From b8728884fc900dd43f6c565dbe686d5eb5a68d06 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Mon, 10 Oct 2022 10:33:47 -0600 Subject: [PATCH 001/719] Drafting stress controls in fix deform --- src/fix_deform.cpp | 505 ++++++++++++++++++++++++++++++++++++--------- src/fix_deform.h | 21 +- 2 files changed, 430 insertions(+), 96 deletions(-) diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index bc6e61a69ed..40221df839b 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -16,6 +16,11 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +// Save previous state to restart file for derivatives +// define hrate_lo/hi for volume +// add modify command +// add pressure code + #include "fix_deform.h" #include "atom.h" @@ -39,8 +44,9 @@ using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; -enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE}; +enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE,PRESSURE,PISOTROPIC}; enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE}; +enum{NOCOUPLE=0,XYZ,XY,YZ,XZ}; /* ---------------------------------------------------------------------- */ @@ -52,6 +58,8 @@ irregular(nullptr), set(nullptr) no_change_box = 1; restart_global = 1; pre_exchange_migrate = 1; + pcouple = NOCOUPLE; + dimension = domain->dimension; nevery = utils::inumeric(FLERR,arg[3],false,lmp); if (nevery <= 0) error->all(FLERR,"Illegal fix deform command"); @@ -132,7 +140,35 @@ irregular(nullptr), set(nullptr) set[index].hstr = utils::strdup(&arg[iarg+2][2]); set[index].hratestr = utils::strdup(&arg[iarg+3][2]); iarg += 4; - } else error->all(FLERR,"Illegal fix deform command"); + } else if (strcmp(arg[iarg+1],"pressure") == 0) { + if (iarg+4 > narg) error->all(FLERR, "Illegal fix deform command"); + set[index].style = PRESSURE; + if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) { + set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp); + } else { + if (iarg+ > narg) error->all(FLERR,"Illegal fix deform command"); + set[index].pstr = utils::strdup(&arg[iarg+2][2]); + set[index].pvar = 1; + } + set[index].pgain = utils::numeric(FLERR,arg[iarg+3],false,lmp); + if (set[index].pgain <= 0.0) + error->all(FLERR,"Illegal fix deform command"); + iarg += 4; + } else if (strcmp(arg[iarg+1],"pressure/isotropic") == 0) { + if (iarg+4 > narg) error->all(FLERR, "Illegal fix deform command"); + set[index].style = PISOTROPIC; + if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) { + set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp); + } else { + if (iarg+ > narg) error->all(FLERR,"Illegal fix deform command"); + set[index].pstr = utils::strdup(&arg[iarg+2][2]); + set[index].pvar = 1; + } + set[index].pgain = utils::numeric(FLERR,arg[iarg+3],false,lmp); + if (set[index].pgain <= 0.0) + error->all(FLERR,"Illegal fix deform command"); + iarg += 4; + } error->all(FLERR,"Illegal fix deform command"); } else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 || @@ -190,8 +226,21 @@ irregular(nullptr), set(nullptr) set[index].hstr = utils::strdup(&arg[iarg+2][2]); set[index].hratestr = utils::strdup(&arg[iarg+3][2]); iarg += 4; + } else if (strcmp(arg[iarg+1],"pressure") == 0) { + if (iarg+4 > narg) error->all(FLERR, "Illegal fix deform command"); + set[index].style = PRESSURE; + if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) { + set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp); + } else { + if (iarg+ > narg) error->all(FLERR,"Illegal fix deform command"); + set[index].pstr = utils::strdup(&arg[iarg+2][2]); + set[index].pvar = 1; + } + set[index].pgain = utils::numeric(FLERR,arg[iarg+3],false,lmp); + if (set[index].pgain <= 0.0) + error->all(FLERR,"Illegal fix deform command"); + iarg += 4; } else error->all(FLERR,"Illegal fix deform command"); - } else break; } @@ -201,6 +250,63 @@ irregular(nullptr), set(nullptr) options(narg-iarg,&arg[iarg]); if (remapflag != Domain::X_REMAP) restart_pbc = 1; + // populate coupled pressure controls + + if (pcouple != NOCOUPLE) { + int coupled_indices[3] = {0}; + int j = -1; + double couple_gain, coupled_pressure; + char *couple_str; + + if (pcouple == XYZ || pcouple == XY || pcouple == XZ) + coupled_indices[0] = 1; + if (pcouple == XYZ || pcouple == XY || pcouple == YZ) + coupled_indices[1] = 1; + if (pcouple == XYZ || pcouple == XZ || pcouple == YZ) + coupled_indices[2] = 1; + + // Check coupled styles and find reference + for (int i = 0; i < 3; i++) { + if (coupled_indices[i]) { + set[i].coupled_flag = 1; + if (set[i].style != VOLUME && set[i].style != PRESSURE && set[i].style != NONE) + error->all(FLERR, "Cannot couple dimensions not controlled by pressure or volume in fix deform"); + if (set[i].style == PRESSURE || set[i].style == VOLUME) + j = i; + } + } + + if (j == -1) + error->all(FLERR, "Must specify pressure style for a coupled dimension in fix deform"); + + // Copy data to each coupled dimension + for (int i = 0; i < 3; i++) { + if (coupled_indices[i]) { + if (set[j].style != set[i].style && set[i].style != NONE) + error->all(FLERR, "Cannot couple dimensions with different control options"); + + if (set[j].style == PRESSURE && set[i].style == NONE) { + set[i].style = PRESSURE; + set[i].pgain = set[j].pgain; + if (set[j].pvar == 1) { + set[i].pstr = set[j].pstr; + set[i].pvar = 1; + } else { + set[i].ptarget = set[j].ptarget; + } + } else if (set[j].style == VOLUME && set[i].style == NONE) { + set[i].style = VOLUME; + set[i].saved = -1; + if (domain->dimension == 2) + error->all(FLERR, "Cannot couple pressure with constant volume in two dimensions"); + } + } else { + if (set[i].style == VOLUME && set[j].style == VOLUME) + error->all(FLERR, "Dimensions used to maintain constant volume must either be all be coupled or not coupled"); + } + } + } + // setup dimflags used by other classes to check for volume-change conflicts for (int i = 0; i < 6; i++) @@ -285,32 +391,31 @@ irregular(nullptr), set(nullptr) // for VOLUME, setup links to other dims // fixed, dynamic1, dynamic2 + volume_flag = 0; for (int i = 0; i < 3; i++) { if (set[i].style != VOLUME) continue; + volume_flag = 1; int other1 = (i+1) % 3; int other2 = (i+2) % 3; - if (set[other1].style == NONE) { + // Cannot use VOLUME option without at least one deformed dimension + if (set[other1].style == NONE || set[other1].style == VOLUME) if (set[other2].style == NONE || set[other2].style == VOLUME) error->all(FLERR,"Fix deform volume setting is invalid"); + + if (set[other1].style == NONE) { set[i].substyle = ONE_FROM_ONE; set[i].fixed = other1; set[i].dynamic1 = other2; } else if (set[other2].style == NONE) { - if (set[other1].style == NONE || set[other1].style == VOLUME) - error->all(FLERR,"Fix deform volume setting is invalid"); set[i].substyle = ONE_FROM_ONE; set[i].fixed = other2; set[i].dynamic1 = other1; } else if (set[other1].style == VOLUME) { - if (set[other2].style == NONE || set[other2].style == VOLUME) - error->all(FLERR,"Fix deform volume setting is invalid"); set[i].substyle = TWO_FROM_ONE; set[i].fixed = other1; set[i].dynamic1 = other2; } else if (set[other2].style == VOLUME) { - if (set[other1].style == NONE || set[other1].style == VOLUME) - error->all(FLERR,"Fix deform volume setting is invalid"); set[i].substyle = TWO_FROM_ONE; set[i].fixed = other2; set[i].dynamic1 = other1; @@ -321,12 +426,34 @@ irregular(nullptr), set(nullptr) } } + // set strain_flag + strain_flag = 0; + for (int i = 0; i < 6; i++) + if (set[i].style != NONE && set[i].style != VOLUME && + set[i].style != PRESSURE && set[i].style != PISOTROPIC) + strain_flag = 1; + // set varflag varflag = 0; for (int i = 0; i < 6; i++) if (set[i].style == VARIABLE) varflag = 1; + // set pressure_flag + + pressure_flag = 0; + for (int i = 0; i < 6; i++) { + if (set[i].style == PRESSURE || set[i].style == PISOTROPIC) pressure_flag = 1; + if (set[i].coupled_flag) pressure_flag = 1; + } + + // check conflict between constant volume/pressure + + if (volume_flag) + for (int i = 0; i < 6; i++) + if (set[i].style == PISOTROPIC) + error->all(FLERR, "Cannot use fix deform to assign constant volume and pressure"); + // set initial values at time fix deform is issued for (int i = 0; i < 3; i++) { @@ -350,6 +477,29 @@ irregular(nullptr), set(nullptr) else irregular = nullptr; TWOPI = 2.0*MY_PI; + + // Create pressure compute, if needed + + pflag = 0; + tflag = 0; + if (pressure_flag) { + // create a new compute temp style + // id = fix-ID + temp + // compute group = all since pressure is always global (group all) + // and thus its KE/temperature contribution should use group all + + id_temp = utils::strdup(std::string(id) + "_temp"); + modify->add_compute(fmt::format("{} all temp",id_temp)); + tflag = 1; + + // create a new compute pressure style + // id = fix-ID + press, compute group = all + // pass id_temp as 4th arg to pressure constructor + + id_press = utils::strdup(std::string(id) + "_press"); + modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); + pflag = 1; + } } /* ---------------------------------------------------------------------- */ @@ -360,6 +510,7 @@ FixDeform::~FixDeform() for (int i = 0; i < 6; i++) { delete[] set[i].hstr; delete[] set[i].hratestr; + delete[] set[i].pstr; } } delete[] set; @@ -374,6 +525,13 @@ FixDeform::~FixDeform() h_rate[0] = h_rate[1] = h_rate[2] = h_rate[3] = h_rate[4] = h_rate[5] = 0.0; h_ratelo[0] = h_ratelo[1] = h_ratelo[2] = 0.0; + + // delete temperature and pressure if fix created them + + if (tflag) modify->delete_compute(id_temp); + if (pflag) modify->delete_compute(id_press); + delete [] id_temp; + delete [] id_press; } /* ---------------------------------------------------------------------- */ @@ -574,7 +732,7 @@ void FixDeform::init() // set domain->h_rate values for use by domain and other fixes/computes // initialize all rates to 0.0 - // cannot set here for TRATE,VOLUME,WIGGLE,VARIABLE since not constant + // cannot set here for TRATE,VOLUME,WIGGLE,VARIABLE,PRESSURE since not constant h_rate = domain->h_rate; h_ratelo = domain->h_ratelo; @@ -611,6 +769,31 @@ void FixDeform::init() for (auto ifix : modify->get_fix_list()) if (ifix->rigid_flag) rfix.push_back(ifix); + + // Find pressure/temp computes if needed + + if (pressure_flag) { + int icompute = modify->find_compute(id_temp); + if (icompute < 0) + error->all(FLERR,"Temperature ID for fix deform does not exist"); + temperature = modify->compute[icompute]; + + icompute = modify->find_compute(id_press); + if (icompute < 0) + error->all(FLERR,"Pressure ID for fix deform does not exist"); + pressure = modify->compute[icompute]; + } +} + +/* ---------------------------------------------------------------------- + compute T,P if needed before integrator starts +------------------------------------------------------------------------- */ + +void FixDeform::setup(int /*vflag*/) +{ + // trigger virial computation on next timestep + + if (pressure_flag) pressure->addstep(update->ntimestep+1); } /* ---------------------------------------------------------------------- @@ -660,95 +843,40 @@ void FixDeform::end_of_step() if (varflag) modify->clearstep_compute(); - // set new box size - // for NONE, target is current box size - // for TRATE, set target directly based on current time, also set h_rate - // for WIGGLE, set target directly based on current time, also set h_rate - // for VARIABLE, set target directly via variable eval, also set h_rate - // for others except VOLUME, target is linear value between start and stop + // set new box size for strain-based dims - for (i = 0; i < 3; i++) { - if (set[i].style == NONE) { - set[i].lo_target = domain->boxlo[i]; - set[i].hi_target = domain->boxhi[i]; - } else if (set[i].style == TRATE) { - double delt = (update->ntimestep - update->beginstep) * update->dt; - set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt)); - set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt)); - h_rate[i] = set[i].rate * domain->h[i]; - h_ratelo[i] = -0.5*h_rate[i]; - } else if (set[i].style == WIGGLE) { - double delt = (update->ntimestep - update->beginstep) * update->dt; - set[i].lo_target = set[i].lo_start - - 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); - set[i].hi_target = set[i].hi_start + - 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); - h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude * - cos(TWOPI*delt/set[i].tperiod); - h_ratelo[i] = -0.5*h_rate[i]; - } else if (set[i].style == VARIABLE) { - double del = input->variable->compute_equal(set[i].hvar); - set[i].lo_target = set[i].lo_start - 0.5*del; - set[i].hi_target = set[i].hi_start + 0.5*del; - h_rate[i] = input->variable->compute_equal(set[i].hratevar); - h_ratelo[i] = -0.5*h_rate[i]; - } else if (set[i].style != VOLUME) { - set[i].lo_target = set[i].lo_start + - delta*(set[i].lo_stop - set[i].lo_start); - set[i].hi_target = set[i].hi_start + - delta*(set[i].hi_stop - set[i].hi_start); + set_strain(); + + // set new box size for pressure-based dims + + if (pressure_flag) { + temperature->compute_vector(); + pressure->compute_vector(); + for (int i = 0; i < 3; i++) { + if (set[i].saved == -1) { + set[i].saved = 1; + set[i].rate = 0.0; + set[i].prior_pressure = pressure->vector[i]; + if (i == 0) set[i].box_length = domain->xprd; + else if (i == 1) set[i].box_length = domain->yprd; + else (i == 2) set[i].box_length = domain->zprd; + } } + set_pressure(); } // set new box size for VOLUME dims that are linked to other dims // NOTE: still need to set h_rate for these dims - for (i = 0; i < 3; i++) { - if (set[i].style != VOLUME) continue; - - if (set[i].substyle == ONE_FROM_ONE) { - set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*(set[i].vol_start / - (set[set[i].dynamic1].hi_target - - set[set[i].dynamic1].lo_target) / - (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start)); - set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*(set[i].vol_start / - (set[set[i].dynamic1].hi_target - - set[set[i].dynamic1].lo_target) / - (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start)); + if (volume_flag) set_volume(); - } else if (set[i].substyle == ONE_FROM_TWO) { - set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*(set[i].vol_start / - (set[set[i].dynamic1].hi_target - - set[set[i].dynamic1].lo_target) / - (set[set[i].dynamic2].hi_target - - set[set[i].dynamic2].lo_target)); - set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*(set[i].vol_start / - (set[set[i].dynamic1].hi_target - - set[set[i].dynamic1].lo_target) / - (set[set[i].dynamic2].hi_target - - set[set[i].dynamic2].lo_target)); + // Save pressure/strain rate if required - } else if (set[i].substyle == TWO_FROM_ONE) { - set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*sqrt(set[i].vol_start / - (set[set[i].dynamic1].hi_target - - set[set[i].dynamic1].lo_target) / - (set[set[i].fixed].hi_start - - set[set[i].fixed].lo_start) * - (set[i].hi_start - set[i].lo_start)); - set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*sqrt(set[i].vol_start / - (set[set[i].dynamic1].hi_target - - set[set[i].dynamic1].lo_target) / - (set[set[i].fixed].hi_start - - set[set[i].fixed].lo_start) * - (set[i].hi_start - set[i].lo_start)); + if (pressure_flag) { + double dt_inv = 1.0 / update->dt; + for (int i = 0; i < 3; i++) { + set[i].prior_pressure = pressure->vector[i]; + set[i].prior_rate = ((set[i].hi_target - set[i].lo_target) / set[i].box_length - 1.0) * dt_inv; } } @@ -882,7 +1010,7 @@ void FixDeform::end_of_step() if (mask[i] & groupbit) domain->x2lamda(x[i],x[i]); - for (auto &ifix : rfix) + for (auto ifix : rfix) ifix->deform(0); } @@ -921,13 +1049,134 @@ void FixDeform::end_of_step() if (mask[i] & groupbit) domain->lamda2x(x[i],x[i]); - for (auto &ifix : rfix) + for (auto ifix : rfix) ifix->deform(1); } // redo KSpace coeffs since box has changed if (kspace_flag) force->kspace->setup(); + + // trigger virial computation, if needed, on next timestep + + if (pressure_flag) { + pressure->addstep(update->ntimestep+1); + set[0].box_length = domain->xprd; + set[1].box_length = domain->yprd; + set[2].box_length = domain->zprd; + } +} + +/* ---------------------------------------------------------------------- + set box size for strain-based dimensions +------------------------------------------------------------------------- */ + +void FixDeform::set_strain() +{ + // for NONE, target is current box size + // for TRATE, set target directly based on current time, also set h_rate + // for WIGGLE, set target directly based on current time, also set h_rate + // for VARIABLE, set target directly via variable eval, also set h_rate + // for others except VOLUME, target is linear value between start and stop + + for (int i = 0; i < 3; i++) { + if (set[i].style == NONE) { + set[i].lo_target = domain->boxlo[i]; + set[i].hi_target = domain->boxhi[i]; + } else if (set[i].style == TRATE) { + double delt = (update->ntimestep - update->beginstep) * update->dt; + set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) - + 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt)); + set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) + + 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt)); + h_rate[i] = set[i].rate * domain->h[i]; + h_ratelo[i] = -0.5*h_rate[i]; + } else if (set[i].style == WIGGLE) { + double delt = (update->ntimestep - update->beginstep) * update->dt; + set[i].lo_target = set[i].lo_start - + 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); + set[i].hi_target = set[i].hi_start + + 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); + h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude * + cos(TWOPI*delt/set[i].tperiod); + h_ratelo[i] = -0.5*h_rate[i]; + } else if (set[i].style == VARIABLE) { + double del = input->variable->compute_equal(set[i].hvar); + set[i].lo_target = set[i].lo_start - 0.5*del; + set[i].hi_target = set[i].hi_start + 0.5*del; + h_rate[i] = input->variable->compute_equal(set[i].hratevar); + h_ratelo[i] = -0.5*h_rate[i]; + } else if (set[i].style != VOLUME) { + set[i].lo_target = set[i].lo_start + + delta*(set[i].lo_stop - set[i].lo_start); + set[i].hi_target = set[i].hi_start + + delta*(set[i].hi_stop - set[i].hi_start); + } + } +} + +/* ---------------------------------------------------------------------- + set box size for pressure-based dimensions +------------------------------------------------------------------------- */ + +void FixDeform::set_pressure() +{ + for (int i = 0; i < 3; i++) { + + + } + // must define hi+lo target + // + +} + +/* ---------------------------------------------------------------------- + set box size for VOLUME dimensions +------------------------------------------------------------------------- */ + +void FixDeform::set_volume() +{ + for (int i = 0; i < 3; i++) { + if (set[i].style != VOLUME) continue; + + double v0 = set[i].vol_start; + double center_start = 0.5 * (set[i].lo_start + set[i].hi_start); + double offset; + + if (set[i].substyle == ONE_FROM_ONE) { + offset = 0.5 * (v0 / + (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) / + (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start)); + } else if (set[i].substyle == ONE_FROM_TWO) { + offset = 0.5 * (v0 / + (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) / + (set[set[i].dynamic2].hi_target - set[set[i].dynamic2].lo_target)) + } else if (set[i].substyle == TWO_FROM_ONE) { + if (!set[i].coupled_flag) { + offset = 0.5 * sqrt(v0 * (set[i].hi_start - set[i].lo_start) / + (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) / + (set[set[i].fixed].hi_start - set[set[i].fixed].lo_start)) + } else { + double p1 = pressure->vector[i]; + double p2 = pressure->vector[set[i].fixed]; + double p1i = set[i].prior_pressure; + double p2i = set[set[i].fixed].prior_pressure; + double e1i = set[i].prior_rate; + double e2i = set[set[i].fixed].prior_rate; + double L3 = (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target); + double dt = update->dt; + + double e3 = (L3 / set[set[i].dynamic1].box_length - 1.0) / dt; + double e1 = -e3 * dt / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2); + e1 /= (p2 - p2i + (p1 - p1i) / e1p * e2p); + double e2 = (1.0 - (1 + e3 * dt) * (1 + e1 * dt)); + e2 /= (1 + e3 * dt) * (1 + e1 * dt) * dt; + offset = 0.5 * set[i].box_length * (1.0 - e3 * dt); + } + } + set[i].lo_target = center_start - offset; + set[i].hi_target = center_start + offset; + } } /* ---------------------------------------------------------------------- @@ -937,7 +1186,7 @@ void FixDeform::end_of_step() void FixDeform::write_restart(FILE *fp) { if (comm->me == 0) { - int size = 6*sizeof(Set); + int size = 6 * sizeof(Set); fwrite(&size,sizeof(int),1,fp); fwrite(set,sizeof(Set),6,fp); } @@ -996,8 +1245,22 @@ void FixDeform::options(int narg, char **arg) if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command"); flipflag = utils::logical(FLERR,arg[iarg+1],false,lmp); iarg += 2; + } else if (strcmp(arg[iarg],"couple") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal fix fix deform command"); + if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ; + else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY; + else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ; + else if (strcmp(arg[iarg+1],"xz") == 0) pcouple = XZ; + else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NOCOUPLE; + else error->all(FLERR,"Illegal fix fix deform command"); + iarg += 2; } else error->all(FLERR,"Illegal fix deform command"); } + + if (dimension == 2) + if (pcouple == XYZ || pcouple == XZ || pcouple == YZ) + error->all(FLERR, "Cannot couple Z dimension in fix deform in 2D"); } /* ---------------------------------------------------------------------- @@ -1010,3 +1273,57 @@ double FixDeform::memory_usage() if (irregular) bytes += irregular->memory_usage(); return bytes; } + + +/* ---------------------------------------------------------------------- */ + +int FixDeform::modify_param(int narg, char **arg) +{ + if (!pressure_flag) error->all(FLERR,"Cannot modify fix deform without a pressure control"); + if (strcmp(arg[0],"temp") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (tflag) { + modify->delete_compute(id_temp); + tflag = 0; + } + delete [] id_temp; + id_temp = utils::strdup(arg[1]); + + int icompute = modify->find_compute(arg[1]); + if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID"); + temperature = modify->compute[icompute]; + + if (temperature->tempflag == 0) + error->all(FLERR,"Fix_modify temperature ID does not compute temperature"); + if (temperature->igroup != 0 && comm->me == 0) + error->warning(FLERR,"Temperature for deform is not for group all"); + + // reset id_temp of pressure to new temperature ID + + icompute = modify->find_compute(id_press); + if (icompute < 0) + error->all(FLERR,"Pressure ID for fix deform does not exist"); + modify->compute[icompute]->reset_extra_compute_fix(id_temp); + + return 2; + + } else if (strcmp(arg[0],"press") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (pflag) { + modify->delete_compute(id_press); + pflag = 0; + } + delete [] id_press; + id_press = utils::strdup(arg[1]); + + int icompute = modify->find_compute(arg[1]); + if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); + pressure = modify->compute[icompute]; + + if (pressure->pressflag == 0) + error->all(FLERR,"Fix_modify pressure ID does not compute pressure"); + return 2; + } + + return 0; +} diff --git a/src/fix_deform.h b/src/fix_deform.h index 76f5fc9d4a2..7297874258c 100644 --- a/src/fix_deform.h +++ b/src/fix_deform.h @@ -33,23 +33,32 @@ class FixDeform : public Fix { ~FixDeform() override; int setmask() override; void init() override; + void setup(int) override; void pre_exchange() override; void end_of_step() override; void write_restart(FILE *) override; void restart(char *buf) override; double memory_usage() override; + int modify_param(int, char **) override; protected: - int triclinic, scaleflag, flipflag; + int dimension, triclinic, scaleflag, flipflag, pcouple; int flip, flipxy, flipxz, flipyz; double *h_rate, *h_ratelo; int varflag; // 1 if VARIABLE option is used, 0 if not + int strain_flag; // 1 if strain-based option is used, 0 if not + int volume_flag; // 1 if VOLUME option is used, 0 if not + int pressure_flag; // 1 if pressure tensor used, 0 if not int kspace_flag; // 1 if KSpace invoked, 0 if not std::vector rfix; // pointers to rigid fixes class Irregular *irregular; // for migrating atoms after box flips double TWOPI; + char *id_temp, *id_press; + class Compute *temperature, *pressure; + int tflag, pflag; + struct Set { int style, substyle; double flo, fhi, ftilt; @@ -61,13 +70,21 @@ class FixDeform : public Fix { double tilt_initial, tilt_start, tilt_stop, tilt_target, tilt_flip; double tilt_min, tilt_max; double vol_initial, vol_start; + double ptarget, pgain; + double prior_pressure, prior_rate; + double box_length; + int saved; int fixed, dynamic1, dynamic2; - char *hstr, *hratestr; + char *hstr, *hratestr, *pstr; int hvar, hratevar; + int pvar; + int coupled_flag; }; Set *set; void options(int, char **); + void set_volume(); + void couple(); }; } // namespace LAMMPS_NS From 66471c146537d8d1a32e00c8c7d9e68c4bc8ff07 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 11 Oct 2022 16:52:02 -0600 Subject: [PATCH 002/719] Adding pressure controls and fixing misc errors --- src/fix_deform.cpp | 377 ++++++++++++++++++++++++++++----------------- src/fix_deform.h | 4 +- 2 files changed, 236 insertions(+), 145 deletions(-) diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 40221df839b..766d7c22ae6 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -17,14 +17,14 @@ ------------------------------------------------------------------------- */ // Save previous state to restart file for derivatives -// define hrate_lo/hi for volume -// add modify command -// add pressure code +// define hrate_lo/hi for volume/pressure +// add logic for hi_stop and flip flag #include "fix_deform.h" #include "atom.h" #include "comm.h" +#include "compute.h" #include "domain.h" #include "error.h" #include "force.h" @@ -84,36 +84,36 @@ irregular(nullptr), set(nullptr) else if (strcmp(arg[iarg],"y") == 0) index = 1; else if (strcmp(arg[iarg],"z") == 0) index = 2; - if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform", error); if (strcmp(arg[iarg+1],"final") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform final", error); set[index].style = FINAL; set[index].flo = utils::numeric(FLERR,arg[iarg+2],false,lmp); set[index].fhi = utils::numeric(FLERR,arg[iarg+3],false,lmp); iarg += 4; } else if (strcmp(arg[iarg+1],"delta") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform delta", error); set[index].style = DELTA; set[index].dlo = utils::numeric(FLERR,arg[iarg+2],false,lmp); set[index].dhi = utils::numeric(FLERR,arg[iarg+3],false,lmp); iarg += 4; } else if (strcmp(arg[iarg+1],"scale") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix deform scale", error); set[index].style = SCALE; set[index].scale = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; } else if (strcmp(arg[iarg+1],"vel") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix deform vel", error); set[index].style = VEL; set[index].vel = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; } else if (strcmp(arg[iarg+1],"erate") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix deform erate", error); set[index].style = ERATE; set[index].rate = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; } else if (strcmp(arg[iarg+1],"trate") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix deform trate", error); set[index].style = TRATE; set[index].rate = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; @@ -121,54 +121,52 @@ irregular(nullptr), set(nullptr) set[index].style = VOLUME; iarg += 2; } else if (strcmp(arg[iarg+1],"wiggle") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform wiggle", error); set[index].style = WIGGLE; set[index].amplitude = utils::numeric(FLERR,arg[iarg+2],false,lmp); set[index].tperiod = utils::numeric(FLERR,arg[iarg+3],false,lmp); if (set[index].tperiod <= 0.0) - error->all(FLERR,"Illegal fix deform command"); + error->all(FLERR,"Illegal fix deform wiggle period, must be positive"); iarg += 4; } else if (strcmp(arg[iarg+1],"variable") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform variable", error); set[index].style = VARIABLE; if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) - error->all(FLERR,"Illegal fix deform command"); + error->all(FLERR,"Illegal fix deform variable name {}", arg[iarg+2]); if (strstr(arg[iarg+3],"v_") != arg[iarg+3]) - error->all(FLERR,"Illegal fix deform command"); + error->all(FLERR,"Illegal fix deform variable name {}", arg[iarg+3]); delete[] set[index].hstr; delete[] set[index].hratestr; set[index].hstr = utils::strdup(&arg[iarg+2][2]); set[index].hratestr = utils::strdup(&arg[iarg+3][2]); iarg += 4; } else if (strcmp(arg[iarg+1],"pressure") == 0) { - if (iarg+4 > narg) error->all(FLERR, "Illegal fix deform command"); + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform pressure", error); set[index].style = PRESSURE; if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) { set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp); } else { - if (iarg+ > narg) error->all(FLERR,"Illegal fix deform command"); set[index].pstr = utils::strdup(&arg[iarg+2][2]); - set[index].pvar = 1; + set[index].pvar_flag = 1; } set[index].pgain = utils::numeric(FLERR,arg[iarg+3],false,lmp); if (set[index].pgain <= 0.0) - error->all(FLERR,"Illegal fix deform command"); + error->all(FLERR,"Illegal fix deform pressure gain, must be positive"); iarg += 4; } else if (strcmp(arg[iarg+1],"pressure/isotropic") == 0) { - if (iarg+4 > narg) error->all(FLERR, "Illegal fix deform command"); + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform pressure/isotropic", error); set[index].style = PISOTROPIC; if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) { set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp); } else { - if (iarg+ > narg) error->all(FLERR,"Illegal fix deform command"); set[index].pstr = utils::strdup(&arg[iarg+2][2]); - set[index].pvar = 1; + set[index].pvar_flag = 1; } set[index].pgain = utils::numeric(FLERR,arg[iarg+3],false,lmp); if (set[index].pgain <= 0.0) - error->all(FLERR,"Illegal fix deform command"); + error->all(FLERR,"Illegal fix deform pressure gain, must be positive"); iarg += 4; - } error->all(FLERR,"Illegal fix deform command"); + } else error->all(FLERR,"Illegal fix deform command argument: {}", arg[iarg+1]); } else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 || @@ -180,67 +178,66 @@ irregular(nullptr), set(nullptr) else if (strcmp(arg[iarg],"xz") == 0) index = 4; else if (strcmp(arg[iarg],"yz") == 0) index = 3; - if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform", error); if (strcmp(arg[iarg+1],"final") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix deform final", error); set[index].style = FINAL; set[index].ftilt = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; } else if (strcmp(arg[iarg+1],"delta") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix deform delta", error); set[index].style = DELTA; set[index].dtilt = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; } else if (strcmp(arg[iarg+1],"vel") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix deform vel", error); set[index].style = VEL; set[index].vel = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; } else if (strcmp(arg[iarg+1],"erate") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix deform erate", error); set[index].style = ERATE; set[index].rate = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; } else if (strcmp(arg[iarg+1],"trate") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix deform trate", error); set[index].style = TRATE; set[index].rate = utils::numeric(FLERR,arg[iarg+2],false,lmp); iarg += 3; } else if (strcmp(arg[iarg+1],"wiggle") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform wiggle", error); set[index].style = WIGGLE; set[index].amplitude = utils::numeric(FLERR,arg[iarg+2],false,lmp); set[index].tperiod = utils::numeric(FLERR,arg[iarg+3],false,lmp); if (set[index].tperiod <= 0.0) - error->all(FLERR,"Illegal fix deform command"); + error->all(FLERR,"Illegal fix deform wiggle period, must be positive"); iarg += 4; } else if (strcmp(arg[iarg+1],"variable") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform variable", error); set[index].style = VARIABLE; if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) - error->all(FLERR,"Illegal fix deform command"); + error->all(FLERR,"Illegal fix deform variable name {}", arg[iarg+2]); if (strstr(arg[iarg+3],"v_") != arg[iarg+3]) - error->all(FLERR,"Illegal fix deform command"); + error->all(FLERR,"Illegal fix deform variable name {}", arg[iarg+3]); delete[] set[index].hstr; delete[] set[index].hratestr; set[index].hstr = utils::strdup(&arg[iarg+2][2]); set[index].hratestr = utils::strdup(&arg[iarg+3][2]); iarg += 4; } else if (strcmp(arg[iarg+1],"pressure") == 0) { - if (iarg+4 > narg) error->all(FLERR, "Illegal fix deform command"); + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform pressure", error); set[index].style = PRESSURE; if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) { set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp); } else { - if (iarg+ > narg) error->all(FLERR,"Illegal fix deform command"); set[index].pstr = utils::strdup(&arg[iarg+2][2]); - set[index].pvar = 1; + set[index].pvar_flag = 1; } set[index].pgain = utils::numeric(FLERR,arg[iarg+3],false,lmp); if (set[index].pgain <= 0.0) - error->all(FLERR,"Illegal fix deform command"); + error->all(FLERR,"Illegal fix deform pressure gain, must be positive"); iarg += 4; - } else error->all(FLERR,"Illegal fix deform command"); + } else error->all(FLERR,"Illegal fix deform command: {}", arg[iarg+1]); } else break; } @@ -270,7 +267,7 @@ irregular(nullptr), set(nullptr) if (coupled_indices[i]) { set[i].coupled_flag = 1; if (set[i].style != VOLUME && set[i].style != PRESSURE && set[i].style != NONE) - error->all(FLERR, "Cannot couple dimensions not controlled by pressure or volume in fix deform"); + error->all(FLERR, "Cannot couple dimensions unless they are controlled using the pressure or volume option in fix deform"); if (set[i].style == PRESSURE || set[i].style == VOLUME) j = i; } @@ -279,30 +276,45 @@ irregular(nullptr), set(nullptr) if (j == -1) error->all(FLERR, "Must specify pressure style for a coupled dimension in fix deform"); - // Copy data to each coupled dimension + // Copy or compare data for each coupled dimension for (int i = 0; i < 3; i++) { if (coupled_indices[i]) { - if (set[j].style != set[i].style && set[i].style != NONE) - error->all(FLERR, "Cannot couple dimensions with different control options"); - + // Copy coupling information if dimension style is undefined if (set[j].style == PRESSURE && set[i].style == NONE) { set[i].style = PRESSURE; set[i].pgain = set[j].pgain; - if (set[j].pvar == 1) { + if (set[j].pvar_flag) { set[i].pstr = set[j].pstr; - set[i].pvar = 1; + set[i].pvar_flag = 1; } else { set[i].ptarget = set[j].ptarget; } } else if (set[j].style == VOLUME && set[i].style == NONE) { set[i].style = VOLUME; - set[i].saved = -1; if (domain->dimension == 2) error->all(FLERR, "Cannot couple pressure with constant volume in two dimensions"); } + + // Check for incompatibilities in style + if (set[j].style != set[i].style && set[i].style != NONE) + error->all(FLERR, "Cannot couple dimensions with different control options"); + if (set[j].style != PRESSURE) continue; + + // If pressure controlled, check for incompatibilities in parameters + if (set[i].pgain != set[j].pgain) + error->all(FLERR, "Coupled dimensions must have identical gain parameters\n"); + + if (set[i].pvar_flag != set[j].pvar_flag) + error->all(FLERR, "Coupled dimensions must have the same target pressure\n"); + if (set[j].pvar_flag) + if (strcmp(set[i].pstr, set[j].pstr) != 0) + error->all(FLERR, "Coupled dimensions must have the same target pressure\n"); + if (set[i].ptarget != set[j].ptarget) + error->all(FLERR, "Coupled dimensions must have the same target pressure\n"); + } else { if (set[i].style == VOLUME && set[j].style == VOLUME) - error->all(FLERR, "Dimensions used to maintain constant volume must either be all be coupled or not coupled"); + error->all(FLERR, "Dimensions used to maintain constant volume must either all be coupled or uncoupled"); } } } @@ -427,6 +439,7 @@ irregular(nullptr), set(nullptr) } // set strain_flag + strain_flag = 0; for (int i = 0; i < 6; i++) if (set[i].style != NONE && set[i].style != VOLUME && @@ -569,14 +582,25 @@ void FixDeform::init() if (set[i].style != VARIABLE) continue; set[i].hvar = input->variable->find(set[i].hstr); if (set[i].hvar < 0) - error->all(FLERR,"Variable name for fix deform does not exist"); + error->all(FLERR,"Variable name {} for fix deform does not exist", set[i].hstr); if (!input->variable->equalstyle(set[i].hvar)) - error->all(FLERR,"Variable for fix deform is invalid style"); + error->all(FLERR,"Variable {} for fix deform is invalid style", set[i].hstr); set[i].hratevar = input->variable->find(set[i].hratestr); if (set[i].hratevar < 0) - error->all(FLERR,"Variable name for fix deform does not exist"); + error->all(FLERR,"Variable name {} for fix deform does not exist", set[i].hratestr); if (!input->variable->equalstyle(set[i].hratevar)) - error->all(FLERR,"Variable for fix deform is invalid style"); + error->all(FLERR,"Variable {} for fix deform is invalid style", set[i].hratestr); + } + + // check optional variables for PRESSURE or PISOTROPIC style + + for (int i = 0; i < 6; i++) { + if (!set[i].pvar_flag) continue; + set[i].pvar = input->variable->find(set[i].pstr); + if (set[i].pvar < 0) + error->all(FLERR,"Variable name {} for fix deform does not exist", set[i].pstr); + if (!input->variable->equalstyle(set[i].pvar)) + error->all(FLERR,"Variable {} for fix deform is invalid style", set[i].pstr); } // set start/stop values for box size and shape @@ -834,11 +858,6 @@ void FixDeform::pre_exchange() void FixDeform::end_of_step() { - int i; - - double delta = update->ntimestep - update->beginstep; - if (delta != 0.0) delta /= update->endstep - update->beginstep; - // wrap variable evaluations with clear/add if (varflag) modify->clearstep_compute(); @@ -853,13 +872,13 @@ void FixDeform::end_of_step() temperature->compute_vector(); pressure->compute_vector(); for (int i = 0; i < 3; i++) { - if (set[i].saved == -1) { + if (! set[i].saved) { set[i].saved = 1; - set[i].rate = 0.0; + set[i].prior_rate = 0.0; set[i].prior_pressure = pressure->vector[i]; if (i == 0) set[i].box_length = domain->xprd; else if (i == 1) set[i].box_length = domain->yprd; - else (i == 2) set[i].box_length = domain->zprd; + else set[i].box_length = domain->zprd; } } set_pressure(); @@ -880,61 +899,6 @@ void FixDeform::end_of_step() } } - // for triclinic, set new box shape - // for NONE, target is current tilt - // for TRATE, set target directly based on current time. also set h_rate - // for WIGGLE, set target directly based on current time. also set h_rate - // for VARIABLE, set target directly via variable eval. also set h_rate - // for other styles, target is linear value between start and stop values - - if (triclinic) { - double *h = domain->h; - - for (i = 3; i < 6; i++) { - if (set[i].style == NONE) { - if (i == 5) set[i].tilt_target = domain->xy; - else if (i == 4) set[i].tilt_target = domain->xz; - else if (i == 3) set[i].tilt_target = domain->yz; - } else if (set[i].style == TRATE) { - double delt = (update->ntimestep - update->beginstep) * update->dt; - set[i].tilt_target = set[i].tilt_start * exp(set[i].rate*delt); - h_rate[i] = set[i].rate * domain->h[i]; - } else if (set[i].style == WIGGLE) { - double delt = (update->ntimestep - update->beginstep) * update->dt; - set[i].tilt_target = set[i].tilt_start + - set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); - h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude * - cos(TWOPI*delt/set[i].tperiod); - } else if (set[i].style == VARIABLE) { - double delta_tilt = input->variable->compute_equal(set[i].hvar); - set[i].tilt_target = set[i].tilt_start + delta_tilt; - h_rate[i] = input->variable->compute_equal(set[i].hratevar); - } else { - set[i].tilt_target = set[i].tilt_start + - delta*(set[i].tilt_stop - set[i].tilt_start); - } - - // tilt_target can be large positive or large negative value - // add/subtract box lengths until tilt_target is closest to current value - - int idenom = 0; - if (i == 5) idenom = 0; - else if (i == 4) idenom = 0; - else if (i == 3) idenom = 1; - double denom = set[idenom].hi_target - set[idenom].lo_target; - - double current = h[i]/h[idenom]; - - while (set[i].tilt_target/denom - current > 0.0) - set[i].tilt_target -= denom; - while (set[i].tilt_target/denom - current < 0.0) - set[i].tilt_target += denom; - if (fabs(set[i].tilt_target/denom - 1.0 - current) < - fabs(set[i].tilt_target/denom - current)) - set[i].tilt_target -= denom; - } - } - if (varflag) modify->addstep_compute(update->ntimestep + nevery); // if any tilt ratios exceed 0.5, set flip = 1 and compute new tilt values @@ -1006,7 +970,7 @@ void FixDeform::end_of_step() int *mask = atom->mask; int nlocal = atom->nlocal; - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) domain->x2lamda(x[i],x[i]); @@ -1045,7 +1009,7 @@ void FixDeform::end_of_step() int *mask = atom->mask; int nlocal = atom->nlocal; - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) domain->lamda2x(x[i],x[i]); @@ -1079,6 +1043,9 @@ void FixDeform::set_strain() // for VARIABLE, set target directly via variable eval, also set h_rate // for others except VOLUME, target is linear value between start and stop + double delta = update->ntimestep - update->beginstep; + if (delta != 0.0) delta /= update->endstep - update->beginstep; + for (int i = 0; i < 3; i++) { if (set[i].style == NONE) { set[i].lo_target = domain->boxlo[i]; @@ -1113,6 +1080,62 @@ void FixDeform::set_strain() delta*(set[i].hi_stop - set[i].hi_start); } } + + + // for triclinic, set new box shape + // for NONE, target is current tilt + // for TRATE, set target directly based on current time. also set h_rate + // for WIGGLE, set target directly based on current time. also set h_rate + // for VARIABLE, set target directly via variable eval. also set h_rate + // for other styles, target is linear value between start and stop values + + if (triclinic) { + double *h = domain->h; + + for (int i = 3; i < 6; i++) { + if (set[i].style == NONE) { + if (i == 5) set[i].tilt_target = domain->xy; + else if (i == 4) set[i].tilt_target = domain->xz; + else if (i == 3) set[i].tilt_target = domain->yz; + } else if (set[i].style == TRATE) { + double delt = (update->ntimestep - update->beginstep) * update->dt; + set[i].tilt_target = set[i].tilt_start * exp(set[i].rate*delt); + h_rate[i] = set[i].rate * domain->h[i]; + } else if (set[i].style == WIGGLE) { + double delt = (update->ntimestep - update->beginstep) * update->dt; + set[i].tilt_target = set[i].tilt_start + + set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); + h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude * + cos(TWOPI*delt/set[i].tperiod); + } else if (set[i].style == VARIABLE) { + double delta_tilt = input->variable->compute_equal(set[i].hvar); + set[i].tilt_target = set[i].tilt_start + delta_tilt; + h_rate[i] = input->variable->compute_equal(set[i].hratevar); + } else { + set[i].tilt_target = set[i].tilt_start + + delta*(set[i].tilt_stop - set[i].tilt_start); + } + + // tilt_target can be large positive or large negative value + // add/subtract box lengths until tilt_target is closest to current value + + int idenom = 0; + if (i == 5) idenom = 0; + else if (i == 4) idenom = 0; + else if (i == 3) idenom = 1; + double denom = set[idenom].hi_target - set[idenom].lo_target; + + double current = h[i]/h[idenom]; + + while (set[i].tilt_target/denom - current > 0.0) + set[i].tilt_target -= denom; + while (set[i].tilt_target/denom - current < 0.0) + set[i].tilt_target += denom; + if (fabs(set[i].tilt_target/denom - 1.0 - current) < + fabs(set[i].tilt_target/denom - current)) + set[i].tilt_target -= denom; + } + } } /* ---------------------------------------------------------------------- @@ -1121,13 +1144,59 @@ void FixDeform::set_strain() void FixDeform::set_pressure() { - for (int i = 0; i < 3; i++) { - + // If variable pressure, calculate current target + for (int i = 0; i < 6; i++) + if (set[i].style == PRESSURE) + if (set[i].pvar_flag) + set[i].ptarget = input->variable->compute_equal(set[i].pvar); + + // Find current (possibly coupled/hydrostatic) pressure for X, Y, Z + double *tensor = pressure->vector; + double scalar = pressure->scalar; + double p_current[3]; + + if (pcouple == XYZ) { + double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]); + p_current[0] = p_current[1] = p_current[2] = ave; + } else if (pcouple == XY) { + double ave = 0.5 * (tensor[0] + tensor[1]); + p_current[0] = p_current[1] = ave; + p_current[2] = tensor[2]; + } else if (pcouple == YZ) { + double ave = 0.5 * (tensor[1] + tensor[2]); + p_current[1] = p_current[2] = ave; + p_current[0] = tensor[0]; + } else if (pcouple == XZ) { + double ave = 0.5 * (tensor[0] + tensor[2]); + p_current[0] = p_current[2] = ave; + p_current[1] = tensor[1]; + } else { + if (set[0].style == PRESSURE) p_current[0] = tensor[0]; + else if (set[0].style == PISOTROPIC) p_current[0] = scalar; + + if (set[1].style == PRESSURE) p_current[1] = tensor[1]; + else if (set[1].style == PISOTROPIC) p_current[1] = scalar; + + if (set[2].style == PRESSURE) p_current[2] = tensor[2]; + else if (set[2].style == PISOTROPIC) p_current[2] = scalar; + } + for (int i = 0; i < 3; i++) { + if (set[i].style != PRESSURE && set[i].style != PISOTROPIC) continue; + double dilation = 1.0 - update->dt * set[i].pgain * (set[i].ptarget - p_current[i]); + double center_start = 0.5 * (set[i].lo_start + set[i].hi_start); + double offset = 0.5 * set[i].box_length * dilation; + //printf("ptarget %g vs %g, dilation %g cs %g ofset %g box %g\n", set[i].ptarget, p_current[i], dilation, center_start, offset, set[i].box_length); + set[i].lo_target = center_start - offset; + set[i].hi_target = center_start + offset; } - // must define hi+lo target - // + for (int i = 3; i < 6; i++) { + double shift = update->dt * set[i].pgain * (set[i].ptarget - tensor[i]); + if (i == 3) set[i].tilt_target = domain->xy + shift * domain->xprd; + else if (i == 4) set[i].tilt_target = domain->xz + shift * domain->xprd; + else set[i].tilt_target = domain->yz + shift * domain->yprd; + } } /* ---------------------------------------------------------------------- @@ -1136,6 +1205,9 @@ void FixDeform::set_pressure() void FixDeform::set_volume() { + double e1, e2; + int linked_pressure = 0; + for (int i = 0; i < 3; i++) { if (set[i].style != VOLUME) continue; @@ -1150,28 +1222,46 @@ void FixDeform::set_volume() } else if (set[i].substyle == ONE_FROM_TWO) { offset = 0.5 * (v0 / (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) / - (set[set[i].dynamic2].hi_target - set[set[i].dynamic2].lo_target)) + (set[set[i].dynamic2].hi_target - set[set[i].dynamic2].lo_target)); } else if (set[i].substyle == TWO_FROM_ONE) { if (!set[i].coupled_flag) { offset = 0.5 * sqrt(v0 * (set[i].hi_start - set[i].lo_start) / (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) / - (set[set[i].fixed].hi_start - set[set[i].fixed].lo_start)) + (set[set[i].fixed].hi_start - set[set[i].fixed].lo_start)); } else { + double dt = update->dt; + double e1i = set[i].prior_rate; + double e2i = set[set[i].fixed].prior_rate; + double L3 = (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target); + double e3 = (L3 / set[set[i].dynamic1].box_length - 1.0) / dt; double p1 = pressure->vector[i]; double p2 = pressure->vector[set[i].fixed]; double p1i = set[i].prior_pressure; double p2i = set[set[i].fixed].prior_pressure; - double e1i = set[i].prior_rate; - double e2i = set[set[i].fixed].prior_rate; - double L3 = (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target); - double dt = update->dt; - double e3 = (L3 / set[set[i].dynamic1].box_length - 1.0) / dt; - double e1 = -e3 * dt / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2); - e1 /= (p2 - p2i + (p1 - p1i) / e1p * e2p); - double e2 = (1.0 - (1 + e3 * dt) * (1 + e1 * dt)); - e2 /= (1 + e3 * dt) * (1 + e1 * dt) * dt; - offset = 0.5 * set[i].box_length * (1.0 - e3 * dt); + if (e3 == 0) { + e1 = 0.0; + e2 = 0.0; + offset = 0.5 * set[i].box_length; + } else if (e1i == 0 || e2i == 0 || (p2 == p2i && p1 == p1i)) { + // If no prior strain or no change in pressure (initial step) just scale offset by relative box lengths + offset = 0.5 * sqrt(v0 * set[i].box_length / L3 / set[set[i].fixed].box_length); + } else { + if (! linked_pressure) { + // Calculate first strain rate by expanding stress to linear order in strain to achieve p1(t+dt) = p2(t+dt) + e1 = -e3 / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2); + e1 /= (p2 - p2i + (p1 - p1i) / e1i * e2i); + + // Calculate second strain rate to preserve volume + e2 = (1.0 - (1 + e3 * dt) * (1 + e1 * dt)); + e2 /= (1 + e3 * dt) * (1 + e1 * dt) * dt; + + offset = 0.5 * set[i].box_length * (1.0 + e1 * dt); + linked_pressure = 1; + } else { + offset = 0.5 * set[i].box_length * (1.0 + e2 * dt); + } + } } } set[i].lo_target = center_start - offset; @@ -1229,33 +1319,32 @@ void FixDeform::options(int narg, char **arg) int iarg = 0; while (iarg < narg) { if (strcmp(arg[iarg],"remap") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform remap", error); if (strcmp(arg[iarg+1],"x") == 0) remapflag = Domain::X_REMAP; else if (strcmp(arg[iarg+1],"v") == 0) remapflag = Domain::V_REMAP; else if (strcmp(arg[iarg+1],"none") == 0) remapflag = Domain::NO_REMAP; - else error->all(FLERR,"Illegal fix deform command"); + else error->all(FLERR,"Illegal fix deform remap command: {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"units") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform units", error); if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; - else error->all(FLERR,"Illegal fix deform command"); + else error->all(FLERR,"Illegal fix deform units command: {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"flip") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform flip", error); flipflag = utils::logical(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"couple") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix fix deform command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform couple", error); if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ; else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY; else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ; else if (strcmp(arg[iarg+1],"xz") == 0) pcouple = XZ; else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NOCOUPLE; - else error->all(FLERR,"Illegal fix fix deform command"); + else error->all(FLERR,"Illegal fix fix deform couple command: {}", arg[iarg+1]); iarg += 2; - } else error->all(FLERR,"Illegal fix deform command"); + } else error->all(FLERR,"Illegal fix deform command: {}", arg[iarg]); } if (dimension == 2) @@ -1281,7 +1370,7 @@ int FixDeform::modify_param(int narg, char **arg) { if (!pressure_flag) error->all(FLERR,"Cannot modify fix deform without a pressure control"); if (strcmp(arg[0],"temp") == 0) { - if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (narg < 2) utils::missing_cmd_args(FLERR, "fix_modify deform", error); if (tflag) { modify->delete_compute(id_temp); tflag = 0; diff --git a/src/fix_deform.h b/src/fix_deform.h index 7297874258c..9ecb9a577dd 100644 --- a/src/fix_deform.h +++ b/src/fix_deform.h @@ -77,12 +77,14 @@ class FixDeform : public Fix { int fixed, dynamic1, dynamic2; char *hstr, *hratestr, *pstr; int hvar, hratevar; - int pvar; + int pvar, pvar_flag; int coupled_flag; }; Set *set; void options(int, char **); + void set_strain(); + void set_pressure(); void set_volume(); void couple(); }; From 173e2382b3c3752439b601e7fa88f1a7523b50ce Mon Sep 17 00:00:00 2001 From: jtclemm Date: Sat, 22 Oct 2022 19:03:52 -0600 Subject: [PATCH 003/719] Adding documentation, various updates --- doc/src/fix_deform.rst | 169 ++++++++++++++- src/fix_deform.cpp | 482 ++++++++++++++++++++++------------------- src/fix_deform.h | 7 +- 3 files changed, 425 insertions(+), 233 deletions(-) diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 805bd843827..d46f1204f5e 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -34,6 +34,12 @@ Syntax effectively an engineering strain rate *erate* value = R R = engineering strain rate (1/time units) + *pressure* values = target gain + target = target pressure (pressure units) + gain = proportional gain constant (1/(time * pressure) or 1/time units) + *pressure/mean* values = target gain + target = target pressure (pressure units) + gain = proportional gain constant (1/(time * pressure) or 1/time units) *trate* value = R R = true strain rate (1/time units) *volume* value = none = adjust this dim to preserve volume of system @@ -54,6 +60,9 @@ Syntax effectively an engineering shear strain rate *erate* value = R R = engineering shear strain rate (1/time units) + *pressure* values = target gain + target = target pressure (pressure units) + gain = proportional gain constant (1/(time * pressure) or 1/time units) *trate* value = R R = true shear strain rate (1/time units) *wiggle* values = A Tp @@ -64,7 +73,7 @@ Syntax v_name2 = variable with name2 for change rate as function of time * zero or more keyword/value pairs may be appended -* keyword = *remap* or *flip* or *units* +* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure* .. parsed-literal:: @@ -77,6 +86,14 @@ Syntax *units* value = *lattice* or *box* lattice = distances are defined in lattice units box = distances are defined in simulation box units + *couple* value = *none* or *xyz* or *xy* or *yz* or *xz* + couple pressure values of various dimensions + *vol/balance/p* = *yes* or *no* + Modifies the behavior of the *volume* option to try and balance pressures + *max/rate* value = *rate* + rate = maximum strain rate for pressure control + *normalize/pressure* value = *yes* or *no* + determine whether pressure deviation is normalized by target pressure Examples """""""" @@ -87,6 +104,9 @@ Examples fix 1 all deform 1 x trate 0.1 y volume z volume fix 1 all deform 1 xy erate 0.001 remap v fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0 + fix 1 all deform 1 x pressure 2.0 0.1 normalize/pressure yes max/rate 0.001 + fix 1 all deform 1 x trate 0.1 y volume z volume vol/balance/p yes + fix 1 all deform 1 x trate 0.1 y pressure/mean 0.0 1.0 z pressure/mean 0.0 1.0 Description """"""""""" @@ -230,7 +250,11 @@ the product of x,z lengths constant. If "x scale 1.1 y volume z volume" is specified, then both the y,z box lengths will shrink as x increases to keep the volume constant (product of x,y,z lengths). In this case, the y,z box lengths shrink so as to keep their relative -aspect ratio constant. +aspect ratio constant. When maintaining a constant volume using two +separate dimensions, one can alternatively allow the two dimensions +to adjust their aspect ratio to attempt to maintain equivalent +pressures along the two dimensions. See the +:ref:`vol/balance/p ` option for more details. For solids or liquids, note that when one dimension of the box is expanded via fix deform (i.e. tensile strain), it may be physically @@ -292,6 +316,38 @@ For the *scale*, *vel*, *erate*, *trate*, *volume*, *wiggle*, and *variable* styles, the box length is expanded or compressed around its mid point. +The *pressure* style adjusts a dimensions's box length to control that +component of the pressure tensor. This option attempts to maintain a +specified target value using a linear controller where the box length L +evolves according to the equation + +.. parsed-literal:: + + \frac{d L(t)}{dt} = L(t) k (P_t - P) + +where :math:`k` is a proportional gain constant, :math:`P_t` is the target +pressure, and :math:`P` is the current pressure along that dimension. This +approach is similar to the method used to control the pressure by +:doc:`fix press/berendsen `. The target pressure +accepts either a constant numeric value or a LAMMPS :ref:`variable `. +Notably, this variable can be a function of time or other components of +the pressure tensor. By default, :math:`k` has units of 1/(time * pressure) +although this will change if the *normalize/pessure* option is set as +:ref:`discussed below `. There is no proven method +to choosing an appropriate value of :math:`k` as it will depend on the +specific details of a simulation and testing different values is +recommended. One can also apply a maximum limit to the magnitude of the +applied strain using the :ref:`max/rate ` option and couple +pressures in different dimensions using the :ref:`couple ` +option. + +The *pressure/mean* style is changes a dimension in order to maintain +a constant mean pressure defined as the trace of the pressure tensor. +This option is therefore very similar to the *presssure* style with +identical arguments except the current and target pressures refer to the +mean trace of the pressure tensor. The same options also apply except +for the :ref:`couple ` option. + ---------- For the *xy*, *xz*, and *yz* parameters, this is the meaning of their @@ -433,6 +489,27 @@ assume that the current timestep = 0. variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)" fix 2 all deform 1 xy variable v_displace v_rate remap v +The *pressure* style adjusts a tilt factor to control the corresponding +off-diagonal component of the pressure tensor. This option attempts to +maintain a specified target value using a linear controller where the +tilt factor T evolves according to the equation + +.. parsed-literal:: + + \frac{d T(t)}{dt} = L(t) k (P - P_t) + +where :math:`k` is a proportional gain constant, :math:`P_t` is the target +pressure, :math:`P` is the current pressure, and :math:`L` is the perpendicular +box length. The target pressure accepts either a constant numeric value or a +LAMMPS :ref:`variable `. Notably, this variable can be a function +of time or other components of the pressure tensor. By default, :math:`k` +has units of 1/(time * pressure) although this will change if the +*normalize/pessure* option is set as :ref:`discussed below `. +There is no proven method to choosing an appropriate value of :math:`k` as it +will depend on thespecific details of a simulation and testing different +values isrecommended. One can also apply a maximum limit to the magnitude +of the applied strain using the :ref:`max/rate ` option. + ---------- All of the tilt styles change the xy, xz, yz tilt factors during a @@ -561,6 +638,73 @@ does not affect the *variable* style. You should use the *xlat*, *ylat*, *zlat* keywords of the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. +.. _deform_normalize: + +The *normalize/pressure* keyword changes how box dimensions evolve when +using the *pressure* or *pressure/mean* deformation options. If the +*deform/normalize* value is set to *yes*, then the deviation from the +target pressure is normalized by the absolute value of the target +pressure such that the proportional gain constant scales a percentage +error and has units of 1/time. If the target pressure is ever zero, this +will produce an error unless the *max/rate* keyword is defined, +described below, which will cap the divergence. + +.. _deform_max_rate: + +The *max/rate* keyword sets an upper threshold, *rate*, that limits the +maximum magnitude of the strain rate applied in any dimension. This keyword +only applies to the *pressure* and *pressure/mean* options. + +.. _deform_couple: + +The *couple* keyword allows two or three of the diagonal components of +the pressure tensor to be "coupled" together for the *pressure* option. +The value specified with the keyword determines which are coupled. For +example, *xz* means the *Pxx* and *Pzz* components of the stress tensor +are coupled. *Xyz* means all 3 diagonal components are coupled. Coupling +means two things: the instantaneous stress will be computed as an average +of the corresponding diagonal components, and the coupled box dimensions +will be changed together in lockstep, meaning coupled dimensions will be +dilated or contracted by the same percentage every timestep. The target +pressures and gain constants for any coupled dimensions must be identical. +*Couple xyz* can be used for a 2d simulation; the *z* dimension is simply +ignored. + +.. _deform_balance: + +The *vol/balance/p* keyword modifies the behavior of *volume* when two +dimensions are used to maintain a fixed volume. Instead of straining +the two dimensions in lockstep, the two dimensions are allowed to +separately dilate or contract in a manner to maintain a constant +volume while simultaneously trying to keep the pressure along each +dimension equal using a method described in :ref:`(Huang2014) `. + +---------- + +If any pressure controls are used, this fix computes a temperature and +pressure each timestep. To do this, the fix creates its own computes of +style "temp" and "pressure", as if these commands had been issued: + +.. code-block:: LAMMPS + + compute fix-ID_temp group-ID temp + compute fix-ID_press group-ID pressure fix-ID_temp + +See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press", and the group for the new computes is the same +as the fix group. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the +:doc:`thermo_style custom ` command using the appropriate +compute-ID. It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + ---------- .. include:: accel_styles.rst @@ -574,6 +718,15 @@ command. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. +If any pressure controls are used, the :doc:`fix_modify ` *temp* +and *press* options are supported by this fix. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its temperature and pressure calculations. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + This fix can perform deformation over multiple runs, using the *start* and *stop* keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. @@ -597,4 +750,14 @@ Related commands Default """"""" -The option defaults are remap = x, flip = yes, and units = lattice. +The option defaults are remap = x, flip = yes, units = lattice, and +normalize/pressure = no. + +---------- + +.. _Li2014b: + +**(Huang2014)** X. Huang, +"Exploring critical-state behavior using DEM", +Doctoral dissertation, Imperial College. +(2014). https://doi.org/10.25560/25316 diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 766d7c22ae6..db3fad6a958 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -13,13 +13,9 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Pieter in 't Veld (SNL) + Contributing author: Pieter in 't Veld (SNL), Joel Clemmer (SNL) ------------------------------------------------------------------------- */ -// Save previous state to restart file for derivatives -// define hrate_lo/hi for volume/pressure -// add logic for hi_stop and flip flag - #include "fix_deform.h" #include "atom.h" @@ -44,7 +40,7 @@ using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; -enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE,PRESSURE,PISOTROPIC}; +enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE,PRESSURE,PMEAN}; enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE}; enum{NOCOUPLE=0,XYZ,XY,YZ,XZ}; @@ -60,6 +56,9 @@ irregular(nullptr), set(nullptr) pre_exchange_migrate = 1; pcouple = NOCOUPLE; dimension = domain->dimension; + max_h_rate = 0.0; + vol_balance_flag = 0; + normalize_pressure_flag = 0; nevery = utils::inumeric(FLERR,arg[3],false,lmp); if (nevery <= 0) error->all(FLERR,"Illegal fix deform command"); @@ -153,9 +152,9 @@ irregular(nullptr), set(nullptr) if (set[index].pgain <= 0.0) error->all(FLERR,"Illegal fix deform pressure gain, must be positive"); iarg += 4; - } else if (strcmp(arg[iarg+1],"pressure/isotropic") == 0) { - if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform pressure/isotropic", error); - set[index].style = PISOTROPIC; + } else if (strcmp(arg[iarg+1],"pressure/mean") == 0) { + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform pressure/mean", error); + set[index].style = PMEAN; if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) { set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp); } else { @@ -266,21 +265,21 @@ irregular(nullptr), set(nullptr) for (int i = 0; i < 3; i++) { if (coupled_indices[i]) { set[i].coupled_flag = 1; - if (set[i].style != VOLUME && set[i].style != PRESSURE && set[i].style != NONE) - error->all(FLERR, "Cannot couple dimensions unless they are controlled using the pressure or volume option in fix deform"); - if (set[i].style == PRESSURE || set[i].style == VOLUME) + if (set[i].style != PRESSURE && set[i].style != NONE) + error->all(FLERR, "Cannot couple non-pressure-controlled dimensions"); + if (set[i].style == PRESSURE) j = i; } } if (j == -1) - error->all(FLERR, "Must specify pressure style for a coupled dimension in fix deform"); + error->all(FLERR, "Must specify deformation style for at least one coupled dimension"); // Copy or compare data for each coupled dimension for (int i = 0; i < 3; i++) { if (coupled_indices[i]) { // Copy coupling information if dimension style is undefined - if (set[j].style == PRESSURE && set[i].style == NONE) { + if (set[i].style == NONE) { set[i].style = PRESSURE; set[i].pgain = set[j].pgain; if (set[j].pvar_flag) { @@ -289,32 +288,21 @@ irregular(nullptr), set(nullptr) } else { set[i].ptarget = set[j].ptarget; } - } else if (set[j].style == VOLUME && set[i].style == NONE) { - set[i].style = VOLUME; - if (domain->dimension == 2) - error->all(FLERR, "Cannot couple pressure with constant volume in two dimensions"); + } else { + // Check for incompatibilities in style + if (set[j].style != set[i].style && set[i].style != NONE) + error->all(FLERR, "Cannot couple dimensions with different control options"); + if (set[j].style != PRESSURE) continue; + + // If pressure controlled, check for incompatibilities in parameters + if (set[i].pgain != set[j].pgain || set[i].pvar_flag != set[j].pvar_flag || + set[i].ptarget != set[j].ptarget) + error->all(FLERR, "Coupled dimensions must have identical gain parameters"); + + if (set[j].pvar_flag) + if (strcmp(set[i].pstr, set[j].pstr) != 0) + error->all(FLERR, "Coupled dimensions must have the same target pressure"); } - - // Check for incompatibilities in style - if (set[j].style != set[i].style && set[i].style != NONE) - error->all(FLERR, "Cannot couple dimensions with different control options"); - if (set[j].style != PRESSURE) continue; - - // If pressure controlled, check for incompatibilities in parameters - if (set[i].pgain != set[j].pgain) - error->all(FLERR, "Coupled dimensions must have identical gain parameters\n"); - - if (set[i].pvar_flag != set[j].pvar_flag) - error->all(FLERR, "Coupled dimensions must have the same target pressure\n"); - if (set[j].pvar_flag) - if (strcmp(set[i].pstr, set[j].pstr) != 0) - error->all(FLERR, "Coupled dimensions must have the same target pressure\n"); - if (set[i].ptarget != set[j].ptarget) - error->all(FLERR, "Coupled dimensions must have the same target pressure\n"); - - } else { - if (set[i].style == VOLUME && set[j].style == VOLUME) - error->all(FLERR, "Dimensions used to maintain constant volume must either all be coupled or uncoupled"); } } } @@ -335,27 +323,18 @@ irregular(nullptr), set(nullptr) // no tensile deformation on shrink-wrapped dims // b/c shrink wrap will change box-length - if (set[0].style && - (domain->boundary[0][0] >= 2 || domain->boundary[0][1] >= 2)) - error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary"); - if (set[1].style && - (domain->boundary[1][0] >= 2 || domain->boundary[1][1] >= 2)) - error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary"); - if (set[2].style && - (domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2)) + for (int i = 0; i < 3; i++) + if (set[i].style && (domain->boundary[i][0] >= 2 || domain->boundary[i][1] >= 2)) error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary"); // no tilt deformation on shrink-wrapped 2nd dim // b/c shrink wrap will change tilt factor in domain::reset_box() - if (set[3].style && - (domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2)) + if (set[3].style && (domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2)) error->all(FLERR,"Cannot use fix deform tilt on a shrink-wrapped 2nd dim"); - if (set[4].style && - (domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2)) + if (set[4].style && (domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2)) error->all(FLERR,"Cannot use fix deform tilt on a shrink-wrapped 2nd dim"); - if (set[5].style && - (domain->boundary[1][0] >= 2 || domain->boundary[1][1] >= 2)) + if (set[5].style && (domain->boundary[1][0] >= 2 || domain->boundary[1][1] >= 2)) error->all(FLERR,"Cannot use fix deform tilt on a shrink-wrapped 2nd dim"); // apply scaling to FINAL,DELTA,VEL,WIGGLE since they have dist/vel units @@ -436,6 +415,9 @@ irregular(nullptr), set(nullptr) set[i].dynamic1 = other1; set[i].dynamic2 = other2; } + + if (vol_balance_flag && set[i].substyle != TWO_FROM_ONE) + error->all(FLERR, "Two dimensions must maintain constant volume to use the vol/balance/p option"); } // set strain_flag @@ -443,30 +425,41 @@ irregular(nullptr), set(nullptr) strain_flag = 0; for (int i = 0; i < 6; i++) if (set[i].style != NONE && set[i].style != VOLUME && - set[i].style != PRESSURE && set[i].style != PISOTROPIC) + set[i].style != PRESSURE && set[i].style != PMEAN) strain_flag = 1; // set varflag varflag = 0; - for (int i = 0; i < 6; i++) + for (int i = 0; i < 6; i++) { if (set[i].style == VARIABLE) varflag = 1; + if (set[i].pvar_flag) varflag = 1; + } // set pressure_flag pressure_flag = 0; for (int i = 0; i < 6; i++) { - if (set[i].style == PRESSURE || set[i].style == PISOTROPIC) pressure_flag = 1; + if (set[i].style == PRESSURE || set[i].style == PMEAN) pressure_flag = 1; if (set[i].coupled_flag) pressure_flag = 1; } + if (vol_balance_flag) pressure_flag = 1; // check conflict between constant volume/pressure if (volume_flag) for (int i = 0; i < 6; i++) - if (set[i].style == PISOTROPIC) + if (set[i].style == PMEAN) error->all(FLERR, "Cannot use fix deform to assign constant volume and pressure"); + // check pressure used for max rate and normalize error flag + + if (!pressure_flag && max_h_rate != 0) + error->all(FLERR, "Can only assign a maximum strain rate using pressure-controlled dimensions"); + + if (!pressure_flag && normalize_pressure_flag) + error->all(FLERR, "Can only normalize error using pressure-controlled dimensions"); + // set initial values at time fix deform is issued for (int i = 0; i < 3; i++) { @@ -489,8 +482,6 @@ irregular(nullptr), set(nullptr) if (force_reneighbor) irregular = new Irregular(lmp); else irregular = nullptr; - TWOPI = 2.0*MY_PI; - // Create pressure compute, if needed pflag = 0; @@ -592,7 +583,7 @@ void FixDeform::init() error->all(FLERR,"Variable {} for fix deform is invalid style", set[i].hratestr); } - // check optional variables for PRESSURE or PISOTROPIC style + // check optional variables for PRESSURE or PMEAN style for (int i = 0; i < 6; i++) { if (!set[i].pvar_flag) continue; @@ -627,30 +618,26 @@ void FixDeform::init() set[i].lo_stop = set[i].lo_start + set[i].dlo; set[i].hi_stop = set[i].hi_start + set[i].dhi; } else if (set[i].style == SCALE) { - set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*set[i].scale*(set[i].hi_start-set[i].lo_start); - set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*set[i].scale*(set[i].hi_start-set[i].lo_start); + double shift = 0.5 * set[i].scale * (set[i].hi_start - set[i].lo_start); + set[i].lo_stop = 0.5 * (set[i].lo_start + set[i].hi_start) - shift; + set[i].hi_stop = 0.5 * (set[i].lo_start + set[i].hi_start) + shift; } else if (set[i].style == VEL) { - set[i].lo_stop = set[i].lo_start - 0.5*delt*set[i].vel; - set[i].hi_stop = set[i].hi_start + 0.5*delt*set[i].vel; + set[i].lo_stop = set[i].lo_start - 0.5 * delt * set[i].vel; + set[i].hi_stop = set[i].hi_start + 0.5 * delt * set[i].vel; } else if (set[i].style == ERATE) { - set[i].lo_stop = set[i].lo_start - - 0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start); - set[i].hi_stop = set[i].hi_start + - 0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start); + double shift = 0.5 * delt * set[i].rate * (set[i].hi_start - set[i].lo_start); + set[i].lo_stop = set[i].lo_start - shift; + set[i].hi_stop = set[i].hi_start + shift; if (set[i].hi_stop <= set[i].lo_stop) error->all(FLERR,"Final box dimension due to fix deform is < 0.0"); } else if (set[i].style == TRATE) { - set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt)); - set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt)); + double shift = 0.5 * ((set[i].hi_start - set[i].lo_start) * exp(set[i].rate * delt)); + set[i].lo_stop = 0.5 * (set[i].lo_start + set[i].hi_start) - shift; + set[i].hi_stop = 0.5 * (set[i].lo_start + set[i].hi_start) + shift; } else if (set[i].style == WIGGLE) { - set[i].lo_stop = set[i].lo_start - - 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); - set[i].hi_stop = set[i].hi_start + - 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); + double shift = 0.5 * set[i].amplitude * sin(MY_2PI * delt / set[i].tperiod); + set[i].lo_stop = set[i].lo_start - shift; + set[i].hi_stop = set[i].hi_start + shift; } } @@ -666,50 +653,46 @@ void FixDeform::init() } else if (set[i].style == DELTA) { set[i].tilt_stop = set[i].tilt_start + set[i].dtilt; } else if (set[i].style == VEL) { - set[i].tilt_stop = set[i].tilt_start + delt*set[i].vel; + set[i].tilt_stop = set[i].tilt_start + delt * set[i].vel; } else if (set[i].style == ERATE) { if (i == 3) set[i].tilt_stop = set[i].tilt_start + - delt*set[i].rate * (set[2].hi_start-set[2].lo_start); + delt * set[i].rate * (set[2].hi_start - set[2].lo_start); if (i == 4) set[i].tilt_stop = set[i].tilt_start + - delt*set[i].rate * (set[2].hi_start-set[2].lo_start); + delt * set[i].rate * (set[2].hi_start - set[2].lo_start); if (i == 5) set[i].tilt_stop = set[i].tilt_start + - delt*set[i].rate * (set[1].hi_start-set[1].lo_start); + delt * set[i].rate * (set[1].hi_start - set[1].lo_start); } else if (set[i].style == TRATE) { - set[i].tilt_stop = set[i].tilt_start * exp(set[i].rate*delt); + set[i].tilt_stop = set[i].tilt_start * exp(set[i].rate * delt); } else if (set[i].style == WIGGLE) { - set[i].tilt_stop = set[i].tilt_start + - set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); + double shift = set[i].amplitude * sin(MY_2PI * delt / set[i].tperiod); + set[i].tilt_stop = set[i].tilt_start + shift; // compute min/max for WIGGLE = extrema tilt factor will ever reach if (set[i].amplitude >= 0.0) { - if (delt < 0.25*set[i].tperiod) { + if (delt < 0.25 * set[i].tperiod) { set[i].tilt_min = set[i].tilt_start; - set[i].tilt_max = set[i].tilt_start + - set[i].amplitude*sin(TWOPI*delt/set[i].tperiod); - } else if (delt < 0.5*set[i].tperiod) { + set[i].tilt_max = set[i].tilt_start + shift; + } else if (delt < 0.5 * set[i].tperiod) { set[i].tilt_min = set[i].tilt_start; set[i].tilt_max = set[i].tilt_start + set[i].amplitude; - } else if (delt < 0.75*set[i].tperiod) { - set[i].tilt_min = set[i].tilt_start - - set[i].amplitude*sin(TWOPI*delt/set[i].tperiod); + } else if (delt < 0.75 * set[i].tperiod) { + set[i].tilt_min = set[i].tilt_start - shift; set[i].tilt_max = set[i].tilt_start + set[i].amplitude; } else { set[i].tilt_min = set[i].tilt_start - set[i].amplitude; set[i].tilt_max = set[i].tilt_start + set[i].amplitude; } } else { - if (delt < 0.25*set[i].tperiod) { - set[i].tilt_min = set[i].tilt_start - - set[i].amplitude*sin(TWOPI*delt/set[i].tperiod); + if (delt < 0.25 * set[i].tperiod) { + set[i].tilt_min = set[i].tilt_start - shift; set[i].tilt_max = set[i].tilt_start; - } else if (delt < 0.5*set[i].tperiod) { + } else if (delt < 0.5 * set[i].tperiod) { set[i].tilt_min = set[i].tilt_start - set[i].amplitude; set[i].tilt_max = set[i].tilt_start; - } else if (delt < 0.75*set[i].tperiod) { + } else if (delt < 0.75 * set[i].tperiod) { set[i].tilt_min = set[i].tilt_start - set[i].amplitude; - set[i].tilt_max = set[i].tilt_start + - set[i].amplitude*sin(TWOPI*delt/set[i].tperiod); + set[i].tilt_max = set[i].tilt_start + shift; } else { set[i].tilt_min = set[i].tilt_start - set[i].amplitude; set[i].tilt_max = set[i].tilt_start + set[i].amplitude; @@ -729,25 +712,25 @@ void FixDeform::init() // this is b/c the flips would induce continuous changes in xz // in order to keep the edge vectors of the flipped shape matrix // an integer combination of the edge vectors of the unflipped shape matrix - // VARIABLE for yz is error, since no way to calculate if box flip occurs + // VARIABLE or PRESSURE for yz is error, since no way to calculate if box flip occurs // WIGGLE lo/hi flip test is on min/max oscillation limit, not tilt_stop // only trigger actual errors if flipflag is set if (set[3].style && set[5].style) { int flag = 0; double lo,hi; - if (flipflag && set[3].style == VARIABLE) - error->all(FLERR,"Fix deform cannot use yz variable with xy"); + if (flipflag && (set[3].style == VARIABLE || set[3].style == PRESSURE)) + error->all(FLERR,"Fix deform cannot use yz variable or pressure with xy"); if (set[3].style == WIGGLE) { lo = set[3].tilt_min; hi = set[3].tilt_max; } else lo = hi = set[3].tilt_stop; if (flipflag) { - if (lo/(set[1].hi_start-set[1].lo_start) < -0.5 || - hi/(set[1].hi_start-set[1].lo_start) > 0.5) flag = 1; + if (lo / (set[1].hi_start - set[1].lo_start) < -0.5 || + hi / (set[1].hi_start - set[1].lo_start) > 0.5) flag = 1; if (set[1].style) { - if (lo/(set[1].hi_stop-set[1].lo_stop) < -0.5 || - hi/(set[1].hi_stop-set[1].lo_stop) > 0.5) flag = 1; + if (lo / (set[1].hi_stop - set[1].lo_stop) < -0.5 || + hi / (set[1].hi_stop - set[1].lo_stop) > 0.5) flag = 1; } if (flag) error->all(FLERR,"Fix deform is changing yz too much with xy"); @@ -798,13 +781,11 @@ void FixDeform::init() if (pressure_flag) { int icompute = modify->find_compute(id_temp); - if (icompute < 0) - error->all(FLERR,"Temperature ID for fix deform does not exist"); + if (icompute < 0) error->all(FLERR,"Temperature ID for fix deform does not exist"); temperature = modify->compute[icompute]; icompute = modify->find_compute(id_press); - if (icompute < 0) - error->all(FLERR,"Pressure ID for fix deform does not exist"); + if (icompute < 0) error->all(FLERR,"Pressure ID for fix deform does not exist"); pressure = modify->compute[icompute]; } } @@ -816,7 +797,6 @@ void FixDeform::init() void FixDeform::setup(int /*vflag*/) { // trigger virial computation on next timestep - if (pressure_flag) pressure->addstep(update->ntimestep+1); } @@ -872,13 +852,10 @@ void FixDeform::end_of_step() temperature->compute_vector(); pressure->compute_vector(); for (int i = 0; i < 3; i++) { - if (! set[i].saved) { + if (!set[i].saved) { set[i].saved = 1; set[i].prior_rate = 0.0; set[i].prior_pressure = pressure->vector[i]; - if (i == 0) set[i].box_length = domain->xprd; - else if (i == 1) set[i].box_length = domain->yprd; - else set[i].box_length = domain->zprd; } } set_pressure(); @@ -892,15 +869,39 @@ void FixDeform::end_of_step() // Save pressure/strain rate if required if (pressure_flag) { - double dt_inv = 1.0 / update->dt; for (int i = 0; i < 3; i++) { set[i].prior_pressure = pressure->vector[i]; - set[i].prior_rate = ((set[i].hi_target - set[i].lo_target) / set[i].box_length - 1.0) * dt_inv; + set[i].prior_rate = ((set[i].hi_target - set[i].lo_target) / + (domain->boxhi[i] - domain->boxlo[i]) - 1.0) / update->dt; } } if (varflag) modify->addstep_compute(update->ntimestep + nevery); + // tilt_target can be large positive or large negative value + // add/subtract box lengths until tilt_target is closest to current value + + if (triclinic) { + double *h = domain->h; + for (int i = 3; i < 6; i++) { + int idenom = 0; + if (i == 5) idenom = 0; + else if (i == 4) idenom = 0; + else if (i == 3) idenom = 1; + double denom = set[idenom].hi_target - set[idenom].lo_target; + + double current = h[i] / h[idenom]; + + while (set[i].tilt_target / denom - current > 0.0) + set[i].tilt_target -= denom; + while (set[i].tilt_target / denom - current < 0.0) + set[i].tilt_target += denom; + if (fabs(set[i].tilt_target / denom - 1.0 - current) < + fabs(set[i].tilt_target / denom - current)) + set[i].tilt_target -= denom; + } + } + // if any tilt ratios exceed 0.5, set flip = 1 and compute new tilt values // do not flip in x or y if non-periodic (can tilt but not flip) // this is b/c the box length would be changed (dramatically) by flip @@ -915,12 +916,12 @@ void FixDeform::end_of_step() double yprd = set[1].hi_target - set[1].lo_target; double xprdinv = 1.0 / xprd; double yprdinv = 1.0 / yprd; - if (set[3].tilt_target*yprdinv < -0.5 || - set[3].tilt_target*yprdinv > 0.5 || - set[4].tilt_target*xprdinv < -0.5 || - set[4].tilt_target*xprdinv > 0.5 || - set[5].tilt_target*xprdinv < -0.5 || - set[5].tilt_target*xprdinv > 0.5) { + if (set[3].tilt_target * yprdinv < -0.5 || + set[3].tilt_target * yprdinv > 0.5 || + set[4].tilt_target * xprdinv < -0.5 || + set[4].tilt_target * xprdinv > 0.5 || + set[5].tilt_target * xprdinv < -0.5 || + set[5].tilt_target * xprdinv > 0.5) { set[3].tilt_flip = set[3].tilt_target; set[4].tilt_flip = set[4].tilt_target; set[5].tilt_flip = set[5].tilt_target; @@ -928,30 +929,30 @@ void FixDeform::end_of_step() flipxy = flipxz = flipyz = 0; if (domain->yperiodic) { - if (set[3].tilt_flip*yprdinv < -0.5) { + if (set[3].tilt_flip * yprdinv < -0.5) { set[3].tilt_flip += yprd; set[4].tilt_flip += set[5].tilt_flip; flipyz = 1; - } else if (set[3].tilt_flip*yprdinv > 0.5) { + } else if (set[3].tilt_flip * yprdinv > 0.5) { set[3].tilt_flip -= yprd; set[4].tilt_flip -= set[5].tilt_flip; flipyz = -1; } } if (domain->xperiodic) { - if (set[4].tilt_flip*xprdinv < -0.5) { + if (set[4].tilt_flip * xprdinv < -0.5) { set[4].tilt_flip += xprd; flipxz = 1; } - if (set[4].tilt_flip*xprdinv > 0.5) { + if (set[4].tilt_flip * xprdinv > 0.5) { set[4].tilt_flip -= xprd; flipxz = -1; } - if (set[5].tilt_flip*xprdinv < -0.5) { + if (set[5].tilt_flip * xprdinv < -0.5) { set[5].tilt_flip += xprd; flipxy = 1; } - if (set[5].tilt_flip*xprdinv > 0.5) { + if (set[5].tilt_flip * xprdinv > 0.5) { set[5].tilt_flip -= xprd; flipxy = -1; } @@ -1023,12 +1024,8 @@ void FixDeform::end_of_step() // trigger virial computation, if needed, on next timestep - if (pressure_flag) { + if (pressure_flag) pressure->addstep(update->ntimestep+1); - set[0].box_length = domain->xprd; - set[1].box_length = domain->yprd; - set[2].box_length = domain->zprd; - } } /* ---------------------------------------------------------------------- @@ -1052,36 +1049,31 @@ void FixDeform::set_strain() set[i].hi_target = domain->boxhi[i]; } else if (set[i].style == TRATE) { double delt = (update->ntimestep - update->beginstep) * update->dt; - set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) - - 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt)); - set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) + - 0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt)); + double shift = 0.5 * ((set[i].hi_start - set[i].lo_start) * exp(set[i].rate * delt)); + set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - shift; + set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + shift; h_rate[i] = set[i].rate * domain->h[i]; - h_ratelo[i] = -0.5*h_rate[i]; + h_ratelo[i] = -0.5 * h_rate[i]; } else if (set[i].style == WIGGLE) { double delt = (update->ntimestep - update->beginstep) * update->dt; - set[i].lo_target = set[i].lo_start - - 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); - set[i].hi_target = set[i].hi_start + - 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); - h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude * - cos(TWOPI*delt/set[i].tperiod); - h_ratelo[i] = -0.5*h_rate[i]; + double shift = 0.5 * set[i].amplitude * sin(MY_2PI * delt / set[i].tperiod); + set[i].lo_target = set[i].lo_start - shift; + set[i].hi_target = set[i].hi_start + shift; + h_rate[i] = MY_2PI / set[i].tperiod * set[i].amplitude * + cos(MY_2PI * delt / set[i].tperiod); + h_ratelo[i] = -0.5 * h_rate[i]; } else if (set[i].style == VARIABLE) { double del = input->variable->compute_equal(set[i].hvar); - set[i].lo_target = set[i].lo_start - 0.5*del; - set[i].hi_target = set[i].hi_start + 0.5*del; + set[i].lo_target = set[i].lo_start - 0.5 * del; + set[i].hi_target = set[i].hi_start + 0.5 * del; h_rate[i] = input->variable->compute_equal(set[i].hratevar); - h_ratelo[i] = -0.5*h_rate[i]; + h_ratelo[i] = -0.5 * h_rate[i]; } else if (set[i].style != VOLUME) { - set[i].lo_target = set[i].lo_start + - delta*(set[i].lo_stop - set[i].lo_start); - set[i].hi_target = set[i].hi_start + - delta*(set[i].hi_stop - set[i].hi_start); + set[i].lo_target = set[i].lo_start + delta * (set[i].lo_stop - set[i].lo_start); + set[i].hi_target = set[i].hi_start + delta * (set[i].hi_stop - set[i].hi_start); } } - // for triclinic, set new box shape // for NONE, target is current tilt // for TRATE, set target directly based on current time. also set h_rate @@ -1099,41 +1091,21 @@ void FixDeform::set_strain() else if (i == 3) set[i].tilt_target = domain->yz; } else if (set[i].style == TRATE) { double delt = (update->ntimestep - update->beginstep) * update->dt; - set[i].tilt_target = set[i].tilt_start * exp(set[i].rate*delt); + set[i].tilt_target = set[i].tilt_start * exp(set[i].rate * delt); h_rate[i] = set[i].rate * domain->h[i]; } else if (set[i].style == WIGGLE) { double delt = (update->ntimestep - update->beginstep) * update->dt; set[i].tilt_target = set[i].tilt_start + - set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); - h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude * - cos(TWOPI*delt/set[i].tperiod); + set[i].amplitude * sin(MY_2PI * delt / set[i].tperiod); + h_rate[i] = MY_2PI / set[i].tperiod * set[i].amplitude * + cos(MY_2PI * delt / set[i].tperiod); } else if (set[i].style == VARIABLE) { double delta_tilt = input->variable->compute_equal(set[i].hvar); set[i].tilt_target = set[i].tilt_start + delta_tilt; h_rate[i] = input->variable->compute_equal(set[i].hratevar); } else { - set[i].tilt_target = set[i].tilt_start + - delta*(set[i].tilt_stop - set[i].tilt_start); + set[i].tilt_target = set[i].tilt_start + delta * (set[i].tilt_stop - set[i].tilt_start); } - - // tilt_target can be large positive or large negative value - // add/subtract box lengths until tilt_target is closest to current value - - int idenom = 0; - if (i == 5) idenom = 0; - else if (i == 4) idenom = 0; - else if (i == 3) idenom = 1; - double denom = set[idenom].hi_target - set[idenom].lo_target; - - double current = h[i]/h[idenom]; - - while (set[i].tilt_target/denom - current > 0.0) - set[i].tilt_target -= denom; - while (set[i].tilt_target/denom - current < 0.0) - set[i].tilt_target += denom; - if (fabs(set[i].tilt_target/denom - 1.0 - current) < - fabs(set[i].tilt_target/denom - current)) - set[i].tilt_target -= denom; } } } @@ -1156,7 +1128,7 @@ void FixDeform::set_pressure() double p_current[3]; if (pcouple == XYZ) { - double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]); + double ave = THIRD * (tensor[0] + tensor[1] + tensor[2]); p_current[0] = p_current[1] = p_current[2] = ave; } else if (pcouple == XY) { double ave = 0.5 * (tensor[0] + tensor[1]); @@ -1172,30 +1144,68 @@ void FixDeform::set_pressure() p_current[1] = tensor[1]; } else { if (set[0].style == PRESSURE) p_current[0] = tensor[0]; - else if (set[0].style == PISOTROPIC) p_current[0] = scalar; + else if (set[0].style == PMEAN) p_current[0] = scalar; if (set[1].style == PRESSURE) p_current[1] = tensor[1]; - else if (set[1].style == PISOTROPIC) p_current[1] = scalar; + else if (set[1].style == PMEAN) p_current[1] = scalar; if (set[2].style == PRESSURE) p_current[2] = tensor[2]; - else if (set[2].style == PISOTROPIC) p_current[2] = scalar; + else if (set[2].style == PMEAN) p_current[2] = scalar; } for (int i = 0; i < 3; i++) { - if (set[i].style != PRESSURE && set[i].style != PISOTROPIC) continue; - double dilation = 1.0 - update->dt * set[i].pgain * (set[i].ptarget - p_current[i]); - double center_start = 0.5 * (set[i].lo_start + set[i].hi_start); - double offset = 0.5 * set[i].box_length * dilation; - //printf("ptarget %g vs %g, dilation %g cs %g ofset %g box %g\n", set[i].ptarget, p_current[i], dilation, center_start, offset, set[i].box_length); - set[i].lo_target = center_start - offset; - set[i].hi_target = center_start + offset; + if (set[i].style != PRESSURE && set[i].style != PMEAN) continue; + + h_rate[i] = set[i].pgain * (p_current[i] - set[i].ptarget); + if (normalize_pressure_flag) { + if (set[i].ptarget == 0) { + if (max_h_rate == 0) { + error->all(FLERR, "Cannot normalize error for zero pressure without defining a max rate"); + } else h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]); + } else h_rate[i] /= fabs(set[i].ptarget); + } + + if (max_h_rate != 0) + if (fabs(set[i].ptarget) > max_h_rate) + h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]); + + double offset = 0.5 * (domain->boxhi[i] - domain->boxlo[i]) * (1.0 + update->dt * h_rate[i]); + set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - offset; + set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + offset; } for (int i = 3; i < 6; i++) { - double shift = update->dt * set[i].pgain * (set[i].ptarget - tensor[i]); - if (i == 3) set[i].tilt_target = domain->xy + shift * domain->xprd; - else if (i == 4) set[i].tilt_target = domain->xz + shift * domain->xprd; - else set[i].tilt_target = domain->yz + shift * domain->yprd; + if (set[i].style != PRESSURE) continue; + + double L, tilt, pcurrent; + if (i == 3) { + L = domain->zprd; + tilt = domain->yz; + pcurrent = tensor[5]; + } else if (i == 4) { + L = domain->zprd; + tilt = domain->xz + update->dt; + pcurrent = tensor[4]; + } else { + L = domain->yprd; + tilt = domain->xy; + pcurrent = tensor[3]; + } + + h_rate[i] = L * set[i].pgain * (pcurrent - set[i].ptarget); + if (normalize_pressure_flag) { + if (set[i].ptarget == 0) { + if (max_h_rate == 0) { + error->all(FLERR, "Cannot normalize error for zero pressure without defining a max rate"); + } else h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]); + } else h_rate[i] /= fabs(set[i].ptarget); + } + + if (max_h_rate != 0) + if (fabs(h_rate[i]) > max_h_rate) + h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]); + + set[i].tilt_target = tilt + update->dt * h_rate[i]; } } @@ -1211,61 +1221,65 @@ void FixDeform::set_volume() for (int i = 0; i < 3; i++) { if (set[i].style != VOLUME) continue; + int dynamic1 = set[i].dynamic1; + int dynamic2 = set[i].dynamic2; + int fixed = set[i].fixed; double v0 = set[i].vol_start; - double center_start = 0.5 * (set[i].lo_start + set[i].hi_start); - double offset; + double shift; if (set[i].substyle == ONE_FROM_ONE) { - offset = 0.5 * (v0 / - (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) / - (set[set[i].fixed].hi_start-set[set[i].fixed].lo_start)); + shift = 0.5 * (v0 / (set[dynamic1].hi_target - set[dynamic1].lo_target) / + (set[fixed].hi_start-set[fixed].lo_start)); } else if (set[i].substyle == ONE_FROM_TWO) { - offset = 0.5 * (v0 / - (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) / - (set[set[i].dynamic2].hi_target - set[set[i].dynamic2].lo_target)); + shift = 0.5 * (v0 / (set[dynamic1].hi_target - set[dynamic1].lo_target) / + (set[dynamic2].hi_target - set[dynamic2].lo_target)); } else if (set[i].substyle == TWO_FROM_ONE) { - if (!set[i].coupled_flag) { - offset = 0.5 * sqrt(v0 * (set[i].hi_start - set[i].lo_start) / - (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) / - (set[set[i].fixed].hi_start - set[set[i].fixed].lo_start)); + if (!vol_balance_flag) { + shift = 0.5 * sqrt(v0 * (set[i].hi_start - set[i].lo_start) / + (set[dynamic1].hi_target - set[dynamic1].lo_target) / + (set[fixed].hi_start - set[fixed].lo_start)); } else { double dt = update->dt; double e1i = set[i].prior_rate; - double e2i = set[set[i].fixed].prior_rate; - double L3 = (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target); - double e3 = (L3 / set[set[i].dynamic1].box_length - 1.0) / dt; + double e2i = set[fixed].prior_rate; + double L1i = domain->boxhi[i] - domain->boxlo[i]; + double L2i = domain->boxhi[fixed] - domain->boxlo[fixed]; + double L3i = domain->boxhi[dynamic1] - domain->boxlo[dynamic1]; + double L3 = (set[dynamic1].hi_target - set[dynamic1].lo_target); + double e3 = (L3 / L3i - 1.0) / dt; double p1 = pressure->vector[i]; - double p2 = pressure->vector[set[i].fixed]; + double p2 = pressure->vector[fixed]; double p1i = set[i].prior_pressure; - double p2i = set[set[i].fixed].prior_pressure; + double p2i = set[fixed].prior_pressure; if (e3 == 0) { e1 = 0.0; e2 = 0.0; - offset = 0.5 * set[i].box_length; + shift = 0.5 * L1i; } else if (e1i == 0 || e2i == 0 || (p2 == p2i && p1 == p1i)) { - // If no prior strain or no change in pressure (initial step) just scale offset by relative box lengths - offset = 0.5 * sqrt(v0 * set[i].box_length / L3 / set[set[i].fixed].box_length); + // If no prior strain or no change in pressure (initial step) just scale shift by relative box lengths + shift = 0.5 * sqrt(v0 * L1i / L3 / L2i); } else { - if (! linked_pressure) { - // Calculate first strain rate by expanding stress to linear order in strain to achieve p1(t+dt) = p2(t+dt) - e1 = -e3 / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2); - e1 /= (p2 - p2i + (p1 - p1i) / e1i * e2i); - + if (!linked_pressure) { + // Calculate first strain rate by expanding stress to linear order, p1(t+dt) = p2(t+dt) // Calculate second strain rate to preserve volume - e2 = (1.0 - (1 + e3 * dt) * (1 + e1 * dt)); - e2 /= (1 + e3 * dt) * (1 + e1 * dt) * dt; + e1 = -e3 / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2) / (p2 - p2i + (p1 - p1i) / e1i * e2i); + e2 = (1.0 - (1 + e3 * dt) * (1 + e1 * dt)) / ((1 + e3 * dt) * (1 + e1 * dt) * dt); - offset = 0.5 * set[i].box_length * (1.0 + e1 * dt); + shift = 0.5 * L1i * (1.0 + e1 * dt); linked_pressure = 1; } else { - offset = 0.5 * set[i].box_length * (1.0 + e2 * dt); + // Already calculated value of e2 + shift = 0.5 * L1i * (1.0 + e2 * dt); } } } } - set[i].lo_target = center_start - offset; - set[i].hi_target = center_start + offset; + + h_rate[i] = (2.0 * shift / (domain->boxhi[i] - domain->boxlo[i]) - 1.0) / update->dt; + + set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - shift; + set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + shift; } } @@ -1296,6 +1310,9 @@ void FixDeform::restart(char *buf) set[i].hi_initial = set_restart[i].hi_initial; set[i].vol_initial = set_restart[i].vol_initial; set[i].tilt_initial = set_restart[i].tilt_initial; + set[i].saved = set_restart[i].saved; + set[i].prior_rate = set_restart[i].prior_rate; + set[i].prior_pressure = set_restart[i].prior_pressure; // check if style settings are consistent (should do the whole set?) if (set[i].style != set_restart[i].style) samestyle = 0; @@ -1344,6 +1361,20 @@ void FixDeform::options(int narg, char **arg) else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NOCOUPLE; else error->all(FLERR,"Illegal fix fix deform couple command: {}", arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"max/rate") == 0) { + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform max/rate", error); + max_h_rate = utils::numeric(FLERR,arg[iarg+1],false,lmp); + if (max_h_rate <= 0.0) + error->all(FLERR,"Maximum strain rate must be a positive, non-zero value"); + iarg += 2; + } else if (strcmp(arg[iarg],"normalize/pressure") == 0) { + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform normalize/pressure", error); + normalize_pressure_flag = utils::logical(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + } else if (strcmp(arg[iarg],"vol/balance/p") == 0) { + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform vol/balance/p", error); + vol_balance_flag = utils::logical(FLERR,arg[iarg+1],false,lmp); + iarg += 2; } else error->all(FLERR,"Illegal fix deform command: {}", arg[iarg]); } @@ -1363,7 +1394,6 @@ double FixDeform::memory_usage() return bytes; } - /* ---------------------------------------------------------------------- */ int FixDeform::modify_param(int narg, char **arg) diff --git a/src/fix_deform.h b/src/fix_deform.h index 9ecb9a577dd..eda97f7c908 100644 --- a/src/fix_deform.h +++ b/src/fix_deform.h @@ -44,17 +44,17 @@ class FixDeform : public Fix { protected: int dimension, triclinic, scaleflag, flipflag, pcouple; int flip, flipxy, flipxz, flipyz; - double *h_rate, *h_ratelo; + double *h_rate, *h_ratelo, max_h_rate; int varflag; // 1 if VARIABLE option is used, 0 if not int strain_flag; // 1 if strain-based option is used, 0 if not int volume_flag; // 1 if VOLUME option is used, 0 if not int pressure_flag; // 1 if pressure tensor used, 0 if not int kspace_flag; // 1 if KSpace invoked, 0 if not + int normalize_pressure_flag; // 1 if normalize pressure deviation by target + int vol_balance_flag; // 1 if pressures balanced when maintaining const vol std::vector rfix; // pointers to rigid fixes class Irregular *irregular; // for migrating atoms after box flips - double TWOPI; - char *id_temp, *id_press; class Compute *temperature, *pressure; int tflag, pflag; @@ -72,7 +72,6 @@ class FixDeform : public Fix { double vol_initial, vol_start; double ptarget, pgain; double prior_pressure, prior_rate; - double box_length; int saved; int fixed, dynamic1, dynamic2; char *hstr, *hratestr, *pstr; From 63618d249056b6008d34486301d841fa7bc47ccf Mon Sep 17 00:00:00 2001 From: jtclemm Date: Mon, 24 Oct 2022 10:59:22 -0600 Subject: [PATCH 004/719] Adding scalar pressure compute --- src/fix_deform.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index db3fad6a958..29c286ed029 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -851,6 +851,7 @@ void FixDeform::end_of_step() if (pressure_flag) { temperature->compute_vector(); pressure->compute_vector(); + pressure->compute_scalar(); for (int i = 0; i < 3; i++) { if (!set[i].saved) { set[i].saved = 1; @@ -1157,6 +1158,7 @@ void FixDeform::set_pressure() if (set[i].style != PRESSURE && set[i].style != PMEAN) continue; h_rate[i] = set[i].pgain * (p_current[i] - set[i].ptarget); + if (normalize_pressure_flag) { if (set[i].ptarget == 0) { if (max_h_rate == 0) { From 7160594902f74dd8cb5d88e85a96c1930df67cd0 Mon Sep 17 00:00:00 2001 From: Ludwig Ahrens-Iwers Date: Tue, 31 Jan 2023 07:39:31 +0000 Subject: [PATCH 005/719] Warning for mobile electrode atoms --- src/ELECTRODE/electrode_math.h | 1 + src/ELECTRODE/fix_electrode_conp.cpp | 26 ++- unittest/force-styles/tests/in.conp | 1 + .../tests/kspace-ewald_conp_charge.yaml | 159 +++++++-------- .../tests/kspace-pppm_conp_charge.yaml | 185 +++++++++--------- 5 files changed, 200 insertions(+), 172 deletions(-) diff --git a/src/ELECTRODE/electrode_math.h b/src/ELECTRODE/electrode_math.h index 5992df2289d..08689a5adca 100644 --- a/src/ELECTRODE/electrode_math.h +++ b/src/ELECTRODE/electrode_math.h @@ -18,6 +18,7 @@ #ifndef LMP_ELECTRODE_MATH_H #define LMP_ELECTRODE_MATH_H +#include "math.h" #include "math_const.h" namespace LAMMPS_NS { diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp index dbb508a033f..33632f90996 100644 --- a/src/ELECTRODE/fix_electrode_conp.cpp +++ b/src/ELECTRODE/fix_electrode_conp.cpp @@ -377,6 +377,30 @@ void FixElectrodeConp::init() if (strncmp(modify->fix[i]->style, "electrode", 9) == 0) count++; if (count > 1) error->all(FLERR, "More than one fix electrode"); + // make sure electrode atoms are not integrated if a matrix is used for electrode-electrode interaction + int const nlocal = atom->nlocal; + int *mask = atom->mask; + Fix **fix = modify->fix; + if (matrix_algo) { + std::vector integrate_ids = std::vector(); + for (int i = 0; i < modify->nfix; i++) { + if (fix[i]->time_integrate == 0) continue; + int electrode_mover = 0; + int fix_groupbit = fix[i]->groupbit; + for (int j = 0; j < nlocal; j++) + if ((mask[j] & fix_groupbit) && (mask[j] & groupbit)) electrode_mover = 1; + MPI_Allreduce(MPI_IN_PLACE, &electrode_mover, 1, MPI_INT, MPI_SUM, world); + if (electrode_mover && comm->me == 0) integrate_ids.push_back(fix[i]->id); + } + if (comm->me == 0) + for (char *fix_id : integrate_ids) + error->warning( + FLERR, + "Electrode atoms are integrated by fix {}, but fix electrode is using a matrix method. For " + "mobile electrodes use the conjugate gradient algorithm without matrix ('algo cg').", + fix_id); + } + // check for package intel if (etypes_neighlists) request_etypes_neighlists(); @@ -863,7 +887,7 @@ void FixElectrodeConp::update_charges() update_time += MPI_Wtime() - start; } -std::vector FixElectrodeConp::ele_ele_interaction(const std::vector& q_local) +std::vector FixElectrodeConp::ele_ele_interaction(const std::vector &q_local) { assert(q_local.size() == nlocalele); assert(algo == Algo::CG || algo == Algo::MATRIX_CG); diff --git a/unittest/force-styles/tests/in.conp b/unittest/force-styles/tests/in.conp index 92d2f63cd15..08673ec20bc 100644 --- a/unittest/force-styles/tests/in.conp +++ b/unittest/force-styles/tests/in.conp @@ -22,3 +22,4 @@ angle_coeff * group bot type 1 group top type 2 +group ele type 1 2 diff --git a/unittest/force-styles/tests/kspace-ewald_conp_charge.yaml b/unittest/force-styles/tests/kspace-ewald_conp_charge.yaml index 73fb252226a..9a09a933a40 100644 --- a/unittest/force-styles/tests/kspace-ewald_conp_charge.yaml +++ b/unittest/force-styles/tests/kspace-ewald_conp_charge.yaml @@ -1,7 +1,7 @@ --- -lammps_version: 23 Jun 2022 +lammps_version: 3 Nov 2022 tags: generated -date_generated: Wed Sep 21 13:52:53 2022 +date_generated: Fri Dec 16 10:49:39 2022 epsilon: 1e-12 skip_tests: gpu kokkos_omp omp prerequisites: ! | @@ -17,6 +17,7 @@ post_commands: ! | kspace_modify gewald 0.23118 kspace_modify slab ew2d fix fxcpm bot electrode/conp -1.0 1.805 couple top 1.0 symm on + fix fxforce ele setforce 0 0 0 input_file: in.conp pair_style: coul/long 15.0 pair_coeff: ! | @@ -40,85 +41,85 @@ init_forces: ! |2 10 -3.3526564930579039e-02 -2.3802275431282884e-03 -1.5617801011657175e+00 11 -5.1236396351794389e-02 -4.9531100598979201e-04 -1.5779995894034005e+00 12 -3.3740693032952060e-02 -1.0210406243572182e-03 -1.5630986537874150e+00 - 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From 7d8866891a67878c001e292a21527bb750f7d964 Mon Sep 17 00:00:00 2001 From: Ludwig Ahrens Date: Wed, 1 Feb 2023 10:15:11 +0100 Subject: [PATCH 006/719] Call particle_map in compute of pppm/electrode --- src/ELECTRODE/pppm_electrode.cpp | 137 +++++++++++++++---------------- 1 file changed, 68 insertions(+), 69 deletions(-) diff --git a/src/ELECTRODE/pppm_electrode.cpp b/src/ELECTRODE/pppm_electrode.cpp index 7418a052e65..3bc1364c99e 100644 --- a/src/ELECTRODE/pppm_electrode.cpp +++ b/src/ELECTRODE/pppm_electrode.cpp @@ -445,6 +445,7 @@ void PPPMElectrode::compute(int eflag, int vflag) start_compute(); + /* if (compute_vector_called && last_invert_source) { // electrolyte_density_brick is filled, so we can grab only electrode atoms. // Does not work for direct cg algorithm because electrode charges change after compute_vector. @@ -460,15 +461,17 @@ void PPPMElectrode::compute(int eflag, int vflag) density_brick[nz][ny][nx] += electrolyte_density_brick[nz][ny][nx]; } } else { - make_rho(); + */ + particle_map(); + make_rho(); - // all procs communicate density values from their ghost cells - // to fully sum contribution in their 3d bricks - // remap from 3d decomposition to FFT decomposition + // all procs communicate density values from their ghost cells + // to fully sum contribution in their 3d bricks + // remap from 3d decomposition to FFT decomposition - gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, - MPI_FFT_SCALAR); - } + gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, + MPI_FFT_SCALAR); + //} brick2fft(); @@ -591,6 +594,7 @@ void PPPMElectrode::compute_vector(double *vec, int sensor_grpbit, int source_gr // electrolyte density (without writing an additional function) FFT_SCALAR ***density_brick_real = density_brick; FFT_SCALAR *density_fft_real = density_fft; + particle_map(); make_rho_in_brick(source_grpbit, electrolyte_density_brick, invert_source); density_brick = electrolyte_density_brick; density_fft = electrolyte_density_fft; @@ -674,7 +678,8 @@ void PPPMElectrode::compute_matrix(bigint *imat, double **matrix, bool timer_fla // fft green's function k -> r (double) double *greens_real; memory->create(greens_real, nz_pppm * ny_pppm * nx_pppm, "pppm/electrode:greens_real"); - memset(greens_real, 0, (std::size_t)nz_pppm * (std::size_t)ny_pppm * (std::size_t)nx_pppm * sizeof(double)); + memset(greens_real, 0, + (std::size_t) nz_pppm * (std::size_t) ny_pppm * (std::size_t) nx_pppm * sizeof(double)); for (int i = 0, n = 0; i < nfft; i++) { work2[n++] = greensfn[i]; work2[n++] = ZEROF; @@ -867,7 +872,7 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, double *greens_real, d double **gw; memory->create(gw, nmat, nxyz, "pppm/electrode:gw"); - memset(&(gw[0][0]), 0, (std::size_t)nmat * (std::size_t)nxyz * sizeof(double)); + memset(&(gw[0][0]), 0, (std::size_t) nmat * (std::size_t) nxyz * sizeof(double)); auto fmod = [](int x, int n) { // fast unsigned mod int r = abs(x); @@ -986,17 +991,18 @@ void PPPMElectrode::allocate() // returns local owned and ghost grid bounds // setup communication patterns and buffers - gc = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + gc = new Grid3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_in, nxhi_in, nylo_in, nyhi_in, + nzlo_in, nzhi_in, nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out); - gc->setup_comm(ngc_buf1,ngc_buf2); + gc->setup_comm(ngc_buf1, ngc_buf2); - if (differentiation_flag) npergrid = 1; - else npergrid = 3; + if (differentiation_flag) + npergrid = 1; + else + npergrid = 3; - memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1"); - memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2"); + memory->create(gc_buf1, npergrid * ngc_buf1, "pppm:gc_buf1"); + memory->create(gc_buf2, npergrid * ngc_buf2, "pppm:gc_buf2"); // tally local grid sizes // ngrid = count of owned+ghost grid cells on this proc @@ -1005,67 +1011,63 @@ void PPPMElectrode::allocate() // nfft = FFT points in x-pencil FFT decomposition on this proc // nfft_both = greater of nfft and nfft_brick - ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * - (nzhi_out-nzlo_out+1); + ngrid = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) * (nzhi_out - nzlo_out + 1); - nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * - (nzhi_in-nzlo_in+1); + nfft_brick = (nxhi_in - nxlo_in + 1) * (nyhi_in - nylo_in + 1) * (nzhi_in - nzlo_in + 1); - nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) * - (nzhi_fft-nzlo_fft+1); + nfft = (nxhi_fft - nxlo_fft + 1) * (nyhi_fft - nylo_fft + 1) * (nzhi_fft - nzlo_fft + 1); - nfft_both = MAX(nfft,nfft_brick); + nfft_both = MAX(nfft, nfft_brick); // allocate distributed grid data - memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, - nxlo_out,nxhi_out,"pppm:density_brick"); + memory->create3d_offset(density_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, + "pppm:density_brick"); - memory->create(density_fft,nfft_both,"pppm:density_fft"); - memory->create(greensfn,nfft_both,"pppm:greensfn"); - memory->create(work1,2*nfft_both,"pppm:work1"); - memory->create(work2,2*nfft_both,"pppm:work2"); - memory->create(vg,nfft_both,6,"pppm:vg"); + memory->create(density_fft, nfft_both, "pppm:density_fft"); + memory->create(greensfn, nfft_both, "pppm:greensfn"); + memory->create(work1, 2 * nfft_both, "pppm:work1"); + memory->create(work2, 2 * nfft_both, "pppm:work2"); + memory->create(vg, nfft_both, 6, "pppm:vg"); if (triclinic == 0) { - memory->create1d_offset(fkx,nxlo_fft,nxhi_fft,"pppm:fkx"); - memory->create1d_offset(fky,nylo_fft,nyhi_fft,"pppm:fky"); - memory->create1d_offset(fkz,nzlo_fft,nzhi_fft,"pppm:fkz"); + memory->create1d_offset(fkx, nxlo_fft, nxhi_fft, "pppm:fkx"); + memory->create1d_offset(fky, nylo_fft, nyhi_fft, "pppm:fky"); + memory->create1d_offset(fkz, nzlo_fft, nzhi_fft, "pppm:fkz"); } else { - memory->create(fkx,nfft_both,"pppm:fkx"); - memory->create(fky,nfft_both,"pppm:fky"); - memory->create(fkz,nfft_both,"pppm:fkz"); + memory->create(fkx, nfft_both, "pppm:fkx"); + memory->create(fky, nfft_both, "pppm:fky"); + memory->create(fkz, nfft_both, "pppm:fkz"); } if (differentiation_flag == 1) { - memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, - nxlo_out,nxhi_out,"pppm:u_brick"); + memory->create3d_offset(u_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, + "pppm:u_brick"); - memory->create(sf_precoeff1,nfft_both,"pppm:sf_precoeff1"); - memory->create(sf_precoeff2,nfft_both,"pppm:sf_precoeff2"); - memory->create(sf_precoeff3,nfft_both,"pppm:sf_precoeff3"); - memory->create(sf_precoeff4,nfft_both,"pppm:sf_precoeff4"); - memory->create(sf_precoeff5,nfft_both,"pppm:sf_precoeff5"); - memory->create(sf_precoeff6,nfft_both,"pppm:sf_precoeff6"); + memory->create(sf_precoeff1, nfft_both, "pppm:sf_precoeff1"); + memory->create(sf_precoeff2, nfft_both, "pppm:sf_precoeff2"); + memory->create(sf_precoeff3, nfft_both, "pppm:sf_precoeff3"); + memory->create(sf_precoeff4, nfft_both, "pppm:sf_precoeff4"); + memory->create(sf_precoeff5, nfft_both, "pppm:sf_precoeff5"); + memory->create(sf_precoeff6, nfft_both, "pppm:sf_precoeff6"); } else { - memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, - nxlo_out,nxhi_out,"pppm:vdx_brick"); - memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, - nxlo_out,nxhi_out,"pppm:vdy_brick"); - memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, - nxlo_out,nxhi_out,"pppm:vdz_brick"); + memory->create3d_offset(vdx_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, + "pppm:vdx_brick"); + memory->create3d_offset(vdy_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, + "pppm:vdy_brick"); + memory->create3d_offset(vdz_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, + "pppm:vdz_brick"); } // summation coeffs order_allocated = order; - if (!stagger_flag) memory->create(gf_b,order,"pppm:gf_b"); - memory->create2d_offset(rho1d,3,-order/2,order/2,"pppm:rho1d"); - memory->create2d_offset(drho1d,3,-order/2,order/2,"pppm:drho1d"); - memory->create2d_offset(rho_coeff,order,(1-order)/2,order/2,"pppm:rho_coeff"); - memory->create2d_offset(drho_coeff,order,(1-order)/2,order/2, - "pppm:drho_coeff"); + if (!stagger_flag) memory->create(gf_b, order, "pppm:gf_b"); + memory->create2d_offset(rho1d, 3, -order / 2, order / 2, "pppm:rho1d"); + memory->create2d_offset(drho1d, 3, -order / 2, order / 2, "pppm:drho1d"); + memory->create2d_offset(rho_coeff, order, (1 - order) / 2, order / 2, "pppm:rho_coeff"); + memory->create2d_offset(drho_coeff, order, (1 - order) / 2, order / 2, "pppm:drho_coeff"); // create 2 FFTs and a Remap // 1st FFT keeps data in FFT decomposition @@ -1074,20 +1076,17 @@ void PPPMElectrode::allocate() int tmp; - fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, - nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, - 0,0,&tmp,collective_flag); + fft1 = new FFT3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_fft, nxhi_fft, nylo_fft, nyhi_fft, + nzlo_fft, nzhi_fft, nxlo_fft, nxhi_fft, nylo_fft, nyhi_fft, nzlo_fft, nzhi_fft, + 0, 0, &tmp, collective_flag); - fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - 0,0,&tmp,collective_flag); + fft2 = new FFT3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_fft, nxhi_fft, nylo_fft, nyhi_fft, + nzlo_fft, nzhi_fft, nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, 0, 0, + &tmp, collective_flag); - remap = new Remap(lmp,world, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, - 1,0,0,FFT_PRECISION,collective_flag); + remap = new Remap(lmp, world, nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, nxlo_fft, + nxhi_fft, nylo_fft, nyhi_fft, nzlo_fft, nzhi_fft, 1, 0, 0, FFT_PRECISION, + collective_flag); // ELECTRODE specific allocations From 59bdb136dcada2c62d7c8be7ea298eb3fa26ce00 Mon Sep 17 00:00:00 2001 From: Shern Tee Date: Wed, 31 May 2023 14:50:55 +0000 Subject: [PATCH 007/719] added qtotal keyword --- doc/src/fix_electrode.rst | 17 +++- .../PACKAGES/electrode/graph-il/in.nonneut | 31 +++++++ .../PACKAGES/electrode/graph-il/in.nonneut2 | 33 +++++++ src/ELECTRODE/fix_electrode_conp.cpp | 86 ++++++++++++++++--- src/ELECTRODE/fix_electrode_conp.h | 10 ++- src/ELECTRODE/fix_electrode_thermo.cpp | 5 +- 6 files changed, 168 insertions(+), 14 deletions(-) create mode 100644 examples/PACKAGES/electrode/graph-il/in.nonneut create mode 100644 examples/PACKAGES/electrode/graph-il/in.nonneut2 diff --git a/doc/src/fix_electrode.rst b/doc/src/fix_electrode.rst index 3d543f08d2b..5685482a716 100644 --- a/doc/src/fix_electrode.rst +++ b/doc/src/fix_electrode.rst @@ -45,7 +45,7 @@ Syntax rng_v = integer used to initialize random number generator * zero or more keyword/value pairs may be appended -* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* +* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* or *qtotal* .. parsed-literal:: @@ -68,6 +68,8 @@ Syntax filename = file from which to read elastance matrix *read_inv* value = filename filename = file from which to read inverted matrix + *qtotal* value = number or *v_* equal-style variable + add overall potential so that all electrode charges add up to *qtotal* Examples """""""" @@ -249,6 +251,19 @@ be enabled if any electrode particle has the same type as any electrolyte particle (which would be unusual in a typical simulation) and the fix will issue an error in that case. +.. versionchanged:: qtotal + +The keyword *qtotal* causes *fix electrode/conp* and *fix electrode/thermo* +to add an overall potential to all electrodes so that the total charge on +the electrodes is a specified amount (which may be an equal-style variable). +For example, if a user wanted to simulate a solution of excess cations +such that the total electrolyte charge is +2, setting *qtotal -2* would cause +the total electrode charge to be -2, so that the simulation box remains overall +electroneutral. Since *fix electrode/conq* constrains the total charges of +individual electrodes, and since *symm on* constrains the total charge of all +electrodes to be zero, either option is incompatible with the *qtotal* keyword +(even if *qtotal* is set to zero). + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/examples/PACKAGES/electrode/graph-il/in.nonneut b/examples/PACKAGES/electrode/graph-il/in.nonneut new file mode 100644 index 00000000000..3027faf0cc4 --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/in.nonneut @@ -0,0 +1,31 @@ +# electrodes, overall non-neutral +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +kspace_modify slab 3.0 + +# make an extra anion +variable qmodify index 1 +variable vdiff index 1 +# these values can be changed, e.g. ${LAMMPS_EXECUTABLE} -i in.nonneut -var qmodify 0.9 -var vdiff -2 +# fix electrode/* needs equal style variables: +variable qmodify_equal equal v_qmodify +variable vdiff_equal equal v_vdiff + +create_atoms 4 single 16.1 17.2 0 +set atom 3777 charge $(-v_qmodify) + +fix c top electrode/conp v_vdiff_equal 1.979 couple bot 0 etypes on qtotal v_qmodify_equal +# to test electrode/thermo: +# variable vbot equal 0 +# fix c top electrode/thermo v_vdiff_equal 1.979 couple bot v_vbot etypes on qtotal v_qmodify_equal temp 310 100 12309 # symm on + +variable dv equal f_c[1]-f_c[2] + +variable qelec equal c_qbot+c_qtop +compute qall all reduce sum v_q # total system charge + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_c[1] f_c[2] v_dv v_qelec c_qall +run 500 diff --git a/examples/PACKAGES/electrode/graph-il/in.nonneut2 b/examples/PACKAGES/electrode/graph-il/in.nonneut2 new file mode 100644 index 00000000000..c73eee5db3d --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/in.nonneut2 @@ -0,0 +1,33 @@ +# electrodes, overall non-neutral +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +kspace_modify slab 3.0 + +# make an extra anion +variable qmodify index 1 +variable vdiff index 1 +# these values can be changed, e.g. ${LAMMPS_EXECUTABLE} -i in.nonneut -var qmodify 0.9 -var vdiff -2 +create_atoms 4 single 16.1 17.2 0 +set atom 3777 charge $(-v_qmodify) + +fix c top electrode/conp v_vtop 1.979 couple bot v_vbot etypes on # symm on +# to test electrode/thermo: +#fix c top electrode/thermo v_vtop 1.979 couple bot v_vbot etypes on temp 310 100 12309 symm off +#but it looks like update_psi() is hardwired to impose electroneutrality + +variable csum equal f_c[1][2]+f_c[1][3]+f_c[2][2]+f_c[2][3] +variable cdiff equal 0.5*(f_c[1][2]-f_c[2][3]) +variable qdeficit equal v_qmodify-f_c[1][1]-f_c[2][1]-v_cdiff*v_vdiff +variable vphi equal v_qdeficit/v_csum +variable vtop equal v_vphi+0.5*v_vdiff +variable vbot equal v_vphi-0.5*v_vdiff +variable dv equal v_vtop-v_vbot + +variable qelec equal c_qbot+c_qtop +compute qall all reduce sum v_q # total system charge + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_c[1] f_c[2] v_dv v_qelec c_qall +run 500 diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp index 33632f90996..a7e6cbe922a 100644 --- a/src/ELECTRODE/fix_electrode_conp.cpp +++ b/src/ELECTRODE/fix_electrode_conp.cpp @@ -103,20 +103,23 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : mult_time = 0; n_call = n_cg_step = 0; + qtotal = 0.; + qtotal_var_style = VarStyle::UNSET; + // read fix command fixname = std::string(arg[0]); groups = std::vector(1, igroup); group_bits = std::vector(1, groupbit); group_psi_var_names = std::vector(1); group_psi_var_styles = std::vector(1, VarStyle::CONST); - group_psi = std::vector(1); + group_psi_const = std::vector(1); etypes_neighlists = false; if (strstr(arg[3], "v_") == arg[3]) { std::string vname = arg[3]; group_psi_var_names[0] = vname.substr(2); group_psi_var_styles[0] = VarStyle::EQUAL; } else - group_psi[0] = utils::numeric(FLERR, arg[3], false, lmp); + group_psi_const[0] = utils::numeric(FLERR, arg[3], false, lmp); char *eta_str = arg[4]; eta = utils::numeric(FLERR, eta_str, false, lmp); int iarg = 5; @@ -132,12 +135,12 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : std::string vname = arg[iarg]; group_psi_var_names.push_back(vname.substr(2)); group_psi_var_styles.push_back(VarStyle::EQUAL); - group_psi.push_back(0.); + group_psi_const.push_back(0.); } else { std::string null; group_psi_var_names.push_back(null); group_psi_var_styles.push_back(VarStyle::CONST); - group_psi.push_back(utils::numeric(FLERR, arg[iarg], false, lmp)); + group_psi_const.push_back(utils::numeric(FLERR, arg[iarg], false, lmp)); } } else if ((strcmp(arg[iarg], "algo") == 0)) { if (!default_algo) error->one(FLERR, fmt::format("Algorithm can be set once, only")); @@ -195,6 +198,19 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : thermo_temp = force->boltz / force->qe2f * utils::numeric(FLERR, arg[++iarg], false, lmp); thermo_time = utils::numeric(FLERR, arg[++iarg], false, lmp); thermo_init = utils::inumeric(FLERR, arg[++iarg], false, lmp); + } else if ((strcmp(arg[iarg], "qtotal") == 0)) { + if (iarg + 2 > narg) error->all(FLERR, "Need one argument after qtotal keyword"); + if (strcmp(this->style, "electrode/conq") == 0) + error->all(FLERR, "qtotal keyword not available for electrode/conq"); + ++iarg; + if (strstr(arg[iarg], "v_") == arg[iarg]) { + std::string vname = arg[iarg]; + qtotal_var_name = vname.substr(2); + qtotal_var_style = VarStyle::EQUAL; + } else { + qtotal = utils::numeric(FLERR, arg[iarg], false, lmp); + qtotal_var_style = VarStyle::CONST; + } // toggle parameters } else if ((strcmp(arg[iarg], "etypes") == 0)) { etypes_neighlists = utils::logical(FLERR, arg[++iarg], false, lmp); @@ -208,6 +224,12 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : iarg++; } + if (qtotal_var_style != VarStyle::UNSET) { + if (symm) error->all(FLERR, "{} cannot use qtotal keyword with symm on", this->style); + } + + // computatonal potential + group_psi = std::vector(groups.size()); // union of all coupled groups std::string union_group = "conp_group"; std::string group_cmd = union_group + " union"; @@ -225,6 +247,7 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : if (need_elec_vector) elec_vector = new ElectrodeVector(lmp, igroup, igroup, eta, false); assert(groups.size() == group_bits.size()); assert(groups.size() == group_psi.size()); + assert(groups.size() == group_psi_const.size()); assert(groups.size() == group_psi_var_styles.size()); assert(groups.size() == group_psi_var_names.size()); assert(igroup == elyt_vector->igroup); @@ -396,7 +419,8 @@ void FixElectrodeConp::init() for (char *fix_id : integrate_ids) error->warning( FLERR, - "Electrode atoms are integrated by fix {}, but fix electrode is using a matrix method. For " + "Electrode atoms are integrated by fix {}, but fix electrode is using a matrix method. " + "For " "mobile electrodes use the conjugate gradient algorithm without matrix ('algo cg').", fix_id); } @@ -475,6 +499,7 @@ void FixElectrodeConp::setup_post_neighbor() // get equal-style variable ids: group_psi_var_ids = std::vector(num_of_groups, -1); for (int g = 0; g < num_of_groups; g++) { + assert(group_psi_var_styles[g] != VarStyle::UNSET); if (group_psi_var_styles[g] == VarStyle::CONST) continue; const char *var_name = group_psi_var_names[g].c_str(); int var_id = input->variable->find(var_name); @@ -485,6 +510,16 @@ void FixElectrodeConp::setup_post_neighbor() fmt::format("Variable '{}' for fix electrode is not equal-style", var_name)); group_psi_var_ids[g] = var_id; } + if (qtotal_var_style == VarStyle::EQUAL) { + const char *var_name = qtotal_var_name.c_str(); + int var_id = input->variable->find(var_name); + if (var_id < 0) + error->all(FLERR, fmt::format("Variable '{}' for fix electrode does not exist", var_name)); + if (!input->variable->equalstyle(var_id)) + error->all(FLERR, + fmt::format("Variable '{}' for fix electrode is not equal-style", var_name)); + qtotal_var_id = var_id; + } // pair and list setups: @@ -834,6 +869,8 @@ void FixElectrodeConp::update_charges() } MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); update_psi(); // use for equal-style and conq + if (qtotal_var_style != VarStyle::UNSET) + update_psi_qtotal(); // use for qtotal; same for thermo for (int g = 0; g < num_of_groups; g++) for (int j = 0; j < nlocalele; j++) q_local[j] += sd_vectors[g][list_iele[j]] * group_psi[g]; MPI_Barrier(world); @@ -936,12 +973,22 @@ std::vector FixElectrodeConp::gather_ngroup(std::vector x_local) } /* ---------------------------------------------------------------------- - ensure total electrode charge is 0 if symm + ensure total electrode charge is 0 if symm and qtotal if qtotal is used ------------------------------------------------------------------------- */ std::vector FixElectrodeConp::constraint_correction(std::vector x) { - return constraint_projection(x); + if (symm || qtotal_var_style != VarStyle::UNSET) { + if (qtotal_var_style == VarStyle::EQUAL) qtotal = input->variable->compute_equal(qtotal_var_id); + double sum = 0.; + for (double xi : x) sum += xi; + MPI_Allreduce(MPI_IN_PLACE, &sum, 1, MPI_DOUBLE, MPI_SUM, world); + if (qtotal_var_style != VarStyle::UNSET) sum -= qtotal; + sum /= ngroup; + for (double &xi : x) xi -= sum; + return x; + } + return x; } /* ---------------------------------------------------------------------- @@ -950,7 +997,7 @@ std::vector FixElectrodeConp::constraint_correction(std::vector std::vector FixElectrodeConp::constraint_projection(std::vector x) { - if (symm) { + if (symm || qtotal_var_style != VarStyle::UNSET) { double sum = 0.; for (double xi : x) sum += xi; MPI_Allreduce(MPI_IN_PLACE, &sum, 1, MPI_DOUBLE, MPI_SUM, world); @@ -1008,13 +1055,28 @@ std::vector FixElectrodeConp::times_elastance(std::vector x) void FixElectrodeConp::update_psi() { for (int g = 0; g < num_of_groups; g++) { - if (group_psi_var_styles[g] == VarStyle::CONST) continue; - group_psi[g] = input->variable->compute_equal(group_psi_var_ids[g]); + if (group_psi_var_styles[g] == VarStyle::CONST) + group_psi[g] = group_psi_const[g]; + else + group_psi[g] = input->variable->compute_equal(group_psi_var_ids[g]); } } /* ---------------------------------------------------------------------- */ +void FixElectrodeConp::update_psi_qtotal() +{ + if (qtotal_var_style == VarStyle::EQUAL) qtotal = input->variable->compute_equal(qtotal_var_id); + double q_current = 0.; + for (int i = 0; i < num_of_groups; i++) { + q_current += sb_charges[i]; + for (int j = 0; j < num_of_groups; j++) q_current += macro_capacitance[i][j] * group_psi[j]; + } + double add_psi = (qtotal - q_current) / macro_capacitance_sum; + for (int i = 0; i < num_of_groups; i++) group_psi[i] += add_psi; +} +/* ---------------------------------------------------------------------- */ + void FixElectrodeConp::compute_macro_matrices() { assert(algo == Algo::MATRIX_INV); @@ -1070,6 +1132,10 @@ void FixElectrodeConp::compute_macro_matrices() } } } + + macro_capacitance_sum = 0.; + for (int i = 0; i < num_of_groups; i++) + for (int j = 0; j < num_of_groups; j++) macro_capacitance_sum += macro_capacitance[i][j]; } /* ---------------------------------------------------------------------- */ diff --git a/src/ELECTRODE/fix_electrode_conp.h b/src/ELECTRODE/fix_electrode_conp.h index 1289d96281e..689a44053ca 100644 --- a/src/ELECTRODE/fix_electrode_conp.h +++ b/src/ELECTRODE/fix_electrode_conp.h @@ -71,7 +71,7 @@ class FixElectrodeConp : public Fix { protected: enum class Algo { MATRIX_INV, MATRIX_CG, CG }; - enum class VarStyle { CONST, EQUAL }; + enum class VarStyle { CONST, EQUAL, UNSET }; virtual void update_psi(); virtual void pre_update(){}; virtual void recompute_potential(std::vector, std::vector){}; @@ -80,6 +80,7 @@ class FixElectrodeConp : public Fix { virtual void compute_macro_matrices(); std::vector ele_ele_interaction(const std::vector &); std::vector group_psi; + std::vector group_psi_const; // needed to undo qtotal psi updates std::vector group_bits; std::vector groups; int num_of_groups; @@ -101,6 +102,10 @@ class FixElectrodeConp : public Fix { std::string fixname; // used by electrode/ffield to set up internal efield bool intelflag; inline virtual void intel_pack_buffers() {} + double qtotal; + std::string qtotal_var_name; + int qtotal_var_id; + VarStyle qtotal_var_style; private: std::string output_file_inv, output_file_mat, output_file_vec; @@ -143,6 +148,9 @@ class FixElectrodeConp : public Fix { std::vector gather_ngroup(std::vector); std::vector gather_elevec_local(ElectrodeVector *); void set_charges(std::vector); + // qtotal + double macro_capacitance_sum; + void update_psi_qtotal(); // fix-specific electrode ID storage system: diff --git a/src/ELECTRODE/fix_electrode_thermo.cpp b/src/ELECTRODE/fix_electrode_thermo.cpp index 52c0a3ce4cf..3883aa40a24 100644 --- a/src/ELECTRODE/fix_electrode_thermo.cpp +++ b/src/ELECTRODE/fix_electrode_thermo.cpp @@ -47,7 +47,8 @@ FixElectrodeThermo::FixElectrodeThermo(LAMMPS *lmp, int narg, char **arg) : if (thermo_time < SMALL) error->all(FLERR, "Keyword temp not set or zero in electrode/thermo"); thermo_random = new RanMars(lmp, thermo_init); - if (group_psi_var_styles[0] == VarStyle::CONST) delta_psi_0 = group_psi[1] - group_psi[0]; + if (group_psi_var_styles[0] == VarStyle::CONST) + delta_psi_0 = group_psi_const[1] - group_psi_const[0]; } /* ----------------------------------------------------------------------- */ @@ -102,7 +103,7 @@ void FixElectrodeThermo::update_psi() double const delta_psi = group_psi_old[1] - group_psi_old[0]; // target potential difference from input parameters - if (group_psi_var_styles[0] != VarStyle::CONST) { + if (group_psi_var_styles[0] == VarStyle::EQUAL) { delta_psi_0 = input->variable->compute_equal(group_psi_var_ids[1]) - input->variable->compute_equal(group_psi_var_ids[0]); } From 6de50fbd33a130e8a2ecac07a5bc31ac5467969d Mon Sep 17 00:00:00 2001 From: jtclemm Date: Wed, 14 Jun 2023 13:39:24 -0600 Subject: [PATCH 008/719] Adding iso options to fix deform --- doc/src/fix_deform.rst | 46 ++++++++++++--- src/fix_deform.cpp | 129 ++++++++++++++++++++++++++++++++++++----- src/fix_deform.h | 2 + 3 files changed, 155 insertions(+), 22 deletions(-) diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index d46f1204f5e..7a17f14fed0 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -20,7 +20,7 @@ Syntax .. parsed-literal:: - parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* + parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *iso* *x*, *y*, *z* args = style value(s) style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* *final* values = lo hi @@ -71,6 +71,12 @@ Syntax *variable* values = v_name1 v_name2 v_name1 = variable with name1 for tilt change as function of time v_name2 = variable with name2 for change rate as function of time + *iso* = style value + style = *volume* or *pressure* + *volume* value = none = isotropically adjust system to preserve volume of system + *pressure* values = target gain + target = target mean pressure (pressure units) + gain = proportional gain constant (1/(time * pressure) or 1/time units) * zero or more keyword/value pairs may be appended * keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure* @@ -88,12 +94,10 @@ Syntax box = distances are defined in simulation box units *couple* value = *none* or *xyz* or *xy* or *yz* or *xz* couple pressure values of various dimensions - *vol/balance/p* = *yes* or *no* + *vol/balance/p* value = *yes* or *no* Modifies the behavior of the *volume* option to try and balance pressures *max/rate* value = *rate* rate = maximum strain rate for pressure control - *normalize/pressure* value = *yes* or *no* - determine whether pressure deviation is normalized by target pressure Examples """""""" @@ -107,6 +111,7 @@ Examples fix 1 all deform 1 x pressure 2.0 0.1 normalize/pressure yes max/rate 0.001 fix 1 all deform 1 x trate 0.1 y volume z volume vol/balance/p yes fix 1 all deform 1 x trate 0.1 y pressure/mean 0.0 1.0 z pressure/mean 0.0 1.0 + fix 1 all deform 1 x trate 0.1 y trate -0.1 overlay/pressure/mean 1.0 0.1 Description """"""""""" @@ -318,8 +323,8 @@ mid point. The *pressure* style adjusts a dimensions's box length to control that component of the pressure tensor. This option attempts to maintain a -specified target value using a linear controller where the box length L -evolves according to the equation +specified target value using a linear controller where the box length +:math:`L` evolves according to the equation .. parsed-literal:: @@ -343,7 +348,7 @@ option. The *pressure/mean* style is changes a dimension in order to maintain a constant mean pressure defined as the trace of the pressure tensor. -This option is therefore very similar to the *presssure* style with +This option is therefore very similar to the *pressure* style with identical arguments except the current and target pressures refer to the mean trace of the pressure tensor. The same options also apply except for the :ref:`couple ` option. @@ -512,6 +517,25 @@ of the applied strain using the :ref:`max/rate ` option. ---------- +The *iso* parameter provides an additonal control over the x, y, +and z box lengths. This parameter can only be used in combination with +the *x*, *y*, or *z* comamnds: *vel*, *erate*, *trate*, *pressure*, or +*wiggle*. Note that this parameter will change the overall strain rate in +the *x*, *y*, or *z* dimensions. This is the meaning of its styles and values. + +The *volume* style isotropically scales box lengths to maintain a constant +box volume in response to deformation from other parameters. + +The *pressure* style controls the box volume to maintain the mean pressure +of the system. This is accomplished by isotropically scaling all box +lengths :math:`L` by an additional factor of :math:`k (P_t - P_m)` where +:math:`k` is the proportional gain constant, :math:`P_t` is the target +pressure, and :math:`P_m` is the current mean pressure (the trace of the +pressure tensor). This style allows one to control the deviatoric strain +tensor while maintaining a fixed mean pressure. + +---------- + All of the tilt styles change the xy, xz, yz tilt factors during a simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes are normally bounded by half the distance of the parallel box length. @@ -652,8 +676,12 @@ described below, which will cap the divergence. .. _deform_max_rate: The *max/rate* keyword sets an upper threshold, *rate*, that limits the -maximum magnitude of the strain rate applied in any dimension. This keyword -only applies to the *pressure* and *pressure/mean* options. +maximum magnitude of the instantaneous strain rate applied in any dimension. +This keyword only applies to the *pressure* and *pressure/mean* options. If +a pressure-controlled rate is used for both *iso* and either *x*, *y*, or +*z*, then this threshold will apply separately to each individual controller +such that the cumulative strain rate on a box dimension may be up to twice +the value of *rate*. .. _deform_couple: diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 29c286ed029..e76b34f302b 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -65,8 +65,8 @@ irregular(nullptr), set(nullptr) // set defaults - set = new Set[6]; - memset(set,0,6*sizeof(Set)); + set = new Set[7]; + memset(set,0,7*sizeof(Set)); // parse arguments @@ -237,6 +237,25 @@ irregular(nullptr), set(nullptr) error->all(FLERR,"Illegal fix deform pressure gain, must be positive"); iarg += 4; } else error->all(FLERR,"Illegal fix deform command: {}", arg[iarg+1]); + } else if (strcmp(arg[iarg],"iso") == 0) { + index = 6; + if (strcmp(arg[iarg+1],"volume") == 0) { + set[index].style = VOLUME; + iarg += 2; + } else if (strcmp(arg[iarg+1],"pressure") == 0) { + if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform pressure", error); + set[index].style = PRESSURE; + if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) { + set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp); + } else { + set[index].pstr = utils::strdup(&arg[iarg+2][2]); + set[index].pvar_flag = 1; + } + set[index].pgain = utils::numeric(FLERR,arg[iarg+3],false,lmp); + if (set[index].pgain <= 0.0) + error->all(FLERR,"Illegal fix deform pressure gain, must be positive"); + iarg += 4; + } } else break; } @@ -313,6 +332,12 @@ irregular(nullptr), set(nullptr) if (set[i].style == NONE) dimflag[i] = 0; else dimflag[i] = 1; + if (set[6].style != NONE) { + dimflag[0] = 1; + dimflag[1] = 1; + dimflag[2] = 1; + } + if (dimflag[0]) box_change |= BOX_CHANGE_X; if (dimflag[1]) box_change |= BOX_CHANGE_Y; if (dimflag[2]) box_change |= BOX_CHANGE_Z; @@ -324,7 +349,7 @@ irregular(nullptr), set(nullptr) // b/c shrink wrap will change box-length for (int i = 0; i < 3; i++) - if (set[i].style && (domain->boundary[i][0] >= 2 || domain->boundary[i][1] >= 2)) + if ((set[i].style || set[6].style) && (domain->boundary[i][0] >= 2 || domain->boundary[i][1] >= 2)) error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary"); // no tilt deformation on shrink-wrapped 2nd dim @@ -431,7 +456,7 @@ irregular(nullptr), set(nullptr) // set varflag varflag = 0; - for (int i = 0; i < 6; i++) { + for (int i = 0; i < 7; i++) { if (set[i].style == VARIABLE) varflag = 1; if (set[i].pvar_flag) varflag = 1; } @@ -439,7 +464,7 @@ irregular(nullptr), set(nullptr) // set pressure_flag pressure_flag = 0; - for (int i = 0; i < 6; i++) { + for (int i = 0; i < 7; i++) { if (set[i].style == PRESSURE || set[i].style == PMEAN) pressure_flag = 1; if (set[i].coupled_flag) pressure_flag = 1; } @@ -452,6 +477,14 @@ irregular(nullptr), set(nullptr) if (set[i].style == PMEAN) error->all(FLERR, "Cannot use fix deform to assign constant volume and pressure"); + // check conflicts between x,y,z styles and iso + + if (set[6].style) + for (int i = 0; i < 3; i++) { + if (set[i].style == FINAL || set[i].style == DELTA || set[i].style == SCALE || set[i].style == PMEAN || set[i].style == VARIABLE) + error->all(FLERR, "Cannot use fix deform iso parameter with x, y, or z styles other than vel, erate, trate, pressure, and wiggle"); + } + // check pressure used for max rate and normalize error flag if (!pressure_flag && max_h_rate != 0) @@ -470,6 +503,7 @@ irregular(nullptr), set(nullptr) set[3].tilt_initial = domain->yz; set[4].tilt_initial = domain->xz; set[5].tilt_initial = domain->xy; + set[6].vol_initial = domain->xprd * domain->yprd * domain->zprd; // reneighboring only forced if flips can occur due to shape changes @@ -511,7 +545,7 @@ irregular(nullptr), set(nullptr) FixDeform::~FixDeform() { if (set) { - for (int i = 0; i < 6; i++) { + for (int i = 0; i < 7; i++) { delete[] set[i].hstr; delete[] set[i].hratestr; delete[] set[i].pstr; @@ -569,7 +603,7 @@ void FixDeform::init() // check variables for VARIABLE style - for (int i = 0; i < 6; i++) { + for (int i = 0; i < 7; i++) { if (set[i].style != VARIABLE) continue; set[i].hvar = input->variable->find(set[i].hstr); if (set[i].hvar < 0) @@ -585,7 +619,7 @@ void FixDeform::init() // check optional variables for PRESSURE or PMEAN style - for (int i = 0; i < 6; i++) { + for (int i = 0; i < 7; i++) { if (!set[i].pvar_flag) continue; set[i].pvar = input->variable->find(set[i].pstr); if (set[i].pvar < 0) @@ -701,6 +735,8 @@ void FixDeform::init() } } + set[6].vol_start = domain->xprd * domain->yprd * domain->zprd; + // if using tilt TRATE, then initial tilt must be non-zero for (int i = 3; i < 6; i++) @@ -740,6 +776,7 @@ void FixDeform::init() // set domain->h_rate values for use by domain and other fixes/computes // initialize all rates to 0.0 // cannot set here for TRATE,VOLUME,WIGGLE,VARIABLE,PRESSURE since not constant + // if iso style is used, these will also not be constant h_rate = domain->h_rate; h_ratelo = domain->h_ratelo; @@ -867,6 +904,10 @@ void FixDeform::end_of_step() if (volume_flag) set_volume(); + // apply any final isotropic scalings + + if (set[6].style) set_iso(); + // Save pressure/strain rate if required if (pressure_flag) { @@ -983,15 +1024,15 @@ void FixDeform::end_of_step() // reset global and local box to new size/shape // only if deform fix is controlling the dimension - if (set[0].style) { + if (set[0].style || set[6].style) { domain->boxlo[0] = set[0].lo_target; domain->boxhi[0] = set[0].hi_target; } - if (set[1].style) { + if (set[1].style || set[6].style) { domain->boxlo[1] = set[1].lo_target; domain->boxhi[1] = set[1].hi_target; } - if (set[2].style) { + if (set[2].style || set[6].style) { domain->boxlo[2] = set[2].lo_target; domain->boxhi[2] = set[2].hi_target; } @@ -1285,6 +1326,67 @@ void FixDeform::set_volume() } } +/* ---------------------------------------------------------------------- + apply isotropic controls +------------------------------------------------------------------------- */ + +void FixDeform::set_iso() +{ + int i; + double scale, shift; + double v_rate; + + if (set[6].style == VOLUME) { + double v0 = set[6].vol_start; + double v = 1.0; + for (i = 0; i < 3; i++) + v *= (set[i].hi_target - set[i].lo_target); + + scale = std::pow(v0 / v, THIRD); + for (i = 0; i < 3; i++) { + shift = 0.5 * (set[i].hi_target - set[i].lo_target) * scale; + set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - shift; + set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + shift; + + // Recalculate h_rate + h_rate[i] = (set[i].hi_target - set[i].lo_target) / (domain->boxhi[i] - domain->boxlo[i]) - 1.0; + h_rate[i] /= update->dt; + } + + } else if (set[6].style == PRESSURE) { + + // If variable pressure, calculate current target + if (set[6].pvar_flag) + set[6].ptarget = input->variable->compute_equal(set[6].pvar); + + v_rate = set[6].pgain * (pressure->scalar- set[6].ptarget); + + if (normalize_pressure_flag) { + if (set[6].ptarget == 0) { + if (max_h_rate == 0) { + error->all(FLERR, "Cannot normalize error for zero pressure without defining a max rate"); + } else v_rate = max_h_rate * v_rate / fabs(v_rate); + } else v_rate /= fabs(set[6].ptarget); + } + + if (max_h_rate != 0) + if (fabs(set[6].ptarget) > max_h_rate) + v_rate = max_h_rate * v_rate / fabs(v_rate); + + set[6].cumulative_strain += update->dt * v_rate; + scale = (1.0 + set[6].cumulative_strain); + for (i = 0; i < 3; i++) { + shift = 0.5 * (set[i].hi_target - set[i].lo_target) * scale; + set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - shift; + set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + shift; + + // Recalculate h_rate + h_rate[i] = (set[i].hi_target - set[i].lo_target) / (domain->boxhi[i] - domain->boxlo[i]) - 1.0; + h_rate[i] /= update->dt; + } + } +} + /* ---------------------------------------------------------------------- write Set data to restart file ------------------------------------------------------------------------- */ @@ -1294,7 +1396,7 @@ void FixDeform::write_restart(FILE *fp) if (comm->me == 0) { int size = 6 * sizeof(Set); fwrite(&size,sizeof(int),1,fp); - fwrite(set,sizeof(Set),6,fp); + fwrite(set,sizeof(Set),7,fp); } } @@ -1306,7 +1408,7 @@ void FixDeform::restart(char *buf) { int samestyle = 1; Set *set_restart = (Set *) buf; - for (int i=0; i<6; ++i) { + for (int i=0; i<7; ++i) { // restore data from initial state set[i].lo_initial = set_restart[i].lo_initial; set[i].hi_initial = set_restart[i].hi_initial; @@ -1315,6 +1417,7 @@ void FixDeform::restart(char *buf) set[i].saved = set_restart[i].saved; set[i].prior_rate = set_restart[i].prior_rate; set[i].prior_pressure = set_restart[i].prior_pressure; + set[i].cumulative_strain = set_restart[i].cumulative_strain; // check if style settings are consistent (should do the whole set?) if (set[i].style != set_restart[i].style) samestyle = 0; diff --git a/src/fix_deform.h b/src/fix_deform.h index eda97f7c908..e8a4766b124 100644 --- a/src/fix_deform.h +++ b/src/fix_deform.h @@ -72,6 +72,7 @@ class FixDeform : public Fix { double vol_initial, vol_start; double ptarget, pgain; double prior_pressure, prior_rate; + double cumulative_strain; int saved; int fixed, dynamic1, dynamic2; char *hstr, *hratestr, *pstr; @@ -85,6 +86,7 @@ class FixDeform : public Fix { void set_strain(); void set_pressure(); void set_volume(); + void set_iso(); void couple(); }; From f75eda4bf4f5d223eaf469a5f42d7b8377c0547b Mon Sep 17 00:00:00 2001 From: jtclemm Date: Wed, 14 Jun 2023 14:16:46 -0600 Subject: [PATCH 009/719] Updating size of set in restart --- src/fix_deform.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index e76b34f302b..34e73b4e10f 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -1394,7 +1394,7 @@ void FixDeform::set_iso() void FixDeform::write_restart(FILE *fp) { if (comm->me == 0) { - int size = 6 * sizeof(Set); + int size = 7 * sizeof(Set); fwrite(&size,sizeof(int),1,fp); fwrite(set,sizeof(Set),7,fp); } From 60173c477d59c770e1bbac40e68111a01f28fd67 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Wed, 14 Jun 2023 15:14:19 -0600 Subject: [PATCH 010/719] Creating persistent h_rate variable --- src/fix_deform.cpp | 33 +++++++++++++++++++++++---------- 1 file changed, 23 insertions(+), 10 deletions(-) diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 34e73b4e10f..b595901a058 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -47,7 +47,7 @@ enum{NOCOUPLE=0,XYZ,XY,YZ,XZ}; /* ---------------------------------------------------------------------- */ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), -irregular(nullptr), set(nullptr) +irregular(nullptr), set(nullptr), id_temp(nullptr), id_press(nullptr) { if (narg < 4) error->all(FLERR,"Illegal fix deform command"); @@ -538,6 +538,16 @@ irregular(nullptr), set(nullptr) modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp)); pflag = 1; } + + // initialize all rates to 0.0 in constructor instead of init so values persist + // across run statements and ghosts have correct velocities until the destructor + h_rate = domain->h_rate; + h_ratelo = domain->h_ratelo; + + for (int i = 0; i < 3; i++) + h_rate[i] = h_ratelo[i] = 0.0; + for (int i = 3; i < 6; i++) + h_rate[i] = 0.0; } /* ---------------------------------------------------------------------- */ @@ -774,15 +784,10 @@ void FixDeform::init() } // set domain->h_rate values for use by domain and other fixes/computes - // initialize all rates to 0.0 // cannot set here for TRATE,VOLUME,WIGGLE,VARIABLE,PRESSURE since not constant // if iso style is used, these will also not be constant - h_rate = domain->h_rate; - h_ratelo = domain->h_ratelo; - for (int i = 0; i < 3; i++) { - h_rate[i] = h_ratelo[i] = 0.0; if (set[i].style == FINAL || set[i].style == DELTA || set[i].style == SCALE || set[i].style == VEL || set[i].style == ERATE) { @@ -797,7 +802,6 @@ void FixDeform::init() } for (int i = 3; i < 6; i++) { - h_rate[i] = 0.0; if (set[i].style == FINAL || set[i].style == DELTA || set[i].style == VEL || set[i].style == ERATE) { if (delt != 0.0) @@ -1394,8 +1398,10 @@ void FixDeform::set_iso() void FixDeform::write_restart(FILE *fp) { if (comm->me == 0) { - int size = 7 * sizeof(Set); + int size = 9 * sizeof(double) + 7 * sizeof(Set); fwrite(&size,sizeof(int),1,fp); + fwrite(h_rate,sizeof(double),6,fp); + fwrite(h_ratelo,sizeof(double),3,fp); fwrite(set,sizeof(Set),7,fp); } } @@ -1406,9 +1412,16 @@ void FixDeform::write_restart(FILE *fp) void FixDeform::restart(char *buf) { + int n = 0; + auto list = (double *) buf; + for (int i = 0; i < 6; i++) + h_rate[i] = list[n++]; + for (int i = 0; i < 3; i++) + h_ratelo[i] = list[n++]; + int samestyle = 1; - Set *set_restart = (Set *) buf; - for (int i=0; i<7; ++i) { + Set *set_restart = (Set *) &buf[n * sizeof(double)]; + for (int i = 0; i < 7; ++i) { // restore data from initial state set[i].lo_initial = set_restart[i].lo_initial; set[i].hi_initial = set_restart[i].hi_initial; From d6532d3550694d3f5ce4a1ae83ff4b57ce1598a6 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Fri, 23 Jun 2023 14:13:32 -0600 Subject: [PATCH 011/719] Adding h_ratelo calculation --- src/fix_deform.cpp | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index b595901a058..8da904100e1 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -1114,7 +1114,8 @@ void FixDeform::set_strain() set[i].hi_target = set[i].hi_start + 0.5 * del; h_rate[i] = input->variable->compute_equal(set[i].hratevar); h_ratelo[i] = -0.5 * h_rate[i]; - } else if (set[i].style != VOLUME) { + } else if (set[i].style == FINAL || set[i].style == DELTA || set[i].style == SCALE || + set[i].style == VEL || set[i].style == ERATE) { set[i].lo_target = set[i].lo_start + delta * (set[i].lo_stop - set[i].lo_start); set[i].hi_target = set[i].hi_start + delta * (set[i].hi_stop - set[i].hi_start); } @@ -1215,6 +1216,7 @@ void FixDeform::set_pressure() if (max_h_rate != 0) if (fabs(set[i].ptarget) > max_h_rate) h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]); + h_ratelo[i] = -0.5 * h_rate[i]; double offset = 0.5 * (domain->boxhi[i] - domain->boxlo[i]) * (1.0 + update->dt * h_rate[i]); set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - offset; @@ -1324,6 +1326,7 @@ void FixDeform::set_volume() } h_rate[i] = (2.0 * shift / (domain->boxhi[i] - domain->boxlo[i]) - 1.0) / update->dt; + h_ratelo[i] = -0.5 * h_rate[i]; set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - shift; set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + shift; @@ -1355,6 +1358,7 @@ void FixDeform::set_iso() // Recalculate h_rate h_rate[i] = (set[i].hi_target - set[i].lo_target) / (domain->boxhi[i] - domain->boxlo[i]) - 1.0; h_rate[i] /= update->dt; + h_ratelo[i] = -0.5 * h_rate[i]; } } else if (set[6].style == PRESSURE) { @@ -1387,6 +1391,7 @@ void FixDeform::set_iso() // Recalculate h_rate h_rate[i] = (set[i].hi_target - set[i].lo_target) / (domain->boxhi[i] - domain->boxlo[i]) - 1.0; h_rate[i] /= update->dt; + h_ratelo[i] = -0.5 * h_rate[i]; } } } From 2ef326273d703eeee71cbb894a451810ea3055db Mon Sep 17 00:00:00 2001 From: jtclemm Date: Sat, 15 Jul 2023 16:09:53 -0600 Subject: [PATCH 012/719] Fixing bug in max rate threshold --- src/fix_deform.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 8da904100e1..ff6caf5a1db 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -1214,8 +1214,9 @@ void FixDeform::set_pressure() } if (max_h_rate != 0) - if (fabs(set[i].ptarget) > max_h_rate) + if (fabs(h_rate[i]) > max_h_rate) h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]); + h_ratelo[i] = -0.5 * h_rate[i]; double offset = 0.5 * (domain->boxhi[i] - domain->boxlo[i]) * (1.0 + update->dt * h_rate[i]); @@ -1378,7 +1379,7 @@ void FixDeform::set_iso() } if (max_h_rate != 0) - if (fabs(set[6].ptarget) > max_h_rate) + if (fabs(v_rate) > max_h_rate) v_rate = max_h_rate * v_rate / fabs(v_rate); set[6].cumulative_strain += update->dt * v_rate; From ec65fc48adbe1d2edb40db35e1ae6f85f7b5f7fb Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 18 Jul 2023 09:25:22 -0600 Subject: [PATCH 013/719] Cleaning up files, fixing bug in berendsen --- doc/src/fix_deform.rst | 10 ++++++---- src/fix_deform.cpp | 35 +++++++++++++++++------------------ src/fix_press_berendsen.cpp | 2 +- 3 files changed, 24 insertions(+), 23 deletions(-) diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 7a17f14fed0..a4d449850ed 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -98,6 +98,8 @@ Syntax Modifies the behavior of the *volume* option to try and balance pressures *max/rate* value = *rate* rate = maximum strain rate for pressure control + *normalize/pressure* value = *yes* or *no* + Modifies pressure controls such that the deviation in pressure is normalized by the target pressure Examples """""""" @@ -111,7 +113,6 @@ Examples fix 1 all deform 1 x pressure 2.0 0.1 normalize/pressure yes max/rate 0.001 fix 1 all deform 1 x trate 0.1 y volume z volume vol/balance/p yes fix 1 all deform 1 x trate 0.1 y pressure/mean 0.0 1.0 z pressure/mean 0.0 1.0 - fix 1 all deform 1 x trate 0.1 y trate -0.1 overlay/pressure/mean 1.0 0.1 Description """"""""""" @@ -346,12 +347,13 @@ applied strain using the :ref:`max/rate ` option and couple pressures in different dimensions using the :ref:`couple ` option. -The *pressure/mean* style is changes a dimension in order to maintain +The *pressure/mean* style changes a dimension's box length to maintain a constant mean pressure defined as the trace of the pressure tensor. This option is therefore very similar to the *pressure* style with identical arguments except the current and target pressures refer to the -mean trace of the pressure tensor. The same options also apply except -for the :ref:`couple ` option. +mean trace of the pressure tensor. All options for the *pressure* style +also apply to the *pressure/mean* style except for the +:ref:`couple ` option. ---------- diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index ff6caf5a1db..79f9b3a5ba2 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -24,6 +24,7 @@ #include "domain.h" #include "error.h" #include "force.h" +#include "group.h" #include "input.h" #include "irregular.h" #include "kspace.h" @@ -1522,31 +1523,31 @@ double FixDeform::memory_usage() int FixDeform::modify_param(int narg, char **arg) { - if (!pressure_flag) error->all(FLERR,"Cannot modify fix deform without a pressure control"); if (strcmp(arg[0],"temp") == 0) { - if (narg < 2) utils::missing_cmd_args(FLERR, "fix_modify deform", error); + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); if (tflag) { modify->delete_compute(id_temp); tflag = 0; } - delete [] id_temp; + delete[] id_temp; id_temp = utils::strdup(arg[1]); - int icompute = modify->find_compute(arg[1]); - if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID"); - temperature = modify->compute[icompute]; + temperature = modify->get_compute_by_id(arg[1]); + if (!temperature) + error->all(FLERR,"Could not find fix_modify temperature compute ID: ", arg[1]); if (temperature->tempflag == 0) - error->all(FLERR,"Fix_modify temperature ID does not compute temperature"); + error->all(FLERR,"Fix_modify temperature compute {} does not compute temperature", arg[1]); if (temperature->igroup != 0 && comm->me == 0) - error->warning(FLERR,"Temperature for deform is not for group all"); + error->warning(FLERR,"Temperature compute {} for fix {} is not for group all: {}", + arg[1], style, group->names[temperature->igroup]); // reset id_temp of pressure to new temperature ID - icompute = modify->find_compute(id_press); - if (icompute < 0) - error->all(FLERR,"Pressure ID for fix deform does not exist"); - modify->compute[icompute]->reset_extra_compute_fix(id_temp); + auto icompute = modify->get_compute_by_id(id_press); + if (!icompute) + error->all(FLERR,"Pressure compute ID {} for fix {} does not exist", id_press, style); + icompute->reset_extra_compute_fix(id_temp); return 2; @@ -1556,15 +1557,13 @@ int FixDeform::modify_param(int narg, char **arg) modify->delete_compute(id_press); pflag = 0; } - delete [] id_press; + delete[] id_press; id_press = utils::strdup(arg[1]); - int icompute = modify->find_compute(arg[1]); - if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); - pressure = modify->compute[icompute]; - + pressure = modify->get_compute_by_id(arg[1]); + if (!pressure) error->all(FLERR,"Could not find fix_modify pressure compute ID: {}", arg[1]); if (pressure->pressflag == 0) - error->all(FLERR,"Fix_modify pressure ID does not compute pressure"); + error->all(FLERR,"Fix_modify pressure compute {} does not compute pressure", arg[1]); return 2; } diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index 67802654ba4..ee9a8796160 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -491,7 +491,7 @@ int FixPressBerendsen::modify_param(int narg, char **arg) id_press = utils::strdup(arg[1]); pressure = modify->get_compute_by_id(arg[1]); - if (pressure) error->all(FLERR,"Could not find fix_modify pressure compute ID: {}", arg[1]); + if (!pressure) error->all(FLERR,"Could not find fix_modify pressure compute ID: {}", arg[1]); if (pressure->pressflag == 0) error->all(FLERR,"Fix_modify pressure compute {} does not compute pressure", arg[1]); return 2; From e3792616ad1d749f526e9e9ae2d4a0b1e76e4214 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 1 Aug 2023 12:54:23 -0600 Subject: [PATCH 014/719] Moving line break in BPM doc pages for link, fixing prop/atom syntax --- doc/src/bond_bpm_rotational.rst | 4 ++-- doc/src/bond_bpm_spring.rst | 4 ++-- src/BPM/bond_bpm.cpp | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst index 7459d491d60..6734bd7bfee 100644 --- a/doc/src/bond_bpm_rotational.rst +++ b/doc/src/bond_bpm_rotational.rst @@ -147,8 +147,8 @@ By default, pair forces are not calculated between bonded particles. Pair forces can alternatively be overlaid on top of bond forces by setting the *overlay/pair* keyword to *yes*. These settings require specific :doc:`special_bonds ` settings described in the -restrictions. Further details can be found in the :doc:`how to -` page on BPMs. +restrictions. Further details can be found in the :doc:`how to ` +page on BPMs. .. versionadded:: 28Mar2023 diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 04ff4d59912..a03c8322494 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -113,8 +113,8 @@ By default, pair forces are not calculated between bonded particles. Pair forces can alternatively be overlaid on top of bond forces by setting the *overlay/pair* keyword to *yes*. These settings require specific :doc:`special_bonds ` settings described in the -restrictions. Further details can be found in the :doc:`how to -` page on BPMs. +restrictions. Further details can be found in the :doc:`how to ` +page on BPMs. .. versionadded:: 28Mar2023 diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp index 3ebeed3f1d9..b484df7fabc 100644 --- a/src/BPM/bond_bpm.cpp +++ b/src/BPM/bond_bpm.cpp @@ -224,7 +224,7 @@ void BondBPM::settings(int narg, char **arg) ifix = modify->get_fix_by_id(id_fix_prop_atom); if (!ifix) - ifix = modify->add_fix(fmt::format("{} all property/atom {} {} {} ghost yes", + ifix = modify->add_fix(fmt::format("{} all property/atom d_{} d_{} d_{} ghost yes", id_fix_prop_atom, x_ref_id, y_ref_id, z_ref_id)); int type_flag; From e5bcbd4213ceaad5297cea609a70b26c7c31ee90 Mon Sep 17 00:00:00 2001 From: Ludwig Ahrens Date: Wed, 2 Aug 2023 13:03:45 +0200 Subject: [PATCH 015/719] Bugfix electrode/conq after changes for qtotal --- src/ELECTRODE/fix_electrode_conq.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ELECTRODE/fix_electrode_conq.cpp b/src/ELECTRODE/fix_electrode_conq.cpp index 0d3d1d2aafc..a6baa1e1221 100644 --- a/src/ELECTRODE/fix_electrode_conq.cpp +++ b/src/ELECTRODE/fix_electrode_conq.cpp @@ -30,7 +30,7 @@ FixElectrodeConq::FixElectrodeConq(LAMMPS *lmp, int narg, char **arg) : FixElectrodeConp(lmp, narg, arg) { // copy const-style values across because update_psi will change group_psi - group_q = group_psi; + group_q = group_psi_const; if (symm) { if (num_of_groups == 1) From cd5ebb86c870ebdceb842130aeea6b9bdf067a30 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Fri, 25 Aug 2023 21:37:57 -0400 Subject: [PATCH 016/719] inserting atoms: correct logic for per-atom mass --- src/REACTION/fix_bond_react.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index d124b06dc27..9254c3f5d1e 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -3895,7 +3895,8 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate) // guess a somewhat reasonable initial velocity based on reaction site // further control is possible using bond_react_MASTER_group // compute |velocity| corresponding to a given temperature t, using specific atom's mass - double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / atom->mass[twomol->type[m]]); + double mymass = atom->rmass ? atom->rmass[n] : atom->mass[twomol->type[m]]; + double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / mymass); v[n][0] = random[rxnID]->uniform(); v[n][1] = random[rxnID]->uniform(); v[n][2] = random[rxnID]->uniform(); From 999c364b83d69195dfbfeaeb47397feb2d6d7dc7 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Fri, 25 Aug 2023 21:44:42 -0400 Subject: [PATCH 017/719] better way to list rxn counts --- .../reaction/create_atoms_polystyrene/in.grow_styrene | 2 +- examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt | 4 ++-- .../PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized | 2 +- .../PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized | 2 +- .../tiny_nylon/in.tiny_nylon.stabilized_variable_probability | 2 +- .../PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized | 2 +- .../reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized | 2 +- 7 files changed, 8 insertions(+), 8 deletions(-) diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene b/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene index 7860db4e55c..dcca29c0267 100644 --- a/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene +++ b/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene @@ -40,7 +40,7 @@ fix 1 statted_grp_REACT nvt temp $T $T 100 fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1 -thermo_style custom step temp press density f_myrxns[1] +thermo_style custom step temp press density f_myrxns[*] thermo 100 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt index 9678a714d62..635b2c97509 100644 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt @@ -26,7 +26,7 @@ read_data large_nylon_melt.data.gz & extra/angle/per/atom 15 & extra/dihedral/per/atom 15 & extra/improper/per/atom 25 & - extra/special/per/atom 25 + extra/special/per/atom 25 velocity all create 800.0 4928459 dist gaussian @@ -50,7 +50,7 @@ fix 1 statted_grp_REACT nvt temp 800 800 100 # you can use the internally created 'bond_react_MASTER_group', like so: # fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts +thermo_style custom step temp press density f_myrxns[*] # cumulative reaction counts # restart 100 restart1 restart2 diff --git a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized index 57b03b630ff..ea09d068934 100644 --- a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized +++ b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized @@ -44,7 +44,7 @@ fix rxns all bond/react stabilization yes statted_grp .03 & fix 1 statted_grp_REACT nvt temp 300 300 100 -thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] +thermo_style custom step temp f_rxns[*] run 2000 diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized index 95b39033db9..853bc45f1ea 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized @@ -50,7 +50,7 @@ fix 1 statted_grp_REACT nvt temp 300 300 100 # by using the internally-created 'bond_react_MASTER_group', like so: fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] +thermo_style custom step temp press density f_myrxns[*] # restart 100 restart1 restart2 diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability index 88b5a95a413..f3c32f3cbd2 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability @@ -54,7 +54,7 @@ fix 1 statted_grp_REACT nvt temp 300 300 100 # by using the internally-created 'bond_react_MASTER_group', like so: fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 -thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] +thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[*] # restart 100 restart1 restart2 diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized index a569e28d43c..e5cbaaaf868 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized @@ -47,7 +47,7 @@ fix myrxns all bond/react stabilization no & fix 1 all nve/limit .03 -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] +thermo_style custom step temp press density f_myrxns[*] # restart 100 restart1 restart2 diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized index 4ecc4817195..230998fcd3b 100644 --- a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized +++ b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized @@ -51,7 +51,7 @@ fix 1 statted_grp_REACT nvt temp $T $T 100 fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1 -thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3] +thermo_style custom step temp press density f_rxn1[*] run 10000 From 1039f86037f2870062a0a79108a933ab96063494 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sat, 26 Aug 2023 14:29:07 -0400 Subject: [PATCH 018/719] remove unnecessary restriction do not check for comm cutoff when initiator atoms are directly bonded --- src/REACTION/fix_bond_react.cpp | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 9254c3f5d1e..1da26e32a10 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -827,11 +827,10 @@ void FixBondReact::init() nlevels_respa = (dynamic_cast(update->integrate))->nlevels; // check cutoff for iatomtype,jatomtype - for (int i = 0; i < nreacts; i++) { - if (!utils::strmatch(force->pair_style,"^hybrid")) - if (force->pair == nullptr || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]) + if (!utils::strmatch(force->pair_style,"^hybrid")) + for (int i = 0; i < nreacts; i++) + if (force->pair == nullptr || (closeneigh[i] < 0 && cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])) error->all(FLERR,"Fix bond/react: Fix bond/react cutoff is longer than pairwise cutoff"); - } // need a half neighbor list, built every Nevery steps neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); From db72d4b73a0e30285065c5de0d1bf26081a333f7 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 31 Aug 2023 14:34:37 -0600 Subject: [PATCH 019/719] add general tri options to read and write data commands and Domain class --- src/atom.cpp | 29 +++++++- src/atom.h | 3 +- src/domain.cpp | 181 ++++++++++++++++++++++++++++++++++++++++++++- src/domain.h | 32 +++++--- src/math_extra.h | 16 ++++ src/read_data.cpp | 173 ++++++++++++++++++++++++++++++++----------- src/read_data.h | 7 +- src/write_data.cpp | 61 ++++++++++++--- src/write_data.h | 1 + 9 files changed, 428 insertions(+), 75 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index c4521a244e8..0249547253c 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1041,7 +1041,8 @@ void Atom::deallocate_topology() ------------------------------------------------------------------------- */ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, - int type_offset, int shiftflag, double *shift, + int type_offset, int triclinic_general, + int shiftflag, double *shift, int labelflag, int *ilabel) { int xptr,iptr; @@ -1053,6 +1054,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, auto location = "Atoms section of data file"; // use the first line to detect and validate the number of words/tokens per line + next = strchr(buf,'\n'); if (!next) error->all(FLERR, "Missing data in {}", location); *next = '\0'; @@ -1069,6 +1071,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, error->all(FLERR,"Incorrect format in {}: {}", location, utils::trim(buf)); *next = '\n'; + // set bounds for my proc // if periodic and I am lo/hi proc, adjust bounds by EPSILON // ensures all data atoms will be owned even with round-off @@ -1143,11 +1146,19 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, *next = '\0'; auto values = Tokenizer(buf).as_vector(); int nvalues = values.size(); - if ((nvalues == 0) || (utils::strmatch(values[0],"^#.*"))) { - // skip over empty or comment lines + + // skip comment lines + + if ((nvalues == 0) || (utils::strmatch(values[0],"^#.*"))) { + + // check that line has correct # of words + } else if ((nvalues < nwords) || ((nvalues > nwords) && (!utils::strmatch(values[nwords],"^#")))) { error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + + // extract the atom coords and image flags (if they exist) + } else { int imx = 0, imy = 0, imz = 0; if (imageflag) { @@ -1167,13 +1178,25 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, xdata[0] = utils::numeric(FLERR,values[xptr],false,lmp); xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp); xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp); + + // convert atom coords from general triclinic to restricted triclinic + + if (triclinic_general) domain->general_to_restricted(xdata); + + // apply shift if requested by read_data command + if (shiftflag) { xdata[0] += shift[0]; xdata[1] += shift[1]; xdata[2] += shift[2]; } + // map atom into simulation box for periodic dimensions + domain->remap(xdata,imagedata); + + // determine if this proc owns the atom + if (triclinic) { domain->x2lamda(xdata,lamda); coord = lamda; diff --git a/src/atom.h b/src/atom.h index 548168ac599..cf5fa108149 100644 --- a/src/atom.h +++ b/src/atom.h @@ -328,7 +328,8 @@ class Atom : protected Pointers { void deallocate_topology(); - void data_atoms(int, char *, tagint, tagint, int, int, double *, int, int *); + void data_atoms(int, char *, tagint, tagint, int, int, + int, double *, int, int *); void data_vels(int, char *, tagint); void data_bonds(int, char *, int *, tagint, int, int, int *); void data_angles(int, char *, int *, tagint, int, int, int *); diff --git a/src/domain.cpp b/src/domain.cpp index 3627af26cfe..6523bfc8c77 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -28,6 +28,7 @@ #include "force.h" #include "kspace.h" #include "lattice.h" +#include "math_extra.h" #include "memory.h" #include "modify.h" #include "molecule.h" @@ -41,6 +42,7 @@ #include using namespace LAMMPS_NS; +using namespace MathExtra; #define BIG 1.0e20 #define SMALL 1.0e-4 @@ -81,7 +83,7 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp) minylo = minyhi = 0.0; minzlo = minzhi = 0.0; - triclinic = 0; + triclinic = triclinic_general = 0; boxlo[0] = boxlo[1] = boxlo[2] = -0.5; boxhi[0] = boxhi[1] = boxhi[2] = 0.5; @@ -516,6 +518,180 @@ void Domain::reset_box() } } +/* ---------------------------------------------------------------------- + define and store a general triclinic simulation box + 3 edge vectors of box = avec/bvec/cvec caller + origin of edge vectors = origin_caller = lower left corner of box + create mapping to restricted triclinic box + set boxlo[3], boxhi[3] and 3 tilt factors + create rotation matrices for general <--> restricted transformations +------------------------------------------------------------------------- */ + +void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, + double *cvec_caller, double *origin_caller) +{ + if (triclinic || triclinic_general) + error->all(FLERR,"General triclinic box edge vectors are already set"); + + triclinic = triclinic_general = 1; + + avec[0] = avec_caller[0]; + avec[1] = avec_caller[1]; + avec[2] = avec_caller[2]; + + bvec[0] = bvec_caller[0]; + bvec[1] = bvec_caller[1]; + bvec[2] = bvec_caller[2]; + + cvec[0] = cvec_caller[0]; + cvec[1] = cvec_caller[1]; + cvec[2] = cvec_caller[2]; + + tri_origin[0] = origin_caller[0]; + tri_origin[1] = origin_caller[1]; + tri_origin[2] = origin_caller[2]; + + // error check for co-planar A,B,C + + double abcross[3]; + MathExtra::cross3(avec,bvec,abcross); + double dot = MathExtra::dot3(abcross,cvec); + if (dot == 0.0) + error->all(FLERR,"General triclinic box edge vectors are co-planar"); + + // quat1 = convert A into A' along x-axis + // rot1 = unit vector to rotate A around + // theta1 = angle of rotation calculated from + // A dot xunit = Ax = |A| cos(theta1) + + double rot1[3],quat1[4]; + double xaxis[3] = {1.0, 0.0, 0.0}; + + double avec_len = MathExtra::len3(avec); + MathExtra::cross3(avec,xaxis,rot1); + MathExtra::norm3(rot1); + double theta1 = acos(avec[0]/avec_len); + MathExtra::axisangle_to_quat(rot1,theta1,quat1); + + // rotmat1 = rotation matrix associated with quat1 + + double rotmat1[3][3]; + MathExtra::quat_to_mat(quat1,rotmat1); + + // B1 = rotation of B by quat1 rotation matrix + + double bvec1[3]; + + MathExtra::matvec(rotmat1,bvec,bvec1); + + // quat2 = rotation to convert B1 into B' in xy plane + // Byz1 = projection of B1 into yz plane + // rot2 = unit vector to rotate B1 around = -x axis + // theta2 = angle of rotation calculated from + // Byz1 dot yunit = B1y = |Byz1} cos(theta2) + + double byzvec1[3],quat2[4]; + MathExtra::copy3(bvec1,byzvec1); + byzvec1[0] = 0.0; + double byzvec1_len = MathExtra::len3(byzvec1); + double rot2[3] = {-1.0, 0.0, 0.0}; + double theta2 = acos(bvec1[1]/byzvec1_len); + MathExtra::axisangle_to_quat(rot2,theta2,quat2); + + // quat = product of quat2 * quat1 = transformation via single quat + // rotate_g2r = general to restricted transformation matrix + // rotate_r2g = restricted to general transformation matrix + // if A x B not in direction of C, flip sign of z component of transform + // done by flipping sign of 3rd row of rotate_g2r matrix + + double quat[4]; + MathExtra::quatquat(quat2,quat1,quat); + MathExtra::quat_to_mat(quat,rotate_g2r); + + if (dot < 0.0) { + rotate_g2r[2][0] = -rotate_g2r[2][0]; + rotate_g2r[2][1] = -rotate_g2r[2][1]; + rotate_g2r[2][2] = -rotate_g2r[2][2]; + } + + MathExtra::transpose3(rotate_g2r,rotate_r2g); + + // A',B',C' = transformation of A,B,C to restricted triclinic + + double aprime[3],bprime[3],cprime[3]; + MathExtra::matvec(rotate_g2r,avec,aprime); + MathExtra::matvec(rotate_g2r,bvec,bprime); + MathExtra::matvec(rotate_g2r,cvec,cprime); + + // set restricted triclinic boxlo, boxhi, and tilt factors + + boxlo[0] = tri_origin[0]; + boxlo[1] = tri_origin[1]; + boxlo[2] = tri_origin[2]; + + boxhi[0] = boxlo[0] + aprime[0]; + boxhi[1] = boxlo[1] + bprime[1]; + boxhi[2] = boxlo[2] + cprime[2]; + + xy = bprime[1]; + xz = cprime[0]; + yz = cprime[1]; + + // debug + + /* + printf("Quat: %g %g %g %g\n",quat[0],quat[1],quat[2],quat[3]); + double angle = 2.0*acos(quat[0]); + printf("Theta: %g\n",angle); + printf("Rotvec: %g %g %g\n",quat[1]/sin(0.5*angle),quat[2]/sin(0.5*angle),quat[3]/sin(0.5*angle)); + printf("Aprime: %g %g %g\n",aprime[0],aprime[1],aprime[2]); + printf("Bprime: %g %g %g\n",bprime[0],bprime[1],bprime[2]); + printf("Cprime: %g %g %g\n",cprime[0],cprime[1],cprime[2]); + printf("Length A: %g %g\n",MathExtra::len3(avec),MathExtra::len3(aprime)); + printf("Length B: %g %g\n",MathExtra::len3(bvec),MathExtra::len3(bprime)); + printf("Length C: %g %g\n",MathExtra::len3(cvec),MathExtra::len3(cprime)); + + double coord1[3] = {0.5,0.0,0.0}; + double coord2[3] = {0.5,0.0,0.3}; + double newcoord[3]; + MathExtra::matvec(rotate_g2r,coord1,newcoord); + printf("Atom1: %g %g %g\n",newcoord[0],newcoord[1],newcoord[2]); + MathExtra::matvec(rotate_g2r,coord2,newcoord); + printf("Atom2: %g %g %g\n",newcoord[0],newcoord[1],newcoord[2]); + */ +} + +/* ---------------------------------------------------------------------- + transform one atom's coords from general triclinic to restricted triclinic +------------------------------------------------------------------------- */ + +void Domain::general_to_restricted(double *x) +{ + double xnew[3]; + + MathExtra::matvec(rotate_g2r,x,xnew); + x[0] = xnew[0] + tri_origin[0]; + x[1] = xnew[1] + tri_origin[1]; + x[2] = xnew[2] + tri_origin[2]; +} + +/* ---------------------------------------------------------------------- + transform one atom's coords from restricted triclinic to general triclinic +------------------------------------------------------------------------- */ + +void Domain::restricted_to_general(double *x) +{ + double xshift[3],xnew[3]; + + xshift[0] = x[0] - tri_origin[0]; + xshift[1] = x[1] - tri_origin[1]; + xshift[2] = x[2] - tri_origin[2]; + MathExtra::matvec(rotate_r2g,xshift,xnew); + x[0] = xnew[0]; + x[1] = xnew[1]; + x[2] = xnew[2]; +} + /* ---------------------------------------------------------------------- enforce PBC and modify box image flags for each atom called every reneighboring and by other commands that change atoms @@ -676,9 +852,7 @@ int Domain::inside(double* x) lamda[1] < lo[1] || lamda[1] >= hi[1] || lamda[2] < lo[2] || lamda[2] >= hi[2]) return 0; else return 1; - } - } /* ---------------------------------------------------------------------- @@ -713,7 +887,6 @@ int Domain::inside_nonperiodic(double* x) if (!zperiodic && (lamda[2] < lo[2] || lamda[2] >= hi[2])) return 0; return 1; } - } /* ---------------------------------------------------------------------- diff --git a/src/domain.h b/src/domain.h index ab054f1b501..e77af5d968c 100644 --- a/src/domain.h +++ b/src/domain.h @@ -39,8 +39,9 @@ class Domain : protected Pointers { // 2 = shrink-wrap non-periodic // 3 = shrink-wrap non-per w/ min - int triclinic; // 0 = orthog box, 1 = triclinic - + int triclinic; // 0 = orthog box, 1 = triclinic (restricted or general) + int triclinic_general; // 1 if mapping to/from general triclinic is stored, 0 if not + // orthogonal box double xprd, yprd, zprd; // global box dimensions @@ -48,8 +49,8 @@ class Domain : protected Pointers { double prd[3]; // array form of dimensions double prd_half[3]; // array form of half dimensions - // triclinic box - // xyzprd,xyzprd_half and prd,prd_half = same as if untilted + // restricted triclinic box + // xyzprd,xyzprd_half and prd,prd_half = same as if not tilted double prd_lamda[3]; // lamda box = (1,1,1) double prd_half_lamda[3]; // lamda half box = (0.5,0.5,0.5) @@ -58,14 +59,14 @@ class Domain : protected Pointers { double boxlo[3], boxhi[3]; - // triclinic box - // boxlo/hi = same as if untilted + // restricted triclinic box + // boxlo/hi = same as if not tilted double boxlo_lamda[3], boxhi_lamda[3]; // lamda box = (0,1) double boxlo_bound[3], boxhi_bound[3]; // bounding box of tilted domain double corners[8][3]; // 8 corner points - // orthogonal box & triclinic box + // orthogonal box & restricted triclinic box double minxlo, minxhi; // minimum size of global box double minylo, minyhi; // when shrink-wrapping @@ -75,18 +76,27 @@ class Domain : protected Pointers { double sublo[3], subhi[3]; // sub-box bounds on this proc - // triclinic box + // restricted triclinic box // sublo/hi = undefined double sublo_lamda[3], subhi_lamda[3]; // bounds of subbox in lamda - // triclinic box + // restricted triclinic box double xy, xz, yz; // 3 tilt factors double h[6], h_inv[6]; // shape matrix in Voigt ordering // Voigt = xx,yy,zz,yz,xz,xy double h_rate[6], h_ratelo[3]; // rate of box size/shape change + // general triclinic box + + double avec[3], bvec[3], cvec[3]; // ABC edge vectors of general triclinic box + double tri_origin[3]; // origin of general triclinic box + double rotate_g2r[3][3]; // rotation matrix from general --> restricted tri + double rotate_r2g[3][3]; // rotation matrix from restricted --> general tri + + // box flags + int box_change; // 1 if any of next 3 flags are set, else 0 int box_change_size; // 1 if box size changes, 0 if not int box_change_shape; // 1 if box shape changes, 0 if not @@ -131,6 +141,10 @@ class Domain : protected Pointers { void image_flip(int, int, int); int ownatom(int, double *, imageint *, int); + void set_general_triclinic(double *, double *, double *, double *); + void general_to_restricted(double *); + void restricted_to_general(double *); + void set_lattice(int, char **); void add_region(int, char **); void delete_region(Region *); diff --git a/src/math_extra.h b/src/math_extra.h index 1efacea463e..49e128c3df4 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -47,6 +47,7 @@ inline void cross3(const double *v1, const double *v2, double *ans); inline void zeromat3(double m[3][3]); inline void zeromat3(double **m); +inline void transpose3(const double m[3][3], double ans[3][3]); inline void col2mat(const double *ex, const double *ey, const double *ez, double m[3][3]); inline double det3(const double mat[3][3]); @@ -763,6 +764,21 @@ inline void MathExtra::zeromat3(double **m) m[2][0] = m[2][1] = m[2][2] = 0.0; } +// transpose a matrix + +inline void MathExtra::transpose3(const double m[3][3], double ans[3][3]) +{ + ans[0][0] = m[0][0]; + ans[0][1] = m[1][0]; + ans[0][2] = m[2][0]; + ans[1][0] = m[0][1]; + ans[1][1] = m[1][1]; + ans[1][2] = m[2][1]; + ans[2][0] = m[0][2]; + ans[2][1] = m[1][2]; + ans[2][2] = m[2][2]; +} + // add two matrices inline void MathExtra::plus3(const double m[3][3], double **m2, double **ans) diff --git a/src/read_data.cpp b/src/read_data.cpp index 4b4602f1fce..8df901062c1 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -474,11 +474,14 @@ void ReadData::command(int narg, char **arg) int atomflag, topoflag; int bondflag, angleflag, dihedralflag, improperflag; int ellipsoidflag, lineflag, triflag, bodyflag; - + atomflag = topoflag = 0; bondflag = angleflag = dihedralflag = improperflag = 0; ellipsoidflag = lineflag = triflag = bodyflag = 0; + xloxhi_flag = yloyhi_flag = zlozhi_flag = tilt_flag = 0; + avec_flag = bvec_flag = cvec_flag = 0; + // values in this data file natoms = 0; @@ -488,7 +491,12 @@ void ReadData::command(int narg, char **arg) boxlo[0] = boxlo[1] = boxlo[2] = -0.5; boxhi[0] = boxhi[1] = boxhi[2] = 0.5; - triclinic = 0; + avec[0] = avec[1] = avec[2] = 0.0; + bvec[0] = bvec[1] = bvec[2] = 0.0; + cvec[0] = cvec[1] = cvec[2] = 0.0; + avec[0] = bvec[1] = cvec[2] = 1.0; + tri_origin[0] = tri_origin[1] = tri_origin[2] = 0.0; + keyword[0] = '\0'; nlocal_previous = atom->nlocal; @@ -508,6 +516,17 @@ void ReadData::command(int narg, char **arg) header(firstpass); + // check if simulation box specified consistently + + if (!avec_flag && !bvec_flag && !cvec_flag) { + triclinic = triclinic_general = 0; + if (tilt_flag) triclinic = 1; + } else { + if (xloxhi_flag || yloyhi_flag || zlozhi_flag || tilt_flag) + error->all(FLERR,"Read_data header cannot specify simulation box lo/hi/tilt and ABC vectors"); + triclinic = triclinic_general = 1; + } + // problem setup using info from header // only done once, if firstpass and first data file // apply extra settings before grow(), even if no topology in file @@ -536,31 +555,69 @@ void ReadData::command(int narg, char **arg) n = static_cast(nbig); atom->avec->grow(n); - domain->boxlo[0] = boxlo[0]; - domain->boxhi[0] = boxhi[0]; - domain->boxlo[1] = boxlo[1]; - domain->boxhi[1] = boxhi[1]; - domain->boxlo[2] = boxlo[2]; - domain->boxhi[2] = boxhi[2]; - - if (triclinic) { - domain->triclinic = 1; - domain->xy = xy; - domain->xz = xz; - domain->yz = yz; - } + // setup simulation box + // 3 options: orthogonal, restricted triclinic, general triclinic + // for general triclinic: convect general ABC edge vectors to LAMMPS restricted triclinic + + if (!triclinic_general) { + domain->boxlo[0] = boxlo[0]; + domain->boxhi[0] = boxhi[0]; + domain->boxlo[1] = boxlo[1]; + domain->boxhi[1] = boxhi[1]; + domain->boxlo[2] = boxlo[2]; + domain->boxhi[2] = boxhi[2]; + + if (triclinic) { + domain->triclinic = 1; + domain->xy = xy; + domain->xz = xz; + domain->yz = yz; + } - domain->print_box(" "); - domain->set_initial_box(); - domain->set_global_box(); - comm->set_proc_grid(); - domain->set_local_box(); + } else if (triclinic_general) { + domain->set_general_triclinic(avec,bvec,cvec,tri_origin); + } } // change simulation box to be union of existing box and new box + shift // only done if firstpass and not first data file + // shift not allowed for general triclinic if (firstpass && addflag != NONE) { + + // general triclinic + // first data file must also be general triclinic + // avec,bvec,vec must match first data file + // shift not allowed + + if (triclinic_general) { + if (!domain->triclinic_general) + error->all(FLERR,"Read_data subsequent file cannot switch to general triclinic"); + int errflag = 0; + if (avec[0] != domain->avec[0] || avec[1] != domain->avec[1] || avec[2] != domain->avec[2]) + errflag = 1; + if (bvec[0] != domain->bvec[0] || bvec[1] != domain->bvec[1] || bvec[2] != domain->bvec[2]) + errflag = 1; + if (cvec[0] != domain->cvec[0] || cvec[1] != domain->cvec[1] || cvec[2] != domain->cvec[2]) + errflag = 1; + if (tri_origin[0] != domain->tri_origin[0] || tri_origin[1] != domain->tri_origin[1] || + tri_origin[2] != domain->tri_origin[2]) + errflag = 1; + if (errflag) + error->all(FLERR,"Read_data subsequent file ABC vectors must be same as first file"); + if (shift[0] != 0.0 || shift[1] != 0.0 || shift[2] != 0.0) + error->all(FLERR,"Read_data subsequent file with ABC vectors cannot define shift"); + + // restricted triclinic + // tilt factors must match first data file + + } else if (triclinic) { + if (!domain->triclinic || domain->triclinic_general) + error->all(FLERR,"Read_data subsequent file cannot switch to restricted triclinic"); + if (xy != domain->xy || xz != domain->xz || yz != domain->yz) + error->all(FLERR,"Read_data subsequent file tilt factors must be same as first file"); + } + double oldboxlo[3] = {domain->boxlo[0], domain->boxlo[1], domain->boxlo[2]}; double oldboxhi[3] = {domain->boxhi[0], domain->boxhi[1], domain->boxhi[2]}; domain->boxlo[0] = MIN(domain->boxlo[0], boxlo[0] + shift[0]); @@ -570,7 +627,9 @@ void ReadData::command(int narg, char **arg) domain->boxlo[2] = MIN(domain->boxlo[2], boxlo[2] + shift[2]); domain->boxhi[2] = MAX(domain->boxhi[2], boxhi[2] + shift[2]); - // check of box has changed. If yes, warn about non-zero image flags + // check if box has changed + // if yes, warn about non-zero image flags + if ((oldboxlo[0] != domain->boxlo[0]) || (oldboxlo[1] != domain->boxlo[1]) || (oldboxlo[2] != domain->boxlo[2]) || (oldboxhi[0] != domain->boxhi[0]) || (oldboxhi[1] != domain->boxhi[1]) || (oldboxhi[2] != domain->boxhi[2])) { @@ -588,19 +647,16 @@ void ReadData::command(int narg, char **arg) if ((flag_all > 0) && (comm->me == 0)) error->warning(FLERR, "Non-zero image flags with growing box leads to bad coordinates"); } - - // NOTE: not sure what to do about tilt value in subsequent data files - //if (triclinic) { - // domain->xy = xy; domain->xz = xz; domain->yz = yz; - // } - - domain->print_box(" "); - domain->set_initial_box(); - domain->set_global_box(); - comm->set_proc_grid(); - domain->set_local_box(); } + // setup simulation box and paritioning in Domain and Comm classes + + domain->print_box(" "); + domain->set_initial_box(); + domain->set_global_box(); + comm->set_proc_grid(); + domain->set_local_box(); + // allocate space for type label map if (firstpass) { @@ -608,8 +664,9 @@ void ReadData::command(int narg, char **arg) lmap = new LabelMap(lmp, ntypes, nbondtypes, nangletypes, ndihedraltypes, nimpropertypes); } + // rest of data file is Sections + // read in any order, except where error checks // customize for new sections - // read rest of file in free format while (strlen(keyword)) { @@ -1140,7 +1197,8 @@ void ReadData::header(int firstpass) // initialize type counts by the "extra" numbers so they get counted // in case the corresponding "types" line is missing and thus the extra - // value will not be processed. + // value will not be processed + if (addflag == NONE) { atom->ntypes = extra_atom_types; atom->nbondtypes = extra_bond_types; @@ -1156,6 +1214,7 @@ void ReadData::header(int firstpass) if (eof == nullptr) error->one(FLERR, "Unexpected end of data file"); // check for units keyword in first line and print warning on mismatch + auto units = Tokenizer(utils::strfind(line, "units = \\w+")).as_vector(); if (units.size() > 2) { if (units[2] != update->unit_style) @@ -1278,7 +1337,7 @@ void ReadData::header(int firstpass) else if (firstpass) atom->nimpropers += nimpropers; - // Atom class type settings are only set by first data file + // Atom class type settings are only set by first data file } else if (utils::strmatch(line, "^\\s*\\d+\\s+atom\\s+types\\s")) { ntypes = utils::inumeric(FLERR, words[0], false, lmp); @@ -1300,11 +1359,11 @@ void ReadData::header(int firstpass) nimpropertypes = utils::inumeric(FLERR, words[0], false, lmp); if (addflag == NONE) atom->nimpropertypes = nimpropertypes + extra_improper_types; - // these settings only used by first data file - // also, these are obsolescent. we parse them to maintain backward - // compatibility, but the recommended way is to set them via keywords - // in the LAMMPS input file. In case these flags are set in both, - // the input and the data file, we use the larger of the two. + // these settings only used by first data file + // also, these are obsolescent. we parse them to maintain backward + // compatibility, but the recommended way is to set them via keywords + // in the LAMMPS input file. In case these flags are set in both, + // the input and the data file, we use the larger of the two. } else if (strstr(line, "extra bond per atom")) { if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp); @@ -1322,26 +1381,50 @@ void ReadData::header(int firstpass) if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp); force->special_extra = MAX(force->special_extra, extra_flag_value); - // local copy of box info - // so can treat differently for first vs subsequent data files + // local copy of box info + // so can treat differently for first vs subsequent data files } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi\\s")) { + xloxhi_flag = 1; boxlo[0] = utils::numeric(FLERR, words[0], false, lmp); boxhi[0] = utils::numeric(FLERR, words[1], false, lmp); } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi\\s")) { + yloyhi_flag = 1; boxlo[1] = utils::numeric(FLERR, words[0], false, lmp); boxhi[1] = utils::numeric(FLERR, words[1], false, lmp); } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+zlo\\s+zhi\\s")) { + zlozhi_flag = 1; boxlo[2] = utils::numeric(FLERR, words[0], false, lmp); boxhi[2] = utils::numeric(FLERR, words[1], false, lmp); } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+xy\\s+xz\\s+yz\\s")) { - triclinic = 1; + tilt_flag = 1; xy = utils::numeric(FLERR, words[0], false, lmp); xz = utils::numeric(FLERR, words[1], false, lmp); yz = utils::numeric(FLERR, words[2], false, lmp); + + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\avec\\s")) { + avec_flag = 1; + avec[0] = utils::numeric(FLERR, words[0], false, lmp); + avec[1] = utils::numeric(FLERR, words[1], false, lmp); + avec[2] = utils::numeric(FLERR, words[2], false, lmp); + tri_origin[0] = utils::numeric(FLERR, words[3], false, lmp); + + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\bvec\\s")) { + bvec_flag = 1; + bvec[0] = utils::numeric(FLERR, words[0], false, lmp); + bvec[1] = utils::numeric(FLERR, words[1], false, lmp); + bvec[2] = utils::numeric(FLERR, words[2], false, lmp); + tri_origin[1] = utils::numeric(FLERR, words[3], false, lmp); + + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\cvec\\s")) { + cvec_flag = 1; + cvec[0] = utils::numeric(FLERR, words[0], false, lmp); + cvec[1] = utils::numeric(FLERR, words[1], false, lmp); + cvec[2] = utils::numeric(FLERR, words[2], false, lmp); + tri_origin[2] = utils::numeric(FLERR, words[3], false, lmp); } else break; @@ -1407,8 +1490,8 @@ void ReadData::atoms() if (eof) error->all(FLERR, "Unexpected end of data file"); if (tlabelflag && !lmap->is_complete(Atom::ATOM)) error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label"); - atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, shiftflag, shift, tlabelflag, - lmap->lmap2lmap.atom); + atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, triclinic_general, + shiftflag, shift, tlabelflag, lmap->lmap2lmap.atom); nread += nchunk; } diff --git a/src/read_data.h b/src/read_data.h index e97f2259973..6439fbd0965 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -63,8 +63,11 @@ class ReadData : public Command { double boxlo[3], boxhi[3]; double xy, xz, yz; - int triclinic; - + double avec[3], bvec[3], cvec[3], tri_origin[3]; + int triclinic, triclinic_general; + int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag; + int avec_flag, bvec_flag, cvec_flag; + // optional args int addflag, offsetflag, shiftflag, coeffflag, settypeflag; diff --git a/src/write_data.cpp b/src/write_data.cpp index dd5b056ae8e..0ab72f857a7 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -72,8 +72,11 @@ void WriteData::command(int narg, char **arg) pairflag = II; coeffflag = 1; fixflag = 1; + triclinic_general = 0; lmapflag = 1; - // store current (default) setting since we may change it. + + // store current (default) setting since we may change it + int types_style = atom->types_style; int noinit = 0; @@ -94,6 +97,9 @@ void WriteData::command(int narg, char **arg) } else if (strcmp(arg[iarg],"nofix") == 0) { fixflag = 0; iarg++; + } else if (strcmp(arg[iarg],"triclinic") == 0) { + triclinic_general = 1; + iarg++; } else if (strcmp(arg[iarg],"nolabelmap") == 0) { lmapflag = 0; iarg++; @@ -135,7 +141,9 @@ void WriteData::command(int narg, char **arg) } write(file); + // restore saved setting + atom->types_style = types_style; } @@ -206,8 +214,32 @@ void WriteData::write(const std::string &file) } // per atom info in Atoms and Velocities sections - + // if general triclinic: + // save restricted triclinic atom coords + // transform atom coords from restricted to general + // restore save atom coords after output + // NOTE: do same for velocities as well ? + + double **xstore = nullptr; + + if (triclinic_general) { + double **x = atom->x; + int nlocal = atom->nlocal; + memory->create(xstore,nlocal,3,"write_data:xstore"); + if (nlocal) memcpy(&xstore[0][0],&x[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general(x[i]); + } + if (natoms) atoms(); + + if (triclinic_general) { + double **x = atom->x; + int nlocal = atom->nlocal; + if (nlocal) memcpy(&x[0][0],&xstore[0][0],3*nlocal*sizeof(double)); + memory->destroy(xstore); + } + if (natoms) velocities(); // molecular topology info if defined @@ -289,15 +321,22 @@ void WriteData::header() for (int m = 0; m < ifix->wd_header; m++) ifix->write_data_header(fp,m); - // box info - - auto box = fmt::format("\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n", - domain->boxlo[0],domain->boxhi[0], - domain->boxlo[1],domain->boxhi[1], - domain->boxlo[2],domain->boxhi[2]); - if (domain->triclinic) - box += fmt::format("{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz); - fputs(box.c_str(),fp); + // box info: orthogonal, restricted triclinic, or general triclinic (if requested) + + if (!triclinic_general) { + fmt::print(fp,"\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n", + domain->boxlo[0],domain->boxhi[0], + domain->boxlo[1],domain->boxhi[1], + domain->boxlo[2],domain->boxhi[2]); + if (domain->triclinic) + fmt::print(fp,"{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz); + + } else if (triclinic_general) { + fmt::print(fp,"\n{} {} {} {} avec\n{} {} {} {} bvec\n{} {} {} {} cvec\n", + domain->avec[0],domain->avec[1],domain->avec[2],domain->tri_origin[0], + domain->bvec[0],domain->bvec[1],domain->bvec[2],domain->tri_origin[1], + domain->cvec[0],domain->cvec[1],domain->cvec[2],domain->tri_origin[2]); + } } /* ---------------------------------------------------------------------- diff --git a/src/write_data.h b/src/write_data.h index f0df9b0c5fd..ebaa97ffc0d 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -35,6 +35,7 @@ class WriteData : public Command { int pairflag; int coeffflag; int fixflag; + int triclinic_general; int lmapflag; FILE *fp; bigint nbonds_local, nbonds; From 932a08024645d0f4ca7db8a09704e03b94110551 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 31 Aug 2023 14:45:24 -0600 Subject: [PATCH 020/719] tweak comments --- src/write_data.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/write_data.cpp b/src/write_data.cpp index 0ab72f857a7..03e09cf4620 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -217,8 +217,7 @@ void WriteData::write(const std::string &file) // if general triclinic: // save restricted triclinic atom coords // transform atom coords from restricted to general - // restore save atom coords after output - // NOTE: do same for velocities as well ? + // restore saved atom coords after output double **xstore = nullptr; From 7462439b5d818f7d2fbc8ab74b344f9b76e4eeee Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 1 Sep 2023 12:15:51 -0600 Subject: [PATCH 021/719] mods to change_box --- src/create_atoms.cpp | 2 +- src/create_box.cpp | 142 ++++++++++++++++++++++++++++++++----------- src/domain.cpp | 5 ++ src/lattice.cpp | 30 +++++++++ src/lattice.h | 10 ++- src/read_data.cpp | 13 +++- 6 files changed, 161 insertions(+), 41 deletions(-) diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 32be85e6475..aa95c8397fa 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -1178,7 +1178,7 @@ void CreateAtoms::add_lattice() } else domain->bbox(domain->sublo_lamda, domain->subhi_lamda, bboxlo, bboxhi); - // narrow down the subbox by the bounding box of the given region, if available. + // narrow down the subbox by the bounding box of the given region, if available // for small regions in large boxes, this can result in a significant speedup if ((style == REGION) && region->bboxflag) { diff --git a/src/create_box.cpp b/src/create_box.cpp index 02aa63acf0a..74a8db8bb36 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -19,6 +19,7 @@ #include "domain.h" #include "error.h" #include "force.h" +#include "lattice.h" #include "region.h" #include "region_prism.h" #include "update.h" @@ -45,40 +46,112 @@ void CreateBox::command(int narg, char **arg) // region check - auto region = domain->get_region_by_id(arg[1]); - if (!region) error->all(FLERR, "Create_box region {} does not exist", arg[1]); - if (region->bboxflag == 0) error->all(FLERR, "Create_box region does not support a bounding box"); - - region->init(); - - // if region not prism: - // setup orthogonal domain - // set simulation domain from region extent - // if region is prism: - // seutp triclinic domain - // set simulation domain params from prism params - - if (strcmp(region->style, "prism") != 0) { - domain->triclinic = 0; - domain->boxlo[0] = region->extent_xlo; - domain->boxhi[0] = region->extent_xhi; - domain->boxlo[1] = region->extent_ylo; - domain->boxhi[1] = region->extent_yhi; - domain->boxlo[2] = region->extent_zlo; - domain->boxhi[2] = region->extent_zhi; - - } else { - domain->triclinic = 1; - auto prism = dynamic_cast(region); - domain->boxlo[0] = prism->xlo; - domain->boxhi[0] = prism->xhi; - domain->boxlo[1] = prism->ylo; - domain->boxhi[1] = prism->yhi; - domain->boxlo[2] = prism->zlo; - domain->boxhi[2] = prism->zhi; - domain->xy = prism->xy; - domain->xz = prism->xz; - domain->yz = prism->yz; + Region *region = nullptr; + int triclinic_general = 0; + + if (strcmp(arg[1],"NULL") == 0) triclinic_general = 1; + else { + region = domain->get_region_by_id(arg[1]); + if (!region) error->all(FLERR, "Create_box region {} does not exist", arg[1]); + if (region->bboxflag == 0) error->all(FLERR, "Create_box region does not support a bounding box"); + region->init(); + } + + // setup simulation box + // 3 options: orthogonal, restricted triclinic, general triclinic + + int iarg = 2; + + if (region) { + // region is not prism + // setup orthogonal box + // set simulation domain from region extent + + if (strcmp(region->style, "prism") != 0) { + domain->triclinic = 0; + domain->boxlo[0] = region->extent_xlo; + domain->boxhi[0] = region->extent_xhi; + domain->boxlo[1] = region->extent_ylo; + domain->boxhi[1] = region->extent_yhi; + domain->boxlo[2] = region->extent_zlo; + domain->boxhi[2] = region->extent_zhi; + + // region is prism + // seutp restricted triclinic box + // set simulation domain from prism params + + } else { + domain->triclinic = 1; + auto prism = dynamic_cast(region); + domain->boxlo[0] = prism->xlo; + domain->boxhi[0] = prism->xhi; + domain->boxlo[1] = prism->ylo; + domain->boxhi[1] = prism->yhi; + domain->boxlo[2] = prism->zlo; + domain->boxhi[2] = prism->zhi; + domain->xy = prism->xy; + domain->xz = prism->xz; + domain->yz = prism->yz; + } + + // setup general triclinic box (with no region) + // read next box extent arguments to create ABC edge vectors + origin + // set_general_triclinic() converts + // ABC edge vectors + origin to restricted triclinic + + } else if (triclinic_general) { + if (!domain->lattice->is_custom()) + error->all(FLERR,"Create_box with no region requires custom lattice"); + if (domain->lattice->is_oriented()) + error->all(FLERR,"Create_box with no region requires lattice with default orientation"); + + if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "create_box general triclinic", error); + + double alo = utils::numeric(FLERR, arg[iarg + 0], false, lmp); + double ahi = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + double blo = utils::numeric(FLERR, arg[iarg + 2], false, lmp); + double bhi = utils::numeric(FLERR, arg[iarg + 3], false, lmp); + double clo = utils::numeric(FLERR, arg[iarg + 4], false, lmp); + double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp); + iarg += 6; + + // use lattice2box() to generate avec, bvec, cvec and origin + + double avec[3],bvec[3],cvec[3],origin[3]; + double px,py,pz; + + px = alo; py = blo; pz = clo; + domain->lattice->lattice2box(px,py,pz); + origin[0] = px; + origin[1] = py; + origin[2] = pz; + + px = ahi; py = blo; pz = clo; + domain->lattice->lattice2box(px,py,pz); + avec[0] = px - origin[0]; + avec[1] = py - origin[1]; + avec[2] = pz - origin[2]; + + px = alo; py = bhi; pz = clo; + domain->lattice->lattice2box(px,py,pz); + bvec[0] = px - origin[0]; + bvec[1] = py - origin[1]; + bvec[2] = pz - origin[2]; + + px = alo; py = blo; pz = chi; + domain->lattice->lattice2box(px,py,pz); + cvec[0] = px - origin[0]; + cvec[1] = py - origin[1]; + cvec[2] = pz - origin[2]; + + printf("ORIGIN %g %g %g\n",origin[0],origin[1],origin[2]); + printf("AVEC %g %g %g\n",avec[0],avec[1],avec[2]); + printf("BVEC %g %g %g\n",bvec[0],bvec[1],bvec[2]); + printf("CVEC %g %g %g\n",cvec[0],cvec[1],cvec[2]); + + // setup general triclinic box in Domain + + domain->set_general_triclinic(avec,bvec,cvec,origin); } // if molecular, zero out topology info @@ -104,7 +177,6 @@ void CreateBox::command(int narg, char **arg) // process optional args that can overwrite default settings - int iarg = 2; while (iarg < narg) { if (strcmp(arg[iarg], "bond/types") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box bond/type", error); diff --git a/src/domain.cpp b/src/domain.cpp index 6523bfc8c77..9629645aa65 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -551,6 +551,11 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, tri_origin[1] = origin_caller[1]; tri_origin[2] = origin_caller[2]; + // error check on cvec for 2d systems + + if (dimension == 2 && (cvec[0] != 0.0 || cvec[1] != 0.0)) + error->all(FLERR,"General triclinic box edge vector C invalid for 2d system"); + // error check for co-planar A,B,C double abcross[3]; diff --git a/src/lattice.cpp b/src/lattice.cpp index edb482cfac7..539ec735316 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -262,6 +262,14 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) scale = pow(nbasis/volume/scale,1.0/dimension); } + // set orientflag + // for general triclinic, create_box and create_atoms require orientflag = 0 + + oriented = 0; + if (orientx[0] != 1 || orientx[1] != 0 || orientx[2] != 0) oriented = 1; + if (orienty[0] != 0 || orienty[1] != 1 || orienty[2] != 0) oriented = 1; + if (orientz[0] != 0 || orientz[1] != 0 || orientz[2] != 1) oriented = 1; + // initialize lattice <-> box transformation matrices setup_transform(); @@ -311,6 +319,28 @@ Lattice::~Lattice() memory->destroy(basis); } +/* ---------------------------------------------------------------------- + return 1 if style = CUSTOM, else 0 + queried by create_box and create_atoms for general triclinic +------------------------------------------------------------------------- */ + +int Lattice::is_custom() +{ + if (style == CUSTOM) return 1; + return 0; +} + +/* ---------------------------------------------------------------------- + return 1 any orient vectors are non-default, else 0 + queried by create_box and create_atoms for general triclinic +------------------------------------------------------------------------- */ + +int Lattice::is_oriented() +{ + if (oriented) return 1; + return 0; +} + /* ---------------------------------------------------------------------- check if 3 orientation vectors are mutually orthogonal ------------------------------------------------------------------------- */ diff --git a/src/lattice.h b/src/lattice.h index 5b98f580b7a..d91b5cc834f 100644 --- a/src/lattice.h +++ b/src/lattice.h @@ -33,15 +33,19 @@ class Lattice : protected Pointers { ~Lattice() override; void lattice2box(double &, double &, double &); void box2lattice(double &, double &, double &); - void bbox(int, double, double, double, double &, double &, double &, double &, double &, - double &); - + void bbox(int, double, double, double, + double &, double &, double &, double &, double &, double &); + int is_custom(); + int is_oriented(); + private: double scale; double origin[3]; // lattice origin + int oriented; // 1 if non-default orient xyz, else 0 int orientx[3]; // lattice orientation vecs int orienty[3]; // orientx = what lattice dir lies int orientz[3]; // along x dim in box + double primitive[3][3]; // lattice <-> box transform matrices double priminv[3][3]; diff --git a/src/read_data.cpp b/src/read_data.cpp index 8df901062c1..bd998ed3f55 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -557,9 +557,11 @@ void ReadData::command(int narg, char **arg) // setup simulation box // 3 options: orthogonal, restricted triclinic, general triclinic - // for general triclinic: convect general ABC edge vectors to LAMMPS restricted triclinic if (!triclinic_general) { + + // orthongal box + domain->boxlo[0] = boxlo[0]; domain->boxhi[0] = boxhi[0]; domain->boxlo[1] = boxlo[1]; @@ -567,6 +569,8 @@ void ReadData::command(int narg, char **arg) domain->boxlo[2] = boxlo[2]; domain->boxhi[2] = boxhi[2]; + // restricted triclinic box + if (triclinic) { domain->triclinic = 1; domain->xy = xy; @@ -574,6 +578,10 @@ void ReadData::command(int narg, char **arg) domain->yz = yz; } + // general triclinic box + // set_general_triclinic() converts + // ABC edge vectors + origin to restricted triclinic + } else if (triclinic_general) { domain->set_general_triclinic(avec,bvec,cvec,tri_origin); } @@ -581,7 +589,8 @@ void ReadData::command(int narg, char **arg) // change simulation box to be union of existing box and new box + shift // only done if firstpass and not first data file - // shift not allowed for general triclinic + // for restricted triclinic, new tilt factors not allowed + // for general triclinic, different new box and shift not allowed if (firstpass && addflag != NONE) { From 817a16b48c43d50a153cba0e1693118bd9325eca Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 1 Sep 2023 14:38:22 -0600 Subject: [PATCH 022/719] work on create_atoms command --- src/create_atoms.cpp | 94 ++++++++++++++++++++++++++++++++++++++------ src/create_atoms.h | 1 + src/create_box.cpp | 13 +++--- src/domain.cpp | 4 +- src/lattice.cpp | 5 ++- 5 files changed, 92 insertions(+), 25 deletions(-) diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index aa95c8397fa..9a345446270 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -450,8 +450,8 @@ void CreateAtoms::command(int narg, char **arg) atom->nghost = 0; atom->avec->clear_bonus(); - // add atoms/molecules in one of 3 ways - + // add atoms/molecules with appropriate add() method + bigint natoms_previous = atom->natoms; int nlocal_previous = atom->nlocal; @@ -1155,12 +1155,34 @@ void CreateAtoms::add_mesh(const char *filename) } } +/* ---------------------------------------------------------------------- + add many atoms to general triclinic box by looping over lattice +------------------------------------------------------------------------- */ + +void CreateAtoms::add_lattice_triclinic_general() +{ + + +} + /* ---------------------------------------------------------------------- add many atoms by looping over lattice ------------------------------------------------------------------------- */ void CreateAtoms::add_lattice() { + // add atoms on general triclinic lattice if Domain has setting for it + // verify lattice is valid for general triclinic + + int triclinic_general = domain->triclinic_general; + + if (triclinic_general) { + if (!domain->lattice->is_custom()) + error->all(FLERR,"Create_atoms for general triclinic requires custom lattice"); + if (domain->lattice->is_oriented()) + error->all(FLERR,"Create_atoms for general triclinic requires lattice with default orientation"); + } + // convert 8 corners of my subdomain from box coords to lattice coords // for orthogonal, use corner pts of my subbox // for triclinic, use bounding box of my subbox @@ -1202,17 +1224,56 @@ void CreateAtoms::add_lattice() xmin = ymin = zmin = BIG; xmax = ymax = zmax = -BIG; - // convert to lattice coordinates and set bounding box - - domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); - domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); - + // convert 8 corner points of bounding box to lattice coordinates + // compute new bounding box (xyz min/max) in lattice coords + // for orthogonal or restricted triclinic, use 8 corner points of bbox lo/hi + + if (!triclinic_general) { + domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); + domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax); + + // for general triclinic, convert 8 corner points of bbox to general triclinic coords + // new set of 8 points is no longer an orthogonal bounding box + // instead invoke lattice->bbox() on each of 8 points + + } else if (triclinic_general) { + double point[3]; + + point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2]; + domain->restricted_to_general(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2]; + domain->restricted_to_general(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + + point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2]; + domain->restricted_to_general(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2]; + domain->restricted_to_general(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + + point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2]; + domain->restricted_to_general(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2]; + domain->restricted_to_general(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + + point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2]; + domain->restricted_to_general(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2]; + domain->restricted_to_general(point); + domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); + } + // ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox // overlap = any part of a unit cell (face,edge,pt) in common with my subbox // in lattice space, subbox is a tilted box @@ -1233,6 +1294,8 @@ void CreateAtoms::add_lattice() if (ymin < 0.0) jlo--; if (zmin < 0.0) klo--; + printf("LOOP LATTICE bounds: %d %d: %d %d: %d %d\n",ilo,ihi,jlo,jhi,klo,khi); + // count lattice sites on each proc nlatt_overflow = 0; @@ -1298,6 +1361,7 @@ void CreateAtoms::loop_lattice(int action) { int i, j, k, m; + int triclinic_general = domain->triclinic_general; const double *const *const basis = domain->lattice->basis; nlatt = 0; @@ -1317,6 +1381,10 @@ void CreateAtoms::loop_lattice(int action) domain->lattice->lattice2box(x[0], x[1], x[2]); + // convert from general to restricted triclinic coords + + if (triclinic_general) domain->general_to_restricted(x); + // if a region was specified, test if atom is in it if (style == REGION) diff --git a/src/create_atoms.h b/src/create_atoms.h index ae6f1b9d33c..58509171121 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -69,6 +69,7 @@ class CreateAtoms : public Command { void add_mesh(const char *); int add_bisection(const double[3][3], tagint); int add_quasirandom(const double[3][3], tagint); + void add_lattice_triclinic_general(); void add_lattice(); void loop_lattice(int); void add_molecule(double *); diff --git a/src/create_box.cpp b/src/create_box.cpp index 74a8db8bb36..24dff6c01f3 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -115,8 +115,10 @@ void CreateBox::command(int narg, char **arg) double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp); iarg += 6; - // use lattice2box() to generate avec, bvec, cvec and origin - + // use lattice2box() to generate origin and ABC vectors + // origin = abc lo + // ABC vector = hi in one dim - orign + double avec[3],bvec[3],cvec[3],origin[3]; double px,py,pz; @@ -144,12 +146,7 @@ void CreateBox::command(int narg, char **arg) cvec[1] = py - origin[1]; cvec[2] = pz - origin[2]; - printf("ORIGIN %g %g %g\n",origin[0],origin[1],origin[2]); - printf("AVEC %g %g %g\n",avec[0],avec[1],avec[2]); - printf("BVEC %g %g %g\n",bvec[0],bvec[1],bvec[2]); - printf("CVEC %g %g %g\n",cvec[0],cvec[1],cvec[2]); - - // setup general triclinic box in Domain + // setup general triclinic box within Domain domain->set_general_triclinic(avec,bvec,cvec,origin); } diff --git a/src/domain.cpp b/src/domain.cpp index 9629645aa65..d86ced496be 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -667,7 +667,7 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, } /* ---------------------------------------------------------------------- - transform one atom's coords from general triclinic to restricted triclinic + transform atom coords from general triclinic to restricted triclinic ------------------------------------------------------------------------- */ void Domain::general_to_restricted(double *x) @@ -681,7 +681,7 @@ void Domain::general_to_restricted(double *x) } /* ---------------------------------------------------------------------- - transform one atom's coords from restricted triclinic to general triclinic + transform atom coords from restricted triclinic to general triclinic ------------------------------------------------------------------------- */ void Domain::restricted_to_general(double *x) diff --git a/src/lattice.cpp b/src/lattice.cpp index 539ec735316..2e7e740fb86 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -582,8 +582,9 @@ void Lattice::cross(double *x, double *y, double *z) } /* ---------------------------------------------------------------------- - convert x,y,z from lattice coords to box coords (flag = 0) or vice versa - use new point to expand bounding box (min to max) + convert x,y,z from lattice coords to box coords (flag = 0) + or from box coords to lattice coords (flag = 1) + either way, use new point to expand bounding box (min to max) ------------------------------------------------------------------------- */ void Lattice::bbox(int flag, double x, double y, double z, From 7918f14499d86714aec7c5edb7a985795829044b Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 1 Sep 2023 14:45:00 -0600 Subject: [PATCH 023/719] remove unneeded method --- src/create_atoms.cpp | 10 ---------- src/create_atoms.h | 1 - 2 files changed, 11 deletions(-) diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 9a345446270..ac29387ff39 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -1155,16 +1155,6 @@ void CreateAtoms::add_mesh(const char *filename) } } -/* ---------------------------------------------------------------------- - add many atoms to general triclinic box by looping over lattice -------------------------------------------------------------------------- */ - -void CreateAtoms::add_lattice_triclinic_general() -{ - - -} - /* ---------------------------------------------------------------------- add many atoms by looping over lattice ------------------------------------------------------------------------- */ diff --git a/src/create_atoms.h b/src/create_atoms.h index 58509171121..ae6f1b9d33c 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -69,7 +69,6 @@ class CreateAtoms : public Command { void add_mesh(const char *); int add_bisection(const double[3][3], tagint); int add_quasirandom(const double[3][3], tagint); - void add_lattice_triclinic_general(); void add_lattice(); void loop_lattice(int); void add_molecule(double *); From 40def67942ea62d62b487d3aeab5e5e5962c4513 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 1 Sep 2023 17:46:52 -0600 Subject: [PATCH 024/719] debugging --- src/domain.cpp | 4 +--- src/pair_lj_cut.cpp | 2 ++ 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/domain.cpp b/src/domain.cpp index d86ced496be..69ca63169cd 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -638,13 +638,12 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, boxhi[1] = boxlo[1] + bprime[1]; boxhi[2] = boxlo[2] + cprime[2]; - xy = bprime[1]; + xy = bprime[0]; xz = cprime[0]; yz = cprime[1]; // debug - /* printf("Quat: %g %g %g %g\n",quat[0],quat[1],quat[2],quat[3]); double angle = 2.0*acos(quat[0]); printf("Theta: %g\n",angle); @@ -663,7 +662,6 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, printf("Atom1: %g %g %g\n",newcoord[0],newcoord[1],newcoord[2]); MathExtra::matvec(rotate_g2r,coord2,newcoord); printf("Atom2: %g %g %g\n",newcoord[0],newcoord[1],newcoord[2]); - */ } /* ---------------------------------------------------------------------- diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index fae308c57f4..0e4398f676d 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -111,6 +111,8 @@ void PairLJCut::compute(int eflag, int vflag) jtype = type[j]; if (rsq < cutsq[itype][jtype]) { + printf("AAA tags %d %d ij %d %d nlocal %d dist %g\n", + atom->tag[i],atom->tag[j],i,j,atom->nlocal,sqrt(rsq)); r2inv = 1.0 / rsq; r6inv = r2inv * r2inv * r2inv; forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); From 8c3ab47fd6d458dc42a0404cd9b80b6c13f74d34 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 1 Sep 2023 22:58:10 -0600 Subject: [PATCH 025/719] more debugging for fcc example --- src/create_box.cpp | 2 ++ src/domain.cpp | 28 +++++++++++++++++++++++++--- src/lattice.cpp | 10 ++++++---- 3 files changed, 33 insertions(+), 7 deletions(-) diff --git a/src/create_box.cpp b/src/create_box.cpp index 24dff6c01f3..99dd74d5669 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -129,10 +129,12 @@ void CreateBox::command(int narg, char **arg) origin[2] = pz; px = ahi; py = blo; pz = clo; + printf("CB PXYZ %g %g %g\n",px,py,pz); domain->lattice->lattice2box(px,py,pz); avec[0] = px - origin[0]; avec[1] = py - origin[1]; avec[2] = pz - origin[2]; + printf("CB AVEC %g %g %g\n",avec[0],avec[1],avec[2]); px = alo; py = bhi; pz = clo; domain->lattice->lattice2box(px,py,pz); diff --git a/src/domain.cpp b/src/domain.cpp index 69ca63169cd..f1b0c5a20e8 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -577,32 +577,46 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, MathExtra::norm3(rot1); double theta1 = acos(avec[0]/avec_len); MathExtra::axisangle_to_quat(rot1,theta1,quat1); - + // rotmat1 = rotation matrix associated with quat1 double rotmat1[3][3]; MathExtra::quat_to_mat(quat1,rotmat1); + // DEBUG + double afinal[3]; + MathExtra::matvec(rotmat1,avec,afinal); + printf("AFINAL %g %g %g\n",afinal[0],afinal[1],afinal[2]); + // B1 = rotation of B by quat1 rotation matrix double bvec1[3]; - MathExtra::matvec(rotmat1,bvec,bvec1); + printf("BVEC1 %g %g %g\n",bvec1[0],bvec1[1],bvec1[2]); + // quat2 = rotation to convert B1 into B' in xy plane // Byz1 = projection of B1 into yz plane // rot2 = unit vector to rotate B1 around = -x axis // theta2 = angle of rotation calculated from - // Byz1 dot yunit = B1y = |Byz1} cos(theta2) + // Byz1 dot yunit = B1y = |Byz1| cos(theta2) double byzvec1[3],quat2[4]; MathExtra::copy3(bvec1,byzvec1); byzvec1[0] = 0.0; double byzvec1_len = MathExtra::len3(byzvec1); double rot2[3] = {-1.0, 0.0, 0.0}; + if (byzvec1[2] < 0.0) rot2[0] = 1.0; double theta2 = acos(bvec1[1]/byzvec1_len); MathExtra::axisangle_to_quat(rot2,theta2,quat2); + // DEBUG + double rotmat2[3][3]; + MathExtra::quat_to_mat(quat2,rotmat2); + double bfinal[3]; + MathExtra::matvec(rotmat1,bvec1,bfinal); + printf("BFINAL %g %g %g\n",bfinal[0],bfinal[1],bfinal[2]); + // quat = product of quat2 * quat1 = transformation via single quat // rotate_g2r = general to restricted transformation matrix // rotate_r2g = restricted to general transformation matrix @@ -644,6 +658,14 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, // debug + printf("Cvec: %g %g %g\n",cvec[0],cvec[1],cvec[2]); + printf("ABcross: %g %g %g\n",abcross[0],abcross[1],abcross[2]); + printf("Dot: %g\n",dot); + printf("Avec: %g %g %g\n",avec[0],avec[1],avec[2]); + printf("Theta1: %g\n",theta1); + printf("Rotvec1: %g %g %g\n",rot1[0],rot1[1],rot1[2]); + printf("Theta2: %g\n",theta2); + printf("Rotvec2: %g %g %g\n",rot2[0],rot2[1],rot2[2]); printf("Quat: %g %g %g %g\n",quat[0],quat[1],quat[2],quat[3]); double angle = 2.0*acos(quat[0]); printf("Theta: %g\n",angle); diff --git a/src/lattice.cpp b/src/lattice.cpp index 2e7e740fb86..a5dc9714cf3 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -186,6 +186,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) a1[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); a1[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); iarg += 4; + } else if (strcmp(arg[iarg],"a2") == 0) { if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "lattice a2", error); if (style != CUSTOM) @@ -254,11 +255,12 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // reset scale for LJ units (input scale is rho*) // scale = (Nbasis/(Vprimitive * rho*)) ^ (1/dim) - + // use fabs() in case a1,a2,a3 are not right-handed for general triclinic + if (strcmp(update->unit_style,"lj") == 0) { double vec[3]; cross(a2,a3,vec); - double volume = dot(a1,vec); + double volume = fabs(dot(a1,vec)); scale = pow(nbasis/volume/scale,1.0/dimension); } @@ -497,7 +499,7 @@ void Lattice::setup_transform() ------------------------------------------------------------------------- */ void Lattice::lattice2box(double &x, double &y, double &z) -{ +{ double x1 = primitive[0][0]*x + primitive[0][1]*y + primitive[0][2]*z; double y1 = primitive[1][0]*x + primitive[1][1]*y + primitive[1][2]*z; double z1 = primitive[2][0]*x + primitive[2][1]*y + primitive[2][2]*z; @@ -590,7 +592,7 @@ void Lattice::cross(double *x, double *y, double *z) void Lattice::bbox(int flag, double x, double y, double z, double &xmin, double &ymin, double &zmin, double &xmax, double &ymax, double &zmax) -{ +{ if (flag == 0) lattice2box(x,y,z); else box2lattice(x,y,z); From 57f6526e53655f9027ddab0f34c2fc99b7cb8b58 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Sat, 2 Sep 2023 18:45:37 -0600 Subject: [PATCH 026/719] code cleanup --- src/create_box.cpp | 8 ++--- src/domain.cpp | 81 +++++++++++++++++----------------------------- src/domain.h | 4 +-- src/read_data.cpp | 31 ++++++++++-------- src/read_data.h | 4 +-- src/write_data.cpp | 10 +++--- 6 files changed, 59 insertions(+), 79 deletions(-) diff --git a/src/create_box.cpp b/src/create_box.cpp index 99dd74d5669..e42c7c32f05 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -96,7 +96,7 @@ void CreateBox::command(int narg, char **arg) // setup general triclinic box (with no region) // read next box extent arguments to create ABC edge vectors + origin - // set_general_triclinic() converts + // setup_general_triclinic() converts // ABC edge vectors + origin to restricted triclinic } else if (triclinic_general) { @@ -117,7 +117,7 @@ void CreateBox::command(int narg, char **arg) // use lattice2box() to generate origin and ABC vectors // origin = abc lo - // ABC vector = hi in one dim - orign + // ABC vectors = hi in one dim - orign double avec[3],bvec[3],cvec[3],origin[3]; double px,py,pz; @@ -129,12 +129,10 @@ void CreateBox::command(int narg, char **arg) origin[2] = pz; px = ahi; py = blo; pz = clo; - printf("CB PXYZ %g %g %g\n",px,py,pz); domain->lattice->lattice2box(px,py,pz); avec[0] = px - origin[0]; avec[1] = py - origin[1]; avec[2] = pz - origin[2]; - printf("CB AVEC %g %g %g\n",avec[0],avec[1],avec[2]); px = alo; py = bhi; pz = clo; domain->lattice->lattice2box(px,py,pz); @@ -150,7 +148,7 @@ void CreateBox::command(int narg, char **arg) // setup general triclinic box within Domain - domain->set_general_triclinic(avec,bvec,cvec,origin); + domain->setup_general_triclinic(avec,bvec,cvec,origin); } // if molecular, zero out topology info diff --git a/src/domain.cpp b/src/domain.cpp index f1b0c5a20e8..29e0e2cd896 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -527,8 +527,8 @@ void Domain::reset_box() create rotation matrices for general <--> restricted transformations ------------------------------------------------------------------------- */ -void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, - double *cvec_caller, double *origin_caller) +void Domain::setup_general_triclinic(double *avec_caller, double *bvec_caller, + double *cvec_caller, double *origin_caller) { if (triclinic || triclinic_general) error->all(FLERR,"General triclinic box edge vectors are already set"); @@ -547,15 +547,15 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, cvec[1] = cvec_caller[1]; cvec[2] = cvec_caller[2]; - tri_origin[0] = origin_caller[0]; - tri_origin[1] = origin_caller[1]; - tri_origin[2] = origin_caller[2]; + gtri_origin[0] = origin_caller[0]; + gtri_origin[1] = origin_caller[1]; + gtri_origin[2] = origin_caller[2]; // error check on cvec for 2d systems if (dimension == 2 && (cvec[0] != 0.0 || cvec[1] != 0.0)) error->all(FLERR,"General triclinic box edge vector C invalid for 2d system"); - + // error check for co-planar A,B,C double abcross[3]; @@ -563,8 +563,8 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, double dot = MathExtra::dot3(abcross,cvec); if (dot == 0.0) error->all(FLERR,"General triclinic box edge vectors are co-planar"); - - // quat1 = convert A into A' along x-axis + + // quat1 = convert A into A' along +x-axis // rot1 = unit vector to rotate A around // theta1 = angle of rotation calculated from // A dot xunit = Ax = |A| cos(theta1) @@ -583,45 +583,34 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, double rotmat1[3][3]; MathExtra::quat_to_mat(quat1,rotmat1); - // DEBUG - double afinal[3]; - MathExtra::matvec(rotmat1,avec,afinal); - printf("AFINAL %g %g %g\n",afinal[0],afinal[1],afinal[2]); - // B1 = rotation of B by quat1 rotation matrix double bvec1[3]; MathExtra::matvec(rotmat1,bvec,bvec1); - printf("BVEC1 %g %g %g\n",bvec1[0],bvec1[1],bvec1[2]); - // quat2 = rotation to convert B1 into B' in xy plane // Byz1 = projection of B1 into yz plane - // rot2 = unit vector to rotate B1 around = -x axis + // +xaxis = unit vector to rotate B1 around // theta2 = angle of rotation calculated from // Byz1 dot yunit = B1y = |Byz1| cos(theta2) - + // theta2 via acos() is positive (0 to PI) + // positive is valid if B1z < 0.0 else flip sign of theta2 + double byzvec1[3],quat2[4]; MathExtra::copy3(bvec1,byzvec1); byzvec1[0] = 0.0; double byzvec1_len = MathExtra::len3(byzvec1); - double rot2[3] = {-1.0, 0.0, 0.0}; - if (byzvec1[2] < 0.0) rot2[0] = 1.0; double theta2 = acos(bvec1[1]/byzvec1_len); - MathExtra::axisangle_to_quat(rot2,theta2,quat2); + if (bvec1[2] > 0.0) theta2 = -theta2; + MathExtra::axisangle_to_quat(xaxis,theta2,quat2); - // DEBUG - double rotmat2[3][3]; - MathExtra::quat_to_mat(quat2,rotmat2); - double bfinal[3]; - MathExtra::matvec(rotmat1,bvec1,bfinal); - printf("BFINAL %g %g %g\n",bfinal[0],bfinal[1],bfinal[2]); - - // quat = product of quat2 * quat1 = transformation via single quat + // quat = transformation via single quat = quat2 * quat1 // rotate_g2r = general to restricted transformation matrix + // if dot < 0.0 (A x B not in C direction) + // flip sign of z component of transform, + // by flipping sign of 3rd row of rotate_g2r matrix // rotate_r2g = restricted to general transformation matrix - // if A x B not in direction of C, flip sign of z component of transform - // done by flipping sign of 3rd row of rotate_g2r matrix + // simply a transpose of rotate_g2r since orthonormal double quat[4]; MathExtra::quatquat(quat2,quat1,quat); @@ -644,9 +633,9 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, // set restricted triclinic boxlo, boxhi, and tilt factors - boxlo[0] = tri_origin[0]; - boxlo[1] = tri_origin[1]; - boxlo[2] = tri_origin[2]; + boxlo[0] = gtri_origin[0]; + boxlo[1] = gtri_origin[1]; + boxlo[2] = gtri_origin[2]; boxhi[0] = boxlo[0] + aprime[0]; boxhi[1] = boxlo[1] + bprime[1]; @@ -658,14 +647,10 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, // debug - printf("Cvec: %g %g %g\n",cvec[0],cvec[1],cvec[2]); - printf("ABcross: %g %g %g\n",abcross[0],abcross[1],abcross[2]); - printf("Dot: %g\n",dot); - printf("Avec: %g %g %g\n",avec[0],avec[1],avec[2]); printf("Theta1: %g\n",theta1); printf("Rotvec1: %g %g %g\n",rot1[0],rot1[1],rot1[2]); printf("Theta2: %g\n",theta2); - printf("Rotvec2: %g %g %g\n",rot2[0],rot2[1],rot2[2]); + printf("Rotvec2: %g %g %g\n",xaxis[0],xaxis[1],xaxis[2]); printf("Quat: %g %g %g %g\n",quat[0],quat[1],quat[2],quat[3]); double angle = 2.0*acos(quat[0]); printf("Theta: %g\n",angle); @@ -676,14 +661,6 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller, printf("Length A: %g %g\n",MathExtra::len3(avec),MathExtra::len3(aprime)); printf("Length B: %g %g\n",MathExtra::len3(bvec),MathExtra::len3(bprime)); printf("Length C: %g %g\n",MathExtra::len3(cvec),MathExtra::len3(cprime)); - - double coord1[3] = {0.5,0.0,0.0}; - double coord2[3] = {0.5,0.0,0.3}; - double newcoord[3]; - MathExtra::matvec(rotate_g2r,coord1,newcoord); - printf("Atom1: %g %g %g\n",newcoord[0],newcoord[1],newcoord[2]); - MathExtra::matvec(rotate_g2r,coord2,newcoord); - printf("Atom2: %g %g %g\n",newcoord[0],newcoord[1],newcoord[2]); } /* ---------------------------------------------------------------------- @@ -695,9 +672,9 @@ void Domain::general_to_restricted(double *x) double xnew[3]; MathExtra::matvec(rotate_g2r,x,xnew); - x[0] = xnew[0] + tri_origin[0]; - x[1] = xnew[1] + tri_origin[1]; - x[2] = xnew[2] + tri_origin[2]; + x[0] = xnew[0] + gtri_origin[0]; + x[1] = xnew[1] + gtri_origin[1]; + x[2] = xnew[2] + gtri_origin[2]; } /* ---------------------------------------------------------------------- @@ -708,9 +685,9 @@ void Domain::restricted_to_general(double *x) { double xshift[3],xnew[3]; - xshift[0] = x[0] - tri_origin[0]; - xshift[1] = x[1] - tri_origin[1]; - xshift[2] = x[2] - tri_origin[2]; + xshift[0] = x[0] - gtri_origin[0]; + xshift[1] = x[1] - gtri_origin[1]; + xshift[2] = x[2] - gtri_origin[2]; MathExtra::matvec(rotate_r2g,xshift,xnew); x[0] = xnew[0]; x[1] = xnew[1]; diff --git a/src/domain.h b/src/domain.h index e77af5d968c..d09f4cf70d4 100644 --- a/src/domain.h +++ b/src/domain.h @@ -91,7 +91,7 @@ class Domain : protected Pointers { // general triclinic box double avec[3], bvec[3], cvec[3]; // ABC edge vectors of general triclinic box - double tri_origin[3]; // origin of general triclinic box + double gtri_origin[3]; // origin of general triclinic box double rotate_g2r[3][3]; // rotation matrix from general --> restricted tri double rotate_r2g[3][3]; // rotation matrix from restricted --> general tri @@ -141,7 +141,7 @@ class Domain : protected Pointers { void image_flip(int, int, int); int ownatom(int, double *, imageint *, int); - void set_general_triclinic(double *, double *, double *, double *); + void setup_general_triclinic(double *, double *, double *, double *); void general_to_restricted(double *); void restricted_to_general(double *); diff --git a/src/read_data.cpp b/src/read_data.cpp index bd998ed3f55..75d1c23b753 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -480,7 +480,7 @@ void ReadData::command(int narg, char **arg) ellipsoidflag = lineflag = triflag = bodyflag = 0; xloxhi_flag = yloyhi_flag = zlozhi_flag = tilt_flag = 0; - avec_flag = bvec_flag = cvec_flag = 0; + avec_flag = bvec_flag = cvec_flag = gtri_origin_flag = 0; // values in this data file @@ -495,7 +495,7 @@ void ReadData::command(int narg, char **arg) bvec[0] = bvec[1] = bvec[2] = 0.0; cvec[0] = cvec[1] = cvec[2] = 0.0; avec[0] = bvec[1] = cvec[2] = 1.0; - tri_origin[0] = tri_origin[1] = tri_origin[2] = 0.0; + gtri_origin[0] = gtri_origin[1] = gtri_origin[2] = 0.0; keyword[0] = '\0'; @@ -518,7 +518,7 @@ void ReadData::command(int narg, char **arg) // check if simulation box specified consistently - if (!avec_flag && !bvec_flag && !cvec_flag) { + if (!avec_flag && !bvec_flag && !cvec_flag && !gtri_origin_flag) { triclinic = triclinic_general = 0; if (tilt_flag) triclinic = 1; } else { @@ -579,11 +579,11 @@ void ReadData::command(int narg, char **arg) } // general triclinic box - // set_general_triclinic() converts - // ABC edge vectors + origin to restricted triclinic + // setup_general_triclinic() converts + // ABC edge vectors + gtri_origin to restricted triclinic } else if (triclinic_general) { - domain->set_general_triclinic(avec,bvec,cvec,tri_origin); + domain->setup_general_triclinic(avec,bvec,cvec,gtri_origin); } } @@ -609,8 +609,8 @@ void ReadData::command(int narg, char **arg) errflag = 1; if (cvec[0] != domain->cvec[0] || cvec[1] != domain->cvec[1] || cvec[2] != domain->cvec[2]) errflag = 1; - if (tri_origin[0] != domain->tri_origin[0] || tri_origin[1] != domain->tri_origin[1] || - tri_origin[2] != domain->tri_origin[2]) + if (gtri_origin[0] != domain->gtri_origin[0] || gtri_origin[1] != domain->gtri_origin[1] || + gtri_origin[2] != domain->gtri_origin[2]) errflag = 1; if (errflag) error->all(FLERR,"Read_data subsequent file ABC vectors must be same as first file"); @@ -1414,26 +1414,29 @@ void ReadData::header(int firstpass) xz = utils::numeric(FLERR, words[1], false, lmp); yz = utils::numeric(FLERR, words[2], false, lmp); - } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\avec\\s")) { + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\avec\\s")) { avec_flag = 1; avec[0] = utils::numeric(FLERR, words[0], false, lmp); avec[1] = utils::numeric(FLERR, words[1], false, lmp); avec[2] = utils::numeric(FLERR, words[2], false, lmp); - tri_origin[0] = utils::numeric(FLERR, words[3], false, lmp); - } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\bvec\\s")) { + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\bvec\\s")) { bvec_flag = 1; bvec[0] = utils::numeric(FLERR, words[0], false, lmp); bvec[1] = utils::numeric(FLERR, words[1], false, lmp); bvec[2] = utils::numeric(FLERR, words[2], false, lmp); - tri_origin[1] = utils::numeric(FLERR, words[3], false, lmp); - } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\cvec\\s")) { + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\cvec\\s")) { cvec_flag = 1; cvec[0] = utils::numeric(FLERR, words[0], false, lmp); cvec[1] = utils::numeric(FLERR, words[1], false, lmp); cvec[2] = utils::numeric(FLERR, words[2], false, lmp); - tri_origin[2] = utils::numeric(FLERR, words[3], false, lmp); + + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\gtri\\s+origin\\s")) { + gtri_origin_flag = 1; + gtri_origin[0] = utils::numeric(FLERR, words[0], false, lmp); + gtri_origin[1] = utils::numeric(FLERR, words[1], false, lmp); + gtri_origin[2] = utils::numeric(FLERR, words[2], false, lmp); } else break; diff --git a/src/read_data.h b/src/read_data.h index 6439fbd0965..e3c269e6850 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -63,10 +63,10 @@ class ReadData : public Command { double boxlo[3], boxhi[3]; double xy, xz, yz; - double avec[3], bvec[3], cvec[3], tri_origin[3]; + double avec[3], bvec[3], cvec[3], gtri_origin[3]; int triclinic, triclinic_general; int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag; - int avec_flag, bvec_flag, cvec_flag; + int avec_flag, bvec_flag, cvec_flag, gtri_origin_flag; // optional args diff --git a/src/write_data.cpp b/src/write_data.cpp index 03e09cf4620..ad0c508d156 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -331,10 +331,12 @@ void WriteData::header() fmt::print(fp,"{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz); } else if (triclinic_general) { - fmt::print(fp,"\n{} {} {} {} avec\n{} {} {} {} bvec\n{} {} {} {} cvec\n", - domain->avec[0],domain->avec[1],domain->avec[2],domain->tri_origin[0], - domain->bvec[0],domain->bvec[1],domain->bvec[2],domain->tri_origin[1], - domain->cvec[0],domain->cvec[1],domain->cvec[2],domain->tri_origin[2]); + fmt::print(fp,"\n{} {} {} avec\n{} {} {} bvec\n{} {} {} cvec\n", + domain->avec[0],domain->avec[1],domain->avec[2], + domain->bvec[0],domain->bvec[1],domain->bvec[2], + domain->cvec[0],domain->cvec[1],domain->cvec[2]); + fmt::print(fp,"{} {} {} gtri origin\n", + domain->gtri_origin[0],domain->gtri_origin[1],domain->gtri_origin[2]); } } From 78fbdad59e4039d113cc04b95580b6271b062923 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Sat, 2 Sep 2023 18:46:58 -0600 Subject: [PATCH 027/719] code cleanup --- src/create_box.cpp | 2 +- src/lattice.cpp | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/create_box.cpp b/src/create_box.cpp index e42c7c32f05..c534bf63f86 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -117,7 +117,7 @@ void CreateBox::command(int narg, char **arg) // use lattice2box() to generate origin and ABC vectors // origin = abc lo - // ABC vectors = hi in one dim - orign + // ABC vectors = hi in one dim - origin double avec[3],bvec[3],cvec[3],origin[3]; double px,py,pz; diff --git a/src/lattice.cpp b/src/lattice.cpp index a5dc9714cf3..6d7450fd2b0 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -239,11 +239,11 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (origin[2] != 0.0) error->all(FLERR, "Lattice settings are not compatible with 2d simulation"); - if (orientx[2] != 0 || orienty[2] != 0 || - orientz[0] != 0 || orientz[1] != 0) + if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0) error->all(FLERR, "Lattice settings are not compatible with 2d simulation"); - if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0) + if (orientx[2] != 0 || orienty[2] != 0 || + orientz[0] != 0 || orientz[1] != 0) error->all(FLERR, "Lattice settings are not compatible with 2d simulation"); } From 1ed8dd69063abf9348aa64620e01b1394644c09e Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 4 Sep 2023 15:26:55 -0600 Subject: [PATCH 028/719] add general triclinic options to dump custom --- src/atom.cpp | 2 +- src/create_atoms.cpp | 18 +-- src/create_box.cpp | 6 +- src/domain.cpp | 107 ++++++++++++--- src/domain.h | 15 +- src/dump_custom.cpp | 310 ++++++++++++++++++++++++++++++++++++++++-- src/dump_custom.h | 25 +++- src/lmprestart.h | 1 + src/pair_lj_cut.cpp | 2 - src/read_data.cpp | 28 ++-- src/read_data.h | 5 +- src/read_restart.cpp | 7 + src/write_data.cpp | 6 +- src/write_restart.cpp | 6 + 14 files changed, 461 insertions(+), 77 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index 0249547253c..2c2ebd911fd 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1181,7 +1181,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, // convert atom coords from general triclinic to restricted triclinic - if (triclinic_general) domain->general_to_restricted(xdata); + if (triclinic_general) domain->general_to_restricted_coords(xdata); // apply shift if requested by read_data command diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index ac29387ff39..f7347f9ad10 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -1236,31 +1236,31 @@ void CreateAtoms::add_lattice() double point[3]; point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2]; - domain->restricted_to_general(point); + domain->restricted_to_general_coords(point); domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2]; - domain->restricted_to_general(point); + domain->restricted_to_general_coords(point); domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2]; - domain->restricted_to_general(point); + domain->restricted_to_general_coords(point); domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2]; - domain->restricted_to_general(point); + domain->restricted_to_general_coords(point); domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2]; - domain->restricted_to_general(point); + domain->restricted_to_general_coords(point); domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2]; - domain->restricted_to_general(point); + domain->restricted_to_general_coords(point); domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2]; - domain->restricted_to_general(point); + domain->restricted_to_general_coords(point); domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2]; - domain->restricted_to_general(point); + domain->restricted_to_general_coords(point); domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); } @@ -1373,7 +1373,7 @@ void CreateAtoms::loop_lattice(int action) // convert from general to restricted triclinic coords - if (triclinic_general) domain->general_to_restricted(x); + if (triclinic_general) domain->general_to_restricted_coords(x); // if a region was specified, test if atom is in it diff --git a/src/create_box.cpp b/src/create_box.cpp index c534bf63f86..6a047448260 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -96,7 +96,7 @@ void CreateBox::command(int narg, char **arg) // setup general triclinic box (with no region) // read next box extent arguments to create ABC edge vectors + origin - // setup_general_triclinic() converts + // define_general_triclinic() converts // ABC edge vectors + origin to restricted triclinic } else if (triclinic_general) { @@ -146,9 +146,9 @@ void CreateBox::command(int narg, char **arg) cvec[1] = py - origin[1]; cvec[2] = pz - origin[2]; - // setup general triclinic box within Domain + // define general triclinic box within Domain - domain->setup_general_triclinic(avec,bvec,cvec,origin); + domain->define_general_triclinic(avec,bvec,cvec,origin); } // if molecular, zero out topology info diff --git a/src/domain.cpp b/src/domain.cpp index 29e0e2cd896..810814a80f6 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -290,6 +290,29 @@ void Domain::set_global_box() boxhi_bound[1] = MAX(boxhi[1],boxhi[1]+yz); boxhi_bound[2] = boxhi[2]; } + + // update general triclinic box if defined + // reset ABC edge vectors from restricted triclinic box + // boxlo = lower left corner of general triclinic box + + if (triclinic_general) { + double aprime[3],bprime[3],cprime[3]; + + aprime[0] = boxhi[0] - boxlo[0]; + aprime[1] = aprime[2] = 0.0; + bprime[0] = xy; + bprime[1] = boxhi[1] - boxlo[1]; + bprime[2] = 0.0; + cprime[0] = xz; + cprime[1] = yz; + cprime[2] = boxhi[2] - boxlo[2]; + + // transform restricted A'B'C' to general triclinic A,B,C + + MathExtra::matvec(rotate_r2g,aprime,avec); + MathExtra::matvec(rotate_r2g,bprime,bvec); + MathExtra::matvec(rotate_r2g,cprime,cvec); + } } /* ---------------------------------------------------------------------- @@ -527,8 +550,8 @@ void Domain::reset_box() create rotation matrices for general <--> restricted transformations ------------------------------------------------------------------------- */ -void Domain::setup_general_triclinic(double *avec_caller, double *bvec_caller, - double *cvec_caller, double *origin_caller) +void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, + double *cvec_caller, double *origin_caller) { if (triclinic || triclinic_general) error->all(FLERR,"General triclinic box edge vectors are already set"); @@ -547,9 +570,9 @@ void Domain::setup_general_triclinic(double *avec_caller, double *bvec_caller, cvec[1] = cvec_caller[1]; cvec[2] = cvec_caller[2]; - gtri_origin[0] = origin_caller[0]; - gtri_origin[1] = origin_caller[1]; - gtri_origin[2] = origin_caller[2]; + boxlo[0] = origin_caller[0]; + boxlo[1] = origin_caller[1]; + boxlo[2] = origin_caller[2]; // error check on cvec for 2d systems @@ -623,9 +646,9 @@ void Domain::setup_general_triclinic(double *avec_caller, double *bvec_caller, } MathExtra::transpose3(rotate_g2r,rotate_r2g); - - // A',B',C' = transformation of A,B,C to restricted triclinic - + + // transform general ABC to restricted triclinic A'B'C' + double aprime[3],bprime[3],cprime[3]; MathExtra::matvec(rotate_g2r,avec,aprime); MathExtra::matvec(rotate_g2r,bvec,bprime); @@ -633,10 +656,6 @@ void Domain::setup_general_triclinic(double *avec_caller, double *bvec_caller, // set restricted triclinic boxlo, boxhi, and tilt factors - boxlo[0] = gtri_origin[0]; - boxlo[1] = gtri_origin[1]; - boxlo[2] = gtri_origin[2]; - boxhi[0] = boxlo[0] + aprime[0]; boxhi[1] = boxlo[1] + bprime[1]; boxhi[2] = boxlo[2] + cprime[2]; @@ -667,28 +686,72 @@ void Domain::setup_general_triclinic(double *avec_caller, double *bvec_caller, transform atom coords from general triclinic to restricted triclinic ------------------------------------------------------------------------- */ -void Domain::general_to_restricted(double *x) +void Domain::general_to_restricted_coords(double *x) { - double xnew[3]; + double xshift[3],xnew[3]; - MathExtra::matvec(rotate_g2r,x,xnew); - x[0] = xnew[0] + gtri_origin[0]; - x[1] = xnew[1] + gtri_origin[1]; - x[2] = xnew[2] + gtri_origin[2]; + xshift[0] = x[0] - boxlo[0]; + xshift[1] = x[1] - boxlo[1]; + xshift[2] = x[2] - boxlo[2]; + MathExtra::matvec(rotate_g2r,xshift,xnew); + x[0] = xnew[0] + boxlo[0]; + x[1] = xnew[1] + boxlo[1]; + x[2] = xnew[2] + boxlo[2]; } /* ---------------------------------------------------------------------- transform atom coords from restricted triclinic to general triclinic ------------------------------------------------------------------------- */ -void Domain::restricted_to_general(double *x) +void Domain::restricted_to_general_coords(double *x) { double xshift[3],xnew[3]; - xshift[0] = x[0] - gtri_origin[0]; - xshift[1] = x[1] - gtri_origin[1]; - xshift[2] = x[2] - gtri_origin[2]; + xshift[0] = x[0] - boxlo[0]; + xshift[1] = x[1] - boxlo[1]; + xshift[2] = x[2] - boxlo[2]; MathExtra::matvec(rotate_r2g,xshift,xnew); + x[0] = xnew[0] + boxlo[0]; + x[1] = xnew[1] + boxlo[1]; + x[2] = xnew[2] + boxlo[2]; +} + +void Domain::restricted_to_general_coords(double *x, double *xnew) +{ + double xshift[3]; + + xshift[0] = x[0] - boxlo[0]; + xshift[1] = x[1] - boxlo[1]; + xshift[2] = x[2] - boxlo[2]; + MathExtra::matvec(rotate_r2g,xshift,xnew); + xnew[0] += boxlo[0]; + xnew[1] += boxlo[1]; + xnew[2] += boxlo[2]; +} + +/* ---------------------------------------------------------------------- + transform atom vector from general triclinic to restricted triclinic +------------------------------------------------------------------------- */ + +void Domain::general_to_restricted_vector(double *x) +{ + double xnew[3]; + + MathExtra::matvec(rotate_g2r,x,xnew); + x[0] = xnew[0]; + x[1] = xnew[1]; + x[2] = xnew[2]; +} + +/* ---------------------------------------------------------------------- + transform atom vector from restricted triclinic to general triclinic +------------------------------------------------------------------------- */ + +void Domain::restricted_to_general_vector(double *x) +{ + double xnew[3]; + + MathExtra::matvec(rotate_r2g,x,xnew); x[0] = xnew[0]; x[1] = xnew[1]; x[2] = xnew[2]; diff --git a/src/domain.h b/src/domain.h index d09f4cf70d4..7b306a9426c 100644 --- a/src/domain.h +++ b/src/domain.h @@ -89,9 +89,9 @@ class Domain : protected Pointers { double h_rate[6], h_ratelo[3]; // rate of box size/shape change // general triclinic box - + // boxlo = lower left corner + double avec[3], bvec[3], cvec[3]; // ABC edge vectors of general triclinic box - double gtri_origin[3]; // origin of general triclinic box double rotate_g2r[3][3]; // rotation matrix from general --> restricted tri double rotate_r2g[3][3]; // rotation matrix from restricted --> general tri @@ -141,10 +141,13 @@ class Domain : protected Pointers { void image_flip(int, int, int); int ownatom(int, double *, imageint *, int); - void setup_general_triclinic(double *, double *, double *, double *); - void general_to_restricted(double *); - void restricted_to_general(double *); - + void define_general_triclinic(double *, double *, double *, double *); + void general_to_restricted_coords(double *); + void restricted_to_general_coords(double *); + void restricted_to_general_coords(double *, double *); + void general_to_restricted_vector(double *); + void restricted_to_general_vector(double *); + void set_lattice(int, char **); void add_region(int, char **); void delete_region(Region *); diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 1e60295bbe2..d96800554db 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -34,7 +34,7 @@ using namespace LAMMPS_NS; // customize by adding keyword -// also customize compute_atom_property.cpp +// also customize compute_property_atom.cpp enum{ID,MOL,PROC,PROCP1,TYPE,ELEMENT,MASS, X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI, @@ -88,6 +88,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) : buffer_allow = 1; buffer_flag = 1; + triclinic_general = 0; nthresh = 0; nthreshlast = 0; @@ -294,10 +295,14 @@ void DumpCustom::init_style() if (binary && domain->triclinic == 0) header_choice = &DumpCustom::header_binary; + else if (binary && triclinic_general == 1) + header_choice = &DumpCustom::header_binary_triclinic_general; else if (binary && domain->triclinic == 1) header_choice = &DumpCustom::header_binary_triclinic; else if (!binary && domain->triclinic == 0) header_choice = &DumpCustom::header_item; + else if (!binary && triclinic_general == 1) + header_choice = &DumpCustom::header_item_triclinic_general; else if (!binary && domain->triclinic == 1) header_choice = &DumpCustom::header_item_triclinic; @@ -489,6 +494,31 @@ void DumpCustom::header_binary_triclinic(bigint ndump) /* ---------------------------------------------------------------------- */ +void DumpCustom::header_binary_triclinic_general(bigint ndump) +{ + header_format_binary(); + + fwrite(&update->ntimestep,sizeof(bigint),1,fp); + fwrite(&ndump,sizeof(bigint),1,fp); + fwrite(&domain->triclinic,sizeof(int),1,fp); + fwrite(&domain->triclinic_general,sizeof(int),1,fp); + fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); + fwrite(domain->avec,3*sizeof(double),1,fp); + fwrite(domain->bvec,3*sizeof(double),1,fp); + fwrite(domain->cvec,3*sizeof(double),1,fp); + fwrite(domain->boxlo,3*sizeof(double),1,fp); + fwrite(&nfield,sizeof(int),1,fp); + + header_unit_style_binary(); + header_time_binary(); + header_columns_binary(); + + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::header_item(bigint ndump) { if (unit_flag && !unit_count) { @@ -535,6 +565,32 @@ void DumpCustom::header_item_triclinic(bigint ndump) /* ---------------------------------------------------------------------- */ +void DumpCustom::header_item_triclinic_general(bigint ndump) +{ + if (unit_flag && !unit_count) { + ++unit_count; + fmt::print(fp,"ITEM: UNITS\n{}\n",update->unit_style); + } + if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time()); + + fmt::print(fp,"ITEM: TIMESTEP\n{}\n" + "ITEM: NUMBER OF ATOMS\n{}\n", + update->ntimestep, ndump); + + fmt::print(fp,"ITEM: BOX BOUNDS abc origin {}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n", + boundstr, + domain->avec[0],domain->avec[1],domain->avec[2],domain->boxlo[0], + domain->bvec[0],domain->bvec[1],domain->bvec[2],domain->boxlo[1], + domain->cvec[0],domain->cvec[1],domain->cvec[2],domain->boxlo[2]); + + fmt::print(fp,"ITEM: ATOMS {}\n",columns); +} + +/* ---------------------------------------------------------------------- */ + int DumpCustom::count() { int i; @@ -1286,13 +1342,16 @@ int DumpCustom::parse_fields(int narg, char **arg) vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"x") == 0) { - pack_choice[iarg] = &DumpCustom::pack_x; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_x_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_x; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"y") == 0) { - pack_choice[iarg] = &DumpCustom::pack_y; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_y_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_y; vtype[iarg] = Dump::DOUBLE; - } else if (strcmp(arg[iarg],"z") == 0) { - pack_choice[iarg] = &DumpCustom::pack_z; + } else if (strcmp(arg[iarg],"z") == 0) { + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_z_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_z; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"xs") == 0) { if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xs_triclinic; @@ -1307,15 +1366,18 @@ int DumpCustom::parse_fields(int narg, char **arg) else pack_choice[iarg] = &DumpCustom::pack_zs; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"xu") == 0) { - if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xu_triclinic; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_xu_triclinic_general; + else if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_xu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"yu") == 0) { - if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_yu_triclinic; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_yu_triclinic_general; + else if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_yu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_yu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"zu") == 0) { - if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zu_triclinic; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_zu_triclinic_general; + else if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_zu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"xsu") == 0) { @@ -1341,22 +1403,28 @@ int DumpCustom::parse_fields(int narg, char **arg) vtype[iarg] = Dump::INT; } else if (strcmp(arg[iarg],"vx") == 0) { - pack_choice[iarg] = &DumpCustom::pack_vx; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_vx_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_vx; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"vy") == 0) { - pack_choice[iarg] = &DumpCustom::pack_vy; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_vy_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_vy; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"vz") == 0) { - pack_choice[iarg] = &DumpCustom::pack_vz; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_vz_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_vz; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"fx") == 0) { - pack_choice[iarg] = &DumpCustom::pack_fx; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_fx_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_fx; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"fy") == 0) { - pack_choice[iarg] = &DumpCustom::pack_fy; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_fy_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_fy; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"fz") == 0) { - pack_choice[iarg] = &DumpCustom::pack_fz; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_fz_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_fz; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"q") == 0) { @@ -1395,6 +1463,7 @@ int DumpCustom::parse_fields(int narg, char **arg) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_diameter; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"heatflow") == 0) { if (!atom->heatflow_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1405,6 +1474,7 @@ int DumpCustom::parse_fields(int narg, char **arg) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_temperature; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"omegax") == 0) { if (!atom->omega_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1702,6 +1772,14 @@ int DumpCustom::modify_param(int narg, char **arg) return 2; } + if (strcmp(arg[0],"triclinic/general") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + triclinic_general = utils::logical(FLERR,arg[1],false,lmp); + if (triclinic_general && !domain->triclinic_general) + error->all(FLERR,"Dump_modify triclinic/general invalid b/c simulation box is not"); + return 2; + } + if (strcmp(arg[0],"format") == 0) { if (narg < 2) utils::missing_cmd_args(FLERR, "dump_modify format", error); @@ -2283,6 +2361,48 @@ void DumpCustom::pack_z(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_x_triclinic_general(int n) +{ + double **x = atom->x; + double xtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(x[clist[i]],xtri); + buf[n] = xtri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_y_triclinic_general(int n) +{ + double **x = atom->x; + double xtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(x[clist[i]],xtri); + buf[n] = xtri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_z_triclinic_general(int n) +{ + double **x = atom->x; + double xtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(x[clist[i]],xtri); + buf[n] = xtri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_xs(int n) { double **x = atom->x; @@ -2489,6 +2609,84 @@ void DumpCustom::pack_zu_triclinic(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_xu_triclinic_general(int n) +{ + int j; + double **x = atom->x; + imageint *image = atom->image; + + double *h = domain->h; + double xu[3]; + int xbox,ybox,zbox; + + for (int i = 0; i < nchoose; i++) { + j = clist[i]; + xbox = (image[j] & IMGMASK) - IMGMAX; + ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX; + zbox = (image[j] >> IMG2BITS) - IMGMAX; + xu[0] = x[j][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox; + xu[1] = x[j][1] + h[1]*ybox + h[3]*zbox; + xu[2] = x[j][2] + h[2]*zbox; + domain->restricted_to_general_coords(xu); + buf[n] = xu[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_yu_triclinic_general(int n) +{ + int j; + double **x = atom->x; + imageint *image = atom->image; + + double *h = domain->h; + double xu[3]; + int xbox,ybox,zbox; + + for (int i = 0; i < nchoose; i++) { + j = clist[i]; + xbox = (image[j] & IMGMASK) - IMGMAX; + ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX; + zbox = (image[j] >> IMG2BITS) - IMGMAX; + xu[0] = x[j][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox; + xu[1] = x[j][1] + h[1]*ybox + h[3]*zbox; + xu[2] = x[j][2] + h[2]*zbox; + domain->restricted_to_general_coords(xu); + buf[n] = xu[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_zu_triclinic_general(int n) +{ + int j; + double **x = atom->x; + imageint *image = atom->image; + + double *h = domain->h; + double xu[3]; + int xbox,ybox,zbox; + + for (int i = 0; i < nchoose; i++) { + j = clist[i]; + xbox = (image[j] & IMGMASK) - IMGMAX; + ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX; + zbox = (image[j] >> IMG2BITS) - IMGMAX; + xu[0] = x[j][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox; + xu[1] = x[j][1] + h[1]*ybox + h[3]*zbox; + xu[2] = x[j][2] + h[2]*zbox; + domain->restricted_to_general_coords(xu); + buf[n] = xu[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_xsu(int n) { int j; @@ -2671,6 +2869,48 @@ void DumpCustom::pack_vz(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_vx_triclinic_general(int n) +{ + double **v = atom->v; + double vtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(v[clist[i]],vtri); + buf[n] = vtri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_vy_triclinic_general(int n) +{ + double **v = atom->v; + double vtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(v[clist[i]],vtri); + buf[n] = vtri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_vz_triclinic_general(int n) +{ + double **v = atom->v; + double vtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(v[clist[i]],vtri); + buf[n] = vtri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_fx(int n) { double **f = atom->f; @@ -2707,6 +2947,48 @@ void DumpCustom::pack_fz(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_fx_triclinic_general(int n) +{ + double **f = atom->f; + double ftri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(f[clist[i]],ftri); + buf[n] = ftri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_fy_triclinic_general(int n) +{ + double **f = atom->f; + double ftri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(f[clist[i]],ftri); + buf[n] = ftri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_fz_triclinic_general(int n) +{ + double **f = atom->f; + double ftri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_coords(f[clist[i]],ftri); + buf[n] = ftri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_q(int n) { double *q = atom->q; diff --git a/src/dump_custom.h b/src/dump_custom.h index 2b04944ec32..83adbe0d7f8 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -37,6 +37,8 @@ class DumpCustom : public Dump { int nevery; // dump frequency for output char *idregion; // region ID, nullptr if no region + int triclinic_general; // set by dump_modify + int nthresh; // # of defined thresholds int nthreshlast; // # of defined thresholds with value = LAST // @@ -124,8 +126,10 @@ class DumpCustom : public Dump { FnPtrHeader header_choice; // ptr to write header functions void header_binary(bigint); void header_binary_triclinic(bigint); + void header_binary_triclinic_general(bigint); void header_item(bigint); void header_item_triclinic(bigint); + void header_item_triclinic_general(bigint); typedef void (DumpCustom::*FnPtrWrite)(int, double *); FnPtrWrite write_choice; // ptr to write data functions @@ -153,34 +157,52 @@ class DumpCustom : public Dump { void pack_x(int); void pack_y(int); void pack_z(int); + void pack_x_triclinic_general(int); + void pack_y_triclinic_general(int); + void pack_z_triclinic_general(int); + void pack_xs(int); void pack_ys(int); void pack_zs(int); void pack_xs_triclinic(int); void pack_ys_triclinic(int); void pack_zs_triclinic(int); + void pack_xu(int); void pack_yu(int); void pack_zu(int); void pack_xu_triclinic(int); void pack_yu_triclinic(int); void pack_zu_triclinic(int); + void pack_xu_triclinic_general(int); + void pack_yu_triclinic_general(int); + void pack_zu_triclinic_general(int); + void pack_xsu(int); void pack_ysu(int); void pack_zsu(int); void pack_xsu_triclinic(int); void pack_ysu_triclinic(int); void pack_zsu_triclinic(int); + void pack_ix(int); void pack_iy(int); void pack_iz(int); void pack_vx(int); void pack_vy(int); - void pack_vz(int); + void pack_vz(int); + void pack_vx_triclinic_general(int); + void pack_vy_triclinic_general(int); + void pack_vz_triclinic_general(int); + void pack_fx(int); void pack_fy(int); void pack_fz(int); + void pack_fx_triclinic_general(int); + void pack_fy_triclinic_general(int); + void pack_fz_triclinic_general(int); + void pack_q(int); void pack_mux(int); void pack_muy(int); @@ -188,6 +210,7 @@ class DumpCustom : public Dump { void pack_mu(int); void pack_radius(int); void pack_diameter(int); + void pack_heatflow(int); void pack_temperature(int); diff --git a/src/lmprestart.h b/src/lmprestart.h index e5e1da7edf2..b3982ac8c10 100644 --- a/src/lmprestart.h +++ b/src/lmprestart.h @@ -29,6 +29,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, NDIHEDRALS,NDIHEDRALTYPES,DIHEDRAL_PER_ATOM, NIMPROPERS,NIMPROPERTYPES,IMPROPER_PER_ATOM, TRICLINIC,BOXLO,BOXHI,XY,XZ,YZ, + TRICLINIC_GENERAL,ROTATE_G2R,ROTATE_R2G, SPECIAL_LJ,SPECIAL_COUL, MASS,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER, MULTIPROC,MPIIO,PROCSPERFILE,PERPROC, diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 0e4398f676d..fae308c57f4 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -111,8 +111,6 @@ void PairLJCut::compute(int eflag, int vflag) jtype = type[j]; if (rsq < cutsq[itype][jtype]) { - printf("AAA tags %d %d ij %d %d nlocal %d dist %g\n", - atom->tag[i],atom->tag[j],i,j,atom->nlocal,sqrt(rsq)); r2inv = 1.0 / rsq; r6inv = r2inv * r2inv * r2inv; forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); diff --git a/src/read_data.cpp b/src/read_data.cpp index 75d1c23b753..c19250c2aaa 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -480,7 +480,7 @@ void ReadData::command(int narg, char **arg) ellipsoidflag = lineflag = triflag = bodyflag = 0; xloxhi_flag = yloyhi_flag = zlozhi_flag = tilt_flag = 0; - avec_flag = bvec_flag = cvec_flag = gtri_origin_flag = 0; + avec_flag = bvec_flag = cvec_flag = abc_origin_flag = 0; // values in this data file @@ -495,7 +495,7 @@ void ReadData::command(int narg, char **arg) bvec[0] = bvec[1] = bvec[2] = 0.0; cvec[0] = cvec[1] = cvec[2] = 0.0; avec[0] = bvec[1] = cvec[2] = 1.0; - gtri_origin[0] = gtri_origin[1] = gtri_origin[2] = 0.0; + abc_origin[0] = abc_origin[1] = abc_origin[2] = 0.0; keyword[0] = '\0'; @@ -518,7 +518,7 @@ void ReadData::command(int narg, char **arg) // check if simulation box specified consistently - if (!avec_flag && !bvec_flag && !cvec_flag && !gtri_origin_flag) { + if (!avec_flag && !bvec_flag && !cvec_flag && !abc_origin_flag) { triclinic = triclinic_general = 0; if (tilt_flag) triclinic = 1; } else { @@ -579,11 +579,11 @@ void ReadData::command(int narg, char **arg) } // general triclinic box - // setup_general_triclinic() converts - // ABC edge vectors + gtri_origin to restricted triclinic + // define_general_triclinic() converts + // ABC edge vectors + abc_origin to restricted triclinic } else if (triclinic_general) { - domain->setup_general_triclinic(avec,bvec,cvec,gtri_origin); + domain->define_general_triclinic(avec,bvec,cvec,abc_origin); } } @@ -596,7 +596,7 @@ void ReadData::command(int narg, char **arg) // general triclinic // first data file must also be general triclinic - // avec,bvec,vec must match first data file + // avec,bvec,vec and origin must match first data file // shift not allowed if (triclinic_general) { @@ -609,8 +609,8 @@ void ReadData::command(int narg, char **arg) errflag = 1; if (cvec[0] != domain->cvec[0] || cvec[1] != domain->cvec[1] || cvec[2] != domain->cvec[2]) errflag = 1; - if (gtri_origin[0] != domain->gtri_origin[0] || gtri_origin[1] != domain->gtri_origin[1] || - gtri_origin[2] != domain->gtri_origin[2]) + if (abc_origin[0] != domain->boxlo[0] || abc_origin[1] != domain->boxlo[1] || + abc_origin[2] != domain->boxlo[2]) errflag = 1; if (errflag) error->all(FLERR,"Read_data subsequent file ABC vectors must be same as first file"); @@ -1432,11 +1432,11 @@ void ReadData::header(int firstpass) cvec[1] = utils::numeric(FLERR, words[1], false, lmp); cvec[2] = utils::numeric(FLERR, words[2], false, lmp); - } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\gtri\\s+origin\\s")) { - gtri_origin_flag = 1; - gtri_origin[0] = utils::numeric(FLERR, words[0], false, lmp); - gtri_origin[1] = utils::numeric(FLERR, words[1], false, lmp); - gtri_origin[2] = utils::numeric(FLERR, words[2], false, lmp); + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\abc\\s+origin\\s")) { + abc_origin_flag = 1; + abc_origin[0] = utils::numeric(FLERR, words[0], false, lmp); + abc_origin[1] = utils::numeric(FLERR, words[1], false, lmp); + abc_origin[2] = utils::numeric(FLERR, words[2], false, lmp); } else break; diff --git a/src/read_data.h b/src/read_data.h index e3c269e6850..28b277860a1 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -63,10 +63,11 @@ class ReadData : public Command { double boxlo[3], boxhi[3]; double xy, xz, yz; - double avec[3], bvec[3], cvec[3], gtri_origin[3]; + double avec[3], bvec[3], cvec[3]; + double abc_origin[3]; int triclinic, triclinic_general; int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag; - int avec_flag, bvec_flag, cvec_flag, gtri_origin_flag; + int avec_flag, bvec_flag, cvec_flag, abc_origin_flag; // optional args diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 6925bd6096a..372d1bcfe89 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -783,6 +783,13 @@ void ReadRestart::header() } else if (flag == YZ) { domain->yz = read_double(); + } else if (flag == TRICLINIC_GENERAL) { + domain->triclinic_general = read_int(); + } else if (flag == ROTATE_G2R) { + read_double_vec(9,&domain->rotate_g2r[0][0]); + } else if (flag == ROTATE_R2G) { + read_double_vec(9,&domain->rotate_r2g[0][0]); + } else if (flag == SPECIAL_LJ) { read_int(); read_double_vec(3,&force->special_lj[1]); diff --git a/src/write_data.cpp b/src/write_data.cpp index ad0c508d156..960a4ff1cfd 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -227,7 +227,7 @@ void WriteData::write(const std::string &file) memory->create(xstore,nlocal,3,"write_data:xstore"); if (nlocal) memcpy(&xstore[0][0],&x[0][0],3*nlocal*sizeof(double)); for (int i = 0; i < nlocal; i++) - domain->restricted_to_general(x[i]); + domain->restricted_to_general_coords(x[i]); } if (natoms) atoms(); @@ -335,8 +335,8 @@ void WriteData::header() domain->avec[0],domain->avec[1],domain->avec[2], domain->bvec[0],domain->bvec[1],domain->bvec[2], domain->cvec[0],domain->cvec[1],domain->cvec[2]); - fmt::print(fp,"{} {} {} gtri origin\n", - domain->gtri_origin[0],domain->gtri_origin[1],domain->gtri_origin[2]); + fmt::print(fp,"{} {} {} abc origin\n", + domain->boxlo[0],domain->boxlo[1],domain->boxhi[2]); } } diff --git a/src/write_restart.cpp b/src/write_restart.cpp index a996532687e..fb5b41eb02d 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -448,6 +448,12 @@ void WriteRestart::header() write_double(XZ,domain->xz); write_double(YZ,domain->yz); + write_int(TRICLINIC_GENERAL,domain->triclinic_general); + if (domain->triclinic_general) { + write_double_vec(ROTATE_G2R,9,&domain->rotate_g2r[0][0]); + write_double_vec(ROTATE_R2G,9,&domain->rotate_r2g[0][0]); + } + write_double_vec(SPECIAL_LJ,3,&force->special_lj[1]); write_double_vec(SPECIAL_COUL,3,&force->special_coul[1]); From 6f01b27e7ebf865f7670c56fe46ba37dfb492edc Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 5 Sep 2023 16:50:38 -0600 Subject: [PATCH 029/719] add general triclinic pressure tensor to thermo_style --- doc/src/Howto_triclinic.rst | 373 +++++++++++++++++++++--------------- src/thermo.cpp | 123 ++++++++++-- src/thermo.h | 12 ++ 3 files changed, 345 insertions(+), 163 deletions(-) diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 0efadbcc8c0..5fc42e01c64 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -2,42 +2,140 @@ Triclinic (non-orthogonal) simulation boxes =========================================== By default, LAMMPS uses an orthogonal simulation box to encompass the -particles. The :doc:`boundary ` command sets the boundary -conditions of the box (periodic, non-periodic, etc). The orthogonal -box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors -starting from the origin given by **a** = (xhi-xlo,0,0); **b** = -(0,yhi-ylo,0); **c** = (0,0,zhi-zlo). The 6 parameters +particles. The orthogonal box has its "origin" at (xlo,ylo,zlo) and +extends to (xhi,yhi,zhi). Conceptually it is defined by 3 edge +vectors starting from the origin given by **A** = (xhi-xlo,0,0); **B** += (0,yhi-ylo,0); **C** = (0,0,zhi-zlo). The :doc:`boundary +` command sets the boundary conditions for the 6 faces of +the box (periodic, non-periodic, etc). The 6 parameters (xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box -is created, e.g. by the :doc:`create_box ` or -:doc:`read_data ` or :doc:`read_restart ` -commands. Additionally, LAMMPS defines box size parameters lx,ly,lz -where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 -parameters, as well as lx,ly,lz, can be output via the :doc:`thermo_style custom ` command. +is created by one of these commands: -LAMMPS also allows simulations to be performed in triclinic +* :doc:`create_box ` +* :doc:`read_data ` +* :doc:`read_restart ` +* :doc:`read_dump ` + +Internally, LAMMPS defines box size parameters lx,ly,lz where lx = +xhi-xlo, and similarly in the y and z dimensions. The 6 parameters, +as well as lx,ly,lz, can be output via the :doc:`thermo_style custom +` command. See the :doc:'Howto 2d ` doc page +for info on how zlo and zhi are defined for 2d simulations. + +---------- + +LAMMPS also allows simulations to be performed using triclinic (non-orthogonal) simulation boxes shaped as a parallelepiped with -triclinic symmetry. The parallelepiped has its "origin" at -(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the -origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** = -(xz,yz,zhi-zlo). *xy,xz,yz* can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. In LAMMPS the triclinic -simulation box edge vectors **a**, **b**, and **c** cannot be arbitrary -vectors. As indicated, **a** must lie on the positive x axis. **b** must -lie in the xy plane, with strictly positive y component. **c** may have -any orientation with strictly positive z component. The requirement -that **a**, **b**, and **c** have strictly positive x, y, and z components, -respectively, ensures that **a**, **b**, and **c** form a complete -right-handed basis. These restrictions impose no loss of generality, -since it is possible to rotate/invert any set of 3 crystal basis -vectors so that they conform to the restrictions. - -For example, assume that the 3 vectors **A**,\ **B**,\ **C** are the edge -vectors of a general parallelepiped, where there is no restriction on -**A**,\ **B**,\ **C** other than they form a complete right-handed basis i.e. -**A** x **B** . **C** > 0. The equivalent LAMMPS **a**,\ **b**,\ **c** are a linear -rotation of **A**, **B**, and **C** and can be computed as follows: +triclinic symmetry. + +One use of triclinic simulation boxes is to model solid-state crystals +with triclinic symmetry. The :doc:`lattice ` command can be +used with non-orthogonal basis vectors to define a lattice that will +tile a triclinic simulation box via the :doc:`create_atoms +` command. + +A second use is to run Parrinello-Rahman dynamics via the :doc:`fix +npt ` command, which will adjust the xy, xz, yz tilt factors +to compensate for off-diagonal components of the pressure tensor. The +analog for an :doc:`energy minimization ` is the :doc:`fix +box/relax ` command. + +A third use is to shear a bulk solid to study the response of the +material. The :doc:`fix deform ` command can be used for +this purpose. It allows dynamic control of the xy, xz, yz tilt +factors as a simulation runs. This is discussed in the next section +on non-equilibrium MD (NEMD) simulations. + +Conceptually, the tricliic parallelepiped is defined with an "origin" +at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** = +(bx,by,bz), **C** = (cx,cy,cz) which can now be arbitrary vectors, so +long as they are distinct and are not co-planar. + +The 4 commands listed above for defining orthogonal simulation boxes +have triclinic options which allow for specification of the origin and +edge vectors **A**, **B**, **C**. For each command, this can be done +in one of two ways, for what LAMMPS calls a *general* triclinic box, +or a *restricited* triclinic box. A *general* triclinic box is +specified by an origin and 9 parameters (ax,ay,az), (bx,by,bz), +(cx,cy,cz), or 12 parameters in total. A *restricted* triclinic box +also has an origin, but its edge vectors are of the following form: +**A** = (xhi-xlo,0,0), **B** = (xy,yhi-ylo,0), **C** = +(xz,yz,zhi-zlo). So 9 parameters in total. + +The restricted form of edge vectors means that **A** is along the +x-axis, **B** is in the x-y plane with a y-component in the +y +direction, and **C** has a z-component in the +z direction. +*Xy,xz,yz* can be 0.0 or positive or negative values and are called +"tilt factors" because they are the amount of displacement applied to +faces of an originally orthogonal box to transform it into a +restricted parallelepiped. + +.. note:: + + Any general triclinic box (i.e. any solid-state crystal basis + vectors) can be rotated/inverted in 3d around its origin to conform + to the definition of a restricted triclinic box. An inversion may + need to be applied to the rotated **C** vector to ensure its final + z-component is in the +z direction. + +.. note:: + + While LAMMPS allows specification of a triclinic simulation box in + either **general** or **restricted** form, internally LAMMPS only + uses restricted triclinic simulation boxes. This is for parallel + efficiency and to formulate partitioning of the simulation box + across processors, neighbor list building, and inter-processor + communication of per-atom data with methods similar to those used + for orthogonal boxes. This means 3 things. (1) Input of a general + triclinic is immediately converted to restricted form. + (2) If output in general triclinic form is requested (e.g. for atom + coordinates in a dump file), then conversion from restricted + triclinic coordinates is done at the time of output. (3) Most + importantly, other LAMMPS commands such as the :doc:`region + ` command, that refer to the simulation box geometry, + operate on restricted triclinic boxes, even if a general triclinic + box was specified as input. + +Note that for 2d simulations a triclinic simulation box is effectively +a parallelogram; see the :doc:'Howto 2d ` doc page for +details. + +The :doc:`boundary ` command sets the boundary conditions +for the 6 faces of a restricted triclinix box (periodic, non-periodic, +etc), similar to the way the settings apply to the 6 faces of an +orthogonal box. Note that if a restricted triclinic box is periodic +in the y-dimension and has a non-zero xy tilt factor, then particles +which exit the -y face of the box will re-enter the +y face but will +be displaced in x by the xy tilt factor. Similarly for z-periodicity, +if the xz and/or yz tilt factors are non-zero, then particles which +exit the -z face of the box will be displaced in x by the xz tilt +factor and in y by the yz tilt factor. + +For general and restricted triclinic boxes, their **A**, **B**, **C** +edge vector components can be output via + +The :doc:`thermo_style custom ` command also has options +for outputting the parameters that define general and restricted +triclinic simulation boxes. For general triclinic, this is the +(xlo,ylo,zhi) origin and the 9 components of the **A**, **B**, **C** +edge vectors. For restricted triclinic, this is (xlo,ylo,zlo), +(xhi,yhi,zhi), and the xy,xz,yz tilt factors. For both orthogonal and +restricted triclinic boxes, lx/ly/lz refer to the same box sizes, +namely lx = xhi - xlo, etc. + +The remainder of this doc page explains mathematical transformations +between different ways of representing general and restrictied +triclinic boxes, which may be useful when creating LAMMPS inputs for +triclinic simulations or interpreting outputs. How LAMMPS uses tilt +factors for restricted triclinic simulation boxes is also discussed. + +---------- + +Let **A**,\ **B**,\ **C** be the edge vectors of a general triclinic +simulation box. Assume that **A** x **B** . **C** > 0. The +equivalent LAMMPS **a**,\ **b**,\ **c** for a restricted triclinic box +are a linear rotation of **A**, **B**, and **C** and can be computed +as follows: .. math:: @@ -54,23 +152,23 @@ rotation of **A**, **B**, and **C** and can be computed as follows: c_y = & \mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})} \times \mathbf{\hat{A}} \quad = \quad \frac{\mathbf{B} \cdot \mathbf{C} - b_x c_x}{b_y} \\ c_z = & |\mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})}|\quad = \quad \sqrt{C^2 - {c_x}^2 - {c_y}^2} -where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^) -indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles -between the vectors described below. Note that by construction, -**a**, **b**, and **c** have strictly positive x, y, and z components, respectively. -If it should happen that -**A**, **B**, and **C** form a left-handed basis, then the above equations -are not valid for **c**\ . In this case, it is necessary -to first apply an inversion. This can be achieved -by interchanging two basis vectors or by changing the sign of one of them. - -For consistency, the same rotation/inversion applied to the basis vectors -must also be applied to atom positions, velocities, -and any other vector quantities. -This can be conveniently achieved by first converting to -fractional coordinates in the -old basis and then converting to distance coordinates in the new basis. -The transformation is given by the following equation: +where A = \| **A** \| indicates the scalar length of **A**\ . The hat +symbol (\^) indicates the corresponding unit vector. :math:`\beta` and +:math:`\gamma` are angles between the **A**, **B**, **C** vectors +as described below. + +If **A** x **B** . **C** < 0 the above equations are not valid for +**c**\ . In this case, it is necessary to first apply an +inversion. This can be achieved by interchanging two of the **A**, +**B**, **C** vectors or by changing the sign of one of them. + +For consistency, the same rotation/inversion applied to the triclinic +box edge vectors also typically needs to be applied to atom positions, +velocities, and other vector quantities. This can be conveniently +achieved by first converting to fractional coordinates in the general +triclinic coordinates and then converting to coordinates in the +resetricted triclinic basis. The transformation is given by the +following equation: .. math:: @@ -81,87 +179,21 @@ The transformation is given by the following equation: \mathbf{A \times B} \end{pmatrix} \cdot \mathbf{X} -where *V* is the volume of the box, **X** is the original vector quantity and -**x** is the vector in the LAMMPS basis. +where *V* is the volume of the box (same in either basis), **X** is +the fractional vector in the general triclinic basis and **x** is the +resulting vector in the restricted triclinic basis. -There is no requirement that a triclinic box be periodic in any -dimension, though it typically should be in at least the second dimension -of the tilt (y in xy) if you want to enforce a shift in periodic -boundary conditions across that boundary. Some commands that work -with triclinic boxes, e.g. the :doc:`fix deform ` and :doc:`fix npt ` commands, require periodicity or non-shrink-wrap -boundary conditions in specific dimensions. See the command doc pages -for details. - -The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the -time the simulation box is created. This happens in one of 3 ways. -If the :doc:`create_box ` command is used with a region of -style *prism*, then a triclinic box is setup. See the -:doc:`region ` command for details. If the -:doc:`read_data ` command is used to define the simulation -box, and the header of the data file contains a line with the "xy xz -yz" keyword, then a triclinic box is setup. See the -:doc:`read_data ` command for details. Finally, if the -:doc:`read_restart ` command reads a restart file which -was written from a simulation using a triclinic box, then a triclinic -box will be setup for the restarted simulation. - -Note that you can define a triclinic box with all 3 tilt factors = -0.0, so that it is initially orthogonal. This is necessary if the box -will become non-orthogonal, e.g. due to the :doc:`fix npt ` or -:doc:`fix deform ` commands. Alternatively, you can use the -:doc:`change_box ` command to convert a simulation box from -orthogonal to triclinic and vice versa. - -As with orthogonal boxes, LAMMPS defines triclinic box size parameters -lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. -The 9 parameters, as well as lx,ly,lz, can be output via the -:doc:`thermo_style custom ` command. - -To avoid extremely tilted boxes (which would be computationally -inefficient), LAMMPS normally requires that no tilt factor can skew -the box more than half the distance of the parallel box length, which -is the first dimension in the tilt factor (x for xz). This is required -both when the simulation box is created, e.g. via the -:doc:`create_box ` or :doc:`read_data ` commands, -as well as when the box shape changes dynamically during a simulation, -e.g. via the :doc:`fix deform ` or :doc:`fix npt ` -commands. +---------- -For example, if xlo = 2 and xhi = 12, then the x box length is 10 and -the xy tilt factor must be between -5 and 5. Similarly, both xz and -yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is -not a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are geometrically all equivalent. If the box tilt exceeds this -limit during a dynamics run (e.g. via the :doc:`fix deform ` -command), then the box is "flipped" to an equivalent shape with a tilt -factor within the bounds, so the run can continue. See the :doc:`fix deform ` page for further details. - -One exception to this rule is if the first dimension in the tilt -factor (x for xy) is non-periodic. In that case, the limits on the -tilt factor are not enforced, since flipping the box in that dimension -does not change the atom positions due to non-periodicity. In this -mode, if you tilt the system to extreme angles, the simulation will -simply become inefficient, due to the highly skewed simulation box. - -Box flips that may occur using the :doc:`fix deform ` or -:doc:`fix npt ` commands can be turned off using the *flip no* -option with either of the commands. - -Note that if a simulation box has a large tilt factor, LAMMPS will run -less efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped subdomain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. - -Triclinic crystal structures are often defined using three lattice -constants *a*, *b*, and *c*, and three angles :math:`\alpha`, -:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, -the a, b, and c lattice constants are the scalar lengths of the edge +General triclinic crystal structures are often defined using three +lattice constants *a*, *b*, and *c*, and three angles :math:`\alpha`, +:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, the +a, b, and c lattice constants are the scalar lengths of the edge vectors **a**, **b**, and **c** defined above. The relationship between these 6 quantities (a, b, c, :math:`\alpha`, :math:`\beta`, -:math:`\gamma`) and the LAMMPS box sizes (lx,ly,lz) = -(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: +:math:`\gamma`) and the LAMMPS restricted triclinic box sizes +(lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is +as follows: .. math:: @@ -185,15 +217,16 @@ The inverse relationship can be written as follows: The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and :math:`\gamma` can be printed out or accessed by computes using the -:doc:`thermo_style custom ` keywords -*cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*, -respectively. +:doc:`thermo_style custom ` keywords *cella*, *cellb*, +*cellc*, *cellalpha*, *cellbeta*, *cellgamma*, respectively. + +---------- As discussed on the :doc:`dump ` command doc page, when the BOX -BOUNDS for a snapshot is written to a dump file for a triclinic box, -an orthogonal bounding box which encloses the triclinic simulation box -is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic -box, formatted as follows: +BOUNDS for a snapshot is written to a dump file for a resticted +triclinic box, an orthogonal bounding box which encloses the triclinic +simulation box is output, along with the 3 tilt factors (xy, xz, yz) +of the restricted triclinic box, formatted as follows: .. parsed-literal:: @@ -203,7 +236,7 @@ box, formatted as follows: zlo_bound zhi_bound yz This bounding box is convenient for many visualization programs and is -calculated from the 9 triclinic box parameters +calculated from the 9 restricted triclinic box parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows: .. parsed-literal:: @@ -216,22 +249,60 @@ calculated from the 9 triclinic box parameters zhi_bound = zhi These formulas can be inverted if you need to convert the bounding box -back into the triclinic box parameters, e.g. xlo = xlo_bound - -MIN(0.0,xy,xz,xy+xz). +back into the restricted triclinic box parameters, e.g. xlo = +xlo_bound - MIN(0.0,xy,xz,xy+xz). -One use of triclinic simulation boxes is to model solid-state crystals -with triclinic symmetry. The :doc:`lattice ` command can be -used with non-orthogonal basis vectors to define a lattice that will -tile a triclinic simulation box via the -:doc:`create_atoms ` command. +---------- -A second use is to run Parrinello-Rahman dynamics via the :doc:`fix npt ` command, which will adjust the xy, xz, yz tilt -factors to compensate for off-diagonal components of the pressure -tensor. The analog for an :doc:`energy minimization ` is -the :doc:`fix box/relax ` command. +There is no requirement that a triclinic box be periodic in any +dimension, though as explained above it typically should be in y or z +if you wish enforce a shift in coordinates due to periodic boundary +conditions across the y or z boundaries. + +Some commands that work with triclinic boxes, e.g. the :doc:`fix +deform ` and :doc:`fix npt ` commands, require +periodicity or non-shrink-wrap boundary conditions in specific +dimensions. See the command doc pages for details. + +A restricted triclinic box can be defined with all 3 tilt factors = +0.0, so that it is initially orthogonal. This is necessary if the box +will become non-orthogonal, e.g. due to use of the :doc:`fix npt +` or :doc:`fix deform ` commands. Alternatively, +you can use the :doc:`change_box ` command to convert a +simulation box from orthogonal to restricted triclinic and vice versa. + +Highly tilted restricted triclinic simulation boxes can be +computationally inefficient. This is due to the large volume of +communication needed to acquire ghost atoms around a processor's +irregular-shaped subdomain. For extreme values of tilt, LAMMPS may +also lose atoms and generate an error. + +LAMMPS will issue a warning if you define a restricted triclinic box +with a tilt factor which skews the box more than half the distance of +the parallel box length, which is the first dimension in the tilt +factor (x for xz). + +For example, if xlo = 2 and xhi = 12, then the x box length is 10 and +the xy tilt factor should be between -5 and 5 to avoid the warning. +Similarly, both xz and yz should be between -(xhi-xlo)/2 and ++(yhi-ylo)/2. Note that these are not limitations, since if the +maximum tilt factor is 5 (as in this example), then simulations boxes +and atom configurations with tilt = ..., -15, -5, 5, 15, 25, ... are +geometrically all equivalent. + +If the box tilt exceeds this limit during a dynamics run (e.g. due to +the :doc:`fix deform ` command), then by default the box +is "flipped" to an equivalent shape with a tilt factor within the +warning bounds, and the run continues. See the :doc:`fix deform +` page for further details. Box flips that would normally +occur using the :doc:`fix deform ` or :doc:`fix npt +` commands can be suppressed using the *flip no* option with +either of the commands. + +One exception to box flipping is if the first dimension in the tilt +factor (x for xy) is non-periodic. In that case, the limits on the +tilt factor are not enforced, since flipping the box in that dimension +does not change the atom positions due to non-periodicity. In this +mode, the system tilts to large angles, the simulation will simply +become inefficient, due to the highly skewed simulation box. -A third use is to shear a bulk solid to study the response of the -material. The :doc:`fix deform ` command can be used for -this purpose. It allows dynamic control of the xy, xz, yz tilt -factors as a simulation runs. This is discussed in the next section -on non-equilibrium MD (NEMD) simulations. diff --git a/src/thermo.cpp b/src/thermo.cpp index 9f211465886..9a8adcd4193 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -34,6 +34,7 @@ #include "kspace.h" #include "lattice.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" #include "modify.h" #include "neighbor.h" @@ -51,6 +52,7 @@ using namespace LAMMPS_NS; using namespace MathConst; +using namespace MathExtra; // CUSTOMIZATION: add a new keyword by adding it to this list: @@ -111,6 +113,7 @@ Thermo::Thermo(LAMMPS *_lmp, int narg, char **arg) : lostflag = lostbond = Thermo::ERROR; lostbefore = warnbefore = 0; flushflag = 0; + triclinic_general = 0; ntimestep = -1; // set style and corresponding lineflag @@ -569,6 +572,13 @@ void Thermo::modify_params(int narg, char **arg) iarg += 2; + } else if (strcmp(arg[iarg],"triclinic/general") == 0) { + if (iarg + 2 > narg) error->all(FLERR,"Illegal thermo_modify command"); + triclinic_general = utils::logical(FLERR,arg[iarg+1],false,lmp); + if (triclinic_general && !domain->triclinic_general) + error->all(FLERR,"Thermo_modify triclinic/general invalid b/c simulation box is not"); + iarg += 2; + } else if (strcmp(arg[iarg], "lost") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "thermo_modify lost", error); if (strcmp(arg[iarg + 1], "ignore") == 0) @@ -947,21 +957,33 @@ void Thermo::parse_fields(const std::string &str) addfield("Impros", &Thermo::compute_impropers, BIGINT); } else if (word == "pxx") { - addfield("Pxx", &Thermo::compute_pxx, FLOAT); + if (triclinic_general) + addfield("Pxx", &Thermo::compute_pxx_triclinic_general, FLOAT); + else addfield("Pxx", &Thermo::compute_pxx, FLOAT); index_press_vector = add_compute(id_press, VECTOR); } else if (word == "pyy") { - addfield("Pyy", &Thermo::compute_pyy, FLOAT); + if (triclinic_general) + addfield("Pyy", &Thermo::compute_pyy_triclinic_general, FLOAT); + else addfield("Pyy", &Thermo::compute_pyy, FLOAT); index_press_vector = add_compute(id_press, VECTOR); } else if (word == "pzz") { - addfield("Pzz", &Thermo::compute_pzz, FLOAT); + if (triclinic_general) + addfield("Pzz", &Thermo::compute_pzz_triclinic_general, FLOAT); + else addfield("Pzz", &Thermo::compute_pzz, FLOAT); index_press_vector = add_compute(id_press, VECTOR); } else if (word == "pxy") { - addfield("Pxy", &Thermo::compute_pxy, FLOAT); + if (triclinic_general) + addfield("Pxy", &Thermo::compute_pxy_triclinic_general, FLOAT); + else addfield("Pxy", &Thermo::compute_pxy, FLOAT); index_press_vector = add_compute(id_press, VECTOR); - } else if (word == "pxz") { - addfield("Pxz", &Thermo::compute_pxz, FLOAT); + } else if (word == "pxz") { + if (triclinic_general) + addfield("Pxz", &Thermo::compute_pxz_triclinic_general, FLOAT); + else addfield("Pxz", &Thermo::compute_pxz, FLOAT); index_press_vector = add_compute(id_press, VECTOR); } else if (word == "pyz") { + if (triclinic_general) + addfield("Pyz", &Thermo::compute_pyz_triclinic_general, FLOAT); addfield("Pyz", &Thermo::compute_pyz, FLOAT); index_press_vector = add_compute(id_press, VECTOR); @@ -1195,6 +1217,17 @@ void Thermo::check_press_vector(const std::string &keyword) if (!(pressure->invoked_flag & Compute::INVOKED_VECTOR)) { pressure->compute_vector(); pressure->invoked_flag |= Compute::INVOKED_VECTOR; + + // store 3x3 matrix form of symmetric pressure tensor for use in triclinic_general() + + if (triclinic_general) { + press_tensor[0][0] = pressure->vector[0]; + press_tensor[1][1] = pressure->vector[1]; + press_tensor[2][2] = pressure->vector[2]; + press_tensor[0][1] = press_tensor[1][0] = pressure->vector[3]; + press_tensor[0][2] = press_tensor[2][0] = pressure->vector[4]; + press_tensor[1][2] = press_tensor[2][1] = pressure->vector[5]; + } } } @@ -1412,27 +1445,33 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer) else if (word == "pxx") { check_press_vector(word); - compute_pxx(); + if (triclinic_general) compute_pxx_triclinic_general(); + else compute_pxx(); } else if (word == "pyy") { check_press_vector(word); - compute_pyy(); + if (triclinic_general) compute_pyy_triclinic_general(); + else compute_pyy(); } else if (word == "pzz") { check_press_vector(word); - compute_pzz(); + if (triclinic_general) compute_pzz_triclinic_general(); + else compute_pzz(); } else if (word == "pxy") { check_press_vector(word); - compute_pxy(); + if (triclinic_general) compute_pxy_triclinic_general(); + else compute_pxy(); } else if (word == "pxz") { check_press_vector(word); - compute_pxz(); + if (triclinic_general) compute_pxz_triclinic_general(); + else compute_pxz(); } else if (word == "pyz") { check_press_vector(word); - compute_pyz(); + if (triclinic_general) compute_pyz_triclinic_general(); + else compute_pyz(); } else if (word == "fmax") @@ -2084,6 +2123,66 @@ void Thermo::compute_pyz() /* ---------------------------------------------------------------------- */ +void Thermo::compute_pxx_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[0][0]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pyy_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[1][1]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pzz_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[2][2]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pxy_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[0][1]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pxz_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[0][2]; +} + +/* ---------------------------------------------------------------------- */ + +void Thermo::compute_pyz_triclinic_general() +{ + double middle[3][3],final[3][3]; + MathExtra::times3(domain->rotate_r2g,press_tensor,middle); + MathExtra::times3(middle,domain->rotate_g2r,final); + dvalue = final[1][2]; +} + +/* ---------------------------------------------------------------------- */ + void Thermo::compute_fmax() { double **f = atom->f; diff --git a/src/thermo.h b/src/thermo.h index 333a282ca0a..213415046e3 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -51,6 +51,8 @@ class Thermo : protected Pointers { private: int nfield, nfield_initial; int *vtype; + + int triclinic_general; // set by thermo_modify std::string line; std::vector keyword, format, format_column_user, keyword_user; std::string format_line_user, format_float_user, format_int_user, format_bigint_user; @@ -73,6 +75,7 @@ class Thermo : protected Pointers { bigint ntimestep; // data used by routines that compute single values + int ivalue; // integer value to print double dvalue; // double value to print bigint bivalue; // big integer value to print @@ -85,8 +88,10 @@ class Thermo : protected Pointers { // index = where they are in computes list // id = ID of Compute objects // Compute * = ptrs to the Compute objects + int index_temp, index_press_scalar, index_press_vector, index_pe; class Compute *temperature, *pressure, *pe; + double press_tensor[3][3]; int ncompute; // # of Compute objects called by thermo char **id_compute; // their IDs @@ -194,6 +199,13 @@ class Thermo : protected Pointers { void compute_pyz(); void compute_pxz(); + void compute_pxx_triclinic_general(); + void compute_pyy_triclinic_general(); + void compute_pzz_triclinic_general(); + void compute_pxy_triclinic_general(); + void compute_pyz_triclinic_general(); + void compute_pxz_triclinic_general(); + void compute_fmax(); void compute_fnorm(); From d6d65f001aa67f865f2dee9bb828dff8d1c2ff94 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 6 Sep 2023 09:04:10 -0600 Subject: [PATCH 030/719] enforce atom z coords = 0.0 for 2d simulations --- src/atom.cpp | 13 ++++++++++++- src/create_atoms.cpp | 23 ++++++++++++++++++----- src/create_box.cpp | 13 ++++++++++++- src/lattice.cpp | 6 +++--- src/read_data.cpp | 22 +++++++++++++++++++--- 5 files changed, 64 insertions(+), 13 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index 2c2ebd911fd..fb444e3e797 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -49,6 +49,7 @@ using namespace MathConst; #define DELTA 1 #define EPSILON 1.0e-6 +#define EPS_ZCOORD 1.0e-12 #define MAXLINE 256 /* ---------------------------------------------------------------------- @@ -1076,6 +1077,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, // if periodic and I am lo/hi proc, adjust bounds by EPSILON // ensures all data atoms will be owned even with round-off + int dimension = domain->dimension; int triclinic = domain->triclinic; double epsilon[3]; @@ -1165,7 +1167,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, imx = utils::inumeric(FLERR,values[iptr],false,lmp); imy = utils::inumeric(FLERR,values[iptr+1],false,lmp); imz = utils::inumeric(FLERR,values[iptr+2],false,lmp); - if ((domain->dimension == 2) && (imz != 0)) + if ((dimension == 2) && (imz != 0)) error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems"); if ((!domain->xperiodic) && (imx != 0)) { reset_image_flag[0] = true; imx = 0; } if ((!domain->yperiodic) && (imy != 0)) { reset_image_flag[1] = true; imy = 0; } @@ -1179,6 +1181,15 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp); xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp); + // for 2d simulation, check if z coord is within EPS_ZCOORD of zero + // then set to zero + + if (dimension == 2) { + if (fabs(xdata[2]) > EPS_ZCOORD) + error->all(FLERR,"Read_data atom z coord is non-zero for 2d simulation"); + xdata[2] = 0.0; + } + // convert atom coords from general triclinic to restricted triclinic if (triclinic_general) domain->general_to_restricted_coords(xdata); diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index f7347f9ad10..0a8c4626882 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -54,6 +54,8 @@ static constexpr double INV_P_CONST = 0.7548777; static constexpr double INV_SQ_P_CONST = 0.5698403; static constexpr int DEFAULT_MAXTRY = 1000; +#define EPS_ZCOORD 1.0e-12 + enum { BOX, REGION, SINGLE, RANDOM, MESH }; enum { ATOM, MOLECULE }; enum { COUNT, INSERT, INSERT_SELECTED }; @@ -1163,7 +1165,7 @@ void CreateAtoms::add_lattice() { // add atoms on general triclinic lattice if Domain has setting for it // verify lattice is valid for general triclinic - + int triclinic_general = domain->triclinic_general; if (triclinic_general) { @@ -1272,7 +1274,8 @@ void CreateAtoms::add_lattice() // decrement lo, increment hi to avoid round-off issues in lattice->bbox(), // which can lead to missing atoms in rare cases // extra decrement of lo if min < 0, since static_cast(-1.5) = -1 - + // for 2d simulation, klo = khi = 0 so just one plane of atoms + ilo = static_cast(xmin) - 1; jlo = static_cast(ymin) - 1; klo = static_cast(zmin) - 1; @@ -1284,7 +1287,7 @@ void CreateAtoms::add_lattice() if (ymin < 0.0) jlo--; if (zmin < 0.0) klo--; - printf("LOOP LATTICE bounds: %d %d: %d %d: %d %d\n",ilo,ihi,jlo,jhi,klo,khi); + if (domain->dimension == 2) klo = khi = 0; // count lattice sites on each proc @@ -1351,6 +1354,7 @@ void CreateAtoms::loop_lattice(int action) { int i, j, k, m; + int dimension = domain->dimension; int triclinic_general = domain->triclinic_general; const double *const *const basis = domain->lattice->basis; @@ -1372,9 +1376,18 @@ void CreateAtoms::loop_lattice(int action) domain->lattice->lattice2box(x[0], x[1], x[2]); // convert from general to restricted triclinic coords + // for 2d simulation, check if z coord is within EPS_ZCOORD of zero + // then set to zero + + if (triclinic_general) { + domain->general_to_restricted_coords(x); + if (dimension == 2) { + if (fabs(x[2]) > EPS_ZCOORD) + error->all(FLERR,"Create_atoms atom z coord is non-zero for 2d simulation"); + x[2] = 0.0; + } + } - if (triclinic_general) domain->general_to_restricted_coords(x); - // if a region was specified, test if atom is in it if (style == REGION) diff --git a/src/create_box.cpp b/src/create_box.cpp index 6a047448260..8cf60659627 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -63,6 +63,7 @@ void CreateBox::command(int narg, char **arg) int iarg = 2; if (region) { + // region is not prism // setup orthogonal box // set simulation domain from region extent @@ -94,6 +95,11 @@ void CreateBox::command(int narg, char **arg) domain->yz = prism->yz; } + if (domain->dimension == 2) { + if (domain->boxlo[2] >= 0.0 || domain->boxhi[2] <= 0.0) + error->all(FLERR,"Create_box region zlo/zhi for 2d simulation must straddle 0.0"); + } + // setup general triclinic box (with no region) // read next box extent arguments to create ABC edge vectors + origin // define_general_triclinic() converts @@ -114,7 +120,12 @@ void CreateBox::command(int narg, char **arg) double clo = utils::numeric(FLERR, arg[iarg + 4], false, lmp); double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp); iarg += 6; - + + if (domain->dimension == 2) { + if (clo >= 0.0 || clo <= 0.0) + error->all(FLERR,"Create_box region clo/chi for 2d simulation must straddle 0.0"); + } + // use lattice2box() to generate origin and ABC vectors // origin = abc lo // ABC vectors = hi in one dim - origin diff --git a/src/lattice.cpp b/src/lattice.cpp index 6d7450fd2b0..ef2b4c344d0 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -238,14 +238,14 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (dimension == 2) { if (origin[2] != 0.0) error->all(FLERR, - "Lattice settings are not compatible with 2d simulation"); + "Lattice origin not compatible with 2d simulation"); if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0) error->all(FLERR, - "Lattice settings are not compatible with 2d simulation"); + "Lattice a1/a2/a3 vectors are not compatible with 2d simulation"); if (orientx[2] != 0 || orienty[2] != 0 || orientz[0] != 0 || orientz[1] != 0) error->all(FLERR, - "Lattice settings are not compatible with 2d simulation"); + "Lattice orient vectors are not compatible with 2d simulation"); } if (spaceflag) { diff --git a/src/read_data.cpp b/src/read_data.cpp index c19250c2aaa..c59bec74761 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -491,11 +491,14 @@ void ReadData::command(int narg, char **arg) boxlo[0] = boxlo[1] = boxlo[2] = -0.5; boxhi[0] = boxhi[1] = boxhi[2] = 0.5; - avec[0] = avec[1] = avec[2] = 0.0; - bvec[0] = bvec[1] = bvec[2] = 0.0; - cvec[0] = cvec[1] = cvec[2] = 0.0; + xy = xz = yz = 0.0; + avec[0] = bvec[1] = cvec[2] = 1.0; + avec[1] = avec[2] = 0.0; + bvec[0] = bvec[2] = 0.0; + cvec[0] = cvec[1] = 0.0; abc_origin[0] = abc_origin[1] = abc_origin[2] = 0.0; + if (domain->dimension == 2) abc_origin[2] = -0.5; keyword[0] = '\0'; @@ -526,6 +529,19 @@ void ReadData::command(int narg, char **arg) error->all(FLERR,"Read_data header cannot specify simulation box lo/hi/tilt and ABC vectors"); triclinic = triclinic_general = 1; } + + // check if simulation box specified correctly for 2d + + if (domain->dimension == 2) { + if (triclinic_general == 0) { + if (boxlo[2] >= 0.0 || boxhi[2] <= 0.0) + error->all(FLERR,"Read_data zlo/zhi for 2d simulation must straddle 0.0"); + } else if (triclinic_general == 1) { + if (cvec[0] != 0.0 || cvec[1] != 0.0 || cvec[2] != 1.0 || abc_origin[2] != -0.5) + error->all(FLERR,"Read_data cvec and/or abc_origin is invalid for " + "2d simulation with general triclinic box"); + } + } // problem setup using info from header // only done once, if firstpass and first data file From 4735534139f0b259b0d54a97943e5380169c1aea Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 6 Sep 2023 09:05:02 -0600 Subject: [PATCH 031/719] enforce atom z coords = 0.0 for 2d simulations --- src/lattice.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/lattice.cpp b/src/lattice.cpp index ef2b4c344d0..815700003df 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -238,7 +238,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (dimension == 2) { if (origin[2] != 0.0) error->all(FLERR, - "Lattice origin not compatible with 2d simulation"); + "Lattice origin z coord must be 0.0 for 2d simulation"); if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0) error->all(FLERR, "Lattice a1/a2/a3 vectors are not compatible with 2d simulation"); @@ -246,6 +246,9 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) orientz[0] != 0 || orientz[1] != 0) error->all(FLERR, "Lattice orient vectors are not compatible with 2d simulation"); + for (int i = 0; i < nbasis; i++) + if (basis[i][2] != 0.0) + error->all(FLERR,"Lattice basis atom z coords must be zero for 2d simulation"); } if (spaceflag) { From 1ab26e083abbde65b30f28fab114c0066456aaf2 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 6 Sep 2023 10:11:04 -0600 Subject: [PATCH 032/719] more general tri support in dump atom and dump custom --- src/dump_atom.cpp | 147 +++++++++++++++++++++++++++++++++++++++++--- src/dump_atom.h | 9 ++- src/dump_custom.cpp | 17 ++++- 3 files changed, 161 insertions(+), 12 deletions(-) diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 2d047dc0a05..dd46452d9ee 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -36,6 +36,7 @@ DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : scale_flag = 1; image_flag = 0; + triclinic_general = 0; buffer_allow = 1; buffer_flag = 1; format_default = nullptr; @@ -90,12 +91,19 @@ void DumpAtom::init_style() // setup function ptrs + if (scale_flag && triclinic_general) + error->all(FLERR,"Dump atom cannot use scale and triclinic/general settings"); + if (binary && domain->triclinic == 0) header_choice = &DumpAtom::header_binary; + else if (binary && triclinic_general == 1) + header_choice = &DumpAtom::header_binary_triclinic_general; else if (binary && domain->triclinic == 1) header_choice = &DumpAtom::header_binary_triclinic; else if (!binary && domain->triclinic == 0) header_choice = &DumpAtom::header_item; + else if (!binary && triclinic_general == 1) + header_choice = &DumpAtom::header_item_triclinic_general; else if (!binary && domain->triclinic == 1) header_choice = &DumpAtom::header_item_triclinic; @@ -103,10 +111,17 @@ void DumpAtom::init_style() pack_choice = &DumpAtom::pack_scale_noimage; else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0) pack_choice = &DumpAtom::pack_scale_image; + + else if (scale_flag == 0 && image_flag == 0 && triclinic_general == 1) + pack_choice = &DumpAtom::pack_noscale_noimage_triclinic_general; + else if (scale_flag == 0 && image_flag == 1 && triclinic_general == 1) + pack_choice = &DumpAtom::pack_noscale_image_triclinic_general; + else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1) pack_choice = &DumpAtom::pack_scale_noimage_triclinic; else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1) pack_choice = &DumpAtom::pack_scale_image_triclinic; + else if (scale_flag == 0 && image_flag == 0) pack_choice = &DumpAtom::pack_noscale_noimage; else if (scale_flag == 0 && image_flag == 1) @@ -139,7 +154,14 @@ int DumpAtom::modify_param(int narg, char **arg) image_flag = utils::logical(FLERR,arg[1],false,lmp); for (auto &item : keyword_user) item.clear(); return 2; + } else if (strcmp(arg[0],"triclinic/general") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + triclinic_general = utils::logical(FLERR,arg[1],false,lmp); + if (triclinic_general && !domain->triclinic_general) + error->all(FLERR,"Dump_modify triclinic/general invalid b/c simulation box is not"); + return 2; } + return 0; } @@ -306,6 +328,30 @@ void DumpAtom::header_binary_triclinic(bigint ndump) /* ---------------------------------------------------------------------- */ +void DumpAtom::header_binary_triclinic_general(bigint ndump) +{ + header_format_binary(); + + fwrite(&update->ntimestep,sizeof(bigint),1,fp); + fwrite(&ndump,sizeof(bigint),1,fp); + int general_tri = 2; + fwrite(&general_tri,sizeof(int),1,fp); + fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); + fwrite(domain->avec,3*sizeof(double),1,fp); + fwrite(domain->bvec,3*sizeof(double),1,fp); + fwrite(domain->cvec,3*sizeof(double),1,fp); + fwrite(domain->boxlo,3*sizeof(double),1,fp); + + header_unit_style_binary(); + header_time_binary(); + header_columns_binary(); + + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- */ + void DumpAtom::header_item(bigint ndump) { if (unit_flag && !unit_count) { @@ -348,6 +394,32 @@ void DumpAtom::header_item_triclinic(bigint ndump) /* ---------------------------------------------------------------------- */ +void DumpAtom::header_item_triclinic_general(bigint ndump) +{ + if (unit_flag && !unit_count) { + ++unit_count; + fmt::print(fp,"ITEM: UNITS\n{}\n",update->unit_style); + } + if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time()); + + fmt::print(fp,"ITEM: TIMESTEP\n{}\n" + "ITEM: NUMBER OF ATOMS\n{}\n", + update->ntimestep, ndump); + + fmt::print(fp,"ITEM: BOX BOUNDS abc origin {}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n", + boundstr, + domain->avec[0],domain->avec[1],domain->avec[2],domain->boxlo[0], + domain->bvec[0],domain->bvec[1],domain->bvec[2],domain->boxlo[1], + domain->cvec[0],domain->cvec[1],domain->cvec[2],domain->boxlo[2]); + + fmt::print(fp,"ITEM: ATOMS {}\n",columns); +} + +/* ---------------------------------------------------------------------- */ + void DumpAtom::pack_scale_image(tagint *ids) { int m,n; @@ -406,6 +478,59 @@ void DumpAtom::pack_scale_noimage(tagint *ids) } } +/* ---------------------------------------------------------------------- */ + +void DumpAtom::pack_noscale_image(tagint *ids) +{ + int m,n; + + tagint *tag = atom->tag; + int *type = atom->type; + imageint *image = atom->image; + int *mask = atom->mask; + double **x = atom->x; + int nlocal = atom->nlocal; + + m = n = 0; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + buf[m++] = tag[i]; + buf[m++] = type[i]; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = (image[i] & IMGMASK) - IMGMAX; + buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; + buf[m++] = (image[i] >> IMG2BITS) - IMGMAX; + if (ids) ids[n++] = tag[i]; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpAtom::pack_noscale_noimage(tagint *ids) +{ + int m,n; + + tagint *tag = atom->tag; + int *type = atom->type; + int *mask = atom->mask; + double **x = atom->x; + int nlocal = atom->nlocal; + + m = n = 0; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + buf[m++] = tag[i]; + buf[m++] = type[i]; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + if (ids) ids[n++] = tag[i]; + } +} + + /* ---------------------------------------------------------------------- */ void DumpAtom::pack_scale_image_triclinic(tagint *ids) @@ -466,7 +591,7 @@ void DumpAtom::pack_scale_noimage_triclinic(tagint *ids) /* ---------------------------------------------------------------------- */ -void DumpAtom::pack_noscale_image(tagint *ids) +void DumpAtom::pack_noscale_image_triclinic_general(tagint *ids) { int m,n; @@ -477,14 +602,17 @@ void DumpAtom::pack_noscale_image(tagint *ids) double **x = atom->x; int nlocal = atom->nlocal; + double xtri[3]; + m = n = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; - buf[m++] = x[i][0]; - buf[m++] = x[i][1]; - buf[m++] = x[i][2]; + domain->restricted_to_general_coords(x[i],xtri); + buf[m++] = xtri[0]; + buf[m++] = xtri[1]; + buf[m++] = xtri[2]; buf[m++] = (image[i] & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; buf[m++] = (image[i] >> IMG2BITS) - IMGMAX; @@ -494,7 +622,7 @@ void DumpAtom::pack_noscale_image(tagint *ids) /* ---------------------------------------------------------------------- */ -void DumpAtom::pack_noscale_noimage(tagint *ids) +void DumpAtom::pack_noscale_noimage_triclinic_general(tagint *ids) { int m,n; @@ -504,14 +632,17 @@ void DumpAtom::pack_noscale_noimage(tagint *ids) double **x = atom->x; int nlocal = atom->nlocal; + double xtri[3]; + m = n = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { buf[m++] = tag[i]; buf[m++] = type[i]; - buf[m++] = x[i][0]; - buf[m++] = x[i][1]; - buf[m++] = x[i][2]; + domain->restricted_to_general_coords(x[i],xtri); + buf[m++] = xtri[0]; + buf[m++] = xtri[1]; + buf[m++] = xtri[2]; if (ids) ids[n++] = tag[i]; } } diff --git a/src/dump_atom.h b/src/dump_atom.h index e28b390520f..df21c7788c8 100644 --- a/src/dump_atom.h +++ b/src/dump_atom.h @@ -33,8 +33,9 @@ class DumpAtom : public Dump { const int ENDIAN = 0x0001; protected: - int scale_flag; // 1 if atom coords are scaled, 0 if no - int image_flag; // 1 if append box count to atom coords, 0 if no + int scale_flag; // 1 if atom coords are scaled, 0 if no + int image_flag; // 1 if append box count to atom coords, 0 if no + int triclinic_general; // 1 if output box,coords for general triclinic std::string columns; // column labels @@ -57,8 +58,10 @@ class DumpAtom : public Dump { FnPtrHeader header_choice; // ptr to write header functions void header_binary(bigint); void header_binary_triclinic(bigint); + void header_binary_triclinic_general(bigint); void header_item(bigint); void header_item_triclinic(bigint); + void header_item_triclinic_general(bigint); typedef void (DumpAtom::*FnPtrPack)(tagint *); FnPtrPack pack_choice; // ptr to pack functions @@ -68,6 +71,8 @@ class DumpAtom : public Dump { void pack_noscale_noimage(tagint *); void pack_scale_image_triclinic(tagint *); void pack_scale_noimage_triclinic(tagint *); + void pack_noscale_image_triclinic_general(tagint *); + void pack_noscale_noimage_triclinic_general(tagint *); typedef int (DumpAtom::*FnPtrConvert)(int, double *); FnPtrConvert convert_choice; // ptr to convert data functions diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index d96800554db..da9bbd013e6 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -500,8 +500,8 @@ void DumpCustom::header_binary_triclinic_general(bigint ndump) fwrite(&update->ntimestep,sizeof(bigint),1,fp); fwrite(&ndump,sizeof(bigint),1,fp); - fwrite(&domain->triclinic,sizeof(int),1,fp); - fwrite(&domain->triclinic_general,sizeof(int),1,fp); + int general_tri = 2; + fwrite(&general_tri,sizeof(int),1,fp); fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); fwrite(domain->avec,3*sizeof(double),1,fp); fwrite(domain->bvec,3*sizeof(double),1,fp); @@ -1354,14 +1354,20 @@ int DumpCustom::parse_fields(int narg, char **arg) else pack_choice[iarg] = &DumpCustom::pack_z; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"xs") == 0) { + if (triclinic_general) + error->all(FLERR,"Dump custom xs property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xs_triclinic; else pack_choice[iarg] = &DumpCustom::pack_xs; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"ys") == 0) { + if (triclinic_general) + error->all(FLERR,"Dump custom ys property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_ys_triclinic; else pack_choice[iarg] = &DumpCustom::pack_ys; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"zs") == 0) { + if (triclinic_general) + error->all(FLERR,"Dump custom zs property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zs_triclinic; else pack_choice[iarg] = &DumpCustom::pack_zs; vtype[iarg] = Dump::DOUBLE; @@ -1381,17 +1387,24 @@ int DumpCustom::parse_fields(int narg, char **arg) else pack_choice[iarg] = &DumpCustom::pack_zu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"xsu") == 0) { + if (triclinic_general) + error->all(FLERR,"Dump custom xsu property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xsu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_xsu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"ysu") == 0) { + if (triclinic_general) + error->all(FLERR,"Dump custom ysu property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_ysu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_ysu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"zsu") == 0) { + if (triclinic_general) + error->all(FLERR,"Dump custom zsu property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zsu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_zsu; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"ix") == 0) { pack_choice[iarg] = &DumpCustom::pack_ix; vtype[iarg] = Dump::INT; From ceed2e723e4bcb0c44adccd4b6cdca33ca82cbad Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 6 Sep 2023 10:11:28 -0600 Subject: [PATCH 033/719] more general tri support in dump atom and dump custom --- src/dump_custom.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dump_custom.h b/src/dump_custom.h index 83adbe0d7f8..b1ef2c64007 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -37,7 +37,7 @@ class DumpCustom : public Dump { int nevery; // dump frequency for output char *idregion; // region ID, nullptr if no region - int triclinic_general; // set by dump_modify + int triclinic_general; // 1 if output box,x,v,f for general triclinic int nthresh; // # of defined thresholds int nthreshlast; // # of defined thresholds with value = LAST From e20e3972d264bd7c316764f40f557b48afb9a7bb Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 7 Sep 2023 17:21:15 -0600 Subject: [PATCH 034/719] doc page updates --- doc/src/Howto_triclinic.rst | 156 +++++++++++------- doc/src/read_data.rst | 307 ++++++++++++++++++++++++------------ 2 files changed, 300 insertions(+), 163 deletions(-) diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 5fc42e01c64..9780ec8c63d 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -24,6 +24,9 @@ for info on how zlo and zhi are defined for 2d simulations. ---------- +Triclinic simulation boxes +"""""""""""""""""""""""""" + LAMMPS also allows simulations to be performed using triclinic (non-orthogonal) simulation boxes shaped as a parallelepiped with triclinic symmetry. @@ -46,55 +49,41 @@ this purpose. It allows dynamic control of the xy, xz, yz tilt factors as a simulation runs. This is discussed in the next section on non-equilibrium MD (NEMD) simulations. -Conceptually, the tricliic parallelepiped is defined with an "origin" +Conceptually, a triclinic parallelepiped is defined with an "origin" at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), **C** = (cx,cy,cz) which can now be arbitrary vectors, so -long as they are distinct and are not co-planar. +long as they are non-zero, distinct, and not co-planar. There is no +"right-hand rule" requirement that (**A** x **B**) point in the +direction of **C**. The 4 commands listed above for defining orthogonal simulation boxes have triclinic options which allow for specification of the origin and edge vectors **A**, **B**, **C**. For each command, this can be done -in one of two ways, for what LAMMPS calls a *general* triclinic box, -or a *restricited* triclinic box. A *general* triclinic box is -specified by an origin and 9 parameters (ax,ay,az), (bx,by,bz), -(cx,cy,cz), or 12 parameters in total. A *restricted* triclinic box -also has an origin, but its edge vectors are of the following form: -**A** = (xhi-xlo,0,0), **B** = (xy,yhi-ylo,0), **C** = -(xz,yz,zhi-zlo). So 9 parameters in total. - -The restricted form of edge vectors means that **A** is along the -x-axis, **B** is in the x-y plane with a y-component in the +y +in one of two ways, for what LAMMPS calls a *general* triclinic box or +a *restricted* triclinic box. + +A *general* triclinic box is specified by an origin and 9 parameters +(ax,ay,az), (bx,by,bz), (cx,cy,cz), or 12 parameters in total. A +*restricted* triclinic box also has an origin, but its edge vectors +are of the following form: **A** = (xhi-xlo,0,0), **B** = +(xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So 9 parameters in total. + +The restricted form of edge vectors requires that **A** is along the +x-axis, **B** is in the xy plane with a y-component in the +y direction, and **C** has a z-component in the +z direction. -*Xy,xz,yz* can be 0.0 or positive or negative values and are called +*Xy,xz,yz* can be zero or positive or negative values and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into a -restricted parallelepiped. +restricted triclinic parallelepiped. .. note:: - Any general triclinic box (i.e. any solid-state crystal basis - vectors) can be rotated/inverted in 3d around its origin to conform - to the definition of a restricted triclinic box. An inversion may + Any general triclinic box (i.e. solid-state crystal basis vectors) + can be rotated/inverted in 3d around its origin to conform to the + LAMMPS definition of a restricted triclinic box. An inversion may need to be applied to the rotated **C** vector to ensure its final - z-component is in the +z direction. - -.. note:: - - While LAMMPS allows specification of a triclinic simulation box in - either **general** or **restricted** form, internally LAMMPS only - uses restricted triclinic simulation boxes. This is for parallel - efficiency and to formulate partitioning of the simulation box - across processors, neighbor list building, and inter-processor - communication of per-atom data with methods similar to those used - for orthogonal boxes. This means 3 things. (1) Input of a general - triclinic is immediately converted to restricted form. - (2) If output in general triclinic form is requested (e.g. for atom - coordinates in a dump file), then conversion from restricted - triclinic coordinates is done at the time of output. (3) Most - importantly, other LAMMPS commands such as the :doc:`region - ` command, that refer to the simulation box geometry, - operate on restricted triclinic boxes, even if a general triclinic - box was specified as input. + z-component is in the +z direction. See the discussion in the next + sub-section about general triclinic simulation boxes in LAMMPS. Note that for 2d simulations a triclinic simulation box is effectively a parallelogram; see the :doc:'Howto 2d ` doc page for @@ -111,26 +100,68 @@ if the xz and/or yz tilt factors are non-zero, then particles which exit the -z face of the box will be displaced in x by the xz tilt factor and in y by the yz tilt factor. -For general and restricted triclinic boxes, their **A**, **B**, **C** -edge vector components can be output via +The :doc:`thermo_style custom ` command has keywords for +outputting the parameters that define restricted and general triclinic +simulation boxes. For restricted triclinic, this is (xlo,ylo,zlo), +(xhi,yhi,zhi), and the xy,xz,yz tilt factors. For general triclinic, +this is the (xlo,ylo,zhi) origin and the 9 components of the **A**, +**B**, **C** edge vectors. For both orthogonal and restricted +triclinic boxes, lx/ly/lz refer to the same box sizes, namely lx = +xhi - xlo, etc. + +The remainder of this doc page explains (a) how LAMMPS operates with +general triclinic simulation boxes, (b) mathematical transformations +between general and restricted triclinic boxes (which may be useful +when creating LAMMPS inputs or interpreting outputs for triclinic +simulations, and (c) how LAMMPS uses tilt factors for restricted +triclinic simulation boxes. -The :doc:`thermo_style custom ` command also has options -for outputting the parameters that define general and restricted -triclinic simulation boxes. For general triclinic, this is the -(xlo,ylo,zhi) origin and the 9 components of the **A**, **B**, **C** -edge vectors. For restricted triclinic, this is (xlo,ylo,zlo), -(xhi,yhi,zhi), and the xy,xz,yz tilt factors. For both orthogonal and -restricted triclinic boxes, lx/ly/lz refer to the same box sizes, -namely lx = xhi - xlo, etc. +---------- -The remainder of this doc page explains mathematical transformations -between different ways of representing general and restrictied -triclinic boxes, which may be useful when creating LAMMPS inputs for -triclinic simulations or interpreting outputs. How LAMMPS uses tilt -factors for restricted triclinic simulation boxes is also discussed. +General triclinic simulation boxes in LAMMPS +"""""""""""""""""""""""""""""""""""""""""""" + +LAMMPS allows specification of general triclinic simulation boxes as a +convenience for users who may be converting data from solid-state +crystallograhic representations for input to LAMMPS. + +However, internally LAMMPS only uses restricted triclinic simulation +boxes. This is for parallel efficiency and to formulate partitioning +of the simulation box across processors, neighbor list building, and +inter-processor communication of per-atom data with methods similar to +those used for orthogonal boxes. + +This means 3 things which it is important to understand: + +* Input of a general triclinic system is immediately converted to a + restricted triclinic system. +* If output of general triclinic data is requested (e.g. for atom + coordinates in a dump file), then conversion from restricted + triclinic data is done at the time of output. +* Most importantly, other LAMMPS commands such as the :doc:`boundary + ` command or :doc:`region ` command, that refer to + the simulation box geometry, operate on restricted triclinic boxes, + even if a general triclinic box was defined initially. + +This is the list of commands that have specific general triclinic +options: + +create_box +create_atoms +lattice +read_data +write_data +dump atoms, dump custom +dump_modify +thermo_style +thermo_modify +read_restart, write_restart ---------- +Transformation from general to restricted triclinic boxes +""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + Let **A**,\ **B**,\ **C** be the edge vectors of a general triclinic simulation box. Assume that **A** x **B** . **C** > 0. The equivalent LAMMPS **a**,\ **b**,\ **c** for a restricted triclinic box @@ -163,12 +194,12 @@ inversion. This can be achieved by interchanging two of the **A**, **B**, **C** vectors or by changing the sign of one of them. For consistency, the same rotation/inversion applied to the triclinic -box edge vectors also typically needs to be applied to atom positions, -velocities, and other vector quantities. This can be conveniently -achieved by first converting to fractional coordinates in the general -triclinic coordinates and then converting to coordinates in the -resetricted triclinic basis. The transformation is given by the -following equation: +box edge vectors can also be applied to atom positions, velocities, +and other vector quantities. This can be conveniently achieved by +first converting to fractional coordinates in the general triclinic +coordinates and then converting to coordinates in the resetricted +triclinic basis. The transformation is given by the following +equation: .. math:: @@ -185,6 +216,9 @@ resulting vector in the restricted triclinic basis. ---------- +Crystallographic general triclinic representation of a simulation box +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + General triclinic crystal structures are often defined using three lattice constants *a*, *b*, and *c*, and three angles :math:`\alpha`, :math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, the @@ -222,6 +256,9 @@ The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and ---------- +Output of restricted and general triclinic boxes in a dump file +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + As discussed on the :doc:`dump ` command doc page, when the BOX BOUNDS for a snapshot is written to a dump file for a resticted triclinic box, an orthogonal bounding box which encloses the triclinic @@ -254,6 +291,9 @@ xlo_bound - MIN(0.0,xy,xz,xy+xz). ---------- +Periodicity and tilt factors for triclinic simulation boxes +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + There is no requirement that a triclinic box be periodic in any dimension, though as explained above it typically should be in y or z if you wish enforce a shift in coordinates due to periodic boundary @@ -288,7 +328,7 @@ Similarly, both xz and yz should be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that these are not limitations, since if the maximum tilt factor is 5 (as in this example), then simulations boxes and atom configurations with tilt = ..., -15, -5, 5, 15, 25, ... are -geometrically all equivalent. +all geometrically equivalent. If the box tilt exceeds this limit during a dynamics run (e.g. due to the :doc:`fix deform ` command), then by default the box diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 0ecd2b6fa23..2709bf87e59 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -122,16 +122,16 @@ keyword must be used. .. note:: - The simulation box size (xlo to xhi, ylo to yhi, zlo to zhi) in - the new data file will be merged with the existing simulation box to - create a large enough box in each dimension to contain both the - existing and new atoms. Each box dimension never shrinks due to this - merge operation, it only stays the same or grows. Care must be used if - you are growing the existing simulation box in a periodic dimension. - If there are existing atoms with bonds that straddle that periodic - boundary, then the atoms may become far apart if the box size grows. - This will separate the atoms in the bond, which can lead to "lost" - bond atoms or bad dynamics. + The simulation box size in the new data file will be merged with + the existing simulation box to create a large enough box in each + dimension to contain both the existing and new atoms. Each box + dimension never shrinks due to this merge operation, it only stays + the same or grows. Care must be used if you are growing the + existing simulation box in a periodic dimension. If there are + existing atoms with bonds that straddle that periodic boundary, + then the atoms may become far apart if the box size grows. This + will separate the atoms in the bond, which can lead to "lost" bond + atoms or bad dynamics. The three choices for the *add* argument affect how the atom IDs and molecule IDs of atoms in the data file are treated. If *append* is @@ -288,13 +288,16 @@ Format of the header of a data file """"""""""""""""""""""""""""""""""" These are the recognized header keywords. Header lines can come in -any order. The value(s) are read from the beginning of the line. +any order. Each keyword takes a single value unless noted in this +list. The value(s) are read from the beginning of the line. Thus the keyword *atoms* should be in a line like "1000 atoms"; the keyword *ylo yhi* should be in a line like "-10.0 10.0 ylo yhi"; the keyword *xy xz yz* should be in a line like "0.0 5.0 6.0 xy xz yz". -All these settings have a default value of 0, except the lo/hi box -size defaults are -0.5 and 0.5. A line need only appear if the value -is different than the default. + +All these settings have a default value of 0, except for the +simulation box size settings; their defaults are explained below. A +keyword line need only appear if its value is different than the +default. * *atoms* = # of atoms in system * *bonds* = # of bonds in system @@ -315,73 +318,150 @@ is different than the default. * *lines* = # of line segments in system * *triangles* = # of triangles in system * *bodies* = # of bodies in system -* *xlo xhi* = simulation box boundaries in x dimension -* *ylo yhi* = simulation box boundaries in y dimension -* *zlo zhi* = simulation box boundaries in z dimension -* *xy xz yz* = simulation box tilt factors for triclinic system - -The initial simulation box size is determined by the lo/hi settings. -In any dimension, the system may be periodic or non-periodic; see the -:doc:`boundary ` command. When the simulation box is created -it is also partitioned into a regular 3d grid of rectangular bricks, -one per processor, based on the number of processors being used and -the settings of the :doc:`processors ` command. The -partitioning can later be changed by the :doc:`balance ` or -:doc:`fix balance ` commands. - -If the *xy xz yz* line does not appear, LAMMPS will set up an -axis-aligned (orthogonal) simulation box. If the line does appear, -LAMMPS creates a non-orthogonal simulation domain shaped as a -parallelepiped with triclinic symmetry. The parallelepiped has its -"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting -from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = -(xz,yz,zhi-zlo). *Xy,xz,yz* can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. - -The tilt factors (xy,xz,yz) should not skew the box more than half the -distance of the corresponding parallel box length. For example, if -:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x` -box length is 10 and the :math:`xy` tilt factor must be between -:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz` -must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and -:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a -limitation, since if the maximum tilt factor is 5 (as in this example), -then configurations with tilt :math:`= \dots, -15`, :math:`-5`, -:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically -equivalent. Simulations with large tilt factors will run inefficiently, -since they require more ghost atoms and thus more communication. With -very large tilt factors, LAMMPS will eventually produce incorrect -trajectories and stop with errors due to lost atoms or similar. - -See the :doc:`Howto triclinic ` page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. - -When a triclinic system is used, the simulation domain should normally -be periodic in the dimension that the tilt is applied to, which is -given by the second dimension of the tilt factor (e.g. y for xy tilt). -This is so that pairs of atoms interacting across that boundary will -have one of them shifted by the tilt factor. Periodicity is set by -the :doc:`boundary ` command. For example, if the xy tilt -factor is non-zero, then the y dimension should be periodic. -Similarly, the z dimension should be periodic if xz or yz is non-zero. -LAMMPS does not require this periodicity, but you may lose atoms if -this is not the case. - -Also note that if your simulation will tilt the box, e.g. via the -:doc:`fix deform ` command, the simulation box must be setup -to be triclinic, even if the tilt factors are initially 0.0. You can -also change an orthogonal box to a triclinic box or vice versa by using -the :doc:`change box ` command with its *ortho* and -*triclinic* options. - -For 2d simulations, the *zlo zhi* values should be set to bound the z -coords for atoms that appear in the file; the default of -0.5 0.5 is -valid if all z coords are 0.0. For 2d triclinic simulations, the xz -and yz tilt factors must be 0.0. +* *xlo xhi* = simulation box boundaries in x dimension (2 values) +* *ylo yhi* = simulation box boundaries in y dimension (2 values) +* *zlo zhi* = simulation box boundaries in z dimension (2 values) +* *xy xz yz* = simulation box tilt factors for triclinic system (3 values) +* *avec* = first edge vector of a general triclinic simulation box (3 values) +* *bvec* = second edge vector of a general triclinic simulation box (3 values) +* *cvec* = third edge vector of a general triclinic simulation box (3 values) +* *abc origin* = origin on a general triclinic simulation box (3 values) + +---------- + +Header specification of the simulation box size and shape +""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +The final 8 keywords in the list of header keywords are for simulation +boxes of 3 kinds which LAMMPS supports: + +* orthogonal box = faces are perpendicular to the xyz coordinate axes +* restricted triclinic box = a parallelepiped defined by 3 edge vectors oriented in a constrained manner +* general triclinic box = a parallelepiped defined by 3 arbitrary edge vectors + +For restricted and general triclinic boxes, see the +:doc:`Howto_triclinic ` doc page for a fuller +description than is given here. + +The units of the values for all 8 keywords in in distance units; see +the :doc:`units ` command for details. + +For all 3 kinds of simulation boxes, the system may be periodic or +non-periodic in any dimension; see the :doc:`boundary ` +command. When the simulation box is created by the read_data command, +it is also partitioned into a regular 3d grid of subdomains, one per +processor, based on the number of processors being used and the +settings of the :doc:`processors ` command. For each kind +of simulatino box the subdomains have the same shape as the simulation +box, i.e. smaller orthogonal bricks for orthogonal boxes, smaller +tilted bricks for triclinic boxes. The partitioning can later be +changed by the :doc:`balance ` or :doc:`fix balance +` commands. + +For an orthogonal box, only the *xlo xhi*, *ylo yhi*, *zlo zhi* +keywords are used. They define the extent of the simulation box in +each dimension. The origin (lower left corner) of the orthogonal box +is at (xlo,ylo,zlo). The default values for these 3 keywords are -0.5 +and 0.5 for each lo/hi pair. For a 2d simulation, the zlo and zhi +values must straddle zero. The default zlo/zhi values do this, so +that keyword is not needed in 2d. + +For a restricted triclinic box, the *xy xz yz* keyword is used in +addition to the *xlo xhi*, *ylo yhi*, *zlo zhi* keywords. The three +*xy,xz,yz* values can be 0.0 or positive or negative, and are called +"tilt factors" because they are the amount of displacement applied to +faces of an orthogonal box to transform it into a restricted triclinic +parallelepiped. + +The :doc:`Howto_triclinic ` doc page discusses the +tilt factors in detail and explains that the resulting edge vectors of +the restricted triclinic box are: + +* **A** = (xhi-xlo,0,0) +* **B** = (xy,yhi-ylo,0) +* **C** = (xz,yz,zhi-zlo) + +This restricted form of edge vectors means that **A** is along the +x-axis, **B** is in the xy plane with a y-component in the +y +direction, and **C** has a z-component in the +z direction. The +origin (lower left corner) of the restricted triclinic box is at +(xlo,ylo,zlo). + +For a 2d simulation, the zlo and zhi values must straddle zero. The +default zlo/zhi values do this, so that keyword is not needed in 2d. +The xz and yz values must also be zero in 2d. The shape of the 2d +restricted triclinic simulation box is effectively a parallelogram. + +.. note:: + + When a restricted triclinic box is used, the simulation domain + should normally be periodic in any dimensions that tilt is applied + to, which is given by the second dimension of the tilt factor + (e.g. y for xy tilt). This is so that pairs of atoms interacting + across that boundary will have one of them shifted by the tilt + factor. Periodicity is set by the :doc:`boundary ` + command. For example, if the xy tilt factor is non-zero, then the + y dimension should be periodic. Similarly, the z dimension should + be periodic if xz or yz is non-zero. LAMMPS does not require this + periodicity, but you may lose atoms if this is not the case. + +.. note:: + + Normally, the specified tilt factors (xy,xz,yz) should not skew the + simulation box by more than half the distance of the corresponding + parallel box length for computational efficiency. For example, if + :math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the + :math:`x` box length is 10 and the :math:`xy` tilt factor should be + between :math:`-5` and :math:`5`. LAMMPS will issue a warning if + this is not the case. See the :doc:`Howto_triclinic + ` doc page for more details. + +.. note:: + + If a simulation box is initially orthogonal, but will tilt during a + simulation, e.g. via the :doc:`fix deform ` command, + then the box should be defined as restricted triclinic with all 3 + tilt factors = 0.0. Alternatively, the :doc:`change box + ` command can be used to convert an orthogonal box to a + restricted triclinic box. + +For a general triclinic box, the *avec*, *bvec*, *cvec*, and *abc +origin* keywords are used. The *xlo xhi*, *ylo yhi*, *zlo zhi*, and +*xy xz yz* keywords are not used. The first 3 keywords define the 3 +edge vectors **A**, **B**, **C** of a general triclinic box. They can +be arbitrary vectors so long as they are distinct, non-zero, and not +co-planar. There is no "right-hand rule" requirement that (**A** x +**B**) point in the direction of **C**. The origin of the box (origin +of the 3 edge vectors) is set by the *abc origin* keyword. + +The default values for these 4 keywords are as follows: + +* avec = (1,0,0) +* bvec = (0,1,0) +* cvec = (0,0,1) +* *abc origin = (0,0,0) for 3d, (0,0,-0.5) for 2d + +For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of +*abc origin* must be -0.5. These are the default values, so the +*cvec* keyword is not needed in 2d. + +.. note:: + + LAMMPS allows specification of general triclinic simulation boxes + as a convenience for users who may be converting data from + solid-state crystallograhic representations for input to LAMMPS. + However, as explained on the :doc:`Howto_triclinic + ` doc page, internally LAMMPS only uses restricted + triclinic simulation boxes. This means the box and atom + information (coordinates, velocities) in the data file are + converted from general to restricted triclinic form as soon as the + file is read. The :doc:`Howto_triclinic ` doc + page also discusses other LAMMPS commands which can input/output + general triclinic representations of the simulation box and + per-atom data. + +The following explanations apply to all 3 kinds of simulation boxes: +orthogonal, restricted triclinic, and general triclinic. If the system is periodic (in a dimension), then atom coordinates can be outside the bounds (in that dimension); they will be remapped (in a @@ -406,7 +486,6 @@ individually back into the principal unit cell in that direction. This operation is equivalent to the behavior of the :doc:`change_box command ` when used to change periodicity. - If those atoms with non-zero image flags are involved in bonded interactions, this reset can lead to undesired changes, when the image flag values differ between the atoms, i.e. the bonded interaction @@ -440,25 +519,32 @@ needed, so that the image flag would be zero. to lose atoms when LAMMPS shrink-wraps the box around the atoms. The read_data command will generate an error in this case. +---------- + +Meaning of other header keywords +"""""""""""""""""""""""""""""""" + The "extra bond per atom" setting (angle, dihedral, improper) is only needed if new bonds (angles, dihedrals, impropers) will be added to -the system when a simulation runs, e.g. by using the :doc:`fix bond/create ` command. Using this header flag -is deprecated; please use the *extra/bond/per/atom* keyword (and +the system when a simulation runs, e.g. by using the :doc:`fix +bond/create ` command. Using this header flag is +deprecated; please use the *extra/bond/per/atom* keyword (and correspondingly for angles, dihedrals and impropers) in the read_data command instead. Either will pre-allocate space in LAMMPS data structures for storing the new bonds (angles, dihedrals, impropers). The "extra special per atom" setting is typically only needed if new -bonds/angles/etc will be added to the system, e.g. by using the :doc:`fix bond/create ` command. Or if entire new molecules -will be added to the system, e.g. by using the -:doc:`fix deposit ` or :doc:`fix pour ` commands, -which will have more special 1-2,1-3,1-4 neighbors than any other -molecules defined in the data file. Using this header flag is -deprecated; please use the *extra/special/per/atom* keyword instead. -Using this setting will pre-allocate space in the LAMMPS data -structures for storing these neighbors. See the -:doc:`special_bonds ` and :doc:`molecule ` doc -pages for more discussion of 1-2,1-3,1-4 neighbors. +bonds/angles/etc will be added to the system, e.g. by using the +:doc:`fix bond/create ` command. Or if entire new +molecules will be added to the system, e.g. by using the :doc:`fix +deposit ` or :doc:`fix pour ` commands, which +will have more special 1-2,1-3,1-4 neighbors than any other molecules +defined in the data file. Using this header flag is deprecated; +please use the *extra/special/per/atom* keyword instead. Using this +setting will pre-allocate space in the LAMMPS data structures for +storing these neighbors. See the :doc:`special_bonds ` +and :doc:`molecule ` doc pages for more discussion of +1-2,1-3,1-4 neighbors. .. note:: @@ -470,13 +556,13 @@ pages for more discussion of 1-2,1-3,1-4 neighbors. If they appear in later data files, they are ignored. The "ellipsoids" and "lines" and "triangles" and "bodies" settings are -only used with :doc:`atom_style ellipsoid or line or tri or body ` and specify how many of the atoms are -finite-size ellipsoids or lines or triangles or bodies; the remainder -are point particles. See the discussion of ellipsoidflag and the -*Ellipsoids* section below. See the discussion of lineflag and the -*Lines* section below. See the discussion of triangleflag and the -*Triangles* section below. See the discussion of bodyflag and the -*Bodies* section below. +only used with :doc:`atom_style ellipsoid or line or tri or body +` and specify how many of the atoms are finite-size +ellipsoids or lines or triangles or bodies; the remainder are point +particles. See the discussion of ellipsoidflag and the *Ellipsoids* +section below. See the discussion of lineflag and the *Lines* section +below. See the discussion of triangleflag and the *Triangles* section +below. See the discussion of bodyflag and the *Bodies* section below. .. note:: @@ -680,6 +766,16 @@ appended to it, which indicate which image of a periodic simulation box the atom is in. These may be important to include for some kinds of analysis. +.. note:: + + For orthogonal and restricted and general triclinic simulation + boxes, the atom coordinates (x,y,z) listed in this section should + be inside the corresponding simulation box. For general triclinic + boxes that means the box defined by the 3 edge vectors specified by + the *avec*, *bvec*, *cvec* header keywords. See the discussion + above in the header section about how atom coordinates outside the + simulation box are (or are not) remapped to be inside the box. + .. list-table:: * - angle @@ -773,8 +869,9 @@ The per-atom values have these meanings and units, listed alphabetically: The units for these quantities depend on the unit style; see the :doc:`units ` command for details. -For 2d simulations specify z as 0.0, or a value within the *zlo zhi* -setting in the data file header. +For 2d simulations, z must be specified as 0.0. If the data file is +created by another program, then z values for a 2d simulation can be +within epsilon of 0.0, and LAMMPS will force them to zero. The atom-ID is used to identify the atom throughout the simulation and in dump files. Normally, it is a unique value from 1 to Natoms for @@ -1513,8 +1610,8 @@ fields: atom-ID vx vy vz ervel wx wy wz -Translational velocities can also be set by the -:doc:`velocity ` command in the input script. +Translational velocities can also be (re)set by the :doc:`velocity +` command in the input script. ---------- From dec245c67bbe43075aa444831058c9e5d05787db Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 13 Sep 2023 09:29:56 -0600 Subject: [PATCH 035/719] support for other vector fields in read_data --- doc/src/Errors_messages.rst | 6 ----- doc/src/Errors_warnings.rst | 7 ------ src/DIELECTRIC/atom_vec_dielectric.cpp | 15 ++++++++++++ src/DIELECTRIC/atom_vec_dielectric.h | 1 + src/DIPOLE/atom_vec_dipole.cpp | 15 ++++++++++++ src/DIPOLE/atom_vec_dipole.h | 1 + src/MACHDYN/atom_vec_smd.cpp | 7 ++++++ src/SPIN/atom_vec_spin.cpp | 17 ++++++++++++-- src/SPIN/atom_vec_spin.h | 1 + src/atom.cpp | 14 +++++------ src/atom.h | 3 +-- src/atom_vec.cpp | 32 +++++++++++++++++++++++++- src/atom_vec.h | 5 +++- src/create_atoms.cpp | 4 ++-- src/lmprestart.h | 4 ++-- src/read_data.cpp | 10 ++++++-- 16 files changed, 110 insertions(+), 32 deletions(-) diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index bfdba4f6a1a..2a146a91845 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -7883,12 +7883,6 @@ keyword to allow for additional bonds to be formed Fix poems cannot (yet) work with coupled bodies whose joints connect the bodies in a tree structure. -*Triclinic box skew is too large* - The displacement in a skewed direction must be less than half the box - length in that dimension. E.g. the xy tilt must be between -half and - +half of the x box length. This constraint can be relaxed by using - the box tilt command. - *Tried to convert a double to int, but input_double > INT_MAX* Self-explanatory. diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index b0fa2e21739..d244818cc97 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -752,13 +752,6 @@ This will most likely cause errors in kinetic fluctuations. More than the maximum # of neighbors was found multiple times. This was unexpected. -*Triclinic box skew is large* - The displacement in a skewed direction is normally required to be less - than half the box length in that dimension. E.g. the xy tilt must be - between -half and +half of the x box length. You have relaxed the - constraint using the box tilt command, but the warning means that a - LAMMPS simulation may be inefficient as a result. - *Use special bonds = 0,1,1 with bond style fene* Most FENE models need this setting for the special_bonds command. diff --git a/src/DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp index 3b25ad4e17b..a06b4d599ba 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -15,6 +15,7 @@ #include "atom.h" #include "citeme.h" +#include "domain.h" #include "error.h" #include "force.h" #include "pair.h" @@ -187,6 +188,20 @@ void AtomVecDielectric::data_atom_post(int ilocal) mu_one[3] = sqrt(mu_one[0] * mu_one[0] + mu_one[1] * mu_one[1] + mu_one[2] * mu_one[2]); } +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on dipole moment mu +------------------------------------------------------------------------- */ + +void AtomVecDielectric::data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::data_general_to_restricted(nlocal_previous, nlocal); + + for (int i = nlocal_previous; i < nlocal; i++) + domain->general_to_restricted_vector(mu[i]); +} + /* ---------------------------------------------------------------------- initialize other atom quantities after AtomVec::unpack_restart() ------------------------------------------------------------------------- */ diff --git a/src/DIELECTRIC/atom_vec_dielectric.h b/src/DIELECTRIC/atom_vec_dielectric.h index 28bf7abb33c..fefbc99c4f5 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.h +++ b/src/DIELECTRIC/atom_vec_dielectric.h @@ -35,6 +35,7 @@ class AtomVecDielectric : virtual public AtomVec { void grow_pointers() override; void create_atom_post(int) override; void data_atom_post(int) override; + void data_general_to_restricted(int, int); void unpack_restart_init(int) override; int property_atom(const std::string &) override; void pack_property_atom(int, double *, int, int) override; diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 3f160787b27..5323e33f177 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -14,6 +14,7 @@ #include "atom_vec_dipole.h" #include "atom.h" +#include "domain.h" #include @@ -68,3 +69,17 @@ void AtomVecDipole::data_atom_post(int ilocal) double *mu_one = mu[ilocal]; mu_one[3] = sqrt(mu_one[0] * mu_one[0] + mu_one[1] * mu_one[1] + mu_one[2] * mu_one[2]); } + +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on mu +------------------------------------------------------------------------- */ + +void AtomVecDipole::data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::data_general_to_restricted(nlocal_previous, nlocal); + + for (int i = nlocal_previous; i < nlocal; i++) + domain->general_to_restricted_vector(mu[i]); +} diff --git a/src/DIPOLE/atom_vec_dipole.h b/src/DIPOLE/atom_vec_dipole.h index d2f5746462b..d688fd98ddb 100644 --- a/src/DIPOLE/atom_vec_dipole.h +++ b/src/DIPOLE/atom_vec_dipole.h @@ -30,6 +30,7 @@ class AtomVecDipole : virtual public AtomVec { void grow_pointers() override; void data_atom_post(int) override; + void data_general_to_restricted(int, int); protected: double **mu; diff --git a/src/MACHDYN/atom_vec_smd.cpp b/src/MACHDYN/atom_vec_smd.cpp index d1bae9ecb74..0f5e7f82f02 100644 --- a/src/MACHDYN/atom_vec_smd.cpp +++ b/src/MACHDYN/atom_vec_smd.cpp @@ -156,6 +156,13 @@ void AtomVecSMD::create_atom_post(int ilocal) void AtomVecSMD::data_atom_post(int ilocal) { esph[ilocal] = 0.0; + + // x and x0 are in Atoms section of data file + // reset x0 b/c x may have been modified in Atom::data_atoms() + // for PBC, shift, etc + // this also means no need for data_general_to_restricted() method + // to rotate x0 for general triclinic + x0[ilocal][0] = x[ilocal][0]; x0[ilocal][1] = x[ilocal][1]; x0[ilocal][2] = x[ilocal][2]; diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 9a7e4c6aac6..1ea57516f67 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -1,5 +1,4 @@ /* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories LAMMPS development team: developers@lammps.org @@ -10,7 +9,6 @@ the GNU General Public License. See the README file in the top-level LAMMPS directory. - ------------------------------------------------------------------------- */ /* ------------------------------------------------------------------------ @@ -26,6 +24,7 @@ #include "atom_vec_spin.h" #include "atom.h" +#include "domain.h" #include #include @@ -100,3 +99,17 @@ void AtomVecSpin::data_atom_post(int ilocal) sp_one[1] *= norm; sp_one[2] *= norm; } + +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on spin vector sp +------------------------------------------------------------------------- */ + +void AtomVecSpin::data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::data_general_to_restricted(nlocal_previous, nlocal); + + for (int i = nlocal_previous; i < nlocal; i++) + domain->general_to_restricted_vector(sp[i]); +} diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h index bf11d5856e5..effbe232f4e 100644 --- a/src/SPIN/atom_vec_spin.h +++ b/src/SPIN/atom_vec_spin.h @@ -31,6 +31,7 @@ class AtomVecSpin : virtual public AtomVec { void grow_pointers() override; void force_clear(int, size_t) override; void data_atom_post(int) override; + void data_general_to_restricted(int, int); protected: double **sp, **fm, **fm_long; diff --git a/src/atom.cpp b/src/atom.cpp index fb444e3e797..4674ded045b 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1039,12 +1039,12 @@ void Atom::deallocate_topology() /* ---------------------------------------------------------------------- unpack N lines from Atom section of data file call style-specific routine to parse line + triclinic_general = 1 if data file defines a general triclinic box ------------------------------------------------------------------------- */ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, - int type_offset, int triclinic_general, - int shiftflag, double *shift, - int labelflag, int *ilabel) + int type_offset, int shiftflag, double *shift, + int labelflag, int *ilabel, int triclinic_general) { int xptr,iptr; imageint imagedata; @@ -1181,8 +1181,8 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp); xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp); - // for 2d simulation, check if z coord is within EPS_ZCOORD of zero - // then set to zero + // for 2d simulation: + // check if z coord is within EPS_ZCOORD of zero and set to zero if (dimension == 2) { if (fabs(xdata[2]) > EPS_ZCOORD) @@ -1255,8 +1255,8 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, /* ---------------------------------------------------------------------- unpack N lines from Velocity section of data file check that atom IDs are > 0 and <= map_tag_max - call style-specific routine to parse line -------------------------------------------------------------------------- */ + call style-specific routine to parse line- +------------------------------------------------------------------------ */ void Atom::data_vels(int n, char *buf, tagint id_offset) { diff --git a/src/atom.h b/src/atom.h index cf5fa108149..5c4ad80e626 100644 --- a/src/atom.h +++ b/src/atom.h @@ -328,8 +328,7 @@ class Atom : protected Pointers { void deallocate_topology(); - void data_atoms(int, char *, tagint, tagint, int, int, - int, double *, int, int *); + void data_atoms(int, char *, tagint, tagint, int, int, double *, int, int *, int); void data_vels(int, char *, tagint); void data_bonds(int, char *, int *, tagint, int, int, int *); void data_angles(int, char *, int *, tagint, int, int, int *); diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index bfda9518238..d8684aaf944 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -1656,6 +1656,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vectornlocal; if (nlocal == nmax) grow(0); @@ -1684,7 +1685,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vectorgeneral_to_restricted_vector(array[i]); + } + } + } +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/atom_vec.h b/src/atom_vec.h index a4db0547529..b0c77635f80 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -123,7 +123,8 @@ class AtomVec : protected Pointers { virtual void create_atom(int, double *); virtual void create_atom_post(int) {} - virtual void data_atom(double *, imageint, const std::vector &, std::string &); + virtual void data_atom(double *, imageint, const std::vector &, + std::string &); virtual void data_atom_post(int) {} virtual void data_atom_bonus(int, const std::vector &) {} virtual void data_body(int, int, int, int *, double *) {} @@ -151,6 +152,8 @@ class AtomVec : protected Pointers { virtual int pack_data_bonus(double *, int) { return 0; } virtual void write_data_bonus(FILE *, int, double *, int) {} + virtual void data_general_to_restricted(int, int); + virtual int property_atom(const std::string &) { return -1; } virtual void pack_property_atom(int, double *, int, int) {} diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 0a8c4626882..fb9b83413f2 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -1376,8 +1376,8 @@ void CreateAtoms::loop_lattice(int action) domain->lattice->lattice2box(x[0], x[1], x[2]); // convert from general to restricted triclinic coords - // for 2d simulation, check if z coord is within EPS_ZCOORD of zero - // then set to zero + // for 2d simulation: + // check if z coord is within EPS_ZCOORD of zero and set to zero if (triclinic_general) { domain->general_to_restricted_coords(x); diff --git a/src/lmprestart.h b/src/lmprestart.h index b3982ac8c10..2ed1d7db11f 100644 --- a/src/lmprestart.h +++ b/src/lmprestart.h @@ -29,7 +29,6 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, NDIHEDRALS,NDIHEDRALTYPES,DIHEDRAL_PER_ATOM, NIMPROPERS,NIMPROPERTYPES,IMPROPER_PER_ATOM, TRICLINIC,BOXLO,BOXHI,XY,XZ,YZ, - TRICLINIC_GENERAL,ROTATE_G2R,ROTATE_R2G, SPECIAL_LJ,SPECIAL_COUL, MASS,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER, MULTIPROC,MPIIO,PROCSPERFILE,PERPROC, @@ -38,7 +37,8 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL, - NELLIPSOIDS,NLINES,NTRIS,NBODIES,ATIME,ATIMESTEP,LABELMAP}; + NELLIPSOIDS,NLINES,NTRIS,NBODIES,ATIME,ATIMESTEP,LABELMAP, + TRICLINIC_GENERAL,ROTATE_G2R,ROTATE_R2G}; #define LB_FACTOR 1.1 diff --git a/src/read_data.cpp b/src/read_data.cpp index c59bec74761..219a3615848 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1062,6 +1062,12 @@ void ReadData::command(int narg, char **arg) atom->avec->grow(atom->nmax); } + // if general triclinic, perform general to restricted rotation operation + // on any quantities read from data file which require it + + if (triclinic_general) + atom->avec->data_general_to_restricted(nlocal_previous, atom->nlocal); + // init per-atom fix/compute/variable values for created atoms atom->data_fix_compute_variable(nlocal_previous, atom->nlocal); @@ -1518,8 +1524,8 @@ void ReadData::atoms() if (eof) error->all(FLERR, "Unexpected end of data file"); if (tlabelflag && !lmap->is_complete(Atom::ATOM)) error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label"); - atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, triclinic_general, - shiftflag, shift, tlabelflag, lmap->lmap2lmap.atom); + atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, + shiftflag, shift, tlabelflag, lmap->lmap2lmap.atom, triclinic_general); nread += nchunk; } From c7e794146f9cd04d3e5b2a57bb7e5dc096547a08 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 13 Sep 2023 10:03:05 -0600 Subject: [PATCH 036/719] initial support for write_data --- src/DIELECTRIC/atom_vec_dielectric.cpp | 4 +- src/DIELECTRIC/atom_vec_dielectric.h | 2 +- src/MACHDYN/atom_vec_smd.cpp | 2 +- src/atom.cpp | 2 + src/atom_vec.cpp | 102 ++++++++++++++++++++++++- src/atom_vec.h | 9 ++- src/read_data.cpp | 2 +- src/write_data.cpp | 33 +++----- 8 files changed, 124 insertions(+), 32 deletions(-) diff --git a/src/DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp index a06b4d599ba..735d770b04f 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -194,9 +194,9 @@ void AtomVecDielectric::data_atom_post(int ilocal) child class operates on dipole moment mu ------------------------------------------------------------------------- */ -void AtomVecDielectric::data_general_to_restricted(int nlocal_previous, int nlocal) +void AtomVecDielectric::read_data_general_to_restricted(int nlocal_previous, int nlocal) { - AtomVec::data_general_to_restricted(nlocal_previous, nlocal); + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); for (int i = nlocal_previous; i < nlocal; i++) domain->general_to_restricted_vector(mu[i]); diff --git a/src/DIELECTRIC/atom_vec_dielectric.h b/src/DIELECTRIC/atom_vec_dielectric.h index fefbc99c4f5..8bef111cb4b 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.h +++ b/src/DIELECTRIC/atom_vec_dielectric.h @@ -35,7 +35,7 @@ class AtomVecDielectric : virtual public AtomVec { void grow_pointers() override; void create_atom_post(int) override; void data_atom_post(int) override; - void data_general_to_restricted(int, int); + void read_data_general_to_restricted(int, int); void unpack_restart_init(int) override; int property_atom(const std::string &) override; void pack_property_atom(int, double *, int, int) override; diff --git a/src/MACHDYN/atom_vec_smd.cpp b/src/MACHDYN/atom_vec_smd.cpp index 0f5e7f82f02..27f23c53628 100644 --- a/src/MACHDYN/atom_vec_smd.cpp +++ b/src/MACHDYN/atom_vec_smd.cpp @@ -160,7 +160,7 @@ void AtomVecSMD::data_atom_post(int ilocal) // x and x0 are in Atoms section of data file // reset x0 b/c x may have been modified in Atom::data_atoms() // for PBC, shift, etc - // this also means no need for data_general_to_restricted() method + // this also means no need for read_data_general_to_restricted() method // to rotate x0 for general triclinic x0[ilocal][0] = x[ilocal][0]; diff --git a/src/atom.cpp b/src/atom.cpp index 4674ded045b..7f472e44f4b 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1191,6 +1191,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, } // convert atom coords from general triclinic to restricted triclinic + // so can decide which proc owns the atom if (triclinic_general) domain->general_to_restricted_coords(xdata); @@ -1216,6 +1217,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, if (coord[0] >= sublo[0] && coord[0] < subhi[0] && coord[1] >= sublo[1] && coord[1] < subhi[1] && coord[2] >= sublo[2] && coord[2] < subhi[2]) { + avec->data_atom(xdata,imagedata,values,typestr); typestr = utils::utf8_subst(typestr); if (id_offset) tag[nlocal-1] += id_offset; diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index d8684aaf944..f7a0f6f5663 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -68,6 +68,9 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp) image = nullptr; x = v = f = nullptr; + x_hold = nullptr; + v_hold = omega_hold = angmom_hold = nullptr; + threads = nullptr; } @@ -2223,12 +2226,12 @@ void AtomVec::write_improper(FILE *fp, int n, tagint **buf, int index) } /* ---------------------------------------------------------------------- - convert read_data file info from general to restricted triclinic + convert info input by read_data from general to restricted triclinic parent class only operates on data from Velocities section of data file child classes operate on all other data: Atoms, Ellipsoids, Lines, Triangles, etc ------------------------------------------------------------------------- */ -void AtomVec::data_general_to_restricted(int nlocal_previous, int nlocal) +void AtomVec::read_data_general_to_restricted(int nlocal_previous, int nlocal) { int datatype, cols; void *pdata; @@ -2239,7 +2242,7 @@ void AtomVec::data_general_to_restricted(int nlocal_previous, int nlocal) cols = mdata_vel.cols[n]; // operate on v, omega, angmom - // no other read_data atom fields are Nx3 double arrays + // no other read_data Velocities fields are Nx3 double arrays if (datatype == Atom::DOUBLE) { if (cols == 3) { @@ -2251,6 +2254,99 @@ void AtomVec::data_general_to_restricted(int nlocal_previous, int nlocal) } } +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class only operates on x and data from Velocities section of data file + child classes operate on all other data: Atoms, Ellipsoids, Lines, Triangles, etc +------------------------------------------------------------------------- */ + +void AtomVec::write_data_restricted_to_general() +{ + int datatype, cols; + void *pdata; + + int nlocal = atom->nlocal; + + memory->create(x_hold,nlocal,3,"atomvec:x_hold"); + if (nlocal) memcpy(&x_hold[0][0],&x[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_coords(x[i]); + + double **omega = atom->omega; + double **angmom = atom->angmom; + + for (int n = 1; n < ndata_vel; n++) { + pdata = mdata_vel.pdata[n]; + datatype = mdata_vel.datatype[n]; + cols = mdata_vel.cols[n]; + + // operate on v, omega, angmom + // no other write_data Velocities fields are Nx3 double arrays + + if (datatype == Atom::DOUBLE) { + if (cols == 3) { + double **array = *((double ***) pdata); + + if (array == v) { + memory->create(v_hold,nlocal,3,"atomvec:v_hold"); + if (nlocal) memcpy(&v_hold[0][0],&v[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_vector(v[i]); + } else if (array == omega) { + memory->create(omega_hold,nlocal,3,"atomvec:omega_hold"); + if (nlocal) memcpy(&omega_hold[0][0],&omega[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_vector(omega[i]); + } else if (array == angmom) { + memory->create(angmom_hold,nlocal,3,"atomvec:angmom_hold"); + if (nlocal) memcpy(&angmom_hold[0][0],&angmom[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_vector(angmom[i]); + } + } + } + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class only operates on x and data from Velocities section of data file + child classes operate on all other data: Atoms, Ellipsoids, Lines, Triangles, etc +------------------------------------------------------------------------- */ + +void AtomVec::write_data_restore_restricted() +{ + int nlocal = atom->nlocal; + + if (x_hold) { + memcpy(&x[0][0],&x_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(x_hold); + x_hold = nullptr; + } + + // operate on v, omega, angmom + // no other write_data Velocities fields are Nx3 double arrays + + if (v_hold) { + memcpy(&v[0][0],&v_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(v_hold); + v_hold = nullptr; + } + + if (omega_hold) { + memcpy(&atom->omega[0][0],&omega_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(omega_hold); + omega_hold = nullptr; + } + + if (angmom_hold) { + memcpy(&atom->angmom[0][0],&angmom_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(angmom_hold); + angmom_hold = nullptr; + } +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/atom_vec.h b/src/atom_vec.h index b0c77635f80..55fe7e2f7d2 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -152,7 +152,9 @@ class AtomVec : protected Pointers { virtual int pack_data_bonus(double *, int) { return 0; } virtual void write_data_bonus(FILE *, int, double *, int) {} - virtual void data_general_to_restricted(int, int); + virtual void read_data_general_to_restricted(int, int); + virtual void write_data_restricted_to_general(); + virtual void write_data_restore_restricted(); virtual int property_atom(const std::string &) { return -1; } virtual void pack_property_atom(int, double *, int, int) {} @@ -171,6 +173,11 @@ class AtomVec : protected Pointers { imageint *image; double **x, **v, **f; + // copies of original unrotated fields for write_data for general triclinic + + double **x_hold; + double **v_hold, **omega_hold, **angmom_hold; + // standard list of peratom fields always operated on by different methods // common to all styles, so not listed in field strings diff --git a/src/read_data.cpp b/src/read_data.cpp index 219a3615848..ab3876a25ef 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1066,7 +1066,7 @@ void ReadData::command(int narg, char **arg) // on any quantities read from data file which require it if (triclinic_general) - atom->avec->data_general_to_restricted(nlocal_previous, atom->nlocal); + atom->avec->read_data_general_to_restricted(nlocal_previous, atom->nlocal); // init per-atom fix/compute/variable values for created atoms diff --git a/src/write_data.cpp b/src/write_data.cpp index 960a4ff1cfd..49e041b6ce2 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -97,7 +97,7 @@ void WriteData::command(int narg, char **arg) } else if (strcmp(arg[iarg],"nofix") == 0) { fixflag = 0; iarg++; - } else if (strcmp(arg[iarg],"triclinic") == 0) { + } else if (strcmp(arg[iarg],"triclinic/general") == 0) { triclinic_general = 1; iarg++; } else if (strcmp(arg[iarg],"nolabelmap") == 0) { @@ -213,32 +213,14 @@ void WriteData::write(const std::string &file) if (coeffflag) force_fields(); } - // per atom info in Atoms and Velocities sections // if general triclinic: - // save restricted triclinic atom coords - // transform atom coords from restricted to general - // restore saved atom coords after output - - double **xstore = nullptr; + // reset internal per-atom data that needs rotation + + atom->avec->write_data_restricted_to_general(); - if (triclinic_general) { - double **x = atom->x; - int nlocal = atom->nlocal; - memory->create(xstore,nlocal,3,"write_data:xstore"); - if (nlocal) memcpy(&xstore[0][0],&x[0][0],3*nlocal*sizeof(double)); - for (int i = 0; i < nlocal; i++) - domain->restricted_to_general_coords(x[i]); - } + // per atom info in Atoms and Velocities sections if (natoms) atoms(); - - if (triclinic_general) { - double **x = atom->x; - int nlocal = atom->nlocal; - if (nlocal) memcpy(&x[0][0],&xstore[0][0],3*nlocal*sizeof(double)); - memory->destroy(xstore); - } - if (natoms) velocities(); // molecular topology info if defined @@ -265,6 +247,11 @@ void WriteData::write(const std::string &file) if (ifix->wd_section) for (int m = 0; m < ifix->wd_section; m++) fix(ifix,m); + // if general triclinic: + // restore internal per-atom data that was rotated + + atom->avec->write_data_restore_restricted(); + // close data file if (me == 0) fclose(fp); From e5f3fcbbf41e47decbce9deed926d4dde1bd2fd8 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 13 Sep 2023 13:29:37 -0600 Subject: [PATCH 037/719] more work on read_data and write_data --- src/DIELECTRIC/atom_vec_dielectric.cpp | 39 ++++++++++++ src/DIELECTRIC/atom_vec_dielectric.h | 5 ++ src/DIPOLE/atom_vec_dipole.cpp | 45 ++++++++++++- src/DIPOLE/atom_vec_dipole.h | 5 +- src/MACHDYN/atom_vec_smd.cpp | 41 ++++++++++++ src/MACHDYN/atom_vec_smd.h | 4 ++ src/SPIN/atom_vec_spin.cpp | 43 ++++++++++++- src/SPIN/atom_vec_spin.h | 5 +- src/atom_vec_body.cpp | 88 ++++++++++++++++++++++++++ src/atom_vec_body.h | 5 ++ src/atom_vec_ellipsoid.cpp | 87 +++++++++++++++++++++++++ src/atom_vec_ellipsoid.h | 5 ++ src/atom_vec_line.cpp | 23 +++++++ src/atom_vec_line.h | 1 + src/atom_vec_tri.cpp | 86 +++++++++++++++++++++++++ src/atom_vec_tri.h | 5 ++ src/domain.cpp | 14 ++-- src/domain.h | 1 + 18 files changed, 488 insertions(+), 14 deletions(-) diff --git a/src/DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp index 735d770b04f..516c08bd986 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -18,6 +18,7 @@ #include "domain.h" #include "error.h" #include "force.h" +#include "memory.h" #include "pair.h" #include "pair_hybrid.h" @@ -51,6 +52,8 @@ AtomVecDielectric::AtomVecDielectric(LAMMPS *_lmp) : AtomVec(_lmp) atom->molecule_flag = atom->q_flag = atom->mu_flag = 1; atom->dielectric_flag = 1; + mu_hold = nullptr; + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -202,6 +205,42 @@ void AtomVecDielectric::read_data_general_to_restricted(int nlocal_previous, int domain->general_to_restricted_vector(mu[i]); } +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on dipole momemt mu +------------------------------------------------------------------------- */ + +void AtomVecDielectric::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + int nlocal = atom->nlocal; + memory->create(mu_hold,nlocal,3,"atomvec:mu_hold"); + if (nlocal) memcpy(&mu_hold[0][0],&mu[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_vector(mu[i]); +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on dipole moment mu +------------------------------------------------------------------------- */ + +void AtomVecDielectric::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!mu_hold) return; + + int nlocal = atom->nlocal; + memcpy(&mu[0][0],&mu_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(mu_hold); + mu_hold = nullptr; +} + /* ---------------------------------------------------------------------- initialize other atom quantities after AtomVec::unpack_restart() ------------------------------------------------------------------------- */ diff --git a/src/DIELECTRIC/atom_vec_dielectric.h b/src/DIELECTRIC/atom_vec_dielectric.h index 8bef111cb4b..b6b7ebd676c 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.h +++ b/src/DIELECTRIC/atom_vec_dielectric.h @@ -36,6 +36,9 @@ class AtomVecDielectric : virtual public AtomVec { void create_atom_post(int) override; void data_atom_post(int) override; void read_data_general_to_restricted(int, int); + void write_data_restricted_to_general(); + void write_data_restore_restricted(); + void unpack_restart_init(int) override; int property_atom(const std::string &) override; void pack_property_atom(int, double *, int, int) override; @@ -49,6 +52,8 @@ class AtomVecDielectric : virtual public AtomVec { double **mu; double *area, *ed, *em, *epsilon, *curvature, *q_scaled; + + double **mu_hold; }; } // namespace LAMMPS_NS diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 5323e33f177..025624c6c0d 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -15,6 +15,7 @@ #include "atom.h" #include "domain.h" +#include "memory.h" #include @@ -28,6 +29,8 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp) mass_type = PER_TYPE; atom->q_flag = atom->mu_flag = 1; + + mu_hold = nullptr; // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings @@ -73,13 +76,49 @@ void AtomVecDipole::data_atom_post(int ilocal) /* ---------------------------------------------------------------------- convert read_data file info from general to restricted triclinic parent class operates on data from Velocities section of data file - child class operates on mu + child class operates on dipole moment mu ------------------------------------------------------------------------- */ -void AtomVecDipole::data_general_to_restricted(int nlocal_previous, int nlocal) +void AtomVecDipole::read_data_general_to_restricted(int nlocal_previous, int nlocal) { - AtomVec::data_general_to_restricted(nlocal_previous, nlocal); + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); for (int i = nlocal_previous; i < nlocal; i++) domain->general_to_restricted_vector(mu[i]); } + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on dipole momemt mu +------------------------------------------------------------------------- */ + +void AtomVecDipole::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + int nlocal = atom->nlocal; + memory->create(mu_hold,nlocal,3,"atomvec:mu_hold"); + if (nlocal) memcpy(&mu_hold[0][0],&mu[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_vector(mu[i]); +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on dipole moment mu +------------------------------------------------------------------------- */ + +void AtomVecDipole::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!mu_hold) return; + + int nlocal = atom->nlocal; + memcpy(&mu[0][0],&mu_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(mu_hold); + mu_hold = nullptr; +} diff --git a/src/DIPOLE/atom_vec_dipole.h b/src/DIPOLE/atom_vec_dipole.h index d688fd98ddb..1f6d6fe2bef 100644 --- a/src/DIPOLE/atom_vec_dipole.h +++ b/src/DIPOLE/atom_vec_dipole.h @@ -30,10 +30,13 @@ class AtomVecDipole : virtual public AtomVec { void grow_pointers() override; void data_atom_post(int) override; - void data_general_to_restricted(int, int); + void read_data_general_to_restricted(int, int); + void write_data_restricted_to_general(); + void write_data_restore_restricted(); protected: double **mu; + double **mu_hold; }; } // namespace LAMMPS_NS diff --git a/src/MACHDYN/atom_vec_smd.cpp b/src/MACHDYN/atom_vec_smd.cpp index 27f23c53628..5ba2c010386 100644 --- a/src/MACHDYN/atom_vec_smd.cpp +++ b/src/MACHDYN/atom_vec_smd.cpp @@ -25,6 +25,8 @@ #include "atom_vec_smd.h" #include "atom.h" +#include "domain.h" +#include "memory.h" #include @@ -57,6 +59,8 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp) atom->damage_flag = 1; atom->eff_plastic_strain_rate_flag = 1; + x0_hold = nullptr; + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -184,3 +188,40 @@ void AtomVecSMD::data_atom_post(int ilocal) smd_data_9[ilocal][4] = 1.0; // yy smd_data_9[ilocal][8] = 1.0; // zz } + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on original coords x0 +------------------------------------------------------------------------- */ + +void AtomVecSMD::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + int nlocal = atom->nlocal; + memory->create(x0_hold,nlocal,3,"atomvec:x0_hold"); + if (nlocal) memcpy(&x0_hold[0][0],&x0[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_coords(x0[i]); + +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on original coords x0 +------------------------------------------------------------------------- */ + +void AtomVecSMD::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!x0_hold) return; + + int nlocal = atom->nlocal; + memcpy(&x0[0][0],&x0_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(x0_hold); + x0_hold = nullptr; +} diff --git a/src/MACHDYN/atom_vec_smd.h b/src/MACHDYN/atom_vec_smd.h index 6ca7f08b4d1..322136ebd35 100644 --- a/src/MACHDYN/atom_vec_smd.h +++ b/src/MACHDYN/atom_vec_smd.h @@ -43,12 +43,16 @@ class AtomVecSMD : virtual public AtomVec { void force_clear(int, size_t) override; void create_atom_post(int) override; void data_atom_post(int) override; + void write_data_restricted_to_general(); + void write_data_restore_restricted(); private: tagint *molecule; double *esph, *desph, *vfrac, *rmass, *radius, *contact_radius; double *eff_plastic_strain, *eff_plastic_strain_rate, *damage; double **x0, **smd_data_9, **smd_stress, **vest; + + double **x0_hold; }; } // namespace LAMMPS_NS diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 1ea57516f67..a68a59ef389 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -25,6 +25,7 @@ #include "atom.h" #include "domain.h" +#include "memory.h" #include #include @@ -41,6 +42,8 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp) atom->sp_flag = 1; + sp_hold = nullptr; + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -106,10 +109,46 @@ void AtomVecSpin::data_atom_post(int ilocal) child class operates on spin vector sp ------------------------------------------------------------------------- */ -void AtomVecSpin::data_general_to_restricted(int nlocal_previous, int nlocal) +void AtomVecSpin::read_data_general_to_restricted(int nlocal_previous, int nlocal) { - AtomVec::data_general_to_restricted(nlocal_previous, nlocal); + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); for (int i = nlocal_previous; i < nlocal; i++) domain->general_to_restricted_vector(sp[i]); } + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on spin vector sp +------------------------------------------------------------------------- */ + +void AtomVecSpin::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + int nlocal = atom->nlocal; + memory->create(sp_hold,nlocal,3,"atomvec:sp_hold"); + if (nlocal) memcpy(&sp_hold[0][0],&sp[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + domain->restricted_to_general_vector(sp[i]); +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on spin vector sp +------------------------------------------------------------------------- */ + +void AtomVecSpin::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!sp_hold) return; + + int nlocal = atom->nlocal; + memcpy(&sp[0][0],&sp_hold[0][0],3*nlocal*sizeof(double)); + memory->destroy(sp_hold); + sp_hold = nullptr; +} diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h index effbe232f4e..93bbc82ab8a 100644 --- a/src/SPIN/atom_vec_spin.h +++ b/src/SPIN/atom_vec_spin.h @@ -31,10 +31,13 @@ class AtomVecSpin : virtual public AtomVec { void grow_pointers() override; void force_clear(int, size_t) override; void data_atom_post(int) override; - void data_general_to_restricted(int, int); + void read_data_general_to_restricted(int, int); + void write_data_restricted_to_general(); + void write_data_restore_restricted(); protected: double **sp, **fm, **fm_long; + double **sp_hold; }; } // namespace LAMMPS_NS diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 538e9783df3..7721e1540b7 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -16,8 +16,10 @@ #include "atom.h" #include "body.h" +#include "domain.h" #include "error.h" #include "fix.h" +#include "math_extra.h" #include "memory.h" #include "modify.h" #include "my_pool_chunk.h" @@ -51,6 +53,8 @@ AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp) nlocal_bonus = nghost_bonus = nmax_bonus = 0; bonus = nullptr; + quat_hold = nullptr; + bptr = nullptr; if (sizeof(double) == sizeof(int)) @@ -547,6 +551,90 @@ void AtomVecBody::data_atom_post(int ilocal) angmom[ilocal][2] = 0.0; } +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on bonus quat +------------------------------------------------------------------------- */ + +void AtomVecBody::read_data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + double quat[4]; + double *bquat; + + for (int i = nlocal_previous; i < nlocal; i++) { + if (body[i] < 0) continue; + bquat = bonus[body[i]].quat; + MathExtra::quatquat(domain->quat_g2r,bquat,quat); + bquat[0] = quat[0]; + bquat[1] = quat[1]; + bquat[2] = quat[2]; + bquat[3] = quat[3]; + MathExtra::qnormalize(bquat); + } +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on bonus quat +------------------------------------------------------------------------- */ + +void AtomVecBody::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + double quat[4],quat_r2g[4]; + double *bquat; + + memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); + MathExtra::qconjugate(domain->quat_g2r,quat_r2g); + + for (int i = 0; i < nlocal_bonus; i++) { + bquat = bonus[i].quat; + quat_hold[i][0] = bquat[0]; + quat_hold[i][1] = bquat[1]; + quat_hold[i][2] = bquat[2]; + quat_hold[i][3] = bquat[3]; + + MathExtra::quatquat(quat_r2g,bquat,quat); + bquat[0] = quat[0]; + bquat[1] = quat[1]; + bquat[2] = quat[2]; + bquat[3] = quat[3]; + MathExtra::qnormalize(bquat); + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on bonus quat +------------------------------------------------------------------------- */ + +void AtomVecBody::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!quat_hold) return; + + double *bquat; + + for (int i = 0; i < nlocal_bonus; i++) { + bquat = bonus[i].quat; + bquat[0] = quat_hold[i][0]; + bquat[1] = quat_hold[i][1]; + bquat[2] = quat_hold[i][2]; + bquat[3] = quat_hold[i][3]; + } + + memory->destroy(quat_hold); + quat_hold = nullptr; +} + /* ---------------------------------------------------------------------- unpack one body from Bodies section of data file ------------------------------------------------------------------------- */ diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index e02fd3bbb0d..955b4f45874 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -60,6 +60,9 @@ class AtomVecBody : public AtomVec { void create_atom_post(int) override; void data_atom_post(int) override; + void read_data_general_to_restricted(int, int); + void write_data_restricted_to_general(); + void write_data_restore_restricted(); void pack_data_pre(int) override; void pack_data_post(int) override; @@ -78,6 +81,8 @@ class AtomVecBody : public AtomVec { double *rmass, *radius; double **angmom; + double **quat_hold; + int nghost_bonus, nmax_bonus; int intdoubleratio; // sizeof(double) / sizeof(int) int body_flag; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 3eaa9273844..ceb813cbe2f 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -18,6 +18,7 @@ #include "atom_vec_ellipsoid.h" #include "atom.h" +#include "domain.h" #include "error.h" #include "fix.h" #include "math_const.h" @@ -48,6 +49,8 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp) nlocal_bonus = nghost_bonus = nmax_bonus = 0; bonus = nullptr; + quat_hold = nullptr; + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -457,6 +460,90 @@ void AtomVecEllipsoid::data_atom_post(int ilocal) angmom[ilocal][2] = 0.0; } +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on bonus quat +------------------------------------------------------------------------- */ + +void AtomVecEllipsoid::read_data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + double quat[4]; + double *bquat; + + for (int i = nlocal_previous; i < nlocal; i++) { + if (ellipsoid[i] < 0) continue; + bquat = bonus[ellipsoid[i]].quat; + MathExtra::quatquat(domain->quat_g2r,bquat,quat); + bquat[0] = quat[0]; + bquat[1] = quat[1]; + bquat[2] = quat[2]; + bquat[3] = quat[3]; + MathExtra::qnormalize(bquat); + } +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on bonus quat +------------------------------------------------------------------------- */ + +void AtomVecEllipsoid::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + double quat[4],quat_r2g[4]; + double *bquat; + + memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); + MathExtra::qconjugate(domain->quat_g2r,quat_r2g); + + for (int i = 0; i < nlocal_bonus; i++) { + bquat = bonus[i].quat; + quat_hold[i][0] = bquat[0]; + quat_hold[i][1] = bquat[1]; + quat_hold[i][2] = bquat[2]; + quat_hold[i][3] = bquat[3]; + + MathExtra::quatquat(quat_r2g,bquat,quat); + bquat[0] = quat[0]; + bquat[1] = quat[1]; + bquat[2] = quat[2]; + bquat[3] = quat[3]; + MathExtra::qnormalize(bquat); + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on bonus quat +------------------------------------------------------------------------- */ + +void AtomVecEllipsoid::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!quat_hold) return; + + double *bquat; + + for (int i = 0; i < nlocal_bonus; i++) { + bquat = bonus[i].quat; + bquat[0] = quat_hold[i][0]; + bquat[1] = quat_hold[i][1]; + bquat[2] = quat_hold[i][2]; + bquat[3] = quat_hold[i][3]; + } + + memory->destroy(quat_hold); + quat_hold = nullptr; +} + /* ---------------------------------------------------------------------- modify values for AtomVec::pack_data() to pack ------------------------------------------------------------------------- */ diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h index 6e06d773fcb..3d6815fff03 100644 --- a/src/atom_vec_ellipsoid.h +++ b/src/atom_vec_ellipsoid.h @@ -53,6 +53,9 @@ class AtomVecEllipsoid : public AtomVec { void create_atom_post(int) override; void data_atom_post(int) override; + void read_data_general_to_restricted(int, int); + void write_data_restricted_to_general(); + void write_data_restore_restricted(); void pack_data_pre(int) override; void pack_data_post(int) override; @@ -70,6 +73,8 @@ class AtomVecEllipsoid : public AtomVec { double *rmass; double **angmom; + double **quat_hold; + int nghost_bonus, nmax_bonus; int ellipsoid_flag; double rmass_one; diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index ff09bed6d01..95ccfe31bd1 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -437,6 +437,29 @@ void AtomVecLine::data_atom_post(int ilocal) omega[ilocal][2] = 0.0; } +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on bonus theta +------------------------------------------------------------------------- */ + +void AtomVecLine::read_data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + double btheta; + double theta_g2r = 2.0*acos(domain->quat_g2r[0]); + + for (int i = nlocal_previous; i < nlocal; i++) { + if (line[i] < 0) continue; + btheta = bonus[line[i]].theta; + btheta += theta_g2r; + if (btheta > MathConst::MY_PI) btheta -= MathConst::MY_2PI; + else if (btheta <= -MathConst::MY_PI) btheta += MathConst::MY_2PI; + bonus[line[i]].theta = btheta; + } +} + /* ---------------------------------------------------------------------- modify values for AtomVec::pack_data() to pack ------------------------------------------------------------------------- */ diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h index 740c541916f..2503f55d8d6 100644 --- a/src/atom_vec_line.h +++ b/src/atom_vec_line.h @@ -53,6 +53,7 @@ class AtomVecLine : public AtomVec { void create_atom_post(int) override; void data_atom_post(int) override; + void read_data_general_to_restricted(int, int); void pack_data_pre(int) override; void pack_data_post(int) override; diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index a46609b02c6..7dfb50093bb 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -52,6 +52,8 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp) nlocal_bonus = nghost_bonus = nmax_bonus = 0; bonus = nullptr; + double **quat_hold = nullptr; + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -657,6 +659,90 @@ void AtomVecTri::data_atom_post(int ilocal) angmom[ilocal][2] = 0.0; } +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on bonus quat +------------------------------------------------------------------------- */ + +void AtomVecTri::read_data_general_to_restricted(int nlocal_previous, int nlocal) +{ + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + double quat[4]; + double *bquat; + + for (int i = nlocal_previous; i < nlocal; i++) { + if (tri[i] < 0) continue; + bquat = bonus[tri[i]].quat; + MathExtra::quatquat(domain->quat_g2r,bquat,quat); + bquat[0] = quat[0]; + bquat[1] = quat[1]; + bquat[2] = quat[2]; + bquat[3] = quat[3]; + MathExtra::qnormalize(bquat); + } +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on bonus quat +------------------------------------------------------------------------- */ + +void AtomVecTri::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + double quat[4],quat_r2g[4]; + double *bquat; + + memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); + MathExtra::qconjugate(domain->quat_g2r,quat_r2g); + + for (int i = 0; i < nlocal_bonus; i++) { + bquat = bonus[i].quat; + quat_hold[i][0] = bquat[0]; + quat_hold[i][1] = bquat[1]; + quat_hold[i][2] = bquat[2]; + quat_hold[i][3] = bquat[3]; + + MathExtra::quatquat(quat_r2g,bquat,quat); + bquat[0] = quat[0]; + bquat[1] = quat[1]; + bquat[2] = quat[2]; + bquat[3] = quat[3]; + MathExtra::qnormalize(bquat); + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on bonus quat +------------------------------------------------------------------------- */ + +void AtomVecTri::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + if (!quat_hold) return; + + double *bquat; + + for (int i = 0; i < nlocal_bonus; i++) { + bquat = bonus[i].quat; + bquat[0] = quat_hold[i][0]; + bquat[1] = quat_hold[i][1]; + bquat[2] = quat_hold[i][2]; + bquat[3] = quat_hold[i][3]; + } + + memory->destroy(quat_hold); + quat_hold = nullptr; +} + /* ---------------------------------------------------------------------- modify values for AtomVec::pack_data() to pack ------------------------------------------------------------------------- */ diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h index 424bd8ea0ae..91a7a20e6dd 100644 --- a/src/atom_vec_tri.h +++ b/src/atom_vec_tri.h @@ -55,6 +55,9 @@ class AtomVecTri : public AtomVec { void create_atom_post(int) override; void data_atom_post(int) override; + void read_data_general_to_restricted(int, int); + void write_data_restricted_to_general(); + void write_data_restore_restricted(); void pack_data_pre(int) override; void pack_data_post(int) override; @@ -72,6 +75,8 @@ class AtomVecTri : public AtomVec { double *radius, *rmass; double **omega, **angmom; + double **quat_hold; + int nghost_bonus, nmax_bonus; int tri_flag; double rmass_one; diff --git a/src/domain.cpp b/src/domain.cpp index 810814a80f6..9c6e1a936c0 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -627,7 +627,7 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, if (bvec1[2] > 0.0) theta2 = -theta2; MathExtra::axisangle_to_quat(xaxis,theta2,quat2); - // quat = transformation via single quat = quat2 * quat1 + // quat_g2r = transformation via single quat = quat2 * quat1 // rotate_g2r = general to restricted transformation matrix // if dot < 0.0 (A x B not in C direction) // flip sign of z component of transform, @@ -635,9 +635,8 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, // rotate_r2g = restricted to general transformation matrix // simply a transpose of rotate_g2r since orthonormal - double quat[4]; - MathExtra::quatquat(quat2,quat1,quat); - MathExtra::quat_to_mat(quat,rotate_g2r); + MathExtra::quatquat(quat2,quat1,quat_g2r); + MathExtra::quat_to_mat(quat_g2r,rotate_g2r); if (dot < 0.0) { rotate_g2r[2][0] = -rotate_g2r[2][0]; @@ -670,10 +669,11 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, printf("Rotvec1: %g %g %g\n",rot1[0],rot1[1],rot1[2]); printf("Theta2: %g\n",theta2); printf("Rotvec2: %g %g %g\n",xaxis[0],xaxis[1],xaxis[2]); - printf("Quat: %g %g %g %g\n",quat[0],quat[1],quat[2],quat[3]); - double angle = 2.0*acos(quat[0]); + printf("Quat: %g %g %g %g\n",quat_g2r[0],quat_g2r[1],quat_g2r[2],quat_g2r[3]); + double angle = 2.0*acos(quat_g2r[0]); printf("Theta: %g\n",angle); - printf("Rotvec: %g %g %g\n",quat[1]/sin(0.5*angle),quat[2]/sin(0.5*angle),quat[3]/sin(0.5*angle)); + printf("Rotvec: %g %g %g\n",quat_g2r[1]/sin(0.5*angle),quat_g2r[2]/sin(0.5*angle), + quat_g2r[3]/sin(0.5*angle)); printf("Aprime: %g %g %g\n",aprime[0],aprime[1],aprime[2]); printf("Bprime: %g %g %g\n",bprime[0],bprime[1],bprime[2]); printf("Cprime: %g %g %g\n",cprime[0],cprime[1],cprime[2]); diff --git a/src/domain.h b/src/domain.h index 7b306a9426c..3e8b215d291 100644 --- a/src/domain.h +++ b/src/domain.h @@ -92,6 +92,7 @@ class Domain : protected Pointers { // boxlo = lower left corner double avec[3], bvec[3], cvec[3]; // ABC edge vectors of general triclinic box + double quat_g2r[4]; // quaternion for general --> restricted rotation double rotate_g2r[3][3]; // rotation matrix from general --> restricted tri double rotate_r2g[3][3]; // rotation matrix from restricted --> general tri From 30f73288417e5dc159b76ccf9c6a25d1a91851bb Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 14 Sep 2023 16:00:25 -0600 Subject: [PATCH 038/719] more dump custom fields rotated --- src/domain.cpp | 30 +++--- src/domain.h | 1 + src/dump_custom.cpp | 219 ++++++++++++++++++++++++++++++++++++++++---- src/dump_custom.h | 16 ++++ 4 files changed, 236 insertions(+), 30 deletions(-) diff --git a/src/domain.cpp b/src/domain.cpp index 9c6e1a936c0..e6ef232a6de 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -733,28 +733,34 @@ void Domain::restricted_to_general_coords(double *x, double *xnew) transform atom vector from general triclinic to restricted triclinic ------------------------------------------------------------------------- */ -void Domain::general_to_restricted_vector(double *x) +void Domain::general_to_restricted_vector(double *v) { - double xnew[3]; + double vnew[3]; - MathExtra::matvec(rotate_g2r,x,xnew); - x[0] = xnew[0]; - x[1] = xnew[1]; - x[2] = xnew[2]; + MathExtra::matvec(rotate_g2r,v,vnew); + v[0] = vnew[0]; + v[1] = vnew[1]; + v[2] = vnew[2]; } /* ---------------------------------------------------------------------- transform atom vector from restricted triclinic to general triclinic ------------------------------------------------------------------------- */ -void Domain::restricted_to_general_vector(double *x) +void Domain::restricted_to_general_vector(double *v) { - double xnew[3]; + double vnew[3]; - MathExtra::matvec(rotate_r2g,x,xnew); - x[0] = xnew[0]; - x[1] = xnew[1]; - x[2] = xnew[2]; + MathExtra::matvec(rotate_r2g,v,vnew); + v[0] = vnew[0]; + v[1] = vnew[1]; + v[2] = vnew[2]; +} + + +void Domain::restricted_to_general_vector(double *v, double *vnew) +{ + MathExtra::matvec(rotate_r2g,v,vnew); } /* ---------------------------------------------------------------------- diff --git a/src/domain.h b/src/domain.h index 3e8b215d291..7c5510d4c2a 100644 --- a/src/domain.h +++ b/src/domain.h @@ -148,6 +148,7 @@ class Domain : protected Pointers { void restricted_to_general_coords(double *, double *); void general_to_restricted_vector(double *); void restricted_to_general_vector(double *); + void restricted_to_general_vector(double *, double *x); void set_lattice(int, char **); void add_region(int, char **); diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index da9bbd013e6..2e478fd5e92 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -1445,20 +1445,24 @@ int DumpCustom::parse_fields(int narg, char **arg) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_q; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"mux") == 0) { if (!atom->mu_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_mux; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_mux_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_mux; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"muy") == 0) { if (!atom->mu_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_muy; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_muy_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_muy; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"muz") == 0) { if (!atom->mu_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_muz; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_muz_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_muz; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"mu") == 0) { if (!atom->mu_flag) @@ -1491,47 +1495,58 @@ int DumpCustom::parse_fields(int narg, char **arg) } else if (strcmp(arg[iarg],"omegax") == 0) { if (!atom->omega_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_omegax; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_omegax_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_omegax; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"omegay") == 0) { if (!atom->omega_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_omegay; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_omegay_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_omegay; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"omegaz") == 0) { if (!atom->omega_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_omegaz; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_omegaz_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_omegaz; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"angmomx") == 0) { if (!atom->angmom_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_angmomx; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_angmomx_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_angmomx; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"angmomy") == 0) { if (!atom->angmom_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_angmomy; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_angmomy_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_angmomy; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"angmomz") == 0) { if (!atom->angmom_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_angmomz; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_angmomz_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_angmomz; vtype[iarg] = Dump::DOUBLE; + } else if (strcmp(arg[iarg],"tqx") == 0) { if (!atom->torque_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_tqx; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_tqx_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_tqx; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"tqy") == 0) { if (!atom->torque_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_tqy; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_tqy_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_tqy; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"tqz") == 0) { if (!atom->torque_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); - pack_choice[iarg] = &DumpCustom::pack_tqz; + if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_tqz_triclinic_general; + else pack_choice[iarg] = &DumpCustom::pack_tqz; vtype[iarg] = Dump::DOUBLE; // compute or fix or variable or custom vector/array @@ -2888,7 +2903,7 @@ void DumpCustom::pack_vx_triclinic_general(int n) double vtri[3]; for (int i = 0; i < nchoose; i++) { - domain->restricted_to_general_coords(v[clist[i]],vtri); + domain->restricted_to_general_vector(v[clist[i]],vtri); buf[n] = vtri[0]; n += size_one; } @@ -2902,7 +2917,7 @@ void DumpCustom::pack_vy_triclinic_general(int n) double vtri[3]; for (int i = 0; i < nchoose; i++) { - domain->restricted_to_general_coords(v[clist[i]],vtri); + domain->restricted_to_general_vector(v[clist[i]],vtri); buf[n] = vtri[1]; n += size_one; } @@ -2916,7 +2931,7 @@ void DumpCustom::pack_vz_triclinic_general(int n) double vtri[3]; for (int i = 0; i < nchoose; i++) { - domain->restricted_to_general_coords(v[clist[i]],vtri); + domain->restricted_to_general_vector(v[clist[i]],vtri); buf[n] = vtri[2]; n += size_one; } @@ -2966,7 +2981,7 @@ void DumpCustom::pack_fx_triclinic_general(int n) double ftri[3]; for (int i = 0; i < nchoose; i++) { - domain->restricted_to_general_coords(f[clist[i]],ftri); + domain->restricted_to_general_vector(f[clist[i]],ftri); buf[n] = ftri[0]; n += size_one; } @@ -2980,7 +2995,7 @@ void DumpCustom::pack_fy_triclinic_general(int n) double ftri[3]; for (int i = 0; i < nchoose; i++) { - domain->restricted_to_general_coords(f[clist[i]],ftri); + domain->restricted_to_general_vector(f[clist[i]],ftri); buf[n] = ftri[1]; n += size_one; } @@ -2994,7 +3009,7 @@ void DumpCustom::pack_fz_triclinic_general(int n) double ftri[3]; for (int i = 0; i < nchoose; i++) { - domain->restricted_to_general_coords(f[clist[i]],ftri); + domain->restricted_to_general_vector(f[clist[i]],ftri); buf[n] = ftri[2]; n += size_one; } @@ -3062,6 +3077,48 @@ void DumpCustom::pack_mu(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_mux_triclinic_general(int n) +{ + double **mu = atom->mu; + double mutri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(mu[clist[i]],mutri); + buf[n] = mutri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_muy_triclinic_general(int n) +{ + double **mu = atom->mu; + double mutri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(mu[clist[i]],mutri); + buf[n] = mutri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_muz_triclinic_general(int n) +{ + double **mu = atom->mu; + double mutri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(mu[clist[i]],mutri); + buf[n] = mutri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_radius(int n) { double *radius = atom->radius; @@ -3146,6 +3203,48 @@ void DumpCustom::pack_omegaz(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_omegax_triclinic_general(int n) +{ + double **omega = atom->omega; + double omegatri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(omega[clist[i]],omegatri); + buf[n] = omegatri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_omegay_triclinic_general(int n) +{ + double **omega = atom->omega; + double omegatri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(omega[clist[i]],omegatri); + buf[n] = omegatri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_omegaz_triclinic_general(int n) +{ + double **omega = atom->omega; + double omegatri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(omega[clist[i]],omegatri); + buf[n] = omegatri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_angmomx(int n) { double **angmom = atom->angmom; @@ -3182,6 +3281,48 @@ void DumpCustom::pack_angmomz(int n) /* ---------------------------------------------------------------------- */ +void DumpCustom::pack_angmomx_triclinic_general(int n) +{ + double **angmom = atom->angmom; + double angmomtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(angmom[clist[i]],angmomtri); + buf[n] = angmomtri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_angmomy_triclinic_general(int n) +{ + double **angmom = atom->angmom; + double angmomtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(angmom[clist[i]],angmomtri); + buf[n] = angmomtri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_angmomz_triclinic_general(int n) +{ + double **angmom = atom->angmom; + double angmomtri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(angmom[clist[i]],angmomtri); + buf[n] = angmomtri[2]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + void DumpCustom::pack_tqx(int n) { double **torque = atom->torque; @@ -3215,3 +3356,45 @@ void DumpCustom::pack_tqz(int n) n += size_one; } } + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_tqx_triclinic_general(int n) +{ + double **torque = atom->torque; + double torquetri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(torque[clist[i]],torquetri); + buf[n] = torquetri[0]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_tqy_triclinic_general(int n) +{ + double **torque = atom->torque; + double torquetri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(torque[clist[i]],torquetri); + buf[n] = torquetri[1]; + n += size_one; + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustom::pack_tqz_triclinic_general(int n) +{ + double **torque = atom->torque; + double torquetri[3]; + + for (int i = 0; i < nchoose; i++) { + domain->restricted_to_general_vector(torque[clist[i]],torquetri); + buf[n] = torquetri[2]; + n += size_one; + } +} diff --git a/src/dump_custom.h b/src/dump_custom.h index b1ef2c64007..60070ddf629 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -204,10 +204,15 @@ class DumpCustom : public Dump { void pack_fz_triclinic_general(int); void pack_q(int); + void pack_mux(int); void pack_muy(int); void pack_muz(int); void pack_mu(int); + void pack_mux_triclinic_general(int); + void pack_muy_triclinic_general(int); + void pack_muz_triclinic_general(int); + void pack_radius(int); void pack_diameter(int); @@ -217,12 +222,23 @@ class DumpCustom : public Dump { void pack_omegax(int); void pack_omegay(int); void pack_omegaz(int); + void pack_omegax_triclinic_general(int); + void pack_omegay_triclinic_general(int); + void pack_omegaz_triclinic_general(int); + void pack_angmomx(int); void pack_angmomy(int); void pack_angmomz(int); + void pack_angmomx_triclinic_general(int); + void pack_angmomy_triclinic_general(int); + void pack_angmomz_triclinic_general(int); + void pack_tqx(int); void pack_tqy(int); void pack_tqz(int); + void pack_tqx_triclinic_general(int); + void pack_tqy_triclinic_general(int); + void pack_tqz_triclinic_general(int); }; } // namespace LAMMPS_NS From c5b2d662833a80a5bf2fb8b8294292313872f475 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 15 Sep 2023 16:49:56 -0600 Subject: [PATCH 039/719] upgrades to read/write data commands --- src/atom_vec_body.cpp | 6 +++--- src/atom_vec_ellipsoid.cpp | 6 +++--- src/atom_vec_tri.cpp | 4 ++-- src/domain.cpp | 24 +++++++++++++++--------- src/domain.h | 5 +++-- src/dump_atom.cpp | 5 +++-- src/lmprestart.h | 2 +- src/read_restart.cpp | 24 ++++++++++++++++++++---- src/write_restart.cpp | 4 ++-- 9 files changed, 52 insertions(+), 28 deletions(-) diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 7721e1540b7..898b0657495 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -586,11 +586,11 @@ void AtomVecBody::write_data_restricted_to_general() { AtomVec::write_data_restricted_to_general(); - double quat[4],quat_r2g[4]; + double quat[4]; double *bquat; - + double *quat_r2g = domain->quat_r2g; + memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); - MathExtra::qconjugate(domain->quat_g2r,quat_r2g); for (int i = 0; i < nlocal_bonus; i++) { bquat = bonus[i].quat; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index ceb813cbe2f..d51f7af78ff 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -495,11 +495,11 @@ void AtomVecEllipsoid::write_data_restricted_to_general() { AtomVec::write_data_restricted_to_general(); - double quat[4],quat_r2g[4]; + double quat[4]; double *bquat; - + double *quat_r2g = domain->quat_r2g; + memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); - MathExtra::qconjugate(domain->quat_g2r,quat_r2g); for (int i = 0; i < nlocal_bonus; i++) { bquat = bonus[i].quat; diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 7dfb50093bb..f83a282c356 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -694,11 +694,11 @@ void AtomVecTri::write_data_restricted_to_general() { AtomVec::write_data_restricted_to_general(); - double quat[4],quat_r2g[4]; + double quat[4]; double *bquat; + double *quat_r2g = domain->quat_r2g; memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); - MathExtra::qconjugate(domain->quat_g2r,quat_r2g); for (int i = 0; i < nlocal_bonus; i++) { bquat = bonus[i].quat; diff --git a/src/domain.cpp b/src/domain.cpp index e6ef232a6de..68eafab356e 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -580,13 +580,18 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, error->all(FLERR,"General triclinic box edge vector C invalid for 2d system"); // error check for co-planar A,B,C + // if A x B is in C direction, only a rotation to restricted tri is needed + // since restricted tri box will obey right-hand rule + // if not, an inversion (flip) of C vector is also needed double abcross[3]; MathExtra::cross3(avec,bvec,abcross); double dot = MathExtra::dot3(abcross,cvec); if (dot == 0.0) error->all(FLERR,"General triclinic box edge vectors are co-planar"); - + if (dot > 0.0) triclinic_general_flip = 0; + else triclinic_general_flip = 1; + // quat1 = convert A into A' along +x-axis // rot1 = unit vector to rotate A around // theta1 = angle of rotation calculated from @@ -627,18 +632,19 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, if (bvec1[2] > 0.0) theta2 = -theta2; MathExtra::axisangle_to_quat(xaxis,theta2,quat2); - // quat_g2r = transformation via single quat = quat2 * quat1 - // rotate_g2r = general to restricted transformation matrix - // if dot < 0.0 (A x B not in C direction) - // flip sign of z component of transform, - // by flipping sign of 3rd row of rotate_g2r matrix - // rotate_r2g = restricted to general transformation matrix + // quat_g2r = rotation via single quat = quat2 * quat1 + // quat_r2g = rotation from restricted to general + // rotate_g2r = general to restricted rotation matrix + // include flip of C vector if needed to obey right-hand rule + // rotate_r2g = restricted to general rotation matrix // simply a transpose of rotate_g2r since orthonormal MathExtra::quatquat(quat2,quat1,quat_g2r); + MathExtra::qconjugate(quat_g2r,quat_r2g); + MathExtra::quat_to_mat(quat_g2r,rotate_g2r); - if (dot < 0.0) { + if (triclinic_general_flip) { rotate_g2r[2][0] = -rotate_g2r[2][0]; rotate_g2r[2][1] = -rotate_g2r[2][1]; rotate_g2r[2][2] = -rotate_g2r[2][2]; @@ -646,7 +652,7 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, MathExtra::transpose3(rotate_g2r,rotate_r2g); - // transform general ABC to restricted triclinic A'B'C' + // rotate general ABC to restricted triclinic A'B'C' double aprime[3],bprime[3],cprime[3]; MathExtra::matvec(rotate_g2r,avec,aprime); diff --git a/src/domain.h b/src/domain.h index 7c5510d4c2a..61a88724e7f 100644 --- a/src/domain.h +++ b/src/domain.h @@ -41,6 +41,7 @@ class Domain : protected Pointers { int triclinic; // 0 = orthog box, 1 = triclinic (restricted or general) int triclinic_general; // 1 if mapping to/from general triclinic is stored, 0 if not + int triclinic_general_flip; // 1 if general tri rotation needs to invert C edge vector // orthogonal box @@ -90,9 +91,9 @@ class Domain : protected Pointers { // general triclinic box // boxlo = lower left corner - + double avec[3], bvec[3], cvec[3]; // ABC edge vectors of general triclinic box - double quat_g2r[4]; // quaternion for general --> restricted rotation + double quat_g2r[4], quat_r2g[4]; // quaternions for general <--> restricted rotations double rotate_g2r[3][3]; // rotation matrix from general --> restricted tri double rotate_r2g[3][3]; // rotation matrix from restricted --> general tri diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index dd46452d9ee..151446bdfd5 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -334,13 +334,14 @@ void DumpAtom::header_binary_triclinic_general(bigint ndump) fwrite(&update->ntimestep,sizeof(bigint),1,fp); fwrite(&ndump,sizeof(bigint),1,fp); - int general_tri = 2; - fwrite(&general_tri,sizeof(int),1,fp); + int triclinic_general_flag = 2; + fwrite(&triclinic_general_flag,sizeof(int),1,fp); fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); fwrite(domain->avec,3*sizeof(double),1,fp); fwrite(domain->bvec,3*sizeof(double),1,fp); fwrite(domain->cvec,3*sizeof(double),1,fp); fwrite(domain->boxlo,3*sizeof(double),1,fp); + fwrite(&size_one,sizeof(int),1,fp); header_unit_style_binary(); header_time_binary(); diff --git a/src/lmprestart.h b/src/lmprestart.h index 2ed1d7db11f..43ef5766ac1 100644 --- a/src/lmprestart.h +++ b/src/lmprestart.h @@ -38,7 +38,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL, NELLIPSOIDS,NLINES,NTRIS,NBODIES,ATIME,ATIMESTEP,LABELMAP, - TRICLINIC_GENERAL,ROTATE_G2R,ROTATE_R2G}; + TRICLINIC_GENERAL,TRICLINIC_GENERAL_FLIP,QUAT_G2R}; #define LB_FACTOR 1.1 diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 372d1bcfe89..ca5eb25762f 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -28,6 +28,7 @@ #include "improper.h" #include "irregular.h" #include "label_map.h" +#include "math_extra.h" #include "memory.h" #include "modify.h" #include "pair.h" @@ -136,6 +137,21 @@ void ReadRestart::command(int narg, char **arg) atom->avec->grow(n); n = atom->nmax; + // setup simulation box + // for general triclinic, need to generate additional info which + // Domain::define_general_triclinic() would have created + + if (domain->triclinic_general) { + MathExtra::qconjugate(domain->quat_g2r,domain->quat_r2g); + MathExtra::quat_to_mat(domain->quat_g2r,domain->rotate_g2r); + if (domain->triclinic_general_flip) { + domain->rotate_g2r[2][0] = -domain->rotate_g2r[2][0]; + domain->rotate_g2r[2][1] = -domain->rotate_g2r[2][1]; + domain->rotate_g2r[2][2] = -domain->rotate_g2r[2][2]; + } + MathExtra::transpose3(domain->rotate_g2r,domain->rotate_r2g); + } + domain->print_box(" "); domain->set_initial_box(0); domain->set_global_box(); @@ -785,10 +801,10 @@ void ReadRestart::header() } else if (flag == TRICLINIC_GENERAL) { domain->triclinic_general = read_int(); - } else if (flag == ROTATE_G2R) { - read_double_vec(9,&domain->rotate_g2r[0][0]); - } else if (flag == ROTATE_R2G) { - read_double_vec(9,&domain->rotate_r2g[0][0]); + } else if (flag == TRICLINIC_GENERAL_FLIP) { + domain->triclinic_general_flip = read_int(); + } else if (flag == QUAT_G2R) { + read_double_vec(4,domain->quat_g2r); } else if (flag == SPECIAL_LJ) { read_int(); diff --git a/src/write_restart.cpp b/src/write_restart.cpp index fb5b41eb02d..16a59ebc208 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -450,8 +450,8 @@ void WriteRestart::header() write_int(TRICLINIC_GENERAL,domain->triclinic_general); if (domain->triclinic_general) { - write_double_vec(ROTATE_G2R,9,&domain->rotate_g2r[0][0]); - write_double_vec(ROTATE_R2G,9,&domain->rotate_r2g[0][0]); + write_int(TRICLINIC_GENERAL_FLIP,domain->triclinic_general_flip); + write_double_vec(QUAT_G2R,4,domain->quat_g2r); } write_double_vec(SPECIAL_LJ,3,&force->special_lj[1]); From 21d3f3240e6e17c532f8f6bba5bcadf396c49630 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Sat, 16 Sep 2023 10:09:26 -0600 Subject: [PATCH 040/719] more work on restart support --- src/atom.cpp | 2 +- src/atom_vec_line.cpp | 66 ++++++++++++++--------- src/atom_vec_line.h | 1 - src/atom_vec_tri.cpp | 121 +++++++++++------------------------------- src/atom_vec_tri.h | 3 -- src/lmprestart.h | 2 +- src/read_restart.cpp | 20 ++----- src/write_restart.cpp | 2 +- 8 files changed, 78 insertions(+), 139 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index 7f472e44f4b..c7c13013c81 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1190,7 +1190,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, xdata[2] = 0.0; } - // convert atom coords from general triclinic to restricted triclinic + // convert atom coords from general to restricted triclinic // so can decide which proc owns the atom if (triclinic_general) domain->general_to_restricted_coords(xdata); diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index 95ccfe31bd1..73f2e702f6a 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -352,6 +352,22 @@ void AtomVecLine::data_atom_bonus(int m, const std::vector &values) double y1 = utils::numeric(FLERR, values[ivalue++], true, lmp); double x2 = utils::numeric(FLERR, values[ivalue++], true, lmp); double y2 = utils::numeric(FLERR, values[ivalue++], true, lmp); + + // convert x1/y1 and x2/y2 from general to restricted triclniic + // x is already restricted triclinic + + if (domain->triclinic_general) { + double coords[3]; + coords[0] = x1; coords[1] = y1; coords[2] = 0.0; + domain->general_to_restricted_coords(coords); + x1 = coords[0]; y1 = coords[1]; + coords[0] = x2; coords[1] = y2; coords[2] = 0.0; + domain->general_to_restricted_coords(coords); + x2 = coords[0]; y2 = coords[1]; + } + + // calculate length and theta + double dx = x2 - x1; double dy = y2 - y1; double length = sqrt(dx * dx + dy * dy); @@ -437,29 +453,6 @@ void AtomVecLine::data_atom_post(int ilocal) omega[ilocal][2] = 0.0; } -/* ---------------------------------------------------------------------- - convert read_data file info from general to restricted triclinic - parent class operates on data from Velocities section of data file - child class operates on bonus theta -------------------------------------------------------------------------- */ - -void AtomVecLine::read_data_general_to_restricted(int nlocal_previous, int nlocal) -{ - AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); - - double btheta; - double theta_g2r = 2.0*acos(domain->quat_g2r[0]); - - for (int i = nlocal_previous; i < nlocal; i++) { - if (line[i] < 0) continue; - btheta = bonus[line[i]].theta; - btheta += theta_g2r; - if (btheta > MathConst::MY_PI) btheta -= MathConst::MY_2PI; - else if (btheta <= -MathConst::MY_PI) btheta += MathConst::MY_2PI; - bonus[line[i]].theta = btheta; - } -} - /* ---------------------------------------------------------------------- modify values for AtomVec::pack_data() to pack ------------------------------------------------------------------------- */ @@ -501,8 +494,14 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/) int i, j; double length, theta; double xc, yc, x1, x2, y1, y2; + double coords[3]; + + int triclinic_general = domain->triclinic_general; + + double **x_bonus; + if (triclinic_general) x_bonus = x_hold; + else x_bonus = x; - double **x = atom->x; tagint *tag = atom->tag; int nlocal = atom->nlocal; @@ -514,8 +513,9 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/) j = line[i]; length = bonus[j].length; theta = bonus[j].theta; - xc = x[i][0]; - yc = x[i][1]; + + xc = x_bonus[i][0]; + yc = x_bonus[i][1]; x1 = xc - 0.5 * cos(theta) * length; y1 = yc - 0.5 * sin(theta) * length; x2 = xc + 0.5 * cos(theta) * length; @@ -524,6 +524,20 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/) buf[m++] = y1; buf[m++] = x2; buf[m++] = y2; + + // if triclinic_general: + // rotate 4 buf values from restricted to general triclinic + // output by write_data_bonus() as x1/y1 and x2/y2 + + if (triclinic_general) { + coords[0] = buf[m-4]; coords[1] = buf[m-3]; coords[2] = 0.0; + domain->restricted_to_general_coords(coords); + buf[m-4] = coords[0]; buf[m-3] = coords[1]; + coords[0] = buf[m-2]; coords[1] = buf[m-1]; coords[2] = 0.0; + domain->restricted_to_general_coords(coords); + buf[m-2] = coords[0]; buf[m-1] = coords[1]; + } + } else m += size_data_bonus; } diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h index 2503f55d8d6..740c541916f 100644 --- a/src/atom_vec_line.h +++ b/src/atom_vec_line.h @@ -53,7 +53,6 @@ class AtomVecLine : public AtomVec { void create_atom_post(int) override; void data_atom_post(int) override; - void read_data_general_to_restricted(int, int); void pack_data_pre(int) override; void pack_data_post(int) override; diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index f83a282c356..b0849e67175 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -510,8 +510,18 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector &values) MathExtra::sub3(c3, c1, c3mc1); double size = MAX(MathExtra::len3(c2mc1), MathExtra::len3(c3mc1)); + // convert c1,c2,c3 from general to restricted triclniic + // x is already restricted triclinic + + if (domain->triclinic_general) { + domain->general_to_restricted_coords(c1); + domain->general_to_restricted_coords(c2); + domain->general_to_restricted_coords(c3); + } + // centroid = 1/3 of sum of vertices - + // error if centroid is not within EPSILON of Atoms section coord + double centroid[3]; centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0; centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0; @@ -659,90 +669,6 @@ void AtomVecTri::data_atom_post(int ilocal) angmom[ilocal][2] = 0.0; } -/* ---------------------------------------------------------------------- - convert read_data file info from general to restricted triclinic - parent class operates on data from Velocities section of data file - child class operates on bonus quat -------------------------------------------------------------------------- */ - -void AtomVecTri::read_data_general_to_restricted(int nlocal_previous, int nlocal) -{ - AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); - - double quat[4]; - double *bquat; - - for (int i = nlocal_previous; i < nlocal; i++) { - if (tri[i] < 0) continue; - bquat = bonus[tri[i]].quat; - MathExtra::quatquat(domain->quat_g2r,bquat,quat); - bquat[0] = quat[0]; - bquat[1] = quat[1]; - bquat[2] = quat[2]; - bquat[3] = quat[3]; - MathExtra::qnormalize(bquat); - } -} - -/* ---------------------------------------------------------------------- - convert info output by write_data from restricted to general triclinic - parent class operates on x and data from Velocities section of data file - child class operates on bonus quat -------------------------------------------------------------------------- */ - -void AtomVecTri::write_data_restricted_to_general() -{ - AtomVec::write_data_restricted_to_general(); - - double quat[4]; - double *bquat; - double *quat_r2g = domain->quat_r2g; - - memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); - - for (int i = 0; i < nlocal_bonus; i++) { - bquat = bonus[i].quat; - quat_hold[i][0] = bquat[0]; - quat_hold[i][1] = bquat[1]; - quat_hold[i][2] = bquat[2]; - quat_hold[i][3] = bquat[3]; - - MathExtra::quatquat(quat_r2g,bquat,quat); - bquat[0] = quat[0]; - bquat[1] = quat[1]; - bquat[2] = quat[2]; - bquat[3] = quat[3]; - MathExtra::qnormalize(bquat); - } -} - -/* ---------------------------------------------------------------------- - restore info output by write_data to restricted triclinic - original data is in "hold" arrays - parent class operates on x and data from Velocities section of data file - child class operates on bonus quat -------------------------------------------------------------------------- */ - -void AtomVecTri::write_data_restore_restricted() -{ - AtomVec::write_data_restore_restricted(); - - if (!quat_hold) return; - - double *bquat; - - for (int i = 0; i < nlocal_bonus; i++) { - bquat = bonus[i].quat; - bquat[0] = quat_hold[i][0]; - bquat[1] = quat_hold[i][1]; - bquat[2] = quat_hold[i][2]; - bquat[3] = quat_hold[i][3]; - } - - memory->destroy(quat_hold); - quat_hold = nullptr; -} - /* ---------------------------------------------------------------------- modify values for AtomVec::pack_data() to pack ------------------------------------------------------------------------- */ @@ -792,7 +718,12 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/) double dc1[3], dc2[3], dc3[3]; double p[3][3]; - double **x = atom->x; + int triclinic_general = domain->triclinic_general; + + double **x_bonus; + if (triclinic_general) x_bonus = x_hold; + else x_bonus = x; + tagint *tag = atom->tag; int nlocal = atom->nlocal; @@ -806,9 +737,10 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/) MathExtra::matvec(p, bonus[j].c1, dc1); MathExtra::matvec(p, bonus[j].c2, dc2); MathExtra::matvec(p, bonus[j].c3, dc3); - xc = x[i][0]; - yc = x[i][1]; - zc = x[i][2]; + + xc = x_bonus[i][0]; + yc = x_bonus[i][1]; + zc = x_bonus[i][2]; buf[m++] = xc + dc1[0]; buf[m++] = yc + dc1[1]; buf[m++] = zc + dc1[2]; @@ -818,6 +750,17 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/) buf[m++] = xc + dc3[0]; buf[m++] = yc + dc3[1]; buf[m++] = zc + dc3[2]; + + // if triclinic_general: + // rotate 9 buf values from restricted to general triclinic + // output by write_data_bonus() as c1,c2,c3 + + if (triclinic_general) { + domain->restricted_to_general_coords(&buf[m-9]); + domain->restricted_to_general_coords(&buf[m-6]); + domain->restricted_to_general_coords(&buf[m-3]); + } + } else m += size_data_bonus; } diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h index 91a7a20e6dd..5a3b831c0da 100644 --- a/src/atom_vec_tri.h +++ b/src/atom_vec_tri.h @@ -55,9 +55,6 @@ class AtomVecTri : public AtomVec { void create_atom_post(int) override; void data_atom_post(int) override; - void read_data_general_to_restricted(int, int); - void write_data_restricted_to_general(); - void write_data_restore_restricted(); void pack_data_pre(int) override; void pack_data_post(int) override; diff --git a/src/lmprestart.h b/src/lmprestart.h index 43ef5766ac1..73eb5e618e1 100644 --- a/src/lmprestart.h +++ b/src/lmprestart.h @@ -38,7 +38,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL, NELLIPSOIDS,NLINES,NTRIS,NBODIES,ATIME,ATIMESTEP,LABELMAP, - TRICLINIC_GENERAL,TRICLINIC_GENERAL_FLIP,QUAT_G2R}; + TRICLINIC_GENERAL,TRICLINIC_GENERAL_FLIP,ROTATE_G2R}; #define LB_FACTOR 1.1 diff --git a/src/read_restart.cpp b/src/read_restart.cpp index ca5eb25762f..2224b9eeacb 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -137,21 +137,6 @@ void ReadRestart::command(int narg, char **arg) atom->avec->grow(n); n = atom->nmax; - // setup simulation box - // for general triclinic, need to generate additional info which - // Domain::define_general_triclinic() would have created - - if (domain->triclinic_general) { - MathExtra::qconjugate(domain->quat_g2r,domain->quat_r2g); - MathExtra::quat_to_mat(domain->quat_g2r,domain->rotate_g2r); - if (domain->triclinic_general_flip) { - domain->rotate_g2r[2][0] = -domain->rotate_g2r[2][0]; - domain->rotate_g2r[2][1] = -domain->rotate_g2r[2][1]; - domain->rotate_g2r[2][2] = -domain->rotate_g2r[2][2]; - } - MathExtra::transpose3(domain->rotate_g2r,domain->rotate_r2g); - } - domain->print_box(" "); domain->set_initial_box(0); domain->set_global_box(); @@ -803,8 +788,9 @@ void ReadRestart::header() domain->triclinic_general = read_int(); } else if (flag == TRICLINIC_GENERAL_FLIP) { domain->triclinic_general_flip = read_int(); - } else if (flag == QUAT_G2R) { - read_double_vec(4,domain->quat_g2r); + } else if (flag == ROTATE_G2R) { + read_double_vec(9,&domain->rotate_g2r[0][0]); + MathExtra::transpose3(domain->rotate_g2r,domain->rotate_r2g); } else if (flag == SPECIAL_LJ) { read_int(); diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 16a59ebc208..e265ceadc1e 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -451,7 +451,7 @@ void WriteRestart::header() write_int(TRICLINIC_GENERAL,domain->triclinic_general); if (domain->triclinic_general) { write_int(TRICLINIC_GENERAL_FLIP,domain->triclinic_general_flip); - write_double_vec(QUAT_G2R,4,domain->quat_g2r); + write_double_vec(ROTATE_G2R,9,&domain->rotate_g2r[0][0]); } write_double_vec(SPECIAL_LJ,3,&force->special_lj[1]); From 77a5fd16dd5309d1955aae573ed41d66bc0caede Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 19 Sep 2023 13:37:47 +0200 Subject: [PATCH 041/719] Fixing bug in link pressure --- src/fix_deform.cpp | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 79f9b3a5ba2..139f1e08352 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -1302,6 +1302,7 @@ void FixDeform::set_volume() double p2 = pressure->vector[fixed]; double p1i = set[i].prior_pressure; double p2i = set[fixed].prior_pressure; + double denominator; if (e3 == 0) { e1 = 0.0; @@ -1314,7 +1315,12 @@ void FixDeform::set_volume() if (!linked_pressure) { // Calculate first strain rate by expanding stress to linear order, p1(t+dt) = p2(t+dt) // Calculate second strain rate to preserve volume - e1 = -e3 / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2) / (p2 - p2i + (p1 - p1i) / e1i * e2i); + denominator = (p2 - p2i + (p1 - p1i) / e1i * e2i); + if (denominator != 0.0 && e1i != 0.0) { + e1 = (-e3 / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2)) / denominator; + } else { + e1 = e2i; + } e2 = (1.0 - (1 + e3 * dt) * (1 + e1 * dt)) / ((1 + e3 * dt) * (1 + e1 * dt) * dt); shift = 0.5 * L1i * (1.0 + e1 * dt); From 94a0d85b33007838bc0170c37a56ecff5a684dc4 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 20 Sep 2023 15:20:02 -0600 Subject: [PATCH 042/719] doc page updates --- doc/src/Howto_2d.rst | 53 +++++----- doc/src/Howto_triclinic.rst | 199 ++++++++++++++++++++++-------------- doc/src/boundary.rst | 54 ++++++---- doc/src/read_data.rst | 145 ++++++++++++++++++-------- 4 files changed, 287 insertions(+), 164 deletions(-) diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index ae58711063a..06e6d57be8b 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -1,42 +1,49 @@ 2d simulations ============== -Use the :doc:`dimension ` command to specify a 2d simulation. +You must use the :doc:`dimension ` command to specify a 2d +simulation. The default is 3d. Make the simulation box periodic in z via the :doc:`boundary ` command. This is the default. -If using the :doc:`create_box ` command to define a -simulation box, set the z dimensions narrow, but finite, so that the -:doc:`create_atoms ` command will fill the 3d simulation -box with a single z plane of atoms - e.g. +If using the :doc:`create_box ` command, you must define a +simulation box which straddes z = 0.0 in the z dimension since all the +atoms will have a z coordinate of zero. Typicaily the width of box in +the z dimension should be narrow, e.g. -0.5 to 0.5, but that is not +required. An example is: .. code-block:: LAMMPS - create_box 1 -10 10 -10 10 -0.25 0.25 + create_box 1 -10 10 0 10 -0.25 0.25 -If using the :doc:`read_data ` command to read in a file of -atom coordinates, set the "zlo zhi" values to be finite but narrow, -similar to the create_box command settings just described. For each -atom in the file, assign a z coordinate so it falls inside the -z-boundaries of the box - e.g. 0.0. +Likewise, If using the :doc:`read_data ` command to define +the simulation box and read in a file of atom coordinates, the default +"zlo zhi" values are -0.5 0.5 for 2d simulations. If the data file +includes that header keyword the zlo/zhi values must straddle z = 0.0. +The z coords for atoms listed in the file must be 0.0 (within epsilon +of zero is also allowed in case the data file was generated by another +program with finite precision). -Use the :doc:`fix enforce2d ` command as the last -defined fix to ensure that the z-components of velocities and forces -are zeroed out every timestep. The reason to make it the last fix is -so that any forces induced by other fixes will be zeroed out. +Use the :doc:`fix enforce2d ` command as the last fix +defined in the input script. It ensures that the z-components of +velocities and forces are zeroed out every timestep. The reason to +make it the last fix is so that any forces added by other fixes will +also be zeroed out. -Many of the example input scripts included in the LAMMPS distribution +Many of the example input scripts included in the examples directory are for 2d models. .. note:: Some models in LAMMPS treat particles as finite-size spheres, as - opposed to point particles. See the :doc:`atom_style sphere ` and :doc:`fix nve/sphere ` - commands for details. By default, for 2d simulations, such particles - will still be modeled as 3d spheres, not 2d discs (circles), meaning + opposed to point particles. See the :doc:`atom_style sphere + ` and :doc:`fix nve/sphere ` commands + for details. By default, for 2d simulations, such particles will + still be modeled as 3d spheres, not 2d discs (circles), meaning their moment of inertia will be that of a sphere. If you wish to - model them as 2d discs, see the :doc:`set density/disc ` command - and the *disc* option for the :doc:`fix nve/sphere `, - :doc:`fix nvt/sphere `, :doc:`fix nph/sphere `, :doc:`fix npt/sphere ` - commands. + model them as 2d discs, see the :doc:`set density/disc ` + command and the *disc* option for the :doc:`fix nve/sphere + `, :doc:`fix nvt/sphere `, + :doc:`fix nph/sphere `, :doc:`fix npt/sphere + ` commands. diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 9780ec8c63d..c84f4243567 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -28,8 +28,10 @@ Triclinic simulation boxes """""""""""""""""""""""""" LAMMPS also allows simulations to be performed using triclinic -(non-orthogonal) simulation boxes shaped as a parallelepiped with -triclinic symmetry. +(non-orthogonal) simulation boxes shaped as a 3d parallelepiped with +triclinic symmetry. For 2d simulations a triclinic simulation box is +effectively a parallelogram; see the :doc:'Howto 2d ` doc +page for details. One use of triclinic simulation boxes is to model solid-state crystals with triclinic symmetry. The :doc:`lattice ` command can be @@ -52,9 +54,7 @@ on non-equilibrium MD (NEMD) simulations. Conceptually, a triclinic parallelepiped is defined with an "origin" at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), **C** = (cx,cy,cz) which can now be arbitrary vectors, so -long as they are non-zero, distinct, and not co-planar. There is no -"right-hand rule" requirement that (**A** x **B**) point in the -direction of **C**. +long as they are non-zero, distinct, and not co-planar. The 4 commands listed above for defining orthogonal simulation boxes have triclinic options which allow for specification of the origin and @@ -62,56 +62,52 @@ edge vectors **A**, **B**, **C**. For each command, this can be done in one of two ways, for what LAMMPS calls a *general* triclinic box or a *restricted* triclinic box. -A *general* triclinic box is specified by an origin and 9 parameters -(ax,ay,az), (bx,by,bz), (cx,cy,cz), or 12 parameters in total. A -*restricted* triclinic box also has an origin, but its edge vectors -are of the following form: **A** = (xhi-xlo,0,0), **B** = -(xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So 9 parameters in total. - -The restricted form of edge vectors requires that **A** is along the -x-axis, **B** is in the xy plane with a y-component in the +y -direction, and **C** has a z-component in the +z direction. -*Xy,xz,yz* can be zero or positive or negative values and are called -"tilt factors" because they are the amount of displacement applied to -faces of an originally orthogonal box to transform it into a -restricted triclinic parallelepiped. +A *general* triclinic box is specified by an origin (xlo, ylo, zlo) +and arbitrary edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), and +**C** = (cx,cy,cz). So there are 12 parameters in total. Note that a +general triclinic box can either be *right-handed* if (**A** x **B**) +points in the direction of **C**, or it can be *left-handed* if (**A** +x **B**) points opposite to **C**. + +A *restricted* triclinic box also has an origin (xlo,ylo,zlo), but its +edge vectors are of the following form: **A** = (xhi-xlo,0,0), **B** = +(xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So there are 9 parameters in +total. The restricted form of edge vectors requires that **A** is +along the x-axis, **B** is in the xy plane with a y-component in +the +y direction, and **C** has a z-component in the +z direction. +Note that a restricted triclinic box is always *right-handed* so +that (**A** x **B**) points in the direction of **C**. + +The *xy,xz,yz* values can be zero or positive or negative. They are +called "tilt factors" because they are the amount of displacement +applied to edges of faces of an originally orthogonal box to change it +into a restricted triclinic parallelepiped. .. note:: Any general triclinic box (i.e. solid-state crystal basis vectors) - can be rotated/inverted in 3d around its origin to conform to the - LAMMPS definition of a restricted triclinic box. An inversion may - need to be applied to the rotated **C** vector to ensure its final - z-component is in the +z direction. See the discussion in the next + can be rotated in 3d around its origin (and reflected across a + plane if necessary to flip from a left-handed coordinate system to + right-handed) in order to conform to the LAMMPS definition of a + restricted triclinic box. See the discussion in the next sub-section about general triclinic simulation boxes in LAMMPS. - -Note that for 2d simulations a triclinic simulation box is effectively -a parallelogram; see the :doc:'Howto 2d ` doc page for -details. - -The :doc:`boundary ` command sets the boundary conditions -for the 6 faces of a restricted triclinix box (periodic, non-periodic, -etc), similar to the way the settings apply to the 6 faces of an -orthogonal box. Note that if a restricted triclinic box is periodic -in the y-dimension and has a non-zero xy tilt factor, then particles -which exit the -y face of the box will re-enter the +y face but will -be displaced in x by the xy tilt factor. Similarly for z-periodicity, -if the xz and/or yz tilt factors are non-zero, then particles which -exit the -z face of the box will be displaced in x by the xz tilt -factor and in y by the yz tilt factor. - -The :doc:`thermo_style custom ` command has keywords for -outputting the parameters that define restricted and general triclinic -simulation boxes. For restricted triclinic, this is (xlo,ylo,zlo), -(xhi,yhi,zhi), and the xy,xz,yz tilt factors. For general triclinic, -this is the (xlo,ylo,zhi) origin and the 9 components of the **A**, -**B**, **C** edge vectors. For both orthogonal and restricted -triclinic boxes, lx/ly/lz refer to the same box sizes, namely lx = -xhi - xlo, etc. + +Note that the :doc:`thermo_style custom ` command has +keywords for outputting the various parameters that define both +restricted and general triclinic simulation boxes. Thus you can check +the restricted triclinic box parameters LAMMPS generates to +rotate/reflect a general triclinic box to restricted triclinic form. + +For restricted triclinic boxes there are 9 thermo keywords for +(xlo,ylo,zlo), (xhi,yhi,zhi), and the (xy,xz,yz) tilt factors. For +general triclinic boxes there are 12 thermo keywords for (xlo,ylo,zhi) +and the components of the **A**, **B**, **C** edge vectors. For both +orthogonal and restricted triclinic boxes, the thermo keywords +lx/ly/lz refer to the box sizes, namely lx = xhi - xlo, etc. The remainder of this doc page explains (a) how LAMMPS operates with general triclinic simulation boxes, (b) mathematical transformations -between general and restricted triclinic boxes (which may be useful +between general and restricted triclinic boxes which may be useful when creating LAMMPS inputs or interpreting outputs for triclinic simulations, and (c) how LAMMPS uses tilt factors for restricted triclinic simulation boxes. @@ -121,41 +117,85 @@ triclinic simulation boxes. General triclinic simulation boxes in LAMMPS """""""""""""""""""""""""""""""""""""""""""" -LAMMPS allows specification of general triclinic simulation boxes as a -convenience for users who may be converting data from solid-state -crystallograhic representations for input to LAMMPS. +LAMMPS allows specification of general triclinic simulation boxes with +their atoms as a convenience for users who may be converting data from +solid-state crystallograhic representations or from DFT codes for +input to LAMMPS. Likewise it allows output of dump files, data files, +and thermodynamic data (e.g. pressure tensor) in a general triclinic +format. -However, internally LAMMPS only uses restricted triclinic simulation +However, internally, LAMMPS only uses restricted triclinic simulation boxes. This is for parallel efficiency and to formulate partitioning of the simulation box across processors, neighbor list building, and inter-processor communication of per-atom data with methods similar to those used for orthogonal boxes. -This means 3 things which it is important to understand: +This means 4 things which are important to understand: * Input of a general triclinic system is immediately converted to a restricted triclinic system. -* If output of general triclinic data is requested (e.g. for atom - coordinates in a dump file), then conversion from restricted - triclinic data is done at the time of output. -* Most importantly, other LAMMPS commands such as the :doc:`boundary - ` command or :doc:`region ` command, that refer to - the simulation box geometry, operate on restricted triclinic boxes, - even if a general triclinic box was defined initially. - -This is the list of commands that have specific general triclinic -options: - -create_box -create_atoms -lattice -read_data -write_data -dump atoms, dump custom -dump_modify -thermo_style -thermo_modify -read_restart, write_restart +* If output of per-atom data for a general triclinic system is + requested (e.g. for atom coordinates in a dump file), + conversion from a restricted to general triclinic system is done at + the time of output. +* The conversion of the simulation box and per-atom data from general + triclinic to restriced triclinic (and vice versa) is a rotation + + optional reflection from one set of coordinate axes to another. For + orthogonal and restricted triclinic systems, the coordinate axes are + the standard x,y,z axes. For a general triclinic system, those + coordinate axes are rotated in 3d. The optional reflection flips + the axes from right-handed to left-handed if necessary. The 3 + rotated/reflected axes remain mutually orthogonal. For all 3 kinds + of systems (orthogonal, restricted, general), per-atom quantities + (e.g. coords, velocities) are input/output as values consistent with + the corresponding coordinate axes. +* Other LAMMPS commands such as the :doc:`boundary ` or + :doc:`region ` or :doc:`velocity ` or :doc:`set + ` commands, operate on restricted triclinic systems even if a + general triclinic system was defined initially. For an example, see + the paragraph below the folliowing list. + +This is the list of commands which have general triclinic options: + +* :doc:`create_box ` - define a general triclinic box +* :doc:`create_atoms ` - add atoms to a general triclinic box +* :doc:`lattice ` - define a custom lattice consistent with **A**, **B**, **C** edge vectors of a general triclinic box +* :doc:`read_data ` - read a data file for a general triclinic system +* :doc:`write_data ` - write a data file for a general triclinic system +* :doc:`dump atom, dump custom ` - output dump snapshots in general triclinic format +* :doc:`dump_modify ` - switch a dump file between restrictied and general triclinic format +* :doc:`thermo_style ` - output the pressure tensor in + general triclinic format +* :doc:`thermo_modify ` - toggle thermo-style output + between restricted and general triclinic format +* :doc:`read_restart ` - read a restart file for a general tricliinc system +* :doc:`write_restart ` - write a restart file for a general tricliinc system + +As an example, consider the velocity of each atom in a general +triclinic system. In a general triclinic data file, each atom will +have coordinates inside a general triclinic box with arbitrary edge +vectors **A**, **B**, **C**. If the file has a "Velocities" section +then the velocity vector of each atom should be in a direction +consistent with the orientation of the general triclnic coordinate +axes. + +When LAMMPS internally converts the general triclinic system to +restricted triclinic, the coordinates of all atoms are transformed +(rotation + optional reflection) to be inside the new restricted +triclinic box. Likewise the velocity vectors are transformed. + +If the :doc:`velocity ` command is used to set an x-velocity +component, it will use the coordinate axes of the restricted box. + +If the atoms and their velocities are output via the :doc:`write_data +` or :doc:`dump custom ` commands, the coordinates +will be transformed (inverse rotation + optional reflection) to be +inside the general triclinic box. Likewise the velocity vector for +each atom will be transformed from restricted to general triclinic. + +Any other vector quantities associated with atoms (magnetic moments, +spins, etc) are transformed in a similar manner back-and-forth between +general and restricted box orientations. ---------- @@ -295,9 +335,11 @@ Periodicity and tilt factors for triclinic simulation boxes """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" There is no requirement that a triclinic box be periodic in any -dimension, though as explained above it typically should be in y or z -if you wish enforce a shift in coordinates due to periodic boundary -conditions across the y or z boundaries. +dimension, though it typically should be in y or z if you wish enforce +a shift in coordinates due to periodic boundary conditions across the +y or z boundaries. See the doc page for the :doc:`boundary +` command for an explanation of shifted coordinates for +restricted triclinic boxes which are periodic. Some commands that work with triclinic boxes, e.g. the :doc:`fix deform ` and :doc:`fix npt ` commands, require @@ -342,7 +384,6 @@ either of the commands. One exception to box flipping is if the first dimension in the tilt factor (x for xy) is non-periodic. In that case, the limits on the tilt factor are not enforced, since flipping the box in that dimension -does not change the atom positions due to non-periodicity. In this -mode, the system tilts to large angles, the simulation will simply +would not change the atom positions due to non-periodicity. In this +mode, if the system tilts to large angles, the simulation will simply become inefficient, due to the highly skewed simulation box. - diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index 8e019e801c9..772c72cd314 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -42,8 +42,10 @@ commands. The style *p* means the box is periodic, so that particles interact across the boundary, and they can exit one end of the box and re-enter the other end. A periodic dimension can change in size due to -constant pressure boundary conditions or box deformation (see the :doc:`fix npt ` and :doc:`fix deform ` commands). The *p* -style must be applied to both faces of a dimension. +constant pressure boundary conditions or box deformation (see the +:doc:`fix npt ` and :doc:`fix deform ` commands). +The *p* style must be applied to both faces of a dimension. For 2d +simulations the z dimension must be periodic (which is the default). The styles *f*, *s*, and *m* mean the box is non-periodic, so that particles do not interact across the boundary and do not move from one @@ -76,28 +78,44 @@ atoms becomes less than 50.0. This can be useful if you start a simulation with an empty box or if you wish to leave room on one side of the box, e.g. for atoms to evaporate from a surface. -For triclinic (non-orthogonal) simulation boxes, if the second dimension -of a tilt factor (e.g. y for xy) is periodic, then the periodicity is -enforced with the tilt factor offset. If the first dimension is -shrink-wrapped, then the shrink wrapping is applied to the tilted box -face, to encompass the atoms. E.g. for a positive xy tilt, the xlo -and xhi faces of the box are planes tilting in the +y direction as y -increases. These tilted planes are shrink-wrapped around the atoms to -determine the x extent of the box. - +LAMMPS also allows use of triclinic (non-orthogonal) simulation boxes. See the :doc:`Howto triclinic ` page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. +description of both general and restricted triclinic boxes and how to +define them. General triclinic boxes (arbitrary edge vectors **A**, +**B**, and **C**) are converted internally to restricted triclinic +boxes with tilt factors (xy,xz,yz) added to skew an otherwise +orthogonal box. + +The boundary command settings expalined above for the 6 +faces of an orthogonal box also apply in similar manner to the 6 faces +of a restricted triclinix box (and thus to the corresponding 6 faces +of a general triclinic box), with the following context. + +if the second dimension of a tilt factor (e.g. y for xy) is periodic, +then the periodicity is enforced with the tilt factor offset. This +means that for y periodicity a particle which exits the lower y +boundary is displaced in the x-direction by xy before it re-enters the +upper y boundary. And vice versa if a particle exits the upper y +boundary. Likewise the ghost atoms surrounding a particle near the +lower y boundary include images of particles near the upper y-boundary +which are displaced in the x-direction by xy. Similar rules apply for +z-periodicity and the xz and/or yz tilt factors. + +If the first dimension of a tilt factor is shrink-wrapped, then the +shrink wrapping is applied to the tilted box face, to encompass the +atoms. E.g. for a positive xy tilt, the xlo and xhi faces of the box +are planes tilting in the +y direction as y increases. The position +of these tilted planes are adjusted dynamically to shrink-wrap around +the atoms to determine the xlo and xhi extents of the box. Restrictions """""""""""" This command cannot be used after the simulation box is defined by a -:doc:`read_data ` or :doc:`create_box ` command or -:doc:`read_restart ` command. See the -:doc:`change_box ` command for how to change the simulation -box boundaries after it has been defined. +:doc:`read_data ` or :doc:`create_box ` command +or :doc:`read_restart ` command. See the +:doc:`change_box ` command for how to change the +simulation box boundaries after it has been defined. For 2d simulations, the z dimension must be periodic. diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 2709bf87e59..1d81acb51ed 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -325,14 +325,14 @@ default. * *avec* = first edge vector of a general triclinic simulation box (3 values) * *bvec* = second edge vector of a general triclinic simulation box (3 values) * *cvec* = third edge vector of a general triclinic simulation box (3 values) -* *abc origin* = origin on a general triclinic simulation box (3 values) +* *abc origin* = origin of a general triclinic simulation box (3 values) ---------- Header specification of the simulation box size and shape """"""""""""""""""""""""""""""""""""""""""""""""""""""""" -The final 8 keywords in the list of header keywords are for simulation +The last 8 keywords in the list of header keywords are for simulation boxes of 3 kinds which LAMMPS supports: * orthogonal box = faces are perpendicular to the xyz coordinate axes @@ -348,13 +348,15 @@ the :doc:`units ` command for details. For all 3 kinds of simulation boxes, the system may be periodic or non-periodic in any dimension; see the :doc:`boundary ` -command. When the simulation box is created by the read_data command, -it is also partitioned into a regular 3d grid of subdomains, one per +command for details. + +When the simulation box is created by the read_data command, it is +also partitioned into a regular 3d grid of subdomains, one per processor, based on the number of processors being used and the settings of the :doc:`processors ` command. For each kind -of simulatino box the subdomains have the same shape as the simulation +of simulation box the subdomains have the same shape as the simulation box, i.e. smaller orthogonal bricks for orthogonal boxes, smaller -tilted bricks for triclinic boxes. The partitioning can later be +parallelepipeds for triclinic boxes. The partitioning can later be changed by the :doc:`balance ` or :doc:`fix balance ` commands. @@ -375,7 +377,7 @@ parallelepiped. The :doc:`Howto_triclinic ` doc page discusses the tilt factors in detail and explains that the resulting edge vectors of -the restricted triclinic box are: +a restricted triclinic box are: * **A** = (xhi-xlo,0,0) * **B** = (xy,yhi-ylo,0) @@ -400,10 +402,11 @@ restricted triclinic simulation box is effectively a parallelogram. (e.g. y for xy tilt). This is so that pairs of atoms interacting across that boundary will have one of them shifted by the tilt factor. Periodicity is set by the :doc:`boundary ` - command. For example, if the xy tilt factor is non-zero, then the - y dimension should be periodic. Similarly, the z dimension should - be periodic if xz or yz is non-zero. LAMMPS does not require this - periodicity, but you may lose atoms if this is not the case. + command which also describes the shifting by the tilt factor. For + example, if the xy tilt factor is non-zero, then the y dimension + should be periodic. Similarly, the z dimension should be periodic + if xz or yz is non-zero. LAMMPS does not require this periodicity, + but you may lose atoms if this is not the case. .. note:: @@ -413,8 +416,8 @@ restricted triclinic simulation box is effectively a parallelogram. :math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x` box length is 10 and the :math:`xy` tilt factor should be between :math:`-5` and :math:`5`. LAMMPS will issue a warning if - this is not the case. See the :doc:`Howto_triclinic - ` doc page for more details. + this is not the case. See the last sub-section of the + :doc:`Howto_triclinic ` doc page for more details. .. note:: @@ -449,27 +452,33 @@ For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of LAMMPS allows specification of general triclinic simulation boxes as a convenience for users who may be converting data from - solid-state crystallograhic representations for input to LAMMPS. - However, as explained on the :doc:`Howto_triclinic - ` doc page, internally LAMMPS only uses restricted - triclinic simulation boxes. This means the box and atom - information (coordinates, velocities) in the data file are - converted from general to restricted triclinic form as soon as the - file is read. The :doc:`Howto_triclinic ` doc - page also discusses other LAMMPS commands which can input/output - general triclinic representations of the simulation box and - per-atom data. + solid-state crystallograhic representations or ftom DFT codes for + input to LAMMPS. However, as explained on the + :doc:`Howto_triclinic ` doc page, internally + LAMMPS only uses restricted triclinic simulation boxes. This means + the box and per-atom information (e.g. coordinates, velocities) in + the data file are converted from general to restricted triclinic + form as soon as the file is read. This means other sections of the + data file must specify their per-atom data appropriately. This + requirement is explained below for the relevant sections. The + :doc:`Howto_triclinic ` doc page also discusses + other LAMMPS commands which can input/output general triclinic + representations of the simulation box and per-atom data. The following explanations apply to all 3 kinds of simulation boxes: orthogonal, restricted triclinic, and general triclinic. If the system is periodic (in a dimension), then atom coordinates can be outside the bounds (in that dimension); they will be remapped (in a -periodic sense) back inside the box. Note that if the *add* option is -being used to add atoms to a simulation box that already exists, this -periodic remapping will be performed using simulation box bounds that -are the union of the existing box and the box boundaries in the new -data file. +periodic sense) back inside the box. For triclinic boxes, periodicity +in x,y,z refers to the faces of the parallelepided defined by the +**A**,**B**,**C** edge vectors of the simuation box. See the +:doc:`boundary ` command doc page for a fuller discussion. + +Note that if the *add* option is being used to add atoms to a +simulation box that already exists, this periodic remapping will be +performed using simulation box bounds that are the union of the +existing box and the box boundaries in the new data file. If the system is non-periodic (in a dimension), then an image flag for that direction has no meaning, since there cannot be periodic images @@ -770,10 +779,13 @@ of analysis. For orthogonal and restricted and general triclinic simulation boxes, the atom coordinates (x,y,z) listed in this section should - be inside the corresponding simulation box. For general triclinic - boxes that means the box defined by the 3 edge vectors specified by - the *avec*, *bvec*, *cvec* header keywords. See the discussion - above in the header section about how atom coordinates outside the + be inside the corresponding simulation box. For restricted + triclinic boxes that means the parallelepiped defined by the by the + *xlo xhi*, *ylo yhi*, *zlo zhi*, and *xy xz yz*, keywords. For + general triclinic boxes that means the parallelepiped defined by + the 3 edge vectors and origin specified by the *avec*, *bvec*, + *cvec*, and *abc origin* header keywords. See the discussion in + the header section above about how atom coordinates outside the simulation box are (or are not) remapped to be inside the box. .. list-table:: @@ -853,18 +865,21 @@ The per-atom values have these meanings and units, listed alphabetically: * lineflag = 1 for line segment particles, 0 for point or spherical particles * mass = mass of particle (mass units) * molecule-ID = integer ID of molecule the atom belongs to -* mux,muy,muz = components of dipole moment of atom (dipole units) +* mux,muy,muz = components of dipole moment of atom (dipole units) (see general triclinic comment below) +* normx,normy,normz = components of dielectric dipole moment of atom (dipole + units) (see general triclinic comment below) * q = charge on atom (charge units) * rho = density (need units) for SPH particles * sp = magnitude of magnetic spin of atom (Bohr magnetons) -* spx,spy,spz = components of magnetic spin of atom (unit vector) +* spx,spy,spz = components of magnetic spin of atom (unit vector) (see general triclinic comment below) * template-atom = which atom within a template molecule the atom is * template-index = which molecule within the molecule template the atom is part of * theta = internal temperature of a DPD particle * triangleflag = 1 for triangular particles, 0 for point or spherical particles * volume = volume of Peridynamic particle (distance\^3 units) * x,y,z = coordinates of atom (distance units) -* x0,y0,z0 = original (strain-free) coordinates of atom (distance units) +* x0,y0,z0 = original (strain-free) coordinates of atom (distance + units) (see general triclinic comment below) The units for these quantities depend on the unit style; see the :doc:`units ` command for details. @@ -873,6 +888,21 @@ For 2d simulations, z must be specified as 0.0. If the data file is created by another program, then z values for a 2d simulation can be within epsilon of 0.0, and LAMMPS will force them to zero. +If the data file defines a general triclinic box, then the following +per-atom values in the list above are per-atom vectors: (mux,muy,muz), +(normx,normy,normz), (spx,spy,spz). They should be specified with +values for the rotated coordinate axes of the general triclinic box. +Likewise, (x0,y0,z0) are per-atom coordinates and should be values +inside the general triclinic box, the same as explained for (x,y,z) +above. See the :doc:`Howto triclinic ` doc page for +more details. + +If the data file defines a general triclinic box, then each of the 3 +vectors (translational velocity, angular momentum, angule velocity) +sholld be specified for the rotated coordinate axes of the general +triclinic box. See the :doc:`Howto triclinic ` doc +page for more details. + The atom-ID is used to identify the atom throughout the simulation and in dump files. Normally, it is a unique value from 1 to Natoms for each atom. Unique values larger than Natoms can be used, but they @@ -1060,8 +1090,9 @@ the "bodies" keyword. Each body can have a variable number of integer and/or floating-point values. The number and meaning of the values is defined by the body -style, as described in the :doc:`Howto body ` doc page. The -body style is given as an argument to the :doc:`atom_style body ` command. +style, as described in the :doc:`Howto body ` doc page. +The body style is given as an argument to the :doc:`atom_style body +` command. The Ninteger and Ndouble values determine how many integer and floating-point values are specified for this particle. Ninteger and @@ -1276,10 +1307,10 @@ and a general discussion of how type labels can be used. 12 1 2 1 1 0 0 0 -The *Ellipsoids* section must appear if :doc:`atom_style ellipsoid ` is used and any atoms are listed in the -*Atoms* section with an ellipsoidflag = 1. The number of ellipsoids -should be specified in the header section via the "ellipsoids" -keyword. +The *Ellipsoids* section must appear if :doc:`atom_style ellipsoid +` is used and any atoms are listed in the *Atoms* section +with an ellipsoidflag = 1. The number of ellipsoids should be +specified in the header section via the "ellipsoids" keyword. The 3 shape values specify the 3 diameters or aspect ratios of a finite-size ellipsoidal particle, when it is oriented along the 3 @@ -1297,6 +1328,13 @@ the quaternion that represents its new orientation is given by LAMMPS normalizes each atom's quaternion in case (a,b,c) is not specified as a unit vector. +If the data file defines a general triclinic box, then the quaternion +for each ellipsoid should be specified for its orientation in the +general triclinic system with respect to the standard xyz axes (not +the rotated coordinate axes of the general triclinic system). When +the general triclinic box is transformed to a restricted triclinic +box, the ellipsoid quaternions will be altered appropriately. + The *Ellipsoids* section must appear after the *Atoms* section. ---------- @@ -1420,6 +1458,12 @@ the line segment with a unit vector in the +z direction, gives an I.e. normal = (c2-c1) x (0,0,1). This orientation may be important for defining some interactions. +If the data file defines a general triclinic box, the (x1,y1) and +(x2,y2) values should be within (or near) its parallelogram area, +i.e. near the x,y coordinates of the line segment as defined in the +Atoms section. See the :doc:`Howto triclinic ` doc +page for more details. + The *Lines* section must appear after the *Atoms* section. ---------- @@ -1541,9 +1585,10 @@ via the :doc:`pair_coeff ` command in the input script. 12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0 -The *Triangles* section must appear if :doc:`atom_style tri ` is used and any atoms are listed in the *Atoms* -section with a triangleflag = 1. The number of lines should be -specified in the header section via the "triangles" keyword. +The *Triangles* section must appear if :doc:`atom_style tri +` is used and any atoms are listed in the *Atoms* section +with a triangleflag = 1. The number of lines should be specified in +the header section via the "triangles" keyword. The 3 corner points are the corner points of the triangle. The ordering of the 3 points should be such that using a right-hand rule @@ -1551,6 +1596,12 @@ to go from point1 to point2 to point3 gives an "outward" normal vector to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This orientation may be important for defining some interactions. +If the data file defines a general triclinic box, the (x1,y1,z1), +(x2,y2,z2), (x3,y3,z3) corner points should be within (or near) its +parallelepiped volume, i.e. near the x,y,z coordinates of the triangle +as defined in the Atoms section. See the :doc:`Howto triclinic +` doc page for more details. + The *Triangles* section must appear after the *Atoms* section. ---------- @@ -1590,6 +1641,12 @@ Vx, vy, vz, and ervel are in :doc:`units ` of velocity. Lx, ly, lz are in units of angular momentum (distance-velocity-mass). Wx, Wy, Wz are in units of angular velocity (radians/time). +If the data file defines a general triclinic box, then each of the 3 +vectors (translational velocity, angular momentum, angular velocity) +should be specified for the rotated coordinate axes of the general +triclinic box. See the :doc:`Howto triclinic ` doc +page for more details. + For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz), specific values for each sub-style must be listed. The order of the sub-styles is the same as they were listed in the From 5ff16da2725e641c3a4eae7db763dd8f0d2cf8fa Mon Sep 17 00:00:00 2001 From: jtclemm Date: Thu, 21 Sep 2023 12:17:47 +0200 Subject: [PATCH 043/719] Adding rate cap on vol link pressure --- src/fix_deform.cpp | 48 +++++++++++++++++++++++++++++++++++++++++++--- src/fix_deform.h | 1 + 2 files changed, 46 insertions(+), 3 deletions(-) diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 139f1e08352..3430c26061f 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -1297,6 +1297,8 @@ void FixDeform::set_volume() double L2i = domain->boxhi[fixed] - domain->boxlo[fixed]; double L3i = domain->boxhi[dynamic1] - domain->boxlo[dynamic1]; double L3 = (set[dynamic1].hi_target - set[dynamic1].lo_target); + double Vi = L1i * L2i * L3i; + double V = L3 * L1i * L2i; double e3 = (L3 / L3i - 1.0) / dt; double p1 = pressure->vector[i]; double p2 = pressure->vector[fixed]; @@ -1315,13 +1317,22 @@ void FixDeform::set_volume() if (!linked_pressure) { // Calculate first strain rate by expanding stress to linear order, p1(t+dt) = p2(t+dt) // Calculate second strain rate to preserve volume - denominator = (p2 - p2i + (p1 - p1i) / e1i * e2i); + denominator = p2 - p2i + e2i * ((p1 - p1i) / e1i); if (denominator != 0.0 && e1i != 0.0) { - e1 = (-e3 / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2)) / denominator; + e1 = (((p2 - p2i) * (Vi - V) / (V * dt)) - e2i * (p1 - p2)) / denominator; } else { e1 = e2i; } - e2 = (1.0 - (1 + e3 * dt) * (1 + e1 * dt)) / ((1 + e3 * dt) * (1 + e1 * dt) * dt); + e2 = (Vi - V * (1 + e1 * dt)) / (V * (1 + e1 * dt) * dt); + + // If strain rate exceeds limit in either dimension, cap it at the maximum compatible rate + if (max_h_rate != 0) + if (fabs(e1) > max_h_rate || fabs(e2) > max_h_rate) + if (fabs(e1) > fabs(e2)) + adjust_linked_rates(e1, e2, e3, Vi, V); + else + adjust_linked_rates(e2, e1, e3, Vi, V); + shift = 0.5 * L1i * (1.0 + e1 * dt); linked_pressure = 1; @@ -1341,6 +1352,37 @@ void FixDeform::set_volume() } } + +/* ---------------------------------------------------------------------- + Rescale volume preserving strain rates to enforce max rate +------------------------------------------------------------------------- */ + +void FixDeform::adjust_linked_rates(double &e_larger, double &e_smaller, double e3, double Vi, double V) +{ + double dt = update->dt; + double e_lim_positive = (Vi - V * (1 + max_h_rate * dt)) / (V * (1 + max_h_rate * dt) * dt); + double e_lim_negative = (Vi - V * (1 - max_h_rate * dt)) / (V * (1 - max_h_rate * dt) * dt); + if ((e_larger * e3) >= 0) { + if (e_larger > 0.0) { + // Same sign as primary strain rate, cap third dimension + e_smaller = -max_h_rate; + e_larger = e_lim_negative; + } else { + e_smaller = max_h_rate; + e_larger = e_lim_positive; + } + } else { + // Opposite sign, set to maxrate. + if (e_larger > 0.0) { + e_larger = max_h_rate; + e_smaller = e_lim_positive; + } else { + e_larger = -max_h_rate; + e_smaller = e_lim_negative; + } + } +} + /* ---------------------------------------------------------------------- apply isotropic controls ------------------------------------------------------------------------- */ diff --git a/src/fix_deform.h b/src/fix_deform.h index e8a4766b124..2f0b66aa714 100644 --- a/src/fix_deform.h +++ b/src/fix_deform.h @@ -88,6 +88,7 @@ class FixDeform : public Fix { void set_volume(); void set_iso(); void couple(); + void adjust_linked_rates(double&, double&, double, double, double); }; } // namespace LAMMPS_NS From 857cc5392385f1799b222af2996c6b684ee613da Mon Sep 17 00:00:00 2001 From: Ludwig Ahrens-Iwers Date: Wed, 4 Oct 2023 10:32:50 +0200 Subject: [PATCH 044/719] README file for the ELECTRODE package --- src/ELECTRODE/README | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 src/ELECTRODE/README diff --git a/src/ELECTRODE/README b/src/ELECTRODE/README new file mode 100644 index 00000000000..56894943a0c --- /dev/null +++ b/src/ELECTRODE/README @@ -0,0 +1,15 @@ +This package provides the "fix electrode/*" commands which can be used in a +LAMMPS input script. These fixes implement the constant potential method, which +minimizes the energy of electrodes as a function of atom charges at given +electric potentials or electrode charges. + +See the doc page for the fix electrode/conp command to get started. There are +example scripts for using this package in examples/PACKAGES/electrode. + +This package uses an external library in lib/electrode which must be compiled +before making LAMMPS. See the doc page on "Packages with extra build options" +for more information. + +The primary people who created this package are Ludwig Ahrens-Iwers, Shern Tee +(s.tee@griffith.edu.au) and Robert Meißner (robert.meissner@tuhh.de). Contact +them directly if you have questions. From 201f8cda9a72f25bc6ad9d7da7afc0ed97c62ff8 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 12 Oct 2023 06:49:59 -0600 Subject: [PATCH 045/719] more updates --- src/atom_vec_body.cpp | 86 -------------------------------------- src/atom_vec_body.h | 5 --- src/atom_vec_ellipsoid.cpp | 86 -------------------------------------- src/atom_vec_ellipsoid.h | 5 --- src/domain.cpp | 18 ++++---- src/domain.h | 1 - src/dump_atom.cpp | 51 ++++++++++++---------- src/dump_custom.cpp | 12 ------ 8 files changed, 39 insertions(+), 225 deletions(-) diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 898b0657495..fd590ad5fe5 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -53,8 +53,6 @@ AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp) nlocal_bonus = nghost_bonus = nmax_bonus = 0; bonus = nullptr; - quat_hold = nullptr; - bptr = nullptr; if (sizeof(double) == sizeof(int)) @@ -551,90 +549,6 @@ void AtomVecBody::data_atom_post(int ilocal) angmom[ilocal][2] = 0.0; } -/* ---------------------------------------------------------------------- - convert read_data file info from general to restricted triclinic - parent class operates on data from Velocities section of data file - child class operates on bonus quat -------------------------------------------------------------------------- */ - -void AtomVecBody::read_data_general_to_restricted(int nlocal_previous, int nlocal) -{ - AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); - - double quat[4]; - double *bquat; - - for (int i = nlocal_previous; i < nlocal; i++) { - if (body[i] < 0) continue; - bquat = bonus[body[i]].quat; - MathExtra::quatquat(domain->quat_g2r,bquat,quat); - bquat[0] = quat[0]; - bquat[1] = quat[1]; - bquat[2] = quat[2]; - bquat[3] = quat[3]; - MathExtra::qnormalize(bquat); - } -} - -/* ---------------------------------------------------------------------- - convert info output by write_data from restricted to general triclinic - parent class operates on x and data from Velocities section of data file - child class operates on bonus quat -------------------------------------------------------------------------- */ - -void AtomVecBody::write_data_restricted_to_general() -{ - AtomVec::write_data_restricted_to_general(); - - double quat[4]; - double *bquat; - double *quat_r2g = domain->quat_r2g; - - memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); - - for (int i = 0; i < nlocal_bonus; i++) { - bquat = bonus[i].quat; - quat_hold[i][0] = bquat[0]; - quat_hold[i][1] = bquat[1]; - quat_hold[i][2] = bquat[2]; - quat_hold[i][3] = bquat[3]; - - MathExtra::quatquat(quat_r2g,bquat,quat); - bquat[0] = quat[0]; - bquat[1] = quat[1]; - bquat[2] = quat[2]; - bquat[3] = quat[3]; - MathExtra::qnormalize(bquat); - } -} - -/* ---------------------------------------------------------------------- - restore info output by write_data to restricted triclinic - original data is in "hold" arrays - parent class operates on x and data from Velocities section of data file - child class operates on bonus quat -------------------------------------------------------------------------- */ - -void AtomVecBody::write_data_restore_restricted() -{ - AtomVec::write_data_restore_restricted(); - - if (!quat_hold) return; - - double *bquat; - - for (int i = 0; i < nlocal_bonus; i++) { - bquat = bonus[i].quat; - bquat[0] = quat_hold[i][0]; - bquat[1] = quat_hold[i][1]; - bquat[2] = quat_hold[i][2]; - bquat[3] = quat_hold[i][3]; - } - - memory->destroy(quat_hold); - quat_hold = nullptr; -} - /* ---------------------------------------------------------------------- unpack one body from Bodies section of data file ------------------------------------------------------------------------- */ diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index 955b4f45874..e02fd3bbb0d 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -60,9 +60,6 @@ class AtomVecBody : public AtomVec { void create_atom_post(int) override; void data_atom_post(int) override; - void read_data_general_to_restricted(int, int); - void write_data_restricted_to_general(); - void write_data_restore_restricted(); void pack_data_pre(int) override; void pack_data_post(int) override; @@ -81,8 +78,6 @@ class AtomVecBody : public AtomVec { double *rmass, *radius; double **angmom; - double **quat_hold; - int nghost_bonus, nmax_bonus; int intdoubleratio; // sizeof(double) / sizeof(int) int body_flag; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index d51f7af78ff..3cc8f6362d2 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -49,8 +49,6 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp) nlocal_bonus = nghost_bonus = nmax_bonus = 0; bonus = nullptr; - quat_hold = nullptr; - // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -460,90 +458,6 @@ void AtomVecEllipsoid::data_atom_post(int ilocal) angmom[ilocal][2] = 0.0; } -/* ---------------------------------------------------------------------- - convert read_data file info from general to restricted triclinic - parent class operates on data from Velocities section of data file - child class operates on bonus quat -------------------------------------------------------------------------- */ - -void AtomVecEllipsoid::read_data_general_to_restricted(int nlocal_previous, int nlocal) -{ - AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); - - double quat[4]; - double *bquat; - - for (int i = nlocal_previous; i < nlocal; i++) { - if (ellipsoid[i] < 0) continue; - bquat = bonus[ellipsoid[i]].quat; - MathExtra::quatquat(domain->quat_g2r,bquat,quat); - bquat[0] = quat[0]; - bquat[1] = quat[1]; - bquat[2] = quat[2]; - bquat[3] = quat[3]; - MathExtra::qnormalize(bquat); - } -} - -/* ---------------------------------------------------------------------- - convert info output by write_data from restricted to general triclinic - parent class operates on x and data from Velocities section of data file - child class operates on bonus quat -------------------------------------------------------------------------- */ - -void AtomVecEllipsoid::write_data_restricted_to_general() -{ - AtomVec::write_data_restricted_to_general(); - - double quat[4]; - double *bquat; - double *quat_r2g = domain->quat_r2g; - - memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); - - for (int i = 0; i < nlocal_bonus; i++) { - bquat = bonus[i].quat; - quat_hold[i][0] = bquat[0]; - quat_hold[i][1] = bquat[1]; - quat_hold[i][2] = bquat[2]; - quat_hold[i][3] = bquat[3]; - - MathExtra::quatquat(quat_r2g,bquat,quat); - bquat[0] = quat[0]; - bquat[1] = quat[1]; - bquat[2] = quat[2]; - bquat[3] = quat[3]; - MathExtra::qnormalize(bquat); - } -} - -/* ---------------------------------------------------------------------- - restore info output by write_data to restricted triclinic - original data is in "hold" arrays - parent class operates on x and data from Velocities section of data file - child class operates on bonus quat -------------------------------------------------------------------------- */ - -void AtomVecEllipsoid::write_data_restore_restricted() -{ - AtomVec::write_data_restore_restricted(); - - if (!quat_hold) return; - - double *bquat; - - for (int i = 0; i < nlocal_bonus; i++) { - bquat = bonus[i].quat; - bquat[0] = quat_hold[i][0]; - bquat[1] = quat_hold[i][1]; - bquat[2] = quat_hold[i][2]; - bquat[3] = quat_hold[i][3]; - } - - memory->destroy(quat_hold); - quat_hold = nullptr; -} - /* ---------------------------------------------------------------------- modify values for AtomVec::pack_data() to pack ------------------------------------------------------------------------- */ diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h index 3d6815fff03..6e06d773fcb 100644 --- a/src/atom_vec_ellipsoid.h +++ b/src/atom_vec_ellipsoid.h @@ -53,9 +53,6 @@ class AtomVecEllipsoid : public AtomVec { void create_atom_post(int) override; void data_atom_post(int) override; - void read_data_general_to_restricted(int, int); - void write_data_restricted_to_general(); - void write_data_restore_restricted(); void pack_data_pre(int) override; void pack_data_post(int) override; @@ -73,8 +70,6 @@ class AtomVecEllipsoid : public AtomVec { double *rmass; double **angmom; - double **quat_hold; - int nghost_bonus, nmax_bonus; int ellipsoid_flag; double rmass_one; diff --git a/src/domain.cpp b/src/domain.cpp index 68eafab356e..379b626d800 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -632,17 +632,17 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, if (bvec1[2] > 0.0) theta2 = -theta2; MathExtra::axisangle_to_quat(xaxis,theta2,quat2); - // quat_g2r = rotation via single quat = quat2 * quat1 + // quat_single = rotation via single quat = quat2 * quat1 // quat_r2g = rotation from restricted to general // rotate_g2r = general to restricted rotation matrix // include flip of C vector if needed to obey right-hand rule // rotate_r2g = restricted to general rotation matrix // simply a transpose of rotate_g2r since orthonormal - MathExtra::quatquat(quat2,quat1,quat_g2r); - MathExtra::qconjugate(quat_g2r,quat_r2g); + double quat_single[4]; + MathExtra::quatquat(quat2,quat1,quat_single); - MathExtra::quat_to_mat(quat_g2r,rotate_g2r); + MathExtra::quat_to_mat(quat_single,rotate_g2r); if (triclinic_general_flip) { rotate_g2r[2][0] = -rotate_g2r[2][0]; @@ -675,11 +675,13 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, printf("Rotvec1: %g %g %g\n",rot1[0],rot1[1],rot1[2]); printf("Theta2: %g\n",theta2); printf("Rotvec2: %g %g %g\n",xaxis[0],xaxis[1],xaxis[2]); - printf("Quat: %g %g %g %g\n",quat_g2r[0],quat_g2r[1],quat_g2r[2],quat_g2r[3]); - double angle = 2.0*acos(quat_g2r[0]); + printf("Quat: %g %g %g %g\n", + quat_single[0],quat_single[1],quat_single[2],quat_single[3]); + double angle = 2.0*acos(quat_single[0]); printf("Theta: %g\n",angle); - printf("Rotvec: %g %g %g\n",quat_g2r[1]/sin(0.5*angle),quat_g2r[2]/sin(0.5*angle), - quat_g2r[3]/sin(0.5*angle)); + printf("Rotvec: %g %g %g\n", + quat_single[1]/sin(0.5*angle),quat_single[2]/sin(0.5*angle), + quat_single[3]/sin(0.5*angle)); printf("Aprime: %g %g %g\n",aprime[0],aprime[1],aprime[2]); printf("Bprime: %g %g %g\n",bprime[0],bprime[1],bprime[2]); printf("Cprime: %g %g %g\n",cprime[0],cprime[1],cprime[2]); diff --git a/src/domain.h b/src/domain.h index 61a88724e7f..34714cf6e38 100644 --- a/src/domain.h +++ b/src/domain.h @@ -93,7 +93,6 @@ class Domain : protected Pointers { // boxlo = lower left corner double avec[3], bvec[3], cvec[3]; // ABC edge vectors of general triclinic box - double quat_g2r[4], quat_r2g[4]; // quaternions for general <--> restricted rotations double rotate_g2r[3][3]; // rotation matrix from general --> restricted tri double rotate_r2g[3][3]; // rotation matrix from restricted --> general tri diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 151446bdfd5..38c8431269d 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -91,9 +91,6 @@ void DumpAtom::init_style() // setup function ptrs - if (scale_flag && triclinic_general) - error->all(FLERR,"Dump atom cannot use scale and triclinic/general settings"); - if (binary && domain->triclinic == 0) header_choice = &DumpAtom::header_binary; else if (binary && triclinic_general == 1) @@ -107,26 +104,36 @@ void DumpAtom::init_style() else if (!binary && domain->triclinic == 1) header_choice = &DumpAtom::header_item_triclinic; - if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0) - pack_choice = &DumpAtom::pack_scale_noimage; - else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0) - pack_choice = &DumpAtom::pack_scale_image; - - else if (scale_flag == 0 && image_flag == 0 && triclinic_general == 1) - pack_choice = &DumpAtom::pack_noscale_noimage_triclinic_general; - else if (scale_flag == 0 && image_flag == 1 && triclinic_general == 1) - pack_choice = &DumpAtom::pack_noscale_image_triclinic_general; - - else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1) - pack_choice = &DumpAtom::pack_scale_noimage_triclinic; - else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1) - pack_choice = &DumpAtom::pack_scale_image_triclinic; + if (scale_flag == 0) { + if (image_flag == 0) { + if (triclinic_general == 1) { + pack_choice = &DumpAtom::pack_noscale_noimage_triclinic_general; + } else { + pack_choice = &DumpAtom::pack_noscale_noimage; + } + } else if (image_flag == 1) { + if (triclinic_general == 1) { + pack_choice = &DumpAtom::pack_noscale_image_triclinic_general; + } else { + pack_choice = &DumpAtom::pack_noscale_image; + } + } + } else if (scale_flag == 1) { + if (image_flag == 0) { + if (domain->triclinic == 0) { + pack_choice = &DumpAtom::pack_scale_noimage; + } else { + pack_choice = &DumpAtom::pack_scale_noimage_triclinic; + } + } else if (image_flag == 1) { + if (domain->triclinic == 0) { + pack_choice = &DumpAtom::pack_scale_image; + } else { + pack_choice = &DumpAtom::pack_scale_image_triclinic; + } + } + } - else if (scale_flag == 0 && image_flag == 0) - pack_choice = &DumpAtom::pack_noscale_noimage; - else if (scale_flag == 0 && image_flag == 1) - pack_choice = &DumpAtom::pack_noscale_image; - if (image_flag == 0) convert_choice = &DumpAtom::convert_noimage; else convert_choice = &DumpAtom::convert_image; diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 2e478fd5e92..9554247aff0 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -1354,20 +1354,14 @@ int DumpCustom::parse_fields(int narg, char **arg) else pack_choice[iarg] = &DumpCustom::pack_z; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"xs") == 0) { - if (triclinic_general) - error->all(FLERR,"Dump custom xs property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xs_triclinic; else pack_choice[iarg] = &DumpCustom::pack_xs; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"ys") == 0) { - if (triclinic_general) - error->all(FLERR,"Dump custom ys property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_ys_triclinic; else pack_choice[iarg] = &DumpCustom::pack_ys; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"zs") == 0) { - if (triclinic_general) - error->all(FLERR,"Dump custom zs property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zs_triclinic; else pack_choice[iarg] = &DumpCustom::pack_zs; vtype[iarg] = Dump::DOUBLE; @@ -1387,20 +1381,14 @@ int DumpCustom::parse_fields(int narg, char **arg) else pack_choice[iarg] = &DumpCustom::pack_zu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"xsu") == 0) { - if (triclinic_general) - error->all(FLERR,"Dump custom xsu property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xsu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_xsu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"ysu") == 0) { - if (triclinic_general) - error->all(FLERR,"Dump custom ysu property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_ysu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_ysu; vtype[iarg] = Dump::DOUBLE; } else if (strcmp(arg[iarg],"zsu") == 0) { - if (triclinic_general) - error->all(FLERR,"Dump custom zsu property not supported for general triclinic"); if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zsu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_zsu; vtype[iarg] = Dump::DOUBLE; From a4a7b9c5007df4c63c98c31807edb82b3c29820f Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 20 Oct 2023 14:01:24 -0600 Subject: [PATCH 046/719] formatting --- src/domain.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/domain.cpp b/src/domain.cpp index d5414ece56a..47295c338c9 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -756,7 +756,6 @@ void Domain::restricted_to_general_vector(double *v) v[2] = vnew[2]; } - void Domain::restricted_to_general_vector(double *v, double *vnew) { MathExtra::matvec(rotate_r2g,v,vnew); From 6fe6395ab29a002f0f264573359fee7563ecc640 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 3 Nov 2023 14:52:41 -0600 Subject: [PATCH 047/719] reset quats for ellipsoids for general <-> restriced triclinic --- src/atom_vec_ellipsoid.cpp | 77 ++++++++++++++++++++++++++++++++++++++ src/atom_vec_ellipsoid.h | 7 +++- src/domain.cpp | 2 +- src/math_extra.cpp | 25 ++++++++++++- src/math_extra.h | 1 + 5 files changed, 109 insertions(+), 3 deletions(-) diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 3cc8f6362d2..9b64426224c 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -536,6 +536,83 @@ void AtomVecEllipsoid::write_data_bonus(FILE *fp, int n, double *buf, int /*flag } } +/* ---------------------------------------------------------------------- + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on ellipsoid quaternion +------------------------------------------------------------------------- */ + +void AtomVecEllipsoid::read_data_general_to_restricted(int nlocal_previous, int nlocal) +{ + int j; + + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + // quat_g2r = quat that rotates from general to restricted triclinic + // quat_new = ellipsoid quat converted to restricted triclinic + + double quat_g2r[4],quat_new[4]; + MathExtra::mat_to_quat(domain->rotate_g2r,quat_g2r); + + for (int i = nlocal_previous; i < nlocal; i++) { + if (ellipsoid[i] < 0) continue; + j = ellipsoid[i]; + MathExtra::quatquat(quat_g2r,bonus[j].quat,quat_new); + bonus[j].quat[0] = quat_new[0]; + bonus[j].quat[1] = quat_new[1]; + bonus[j].quat[2] = quat_new[2]; + bonus[j].quat[3] = quat_new[3]; + } +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on ellipsoid quaternion +------------------------------------------------------------------------- */ + +void AtomVecEllipsoid::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); + + for (int i = 0; i < nlocal_bonus; i++) + memcpy(quat_hold[i],bonus[i].quat,4*sizeof(double)); + + // quat_r2g = quat that rotates from restricted to general triclinic + // quat_new = ellipsoid quat converted to general triclinic + + double quat_r2g[4],quat_new[4]; + MathExtra::mat_to_quat(domain->rotate_r2g,quat_r2g); + + for (int i = 0; i < nlocal_bonus; i++) { + MathExtra::quatquat(quat_r2g,bonus[i].quat,quat_new); + bonus[i].quat[0] = quat_new[0]; + bonus[i].quat[1] = quat_new[1]; + bonus[i].quat[2] = quat_new[2]; + bonus[i].quat[3] = quat_new[3]; + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on ellipsoid quaternion +------------------------------------------------------------------------- */ + +void AtomVecEllipsoid::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + for (int i = 0; i < nlocal_bonus; i++) + memcpy(bonus[i].quat,quat_hold[i],4*sizeof(double)); + + memory->destroy(quat_hold); + quat_hold = nullptr; +} + /* ---------------------------------------------------------------------- set shape values in bonus data for particle I oriented aligned with xyz axes diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h index 6e06d773fcb..23c824dbf03 100644 --- a/src/atom_vec_ellipsoid.h +++ b/src/atom_vec_ellipsoid.h @@ -59,6 +59,10 @@ class AtomVecEllipsoid : public AtomVec { int pack_data_bonus(double *, int) override; void write_data_bonus(FILE *, int, double *, int) override; + void read_data_general_to_restricted(int, int); + void write_data_restricted_to_general(); + void write_data_restore_restricted(); + // unique to AtomVecEllipsoid void set_shape(int, double, double, double); @@ -69,7 +73,8 @@ class AtomVecEllipsoid : public AtomVec { int *ellipsoid; double *rmass; double **angmom; - + double **quat_hold; + int nghost_bonus, nmax_bonus; int ellipsoid_flag; double rmass_one; diff --git a/src/domain.cpp b/src/domain.cpp index 47295c338c9..439dafd7659 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -307,7 +307,7 @@ void Domain::set_global_box() cprime[1] = yz; cprime[2] = boxhi[2] - boxlo[2]; - // transform restricted A'B'C' to general triclinic A,B,C + // transform restricted A'B'C' to general triclinic ABC MathExtra::matvec(rotate_r2g,aprime,avec); MathExtra::matvec(rotate_r2g,bprime,bvec); diff --git a/src/math_extra.cpp b/src/math_extra.cpp index 83e548f79fa..b8c9bd98df2 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -362,6 +362,29 @@ void exyz_to_q(double *ex, double *ey, double *ez, double *q) qnormalize(q); } +/* ---------------------------------------------------------------------- + create unit quaternion from a rotation matrix + just a wrapper on exyz_to_q() + ex,ey,ez are columns of a rotation matrix +------------------------------------------------------------------------- */ + +void mat_to_quat(double mat[3][3], double *q) +{ + double ex[3],ey[3],ez[3]; + + ex[0] = mat[0][0]; + ex[1] = mat[1][0]; + ex[2] = mat[2][0]; + ey[0] = mat[0][1]; + ey[1] = mat[1][1]; + ey[2] = mat[2][1]; + ez[0] = mat[0][2]; + ez[1] = mat[1][2]; + ez[2] = mat[2][2]; + + MathExtra::exyz_to_q(ex,ey,ez,q); +} + /* ---------------------------------------------------------------------- compute space-frame ex,ey,ez from current quaternion q ex,ey,ez = space-frame coords of 1st,2nd,3rd principal axis @@ -417,6 +440,7 @@ void quat_to_mat(const double *quat, double mat[3][3]) /* ---------------------------------------------------------------------- compute rotation matrix from quaternion conjugate quat = [w i j k] + similar logic to quat_to_mat() ------------------------------------------------------------------------- */ void quat_to_mat_trans(const double *quat, double mat[3][3]) @@ -647,5 +671,4 @@ void tribbox(double *h, double radius, double *dist) /* ---------------------------------------------------------------------- */ - } diff --git a/src/math_extra.h b/src/math_extra.h index 49e128c3df4..52d1d838ffb 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -100,6 +100,7 @@ void angmom_to_omega(double *m, double *ex, double *ey, double *ez, double *idia void omega_to_angmom(double *w, double *ex, double *ey, double *ez, double *idiag, double *m); void mq_to_omega(double *m, double *q, double *moments, double *w); void exyz_to_q(double *ex, double *ey, double *ez, double *q); +void mat_to_quat(double mat[3][3], double *quat); void q_to_exyz(double *q, double *ex, double *ey, double *ez); void quat_to_mat(const double *quat, double mat[3][3]); void quat_to_mat_trans(const double *quat, double mat[3][3]); From 612a919e939502d32d630f6bbeee7f97e22fd93d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 6 Nov 2023 16:56:33 -0700 Subject: [PATCH 048/719] more work on read_data and doc pages --- doc/src/Howto_2d.rst | 33 ++++---- doc/src/Howto_triclinic.rst | 161 ++++++++++++++++-------------------- doc/src/boundary.rst | 6 +- src/atom.cpp | 4 +- src/atom_vec.cpp | 5 +- src/domain.cpp | 5 +- src/domain.h | 4 +- src/read_data.cpp | 14 ++-- src/read_data.h | 9 +- 9 files changed, 113 insertions(+), 128 deletions(-) diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index 06e6d57be8b..b80a424690d 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -1,29 +1,32 @@ -2d simulations -============== +================ + 2d simulations +================ You must use the :doc:`dimension ` command to specify a 2d simulation. The default is 3d. -Make the simulation box periodic in z via the :doc:`boundary ` -command. This is the default. +A 2d simulation box must be periodic in z as set by the :doc:`boundary +` command. This is the default. If using the :doc:`create_box ` command, you must define a -simulation box which straddes z = 0.0 in the z dimension since all the -atoms will have a z coordinate of zero. Typicaily the width of box in -the z dimension should be narrow, e.g. -0.5 to 0.5, but that is not -required. An example is: +simulation box which straddles z = 0.0 in the z dimension since all +the atoms will have a z coordinate of zero. Typicaily the width of +box in the z dimension should be narrow, e.g. -0.5 to 0.5, but that is +not required. Example are: .. code-block:: LAMMPS + create_box 1 -10 10 0 10 -0.5 0.5 create_box 1 -10 10 0 10 -0.25 0.25 -Likewise, If using the :doc:`read_data ` command to define -the simulation box and read in a file of atom coordinates, the default -"zlo zhi" values are -0.5 0.5 for 2d simulations. If the data file -includes that header keyword the zlo/zhi values must straddle z = 0.0. -The z coords for atoms listed in the file must be 0.0 (within epsilon -of zero is also allowed in case the data file was generated by another -program with finite precision). +Likewise, if using the :doc:`read_data ` command to define +the simulation box and read in a data file of atom coordinates, the +default "zlo zhi" values are -0.5 0.5 for 2d simulations. If the data +file includes that header keyword the zlo/zhi values must straddle z = +0.0. Also, the z coord for each atom listed in the file must be 0.0. +A value within epsilon of zero is also allowed in case the data file +was generated by another program with finite precision, in which case +the z coord for the atom will be set to 0.0. Use the :doc:`fix enforce2d ` command as the last fix defined in the input script. It ensures that the z-components of diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index c84f4243567..0a66af4b36b 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -48,13 +48,17 @@ box/relax ` command. A third use is to shear a bulk solid to study the response of the material. The :doc:`fix deform ` command can be used for this purpose. It allows dynamic control of the xy, xz, yz tilt -factors as a simulation runs. This is discussed in the next section -on non-equilibrium MD (NEMD) simulations. +factors as a simulation runs. This is discussed in the :doc:`Howto +NEMD ` doc page on non-equilibrium MD (NEMD) simulations. Conceptually, a triclinic parallelepiped is defined with an "origin" at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** = -(bx,by,bz), **C** = (cx,cy,cz) which can now be arbitrary vectors, so -long as they are non-zero, distinct, and not co-planar. +(bx,by,bz), **C** = (cx,cy,cz) which can be arbitrary vectors, so long +as they are non-zero, distinct, and not co-planar. In addition, they +must define a right-handed system, such that (**A** cross **B**) +points in the direction of **C**. Note that a left-handed system can +be converted to a right-handed system by simply swapping the order of +any two of the **A**, **B**, **C** vectors. The 4 commands listed above for defining orthogonal simulation boxes have triclinic options which allow for specification of the origin and @@ -64,46 +68,45 @@ a *restricted* triclinic box. A *general* triclinic box is specified by an origin (xlo, ylo, zlo) and arbitrary edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), and -**C** = (cx,cy,cz). So there are 12 parameters in total. Note that a -general triclinic box can either be *right-handed* if (**A** x **B**) -points in the direction of **C**, or it can be *left-handed* if (**A** -x **B**) points opposite to **C**. +**C** = (cx,cy,cz). So there are 12 parameters in total. A *restricted* triclinic box also has an origin (xlo,ylo,zlo), but its -edge vectors are of the following form: **A** = (xhi-xlo,0,0), **B** = -(xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So there are 9 parameters in -total. The restricted form of edge vectors requires that **A** is -along the x-axis, **B** is in the xy plane with a y-component in -the +y direction, and **C** has a z-component in the +z direction. -Note that a restricted triclinic box is always *right-handed* so -that (**A** x **B**) points in the direction of **C**. +edge vectors are of the following restricted form: **A** = +(xhi-xlo,0,0), **B** = (xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So +there are 9 parameters in total. Note that the restricted form +requires **A** to be along the x-axis, **B** to be in the xy plane +with a y-component in the +y direction, and **C** to have its +z-component in the +z direction. Note that a restricted triclinic box +is *right-handed* by construction since (**A** cross **B**) points in +the direction of **C**. The *xy,xz,yz* values can be zero or positive or negative. They are called "tilt factors" because they are the amount of displacement -applied to edges of faces of an originally orthogonal box to change it -into a restricted triclinic parallelepiped. +applied to edges of faces of an orthogonal box to change it into a +restricted triclinic parallelepiped. .. note:: - Any general triclinic box (i.e. solid-state crystal basis vectors) - can be rotated in 3d around its origin (and reflected across a - plane if necessary to flip from a left-handed coordinate system to - right-handed) in order to conform to the LAMMPS definition of a - restricted triclinic box. See the discussion in the next - sub-section about general triclinic simulation boxes in LAMMPS. + Any right-handed general triclinic box (i.e. solid-state crystal + basis vectors) can be rotated in 3d around its origin in order to + conform to the LAMMPS definition of a restricted triclinic box. + See the discussion in the next sub-section about general triclinic + simulation boxes in LAMMPS. Note that the :doc:`thermo_style custom ` command has keywords for outputting the various parameters that define both restricted and general triclinic simulation boxes. Thus you can check -the restricted triclinic box parameters LAMMPS generates to -rotate/reflect a general triclinic box to restricted triclinic form. +the restricted triclinic box parameters LAMMPS generates to rotate a +general triclinic box to restricted triclinic form. -For restricted triclinic boxes there are 9 thermo keywords for +For restricted triclinic boxes these are the 9 thermo keywords for (xlo,ylo,zlo), (xhi,yhi,zhi), and the (xy,xz,yz) tilt factors. For -general triclinic boxes there are 12 thermo keywords for (xlo,ylo,zhi) -and the components of the **A**, **B**, **C** edge vectors. For both -orthogonal and restricted triclinic boxes, the thermo keywords -lx/ly/lz refer to the box sizes, namely lx = xhi - xlo, etc. +general triclinic boxes these are the 12 thermo keywords for +(xlo,ylo,zhi) and the components of the **A**, **B**, **C** edge +vectors. For both orthogonal and restricted triclinic boxes, the +thermo keywords lx/ly/lz refer to the box sizes, namely lx = xhi - +xlo, etc. Lx,ly,lz are the box edge vector lengths for orthogonal and +restricted/general triclinic simulation boxes. The remainder of this doc page explains (a) how LAMMPS operates with general triclinic simulation boxes, (b) mathematical transformations @@ -124,7 +127,7 @@ input to LAMMPS. Likewise it allows output of dump files, data files, and thermodynamic data (e.g. pressure tensor) in a general triclinic format. -However, internally, LAMMPS only uses restricted triclinic simulation +However internally, LAMMPS only uses restricted triclinic simulation boxes. This is for parallel efficiency and to formulate partitioning of the simulation box across processors, neighbor list building, and inter-processor communication of per-atom data with methods similar to @@ -139,31 +142,39 @@ This means 4 things which are important to understand: conversion from a restricted to general triclinic system is done at the time of output. * The conversion of the simulation box and per-atom data from general - triclinic to restriced triclinic (and vice versa) is a rotation + - optional reflection from one set of coordinate axes to another. For - orthogonal and restricted triclinic systems, the coordinate axes are - the standard x,y,z axes. For a general triclinic system, those - coordinate axes are rotated in 3d. The optional reflection flips - the axes from right-handed to left-handed if necessary. The 3 - rotated/reflected axes remain mutually orthogonal. For all 3 kinds - of systems (orthogonal, restricted, general), per-atom quantities - (e.g. coords, velocities) are input/output as values consistent with - the corresponding coordinate axes. -* Other LAMMPS commands such as the :doc:`boundary ` or - :doc:`region ` or :doc:`velocity ` or :doc:`set - ` commands, operate on restricted triclinic systems even if a - general triclinic system was defined initially. For an example, see - the paragraph below the folliowing list. + triclinic to restricted triclinic (and vice versa) is a 3d rotation + operation around an origin, which is the lower left corner of the + simulation box. This means an input data file for a general + triclinic system should specify all per-atom quantities consistent + with the general triclinic box and its orientation relative to the + standard x,y,z coordinate axes. For example, atom coordinates + should be inside the general triclinic simulation box defined by the + edge vectors **A**, **B**, **C** and its origin. Likewise per-atom + velocities should be in directions consistent with the general + triclinic box orientation. I.e. a velocity vector that will be in + the +x direction once LAMMPS converts from a general to restricted + triclinic box, should be specified in the data file in the direction + of the **A** edge vector. See the :doc:`read_data ` doc + page for info on all the per-atom vector quantities this rule + affects when the data file for a general triclinic box is input. +* If commands such as :doc:`write_data ` or :doc:`dump + custom ` are used to output general triclinic information, it + is effectively the inverse of the operation described in the + preceeding bullet. +* Other LAMMPS commands such as :doc:`region ` or + :doc:`velocity ` or :doc:`set `, operate on a + restricted triclinic system even if a general triclinic system was + defined initially. This is the list of commands which have general triclinic options: * :doc:`create_box ` - define a general triclinic box * :doc:`create_atoms ` - add atoms to a general triclinic box -* :doc:`lattice ` - define a custom lattice consistent with **A**, **B**, **C** edge vectors of a general triclinic box +* :doc:`lattice ` - define a custom lattice consistent with the **A**, **B**, **C** edge vectors of a general triclinic box * :doc:`read_data ` - read a data file for a general triclinic system * :doc:`write_data ` - write a data file for a general triclinic system * :doc:`dump atom, dump custom ` - output dump snapshots in general triclinic format -* :doc:`dump_modify ` - switch a dump file between restrictied and general triclinic format +* :doc:`dump_modify ` - toggle a dump file between restrictied and general triclinic format * :doc:`thermo_style ` - output the pressure tensor in general triclinic format * :doc:`thermo_modify ` - toggle thermo-style output @@ -171,42 +182,15 @@ This is the list of commands which have general triclinic options: * :doc:`read_restart ` - read a restart file for a general tricliinc system * :doc:`write_restart ` - write a restart file for a general tricliinc system -As an example, consider the velocity of each atom in a general -triclinic system. In a general triclinic data file, each atom will -have coordinates inside a general triclinic box with arbitrary edge -vectors **A**, **B**, **C**. If the file has a "Velocities" section -then the velocity vector of each atom should be in a direction -consistent with the orientation of the general triclnic coordinate -axes. - -When LAMMPS internally converts the general triclinic system to -restricted triclinic, the coordinates of all atoms are transformed -(rotation + optional reflection) to be inside the new restricted -triclinic box. Likewise the velocity vectors are transformed. - -If the :doc:`velocity ` command is used to set an x-velocity -component, it will use the coordinate axes of the restricted box. - -If the atoms and their velocities are output via the :doc:`write_data -` or :doc:`dump custom ` commands, the coordinates -will be transformed (inverse rotation + optional reflection) to be -inside the general triclinic box. Likewise the velocity vector for -each atom will be transformed from restricted to general triclinic. - -Any other vector quantities associated with atoms (magnetic moments, -spins, etc) are transformed in a similar manner back-and-forth between -general and restricted box orientations. - ---------- Transformation from general to restricted triclinic boxes """"""""""""""""""""""""""""""""""""""""""""""""""""""""" -Let **A**,\ **B**,\ **C** be the edge vectors of a general triclinic -simulation box. Assume that **A** x **B** . **C** > 0. The -equivalent LAMMPS **a**,\ **b**,\ **c** for a restricted triclinic box -are a linear rotation of **A**, **B**, and **C** and can be computed -as follows: +Let **A**,\ **B**,\ **C** be the right-handed edge vectors of a +general triclinic simulation box. The equivalent LAMMPS **a**,\ +**b**,\ **c** for a restricted triclinic box are a 3d rotation of +**A**, **B**, and **C** and can be computed as follows: .. math:: @@ -228,15 +212,10 @@ symbol (\^) indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles between the **A**, **B**, **C** vectors as described below. -If **A** x **B** . **C** < 0 the above equations are not valid for -**c**\ . In this case, it is necessary to first apply an -inversion. This can be achieved by interchanging two of the **A**, -**B**, **C** vectors or by changing the sign of one of them. - -For consistency, the same rotation/inversion applied to the triclinic -box edge vectors can also be applied to atom positions, velocities, -and other vector quantities. This can be conveniently achieved by -first converting to fractional coordinates in the general triclinic +For consistency, the same rotation applied to the triclinic box edge +vectors can also be applied to atom positions, velocities, and other +vector quantities. This can be conveniently achieved by first +converting to fractional coordinates in the general triclinic coordinates and then converting to coordinates in the resetricted triclinic basis. The transformation is given by the following equation: @@ -335,9 +314,9 @@ Periodicity and tilt factors for triclinic simulation boxes """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" There is no requirement that a triclinic box be periodic in any -dimension, though it typically should be in y or z if you wish enforce -a shift in coordinates due to periodic boundary conditions across the -y or z boundaries. See the doc page for the :doc:`boundary +dimension, though it typically should be in y or z if you wish to +enforce a shift in coordinates due to periodic boundary conditions +across the y or z boundaries. See the doc page for the :doc:`boundary ` command for an explanation of shifted coordinates for restricted triclinic boxes which are periodic. diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index 772c72cd314..c1adeb1009b 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -83,10 +83,10 @@ See the :doc:`Howto triclinic ` page for a description of both general and restricted triclinic boxes and how to define them. General triclinic boxes (arbitrary edge vectors **A**, **B**, and **C**) are converted internally to restricted triclinic -boxes with tilt factors (xy,xz,yz) added to skew an otherwise -orthogonal box. +boxes with tilt factors (xy,xz,yz) which skew an otherwise orthogonal +box. -The boundary command settings expalined above for the 6 +The boundary command settings explained above for the 6 faces of an orthogonal box also apply in similar manner to the 6 faces of a restricted triclinix box (and thus to the corresponding 6 faces of a general triclinic box), with the following context. diff --git a/src/atom.cpp b/src/atom.cpp index c7c13013c81..6d983cd7f17 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1038,7 +1038,7 @@ void Atom::deallocate_topology() /* ---------------------------------------------------------------------- unpack N lines from Atom section of data file - call style-specific routine to parse line + call atom-style specific method to parse each line triclinic_general = 1 if data file defines a general triclinic box ------------------------------------------------------------------------- */ @@ -1217,6 +1217,8 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, if (coord[0] >= sublo[0] && coord[0] < subhi[0] && coord[1] >= sublo[1] && coord[1] < subhi[1] && coord[2] >= sublo[2] && coord[2] < subhi[2]) { + + // atom-style specific method parses single line avec->data_atom(xdata,imagedata,values,typestr); typestr = utils::utf8_subst(typestr); diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index f7a0f6f5663..d94365db438 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -1659,7 +1659,6 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vectornlocal; if (nlocal == nmax) grow(0); @@ -2227,7 +2226,8 @@ void AtomVec::write_improper(FILE *fp, int n, tagint **buf, int index) /* ---------------------------------------------------------------------- convert info input by read_data from general to restricted triclinic - parent class only operates on data from Velocities section of data file + atom coords are converted in Atom::data_atoms() + parent class operates on data from Velocities section of data file child classes operate on all other data: Atoms, Ellipsoids, Lines, Triangles, etc ------------------------------------------------------------------------- */ @@ -2256,6 +2256,7 @@ void AtomVec::read_data_general_to_restricted(int nlocal_previous, int nlocal) /* ---------------------------------------------------------------------- convert info output by write_data from restricted to general triclinic + create "hold" copy of original restricted data to restore after data file is written parent class only operates on x and data from Velocities section of data file child classes operate on all other data: Atoms, Ellipsoids, Lines, Triangles, etc ------------------------------------------------------------------------- */ diff --git a/src/domain.cpp b/src/domain.cpp index 439dafd7659..700cf79a82e 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -292,12 +292,13 @@ void Domain::set_global_box() } // update general triclinic box if defined - // reset ABC edge vectors from restricted triclinic box - // boxlo = lower left corner of general triclinic box + // reset general tri ABC edge vectors from restricted tri box if (triclinic_general) { double aprime[3],bprime[3],cprime[3]; + // A'B'C' = edge vectors of restricted triclinic box + aprime[0] = boxhi[0] - boxlo[0]; aprime[1] = aprime[2] = 0.0; bprime[0] = xy; diff --git a/src/domain.h b/src/domain.h index 206038f2952..41994e21407 100644 --- a/src/domain.h +++ b/src/domain.h @@ -40,7 +40,7 @@ class Domain : protected Pointers { // 3 = shrink-wrap non-per w/ min int triclinic; // 0 = orthog box, 1 = triclinic (restricted or general) - int triclinic_general; // 1 if mapping to/from general triclinic is stored, 0 if not + int triclinic_general; // 1 if general <-> restricted tri mapping is stored, 0 if not // orthogonal box @@ -50,7 +50,7 @@ class Domain : protected Pointers { double prd_half[3]; // array form of half dimensions // restricted triclinic box - // xyzprd,xyzprd_half and prd,prd_half = same as if not tilted + // xyz prd,xyz prd_half and prd,prd_half = same as if not tilted double prd_lamda[3]; // lamda box = (1,1,1) double prd_half_lamda[3]; // lamda half box = (0.5,0.5,0.5) diff --git a/src/read_data.cpp b/src/read_data.cpp index 7b885904525..b34dac54eb1 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -576,7 +576,7 @@ void ReadData::command(int narg, char **arg) if (!triclinic_general) { - // orthongal box + // orthogonal or restricted triclinic box domain->boxlo[0] = boxlo[0]; domain->boxhi[0] = boxhi[0]; @@ -605,8 +605,6 @@ void ReadData::command(int narg, char **arg) // change simulation box to be union of existing box and new box + shift // only done if firstpass and not first data file - // for restricted triclinic, new tilt factors not allowed - // for general triclinic, different new box and shift not allowed if (firstpass && addflag != NONE) { @@ -670,7 +668,7 @@ void ReadData::command(int narg, char **arg) int flag_all; MPI_Allreduce(&iflag, &flag_all, 1, MPI_INT, MPI_SUM, world); if ((flag_all > 0) && (comm->me == 0)) - error->warning(FLERR, "Non-zero image flags with growing box leads to bad coordinates"); + error->warning(FLERR, "Non-zero image flags with growing box can produce bad coordinates"); } } @@ -689,6 +687,7 @@ void ReadData::command(int narg, char **arg) lmap = new LabelMap(lmp, ntypes, nbondtypes, nangletypes, ndihedraltypes, nimpropertypes); } + // ------------------------------------------------------------------------------------- // rest of data file is Sections // read in any order, except where error checks // customize for new sections @@ -1391,10 +1390,9 @@ void ReadData::header(int firstpass) if (addflag == NONE) atom->nimpropertypes = nimpropertypes + extra_improper_types; // these settings only used by first data file - // also, these are obsolescent. we parse them to maintain backward - // compatibility, but the recommended way is to set them via keywords - // in the LAMMPS input file. In case these flags are set in both, - // the input and the data file, we use the larger of the two. + // NOTEL these are now obsolete, we parse them to maintain backward compatibility + // the recommended way is to set them via command keywords in the input script + // if these flags are set both ways, the larger of the two values is used } else if (strstr(line, "extra bond per atom")) { if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp); diff --git a/src/read_data.h b/src/read_data.h index 28b277860a1..495c17d500c 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -59,15 +59,16 @@ class ReadData : public Command { class LabelMap *lmap; - // box info + // box info read from file + int triclinic, triclinic_general; + int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag; + int avec_flag, bvec_flag, cvec_flag, abc_origin_flag; + double boxlo[3], boxhi[3]; double xy, xz, yz; double avec[3], bvec[3], cvec[3]; double abc_origin[3]; - int triclinic, triclinic_general; - int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag; - int avec_flag, bvec_flag, cvec_flag, abc_origin_flag; // optional args From e57079768f973aa7b070cfdc17ef7f799b5ca41c Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 9 Nov 2023 17:58:12 -0700 Subject: [PATCH 049/719] update some doc pages --- doc/src/Howto_triclinic.rst | 36 ++--- doc/src/fix_rigid.rst | 281 +++++++++++++++++++----------------- doc/src/read_data.rst | 202 +++++++++++++++----------- 3 files changed, 280 insertions(+), 239 deletions(-) diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 0a66af4b36b..6cbc0644cd5 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -56,9 +56,9 @@ at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), **C** = (cx,cy,cz) which can be arbitrary vectors, so long as they are non-zero, distinct, and not co-planar. In addition, they must define a right-handed system, such that (**A** cross **B**) -points in the direction of **C**. Note that a left-handed system can -be converted to a right-handed system by simply swapping the order of -any two of the **A**, **B**, **C** vectors. +points in the direction of **C**. A left-handed system can be +converted to a right-handed system by simply swapping the order of any +pair of the **A**, **B**, **C** vectors. The 4 commands listed above for defining orthogonal simulation boxes have triclinic options which allow for specification of the origin and @@ -151,12 +151,12 @@ This means 4 things which are important to understand: should be inside the general triclinic simulation box defined by the edge vectors **A**, **B**, **C** and its origin. Likewise per-atom velocities should be in directions consistent with the general - triclinic box orientation. I.e. a velocity vector that will be in + triclinic box orientation. E.g. a velocity vector which will be in the +x direction once LAMMPS converts from a general to restricted triclinic box, should be specified in the data file in the direction of the **A** edge vector. See the :doc:`read_data ` doc - page for info on all the per-atom vector quantities this rule - affects when the data file for a general triclinic box is input. + page for info on all the per-atom vector quantities to which this + rule applies when a data file for a general triclinic box is input. * If commands such as :doc:`write_data ` or :doc:`dump custom ` are used to output general triclinic information, it is effectively the inverse of the operation described in the @@ -332,16 +332,18 @@ will become non-orthogonal, e.g. due to use of the :doc:`fix npt you can use the :doc:`change_box ` command to convert a simulation box from orthogonal to restricted triclinic and vice versa. -Highly tilted restricted triclinic simulation boxes can be -computationally inefficient. This is due to the large volume of -communication needed to acquire ghost atoms around a processor's -irregular-shaped subdomain. For extreme values of tilt, LAMMPS may -also lose atoms and generate an error. +.. note:: + + Highly tilted restricted triclinic simulation boxes can be + computationally inefficient. This is due to the large volume of + communication needed to acquire ghost atoms around a processor's + irregular-shaped subdomain. For extreme values of tilt, LAMMPS may + also lose atoms and generate an error. LAMMPS will issue a warning if you define a restricted triclinic box with a tilt factor which skews the box more than half the distance of the parallel box length, which is the first dimension in the tilt -factor (x for xz). +factor (e.g. x for xz). For example, if xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt factor should be between -5 and 5 to avoid the warning. @@ -361,8 +363,8 @@ occur using the :doc:`fix deform ` or :doc:`fix npt either of the commands. One exception to box flipping is if the first dimension in the tilt -factor (x for xy) is non-periodic. In that case, the limits on the -tilt factor are not enforced, since flipping the box in that dimension -would not change the atom positions due to non-periodicity. In this -mode, if the system tilts to large angles, the simulation will simply -become inefficient, due to the highly skewed simulation box. +factor (e.g. x for xy) is non-periodic. In that case, the limits on +the tilt factor are not enforced, since flipping the box in that +dimension would not change the atom positions due to non-periodicity. +In this mode, if the system tilts to large angles, the simulation will +simply become inefficient, due to the highly skewed simulation box. diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index a50e2156812..2192f9ed1f6 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -169,14 +169,15 @@ Examples of large rigid bodies are a colloidal particle, or portions of a biomolecule such as a protein. Example of small rigid bodies are patchy nanoparticles, such as those -modeled in :ref:`this paper ` by Sharon Glotzer's group, clumps of -granular particles, lipid molecules consisting of one or more point -dipoles connected to other spheroids or ellipsoids, irregular -particles built from line segments (2d) or triangles (3d), and -coarse-grain models of nano or colloidal particles consisting of a -small number of constituent particles. Note that the :doc:`fix shake ` command can also be used to rigidify small -molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats -the constituent atoms as point masses. +modeled in :ref:`this paper ` by Sharon Glotzer's group, +clumps of granular particles, lipid molecules consisting of one or +more point dipoles connected to other spheroids or ellipsoids, +irregular particles built from line segments (2d) or triangles (3d), +and coarse-grain models of nano or colloidal particles consisting of a +small number of constituent particles. Note that the :doc:`fix shake +` command can also be used to rigidify small molecules of +2, 3, or 4 atoms, e.g. water molecules. That fix treats the +constituent atoms as point masses. These fixes also update the positions and velocities of the atoms in each rigid body via time integration, in the NVE, NVT, NPT, or NPH @@ -210,13 +211,14 @@ processors when ghost atom info is accumulated. .. note:: - To use the *rigid/small* styles the ghost atom cutoff must be - large enough to span the distance between the atom that owns the body - and every other atom in the body. This distance value is printed out - when the rigid bodies are defined. If the - :doc:`pair_style ` cutoff plus neighbor skin does not span - this distance, then you should use the :doc:`comm_modify cutoff ` command with a setting epsilon larger than - the distance. + To use the *rigid/small* styles the ghost atom cutoff must be large + enough to span the distance between the atom that owns the body and + every other atom in the body. This distance value is printed out + when the rigid bodies are defined. If the :doc:`pair_style + ` cutoff plus neighbor skin does not span this + distance, then you should use the :doc:`comm_modify cutoff + ` command with a setting epsilon larger than the + distance. Which of the two variants is faster for a particular problem is hard to predict. The best way to decide is to perform a short test run. @@ -227,49 +229,54 @@ differences may accumulate to produce divergent trajectories. .. note:: You should not update the atoms in rigid bodies via other - time-integration fixes (e.g. :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix npt `, :doc:`fix move `), - or you will have conflicting updates to positions and velocities - resulting in unphysical behavior in most cases. When performing a hybrid - simulation with some atoms in rigid bodies, and some not, a separate - time integration fix like :doc:`fix nve ` or :doc:`fix nvt ` should be used for the non-rigid particles. + time-integration fixes (e.g. :doc:`fix nve `, :doc:`fix + nvt `, :doc:`fix npt `, :doc:`fix move + `), or you will have conflicting updates to positions and + velocities resulting in unphysical behavior in most cases. When + performing a hybrid simulation with some atoms in rigid bodies, and + some not, a separate time integration fix like :doc:`fix nve + ` or :doc:`fix nvt ` should be used for the + non-rigid particles. .. note:: - These fixes are overkill if you simply want to hold a collection - of atoms stationary or have them move with a constant velocity. A - simpler way to hold atoms stationary is to not include those atoms in - your time integration fix. E.g. use "fix 1 mobile nve" instead of - "fix 1 all nve", where "mobile" is the group of atoms that you want to - move. You can move atoms with a constant velocity by assigning them - an initial velocity (via the :doc:`velocity ` command), - setting the force on them to 0.0 (via the :doc:`fix setforce ` command), and integrating them as usual - (e.g. via the :doc:`fix nve ` command). + These fixes are overkill if you simply want to hold a collection of + atoms stationary or have them move with a constant velocity. A + simpler way to hold atoms stationary is to not include those atoms + in your time integration fix. E.g. use "fix 1 mobile nve" instead + of "fix 1 all nve", where "mobile" is the group of atoms that you + want to move. You can move atoms with a constant velocity by + assigning them an initial velocity (via the :doc:`velocity + ` command), setting the force on them to 0.0 (via the + :doc:`fix setforce ` command), and integrating them + as usual (e.g. via the :doc:`fix nve ` command). .. warning:: - The aggregate properties of each rigid body are - calculated at the start of a simulation run and are maintained in - internal data structures. The properties include the position and - velocity of the center-of-mass of the body, its moments of inertia, and - its angular momentum. This is done using the properties of the - constituent atoms of the body at that point in time (or see the *infile* - keyword option). Thereafter, changing these properties of individual - atoms in the body will have no effect on a rigid body's dynamics, unless - they effect any computation of per-atom forces or torques. If the - keyword *reinit* is set to *yes* (the default), the rigid body data - structures will be recreated at the beginning of each *run* command; - if the keyword *reinit* is set to *no*, the rigid body data structures - will be built only at the very first *run* command and maintained for - as long as the rigid fix is defined. For example, you might think you - could displace the atoms in a body or add a large velocity to each atom - in a body to make it move in a desired direction before a second run is - performed, using the :doc:`set ` or - :doc:`displace_atoms ` or :doc:`velocity ` - commands. But these commands will not affect the internal attributes - of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no* - (or using the *infile* option, which implies *reinit* *no*\ ) the position - and velocity of individual atoms in the body will be reset when time - integration starts again. + The aggregate properties of each rigid body are calculated at the + start of a simulation run and are maintained in internal data + structures. The properties include the position and velocity of the + center-of-mass of the body, its moments of inertia, and its angular + momentum. This is done using the properties of the constituent + atoms of the body at that point in time (or see the *infile* + keyword option). Thereafter, changing these properties of + individual atoms in the body will have no effect on a rigid body's + dynamics, unless they effect any computation of per-atom forces or + torques. If the keyword *reinit* is set to *yes* (the default), the + rigid body data structures will be recreated at the beginning of + each *run* command; if the keyword *reinit* is set to *no*, the + rigid body data structures will be built only at the very first + *run* command and maintained for as long as the rigid fix is + defined. For example, you might think you could displace the atoms + in a body or add a large velocity to each atom in a body to make it + move in a desired direction before a second run is performed, using + the :doc:`set ` or :doc:`displace_atoms ` or + :doc:`velocity ` commands. But these commands will not + affect the internal attributes of the body unless *reinit* is set + to *yes*\ . With *reinit* set to *no* (or using the *infile* + option, which implies *reinit* *no*\ ) the position and velocity of + individual atoms in the body will be reset when time integration + starts again. ---------- @@ -314,17 +321,17 @@ to be part of rigid bodies. .. note:: - To compute the initial center-of-mass position and other - properties of each rigid body, the image flags for each atom in the - body are used to "unwrap" the atom coordinates. Thus you must ensure - that these image flags are consistent so that the unwrapping creates a + To compute the initial center-of-mass position and other properties + of each rigid body, the image flags for each atom in the body are + used to "unwrap" the atom coordinates. Thus you must ensure that + these image flags are consistent so that the unwrapping creates a valid rigid body (one where the atoms are close together), - particularly if the atoms in a single rigid body straddle a periodic - boundary. This means the input data file or restart file must define - the image flags for each atom consistently or that you have used the - :doc:`set ` command to specify them correctly. If a dimension is - non-periodic then the image flag of each atom must be 0 in that - dimension, else an error is generated. + particularly if the atoms in a single rigid body straddle a + periodic boundary. This means the input data file or restart file + must define the image flags for each atom consistently or that you + have used the :doc:`set ` command to specify them correctly. + If a dimension is non-periodic then the image flag of each atom + must be 0 in that dimension, else an error is generated. The *force* and *torque* keywords discussed next are only allowed for the *rigid* styles. @@ -360,12 +367,13 @@ settings from the final keyword are used. .. note:: - For computational efficiency, you may wish to turn off pairwise - and bond interactions within each rigid body, as they no longer - contribute to the motion. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` - commands are used to do this. If the rigid bodies have strongly - overlapping atoms, you may need to turn off these interactions to - avoid numerical problems due to large equal/opposite intra-body forces + For computational efficiency, you may wish to turn off pairwise and + bond interactions within each rigid body, as they no longer + contribute to the motion. The :doc:`neigh_modify exclude + ` and :doc:`delete_bonds ` commands are + used to do this. If the rigid bodies have strongly overlapping + atoms, you may need to turn off these interactions to avoid + numerical problems due to large equal/opposite intra-body forces swamping the contribution of small inter-body forces. For computational efficiency, you should typically define one fix @@ -377,7 +385,8 @@ is more expensive. The constituent particles within a rigid body can be point particles (the default in LAMMPS) or finite-size particles, such as spheres or -ellipsoids or line segments or triangles. See the :doc:`atom_style sphere and ellipsoid and line and tri ` commands for more +ellipsoids or line segments or triangles. See the :doc:`atom_style +sphere and ellipsoid and line and tri ` commands for more details on these kinds of particles. Finite-size particles contribute differently to the moment of inertia of a rigid body than do point particles. Finite-size particles can also experience torque (e.g. due @@ -387,7 +396,8 @@ orientation. These contributions are accounted for by these fixes. Forces between particles within a body do not contribute to the external force or torque on the body. Thus for computational efficiency, you may wish to turn off pairwise and bond interactions -between particles within each rigid body. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` +between particles within each rigid body. The :doc:`neigh_modify +exclude ` and :doc:`delete_bonds ` commands are used to do this. For finite-size particles this also means the particles can be highly overlapped when creating the rigid body. @@ -399,16 +409,17 @@ perform constant NVE time integration. They are referred to below as the 4 NVE rigid styles. The only difference is that the *rigid* and *rigid/small* styles use an integration technique based on Richardson iterations. The *rigid/nve* and *rigid/small/nve* styles uses the -methods described in the paper by :ref:`Miller `, which are thought -to provide better energy conservation than an iterative approach. +methods described in the paper by :ref:`Miller `, which are +thought to provide better energy conservation than an iterative +approach. The *rigid/nvt* and *rigid/nvt/small* styles performs constant NVT integration using a Nose/Hoover thermostat with chains as described -originally in :ref:`(Hoover) ` and :ref:`(Martyna) `, which -thermostats both the translational and rotational degrees of freedom -of the rigid bodies. They are referred to below as the 2 NVT rigid -styles. The rigid-body algorithm used by *rigid/nvt* is described in -the paper by :ref:`Kamberaj `. +originally in :ref:`(Hoover) ` and :ref:`(Martyna) +`, which thermostats both the translational and rotational +degrees of freedom of the rigid bodies. They are referred to below as +the 2 NVT rigid styles. The rigid-body algorithm used by *rigid/nvt* +is described in the paper by :ref:`Kamberaj `. The *rigid/npt*, *rigid/nph*, *rigid/npt/small*, and *rigid/nph/small* styles perform constant NPT or NPH integration using a Nose/Hoover @@ -434,12 +445,12 @@ The target pressures for each of the 6 components of the stress tensor can be specified independently via the *x*, *y*, *z* keywords, which correspond to the 3 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped -value during the run from *Pstart* to *Pstop*\ . If a target pressure is -specified for a component, then the corresponding box dimension will -change during a simulation. For example, if the *y* keyword is used, -the y-box length will change. A box dimension will not change if that -component is not specified, although you have the option to change -that dimension via the :doc:`fix deform ` command. +value during the run from *Pstart* to *Pstop*\ . If a target pressure +is specified for a component, then the corresponding box dimension +will change during a simulation. For example, if the *y* keyword is +used, the y-box length will change. A box dimension will not change +if that component is not specified, although you have the option to +change that dimension via the :doc:`fix deform ` command. For all barostat keywords, the *Pdamp* parameter operates like the *Tdamp* parameter, determining the time scale on which pressure is @@ -523,11 +534,11 @@ discussed below. The *langevin* keyword applies a Langevin thermostat to the constant NVE time integration performed by any of the 4 NVE rigid styles: -*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot be -used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ . The -desired temperature at each timestep is a ramped value during the run -from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in time -units and determines how rapidly the temperature is relaxed. For +*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot +be used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ . +The desired temperature at each timestep is a ramped value during the +run from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in +time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 means to relax the temperature in a timespan of (roughly) 100 time units (:math:`\tau` or fs or ps - see the :doc:`units ` command). The random # *seed* must be a positive @@ -562,29 +573,30 @@ used. *Tchain* is the number of thermostats in the Nose Hoover chain. This value, along with *Tdamp* can be varied to dampen undesirable oscillations in temperature that can occur in a simulation. As a rule of thumb, increasing the chain length should lead to smaller -oscillations. The keyword *pchain* specifies the number of -thermostats in the chain thermostatting the barostat degrees of -freedom. +oscillations. The keyword *pchain* specifies the number of thermostats +in the chain thermostatting the barostat degrees of freedom. .. note:: There are alternate ways to thermostat a system of rigid bodies. - You can use :doc:`fix langevin ` to treat the individual - particles in the rigid bodies as effectively immersed in an implicit - solvent, e.g. a Brownian dynamics model. For hybrid systems with both - rigid bodies and solvent particles, you can thermostat only the - solvent particles that surround one or more rigid bodies by - appropriate choice of groups in the compute and fix commands for - temperature and thermostatting. The solvent interactions with the - rigid bodies should then effectively thermostat the rigid body - temperature as well without use of the Langevin or Nose/Hoover options - associated with the fix rigid commands. + You can use :doc:`fix langevin ` to treat the + individual particles in the rigid bodies as effectively immersed in + an implicit solvent, e.g. a Brownian dynamics model. For hybrid + systems with both rigid bodies and solvent particles, you can + thermostat only the solvent particles that surround one or more + rigid bodies by appropriate choice of groups in the compute and fix + commands for temperature and thermostatting. The solvent + interactions with the rigid bodies should then effectively + thermostat the rigid body temperature as well without use of the + Langevin or Nose/Hoover options associated with the fix rigid + commands. ---------- The *mol* keyword can only be used with the *rigid/small* styles. It -must be used when other commands, such as :doc:`fix deposit ` or :doc:`fix pour `, add rigid -bodies on-the-fly during a simulation. You specify a *template-ID* +must be used when other commands, such as :doc:`fix deposit +` or :doc:`fix pour `, add rigid bodies +on-the-fly during a simulation. You specify a *template-ID* previously defined using the :doc:`molecule ` command, which reads a file that defines the molecule. You must use the same *template-ID* that the other fix which is adding rigid bodies uses. @@ -668,16 +680,16 @@ cross periodic boundaries during the simulation. .. note:: - If you use the *infile* or *mol* keywords and write restart - files during a simulation, then each time a restart file is written, - the fix also write an auxiliary restart file with the name - rfile.rigid, where "rfile" is the name of the restart file, + If you use the *infile* or *mol* keywords and write restart files + during a simulation, then each time a restart file is written, the + fix also write an auxiliary restart file with the name rfile.rigid, + where "rfile" is the name of the restart file, e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary - file is in the same format described above. Thus it can be used in a - new input script that restarts the run and re-specifies a rigid fix - using an *infile* keyword and the appropriate filename. Note that the - auxiliary file will contain one line for every rigid body, even if the - original file only listed a subset of the rigid bodies. + file is in the same format described above. Thus it can be used in + a new input script that restarts the run and re-specifies a rigid + fix using an *infile* keyword and the appropriate filename. Note + that the auxiliary file will contain one line for every rigid body, + even if the original file only listed a subset of the rigid bodies. If the system has rigid bodies with finite-size overlapping particles and the model uses the :doc:`fix gravity ` command to @@ -726,10 +738,11 @@ also accounted for by this fix. ---------- -If your simulation is a hybrid model with a mixture of rigid bodies and -non-rigid particles (e.g. solvent) there are several ways these rigid -fixes can be used in tandem with :doc:`fix nve `, :doc:`fix nvt -`, :doc:`fix npt `, and :doc:`fix nph `. +If your simulation is a hybrid model with a mixture of rigid bodies +and non-rigid particles (e.g. solvent) there are several ways these +rigid fixes can be used in tandem with :doc:`fix nve `, +:doc:`fix nvt `, :doc:`fix npt `, and :doc:`fix nph +`. If you wish to perform NVE dynamics (no thermostatting or barostatting), use one of 4 NVE rigid styles to integrate the rigid @@ -739,14 +752,14 @@ particles. If you wish to perform NVT dynamics (thermostatting, but no barostatting), you can use one of the 2 NVT rigid styles for the rigid bodies, and any thermostatting fix for the non-rigid particles -(:doc:`fix nvt `, :doc:`fix langevin `, :doc:`fix -temp/berendsen `). You can also use one of the 4 -NVE rigid styles for the rigid bodies and thermostat them using -:doc:`fix langevin ` on the group that contains all the -particles in the rigid bodies. The net force added by :doc:`fix -langevin ` to each rigid body effectively thermostats its -translational center-of-mass motion. Not sure how well it does at -thermostatting its rotational motion. +(:doc:`fix nvt `, :doc:`fix langevin `, +:doc:`fix temp/berendsen `). You can also use one +of the 4 NVE rigid styles for the rigid bodies and thermostat them +using :doc:`fix langevin ` on the group that contains +all the particles in the rigid bodies. The net force added by +:doc:`fix langevin ` to each rigid body effectively +thermostats its translational center-of-mass motion. Not sure how +well it does at thermostatting its rotational motion. If you wish to perform NPT or NPH dynamics (barostatting), you cannot use both :doc:`fix npt ` and the NPT or NPH rigid styles. This @@ -772,12 +785,12 @@ to the global pressure and the box is scaled the same by any of the barostatting fixes. You could even use the second and third options for a non-hybrid -simulation consisting of only rigid bodies, assuming you give :doc:`fix -npt ` an empty group, though it's an odd thing to do. The -barostatting fixes (:doc:`fix npt ` and :doc:`fix press/berensen -`) will monitor the pressure and change the box -dimensions, but not time integrate any particles. The integration of -the rigid bodies will be performed by fix rigid/nvt. +simulation consisting of only rigid bodies, assuming you give +:doc:`fix npt ` an empty group, though it's an odd thing to +do. The barostatting fixes (:doc:`fix npt ` and :doc:`fix +press/berensen `) will monitor the pressure and +change the box dimensions, but not time integrate any particles. The +integration of the rigid bodies will be performed by fix rigid/nvt. ---------- @@ -822,10 +835,10 @@ various :doc:`output commands `. The scalar value calculated by these fixes is "intensive". The scalar is the current temperature of the collection of rigid bodies. This is averaged over all rigid bodies and their translational and rotational degrees of -freedom. The translational energy of a rigid body is 1/2 m v\^2, where -m = total mass of the body and v = the velocity of its center of mass. -The rotational energy of a rigid body is 1/2 I w\^2, where I = the -moment of inertia tensor of the body and w = its angular velocity. +freedom. The translational energy of a rigid body is 1/2 m v\^2, +where m = total mass of the body and v = the velocity of its center of +mass. The rotational energy of a rigid body is 1/2 I w\^2, where I = +the moment of inertia tensor of the body and w = its angular velocity. Degrees of freedom constrained by the *force* and *torque* keywords are removed from this calculation, but only for the *rigid* and *rigid/nve* fixes. diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 1d81acb51ed..7dda35d7bbd 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -63,11 +63,16 @@ Description Read in a data file containing information LAMMPS needs to run a simulation. The file can be ASCII text or a gzipped text file -(detected by a .gz suffix). This is one of 3 ways to specify initial -atom coordinates; see the :doc:`read_restart ` and -:doc:`create_atoms ` commands for alternative methods. -Also see the explanation of the :doc:`-restart command-line switch -` which can convert a restart file to a data file. +(detected by a .gz suffix). + +This is one of 3 ways to specify the simulation box: see the +:doc:`create_box ` and :doc:`read_restart ` +and commands for alternative methods. It is also one of 3 ways to +specify initial atom coordinates: see the :doc:`create_atoms +` and :doc:`read_restart ` and commands +for alternative methods. Also see the explanation of the +:doc:`-restart command-line switch ` which can convert a +restart file to a data file. This command can be used multiple times to add new atoms and their properties to an existing system by using the *add*, *offset*, and @@ -133,6 +138,17 @@ keyword must be used. will separate the atoms in the bond, which can lead to "lost" bond atoms or bad dynamics. +.. note:: + + If the first read_data command defined a restricted or general + triclinic simulation box (see the sub-section below on header + keywords), then subsequent data files have restrictions. For a + restricted triclinic box, the 3 tilt factors ("xy xz yz" keyword) + must have the same values in subsequent data files. For a general + triclinic box, the avec, bvec, cvec, and "abc origin" keywords must + have the same values in subsequent data files. Also the *shift* + keyword cannot be used in subsequent read_data commands. + The three choices for the *add* argument affect how the atom IDs and molecule IDs of atoms in the data file are treated. If *append* is specified, atoms in the data file are added to the current system, @@ -372,8 +388,8 @@ For a restricted triclinic box, the *xy xz yz* keyword is used in addition to the *xlo xhi*, *ylo yhi*, *zlo zhi* keywords. The three *xy,xz,yz* values can be 0.0 or positive or negative, and are called "tilt factors" because they are the amount of displacement applied to -faces of an orthogonal box to transform it into a restricted triclinic -parallelepiped. +edges of faces of an orthogonal box to transform it into a restricted +triclinic parallelepiped. The :doc:`Howto_triclinic ` doc page discusses the tilt factors in detail and explains that the resulting edge vectors of @@ -383,11 +399,11 @@ a restricted triclinic box are: * **B** = (xy,yhi-ylo,0) * **C** = (xz,yz,zhi-zlo) -This restricted form of edge vectors means that **A** is along the -x-axis, **B** is in the xy plane with a y-component in the +y -direction, and **C** has a z-component in the +z direction. The -origin (lower left corner) of the restricted triclinic box is at -(xlo,ylo,zlo). +This restricted form of edge vectors requires that **A** be in the +direction of the x-axis, **B** be in the xy plane with its y-component +in the +y direction, and **C** have its z-component in the +z +direction. The origin (lower left corner) of the restricted triclinic +box is at (xlo,ylo,zlo). For a 2d simulation, the zlo and zhi values must straddle zero. The default zlo/zhi values do this, so that keyword is not needed in 2d. @@ -433,16 +449,19 @@ origin* keywords are used. The *xlo xhi*, *ylo yhi*, *zlo zhi*, and *xy xz yz* keywords are not used. The first 3 keywords define the 3 edge vectors **A**, **B**, **C** of a general triclinic box. They can be arbitrary vectors so long as they are distinct, non-zero, and not -co-planar. There is no "right-hand rule" requirement that (**A** x -**B**) point in the direction of **C**. The origin of the box (origin -of the 3 edge vectors) is set by the *abc origin* keyword. +co-planar. They must also define a right-handed system requirement +such that (**A** x **B**) points in the direction of **C**. A +left-handed system can be converted to a right-handed system by simply +swapping the order of any pair of the **A**, **B**, **C** vectors. +The origin of the box (origin of the 3 edge vectors) is set by the +*abc origin* keyword. The default values for these 4 keywords are as follows: * avec = (1,0,0) * bvec = (0,1,0) * cvec = (0,0,1) -* *abc origin = (0,0,0) for 3d, (0,0,-0.5) for 2d +* abc origin = (0,0,0) for 3d, (0,0,-0.5) for 2d For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of *abc origin* must be -0.5. These are the default values, so the @@ -452,18 +471,18 @@ For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of LAMMPS allows specification of general triclinic simulation boxes as a convenience for users who may be converting data from - solid-state crystallograhic representations or ftom DFT codes for + solid-state crystallograhic representations or from DFT codes for input to LAMMPS. However, as explained on the - :doc:`Howto_triclinic ` doc page, internally + :doc:`Howto_triclinic ` doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means the box and per-atom information (e.g. coordinates, velocities) in the data file are converted from general to restricted triclinic - form as soon as the file is read. This means other sections of the - data file must specify their per-atom data appropriately. This - requirement is explained below for the relevant sections. The - :doc:`Howto_triclinic ` doc page also discusses - other LAMMPS commands which can input/output general triclinic - representations of the simulation box and per-atom data. + form when the file is read. Other sections of the data file must + also list their per-atom data appropriately if vector quantities + are specified. This requirement is explained below for the relevant + sections. The :doc:`Howto_triclinic ` doc page + also discusses other LAMMPS commands which can input/output general + triclinic representations of the simulation box and per-atom data. The following explanations apply to all 3 kinds of simulation boxes: orthogonal, restricted triclinic, and general triclinic. @@ -509,24 +528,25 @@ needed, so that the image flag would be zero. .. note:: - If the system is non-periodic (in a dimension), then all atoms in the - data file must have coordinates (in that dimension) that are "greater - than or equal to" the lo value and "less than or equal to" the hi - value. If the non-periodic dimension is of style "fixed" (see the - :doc:`boundary ` command), then the atom coords must be - strictly "less than" the hi value, due to the way LAMMPS assign atoms - to processors. Note that you should not make the lo/hi values - radically smaller/larger than the extent of the atoms. For example, - if your atoms extend from 0 to 50, you should not specify the box - bounds as -10000 and 10000 unless you also use the :doc:`processors - command `. This is because LAMMPS uses the specified box - size to layout the 3d grid of processors. A huge (mostly empty) box - will be sub-optimal for performance when using "fixed" boundary - conditions (see the :doc:`boundary ` command). When using - "shrink-wrap" boundary conditions (see the :doc:`boundary ` - command), a huge (mostly empty) box may cause a parallel simulation - to lose atoms when LAMMPS shrink-wraps the box around the atoms. The - read_data command will generate an error in this case. + If the system is non-periodic (in a dimension), then all atoms in + the data file must have coordinates (in that dimension) that are + "greater than or equal to" the lo value and "less than or equal to" + the hi value. If the non-periodic dimension is of style "fixed" + (see the :doc:`boundary ` command), then the atom coords + must be strictly "less than" the hi value, due to the way LAMMPS + assign atoms to processors. Note that you should not make the + lo/hi values radically smaller/larger than the extent of the atoms. + For example, if atoms extend from 0 to 50, you should not specify + the box bounds as -10000 and 10000 unless you also use the + :doc:`processors command `. This is because LAMMPS + uses the specified box size to layout the 3d grid of processors. A + huge (mostly empty) box will be sub-optimal for performance when + using "fixed" boundary conditions (see the :doc:`boundary + ` command). When using "shrink-wrap" boundary conditions + (see the :doc:`boundary ` command), a huge (mostly empty) + box may cause a parallel simulation to lose atoms when LAMMPS + shrink-wraps the box around the atoms. The read_data command will + generate an error in this case. ---------- @@ -557,12 +577,12 @@ and :doc:`molecule ` doc pages for more discussion of .. note:: - All of the "extra" settings are only applied in the first data - file read and when no simulation box has yet been created; as soon as + All of the "extra" settings are only applied in the first data file + read and when no simulation box has yet been created; as soon as the simulation box is created (and read_data implies that), these settings are *locked* and cannot be changed anymore. Please see the - description of the *add* keyword above for reading multiple data files. - If they appear in later data files, they are ignored. + description of the *add* keyword above for reading multiple data + files. If they appear in later data files, they are ignored. The "ellipsoids" and "lines" and "triangles" and "bodies" settings are only used with :doc:`atom_style ellipsoid or line or tri or body @@ -575,14 +595,14 @@ below. See the discussion of bodyflag and the *Bodies* section below. .. note:: - For :doc:`atom_style template `, the molecular - topology (bonds,angles,etc) is contained in the molecule templates - read-in by the :doc:`molecule ` command. This means you - cannot set the *bonds*, *angles*, etc header keywords in the data - file, nor can you define *Bonds*, *Angles*, etc sections as discussed + For :doc:`atom_style template `, the molecular topology + (bonds,angles,etc) is contained in the molecule templates read-in + by the :doc:`molecule ` command. This means you cannot + set the *bonds*, *angles*, etc header keywords in the data file, + nor can you define *Bonds*, *Angles*, etc sections as discussed below. You can set the *bond types*, *angle types*, etc header - keywords, though it is not necessary. If specified, they must match - the maximum values defined in any of the template molecules. + keywords, though it is not necessary. If specified, they must + match the maximum values defined in any of the template molecules. ---------- @@ -780,13 +800,13 @@ of analysis. For orthogonal and restricted and general triclinic simulation boxes, the atom coordinates (x,y,z) listed in this section should be inside the corresponding simulation box. For restricted - triclinic boxes that means the parallelepiped defined by the by the - *xlo xhi*, *ylo yhi*, *zlo zhi*, and *xy xz yz*, keywords. For - general triclinic boxes that means the parallelepiped defined by - the 3 edge vectors and origin specified by the *avec*, *bvec*, - *cvec*, and *abc origin* header keywords. See the discussion in - the header section above about how atom coordinates outside the - simulation box are (or are not) remapped to be inside the box. + triclinic boxes that means the parallelepiped defined by the *xlo + xhi*, *ylo yhi*, *zlo zhi*, and *xy xz yz*, keywords. For general + triclinic boxes that means the parallelepiped defined by the 3 edge + vectors and origin specified by the *avec*, *bvec*, *cvec*, and + *abc origin* header keywords. See the discussion in the header + section above about how atom coordinates outside the simulation box + are (or are not) remapped to be inside the box. .. list-table:: @@ -865,13 +885,13 @@ The per-atom values have these meanings and units, listed alphabetically: * lineflag = 1 for line segment particles, 0 for point or spherical particles * mass = mass of particle (mass units) * molecule-ID = integer ID of molecule the atom belongs to -* mux,muy,muz = components of dipole moment of atom (dipole units) (see general triclinic comment below) +* mux,muy,muz = components of dipole moment of atom (dipole units) (see general triclinic note below) * normx,normy,normz = components of dielectric dipole moment of atom (dipole - units) (see general triclinic comment below) + units) (see general triclinic note below) * q = charge on atom (charge units) * rho = density (need units) for SPH particles * sp = magnitude of magnetic spin of atom (Bohr magnetons) -* spx,spy,spz = components of magnetic spin of atom (unit vector) (see general triclinic comment below) +* spx,spy,spz = components of magnetic spin of atom (unit vector) (see general triclinic note below) * template-atom = which atom within a template molecule the atom is * template-index = which molecule within the molecule template the atom is part of * theta = internal temperature of a DPD particle @@ -879,29 +899,31 @@ The per-atom values have these meanings and units, listed alphabetically: * volume = volume of Peridynamic particle (distance\^3 units) * x,y,z = coordinates of atom (distance units) * x0,y0,z0 = original (strain-free) coordinates of atom (distance - units) (see general triclinic comment below) + units) (see general triclinic note below) The units for these quantities depend on the unit style; see the :doc:`units ` command for details. -For 2d simulations, z must be specified as 0.0. If the data file is -created by another program, then z values for a 2d simulation can be -within epsilon of 0.0, and LAMMPS will force them to zero. +For 2d simulations, the atom coordinate z must be specified as 0.0. +If the data file is created by another program, then z values for a 2d +simulation can be within epsilon of 0.0, and LAMMPS will force them to +zero. -If the data file defines a general triclinic box, then the following -per-atom values in the list above are per-atom vectors: (mux,muy,muz), -(normx,normy,normz), (spx,spy,spz). They should be specified with -values for the rotated coordinate axes of the general triclinic box. -Likewise, (x0,y0,z0) are per-atom coordinates and should be values -inside the general triclinic box, the same as explained for (x,y,z) -above. See the :doc:`Howto triclinic ` doc page for -more details. +.. note:: -If the data file defines a general triclinic box, then each of the 3 -vectors (translational velocity, angular momentum, angule velocity) -sholld be specified for the rotated coordinate axes of the general -triclinic box. See the :doc:`Howto triclinic ` doc -page for more details. + If the data file defines a general triclinic box, then the + following per-atom values in the list above are per-atom vectors + which imply an orientation: (mux,muy,muz), (normx,normy,normz), + (spx,spy,spz). This menas they should be specified consistent with + the general triclinic box and its orientation relative to the + standard x,y,z coordinate axes. For example a dipole moment vector + which will be in the +x direction once LAMMPS converts from a + general to restricted triclinic box, should be specified in the + data file in the direction of the **A** edge vector. Likewise the + (x0,y0,z0) per-atom strain-free coordinates should be inside the + general triclinic simulation box as explained in the note above. + See the :doc:`Howto triclinic ` doc page for more + details. The atom-ID is used to identify the atom throughout the simulation and in dump files. Normally, it is a unique value from 1 to Natoms for @@ -1049,9 +1071,8 @@ that use unwrapped coordinates internally are as follows: Atom velocities and other atom quantities not defined above are set to 0.0 when the *Atoms* section is read. Velocities can be set later by -a *Velocities* section in the data file or by a -:doc:`velocity ` or :doc:`set ` command in the input -script. +a *Velocities* section in the data file or by a :doc:`velocity +` or :doc:`set ` command in the input script. ---------- @@ -1329,11 +1350,10 @@ LAMMPS normalizes each atom's quaternion in case (a,b,c) is not specified as a unit vector. If the data file defines a general triclinic box, then the quaternion -for each ellipsoid should be specified for its orientation in the -general triclinic system with respect to the standard xyz axes (not -the rotated coordinate axes of the general triclinic system). When -the general triclinic box is transformed to a restricted triclinic -box, the ellipsoid quaternions will be altered appropriately. +for each ellipsoid should be specified for its orientation relative to +the standard x,y,z coordinate axes. When the system is converted to a +restricted triclinic box, the ellipsoid quaternions will be altered +appropriately. The *Ellipsoids* section must appear after the *Atoms* section. @@ -1458,6 +1478,12 @@ the line segment with a unit vector in the +z direction, gives an I.e. normal = (c2-c1) x (0,0,1). This orientation may be important for defining some interactions. +If the data file defines a general triclinic box, then the quaternion +for each ellipsoid should be specified for its orientation relative to +the standard x,y,z coordinate axes. When the system is converted to a +restricted triclinic box, the ellipsoid quaternions will be altered +appropriately. + If the data file defines a general triclinic box, the (x1,y1) and (x2,y2) values should be within (or near) its parallelogram area, i.e. near the x,y coordinates of the line segment as defined in the From a651697d2e8477927c04eaf1db5ba0a5ef4b6f5c Mon Sep 17 00:00:00 2001 From: Ludwig Ahrens-Iwers Date: Mon, 13 Nov 2023 14:41:13 +0100 Subject: [PATCH 050/719] Mix eta in Electrode package --- doc/src/fix_electrode.rst | 7 + examples/PACKAGES/electrode/madelung/data.eta | 34 +++++ .../PACKAGES/electrode/madelung/data.eta_mix | 34 +++++ examples/PACKAGES/electrode/madelung/eval.py | 4 +- examples/PACKAGES/electrode/madelung/in.eta | 17 +++ .../PACKAGES/electrode/madelung/in.eta_cg | 17 +++ .../PACKAGES/electrode/madelung/in.eta_mix | 17 +++ .../PACKAGES/electrode/madelung/plate_cap.py | 125 +++++++++--------- .../electrode/madelung/settings_eta.mod | 19 +++ examples/PACKAGES/electrode/madelung/test.sh | 16 ++- src/ELECTRODE/electrode_matrix.cpp | 20 ++- src/ELECTRODE/electrode_matrix.h | 3 + src/ELECTRODE/electrode_vector.cpp | 35 +++-- src/ELECTRODE/electrode_vector.h | 3 + src/ELECTRODE/fix_electrode_conp.cpp | 36 ++++- src/ELECTRODE/fix_electrode_conp.h | 2 + 16 files changed, 307 insertions(+), 82 deletions(-) create mode 100644 examples/PACKAGES/electrode/madelung/data.eta create mode 100644 examples/PACKAGES/electrode/madelung/data.eta_mix create mode 100644 examples/PACKAGES/electrode/madelung/in.eta create mode 100644 examples/PACKAGES/electrode/madelung/in.eta_cg create mode 100644 examples/PACKAGES/electrode/madelung/in.eta_mix create mode 100644 examples/PACKAGES/electrode/madelung/settings_eta.mod diff --git a/doc/src/fix_electrode.rst b/doc/src/fix_electrode.rst index 5685482a716..d807da7fd28 100644 --- a/doc/src/fix_electrode.rst +++ b/doc/src/fix_electrode.rst @@ -70,6 +70,8 @@ Syntax filename = file from which to read inverted matrix *qtotal* value = number or *v_* equal-style variable add overall potential so that all electrode charges add up to *qtotal* + *eta* value = d_propname + d_propname = a custom double vector defined via fix property/atom Examples """""""" @@ -264,6 +266,11 @@ individual electrodes, and since *symm on* constrains the total charge of all electrodes to be zero, either option is incompatible with the *qtotal* keyword (even if *qtotal* is set to zero). +The keyword *eta* takes the name of a custom double vector defined via fix +property/atom. The values will be used instead of the standard eta value. The +property/atom fix must be for vector of double values and use the *ghost on* +option. + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/examples/PACKAGES/electrode/madelung/data.eta b/examples/PACKAGES/electrode/madelung/data.eta new file mode 100644 index 00000000000..b05700a4ab2 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/data.eta @@ -0,0 +1,34 @@ +LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0 + +4 atoms +3 atom types + +0 1 xlo xhi +0 1 ylo yhi +-10 10 zlo zhi + +Masses + +1 196.966553 +2 196.966553 +3 1.0 + +Pair Coeffs # lj/cut/coul/long + +1 0 0 +2 0 0 +3 0 0 + +Atoms # full + +1 1 1 0.00 0.00 0.00 -2.00 # bottom electrode +2 2 2 0.00 0.00 0.00 2.00 # top electrode +3 3 3 0.50 0.00 0.00 -1.00 # bottom electrolyte +4 3 3 -0.50 0.00 0.00 1.00 # top electrolyte + +ETA + +1 2.0 +2 2.0 +3 0 +4 0 diff --git a/examples/PACKAGES/electrode/madelung/data.eta_mix b/examples/PACKAGES/electrode/madelung/data.eta_mix new file mode 100644 index 00000000000..9322ebd6622 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/data.eta_mix @@ -0,0 +1,34 @@ +LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0 + +4 atoms +3 atom types + +0 1 xlo xhi +0 1 ylo yhi +-10 10 zlo zhi + +Masses + +1 196.966553 +2 196.966553 +3 1.0 + +Pair Coeffs # lj/cut/coul/long + +1 0 0 +2 0 0 +3 0 0 + +Atoms # full + +1 1 1 0.00 0.00 0.00 -2.00 # bottom electrode +2 2 2 0.00 0.00 0.00 2.00 # top electrode +3 3 3 0.50 0.00 0.00 -1.00 # bottom electrolyte +4 3 3 -0.50 0.00 0.00 1.00 # top electrolyte + +ETA + +1 0.5 +2 3.0 +3 0 +4 0 diff --git a/examples/PACKAGES/electrode/madelung/eval.py b/examples/PACKAGES/electrode/madelung/eval.py index 2f5a355d9bc..feda0e384ed 100644 --- a/examples/PACKAGES/electrode/madelung/eval.py +++ b/examples/PACKAGES/electrode/madelung/eval.py @@ -1,7 +1,7 @@ #!/usr/env/python3 -import sys import os.path as op +import sys def rel_error(out, ref): @@ -49,5 +49,5 @@ def rel_error(out, ref): error = rel_error(out, ref) lines.append(f"{label}: {out:.5f}, {error:.5f}\n") -with open("madelung.txt", 'a') as f: +with open("madelung.txt", "a") as f: f.writelines(lines) diff --git a/examples/PACKAGES/electrode/madelung/in.eta b/examples/PACKAGES/electrode/madelung/in.eta new file mode 100644 index 00000000000..d928f8fed08 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.eta @@ -0,0 +1,17 @@ +atom_style full +units real +boundary p p f + +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc +pair_style lj/cut/coul/long 12 + +fix feta all property/atom d_eta ghost yes +read_data data.eta fix feta NULL ETA + +include "settings_eta.mod" + +fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.eta_cg b/examples/PACKAGES/electrode/madelung/in.eta_cg new file mode 100644 index 00000000000..e04db318d57 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.eta_cg @@ -0,0 +1,17 @@ +atom_style full +units real +boundary p p f + +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc +pair_style lj/cut/coul/long 12 + +fix feta all property/atom d_eta ghost yes +read_data data.eta_mix fix feta NULL ETA + +include "settings_eta.mod" + +fix conp bot electrode/conp 0 2 couple top 1 symm on algo cg 1e-6 eta d_eta + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.eta_mix b/examples/PACKAGES/electrode/madelung/in.eta_mix new file mode 100644 index 00000000000..d4bcf712251 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.eta_mix @@ -0,0 +1,17 @@ +atom_style full +units real +boundary p p f + +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc +pair_style lj/cut/coul/long 12 + +fix feta all property/atom d_eta ghost on +read_data data.eta_mix fix feta NULL ETA + +include "settings_eta.mod" + +fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/plate_cap.py b/examples/PACKAGES/electrode/madelung/plate_cap.py index 62d52fe102a..fcca1668691 100755 --- a/examples/PACKAGES/electrode/madelung/plate_cap.py +++ b/examples/PACKAGES/electrode/madelung/plate_cap.py @@ -3,7 +3,6 @@ import numpy as np from scipy.special import erf -ETA = 2 SQRT2 = np.sqrt(2) COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units QE2F = 23.060549 @@ -17,14 +16,14 @@ def lattice(length): return np.array(np.meshgrid(x, y)).T.reshape(-1, 2) -def a_element(r): +def a_element(r, eta): """Coulomb contribution of two Gaussians""" - return erf(ETA / SQRT2 * r) / r + return erf(eta * r) / r -def b_element(r, q): +def b_element(r, q, eta): """Coulomb contribution of a Gaussian with a point charge""" - return q * erf(ETA * r) / r + return q * erf(eta * r) / r a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2) @@ -36,59 +35,65 @@ def b_element(r, q): # distances to images within electrode and to opposite electrode distances = a * np.linalg.norm(lattice(LENGTH), axis=1) -opposite_distances = np.sqrt(np.square(distances) + distance_plates ** 2) - -# self interaction and within original box -A_11 = np.sqrt(2 / np.pi) * ETA -A_12 = erf(ETA * distance_plates / SQRT2) / distance_plates - -# interaction with periodic images -A_11 += 4 * np.sum(a_element(distances)) -A_12 += 4 * np.sum(a_element(opposite_distances)) -A = np.array([[A_11, A_12], [A_12, A_11]]) -inv = np.linalg.inv(A) -e = np.array([1, 1]) -inv -= np.matmul(inv, np.matmul(np.outer(e, e), inv)) / np.dot(e, np.dot(inv, e)) - -# electrode-electrolyte interaction -b = [] -for x in x_elec: - bi = 0 - for y, q in zip(x_elyt, q_elyt): - d = abs(y - x) - bi += b_element(d, q) - image_distances = np.sqrt(np.square(distances) + d ** 2) - bi += 4 * np.sum(b_element(image_distances, q)) - b.append(bi) -b = np.array(b) - -# electrolyte-electrolyte energy -elyt_11 = 4 * np.sum(1 / distances) -distance_elyt = x_elyt[1] - x_elyt[0] -elyt_12 = 1 / distance_elyt + 4 * np.sum( - 1 / np.sqrt(np.square(distances) + distance_elyt ** 2) -) -elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]]) -energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt)) - -# electrode charges and energy -q = np.dot(inv, v - b) -energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt) - -print( - "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A" -) -print( - ", ".join( - [ - str(LENGTH), - f"{energy:.8f}", - f"{q[0]:.10f}", - f"{q[1]:.10f}", - f"{inv[0, 0]:.10f}", - f"{inv[0, 1]:.10f}", - f"{b[0]:.8f}", - f"{b[1]:.8f}", - ] +opposite_distances = np.sqrt(np.square(distances) + distance_plates**2) + +for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]: + eta_mix = np.prod(eta_elec) / np.sqrt(np.sum(np.square(eta_elec))) + # self interaction and within original box + A_11 = np.sqrt(2 / np.pi) * eta_elec[0] + A_22 = np.sqrt(2 / np.pi) * eta_elec[1] + A_12 = erf(eta_mix * distance_plates) / distance_plates + + # interaction with periodic images + A_11 += 4 * np.sum(a_element(distances, eta_elec[0] / SQRT2)) + A_22 += 4 * np.sum(a_element(distances, eta_elec[1] / SQRT2)) + A_12 += 4 * np.sum(a_element(opposite_distances, eta_mix)) + A = np.array([[A_11, A_12], [A_12, A_22]]) + inv = np.linalg.inv(A) + e = np.array([1, 1]) + inv -= np.matmul(inv, np.matmul(np.outer(e, e), inv)) / np.dot(e, np.dot(inv, e)) + + # electrode-electrolyte interaction + b = [] + for x, eta in zip(x_elec, eta_elec): + bi = 0 + for y, q in zip(x_elyt, q_elyt): + d = abs(y - x) + bi += b_element(d, q, eta) + image_distances = np.sqrt(np.square(distances) + d**2) + bi += 4 * np.sum(b_element(image_distances, q, eta)) + b.append(bi) + b = np.array(b) + + # electrolyte-electrolyte energy + elyt_11 = 4 * np.sum(1 / distances) + distance_elyt = x_elyt[1] - x_elyt[0] + elyt_12 = 1 / distance_elyt + 4 * np.sum( + 1 / np.sqrt(np.square(distances) + distance_elyt**2) ) -) + elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]]) + energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt)) + + # electrode charges and energy + q = np.dot(inv, v - b) + energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt) + + with open(f"plate_cap{name}.csv", "w") as f: + f.write( + "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A\n" + ) + f.write( + ", ".join( + [ + str(LENGTH), + f"{energy:.8f}", + f"{q[0]:.10f}", + f"{q[1]:.10f}", + f"{inv[0, 0]:.10f}", + f"{inv[0, 1]:.10f}", + f"{b[0]:.8f}", + f"{b[1]:.8f}", + ] + ) + + "\n" + ) diff --git a/examples/PACKAGES/electrode/madelung/settings_eta.mod b/examples/PACKAGES/electrode/madelung/settings_eta.mod new file mode 100644 index 00000000000..aee63bf2e96 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/settings_eta.mod @@ -0,0 +1,19 @@ + +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +group bot type 1 +group top type 2 + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop + diff --git a/examples/PACKAGES/electrode/madelung/test.sh b/examples/PACKAGES/electrode/madelung/test.sh index edac04f5b1f..a558ee67110 100644 --- a/examples/PACKAGES/electrode/madelung/test.sh +++ b/examples/PACKAGES/electrode/madelung/test.sh @@ -7,17 +7,27 @@ if [ ! -f $lmpbin ]; then fi ref_out="plate_cap.csv" -if [ ! -f $ref_out ]; then +ref_mix_out="plate_cap_eta_mix.csv" +if [ ! -f $ref_out ] || [ ! -f $ref_mix_out ]; then echo "Generating reference data" - python3 plate_cap.py > $ref_out + python3 plate_cap.py fi echo "Running Lammps inputs" +# w/o eta mixing rm -rf madelung.txt && touch madelung.txt -for file in in.*; do +for file in in.eta in.ewald-ew3dc in.ewald-ew2d in.pppm-ew3dc in.cg; do printf "\n$file\n" >> madelung.txt rm -f out.csv inv.csv vec.csv $lmpbin -i $file &> /dev/null python3 eval.py $ref_out out.csv inv.csv vec.csv done + +# with eta mixing +for file in in.eta_mix in.eta_cg; do + printf "\n$file\n" >> madelung.txt + rm -f out.csv inv.csv vec.csv + $lmpbin -i $file &> /dev/null + python3 eval.py $ref_mix_out out.csv inv.csv vec.csv +done cat madelung.txt diff --git a/src/ELECTRODE/electrode_matrix.cpp b/src/ELECTRODE/electrode_matrix.cpp index 7be9119c627..d917fb1f975 100644 --- a/src/ELECTRODE/electrode_matrix.cpp +++ b/src/ELECTRODE/electrode_matrix.cpp @@ -43,6 +43,7 @@ ElectrodeMatrix::ElectrodeMatrix(LAMMPS *lmp, int electrode_group, double eta) : groupbit = group->bitmask[igroup]; ngroup = group->count(igroup); this->eta = eta; + etaflag = false; tfflag = false; } @@ -72,6 +73,14 @@ void ElectrodeMatrix::setup_tf(const std::map &tf_types) /* ---------------------------------------------------------------------- */ +void ElectrodeMatrix::setup_eta(int index) +{ + etaflag = true; + eta_index = index; +} + +/* ---------------------------------------------------------------------- */ + void ElectrodeMatrix::compute_array(double **array, bool timer_flag) { // setting all entries of coulomb matrix to zero @@ -115,8 +124,6 @@ void ElectrodeMatrix::pair_contribution(double **array) int nlocal = atom->nlocal; int newton_pair = force->newton_pair; - double const etaij = eta * eta / sqrt(2.0 * eta * eta); // see mw ewald theory eq. (29)-(30) - // neighbor list will be ready because called from post_neighbor inum = list->inum; ilist = list->ilist; @@ -135,6 +142,7 @@ void ElectrodeMatrix::pair_contribution(double **array) xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; @@ -152,6 +160,9 @@ void ElectrodeMatrix::pair_contribution(double **array) jtype = type[j]; if (rsq < cutsq[itype][jtype]) { + double const eta_j = etaflag ? atom->dvector[eta_index][j] : eta; + double const etaij = eta_i * eta_j / sqrt(eta_i * eta_i + eta_j * eta_j); + r = sqrt(rsq); rinv = 1.0 / r; aij = rinv; @@ -178,7 +189,10 @@ void ElectrodeMatrix::self_contribution(double **array) const double preta = MY_SQRT2 / MY_PIS; for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { array[mpos[i]][mpos[i]] += preta * eta - selfint; } + if (mask[i] & groupbit) { + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; + array[mpos[i]][mpos[i]] += preta * eta_i - selfint; + } } /* ---------------------------------------------------------------------- */ diff --git a/src/ELECTRODE/electrode_matrix.h b/src/ELECTRODE/electrode_matrix.h index 8499cfdb342..1c64d8a4c45 100644 --- a/src/ELECTRODE/electrode_matrix.h +++ b/src/ELECTRODE/electrode_matrix.h @@ -30,6 +30,7 @@ class ElectrodeMatrix : protected Pointers { ElectrodeMatrix(class LAMMPS *, int, double); void setup(const std::unordered_map &, class Pair *, class NeighList *); void setup_tf(const std::map &); + void setup_eta(int); void compute_array(double **, bool); int igroup; @@ -39,6 +40,8 @@ class ElectrodeMatrix : protected Pointers { double **cutsq; double g_ewald, eta; bool tfflag; + bool etaflag; + int eta_index; std::map tf_types; std::unordered_map tag_to_iele; bool assigned; diff --git a/src/ELECTRODE/electrode_vector.cpp b/src/ELECTRODE/electrode_vector.cpp index 245ba577273..a2eaf784c50 100644 --- a/src/ELECTRODE/electrode_vector.cpp +++ b/src/ELECTRODE/electrode_vector.cpp @@ -29,6 +29,7 @@ #include "neigh_list.h" #include "pair.h" +#include #include #include @@ -47,6 +48,7 @@ ElectrodeVector::ElectrodeVector(LAMMPS *lmp, int sensor_group, int source_group source_grpbit = group->bitmask[source_group]; this->eta = eta; tfflag = false; + etaflag = false; kspace_time_total = 0; pair_time_total = 0; @@ -93,6 +95,14 @@ void ElectrodeVector::setup_tf(const std::map &tf_types) /* ---------------------------------------------------------------------- */ +void ElectrodeVector::setup_eta(int index) +{ + etaflag = true; + eta_index = index; +} + +/* ---------------------------------------------------------------------- */ + void ElectrodeVector::compute_vector(double *vector) { MPI_Barrier(world); @@ -121,7 +131,6 @@ void ElectrodeVector::compute_vector(double *vector) void ElectrodeVector::pair_contribution(double *vector) { - double const etaij = eta * MY_ISQRT2; double **x = atom->x; double *q = atom->q; int *type = atom->type; @@ -142,6 +151,7 @@ void ElectrodeVector::pair_contribution(double *vector) double const xtmp = x[i][0]; double const ytmp = x[i][1]; double const ztmp = x[i][2]; + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; int itype = type[i]; int *jlist = firstneigh[i]; int jnum = numneigh[i]; @@ -158,18 +168,22 @@ void ElectrodeVector::pair_contribution(double *vector) double const rsq = delx * delx + dely * dely + delz * delz; int jtype = type[j]; if (rsq >= cutsq[itype][jtype]) continue; + double const eta_j = etaflag ? atom->dvector[eta_index][j] : eta; + double etaij; + if (i_in_sensor && j_in_sensor) + etaij = eta_i * eta_j / sqrt(eta_i * eta_i + eta_j * eta_j); + else if (i_in_sensor) + etaij = eta_i; + else { + assert(j_in_sensor); + etaij = eta_j; + } double const r = sqrt(rsq); double const rinv = 1.0 / r; double aij = rinv; aij *= ElectrodeMath::safe_erfc(g_ewald * r); - if (invert_source) - aij -= ElectrodeMath::safe_erfc(eta * r) * rinv; - else - aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv; - if (i_in_sensor) { - vector[i] += aij * q[j]; - //} else if (j_in_sensor) { - } + aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv; + if (i_in_sensor) { vector[i] += aij * q[j]; } if (j_in_sensor && (!invert_source || !i_in_sensor)) { vector[j] += aij * q[i]; } } } @@ -189,9 +203,10 @@ void ElectrodeVector::self_contribution(double *vector) for (int ii = 0; ii < inum; ii++) { int const i = ilist[ii]; + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; bool const i_in_sensor = (mask[i] & groupbit); bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source; - if (i_in_sensor && i_in_source) vector[i] += (preta * eta - selfint) * q[i]; + if (i_in_sensor && i_in_source) vector[i] += (preta * eta_i - selfint) * q[i]; } } diff --git a/src/ELECTRODE/electrode_vector.h b/src/ELECTRODE/electrode_vector.h index e7f637dd2df..a4f274a0493 100644 --- a/src/ELECTRODE/electrode_vector.h +++ b/src/ELECTRODE/electrode_vector.h @@ -29,6 +29,7 @@ class ElectrodeVector : protected Pointers { ~ElectrodeVector() override; void setup(class Pair *, class NeighList *, bool); void setup_tf(const std::map &); + void setup_eta(int); void compute_vector(double *); int igroup, source_group; @@ -39,6 +40,8 @@ class ElectrodeVector : protected Pointers { double **cutsq; double g_ewald, eta; bool tfflag; + bool etaflag; + int eta_index; std::map tf_types; class Pair *pair; class NeighList *list; diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp index 13866cd3946..a87642182b0 100644 --- a/src/ELECTRODE/fix_electrode_conp.cpp +++ b/src/ELECTRODE/fix_electrode_conp.cpp @@ -97,6 +97,7 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : top_group = 0; intelflag = false; tfflag = false; + etaflag = false; timer_flag = false; update_time = 0; @@ -211,6 +212,19 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : qtotal = utils::numeric(FLERR, arg[iarg], false, lmp); qtotal_var_style = VarStyle::CONST; } + } else if ((strcmp(arg[iarg], "eta") == 0)) { + if (iarg + 2 > narg) error->all(FLERR, "Need two arguments after eta command"); + etaflag = true; + int is_double, cols; + eta_index = atom->find_custom(arg[++iarg] + 2, is_double, cols); + if (eta_index == -1) + error->all(FLERR, "eta keyword requires name of previously defined property"); + if (!is_double) error->all(FLERR, "eta keyword requires double-valued property/atom vector"); + if (cols != 0) error->all(FLERR, "eta keyword requires property/atom vector not an array"); + if (!atom->nextra_border) + error->all(FLERR, + "There is no fix with ghost on, but the eta keyword requires a property/atom " + "fix with ghost on"); // toggle parameters } else if ((strcmp(arg[iarg], "etypes") == 0)) { etypes_neighlists = utils::logical(FLERR, arg[++iarg], false, lmp); @@ -520,8 +534,10 @@ void FixElectrodeConp::setup_post_neighbor() evscale = force->qe2f / force->qqrd2e; elyt_vector->setup(pair, vec_neighlist, timer_flag); + if (etaflag) elyt_vector->setup_eta(eta_index); if (need_elec_vector) { elec_vector->setup(pair, mat_neighlist, timer_flag); + if (etaflag) elec_vector->setup_eta(eta_index); if (tfflag) elec_vector->setup_tf(tf_types); } @@ -556,7 +572,8 @@ void FixElectrodeConp::setup_post_neighbor() if (etypes_neighlists) neighbor->build_one(mat_neighlist, 0); auto array_compute = std::unique_ptr(new ElectrodeMatrix(lmp, igroup, eta)); array_compute->setup(tag_to_iele, pair, mat_neighlist); - if (tfflag) { array_compute->setup_tf(tf_types); } + if (etaflag) array_compute->setup_eta(eta_index); + if (tfflag) array_compute->setup_tf(tf_types); array_compute->compute_array(elastance, timer_flag); } // write_mat before proceeding if (comm->me == 0 && write_mat) { @@ -1186,7 +1203,7 @@ double FixElectrodeConp::self_energy(int eflag) // corrections to energy due to self interaction double const qqrd2e = force->qqrd2e; int const nlocal = atom->nlocal; - double const pre = eta / sqrt(MY_2PI) * qqrd2e; + double const pre = 1. / sqrt(MY_2PI) * qqrd2e; int *mask = atom->mask; int *type = atom->type; double *q = atom->q; @@ -1194,7 +1211,8 @@ double FixElectrodeConp::self_energy(int eflag) for (int i = 0; i < nlocal; i++) { if (groupbit & mask[i]) { double const q2 = q[i] * q[i]; - double e = pre * q2; + double ieta = etaflag ? atom->dvector[eta_index][i] : eta; + double e = ieta * pre * q2; if (tfflag && (groupbit & mask[i])) e += 0.5 * qqrd2e * q2 * tf_types[type[i]]; energy += e; if (eflag) { @@ -1234,6 +1252,7 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag) double xtmp = x[i][0]; double ytmp = x[i][1]; double ztmp = x[i][2]; + double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta; int itype = type[i]; int *jlist = firstneigh[i]; int jnum = numneigh[i]; @@ -1242,7 +1261,6 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag) int const j = jlist[jj] & NEIGHMASK; bool j_in_ele = groupbit & mask[j]; if (!(i_in_ele || j_in_ele)) continue; - double eta_ij = (i_in_ele && j_in_ele) ? eta / MY_SQRT2 : eta; double delx = xtmp - x[j][0]; double dely = ytmp - x[j][1]; @@ -1251,6 +1269,16 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag) int jtype = type[j]; if (rsq < force->pair->cutsq[itype][jtype]) { + double const eta_j = etaflag ? atom->dvector[eta_index][j] : eta; + double eta_ij; + if (i_in_ele && j_in_ele) + eta_ij = eta_i * eta_j / sqrt(eta_i * eta_i + eta_j * eta_j); + else if (i_in_ele) + eta_ij = eta_i; + else { + assert(j_in_ele); + eta_ij = eta_j; + } double r2inv = 1.0 / rsq; double r = sqrt(rsq); double erfc_etar = 0.; diff --git a/src/ELECTRODE/fix_electrode_conp.h b/src/ELECTRODE/fix_electrode_conp.h index 689a44053ca..fa972c0acc5 100644 --- a/src/ELECTRODE/fix_electrode_conp.h +++ b/src/ELECTRODE/fix_electrode_conp.h @@ -138,6 +138,8 @@ class FixElectrodeConp : public Fix { int get_top_group(); // used by ffield int top_group; // used by ffield bool tfflag; + int eta_index; // index of atom property for eta + bool etaflag; // eta specified as atom property bool timer_flag; std::map tf_types; // cg From 4da49c6d85673952c4a7f58916607bbcb2590142 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 13 Nov 2023 15:22:17 -0700 Subject: [PATCH 051/719] more updates to doc page and read_data functionality --- doc/src/Howto_body.rst | 4 +- doc/src/read_data.rst | 62 ++++++++++++++------------ src/DIELECTRIC/atom_vec_dielectric.cpp | 12 ++--- src/DIPOLE/atom_vec_dipole.cpp | 12 ++--- src/MACHDYN/atom_vec_smd.cpp | 2 +- src/SPIN/atom_vec_spin.cpp | 12 ++--- src/atom_vec_line.cpp | 19 ++++++-- src/atom_vec_line.h | 1 - src/atom_vec_tri.cpp | 12 +++-- src/atom_vec_tri.h | 2 - src/domain.cpp | 2 +- src/write_data.cpp | 11 +++-- 12 files changed, 90 insertions(+), 61 deletions(-) diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 88fa2d9c974..15d6aee8459 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -102,8 +102,8 @@ particles of different styles | :doc:`dump image ` | output body particle attributes as an image | +------------------------------------------------+-----------------------------------------------------+ -The pair styles defined for use with specific body styles are listed -in the sections below. +The pair styles currently defined for use with specific body styles +are listed in the sections below. ---------- diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 7dda35d7bbd..d26d0ab5778 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -914,7 +914,7 @@ zero. If the data file defines a general triclinic box, then the following per-atom values in the list above are per-atom vectors which imply an orientation: (mux,muy,muz), (normx,normy,normz), - (spx,spy,spz). This menas they should be specified consistent with + (spx,spy,spz). This means they should be specified consistent with the general triclinic box and its orientation relative to the standard x,y,z coordinate axes. For example a dipole moment vector which will be in the +x direction once LAMMPS converts from a @@ -1352,8 +1352,8 @@ specified as a unit vector. If the data file defines a general triclinic box, then the quaternion for each ellipsoid should be specified for its orientation relative to the standard x,y,z coordinate axes. When the system is converted to a -restricted triclinic box, the ellipsoid quaternions will be altered -appropriately. +restricted triclinic box, the ellipsoid quaternions will be altered to +reflect the new orientation of the ellipsoid. The *Ellipsoids* section must appear after the *Atoms* section. @@ -1471,24 +1471,23 @@ is used and any atoms are listed in the *Atoms* section with a lineflag = 1. The number of lines should be specified in the header section via the "lines" keyword. -The 2 end points are the end points of the line segment. The ordering -of the 2 points should be such that using a right-hand rule to cross -the line segment with a unit vector in the +z direction, gives an -"outward" normal vector perpendicular to the line segment. +The 2 end points are the end points of the line segment. They should +be values close to the center point of the line segment specified in +the Atoms section of the data file, even if individual end points are +outside the simulation box. + +The ordering of the 2 points should be such that using a right-hand +rule to cross the line segment with a unit vector in the +z direction, +gives an "outward" normal vector perpendicular to the line segment. I.e. normal = (c2-c1) x (0,0,1). This orientation may be important for defining some interactions. -If the data file defines a general triclinic box, then the quaternion -for each ellipsoid should be specified for its orientation relative to -the standard x,y,z coordinate axes. When the system is converted to a -restricted triclinic box, the ellipsoid quaternions will be altered -appropriately. - -If the data file defines a general triclinic box, the (x1,y1) and -(x2,y2) values should be within (or near) its parallelogram area, -i.e. near the x,y coordinates of the line segment as defined in the -Atoms section. See the :doc:`Howto triclinic ` doc -page for more details. +If the data file defines a general triclinic box, then the x1,y1 and +x2,y2 values for each line segment should be specified for its +orientation relative to the standard x,y,z coordinate axes. When the +system is converted to a restricted triclinic box, the x1,y1,x2,y2 +values will be altered to reflect the new orientation of the line +segment. The *Lines* section must appear after the *Atoms* section. @@ -1616,17 +1615,22 @@ The *Triangles* section must appear if :doc:`atom_style tri with a triangleflag = 1. The number of lines should be specified in the header section via the "triangles" keyword. -The 3 corner points are the corner points of the triangle. The -ordering of the 3 points should be such that using a right-hand rule -to go from point1 to point2 to point3 gives an "outward" normal vector -to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This -orientation may be important for defining some interactions. - -If the data file defines a general triclinic box, the (x1,y1,z1), -(x2,y2,z2), (x3,y3,z3) corner points should be within (or near) its -parallelepiped volume, i.e. near the x,y,z coordinates of the triangle -as defined in the Atoms section. See the :doc:`Howto triclinic -` doc page for more details. +The 3 corner points are the corner points of the triangle. They +should be values close to the center point of the triangle specified +in the Atoms section of the data file, even if individual corner +points are outside the simulation box. + +The ordering of the 3 points should be such that using a right-hand +rule to go from point1 to point2 to point3 gives an "outward" normal +vector to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). +This orientation may be important for defining some interactions. + +If the data file defines a general triclinic box, then the x1,y1,z1 +and x2,y2,z2 and x3,y3,z3 values for each triangle should be specified +for its orientation relative to the standard x,y,z coordinate axes. +When the system is converted to a restricted triclinic box, the +x1,y1,z1,x2,y2,z2,x3,y3,z3 values will be altered to reflect the new +orientation of the triangle. The *Triangles* section must appear after the *Atoms* section. diff --git a/src/DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp index 516c08bd986..617ad4ebea5 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -208,7 +208,7 @@ void AtomVecDielectric::read_data_general_to_restricted(int nlocal_previous, int /* ---------------------------------------------------------------------- convert info output by write_data from restricted to general triclinic parent class operates on x and data from Velocities section of data file - child class operates on dipole momemt mu + child class operates on dipole momemt mu which has 4 values per atom ------------------------------------------------------------------------- */ void AtomVecDielectric::write_data_restricted_to_general() @@ -217,16 +217,17 @@ void AtomVecDielectric::write_data_restricted_to_general() int nlocal = atom->nlocal; memory->create(mu_hold,nlocal,3,"atomvec:mu_hold"); - if (nlocal) memcpy(&mu_hold[0][0],&mu[0][0],3*nlocal*sizeof(double)); - for (int i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) { + memcpy(&mu_hold[i],&mu[i],3*sizeof(double)); domain->restricted_to_general_vector(mu[i]); + } } /* ---------------------------------------------------------------------- restore info output by write_data to restricted triclinic original data is in "hold" arrays parent class operates on x and data from Velocities section of data file - child class operates on dipole moment mu + child class operates on dipole moment mu which has 4 values per atom ------------------------------------------------------------------------- */ void AtomVecDielectric::write_data_restore_restricted() @@ -236,7 +237,8 @@ void AtomVecDielectric::write_data_restore_restricted() if (!mu_hold) return; int nlocal = atom->nlocal; - memcpy(&mu[0][0],&mu_hold[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + memcpy(&mu[i],&mu_hold[i],3*sizeof(double)); memory->destroy(mu_hold); mu_hold = nullptr; } diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 025624c6c0d..38ecd63dddf 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -90,7 +90,7 @@ void AtomVecDipole::read_data_general_to_restricted(int nlocal_previous, int nlo /* ---------------------------------------------------------------------- convert info output by write_data from restricted to general triclinic parent class operates on x and data from Velocities section of data file - child class operates on dipole momemt mu + child class operates on dipole momemt mu which has 4 values per atom ------------------------------------------------------------------------- */ void AtomVecDipole::write_data_restricted_to_general() @@ -99,16 +99,17 @@ void AtomVecDipole::write_data_restricted_to_general() int nlocal = atom->nlocal; memory->create(mu_hold,nlocal,3,"atomvec:mu_hold"); - if (nlocal) memcpy(&mu_hold[0][0],&mu[0][0],3*nlocal*sizeof(double)); - for (int i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) { + memcpy(&mu_hold[i],&mu[i],3*sizeof(double)); domain->restricted_to_general_vector(mu[i]); + } } /* ---------------------------------------------------------------------- restore info output by write_data to restricted triclinic original data is in "hold" arrays parent class operates on x and data from Velocities section of data file - child class operates on dipole moment mu + child class operates on dipole moment mu which has 4 values per atom ------------------------------------------------------------------------- */ void AtomVecDipole::write_data_restore_restricted() @@ -118,7 +119,8 @@ void AtomVecDipole::write_data_restore_restricted() if (!mu_hold) return; int nlocal = atom->nlocal; - memcpy(&mu[0][0],&mu_hold[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + memcpy(&mu[i],&mu_hold[i],3*sizeof(double)); memory->destroy(mu_hold); mu_hold = nullptr; } diff --git a/src/MACHDYN/atom_vec_smd.cpp b/src/MACHDYN/atom_vec_smd.cpp index 5ba2c010386..05c73d5b33d 100644 --- a/src/MACHDYN/atom_vec_smd.cpp +++ b/src/MACHDYN/atom_vec_smd.cpp @@ -164,7 +164,7 @@ void AtomVecSMD::data_atom_post(int ilocal) // x and x0 are in Atoms section of data file // reset x0 b/c x may have been modified in Atom::data_atoms() // for PBC, shift, etc - // this also means no need for read_data_general_to_restricted() method + // this means no need for read_data_general_to_restricted() method // to rotate x0 for general triclinic x0[ilocal][0] = x[ilocal][0]; diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index a68a59ef389..8844755cd81 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -120,7 +120,7 @@ void AtomVecSpin::read_data_general_to_restricted(int nlocal_previous, int nloca /* ---------------------------------------------------------------------- convert info output by write_data from restricted to general triclinic parent class operates on x and data from Velocities section of data file - child class operates on spin vector sp + child class operates on spin vector sp which has 4 values per atom ------------------------------------------------------------------------- */ void AtomVecSpin::write_data_restricted_to_general() @@ -129,16 +129,17 @@ void AtomVecSpin::write_data_restricted_to_general() int nlocal = atom->nlocal; memory->create(sp_hold,nlocal,3,"atomvec:sp_hold"); - if (nlocal) memcpy(&sp_hold[0][0],&sp[0][0],3*nlocal*sizeof(double)); - for (int i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) { + memcpy(&sp_hold[i],&sp[i],3*sizeof(double)); domain->restricted_to_general_vector(sp[i]); + } } /* ---------------------------------------------------------------------- restore info output by write_data to restricted triclinic original data is in "hold" arrays parent class operates on x and data from Velocities section of data file - child class operates on spin vector sp + child class operates on spin vector sp which has 4 values per atom ------------------------------------------------------------------------- */ void AtomVecSpin::write_data_restore_restricted() @@ -148,7 +149,8 @@ void AtomVecSpin::write_data_restore_restricted() if (!sp_hold) return; int nlocal = atom->nlocal; - memcpy(&sp[0][0],&sp_hold[0][0],3*nlocal*sizeof(double)); + for (int i = 0; i < nlocal; i++) + memcpy(&sp[i],&sp_hold[i],3*sizeof(double)); memory->destroy(sp_hold); sp_hold = nullptr; } diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index 73f2e702f6a..f5544c08ee7 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -355,9 +355,10 @@ void AtomVecLine::data_atom_bonus(int m, const std::vector &values) // convert x1/y1 and x2/y2 from general to restricted triclniic // x is already restricted triclinic - + + double coords[3]; + if (domain->triclinic_general) { - double coords[3]; coords[0] = x1; coords[1] = y1; coords[2] = 0.0; domain->general_to_restricted_coords(coords); x1 = coords[0]; y1 = coords[1]; @@ -366,8 +367,20 @@ void AtomVecLine::data_atom_bonus(int m, const std::vector &values) x2 = coords[0]; y2 = coords[1]; } + // remap end points to be near x + // necessary if atom x was remapped into periodic box + + coords[0] = x1; coords[1] = y1; coords[2] = 0.0; + domain->remap_near(coords,x[m]); + x1 = coords[0]; y1 = coords[1]; + coords[0] = x2; coords[1] = y2; coords[2] = 0.0; + domain->remap_near(c2,x[m]); + x2 = coords[0]; y2 = coords[1]; + // calculate length and theta - + // error if segment center is not within EPSILON of atom x + // reset atom x to center point + double dx = x2 - x1; double dy = y2 - y1; double length = sqrt(dx * dx + dy * dy); diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h index 740c541916f..0f5e5800f52 100644 --- a/src/atom_vec_line.h +++ b/src/atom_vec_line.h @@ -76,7 +76,6 @@ class AtomVecLine : public AtomVec { void grow_bonus(); void copy_bonus_all(int, int); - // void consistency_check(int, char *); }; } // namespace LAMMPS_NS diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index b0849e67175..69665c6a94b 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -52,8 +52,6 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp) nlocal_bonus = nghost_bonus = nmax_bonus = 0; bonus = nullptr; - double **quat_hold = nullptr; - // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -518,9 +516,17 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector &values) domain->general_to_restricted_coords(c2); domain->general_to_restricted_coords(c3); } + + // remap corner points to be near x + // necessary if atom x was remapped into periodic box + + domain->remap_near(c1,x[m]); + domain->remap_near(c2,x[m]); + domain->remap_near(c3,x[m]); // centroid = 1/3 of sum of vertices - // error if centroid is not within EPSILON of Atoms section coord + // error if centroid is not within EPSILON of atom x + // reset atom x to centroid double centroid[3]; centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0; diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h index 5a3b831c0da..424bd8ea0ae 100644 --- a/src/atom_vec_tri.h +++ b/src/atom_vec_tri.h @@ -72,8 +72,6 @@ class AtomVecTri : public AtomVec { double *radius, *rmass; double **omega, **angmom; - double **quat_hold; - int nghost_bonus, nmax_bonus; int tri_flag; double rmass_one; diff --git a/src/domain.cpp b/src/domain.cpp index 700cf79a82e..e9a18b897e3 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1361,7 +1361,7 @@ int Domain::closest_image(const double * const pos, int j) /* ---------------------------------------------------------------------- find and return Xj image = periodic image of Xj that is closest to Xi for triclinic, add/subtract tilt factors in other dims as needed - called by ServerMD class and LammpsInterface in lib/atc. + called by ServerMD class and LammpsInterface in lib/atc ------------------------------------------------------------------------- */ void Domain::closest_image(const double * const xi, const double * const xj, double * const xjimage) diff --git a/src/write_data.cpp b/src/write_data.cpp index 49e041b6ce2..e945f85c3be 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -98,6 +98,9 @@ void WriteData::command(int narg, char **arg) fixflag = 0; iarg++; } else if (strcmp(arg[iarg],"triclinic/general") == 0) { + if (!domain->triclinic_general) + error->all(FLERR,"Write_data triclinic/general for system " + "that is not general triclinic"); triclinic_general = 1; iarg++; } else if (strcmp(arg[iarg],"nolabelmap") == 0) { @@ -213,10 +216,10 @@ void WriteData::write(const std::string &file) if (coeffflag) force_fields(); } - // if general triclinic: + // if general triclinic requested: // reset internal per-atom data that needs rotation - atom->avec->write_data_restricted_to_general(); + if (triclinic_general) atom->avec->write_data_restricted_to_general(); // per atom info in Atoms and Velocities sections @@ -247,10 +250,10 @@ void WriteData::write(const std::string &file) if (ifix->wd_section) for (int m = 0; m < ifix->wd_section; m++) fix(ifix,m); - // if general triclinic: + // if general triclinic requested: // restore internal per-atom data that was rotated - atom->avec->write_data_restore_restricted(); + if (triclinic_general) atom->avec->write_data_restore_restricted(); // close data file From a0a21fab64b8087257f2bb46d17b827062002258 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 14 Nov 2023 17:03:56 -0700 Subject: [PATCH 052/719] changes for body particles in general triclinic --- doc/src/Howto_body.rst | 30 ++++++++++ src/BODY/body_nparticle.cpp | 2 +- src/BODY/body_rounded_polygon.cpp | 2 +- src/BODY/body_rounded_polyhedron.cpp | 2 +- src/atom_vec_body.cpp | 83 +++++++++++++++++++++++++++- src/atom_vec_body.h | 6 +- src/write_data.cpp | 31 +++++++---- 7 files changed, 137 insertions(+), 19 deletions(-) diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 15d6aee8459..41d3cd8efe3 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -154,12 +154,22 @@ values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. + The coordinates of each sub-particle are specified as its x,y,z displacement from the center-of-mass of the body particle. The center-of-mass position of the particle is specified by the x,y,z values in the *Atoms* section of the data file, as is the total mass of the body particle. +If the data file defines a general triclinic box, then the orientation +of the body particle and its corresponding 6 moments of inertia and +sub-particle displacements should reflect the fact the body is defined +withing a general triclinic box with edge vectors **A**,**B**,**C**. +LAMMPS will rotate the box to convert it to a restricted triclinic +box. This operation will also rotate the orientation of the body +particles. See the :doc:`Howto triclinic ` doc page +for more details. + The :doc:`pair_style body/nparticle ` command can be used with this body style to compute body/body and body/non-body interactions. @@ -226,6 +236,7 @@ values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. + The coordinates of each vertex are specified as its x,y,z displacement from the center-of-mass of the body particle. The center-of-mass position of the particle is specified by the x,y,z values in the @@ -270,6 +281,15 @@ A disk, whose diameter is 3.0, mass 1.0, is specified as follows: 0 0 0 3.0 +If the data file defines a general triclinic box, then the orientation +of the body particle and its corresponding 6 moments of inertia and +polygon vertex displacements should reflect the fact the body is +defined withing a general triclinic box with edge vectors +**A**,**B**,**C**. LAMMPS will rotate the box to convert it to a +restricted triclinic box. This operation will also rotate the +orientation of the body particles. See the :doc:`Howto triclinic +` doc page for more details. + The :doc:`pair_style body/rounded/polygon ` command can be used with this body style to compute body/body interactions. The :doc:`fix wall/body/polygon ` @@ -366,6 +386,7 @@ values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. + The coordinates of each vertex are specified as its x,y,z displacement from the center-of-mass of the body particle. The center-of-mass position of the particle is specified by the x,y,z values in the @@ -435,6 +456,15 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows: The number of edges and faces for a rod or sphere must be listed, but is ignored. +If the data file defines a general triclinic box, then the orientation +of the body particle and its corresponding 6 moments of inertia and +polyhedron vertex displacements should reflect the fact the body is +defined withing a general triclinic box with edge vectors +**A**,**B**,**C**. LAMMPS will rotate the box to convert it to a +restricted triclinic box. This operation will also rotate the +orientation of the body particles. See the :doc:`Howto triclinic +` doc page for more details. + The :doc:`pair_style body/rounded/polhedron ` command can be used with this body style to compute body/body interactions. The :doc:`fix diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 62e6ee802ae..05df63ff44f 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -99,7 +99,7 @@ int BodyNparticle::unpack_border_body(AtomVecBody::Bonus *bonus, double *buf) } /* ---------------------------------------------------------------------- - populate bonus data structure with data file values + populate bonus data structure with data file values for one body ------------------------------------------------------------------------- */ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble, diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index 2fb2a991f1b..b84a2717794 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -155,7 +155,7 @@ int BodyRoundedPolygon::unpack_border_body(AtomVecBody::Bonus *bonus, } /* ---------------------------------------------------------------------- - populate bonus data structure with data file values + populate bonus data structure with data file values for one body ------------------------------------------------------------------------- */ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble, diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 1d11644618e..111e41dbd16 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -185,7 +185,7 @@ int BodyRoundedPolyhedron::unpack_border_body(AtomVecBody::Bonus *bonus, double } /* ---------------------------------------------------------------------- - populate bonus data structure with data file values + populate bonus data structure with data file values for one body ------------------------------------------------------------------------- */ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble, diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index fd590ad5fe5..108d94bbecb 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -597,6 +597,15 @@ void AtomVecBody::pack_data_pre(int ilocal) body[ilocal] = 1; } +/* ---------------------------------------------------------------------- + unmodify values packed by AtomVec::pack_data() +------------------------------------------------------------------------- */ + +void AtomVecBody::pack_data_post(int ilocal) +{ + body[ilocal] = body_flag; +} + /* ---------------------------------------------------------------------- pack bonus body info for writing to data file if buf is nullptr, just return buffer size @@ -631,12 +640,80 @@ void AtomVecBody::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/) } /* ---------------------------------------------------------------------- - unmodify values packed by AtomVec::pack_data() + convert read_data file info from general to restricted triclinic + parent class operates on data from Velocities section of data file + child class operates on body quaternion ------------------------------------------------------------------------- */ -void AtomVecBody::pack_data_post(int ilocal) +void AtomVecBody::read_data_general_to_restricted(int nlocal_previous, int nlocal) { - body[ilocal] = body_flag; + int j; + + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); + + // quat_g2r = quat that rotates from general to restricted triclinic + // quat_new = body quat converted to restricted triclinic + + double quat_g2r[4],quat_new[4]; + MathExtra::mat_to_quat(domain->rotate_g2r,quat_g2r); + + for (int i = nlocal_previous; i < nlocal; i++) { + if (body[i] < 0) continue; + j = body[i]; + MathExtra::quatquat(quat_g2r,bonus[j].quat,quat_new); + bonus[j].quat[0] = quat_new[0]; + bonus[j].quat[1] = quat_new[1]; + bonus[j].quat[2] = quat_new[2]; + bonus[j].quat[3] = quat_new[3]; + } +} + +/* ---------------------------------------------------------------------- + convert info output by write_data from restricted to general triclinic + parent class operates on x and data from Velocities section of data file + child class operates on body quaternion +------------------------------------------------------------------------- */ + +void AtomVecBody::write_data_restricted_to_general() +{ + AtomVec::write_data_restricted_to_general(); + + memory->create(quat_hold,nlocal_bonus,4,"atomvec:quat_hold"); + + for (int i = 0; i < nlocal_bonus; i++) + memcpy(quat_hold[i],bonus[i].quat,4*sizeof(double)); + + // quat_r2g = quat that rotates from restricted to general triclinic + // quat_new = ellipsoid quat converted to general triclinic + + double quat_r2g[4],quat_new[4]; + MathExtra::mat_to_quat(domain->rotate_r2g,quat_r2g); + + for (int i = 0; i < nlocal_bonus; i++) { + MathExtra::quatquat(quat_r2g,bonus[i].quat,quat_new); + bonus[i].quat[0] = quat_new[0]; + bonus[i].quat[1] = quat_new[1]; + bonus[i].quat[2] = quat_new[2]; + bonus[i].quat[3] = quat_new[3]; + } +} + +/* ---------------------------------------------------------------------- + restore info output by write_data to restricted triclinic + original data is in "hold" arrays + parent class operates on x and data from Velocities section of data file + child class operates on body quaternion +------------------------------------------------------------------------- */ + +void AtomVecBody::write_data_restore_restricted() +{ + AtomVec::write_data_restore_restricted(); + + for (int i = 0; i < nlocal_bonus; i++) + memcpy(bonus[i].quat,quat_hold[i],4*sizeof(double)); + + memory->destroy(quat_hold); + quat_hold = nullptr; } /* ---------------------------------------------------------------------- diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index e02fd3bbb0d..5ba90a6dc1d 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -66,6 +66,10 @@ class AtomVecBody : public AtomVec { int pack_data_bonus(double *, int) override; void write_data_bonus(FILE *, int, double *, int) override; + void read_data_general_to_restricted(int, int); + void write_data_restricted_to_general(); + void write_data_restore_restricted(); + // methods used by other classes to query/set body info double radius_body(int, int, int *, double *); @@ -77,6 +81,7 @@ class AtomVecBody : public AtomVec { int *body; double *rmass, *radius; double **angmom; + double **quat_hold; int nghost_bonus, nmax_bonus; int intdoubleratio; // sizeof(double) / sizeof(int) @@ -87,7 +92,6 @@ class AtomVecBody : public AtomVec { void grow_bonus(); void copy_bonus_all(int, int); - // check(int); }; } // namespace LAMMPS_NS diff --git a/src/write_data.cpp b/src/write_data.cpp index e945f85c3be..06512a0f20b 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -76,7 +76,8 @@ void WriteData::command(int narg, char **arg) lmapflag = 1; // store current (default) setting since we may change it - + + int domain_triclinic_general = domain->triclinic_general; int types_style = atom->types_style; int noinit = 0; @@ -98,9 +99,6 @@ void WriteData::command(int narg, char **arg) fixflag = 0; iarg++; } else if (strcmp(arg[iarg],"triclinic/general") == 0) { - if (!domain->triclinic_general) - error->all(FLERR,"Write_data triclinic/general for system " - "that is not general triclinic"); triclinic_general = 1; iarg++; } else if (strcmp(arg[iarg],"nolabelmap") == 0) { @@ -115,6 +113,14 @@ void WriteData::command(int narg, char **arg) } else error->all(FLERR,"Unknown write_data keyword: {}", arg[iarg]); } + // temporarily disable domain->triclinic_general if output not requested + + if (triclinic_general && !domain->triclinic_general) + error->all(FLERR,"Write_data triclinic/general for system " + "that is not general triclinic"); + if (!triclinic_general && domain->triclinic_general) + domain->triclinic_general = 0; + // init entire system since comm->exchange is done // comm::init needs neighbor::init needs pair::init needs kspace::init, etc // exception is when called by -r command-line switch @@ -145,8 +151,9 @@ void WriteData::command(int narg, char **arg) write(file); - // restore saved setting - + // restore saved settings + + domain->triclinic_general = domain_triclinic_general; atom->types_style = types_style; } @@ -216,10 +223,10 @@ void WriteData::write(const std::string &file) if (coeffflag) force_fields(); } - // if general triclinic requested: + // if general triclinic output: // reset internal per-atom data that needs rotation - if (triclinic_general) atom->avec->write_data_restricted_to_general(); + if (domain->triclinic_general) atom->avec->write_data_restricted_to_general(); // per atom info in Atoms and Velocities sections @@ -250,10 +257,10 @@ void WriteData::write(const std::string &file) if (ifix->wd_section) for (int m = 0; m < ifix->wd_section; m++) fix(ifix,m); - // if general triclinic requested: + // if general triclinic output: // restore internal per-atom data that was rotated - if (triclinic_general) atom->avec->write_data_restore_restricted(); + if (domain->triclinic_general) atom->avec->write_data_restore_restricted(); // close data file @@ -312,7 +319,7 @@ void WriteData::header() // box info: orthogonal, restricted triclinic, or general triclinic (if requested) - if (!triclinic_general) { + if (!domain->triclinic_general) { fmt::print(fp,"\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n", domain->boxlo[0],domain->boxhi[0], domain->boxlo[1],domain->boxhi[1], @@ -320,7 +327,7 @@ void WriteData::header() if (domain->triclinic) fmt::print(fp,"{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz); - } else if (triclinic_general) { + } else if (domain->triclinic_general) { fmt::print(fp,"\n{} {} {} avec\n{} {} {} bvec\n{} {} {} cvec\n", domain->avec[0],domain->avec[1],domain->avec[2], domain->bvec[0],domain->bvec[1],domain->bvec[2], From fc5803188fb478cdb280fc99a2e45151d7585bf5 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 15 Nov 2023 09:29:04 -0700 Subject: [PATCH 053/719] doc page for write_data --- doc/src/write_data.rst | 28 ++++++++++++++++++++++++---- 1 file changed, 24 insertions(+), 4 deletions(-) diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index c598ebe4810..e083f834b88 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -19,6 +19,7 @@ Syntax *nocoeff* = do not write out force field info *nofix* = do not write out extra sections read by fixes *nolabelmap* = do not write out type labels + *triclinic/general = write data file in general triclinic format *types* value = *numeric* or *labels* *pair* value = *ii* or *ij* *ii* = write one line of pair coefficient info per atom type @@ -31,6 +32,7 @@ Examples write_data data.polymer write_data data.* + write_data data.solid triclinic/general Description """"""""""" @@ -85,10 +87,11 @@ using the :doc:`-r command-line switch `. :doc:`fixes ` are stored. :doc:`Binary restart files ` store more information. -Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake ` or :doc:`delete_bonds ` command will -be written to a data file as if they are turned on. This means they -will need to be turned off again in a new run after the data file is -read. +Bond interactions (angle, etc) that have been turned off by the +:doc:`fix shake ` or :doc:`delete_bonds ` +command will be written to a data file as if they are turned on. This +means they will need to be turned off again in a new run after the +data file is read. Bonds that are broken (e.g. by a bond-breaking potential) are not written to the data file. Thus these bonds will not exist when the @@ -122,6 +125,23 @@ not written to the data file. By default, they are written if they exist. A type label must be defined for every numeric type (within a given type-kind) to be written to the data file. +Use of the *triclinic/general* keyword will output a data file which +specifies a general triclinic simulation box as well as per-atom +quantities consistent with the general triclinic box. The latter +means that per-atom vectors, such as velocities and dipole moments +will be oriented conistent with the 3d rotation implied by the general +triclinic box (relative to the associated restricted triclinic box). + +This option can only be requested if the simulation box was initially +defined to be general triclinic. If if was and the +*triclinic/general* keyword is not used, then the data file will +specify a restricted triclinic box, since that is the internal format +LAMMPS uses for both general and restricited triclinic simulations. +See the :doc:`Howto triclinic ` doc page for more +explanation of how general triclinic simulation boxes are supported by +LAMMPS. And see the :doc:`read_data ` doc page for details +of how the format is altered for general triclinic data files. + The *types* keyword determines how atom types, bond types, angle types, etc are written into these data file sections: Atoms, Bonds, Angles, etc. The default is the *numeric* setting, even if type label From 4057ee3d6236b7c0ce8a355c311125a8743a47cf Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 16 Nov 2023 16:35:16 -0700 Subject: [PATCH 054/719] more doc page updates for general tri --- doc/src/create_box.rst | 226 ++++++++++++++++++++++++++------------ doc/src/lattice.rst | 6 +- doc/src/read_data.rst | 8 +- doc/src/write_restart.rst | 21 ++-- src/create_box.cpp | 11 +- 5 files changed, 183 insertions(+), 89 deletions(-) diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index f930ecea83a..b5ac4ac9077 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -9,9 +9,11 @@ Syntax .. code-block:: LAMMPS create_box N region-ID keyword value ... + create_box N NULL alo ahi blo bhi clo chi keyword value ... * N = # of atom types to use in this simulation -* region-ID = ID of region to use as simulation domain +* region-ID = ID of region to use as simulation domain or NULL for general triclinic box +* alo,ahi,blo,bhi,clo,chi = multipliers on a1,a2,a3 vectors defined by :doc"`lattice ` command (only when region-ID = NULL) * zero or more keyword/value pairs may be appended * keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom* @@ -32,95 +34,183 @@ Examples .. code-block:: LAMMPS + # orthogonal or restricted triclinic box using regionID = mybox create_box 2 mybox create_box 2 mybox bond/types 2 extra/bond/per/atom 1 +.. code-block:: LAMMPS + + # 2d general triclinic box using primitive cell for 2d hex lattice + lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 & + a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 + create_box 1 NULL 0 5 0 5 -0.5 0.5 + +.. code-block:: LAMMPS + + # 3d general triclinic box using primitive cell for 3d fcc lattice + lattice custom 1.0 a2 0.0 0.5 0.5 a1 0.5 0.0 0.5 a3 0.5 0.5 0.0 basis 0.0 0.0 0.0 + create box 1 NULL -5 5 -10 10 0 20 + Description """"""""""" -This command creates a simulation box based on the specified region. -Thus a :doc:`region ` command must first be used to define a -geometric domain. It also partitions the simulation box into a -regular 3d grid of rectangular bricks, one per processor, based on the -number of processors being used and the settings of the -:doc:`processors ` command. The partitioning can later be -changed by the :doc:`balance ` or :doc:`fix balance ` commands. - -The argument N is the number of atom types that will be used in the +This command creates a simulation box. It also partitions the box into +a regular 3d grid of smaller sub-boxes, one per procssor (MPI task). +The geometry of the partitioning is based on the size and shape of the +simulation box, the number of processors being used and the settings +of the :doc:`processors ` command. The partitioning can +later be changed by the :doc:`balance ` or :doc:`fix balance +` commands. + +Simulation boxes in LAMMPS can be either orthogonal or triclinic in +shape. Orthogonal boxes are a brick in 3d (rectangle in 2d) with 6 +faces that are each perpendicular to one of the standard xyz +coordinate axes. Triclinic boxes are a parallelepiped in 3d +(parallelogram in 2d) with opposite pairs of faces parallel to each +other. LAMMPS supports two forms of triclinic boxes, restricted and +general, which differ in how the box is oriented with respect to the +xyz coordinate axes. See the :doc:`Howto triclinic ` +for a detailed description of all 3 kinds of simulation boxes. + +The argument *N* is the number of atom types that will be used in the simulation. +Orthogonal and restricted triclinic boxes are created by specifying a +region ID previously defined by the :doc:`region ` command. +General triclinic boxes are discussed below. + If the region is not of style *prism*, then LAMMPS encloses the region (block, sphere, etc.) with an axis-aligned orthogonal bounding box -which becomes the simulation domain. +which becomes the simulation domain. For a 2d simulation, the zlo and +zhi values of the simulation box must straddle zero. If the region is of style *prism*, LAMMPS creates a non-orthogonal simulation domain shaped as a parallelepiped with triclinic symmetry. As defined by the :doc:`region prism ` command, the -parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by three -edge vectors starting from the origin given by -:math:`\vec a = (x_\text{hi}-x_\text{lo},0,0)`; -:math:`\vec b = (xy,y_\text{hi}-y_\text{lo},0)`; and -:math:`\vec c = (xz,yz,z_\text{hi}-z_\text{lo})`. -The parameters *xy*\ , *xz*\ , and *yz* can be 0.0 or -positive or negative values and are called "tilt factors" because they -are the amount of displacement applied to faces of an originally -orthogonal box to transform it into the parallelepiped. - -By default, a *prism* region used with the create_box command must have -tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half -the distance of the parallel box length. For example, if -:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x` -box length is 10 and the :math:`xy` tilt factor must be between -:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz` -must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and +parallelepiped has an "origin" at (xlo,ylo,zlo) and three edge vectors +starting from the origin given by :math:`\vec a = +(x_\text{hi}-x_\text{lo},0,0)`; :math:`\vec b = +(xy,y_\text{hi}-y_\text{lo},0)`; and :math:`\vec c = +(xz,yz,z_\text{hi}-z_\text{lo})`. This is a restricted triclinic box +because the three edge vectors cannot be defined in arbitrary +(general) directions. The parameters *xy*\ , *xz*\ , and *yz* can be +0.0 or positive or negative values and are called "tilt factors" +because they are the amount of displacement applied to faces of an +originally orthogonal box to transform it into the parallelepiped. +For a 2d simulation, the zlo and zhi values of the simulation box must +straddle zero. + +Typically a *prism* region used with the create_box command should +have tilt factors :math:`(xy,xz,yz)` that do not skew the box more +than half the distance of the parallel box length. For example, if +:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the +:math:`x` box length is 10 and the :math:`xy` tilt factor must be +between :math:`-5` and :math:`5`. Similarly, both :math:`xz` and +:math:`yz` must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and :math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a -limitation, since if the maximum tilt factor is 5 (as in this example), -then configurations with tilt :math:`= \dots, -15`, :math:`-5`, -:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically -equivalent. Simulations with large tilt factors will run inefficiently, -since they require more ghost atoms and thus more communication. With -very large tilt factors, LAMMPS will eventually produce incorrect -trajectories and stop with errors due to lost atoms or similar. - -See the :doc:`Howto triclinic ` page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. - -When a prism region is used, the simulation domain should normally be periodic -in the dimension that the tilt is applied to, which is given by the second -dimension of the tilt factor (e.g., :math:`y` for :math:`xy` tilt). This is so -that pairs of atoms interacting across that boundary will have one of them -shifted by the tilt factor. Periodicity is set by the -:doc:`boundary ` command. For example, if the :math:`xy` tilt factor -is non-zero, then the :math:`y` dimension should be periodic. Similarly, the -:math:`z` dimension should be periodic if :math:`xz` or :math:`yz` is non-zero. -LAMMPS does not require this periodicity, but you may lose atoms if this is not -the case. +limitation, since if the maximum tilt factor is 5 (as in this +example), then configurations with tilt :math:`= \dots, -15`, +:math:`-5`, :math:`5`, :math:`15`, :math:`25, \dots` are all +geometrically equivalent. + +LAMMPS will issue a warning if the tilt factors of the created box do +not meet this criterion. This is because simulations with large tilt +factors may run inefficiently, since they require more ghost atoms and +thus more communication. With very large tilt factors, LAMMPS may +eventually produce incorrect trajectories and stop with errors due to +lost atoms or similar issues. + +See the :doc:`Howto triclinic ` page for geometric +descriptions of triclinic boxes and tilt factors, as well as how to +transform the restricted triclinic parameters to and from other +commonly used triclinic representations. + +When a prism region is used, the simulation domain should normally be +periodic in the dimension that the tilt is applied to, which is given +by the second dimension of the tilt factor (e.g., :math:`y` for +:math:`xy` tilt). This is so that pairs of atoms interacting across +that boundary will have one of them shifted by the tilt factor. +Periodicity is set by the :doc:`boundary ` command. For +example, if the :math:`xy` tilt factor is non-zero, then the :math:`y` +dimension should be periodic. Similarly, the :math:`z` dimension +should be periodic if :math:`xz` or :math:`yz` is non-zero. LAMMPS +does not require this periodicity, but you may lose atoms if this is +not the case. Note that if your simulation will tilt the box (e.g., via the -:doc:`fix deform ` command), the simulation box must be set up to -be triclinic, even if the tilt factors are initially 0.0. You can -also change an orthogonal box to a triclinic box or vice versa by +:doc:`fix deform ` command), the simulation box must be +created as triclinic, even if the tilt factors are initially 0.0. You +can also change an orthogonal box to a triclinic box or vice versa by using the :doc:`change box ` command with its *ortho* and *triclinic* options. .. note:: - If the system is non-periodic (in a dimension), then you should - not make the lo/hi box dimensions (as defined in your - :doc:`region ` command) radically smaller/larger than the extent - of the atoms you eventually plan to create (e.g., via the - :doc:`create_atoms ` command). For example, if your atoms - extend from 0 to 50, you should not specify the box bounds as :math:`-10000` - and :math:`10000`. This is because as described above, LAMMPS uses the - specified box size to lay out the 3d grid of processors. A huge - (mostly empty) box will be sub-optimal for performance when using - "fixed" boundary conditions (see the :doc:`boundary ` - command). When using "shrink-wrap" boundary conditions (see the - :doc:`boundary ` command), a huge (mostly empty) box may cause - a parallel simulation to lose atoms the first time that LAMMPS - shrink-wraps the box around the atoms. + If the system is non-periodic (in a dimension), then you should not + make the lo/hi box dimensions (as defined in your :doc:`region + ` command) radically smaller/larger than the extent of the + atoms you eventually plan to create (e.g., via the + :doc:`create_atoms ` command). For example, if your + atoms extend from 0 to 50, you should not specify the box bounds as + :math:`-10000` and :math:`10000`. This is because as described + above, LAMMPS uses the specified box size to lay out the 3d grid of + processors. A huge (mostly empty) box will be sub-optimal for + performance when using "fixed" boundary conditions (see the + :doc:`boundary ` command). When using "shrink-wrap" + boundary conditions (see the :doc:`boundary ` command), a + huge (mostly empty) box may cause a parallel simulation to lose + atoms the first time that LAMMPS shrink-wraps the box around the + atoms. + +---------- + +As noted above, general triclinic boxes allow for arbitrary edge +vectors **A**, **B**, **C*. The only restrictions are that the three +vectors be distinct, non-zero, and not co-planar. They must also +define a right-handed system such that (**A** x **B**) points in the +direction of **C**. Note that a left-handed system can be converted +to a right-handed system by simply swapping the order of any pair of +the **A**, **B**, **C** vectors. + +To create a general triclinic boxes, the region is specified as NULL +and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three +edge vectors **A**, **B**, **C** using additional information +previousl set by the :doc:`lattice ` command. + +The lattice must be of style *custom* with a default orientation (no +use of the *orient* keyword to change the default values). The *a1, +*a2*, *a3* settings of the :doc:`lattice ` command define the +edge vectors of a unit cell of the lattice. The three edge vectors of +the general triclinic box are defined as + +* **A** = (ahi-alo) * *a1* +* **B** = (bhi-blo) * *a2* +* **C** = (chi-clo) * *a3* + +The origin of the general triclinic box is at (alo*a1 + blo*a2 + +clo*a3) with an additional offset due to the *origin* setting of the +lattice command (zero vector by default). + +For 2d simulations, **C** = (0,0,1) is required, and the z-component +of the simulation box origin must be -0.5. The easy way to do this is +to specify clo = -0.5 and chi = 0.5 with the :doc:`lattice ` +command default of a3 = (0,0,1). + +.. note:: + + LAMMPS allows specification of general triclinic simulation boxes + as a convenience for users who may be converting data from + solid-state crystallograhic representations or from DFT codes for + input to LAMMPS. However, as explained on the + :doc:`Howto_triclinic ` doc page, internally, + LAMMPS only uses restricted triclinic simulation boxes. This means + the box defined by this command and per-atom information + (e.g. coordinates, velocities) defined by the :doc:`create_atoms + ` command are converted from general to restricted + triclinic form when the two commands are invoked. The + ` doc page also discusses other LAMMPS commands + which can input/output general triclinic representations of the + simulation box and per-atom data. ---------- diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index 7dc9c579e53..277f6485150 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -131,8 +131,10 @@ so that they describe a tilted parallelepiped. Via the *basis* keyword you add atoms, one at a time, to the unit cell. Its arguments are fractional coordinates (0.0 <= x,y,z < 1.0). The position vector x of a basis atom within the unit cell is thus a linear combination of -the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, -where bx,by,bz are the 3 values specified for the *basis* keyword. +the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, where +bx,by,bz are the 3 values specified for the *basis* keyword. For 2d +simulations, the fractional z coordinate for any basis atom must be +0.0. ---------- diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index d26d0ab5778..56c92355a86 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -449,8 +449,8 @@ origin* keywords are used. The *xlo xhi*, *ylo yhi*, *zlo zhi*, and *xy xz yz* keywords are not used. The first 3 keywords define the 3 edge vectors **A**, **B**, **C** of a general triclinic box. They can be arbitrary vectors so long as they are distinct, non-zero, and not -co-planar. They must also define a right-handed system requirement -such that (**A** x **B**) points in the direction of **C**. A +co-planar. They must also define a right-handed system such that +(**A** x **B**) points in the direction of **C**. Note that a left-handed system can be converted to a right-handed system by simply swapping the order of any pair of the **A**, **B**, **C** vectors. The origin of the box (origin of the 3 edge vectors) is set by the @@ -818,6 +818,8 @@ of analysis. - atom-ID atom-type bodyflag mass x y z * - bond - atom-ID molecule-ID atom-type x y z + * - bpm/sphere + - atom-ID molecule-ID atom-type diameter density x y z * - charge - atom-ID atom-type q x y z * - dielectric @@ -848,8 +850,6 @@ of analysis. - atom-ID atom-type rho esph cv x y z * - sphere - atom-ID atom-type diameter density x y z - * - bpm/sphere - - atom-ID molecule-ID atom-type diameter density x y z * - spin - atom-ID atom-type x y z spx spy spz sp * - tdpd diff --git a/doc/src/write_restart.rst b/doc/src/write_restart.rst index a35adffe567..6205f24faff 100644 --- a/doc/src/write_restart.rst +++ b/doc/src/write_restart.rst @@ -55,21 +55,22 @@ alter the number of files written. Restart files can be read by a :doc:`read_restart ` command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on -another machine. In this case, you can use the :doc:`-r command-line switch ` to convert a restart file to a data file. +another machine. In this case, you can use the :doc:`-r command-line +switch ` to convert a restart file to a data file. .. note:: Although the purpose of restart files is to enable restarting a simulation from where it left off, not all information about a - simulation is stored in the file. For example, the list of fixes that - were specified during the initial run is not stored, which means the - new input script must specify any fixes you want to use. Even when - restart information is stored in the file, as it is for some fixes, - commands may need to be re-specified in the new input script, in order - to re-use that information. Details are usually given in the - documentation of the respective command. Also, see the - :doc:`read_restart ` command for general information about - what is stored in a restart file. + simulation is stored in the file. For example, the list of fixes + that were specified during the initial run is not stored, which + means the new input script must specify any fixes you want to use. + Even when restart information is stored in the file, as it is for + some fixes, commands may need to be re-specified in the new input + script, in order to re-use that information. Details are usually + given in the documentation of the respective command. Also, see the + :doc:`read_restart ` command for general information + about what is stored in a restart file. ---------- diff --git a/src/create_box.cpp b/src/create_box.cpp index 8cf60659627..4df23d286f7 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -121,11 +121,6 @@ void CreateBox::command(int narg, char **arg) double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp); iarg += 6; - if (domain->dimension == 2) { - if (clo >= 0.0 || clo <= 0.0) - error->all(FLERR,"Create_box region clo/chi for 2d simulation must straddle 0.0"); - } - // use lattice2box() to generate origin and ABC vectors // origin = abc lo // ABC vectors = hi in one dim - origin @@ -157,6 +152,12 @@ void CreateBox::command(int narg, char **arg) cvec[1] = py - origin[1]; cvec[2] = pz - origin[2]; + if (domain->dimension == 2) { + if (cvec[0] != 0.0 || cvec[1] != 0.0 || cvec[2] != 1.0 || origin[2] != -0.5) + error->all(FLERR,"Create_box C vector and/or origin is invalid " + "for 2d simulation with general triclinic box"); + } + // define general triclinic box within Domain domain->define_general_triclinic(avec,bvec,cvec,origin); From 4ccd59af804424d7349e9f915e0fc7b22d21499c Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 16 Nov 2023 16:37:43 -0700 Subject: [PATCH 055/719] another doc tweak for 2d --- doc/src/lattice.rst | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index 277f6485150..3306c58e8c8 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -129,12 +129,13 @@ and a3 are 3 orthogonal unit vectors (edges of a unit cube). But you can specify them to be of any length and non-orthogonal to each other, so that they describe a tilted parallelepiped. Via the *basis* keyword you add atoms, one at a time, to the unit cell. Its arguments -are fractional coordinates (0.0 <= x,y,z < 1.0). The position vector -x of a basis atom within the unit cell is thus a linear combination of -the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, where -bx,by,bz are the 3 values specified for the *basis* keyword. For 2d -simulations, the fractional z coordinate for any basis atom must be -0.0. +are fractional coordinates (0.0 <= x,y,z < 1.0). For 2d simulations, +the fractional z coordinate for any basis atom must be 0.0. + +The position vector x of a basis atom within the unit cell is a linear +combination of the unit cell's 3 edge vectors, i.e. x = bx a1 + by +a2 + bz a3, where bx,by,bz are the 3 values specified for the *basis* +keyword. ---------- From 56b2c7ed4651c3bbb3ba7457d7aa9f5cc0ba4c03 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 17 Nov 2023 17:10:45 -0700 Subject: [PATCH 056/719] alter how lattice interacts with create_box and create_atoms for general triclinic --- doc/src/Howto_triclinic.rst | 6 +- doc/src/create_atoms.rst | 112 +++++++++++++++++++++++++------ doc/src/create_box.rst | 56 ++++++++-------- doc/src/lattice.rst | 68 ++++++++++++++++++- src/atom_vec_line.cpp | 2 +- src/create_atoms.cpp | 54 +++++++-------- src/create_box.cpp | 12 ++-- src/domain.cpp | 130 ++++++++++++++++++++---------------- src/domain.h | 3 + src/lattice.cpp | 91 +++++++++++++++---------- src/lattice.h | 25 ++++--- 11 files changed, 368 insertions(+), 191 deletions(-) diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 6cbc0644cd5..525c3e0f1b3 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -56,9 +56,9 @@ at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), **C** = (cx,cy,cz) which can be arbitrary vectors, so long as they are non-zero, distinct, and not co-planar. In addition, they must define a right-handed system, such that (**A** cross **B**) -points in the direction of **C**. A left-handed system can be -converted to a right-handed system by simply swapping the order of any -pair of the **A**, **B**, **C** vectors. +points in the direction of **C**. Note that a left-handed system can +be converted to a right-handed system by simply swapping the order of +any pair of the **A**, **B**, **C** vectors. The 4 commands listed above for defining orthogonal simulation boxes have triclinic options which allow for specification of the origin and diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 5d1e7c872c8..c9e8f3e8408 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -86,25 +86,25 @@ Description """"""""""" This command creates atoms (or molecules) within the simulation box, -either on a lattice, or a single atom (or molecule), or on a surface -defined by a triangulated mesh, or a random collection of atoms (or -molecules). It is an alternative to reading in atom coordinates -explicitly via a :doc:`read_data ` or :doc:`read_restart -` command. A simulation box must already exist, which is -typically created via the :doc:`create_box ` command. -Before using this command, a lattice must also be defined using the -:doc:`lattice ` command, unless you specify the *single* style -with units = box or the *random* style. For the remainder of this doc -page, a created atom or molecule is referred to as a "particle". +either on a lattice, or at a single specified location, or randomly, +or on a surface defined by a triangulated mesh. It is an alternative +to reading in atom coordinates explicitly via a :doc:`read_data +` or :doc:`read_restart ` command. A +simulation box must already exist, which is typically created via the +:doc:`create_box ` command. Before using this command, a +lattice must typically also be defined using the :doc:`lattice +` command, unless you specify the *single* style with units = +box or the *random* style. For the remainder of this doc page, a +created atom or molecule is referred to as a "particle". If created particles are individual atoms, they are assigned the specified atom *type*, though this can be altered via the *basis* keyword as discussed below. If molecules are being created, the type -of each atom in the created molecule is specified in the file read by -the :doc:`molecule ` command, and those values are added to -the specified atom *type* (e.g., if *type* = 2 and the file specifies -atom types 1, 2, and 3, then each created molecule will have atom types -3, 4, and 5). +of each atom in the created molecule is specified in a specified file +read by the :doc:`molecule ` command, and those values are +added to the specified atom *type* (e.g., if *type* = 2 and the file +specifies atom types 1, 2, and 3, then each created molecule will have +atom types 3, 4, and 5). For the *box* style, the create_atoms command fills the entire simulation box with particles on the lattice. If your simulation box @@ -126,6 +126,69 @@ periodic boundaries. If this is desired, you should either use the *box* style, or tweak the region size to get precisely the particles you want. + +------------------ + +WORK on this + + +If a general triclinic simulation box is defined ... + + + +As noted above, general triclinic boxes in LAMMPS allow for arbitrary +edge vectors **A**, **B**, **C**. The only restrictions are that the +three vectors be distinct, non-zero, and not co-planar. They must +also define a right-handed system such that (**A** x **B**) points in +the direction of **C**. Note that a left-handed system can be +converted to a right-handed system by simply swapping the order of any +pair of the **A**, **B**, **C** vectors. + +To create a general triclinic boxes, the region is specified as NULL +and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three +edge vectors **A**, **B**, **C** using additional information +previously defind by the :doc:`lattice ` command. + +The lattice must be of style *custom* and use its *triclinic/general* +option. This insures the lattice satisfies the restrictions listed +above. The *a1, *a2*, *a3* settings of the :doc:`lattice ` +command define the edge vectors of a unit cell of the general +triclinic lattice. This command uses them to define the three edge +vectors and origin of the general triclinic box as: + + +explain region is applied after conversion to restricted triclinic atom coords + +explain general tri for box and region styles +must use lattice triclinic/general +paragraph about DFT motivation +doc that single, random, mesh operate on restricted triclinic box + +------------------ + + +.. note:: + + LAMMPS allows specification of general triclinic simulation boxes + as a convenience for users who may be converting data from + solid-state crystallograhic representations or from DFT codes for + input to LAMMPS. However, as explained on the + :doc:`Howto_triclinic ` doc page, internally, + LAMMPS only uses restricted triclinic simulation boxes. This means + the box defined by this command and per-atom information + (e.g. coordinates, velocities) defined by the :doc:`create_atoms + ` command are converted from general to restricted + triclinic form when the two commands are invoked. The + ` doc page also discusses other LAMMPS commands + which can input/output general triclinic representations of the + simulation box and per-atom data. + + + + + + + For the *single* style, a single particle is added to the system at the specified coordinates. This can be useful for debugging purposes or to create a tiny system with a handful of particles at specified @@ -463,12 +526,19 @@ on a single CPU core. ----- The *units* keyword determines the meaning of the distance units used -to specify the coordinates of the one particle created by the *single* -style, or the overlap distance *Doverlap* by the *overlap* keyword. A -*box* value selects standard distance units as defined by the -:doc:`units ` command (e.g., :math:`\AA` for -units = *real* or *metal*\ . A *lattice* value means the distance units are in -lattice spacings. +by parameters for various styles. A *box* value selects standard +distance units as defined by the :doc:`units ` command (e.g., +:math:`\AA` for units = *real* or *metal*\ . A *lattice* value means +the distance units are in lattice spacings. These are affected settings: + +* for *single* style: coordinates of the particle created +* for *random* style: overlap distance *Doverlap* by the *overlap* keyword +* for *mesh* style: *bisect* threshold valeu for *meshmode* = *bisect* +* for *mesh* style: *radthresh* value for *meshmode* = *bisect* +* for *mesh* style: *density* value for *meshmode* = *qrand* + +Since *density* represents an area (distance ^2), the lattice spacing +factor is also squared. ---------- diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index b5ac4ac9077..11b2878fe4c 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -91,14 +91,14 @@ parallelepiped has an "origin" at (xlo,ylo,zlo) and three edge vectors starting from the origin given by :math:`\vec a = (x_\text{hi}-x_\text{lo},0,0)`; :math:`\vec b = (xy,y_\text{hi}-y_\text{lo},0)`; and :math:`\vec c = -(xz,yz,z_\text{hi}-z_\text{lo})`. This is a restricted triclinic box -because the three edge vectors cannot be defined in arbitrary -(general) directions. The parameters *xy*\ , *xz*\ , and *yz* can be -0.0 or positive or negative values and are called "tilt factors" -because they are the amount of displacement applied to faces of an -originally orthogonal box to transform it into the parallelepiped. -For a 2d simulation, the zlo and zhi values of the simulation box must -straddle zero. +(xz,yz,z_\text{hi}-z_\text{lo})`. In LAMMPS lingo, this is a +restricted triclinic box because the three edge vectors cannot be +defined in arbitrary (general) directions. The parameters *xy*\ , +*xz*\ , and *yz* can be 0.0 or positive or negative values and are +called "tilt factors" because they are the amount of displacement +applied to faces of an originally orthogonal box to transform it into +the parallelepiped. For a 2d simulation, the zlo and zhi values of +the simulation box must straddle zero. Typically a *prism* region used with the create_box command should have tilt factors :math:`(xy,xz,yz)` that do not skew the box more @@ -164,37 +164,35 @@ using the :doc:`change box ` command with its *ortho* and ---------- -As noted above, general triclinic boxes allow for arbitrary edge -vectors **A**, **B**, **C*. The only restrictions are that the three -vectors be distinct, non-zero, and not co-planar. They must also -define a right-handed system such that (**A** x **B**) points in the -direction of **C**. Note that a left-handed system can be converted -to a right-handed system by simply swapping the order of any pair of -the **A**, **B**, **C** vectors. +As noted above, general triclinic boxes in LAMMPS allow for arbitrary +edge vectors **A**, **B**, **C**. The only restrictions are that the +three vectors be distinct, non-zero, and not co-planar. They must +also define a right-handed system such that (**A** x **B**) points in +the direction of **C**. Note that a left-handed system can be +converted to a right-handed system by simply swapping the order of any +pair of the **A**, **B**, **C** vectors. To create a general triclinic boxes, the region is specified as NULL and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three edge vectors **A**, **B**, **C** using additional information -previousl set by the :doc:`lattice ` command. +previously defind by the :doc:`lattice ` command. -The lattice must be of style *custom* with a default orientation (no -use of the *orient* keyword to change the default values). The *a1, -*a2*, *a3* settings of the :doc:`lattice ` command define the -edge vectors of a unit cell of the lattice. The three edge vectors of -the general triclinic box are defined as +The lattice must be of style *custom* and use its *triclinic/general* +option. This insures the lattice satisfies the restrictions listed +above. The *a1, *a2*, *a3* settings of the :doc:`lattice ` +command define the edge vectors of a unit cell of the general +triclinic lattice. This command uses them to define the three edge +vectors and origin of the general triclinic box as: * **A** = (ahi-alo) * *a1* * **B** = (bhi-blo) * *a2* * **C** = (chi-clo) * *a3* +* origin = (alo*a1 + blo*a2 + clo*a3) -The origin of the general triclinic box is at (alo*a1 + blo*a2 + -clo*a3) with an additional offset due to the *origin* setting of the -lattice command (zero vector by default). - -For 2d simulations, **C** = (0,0,1) is required, and the z-component -of the simulation box origin must be -0.5. The easy way to do this is -to specify clo = -0.5 and chi = 0.5 with the :doc:`lattice ` -command default of a3 = (0,0,1). +For 2d general triclinic boxes, **C** = (0,0,1) is required, and the +z-component of the simulation box origin must be -0.5. The easy way +to do this is to specify clo = -0.5 and chi = 0.5 and use the +:doc:`lattice ` command default for a3 = (0,0,1). .. note:: diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index 3306c58e8c8..235b8b30daa 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -19,7 +19,7 @@ Syntax scale = lattice constant in distance units (for all other units) * zero or more keyword/value pairs may be appended -* keyword = *origin* or *orient* or *spacing* or *a1* or *a2* or *a3* or *basis* +* keyword = *origin* or *orient* or *spacing* or *a1* or *a2* or *a3* or *basis* or *triclinic/general* .. parsed-literal:: @@ -34,6 +34,7 @@ Syntax x,y,z = primitive vector components that define unit cell *basis* values = x y z x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) + *triclinic/general* values = no values, assume lattice tiles Examples """""""" @@ -44,7 +45,7 @@ Examples lattice hex 0.85 lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0 lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 & - basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 + basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 triclinic/general lattice none 2.0 Description @@ -196,6 +197,57 @@ the Z direction. ---------- +The *triclinic/general* option specifies that the defined lattice is +for use with a general triclinic simulation box, as opposed to an +orthogonal or restricted triclinic box. The :doc:`Howto triclinic +` doc page explains all 3 kinds of simluation boxes +LAMMPS supports. + +If this option is specified, a *custom* lattice style must be used. +The *a1*, *a2*, *a3* vectors should define the edge vectors of a +single unit cell of the lattice with one or more basis atoms. They +edge vectors can be arbitrary so long as they are non-zero, distinct, +and not co-planar. In addition, they must define a right-handed +system, such that (*a1* cross *a2*) points in the direction of *a3*. +Note that a left-handed system can be converted to a right-handed +system by simply swapping the order of any pair of the *a1*, *a2*, +*a3* vectors. + +If this option is used, the *origin* and *orient* settings must have +their default values. + +The :doc:`create_box ` command can be used to create a +general triclinic box that replicates the *a1*, *a2*, *a3* unit cell +vectors in each direction to create the 3 arbitrary edge vectors of +the overall simulation box. It requires a lattice with the +*triclinic/general* option. + +Likewise, the :doc:`create_atoms ` command can be used +to add atoms (or molecules) to a general triclinic box which lie on +the lattice points defined by *a1*, *a2*, *a3* and the unit cell basis +atoms. To do this, it also requires a lattice with the +*triclinic/general* option. + +.. note:: + + LAMMPS allows specification of general triclinic lattices and + simulation boxes as a convenience for users who may be converting + data from solid-state crystallograhic representations or from DFT + codes for input to LAMMPS. However, as explained on the + :doc:`Howto_triclinic ` doc page, internally, + LAMMPS only uses restricted triclinic simulation boxes. This means + the box and per-atom information (e.g. coordinates, velocities) + defined by the :doc:`create_box ` and + :doc:`create_atoms ` commands are converted from + general to restricted triclinic form when the two commands are + invoked. It also means that any other commands which use lattice + spacings from this command (e.g. the region command), will be + operating on a restricted triclinic simulation box, even if the + *triclinic/general* option was used to define the lattice. See the + next section for details. + +---------- + Several LAMMPS commands have the option to use distance units that are inferred from "lattice spacings" in the x,y,z box directions. E.g. the :doc:`region ` command can create a block of size @@ -219,6 +271,18 @@ coordinates of the 8 corner points of the modified unit cell (4 in 2d). Similarly, the Y and Z lattice spacings are defined as the difference in the min/max of the y and z coordinates. +.. note:: + + If the *triclinic/general* option is specified, the unit cell + defined by *a1*, *a2*, *a3* edge vectors is first converted to a + restricted triclinic orientation, which is a rotation operation. + The min/max extent of the 8 corner points is then determined, as + described in the preceeding paragraph, to set the lattice + spacings. As explained for the *triclinic/general* option above, + this is because any use of the lattice spacings by other commands + will be for a restricted triclinic simulation box, not a general + triclinic box. + Note that if the unit cell is orthogonal with axis-aligned edges (no rotation via the *orient* keyword), then the lattice spacings in each dimension are simply the scale factor (described above) multiplied by diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index f5544c08ee7..21a9cc880a7 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -374,7 +374,7 @@ void AtomVecLine::data_atom_bonus(int m, const std::vector &values) domain->remap_near(coords,x[m]); x1 = coords[0]; y1 = coords[1]; coords[0] = x2; coords[1] = y2; coords[2] = 0.0; - domain->remap_near(c2,x[m]); + domain->remap_near(coords,x[m]); x2 = coords[0]; y2 = coords[1]; // calculate length and theta diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index ef19085ce50..a24fba4612e 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -154,9 +154,10 @@ void CreateAtoms::command(int narg, char **arg) overlapflag = 0; maxtry = DEFAULT_MAXTRY; radscale = 1.0; - radthresh = domain->lattice->xlattice; mesh_style = BISECTION; - mesh_density = 1.0; + radthresh = domain->lattice->xlattice; // NOTE to Axel - I think this should be 1.0 by default + mesh_density = 1.0; // similar to how this setting is 1.0 + // see rescaling of both below if units = lattice nbasis = domain->lattice->nbasis; basistype = new int[nbasis]; for (int i = 0; i < nbasis; i++) basistype[i] = ntype; @@ -354,19 +355,27 @@ void CreateAtoms::command(int narg, char **arg) } } - // demand non-none lattice be defined for BOX and REGION - // else setup scaling for SINGLE and RANDOM - // could use domain->lattice->lattice2box() to do conversion of - // lattice to box, but not consistent with other uses of units=lattice - // triclinic remapping occurs in add_single() - + // require non-none lattice be defined for BOX or REGION styles + if ((style == BOX) || (style == REGION)) { if (nbasis == 0) error->all(FLERR, "Cannot create atoms with undefined lattice"); - } else if (scaleflag == 1) { + + // apply scaling factor for styles that use distance-dependent factors + + if (scaleflag) { + if (style == SINGLE) { xone[0] *= domain->lattice->xlattice; xone[1] *= domain->lattice->ylattice; xone[2] *= domain->lattice->zlattice; - overlap *= domain->lattice->xlattice; + } else if (style == RANDOM) { + if (overlapflag) overlap *= domain->lattice->xlattice; + } else if (style == MESH) { // NOTE to Axel - here is the rescaling of both params + if (mesh_style == BISECT) { // by lattice spacings if units = lattice, similar to xone,overlap + radthresh *= domain->lattice->xlattice; + } else if (mesh_style = QUASIRANDOM) { + mesh_density /= (domain->lattice->xlattice * domain->lattice->xlattice); + } + } } // set bounds for my proc in sublo[3] & subhi[3] @@ -710,7 +719,7 @@ void CreateAtoms::add_single() void CreateAtoms::add_random() { - double xlo, ylo, zlo, xhi, yhi, zhi, zmid; + double xlo, ylo, zlo, xhi, yhi, zhi; double delx, dely, delz, distsq, odistsq; double lamda[3], *coord; double *boxlo, *boxhi; @@ -729,7 +738,6 @@ void CreateAtoms::add_random() for (int ii = 0; ii < 30; ii++) random->uniform(); // bounding box for atom creation - // in real units, even if triclinic // only limit bbox by region if its bboxflag is set (interior region) if (triclinic == 0) { @@ -739,7 +747,6 @@ void CreateAtoms::add_random() yhi = domain->boxhi[1]; zlo = domain->boxlo[2]; zhi = domain->boxhi[2]; - zmid = zlo + 0.5 * (zhi - zlo); } else { xlo = domain->boxlo_bound[0]; xhi = domain->boxhi_bound[0]; @@ -747,7 +754,6 @@ void CreateAtoms::add_random() yhi = domain->boxhi_bound[1]; zlo = domain->boxlo_bound[2]; zhi = domain->boxhi_bound[2]; - zmid = zlo + 0.5 * (zhi - zlo); boxlo = domain->boxlo_lamda; boxhi = domain->boxhi_lamda; } @@ -783,7 +789,7 @@ void CreateAtoms::add_random() xone[0] = xlo + random->uniform() * (xhi - xlo); xone[1] = ylo + random->uniform() * (yhi - ylo); xone[2] = zlo + random->uniform() * (zhi - zlo); - if (domain->dimension == 2) xone[2] = zmid; + if (domain->dimension == 2) xone[2] = 0.0; if (region && (region->match(xone[0], xone[1], xone[2]) == 0)) continue; if (varflag && vartest(xone) == 0) continue; @@ -1168,16 +1174,12 @@ void CreateAtoms::add_mesh(const char *filename) void CreateAtoms::add_lattice() { // add atoms on general triclinic lattice if Domain has setting for it - // verify lattice is valid for general triclinic - - int triclinic_general = domain->triclinic_general; + // verify lattice was defined with triclinic/general option - if (triclinic_general) { - if (!domain->lattice->is_custom()) - error->all(FLERR,"Create_atoms for general triclinic requires custom lattice"); - if (domain->lattice->is_oriented()) - error->all(FLERR,"Create_atoms for general triclinic requires lattice with default orientation"); - } + if (!domain->triclinic_general && domain->lattice->is_general_triclinic()) + error->all(FLERR,"Create_atoms for non general triclinic box cannot use triclinic/general lattice"); + if (domain->triclinic_general && !domain->lattice->is_general_triclinic()) + error->all(FLERR,"Create_atoms for general triclinic box requires triclnic/general lattice"); // convert 8 corners of my subdomain from box coords to lattice coords // for orthogonal, use corner pts of my subbox @@ -1224,7 +1226,7 @@ void CreateAtoms::add_lattice() // compute new bounding box (xyz min/max) in lattice coords // for orthogonal or restricted triclinic, use 8 corner points of bbox lo/hi - if (!triclinic_general) { + if (!domain->triclinic_general) { domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); @@ -1238,7 +1240,7 @@ void CreateAtoms::add_lattice() // new set of 8 points is no longer an orthogonal bounding box // instead invoke lattice->bbox() on each of 8 points - } else if (triclinic_general) { + } else if (domain->triclinic_general) { double point[3]; point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2]; diff --git a/src/create_box.cpp b/src/create_box.cpp index 4df23d286f7..e4ebe4c0cb4 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -106,10 +106,8 @@ void CreateBox::command(int narg, char **arg) // ABC edge vectors + origin to restricted triclinic } else if (triclinic_general) { - if (!domain->lattice->is_custom()) - error->all(FLERR,"Create_box with no region requires custom lattice"); - if (domain->lattice->is_oriented()) - error->all(FLERR,"Create_box with no region requires lattice with default orientation"); + if (!domain->lattice->is_general_triclinic()) + error->all(FLERR,"Create_box for general triclinic requires triclnic/general lattice"); if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "create_box general triclinic", error); @@ -154,11 +152,11 @@ void CreateBox::command(int narg, char **arg) if (domain->dimension == 2) { if (cvec[0] != 0.0 || cvec[1] != 0.0 || cvec[2] != 1.0 || origin[2] != -0.5) - error->all(FLERR,"Create_box C vector and/or origin is invalid " + error->all(FLERR,"Create_box C edge vector and/or origin is invalid " "for 2d simulation with general triclinic box"); } - // define general triclinic box within Domain + // define general triclinic box within Domain class domain->define_general_triclinic(avec,bvec,cvec,origin); } @@ -247,7 +245,7 @@ void CreateBox::command(int narg, char **arg) error->all(FLERR, "Unknown create_box keyword: {}", arg[iarg]); } - // problem setup using info from header + // setup the simulation box and initial system // deallocate/grow ensures any extra settings are used for topology arrays // necessary in case no create_atoms is performed diff --git a/src/domain.cpp b/src/domain.cpp index e9a18b897e3..3e49255b573 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -571,27 +571,78 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, cvec[1] = cvec_caller[1]; cvec[2] = cvec_caller[2]; + // error check on cvec for 2d systems + + if (dimension == 2 && (cvec[0] != 0.0 || cvec[1] != 0.0)) + error->all(FLERR,"General triclinic box edge vector C invalid for 2d system"); + + // rotate_g2r = rotation matrix from general to restricted triclnic + // rotate_r2g = rotation matrix from restricted to general triclnic + + double aprime[3],bprime[3],cprime[3]; + general_to_restricted_rotation(avec,bvec,cvec,rotate_g2r,aprime,bprime,cprime); + MathExtra::transpose3(rotate_g2r,rotate_r2g); + + // set restricted triclinic boxlo, boxhi, and tilt factors + boxlo[0] = origin_caller[0]; boxlo[1] = origin_caller[1]; boxlo[2] = origin_caller[2]; - // error check on cvec for 2d systems + boxhi[0] = boxlo[0] + aprime[0]; + boxhi[1] = boxlo[1] + bprime[1]; + boxhi[2] = boxlo[2] + cprime[2]; - if (dimension == 2 && (cvec[0] != 0.0 || cvec[1] != 0.0)) - error->all(FLERR,"General triclinic box edge vector C invalid for 2d system"); + xy = bprime[0]; + xz = cprime[0]; + yz = cprime[1]; + + // debug - // error checks for 3d systems + /* + printf("Theta1: %g\n",theta1); + printf("Rotvec1: %g %g %g\n",rot1[0],rot1[1],rot1[2]); + printf("Theta2: %g\n",theta2); + printf("Rotvec2: %g %g %g\n",xaxis[0],xaxis[1],xaxis[2]); + printf("Quat: %g %g %g %g\n", + quat_single[0],quat_single[1],quat_single[2],quat_single[3]); + double angle = 2.0*acos(quat_single[0]); + printf("Theta: %g\n",angle); + printf("Rotvec: %g %g %g\n", + quat_single[1]/sin(0.5*angle),quat_single[2]/sin(0.5*angle), + quat_single[3]/sin(0.5*angle)); + printf("Aprime: %g %g %g\n",aprime[0],aprime[1],aprime[2]); + printf("Bprime: %g %g %g\n",bprime[0],bprime[1],bprime[2]); + printf("Cprime: %g %g %g\n",cprime[0],cprime[1],cprime[2]); + printf("Length A: %g %g\n",MathExtra::len3(avec),MathExtra::len3(aprime)); + printf("Length B: %g %g\n",MathExtra::len3(bvec),MathExtra::len3(bprime)); + printf("Length C: %g %g\n",MathExtra::len3(cvec),MathExtra::len3(cprime)); + */ +} + +/* ---------------------------------------------------------------------- + compute rotation matrix to transform from general to restricted triclinic + ABC = 3 general triclinic edge vectors + rotmat = rotation matrix + A`B`C` = 3 restricited triclinic edge vectors +------------------------------------------------------------------------- */ + +void Domain::general_to_restricted_rotation(double *a, double *b, double *c, + double rotmat[3][3], + double *aprime, double *bprime, double *cprime) +{ + // error checks // A,B,C cannot be co-planar // A x B must point in C direction (right-handed) double abcross[3]; - MathExtra::cross3(avec,bvec,abcross); - double dot = MathExtra::dot3(abcross,cvec); + MathExtra::cross3(a,b,abcross); + double dot = MathExtra::dot3(abcross,c); if (dot == 0.0) - error->all(FLERR,"General triclinic box edge vectors are co-planar"); + error->all(FLERR,"General triclinic edge vectors are co-planar"); if (dot < 0.0) - error->all(FLERR,"General triclinic box edge vectors must be right-handed"); - + error->all(FLERR,"General triclinic edge vectors must be right-handed"); + // quat1 = convert A into A' along +x-axis // rot1 = unit vector to rotate A around // theta1 = angle of rotation calculated from @@ -600,10 +651,10 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, double rot1[3],quat1[4]; double xaxis[3] = {1.0, 0.0, 0.0}; - double avec_len = MathExtra::len3(avec); - MathExtra::cross3(avec,xaxis,rot1); + double alen = MathExtra::len3(a); + MathExtra::cross3(a,xaxis,rot1); MathExtra::norm3(rot1); - double theta1 = acos(avec[0]/avec_len); + double theta1 = acos(a[0]/alen); MathExtra::axisangle_to_quat(rot1,theta1,quat1); // rotmat1 = rotation matrix associated with quat1 @@ -613,8 +664,8 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, // B1 = rotation of B by quat1 rotation matrix - double bvec1[3]; - MathExtra::matvec(rotmat1,bvec,bvec1); + double b1[3]; + MathExtra::matvec(rotmat1,b,b1); // quat2 = rotation to convert B1 into B' in xy plane // Byz1 = projection of B1 into yz plane @@ -625,61 +676,26 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, // positive is valid if B1z < 0.0 else flip sign of theta2 double byzvec1[3],quat2[4]; - MathExtra::copy3(bvec1,byzvec1); + MathExtra::copy3(b1,byzvec1); byzvec1[0] = 0.0; double byzvec1_len = MathExtra::len3(byzvec1); - double theta2 = acos(bvec1[1]/byzvec1_len); - if (bvec1[2] > 0.0) theta2 = -theta2; + double theta2 = acos(b1[1]/byzvec1_len); + if (b1[2] > 0.0) theta2 = -theta2; MathExtra::axisangle_to_quat(xaxis,theta2,quat2); // quat_single = rotation via single quat = quat2 * quat1 // quat_r2g = rotation from restricted to general - // rotate_g2r = general to restricted rotation matrix - // include flip of C vector if needed to obey right-hand rule - // rotate_r2g = restricted to general rotation matrix - // simply a transpose of rotate_g2r since orthonormal + // rotmat = general to restricted rotation matrix double quat_single[4]; MathExtra::quatquat(quat2,quat1,quat_single); - MathExtra::quat_to_mat(quat_single,rotate_g2r); - MathExtra::transpose3(rotate_g2r,rotate_r2g); + MathExtra::quat_to_mat(quat_single,rotmat); // rotate general ABC to restricted triclinic A'B'C' - double aprime[3],bprime[3],cprime[3]; - MathExtra::matvec(rotate_g2r,avec,aprime); - MathExtra::matvec(rotate_g2r,bvec,bprime); - MathExtra::matvec(rotate_g2r,cvec,cprime); - - // set restricted triclinic boxlo, boxhi, and tilt factors - - boxhi[0] = boxlo[0] + aprime[0]; - boxhi[1] = boxlo[1] + bprime[1]; - boxhi[2] = boxlo[2] + cprime[2]; - - xy = bprime[0]; - xz = cprime[0]; - yz = cprime[1]; - - // debug - - printf("Theta1: %g\n",theta1); - printf("Rotvec1: %g %g %g\n",rot1[0],rot1[1],rot1[2]); - printf("Theta2: %g\n",theta2); - printf("Rotvec2: %g %g %g\n",xaxis[0],xaxis[1],xaxis[2]); - printf("Quat: %g %g %g %g\n", - quat_single[0],quat_single[1],quat_single[2],quat_single[3]); - double angle = 2.0*acos(quat_single[0]); - printf("Theta: %g\n",angle); - printf("Rotvec: %g %g %g\n", - quat_single[1]/sin(0.5*angle),quat_single[2]/sin(0.5*angle), - quat_single[3]/sin(0.5*angle)); - printf("Aprime: %g %g %g\n",aprime[0],aprime[1],aprime[2]); - printf("Bprime: %g %g %g\n",bprime[0],bprime[1],bprime[2]); - printf("Cprime: %g %g %g\n",cprime[0],cprime[1],cprime[2]); - printf("Length A: %g %g\n",MathExtra::len3(avec),MathExtra::len3(aprime)); - printf("Length B: %g %g\n",MathExtra::len3(bvec),MathExtra::len3(bprime)); - printf("Length C: %g %g\n",MathExtra::len3(cvec),MathExtra::len3(cprime)); + MathExtra::matvec(rotate_g2r,a,aprime); + MathExtra::matvec(rotate_g2r,b,bprime); + MathExtra::matvec(rotate_g2r,c,cprime); } /* ---------------------------------------------------------------------- diff --git a/src/domain.h b/src/domain.h index 41994e21407..c54c08df3d5 100644 --- a/src/domain.h +++ b/src/domain.h @@ -142,6 +142,9 @@ class Domain : protected Pointers { int ownatom(int, double *, imageint *, int); void define_general_triclinic(double *, double *, double *, double *); + void general_to_restricted_rotation(double *, double *, double *, + double [3][3], + double *, double *, double *); void general_to_restricted_coords(double *); void restricted_to_general_coords(double *); void restricted_to_general_coords(double *, double *); diff --git a/src/lattice.cpp b/src/lattice.cpp index 815700003df..d29a378589a 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -138,6 +138,8 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // process optional args + int triclinic_general = 0; + int iarg = 2; while (iarg < narg) { if (strcmp(arg[iarg],"origin") == 0) { @@ -222,6 +224,11 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) error->all(FLERR, "Invalid lattice basis argument: {}", z); add_basis(x,y,z); iarg += 4; + + } else if (strcmp(arg[iarg],"triclinic/general") == 0) { + triclinic_general = 1; + iarg++; + } else error->all(FLERR,"Unknown lattice keyword: {}", arg[iarg]); } @@ -256,6 +263,26 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) error->all(FLERR,"Lattice spacings are invalid"); } + // requirements for a general triclinic lattice + // right-handed requirement is checked by domain->general_to_restricted_rotation() + // a123 prime are used to compute lattice spacings + + if (triclinic_general) { + if (style != CUSTOM) + error->all(FLERR,"Lattice triclnic/general must be style = CUSTOM"); + if (origin[0] != 0.0 || origin[1] != 0.0 || origin[2] != 0.0) + error->all(FLERR,"Lattice triclnic/general must have default origin"); + int oriented = 0; + if (orientx[0] != 1 || orientx[1] != 0 || orientx[2] != 0) oriented = 1; + if (orienty[0] != 0 || orienty[1] != 1 || orienty[2] != 0) oriented = 1; + if (orientz[0] != 0 || orientz[1] != 0 || orientz[2] != 1) oriented = 1; + if (oriented) + error->all(FLERR,"Lattice triclnic/general must have default orientation"); + + double rotmat[3][3]; + domain->general_to_restricted_rotation(a1,a2,a3,rotmat,a1_prime,a2_prime,a3_prime); + } + // reset scale for LJ units (input scale is rho*) // scale = (Nbasis/(Vprimitive * rho*)) ^ (1/dim) // use fabs() in case a1,a2,a3 are not right-handed for general triclinic @@ -267,18 +294,11 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) scale = pow(nbasis/volume/scale,1.0/dimension); } - // set orientflag - // for general triclinic, create_box and create_atoms require orientflag = 0 - - oriented = 0; - if (orientx[0] != 1 || orientx[1] != 0 || orientx[2] != 0) oriented = 1; - if (orienty[0] != 0 || orienty[1] != 1 || orienty[2] != 0) oriented = 1; - if (orientz[0] != 0 || orientz[1] != 0 || orientz[2] != 1) oriented = 1; - // initialize lattice <-> box transformation matrices - setup_transform(); + setup_transform(a1,a2,a3); + // automatic calculation of lattice spacings // convert 8 corners of primitive unit cell from lattice coords to box coords // min to max = bounding box around the pts in box space // xlattice,ylattice,zlattice = extent of bbox in box space @@ -291,6 +311,14 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) xmax = ymax = zmax = -BIG; xlattice = ylattice = zlattice = 0.0; + // for general triclinic, bounding box is around unit cell + // in restricted triclinic orientation, NOT general + // this enables lattice spacings to be used for other commands (e.g. region) + // after create_box and create_atoms create the restricted triclnic system + // reset transform used by bbox() to be based on rotated a123 prime vectors + + if (triclinic_general) setup_transform(a1_prime,a2_prime,a3_prime); + bbox(0,0.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax); bbox(0,1.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax); bbox(0,0.0,1.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax); @@ -300,10 +328,16 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) bbox(0,0.0,1.0,1.0,xmin,ymin,zmin,xmax,ymax,zmax); bbox(0,1.0,1.0,1.0,xmin,ymin,zmin,xmax,ymax,zmax); + // restore original general triclinic a123 transform + + if (triclinic_general) setup_transform(a2,a2,a3); + xlattice = xmax - xmin; ylattice = ymax - ymin; zlattice = zmax - zmin; + // user-defined lattice spacings + } else { xlattice *= scale; ylattice *= scale; @@ -325,24 +359,13 @@ Lattice::~Lattice() } /* ---------------------------------------------------------------------- - return 1 if style = CUSTOM, else 0 - queried by create_box and create_atoms for general triclinic -------------------------------------------------------------------------- */ - -int Lattice::is_custom() -{ - if (style == CUSTOM) return 1; - return 0; -} - -/* ---------------------------------------------------------------------- - return 1 any orient vectors are non-default, else 0 - queried by create_box and create_atoms for general triclinic + return 1 if lattice is for a general triclinic simulation box + queried by create_box and create_atoms ------------------------------------------------------------------------- */ -int Lattice::is_oriented() +int Lattice::is_general_triclinic() { - if (oriented) return 1; + if (triclinic_general) return 1; return 0; } @@ -395,21 +418,21 @@ int Lattice::collinear() initialize lattice <-> box transformation matrices ------------------------------------------------------------------------- */ -void Lattice::setup_transform() +void Lattice::setup_transform(double *a, double *b, double *c) { double length; // primitive = 3x3 matrix with primitive vectors as columns - primitive[0][0] = a1[0]; - primitive[1][0] = a1[1]; - primitive[2][0] = a1[2]; - primitive[0][1] = a2[0]; - primitive[1][1] = a2[1]; - primitive[2][1] = a2[2]; - primitive[0][2] = a3[0]; - primitive[1][2] = a3[1]; - primitive[2][2] = a3[2]; + primitive[0][0] = a[0]; + primitive[1][0] = a[1]; + primitive[2][0] = a[2]; + primitive[0][1] = b[0]; + primitive[1][1] = b[1]; + primitive[2][1] = b[2]; + primitive[0][2] = c[0]; + primitive[1][2] = c[1]; + primitive[2][2] = c[2]; // priminv = inverse of primitive diff --git a/src/lattice.h b/src/lattice.h index d91b5cc834f..74f213bdb4c 100644 --- a/src/lattice.h +++ b/src/lattice.h @@ -28,34 +28,37 @@ class Lattice : protected Pointers { int nbasis; // # of basis atoms in unit cell double **basis; // fractional coords of each basis atom // within unit cell (0 <= coord < 1) - + Lattice(class LAMMPS *, int, char **); ~Lattice() override; void lattice2box(double &, double &, double &); void box2lattice(double &, double &, double &); void bbox(int, double, double, double, double &, double &, double &, double &, double &, double &); - int is_custom(); - int is_oriented(); + int is_general_triclinic(); private: + int triclinic_general; // 1 if general triclinic, else 0 + int oriented; // 1 if non-default orient xyz, else 0 double scale; - double origin[3]; // lattice origin - int oriented; // 1 if non-default orient xyz, else 0 - int orientx[3]; // lattice orientation vecs - int orienty[3]; // orientx = what lattice dir lies - int orientz[3]; // along x dim in box - + double origin[3]; // lattice origin + int orientx[3]; // lattice orientation vecs + int orienty[3]; // orientx = what lattice dir lies + int orientz[3]; // along x dim in box - double primitive[3][3]; // lattice <-> box transform matrices + double primitive[3][3]; // lattice <-> box transformation matrices double priminv[3][3]; double rotaterow[3][3]; double rotatecol[3][3]; + double a1_prime[3]; // a123 rotated to restricted triclinic orientation + double a2_prime[3]; + double a3_prime[3]; + int orthogonal(); int right_handed(); int collinear(); - void setup_transform(); + void setup_transform(double *, double *, double *); void add_basis(double, double, double); double dot(double *, double *); void cross(double *, double *, double *); From 92b02041cbf768a16ac7109189db3b3ec5094c12 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Sat, 18 Nov 2023 17:16:29 -0700 Subject: [PATCH 057/719] more edits on create_atoms doc page --- doc/src/create_atoms.rst | 110 ++++++++++++++++++--------------------- doc/src/create_box.rst | 4 +- doc/src/read_data.rst | 15 +++--- src/create_atoms.cpp | 2 +- 4 files changed, 61 insertions(+), 70 deletions(-) diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index c9e8f3e8408..26681468521 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -86,16 +86,22 @@ Description """"""""""" This command creates atoms (or molecules) within the simulation box, -either on a lattice, or at a single specified location, or randomly, -or on a surface defined by a triangulated mesh. It is an alternative -to reading in atom coordinates explicitly via a :doc:`read_data -` or :doc:`read_restart ` command. A -simulation box must already exist, which is typically created via the -:doc:`create_box ` command. Before using this command, a -lattice must typically also be defined using the :doc:`lattice -` command, unless you specify the *single* style with units = -box or the *random* style. For the remainder of this doc page, a -created atom or molecule is referred to as a "particle". +either on a lattice, or at random points, or on a surface defined by a +triangulated mesh. Or it creates a single atom (or molecule) at a +specified point. It is an alternative to reading in atom coordinates +explicitly via a :doc:`read_data ` or :doc:`read_restart +` command. + +To use this command a simulation box must already exist, which is +typically created via the :doc:`create_box ` command. +Before using this command, a lattice must typically also be defined +using the :doc:`lattice ` command, unless you specify the +*single* or *mesh* style with units = box or the *random* style. To +create atoms on a lattice for general triclinic boxes, see the +disucssion below. + +For the remainder of this doc page, a created atom or molecule is +referred to as a "particle". If created particles are individual atoms, they are assigned the specified atom *type*, though this can be altered via the *basis* @@ -126,46 +132,21 @@ periodic boundaries. If this is desired, you should either use the *box* style, or tweak the region size to get precisely the particles you want. +---------- ------------------- - -WORK on this - - -If a general triclinic simulation box is defined ... - - - -As noted above, general triclinic boxes in LAMMPS allow for arbitrary -edge vectors **A**, **B**, **C**. The only restrictions are that the -three vectors be distinct, non-zero, and not co-planar. They must -also define a right-handed system such that (**A** x **B**) points in -the direction of **C**. Note that a left-handed system can be -converted to a right-handed system by simply swapping the order of any -pair of the **A**, **B**, **C** vectors. - -To create a general triclinic boxes, the region is specified as NULL -and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three -edge vectors **A**, **B**, **C** using additional information -previously defind by the :doc:`lattice ` command. - -The lattice must be of style *custom* and use its *triclinic/general* -option. This insures the lattice satisfies the restrictions listed -above. The *a1, *a2*, *a3* settings of the :doc:`lattice ` +If the simulation box is formulated as a general triclinic box defined +by arbitary edge vectors **A**, **B**, **C**, then the *box* and +*region* styles will create atoms on a lattice commensurate with those +edge vectors. See the :doc:`Howto_triclinic ` doc +page for a detailed explanation of orthogonal, restricted triclinic, +and general triclinic simulation boxes. As with the :doc:`create_box +` command, the :doc:`lattice ` command used by +this command must be of style *custom* and use its *triclinic/general* +option. The *a1, *a2*, *a3* settings of the :doc:`lattice ` command define the edge vectors of a unit cell of the general -triclinic lattice. This command uses them to define the three edge -vectors and origin of the general triclinic box as: - - -explain region is applied after conversion to restricted triclinic atom coords - -explain general tri for box and region styles -must use lattice triclinic/general -paragraph about DFT motivation -doc that single, random, mesh operate on restricted triclinic box - ------------------- - +triclinic lattice. The :doc:`create_box ` command creates +a simulation box which replicates that unit cell along each of the +**A**, **B**, **C** edge vectors. .. note:: @@ -175,19 +156,28 @@ doc that single, random, mesh operate on restricted triclinic box input to LAMMPS. However, as explained on the :doc:`Howto_triclinic ` doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means - the box defined by this command and per-atom information - (e.g. coordinates, velocities) defined by the :doc:`create_atoms - ` command are converted from general to restricted - triclinic form when the two commands are invoked. The - ` doc page also discusses other LAMMPS commands - which can input/output general triclinic representations of the - simulation box and per-atom data. - - - - - + the box created by the :doc:`create_box ` command and + the atoms with their per-atom information (e.g. coordinates, + velocities) created by this command are converted (rotated) from + general to restricted triclinic form when the two commands are + invoked. The ` doc page also discusses other + LAMMPS commands which can input/output general triclinic + representations of the simulation box and per-atom data. + +The *box* style will fill the entire general triclinic box with +particles on the lattice, as explained above. The *region* style also +operates as explained above, but the check for particles inside the +region is performed *after* the particle coordinates have been +converted to the restricted triclinic box. This means the region must +also be defined with respect to the restricted triclinic box, not the +general triclinic box. + +If the simulation box is general triclinic, the *single*, *random*, +and *mesh* styles described next operate on the box after it has been +converted to restricted triclinic. So all the settings for those +styles should be made in that context. +---------- For the *single* style, a single particle is added to the system at the specified coordinates. This can be useful for debugging purposes diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 11b2878fe4c..79aa839d11a 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -204,8 +204,8 @@ to do this is to specify clo = -0.5 and chi = 0.5 and use the LAMMPS only uses restricted triclinic simulation boxes. This means the box defined by this command and per-atom information (e.g. coordinates, velocities) defined by the :doc:`create_atoms - ` command are converted from general to restricted - triclinic form when the two commands are invoked. The + ` command are converted (rotated) from general to + restricted triclinic form when the two commands are invoked. The ` doc page also discusses other LAMMPS commands which can input/output general triclinic representations of the simulation box and per-atom data. diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 56c92355a86..897f6878b05 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -476,13 +476,14 @@ For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of :doc:`Howto_triclinic ` doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means the box and per-atom information (e.g. coordinates, velocities) in - the data file are converted from general to restricted triclinic - form when the file is read. Other sections of the data file must - also list their per-atom data appropriately if vector quantities - are specified. This requirement is explained below for the relevant - sections. The :doc:`Howto_triclinic ` doc page - also discusses other LAMMPS commands which can input/output general - triclinic representations of the simulation box and per-atom data. + the data file are converted (rotated) from general to restricted + triclinic form when the file is read. Other sections of the data + file must also list their per-atom data appropriately if vector + quantities are specified. This requirement is explained below for + the relevant sections. The :doc:`Howto_triclinic + ` doc page also discusses other LAMMPS commands + which can input/output general triclinic representations of the + simulation box and per-atom data. The following explanations apply to all 3 kinds of simulation boxes: orthogonal, restricted triclinic, and general triclinic. diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index a24fba4612e..d510014191e 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -1179,7 +1179,7 @@ void CreateAtoms::add_lattice() if (!domain->triclinic_general && domain->lattice->is_general_triclinic()) error->all(FLERR,"Create_atoms for non general triclinic box cannot use triclinic/general lattice"); if (domain->triclinic_general && !domain->lattice->is_general_triclinic()) - error->all(FLERR,"Create_atoms for general triclinic box requires triclnic/general lattice"); + error->all(FLERR,"Create_atoms for general triclinic box requires triclinic/general lattice"); // convert 8 corners of my subdomain from box coords to lattice coords // for orthogonal, use corner pts of my subbox From dfafdff2093fa347c44ff23fea381b620e670df8 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 20 Nov 2023 12:06:58 -0700 Subject: [PATCH 058/719] finalized dump command support for general triclinic --- doc/src/create_atoms.rst | 141 ++++++++++++++++++++------------------- doc/src/dump.rst | 108 +++++++++++++++++++++++++++--- doc/src/dump_modify.rst | 45 +++++++++++-- src/create_atoms.cpp | 9 ++- src/dump_atom.cpp | 20 +++--- src/dump_atom.h | 2 +- src/dump_custom.cpp | 34 ++++++---- src/dump_custom.h | 3 +- src/lattice.cpp | 61 ++++++++--------- src/lattice.h | 3 +- tools/binary2txt.cpp | 46 ++++++++++--- 11 files changed, 319 insertions(+), 153 deletions(-) diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 26681468521..71303a7d4f3 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -112,6 +112,21 @@ added to the specified atom *type* (e.g., if *type* = 2 and the file specifies atom types 1, 2, and 3, then each created molecule will have atom types 3, 4, and 5). +.. note:: + + You cannot use this command to create atoms that are outside the + simulation box; they will just be ignored by LAMMPS. This is true + even if you are using shrink-wrapped box boundaries, as specified + by the :doc:`boundary ` command. However, you can first + use the :doc:`change_box ` command to temporarily + expand the box, then add atoms via create_atoms, then finally use + change_box command again if needed to re-shrink-wrap the new atoms. + See the :doc:`change_box ` doc page for an example of + how to do this, using the create_atoms *single* style to insert a + new atom outside the current simulation box. + +---------- + For the *box* style, the create_atoms command fills the entire simulation box with particles on the lattice. If your simulation box is periodic, you should ensure its size is a multiple of the lattice @@ -182,7 +197,64 @@ styles should be made in that context. For the *single* style, a single particle is added to the system at the specified coordinates. This can be useful for debugging purposes or to create a tiny system with a handful of particles at specified -positions. +positions. For a 2d simulation the specified z coordinate must be +0.0. + +.. versionchanged:: 2Jun2022 + +The *porosity* style has been renamed to *random* with added functionality. + +For the *random* style, *N* particles are added to the system at +randomly generated coordinates, which can be useful for generating an +amorphous system. For 2d simulations, the z coordinates of all added +atoms will be 0.0. + +The particles are created one by one using the specified random number +*seed*, resulting in the same set of particle coordinates, independent +of how many processors are being used in the simulation. Unless the +*overlap* keyword is specified, particles created by the *random* +style will typically be highly overlapped. Various additional +criteria can be used to accept or reject a random particle insertion; +see the keyword discussion below. Multiple attempts per particle are +made (see the *maxtry* keyword) until the insertion is either +successful or fails. If this command fails to add all requested *N* +particles, a warning will be output. + +If the *region-ID* argument is specified as NULL, then the randomly +created particles will be anywhere in the simulation box. If a +*region-ID* is specified, a geometric volume is filled that is both +inside the simulation box and is also consistent with the region +volume. See the :doc:`region ` command for details. Note +that a region can be specified so that its "volume" is either inside +or outside its geometric boundary. + +Note that the create_atoms command adds particles to those that +already exist. This means it can be used to add particles to a system +previously read in from a data or restart file. Or the create_atoms +command can be used multiple times, to add multiple sets of particles +to the simulation. For example, grain boundaries can be created, by +interleaving the create_atoms command with :doc:`lattice ` +commands specifying different orientations. + +When this command is used, care should be taken to ensure the +resulting system does not contain particles that are highly +overlapped. Such overlaps will cause many interatomic potentials to +compute huge energies and forces, leading to bad dynamics. There are +several strategies to avoid this problem: + +* Use the :doc:`delete_atoms overlap ` command after + create_atoms. For example, this strategy can be used to overlay and + surround a large protein molecule with a volume of water molecules, + then delete water molecules that overlap with the protein atoms. + +* For the *random* style, use the optional *overlap* keyword to avoid + overlaps when each new particle is created. + +* Before running dynamics on an overlapped system, perform an + :doc:`energy minimization `. Or run initial dynamics with + :doc:`pair_style soft ` or with :doc:`fix nve/limit + ` to un-overlap the particles, before running normal + dynamics. .. figure:: img/marble_race.jpg :figwidth: 33% @@ -242,73 +314,6 @@ to the area of that triangle. beneficial to exclude computing interactions between the created particles using :doc:`neigh_modify exclude `. -.. versionchanged:: 2Jun2022 - -The *porosity* style has been renamed to *random* with added functionality. - -For the *random* style, *N* particles are added to the system at -randomly generated coordinates, which can be useful for generating an -amorphous system. The particles are created one by one using the -specified random number *seed*, resulting in the same set of particle -coordinates, independent of how many processors are being used in the -simulation. Unless the *overlap* keyword is specified, particles -created by the *random* style will typically be highly overlapped. -Various additional criteria can be used to accept or reject a random -particle insertion; see the keyword discussion below. Multiple -attempts per particle are made (see the *maxtry* keyword) until the -insertion is either successful or fails. If this command fails to add -all requested *N* particles, a warning will be output. - -If the *region-ID* argument is specified as NULL, then the randomly -created particles will be anywhere in the simulation box. If a -*region-ID* is specified, a geometric volume is filled that is both -inside the simulation box and is also consistent with the region -volume. See the :doc:`region ` command for details. Note -that a region can be specified so that its "volume" is either inside -or outside its geometric boundary. - -Note that the create_atoms command adds particles to those that -already exist. This means it can be used to add particles to a system -previously read in from a data or restart file. Or the create_atoms -command can be used multiple times, to add multiple sets of particles -to the simulation. For example, grain boundaries can be created, by -interleaving the create_atoms command with :doc:`lattice ` -commands specifying different orientations. - -When this command is used, care should be taken to ensure the -resulting system does not contain particles that are highly -overlapped. Such overlaps will cause many interatomic potentials to -compute huge energies and forces, leading to bad dynamics. There are -several strategies to avoid this problem: - -* Use the :doc:`delete_atoms overlap ` command after - create_atoms. For example, this strategy can be used to overlay and - surround a large protein molecule with a volume of water molecules, - then delete water molecules that overlap with the protein atoms. - -* For the *random* style, use the optional *overlap* keyword to avoid - overlaps when each new particle is created. - -* Before running dynamics on an overlapped system, perform an - :doc:`energy minimization `. Or run initial dynamics with - :doc:`pair_style soft ` or with :doc:`fix nve/limit - ` to un-overlap the particles, before running normal - dynamics. - -.. note:: - - You cannot use any of the styles explained above to create atoms - that are outside the simulation box; they will just be ignored by - LAMMPS. This is true even if you are using shrink-wrapped box - boundaries, as specified by the :doc:`boundary ` command. - However, you can first use the :doc:`change_box ` - command to temporarily expand the box, then add atoms via - create_atoms, then finally use change_box command again if needed - to re-shrink-wrap the new atoms. See the :doc:`change_box - ` doc page for an example of how to do this, using the - create_atoms *single* style to insert a new atom outside the - current simulation box. - ---------- Individual atoms are inserted by this command, unless the *mol* diff --git a/doc/src/dump.rst b/doc/src/dump.rst index e5885dc25df..93bffa3fdcf 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -278,16 +278,20 @@ format ` command and its options. Format of native LAMMPS format dump files: The *atom*, *custom*, *grid*, and *local* styles create files in a -simple LAMMPS-specific text format that is self-explanatory when -viewing a dump file. Many post-processing tools either included with -LAMMPS or third-party tools can read this format, as does the +simple LAMMPS-specific text format that is mostly self-explanatory +when viewing a dump file. Many post-processing tools either included +with LAMMPS or third-party tools can read this format, as does the :doc:`rerun ` command. See tools described on the :doc:`Tools ` doc page for examples, including `Pizza.py `_. For all these styles, the dimensions of the simulation box are -included in each snapshot. For an orthogonal simulation box this -information is formatted as: +included in each snapshot. The simulation box in LAMMPS can be +defined in one of 3 ways: orthogonal, restricted triclinic, and +general triclinic. See the :doc:`Howto triclinic ` +doc page for a detailed description of all 3 options. + +For an orthogonal simulation box the box information is formatted as: .. parsed-literal:: @@ -304,10 +308,10 @@ the six characters is one of *p* (periodic), *f* (fixed), *s* (shrink wrap), or *m* (shrink wrapped with a minimum value). See the :doc:`boundary ` command for details. -For triclinic simulation boxes (non-orthogonal), an orthogonal -bounding box which encloses the triclinic simulation box is output, -along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic box, -formatted as follows: +For a restricted triclinic simulation box, an orthogonal bounding box +which encloses the restricted triclinic simulation box is output, +along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic +box, formatted as follows: .. parsed-literal:: @@ -329,6 +333,10 @@ bounding box extents (xlo_bound, xhi_bound, etc.) are calculated from the triclinic parameters, and how to transform those parameters to and from other commonly used triclinic representations. +For a general triclinic simulation box, see the "General triclinic" +section below for a description of the ITEM: BOX BOUNDS format as well +as how per-atom coordinates and per-atom vector quantities are output. + The *atom* and *custom* styles output a "ITEM: NUMBER OF ATOMS" line with the count of atoms in the snapshot. Likewise they output an "ITEM: ATOMS" line which includes column descriptors for the per-atom @@ -400,7 +408,6 @@ command. Dump files in other popular formats: - .. note:: This section only discusses file formats relevant to this doc page. @@ -656,6 +663,87 @@ how to control the compression level in both variants. ---------- +General triclinic simulation box output for the *atom* and *custom* styles: + +As mentioned above, the simulation box can be defined as a general +triclinic box, which means that 3 arbitrary box edge vectors **A**, +**B**, **C** can be specified. See the :doc:`Howto triclinic +` doc page for a detailed description of general +triclinic boxes. + +This option is provided as a convenience for users who may be +converting data from solid-state crystallograhic representations or +from DFT codes for input to LAMMPS. However, as explained on the +:doc:`Howto_triclinic ` doc page, internally, LAMMPS +only uses restricted triclinic simulation boxes. This means the box +and per-atom information (e.g. coordinates, velocities) LAMMPS stores +are converted (rotated) from general to restricted triclinic form when +the system is created. + +For dump output, if the :doc:`dump_modify triclinic/general +` command is used, the box description and per-atom +coordinates and other per-atom vectors will be converted (rotated) +from restricted to general form when each dump file snapshots is +output. This option can only be used if the simulation box was +initially created as general triclinic. If the option is not used, +and the simulation box is general triclinic, then the dump file +snapshots will reflect the internal restricted triclinic geometry. + +The dump_modify triclinic/general option affects 3 aspects of the dump +file output. + +First, the format for the BOX BOUNDS is as follows + +.. parsed-literal:: + + ITEM: BOX BOUNDS abc origin + ax ay az originx + bx by bz originy + cx cy cz originz + +where the **A** edge vector of the box is (ax,ay,az) and similarly +for **B** and **C**. The origin of all 3 edge vectors is (originx, +originy, originz). + +Second, the coordinates of each atom are converted (rotated) so that +the atom is inside (or near) the general triclinic box defined by the +**A**, **B**, **C** edge vectors. For style *atom*, this only alters +output for unscaled atom coords, via the :doc:`dump_modify scaled no +` setting. For style *custom*, this alters output for +either unscaled or unwrapped output of atom coords, via the *x,y,z* or +*xu,yu,zu* attributes. For output of scaled atom coords by both +styles, there is no difference bewteen restricted and general +triclinic values. + +Third, the output for any attribute of the *custom* style which +represents a per-atom vector quantity will be converted (rotated) to +be oriented consistent with the general tricinic box and its +orientation relative to the standard xyz coordinate axes. + +This applies to the following *custom* style attributes: + +* vx,vy,vz = atom velocities +* fx,fy,fz = forces on atoms +* mux,muy,muz = orientation of dipole moment of atom +* omegax,omegay,omegaz = angular velocity of spherical particle +* angmomx,angmomy,angmomz = angular momentum of aspherical particle +* tqx,tqy,tqz = torque on finite-size particles + +For example, if the velocity of an atom in a restricted triclinic box +is along the x-axis, then it will be output for a general triclinic +box as a vector along the **A** edge vector of the box. + +.. note:: + + For style *custom*, the :doc:`dump_modify thresh ` + command may access per-atom attributes either directly or + indirectly through a compute or variable. If the attribute is an + atom coordinate or one of the vectors mentioned above, its value + will *NOT* be a general triclinic (rotated) value. Rather it will + be a restricted triclinic value. + +---------- + Arguments for different styles: The sections below describe per-atom, local, and per grid cell diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 2d84f28836b..31f1cd214e9 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -17,7 +17,7 @@ Syntax * one or more keyword/value pairs may be appended * these keywords apply to various dump styles -* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap* +* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *triclinic/general* or *units* or *unwrap* .. parsed-literal:: @@ -74,12 +74,13 @@ Syntax -N = sort per-atom lines in descending order by the Nth column *tfactor* arg = time scaling factor (> 0.0) *thermo* arg = *yes* or *no* - *time* arg = *yes* or *no* *thresh* args = attribute operator value attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^" value = numeric value to compare to, or LAST these 3 args can be replaced by the word "none" to turn off thresholding + *time* arg = *yes* or *no* + *triclinic/general* arg = none *units* arg = *yes* or *no* *unwrap* arg = *yes* or *no* @@ -802,8 +803,9 @@ region since the last dump. dump_modify ... thresh v_charge |^ LAST This will dump atoms whose charge has changed from an absolute value -less than :math:`\frac12` to greater than :math:`\frac12` (or vice versa) since the last dump (e.g., due to reactions and subsequent charge equilibration in a -reactive force field). +less than :math:`\frac12` to greater than :math:`\frac12` (or vice +versa) since the last dump (e.g., due to reactions and subsequent +charge equilibration in a reactive force field). The choice of operators listed above are the usual comparison operators. The XOR operation (exclusive or) is also included as "\|\^". @@ -811,6 +813,18 @@ In this context, XOR means that if either the attribute or value is 0.0 and the other is non-zero, then the result is "true" and the threshold criterion is met. Otherwise it is not met. +.. note:: + + For style *custom*, the *triclinic/general* keyword alters dump + output for general triclinic simulation boxes and their atoms. See + the :doc:`dump ` command for details of how this changes the + format of dump file snapstots. The thresh keyword may access + per-atom attributes either directly or indirectly through a compute + or variable. If the attribute is an atom coordinate or a per-atom + vector (such as velocity, force, or dipole moment), its value will + *NOT* be a general triclinic (rotated) value. Rather it will be a + restricted triclinic value. + ---------- The *time* keyword only applies to the dump *atom*, *custom*, *local*, @@ -835,6 +849,27 @@ The default setting is *no*\ . ---------- +The *triclinic/general* keyword only applies to the dump *atom* and +*custom* styles. It can only be used if the simulation box was +created as a general triclinic box. See the :doc:`Howto_triclinic +` doc page for a detailed explanation of orthogonal, +restricted triclinic, and general triclinic simulation boxes. + +If this keyword is used, the box information at the beginning of each +snapshot will include information about the 3 arbitrary edge vectors +**A**, **B**, **C** that define the general triclinic box as well as +their origin. The format is described on the :doc:`dump ` doc +page. + +The coordinates of each atom will be output as values in (or near) the +general triclinic box. Likewise, per-atom vector quantities such as +velocity, omega, dipole moment, etc will have orientations consistent +with the general triclinic box, meaning they will be rotated relative +to the standard xyz coordinate axes. See the :doc:`dump ` doc +page for a full list of which dump attributes this affects. + +---------- + The *units* keyword only applies to the dump *atom*, *custom*, and *local* styles (and their COMPRESS package versions *atom/gz*, *custom/gz* and *local/gz*\ ). If set to *yes*, each individual dump @@ -922,6 +957,8 @@ The option defaults are * sort = off for dump styles *atom*, *custom*, *cfg*, and *local* * sort = id for dump styles *dcd*, *xtc*, and *xyz* * thresh = none +* time = no +* triclinic/general not specified * units = no * unwrap = no diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index d510014191e..59b0ad4ab6f 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -113,6 +113,8 @@ void CreateAtoms::command(int narg, char **arg) xone[0] = utils::numeric(FLERR, arg[2], false, lmp); xone[1] = utils::numeric(FLERR, arg[3], false, lmp); xone[2] = utils::numeric(FLERR, arg[4], false, lmp); + if (domain->dimension == 2 && xone[2] != 0.0) + error->all(FLERR,"Create_atoms single for 2d simulation requires z coord = 0.0"); iarg = 5; } else if (strcmp(arg[1], "random") == 0) { style = RANDOM; @@ -359,7 +361,8 @@ void CreateAtoms::command(int narg, char **arg) if ((style == BOX) || (style == REGION)) { if (nbasis == 0) error->all(FLERR, "Cannot create atoms with undefined lattice"); - + } + // apply scaling factor for styles that use distance-dependent factors if (scaleflag) { @@ -369,8 +372,8 @@ void CreateAtoms::command(int narg, char **arg) xone[2] *= domain->lattice->zlattice; } else if (style == RANDOM) { if (overlapflag) overlap *= domain->lattice->xlattice; - } else if (style == MESH) { // NOTE to Axel - here is the rescaling of both params - if (mesh_style == BISECT) { // by lattice spacings if units = lattice, similar to xone,overlap + } else if (style == MESH) { // NOTE to Axel - here is the rescaling of both params + if (mesh_style == BISECTION) { // by lattice spacings if units = lattice, similar to xone,overlap radthresh *= domain->lattice->xlattice; } else if (mesh_style = QUASIRANDOM) { mesh_density /= (domain->lattice->xlattice * domain->lattice->xlattice); diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 38c8431269d..a029a68135b 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -156,17 +156,21 @@ int DumpAtom::modify_param(int narg, char **arg) scale_flag = utils::logical(FLERR,arg[1],false,lmp); for (auto &item : keyword_user) item.clear(); return 2; - } else if (strcmp(arg[0],"image") == 0) { + } + + if (strcmp(arg[0],"image") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); image_flag = utils::logical(FLERR,arg[1],false,lmp); for (auto &item : keyword_user) item.clear(); return 2; - } else if (strcmp(arg[0],"triclinic/general") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - triclinic_general = utils::logical(FLERR,arg[1],false,lmp); + } + + if (strcmp(arg[0],"triclinic/general") == 0) { + triclinic_general = 1; if (triclinic_general && !domain->triclinic_general) - error->all(FLERR,"Dump_modify triclinic/general invalid b/c simulation box is not"); - return 2; + error->all(FLERR,"Dump_modify triclinic/general cannot be used " + "if simulation box is not general triclinic"); + return 1; } return 0; @@ -410,9 +414,7 @@ void DumpAtom::header_item_triclinic_general(bigint ndump) } if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time()); - fmt::print(fp,"ITEM: TIMESTEP\n{}\n" - "ITEM: NUMBER OF ATOMS\n{}\n", - update->ntimestep, ndump); + fmt::print(fp,"ITEM: TIMESTEP\n{}\nITEM: NUMBER OF ATOMS\n{}\n", update->ntimestep, ndump); fmt::print(fp,"ITEM: BOX BOUNDS abc origin {}\n" "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" diff --git a/src/dump_atom.h b/src/dump_atom.h index df21c7788c8..0b0d3a4f05a 100644 --- a/src/dump_atom.h +++ b/src/dump_atom.h @@ -35,7 +35,7 @@ class DumpAtom : public Dump { protected: int scale_flag; // 1 if atom coords are scaled, 0 if no int image_flag; // 1 if append box count to atom coords, 0 if no - int triclinic_general; // 1 if output box,coords for general triclinic + int triclinic_general; // 1 if output box & coords for general triclinic, 0 if no std::string columns; // column labels diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 9554247aff0..6708a7c4103 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -500,8 +500,8 @@ void DumpCustom::header_binary_triclinic_general(bigint ndump) fwrite(&update->ntimestep,sizeof(bigint),1,fp); fwrite(&ndump,sizeof(bigint),1,fp); - int general_tri = 2; - fwrite(&general_tri,sizeof(int),1,fp); + int triclinic_general_flag = 2; + fwrite(&triclinic_general_flag,sizeof(int),1,fp); fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); fwrite(domain->avec,3*sizeof(double),1,fp); fwrite(domain->bvec,3*sizeof(double),1,fp); @@ -573,9 +573,7 @@ void DumpCustom::header_item_triclinic_general(bigint ndump) } if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time()); - fmt::print(fp,"ITEM: TIMESTEP\n{}\n" - "ITEM: NUMBER OF ATOMS\n{}\n", - update->ntimestep, ndump); + fmt::print(fp,"ITEM: TIMESTEP\n{}\nITEM: NUMBER OF ATOMS\n{}\n", update->ntimestep, ndump); fmt::print(fp,"ITEM: BOX BOUNDS abc origin {}\n" "{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n" @@ -1788,6 +1786,14 @@ int DumpCustom::modify_param(int narg, char **arg) return 2; } + if (strcmp(arg[0],"triclinic/general") == 0) { + triclinic_general = 1; + if (triclinic_general && !domain->triclinic_general) + error->all(FLERR,"Dump_modify triclinic/general cannot be used " + "if simulation box is not general triclinic"); + return 1; + } + if (strcmp(arg[0],"triclinic/general") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); triclinic_general = utils::logical(FLERR,arg[1],false,lmp); @@ -3350,11 +3356,11 @@ void DumpCustom::pack_tqz(int n) void DumpCustom::pack_tqx_triclinic_general(int n) { double **torque = atom->torque; - double torquetri[3]; + double tqtri[3]; for (int i = 0; i < nchoose; i++) { - domain->restricted_to_general_vector(torque[clist[i]],torquetri); - buf[n] = torquetri[0]; + domain->restricted_to_general_vector(torque[clist[i]],tqtri); + buf[n] = tqtri[0]; n += size_one; } } @@ -3364,11 +3370,11 @@ void DumpCustom::pack_tqx_triclinic_general(int n) void DumpCustom::pack_tqy_triclinic_general(int n) { double **torque = atom->torque; - double torquetri[3]; + double tqtri[3]; for (int i = 0; i < nchoose; i++) { - domain->restricted_to_general_vector(torque[clist[i]],torquetri); - buf[n] = torquetri[1]; + domain->restricted_to_general_vector(torque[clist[i]],tqtri); + buf[n] = tqtri[1]; n += size_one; } } @@ -3378,11 +3384,11 @@ void DumpCustom::pack_tqy_triclinic_general(int n) void DumpCustom::pack_tqz_triclinic_general(int n) { double **torque = atom->torque; - double torquetri[3]; + double tqtri[3]; for (int i = 0; i < nchoose; i++) { - domain->restricted_to_general_vector(torque[clist[i]],torquetri); - buf[n] = torquetri[2]; + domain->restricted_to_general_vector(torque[clist[i]],tqtri); + buf[n] = tqtri[2]; n += size_one; } } diff --git a/src/dump_custom.h b/src/dump_custom.h index 60070ddf629..b22d03f9b53 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -36,8 +36,7 @@ class DumpCustom : public Dump { protected: int nevery; // dump frequency for output char *idregion; // region ID, nullptr if no region - - int triclinic_general; // 1 if output box,x,v,f for general triclinic + int triclinic_general; // 1 if output box & per-atom info for general triclinic int nthresh; // # of defined thresholds int nthreshlast; // # of defined thresholds with value = LAST diff --git a/src/lattice.cpp b/src/lattice.cpp index d29a378589a..6992828e3a6 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -17,6 +17,7 @@ #include "comm.h" #include "domain.h" #include "error.h" +#include "math_extra.h" #include "memory.h" #include "update.h" @@ -24,6 +25,7 @@ #include using namespace LAMMPS_NS; +using namespace MathExtra; #define BIG 1.0e30 @@ -237,7 +239,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (nbasis == 0) error->all(FLERR,"No basis atoms in lattice"); if (!orthogonal()) error->all(FLERR,"Lattice orient vectors are not orthogonal"); - if (!right_handed()) + if (!right_handed_orientation()) error->all(FLERR,"Lattice orient vectors are not right-handed"); if (collinear()) error->all(FLERR,"Lattice primitive vectors are collinear"); @@ -263,8 +265,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) error->all(FLERR,"Lattice spacings are invalid"); } - // requirements for a general triclinic lattice - // right-handed requirement is checked by domain->general_to_restricted_rotation() + // additional requirements for a general triclinic lattice // a123 prime are used to compute lattice spacings if (triclinic_general) { @@ -278,6 +279,8 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (orientz[0] != 0 || orientz[1] != 0 || orientz[2] != 1) oriented = 1; if (oriented) error->all(FLERR,"Lattice triclnic/general must have default orientation"); + if (!right_handed_primitive()) + error->all(FLERR,"Lattice triclnic/general a1,a2,a3 must be right-handed"); double rotmat[3][3]; domain->general_to_restricted_rotation(a1,a2,a3,rotmat,a1_prime,a2_prime,a3_prime); @@ -289,8 +292,8 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (strcmp(update->unit_style,"lj") == 0) { double vec[3]; - cross(a2,a3,vec); - double volume = fabs(dot(a1,vec)); + MathExtra::cross3(a2,a3,vec); + double volume = fabs(MathExtra::dot3(a1,vec)); scale = pow(nbasis/volume/scale,1.0/dimension); } @@ -389,7 +392,7 @@ int Lattice::orthogonal() x cross y must be in same direction as z ------------------------------------------------------------------------- */ -int Lattice::right_handed() +int Lattice::right_handed_orientation() { int xy0 = orientx[1]*orienty[2] - orientx[2]*orienty[1]; int xy1 = orientx[2]*orienty[0] - orientx[0]*orienty[2]; @@ -398,19 +401,33 @@ int Lattice::right_handed() return 1; } +/* ---------------------------------------------------------------------- + check righthandedness of a1,a2,a3 primitive vectors + x cross y must be in same direction as z +------------------------------------------------------------------------- */ + +int Lattice::right_handed_primitive() +{ + double vec[3]; + MathExtra::cross3(a1,a2,vec); + if (MathExtra::dot3(vec,a3) <= 0.0) return 0; + return 1; +} + /* ---------------------------------------------------------------------- check collinearity of each pair of primitive vectors + also checks if any primitive vector is zero-length ------------------------------------------------------------------------- */ int Lattice::collinear() { double vec[3]; - cross(a1,a2,vec); - if (dot(vec,vec) == 0.0) return 1; - cross(a2,a3,vec); - if (dot(vec,vec) == 0.0) return 1; - cross(a1,a3,vec); - if (dot(vec,vec) == 0.0) return 1; + MathExtra::cross3(a1,a2,vec); + if (MathExtra::len3(vec) == 0.0) return 1; + MathExtra::cross3(a2,a3,vec); + if (MathExtra::len3(vec) == 0.0) return 1; + MathExtra::cross3(a1,a3,vec); + if (MathExtra::len3(vec) == 0.0) return 1; return 0; } @@ -589,26 +606,6 @@ void Lattice::add_basis(double x, double y, double z) nbasis++; } -/* ---------------------------------------------------------------------- - return x dot y -------------------------------------------------------------------------- */ - -double Lattice::dot(double *x, double *y) -{ - return x[0]*y[0] + x[1]*y[1] + x[2]*y[2]; -} - -/* ---------------------------------------------------------------------- - z = x cross y -------------------------------------------------------------------------- */ - -void Lattice::cross(double *x, double *y, double *z) -{ - z[0] = x[1]*y[2] - x[2]*y[1]; - z[1] = x[2]*y[0] - x[0]*y[2]; - z[2] = x[0]*y[1] - x[1]*y[0]; -} - /* ---------------------------------------------------------------------- convert x,y,z from lattice coords to box coords (flag = 0) or from box coords to lattice coords (flag = 1) diff --git a/src/lattice.h b/src/lattice.h index 74f213bdb4c..8f545de2abc 100644 --- a/src/lattice.h +++ b/src/lattice.h @@ -56,7 +56,8 @@ class Lattice : protected Pointers { double a3_prime[3]; int orthogonal(); - int right_handed(); + int right_handed_orientation(); + int right_handed_primitive(); int collinear(); void setup_transform(double *, double *, double *); void add_basis(double, double, double); diff --git a/tools/binary2txt.cpp b/tools/binary2txt.cpp index b77614a8fcb..2369057324e 100644 --- a/tools/binary2txt.cpp +++ b/tools/binary2txt.cpp @@ -60,6 +60,7 @@ int main(int narg, char **arg) bigint ntimestep, natoms; int size_one, nchunk, triclinic; double xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz; + double ax, ay, az, bx, by, bz, cx, cy, cz, abcx, abcy, abcz; int boundary[3][2]; char boundstr[9]; @@ -133,17 +134,39 @@ int main(int narg, char **arg) fread(&natoms, sizeof(bigint), 1, fp); fread(&triclinic, sizeof(int), 1, fp); fread(&boundary[0][0], 6 * sizeof(int), 1, fp); - fread(&xlo, sizeof(double), 1, fp); - fread(&xhi, sizeof(double), 1, fp); - fread(&ylo, sizeof(double), 1, fp); - fread(&yhi, sizeof(double), 1, fp); - fread(&zlo, sizeof(double), 1, fp); - fread(&zhi, sizeof(double), 1, fp); - if (triclinic) { + + if (triclinic == 0) { + fread(&xlo, sizeof(double), 1, fp); + fread(&xhi, sizeof(double), 1, fp); + fread(&ylo, sizeof(double), 1, fp); + fread(&yhi, sizeof(double), 1, fp); + fread(&zlo, sizeof(double), 1, fp); + fread(&zhi, sizeof(double), 1, fp); + } else if (triclinic == 1) { + fread(&xlo, sizeof(double), 1, fp); + fread(&xhi, sizeof(double), 1, fp); + fread(&ylo, sizeof(double), 1, fp); + fread(&yhi, sizeof(double), 1, fp); + fread(&zlo, sizeof(double), 1, fp); + fread(&zhi, sizeof(double), 1, fp); fread(&xy, sizeof(double), 1, fp); fread(&xz, sizeof(double), 1, fp); fread(&yz, sizeof(double), 1, fp); + } else if (triclinic == 2) { + fread(&ax, sizeof(double), 1, fp); + fread(&ay, sizeof(double), 1, fp); + fread(&az, sizeof(double), 1, fp); + fread(&bx, sizeof(double), 1, fp); + fread(&by, sizeof(double), 1, fp); + fread(&bz, sizeof(double), 1, fp); + fread(&cx, sizeof(double), 1, fp); + fread(&cy, sizeof(double), 1, fp); + fread(&cz, sizeof(double), 1, fp); + fread(&abcx, sizeof(double), 1, fp); + fread(&abcy, sizeof(double), 1, fp); + fread(&abcz, sizeof(double), 1, fp); } + fread(&size_one, sizeof(int), 1, fp); if (magic_string && revision > 0x0001) { @@ -201,16 +224,21 @@ int main(int narg, char **arg) } boundstr[8] = '\0'; - if (!triclinic) { + if (triclinic == 0) { fprintf(fptxt, "ITEM: BOX BOUNDS %s\n", boundstr); fprintf(fptxt, "%-1.16e %-1.16e\n", xlo, xhi); fprintf(fptxt, "%-1.16e %-1.16e\n", ylo, yhi); fprintf(fptxt, "%-1.16e %-1.16e\n", zlo, zhi); - } else { + } else if (triclinic == 1) { fprintf(fptxt, "ITEM: BOX BOUNDS xy xz yz %s\n", boundstr); fprintf(fptxt, "%-1.16e %-1.16e %-1.16e\n", xlo, xhi, xy); fprintf(fptxt, "%-1.16e %-1.16e %-1.16e\n", ylo, yhi, xz); fprintf(fptxt, "%-1.16e %-1.16e %-1.16e\n", zlo, zhi, yz); + } else if (triclinic == 2) { + fprintf(fptxt, "ITEM: BOX BOUNDS abc origin %s\n", boundstr); + fprintf(fptxt, "%-1.16e %-1.16e %-1.16e %-1.16e\n", ax, ay, az, abcx); + fprintf(fptxt, "%-1.16e %-1.16e %-1.16e %-1.16e\n", bx, by, bz, abcy); + fprintf(fptxt, "%-1.16e %-1.16e %-1.16e %-1.16e\n", cx, cy, cz, abcz); } if (columns) From 18c5cdb327fb1e4f0a0e903e4a971196ec69b2ba Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 21 Nov 2023 15:03:32 -0700 Subject: [PATCH 059/719] doc page for thermo output difference with triclinic/general --- doc/src/thermo_modify.rst | 15 ++++++++++++- doc/src/thermo_style.rst | 46 +++++++++++++++++++++++++++++---------- src/thermo.cpp | 3 ++- src/thermo.h | 2 +- 4 files changed, 52 insertions(+), 14 deletions(-) diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 3d2c19614e8..72f36b11982 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -11,7 +11,7 @@ Syntax thermo_modify keyword value ... * one or more keyword/value pairs may be listed -* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press* +* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press* or *triclinic/general* .. parsed-literal:: @@ -32,6 +32,8 @@ Syntax *or* a thermo keyword or reference to compute, fix, property or variable. *temp* value = compute ID that calculates a temperature *press* value = compute ID that calculates a pressure + *triclinic/general* arg = none + Examples """""""" @@ -240,6 +242,17 @@ command, thermo output uses a default compute for pressure with ID = keyword, then the new pressure compute specified by the *press* keyword will be unaffected by the *temp* setting. +The *triclinic/general* keyword can only be used if the simulation box +was created as a general triclinic box. See the :doc:`Howto_triclinic +` doc page for a detailed explanation of orthogonal, +restricted triclinic, and general triclinic simulation boxes. + +If this keyword is used, the output of pressure tensor components for +the system is affected. These components are specified by the +*pxx,pyy,pzz,pxy,pxz,pyz* keywords of the :doc:`thermo_style +` command. See the :doc:`thermo_style ` +doc page for details. + Restrictions """""""""""" none diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 89a2c0b7405..504a7d1d6da 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -68,7 +68,7 @@ Syntax density = mass density of system lx,ly,lz = box lengths in x,y,z xlo,xhi,ylo,yhi,zlo,zhi = box boundaries - xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes + xy,xz,yz = box tilt for restricted triclinic (non-orthogonal) simulation boxes xlat,ylat,zlat = lattice spacings as calculated by :doc:`lattice ` command bonds,angles,dihedrals,impropers = # of these interactions defined pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor @@ -102,9 +102,12 @@ Examples Description """"""""""" -Set the style and content for printing thermodynamic data to the screen -and log files. - +Set the style and content for printing thermodynamic data to the +screen and log files. The units for each column of output +corresponding to the list of keywords is determined by the :doc:`units +` command for the simulation. E.g. energies will be in energy +units, temperature in temperature units, pressure in pressure units. + Style *one* prints a single line of thermodynamic info that is the equivalent of "thermo_style custom step temp epair emol etotal press". The line contains only numeric values. @@ -319,6 +322,27 @@ thermostatting or barostatting to their coupling reservoirs -- that is, the NVT, NPH, or NPT ensembles, the *econserve* quantity should remain constant over time even though *etotal* may change. +The *pxx,pyy,pzz,pxy,pxz,pyz* keywords are the 6 components of the +symmetric pressure tensor for the system. See the :doc:`compute +pressure ` command doc page for details of how it is +calculated. + +If the :doc:`thermo_modify triclinic/general ` option +is set and the simulation box was created as a geenral triclinic box, +then the components will be output as values consistent with the +orientation of the general triclinic box relative to the standard xyz +coordinate axes. If this keyword is not used, the values will be +consistent with the orientation of the restricted triclinic box (which +aligns with the xyz coordinate axes). As explained on the +:doc:`Howto_triclinic ` doc page, even if the +simulation box is created as a general triclinic box, internally +LAMMPS uses a restricted triclinic box. + +Note that because the pressure tensor components are computed using +force vectors and atom coordinates, both of which are rotated in the +general versus restricted triclinic representation, the values will +typically be different for the two cases. + The *fmax* and *fnorm* keywords are useful for monitoring the progress of an :doc:`energy minimization `. The *fmax* keyword calculates the maximum force in any dimension on any atom in the @@ -338,13 +362,13 @@ to reduce the delay factor to ensure no force interactions are missed by atoms moving beyond the neighbor skin distance before a rebuild takes place. -The keywords *cella*, *cellb*, *cellc*, *cellalpha*, -*cellbeta*, *cellgamma*, correspond to the usual crystallographic -quantities that define the periodic unit cell of a crystal. See the -:doc:`Howto triclinic ` page for a geometric -description of triclinic periodic cells, including a precise -definition of these quantities in terms of the internal LAMMPS cell -dimensions *lx*, *ly*, *lz*, *yz*, *xz*, *xy*\ . +The keywords *cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, +*cellgamma*, correspond to the usual crystallographic quantities that +define the periodic unit cell of a crystal. See the :doc:`Howto +triclinic ` page for a geometric description of +restricted triclinic periodic cells, including a precise definition of +these quantities in terms of the internal LAMMPS cell dimensions *lx*, +*ly*, *lz*, *yz*, *xz*, *xy*\ . ---------- diff --git a/src/thermo.cpp b/src/thermo.cpp index 082bebe80d7..d791f5f856f 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -579,7 +579,8 @@ void Thermo::modify_params(int narg, char **arg) if (iarg + 2 > narg) error->all(FLERR,"Illegal thermo_modify command"); triclinic_general = utils::logical(FLERR,arg[iarg+1],false,lmp); if (triclinic_general && !domain->triclinic_general) - error->all(FLERR,"Thermo_modify triclinic/general invalid b/c simulation box is not"); + error->all(FLERR,"Thermo_modify triclinic/general cannot be used " + "if simulation box is not general triclinic"); iarg += 2; } else if (strcmp(arg[iarg], "lost") == 0) { diff --git a/src/thermo.h b/src/thermo.h index b7c973fff5a..1829349b96c 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -57,8 +57,8 @@ class Thermo : protected Pointers { private: int nfield, nfield_initial; int *vtype; + int triclinic_general; // set by thermo_modify - int triclinic_general; // set by thermo_modify std::string line; std::vector keyword, format, format_column_user, keyword_user; std::string format_line_user, format_float_user, format_int_user, format_bigint_user; From 61993d16432314055cc263779095f550c7d7a1db Mon Sep 17 00:00:00 2001 From: Leidy Lorena Alzate Vargas - 373576 Date: Wed, 22 Nov 2023 14:36:59 -0700 Subject: [PATCH 060/719] MLIAP Unified fix for multi layer models CPU only --- src/ML-IAP/mliap_unified.cpp | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/src/ML-IAP/mliap_unified.cpp b/src/ML-IAP/mliap_unified.cpp index de1d0bcb7df..6dcdf94c2d2 100644 --- a/src/ML-IAP/mliap_unified.cpp +++ b/src/ML-IAP/mliap_unified.cpp @@ -254,10 +254,8 @@ void LAMMPS_NS::update_pair_energy(MLIAPData *data, double *eij) double e = 0.5 * eij[ii]; // must not count any contribution where i is not a local atom - if (i < nlocal) { - data->eatoms[i] += e; - e_total += e; - } + data->eatoms[i] += e; + e_total += e; } data->energy = e_total; } @@ -278,16 +276,14 @@ void LAMMPS_NS::update_pair_forces(MLIAPData *data, double *fij) int j = data->jatoms[ii]; // must not count any contribution where i is not a local atom - if (i < nlocal) { - f[i][0] += fij[ii3]; - f[i][1] += fij[ii3 + 1]; - f[i][2] += fij[ii3 + 2]; - f[j][0] -= fij[ii3]; - f[j][1] -= fij[ii3 + 1]; - f[j][2] -= fij[ii3 + 2]; - - if (data->vflag) data->pairmliap->v_tally(i, j, &fij[ii3], data->rij[ii]); - } + f[i][0] += fij[ii3]; + f[i][1] += fij[ii3 + 1]; + f[i][2] += fij[ii3 + 2]; + f[j][0] -= fij[ii3]; + f[j][1] -= fij[ii3 + 1]; + f[j][2] -= fij[ii3 + 2]; + + if (data->vflag) data->pairmliap->v_tally(i, j, &fij[ii3], data->rij[ii]); } } From 469358cbf4951c51472777bcd51055de9aaf2ed7 Mon Sep 17 00:00:00 2001 From: Leidy Lorena Alzate Vargas - 373576 Date: Wed, 22 Nov 2023 14:38:13 -0700 Subject: [PATCH 061/719] UPDATE KOKKOS --- src/KOKKOS/mliap_unified_kokkos.cpp | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/KOKKOS/mliap_unified_kokkos.cpp b/src/KOKKOS/mliap_unified_kokkos.cpp index 4c38e4f1d61..4a8c14d7230 100644 --- a/src/KOKKOS/mliap_unified_kokkos.cpp +++ b/src/KOKKOS/mliap_unified_kokkos.cpp @@ -315,7 +315,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij) int i = pair_i[ii]; int j = j_atoms[ii]; // must not count any contribution where i is not a local atom - if (i < nlocal) { Kokkos::atomic_add(&f[i*3+0], fij[ii3+0]); Kokkos::atomic_add(&f[i*3+1], fij[ii3+1]); Kokkos::atomic_add(&f[i*3+2], fij[ii3+2]); @@ -352,7 +351,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij) Kokkos::atomic_add(&d_vatom(j,3), 0.5*v[3]); Kokkos::atomic_add(&d_vatom(j,4), 0.5*v[4]); Kokkos::atomic_add(&d_vatom(j,5), 0.5*v[5]); - } } } }); @@ -383,10 +381,8 @@ void LAMMPS_NS::update_atom_energy(MLIAPDataKokkosDevice *data, double *ei) Kokkos::parallel_reduce(nlocal, KOKKOS_LAMBDA(int i, double &local_sum){ double e = ei[i]; // must not count any contribution where i is not a local atom - if (i < nlocal) { - d_eatoms[i] = e; - local_sum += e; - } + d_eatoms[i] = e; + local_sum += e; },*data->energy); } From c57ed87e9a9f73dfbc4e6e62a5f98ac46e083f48 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 23 Nov 2023 15:36:27 +0200 Subject: [PATCH 062/719] Addition of conical indenter --- src/fix_indent.h | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/fix_indent.h b/src/fix_indent.h index 527e9ec2772..6f33f6fbb10 100644 --- a/src/fix_indent.h +++ b/src/fix_indent.h @@ -49,6 +49,10 @@ class FixIndent : public Fix { int cdim, varflag; int ilevel_respa; + char *rlostr, *rhistr, *lostr, *histr; + int rlovar, rhivar, lovar, hivar; + double rlovalue, rhivalue, lovalue, hivalue; + void options(int, char **); }; From a90c7b42f99bf61d79a7cdacc69394b56de829b0 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 23 Nov 2023 15:40:34 +0200 Subject: [PATCH 063/719] Include code for conical indenter in fix_indent.cpp --- src/fix_indent.cpp | 466 ++++++++++++++++++++++++++++++++++++++------- 1 file changed, 398 insertions(+), 68 deletions(-) diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index 9adb337dd66..d3e80ecd793 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -23,6 +23,7 @@ #include "error.h" #include "input.h" #include "lattice.h" +#include "math_extra.h" #include "modify.h" #include "respa.h" #include "update.h" @@ -34,14 +35,30 @@ using namespace LAMMPS_NS; using namespace FixConst; -enum{NONE,SPHERE,CYLINDER,PLANE}; -enum{INSIDE,OUTSIDE}; +enum{NONE, SPHERE, CYLINDER, PLANE, CONE}; +enum{INSIDE, OUTSIDE}; + +static bool PointInsideCone(int dir, double *center, double lo, + double hi, double rlo, double rhi, double *point); + +static void DistanceExteriorPoint(int dir, double *center, + double lo, double hi, double rlo, double rhi, double &x, + double &y, double &z); + +static void DistanceInteriorPoint(int dir, double *center, + double lo, double hi, double rlo, double rhi, double &x, + double &y, double &z); + +static void point_on_line_segment(double *a, double *b, double *c, double *d); + +static double closest(double *x, double *near, double *nearest, double dsq); /* ---------------------------------------------------------------------- */ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - xstr(nullptr), ystr(nullptr), zstr(nullptr), rstr(nullptr), pstr(nullptr) + xstr(nullptr), ystr(nullptr), zstr(nullptr), rstr(nullptr), pstr(nullptr), + rlostr(nullptr), rhistr(nullptr), lostr(nullptr), histr(nullptr) { if (narg < 4) utils::missing_cmd_args(FLERR, "fix indent", error); @@ -56,6 +73,7 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) : ilevel_respa = 0; k = utils::numeric(FLERR,arg[3],false,lmp); + if (k < 0.0) error->all(FLERR, "Illegal fix indent force constant: {}", k); k3 = k/3.0; // read options from end of input line @@ -79,6 +97,30 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) : if (!ystr) yvalue *= yscale; if (!zstr) zvalue *= zscale; if (!rstr) rvalue *= xscale; + } else if (istyle == CONE) { + + if (!xstr) xvalue *= xscale; + if (!ystr) yvalue *= yscale; + if (!zstr) zvalue *= zscale; + + double scaling_factor = 1.0; + switch (cdim) { + case 0: + scaling_factor = xscale; + break; + case 1: + scaling_factor = yscale; + break; + case 2: + scaling_factor = zscale; + break; + } + + if (!rlostr) rlovalue *= scaling_factor; + if (!rhistr) rhivalue *= scaling_factor; + if (!lostr) lovalue *= scaling_factor; + if (!histr) hivalue *= scaling_factor; + } else if (istyle == PLANE) { if (cdim == 0 && !pstr) pvalue *= xscale; else if (cdim == 1 && !pstr) pvalue *= yscale; @@ -86,7 +128,7 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR,"Unknown fix indent keyword: {}", istyle); varflag = 0; - if (xstr || ystr || zstr || rstr || pstr) varflag = 1; + if (xstr || ystr || zstr || rstr || pstr || rlostr || rhistr || lostr || histr) varflag = 1; indenter_flag = 0; indenter[0] = indenter[1] = indenter[2] = indenter[3] = 0.0; @@ -101,6 +143,10 @@ FixIndent::~FixIndent() delete [] zstr; delete [] rstr; delete [] pstr; + delete [] rlostr; + delete [] rhistr; + delete [] lostr; + delete [] histr; } /* ---------------------------------------------------------------------- */ @@ -154,6 +200,38 @@ void FixIndent::init() error->all(FLERR,"Variable {} for fix indent is invalid style", pstr); } + if (rlostr) { + rlovar = input->variable->find(rlostr); + if (rlovar < 0) + error->all(FLERR,"Variable {} for fix indent does not exist", rlostr); + if (!input->variable->equalstyle(rlovar)) + error->all(FLERR,"Variable {} for fix indent is invalid style", rlostr); + } + + if (rhistr) { + rhivar = input->variable->find(rhistr); + if (rhivar < 0) + error->all(FLERR,"Variable {} for fix indent does not exist", rhistr); + if (!input->variable->equalstyle(rhivar)) + error->all(FLERR,"Variable {} for fix indent is invalid style", rhistr); + } + + if (lostr) { + lovar = input->variable->find(lostr); + if (lovar < 0) + error->all(FLERR,"Variable {} for fix indent does not exist", lostr); + if (!input->variable->equalstyle(lovar)) + error->all(FLERR,"Variable {} for fix indent is invalid style", lostr); + } + + if (histr) { + hivar = input->variable->find(histr); + if (hivar < 0) + error->all(FLERR,"Variable {} for fix indent does not exist", histr); + if (!input->variable->equalstyle(hivar)) + error->all(FLERR,"Variable {} for fix indent is invalid style", histr); + } + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = (dynamic_cast(update->integrate))->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); @@ -192,32 +270,28 @@ void FixIndent::post_force(int /*vflag*/) indenter_flag = 0; indenter[0] = indenter[1] = indenter[2] = indenter[3] = 0.0; - // spherical indenter + // ctr = current indenter centerz + double ctr[3] {xvalue, yvalue, zvalue}; + if (xstr) ctr[0] = input->variable->compute_equal(xvar); + if (ystr) ctr[1] = input->variable->compute_equal(yvar); + if (zstr) ctr[2] = input->variable->compute_equal(zvar); - if (istyle == SPHERE) { + double **x = atom->x; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; - // ctr = current indenter center - // remap into periodic box + double delx, dely, delz, r, dr, fmag, fx, fy, fz; - double ctr[3]; - if (xstr) ctr[0] = input->variable->compute_equal(xvar); - else ctr[0] = xvalue; - if (ystr) ctr[1] = input->variable->compute_equal(yvar); - else ctr[1] = yvalue; - if (zstr) ctr[2] = input->variable->compute_equal(zvar); - else ctr[2] = zvalue; - domain->remap(ctr); + // spherical indenter - double radius; - if (rstr) radius = input->variable->compute_equal(rvar); - else radius = rvalue; + if (istyle == SPHERE) { - double **x = atom->x; - double **f = atom->f; - int *mask = atom->mask; - int nlocal = atom->nlocal; + // remap indenter center into periodic box + domain->remap(ctr); - double delx,dely,delz,r,dr,fmag,fx,fy,fz; + double radius { rstr ? input->variable->compute_equal(rvar) : rvalue}; + if (radius < 0.0) error->all(FLERR, "Illegal fix indent sphere radius: {}", radius); for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { @@ -254,38 +328,11 @@ void FixIndent::post_force(int /*vflag*/) // remap into periodic box // 3rd coord is just near box for remap(), since isn't used - double ctr[3]; - if (cdim == 0) { - ctr[0] = domain->boxlo[0]; - if (ystr) ctr[1] = input->variable->compute_equal(yvar); - else ctr[1] = yvalue; - if (zstr) ctr[2] = input->variable->compute_equal(zvar); - else ctr[2] = zvalue; - } else if (cdim == 1) { - if (xstr) ctr[0] = input->variable->compute_equal(xvar); - else ctr[0] = xvalue; - ctr[1] = domain->boxlo[1]; - if (zstr) ctr[2] = input->variable->compute_equal(zvar); - else ctr[2] = zvalue; - } else { - if (xstr) ctr[0] = input->variable->compute_equal(xvar); - else ctr[0] = xvalue; - if (ystr) ctr[1] = input->variable->compute_equal(yvar); - else ctr[1] = yvalue; - ctr[2] = domain->boxlo[2]; - } + ctr[cdim] = domain->boxlo[cdim]; domain->remap(ctr); - double radius; - if (rstr) radius = input->variable->compute_equal(rvar); - else radius = rvalue; - - double **x = atom->x; - double **f = atom->f; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - double delx,dely,delz,r,dr,fmag,fx,fy,fz; + double radius { rstr ? input->variable->compute_equal(rvar) : rvalue}; + if (radius < 0.0) error->all(FLERR, "Illegal fix indent cylinder radius: {}", radius); for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { @@ -324,31 +371,85 @@ void FixIndent::post_force(int /*vflag*/) indenter[3] -= fz; } + // conical indenter + + } else if (istyle == CONE) { + + double radiuslo { rlostr ? input->variable->compute_equal(rlovar) : rlovalue }; + if (radiuslo < 0.0) error->all(FLERR, "Illegal fix indent cone lower radius: {}", radiuslo); + + double radiushi { rhistr ? input->variable->compute_equal(rhivar) : rhivalue }; + if (radiushi < 0.0) error->all(FLERR, "Illegal fix indent cone high radius: {}", radiushi); + + double initial_lo { lostr ? input->variable->compute_equal(lovar) : lovalue }; + double initial_hi { histr ? input->variable->compute_equal(hivar) : hivalue }; + + ctr[cdim] = 0.5 * (initial_hi + initial_lo); + + domain->remap(ctr); + + double hi = ctr[cdim] + 0.5 * (initial_hi - initial_lo); + double lo = ctr[cdim] - 0.5 * (initial_hi - initial_lo); + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + delx = x[i][0] - ctr[0]; + dely = x[i][1] - ctr[1]; + delz = x[i][2] - ctr[2]; + domain->minimum_image(delx, dely, delz); + + double x0[3] {delx + ctr[0], dely + ctr[1], delz + ctr[2]}; + r = sqrt(delx * delx + dely * dely + delz * delz); + + // find if the particle is inside or outside the cone + bool point_inside_cone = PointInsideCone(cdim, ctr, lo, hi, radiuslo, radiushi, x0); + + if (side == INSIDE && point_inside_cone) continue; + if (side == OUTSIDE && !point_inside_cone) continue; + + // find the distance between the point and the cone + if (point_inside_cone) { + DistanceInteriorPoint(cdim, ctr, lo, hi, radiuslo, radiushi, x0[0], x0[1], x0[2]); + } else { + DistanceExteriorPoint(cdim, ctr, lo, hi, radiuslo, radiushi, x0[0], x0[1], x0[2]); + } + + // compute the force from the center of the cone - it is different from the approach of fix wall/region + dr = sqrt(x0[0] * x0[0] + x0[1] * x0[1] + x0[2] * x0[2]); + + int force_sign = { point_inside_cone ? 1 : -1 }; + fmag = force_sign * k * dr * dr; + + fx = delx*fmag/r; + fy = dely*fmag/r; + fz = delz*fmag/r; + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + indenter[0] -= k3 * dr * dr * dr; + indenter[1] -= fx; + indenter[2] -= fy; + indenter[3] -= fz; + } + } + // planar indenter } else { // plane = current plane position - double plane; - if (pstr) plane = input->variable->compute_equal(pvar); - else plane = pvalue; - - double **x = atom->x; - double **f = atom->f; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - double dr,fatom; + double plane { pstr ? input->variable->compute_equal(pvar) : pvalue}; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { dr = planeside * (plane - x[i][cdim]); if (dr >= 0.0) continue; - fatom = -planeside * k*dr*dr; - f[i][cdim] += fatom; - indenter[0] -= k3 * dr*dr*dr; - indenter[cdim+1] -= fatom; + fmag = -planeside * k * dr * dr; + f[i][cdim] += fmag; + indenter[0] -= k3 * dr * dr * dr; + indenter[cdim+1] -= fmag; } } @@ -487,6 +588,64 @@ void FixIndent::options(int narg, char **arg) istyle = PLANE; iarg += 4; + } else if (strcmp(arg[iarg],"cone") == 0) { + + if (iarg+8 > narg) utils::missing_cmd_args(FLERR, "fix indent cone", error); + + if (strcmp(arg[iarg+1],"x") == 0) { + cdim = 0; + + if (utils::strmatch(arg[iarg+2],"^v_")) { + ystr = utils::strdup(arg[iarg+2]+2); + } else yvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp); + + if (utils::strmatch(arg[iarg+3],"^v_")) { + zstr = utils::strdup(arg[iarg+3]+2); + } else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp); + + } else if (strcmp(arg[iarg+1],"y") == 0) { + cdim = 1; + + if (utils::strmatch(arg[iarg+2],"^v_")) { + xstr = utils::strdup(arg[iarg+2]+2); + } else xvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp); + + if (utils::strmatch(arg[iarg+3],"^v_")) { + zstr = utils::strdup(arg[iarg+3]+2); + } else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp); + + } else if (strcmp(arg[iarg+1],"z") == 0) { + cdim = 2; + + if (utils::strmatch(arg[iarg+2],"^v_")) { + xstr = utils::strdup(arg[iarg+2]+2); + } else xvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp); + + if (utils::strmatch(arg[iarg+3],"^v_")) { + ystr = utils::strdup(arg[iarg+3]+2); + } else yvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp); + + } else error->all(FLERR,"Unknown fix indent cone argument: {}", arg[iarg+1]); + + if (utils::strmatch(arg[iarg+4],"^v_")) { + rlostr = utils::strdup(arg[iarg+4]+2); + } else rlovalue = utils::numeric(FLERR,arg[iarg+4],false,lmp); + + if (utils::strmatch(arg[iarg+5],"^v_")) { + rhistr = utils::strdup(arg[iarg+5]+2); + } else rhivalue = utils::numeric(FLERR,arg[iarg+5],false,lmp); + + if (utils::strmatch(arg[iarg+6],"^v_")) { + lostr = utils::strdup(arg[iarg+6]+2); + } else lovalue = utils::numeric(FLERR,arg[iarg+6],false,lmp); + + if (utils::strmatch(arg[iarg+7],"^v_")) { + histr = utils::strdup(arg[iarg+7]+2); + } else hivalue = utils::numeric(FLERR,arg[iarg+7],false,lmp); + + istyle = CONE; + iarg += 8; + } else if (strcmp(arg[iarg],"units") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix indent units", error); if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; @@ -503,3 +662,174 @@ void FixIndent::options(int narg, char **arg) } else error->all(FLERR,"Unknown fix indent argument: {}", arg[iarg]); } } + +/* ---------------------------------------------------------------------- + determines if a point is inside (true) or outside (false) of a cone +------------------------------------------------------------------------- */ + +bool PointInsideCone(int dir, double *center, double lo, + double hi, double rlo, double rhi, double *x) +{ + if ((x[dir] > hi) || (x[dir] < lo)) return false; + + double del[3] {x[0] - center[0], x[1] - center[1], x[2] - center[2]}; + del[dir] = 0.0; + + double dist = sqrt(del[0] * del[0] + del[1] * del[1] + del[2] * del[2]); + double currentradius = rlo + (x[dir] - lo) * (rhi - rlo) / (hi - lo); + + if (dist > currentradius) return false; + + return true; +} + +/* ---------------------------------------------------------------------- + distance between an exterior point and a cone +------------------------------------------------------------------------- */ +void DistanceExteriorPoint(int dir, double *center, double lo, double hi, + double rlo, double rhi, double &x, double &y, double &z) +{ + double xp[3], nearest[3], corner1[3], corner2[3]; + + double point[3] {x, y, z}; + + double del[3] {x - center[0], y - center[1], z - center[2]}; + del[dir] = 0.0; + + double r = sqrt(del[0] * del[0] + del[1] * del[1] + del[2] * del[2]); + + corner1[0] = center[0] + del[0] * rlo / r; + corner1[1] = center[1] + del[1] * rlo / r; + corner1[2] = center[2] + del[2] * rlo / r; + corner1[dir] = lo; + + corner2[0] = center[0] + del[0] * rhi / r; + corner2[1] = center[1] + del[1] * rhi / r; + corner2[2] = center[2] + del[2] * rhi / r; + corner2[dir] = hi; + + double corner3[3] {center[0], center[1], center[2]}; + corner3[dir] = lo; + + double corner4[3] {center[0], center[1], center[2]}; + corner4[dir] = hi; + + // initialize distance to a big number + double distsq = 1.0e20; + + // check the first triangle + point_on_line_segment(corner1, corner2, point, xp); + distsq = closest(point, xp, nearest, distsq); + + // check the second triangle + point_on_line_segment(corner1, corner3, point, xp); + distsq = closest(point, xp, nearest, distsq); + + // check the third triangle + point_on_line_segment(corner2, corner4, point, xp); + distsq = closest(point, xp, nearest, distsq); + + x -= nearest[0]; + y -= nearest[1]; + z -= nearest[2]; + + return; +} + +/* ---------------------------------------------------------------------- + distance between an interior point and a cone +------------------------------------------------------------------------- */ + +void DistanceInteriorPoint(int dir, double *center, + double lo, double hi, double rlo, double rhi, double &x, + double &y, double &z) +{ + double r, dist_disk, dist_surf; + double surflo[3], surfhi[3], xs[3]; + double initial_point[3] {x, y, z}; + double point[3] {0.0, 0.0, 0.0}; + + // initial check with the two disks + if ( (initial_point[dir] - lo) < (hi - initial_point[dir]) ) { + dist_disk = (initial_point[dir] - lo) * (initial_point[dir] - lo); + point[dir] = initial_point[dir] - lo; + } else { + dist_disk = (hi - initial_point[dir]) * (hi - initial_point[dir]); + point[dir] = initial_point[dir] - hi; + } + + // check with the points in the conical surface + double del[3] {x - center[0], y - center[1], z - center[2]}; + del[dir] = 0.0; + r = sqrt(del[0] * del[0] + del[1] * del[1] + del[2] * del[2]); + + surflo[0] = center[0] + del[0] * rlo / r; + surflo[1] = center[1] + del[1] * rlo / r; + surflo[2] = center[2] + del[2] * rlo / r; + surflo[dir] = lo; + + surfhi[0] = center[0] + del[0] * rhi / r; + surfhi[1] = center[1] + del[1] * rhi / r; + surfhi[2] = center[2] + del[2] * rhi / r; + surfhi[dir] = hi; + + point_on_line_segment(surflo, surfhi, initial_point, xs); + + double dx[3] {initial_point[0] - xs[0], initial_point[1] - xs[1], initial_point[2] - xs[2]}; + dist_surf = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2]; + if (dist_surf < dist_disk) { + x = dx[0]; + y = dx[1]; + z = dx[2]; + } else { + x = point[0]; + y = point[1]; + z = point[2]; + } + + return; +} + +/* ---------------------------------------------------------------------- + helper function extracted from region.cpp +------------------------------------------------------------------------- */ + +void point_on_line_segment(double *a, double *b, double *c, double *d) +{ + double ba[3], ca[3]; + + MathExtra::sub3(b, a, ba); + MathExtra::sub3(c, a, ca); + double t = MathExtra::dot3(ca, ba) / MathExtra::dot3(ba, ba); + if (t <= 0.0) { + d[0] = a[0]; + d[1] = a[1]; + d[2] = a[2]; + } else if (t >= 1.0) { + d[0] = b[0]; + d[1] = b[1]; + d[2] = b[2]; + } else { + d[0] = a[0] + t * ba[0]; + d[1] = a[1] + t * ba[1]; + d[2] = a[2] + t * ba[2]; + } +} + +/* ---------------------------------------------------------------------- + helper function extracted from region_cone.cpp +------------------------------------------------------------------------- */ + +double closest(double *x, double *near, double *nearest, double dsq) +{ + double dx = x[0] - near[0]; + double dy = x[1] - near[1]; + double dz = x[2] - near[2]; + double rsq = dx * dx + dy * dy + dz * dz; + if (rsq >= dsq) return dsq; + + nearest[0] = near[0]; + nearest[1] = near[1]; + nearest[2] = near[2]; + return rsq; +} From e1c028c785fface11d8eba7d6ab57e42d278e654 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 23 Nov 2023 16:02:22 +0200 Subject: [PATCH 064/719] Update documentation Describe the arguments for cone indenter style --- doc/src/fix_indent.rst | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index 15790e15d02..d478d7dc506 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -14,17 +14,23 @@ Syntax * indent = style name of this fix command * K = force constant for indenter surface (force/distance\^2 units) * one or more keyword/value pairs may be appended -* keyword = *sphere* or *cylinder* or *plane* or *side* or *units* +* keyword = *sphere* or *cone* or *cylinder* or *plane* or *side* or *units* .. parsed-literal:: *sphere* args = x y z R - x,y,z = position of center of indenter (distance units) + x, y, z = position of center of indenter (distance units) R = sphere radius of indenter (distance units) - any of x,y,z,R can be a variable (see below) + any of x, y, z, R can be a variable (see below) + *cone* args = dim c1 c2 radlo radhi lo hi + dim = *x* or *y* or *z* = axis of cone + c1, c2 = coords of cone axis in other 2 dimensions (distance units) + radlo,radhi = cone radii at lo and hi end (distance units) + lo,hi = bounds of cone in dim (distance units) + any of c1, c2, radlo, radhi, lo, hi can be a variable (see below) *cylinder* args = dim c1 c2 R dim = *x* or *y* or *z* = axis of cylinder - c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) + c1, c2 = coords of cylinder axis in other 2 dimensions (distance units) R = cylinder radius of indenter (distance units) any of c1,c2,R can be a variable (see below) *plane* args = dim pos side @@ -57,7 +63,7 @@ material or as an obstacle in a flow. Or it can be used as a constraining wall around a simulation; see the discussion of the *side* keyword below. -The indenter can either be spherical or cylindrical or planar. You +The indenter can either be spherical or conical or cylindrical or planar. You must set one of those 3 keywords. A spherical indenter exerts a force of magnitude @@ -75,9 +81,9 @@ A cylindrical indenter exerts the same force, except that *r* is the distance from the atom to the center axis of the cylinder. The cylinder extends infinitely along its axis. -Spherical and cylindrical indenters account for periodic boundaries in +Spherical, conical and cylindrical indenters account for periodic boundaries in two ways. First, the center point of a spherical indenter (x,y,z) or -axis of a cylindrical indenter (c1,c2) is remapped back into the +axis of a conical/cylindrical indenter (c1,c2) is remapped back into the simulation box, if the box is periodic in a particular dimension. This occurs every timestep if the indenter geometry is specified with a variable (see below), e.g. it is moving over time. Second, the From fb243eba9b0ca50efb02e9fa4df05614ab7c8dcc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 1 Dec 2023 14:41:12 -0500 Subject: [PATCH 065/719] update lattice death tests for changed error messages --- unittest/commands/test_lattice_region.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/unittest/commands/test_lattice_region.cpp b/unittest/commands/test_lattice_region.cpp index da36628b7f1..6eac1f45dfa 100644 --- a/unittest/commands/test_lattice_region.cpp +++ b/unittest/commands/test_lattice_region.cpp @@ -322,7 +322,7 @@ TEST_F(LatticeRegionTest, lattice_sq) ASSERT_EQ(lattice->basis[0][1], 0.0); ASSERT_EQ(lattice->basis[0][2], 0.0); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice orient vectors are not compatible with 2d simulation.*", command("lattice sq 1.0 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1");); BEGIN_HIDE_OUTPUT(); @@ -463,13 +463,13 @@ TEST_F(LatticeRegionTest, lattice_custom) command("dimension 2"); END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: No basis atoms in lattice.*", command("lattice custom 1.0");); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice origin z coord must be 0.0 for 2d simulation.*", command("lattice custom 1.0 origin 0.5 0.5 0.5 basis 0.0 0.0 0.0");); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice a1/a2/a3 vectors are not compatible with 2d simulation.*", command("lattice custom 1.0 a1 1.0 1.0 1.0 basis 0.0 0.0 0.0");); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice a1/a2/a3 vectors are not compatible with 2d simulation.*", command("lattice custom 1.0 a2 1.0 1.0 1.0 basis 0.0 0.0 0.0");); - TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*", + TEST_FAILURE(".*ERROR: Lattice a1/a2/a3 vectors are not compatible with 2d simulation.*", command("lattice custom 1.0 a3 1.0 1.0 1.0 basis 0.0 0.0 0.0");); } From 45372937dbf81a04b49b78341e27ca254a7549fe Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 1 Dec 2023 14:52:47 -0500 Subject: [PATCH 066/719] loads of whitespace fixes --- doc/src/Howto_triclinic.rst | 2 +- doc/src/create_box.rst | 4 +-- doc/src/dump.rst | 4 +-- doc/src/read_data.rst | 4 +-- doc/src/thermo_style.rst | 2 +- src/DIELECTRIC/atom_vec_dielectric.cpp | 2 +- src/DIPOLE/atom_vec_dipole.cpp | 4 +-- src/MACHDYN/atom_vec_smd.cpp | 4 +-- src/SPIN/atom_vec_spin.cpp | 4 +-- src/atom.cpp | 22 ++++++------- src/atom_vec.cpp | 12 +++---- src/atom_vec.h | 4 +-- src/atom_vec_body.cpp | 8 ++--- src/atom_vec_body.h | 2 +- src/atom_vec_ellipsoid.cpp | 8 ++--- src/atom_vec_ellipsoid.h | 2 +- src/atom_vec_line.cpp | 4 +-- src/atom_vec_tri.cpp | 10 +++--- src/create_atoms.cpp | 18 +++++------ src/create_box.cpp | 18 +++++------ src/domain.cpp | 24 +++++++------- src/domain.h | 12 +++---- src/dump_atom.cpp | 8 ++--- src/dump_custom.cpp | 44 +++++++++++++------------- src/dump_custom.h | 14 ++++---- src/lattice.cpp | 20 ++++++------ src/lattice.h | 8 ++--- src/math_extra.cpp | 2 +- src/read_data.cpp | 32 +++++++++---------- src/read_data.h | 4 +-- src/thermo.cpp | 4 +-- src/thermo.h | 4 +-- src/write_data.cpp | 10 +++--- src/write_restart.cpp | 2 +- 34 files changed, 163 insertions(+), 163 deletions(-) diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 525c3e0f1b3..1461f32187d 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -92,7 +92,7 @@ restricted triclinic parallelepiped. conform to the LAMMPS definition of a restricted triclinic box. See the discussion in the next sub-section about general triclinic simulation boxes in LAMMPS. - + Note that the :doc:`thermo_style custom ` command has keywords for outputting the various parameters that define both restricted and general triclinic simulation boxes. Thus you can check diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 79aa839d11a..f2b58755393 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -46,11 +46,11 @@ Examples create_box 1 NULL 0 5 0 5 -0.5 0.5 .. code-block:: LAMMPS - + # 3d general triclinic box using primitive cell for 3d fcc lattice lattice custom 1.0 a2 0.0 0.5 0.5 a1 0.5 0.0 0.5 a3 0.5 0.5 0.0 basis 0.0 0.0 0.0 create box 1 NULL -5 5 -10 10 0 20 - + Description """"""""""" diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 77faa5ffe7f..8cba1d760bf 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -719,9 +719,9 @@ Third, the output for any attribute of the *custom* style which represents a per-atom vector quantity will be converted (rotated) to be oriented consistent with the general tricinic box and its orientation relative to the standard xyz coordinate axes. - + This applies to the following *custom* style attributes: - + * vx,vy,vz = atom velocities * fx,fy,fz = forces on atoms * mux,muy,muz = orientation of dipole moment of atom diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 897f6878b05..dd028ec23e4 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -148,7 +148,7 @@ keyword must be used. triclinic box, the avec, bvec, cvec, and "abc origin" keywords must have the same values in subsequent data files. Also the *shift* keyword cannot be used in subsequent read_data commands. - + The three choices for the *add* argument affect how the atom IDs and molecule IDs of atoms in the data file are treated. If *append* is specified, atoms in the data file are added to the current system, @@ -494,7 +494,7 @@ periodic sense) back inside the box. For triclinic boxes, periodicity in x,y,z refers to the faces of the parallelepided defined by the **A**,**B**,**C** edge vectors of the simuation box. See the :doc:`boundary ` command doc page for a fuller discussion. - + Note that if the *add* option is being used to add atoms to a simulation box that already exists, this periodic remapping will be performed using simulation box bounds that are the union of the diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 504a7d1d6da..45a1eaa2a81 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -107,7 +107,7 @@ screen and log files. The units for each column of output corresponding to the list of keywords is determined by the :doc:`units ` command for the simulation. E.g. energies will be in energy units, temperature in temperature units, pressure in pressure units. - + Style *one* prints a single line of thermodynamic info that is the equivalent of "thermo_style custom step temp epair emol etotal press". The line contains only numeric values. diff --git a/src/DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp index 617ad4ebea5..7412df118f9 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -235,7 +235,7 @@ void AtomVecDielectric::write_data_restore_restricted() AtomVec::write_data_restore_restricted(); if (!mu_hold) return; - + int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) memcpy(&mu[i],&mu_hold[i],3*sizeof(double)); diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 38ecd63dddf..470dfc77eff 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -29,7 +29,7 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp) mass_type = PER_TYPE; atom->q_flag = atom->mu_flag = 1; - + mu_hold = nullptr; // strings with peratom variables to include in each AtomVec method @@ -117,7 +117,7 @@ void AtomVecDipole::write_data_restore_restricted() AtomVec::write_data_restore_restricted(); if (!mu_hold) return; - + int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) memcpy(&mu[i],&mu_hold[i],3*sizeof(double)); diff --git a/src/MACHDYN/atom_vec_smd.cpp b/src/MACHDYN/atom_vec_smd.cpp index 05c73d5b33d..9d4e5dcce5a 100644 --- a/src/MACHDYN/atom_vec_smd.cpp +++ b/src/MACHDYN/atom_vec_smd.cpp @@ -60,7 +60,7 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp) atom->eff_plastic_strain_rate_flag = 1; x0_hold = nullptr; - + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -166,7 +166,7 @@ void AtomVecSMD::data_atom_post(int ilocal) // for PBC, shift, etc // this means no need for read_data_general_to_restricted() method // to rotate x0 for general triclinic - + x0[ilocal][0] = x[ilocal][0]; x0[ilocal][1] = x[ilocal][1]; x0[ilocal][2] = x[ilocal][2]; diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 8844755cd81..f941ddc990a 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -43,7 +43,7 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp) atom->sp_flag = 1; sp_hold = nullptr; - + // strings with peratom variables to include in each AtomVec method // strings cannot contain fields in corresponding AtomVec default strings // order of fields in a string does not matter @@ -147,7 +147,7 @@ void AtomVecSpin::write_data_restore_restricted() AtomVec::write_data_restore_restricted(); if (!sp_hold) return; - + int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) memcpy(&sp[i],&sp_hold[i],3*sizeof(double)); diff --git a/src/atom.cpp b/src/atom.cpp index 33bd5d517fb..a0d5b4ba08e 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1052,7 +1052,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, auto location = "Atoms section of data file"; // use the first line to detect and validate the number of words/tokens per line - + next = strchr(buf,'\n'); if (!next) error->all(FLERR, "Missing data in {}", location); *next = '\0'; @@ -1069,7 +1069,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, error->all(FLERR,"Incorrect format in {}: {}", location, utils::trim(buf)); *next = '\n'; - + // set bounds for my proc // if periodic and I am lo/hi proc, adjust bounds by EPSILON // ensures all data atoms will be owned even with round-off @@ -1147,17 +1147,17 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, int nvalues = values.size(); // skip comment lines - + if ((nvalues == 0) || (utils::strmatch(values[0],"^#.*"))) { // check that line has correct # of words - + } else if ((nvalues < nwords) || ((nvalues > nwords) && (!utils::strmatch(values[nwords],"^#")))) { error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); // extract the atom coords and image flags (if they exist) - + } else { int imx = 0, imy = 0, imz = 0; if (imageflag) { @@ -1186,14 +1186,14 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, error->all(FLERR,"Read_data atom z coord is non-zero for 2d simulation"); xdata[2] = 0.0; } - + // convert atom coords from general to restricted triclinic // so can decide which proc owns the atom - + if (triclinic_general) domain->general_to_restricted_coords(xdata); // apply shift if requested by read_data command - + if (shiftflag) { xdata[0] += shift[0]; xdata[1] += shift[1]; @@ -1201,11 +1201,11 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, } // map atom into simulation box for periodic dimensions - + domain->remap(xdata,imagedata); // determine if this proc owns the atom - + if (triclinic) { domain->x2lamda(xdata,lamda); coord = lamda; @@ -1216,7 +1216,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, coord[2] >= sublo[2] && coord[2] < subhi[2]) { // atom-style specific method parses single line - + avec->data_atom(xdata,imagedata,values,typestr); typestr = utils::utf8_subst(typestr); if (id_offset) tag[nlocal-1] += id_offset; diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index d94365db438..1942d2a6d2a 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -70,7 +70,7 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp) x_hold = nullptr; v_hold = omega_hold = angmom_hold = nullptr; - + threads = nullptr; } @@ -2243,7 +2243,7 @@ void AtomVec::read_data_general_to_restricted(int nlocal_previous, int nlocal) // operate on v, omega, angmom // no other read_data Velocities fields are Nx3 double arrays - + if (datatype == Atom::DOUBLE) { if (cols == 3) { double **array = *((double ***) pdata); @@ -2283,7 +2283,7 @@ void AtomVec::write_data_restricted_to_general() // operate on v, omega, angmom // no other write_data Velocities fields are Nx3 double arrays - + if (datatype == Atom::DOUBLE) { if (cols == 3) { double **array = *((double ***) pdata); @@ -2325,10 +2325,10 @@ void AtomVec::write_data_restore_restricted() memory->destroy(x_hold); x_hold = nullptr; } - + // operate on v, omega, angmom // no other write_data Velocities fields are Nx3 double arrays - + if (v_hold) { memcpy(&v[0][0],&v_hold[0][0],3*nlocal*sizeof(double)); memory->destroy(v_hold); @@ -2340,7 +2340,7 @@ void AtomVec::write_data_restore_restricted() memory->destroy(omega_hold); omega_hold = nullptr; } - + if (angmom_hold) { memcpy(&atom->angmom[0][0],&angmom_hold[0][0],3*nlocal*sizeof(double)); memory->destroy(angmom_hold); diff --git a/src/atom_vec.h b/src/atom_vec.h index 55fe7e2f7d2..23429647972 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -174,8 +174,8 @@ class AtomVec : protected Pointers { double **x, **v, **f; // copies of original unrotated fields for write_data for general triclinic - - double **x_hold; + + double **x_hold; double **v_hold, **omega_hold, **angmom_hold; // standard list of peratom fields always operated on by different methods diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 108d94bbecb..5ff84d6b1f3 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -648,15 +648,15 @@ void AtomVecBody::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/) void AtomVecBody::read_data_general_to_restricted(int nlocal_previous, int nlocal) { int j; - + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); // quat_g2r = quat that rotates from general to restricted triclinic // quat_new = body quat converted to restricted triclinic - + double quat_g2r[4],quat_new[4]; MathExtra::mat_to_quat(domain->rotate_g2r,quat_g2r); - + for (int i = nlocal_previous; i < nlocal; i++) { if (body[i] < 0) continue; j = body[i]; @@ -685,7 +685,7 @@ void AtomVecBody::write_data_restricted_to_general() // quat_r2g = quat that rotates from restricted to general triclinic // quat_new = ellipsoid quat converted to general triclinic - + double quat_r2g[4],quat_new[4]; MathExtra::mat_to_quat(domain->rotate_r2g,quat_r2g); diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index 5ba90a6dc1d..0aa83e833f1 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -69,7 +69,7 @@ class AtomVecBody : public AtomVec { void read_data_general_to_restricted(int, int); void write_data_restricted_to_general(); void write_data_restore_restricted(); - + // methods used by other classes to query/set body info double radius_body(int, int, int *, double *); diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 9b64426224c..417c3cf5fab 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -545,15 +545,15 @@ void AtomVecEllipsoid::write_data_bonus(FILE *fp, int n, double *buf, int /*flag void AtomVecEllipsoid::read_data_general_to_restricted(int nlocal_previous, int nlocal) { int j; - + AtomVec::read_data_general_to_restricted(nlocal_previous, nlocal); // quat_g2r = quat that rotates from general to restricted triclinic // quat_new = ellipsoid quat converted to restricted triclinic - + double quat_g2r[4],quat_new[4]; MathExtra::mat_to_quat(domain->rotate_g2r,quat_g2r); - + for (int i = nlocal_previous; i < nlocal; i++) { if (ellipsoid[i] < 0) continue; j = ellipsoid[i]; @@ -582,7 +582,7 @@ void AtomVecEllipsoid::write_data_restricted_to_general() // quat_r2g = quat that rotates from restricted to general triclinic // quat_new = ellipsoid quat converted to general triclinic - + double quat_r2g[4],quat_new[4]; MathExtra::mat_to_quat(domain->rotate_r2g,quat_r2g); diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h index 23c824dbf03..03850837d8e 100644 --- a/src/atom_vec_ellipsoid.h +++ b/src/atom_vec_ellipsoid.h @@ -74,7 +74,7 @@ class AtomVecEllipsoid : public AtomVec { double *rmass; double **angmom; double **quat_hold; - + int nghost_bonus, nmax_bonus; int ellipsoid_flag; double rmass_one; diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index 21a9cc880a7..d6f1b561713 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -526,7 +526,7 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/) j = line[i]; length = bonus[j].length; theta = bonus[j].theta; - + xc = x_bonus[i][0]; yc = x_bonus[i][1]; x1 = xc - 0.5 * cos(theta) * length; @@ -541,7 +541,7 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/) // if triclinic_general: // rotate 4 buf values from restricted to general triclinic // output by write_data_bonus() as x1/y1 and x2/y2 - + if (triclinic_general) { coords[0] = buf[m-4]; coords[1] = buf[m-3]; coords[2] = 0.0; domain->restricted_to_general_coords(coords); diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 69665c6a94b..e3cfab7d59a 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -510,7 +510,7 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector &values) // convert c1,c2,c3 from general to restricted triclniic // x is already restricted triclinic - + if (domain->triclinic_general) { domain->general_to_restricted_coords(c1); domain->general_to_restricted_coords(c2); @@ -523,11 +523,11 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector &values) domain->remap_near(c1,x[m]); domain->remap_near(c2,x[m]); domain->remap_near(c3,x[m]); - + // centroid = 1/3 of sum of vertices // error if centroid is not within EPSILON of atom x // reset atom x to centroid - + double centroid[3]; centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0; centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0; @@ -729,7 +729,7 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/) double **x_bonus; if (triclinic_general) x_bonus = x_hold; else x_bonus = x; - + tagint *tag = atom->tag; int nlocal = atom->nlocal; @@ -760,7 +760,7 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/) // if triclinic_general: // rotate 9 buf values from restricted to general triclinic // output by write_data_bonus() as c1,c2,c3 - + if (triclinic_general) { domain->restricted_to_general_coords(&buf[m-9]); domain->restricted_to_general_coords(&buf[m-6]); diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 59b0ad4ab6f..d3c3e200bc7 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -358,11 +358,11 @@ void CreateAtoms::command(int narg, char **arg) } // require non-none lattice be defined for BOX or REGION styles - + if ((style == BOX) || (style == REGION)) { if (nbasis == 0) error->all(FLERR, "Cannot create atoms with undefined lattice"); } - + // apply scaling factor for styles that use distance-dependent factors if (scaleflag) { @@ -465,7 +465,7 @@ void CreateAtoms::command(int narg, char **arg) atom->avec->clear_bonus(); // add atoms/molecules with appropriate add() method - + bigint natoms_previous = atom->natoms; int nlocal_previous = atom->nlocal; @@ -1178,7 +1178,7 @@ void CreateAtoms::add_lattice() { // add atoms on general triclinic lattice if Domain has setting for it // verify lattice was defined with triclinic/general option - + if (!domain->triclinic_general && domain->lattice->is_general_triclinic()) error->all(FLERR,"Create_atoms for non general triclinic box cannot use triclinic/general lattice"); if (domain->triclinic_general && !domain->lattice->is_general_triclinic()) @@ -1228,7 +1228,7 @@ void CreateAtoms::add_lattice() // convert 8 corner points of bounding box to lattice coordinates // compute new bounding box (xyz min/max) in lattice coords // for orthogonal or restricted triclinic, use 8 corner points of bbox lo/hi - + if (!domain->triclinic_general) { domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax); @@ -1274,7 +1274,7 @@ void CreateAtoms::add_lattice() domain->restricted_to_general_coords(point); domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax); } - + // ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox // overlap = any part of a unit cell (face,edge,pt) in common with my subbox // in lattice space, subbox is a tilted box @@ -1284,7 +1284,7 @@ void CreateAtoms::add_lattice() // which can lead to missing atoms in rare cases // extra decrement of lo if min < 0, since static_cast(-1.5) = -1 // for 2d simulation, klo = khi = 0 so just one plane of atoms - + ilo = static_cast(xmin) - 1; jlo = static_cast(ymin) - 1; klo = static_cast(zmin) - 1; @@ -1297,7 +1297,7 @@ void CreateAtoms::add_lattice() if (zmin < 0.0) klo--; if (domain->dimension == 2) klo = khi = 0; - + // count lattice sites on each proc nlatt_overflow = 0; @@ -1395,7 +1395,7 @@ void CreateAtoms::loop_lattice(int action) error->all(FLERR,"Create_atoms atom z coord is non-zero for 2d simulation"); x[2] = 0.0; } - } + } // if a region was specified, test if atom is in it diff --git a/src/create_box.cpp b/src/create_box.cpp index e4ebe4c0cb4..7dd6f52e9d0 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -48,7 +48,7 @@ void CreateBox::command(int narg, char **arg) Region *region = nullptr; int triclinic_general = 0; - + if (strcmp(arg[1],"NULL") == 0) triclinic_general = 1; else { region = domain->get_region_by_id(arg[1]); @@ -61,13 +61,13 @@ void CreateBox::command(int narg, char **arg) // 3 options: orthogonal, restricted triclinic, general triclinic int iarg = 2; - + if (region) { - + // region is not prism // setup orthogonal box // set simulation domain from region extent - + if (strcmp(region->style, "prism") != 0) { domain->triclinic = 0; domain->boxlo[0] = region->extent_xlo; @@ -108,7 +108,7 @@ void CreateBox::command(int narg, char **arg) } else if (triclinic_general) { if (!domain->lattice->is_general_triclinic()) error->all(FLERR,"Create_box for general triclinic requires triclnic/general lattice"); - + if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "create_box general triclinic", error); double alo = utils::numeric(FLERR, arg[iarg + 0], false, lmp); @@ -118,14 +118,14 @@ void CreateBox::command(int narg, char **arg) double clo = utils::numeric(FLERR, arg[iarg + 4], false, lmp); double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp); iarg += 6; - + // use lattice2box() to generate origin and ABC vectors // origin = abc lo // ABC vectors = hi in one dim - origin - + double avec[3],bvec[3],cvec[3],origin[3]; double px,py,pz; - + px = alo; py = blo; pz = clo; domain->lattice->lattice2box(px,py,pz); origin[0] = px; @@ -157,7 +157,7 @@ void CreateBox::command(int narg, char **arg) } // define general triclinic box within Domain class - + domain->define_general_triclinic(avec,bvec,cvec,origin); } diff --git a/src/domain.cpp b/src/domain.cpp index 3e49255b573..a27b52e49b0 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -293,12 +293,12 @@ void Domain::set_global_box() // update general triclinic box if defined // reset general tri ABC edge vectors from restricted tri box - + if (triclinic_general) { double aprime[3],bprime[3],cprime[3]; // A'B'C' = edge vectors of restricted triclinic box - + aprime[0] = boxhi[0] - boxlo[0]; aprime[1] = aprime[2] = 0.0; bprime[0] = xy; @@ -309,7 +309,7 @@ void Domain::set_global_box() cprime[2] = boxhi[2] - boxlo[2]; // transform restricted A'B'C' to general triclinic ABC - + MathExtra::matvec(rotate_r2g,aprime,avec); MathExtra::matvec(rotate_r2g,bprime,bvec); MathExtra::matvec(rotate_r2g,cprime,cvec); @@ -556,7 +556,7 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, { if (triclinic || triclinic_general) error->all(FLERR,"General triclinic box edge vectors are already set"); - + triclinic = triclinic_general = 1; avec[0] = avec_caller[0]; @@ -596,7 +596,7 @@ void Domain::define_general_triclinic(double *avec_caller, double *bvec_caller, xy = bprime[0]; xz = cprime[0]; yz = cprime[1]; - + // debug /* @@ -656,7 +656,7 @@ void Domain::general_to_restricted_rotation(double *a, double *b, double *c, MathExtra::norm3(rot1); double theta1 = acos(a[0]/alen); MathExtra::axisangle_to_quat(rot1,theta1,quat1); - + // rotmat1 = rotation matrix associated with quat1 double rotmat1[3][3]; @@ -674,7 +674,7 @@ void Domain::general_to_restricted_rotation(double *a, double *b, double *c, // Byz1 dot yunit = B1y = |Byz1| cos(theta2) // theta2 via acos() is positive (0 to PI) // positive is valid if B1z < 0.0 else flip sign of theta2 - + double byzvec1[3],quat2[4]; MathExtra::copy3(b1,byzvec1); byzvec1[0] = 0.0; @@ -705,7 +705,7 @@ void Domain::general_to_restricted_rotation(double *a, double *b, double *c, void Domain::general_to_restricted_coords(double *x) { double xshift[3],xnew[3]; - + xshift[0] = x[0] - boxlo[0]; xshift[1] = x[1] - boxlo[1]; xshift[2] = x[2] - boxlo[2]; @@ -722,7 +722,7 @@ void Domain::general_to_restricted_coords(double *x) void Domain::restricted_to_general_coords(double *x) { double xshift[3],xnew[3]; - + xshift[0] = x[0] - boxlo[0]; xshift[1] = x[1] - boxlo[1]; xshift[2] = x[2] - boxlo[2]; @@ -735,7 +735,7 @@ void Domain::restricted_to_general_coords(double *x) void Domain::restricted_to_general_coords(double *x, double *xnew) { double xshift[3]; - + xshift[0] = x[0] - boxlo[0]; xshift[1] = x[1] - boxlo[1]; xshift[2] = x[2] - boxlo[2]; @@ -752,7 +752,7 @@ void Domain::restricted_to_general_coords(double *x, double *xnew) void Domain::general_to_restricted_vector(double *v) { double vnew[3]; - + MathExtra::matvec(rotate_g2r,v,vnew); v[0] = vnew[0]; v[1] = vnew[1]; @@ -766,7 +766,7 @@ void Domain::general_to_restricted_vector(double *v) void Domain::restricted_to_general_vector(double *v) { double vnew[3]; - + MathExtra::matvec(rotate_r2g,v,vnew); v[0] = vnew[0]; v[1] = vnew[1]; diff --git a/src/domain.h b/src/domain.h index c54c08df3d5..d0991c37688 100644 --- a/src/domain.h +++ b/src/domain.h @@ -41,7 +41,7 @@ class Domain : protected Pointers { int triclinic; // 0 = orthog box, 1 = triclinic (restricted or general) int triclinic_general; // 1 if general <-> restricted tri mapping is stored, 0 if not - + // orthogonal box double xprd, yprd, zprd; // global box dimensions @@ -96,7 +96,7 @@ class Domain : protected Pointers { double rotate_r2g[3][3]; // rotation matrix from restricted --> general tri // box flags - + int box_change; // 1 if any of next 3 flags are set, else 0 int box_change_size; // 1 if box size changes, 0 if not int box_change_shape; // 1 if box shape changes, 0 if not @@ -145,13 +145,13 @@ class Domain : protected Pointers { void general_to_restricted_rotation(double *, double *, double *, double [3][3], double *, double *, double *); - void general_to_restricted_coords(double *); + void general_to_restricted_coords(double *); void restricted_to_general_coords(double *); void restricted_to_general_coords(double *, double *); - void general_to_restricted_vector(double *); + void general_to_restricted_vector(double *); void restricted_to_general_vector(double *); - void restricted_to_general_vector(double *, double *x); - + void restricted_to_general_vector(double *, double *x); + void set_lattice(int, char **); void add_region(int, char **); void delete_region(Region *); diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index a029a68135b..8d77efcea05 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -133,7 +133,7 @@ void DumpAtom::init_style() } } } - + if (image_flag == 0) convert_choice = &DumpAtom::convert_noimage; else convert_choice = &DumpAtom::convert_image; @@ -157,14 +157,14 @@ int DumpAtom::modify_param(int narg, char **arg) for (auto &item : keyword_user) item.clear(); return 2; } - + if (strcmp(arg[0],"image") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); image_flag = utils::logical(FLERR,arg[1],false,lmp); for (auto &item : keyword_user) item.clear(); return 2; } - + if (strcmp(arg[0],"triclinic/general") == 0) { triclinic_general = 1; if (triclinic_general && !domain->triclinic_general) @@ -172,7 +172,7 @@ int DumpAtom::modify_param(int narg, char **arg) "if simulation box is not general triclinic"); return 1; } - + return 0; } diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 6708a7c4103..c06ee0a2901 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -1347,7 +1347,7 @@ int DumpCustom::parse_fields(int narg, char **arg) if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_y_triclinic_general; else pack_choice[iarg] = &DumpCustom::pack_y; vtype[iarg] = Dump::DOUBLE; - } else if (strcmp(arg[iarg],"z") == 0) { + } else if (strcmp(arg[iarg],"z") == 0) { if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_z_triclinic_general; else pack_choice[iarg] = &DumpCustom::pack_z; vtype[iarg] = Dump::DOUBLE; @@ -1390,7 +1390,7 @@ int DumpCustom::parse_fields(int narg, char **arg) if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zsu_triclinic; else pack_choice[iarg] = &DumpCustom::pack_zsu; vtype[iarg] = Dump::DOUBLE; - + } else if (strcmp(arg[iarg],"ix") == 0) { pack_choice[iarg] = &DumpCustom::pack_ix; vtype[iarg] = Dump::INT; @@ -1431,7 +1431,7 @@ int DumpCustom::parse_fields(int narg, char **arg) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_q; vtype[iarg] = Dump::DOUBLE; - + } else if (strcmp(arg[iarg],"mux") == 0) { if (!atom->mu_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1466,7 +1466,7 @@ int DumpCustom::parse_fields(int narg, char **arg) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_diameter; vtype[iarg] = Dump::DOUBLE; - + } else if (strcmp(arg[iarg],"heatflow") == 0) { if (!atom->heatflow_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1477,7 +1477,7 @@ int DumpCustom::parse_fields(int narg, char **arg) error->all(FLERR,"Dumping an atom property that isn't allocated"); pack_choice[iarg] = &DumpCustom::pack_temperature; vtype[iarg] = Dump::DOUBLE; - + } else if (strcmp(arg[iarg],"omegax") == 0) { if (!atom->omega_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1496,7 +1496,7 @@ int DumpCustom::parse_fields(int narg, char **arg) if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_omegaz_triclinic_general; else pack_choice[iarg] = &DumpCustom::pack_omegaz; vtype[iarg] = Dump::DOUBLE; - + } else if (strcmp(arg[iarg],"angmomx") == 0) { if (!atom->angmom_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1515,7 +1515,7 @@ int DumpCustom::parse_fields(int narg, char **arg) if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_angmomz_triclinic_general; else pack_choice[iarg] = &DumpCustom::pack_angmomz; vtype[iarg] = Dump::DOUBLE; - + } else if (strcmp(arg[iarg],"tqx") == 0) { if (!atom->torque_flag) error->all(FLERR,"Dumping an atom property that isn't allocated"); @@ -1793,7 +1793,7 @@ int DumpCustom::modify_param(int narg, char **arg) "if simulation box is not general triclinic"); return 1; } - + if (strcmp(arg[0],"triclinic/general") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); triclinic_general = utils::logical(FLERR,arg[1],false,lmp); @@ -2387,7 +2387,7 @@ void DumpCustom::pack_x_triclinic_general(int n) { double **x = atom->x; double xtri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_coords(x[clist[i]],xtri); buf[n] = xtri[0]; @@ -2973,7 +2973,7 @@ void DumpCustom::pack_fx_triclinic_general(int n) { double **f = atom->f; double ftri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(f[clist[i]],ftri); buf[n] = ftri[0]; @@ -3075,7 +3075,7 @@ void DumpCustom::pack_mux_triclinic_general(int n) { double **mu = atom->mu; double mutri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(mu[clist[i]],mutri); buf[n] = mutri[0]; @@ -3089,7 +3089,7 @@ void DumpCustom::pack_muy_triclinic_general(int n) { double **mu = atom->mu; double mutri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(mu[clist[i]],mutri); buf[n] = mutri[1]; @@ -3103,7 +3103,7 @@ void DumpCustom::pack_muz_triclinic_general(int n) { double **mu = atom->mu; double mutri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(mu[clist[i]],mutri); buf[n] = mutri[2]; @@ -3201,7 +3201,7 @@ void DumpCustom::pack_omegax_triclinic_general(int n) { double **omega = atom->omega; double omegatri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(omega[clist[i]],omegatri); buf[n] = omegatri[0]; @@ -3215,7 +3215,7 @@ void DumpCustom::pack_omegay_triclinic_general(int n) { double **omega = atom->omega; double omegatri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(omega[clist[i]],omegatri); buf[n] = omegatri[1]; @@ -3229,7 +3229,7 @@ void DumpCustom::pack_omegaz_triclinic_general(int n) { double **omega = atom->omega; double omegatri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(omega[clist[i]],omegatri); buf[n] = omegatri[2]; @@ -3279,7 +3279,7 @@ void DumpCustom::pack_angmomx_triclinic_general(int n) { double **angmom = atom->angmom; double angmomtri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(angmom[clist[i]],angmomtri); buf[n] = angmomtri[0]; @@ -3293,7 +3293,7 @@ void DumpCustom::pack_angmomy_triclinic_general(int n) { double **angmom = atom->angmom; double angmomtri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(angmom[clist[i]],angmomtri); buf[n] = angmomtri[1]; @@ -3307,7 +3307,7 @@ void DumpCustom::pack_angmomz_triclinic_general(int n) { double **angmom = atom->angmom; double angmomtri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(angmom[clist[i]],angmomtri); buf[n] = angmomtri[2]; @@ -3357,7 +3357,7 @@ void DumpCustom::pack_tqx_triclinic_general(int n) { double **torque = atom->torque; double tqtri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(torque[clist[i]],tqtri); buf[n] = tqtri[0]; @@ -3371,7 +3371,7 @@ void DumpCustom::pack_tqy_triclinic_general(int n) { double **torque = atom->torque; double tqtri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(torque[clist[i]],tqtri); buf[n] = tqtri[1]; @@ -3385,7 +3385,7 @@ void DumpCustom::pack_tqz_triclinic_general(int n) { double **torque = atom->torque; double tqtri[3]; - + for (int i = 0; i < nchoose; i++) { domain->restricted_to_general_vector(torque[clist[i]],tqtri); buf[n] = tqtri[2]; diff --git a/src/dump_custom.h b/src/dump_custom.h index b22d03f9b53..ceb85ea3c2a 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -37,7 +37,7 @@ class DumpCustom : public Dump { int nevery; // dump frequency for output char *idregion; // region ID, nullptr if no region int triclinic_general; // 1 if output box & per-atom info for general triclinic - + int nthresh; // # of defined thresholds int nthreshlast; // # of defined thresholds with value = LAST // @@ -159,7 +159,7 @@ class DumpCustom : public Dump { void pack_x_triclinic_general(int); void pack_y_triclinic_general(int); void pack_z_triclinic_general(int); - + void pack_xs(int); void pack_ys(int); void pack_zs(int); @@ -190,11 +190,11 @@ class DumpCustom : public Dump { void pack_vx(int); void pack_vy(int); - void pack_vz(int); + void pack_vz(int); void pack_vx_triclinic_general(int); void pack_vy_triclinic_general(int); void pack_vz_triclinic_general(int); - + void pack_fx(int); void pack_fy(int); void pack_fz(int); @@ -214,7 +214,7 @@ class DumpCustom : public Dump { void pack_radius(int); void pack_diameter(int); - + void pack_heatflow(int); void pack_temperature(int); @@ -224,14 +224,14 @@ class DumpCustom : public Dump { void pack_omegax_triclinic_general(int); void pack_omegay_triclinic_general(int); void pack_omegaz_triclinic_general(int); - + void pack_angmomx(int); void pack_angmomy(int); void pack_angmomz(int); void pack_angmomx_triclinic_general(int); void pack_angmomy_triclinic_general(int); void pack_angmomz_triclinic_general(int); - + void pack_tqx(int); void pack_tqy(int); void pack_tqz(int); diff --git a/src/lattice.cpp b/src/lattice.cpp index 6992828e3a6..64bde35c26e 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -141,7 +141,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // process optional args int triclinic_general = 0; - + int iarg = 2; while (iarg < narg) { if (strcmp(arg[iarg],"origin") == 0) { @@ -230,7 +230,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) } else if (strcmp(arg[iarg],"triclinic/general") == 0) { triclinic_general = 1; iarg++; - + } else error->all(FLERR,"Unknown lattice keyword: {}", arg[iarg]); } @@ -267,7 +267,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // additional requirements for a general triclinic lattice // a123 prime are used to compute lattice spacings - + if (triclinic_general) { if (style != CUSTOM) error->all(FLERR,"Lattice triclnic/general must be style = CUSTOM"); @@ -285,11 +285,11 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) double rotmat[3][3]; domain->general_to_restricted_rotation(a1,a2,a3,rotmat,a1_prime,a2_prime,a3_prime); } - + // reset scale for LJ units (input scale is rho*) // scale = (Nbasis/(Vprimitive * rho*)) ^ (1/dim) // use fabs() in case a1,a2,a3 are not right-handed for general triclinic - + if (strcmp(update->unit_style,"lj") == 0) { double vec[3]; MathExtra::cross3(a2,a3,vec); @@ -321,7 +321,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // reset transform used by bbox() to be based on rotated a123 prime vectors if (triclinic_general) setup_transform(a1_prime,a2_prime,a3_prime); - + bbox(0,0.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax); bbox(0,1.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax); bbox(0,0.0,1.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax); @@ -334,13 +334,13 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // restore original general triclinic a123 transform if (triclinic_general) setup_transform(a2,a2,a3); - + xlattice = xmax - xmin; ylattice = ymax - ymin; zlattice = zmax - zmin; // user-defined lattice spacings - + } else { xlattice *= scale; ylattice *= scale; @@ -542,7 +542,7 @@ void Lattice::setup_transform(double *a, double *b, double *c) ------------------------------------------------------------------------- */ void Lattice::lattice2box(double &x, double &y, double &z) -{ +{ double x1 = primitive[0][0]*x + primitive[0][1]*y + primitive[0][2]*z; double y1 = primitive[1][0]*x + primitive[1][1]*y + primitive[1][2]*z; double z1 = primitive[2][0]*x + primitive[2][1]*y + primitive[2][2]*z; @@ -615,7 +615,7 @@ void Lattice::add_basis(double x, double y, double z) void Lattice::bbox(int flag, double x, double y, double z, double &xmin, double &ymin, double &zmin, double &xmax, double &ymax, double &zmax) -{ +{ if (flag == 0) lattice2box(x,y,z); else box2lattice(x,y,z); diff --git a/src/lattice.h b/src/lattice.h index 8f545de2abc..85ffd27c0a6 100644 --- a/src/lattice.h +++ b/src/lattice.h @@ -28,7 +28,7 @@ class Lattice : protected Pointers { int nbasis; // # of basis atoms in unit cell double **basis; // fractional coords of each basis atom // within unit cell (0 <= coord < 1) - + Lattice(class LAMMPS *, int, char **); ~Lattice() override; void lattice2box(double &, double &, double &); @@ -36,7 +36,7 @@ class Lattice : protected Pointers { void bbox(int, double, double, double, double &, double &, double &, double &, double &, double &); int is_general_triclinic(); - + private: int triclinic_general; // 1 if general triclinic, else 0 int oriented; // 1 if non-default orient xyz, else 0 @@ -51,10 +51,10 @@ class Lattice : protected Pointers { double rotaterow[3][3]; double rotatecol[3][3]; - double a1_prime[3]; // a123 rotated to restricted triclinic orientation + double a1_prime[3]; // a123 rotated to restricted triclinic orientation double a2_prime[3]; double a3_prime[3]; - + int orthogonal(); int right_handed_orientation(); int right_handed_primitive(); diff --git a/src/math_extra.cpp b/src/math_extra.cpp index b8c9bd98df2..a36600d970a 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -381,7 +381,7 @@ void mat_to_quat(double mat[3][3], double *q) ez[0] = mat[0][2]; ez[1] = mat[1][2]; ez[2] = mat[2][2]; - + MathExtra::exyz_to_q(ex,ey,ez,q); } diff --git a/src/read_data.cpp b/src/read_data.cpp index b34dac54eb1..5642c61920c 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -474,7 +474,7 @@ void ReadData::command(int narg, char **arg) int atomflag, topoflag; int bondflag, angleflag, dihedralflag, improperflag; int ellipsoidflag, lineflag, triflag, bodyflag; - + atomflag = topoflag = 0; bondflag = angleflag = dihedralflag = improperflag = 0; ellipsoidflag = lineflag = triflag = bodyflag = 0; @@ -492,14 +492,14 @@ void ReadData::command(int narg, char **arg) boxlo[0] = boxlo[1] = boxlo[2] = -0.5; boxhi[0] = boxhi[1] = boxhi[2] = 0.5; xy = xz = yz = 0.0; - + avec[0] = bvec[1] = cvec[2] = 1.0; avec[1] = avec[2] = 0.0; bvec[0] = bvec[2] = 0.0; cvec[0] = cvec[1] = 0.0; abc_origin[0] = abc_origin[1] = abc_origin[2] = 0.0; if (domain->dimension == 2) abc_origin[2] = -0.5; - + keyword[0] = '\0'; nlocal_previous = atom->nlocal; @@ -542,7 +542,7 @@ void ReadData::command(int narg, char **arg) "2d simulation with general triclinic box"); } } - + // problem setup using info from header // only done once, if firstpass and first data file // apply extra settings before grow(), even if no topology in file @@ -577,7 +577,7 @@ void ReadData::command(int narg, char **arg) if (!triclinic_general) { // orthogonal or restricted triclinic box - + domain->boxlo[0] = boxlo[0]; domain->boxhi[0] = boxhi[0]; domain->boxlo[1] = boxlo[1]; @@ -586,7 +586,7 @@ void ReadData::command(int narg, char **arg) domain->boxhi[2] = boxhi[2]; // restricted triclinic box - + if (triclinic) { domain->triclinic = 1; domain->xy = xy; @@ -597,7 +597,7 @@ void ReadData::command(int narg, char **arg) // general triclinic box // define_general_triclinic() converts // ABC edge vectors + abc_origin to restricted triclinic - + } else if (triclinic_general) { domain->define_general_triclinic(avec,bvec,cvec,abc_origin); } @@ -612,7 +612,7 @@ void ReadData::command(int narg, char **arg) // first data file must also be general triclinic // avec,bvec,vec and origin must match first data file // shift not allowed - + if (triclinic_general) { if (!domain->triclinic_general) error->all(FLERR,"Read_data subsequent file cannot switch to general triclinic"); @@ -633,14 +633,14 @@ void ReadData::command(int narg, char **arg) // restricted triclinic // tilt factors must match first data file - + } else if (triclinic) { if (!domain->triclinic || domain->triclinic_general) error->all(FLERR,"Read_data subsequent file cannot switch to restricted triclinic"); if (xy != domain->xy || xz != domain->xz || yz != domain->yz) error->all(FLERR,"Read_data subsequent file tilt factors must be same as first file"); } - + double oldboxlo[3] = {domain->boxlo[0], domain->boxlo[1], domain->boxlo[2]}; double oldboxhi[3] = {domain->boxhi[0], domain->boxhi[1], domain->boxhi[2]}; domain->boxlo[0] = MIN(domain->boxlo[0], boxlo[0] + shift[0]); @@ -652,7 +652,7 @@ void ReadData::command(int narg, char **arg) // check if box has changed // if yes, warn about non-zero image flags - + if ((oldboxlo[0] != domain->boxlo[0]) || (oldboxlo[1] != domain->boxlo[1]) || (oldboxlo[2] != domain->boxlo[2]) || (oldboxhi[0] != domain->boxhi[0]) || (oldboxhi[1] != domain->boxhi[1]) || (oldboxhi[2] != domain->boxhi[2])) { @@ -673,7 +673,7 @@ void ReadData::command(int narg, char **arg) } // setup simulation box and paritioning in Domain and Comm classes - + domain->print_box(" "); domain->set_initial_box(); domain->set_global_box(); @@ -1228,7 +1228,7 @@ void ReadData::header(int firstpass) // initialize type counts by the "extra" numbers so they get counted // in case the corresponding "types" line is missing and thus the extra // value will not be processed - + if (addflag == NONE) { atom->ntypes = extra_atom_types; atom->nbondtypes = extra_bond_types; @@ -1244,7 +1244,7 @@ void ReadData::header(int firstpass) if (eof == nullptr) error->one(FLERR, "Unexpected end of data file"); // check for units keyword in first line and print warning on mismatch - + auto units = Tokenizer(utils::strfind(line, "units = \\w+")).as_vector(); if (units.size() > 2) { if (units[2] != update->unit_style) @@ -1433,7 +1433,7 @@ void ReadData::header(int firstpass) xy = utils::numeric(FLERR, words[0], false, lmp); xz = utils::numeric(FLERR, words[1], false, lmp); yz = utils::numeric(FLERR, words[2], false, lmp); - + } else if (utils::strmatch(line, "^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\avec\\s")) { avec_flag = 1; avec[0] = utils::numeric(FLERR, words[0], false, lmp); @@ -1522,7 +1522,7 @@ void ReadData::atoms() if (eof) error->all(FLERR, "Unexpected end of data file"); if (tlabelflag && !lmap->is_complete(Atom::ATOM)) error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label"); - atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, + atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, shiftflag, shift, tlabelflag, lmap->lmap2lmap.atom, triclinic_general); nread += nchunk; } diff --git a/src/read_data.h b/src/read_data.h index 495c17d500c..008283251cd 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -64,12 +64,12 @@ class ReadData : public Command { int triclinic, triclinic_general; int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag; int avec_flag, bvec_flag, cvec_flag, abc_origin_flag; - + double boxlo[3], boxhi[3]; double xy, xz, yz; double avec[3], bvec[3], cvec[3]; double abc_origin[3]; - + // optional args int addflag, offsetflag, shiftflag, coeffflag, settypeflag; diff --git a/src/thermo.cpp b/src/thermo.cpp index d791f5f856f..76355849bee 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -980,7 +980,7 @@ void Thermo::parse_fields(const std::string &str) addfield("Pxy", &Thermo::compute_pxy_triclinic_general, FLOAT); else addfield("Pxy", &Thermo::compute_pxy, FLOAT); index_press_vector = add_compute(id_press, VECTOR); - } else if (word == "pxz") { + } else if (word == "pxz") { if (triclinic_general) addfield("Pxz", &Thermo::compute_pxz_triclinic_general, FLOAT); else addfield("Pxz", &Thermo::compute_pxz, FLOAT); @@ -1223,7 +1223,7 @@ void Thermo::check_press_vector(const std::string &keyword) pressure->invoked_flag |= Compute::INVOKED_VECTOR; // store 3x3 matrix form of symmetric pressure tensor for use in triclinic_general() - + if (triclinic_general) { press_tensor[0][0] = pressure->vector[0]; press_tensor[1][1] = pressure->vector[1]; diff --git a/src/thermo.h b/src/thermo.h index 1829349b96c..a82d4625855 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -83,7 +83,7 @@ class Thermo : protected Pointers { std::string image_fname; // data used by routines that compute single values - + int ivalue; // integer value to print double dvalue; // double value to print bigint bivalue; // big integer value to print @@ -96,7 +96,7 @@ class Thermo : protected Pointers { // index = where they are in computes list // id = ID of Compute objects // Compute * = ptrs to the Compute objects - + int index_temp, index_press_scalar, index_press_vector, index_pe; class Compute *temperature, *pressure, *pe; double press_tensor[3][3]; diff --git a/src/write_data.cpp b/src/write_data.cpp index 06512a0f20b..f9c9ec383f4 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -74,7 +74,7 @@ void WriteData::command(int narg, char **arg) fixflag = 1; triclinic_general = 0; lmapflag = 1; - + // store current (default) setting since we may change it int domain_triclinic_general = domain->triclinic_general; @@ -227,9 +227,9 @@ void WriteData::write(const std::string &file) // reset internal per-atom data that needs rotation if (domain->triclinic_general) atom->avec->write_data_restricted_to_general(); - + // per atom info in Atoms and Velocities sections - + if (natoms) atoms(); if (natoms) velocities(); @@ -261,7 +261,7 @@ void WriteData::write(const std::string &file) // restore internal per-atom data that was rotated if (domain->triclinic_general) atom->avec->write_data_restore_restricted(); - + // close data file if (me == 0) fclose(fp); @@ -326,7 +326,7 @@ void WriteData::header() domain->boxlo[2],domain->boxhi[2]); if (domain->triclinic) fmt::print(fp,"{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz); - + } else if (domain->triclinic_general) { fmt::print(fp,"\n{} {} {} avec\n{} {} {} bvec\n{} {} {} cvec\n", domain->avec[0],domain->avec[1],domain->avec[2], diff --git a/src/write_restart.cpp b/src/write_restart.cpp index ae5cfa5a3bd..4c7835fa407 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -451,7 +451,7 @@ void WriteRestart::header() write_int(TRICLINIC_GENERAL,domain->triclinic_general); if (domain->triclinic_general) write_double_vec(ROTATE_G2R,9,&domain->rotate_g2r[0][0]); - + write_double_vec(SPECIAL_LJ,3,&force->special_lj[1]); write_double_vec(SPECIAL_COUL,3,&force->special_coul[1]); From ef400cc13f86aa9453a7bed69ae598357d15f20b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 1 Dec 2023 15:25:51 -0500 Subject: [PATCH 067/719] fix broken links --- doc/src/Howto_body.rst | 6 +++--- doc/src/Howto_triclinic.rst | 8 ++++---- doc/src/dump.rst | 4 ++-- doc/src/lattice.rst | 2 +- doc/src/read_data.rst | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-) diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 80bed7d4c64..19ae10b9a0d 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -167,7 +167,7 @@ sub-particle displacements should reflect the fact the body is defined withing a general triclinic box with edge vectors **A**,**B**,**C**. LAMMPS will rotate the box to convert it to a restricted triclinic box. This operation will also rotate the orientation of the body -particles. See the :doc:`Howto triclinic ` doc page +particles. See the :doc:`Howto triclinic ` doc page for more details. The :doc:`pair_style body/nparticle ` command can be used @@ -288,7 +288,7 @@ defined withing a general triclinic box with edge vectors **A**,**B**,**C**. LAMMPS will rotate the box to convert it to a restricted triclinic box. This operation will also rotate the orientation of the body particles. See the :doc:`Howto triclinic -` doc page for more details. +` doc page for more details. The :doc:`pair_style body/rounded/polygon ` command can be used with this body style to compute body/body @@ -463,7 +463,7 @@ defined withing a general triclinic box with edge vectors **A**,**B**,**C**. LAMMPS will rotate the box to convert it to a restricted triclinic box. This operation will also rotate the orientation of the body particles. See the :doc:`Howto triclinic -` doc page for more details. +` doc page for more details. The :doc:`pair_style body/rounded/polhedron ` command can be used with this body diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 1461f32187d..d98a4eca426 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -17,9 +17,9 @@ is created by one of these commands: * :doc:`read_dump ` Internally, LAMMPS defines box size parameters lx,ly,lz where lx = -xhi-xlo, and similarly in the y and z dimensions. The 6 parameters, -as well as lx,ly,lz, can be output via the :doc:`thermo_style custom -` command. See the :doc:'Howto 2d ` doc page +xhi-xlo, and similarly in the y and z dimensions. The 6 parameters, as +well as lx,ly,lz, can be output via the :doc:`thermo_style custom +` command. See the :doc:`Howto 2d ` doc page for info on how zlo and zhi are defined for 2d simulations. ---------- @@ -30,7 +30,7 @@ Triclinic simulation boxes LAMMPS also allows simulations to be performed using triclinic (non-orthogonal) simulation boxes shaped as a 3d parallelepiped with triclinic symmetry. For 2d simulations a triclinic simulation box is -effectively a parallelogram; see the :doc:'Howto 2d ` doc +effectively a parallelogram; see the :doc:`Howto 2d ` doc page for details. One use of triclinic simulation boxes is to model solid-state crystals diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 8cba1d760bf..bfb1cb15560 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -288,7 +288,7 @@ with LAMMPS or third-party tools can read this format, as does the For all these styles, the dimensions of the simulation box are included in each snapshot. The simulation box in LAMMPS can be defined in one of 3 ways: orthogonal, restricted triclinic, and -general triclinic. See the :doc:`Howto triclinic ` +general triclinic. See the :doc:`Howto triclinic ` doc page for a detailed description of all 3 options. For an orthogonal simulation box the box information is formatted as: @@ -668,7 +668,7 @@ General triclinic simulation box output for the *atom* and *custom* styles: As mentioned above, the simulation box can be defined as a general triclinic box, which means that 3 arbitrary box edge vectors **A**, **B**, **C** can be specified. See the :doc:`Howto triclinic -` doc page for a detailed description of general +` doc page for a detailed description of general triclinic boxes. This option is provided as a convenience for users who may be diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index 235b8b30daa..ae4b9267a68 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -200,7 +200,7 @@ the Z direction. The *triclinic/general* option specifies that the defined lattice is for use with a general triclinic simulation box, as opposed to an orthogonal or restricted triclinic box. The :doc:`Howto triclinic -` doc page explains all 3 kinds of simluation boxes +` doc page explains all 3 kinds of simluation boxes LAMMPS supports. If this option is specified, a *custom* lattice style must be used. diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index dd028ec23e4..9bea4e9df73 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -923,7 +923,7 @@ zero. data file in the direction of the **A** edge vector. Likewise the (x0,y0,z0) per-atom strain-free coordinates should be inside the general triclinic simulation box as explained in the note above. - See the :doc:`Howto triclinic ` doc page for more + See the :doc:`Howto triclinic ` doc page for more details. The atom-ID is used to identify the atom throughout the simulation and @@ -1675,7 +1675,7 @@ Wz are in units of angular velocity (radians/time). If the data file defines a general triclinic box, then each of the 3 vectors (translational velocity, angular momentum, angular velocity) should be specified for the rotated coordinate axes of the general -triclinic box. See the :doc:`Howto triclinic ` doc +triclinic box. See the :doc:`Howto triclinic ` doc page for more details. For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz), From acdb0481f0d3ce075968cf072f07c285f3af9a2f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 1 Dec 2023 15:54:54 -0500 Subject: [PATCH 068/719] loads of spelling fixes --- doc/src/Howto_2d.rst | 2 +- doc/src/Howto_triclinic.rst | 21 ++++++++++----------- doc/src/boundary.rst | 2 +- doc/src/create_atoms.rst | 8 ++++---- doc/src/create_box.rst | 6 +++--- doc/src/dump.rst | 6 +++--- doc/src/dump_modify.rst | 2 +- doc/src/lattice.rst | 6 +++--- doc/src/read_data.rst | 6 +++--- doc/src/thermo_style.rst | 2 +- doc/src/write_data.rst | 8 ++++---- doc/utils/sphinx-config/false_positives.txt | 17 +++++++++++++++++ 12 files changed, 51 insertions(+), 35 deletions(-) diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index b80a424690d..8bce7000bd0 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -10,7 +10,7 @@ A 2d simulation box must be periodic in z as set by the :doc:`boundary If using the :doc:`create_box ` command, you must define a simulation box which straddles z = 0.0 in the z dimension since all -the atoms will have a z coordinate of zero. Typicaily the width of +the atoms will have a z coordinate of zero. Typically the width of box in the z dimension should be narrow, e.g. -0.5 to 0.5, but that is not required. Example are: diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index d98a4eca426..2f2ffe85cf2 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -122,7 +122,7 @@ General triclinic simulation boxes in LAMMPS LAMMPS allows specification of general triclinic simulation boxes with their atoms as a convenience for users who may be converting data from -solid-state crystallograhic representations or from DFT codes for +solid-state crystallographic representations or from DFT codes for input to LAMMPS. Likewise it allows output of dump files, data files, and thermodynamic data (e.g. pressure tensor) in a general triclinic format. @@ -160,7 +160,7 @@ This means 4 things which are important to understand: * If commands such as :doc:`write_data ` or :doc:`dump custom ` are used to output general triclinic information, it is effectively the inverse of the operation described in the - preceeding bullet. + preceding bullet. * Other LAMMPS commands such as :doc:`region ` or :doc:`velocity ` or :doc:`set `, operate on a restricted triclinic system even if a general triclinic system was @@ -174,13 +174,13 @@ This is the list of commands which have general triclinic options: * :doc:`read_data ` - read a data file for a general triclinic system * :doc:`write_data ` - write a data file for a general triclinic system * :doc:`dump atom, dump custom ` - output dump snapshots in general triclinic format -* :doc:`dump_modify ` - toggle a dump file between restrictied and general triclinic format +* :doc:`dump_modify ` - toggle a dump file between restricted and general triclinic format * :doc:`thermo_style ` - output the pressure tensor in general triclinic format * :doc:`thermo_modify ` - toggle thermo-style output between restricted and general triclinic format -* :doc:`read_restart ` - read a restart file for a general tricliinc system -* :doc:`write_restart ` - write a restart file for a general tricliinc system +* :doc:`read_restart ` - read a restart file for a general triclinic system +* :doc:`write_restart ` - write a restart file for a general triclinic system ---------- @@ -216,9 +216,8 @@ For consistency, the same rotation applied to the triclinic box edge vectors can also be applied to atom positions, velocities, and other vector quantities. This can be conveniently achieved by first converting to fractional coordinates in the general triclinic -coordinates and then converting to coordinates in the resetricted -triclinic basis. The transformation is given by the following -equation: +coordinates and then converting to coordinates in the restricted +triclinic basis. The transformation is given by the following equation: .. math:: @@ -279,10 +278,10 @@ Output of restricted and general triclinic boxes in a dump file """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" As discussed on the :doc:`dump ` command doc page, when the BOX -BOUNDS for a snapshot is written to a dump file for a resticted +BOUNDS for a snapshot is written to a dump file for a restricted triclinic box, an orthogonal bounding box which encloses the triclinic -simulation box is output, along with the 3 tilt factors (xy, xz, yz) -of the restricted triclinic box, formatted as follows: +simulation box is output, along with the 3 tilt factors (xy, xz, yz) of +the restricted triclinic box, formatted as follows: .. parsed-literal:: diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index c1adeb1009b..06f125ed4f7 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -88,7 +88,7 @@ box. The boundary command settings explained above for the 6 faces of an orthogonal box also apply in similar manner to the 6 faces -of a restricted triclinix box (and thus to the corresponding 6 faces +of a restricted triclinic box (and thus to the corresponding 6 faces of a general triclinic box), with the following context. if the second dimension of a tilt factor (e.g. y for xy) is periodic, diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 71303a7d4f3..2282cd6e0c0 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -98,7 +98,7 @@ Before using this command, a lattice must typically also be defined using the :doc:`lattice ` command, unless you specify the *single* or *mesh* style with units = box or the *random* style. To create atoms on a lattice for general triclinic boxes, see the -disucssion below. +discussion below. For the remainder of this doc page, a created atom or molecule is referred to as a "particle". @@ -150,7 +150,7 @@ you want. ---------- If the simulation box is formulated as a general triclinic box defined -by arbitary edge vectors **A**, **B**, **C**, then the *box* and +by arbitrary edge vectors **A**, **B**, **C**, then the *box* and *region* styles will create atoms on a lattice commensurate with those edge vectors. See the :doc:`Howto_triclinic ` doc page for a detailed explanation of orthogonal, restricted triclinic, @@ -167,7 +167,7 @@ a simulation box which replicates that unit cell along each of the LAMMPS allows specification of general triclinic simulation boxes as a convenience for users who may be converting data from - solid-state crystallograhic representations or from DFT codes for + solid-state crystallographic representations or from DFT codes for input to LAMMPS. However, as explained on the :doc:`Howto_triclinic ` doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means @@ -528,7 +528,7 @@ the distance units are in lattice spacings. These are affected settings: * for *single* style: coordinates of the particle created * for *random* style: overlap distance *Doverlap* by the *overlap* keyword -* for *mesh* style: *bisect* threshold valeu for *meshmode* = *bisect* +* for *mesh* style: *bisect* threshold value for *meshmode* = *bisect* * for *mesh* style: *radthresh* value for *meshmode* = *bisect* * for *mesh* style: *density* value for *meshmode* = *qrand* diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index f2b58755393..e7f76f075a9 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -55,7 +55,7 @@ Description """"""""""" This command creates a simulation box. It also partitions the box into -a regular 3d grid of smaller sub-boxes, one per procssor (MPI task). +a regular 3d grid of smaller sub-boxes, one per processor (MPI task). The geometry of the partitioning is based on the size and shape of the simulation box, the number of processors being used and the settings of the :doc:`processors ` command. The partitioning can @@ -175,7 +175,7 @@ pair of the **A**, **B**, **C** vectors. To create a general triclinic boxes, the region is specified as NULL and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three edge vectors **A**, **B**, **C** using additional information -previously defind by the :doc:`lattice ` command. +previously defined by the :doc:`lattice ` command. The lattice must be of style *custom* and use its *triclinic/general* option. This insures the lattice satisfies the restrictions listed @@ -198,7 +198,7 @@ to do this is to specify clo = -0.5 and chi = 0.5 and use the LAMMPS allows specification of general triclinic simulation boxes as a convenience for users who may be converting data from - solid-state crystallograhic representations or from DFT codes for + solid-state crystallographic representations or from DFT codes for input to LAMMPS. However, as explained on the :doc:`Howto_triclinic ` doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means diff --git a/doc/src/dump.rst b/doc/src/dump.rst index bfb1cb15560..2df4f984cf8 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -672,7 +672,7 @@ triclinic box, which means that 3 arbitrary box edge vectors **A**, triclinic boxes. This option is provided as a convenience for users who may be -converting data from solid-state crystallograhic representations or +converting data from solid-state crystallographic representations or from DFT codes for input to LAMMPS. However, as explained on the :doc:`Howto_triclinic ` doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means the box @@ -712,12 +712,12 @@ output for unscaled atom coords, via the :doc:`dump_modify scaled no ` setting. For style *custom*, this alters output for either unscaled or unwrapped output of atom coords, via the *x,y,z* or *xu,yu,zu* attributes. For output of scaled atom coords by both -styles, there is no difference bewteen restricted and general +styles, there is no difference between restricted and general triclinic values. Third, the output for any attribute of the *custom* style which represents a per-atom vector quantity will be converted (rotated) to -be oriented consistent with the general tricinic box and its +be oriented consistent with the general triclinic box and its orientation relative to the standard xyz coordinate axes. This applies to the following *custom* style attributes: diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 31f1cd214e9..6bc1bb8b3ec 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -818,7 +818,7 @@ threshold criterion is met. Otherwise it is not met. For style *custom*, the *triclinic/general* keyword alters dump output for general triclinic simulation boxes and their atoms. See the :doc:`dump ` command for details of how this changes the - format of dump file snapstots. The thresh keyword may access + format of dump file snapshots. The thresh keyword may access per-atom attributes either directly or indirectly through a compute or variable. If the attribute is an atom coordinate or a per-atom vector (such as velocity, force, or dipole moment), its value will diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index ae4b9267a68..ad5ab364bdb 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -200,7 +200,7 @@ the Z direction. The *triclinic/general* option specifies that the defined lattice is for use with a general triclinic simulation box, as opposed to an orthogonal or restricted triclinic box. The :doc:`Howto triclinic -` doc page explains all 3 kinds of simluation boxes +` doc page explains all 3 kinds of simulation boxes LAMMPS supports. If this option is specified, a *custom* lattice style must be used. @@ -232,7 +232,7 @@ atoms. To do this, it also requires a lattice with the LAMMPS allows specification of general triclinic lattices and simulation boxes as a convenience for users who may be converting - data from solid-state crystallograhic representations or from DFT + data from solid-state crystallographic representations or from DFT codes for input to LAMMPS. However, as explained on the :doc:`Howto_triclinic ` doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means @@ -277,7 +277,7 @@ difference in the min/max of the y and z coordinates. defined by *a1*, *a2*, *a3* edge vectors is first converted to a restricted triclinic orientation, which is a rotation operation. The min/max extent of the 8 corner points is then determined, as - described in the preceeding paragraph, to set the lattice + described in the preceding paragraph, to set the lattice spacings. As explained for the *triclinic/general* option above, this is because any use of the lattice spacings by other commands will be for a restricted triclinic simulation box, not a general diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 9bea4e9df73..3bf3e8643a6 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -471,7 +471,7 @@ For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of LAMMPS allows specification of general triclinic simulation boxes as a convenience for users who may be converting data from - solid-state crystallograhic representations or from DFT codes for + solid-state crystallographic representations or from DFT codes for input to LAMMPS. However, as explained on the :doc:`Howto_triclinic ` doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means @@ -491,8 +491,8 @@ orthogonal, restricted triclinic, and general triclinic. If the system is periodic (in a dimension), then atom coordinates can be outside the bounds (in that dimension); they will be remapped (in a periodic sense) back inside the box. For triclinic boxes, periodicity -in x,y,z refers to the faces of the parallelepided defined by the -**A**,**B**,**C** edge vectors of the simuation box. See the +in x,y,z refers to the faces of the parallelepiped defined by the +**A**,**B**,**C** edge vectors of the simulation box. See the :doc:`boundary ` command doc page for a fuller discussion. Note that if the *add* option is being used to add atoms to a diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 45a1eaa2a81..f73c4baa3da 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -328,7 +328,7 @@ pressure ` command doc page for details of how it is calculated. If the :doc:`thermo_modify triclinic/general ` option -is set and the simulation box was created as a geenral triclinic box, +is set and the simulation box was created as a general triclinic box, then the components will be output as values consistent with the orientation of the general triclinic box relative to the standard xyz coordinate axes. If this keyword is not used, the values will be diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index e083f834b88..516685f4fea 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -127,16 +127,16 @@ given type-kind) to be written to the data file. Use of the *triclinic/general* keyword will output a data file which specifies a general triclinic simulation box as well as per-atom -quantities consistent with the general triclinic box. The latter -means that per-atom vectors, such as velocities and dipole moments -will be oriented conistent with the 3d rotation implied by the general +quantities consistent with the general triclinic box. The latter means +that per-atom vectors, such as velocities and dipole moments will be +oriented consistent with the 3d rotation implied by the general triclinic box (relative to the associated restricted triclinic box). This option can only be requested if the simulation box was initially defined to be general triclinic. If if was and the *triclinic/general* keyword is not used, then the data file will specify a restricted triclinic box, since that is the internal format -LAMMPS uses for both general and restricited triclinic simulations. +LAMMPS uses for both general and restricted triclinic simulations. See the :doc:`Howto triclinic ` doc page for more explanation of how general triclinic simulation boxes are supported by LAMMPS. And see the :doc:`read_data ` doc page for details diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 75589e31157..1a19840c177 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -50,6 +50,7 @@ agilio Agilio agni Agnolin +ahi Ahrens Ai Aidan @@ -85,6 +86,7 @@ allocator allocators allosws AlO +alo Alonso Alperen alphak @@ -184,6 +186,7 @@ automagically Auvergne Avalos avalue +avec aveforce Avendano Averett @@ -191,11 +194,14 @@ avi AVX awpmd AWPMD +ax Axel Axilrod Ay +ay Ayton Az +az Azevedo azimuthal Azuri @@ -268,6 +274,7 @@ Bext Bfrac bgq Bh +bhi Bialke biaxial bicrystal @@ -304,6 +311,7 @@ Bkappa blabel Blaise blanchedalmond +blo blocksize blueviolet bn @@ -383,6 +391,7 @@ burlywood Bussi Buturigakkwaishi Buyl +bvec Bybee bz Cadarache @@ -645,14 +654,18 @@ cv Cv Cval cvar +cvec cvff cwiggle +cx +cy cygwin Cygwin cylindrically Cyrot cyrstals cython +cz Daivis Dammak dampflag @@ -2655,6 +2668,9 @@ organometallic orientational orientationsFile orientorder +originx +originy +originz Orlikowski ornl Ornstein @@ -2698,6 +2714,7 @@ papayawhip paquay Paquay parallelepiped +parallelepipeds Parallelizable parallelization parallelized From fbb9c697717a158fa0e43658e8fafab587bb151e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 1 Dec 2023 16:23:49 -0500 Subject: [PATCH 069/719] fix initialization bug --- src/lattice.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/lattice.cpp b/src/lattice.cpp index 64bde35c26e..9843a00438e 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -140,7 +140,8 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // process optional args - int triclinic_general = 0; + triclinic_general = 0; + oriented = 0; int iarg = 2; while (iarg < narg) { From dab47d518dff440eee95c0f79b131eb8ca4f045e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 1 Dec 2023 16:23:59 -0500 Subject: [PATCH 070/719] apply clang-format --- src/lattice.h | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/lattice.h b/src/lattice.h index 85ffd27c0a6..b5eca8c13aa 100644 --- a/src/lattice.h +++ b/src/lattice.h @@ -33,25 +33,25 @@ class Lattice : protected Pointers { ~Lattice() override; void lattice2box(double &, double &, double &); void box2lattice(double &, double &, double &); - void bbox(int, double, double, double, - double &, double &, double &, double &, double &, double &); + void bbox(int, double, double, double, double &, double &, double &, double &, double &, + double &); int is_general_triclinic(); private: - int triclinic_general; // 1 if general triclinic, else 0 - int oriented; // 1 if non-default orient xyz, else 0 + int triclinic_general; // 1 if general triclinic, else 0 + int oriented; // 1 if non-default orient xyz, else 0 double scale; - double origin[3]; // lattice origin - int orientx[3]; // lattice orientation vecs - int orienty[3]; // orientx = what lattice dir lies - int orientz[3]; // along x dim in box + double origin[3]; // lattice origin + int orientx[3]; // lattice orientation vecs + int orienty[3]; // orientx = what lattice dir lies + int orientz[3]; // along x dim in box double primitive[3][3]; // lattice <-> box transformation matrices double priminv[3][3]; double rotaterow[3][3]; double rotatecol[3][3]; - double a1_prime[3]; // a123 rotated to restricted triclinic orientation + double a1_prime[3]; // a123 rotated to restricted triclinic orientation double a2_prime[3]; double a3_prime[3]; From 82868cd583c1dab43c541340f43161e4e9a4f1aa Mon Sep 17 00:00:00 2001 From: Ludwig Ahrens Date: Mon, 4 Dec 2023 13:59:07 +0100 Subject: [PATCH 071/719] Simplify Madelung examples with mixed eta --- examples/PACKAGES/electrode/madelung/data.eta | 34 ------------------- .../PACKAGES/electrode/madelung/data.eta_mix | 34 ------------------- examples/PACKAGES/electrode/madelung/in.eta | 13 +++---- .../PACKAGES/electrode/madelung/in.eta_cg | 15 ++++---- .../PACKAGES/electrode/madelung/in.eta_mix | 13 +++---- .../electrode/madelung/settings_eta.mod | 19 ----------- 6 files changed, 16 insertions(+), 112 deletions(-) delete mode 100644 examples/PACKAGES/electrode/madelung/data.eta delete mode 100644 examples/PACKAGES/electrode/madelung/data.eta_mix delete mode 100644 examples/PACKAGES/electrode/madelung/settings_eta.mod diff --git a/examples/PACKAGES/electrode/madelung/data.eta b/examples/PACKAGES/electrode/madelung/data.eta deleted file mode 100644 index b05700a4ab2..00000000000 --- a/examples/PACKAGES/electrode/madelung/data.eta +++ /dev/null @@ -1,34 +0,0 @@ -LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0 - -4 atoms -3 atom types - -0 1 xlo xhi -0 1 ylo yhi --10 10 zlo zhi - -Masses - -1 196.966553 -2 196.966553 -3 1.0 - -Pair Coeffs # lj/cut/coul/long - -1 0 0 -2 0 0 -3 0 0 - -Atoms # full - -1 1 1 0.00 0.00 0.00 -2.00 # bottom electrode -2 2 2 0.00 0.00 0.00 2.00 # top electrode -3 3 3 0.50 0.00 0.00 -1.00 # bottom electrolyte -4 3 3 -0.50 0.00 0.00 1.00 # top electrolyte - -ETA - -1 2.0 -2 2.0 -3 0 -4 0 diff --git a/examples/PACKAGES/electrode/madelung/data.eta_mix b/examples/PACKAGES/electrode/madelung/data.eta_mix deleted file mode 100644 index 9322ebd6622..00000000000 --- a/examples/PACKAGES/electrode/madelung/data.eta_mix +++ /dev/null @@ -1,34 +0,0 @@ -LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0 - -4 atoms -3 atom types - -0 1 xlo xhi -0 1 ylo yhi --10 10 zlo zhi - -Masses - -1 196.966553 -2 196.966553 -3 1.0 - -Pair Coeffs # lj/cut/coul/long - -1 0 0 -2 0 0 -3 0 0 - -Atoms # full - -1 1 1 0.00 0.00 0.00 -2.00 # bottom electrode -2 2 2 0.00 0.00 0.00 2.00 # top electrode -3 3 3 0.50 0.00 0.00 -1.00 # bottom electrolyte -4 3 3 -0.50 0.00 0.00 1.00 # top electrolyte - -ETA - -1 0.5 -2 3.0 -3 0 -4 0 diff --git a/examples/PACKAGES/electrode/madelung/in.eta b/examples/PACKAGES/electrode/madelung/in.eta index d928f8fed08..3a45bb1bf5d 100644 --- a/examples/PACKAGES/electrode/madelung/in.eta +++ b/examples/PACKAGES/electrode/madelung/in.eta @@ -1,16 +1,13 @@ -atom_style full -units real boundary p p f - kspace_style ewald/electrode 1.0e-8 kspace_modify slab 8.0 # ew3dc -pair_style lj/cut/coul/long 12 - -fix feta all property/atom d_eta ghost yes -read_data data.eta fix feta NULL ETA -include "settings_eta.mod" +include "settings.mod" # styles, computes, groups and fixes +thermo_style custom step pe c_qbot c_qtop +fix feta all property/atom d_eta ghost on +set group bot d_eta 2.0 +set group top d_eta 2.0 fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv run 0 diff --git a/examples/PACKAGES/electrode/madelung/in.eta_cg b/examples/PACKAGES/electrode/madelung/in.eta_cg index e04db318d57..5ac8cddf17d 100644 --- a/examples/PACKAGES/electrode/madelung/in.eta_cg +++ b/examples/PACKAGES/electrode/madelung/in.eta_cg @@ -1,17 +1,14 @@ -atom_style full -units real boundary p p f - kspace_style ewald/electrode 1.0e-8 kspace_modify slab 8.0 # ew3dc -pair_style lj/cut/coul/long 12 - -fix feta all property/atom d_eta ghost yes -read_data data.eta_mix fix feta NULL ETA -include "settings_eta.mod" +include "settings.mod" # styles, computes, groups and fixes -fix conp bot electrode/conp 0 2 couple top 1 symm on algo cg 1e-6 eta d_eta +thermo_style custom step pe c_qbot c_qtop +fix feta all property/atom d_eta ghost on +set group bot d_eta 0.5 +set group top d_eta 3.0 +fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6 run 0 diff --git a/examples/PACKAGES/electrode/madelung/in.eta_mix b/examples/PACKAGES/electrode/madelung/in.eta_mix index d4bcf712251..d00e008fa43 100644 --- a/examples/PACKAGES/electrode/madelung/in.eta_mix +++ b/examples/PACKAGES/electrode/madelung/in.eta_mix @@ -1,16 +1,13 @@ -atom_style full -units real boundary p p f - kspace_style ewald/electrode 1.0e-8 kspace_modify slab 8.0 # ew3dc -pair_style lj/cut/coul/long 12 - -fix feta all property/atom d_eta ghost on -read_data data.eta_mix fix feta NULL ETA -include "settings_eta.mod" +include "settings.mod" # styles, computes, groups and fixes +thermo_style custom step pe c_qbot c_qtop +fix feta all property/atom d_eta ghost on +set group bot d_eta 0.5 +set group top d_eta 3.0 fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv run 0 diff --git a/examples/PACKAGES/electrode/madelung/settings_eta.mod b/examples/PACKAGES/electrode/madelung/settings_eta.mod deleted file mode 100644 index aee63bf2e96..00000000000 --- a/examples/PACKAGES/electrode/madelung/settings_eta.mod +++ /dev/null @@ -1,19 +0,0 @@ - -# distribute electrode atoms among all processors: -if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" - -group bot type 1 -group top type 2 - -# get electrode charges -variable q atom q -compute qbot bot reduce sum v_q -compute qtop top reduce sum v_q - -compute compute_pe all pe -variable vpe equal c_compute_pe -variable charge equal c_qtop -fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" - -thermo_style custom step pe c_qbot c_qtop - From ae4b65430acfa9d05ac8de8e08c06cd16bd157c8 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 5 Dec 2023 15:58:40 -0700 Subject: [PATCH 072/719] clarify rules for reading multiple data files with read_data --- doc/src/read_data.rst | 82 ++++++++++++++++++++++++------------------- src/read_data.cpp | 4 +++ 2 files changed, 49 insertions(+), 37 deletions(-) diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 897f6878b05..95f08a84833 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -127,48 +127,56 @@ keyword must be used. .. note:: - The simulation box size in the new data file will be merged with - the existing simulation box to create a large enough box in each - dimension to contain both the existing and new atoms. Each box - dimension never shrinks due to this merge operation, it only stays - the same or grows. Care must be used if you are growing the - existing simulation box in a periodic dimension. If there are - existing atoms with bonds that straddle that periodic boundary, - then the atoms may become far apart if the box size grows. This - will separate the atoms in the bond, which can lead to "lost" bond - atoms or bad dynamics. + If the first read_data command defined an orthogonal or restricted + triclinic or general triclinic simulation box (see the sub-section + below on header keywords), then subsequent data files must define + the same kind of simulation box. For orthogonal boxes, the new box + can be a different size; see the next Note. For a restricted + triclinic box, the 3 new tilt factors ("xy xz yz" keyword) must + have the same values as in the original data file. For a general + triclinic box, the new avec, bvec, cvec, and "abc origin" keywords + must have the same values in the original data file. files. Also + the *shift* keyword cannot be used in subsequent read_data commands + for a general triclinic box. .. note:: - If the first read_data command defined a restricted or general - triclinic simulation box (see the sub-section below on header - keywords), then subsequent data files have restrictions. For a - restricted triclinic box, the 3 tilt factors ("xy xz yz" keyword) - must have the same values in subsequent data files. For a general - triclinic box, the avec, bvec, cvec, and "abc origin" keywords must - have the same values in subsequent data files. Also the *shift* - keyword cannot be used in subsequent read_data commands. + For orthogonal boxes, the simulation box size in the new data file + will be merged with the existing simulation box to create a large + enough box in each dimension to contain both the existing and new + atoms. Each box dimension never shrinks due to this merge + operation, it only stays the same or grows. Care must be used if + you are growing the existing simulation box in a periodic + dimension. If there are existing atoms with bonds that straddle + that periodic boundary, then the atoms may become far apart if the + box size grows. This will separate the atoms in the bond, which + can lead to "lost" bond atoms or bad dynamics. + The three choices for the *add* argument affect how the atom IDs and -molecule IDs of atoms in the data file are treated. If *append* is -specified, atoms in the data file are added to the current system, -with their atom IDs reset so that an atom-ID = M in the data file -becomes atom-ID = N+M, where N is the largest atom ID in the current -system. This rule is applied to all occurrences of atom IDs in the -data file, e.g. in the Velocity or Bonds section. This is also done -for molecule IDs, if the atom style does support molecule IDs or -they are enabled via fix property/atom. If *IDoffset* is specified, -then *IDoffset* is a numeric value is given, e.g. 1000, so that an -atom-ID = M in the data file becomes atom-ID = 1000+M. For systems -with enabled molecule IDs, another numerical argument *MOLoffset* -is required representing the equivalent offset for molecule IDs. -If *merge* is specified, the data file atoms -are added to the current system without changing their IDs. They are -assumed to merge (without duplication) with the currently defined -atoms. It is up to you to ensure there are no multiply defined atom -IDs, as LAMMPS only performs an incomplete check that this is the case -by ensuring the resulting max atom-ID >= the number of atoms. For -molecule IDs, there is no check done at all. +molecule IDs of atoms in the data file are treated. + +If *append* is specified, atoms in the data file are added to the +current system, with their atom IDs reset so that an atom-ID = M in +the data file becomes atom-ID = N+M, where N is the largest atom ID in +the current system. This rule is applied to all occurrences of atom +IDs in the data file, e.g. in the Velocity or Bonds section. This is +also done for molecule IDs, if the atom style does support molecule +IDs or they are enabled via fix property/atom. + +If *IDoffset* is specified, then *IDoffset* is a numeric value is +given, e.g. 1000, so that an atom-ID = M in the data file becomes +atom-ID = 1000+M. For systems with enabled molecule IDs, another +numerical argument *MOLoffset* is required representing the equivalent +offset for molecule IDs. + +If *merge* is specified, the data file atoms are added to the current +system without changing their IDs. They are assumed to merge (without +duplication) with the currently defined atoms. It is up to you to +ensure there are no multiply defined atom IDs, as LAMMPS only performs +an incomplete check that this is the case by ensuring the resulting +max atom-ID >= the number of atoms. For molecule IDs, there is no +check done at all. The *offset* and *shift* keywords can only be used if the *add* keyword is also specified. diff --git a/src/read_data.cpp b/src/read_data.cpp index b34dac54eb1..46bd4ba76ca 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -639,6 +639,10 @@ void ReadData::command(int narg, char **arg) error->all(FLERR,"Read_data subsequent file cannot switch to restricted triclinic"); if (xy != domain->xy || xz != domain->xz || yz != domain->yz) error->all(FLERR,"Read_data subsequent file tilt factors must be same as first file"); + + } else { + if (domain->triclinic) + error->all(FLERR,"Read_data subsequent file cannot switch to orthogonal"); } double oldboxlo[3] = {domain->boxlo[0], domain->boxlo[1], domain->boxlo[2]}; From c172dceb9f74b01929ffccdb2e38f5d6a7edc8e3 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 5 Dec 2023 16:05:07 -0700 Subject: [PATCH 073/719] white space update --- src/read_data.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/read_data.cpp b/src/read_data.cpp index c038d463e85..dc3949ea562 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -639,7 +639,7 @@ void ReadData::command(int narg, char **arg) error->all(FLERR,"Read_data subsequent file cannot switch to restricted triclinic"); if (xy != domain->xy || xz != domain->xz || yz != domain->yz) error->all(FLERR,"Read_data subsequent file tilt factors must be same as first file"); - + } else { if (domain->triclinic) error->all(FLERR,"Read_data subsequent file cannot switch to orthogonal"); From 58787ddecd6ba520004dc7a4ddc1b937cbbd5c5c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 6 Dec 2023 07:36:29 -0500 Subject: [PATCH 074/719] make 2d system box center on 0.0 --- examples/voronoi/in.voronoi.2d | 30 ++-- examples/voronoi/in.voronoi.data | 38 ++-- .../voronoi/log.27Nov18.voronoi.data.g++.1 | 170 ------------------ .../voronoi/log.27Nov18.voronoi.data.g++.4 | 170 ------------------ ...i.2d.g++.1 => log.6Dec23.voronoi.2d.g++.1} | 90 +++++----- ...i.2d.g++.4 => log.6Dec23.voronoi.2d.g++.4} | 92 +++++----- .../voronoi/log.6Dec23.voronoi.data.g++.1 | 168 +++++++++++++++++ .../voronoi/log.6Dec23.voronoi.data.g++.4 | 168 +++++++++++++++++ 8 files changed, 465 insertions(+), 461 deletions(-) delete mode 100644 examples/voronoi/log.27Nov18.voronoi.data.g++.1 delete mode 100644 examples/voronoi/log.27Nov18.voronoi.data.g++.4 rename examples/voronoi/{log.27Nov18.voronoi.2d.g++.1 => log.6Dec23.voronoi.2d.g++.1} (53%) rename examples/voronoi/{log.27Nov18.voronoi.2d.g++.4 => log.6Dec23.voronoi.2d.g++.4} (51%) create mode 100644 examples/voronoi/log.6Dec23.voronoi.data.g++.1 create mode 100644 examples/voronoi/log.6Dec23.voronoi.data.g++.4 diff --git a/examples/voronoi/in.voronoi.2d b/examples/voronoi/in.voronoi.2d index 74bde73f1b5..25628bd19a5 100644 --- a/examples/voronoi/in.voronoi.2d +++ b/examples/voronoi/in.voronoi.2d @@ -7,46 +7,46 @@ variable len equal 4.0 variable lenz equal 10.0 dimension 2 -units metal -boundary p p p +units metal +boundary p p p #lattice sq 1.0 origin 0.5 0.5 0.0 lattice hex 1.0 origin 0.5 0.5 0.0 -atom_style atomic +atom_style atomic -region box block 0 ${len} 0 ${len} 0.0 ${lenz} +region box block 0 ${len} 0 ${len} -0.5 0.5 region atoms block 0 ${len} 0 ${len} 0.0 0.0 create_box 1 box create_atoms 1 region atoms -mass 1 1.0 +mass 1 1.0 pair_style lj/cut ${rcut} pair_coeff 1 1 0.0 1.0 -neighbor ${rskin} nsq +neighbor ${rskin} nsq # set the minimum communication cut-off comm_modify cutoff ${rcomm} -compute v1 all voronoi/atom neighbors yes -compute volvor all reduce sum c_v1[1] -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys -thermo_style custom c_volvor v_volsys vol v_err -thermo 1 +compute v1 all voronoi/atom neighbors yes +compute volvor all reduce sum c_v1[1] +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys +thermo_style custom c_volvor v_volsys vol v_err +thermo 1 # # TEST 1: Volume check for 2d bulk system # -run 0 +run 0 # # TEST 2: Volume check for 2d finite system # add margins in x and y directions # -change_box all boundary f f p -run 0 +change_box all boundary f f p +run 0 diff --git a/examples/voronoi/in.voronoi.data b/examples/voronoi/in.voronoi.data index e5d925c4982..cbcc530649e 100644 --- a/examples/voronoi/in.voronoi.data +++ b/examples/voronoi/in.voronoi.data @@ -4,24 +4,24 @@ variable len equal 4.0 variable lenz equal 10.0 dimension 2 -units metal -boundary f f p +units metal +boundary f f p lattice hex 1.0 origin 0.25 0.25 0.0 -atom_style atomic +atom_style atomic -region box block 0 ${len} 0 ${len} 0.0 ${lenz} +region box block 0 ${len} 0 ${len} -0.5 0.5 region atoms block 0 ${len} 0 ${len} 0.0 0.0 create_box 1 box create_atoms 1 region atoms -mass 1 1.0 +mass 1 1.0 pair_style lj/cut 2.5 pair_coeff 1 1 0.0 1.0 -neighbor 1.0 nsq +neighbor 1.0 nsq # # TEST 1: @@ -30,11 +30,11 @@ neighbor 1.0 nsq # This compute voronoi generates all three # types of quantity: per-atom, local, and global -compute v1 all voronoi/atom neighbors yes edge_histo 6 +compute v1 all voronoi/atom neighbors yes edge_histo 6 # write voronoi per-atom quantities to a file -dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] +dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] # writing voronoi local quantities to a file @@ -42,17 +42,17 @@ dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] # sum up a voronoi per-atom quantity -compute volvor all reduce sum c_v1[1] +compute volvor all reduce sum c_v1[1] -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys # output voronoi global quantities -thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] -thermo 1 +thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +thermo 1 -run 0 +run 0 uncompute v1 uncompute volvor @@ -65,7 +65,7 @@ undump dlocal # This compute voronoi generates peratom and local and global quantities -compute v2 all voronoi/atom neighbors yes edge_histo 6 +compute v2 all voronoi/atom neighbors yes edge_histo 6 # write voronoi local quantities to a file @@ -73,11 +73,11 @@ dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] # sum up a voronoi local quantity -compute sumarea all reduce sum c_v2[3] inputs local +compute sumarea all reduce sum c_v2[3] inputs local # output voronoi global quantities -thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] -thermo 1 +thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] +thermo 1 -run 0 +run 0 diff --git a/examples/voronoi/log.27Nov18.voronoi.data.g++.1 b/examples/voronoi/log.27Nov18.voronoi.data.g++.1 deleted file mode 100644 index 04bc629d87d..00000000000 --- a/examples/voronoi/log.27Nov18.voronoi.data.g++.1 +++ /dev/null @@ -1,170 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Exercise different output data options - -variable len equal 4.0 -variable lenz equal 10.0 - -dimension 2 -units metal -boundary f f p - -lattice hex 1.0 origin 0.25 0.25 0.0 -Lattice spacing in x,y,z = 1 1.73205 1 - -atom_style atomic - -region box block 0 ${len} 0 ${len} 0.0 ${lenz} -region box block 0 4 0 ${len} 0.0 ${lenz} -region box block 0 4 0 4 0.0 ${lenz} -region box block 0 4 0 4 0.0 10 -region atoms block 0 ${len} 0 ${len} 0.0 0.0 -region atoms block 0 4 0 ${len} 0.0 0.0 -region atoms block 0 4 0 4 0.0 0.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (4 6.9282 10) - 1 by 1 by 1 MPI processor grid -create_atoms 1 region atoms -Created 32 atoms - Time spent = 0.000315666 secs - -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 0.0 1.0 - -neighbor 1.0 nsq - -# -# TEST 1: -# - -# This compute voronoi generates all three -# types of quantity: per-atom, local, and global - -compute v1 all voronoi/atom neighbors yes edge_histo 6 - -# write voronoi per-atom quantities to a file - -dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] - -# writing voronoi local quantities to a file - -dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] - -# sum up a voronoi per-atom quantity - -compute volvor all reduce sum c_v1[1] - -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys - -# output voronoi global quantities - -thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] -thermo 1 - -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.5 - ghost atom cutoff = 3.5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/nsq/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 10.04 | 10.04 | 10.04 Mbytes -c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] - 277.12813 277.12813 27.712813 3.9790393e-13 0 186 12 36 0 -Loop time of 7.15256e-07 on 1 procs for 0 steps with 32 atoms - -0.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 7.153e-07 | | |100.00 - -Nlocal: 32 ave 32 max 32 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 325 ave 325 max 325 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 325 -Ave neighs/atom = 10.1562 -Neighbor list builds = 0 -Dangerous builds = 0 - -uncompute v1 -uncompute volvor -undump dperatom -undump dlocal - -# -# TEST 2: -# - -# This compute voronoi generates -# local and global quantities, but -# not per-atom quantities - -compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no - -# write voronoi local quantities to a file - -dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] - -# sum up a voronoi local quantity - -compute sumarea all reduce sum c_v2[3] - -# output voronoi global quantities - -thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] -thermo 1 - -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Per MPI rank memory allocation (min/avg/max) = 8.787 | 8.787 | 8.787 Mbytes -c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] - 1215.0706 0 186 12 36 0 -Loop time of 7.15256e-07 on 1 procs for 0 steps with 32 atoms - -139.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 7.153e-07 | | |100.00 - -Nlocal: 32 ave 32 max 32 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 325 ave 325 max 325 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 325 -Ave neighs/atom = 10.1562 -Neighbor list builds = 0 -Dangerous builds = 0 - - - -Total wall time: 0:00:00 diff --git a/examples/voronoi/log.27Nov18.voronoi.data.g++.4 b/examples/voronoi/log.27Nov18.voronoi.data.g++.4 deleted file mode 100644 index be028e4d2f1..00000000000 --- a/examples/voronoi/log.27Nov18.voronoi.data.g++.4 +++ /dev/null @@ -1,170 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Exercise different output data options - -variable len equal 4.0 -variable lenz equal 10.0 - -dimension 2 -units metal -boundary f f p - -lattice hex 1.0 origin 0.25 0.25 0.0 -Lattice spacing in x,y,z = 1 1.73205 1 - -atom_style atomic - -region box block 0 ${len} 0 ${len} 0.0 ${lenz} -region box block 0 4 0 ${len} 0.0 ${lenz} -region box block 0 4 0 4 0.0 ${lenz} -region box block 0 4 0 4 0.0 10 -region atoms block 0 ${len} 0 ${len} 0.0 0.0 -region atoms block 0 4 0 ${len} 0.0 0.0 -region atoms block 0 4 0 4 0.0 0.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (4 6.9282 10) - 2 by 2 by 1 MPI processor grid -create_atoms 1 region atoms -Created 32 atoms - Time spent = 0.000311136 secs - -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 0.0 1.0 - -neighbor 1.0 nsq - -# -# TEST 1: -# - -# This compute voronoi generates all three -# types of quantity: per-atom, local, and global - -compute v1 all voronoi/atom neighbors yes edge_histo 6 - -# write voronoi per-atom quantities to a file - -dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] - -# writing voronoi local quantities to a file - -dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] - -# sum up a voronoi per-atom quantity - -compute volvor all reduce sum c_v1[1] - -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys - -# output voronoi global quantities - -thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] -thermo 1 - -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.5 - ghost atom cutoff = 3.5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/nsq/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 9.922 | 9.922 | 9.922 Mbytes -c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] - 277.12813 277.12813 27.712813 3.4106051e-13 0 186 12 36 0 -Loop time of 1.40667e-05 on 4 procs for 0 steps with 32 atoms - -46.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.407e-05 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 24 ave 24 max 24 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 81.25 ave 84 max 77 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 325 -Ave neighs/atom = 10.1562 -Neighbor list builds = 0 -Dangerous builds = 0 - -uncompute v1 -uncompute volvor -undump dperatom -undump dlocal - -# -# TEST 2: -# - -# This compute voronoi generates -# local and global quantities, but -# not per-atom quantities - -compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no - -# write voronoi local quantities to a file - -dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] - -# sum up a voronoi local quantity - -compute sumarea all reduce sum c_v2[3] - -# output voronoi global quantities - -thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] -thermo 1 - -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Per MPI rank memory allocation (min/avg/max) = 8.671 | 8.671 | 8.671 Mbytes -c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] - 1215.0706 0 186 12 36 0 -Loop time of 2.71797e-05 on 4 procs for 0 steps with 32 atoms - -57.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.718e-05 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 24 ave 24 max 24 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 81.25 ave 84 max 77 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 325 -Ave neighs/atom = 10.1562 -Neighbor list builds = 0 -Dangerous builds = 0 - - - -Total wall time: 0:00:00 diff --git a/examples/voronoi/log.27Nov18.voronoi.2d.g++.1 b/examples/voronoi/log.6Dec23.voronoi.2d.g++.1 similarity index 53% rename from examples/voronoi/log.27Nov18.voronoi.2d.g++.1 rename to examples/voronoi/log.6Dec23.voronoi.2d.g++.1 index a591db8b4f6..0f1bc89bb99 100644 --- a/examples/voronoi/log.27Nov18.voronoi.2d.g++.1 +++ b/examples/voronoi/log.6Dec23.voronoi.2d.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (27 Nov 2018) +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Test volume definitions for 2d and finite systems @@ -9,57 +10,58 @@ variable len equal 4.0 variable lenz equal 10.0 dimension 2 -units metal -boundary p p p +units metal +boundary p p p #lattice sq 1.0 origin 0.5 0.5 0.0 lattice hex 1.0 origin 0.5 0.5 0.0 -Lattice spacing in x,y,z = 1 1.73205 1 +Lattice spacing in x,y,z = 1 1.7320508 1 -atom_style atomic +atom_style atomic -region box block 0 ${len} 0 ${len} 0.0 ${lenz} -region box block 0 4 0 ${len} 0.0 ${lenz} -region box block 0 4 0 4 0.0 ${lenz} -region box block 0 4 0 4 0.0 10 +region box block 0 ${len} 0 ${len} -0.5 0.5 +region box block 0 4 0 ${len} -0.5 0.5 +region box block 0 4 0 4 -0.5 0.5 region atoms block 0 ${len} 0 ${len} 0.0 0.0 region atoms block 0 4 0 ${len} 0.0 0.0 region atoms block 0 4 0 4 0.0 0.0 create_box 1 box -Created orthogonal box = (0 0 0) to (4 6.9282 10) +Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) 1 by 1 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms - Time spent = 0.000315905 secs + using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + create_atoms CPU = 0.000 seconds -mass 1 1.0 +mass 1 1.0 pair_style lj/cut ${rcut} pair_style lj/cut 10 pair_coeff 1 1 0.0 1.0 -neighbor ${rskin} nsq -neighbor 2 nsq +neighbor ${rskin} nsq +neighbor 2 nsq # set the minimum communication cut-off comm_modify cutoff ${rcomm} comm_modify cutoff 20 -compute v1 all voronoi/atom neighbors yes -compute volvor all reduce sum c_v1[1] -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys -thermo_style custom c_volvor v_volsys vol v_err -thermo 1 +compute v1 all voronoi/atom neighbors yes +compute volvor all reduce sum c_v1[1] +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys +thermo_style custom c_volvor v_volsys vol v_err +thermo 1 # # TEST 1: Volume check for 2d bulk system # -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 20 @@ -69,12 +71,12 @@ Neighbor list info ... pair build: half/nsq/newton stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 3.007 | 3.007 | 3.007 Mbytes -c_volvor v_volsys Volume v_err - 277.12813 277.12813 27.712813 5.6843419e-14 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms +Per MPI rank memory allocation (min/avg/max) = 3.008 | 3.008 | 3.008 Mbytes + c_volvor v_volsys Volume v_err + 27.712813 27.712813 27.712813 -3.5527137e-15 +Loop time of 6.33e-07 on 1 procs for 0 steps with 32 atoms -209.7% CPU use with 1 MPI tasks x 1 OpenMP threads +316.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -84,13 +86,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 6.33e-07 | | |100.00 -Nlocal: 32 ave 32 max 32 min +Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2415 ave 2415 max 2415 min +Nghost: 2415 ave 2415 max 2415 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8256 ave 8256 max 8256 min +Neighs: 8256 ave 8256 max 8256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8256 @@ -103,15 +105,17 @@ Dangerous builds = 0 # add margins in x and y directions # -change_box all boundary f f p -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +change_box all boundary f f p +Changing box ... +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 7.688 | 7.688 | 7.688 Mbytes -c_volvor v_volsys Volume v_err - 277.12813 277.12813 27.712813 3.4106051e-13 -Loop time of 4.76837e-07 on 1 procs for 0 steps with 32 atoms + c_volvor v_volsys Volume v_err + 27.712813 27.712813 27.712813 3.5527137e-14 +Loop time of 3.93e-07 on 1 procs for 0 steps with 32 atoms -209.7% CPU use with 1 MPI tasks x 1 OpenMP threads +254.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -121,13 +125,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 4.768e-07 | | |100.00 +Other | | 3.93e-07 | | |100.00 -Nlocal: 32 ave 32 max 32 min +Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min +Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 496 ave 496 max 496 min +Neighs: 496 ave 496 max 496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496 diff --git a/examples/voronoi/log.27Nov18.voronoi.2d.g++.4 b/examples/voronoi/log.6Dec23.voronoi.2d.g++.4 similarity index 51% rename from examples/voronoi/log.27Nov18.voronoi.2d.g++.4 rename to examples/voronoi/log.6Dec23.voronoi.2d.g++.4 index 841f8dcb81d..f5a5052c4fd 100644 --- a/examples/voronoi/log.27Nov18.voronoi.2d.g++.4 +++ b/examples/voronoi/log.6Dec23.voronoi.2d.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (27 Nov 2018) +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Test volume definitions for 2d and finite systems @@ -9,57 +10,58 @@ variable len equal 4.0 variable lenz equal 10.0 dimension 2 -units metal -boundary p p p +units metal +boundary p p p #lattice sq 1.0 origin 0.5 0.5 0.0 lattice hex 1.0 origin 0.5 0.5 0.0 -Lattice spacing in x,y,z = 1 1.73205 1 +Lattice spacing in x,y,z = 1 1.7320508 1 -atom_style atomic +atom_style atomic -region box block 0 ${len} 0 ${len} 0.0 ${lenz} -region box block 0 4 0 ${len} 0.0 ${lenz} -region box block 0 4 0 4 0.0 ${lenz} -region box block 0 4 0 4 0.0 10 +region box block 0 ${len} 0 ${len} -0.5 0.5 +region box block 0 4 0 ${len} -0.5 0.5 +region box block 0 4 0 4 -0.5 0.5 region atoms block 0 ${len} 0 ${len} 0.0 0.0 region atoms block 0 4 0 ${len} 0.0 0.0 region atoms block 0 4 0 4 0.0 0.0 create_box 1 box -Created orthogonal box = (0 0 0) to (4 6.9282 10) +Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) 2 by 2 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms - Time spent = 0.000319481 secs + using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + create_atoms CPU = 0.000 seconds -mass 1 1.0 +mass 1 1.0 pair_style lj/cut ${rcut} pair_style lj/cut 10 pair_coeff 1 1 0.0 1.0 -neighbor ${rskin} nsq -neighbor 2 nsq +neighbor ${rskin} nsq +neighbor 2 nsq # set the minimum communication cut-off comm_modify cutoff ${rcomm} comm_modify cutoff 20 -compute v1 all voronoi/atom neighbors yes -compute volvor all reduce sum c_v1[1] -variable volsys equal lz*lx*ly -variable err equal c_volvor-v_volsys -thermo_style custom c_volvor v_volsys vol v_err -thermo 1 +compute v1 all voronoi/atom neighbors yes +compute volvor all reduce sum c_v1[1] +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys +thermo_style custom c_volvor v_volsys vol v_err +thermo 1 # # TEST 1: Volume check for 2d bulk system # -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 20 @@ -69,12 +71,12 @@ Neighbor list info ... pair build: half/nsq/newton stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 3.042 | 3.042 | 3.042 Mbytes -c_volvor v_volsys Volume v_err - 277.12813 277.12813 27.712813 5.1159077e-13 -Loop time of 2.79546e-05 on 4 procs for 0 steps with 32 atoms +Per MPI rank memory allocation (min/avg/max) = 3.038 | 3.038 | 3.038 Mbytes + c_volvor v_volsys Volume v_err + 27.712813 27.712813 27.712813 2.1316282e-14 +Loop time of 2.18725e-06 on 4 procs for 0 steps with 32 atoms -51.9% CPU use with 4 MPI tasks x 1 OpenMP threads +45.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -84,13 +86,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.795e-05 | | |100.00 +Other | | 2.187e-06 | | |100.00 -Nlocal: 8 ave 8 max 8 min +Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 2159 ave 2159 max 2159 min +Nghost: 2159 ave 2159 max 2159 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 2064 ave 2077 max 2051 min +Neighs: 2064 ave 2077 max 2051 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 8256 @@ -103,15 +105,17 @@ Dangerous builds = 0 # add margins in x and y directions # -change_box all boundary f f p -run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) -Per MPI rank memory allocation (min/avg/max) = 7.678 | 7.678 | 7.678 Mbytes -c_volvor v_volsys Volume v_err - 277.12813 277.12813 27.712813 3.4106051e-13 -Loop time of 1.88947e-05 on 4 procs for 0 steps with 32 atoms +change_box all boundary f f p +Changing box ... +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.671 | 7.671 | 7.671 Mbytes + c_volvor v_volsys Volume v_err + 27.712813 27.712813 27.712813 3.907985e-14 +Loop time of 2.22e-06 on 4 procs for 0 steps with 32 atoms -47.6% CPU use with 4 MPI tasks x 1 OpenMP threads +112.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -121,13 +125,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.889e-05 | | |100.00 +Other | | 2.22e-06 | | |100.00 -Nlocal: 8 ave 8 max 8 min +Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 24 ave 24 max 24 min +Nghost: 24 ave 24 max 24 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 124 ave 124 max 124 min +Neighs: 124 ave 124 max 124 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496 diff --git a/examples/voronoi/log.6Dec23.voronoi.data.g++.1 b/examples/voronoi/log.6Dec23.voronoi.data.g++.1 new file mode 100644 index 00000000000..b598b251dcb --- /dev/null +++ b/examples/voronoi/log.6Dec23.voronoi.data.g++.1 @@ -0,0 +1,168 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Exercise different output data options + +variable len equal 4.0 +variable lenz equal 10.0 + +dimension 2 +units metal +boundary f f p + +lattice hex 1.0 origin 0.25 0.25 0.0 +Lattice spacing in x,y,z = 1 1.7320508 1 + +atom_style atomic + +region box block 0 ${len} 0 ${len} -0.5 0.5 +region box block 0 4 0 ${len} -0.5 0.5 +region box block 0 4 0 4 -0.5 0.5 +region atoms block 0 ${len} 0 ${len} 0.0 0.0 +region atoms block 0 4 0 ${len} 0.0 0.0 +region atoms block 0 4 0 4 0.0 0.0 +create_box 1 box +Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region atoms +Created 32 atoms + using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + create_atoms CPU = 0.000 seconds + +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 0.0 1.0 + +neighbor 1.0 nsq + +# +# TEST 1: +# + +# This compute voronoi generates all three +# types of quantity: per-atom, local, and global + +compute v1 all voronoi/atom neighbors yes edge_histo 6 + +# write voronoi per-atom quantities to a file + +dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] + +# writing voronoi local quantities to a file + +dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] + +# sum up a voronoi per-atom quantity + +compute volvor all reduce sum c_v1[1] + +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys + +# output voronoi global quantities + +thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +thermo 1 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.5 + ghost atom cutoff = 3.5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/nsq/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.03 | 3.03 | 3.03 Mbytes + c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] + 27.712813 27.712813 27.712813 3.1974423e-14 0 186 12 36 0 +Loop time of 7.96e-07 on 1 procs for 0 steps with 32 atoms + +125.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.96e-07 | | |100.00 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 325 ave 325 max 325 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 325 +Ave neighs/atom = 10.15625 +Neighbor list builds = 0 +Dangerous builds = 0 + +uncompute v1 +uncompute volvor +undump dperatom +undump dlocal + +# +# TEST 2: +# + +# This compute voronoi generates peratom and local and global quantities + +compute v2 all voronoi/atom neighbors yes edge_histo 6 + +# write voronoi local quantities to a file + +dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] + +# sum up a voronoi local quantity + +compute sumarea all reduce sum c_v2[3] inputs local + +# output voronoi global quantities + +thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] +thermo 1 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.03 | 3.03 | 3.03 Mbytes + c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] + 171.39013 0 186 12 36 0 +Loop time of 3.74e-07 on 1 procs for 0 steps with 32 atoms + +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.74e-07 | | |100.00 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 325 ave 325 max 325 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 325 +Ave neighs/atom = 10.15625 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/voronoi/log.6Dec23.voronoi.data.g++.4 b/examples/voronoi/log.6Dec23.voronoi.data.g++.4 new file mode 100644 index 00000000000..dc0855c2c78 --- /dev/null +++ b/examples/voronoi/log.6Dec23.voronoi.data.g++.4 @@ -0,0 +1,168 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Exercise different output data options + +variable len equal 4.0 +variable lenz equal 10.0 + +dimension 2 +units metal +boundary f f p + +lattice hex 1.0 origin 0.25 0.25 0.0 +Lattice spacing in x,y,z = 1 1.7320508 1 + +atom_style atomic + +region box block 0 ${len} 0 ${len} -0.5 0.5 +region box block 0 4 0 ${len} -0.5 0.5 +region box block 0 4 0 4 -0.5 0.5 +region atoms block 0 ${len} 0 ${len} 0.0 0.0 +region atoms block 0 4 0 ${len} 0.0 0.0 +region atoms block 0 4 0 4 0.0 0.0 +create_box 1 box +Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + 2 by 2 by 1 MPI processor grid +create_atoms 1 region atoms +Created 32 atoms + using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5) + create_atoms CPU = 0.000 seconds + +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 0.0 1.0 + +neighbor 1.0 nsq + +# +# TEST 1: +# + +# This compute voronoi generates all three +# types of quantity: per-atom, local, and global + +compute v1 all voronoi/atom neighbors yes edge_histo 6 + +# write voronoi per-atom quantities to a file + +dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] + +# writing voronoi local quantities to a file + +dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] + +# sum up a voronoi per-atom quantity + +compute volvor all reduce sum c_v1[1] + +variable volsys equal lz*lx*ly +variable err equal c_volvor-v_volsys + +# output voronoi global quantities + +thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +thermo 1 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.5 + ghost atom cutoff = 3.5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/nsq/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 2.921 | 2.921 | 2.921 Mbytes + c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] + 27.712813 27.712813 27.712813 3.907985e-14 0 186 12 36 0 +Loop time of 2.21425e-06 on 4 procs for 0 steps with 32 atoms + +45.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.214e-06 | | |100.00 + +Nlocal: 8 ave 8 max 8 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 24 ave 24 max 24 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 81.25 ave 84 max 77 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 325 +Ave neighs/atom = 10.15625 +Neighbor list builds = 0 +Dangerous builds = 0 + +uncompute v1 +uncompute volvor +undump dperatom +undump dlocal + +# +# TEST 2: +# + +# This compute voronoi generates peratom and local and global quantities + +compute v2 all voronoi/atom neighbors yes edge_histo 6 + +# write voronoi local quantities to a file + +dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] + +# sum up a voronoi local quantity + +compute sumarea all reduce sum c_v2[3] inputs local + +# output voronoi global quantities + +thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] +thermo 1 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 2.921 | 2.921 | 2.921 Mbytes + c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] + 171.39013 0 186 12 36 0 +Loop time of 1.82375e-06 on 4 procs for 0 steps with 32 atoms + +82.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.824e-06 | | |100.00 + +Nlocal: 8 ave 8 max 8 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 24 ave 24 max 24 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 81.25 ave 84 max 77 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 325 +Ave neighs/atom = 10.15625 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 From 8eaaae1e996e65d0a123d98b1932c104b23d7370 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 6 Dec 2023 08:31:41 -0500 Subject: [PATCH 075/719] recenter 2d boxes around 0.0 --- examples/PACKAGES/flow_gauss/in.GD | 2 +- .../PACKAGES/flow_gauss/log.6Dec23.GD.g++.1 | 941 + .../PACKAGES/flow_gauss/log.6Dec23.GD.g++.4 | 941 + .../PACKAGES/flow_gauss/log.6Jul17.GD.g++.1 | 909 - .../PACKAGES/flow_gauss/log.6Jul17.GD.g++.4 | 909 - .../PACKAGES/phonon/2-1D-diatomic/data.pos | 2 +- .../phonon/2-1D-diatomic/log.6Dec23.Ana.g++.1 | 20125 ++++++++++++++++ .../phonon/2-1D-diatomic/log.6Dec23.Ana.g++.4 | 20125 ++++++++++++++++ .../PACKAGES/phonon/2-1D-diatomic/log.lammps | 20088 --------------- .../phonon/2-1D-diatomic/phonon.bin.2000000 | Bin 2196 -> 0 bytes .../PACKAGES/phonon/2-1D-diatomic/phonon.log | 206 - 11 files changed, 42134 insertions(+), 22114 deletions(-) create mode 100644 examples/PACKAGES/flow_gauss/log.6Dec23.GD.g++.1 create mode 100644 examples/PACKAGES/flow_gauss/log.6Dec23.GD.g++.4 delete mode 100644 examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.1 delete mode 100644 examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.4 create mode 100644 examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.1 create mode 100644 examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.4 delete mode 100644 examples/PACKAGES/phonon/2-1D-diatomic/log.lammps delete mode 100644 examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 delete mode 100644 examples/PACKAGES/phonon/2-1D-diatomic/phonon.log diff --git a/examples/PACKAGES/flow_gauss/in.GD b/examples/PACKAGES/flow_gauss/in.GD index bcff4d4c57b..a22b440eb67 100644 --- a/examples/PACKAGES/flow_gauss/in.GD +++ b/examples/PACKAGES/flow_gauss/in.GD @@ -68,7 +68,7 @@ variable Lx1 equal round(${Lx}/${aWall})*${aWall} #create simulation box variable lx2 equal ${Lx1}/2 variable ly2 equal ${Ly1}/2 -region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box +region simbox block -${lx2} ${lx2} -${ly2} ${ly2} -0.1 0.1 units box create_box 2 simbox ##################################################################### diff --git a/examples/PACKAGES/flow_gauss/log.6Dec23.GD.g++.1 b/examples/PACKAGES/flow_gauss/log.6Dec23.GD.g++.1 new file mode 100644 index 00000000000..566ef572bc8 --- /dev/null +++ b/examples/PACKAGES/flow_gauss/log.6Dec23.GD.g++.1 @@ -0,0 +1,941 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +#LAMMPS input script +#in.GD +#see README for details + +############################################################################### +#initialize variables +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task + +#frequency for outputting info (timesteps) +variable dump_rate equal 50 +variable thermo_rate equal 10 + +#equilibration time (timesteps) +variable equil equal 1000 + +#stabilization time (timesteps to reach steady-state) +variable stabil equal 1000 + +#data collection time (timesteps) +variable run equal 2000 + +#length of pipe +variable L equal 30 + +#width of pipe +variable d equal 20 + +#flux (mass/sigma*tau) +variable J equal 0.1 + +#simulation box dimensions +variable Lx equal 100 +variable Ly equal 40 + +#bulk fluid density +variable dens equal 0.8 + +#lattice spacing for wall atoms +variable aWall equal 1.0 #1.7472 + +#timestep +variable ts equal 0.001 + +#temperature +variable T equal 2.0 + +#thermostat damping constant +variable tdamp equal ${ts}*100 +variable tdamp equal 0.001*100 + +units lj +dimension 2 +atom_style atomic + + +############################################################################### +#create box + +#create lattice with the spacing aWall +variable rhoWall equal ${aWall}^(-2) +variable rhoWall equal 1^(-2) +lattice sq ${rhoWall} +lattice sq 1 +Lattice spacing in x,y,z = 1 1 1 + +#modify input dimensions to be multiples of aWall +variable L1 equal round($L/${aWall})*${aWall} +variable L1 equal round(30/${aWall})*${aWall} +variable L1 equal round(30/1)*${aWall} +variable L1 equal round(30/1)*1 +variable d1 equal round($d/${aWall})*${aWall} +variable d1 equal round(20/${aWall})*${aWall} +variable d1 equal round(20/1)*${aWall} +variable d1 equal round(20/1)*1 +variable Ly1 equal round(${Ly}/${aWall})*${aWall} +variable Ly1 equal round(40/${aWall})*${aWall} +variable Ly1 equal round(40/1)*${aWall} +variable Ly1 equal round(40/1)*1 +variable Lx1 equal round(${Lx}/${aWall})*${aWall} +variable Lx1 equal round(100/${aWall})*${aWall} +variable Lx1 equal round(100/1)*${aWall} +variable Lx1 equal round(100/1)*1 + +#create simulation box +variable lx2 equal ${Lx1}/2 +variable lx2 equal 100/2 +variable ly2 equal ${Ly1}/2 +variable ly2 equal 40/2 +region simbox block -${lx2} ${lx2} -${ly2} ${ly2} -0.1 0.1 units box +region simbox block -50 ${lx2} -${ly2} ${ly2} -0.1 0.1 units box +region simbox block -50 50 -${ly2} ${ly2} -0.1 0.1 units box +region simbox block -50 50 -20 ${ly2} -0.1 0.1 units box +region simbox block -50 50 -20 20 -0.1 0.1 units box +create_box 2 simbox +Created orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + 1 by 1 by 1 MPI processor grid + +##################################################################### +#set up potential + +mass 1 1.0 #fluid atoms +mass 2 1.0 #wall atoms + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 1.12246 +pair_coeff 2 2 0.0 0.0 + +neigh_modify exclude type 2 2 + +timestep ${ts} +timestep 0.001 + +##################################################################### +#create atoms + +#create wall atoms everywhere +create_atoms 2 box +Created 4000 atoms + using lattice units in orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + create_atoms CPU = 0.002 seconds + +#define region which is "walled off" +variable dhalf equal ${d1}/2 +variable dhalf equal 20/2 +variable Lhalf equal ${L1}/2 +variable Lhalf equal 30/2 +region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box +region walltop block -15 ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box +region walltop block -15 15 ${dhalf} EDGE -0.1 0.1 units box +region walltop block -15 15 10 EDGE -0.1 0.1 units box +region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box +region wallbot block -15 ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box +region wallbot block -15 15 EDGE -${dhalf} -0.1 0.1 units box +region wallbot block -15 15 EDGE -10 -0.1 0.1 units box +region outsidewall union 2 walltop wallbot side out + +#remove wall atoms outside wall region +group outside region outsidewall +3349 atoms in group outside +delete_atoms group outside +Deleted 3349 atoms, new total = 651 + +#remove wall atoms that aren't on edge of wall region +variable x1 equal ${Lhalf}-${aWall} +variable x1 equal 15-${aWall} +variable x1 equal 15-1 +variable y1 equal ${dhalf}+${aWall} +variable y1 equal 10+${aWall} +variable y1 equal 10+1 +region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box +region insideTop block -14 ${x1} ${y1} EDGE -0.1 0.1 units box +region insideTop block -14 14 ${y1} EDGE -0.1 0.1 units box +region insideTop block -14 14 11 EDGE -0.1 0.1 units box +region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box +region insideBot block -14 ${x1} EDGE -${y1} -0.1 0.1 units box +region insideBot block -14 14 EDGE -${y1} -0.1 0.1 units box +region insideBot block -14 14 EDGE -11 -0.1 0.1 units box +region insideWall union 2 insideTop insideBot +group insideWall region insideWall +551 atoms in group insideWall +delete_atoms group insideWall +Deleted 551 atoms, new total = 100 + +#define new lattice, to give correct fluid density +#y lattice const must be a multiple of aWall +variable atrue equal ${dens}^(-1/2) +variable atrue equal 0.8^(-1/2) +variable ay equal round(${atrue}/${aWall})*${aWall} +variable ay equal round(1.11803398874989/${aWall})*${aWall} +variable ay equal round(1.11803398874989/1)*${aWall} +variable ay equal round(1.11803398874989/1)*1 + +#choose x lattice const to give correct density +variable ax equal (${ay}*${dens})^(-1) +variable ax equal (1*${dens})^(-1) +variable ax equal (1*0.8)^(-1) + +#change Lx to be multiple of ax +variable Lx1 equal round(${Lx}/${ax})*${ax} +variable Lx1 equal round(100/${ax})*${ax} +variable Lx1 equal round(100/1.25)*${ax} +variable Lx1 equal round(100/1.25)*1.25 +variable lx2 equal ${Lx1}/2 +variable lx2 equal 100/2 +change_box all x final -${lx2} ${lx2} units box +change_box all x final -50 ${lx2} units box +change_box all x final -50 50 units box +Changing box ... + orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + +#define new lattice +lattice custom ${dens} a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 +lattice custom 0.8 a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 +lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 +lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 1 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 +Lattice spacing in x,y,z = 1.25 1 1 + +#fill in rest of box with bulk particles +variable delta equal 0.001 +variable Ldelt equal ${Lhalf}+${delta} +variable Ldelt equal 15+${delta} +variable Ldelt equal 15+0.001 +variable dDelt equal ${dhalf}-${delta} +variable dDelt equal 10-${delta} +variable dDelt equal 10-0.001 +region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box +region left block EDGE -15.001 EDGE EDGE -0.1 0.1 units box +region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box +region right block 15.001 EDGE EDGE EDGE -0.1 0.1 units box +region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box +region pipe block -15.001 ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box +region pipe block -15.001 15.001 -${dDelt} ${dDelt} -0.1 0.1 units box +region pipe block -15.001 15.001 -9.999 ${dDelt} -0.1 0.1 units box +region pipe block -15.001 15.001 -9.999 9.999 -0.1 0.1 units box + +region bulk union 3 left pipe right +create_atoms 1 region bulk +Created 2675 atoms + using lattice units in orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + create_atoms CPU = 0.002 seconds + +group bulk type 1 +2675 atoms in group bulk +group wall type 2 +100 atoms in group wall + +#remove atoms that are too close to wall +delete_atoms overlap 0.9 bulk wall +System init for delete_atoms ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 72 29 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command delete_atoms, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Deleted 0 atoms, new total = 2775 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes +neigh_modify exclude group wall wall + +velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom +velocity bulk create 2 78915 dist gaussian rot yes mom yes loop geom + +##################################################################### +#set up PUT +#see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172 + +#average number of particles per box, Evans and Morriss used 2.0 +variable NperBox equal 8.0 + +#calculate box sizes +variable boxSide equal sqrt(${NperBox}/${dens}) +variable boxSide equal sqrt(8/${dens}) +variable boxSide equal sqrt(8/0.8) +variable nX equal round(lx/${boxSide}) +variable nX equal round(lx/3.16227766016838) +variable nY equal round(ly/${boxSide}) +variable nY equal round(ly/3.16227766016838) +variable dX equal lx/${nX} +variable dX equal lx/32 +variable dY equal ly/${nY} +variable dY equal ly/13 + +#temperature of fluid (excluding wall) +compute myT bulk temp + +#profile-unbiased temperature of fluid +compute myTp bulk temp/profile 1 1 0 xy ${nX} ${nY} +compute myTp bulk temp/profile 1 1 0 xy 32 ${nY} +compute myTp bulk temp/profile 1 1 0 xy 32 13 + +#thermo setup +thermo ${thermo_rate} +thermo 10 +thermo_style custom step c_myT c_myTp etotal press + +#dump initial configuration +# dump 55 all custom 1 all.init.lammpstrj id type x y z vx vy vz +# dump 56 wall custom 1 wall.init.lammpstrj id type x y z +# dump_modify 55 sort id +# dump_modify 56 sort id +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 72 29 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.104 | 3.104 | 3.104 Mbytes + Step c_myT c_myTp TotEng Press + 0 2 2.054601 0.77892922 7.3417096 +Loop time of 6.85e-07 on 1 procs for 0 steps with 2775 atoms + +146.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 6.85e-07 | | |100.00 + +Nlocal: 2775 ave 2775 max 2775 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 510 ave 510 max 510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 26406 ave 26406 max 26406 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 26406 +Ave neighs/atom = 9.5156757 +Neighbor list builds = 0 +Dangerous builds = 0 +# undump 55 +# undump 56 + +##################################################################### +#equilibrate without GD + +fix nvt bulk nvt temp $T $T ${tdamp} +fix nvt bulk nvt temp 2 $T ${tdamp} +fix nvt bulk nvt temp 2 2 ${tdamp} +fix nvt bulk nvt temp 2 2 0.1 +fix_modify nvt temp myTp +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1391) +fix 2 bulk enforce2d + +run ${equil} +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.166 | 3.166 | 3.166 Mbytes + Step c_myT c_myTp TotEng Press + 0 2 2.054601 0.77892922 7.3417096 + 10 1.9173668 1.9381538 0.77877698 7.6702283 + 20 1.7033651 1.6967466 0.7798044 8.5615039 + 30 1.5026644 1.4718046 0.78461914 9.4308883 + 40 1.4881235 1.4586031 0.79494919 9.6135307 + 50 1.6193439 1.6144665 0.81119835 9.2594114 + 60 1.7405127 1.7576881 0.82966956 8.9525458 + 70 1.7758506 1.7999706 0.84538866 8.9719793 + 80 1.7574736 1.7806782 0.85780732 9.1938511 + 90 1.7492232 1.7720284 0.86895259 9.3714617 + 100 1.7800292 1.807315 0.88044504 9.3874107 + 110 1.8442295 1.878681 0.89278276 9.2585436 + 120 1.9193695 1.9667163 0.90556381 9.0683654 + 130 1.9885753 2.0478097 0.91782871 8.8815507 + 140 2.04662 2.1105827 0.92850319 8.718882 + 150 2.0957046 2.1672706 0.93677238 8.5718869 + 160 2.144595 2.2210801 0.94188484 8.4089161 + 170 2.1802133 2.2626399 0.9429713 8.2775682 + 180 2.1868284 2.2696504 0.93931537 8.2321283 + 190 2.1838369 2.2706873 0.93069783 8.1970105 + 200 2.1943436 2.2865542 0.91717737 8.0854148 + 210 2.2029439 2.2912731 0.89906796 7.9589187 + 220 2.1891494 2.2768232 0.87764254 7.9016509 + 230 2.1677848 2.2493747 0.85497463 7.8690125 + 240 2.156695 2.2377486 0.83255207 7.8020978 + 250 2.142758 2.2237662 0.81090722 7.7510242 + 260 2.1177881 2.1967699 0.79016944 7.7477503 + 270 2.0862408 2.1669583 0.77040874 7.7740216 + 280 2.0676515 2.1446262 0.75157955 7.7544068 + 290 2.0645498 2.1425534 0.73343008 7.6746729 + 300 2.0563664 2.1358776 0.71562279 7.6114783 + 310 2.0390115 2.1198472 0.69809211 7.581719 + 320 2.0209035 2.1063385 0.68093855 7.5540946 + 330 2.012488 2.1037583 0.66418283 7.4896097 + 340 2.0166095 2.1094212 0.64762479 7.3779677 + 350 2.0172861 2.1072653 0.63109595 7.2807114 + 360 2.0065768 2.0803788 0.6147802 7.2283814 + 370 1.9970858 2.0639903 0.59905362 7.1747592 + 380 1.9925189 2.056563 0.58395055 7.103506 + 390 1.9935388 2.0546596 0.56945318 7.010305 + 400 2.0020199 2.0632095 0.55532013 6.8883647 + 410 2.009157 2.0732883 0.54128082 6.771521 + 420 2.0081687 2.0785184 0.52711525 6.6868076 + 430 1.9990498 2.0705469 0.51283203 6.6343482 + 440 1.9891528 2.0586814 0.4986104 6.5888679 + 450 1.9829175 2.0465778 0.4846738 6.5332233 + 460 1.9745599 2.031067 0.4711878 6.4903915 + 470 1.9581101 2.006674 0.45837961 6.4836654 + 480 1.9367964 1.9732882 0.44656667 6.501731 + 490 1.9258333 1.9561395 0.43605676 6.4879447 + 500 1.9287 1.9571319 0.42678362 6.4296036 + 510 1.9274696 1.9569118 0.41856553 6.3949919 + 520 1.9100149 1.9392424 0.41134511 6.4307452 + 530 1.8827127 1.9059412 0.40536565 6.5126603 + 540 1.8660696 1.8912024 0.40096324 6.5610607 + 550 1.8701883 1.9043254 0.3982457 6.536251 + 560 1.8842923 1.9289528 0.39698123 6.4785367 + 570 1.8906147 1.9462124 0.39684504 6.4547374 + 580 1.8895472 1.9472747 0.39763233 6.4630103 + 590 1.895375 1.9551336 0.39926725 6.449517 + 600 1.9115711 1.9737109 0.40163655 6.3995241 + 610 1.92823 1.9851787 0.404506 6.3499339 + 620 1.9360678 1.9889572 0.40767569 6.3367514 + 630 1.9346853 1.9836719 0.41105958 6.3637995 + 640 1.9266095 1.9757908 0.41472954 6.4212842 + 650 1.9213863 1.9719496 0.41879537 6.4707692 + 660 1.922962 1.9702923 0.42332926 6.4949933 + 670 1.9238956 1.9707534 0.42836303 6.5212631 + 680 1.9212675 1.9740379 0.43388709 6.5608915 + 690 1.9210314 1.976311 0.43982007 6.5904702 + 700 1.928081 1.9868449 0.44610463 6.5915021 + 710 1.9428895 2.0044235 0.45257857 6.5616141 + 720 1.9554783 2.0176139 0.45898384 6.5367529 + 730 1.969838 2.0327907 0.46505662 6.5017635 + 740 1.9840204 2.0467126 0.47058703 6.4649226 + 750 1.9946633 2.0526929 0.47535832 6.4399342 + 760 2.0018048 2.0535606 0.47924291 6.4280737 + 770 1.9991703 2.0483426 0.48222842 6.4537535 + 780 1.9850797 2.0312444 0.48443072 6.5234271 + 790 1.9691589 2.0154006 0.4861158 6.5995894 + 800 1.9612641 2.0031407 0.48754831 6.6430968 + 810 1.9637155 2.0074142 0.48891261 6.6444644 + 820 1.9691691 2.0110229 0.49018604 6.6304512 + 830 1.9763962 2.0190998 0.49130448 6.6060594 + 840 1.9908278 2.0352615 0.49213189 6.5510683 + 850 2.0105715 2.0558403 0.49238435 6.4743276 + 860 2.0227982 2.0645732 0.49173076 6.4260863 + 870 2.015555 2.064081 0.48998228 6.4528588 + 880 1.9889672 2.0320831 0.48722022 6.5532269 + 890 1.9632172 2.0025881 0.48392295 6.6494723 + 900 1.9527429 1.9887196 0.48054642 6.6846937 + 910 1.9567815 1.9953408 0.47726539 6.6606541 + 920 1.9666996 2.0084955 0.47397593 6.6100666 + 930 1.9702885 2.014774 0.47048741 6.5805871 + 940 1.9661802 2.0116846 0.46671831 6.579539 + 950 1.9576953 1.9960728 0.46273983 6.5967841 + 960 1.9428073 1.9802284 0.45879028 6.6395002 + 970 1.9256011 1.9584581 0.45515059 6.6916425 + 980 1.913512 1.9478848 0.45214528 6.7233279 + 990 1.9174938 1.9449699 0.44994026 6.6943867 + 1000 1.9365527 1.9663901 0.44852349 6.6101761 +Loop time of 0.324261 on 1 procs for 1000 steps with 2775 atoms + +Performance: 266452.077 tau/day, 3083.936 timesteps/s, 8.558 Matom-step/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.19361 | 0.19361 | 0.19361 | 0.0 | 59.71 +Neigh | 0.025544 | 0.025544 | 0.025544 | 0.0 | 7.88 +Comm | 0.0023292 | 0.0023292 | 0.0023292 | 0.0 | 0.72 +Output | 0.0046269 | 0.0046269 | 0.0046269 | 0.0 | 1.43 +Modify | 0.092779 | 0.092779 | 0.092779 | 0.0 | 28.61 +Other | | 0.005374 | | | 1.66 + +Nlocal: 2775 ave 2775 max 2775 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 527 ave 527 max 527 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 24332 ave 24332 max 24332 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 24332 +Ave neighs/atom = 8.7682883 +Neighbor list builds = 38 +Dangerous builds = 0 + +##################################################################### +#initialize the COM velocity and run to achieve steady-state + +#calculate velocity to add: V=J/rho_total +variable Vadd equal $J*lx*ly/count(bulk) +variable Vadd equal 0.1*lx*ly/count(bulk) + +#first remove any COM velocity, then add back the streaming velocity +velocity bulk zero linear +velocity bulk set ${Vadd} 0.0 0.0 units box sum yes mom no +velocity bulk set 0.149532710280374 0.0 0.0 units box sum yes mom no + +fix GD bulk flow/gauss 1 0 0 #energy yes +#fix_modify GD energy yes + +run ${stabil} +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Gaussian dynamics package: doi:10.1021/acs.jpcb.6b09387 + +@Article{strong_water_2017, +title = {The Dynamics of Water in Porous Two-Dimensional Crystals}, +volume = {121}, +number = {1}, +url = {https://doi.org/10.1021/acs.jpcb.6b09387}, +doi = {10.1021/acs.jpcb.6b09387}, +urldate = {2016-12-07}, +journal = {J.~Phys.\ Chem.~B}, +author = {Strong, Steven E. and Eaves, Joel D.}, +year = {2017}, +pages = {189--207} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.166 | 3.166 | 3.166 Mbytes + Step c_myT c_myTp TotEng Press + 1000 1.9477212 1.9663901 0.45928547 6.6176422 + 1010 1.9617328 1.9828061 0.45840963 6.555968 + 1020 1.9570976 1.9825696 0.45782895 6.5690613 + 1030 1.9356292 1.9690101 0.45753984 6.6493822 + 1040 1.9174914 1.9448868 0.4577768 6.7171474 + 1050 1.9202482 1.9432766 0.4588733 6.7039634 + 1060 1.9419998 1.9718217 0.46086407 6.617366 + 1070 1.9666048 1.996346 0.46339522 6.5207175 + 1080 1.9775489 2.0078489 0.46608862 6.4794239 + 1090 1.9725172 2.0005028 0.46876174 6.5044299 + 1100 1.9659582 1.9931537 0.47147394 6.5409107 + 1110 1.9670607 1.9965504 0.47432892 6.5527414 + 1120 1.9716302 1.9984924 0.47732198 6.5530022 + 1130 1.9752703 2.0057031 0.48043914 6.5579379 + 1140 1.976368 2.0061152 0.48358744 6.5719123 + 1150 1.9748014 2.0056689 0.48673155 6.5957896 + 1160 1.9729115 2.0036854 0.48986563 6.6200102 + 1170 1.9702742 2.0016461 0.49302426 6.6455948 + 1180 1.9680418 1.9978705 0.49625385 6.6697165 + 1190 1.9640159 1.9937501 0.49962311 6.7004634 + 1200 1.9616719 1.9932085 0.50320747 6.7253219 + 1210 1.9658831 1.9985624 0.50702861 6.7242078 + 1220 1.9790884 2.0132679 0.51100573 6.688483 + 1230 1.9946749 2.0324782 0.51491484 6.6422423 + 1240 2.0039182 2.0484588 0.5184382 6.6190292 + 1250 2.0033685 2.0545791 0.52130299 6.6322608 + 1260 1.9991533 2.0533011 0.52339221 6.6590872 + 1270 1.9969511 2.0571182 0.5246505 6.6789676 + 1280 1.9911353 2.0488281 0.52501304 6.7125634 + 1290 1.9712819 2.0209437 0.52460315 6.7967237 + 1300 1.9486195 1.9967749 0.5238106 6.886265 + 1310 1.951612 2.0051749 0.52294383 6.8723332 + 1320 1.9800953 2.0397207 0.52186525 6.7537937 + 1330 2.0084961 2.0723584 0.52001894 6.6279995 + 1340 2.021654 2.085105 0.51675149 6.554461 + 1350 2.0193685 2.0672662 0.5117514 6.5349176 + 1360 2.0084017 2.0471065 0.50518646 6.5453141 + 1370 1.994978 2.030683 0.49737164 6.5627932 + 1380 1.9781978 2.0044236 0.48871071 6.5903683 + 1390 1.9572368 1.9833426 0.47978207 6.6326472 + 1400 1.9400481 1.956474 0.47117436 6.6600696 + 1410 1.9380218 1.9552501 0.46336325 6.6314231 + 1420 1.9494747 1.9681145 0.45642218 6.5527615 + 1430 1.9610978 1.9824506 0.4501938 6.4763851 + 1440 1.9639503 1.9890985 0.44452289 6.4375535 + 1450 1.9560428 1.9821594 0.43936988 6.4453654 + 1460 1.9399344 1.9627639 0.43486138 6.488055 + 1470 1.9247229 1.9440629 0.43123378 6.5292381 + 1480 1.9213375 1.9369273 0.42866841 6.5271097 + 1490 1.9265729 1.9383637 0.42719968 6.4940959 + 1500 1.930987 1.9416689 0.4267225 6.4673585 + 1510 1.9303444 1.9418498 0.42714462 6.4648027 + 1520 1.9258423 1.940384 0.42844066 6.4834098 + 1530 1.9131202 1.9296653 0.4306338 6.5390881 + 1540 1.8990016 1.9101025 0.43386405 6.6052091 + 1550 1.9012878 1.9120047 0.43834036 6.6147792 + 1560 1.9153287 1.9388751 0.44404054 6.5851781 + 1570 1.9266928 1.9596147 0.45057056 6.5705776 + 1580 1.9358289 1.9745564 0.45744022 6.5674622 + 1590 1.9415248 1.9818707 0.46425451 6.5778534 + 1600 1.9466876 1.98498 0.47075833 6.5878483 + 1610 1.9557175 1.9930268 0.47674103 6.5777205 + 1620 1.9712902 2.0112337 0.48200984 6.5367922 + 1630 1.9900646 2.0303946 0.48631888 6.4790095 + 1640 1.9960901 2.039173 0.48947508 6.4661574 + 1650 1.9879046 2.0329046 0.49151173 6.504063 + 1660 1.9832967 2.0325843 0.49266284 6.5255647 + 1670 1.9875656 2.034783 0.49313513 6.5093662 + 1680 1.9967654 2.0492931 0.49299896 6.4699787 + 1690 2.0025957 2.0532539 0.49216931 6.4389613 + 1700 2.0022202 2.0424508 0.49070612 6.4276702 + 1710 2.0083188 2.0437945 0.48879489 6.3909243 + 1720 2.0178792 2.0439212 0.48646135 6.3411063 + 1730 2.0210944 2.0444299 0.48367905 6.3141106 + 1740 2.0170566 2.0337564 0.48044951 6.3158785 + 1750 2.0099049 2.0231598 0.47693196 6.3313851 + 1760 1.9990395 2.0132651 0.47329842 6.3631889 + 1770 1.9823237 1.9969291 0.46970233 6.4208124 + 1780 1.9640169 1.9798655 0.4663519 6.4879798 + 1790 1.9457657 1.9626633 0.46348315 6.557165 + 1800 1.9253222 1.9443136 0.46134123 6.6365286 + 1810 1.9123385 1.9339816 0.46011796 6.6879846 + 1820 1.9098744 1.9287702 0.45993599 6.7001355 + 1830 1.9096278 1.9220243 0.460898 6.7020982 + 1840 1.9223081 1.9378963 0.46303724 6.6558132 + 1850 1.9481113 1.9718786 0.46616351 6.5618175 + 1860 1.9704143 1.9931969 0.46987208 6.484088 + 1870 1.9864974 2.017655 0.47377416 6.4360445 + 1880 1.993165 2.0276398 0.47750238 6.4296162 + 1890 1.9852177 2.0249022 0.48088382 6.4843765 + 1900 1.9692398 2.0101062 0.4839255 6.5735477 + 1910 1.9516968 1.9893586 0.48689095 6.6692995 + 1920 1.9380452 1.9750949 0.49014596 6.7488323 + 1930 1.9323223 1.9719977 0.49399992 6.7947629 + 1940 1.9402144 1.9786701 0.49859677 6.7846787 + 1950 1.9589972 1.9956447 0.50392573 6.7291499 + 1960 1.979631 2.0201087 0.50984934 6.6648708 + 1970 2.0002749 2.0392081 0.51605302 6.6026647 + 1980 2.0143746 2.0524405 0.52221277 6.5687042 + 1990 2.0166553 2.0466885 0.5281276 6.5835144 + 2000 2.0130617 2.0424179 0.53381506 6.6234083 +Loop time of 0.33442 on 1 procs for 1000 steps with 2775 atoms + +Performance: 258357.633 tau/day, 2990.250 timesteps/s, 8.298 Matom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.19616 | 0.19616 | 0.19616 | 0.0 | 58.66 +Neigh | 0.023799 | 0.023799 | 0.023799 | 0.0 | 7.12 +Comm | 0.0022819 | 0.0022819 | 0.0022819 | 0.0 | 0.68 +Output | 0.0046967 | 0.0046967 | 0.0046967 | 0.0 | 1.40 +Modify | 0.10212 | 0.10212 | 0.10212 | 0.0 | 30.54 +Other | | 0.005366 | | | 1.60 + +Nlocal: 2775 ave 2775 max 2775 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 530 ave 530 max 530 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 24370 ave 24370 max 24370 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 24370 +Ave neighs/atom = 8.781982 +Neighbor list builds = 35 +Dangerous builds = 0 + +##################################################################### +#collect data + +#print the applied force and total flux to ensure conservation of Jx +variable Fapp equal f_GD[1] +compute vxBulk bulk reduce sum vx +compute vyBulk bulk reduce sum vy +variable invVol equal 1.0/(lx*ly) +variable jx equal c_vxBulk*${invVol} +variable jx equal c_vxBulk*0.00025 +variable jy equal c_vyBulk*${invVol} +variable jy equal c_vyBulk*0.00025 +variable curr_step equal step +variable p_Fapp format Fapp %.3f +variable p_jx format jx %.5g +variable p_jy format jy %.5g +fix print_vCOM all print ${dump_rate} "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy" +fix print_vCOM all print 50 "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy" + +#compute IK1 pressure profile +#see Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627 +#use profile-unbiased temperature to remove the streaming velocity +#from the kinetic part of the pressure +compute spa bulk stress/atom myTp + +#for the pressure profile, use the same grid as the PUT +compute chunkX bulk chunk/atom bin/1d x lower ${dX} units box +compute chunkX bulk chunk/atom bin/1d x lower 3.125 units box + +#output pressure profile and other profiles +#the pressure profile is (-1/2V)*(c_spa[1] + c_spa[2]), where +#V is the volume of a slice +fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite +fix profiles bulk ave/chunk 1 1 50 chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite + +#compute velocity profile across the pipe with a finer grid +variable dYnew equal ${dY}/10 +variable dYnew equal 3.07692307692308/10 +compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box region pipe +compute chunkY bulk chunk/atom bin/1d y center 0.307692307692308 units box region pipe +fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY vx file Vy_profile ave running overwrite +fix velYprof bulk ave/chunk 1 1 50 chunkY vx file Vy_profile ave running overwrite + +#full trajectory +# dump 7 bulk custom ${dump_rate} bulk.lammpstrj id type x y z +# dump_modify 7 sort id + +run ${run} +run 2000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 5.175 | 5.175 | 5.175 Mbytes + Step c_myT c_myTp TotEng Press + 2000 2.0130617 2.0424179 0.53381506 6.6234083 + 2010 2.011712 2.0399428 0.53937165 6.6546944 + 2020 2.0177252 2.0516588 0.54483848 6.6575988 + 2030 2.0192267 2.054258 0.55012466 6.6761208 + 2040 2.0155308 2.0513866 0.55518707 6.7132509 + 2050 2.016831 2.0539288 0.56007247 6.7306192 + 2060 2.0213378 2.0690043 0.56479732 6.7330132 + 2070 2.0292987 2.0799825 0.56913353 6.7186216 + 2080 2.0342188 2.0900923 0.57283821 6.7098434 + 2090 2.0376411 2.096351 0.57566175 6.6998818 + 2100 2.053128 2.1238481 0.57727694 6.637431 + 2110 2.0783941 2.1609599 0.5768993 6.5304031 + 2120 2.0887269 2.1760645 0.57341638 6.4706853 + 2130 2.06944 2.1522354 0.5659988 6.5099284 + 2140 2.0380605 2.115767 0.55466476 6.5802578 + 2150 2.0195872 2.0868424 0.54025148 6.5885111 + 2160 2.0061251 2.069266 0.52417244 6.5682875 + 2170 1.992682 2.0526743 0.50812177 6.5470052 + 2180 1.9816004 2.0352692 0.49354583 6.5244099 + 2190 1.9688265 2.0226679 0.4811848 6.5185172 + 2200 1.9574266 2.000155 0.47107703 6.5176047 + 2210 1.9502736 1.9925522 0.46298224 6.5078398 + 2220 1.9475332 1.9936032 0.45641728 6.4850252 + 2230 1.9545128 2.0045053 0.45087489 6.4291405 + 2240 1.9627871 2.0112148 0.44588526 6.3715676 + 2250 1.9617694 2.0073769 0.44121477 6.3541518 + 2260 1.9579423 2.0079137 0.43675541 6.3542735 + 2270 1.9475845 1.998983 0.43243494 6.3854071 + 2280 1.9253275 1.9715083 0.42839782 6.464845 + 2290 1.8996763 1.9456257 0.42496367 6.5591177 + 2300 1.8823546 1.9240543 0.42247729 6.6211062 + 2310 1.8844318 1.9216768 0.42116372 6.6085376 + 2320 1.8965287 1.933936 0.42103218 6.5584198 + 2330 1.902103 1.9433708 0.421956 6.5350698 + 2340 1.9061826 1.950462 0.42378825 6.5228738 + 2350 1.9180306 1.961141 0.42644522 6.489172 + 2360 1.9296124 1.9748542 0.42981448 6.4628168 + 2370 1.9328566 1.9718181 0.43373762 6.4721746 + 2380 1.9360042 1.9769998 0.43819906 6.4840942 + 2390 1.9387073 1.9778749 0.44317927 6.49778 + 2400 1.9445619 1.9882647 0.4486142 6.4971899 + 2410 1.9553344 1.9997412 0.45435544 6.4749774 + 2420 1.9710783 2.0211926 0.46019236 6.4320181 + 2430 1.9903873 2.046553 0.46575694 6.3751343 + 2440 2.0041158 2.0721071 0.47060398 6.3415121 + 2450 2.0020392 2.0728953 0.47431806 6.3708096 + 2460 1.9839851 2.0568906 0.47681718 6.465129 + 2470 1.9566365 2.0258852 0.47838596 6.5966256 + 2480 1.929674 2.0032606 0.47952215 6.7260074 + 2490 1.9153613 1.990031 0.48061628 6.8035919 + 2500 1.9188373 1.9920514 0.4819225 6.8075788 + 2510 1.9371656 2.0138698 0.48343533 6.7492701 + 2520 1.9566481 2.0340995 0.48485699 6.6821181 + 2530 1.9636141 2.0389496 0.48583392 6.6581326 + 2540 1.9585172 2.0207113 0.48622314 6.6762792 + 2550 1.9516934 2.0024186 0.48621721 6.6980104 + 2560 1.9509543 1.9960852 0.48612286 6.6946311 + 2570 1.9601672 2.0072552 0.48602872 6.6528934 + 2580 1.973804 2.0230879 0.48576601 6.5942862 + 2590 1.9788378 2.034436 0.48505027 6.5689819 + 2600 1.9716493 2.0208578 0.48368043 6.5897554 + 2610 1.9618006 2.007098 0.48174365 6.6188626 + 2620 1.9631458 2.0075461 0.4793429 6.6026194 + 2630 1.9706918 2.0174955 0.47638698 6.5591053 + 2640 1.9759585 2.0213828 0.47264742 6.5198595 + 2650 1.9761708 2.0225139 0.46794373 6.4977306 + 2660 1.9611574 2.0083871 0.46221598 6.5299021 + 2670 1.9342882 1.9720247 0.45576624 6.6034695 + 2680 1.9142009 1.9520382 0.44913109 6.6474082 + 2690 1.9052096 1.9428107 0.4426988 6.645123 + 2700 1.902446 1.9459937 0.43672046 6.6152926 + 2710 1.9099036 1.9594727 0.43120889 6.5473804 + 2720 1.9180788 1.9767479 0.42599739 6.4792536 + 2730 1.9142892 1.9798275 0.42092791 6.4604982 + 2740 1.9019844 1.9674244 0.41601841 6.4795855 + 2750 1.8895632 1.958412 0.41144638 6.5037424 + 2760 1.8824401 1.9494985 0.40739848 6.5113925 + 2770 1.8852759 1.9525073 0.40398809 6.484535 + 2780 1.8998168 1.9664907 0.40114076 6.4159782 + 2790 1.9153937 1.9810349 0.39863439 6.346934 + 2800 1.9162707 1.9824285 0.39627973 6.3364828 + 2810 1.9087999 1.9666258 0.39408314 6.360755 + 2820 1.9073152 1.956153 0.39226387 6.3655719 + 2830 1.9091743 1.9493705 0.39098546 6.3595054 + 2840 1.9042021 1.9424118 0.39036698 6.381752 + 2850 1.8901401 1.9353495 0.39057524 6.4417859 + 2860 1.872943 1.915215 0.39190057 6.5158585 + 2870 1.8732626 1.9181551 0.39474702 6.5269257 + 2880 1.8931021 1.9396049 0.39938934 6.467715 + 2890 1.9217069 1.9733171 0.40581935 6.3811936 + 2900 1.9452213 1.9949806 0.41374968 6.3217226 + 2910 1.9591065 2.0105363 0.42280483 6.3087055 + 2920 1.9649158 2.0234068 0.43256139 6.3353204 + 2930 1.9647653 2.0265233 0.4425691 6.3902862 + 2940 1.9623876 2.0281154 0.45237409 6.4560778 + 2950 1.9591057 2.0276078 0.46164197 6.5239614 + 2960 1.9556907 2.0254377 0.47016674 6.5883236 + 2970 1.9524475 2.0203546 0.47782337 6.6457078 + 2980 1.9556442 2.0212175 0.48459527 6.6731473 + 2990 1.9663638 2.0285202 0.49047217 6.667322 + 3000 1.976263 2.0326354 0.49540098 6.6601492 + 3010 1.9734917 2.0251301 0.49938916 6.6970878 + 3020 1.955368 1.9974693 0.50265656 6.7865104 + 3030 1.9476644 1.9780945 0.50564273 6.8327176 + 3040 1.9584769 1.9887952 0.50867872 6.8046262 + 3050 1.9705616 2.0030557 0.51168699 6.7669575 + 3060 1.9766986 2.0112576 0.51444822 6.74919 + 3070 1.9766671 2.0076853 0.51685838 6.7523339 + 3080 1.9763383 2.0045916 0.51896849 6.7532253 + 3090 1.9855877 2.0260371 0.52081442 6.7160131 + 3100 2.0011042 2.042205 0.52215192 6.653598 + 3110 2.0039819 2.0511266 0.52275172 6.6355885 + 3120 1.9958773 2.0457899 0.52253307 6.6565817 + 3130 1.9933925 2.04521 0.52158082 6.6543706 + 3140 1.9936643 2.0477262 0.51996279 6.639564 + 3150 1.9921223 2.0455965 0.51768794 6.6291901 + 3160 1.9914788 2.0365842 0.51483187 6.6154874 + 3170 1.9922866 2.0422451 0.51144092 6.5976334 + 3180 1.9872806 2.0376593 0.50747923 6.6043774 + 3190 1.9708577 2.0198422 0.50308657 6.6551127 + 3200 1.9534272 1.9982319 0.49857904 6.7093718 + 3210 1.9423425 1.9876311 0.49429833 6.7370529 + 3220 1.941974 1.984738 0.49043179 6.7218879 + 3230 1.9456357 1.9916666 0.48697785 6.6917144 + 3240 1.9392412 1.9874858 0.48388805 6.7004046 + 3250 1.9312152 1.9814714 0.4812083 6.7175714 + 3260 1.9364393 1.9840125 0.47897357 6.6870787 + 3270 1.9490184 1.9871802 0.47715672 6.6308261 + 3280 1.9578901 1.9917218 0.47568803 6.589659 + 3290 1.9598612 1.9918098 0.47449561 6.5756965 + 3300 1.9538424 1.9845316 0.47357576 6.5931068 + 3310 1.944957 1.9676243 0.47302774 6.6211221 + 3320 1.9479975 1.9720828 0.47296613 6.6058089 + 3330 1.9569283 1.98719 0.47330356 6.5698601 + 3340 1.9558114 1.9861834 0.47383928 6.5729191 + 3350 1.9461606 1.9777192 0.47452365 6.6090135 + 3360 1.942095 1.9776297 0.47540879 6.6255417 + 3370 1.9482423 1.981145 0.47643851 6.6032207 + 3380 1.9564098 1.992645 0.47752314 6.5736007 + 3390 1.9607986 2.0006048 0.47852085 6.5587348 + 3400 1.9595637 2.0047228 0.47933656 6.5656692 + 3410 1.9628181 2.013785 0.47991082 6.5570579 + 3420 1.9698466 2.0200788 0.48018617 6.536373 + 3430 1.969877 2.0210764 0.48013786 6.543084 + 3440 1.96327 2.0103631 0.47979187 6.5761448 + 3450 1.9566516 1.9996494 0.47933398 6.6098616 + 3460 1.9511915 1.9976175 0.47891646 6.6401481 + 3470 1.9410601 1.9950284 0.47859124 6.6862584 + 3480 1.9307395 1.98193 0.47840998 6.7307929 + 3490 1.9206678 1.9678856 0.47853003 6.7702613 + 3500 1.9139405 1.955324 0.47914241 6.7934071 + 3510 1.9206383 1.957176 0.48041531 6.763312 + 3520 1.9449301 1.9816996 0.4823109 6.6651453 + 3530 1.9752924 2.0115126 0.48452681 6.5438659 + 3540 1.9951599 2.037759 0.48660439 6.463461 + 3550 2.00071 2.0413872 0.48813252 6.4405933 + 3560 1.9939017 2.0277566 0.48901382 6.4684771 + 3570 1.9766844 2.0031366 0.48946452 6.5392906 + 3580 1.9600495 1.9790718 0.48988281 6.6106541 + 3590 1.9522334 1.9727673 0.49062615 6.6517495 + 3600 1.9522007 1.9829458 0.49183552 6.6635632 + 3610 1.9614098 1.9992781 0.49340617 6.6407777 + 3620 1.9739926 2.0159629 0.49511752 6.6062456 + 3630 1.9726539 2.0152219 0.49675445 6.6254361 + 3640 1.9613098 2.0017247 0.49829011 6.6828523 + 3650 1.9577727 2.0000723 0.49991877 6.7111788 + 3660 1.9626403 2.0037309 0.50175296 6.7072182 + 3670 1.9603974 1.9937256 0.50383808 6.7277464 + 3680 1.9532611 1.9846903 0.50638428 6.766139 + 3690 1.9541656 1.9798331 0.50962883 6.7752527 + 3700 1.9656726 1.9951191 0.51377056 6.7462001 + 3710 1.9834474 2.0193011 0.5187681 6.6957856 + 3720 2.0017372 2.0396413 0.52433682 6.6470375 + 3730 2.0109702 2.0469463 0.53011728 6.6363717 + 3740 2.0096859 2.0458572 0.53588234 6.6682277 + 3750 2.0066189 2.0519843 0.54153099 6.7085484 + 3760 2.0096126 2.0561094 0.54689937 6.7250788 + 3770 2.0117777 2.0668795 0.55183559 6.7400961 + 3780 2.0154601 2.0763941 0.55607392 6.7423369 + 3790 2.0313954 2.0972106 0.55930714 6.6920109 + 3800 2.0496133 2.1176374 0.56110467 6.6271089 + 3810 2.0553084 2.1205041 0.56098738 6.6034667 + 3820 2.0478771 2.1131255 0.5587031 6.6239895 + 3830 2.0342107 2.0991257 0.55418078 6.6632309 + 3840 2.0142205 2.0767164 0.5475632 6.7196407 + 3850 1.9879527 2.0516847 0.53919956 6.7932756 + 3860 1.9593315 2.0232738 0.52966135 6.8686984 + 3870 1.9362884 1.9952027 0.51970091 6.9156688 + 3880 1.9292997 1.988308 0.50996281 6.8957697 + 3890 1.9372437 1.9978667 0.50073928 6.8160964 + 3900 1.949918 2.0107188 0.49208883 6.7186535 + 3910 1.9547594 2.0160936 0.48397839 6.6537347 + 3920 1.9543568 2.0191268 0.47640162 6.6136066 + 3930 1.9582199 2.020036 0.46933873 6.5629723 + 3940 1.9644632 2.0304626 0.4627222 6.5077173 + 3950 1.9645883 2.030183 0.45644411 6.4795254 + 3960 1.9546999 2.0197243 0.45050582 6.4943661 + 3970 1.9424307 2.0063453 0.44500624 6.5237706 + 3980 1.9281472 1.9910524 0.44010499 6.5640156 + 3990 1.9168821 1.976369 0.43594016 6.592621 + 4000 1.9150056 1.9752502 0.43256473 6.5855641 +Loop time of 0.696491 on 1 procs for 2000 steps with 2775 atoms + +Performance: 248100.709 tau/day, 2871.536 timesteps/s, 7.969 Matom-step/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.39664 | 0.39664 | 0.39664 | 0.0 | 56.95 +Neigh | 0.051502 | 0.051502 | 0.051502 | 0.0 | 7.39 +Comm | 0.0047546 | 0.0047546 | 0.0047546 | 0.0 | 0.68 +Output | 0.0095092 | 0.0095092 | 0.0095092 | 0.0 | 1.37 +Modify | 0.22322 | 0.22322 | 0.22322 | 0.0 | 32.05 +Other | | 0.01087 | | | 1.56 + +Nlocal: 2775 ave 2775 max 2775 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 24313 ave 24313 max 24313 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 24313 +Ave neighs/atom = 8.7614414 +Neighbor list builds = 75 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/flow_gauss/log.6Dec23.GD.g++.4 b/examples/PACKAGES/flow_gauss/log.6Dec23.GD.g++.4 new file mode 100644 index 00000000000..089e8d003de --- /dev/null +++ b/examples/PACKAGES/flow_gauss/log.6Dec23.GD.g++.4 @@ -0,0 +1,941 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +#LAMMPS input script +#in.GD +#see README for details + +############################################################################### +#initialize variables +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task + +#frequency for outputting info (timesteps) +variable dump_rate equal 50 +variable thermo_rate equal 10 + +#equilibration time (timesteps) +variable equil equal 1000 + +#stabilization time (timesteps to reach steady-state) +variable stabil equal 1000 + +#data collection time (timesteps) +variable run equal 2000 + +#length of pipe +variable L equal 30 + +#width of pipe +variable d equal 20 + +#flux (mass/sigma*tau) +variable J equal 0.1 + +#simulation box dimensions +variable Lx equal 100 +variable Ly equal 40 + +#bulk fluid density +variable dens equal 0.8 + +#lattice spacing for wall atoms +variable aWall equal 1.0 #1.7472 + +#timestep +variable ts equal 0.001 + +#temperature +variable T equal 2.0 + +#thermostat damping constant +variable tdamp equal ${ts}*100 +variable tdamp equal 0.001*100 + +units lj +dimension 2 +atom_style atomic + + +############################################################################### +#create box + +#create lattice with the spacing aWall +variable rhoWall equal ${aWall}^(-2) +variable rhoWall equal 1^(-2) +lattice sq ${rhoWall} +lattice sq 1 +Lattice spacing in x,y,z = 1 1 1 + +#modify input dimensions to be multiples of aWall +variable L1 equal round($L/${aWall})*${aWall} +variable L1 equal round(30/${aWall})*${aWall} +variable L1 equal round(30/1)*${aWall} +variable L1 equal round(30/1)*1 +variable d1 equal round($d/${aWall})*${aWall} +variable d1 equal round(20/${aWall})*${aWall} +variable d1 equal round(20/1)*${aWall} +variable d1 equal round(20/1)*1 +variable Ly1 equal round(${Ly}/${aWall})*${aWall} +variable Ly1 equal round(40/${aWall})*${aWall} +variable Ly1 equal round(40/1)*${aWall} +variable Ly1 equal round(40/1)*1 +variable Lx1 equal round(${Lx}/${aWall})*${aWall} +variable Lx1 equal round(100/${aWall})*${aWall} +variable Lx1 equal round(100/1)*${aWall} +variable Lx1 equal round(100/1)*1 + +#create simulation box +variable lx2 equal ${Lx1}/2 +variable lx2 equal 100/2 +variable ly2 equal ${Ly1}/2 +variable ly2 equal 40/2 +region simbox block -${lx2} ${lx2} -${ly2} ${ly2} -0.1 0.1 units box +region simbox block -50 ${lx2} -${ly2} ${ly2} -0.1 0.1 units box +region simbox block -50 50 -${ly2} ${ly2} -0.1 0.1 units box +region simbox block -50 50 -20 ${ly2} -0.1 0.1 units box +region simbox block -50 50 -20 20 -0.1 0.1 units box +create_box 2 simbox +Created orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + 4 by 1 by 1 MPI processor grid + +##################################################################### +#set up potential + +mass 1 1.0 #fluid atoms +mass 2 1.0 #wall atoms + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 1.12246 +pair_coeff 2 2 0.0 0.0 + +neigh_modify exclude type 2 2 + +timestep ${ts} +timestep 0.001 + +##################################################################### +#create atoms + +#create wall atoms everywhere +create_atoms 2 box +Created 4000 atoms + using lattice units in orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + create_atoms CPU = 0.000 seconds + +#define region which is "walled off" +variable dhalf equal ${d1}/2 +variable dhalf equal 20/2 +variable Lhalf equal ${L1}/2 +variable Lhalf equal 30/2 +region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box +region walltop block -15 ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box +region walltop block -15 15 ${dhalf} EDGE -0.1 0.1 units box +region walltop block -15 15 10 EDGE -0.1 0.1 units box +region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box +region wallbot block -15 ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box +region wallbot block -15 15 EDGE -${dhalf} -0.1 0.1 units box +region wallbot block -15 15 EDGE -10 -0.1 0.1 units box +region outsidewall union 2 walltop wallbot side out + +#remove wall atoms outside wall region +group outside region outsidewall +3349 atoms in group outside +delete_atoms group outside +Deleted 3349 atoms, new total = 651 + +#remove wall atoms that aren't on edge of wall region +variable x1 equal ${Lhalf}-${aWall} +variable x1 equal 15-${aWall} +variable x1 equal 15-1 +variable y1 equal ${dhalf}+${aWall} +variable y1 equal 10+${aWall} +variable y1 equal 10+1 +region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box +region insideTop block -14 ${x1} ${y1} EDGE -0.1 0.1 units box +region insideTop block -14 14 ${y1} EDGE -0.1 0.1 units box +region insideTop block -14 14 11 EDGE -0.1 0.1 units box +region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box +region insideBot block -14 ${x1} EDGE -${y1} -0.1 0.1 units box +region insideBot block -14 14 EDGE -${y1} -0.1 0.1 units box +region insideBot block -14 14 EDGE -11 -0.1 0.1 units box +region insideWall union 2 insideTop insideBot +group insideWall region insideWall +551 atoms in group insideWall +delete_atoms group insideWall +Deleted 551 atoms, new total = 100 + +#define new lattice, to give correct fluid density +#y lattice const must be a multiple of aWall +variable atrue equal ${dens}^(-1/2) +variable atrue equal 0.8^(-1/2) +variable ay equal round(${atrue}/${aWall})*${aWall} +variable ay equal round(1.11803398874989/${aWall})*${aWall} +variable ay equal round(1.11803398874989/1)*${aWall} +variable ay equal round(1.11803398874989/1)*1 + +#choose x lattice const to give correct density +variable ax equal (${ay}*${dens})^(-1) +variable ax equal (1*${dens})^(-1) +variable ax equal (1*0.8)^(-1) + +#change Lx to be multiple of ax +variable Lx1 equal round(${Lx}/${ax})*${ax} +variable Lx1 equal round(100/${ax})*${ax} +variable Lx1 equal round(100/1.25)*${ax} +variable Lx1 equal round(100/1.25)*1.25 +variable lx2 equal ${Lx1}/2 +variable lx2 equal 100/2 +change_box all x final -${lx2} ${lx2} units box +change_box all x final -50 ${lx2} units box +change_box all x final -50 50 units box +Changing box ... + orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + +#define new lattice +lattice custom ${dens} a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 +lattice custom 0.8 a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 +lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 +lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 1 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 +Lattice spacing in x,y,z = 1.25 1 1 + +#fill in rest of box with bulk particles +variable delta equal 0.001 +variable Ldelt equal ${Lhalf}+${delta} +variable Ldelt equal 15+${delta} +variable Ldelt equal 15+0.001 +variable dDelt equal ${dhalf}-${delta} +variable dDelt equal 10-${delta} +variable dDelt equal 10-0.001 +region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box +region left block EDGE -15.001 EDGE EDGE -0.1 0.1 units box +region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box +region right block 15.001 EDGE EDGE EDGE -0.1 0.1 units box +region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box +region pipe block -15.001 ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box +region pipe block -15.001 15.001 -${dDelt} ${dDelt} -0.1 0.1 units box +region pipe block -15.001 15.001 -9.999 ${dDelt} -0.1 0.1 units box +region pipe block -15.001 15.001 -9.999 9.999 -0.1 0.1 units box + +region bulk union 3 left pipe right +create_atoms 1 region bulk +Created 2675 atoms + using lattice units in orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + create_atoms CPU = 0.000 seconds + +group bulk type 1 +2675 atoms in group bulk +group wall type 2 +100 atoms in group wall + +#remove atoms that are too close to wall +delete_atoms overlap 0.9 bulk wall +System init for delete_atoms ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 72 29 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command delete_atoms, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Deleted 0 atoms, new total = 2775 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes +neigh_modify exclude group wall wall + +velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom +velocity bulk create 2 78915 dist gaussian rot yes mom yes loop geom + +##################################################################### +#set up PUT +#see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172 + +#average number of particles per box, Evans and Morriss used 2.0 +variable NperBox equal 8.0 + +#calculate box sizes +variable boxSide equal sqrt(${NperBox}/${dens}) +variable boxSide equal sqrt(8/${dens}) +variable boxSide equal sqrt(8/0.8) +variable nX equal round(lx/${boxSide}) +variable nX equal round(lx/3.16227766016838) +variable nY equal round(ly/${boxSide}) +variable nY equal round(ly/3.16227766016838) +variable dX equal lx/${nX} +variable dX equal lx/32 +variable dY equal ly/${nY} +variable dY equal ly/13 + +#temperature of fluid (excluding wall) +compute myT bulk temp + +#profile-unbiased temperature of fluid +compute myTp bulk temp/profile 1 1 0 xy ${nX} ${nY} +compute myTp bulk temp/profile 1 1 0 xy 32 ${nY} +compute myTp bulk temp/profile 1 1 0 xy 32 13 + +#thermo setup +thermo ${thermo_rate} +thermo 10 +thermo_style custom step c_myT c_myTp etotal press + +#dump initial configuration +# dump 55 all custom 1 all.init.lammpstrj id type x y z vx vy vz +# dump 56 wall custom 1 wall.init.lammpstrj id type x y z +# dump_modify 55 sort id +# dump_modify 56 sort id +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 72 29 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.068 | 3.069 | 3.071 Mbytes + Step c_myT c_myTp TotEng Press + 0 2 2.054601 0.77892922 7.3417096 +Loop time of 1.90125e-06 on 4 procs for 0 steps with 2775 atoms + +26.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.901e-06 | | |100.00 + +Nlocal: 693.75 ave 800 max 578 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 266.25 ave 325 max 198 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 6601.5 ave 8000 max 5147 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 26406 +Ave neighs/atom = 9.5156757 +Neighbor list builds = 0 +Dangerous builds = 0 +# undump 55 +# undump 56 + +##################################################################### +#equilibrate without GD + +fix nvt bulk nvt temp $T $T ${tdamp} +fix nvt bulk nvt temp 2 $T ${tdamp} +fix nvt bulk nvt temp 2 2 ${tdamp} +fix nvt bulk nvt temp 2 2 0.1 +fix_modify nvt temp myTp +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1391) +fix 2 bulk enforce2d + +run ${equil} +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.131 | 3.132 | 3.133 Mbytes + Step c_myT c_myTp TotEng Press + 0 2 2.054601 0.77892922 7.3417096 + 10 1.9173668 1.9381538 0.77877698 7.6702283 + 20 1.7033651 1.6967466 0.7798044 8.5615039 + 30 1.5026644 1.4718046 0.78461914 9.4308883 + 40 1.4881235 1.4586031 0.79494919 9.6135307 + 50 1.6193439 1.6144665 0.81119835 9.2594114 + 60 1.7405127 1.7576881 0.82966956 8.9525458 + 70 1.7758506 1.7999706 0.84538866 8.9719793 + 80 1.7574736 1.7806782 0.85780732 9.1938511 + 90 1.7492232 1.7720284 0.86895259 9.3714617 + 100 1.7800292 1.807315 0.88044504 9.3874107 + 110 1.8442295 1.878681 0.89278276 9.2585436 + 120 1.9193695 1.9667163 0.90556381 9.0683654 + 130 1.9885753 2.0478097 0.91782871 8.8815507 + 140 2.04662 2.1105827 0.92850319 8.718882 + 150 2.0957046 2.1672706 0.93677238 8.5718869 + 160 2.144595 2.2210801 0.94188484 8.4089161 + 170 2.1802133 2.2626399 0.9429713 8.2775682 + 180 2.1868284 2.2696504 0.93931537 8.2321283 + 190 2.1838369 2.2706873 0.93069783 8.1970105 + 200 2.1943436 2.2865542 0.91717737 8.0854148 + 210 2.2029439 2.2912731 0.89906796 7.9589187 + 220 2.1891494 2.2768232 0.87764254 7.9016509 + 230 2.1677848 2.2493747 0.85497463 7.8690125 + 240 2.156695 2.2377486 0.83255207 7.8020978 + 250 2.142758 2.2237662 0.81090722 7.7510242 + 260 2.1177881 2.1967699 0.79016944 7.7477503 + 270 2.0862408 2.1669583 0.77040874 7.7740216 + 280 2.0676515 2.1446262 0.75157955 7.7544068 + 290 2.0645498 2.1425534 0.73343008 7.6746729 + 300 2.0563664 2.1358776 0.71562279 7.6114783 + 310 2.0390115 2.1198472 0.69809211 7.581719 + 320 2.0209035 2.1063385 0.68093855 7.5540946 + 330 2.012488 2.1037583 0.66418283 7.4896097 + 340 2.0166095 2.1094212 0.64762479 7.3779677 + 350 2.0172861 2.1072653 0.63109595 7.2807114 + 360 2.0065768 2.0803788 0.6147802 7.2283814 + 370 1.9970858 2.0639903 0.59905362 7.1747592 + 380 1.9925189 2.056563 0.58395055 7.103506 + 390 1.9935388 2.0546596 0.56945318 7.010305 + 400 2.0020199 2.0632095 0.55532013 6.8883647 + 410 2.009157 2.0732883 0.54128082 6.771521 + 420 2.0081687 2.0785184 0.52711525 6.6868076 + 430 1.9990498 2.0705469 0.51283203 6.6343482 + 440 1.9891528 2.0586814 0.4986104 6.5888679 + 450 1.9829175 2.0465778 0.4846738 6.5332233 + 460 1.9745599 2.031067 0.4711878 6.4903915 + 470 1.9581101 2.006674 0.45837961 6.4836654 + 480 1.9367964 1.9732882 0.44656667 6.501731 + 490 1.9258333 1.9561395 0.43605676 6.4879447 + 500 1.9287 1.9571319 0.42678362 6.4296036 + 510 1.9274696 1.9569118 0.41856553 6.3949919 + 520 1.9100149 1.9392424 0.41134511 6.4307452 + 530 1.8827127 1.9059412 0.40536565 6.5126603 + 540 1.8660696 1.8912024 0.40096324 6.5610607 + 550 1.8701883 1.9043254 0.3982457 6.536251 + 560 1.8842923 1.9289528 0.39698123 6.4785367 + 570 1.8906147 1.9462124 0.39684504 6.4547374 + 580 1.8895472 1.9472747 0.39763233 6.4630103 + 590 1.895375 1.9551336 0.39926725 6.449517 + 600 1.9115711 1.9737109 0.40163655 6.3995241 + 610 1.92823 1.9851787 0.404506 6.3499339 + 620 1.9360678 1.9889572 0.40767569 6.3367514 + 630 1.9346853 1.9836719 0.41105958 6.3637995 + 640 1.9266095 1.9757908 0.41472954 6.4212842 + 650 1.9213863 1.9719496 0.41879537 6.4707692 + 660 1.922962 1.9702923 0.42332926 6.4949933 + 670 1.9238956 1.9707534 0.42836303 6.5212631 + 680 1.9212675 1.9740379 0.43388709 6.5608915 + 690 1.9210314 1.976311 0.43982007 6.5904702 + 700 1.928081 1.9868449 0.44610463 6.5915021 + 710 1.9428895 2.0044235 0.45257857 6.5616141 + 720 1.9554783 2.0176139 0.45898384 6.5367529 + 730 1.969838 2.0327907 0.46505662 6.5017635 + 740 1.9840204 2.0467126 0.47058703 6.4649226 + 750 1.9946633 2.0526929 0.47535832 6.4399342 + 760 2.0018048 2.0535606 0.47924291 6.4280737 + 770 1.9991703 2.0483426 0.48222842 6.4537535 + 780 1.9850797 2.0312444 0.48443072 6.5234271 + 790 1.9691589 2.0154006 0.4861158 6.5995894 + 800 1.9612641 2.0031407 0.48754831 6.6430968 + 810 1.9637155 2.0074142 0.48891261 6.6444644 + 820 1.9691691 2.0110229 0.49018604 6.6304512 + 830 1.9763962 2.0190998 0.49130448 6.6060594 + 840 1.9908278 2.0352615 0.49213189 6.5510683 + 850 2.0105715 2.0558403 0.49238435 6.4743276 + 860 2.0227982 2.0645732 0.49173076 6.4260863 + 870 2.015555 2.064081 0.48998228 6.4528588 + 880 1.9889672 2.0320831 0.48722022 6.5532269 + 890 1.9632172 2.0025881 0.48392295 6.6494723 + 900 1.9527429 1.9887196 0.48054642 6.6846937 + 910 1.9567815 1.9953408 0.47726539 6.6606541 + 920 1.9666996 2.0084955 0.47397593 6.6100666 + 930 1.9702885 2.014774 0.47048741 6.5805871 + 940 1.9661802 2.0116846 0.46671831 6.579539 + 950 1.9576953 1.9960728 0.46273983 6.5967841 + 960 1.9428073 1.9802284 0.45879028 6.6395002 + 970 1.9256011 1.9584581 0.45515059 6.6916425 + 980 1.913512 1.9478848 0.45214528 6.7233279 + 990 1.9174938 1.9449699 0.44994026 6.6943867 + 1000 1.9365527 1.9663901 0.44852349 6.6101761 +Loop time of 0.136245 on 4 procs for 1000 steps with 2775 atoms + +Performance: 634150.810 tau/day, 7339.708 timesteps/s, 20.368 Matom-step/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.05652 | 0.058835 | 0.061144 | 0.7 | 43.18 +Neigh | 0.0077706 | 0.0082387 | 0.0086435 | 0.4 | 6.05 +Comm | 0.0079304 | 0.010631 | 0.013709 | 2.5 | 7.80 +Output | 0.003516 | 0.0036313 | 0.0038326 | 0.2 | 2.67 +Modify | 0.045283 | 0.048616 | 0.052008 | 1.3 | 35.68 +Other | | 0.006293 | | | 4.62 + +Nlocal: 693.75 ave 800 max 584 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 255.25 ave 323 max 192 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 6083 ave 7383 max 4741 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 24332 +Ave neighs/atom = 8.7682883 +Neighbor list builds = 38 +Dangerous builds = 0 + +##################################################################### +#initialize the COM velocity and run to achieve steady-state + +#calculate velocity to add: V=J/rho_total +variable Vadd equal $J*lx*ly/count(bulk) +variable Vadd equal 0.1*lx*ly/count(bulk) + +#first remove any COM velocity, then add back the streaming velocity +velocity bulk zero linear +velocity bulk set ${Vadd} 0.0 0.0 units box sum yes mom no +velocity bulk set 0.149532710280374 0.0 0.0 units box sum yes mom no + +fix GD bulk flow/gauss 1 0 0 #energy yes +#fix_modify GD energy yes + +run ${stabil} +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Gaussian dynamics package: doi:10.1021/acs.jpcb.6b09387 + +@Article{strong_water_2017, +title = {The Dynamics of Water in Porous Two-Dimensional Crystals}, +volume = {121}, +number = {1}, +url = {https://doi.org/10.1021/acs.jpcb.6b09387}, +doi = {10.1021/acs.jpcb.6b09387}, +urldate = {2016-12-07}, +journal = {J.~Phys.\ Chem.~B}, +author = {Strong, Steven E. and Eaves, Joel D.}, +year = {2017}, +pages = {189--207} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.131 | 3.132 | 3.133 Mbytes + Step c_myT c_myTp TotEng Press + 1000 1.9477212 1.9663901 0.45928547 6.6176422 + 1010 1.9617328 1.9828061 0.45840963 6.555968 + 1020 1.9570976 1.9825696 0.45782895 6.5690613 + 1030 1.9356292 1.9690101 0.45753984 6.6493822 + 1040 1.9174914 1.9448868 0.4577768 6.7171474 + 1050 1.9202482 1.9432766 0.4588733 6.7039634 + 1060 1.9419998 1.9718217 0.46086407 6.617366 + 1070 1.9666048 1.996346 0.46339522 6.5207175 + 1080 1.9775489 2.0078489 0.46608862 6.4794239 + 1090 1.9725172 2.0005028 0.46876174 6.5044299 + 1100 1.9659582 1.9931537 0.47147394 6.5409107 + 1110 1.9670607 1.9965504 0.47432892 6.5527414 + 1120 1.9716302 1.9984924 0.47732198 6.5530022 + 1130 1.9752703 2.0057031 0.48043914 6.5579379 + 1140 1.976368 2.0061152 0.48358744 6.5719123 + 1150 1.9748014 2.0056689 0.48673155 6.5957896 + 1160 1.9729115 2.0036854 0.48986563 6.6200102 + 1170 1.9702742 2.0016461 0.49302426 6.6455948 + 1180 1.9680418 1.9978705 0.49625385 6.6697165 + 1190 1.9640159 1.9937501 0.49962311 6.7004634 + 1200 1.9616719 1.9932085 0.50320747 6.7253219 + 1210 1.9658831 1.9985624 0.50702861 6.7242078 + 1220 1.9790884 2.0132679 0.51100573 6.688483 + 1230 1.9946749 2.0324782 0.51491484 6.6422423 + 1240 2.0039182 2.0484588 0.5184382 6.6190292 + 1250 2.0033685 2.0545791 0.52130299 6.6322608 + 1260 1.9991533 2.0533011 0.52339221 6.6590872 + 1270 1.9969511 2.0571182 0.5246505 6.6789676 + 1280 1.9911353 2.0488281 0.52501304 6.7125634 + 1290 1.9712819 2.0209437 0.52460315 6.7967237 + 1300 1.9486195 1.9967749 0.5238106 6.886265 + 1310 1.951612 2.0051749 0.52294383 6.8723332 + 1320 1.9800953 2.0397207 0.52186525 6.7537937 + 1330 2.0084961 2.0723584 0.52001894 6.6279995 + 1340 2.021654 2.085105 0.51675149 6.554461 + 1350 2.0193685 2.0672662 0.5117514 6.5349176 + 1360 2.0084017 2.0471065 0.50518646 6.5453141 + 1370 1.994978 2.030683 0.49737164 6.5627932 + 1380 1.9781978 2.0044236 0.48871071 6.5903683 + 1390 1.9572368 1.9833426 0.47978207 6.6326472 + 1400 1.9400481 1.956474 0.47117436 6.6600696 + 1410 1.9380218 1.9552501 0.46336325 6.6314231 + 1420 1.9494747 1.9681145 0.45642218 6.5527615 + 1430 1.9610978 1.9824506 0.4501938 6.4763851 + 1440 1.9639503 1.9890985 0.44452289 6.4375535 + 1450 1.9560428 1.9821594 0.43936988 6.4453654 + 1460 1.9399344 1.9627639 0.43486138 6.488055 + 1470 1.9247229 1.9440629 0.43123378 6.5292381 + 1480 1.9213375 1.9369273 0.42866841 6.5271097 + 1490 1.9265729 1.9383637 0.42719968 6.4940959 + 1500 1.930987 1.9416689 0.4267225 6.4673585 + 1510 1.9303444 1.9418498 0.42714462 6.4648027 + 1520 1.9258423 1.940384 0.42844066 6.4834098 + 1530 1.9131202 1.9296653 0.4306338 6.5390881 + 1540 1.8990016 1.9101025 0.43386405 6.6052091 + 1550 1.9012878 1.9120047 0.43834036 6.6147792 + 1560 1.9153287 1.9388751 0.44404054 6.5851781 + 1570 1.9266928 1.9596147 0.45057056 6.5705776 + 1580 1.9358289 1.9745564 0.45744022 6.5674622 + 1590 1.9415248 1.9818707 0.46425451 6.5778534 + 1600 1.9466876 1.98498 0.47075833 6.5878483 + 1610 1.9557175 1.9930268 0.47674103 6.5777205 + 1620 1.9712902 2.0112337 0.48200984 6.5367922 + 1630 1.9900646 2.0303946 0.48631888 6.4790095 + 1640 1.9960901 2.039173 0.48947508 6.4661574 + 1650 1.9879046 2.0329046 0.49151173 6.504063 + 1660 1.9832967 2.0325843 0.49266284 6.5255647 + 1670 1.9875656 2.034783 0.49313513 6.5093662 + 1680 1.9967654 2.0492931 0.49299896 6.4699787 + 1690 2.0025957 2.0532539 0.49216931 6.4389613 + 1700 2.0022202 2.0424508 0.49070612 6.4276702 + 1710 2.0083188 2.0437945 0.48879489 6.3909243 + 1720 2.0178792 2.0439212 0.48646135 6.3411063 + 1730 2.0210944 2.0444299 0.48367905 6.3141106 + 1740 2.0170566 2.0337564 0.48044951 6.3158785 + 1750 2.0099049 2.0231598 0.47693196 6.3313851 + 1760 1.9990395 2.0132651 0.47329842 6.3631889 + 1770 1.9823237 1.9969291 0.46970233 6.4208124 + 1780 1.9640169 1.9798655 0.4663519 6.4879798 + 1790 1.9457657 1.9626633 0.46348315 6.557165 + 1800 1.9253222 1.9443136 0.46134123 6.6365286 + 1810 1.9123385 1.9339816 0.46011796 6.6879846 + 1820 1.9098744 1.9287702 0.45993599 6.7001355 + 1830 1.9096278 1.9220243 0.460898 6.7020982 + 1840 1.9223081 1.9378963 0.46303724 6.6558132 + 1850 1.9481113 1.9718786 0.46616351 6.5618175 + 1860 1.9704143 1.9931969 0.46987208 6.484088 + 1870 1.9864974 2.017655 0.47377416 6.4360445 + 1880 1.993165 2.0276398 0.47750238 6.4296162 + 1890 1.9852177 2.0249022 0.48088382 6.4843765 + 1900 1.9692398 2.0101062 0.4839255 6.5735477 + 1910 1.9516968 1.9893586 0.48689095 6.6692995 + 1920 1.9380452 1.9750949 0.49014596 6.7488323 + 1930 1.9323223 1.9719977 0.49399992 6.7947629 + 1940 1.9402144 1.9786701 0.49859677 6.7846787 + 1950 1.9589972 1.9956447 0.50392573 6.7291499 + 1960 1.979631 2.0201087 0.50984934 6.6648708 + 1970 2.0002749 2.0392081 0.51605302 6.6026647 + 1980 2.0143746 2.0524405 0.52221277 6.5687042 + 1990 2.0166553 2.0466885 0.5281276 6.5835144 + 2000 2.0130617 2.0424179 0.53381506 6.6234083 +Loop time of 0.141455 on 4 procs for 1000 steps with 2775 atoms + +Performance: 610793.635 tau/day, 7069.371 timesteps/s, 19.618 Matom-step/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.05683 | 0.060353 | 0.062989 | 1.0 | 42.67 +Neigh | 0.0072596 | 0.0077408 | 0.0081397 | 0.4 | 5.47 +Comm | 0.0075975 | 0.010647 | 0.014725 | 3.0 | 7.53 +Output | 0.0035631 | 0.0036749 | 0.0038919 | 0.2 | 2.60 +Modify | 0.050043 | 0.052936 | 0.05613 | 1.2 | 37.42 +Other | | 0.006104 | | | 4.32 + +Nlocal: 693.75 ave 799 max 589 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 259 ave 320 max 196 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 6092.5 ave 7344 max 4845 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 24370 +Ave neighs/atom = 8.781982 +Neighbor list builds = 35 +Dangerous builds = 0 + +##################################################################### +#collect data + +#print the applied force and total flux to ensure conservation of Jx +variable Fapp equal f_GD[1] +compute vxBulk bulk reduce sum vx +compute vyBulk bulk reduce sum vy +variable invVol equal 1.0/(lx*ly) +variable jx equal c_vxBulk*${invVol} +variable jx equal c_vxBulk*0.00025 +variable jy equal c_vyBulk*${invVol} +variable jy equal c_vyBulk*0.00025 +variable curr_step equal step +variable p_Fapp format Fapp %.3f +variable p_jx format jx %.5g +variable p_jy format jy %.5g +fix print_vCOM all print ${dump_rate} "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy" +fix print_vCOM all print 50 "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy" + +#compute IK1 pressure profile +#see Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627 +#use profile-unbiased temperature to remove the streaming velocity +#from the kinetic part of the pressure +compute spa bulk stress/atom myTp + +#for the pressure profile, use the same grid as the PUT +compute chunkX bulk chunk/atom bin/1d x lower ${dX} units box +compute chunkX bulk chunk/atom bin/1d x lower 3.125 units box + +#output pressure profile and other profiles +#the pressure profile is (-1/2V)*(c_spa[1] + c_spa[2]), where +#V is the volume of a slice +fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite +fix profiles bulk ave/chunk 1 1 50 chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite + +#compute velocity profile across the pipe with a finer grid +variable dYnew equal ${dY}/10 +variable dYnew equal 3.07692307692308/10 +compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box region pipe +compute chunkY bulk chunk/atom bin/1d y center 0.307692307692308 units box region pipe +fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY vx file Vy_profile ave running overwrite +fix velYprof bulk ave/chunk 1 1 50 chunkY vx file Vy_profile ave running overwrite + +#full trajectory +# dump 7 bulk custom ${dump_rate} bulk.lammpstrj id type x y z +# dump_modify 7 sort id + +run ${run} +run 2000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 5.139 | 5.14 | 5.141 Mbytes + Step c_myT c_myTp TotEng Press + 2000 2.0130617 2.0424179 0.53381506 6.6234083 + 2010 2.011712 2.0399428 0.53937165 6.6546944 + 2020 2.0177252 2.0516588 0.54483848 6.6575988 + 2030 2.0192267 2.054258 0.55012466 6.6761208 + 2040 2.0155308 2.0513866 0.55518707 6.7132509 + 2050 2.016831 2.0539288 0.56007247 6.7306192 + 2060 2.0213378 2.0690043 0.56479732 6.7330132 + 2070 2.0292987 2.0799825 0.56913353 6.7186216 + 2080 2.0342188 2.0900923 0.57283821 6.7098434 + 2090 2.0376411 2.096351 0.57566175 6.6998818 + 2100 2.053128 2.1238481 0.57727694 6.637431 + 2110 2.0783941 2.1609599 0.5768993 6.5304031 + 2120 2.0887269 2.1760645 0.57341638 6.4706853 + 2130 2.06944 2.1522354 0.5659988 6.5099284 + 2140 2.0380605 2.115767 0.55466476 6.5802578 + 2150 2.0195872 2.0868424 0.54025148 6.5885111 + 2160 2.0061251 2.069266 0.52417244 6.5682875 + 2170 1.992682 2.0526743 0.50812177 6.5470052 + 2180 1.9816004 2.0352692 0.49354583 6.5244099 + 2190 1.9688265 2.0226679 0.4811848 6.5185172 + 2200 1.9574266 2.000155 0.47107703 6.5176047 + 2210 1.9502736 1.9925522 0.46298224 6.5078398 + 2220 1.9475332 1.9936032 0.45641728 6.4850252 + 2230 1.9545128 2.0045053 0.45087489 6.4291405 + 2240 1.9627871 2.0112148 0.44588526 6.3715676 + 2250 1.9617694 2.0073769 0.44121477 6.3541518 + 2260 1.9579423 2.0079137 0.43675541 6.3542735 + 2270 1.9475845 1.998983 0.43243494 6.3854071 + 2280 1.9253275 1.9715083 0.42839782 6.464845 + 2290 1.8996763 1.9456257 0.42496367 6.5591177 + 2300 1.8823546 1.9240543 0.42247729 6.6211062 + 2310 1.8844318 1.9216768 0.42116372 6.6085376 + 2320 1.8965287 1.933936 0.42103218 6.5584198 + 2330 1.902103 1.9433708 0.421956 6.5350698 + 2340 1.9061826 1.950462 0.42378825 6.5228738 + 2350 1.9180306 1.961141 0.42644522 6.489172 + 2360 1.9296124 1.9748542 0.42981448 6.4628168 + 2370 1.9328566 1.9718181 0.43373762 6.4721746 + 2380 1.9360042 1.9769998 0.43819906 6.4840942 + 2390 1.9387073 1.9778749 0.44317927 6.49778 + 2400 1.9445619 1.9882647 0.4486142 6.4971899 + 2410 1.9553344 1.9997412 0.45435544 6.4749774 + 2420 1.9710783 2.0211926 0.46019236 6.4320181 + 2430 1.9903873 2.046553 0.46575694 6.3751343 + 2440 2.0041158 2.0721071 0.47060398 6.3415121 + 2450 2.0020392 2.0728953 0.47431806 6.3708096 + 2460 1.9839851 2.0568906 0.47681718 6.465129 + 2470 1.9566365 2.0258852 0.47838596 6.5966256 + 2480 1.929674 2.0032606 0.47952215 6.7260074 + 2490 1.9153613 1.990031 0.48061628 6.8035919 + 2500 1.9188373 1.9920514 0.4819225 6.8075788 + 2510 1.9371656 2.0138698 0.48343533 6.7492701 + 2520 1.9566481 2.0340995 0.48485699 6.6821181 + 2530 1.9636141 2.0389496 0.48583392 6.6581326 + 2540 1.9585172 2.0207113 0.48622314 6.6762792 + 2550 1.9516934 2.0024186 0.48621721 6.6980104 + 2560 1.9509543 1.9960852 0.48612286 6.6946311 + 2570 1.9601672 2.0072552 0.48602872 6.6528934 + 2580 1.973804 2.0230879 0.48576601 6.5942862 + 2590 1.9788378 2.034436 0.48505027 6.5689819 + 2600 1.9716493 2.0208578 0.48368043 6.5897554 + 2610 1.9618006 2.007098 0.48174365 6.6188626 + 2620 1.9631458 2.0075461 0.4793429 6.6026194 + 2630 1.9706918 2.0174955 0.47638698 6.5591053 + 2640 1.9759585 2.0213828 0.47264742 6.5198595 + 2650 1.9761708 2.0225139 0.46794373 6.4977306 + 2660 1.9611574 2.0083871 0.46221598 6.5299021 + 2670 1.9342882 1.9720247 0.45576624 6.6034695 + 2680 1.9142009 1.9520382 0.44913109 6.6474082 + 2690 1.9052096 1.9428107 0.4426988 6.645123 + 2700 1.902446 1.9459937 0.43672046 6.6152926 + 2710 1.9099036 1.9594727 0.43120889 6.5473804 + 2720 1.9180788 1.9767479 0.42599739 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6.3902862 + 2940 1.9623876 2.0281154 0.45237409 6.4560778 + 2950 1.9591057 2.0276078 0.46164197 6.5239614 + 2960 1.9556907 2.0254377 0.47016674 6.5883236 + 2970 1.9524475 2.0203546 0.47782337 6.6457078 + 2980 1.9556442 2.0212175 0.48459527 6.6731473 + 2990 1.9663638 2.0285202 0.49047217 6.667322 + 3000 1.976263 2.0326354 0.49540098 6.6601492 + 3010 1.9734917 2.0251301 0.49938916 6.6970878 + 3020 1.955368 1.9974693 0.50265656 6.7865104 + 3030 1.9476644 1.9780945 0.50564273 6.8327176 + 3040 1.9584769 1.9887952 0.50867872 6.8046262 + 3050 1.9705616 2.0030557 0.51168699 6.7669575 + 3060 1.9766986 2.0112576 0.51444822 6.74919 + 3070 1.9766671 2.0076853 0.51685838 6.7523339 + 3080 1.9763383 2.0045916 0.51896849 6.7532253 + 3090 1.9855877 2.0260371 0.52081441 6.7160131 + 3100 2.0011042 2.042205 0.52215192 6.653598 + 3110 2.0039819 2.0511266 0.52275172 6.6355885 + 3120 1.9958773 2.0457899 0.52253307 6.6565817 + 3130 1.9933925 2.04521 0.52158082 6.6543706 + 3140 1.9936643 2.0477262 0.51996279 6.639564 + 3150 1.9921223 2.0455965 0.51768794 6.6291901 + 3160 1.9914788 2.0365842 0.51483187 6.6154874 + 3170 1.9922866 2.0422451 0.51144091 6.5976334 + 3180 1.9872806 2.0376593 0.50747923 6.6043774 + 3190 1.9708577 2.0198422 0.50308657 6.6551127 + 3200 1.9534272 1.9982319 0.49857904 6.7093718 + 3210 1.9423425 1.9876311 0.49429833 6.7370529 + 3220 1.941974 1.984738 0.49043179 6.7218879 + 3230 1.9456357 1.9916666 0.48697785 6.6917144 + 3240 1.9392412 1.9874858 0.48388805 6.7004046 + 3250 1.9312152 1.9814714 0.4812083 6.7175714 + 3260 1.9364393 1.9840125 0.47897357 6.6870787 + 3270 1.9490184 1.9871802 0.47715672 6.6308261 + 3280 1.9578901 1.9917218 0.47568803 6.5896589 + 3290 1.9598612 1.9918098 0.47449561 6.5756965 + 3300 1.9538424 1.9845316 0.47357576 6.5931068 + 3310 1.944957 1.9676243 0.47302774 6.6211221 + 3320 1.9479975 1.9720828 0.47296613 6.6058089 + 3330 1.9569283 1.98719 0.47330356 6.5698601 + 3340 1.9558114 1.9861834 0.47383928 6.5729191 + 3350 1.9461606 1.9777192 0.47452365 6.6090135 + 3360 1.942095 1.9776297 0.47540879 6.6255417 + 3370 1.9482423 1.981145 0.47643851 6.6032207 + 3380 1.9564098 1.992645 0.47752314 6.5736007 + 3390 1.9607986 2.0006048 0.47852085 6.5587349 + 3400 1.9595637 2.0047228 0.47933656 6.5656692 + 3410 1.9628181 2.013785 0.47991082 6.5570579 + 3420 1.9698466 2.0200788 0.48018617 6.536373 + 3430 1.969877 2.0210764 0.48013786 6.543084 + 3440 1.96327 2.0103631 0.47979187 6.5761448 + 3450 1.9566516 1.9996494 0.47933398 6.6098616 + 3460 1.9511915 1.9976175 0.47891646 6.6401481 + 3470 1.9410601 1.9950284 0.47859124 6.6862584 + 3480 1.9307395 1.98193 0.47840998 6.7307929 + 3490 1.9206678 1.9678856 0.47853003 6.7702613 + 3500 1.9139405 1.955324 0.47914241 6.7934071 + 3510 1.9206383 1.9571761 0.48041531 6.763312 + 3520 1.9449301 1.9816996 0.4823109 6.6651452 + 3530 1.9752924 2.0115126 0.48452681 6.5438659 + 3540 1.9951599 2.037759 0.48660438 6.463461 + 3550 2.00071 2.0413872 0.48813252 6.4405933 + 3560 1.9939017 2.0277566 0.48901382 6.4684771 + 3570 1.9766844 2.0031366 0.48946452 6.5392906 + 3580 1.9600494 1.9790718 0.48988281 6.6106542 + 3590 1.9522334 1.9727673 0.49062615 6.6517495 + 3600 1.9522007 1.9829458 0.49183552 6.6635632 + 3610 1.9614098 1.9992781 0.49340617 6.6407777 + 3620 1.9739926 2.0159629 0.49511752 6.6062456 + 3630 1.9726539 2.0152219 0.49675445 6.6254361 + 3640 1.9613098 2.0017247 0.49829012 6.6828523 + 3650 1.9577727 2.0000723 0.49991877 6.7111789 + 3660 1.9626403 2.0037309 0.50175296 6.7072182 + 3670 1.9603974 1.9937256 0.50383808 6.7277464 + 3680 1.9532611 1.9846903 0.50638429 6.766139 + 3690 1.9541656 1.9798331 0.50962883 6.7752527 + 3700 1.9656726 1.9951191 0.51377056 6.7462001 + 3710 1.9834474 2.0193011 0.5187681 6.6957856 + 3720 2.0017373 2.0396413 0.52433682 6.6470375 + 3730 2.0109702 2.0469463 0.53011728 6.6363717 + 3740 2.0096858 2.0458572 0.53588234 6.6682278 + 3750 2.0066189 2.0519842 0.54153099 6.7085484 + 3760 2.0096126 2.0561094 0.54689937 6.7250789 + 3770 2.0117777 2.0668795 0.55183559 6.7400962 + 3780 2.0154601 2.0763941 0.55607392 6.7423369 + 3790 2.0313954 2.0972106 0.55930714 6.6920109 + 3800 2.0496133 2.1176374 0.56110467 6.6271089 + 3810 2.0553084 2.1205041 0.56098738 6.6034668 + 3820 2.0478771 2.1131255 0.5587031 6.6239896 + 3830 2.0342107 2.0991257 0.55418078 6.6632309 + 3840 2.0142205 2.0767165 0.54756321 6.7196407 + 3850 1.9879527 2.0516847 0.53919957 6.7932756 + 3860 1.9593315 2.0232738 0.52966136 6.8686983 + 3870 1.9362884 1.9952027 0.51970092 6.9156687 + 3880 1.9292997 1.9883081 0.50996282 6.8957696 + 3890 1.9372438 1.9978667 0.50073929 6.8160963 + 3900 1.949918 2.0107188 0.49208883 6.7186535 + 3910 1.9547594 2.0160936 0.48397839 6.6537348 + 3920 1.9543567 2.0191268 0.47640162 6.6136067 + 3930 1.9582199 2.0200359 0.46933873 6.5629726 + 3940 1.9644631 2.0304625 0.4627222 6.5077177 + 3950 1.9645882 2.0301829 0.45644411 6.4795258 + 3960 1.9546999 2.0197242 0.45050583 6.4943664 + 3970 1.9424307 2.0063453 0.44500625 6.5237707 + 3980 1.9281472 1.9910524 0.440105 6.5640156 + 3990 1.9168821 1.9763691 0.43594018 6.592621 + 4000 1.9150056 1.9752502 0.43256475 6.585564 +Loop time of 0.29535 on 4 procs for 2000 steps with 2775 atoms + +Performance: 585068.702 tau/day, 6771.628 timesteps/s, 18.791 Matom-step/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.11499 | 0.12105 | 0.12753 | 1.6 | 40.99 +Neigh | 0.015593 | 0.01655 | 0.017426 | 0.6 | 5.60 +Comm | 0.011343 | 0.020696 | 0.029105 | 5.0 | 7.01 +Output | 0.0076551 | 0.010557 | 0.01165 | 1.6 | 3.57 +Modify | 0.10677 | 0.11421 | 0.1196 | 1.4 | 38.67 +Other | | 0.01228 | | | 4.16 + +Nlocal: 693.75 ave 801 max 584 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 256.25 ave 313 max 200 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 6078.25 ave 7398 max 4746 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 24313 +Ave neighs/atom = 8.7614414 +Neighbor list builds = 75 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.1 b/examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.1 deleted file mode 100644 index bb9167f4901..00000000000 --- a/examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.1 +++ /dev/null @@ -1,909 +0,0 @@ -LAMMPS (6 Jul 2017) - using 1 OpenMP thread(s) per MPI task -#LAMMPS input script -#in.GD -#see README for details - -############################################################################### -#initialize variables -clear - using 1 OpenMP thread(s) per MPI task - -#frequency for outputting info (timesteps) -variable dump_rate equal 50 -variable thermo_rate equal 10 - -#equilibration time (timesteps) -variable equil equal 1000 - -#stabilization time (timesteps to reach steady-state) -variable stabil equal 1000 - -#data collection time (timesteps) -variable run equal 2000 - -#length of pipe -variable L equal 30 - -#width of pipe -variable d equal 20 - -#flux (mass/sigma*tau) -variable J equal 0.1 - -#simulation box dimensions -variable Lx equal 100 -variable Ly equal 40 - -#bulk fluid density -variable dens equal 0.8 - -#lattice spacing for wall atoms -variable aWall equal 1.0 #1.7472 - -#timestep -variable ts equal 0.001 - -#temperature -variable T equal 2.0 - -#thermostat damping constant -variable tdamp equal ${ts}*100 -variable tdamp equal 0.001*100 - -units lj -dimension 2 -atom_style atomic - - -############################################################################### -#create box - -#create lattice with the spacing aWall -variable rhoWall equal ${aWall}^(-2) -variable rhoWall equal 1^(-2) -lattice sq ${rhoWall} -lattice sq 1 -Lattice spacing in x,y,z = 1 1 1 - -#modify input dimensions to be multiples of aWall -variable L1 equal round($L/${aWall})*${aWall} -variable L1 equal round(30/${aWall})*${aWall} -variable L1 equal round(30/1)*${aWall} -variable L1 equal round(30/1)*1 -variable d1 equal round($d/${aWall})*${aWall} -variable d1 equal round(20/${aWall})*${aWall} -variable d1 equal round(20/1)*${aWall} -variable d1 equal round(20/1)*1 -variable Ly1 equal round(${Ly}/${aWall})*${aWall} -variable Ly1 equal round(40/${aWall})*${aWall} -variable Ly1 equal round(40/1)*${aWall} -variable Ly1 equal round(40/1)*1 -variable Lx1 equal round(${Lx}/${aWall})*${aWall} -variable Lx1 equal round(100/${aWall})*${aWall} -variable Lx1 equal round(100/1)*${aWall} -variable Lx1 equal round(100/1)*1 - -#create simulation box -variable lx2 equal ${Lx1}/2 -variable lx2 equal 100/2 -variable ly2 equal ${Ly1}/2 -variable ly2 equal 40/2 -region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box -region simbox block -50 ${lx2} -${ly2} ${ly2} 0 0.1 units box -region simbox block -50 50 -${ly2} ${ly2} 0 0.1 units box -region simbox block -50 50 -20 ${ly2} 0 0.1 units box -region simbox block -50 50 -20 20 0 0.1 units box -create_box 2 simbox -Created orthogonal box = (-50 -20 0) to (50 20 0.1) - 1 by 1 by 1 MPI processor grid - -##################################################################### -#set up potential - -mass 1 1.0 #fluid atoms -mass 2 1.0 #wall atoms - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 1.12246 -pair_coeff 2 2 0.0 0.0 - -neigh_modify exclude type 2 2 - -timestep ${ts} -timestep 0.001 - -##################################################################### -#create atoms - -#create wall atoms everywhere -create_atoms 2 box -Created 4000 atoms - -#define region which is "walled off" -variable dhalf equal ${d1}/2 -variable dhalf equal 20/2 -variable Lhalf equal ${L1}/2 -variable Lhalf equal 30/2 -region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box -region walltop block -15 ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box -region walltop block -15 15 ${dhalf} EDGE -0.1 0.1 units box -region walltop block -15 15 10 EDGE -0.1 0.1 units box -region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box -region wallbot block -15 ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box -region wallbot block -15 15 EDGE -${dhalf} -0.1 0.1 units box -region wallbot block -15 15 EDGE -10 -0.1 0.1 units box -region outsidewall union 2 walltop wallbot side out - -#remove wall atoms outside wall region -group outside region outsidewall -3349 atoms in group outside -delete_atoms group outside -Deleted 3349 atoms, new total = 651 - -#remove wall atoms that aren't on edge of wall region -variable x1 equal ${Lhalf}-${aWall} -variable x1 equal 15-${aWall} -variable x1 equal 15-1 -variable y1 equal ${dhalf}+${aWall} -variable y1 equal 10+${aWall} -variable y1 equal 10+1 -region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box -region insideTop block -14 ${x1} ${y1} EDGE -0.1 0.1 units box -region insideTop block -14 14 ${y1} EDGE -0.1 0.1 units box -region insideTop block -14 14 11 EDGE -0.1 0.1 units box -region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box -region insideBot block -14 ${x1} EDGE -${y1} -0.1 0.1 units box -region insideBot block -14 14 EDGE -${y1} -0.1 0.1 units box -region insideBot block -14 14 EDGE -11 -0.1 0.1 units box -region insideWall union 2 insideTop insideBot -group insideWall region insideWall -551 atoms in group insideWall -delete_atoms group insideWall -Deleted 551 atoms, new total = 100 - -#define new lattice, to give correct fluid density -#y lattice const must be a multiple of aWall -variable atrue equal ${dens}^(-1/2) -variable atrue equal 0.8^(-1/2) -variable ay equal round(${atrue}/${aWall})*${aWall} -variable ay equal round(1.11803398874989/${aWall})*${aWall} -variable ay equal round(1.11803398874989/1)*${aWall} -variable ay equal round(1.11803398874989/1)*1 - -#choose x lattice const to give correct density -variable ax equal (${ay}*${dens})^(-1) -variable ax equal (1*${dens})^(-1) -variable ax equal (1*0.8)^(-1) - -#change Lx to be multiple of ax -variable Lx1 equal round(${Lx}/${ax})*${ax} -variable Lx1 equal round(100/${ax})*${ax} -variable Lx1 equal round(100/1.25)*${ax} -variable Lx1 equal round(100/1.25)*1.25 -variable lx2 equal ${Lx1}/2 -variable lx2 equal 100/2 -change_box all x final -${lx2} ${lx2} units box -change_box all x final -50 ${lx2} units box -change_box all x final -50 50 units box - orthogonal box = (-50 -20 0) to (50 20 0.1) - -#define new lattice -lattice custom ${dens} a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 -lattice custom 0.8 a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 -lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 -lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 1 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 -Lattice spacing in x,y,z = 1.25 1 1 - -#fill in rest of box with bulk particles -variable delta equal 0.001 -variable Ldelt equal ${Lhalf}+${delta} -variable Ldelt equal 15+${delta} -variable Ldelt equal 15+0.001 -variable dDelt equal ${dhalf}-${delta} -variable dDelt equal 10-${delta} -variable dDelt equal 10-0.001 -region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box -region left block EDGE -15.001 EDGE EDGE -0.1 0.1 units box -region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box -region right block 15.001 EDGE EDGE EDGE -0.1 0.1 units box -region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box -region pipe block -15.001 ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box -region pipe block -15.001 15.001 -${dDelt} ${dDelt} -0.1 0.1 units box -region pipe block -15.001 15.001 -9.999 ${dDelt} -0.1 0.1 units box -region pipe block -15.001 15.001 -9.999 9.999 -0.1 0.1 units box - -region bulk union 3 left pipe right -create_atoms 1 region bulk -Created 2675 atoms - -group bulk type 1 -2675 atoms in group bulk -group wall type 2 -100 atoms in group wall - -#remove atoms that are too close to wall -delete_atoms overlap 0.9 bulk wall -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 72 29 1 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) command delete_atoms, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/2d - bin: standard - (2) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Deleted 0 atoms, new total = 2775 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes -neigh_modify exclude group wall wall - -velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom -velocity bulk create 2 78915 dist gaussian rot yes mom yes loop geom - -##################################################################### -#set up PUT -#see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172 - -#average number of particles per box, Evans and Morriss used 2.0 -variable NperBox equal 8.0 - -#calculate box sizes -variable boxSide equal sqrt(${NperBox}/${dens}) -variable boxSide equal sqrt(8/${dens}) -variable boxSide equal sqrt(8/0.8) -variable nX equal round(lx/${boxSide}) -variable nX equal round(lx/3.16227766016838) -variable nY equal round(ly/${boxSide}) -variable nY equal round(ly/3.16227766016838) -variable dX equal lx/${nX} -variable dX equal lx/32 -variable dY equal ly/${nY} -variable dY equal ly/13 - -#temperature of fluid (excluding wall) -compute myT bulk temp - -#profile-unbiased temperature of fluid -compute myTp bulk temp/profile 1 1 0 xy ${nX} ${nY} -compute myTp bulk temp/profile 1 1 0 xy 32 ${nY} -compute myTp bulk temp/profile 1 1 0 xy 32 13 - -#thermo setup -thermo ${thermo_rate} -thermo 10 -thermo_style custom step c_myT c_myTp etotal press - -#dump initial configuration -# dump 55 all custom 1 all.init.lammpstrj id type x y z vx vy vz -# dump 56 wall custom 1 wall.init.lammpstrj id type x y z -# dump_modify 55 sort id -# dump_modify 56 sort id -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 72 29 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes -Step c_myT c_myTp TotEng Press - 0 2 2.0555109 0.77892922 7.3417096 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 2775 atoms - -314.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 2775 ave 2775 max 2775 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 510 ave 510 max 510 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 26406 ave 26406 max 26406 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 26406 -Ave neighs/atom = 9.51568 -Neighbor list builds = 0 -Dangerous builds = 0 -# undump 55 -# undump 56 - -##################################################################### -#equilibrate without GD - -fix nvt bulk nvt temp $T $T ${tdamp} -fix nvt bulk nvt temp 2 $T ${tdamp} -fix nvt bulk nvt temp 2 2 ${tdamp} -fix nvt bulk nvt temp 2 2 0.1 -fix_modify nvt temp myTp -WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1395) -fix 2 bulk enforce2d - -run ${equil} -run 1000 -Per MPI rank memory allocation (min/avg/max) = 3.166 | 3.166 | 3.166 Mbytes -Step c_myT c_myTp TotEng Press - 0 2 2.0555109 0.77892922 7.3417096 - 10 1.9173594 1.9390034 0.77876976 7.6702228 - 20 1.7033394 1.6974676 0.77977799 8.5614784 - 30 1.5026161 1.4723993 0.78456655 9.4308258 - 40 1.4880481 1.4591602 0.79486693 9.6134304 - 50 1.6192437 1.6150635 0.81109069 9.2592835 - 60 1.7404087 1.7583444 0.82955456 8.952392 - 70 1.7757591 1.8006606 0.8452778 8.9717917 - 80 1.7573847 1.7813629 0.85769389 9.1936368 - 90 1.7491183 1.7726908 0.86882429 9.3712357 - 100 1.7798944 1.8079583 0.88029084 9.3871755 - 110 1.8440582 1.8793133 0.89259397 9.2582848 - 120 1.9191606 1.9673434 0.90533438 9.0680574 - 130 1.9883299 2.0484299 0.91755461 8.88117 - 140 2.0463366 2.1111872 0.92818114 8.7184178 - 150 2.0953769 2.167849 0.93639789 8.5713408 - 160 2.1442147 2.2216228 0.94145082 8.4082835 - 170 2.1797848 2.2631458 0.94246877 8.2767903 - 180 2.1863476 2.2700986 0.93873326 8.2311689 - 190 2.1832866 2.2710551 0.93003012 8.1959062 - 200 2.1937154 2.2868403 0.91642537 8.0842007 - 210 2.2022708 2.2915142 0.89824533 7.9575312 - 220 2.1884715 2.2770564 0.87677613 7.9000591 - 230 2.1671124 2.2496063 0.85409501 7.8673156 - 240 2.1560417 2.2379998 0.83167878 7.8003228 - 250 2.1421449 2.2240624 0.81004723 7.7491508 - 260 2.1172164 2.1971044 0.78931978 7.7457415 - 270 2.0856847 2.1672998 0.76956352 7.7719788 - 280 2.0670685 2.1449303 0.75073364 7.7524614 - 290 2.0639481 2.1428374 0.73258016 7.6727716 - 300 2.055776 2.1361719 0.7147669 7.6095248 - 310 2.038425 2.1209353 0.69722853 7.5797085 - 320 2.0203023 2.1066031 0.68006634 7.5521081 - 330 2.0118478 2.1039797 0.66330302 7.4877535 - 340 2.0159442 2.1096258 0.64673694 7.3761703 - 350 2.0166408 2.1075061 0.63020017 7.2788 - 360 2.0059407 2.0806316 0.61387618 7.2263941 - 370 1.9964281 2.0642074 0.59814148 7.1728041 - 380 1.9918446 2.0567527 0.58303017 7.101597 - 390 1.992835 2.0548138 0.56852431 7.0084774 - 400 2.0012934 2.0615016 0.55438401 6.8865948 - 410 2.0084291 2.073418 0.54034073 6.7697478 - 420 2.007464 2.0786717 0.52617041 6.6849032 - 430 1.9983712 2.0704366 0.51188183 6.6323103 - 440 1.9884651 2.0588515 0.49765394 6.5868356 - 450 1.982221 2.0467396 0.4837102 6.5311681 - 460 1.9738673 2.031238 0.47021649 6.4882783 - 470 1.9574246 2.0060447 0.45740021 6.4814923 - 480 1.9361065 1.9734507 0.44557947 6.4995199 - 490 1.9251024 1.9562469 0.43506067 6.4858343 - 500 1.9279545 1.9572145 0.42577835 6.4274765 - 510 1.9267504 1.9570246 0.41755013 6.3927027 - 520 1.9093405 1.9393872 0.41031829 6.4281888 - 530 1.8820555 1.9060756 0.40432569 6.5099401 - 540 1.86537 1.8912682 0.3999087 6.55843 - 550 1.8694252 1.9043192 0.39717519 6.5337875 - 560 1.8835224 1.9294105 0.39589322 6.4760141 - 570 1.8898719 1.9462433 0.39573596 6.4520041 - 580 1.8887698 1.9472764 0.39649878 6.4602989 - 590 1.8945125 1.9550624 0.39810844 6.4470226 - 600 1.9106571 1.9735939 0.40045321 6.3971026 - 610 1.9273243 1.98509 0.40330026 6.3474421 - 620 1.9351802 1.9888986 0.4064498 6.3340566 - 630 1.9337889 1.9846794 0.40981479 6.3610556 - 640 1.9257018 1.9757153 0.4134641 6.4184721 - 650 1.9204429 1.9718256 0.41750942 6.4679594 - 660 1.9220449 1.9701963 0.42202455 6.4919724 - 670 1.9230578 1.9707406 0.4270412 6.5178484 - 680 1.9204554 1.9740485 0.43255127 6.5572507 - 690 1.9201811 1.9762854 0.43847123 6.5869126 - 700 1.9271511 1.9867455 0.44474356 6.5882669 - 710 1.9418851 2.0042477 0.45120727 6.558573 - 720 1.9544547 2.0186724 0.4576061 6.5338329 - 730 1.9687971 2.0326169 0.46367507 6.4988775 - 740 1.9830308 2.0466267 0.46920367 6.4618136 - 750 1.9936981 2.0526606 0.47397868 6.4367349 - 760 2.0008431 2.0535449 0.47786748 6.4249001 - 770 1.9982133 2.0483219 0.48085757 6.4504786 - 780 1.9841544 2.0311693 0.48306488 6.5200512 - 790 1.9683122 2.0158738 0.48475632 6.5959263 - 800 1.9604618 2.003224 0.48619405 6.6392559 - 810 1.9629155 2.0075077 0.48756075 6.6406486 - 820 1.9683056 2.0110554 0.48883443 6.6269424 - 830 1.975409 2.0189161 0.48995399 6.6030215 - 840 1.9897264 2.035016 0.4907852 6.5485575 - 850 2.0094338 2.0555358 0.49104505 6.4719926 - 860 2.0217589 2.0643603 0.49040437 6.4233305 - 870 2.0147718 2.0641627 0.48866908 6.4491964 - 880 1.9883859 2.0324092 0.48592007 6.5488061 - 890 1.9625853 2.0028776 0.48263002 6.6452734 - 900 1.9520401 1.9889124 0.47925524 6.6808078 - 910 1.9559583 1.9952984 0.47597346 6.6573059 - 920 1.9657244 2.0083503 0.47268726 6.6073704 - 930 1.969288 2.0152339 0.4692054 6.5780416 - 940 1.9652206 2.0116384 0.4654438 6.5769812 - 950 1.9567495 1.9960693 0.46147541 6.5942022 - 960 1.9418452 1.980858 0.45753557 6.6369454 - 970 1.9247196 1.9585585 0.45390337 6.6888821 - 980 1.9128262 1.9481721 0.45090045 6.7198221 - 990 1.9167211 1.9451096 0.44869731 6.6912394 - 1000 1.935529 1.9662384 0.44728238 6.6079829 -Loop time of 1.307 on 1 procs for 1000 steps with 2775 atoms - -Performance: 66105.601 tau/day, 765.111 timesteps/s -98.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.7676 | 0.7676 | 0.7676 | 0.0 | 58.73 -Neigh | 0.088947 | 0.088947 | 0.088947 | 0.0 | 6.81 -Comm | 0.0094135 | 0.0094135 | 0.0094135 | 0.0 | 0.72 -Output | 0.019547 | 0.019547 | 0.019547 | 0.0 | 1.50 -Modify | 0.39755 | 0.39755 | 0.39755 | 0.0 | 30.42 -Other | | 0.02394 | | | 1.83 - -Nlocal: 2775 ave 2775 max 2775 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 527 ave 527 max 527 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 24332 ave 24332 max 24332 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 24332 -Ave neighs/atom = 8.76829 -Neighbor list builds = 38 -Dangerous builds = 0 - -##################################################################### -#initialize the COM velocity and run to achieve steady-state - -#calculate velocity to add: V=J/rho_total -variable Vadd equal $J*lx*ly/count(bulk) -variable Vadd equal 0.1*lx*ly/count(bulk) - -#first remove any COM velocity, then add back the streaming velocity -velocity bulk zero linear -velocity bulk set ${Vadd} 0.0 0.0 units box sum yes mom no -velocity bulk set 0.149532710280374 0.0 0.0 units box sum yes mom no - -fix GD bulk flow/gauss 1 0 0 #energy yes -#fix_modify GD energy yes - -run ${stabil} -run 1000 -Per MPI rank memory allocation (min/avg/max) = 3.166 | 3.166 | 3.166 Mbytes -Step c_myT c_myTp TotEng Press - 1000 1.9466974 1.9662384 0.45804438 6.615449 - 1010 1.9605467 1.9815754 0.45717241 6.5545496 - 1020 1.9560139 1.9823875 0.45660431 6.5672421 - 1030 1.9348326 1.9691606 0.45633148 6.6463667 - 1040 1.9167809 1.9449522 0.45657707 6.7139486 - 1050 1.9193541 1.943342 0.45767968 6.7014054 - 1060 1.9410751 1.9720491 0.45967742 6.6150379 - 1070 1.9658493 1.9964883 0.46221539 6.5178418 - 1080 1.9767205 2.0074304 0.46491236 6.4768594 - 1090 1.9714544 2.0003054 0.46759126 6.5026957 - 1100 1.9647035 1.9927455 0.4703109 6.5400181 - 1110 1.9657667 1.9959656 0.47317481 6.5519094 - 1120 1.9706062 1.9980802 0.476185 6.5512675 - 1130 1.9747655 2.0062292 0.47932281 6.554091 - 1140 1.9761245 2.0075076 0.48248327 6.5670381 - 1150 1.9744197 2.0073027 0.48562483 6.5914441 - 1160 1.9722698 2.0046687 0.48874207 6.6165575 - 1170 1.9692145 2.0013845 0.49187442 6.6438115 - 1180 1.9665609 1.9970724 0.49508053 6.6693821 - 1190 1.9625031 1.9908427 0.49843816 6.7002606 - 1200 1.960528 1.993084 0.50203044 6.7237076 - 1210 1.9649156 1.9981485 0.50587066 6.7217755 - 1220 1.9788059 2.0134511 0.50987442 6.6833452 - 1230 1.9952283 2.0343101 0.51379781 6.6340278 - 1240 2.0039391 2.0494196 0.51730872 6.6129751 - 1250 2.0019006 2.0526773 0.52014603 6.6320217 - 1260 1.9974025 2.0528914 0.52221385 6.6601786 - 1270 1.9953949 2.0561121 0.5234754 6.6796142 - 1280 1.9893864 2.0470375 0.5238632 6.7140134 - 1290 1.9694951 2.019253 0.5235093 6.798442 - 1300 1.9473901 1.9965919 0.52280384 6.8863369 - 1310 1.9511151 2.006161 0.52203882 6.8700917 - 1320 1.979341 2.0388959 0.52106938 6.7529595 - 1330 2.0073235 2.0720045 0.51935291 6.6297731 - 1340 2.0202482 2.0841419 0.51624273 6.55803 - 1350 2.0177489 2.0669046 0.51142591 6.5401753 - 1360 2.0069274 2.04717 0.50505824 6.5506533 - 1370 1.994854 2.0311383 0.49743042 6.5633001 - 1380 1.9793176 2.0077184 0.48890503 6.5859072 - 1390 1.9580907 1.9839831 0.48004316 6.6288992 - 1400 1.9415542 1.9594192 0.47143599 6.6534105 - 1410 1.9405188 1.9591825 0.46353105 6.620549 - 1420 1.9504784 1.9730647 0.45640199 6.5471784 - 1430 1.9594158 1.9819854 0.44995052 6.4802874 - 1440 1.9615108 1.9863792 0.44406411 6.44391 - 1450 1.9544127 1.9806249 0.43873409 6.4484818 - 1460 1.9384927 1.9614953 0.43408605 6.4905259 - 1470 1.9214711 1.9425515 0.43035972 6.5390434 - 1480 1.9170761 1.9300809 0.42775046 6.5409502 - 1490 1.9242904 1.9385731 0.42631007 6.5005057 - 1500 1.9307133 1.9446119 0.4258836 6.4660754 - 1510 1.9303576 1.9435389 0.42633976 6.4616415 - 1520 1.9248382 1.9408306 0.42765441 6.4832059 - 1530 1.9120794 1.9278123 0.42986958 6.5380951 - 1540 1.899122 1.9125029 0.4331459 6.5987181 - 1550 1.9030956 1.9187821 0.43765067 6.6012019 - 1560 1.9182961 1.9453782 0.44330842 6.5674222 - 1570 1.9272863 1.9613129 0.44971962 6.5619794 - 1580 1.931679 1.9698134 0.45643436 6.5780809 - 1590 1.9336692 1.9728684 0.46314752 6.6035675 - 1600 1.938895 1.9823104 0.46964519 6.6138411 - 1610 1.9510838 1.9937914 0.47568807 6.5916989 - 1620 1.9685387 2.0087314 0.48102339 6.5424432 - 1630 1.9894416 2.0295715 0.48539861 6.4757743 - 1640 1.9982699 2.0426949 0.48860411 6.4512418 - 1650 1.9901677 2.0363837 0.49062424 6.4879985 - 1660 1.9814216 2.0291326 0.49172203 6.5248034 - 1670 1.9812111 2.0293629 0.49218297 6.5253876 - 1680 1.9903906 2.0408376 0.49211747 6.4852787 - 1690 2.0015983 2.0538843 0.4914581 6.4325081 - 1700 2.009727 2.0503407 0.49011163 6.3878577 - 1710 2.0167822 2.0531002 0.4881688 6.3477054 - 1720 2.0189021 2.0445033 0.48564798 6.3273063 - 1730 2.0129713 2.0354734 0.48270666 6.3385541 - 1740 2.0048763 2.0199836 0.47950943 6.3587586 - 1750 1.9994843 2.0085942 0.47624908 6.3694119 - 1760 1.9940025 2.0072098 0.47305283 6.3816295 - 1770 1.9817431 1.9974066 0.46994486 6.4224295 - 1780 1.965171 1.9805421 0.4670779 6.4832371 - 1790 1.9474078 1.9662605 0.46466823 6.5516524 - 1800 1.9286009 1.9507751 0.46292015 6.6263366 - 1810 1.9168087 1.9437961 0.46199899 6.6759834 - 1820 1.9107555 1.9306323 0.46204129 6.7029857 - 1830 1.9135569 1.930819 0.46316484 6.6949737 - 1840 1.9345342 1.9553413 0.46532704 6.6178988 - 1850 1.9630349 1.9929548 0.46822932 6.5137866 - 1860 1.9820746 2.0188839 0.47135068 6.4489028 - 1870 1.9834959 2.0217145 0.47427805 6.4552721 - 1880 1.9731564 2.0120293 0.47692755 6.5100251 - 1890 1.9653605 2.0070624 0.47943307 6.5594235 - 1900 1.9630631 2.0095488 0.48192185 6.5912876 - 1910 1.9556778 2.0035006 0.48443107 6.6437189 - 1920 1.9408788 1.9828296 0.48710124 6.7228731 - 1930 1.9292393 1.9732376 0.49025327 6.7880112 - 1940 1.9263081 1.9708942 0.49416086 6.8162477 - 1950 1.9358375 1.976323 0.49899895 6.7946964 - 1960 1.9520543 1.9936542 0.50485961 6.7467481 - 1970 1.9709064 2.0108957 0.51165586 6.6909455 - 1980 1.9940026 2.0375428 0.51918913 6.6250463 - 1990 2.0171261 2.0646948 0.52705638 6.5649879 - 2000 2.0302713 2.0802515 0.53472229 6.5470853 -Loop time of 1.34877 on 1 procs for 1000 steps with 2775 atoms - -Performance: 64058.154 tau/day, 741.414 timesteps/s -98.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.77091 | 0.77091 | 0.77091 | 0.0 | 57.16 -Neigh | 0.085835 | 0.085835 | 0.085835 | 0.0 | 6.36 -Comm | 0.0093472 | 0.0093472 | 0.0093472 | 0.0 | 0.69 -Output | 0.019047 | 0.019047 | 0.019047 | 0.0 | 1.41 -Modify | 0.43949 | 0.43949 | 0.43949 | 0.0 | 32.58 -Other | | 0.02415 | | | 1.79 - -Nlocal: 2775 ave 2775 max 2775 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 530 ave 530 max 530 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 24404 ave 24404 max 24404 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 24404 -Ave neighs/atom = 8.79423 -Neighbor list builds = 36 -Dangerous builds = 0 - -##################################################################### -#collect data - -#print the applied force and total flux to ensure conservation of Jx -variable Fapp equal f_GD[1] -compute vxBulk bulk reduce sum vx -compute vyBulk bulk reduce sum vy -variable invVol equal 1.0/(lx*ly) -variable jx equal c_vxBulk*${invVol} -variable jx equal c_vxBulk*0.00025 -variable jy equal c_vyBulk*${invVol} -variable jy equal c_vyBulk*0.00025 -variable curr_step equal step -variable p_Fapp format Fapp %.3f -variable p_jx format jx %.5g -variable p_jy format jy %.5g -fix print_vCOM all print ${dump_rate} "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy" -fix print_vCOM all print 50 "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy" - -#compute IK1 pressure profile -#see Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627 -#use profile-unbiased temperature to remove the streaming velocity -#from the kinetic part of the pressure -compute spa bulk stress/atom myTp - -#for the pressure profile, use the same grid as the PUT -compute chunkX bulk chunk/atom bin/1d x lower ${dX} units box -compute chunkX bulk chunk/atom bin/1d x lower 3.125 units box - -#output pressure profile and other profiles -#the pressure profile is (-1/2V)*(c_spa[1] + c_spa[2]), where -#V is the volume of a slice -fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite -fix profiles bulk ave/chunk 1 1 50 chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite - -#compute velocity profile across the pipe with a finer grid -variable dYnew equal ${dY}/10 -variable dYnew equal 3.07692307692308/10 -compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box region pipe -compute chunkY bulk chunk/atom bin/1d y center 0.307692307692308 units box region pipe -fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY vx file Vy_profile ave running overwrite -fix velYprof bulk ave/chunk 1 1 50 chunkY vx file Vy_profile ave running overwrite - -#full trajectory -# dump 7 bulk custom ${dump_rate} bulk.lammpstrj id type x y z -# dump_modify 7 sort id - -run ${run} -run 2000 -Per MPI rank memory allocation (min/avg/max) = 5.174 | 5.174 | 5.174 Mbytes -Step c_myT c_myTp TotEng Press - 2000 2.0302713 2.0802515 0.53472229 6.5470853 - 2010 2.0303419 2.0806129 0.54177821 6.5808527 - 2020 2.0245167 2.0792991 0.54803523 6.6381758 - 2030 2.0169072 2.065404 0.55345227 6.7008962 - 2040 2.0052526 2.0513817 0.55818432 6.7755868 - 2050 1.9953625 2.0366564 0.56245299 6.8382569 - 2060 2.0003667 2.0462109 0.56649798 6.8390557 - 2070 2.0238288 2.0834553 0.57023651 6.7637821 - 2080 2.045765 2.1173867 0.5730944 6.6861321 - 2090 2.0563925 2.1370313 0.57430831 6.6422581 - 2100 2.0620437 2.1480293 0.57319824 6.6080678 - 2110 2.0584437 2.1473173 0.56913597 6.5969671 - 2120 2.0532825 2.1393006 0.56154606 6.5799417 - 2130 2.0450143 2.1234905 0.55009479 6.5616931 - 2140 2.0229537 2.1004507 0.53511912 6.5854627 - 2150 1.9832556 2.0554119 0.51812599 6.6700591 - 2160 1.9444027 2.0110758 0.50163049 6.7534263 - 2170 1.9267473 1.9904528 0.48759542 6.76469 - 2180 1.9262232 1.9809353 0.47662199 6.7188048 - 2190 1.9359331 1.9854626 0.46836289 6.6406985 - 2200 1.9530728 1.9971865 0.4620366 6.5409943 - 2210 1.9657099 2.0056761 0.45692542 6.4639397 - 2220 1.9661008 2.0046161 0.45253504 6.4388081 - 2230 1.9574696 1.9947839 0.44864257 6.4528687 - 2240 1.9522284 1.9922663 0.44518111 6.4584458 - 2250 1.9518203 1.9950044 0.44206844 6.4491722 - 2260 1.9527908 1.9989603 0.4391804 6.4377912 - 2270 1.9452231 1.9932538 0.43643529 6.4607516 - 2280 1.9249341 1.9759145 0.43392742 6.5320897 - 2290 1.9087464 1.960985 0.43186869 6.5875176 - 2300 1.9103289 1.964731 0.43039882 6.5765021 - 2310 1.9182062 1.9783814 0.4294628 6.5434488 - 2320 1.9204281 1.9796609 0.42889381 6.5351629 - 2330 1.916279 1.9720659 0.42866391 6.5562619 - 2340 1.9062866 1.9587628 0.42890166 6.6033936 - 2350 1.9024117 1.9566812 0.42979475 6.6297969 - 2360 1.908153 1.960687 0.43141898 6.6215148 - 2370 1.9115944 1.9663337 0.43376668 6.6236491 - 2380 1.9086193 1.9637867 0.4367911 6.6529568 - 2390 1.9039907 1.9610268 0.44053991 6.6926343 - 2400 1.9034944 1.9609406 0.44508818 6.7193441 - 2410 1.9151521 1.9753641 0.4504458 6.7015957 - 2420 1.9314517 1.9925924 0.45644382 6.6669864 - 2430 1.9433933 2.0062001 0.46277215 6.6481527 - 2440 1.9504631 2.0087015 0.46917209 6.6475757 - 2450 1.9550092 2.0094957 0.47550077 6.6556459 - 2460 1.9609689 2.0147997 0.48170141 6.6568282 - 2470 1.9730726 2.0328127 0.48763131 6.6337545 - 2480 1.9838562 2.0466643 0.49303443 6.6143423 - 2490 1.9862031 2.0473388 0.49767532 6.6245587 - 2500 1.9817565 2.0455432 0.50152131 6.6573893 - 2510 1.9785788 2.0423176 0.50460561 6.6808042 - 2520 1.9823006 2.0505106 0.50696374 6.6726698 - 2530 1.9907178 2.0553736 0.50852885 6.6402082 - 2540 2.0005205 2.0690408 0.50919421 6.5966469 - 2550 2.0079727 2.0809816 0.50872954 6.5568419 - 2560 2.0133128 2.096271 0.50682742 6.5199915 - 2570 2.0141298 2.0990846 0.50314491 6.4951991 - 2580 2.0048768 2.0874319 0.49750096 6.5025454 - 2590 1.9876498 2.0638834 0.4900201 6.5333038 - 2600 1.9720479 2.0474479 0.48105263 6.5527157 - 2610 1.9596324 2.0355764 0.4710001 6.5547867 - 2620 1.9439039 2.0106405 0.46046644 6.5646889 - 2630 1.9321714 1.9924346 0.45021207 6.5589454 - 2640 1.9349378 1.9923889 0.44082833 6.5012762 - 2650 1.9448459 2.0069955 0.43251999 6.4228945 - 2660 1.9446852 2.0050346 0.42525857 6.3921645 - 2670 1.9325594 1.9884937 0.41913362 6.4169726 - 2680 1.9121687 1.9606084 0.41434428 6.4821267 - 2690 1.8923613 1.9339385 0.41105831 6.5517615 - 2700 1.8807238 1.9191801 0.40933203 6.5949447 - 2710 1.8797367 1.918758 0.40906826 6.6001309 - 2720 1.8852961 1.9225996 0.41005611 6.58191 - 2730 1.8937478 1.9357751 0.41204348 6.5541946 - 2740 1.9019279 1.9449374 0.41476104 6.5278575 - 2750 1.9134396 1.9614415 0.41800066 6.4890769 - 2760 1.9339551 1.9913779 0.42150554 6.4159805 - 2770 1.9597826 2.0220988 0.42487614 6.3232273 - 2780 1.9753466 2.0414907 0.42771704 6.2715489 - 2790 1.9720423 2.0402016 0.42976012 6.2949288 - 2800 1.9512893 2.0172711 0.43109201 6.3878056 - 2810 1.9232302 1.9870212 0.4320928 6.5101822 - 2820 1.9026913 1.959286 0.43326424 6.6024967 - 2830 1.9033802 1.9621601 0.43500785 6.6114274 - 2840 1.9214292 1.9833838 0.43733454 6.5508757 - 2850 1.9440563 2.0087358 0.43995473 6.4713496 - 2860 1.9589136 2.0211107 0.44250821 6.4232961 - 2870 1.9588429 2.022232 0.44477492 6.4355861 - 2880 1.9456751 2.0009513 0.44676532 6.5021746 - 2890 1.9269155 1.9782929 0.44877858 6.5926531 - 2900 1.9125262 1.9554653 0.45121196 6.6657808 - 2910 1.9187855 1.9572583 0.45438665 6.6589954 - 2920 1.9416112 1.9784518 0.45839212 6.5888253 - 2930 1.9613579 1.9975032 0.46305788 6.5317424 - 2940 1.9711529 2.0102501 0.46812715 6.5148943 - 2950 1.9707865 2.0133283 0.47345305 6.5389543 - 2960 1.9732526 2.0170219 0.47898306 6.5537092 - 2970 1.9871126 2.0282309 0.48465048 6.5273492 - 2980 1.9953449 2.0404164 0.49032615 6.5227325 - 2990 1.9909136 2.037246 0.49581423 6.5664662 - 3000 1.9872474 2.0307896 0.5011051 6.6060698 - 3010 1.9944885 2.0457308 0.5062755 6.6031811 - 3020 2.0103461 2.0599491 0.51116655 6.5654871 - 3030 2.0240275 2.077342 0.5154921 6.5358852 - 3040 2.0205953 2.0704954 0.51898871 6.5708937 - 3050 2.0032184 2.0463036 0.52167438 6.657741 - 3060 1.9889341 2.0265284 0.52385964 6.7329171 - 3070 1.9795143 2.0201081 0.52588914 6.7881407 - 3080 1.9713362 2.0123964 0.52797238 6.8362858 - 3090 1.9692592 2.0106467 0.53025538 6.8616268 - 3100 1.9722487 2.0259566 0.53277635 6.8689898 - 3110 1.9703322 2.0314028 0.53541462 6.895271 - 3120 1.9594359 2.0217586 0.53808512 6.954362 - 3130 1.9524729 2.0148628 0.5409094 6.9965233 - 3140 1.9630381 2.0260807 0.54400259 6.968082 - 3150 1.9902598 2.0549364 0.54720142 6.8698796 - 3160 2.029715 2.0923999 0.54995378 6.7193678 - 3170 2.0581544 2.1137995 0.55150021 6.6053728 - 3180 2.0590739 2.1156535 0.55123668 6.5919337 - 3190 2.0400682 2.0904721 0.54894762 6.6505757 - 3200 2.0211594 2.0682597 0.54484887 6.7046468 - 3210 2.012712 2.0573114 0.53922056 6.7130909 - 3220 2.0102377 2.0554701 0.53219251 6.6919068 - 3230 2.0017671 2.0505068 0.52386898 6.6867054 - 3240 1.9854941 2.0308454 0.51458791 6.7051085 - 3250 1.9767009 2.0187664 0.50486784 6.6916859 - 3260 1.9771733 2.0186148 0.49510721 6.6424305 - 3270 1.974003 2.0136039 0.48556818 6.6078903 - 3280 1.9627665 1.9989122 0.47654147 6.6067904 - 3290 1.9491247 1.9826247 0.46834865 6.6186709 - 3300 1.9414093 1.9724941 0.4612122 6.6119543 - 3310 1.9433901 1.9715482 0.45518879 6.570612 - 3320 1.9518837 1.9872717 0.45010165 6.5057947 - 3330 1.9603874 1.9957995 0.44566728 6.4428221 - 3340 1.9615962 1.9945224 0.44167201 6.4099339 - 3350 1.955918 1.9882866 0.4380303 6.4070811 - 3360 1.9463445 1.9763654 0.43480086 6.4241178 - 3370 1.9411187 1.9683081 0.4320639 6.4296577 - 3380 1.9407224 1.9580074 0.42991627 6.4210217 - 3390 1.9402479 1.9530447 0.42850635 6.4170536 - 3400 1.9451337 1.9555771 0.42787382 6.3990336 - 3410 1.9475586 1.9612432 0.42797178 6.3953251 - 3420 1.9434927 1.960532 0.4286887 6.4210681 - 3430 1.9339054 1.9516935 0.43003682 6.4707071 - 3440 1.9234014 1.9464343 0.43214965 6.5248205 - 3450 1.9191846 1.9444777 0.43516361 6.5558451 - 3460 1.923218 1.9594606 0.43915611 6.5549213 - 3470 1.9328953 1.9792053 0.44397878 6.5327637 - 3480 1.9466227 1.9997841 0.44940599 6.4954965 - 3490 1.9672374 2.0323219 0.45511091 6.4358811 - 3500 1.9799622 2.0479841 0.46061029 6.4100217 - 3510 1.97942 2.0493411 0.46551964 6.4368108 - 3520 1.9725674 2.0389602 0.46976379 6.4892049 - 3530 1.9716429 2.0389798 0.47344292 6.5200899 - 3540 1.9789254 2.0486162 0.47659268 6.5198212 - 3550 1.9872455 2.0577517 0.47908145 6.5144586 - 3560 1.9808834 2.0545963 0.48076562 6.5633282 - 3570 1.9637165 2.0335394 0.4816783 6.6519124 - 3580 1.9407948 2.0067763 0.48212406 6.7605224 - 3590 1.9226532 1.9825887 0.482523 6.8486041 - 3600 1.9135067 1.9700999 0.48328349 6.8977859 - 3610 1.9157516 1.9720028 0.48470695 6.8977759 - 3620 1.9328644 2.0001154 0.48688778 6.8361569 - 3630 1.9568208 2.0243053 0.48963934 6.7442107 - 3640 1.9824587 2.0569223 0.49259174 6.6452535 - 3650 1.9934906 2.0686357 0.49529039 6.6020218 - 3660 1.9996281 2.0747054 0.49732231 6.5808905 - 3670 2.0038801 2.0772777 0.49838834 6.5691351 - 3680 1.9941342 2.0712365 0.49826732 6.6088108 - 3690 1.9762631 2.0486045 0.49689109 6.6739003 - 3700 1.9667284 2.034939 0.49438991 6.7010266 - 3710 1.9615089 2.0168112 0.49093736 6.7040385 - 3720 1.9613068 2.014749 0.48673789 6.6813041 - 3730 1.9731234 2.0290151 0.48175562 6.6096756 - 3740 1.9829764 2.0461907 0.47575174 6.5424752 - 3750 1.9792839 2.0454423 0.4685271 6.5237752 - 3760 1.9599692 2.0287015 0.46022485 6.5616271 - 3770 1.935975 2.0000948 0.45138017 6.6136471 - 3780 1.9236713 1.9834802 0.44262437 6.6187463 - 3790 1.9268004 1.9875324 0.43430113 6.5632772 - 3800 1.932601 1.9872595 0.42649564 6.4984765 - 3810 1.9322506 1.9814946 0.41928856 6.4617054 - 3820 1.9245737 1.9712821 0.4128224 6.461378 - 3830 1.9148568 1.9555602 0.40721003 6.4774474 - 3840 1.9049961 1.9457058 0.4026118 6.5029211 - 3850 1.8915137 1.9265199 0.39914962 6.5483592 - 3860 1.8784768 1.9058055 0.39700153 6.5962113 - 3870 1.8755236 1.9045158 0.39632769 6.6079033 - 3880 1.8841415 1.9140314 0.39710038 6.5777071 - 3890 1.8958027 1.9331148 0.39918951 6.5359786 - 3900 1.9064085 1.948805 0.40238576 6.4998591 - 3910 1.9185092 1.9675732 0.40647523 6.4610682 - 3920 1.9342595 1.9933225 0.41115392 6.4122308 - 3930 1.9482664 2.007614 0.41603495 6.373684 - 3940 1.9557759 2.0161573 0.42084462 6.3636707 - 3950 1.9573687 2.016612 0.42540421 6.3804123 - 3960 1.9486354 1.9998027 0.42974612 6.4404943 - 3970 1.936214 1.980721 0.43412037 6.5176787 - 3980 1.9274292 1.9595259 0.43885103 6.5846211 - 3990 1.9233082 1.953436 0.44425085 6.6354275 - 4000 1.9289165 1.9522097 0.45042645 6.6513836 -Loop time of 2.49114 on 1 procs for 2000 steps with 2775 atoms - -Performance: 69365.902 tau/day, 802.846 timesteps/s -98.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.4257 | 1.4257 | 1.4257 | 0.0 | 57.23 -Neigh | 0.15501 | 0.15501 | 0.15501 | 0.0 | 6.22 -Comm | 0.017206 | 0.017206 | 0.017206 | 0.0 | 0.69 -Output | 0.034183 | 0.034183 | 0.034183 | 0.0 | 1.37 -Modify | 0.81531 | 0.81531 | 0.81531 | 0.0 | 32.73 -Other | | 0.04374 | | | 1.76 - -Nlocal: 2775 ave 2775 max 2775 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 517 ave 517 max 517 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 24366 ave 24366 max 24366 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 24366 -Ave neighs/atom = 8.78054 -Neighbor list builds = 72 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:05 diff --git a/examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.4 b/examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.4 deleted file mode 100644 index 6171c0da5cf..00000000000 --- a/examples/PACKAGES/flow_gauss/log.6Jul17.GD.g++.4 +++ /dev/null @@ -1,909 +0,0 @@ -LAMMPS (6 Jul 2017) - using 1 OpenMP thread(s) per MPI task -#LAMMPS input script -#in.GD -#see README for details - -############################################################################### -#initialize variables -clear - using 1 OpenMP thread(s) per MPI task - -#frequency for outputting info (timesteps) -variable dump_rate equal 50 -variable thermo_rate equal 10 - -#equilibration time (timesteps) -variable equil equal 1000 - -#stabilization time (timesteps to reach steady-state) -variable stabil equal 1000 - -#data collection time (timesteps) -variable run equal 2000 - -#length of pipe -variable L equal 30 - -#width of pipe -variable d equal 20 - -#flux (mass/sigma*tau) -variable J equal 0.1 - -#simulation box dimensions -variable Lx equal 100 -variable Ly equal 40 - -#bulk fluid density -variable dens equal 0.8 - -#lattice spacing for wall atoms -variable aWall equal 1.0 #1.7472 - -#timestep -variable ts equal 0.001 - -#temperature -variable T equal 2.0 - -#thermostat damping constant -variable tdamp equal ${ts}*100 -variable tdamp equal 0.001*100 - -units lj -dimension 2 -atom_style atomic - - -############################################################################### -#create box - -#create lattice with the spacing aWall -variable rhoWall equal ${aWall}^(-2) -variable rhoWall equal 1^(-2) -lattice sq ${rhoWall} -lattice sq 1 -Lattice spacing in x,y,z = 1 1 1 - -#modify input dimensions to be multiples of aWall -variable L1 equal round($L/${aWall})*${aWall} -variable L1 equal round(30/${aWall})*${aWall} -variable L1 equal round(30/1)*${aWall} -variable L1 equal round(30/1)*1 -variable d1 equal round($d/${aWall})*${aWall} -variable d1 equal round(20/${aWall})*${aWall} -variable d1 equal round(20/1)*${aWall} -variable d1 equal round(20/1)*1 -variable Ly1 equal round(${Ly}/${aWall})*${aWall} -variable Ly1 equal round(40/${aWall})*${aWall} -variable Ly1 equal round(40/1)*${aWall} -variable Ly1 equal round(40/1)*1 -variable Lx1 equal round(${Lx}/${aWall})*${aWall} -variable Lx1 equal round(100/${aWall})*${aWall} -variable Lx1 equal round(100/1)*${aWall} -variable Lx1 equal round(100/1)*1 - -#create simulation box -variable lx2 equal ${Lx1}/2 -variable lx2 equal 100/2 -variable ly2 equal ${Ly1}/2 -variable ly2 equal 40/2 -region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box -region simbox block -50 ${lx2} -${ly2} ${ly2} 0 0.1 units box -region simbox block -50 50 -${ly2} ${ly2} 0 0.1 units box -region simbox block -50 50 -20 ${ly2} 0 0.1 units box -region simbox block -50 50 -20 20 0 0.1 units box -create_box 2 simbox -Created orthogonal box = (-50 -20 0) to (50 20 0.1) - 4 by 1 by 1 MPI processor grid - -##################################################################### -#set up potential - -mass 1 1.0 #fluid atoms -mass 2 1.0 #wall atoms - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 1.12246 -pair_coeff 2 2 0.0 0.0 - -neigh_modify exclude type 2 2 - -timestep ${ts} -timestep 0.001 - -##################################################################### -#create atoms - -#create wall atoms everywhere -create_atoms 2 box -Created 4000 atoms - -#define region which is "walled off" -variable dhalf equal ${d1}/2 -variable dhalf equal 20/2 -variable Lhalf equal ${L1}/2 -variable Lhalf equal 30/2 -region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box -region walltop block -15 ${Lhalf} ${dhalf} EDGE -0.1 0.1 units box -region walltop block -15 15 ${dhalf} EDGE -0.1 0.1 units box -region walltop block -15 15 10 EDGE -0.1 0.1 units box -region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box -region wallbot block -15 ${Lhalf} EDGE -${dhalf} -0.1 0.1 units box -region wallbot block -15 15 EDGE -${dhalf} -0.1 0.1 units box -region wallbot block -15 15 EDGE -10 -0.1 0.1 units box -region outsidewall union 2 walltop wallbot side out - -#remove wall atoms outside wall region -group outside region outsidewall -3349 atoms in group outside -delete_atoms group outside -Deleted 3349 atoms, new total = 651 - -#remove wall atoms that aren't on edge of wall region -variable x1 equal ${Lhalf}-${aWall} -variable x1 equal 15-${aWall} -variable x1 equal 15-1 -variable y1 equal ${dhalf}+${aWall} -variable y1 equal 10+${aWall} -variable y1 equal 10+1 -region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box -region insideTop block -14 ${x1} ${y1} EDGE -0.1 0.1 units box -region insideTop block -14 14 ${y1} EDGE -0.1 0.1 units box -region insideTop block -14 14 11 EDGE -0.1 0.1 units box -region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box -region insideBot block -14 ${x1} EDGE -${y1} -0.1 0.1 units box -region insideBot block -14 14 EDGE -${y1} -0.1 0.1 units box -region insideBot block -14 14 EDGE -11 -0.1 0.1 units box -region insideWall union 2 insideTop insideBot -group insideWall region insideWall -551 atoms in group insideWall -delete_atoms group insideWall -Deleted 551 atoms, new total = 100 - -#define new lattice, to give correct fluid density -#y lattice const must be a multiple of aWall -variable atrue equal ${dens}^(-1/2) -variable atrue equal 0.8^(-1/2) -variable ay equal round(${atrue}/${aWall})*${aWall} -variable ay equal round(1.11803398874989/${aWall})*${aWall} -variable ay equal round(1.11803398874989/1)*${aWall} -variable ay equal round(1.11803398874989/1)*1 - -#choose x lattice const to give correct density -variable ax equal (${ay}*${dens})^(-1) -variable ax equal (1*${dens})^(-1) -variable ax equal (1*0.8)^(-1) - -#change Lx to be multiple of ax -variable Lx1 equal round(${Lx}/${ax})*${ax} -variable Lx1 equal round(100/${ax})*${ax} -variable Lx1 equal round(100/1.25)*${ax} -variable Lx1 equal round(100/1.25)*1.25 -variable lx2 equal ${Lx1}/2 -variable lx2 equal 100/2 -change_box all x final -${lx2} ${lx2} units box -change_box all x final -50 ${lx2} units box -change_box all x final -50 50 units box - orthogonal box = (-50 -20 0) to (50 20 0.1) - -#define new lattice -lattice custom ${dens} a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 -lattice custom 0.8 a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 -lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 -lattice custom 0.8 a1 1.25 0.0 0.0 a2 0.0 1 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 -Lattice spacing in x,y,z = 1.25 1 1 - -#fill in rest of box with bulk particles -variable delta equal 0.001 -variable Ldelt equal ${Lhalf}+${delta} -variable Ldelt equal 15+${delta} -variable Ldelt equal 15+0.001 -variable dDelt equal ${dhalf}-${delta} -variable dDelt equal 10-${delta} -variable dDelt equal 10-0.001 -region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box -region left block EDGE -15.001 EDGE EDGE -0.1 0.1 units box -region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box -region right block 15.001 EDGE EDGE EDGE -0.1 0.1 units box -region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box -region pipe block -15.001 ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 units box -region pipe block -15.001 15.001 -${dDelt} ${dDelt} -0.1 0.1 units box -region pipe block -15.001 15.001 -9.999 ${dDelt} -0.1 0.1 units box -region pipe block -15.001 15.001 -9.999 9.999 -0.1 0.1 units box - -region bulk union 3 left pipe right -create_atoms 1 region bulk -Created 2675 atoms - -group bulk type 1 -2675 atoms in group bulk -group wall type 2 -100 atoms in group wall - -#remove atoms that are too close to wall -delete_atoms overlap 0.9 bulk wall -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 72 29 1 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) command delete_atoms, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/2d - bin: standard - (2) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Deleted 0 atoms, new total = 2775 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes -neigh_modify exclude group wall wall - -velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom -velocity bulk create 2 78915 dist gaussian rot yes mom yes loop geom - -##################################################################### -#set up PUT -#see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172 - -#average number of particles per box, Evans and Morriss used 2.0 -variable NperBox equal 8.0 - -#calculate box sizes -variable boxSide equal sqrt(${NperBox}/${dens}) -variable boxSide equal sqrt(8/${dens}) -variable boxSide equal sqrt(8/0.8) -variable nX equal round(lx/${boxSide}) -variable nX equal round(lx/3.16227766016838) -variable nY equal round(ly/${boxSide}) -variable nY equal round(ly/3.16227766016838) -variable dX equal lx/${nX} -variable dX equal lx/32 -variable dY equal ly/${nY} -variable dY equal ly/13 - -#temperature of fluid (excluding wall) -compute myT bulk temp - -#profile-unbiased temperature of fluid -compute myTp bulk temp/profile 1 1 0 xy ${nX} ${nY} -compute myTp bulk temp/profile 1 1 0 xy 32 ${nY} -compute myTp bulk temp/profile 1 1 0 xy 32 13 - -#thermo setup -thermo ${thermo_rate} -thermo 10 -thermo_style custom step c_myT c_myTp etotal press - -#dump initial configuration -# dump 55 all custom 1 all.init.lammpstrj id type x y z vx vy vz -# dump 56 wall custom 1 wall.init.lammpstrj id type x y z -# dump_modify 55 sort id -# dump_modify 56 sort id -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 72 29 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.067 | 3.068 | 3.07 Mbytes -Step c_myT c_myTp TotEng Press - 0 2 2.0555109 0.77892922 7.3417096 -Loop time of 4.35114e-06 on 4 procs for 0 steps with 2775 atoms - -114.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 4.351e-06 | | |100.00 - -Nlocal: 693.75 ave 800 max 578 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 266.25 ave 325 max 198 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Neighs: 6601.5 ave 8000 max 5147 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 26406 -Ave neighs/atom = 9.51568 -Neighbor list builds = 0 -Dangerous builds = 0 -# undump 55 -# undump 56 - -##################################################################### -#equilibrate without GD - -fix nvt bulk nvt temp $T $T ${tdamp} -fix nvt bulk nvt temp 2 $T ${tdamp} -fix nvt bulk nvt temp 2 2 ${tdamp} -fix nvt bulk nvt temp 2 2 0.1 -fix_modify nvt temp myTp -WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1395) -fix 2 bulk enforce2d - -run ${equil} -run 1000 -Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.131 | 3.132 Mbytes -Step c_myT c_myTp TotEng Press - 0 2 2.0555109 0.77892922 7.3417096 - 10 1.9173594 1.9390034 0.77876976 7.6702228 - 20 1.7033394 1.6974676 0.77977799 8.5614784 - 30 1.5026161 1.4723993 0.78456655 9.4308258 - 40 1.4880481 1.4591602 0.79486693 9.6134304 - 50 1.6192437 1.6150635 0.81109069 9.2592835 - 60 1.7404087 1.7583444 0.82955456 8.952392 - 70 1.7757591 1.8006606 0.8452778 8.9717917 - 80 1.7573847 1.7813629 0.85769389 9.1936368 - 90 1.7491183 1.7726908 0.86882429 9.3712357 - 100 1.7798944 1.8079583 0.88029084 9.3871755 - 110 1.8440582 1.8793133 0.89259397 9.2582848 - 120 1.9191606 1.9673434 0.90533438 9.0680574 - 130 1.9883299 2.0484299 0.91755461 8.88117 - 140 2.0463366 2.1111872 0.92818114 8.7184178 - 150 2.0953769 2.167849 0.93639789 8.5713408 - 160 2.1442147 2.2216228 0.94145082 8.4082835 - 170 2.1797848 2.2631458 0.94246877 8.2767903 - 180 2.1863476 2.2700986 0.93873326 8.2311689 - 190 2.1832866 2.2710551 0.93003012 8.1959062 - 200 2.1937154 2.2868403 0.91642537 8.0842007 - 210 2.2022708 2.2915142 0.89824533 7.9575312 - 220 2.1884715 2.2770564 0.87677613 7.9000591 - 230 2.1671124 2.2496063 0.85409501 7.8673156 - 240 2.1560417 2.2379998 0.83167878 7.8003228 - 250 2.1421449 2.2240624 0.81004723 7.7491508 - 260 2.1172164 2.1971044 0.78931978 7.7457415 - 270 2.0856847 2.1672998 0.76956352 7.7719788 - 280 2.0670685 2.1449303 0.75073364 7.7524614 - 290 2.0639481 2.1428374 0.73258016 7.6727716 - 300 2.055776 2.1361719 0.7147669 7.6095248 - 310 2.038425 2.1209353 0.69722853 7.5797085 - 320 2.0203023 2.1066031 0.68006634 7.5521081 - 330 2.0118478 2.1039797 0.66330302 7.4877535 - 340 2.0159442 2.1096258 0.64673694 7.3761703 - 350 2.0166408 2.1075061 0.63020017 7.2788 - 360 2.0059407 2.0806316 0.61387618 7.2263941 - 370 1.9964281 2.0642074 0.59814148 7.1728041 - 380 1.9918446 2.0567527 0.58303017 7.101597 - 390 1.992835 2.0548138 0.56852431 7.0084774 - 400 2.0012934 2.0615016 0.55438401 6.8865948 - 410 2.0084291 2.073418 0.54034073 6.7697478 - 420 2.007464 2.0786717 0.52617041 6.6849032 - 430 1.9983712 2.0704366 0.51188183 6.6323103 - 440 1.9884651 2.0588515 0.49765394 6.5868356 - 450 1.982221 2.0467396 0.4837102 6.5311681 - 460 1.9738673 2.031238 0.47021649 6.4882783 - 470 1.9574246 2.0060447 0.45740021 6.4814923 - 480 1.9361065 1.9734507 0.44557947 6.4995199 - 490 1.9251024 1.9562469 0.43506067 6.4858343 - 500 1.9279545 1.9572145 0.42577835 6.4274765 - 510 1.9267504 1.9570246 0.41755013 6.3927027 - 520 1.9093405 1.9393872 0.41031829 6.4281888 - 530 1.8820555 1.9060756 0.40432569 6.5099401 - 540 1.86537 1.8912682 0.3999087 6.55843 - 550 1.8694252 1.9043192 0.39717519 6.5337875 - 560 1.8835224 1.9294105 0.39589322 6.4760141 - 570 1.8898719 1.9462433 0.39573596 6.4520041 - 580 1.8887698 1.9472764 0.39649878 6.4602989 - 590 1.8945125 1.9550624 0.39810844 6.4470226 - 600 1.9106571 1.9735939 0.40045321 6.3971026 - 610 1.9273243 1.98509 0.40330026 6.3474421 - 620 1.9351802 1.9888986 0.4064498 6.3340566 - 630 1.9337889 1.9846794 0.40981479 6.3610556 - 640 1.9257018 1.9757153 0.4134641 6.4184721 - 650 1.9204429 1.9718256 0.41750942 6.4679594 - 660 1.9220449 1.9701963 0.42202455 6.4919724 - 670 1.9230578 1.9707406 0.4270412 6.5178484 - 680 1.9204554 1.9740485 0.43255127 6.5572507 - 690 1.9201811 1.9762854 0.43847123 6.5869126 - 700 1.9271511 1.9867455 0.44474356 6.5882669 - 710 1.9418851 2.0042477 0.45120727 6.558573 - 720 1.9544547 2.0186724 0.4576061 6.5338329 - 730 1.9687971 2.0326169 0.46367507 6.4988775 - 740 1.9830308 2.0466267 0.46920367 6.4618136 - 750 1.9936981 2.0526606 0.47397868 6.4367349 - 760 2.0008431 2.0535449 0.47786748 6.4249001 - 770 1.9982133 2.0483219 0.48085757 6.4504786 - 780 1.9841544 2.0311693 0.48306488 6.5200512 - 790 1.9683122 2.0158738 0.48475632 6.5959263 - 800 1.9604618 2.003224 0.48619405 6.6392559 - 810 1.9629155 2.0075077 0.48756075 6.6406486 - 820 1.9683056 2.0110554 0.48883443 6.6269424 - 830 1.975409 2.0189161 0.48995399 6.6030215 - 840 1.9897264 2.035016 0.4907852 6.5485575 - 850 2.0094338 2.0555358 0.49104505 6.4719926 - 860 2.0217589 2.0643603 0.49040437 6.4233305 - 870 2.0147718 2.0641627 0.48866908 6.4491964 - 880 1.9883859 2.0324092 0.48592007 6.5488061 - 890 1.9625853 2.0028776 0.48263002 6.6452734 - 900 1.9520401 1.9889124 0.47925524 6.6808078 - 910 1.9559583 1.9952984 0.47597346 6.6573059 - 920 1.9657244 2.0083503 0.47268726 6.6073704 - 930 1.969288 2.0152339 0.4692054 6.5780416 - 940 1.9652206 2.0116384 0.4654438 6.5769812 - 950 1.9567495 1.9960693 0.46147541 6.5942022 - 960 1.9418452 1.980858 0.45753557 6.6369454 - 970 1.9247196 1.9585585 0.45390337 6.6888821 - 980 1.9128262 1.9481721 0.45090045 6.7198221 - 990 1.9167211 1.9451096 0.44869731 6.6912394 - 1000 1.935529 1.9662384 0.44728238 6.6079829 -Loop time of 0.474418 on 4 procs for 1000 steps with 2775 atoms - -Performance: 182118.045 tau/day, 2107.848 timesteps/s -98.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.13953 | 0.19068 | 0.23764 | 10.4 | 40.19 -Neigh | 0.016439 | 0.022345 | 0.027069 | 3.2 | 4.71 -Comm | 0.018215 | 0.068071 | 0.12178 | 18.6 | 14.35 -Output | 0.011982 | 0.012633 | 0.013047 | 0.4 | 2.66 -Modify | 0.14494 | 0.15597 | 0.16628 | 2.4 | 32.88 -Other | | 0.02472 | | | 5.21 - -Nlocal: 693.75 ave 800 max 584 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 255.5 ave 323 max 192 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 6083 ave 7384 max 4742 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 24332 -Ave neighs/atom = 8.76829 -Neighbor list builds = 38 -Dangerous builds = 0 - -##################################################################### -#initialize the COM velocity and run to achieve steady-state - -#calculate velocity to add: V=J/rho_total -variable Vadd equal $J*lx*ly/count(bulk) -variable Vadd equal 0.1*lx*ly/count(bulk) - -#first remove any COM velocity, then add back the streaming velocity -velocity bulk zero linear -velocity bulk set ${Vadd} 0.0 0.0 units box sum yes mom no -velocity bulk set 0.149532710280374 0.0 0.0 units box sum yes mom no - -fix GD bulk flow/gauss 1 0 0 #energy yes -#fix_modify GD energy yes - -run ${stabil} -run 1000 -Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.131 | 3.132 Mbytes -Step c_myT c_myTp TotEng Press - 1000 1.9466974 1.9662384 0.45804438 6.615449 - 1010 1.9605467 1.9815754 0.45717241 6.5545496 - 1020 1.9560139 1.9823875 0.45660431 6.5672421 - 1030 1.9348326 1.9691606 0.45633148 6.6463667 - 1040 1.9167809 1.9449522 0.45657707 6.7139486 - 1050 1.9193541 1.943342 0.45767968 6.7014054 - 1060 1.9410751 1.9720491 0.45967742 6.6150379 - 1070 1.9658493 1.9964883 0.46221539 6.5178418 - 1080 1.9767205 2.0074304 0.46491236 6.4768594 - 1090 1.9714544 2.0003054 0.46759126 6.5026957 - 1100 1.9647035 1.9927455 0.4703109 6.5400181 - 1110 1.9657667 1.9959656 0.47317481 6.5519094 - 1120 1.9706062 1.9980802 0.476185 6.5512675 - 1130 1.9747655 2.0062292 0.47932281 6.554091 - 1140 1.9761245 2.0075076 0.48248327 6.5670381 - 1150 1.9744197 2.0073027 0.48562483 6.5914441 - 1160 1.9722698 2.0046687 0.48874207 6.6165575 - 1170 1.9692145 2.0013845 0.49187442 6.6438115 - 1180 1.9665609 1.9970724 0.49508053 6.6693821 - 1190 1.9625031 1.9908427 0.49843816 6.7002606 - 1200 1.960528 1.993084 0.50203044 6.7237076 - 1210 1.9649156 1.9981485 0.50587066 6.7217755 - 1220 1.9788059 2.0134511 0.50987442 6.6833452 - 1230 1.9952283 2.0343101 0.51379781 6.6340278 - 1240 2.0039391 2.0494196 0.51730872 6.6129751 - 1250 2.0019006 2.0526773 0.52014603 6.6320217 - 1260 1.9974025 2.0528914 0.52221385 6.6601786 - 1270 1.9953949 2.0561121 0.5234754 6.6796142 - 1280 1.9893864 2.0470375 0.5238632 6.7140134 - 1290 1.9694951 2.019253 0.5235093 6.798442 - 1300 1.9473901 1.9965919 0.52280384 6.8863369 - 1310 1.9511151 2.006161 0.52203882 6.8700917 - 1320 1.979341 2.0388959 0.52106938 6.7529595 - 1330 2.0073235 2.0720045 0.51935291 6.6297731 - 1340 2.0202482 2.0841419 0.51624273 6.55803 - 1350 2.0177489 2.0669046 0.51142591 6.5401753 - 1360 2.0069274 2.04717 0.50505824 6.5506533 - 1370 1.994854 2.0311383 0.49743042 6.5633001 - 1380 1.9793176 2.0077184 0.48890503 6.5859072 - 1390 1.9580907 1.9839831 0.48004316 6.6288992 - 1400 1.9415542 1.9594192 0.47143599 6.6534105 - 1410 1.9405188 1.9591825 0.46353105 6.620549 - 1420 1.9504784 1.9730647 0.45640199 6.5471784 - 1430 1.9594158 1.9819854 0.44995052 6.4802874 - 1440 1.9615108 1.9863792 0.44406411 6.44391 - 1450 1.9544127 1.9806249 0.43873409 6.4484818 - 1460 1.9384927 1.9614953 0.43408605 6.4905259 - 1470 1.9214711 1.9425515 0.43035972 6.5390434 - 1480 1.9170761 1.9300809 0.42775046 6.5409502 - 1490 1.9242904 1.9385731 0.42631007 6.5005057 - 1500 1.9307133 1.9446119 0.4258836 6.4660754 - 1510 1.9303576 1.9435389 0.42633976 6.4616415 - 1520 1.9248382 1.9408306 0.42765441 6.4832059 - 1530 1.9120794 1.9278123 0.42986958 6.5380951 - 1540 1.899122 1.9125029 0.4331459 6.5987181 - 1550 1.9030956 1.9187821 0.43765067 6.6012019 - 1560 1.9182961 1.9453782 0.44330842 6.5674222 - 1570 1.9272863 1.9613129 0.44971962 6.5619794 - 1580 1.931679 1.9698134 0.45643436 6.5780809 - 1590 1.9336692 1.9728684 0.46314752 6.6035675 - 1600 1.938895 1.9823104 0.46964519 6.6138411 - 1610 1.9510838 1.9937914 0.47568807 6.5916989 - 1620 1.9685387 2.0087314 0.48102339 6.5424432 - 1630 1.9894416 2.0295715 0.48539861 6.4757743 - 1640 1.9982699 2.0426949 0.48860411 6.4512418 - 1650 1.9901677 2.0363837 0.49062424 6.4879985 - 1660 1.9814216 2.0291326 0.49172203 6.5248034 - 1670 1.9812111 2.0293629 0.49218297 6.5253876 - 1680 1.9903906 2.0408376 0.49211747 6.4852787 - 1690 2.0015983 2.0538843 0.4914581 6.4325081 - 1700 2.009727 2.0503407 0.49011163 6.3878577 - 1710 2.0167822 2.0531002 0.4881688 6.3477054 - 1720 2.0189021 2.0445033 0.48564798 6.3273063 - 1730 2.0129713 2.0354734 0.48270666 6.3385541 - 1740 2.0048763 2.0199836 0.47950943 6.3587586 - 1750 1.9994843 2.0085942 0.47624908 6.3694119 - 1760 1.9940025 2.0072098 0.47305283 6.3816295 - 1770 1.9817431 1.9974066 0.46994486 6.4224295 - 1780 1.965171 1.9805421 0.4670779 6.4832371 - 1790 1.9474078 1.9662605 0.46466823 6.5516524 - 1800 1.9286009 1.9507751 0.46292015 6.6263366 - 1810 1.9168087 1.9437961 0.46199899 6.6759834 - 1820 1.9107555 1.9306323 0.46204129 6.7029857 - 1830 1.9135569 1.930819 0.46316484 6.6949737 - 1840 1.9345342 1.9553413 0.46532704 6.6178988 - 1850 1.9630349 1.9929548 0.46822932 6.5137866 - 1860 1.9820746 2.0188839 0.47135068 6.4489028 - 1870 1.9834959 2.0217145 0.47427805 6.4552721 - 1880 1.9731564 2.0120293 0.47692755 6.5100251 - 1890 1.9653605 2.0070624 0.47943307 6.5594235 - 1900 1.9630631 2.0095488 0.48192185 6.5912876 - 1910 1.9556778 2.0035006 0.48443107 6.6437189 - 1920 1.9408788 1.9828296 0.48710124 6.7228731 - 1930 1.9292393 1.9732376 0.49025327 6.7880112 - 1940 1.9263081 1.9708942 0.49416086 6.8162477 - 1950 1.9358375 1.976323 0.49899895 6.7946964 - 1960 1.9520543 1.9936542 0.50485961 6.7467481 - 1970 1.9709064 2.0108957 0.51165586 6.6909455 - 1980 1.9940026 2.0375428 0.51918913 6.6250463 - 1990 2.0171261 2.0646948 0.52705638 6.5649879 - 2000 2.0302713 2.0802515 0.53472229 6.5470853 -Loop time of 0.482133 on 4 procs for 1000 steps with 2775 atoms - -Performance: 179203.608 tau/day, 2074.116 timesteps/s -98.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.1081 | 0.18228 | 0.23471 | 12.7 | 37.81 -Neigh | 0.011443 | 0.019967 | 0.025651 | 4.1 | 4.14 -Comm | 0.01639 | 0.073615 | 0.15634 | 21.8 | 15.27 -Output | 0.011851 | 0.012603 | 0.013287 | 0.5 | 2.61 -Modify | 0.14306 | 0.16634 | 0.18018 | 3.6 | 34.50 -Other | | 0.02733 | | | 5.67 - -Nlocal: 693.75 ave 797 max 590 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 259 ave 320 max 195 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 6101 ave 7360 max 4853 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 24404 -Ave neighs/atom = 8.79423 -Neighbor list builds = 36 -Dangerous builds = 0 - -##################################################################### -#collect data - -#print the applied force and total flux to ensure conservation of Jx -variable Fapp equal f_GD[1] -compute vxBulk bulk reduce sum vx -compute vyBulk bulk reduce sum vy -variable invVol equal 1.0/(lx*ly) -variable jx equal c_vxBulk*${invVol} -variable jx equal c_vxBulk*0.00025 -variable jy equal c_vyBulk*${invVol} -variable jy equal c_vyBulk*0.00025 -variable curr_step equal step -variable p_Fapp format Fapp %.3f -variable p_jx format jx %.5g -variable p_jy format jy %.5g -fix print_vCOM all print ${dump_rate} "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy" -fix print_vCOM all print 50 "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no title "timestep Fapp Jx Jy" - -#compute IK1 pressure profile -#see Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627 -#use profile-unbiased temperature to remove the streaming velocity -#from the kinetic part of the pressure -compute spa bulk stress/atom myTp - -#for the pressure profile, use the same grid as the PUT -compute chunkX bulk chunk/atom bin/1d x lower ${dX} units box -compute chunkX bulk chunk/atom bin/1d x lower 3.125 units box - -#output pressure profile and other profiles -#the pressure profile is (-1/2V)*(c_spa[1] + c_spa[2]), where -#V is the volume of a slice -fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite -fix profiles bulk ave/chunk 1 1 50 chunkX vx density/mass c_spa[1] c_spa[2] file x_profiles ave running overwrite - -#compute velocity profile across the pipe with a finer grid -variable dYnew equal ${dY}/10 -variable dYnew equal 3.07692307692308/10 -compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box region pipe -compute chunkY bulk chunk/atom bin/1d y center 0.307692307692308 units box region pipe -fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY vx file Vy_profile ave running overwrite -fix velYprof bulk ave/chunk 1 1 50 chunkY vx file Vy_profile ave running overwrite - -#full trajectory -# dump 7 bulk custom ${dump_rate} bulk.lammpstrj id type x y z -# dump_modify 7 sort id - -run ${run} -run 2000 -Per MPI rank memory allocation (min/avg/max) = 5.138 | 5.139 | 5.14 Mbytes -Step c_myT c_myTp TotEng Press - 2000 2.0302713 2.0802515 0.53472229 6.5470853 - 2010 2.0303419 2.0806129 0.54177821 6.5808527 - 2020 2.0245167 2.0792991 0.54803523 6.6381758 - 2030 2.0169072 2.065404 0.55345227 6.7008962 - 2040 2.0052526 2.0513817 0.55818432 6.7755868 - 2050 1.9953625 2.0366564 0.56245299 6.8382569 - 2060 2.0003667 2.0462109 0.56649798 6.8390557 - 2070 2.0238288 2.0834553 0.57023651 6.7637821 - 2080 2.045765 2.1173867 0.5730944 6.6861321 - 2090 2.0563925 2.1370313 0.57430831 6.6422581 - 2100 2.0620437 2.1480293 0.57319824 6.6080678 - 2110 2.0584437 2.1473173 0.56913597 6.5969671 - 2120 2.0532825 2.1393006 0.56154606 6.5799417 - 2130 2.0450143 2.1234905 0.55009479 6.5616931 - 2140 2.0229537 2.1004507 0.53511912 6.5854627 - 2150 1.9832556 2.0554119 0.51812599 6.6700591 - 2160 1.9444027 2.0110758 0.50163049 6.7534263 - 2170 1.9267473 1.9904528 0.48759542 6.76469 - 2180 1.9262232 1.9809353 0.47662199 6.7188048 - 2190 1.9359331 1.9854626 0.46836289 6.6406985 - 2200 1.9530728 1.9971865 0.4620366 6.5409943 - 2210 1.9657099 2.0056761 0.45692542 6.4639397 - 2220 1.9661008 2.0046161 0.45253504 6.4388081 - 2230 1.9574696 1.9947839 0.44864257 6.4528687 - 2240 1.9522284 1.9922663 0.44518111 6.4584458 - 2250 1.9518203 1.9950044 0.44206844 6.4491722 - 2260 1.9527908 1.9989603 0.4391804 6.4377912 - 2270 1.9452231 1.9932538 0.43643529 6.4607516 - 2280 1.9249341 1.9759145 0.43392742 6.5320897 - 2290 1.9087464 1.960985 0.43186869 6.5875176 - 2300 1.9103289 1.964731 0.43039882 6.5765021 - 2310 1.9182062 1.9783814 0.4294628 6.5434488 - 2320 1.9204281 1.9796609 0.42889381 6.5351629 - 2330 1.916279 1.9720659 0.42866391 6.5562619 - 2340 1.9062866 1.9587628 0.42890166 6.6033936 - 2350 1.9024117 1.9566812 0.42979475 6.6297969 - 2360 1.908153 1.960687 0.43141898 6.6215148 - 2370 1.9115944 1.9663337 0.43376668 6.6236491 - 2380 1.9086193 1.9637867 0.4367911 6.6529568 - 2390 1.9039907 1.9610268 0.44053991 6.6926343 - 2400 1.9034944 1.9609406 0.44508818 6.7193441 - 2410 1.9151521 1.9753641 0.4504458 6.7015957 - 2420 1.9314517 1.9925924 0.45644382 6.6669864 - 2430 1.9433933 2.0062001 0.46277215 6.6481527 - 2440 1.9504631 2.0087015 0.46917209 6.6475757 - 2450 1.9550092 2.0094957 0.47550077 6.6556459 - 2460 1.9609689 2.0147997 0.48170141 6.6568282 - 2470 1.9730726 2.0328127 0.48763131 6.6337545 - 2480 1.9838562 2.0466643 0.49303443 6.6143423 - 2490 1.9862031 2.0473388 0.49767532 6.6245587 - 2500 1.9817565 2.0455432 0.50152131 6.6573893 - 2510 1.9785788 2.0423176 0.50460561 6.6808042 - 2520 1.9823006 2.0505106 0.50696374 6.6726698 - 2530 1.9907178 2.0553736 0.50852885 6.6402082 - 2540 2.0005205 2.0690408 0.50919421 6.5966469 - 2550 2.0079727 2.0809816 0.50872954 6.5568419 - 2560 2.0133128 2.096271 0.50682742 6.5199915 - 2570 2.0141298 2.0990846 0.50314491 6.4951991 - 2580 2.0048768 2.0874319 0.49750096 6.5025454 - 2590 1.9876498 2.0638834 0.4900201 6.5333038 - 2600 1.9720479 2.0474479 0.48105263 6.5527157 - 2610 1.9596324 2.0355764 0.4710001 6.5547867 - 2620 1.9439039 2.0106405 0.46046644 6.5646889 - 2630 1.9321714 1.9924346 0.45021207 6.5589454 - 2640 1.9349378 1.9923889 0.44082833 6.5012762 - 2650 1.9448459 2.0069955 0.43251999 6.4228945 - 2660 1.9446852 2.0050346 0.42525857 6.3921645 - 2670 1.9325594 1.9884937 0.41913362 6.4169726 - 2680 1.9121687 1.9606084 0.41434428 6.4821267 - 2690 1.8923613 1.9339385 0.41105831 6.5517615 - 2700 1.8807238 1.9191801 0.40933203 6.5949447 - 2710 1.8797367 1.918758 0.40906826 6.6001309 - 2720 1.8852961 1.9225996 0.41005611 6.58191 - 2730 1.8937478 1.9357751 0.41204348 6.5541946 - 2740 1.9019279 1.9449374 0.41476104 6.5278575 - 2750 1.9134396 1.9614415 0.41800066 6.4890769 - 2760 1.9339551 1.9913779 0.42150554 6.4159805 - 2770 1.9597826 2.0220988 0.42487614 6.3232273 - 2780 1.9753466 2.0414907 0.42771704 6.2715489 - 2790 1.9720423 2.0402016 0.42976012 6.2949288 - 2800 1.9512893 2.0172711 0.43109201 6.3878056 - 2810 1.9232302 1.9870212 0.4320928 6.5101822 - 2820 1.9026913 1.959286 0.43326424 6.6024967 - 2830 1.9033802 1.9621601 0.43500785 6.6114274 - 2840 1.9214292 1.9833838 0.43733454 6.5508757 - 2850 1.9440563 2.0087358 0.43995473 6.4713496 - 2860 1.9589136 2.0211107 0.44250821 6.4232961 - 2870 1.9588429 2.022232 0.44477492 6.4355861 - 2880 1.9456751 2.0009513 0.44676532 6.5021746 - 2890 1.9269155 1.9782929 0.44877858 6.5926531 - 2900 1.9125262 1.9554653 0.45121196 6.6657808 - 2910 1.9187855 1.9572583 0.45438665 6.6589954 - 2920 1.9416112 1.9784518 0.45839212 6.5888253 - 2930 1.9613579 1.9975032 0.46305788 6.5317424 - 2940 1.9711529 2.0102501 0.46812715 6.5148943 - 2950 1.9707865 2.0133283 0.47345305 6.5389543 - 2960 1.9732526 2.0170219 0.47898306 6.5537092 - 2970 1.9871126 2.0282309 0.48465048 6.5273492 - 2980 1.9953449 2.0404164 0.49032615 6.5227325 - 2990 1.9909136 2.037246 0.49581423 6.5664662 - 3000 1.9872474 2.0307896 0.50110509 6.6060698 - 3010 1.9944885 2.0457308 0.5062755 6.6031811 - 3020 2.0103461 2.0599491 0.51116655 6.5654871 - 3030 2.0240275 2.077342 0.5154921 6.5358852 - 3040 2.0205953 2.0704954 0.51898871 6.5708937 - 3050 2.0032184 2.0463036 0.52167438 6.657741 - 3060 1.9889341 2.0265284 0.52385964 6.7329171 - 3070 1.9795143 2.0201081 0.52588914 6.7881407 - 3080 1.9713362 2.0123964 0.52797238 6.8362858 - 3090 1.9692592 2.0106467 0.53025538 6.8616268 - 3100 1.9722487 2.0259566 0.53277635 6.8689898 - 3110 1.9703322 2.0314028 0.53541462 6.895271 - 3120 1.9594359 2.0217586 0.53808512 6.954362 - 3130 1.9524729 2.0148628 0.5409094 6.9965233 - 3140 1.9630381 2.0260807 0.54400259 6.968082 - 3150 1.9902598 2.0549364 0.54720142 6.8698796 - 3160 2.029715 2.0923999 0.54995378 6.7193678 - 3170 2.0581544 2.1137995 0.55150021 6.6053728 - 3180 2.059074 2.1156535 0.55123668 6.5919337 - 3190 2.0400682 2.0904721 0.54894762 6.6505757 - 3200 2.0211594 2.0682597 0.54484887 6.7046468 - 3210 2.012712 2.0573114 0.53922057 6.7130909 - 3220 2.0102377 2.0554701 0.53219251 6.6919069 - 3230 2.0017671 2.0505068 0.52386898 6.6867054 - 3240 1.9854941 2.0308454 0.51458792 6.7051085 - 3250 1.9767009 2.0187664 0.50486785 6.6916859 - 3260 1.9771733 2.0186148 0.49510722 6.6424305 - 3270 1.974003 2.0136039 0.48556819 6.6078903 - 3280 1.9627665 1.9989122 0.47654147 6.6067904 - 3290 1.9491247 1.9826248 0.46834866 6.6186709 - 3300 1.9414093 1.9724941 0.4612122 6.6119543 - 3310 1.9433901 1.9715482 0.45518879 6.570612 - 3320 1.9518837 1.9872717 0.45010165 6.5057947 - 3330 1.9603874 1.9957995 0.44566728 6.4428221 - 3340 1.9615962 1.9945224 0.44167201 6.4099339 - 3350 1.955918 1.9882866 0.4380303 6.4070811 - 3360 1.9463445 1.9763654 0.43480086 6.4241178 - 3370 1.9411187 1.9683081 0.43206391 6.4296577 - 3380 1.9407224 1.9580074 0.42991627 6.4210217 - 3390 1.9402479 1.9530447 0.42850635 6.4170536 - 3400 1.9451337 1.9555771 0.42787382 6.3990336 - 3410 1.9475586 1.9612432 0.42797178 6.3953251 - 3420 1.9434927 1.960532 0.4286887 6.4210681 - 3430 1.9339054 1.9516935 0.43003682 6.4707071 - 3440 1.9234014 1.9464343 0.43214965 6.5248205 - 3450 1.9191846 1.9444777 0.43516361 6.5558451 - 3460 1.923218 1.9594606 0.43915611 6.5549213 - 3470 1.9328953 1.9792053 0.44397878 6.5327637 - 3480 1.9466227 1.9997841 0.44940599 6.4954965 - 3490 1.9672374 2.0323219 0.45511091 6.4358811 - 3500 1.9799622 2.0479841 0.46061029 6.4100217 - 3510 1.97942 2.0493411 0.46551964 6.4368108 - 3520 1.9725674 2.0389602 0.46976378 6.4892049 - 3530 1.9716429 2.0389798 0.47344292 6.5200899 - 3540 1.9789254 2.0486162 0.47659268 6.5198212 - 3550 1.9872455 2.0577517 0.47908145 6.5144586 - 3560 1.9808834 2.0545962 0.48076561 6.5633282 - 3570 1.9637165 2.0335394 0.4816783 6.6519124 - 3580 1.9407948 2.0067763 0.48212405 6.7605224 - 3590 1.9226532 1.9825887 0.48252299 6.8486041 - 3600 1.9135067 1.9700999 0.48328348 6.8977858 - 3610 1.9157516 1.9720028 0.48470695 6.8977759 - 3620 1.9328644 2.0001154 0.48688777 6.8361569 - 3630 1.9568208 2.0243053 0.48963933 6.7442107 - 3640 1.9824587 2.0569223 0.49259173 6.6452535 - 3650 1.9934906 2.0686356 0.49529038 6.6020218 - 3660 1.9996281 2.0747054 0.4973223 6.5808904 - 3670 2.0038801 2.0772777 0.49838833 6.5691351 - 3680 1.9941342 2.0712365 0.49826732 6.6088107 - 3690 1.9762631 2.0486045 0.49689108 6.6739002 - 3700 1.9667284 2.0349391 0.4943899 6.7010265 - 3710 1.9615089 2.0168112 0.49093735 6.7040384 - 3720 1.9613068 2.0147489 0.48673788 6.6813041 - 3730 1.9731234 2.0290151 0.48175561 6.6096757 - 3740 1.9829764 2.0461907 0.47575173 6.5424752 - 3750 1.9792839 2.0454423 0.46852709 6.5237753 - 3760 1.9599692 2.0287014 0.46022484 6.5616271 - 3770 1.935975 2.0000948 0.45138016 6.6136471 - 3780 1.9236713 1.9834802 0.44262435 6.6187463 - 3790 1.9268004 1.9875324 0.43430112 6.5632772 - 3800 1.932601 1.9872595 0.42649563 6.4984764 - 3810 1.9322506 1.9814946 0.41928855 6.4617054 - 3820 1.9245737 1.9712821 0.4128224 6.4613779 - 3830 1.9148568 1.9555602 0.40721003 6.4774474 - 3840 1.9049961 1.9457058 0.40261179 6.5029211 - 3850 1.8915137 1.9265199 0.39914961 6.5483592 - 3860 1.8784768 1.9058055 0.39700153 6.5962113 - 3870 1.8755236 1.9045158 0.39632768 6.6079033 - 3880 1.8841415 1.9140314 0.39710037 6.577707 - 3890 1.8958027 1.9331149 0.39918951 6.5359785 - 3900 1.9064085 1.948805 0.40238576 6.499859 - 3910 1.9185092 1.9675733 0.40647523 6.4610682 - 3920 1.9342595 1.9933225 0.41115392 6.4122308 - 3930 1.9482664 2.0076139 0.41603495 6.3736841 - 3940 1.9557759 2.0161573 0.42084462 6.3636708 - 3950 1.9573687 2.016612 0.42540421 6.3804124 - 3960 1.9486354 1.9998027 0.42974612 6.4404944 - 3970 1.936214 1.9807209 0.43412037 6.5176788 - 3980 1.9274292 1.9595259 0.43885103 6.5846212 - 3990 1.9233082 1.953436 0.44425085 6.6354276 - 4000 1.9289166 1.9522097 0.45042645 6.6513835 -Loop time of 0.998413 on 4 procs for 2000 steps with 2775 atoms - -Performance: 173074.634 tau/day, 2003.179 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.25646 | 0.3672 | 0.47947 | 15.7 | 36.78 -Neigh | 0.027925 | 0.039163 | 0.050221 | 4.5 | 3.92 -Comm | 0.032807 | 0.14565 | 0.27684 | 25.4 | 14.59 -Output | 0.025572 | 0.032272 | 0.035355 | 2.2 | 3.23 -Modify | 0.31519 | 0.35781 | 0.375 | 4.1 | 35.84 -Other | | 0.05632 | | | 5.64 - -Nlocal: 693.75 ave 805 max 582 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 255.5 ave 312 max 199 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 6091.5 ave 7423 max 4780 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 24366 -Ave neighs/atom = 8.78054 -Neighbor list builds = 72 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/data.pos b/examples/PACKAGES/phonon/2-1D-diatomic/data.pos index cba35b49c94..3ab4033aee5 100644 --- a/examples/PACKAGES/phonon/2-1D-diatomic/data.pos +++ b/examples/PACKAGES/phonon/2-1D-diatomic/data.pos @@ -8,7 +8,7 @@ 0.00000000 64.00000000 xlo xhi 0.00000000 1.00000000 ylo yhi - 0.00000000 1.00000000 zlo zhi + -0.50000000 0.50000000 zlo zhi Atoms diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.1 b/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.1 new file mode 100644 index 00000000000..e84bcf8dfff --- /dev/null +++ b/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.1 @@ -0,0 +1,20125 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# 3D simple cubic lattice simulation +dimension 2 +boundary p f p + +units lj +atom_style bond +atom_modify sort 0 1. +bond_style harmonic +pair_style none +comm_modify cutoff 2.0 + +# geometry +read_data data.pos +Reading data file ... + orthogonal box = (0 0 -0.5) to (64 1 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 64 atoms + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 64 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.002 seconds + +# +neighbor 1.0 nsq +neigh_modify delay 0 check no + +#Langevin random seed +variable r equal 571101 + +#Langevin Temperature +variable t equal 0.005 + +# Langevin Damping variable +variable d equal 0.5 + +# Create velocities and equilibrate +compute MyTemp all temp/partial 1 0 0 +velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all create 0.005 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all set NULL 0.0 0.0 units box +# +fix 1 all langevin $t $t $d $r +fix 1 all langevin 0.005 $t $d $r +fix 1 all langevin 0.005 0.005 $d $r +fix 1 all langevin 0.005 0.005 0.5 $r +fix 1 all langevin 0.005 0.005 0.5 571101 +fix_modify 1 temp MyTemp +fix 2 all setforce NULL 0. 0. +fix 3 all nve +fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1 +fix_modify 4 temp MyTemp + +# 1 2 3 4 +thermo_style custom step temp pe etotal +thermo_modify temp MyTemp +thermo 100 + +# +run 2000000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix phonon command: doi:10.1016/j.cpc.2011.04.019 + +@Article{Kong11, + author = {L. T. Kong}, + title = {Phonon Dispersion Measured Directly from Molecular Dynamics Simulations}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2011, + volume = 182, + pages = {2201--2207} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. (src/comm.cpp:723) +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. (src/comm.cpp:723) +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 3.24 | 3.24 | 3.24 Mbytes + Step Temp PotEng TotEng + 0 0.005 0 0.0024609375 + 100 0.0043574392 0.00069805582 0.0028427329 + 200 0.0050747182 0.001248215 0.0037459279 + 300 0.0042939525 0.0012759486 0.0033893784 + 400 0.0047484976 0.001437393 0.0037745442 + 500 0.004627561 0.0016348645 0.0039124922 + 600 0.0053777922 0.0016710534 0.0043179355 + 700 0.0052695823 0.001835953 0.0044295755 + 800 0.0058609694 0.0019759698 0.0048606657 + 900 0.0041391777 0.0023023409 0.0043395924 + 1000 0.0056759231 0.0025899311 0.0053835496 + 1100 0.0040035566 0.0026989975 0.004669498 + 1200 0.0046087446 0.0024368196 0.004705186 + 1300 0.0044194669 0.0024664612 0.0046416676 + 1400 0.0073096222 0.001870287 0.0054679916 + 1500 0.0051897883 0.0017108961 0.004265245 + 1600 0.0044584884 0.001752323 0.0039467352 + 1700 0.005428529 0.0021271098 0.0047989639 + 1800 0.0051009277 0.0024399413 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threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0.86381 | 0.86381 | 0.86381 | 0.0 | 6.82 +Neigh | 1.2565 | 1.2565 | 1.2565 | 0.0 | 9.92 +Comm | 1.0357 | 1.0357 | 1.0357 | 0.0 | 8.18 +Output | 0.071243 | 0.071243 | 0.071243 | 0.0 | 0.56 +Modify | 7.5928 | 7.5928 | 7.5928 | 0.0 | 59.94 +Other | | 1.848 | | | 14.59 + +Nlocal: 64 ave 64 max 64 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 6 +Neighbor list builds = 2000000 +Dangerous builds not checked +Total wall time: 0:00:12 diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.4 b/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.4 new file mode 100644 index 00000000000..2bb0c1c972b --- /dev/null +++ b/examples/PACKAGES/phonon/2-1D-diatomic/log.6Dec23.Ana.g++.4 @@ -0,0 +1,20125 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# 3D simple cubic lattice simulation +dimension 2 +boundary p f p + +units lj +atom_style bond +atom_modify sort 0 1. +bond_style harmonic +pair_style none +comm_modify cutoff 2.0 + +# geometry +read_data data.pos +Reading data file ... + orthogonal box = (0 0 -0.5) to (64 1 0.5) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 64 atoms + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 64 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# +neighbor 1.0 nsq +neigh_modify delay 0 check no + +#Langevin random seed +variable r equal 571101 + +#Langevin Temperature +variable t equal 0.005 + +# Langevin Damping variable +variable d equal 0.5 + +# Create velocities and equilibrate +compute MyTemp all temp/partial 1 0 0 +velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all create 0.005 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all set NULL 0.0 0.0 units box +# +fix 1 all langevin $t $t $d $r +fix 1 all langevin 0.005 $t $d $r +fix 1 all langevin 0.005 0.005 $d $r +fix 1 all langevin 0.005 0.005 0.5 $r +fix 1 all langevin 0.005 0.005 0.5 571101 +fix_modify 1 temp MyTemp +fix 2 all setforce NULL 0. 0. +fix 3 all nve +fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1 +fix_modify 4 temp MyTemp + +# 1 2 3 4 +thermo_style custom step temp pe etotal +thermo_modify temp MyTemp +thermo 100 + +# +run 2000000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix phonon command: doi:10.1016/j.cpc.2011.04.019 + +@Article{Kong11, + author = {L. T. Kong}, + title = {Phonon Dispersion Measured Directly from Molecular Dynamics Simulations}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2011, + volume = 182, + pages = {2201--2207} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. (src/comm.cpp:723) +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. 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0.0022659689 0.0050292709 + 1998200 0.0043151851 0.0025546655 0.0046785456 + 1998300 0.0052712957 0.0024152156 0.0050096815 + 1998400 0.0042348839 0.0024296798 0.0045140367 + 1998500 0.0030287342 0.002623803 0.0041145081 + 1998600 0.0055051309 0.0021173655 0.0048269221 + 1998700 0.0057217041 0.0017686861 0.0045848373 + 1998800 0.0048875419 0.0018746291 0.0042802161 + 1998900 0.007364676 0.0019868413 0.0056116428 + 1999000 0.0053002642 0.0021333448 0.0047420686 + 1999100 0.0044239819 0.0026956169 0.0048730454 + 1999200 0.0037866761 0.0031115123 0.0049752669 + 1999300 0.0045921308 0.0027207583 0.0049809477 + 1999400 0.0052107996 0.0020772636 0.004641954 + 1999500 0.0049143451 0.001868372 0.0042871512 + 1999600 0.0059949807 0.0022728405 0.0052234951 + 1999700 0.0050216233 0.002669087 0.0051406673 + 1999800 0.0049219953 0.0025093587 0.0049319033 + 1999900 0.0045165212 0.0022190108 0.004441986 + 2000000 0.0049904073 0.001955233 0.0044114491 +Loop time of 22.6651 on 4 procs for 2000000 steps with 64 atoms + +Performance: 38120276.772 tau/day, 88241.381 timesteps/s, 5.647 Matom-step/s +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0.37899 | 0.39755 | 0.41982 | 2.3 | 1.75 +Neigh | 2.9184 | 3.0178 | 3.1717 | 5.4 | 13.31 +Comm | 10.429 | 10.694 | 11.003 | 6.2 | 47.18 +Output | 0.12974 | 0.14293 | 0.17878 | 5.5 | 0.63 +Modify | 6.4203 | 6.5794 | 6.7365 | 4.5 | 29.03 +Other | | 1.833 | | | 8.09 + +Nlocal: 16 ave 16 max 16 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4 ave 4 max 4 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 6 +Neighbor list builds = 2000000 +Dangerous builds not checked +Total wall time: 0:00:22 diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/log.lammps b/examples/PACKAGES/phonon/2-1D-diatomic/log.lammps deleted file mode 100644 index b5867bb6582..00000000000 --- a/examples/PACKAGES/phonon/2-1D-diatomic/log.lammps +++ /dev/null @@ -1,20088 +0,0 @@ -LAMMPS (23 Sep 2013) -# 3D simple cubic lattice simulation -dimension 2 -boundary p f p - -units lj -atom_style bond -atom_modify sort 0 1. -bond_style harmonic -pair_style none -communicate single cutoff 2.0 - -# geometry -read_data data.pos - 2 = max bonds/atom - orthogonal box = (0 0 0) to (64 1 1) - 1 by 1 by 1 MPI processor grid - 64 atoms - 64 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -# -neighbor 1.0 nsq -neigh_modify delay 0 check no - -#Langevin random seed -variable r equal 571101 - -#Langevin Temperature -variable t equal 0.005 - -# Langevin Damping variable -variable d equal 0.5 - -# Create velocities and equilibrate -compute MyTemp all temp/partial 1 0 0 -velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp -velocity all create 0.0050000000000000001041 28711 mom yes rot yes dist gaussian temp MyTemp -velocity all set NULL 0.0 0.0 units box -# -fix 1 all langevin $t $t $d $r -fix 1 all langevin 0.0050000000000000001041 $t $d $r -fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 $d $r -fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 $r -fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 571101 -fix_modify 1 temp MyTemp -fix 2 all setforce NULL 0. 0. -fix 3 all nve -fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1 -fix_modify 4 temp MyTemp - -# 1 2 3 4 -thermo_style custom step temp pe etotal -thermo_modify temp MyTemp -thermo 100 - -# -run 2000000 -Memory usage per processor = 2.01061 Mbytes -Step Temp PotEng TotEng - 0 0.005 0 0.002421875 - 100 0.0044233185 0.00069227571 0.0028348206 - 200 0.0051557212 0.0012425996 0.003739902 - 300 0.004357315 0.0012750554 0.0033856298 - 400 0.0048269093 0.0014376622 0.0037756964 - 500 0.0047025425 0.0016352541 0.0039130482 - 600 0.0054651713 0.0016709504 0.0043181428 - 700 0.0053552729 0.0018353947 0.0044293551 - 800 0.005954909 0.0019755263 0.0048599354 - 900 0.0042057592 0.0023020508 0.0043392155 - 1000 0.0057669621 0.0025897902 0.0053831625 - 1100 0.0040680049 0.0026989519 0.0046693918 - 1200 0.0046829459 0.0024368094 0.0047051113 - 1300 0.0044905385 0.0024665322 0.0046416368 - 1400 0.0074275036 0.0018704053 0.0054681024 - 1500 0.0052733986 0.0017110596 0.0042653621 - 1600 0.0045302499 0.0017525366 0.0039468764 - 1700 0.0055159362 0.002127395 0.0047991766 - 1800 0.0051833134 0.0024402092 0.0049508766 - 1900 0.0052803653 0.0024879535 0.0050456305 - 2000 0.0056694273 0.0023283837 0.0050745125 - 2100 0.0057566849 0.0021451166 0.0049335108 - 2200 0.00386807 0.0021520647 0.0040256611 - 2300 0.0058041566 0.0023206647 0.0051320531 - 2400 0.0049628786 0.0021353417 0.004539236 - 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4700 0.004112287 0.0028318222 0.0048237112 - 4800 0.0049222174 0.0026333499 0.0050175489 - 4900 0.0053288359 0.0023349026 0.0049160575 - 5000 0.0052122846 0.0020219366 0.0045466369 - 5100 0.0058812614 0.0021999893 0.0050487252 - 5200 0.0051967264 0.0018998782 0.0044170426 - 5300 0.005879625 0.0019625602 0.0048105036 - 5400 0.0059624731 0.0021443126 0.0050323855 - 5500 0.0059591574 0.0023506099 0.0052370768 - 5600 0.003079608 0.0029662562 0.0044579413 - 5700 0.0056499809 0.0030961313 0.0058328408 - 5800 0.004573757 0.0024716554 0.004687069 - 5900 0.0061564453 0.0021550869 0.0051371151 - 6000 0.0075508592 0.0021537409 0.0058111883 - 6100 0.0063879372 0.0024185024 0.0055126595 - 6200 0.0041526115 0.0027590092 0.0047704304 - 6300 0.0053061863 0.0025648127 0.0051349967 - 6400 0.006060304 0.0027159393 0.0056513991 - 6500 0.0056452086 0.0030946398 0.0058290377 - 6600 0.0041209765 0.0033636656 0.0053597636 - 6700 0.0045845779 0.0028218743 0.0050425293 - 6800 0.0059546759 0.0023227413 0.0052070374 - 6900 0.0040117754 0.0023341431 0.0042773468 - 7000 0.0042824332 0.0023350167 0.0044093203 - 7100 0.0055815793 0.0020343862 0.0047379636 - 7200 0.0047361478 0.0021430515 0.0044371231 - 7300 0.0046591248 0.0021899851 0.0044467487 - 7400 0.0055490678 0.0024363348 0.0051241645 - 7500 0.0062602828 0.0022183901 0.0052507145 - 7600 0.0071038558 0.0023618503 0.0058027804 - 7700 0.0049840045 0.0028164024 0.0052305296 - 7800 0.0060742119 0.0028555113 0.0057977076 - 7900 0.0057662888 0.0026868797 0.0054799259 - 8000 0.0055472766 0.0026213197 0.0053082818 - 8100 0.0061220787 0.0024665333 0.0054319151 - 8200 0.0035301258 0.0022766722 0.0039865769 - 8300 0.0047057949 0.0020748339 0.0043542033 - 8400 0.0056584891 0.0025104488 0.0052512795 - 8500 0.0052931944 0.0031335003 0.0056973914 - 8600 0.006813214 0.0031081279 0.0064082784 - 8700 0.0057000798 0.0031294549 0.0058904311 - 8800 0.0063988595 0.0029939656 0.0060934132 - 8900 0.0050809819 0.0033860223 0.0058471229 - 9000 0.0058880586 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0.0057155358 - 190700 0.006697174 0.003039924 0.0062838677 - 190800 0.0053998872 0.0029342198 0.0055497901 - 190900 0.0050070716 0.0032378488 0.0056631491 - 191000 0.0044775182 0.0032919033 0.0054607011 - 191100 0.0048496929 0.0029186711 0.0052677411 - 191200 0.0046411987 0.0026224616 0.0048705422 - 191300 0.0055062313 0.0028360695 0.0055031503 - 191400 0.0043036098 0.0030423482 0.0051269092 - 191500 0.0047557858 0.0028837441 0.0051873279 - 191600 0.0049657398 0.0031398468 0.0055451271 - 191700 0.0057967036 0.0027231302 0.0055309085 - 191800 0.0046446397 0.0023950176 0.0046447649 - 191900 0.0060831854 0.0021788919 0.0051254348 - 192000 0.0050062294 0.0025966413 0.0050215337 - 192100 0.0043299953 0.0029248104 0.0050221519 - 192200 0.0055555236 0.0024065811 0.0050975378 - 192300 0.0055035662 0.0023360749 0.0050018648 - 192400 0.0035013393 0.0024301448 0.004126106 - 192500 0.0039670881 0.0021160113 0.0040375696 - 192600 0.0054090169 0.0020258664 0.0046458589 - 192700 0.0043622174 0.0025770528 0.0046900019 - 192800 0.0044188753 0.0025913243 0.004731717 - 192900 0.0054753877 0.0025689278 0.0052210687 - 193000 0.0030370073 0.0026801634 0.0041512138 - 193100 0.004409951 0.0022050277 0.0043410977 - 193200 0.0057759185 0.001896822 0.0046945325 - 193300 0.0042752982 0.0025307205 0.0046015681 - 193400 0.0055186183 0.0031917268 0.0058648075 - 193500 0.0060706248 0.0030096467 0.0059501056 - 193600 0.0042938989 0.00264227 0.0047221273 - 193700 0.0055878445 0.0026675461 0.0053741583 - 193800 0.0041577783 0.0032179247 0.0052318486 - 193900 0.0044302076 0.0028307011 0.004976583 - 194000 0.0045536136 0.0026532486 0.0048589052 - 194100 0.0042068026 0.0024913282 0.0045289982 - 194200 0.0037699595 0.0026229049 0.004448979 - 194300 0.0037420602 0.0026526448 0.0044652052 - 194400 0.003878494 0.0026486011 0.0045272466 - 194500 0.0046998411 0.0024972143 0.0047736999 - 194600 0.0074446112 0.0023454877 0.0059514713 - 194700 0.0035616348 0.0025592457 0.0042844125 - 194800 0.004454451 0.0026486558 0.0048062805 - 194900 0.0041375053 0.0031289022 0.0051330063 - 195000 0.0055855352 0.0023818302 0.0050873238 - 195100 0.0049993147 0.0022307876 0.0046523307 - 195200 0.0050902708 0.0024878171 0.004953417 - 195300 0.0052889476 0.0028110914 0.0053729254 - 195400 0.0069216615 0.0026928476 0.0060455273 - 195500 0.0056653594 0.0028165203 0.0055606787 - 195600 0.0068159974 0.0033075535 0.0066090523 - 195700 0.0038892912 0.0033528858 0.0052367612 - 195800 0.0050771126 0.0029442862 0.0054035126 - 195900 0.0049673801 0.0024786018 0.0048846766 - 196000 0.0045366143 0.0023858427 0.0045832652 - 196100 0.0034262945 0.0023407836 0.004000395 - 196200 0.0080690464 0.002105792 0.0060142364 - 196300 0.0055825313 0.0026808195 0.0053848581 - 196400 0.0058569898 0.0025960602 0.0054330397 - 196500 0.0049358445 0.0023874592 0.0047782588 - 196600 0.0057120089 0.0030756087 0.005842363 - 196700 0.0065281028 0.0036266314 0.0067886812 - 196800 0.0083678972 0.002787348 0.0068405482 - 196900 0.0053579919 0.0027321079 0.0053273852 - 197000 0.0051319658 0.0031094842 0.0055952801 - 197100 0.0051893931 0.0026560568 0.0051696691 - 197200 0.0057025248 0.0025227845 0.005284945 - 197300 0.0057190745 0.0021218735 0.0048920502 - 197400 0.0054308536 0.0021085758 0.0047391455 - 197500 0.0061738386 0.0024553693 0.0054458224 - 197600 0.0073637833 0.0034092835 0.006976116 - 197700 0.006880961 0.0038654894 0.0071984549 - 197800 0.0045154568 0.003905548 0.0060927224 - 197900 0.0058546478 0.0034661516 0.0063019967 - 198000 0.006251792 0.0032547858 0.0062829976 - 198100 0.0047231964 0.0027934021 0.0050812004 - 198200 0.0050989071 0.0024584673 0.0049282504 - 198300 0.0066451305 0.0021919512 0.0054106863 - 198400 0.0052993565 0.0027496567 0.0053165324 - 198500 0.0048914502 0.0030021438 0.00537144 - 198600 0.0045970991 0.0028914871 0.005118207 - 198700 0.0046075146 0.0028712859 0.0051030508 - 198800 0.0044019458 0.0030324028 0.0051645953 - 198900 0.0064983384 0.0028781354 0.006025768 - 199000 0.0043115478 0.0026259277 0.0047143336 - 199100 0.0052927869 0.0030187438 0.0055824374 - 199200 0.0046158741 0.0034427209 0.0056785349 - 199300 0.0057827879 0.0033809411 0.0061819789 - 199400 0.0047102404 0.0030595364 0.0053410591 - 199500 0.0065787425 0.0026770398 0.0058636182 - 199600 0.0051927359 0.0026411966 0.005156428 - 199700 0.0045327092 0.0027294203 0.0049249513 - 199800 0.0048496623 0.0025053467 0.0048544019 - 199900 0.0054228679 0.0020631595 0.0046898612 - 200000 0.0055794195 0.0018362356 0.0045387669 - 200100 0.0046262225 0.0020656778 0.0043065043 - 200200 0.003627737 0.002270457 0.0040276421 - 200300 0.0038479801 0.0021699958 0.0040338612 - 200400 0.0050120202 0.002216547 0.0046442443 - 200500 0.0049172792 0.0023821287 0.0047639358 - 200600 0.0036694163 0.0025848857 0.0043622592 - 200700 0.0041600694 0.0027527852 0.0047678188 - 200800 0.004511666 0.0024639128 0.004649251 - 200900 0.0066329627 0.0025066272 0.0057194686 - 201000 0.0050300515 0.0032750403 0.0057114715 - 201100 0.0059981294 0.0034641684 0.0063695123 - 201200 0.0053221902 0.0032550253 0.0058329612 - 201300 0.004780854 0.0027813602 0.0050970863 - 201400 0.0047724553 0.0027331203 0.0050447783 - 201500 0.0083500719 0.0026781623 0.0067227284 - 201600 0.0057064719 0.0026443441 0.0054084164 - 201700 0.0053270485 0.0031907506 0.0057710397 - 201800 0.0056772678 0.0027345683 0.0054844949 - 201900 0.0051556952 0.0026502128 0.0051475027 - 202000 0.0054386571 0.0024793145 0.0051136641 - 202100 0.0060716989 0.002756279 0.0056972581 - 202200 0.0040641357 0.0033367206 0.0053052863 - 202300 0.0046033751 0.0032435963 0.0054733561 - 202400 0.004246771 0.0028810152 0.0049380449 - 202500 0.0058791109 0.002499567 0.0053472613 - 202600 0.0044302003 0.0030500904 0.0051959687 - 202700 0.0045842744 0.0028628921 0.0050834 - 202800 0.0056273109 0.0031744904 0.0059002191 - 202900 0.0066554885 0.0030585302 0.0062822825 - 203000 0.0059381392 0.0028487683 0.0057250544 - 203100 0.0051322804 0.0031226977 0.005608646 - 203200 0.0055475824 0.0025834209 0.0052705311 - 203300 0.0049699258 0.0025155703 0.0049228781 - 203400 0.0050097429 0.0023647721 0.0047913663 - 203500 0.0044111825 0.0023675111 0.0045041776 - 203600 0.0040262051 0.0027285627 0.0046787558 - 203700 0.0053123872 0.003257171 0.0058303585 - 203800 0.005475602 0.0030955672 0.0057478119 - 203900 0.0063764118 0.0027558197 0.0058443942 - 204000 0.0063038368 0.0024937674 0.0055471884 - 204100 0.0050449743 0.0026723037 0.0051159631 - 204200 0.0067524323 0.0025882042 0.0058589137 - 204300 0.0073031627 0.0026445353 0.0061820047 - 204400 0.0050223894 0.002810413 0.0052431329 - 204500 0.0037718568 0.0030748839 0.004901877 - 204600 0.0062012174 0.0032083521 0.0062120668 - 204700 0.0054393438 0.0028176179 0.0054523 - 204800 0.0088331665 0.002493314 0.006771879 - 204900 0.0053942416 0.0025172599 0.0051300957 - 205000 0.0037609622 0.0030769793 0.0048986954 - 205100 0.0063160379 0.0030003872 0.006059718 - 205200 0.0042026933 0.0026768992 0.0047125788 - 205300 0.0058727251 0.0025895103 0.0054341116 - 205400 0.0067897991 0.002280172 0.005568981 - 205500 0.0055292419 0.002319809 0.0049980356 - 205600 0.0052534527 0.0026419529 0.0051865941 - 205700 0.0043953817 0.0023659035 0.0044949165 - 205800 0.0045353981 0.0024362533 0.0046330868 - 205900 0.0031392895 0.0024728119 0.0039934052 - 206000 0.0045591585 0.0023565796 0.004564922 - 206100 0.0053648652 0.0021715123 0.0047701189 - 206200 0.0051829247 0.0019909078 0.0045013869 - 206300 0.0050365147 0.0026592167 0.0050987785 - 206400 0.0050082255 0.0028922498 0.005318109 - 206500 0.0052750194 0.0029120324 0.0054671199 - 206600 0.0055912708 0.0023448232 0.005053095 - 206700 0.0046981304 0.0021110812 0.0043867381 - 206800 0.0058175925 0.0023570336 0.00517493 - 206900 0.0049001501 0.002548525 0.0049220352 - 207000 0.005069773 0.0027047998 0.005160471 - 207100 0.0051734466 0.002815373 0.0053212611 - 207200 0.0060320982 0.0024832317 0.0054050292 - 207300 0.0057246583 0.0025824224 0.0053553038 - 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209500 0.004197963 0.0032123208 0.0052457091 - 209600 0.004950149 0.0030137388 0.0054114672 - 209700 0.0056623336 0.0031856888 0.0059283816 - 209800 0.0037767196 0.0031179024 0.004947251 - 209900 0.0054877261 0.0030862769 0.0057443942 - 210000 0.0067233116 0.0032367487 0.0064933527 - 210100 0.0059930893 0.0035364581 0.0064393608 - 210200 0.0059538067 0.0030089911 0.0058928662 - 210300 0.0052167989 0.0027591159 0.0052860029 - 210400 0.0057580904 0.0023534834 0.0051425584 - 210500 0.0057889341 0.0019918568 0.0047958718 - 210600 0.0048658675 0.0022582845 0.0046151891 - 210700 0.0049044132 0.0027921752 0.0051677504 - 210800 0.006885278 0.0028135277 0.0061485842 - 210900 0.0066110515 0.0031688163 0.0063710444 - 211000 0.0054439086 0.0030748344 0.0057117276 - 211100 0.0053383283 0.0029234553 0.0055092081 - 211200 0.0068191874 0.0024696249 0.0057726689 - 211300 0.0057627794 0.0026758586 0.0054672049 - 211400 0.0045150576 0.0032959442 0.0054829253 - 211500 0.0060131577 0.0032466078 0.0061592311 - 211600 0.0062034207 0.0034196759 0.0064244579 - 211700 0.0065560387 0.0034097479 0.0065853292 - 211800 0.0045648133 0.0033793404 0.0055904218 - 211900 0.0033423538 0.0033912292 0.0050101818 - 212000 0.0055023199 0.003326599 0.0059917852 - 212100 0.0065361398 0.0031275845 0.0062935272 - 212200 0.004875831 0.0032259827 0.0055877133 - 212300 0.0054858679 0.0029599265 0.0056171438 - 212400 0.0061264953 0.002381524 0.0053490452 - 212500 0.005214498 0.001990062 0.0045158345 - 212600 0.0057493994 0.0019943938 0.0047792592 - 212700 0.005623798 0.0020935105 0.0048175377 - 212800 0.0065557591 0.002189019 0.0053644648 - 212900 0.0059814045 0.0023138649 0.0052111077 - 213000 0.0043864828 0.002104435 0.0042291376 - 213100 0.0051890328 0.0025328931 0.0050463308 - 213200 0.005177568 0.0024633304 0.0049712149 - 213300 0.0043030541 0.0023018382 0.00438613 - 213400 0.0053245053 0.0023578072 0.0049368645 - 213500 0.0052064675 0.0024410219 0.0049629046 - 213600 0.0040067453 0.0023947802 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0.0018770499 0.004582572 - 215800 0.0058154559 0.0018535909 0.0046704524 - 215900 0.0047862493 0.0022969899 0.0046153294 - 216000 0.0066111398 0.0024597439 0.0056620148 - 216100 0.0044377463 0.0032458319 0.0053953653 - 216200 0.0033917 0.0030578865 0.0047007412 - 216300 0.0053549289 0.0027917723 0.005385566 - 216400 0.0057641906 0.0027734806 0.0055655104 - 216500 0.0035664256 0.0030744324 0.0048019198 - 216600 0.0053216588 0.0028866069 0.0054642854 - 216700 0.0060473874 0.0025742992 0.0055035025 - 216800 0.00527329 0.0024363575 0.0049906074 - 216900 0.0041275952 0.0028042369 0.0048035408 - 217000 0.0052517655 0.0027585654 0.0053023893 - 217100 0.0041891447 0.0022853911 0.0043145081 - 217200 0.0056755423 0.0024929182 0.005242009 - 217300 0.0048143059 0.0034005223 0.0057324517 - 217400 0.0051420074 0.0035189033 0.0060095632 - 217500 0.0050148067 0.0033553455 0.0057843924 - 217600 0.0061779397 0.002547201 0.0055396405 - 217700 0.0046718327 0.002432099 0.0046950179 - 217800 0.0054400962 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- 1974700 0.0074740317 0.0022399864 0.0058602206 - 1974800 0.0060482682 0.0025337519 0.0054633817 - 1974900 0.0050154909 0.0027719504 0.0052013288 - 1975000 0.0045335664 0.0030395025 0.0052354487 - 1975100 0.0046638217 0.0028020992 0.0050611378 - 1975200 0.004873034 0.002848826 0.0052092018 - 1975300 0.0042910303 0.002913311 0.0049917787 - 1975400 0.0051556367 0.0031093931 0.0056066547 - 1975500 0.0040694394 0.0030316112 0.0050027459 - 1975600 0.0058378983 0.002423874 0.005251606 - 1975700 0.0053371129 0.0021502419 0.004735406 - 1975800 0.0070446923 0.0021047481 0.0055170209 - 1975900 0.006559973 0.0023314058 0.0055088927 - 1976000 0.0052979827 0.0023618796 0.00492809 - 1976100 0.0045817236 0.0026409467 0.0048602191 - 1976200 0.004473997 0.0024717308 0.0046388231 - 1976300 0.0037308915 0.0021052169 0.0039123675 - 1976400 0.0050736595 0.0021350389 0.0045925927 - 1976500 0.0047211873 0.0026576123 0.0049444374 - 1976600 0.0051823742 0.002915772 0.0054259845 - 1976700 0.0055667224 0.0029714565 0.0056678377 - 1976800 0.0038088425 0.0026669281 0.0045118362 - 1976900 0.0052066277 0.0022477273 0.0047696876 - 1977000 0.0042668185 0.0028161513 0.0048828915 - 1977100 0.0040233428 0.0032010428 0.0051498494 - 1977200 0.0059016387 0.0025410678 0.0053996741 - 1977300 0.0060788044 0.0025806854 0.0055251063 - 1977400 0.0062889813 0.0028776728 0.0059238981 - 1977500 0.0032107879 0.003219768 0.0047749934 - 1977600 0.0048271814 0.0031008448 0.0054390108 - 1977700 0.0039721478 0.0031140292 0.0050380383 - 1977800 0.0049130448 0.0027406432 0.0051203993 - 1977900 0.0039220526 0.0026374838 0.004537228 - 1978000 0.0049530761 0.0026458429 0.0050449892 - 1978100 0.0058477313 0.0027040842 0.0055365791 - 1978200 0.0046354224 0.0029584259 0.0052037086 - 1978300 0.005457118 0.0031401241 0.0057834156 - 1978400 0.0043750854 0.0035560459 0.0056752279 - 1978500 0.0050376813 0.0029973742 0.0054375011 - 1978600 0.0055113232 0.0025874049 0.005256952 - 1978700 0.0048874684 0.0028211325 0.0051885 - 1978800 0.004561218 0.0030247895 0.0052341295 - 1978900 0.004649609 0.0029502179 0.0052023723 - 1979000 0.0061386174 0.0029548338 0.0059282266 - 1979100 0.0043850939 0.0030199504 0.0051439803 - 1979200 0.0059819611 0.0027335317 0.0056310441 - 1979300 0.0048187475 0.0027734638 0.0051075446 - 1979400 0.0045799377 0.0029437671 0.0051621745 - 1979500 0.005523774 0.0024135131 0.0050890911 - 1979600 0.0040420342 0.0019942777 0.003952138 - 1979700 0.0057359773 0.0017813829 0.0045597469 - 1979800 0.0042200444 0.0023567126 0.0044007966 - 1979900 0.0051318171 0.0028423141 0.005328038 - 1980000 0.0064015161 0.0024439437 0.0055446781 - 1980100 0.0053352823 0.0025956758 0.0051799532 - 1980200 0.0050231942 0.002769345 0.0052024547 - 1980300 0.006619252 0.0020366298 0.00524283 - 1980400 0.0062049134 0.0018875618 0.0048930668 - 1980500 0.0051416895 0.0021138048 0.0046043107 - 1980600 0.0052995442 0.0028344629 0.0054014297 - 1980700 0.0056324243 0.0026775714 0.0054057769 - 1980800 0.0070507367 0.0029468265 0.0063620271 - 1980900 0.0048590894 0.0028670738 0.0052206952 - 1981000 0.0043643056 0.0030986563 0.0052126168 - 1981100 0.0059884883 0.0028801275 0.0057808015 - 1981200 0.0052383865 0.0025165771 0.0050539206 - 1981300 0.0042253591 0.0024423829 0.0044890413 - 1981400 0.0041889244 0.0027406088 0.0047696191 - 1981500 0.0042360903 0.003124121 0.0051759772 - 1981600 0.0055854364 0.0025034131 0.0052088588 - 1981700 0.0060298884 0.0023962616 0.0053169888 - 1981800 0.0051099318 0.0029115977 0.0053867209 - 1981900 0.007432557 0.0031682516 0.0067683964 - 1982000 0.0051651015 0.0027414071 0.0052432531 - 1982100 0.0031482323 0.0023919215 0.0039168466 - 1982200 0.0050324706 0.0019992191 0.004436822 - 1982300 0.0045776837 0.0022314753 0.0044487909 - 1982400 0.0050757808 0.0025842099 0.0050427912 - 1982500 0.0038937605 0.0025762614 0.0044623017 - 1982600 0.0048099064 0.0020768117 0.0044066102 - 1982700 0.0048078708 0.0020836694 0.0044124818 - 1982800 0.0038340538 0.0027345713 0.0045916911 - 1982900 0.0046449049 0.0026494406 0.0048993164 - 1983000 0.0055783579 0.0021691463 0.0048711634 - 1983100 0.0047203041 0.0019030225 0.0041894198 - 1983200 0.0055060166 0.0022998265 0.0049668032 - 1983300 0.0055737916 0.0024850769 0.0051848822 - 1983400 0.0050966465 0.0024651767 0.0049338649 - 1983500 0.0034818344 0.0028266297 0.0045131432 - 1983600 0.0059945363 0.0026177563 0.0055213598 - 1983700 0.004267897 0.0022676125 0.0043348751 - 1983800 0.0056603714 0.0022174523 0.0049591946 - 1983900 0.0051517181 0.0022974572 0.0047928206 - 1984000 0.0051474378 0.0025681994 0.0050614896 - 1984100 0.005460167 0.0024815444 0.0051263129 - 1984200 0.0054376744 0.0018492774 0.0044831509 - 1984300 0.0055410768 0.0018767829 0.004560742 - 1984400 0.0050647983 0.0021000771 0.0045533388 - 1984500 0.0043126595 0.0030772223 0.0051661667 - 1984600 0.0037685928 0.0029275743 0.0047529864 - 1984700 0.0081352754 0.0023483682 0.0062888923 - 1984800 0.0057769913 0.0024488912 0.0052471214 - 1984900 0.004978804 0.001879708 0.0042913162 - 1985000 0.0048145303 0.0016232973 0.0039553354 - 1985100 0.0051224975 0.0016960054 0.0041772151 - 1985200 0.0069831704 0.0019689625 0.0053514357 - 1985300 0.0060294024 0.002259717 0.0051802088 - 1985400 0.0057887876 0.0023596115 0.0051635555 - 1985500 0.005588287 0.0019500888 0.0046569153 - 1985600 0.0056547797 0.0018248935 0.0045639275 - 1985700 0.0033519597 0.0015875152 0.0032111206 - 1985800 0.0047733698 0.0019011104 0.0042132115 - 1985900 0.0049710853 0.0020709354 0.0044788048 - 1986000 0.0051061302 0.0020213273 0.0044946091 - 1986100 0.0054134899 0.0021487742 0.0047709334 - 1986200 0.0040267681 0.002647106 0.0045975718 - 1986300 0.0043519756 0.0028408882 0.0049488764 - 1986400 0.0067032628 0.0024620465 0.0057089395 - 1986500 0.005056597 0.0022323524 0.0046816416 - 1986600 0.0051228808 0.0019012453 0.0043826406 - 1986700 0.0058110347 0.0019400205 0.0047547404 - 1986800 0.0050110146 0.002240595 0.0046678052 - 1986900 0.005864026 0.0020852965 0.0049256841 - 1987000 0.0056545357 0.0017174938 0.0044564095 - 1987100 0.0056803806 0.0017661794 0.0045176137 - 1987200 0.0062633742 0.0024604312 0.0054942531 - 1987300 0.0054471498 0.0024218447 0.0050603078 - 1987400 0.0044758873 0.0021148092 0.0042828171 - 1987500 0.0051304638 0.0026949514 0.0051800198 - 1987600 0.0033567354 0.0028827272 0.0045086459 - 1987700 0.0057063021 0.0026394497 0.0054034398 - 1987800 0.0046798921 0.0024753942 0.004742217 - 1987900 0.0054774371 0.0019866846 0.0046398182 - 1988000 0.0050890975 0.0021466774 0.004611709 - 1988100 0.0038729382 0.0023440655 0.0042200199 - 1988200 0.0055760036 0.0018172397 0.0045181165 - 1988300 0.0047048483 0.0017158983 0.0039948092 - 1988400 0.0046541239 0.0018986344 0.0041529757 - 1988500 0.0042934389 0.0021489599 0.0042285943 - 1988600 0.0047159057 0.0027011784 0.0049854453 - 1988700 0.005847541 0.0027889251 0.0056213278 - 1988800 0.004829912 0.0025011755 0.0048406641 - 1988900 0.0056956836 0.0020999981 0.0048588448 - 1989000 0.0047076006 0.0022881468 0.0045683908 - 1989100 0.005091665 0.0021371748 0.0046034501 - 1989200 0.004117067 0.0018519146 0.0038461189 - 1989300 0.0060880931 0.0015364795 0.0044853996 - 1989400 0.0035161215 0.0018072419 0.0035103633 - 1989500 0.0043151298 0.0020787266 0.0041688676 - 1989600 0.0052430814 0.002514277 0.0050538946 - 1989700 0.0043809065 0.0025939534 0.0047159549 - 1989800 0.0041960335 0.0025453096 0.0045777634 - 1989900 0.0039563302 0.0026856849 0.0046020323 - 1990000 0.0057348699 0.0022228385 0.0050006661 - 1990100 0.0047898563 0.0022843105 0.0046043972 - 1990200 0.0051976815 0.0025090598 0.0050266868 - 1990300 0.0050077625 0.0023855288 0.0048111637 - 1990400 0.0053204764 0.0023640181 0.0049411239 - 1990500 0.0052841198 0.0020073376 0.0045668331 - 1990600 0.0053451514 0.0018676685 0.0044567262 - 1990700 0.0033328477 0.0019433734 0.0035577215 - 1990800 0.0044006934 0.0019865754 0.0041181613 - 1990900 0.0050452301 0.0020408853 0.0044846686 - 1991000 0.0065300025 0.0023365408 0.0054995107 - 1991100 0.0051928278 0.0024265468 0.0049418228 - 1991200 0.0053469544 0.0028286653 0.0054185964 - 1991300 0.0034592909 0.0029405703 0.0046161643 - 1991400 0.0057569225 0.002730733 0.0055192423 - 1991500 0.0057598209 0.002308152 0.0050980653 - 1991600 0.005152249 0.0025708244 0.005066445 - 1991700 0.0044006429 0.0029145105 0.0050460719 - 1991800 0.0053758242 0.0030241416 0.0056280565 - 1991900 0.0049695684 0.0032815402 0.0056886749 - 1992000 0.0055769618 0.0034554958 0.0061568366 - 1992100 0.0059583852 0.0032399942 0.006126087 - 1992200 0.0046716994 0.002824056 0.0050869104 - 1992300 0.0048192819 0.0025829998 0.0049173394 - 1992400 0.0038993345 0.002542284 0.0044310241 - 1992500 0.0058376134 0.0024547601 0.0052823541 - 1992600 0.0060848393 0.0020066323 0.0049539764 - 1992700 0.0052477907 0.0020321311 0.0045740297 - 1992800 0.005249679 0.0025529926 0.0050958058 - 1992900 0.0053727672 0.0029005984 0.0055030325 - 1993000 0.0052625154 0.002932028 0.0054810588 - 1993100 0.0047142363 0.0029994144 0.0052828727 - 1993200 0.0053191154 0.0028774698 0.0054539163 - 1993300 0.0048289049 0.0025951217 0.0049341224 - 1993400 0.0076168859 0.0025009687 0.0061903978 - 1993500 0.0039761104 0.0032317131 0.0051576416 - 1993600 0.0044341498 0.0032938349 0.0054416262 - 1993700 0.0044275168 0.0031057684 0.0052503469 - 1993800 0.0075731693 0.0026348982 0.0063031521 - 1993900 0.0038286962 0.0026274942 0.0044820189 - 1994000 0.0050633462 0.0021650901 0.0046176484 - 1994100 0.0056199345 0.0020324649 0.0047546207 - 1994200 0.0048056788 0.0024693387 0.0047970894 - 1994300 0.006459677 0.0024678261 0.0055967322 - 1994400 0.0053801503 0.0024082668 0.0050142771 - 1994500 0.0048374889 0.0022730389 0.0046161976 - 1994600 0.0071441213 0.0018187729 0.0052792067 - 1994700 0.0064209046 0.0015227998 0.0046329255 - 1994800 0.0059406221 0.0016856726 0.0045631614 - 1994900 0.0045269071 0.0019621556 0.0041548762 - 1995000 0.0052455402 0.0020446714 0.0045854799 - 1995100 0.0042616975 0.00222956 0.0042938197 - 1995200 0.0039930582 0.0022136127 0.0041477503 - 1995300 0.0041277274 0.0018235115 0.0038228795 - 1995400 0.0050126134 0.0016191577 0.0040471423 - 1995500 0.0051791589 0.0019933343 0.0045019894 - 1995600 0.0063261234 0.0020172697 0.0050814857 - 1995700 0.0040529898 0.0017794217 0.0037425886 - 1995800 0.004570197 0.0017709365 0.0039846257 - 1995900 0.0054443845 0.0021039712 0.0047410949 - 1996000 0.0065881402 0.0020022043 0.0051933347 - 1996100 0.0047293703 0.0021049099 0.0043956986 - 1996200 0.0058157538 0.002259823 0.0050768287 - 1996300 0.0040998142 0.0023433742 0.0043292217 - 1996400 0.0052792745 0.0026857358 0.0052428843 - 1996500 0.0044951832 0.0025509056 0.00472826 - 1996600 0.0066010422 0.0021231854 0.0053205652 - 1996700 0.0038160025 0.0020482724 0.0038966486 - 1996800 0.0039766657 0.0021095955 0.0040357929 - 1996900 0.0044950258 0.002243618 0.0044208961 - 1997000 0.0045608723 0.0024545671 0.0046637396 - 1997100 0.005528286 0.0025390388 0.0052168023 - 1997200 0.0045379632 0.0023606972 0.0045587731 - 1997300 0.004636872 0.0025142273 0.0047602122 - 1997400 0.0053189046 0.0027464507 0.0053227951 - 1997500 0.0048530074 0.002783892 0.0051345675 - 1997600 0.0057274054 0.0021685357 0.0049427477 - 1997700 0.0038524705 0.0019583496 0.00382439 - 1997800 0.0051296654 0.0022335132 0.0047181949 - 1997900 0.0051018744 0.0027812269 0.0052524473 - 1998000 0.0047275885 0.0028043102 0.0050942359 - 1998100 0.0070847667 0.0019055429 0.0053372267 - 1998200 0.0065207742 0.0018082562 0.0049667562 - 1998300 0.0061191428 0.0020378316 0.0050017913 - 1998400 0.0063659105 0.0026460546 0.0057295425 - 1998500 0.0043373725 0.0027045125 0.0048054273 - 1998600 0.0048756101 0.0024999167 0.0048615404 - 1998700 0.0046508855 0.0023965866 0.0046493593 - 1998800 0.0062661518 0.0022217336 0.0052569009 - 1998900 0.0061555738 0.0023546222 0.0053362283 - 1999000 0.0043069574 0.0024786217 0.0045648042 - 1999100 0.0055141568 0.0028549884 0.0055259081 - 1999200 0.0034372635 0.0027990632 0.0044639877 - 1999300 0.0048351937 0.0023526277 0.0046946746 - 1999400 0.0057087851 0.0020335116 0.0047987044 - 1999500 0.0033912965 0.0023030393 0.0039456986 - 1999600 0.0054813169 0.0023096891 0.004964702 - 1999700 0.0048389727 0.0021943385 0.0045382159 - 1999800 0.0059277298 0.0020055057 0.0048767498 - 1999900 0.0059290305 0.002299977 0.0051718512 - 2000000 0.0047343315 0.0026625608 0.0049557526 -Loop time of 36.7413 on 1 procs for 2000000 steps with 64 atoms - -Pair time (%) = 0 (0) -Bond time (%) = 6.21948 (16.9278) -Neigh time (%) = 3.63757 (9.9005) -Comm time (%) = 3.27223 (8.90612) -Outpt time (%) = 2.95884 (8.05317) -Other time (%) = 20.6532 (56.2125) - -Nlocal: 64 ave 64 max 64 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 4 ave 4 max 4 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 6 -Neighbor list builds = 2000000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 b/examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 deleted file mode 100644 index e68a1d56d40a4afcdd5fe174355874b470241ad3..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2196 zcmai$3oMmk7{`xeGRmmdjaEll5=&yX*5^EDWNECL(nUxmmL1lXbtp?~Ho790b(}8B zN%tEK<;$Ze33JaS4H;?FkuK{bP8!Es&(^-Pef#$N-plh|p6CBR1|pG2GWHluJmRtU z_-_zu=KBVH>ehk&OP6d-t!t+a|Hm8Se?7A^6v_1Mp<8T=>ZObg=eozBxv1n};PI8F zQ!9Wl`bXB5M+57hYg*WrI;?|JUWcw##iVf+iyhqpYDO`7DAs4Te+v-C>@(q|`C>M{ z)4pzj`!vRh=bLUV4;jI@V(U~7br%rES828*cU#$h#Z!;*OWx=pLBWNzm%rrRo!yao z+GQA%Ej%mdMD#+(1ZR#jTGuw-^efb_w~Vv$c=2{sxJWj>el_>=eMyDmVJ$i=d|K`K zxgQAQvdm4prtfF#UHC(pq&%meFO8E{`KphMe#1Mmd3l)$13(xnCEDEKUbg;ws@o6u zPhs<2FqR*PivNPA0%rxM9Mk||43n>IO3||MeMzdEY!&0iwrUHfSPjY(_r=vzeFDN5 z7TogF{tD}#;{UN-@}99ztC7i!Js+?*qV7b%W(^QV7e&Ncr?K;%xNqKJqqv;6VC!#a zSNM0Ac4N_r+jc9=KLTNNZ7OWLtObJTm$ya6DLsaf0j zDtFf3#KBc*IhS#%OK7!YPy^cB>UkX5(F25WyYVJ@#&s57yF0YREuFEKa%a-gInVLt zR*y?E?=B#WlKVE_Lo!%Ad#pDfddbG;pK%UpHOt3H>F5osyw^Y&59IXQwmFMreS3Va zg{#+bG6(6tJU2FH+1-vac#{JJw$yK9cxA;`0LgN3wq)`{xDDAIbRxJ%54wM{@r_?_VJQ zkmMiG{1eE3B>4|C{{`v~N&Nw-KTe?jk<>rX`WMh2B>DqXe~A9^RPP7_)jy)YJk?vm zK=qgCKTq@@iT(r8e_p_UkoXT!{~`XzQ@ diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/phonon.log b/examples/PACKAGES/phonon/2-1D-diatomic/phonon.log deleted file mode 100644 index 86c0a385cec..00000000000 --- a/examples/PACKAGES/phonon/2-1D-diatomic/phonon.log +++ /dev/null @@ -1,206 +0,0 @@ -############################################################ -# group name of the atoms under study : all -# total number of atoms in the group : 64 -# dimension of the system : 1 D -# number of atoms per unit cell : 2 -# dimension of the FFT mesh : 32 x 1 x 1 -# number of wait steps before measurement : 500000 -# frequency of the measurement : 10 -# output result after this many measurement: 50000 -# number of processors used by this run : 1 -############################################################ -# mapping information between lattice index and atom id -# nx ny nz nucell -32 1 1 2 -# l1 l2 l3 k atom_id -0 0 0 0 1 -0 0 0 1 2 -1 0 0 0 3 -1 0 0 1 4 -2 0 0 0 5 -2 0 0 1 6 -3 0 0 0 7 -3 0 0 1 8 -4 0 0 0 9 -4 0 0 1 10 -5 0 0 0 11 -5 0 0 1 12 -6 0 0 0 13 -6 0 0 1 14 -7 0 0 0 15 -7 0 0 1 16 -8 0 0 0 17 -8 0 0 1 18 -9 0 0 0 19 -9 0 0 1 20 -10 0 0 0 21 -10 0 0 1 22 -11 0 0 0 23 -11 0 0 1 24 -12 0 0 0 25 -12 0 0 1 26 -13 0 0 0 27 -13 0 0 1 28 -14 0 0 0 29 -14 0 0 1 30 -15 0 0 0 31 -15 0 0 1 32 -16 0 0 0 33 -16 0 0 1 34 -17 0 0 0 35 -17 0 0 1 36 -18 0 0 0 37 -18 0 0 1 38 -19 0 0 0 39 -19 0 0 1 40 -20 0 0 0 41 -20 0 0 1 42 -21 0 0 0 43 -21 0 0 1 44 -22 0 0 0 45 -22 0 0 1 46 -23 0 0 0 47 -23 0 0 1 48 -24 0 0 0 49 -24 0 0 1 50 -25 0 0 0 51 -25 0 0 1 52 -26 0 0 0 53 -26 0 0 1 54 -27 0 0 0 55 -27 0 0 1 56 -28 0 0 0 57 -28 0 0 1 58 -29 0 0 0 59 -29 0 0 1 60 -30 0 0 0 61 -30 0 0 1 62 -31 0 0 0 63 -31 0 0 1 64 -############################################################ -############################################################ -# Current time step : 1000000 -# Total number of measurements : 50000 -# Average temperature of the measurement : 0.00499889 -# Boltzmann constant under current units : 1 -# basis vector A1 = [2 0 0] -# basis vector A2 = [0 1 0] -# basis vector A3 = [0 0 1] -############################################################ -# qx qy qz Phi(q) -0 0 0 2.0269 0 -1.43323 0 -1.43323 0 1.01345 0 -0.03125 0 0 2.06958 0 -1.44367 0.144297 -1.44367 -0.144297 1.03745 0 -0.0625 0 0 2.00734 -7.10386e-17 -1.36818 0.273607 -1.36818 -0.273607 1.02097 0 -0.09375 0 0 2.06033 7.36546e-16 -1.32894 0.389454 -1.32894 -0.389454 1.00889 3.19674e-16 -0.125 0 0 2.04516 7.25738e-16 -1.20961 0.516478 -1.20961 -0.516478 1.0073 2.84154e-16 -0.15625 0 0 2.05756 0 -1.12954 0.615757 -1.12954 -0.615757 1.02862 0 -0.1875 0 0 2.01319 0 -0.970491 0.627631 -0.970491 -0.627631 0.998014 0 -0.21875 0 0 1.92269 1.42077e-16 -0.863486 0.66779 -0.863486 -0.66779 1.00343 8.73509e-17 -0.25 0 0 1.99044 1.71855e-16 -0.671658 0.661397 -0.671658 -0.661397 0.956893 7.10386e-17 -0.28125 0 0 1.96341 -7.10386e-17 -0.556809 0.66713 -0.556809 -0.66713 0.987126 4.2268e-17 -0.3125 0 0 2.04354 0 -0.442943 0.661601 -0.442943 -0.661601 0.961726 1.77596e-17 -0.34375 0 0 1.98412 0 -0.313464 0.632666 -0.313464 -0.632666 1.01134 -2.21836e-17 -0.375 0 0 2.00509 2.17993e-17 -0.187554 0.499349 -0.187554 -0.499349 0.953607 -8.87982e-18 -0.40625 0 0 1.91679 0 -0.0962947 0.408121 -0.0962947 -0.408121 1.02919 0 -0.4375 0 0 1.98963 0 -0.0137565 0.277826 -0.0137565 -0.277826 1.01624 0 -0.46875 0 0 2.08228 0 -0.0312083 0.0872272 -0.0312083 -0.0872272 0.991567 0 -0.5 0 0 1.95481 0 0.0542224 0 0.0542224 0 1.00583 0 -0.53125 0 0 2.08228 0 -0.0312083 -0.0872272 -0.0312083 0.0872272 0.991567 0 -0.5625 0 0 1.98963 0 -0.0137565 -0.277826 -0.0137565 0.277826 1.01624 0 -0.59375 0 0 1.91679 0 -0.0962947 -0.408121 -0.0962947 0.408121 1.02919 0 -0.625 0 0 2.00509 -2.17993e-17 -0.187554 -0.499349 -0.187554 0.499349 0.953607 8.87982e-18 -0.65625 0 0 1.98412 0 -0.313464 -0.632666 -0.313464 0.632666 1.01134 2.21836e-17 -0.6875 0 0 2.04354 0 -0.442943 -0.661601 -0.442943 0.661601 0.961726 -1.77596e-17 -0.71875 0 0 1.96341 7.10386e-17 -0.556809 -0.66713 -0.556809 0.66713 0.987126 -4.2268e-17 -0.75 0 0 1.99044 -1.71855e-16 -0.671658 -0.661397 -0.671658 0.661397 0.956893 -7.10386e-17 -0.78125 0 0 1.92269 -1.42077e-16 -0.863486 -0.66779 -0.863486 0.66779 1.00343 -8.73509e-17 -0.8125 0 0 2.01319 0 -0.970491 -0.627631 -0.970491 0.627631 0.998014 0 -0.84375 0 0 2.05756 0 -1.12954 -0.615757 -1.12954 0.615757 1.02862 0 -0.875 0 0 2.04516 -7.25738e-16 -1.20961 -0.516478 -1.20961 0.516478 1.0073 -2.84154e-16 -0.90625 0 0 2.06033 -7.36546e-16 -1.32894 -0.389454 -1.32894 0.389454 1.00889 -3.19674e-16 -0.9375 0 0 2.00734 7.10386e-17 -1.36818 -0.273607 -1.36818 0.273607 1.02097 0 -0.96875 0 0 2.06958 0 -1.44367 -0.144297 -1.44367 0.144297 1.03745 0 -############################################################ -# Current time step : 1500000 -# Total number of measurements : 100000 -# Average temperature of the measurement : 0.00499969 -# Boltzmann constant under current units : 1 -# basis vector A1 = [2 0 0] -# basis vector A2 = [0 1 0] -# basis vector A3 = [0 0 1] -############################################################ -# qx qy qz Phi(q) -0 0 0 2.00227 0 -1.41582 0 -1.41582 0 1.00114 0 -0.03125 0 0 2.06839 -2.94857e-15 -1.44775 0.141336 -1.44775 -0.141336 1.03568 -1.48867e-15 -0.0625 0 0 1.99449 0 -1.35985 0.267438 -1.35985 -0.267438 0.997747 0 -0.09375 0 0 2.01906 7.07225e-16 -1.30258 0.390432 -1.30258 -0.390432 1.00279 3.55249e-16 -0.125 0 0 2.0047 0 -1.19787 0.503497 -1.19787 -0.503497 1.00067 -3.55249e-17 -0.15625 0 0 2.05042 4.26299e-16 -1.12849 0.613659 -1.12849 -0.613659 1.03457 1.85685e-16 -0.1875 0 0 1.99151 0 -0.971684 0.625667 -0.971684 -0.625667 0.990665 0 -0.21875 0 0 1.96519 -7.10498e-17 -0.861495 0.687109 -0.861495 -0.687109 1.0008 0 -0.25 0 0 2.01865 0 -0.687312 0.684014 -0.687312 -0.684014 0.977055 0 -0.28125 0 0 1.9933 0 -0.560168 0.698726 -0.560168 -0.698726 1.00805 -4.40715e-17 -0.3125 0 0 2.01323 0 -0.446505 0.648764 -0.446505 -0.648764 1.00283 -1.77625e-17 -0.34375 0 0 2.00398 0 -0.313827 0.630741 -0.313827 -0.630741 0.996834 0 -0.375 0 0 2.0191 0 -0.216211 0.499651 -0.216211 -0.499651 0.978322 0 -0.40625 0 0 1.97734 -4.44061e-18 -0.102328 0.398954 -0.102328 -0.398954 1.03793 0 -0.4375 0 0 1.99332 -2.22031e-18 -0.0639782 0.238226 -0.0639782 -0.238226 1.00811 -1.3774e-18 -0.46875 0 0 2.02854 0 -0.0151203 0.0911116 -0.0151203 -0.0911116 1.00593 0 -0.5 0 0 1.99466 0 0.0671755 0 0.0671755 0 0.967275 0 -0.53125 0 0 2.02854 0 -0.0151203 -0.0911116 -0.0151203 0.0911116 1.00593 0 -0.5625 0 0 1.99332 2.22031e-18 -0.0639782 -0.238226 -0.0639782 0.238226 1.00811 1.3774e-18 -0.59375 0 0 1.97734 4.44061e-18 -0.102328 -0.398954 -0.102328 0.398954 1.03793 0 -0.625 0 0 2.0191 0 -0.216211 -0.499651 -0.216211 0.499651 0.978322 0 -0.65625 0 0 2.00398 0 -0.313827 -0.630741 -0.313827 0.630741 0.996834 0 -0.6875 0 0 2.01323 0 -0.446505 -0.648764 -0.446505 0.648764 1.00283 1.77625e-17 -0.71875 0 0 1.9933 0 -0.560168 -0.698726 -0.560168 0.698726 1.00805 4.40715e-17 -0.75 0 0 2.01865 0 -0.687312 -0.684014 -0.687312 0.684014 0.977055 0 -0.78125 0 0 1.96519 7.10498e-17 -0.861495 -0.687109 -0.861495 0.687109 1.0008 0 -0.8125 0 0 1.99151 0 -0.971684 -0.625667 -0.971684 0.625667 0.990665 0 -0.84375 0 0 2.05042 -4.26299e-16 -1.12849 -0.613659 -1.12849 0.613659 1.03457 -1.85685e-16 -0.875 0 0 2.0047 0 -1.19787 -0.503497 -1.19787 0.503497 1.00067 3.55249e-17 -0.90625 0 0 2.01906 -7.07225e-16 -1.30258 -0.390432 -1.30258 0.390432 1.00279 -3.55249e-16 -0.9375 0 0 1.99449 0 -1.35985 -0.267438 -1.35985 0.267438 0.997747 0 -0.96875 0 0 2.06839 2.94857e-15 -1.44775 -0.141336 -1.44775 0.141336 1.03568 1.48867e-15 -############################################################ -# Current time step : 2000000 -# Total number of measurements : 150000 -# Average temperature of the measurement : 0.00499897 -# Boltzmann constant under current units : 1 -# basis vector A1 = [2 0 0] -# basis vector A2 = [0 1 0] -# basis vector A3 = [0 0 1] -############################################################ -# qx qy qz Phi(q) -0 0 0 1.99479 0 -1.41053 0 -1.41053 0 0.997396 0 -0.03125 0 0 2.03068 0 -1.41965 0.138345 -1.41965 -0.138345 1.0155 0 -0.0625 0 0 1.99892 7.10396e-17 -1.36162 0.269053 -1.36162 -0.269053 1.00066 0 -0.09375 0 0 2.00599 0 -1.29893 0.389829 -1.29893 -0.389829 0.995323 0 -0.125 0 0 1.991 6.87803e-16 -1.20232 0.495552 -1.20232 -0.495552 0.991252 2.84159e-16 -0.15625 0 0 2.05187 1.42079e-16 -1.12612 0.617447 -1.12612 -0.617447 1.02736 0 -0.1875 0 0 1.97476 7.10396e-17 -0.972012 0.630423 -0.972012 -0.630423 0.996946 0 -0.21875 0 0 2.00314 0 -0.862555 0.695244 -0.862555 -0.695244 0.999215 0 -0.25 0 0 1.9755 0 -0.69573 0.680591 -0.69573 -0.680591 0.988546 0 -0.28125 0 0 1.99393 0 -0.560979 0.692292 -0.560979 -0.692292 0.995507 -3.55198e-17 -0.3125 0 0 2.00817 0 -0.436753 0.642127 -0.436753 -0.642127 0.989051 0 -0.34375 0 0 2.02348 0 -0.310766 0.620888 -0.310766 -0.620888 1.01631 0 -0.375 0 0 2.01177 0 -0.213987 0.483325 -0.213987 -0.483325 0.98933 0 -0.40625 0 0 1.97394 0 -0.116509 0.382146 -0.116509 -0.382146 1.03672 0 -0.4375 0 0 1.98656 0 -0.0609164 0.250798 -0.0609164 -0.250798 1.01266 1.39007e-18 -0.46875 0 0 2.03013 0 -0.0242785 0.120597 -0.0242785 -0.120597 1.02741 1.78858e-19 -0.5 0 0 1.98872 0 0.0648313 0 0.0648313 0 0.973791 0 -0.53125 0 0 2.03013 0 -0.0242785 -0.120597 -0.0242785 0.120597 1.02741 -1.78858e-19 -0.5625 0 0 1.98656 0 -0.0609164 -0.250798 -0.0609164 0.250798 1.01266 -1.39007e-18 -0.59375 0 0 1.97394 0 -0.116509 -0.382146 -0.116509 0.382146 1.03672 0 -0.625 0 0 2.01177 0 -0.213987 -0.483325 -0.213987 0.483325 0.98933 0 -0.65625 0 0 2.02348 0 -0.310766 -0.620888 -0.310766 0.620888 1.01631 0 -0.6875 0 0 2.00817 0 -0.436753 -0.642127 -0.436753 0.642127 0.989051 0 -0.71875 0 0 1.99393 0 -0.560979 -0.692292 -0.560979 0.692292 0.995507 3.55198e-17 -0.75 0 0 1.9755 0 -0.69573 -0.680591 -0.69573 0.680591 0.988546 0 -0.78125 0 0 2.00314 0 -0.862555 -0.695244 -0.862555 0.695244 0.999215 0 -0.8125 0 0 1.97476 -7.10396e-17 -0.972012 -0.630423 -0.972012 0.630423 0.996946 0 -0.84375 0 0 2.05187 -1.42079e-16 -1.12612 -0.617447 -1.12612 0.617447 1.02736 0 -0.875 0 0 1.991 -6.87803e-16 -1.20232 -0.495552 -1.20232 0.495552 0.991252 -2.84159e-16 -0.90625 0 0 2.00599 0 -1.29893 -0.389829 -1.29893 0.389829 0.995323 0 -0.9375 0 0 1.99892 -7.10396e-17 -1.36162 -0.269053 -1.36162 0.269053 1.00066 0 -0.96875 0 0 2.03068 0 -1.41965 -0.138345 -1.41965 0.138345 1.0155 0 From fc897512a029cee3a57b299c9dd4b93ab6bbff02 Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Wed, 6 Dec 2023 11:13:34 -0500 Subject: [PATCH 076/719] Initial conversion of all FFT_ settings in the KOKKOS subdirectory to FFT_KOKKOS_ --- src/KOKKOS/fft3d_kokkos.cpp | 84 ++++++++++++++++++------------------ src/KOKKOS/fft3d_kokkos.h | 10 ++--- src/KOKKOS/fftdata_kokkos.h | 86 ++++++++++++++++++------------------- src/KOKKOS/pppm_kokkos.cpp | 4 +- src/KOKKOS/pppm_kokkos.h | 32 +++++++------- 5 files changed, 108 insertions(+), 108 deletions(-) diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index 82e4140f779..ca3d18e11a5 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -44,20 +44,20 @@ FFT3dKokkos::FFT3dKokkos(LAMMPS *lmp, MPI_Comm comm, int nfast, int int ngpus = lmp->kokkos->ngpus; ExecutionSpace execution_space = ExecutionSpaceFromDevice::space; -#if defined(FFT_MKL) +#if defined(FFT_KOKKOS_MKL) if (ngpus > 0 && execution_space == Device) lmp->error->all(FLERR,"Cannot use the MKL library with Kokkos on GPUs"); -#elif defined(FFT_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) if (ngpus > 0 && execution_space == Device) lmp->error->all(FLERR,"Cannot use the FFTW library with Kokkos on GPUs"); -#elif defined(FFT_CUFFT) +#elif defined(FFT_KOKKOS_CUFFT) if (ngpus > 0 && execution_space == Host) lmp->error->all(FLERR,"Cannot use the cuFFT library with Kokkos on the host CPUs"); -#elif defined(FFT_HIPFFT) +#elif defined(FFT_KOKKOS_HIPFFT) if (ngpus > 0 && execution_space == Host) lmp->error->all(FLERR,"Cannot use the hipFFT library with Kokkos on the host CPUs"); -#elif defined(FFT_KISSFFT) +#elif defined(FFT_KOKKOS_KISSFFT) // The compiler can't statically determine the stack size needed for // recursive function calls in KISS FFT and the default per-thread // stack size on GPUs needs to be increased to prevent stack overflows @@ -149,20 +149,20 @@ struct norm_functor { KOKKOS_INLINE_FUNCTION void operator() (const int &i) const { -#if defined(FFT_FFTW3) || defined(FFT_CUFFT) || defined(FFT_HIPFFT) +#if defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_CUFFT) || defined(FFT_KOKKOS_HIPFFT) FFT_SCALAR* out_ptr = (FFT_SCALAR *)(d_out.data()+i); *(out_ptr++) *= norm; *(out_ptr++) *= norm; -#elif defined(FFT_MKL) +#elif defined(FFT_KOKKOS_MKL) d_out(i) *= norm; -#else // FFT_KISS +#else // FFT_KOKKOS_KISS d_out(i).re *= norm; d_out(i).im *= norm; #endif } }; -#ifdef FFT_KISSFFT +#ifdef FFT_KOKKOS_KISSFFT template struct kiss_fft_functor { public: @@ -219,19 +219,19 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, total = plan->total1; length = plan->length1; - #if defined(FFT_MKL) + #if defined(FFT_KOKKOS_MKL) if (flag == 1) DftiComputeForward(plan->handle_fast,d_data.data()); else DftiComputeBackward(plan->handle_fast,d_data.data()); - #elif defined(FFT_FFTW3) + #elif defined(FFT_KOKKOS_FFTW3) if (flag == 1) FFTW_API(execute_dft)(plan->plan_fast_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); else FFTW_API(execute_dft)(plan->plan_fast_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); - #elif defined(FFT_CUFFT) + #elif defined(FFT_KOKKOS_CUFFT) cufftExec(plan->plan_fast,d_data.data(),d_data.data(),-flag); - #elif defined(FFT_HIPFFT) + #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_fast,d_data.data(),d_data.data(),-flag); #else typename FFT_AT::t_FFT_DATA_1d d_tmp = @@ -265,19 +265,19 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, total = plan->total2; length = plan->length2; - #if defined(FFT_MKL) + #if defined(FFT_KOKKOS_MKL) if (flag == 1) DftiComputeForward(plan->handle_mid,d_data.data()); else DftiComputeBackward(plan->handle_mid,d_data.data()); - #elif defined(FFT_FFTW3) + #elif defined(FFT_KOKKOS_FFTW3) if (flag == 1) FFTW_API(execute_dft)(plan->plan_mid_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); else FFTW_API(execute_dft)(plan->plan_mid_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); - #elif defined(FFT_CUFFT) + #elif defined(FFT_KOKKOS_CUFFT) cufftExec(plan->plan_mid,d_data.data(),d_data.data(),-flag); - #elif defined(FFT_HIPFFT) + #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_mid,d_data.data(),d_data.data(),-flag); #else d_tmp = typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); @@ -309,19 +309,19 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, total = plan->total3; length = plan->length3; - #if defined(FFT_MKL) + #if defined(FFT_KOKKOS_MKL) if (flag == 1) DftiComputeForward(plan->handle_slow,d_data.data()); else DftiComputeBackward(plan->handle_slow,d_data.data()); - #elif defined(FFT_FFTW3) + #elif defined(FFT_KOKKOS_FFTW3) if (flag == 1) FFTW_API(execute_dft)(plan->plan_slow_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); else FFTW_API(execute_dft)(plan->plan_slow_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); - #elif defined(FFT_CUFFT) + #elif defined(FFT_KOKKOS_CUFFT) cufftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); - #elif defined(FFT_HIPFFT) + #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); #else d_tmp = typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); @@ -609,46 +609,46 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl // system specific pre-computation of 1d FFT coeffs // and scaling normalization -#if defined(FFT_MKL) - DftiCreateDescriptor( &(plan->handle_fast), FFT_MKL_PREC, DFTI_COMPLEX, 1, +#if defined(FFT_KOKKOS_MKL) + DftiCreateDescriptor( &(plan->handle_fast), FFT_KOKKOS_MKL_PREC, DFTI_COMPLEX, 1, (MKL_LONG)nfast); DftiSetValue(plan->handle_fast, DFTI_NUMBER_OF_TRANSFORMS, (MKL_LONG)plan->total1/nfast); DftiSetValue(plan->handle_fast, DFTI_PLACEMENT,DFTI_INPLACE); DftiSetValue(plan->handle_fast, DFTI_INPUT_DISTANCE, (MKL_LONG)nfast); DftiSetValue(plan->handle_fast, DFTI_OUTPUT_DISTANCE, (MKL_LONG)nfast); -#if defined(FFT_MKL_THREADS) +#if defined(FFT_KOKKOS_MKL_THREADS) DftiSetValue(plan->handle_fast, DFTI_NUMBER_OF_USER_THREADS, nthreads); #endif DftiCommitDescriptor(plan->handle_fast); - DftiCreateDescriptor( &(plan->handle_mid), FFT_MKL_PREC, DFTI_COMPLEX, 1, + DftiCreateDescriptor( &(plan->handle_mid), FFT_KOKKOS_MKL_PREC, DFTI_COMPLEX, 1, (MKL_LONG)nmid); DftiSetValue(plan->handle_mid, DFTI_NUMBER_OF_TRANSFORMS, (MKL_LONG)plan->total2/nmid); DftiSetValue(plan->handle_mid, DFTI_PLACEMENT,DFTI_INPLACE); DftiSetValue(plan->handle_mid, DFTI_INPUT_DISTANCE, (MKL_LONG)nmid); DftiSetValue(plan->handle_mid, DFTI_OUTPUT_DISTANCE, (MKL_LONG)nmid); -#if defined(FFT_MKL_THREADS) +#if defined(FFT_KOKKOS_MKL_THREADS) DftiSetValue(plan->handle_mid, DFTI_NUMBER_OF_USER_THREADS, nthreads); #endif DftiCommitDescriptor(plan->handle_mid); - DftiCreateDescriptor( &(plan->handle_slow), FFT_MKL_PREC, DFTI_COMPLEX, 1, + DftiCreateDescriptor( &(plan->handle_slow), FFT_KOKKOS_MKL_PREC, DFTI_COMPLEX, 1, (MKL_LONG)nslow); DftiSetValue(plan->handle_slow, DFTI_NUMBER_OF_TRANSFORMS, (MKL_LONG)plan->total3/nslow); DftiSetValue(plan->handle_slow, DFTI_PLACEMENT,DFTI_INPLACE); DftiSetValue(plan->handle_slow, DFTI_INPUT_DISTANCE, (MKL_LONG)nslow); DftiSetValue(plan->handle_slow, DFTI_OUTPUT_DISTANCE, (MKL_LONG)nslow); -#if defined(FFT_MKL_THREADS) +#if defined(FFT_KOKKOS_MKL_THREADS) DftiSetValue(plan->handle_slow, DFTI_NUMBER_OF_USER_THREADS, nthreads); #endif DftiCommitDescriptor(plan->handle_slow); -#elif defined(FFT_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) -#if defined (FFT_FFTW_THREADS) +#if defined (FFT_KOKKOS_FFTW_THREADS) if (nthreads > 1) { FFTW_API(init_threads)(); FFTW_API(plan_with_nthreads)(nthreads); @@ -692,7 +692,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl nullptr,&nslow,1,plan->length3, FFTW_BACKWARD,FFTW_ESTIMATE); -#elif defined(FFT_CUFFT) +#elif defined(FFT_KOKKOS_CUFFT) cufftPlanMany(&(plan->plan_fast), 1, &nfast, &nfast,1,plan->length1, @@ -709,7 +709,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl &nslow,1,plan->length3, CUFFT_TYPE,plan->total3/plan->length3); -#elif defined(FFT_HIPFFT) +#elif defined(FFT_KOKKOS_HIPFFT) hipfftPlanMany(&(plan->plan_fast), 1, &nfast, &nfast,1,plan->length1, @@ -726,7 +726,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl &nslow,1,plan->length3, HIPFFT_TYPE,plan->total3/plan->length3); -#else /* FFT_KISS */ +#else /* FFT_KOKKOS_KISS */ kissfftKK = new KissFFTKokkos(); @@ -781,11 +781,11 @@ void FFT3dKokkos::fft_3d_destroy_plan_kokkos(struct fft_plan_3d_kokk if (plan->mid2_plan) remapKK->remap_3d_destroy_plan_kokkos(plan->mid2_plan); if (plan->post_plan) remapKK->remap_3d_destroy_plan_kokkos(plan->post_plan); -#if defined(FFT_MKL) +#if defined(FFT_KOKKOS_MKL) DftiFreeDescriptor(&(plan->handle_fast)); DftiFreeDescriptor(&(plan->handle_mid)); DftiFreeDescriptor(&(plan->handle_slow)); -#elif defined(FFT_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) FFTW_API(destroy_plan)(plan->plan_slow_forward); FFTW_API(destroy_plan)(plan->plan_slow_backward); FFTW_API(destroy_plan)(plan->plan_mid_forward); @@ -793,11 +793,11 @@ void FFT3dKokkos::fft_3d_destroy_plan_kokkos(struct fft_plan_3d_kokk FFTW_API(destroy_plan)(plan->plan_fast_forward); FFTW_API(destroy_plan)(plan->plan_fast_backward); -#if defined (FFT_FFTW_THREADS) +#if defined (FFT_KOKKOS_FFTW_THREADS) FFTW_API(cleanup_threads)(); #endif -#elif defined (FFT_KISSFFT) +#elif defined (FFT_KOKKOS_KISSFFT) delete kissfftKK; #endif @@ -855,7 +855,7 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ // fftw3 and Dfti in MKL encode the number of transforms // into the plan, so we cannot operate on a smaller data set -#if defined(FFT_MKL) || defined(FFT_FFTW3) +#if defined(FFT_KOKKOS_MKL) || defined(FFT_KOKKOS_FFTW3) if ((total1 > nsize) || (total2 > nsize) || (total3 > nsize)) return; #endif @@ -866,7 +866,7 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ // perform 1d FFTs in each of 3 dimensions // data is just an array of 0.0 -#if defined(FFT_MKL) +#if defined(FFT_KOKKOS_MKL) if (flag == -1) { DftiComputeForward(plan->handle_fast,d_data.data()); DftiComputeForward(plan->handle_mid,d_data.data()); @@ -876,7 +876,7 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ DftiComputeBackward(plan->handle_mid,d_data.data()); DftiComputeBackward(plan->handle_slow,d_data.data()); } -#elif defined(FFT_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) if (flag == -1) { FFTW_API(execute_dft)(plan->plan_fast_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); FFTW_API(execute_dft)(plan->plan_mid_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); @@ -886,11 +886,11 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ FFTW_API(execute_dft)(plan->plan_mid_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); FFTW_API(execute_dft)(plan->plan_slow_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); } -#elif defined(FFT_CUFFT) +#elif defined(FFT_KOKKOS_CUFFT) cufftExec(plan->plan_fast,d_data.data(),d_data.data(),-flag); cufftExec(plan->plan_mid,d_data.data(),d_data.data(),-flag); cufftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); -#elif defined(FFT_HIPFFT) +#elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_fast,d_data.data(),d_data.data(),-flag); hipfftExec(plan->plan_mid,d_data.data(),d_data.data(),-flag); hipfftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); diff --git a/src/KOKKOS/fft3d_kokkos.h b/src/KOKKOS/fft3d_kokkos.h index a0489f69bbd..ed49c4b1eed 100644 --- a/src/KOKKOS/fft3d_kokkos.h +++ b/src/KOKKOS/fft3d_kokkos.h @@ -45,22 +45,22 @@ struct fft_plan_3d_kokkos { double norm; // normalization factor for rescaling // system specific 1d FFT info -#if defined(FFT_MKL) +#if defined(FFT_KOKKOS_MKL) DFTI_DESCRIPTOR *handle_fast; DFTI_DESCRIPTOR *handle_mid; DFTI_DESCRIPTOR *handle_slow; -#elif defined(FFT_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) FFTW_API(plan) plan_fast_forward; FFTW_API(plan) plan_fast_backward; FFTW_API(plan) plan_mid_forward; FFTW_API(plan) plan_mid_backward; FFTW_API(plan) plan_slow_forward; FFTW_API(plan) plan_slow_backward; -#elif defined(FFT_CUFFT) +#elif defined(FFT_KOKKOS_CUFFT) cufftHandle plan_fast; cufftHandle plan_mid; cufftHandle plan_slow; -#elif defined(FFT_HIPFFT) +#elif defined(FFT_KOKKOS_HIPFFT) hipfftHandle plan_fast; hipfftHandle plan_mid; hipfftHandle plan_slow; @@ -92,7 +92,7 @@ class FFT3dKokkos : protected Pointers { struct fft_plan_3d_kokkos *plan; RemapKokkos *remapKK; -#ifdef FFT_KISSFFT +#ifdef FFT_KOKKOS_KISSFFT KissFFTKokkos *kissfftKK; #endif diff --git a/src/KOKKOS/fftdata_kokkos.h b/src/KOKKOS/fftdata_kokkos.h index a3812a1cf0b..bed2c7faf0b 100644 --- a/src/KOKKOS/fftdata_kokkos.h +++ b/src/KOKKOS/fftdata_kokkos.h @@ -29,10 +29,10 @@ // Data types for single-precision complex -#if FFT_PRECISION == 1 -#elif FFT_PRECISION == 2 +#if FFT_KOKKOS_PRECISION == 1 +#elif FFT_KOKKOS_PRECISION == 2 #else -#error "FFT_PRECISION needs to be either 1 (=single) or 2 (=double)" +#error "FFT_KOKKOS_PRECISION needs to be either 1 (=single) or 2 (=double)" #endif @@ -41,70 +41,70 @@ // FFTs here, since they may be valid in fft3d.cpp #ifdef KOKKOS_ENABLE_CUDA -# if defined(FFT_FFTW) -# undef FFT_FFTW +# if defined(FFT_KOKKOS_FFTW) +# undef FFT_KOKKOS_FFTW # endif -# if defined(FFT_FFTW3) -# undef FFT_FFTW3 +# if defined(FFT_KOKKOS_FFTW3) +# undef FFT_KOKKOS_FFTW3 # endif -# if defined(FFT_MKL) -# undef FFT_MKL +# if defined(FFT_KOKKOS_MKL) +# undef FFT_KOKKOS_MKL # endif -# if !defined(FFT_CUFFT) && !defined(FFT_KISSFFT) -# define FFT_KISSFFT +# if !defined(FFT_KOKKOS_CUFFT) && !defined(FFT_KOKKOS_KISSFFT) +# define FFT_KOKKOS_KISSFFT # endif #elif defined(KOKKOS_ENABLE_HIP) -# if defined(FFT_FFTW) -# undef FFT_FFTW +# if defined(FFT_KOKKOS_FFTW) +# undef FFT_KOKKOS_FFTW # endif -# if defined(FFT_FFTW3) -# undef FFT_FFTW3 +# if defined(FFT_KOKKOS_FFTW3) +# undef FFT_KOKKOS_FFTW3 # endif -# if defined(FFT_MKL) -# undef FFT_MKL +# if defined(FFT_KOKKOS_MKL) +# undef FFT_KOKKOS_MKL # endif -# if !defined(FFT_HIPFFT) && !defined(FFT_KISSFFT) -# define FFT_KISSFFT +# if !defined(FFT_KOKKOS_HIPFFT) && !defined(FFT_KOKKOS_KISSFFT) +# define FFT_KOKKOS_KISSFFT # endif #else -# if defined(FFT_CUFFT) -# error "Must enable CUDA with KOKKOS to use -DFFT_CUFFT" +# if defined(FFT_KOKKOS_CUFFT) +# error "Must enable CUDA with KOKKOS to use -DFFT_KOKKOS_CUFFT" # endif -# if defined(FFT_HIPFFT) -# error "Must enable HIP with KOKKOS to use -DFFT_HIPFFT" +# if defined(FFT_KOKKOS_HIPFFT) +# error "Must enable HIP with KOKKOS to use -DFFT_KOKKOS_HIPFFT" # endif // if user set FFTW, it means FFTW3 -# ifdef FFT_FFTW -# define FFT_FFTW3 +# ifdef FFT_KOKKOS_FFTW +# define FFT_KOKKOS_FFTW3 # endif -# ifdef FFT_FFTW_THREADS -# if !defined(FFT_FFTW3) -# error "Must use -DFFT_FFTW3 with -DFFT_FFTW_THREADS" +# ifdef FFT_KOKKOS_FFTW_THREADS +# if !defined(FFT_KOKKOS_FFTW3) +# error "Must use -DFFT_KOKKOS_FFTW3 with -DFFT_KOKKOS_FFTW_THREADS" # endif # endif #endif -#if defined(FFT_MKL) +#if defined(FFT_KOKKOS_MKL) #include "mkl_dfti.h" - #if defined(FFT_SINGLE) + #if defined(FFT_KOKKOS_SINGLE) typedef float _Complex FFT_DATA; - #define FFT_MKL_PREC DFTI_SINGLE + #define FFT_KOKKOS_MKL_PREC DFTI_SINGLE #else typedef double _Complex FFT_DATA; - #define FFT_MKL_PREC DFTI_DOUBLE + #define FFT_KOKKOS_MKL_PREC DFTI_DOUBLE #endif -#elif defined(FFT_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) #include "fftw3.h" - #if defined(FFT_SINGLE) + #if defined(FFT_KOKKOS_SINGLE) typedef fftwf_complex FFT_DATA; #define FFTW_API(function) fftwf_ ## function #else typedef fftw_complex FFT_DATA; #define FFTW_API(function) fftw_ ## function #endif -#elif defined(FFT_CUFFT) +#elif defined(FFT_KOKKOS_CUFFT) #include "cufft.h" - #if defined(FFT_SINGLE) + #if defined(FFT_KOKKOS_SINGLE) #define cufftExec cufftExecC2C #define CUFFT_TYPE CUFFT_C2C typedef cufftComplex FFT_DATA; @@ -113,9 +113,9 @@ #define CUFFT_TYPE CUFFT_Z2Z typedef cufftDoubleComplex FFT_DATA; #endif -#elif defined(FFT_HIPFFT) +#elif defined(FFT_KOKKOS_HIPFFT) #include - #if defined(FFT_SINGLE) + #if defined(FFT_KOKKOS_SINGLE) #define hipfftExec hipfftExecC2C #define HIPFFT_TYPE HIPFFT_C2C typedef hipfftComplex FFT_DATA; @@ -125,7 +125,7 @@ typedef hipfftDoubleComplex FFT_DATA; #endif #else - #if defined(FFT_SINGLE) + #if defined(FFT_KOKKOS_SINGLE) #define kiss_fft_scalar float #else #define kiss_fft_scalar double @@ -134,13 +134,13 @@ kiss_fft_scalar re; kiss_fft_scalar im; } FFT_DATA; - #ifndef FFT_KISSFFT - #define FFT_KISSFFT + #ifndef FFT_KOKKOS_KISSFFT + #define FFT_KOKKOS_KISSFFT #endif #endif // (double[2]*) is not a 1D pointer -#if defined(FFT_FFTW3) +#if defined(FFT_KOKKOS_FFTW3) typedef FFT_SCALAR* FFT_DATA_POINTER; #else typedef FFT_DATA* FFT_DATA_POINTER; @@ -216,7 +216,7 @@ typedef struct FFTArrayTypes FFT_DAT; typedef struct FFTArrayTypes FFT_HAT; -#if defined(FFT_KISSFFT) +#if defined(FFT_KOKKOS_KISSFFT) #include "kissfft_kokkos.h" // uses t_FFT_DATA_1d, needs to come last #endif diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 912ae36f6f3..17a9c82bdb8 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -48,7 +48,7 @@ using namespace MathSpecialKokkos; enum{REVERSE_RHO}; enum{FORWARD_IK,FORWARD_IK_PERATOM}; -#ifdef FFT_SINGLE +#ifdef FFT_KOKKOS_SINGLE #define ZEROF 0.0f #define ONEF 1.0f #else @@ -2390,7 +2390,7 @@ void PPPMKokkos::compute_rho_coeff() s = 0.0; for (l = 0; l < j; l++) { a[l+1][k+order] = (a[l][k+1+order]-a[l][k-1+order]) / (l+1); -#ifdef FFT_SINGLE +#ifdef FFT_KOKKOS_SINGLE s += powf(0.5,(float) l+1) * (a[l][k-1+order] + powf(-1.0,(float) l) * a[l][k+1+order]) / (l+1); #else diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h index d621313873f..14d4670dbdf 100644 --- a/src/KOKKOS/pppm_kokkos.h +++ b/src/KOKKOS/pppm_kokkos.h @@ -36,30 +36,30 @@ KSpaceStyle(pppm/kk/host,PPPMKokkos); // fix up FFT defines for KOKKOS with CUDA and HIP #ifdef KOKKOS_ENABLE_CUDA -# if defined(FFT_FFTW) -# undef FFT_FFTW +# if defined(FFT_KOKKOS_FFTW) +# undef FFT_KOKKOS_FFTW # endif -# if defined(FFT_FFTW3) -# undef FFT_FFTW3 +# if defined(FFT_KOKKOS_FFTW3) +# undef FFT_KOKKOS_FFTW3 # endif -# if defined(FFT_MKL) -# undef FFT_MKL +# if defined(FFT_KOKKOS_MKL) +# undef FFT_KOKKOS_MKL # endif -# if !defined(FFT_CUFFT) && !defined(FFT_KISSFFT) -# define FFT_KISSFFT +# if !defined(FFT_KOKKOS_CUFFT) && !defined(FFT_KOKKOS_KISSFFT) +# define FFT_KOKKOS_KISSFFT # endif #elif defined(KOKKOS_ENABLE_HIP) -# if defined(FFT_FFTW) -# undef FFT_FFTW +# if defined(FFT_KOKKOS_FFTW) +# undef FFT_KOKKOS_FFTW # endif -# if defined(FFT_FFTW3) -# undef FFT_FFTW3 +# if defined(FFT_KOKKOS_FFTW3) +# undef FFT_KOKKOS_FFTW3 # endif -# if defined(FFT_MKL) -# undef FFT_MKL +# if defined(FFT_KOKKOS_MKL) +# undef FFT_KOKKOS_MKL # endif -# if !defined(FFT_HIPFFT) && !defined(FFT_KISSFFT) -# define FFT_KISSFFT +# if !defined(FFT_KOKKOS_HIPFFT) && !defined(FFT_KOKKOS_KISSFFT) +# define FFT_KOKKOS_KISSFFT # endif #endif From 0e98e706c69881f5562ce12285f80687ac8baf6c Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Wed, 6 Dec 2023 11:49:54 -0500 Subject: [PATCH 077/719] Added LMPFFT settings for Kokkos-specific FFTs --- src/KOKKOS/lmpfftsettings_kokkos.h | 54 ++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 src/KOKKOS/lmpfftsettings_kokkos.h diff --git a/src/KOKKOS/lmpfftsettings_kokkos.h b/src/KOKKOS/lmpfftsettings_kokkos.h new file mode 100644 index 00000000000..148e001de38 --- /dev/null +++ b/src/KOKKOS/lmpfftsettings_kokkos.h @@ -0,0 +1,54 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +// common FFT library related defines and compilation settings + +#ifndef LMP_FFT_KOKKOS_SETTINGS_H +#define LMP_FFT_KOKKOS_SETTINGS_H + +// if user set FFTW, it means FFTW3 + +#ifdef FFT_KOKKOS_FFTW +#ifndef FFT_KOKKOS_FFTW3 +#define FFT_KOKKOS_FFTW3 +#endif +#endif + +// set strings for library info output + +#if defined(FFT_KOKKOS_FFTW3) +#define LMP_FFT_KOKKOS_LIB "FFTW3" +#elif defined(FFT_KOKKOS_MKL) +#define LMP_FFT_KOKKOS_LIB "MKL FFT" +#elif defined(FFT_KOKKOS_CUFFT) +#define LMP_FFT_KOKKOS_LIB "cuFFT" +#elif defined(FFT_KOKKOS_HIPFFT) +#define LMP_FFT_KOKKOS_LIB "hipFFT" +#else +#define LMP_FFT_KOKKOS_LIB "KISS FFT" +#endif + +#ifdef FFT_KOKKOS_SINGLE +typedef float FFT_KOKKOS_SCALAR; +#define FFT_KOKKOS_PRECISION 1 +#define LMP_FFT_KOKKOS_PREC "single" +#define MPI_FFT_KOKKOS_SCALAR MPI_FLOAT +#else + +typedef double FFT_KOKKOS_SCALAR; +#define FFT_KOKKOS_PRECISION 2 +#define LMP_FFT_KOKKOS_PREC "double" +#define MPI_FFT_KOKKOS_SCALAR MPI_DOUBLE +#endif + +#endif From 48ef968dd21c4e474fdbf927a89b0585f5235568 Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Wed, 6 Dec 2023 12:01:06 -0500 Subject: [PATCH 078/719] Decoupled all variable typenames from the non-kokkos FFT --- src/KOKKOS/fft3d_kokkos.cpp | 120 +++++++++++++++++------------------ src/KOKKOS/fft3d_kokkos.h | 16 ++--- src/KOKKOS/fftdata_kokkos.h | 90 +++++++++++++------------- src/KOKKOS/grid3d_kokkos.cpp | 28 ++++---- src/KOKKOS/grid3d_kokkos.h | 14 ++-- src/KOKKOS/kissfft_kokkos.h | 76 +++++++++++----------- src/KOKKOS/kokkos_base_fft.h | 12 ++-- src/KOKKOS/pack_kokkos.h | 52 +++++++-------- src/KOKKOS/pppm_kokkos.cpp | 114 ++++++++++++++++----------------- src/KOKKOS/pppm_kokkos.h | 50 +++++++-------- src/KOKKOS/remap_kokkos.cpp | 20 +++--- src/KOKKOS/remap_kokkos.h | 20 +++--- 12 files changed, 306 insertions(+), 306 deletions(-) diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index ca3d18e11a5..7093136fe6e 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -88,10 +88,10 @@ FFT3dKokkos::~FFT3dKokkos() /* ---------------------------------------------------------------------- */ template -void FFT3dKokkos::compute(typename FFT_AT::t_FFT_SCALAR_1d d_in, typename FFT_AT::t_FFT_SCALAR_1d d_out, int flag) +void FFT3dKokkos::compute(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_out, int flag) { - typename FFT_AT::t_FFT_DATA_1d d_in_data((FFT_DATA_POINTER)d_in.data(),d_in.size()/2); - typename FFT_AT::t_FFT_DATA_1d d_out_data((FFT_DATA_POINTER)d_out.data(),d_out.size()/2); + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_out_data((FFT_KOKKOS_DATA_POINTER)d_out.data(),d_out.size()/2); fft_3d_kokkos(d_in_data,d_out_data,flag,plan); } @@ -99,9 +99,9 @@ void FFT3dKokkos::compute(typename FFT_AT::t_FFT_SCALAR_1d d_in, typ /* ---------------------------------------------------------------------- */ template -void FFT3dKokkos::timing1d(typename FFT_AT::t_FFT_SCALAR_1d d_in, int nsize, int flag) +void FFT3dKokkos::timing1d(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in, int nsize, int flag) { - typename FFT_AT::t_FFT_DATA_1d d_in_data((FFT_DATA_POINTER)d_in.data(),d_in.size()/2); + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); fft_3d_1d_only_kokkos(d_in_data,nsize,flag,plan); } @@ -140,17 +140,17 @@ template struct norm_functor { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; - typename FFT_AT::t_FFT_DATA_1d_um d_out; + typedef FFTArrayTypes FFT_KOKKOS_AT; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_out; int norm; - norm_functor(typename FFT_AT::t_FFT_DATA_1d &d_out_, int norm_): + norm_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d &d_out_, int norm_): d_out(d_out_),norm(norm_) {} KOKKOS_INLINE_FUNCTION void operator() (const int &i) const { #if defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_CUFFT) || defined(FFT_KOKKOS_HIPFFT) - FFT_SCALAR* out_ptr = (FFT_SCALAR *)(d_out.data()+i); + FFT_KOKKOS_SCALAR* out_ptr = (FFT_KOKKOS_SCALAR *)(d_out.data()+i); *(out_ptr++) *= norm; *(out_ptr++) *= norm; #elif defined(FFT_KOKKOS_MKL) @@ -167,14 +167,14 @@ template struct kiss_fft_functor { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; - typename FFT_AT::t_FFT_DATA_1d_um d_data,d_tmp; + typedef FFTArrayTypes FFT_KOKKOS_AT; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_data,d_tmp; kiss_fft_state_kokkos st; int length; kiss_fft_functor() = default; - kiss_fft_functor(typename FFT_AT::t_FFT_DATA_1d &d_data_,typename FFT_AT::t_FFT_DATA_1d &d_tmp_, kiss_fft_state_kokkos &st_, int length_): + kiss_fft_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d &d_data_,typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d &d_tmp_, kiss_fft_state_kokkos &st_, int length_): d_data(d_data_), d_tmp(d_tmp_), st(st_) @@ -191,11 +191,11 @@ struct kiss_fft_functor { #endif template -void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, typename FFT_AT::t_FFT_DATA_1d d_out, int flag, struct fft_plan_3d_kokkos *plan) +void FFT3dKokkos::fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_in, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_out, int flag, struct fft_plan_3d_kokkos *plan) { int total,length; - typename FFT_AT::t_FFT_DATA_1d d_data,d_copy; - typename FFT_AT::t_FFT_SCALAR_1d d_in_scalar,d_data_scalar,d_out_scalar,d_copy_scalar,d_scratch_scalar; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_data,d_copy; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in_scalar,d_data_scalar,d_out_scalar,d_copy_scalar,d_scratch_scalar; // pre-remap to prepare for 1st FFTs if needed // copy = loc for remap result @@ -204,9 +204,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, if (plan->pre_target == 0) d_copy = d_out; else d_copy = plan->d_copy; - d_in_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_in.data(),d_in.size()*2); - d_copy_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_copy.data(),d_copy.size()*2); - d_scratch_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_in_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_in.data(),d_in.size()*2); + d_copy_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); + d_scratch_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_in_scalar, d_copy_scalar, d_scratch_scalar, plan->pre_plan); @@ -226,16 +226,16 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, DftiComputeBackward(plan->handle_fast,d_data.data()); #elif defined(FFT_KOKKOS_FFTW3) if (flag == 1) - FFTW_API(execute_dft)(plan->plan_fast_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_fast_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); else - FFTW_API(execute_dft)(plan->plan_fast_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_fast_backward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); #elif defined(FFT_KOKKOS_CUFFT) cufftExec(plan->plan_fast,d_data.data(),d_data.data(),-flag); #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_fast,d_data.data(),d_data.data(),-flag); #else - typename FFT_AT::t_FFT_DATA_1d d_tmp = - typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_tmp = + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); kiss_fft_functor f; if (flag == 1) f = kiss_fft_functor(d_data,d_tmp,plan->cfg_fast_forward,length); @@ -251,9 +251,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, if (plan->mid1_target == 0) d_copy = d_out; else d_copy = plan->d_copy; - d_data_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_data.data(),d_data.size()*2); - d_copy_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_copy.data(),d_copy.size()*2); - d_scratch_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_data_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); + d_copy_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); + d_scratch_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_data_scalar, d_copy_scalar, d_scratch_scalar, plan->mid1_plan); @@ -272,15 +272,15 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, DftiComputeBackward(plan->handle_mid,d_data.data()); #elif defined(FFT_KOKKOS_FFTW3) if (flag == 1) - FFTW_API(execute_dft)(plan->plan_mid_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_mid_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); else - FFTW_API(execute_dft)(plan->plan_mid_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_mid_backward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); #elif defined(FFT_KOKKOS_CUFFT) cufftExec(plan->plan_mid,d_data.data(),d_data.data(),-flag); #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_mid,d_data.data(),d_data.data(),-flag); #else - d_tmp = typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + d_tmp = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); if (flag == 1) f = kiss_fft_functor(d_data,d_tmp,plan->cfg_mid_forward,length); else @@ -295,9 +295,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, if (plan->mid2_target == 0) d_copy = d_out; else d_copy = plan->d_copy; - d_data_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_data.data(),d_data.size()*2); - d_copy_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_copy.data(),d_copy.size()*2); - d_scratch_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_data_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); + d_copy_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); + d_scratch_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_data_scalar, d_copy_scalar, d_scratch_scalar, plan->mid2_plan); @@ -316,15 +316,15 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, DftiComputeBackward(plan->handle_slow,d_data.data()); #elif defined(FFT_KOKKOS_FFTW3) if (flag == 1) - FFTW_API(execute_dft)(plan->plan_slow_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_slow_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); else - FFTW_API(execute_dft)(plan->plan_slow_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_slow_backward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); #elif defined(FFT_KOKKOS_CUFFT) cufftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); #else - d_tmp = typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + d_tmp = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); if (flag == 1) f = kiss_fft_functor(d_data,d_tmp,plan->cfg_slow_forward,length); else @@ -337,9 +337,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, // destination is always out if (plan->post_plan) { - d_data_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_data.data(),d_data.size()*2); - d_out_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_out.data(),d_out.size()*2); - d_scratch_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_data_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); + d_out_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_out.data(),d_out.size()*2); + d_scratch_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_data_scalar, d_out_scalar, d_scratch_scalar, plan->post_plan); @@ -348,7 +348,7 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, // scaling if required if (flag == -1 && plan->scaled) { - FFT_SCALAR norm = plan->norm; + FFT_KOKKOS_SCALAR norm = plan->norm; int num = plan->normnum; norm_functor f(d_out,norm); @@ -443,7 +443,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl plan->pre_plan = remapKK->remap_3d_create_plan_kokkos(comm,in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi, first_ilo,first_ihi,first_jlo,first_jhi, - first_klo,first_khi,2,0,0,FFT_PRECISION, + first_klo,first_khi,2,0,0,FFT_KOKKOS_PRECISION, usecollective,usecuda_aware); if (plan->pre_plan == nullptr) return nullptr; } @@ -468,7 +468,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl first_ilo,first_ihi,first_jlo,first_jhi, first_klo,first_khi, second_ilo,second_ihi,second_jlo,second_jhi, - second_klo,second_khi,2,1,0,FFT_PRECISION, + second_klo,second_khi,2,1,0,FFT_KOKKOS_PRECISION, usecollective,usecuda_aware); if (plan->mid1_plan == nullptr) return nullptr; @@ -509,7 +509,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl second_jlo,second_jhi,second_klo,second_khi, second_ilo,second_ihi, third_jlo,third_jhi,third_klo,third_khi, - third_ilo,third_ihi,2,1,0,FFT_PRECISION, + third_ilo,third_ihi,2,1,0,FFT_KOKKOS_PRECISION, usecollective,usecuda_aware); if (plan->mid2_plan == nullptr) return nullptr; @@ -537,7 +537,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl third_klo,third_khi,third_ilo,third_ihi, third_jlo,third_jhi, out_klo,out_khi,out_ilo,out_ihi, - out_jlo,out_jhi,2,(permute+1)%3,0,FFT_PRECISION, + out_jlo,out_jhi,2,(permute+1)%3,0,FFT_KOKKOS_PRECISION, usecollective,usecuda_aware); if (plan->post_plan == nullptr) return nullptr; } @@ -599,11 +599,11 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl *nbuf = copy_size + scratch_size; if (copy_size) { - plan->d_copy = typename FFT_AT::t_FFT_DATA_1d("fft3d:copy",copy_size); + plan->d_copy = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d("fft3d:copy",copy_size); } if (scratch_size) { - plan->d_scratch = typename FFT_AT::t_FFT_DATA_1d("fft3d:scratch",scratch_size); + plan->d_scratch = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d("fft3d:scratch",scratch_size); } // system specific pre-computation of 1d FFT coeffs @@ -697,34 +697,34 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl cufftPlanMany(&(plan->plan_fast), 1, &nfast, &nfast,1,plan->length1, &nfast,1,plan->length1, - CUFFT_TYPE,plan->total1/plan->length1); + CUFFT_KOKKOS_TYPE,plan->total1/plan->length1); cufftPlanMany(&(plan->plan_mid), 1, &nmid, &nmid,1,plan->length2, &nmid,1,plan->length2, - CUFFT_TYPE,plan->total2/plan->length2); + CUFFT_KOKKOS_TYPE,plan->total2/plan->length2); cufftPlanMany(&(plan->plan_slow), 1, &nslow, &nslow,1,plan->length3, &nslow,1,plan->length3, - CUFFT_TYPE,plan->total3/plan->length3); + CUFFT_KOKKOS_TYPE,plan->total3/plan->length3); #elif defined(FFT_KOKKOS_HIPFFT) hipfftPlanMany(&(plan->plan_fast), 1, &nfast, &nfast,1,plan->length1, &nfast,1,plan->length1, - HIPFFT_TYPE,plan->total1/plan->length1); + HIPFFT_KOKKOS_TYPE,plan->total1/plan->length1); hipfftPlanMany(&(plan->plan_mid), 1, &nmid, &nmid,1,plan->length2, &nmid,1,plan->length2, - HIPFFT_TYPE,plan->total2/plan->length2); + HIPFFT_KOKKOS_TYPE,plan->total2/plan->length2); hipfftPlanMany(&(plan->plan_slow), 1, &nslow, &nslow,1,plan->length3, &nslow,1,plan->length3, - HIPFFT_TYPE,plan->total3/plan->length3); + HIPFFT_KOKKOS_TYPE,plan->total3/plan->length3); #else /* FFT_KOKKOS_KISS */ @@ -838,7 +838,7 @@ void FFT3dKokkos::bifactor(int n, int *factor1, int *factor2) ------------------------------------------------------------------------- */ template -void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_1d d_data, int nsize, int flag, +void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_data, int nsize, int flag, struct fft_plan_3d_kokkos *plan) { // total = size of data needed in each dim @@ -878,13 +878,13 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ } #elif defined(FFT_KOKKOS_FFTW3) if (flag == -1) { - FFTW_API(execute_dft)(plan->plan_fast_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); - FFTW_API(execute_dft)(plan->plan_mid_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); - FFTW_API(execute_dft)(plan->plan_slow_forward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_fast_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_mid_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_slow_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); } else { - FFTW_API(execute_dft)(plan->plan_fast_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); - FFTW_API(execute_dft)(plan->plan_mid_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); - FFTW_API(execute_dft)(plan->plan_slow_backward,(FFT_DATA*)d_data.data(),(FFT_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_fast_backward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_mid_backward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); + FFTW_API(execute_dft)(plan->plan_slow_backward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); } #elif defined(FFT_KOKKOS_CUFFT) cufftExec(plan->plan_fast,d_data.data(),d_data.data(),-flag); @@ -896,8 +896,8 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ hipfftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); #else kiss_fft_functor f; - typename FFT_AT::t_FFT_DATA_1d d_tmp = - typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_tmp = + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); if (flag == -1) { f = kiss_fft_functor(d_data,d_tmp,plan->cfg_fast_forward,length1); Kokkos::parallel_for(total1/length1,f); @@ -923,7 +923,7 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ // limit num to size of data if (flag == 1 && plan->scaled) { - FFT_SCALAR norm = plan->norm; + FFT_KOKKOS_SCALAR norm = plan->norm; int num = MIN(plan->normnum,nsize); norm_functor f(d_data,norm); diff --git a/src/KOKKOS/fft3d_kokkos.h b/src/KOKKOS/fft3d_kokkos.h index ed49c4b1eed..bb552ec4efd 100644 --- a/src/KOKKOS/fft3d_kokkos.h +++ b/src/KOKKOS/fft3d_kokkos.h @@ -28,14 +28,14 @@ namespace LAMMPS_NS { template struct fft_plan_3d_kokkos { typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; + typedef FFTArrayTypes FFT_KOKKOS_AT; struct remap_plan_3d_kokkos *pre_plan; // remap from input -> 1st FFTs struct remap_plan_3d_kokkos *mid1_plan; // remap from 1st -> 2nd FFTs struct remap_plan_3d_kokkos *mid2_plan; // remap from 2nd -> 3rd FFTs struct remap_plan_3d_kokkos *post_plan; // remap from 3rd FFTs -> output - typename FFT_AT::t_FFT_DATA_1d d_copy; // memory for remap results (if needed) - typename FFT_AT::t_FFT_DATA_1d d_scratch; // scratch space for remaps + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_copy; // memory for remap results (if needed) + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_scratch; // scratch space for remaps int total1,total2,total3; // # of 1st,2nd,3rd FFTs (times length) int length1,length2,length3; // length of 1st,2nd,3rd FFTs int pre_target; // where to put remap results @@ -79,14 +79,14 @@ class FFT3dKokkos : protected Pointers { public: enum{FORWARD=1,BACKWARD=-1}; typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; + typedef FFTArrayTypes FFT_KOKKOS_AT; FFT3dKokkos(class LAMMPS *, MPI_Comm, int,int,int,int,int,int,int,int,int,int,int,int,int,int,int, int,int,int *,int,int); ~FFT3dKokkos() override; - void compute(typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, int); - void timing1d(typename FFT_AT::t_FFT_SCALAR_1d, int, int); + void compute(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, int); + void timing1d(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, int, int); private: struct fft_plan_3d_kokkos *plan; @@ -96,7 +96,7 @@ class FFT3dKokkos : protected Pointers { KissFFTKokkos *kissfftKK; #endif - void fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d, typename FFT_AT::t_FFT_DATA_1d, int, struct fft_plan_3d_kokkos *); + void fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d, int, struct fft_plan_3d_kokkos *); struct fft_plan_3d_kokkos *fft_3d_create_plan_kokkos(MPI_Comm, int, int, int, int, int, int, int, int, @@ -105,7 +105,7 @@ class FFT3dKokkos : protected Pointers { void fft_3d_destroy_plan_kokkos(struct fft_plan_3d_kokkos *); - void fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_1d, int, int, struct fft_plan_3d_kokkos *); + void fft_3d_1d_only_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d, int, int, struct fft_plan_3d_kokkos *); void bifactor(int, int *, int *); }; diff --git a/src/KOKKOS/fftdata_kokkos.h b/src/KOKKOS/fftdata_kokkos.h index bed2c7faf0b..a9ea2de8963 100644 --- a/src/KOKKOS/fftdata_kokkos.h +++ b/src/KOKKOS/fftdata_kokkos.h @@ -20,10 +20,10 @@ // data types for 2d/3d FFTs -#ifndef LMP_FFT_DATA_KOKKOS_H -#define LMP_FFT_DATA_KOKKOS_H +#ifndef LMP_FFT_KOKKOS_DATA_H +#define LMP_FFT_KOKKOS_DATA_H -#include "lmpfftsettings.h" +#include "lmpfftsettings_kokkos.h" // ------------------------------------------------------------------------- @@ -87,42 +87,42 @@ #if defined(FFT_KOKKOS_MKL) #include "mkl_dfti.h" #if defined(FFT_KOKKOS_SINGLE) - typedef float _Complex FFT_DATA; + typedef float _Complex FFT_KOKKOS_DATA; #define FFT_KOKKOS_MKL_PREC DFTI_SINGLE #else - typedef double _Complex FFT_DATA; + typedef double _Complex FFT_KOKKOS_DATA; #define FFT_KOKKOS_MKL_PREC DFTI_DOUBLE #endif #elif defined(FFT_KOKKOS_FFTW3) #include "fftw3.h" #if defined(FFT_KOKKOS_SINGLE) - typedef fftwf_complex FFT_DATA; + typedef fftwf_complex FFT_KOKKOS_DATA; #define FFTW_API(function) fftwf_ ## function #else - typedef fftw_complex FFT_DATA; + typedef fftw_complex FFT_KOKKOS_DATA; #define FFTW_API(function) fftw_ ## function #endif #elif defined(FFT_KOKKOS_CUFFT) #include "cufft.h" #if defined(FFT_KOKKOS_SINGLE) #define cufftExec cufftExecC2C - #define CUFFT_TYPE CUFFT_C2C - typedef cufftComplex FFT_DATA; + #define CUFFT_KOKKOS_TYPE CUFFT_KOKKOS_C2C + typedef cufftComplex FFT_KOKKOS_DATA; #else #define cufftExec cufftExecZ2Z - #define CUFFT_TYPE CUFFT_Z2Z - typedef cufftDoubleComplex FFT_DATA; + #define CUFFT_KOKKOS_TYPE CUFFT_KOKKOS_Z2Z + typedef cufftDoubleComplex FFT_KOKKOS_DATA; #endif #elif defined(FFT_KOKKOS_HIPFFT) #include #if defined(FFT_KOKKOS_SINGLE) #define hipfftExec hipfftExecC2C - #define HIPFFT_TYPE HIPFFT_C2C - typedef hipfftComplex FFT_DATA; + #define HIPFFT_KOKKOS_TYPE HIPFFT_KOKKOS_C2C + typedef hipfftComplex FFT_KOKKOS_DATA; #else #define hipfftExec hipfftExecZ2Z - #define HIPFFT_TYPE HIPFFT_Z2Z - typedef hipfftDoubleComplex FFT_DATA; + #define HIPFFT_KOKKOS_TYPE HIPFFT_KOKKOS_Z2Z + typedef hipfftDoubleComplex FFT_KOKKOS_DATA; #endif #else #if defined(FFT_KOKKOS_SINGLE) @@ -133,7 +133,7 @@ typedef struct { kiss_fft_scalar re; kiss_fft_scalar im; - } FFT_DATA; + } FFT_KOKKOS_DATA; #ifndef FFT_KOKKOS_KISSFFT #define FFT_KOKKOS_KISSFFT #endif @@ -141,9 +141,9 @@ // (double[2]*) is not a 1D pointer #if defined(FFT_KOKKOS_FFTW3) - typedef FFT_SCALAR* FFT_DATA_POINTER; + typedef FFT_KOKKOS_SCALAR* FFT_KOKKOS_DATA_POINTER; #else - typedef FFT_DATA* FFT_DATA_POINTER; + typedef FFT_KOKKOS_DATA* FFT_KOKKOS_DATA_POINTER; #endif @@ -154,23 +154,23 @@ template <> struct FFTArrayTypes { typedef Kokkos:: - DualView tdual_FFT_SCALAR_1d; -typedef tdual_FFT_SCALAR_1d::t_dev t_FFT_SCALAR_1d; -typedef tdual_FFT_SCALAR_1d::t_dev_um t_FFT_SCALAR_1d_um; + DualView tdual_FFT_KOKKOS_SCALAR_1d; +typedef tdual_FFT_KOKKOS_SCALAR_1d::t_dev t_FFT_KOKKOS_SCALAR_1d; +typedef tdual_FFT_KOKKOS_SCALAR_1d::t_dev_um t_FFT_KOKKOS_SCALAR_1d_um; -typedef Kokkos::DualView tdual_FFT_SCALAR_2d; -typedef tdual_FFT_SCALAR_2d::t_dev t_FFT_SCALAR_2d; +typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_2d; +typedef tdual_FFT_KOKKOS_SCALAR_2d::t_dev t_FFT_KOKKOS_SCALAR_2d; -typedef Kokkos::DualView tdual_FFT_SCALAR_2d_3; -typedef tdual_FFT_SCALAR_2d_3::t_dev t_FFT_SCALAR_2d_3; +typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_2d_3; +typedef tdual_FFT_KOKKOS_SCALAR_2d_3::t_dev t_FFT_KOKKOS_SCALAR_2d_3; -typedef Kokkos::DualView tdual_FFT_SCALAR_3d; -typedef tdual_FFT_SCALAR_3d::t_dev t_FFT_SCALAR_3d; +typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_3d; +typedef tdual_FFT_KOKKOS_SCALAR_3d::t_dev t_FFT_KOKKOS_SCALAR_3d; typedef Kokkos:: - DualView tdual_FFT_DATA_1d; -typedef tdual_FFT_DATA_1d::t_dev t_FFT_DATA_1d; -typedef tdual_FFT_DATA_1d::t_dev_um t_FFT_DATA_1d_um; + DualView tdual_FFT_KOKKOS_DATA_1d; +typedef tdual_FFT_KOKKOS_DATA_1d::t_dev t_FFT_KOKKOS_DATA_1d; +typedef tdual_FFT_KOKKOS_DATA_1d::t_dev_um t_FFT_KOKKOS_DATA_1d_um; typedef Kokkos:: DualView tdual_int_64; @@ -186,23 +186,23 @@ struct FFTArrayTypes { //Kspace typedef Kokkos:: - DualView tdual_FFT_SCALAR_1d; -typedef tdual_FFT_SCALAR_1d::t_host t_FFT_SCALAR_1d; -typedef tdual_FFT_SCALAR_1d::t_host_um t_FFT_SCALAR_1d_um; + DualView tdual_FFT_KOKKOS_SCALAR_1d; +typedef tdual_FFT_KOKKOS_SCALAR_1d::t_host t_FFT_KOKKOS_SCALAR_1d; +typedef tdual_FFT_KOKKOS_SCALAR_1d::t_host_um t_FFT_KOKKOS_SCALAR_1d_um; -typedef Kokkos::DualView tdual_FFT_SCALAR_2d; -typedef tdual_FFT_SCALAR_2d::t_host t_FFT_SCALAR_2d; +typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_2d; +typedef tdual_FFT_KOKKOS_SCALAR_2d::t_host t_FFT_KOKKOS_SCALAR_2d; -typedef Kokkos::DualView tdual_FFT_SCALAR_2d_3; -typedef tdual_FFT_SCALAR_2d_3::t_host t_FFT_SCALAR_2d_3; +typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_2d_3; +typedef tdual_FFT_KOKKOS_SCALAR_2d_3::t_host t_FFT_KOKKOS_SCALAR_2d_3; -typedef Kokkos::DualView tdual_FFT_SCALAR_3d; -typedef tdual_FFT_SCALAR_3d::t_host t_FFT_SCALAR_3d; +typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_3d; +typedef tdual_FFT_KOKKOS_SCALAR_3d::t_host t_FFT_KOKKOS_SCALAR_3d; typedef Kokkos:: - DualView tdual_FFT_DATA_1d; -typedef tdual_FFT_DATA_1d::t_host t_FFT_DATA_1d; -typedef tdual_FFT_DATA_1d::t_host_um t_FFT_DATA_1d_um; + DualView tdual_FFT_KOKKOS_DATA_1d; +typedef tdual_FFT_KOKKOS_DATA_1d::t_host t_FFT_KOKKOS_DATA_1d; +typedef tdual_FFT_KOKKOS_DATA_1d::t_host_um t_FFT_KOKKOS_DATA_1d_um; typedef Kokkos:: DualView tdual_int_64; @@ -212,12 +212,12 @@ typedef tdual_int_64::t_host_um t_int_64_um; }; #endif -typedef struct FFTArrayTypes FFT_DAT; -typedef struct FFTArrayTypes FFT_HAT; +typedef struct FFTArrayTypes FFT_KOKKOS_DAT; +typedef struct FFTArrayTypes FFT_KOKKOS_HAT; #if defined(FFT_KOKKOS_KISSFFT) -#include "kissfft_kokkos.h" // uses t_FFT_DATA_1d, needs to come last +#include "kissfft_kokkos.h" // uses t_FFT_KOKKOS_DATA_1d, needs to come last #endif diff --git a/src/KOKKOS/grid3d_kokkos.cpp b/src/KOKKOS/grid3d_kokkos.cpp index 9a82e0157db..0f8e0bdc4e7 100644 --- a/src/KOKKOS/grid3d_kokkos.cpp +++ b/src/KOKKOS/grid3d_kokkos.cpp @@ -636,7 +636,7 @@ void Grid3dKokkos::setup_comm_tiled(int &nbuf1, int &nbuf2) template void Grid3dKokkos::forward_comm(int caller, void *ptr, int which, int nper, int nbyte, - FFT_DAT::tdual_FFT_SCALAR_1d& k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d& k_buf2, + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d& k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d& k_buf2, MPI_Datatype datatype) { if (caller == KSPACE) { @@ -655,14 +655,14 @@ void Grid3dKokkos::forward_comm(int caller, void *ptr, int which, in template void Grid3dKokkos:: forward_comm_kspace_brick(KSpace *kspace, int which, int nper, - FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int m; MPI_Request request; KokkosBaseFFT* kspaceKKBase = dynamic_cast(kspace); - FFT_SCALAR* buf1; - FFT_SCALAR* buf2; + FFT_KOKKOS_SCALAR* buf1; + FFT_KOKKOS_SCALAR* buf2; if (lmp->kokkos->gpu_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); @@ -709,13 +709,13 @@ forward_comm_kspace_brick(KSpace *kspace, int which, int nper, template void Grid3dKokkos:: forward_comm_kspace_tiled(KSpace *kspace, int which, int nper, - FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int i,m,offset; KokkosBaseFFT* kspaceKKBase = dynamic_cast(kspace); - FFT_SCALAR* buf1; - FFT_SCALAR* buf2; + FFT_KOKKOS_SCALAR* buf1; + FFT_KOKKOS_SCALAR* buf2; if (lmp->kokkos->gpu_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); @@ -776,7 +776,7 @@ forward_comm_kspace_tiled(KSpace *kspace, int which, int nper, template void Grid3dKokkos::reverse_comm(int caller, void *ptr, int which, int nper, int nbyte, - FFT_DAT::tdual_FFT_SCALAR_1d& k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d& k_buf2, + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d& k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d& k_buf2, MPI_Datatype datatype) { if (caller == KSPACE) { @@ -795,14 +795,14 @@ void Grid3dKokkos::reverse_comm(int caller, void *ptr, int which, in template void Grid3dKokkos:: reverse_comm_kspace_brick(KSpace *kspace, int which, int nper, - FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int m; MPI_Request request; KokkosBaseFFT* kspaceKKBase = dynamic_cast(kspace); - FFT_SCALAR* buf1; - FFT_SCALAR* buf2; + FFT_KOKKOS_SCALAR* buf1; + FFT_KOKKOS_SCALAR* buf2; if (lmp->kokkos->gpu_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); @@ -850,14 +850,14 @@ reverse_comm_kspace_brick(KSpace *kspace, int which, int nper, template void Grid3dKokkos:: reverse_comm_kspace_tiled(KSpace *kspace, int which, int nper, - FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int i,m,offset; KokkosBaseFFT* kspaceKKBase = dynamic_cast(kspace); - FFT_SCALAR* buf1; - FFT_SCALAR* buf2; + FFT_KOKKOS_SCALAR* buf1; + FFT_KOKKOS_SCALAR* buf2; if (lmp->kokkos->gpu_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); diff --git a/src/KOKKOS/grid3d_kokkos.h b/src/KOKKOS/grid3d_kokkos.h index 19751d83c9c..8e9f6cd051f 100644 --- a/src/KOKKOS/grid3d_kokkos.h +++ b/src/KOKKOS/grid3d_kokkos.h @@ -27,16 +27,16 @@ class Grid3dKokkos : public Grid3d { enum { KSPACE = 0, PAIR = 1, FIX = 2 }; // calling classes typedef DeviceType device_type; typedef ArrayTypes AT; - typedef FFTArrayTypes FFT_AT; + typedef FFTArrayTypes FFT_KOKKOS_AT; Grid3dKokkos(class LAMMPS *, MPI_Comm, int, int, int); Grid3dKokkos(class LAMMPS *, MPI_Comm, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int); ~Grid3dKokkos() override; void forward_comm(int, void *, int, int, int, - FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); void reverse_comm(int, void *, int, int, int, - FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); private: DAT::tdual_int_2d k_swap_packlist; @@ -57,13 +57,13 @@ class Grid3dKokkos : public Grid3d { void setup_comm_tiled(int &, int &) override; void forward_comm_kspace_brick(class KSpace *, int, int, - FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); void forward_comm_kspace_tiled(class KSpace *, int, int, - FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); void reverse_comm_kspace_brick(class KSpace *, int, int, - FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); void reverse_comm_kspace_tiled(class KSpace *, int, int, - FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); void grow_swap() override; diff --git a/src/KOKKOS/kissfft_kokkos.h b/src/KOKKOS/kissfft_kokkos.h index 265677a21c7..fc23bf7891c 100644 --- a/src/KOKKOS/kissfft_kokkos.h +++ b/src/KOKKOS/kissfft_kokkos.h @@ -119,14 +119,14 @@ }while(0) */ -#define KISS_FFT_COS(phase) (FFT_SCALAR) cos(phase) -#define KISS_FFT_SIN(phase) (FFT_SCALAR) sin(phase) +#define KISS_FFT_KOKKOS_COS(phase) (FFT_KOKKOS_SCALAR) cos(phase) +#define KISS_FFT_KOKKOS_SIN(phase) (FFT_KOKKOS_SCALAR) sin(phase) #define HALF_OF(x) ((x)*.5) #define kf_cexp(x,x_index,phase) \ do{ \ - (x)(x_index).re = KISS_FFT_COS(phase);\ - (x)(x_index).im = KISS_FFT_SIN(phase);\ + (x)(x_index).re = KISS_FFT_KOKKOS_COS(phase);\ + (x)(x_index).im = KISS_FFT_KOKKOS_SIN(phase);\ }while(0) @@ -138,26 +138,26 @@ namespace LAMMPS_NS { template struct kiss_fft_state_kokkos { typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; + typedef FFTArrayTypes FFT_KOKKOS_AT; int nfft; int inverse; - typename FFT_AT::t_int_64 d_factors; - typename FFT_AT::t_FFT_DATA_1d d_twiddles; - typename FFT_AT::t_FFT_DATA_1d d_scratch; + typename FFT_KOKKOS_AT::t_int_64 d_factors; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_twiddles; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_scratch; }; template class KissFFTKokkos { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; + typedef FFTArrayTypes FFT_KOKKOS_AT; KOKKOS_INLINE_FUNCTION - static void kf_bfly2(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly2(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, int m, int Fout_count) { - typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_SCALAR t[2]; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_KOKKOS_SCALAR t[2]; int Fout2_count; int tw1_count = 0; @@ -179,11 +179,11 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kf_bfly4(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly4(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, const size_t m, int Fout_count) { - typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_SCALAR scratch[6][2]; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_KOKKOS_SCALAR scratch[6][2]; size_t k=m; const size_t m2=2*m; const size_t m3=3*m; @@ -237,14 +237,14 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kf_bfly3(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly3(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, size_t m, int Fout_count) { size_t k=m; const size_t m2 = 2*m; - typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_SCALAR scratch[5][2]; - FFT_SCALAR epi3[2]; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_KOKKOS_SCALAR scratch[5][2]; + FFT_KOKKOS_SCALAR epi3[2]; //C_EQ(epi3,d_twiddles[fstride*m]); epi3[0] = d_twiddles(fstride*m).re; epi3[1] = d_twiddles(fstride*m).im; @@ -289,13 +289,13 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kf_bfly5(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly5(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, int m, int Fout_count) { int u; - FFT_SCALAR scratch[13][2]; - typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_SCALAR ya[2],yb[2]; + FFT_KOKKOS_SCALAR scratch[13][2]; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_KOKKOS_SCALAR ya[2],yb[2]; //C_EQ(ya,d_twiddles[fstride*m]); ya[1] = d_twiddles(fstride*m).im; ya[0] = d_twiddles(fstride*m).re; @@ -369,15 +369,15 @@ class KissFFTKokkos { /* perform the butterfly for one stage of a mixed radix FFT */ KOKKOS_INLINE_FUNCTION - static void kf_bfly_generic(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly_generic(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, int m, int p, int Fout_count) { int u,k,q1,q; - typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_SCALAR t[2]; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_KOKKOS_SCALAR t[2]; int Norig = st.nfft; - typename FFT_AT::t_FFT_DATA_1d_um d_scratch = st.d_scratch; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_scratch = st.d_scratch; for ( u=0; u &st, int Fout_count, int f_count, int factors_count) + const typename FFT_KOKKOS_AT::t_int_64_um &d_factors, const kiss_fft_state_kokkos &st, int Fout_count, int f_count, int factors_count) { const int beg = Fout_count; const int p = d_factors[factors_count++]; /* the radix */ @@ -452,7 +452,7 @@ class KissFFTKokkos { p[i] * m[i] = m[i-1] m0 = n */ - static int kf_factor(int n, FFT_HAT::t_int_64 h_facbuf) + static int kf_factor(int n, FFT_KOKKOS_HAT::t_int_64 h_facbuf) { int p=4, nf=0; double floor_sqrt; @@ -496,12 +496,12 @@ class KissFFTKokkos { st.nfft = nfft; st.inverse = inverse_fft; - typename FFT_AT::tdual_int_64 k_factors = typename FFT_AT::tdual_int_64(); - typename FFT_AT::tdual_FFT_DATA_1d k_twiddles = typename FFT_AT::tdual_FFT_DATA_1d(); + typename FFT_KOKKOS_AT::tdual_int_64 k_factors = typename FFT_KOKKOS_AT::tdual_int_64(); + typename FFT_KOKKOS_AT::tdual_FFT_KOKKOS_DATA_1d k_twiddles = typename FFT_KOKKOS_AT::tdual_FFT_KOKKOS_DATA_1d(); if (nfft > 0) { - k_factors = typename FFT_AT::tdual_int_64("kissfft:factors",MAXFACTORS*2); - k_twiddles = typename FFT_AT::tdual_FFT_DATA_1d("kissfft:twiddles",nfft); + k_factors = typename FFT_KOKKOS_AT::tdual_int_64("kissfft:factors",MAXFACTORS*2); + k_twiddles = typename FFT_KOKKOS_AT::tdual_FFT_KOKKOS_DATA_1d("kissfft:twiddles",nfft); for (i=0;i(); @@ -524,12 +524,12 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kiss_fft_stride(const kiss_fft_state_kokkos &st, const typename FFT_AT::t_FFT_DATA_1d_um &d_fin, typename FFT_AT::t_FFT_DATA_1d_um &d_fout, int in_stride, int offset) + static void kiss_fft_stride(const kiss_fft_state_kokkos &st, const typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_fin, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_fout, int in_stride, int offset) { //if (d_fin.data() == d_fout.data()) { // // NOTE: this is not really an in-place FFT algorithm. // // It just performs an out-of-place FFT into a temp buffer - // typename FFT_AT::t_FFT_DATA_1d_um d_tmpbuf = typename FFT_AT::t_FFT_DATA_1d("kissfft:tmpbuf",d_fin.extent(1)); + // typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_tmpbuf = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d("kissfft:tmpbuf",d_fin.extent(1)); // kf_work(d_tmpbuf,d_fin,1,in_stride,st.d_factors,st,offset,offset).re; // Kokkos::deep_copy(d_fout,d_tmpbuf); //} else { @@ -538,7 +538,7 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kiss_fft_kokkos(const kiss_fft_state_kokkos &cfg, const typename FFT_AT::t_FFT_DATA_1d_um d_fin, typename FFT_AT::t_FFT_DATA_1d_um d_fout, int offset) + static void kiss_fft_kokkos(const kiss_fft_state_kokkos &cfg, const typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_fin, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_fout, int offset) { kiss_fft_stride(cfg,d_fin,d_fout,1,offset); } diff --git a/src/KOKKOS/kokkos_base_fft.h b/src/KOKKOS/kokkos_base_fft.h index 08369b3c78e..567dc02ff3a 100644 --- a/src/KOKKOS/kokkos_base_fft.h +++ b/src/KOKKOS/kokkos_base_fft.h @@ -12,8 +12,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifndef LMP_KOKKOS_BASE_FFT_H -#define LMP_KOKKOS_BASE_FFT_H +#ifndef LMP_KOKKOS_BASE_FFT_KOKKOS_H +#define LMP_KOKKOS_BASE_FFT_KOKKOS_H #include "fftdata_kokkos.h" @@ -24,10 +24,10 @@ class KokkosBaseFFT { KokkosBaseFFT() {} // Kspace - virtual void pack_forward_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {}; - virtual void unpack_forward_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) {}; - virtual void pack_reverse_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {}; - virtual void unpack_reverse_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) {}; + virtual void pack_forward_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {}; + virtual void unpack_forward_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) {}; + virtual void pack_reverse_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {}; + virtual void unpack_reverse_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) {}; }; } diff --git a/src/KOKKOS/pack_kokkos.h b/src/KOKKOS/pack_kokkos.h index fe90d294a67..97d35afe268 100644 --- a/src/KOKKOS/pack_kokkos.h +++ b/src/KOKKOS/pack_kokkos.h @@ -38,13 +38,13 @@ template class PackKokkos { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; + typedef FFTArrayTypes FFT_KOKKOS_AT; struct pack_3d_functor { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; - typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; + typedef FFTArrayTypes FFT_KOKKOS_AT; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -52,7 +52,7 @@ struct pack_3d_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - pack_3d_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + pack_3d_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -80,7 +80,7 @@ struct pack_3d_functor { } }; -static void pack_3d(typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, struct pack_plan_3d *plan) +static void pack_3d(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -98,7 +98,7 @@ struct unpack_3d_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -106,7 +106,7 @@ struct unpack_3d_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -134,7 +134,7 @@ struct unpack_3d_functor { } }; -static void unpack_3d(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -153,7 +153,7 @@ struct unpack_3d_permute1_1_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -161,7 +161,7 @@ struct unpack_3d_permute1_1_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute1_1_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute1_1_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -189,7 +189,7 @@ struct unpack_3d_permute1_1_functor { } }; -static void unpack_3d_permute1_1(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute1_1(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -206,7 +206,7 @@ struct unpack_3d_permute1_2_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -214,7 +214,7 @@ struct unpack_3d_permute1_2_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute1_2_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute1_2_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -243,7 +243,7 @@ struct unpack_3d_permute1_2_functor { } }; -static void unpack_3d_permute1_2(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute1_2(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -261,7 +261,7 @@ struct unpack_3d_permute1_n_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -270,7 +270,7 @@ struct unpack_3d_permute1_n_functor { int nstride_plane; // stride between successive slow indices int nqty; // # of values/element - unpack_3d_permute1_n_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute1_n_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -299,7 +299,7 @@ struct unpack_3d_permute1_n_functor { } }; -static void unpack_3d_permute1_n(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute1_n(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -317,7 +317,7 @@ struct unpack_3d_permute2_1_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -325,7 +325,7 @@ struct unpack_3d_permute2_1_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute2_1_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute2_1_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -352,7 +352,7 @@ struct unpack_3d_permute2_1_functor { } }; -static void unpack_3d_permute2_1(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute2_1(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -370,7 +370,7 @@ struct unpack_3d_permute2_2_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -378,7 +378,7 @@ struct unpack_3d_permute2_2_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute2_2_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute2_2_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -406,7 +406,7 @@ struct unpack_3d_permute2_2_functor { } }; -static void unpack_3d_permute2_2(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute2_2(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -423,7 +423,7 @@ struct unpack_3d_permute2_n_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -432,7 +432,7 @@ struct unpack_3d_permute2_n_functor { int nstride_plane; // stride between successive slow indices int nqty; // # of values/element - unpack_3d_permute2_n_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute2_n_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -460,7 +460,7 @@ struct unpack_3d_permute2_n_functor { } }; -static void unpack_3d_permute2_n(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute2_n(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 17a9c82bdb8..3fc90c088d2 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -285,7 +285,7 @@ void PPPMKokkos::init() estimated_accuracy); mesg += fmt::format(" estimated relative force accuracy = {:.8g}\n", estimated_accuracy/two_charge_force); - mesg += " using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"; + mesg += " using " LMP_FFT_KOKKOS_PREC " precision " LMP_FFT_KOKKOS_LIB "\n"; mesg += fmt::format(" 3d grid and FFT values/proc = {} {}\n", ngrid_max,nfft_both_max); utils::logmesg(lmp,mesg); @@ -582,7 +582,7 @@ void PPPMKokkos::compute(int eflag, int vflag) if (atom->nmax > nmax) { nmax = atomKK->nmax; d_part2grid = typename AT::t_int_1d_3("pppm:part2grid",nmax); - d_rho1d = typename FFT_AT::t_FFT_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); + d_rho1d = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); } // find grid points for all my particles @@ -595,8 +595,8 @@ void PPPMKokkos::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), - k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_KOKKOS_SCALAR), + k_gc_buf1,k_gc_buf2,MPI_FFT_KOKKOS_SCALAR); brick2fft(); // compute potential gradient on my FFT grid and @@ -609,14 +609,14 @@ void PPPMKokkos::compute(int eflag, int vflag) // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks - gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), - k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_KOKKOS_SCALAR), + k_gc_buf1,k_gc_buf2,MPI_FFT_KOKKOS_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) - gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), - k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_KOKKOS_SCALAR), + k_gc_buf1,k_gc_buf2,MPI_FFT_KOKKOS_SCALAR); // calculate the force on my particles @@ -730,8 +730,8 @@ void PPPMKokkos::allocate() npergrid = 3; - k_gc_buf1 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); - k_gc_buf2 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); + k_gc_buf1 = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); + k_gc_buf2 = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); // tally local grid sizes // ngrid = count of owned+ghost grid cells on this proc @@ -753,7 +753,7 @@ void PPPMKokkos::allocate() // allocate distributed grid data - d_density_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:density_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_density_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:density_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); memoryKK->create_kokkos(k_density_fft,density_fft,nfft_both,"pppm:d_density_fft"); d_density_fft = k_density_fft.view(); @@ -775,17 +775,17 @@ void PPPMKokkos::allocate() d_fkz = typename AT::t_float_1d("pppm:d_fkz",nfft_both); } - d_vdx_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_vdx_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_vdy_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_vdy_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_vdz_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_vdz_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_vdx_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdx_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_vdy_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdy_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_vdz_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdz_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); // summation coeffs order_allocated = order; k_gf_b = typename DAT::tdual_float_1d("pppm:gf_b",order); d_gf_b = k_gf_b.view(); - d_rho1d = typename FFT_AT::t_FFT_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); - k_rho_coeff = FFT_DAT::tdual_FFT_SCALAR_2d("pppm:rho_coeff",order,order/2-(1-order)/2+1); + d_rho1d = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); + k_rho_coeff = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_2d("pppm:rho_coeff",order,order/2-(1-order)/2+1); d_rho_coeff = k_rho_coeff.view(); h_rho_coeff = k_rho_coeff.h_view; @@ -810,7 +810,7 @@ void PPPMKokkos::allocate() remap = new RemapKokkos(lmp,world, nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, - 1,0,0,FFT_PRECISION,collective_flag,gpu_aware_flag); + 1,0,0,FFT_KOKKOS_PRECISION,collective_flag,gpu_aware_flag); } /* ---------------------------------------------------------------------- @@ -847,14 +847,14 @@ void PPPMKokkos::allocate_peratom() { peratom_allocate_flag = 1; - d_u_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:u_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_u_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:u_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v0_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v0_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v1_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v1_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v2_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v2_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v3_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v3_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v4_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v4_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v5_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v5_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v0_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v0_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v1_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v1_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v2_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v2_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v3_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v3_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v4_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v4_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v5_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v5_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); // use same GC ghost grid object for peratom grid communication @@ -862,8 +862,8 @@ void PPPMKokkos::allocate_peratom() npergrid = 7; - k_gc_buf1 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); - k_gc_buf2 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); + k_gc_buf1 = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); + k_gc_buf2 = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); } /* ---------------------------------------------------------------------- @@ -1234,14 +1234,14 @@ KOKKOS_INLINE_FUNCTION void PPPMKokkos::operator()(TagPPPM_make_rho_atomic, const int &i) const { // The density_brick array is atomic for Half/Thread neighbor style - Kokkos::View::value,Kokkos::MemoryTraits > a_density_brick = d_density_brick; + Kokkos::View::value,Kokkos::MemoryTraits > a_density_brick = d_density_brick; int nx = d_part2grid(i,0); int ny = d_part2grid(i,1); int nz = d_part2grid(i,2); - const FFT_SCALAR dx = nx+shiftone - (x(i,0)-boxlo[0])*delxinv; - const FFT_SCALAR dy = ny+shiftone - (x(i,1)-boxlo[1])*delyinv; - const FFT_SCALAR dz = nz+shiftone - (x(i,2)-boxlo[2])*delzinv; + const FFT_KOKKOS_SCALAR dx = nx+shiftone - (x(i,0)-boxlo[0])*delxinv; + const FFT_KOKKOS_SCALAR dy = ny+shiftone - (x(i,1)-boxlo[1])*delyinv; + const FFT_KOKKOS_SCALAR dz = nz+shiftone - (x(i,2)-boxlo[2])*delzinv; nz -= nzlo_out; @@ -1250,13 +1250,13 @@ void PPPMKokkos::operator()(TagPPPM_make_rho_atomic, const int &i) c compute_rho1d(i,dx,dy,dz); - const FFT_SCALAR z0 = delvolinv * q[i]; + const FFT_KOKKOS_SCALAR z0 = delvolinv * q[i]; for (int n = nlower; n <= nupper; n++) { const int mz = n+nz; - const FFT_SCALAR y0 = z0*d_rho1d(i,n+order/2,2); + const FFT_KOKKOS_SCALAR y0 = z0*d_rho1d(i,n+order/2,2); for (int m = nlower; m <= nupper; m++) { const int my = m+ny; - const FFT_SCALAR x0 = y0*d_rho1d(i,m+order/2,1); + const FFT_KOKKOS_SCALAR x0 = y0*d_rho1d(i,m+order/2,1); for (int l = nlower; l <= nupper; l++) { const int mx = l+nx; a_density_brick(mz,my,mx) += x0*d_rho1d(i,l+order/2,0); @@ -1294,9 +1294,9 @@ void PPPMKokkos::operator() (TagPPPM_make_rho, typename Kokkos::Team if ( ((nz+nlower-nzlo_out)*ix*iy >= ito) || ((nz+nupper-nzlo_out+1)*ix*iy < ifrom) ) continue; - const FFT_SCALAR dx = nx+shiftone - (x(i,0)-boxlo[0])*delxinv; - const FFT_SCALAR dy = ny+shiftone - (x(i,1)-boxlo[1])*delyinv; - const FFT_SCALAR dz = nz+shiftone - (x(i,2)-boxlo[2])*delzinv; + const FFT_KOKKOS_SCALAR dx = nx+shiftone - (x(i,0)-boxlo[0])*delxinv; + const FFT_KOKKOS_SCALAR dy = ny+shiftone - (x(i,1)-boxlo[1])*delyinv; + const FFT_KOKKOS_SCALAR dz = nz+shiftone - (x(i,2)-boxlo[2])*delzinv; nz -= nzlo_out; ny -= nylo_out; @@ -1304,15 +1304,15 @@ void PPPMKokkos::operator() (TagPPPM_make_rho, typename Kokkos::Team compute_rho1d(i,dx,dy,dz); - const FFT_SCALAR z0 = delvolinv * q[i]; + const FFT_KOKKOS_SCALAR z0 = delvolinv * q[i]; for (int n = nlower; n <= nupper; n++) { const int mz = n+nz; const int in = mz*ix*iy; - const FFT_SCALAR y0 = z0*d_rho1d(i,n+order/2,2); + const FFT_KOKKOS_SCALAR y0 = z0*d_rho1d(i,n+order/2,2); for (int m = nlower; m <= nupper; m++) { const int my = m+ny; const int im = in+my*ix; - const FFT_SCALAR x0 = y0*d_rho1d(i,m+order/2,1); + const FFT_KOKKOS_SCALAR x0 = y0*d_rho1d(i,m+order/2,1); for (int l = nlower; l <= nupper; l++) { const int mx = l+nx; const int il = im+mx; @@ -2040,8 +2040,8 @@ KOKKOS_INLINE_FUNCTION void PPPMKokkos::operator()(TagPPPM_fieldforce_ik, const int &i) const { int l,m,n,nx,ny,nz,mx,my,mz; - FFT_SCALAR x0,y0,z0; - FFT_SCALAR ekx,eky,ekz; + FFT_KOKKOS_SCALAR x0,y0,z0; + FFT_KOKKOS_SCALAR ekx,eky,ekz; nx = d_part2grid(i,0); ny = d_part2grid(i,1); @@ -2100,8 +2100,8 @@ KOKKOS_INLINE_FUNCTION void PPPMKokkos::operator()(TagPPPM_fieldforce_peratom, const int &i) const { int l,m,n,nx,ny,nz,mx,my,mz; - FFT_SCALAR dx,dy,dz,x0,y0,z0; - FFT_SCALAR u,v0,v1,v2,v3,v4,v5; + FFT_KOKKOS_SCALAR dx,dy,dz,x0,y0,z0; + FFT_KOKKOS_SCALAR u,v0,v1,v2,v3,v4,v5; nx = d_part2grid(i,0); ny = d_part2grid(i,1); @@ -2155,7 +2155,7 @@ void PPPMKokkos::operator()(TagPPPM_fieldforce_peratom, const int &i ------------------------------------------------------------------------- */ template -void PPPMKokkos::pack_forward_grid_kokkos(int flag, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index) +void PPPMKokkos::pack_forward_grid_kokkos(int flag, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index) { typename AT::t_int_2d_um d_list = k_list.view(); d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL()); @@ -2211,7 +2211,7 @@ void PPPMKokkos::operator()(TagPPPM_pack_forward2, const int &i) con ------------------------------------------------------------------------- */ template -void PPPMKokkos::unpack_forward_grid_kokkos(int flag, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int offset, int nlist, DAT::tdual_int_2d &k_list, int index) +void PPPMKokkos::unpack_forward_grid_kokkos(int flag, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf, int offset, int nlist, DAT::tdual_int_2d &k_list, int index) { typename AT::t_int_2d_um d_list = k_list.view(); d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL()); @@ -2269,7 +2269,7 @@ void PPPMKokkos::operator()(TagPPPM_unpack_forward2, const int &i) c ------------------------------------------------------------------------- */ template -void PPPMKokkos::pack_reverse_grid_kokkos(int /*flag*/, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index) +void PPPMKokkos::pack_reverse_grid_kokkos(int /*flag*/, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index) { typename AT::t_int_2d_um d_list = k_list.view(); d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL()); @@ -2299,7 +2299,7 @@ void PPPMKokkos::operator()(TagPPPM_pack_reverse, const int &i) cons ------------------------------------------------------------------------- */ template -void PPPMKokkos::unpack_reverse_grid_kokkos(int /*flag*/, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int offset, int nlist, DAT::tdual_int_2d &k_list, int index) +void PPPMKokkos::unpack_reverse_grid_kokkos(int /*flag*/, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf, int offset, int nlist, DAT::tdual_int_2d &k_list, int index) { typename AT::t_int_2d_um d_list = k_list.view(); d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL()); @@ -2332,11 +2332,11 @@ void PPPMKokkos::operator()(TagPPPM_unpack_reverse, const int &i) co template KOKKOS_INLINE_FUNCTION -void PPPMKokkos::compute_rho1d(const int i, const FFT_SCALAR &dx, const FFT_SCALAR &dy, - const FFT_SCALAR &dz) const +void PPPMKokkos::compute_rho1d(const int i, const FFT_KOKKOS_SCALAR &dx, const FFT_KOKKOS_SCALAR &dy, + const FFT_KOKKOS_SCALAR &dz) const { int k,l; - FFT_SCALAR r1,r2,r3; + FFT_KOKKOS_SCALAR r1,r2,r3; for (k = (1-order)/2; k <= order/2; k++) { r1 = r2 = r3 = ZEROF; @@ -2375,10 +2375,10 @@ template void PPPMKokkos::compute_rho_coeff() { int j,k,l,m; - FFT_SCALAR s; - FFT_SCALAR **a = new FFT_SCALAR *[order]; + FFT_KOKKOS_SCALAR s; + FFT_KOKKOS_SCALAR **a = new FFT_KOKKOS_SCALAR *[order]; for (int i = 0; i < order; ++i) - a[i] = new FFT_SCALAR[2*order+1]; + a[i] = new FFT_KOKKOS_SCALAR[2*order+1]; for (k = 0; k <= 2*order; k++) for (l = 0; l < order; l++) @@ -2586,18 +2586,18 @@ double PPPMKokkos::memory_usage() double bytes = (double)nmax*3 * sizeof(double); int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * (nzhi_out-nzlo_out+1); - bytes += (double)4 * nbrick * sizeof(FFT_SCALAR); + bytes += (double)4 * nbrick * sizeof(FFT_KOKKOS_SCALAR); if (triclinic) bytes += (double)3 * nfft_both * sizeof(double); bytes += (double)6 * nfft_both * sizeof(double); bytes += (double)nfft_both * sizeof(double); - bytes += (double)nfft_both*5 * sizeof(FFT_SCALAR); + bytes += (double)nfft_both*5 * sizeof(FFT_KOKKOS_SCALAR); if (peratom_allocate_flag) - bytes += (double)6 * nbrick * sizeof(FFT_SCALAR); + bytes += (double)6 * nbrick * sizeof(FFT_KOKKOS_SCALAR); // two Grid3d bufs - bytes += (double)(ngc_buf1 + ngc_buf2) * npergrid * sizeof(FFT_SCALAR); + bytes += (double)(ngc_buf1 + ngc_buf2) * npergrid * sizeof(FFT_KOKKOS_SCALAR); return bytes; } diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h index 14d4670dbdf..dc0fbd88e52 100644 --- a/src/KOKKOS/pppm_kokkos.h +++ b/src/KOKKOS/pppm_kokkos.h @@ -131,7 +131,7 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typedef FFTArrayTypes FFT_AT; + typedef FFTArrayTypes FFT_KOKKOS_AT; PPPMKokkos(class LAMMPS *); ~PPPMKokkos() override; @@ -350,7 +350,7 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { int nx,ny,nz; typename AT::t_int_1d_um d_list_index; - typename FFT_AT::t_FFT_SCALAR_1d_um d_buf; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf; int unpack_offset; DAT::tdual_int_scalar k_flag; @@ -364,31 +364,31 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; - typename FFT_AT::t_FFT_SCALAR_3d d_density_brick; - typename FFT_AT::t_FFT_SCALAR_3d d_vdx_brick,d_vdy_brick,d_vdz_brick; - typename FFT_AT::t_FFT_SCALAR_3d d_u_brick; - typename FFT_AT::t_FFT_SCALAR_3d d_v0_brick,d_v1_brick,d_v2_brick; - typename FFT_AT::t_FFT_SCALAR_3d d_v3_brick,d_v4_brick,d_v5_brick; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_density_brick; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_vdx_brick,d_vdy_brick,d_vdz_brick; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_u_brick; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_v0_brick,d_v1_brick,d_v2_brick; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_v3_brick,d_v4_brick,d_v5_brick; typename AT::t_float_1d d_greensfn; typename AT::t_virial_array d_vg; typename AT::t_float_1d d_fkx; typename AT::t_float_1d d_fky; typename AT::t_float_1d d_fkz; - FFT_DAT::tdual_FFT_SCALAR_1d k_density_fft; - FFT_DAT::tdual_FFT_SCALAR_1d k_work1; - FFT_DAT::tdual_FFT_SCALAR_1d k_work2; - typename FFT_AT::t_FFT_SCALAR_1d d_density_fft; - typename FFT_AT::t_FFT_SCALAR_1d d_work1; - typename FFT_AT::t_FFT_SCALAR_1d d_work2; + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_density_fft; + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_work1; + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_work2; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_density_fft; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_work1; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_work2; DAT::tdual_float_1d k_gf_b; typename AT::t_float_1d d_gf_b; - //FFT_SCALAR **rho1d,**rho_coeff,**drho1d,**drho_coeff; - typename FFT_AT::t_FFT_SCALAR_2d_3 d_rho1d; - FFT_DAT::tdual_FFT_SCALAR_2d k_rho_coeff; - typename FFT_AT::t_FFT_SCALAR_2d d_rho_coeff; - FFT_HAT::t_FFT_SCALAR_2d h_rho_coeff; + //FFT_KOKKOS_SCALAR **rho1d,**rho_coeff,**drho1d,**drho_coeff; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_2d_3 d_rho1d; + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_2d k_rho_coeff; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_2d d_rho_coeff; + FFT_KOKKOS_HAT::t_FFT_KOKKOS_SCALAR_2d h_rho_coeff; //double **acons; typename Kokkos::DualView::t_host acons; @@ -398,7 +398,7 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { RemapKokkos *remap; Grid3dKokkos *gc; - FFT_DAT::tdual_FFT_SCALAR_1d k_gc_buf1,k_gc_buf2; + FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_gc_buf1,k_gc_buf2; int ngc_buf1,ngc_buf2,npergrid; //int **part2grid; // storage for particle -> grid mapping @@ -429,17 +429,17 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { void fieldforce_peratom() override; KOKKOS_INLINE_FUNCTION - void compute_rho1d(const int i, const FFT_SCALAR &, const FFT_SCALAR &, - const FFT_SCALAR &) const; + void compute_rho1d(const int i, const FFT_KOKKOS_SCALAR &, const FFT_KOKKOS_SCALAR &, + const FFT_KOKKOS_SCALAR &) const; void compute_rho_coeff(); void slabcorr() override; // grid communication - void pack_forward_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) override; - void unpack_forward_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) override; - void pack_reverse_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) override; - void unpack_reverse_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) override; + void pack_forward_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, DAT::tdual_int_2d &, int) override; + void unpack_forward_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) override; + void pack_reverse_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, DAT::tdual_int_2d &, int) override; + void unpack_reverse_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) override; // triclinic diff --git a/src/KOKKOS/remap_kokkos.cpp b/src/KOKKOS/remap_kokkos.cpp index efc6742a259..d6b8a5691c1 100644 --- a/src/KOKKOS/remap_kokkos.cpp +++ b/src/KOKKOS/remap_kokkos.cpp @@ -59,7 +59,7 @@ RemapKokkos::~RemapKokkos() /* ---------------------------------------------------------------------- */ template -void RemapKokkos::perform(typename FFT_AT::t_FFT_SCALAR_1d d_in, typename FFT_AT::t_FFT_SCALAR_1d d_out, typename FFT_AT::t_FFT_SCALAR_1d d_buf) +void RemapKokkos::perform(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_out, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_buf) { remap_3d_kokkos(d_in,d_out,d_buf,plan); } @@ -103,7 +103,7 @@ void RemapKokkos::perform(typename FFT_AT::t_FFT_SCALAR_1d d_in, typ ------------------------------------------------------------------------- */ template -void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d d_in, typename FFT_AT::t_FFT_SCALAR_1d d_out, typename FFT_AT::t_FFT_SCALAR_1d d_buf, +void RemapKokkos::remap_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_out, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_buf, struct remap_plan_3d_kokkos *plan) { // collective flag not yet supported @@ -111,7 +111,7 @@ void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d d // use point-to-point communication int i,isend,irecv; - typename FFT_AT::t_FFT_SCALAR_1d d_scratch; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_scratch; if (plan->memory == 0) d_scratch = d_buf; @@ -120,20 +120,20 @@ void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d d // post all recvs into scratch space - FFT_SCALAR* v_scratch = d_scratch.data(); + FFT_KOKKOS_SCALAR* v_scratch = d_scratch.data(); if (!plan->usecuda_aware) { plan->h_scratch = Kokkos::create_mirror_view(d_scratch); v_scratch = plan->h_scratch.data(); } for (irecv = 0; irecv < plan->nrecv; irecv++) { - FFT_SCALAR* scratch = v_scratch + plan->recv_bufloc[irecv]; + FFT_KOKKOS_SCALAR* scratch = v_scratch + plan->recv_bufloc[irecv]; MPI_Irecv(scratch,plan->recv_size[irecv], - MPI_FFT_SCALAR,plan->recv_proc[irecv],0, + MPI_FFT_KOKKOS_SCALAR,plan->recv_proc[irecv],0, plan->comm,&plan->request[irecv]); } - FFT_SCALAR* v_sendbuf = plan->d_sendbuf.data(); + FFT_KOKKOS_SCALAR* v_sendbuf = plan->d_sendbuf.data(); if (!plan->usecuda_aware) { plan->h_sendbuf = Kokkos::create_mirror_view(plan->d_sendbuf); v_sendbuf = plan->h_sendbuf.data(); @@ -149,7 +149,7 @@ void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d d if (!plan->usecuda_aware) Kokkos::deep_copy(plan->h_sendbuf,plan->d_sendbuf); - MPI_Send(v_sendbuf,plan->send_size[isend],MPI_FFT_SCALAR, + MPI_Send(v_sendbuf,plan->send_size[isend],MPI_FFT_KOKKOS_SCALAR, plan->send_proc[isend],0,plan->comm); } @@ -465,7 +465,7 @@ struct remap_plan_3d_kokkos* RemapKokkos::remap_3d_creat size = MAX(size,plan->send_size[nsend]); if (size) { - plan->d_sendbuf = typename FFT_AT::t_FFT_SCALAR_1d("remap3d:sendbuf",size); + plan->d_sendbuf = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d("remap3d:sendbuf",size); if (!plan->d_sendbuf.data()) return nullptr; } @@ -475,7 +475,7 @@ struct remap_plan_3d_kokkos* RemapKokkos::remap_3d_creat if (memory == 1) { if (nrecv > 0) { plan->d_scratch = - typename FFT_AT::t_FFT_SCALAR_1d("remap3d:scratch",nqty*out.isize*out.jsize*out.ksize); + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d("remap3d:scratch",nqty*out.isize*out.jsize*out.ksize); if (!plan->d_scratch.data()) return nullptr; } } diff --git a/src/KOKKOS/remap_kokkos.h b/src/KOKKOS/remap_kokkos.h index a62c14f00b9..035b58260e8 100644 --- a/src/KOKKOS/remap_kokkos.h +++ b/src/KOKKOS/remap_kokkos.h @@ -27,14 +27,14 @@ namespace LAMMPS_NS { template struct remap_plan_3d_kokkos { typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; - typename FFT_AT::t_FFT_SCALAR_1d d_sendbuf; // buffer for MPI sends - FFT_HAT::t_FFT_SCALAR_1d h_sendbuf; // host buffer for MPI sends - typename FFT_AT::t_FFT_SCALAR_1d d_scratch; // scratch buffer for MPI recvs - FFT_HAT::t_FFT_SCALAR_1d h_scratch; // host scratch buffer for MPI recvs - void (*pack)(typename FFT_AT::t_FFT_SCALAR_1d_um, int, typename FFT_AT::t_FFT_SCALAR_1d_um, int, struct pack_plan_3d *); + typedef FFTArrayTypes FFT_KOKKOS_AT; + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_sendbuf; // buffer for MPI sends + FFT_KOKKOS_HAT::t_FFT_KOKKOS_SCALAR_1d h_sendbuf; // host buffer for MPI sends + typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_scratch; // scratch buffer for MPI recvs + FFT_KOKKOS_HAT::t_FFT_KOKKOS_SCALAR_1d h_scratch; // host scratch buffer for MPI recvs + void (*pack)(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, struct pack_plan_3d *); // which pack function to use - void (*unpack)(typename FFT_AT::t_FFT_SCALAR_1d_um, int, typename FFT_AT::t_FFT_SCALAR_1d_um, int, struct pack_plan_3d *); + void (*unpack)(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, struct pack_plan_3d *); // which unpack function to use int *send_offset; // extraction loc for each send int *send_size; // size of each send message @@ -61,16 +61,16 @@ template class RemapKokkos : protected Pointers { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_AT; + typedef FFTArrayTypes FFT_KOKKOS_AT; RemapKokkos(class LAMMPS *); RemapKokkos(class LAMMPS *, MPI_Comm,int,int,int,int,int,int, int,int,int,int,int,int,int,int,int,int,int,int); ~RemapKokkos() override; - void perform(typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d); + void perform(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d); struct remap_plan_3d_kokkos *plan; - void remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, struct remap_plan_3d_kokkos *); + void remap_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, struct remap_plan_3d_kokkos *); struct remap_plan_3d_kokkos *remap_3d_create_plan_kokkos(MPI_Comm, int, int, int, int, int, int, int, int, int, int, int, int, From 51eebf311fde2f3848feae35ce3692a35d90fe9f Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Wed, 6 Dec 2023 12:40:11 -0500 Subject: [PATCH 079/719] Added fft settings to Install.sh, fixed typo in HIPFFT_C2C and HIPFFT_Z2Z --- src/KOKKOS/Install.sh | 1 + src/KOKKOS/fftdata_kokkos.h | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 489efc55a04..ba6c4ed427c 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -200,6 +200,7 @@ action kokkos_few.h action kokkos_type.h action kokkos.cpp action kokkos.h +action lmpfftsettings_kokkos.h action math_special_kokkos.cpp action math_special_kokkos.h action meam_dens_final_kokkos.h meam_dens_final.cpp diff --git a/src/KOKKOS/fftdata_kokkos.h b/src/KOKKOS/fftdata_kokkos.h index a9ea2de8963..d52bc0b968a 100644 --- a/src/KOKKOS/fftdata_kokkos.h +++ b/src/KOKKOS/fftdata_kokkos.h @@ -117,11 +117,11 @@ #include #if defined(FFT_KOKKOS_SINGLE) #define hipfftExec hipfftExecC2C - #define HIPFFT_KOKKOS_TYPE HIPFFT_KOKKOS_C2C + #define HIPFFT_KOKKOS_TYPE HIPFFT_C2C typedef hipfftComplex FFT_KOKKOS_DATA; #else #define hipfftExec hipfftExecZ2Z - #define HIPFFT_KOKKOS_TYPE HIPFFT_KOKKOS_Z2Z + #define HIPFFT_KOKKOS_TYPE HIPFFT_Z2Z typedef hipfftDoubleComplex FFT_KOKKOS_DATA; #endif #else From e80c3d3215a9de1f8e1c9041fc96c9713cb156ca Mon Sep 17 00:00:00 2001 From: Stan Gerald Moore Date: Tue, 12 Dec 2023 12:20:24 -0700 Subject: [PATCH 080/719] Revert FFT_AT name change --- src/KOKKOS/fft3d_kokkos.cpp | 70 ++++++++++++++++++------------------- src/KOKKOS/fft3d_kokkos.h | 16 ++++----- src/KOKKOS/grid3d_kokkos.h | 2 +- src/KOKKOS/kissfft_kokkos.h | 52 +++++++++++++-------------- src/KOKKOS/pack_kokkos.h | 52 +++++++++++++-------------- src/KOKKOS/pppm_kokkos.cpp | 26 +++++++------- src/KOKKOS/pppm_kokkos.h | 24 ++++++------- src/KOKKOS/remap_kokkos.cpp | 10 +++--- src/KOKKOS/remap_kokkos.h | 16 ++++----- 9 files changed, 134 insertions(+), 134 deletions(-) diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index 7093136fe6e..9e7b87b8d8a 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -88,10 +88,10 @@ FFT3dKokkos::~FFT3dKokkos() /* ---------------------------------------------------------------------- */ template -void FFT3dKokkos::compute(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_out, int flag) +void FFT3dKokkos::compute(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_out, int flag) { - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_out_data((FFT_KOKKOS_DATA_POINTER)d_out.data(),d_out.size()/2); + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_out_data((FFT_KOKKOS_DATA_POINTER)d_out.data(),d_out.size()/2); fft_3d_kokkos(d_in_data,d_out_data,flag,plan); } @@ -99,9 +99,9 @@ void FFT3dKokkos::compute(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALA /* ---------------------------------------------------------------------- */ template -void FFT3dKokkos::timing1d(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in, int nsize, int flag) +void FFT3dKokkos::timing1d(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in, int nsize, int flag) { - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); fft_3d_1d_only_kokkos(d_in_data,nsize,flag,plan); } @@ -140,11 +140,11 @@ template struct norm_functor { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_out; + typedef FFTArrayTypes FFT_AT; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_out; int norm; - norm_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d &d_out_, int norm_): + norm_functor(typename FFT_AT::t_FFT_KOKKOS_DATA_1d &d_out_, int norm_): d_out(d_out_),norm(norm_) {} KOKKOS_INLINE_FUNCTION @@ -167,14 +167,14 @@ template struct kiss_fft_functor { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_data,d_tmp; + typedef FFTArrayTypes FFT_AT; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_data,d_tmp; kiss_fft_state_kokkos st; int length; kiss_fft_functor() = default; - kiss_fft_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d &d_data_,typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d &d_tmp_, kiss_fft_state_kokkos &st_, int length_): + kiss_fft_functor(typename FFT_AT::t_FFT_KOKKOS_DATA_1d &d_data_,typename FFT_AT::t_FFT_KOKKOS_DATA_1d &d_tmp_, kiss_fft_state_kokkos &st_, int length_): d_data(d_data_), d_tmp(d_tmp_), st(st_) @@ -191,11 +191,11 @@ struct kiss_fft_functor { #endif template -void FFT3dKokkos::fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_in, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_out, int flag, struct fft_plan_3d_kokkos *plan) +void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_in, typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_out, int flag, struct fft_plan_3d_kokkos *plan) { int total,length; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_data,d_copy; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in_scalar,d_data_scalar,d_out_scalar,d_copy_scalar,d_scratch_scalar; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_data,d_copy; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in_scalar,d_data_scalar,d_out_scalar,d_copy_scalar,d_scratch_scalar; // pre-remap to prepare for 1st FFTs if needed // copy = loc for remap result @@ -204,9 +204,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS if (plan->pre_target == 0) d_copy = d_out; else d_copy = plan->d_copy; - d_in_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_in.data(),d_in.size()*2); - d_copy_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); - d_scratch_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_in_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_in.data(),d_in.size()*2); + d_copy_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); + d_scratch_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_in_scalar, d_copy_scalar, d_scratch_scalar, plan->pre_plan); @@ -234,8 +234,8 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_fast,d_data.data(),d_data.data(),-flag); #else - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_tmp = - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_tmp = + typename FFT_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); kiss_fft_functor f; if (flag == 1) f = kiss_fft_functor(d_data,d_tmp,plan->cfg_fast_forward,length); @@ -251,9 +251,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS if (plan->mid1_target == 0) d_copy = d_out; else d_copy = plan->d_copy; - d_data_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); - d_copy_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); - d_scratch_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_data_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); + d_copy_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); + d_scratch_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_data_scalar, d_copy_scalar, d_scratch_scalar, plan->mid1_plan); @@ -280,7 +280,7 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_mid,d_data.data(),d_data.data(),-flag); #else - d_tmp = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + d_tmp = typename FFT_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); if (flag == 1) f = kiss_fft_functor(d_data,d_tmp,plan->cfg_mid_forward,length); else @@ -295,9 +295,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS if (plan->mid2_target == 0) d_copy = d_out; else d_copy = plan->d_copy; - d_data_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); - d_copy_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); - d_scratch_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_data_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); + d_copy_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); + d_scratch_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_data_scalar, d_copy_scalar, d_scratch_scalar, plan->mid2_plan); @@ -324,7 +324,7 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); #else - d_tmp = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + d_tmp = typename FFT_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); if (flag == 1) f = kiss_fft_functor(d_data,d_tmp,plan->cfg_slow_forward,length); else @@ -337,9 +337,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS // destination is always out if (plan->post_plan) { - d_data_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); - d_out_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_out.data(),d_out.size()*2); - d_scratch_scalar = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_data_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); + d_out_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_out.data(),d_out.size()*2); + d_scratch_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_data_scalar, d_out_scalar, d_scratch_scalar, plan->post_plan); @@ -599,11 +599,11 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl *nbuf = copy_size + scratch_size; if (copy_size) { - plan->d_copy = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d("fft3d:copy",copy_size); + plan->d_copy = typename FFT_AT::t_FFT_KOKKOS_DATA_1d("fft3d:copy",copy_size); } if (scratch_size) { - plan->d_scratch = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d("fft3d:scratch",scratch_size); + plan->d_scratch = typename FFT_AT::t_FFT_KOKKOS_DATA_1d("fft3d:scratch",scratch_size); } // system specific pre-computation of 1d FFT coeffs @@ -838,7 +838,7 @@ void FFT3dKokkos::bifactor(int n, int *factor1, int *factor2) ------------------------------------------------------------------------- */ template -void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_data, int nsize, int flag, +void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_data, int nsize, int flag, struct fft_plan_3d_kokkos *plan) { // total = size of data needed in each dim @@ -896,8 +896,8 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_KOKKOS_AT::t_FF hipfftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); #else kiss_fft_functor f; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_tmp = - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_tmp = + typename FFT_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); if (flag == -1) { f = kiss_fft_functor(d_data,d_tmp,plan->cfg_fast_forward,length1); Kokkos::parallel_for(total1/length1,f); diff --git a/src/KOKKOS/fft3d_kokkos.h b/src/KOKKOS/fft3d_kokkos.h index bb552ec4efd..9729bc6a63e 100644 --- a/src/KOKKOS/fft3d_kokkos.h +++ b/src/KOKKOS/fft3d_kokkos.h @@ -28,14 +28,14 @@ namespace LAMMPS_NS { template struct fft_plan_3d_kokkos { typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; + typedef FFTArrayTypes FFT_AT; struct remap_plan_3d_kokkos *pre_plan; // remap from input -> 1st FFTs struct remap_plan_3d_kokkos *mid1_plan; // remap from 1st -> 2nd FFTs struct remap_plan_3d_kokkos *mid2_plan; // remap from 2nd -> 3rd FFTs struct remap_plan_3d_kokkos *post_plan; // remap from 3rd FFTs -> output - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_copy; // memory for remap results (if needed) - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_scratch; // scratch space for remaps + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_copy; // memory for remap results (if needed) + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_scratch; // scratch space for remaps int total1,total2,total3; // # of 1st,2nd,3rd FFTs (times length) int length1,length2,length3; // length of 1st,2nd,3rd FFTs int pre_target; // where to put remap results @@ -79,14 +79,14 @@ class FFT3dKokkos : protected Pointers { public: enum{FORWARD=1,BACKWARD=-1}; typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; + typedef FFTArrayTypes FFT_AT; FFT3dKokkos(class LAMMPS *, MPI_Comm, int,int,int,int,int,int,int,int,int,int,int,int,int,int,int, int,int,int *,int,int); ~FFT3dKokkos() override; - void compute(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, int); - void timing1d(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, int, int); + void compute(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, int); + void timing1d(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, int, int); private: struct fft_plan_3d_kokkos *plan; @@ -96,7 +96,7 @@ class FFT3dKokkos : protected Pointers { KissFFTKokkos *kissfftKK; #endif - void fft_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d, int, struct fft_plan_3d_kokkos *); + void fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1d, typename FFT_AT::t_FFT_KOKKOS_DATA_1d, int, struct fft_plan_3d_kokkos *); struct fft_plan_3d_kokkos *fft_3d_create_plan_kokkos(MPI_Comm, int, int, int, int, int, int, int, int, @@ -105,7 +105,7 @@ class FFT3dKokkos : protected Pointers { void fft_3d_destroy_plan_kokkos(struct fft_plan_3d_kokkos *); - void fft_3d_1d_only_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d, int, int, struct fft_plan_3d_kokkos *); + void fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1d, int, int, struct fft_plan_3d_kokkos *); void bifactor(int, int *, int *); }; diff --git a/src/KOKKOS/grid3d_kokkos.h b/src/KOKKOS/grid3d_kokkos.h index 8e9f6cd051f..864ac19c060 100644 --- a/src/KOKKOS/grid3d_kokkos.h +++ b/src/KOKKOS/grid3d_kokkos.h @@ -27,7 +27,7 @@ class Grid3dKokkos : public Grid3d { enum { KSPACE = 0, PAIR = 1, FIX = 2 }; // calling classes typedef DeviceType device_type; typedef ArrayTypes AT; - typedef FFTArrayTypes FFT_KOKKOS_AT; + typedef FFTArrayTypes FFT_AT; Grid3dKokkos(class LAMMPS *, MPI_Comm, int, int, int); Grid3dKokkos(class LAMMPS *, MPI_Comm, int, int, int, int, int, int, int, int, int, int, int, int, int, int, int); diff --git a/src/KOKKOS/kissfft_kokkos.h b/src/KOKKOS/kissfft_kokkos.h index fc23bf7891c..66f32d29fb1 100644 --- a/src/KOKKOS/kissfft_kokkos.h +++ b/src/KOKKOS/kissfft_kokkos.h @@ -138,25 +138,25 @@ namespace LAMMPS_NS { template struct kiss_fft_state_kokkos { typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; + typedef FFTArrayTypes FFT_AT; int nfft; int inverse; - typename FFT_KOKKOS_AT::t_int_64 d_factors; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_twiddles; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d d_scratch; + typename FFT_AT::t_int_64 d_factors; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_twiddles; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_scratch; }; template class KissFFTKokkos { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; + typedef FFTArrayTypes FFT_AT; KOKKOS_INLINE_FUNCTION - static void kf_bfly2(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly2(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, int m, int Fout_count) { - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; FFT_KOKKOS_SCALAR t[2]; int Fout2_count; int tw1_count = 0; @@ -179,10 +179,10 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kf_bfly4(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly4(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, const size_t m, int Fout_count) { - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; FFT_KOKKOS_SCALAR scratch[6][2]; size_t k=m; const size_t m2=2*m; @@ -237,12 +237,12 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kf_bfly3(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly3(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, size_t m, int Fout_count) { size_t k=m; const size_t m2 = 2*m; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; FFT_KOKKOS_SCALAR scratch[5][2]; FFT_KOKKOS_SCALAR epi3[2]; //C_EQ(epi3,d_twiddles[fstride*m]); @@ -289,12 +289,12 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kf_bfly5(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly5(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, int m, int Fout_count) { int u; FFT_KOKKOS_SCALAR scratch[13][2]; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; FFT_KOKKOS_SCALAR ya[2],yb[2]; //C_EQ(ya,d_twiddles[fstride*m]); ya[1] = d_twiddles(fstride*m).im; @@ -369,15 +369,15 @@ class KissFFTKokkos { /* perform the butterfly for one stage of a mixed radix FFT */ KOKKOS_INLINE_FUNCTION - static void kf_bfly_generic(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly_generic(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, int m, int p, int Fout_count) { int u,k,q1,q; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; FFT_KOKKOS_SCALAR t[2]; int Norig = st.nfft; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_scratch = st.d_scratch; + typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_scratch = st.d_scratch; for ( u=0; u &st, int Fout_count, int f_count, int factors_count) + const typename FFT_AT::t_int_64_um &d_factors, const kiss_fft_state_kokkos &st, int Fout_count, int f_count, int factors_count) { const int beg = Fout_count; const int p = d_factors[factors_count++]; /* the radix */ @@ -496,12 +496,12 @@ class KissFFTKokkos { st.nfft = nfft; st.inverse = inverse_fft; - typename FFT_KOKKOS_AT::tdual_int_64 k_factors = typename FFT_KOKKOS_AT::tdual_int_64(); - typename FFT_KOKKOS_AT::tdual_FFT_KOKKOS_DATA_1d k_twiddles = typename FFT_KOKKOS_AT::tdual_FFT_KOKKOS_DATA_1d(); + typename FFT_AT::tdual_int_64 k_factors = typename FFT_AT::tdual_int_64(); + typename FFT_AT::tdual_FFT_KOKKOS_DATA_1d k_twiddles = typename FFT_AT::tdual_FFT_KOKKOS_DATA_1d(); if (nfft > 0) { - k_factors = typename FFT_KOKKOS_AT::tdual_int_64("kissfft:factors",MAXFACTORS*2); - k_twiddles = typename FFT_KOKKOS_AT::tdual_FFT_KOKKOS_DATA_1d("kissfft:twiddles",nfft); + k_factors = typename FFT_AT::tdual_int_64("kissfft:factors",MAXFACTORS*2); + k_twiddles = typename FFT_AT::tdual_FFT_KOKKOS_DATA_1d("kissfft:twiddles",nfft); for (i=0;i(); @@ -524,12 +524,12 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kiss_fft_stride(const kiss_fft_state_kokkos &st, const typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_fin, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um &d_fout, int in_stride, int offset) + static void kiss_fft_stride(const kiss_fft_state_kokkos &st, const typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_fin, typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_fout, int in_stride, int offset) { //if (d_fin.data() == d_fout.data()) { // // NOTE: this is not really an in-place FFT algorithm. // // It just performs an out-of-place FFT into a temp buffer - // typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_tmpbuf = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d("kissfft:tmpbuf",d_fin.extent(1)); + // typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_tmpbuf = typename FFT_AT::t_FFT_KOKKOS_DATA_1d("kissfft:tmpbuf",d_fin.extent(1)); // kf_work(d_tmpbuf,d_fin,1,in_stride,st.d_factors,st,offset,offset).re; // Kokkos::deep_copy(d_fout,d_tmpbuf); //} else { @@ -538,7 +538,7 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kiss_fft_kokkos(const kiss_fft_state_kokkos &cfg, const typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_fin, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_DATA_1d_um d_fout, int offset) + static void kiss_fft_kokkos(const kiss_fft_state_kokkos &cfg, const typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_fin, typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_fout, int offset) { kiss_fft_stride(cfg,d_fin,d_fout,1,offset); } diff --git a/src/KOKKOS/pack_kokkos.h b/src/KOKKOS/pack_kokkos.h index 97d35afe268..5e014db020e 100644 --- a/src/KOKKOS/pack_kokkos.h +++ b/src/KOKKOS/pack_kokkos.h @@ -38,13 +38,13 @@ template class PackKokkos { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; + typedef FFTArrayTypes FFT_AT; struct pack_3d_functor { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typedef FFTArrayTypes FFT_AT; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -52,7 +52,7 @@ struct pack_3d_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - pack_3d_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + pack_3d_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -80,7 +80,7 @@ struct pack_3d_functor { } }; -static void pack_3d(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, struct pack_plan_3d *plan) +static void pack_3d(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -98,7 +98,7 @@ struct unpack_3d_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -106,7 +106,7 @@ struct unpack_3d_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -134,7 +134,7 @@ struct unpack_3d_functor { } }; -static void unpack_3d(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -153,7 +153,7 @@ struct unpack_3d_permute1_1_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -161,7 +161,7 @@ struct unpack_3d_permute1_1_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute1_1_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute1_1_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -189,7 +189,7 @@ struct unpack_3d_permute1_1_functor { } }; -static void unpack_3d_permute1_1(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute1_1(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -206,7 +206,7 @@ struct unpack_3d_permute1_2_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -214,7 +214,7 @@ struct unpack_3d_permute1_2_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute1_2_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute1_2_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -243,7 +243,7 @@ struct unpack_3d_permute1_2_functor { } }; -static void unpack_3d_permute1_2(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute1_2(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -261,7 +261,7 @@ struct unpack_3d_permute1_n_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -270,7 +270,7 @@ struct unpack_3d_permute1_n_functor { int nstride_plane; // stride between successive slow indices int nqty; // # of values/element - unpack_3d_permute1_n_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute1_n_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -299,7 +299,7 @@ struct unpack_3d_permute1_n_functor { } }; -static void unpack_3d_permute1_n(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute1_n(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -317,7 +317,7 @@ struct unpack_3d_permute2_1_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -325,7 +325,7 @@ struct unpack_3d_permute2_1_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute2_1_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute2_1_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -352,7 +352,7 @@ struct unpack_3d_permute2_1_functor { } }; -static void unpack_3d_permute2_1(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute2_1(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -370,7 +370,7 @@ struct unpack_3d_permute2_2_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -378,7 +378,7 @@ struct unpack_3d_permute2_2_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute2_2_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute2_2_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -406,7 +406,7 @@ struct unpack_3d_permute2_2_functor { } }; -static void unpack_3d_permute2_2(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute2_2(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -423,7 +423,7 @@ struct unpack_3d_permute2_n_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -432,7 +432,7 @@ struct unpack_3d_permute2_n_functor { int nstride_plane; // stride between successive slow indices int nqty; // # of values/element - unpack_3d_permute2_n_functor(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute2_n_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -460,7 +460,7 @@ struct unpack_3d_permute2_n_functor { } }; -static void unpack_3d_permute2_n(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute2_n(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 3fc90c088d2..ed7ace08c16 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -582,7 +582,7 @@ void PPPMKokkos::compute(int eflag, int vflag) if (atom->nmax > nmax) { nmax = atomKK->nmax; d_part2grid = typename AT::t_int_1d_3("pppm:part2grid",nmax); - d_rho1d = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); + d_rho1d = typename FFT_AT::t_FFT_KOKKOS_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); } // find grid points for all my particles @@ -753,7 +753,7 @@ void PPPMKokkos::allocate() // allocate distributed grid data - d_density_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:density_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_density_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:density_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); memoryKK->create_kokkos(k_density_fft,density_fft,nfft_both,"pppm:d_density_fft"); d_density_fft = k_density_fft.view(); @@ -775,16 +775,16 @@ void PPPMKokkos::allocate() d_fkz = typename AT::t_float_1d("pppm:d_fkz",nfft_both); } - d_vdx_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdx_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_vdy_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdy_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_vdz_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdz_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_vdx_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdx_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_vdy_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdy_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_vdz_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdz_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); // summation coeffs order_allocated = order; k_gf_b = typename DAT::tdual_float_1d("pppm:gf_b",order); d_gf_b = k_gf_b.view(); - d_rho1d = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); + d_rho1d = typename FFT_AT::t_FFT_KOKKOS_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); k_rho_coeff = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_2d("pppm:rho_coeff",order,order/2-(1-order)/2+1); d_rho_coeff = k_rho_coeff.view(); h_rho_coeff = k_rho_coeff.h_view; @@ -847,14 +847,14 @@ void PPPMKokkos::allocate_peratom() { peratom_allocate_flag = 1; - d_u_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:u_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_u_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:u_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v0_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v0_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v1_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v1_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v2_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v2_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v3_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v3_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v4_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v4_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v5_brick = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v5_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v0_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v0_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v1_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v1_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v2_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v2_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v3_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v3_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v4_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v4_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v5_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v5_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); // use same GC ghost grid object for peratom grid communication diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h index dc0fbd88e52..09513c9a2fb 100644 --- a/src/KOKKOS/pppm_kokkos.h +++ b/src/KOKKOS/pppm_kokkos.h @@ -131,7 +131,7 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typedef FFTArrayTypes FFT_KOKKOS_AT; + typedef FFTArrayTypes FFT_AT; PPPMKokkos(class LAMMPS *); ~PPPMKokkos() override; @@ -350,7 +350,7 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { int nx,ny,nz; typename AT::t_int_1d_um d_list_index; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf; int unpack_offset; DAT::tdual_int_scalar k_flag; @@ -364,11 +364,11 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_density_brick; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_vdx_brick,d_vdy_brick,d_vdz_brick; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_u_brick; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_v0_brick,d_v1_brick,d_v2_brick; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_3d d_v3_brick,d_v4_brick,d_v5_brick; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_density_brick; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_vdx_brick,d_vdy_brick,d_vdz_brick; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_u_brick; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_v0_brick,d_v1_brick,d_v2_brick; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_v3_brick,d_v4_brick,d_v5_brick; typename AT::t_float_1d d_greensfn; typename AT::t_virial_array d_vg; typename AT::t_float_1d d_fkx; @@ -377,17 +377,17 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_density_fft; FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_work1; FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_work2; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_density_fft; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_work1; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_work2; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_density_fft; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_work1; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_work2; DAT::tdual_float_1d k_gf_b; typename AT::t_float_1d d_gf_b; //FFT_KOKKOS_SCALAR **rho1d,**rho_coeff,**drho1d,**drho_coeff; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_2d_3 d_rho1d; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_2d_3 d_rho1d; FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_2d k_rho_coeff; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_2d d_rho_coeff; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_2d d_rho_coeff; FFT_KOKKOS_HAT::t_FFT_KOKKOS_SCALAR_2d h_rho_coeff; //double **acons; typename Kokkos::DualView::t_host acons; diff --git a/src/KOKKOS/remap_kokkos.cpp b/src/KOKKOS/remap_kokkos.cpp index d6b8a5691c1..18ba6264605 100644 --- a/src/KOKKOS/remap_kokkos.cpp +++ b/src/KOKKOS/remap_kokkos.cpp @@ -59,7 +59,7 @@ RemapKokkos::~RemapKokkos() /* ---------------------------------------------------------------------- */ template -void RemapKokkos::perform(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_out, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_buf) +void RemapKokkos::perform(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_out, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_buf) { remap_3d_kokkos(d_in,d_out,d_buf,plan); } @@ -103,7 +103,7 @@ void RemapKokkos::perform(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALA ------------------------------------------------------------------------- */ template -void RemapKokkos::remap_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_out, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_buf, +void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_out, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_buf, struct remap_plan_3d_kokkos *plan) { // collective flag not yet supported @@ -111,7 +111,7 @@ void RemapKokkos::remap_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKK // use point-to-point communication int i,isend,irecv; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_scratch; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_scratch; if (plan->memory == 0) d_scratch = d_buf; @@ -465,7 +465,7 @@ struct remap_plan_3d_kokkos* RemapKokkos::remap_3d_creat size = MAX(size,plan->send_size[nsend]); if (size) { - plan->d_sendbuf = typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d("remap3d:sendbuf",size); + plan->d_sendbuf = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d("remap3d:sendbuf",size); if (!plan->d_sendbuf.data()) return nullptr; } @@ -475,7 +475,7 @@ struct remap_plan_3d_kokkos* RemapKokkos::remap_3d_creat if (memory == 1) { if (nrecv > 0) { plan->d_scratch = - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d("remap3d:scratch",nqty*out.isize*out.jsize*out.ksize); + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d("remap3d:scratch",nqty*out.isize*out.jsize*out.ksize); if (!plan->d_scratch.data()) return nullptr; } } diff --git a/src/KOKKOS/remap_kokkos.h b/src/KOKKOS/remap_kokkos.h index 035b58260e8..ad5fa9833d2 100644 --- a/src/KOKKOS/remap_kokkos.h +++ b/src/KOKKOS/remap_kokkos.h @@ -27,14 +27,14 @@ namespace LAMMPS_NS { template struct remap_plan_3d_kokkos { typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_sendbuf; // buffer for MPI sends + typedef FFTArrayTypes FFT_AT; + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_sendbuf; // buffer for MPI sends FFT_KOKKOS_HAT::t_FFT_KOKKOS_SCALAR_1d h_sendbuf; // host buffer for MPI sends - typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d d_scratch; // scratch buffer for MPI recvs + typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_scratch; // scratch buffer for MPI recvs FFT_KOKKOS_HAT::t_FFT_KOKKOS_SCALAR_1d h_scratch; // host scratch buffer for MPI recvs - void (*pack)(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, struct pack_plan_3d *); + void (*pack)(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, struct pack_plan_3d *); // which pack function to use - void (*unpack)(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, struct pack_plan_3d *); + void (*unpack)(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, struct pack_plan_3d *); // which unpack function to use int *send_offset; // extraction loc for each send int *send_size; // size of each send message @@ -61,16 +61,16 @@ template class RemapKokkos : protected Pointers { public: typedef DeviceType device_type; - typedef FFTArrayTypes FFT_KOKKOS_AT; + typedef FFTArrayTypes FFT_AT; RemapKokkos(class LAMMPS *); RemapKokkos(class LAMMPS *, MPI_Comm,int,int,int,int,int,int, int,int,int,int,int,int,int,int,int,int,int,int); ~RemapKokkos() override; - void perform(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d); + void perform(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d); struct remap_plan_3d_kokkos *plan; - void remap_3d_kokkos(typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_KOKKOS_AT::t_FFT_KOKKOS_SCALAR_1d, struct remap_plan_3d_kokkos *); + void remap_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, struct remap_plan_3d_kokkos *); struct remap_plan_3d_kokkos *remap_3d_create_plan_kokkos(MPI_Comm, int, int, int, int, int, int, int, int, int, int, int, int, From 665785f41e064a84e14904d463a5bda4dc561dbb Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 13 Dec 2023 09:04:23 -0700 Subject: [PATCH 081/719] adjust 2d box bounds --- examples/PACKAGES/phonon/2-1D-diatomic/data.pos | 2 +- examples/PACKAGES/phonon/2-1D-diatomic/in.Ana | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/data.pos b/examples/PACKAGES/phonon/2-1D-diatomic/data.pos index cba35b49c94..130c6e7cd68 100644 --- a/examples/PACKAGES/phonon/2-1D-diatomic/data.pos +++ b/examples/PACKAGES/phonon/2-1D-diatomic/data.pos @@ -8,7 +8,7 @@ 0.00000000 64.00000000 xlo xhi 0.00000000 1.00000000 ylo yhi - 0.00000000 1.00000000 zlo zhi + -0.5 0.5 zlo zhi Atoms diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana b/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana index ca49cd50c6c..5209adeb4a4 100644 --- a/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana +++ b/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana @@ -1,4 +1,5 @@ -# 3D simple cubic lattice simulation +# 2D slice of 3D simple cubic lattice simulation + dimension 2 boundary p f p From 68c53886b8f52ec1f4af801783c87d368cef10e2 Mon Sep 17 00:00:00 2001 From: Stan Gerald Moore Date: Wed, 13 Dec 2023 15:09:02 -0700 Subject: [PATCH 082/719] Revert some name changes --- src/KOKKOS/Install.sh | 2 +- src/KOKKOS/fft3d_kokkos.cpp | 88 +++++++++++----------- src/KOKKOS/fft3d_kokkos.h | 12 +-- src/KOKKOS/fftdata_kokkos.h | 80 ++++++++++---------- src/KOKKOS/grid3d_kokkos.cpp | 28 +++---- src/KOKKOS/grid3d_kokkos.h | 12 +-- src/KOKKOS/kissfft_kokkos.h | 64 ++++++++-------- src/KOKKOS/kokkos_base_fft.h | 12 +-- src/KOKKOS/lmpfftsettings_kokkos.h | 15 +--- src/KOKKOS/pack_kokkos.h | 48 ++++++------ src/KOKKOS/pppm_kokkos.cpp | 116 ++++++++++++++--------------- src/KOKKOS/pppm_kokkos.h | 48 ++++++------ src/KOKKOS/remap_kokkos.cpp | 20 ++--- src/KOKKOS/remap_kokkos.h | 16 ++-- 14 files changed, 275 insertions(+), 286 deletions(-) diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index ba6c4ed427c..2dcf49ce067 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -200,7 +200,7 @@ action kokkos_few.h action kokkos_type.h action kokkos.cpp action kokkos.h -action lmpfftsettings_kokkos.h +action lmpfftsettings_kokkos.h lmpfftsettings.h action math_special_kokkos.cpp action math_special_kokkos.h action meam_dens_final_kokkos.h meam_dens_final.cpp diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index 9e7b87b8d8a..d78239606e1 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -88,10 +88,10 @@ FFT3dKokkos::~FFT3dKokkos() /* ---------------------------------------------------------------------- */ template -void FFT3dKokkos::compute(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_out, int flag) +void FFT3dKokkos::compute(typename FFT_AT::t_FFT_SCALAR_1d d_in, typename FFT_AT::t_FFT_SCALAR_1d d_out, int flag) { - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_out_data((FFT_KOKKOS_DATA_POINTER)d_out.data(),d_out.size()/2); + typename FFT_AT::t_FFT_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); + typename FFT_AT::t_FFT_DATA_1d d_out_data((FFT_KOKKOS_DATA_POINTER)d_out.data(),d_out.size()/2); fft_3d_kokkos(d_in_data,d_out_data,flag,plan); } @@ -99,9 +99,9 @@ void FFT3dKokkos::compute(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_ /* ---------------------------------------------------------------------- */ template -void FFT3dKokkos::timing1d(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in, int nsize, int flag) +void FFT3dKokkos::timing1d(typename FFT_AT::t_FFT_SCALAR_1d d_in, int nsize, int flag) { - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); + typename FFT_AT::t_FFT_DATA_1d d_in_data((FFT_KOKKOS_DATA_POINTER)d_in.data(),d_in.size()/2); fft_3d_1d_only_kokkos(d_in_data,nsize,flag,plan); } @@ -141,21 +141,21 @@ struct norm_functor { public: typedef DeviceType device_type; typedef FFTArrayTypes FFT_AT; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_out; + typename FFT_AT::t_FFT_DATA_1d_um d_out; int norm; - norm_functor(typename FFT_AT::t_FFT_KOKKOS_DATA_1d &d_out_, int norm_): + norm_functor(typename FFT_AT::t_FFT_DATA_1d &d_out_, int norm_): d_out(d_out_),norm(norm_) {} KOKKOS_INLINE_FUNCTION void operator() (const int &i) const { #if defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_CUFFT) || defined(FFT_KOKKOS_HIPFFT) - FFT_KOKKOS_SCALAR* out_ptr = (FFT_KOKKOS_SCALAR *)(d_out.data()+i); + FFT_SCALAR* out_ptr = (FFT_SCALAR *)(d_out.data()+i); *(out_ptr++) *= norm; *(out_ptr++) *= norm; #elif defined(FFT_KOKKOS_MKL) d_out(i) *= norm; -#else // FFT_KOKKOS_KISS +#else // FFT_KISS d_out(i).re *= norm; d_out(i).im *= norm; #endif @@ -168,13 +168,13 @@ struct kiss_fft_functor { public: typedef DeviceType device_type; typedef FFTArrayTypes FFT_AT; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_data,d_tmp; + typename FFT_AT::t_FFT_DATA_1d_um d_data,d_tmp; kiss_fft_state_kokkos st; int length; kiss_fft_functor() = default; - kiss_fft_functor(typename FFT_AT::t_FFT_KOKKOS_DATA_1d &d_data_,typename FFT_AT::t_FFT_KOKKOS_DATA_1d &d_tmp_, kiss_fft_state_kokkos &st_, int length_): + kiss_fft_functor(typename FFT_AT::t_FFT_DATA_1d &d_data_,typename FFT_AT::t_FFT_DATA_1d &d_tmp_, kiss_fft_state_kokkos &st_, int length_): d_data(d_data_), d_tmp(d_tmp_), st(st_) @@ -191,11 +191,11 @@ struct kiss_fft_functor { #endif template -void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_in, typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_out, int flag, struct fft_plan_3d_kokkos *plan) +void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, typename FFT_AT::t_FFT_DATA_1d d_out, int flag, struct fft_plan_3d_kokkos *plan) { int total,length; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_data,d_copy; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in_scalar,d_data_scalar,d_out_scalar,d_copy_scalar,d_scratch_scalar; + typename FFT_AT::t_FFT_DATA_1d d_data,d_copy; + typename FFT_AT::t_FFT_SCALAR_1d d_in_scalar,d_data_scalar,d_out_scalar,d_copy_scalar,d_scratch_scalar; // pre-remap to prepare for 1st FFTs if needed // copy = loc for remap result @@ -204,9 +204,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1 if (plan->pre_target == 0) d_copy = d_out; else d_copy = plan->d_copy; - d_in_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_in.data(),d_in.size()*2); - d_copy_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); - d_scratch_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_in_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_in.data(),d_in.size()*2); + d_copy_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_copy.data(),d_copy.size()*2); + d_scratch_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_in_scalar, d_copy_scalar, d_scratch_scalar, plan->pre_plan); @@ -234,8 +234,8 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1 #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_fast,d_data.data(),d_data.data(),-flag); #else - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_tmp = - typename FFT_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + typename FFT_AT::t_FFT_DATA_1d d_tmp = + typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); kiss_fft_functor f; if (flag == 1) f = kiss_fft_functor(d_data,d_tmp,plan->cfg_fast_forward,length); @@ -251,9 +251,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1 if (plan->mid1_target == 0) d_copy = d_out; else d_copy = plan->d_copy; - d_data_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); - d_copy_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); - d_scratch_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_data_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_data.data(),d_data.size()*2); + d_copy_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_copy.data(),d_copy.size()*2); + d_scratch_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_data_scalar, d_copy_scalar, d_scratch_scalar, plan->mid1_plan); @@ -280,7 +280,7 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1 #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_mid,d_data.data(),d_data.data(),-flag); #else - d_tmp = typename FFT_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + d_tmp = typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); if (flag == 1) f = kiss_fft_functor(d_data,d_tmp,plan->cfg_mid_forward,length); else @@ -295,9 +295,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1 if (plan->mid2_target == 0) d_copy = d_out; else d_copy = plan->d_copy; - d_data_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); - d_copy_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_copy.data(),d_copy.size()*2); - d_scratch_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_data_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_data.data(),d_data.size()*2); + d_copy_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_copy.data(),d_copy.size()*2); + d_scratch_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_data_scalar, d_copy_scalar, d_scratch_scalar, plan->mid2_plan); @@ -324,7 +324,7 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1 #elif defined(FFT_KOKKOS_HIPFFT) hipfftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); #else - d_tmp = typename FFT_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + d_tmp = typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); if (flag == 1) f = kiss_fft_functor(d_data,d_tmp,plan->cfg_slow_forward,length); else @@ -337,9 +337,9 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1 // destination is always out if (plan->post_plan) { - d_data_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_data.data(),d_data.size()*2); - d_out_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)d_out.data(),d_out.size()*2); - d_scratch_scalar = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d((FFT_KOKKOS_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); + d_data_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_data.data(),d_data.size()*2); + d_out_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)d_out.data(),d_out.size()*2); + d_scratch_scalar = typename FFT_AT::t_FFT_SCALAR_1d((FFT_SCALAR*)plan->d_scratch.data(),plan->d_scratch.size()*2); remapKK->remap_3d_kokkos(d_data_scalar, d_out_scalar, d_scratch_scalar, plan->post_plan); @@ -348,7 +348,7 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1 // scaling if required if (flag == -1 && plan->scaled) { - FFT_KOKKOS_SCALAR norm = plan->norm; + FFT_SCALAR norm = plan->norm; int num = plan->normnum; norm_functor f(d_out,norm); @@ -443,7 +443,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl plan->pre_plan = remapKK->remap_3d_create_plan_kokkos(comm,in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi, first_ilo,first_ihi,first_jlo,first_jhi, - first_klo,first_khi,2,0,0,FFT_KOKKOS_PRECISION, + first_klo,first_khi,2,0,0,FFT_PRECISION, usecollective,usecuda_aware); if (plan->pre_plan == nullptr) return nullptr; } @@ -468,7 +468,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl first_ilo,first_ihi,first_jlo,first_jhi, first_klo,first_khi, second_ilo,second_ihi,second_jlo,second_jhi, - second_klo,second_khi,2,1,0,FFT_KOKKOS_PRECISION, + second_klo,second_khi,2,1,0,FFT_PRECISION, usecollective,usecuda_aware); if (plan->mid1_plan == nullptr) return nullptr; @@ -509,7 +509,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl second_jlo,second_jhi,second_klo,second_khi, second_ilo,second_ihi, third_jlo,third_jhi,third_klo,third_khi, - third_ilo,third_ihi,2,1,0,FFT_KOKKOS_PRECISION, + third_ilo,third_ihi,2,1,0,FFT_PRECISION, usecollective,usecuda_aware); if (plan->mid2_plan == nullptr) return nullptr; @@ -537,7 +537,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl third_klo,third_khi,third_ilo,third_ihi, third_jlo,third_jhi, out_klo,out_khi,out_ilo,out_ihi, - out_jlo,out_jhi,2,(permute+1)%3,0,FFT_KOKKOS_PRECISION, + out_jlo,out_jhi,2,(permute+1)%3,0,FFT_PRECISION, usecollective,usecuda_aware); if (plan->post_plan == nullptr) return nullptr; } @@ -599,11 +599,11 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl *nbuf = copy_size + scratch_size; if (copy_size) { - plan->d_copy = typename FFT_AT::t_FFT_KOKKOS_DATA_1d("fft3d:copy",copy_size); + plan->d_copy = typename FFT_AT::t_FFT_DATA_1d("fft3d:copy",copy_size); } if (scratch_size) { - plan->d_scratch = typename FFT_AT::t_FFT_KOKKOS_DATA_1d("fft3d:scratch",scratch_size); + plan->d_scratch = typename FFT_AT::t_FFT_DATA_1d("fft3d:scratch",scratch_size); } // system specific pre-computation of 1d FFT coeffs @@ -697,17 +697,17 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl cufftPlanMany(&(plan->plan_fast), 1, &nfast, &nfast,1,plan->length1, &nfast,1,plan->length1, - CUFFT_KOKKOS_TYPE,plan->total1/plan->length1); + CUFFT_TYPE,plan->total1/plan->length1); cufftPlanMany(&(plan->plan_mid), 1, &nmid, &nmid,1,plan->length2, &nmid,1,plan->length2, - CUFFT_KOKKOS_TYPE,plan->total2/plan->length2); + CUFFT_TYPE,plan->total2/plan->length2); cufftPlanMany(&(plan->plan_slow), 1, &nslow, &nslow,1,plan->length3, &nslow,1,plan->length3, - CUFFT_KOKKOS_TYPE,plan->total3/plan->length3); + CUFFT_TYPE,plan->total3/plan->length3); #elif defined(FFT_KOKKOS_HIPFFT) @@ -838,7 +838,7 @@ void FFT3dKokkos::bifactor(int n, int *factor1, int *factor2) ------------------------------------------------------------------------- */ template -void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_data, int nsize, int flag, +void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_1d d_data, int nsize, int flag, struct fft_plan_3d_kokkos *plan) { // total = size of data needed in each dim @@ -896,8 +896,8 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_KOKKO hipfftExec(plan->plan_slow,d_data.data(),d_data.data(),-flag); #else kiss_fft_functor f; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_tmp = - typename FFT_AT::t_FFT_KOKKOS_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); + typename FFT_AT::t_FFT_DATA_1d d_tmp = + typename FFT_AT::t_FFT_DATA_1d(Kokkos::view_alloc("fft_3d:tmp",Kokkos::WithoutInitializing),d_data.extent(0)); if (flag == -1) { f = kiss_fft_functor(d_data,d_tmp,plan->cfg_fast_forward,length1); Kokkos::parallel_for(total1/length1,f); @@ -923,7 +923,7 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_KOKKO // limit num to size of data if (flag == 1 && plan->scaled) { - FFT_KOKKOS_SCALAR norm = plan->norm; + FFT_SCALAR norm = plan->norm; int num = MIN(plan->normnum,nsize); norm_functor f(d_data,norm); diff --git a/src/KOKKOS/fft3d_kokkos.h b/src/KOKKOS/fft3d_kokkos.h index 9729bc6a63e..ed49c4b1eed 100644 --- a/src/KOKKOS/fft3d_kokkos.h +++ b/src/KOKKOS/fft3d_kokkos.h @@ -34,8 +34,8 @@ struct fft_plan_3d_kokkos { struct remap_plan_3d_kokkos *mid1_plan; // remap from 1st -> 2nd FFTs struct remap_plan_3d_kokkos *mid2_plan; // remap from 2nd -> 3rd FFTs struct remap_plan_3d_kokkos *post_plan; // remap from 3rd FFTs -> output - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_copy; // memory for remap results (if needed) - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_scratch; // scratch space for remaps + typename FFT_AT::t_FFT_DATA_1d d_copy; // memory for remap results (if needed) + typename FFT_AT::t_FFT_DATA_1d d_scratch; // scratch space for remaps int total1,total2,total3; // # of 1st,2nd,3rd FFTs (times length) int length1,length2,length3; // length of 1st,2nd,3rd FFTs int pre_target; // where to put remap results @@ -85,8 +85,8 @@ class FFT3dKokkos : protected Pointers { int,int,int,int,int,int,int,int,int,int,int,int,int,int,int, int,int,int *,int,int); ~FFT3dKokkos() override; - void compute(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, int); - void timing1d(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, int, int); + void compute(typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, int); + void timing1d(typename FFT_AT::t_FFT_SCALAR_1d, int, int); private: struct fft_plan_3d_kokkos *plan; @@ -96,7 +96,7 @@ class FFT3dKokkos : protected Pointers { KissFFTKokkos *kissfftKK; #endif - void fft_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1d, typename FFT_AT::t_FFT_KOKKOS_DATA_1d, int, struct fft_plan_3d_kokkos *); + void fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d, typename FFT_AT::t_FFT_DATA_1d, int, struct fft_plan_3d_kokkos *); struct fft_plan_3d_kokkos *fft_3d_create_plan_kokkos(MPI_Comm, int, int, int, int, int, int, int, int, @@ -105,7 +105,7 @@ class FFT3dKokkos : protected Pointers { void fft_3d_destroy_plan_kokkos(struct fft_plan_3d_kokkos *); - void fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_KOKKOS_DATA_1d, int, int, struct fft_plan_3d_kokkos *); + void fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_1d, int, int, struct fft_plan_3d_kokkos *); void bifactor(int, int *, int *); }; diff --git a/src/KOKKOS/fftdata_kokkos.h b/src/KOKKOS/fftdata_kokkos.h index d52bc0b968a..15dca33bcc1 100644 --- a/src/KOKKOS/fftdata_kokkos.h +++ b/src/KOKKOS/fftdata_kokkos.h @@ -20,8 +20,8 @@ // data types for 2d/3d FFTs -#ifndef LMP_FFT_KOKKOS_DATA_H -#define LMP_FFT_KOKKOS_DATA_H +#ifndef LMP_FFT_DATA_KOKKOS_H +#define LMP_FFT_DATA_KOKKOS_H #include "lmpfftsettings_kokkos.h" @@ -29,10 +29,10 @@ // Data types for single-precision complex -#if FFT_KOKKOS_PRECISION == 1 -#elif FFT_KOKKOS_PRECISION == 2 +#if FFT_PRECISION == 1 +#elif FFT_PRECISION == 2 #else -#error "FFT_KOKKOS_PRECISION needs to be either 1 (=single) or 2 (=double)" +#error "FFT_PRECISION needs to be either 1 (=single) or 2 (=double)" #endif @@ -86,7 +86,7 @@ #if defined(FFT_KOKKOS_MKL) #include "mkl_dfti.h" - #if defined(FFT_KOKKOS_SINGLE) + #if defined(FFT_SINGLE) typedef float _Complex FFT_KOKKOS_DATA; #define FFT_KOKKOS_MKL_PREC DFTI_SINGLE #else @@ -95,7 +95,7 @@ #endif #elif defined(FFT_KOKKOS_FFTW3) #include "fftw3.h" - #if defined(FFT_KOKKOS_SINGLE) + #if defined(FFT_SINGLE) typedef fftwf_complex FFT_KOKKOS_DATA; #define FFTW_API(function) fftwf_ ## function #else @@ -104,18 +104,18 @@ #endif #elif defined(FFT_KOKKOS_CUFFT) #include "cufft.h" - #if defined(FFT_KOKKOS_SINGLE) + #if defined(FFT_SINGLE) #define cufftExec cufftExecC2C - #define CUFFT_KOKKOS_TYPE CUFFT_KOKKOS_C2C + #define CUFFT_TYPE CUFFT_C2C typedef cufftComplex FFT_KOKKOS_DATA; #else #define cufftExec cufftExecZ2Z - #define CUFFT_KOKKOS_TYPE CUFFT_KOKKOS_Z2Z + #define CUFFT_TYPE CUFFT_Z2Z typedef cufftDoubleComplex FFT_KOKKOS_DATA; #endif #elif defined(FFT_KOKKOS_HIPFFT) #include - #if defined(FFT_KOKKOS_SINGLE) + #if defined(FFT_SINGLE) #define hipfftExec hipfftExecC2C #define HIPFFT_KOKKOS_TYPE HIPFFT_C2C typedef hipfftComplex FFT_KOKKOS_DATA; @@ -125,7 +125,7 @@ typedef hipfftDoubleComplex FFT_KOKKOS_DATA; #endif #else - #if defined(FFT_KOKKOS_SINGLE) + #if defined(FFT_SINGLE) #define kiss_fft_scalar float #else #define kiss_fft_scalar double @@ -141,7 +141,7 @@ // (double[2]*) is not a 1D pointer #if defined(FFT_KOKKOS_FFTW3) - typedef FFT_KOKKOS_SCALAR* FFT_KOKKOS_DATA_POINTER; + typedef FFT_SCALAR* FFT_KOKKOS_DATA_POINTER; #else typedef FFT_KOKKOS_DATA* FFT_KOKKOS_DATA_POINTER; #endif @@ -154,23 +154,23 @@ template <> struct FFTArrayTypes { typedef Kokkos:: - DualView tdual_FFT_KOKKOS_SCALAR_1d; -typedef tdual_FFT_KOKKOS_SCALAR_1d::t_dev t_FFT_KOKKOS_SCALAR_1d; -typedef tdual_FFT_KOKKOS_SCALAR_1d::t_dev_um t_FFT_KOKKOS_SCALAR_1d_um; + DualView tdual_FFT_SCALAR_1d; +typedef tdual_FFT_SCALAR_1d::t_dev t_FFT_SCALAR_1d; +typedef tdual_FFT_SCALAR_1d::t_dev_um t_FFT_SCALAR_1d_um; -typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_2d; -typedef tdual_FFT_KOKKOS_SCALAR_2d::t_dev t_FFT_KOKKOS_SCALAR_2d; +typedef Kokkos::DualView tdual_FFT_SCALAR_2d; +typedef tdual_FFT_SCALAR_2d::t_dev t_FFT_SCALAR_2d; -typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_2d_3; -typedef tdual_FFT_KOKKOS_SCALAR_2d_3::t_dev t_FFT_KOKKOS_SCALAR_2d_3; +typedef Kokkos::DualView tdual_FFT_SCALAR_2d_3; +typedef tdual_FFT_SCALAR_2d_3::t_dev t_FFT_SCALAR_2d_3; -typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_3d; -typedef tdual_FFT_KOKKOS_SCALAR_3d::t_dev t_FFT_KOKKOS_SCALAR_3d; +typedef Kokkos::DualView tdual_FFT_SCALAR_3d; +typedef tdual_FFT_SCALAR_3d::t_dev t_FFT_SCALAR_3d; typedef Kokkos:: - DualView tdual_FFT_KOKKOS_DATA_1d; -typedef tdual_FFT_KOKKOS_DATA_1d::t_dev t_FFT_KOKKOS_DATA_1d; -typedef tdual_FFT_KOKKOS_DATA_1d::t_dev_um t_FFT_KOKKOS_DATA_1d_um; + DualView tdual_FFT_DATA_1d; +typedef tdual_FFT_DATA_1d::t_dev t_FFT_DATA_1d; +typedef tdual_FFT_DATA_1d::t_dev_um t_FFT_DATA_1d_um; typedef Kokkos:: DualView tdual_int_64; @@ -186,23 +186,23 @@ struct FFTArrayTypes { //Kspace typedef Kokkos:: - DualView tdual_FFT_KOKKOS_SCALAR_1d; -typedef tdual_FFT_KOKKOS_SCALAR_1d::t_host t_FFT_KOKKOS_SCALAR_1d; -typedef tdual_FFT_KOKKOS_SCALAR_1d::t_host_um t_FFT_KOKKOS_SCALAR_1d_um; + DualView tdual_FFT_SCALAR_1d; +typedef tdual_FFT_SCALAR_1d::t_host t_FFT_SCALAR_1d; +typedef tdual_FFT_SCALAR_1d::t_host_um t_FFT_SCALAR_1d_um; -typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_2d; -typedef tdual_FFT_KOKKOS_SCALAR_2d::t_host t_FFT_KOKKOS_SCALAR_2d; +typedef Kokkos::DualView tdual_FFT_SCALAR_2d; +typedef tdual_FFT_SCALAR_2d::t_host t_FFT_SCALAR_2d; -typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_2d_3; -typedef tdual_FFT_KOKKOS_SCALAR_2d_3::t_host t_FFT_KOKKOS_SCALAR_2d_3; +typedef Kokkos::DualView tdual_FFT_SCALAR_2d_3; +typedef tdual_FFT_SCALAR_2d_3::t_host t_FFT_SCALAR_2d_3; -typedef Kokkos::DualView tdual_FFT_KOKKOS_SCALAR_3d; -typedef tdual_FFT_KOKKOS_SCALAR_3d::t_host t_FFT_KOKKOS_SCALAR_3d; +typedef Kokkos::DualView tdual_FFT_SCALAR_3d; +typedef tdual_FFT_SCALAR_3d::t_host t_FFT_SCALAR_3d; typedef Kokkos:: - DualView tdual_FFT_KOKKOS_DATA_1d; -typedef tdual_FFT_KOKKOS_DATA_1d::t_host t_FFT_KOKKOS_DATA_1d; -typedef tdual_FFT_KOKKOS_DATA_1d::t_host_um t_FFT_KOKKOS_DATA_1d_um; + DualView tdual_FFT_DATA_1d; +typedef tdual_FFT_DATA_1d::t_host t_FFT_DATA_1d; +typedef tdual_FFT_DATA_1d::t_host_um t_FFT_DATA_1d_um; typedef Kokkos:: DualView tdual_int_64; @@ -212,12 +212,12 @@ typedef tdual_int_64::t_host_um t_int_64_um; }; #endif -typedef struct FFTArrayTypes FFT_KOKKOS_DAT; -typedef struct FFTArrayTypes FFT_KOKKOS_HAT; +typedef struct FFTArrayTypes FFT_DAT; +typedef struct FFTArrayTypes FFT_HAT; #if defined(FFT_KOKKOS_KISSFFT) -#include "kissfft_kokkos.h" // uses t_FFT_KOKKOS_DATA_1d, needs to come last +#include "kissfft_kokkos.h" // uses t_FFT_DATA_1d, needs to come last #endif diff --git a/src/KOKKOS/grid3d_kokkos.cpp b/src/KOKKOS/grid3d_kokkos.cpp index 0f8e0bdc4e7..9a82e0157db 100644 --- a/src/KOKKOS/grid3d_kokkos.cpp +++ b/src/KOKKOS/grid3d_kokkos.cpp @@ -636,7 +636,7 @@ void Grid3dKokkos::setup_comm_tiled(int &nbuf1, int &nbuf2) template void Grid3dKokkos::forward_comm(int caller, void *ptr, int which, int nper, int nbyte, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d& k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d& k_buf2, + FFT_DAT::tdual_FFT_SCALAR_1d& k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d& k_buf2, MPI_Datatype datatype) { if (caller == KSPACE) { @@ -655,14 +655,14 @@ void Grid3dKokkos::forward_comm(int caller, void *ptr, int which, in template void Grid3dKokkos:: forward_comm_kspace_brick(KSpace *kspace, int which, int nper, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf2, MPI_Datatype datatype) + FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int m; MPI_Request request; KokkosBaseFFT* kspaceKKBase = dynamic_cast(kspace); - FFT_KOKKOS_SCALAR* buf1; - FFT_KOKKOS_SCALAR* buf2; + FFT_SCALAR* buf1; + FFT_SCALAR* buf2; if (lmp->kokkos->gpu_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); @@ -709,13 +709,13 @@ forward_comm_kspace_brick(KSpace *kspace, int which, int nper, template void Grid3dKokkos:: forward_comm_kspace_tiled(KSpace *kspace, int which, int nper, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf2, MPI_Datatype datatype) + FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int i,m,offset; KokkosBaseFFT* kspaceKKBase = dynamic_cast(kspace); - FFT_KOKKOS_SCALAR* buf1; - FFT_KOKKOS_SCALAR* buf2; + FFT_SCALAR* buf1; + FFT_SCALAR* buf2; if (lmp->kokkos->gpu_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); @@ -776,7 +776,7 @@ forward_comm_kspace_tiled(KSpace *kspace, int which, int nper, template void Grid3dKokkos::reverse_comm(int caller, void *ptr, int which, int nper, int nbyte, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d& k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d& k_buf2, + FFT_DAT::tdual_FFT_SCALAR_1d& k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d& k_buf2, MPI_Datatype datatype) { if (caller == KSPACE) { @@ -795,14 +795,14 @@ void Grid3dKokkos::reverse_comm(int caller, void *ptr, int which, in template void Grid3dKokkos:: reverse_comm_kspace_brick(KSpace *kspace, int which, int nper, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf2, MPI_Datatype datatype) + FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int m; MPI_Request request; KokkosBaseFFT* kspaceKKBase = dynamic_cast(kspace); - FFT_KOKKOS_SCALAR* buf1; - FFT_KOKKOS_SCALAR* buf2; + FFT_SCALAR* buf1; + FFT_SCALAR* buf2; if (lmp->kokkos->gpu_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); @@ -850,14 +850,14 @@ reverse_comm_kspace_brick(KSpace *kspace, int which, int nper, template void Grid3dKokkos:: reverse_comm_kspace_tiled(KSpace *kspace, int which, int nper, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf1, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf2, MPI_Datatype datatype) + FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int i,m,offset; KokkosBaseFFT* kspaceKKBase = dynamic_cast(kspace); - FFT_KOKKOS_SCALAR* buf1; - FFT_KOKKOS_SCALAR* buf2; + FFT_SCALAR* buf1; + FFT_SCALAR* buf2; if (lmp->kokkos->gpu_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); diff --git a/src/KOKKOS/grid3d_kokkos.h b/src/KOKKOS/grid3d_kokkos.h index 864ac19c060..19751d83c9c 100644 --- a/src/KOKKOS/grid3d_kokkos.h +++ b/src/KOKKOS/grid3d_kokkos.h @@ -34,9 +34,9 @@ class Grid3dKokkos : public Grid3d { ~Grid3dKokkos() override; void forward_comm(int, void *, int, int, int, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); + FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); void reverse_comm(int, void *, int, int, int, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); + FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); private: DAT::tdual_int_2d k_swap_packlist; @@ -57,13 +57,13 @@ class Grid3dKokkos : public Grid3d { void setup_comm_tiled(int &, int &) override; void forward_comm_kspace_brick(class KSpace *, int, int, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); + FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); void forward_comm_kspace_tiled(class KSpace *, int, int, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); + FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); void reverse_comm_kspace_brick(class KSpace *, int, int, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); + FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); void reverse_comm_kspace_tiled(class KSpace *, int, int, - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, MPI_Datatype); + FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); void grow_swap() override; diff --git a/src/KOKKOS/kissfft_kokkos.h b/src/KOKKOS/kissfft_kokkos.h index 66f32d29fb1..265677a21c7 100644 --- a/src/KOKKOS/kissfft_kokkos.h +++ b/src/KOKKOS/kissfft_kokkos.h @@ -119,14 +119,14 @@ }while(0) */ -#define KISS_FFT_KOKKOS_COS(phase) (FFT_KOKKOS_SCALAR) cos(phase) -#define KISS_FFT_KOKKOS_SIN(phase) (FFT_KOKKOS_SCALAR) sin(phase) +#define KISS_FFT_COS(phase) (FFT_SCALAR) cos(phase) +#define KISS_FFT_SIN(phase) (FFT_SCALAR) sin(phase) #define HALF_OF(x) ((x)*.5) #define kf_cexp(x,x_index,phase) \ do{ \ - (x)(x_index).re = KISS_FFT_KOKKOS_COS(phase);\ - (x)(x_index).im = KISS_FFT_KOKKOS_SIN(phase);\ + (x)(x_index).re = KISS_FFT_COS(phase);\ + (x)(x_index).im = KISS_FFT_SIN(phase);\ }while(0) @@ -142,8 +142,8 @@ struct kiss_fft_state_kokkos { int nfft; int inverse; typename FFT_AT::t_int_64 d_factors; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_twiddles; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d d_scratch; + typename FFT_AT::t_FFT_DATA_1d d_twiddles; + typename FFT_AT::t_FFT_DATA_1d d_scratch; }; template @@ -153,11 +153,11 @@ class KissFFTKokkos { typedef FFTArrayTypes FFT_AT; KOKKOS_INLINE_FUNCTION - static void kf_bfly2(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly2(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, int m, int Fout_count) { - typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_KOKKOS_SCALAR t[2]; + typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_SCALAR t[2]; int Fout2_count; int tw1_count = 0; @@ -179,11 +179,11 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kf_bfly4(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly4(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, const size_t m, int Fout_count) { - typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_KOKKOS_SCALAR scratch[6][2]; + typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_SCALAR scratch[6][2]; size_t k=m; const size_t m2=2*m; const size_t m3=3*m; @@ -237,14 +237,14 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kf_bfly3(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly3(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, size_t m, int Fout_count) { size_t k=m; const size_t m2 = 2*m; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_KOKKOS_SCALAR scratch[5][2]; - FFT_KOKKOS_SCALAR epi3[2]; + typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_SCALAR scratch[5][2]; + FFT_SCALAR epi3[2]; //C_EQ(epi3,d_twiddles[fstride*m]); epi3[0] = d_twiddles(fstride*m).re; epi3[1] = d_twiddles(fstride*m).im; @@ -289,13 +289,13 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kf_bfly5(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly5(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, int m, int Fout_count) { int u; - FFT_KOKKOS_SCALAR scratch[13][2]; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_KOKKOS_SCALAR ya[2],yb[2]; + FFT_SCALAR scratch[13][2]; + typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_SCALAR ya[2],yb[2]; //C_EQ(ya,d_twiddles[fstride*m]); ya[1] = d_twiddles(fstride*m).im; ya[0] = d_twiddles(fstride*m).re; @@ -369,15 +369,15 @@ class KissFFTKokkos { /* perform the butterfly for one stage of a mixed radix FFT */ KOKKOS_INLINE_FUNCTION - static void kf_bfly_generic(typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_Fout, const size_t fstride, + static void kf_bfly_generic(typename FFT_AT::t_FFT_DATA_1d_um &d_Fout, const size_t fstride, const kiss_fft_state_kokkos &st, int m, int p, int Fout_count) { int u,k,q1,q; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_twiddles = st.d_twiddles; - FFT_KOKKOS_SCALAR t[2]; + typename FFT_AT::t_FFT_DATA_1d_um d_twiddles = st.d_twiddles; + FFT_SCALAR t[2]; int Norig = st.nfft; - typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_scratch = st.d_scratch; + typename FFT_AT::t_FFT_DATA_1d_um d_scratch = st.d_scratch; for ( u=0; u &st, int Fout_count, int f_count, int factors_count) { @@ -452,7 +452,7 @@ class KissFFTKokkos { p[i] * m[i] = m[i-1] m0 = n */ - static int kf_factor(int n, FFT_KOKKOS_HAT::t_int_64 h_facbuf) + static int kf_factor(int n, FFT_HAT::t_int_64 h_facbuf) { int p=4, nf=0; double floor_sqrt; @@ -497,11 +497,11 @@ class KissFFTKokkos { st.inverse = inverse_fft; typename FFT_AT::tdual_int_64 k_factors = typename FFT_AT::tdual_int_64(); - typename FFT_AT::tdual_FFT_KOKKOS_DATA_1d k_twiddles = typename FFT_AT::tdual_FFT_KOKKOS_DATA_1d(); + typename FFT_AT::tdual_FFT_DATA_1d k_twiddles = typename FFT_AT::tdual_FFT_DATA_1d(); if (nfft > 0) { k_factors = typename FFT_AT::tdual_int_64("kissfft:factors",MAXFACTORS*2); - k_twiddles = typename FFT_AT::tdual_FFT_KOKKOS_DATA_1d("kissfft:twiddles",nfft); + k_twiddles = typename FFT_AT::tdual_FFT_DATA_1d("kissfft:twiddles",nfft); for (i=0;i(); @@ -524,12 +524,12 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kiss_fft_stride(const kiss_fft_state_kokkos &st, const typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_fin, typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um &d_fout, int in_stride, int offset) + static void kiss_fft_stride(const kiss_fft_state_kokkos &st, const typename FFT_AT::t_FFT_DATA_1d_um &d_fin, typename FFT_AT::t_FFT_DATA_1d_um &d_fout, int in_stride, int offset) { //if (d_fin.data() == d_fout.data()) { // // NOTE: this is not really an in-place FFT algorithm. // // It just performs an out-of-place FFT into a temp buffer - // typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_tmpbuf = typename FFT_AT::t_FFT_KOKKOS_DATA_1d("kissfft:tmpbuf",d_fin.extent(1)); + // typename FFT_AT::t_FFT_DATA_1d_um d_tmpbuf = typename FFT_AT::t_FFT_DATA_1d("kissfft:tmpbuf",d_fin.extent(1)); // kf_work(d_tmpbuf,d_fin,1,in_stride,st.d_factors,st,offset,offset).re; // Kokkos::deep_copy(d_fout,d_tmpbuf); //} else { @@ -538,7 +538,7 @@ class KissFFTKokkos { } KOKKOS_INLINE_FUNCTION - static void kiss_fft_kokkos(const kiss_fft_state_kokkos &cfg, const typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_fin, typename FFT_AT::t_FFT_KOKKOS_DATA_1d_um d_fout, int offset) + static void kiss_fft_kokkos(const kiss_fft_state_kokkos &cfg, const typename FFT_AT::t_FFT_DATA_1d_um d_fin, typename FFT_AT::t_FFT_DATA_1d_um d_fout, int offset) { kiss_fft_stride(cfg,d_fin,d_fout,1,offset); } diff --git a/src/KOKKOS/kokkos_base_fft.h b/src/KOKKOS/kokkos_base_fft.h index 567dc02ff3a..08369b3c78e 100644 --- a/src/KOKKOS/kokkos_base_fft.h +++ b/src/KOKKOS/kokkos_base_fft.h @@ -12,8 +12,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifndef LMP_KOKKOS_BASE_FFT_KOKKOS_H -#define LMP_KOKKOS_BASE_FFT_KOKKOS_H +#ifndef LMP_KOKKOS_BASE_FFT_H +#define LMP_KOKKOS_BASE_FFT_H #include "fftdata_kokkos.h" @@ -24,10 +24,10 @@ class KokkosBaseFFT { KokkosBaseFFT() {} // Kspace - virtual void pack_forward_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {}; - virtual void unpack_forward_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) {}; - virtual void pack_reverse_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {}; - virtual void unpack_reverse_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) {}; + virtual void pack_forward_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {}; + virtual void unpack_forward_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) {}; + virtual void pack_reverse_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {}; + virtual void unpack_reverse_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) {}; }; } diff --git a/src/KOKKOS/lmpfftsettings_kokkos.h b/src/KOKKOS/lmpfftsettings_kokkos.h index 148e001de38..6cea9bb63a4 100644 --- a/src/KOKKOS/lmpfftsettings_kokkos.h +++ b/src/KOKKOS/lmpfftsettings_kokkos.h @@ -16,6 +16,8 @@ #ifndef LMP_FFT_KOKKOS_SETTINGS_H #define LMP_FFT_KOKKOS_SETTINGS_H +#include "lmpfftsettings.h" + // if user set FFTW, it means FFTW3 #ifdef FFT_KOKKOS_FFTW @@ -38,17 +40,4 @@ #define LMP_FFT_KOKKOS_LIB "KISS FFT" #endif -#ifdef FFT_KOKKOS_SINGLE -typedef float FFT_KOKKOS_SCALAR; -#define FFT_KOKKOS_PRECISION 1 -#define LMP_FFT_KOKKOS_PREC "single" -#define MPI_FFT_KOKKOS_SCALAR MPI_FLOAT -#else - -typedef double FFT_KOKKOS_SCALAR; -#define FFT_KOKKOS_PRECISION 2 -#define LMP_FFT_KOKKOS_PREC "double" -#define MPI_FFT_KOKKOS_SCALAR MPI_DOUBLE -#endif - #endif diff --git a/src/KOKKOS/pack_kokkos.h b/src/KOKKOS/pack_kokkos.h index 5e014db020e..fe90d294a67 100644 --- a/src/KOKKOS/pack_kokkos.h +++ b/src/KOKKOS/pack_kokkos.h @@ -44,7 +44,7 @@ struct pack_3d_functor { public: typedef DeviceType device_type; typedef FFTArrayTypes FFT_AT; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -52,7 +52,7 @@ struct pack_3d_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - pack_3d_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + pack_3d_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -80,7 +80,7 @@ struct pack_3d_functor { } }; -static void pack_3d(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, struct pack_plan_3d *plan) +static void pack_3d(typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -98,7 +98,7 @@ struct unpack_3d_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -106,7 +106,7 @@ struct unpack_3d_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -134,7 +134,7 @@ struct unpack_3d_functor { } }; -static void unpack_3d(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -153,7 +153,7 @@ struct unpack_3d_permute1_1_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -161,7 +161,7 @@ struct unpack_3d_permute1_1_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute1_1_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute1_1_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -189,7 +189,7 @@ struct unpack_3d_permute1_1_functor { } }; -static void unpack_3d_permute1_1(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute1_1(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -206,7 +206,7 @@ struct unpack_3d_permute1_2_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -214,7 +214,7 @@ struct unpack_3d_permute1_2_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute1_2_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute1_2_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -243,7 +243,7 @@ struct unpack_3d_permute1_2_functor { } }; -static void unpack_3d_permute1_2(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute1_2(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -261,7 +261,7 @@ struct unpack_3d_permute1_n_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -270,7 +270,7 @@ struct unpack_3d_permute1_n_functor { int nstride_plane; // stride between successive slow indices int nqty; // # of values/element - unpack_3d_permute1_n_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute1_n_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -299,7 +299,7 @@ struct unpack_3d_permute1_n_functor { } }; -static void unpack_3d_permute1_n(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute1_n(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -317,7 +317,7 @@ struct unpack_3d_permute2_1_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -325,7 +325,7 @@ struct unpack_3d_permute2_1_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute2_1_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute2_1_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -352,7 +352,7 @@ struct unpack_3d_permute2_1_functor { } }; -static void unpack_3d_permute2_1(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute2_1(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -370,7 +370,7 @@ struct unpack_3d_permute2_2_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -378,7 +378,7 @@ struct unpack_3d_permute2_2_functor { int nstride_line; // stride between successive mid indices int nstride_plane; // stride between successive slow indices - unpack_3d_permute2_2_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute2_2_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -406,7 +406,7 @@ struct unpack_3d_permute2_2_functor { } }; -static void unpack_3d_permute2_2(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute2_2(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; @@ -423,7 +423,7 @@ struct unpack_3d_permute2_n_functor { public: typedef DeviceType device_type; typedef ArrayTypes AT; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf,d_data; + typename FFT_AT::t_FFT_SCALAR_1d_um d_buf,d_data; int buf_offset,data_offset; int nfast; // # of elements in fast index int nmid; // # of elements in mid index @@ -432,7 +432,7 @@ struct unpack_3d_permute2_n_functor { int nstride_plane; // stride between successive slow indices int nqty; // # of values/element - unpack_3d_permute2_n_functor(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): + unpack_3d_permute2_n_functor(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf_, int buf_offset_, typename FFT_AT::t_FFT_SCALAR_1d_um d_data_, int data_offset_, struct pack_plan_3d *plan): d_buf(d_buf_), d_data(d_data_) { @@ -460,7 +460,7 @@ struct unpack_3d_permute2_n_functor { } }; -static void unpack_3d_permute2_n(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) +static void unpack_3d_permute2_n(typename FFT_AT::t_FFT_SCALAR_1d_um d_buf, int buf_offset, typename FFT_AT::t_FFT_SCALAR_1d_um d_data, int data_offset, struct pack_plan_3d *plan) { const int nslow = plan->nslow; const int nmid = plan->nmid; diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index ed7ace08c16..6e1b3a83fa9 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -48,7 +48,7 @@ using namespace MathSpecialKokkos; enum{REVERSE_RHO}; enum{FORWARD_IK,FORWARD_IK_PERATOM}; -#ifdef FFT_KOKKOS_SINGLE +#ifdef FFT_SINGLE #define ZEROF 0.0f #define ONEF 1.0f #else @@ -582,7 +582,7 @@ void PPPMKokkos::compute(int eflag, int vflag) if (atom->nmax > nmax) { nmax = atomKK->nmax; d_part2grid = typename AT::t_int_1d_3("pppm:part2grid",nmax); - d_rho1d = typename FFT_AT::t_FFT_KOKKOS_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); + d_rho1d = typename FFT_AT::t_FFT_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); } // find grid points for all my particles @@ -595,8 +595,8 @@ void PPPMKokkos::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_KOKKOS_SCALAR), - k_gc_buf1,k_gc_buf2,MPI_FFT_KOKKOS_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); brick2fft(); // compute potential gradient on my FFT grid and @@ -609,14 +609,14 @@ void PPPMKokkos::compute(int eflag, int vflag) // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks - gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_KOKKOS_SCALAR), - k_gc_buf1,k_gc_buf2,MPI_FFT_KOKKOS_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), + k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) - gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_KOKKOS_SCALAR), - k_gc_buf1,k_gc_buf2,MPI_FFT_KOKKOS_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); // calculate the force on my particles @@ -730,8 +730,8 @@ void PPPMKokkos::allocate() npergrid = 3; - k_gc_buf1 = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); - k_gc_buf2 = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); + k_gc_buf1 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); + k_gc_buf2 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); // tally local grid sizes // ngrid = count of owned+ghost grid cells on this proc @@ -753,7 +753,7 @@ void PPPMKokkos::allocate() // allocate distributed grid data - d_density_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:density_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_density_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:density_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); memoryKK->create_kokkos(k_density_fft,density_fft,nfft_both,"pppm:d_density_fft"); d_density_fft = k_density_fft.view(); @@ -775,17 +775,17 @@ void PPPMKokkos::allocate() d_fkz = typename AT::t_float_1d("pppm:d_fkz",nfft_both); } - d_vdx_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdx_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_vdy_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdy_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_vdz_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_vdz_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_vdx_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_vdx_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_vdy_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_vdy_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_vdz_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_vdz_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); // summation coeffs order_allocated = order; k_gf_b = typename DAT::tdual_float_1d("pppm:gf_b",order); d_gf_b = k_gf_b.view(); - d_rho1d = typename FFT_AT::t_FFT_KOKKOS_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); - k_rho_coeff = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_2d("pppm:rho_coeff",order,order/2-(1-order)/2+1); + d_rho1d = typename FFT_AT::t_FFT_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); + k_rho_coeff = FFT_DAT::tdual_FFT_SCALAR_2d("pppm:rho_coeff",order,order/2-(1-order)/2+1); d_rho_coeff = k_rho_coeff.view(); h_rho_coeff = k_rho_coeff.h_view; @@ -810,7 +810,7 @@ void PPPMKokkos::allocate() remap = new RemapKokkos(lmp,world, nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, - 1,0,0,FFT_KOKKOS_PRECISION,collective_flag,gpu_aware_flag); + 1,0,0,FFT_PRECISION,collective_flag,gpu_aware_flag); } /* ---------------------------------------------------------------------- @@ -847,14 +847,14 @@ void PPPMKokkos::allocate_peratom() { peratom_allocate_flag = 1; - d_u_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:u_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_u_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:u_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v0_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v0_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v1_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v1_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v2_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v2_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v3_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v3_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v4_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v4_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); - d_v5_brick = typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d("pppm:d_v5_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v0_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v0_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v1_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v1_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v2_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v2_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v3_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v3_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v4_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v4_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); + d_v5_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:d_v5_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); // use same GC ghost grid object for peratom grid communication @@ -862,8 +862,8 @@ void PPPMKokkos::allocate_peratom() npergrid = 7; - k_gc_buf1 = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); - k_gc_buf2 = FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); + k_gc_buf1 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); + k_gc_buf2 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); } /* ---------------------------------------------------------------------- @@ -1234,14 +1234,14 @@ KOKKOS_INLINE_FUNCTION void PPPMKokkos::operator()(TagPPPM_make_rho_atomic, const int &i) const { // The density_brick array is atomic for Half/Thread neighbor style - Kokkos::View::value,Kokkos::MemoryTraits > a_density_brick = d_density_brick; + Kokkos::View::value,Kokkos::MemoryTraits > a_density_brick = d_density_brick; int nx = d_part2grid(i,0); int ny = d_part2grid(i,1); int nz = d_part2grid(i,2); - const FFT_KOKKOS_SCALAR dx = nx+shiftone - (x(i,0)-boxlo[0])*delxinv; - const FFT_KOKKOS_SCALAR dy = ny+shiftone - (x(i,1)-boxlo[1])*delyinv; - const FFT_KOKKOS_SCALAR dz = nz+shiftone - (x(i,2)-boxlo[2])*delzinv; + const FFT_SCALAR dx = nx+shiftone - (x(i,0)-boxlo[0])*delxinv; + const FFT_SCALAR dy = ny+shiftone - (x(i,1)-boxlo[1])*delyinv; + const FFT_SCALAR dz = nz+shiftone - (x(i,2)-boxlo[2])*delzinv; nz -= nzlo_out; @@ -1250,13 +1250,13 @@ void PPPMKokkos::operator()(TagPPPM_make_rho_atomic, const int &i) c compute_rho1d(i,dx,dy,dz); - const FFT_KOKKOS_SCALAR z0 = delvolinv * q[i]; + const FFT_SCALAR z0 = delvolinv * q[i]; for (int n = nlower; n <= nupper; n++) { const int mz = n+nz; - const FFT_KOKKOS_SCALAR y0 = z0*d_rho1d(i,n+order/2,2); + const FFT_SCALAR y0 = z0*d_rho1d(i,n+order/2,2); for (int m = nlower; m <= nupper; m++) { const int my = m+ny; - const FFT_KOKKOS_SCALAR x0 = y0*d_rho1d(i,m+order/2,1); + const FFT_SCALAR x0 = y0*d_rho1d(i,m+order/2,1); for (int l = nlower; l <= nupper; l++) { const int mx = l+nx; a_density_brick(mz,my,mx) += x0*d_rho1d(i,l+order/2,0); @@ -1294,9 +1294,9 @@ void PPPMKokkos::operator() (TagPPPM_make_rho, typename Kokkos::Team if ( ((nz+nlower-nzlo_out)*ix*iy >= ito) || ((nz+nupper-nzlo_out+1)*ix*iy < ifrom) ) continue; - const FFT_KOKKOS_SCALAR dx = nx+shiftone - (x(i,0)-boxlo[0])*delxinv; - const FFT_KOKKOS_SCALAR dy = ny+shiftone - (x(i,1)-boxlo[1])*delyinv; - const FFT_KOKKOS_SCALAR dz = nz+shiftone - (x(i,2)-boxlo[2])*delzinv; + const FFT_SCALAR dx = nx+shiftone - (x(i,0)-boxlo[0])*delxinv; + const FFT_SCALAR dy = ny+shiftone - (x(i,1)-boxlo[1])*delyinv; + const FFT_SCALAR dz = nz+shiftone - (x(i,2)-boxlo[2])*delzinv; nz -= nzlo_out; ny -= nylo_out; @@ -1304,15 +1304,15 @@ void PPPMKokkos::operator() (TagPPPM_make_rho, typename Kokkos::Team compute_rho1d(i,dx,dy,dz); - const FFT_KOKKOS_SCALAR z0 = delvolinv * q[i]; + const FFT_SCALAR z0 = delvolinv * q[i]; for (int n = nlower; n <= nupper; n++) { const int mz = n+nz; const int in = mz*ix*iy; - const FFT_KOKKOS_SCALAR y0 = z0*d_rho1d(i,n+order/2,2); + const FFT_SCALAR y0 = z0*d_rho1d(i,n+order/2,2); for (int m = nlower; m <= nupper; m++) { const int my = m+ny; const int im = in+my*ix; - const FFT_KOKKOS_SCALAR x0 = y0*d_rho1d(i,m+order/2,1); + const FFT_SCALAR x0 = y0*d_rho1d(i,m+order/2,1); for (int l = nlower; l <= nupper; l++) { const int mx = l+nx; const int il = im+mx; @@ -2040,8 +2040,8 @@ KOKKOS_INLINE_FUNCTION void PPPMKokkos::operator()(TagPPPM_fieldforce_ik, const int &i) const { int l,m,n,nx,ny,nz,mx,my,mz; - FFT_KOKKOS_SCALAR x0,y0,z0; - FFT_KOKKOS_SCALAR ekx,eky,ekz; + FFT_SCALAR x0,y0,z0; + FFT_SCALAR ekx,eky,ekz; nx = d_part2grid(i,0); ny = d_part2grid(i,1); @@ -2100,8 +2100,8 @@ KOKKOS_INLINE_FUNCTION void PPPMKokkos::operator()(TagPPPM_fieldforce_peratom, const int &i) const { int l,m,n,nx,ny,nz,mx,my,mz; - FFT_KOKKOS_SCALAR dx,dy,dz,x0,y0,z0; - FFT_KOKKOS_SCALAR u,v0,v1,v2,v3,v4,v5; + FFT_SCALAR dx,dy,dz,x0,y0,z0; + FFT_SCALAR u,v0,v1,v2,v3,v4,v5; nx = d_part2grid(i,0); ny = d_part2grid(i,1); @@ -2155,7 +2155,7 @@ void PPPMKokkos::operator()(TagPPPM_fieldforce_peratom, const int &i ------------------------------------------------------------------------- */ template -void PPPMKokkos::pack_forward_grid_kokkos(int flag, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index) +void PPPMKokkos::pack_forward_grid_kokkos(int flag, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index) { typename AT::t_int_2d_um d_list = k_list.view(); d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL()); @@ -2211,7 +2211,7 @@ void PPPMKokkos::operator()(TagPPPM_pack_forward2, const int &i) con ------------------------------------------------------------------------- */ template -void PPPMKokkos::unpack_forward_grid_kokkos(int flag, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf, int offset, int nlist, DAT::tdual_int_2d &k_list, int index) +void PPPMKokkos::unpack_forward_grid_kokkos(int flag, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int offset, int nlist, DAT::tdual_int_2d &k_list, int index) { typename AT::t_int_2d_um d_list = k_list.view(); d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL()); @@ -2269,7 +2269,7 @@ void PPPMKokkos::operator()(TagPPPM_unpack_forward2, const int &i) c ------------------------------------------------------------------------- */ template -void PPPMKokkos::pack_reverse_grid_kokkos(int /*flag*/, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index) +void PPPMKokkos::pack_reverse_grid_kokkos(int /*flag*/, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index) { typename AT::t_int_2d_um d_list = k_list.view(); d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL()); @@ -2299,7 +2299,7 @@ void PPPMKokkos::operator()(TagPPPM_pack_reverse, const int &i) cons ------------------------------------------------------------------------- */ template -void PPPMKokkos::unpack_reverse_grid_kokkos(int /*flag*/, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &k_buf, int offset, int nlist, DAT::tdual_int_2d &k_list, int index) +void PPPMKokkos::unpack_reverse_grid_kokkos(int /*flag*/, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int offset, int nlist, DAT::tdual_int_2d &k_list, int index) { typename AT::t_int_2d_um d_list = k_list.view(); d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL()); @@ -2332,11 +2332,11 @@ void PPPMKokkos::operator()(TagPPPM_unpack_reverse, const int &i) co template KOKKOS_INLINE_FUNCTION -void PPPMKokkos::compute_rho1d(const int i, const FFT_KOKKOS_SCALAR &dx, const FFT_KOKKOS_SCALAR &dy, - const FFT_KOKKOS_SCALAR &dz) const +void PPPMKokkos::compute_rho1d(const int i, const FFT_SCALAR &dx, const FFT_SCALAR &dy, + const FFT_SCALAR &dz) const { int k,l; - FFT_KOKKOS_SCALAR r1,r2,r3; + FFT_SCALAR r1,r2,r3; for (k = (1-order)/2; k <= order/2; k++) { r1 = r2 = r3 = ZEROF; @@ -2375,10 +2375,10 @@ template void PPPMKokkos::compute_rho_coeff() { int j,k,l,m; - FFT_KOKKOS_SCALAR s; - FFT_KOKKOS_SCALAR **a = new FFT_KOKKOS_SCALAR *[order]; + FFT_SCALAR s; + FFT_SCALAR **a = new FFT_SCALAR *[order]; for (int i = 0; i < order; ++i) - a[i] = new FFT_KOKKOS_SCALAR[2*order+1]; + a[i] = new FFT_SCALAR[2*order+1]; for (k = 0; k <= 2*order; k++) for (l = 0; l < order; l++) @@ -2390,7 +2390,7 @@ void PPPMKokkos::compute_rho_coeff() s = 0.0; for (l = 0; l < j; l++) { a[l+1][k+order] = (a[l][k+1+order]-a[l][k-1+order]) / (l+1); -#ifdef FFT_KOKKOS_SINGLE +#ifdef FFT_SINGLE s += powf(0.5,(float) l+1) * (a[l][k-1+order] + powf(-1.0,(float) l) * a[l][k+1+order]) / (l+1); #else @@ -2586,18 +2586,18 @@ double PPPMKokkos::memory_usage() double bytes = (double)nmax*3 * sizeof(double); int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * (nzhi_out-nzlo_out+1); - bytes += (double)4 * nbrick * sizeof(FFT_KOKKOS_SCALAR); + bytes += (double)4 * nbrick * sizeof(FFT_SCALAR); if (triclinic) bytes += (double)3 * nfft_both * sizeof(double); bytes += (double)6 * nfft_both * sizeof(double); bytes += (double)nfft_both * sizeof(double); - bytes += (double)nfft_both*5 * sizeof(FFT_KOKKOS_SCALAR); + bytes += (double)nfft_both*5 * sizeof(FFT_SCALAR); if (peratom_allocate_flag) - bytes += (double)6 * nbrick * sizeof(FFT_KOKKOS_SCALAR); + bytes += (double)6 * nbrick * sizeof(FFT_SCALAR); // two Grid3d bufs - bytes += (double)(ngc_buf1 + ngc_buf2) * npergrid * sizeof(FFT_KOKKOS_SCALAR); + bytes += (double)(ngc_buf1 + ngc_buf2) * npergrid * sizeof(FFT_SCALAR); return bytes; } diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h index 09513c9a2fb..14d4670dbdf 100644 --- a/src/KOKKOS/pppm_kokkos.h +++ b/src/KOKKOS/pppm_kokkos.h @@ -350,7 +350,7 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { int nx,ny,nz; typename AT::t_int_1d_um d_list_index; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um d_buf; + typename FFT_AT::t_FFT_SCALAR_1d_um d_buf; int unpack_offset; DAT::tdual_int_scalar k_flag; @@ -364,31 +364,31 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_density_brick; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_vdx_brick,d_vdy_brick,d_vdz_brick; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_u_brick; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_v0_brick,d_v1_brick,d_v2_brick; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_3d d_v3_brick,d_v4_brick,d_v5_brick; + typename FFT_AT::t_FFT_SCALAR_3d d_density_brick; + typename FFT_AT::t_FFT_SCALAR_3d d_vdx_brick,d_vdy_brick,d_vdz_brick; + typename FFT_AT::t_FFT_SCALAR_3d d_u_brick; + typename FFT_AT::t_FFT_SCALAR_3d d_v0_brick,d_v1_brick,d_v2_brick; + typename FFT_AT::t_FFT_SCALAR_3d d_v3_brick,d_v4_brick,d_v5_brick; typename AT::t_float_1d d_greensfn; typename AT::t_virial_array d_vg; typename AT::t_float_1d d_fkx; typename AT::t_float_1d d_fky; typename AT::t_float_1d d_fkz; - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_density_fft; - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_work1; - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_work2; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_density_fft; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_work1; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_work2; + FFT_DAT::tdual_FFT_SCALAR_1d k_density_fft; + FFT_DAT::tdual_FFT_SCALAR_1d k_work1; + FFT_DAT::tdual_FFT_SCALAR_1d k_work2; + typename FFT_AT::t_FFT_SCALAR_1d d_density_fft; + typename FFT_AT::t_FFT_SCALAR_1d d_work1; + typename FFT_AT::t_FFT_SCALAR_1d d_work2; DAT::tdual_float_1d k_gf_b; typename AT::t_float_1d d_gf_b; - //FFT_KOKKOS_SCALAR **rho1d,**rho_coeff,**drho1d,**drho_coeff; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_2d_3 d_rho1d; - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_2d k_rho_coeff; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_2d d_rho_coeff; - FFT_KOKKOS_HAT::t_FFT_KOKKOS_SCALAR_2d h_rho_coeff; + //FFT_SCALAR **rho1d,**rho_coeff,**drho1d,**drho_coeff; + typename FFT_AT::t_FFT_SCALAR_2d_3 d_rho1d; + FFT_DAT::tdual_FFT_SCALAR_2d k_rho_coeff; + typename FFT_AT::t_FFT_SCALAR_2d d_rho_coeff; + FFT_HAT::t_FFT_SCALAR_2d h_rho_coeff; //double **acons; typename Kokkos::DualView::t_host acons; @@ -398,7 +398,7 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { RemapKokkos *remap; Grid3dKokkos *gc; - FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d k_gc_buf1,k_gc_buf2; + FFT_DAT::tdual_FFT_SCALAR_1d k_gc_buf1,k_gc_buf2; int ngc_buf1,ngc_buf2,npergrid; //int **part2grid; // storage for particle -> grid mapping @@ -429,17 +429,17 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { void fieldforce_peratom() override; KOKKOS_INLINE_FUNCTION - void compute_rho1d(const int i, const FFT_KOKKOS_SCALAR &, const FFT_KOKKOS_SCALAR &, - const FFT_KOKKOS_SCALAR &) const; + void compute_rho1d(const int i, const FFT_SCALAR &, const FFT_SCALAR &, + const FFT_SCALAR &) const; void compute_rho_coeff(); void slabcorr() override; // grid communication - void pack_forward_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, DAT::tdual_int_2d &, int) override; - void unpack_forward_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) override; - void pack_reverse_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, DAT::tdual_int_2d &, int) override; - void unpack_reverse_grid_kokkos(int, FFT_KOKKOS_DAT::tdual_FFT_KOKKOS_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) override; + void pack_forward_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) override; + void unpack_forward_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) override; + void pack_reverse_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) override; + void unpack_reverse_grid_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, int, DAT::tdual_int_2d &, int) override; // triclinic diff --git a/src/KOKKOS/remap_kokkos.cpp b/src/KOKKOS/remap_kokkos.cpp index 18ba6264605..efc6742a259 100644 --- a/src/KOKKOS/remap_kokkos.cpp +++ b/src/KOKKOS/remap_kokkos.cpp @@ -59,7 +59,7 @@ RemapKokkos::~RemapKokkos() /* ---------------------------------------------------------------------- */ template -void RemapKokkos::perform(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_out, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_buf) +void RemapKokkos::perform(typename FFT_AT::t_FFT_SCALAR_1d d_in, typename FFT_AT::t_FFT_SCALAR_1d d_out, typename FFT_AT::t_FFT_SCALAR_1d d_buf) { remap_3d_kokkos(d_in,d_out,d_buf,plan); } @@ -103,7 +103,7 @@ void RemapKokkos::perform(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_ ------------------------------------------------------------------------- */ template -void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_in, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_out, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_buf, +void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d d_in, typename FFT_AT::t_FFT_SCALAR_1d d_out, typename FFT_AT::t_FFT_SCALAR_1d d_buf, struct remap_plan_3d_kokkos *plan) { // collective flag not yet supported @@ -111,7 +111,7 @@ void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_SCAL // use point-to-point communication int i,isend,irecv; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_scratch; + typename FFT_AT::t_FFT_SCALAR_1d d_scratch; if (plan->memory == 0) d_scratch = d_buf; @@ -120,20 +120,20 @@ void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_SCAL // post all recvs into scratch space - FFT_KOKKOS_SCALAR* v_scratch = d_scratch.data(); + FFT_SCALAR* v_scratch = d_scratch.data(); if (!plan->usecuda_aware) { plan->h_scratch = Kokkos::create_mirror_view(d_scratch); v_scratch = plan->h_scratch.data(); } for (irecv = 0; irecv < plan->nrecv; irecv++) { - FFT_KOKKOS_SCALAR* scratch = v_scratch + plan->recv_bufloc[irecv]; + FFT_SCALAR* scratch = v_scratch + plan->recv_bufloc[irecv]; MPI_Irecv(scratch,plan->recv_size[irecv], - MPI_FFT_KOKKOS_SCALAR,plan->recv_proc[irecv],0, + MPI_FFT_SCALAR,plan->recv_proc[irecv],0, plan->comm,&plan->request[irecv]); } - FFT_KOKKOS_SCALAR* v_sendbuf = plan->d_sendbuf.data(); + FFT_SCALAR* v_sendbuf = plan->d_sendbuf.data(); if (!plan->usecuda_aware) { plan->h_sendbuf = Kokkos::create_mirror_view(plan->d_sendbuf); v_sendbuf = plan->h_sendbuf.data(); @@ -149,7 +149,7 @@ void RemapKokkos::remap_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_SCAL if (!plan->usecuda_aware) Kokkos::deep_copy(plan->h_sendbuf,plan->d_sendbuf); - MPI_Send(v_sendbuf,plan->send_size[isend],MPI_FFT_KOKKOS_SCALAR, + MPI_Send(v_sendbuf,plan->send_size[isend],MPI_FFT_SCALAR, plan->send_proc[isend],0,plan->comm); } @@ -465,7 +465,7 @@ struct remap_plan_3d_kokkos* RemapKokkos::remap_3d_creat size = MAX(size,plan->send_size[nsend]); if (size) { - plan->d_sendbuf = typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d("remap3d:sendbuf",size); + plan->d_sendbuf = typename FFT_AT::t_FFT_SCALAR_1d("remap3d:sendbuf",size); if (!plan->d_sendbuf.data()) return nullptr; } @@ -475,7 +475,7 @@ struct remap_plan_3d_kokkos* RemapKokkos::remap_3d_creat if (memory == 1) { if (nrecv > 0) { plan->d_scratch = - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d("remap3d:scratch",nqty*out.isize*out.jsize*out.ksize); + typename FFT_AT::t_FFT_SCALAR_1d("remap3d:scratch",nqty*out.isize*out.jsize*out.ksize); if (!plan->d_scratch.data()) return nullptr; } } diff --git a/src/KOKKOS/remap_kokkos.h b/src/KOKKOS/remap_kokkos.h index ad5fa9833d2..a62c14f00b9 100644 --- a/src/KOKKOS/remap_kokkos.h +++ b/src/KOKKOS/remap_kokkos.h @@ -28,13 +28,13 @@ template struct remap_plan_3d_kokkos { typedef DeviceType device_type; typedef FFTArrayTypes FFT_AT; - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_sendbuf; // buffer for MPI sends - FFT_KOKKOS_HAT::t_FFT_KOKKOS_SCALAR_1d h_sendbuf; // host buffer for MPI sends - typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d d_scratch; // scratch buffer for MPI recvs - FFT_KOKKOS_HAT::t_FFT_KOKKOS_SCALAR_1d h_scratch; // host scratch buffer for MPI recvs - void (*pack)(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, struct pack_plan_3d *); + typename FFT_AT::t_FFT_SCALAR_1d d_sendbuf; // buffer for MPI sends + FFT_HAT::t_FFT_SCALAR_1d h_sendbuf; // host buffer for MPI sends + typename FFT_AT::t_FFT_SCALAR_1d d_scratch; // scratch buffer for MPI recvs + FFT_HAT::t_FFT_SCALAR_1d h_scratch; // host scratch buffer for MPI recvs + void (*pack)(typename FFT_AT::t_FFT_SCALAR_1d_um, int, typename FFT_AT::t_FFT_SCALAR_1d_um, int, struct pack_plan_3d *); // which pack function to use - void (*unpack)(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d_um, int, struct pack_plan_3d *); + void (*unpack)(typename FFT_AT::t_FFT_SCALAR_1d_um, int, typename FFT_AT::t_FFT_SCALAR_1d_um, int, struct pack_plan_3d *); // which unpack function to use int *send_offset; // extraction loc for each send int *send_size; // size of each send message @@ -66,11 +66,11 @@ class RemapKokkos : protected Pointers { RemapKokkos(class LAMMPS *, MPI_Comm,int,int,int,int,int,int, int,int,int,int,int,int,int,int,int,int,int,int); ~RemapKokkos() override; - void perform(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d); + void perform(typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d); struct remap_plan_3d_kokkos *plan; - void remap_3d_kokkos(typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, typename FFT_AT::t_FFT_KOKKOS_SCALAR_1d, struct remap_plan_3d_kokkos *); + void remap_3d_kokkos(typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, typename FFT_AT::t_FFT_SCALAR_1d, struct remap_plan_3d_kokkos *); struct remap_plan_3d_kokkos *remap_3d_create_plan_kokkos(MPI_Comm, int, int, int, int, int, int, int, int, int, int, int, int, From 6d1d515f3a3f7369f9ace5bef4dfcc1b81d6f80e Mon Sep 17 00:00:00 2001 From: Stan Gerald Moore Date: Wed, 13 Dec 2023 15:32:32 -0700 Subject: [PATCH 083/719] Fix compile issue --- src/KOKKOS/pppm_kokkos.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 6e1b3a83fa9..2a53682df3a 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -285,7 +285,7 @@ void PPPMKokkos::init() estimated_accuracy); mesg += fmt::format(" estimated relative force accuracy = {:.8g}\n", estimated_accuracy/two_charge_force); - mesg += " using " LMP_FFT_KOKKOS_PREC " precision " LMP_FFT_KOKKOS_LIB "\n"; + mesg += " using " LMP_FFT_PREC " precision " LMP_FFT_KOKKOS_LIB "\n"; mesg += fmt::format(" 3d grid and FFT values/proc = {} {}\n", ngrid_max,nfft_both_max); utils::logmesg(lmp,mesg); From b199368c19bdc5f1b5f0fc991473ae7de3f73d31 Mon Sep 17 00:00:00 2001 From: Shern Tee Date: Thu, 14 Dec 2023 10:46:32 +1000 Subject: [PATCH 084/719] add extract function to fix_property_atom --- src/fix_property_atom.cpp | 24 ++++++++++++++++++++++++ src/fix_property_atom.h | 1 + 2 files changed, 25 insertions(+) diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 9613523059d..1e004ae4cb5 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -948,3 +948,27 @@ int FixPropertyAtom::size_restart(int /*nlocal*/) { return values_peratom + 1; } + +/* ---------------------------------------------------------------------- + extract fix property/atom properties +------------------------------------------------------------------------- */ + +void *FixPropertyAtom::extract(const char *str, int &dim) +{ + dim=0; + if (strcmp(str, "nvalue") == 0) { + return &nvalue; + } else if (strcmp(str, "border") == 0) { + return &border; + } + dim=1; + if (strcmp(str, "styles") == 0) { + return &styles; + } else if (strcmp(str, "index") == 0) { + return &index; + } else if (strcmp(str, "cols") == 0) { + return &cols; + } + return nullptr; +} + diff --git a/src/fix_property_atom.h b/src/fix_property_atom.h index c50b6049dce..820acf3a209 100644 --- a/src/fix_property_atom.h +++ b/src/fix_property_atom.h @@ -51,6 +51,7 @@ class FixPropertyAtom : public Fix { void unpack_restart(int, int) override; int size_restart(int) override; int maxsize_restart() override; + void *extract(const char *, int &) override; double memory_usage() override; protected: From c45183d45c98c151ae4227dd415859249afae766 Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Thu, 14 Dec 2023 15:38:45 -0500 Subject: [PATCH 085/719] Updated CMake build system to allow for FFT_KOKKOS parameter. Updated CMakeLists.txt to print the correct value when summarizing. --- cmake/CMakeLists.txt | 16 +--------------- cmake/Modules/Packages/KOKKOS.cmake | 23 +++++++++++++++++++---- 2 files changed, 20 insertions(+), 19 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 28e02bbee7b..aacaca4e6ca 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -984,21 +984,7 @@ if(PKG_KSPACE) message(STATUS "Using non-threaded FFTs") endif() if(PKG_KOKKOS) - if(Kokkos_ENABLE_CUDA) - if(FFT STREQUAL "KISS") - message(STATUS "Kokkos FFT: KISS") - else() - message(STATUS "Kokkos FFT: cuFFT") - endif() - elseif(Kokkos_ENABLE_HIP) - if(FFT STREQUAL "KISS") - message(STATUS "Kokkos FFT: KISS") - else() - message(STATUS "Kokkos FFT: hipFFT") - endif() - else() - message(STATUS "Kokkos FFT: ${FFT}") - endif() + message(STATUS "Kokkos FFT: ${FFT_KOKKOS}") endif() endif() if(BUILD_DOC) diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index 0edd9a3baad..eb20f93956e 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -131,16 +131,31 @@ if(PKG_KSPACE) list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp) + set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT) + set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES}) + validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES) + string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS) + if(Kokkos_ENABLE_CUDA) - if(NOT (FFT STREQUAL "KISS")) - target_compile_definitions(lammps PRIVATE -DFFT_CUFFT) + if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "CUFFT"))) + message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.") + elseif(FFT_KOKKOS STREQUAL "KISS") + message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.") + target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS) + elseif(FFT_KOKKOS STREQUAL "CUFFT") + target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT) target_link_libraries(lammps PRIVATE cufft) endif() elseif(Kokkos_ENABLE_HIP) - if(NOT (FFT STREQUAL "KISS")) + if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT"))) + message(FATAL_ERROR "The HIP backend of Kokkos requires either KISS FFT or HIPFFT.") + elseif(FFT_KOKKOS STREQUAL "KISS") + message(WARNING "Using KISS FFT with the HIP backend of Kokkos may be sub-optimal.") + target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS) + elseif(FFT_KOKKOS STREQUAL "HIPFFT") include(DetectHIPInstallation) find_package(hipfft REQUIRED) - target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT) + target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT) target_link_libraries(lammps PRIVATE hip::hipfft) endif() endif() From 54089fb5abbd18d91ad2b0f1665338df403396f1 Mon Sep 17 00:00:00 2001 From: Shern Tee Date: Fri, 15 Dec 2023 10:58:06 +1000 Subject: [PATCH 086/719] Revert "add extract function to fix_property_atom" This reverts commit b199368c19bdc5f1b5f0fc991473ae7de3f73d31. --- src/fix_property_atom.cpp | 24 ------------------------ src/fix_property_atom.h | 1 - 2 files changed, 25 deletions(-) diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 1e004ae4cb5..9613523059d 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -948,27 +948,3 @@ int FixPropertyAtom::size_restart(int /*nlocal*/) { return values_peratom + 1; } - -/* ---------------------------------------------------------------------- - extract fix property/atom properties -------------------------------------------------------------------------- */ - -void *FixPropertyAtom::extract(const char *str, int &dim) -{ - dim=0; - if (strcmp(str, "nvalue") == 0) { - return &nvalue; - } else if (strcmp(str, "border") == 0) { - return &border; - } - dim=1; - if (strcmp(str, "styles") == 0) { - return &styles; - } else if (strcmp(str, "index") == 0) { - return &index; - } else if (strcmp(str, "cols") == 0) { - return &cols; - } - return nullptr; -} - diff --git a/src/fix_property_atom.h b/src/fix_property_atom.h index 820acf3a209..c50b6049dce 100644 --- a/src/fix_property_atom.h +++ b/src/fix_property_atom.h @@ -51,7 +51,6 @@ class FixPropertyAtom : public Fix { void unpack_restart(int, int) override; int size_restart(int) override; int maxsize_restart() override; - void *extract(const char *, int &) override; double memory_usage() override; protected: From 44fbcf7bfe2b8fd27c2cacf171fdc8dc6219ec69 Mon Sep 17 00:00:00 2001 From: Shern Tee Date: Fri, 15 Dec 2023 11:01:50 +1000 Subject: [PATCH 087/719] reorder "ghost" processing in fix property/atom --- src/fix_property_atom.cpp | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 9613523059d..93e33ca056b 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -51,6 +51,19 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : nvalue = 0; values_peratom = 0; + // get "ghost" first for settings + + border = 0; + while (iarg < narg) { + if (strcmp(arg[iarg], "ghost") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix property/atom command"); + border = utils::logical(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else iarg++; + } + + iarg = 3; + while (iarg < narg) { if (strcmp(arg[iarg], "mol") == 0) { if (atom->molecule_flag) @@ -168,11 +181,8 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : // optional args - border = 0; while (iarg < narg) { if (strcmp(arg[iarg], "ghost") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix property/atom command"); - border = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "writedata") == 0) { if (iarg + 2 > narg) error->all(FLERR, "Illegal fix property/atom command"); From 61ca9b79db605dae37450c2b20d12d1f88ce817e Mon Sep 17 00:00:00 2001 From: Shern Tee Date: Fri, 15 Dec 2023 11:48:46 +1000 Subject: [PATCH 088/719] add custom_border to Atom and AtomKokkos --- src/KOKKOS/atom_kokkos.cpp | 7 ++++++- src/KOKKOS/atom_kokkos.h | 2 +- src/atom.cpp | 13 ++++++++++++- src/atom.h | 4 +++- 4 files changed, 22 insertions(+), 4 deletions(-) diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index bc393b29d8b..ecd618e7ac3 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -297,7 +297,7 @@ void AtomKokkos::grow(unsigned int mask) return index in ivector or dvector of its location ------------------------------------------------------------------------- */ -int AtomKokkos::add_custom(const char *name, int flag, int cols) +int AtomKokkos::add_custom(const char *name, int flag, int cols, int border) { int index; @@ -342,6 +342,11 @@ int AtomKokkos::add_custom(const char *name, int flag, int cols) dcols[index] = cols; } + if (index < 0) + error->all(FLERR,"Invalid call to AtomKokkos::add_custom()"); + else + custom_border[flag + (cols) ? 2 : 0].push_back(border); + return index; } diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index 21a9aeebbd2..000ad5e1126 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -154,7 +154,7 @@ class AtomKokkos : public Atom { void sync_overlapping_device(const ExecutionSpace space, unsigned int mask); void sort() override; virtual void grow(unsigned int mask); - int add_custom(const char *, int, int) override; + int add_custom(const char *, int, int, int border = 0) override; void remove_custom(int, int, int) override; virtual void deallocate_topology(); private: diff --git a/src/atom.cpp b/src/atom.cpp index b604c54e6be..8ac72e89505 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -2605,6 +2605,7 @@ void Atom::update_callback(int ifix) lists of names can have NULL entries if previously removed return flag = 0/1 for int/double return cols = 0/N for vector/array where N = # of columns + return border = 0/1 if fix property/atom has "ghost" no/yes ------------------------------------------------------------------------- */ int Atom::find_custom(const char *name, int &flag, int &cols) @@ -2642,6 +2643,13 @@ int Atom::find_custom(const char *name, int &flag, int &cols) return -1; } +int Atom::find_custom(const char *name, int &flag, int &cols, int &border) +{ + int i = find_custom(name, flag, cols); + if (i != -1) border = custom_border[flag + (cols) ? 2 : 0][i]; + return i; +} + /** \brief Add a custom per-atom property with the given name and type and size \verbatim embed:rst @@ -2654,7 +2662,7 @@ This function is called, e.g. from :doc:`fix property/atom `. * \param cols Number of values: 0 for a single value, 1 or more for a vector of values * \return index of property in the respective list of properties */ -int Atom::add_custom(const char *name, int flag, int cols) +int Atom::add_custom(const char *name, int flag, int cols, int border) { int index = -1; @@ -2697,6 +2705,9 @@ int Atom::add_custom(const char *name, int flag, int cols) if (index < 0) error->all(FLERR,"Invalid call to Atom::add_custom()"); + else + custom_border[flag + (cols) ? 2 : 0].push_back(border); + return index; } diff --git a/src/atom.h b/src/atom.h index 548168ac599..9724e5662ff 100644 --- a/src/atom.h +++ b/src/atom.h @@ -242,6 +242,7 @@ class Atom : protected Pointers { int *icols, *dcols; char **ivname, **dvname, **ianame, **daname; int nivector, ndvector, niarray, ndarray; + std::array, 4> custom_border; // molecule templates // each template can be a set of consecutive molecules @@ -363,7 +364,8 @@ class Atom : protected Pointers { void update_callback(int); int find_custom(const char *, int &, int &); - virtual int add_custom(const char *, int, int); + int find_custom(const char *, int &, int &, int &); + virtual int add_custom(const char *, int, int, int border = 0); virtual void remove_custom(int, int, int); void *extract(const char *); From 09c87040b54b7bea54a0b7528cea0801ef94e81b Mon Sep 17 00:00:00 2001 From: Shern Tee Date: Fri, 15 Dec 2023 11:54:15 +1000 Subject: [PATCH 089/719] add border arguments to FixPropertyAtom add_custom functions --- src/fix_property_atom.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 93e33ca056b..c3af7c2f1af 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -125,7 +125,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : if (index[nvalue] >= 0) error->all(FLERR, "Fix property/atom vector name already exists"); if (ReadData::is_data_section(id)) error->all(FLERR, "Fix property/atom fix ID must not be a data file section name"); - index[nvalue] = atom->add_custom(&arg[iarg][2], 0, 0); + index[nvalue] = atom->add_custom(&arg[iarg][2], 0, 0, border); cols[nvalue] = 0; values_peratom++; nvalue++; @@ -138,7 +138,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : if (index[nvalue] >= 0) error->all(FLERR, "Fix property/atom vector name already exists"); if (ReadData::is_data_section(id)) error->all(FLERR, "Fix property/atom fix ID must not be a data file section name"); - index[nvalue] = atom->add_custom(&arg[iarg][2], 1, 0); + index[nvalue] = atom->add_custom(&arg[iarg][2], 1, 0, border); cols[nvalue] = 0; values_peratom++; nvalue++; @@ -167,7 +167,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : which = 1; styles[nvalue] = DARRAY; } - index[nvalue] = atom->add_custom(&arg[iarg][3], which, ncols); + index[nvalue] = atom->add_custom(&arg[iarg][3], which, ncols, border); cols[nvalue] = ncols; values_peratom += ncols; nvalue++; From a873106790223b3a72ed4d9293f55a2a8ba59bcc Mon Sep 17 00:00:00 2001 From: Shern Tee Date: Fri, 15 Dec 2023 12:26:05 +1000 Subject: [PATCH 090/719] improve AMOEBA fix property/atom checks --- src/AMOEBA/pair_amoeba.cpp | 47 ++++++++++++++++++++------------------ 1 file changed, 25 insertions(+), 22 deletions(-) diff --git a/src/AMOEBA/pair_amoeba.cpp b/src/AMOEBA/pair_amoeba.cpp index cad9e2b6289..c94faf91a76 100644 --- a/src/AMOEBA/pair_amoeba.cpp +++ b/src/AMOEBA/pair_amoeba.cpp @@ -827,28 +827,31 @@ void PairAmoeba::init_style() // check if all custom atom arrays were set via fix property/atom - int flag,cols; - - index_amtype = atom->find_custom("amtype",flag,cols); - if (index_amtype < 0 || flag || cols) - error->all(FLERR,"Pair {} amtype is not defined", mystyle); - index_amgroup = atom->find_custom("amgroup",flag,cols); - if (index_amgroup < 0 || flag || cols) - error->all(FLERR,"Pair {} amgroup is not defined", mystyle); - - index_redID = atom->find_custom("redID",flag,cols); - if (index_redID < 0 || !flag || cols) - error->all(FLERR,"Pair {} redID is not defined", mystyle); - index_xyzaxis = atom->find_custom("xyzaxis",flag,cols); - if (index_xyzaxis < 0 || !flag || cols == 0) - error->all(FLERR,"Pair {} xyzaxis is not defined", mystyle); - - index_polaxe = atom->find_custom("polaxe",flag,cols); - if (index_polaxe < 0 || flag || cols) - error->all(FLERR,"Pair {} polaxe is not defined", mystyle); - index_pval = atom->find_custom("pval",flag,cols); - if (index_pval < 0 || !flag || cols) - error->all(FLERR,"Pair {} pval is not defined", mystyle); + char const * names[6] = {"amtype", "amgroup", "redID", + "xyzaxis", "polaxe", "pval"}; + int const flag_check[6] = {0, 0, 1, 1, 0, 1}; // correct type (0 int, 1 dbl) + int const cols_check[6] = {0, 0, 0, 3, 0, 0}; // xyzaxis 3 cols, all others 0 + int const border_check[6] = {1, 0, 0, 0, 0, 0}; // which types need ghost + int flag, cols, border; + int index[6]; + + for (int i = 0; i < 6; i++) { + index[i] = atom->find_custom(names[i], flag, cols, border); + std::string err = ""; + if (index[i] < 0) err = "was not defined"; + else if (flag_check[i] != flag) err = "has the wrong type"; + else if (cols_check[i] != cols) err = "has the wrong number of columns"; + else if (border_check[i] && !border) err = "must be set by fix property/atom with ghost yes"; + if (err != "") + error->all(FLERR,"Pair {} per-atom variable {} {}", mystyle, names[i], err); + } + + index_amtype = index[0]; + index_amgroup = index[1]; + index_redID = index[2]; + index_xyzaxis = index[3]; + index_polaxe = index[4]; + index_pval = index[5]; // ------------------------------------------------------------------- // one-time initializations From e36a764db2a62ad45024e5c7fbdb8482ece4ec66 Mon Sep 17 00:00:00 2001 From: Shern Tee Date: Fri, 15 Dec 2023 12:44:55 +1000 Subject: [PATCH 091/719] add array and vector STL headers --- src/atom.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/atom.h b/src/atom.h index 9724e5662ff..6f22ebd1609 100644 --- a/src/atom.h +++ b/src/atom.h @@ -18,6 +18,8 @@ #include #include +#include +#include namespace LAMMPS_NS { From 95d1a41ee44a2fe05e4acb266bb550e4fa5dd3bc Mon Sep 17 00:00:00 2001 From: jtclemm Date: Fri, 15 Dec 2023 13:33:45 -0700 Subject: [PATCH 092/719] Fixing bpm/sphere error in fix move, displace atoms --- src/displace_atoms.cpp | 16 +++++++++++---- src/fix_move.cpp | 45 +++++++++++++++++++++++++++++++++--------- src/fix_move.h | 2 +- 3 files changed, 49 insertions(+), 14 deletions(-) diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index fa333f1bc23..5ecf5a2c9e8 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -160,7 +160,7 @@ void DisplaceAtoms::command(int narg, char **arg) int *mask = atom->mask; int nlocal = atom->nlocal; - double fraction,dramp; + double fraction, dramp; for (i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -255,11 +255,12 @@ void DisplaceAtoms::command(int narg, char **arg) int line_flag = atom->line_flag; int tri_flag = atom->tri_flag; int body_flag = atom->body_flag; + int quat_atom_flag = atom->quat_flag; int theta_flag = 0; int quat_flag = 0; if (line_flag) theta_flag = 1; - if (ellipsoid_flag || tri_flag || body_flag) quat_flag = 1; + if (ellipsoid_flag || tri_flag || body_flag || quat_atom_flag) quat_flag = 1; // AtomVec pointers to retrieve per-atom storage of extra quantities @@ -269,6 +270,7 @@ void DisplaceAtoms::command(int narg, char **arg) auto avec_body = dynamic_cast(atom->style_match("body")); double **x = atom->x; + double **quat_atom = atom->quat; int *ellipsoid = atom->ellipsoid; int *line = atom->line; int *tri = atom->tri; @@ -313,7 +315,7 @@ void DisplaceAtoms::command(int narg, char **arg) // quats for ellipsoids, tris, and bodies - if (quat_flag) { + if (quat_flag && !quat_atom_flag) { quat = nullptr; if (ellipsoid_flag && ellipsoid[i] >= 0) quat = avec_ellipsoid->bonus[ellipsoid[i]].quat; @@ -322,12 +324,18 @@ void DisplaceAtoms::command(int narg, char **arg) else if (body_flag && body[i] >= 0) quat = avec_body->bonus[body[i]].quat; if (quat) { - MathExtra::quatquat(qrotate,quat,qnew); + MathExtra::quatquat(qrotate, quat, qnew); quat[0] = qnew[0]; quat[1] = qnew[1]; quat[2] = qnew[2]; quat[3] = qnew[3]; } + } else if (quat_atom_flag) { + MathExtra::quatquat(qrotate, quat_atom[i], qnew); + quat_atom[i][0] = qnew[0]; + quat_atom[i][1] = qnew[1]; + quat_atom[i][2] = qnew[2]; + quat_atom[i][3] = qnew[3]; } } } diff --git a/src/fix_move.cpp b/src/fix_move.cpp index 36bba410fcb..99b5b30bece 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -276,10 +276,11 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) : line_flag = atom->line_flag; tri_flag = atom->tri_flag; body_flag = atom->body_flag; + quat_atom_flag = atom->quat_flag; theta_flag = quat_flag = 0; if (line_flag) theta_flag = 1; - if (ellipsoid_flag || tri_flag || body_flag) quat_flag = 1; + if (ellipsoid_flag || tri_flag || body_flag || quat_atom_flag) quat_flag = 1; extra_flag = 0; if (omega_flag || angmom_flag || theta_flag || quat_flag) extra_flag = 1; @@ -329,7 +330,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) : } } - if (quat_flag) { + if (quat_flag && !quat_atom_flag) { double *quat; for (int i = 0; i < nlocal; i++) { quat = nullptr; @@ -349,6 +350,16 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) : } else qoriginal[i][0] = qoriginal[i][1] = qoriginal[i][2] = qoriginal[i][3] = 0.0; } + } else if (quat_atom_flag) { + double **quat_atom = atom->quat; + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + qoriginal[i][0] = quat_atom[i][0]; + qoriginal[i][1] = quat_atom[i][1]; + qoriginal[i][2] = quat_atom[i][2]; + qoriginal[i][3] = quat_atom[i][3]; + } + } } // nrestart = size of per-atom restart data @@ -521,6 +532,7 @@ void FixMove::initial_integrate(int /*vflag*/) double *radius = atom->radius; double *rmass = atom->rmass; double *mass = atom->mass; + double **quat_atom = atom->quat; int *type = atom->type; int *ellipsoid = atom->ellipsoid; int *line = atom->line; @@ -749,9 +761,9 @@ void FixMove::initial_integrate(int /*vflag*/) avec_line->bonus[atom->line[i]].theta = theta_new; } - // quats for ellipsoids, tris, and bodies + // quats for ellipsoids, tris, bodies, and bpm/sphere - if (quat_flag) { + if (quat_flag && !quat_atom_flag) { quat = nullptr; if (ellipsoid_flag && ellipsoid[i] >= 0) quat = avec_ellipsoid->bonus[ellipsoid[i]].quat; @@ -760,6 +772,8 @@ void FixMove::initial_integrate(int /*vflag*/) else if (body_flag && body[i] >= 0) quat = avec_body->bonus[body[i]].quat; if (quat) MathExtra::quatquat(qrotate, qoriginal[i], quat); + } else if (quat_atom_flag) { + MathExtra::quatquat(qrotate, qoriginal[i], quat_atom[i]); } } @@ -880,9 +894,9 @@ void FixMove::initial_integrate(int /*vflag*/) avec_line->bonus[atom->line[i]].theta = theta_new; } - // quats for ellipsoids, tris, and bodies + // quats for ellipsoids, tris, bodies, and bpm/sphere - if (quat_flag) { + if (quat_flag && !quat_atom_flag) { quat = nullptr; if (ellipsoid_flag && ellipsoid[i] >= 0) quat = avec_ellipsoid->bonus[ellipsoid[i]].quat; @@ -891,6 +905,8 @@ void FixMove::initial_integrate(int /*vflag*/) else if (body_flag && body[i] >= 0) quat = avec_body->bonus[body[i]].quat; if (quat) MathExtra::quatquat(qrotate, qoriginal[i], quat); + } else if (quat_atom_flag) { + MathExtra::quatquat(qrotate, qoriginal[i], quat_atom[i]); } } @@ -1263,6 +1279,7 @@ void FixMove::set_arrays(int i) double *quat; double **x = atom->x; + double **quat_atom = atom->quat; imageint *image = atom->image; int *ellipsoid = atom->ellipsoid; int *line = atom->line; @@ -1341,9 +1358,9 @@ void FixMove::set_arrays(int i) toriginal[i] = theta - 0.0; // NOTE: edit this line } - // quats for ellipsoids, tris, and bodies + // quats for ellipsoids, tris, bodies, and bpm/sphere - if (quat_flag) { + if (quat_flag & !quat_atom_flag) { quat = nullptr; if (ellipsoid_flag && ellipsoid[i] >= 0) quat = avec_ellipsoid->bonus[ellipsoid[i]].quat; @@ -1354,6 +1371,11 @@ void FixMove::set_arrays(int i) if (quat) { // qoriginal = f(quat,-delta); // NOTE: edit this line } + } else if (quat_atom_flag) { + // qoriginal[0] = quat_atom[i][0]; // NOTE: edit this line + // qoriginal[1] = quat_atom[i][1]; // NOTE: edit this line + // qoriginal[2] = quat_atom[i][2]; // NOTE: edit this line + // qoriginal[3] = quat_atom[i][3]; // NOTE: edit this line } } xoriginal[i][0] -= vx * delta; @@ -1400,7 +1422,7 @@ void FixMove::set_arrays(int i) // quats for ellipsoids, tris, and bodies - if (quat_flag) { + if (quat_flag && !quat_atom_flag) { quat = nullptr; if (ellipsoid_flag && ellipsoid[i] >= 0) quat = avec_ellipsoid->bonus[ellipsoid[i]].quat; @@ -1411,6 +1433,11 @@ void FixMove::set_arrays(int i) if (quat) { // qoriginal = f(quat,-delta); // NOTE: edit this line } + } else if (quat_atom_flag) { + // qoriginal[0] = quat_atom[i][0]; // NOTE: edit this line + // qoriginal[1] = quat_atom[i][1]; // NOTE: edit this line + // qoriginal[2] = quat_atom[i][2]; // NOTE: edit this line + // qoriginal[3] = quat_atom[i][3]; // NOTE: edit this line } } } diff --git a/src/fix_move.h b/src/fix_move.h index e3c018f54d7..244a9d704a7 100644 --- a/src/fix_move.h +++ b/src/fix_move.h @@ -61,7 +61,7 @@ class FixMove : public Fix { int xvar, yvar, zvar, vxvar, vyvar, vzvar; int xvarstyle, yvarstyle, zvarstyle, vxvarstyle, vyvarstyle, vzvarstyle; int extra_flag, omega_flag, angmom_flag; - int radius_flag, ellipsoid_flag, line_flag, tri_flag, body_flag; + int radius_flag, ellipsoid_flag, line_flag, tri_flag, body_flag, quat_atom_flag; int theta_flag, quat_flag; int nlevels_respa, nrestart; int time_origin; From 4d2aed89374760f611e23c0d121d92a15b01e5b1 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Mon, 18 Dec 2023 11:15:56 -0500 Subject: [PATCH 093/719] bug fix for when reaction site has angles, but post-reaction template has none (same for dihedrals, impropers) --- src/REACTION/fix_bond_react.cpp | 180 +++++++++++++++++--------------- 1 file changed, 93 insertions(+), 87 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 1da26e32a10..10a7023e170 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -3348,7 +3348,7 @@ void FixBondReact::update_everything() dynamic_cast(ihistory)->clear_cache(); // Angles! First let's delete all angle info: - if (force->angle && twomol->angleflag) { + if (force->angle) { int *num_angle = atom->num_angle; int **angle_type = atom->angle_type; tagint **angle_atom1 = atom->angle_atom1; @@ -3389,33 +3389,35 @@ void FixBondReact::update_everything() } } // now let's add the new angle info. - for (int j = 0; j < twomol->natoms; j++) { - int jj = equivalences[j][1][rxnID]-1; - if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { - if (landlocked_atoms[j][rxnID] == 1) { - num_angle[atom->map(update_mega_glove[jj+1][i])] = twomol->num_angle[j]; - delta_angle += twomol->num_angle[j]; - for (int p = 0; p < twomol->num_angle[j]; p++) { - angle_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->angle_type[j][p]; - angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i]; - angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i]; - angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i]; + if (twomol->angleflag) { + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_angle[atom->map(update_mega_glove[jj+1][i])] = twomol->num_angle[j]; + delta_angle += twomol->num_angle[j]; + for (int p = 0; p < twomol->num_angle[j]; p++) { + angle_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->angle_type[j][p]; + angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i]; + angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i]; + angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i]; + } } - } - if (landlocked_atoms[j][rxnID] == 0) { - for (int p = 0; p < twomol->num_angle[j]; p++) { - if (landlocked_atoms[twomol->angle_atom1[j][p]-1][rxnID] == 1 || - landlocked_atoms[twomol->angle_atom2[j][p]-1][rxnID] == 1 || - landlocked_atoms[twomol->angle_atom3[j][p]-1][rxnID] == 1) { - insert_num = num_angle[atom->map(update_mega_glove[jj+1][i])]; - angle_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->angle_type[j][p]; - angle_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i]; - angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i]; - angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i]; - num_angle[atom->map(update_mega_glove[jj+1][i])]++; - if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom) - error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); - delta_angle++; + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_angle[j]; p++) { + if (landlocked_atoms[twomol->angle_atom1[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->angle_atom2[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->angle_atom3[j][p]-1][rxnID] == 1) { + insert_num = num_angle[atom->map(update_mega_glove[jj+1][i])]; + angle_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->angle_type[j][p]; + angle_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i]; + angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i]; + angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i]; + num_angle[atom->map(update_mega_glove[jj+1][i])]++; + if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom) + error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); + delta_angle++; + } } } } @@ -3425,7 +3427,7 @@ void FixBondReact::update_everything() } // Dihedrals! first let's delete all dihedral info for landlocked atoms - if (force->dihedral && twomol->dihedralflag) { + if (force->dihedral) { int *num_dihedral = atom->num_dihedral; int **dihedral_type = atom->dihedral_type; tagint **dihedral_atom1 = atom->dihedral_atom1; @@ -3469,36 +3471,38 @@ void FixBondReact::update_everything() } } // now let's add new dihedral info - for (int j = 0; j < twomol->natoms; j++) { - int jj = equivalences[j][1][rxnID]-1; - if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { - if (landlocked_atoms[j][rxnID] == 1) { - num_dihedral[atom->map(update_mega_glove[jj+1][i])] = twomol->num_dihedral[j]; - delta_dihed += twomol->num_dihedral[j]; - for (int p = 0; p < twomol->num_dihedral[j]; p++) { - dihedral_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->dihedral_type[j][p]; - dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i]; - dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i]; - dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i]; - dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i]; + if (twomol->dihedralflag) { + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_dihedral[atom->map(update_mega_glove[jj+1][i])] = twomol->num_dihedral[j]; + delta_dihed += twomol->num_dihedral[j]; + for (int p = 0; p < twomol->num_dihedral[j]; p++) { + dihedral_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->dihedral_type[j][p]; + dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i]; + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i]; + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i]; + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i]; + } } - } - if (landlocked_atoms[j][rxnID] == 0) { - for (int p = 0; p < twomol->num_dihedral[j]; p++) { - if (landlocked_atoms[twomol->dihedral_atom1[j][p]-1][rxnID] == 1 || - landlocked_atoms[twomol->dihedral_atom2[j][p]-1][rxnID] == 1 || - landlocked_atoms[twomol->dihedral_atom3[j][p]-1][rxnID] == 1 || - landlocked_atoms[twomol->dihedral_atom4[j][p]-1][rxnID] == 1) { - insert_num = num_dihedral[atom->map(update_mega_glove[jj+1][i])]; - dihedral_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->dihedral_type[j][p]; - dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i]; - dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i]; - dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i]; - dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i]; - num_dihedral[atom->map(update_mega_glove[jj+1][i])]++; - if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom) - error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); - delta_dihed++; + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_dihedral[j]; p++) { + if (landlocked_atoms[twomol->dihedral_atom1[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->dihedral_atom2[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->dihedral_atom3[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->dihedral_atom4[j][p]-1][rxnID] == 1) { + insert_num = num_dihedral[atom->map(update_mega_glove[jj+1][i])]; + dihedral_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->dihedral_type[j][p]; + dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i]; + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i]; + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i]; + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i]; + num_dihedral[atom->map(update_mega_glove[jj+1][i])]++; + if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom) + error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); + delta_dihed++; + } } } } @@ -3508,7 +3512,7 @@ void FixBondReact::update_everything() } // finally IMPROPERS!!!! first let's delete all improper info for landlocked atoms - if (force->improper && twomol->improperflag) { + if (force->improper) { int *num_improper = atom->num_improper; int **improper_type = atom->improper_type; tagint **improper_atom1 = atom->improper_atom1; @@ -3552,36 +3556,38 @@ void FixBondReact::update_everything() } } // now let's add new improper info - for (int j = 0; j < twomol->natoms; j++) { - int jj = equivalences[j][1][rxnID]-1; - if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { - if (landlocked_atoms[j][rxnID] == 1) { - num_improper[atom->map(update_mega_glove[jj+1][i])] = twomol->num_improper[j]; - delta_imprp += twomol->num_improper[j]; - for (int p = 0; p < twomol->num_improper[j]; p++) { - improper_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->improper_type[j][p]; - improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i]; - improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i]; - improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i]; - improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i]; + if (twomol->improperflag) { + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_improper[atom->map(update_mega_glove[jj+1][i])] = twomol->num_improper[j]; + delta_imprp += twomol->num_improper[j]; + for (int p = 0; p < twomol->num_improper[j]; p++) { + improper_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->improper_type[j][p]; + improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i]; + improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i]; + improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i]; + improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i]; + } } - } - if (landlocked_atoms[j][rxnID] == 0) { - for (int p = 0; p < twomol->num_improper[j]; p++) { - if (landlocked_atoms[twomol->improper_atom1[j][p]-1][rxnID] == 1 || - landlocked_atoms[twomol->improper_atom2[j][p]-1][rxnID] == 1 || - landlocked_atoms[twomol->improper_atom3[j][p]-1][rxnID] == 1 || - landlocked_atoms[twomol->improper_atom4[j][p]-1][rxnID] == 1) { - insert_num = num_improper[atom->map(update_mega_glove[jj+1][i])]; - improper_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->improper_type[j][p]; - improper_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i]; - improper_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i]; - improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i]; - improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i]; - num_improper[atom->map(update_mega_glove[jj+1][i])]++; - if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom) - error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); - delta_imprp++; + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_improper[j]; p++) { + if (landlocked_atoms[twomol->improper_atom1[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->improper_atom2[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->improper_atom3[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->improper_atom4[j][p]-1][rxnID] == 1) { + insert_num = num_improper[atom->map(update_mega_glove[jj+1][i])]; + improper_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->improper_type[j][p]; + improper_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i]; + improper_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i]; + improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i]; + improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i]; + num_improper[atom->map(update_mega_glove[jj+1][i])]++; + if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom) + error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); + delta_imprp++; + } } } } From a6addbc90761fd9b3e48e5a3064f8f589a58140e Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Mon, 18 Dec 2023 11:30:56 -0500 Subject: [PATCH 094/719] Updated documentation for FFT_KOKKOS_ flags and CMake variable selection --- doc/src/Build_settings.rst | 18 +++++++++++++++--- doc/src/Howto_cmake.rst | 2 ++ doc/src/kspace_style.rst | 5 ++++- 3 files changed, 21 insertions(+), 4 deletions(-) diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 7576cae3eb2..33b0508fe90 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -51,14 +51,18 @@ LAMMPS can use them if they are available on your system. .. code-block:: bash -D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS + -D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS -D FFT_SINGLE=value # yes or no (default), no = double precision -D FFT_PACK=value # array (default) or pointer or memcpy .. note:: - The values for the FFT variable must be in upper-case. This is - an exception to the rule that all CMake variables can be specified - with lower-case values. + When the Kokkos variant of a package is compiled and selected at run time, + the FFT library selected by the FFT_KOKKOS variable applies. Otherwise, + the FFT library selected by the FFT variable applies. + The same FFT settings apply to both. FFT_KOKKOS must be compatible with the + Kokkos backend - for example, when using the CUDA backend of Kokkos, + you must use either CUFFT or KISS. Usually these settings are all that is needed. If FFTW3 is selected, then CMake will try to detect, if threaded FFTW @@ -87,6 +91,8 @@ LAMMPS can use them if they are available on your system. FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS # default is KISS if not specified + FFT_INC = -DFFT_KOKKOS_CUFFT # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS} + # default is KISS if not specified FFT_INC = -DFFT_SINGLE # do not specify for double precision FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries @@ -97,6 +103,8 @@ LAMMPS can use them if they are available on your system. FFT_INC = -I/usr/local/include FFT_PATH = -L/usr/local/lib + FFT_LIB = -lhipfft # hipFFT either precision + FFT_LIB = -lcufft # cuFFT either precision FFT_LIB = -lfftw3 # FFTW3 double precision FFT_LIB = -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS) FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision @@ -141,6 +149,10 @@ The Intel MKL math library is part of the Intel compiler suite. It can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting above). +The CUFFT and HIPFFT FFT libraries are packaged with NVIDIA's CUDA and AMD's +HIP installations, respectively. These FFT libraries require the Kokkos acceleration +package to be enabled and the Kokkos backend to be GPU-resident (ie, HIP or CUDA). + Performing 3d FFTs in parallel can be time-consuming due to data access and required communication. This cost can be reduced by performing single-precision FFTs instead of double precision. Single precision diff --git a/doc/src/Howto_cmake.rst b/doc/src/Howto_cmake.rst index 42324cf2f10..8b710d10650 100644 --- a/doc/src/Howto_cmake.rst +++ b/doc/src/Howto_cmake.rst @@ -349,6 +349,8 @@ Some common LAMMPS specific variables - when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a`` * - ``FFT`` - select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found) + * - ``FFT_KOKKOS`` + - select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``KISS`` (default) * - ``FFT_SINGLE`` - select whether to use single precision FFTs (default: ``off``) * - ``WITH_JPEG`` diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 38a6fce375a..78d7380c01f 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -450,7 +450,10 @@ relative RMS error. For the KOKKOS package, the *pppm/kk* style performs charge assignment and force interpolation calculations, along with the FFTs themselves, on the GPU or (optionally) threaded on the CPU when - using OpenMP and FFTW3. + using OpenMP and FFTW3. The specific FFT library is selected using + the FFT_KOKKOS CMake parameter. See the + :doc:`Build settings ` doc page for how to select a + 3rd-party FFT library. ---------- From bc47f4f3a32c8499d5bd5fd6bc4a68424b700da5 Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Mon, 18 Dec 2023 11:56:23 -0500 Subject: [PATCH 095/719] Updated CMake preset files for kokkos-cuda and kokkos-hip --- cmake/presets/kokkos-cuda.cmake | 3 +++ cmake/presets/kokkos-hip.cmake | 3 +++ 2 files changed, 6 insertions(+) diff --git a/cmake/presets/kokkos-cuda.cmake b/cmake/presets/kokkos-cuda.cmake index c3ee081898f..3205387044e 100644 --- a/cmake/presets/kokkos-cuda.cmake +++ b/cmake/presets/kokkos-cuda.cmake @@ -9,5 +9,8 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE) get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE) set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE) +# If KSPACE is also enabled, use CUFFT for FFTs +set(FFT_KOKKOS "CUFFT" CACHE STRING FORCE) + # hide deprecation warnings temporarily for stable release set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/kokkos-hip.cmake b/cmake/presets/kokkos-hip.cmake index 827a37152b3..ffc259a2252 100644 --- a/cmake/presets/kokkos-hip.cmake +++ b/cmake/presets/kokkos-hip.cmake @@ -12,6 +12,9 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE) set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE) set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE) +# If KSPACE is also enabled, use CUFFT for FFTs +set(FFT_KOKKOS "HIPFFT" CACHE STRING FORCE) + # hide deprecation warnings temporarily for stable release set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE) From d02ffb0e709cb57ff0959c74d74a7a0ad9b7670e Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Mon, 18 Dec 2023 12:06:41 -0500 Subject: [PATCH 096/719] Updated Summit & Frontier template Makefiles --- src/MAKE/MACHINES/Makefile.frontier_kokkos | 2 +- src/MAKE/MACHINES/Makefile.summit_kokkos | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/MAKE/MACHINES/Makefile.frontier_kokkos b/src/MAKE/MACHINES/Makefile.frontier_kokkos index 86cddd12b77..b58a3d871c2 100644 --- a/src/MAKE/MACHINES/Makefile.frontier_kokkos +++ b/src/MAKE/MACHINES/Makefile.frontier_kokkos @@ -55,7 +55,7 @@ MPI_LIB = -L${MPICH_DIR}/lib -lmpi -L${CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa MY_HIP_EXE = $(shell which hipcc) MY_HIP_PATH = $(dir ${MY_HIP_EXE}) -FFT_INC = -DFFT_HIPFFT +FFT_INC = -DFFT_KOKKOS_HIPFFT FFT_PATH = FFT_LIB = -L${MY_HIP_PATH}../lib -lhipfft diff --git a/src/MAKE/MACHINES/Makefile.summit_kokkos b/src/MAKE/MACHINES/Makefile.summit_kokkos index 557ebd22b2a..d554e09a5ad 100644 --- a/src/MAKE/MACHINES/Makefile.summit_kokkos +++ b/src/MAKE/MACHINES/Makefile.summit_kokkos @@ -57,7 +57,7 @@ MPI_LIB = -L${MY_MPI_PATH}../lib -lmpi_ibm # PATH = path for FFT library # LIB = name of FFT library -FFT_INC = -DFFT_CUFFT +FFT_INC = -DFFT_KOKKOS_CUFFT FFT_PATH = FFT_LIB = -lcufft From bc7050ab5001b4480383d9e16995494a25f1bec8 Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Mon, 18 Dec 2023 12:11:31 -0500 Subject: [PATCH 097/719] Added LMP_HEFFTE to CMakeLists.txt to attempt to fix a merge conflict --- cmake/CMakeLists.txt | 46 +++++++++++++++++++++++++++++++------------- 1 file changed, 33 insertions(+), 13 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index aacaca4e6ca..76248445e91 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -971,20 +971,40 @@ if(PKG_KOKKOS) endif() endif() if(PKG_KSPACE) - message(STATUS "<<< FFT settings >>> --- Primary FFT lib: ${FFT}") - if(FFT_SINGLE) - message(STATUS "Using single precision FFTs") - else() - message(STATUS "Using double precision FFTs") - endif() - if(FFT_FFTW_THREADS OR FFT_MKL_THREADS) - message(STATUS "Using threaded FFTs") + if (LMP_HEFFTE) + message(STATUS "<<< FFT settings >>> +-- Primary FFT lib: heFFTe") + if (HEFFTE_BACKEND) + message(STATUS "heFFTe backend: ${HEFFTE_BACKEND}") + else() + message(STATUS "heFFTe backend: stock (builtin FFT implementation, tested for corrected but not optimized for production)") + endif() + if(FFT_SINGLE) + message(STATUS "Using single precision FFTs") + else() + message(STATUS "Using double precision FFTs") + endif() else() - message(STATUS "Using non-threaded FFTs") - endif() - if(PKG_KOKKOS) - message(STATUS "Kokkos FFT: ${FFT_KOKKOS}") + message(STATUS "<<< FFT settings >>> +-- Primary FFT lib: ${FFT}") + if(FFT_SINGLE) + message(STATUS "Using single precision FFTs") + else() + message(STATUS "Using double precision FFTs") + endif() + if(FFT_FFTW_THREADS OR FFT_MKL_THREADS) + message(STATUS "Using threaded FFTs") + else() + message(STATUS "Using non-threaded FFTs") + endif() + if (FFT_HEFFTE) + message(STATUS "Using distributed algorithms from heFTTe") + else() + message(STATUS "Using builtin distributed algorithms") + endif() + if(PKG_KOKKOS) + message(STATUS "Kokkos FFT: ${FFT_KOKKOS}") + endif() endif() endif() if(BUILD_DOC) From dd1ac640aeec2686b2757d734546d6960804bcc2 Mon Sep 17 00:00:00 2001 From: Nick Hagerty Date: Mon, 18 Dec 2023 12:56:30 -0500 Subject: [PATCH 098/719] Added declaration for FFT_KOKKOS variable --- cmake/Modules/Packages/KOKKOS.cmake | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index eb20f93956e..a0b872ba858 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -131,6 +131,7 @@ if(PKG_KSPACE) list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp) + set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package") set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT) set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES}) validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES) From e72f186123df9d24f1f4f2bac5bdc4fad8d2a8e6 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 19 Dec 2023 22:01:18 -0700 Subject: [PATCH 099/719] check ghost vel in pair bpm/spring --- src/BPM/pair_bpm_spring.cpp | 13 +++++++++++++ src/BPM/pair_bpm_spring.h | 1 + 2 files changed, 14 insertions(+) diff --git a/src/BPM/pair_bpm_spring.cpp b/src/BPM/pair_bpm_spring.cpp index 11771563597..01cee91b4c8 100644 --- a/src/BPM/pair_bpm_spring.cpp +++ b/src/BPM/pair_bpm_spring.cpp @@ -19,6 +19,7 @@ #include "force.h" #include "memory.h" #include "neigh_list.h" +#include "neighbor.h" #include @@ -202,6 +203,18 @@ void PairBPMSpring::coeff(int narg, char **arg) if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairBPMSpring::init_style() +{ + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair bpm/spring requires ghost atoms store velocity"); + + neighbor->add_request(this); +} + /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ diff --git a/src/BPM/pair_bpm_spring.h b/src/BPM/pair_bpm_spring.h index 3cb281bff3b..c10e4a34008 100644 --- a/src/BPM/pair_bpm_spring.h +++ b/src/BPM/pair_bpm_spring.h @@ -31,6 +31,7 @@ class PairBPMSpring : public Pair { void compute(int, int) override; void settings(int, char **) override; void coeff(int, char **) override; + void init_style() override; double init_one(int, int) override; void write_restart(FILE *) override; void read_restart(FILE *) override; From e69a079545dcf9801f0099c268fb781567fe7b61 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Wed, 20 Dec 2023 10:50:54 -0700 Subject: [PATCH 100/719] Fixing invalid variable deform kokkos --- src/KOKKOS/fix_deform_kokkos.cpp | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 104ac41188d..7a2b3e2481a 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -120,11 +120,11 @@ void FixDeformKokkos::end_of_step() } else if (set[i].style == WIGGLE) { double delt = (update->ntimestep - update->beginstep) * update->dt; set[i].lo_target = set[i].lo_start - - 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); + 0.5*set[i].amplitude * sin(MY_2PI*delt/set[i].tperiod); set[i].hi_target = set[i].hi_start + - 0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); - h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude * - cos(TWOPI*delt/set[i].tperiod); + 0.5*set[i].amplitude * sin(MY_2PI*delt/set[i].tperiod); + h_rate[i] = MY_2PI/set[i].tperiod * set[i].amplitude * + cos(MY_2PI*delt/set[i].tperiod); h_ratelo[i] = -0.5*h_rate[i]; } else if (set[i].style == VARIABLE) { double del = input->variable->compute_equal(set[i].hvar); @@ -212,9 +212,9 @@ void FixDeformKokkos::end_of_step() } else if (set[i].style == WIGGLE) { double delt = (update->ntimestep - update->beginstep) * update->dt; set[i].tilt_target = set[i].tilt_start + - set[i].amplitude * sin(TWOPI*delt/set[i].tperiod); - h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude * - cos(TWOPI*delt/set[i].tperiod); + set[i].amplitude * sin(MY_2PI*delt/set[i].tperiod); + h_rate[i] = MY_2PI/set[i].tperiod * set[i].amplitude * + cos(MY_2PI*delt/set[i].tperiod); } else if (set[i].style == VARIABLE) { double delta_tilt = input->variable->compute_equal(set[i].hvar); set[i].tilt_target = set[i].tilt_start + delta_tilt; From d61c379b0caa0b50b6fac0942c7bba191c4b4143 Mon Sep 17 00:00:00 2001 From: Ludwig Ahrens Date: Thu, 21 Dec 2023 14:28:54 +0100 Subject: [PATCH 101/719] Error formatting --- src/ELECTRODE/fix_electrode_conp.cpp | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp index a87642182b0..091840148d4 100644 --- a/src/ELECTRODE/fix_electrode_conp.cpp +++ b/src/ELECTRODE/fix_electrode_conp.cpp @@ -522,11 +522,9 @@ void FixElectrodeConp::setup_post_neighbor() if (qtotal_var_style == VarStyle::EQUAL) { const char *var_name = qtotal_var_name.c_str(); int var_id = input->variable->find(var_name); - if (var_id < 0) - error->all(FLERR, fmt::format("Variable '{}' for fix electrode does not exist", var_name)); + if (var_id < 0) error->all(FLERR, "Variable '{}' for fix electrode does not exist", var_name); if (!input->variable->equalstyle(var_id)) - error->all(FLERR, - fmt::format("Variable '{}' for fix electrode is not equal-style", var_name)); + error->all(FLERR, "Variable '{}' for fix electrode is not equal-style", var_name); qtotal_var_id = var_id; } From ded160cd41653fb9a6d4835045d46279d1245124 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Sun, 31 Dec 2023 10:49:59 -0700 Subject: [PATCH 102/719] Generalizing fix update/special/bonds for pair hybrid --- src/fix_update_special_bonds.cpp | 61 ++++++++++++++++---------------- 1 file changed, 31 insertions(+), 30 deletions(-) diff --git a/src/fix_update_special_bonds.cpp b/src/fix_update_special_bonds.cpp index 159b2a11700..4e8cba47ecb 100644 --- a/src/fix_update_special_bonds.cpp +++ b/src/fix_update_special_bonds.cpp @@ -19,6 +19,7 @@ #include "error.h" #include "force.h" #include "modify.h" +#include "neighbor.h" #include "neigh_list.h" #include "pair.h" @@ -72,9 +73,6 @@ void FixUpdateSpecialBonds::setup(int /*vflag*/) force->special_coul[3] != 1.0) error->all(FLERR, "Fix update/special/bonds requires special Coulomb weights = 1,1,1"); // Implies neighbor->special_flag = [X, 2, 1, 1] - - if (utils::strmatch(force->pair_style, "^hybrid")) - error->all(FLERR, "Cannot use fix update/special/bonds with hybrid pair styles"); } /* ---------------------------------------------------------------------- @@ -155,44 +153,47 @@ void FixUpdateSpecialBonds::pre_exchange() void FixUpdateSpecialBonds::pre_force(int /*vflag*/) { - int i1, i2, j, jj, jnum; + int ilist, nlist, i1, i2, j, jj, jnum; int *jlist, *numneigh, **firstneigh; tagint tag1, tag2; + NeighList *list; int nlocal = atom->nlocal; - tagint *tag = atom->tag; - NeighList *list = force->pair->list; // may need to be generalized for pair hybrid* - numneigh = list->numneigh; - firstneigh = list->firstneigh; // In theory could communicate a list of broken bonds to neighboring processors here // to remove restriction that users use Newton bond off - for (auto const &it : new_broken_pairs) { - tag1 = it.first; - tag2 = it.second; - i1 = atom->map(tag1); - i2 = atom->map(tag2); - - // Loop through atoms of owned atoms i j - if (i1 < nlocal) { - jlist = firstneigh[i1]; - jnum = numneigh[i1]; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= SPECIALMASK; // Clear special bond bits - if (tag[j] == tag2) jlist[jj] = j; + for (int ilist = 0; ilist < neighbor->nlist; ilist ++) { + list = neighbor->lists[ilist]; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + for (auto const &it : new_broken_pairs) { + tag1 = it.first; + tag2 = it.second; + i1 = atom->map(tag1); + i2 = atom->map(tag2); + + // Loop through atoms of owned atoms i j + if (i1 < nlocal) { + jlist = firstneigh[i1]; + jnum = numneigh[i1]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= SPECIALMASK; // Clear special bond bits + if (tag[j] == tag2) jlist[jj] = j; + } } - } - if (i2 < nlocal) { - jlist = firstneigh[i2]; - jnum = numneigh[i2]; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= SPECIALMASK; // Clear special bond bits - if (tag[j] == tag1) jlist[jj] = j; + if (i2 < nlocal) { + jlist = firstneigh[i2]; + jnum = numneigh[i2]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= SPECIALMASK; // Clear special bond bits + if (tag[j] == tag1) jlist[jj] = j; + } } } } From 0562c3113879f38f8fc6db7afb88830ecb3ae10c Mon Sep 17 00:00:00 2001 From: Mitch Murphy Date: Tue, 2 Jan 2024 04:51:10 -0500 Subject: [PATCH 103/719] added pair/lj/charmmfsw/coul/long/kk and dihedral/charmmfsw/kk so that lammps scripts generated by charmm-gui.org can be run without tweaks --- src/KOKKOS/Install.sh | 4 + src/KOKKOS/dihedral_charmmfsw_kokkos.cpp | 991 ++++++++++++++++++ src/KOKKOS/dihedral_charmmfsw_kokkos.h | 267 +++++ .../pair_lj_charmmfsw_coul_long_kokkos.cpp | 941 +++++++++++++++++ .../pair_lj_charmmfsw_coul_long_kokkos.h | 230 ++++ 5 files changed, 2433 insertions(+) create mode 100644 src/KOKKOS/dihedral_charmmfsw_kokkos.cpp create mode 100644 src/KOKKOS/dihedral_charmmfsw_kokkos.h create mode 100644 src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp create mode 100644 src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.h diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index af80420d7a9..462c0cbe575 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -106,6 +106,8 @@ action compute_temp_kokkos.cpp action compute_temp_kokkos.h action dihedral_charmm_kokkos.cpp dihedral_charmm.cpp action dihedral_charmm_kokkos.h dihedral_charmm.h +action dihedral_charmmfsw_kokkos.cpp dihedral_charmmfsw.cpp +action dihedral_charmmfsw_kokkos.h dihedral_charmmfsw.h action dihedral_class2_kokkos.cpp dihedral_class2.cpp action dihedral_class2_kokkos.h dihedral_class2.h action dihedral_harmonic_kokkos.cpp dihedral_harmonic.cpp @@ -310,6 +312,8 @@ action pair_lj_charmm_coul_charmm_kokkos.cpp pair_lj_charmm_coul_charmm.cpp action pair_lj_charmm_coul_charmm_kokkos.h pair_lj_charmm_coul_charmm.h action pair_lj_charmm_coul_long_kokkos.cpp pair_lj_charmm_coul_long.cpp action pair_lj_charmm_coul_long_kokkos.h pair_lj_charmm_coul_long.h +action pair_lj_charmmfsw_coul_long_kokkos.cpp pair_lj_charmmfsw_coul_long.cpp +action pair_lj_charmmfsw_coul_long_kokkos.h pair_lj_charmmfsw_coul_long.h action pair_lj_class2_coul_cut_kokkos.cpp pair_lj_class2_coul_cut.cpp action pair_lj_class2_coul_cut_kokkos.h pair_lj_class2_coul_cut.h action pair_lj_class2_coul_long_kokkos.cpp pair_lj_class2_coul_long.cpp diff --git a/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp b/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp new file mode 100644 index 00000000000..facb7235808 --- /dev/null +++ b/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp @@ -0,0 +1,991 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + + Contributing authors: + + - Stan Moore (SNL) original DihedralCharmmfswKokkos + + - Mitch Murphy (alphataubio) - DihedralCharmmfswKokkos update (2023/12) + + Based on serial dihedral_charmmfsw.cpp lj-fsw sections (force-switched) + provided by Robert Meissner and Lucio Colombi Ciacchi of Bremen + University, Germany, with additional assistance from + Robert A. Latour, Clemson University. + +------------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + + *** DRAFT VERSION 1 (lots of comments to be removed just before merge) *** + + (1) first draft version of DihedralCharmmfswKokkos exactly + same as DihedralCharmmfswKokkos but with new class name + + method: track changes from serial kspace dihedral_charmm to + dihedral_charmmfsw and apply to DihedralCharmmfswKokkos + + % diff dihedral_charmm.cpp dihedral_charmmfsw.cpp + +------------------------------------------------------------------------- */ + +/* + 18c21 + < #include "dihedral_charmm.h" + --- + > #include "dihedral_charmmfsw.h" + + */ + +#include "dihedral_charmmfsw_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "error.h" +#include "force.h" +#include "kokkos.h" +#include "math_const.h" +#include "memory_kokkos.h" +#include "neighbor_kokkos.h" +#include "pair.h" + +#include + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define TOLERANCE 0.05 + +/* ---------------------------------------------------------------------- */ + +/* + + 40c43 + < DihedralCharmm::DihedralCharmm(LAMMPS *_lmp) : Dihedral(_lmp) + --- + > DihedralCharmmfsw::DihedralCharmmfsw(LAMMPS *_lmp) : Dihedral(_lmp) + + */ + +template +DihedralCharmmfswKokkos::DihedralCharmmfswKokkos(LAMMPS *lmp) : DihedralCharmmfsw(lmp) +{ + atomKK = (AtomKokkos *) atom; + neighborKK = (NeighborKokkos *) neighbor; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = X_MASK | F_MASK | Q_MASK | ENERGY_MASK | VIRIAL_MASK | TYPE_MASK; + datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; + + k_warning_flag = Kokkos::DualView("Dihedral:warning_flag"); + d_warning_flag = k_warning_flag.template view(); + h_warning_flag = k_warning_flag.h_view; + + centroidstressflag = CENTROID_NOTAVAIL; +} + +/* ---------------------------------------------------------------------- */ + +/* + + 48c51 + < DihedralCharmm::~DihedralCharmm() + --- + > DihedralCharmmfsw::~DihedralCharmmfsw() + + */ + +template +DihedralCharmmfswKokkos::~DihedralCharmmfswKokkos() +{ + if (!copymode) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->destroy_kokkos(k_vatom,vatom); + } +} + +/* ---------------------------------------------------------------------- */ + +/* + + 73c76 + < double delx, dely, delz, rsq, r2inv, r6inv; + --- + > double delx, dely, delz, rsq, r2inv, r6inv, r; + 255a259,264 + > // modifying coul and LJ force and energies to apply + > // force_shift and force_switch as in CHARMM pairwise + > // LJ interactions between 1-4 atoms should usually be + > // for r < cut_inner, so switching not applied + > + > r = sqrt(rsq); + 258c267 + < else + --- + > else if (dihedflag) + 259a269,270 + > else + > forcecoul = qqrd2e * q[i1] * q[i4] * (sqrt(r2inv) - r * cut_coulinv14 * cut_coulinv14); + 264,265c275,284 + < ecoul = weight[type] * forcecoul; + < evdwl = r6inv * (lj14_3[itype][jtype] * r6inv - lj14_4[itype][jtype]); + --- + > if (dihedflag) + > ecoul = weight[type] * forcecoul; + > else + > ecoul = weight[type] * qqrd2e * q[i1] * q[i4] * + > (sqrt(r2inv) + r * cut_coulinv14 * cut_coulinv14 - 2.0 * cut_coulinv14); + > evdwl14_12 = r6inv * lj14_3[itype][jtype] * r6inv - + > lj14_3[itype][jtype] * cut_lj_inner6inv * cut_lj6inv; + > evdwl14_6 = + > -lj14_4[itype][jtype] * r6inv + lj14_4[itype][jtype] * cut_lj_inner3inv * cut_lj3inv; + > evdwl = evdwl14_12 + evdwl14_6; + + */ + + +/* + + 63c66 + < void DihedralCharmm::compute(int eflag, int vflag) + --- + > void DihedralCharmmfsw::compute(int eflag, int vflag) + + */ + +template +void DihedralCharmmfswKokkos::compute(int eflag_in, int vflag_in) +{ + eflag = eflag_in; + vflag = vflag_in; + + if (lmp->kokkos->neighflag == FULL) + error->all(FLERR,"Dihedral_style charmm/kk requires half neighbor list"); + + ev_init(eflag,vflag,0); + + // ensure pair->ev_tally() will use 1-4 virial contribution + + if (weightflag && vflag_global == VIRIAL_FDOTR) + force->pair->vflag_either = force->pair->vflag_global = 1; + + // reallocate per-atom arrays if necessary + + if (eflag_atom) { + //if(k_eatom.extent(0)destroy_kokkos(k_eatom,eatom); + memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom"); + d_eatom = k_eatom.template view(); + k_eatom_pair = Kokkos::DualView("dihedral:eatom_pair",maxeatom); + d_eatom_pair = k_eatom_pair.template view(); + //} + } + if (vflag_atom) { + //if(k_vatom.extent(0)destroy_kokkos(k_vatom,vatom); + memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"dihedral:vatom"); + d_vatom = k_vatom.template view(); + k_vatom_pair = Kokkos::DualView("dihedral:vatom_pair",maxvatom); + d_vatom_pair = k_vatom_pair.template view(); + //} + } + + x = atomKK->k_x.view(); + f = atomKK->k_f.view(); + q = atomKK->k_q.view(); + atomtype = atomKK->k_type.view(); + neighborKK->k_dihedrallist.template sync(); + dihedrallist = neighborKK->k_dihedrallist.view(); + int ndihedrallist = neighborKK->ndihedrallist; + nlocal = atom->nlocal; + newton_bond = force->newton_bond; + qqrd2e = force->qqrd2e; + + h_warning_flag() = 0; + k_warning_flag.template modify(); + k_warning_flag.template sync(); + + copymode = 1; + + // loop over neighbors of my atoms + + EVM_FLOAT evm; + + if (evflag) { + if (newton_bond) { + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ndihedrallist),*this,evm); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ndihedrallist),*this,evm); + } + } else { + if (newton_bond) { + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ndihedrallist),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ndihedrallist),*this); + } + } + + // error check + + k_warning_flag.template modify(); + k_warning_flag.template sync(); + if (h_warning_flag()) + error->warning(FLERR,"Dihedral problem"); + + if (eflag_global) { + energy += evm.emol; + force->pair->eng_vdwl += evm.evdwl; + force->pair->eng_coul += evm.ecoul; + } + if (vflag_global) { + virial[0] += evm.v[0]; + virial[1] += evm.v[1]; + virial[2] += evm.v[2]; + virial[3] += evm.v[3]; + virial[4] += evm.v[4]; + virial[5] += evm.v[5]; + + force->pair->virial[0] += evm.vp[0]; + force->pair->virial[1] += evm.vp[1]; + force->pair->virial[2] += evm.vp[2]; + force->pair->virial[3] += evm.vp[3]; + force->pair->virial[4] += evm.vp[4]; + force->pair->virial[5] += evm.vp[5]; + } + + // don't yet have dualviews for eatom and vatom in pair_kokkos, + // so need to manually copy these to pair style + + int n = nlocal; + if (newton_bond) n += atom->nghost; + + if (eflag_atom) { + k_eatom.template modify(); + k_eatom.template sync(); + + k_eatom_pair.template modify(); + k_eatom_pair.template sync(); + for (int i = 0; i < n; i++) + force->pair->eatom[i] += k_eatom_pair.h_view(i); + } + + if (vflag_atom) { + k_vatom.template modify(); + k_vatom.template sync(); + + k_vatom_pair.template modify(); + k_vatom_pair.template sync(); + for (int i = 0; i < n; i++) { + force->pair->vatom[i][0] += k_vatom_pair.h_view(i,0); + force->pair->vatom[i][1] += k_vatom_pair.h_view(i,1); + force->pair->vatom[i][2] += k_vatom_pair.h_view(i,2); + force->pair->vatom[i][3] += k_vatom_pair.h_view(i,3); + force->pair->vatom[i][4] += k_vatom_pair.h_view(i,4); + force->pair->vatom[i][5] += k_vatom_pair.h_view(i,5); + } + } + + copymode = 0; +} + +template +template +KOKKOS_INLINE_FUNCTION +void DihedralCharmmfswKokkos::operator()(TagDihedralCharmmCompute, const int &n, EVM_FLOAT& evm) const { + + // The f array is atomic + Kokkos::View::value,Kokkos::MemoryTraits > a_f = f; + + const int i1 = dihedrallist(n,0); + const int i2 = dihedrallist(n,1); + const int i3 = dihedrallist(n,2); + const int i4 = dihedrallist(n,3); + const int type = dihedrallist(n,4); + + // 1st bond + + const F_FLOAT vb1x = x(i1,0) - x(i2,0); + const F_FLOAT vb1y = x(i1,1) - x(i2,1); + const F_FLOAT vb1z = x(i1,2) - x(i2,2); + + // 2nd bond + + const F_FLOAT vb2x = x(i3,0) - x(i2,0); + const F_FLOAT vb2y = x(i3,1) - x(i2,1); + const F_FLOAT vb2z = x(i3,2) - x(i2,2); + + const F_FLOAT vb2xm = -vb2x; + const F_FLOAT vb2ym = -vb2y; + const F_FLOAT vb2zm = -vb2z; + + // 3rd bond + + const F_FLOAT vb3x = x(i4,0) - x(i3,0); + const F_FLOAT vb3y = x(i4,1) - x(i3,1); + const F_FLOAT vb3z = x(i4,2) - x(i3,2); + + const F_FLOAT ax = vb1y*vb2zm - vb1z*vb2ym; + const F_FLOAT ay = vb1z*vb2xm - vb1x*vb2zm; + const F_FLOAT az = vb1x*vb2ym - vb1y*vb2xm; + const F_FLOAT bx = vb3y*vb2zm - vb3z*vb2ym; + const F_FLOAT by = vb3z*vb2xm - vb3x*vb2zm; + const F_FLOAT bz = vb3x*vb2ym - vb3y*vb2xm; + + const F_FLOAT rasq = ax*ax + ay*ay + az*az; + const F_FLOAT rbsq = bx*bx + by*by + bz*bz; + const F_FLOAT rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm; + const F_FLOAT rg = sqrt(rgsq); + + F_FLOAT rginv,ra2inv,rb2inv; + rginv = ra2inv = rb2inv = 0.0; + if (rg > 0) rginv = 1.0/rg; + if (rasq > 0) ra2inv = 1.0/rasq; + if (rbsq > 0) rb2inv = 1.0/rbsq; + const F_FLOAT rabinv = sqrt(ra2inv*rb2inv); + + F_FLOAT c = (ax*bx + ay*by + az*bz)*rabinv; + F_FLOAT s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z); + + // error check + + if ((c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) && !d_warning_flag()) + d_warning_flag() = 1; + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + const int m = d_multiplicity[type]; + F_FLOAT p = 1.0; + F_FLOAT ddf1,df1; + ddf1 = df1 = 0.0; + + for (int i = 0; i < m; i++) { + ddf1 = p*c - df1*s; + df1 = p*s + df1*c; + p = ddf1; + } + + p = p*d_cos_shift[type] + df1*d_sin_shift[type]; + df1 = df1*d_cos_shift[type] - ddf1*d_sin_shift[type]; + df1 *= -m; + p += 1.0; + + if (m == 0) { + p = 1.0 + d_cos_shift[type]; + df1 = 0.0; + } + + E_FLOAT edihedral = 0.0; + if (eflag) edihedral = d_k[type] * p; + + const F_FLOAT fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm; + const F_FLOAT hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm; + const F_FLOAT fga = fg*ra2inv*rginv; + const F_FLOAT hgb = hg*rb2inv*rginv; + const F_FLOAT gaa = -ra2inv*rg; + const F_FLOAT gbb = rb2inv*rg; + + const F_FLOAT dtfx = gaa*ax; + const F_FLOAT dtfy = gaa*ay; + const F_FLOAT dtfz = gaa*az; + const F_FLOAT dtgx = fga*ax - hgb*bx; + const F_FLOAT dtgy = fga*ay - hgb*by; + const F_FLOAT dtgz = fga*az - hgb*bz; + const F_FLOAT dthx = gbb*bx; + const F_FLOAT dthy = gbb*by; + const F_FLOAT dthz = gbb*bz; + + const F_FLOAT df = -d_k[type] * df1; + + const F_FLOAT sx2 = df*dtgx; + const F_FLOAT sy2 = df*dtgy; + const F_FLOAT sz2 = df*dtgz; + + F_FLOAT f1[3],f2[3],f3[3],f4[3]; + f1[0] = df*dtfx; + f1[1] = df*dtfy; + f1[2] = df*dtfz; + + f2[0] = sx2 - f1[0]; + f2[1] = sy2 - f1[1]; + f2[2] = sz2 - f1[2]; + + f4[0] = df*dthx; + f4[1] = df*dthy; + f4[2] = df*dthz; + + f3[0] = -sx2 - f4[0]; + f3[1] = -sy2 - f4[1]; + f3[2] = -sz2 - f4[2]; + + // apply force to each of 4 atoms + + if (NEWTON_BOND || i1 < nlocal) { + a_f(i1,0) += f1[0]; + a_f(i1,1) += f1[1]; + a_f(i1,2) += f1[2]; + } + + if (NEWTON_BOND || i2 < nlocal) { + a_f(i2,0) += f2[0]; + a_f(i2,1) += f2[1]; + a_f(i2,2) += f2[2]; + } + + if (NEWTON_BOND || i3 < nlocal) { + a_f(i3,0) += f3[0]; + a_f(i3,1) += f3[1]; + a_f(i3,2) += f3[2]; + } + + if (NEWTON_BOND || i4 < nlocal) { + a_f(i4,0) += f4[0]; + a_f(i4,1) += f4[1]; + a_f(i4,2) += f4[2]; + } + + if (EVFLAG) + ev_tally(evm,i1,i2,i3,i4,edihedral,f1,f3,f4, + vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); + + // 1-4 LJ and Coulomb interactions + // tally energy/virial in pair, using newton_bond as newton flag + + if (d_weight[type] > 0.0) { + const int itype = atomtype[i1]; + const int jtype = atomtype[i4]; + + const F_FLOAT delx = x(i1,0) - x(i4,0); + const F_FLOAT dely = x(i1,1) - x(i4,1); + const F_FLOAT delz = x(i1,2) - x(i4,2); + const F_FLOAT rsq = delx*delx + dely*dely + delz*delz; + const F_FLOAT r2inv = 1.0/rsq; + const F_FLOAT r6inv = r2inv*r2inv*r2inv; + + F_FLOAT forcecoul; + if (implicit) forcecoul = qqrd2e * q[i1]*q[i4]*r2inv; + else forcecoul = qqrd2e * q[i1]*q[i4]*sqrt(r2inv); + const F_FLOAT forcelj = r6inv * (d_lj14_1(itype,jtype)*r6inv - d_lj14_2(itype,jtype)); + const F_FLOAT fpair = d_weight[type] * (forcelj+forcecoul)*r2inv; + + F_FLOAT ecoul = 0.0; + F_FLOAT evdwl = 0.0; + if (eflag) { + ecoul = d_weight[type] * forcecoul; + evdwl = r6inv * (d_lj14_3(itype,jtype)*r6inv - d_lj14_4(itype,jtype)); + evdwl *= d_weight[type]; + } + + if (newton_bond || i1 < nlocal) { + a_f(i1,0) += delx*fpair; + a_f(i1,1) += dely*fpair; + a_f(i1,2) += delz*fpair; + } + if (newton_bond || i4 < nlocal) { + a_f(i4,0) -= delx*fpair; + a_f(i4,1) -= dely*fpair; + a_f(i4,2) -= delz*fpair; + } + + if (EVFLAG) ev_tally(evm,i1,i4,evdwl,ecoul,fpair,delx,dely,delz); + } +} + +template +template +KOKKOS_INLINE_FUNCTION +void DihedralCharmmfswKokkos::operator()(TagDihedralCharmmCompute, const int &n) const { + EVM_FLOAT evm; + this->template operator()(TagDihedralCharmmCompute(), n, evm); +} + +/* ---------------------------------------------------------------------- */ + +/* + + 288c307 + < void DihedralCharmm::allocate() + --- + > void DihedralCharmmfsw::allocate() + + */ + +template +void DihedralCharmmfswKokkos::allocate() +{ + DihedralCharmmfsw::allocate(); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +/* + + 308c327 + < void DihedralCharmm::coeff(int narg, char **arg) + --- + > void DihedralCharmmfsw::coeff(int narg, char **arg) + + */ + +template +void DihedralCharmmfswKokkos::coeff(int narg, char **arg) +{ + DihedralCharmmfsw::coeff(narg, arg); + + int nd = atom->ndihedraltypes; + typename AT::tdual_ffloat_1d k_k("DihedralCharmm::k",nd+1); + typename AT::tdual_ffloat_1d k_multiplicity("DihedralCharmm::multiplicity",nd+1); + typename AT::tdual_ffloat_1d k_shift("DihedralCharmm::shift",nd+1); + typename AT::tdual_ffloat_1d k_cos_shift("DihedralCharmm::cos_shift",nd+1); + typename AT::tdual_ffloat_1d k_sin_shift("DihedralCharmm::sin_shift",nd+1); + typename AT::tdual_ffloat_1d k_weight("DihedralCharmm::weight",nd+1); + + d_k = k_k.template view(); + d_multiplicity = k_multiplicity.template view(); + d_shift = k_shift.template view(); + d_cos_shift = k_cos_shift.template view(); + d_sin_shift = k_sin_shift.template view(); + d_weight = k_weight.template view(); + + int n = atom->ndihedraltypes; + for (int i = 1; i <= n; i++) { + k_k.h_view[i] = k[i]; + k_multiplicity.h_view[i] = multiplicity[i]; + k_shift.h_view[i] = shift[i]; + k_cos_shift.h_view[i] = cos_shift[i]; + k_sin_shift.h_view[i] = sin_shift[i]; + k_weight.h_view[i] = weight[i]; + } + + k_k.template modify(); + k_multiplicity.template modify(); + k_shift.template modify(); + k_cos_shift.template modify(); + k_sin_shift.template modify(); + k_weight.template modify(); + + k_k.template sync(); + k_multiplicity.template sync(); + k_shift.template sync(); + k_cos_shift.template sync(); + k_sin_shift.template sync(); + k_weight.template sync(); +} + +/* ---------------------------------------------------------------------- + error check and initialize all values needed for force computation +------------------------------------------------------------------------- */ + +/* + + 350c369 + < void DihedralCharmm::init_style() + --- + > void DihedralCharmmfsw::init_style() + 382a402,425 + > + > // constants for applying force switch (LJ) and force_shift (coul) + > // to 1/4 dihedral atoms to match CHARMM pairwise interactions + > + > int itmp; + > int *p_dihedflag = (int *) force->pair->extract("dihedflag", itmp); + > auto p_cutljinner = (double *) force->pair->extract("cut_lj_inner", itmp); + > auto p_cutlj = (double *) force->pair->extract("cut_lj", itmp); + > auto p_cutcoul = (double *) force->pair->extract("cut_coul", itmp); + > + > if (p_cutcoul == nullptr || p_cutljinner == nullptr || p_cutlj == nullptr || + > p_dihedflag == nullptr) + > error->all(FLERR, "Dihedral charmmfsw is incompatible with Pair style"); + > + > dihedflag = *p_dihedflag; + > cut_coul14 = *p_cutcoul; + > cut_lj_inner14 = *p_cutljinner; + > cut_lj14 = *p_cutlj; + > + > cut_coulinv14 = 1 / cut_coul14; + > cut_lj_inner3inv = (1 / cut_lj_inner14) * (1 / cut_lj_inner14) * (1 / cut_lj_inner14); + > cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv; + > cut_lj3inv = (1 / cut_lj14) * (1 / cut_lj14) * (1 / cut_lj14); + > cut_lj6inv = cut_lj3inv * cut_lj3inv; + + */ + +template +void DihedralCharmmfswKokkos::init_style() +{ + DihedralCharmmfsw::init_style(); + + int n = atom->ntypes; + DAT::tdual_ffloat_2d k_lj14_1("DihedralCharmm:lj14_1",n+1,n+1); + DAT::tdual_ffloat_2d k_lj14_2("DihedralCharmm:lj14_2",n+1,n+1); + DAT::tdual_ffloat_2d k_lj14_3("DihedralCharmm:lj14_3",n+1,n+1); + DAT::tdual_ffloat_2d k_lj14_4("DihedralCharmm:lj14_4",n+1,n+1); + + d_lj14_1 = k_lj14_1.template view(); + d_lj14_2 = k_lj14_2.template view(); + d_lj14_3 = k_lj14_3.template view(); + d_lj14_4 = k_lj14_4.template view(); + + + if (weightflag) { + int n = atom->ntypes; + for (int i = 1; i <= n; i++) { + for (int j = 1; j <= n; j++) { + k_lj14_1.h_view(i,j) = lj14_1[i][j]; + k_lj14_2.h_view(i,j) = lj14_2[i][j]; + k_lj14_3.h_view(i,j) = lj14_3[i][j]; + k_lj14_4.h_view(i,j) = lj14_4[i][j]; + } + } + } + + k_lj14_1.template modify(); + k_lj14_2.template modify(); + k_lj14_3.template modify(); + k_lj14_4.template modify(); + + k_lj14_1.template sync(); + k_lj14_2.template sync(); + k_lj14_3.template sync(); + k_lj14_4.template sync(); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +/* + + 402c445 + < void DihedralCharmm::read_restart(FILE *fp) + --- + > void DihedralCharmmfsw::read_restart(FILE *fp) + + */ +template +void DihedralCharmmfswKokkos::read_restart(FILE *fp) +{ + DihedralCharmmfsw::read_restart(fp); + + int nd = atom->ndihedraltypes; + typename AT::tdual_ffloat_1d k_k("DihedralCharmm::k",nd+1); + typename AT::tdual_ffloat_1d k_multiplicity("DihedralCharmm::multiplicity",nd+1); + typename AT::tdual_ffloat_1d k_shift("DihedralCharmm::shift",nd+1); + typename AT::tdual_ffloat_1d k_cos_shift("DihedralCharmm::cos_shift",nd+1); + typename AT::tdual_ffloat_1d k_sin_shift("DihedralCharmm::sin_shift",nd+1); + typename AT::tdual_ffloat_1d k_weight("DihedralCharmm::weight",nd+1); + + d_k = k_k.template view(); + d_multiplicity = k_multiplicity.template view(); + d_shift = k_shift.template view(); + d_cos_shift = k_cos_shift.template view(); + d_sin_shift = k_sin_shift.template view(); + d_weight = k_weight.template view(); + + int n = atom->ndihedraltypes; + for (int i = 1; i <= n; i++) { + k_k.h_view[i] = k[i]; + k_multiplicity.h_view[i] = multiplicity[i]; + k_shift.h_view[i] = shift[i]; + k_cos_shift.h_view[i] = cos_shift[i]; + k_sin_shift.h_view[i] = sin_shift[i]; + k_weight.h_view[i] = weight[i]; + } + + k_k.template modify(); + k_multiplicity.template modify(); + k_shift.template modify(); + k_cos_shift.template modify(); + k_sin_shift.template modify(); + k_weight.template modify(); + + k_k.template sync(); + k_multiplicity.template sync(); + k_shift.template sync(); + k_cos_shift.template sync(); + k_sin_shift.template sync(); + k_weight.template sync(); +} + +/* ---------------------------------------------------------------------- + tally energy and virial into global and per-atom accumulators + virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4 + = (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4 + = vb1*f1 + vb2*f3 + (vb3+vb2)*f4 +------------------------------------------------------------------------- */ + +template +//template +KOKKOS_INLINE_FUNCTION +void DihedralCharmmfswKokkos::ev_tally(EVM_FLOAT &evm, const int i1, const int i2, const int i3, const int i4, + F_FLOAT &edihedral, F_FLOAT *f1, F_FLOAT *f3, F_FLOAT *f4, + const F_FLOAT &vb1x, const F_FLOAT &vb1y, const F_FLOAT &vb1z, + const F_FLOAT &vb2x, const F_FLOAT &vb2y, const F_FLOAT &vb2z, + const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const +{ + E_FLOAT edihedralquarter; + F_FLOAT v[6]; + + if (eflag_either) { + if (eflag_global) { + if (newton_bond) evm.emol += edihedral; + else { + edihedralquarter = 0.25*edihedral; + if (i1 < nlocal) evm.emol += edihedralquarter; + if (i2 < nlocal) evm.emol += edihedralquarter; + if (i3 < nlocal) evm.emol += edihedralquarter; + if (i4 < nlocal) evm.emol += edihedralquarter; + } + } + if (eflag_atom) { + edihedralquarter = 0.25*edihedral; + if (newton_bond || i1 < nlocal) d_eatom[i1] += edihedralquarter; + if (newton_bond || i2 < nlocal) d_eatom[i2] += edihedralquarter; + if (newton_bond || i3 < nlocal) d_eatom[i3] += edihedralquarter; + if (newton_bond || i4 < nlocal) d_eatom[i4] += edihedralquarter; + } + } + + if (vflag_either) { + v[0] = vb1x*f1[0] + vb2x*f3[0] + (vb3x+vb2x)*f4[0]; + v[1] = vb1y*f1[1] + vb2y*f3[1] + (vb3y+vb2y)*f4[1]; + v[2] = vb1z*f1[2] + vb2z*f3[2] + (vb3z+vb2z)*f4[2]; + v[3] = vb1x*f1[1] + vb2x*f3[1] + (vb3x+vb2x)*f4[1]; + v[4] = vb1x*f1[2] + vb2x*f3[2] + (vb3x+vb2x)*f4[2]; + v[5] = vb1y*f1[2] + vb2y*f3[2] + (vb3y+vb2y)*f4[2]; + + if (vflag_global) { + if (newton_bond) { + evm.v[0] += v[0]; + evm.v[1] += v[1]; + evm.v[2] += v[2]; + evm.v[3] += v[3]; + evm.v[4] += v[4]; + evm.v[5] += v[5]; + } else { + if (i1 < nlocal) { + evm.v[0] += 0.25*v[0]; + evm.v[1] += 0.25*v[1]; + evm.v[2] += 0.25*v[2]; + evm.v[3] += 0.25*v[3]; + evm.v[4] += 0.25*v[4]; + evm.v[5] += 0.25*v[5]; + } + if (i2 < nlocal) { + evm.v[0] += 0.25*v[0]; + evm.v[1] += 0.25*v[1]; + evm.v[2] += 0.25*v[2]; + evm.v[3] += 0.25*v[3]; + evm.v[4] += 0.25*v[4]; + evm.v[5] += 0.25*v[5]; + } + if (i3 < nlocal) { + evm.v[0] += 0.25*v[0]; + evm.v[1] += 0.25*v[1]; + evm.v[2] += 0.25*v[2]; + evm.v[3] += 0.25*v[3]; + evm.v[4] += 0.25*v[4]; + evm.v[5] += 0.25*v[5]; + } + if (i4 < nlocal) { + evm.v[0] += 0.25*v[0]; + evm.v[1] += 0.25*v[1]; + evm.v[2] += 0.25*v[2]; + evm.v[3] += 0.25*v[3]; + evm.v[4] += 0.25*v[4]; + evm.v[5] += 0.25*v[5]; + } + } + } + + if (vflag_atom) { + if (newton_bond || i1 < nlocal) { + d_vatom(i1,0) += 0.25*v[0]; + d_vatom(i1,1) += 0.25*v[1]; + d_vatom(i1,2) += 0.25*v[2]; + d_vatom(i1,3) += 0.25*v[3]; + d_vatom(i1,4) += 0.25*v[4]; + d_vatom(i1,5) += 0.25*v[5]; + } + if (newton_bond || i2 < nlocal) { + d_vatom(i2,0) += 0.25*v[0]; + d_vatom(i2,1) += 0.25*v[1]; + d_vatom(i2,2) += 0.25*v[2]; + d_vatom(i2,3) += 0.25*v[3]; + d_vatom(i2,4) += 0.25*v[4]; + d_vatom(i2,5) += 0.25*v[5]; + } + if (newton_bond || i3 < nlocal) { + d_vatom(i3,0) += 0.25*v[0]; + d_vatom(i3,1) += 0.25*v[1]; + d_vatom(i3,2) += 0.25*v[2]; + d_vatom(i3,3) += 0.25*v[3]; + d_vatom(i3,4) += 0.25*v[4]; + d_vatom(i3,5) += 0.25*v[5]; + } + if (newton_bond || i4 < nlocal) { + d_vatom(i4,0) += 0.25*v[0]; + d_vatom(i4,1) += 0.25*v[1]; + d_vatom(i4,2) += 0.25*v[2]; + d_vatom(i4,3) += 0.25*v[3]; + d_vatom(i4,4) += 0.25*v[4]; + d_vatom(i4,5) += 0.25*v[5]; + } + } + } +} + +/* ---------------------------------------------------------------------- + tally eng_vdwl and virial into global and per-atom accumulators + need i < nlocal test since called by bond_quartic and dihedral_charmm +------------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void DihedralCharmmfswKokkos::ev_tally(EVM_FLOAT &evm, const int i, const int j, + const F_FLOAT &evdwl, const F_FLOAT &ecoul, const F_FLOAT &fpair, const F_FLOAT &delx, + const F_FLOAT &dely, const F_FLOAT &delz) const +{ + E_FLOAT evdwlhalf,ecoulhalf,epairhalf; + F_FLOAT v[6]; + + + if (eflag_either) { + if (eflag_global) { + if (newton_bond) { + evm.evdwl += evdwl; + evm.ecoul += ecoul; + } else { + evdwlhalf = 0.5*evdwl; + ecoulhalf = 0.5*ecoul; + if (i < nlocal) { + evm.evdwl += evdwlhalf; + evm.ecoul += ecoulhalf; + } + if (j < nlocal) { + evm.evdwl += evdwlhalf; + evm.ecoul += ecoulhalf; + } + } + } + if (eflag_atom) { + epairhalf = 0.5 * (evdwl + ecoul); + if (newton_bond || i < nlocal) d_eatom_pair[i] += epairhalf; + if (newton_bond || j < nlocal) d_eatom_pair[j] += epairhalf; + } + } + + if (vflag_either) { + v[0] = delx*delx*fpair; + v[1] = dely*dely*fpair; + v[2] = delz*delz*fpair; + v[3] = delx*dely*fpair; + v[4] = delx*delz*fpair; + v[5] = dely*delz*fpair; + + if (vflag_global) { + if (newton_bond) { + evm.vp[0] += v[0]; + evm.vp[1] += v[1]; + evm.vp[2] += v[2]; + evm.vp[3] += v[3]; + evm.vp[4] += v[4]; + evm.vp[5] += v[5]; + } else { + if (i < nlocal) { + evm.vp[0] += 0.5*v[0]; + evm.vp[1] += 0.5*v[1]; + evm.vp[2] += 0.5*v[2]; + evm.vp[3] += 0.5*v[3]; + evm.vp[4] += 0.5*v[4]; + evm.vp[5] += 0.5*v[5]; + } + if (j < nlocal) { + evm.vp[0] += 0.5*v[0]; + evm.vp[1] += 0.5*v[1]; + evm.vp[2] += 0.5*v[2]; + evm.vp[3] += 0.5*v[3]; + evm.vp[4] += 0.5*v[4]; + evm.vp[5] += 0.5*v[5]; + } + } + } + + if (vflag_atom) { + if (newton_bond || i < nlocal) { + d_vatom_pair(i,0) += 0.5*v[0]; + d_vatom_pair(i,1) += 0.5*v[1]; + d_vatom_pair(i,2) += 0.5*v[2]; + d_vatom_pair(i,3) += 0.5*v[3]; + d_vatom_pair(i,4) += 0.5*v[4]; + d_vatom_pair(i,5) += 0.5*v[5]; + } + if (newton_bond || j < nlocal) { + d_vatom_pair(j,0) += 0.5*v[0]; + d_vatom_pair(j,1) += 0.5*v[1]; + d_vatom_pair(j,2) += 0.5*v[2]; + d_vatom_pair(j,3) += 0.5*v[3]; + d_vatom_pair(j,4) += 0.5*v[4]; + d_vatom_pair(j,5) += 0.5*v[5]; + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +namespace LAMMPS_NS { +template class DihedralCharmmfswKokkos; +#ifdef LMP_KOKKOS_GPU +template class DihedralCharmmfswKokkos; +#endif +} + + + +/* + + + 355c374 + < error->all(FLERR, "Dihedral style charmm must be set to same r-RESPA level as 'pair'"); + --- + > error->all(FLERR, "Dihedral style charmmfsw must be set to same r-RESPA level as 'pair'"); + 357c376 + < error->all(FLERR, "Dihedral style charmm must be set to same r-RESPA level as 'outer'"); + --- + > error->all(FLERR, "Dihedral style charmmfsw must be set to same r-RESPA level as 'outer'"); + 373c392 + < error->all(FLERR, "Dihedral charmm is incompatible with Pair style"); + --- + > error->all(FLERR, "Dihedral charmmfsw is incompatible with Pair style"); + 380c399 + < error->all(FLERR, "Dihedral charmm is incompatible with Pair style"); + --- + > error->all(FLERR, "Dihedral charmmfsw is incompatible with Pair style"); + + 389c432 + < void DihedralCharmm::write_restart(FILE *fp) + --- + > void DihedralCharmmfsw::write_restart(FILE *fp) + 430c473 + < void DihedralCharmm::write_data(FILE *fp) + --- + > void DihedralCharmmfsw::write_data(FILE *fp) + + */ + +// nothing to do for all these, inherited from DihedralCharmmfsw diff --git a/src/KOKKOS/dihedral_charmmfsw_kokkos.h b/src/KOKKOS/dihedral_charmmfsw_kokkos.h new file mode 100644 index 00000000000..413945826f9 --- /dev/null +++ b/src/KOKKOS/dihedral_charmmfsw_kokkos.h @@ -0,0 +1,267 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + + *** DRAFT VERSION 1 (lots of comments to be removed just before merge) *** + + (1) first draft version of DihedralCharmmfswKokkos exactly + same as DihedralCharmmKokkos but with new class name + + (2) second draft version: nothing changed in header file + + method: track changes from serial kspace dihedral_charmm to + dihedral_charmmfsw and apply to DihedralCharmmKokkos + + % diff dihedral_charmm.h dihedral_charmmfsw.h + +------------------------------------------------------------------------- */ + +/* + + 16c16 + < DihedralStyle(charmm,DihedralCharmm); + --- + > DihedralStyle(charmmfsw,DihedralCharmmfsw); + + */ + +#ifdef DIHEDRAL_CLASS +// clang-format off +DihedralStyle(charmmfsw/kk,DihedralCharmmfswKokkos); +DihedralStyle(charmmfsw/kk/device,DihedralCharmmfswKokkos); +DihedralStyle(charmmfsw/kk/host,DihedralCharmmfswKokkos); +// clang-format on +#else + +/* + + 20,21c20,21 + < #ifndef LMP_DIHEDRAL_CHARMM_H + < #define LMP_DIHEDRAL_CHARMM_H + --- + > #ifndef LMP_DIHEDRAL_CHARMMFSW_H + > #define LMP_DIHEDRAL_CHARMMFSW_H + + */ + +// clang-format off +#ifndef LMP_DIHEDRAL_CHARMMFSW_KOKKOS_H +#define LMP_DIHEDRAL_CHARMMFSW_KOKKOS_H + +#include "dihedral_charmmfsw.h" +#include "kokkos_type.h" +#include "dihedral_charmm_kokkos.h" + +/* + + s_EVM_FLOAT and TagDihedralCharmmCompute conflict because style_dihedral.h + includes both dihedral_charmm_kokkos.h and dihedral_charmmfsw_kokkos.h + so comment out definitions in here and include dihedral_charmm_kokkos.h + in dihedral_charmmfsw_kokkos.h: + + In file included from /Users/mitch/Dropbox/lammps/lammps/src/force.cpp:18: + In file included from /Users/mitch/Dropbox/lammps/lammps/build/styles/style_dihedral.h:4: + /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmmfsw_kokkos.h:65:8: error: redefinition of 's_EVM_FLOAT' + struct s_EVM_FLOAT { + ^ + /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:31:8: note: previous definition is here + struct s_EVM_FLOAT { + ^ + In file included from /Users/mitch/Dropbox/lammps/lammps/src/force.cpp:18: + In file included from /Users/mitch/Dropbox/lammps/lammps/build/styles/style_dihedral.h:4: + /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmmfsw_kokkos.h:104:8: error: redefinition of 'TagDihedralCharmmCompute' + struct TagDihedralCharmmCompute{}; + ^ + /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:70:8: note: previous definition is here + struct TagDihedralCharmmCompute{}; + ^ + In file included from /Users/mitch/Dropbox/lammps/lammps/src/lammps.cpp:23: + In file included from /Users/mitch/Dropbox/lammps/lammps/build/styles/style_dihedral.h:4: + /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmmfsw_kokkos.h:65:8: error: redefinition of 's_EVM_FLOAT' + struct s_EVM_FLOAT { + ^ + /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:31:8: note: previous definition is here + struct s_EVM_FLOAT { + ^ + In file included from /Users/mitch/Dropbox/lammps/lammps/src/lammps.cpp:23: + In file included from /Users/mitch/Dropbox/lammps/lammps/build/styles/style_dihedral.h:4: + /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmmfsw_kokkos.h:104:8: error: redefinition of 'TagDihedralCharmmCompute' + struct TagDihedralCharmmCompute{}; + ^ + /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:70:8: note: previous definition is here + struct TagDihedralCharmmCompute{}; + ^ + + */ + +namespace LAMMPS_NS { + +/* +struct s_EVM_FLOAT { + E_FLOAT evdwl; + E_FLOAT ecoul; + E_FLOAT emol; + F_FLOAT v[6]; + F_FLOAT vp[6]; + KOKKOS_INLINE_FUNCTION + s_EVM_FLOAT() { + evdwl = 0; + ecoul = 0; + emol = 0; + v[0] = 0; v[1] = 0; v[2] = 0; + v[3] = 0; v[4] = 0; v[5] = 0; + vp[0] = 0; vp[1] = 0; vp[2] = 0; + vp[3] = 0; vp[4] = 0; vp[5] = 0; + } + + KOKKOS_INLINE_FUNCTION + void operator+=(const s_EVM_FLOAT &rhs) { + evdwl += rhs.evdwl; + ecoul += rhs.ecoul; + emol += rhs.emol; + v[0] += rhs.v[0]; + v[1] += rhs.v[1]; + v[2] += rhs.v[2]; + v[3] += rhs.v[3]; + v[4] += rhs.v[4]; + v[5] += rhs.v[5]; + vp[0] += rhs.vp[0]; + vp[1] += rhs.vp[1]; + vp[2] += rhs.vp[2]; + vp[3] += rhs.vp[3]; + vp[4] += rhs.vp[4]; + vp[5] += rhs.vp[5]; + } +}; +typedef struct s_EVM_FLOAT EVM_FLOAT; + +template +struct TagDihedralCharmmCompute{}; + +*/ + +/* + 27c27 + < class DihedralCharmm : public Dihedral { + --- + > class DihedralCharmmfsw : public Dihedral { + 29,30c29,30 + < DihedralCharmm(class LAMMPS *); + < ~DihedralCharmm() override; + --- + > DihedralCharmmfsw(class LAMMPS *); + > ~DihedralCharmmfsw() override; + + */ + +template +class DihedralCharmmfswKokkos : public DihedralCharmmfsw { + public: + typedef DeviceType device_type; + typedef EVM_FLOAT value_type; + typedef ArrayTypes AT; + + DihedralCharmmfswKokkos(class LAMMPS *); + ~DihedralCharmmfswKokkos() override; + void compute(int, int) override; + void coeff(int, char **) override; + void init_style() override; + void read_restart(FILE *) override; + + template + KOKKOS_INLINE_FUNCTION + void operator()(TagDihedralCharmmCompute, const int&, EVM_FLOAT&) const; + + template + KOKKOS_INLINE_FUNCTION + void operator()(TagDihedralCharmmCompute, const int&) const; + + //template + KOKKOS_INLINE_FUNCTION + void ev_tally(EVM_FLOAT &evm, const int i1, const int i2, const int i3, const int i4, + F_FLOAT &edihedral, F_FLOAT *f1, F_FLOAT *f3, F_FLOAT *f4, + const F_FLOAT &vb1x, const F_FLOAT &vb1y, const F_FLOAT &vb1z, + const F_FLOAT &vb2x, const F_FLOAT &vb2y, const F_FLOAT &vb2z, + const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const; + + KOKKOS_INLINE_FUNCTION + void ev_tally(EVM_FLOAT &evm, const int i, const int j, + const F_FLOAT &evdwl, const F_FLOAT &ecoul, const F_FLOAT &fpair, const F_FLOAT &delx, + const F_FLOAT &dely, const F_FLOAT &delz) const; + + protected: + + class NeighborKokkos *neighborKK; + + typename AT::t_x_array_randomread x; + typename AT::t_int_1d_randomread atomtype; + typename AT::t_ffloat_1d_randomread q; + typename AT::t_f_array f; + typename AT::t_int_2d dihedrallist; + + typedef typename KKDevice::value KKDeviceType; + Kokkos::DualView k_eatom; + Kokkos::DualView k_vatom; + Kokkos::View > d_eatom; + Kokkos::View > d_vatom; + + Kokkos::DualView k_eatom_pair; + Kokkos::DualView k_vatom_pair; + Kokkos::View > d_eatom_pair; + Kokkos::View > d_vatom_pair; + + int nlocal,newton_bond; + int eflag,vflag; + double qqrd2e; + + Kokkos::DualView k_warning_flag; + typename Kokkos::DualView::t_dev d_warning_flag; + typename Kokkos::DualView::t_host h_warning_flag; + + typename AT::t_ffloat_2d d_lj14_1; + typename AT::t_ffloat_2d d_lj14_2; + typename AT::t_ffloat_2d d_lj14_3; + typename AT::t_ffloat_2d d_lj14_4; + + typename AT::t_ffloat_1d d_k; + typename AT::t_ffloat_1d d_multiplicity; + typename AT::t_ffloat_1d d_shift; + typename AT::t_ffloat_1d d_sin_shift; + typename AT::t_ffloat_1d d_cos_shift; + typename AT::t_ffloat_1d d_weight; + + void allocate() override; +}; + +} + +#endif +#endif + + + +/* + + 38a39,43 + > int implicit, weightflag, dihedflag; + > double cut_lj_inner14, cut_lj14, cut_coul14; + > double evdwl14_12, evdwl14_6, cut_coulinv14; + > double cut_lj_inner3inv, cut_lj_inner6inv, cut_lj3inv, cut_lj6inv; + > + 42d46 + < int implicit, weightflag; + + */ + +// nothing to do here, inherited from DihedralCharmmfsw diff --git a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp new file mode 100644 index 00000000000..88efec5fda4 --- /dev/null +++ b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp @@ -0,0 +1,941 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + + Contributing authors: + + - Ray Shan (SNL) - original PairLJCharmmCoulLongKokkos + + - Mitch Murphy (alphataubio) - PairLJCharmmfswCoulLongKokkos update (2023/12) + + Based on serial kspace lj-fsw sections (force-switched) provided by + Robert Meissner and Lucio Colombi Ciacchi of Bremen University, Germany, + with additional assistance from Robert A. Latour, Clemson University + + ------------------------------------------------------------------------- */ + + + +/* ---------------------------------------------------------------------- + + *** DRAFT VERSION 1 (lots of comments to be removed just before merge) *** + + (1) first draft version of PairLJCharmmfswCoulLongKokkos almost exactly + same as PairLJCharmmCoulLongKokkos but with new class name + + method: track changes from serial kspace pair_lj_charmm_coul_long to + pair_lj_charmmfsw_coul_long and apply to PairLJCharmmCoulLongKokkos + + ISSUES: + + (A) charmm denom_lj_inv cache , is it to optimize code because division + is slower that multiplication ?? + + + + ------------------------------------------------------------------------- */ + + +/* + 19c23 + < #include "pair_lj_charmm_coul_long.h" + --- + > #include "pair_lj_charmmfsw_coul_long.h" + + */ + +#include "pair_lj_charmmfsw_coul_long_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "error.h" +#include "force.h" +#include "kokkos.h" +#include "memory_kokkos.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" + +#include +#include + +using namespace LAMMPS_NS; + + +#define EWALD_F 1.12837917 +#define EWALD_P 0.3275911 +#define A1 0.254829592 +#define A2 -0.284496736 +#define A3 1.421413741 +#define A4 -1.453152027 +#define A5 1.061405429 + +/* ---------------------------------------------------------------------- */ + +/* + 47c51 + < PairLJCharmmCoulLong::PairLJCharmmCoulLong(LAMMPS *lmp) : Pair(lmp) + --- + > PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(LAMMPS *lmp) : Pair(lmp) + 55a60,72 + > + > // short-range/long-range flag accessed by DihedralCharmmfsw + > + > dihedflag = 1; + > + > // switch qqr2e from LAMMPS value to CHARMM value + > + > if (strcmp(update->unit_style,"real") == 0) { + > if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real)) + > error->message(FLERR,"Switching to CHARMM coulomb energy" + > " conversion constant"); + > force->qqr2e = force->qqr2e_charmm_real; + > } + + */ + +// added superclass constructor to inherit from PairLJCharmmfswCoulLong + +template +PairLJCharmmfswCoulLongKokkos::PairLJCharmmfswCoulLongKokkos(LAMMPS *lmp):PairLJCharmmfswCoulLong(lmp) +{ + + // pair_lj_charmmfsw_coul_long_kokkos.cpp:112:28: error: qualified reference to 'PairLJCharmmfswCoulLong' is a constructor name rather than a type in this context + // ??? PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(lmp); + + respa_enable = 0; + + kokkosable = 1; + atomKK = (AtomKokkos *) atom; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = X_MASK | F_MASK | TYPE_MASK | Q_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; +} + +/* ---------------------------------------------------------------------- */ + +/* + + 60c77 + < PairLJCharmmCoulLong::~PairLJCharmmCoulLong() + --- + > PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong() + 61a79,87 + > // switch qqr2e back from CHARMM value to LAMMPS value + > + > if (update && strcmp(update->unit_style,"real") == 0) { + > if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real)) + > error->message(FLERR,"Restoring original LAMMPS coulomb energy" + > " conversion constant"); + > force->qqr2e = force->qqr2e_lammps_real; + > } + > + + */ + +// added superclass constructor to inherit from PairLJCharmmfswCoulLong + +template +PairLJCharmmfswCoulLongKokkos::~PairLJCharmmfswCoulLongKokkos() +{ + + // pair_lj_charmmfsw_coul_long_kokkos.cpp:150:28: error: qualified reference to 'PairLJCharmmfswCoulLong' is a constructor name rather than a type in this context + // ??? PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(); + + if (copymode) return; + + if (allocated) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->destroy_kokkos(k_cutsq,cutsq); + } +} + +/* ---------------------------------------------------------------------- */ + +/* + 87c112 + < void PairLJCharmmCoulLong::compute(int eflag, int vflag) + --- + > void PairLJCharmmfswCoulLong::compute(int eflag, int vflag) + 90c115 + < double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + --- + > double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwl12,evdwl6,ecoul,fpair; + 92c117 + < double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; + --- + > double r,rinv,r2inv,r3inv,r6inv,rsq,forcecoul,forcelj,factor_coul,factor_lj; + 94c119 + < double philj,switch1,switch2; + --- + > double switch1; + 96d120 + < double rsq; + 174,179c198,200 + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < switch2 = 12.0*rsq * (cut_ljsq-rsq) * + < (rsq-cut_lj_innersq) * denom_lj_inv; + < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + < forcelj = forcelj*switch1 + philj*switch2; + < } + --- + > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + > forcelj = forcelj*switch1; + > } + 205d225 + < evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); + 207,209c227,240 + < switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < evdwl *= switch1; + --- + > r = sqrt(rsq); + > rinv = 1.0/r; + > r3inv = rinv*rinv*rinv; + > evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 * + > (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); + > evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 * + > (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); + > evdwl = evdwl12 + evdwl6; + > } else { + > evdwl12 = r6inv*lj3[itype][jtype]*r6inv - + > lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; + > evdwl6 = -lj4[itype][jtype]*r6inv + + > lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv; + > evdwl = evdwl12 + evdwl6; + + */ + +template +void PairLJCharmmfswCoulLongKokkos::compute(int eflag_in, int vflag_in) +{ + eflag = eflag_in; + vflag = vflag_in; + + if (neighflag == FULL) no_virial_fdotr_compute = 1; + + ev_init(eflag,vflag,0); + + // reallocate per-atom arrays if necessary + + if (eflag_atom) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom"); + d_eatom = k_eatom.view(); + } + if (vflag_atom) { + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"pair:vatom"); + d_vatom = k_vatom.view(); + } + + atomKK->sync(execution_space,datamask_read); + k_cutsq.template sync(); + k_params.template sync(); + if (eflag || vflag) atomKK->modified(execution_space,datamask_modify); + else atomKK->modified(execution_space,F_MASK); + + x = atomKK->k_x.view(); + c_x = atomKK->k_x.view(); + f = atomKK->k_f.view(); + q = atomKK->k_q.view(); + type = atomKK->k_type.view(); + nlocal = atom->nlocal; + nall = atom->nlocal + atom->nghost; + special_lj[0] = force->special_lj[0]; + special_lj[1] = force->special_lj[1]; + special_lj[2] = force->special_lj[2]; + special_lj[3] = force->special_lj[3]; + special_coul[0] = force->special_coul[0]; + special_coul[1] = force->special_coul[1]; + special_coul[2] = force->special_coul[2]; + special_coul[3] = force->special_coul[3]; + qqrd2e = force->qqrd2e; + newton_pair = force->newton_pair; + + // loop over neighbors of my atoms + + copymode = 1; + + EV_FLOAT ev; + if (ncoultablebits) + ev = pair_compute,CoulLongTable<1> > + (this,(NeighListKokkos*)list); + else + ev = pair_compute,CoulLongTable<0> > + (this,(NeighListKokkos*)list); + + + if (eflag) { + eng_vdwl += ev.evdwl; + eng_coul += ev.ecoul; + } + if (vflag_global) { + virial[0] += ev.v[0]; + virial[1] += ev.v[1]; + virial[2] += ev.v[2]; + virial[3] += ev.v[3]; + virial[4] += ev.v[4]; + virial[5] += ev.v[5]; + } + + if (eflag_atom) { + k_eatom.template modify(); + k_eatom.template sync(); + } + + if (vflag_atom) { + k_vatom.template modify(); + k_vatom.template sync(); + } + + if (vflag_fdotr) pair_virial_fdotr_compute(this); + + copymode = 0; +} + +/* ---------------------------------------------------------------------- + compute LJ CHARMM pair force between atoms i and j + ---------------------------------------------------------------------- */ +template +template +KOKKOS_INLINE_FUNCTION +F_FLOAT PairLJCharmmfswCoulLongKokkos:: +compute_fpair(const F_FLOAT& rsq, const int& /*i*/, const int& /*j*/, + const int& itype, const int& jtype) const { + const F_FLOAT r2inv = 1.0/rsq; + const F_FLOAT r6inv = r2inv*r2inv*r2inv; + F_FLOAT forcelj, switch1, switch2, englj; + + forcelj = r6inv * + ((STACKPARAMS?m_params[itype][jtype].lj1:params(itype,jtype).lj1)*r6inv - + (STACKPARAMS?m_params[itype][jtype].lj2:params(itype,jtype).lj2)); + + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + switch2 = 12.0*rsq * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj; + englj = r6inv * + ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv - + (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)); + forcelj = forcelj*switch1 + englj*switch2; + } + + return forcelj*r2inv; +} + +/* ---------------------------------------------------------------------- + compute LJ CHARMM pair potential energy between atoms i and j + ---------------------------------------------------------------------- */ +template +template +KOKKOS_INLINE_FUNCTION +F_FLOAT PairLJCharmmfswCoulLongKokkos:: +compute_evdwl(const F_FLOAT& rsq, const int& /*i*/, const int& /*j*/, + const int& itype, const int& jtype) const { + const F_FLOAT r2inv = 1.0/rsq; + const F_FLOAT r6inv = r2inv*r2inv*r2inv; + F_FLOAT englj, switch1; + + englj = r6inv * + ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv - + (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)); + + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + englj *= switch1; + } + + return englj; + +} + +/* ---------------------------------------------------------------------- + compute coulomb pair force between atoms i and j + ---------------------------------------------------------------------- */ +template +template +KOKKOS_INLINE_FUNCTION +F_FLOAT PairLJCharmmfswCoulLongKokkos:: +compute_fcoul(const F_FLOAT& rsq, const int& /*i*/, const int&j, + const int& /*itype*/, const int& /*jtype*/, + const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const { + if (Specialisation::DoTable && rsq > tabinnersq) { + union_int_float_t rsq_lookup; + rsq_lookup.f = rsq; + const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits; + const F_FLOAT fraction = (rsq_lookup.f - d_rtable[itable]) * d_drtable[itable]; + const F_FLOAT table = d_ftable[itable] + fraction*d_dftable[itable]; + F_FLOAT forcecoul = qtmp*q[j] * table; + if (factor_coul < 1.0) { + const F_FLOAT table = d_ctable[itable] + fraction*d_dctable[itable]; + const F_FLOAT prefactor = qtmp*q[j] * table; + forcecoul -= (1.0-factor_coul)*prefactor; + } + return forcecoul/rsq; + } else { + const F_FLOAT r = sqrt(rsq); + const F_FLOAT grij = g_ewald * r; + const F_FLOAT expm2 = exp(-grij*grij); + const F_FLOAT t = 1.0 / (1.0 + EWALD_P*grij); + const F_FLOAT rinv = 1.0/r; + const F_FLOAT erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + const F_FLOAT prefactor = qqrd2e * qtmp*q[j]*rinv; + F_FLOAT forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + + return forcecoul*rinv*rinv; + } +} + +/* ---------------------------------------------------------------------- + compute coulomb pair potential energy between atoms i and j + ---------------------------------------------------------------------- */ +template +template +KOKKOS_INLINE_FUNCTION +F_FLOAT PairLJCharmmfswCoulLongKokkos:: +compute_ecoul(const F_FLOAT& rsq, const int& /*i*/, const int&j, + const int& /*itype*/, const int& /*jtype*/, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const { + if (Specialisation::DoTable && rsq > tabinnersq) { + union_int_float_t rsq_lookup; + rsq_lookup.f = rsq; + const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits; + const F_FLOAT fraction = (rsq_lookup.f - d_rtable[itable]) * d_drtable[itable]; + const F_FLOAT table = d_etable[itable] + fraction*d_detable[itable]; + F_FLOAT ecoul = qtmp*q[j] * table; + if (factor_coul < 1.0) { + const F_FLOAT table = d_ctable[itable] + fraction*d_dctable[itable]; + const F_FLOAT prefactor = qtmp*q[j] * table; + ecoul -= (1.0-factor_coul)*prefactor; + } + return ecoul; + } else { + const F_FLOAT r = sqrt(rsq); + const F_FLOAT grij = g_ewald * r; + const F_FLOAT expm2 = exp(-grij*grij); + const F_FLOAT t = 1.0 / (1.0 + EWALD_P*grij); + const F_FLOAT erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + const F_FLOAT prefactor = qqrd2e * qtmp*q[j]/r; + F_FLOAT ecoul = prefactor * erfc; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + return ecoul; + } +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +template +void PairLJCharmmfswCoulLongKokkos::allocate() +{ + PairLJCharmmfswCoulLong::allocate(); + + int n = atom->ntypes; + + memory->destroy(cutsq); + memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq"); + d_cutsq = k_cutsq.template view(); + + d_cut_ljsq = typename AT::t_ffloat_2d("pair:cut_ljsq",n+1,n+1); + + d_cut_coulsq = typename AT::t_ffloat_2d("pair:cut_coulsq",n+1,n+1); + + k_params = Kokkos::DualView("PairLJCharmmCoulLong::params",n+1,n+1); + params = k_params.template view(); +} + +template +void PairLJCharmmfswCoulLongKokkos::init_tables(double cut_coul, double *cut_respa) +{ + Pair::init_tables(cut_coul,cut_respa); + + typedef typename ArrayTypes::t_ffloat_1d table_type; + typedef typename ArrayTypes::t_ffloat_1d host_table_type; + + int ntable = 1; + for (int i = 0; i < ncoultablebits; i++) ntable *= 2; + + + // Copy rtable and drtable + { + host_table_type h_table("HostTable",ntable); + table_type d_table("DeviceTable",ntable); + for (int i = 0; i < ntable; i++) { + h_table(i) = rtable[i]; + } + Kokkos::deep_copy(d_table,h_table); + d_rtable = d_table; + } + + { + host_table_type h_table("HostTable",ntable); + table_type d_table("DeviceTable",ntable); + for (int i = 0; i < ntable; i++) { + h_table(i) = drtable[i]; + } + Kokkos::deep_copy(d_table,h_table); + d_drtable = d_table; + } + + { + host_table_type h_table("HostTable",ntable); + table_type d_table("DeviceTable",ntable); + + // Copy ftable and dftable + for (int i = 0; i < ntable; i++) { + h_table(i) = ftable[i]; + } + Kokkos::deep_copy(d_table,h_table); + d_ftable = d_table; + } + + { + host_table_type h_table("HostTable",ntable); + table_type d_table("DeviceTable",ntable); + + for (int i = 0; i < ntable; i++) { + h_table(i) = dftable[i]; + } + Kokkos::deep_copy(d_table,h_table); + d_dftable = d_table; + } + + { + host_table_type h_table("HostTable",ntable); + table_type d_table("DeviceTable",ntable); + + // Copy ctable and dctable + for (int i = 0; i < ntable; i++) { + h_table(i) = ctable[i]; + } + Kokkos::deep_copy(d_table,h_table); + d_ctable = d_table; + } + + { + host_table_type h_table("HostTable",ntable); + table_type d_table("DeviceTable",ntable); + + for (int i = 0; i < ntable; i++) { + h_table(i) = dctable[i]; + } + Kokkos::deep_copy(d_table,h_table); + d_dctable = d_table; + } + + { + host_table_type h_table("HostTable",ntable); + table_type d_table("DeviceTable",ntable); + + // Copy etable and detable + for (int i = 0; i < ntable; i++) { + h_table(i) = etable[i]; + } + Kokkos::deep_copy(d_table,h_table); + d_etable = d_table; + } + + { + host_table_type h_table("HostTable",ntable); + table_type d_table("DeviceTable",ntable); + + for (int i = 0; i < ntable; i++) { + h_table(i) = detable[i]; + } + Kokkos::deep_copy(d_table,h_table); + d_detable = d_table; + } +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +/* + 682c733 + < void PairLJCharmmCoulLong::init_style() + --- + > void PairLJCharmmfswCoulLong::init_style() + 686c737 + < "Pair style lj/charmm/coul/long requires atom attribute q"); + --- + > "Pair style lj/charmmfsw/coul/long requires atom attribute q"); + 688c739 + < // request regular or rRESPA neighbor list + --- + > // request regular or rRESPA neighbor lists + 705a757,766 + > cut_ljinv = 1.0/cut_lj; + > cut_lj_innerinv = 1.0/cut_lj_inner; + > cut_lj3 = cut_lj * cut_lj * cut_lj; + > cut_lj3inv = cut_ljinv * cut_ljinv * cut_ljinv; + > cut_lj_inner3inv = cut_lj_innerinv * cut_lj_innerinv * cut_lj_innerinv; + > cut_lj_inner3 = cut_lj_inner * cut_lj_inner * cut_lj_inner; + > cut_lj6 = cut_ljsq * cut_ljsq * cut_ljsq; + > cut_lj6inv = cut_lj3inv * cut_lj3inv; + > cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv; + > cut_lj_inner6 = cut_lj_innersq * cut_lj_innersq * cut_lj_innersq; + 709,711c770,773 + < denom_lj = ( (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * + < (cut_ljsq-cut_lj_innersq) ); + < denom_lj_inv = 1.0 / denom_lj; + --- + > denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * + > (cut_ljsq-cut_lj_innersq); + > denom_lj12 = 1.0/(cut_lj6 - cut_lj_inner6); + > denom_lj6 = 1.0/(cut_lj3 - cut_lj_inner3); + 718,730d779 + < cut_in_off = cut_respa[0]; + < cut_in_on = cut_respa[1]; + < cut_out_on = cut_respa[2]; + < cut_out_off = cut_respa[3]; + < + < cut_in_diff = cut_in_on - cut_in_off; + < cut_out_diff = cut_out_off - cut_out_on; + < cut_in_diff_inv = 1.0 / (cut_in_diff); + < cut_out_diff_inv = 1.0 / (cut_out_diff); + < cut_in_off_sq = cut_in_off*cut_in_off; + < cut_in_on_sq = cut_in_on*cut_in_on; + < cut_out_on_sq = cut_out_on*cut_out_on; + < cut_out_off_sq = cut_out_off*cut_out_off; + + */ + +template +void PairLJCharmmfswCoulLongKokkos::init_style() +{ + PairLJCharmmfswCoulLong::init_style(); + + Kokkos::deep_copy(d_cut_ljsq,cut_ljsq); + Kokkos::deep_copy(d_cut_coulsq,cut_coulsq); + + // error if rRESPA with inner levels + + if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { + int respa = 0; + if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; + if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + if (respa) + error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle"); + } + + // adjust neighbor list request for KOKKOS + + neighflag = lmp->kokkos->neighflag; + auto request = neighbor->find_request(this); + request->set_kokkos_host(std::is_same_v && + !std::is_same_v); + request->set_kokkos_device(std::is_same_v); + if (neighflag == FULL) request->enable_full(); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +template +double PairLJCharmmfswCoulLongKokkos::init_one(int i, int j) +{ + double cutone = PairLJCharmmfswCoulLong::init_one(i,j); + + k_params.h_view(i,j).lj1 = lj1[i][j]; + k_params.h_view(i,j).lj2 = lj2[i][j]; + k_params.h_view(i,j).lj3 = lj3[i][j]; + k_params.h_view(i,j).lj4 = lj4[i][j]; + //k_params.h_view(i,j).offset = offset[i][j]; + k_params.h_view(i,j).cut_ljsq = cut_ljsq; + k_params.h_view(i,j).cut_coulsq = cut_coulsq; + + k_params.h_view(j,i) = k_params.h_view(i,j); + if (i(); + k_params.template modify(); + + return cutone; +} + +namespace LAMMPS_NS { +template class PairLJCharmmfswCoulLongKokkos; +#ifdef LMP_KOKKOS_GPU +template class PairLJCharmmfswCoulLongKokkos; +#endif +} + + + + +/* + 80d105 + < memory->destroy(offset); + 598c650 + < void PairLJCharmmCoulLong::allocate() + --- + > void PairLJCharmmfswCoulLong::allocate() + 622d673 + < memory->create(offset,n+1,n+1,"pair:offset"); + 631c682 + < void PairLJCharmmCoulLong::settings(int narg, char **arg) + --- + > void PairLJCharmmfswCoulLong::settings(int narg, char **arg) + 645c696 + < void PairLJCharmmCoulLong::coeff(int narg, char **arg) + --- + > void PairLJCharmmfswCoulLong::coeff(int narg, char **arg) + 752c801 + < double PairLJCharmmCoulLong::init_one(int i, int j) + --- + > double PairLJCharmmfswCoulLong::init_one(int i, int j) + 790c839 + < void PairLJCharmmCoulLong::write_restart(FILE *fp) + --- + > void PairLJCharmmfswCoulLong::write_restart(FILE *fp) + 811c860 + < void PairLJCharmmCoulLong::read_restart(FILE *fp) + --- + > void PairLJCharmmfswCoulLong::read_restart(FILE *fp) + 842c891 + < void PairLJCharmmCoulLong::write_restart_settings(FILE *fp) + --- + > void PairLJCharmmfswCoulLong::write_restart_settings(FILE *fp) + 857c906 + < void PairLJCharmmCoulLong::read_restart_settings(FILE *fp) + --- + > void PairLJCharmmfswCoulLong::read_restart_settings(FILE *fp) + 882c931 + < void PairLJCharmmCoulLong::write_data(FILE *fp) + --- + > void PairLJCharmmfswCoulLong::write_data(FILE *fp) + 893c942 + < void PairLJCharmmCoulLong::write_data_all(FILE *fp) + --- + > void PairLJCharmmfswCoulLong::write_data_all(FILE *fp) + 903c952 + < double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype, + --- + > double PairLJCharmmfswCoulLong::single(int i, int j, int itype, int jtype, + 908,909c957,958 + < double r2inv,r6inv,r,grij,expm2,t,erfc,prefactor; + < double switch1,switch2,fraction,table,forcecoul,forcelj,phicoul,philj; + --- + > double r,rinv,r2inv,r3inv,r6inv,grij,expm2,t,erfc,prefactor; + > double switch1,fraction,table,forcecoul,forcelj,phicoul,philj,philj12,philj6; + 911a961,962 + > r = sqrt(rsq); + > rinv = 1.0/r; + 939c990,991 + < r6inv = r2inv*r2inv*r2inv; + --- + > r3inv = rinv*rinv*rinv; + > r6inv = r3inv*r3inv; + 943,947c995,996 + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < switch2 = 12.0*rsq * (cut_ljsq-rsq) * + < (rsq-cut_lj_innersq) * denom_lj_inv; + < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + < forcelj = forcelj*switch1 + philj*switch2; + --- + > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + > forcelj = forcelj*switch1; + 965d1013 + < philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); + 967,969c1015,1025 + < switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < philj *= switch1; + --- + > philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 * + > (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); + > philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 * + > (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); + > philj = philj12 + philj6; + > } else { + > philj12 = r6inv*lj3[itype][jtype]*r6inv - + > lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; + > philj6 = -lj4[itype][jtype]*r6inv + + > lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv; + > philj = philj12 + philj6; + 979c1035 + < void *PairLJCharmmCoulLong::extract(const char *str, int &dim) + --- + > void *PairLJCharmmfswCoulLong::extract(const char *str, int &dim) + 988a1045,1047 + > + > // info extracted by dihedral_charmmfsw + > + 989a1049,1051 + > if (strcmp(str,"cut_lj_inner") == 0) return (void *) &cut_lj_inner; + > if (strcmp(str,"cut_lj") == 0) return (void *) &cut_lj; + > if (strcmp(str,"dihedflag") == 0) return (void *) &dihedflag; + + + */ + +// nothing to do for all these, inherited from PairLJCharmmfswCoulLong + + + + +/* + + 226c257 + < void PairLJCharmmCoulLong::compute_inner() + --- + > void PairLJCharmmfswCoulLong::compute_inner() + 248a280,286 + > double cut_out_on = cut_respa[0]; + > double cut_out_off = cut_respa[1]; + > + > double cut_out_diff = cut_out_off - cut_out_on; + > double cut_out_on_sq = cut_out_on*cut_out_on; + > double cut_out_off_sq = cut_out_off*cut_out_off; + > + 284c322 + < rsw = (sqrt(rsq) - cut_out_on)*cut_out_diff_inv; + --- + > rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; + 303c341 + < void PairLJCharmmCoulLong::compute_middle() + --- + > void PairLJCharmmfswCoulLong::compute_middle() + 308c346 + < double philj,switch1,switch2; + --- + > double switch1; + 326a365,376 + > double cut_in_off = cut_respa[0]; + > double cut_in_on = cut_respa[1]; + > double cut_out_on = cut_respa[2]; + > double cut_out_off = cut_respa[3]; + > + > double cut_in_diff = cut_in_on - cut_in_off; + > double cut_out_diff = cut_out_off - cut_out_on; + > double cut_in_off_sq = cut_in_off*cut_in_off; + > double cut_in_on_sq = cut_in_on*cut_in_on; + > double cut_out_on_sq = cut_out_on*cut_out_on; + > double cut_out_off_sq = cut_out_off*cut_out_off; + > + 361,365c411,412 + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < switch2 = 12.0*rsq * (cut_ljsq-rsq) * + < (rsq-cut_lj_innersq) * denom_lj_inv; + < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + < forcelj = forcelj*switch1 + philj*switch2; + --- + > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + > forcelj = forcelj*switch1; + 370c417 + < rsw = (sqrt(rsq) - cut_in_off)*cut_in_diff_inv; + --- + > rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; + 374c421 + < rsw = (sqrt(rsq) - cut_out_on)*cut_out_diff_inv; + --- + > rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; + 393c440 + < void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag) + --- + > void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) + 396c443 + < double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + --- + > double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwl6,evdwl12,ecoul,fpair; + 398c445 + < double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; + --- + > double r,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; + 400c447 + < double philj,switch1,switch2; + --- + > double switch1; + 422a470,476 + > double cut_in_off = cut_respa[2]; + > double cut_in_on = cut_respa[3]; + > + > double cut_in_diff = cut_in_on - cut_in_off; + > double cut_in_off_sq = cut_in_off*cut_in_off; + > double cut_in_on_sq = cut_in_on*cut_in_on; + > + 448a503 + > r6inv = r2inv*r2inv*r2inv; + 489d543 + < r6inv = r2inv*r2inv*r2inv; + 493,497c547,548 + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < switch2 = 12.0*rsq * (cut_ljsq-rsq) * + < (rsq-cut_lj_innersq) * denom_lj_inv; + < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + < forcelj = forcelj*switch1 + philj*switch2; + --- + > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + > forcelj = forcelj*switch1; + 533d583 + < r6inv = r2inv*r2inv*r2inv; + 536,538c586,598 + < switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < evdwl *= switch1; + --- + > rinv = sqrt(r2inv); + > r3inv = r2inv*rinv; + > evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 * + > (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); + > evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 * + > (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); + > evdwl = evdwl12 + evdwl6; + > } else { + > evdwl12 = r6inv*lj3[itype][jtype]*r6inv - + > lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; + > evdwl6 = -lj4[itype][jtype]*r6inv + + > lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv; + > evdwl = evdwl12 + evdwl6; + 561d620 + < r6inv = r2inv*r2inv*r2inv; + 565,569c624,625 + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < switch2 = 12.0*rsq * (cut_ljsq-rsq) * + < (rsq-cut_lj_innersq) * denom_lj_inv; + < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + < forcelj = forcelj*switch1 + philj*switch2; + --- + > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + > forcelj = forcelj*switch1; + 572d627 + < r6inv = r2inv*r2inv*r2inv; + 576,580c631,632 + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < switch2 = 12.0*rsq * (cut_ljsq-rsq) * + < (rsq-cut_lj_innersq) * denom_lj_inv; + < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + < forcelj = forcelj*switch1 + philj*switch2; + --- + > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + > forcelj = forcelj*switch1; + + */ + +// kokkos doesnt support respa, so ignore compute_inner / compute_middle / compute_outer diff --git a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.h b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.h new file mode 100644 index 00000000000..e9a6b5486f9 --- /dev/null +++ b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.h @@ -0,0 +1,230 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + + *** DRAFT VERSION 1 (lots of comments to be removed just before merge) *** + + (1) first draft version of PairLJCharmmfswCoulLongKokkos exactly + same as PairLJCharmmCoulLongKokkos but with new class name + + method: track changes from serial kspace pair_lj_charmm_coul_long to + pair_lj_charmmfsw_coul_long and apply to PairLJCharmmfswCoulLongKokkos + + % diff pair_lj_charmm_coul_long.h pair_lj_charmmfsw_coul_long.h + + +------------------------------------------------------------------------- */ + +/* + 16c16 + < PairStyle(lj/charmm/coul/long,PairLJCharmmCoulLong); + --- + > PairStyle(lj/charmmfsw/coul/long,PairLJCharmmfswCoulLong); + + */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(lj/charmmfsw/coul/long/kk,PairLJCharmmfswCoulLongKokkos); +PairStyle(lj/charmmfsw/coul/long/kk/device,PairLJCharmmfswCoulLongKokkos); +PairStyle(lj/charmmfsw/coul/long/kk/host,PairLJCharmmfswCoulLongKokkos); +// clang-format on +#else + +/* + + 20,21c20,21 + < #ifndef LMP_PAIR_LJ_CHARMM_COUL_LONG_H + < #define LMP_PAIR_LJ_CHARMM_COUL_LONG_H + --- + > #ifndef LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_H + > #define LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_H + + */ + +// clang-format off +#ifndef LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_KOKKOS_H +#define LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_KOKKOS_H + +#include "pair_kokkos.h" +#include "pair_lj_charmmfsw_coul_long.h" +#include "neigh_list_kokkos.h" + +namespace LAMMPS_NS { + +/* + + 27c27 +< class PairLJCharmmCoulLong : public Pair { +--- +> class PairLJCharmmfswCoulLong : public Pair { + + */ + +template +class PairLJCharmmfswCoulLongKokkos : public PairLJCharmmfswCoulLong { + public: + enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF}; + enum {COUL_FLAG=1}; + typedef DeviceType device_type; + typedef ArrayTypes AT; + + /* + + 29,30c29,30 + < PairLJCharmmCoulLong(class LAMMPS *); + < ~PairLJCharmmCoulLong() override; + --- + > PairLJCharmmfswCoulLong(class LAMMPS *); + > ~PairLJCharmmfswCoulLong() override; + + */ + + PairLJCharmmfswCoulLongKokkos(class LAMMPS *); + ~PairLJCharmmfswCoulLongKokkos() override; + + void compute(int, int) override; + + void init_tables(double cut_coul, double *cut_respa) override; + void init_style() override; + double init_one(int, int) override; + + protected: + + /* + 52c52,54 + < double cut_lj_inner, cut_lj; + --- + > int dihedflag; + > + > double cut_lj_inner, cut_lj, cut_ljinv, cut_lj_innerinv; + 53a56,57 + > double cut_lj3inv, cut_lj_inner3inv, cut_lj3, cut_lj_inner3; + > double cut_lj6inv, cut_lj_inner6inv, cut_lj6, cut_lj_inner6; + 56,60c60 + < double cut_in_off, cut_in_on, cut_out_off, cut_out_on; + < double cut_in_diff, cut_out_diff; + < double cut_in_diff_inv, cut_out_diff_inv; + < double cut_in_off_sq, cut_in_on_sq, cut_out_off_sq, cut_out_on_sq; + < double denom_lj, denom_lj_inv; + --- + > double denom_lj, denom_lj12, denom_lj6; + + */ + + // almost nothing to do here, inherited from PairLJCharmmfswCoulLong + // only temporarily need cut_lj_innersq, denom_coul protected variables + // (removed from pair_lj_charmm_coul_long to pair_lj_charmmfsw_coul_long) + // to compile draft version 1, can be removed by draft version 2 + + + + template + KOKKOS_INLINE_FUNCTION + F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, + const int& itype, const int& jtype) const; + + template + KOKKOS_INLINE_FUNCTION + F_FLOAT compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, + const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const; + + template + KOKKOS_INLINE_FUNCTION + F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, + const int& itype, const int& jtype) const; + + template + KOKKOS_INLINE_FUNCTION + F_FLOAT compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j, + const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const; + + Kokkos::DualView k_params; + typename Kokkos::DualView::t_dev_const_um params; + // hardwired to space for 12 atom types + params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; + + F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; + F_FLOAT m_cut_ljsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; + F_FLOAT m_cut_coulsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; + typename AT::t_x_array_randomread x; + typename AT::t_x_array c_x; + typename AT::t_f_array f; + typename AT::t_int_1d_randomread type; + typename AT::t_float_1d_randomread q; + + DAT::tdual_efloat_1d k_eatom; + DAT::tdual_virial_array k_vatom; + typename AT::t_efloat_1d d_eatom; + typename AT::t_virial_array d_vatom; + + int newton_pair; + + typename AT::tdual_ffloat_2d k_cutsq; + typename AT::t_ffloat_2d d_cutsq; + typename AT::t_ffloat_2d d_cut_ljsq; + typename AT::t_ffloat_2d d_cut_coulsq; + + typename AT::t_ffloat_1d_randomread + d_rtable, d_drtable, d_ftable, d_dftable, + d_ctable, d_dctable, d_etable, d_detable; + + int neighflag; + int nlocal,nall,eflag,vflag; + + double special_coul[4]; + double special_lj[4]; + double qqrd2e; + + void allocate() override; + + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend EV_FLOAT pair_compute_neighlist>(PairLJCharmmfswCoulLongKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist>(PairLJCharmmfswCoulLongKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist>(PairLJCharmmfswCoulLongKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist>(PairLJCharmmfswCoulLongKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute>(PairLJCharmmfswCoulLongKokkos*, + NeighListKokkos*); + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend struct PairComputeFunctor>; + friend EV_FLOAT pair_compute_neighlist>(PairLJCharmmfswCoulLongKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist>(PairLJCharmmfswCoulLongKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist>(PairLJCharmmfswCoulLongKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist>(PairLJCharmmfswCoulLongKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute>(PairLJCharmmfswCoulLongKokkos*, + NeighListKokkos*); + friend void pair_virial_fdotr_compute(PairLJCharmmfswCoulLongKokkos*); + +}; + +} + +#endif +#endif + From 3a1d3bb64d604f48e76a930e88eefd9de062b472 Mon Sep 17 00:00:00 2001 From: Mitch Murphy Date: Wed, 3 Jan 2024 02:42:15 -0500 Subject: [PATCH 104/719] second draft... applied changes to compute methods --- src/KOKKOS/dihedral_charmmfsw_kokkos.cpp | 95 ++++---- src/KOKKOS/dihedral_charmmfsw_kokkos.h | 26 +-- .../pair_lj_charmmfsw_coul_long_kokkos.cpp | 206 +++++++++--------- 3 files changed, 168 insertions(+), 159 deletions(-) diff --git a/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp b/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp index facb7235808..b309f3d97f6 100644 --- a/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp @@ -18,7 +18,7 @@ - Stan Moore (SNL) original DihedralCharmmfswKokkos - - Mitch Murphy (alphataubio) - DihedralCharmmfswKokkos update (2023/12) + - Mitch Murphy (alphataubio) - DihedralCharmmfswKokkos update (2024/01) Based on serial dihedral_charmmfsw.cpp lj-fsw sections (force-switched) provided by Robert Meissner and Lucio Colombi Ciacchi of Bremen @@ -138,21 +138,7 @@ DihedralCharmmfswKokkos::~DihedralCharmmfswKokkos() 259a269,270 > else > forcecoul = qqrd2e * q[i1] * q[i4] * (sqrt(r2inv) - r * cut_coulinv14 * cut_coulinv14); - 264,265c275,284 - < ecoul = weight[type] * forcecoul; - < evdwl = r6inv * (lj14_3[itype][jtype] * r6inv - lj14_4[itype][jtype]); - --- - > if (dihedflag) - > ecoul = weight[type] * forcecoul; - > else - > ecoul = weight[type] * qqrd2e * q[i1] * q[i4] * - > (sqrt(r2inv) + r * cut_coulinv14 * cut_coulinv14 - 2.0 * cut_coulinv14); - > evdwl14_12 = r6inv * lj14_3[itype][jtype] * r6inv - - > lj14_3[itype][jtype] * cut_lj_inner6inv * cut_lj6inv; - > evdwl14_6 = - > -lj14_4[itype][jtype] * r6inv + lj14_4[itype][jtype] * cut_lj_inner3inv * cut_lj3inv; - > evdwl = evdwl14_12 + evdwl14_6; - + */ @@ -225,15 +211,15 @@ void DihedralCharmmfswKokkos::compute(int eflag_in, int vflag_in) if (evflag) { if (newton_bond) { - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ndihedrallist),*this,evm); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ndihedrallist),*this,evm); } else { - Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ndihedrallist),*this,evm); + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ndihedrallist),*this,evm); } } else { if (newton_bond) { - Kokkos::parallel_for(Kokkos::RangePolicy >(0,ndihedrallist),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ndihedrallist),*this); } else { - Kokkos::parallel_for(Kokkos::RangePolicy >(0,ndihedrallist),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ndihedrallist),*this); } } @@ -303,7 +289,7 @@ void DihedralCharmmfswKokkos::compute(int eflag_in, int vflag_in) template template KOKKOS_INLINE_FUNCTION -void DihedralCharmmfswKokkos::operator()(TagDihedralCharmmCompute, const int &n, EVM_FLOAT& evm) const { +void DihedralCharmmfswKokkos::operator()(TagDihedralCharmmfswCompute, const int &n, EVM_FLOAT& evm) const { // The f array is atomic Kokkos::View::value,Kokkos::MemoryTraits > a_f = f; @@ -480,11 +466,38 @@ void DihedralCharmmfswKokkos::operator()(TagDihedralCharmmCompute if (dihedflag) + > ecoul = weight[type] * forcecoul; + > else + > ecoul = weight[type] * qqrd2e * q[i1] * q[i4] * + > (sqrt(r2inv) + r * cut_coulinv14 * cut_coulinv14 - 2.0 * cut_coulinv14); + > evdwl14_12 = r6inv * lj14_3[itype][jtype] * r6inv - + > lj14_3[itype][jtype] * cut_lj_inner6inv * cut_lj6inv; + > evdwl14_6 = + > -lj14_4[itype][jtype] * r6inv + lj14_4[itype][jtype] * cut_lj_inner3inv * cut_lj3inv; + > evdwl = evdwl14_12 + evdwl14_6; + */ + + const F_FLOAT r = sqrt(rsq); F_FLOAT ecoul = 0.0; F_FLOAT evdwl = 0.0; + F_FLOAT evdwl14_12, evdwl14_6; if (eflag) { - ecoul = d_weight[type] * forcecoul; - evdwl = r6inv * (d_lj14_3(itype,jtype)*r6inv - d_lj14_4(itype,jtype)); + if (dihedflag) + ecoul = d_weight[type] * forcecoul; + else + ecoul = d_weight[type] * qqrd2e * q[i1] * q[i4] * + (sqrt(r2inv) + r * cut_coulinv14 * cut_coulinv14 - 2.0 * cut_coulinv14); + evdwl14_12 = r6inv * d_lj14_3(itype,jtype) * r6inv - + d_lj14_3(itype,jtype) * cut_lj_inner6inv * cut_lj6inv; + evdwl14_6 = + -d_lj14_4(itype,jtype) * r6inv + d_lj14_4(itype,jtype) * cut_lj_inner3inv * cut_lj3inv; + evdwl = evdwl14_12 + evdwl14_6; evdwl *= d_weight[type]; } @@ -506,9 +519,9 @@ void DihedralCharmmfswKokkos::operator()(TagDihedralCharmmCompute template KOKKOS_INLINE_FUNCTION -void DihedralCharmmfswKokkos::operator()(TagDihedralCharmmCompute, const int &n) const { +void DihedralCharmmfswKokkos::operator()(TagDihedralCharmmfswCompute, const int &n) const { EVM_FLOAT evm; - this->template operator()(TagDihedralCharmmCompute(), n, evm); + this->template operator()(TagDihedralCharmmfswCompute(), n, evm); } /* ---------------------------------------------------------------------- */ @@ -547,12 +560,12 @@ void DihedralCharmmfswKokkos::coeff(int narg, char **arg) DihedralCharmmfsw::coeff(narg, arg); int nd = atom->ndihedraltypes; - typename AT::tdual_ffloat_1d k_k("DihedralCharmm::k",nd+1); - typename AT::tdual_ffloat_1d k_multiplicity("DihedralCharmm::multiplicity",nd+1); - typename AT::tdual_ffloat_1d k_shift("DihedralCharmm::shift",nd+1); - typename AT::tdual_ffloat_1d k_cos_shift("DihedralCharmm::cos_shift",nd+1); - typename AT::tdual_ffloat_1d k_sin_shift("DihedralCharmm::sin_shift",nd+1); - typename AT::tdual_ffloat_1d k_weight("DihedralCharmm::weight",nd+1); + typename AT::tdual_ffloat_1d k_k("DihedralCharmmfsw::k",nd+1); + typename AT::tdual_ffloat_1d k_multiplicity("DihedralCharmmfsw::multiplicity",nd+1); + typename AT::tdual_ffloat_1d k_shift("DihedralCharmmfsw::shift",nd+1); + typename AT::tdual_ffloat_1d k_cos_shift("DihedralCharmmfsw::cos_shift",nd+1); + typename AT::tdual_ffloat_1d k_sin_shift("DihedralCharmmfsw::sin_shift",nd+1); + typename AT::tdual_ffloat_1d k_weight("DihedralCharmmfsw::weight",nd+1); d_k = k_k.template view(); d_multiplicity = k_multiplicity.template view(); @@ -630,10 +643,10 @@ void DihedralCharmmfswKokkos::init_style() DihedralCharmmfsw::init_style(); int n = atom->ntypes; - DAT::tdual_ffloat_2d k_lj14_1("DihedralCharmm:lj14_1",n+1,n+1); - DAT::tdual_ffloat_2d k_lj14_2("DihedralCharmm:lj14_2",n+1,n+1); - DAT::tdual_ffloat_2d k_lj14_3("DihedralCharmm:lj14_3",n+1,n+1); - DAT::tdual_ffloat_2d k_lj14_4("DihedralCharmm:lj14_4",n+1,n+1); + DAT::tdual_ffloat_2d k_lj14_1("DihedralCharmmfsw:lj14_1",n+1,n+1); + DAT::tdual_ffloat_2d k_lj14_2("DihedralCharmmfsw:lj14_2",n+1,n+1); + DAT::tdual_ffloat_2d k_lj14_3("DihedralCharmmfsw:lj14_3",n+1,n+1); + DAT::tdual_ffloat_2d k_lj14_4("DihedralCharmmfsw:lj14_4",n+1,n+1); d_lj14_1 = k_lj14_1.template view(); d_lj14_2 = k_lj14_2.template view(); @@ -682,12 +695,12 @@ void DihedralCharmmfswKokkos::read_restart(FILE *fp) DihedralCharmmfsw::read_restart(fp); int nd = atom->ndihedraltypes; - typename AT::tdual_ffloat_1d k_k("DihedralCharmm::k",nd+1); - typename AT::tdual_ffloat_1d k_multiplicity("DihedralCharmm::multiplicity",nd+1); - typename AT::tdual_ffloat_1d k_shift("DihedralCharmm::shift",nd+1); - typename AT::tdual_ffloat_1d k_cos_shift("DihedralCharmm::cos_shift",nd+1); - typename AT::tdual_ffloat_1d k_sin_shift("DihedralCharmm::sin_shift",nd+1); - typename AT::tdual_ffloat_1d k_weight("DihedralCharmm::weight",nd+1); + typename AT::tdual_ffloat_1d k_k("DihedralCharmmfsw::k",nd+1); + typename AT::tdual_ffloat_1d k_multiplicity("DihedralCharmmfsw::multiplicity",nd+1); + typename AT::tdual_ffloat_1d k_shift("DihedralCharmmfsw::shift",nd+1); + typename AT::tdual_ffloat_1d k_cos_shift("DihedralCharmmfsw::cos_shift",nd+1); + typename AT::tdual_ffloat_1d k_sin_shift("DihedralCharmmfsw::sin_shift",nd+1); + typename AT::tdual_ffloat_1d k_weight("DihedralCharmmfsw::weight",nd+1); d_k = k_k.template view(); d_multiplicity = k_multiplicity.template view(); diff --git a/src/KOKKOS/dihedral_charmmfsw_kokkos.h b/src/KOKKOS/dihedral_charmmfsw_kokkos.h index 413945826f9..8b57b28d0cd 100644 --- a/src/KOKKOS/dihedral_charmmfsw_kokkos.h +++ b/src/KOKKOS/dihedral_charmmfsw_kokkos.h @@ -78,14 +78,6 @@ DihedralStyle(charmmfsw/kk/host,DihedralCharmmfswKokkos); /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:31:8: note: previous definition is here struct s_EVM_FLOAT { ^ - In file included from /Users/mitch/Dropbox/lammps/lammps/src/force.cpp:18: - In file included from /Users/mitch/Dropbox/lammps/lammps/build/styles/style_dihedral.h:4: - /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmmfsw_kokkos.h:104:8: error: redefinition of 'TagDihedralCharmmCompute' - struct TagDihedralCharmmCompute{}; - ^ - /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:70:8: note: previous definition is here - struct TagDihedralCharmmCompute{}; - ^ In file included from /Users/mitch/Dropbox/lammps/lammps/src/lammps.cpp:23: In file included from /Users/mitch/Dropbox/lammps/lammps/build/styles/style_dihedral.h:4: /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmmfsw_kokkos.h:65:8: error: redefinition of 's_EVM_FLOAT' @@ -94,14 +86,6 @@ DihedralStyle(charmmfsw/kk/host,DihedralCharmmfswKokkos); /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:31:8: note: previous definition is here struct s_EVM_FLOAT { ^ - In file included from /Users/mitch/Dropbox/lammps/lammps/src/lammps.cpp:23: - In file included from /Users/mitch/Dropbox/lammps/lammps/build/styles/style_dihedral.h:4: - /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmmfsw_kokkos.h:104:8: error: redefinition of 'TagDihedralCharmmCompute' - struct TagDihedralCharmmCompute{}; - ^ - /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:70:8: note: previous definition is here - struct TagDihedralCharmmCompute{}; - ^ */ @@ -146,10 +130,12 @@ struct s_EVM_FLOAT { }; typedef struct s_EVM_FLOAT EVM_FLOAT; + */ + template -struct TagDihedralCharmmCompute{}; +struct TagDihedralCharmmfswCompute{}; + -*/ /* 27c27 @@ -181,11 +167,11 @@ class DihedralCharmmfswKokkos : public DihedralCharmmfsw { template KOKKOS_INLINE_FUNCTION - void operator()(TagDihedralCharmmCompute, const int&, EVM_FLOAT&) const; + void operator()(TagDihedralCharmmfswCompute, const int&, EVM_FLOAT&) const; template KOKKOS_INLINE_FUNCTION - void operator()(TagDihedralCharmmCompute, const int&) const; + void operator()(TagDihedralCharmmfswCompute, const int&) const; //template KOKKOS_INLINE_FUNCTION diff --git a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp index 88efec5fda4..7c1da2479ff 100644 --- a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp @@ -18,7 +18,7 @@ - Ray Shan (SNL) - original PairLJCharmmCoulLongKokkos - - Mitch Murphy (alphataubio) - PairLJCharmmfswCoulLongKokkos update (2023/12) + - Mitch Murphy (alphataubio) - PairLJCharmmfswCoulLongKokkos update (2024/01) Based on serial kspace lj-fsw sections (force-switched) provided by Robert Meissner and Lucio Colombi Ciacchi of Bremen University, Germany, @@ -113,9 +113,6 @@ using namespace LAMMPS_NS; template PairLJCharmmfswCoulLongKokkos::PairLJCharmmfswCoulLongKokkos(LAMMPS *lmp):PairLJCharmmfswCoulLong(lmp) { - - // pair_lj_charmmfsw_coul_long_kokkos.cpp:112:28: error: qualified reference to 'PairLJCharmmfswCoulLong' is a constructor name rather than a type in this context - // ??? PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(lmp); respa_enable = 0; @@ -147,15 +144,10 @@ PairLJCharmmfswCoulLongKokkos::PairLJCharmmfswCoulLongKokkos(LAMMPS */ -// added superclass constructor to inherit from PairLJCharmmfswCoulLong - template PairLJCharmmfswCoulLongKokkos::~PairLJCharmmfswCoulLongKokkos() { - // pair_lj_charmmfsw_coul_long_kokkos.cpp:150:28: error: qualified reference to 'PairLJCharmmfswCoulLong' is a constructor name rather than a type in this context - // ??? PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(); - if (copymode) return; if (allocated) { @@ -186,39 +178,7 @@ PairLJCharmmfswCoulLongKokkos::~PairLJCharmmfswCoulLongKokkos() > double switch1; 96d120 < double rsq; - 174,179c198,200 - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < switch2 = 12.0*rsq * (cut_ljsq-rsq) * - < (rsq-cut_lj_innersq) * denom_lj_inv; - < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); - < forcelj = forcelj*switch1 + philj*switch2; - < } - --- - > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; - > forcelj = forcelj*switch1; - > } - 205d225 - < evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); - 207,209c227,240 - < switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < evdwl *= switch1; - --- - > r = sqrt(rsq); - > rinv = 1.0/r; - > r3inv = rinv*rinv*rinv; - > evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 * - > (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); - > evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 * - > (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); - > evdwl = evdwl12 + evdwl6; - > } else { - > evdwl12 = r6inv*lj3[itype][jtype]*r6inv - - > lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; - > evdwl6 = -lj4[itype][jtype]*r6inv + - > lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv; - > evdwl = evdwl12 + evdwl6; - + */ template @@ -320,20 +280,32 @@ compute_fpair(const F_FLOAT& rsq, const int& /*i*/, const int& /*j*/, const int& itype, const int& jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT r6inv = r2inv*r2inv*r2inv; - F_FLOAT forcelj, switch1, switch2, englj; + F_FLOAT forcelj, switch1; forcelj = r6inv * ((STACKPARAMS?m_params[itype][jtype].lj1:params(itype,jtype).lj1)*r6inv - (STACKPARAMS?m_params[itype][jtype].lj2:params(itype,jtype).lj2)); if (rsq > cut_lj_innersq) { + + /* + 174,179c198,200 + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < switch2 = 12.0*rsq * (cut_ljsq-rsq) * + < (rsq-cut_lj_innersq) * denom_lj_inv; + < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + < forcelj = forcelj*switch1 + philj*switch2; + < } + --- + > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + > forcelj = forcelj*switch1; + > } + + */ + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; - switch2 = 12.0*rsq * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj; - englj = r6inv * - ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv - - (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)); - forcelj = forcelj*switch1 + englj*switch2; + forcelj = forcelj*switch1; } return forcelj*r2inv; @@ -350,20 +322,52 @@ compute_evdwl(const F_FLOAT& rsq, const int& /*i*/, const int& /*j*/, const int& itype, const int& jtype) const { const F_FLOAT r2inv = 1.0/rsq; const F_FLOAT r6inv = r2inv*r2inv*r2inv; - F_FLOAT englj, switch1; + const F_FLOAT r = sqrt(rsq); + const F_FLOAT rinv = 1.0/r; + const F_FLOAT r3inv = rinv*rinv*rinv; + F_FLOAT englj, englj12, englj6; + + /* + 205d225 + < evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); + 207,209c227,240 + < switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; + < evdwl *= switch1; + --- + > r = sqrt(rsq); + > rinv = 1.0/r; + > r3inv = rinv*rinv*rinv; + > evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 * + > (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); + > evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 * + > (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); + > evdwl = evdwl12 + evdwl6; + > } else { + > evdwl12 = r6inv*lj3[itype][jtype]*r6inv - + > lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; + > evdwl6 = -lj4[itype][jtype]*r6inv + + > lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv; + > evdwl = evdwl12 + evdwl6; + + */ - englj = r6inv * - ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv - - (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)); if (rsq > cut_lj_innersq) { - switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * - (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; - englj *= switch1; + englj12 = (STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*cut_lj6* + denom_lj12 * (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); + englj6 = -(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)* + cut_lj3*denom_lj6 * (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); + englj = englj12 + englj6; + } else { + englj12 = r6inv*lj3[itype][jtype]*r6inv - + lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; + englj6 = -(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)*r6inv + + (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)* + cut_lj_inner3inv*cut_lj3inv; + englj = englj12 + englj6; } - return englj; - } /* ---------------------------------------------------------------------- @@ -458,7 +462,7 @@ void PairLJCharmmfswCoulLongKokkos::allocate() d_cut_coulsq = typename AT::t_ffloat_2d("pair:cut_coulsq",n+1,n+1); - k_params = Kokkos::DualView("PairLJCharmmCoulLong::params",n+1,n+1); + k_params = Kokkos::DualView("PairLJCharmmfswCoulLong::params",n+1,n+1); params = k_params.template view(); } @@ -574,49 +578,11 @@ void PairLJCharmmfswCoulLongKokkos::init_tables(double cut_coul, dou < void PairLJCharmmCoulLong::init_style() --- > void PairLJCharmmfswCoulLong::init_style() - 686c737 - < "Pair style lj/charmm/coul/long requires atom attribute q"); - --- - > "Pair style lj/charmmfsw/coul/long requires atom attribute q"); - 688c739 + 688c739 < // request regular or rRESPA neighbor list --- > // request regular or rRESPA neighbor lists - 705a757,766 - > cut_ljinv = 1.0/cut_lj; - > cut_lj_innerinv = 1.0/cut_lj_inner; - > cut_lj3 = cut_lj * cut_lj * cut_lj; - > cut_lj3inv = cut_ljinv * cut_ljinv * cut_ljinv; - > cut_lj_inner3inv = cut_lj_innerinv * cut_lj_innerinv * cut_lj_innerinv; - > cut_lj_inner3 = cut_lj_inner * cut_lj_inner * cut_lj_inner; - > cut_lj6 = cut_ljsq * cut_ljsq * cut_ljsq; - > cut_lj6inv = cut_lj3inv * cut_lj3inv; - > cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv; - > cut_lj_inner6 = cut_lj_innersq * cut_lj_innersq * cut_lj_innersq; - 709,711c770,773 - < denom_lj = ( (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * - < (cut_ljsq-cut_lj_innersq) ); - < denom_lj_inv = 1.0 / denom_lj; - --- - > denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * - > (cut_ljsq-cut_lj_innersq); - > denom_lj12 = 1.0/(cut_lj6 - cut_lj_inner6); - > denom_lj6 = 1.0/(cut_lj3 - cut_lj_inner3); - 718,730d779 - < cut_in_off = cut_respa[0]; - < cut_in_on = cut_respa[1]; - < cut_out_on = cut_respa[2]; - < cut_out_off = cut_respa[3]; - < - < cut_in_diff = cut_in_on - cut_in_off; - < cut_out_diff = cut_out_off - cut_out_on; - < cut_in_diff_inv = 1.0 / (cut_in_diff); - < cut_out_diff_inv = 1.0 / (cut_out_diff); - < cut_in_off_sq = cut_in_off*cut_in_off; - < cut_in_on_sq = cut_in_on*cut_in_on; - < cut_out_on_sq = cut_out_on*cut_out_on; - < cut_out_off_sq = cut_out_off*cut_out_off; - + */ template @@ -689,6 +655,8 @@ template class PairLJCharmmfswCoulLongKokkos; + + /* 80d105 < memory->destroy(offset); @@ -706,6 +674,48 @@ template class PairLJCharmmfswCoulLongKokkos; < void PairLJCharmmCoulLong::coeff(int narg, char **arg) --- > void PairLJCharmmfswCoulLong::coeff(int narg, char **arg) + + 686c737 + < "Pair style lj/charmm/coul/long requires atom attribute q"); + --- + > "Pair style lj/charmmfsw/coul/long requires atom attribute q"); + + 705a757,766 + > cut_ljinv = 1.0/cut_lj; + > cut_lj_innerinv = 1.0/cut_lj_inner; + > cut_lj3 = cut_lj * cut_lj * cut_lj; + > cut_lj3inv = cut_ljinv * cut_ljinv * cut_ljinv; + > cut_lj_inner3inv = cut_lj_innerinv * cut_lj_innerinv * cut_lj_innerinv; + > cut_lj_inner3 = cut_lj_inner * cut_lj_inner * cut_lj_inner; + > cut_lj6 = cut_ljsq * cut_ljsq * cut_ljsq; + > cut_lj6inv = cut_lj3inv * cut_lj3inv; + > cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv; + > cut_lj_inner6 = cut_lj_innersq * cut_lj_innersq * cut_lj_innersq; + 709,711c770,773 + < denom_lj = ( (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * + < (cut_ljsq-cut_lj_innersq) ); + < denom_lj_inv = 1.0 / denom_lj; + --- + > denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * + > (cut_ljsq-cut_lj_innersq); + > denom_lj12 = 1.0/(cut_lj6 - cut_lj_inner6); + > denom_lj6 = 1.0/(cut_lj3 - cut_lj_inner3); + 718,730d779 + < cut_in_off = cut_respa[0]; + < cut_in_on = cut_respa[1]; + < cut_out_on = cut_respa[2]; + < cut_out_off = cut_respa[3]; + < + < cut_in_diff = cut_in_on - cut_in_off; + < cut_out_diff = cut_out_off - cut_out_on; + < cut_in_diff_inv = 1.0 / (cut_in_diff); + < cut_out_diff_inv = 1.0 / (cut_out_diff); + < cut_in_off_sq = cut_in_off*cut_in_off; + < cut_in_on_sq = cut_in_on*cut_in_on; + < cut_out_on_sq = cut_out_on*cut_out_on; + < cut_out_off_sq = cut_out_off*cut_out_off; + + 752c801 < double PairLJCharmmCoulLong::init_one(int i, int j) --- From 163805bc33176f58f9ed579f2fac2f7ed8734ce2 Mon Sep 17 00:00:00 2001 From: Mitch Murphy Date: Wed, 3 Jan 2024 15:18:34 -0500 Subject: [PATCH 105/719] removed scaffolding comments and fixed "(STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)" in compute_evdwl --- src/KOKKOS/dihedral_charmmfsw_kokkos.cpp | 117 ----- src/KOKKOS/dihedral_charmmfsw_kokkos.h | 138 +----- .../pair_lj_charmmfsw_coul_long_kokkos.cpp | 450 +----------------- .../pair_lj_charmmfsw_coul_long_kokkos.h | 84 +--- 4 files changed, 7 insertions(+), 782 deletions(-) diff --git a/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp b/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp index b309f3d97f6..831e7d9b229 100644 --- a/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmmfsw_kokkos.cpp @@ -27,29 +27,6 @@ ------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - - *** DRAFT VERSION 1 (lots of comments to be removed just before merge) *** - - (1) first draft version of DihedralCharmmfswKokkos exactly - same as DihedralCharmmfswKokkos but with new class name - - method: track changes from serial kspace dihedral_charmm to - dihedral_charmmfsw and apply to DihedralCharmmfswKokkos - - % diff dihedral_charmm.cpp dihedral_charmmfsw.cpp - -------------------------------------------------------------------------- */ - -/* - 18c21 - < #include "dihedral_charmm.h" - --- - > #include "dihedral_charmmfsw.h" - - */ - #include "dihedral_charmmfsw_kokkos.h" #include "atom_kokkos.h" @@ -526,15 +503,6 @@ void DihedralCharmmfswKokkos::operator()(TagDihedralCharmmfswCompute /* ---------------------------------------------------------------------- */ -/* - - 288c307 - < void DihedralCharmm::allocate() - --- - > void DihedralCharmmfsw::allocate() - - */ - template void DihedralCharmmfswKokkos::allocate() { @@ -545,15 +513,6 @@ void DihedralCharmmfswKokkos::allocate() set coeffs for one or more types ------------------------------------------------------------------------- */ -/* - - 308c327 - < void DihedralCharmm::coeff(int narg, char **arg) - --- - > void DihedralCharmmfsw::coeff(int narg, char **arg) - - */ - template void DihedralCharmmfswKokkos::coeff(int narg, char **arg) { @@ -603,40 +562,6 @@ void DihedralCharmmfswKokkos::coeff(int narg, char **arg) error check and initialize all values needed for force computation ------------------------------------------------------------------------- */ -/* - - 350c369 - < void DihedralCharmm::init_style() - --- - > void DihedralCharmmfsw::init_style() - 382a402,425 - > - > // constants for applying force switch (LJ) and force_shift (coul) - > // to 1/4 dihedral atoms to match CHARMM pairwise interactions - > - > int itmp; - > int *p_dihedflag = (int *) force->pair->extract("dihedflag", itmp); - > auto p_cutljinner = (double *) force->pair->extract("cut_lj_inner", itmp); - > auto p_cutlj = (double *) force->pair->extract("cut_lj", itmp); - > auto p_cutcoul = (double *) force->pair->extract("cut_coul", itmp); - > - > if (p_cutcoul == nullptr || p_cutljinner == nullptr || p_cutlj == nullptr || - > p_dihedflag == nullptr) - > error->all(FLERR, "Dihedral charmmfsw is incompatible with Pair style"); - > - > dihedflag = *p_dihedflag; - > cut_coul14 = *p_cutcoul; - > cut_lj_inner14 = *p_cutljinner; - > cut_lj14 = *p_cutlj; - > - > cut_coulinv14 = 1 / cut_coul14; - > cut_lj_inner3inv = (1 / cut_lj_inner14) * (1 / cut_lj_inner14) * (1 / cut_lj_inner14); - > cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv; - > cut_lj3inv = (1 / cut_lj14) * (1 / cut_lj14) * (1 / cut_lj14); - > cut_lj6inv = cut_lj3inv * cut_lj3inv; - - */ - template void DihedralCharmmfswKokkos::init_style() { @@ -681,14 +606,6 @@ void DihedralCharmmfswKokkos::init_style() proc 0 reads coeffs from restart file, bcasts them ------------------------------------------------------------------------- */ -/* - - 402c445 - < void DihedralCharmm::read_restart(FILE *fp) - --- - > void DihedralCharmmfsw::read_restart(FILE *fp) - - */ template void DihedralCharmmfswKokkos::read_restart(FILE *fp) { @@ -968,37 +885,3 @@ template class DihedralCharmmfswKokkos; #endif } - - -/* - - - 355c374 - < error->all(FLERR, "Dihedral style charmm must be set to same r-RESPA level as 'pair'"); - --- - > error->all(FLERR, "Dihedral style charmmfsw must be set to same r-RESPA level as 'pair'"); - 357c376 - < error->all(FLERR, "Dihedral style charmm must be set to same r-RESPA level as 'outer'"); - --- - > error->all(FLERR, "Dihedral style charmmfsw must be set to same r-RESPA level as 'outer'"); - 373c392 - < error->all(FLERR, "Dihedral charmm is incompatible with Pair style"); - --- - > error->all(FLERR, "Dihedral charmmfsw is incompatible with Pair style"); - 380c399 - < error->all(FLERR, "Dihedral charmm is incompatible with Pair style"); - --- - > error->all(FLERR, "Dihedral charmmfsw is incompatible with Pair style"); - - 389c432 - < void DihedralCharmm::write_restart(FILE *fp) - --- - > void DihedralCharmmfsw::write_restart(FILE *fp) - 430c473 - < void DihedralCharmm::write_data(FILE *fp) - --- - > void DihedralCharmmfsw::write_data(FILE *fp) - - */ - -// nothing to do for all these, inherited from DihedralCharmmfsw diff --git a/src/KOKKOS/dihedral_charmmfsw_kokkos.h b/src/KOKKOS/dihedral_charmmfsw_kokkos.h index 8b57b28d0cd..c3842ca01d9 100644 --- a/src/KOKKOS/dihedral_charmmfsw_kokkos.h +++ b/src/KOKKOS/dihedral_charmmfsw_kokkos.h @@ -11,31 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - - *** DRAFT VERSION 1 (lots of comments to be removed just before merge) *** - - (1) first draft version of DihedralCharmmfswKokkos exactly - same as DihedralCharmmKokkos but with new class name - - (2) second draft version: nothing changed in header file - - method: track changes from serial kspace dihedral_charmm to - dihedral_charmmfsw and apply to DihedralCharmmKokkos - - % diff dihedral_charmm.h dihedral_charmmfsw.h - -------------------------------------------------------------------------- */ - -/* - - 16c16 - < DihedralStyle(charmm,DihedralCharmm); - --- - > DihedralStyle(charmmfsw,DihedralCharmmfsw); - - */ - #ifdef DIHEDRAL_CLASS // clang-format off DihedralStyle(charmmfsw/kk,DihedralCharmmfswKokkos); @@ -44,17 +19,6 @@ DihedralStyle(charmmfsw/kk/host,DihedralCharmmfswKokkos); // clang-format on #else -/* - - 20,21c20,21 - < #ifndef LMP_DIHEDRAL_CHARMM_H - < #define LMP_DIHEDRAL_CHARMM_H - --- - > #ifndef LMP_DIHEDRAL_CHARMMFSW_H - > #define LMP_DIHEDRAL_CHARMMFSW_H - - */ - // clang-format off #ifndef LMP_DIHEDRAL_CHARMMFSW_KOKKOS_H #define LMP_DIHEDRAL_CHARMMFSW_KOKKOS_H @@ -62,95 +26,17 @@ DihedralStyle(charmmfsw/kk/host,DihedralCharmmfswKokkos); #include "dihedral_charmmfsw.h" #include "kokkos_type.h" #include "dihedral_charmm_kokkos.h" - -/* - - s_EVM_FLOAT and TagDihedralCharmmCompute conflict because style_dihedral.h - includes both dihedral_charmm_kokkos.h and dihedral_charmmfsw_kokkos.h - so comment out definitions in here and include dihedral_charmm_kokkos.h - in dihedral_charmmfsw_kokkos.h: - In file included from /Users/mitch/Dropbox/lammps/lammps/src/force.cpp:18: - In file included from /Users/mitch/Dropbox/lammps/lammps/build/styles/style_dihedral.h:4: - /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmmfsw_kokkos.h:65:8: error: redefinition of 's_EVM_FLOAT' - struct s_EVM_FLOAT { - ^ - /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:31:8: note: previous definition is here - struct s_EVM_FLOAT { - ^ - In file included from /Users/mitch/Dropbox/lammps/lammps/src/lammps.cpp:23: - In file included from /Users/mitch/Dropbox/lammps/lammps/build/styles/style_dihedral.h:4: - /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmmfsw_kokkos.h:65:8: error: redefinition of 's_EVM_FLOAT' - struct s_EVM_FLOAT { - ^ - /Users/mitch/Dropbox/lammps/lammps/src/KOKKOS/dihedral_charmm_kokkos.h:31:8: note: previous definition is here - struct s_EVM_FLOAT { - ^ - - */ - namespace LAMMPS_NS { -/* -struct s_EVM_FLOAT { - E_FLOAT evdwl; - E_FLOAT ecoul; - E_FLOAT emol; - F_FLOAT v[6]; - F_FLOAT vp[6]; - KOKKOS_INLINE_FUNCTION - s_EVM_FLOAT() { - evdwl = 0; - ecoul = 0; - emol = 0; - v[0] = 0; v[1] = 0; v[2] = 0; - v[3] = 0; v[4] = 0; v[5] = 0; - vp[0] = 0; vp[1] = 0; vp[2] = 0; - vp[3] = 0; vp[4] = 0; vp[5] = 0; - } - - KOKKOS_INLINE_FUNCTION - void operator+=(const s_EVM_FLOAT &rhs) { - evdwl += rhs.evdwl; - ecoul += rhs.ecoul; - emol += rhs.emol; - v[0] += rhs.v[0]; - v[1] += rhs.v[1]; - v[2] += rhs.v[2]; - v[3] += rhs.v[3]; - v[4] += rhs.v[4]; - v[5] += rhs.v[5]; - vp[0] += rhs.vp[0]; - vp[1] += rhs.vp[1]; - vp[2] += rhs.vp[2]; - vp[3] += rhs.vp[3]; - vp[4] += rhs.vp[4]; - vp[5] += rhs.vp[5]; - } -}; -typedef struct s_EVM_FLOAT EVM_FLOAT; - - */ +// s_EVM_FLOAT definition in here conflicted because style_dihedral.h +// includes both dihedral_charmm_kokkos.h and dihedral_charmmfsw_kokkos.h +// so remove definition of s_EVM_FLOAT in here and include +// dihedral_charmm_kokkos.h template struct TagDihedralCharmmfswCompute{}; - - -/* - 27c27 - < class DihedralCharmm : public Dihedral { - --- - > class DihedralCharmmfsw : public Dihedral { - 29,30c29,30 - < DihedralCharmm(class LAMMPS *); - < ~DihedralCharmm() override; - --- - > DihedralCharmmfsw(class LAMMPS *); - > ~DihedralCharmmfsw() override; - - */ - template class DihedralCharmmfswKokkos : public DihedralCharmmfsw { public: @@ -235,19 +121,3 @@ class DihedralCharmmfswKokkos : public DihedralCharmmfsw { #endif #endif - - -/* - - 38a39,43 - > int implicit, weightflag, dihedflag; - > double cut_lj_inner14, cut_lj14, cut_coul14; - > double evdwl14_12, evdwl14_6, cut_coulinv14; - > double cut_lj_inner3inv, cut_lj_inner6inv, cut_lj3inv, cut_lj6inv; - > - 42d46 - < int implicit, weightflag; - - */ - -// nothing to do here, inherited from DihedralCharmmfsw diff --git a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp index 7c1da2479ff..191626fc9fc 100644 --- a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp @@ -27,35 +27,6 @@ ------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - - *** DRAFT VERSION 1 (lots of comments to be removed just before merge) *** - - (1) first draft version of PairLJCharmmfswCoulLongKokkos almost exactly - same as PairLJCharmmCoulLongKokkos but with new class name - - method: track changes from serial kspace pair_lj_charmm_coul_long to - pair_lj_charmmfsw_coul_long and apply to PairLJCharmmCoulLongKokkos - - ISSUES: - - (A) charmm denom_lj_inv cache , is it to optimize code because division - is slower that multiplication ?? - - - - ------------------------------------------------------------------------- */ - - -/* - 19c23 - < #include "pair_lj_charmm_coul_long.h" - --- - > #include "pair_lj_charmmfsw_coul_long.h" - - */ - #include "pair_lj_charmmfsw_coul_long_kokkos.h" #include "atom_kokkos.h" @@ -86,30 +57,6 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -/* - 47c51 - < PairLJCharmmCoulLong::PairLJCharmmCoulLong(LAMMPS *lmp) : Pair(lmp) - --- - > PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(LAMMPS *lmp) : Pair(lmp) - 55a60,72 - > - > // short-range/long-range flag accessed by DihedralCharmmfsw - > - > dihedflag = 1; - > - > // switch qqr2e from LAMMPS value to CHARMM value - > - > if (strcmp(update->unit_style,"real") == 0) { - > if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real)) - > error->message(FLERR,"Switching to CHARMM coulomb energy" - > " conversion constant"); - > force->qqr2e = force->qqr2e_charmm_real; - > } - - */ - -// added superclass constructor to inherit from PairLJCharmmfswCoulLong - template PairLJCharmmfswCoulLongKokkos::PairLJCharmmfswCoulLongKokkos(LAMMPS *lmp):PairLJCharmmfswCoulLong(lmp) { @@ -125,25 +72,6 @@ PairLJCharmmfswCoulLongKokkos::PairLJCharmmfswCoulLongKokkos(LAMMPS /* ---------------------------------------------------------------------- */ -/* - - 60c77 - < PairLJCharmmCoulLong::~PairLJCharmmCoulLong() - --- - > PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong() - 61a79,87 - > // switch qqr2e back from CHARMM value to LAMMPS value - > - > if (update && strcmp(update->unit_style,"real") == 0) { - > if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real)) - > error->message(FLERR,"Restoring original LAMMPS coulomb energy" - > " conversion constant"); - > force->qqr2e = force->qqr2e_lammps_real; - > } - > - - */ - template PairLJCharmmfswCoulLongKokkos::~PairLJCharmmfswCoulLongKokkos() { @@ -159,28 +87,6 @@ PairLJCharmmfswCoulLongKokkos::~PairLJCharmmfswCoulLongKokkos() /* ---------------------------------------------------------------------- */ -/* - 87c112 - < void PairLJCharmmCoulLong::compute(int eflag, int vflag) - --- - > void PairLJCharmmfswCoulLong::compute(int eflag, int vflag) - 90c115 - < double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; - --- - > double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwl12,evdwl6,ecoul,fpair; - 92c117 - < double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; - --- - > double r,rinv,r2inv,r3inv,r6inv,rsq,forcecoul,forcelj,factor_coul,factor_lj; - 94c119 - < double philj,switch1,switch2; - --- - > double switch1; - 96d120 - < double rsq; - - */ - template void PairLJCharmmfswCoulLongKokkos::compute(int eflag_in, int vflag_in) { @@ -287,22 +193,6 @@ compute_fpair(const F_FLOAT& rsq, const int& /*i*/, const int& /*j*/, (STACKPARAMS?m_params[itype][jtype].lj2:params(itype,jtype).lj2)); if (rsq > cut_lj_innersq) { - - /* - 174,179c198,200 - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < switch2 = 12.0*rsq * (cut_ljsq-rsq) * - < (rsq-cut_lj_innersq) * denom_lj_inv; - < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); - < forcelj = forcelj*switch1 + philj*switch2; - < } - --- - > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; - > forcelj = forcelj*switch1; - > } - - */ - switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; forcelj = forcelj*switch1; @@ -327,32 +217,6 @@ compute_evdwl(const F_FLOAT& rsq, const int& /*i*/, const int& /*j*/, const F_FLOAT r3inv = rinv*rinv*rinv; F_FLOAT englj, englj12, englj6; - /* - 205d225 - < evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); - 207,209c227,240 - < switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < evdwl *= switch1; - --- - > r = sqrt(rsq); - > rinv = 1.0/r; - > r3inv = rinv*rinv*rinv; - > evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 * - > (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); - > evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 * - > (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); - > evdwl = evdwl12 + evdwl6; - > } else { - > evdwl12 = r6inv*lj3[itype][jtype]*r6inv - - > lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; - > evdwl6 = -lj4[itype][jtype]*r6inv + - > lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv; - > evdwl = evdwl12 + evdwl6; - - */ - - if (rsq > cut_lj_innersq) { englj12 = (STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*cut_lj6* denom_lj12 * (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); @@ -360,8 +224,8 @@ compute_evdwl(const F_FLOAT& rsq, const int& /*i*/, const int& /*j*/, cut_lj3*denom_lj6 * (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); englj = englj12 + englj6; } else { - englj12 = r6inv*lj3[itype][jtype]*r6inv - - lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; + englj12 = r6inv*(STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv - + (STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*cut_lj_inner6inv*cut_lj6inv; englj6 = -(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)*r6inv + (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)* cut_lj_inner3inv*cut_lj3inv; @@ -573,18 +437,6 @@ void PairLJCharmmfswCoulLongKokkos::init_tables(double cut_coul, dou init specific to this pair style ------------------------------------------------------------------------- */ -/* - 682c733 - < void PairLJCharmmCoulLong::init_style() - --- - > void PairLJCharmmfswCoulLong::init_style() - 688c739 - < // request regular or rRESPA neighbor list - --- - > // request regular or rRESPA neighbor lists - - */ - template void PairLJCharmmfswCoulLongKokkos::init_style() { @@ -651,301 +503,3 @@ template class PairLJCharmmfswCoulLongKokkos; template class PairLJCharmmfswCoulLongKokkos; #endif } - - - - - - -/* - 80d105 - < memory->destroy(offset); - 598c650 - < void PairLJCharmmCoulLong::allocate() - --- - > void PairLJCharmmfswCoulLong::allocate() - 622d673 - < memory->create(offset,n+1,n+1,"pair:offset"); - 631c682 - < void PairLJCharmmCoulLong::settings(int narg, char **arg) - --- - > void PairLJCharmmfswCoulLong::settings(int narg, char **arg) - 645c696 - < void PairLJCharmmCoulLong::coeff(int narg, char **arg) - --- - > void PairLJCharmmfswCoulLong::coeff(int narg, char **arg) - - 686c737 - < "Pair style lj/charmm/coul/long requires atom attribute q"); - --- - > "Pair style lj/charmmfsw/coul/long requires atom attribute q"); - - 705a757,766 - > cut_ljinv = 1.0/cut_lj; - > cut_lj_innerinv = 1.0/cut_lj_inner; - > cut_lj3 = cut_lj * cut_lj * cut_lj; - > cut_lj3inv = cut_ljinv * cut_ljinv * cut_ljinv; - > cut_lj_inner3inv = cut_lj_innerinv * cut_lj_innerinv * cut_lj_innerinv; - > cut_lj_inner3 = cut_lj_inner * cut_lj_inner * cut_lj_inner; - > cut_lj6 = cut_ljsq * cut_ljsq * cut_ljsq; - > cut_lj6inv = cut_lj3inv * cut_lj3inv; - > cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv; - > cut_lj_inner6 = cut_lj_innersq * cut_lj_innersq * cut_lj_innersq; - 709,711c770,773 - < denom_lj = ( (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * - < (cut_ljsq-cut_lj_innersq) ); - < denom_lj_inv = 1.0 / denom_lj; - --- - > denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * - > (cut_ljsq-cut_lj_innersq); - > denom_lj12 = 1.0/(cut_lj6 - cut_lj_inner6); - > denom_lj6 = 1.0/(cut_lj3 - cut_lj_inner3); - 718,730d779 - < cut_in_off = cut_respa[0]; - < cut_in_on = cut_respa[1]; - < cut_out_on = cut_respa[2]; - < cut_out_off = cut_respa[3]; - < - < cut_in_diff = cut_in_on - cut_in_off; - < cut_out_diff = cut_out_off - cut_out_on; - < cut_in_diff_inv = 1.0 / (cut_in_diff); - < cut_out_diff_inv = 1.0 / (cut_out_diff); - < cut_in_off_sq = cut_in_off*cut_in_off; - < cut_in_on_sq = cut_in_on*cut_in_on; - < cut_out_on_sq = cut_out_on*cut_out_on; - < cut_out_off_sq = cut_out_off*cut_out_off; - - - 752c801 - < double PairLJCharmmCoulLong::init_one(int i, int j) - --- - > double PairLJCharmmfswCoulLong::init_one(int i, int j) - 790c839 - < void PairLJCharmmCoulLong::write_restart(FILE *fp) - --- - > void PairLJCharmmfswCoulLong::write_restart(FILE *fp) - 811c860 - < void PairLJCharmmCoulLong::read_restart(FILE *fp) - --- - > void PairLJCharmmfswCoulLong::read_restart(FILE *fp) - 842c891 - < void PairLJCharmmCoulLong::write_restart_settings(FILE *fp) - --- - > void PairLJCharmmfswCoulLong::write_restart_settings(FILE *fp) - 857c906 - < void PairLJCharmmCoulLong::read_restart_settings(FILE *fp) - --- - > void PairLJCharmmfswCoulLong::read_restart_settings(FILE *fp) - 882c931 - < void PairLJCharmmCoulLong::write_data(FILE *fp) - --- - > void PairLJCharmmfswCoulLong::write_data(FILE *fp) - 893c942 - < void PairLJCharmmCoulLong::write_data_all(FILE *fp) - --- - > void PairLJCharmmfswCoulLong::write_data_all(FILE *fp) - 903c952 - < double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype, - --- - > double PairLJCharmmfswCoulLong::single(int i, int j, int itype, int jtype, - 908,909c957,958 - < double r2inv,r6inv,r,grij,expm2,t,erfc,prefactor; - < double switch1,switch2,fraction,table,forcecoul,forcelj,phicoul,philj; - --- - > double r,rinv,r2inv,r3inv,r6inv,grij,expm2,t,erfc,prefactor; - > double switch1,fraction,table,forcecoul,forcelj,phicoul,philj,philj12,philj6; - 911a961,962 - > r = sqrt(rsq); - > rinv = 1.0/r; - 939c990,991 - < r6inv = r2inv*r2inv*r2inv; - --- - > r3inv = rinv*rinv*rinv; - > r6inv = r3inv*r3inv; - 943,947c995,996 - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < switch2 = 12.0*rsq * (cut_ljsq-rsq) * - < (rsq-cut_lj_innersq) * denom_lj_inv; - < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); - < forcelj = forcelj*switch1 + philj*switch2; - --- - > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; - > forcelj = forcelj*switch1; - 965d1013 - < philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); - 967,969c1015,1025 - < switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < philj *= switch1; - --- - > philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 * - > (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); - > philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 * - > (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); - > philj = philj12 + philj6; - > } else { - > philj12 = r6inv*lj3[itype][jtype]*r6inv - - > lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; - > philj6 = -lj4[itype][jtype]*r6inv + - > lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv; - > philj = philj12 + philj6; - 979c1035 - < void *PairLJCharmmCoulLong::extract(const char *str, int &dim) - --- - > void *PairLJCharmmfswCoulLong::extract(const char *str, int &dim) - 988a1045,1047 - > - > // info extracted by dihedral_charmmfsw - > - 989a1049,1051 - > if (strcmp(str,"cut_lj_inner") == 0) return (void *) &cut_lj_inner; - > if (strcmp(str,"cut_lj") == 0) return (void *) &cut_lj; - > if (strcmp(str,"dihedflag") == 0) return (void *) &dihedflag; - - - */ - -// nothing to do for all these, inherited from PairLJCharmmfswCoulLong - - - - -/* - - 226c257 - < void PairLJCharmmCoulLong::compute_inner() - --- - > void PairLJCharmmfswCoulLong::compute_inner() - 248a280,286 - > double cut_out_on = cut_respa[0]; - > double cut_out_off = cut_respa[1]; - > - > double cut_out_diff = cut_out_off - cut_out_on; - > double cut_out_on_sq = cut_out_on*cut_out_on; - > double cut_out_off_sq = cut_out_off*cut_out_off; - > - 284c322 - < rsw = (sqrt(rsq) - cut_out_on)*cut_out_diff_inv; - --- - > rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; - 303c341 - < void PairLJCharmmCoulLong::compute_middle() - --- - > void PairLJCharmmfswCoulLong::compute_middle() - 308c346 - < double philj,switch1,switch2; - --- - > double switch1; - 326a365,376 - > double cut_in_off = cut_respa[0]; - > double cut_in_on = cut_respa[1]; - > double cut_out_on = cut_respa[2]; - > double cut_out_off = cut_respa[3]; - > - > double cut_in_diff = cut_in_on - cut_in_off; - > double cut_out_diff = cut_out_off - cut_out_on; - > double cut_in_off_sq = cut_in_off*cut_in_off; - > double cut_in_on_sq = cut_in_on*cut_in_on; - > double cut_out_on_sq = cut_out_on*cut_out_on; - > double cut_out_off_sq = cut_out_off*cut_out_off; - > - 361,365c411,412 - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < switch2 = 12.0*rsq * (cut_ljsq-rsq) * - < (rsq-cut_lj_innersq) * denom_lj_inv; - < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); - < forcelj = forcelj*switch1 + philj*switch2; - --- - > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; - > forcelj = forcelj*switch1; - 370c417 - < rsw = (sqrt(rsq) - cut_in_off)*cut_in_diff_inv; - --- - > rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; - 374c421 - < rsw = (sqrt(rsq) - cut_out_on)*cut_out_diff_inv; - --- - > rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; - 393c440 - < void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag) - --- - > void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) - 396c443 - < double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; - --- - > double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwl6,evdwl12,ecoul,fpair; - 398c445 - < double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; - --- - > double r,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; - 400c447 - < double philj,switch1,switch2; - --- - > double switch1; - 422a470,476 - > double cut_in_off = cut_respa[2]; - > double cut_in_on = cut_respa[3]; - > - > double cut_in_diff = cut_in_on - cut_in_off; - > double cut_in_off_sq = cut_in_off*cut_in_off; - > double cut_in_on_sq = cut_in_on*cut_in_on; - > - 448a503 - > r6inv = r2inv*r2inv*r2inv; - 489d543 - < r6inv = r2inv*r2inv*r2inv; - 493,497c547,548 - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < switch2 = 12.0*rsq * (cut_ljsq-rsq) * - < (rsq-cut_lj_innersq) * denom_lj_inv; - < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); - < forcelj = forcelj*switch1 + philj*switch2; - --- - > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; - > forcelj = forcelj*switch1; - 533d583 - < r6inv = r2inv*r2inv*r2inv; - 536,538c586,598 - < switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < evdwl *= switch1; - --- - > rinv = sqrt(r2inv); - > r3inv = r2inv*rinv; - > evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 * - > (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv); - > evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 * - > (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv); - > evdwl = evdwl12 + evdwl6; - > } else { - > evdwl12 = r6inv*lj3[itype][jtype]*r6inv - - > lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv; - > evdwl6 = -lj4[itype][jtype]*r6inv + - > lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv; - > evdwl = evdwl12 + evdwl6; - 561d620 - < r6inv = r2inv*r2inv*r2inv; - 565,569c624,625 - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < switch2 = 12.0*rsq * (cut_ljsq-rsq) * - < (rsq-cut_lj_innersq) * denom_lj_inv; - < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); - < forcelj = forcelj*switch1 + philj*switch2; - --- - > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; - > forcelj = forcelj*switch1; - 572d627 - < r6inv = r2inv*r2inv*r2inv; - 576,580c631,632 - < (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv; - < switch2 = 12.0*rsq * (cut_ljsq-rsq) * - < (rsq-cut_lj_innersq) * denom_lj_inv; - < philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); - < forcelj = forcelj*switch1 + philj*switch2; - --- - > (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; - > forcelj = forcelj*switch1; - - */ - -// kokkos doesnt support respa, so ignore compute_inner / compute_middle / compute_outer diff --git a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.h b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.h index e9a6b5486f9..8fdb8543ed8 100644 --- a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.h +++ b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.h @@ -11,29 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - - *** DRAFT VERSION 1 (lots of comments to be removed just before merge) *** - - (1) first draft version of PairLJCharmmfswCoulLongKokkos exactly - same as PairLJCharmmCoulLongKokkos but with new class name - - method: track changes from serial kspace pair_lj_charmm_coul_long to - pair_lj_charmmfsw_coul_long and apply to PairLJCharmmfswCoulLongKokkos - - % diff pair_lj_charmm_coul_long.h pair_lj_charmmfsw_coul_long.h - - -------------------------------------------------------------------------- */ - -/* - 16c16 - < PairStyle(lj/charmm/coul/long,PairLJCharmmCoulLong); - --- - > PairStyle(lj/charmmfsw/coul/long,PairLJCharmmfswCoulLong); - - */ #ifdef PAIR_CLASS // clang-format off @@ -43,17 +20,6 @@ PairStyle(lj/charmmfsw/coul/long/kk/host,PairLJCharmmfswCoulLongKokkos #ifndef LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_H - > #define LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_H - - */ - // clang-format off #ifndef LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_KOKKOS_H #define LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_KOKKOS_H @@ -64,15 +30,6 @@ PairStyle(lj/charmmfsw/coul/long/kk/host,PairLJCharmmfswCoulLongKokkos class PairLJCharmmfswCoulLong : public Pair { - - */ - template class PairLJCharmmfswCoulLongKokkos : public PairLJCharmmfswCoulLong { public: @@ -80,18 +37,7 @@ class PairLJCharmmfswCoulLongKokkos : public PairLJCharmmfswCoulLong { enum {COUL_FLAG=1}; typedef DeviceType device_type; typedef ArrayTypes AT; - - /* - - 29,30c29,30 - < PairLJCharmmCoulLong(class LAMMPS *); - < ~PairLJCharmmCoulLong() override; - --- - > PairLJCharmmfswCoulLong(class LAMMPS *); - > ~PairLJCharmmfswCoulLong() override; - - */ - + PairLJCharmmfswCoulLongKokkos(class LAMMPS *); ~PairLJCharmmfswCoulLongKokkos() override; @@ -103,34 +49,6 @@ class PairLJCharmmfswCoulLongKokkos : public PairLJCharmmfswCoulLong { protected: - /* - 52c52,54 - < double cut_lj_inner, cut_lj; - --- - > int dihedflag; - > - > double cut_lj_inner, cut_lj, cut_ljinv, cut_lj_innerinv; - 53a56,57 - > double cut_lj3inv, cut_lj_inner3inv, cut_lj3, cut_lj_inner3; - > double cut_lj6inv, cut_lj_inner6inv, cut_lj6, cut_lj_inner6; - 56,60c60 - < double cut_in_off, cut_in_on, cut_out_off, cut_out_on; - < double cut_in_diff, cut_out_diff; - < double cut_in_diff_inv, cut_out_diff_inv; - < double cut_in_off_sq, cut_in_on_sq, cut_out_off_sq, cut_out_on_sq; - < double denom_lj, denom_lj_inv; - --- - > double denom_lj, denom_lj12, denom_lj6; - - */ - - // almost nothing to do here, inherited from PairLJCharmmfswCoulLong - // only temporarily need cut_lj_innersq, denom_coul protected variables - // (removed from pair_lj_charmm_coul_long to pair_lj_charmmfsw_coul_long) - // to compile draft version 1, can be removed by draft version 2 - - - template KOKKOS_INLINE_FUNCTION F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, From 600eaf837b5d911bea54d224b6a3616accc2935d Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 3 Jan 2024 16:20:04 -0500 Subject: [PATCH 106/719] update preferred contact info --- src/REACTION/README | 3 ++- src/REACTION/fix_bond_react.cpp | 2 +- src/REACTION/fix_bond_react.h | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/REACTION/README b/src/REACTION/README index 99a5d604ecc..b9199d6d47b 100644 --- a/src/REACTION/README +++ b/src/REACTION/README @@ -25,4 +25,5 @@ The REACTER methodology is detailed in: https://doi.org/10.1021/acs.macromol.0c02012 This package was created by Jacob Gissinger -(jacob.r.gissinger@gmail.com) at the NASA Langley Research Center. +(jgissing@stevens.edu) while at the NASA Langley Research Center +and Stevens Institute of Technology. diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 10a7023e170..e704160e933 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -13,7 +13,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- -Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com) +Contributing Author: Jacob Gissinger (jgissing@stevens.edu) ------------------------------------------------------------------------- */ #include "fix_bond_react.h" diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h index 534261e11dc..3d56c2fc7bf 100644 --- a/src/REACTION/fix_bond_react.h +++ b/src/REACTION/fix_bond_react.h @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com) + Contributing Author: Jacob Gissinger (jgissing@stevens.edu) ------------------------------------------------------------------------- */ #ifdef FIX_CLASS From a6b00a60b208b17cd25fe6ff2a1d7c0000718bc0 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 3 Jan 2024 20:31:22 -0500 Subject: [PATCH 107/719] additional check/warning for valid templates --- src/REACTION/fix_bond_react.cpp | 33 ++++++++++++++++++++++++++++++--- src/REACTION/fix_bond_react.h | 2 +- 2 files changed, 31 insertions(+), 4 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index e704160e933..00292438ecd 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -2681,16 +2681,43 @@ void FixBondReact::find_landlocked_atoms(int myrxn) } // also, if atoms change number of bonds, but aren't landlocked, that could be bad + int warnflag = 0; if (comm->me == 0) for (int i = 0; i < twomol->natoms; i++) { if ((create_atoms[i][myrxn] == 0) && (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0]) && - (landlocked_atoms[i][myrxn] == 0)) - error->warning(FLERR, "Fix bond/react: Atom affected by reaction {} is too close " - "to template edge",rxn_name[myrxn]); + (landlocked_atoms[i][myrxn] == 0)) { + warnflag = 1; + break; + } + } + + // also, if an atom changes any of its bonds, but is not landlocked, that could be bad + int thereflag; + if (comm->me == 0) + for (int i = 0; i < twomol->natoms; i++) { + if (landlocked_atoms[i][myrxn] == 1) continue; + for (int j = 0; j < twomol_nxspecial[i][0]; j++) { + int oneneighID = equivalences[twomol_xspecial[i][j]-1][1][myrxn]; + int ii = equivalences[i][1][myrxn] - 1; + thereflag = 0; + for (int k = 0; k < onemol_nxspecial[ii][0]; k++) { + if (oneneighID == onemol_xspecial[ii][k]) { + thereflag = 1; + break; + } + } + if (thereflag == 0) { + warnflag = 1; break; + } + } + if (warnflag == 1) break; } + if (comm->me == 0 && warnflag == 1) error->warning(FLERR, "Fix bond/react: Atom affected " + "by reaction {} is too close to template edge",rxn_name[myrxn]); + // finally, if a created atom is not landlocked, bad! for (int i = 0; i < twomol->natoms; i++) { if (create_atoms[i][myrxn] == 1 && landlocked_atoms[i][myrxn] == 0) { diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h index 3d56c2fc7bf..8c9fc9dce4c 100644 --- a/src/REACTION/fix_bond_react.h +++ b/src/REACTION/fix_bond_react.h @@ -139,7 +139,7 @@ class FixBondReact : public Fix { int avail_guesses; // num of restore points available int *guess_branch; // used when there is more than two choices when guessing int **restore_pt; // contains info about restore points - tagint **restore; // contaings info about restore points + tagint **restore; // contains info about restore points int *pioneer_count; // counts pioneers int **edge; // atoms in molecule templates with incorrect valences From 13b6d40062b01a078dd86bd6fe517e15ac731178 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 3 Jan 2024 20:38:10 -0500 Subject: [PATCH 108/719] tiny_epoxy example correction not sure why this issue showed up in recent LAMMPS versions --- examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized index ea09d068934..7e0350cdb08 100644 --- a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized +++ b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized @@ -20,7 +20,8 @@ improper_style class2 special_bonds lj/coul 0 0 1 pair_modify tail yes mix sixthpower -read_data tiny_epoxy.data +read_data tiny_epoxy.data & + extra/special/per/atom 25 velocity all create 300.0 4928459 dist gaussian From de1f6eefd7c167e4980f4173ad1e0b65d48ea4c5 Mon Sep 17 00:00:00 2001 From: Mitch Murphy Date: Wed, 3 Jan 2024 23:00:07 -0500 Subject: [PATCH 109/719] // FIXME: // superclass destructor from KSPACE/pair_lj_charmmfsw_coul_long.cpp:81 // resets force->qqr2e = force->qqr2e_lammps_real at end of timestep 0 // causing ~E-6 errors for steps 1,2,... everywhere in this class when // running kokkos with openmp (and probably with GPUs also). // // WORKAROUND: for now until guidance from lammps devs is to // reset it back force->qqr2e = force->qqr2e_charmm_real here. --- src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp index 191626fc9fc..7701f137685 100644 --- a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp @@ -76,6 +76,17 @@ template PairLJCharmmfswCoulLongKokkos::~PairLJCharmmfswCoulLongKokkos() { + // FIXME: + // superclass destructor from KSPACE/pair_lj_charmmfsw_coul_long.cpp:81 + // resets force->qqr2e = force->qqr2e_lammps_real at end of timestep 0 + // causing ~E-6 errors for steps 1,2,... everywhere in this class when + // running kokkos with openmp (and probably with GPUs also). + // + // WORKAROUND: for now until guidance from lammps devs is to + // reset it back force->qqr2e = force->qqr2e_charmm_real here. + + force->qqr2e = force->qqr2e_charmm_real; + if (copymode) return; if (allocated) { From c065d4bac626bd7fd2912cc1bcd368078a2f587e Mon Sep 17 00:00:00 2001 From: Mitch Murphy Date: Thu, 4 Jan 2024 00:50:06 -0500 Subject: [PATCH 110/719] // FIXME: destructor from this class resets // // force->qqr2e = force->qqr2e_lammps_real // // at end of timestep 0 causing ~E-6 errors for steps 1,2,... // everywhere in pair_lj_charmmfsw_coul_long_kokkos when // running kokkos with openmp (and probably with GPUs also). // // WORKAROUND: for now until guidance from lammps devs is to // comment out this line here (commit to be reversed later). //force->qqr2e = force->qqr2e_lammps_real; --- src/KSPACE/pair_lj_charmmfsw_coul_long.cpp | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index b7635c49c77..83b72931789 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -82,7 +82,19 @@ PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong() if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real)) error->message(FLERR,"Restoring original LAMMPS coulomb energy" " conversion constant"); - force->qqr2e = force->qqr2e_lammps_real; + + // FIXME: destructor from this class resets + // + // force->qqr2e = force->qqr2e_lammps_real + // + // at end of timestep 0 causing ~E-6 errors for steps 1,2,... + // everywhere in pair_lj_charmmfsw_coul_long_kokkos when + // running kokkos with openmp (and probably with GPUs also). + // + // WORKAROUND: for now until guidance from lammps devs is to + // comment out this line here (commit to be reversed later). + + //force->qqr2e = force->qqr2e_lammps_real; } if (copymode) return; From ac9afb26dd7ea27b40bbcd2bd44fcdf1ae3932ae Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 4 Jan 2024 17:38:14 +0200 Subject: [PATCH 111/719] aesthetic optimization for xscale, yscale and zscale --- src/fix_indent.cpp | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index d3e80ecd793..28dcac08d09 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -82,13 +82,9 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) : // setup scaling - double xscale,yscale,zscale; - if (scaleflag) { - xscale = domain->lattice->xlattice; - yscale = domain->lattice->ylattice; - zscale = domain->lattice->zlattice; - } - else xscale = yscale = zscale = 1.0; + const double xscale { scaleflag ? domain->lattice->xlattice : 1.0}; + const double yscale { scaleflag ? domain->lattice->ylattice : 1.0}; + const double zscale { scaleflag ? domain->lattice->zlattice : 1.0}; // apply scaling factors to geometry From 4b4e796c190734090c80b2badd2023a66e08bb6c Mon Sep 17 00:00:00 2001 From: alphataubio Date: Thu, 4 Jan 2024 16:06:41 -0500 Subject: [PATCH 112/719] Revert " // FIXME:" This reverts commit de1f6eefd7c167e4980f4173ad1e0b65d48ea4c5. my first idea to reset back force->qqr2e = force->qqr2e_charmm_real didnt work because class destructor gets called first THEN superclass destructor gets called --- src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp index 7701f137685..191626fc9fc 100644 --- a/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmmfsw_coul_long_kokkos.cpp @@ -76,17 +76,6 @@ template PairLJCharmmfswCoulLongKokkos::~PairLJCharmmfswCoulLongKokkos() { - // FIXME: - // superclass destructor from KSPACE/pair_lj_charmmfsw_coul_long.cpp:81 - // resets force->qqr2e = force->qqr2e_lammps_real at end of timestep 0 - // causing ~E-6 errors for steps 1,2,... everywhere in this class when - // running kokkos with openmp (and probably with GPUs also). - // - // WORKAROUND: for now until guidance from lammps devs is to - // reset it back force->qqr2e = force->qqr2e_charmm_real here. - - force->qqr2e = force->qqr2e_charmm_real; - if (copymode) return; if (allocated) { From f9aafff9928c43f27728647ebcb5b5f245f0ad19 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Jan 2024 22:45:53 -0500 Subject: [PATCH 113/719] must include fmt/ranges.h for fmt::join() --- src/KIM/kim_interactions.cpp | 2 ++ src/KIM/kim_param.cpp | 2 ++ 2 files changed, 4 insertions(+) diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index 1f4f84e6480..ce550bf5da6 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -70,6 +70,8 @@ #include "modify.h" #include "update.h" +#include "fmt/ranges.h" + #include #include diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp index f72df819899..c50474fe67e 100644 --- a/src/KIM/kim_param.cpp +++ b/src/KIM/kim_param.cpp @@ -68,6 +68,8 @@ #include "pair_kim.h" #include "variable.h" +#include "fmt/ranges.h" + #include #include #include From 01482e7a2e0324eabc3dc0b81809573f93ce89b4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Jan 2024 22:46:40 -0500 Subject: [PATCH 114/719] update fmtlib to version 10.2.1 --- src/fmt/args.h | 13 +- src/fmt/chrono.h | 272 +++++++++------- src/fmt/color.h | 77 +++-- src/fmt/compile.h | 17 +- src/fmt/core.h | 647 ++++++++++++++++++++------------------ src/fmt/format-inl.h | 161 +++++----- src/fmt/format.h | 722 ++++++++++++++++++++++--------------------- src/fmt/os.h | 62 ++-- src/fmt/ostream.h | 92 ++++-- src/fmt/printf.h | 34 +- src/fmt/ranges.h | 117 +++++-- src/fmt/std.h | 154 ++++++--- src/fmt/xchar.h | 26 +- src/fmtlib_os.cpp | 67 ++-- 14 files changed, 1381 insertions(+), 1080 deletions(-) diff --git a/src/fmt/args.h b/src/fmt/args.h index 2d684e7cc11..b77a2d06611 100644 --- a/src/fmt/args.h +++ b/src/fmt/args.h @@ -12,7 +12,7 @@ #include // std::unique_ptr #include -#include "core.h" +#include "format.h" // std_string_view FMT_BEGIN_NAMESPACE @@ -22,8 +22,9 @@ template struct is_reference_wrapper : std::false_type {}; template struct is_reference_wrapper> : std::true_type {}; -template const T& unwrap(const T& v) { return v; } -template const T& unwrap(const std::reference_wrapper& v) { +template auto unwrap(const T& v) -> const T& { return v; } +template +auto unwrap(const std::reference_wrapper& v) -> const T& { return static_cast(v); } @@ -50,7 +51,7 @@ class dynamic_arg_list { std::unique_ptr> head_; public: - template const T& push(const Arg& arg) { + template auto push(const Arg& arg) -> const T& { auto new_node = std::unique_ptr>(new typed_node(arg)); auto& value = new_node->value; new_node->next = std::move(head_); @@ -110,14 +111,14 @@ class dynamic_format_arg_store friend class basic_format_args; - unsigned long long get_types() const { + auto get_types() const -> unsigned long long { return detail::is_unpacked_bit | data_.size() | (named_info_.empty() ? 0ULL : static_cast(detail::has_named_args_bit)); } - const basic_format_arg* data() const { + auto data() const -> const basic_format_arg* { return named_info_.empty() ? data_.data() : data_.data() + 1; } diff --git a/src/fmt/chrono.h b/src/fmt/chrono.h index ff3e1445b96..9d54574e168 100644 --- a/src/fmt/chrono.h +++ b/src/fmt/chrono.h @@ -18,7 +18,7 @@ #include #include -#include "format.h" +#include "ostream.h" // formatbuf FMT_BEGIN_NAMESPACE @@ -72,7 +72,8 @@ template ::value && std::numeric_limits::is_signed == std::numeric_limits::is_signed)> -FMT_CONSTEXPR To lossless_integral_conversion(const From from, int& ec) { +FMT_CONSTEXPR auto lossless_integral_conversion(const From from, int& ec) + -> To { ec = 0; using F = std::numeric_limits; using T = std::numeric_limits; @@ -101,7 +102,8 @@ template ::value && std::numeric_limits::is_signed != std::numeric_limits::is_signed)> -FMT_CONSTEXPR To lossless_integral_conversion(const From from, int& ec) { +FMT_CONSTEXPR auto lossless_integral_conversion(const From from, int& ec) + -> To { ec = 0; using F = std::numeric_limits; using T = std::numeric_limits; @@ -133,7 +135,8 @@ FMT_CONSTEXPR To lossless_integral_conversion(const From from, int& ec) { template ::value)> -FMT_CONSTEXPR To lossless_integral_conversion(const From from, int& ec) { +FMT_CONSTEXPR auto lossless_integral_conversion(const From from, int& ec) + -> To { ec = 0; return from; } // function @@ -154,7 +157,7 @@ FMT_CONSTEXPR To lossless_integral_conversion(const From from, int& ec) { // clang-format on template ::value)> -FMT_CONSTEXPR To safe_float_conversion(const From from, int& ec) { +FMT_CONSTEXPR auto safe_float_conversion(const From from, int& ec) -> To { ec = 0; using T = std::numeric_limits; static_assert(std::is_floating_point::value, "From must be floating"); @@ -176,7 +179,7 @@ FMT_CONSTEXPR To safe_float_conversion(const From from, int& ec) { template ::value)> -FMT_CONSTEXPR To safe_float_conversion(const From from, int& ec) { +FMT_CONSTEXPR auto safe_float_conversion(const From from, int& ec) -> To { ec = 0; static_assert(std::is_floating_point::value, "From must be floating"); return from; @@ -188,8 +191,8 @@ FMT_CONSTEXPR To safe_float_conversion(const From from, int& ec) { template ::value), FMT_ENABLE_IF(std::is_integral::value)> -To safe_duration_cast(std::chrono::duration from, - int& ec) { +auto safe_duration_cast(std::chrono::duration from, + int& ec) -> To { using From = std::chrono::duration; ec = 0; // the basic idea is that we need to convert from count() in the from type @@ -240,8 +243,8 @@ To safe_duration_cast(std::chrono::duration from, template ::value), FMT_ENABLE_IF(std::is_floating_point::value)> -To safe_duration_cast(std::chrono::duration from, - int& ec) { +auto safe_duration_cast(std::chrono::duration from, + int& ec) -> To { using From = std::chrono::duration; ec = 0; if (std::isnan(from.count())) { @@ -321,12 +324,12 @@ To safe_duration_cast(std::chrono::duration from, namespace detail { template struct null {}; -inline null<> localtime_r FMT_NOMACRO(...) { return null<>(); } -inline null<> localtime_s(...) { return null<>(); } -inline null<> gmtime_r(...) { return null<>(); } -inline null<> gmtime_s(...) { return null<>(); } +inline auto localtime_r FMT_NOMACRO(...) -> null<> { return null<>(); } +inline auto localtime_s(...) -> null<> { return null<>(); } +inline auto gmtime_r(...) -> null<> { return null<>(); } +inline auto gmtime_s(...) -> null<> { return null<>(); } -inline const std::locale& get_classic_locale() { +inline auto get_classic_locale() -> const std::locale& { static const auto& locale = std::locale::classic(); return locale; } @@ -336,8 +339,6 @@ template struct codecvt_result { CodeUnit buf[max_size]; CodeUnit* end; }; -template -constexpr const size_t codecvt_result::max_size; template void write_codecvt(codecvt_result& out, string_view in_buf, @@ -408,8 +409,7 @@ inline void do_write(buffer& buf, const std::tm& time, auto&& format_buf = formatbuf>(buf); auto&& os = std::basic_ostream(&format_buf); os.imbue(loc); - using iterator = std::ostreambuf_iterator; - const auto& facet = std::use_facet>(loc); + const auto& facet = std::use_facet>(loc); auto end = facet.put(os, os, Char(' '), &time, format, modifier); if (end.failed()) FMT_THROW(format_error("failed to format time")); } @@ -432,6 +432,51 @@ auto write(OutputIt out, const std::tm& time, const std::locale& loc, return write_encoded_tm_str(out, string_view(buf.data(), buf.size()), loc); } +template +struct is_same_arithmetic_type + : public std::integral_constant::value && + std::is_integral::value) || + (std::is_floating_point::value && + std::is_floating_point::value)> { +}; + +template < + typename To, typename FromRep, typename FromPeriod, + FMT_ENABLE_IF(is_same_arithmetic_type::value)> +auto fmt_duration_cast(std::chrono::duration from) -> To { +#if FMT_SAFE_DURATION_CAST + // Throwing version of safe_duration_cast is only available for + // integer to integer or float to float casts. + int ec; + To to = safe_duration_cast::safe_duration_cast(from, ec); + if (ec) FMT_THROW(format_error("cannot format duration")); + return to; +#else + // Standard duration cast, may overflow. + return std::chrono::duration_cast(from); +#endif +} + +template < + typename To, typename FromRep, typename FromPeriod, + FMT_ENABLE_IF(!is_same_arithmetic_type::value)> +auto fmt_duration_cast(std::chrono::duration from) -> To { + // Mixed integer <-> float cast is not supported by safe_duration_cast. + return std::chrono::duration_cast(from); +} + +template +auto to_time_t( + std::chrono::time_point time_point) + -> std::time_t { + // Cannot use std::chrono::system_clock::to_time_t since this would first + // require a cast to std::chrono::system_clock::time_point, which could + // overflow. + return fmt_duration_cast>( + time_point.time_since_epoch()) + .count(); +} } // namespace detail FMT_BEGIN_EXPORT @@ -441,29 +486,29 @@ FMT_BEGIN_EXPORT expressed in local time. Unlike ``std::localtime``, this function is thread-safe on most platforms. */ -inline std::tm localtime(std::time_t time) { +inline auto localtime(std::time_t time) -> std::tm { struct dispatcher { std::time_t time_; std::tm tm_; dispatcher(std::time_t t) : time_(t) {} - bool run() { + auto run() -> bool { using namespace fmt::detail; return handle(localtime_r(&time_, &tm_)); } - bool handle(std::tm* tm) { return tm != nullptr; } + auto handle(std::tm* tm) -> bool { return tm != nullptr; } - bool handle(detail::null<>) { + auto handle(detail::null<>) -> bool { using namespace fmt::detail; return fallback(localtime_s(&tm_, &time_)); } - bool fallback(int res) { return res == 0; } + auto fallback(int res) -> bool { return res == 0; } #if !FMT_MSC_VERSION - bool fallback(detail::null<>) { + auto fallback(detail::null<>) -> bool { using namespace fmt::detail; std::tm* tm = std::localtime(&time_); if (tm) tm_ = *tm; @@ -480,8 +525,8 @@ inline std::tm localtime(std::time_t time) { #if FMT_USE_LOCAL_TIME template inline auto localtime(std::chrono::local_time time) -> std::tm { - return localtime(std::chrono::system_clock::to_time_t( - std::chrono::current_zone()->to_sys(time))); + return localtime( + detail::to_time_t(std::chrono::current_zone()->to_sys(time))); } #endif @@ -490,29 +535,29 @@ inline auto localtime(std::chrono::local_time time) -> std::tm { expressed in Coordinated Universal Time (UTC). Unlike ``std::gmtime``, this function is thread-safe on most platforms. */ -inline std::tm gmtime(std::time_t time) { +inline auto gmtime(std::time_t time) -> std::tm { struct dispatcher { std::time_t time_; std::tm tm_; dispatcher(std::time_t t) : time_(t) {} - bool run() { + auto run() -> bool { using namespace fmt::detail; return handle(gmtime_r(&time_, &tm_)); } - bool handle(std::tm* tm) { return tm != nullptr; } + auto handle(std::tm* tm) -> bool { return tm != nullptr; } - bool handle(detail::null<>) { + auto handle(detail::null<>) -> bool { using namespace fmt::detail; return fallback(gmtime_s(&tm_, &time_)); } - bool fallback(int res) { return res == 0; } + auto fallback(int res) -> bool { return res == 0; } #if !FMT_MSC_VERSION - bool fallback(detail::null<>) { + auto fallback(detail::null<>) -> bool { std::tm* tm = std::gmtime(&time_); if (tm) tm_ = *tm; return tm != nullptr; @@ -525,9 +570,11 @@ inline std::tm gmtime(std::time_t time) { return gt.tm_; } -inline std::tm gmtime( - std::chrono::time_point time_point) { - return gmtime(std::chrono::system_clock::to_time_t(time_point)); +template +inline auto gmtime( + std::chrono::time_point time_point) + -> std::tm { + return gmtime(detail::to_time_t(time_point)); } namespace detail { @@ -566,7 +613,8 @@ inline void write_digit2_separated(char* buf, unsigned a, unsigned b, } } -template FMT_CONSTEXPR inline const char* get_units() { +template +FMT_CONSTEXPR inline auto get_units() -> const char* { if (std::is_same::value) return "as"; if (std::is_same::value) return "fs"; if (std::is_same::value) return "ps"; @@ -584,8 +632,9 @@ template FMT_CONSTEXPR inline const char* get_units() { if (std::is_same::value) return "Ts"; if (std::is_same::value) return "Ps"; if (std::is_same::value) return "Es"; - if (std::is_same>::value) return "m"; + if (std::is_same>::value) return "min"; if (std::is_same>::value) return "h"; + if (std::is_same>::value) return "d"; return nullptr; } @@ -621,9 +670,8 @@ auto write_padding(OutputIt out, pad_type pad) -> OutputIt { // Parses a put_time-like format string and invokes handler actions. template -FMT_CONSTEXPR const Char* parse_chrono_format(const Char* begin, - const Char* end, - Handler&& handler) { +FMT_CONSTEXPR auto parse_chrono_format(const Char* begin, const Char* end, + Handler&& handler) -> const Char* { if (begin == end || *begin == '}') return begin; if (*begin != '%') FMT_THROW(format_error("invalid format")); auto ptr = begin; @@ -954,25 +1002,25 @@ struct tm_format_checker : null_chrono_spec_handler { FMT_CONSTEXPR void on_tz_name() {} }; -inline const char* tm_wday_full_name(int wday) { +inline auto tm_wday_full_name(int wday) -> const char* { static constexpr const char* full_name_list[] = { "Sunday", "Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday"}; return wday >= 0 && wday <= 6 ? full_name_list[wday] : "?"; } -inline const char* tm_wday_short_name(int wday) { +inline auto tm_wday_short_name(int wday) -> const char* { static constexpr const char* short_name_list[] = {"Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat"}; return wday >= 0 && wday <= 6 ? short_name_list[wday] : "???"; } -inline const char* tm_mon_full_name(int mon) { +inline auto tm_mon_full_name(int mon) -> const char* { static constexpr const char* full_name_list[] = { "January", "February", "March", "April", "May", "June", "July", "August", "September", "October", "November", "December"}; return mon >= 0 && mon <= 11 ? full_name_list[mon] : "?"; } -inline const char* tm_mon_short_name(int mon) { +inline auto tm_mon_short_name(int mon) -> const char* { static constexpr const char* short_name_list[] = { "Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec", @@ -1004,21 +1052,21 @@ inline void tzset_once() { // Converts value to Int and checks that it's in the range [0, upper). template ::value)> -inline Int to_nonnegative_int(T value, Int upper) { - FMT_ASSERT(std::is_unsigned::value || - (value >= 0 && to_unsigned(value) <= to_unsigned(upper)), - "invalid value"); - (void)upper; +inline auto to_nonnegative_int(T value, Int upper) -> Int { + if (!std::is_unsigned::value && + (value < 0 || to_unsigned(value) > to_unsigned(upper))) { + FMT_THROW(fmt::format_error("chrono value is out of range")); + } return static_cast(value); } template ::value)> -inline Int to_nonnegative_int(T value, Int upper) { +inline auto to_nonnegative_int(T value, Int upper) -> Int { if (value < 0 || value > static_cast(upper)) FMT_THROW(format_error("invalid value")); return static_cast(value); } -constexpr long long pow10(std::uint32_t n) { +constexpr auto pow10(std::uint32_t n) -> long long { return n == 0 ? 1 : 10 * pow10(n - 1); } @@ -1052,13 +1100,12 @@ void write_fractional_seconds(OutputIt& out, Duration d, int precision = -1) { std::chrono::seconds::rep>::type, std::ratio<1, detail::pow10(num_fractional_digits)>>; - const auto fractional = - d - std::chrono::duration_cast(d); + const auto fractional = d - fmt_duration_cast(d); const auto subseconds = std::chrono::treat_as_floating_point< typename subsecond_precision::rep>::value ? fractional.count() - : std::chrono::duration_cast(fractional).count(); + : fmt_duration_cast(fractional).count(); auto n = static_cast>(subseconds); const int num_digits = detail::count_digits(n); @@ -1109,11 +1156,11 @@ void write_floating_seconds(memory_buffer& buf, Duration duration, num_fractional_digits = 6; } - format_to(std::back_inserter(buf), FMT_STRING("{:.{}f}"), - std::fmod(val * static_cast(Duration::period::num) / - static_cast(Duration::period::den), - static_cast(60)), - num_fractional_digits); + fmt::format_to(std::back_inserter(buf), FMT_STRING("{:.{}f}"), + std::fmod(val * static_cast(Duration::period::num) / + static_cast(Duration::period::den), + static_cast(60)), + num_fractional_digits); } template (l); } - // Algorithm: - // https://en.wikipedia.org/wiki/ISO_week_date#Calculating_the_week_number_from_a_month_and_day_of_the_month_or_ordinal_date + // Algorithm: https://en.wikipedia.org/wiki/ISO_week_date. auto iso_year_weeks(long long curr_year) const noexcept -> int { const auto prev_year = curr_year - 1; const auto curr_p = @@ -1315,7 +1361,7 @@ class tm_writer { subsecs_(subsecs), tm_(tm) {} - OutputIt out() const { return out_; } + auto out() const -> OutputIt { return out_; } FMT_CONSTEXPR void on_text(const Char* begin, const Char* end) { out_ = copy_str(begin, end, out_); @@ -1579,6 +1625,7 @@ struct chrono_format_checker : null_chrono_spec_handler { template FMT_CONSTEXPR void on_text(const Char*, const Char*) {} + FMT_CONSTEXPR void on_day_of_year() {} FMT_CONSTEXPR void on_24_hour(numeric_system, pad_type) {} FMT_CONSTEXPR void on_12_hour(numeric_system, pad_type) {} FMT_CONSTEXPR void on_minute(numeric_system, pad_type) {} @@ -1597,16 +1644,16 @@ struct chrono_format_checker : null_chrono_spec_handler { template ::value&& has_isfinite::value)> -inline bool isfinite(T) { +inline auto isfinite(T) -> bool { return true; } template ::value)> -inline T mod(T x, int y) { +inline auto mod(T x, int y) -> T { return x % static_cast(y); } template ::value)> -inline T mod(T x, int y) { +inline auto mod(T x, int y) -> T { return std::fmod(x, static_cast(y)); } @@ -1621,49 +1668,38 @@ template struct make_unsigned_or_unchanged { using type = typename std::make_unsigned::type; }; -#if FMT_SAFE_DURATION_CAST -// throwing version of safe_duration_cast -template -To fmt_safe_duration_cast(std::chrono::duration from) { - int ec; - To to = safe_duration_cast::safe_duration_cast(from, ec); - if (ec) FMT_THROW(format_error("cannot format duration")); - return to; -} -#endif - template ::value)> -inline std::chrono::duration get_milliseconds( - std::chrono::duration d) { +inline auto get_milliseconds(std::chrono::duration d) + -> std::chrono::duration { // this may overflow and/or the result may not fit in the // target type. #if FMT_SAFE_DURATION_CAST using CommonSecondsType = typename std::common_type::type; - const auto d_as_common = fmt_safe_duration_cast(d); + const auto d_as_common = fmt_duration_cast(d); const auto d_as_whole_seconds = - fmt_safe_duration_cast(d_as_common); + fmt_duration_cast(d_as_common); // this conversion should be nonproblematic const auto diff = d_as_common - d_as_whole_seconds; const auto ms = - fmt_safe_duration_cast>(diff); + fmt_duration_cast>(diff); return ms; #else - auto s = std::chrono::duration_cast(d); - return std::chrono::duration_cast(d - s); + auto s = fmt_duration_cast(d); + return fmt_duration_cast(d - s); #endif } template ::value)> -OutputIt format_duration_value(OutputIt out, Rep val, int) { +auto format_duration_value(OutputIt out, Rep val, int) -> OutputIt { return write(out, val); } template ::value)> -OutputIt format_duration_value(OutputIt out, Rep val, int precision) { +auto format_duration_value(OutputIt out, Rep val, int precision) -> OutputIt { auto specs = format_specs(); specs.precision = precision; specs.type = precision >= 0 ? presentation_type::fixed_lower @@ -1672,12 +1708,12 @@ OutputIt format_duration_value(OutputIt out, Rep val, int precision) { } template -OutputIt copy_unit(string_view unit, OutputIt out, Char) { +auto copy_unit(string_view unit, OutputIt out, Char) -> OutputIt { return std::copy(unit.begin(), unit.end(), out); } template -OutputIt copy_unit(string_view unit, OutputIt out, wchar_t) { +auto copy_unit(string_view unit, OutputIt out, wchar_t) -> OutputIt { // This works when wchar_t is UTF-32 because units only contain characters // that have the same representation in UTF-16 and UTF-32. utf8_to_utf16 u(unit); @@ -1685,7 +1721,7 @@ OutputIt copy_unit(string_view unit, OutputIt out, wchar_t) { } template -OutputIt format_duration_unit(OutputIt out) { +auto format_duration_unit(OutputIt out) -> OutputIt { if (const char* unit = get_units()) return copy_unit(string_view(unit), out, Char()); *out++ = '['; @@ -1752,18 +1788,12 @@ struct chrono_formatter { // this may overflow and/or the result may not fit in the // target type. -#if FMT_SAFE_DURATION_CAST // might need checked conversion (rep!=Rep) - auto tmpval = std::chrono::duration(val); - s = fmt_safe_duration_cast(tmpval); -#else - s = std::chrono::duration_cast( - std::chrono::duration(val)); -#endif + s = fmt_duration_cast(std::chrono::duration(val)); } // returns true if nan or inf, writes to out. - bool handle_nan_inf() { + auto handle_nan_inf() -> bool { if (isfinite(val)) { return false; } @@ -1780,17 +1810,22 @@ struct chrono_formatter { return true; } - Rep hour() const { return static_cast(mod((s.count() / 3600), 24)); } + auto days() const -> Rep { return static_cast(s.count() / 86400); } + auto hour() const -> Rep { + return static_cast(mod((s.count() / 3600), 24)); + } - Rep hour12() const { + auto hour12() const -> Rep { Rep hour = static_cast(mod((s.count() / 3600), 12)); return hour <= 0 ? 12 : hour; } - Rep minute() const { return static_cast(mod((s.count() / 60), 60)); } - Rep second() const { return static_cast(mod(s.count(), 60)); } + auto minute() const -> Rep { + return static_cast(mod((s.count() / 60), 60)); + } + auto second() const -> Rep { return static_cast(mod(s.count(), 60)); } - std::tm time() const { + auto time() const -> std::tm { auto time = std::tm(); time.tm_hour = to_nonnegative_int(hour(), 24); time.tm_min = to_nonnegative_int(minute(), 60); @@ -1858,10 +1893,14 @@ struct chrono_formatter { void on_dec0_week_of_year(numeric_system) {} void on_dec1_week_of_year(numeric_system) {} void on_iso_week_of_year(numeric_system) {} - void on_day_of_year() {} void on_day_of_month(numeric_system) {} void on_day_of_month_space(numeric_system) {} + void on_day_of_year() { + if (handle_nan_inf()) return; + write(days(), 0); + } + void on_24_hour(numeric_system ns, pad_type pad) { if (handle_nan_inf()) return; @@ -1968,7 +2007,7 @@ class weekday { weekday() = default; explicit constexpr weekday(unsigned wd) noexcept : value(static_cast(wd != 7 ? wd : 0)) {} - constexpr unsigned c_encoding() const noexcept { return value; } + constexpr auto c_encoding() const noexcept -> unsigned { return value; } }; class year_month_day {}; @@ -2083,25 +2122,22 @@ struct formatter, period::num != 1 || period::den != 1 || std::is_floating_point::value)) { const auto epoch = val.time_since_epoch(); - auto subsecs = std::chrono::duration_cast( - epoch - std::chrono::duration_cast(epoch)); + auto subsecs = detail::fmt_duration_cast( + epoch - detail::fmt_duration_cast(epoch)); if (subsecs.count() < 0) { auto second = - std::chrono::duration_cast(std::chrono::seconds(1)); + detail::fmt_duration_cast(std::chrono::seconds(1)); if (epoch.count() < ((Duration::min)() + second).count()) FMT_THROW(format_error("duration is too small")); subsecs += second; val -= second; } - return formatter::do_format( - gmtime(std::chrono::time_point_cast(val)), ctx, - &subsecs); + return formatter::do_format(gmtime(val), ctx, &subsecs); } - return formatter::format( - gmtime(std::chrono::time_point_cast(val)), ctx); + return formatter::format(gmtime(val), ctx); } }; @@ -2120,17 +2156,13 @@ struct formatter, Char> if (period::num != 1 || period::den != 1 || std::is_floating_point::value) { const auto epoch = val.time_since_epoch(); - const auto subsecs = std::chrono::duration_cast( - epoch - std::chrono::duration_cast(epoch)); + const auto subsecs = detail::fmt_duration_cast( + epoch - detail::fmt_duration_cast(epoch)); - return formatter::do_format( - localtime(std::chrono::time_point_cast(val)), - ctx, &subsecs); + return formatter::do_format(localtime(val), ctx, &subsecs); } - return formatter::format( - localtime(std::chrono::time_point_cast(val)), - ctx); + return formatter::format(localtime(val), ctx); } }; #endif diff --git a/src/fmt/color.h b/src/fmt/color.h index 8697e1ca0ba..464519e5820 100644 --- a/src/fmt/color.h +++ b/src/fmt/color.h @@ -233,7 +233,7 @@ class text_style { FMT_CONSTEXPR text_style(emphasis em = emphasis()) noexcept : set_foreground_color(), set_background_color(), ems(em) {} - FMT_CONSTEXPR text_style& operator|=(const text_style& rhs) { + FMT_CONSTEXPR auto operator|=(const text_style& rhs) -> text_style& { if (!set_foreground_color) { set_foreground_color = rhs.set_foreground_color; foreground_color = rhs.foreground_color; @@ -257,29 +257,29 @@ class text_style { return *this; } - friend FMT_CONSTEXPR text_style operator|(text_style lhs, - const text_style& rhs) { + friend FMT_CONSTEXPR auto operator|(text_style lhs, const text_style& rhs) + -> text_style { return lhs |= rhs; } - FMT_CONSTEXPR bool has_foreground() const noexcept { + FMT_CONSTEXPR auto has_foreground() const noexcept -> bool { return set_foreground_color; } - FMT_CONSTEXPR bool has_background() const noexcept { + FMT_CONSTEXPR auto has_background() const noexcept -> bool { return set_background_color; } - FMT_CONSTEXPR bool has_emphasis() const noexcept { + FMT_CONSTEXPR auto has_emphasis() const noexcept -> bool { return static_cast(ems) != 0; } - FMT_CONSTEXPR detail::color_type get_foreground() const noexcept { + FMT_CONSTEXPR auto get_foreground() const noexcept -> detail::color_type { FMT_ASSERT(has_foreground(), "no foreground specified for this style"); return foreground_color; } - FMT_CONSTEXPR detail::color_type get_background() const noexcept { + FMT_CONSTEXPR auto get_background() const noexcept -> detail::color_type { FMT_ASSERT(has_background(), "no background specified for this style"); return background_color; } - FMT_CONSTEXPR emphasis get_emphasis() const noexcept { + FMT_CONSTEXPR auto get_emphasis() const noexcept -> emphasis { FMT_ASSERT(has_emphasis(), "no emphasis specified for this style"); return ems; } @@ -297,9 +297,11 @@ class text_style { } } - friend FMT_CONSTEXPR text_style fg(detail::color_type foreground) noexcept; + friend FMT_CONSTEXPR auto fg(detail::color_type foreground) noexcept + -> text_style; - friend FMT_CONSTEXPR text_style bg(detail::color_type background) noexcept; + friend FMT_CONSTEXPR auto bg(detail::color_type background) noexcept + -> text_style; detail::color_type foreground_color; detail::color_type background_color; @@ -309,16 +311,19 @@ class text_style { }; /** Creates a text style from the foreground (text) color. */ -FMT_CONSTEXPR inline text_style fg(detail::color_type foreground) noexcept { +FMT_CONSTEXPR inline auto fg(detail::color_type foreground) noexcept + -> text_style { return text_style(true, foreground); } /** Creates a text style from the background color. */ -FMT_CONSTEXPR inline text_style bg(detail::color_type background) noexcept { +FMT_CONSTEXPR inline auto bg(detail::color_type background) noexcept + -> text_style { return text_style(false, background); } -FMT_CONSTEXPR inline text_style operator|(emphasis lhs, emphasis rhs) noexcept { +FMT_CONSTEXPR inline auto operator|(emphasis lhs, emphasis rhs) noexcept + -> text_style { return text_style(lhs) | rhs; } @@ -384,8 +389,8 @@ template struct ansi_color_escape { } FMT_CONSTEXPR operator const Char*() const noexcept { return buffer; } - FMT_CONSTEXPR const Char* begin() const noexcept { return buffer; } - FMT_CONSTEXPR_CHAR_TRAITS const Char* end() const noexcept { + FMT_CONSTEXPR auto begin() const noexcept -> const Char* { return buffer; } + FMT_CONSTEXPR20 auto end() const noexcept -> const Char* { return buffer + std::char_traits::length(buffer); } @@ -400,25 +405,27 @@ template struct ansi_color_escape { out[2] = static_cast('0' + c % 10); out[3] = static_cast(delimiter); } - static FMT_CONSTEXPR bool has_emphasis(emphasis em, emphasis mask) noexcept { + static FMT_CONSTEXPR auto has_emphasis(emphasis em, emphasis mask) noexcept + -> bool { return static_cast(em) & static_cast(mask); } }; template -FMT_CONSTEXPR ansi_color_escape make_foreground_color( - detail::color_type foreground) noexcept { +FMT_CONSTEXPR auto make_foreground_color(detail::color_type foreground) noexcept + -> ansi_color_escape { return ansi_color_escape(foreground, "\x1b[38;2;"); } template -FMT_CONSTEXPR ansi_color_escape make_background_color( - detail::color_type background) noexcept { +FMT_CONSTEXPR auto make_background_color(detail::color_type background) noexcept + -> ansi_color_escape { return ansi_color_escape(background, "\x1b[48;2;"); } template -FMT_CONSTEXPR ansi_color_escape make_emphasis(emphasis em) noexcept { +FMT_CONSTEXPR auto make_emphasis(emphasis em) noexcept + -> ansi_color_escape { return ansi_color_escape(em); } @@ -427,9 +434,10 @@ template inline void reset_color(buffer& buffer) { buffer.append(reset_color.begin(), reset_color.end()); } -template struct styled_arg { +template struct styled_arg : detail::view { const T& value; text_style style; + styled_arg(const T& v, text_style s) : value(v), style(s) {} }; template @@ -510,9 +518,10 @@ void print(const text_style& ts, const S& format_str, const Args&... args) { } template > -inline std::basic_string vformat( +inline auto vformat( const text_style& ts, const S& format_str, - basic_format_args>> args) { + basic_format_args>> args) + -> std::basic_string { basic_memory_buffer buf; detail::vformat_to(buf, ts, detail::to_string_view(format_str), args); return fmt::to_string(buf); @@ -531,8 +540,8 @@ inline std::basic_string vformat( \endrst */ template > -inline std::basic_string format(const text_style& ts, const S& format_str, - const Args&... args) { +inline auto format(const text_style& ts, const S& format_str, + const Args&... args) -> std::basic_string { return fmt::vformat(ts, detail::to_string_view(format_str), fmt::make_format_args>(args...)); } @@ -542,9 +551,10 @@ inline std::basic_string format(const text_style& ts, const S& format_str, */ template ::value)> -OutputIt vformat_to( - OutputIt out, const text_style& ts, basic_string_view format_str, - basic_format_args>> args) { +auto vformat_to(OutputIt out, const text_style& ts, + basic_string_view format_str, + basic_format_args>> args) + -> OutputIt { auto&& buf = detail::get_buffer(out); detail::vformat_to(buf, ts, format_str, args); return detail::get_iterator(buf, out); @@ -562,9 +572,10 @@ OutputIt vformat_to( fmt::emphasis::bold | fg(fmt::color::red), "{}", 42); \endrst */ -template >::value&& - detail::is_string::value> +template < + typename OutputIt, typename S, typename... Args, + bool enable = detail::is_output_iterator>::value && + detail::is_string::value> inline auto format_to(OutputIt out, const text_style& ts, const S& format_str, Args&&... args) -> typename std::enable_if::type { diff --git a/src/fmt/compile.h b/src/fmt/compile.h index af76507f07f..71fa69c67ec 100644 --- a/src/fmt/compile.h +++ b/src/fmt/compile.h @@ -14,8 +14,8 @@ FMT_BEGIN_NAMESPACE namespace detail { template -FMT_CONSTEXPR inline counting_iterator copy_str(InputIt begin, InputIt end, - counting_iterator it) { +FMT_CONSTEXPR inline auto copy_str(InputIt begin, InputIt end, + counting_iterator it) -> counting_iterator { return it + (end - begin); } @@ -57,7 +57,7 @@ struct udl_compiled_string : compiled_string { #endif template -const T& first(const T& value, const Tail&...) { +auto first(const T& value, const Tail&...) -> const T& { return value; } @@ -489,18 +489,19 @@ FMT_CONSTEXPR OutputIt format_to(OutputIt out, const S&, Args&&... args) { template ::value)> -format_to_n_result format_to_n(OutputIt out, size_t n, - const S& format_str, Args&&... args) { +auto format_to_n(OutputIt out, size_t n, const S& format_str, Args&&... args) + -> format_to_n_result { using traits = detail::fixed_buffer_traits; auto buf = detail::iterator_buffer(out, n); - format_to(std::back_inserter(buf), format_str, std::forward(args)...); + fmt::format_to(std::back_inserter(buf), format_str, + std::forward(args)...); return {buf.out(), buf.count()}; } template ::value)> -FMT_CONSTEXPR20 size_t formatted_size(const S& format_str, - const Args&... args) { +FMT_CONSTEXPR20 auto formatted_size(const S& format_str, const Args&... args) + -> size_t { return fmt::format_to(detail::counting_iterator(), format_str, args...) .count(); } diff --git a/src/fmt/core.h b/src/fmt/core.h index 9f7de781bb2..6a53b8c52c0 100644 --- a/src/fmt/core.h +++ b/src/fmt/core.h @@ -8,17 +8,15 @@ #ifndef FMT_CORE_H_ #define FMT_CORE_H_ -#include // std::byte -#include // std::FILE -#include // std::strlen -#include -#include -#include // std::addressof -#include -#include +#include // std::byte +#include // std::FILE +#include // std::strlen +#include // CHAR_BIT +#include // std::string +#include // std::enable_if // The fmt library version in the form major * 10000 + minor * 100 + patch. -#define FMT_VERSION 100100 +#define FMT_VERSION 100200 #if defined(__clang__) && !defined(__ibmxl__) # define FMT_CLANG_VERSION (__clang_major__ * 100 + __clang_minor__) @@ -58,6 +56,12 @@ # define FMT_MSC_WARNING(...) #endif +#ifdef _GLIBCXX_RELEASE +# define FMT_GLIBCXX_RELEASE _GLIBCXX_RELEASE +#else +# define FMT_GLIBCXX_RELEASE 0 +#endif + #ifdef _MSVC_LANG # define FMT_CPLUSPLUS _MSVC_LANG #else @@ -88,6 +92,20 @@ #define FMT_HAS_CPP17_ATTRIBUTE(attribute) \ (FMT_CPLUSPLUS >= 201703L && FMT_HAS_CPP_ATTRIBUTE(attribute)) +#ifndef FMT_DEPRECATED +# if FMT_HAS_CPP14_ATTRIBUTE(deprecated) || FMT_MSC_VERSION >= 1900 +# define FMT_DEPRECATED [[deprecated]] +# else +# if (defined(__GNUC__) && !defined(__LCC__)) || defined(__clang__) +# define FMT_DEPRECATED __attribute__((deprecated)) +# elif FMT_MSC_VERSION +# define FMT_DEPRECATED __declspec(deprecated) +# else +# define FMT_DEPRECATED /* deprecated */ +# endif +# endif +#endif + // Check if relaxed C++14 constexpr is supported. // GCC doesn't allow throw in constexpr until version 6 (bug 67371). #ifndef FMT_USE_CONSTEXPR @@ -105,30 +123,17 @@ # define FMT_CONSTEXPR #endif -#if ((FMT_CPLUSPLUS >= 202002L) && \ - (!defined(_GLIBCXX_RELEASE) || _GLIBCXX_RELEASE > 9)) || \ - (FMT_CPLUSPLUS >= 201709L && FMT_GCC_VERSION >= 1002) +#if (FMT_CPLUSPLUS >= 202002L || \ + (FMT_CPLUSPLUS >= 201709L && FMT_GCC_VERSION >= 1002)) && \ + ((!FMT_GLIBCXX_RELEASE || FMT_GLIBCXX_RELEASE >= 10) && \ + (!defined(_LIBCPP_VERSION) || _LIBCPP_VERSION >= 10000) && \ + (!FMT_MSC_VERSION || FMT_MSC_VERSION >= 1928)) && \ + defined(__cpp_lib_is_constant_evaluated) # define FMT_CONSTEXPR20 constexpr #else # define FMT_CONSTEXPR20 #endif -// Check if constexpr std::char_traits<>::{compare,length} are supported. -#if defined(__GLIBCXX__) -# if FMT_CPLUSPLUS >= 201703L && defined(_GLIBCXX_RELEASE) && \ - _GLIBCXX_RELEASE >= 7 // GCC 7+ libstdc++ has _GLIBCXX_RELEASE. -# define FMT_CONSTEXPR_CHAR_TRAITS constexpr -# endif -#elif defined(_LIBCPP_VERSION) && FMT_CPLUSPLUS >= 201703L && \ - _LIBCPP_VERSION >= 4000 -# define FMT_CONSTEXPR_CHAR_TRAITS constexpr -#elif FMT_MSC_VERSION >= 1914 && FMT_CPLUSPLUS >= 201703L -# define FMT_CONSTEXPR_CHAR_TRAITS constexpr -#endif -#ifndef FMT_CONSTEXPR_CHAR_TRAITS -# define FMT_CONSTEXPR_CHAR_TRAITS -#endif - // Check if exceptions are disabled. #ifndef FMT_EXCEPTIONS # if (defined(__GNUC__) && !defined(__EXCEPTIONS)) || \ @@ -191,33 +196,25 @@ # define FMT_END_EXPORT #endif +#if FMT_GCC_VERSION || FMT_CLANG_VERSION +# define FMT_VISIBILITY(value) __attribute__((visibility(value))) +#else +# define FMT_VISIBILITY(value) +#endif + #if !defined(FMT_HEADER_ONLY) && defined(_WIN32) -# ifdef FMT_LIB_EXPORT +# if defined(FMT_LIB_EXPORT) # define FMT_API __declspec(dllexport) # elif defined(FMT_SHARED) # define FMT_API __declspec(dllimport) # endif -#else -# if defined(FMT_LIB_EXPORT) || defined(FMT_SHARED) -# if defined(__GNUC__) || defined(__clang__) -# define FMT_API __attribute__((visibility("default"))) -# endif -# endif +#elif defined(FMT_LIB_EXPORT) || defined(FMT_SHARED) +# define FMT_API FMT_VISIBILITY("default") #endif #ifndef FMT_API # define FMT_API #endif -// libc++ supports string_view in pre-c++17. -#if FMT_HAS_INCLUDE() && \ - (FMT_CPLUSPLUS >= 201703L || defined(_LIBCPP_VERSION)) -# include -# define FMT_USE_STRING_VIEW -#elif FMT_HAS_INCLUDE("experimental/string_view") && FMT_CPLUSPLUS >= 201402L -# include -# define FMT_USE_EXPERIMENTAL_STRING_VIEW -#endif - #ifndef FMT_UNICODE # define FMT_UNICODE !FMT_MSC_VERSION #endif @@ -228,8 +225,9 @@ __apple_build_version__ >= 14000029L) && \ FMT_CPLUSPLUS >= 202002L) || \ (defined(__cpp_consteval) && \ - (!FMT_MSC_VERSION || _MSC_FULL_VER >= 193030704)) -// consteval is broken in MSVC before VS2022 and Apple clang before 14. + (!FMT_MSC_VERSION || FMT_MSC_VERSION >= 1929)) +// consteval is broken in MSVC before VS2019 version 16.10 and Apple clang +// before 14. # define FMT_CONSTEVAL consteval # define FMT_HAS_CONSTEVAL # else @@ -248,6 +246,15 @@ # endif #endif +// GCC < 5 requires this-> in decltype. +#ifndef FMT_DECLTYPE_THIS +# if FMT_GCC_VERSION && FMT_GCC_VERSION < 500 +# define FMT_DECLTYPE_THIS this-> +# else +# define FMT_DECLTYPE_THIS +# endif +#endif + // Enable minimal optimizations for more compact code in debug mode. FMT_GCC_PRAGMA("GCC push_options") #if !defined(__OPTIMIZE__) && !defined(__NVCOMPILER) && !defined(__LCC__) && \ @@ -269,20 +276,57 @@ template using remove_const_t = typename std::remove_const::type; template using remove_cvref_t = typename std::remove_cv>::type; -template struct type_identity { using type = T; }; +template struct type_identity { + using type = T; +}; template using type_identity_t = typename type_identity::type; template using underlying_t = typename std::underlying_type::type; -// Checks whether T is a container with contiguous storage. -template struct is_contiguous : std::false_type {}; -template -struct is_contiguous> : std::true_type {}; +#if FMT_GCC_VERSION && FMT_GCC_VERSION < 500 +// A workaround for gcc 4.8 to make void_t work in a SFINAE context. +template struct void_t_impl { + using type = void; +}; +template using void_t = typename void_t_impl::type; +#else +template using void_t = void; +#endif struct monostate { constexpr monostate() {} }; +// An implementation of back_insert_iterator to avoid dependency on . +template class back_insert_iterator { + private: + Container* container_; + + friend auto get_container(back_insert_iterator it) -> Container& { + return *it.container_; + } + + public: + using difference_type = ptrdiff_t; + FMT_UNCHECKED_ITERATOR(back_insert_iterator); + + explicit back_insert_iterator(Container& c) : container_(&c) {} + + auto operator=(const typename Container::value_type& value) + -> back_insert_iterator& { + container_->push_back(value); + return *this; + } + auto operator*() -> back_insert_iterator& { return *this; } + auto operator++() -> back_insert_iterator& { return *this; } + auto operator++(int) -> back_insert_iterator { return *this; } +}; + +template +auto back_inserter(Container& c) -> back_insert_iterator { + return {c}; +} + // An enable_if helper to be used in template parameters which results in much // shorter symbols: https://godbolt.org/z/sWw4vP. Extra parentheses are needed // to workaround a bug in MSVC 2019 (see #1140 and #1186). @@ -310,10 +354,9 @@ template FMT_CONSTEXPR void ignore_unused(const T&...) {} constexpr FMT_INLINE auto is_constant_evaluated( bool default_value = false) noexcept -> bool { // Workaround for incompatibility between libstdc++ consteval-based -// std::is_constant_evaluated() implementation and clang-14. -// https://github.com/fmtlib/fmt/issues/3247 -#if FMT_CPLUSPLUS >= 202002L && defined(_GLIBCXX_RELEASE) && \ - _GLIBCXX_RELEASE >= 12 && \ +// std::is_constant_evaluated() implementation and clang-14: +// https://github.com/fmtlib/fmt/issues/3247. +#if FMT_CPLUSPLUS >= 202002L && FMT_GLIBCXX_RELEASE >= 12 && \ (FMT_CLANG_VERSION >= 1400 && FMT_CLANG_VERSION < 1500) ignore_unused(default_value); return __builtin_is_constant_evaluated(); @@ -346,15 +389,6 @@ FMT_NORETURN FMT_API void assert_fail(const char* file, int line, # endif #endif -#if defined(FMT_USE_STRING_VIEW) -template using std_string_view = std::basic_string_view; -#elif defined(FMT_USE_EXPERIMENTAL_STRING_VIEW) -template -using std_string_view = std::experimental::basic_string_view; -#else -template struct std_string_view {}; -#endif - #ifdef FMT_USE_INT128 // Do nothing. #elif defined(__SIZEOF_INT128__) && !defined(__NVCC__) && \ @@ -386,6 +420,15 @@ FMT_CONSTEXPR auto to_unsigned(Int value) -> return static_cast::type>(value); } +template +struct is_string_like : std::false_type {}; + +// A heuristic to detect std::string and std::string_view. +template +struct is_string_like().find_first_of( + typename T::value_type(), 0))>> : std::true_type { +}; + FMT_CONSTEXPR inline auto is_utf8() -> bool { FMT_MSC_WARNING(suppress : 4566) constexpr unsigned char section[] = "\u00A7"; @@ -394,8 +437,33 @@ FMT_CONSTEXPR inline auto is_utf8() -> bool { return FMT_UNICODE || (sizeof(section) == 3 && uchar(section[0]) == 0xC2 && uchar(section[1]) == 0xA7); } + +template FMT_CONSTEXPR auto length(const Char* s) -> size_t { + size_t len = 0; + while (*s++) ++len; + return len; +} + +template +FMT_CONSTEXPR auto compare(const Char* s1, const Char* s2, std::size_t n) + -> int { + for (; n != 0; ++s1, ++s2, --n) { + if (*s1 < *s2) return -1; + if (*s1 > *s2) return 1; + } + return 0; +} } // namespace detail +template +using basic_string = + std::basic_string, std::allocator>; + +// Checks whether T is a container with contiguous storage. +template struct is_contiguous : std::false_type {}; +template +struct is_contiguous> : std::true_type {}; + /** An implementation of ``std::basic_string_view`` for pre-C++17. It provides a subset of the API. ``fmt::basic_string_view`` is used for format strings even @@ -420,29 +488,25 @@ template class basic_string_view { : data_(s), size_(count) {} /** - \rst - Constructs a string reference object from a C string computing - the size with ``std::char_traits::length``. - \endrst + Constructs a string reference object from a C string. */ - FMT_CONSTEXPR_CHAR_TRAITS + FMT_CONSTEXPR20 FMT_INLINE basic_string_view(const Char* s) : data_(s), size_(detail::const_check(std::is_same::value && - !detail::is_constant_evaluated(true)) + !detail::is_constant_evaluated(false)) ? std::strlen(reinterpret_cast(s)) - : std::char_traits::length(s)) {} - - /** Constructs a string reference from a ``std::basic_string`` object. */ - template - FMT_CONSTEXPR basic_string_view( - const std::basic_string& s) noexcept - : data_(s.data()), size_(s.size()) {} + : detail::length(s)) {} - template >::value)> - FMT_CONSTEXPR basic_string_view(S s) noexcept + /** + Constructs a string reference from a ``std::basic_string`` or a + ``std::basic_string_view`` object. + */ + template ::value&& std::is_same< + typename S::value_type, Char>::value)> + FMT_CONSTEXPR basic_string_view(const S& s) noexcept : data_(s.data()), size_(s.size()) {} /** Returns a pointer to the string data. */ @@ -463,30 +527,28 @@ template class basic_string_view { size_ -= n; } - FMT_CONSTEXPR_CHAR_TRAITS bool starts_with( - basic_string_view sv) const noexcept { - return size_ >= sv.size_ && - std::char_traits::compare(data_, sv.data_, sv.size_) == 0; + FMT_CONSTEXPR auto starts_with(basic_string_view sv) const noexcept + -> bool { + return size_ >= sv.size_ && detail::compare(data_, sv.data_, sv.size_) == 0; } - FMT_CONSTEXPR_CHAR_TRAITS bool starts_with(Char c) const noexcept { - return size_ >= 1 && std::char_traits::eq(*data_, c); + FMT_CONSTEXPR auto starts_with(Char c) const noexcept -> bool { + return size_ >= 1 && *data_ == c; } - FMT_CONSTEXPR_CHAR_TRAITS bool starts_with(const Char* s) const { + FMT_CONSTEXPR auto starts_with(const Char* s) const -> bool { return starts_with(basic_string_view(s)); } // Lexicographically compare this string reference to other. - FMT_CONSTEXPR_CHAR_TRAITS auto compare(basic_string_view other) const -> int { + FMT_CONSTEXPR auto compare(basic_string_view other) const -> int { size_t str_size = size_ < other.size_ ? size_ : other.size_; - int result = std::char_traits::compare(data_, other.data_, str_size); + int result = detail::compare(data_, other.data_, str_size); if (result == 0) result = size_ == other.size_ ? 0 : (size_ < other.size_ ? -1 : 1); return result; } - FMT_CONSTEXPR_CHAR_TRAITS friend auto operator==(basic_string_view lhs, - basic_string_view rhs) - -> bool { + FMT_CONSTEXPR friend auto operator==(basic_string_view lhs, + basic_string_view rhs) -> bool { return lhs.compare(rhs) == 0; } friend auto operator!=(basic_string_view lhs, basic_string_view rhs) -> bool { @@ -526,21 +588,16 @@ template ::value)> FMT_INLINE auto to_string_view(const Char* s) -> basic_string_view { return s; } -template -inline auto to_string_view(const std::basic_string& s) - -> basic_string_view { - return s; +template ::value)> +inline auto to_string_view(const S& s) + -> basic_string_view { + return s; // std::basic_string[_view] } template constexpr auto to_string_view(basic_string_view s) -> basic_string_view { return s; } -template >::value)> -inline auto to_string_view(std_string_view s) -> basic_string_view { - return s; -} template ::value)> constexpr auto to_string_view(const S& s) -> basic_string_view { @@ -609,10 +666,10 @@ FMT_TYPE_CONSTANT(const Char*, cstring_type); FMT_TYPE_CONSTANT(basic_string_view, string_type); FMT_TYPE_CONSTANT(const void*, pointer_type); -constexpr bool is_integral_type(type t) { +constexpr auto is_integral_type(type t) -> bool { return t > type::none_type && t <= type::last_integer_type; } -constexpr bool is_arithmetic_type(type t) { +constexpr auto is_arithmetic_type(type t) -> bool { return t > type::none_type && t <= type::last_numeric_type; } @@ -635,21 +692,10 @@ enum { cstring_set = set(type::cstring_type), pointer_set = set(type::pointer_type) }; - -FMT_NORETURN FMT_API void throw_format_error(const char* message); - -struct error_handler { - constexpr error_handler() = default; - - // This function is intentionally not constexpr to give a compile-time error. - FMT_NORETURN void on_error(const char* message) { - throw_format_error(message); - } -}; } // namespace detail /** Throws ``format_error`` with a given message. */ -using detail::throw_format_error; +FMT_NORETURN FMT_API void throw_format_error(const char* message); /** String's character type. */ template using char_t = typename detail::char_t_impl::type; @@ -701,7 +747,7 @@ template class basic_format_parse_context { */ FMT_CONSTEXPR auto next_arg_id() -> int { if (next_arg_id_ < 0) { - detail::throw_format_error( + throw_format_error( "cannot switch from manual to automatic argument indexing"); return 0; } @@ -716,7 +762,7 @@ template class basic_format_parse_context { */ FMT_CONSTEXPR void check_arg_id(int id) { if (next_arg_id_ > 0) { - detail::throw_format_error( + throw_format_error( "cannot switch from automatic to manual argument indexing"); return; } @@ -769,35 +815,6 @@ class compile_parse_context : public basic_format_parse_context { } }; -// Extracts a reference to the container from back_insert_iterator. -template -inline auto get_container(std::back_insert_iterator it) - -> Container& { - using base = std::back_insert_iterator; - struct accessor : base { - accessor(base b) : base(b) {} - using base::container; - }; - return *accessor(it).container; -} - -template -FMT_CONSTEXPR auto copy_str(InputIt begin, InputIt end, OutputIt out) - -> OutputIt { - while (begin != end) *out++ = static_cast(*begin++); - return out; -} - -template , U>::value&& is_char::value)> -FMT_CONSTEXPR auto copy_str(T* begin, T* end, U* out) -> U* { - if (is_constant_evaluated()) return copy_str(begin, end, out); - auto size = to_unsigned(end - begin); - if (size > 0) memcpy(out, begin, size * sizeof(U)); - return out + size; -} - /** \rst A contiguous memory buffer with an optional growing ability. It is an internal @@ -810,13 +827,18 @@ template class buffer { size_t size_; size_t capacity_; + using grow_fun = void (*)(buffer& buf, size_t capacity); + grow_fun grow_; + protected: // Don't initialize ptr_ since it is not accessed to save a few cycles. FMT_MSC_WARNING(suppress : 26495) - buffer(size_t sz) noexcept : size_(sz), capacity_(sz) {} + FMT_CONSTEXPR buffer(grow_fun grow, size_t sz) noexcept + : size_(sz), capacity_(sz), grow_(grow) {} - FMT_CONSTEXPR20 buffer(T* p = nullptr, size_t sz = 0, size_t cap = 0) noexcept - : ptr_(p), size_(sz), capacity_(cap) {} + FMT_CONSTEXPR20 buffer(grow_fun grow, T* p = nullptr, size_t sz = 0, + size_t cap = 0) noexcept + : ptr_(p), size_(sz), capacity_(cap), grow_(grow) {} FMT_CONSTEXPR20 ~buffer() = default; buffer(buffer&&) = default; @@ -827,9 +849,6 @@ template class buffer { capacity_ = buf_capacity; } - /** Increases the buffer capacity to hold at least *capacity* elements. */ - virtual FMT_CONSTEXPR20 void grow(size_t capacity) = 0; - public: using value_type = T; using const_reference = const T&; @@ -868,7 +887,7 @@ template class buffer { // for at least one additional element either by increasing the capacity or by // flushing the buffer if it is full. FMT_CONSTEXPR20 void try_reserve(size_t new_capacity) { - if (new_capacity > capacity_) grow(new_capacity); + if (new_capacity > capacity_) grow_(*this, new_capacity); } FMT_CONSTEXPR20 void push_back(const T& value) { @@ -917,22 +936,25 @@ class iterator_buffer final : public Traits, public buffer { enum { buffer_size = 256 }; T data_[buffer_size]; - protected: - FMT_CONSTEXPR20 void grow(size_t) override { - if (this->size() == buffer_size) flush(); + static FMT_CONSTEXPR20 void grow(buffer& buf, size_t) { + if (buf.size() == buffer_size) static_cast(buf).flush(); } void flush() { auto size = this->size(); this->clear(); - out_ = copy_str(data_, data_ + this->limit(size), out_); + const T* begin = data_; + const T* end = begin + this->limit(size); + while (begin != end) *out_++ = *begin++; } public: explicit iterator_buffer(OutputIt out, size_t n = buffer_size) - : Traits(n), buffer(data_, 0, buffer_size), out_(out) {} + : Traits(n), buffer(grow, data_, 0, buffer_size), out_(out) {} iterator_buffer(iterator_buffer&& other) - : Traits(other), buffer(data_, 0, buffer_size), out_(other.out_) {} + : Traits(other), + buffer(grow, data_, 0, buffer_size), + out_(other.out_) {} ~iterator_buffer() { flush(); } auto out() -> OutputIt { @@ -951,9 +973,9 @@ class iterator_buffer final enum { buffer_size = 256 }; T data_[buffer_size]; - protected: - FMT_CONSTEXPR20 void grow(size_t) override { - if (this->size() == this->capacity()) flush(); + static FMT_CONSTEXPR20 void grow(buffer& buf, size_t) { + if (buf.size() == buf.capacity()) + static_cast(buf).flush(); } void flush() { @@ -967,10 +989,10 @@ class iterator_buffer final public: explicit iterator_buffer(T* out, size_t n = buffer_size) - : fixed_buffer_traits(n), buffer(out, 0, n), out_(out) {} + : fixed_buffer_traits(n), buffer(grow, out, 0, n), out_(out) {} iterator_buffer(iterator_buffer&& other) : fixed_buffer_traits(other), - buffer(std::move(other)), + buffer(static_cast(other)), out_(other.out_) { if (this->data() != out_) { this->set(data_, buffer_size); @@ -989,38 +1011,37 @@ class iterator_buffer final }; template class iterator_buffer final : public buffer { - protected: - FMT_CONSTEXPR20 void grow(size_t) override {} - public: - explicit iterator_buffer(T* out, size_t = 0) : buffer(out, 0, ~size_t()) {} + explicit iterator_buffer(T* out, size_t = 0) + : buffer([](buffer&, size_t) {}, out, 0, ~size_t()) {} auto out() -> T* { return &*this->end(); } }; // A buffer that writes to a container with the contiguous storage. template -class iterator_buffer, +class iterator_buffer, enable_if_t::value, typename Container::value_type>> final : public buffer { private: + using value_type = typename Container::value_type; Container& container_; - protected: - FMT_CONSTEXPR20 void grow(size_t capacity) override { - container_.resize(capacity); - this->set(&container_[0], capacity); + static FMT_CONSTEXPR20 void grow(buffer& buf, size_t capacity) { + auto& self = static_cast(buf); + self.container_.resize(capacity); + self.set(&self.container_[0], capacity); } public: explicit iterator_buffer(Container& c) - : buffer(c.size()), container_(c) {} - explicit iterator_buffer(std::back_insert_iterator out, size_t = 0) + : buffer(grow, c.size()), container_(c) {} + explicit iterator_buffer(back_insert_iterator out, size_t = 0) : iterator_buffer(get_container(out)) {} - auto out() -> std::back_insert_iterator { - return std::back_inserter(container_); + auto out() -> back_insert_iterator { + return fmt::back_inserter(container_); } }; @@ -1031,15 +1052,14 @@ template class counting_buffer final : public buffer { T data_[buffer_size]; size_t count_ = 0; - protected: - FMT_CONSTEXPR20 void grow(size_t) override { - if (this->size() != buffer_size) return; - count_ += this->size(); - this->clear(); + static FMT_CONSTEXPR20 void grow(buffer& buf, size_t) { + if (buf.size() != buffer_size) return; + static_cast(buf).count_ += buf.size(); + buf.clear(); } public: - counting_buffer() : buffer(data_, 0, buffer_size) {} + counting_buffer() : buffer(grow, data_, 0, buffer_size) {} auto count() -> size_t { return count_ + this->size(); } }; @@ -1053,7 +1073,7 @@ FMT_CONSTEXPR void basic_format_parse_context::do_check_arg_id(int id) { (!FMT_GCC_VERSION || FMT_GCC_VERSION >= 1200)) { using context = detail::compile_parse_context; if (id >= static_cast(this)->num_args()) - detail::throw_format_error("argument not found"); + throw_format_error("argument not found"); } } @@ -1085,18 +1105,29 @@ template using has_formatter = std::is_constructible>; -// An output iterator that appends to a buffer. -// It is used to reduce symbol sizes for the common case. -class appender : public std::back_insert_iterator> { - using base = std::back_insert_iterator>; +// An output iterator that appends to a buffer. It is used instead of +// back_insert_iterator to reduce symbol sizes for the common case. +class appender { + private: + detail::buffer* buffer_; + + friend auto get_container(appender app) -> detail::buffer& { + return *app.buffer_; + } public: - using std::back_insert_iterator>::back_insert_iterator; - appender(base it) noexcept : base(it) {} + using difference_type = ptrdiff_t; FMT_UNCHECKED_ITERATOR(appender); - auto operator++() noexcept -> appender& { return *this; } - auto operator++(int) noexcept -> appender { return *this; } + appender(detail::buffer& buf) : buffer_(&buf) {} + + auto operator=(char c) -> appender& { + buffer_->push_back(c); + return *this; + } + auto operator*() -> appender& { return *this; } + auto operator++() -> appender& { return *this; } + auto operator++(int) -> appender { return *this; } }; namespace detail { @@ -1119,7 +1150,7 @@ constexpr auto has_const_formatter() -> bool { template using buffer_appender = conditional_t::value, appender, - std::back_insert_iterator>>; + back_insert_iterator>>; // Maps an output iterator to a buffer. template @@ -1128,7 +1159,7 @@ auto get_buffer(OutputIt out) -> iterator_buffer { } template , Buf>::value)> -auto get_buffer(std::back_insert_iterator out) -> buffer& { +auto get_buffer(back_insert_iterator out) -> buffer& { return get_container(out); } @@ -1293,7 +1324,13 @@ template class value { template FMT_CONSTEXPR20 FMT_INLINE value(T& val) { using value_type = remove_const_t; - custom.value = const_cast(std::addressof(val)); + // T may overload operator& e.g. std::vector::reference in libc++. +#ifdef __cpp_if_constexpr + if constexpr (std::is_same::value) + custom.value = const_cast(&val); +#endif + if (!is_constant_evaluated()) + custom.value = const_cast(&reinterpret_cast(val)); // Get the formatter type through the context to allow different contexts // have different extension points, e.g. `formatter` for `format` and // `printf_formatter` for `printf`. @@ -1314,6 +1351,7 @@ template class value { parse_ctx.advance_to(f.parse(parse_ctx)); using qualified_type = conditional_t(), const T, T>; + // Calling format through a mutable reference is deprecated. ctx.advance_to(f.format(*static_cast(arg), ctx)); } }; @@ -1327,7 +1365,7 @@ using ulong_type = conditional_t; template struct format_as_result { template ::value || std::is_class::value)> - static auto map(U*) -> decltype(format_as(std::declval())); + static auto map(U*) -> remove_cvref_t()))>; static auto map(...) -> void; using type = decltype(map(static_cast(nullptr))); @@ -1444,7 +1482,8 @@ template struct arg_mapper { // Only map owning types because mapping views can be unsafe. template , FMT_ENABLE_IF(std::is_arithmetic::value)> - FMT_CONSTEXPR FMT_INLINE auto map(const T& val) -> decltype(this->map(U())) { + FMT_CONSTEXPR FMT_INLINE auto map(const T& val) + -> decltype(FMT_DECLTYPE_THIS map(U())) { return map(format_as(val)); } @@ -1468,13 +1507,14 @@ template struct arg_mapper { !is_string::value && !is_char::value && !is_named_arg::value && !std::is_arithmetic>::value)> - FMT_CONSTEXPR FMT_INLINE auto map(T& val) -> decltype(this->do_map(val)) { + FMT_CONSTEXPR FMT_INLINE auto map(T& val) + -> decltype(FMT_DECLTYPE_THIS do_map(val)) { return do_map(val); } template ::value)> FMT_CONSTEXPR FMT_INLINE auto map(const T& named_arg) - -> decltype(this->map(named_arg.value)) { + -> decltype(FMT_DECLTYPE_THIS map(named_arg.value)) { return map(named_arg.value); } @@ -1493,45 +1533,19 @@ enum { max_packed_args = 62 / packed_arg_bits }; enum : unsigned long long { is_unpacked_bit = 1ULL << 63 }; enum : unsigned long long { has_named_args_bit = 1ULL << 62 }; -template -auto copy_str(InputIt begin, InputIt end, appender out) -> appender { - get_container(out).append(begin, end); - return out; -} -template -auto copy_str(InputIt begin, InputIt end, - std::back_insert_iterator out) - -> std::back_insert_iterator { - get_container(out).append(begin, end); - return out; -} - -template -FMT_CONSTEXPR auto copy_str(R&& rng, OutputIt out) -> OutputIt { - return detail::copy_str(rng.begin(), rng.end(), out); -} - -#if FMT_GCC_VERSION && FMT_GCC_VERSION < 500 -// A workaround for gcc 4.8 to make void_t work in a SFINAE context. -template struct void_t_impl { using type = void; }; -template using void_t = typename void_t_impl::type; -#else -template using void_t = void; -#endif - template struct is_output_iterator : std::false_type {}; +template <> struct is_output_iterator : std::true_type {}; + template struct is_output_iterator< - It, T, - void_t::iterator_category, - decltype(*std::declval() = std::declval())>> + It, T, void_t()++ = std::declval())>> : std::true_type {}; template struct is_back_insert_iterator : std::false_type {}; template -struct is_back_insert_iterator> +struct is_back_insert_iterator> : std::true_type {}; // A type-erased reference to an std::locale to avoid a heavy include. @@ -1607,8 +1621,8 @@ FMT_CONSTEXPR inline auto make_arg(T& val) -> basic_format_arg { } // namespace detail FMT_BEGIN_EXPORT -// A formatting argument. It is a trivially copyable/constructible type to -// allow storage in basic_memory_buffer. +// A formatting argument. Context is a template parameter for the compiled API +// where output can be unbuffered. template class basic_format_arg { private: detail::value value_; @@ -1618,11 +1632,6 @@ template class basic_format_arg { friend FMT_CONSTEXPR auto detail::make_arg(T& value) -> basic_format_arg; - template - friend FMT_CONSTEXPR auto visit_format_arg(Visitor&& vis, - const basic_format_arg& arg) - -> decltype(vis(0)); - friend class basic_format_args; friend class dynamic_format_arg_store; @@ -1660,55 +1669,68 @@ template class basic_format_arg { auto is_arithmetic() const -> bool { return detail::is_arithmetic_type(type_); } + + /** + \rst + Visits an argument dispatching to the appropriate visit method based on + the argument type. For example, if the argument type is ``double`` then + ``vis(value)`` will be called with the value of type ``double``. + \endrst + */ + template + FMT_CONSTEXPR auto visit(Visitor&& vis) -> decltype(vis(0)) { + switch (type_) { + case detail::type::none_type: + break; + case detail::type::int_type: + return vis(value_.int_value); + case detail::type::uint_type: + return vis(value_.uint_value); + case detail::type::long_long_type: + return vis(value_.long_long_value); + case detail::type::ulong_long_type: + return vis(value_.ulong_long_value); + case detail::type::int128_type: + return vis(detail::convert_for_visit(value_.int128_value)); + case detail::type::uint128_type: + return vis(detail::convert_for_visit(value_.uint128_value)); + case detail::type::bool_type: + return vis(value_.bool_value); + case detail::type::char_type: + return vis(value_.char_value); + case detail::type::float_type: + return vis(value_.float_value); + case detail::type::double_type: + return vis(value_.double_value); + case detail::type::long_double_type: + return vis(value_.long_double_value); + case detail::type::cstring_type: + return vis(value_.string.data); + case detail::type::string_type: + using sv = basic_string_view; + return vis(sv(value_.string.data, value_.string.size)); + case detail::type::pointer_type: + return vis(value_.pointer); + case detail::type::custom_type: + return vis(typename basic_format_arg::handle(value_.custom)); + } + return vis(monostate()); + } + + FMT_INLINE auto format_custom(const char_type* parse_begin, + typename Context::parse_context_type& parse_ctx, + Context& ctx) -> bool { + if (type_ != detail::type::custom_type) return false; + parse_ctx.advance_to(parse_begin); + value_.custom.format(value_.custom.value, parse_ctx, ctx); + return true; + } }; -/** - \rst - Visits an argument dispatching to the appropriate visit method based on - the argument type. For example, if the argument type is ``double`` then - ``vis(value)`` will be called with the value of type ``double``. - \endrst - */ -// DEPRECATED! template -FMT_CONSTEXPR FMT_INLINE auto visit_format_arg( +FMT_DEPRECATED FMT_CONSTEXPR FMT_INLINE auto visit_format_arg( Visitor&& vis, const basic_format_arg& arg) -> decltype(vis(0)) { - switch (arg.type_) { - case detail::type::none_type: - break; - case detail::type::int_type: - return vis(arg.value_.int_value); - case detail::type::uint_type: - return vis(arg.value_.uint_value); - case detail::type::long_long_type: - return vis(arg.value_.long_long_value); - case detail::type::ulong_long_type: - return vis(arg.value_.ulong_long_value); - case detail::type::int128_type: - return vis(detail::convert_for_visit(arg.value_.int128_value)); - case detail::type::uint128_type: - return vis(detail::convert_for_visit(arg.value_.uint128_value)); - case detail::type::bool_type: - return vis(arg.value_.bool_value); - case detail::type::char_type: - return vis(arg.value_.char_value); - case detail::type::float_type: - return vis(arg.value_.float_value); - case detail::type::double_type: - return vis(arg.value_.double_value); - case detail::type::long_double_type: - return vis(arg.value_.long_double_value); - case detail::type::cstring_type: - return vis(arg.value_.string.data); - case detail::type::string_type: - using sv = basic_string_view; - return vis(sv(arg.value_.string.data, arg.value_.string.size)); - case detail::type::pointer_type: - return vis(arg.value_.pointer); - case detail::type::custom_type: - return vis(typename basic_format_arg::handle(arg.value_.custom)); - } - return vis(monostate()); + return arg.visit(std::forward(vis)); } // Formatting context. @@ -1748,8 +1770,8 @@ template class basic_format_context { } auto args() const -> const format_args& { return args_; } - FMT_CONSTEXPR auto error_handler() -> detail::error_handler { return {}; } - void on_error(const char* message) { error_handler().on_error(message); } + // This function is intentionally not constexpr to give a compile-time error. + void on_error(const char* message) { throw_format_error(message); } // Returns an iterator to the beginning of the output range. FMT_CONSTEXPR auto out() -> iterator { return out_; } @@ -1831,7 +1853,7 @@ class format_arg_store // Arguments are taken by lvalue references to avoid some lifetime issues. template constexpr auto make_format_args(T&... args) - -> format_arg_store...> { + -> format_arg_store...> { return {args...}; } @@ -2107,11 +2129,8 @@ struct dynamic_format_specs : format_specs { }; // Converts a character to ASCII. Returns '\0' on conversion failure. -template ::value)> -constexpr auto to_ascii(Char c) -> char { - return c <= 0xff ? static_cast(c) : '\0'; -} -template ::value)> +template ::value || + std::is_enum::value)> constexpr auto to_ascii(Char c) -> char { return c <= 0xff ? static_cast(c) : '\0'; } @@ -2156,11 +2175,11 @@ FMT_CONSTEXPR auto parse_nonnegative_int(const Char*& begin, const Char* end, } while (p != end && '0' <= *p && *p <= '9'); auto num_digits = p - begin; begin = p; - if (num_digits <= std::numeric_limits::digits10) - return static_cast(value); + int digits10 = static_cast(sizeof(int) * CHAR_BIT * 3 / 10); + if (num_digits <= digits10) return static_cast(value); // Check for overflow. - const unsigned max = to_unsigned((std::numeric_limits::max)()); - return num_digits == std::numeric_limits::digits10 + 1 && + unsigned max = INT_MAX; + return num_digits == digits10 + 1 && prev * 10ull + unsigned(p[-1] - '0') <= max ? static_cast(value) : error_value; @@ -2188,9 +2207,8 @@ FMT_CONSTEXPR auto do_parse_arg_id(const Char* begin, const Char* end, Char c = *begin; if (c >= '0' && c <= '9') { int index = 0; - constexpr int max = (std::numeric_limits::max)(); if (c != '0') - index = parse_nonnegative_int(begin, end, max); + index = parse_nonnegative_int(begin, end, INT_MAX); else ++begin; if (begin == end || (*begin != '}' && *begin != ':')) @@ -2309,9 +2327,12 @@ FMT_CONSTEXPR FMT_INLINE auto parse_format_specs( dynamic_format_specs& specs; type arg_type; - FMT_CONSTEXPR auto operator()(pres type, int set) -> const Char* { - if (!in(arg_type, set)) throw_format_error("invalid format specifier"); - specs.type = type; + FMT_CONSTEXPR auto operator()(pres pres_type, int set) -> const Char* { + if (!in(arg_type, set)) { + if (arg_type == type::none_type) return begin; + throw_format_error("invalid format specifier"); + } + specs.type = pres_type; return begin + 1; } } parse_presentation_type{begin, specs, arg_type}; @@ -2328,6 +2349,7 @@ FMT_CONSTEXPR FMT_INLINE auto parse_format_specs( case '+': case '-': case ' ': + if (arg_type == type::none_type) return begin; enter_state(state::sign, in(arg_type, sint_set | float_set)); switch (c) { case '+': @@ -2343,14 +2365,17 @@ FMT_CONSTEXPR FMT_INLINE auto parse_format_specs( ++begin; break; case '#': + if (arg_type == type::none_type) return begin; enter_state(state::hash, is_arithmetic_type(arg_type)); specs.alt = true; ++begin; break; case '0': enter_state(state::zero); - if (!is_arithmetic_type(arg_type)) + if (!is_arithmetic_type(arg_type)) { + if (arg_type == type::none_type) return begin; throw_format_error("format specifier requires numeric argument"); + } if (specs.align == align::none) { // Ignore 0 if align is specified for compatibility with std::format. specs.align = align::numeric; @@ -2372,12 +2397,14 @@ FMT_CONSTEXPR FMT_INLINE auto parse_format_specs( begin = parse_dynamic_spec(begin, end, specs.width, specs.width_ref, ctx); break; case '.': + if (arg_type == type::none_type) return begin; enter_state(state::precision, in(arg_type, float_set | string_set | cstring_set)); begin = parse_precision(begin, end, specs.precision, specs.precision_ref, ctx); break; case 'L': + if (arg_type == type::none_type) return begin; enter_state(state::locale, is_arithmetic_type(arg_type)); specs.localized = true; ++begin; @@ -2411,6 +2438,8 @@ FMT_CONSTEXPR FMT_INLINE auto parse_format_specs( case 'G': return parse_presentation_type(pres::general_upper, float_set); case 'c': + if (arg_type == type::bool_type) + throw_format_error("invalid format specifier"); return parse_presentation_type(pres::chr, integral_set); case 's': return parse_presentation_type(pres::string, @@ -2550,9 +2579,9 @@ FMT_CONSTEXPR auto parse_format_specs(ParseContext& ctx) decltype(arg_mapper().map(std::declval())), typename strip_named_arg::type>; // LAMMPS customization. Fails to compile with (some) Intel compilers -#if defined(__cpp_if_constexpr) && 0 - if constexpr (std::is_default_constructible_v< - formatter>) { +#if defined(__cpp_if_constexpr) && 1 + if constexpr (std::is_default_constructible< + formatter>::value) { return formatter().parse(ctx); } else { type_is_unformattable_for _; @@ -2675,9 +2704,11 @@ void check_format_string(S format_str) { template struct vformat_args { using type = basic_format_args< - basic_format_context>, Char>>; + basic_format_context>, Char>>; +}; +template <> struct vformat_args { + using type = format_args; }; -template <> struct vformat_args { using type = format_args; }; // Use vformat_args and avoid type_identity to keep symbols short. template @@ -2779,7 +2810,7 @@ using format_string = basic_format_string...>; inline auto runtime(string_view s) -> runtime_format_string<> { return {{s}}; } #endif -FMT_API auto vformat(string_view fmt, format_args args) -> std::string; +FMT_API auto vformat(string_view fmt, format_args args) -> basic_string; /** \rst @@ -2794,7 +2825,7 @@ FMT_API auto vformat(string_view fmt, format_args args) -> std::string; */ template FMT_NODISCARD FMT_INLINE auto format(format_string fmt, T&&... args) - -> std::string { + -> basic_string { return vformat(fmt, fmt::make_format_args(args...)); } @@ -2816,7 +2847,7 @@ auto vformat_to(OutputIt out, string_view fmt, format_args args) -> OutputIt { **Example**:: auto out = std::vector(); - fmt::format_to(std::back_inserter(out), "{}", 42); + fmt::format_to(fmt::back_inserter(out), "{}", 42); \endrst */ template #endif -#ifdef _WIN32 +#if defined(_WIN32) && !defined(FMT_WINDOWS_NO_WCHAR) # include // _isatty #endif @@ -36,10 +36,6 @@ FMT_FUNC void assert_fail(const char* file, int line, const char* message) { std::terminate(); } -FMT_FUNC void throw_format_error(const char* message) { - FMT_THROW(format_error(message)); -} - FMT_FUNC void format_error_code(detail::buffer& out, int error_code, string_view message) noexcept { // Report error code making sure that the output fits into @@ -58,8 +54,8 @@ FMT_FUNC void format_error_code(detail::buffer& out, int error_code, error_code_size += detail::to_unsigned(detail::count_digits(abs_value)); auto it = buffer_appender(out); if (message.size() <= inline_buffer_size - error_code_size) - format_to(it, FMT_STRING("{}{}"), message, SEP); - format_to(it, FMT_STRING("{}{}"), ERROR_STR, error_code); + fmt::format_to(it, FMT_STRING("{}{}"), message, SEP); + fmt::format_to(it, FMT_STRING("{}{}"), ERROR_STR, error_code); FMT_ASSERT(out.size() <= inline_buffer_size, ""); } @@ -73,9 +69,8 @@ FMT_FUNC void report_error(format_func func, int error_code, } // A wrapper around fwrite that throws on error. -inline void fwrite_fully(const void* ptr, size_t size, size_t count, - FILE* stream) { - size_t written = std::fwrite(ptr, size, count, stream); +inline void fwrite_fully(const void* ptr, size_t count, FILE* stream) { + size_t written = std::fwrite(ptr, 1, count, stream); if (written < count) FMT_THROW(system_error(errno, FMT_STRING("cannot write to file"))); } @@ -86,7 +81,7 @@ locale_ref::locale_ref(const Locale& loc) : locale_(&loc) { static_assert(std::is_same::value, ""); } -template Locale locale_ref::get() const { +template auto locale_ref::get() const -> Locale { static_assert(std::is_same::value, ""); return locale_ ? *static_cast(locale_) : std::locale(); } @@ -98,7 +93,8 @@ FMT_FUNC auto thousands_sep_impl(locale_ref loc) -> thousands_sep_result { auto thousands_sep = grouping.empty() ? Char() : facet.thousands_sep(); return {std::move(grouping), thousands_sep}; } -template FMT_FUNC Char decimal_point_impl(locale_ref loc) { +template +FMT_FUNC auto decimal_point_impl(locale_ref loc) -> Char { return std::use_facet>(loc.get()) .decimal_point(); } @@ -127,6 +123,10 @@ FMT_FUNC auto write_loc(appender out, loc_value value, } } // namespace detail +FMT_FUNC void throw_format_error(const char* message) { + FMT_THROW(format_error(message)); +} + template typename Locale::id format_facet::id; #ifndef FMT_STATIC_THOUSANDS_SEPARATOR @@ -144,24 +144,25 @@ FMT_API FMT_FUNC auto format_facet::do_put( } #endif -FMT_FUNC std::system_error vsystem_error(int error_code, string_view fmt, - format_args args) { +FMT_FUNC auto vsystem_error(int error_code, string_view fmt, format_args args) + -> std::system_error { auto ec = std::error_code(error_code, std::generic_category()); return std::system_error(ec, vformat(fmt, args)); } namespace detail { -template inline bool operator==(basic_fp x, basic_fp y) { +template +inline auto operator==(basic_fp x, basic_fp y) -> bool { return x.f == y.f && x.e == y.e; } // Compilers should be able to optimize this into the ror instruction. -FMT_CONSTEXPR inline uint32_t rotr(uint32_t n, uint32_t r) noexcept { +FMT_CONSTEXPR inline auto rotr(uint32_t n, uint32_t r) noexcept -> uint32_t { r &= 31; return (n >> r) | (n << (32 - r)); } -FMT_CONSTEXPR inline uint64_t rotr(uint64_t n, uint32_t r) noexcept { +FMT_CONSTEXPR inline auto rotr(uint64_t n, uint32_t r) noexcept -> uint64_t { r &= 63; return (n >> r) | (n << (64 - r)); } @@ -170,14 +171,14 @@ FMT_CONSTEXPR inline uint64_t rotr(uint64_t n, uint32_t r) noexcept { namespace dragonbox { // Computes upper 64 bits of multiplication of a 32-bit unsigned integer and a // 64-bit unsigned integer. -inline uint64_t umul96_upper64(uint32_t x, uint64_t y) noexcept { +inline auto umul96_upper64(uint32_t x, uint64_t y) noexcept -> uint64_t { return umul128_upper64(static_cast(x) << 32, y); } // Computes lower 128 bits of multiplication of a 64-bit unsigned integer and a // 128-bit unsigned integer. -inline uint128_fallback umul192_lower128(uint64_t x, - uint128_fallback y) noexcept { +inline auto umul192_lower128(uint64_t x, uint128_fallback y) noexcept + -> uint128_fallback { uint64_t high = x * y.high(); uint128_fallback high_low = umul128(x, y.low()); return {high + high_low.high(), high_low.low()}; @@ -185,12 +186,12 @@ inline uint128_fallback umul192_lower128(uint64_t x, // Computes lower 64 bits of multiplication of a 32-bit unsigned integer and a // 64-bit unsigned integer. -inline uint64_t umul96_lower64(uint32_t x, uint64_t y) noexcept { +inline auto umul96_lower64(uint32_t x, uint64_t y) noexcept -> uint64_t { return x * y; } // Various fast log computations. -inline int floor_log10_pow2_minus_log10_4_over_3(int e) noexcept { +inline auto floor_log10_pow2_minus_log10_4_over_3(int e) noexcept -> int { FMT_ASSERT(e <= 2936 && e >= -2985, "too large exponent"); return (e * 631305 - 261663) >> 21; } @@ -204,7 +205,7 @@ FMT_INLINE_VARIABLE constexpr struct { // divisible by pow(10, N). // Precondition: n <= pow(10, N + 1). template -bool check_divisibility_and_divide_by_pow10(uint32_t& n) noexcept { +auto check_divisibility_and_divide_by_pow10(uint32_t& n) noexcept -> bool { // The numbers below are chosen such that: // 1. floor(n/d) = floor(nm / 2^k) where d=10 or d=100, // 2. nm mod 2^k < m if and only if n is divisible by d, @@ -229,7 +230,7 @@ bool check_divisibility_and_divide_by_pow10(uint32_t& n) noexcept { // Computes floor(n / pow(10, N)) for small n and N. // Precondition: n <= pow(10, N + 1). -template uint32_t small_division_by_pow10(uint32_t n) noexcept { +template auto small_division_by_pow10(uint32_t n) noexcept -> uint32_t { constexpr auto info = div_small_pow10_infos[N - 1]; FMT_ASSERT(n <= info.divisor * 10, "n is too large"); constexpr uint32_t magic_number = @@ -238,12 +239,12 @@ template uint32_t small_division_by_pow10(uint32_t n) noexcept { } // Computes floor(n / 10^(kappa + 1)) (float) -inline uint32_t divide_by_10_to_kappa_plus_1(uint32_t n) noexcept { +inline auto divide_by_10_to_kappa_plus_1(uint32_t n) noexcept -> uint32_t { // 1374389535 = ceil(2^37/100) return static_cast((static_cast(n) * 1374389535) >> 37); } // Computes floor(n / 10^(kappa + 1)) (double) -inline uint64_t divide_by_10_to_kappa_plus_1(uint64_t n) noexcept { +inline auto divide_by_10_to_kappa_plus_1(uint64_t n) noexcept -> uint64_t { // 2361183241434822607 = ceil(2^(64+7)/1000) return umul128_upper64(n, 2361183241434822607ull) >> 7; } @@ -255,7 +256,7 @@ template <> struct cache_accessor { using carrier_uint = float_info::carrier_uint; using cache_entry_type = uint64_t; - static uint64_t get_cached_power(int k) noexcept { + static auto get_cached_power(int k) noexcept -> uint64_t { FMT_ASSERT(k >= float_info::min_k && k <= float_info::max_k, "k is out of range"); static constexpr const uint64_t pow10_significands[] = { @@ -297,20 +298,23 @@ template <> struct cache_accessor { bool is_integer; }; - static compute_mul_result compute_mul( - carrier_uint u, const cache_entry_type& cache) noexcept { + static auto compute_mul(carrier_uint u, + const cache_entry_type& cache) noexcept + -> compute_mul_result { auto r = umul96_upper64(u, cache); return {static_cast(r >> 32), static_cast(r) == 0}; } - static uint32_t compute_delta(const cache_entry_type& cache, - int beta) noexcept { + static auto compute_delta(const cache_entry_type& cache, int beta) noexcept + -> uint32_t { return static_cast(cache >> (64 - 1 - beta)); } - static compute_mul_parity_result compute_mul_parity( - carrier_uint two_f, const cache_entry_type& cache, int beta) noexcept { + static auto compute_mul_parity(carrier_uint two_f, + const cache_entry_type& cache, + int beta) noexcept + -> compute_mul_parity_result { FMT_ASSERT(beta >= 1, ""); FMT_ASSERT(beta < 64, ""); @@ -319,22 +323,22 @@ template <> struct cache_accessor { static_cast(r >> (32 - beta)) == 0}; } - static carrier_uint compute_left_endpoint_for_shorter_interval_case( - const cache_entry_type& cache, int beta) noexcept { + static auto compute_left_endpoint_for_shorter_interval_case( + const cache_entry_type& cache, int beta) noexcept -> carrier_uint { return static_cast( (cache - (cache >> (num_significand_bits() + 2))) >> (64 - num_significand_bits() - 1 - beta)); } - static carrier_uint compute_right_endpoint_for_shorter_interval_case( - const cache_entry_type& cache, int beta) noexcept { + static auto compute_right_endpoint_for_shorter_interval_case( + const cache_entry_type& cache, int beta) noexcept -> carrier_uint { return static_cast( (cache + (cache >> (num_significand_bits() + 1))) >> (64 - num_significand_bits() - 1 - beta)); } - static carrier_uint compute_round_up_for_shorter_interval_case( - const cache_entry_type& cache, int beta) noexcept { + static auto compute_round_up_for_shorter_interval_case( + const cache_entry_type& cache, int beta) noexcept -> carrier_uint { return (static_cast( cache >> (64 - num_significand_bits() - 2 - beta)) + 1) / @@ -346,7 +350,7 @@ template <> struct cache_accessor { using carrier_uint = float_info::carrier_uint; using cache_entry_type = uint128_fallback; - static uint128_fallback get_cached_power(int k) noexcept { + static auto get_cached_power(int k) noexcept -> uint128_fallback { FMT_ASSERT(k >= float_info::min_k && k <= float_info::max_k, "k is out of range"); @@ -985,8 +989,7 @@ template <> struct cache_accessor { {0xe0accfa875af45a7, 0x93eb1b80a33b8606}, {0x8c6c01c9498d8b88, 0xbc72f130660533c4}, {0xaf87023b9bf0ee6a, 0xeb8fad7c7f8680b5}, - { 0xdb68c2ca82ed2a05, - 0xa67398db9f6820e2 } + {0xdb68c2ca82ed2a05, 0xa67398db9f6820e2}, #else {0xff77b1fcbebcdc4f, 0x25e8e89c13bb0f7b}, {0xce5d73ff402d98e3, 0xfb0a3d212dc81290}, @@ -1071,19 +1074,22 @@ template <> struct cache_accessor { bool is_integer; }; - static compute_mul_result compute_mul( - carrier_uint u, const cache_entry_type& cache) noexcept { + static auto compute_mul(carrier_uint u, + const cache_entry_type& cache) noexcept + -> compute_mul_result { auto r = umul192_upper128(u, cache); return {r.high(), r.low() == 0}; } - static uint32_t compute_delta(cache_entry_type const& cache, - int beta) noexcept { + static auto compute_delta(cache_entry_type const& cache, int beta) noexcept + -> uint32_t { return static_cast(cache.high() >> (64 - 1 - beta)); } - static compute_mul_parity_result compute_mul_parity( - carrier_uint two_f, const cache_entry_type& cache, int beta) noexcept { + static auto compute_mul_parity(carrier_uint two_f, + const cache_entry_type& cache, + int beta) noexcept + -> compute_mul_parity_result { FMT_ASSERT(beta >= 1, ""); FMT_ASSERT(beta < 64, ""); @@ -1092,35 +1098,35 @@ template <> struct cache_accessor { ((r.high() << beta) | (r.low() >> (64 - beta))) == 0}; } - static carrier_uint compute_left_endpoint_for_shorter_interval_case( - const cache_entry_type& cache, int beta) noexcept { + static auto compute_left_endpoint_for_shorter_interval_case( + const cache_entry_type& cache, int beta) noexcept -> carrier_uint { return (cache.high() - (cache.high() >> (num_significand_bits() + 2))) >> (64 - num_significand_bits() - 1 - beta); } - static carrier_uint compute_right_endpoint_for_shorter_interval_case( - const cache_entry_type& cache, int beta) noexcept { + static auto compute_right_endpoint_for_shorter_interval_case( + const cache_entry_type& cache, int beta) noexcept -> carrier_uint { return (cache.high() + (cache.high() >> (num_significand_bits() + 1))) >> (64 - num_significand_bits() - 1 - beta); } - static carrier_uint compute_round_up_for_shorter_interval_case( - const cache_entry_type& cache, int beta) noexcept { + static auto compute_round_up_for_shorter_interval_case( + const cache_entry_type& cache, int beta) noexcept -> carrier_uint { return ((cache.high() >> (64 - num_significand_bits() - 2 - beta)) + 1) / 2; } }; -FMT_FUNC uint128_fallback get_cached_power(int k) noexcept { +FMT_FUNC auto get_cached_power(int k) noexcept -> uint128_fallback { return cache_accessor::get_cached_power(k); } // Various integer checks template -bool is_left_endpoint_integer_shorter_interval(int exponent) noexcept { +auto is_left_endpoint_integer_shorter_interval(int exponent) noexcept -> bool { const int case_shorter_interval_left_endpoint_lower_threshold = 2; const int case_shorter_interval_left_endpoint_upper_threshold = 3; return exponent >= case_shorter_interval_left_endpoint_lower_threshold && @@ -1132,7 +1138,7 @@ FMT_INLINE int remove_trailing_zeros(uint32_t& n, int s = 0) noexcept { FMT_ASSERT(n != 0, ""); // Modular inverse of 5 (mod 2^32): (mod_inv_5 * 5) mod 2^32 = 1. constexpr uint32_t mod_inv_5 = 0xcccccccd; - constexpr uint32_t mod_inv_25 = 0xc28f5c29; // = mod_inv_5 * mod_inv_5 + constexpr uint32_t mod_inv_25 = 0xc28f5c29; // = mod_inv_5 * mod_inv_5 while (true) { auto q = rotr(n * mod_inv_25, 2); @@ -1168,7 +1174,7 @@ FMT_INLINE int remove_trailing_zeros(uint64_t& n) noexcept { // If n is not divisible by 10^8, work with n itself. constexpr uint64_t mod_inv_5 = 0xcccccccccccccccd; - constexpr uint64_t mod_inv_25 = 0x8f5c28f5c28f5c29; // = mod_inv_5 * mod_inv_5 + constexpr uint64_t mod_inv_25 = 0x8f5c28f5c28f5c29; // mod_inv_5 * mod_inv_5 int s = 0; while (true) { @@ -1234,7 +1240,7 @@ FMT_INLINE decimal_fp shorter_interval_case(int exponent) noexcept { return ret_value; } -template decimal_fp to_decimal(T x) noexcept { +template auto to_decimal(T x) noexcept -> decimal_fp { // Step 1: integer promotion & Schubfach multiplier calculation. using carrier_uint = typename float_info::carrier_uint; @@ -1373,15 +1379,15 @@ template <> struct formatter { for (auto i = n.bigits_.size(); i > 0; --i) { auto value = n.bigits_[i - 1u]; if (first) { - out = format_to(out, FMT_STRING("{:x}"), value); + out = fmt::format_to(out, FMT_STRING("{:x}"), value); first = false; continue; } - out = format_to(out, FMT_STRING("{:08x}"), value); + out = fmt::format_to(out, FMT_STRING("{:08x}"), value); } if (n.exp_ > 0) - out = format_to(out, FMT_STRING("p{}"), - n.exp_ * detail::bigint::bigit_bits); + out = fmt::format_to(out, FMT_STRING("p{}"), + n.exp_ * detail::bigint::bigit_bits); return out; } }; @@ -1417,7 +1423,7 @@ FMT_FUNC void report_system_error(int error_code, report_error(format_system_error, error_code, message); } -FMT_FUNC std::string vformat(string_view fmt, format_args args) { +FMT_FUNC auto vformat(string_view fmt, format_args args) -> std::string { // Don't optimize the "{}" case to keep the binary size small and because it // can be better optimized in fmt::format anyway. auto buffer = memory_buffer(); @@ -1426,33 +1432,38 @@ FMT_FUNC std::string vformat(string_view fmt, format_args args) { } namespace detail { -#ifndef _WIN32 -FMT_FUNC bool write_console(std::FILE*, string_view) { return false; } +#if !defined(_WIN32) || defined(FMT_WINDOWS_NO_WCHAR) +FMT_FUNC auto write_console(int, string_view) -> bool { return false; } #else using dword = conditional_t; extern "C" __declspec(dllimport) int __stdcall WriteConsoleW( // void*, const void*, dword, dword*, void*); -FMT_FUNC bool write_console(std::FILE* f, string_view text) { - auto fd = _fileno(f); - if (!_isatty(fd)) return false; +FMT_FUNC bool write_console(int fd, string_view text) { auto u16 = utf8_to_utf16(text); - auto written = dword(); return WriteConsoleW(reinterpret_cast(_get_osfhandle(fd)), u16.c_str(), - static_cast(u16.size()), &written, nullptr) != 0; + static_cast(u16.size()), nullptr, nullptr) != 0; } +#endif +#ifdef _WIN32 // Print assuming legacy (non-Unicode) encoding. FMT_FUNC void vprint_mojibake(std::FILE* f, string_view fmt, format_args args) { auto buffer = memory_buffer(); - detail::vformat_to(buffer, fmt, - basic_format_args>(args)); - fwrite_fully(buffer.data(), 1, buffer.size(), f); + detail::vformat_to(buffer, fmt, args); + fwrite_fully(buffer.data(), buffer.size(), f); } #endif FMT_FUNC void print(std::FILE* f, string_view text) { - if (!write_console(f, text)) fwrite_fully(text.data(), 1, text.size(), f); +#ifdef _WIN32 + int fd = _fileno(f); + if (_isatty(fd)) { + std::fflush(f); + if (write_console(fd, text)) return; + } +#endif + fwrite_fully(text.data(), text.size(), f); } } // namespace detail diff --git a/src/fmt/format.h b/src/fmt/format.h index 87a34b972ce..8cdf95b7bdf 100644 --- a/src/fmt/format.h +++ b/src/fmt/format.h @@ -37,17 +37,28 @@ #include // uint32_t #include // std::memcpy #include // std::initializer_list -#include // std::numeric_limits -#include // std::uninitialized_copy -#include // std::runtime_error -#include // std::system_error +#include +#include // std::numeric_limits +#include // std::uninitialized_copy +#include // std::runtime_error +#include // std::system_error #ifdef __cpp_lib_bit_cast -# include // std::bitcast +# include // std::bit_cast #endif #include "core.h" +// libc++ supports string_view in pre-c++17. +#if FMT_HAS_INCLUDE() && \ + (FMT_CPLUSPLUS >= 201703L || defined(_LIBCPP_VERSION)) +# include +# define FMT_USE_STRING_VIEW +#elif FMT_HAS_INCLUDE("experimental/string_view") && FMT_CPLUSPLUS >= 201402L +# include +# define FMT_USE_EXPERIMENTAL_STRING_VIEW +#endif + #if defined __cpp_inline_variables && __cpp_inline_variables >= 201606L # define FMT_INLINE_VARIABLE inline #else @@ -65,25 +76,11 @@ # define FMT_FALLTHROUGH #endif -#ifndef FMT_DEPRECATED -# if FMT_HAS_CPP14_ATTRIBUTE(deprecated) || FMT_MSC_VERSION >= 1900 -# define FMT_DEPRECATED [[deprecated]] -# else -# if (defined(__GNUC__) && !defined(__LCC__)) || defined(__clang__) -# define FMT_DEPRECATED __attribute__((deprecated)) -# elif FMT_MSC_VERSION -# define FMT_DEPRECATED __declspec(deprecated) -# else -# define FMT_DEPRECATED /* deprecated */ -# endif -# endif -#endif - #ifndef FMT_NO_UNIQUE_ADDRESS # if FMT_CPLUSPLUS >= 202002L # if FMT_HAS_CPP_ATTRIBUTE(no_unique_address) # define FMT_NO_UNIQUE_ADDRESS [[no_unique_address]] -// VS2019 v16.10 and later except clang-cl (https://reviews.llvm.org/D110485) +// VS2019 v16.10 and later except clang-cl (https://reviews.llvm.org/D110485). # elif (FMT_MSC_VERSION >= 1929) && !FMT_CLANG_VERSION # define FMT_NO_UNIQUE_ADDRESS [[msvc::no_unique_address]] # endif @@ -93,10 +90,11 @@ # define FMT_NO_UNIQUE_ADDRESS #endif -#if FMT_GCC_VERSION || defined(__clang__) -# define FMT_VISIBILITY(value) __attribute__((visibility(value))) +// Visibility when compiled as a shared library/object. +#if defined(FMT_LIB_EXPORT) || defined(FMT_SHARED) +# define FMT_SO_VISIBILITY(value) FMT_VISIBILITY(value) #else -# define FMT_VISIBILITY(value) +# define FMT_SO_VISIBILITY(value) #endif #ifdef __has_builtin @@ -152,7 +150,10 @@ FMT_END_NAMESPACE #ifndef FMT_USE_USER_DEFINED_LITERALS // EDG based compilers (Intel, NVIDIA, Elbrus, etc), GCC and MSVC support UDLs. -# if (FMT_HAS_FEATURE(cxx_user_literals) || FMT_GCC_VERSION >= 407 || \ +// +// GCC before 4.9 requires a space in `operator"" _a` which is invalid in later +// compiler versions. +# if (FMT_HAS_FEATURE(cxx_user_literals) || FMT_GCC_VERSION >= 409 || \ FMT_MSC_VERSION >= 1900) && \ (!defined(__EDG_VERSION__) || __EDG_VERSION__ >= /* UDL feature */ 480) # define FMT_USE_USER_DEFINED_LITERALS 1 @@ -272,20 +273,19 @@ inline auto ctzll(uint64_t x) -> int { FMT_END_NAMESPACE #endif -FMT_BEGIN_NAMESPACE - -template struct disjunction : std::false_type {}; -template struct disjunction

: P {}; -template -struct disjunction - : conditional_t> {}; - -template struct conjunction : std::true_type {}; -template struct conjunction

: P {}; -template -struct conjunction - : conditional_t, P1> {}; +namespace std { +template <> struct iterator_traits { + using value_type = void; + using iterator_category = std::output_iterator_tag; +}; +template +struct iterator_traits> { + using value_type = void; + using iterator_category = std::output_iterator_tag; +}; +} // namespace std +FMT_BEGIN_NAMESPACE namespace detail { FMT_CONSTEXPR inline void abort_fuzzing_if(bool condition) { @@ -295,6 +295,15 @@ FMT_CONSTEXPR inline void abort_fuzzing_if(bool condition) { #endif } +#if defined(FMT_USE_STRING_VIEW) +template using std_string_view = std::basic_string_view; +#elif defined(FMT_USE_EXPERIMENTAL_STRING_VIEW) +template +using std_string_view = std::experimental::basic_string_view; +#else +template struct std_string_view {}; +#endif + template struct string_literal { static constexpr CharT value[sizeof...(C)] = {C...}; constexpr operator basic_string_view() const { @@ -307,37 +316,6 @@ template constexpr CharT string_literal::value[sizeof...(C)]; #endif -template class formatbuf : public Streambuf { - private: - using char_type = typename Streambuf::char_type; - using streamsize = decltype(std::declval().sputn(nullptr, 0)); - using int_type = typename Streambuf::int_type; - using traits_type = typename Streambuf::traits_type; - - buffer& buffer_; - - public: - explicit formatbuf(buffer& buf) : buffer_(buf) {} - - protected: - // The put area is always empty. This makes the implementation simpler and has - // the advantage that the streambuf and the buffer are always in sync and - // sputc never writes into uninitialized memory. A disadvantage is that each - // call to sputc always results in a (virtual) call to overflow. There is no - // disadvantage here for sputn since this always results in a call to xsputn. - - auto overflow(int_type ch) -> int_type override { - if (!traits_type::eq_int_type(ch, traits_type::eof())) - buffer_.push_back(static_cast(ch)); - return ch; - } - - auto xsputn(const char_type* s, streamsize count) -> streamsize override { - buffer_.append(s, s + count); - return count; - } -}; - // Implementation of std::bit_cast for pre-C++20. template FMT_CONSTEXPR20 auto bit_cast(const From& from) -> To { @@ -373,8 +351,8 @@ class uint128_fallback { constexpr uint128_fallback(uint64_t hi, uint64_t lo) : lo_(lo), hi_(hi) {} constexpr uint128_fallback(uint64_t value = 0) : lo_(value), hi_(0) {} - constexpr uint64_t high() const noexcept { return hi_; } - constexpr uint64_t low() const noexcept { return lo_; } + constexpr auto high() const noexcept -> uint64_t { return hi_; } + constexpr auto low() const noexcept -> uint64_t { return lo_; } template ::value)> constexpr explicit operator T() const { @@ -450,7 +428,7 @@ class uint128_fallback { hi_ &= n.hi_; } - FMT_CONSTEXPR20 uint128_fallback& operator+=(uint64_t n) noexcept { + FMT_CONSTEXPR20 auto operator+=(uint64_t n) noexcept -> uint128_fallback& { if (is_constant_evaluated()) { lo_ += n; hi_ += (lo_ < n ? 1 : 0); @@ -546,6 +524,52 @@ FMT_INLINE void assume(bool condition) { #endif } +// Extracts a reference to the container from back_insert_iterator. +template +inline auto get_container(std::back_insert_iterator it) + -> Container& { + using base = std::back_insert_iterator; + struct accessor : base { + accessor(base b) : base(b) {} + using base::container; + }; + return *accessor(it).container; +} + +template +FMT_CONSTEXPR auto copy_str(InputIt begin, InputIt end, OutputIt out) + -> OutputIt { + while (begin != end) *out++ = static_cast(*begin++); + return out; +} + +template , U>::value&& is_char::value)> +FMT_CONSTEXPR auto copy_str(T* begin, T* end, U* out) -> U* { + if (is_constant_evaluated()) return copy_str(begin, end, out); + auto size = to_unsigned(end - begin); + if (size > 0) memcpy(out, begin, size * sizeof(U)); + return out + size; +} + +template +auto copy_str(InputIt begin, InputIt end, appender out) -> appender { + get_container(out).append(begin, end); + return out; +} +template +auto copy_str(InputIt begin, InputIt end, back_insert_iterator out) + -> back_insert_iterator { + get_container(out).append(begin, end); + return out; +} + +template +FMT_CONSTEXPR auto copy_str(R&& rng, OutputIt out) -> OutputIt { + return detail::copy_str(rng.begin(), rng.end(), out); +} + // An approximation of iterator_t for pre-C++20 systems. template using iterator_t = decltype(std::begin(std::declval())); @@ -740,7 +764,7 @@ inline auto compute_width(basic_string_view s) -> size_t { } // Computes approximate display width of a UTF-8 string. -FMT_CONSTEXPR inline size_t compute_width(string_view s) { +FMT_CONSTEXPR inline auto compute_width(string_view s) -> size_t { size_t num_code_points = 0; // It is not a lambda for compatibility with C++14. struct count_code_points { @@ -787,12 +811,17 @@ inline auto code_point_index(basic_string_view s, size_t n) -> size_t { // Calculates the index of the nth code point in a UTF-8 string. inline auto code_point_index(string_view s, size_t n) -> size_t { - const char* data = s.data(); - size_t num_code_points = 0; - for (size_t i = 0, size = s.size(); i != size; ++i) { - if ((data[i] & 0xc0) != 0x80 && ++num_code_points > n) return i; - } - return s.size(); + size_t result = s.size(); + const char* begin = s.begin(); + for_each_codepoint(s, [begin, &n, &result](uint32_t, string_view sv) { + if (n != 0) { + --n; + return true; + } + result = to_unsigned(sv.begin() - begin); + return false; + }); + return result; } inline auto code_point_index(basic_string_view s, size_t n) @@ -902,7 +931,7 @@ enum { inline_buffer_size = 500 }; **Example**:: auto out = fmt::memory_buffer(); - format_to(std::back_inserter(out), "The answer is {}.", 42); + fmt::format_to(std::back_inserter(out), "The answer is {}.", 42); This will append the following output to the ``out`` object: @@ -929,27 +958,29 @@ class basic_memory_buffer final : public detail::buffer { } protected: - FMT_CONSTEXPR20 void grow(size_t size) override { + static FMT_CONSTEXPR20 void grow(detail::buffer& buf, size_t size) { detail::abort_fuzzing_if(size > 5000); - const size_t max_size = std::allocator_traits::max_size(alloc_); - size_t old_capacity = this->capacity(); + auto& self = static_cast(buf); + const size_t max_size = + std::allocator_traits::max_size(self.alloc_); + size_t old_capacity = buf.capacity(); size_t new_capacity = old_capacity + old_capacity / 2; if (size > new_capacity) new_capacity = size; else if (new_capacity > max_size) new_capacity = size > max_size ? size : max_size; - T* old_data = this->data(); + T* old_data = buf.data(); T* new_data = - std::allocator_traits::allocate(alloc_, new_capacity); + std::allocator_traits::allocate(self.alloc_, new_capacity); // Suppress a bogus -Wstringop-overflow in gcc 13.1 (#3481). - detail::assume(this->size() <= new_capacity); + detail::assume(buf.size() <= new_capacity); // The following code doesn't throw, so the raw pointer above doesn't leak. - std::uninitialized_copy_n(old_data, this->size(), new_data); - this->set(new_data, new_capacity); + std::uninitialized_copy_n(old_data, buf.size(), new_data); + self.set(new_data, new_capacity); // deallocate must not throw according to the standard, but even if it does, // the buffer already uses the new storage and will deallocate it in // destructor. - if (old_data != store_) alloc_.deallocate(old_data, old_capacity); + if (old_data != self.store_) self.alloc_.deallocate(old_data, old_capacity); } public: @@ -958,7 +989,7 @@ class basic_memory_buffer final : public detail::buffer { FMT_CONSTEXPR20 explicit basic_memory_buffer( const Allocator& alloc = Allocator()) - : alloc_(alloc) { + : detail::buffer(grow), alloc_(alloc) { this->set(store_, SIZE); if (detail::is_constant_evaluated()) detail::fill_n(store_, SIZE, T()); } @@ -990,7 +1021,8 @@ class basic_memory_buffer final : public detail::buffer { of the other object to it. \endrst */ - FMT_CONSTEXPR20 basic_memory_buffer(basic_memory_buffer&& other) noexcept { + FMT_CONSTEXPR20 basic_memory_buffer(basic_memory_buffer&& other) noexcept + : detail::buffer(grow) { move(other); } @@ -1018,7 +1050,6 @@ class basic_memory_buffer final : public detail::buffer { /** Increases the buffer capacity to *new_capacity*. */ void reserve(size_t new_capacity) { this->try_reserve(new_capacity); } - // Directly append data into the buffer using detail::buffer::append; template void append(const ContiguousRange& range) { @@ -1034,7 +1065,7 @@ struct is_contiguous> : std::true_type { FMT_END_EXPORT namespace detail { -FMT_API bool write_console(std::FILE* f, string_view text); +FMT_API auto write_console(int fd, string_view text) -> bool; FMT_API void print(std::FILE*, string_view); } // namespace detail @@ -1046,7 +1077,7 @@ FMT_BEGIN_EXPORT #endif /** An error reported from a formatting function. */ -class FMT_VISIBILITY("default") format_error : public std::runtime_error { +class FMT_SO_VISIBILITY("default") format_error : public std::runtime_error { public: using std::runtime_error::runtime_error; }; @@ -1089,7 +1120,7 @@ class loc_value { loc_value(T) {} template auto visit(Visitor&& vis) -> decltype(vis(0)) { - return visit_format_arg(vis, value_); + return value_.visit(vis); } }; @@ -1153,13 +1184,13 @@ using uint32_or_64_or_128_t = template using uint64_or_128_t = conditional_t() <= 64, uint64_t, uint128_t>; -#define FMT_POWERS_OF_10(factor) \ - factor * 10, (factor)*100, (factor)*1000, (factor)*10000, (factor)*100000, \ - (factor)*1000000, (factor)*10000000, (factor)*100000000, \ - (factor)*1000000000 +#define FMT_POWERS_OF_10(factor) \ + factor * 10, (factor) * 100, (factor) * 1000, (factor) * 10000, \ + (factor) * 100000, (factor) * 1000000, (factor) * 10000000, \ + (factor) * 100000000, (factor) * 1000000000 // Converts value in the range [0, 100) to a string. -constexpr const char* digits2(size_t value) { +constexpr auto digits2(size_t value) -> const char* { // GCC generates slightly better code when value is pointer-size. return &"0001020304050607080910111213141516171819" "2021222324252627282930313233343536373839" @@ -1169,7 +1200,7 @@ constexpr const char* digits2(size_t value) { } // Sign is a template parameter to workaround a bug in gcc 4.8. -template constexpr Char sign(Sign s) { +template constexpr auto sign(Sign s) -> Char { #if !FMT_GCC_VERSION || FMT_GCC_VERSION >= 604 static_assert(std::is_same::value, ""); #endif @@ -1394,7 +1425,7 @@ FMT_CONSTEXPR inline auto format_uint(It out, UInt value, int num_digits, return out; } // Buffer should be large enough to hold all digits (digits / BASE_BITS + 1). - char buffer[num_bits() / BASE_BITS + 1]; + char buffer[num_bits() / BASE_BITS + 1] = {}; format_uint(buffer, value, num_digits, upper); return detail::copy_str_noinline(buffer, buffer + num_digits, out); } @@ -1430,22 +1461,23 @@ template class to_utf8 { : "invalid utf32")); } operator string_view() const { return string_view(&buffer_[0], size()); } - size_t size() const { return buffer_.size() - 1; } - const char* c_str() const { return &buffer_[0]; } - std::string str() const { return std::string(&buffer_[0], size()); } + auto size() const -> size_t { return buffer_.size() - 1; } + auto c_str() const -> const char* { return &buffer_[0]; } + auto str() const -> std::string { return std::string(&buffer_[0], size()); } // Performs conversion returning a bool instead of throwing exception on // conversion error. This method may still throw in case of memory allocation // error. - bool convert(basic_string_view s, - to_utf8_error_policy policy = to_utf8_error_policy::abort) { + auto convert(basic_string_view s, + to_utf8_error_policy policy = to_utf8_error_policy::abort) + -> bool { if (!convert(buffer_, s, policy)) return false; buffer_.push_back(0); return true; } - static bool convert( - Buffer& buf, basic_string_view s, - to_utf8_error_policy policy = to_utf8_error_policy::abort) { + static auto convert(Buffer& buf, basic_string_view s, + to_utf8_error_policy policy = to_utf8_error_policy::abort) + -> bool { for (auto p = s.begin(); p != s.end(); ++p) { uint32_t c = static_cast(*p); if (sizeof(WChar) == 2 && c >= 0xd800 && c <= 0xdfff) { @@ -1481,7 +1513,7 @@ template class to_utf8 { }; // Computes 128-bit result of multiplication of two 64-bit unsigned integers. -inline uint128_fallback umul128(uint64_t x, uint64_t y) noexcept { +inline auto umul128(uint64_t x, uint64_t y) noexcept -> uint128_fallback { #if FMT_USE_INT128 auto p = static_cast(x) * static_cast(y); return {static_cast(p >> 64), static_cast(p)}; @@ -1512,19 +1544,19 @@ inline uint128_fallback umul128(uint64_t x, uint64_t y) noexcept { namespace dragonbox { // Computes floor(log10(pow(2, e))) for e in [-2620, 2620] using the method from // https://fmt.dev/papers/Dragonbox.pdf#page=28, section 6.1. -inline int floor_log10_pow2(int e) noexcept { +inline auto floor_log10_pow2(int e) noexcept -> int { FMT_ASSERT(e <= 2620 && e >= -2620, "too large exponent"); static_assert((-1 >> 1) == -1, "right shift is not arithmetic"); return (e * 315653) >> 20; } -inline int floor_log2_pow10(int e) noexcept { +inline auto floor_log2_pow10(int e) noexcept -> int { FMT_ASSERT(e <= 1233 && e >= -1233, "too large exponent"); return (e * 1741647) >> 19; } // Computes upper 64 bits of multiplication of two 64-bit unsigned integers. -inline uint64_t umul128_upper64(uint64_t x, uint64_t y) noexcept { +inline auto umul128_upper64(uint64_t x, uint64_t y) noexcept -> uint64_t { #if FMT_USE_INT128 auto p = static_cast(x) * static_cast(y); return static_cast(p >> 64); @@ -1537,14 +1569,14 @@ inline uint64_t umul128_upper64(uint64_t x, uint64_t y) noexcept { // Computes upper 128 bits of multiplication of a 64-bit unsigned integer and a // 128-bit unsigned integer. -inline uint128_fallback umul192_upper128(uint64_t x, - uint128_fallback y) noexcept { +inline auto umul192_upper128(uint64_t x, uint128_fallback y) noexcept + -> uint128_fallback { uint128_fallback r = umul128(x, y.high()); r += umul128_upper64(x, y.low()); return r; } -FMT_API uint128_fallback get_cached_power(int k) noexcept; +FMT_API auto get_cached_power(int k) noexcept -> uint128_fallback; // Type-specific information that Dragonbox uses. template struct float_info; @@ -1598,14 +1630,14 @@ template FMT_API auto to_decimal(T x) noexcept -> decimal_fp; } // namespace dragonbox // Returns true iff Float has the implicit bit which is not stored. -template constexpr bool has_implicit_bit() { +template constexpr auto has_implicit_bit() -> bool { // An 80-bit FP number has a 64-bit significand an no implicit bit. return std::numeric_limits::digits != 64; } // Returns the number of significand bits stored in Float. The implicit bit is // not counted since it is not stored. -template constexpr int num_significand_bits() { +template constexpr auto num_significand_bits() -> int { // std::numeric_limits may not support __float128. return is_float128() ? 112 : (std::numeric_limits::digits - @@ -1698,7 +1730,7 @@ using fp = basic_fp; // Normalizes the value converted from double and multiplied by (1 << SHIFT). template -FMT_CONSTEXPR basic_fp normalize(basic_fp value) { +FMT_CONSTEXPR auto normalize(basic_fp value) -> basic_fp { // Handle subnormals. const auto implicit_bit = F(1) << num_significand_bits(); const auto shifted_implicit_bit = implicit_bit << SHIFT; @@ -1715,7 +1747,7 @@ FMT_CONSTEXPR basic_fp normalize(basic_fp value) { } // Computes lhs * rhs / pow(2, 64) rounded to nearest with half-up tie breaking. -FMT_CONSTEXPR inline uint64_t multiply(uint64_t lhs, uint64_t rhs) { +FMT_CONSTEXPR inline auto multiply(uint64_t lhs, uint64_t rhs) -> uint64_t { #if FMT_USE_INT128 auto product = static_cast<__uint128_t>(lhs) * rhs; auto f = static_cast(product >> 64); @@ -1732,33 +1764,10 @@ FMT_CONSTEXPR inline uint64_t multiply(uint64_t lhs, uint64_t rhs) { #endif } -FMT_CONSTEXPR inline fp operator*(fp x, fp y) { +FMT_CONSTEXPR inline auto operator*(fp x, fp y) -> fp { return {multiply(x.f, y.f), x.e + y.e + 64}; } -template struct basic_data { - // For checking rounding thresholds. - // The kth entry is chosen to be the smallest integer such that the - // upper 32-bits of 10^(k+1) times it is strictly bigger than 5 * 10^k. - static constexpr uint32_t fractional_part_rounding_thresholds[8] = { - 2576980378U, // ceil(2^31 + 2^32/10^1) - 2190433321U, // ceil(2^31 + 2^32/10^2) - 2151778616U, // ceil(2^31 + 2^32/10^3) - 2147913145U, // ceil(2^31 + 2^32/10^4) - 2147526598U, // ceil(2^31 + 2^32/10^5) - 2147487943U, // ceil(2^31 + 2^32/10^6) - 2147484078U, // ceil(2^31 + 2^32/10^7) - 2147483691U // ceil(2^31 + 2^32/10^8) - }; -}; -// This is a struct rather than an alias to avoid shadowing warnings in gcc. -struct data : basic_data<> {}; - -#if FMT_CPLUSPLUS < 201703L -template -constexpr uint32_t basic_data::fractional_part_rounding_thresholds[]; -#endif - template () == num_bits()> using convert_float_result = conditional_t::value || doublish, double, T>; @@ -1939,15 +1948,11 @@ auto write_escaped_cp(OutputIt out, const find_escape_result& escape) *out++ = static_cast('\\'); break; default: - if (escape.cp < 0x100) { - return write_codepoint<2, Char>(out, 'x', escape.cp); - } - if (escape.cp < 0x10000) { + if (escape.cp < 0x100) return write_codepoint<2, Char>(out, 'x', escape.cp); + if (escape.cp < 0x10000) return write_codepoint<4, Char>(out, 'u', escape.cp); - } - if (escape.cp < 0x110000) { + if (escape.cp < 0x110000) return write_codepoint<8, Char>(out, 'U', escape.cp); - } for (Char escape_char : basic_string_view( escape.begin, to_unsigned(escape.end - escape.begin))) { out = write_codepoint<2, Char>(out, 'x', @@ -1977,11 +1982,13 @@ auto write_escaped_string(OutputIt out, basic_string_view str) template auto write_escaped_char(OutputIt out, Char v) -> OutputIt { + Char v_array[1] = {v}; *out++ = static_cast('\''); if ((needs_escape(static_cast(v)) && v != static_cast('"')) || v == static_cast('\'')) { - out = write_escaped_cp( - out, find_escape_result{&v, &v + 1, static_cast(v)}); + out = write_escaped_cp(out, + find_escape_result{v_array, v_array + 1, + static_cast(v)}); } else { *out++ = v; } @@ -2070,10 +2077,10 @@ template class digit_grouping { std::string::const_iterator group; int pos; }; - next_state initial_state() const { return {grouping_.begin(), 0}; } + auto initial_state() const -> next_state { return {grouping_.begin(), 0}; } // Returns the next digit group separator position. - int next(next_state& state) const { + auto next(next_state& state) const -> int { if (thousands_sep_.empty()) return max_value(); if (state.group == grouping_.end()) return state.pos += grouping_.back(); if (*state.group <= 0 || *state.group == max_value()) @@ -2092,9 +2099,9 @@ template class digit_grouping { digit_grouping(std::string grouping, std::basic_string sep) : grouping_(std::move(grouping)), thousands_sep_(std::move(sep)) {} - bool has_separator() const { return !thousands_sep_.empty(); } + auto has_separator() const -> bool { return !thousands_sep_.empty(); } - int count_separators(int num_digits) const { + auto count_separators(int num_digits) const -> int { int count = 0; auto state = initial_state(); while (num_digits > next(state)) ++count; @@ -2103,7 +2110,7 @@ template class digit_grouping { // Applies grouping to digits and write the output to out. template - Out apply(Out out, basic_string_view digits) const { + auto apply(Out out, basic_string_view digits) const -> Out { auto num_digits = static_cast(digits.size()); auto separators = basic_memory_buffer(); separators.push_back(0); @@ -2126,24 +2133,66 @@ template class digit_grouping { } }; +FMT_CONSTEXPR inline void prefix_append(unsigned& prefix, unsigned value) { + prefix |= prefix != 0 ? value << 8 : value; + prefix += (1u + (value > 0xff ? 1 : 0)) << 24; +} + // Writes a decimal integer with digit grouping. template auto write_int(OutputIt out, UInt value, unsigned prefix, const format_specs& specs, const digit_grouping& grouping) -> OutputIt { static_assert(std::is_same, UInt>::value, ""); - int num_digits = count_digits(value); - char digits[40]; - format_decimal(digits, value, num_digits); - unsigned size = to_unsigned((prefix != 0 ? 1 : 0) + num_digits + - grouping.count_separators(num_digits)); + int num_digits = 0; + auto buffer = memory_buffer(); + switch (specs.type) { + case presentation_type::none: + case presentation_type::dec: { + num_digits = count_digits(value); + format_decimal(appender(buffer), value, num_digits); + break; + } + case presentation_type::hex_lower: + case presentation_type::hex_upper: { + bool upper = specs.type == presentation_type::hex_upper; + if (specs.alt) + prefix_append(prefix, unsigned(upper ? 'X' : 'x') << 8 | '0'); + num_digits = count_digits<4>(value); + format_uint<4, char>(appender(buffer), value, num_digits, upper); + break; + } + case presentation_type::bin_lower: + case presentation_type::bin_upper: { + bool upper = specs.type == presentation_type::bin_upper; + if (specs.alt) + prefix_append(prefix, unsigned(upper ? 'B' : 'b') << 8 | '0'); + num_digits = count_digits<1>(value); + format_uint<1, char>(appender(buffer), value, num_digits); + break; + } + case presentation_type::oct: { + num_digits = count_digits<3>(value); + // Octal prefix '0' is counted as a digit, so only add it if precision + // is not greater than the number of digits. + if (specs.alt && specs.precision <= num_digits && value != 0) + prefix_append(prefix, '0'); + format_uint<3, char>(appender(buffer), value, num_digits); + break; + } + case presentation_type::chr: + return write_char(out, static_cast(value), specs); + default: + throw_format_error("invalid format specifier"); + } + + unsigned size = (prefix != 0 ? prefix >> 24 : 0) + to_unsigned(num_digits) + + to_unsigned(grouping.count_separators(num_digits)); return write_padded( out, specs, size, size, [&](reserve_iterator it) { - if (prefix != 0) { - char sign = static_cast(prefix); - *it++ = static_cast(sign); - } - return grouping.apply(it, string_view(digits, to_unsigned(num_digits))); + for (unsigned p = prefix & 0xffffff; p != 0; p >>= 8) + *it++ = static_cast(p & 0xff); + return grouping.apply(it, string_view(buffer.data(), buffer.size())); }); } @@ -2156,11 +2205,6 @@ inline auto write_loc(OutputIt, loc_value, const format_specs&, return false; } -FMT_CONSTEXPR inline void prefix_append(unsigned& prefix, unsigned value) { - prefix |= prefix != 0 ? value << 8 : value; - prefix += (1u + (value > 0xff ? 1 : 0)) << 24; -} - template struct write_int_arg { UInt abs_value; unsigned prefix; @@ -2307,25 +2351,25 @@ class counting_iterator { FMT_CONSTEXPR counting_iterator() : count_(0) {} - FMT_CONSTEXPR size_t count() const { return count_; } + FMT_CONSTEXPR auto count() const -> size_t { return count_; } - FMT_CONSTEXPR counting_iterator& operator++() { + FMT_CONSTEXPR auto operator++() -> counting_iterator& { ++count_; return *this; } - FMT_CONSTEXPR counting_iterator operator++(int) { + FMT_CONSTEXPR auto operator++(int) -> counting_iterator { auto it = *this; ++*this; return it; } - FMT_CONSTEXPR friend counting_iterator operator+(counting_iterator it, - difference_type n) { + FMT_CONSTEXPR friend auto operator+(counting_iterator it, difference_type n) + -> counting_iterator { it.count_ += static_cast(n); return it; } - FMT_CONSTEXPR value_type operator*() const { return {}; } + FMT_CONSTEXPR auto operator*() const -> value_type { return {}; } }; template @@ -2360,9 +2404,10 @@ template FMT_CONSTEXPR auto write(OutputIt out, const Char* s, const format_specs& specs, locale_ref) -> OutputIt { - return specs.type != presentation_type::pointer - ? write(out, basic_string_view(s), specs, {}) - : write_ptr(out, bit_cast(s), &specs); + if (specs.type == presentation_type::pointer) + return write_ptr(out, bit_cast(s), &specs); + if (!s) throw_format_error("string pointer is null"); + return write(out, basic_string_view(s), specs, {}); } template -FMT_CONSTEXPR auto parse_float_type_spec(const format_specs& specs, - ErrorHandler&& eh = {}) +template +FMT_CONSTEXPR auto parse_float_type_spec(const format_specs& specs) -> float_specs { auto result = float_specs(); result.showpoint = specs.alt; @@ -2486,7 +2530,7 @@ FMT_CONSTEXPR auto parse_float_type_spec(const format_specs& specs, result.format = float_format::hex; break; default: - eh.on_error("invalid format specifier"); + throw_format_error("invalid format specifier"); break; } return result; @@ -2725,12 +2769,12 @@ template class fallback_digit_grouping { public: constexpr fallback_digit_grouping(locale_ref, bool) {} - constexpr bool has_separator() const { return false; } + constexpr auto has_separator() const -> bool { return false; } - constexpr int count_separators(int) const { return 0; } + constexpr auto count_separators(int) const -> int { return 0; } template - constexpr Out apply(Out out, basic_string_view) const { + constexpr auto apply(Out out, basic_string_view) const -> Out { return out; } }; @@ -2749,7 +2793,7 @@ FMT_CONSTEXPR20 auto write_float(OutputIt out, const DecimalFP& f, } } -template constexpr bool isnan(T value) { +template constexpr auto isnan(T value) -> bool { return !(value >= value); // std::isnan doesn't support __float128. } @@ -2762,14 +2806,14 @@ struct has_isfinite> template ::value&& has_isfinite::value)> -FMT_CONSTEXPR20 bool isfinite(T value) { +FMT_CONSTEXPR20 auto isfinite(T value) -> bool { constexpr T inf = T(std::numeric_limits::infinity()); if (is_constant_evaluated()) return !detail::isnan(value) && value < inf && value > -inf; return std::isfinite(value); } template ::value)> -FMT_CONSTEXPR bool isfinite(T value) { +FMT_CONSTEXPR auto isfinite(T value) -> bool { T inf = T(std::numeric_limits::infinity()); // std::isfinite doesn't support __float128. return !detail::isnan(value) && value < inf && value > -inf; @@ -2806,10 +2850,10 @@ class bigint { basic_memory_buffer bigits_; int exp_; - FMT_CONSTEXPR20 bigit operator[](int index) const { + FMT_CONSTEXPR20 auto operator[](int index) const -> bigit { return bigits_[to_unsigned(index)]; } - FMT_CONSTEXPR20 bigit& operator[](int index) { + FMT_CONSTEXPR20 auto operator[](int index) -> bigit& { return bigits_[to_unsigned(index)]; } @@ -2905,11 +2949,11 @@ class bigint { assign(uint64_or_128_t(n)); } - FMT_CONSTEXPR20 int num_bigits() const { + FMT_CONSTEXPR20 auto num_bigits() const -> int { return static_cast(bigits_.size()) + exp_; } - FMT_NOINLINE FMT_CONSTEXPR20 bigint& operator<<=(int shift) { + FMT_NOINLINE FMT_CONSTEXPR20 auto operator<<=(int shift) -> bigint& { FMT_ASSERT(shift >= 0, ""); exp_ += shift / bigit_bits; shift %= bigit_bits; @@ -2924,13 +2968,15 @@ class bigint { return *this; } - template FMT_CONSTEXPR20 bigint& operator*=(Int value) { + template + FMT_CONSTEXPR20 auto operator*=(Int value) -> bigint& { FMT_ASSERT(value > 0, ""); multiply(uint32_or_64_or_128_t(value)); return *this; } - friend FMT_CONSTEXPR20 int compare(const bigint& lhs, const bigint& rhs) { + friend FMT_CONSTEXPR20 auto compare(const bigint& lhs, const bigint& rhs) + -> int { int num_lhs_bigits = lhs.num_bigits(), num_rhs_bigits = rhs.num_bigits(); if (num_lhs_bigits != num_rhs_bigits) return num_lhs_bigits > num_rhs_bigits ? 1 : -1; @@ -2947,8 +2993,9 @@ class bigint { } // Returns compare(lhs1 + lhs2, rhs). - friend FMT_CONSTEXPR20 int add_compare(const bigint& lhs1, const bigint& lhs2, - const bigint& rhs) { + friend FMT_CONSTEXPR20 auto add_compare(const bigint& lhs1, + const bigint& lhs2, const bigint& rhs) + -> int { auto minimum = [](int a, int b) { return a < b ? a : b; }; auto maximum = [](int a, int b) { return a > b ? a : b; }; int max_lhs_bigits = maximum(lhs1.num_bigits(), lhs2.num_bigits()); @@ -3029,13 +3076,13 @@ class bigint { bigits_.resize(to_unsigned(num_bigits + exp_difference)); for (int i = num_bigits - 1, j = i + exp_difference; i >= 0; --i, --j) bigits_[j] = bigits_[i]; - std::uninitialized_fill_n(bigits_.data(), exp_difference, 0); + std::uninitialized_fill_n(bigits_.data(), exp_difference, 0u); exp_ -= exp_difference; } // Divides this bignum by divisor, assigning the remainder to this and // returning the quotient. - FMT_CONSTEXPR20 int divmod_assign(const bigint& divisor) { + FMT_CONSTEXPR20 auto divmod_assign(const bigint& divisor) -> int { FMT_ASSERT(this != &divisor, ""); if (compare(*this, divisor) < 0) return 0; FMT_ASSERT(divisor.bigits_[divisor.bigits_.size() - 1u] != 0, ""); @@ -3178,8 +3225,10 @@ FMT_CONSTEXPR20 inline void format_dragon(basic_fp value, } if (buf[0] == overflow) { buf[0] = '1'; - if ((flags & dragon::fixed) != 0) buf.push_back('0'); - else ++exp10; + if ((flags & dragon::fixed) != 0) + buf.push_back('0'); + else + ++exp10; } return; } @@ -3276,6 +3325,17 @@ FMT_CONSTEXPR20 void format_hexfloat(Float value, int precision, format_hexfloat(static_cast(value), precision, specs, buf); } +constexpr auto fractional_part_rounding_thresholds(int index) -> uint32_t { + // For checking rounding thresholds. + // The kth entry is chosen to be the smallest integer such that the + // upper 32-bits of 10^(k+1) times it is strictly bigger than 5 * 10^k. + // It is equal to ceil(2^31 + 2^32/10^(k + 1)). + // These are stored in a string literal because we cannot have static arrays + // in constexpr functions and non-static ones are poorly optimized. + return U"\x9999999a\x828f5c29\x80418938\x80068db9\x8000a7c6\x800010c7" + U"\x800001ae\x8000002b"[index]; +} + template FMT_CONSTEXPR20 auto format_float(Float value, int precision, float_specs specs, buffer& buf) -> int { @@ -3480,12 +3540,12 @@ FMT_CONSTEXPR20 auto format_float(Float value, int precision, float_specs specs, // fractional part is strictly larger than 1/2. if (precision < 9) { uint32_t fractional_part = static_cast(prod); - should_round_up = fractional_part >= - data::fractional_part_rounding_thresholds - [8 - number_of_digits_to_print] || - ((fractional_part >> 31) & - ((digits & 1) | (second_third_subsegments != 0) | - has_more_segments)) != 0; + should_round_up = + fractional_part >= fractional_part_rounding_thresholds( + 8 - number_of_digits_to_print) || + ((fractional_part >> 31) & + ((digits & 1) | (second_third_subsegments != 0) | + has_more_segments)) != 0; } // Rounding at the subsegment boundary. // In this case, the fractional part is at least 1/2 if and only if @@ -3520,12 +3580,12 @@ FMT_CONSTEXPR20 auto format_float(Float value, int precision, float_specs specs, // of 19 digits, so in this case the third segment should be // consisting of a genuine digit from the input. uint32_t fractional_part = static_cast(prod); - should_round_up = fractional_part >= - data::fractional_part_rounding_thresholds - [8 - number_of_digits_to_print] || - ((fractional_part >> 31) & - ((digits & 1) | (third_subsegment != 0) | - has_more_segments)) != 0; + should_round_up = + fractional_part >= fractional_part_rounding_thresholds( + 8 - number_of_digits_to_print) || + ((fractional_part >> 31) & + ((digits & 1) | (third_subsegment != 0) | + has_more_segments)) != 0; } // Rounding at the subsegment boundary. else { @@ -3726,8 +3786,7 @@ FMT_CONSTEXPR auto write(OutputIt out, Char value) -> OutputIt { } template -FMT_CONSTEXPR_CHAR_TRAITS auto write(OutputIt out, const Char* value) - -> OutputIt { +FMT_CONSTEXPR20 auto write(OutputIt out, const Char* value) -> OutputIt { if (value) return write(out, basic_string_view(value)); throw_format_error("string pointer is null"); return out; @@ -3757,8 +3816,11 @@ template enable_if_t::value == type::custom_type, OutputIt> { + auto formatter = typename Context::template formatter_type(); + auto parse_ctx = typename Context::parse_context_type({}); + formatter.parse(parse_ctx); auto ctx = Context(out, {}, {}); - return typename Context::template formatter_type().format(value, ctx); + return formatter.format(value, ctx); } // An argument visitor that formats the argument and writes it via the output @@ -3801,62 +3863,39 @@ template struct arg_formatter { } }; -template struct custom_formatter { - basic_format_parse_context& parse_ctx; - buffer_context& ctx; - - void operator()( - typename basic_format_arg>::handle h) const { - h.format(parse_ctx, ctx); - } - template void operator()(T) const {} -}; - -template class width_checker { - public: - explicit FMT_CONSTEXPR width_checker(ErrorHandler& eh) : handler_(eh) {} - +struct width_checker { template ::value)> FMT_CONSTEXPR auto operator()(T value) -> unsigned long long { - if (is_negative(value)) handler_.on_error("negative width"); + if (is_negative(value)) throw_format_error("negative width"); return static_cast(value); } template ::value)> FMT_CONSTEXPR auto operator()(T) -> unsigned long long { - handler_.on_error("width is not integer"); + throw_format_error("width is not integer"); return 0; } - - private: - ErrorHandler& handler_; }; -template class precision_checker { - public: - explicit FMT_CONSTEXPR precision_checker(ErrorHandler& eh) : handler_(eh) {} - +struct precision_checker { template ::value)> FMT_CONSTEXPR auto operator()(T value) -> unsigned long long { - if (is_negative(value)) handler_.on_error("negative precision"); + if (is_negative(value)) throw_format_error("negative precision"); return static_cast(value); } template ::value)> FMT_CONSTEXPR auto operator()(T) -> unsigned long long { - handler_.on_error("precision is not integer"); + throw_format_error("precision is not integer"); return 0; } - - private: - ErrorHandler& handler_; }; -template