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Fix derive for state variables with ghost cells #707

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merged 4 commits into from
Oct 23, 2023
Merged

Fix derive for state variables with ghost cells #707

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6ccbc93
test for adj-diff-grtr refinement
baperry2 Oct 20, 2023
8c5f4aa
error check for ncomp in physbcfill
baperry2 Oct 20, 2023
c16ae05
fillpatch all state variables together in derive
baperry2 Oct 20, 2023
27b4fd6
always assert, use &&
baperry2 Oct 23, 2023
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9 changes: 7 additions & 2 deletions Exec/RegTests/PMF/pmf-lidryer-arkode.inp
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ pelec.v = 1 # verbosity in PeleC cpp files
amr.v = 1 # verbosity in Amr.cpp
#amr.grid_log = grdlog # name of grid logging file

# REFINEMENT / REGRIDDING
# REFINEMENT / REGRIDDING
amr.max_level = 1 # maximum level number allowed
amr.ref_ratio = 2 2 2 2 # refinement ratio
amr.regrid_int = 2 2 2 2 # how often to regrid
Expand All @@ -49,14 +49,19 @@ pelec.plot_rhoy = 0
pelec.plot_massfrac = 1

# PROBLEM PARAMETERS
prob.pamb = 1013250.0
prob.pamb = 1013250.0
prob.phi_in = -0.5
prob.pertmag = 0.005
prob.pmf_datafile = "LiDryer_H2_p1_phi0_4000tu0300.dat"

tagging.max_ftracerr_lev = 4
tagging.ftracerr = 150.e-6

tagging.refinement_indicators = gtemp
tagging.gtemp.adjacent_difference_greater = 100
tagging.gtemp.field_name = Temp
tagging.gtemp.max_level = 1

extern.new_Jacobian_each_cell = 0

pelec.do_hydro = 1
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7 changes: 5 additions & 2 deletions Source/BCfill.cpp
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Expand Up @@ -21,14 +21,17 @@ struct PCHypFillExtDir
void operator()(
const amrex::IntVect& iv,
amrex::Array4<amrex::Real> const& dest,
const int /*dcomp*/,
const int /*numcomp*/,
const int dcomp,
const int numcomp,
amrex::GeometryData const& geom,
const amrex::Real time,
const amrex::BCRec* bcr,
const int /*bcomp*/,
const int /*orig_comp*/) const
{
// We need the whole state to apply physical BCs
AMREX_ALWAYS_ASSERT(dcomp == 0 && numcomp == NVAR);

const int* domlo = geom.Domain().loVect();
const int* domhi = geom.Domain().hiVect();
const amrex::Real* prob_lo = geom.ProbLo();
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54 changes: 32 additions & 22 deletions Source/PeleC.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1932,29 +1932,21 @@ PeleC::errorEst(
std::unique_ptr<amrex::MultiFab>
PeleC::derive(const std::string& name, amrex::Real time, int ngrow)
{
if ((do_les) && (name == "C_s2")) {
if ((do_les) && ((name == "C_s2") || (name == "C_I") || (name == "Pr_T"))) {
AMREX_ASSERT(ngrow <= LES_Coeffs.nGrow());
std::unique_ptr<amrex::MultiFab> derive_dat(
new amrex::MultiFab(grids, dmap, 1, 0));
amrex::MultiFab::Copy(*derive_dat, LES_Coeffs, comp_Cs2, 0, 1, 0);
return derive_dat;
}
if ((do_les) && (name == "C_I")) {
std::unique_ptr<amrex::MultiFab> derive_dat(
new amrex::MultiFab(grids, dmap, 1, 0));
amrex::MultiFab::Copy(*derive_dat, LES_Coeffs, comp_CI, 0, 1, 0);
return derive_dat;
}
if ((do_les) && (les_model != 1) && (name == "Pr_T")) {
std::unique_ptr<amrex::MultiFab> derive_dat(
new amrex::MultiFab(grids, dmap, 1, 0));
amrex::MultiFab::Copy(*derive_dat, LES_Coeffs, comp_PrT, 0, 1, 0);
return derive_dat;
}
if ((do_les) && (les_model == 1) && (name == "Pr_T")) {
std::unique_ptr<amrex::MultiFab> derive_dat(
new amrex::MultiFab(grids, dmap, 1, 0));
amrex::MultiFab::Copy(*derive_dat, LES_Coeffs, comp_Cs2ovPrT, 0, 1, 0);
amrex::MultiFab::Divide(*derive_dat, LES_Coeffs, comp_Cs2, 0, 1, 0);
new amrex::MultiFab(grids, dmap, 1, ngrow));
if (name == "C_s2") {
amrex::MultiFab::Copy(*derive_dat, LES_Coeffs, comp_Cs2, 0, 1, ngrow);
} else if (name == "C_I") {
amrex::MultiFab::Copy(*derive_dat, LES_Coeffs, comp_CI, 0, 1, ngrow);
} else if ((les_model != 1) && (name == "Pr_T")) {
amrex::MultiFab::Copy(*derive_dat, LES_Coeffs, comp_PrT, 0, 1, ngrow);
} else { // Pr_T, les_model==1
amrex::MultiFab::Copy(
*derive_dat, LES_Coeffs, comp_Cs2ovPrT, 0, 1, ngrow);
amrex::MultiFab::Divide(*derive_dat, LES_Coeffs, comp_Cs2, 0, 1, ngrow);
}
return derive_dat;
}

Expand All @@ -1968,6 +1960,24 @@ PeleC::derive(const std::string& name, amrex::Real time, int ngrow)
return mf;
}

// Can't use the AmrLevel derive for state variables with ghost cells:
// That will fillpatch them individually, but we require the full state
// for physBCs. Therefore, instead fillpatch the full state and then grab
// the component we need.
int index, scomp;
if (isStateVariable(name, index, scomp) && (ngrow > 0)) {
amrex::MultiFab S_data(
get_new_data(State_Type).boxArray(),
get_new_data(State_Type).DistributionMap(), NVAR, ngrow, amrex::MFInfo(),
Factory());
FillPatch(
*this, S_data, S_data.nGrow(), time, State_Type, Density, NVAR, 0);
std::unique_ptr<amrex::MultiFab> derive_dat(
new amrex::MultiFab(grids, dmap, 1, ngrow, amrex::MFInfo(), Factory()));
amrex::MultiFab::Copy(*derive_dat, S_data, scomp, 0, 1, ngrow);
return derive_dat;
}

// For those using GrowBoxByOne we need this
if ((name == "enstrophy") || (name == "magvort") || (name == "divu")) {
ngrow += 1;
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