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Fix BC Types due to breaking AMReX change #758

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merged 6 commits into from
Feb 23, 2024
Merged

Fix BC Types due to breaking AMReX change #758

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765fecb
update pp to update amrex
baperry2 Feb 13, 2024
cc231ba
amrex mathematical bcs changes
baperry2 Feb 13, 2024
746413c
chamnges for physbctype change
baperry2 Feb 13, 2024
e22b4a1
ARLIM_3D to AMREX_ARLIM_3D
baperry2 Feb 13, 2024
b039a16
clang-format
baperry2 Feb 13, 2024
3ef1587
update pp to update amrex
baperry2 Feb 23, 2024
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4 changes: 2 additions & 2 deletions Source/BCfill.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,7 @@ pc_bcfill_hyp(
if (PeleC::turb_inflow.is_initialized()) {
for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) {
auto bndryBoxLO = amrex::Box(amrex::adjCellLo(geom.Domain(), dir) & bx);
if (bcr[1].lo()[dir] == EXT_DIR && bndryBoxLO.ok()) {
if (bcr[1].lo()[dir] == amrex::BCType::ext_dir && bndryBoxLO.ok()) {
// Create box with ghost cells and set them to zero
amrex::IntVect growVect(PeleC::numGrow());
growVect[dir] = 0;
Expand All @@ -179,7 +179,7 @@ pc_bcfill_hyp(
}

auto bndryBoxHI = amrex::Box(amrex::adjCellHi(geom.Domain(), dir) & bx);
if (bcr[1].hi()[dir] == EXT_DIR && bndryBoxHI.ok()) {
if (bcr[1].hi()[dir] == amrex::BCType::ext_dir && bndryBoxHI.ok()) {
// Create box with ghost cells and set them to zero
amrex::IntVect growVect(PeleC::numGrow());
growVect[dir] = 0;
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16 changes: 10 additions & 6 deletions Source/Godunov.H
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Expand Up @@ -1127,13 +1127,17 @@ pc_artif_visc(
divu(iv), 0.5 * (divu(iv) + divu(ivpj)),
0.25 * (divu(iv) + divu(ivpj) + divu(ivpk) + divu(ivpp))));

bool at_bndry = ((dir == 0) && (i == domlo) && (bclo == NoSlipWall)) ||
((dir == 0) && (i == domhi + 1) && (bchi == NoSlipWall)) ||
((dir == 1) && (j == domlo) && (bclo == NoSlipWall)) ||
((dir == 1) && (j == domhi + 1) && (bchi == NoSlipWall));
bool at_bndry =
((dir == 0) && (i == domlo) && (bclo == amrex::PhysBCType::noslipwall)) ||
((dir == 0) && (i == domhi + 1) &&
(bchi == amrex::PhysBCType::noslipwall)) ||
((dir == 1) && (j == domlo) && (bclo == amrex::PhysBCType::noslipwall)) ||
((dir == 1) && (j == domhi + 1) && (bchi == amrex::PhysBCType::noslipwall));
#if (AMREX_SPACEDIM == 3)
at_bndry = at_bndry || ((dir == 2) && (k == domlo) && (bclo == NoSlipWall)) ||
((dir == 2) && (k == domhi + 1) && (bchi == NoSlipWall));
at_bndry =
at_bndry ||
((dir == 2) && (k == domlo) && (bclo == amrex::PhysBCType::noslipwall)) ||
((dir == 2) && (k == domhi + 1) && (bchi == amrex::PhysBCType::noslipwall));
#endif

for (int n = 0; n < NVAR; ++n) {
Expand Down
3 changes: 2 additions & 1 deletion Source/Hydro.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,8 @@ PeleC::construct_hydro_source(
//
// The user should provide a bcnormal routine in bc_fill_module with
// additional optional arguments to temporary fill ghost-cells for
// EXT_DIR and to provide target BC values. See the examples.
// amrex::BCType::ext_dir and to provide target BC values. See the
// examples.

// Allocate fabs for bcMask. Note that we grow in the opposite direction
// because the Riemann solver wants a face value in a ghost-cell
Expand Down
4 changes: 2 additions & 2 deletions Source/InitEB.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -444,8 +444,8 @@ PeleC::eb_distance(const int lev, amrex::MultiFab& signDistLev)
// dummy bcs
amrex::Vector<amrex::BCRec> bcrec_dummy(1);
for (int dir = 0; dir < AMREX_SPACEDIM; dir++) {
bcrec_dummy[0].setLo(dir, INT_DIR);
bcrec_dummy[0].setHi(dir, INT_DIR);
bcrec_dummy[0].setLo(dir, amrex::BCType::int_dir);
bcrec_dummy[0].setHi(dir, amrex::BCType::int_dir);
}

// Interpolate on successive levels up to lev
Expand Down
4 changes: 2 additions & 2 deletions Source/PeleC.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -642,8 +642,8 @@ PeleC::setGridInfo()
const int* domhi_coarse = geom.Domain().hiVect();

for (int dir = 0; dir < 3; dir++) {
domlo_level[dir] = (ARLIM_3D(domlo_coarse))[dir];
domhi_level[dir] = (ARLIM_3D(domhi_coarse))[dir];
domlo_level[dir] = (AMREX_ARLIM_3D(domlo_coarse))[dir];
domhi_level[dir] = (AMREX_ARLIM_3D(domhi_coarse))[dir];
}

for (int lev = 1; lev <= max_level; lev++) {
Expand Down
35 changes: 23 additions & 12 deletions Source/Setup.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -32,18 +32,29 @@ SootModel PeleC::soot_model;

// Components are defined in PCPhysBCType enum in PeleC.H:
// Interior, Inflow, Outflow, Symmetry, SlipWall, NoSlipWall, UserBC
static int scalar_bc[] = {INT_DIR, EXT_DIR, FOEXTRAP, REFLECT_EVEN,
REFLECT_EVEN, REFLECT_EVEN, EXT_DIR};

static int norm_vel_bc[] = {INT_DIR, EXT_DIR, FOEXTRAP, REFLECT_ODD,
REFLECT_ODD, REFLECT_ODD, EXT_DIR};

static int tang_vel_bc[] = {INT_DIR, EXT_DIR, FOEXTRAP, REFLECT_EVEN,
REFLECT_EVEN, REFLECT_ODD, EXT_DIR};

static int react_src_bc[] = {INT_DIR, REFLECT_EVEN, REFLECT_EVEN,
REFLECT_EVEN, REFLECT_EVEN, REFLECT_EVEN,
REFLECT_EVEN};
static int scalar_bc[] = {
amrex::BCType::int_dir, amrex::BCType::ext_dir,
amrex::BCType::foextrap, amrex::BCType::reflect_even,
amrex::BCType::reflect_even, amrex::BCType::reflect_even,
amrex::BCType::ext_dir};

static int norm_vel_bc[] = {
amrex::BCType::int_dir, amrex::BCType::ext_dir,
amrex::BCType::foextrap, amrex::BCType::reflect_odd,
amrex::BCType::reflect_odd, amrex::BCType::reflect_odd,
amrex::BCType::ext_dir};

static int tang_vel_bc[] = {
amrex::BCType::int_dir, amrex::BCType::ext_dir,
amrex::BCType::foextrap, amrex::BCType::reflect_even,
amrex::BCType::reflect_even, amrex::BCType::reflect_odd,
amrex::BCType::ext_dir};

static int react_src_bc[] = {
amrex::BCType::int_dir, amrex::BCType::reflect_even,
amrex::BCType::reflect_even, amrex::BCType::reflect_even,
amrex::BCType::reflect_even, amrex::BCType::reflect_even,
amrex::BCType::reflect_even};

static void
set_scalar_bc(amrex::BCRec& bc, const amrex::BCRec& phys_bc)
Expand Down
2 changes: 1 addition & 1 deletion Submodules/PelePhysics
Open in desktop
Submodule PelePhysics updated 88 files
+18 −1 Docs/sphinx/Ceptr.rst
+32 −21 Mechanisms/Aromatic_KrNara/mechanism.H
+2 −2 Mechanisms/Aromatic_KrNara/mechanism.cpp
+14 −3 Mechanisms/BurkeDryer/mechanism.H
+4 −3 Mechanisms/BurkeDryer/mechanism.cpp
+14 −3 Mechanisms/C1-C2-NO/mechanism.H
+2 −2 Mechanisms/C1-C2-NO/mechanism.cpp
+14 −3 Mechanisms/C1-C2-NO_qss/mechanism.H
+2 −2 Mechanisms/C1-C2-NO_qss/mechanism.cpp
+17 −6 Mechanisms/CH4_lean/mechanism.H
+2 −2 Mechanisms/CH4_lean/mechanism.cpp
+38 −26 Mechanisms/CH4_lean_qss/mechanism.H
+2 −2 Mechanisms/CH4_lean_qss/mechanism.cpp
+14 −3 Mechanisms/Davis/mechanism.H
+4 −4 Mechanisms/Davis/mechanism.cpp
+15 −4 Mechanisms/FFCM1_Red/mechanism.H
+2 −2 Mechanisms/FFCM1_Red/mechanism.cpp
+14 −3 Mechanisms/H2-CO-CO2-3spec/mechanism.H
+14 −3 Mechanisms/IonizedAir/mechanism.H
+14 −3 Mechanisms/JL4/mechanism.H
+2 −2 Mechanisms/JL4/mechanism.cpp
+14 −3 Mechanisms/Kolla/mechanism.H
+4 −4 Mechanisms/Kolla/mechanism.cpp
+14 −3 Mechanisms/LiDryer/mechanism.H
+3 −3 Mechanisms/LiDryer/mechanism.cpp
+17 −6 Mechanisms/LuDME/mechanism.H
+2 −2 Mechanisms/LuDME/mechanism.cpp
+14 −3 Mechanisms/LuEthylene/mechanism.H
+2 −2 Mechanisms/LuEthylene/mechanism.cpp
+14 −3 Mechanisms/LuEthylene_qss/mechanism.H
+2 −2 Mechanisms/LuEthylene_qss/mechanism.cpp
+24 −13 Mechanisms/NUIGalway/mechanism.H
+2 −2 Mechanisms/NUIGalway/mechanism.cpp
+14 −3 Mechanisms/SootReaction/mechanism.H
+2 −2 Mechanisms/SootReaction/mechanism.cpp
+14 −3 Mechanisms/air/mechanism.H
+18 −7 Mechanisms/alzeta/mechanism.H
+2 −2 Mechanisms/alzeta/mechanism.cpp
+14 −3 Mechanisms/chem-CH4-2step/mechanism.H
+2 −2 Mechanisms/chem-CH4-2step/mechanism.cpp
+14 −3 Mechanisms/chem-H/mechanism.H
+4 −3 Mechanisms/chem-H/mechanism.cpp
+14 −3 Mechanisms/decane_3sp/mechanism.H
+14 −3 Mechanisms/dodecane_lu/mechanism.H
+2 −2 Mechanisms/dodecane_lu/mechanism.cpp
+14 −3 Mechanisms/dodecane_lu_qss/mechanism.H
+2 −2 Mechanisms/dodecane_lu_qss/mechanism.cpp
+14 −3 Mechanisms/dodecane_wang/mechanism.H
+2 −2 Mechanisms/dodecane_wang/mechanism.cpp
+14 −3 Mechanisms/dodmethair_4sp/mechanism.H
+15 −4 Mechanisms/drm19/mechanism.H
+7 −7 Mechanisms/drm19/mechanism.cpp
+14 −3 Mechanisms/ethylene_af/mechanism.H
+2 −2 Mechanisms/ethylene_af/mechanism.cpp
+15 −4 Mechanisms/grimech12/mechanism.H
+2 −2 Mechanisms/grimech12/mechanism.cpp
+15 −4 Mechanisms/grimech30-noArN/mechanism.H
+2 −2 Mechanisms/grimech30-noArN/mechanism.cpp
+15 −4 Mechanisms/grimech30/mechanism.H
+2 −2 Mechanisms/grimech30/mechanism.cpp
+14 −3 Mechanisms/heptane_3sp/mechanism.H
+16 −5 Mechanisms/heptane_fc/mechanism.H
+2 −2 Mechanisms/heptane_fc/mechanism.cpp
+19 −8 Mechanisms/heptane_lu_88sk/mechanism.H
+2 −2 Mechanisms/heptane_lu_88sk/mechanism.cpp
+22 −11 Mechanisms/heptane_lu_qss/mechanism.H
+2 −2 Mechanisms/heptane_lu_qss/mechanism.cpp
+54 −43 Mechanisms/isooctane_lu/mechanism.H
+2 −2 Mechanisms/isooctane_lu/mechanism.cpp
+15 −4 Mechanisms/methaneIons_diRenzo/mechanism.H
+2 −2 Mechanisms/methaneIons_diRenzo/mechanism.cpp
+14 −3 Mechanisms/ndodecane_35/mechanism.H
+14 −3 Mechanisms/nitrogens/mechanism.H
+24 −13 Mechanisms/propane_fc/mechanism.H
+2 −2 Mechanisms/propane_fc/mechanism.cpp
+14 −3 Mechanisms/sCO2/mechanism.H
+6 −6 Mechanisms/sCO2/mechanism.cpp
+33 −20 Source/Radiation/PeleLMRad.H
+6 −4 Source/Spray/SprayParticles.cpp
+1 −1 Submodules/amrex
+75 −2 Support/ceptr/ceptr/ceptr.py
+125 −13 Support/ceptr/ceptr/converter.py
+1 −1 Support/ceptr/ceptr/formatter.py
+1 −1 Support/ceptr/ceptr/qssa.py
+48 −13 Support/ceptr/ceptr/reaction_info.py
+3 −0 Support/ceptr/ceptr/species_info.py
+1 −0 Support/ceptr/pyproject.toml
+9 −3 Support/ceptr/tests/test_ceptr.py
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