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Fixing the initialization of the EB data in ghost cells #2635

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Merged
merged 5 commits into from
Dec 13, 2021
Merged

Fixing the initialization of the EB data in ghost cells #2635

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f0aef18
Using ng_FieldSolver ghost cells in the EB data
lgiacome Dec 7, 2021
a6424bb
Removed an unused variable
lgiacome Dec 7, 2021
8aa1ce0
Fixed makeEBFabFactory also in in WarpXRgrid.cpp
lgiacome Dec 7, 2021
683104b
Fixed end of line whitespace
lgiacome Dec 7, 2021
00f6c04
Undoing #2607
lgiacome Dec 8, 2021
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15 changes: 0 additions & 15 deletions Source/Initialization/WarpXInitData.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -887,24 +887,9 @@ void WarpX::InitializeEBGridData (int lev)
ScaleAreas();

const auto &period = Geom(lev).periodicity();
WarpXCommUtil::FillBoundary(*m_edge_lengths[lev][0], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_edge_lengths[lev][1], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_edge_lengths[lev][2], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_face_areas[lev][0], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_face_areas[lev][1], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_face_areas[lev][2], guard_cells.ng_alloc_EB, period);

if (WarpX::maxwell_solver_id == MaxwellSolverAlgo::ECT) {
WarpXCommUtil::FillBoundary(*m_area_mod[lev][0], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_area_mod[lev][1], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_area_mod[lev][2], guard_cells.ng_alloc_EB, period);
MarkCells();
WarpXCommUtil::FillBoundary(*m_flag_info_face[lev][0], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_flag_info_face[lev][1], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_flag_info_face[lev][2], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_flag_ext_face[lev][0], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_flag_ext_face[lev][1], guard_cells.ng_alloc_EB, period);
WarpXCommUtil::FillBoundary(*m_flag_ext_face[lev][2], guard_cells.ng_alloc_EB, period);
ComputeFaceExtensions();
}
}
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85 changes: 50 additions & 35 deletions Source/WarpX.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1422,14 +1422,6 @@ WarpX::ClearLevel (int lev)
void
WarpX::AllocLevelData (int lev, const BoxArray& ba, const DistributionMapping& dm)
{
#ifdef AMREX_USE_EB
m_field_factory[lev] = amrex::makeEBFabFactory(Geom(lev), ba, dm,
{1,1,1}, // Not clear how many ghost cells we need yet
amrex::EBSupport::full);
#else
m_field_factory[lev] = std::make_unique<FArrayBoxFactory>();
#endif

bool aux_is_nodal = (field_gathering_algo == GatheringAlgo::MomentumConserving);

#if (AMREX_SPACEDIM == 1)
Expand Down Expand Up @@ -1461,6 +1453,29 @@ WarpX::AllocLevelData (int lev, const BoxArray& ba, const DistributionMapping& d
WarpX::fft_do_time_averaging,
this->refRatio());


#ifdef AMREX_USE_EB
#ifdef WARPX_DIM_3D
amrex::Vector<int> fs_guard{guard_cells.ng_FieldSolver[0],
guard_cells.ng_FieldSolver[1],
guard_cells.ng_FieldSolver[2]};
#elif defined(WARPX_DIM_XZ) || defined(WARPX_DIM_RZ)
amrex::Vector<int> fs_guard{guard_cells.ng_FieldSolver[0],
guard_cells.ng_FieldSolver[1],
guard_cells.ng_FieldSolver[1]};
#elif defined(WARPX_DIM_1D_Z)
amrex::Vector<int> fs_guard{guard_cells.ng_FieldSolver[0],
guard_cells.ng_FieldSolver[0],
guard_cells.ng_FieldSolver[0]};
#endif
m_field_factory[lev] = amrex::makeEBFabFactory(Geom(lev), ba, dm,
fs_guard,
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@WeiqunZhang WeiqunZhang Dec 7, 2021

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That {1,1,1} is not the number of ghost cells in 3 directions. It's actually for different types of data (e.g., basic like cell flag, volume type like volume fraction, and everything else). Here we want to pass the the max of fs_guard three times in {}.

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@WeiqunZhang WeiqunZhang Dec 7, 2021

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We need to update makeEBFabFacotry in WarpXRegrid.cpp as well.

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@lgiacome lgiacome Dec 7, 2021

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Alright, now everything makes sense. I fixed it, thanks a lot for looking into it.

amrex::EBSupport::full);
#else
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@lgiacome lgiacome Dec 7, 2021

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@WeiqunZhang @RemiLehe makeEBFabFactory always takes a three-dimensional vector for the number of guard cells, no matter the dimensions we use to compile AMReX, while the number of components of guard_cells.ng_FieldSolver depends on the dimensions.
I couldn't find a better solution than the workaround I put in place above, but I am not sure it is ideal.

m_field_factory[lev] = std::make_unique<FArrayBoxFactory>();
#endif


if (mypc->nSpeciesDepositOnMainGrid() && n_current_deposition_buffer == 0) {
n_current_deposition_buffer = 1;
// This forces the allocation of buffers and allows the code associated
Expand Down Expand Up @@ -1618,42 +1633,42 @@ WarpX::AllocLevelMFs (int lev, const BoxArray& ba, const DistributionMapping& dm
if(WarpX::maxwell_solver_id == MaxwellSolverAlgo::Yee
|| WarpX::maxwell_solver_id == MaxwellSolverAlgo::CKC
|| WarpX::maxwell_solver_id == MaxwellSolverAlgo::ECT) {
m_edge_lengths[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Ex_nodal_flag), dm, ncomps, ngE, tag("m_edge_lengths[x]"));
m_edge_lengths[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, Ey_nodal_flag), dm, ncomps, ngE, tag("m_edge_lengths[y]"));
m_edge_lengths[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Ez_nodal_flag), dm, ncomps, ngE, tag("m_edge_lengths[z]"));
m_face_areas[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, ngE, tag("m_face_areas[x]"));
m_face_areas[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, ngE, tag("m_face_areas[y]"));
m_face_areas[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, ngE, tag("m_face_areas[z]"));
m_edge_lengths[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Ex_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_edge_lengths[x]"));
m_edge_lengths[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, Ey_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_edge_lengths[y]"));
m_edge_lengths[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Ez_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_edge_lengths[z]"));
m_face_areas[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_face_areas[x]"));
m_face_areas[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_face_areas[y]"));
m_face_areas[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_face_areas[z]"));
}
constexpr int nc_ls = 1;
constexpr int ng_ls = 2;
m_distance_to_eb[lev] = std::make_unique<MultiFab>(amrex::convert(ba, IntVect::TheNodeVector()), dm, nc_ls, ng_ls, tag("m_distance_to_eb"));
if(WarpX::maxwell_solver_id == MaxwellSolverAlgo::ECT) {
m_edge_lengths[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Ex_nodal_flag), dm, ncomps, ngE, tag("m_edge_lengths[x]"));
m_edge_lengths[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, Ey_nodal_flag), dm, ncomps, ngE, tag("m_edge_lengths[y]"));
m_edge_lengths[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Ez_nodal_flag), dm, ncomps, ngE, tag("m_edge_lengths[z]"));
m_face_areas[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, ngE, tag("m_face_areas[x]"));
m_face_areas[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, ngE, tag("m_face_areas[y]"));
m_face_areas[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, ngE, tag("m_face_areas[z]"));
m_flag_info_face[lev][0] = std::make_unique<iMultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, ngE, tag("m_flag_info_face[x]"));
m_flag_info_face[lev][1] = std::make_unique<iMultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, ngE, tag("m_flag_info_face[y]"));
m_flag_info_face[lev][2] = std::make_unique<iMultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, ngE, tag("m_flag_info_face[z]"));
m_flag_ext_face[lev][0] = std::make_unique<iMultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, ngE, tag("m_flag_ext_face[x]"));
m_flag_ext_face[lev][1] = std::make_unique<iMultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, ngE, tag("m_flag_ext_face[y]"));
m_flag_ext_face[lev][2] = std::make_unique<iMultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, ngE, tag("m_flag_ext_face[z]"));
m_area_mod[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, ngE, tag("m_area_mod[x]"));
m_area_mod[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, ngE, tag("m_area_mod[y]"));
m_area_mod[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, ngE, tag("m_area_mod[z]"));
m_edge_lengths[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Ex_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_edge_lengths[x]"));
m_edge_lengths[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, Ey_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_edge_lengths[y]"));
m_edge_lengths[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Ez_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_edge_lengths[z]"));
m_face_areas[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_face_areas[x]"));
m_face_areas[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_face_areas[y]"));
m_face_areas[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_face_areas[z]"));
m_flag_info_face[lev][0] = std::make_unique<iMultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_flag_info_face[x]"));
m_flag_info_face[lev][1] = std::make_unique<iMultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_flag_info_face[y]"));
m_flag_info_face[lev][2] = std::make_unique<iMultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_flag_info_face[z]"));
m_flag_ext_face[lev][0] = std::make_unique<iMultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_flag_ext_face[x]"));
m_flag_ext_face[lev][1] = std::make_unique<iMultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_flag_ext_face[y]"));
m_flag_ext_face[lev][2] = std::make_unique<iMultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_flag_ext_face[z]"));
m_area_mod[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_area_mod[x]"));
m_area_mod[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_area_mod[y]"));
m_area_mod[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("m_area_mod[z]"));
m_borrowing[lev][0] = std::make_unique<amrex::LayoutData<FaceInfoBox>>(amrex::convert(ba, Bx_nodal_flag), dm);
m_borrowing[lev][1] = std::make_unique<amrex::LayoutData<FaceInfoBox>>(amrex::convert(ba, By_nodal_flag), dm);
m_borrowing[lev][2] = std::make_unique<amrex::LayoutData<FaceInfoBox>>(amrex::convert(ba, Bz_nodal_flag), dm);
Venl[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, ngE, tag("Venl[x]"));
Venl[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, ngE, tag("Venl[y]"));
Venl[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, ngE, tag("Venl[z]"));
Venl[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("Venl[x]"));
Venl[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("Venl[y]"));
Venl[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("Venl[z]"));

ECTRhofield[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, ngE, tag("ECTRhofield[x]"));
ECTRhofield[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, ngE, tag("ECTRhofield[y]"));
ECTRhofield[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, ngE, tag("ECTRhofield[z]"));
ECTRhofield[lev][0] = std::make_unique<MultiFab>(amrex::convert(ba, Bx_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("ECTRhofield[x]"));
ECTRhofield[lev][1] = std::make_unique<MultiFab>(amrex::convert(ba, By_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("ECTRhofield[y]"));
ECTRhofield[lev][2] = std::make_unique<MultiFab>(amrex::convert(ba, Bz_nodal_flag), dm, ncomps, guard_cells.ng_FieldSolver, tag("ECTRhofield[z]"));
ECTRhofield[lev][0]->setVal(0.);
ECTRhofield[lev][1]->setVal(0.);
ECTRhofield[lev][2]->setVal(0.);
Expand Down