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-rw-r--r--Source/Diagnostics/WarpXIO.cpp303
1 files changed, 55 insertions, 248 deletions
diff --git a/Source/Diagnostics/WarpXIO.cpp b/Source/Diagnostics/WarpXIO.cpp
index 0d65b2796..ee1991c21 100644
--- a/Source/Diagnostics/WarpXIO.cpp
+++ b/Source/Diagnostics/WarpXIO.cpp
@@ -1,4 +1,3 @@
-
#include <AMReX_MultiFabUtil.H>
#include <AMReX_PlotFileUtil.H>
#include <AMReX_FillPatchUtil_F.H>
@@ -181,7 +180,6 @@ WarpX::WriteCheckPointFile() const
VisMF::SetHeaderVersion(current_version);
}
-
void
WarpX::InitFromCheckpoint ()
{
@@ -514,130 +512,66 @@ WarpX::WritePlotFile () const
const int nlevels = finestLevel()+1;
for (int lev = 0; lev < nlevels; ++lev)
{
- const std::string raw_plotfilename = plotfilename + "/raw_fields";
- // Plot auxilary patch
- if (plot_raw_fields_guards) {
- VisMF::Write(*Efield_aux[lev][0], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ex_aux"));
- VisMF::Write(*Efield_aux[lev][1], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ey_aux"));
- VisMF::Write(*Efield_aux[lev][2], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ez_aux"));
- VisMF::Write(*Bfield_aux[lev][0], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bx_aux"));
- VisMF::Write(*Bfield_aux[lev][1], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "By_aux"));
- VisMF::Write(*Bfield_aux[lev][2], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bz_aux"));
- } else {
- const DistributionMapping& dm = DistributionMap(lev);
- MultiFab Ex(Efield_aux[lev][0]->boxArray(), dm, 1, 0);
- MultiFab Ey(Efield_aux[lev][1]->boxArray(), dm, 1, 0);
- MultiFab Ez(Efield_aux[lev][2]->boxArray(), dm, 1, 0);
- MultiFab Bx(Bfield_aux[lev][0]->boxArray(), dm, 1, 0);
- MultiFab By(Bfield_aux[lev][1]->boxArray(), dm, 1, 0);
- MultiFab Bz(Bfield_aux[lev][2]->boxArray(), dm, 1, 0);
- MultiFab::Copy(Ex, *Efield_aux[lev][0], 0, 0, 1, 0);
- MultiFab::Copy(Ey, *Efield_aux[lev][1], 0, 0, 1, 0);
- MultiFab::Copy(Ez, *Efield_aux[lev][2], 0, 0, 1, 0);
- MultiFab::Copy(Bx, *Bfield_aux[lev][0], 0, 0, 1, 0);
- MultiFab::Copy(By, *Bfield_aux[lev][1], 0, 0, 1, 0);
- MultiFab::Copy(Bz, *Bfield_aux[lev][2], 0, 0, 1, 0);
- VisMF::Write(Ex, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ex_aux"));
- VisMF::Write(Ey, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ey_aux"));
- VisMF::Write(Ez, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ez_aux"));
- VisMF::Write(Bx, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bx_aux"));
- VisMF::Write(By, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "By_aux"));
- VisMF::Write(Bz, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bz_aux"));
- }
-
- // Plot fine patch
+ const std::unique_ptr<MultiFab> empty_ptr;
+ const std::string raw_pltname = plotfilename + "/raw_fields";
+ const DistributionMapping& dm = DistributionMap(lev);
+
+ // Auxiliary patch
+ WriteRawField( *Efield_aux[lev][0], dm, raw_pltname, level_prefix, "Ex_aux", lev, plot_raw_fields_guards);
+ WriteRawField( *Efield_aux[lev][1], dm, raw_pltname, level_prefix, "Ey_aux", lev, plot_raw_fields_guards);
+ WriteRawField( *Efield_aux[lev][2], dm, raw_pltname, level_prefix, "Ez_aux", lev, plot_raw_fields_guards);
+ WriteRawField( *Bfield_aux[lev][0], dm, raw_pltname, level_prefix, "Bx_aux", lev, plot_raw_fields_guards);
+ WriteRawField( *Bfield_aux[lev][1], dm, raw_pltname, level_prefix, "By_aux", lev, plot_raw_fields_guards);
+ WriteRawField( *Bfield_aux[lev][2], dm, raw_pltname, level_prefix, "Bz_aux", lev, plot_raw_fields_guards);
+
+ // Fine patch
if (plot_finepatch) {
- if (plot_raw_fields_guards) {
- VisMF::Write(*Efield_fp[lev][0], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ex_fp"));
- VisMF::Write(*Efield_fp[lev][1], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ey_fp"));
- VisMF::Write(*Efield_fp[lev][2], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ez_fp"));
- VisMF::Write(*Bfield_fp[lev][0], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bx_fp"));
- VisMF::Write(*Bfield_fp[lev][1], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "By_fp"));
- VisMF::Write(*Bfield_fp[lev][2], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bz_fp"));
- VisMF::Write(*current_fp[lev][0], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "jx_fp"));
- VisMF::Write(*current_fp[lev][1], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "jy_fp"));
- VisMF::Write(*current_fp[lev][2], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "jz_fp"));
- } else {
- const DistributionMapping& dm = DistributionMap(lev);
- MultiFab Ex(Efield_fp[lev][0]->boxArray(), dm, 1, 0);
- MultiFab Ey(Efield_fp[lev][1]->boxArray(), dm, 1, 0);
- MultiFab Ez(Efield_fp[lev][2]->boxArray(), dm, 1, 0);
- MultiFab Bx(Bfield_fp[lev][0]->boxArray(), dm, 1, 0);
- MultiFab By(Bfield_fp[lev][1]->boxArray(), dm, 1, 0);
- MultiFab Bz(Bfield_fp[lev][2]->boxArray(), dm, 1, 0);
- MultiFab jx(current_fp[lev][0]->boxArray(), dm, 1, 0);
- MultiFab jy(current_fp[lev][1]->boxArray(), dm, 1, 0);
- MultiFab jz(current_fp[lev][2]->boxArray(), dm, 1, 0);
- MultiFab::Copy(Ex, *Efield_fp[lev][0], 0, 0, 1, 0);
- MultiFab::Copy(Ey, *Efield_fp[lev][1], 0, 0, 1, 0);
- MultiFab::Copy(Ez, *Efield_fp[lev][2], 0, 0, 1, 0);
- MultiFab::Copy(Bx, *Bfield_fp[lev][0], 0, 0, 1, 0);
- MultiFab::Copy(By, *Bfield_fp[lev][1], 0, 0, 1, 0);
- MultiFab::Copy(Bz, *Bfield_fp[lev][2], 0, 0, 1, 0);
- MultiFab::Copy(jx, *current_fp[lev][0], 0, 0, 1, 0);
- MultiFab::Copy(jy, *current_fp[lev][1], 0, 0, 1, 0);
- MultiFab::Copy(jz, *current_fp[lev][2], 0, 0, 1, 0);
- VisMF::Write(Ex, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ex_fp"));
- VisMF::Write(Ey, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ey_fp"));
- VisMF::Write(Ez, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ez_fp"));
- VisMF::Write(Bx, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bx_fp"));
- VisMF::Write(By, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "By_fp"));
- VisMF::Write(Bz, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bz_fp"));
- VisMF::Write(jx, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "jx_fp"));
- VisMF::Write(jy, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "jy_fp"));
- VisMF::Write(jz, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "jz_fp"));
+ WriteRawField( *Efield_fp[lev][0], dm, raw_pltname, level_prefix, "Ex_fp", lev, plot_raw_fields_guards);
+ WriteRawField( *Efield_fp[lev][1], dm, raw_pltname, level_prefix, "Ey_fp", lev, plot_raw_fields_guards);
+ WriteRawField( *Efield_fp[lev][2], dm, raw_pltname, level_prefix, "Ez_fp", lev, plot_raw_fields_guards);
+ WriteRawField( *current_fp[lev][0], dm, raw_pltname, level_prefix, "jx_fp", lev, plot_raw_fields_guards);
+ WriteRawField( *current_fp[lev][1], dm, raw_pltname, level_prefix, "jy_fp", lev, plot_raw_fields_guards);
+ WriteRawField( *current_fp[lev][2], dm, raw_pltname, level_prefix, "jz_fp", lev, plot_raw_fields_guards);
+ WriteRawField( *Bfield_fp[lev][0], dm, raw_pltname, level_prefix, "Bx_fp", lev, plot_raw_fields_guards);
+ WriteRawField( *Bfield_fp[lev][1], dm, raw_pltname, level_prefix, "By_fp", lev, plot_raw_fields_guards);
+ WriteRawField( *Bfield_fp[lev][2], dm, raw_pltname, level_prefix, "Bz_fp", lev, plot_raw_fields_guards);
+ if (F_fp[lev]) WriteRawField( *F_fp[lev], dm, raw_pltname, level_prefix, "F_fp", lev, plot_raw_fields_guards);
+ if (plot_rho) {
+ // Use the component 1 of `rho_fp`, i.e. rho_new for time synchronization
+ MultiFab rho_new(*rho_fp[lev], amrex::make_alias, 1, 1);
+ WriteRawField( rho_new, dm, raw_pltname, level_prefix, "rho_fp", lev, plot_raw_fields_guards);
}
}
- // Plot coarse patch
- if (plot_crsepatch)
- {
- if (lev == 0)
- {
- const DistributionMapping& dm = DistributionMap(lev);
- MultiFab Ex(Efield_aux[lev][0]->boxArray(), dm, 1, 0);
- MultiFab Ey(Efield_aux[lev][1]->boxArray(), dm, 1, 0);
- MultiFab Ez(Efield_aux[lev][2]->boxArray(), dm, 1, 0);
- MultiFab Bx(Bfield_aux[lev][0]->boxArray(), dm, 1, 0);
- MultiFab By(Bfield_aux[lev][1]->boxArray(), dm, 1, 0);
- MultiFab Bz(Bfield_aux[lev][2]->boxArray(), dm, 1, 0);
-
- Ex.setVal(0.0); Ey.setVal(0.0); Ez.setVal(0.0);
- Bx.setVal(0.0); By.setVal(0.0); Bz.setVal(0.0);
-
- VisMF::Write(Ex, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ex_cp"));
- VisMF::Write(Ey, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ey_cp"));
- VisMF::Write(Ez, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ez_cp"));
- VisMF::Write(Bx, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bx_cp"));
- VisMF::Write(By, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "By_cp"));
- VisMF::Write(Bz, amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bz_cp"));
- } else {
-
- if (plot_raw_fields_guards) {
- VisMF::Write(*Efield_cp[lev][0], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ex_cp"));
- VisMF::Write(*Efield_cp[lev][1], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ey_cp"));
- VisMF::Write(*Efield_cp[lev][2], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ez_cp"));
- VisMF::Write(*Bfield_cp[lev][0], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bx_cp"));
- VisMF::Write(*Bfield_cp[lev][1], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "By_cp"));
- VisMF::Write(*Bfield_cp[lev][2], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bz_cp"));
- } else {
- std::array<std::unique_ptr<MultiFab>, 3> E = getInterpolatedE(lev);
- std::array<std::unique_ptr<MultiFab>, 3> B = getInterpolatedB(lev);
-
- VisMF::Write(*E[0], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ex_cp"));
- VisMF::Write(*E[1], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ey_cp"));
- VisMF::Write(*E[2], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Ez_cp"));
- VisMF::Write(*B[0], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bx_cp"));
- VisMF::Write(*B[1], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "By_cp"));
- VisMF::Write(*B[2], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "Bz_cp"));
- }
- }
+ // Coarse path
+ if (plot_crsepatch) {
+ const Real* dx = Geom(lev-1).CellSize();
+ const int r_ratio = refRatio(lev-1)[0];
+ WriteCoarseVector( "E",
+ Efield_cp[lev][0], Efield_cp[lev][1], Efield_cp[lev][2],
+ Efield_fp[lev][0], Efield_fp[lev][1], Efield_fp[lev][2],
+ dm, raw_pltname, level_prefix, lev, plot_raw_fields_guards,
+ r_ratio, dx );
+ WriteCoarseVector( "B",
+ Bfield_cp[lev][0], Bfield_cp[lev][1], Bfield_cp[lev][2],
+ Bfield_fp[lev][0], Bfield_fp[lev][1], Bfield_fp[lev][2],
+ dm, raw_pltname, level_prefix, lev, plot_raw_fields_guards,
+ r_ratio, dx );
+ WriteCoarseVector( "j",
+ current_cp[lev][0], current_cp[lev][1], current_cp[lev][2],
+ current_fp[lev][0], current_fp[lev][1], current_fp[lev][2],
+ dm, raw_pltname, level_prefix, lev, plot_raw_fields_guards,
+ r_ratio, dx );
+ if (F_cp[lev]) WriteCoarseScalar(
+ "F", F_cp[lev], F_fp[lev],
+ dm, raw_pltname, level_prefix, lev,
+ plot_raw_fields_guards, r_ratio, dx );
+ if (plot_rho) WriteCoarseScalar(
+ "rho", rho_cp[lev], rho_fp[lev],
+ dm, raw_pltname, level_prefix, lev,
+ plot_raw_fields_guards, r_ratio, dx, 1 );
+ // Use the component 1 of `rho_cp`, i.e. rho_new for time synchronization
}
-
- if (F_fp[lev]) {
- VisMF::Write(*F_fp[lev], amrex::MultiFabFileFullPrefix(lev, raw_plotfilename, level_prefix, "F_fp"));
- }
-
}
}
@@ -793,130 +727,3 @@ WarpX::WriteJobInfo (const std::string& dir) const
jobInfoFile.close();
}
}
-
-std::array<std::unique_ptr<MultiFab>, 3> WarpX::getInterpolatedE(int lev) const
-{
-
- const int ngrow = 0;
-
- std::array<std::unique_ptr<MultiFab>, 3> interpolated_E;
- for (int i = 0; i < 3; ++i) {
- interpolated_E[i].reset( new MultiFab(Efield_aux[lev][i]->boxArray(), dmap[lev], 1, ngrow) );
- interpolated_E[i]->setVal(0.0);
- }
-
- const int r_ratio = refRatio(lev-1)[0];
- const int use_limiter = 0;
-#ifdef _OPEMP
-#pragma omp parallel
-#endif
- {
- std::array<FArrayBox,3> efab;
- for (MFIter mfi(*interpolated_E[0]); mfi.isValid(); ++mfi)
- {
- Box ccbx = mfi.fabbox();
- ccbx.enclosedCells();
- ccbx.coarsen(r_ratio).refine(r_ratio); // so that ccbx is coarsenable
-
- const FArrayBox& cxfab = (*Efield_cp[lev][0])[mfi];
- const FArrayBox& cyfab = (*Efield_cp[lev][1])[mfi];
- const FArrayBox& czfab = (*Efield_cp[lev][2])[mfi];
-
- efab[0].resize(amrex::convert(ccbx,Ex_nodal_flag));
- efab[1].resize(amrex::convert(ccbx,Ey_nodal_flag));
- efab[2].resize(amrex::convert(ccbx,Ez_nodal_flag));
-
-#if (AMREX_SPACEDIM == 3)
- amrex_interp_efield(ccbx.loVect(), ccbx.hiVect(),
- BL_TO_FORTRAN_ANYD(efab[0]),
- BL_TO_FORTRAN_ANYD(efab[1]),
- BL_TO_FORTRAN_ANYD(efab[2]),
- BL_TO_FORTRAN_ANYD(cxfab),
- BL_TO_FORTRAN_ANYD(cyfab),
- BL_TO_FORTRAN_ANYD(czfab),
- &r_ratio,&use_limiter);
-#else
- amrex_interp_efield(ccbx.loVect(), ccbx.hiVect(),
- BL_TO_FORTRAN_ANYD(efab[0]),
- BL_TO_FORTRAN_ANYD(efab[2]),
- BL_TO_FORTRAN_ANYD(cxfab),
- BL_TO_FORTRAN_ANYD(czfab),
- &r_ratio,&use_limiter);
- amrex_interp_nd_efield(ccbx.loVect(), ccbx.hiVect(),
- BL_TO_FORTRAN_ANYD(efab[1]),
- BL_TO_FORTRAN_ANYD(cyfab),
- &r_ratio);
-#endif
-
- for (int i = 0; i < 3; ++i) {
- const Box& bx = (*interpolated_E[i])[mfi].box();
- (*interpolated_E[i])[mfi].plus(efab[i], bx, bx, 0, 0, 1);
- }
- }
- }
-
- return interpolated_E;
-}
-
-std::array<std::unique_ptr<MultiFab>, 3> WarpX::getInterpolatedB(int lev) const
-{
- const int ngrow = 0;
-
- std::array<std::unique_ptr<MultiFab>, 3> interpolated_B;
- for (int i = 0; i < 3; ++i) {
- interpolated_B[i].reset( new MultiFab(Bfield_aux[lev][i]->boxArray(), dmap[lev], 1, ngrow) );
- interpolated_B[i]->setVal(0.0);
- }
-
- const Real* dx = Geom(lev-1).CellSize();
- const int r_ratio = refRatio(lev-1)[0];
- const int use_limiter = 0;
-#ifdef _OPEMP
-#pragma omp parallel
-#endif
- {
- std::array<FArrayBox,3> bfab;
- for (MFIter mfi(*interpolated_B[0]); mfi.isValid(); ++mfi)
- {
- Box ccbx = mfi.fabbox();
- ccbx.enclosedCells();
- ccbx.coarsen(r_ratio).refine(r_ratio); // so that ccbx is coarsenable
-
- const FArrayBox& cxfab = (*Bfield_cp[lev][0])[mfi];
- const FArrayBox& cyfab = (*Bfield_cp[lev][1])[mfi];
- const FArrayBox& czfab = (*Bfield_cp[lev][2])[mfi];
-
- bfab[0].resize(amrex::convert(ccbx,Bx_nodal_flag));
- bfab[1].resize(amrex::convert(ccbx,By_nodal_flag));
- bfab[2].resize(amrex::convert(ccbx,Bz_nodal_flag));
-
-#if (AMREX_SPACEDIM == 3)
- amrex_interp_div_free_bfield(ccbx.loVect(), ccbx.hiVect(),
- BL_TO_FORTRAN_ANYD(bfab[0]),
- BL_TO_FORTRAN_ANYD(bfab[1]),
- BL_TO_FORTRAN_ANYD(bfab[2]),
- BL_TO_FORTRAN_ANYD(cxfab),
- BL_TO_FORTRAN_ANYD(cyfab),
- BL_TO_FORTRAN_ANYD(czfab),
- dx, &r_ratio, &use_limiter);
-#else
- amrex_interp_div_free_bfield(ccbx.loVect(), ccbx.hiVect(),
- BL_TO_FORTRAN_ANYD(bfab[0]),
- BL_TO_FORTRAN_ANYD(bfab[2]),
- BL_TO_FORTRAN_ANYD(cxfab),
- BL_TO_FORTRAN_ANYD(czfab),
- dx, &r_ratio, &use_limiter);
- amrex_interp_cc_bfield(ccbx.loVect(), ccbx.hiVect(),
- BL_TO_FORTRAN_ANYD(bfab[1]),
- BL_TO_FORTRAN_ANYD(cyfab),
- &r_ratio, &use_limiter);
-#endif
-
- for (int i = 0; i < 3; ++i) {
- const Box& bx = (*interpolated_B[i])[mfi].box();
- (*interpolated_B[i])[mfi].plus(bfab[i], bx, bx, 0, 0, 1);
- }
- }
- }
- return interpolated_B;
-}
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