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-rw-r--r--Source/Diagnostics/WarpXOpenPMD.cpp209
1 files changed, 118 insertions, 91 deletions
diff --git a/Source/Diagnostics/WarpXOpenPMD.cpp b/Source/Diagnostics/WarpXOpenPMD.cpp
index db2def7c7..6bef287a6 100644
--- a/Source/Diagnostics/WarpXOpenPMD.cpp
+++ b/Source/Diagnostics/WarpXOpenPMD.cpp
@@ -238,32 +238,43 @@ void WarpXOpenPMDPlot::GetFileName(std::string& filename)
}
-void WarpXOpenPMDPlot::SetStep (int ts, const std::string& filePrefix)
+void WarpXOpenPMDPlot::SetStep (int ts, const std::string& filePrefix,
+ bool isBTD)
{
- AMREX_ALWAYS_ASSERT_WITH_MESSAGE(ts >= 0 , "openPMD iterations are unsigned");
-
- if (m_CurrentStep >= ts) {
- // note m_Series is reset in Init(), so using m_Series->iterations.contains(ts) is only able to check the
- // last written step in m_Series's life time, but not other earlier written steps by other m_Series
- std::string warnMsg = " Warning from openPMD writer: Already written iteration:"+std::to_string(ts);
- std::cout<<warnMsg<<std::endl;
- amrex::Warning(warnMsg);
- }
-
- m_CurrentStep = ts;
- Init(openPMD::Access::CREATE, filePrefix);
-
+ AMREX_ALWAYS_ASSERT_WITH_MESSAGE(ts >= 0 , "openPMD iterations are unsigned");
+
+ if( ! isBTD ) {
+ if (m_CurrentStep >= ts) {
+ // note m_Series is reset in Init(), so using m_Series->iterations.contains(ts) is only able to check the
+ // last written step in m_Series's life time, but not other earlier written steps by other m_Series
+ std::string warnMsg =
+ " Warning from openPMD writer: Already written iteration:" + std::to_string(ts);
+ std::cout << warnMsg << std::endl;
+ amrex::Warning(warnMsg);
+ }
+ }
+ m_CurrentStep = ts;
+ Init(openPMD::Access::CREATE, filePrefix, isBTD);
}
-void WarpXOpenPMDPlot::CloseStep ()
+void WarpXOpenPMDPlot::CloseStep (bool isBTD, bool isLastBTDFlush)
{
- if (m_Series)
- m_Series->iterations[m_CurrentStep].close();
+ // default close is true
+ bool callClose = true;
+ // close BTD file only when isLastBTDFlush is true
+ if (isBTD and !isLastBTDFlush) callClose = false;
+ if (callClose) {
+ if (m_Series)
+ m_Series->iterations[m_CurrentStep].close();
+ }
}
void
-WarpXOpenPMDPlot::Init (openPMD::Access access, const std::string& filePrefix)
+WarpXOpenPMDPlot::Init (openPMD::Access access, const std::string& filePrefix, bool isBTD)
{
+ if( isBTD && m_Series != nullptr )
+ return; // already open for this snapshot (aka timestep in lab frame)
+
// either for the next ts file,
// or init a single file for all ts
std::string filename = filePrefix;
@@ -273,8 +284,7 @@ WarpXOpenPMDPlot::Init (openPMD::Access access, const std::string& filePrefix)
// see ADIOS1 limitation: https://github.com/openPMD/openPMD-api/pull/686
m_Series = nullptr;
- if( amrex::ParallelDescriptor::NProcs() > 1 )
- {
+ if (amrex::ParallelDescriptor::NProcs() > 1) {
#if defined(AMREX_USE_MPI)
m_Series = std::make_unique<openPMD::Series>(
filename, access,
@@ -285,9 +295,7 @@ WarpXOpenPMDPlot::Init (openPMD::Access access, const std::string& filePrefix)
#else
amrex::Abort("openPMD-api not built with MPI support!");
#endif
- }
- else
- {
+ } else {
m_Series = std::make_unique<openPMD::Series>(filename, access);
m_MPISize = 1;
m_MPIRank = 1;
@@ -746,30 +754,39 @@ WarpXOpenPMDPlot::SetupPos(
// this is originally copied from FieldIO.cpp
//
void
-WarpXOpenPMDPlot::WriteOpenPMDFields( //const std::string& filename,
+WarpXOpenPMDPlot::WriteOpenPMDFields ( //const std::string& filename,
const std::vector<std::string>& varnames,
const amrex::MultiFab& mf,
- const amrex::Geometry& geom,
+ const amrex::Geometry& geom, // geometry of the mf/Fab
const int iteration,
- const double time ) const
+ const double time, bool isBTD,
+ const amrex::Geometry& full_BTD_snapshot ) const
{
//This is AMReX's tiny profiler. Possibly will apply it later
WARPX_PROFILE("WarpXOpenPMDPlot::WriteOpenPMDFields()");
AMREX_ALWAYS_ASSERT_WITH_MESSAGE(m_Series != nullptr, "openPMD series must be initialized");
+ amrex::Geometry full_geom = geom;
+ if( isBTD )
+ full_geom = full_BTD_snapshot;
+
+ // is this either a regular write (true) or the first write in a
+ // backtransformed diagnostic (BTD):
+ bool const first_write_to_iteration = ! m_Series->iterations.contains( iteration );
+
int const ncomp = mf.nComp();
// Create a few vectors that store info on the global domain
// Swap the indices for each of them, since AMReX data is Fortran order
// and since the openPMD API assumes contiguous C order
// - Size of the box, in integer number of cells
- amrex::Box const & global_box = geom.Domain();
+ amrex::Box const & global_box = full_geom.Domain();
auto const global_size = getReversedVec(global_box.size());
// - Grid spacing
- std::vector<double> const grid_spacing = getReversedVec(geom.CellSize());
+ std::vector<double> const grid_spacing = getReversedVec(full_geom.CellSize());
// - Global offset
- std::vector<double> const global_offset = getReversedVec(geom.ProbLo());
+ std::vector<double> const global_offset = getReversedVec(full_geom.ProbLo());
// - AxisLabels
std::vector<std::string> axis_labels = detail::getFieldAxisLabels();
@@ -779,64 +796,70 @@ WarpXOpenPMDPlot::WriteOpenPMDFields( //const std::string& filename,
// meta data
auto series_iteration = m_Series->iterations[iteration];
- series_iteration.setTime( time );
-
- // meta data for ED-PIC extension
- auto const period = geom.periodicity(); // TODO double-check: is this the proper global bound or of some level?
- std::vector< std::string > fieldBoundary( 6, "reflecting" );
- std::vector< std::string > particleBoundary( 6, "absorbing" );
-#if AMREX_SPACEDIM!=3
- fieldBoundary.resize(4);
- particleBoundary.resize(4);
+ auto meshes = series_iteration.meshes;
+ if( first_write_to_iteration ) {
+ series_iteration.setTime( time );
+
+ // meta data for ED-PIC extension
+ auto const period = full_geom.periodicity(); // TODO double-check: is this the proper global bound or of some level?
+ std::vector<std::string> fieldBoundary(6, "reflecting");
+ std::vector<std::string> particleBoundary(6, "absorbing");
+#if AMREX_SPACEDIM != 3
+ fieldBoundary.resize(4);
+ particleBoundary.resize(4);
#endif
- for( auto i = 0u; i < fieldBoundary.size() / 2u; ++i )
- if( m_fieldPMLdirections.at( i ) )
- fieldBoundary.at( i ) = "open";
-
- for( auto i = 0u; i < fieldBoundary.size() / 2u; ++i )
- if( period.isPeriodic( i ) ) {
- fieldBoundary.at(2u*i ) = "periodic";
- fieldBoundary.at(2u*i + 1u) = "periodic";
- particleBoundary.at(2u*i ) = "periodic";
- particleBoundary.at(2u*i + 1u) = "periodic";
- }
-
- auto meshes = series_iteration.meshes;
- meshes.setAttribute( "fieldSolver", [](){
- switch( WarpX::maxwell_solver_id ) {
- case MaxwellSolverAlgo::Yee : return "Yee";
- case MaxwellSolverAlgo::CKC : return "CK";
- case MaxwellSolverAlgo::PSATD : return "PSATD";
- default: return "other";
- }
- }() );
- meshes.setAttribute( "fieldBoundary", fieldBoundary );
- meshes.setAttribute( "particleBoundary", particleBoundary );
- meshes.setAttribute( "currentSmoothing", [](){
- if( WarpX::use_filter ) return "Binomial";
+ for (auto i = 0u; i < fieldBoundary.size() / 2u; ++i)
+ if (m_fieldPMLdirections.at(i))
+ fieldBoundary.at(i) = "open";
+
+ for (auto i = 0u; i < fieldBoundary.size() / 2u; ++i)
+ if (period.isPeriodic(i)) {
+ fieldBoundary.at(2u * i) = "periodic";
+ fieldBoundary.at(2u * i + 1u) = "periodic";
+ particleBoundary.at(2u * i) = "periodic";
+ particleBoundary.at(2u * i + 1u) = "periodic";
+ }
+
+ meshes.setAttribute("fieldSolver", []() {
+ switch (WarpX::maxwell_solver_id) {
+ case MaxwellSolverAlgo::Yee :
+ return "Yee";
+ case MaxwellSolverAlgo::CKC :
+ return "CK";
+ case MaxwellSolverAlgo::PSATD :
+ return "PSATD";
+ default:
+ return "other";
+ }
+ }());
+ meshes.setAttribute("fieldBoundary", fieldBoundary);
+ meshes.setAttribute("particleBoundary", particleBoundary);
+ meshes.setAttribute("currentSmoothing", []() {
+ if (WarpX::use_filter) return "Binomial";
else return "none";
- }() );
- if( WarpX::use_filter )
- meshes.setAttribute( "currentSmoothingParameters", [](){
- std::stringstream ss;
- ss << "period=1;compensator=false";
- ss << ";numPasses_x=" << WarpX::filter_npass_each_dir[0];
+ }());
+ if (WarpX::use_filter)
+ meshes.setAttribute("currentSmoothingParameters", []() {
+ std::stringstream ss;
+ ss << "period=1;compensator=false";
+ ss << ";numPasses_x=" << WarpX::filter_npass_each_dir[0];
#if (AMREX_SPACEDIM == 3)
- ss << ";numPasses_y=" << WarpX::filter_npass_each_dir[1];
- ss << ";numPasses_z=" << WarpX::filter_npass_each_dir[2];
+ ss << ";numPasses_y=" << WarpX::filter_npass_each_dir[1];
+ ss << ";numPasses_z=" << WarpX::filter_npass_each_dir[2];
#else
- ss << ";numPasses_z=" << WarpX::filter_npass_each_dir[1];
+ ss << ";numPasses_z=" << WarpX::filter_npass_each_dir[1];
#endif
- std::string currentSmoothingParameters = ss.str();
- return currentSmoothingParameters;
- }() );
- meshes.setAttribute("chargeCorrection", [](){
- if( WarpX::do_dive_cleaning ) return "hyperbolic"; // TODO or "spectral" or something? double-check
- else return "none";
- }() );
- if( WarpX::do_dive_cleaning )
- meshes.setAttribute("chargeCorrectionParameters", "period=1");
+ std::string currentSmoothingParameters = ss.str();
+ return currentSmoothingParameters;
+ }());
+ meshes.setAttribute("chargeCorrection", []() {
+ if (WarpX::do_dive_cleaning) return "hyperbolic"; // TODO or "spectral" or something? double-check
+ else return "none";
+ }());
+ if (WarpX::do_dive_cleaning)
+ meshes.setAttribute("chargeCorrectionParameters", "period=1");
+ }
// Loop through the different components, i.e. different fields stored in mf
for (int icomp=0; icomp<ncomp; icomp++){
@@ -871,20 +894,24 @@ WarpXOpenPMDPlot::WriteOpenPMDFields( //const std::string& filename,
// we invert (only) meta-data arrays to assign labels and offsets in the
// order: slowest to fastest varying index when accessing the mesh
// contiguously (as 1D flattened logical memory)
- mesh.setDataOrder( openPMD::Mesh::DataOrder::C );
- mesh.setAxisLabels( axis_labels );
- mesh.setGridSpacing( grid_spacing );
- mesh.setGridGlobalOffset( global_offset );
- mesh.setAttribute( "fieldSmoothing", "none" );
- detail::setOpenPMDUnit( mesh, field_name );
+ if( first_write_to_iteration ) {
+ mesh.setDataOrder(openPMD::Mesh::DataOrder::C);
+ mesh.setAxisLabels(axis_labels);
+ mesh.setGridSpacing(grid_spacing);
+ mesh.setGridGlobalOffset(global_offset);
+ mesh.setAttribute("fieldSmoothing", "none");
+ detail::setOpenPMDUnit(mesh, field_name);
+ }
// Create a new mesh record component, and store the associated metadata
auto mesh_comp = mesh[comp_name];
- mesh_comp.resetDataset( dataset );
+ if( first_write_to_iteration ) {
+ mesh_comp.resetDataset(dataset);
- auto relative_cell_pos = utils::getRelativeCellPosition( mf ); // AMReX Fortran index order
- std::reverse( relative_cell_pos.begin(), relative_cell_pos.end() ); // now in C order
- mesh_comp.setPosition( relative_cell_pos );
+ auto relative_cell_pos = utils::getRelativeCellPosition(mf); // AMReX Fortran index order
+ std::reverse(relative_cell_pos.begin(), relative_cell_pos.end()); // now in C order
+ mesh_comp.setPosition(relative_cell_pos);
+ }
// Loop through the multifab, and store each box as a chunk,
// in the openPMD file.
generated by cgit v1.2.3 (git 2.46.0) at 2025-08-11 19:01:31 +0000