diff options
Diffstat (limited to 'Source')
| -rw-r--r-- | Source/Diagnostics/WarpXIO.cpp | 19 | ||||
| -rw-r--r-- | Source/Diagnostics/WarpXOpenPMD.cpp | 72 |
2 files changed, 68 insertions, 23 deletions
diff --git a/Source/Diagnostics/WarpXIO.cpp b/Source/Diagnostics/WarpXIO.cpp index 31a5f700d..d7a46f7b7 100644 --- a/Source/Diagnostics/WarpXIO.cpp +++ b/Source/Diagnostics/WarpXIO.cpp @@ -527,13 +527,17 @@ WarpX::WritePlotFile () const } #ifdef WARPX_USE_OPENPMD - m_OpenPMDPlotWriter->SetStep(istep[0]); - if (dump_openpmd) - m_OpenPMDPlotWriter->WriteOpenPMDFields(varnames, - *output_mf[0], output_geom[0], istep[0], t_new[0] ); + if (dump_openpmd) { + m_OpenPMDPlotWriter->SetStep(istep[0]); + // fields: only dumped for coarse level + m_OpenPMDPlotWriter->WriteOpenPMDFields( + varnames, *output_mf[0], output_geom[0], istep[0], t_new[0]); + // particles: all (reside only on locally finest level) + m_OpenPMDPlotWriter->WriteOpenPMDParticles(mypc); + } #endif - if (dump_plotfiles || dump_openpmd) { + if (dump_plotfiles) { // Write the fields contained in `mf_avg`, and corresponding to the // names `varnames`, into a plotfile. @@ -616,11 +620,6 @@ WarpX::WritePlotFile () const } } -#ifdef WARPX_USE_OPENPMD - // Write openPMD format: only for level 0 - if (dump_openpmd) - m_OpenPMDPlotWriter->WriteOpenPMDParticles(mypc); -#endif // leaving the option of binary output through AMREx around // regardless of openPMD. This can be adjusted later { diff --git a/Source/Diagnostics/WarpXOpenPMD.cpp b/Source/Diagnostics/WarpXOpenPMD.cpp index 05c2066de..2f1ff7719 100644 --- a/Source/Diagnostics/WarpXOpenPMD.cpp +++ b/Source/Diagnostics/WarpXOpenPMD.cpp @@ -1,6 +1,32 @@ #include "WarpXOpenPMD.H" #include "FieldIO.H" // for getReversedVec +#include <tuple> +#include <utility> + + +namespace detail +{ + /** Unclutter a real_names to openPMD record + * + * @param fullName name as in real_names variable + * @return pair of openPMD record and component name + */ + inline std::pair< std::string, std::string > + name2openPMD( std::string const& fullName ) + { + std::string record_name = fullName; + std::string component_name = openPMD::RecordComponent::SCALAR; + std::size_t startComp = fullName.find_last_of("_"); + + if( startComp != std::string::npos ) { // non-scalar + record_name = fullName.substr(0, startComp); + component_name = fullName.substr(startComp + 1u); + } + return make_pair(record_name, component_name); + } +} + WarpXOpenPMDPlot::WarpXOpenPMDPlot(bool oneFilePerTS, std::string& openPMDFileType) :m_Series(nullptr), @@ -74,8 +100,14 @@ WarpXOpenPMDPlot::Init(openPMD::AccessType accessType) else m_Series = std::make_unique<openPMD::Series>(filename, accessType); - // actually default is "particles" by openPMD. - m_Series->setParticlesPath("particles"); + // more natural naming for PIC + m_Series->setMeshesPath("fields"); + // TODO conform to ED-PIC extension of openPMD + // uint32_t const openPMD_ED_PIC = 1u; + // m_Series->setOpenPMDextension(openPMD_ED_PIC); + // meta info + m_Series->setSoftware("WarpX"); + m_Series->setSoftwareVersion(WARPX_GIT_VERSION); } @@ -93,19 +125,22 @@ WarpXOpenPMDPlot::WriteOpenPMDParticles(const std::unique_ptr<MultiParticleConta amrex::Vector<std::string> int_names; amrex::Vector<int> int_flags; - real_names.push_back("weight"); + // see openPMD ED-PIC extension for namings + // note: an underscore separates the record name from its component + // for non-scalar records + real_names.push_back("weighting"); real_names.push_back("momentum_x"); real_names.push_back("momentum_y"); real_names.push_back("momentum_z"); - real_names.push_back("Ex"); - real_names.push_back("Ey"); - real_names.push_back("Ez"); + real_names.push_back("E_x"); + real_names.push_back("E_y"); + real_names.push_back("E_z"); - real_names.push_back("Bx"); - real_names.push_back("By"); - real_names.push_back("Bz"); + real_names.push_back("B_x"); + real_names.push_back("B_y"); + real_names.push_back("B_z"); #ifdef WARPX_DIM_RZ real_names.push_back("theta"); @@ -224,8 +259,11 @@ WarpXOpenPMDPlot::SetupRealProperties(openPMD::ParticleSpecies& currSpecies, auto counter = std::min(write_real_comp.size(), real_comp_names.size()); for (int i = 0; i < counter; ++i) if (write_real_comp[i]) { - auto& particleVar = currSpecies[real_comp_names[i]]; - auto& particleVarComp = particleVar[openPMD::RecordComponent::SCALAR]; + // handle scalar and non-scalar records by name + std::string record_name, component_name; + std::tie(record_name, component_name) = detail::name2openPMD(real_comp_names[i]); + + auto& particleVarComp = currSpecies[record_name][component_name]; particleVarComp.resetDataset(particlesLineup); } } @@ -253,7 +291,11 @@ WarpXOpenPMDPlot::SaveRealProperty(WarpXParIter& pti, { for (auto idx=0; idx<m_NumAoSRealAttributes; idx++) { if (write_real_comp[idx]) { - auto& currVar = currSpecies[real_comp_names[idx]][openPMD::RecordComponent::SCALAR]; + // handle scalar and non-scalar records by name + std::string record_name, component_name; + std::tie(record_name, component_name) = detail::name2openPMD(real_comp_names[idx]); + + auto& currVar = currSpecies[record_name][component_name]; typename amrex::ParticleReal *d = static_cast<typename amrex::ParticleReal*> (malloc(sizeof(typename amrex::ParticleReal) * numParticleOnTile)); @@ -272,7 +314,11 @@ WarpXOpenPMDPlot::SaveRealProperty(WarpXParIter& pti, for (auto idx=0; idx<m_NumSoARealAttributes; idx++) { auto ii = m_NumAoSRealAttributes + idx; if (write_real_comp[ii]) { - auto& currVar = currSpecies[real_comp_names[ii]][openPMD::RecordComponent::SCALAR]; + // handle scalar and non-scalar records by name + std::string record_name, component_name; + std::tie(record_name, component_name) = detail::name2openPMD(real_comp_names[ii]); + + auto& currVar = currSpecies[record_name][component_name]; currVar.storeChunk(openPMD::shareRaw(soa.GetRealData(idx)), {offset}, {static_cast<unsigned long long>(numParticleOnTile)}); } |