diff options
Diffstat (limited to 'Source/Diagnostics/FieldIO.cpp')
| -rw-r--r-- | Source/Diagnostics/FieldIO.cpp | 35 |
1 files changed, 21 insertions, 14 deletions
diff --git a/Source/Diagnostics/FieldIO.cpp b/Source/Diagnostics/FieldIO.cpp index 5c523804e..540a968a2 100644 --- a/Source/Diagnostics/FieldIO.cpp +++ b/Source/Diagnostics/FieldIO.cpp @@ -13,7 +13,7 @@ using namespace amrex; namespace { // Return true if any element in elems is in vect, false otherwise - static bool is_in_vector(std::vector<std::string> vect, + static bool is_in_vector(std::vector<std::string> vect, std::vector<std::string> elems) { bool value = false; @@ -143,9 +143,16 @@ WriteOpenPMDFields( const std::string& filename, auto dataset = openPMD::Dataset(datatype, global_size); // Create new file and store the time/iteration info - auto series = openPMD::Series( filename, - openPMD::AccessType::CREATE, - MPI_COMM_WORLD ); + auto series = [filename](){ + if( ParallelDescriptor::NProcs() > 1 ) + return openPMD::Series( filename, + openPMD::AccessType::CREATE, + ParallelDescriptor::Communicator() ); + else + return openPMD::Series( filename, + openPMD::AccessType::CREATE ); + }(); + auto series_iteration = series.iterations[iteration]; series_iteration.setTime( time ); @@ -167,7 +174,7 @@ WriteOpenPMDFields( const std::string& filename, } } - // Setup the mesh accordingly + // Setup the mesh record accordingly auto mesh = series_iteration.meshes[field_name]; mesh.setDataOrder(openPMD::Mesh::DataOrder::F); // MultiFab: Fortran order mesh.setAxisLabels( axis_labels ); @@ -175,11 +182,11 @@ WriteOpenPMDFields( const std::string& filename, mesh.setGridGlobalOffset( global_offset ); setOpenPMDUnit( mesh, field_name ); - // Create a new mesh record, and store the associated metadata - auto mesh_record = mesh[comp_name]; - mesh_record.resetDataset( dataset ); + // Create a new mesh record component, and store the associated metadata + auto mesh_comp = mesh[comp_name]; + mesh_comp.resetDataset( dataset ); // Cell-centered data: position is at 0.5 of a cell size. - mesh_record.setPosition(std::vector<double>{AMREX_D_DECL(0.5, 0.5, 0.5)}); + mesh_comp.setPosition(std::vector<double>{AMREX_D_DECL(0.5, 0.5, 0.5)}); // Loop through the multifab, and store each box as a chunk, // in the openPMD file. @@ -195,8 +202,8 @@ WriteOpenPMDFields( const std::string& filename, // Write local data const double* local_data = fab.dataPtr(icomp); - mesh_record.storeChunk(openPMD::shareRaw(local_data), - chunk_offset, chunk_size); + mesh_comp.storeChunk(openPMD::shareRaw(local_data), + chunk_offset, chunk_size); } } // Flush data to disk after looping over all components @@ -318,14 +325,14 @@ WarpX::AverageAndPackFields ( Vector<std::string>& varnames, + static_cast<int>(plot_finepatch)*6 + static_cast<int>(plot_crsepatch)*6 + static_cast<int>(costs[0] != nullptr); - + // Loop over levels of refinement for (int lev = 0; lev <= finest_level; ++lev) { // Allocate pointers to the `ncomp` fields that will be added mf_avg.push_back( MultiFab(grids[lev], dmap[lev], ncomp, ngrow)); - // For E, B and J, if at least one component is requested, + // For E, B and J, if at least one component is requested, // build cell-centered temporary MultiFab with 3 comps MultiFab mf_tmp_E, mf_tmp_B, mf_tmp_J; // Build mf_tmp_E is at least one component of E is requested @@ -420,7 +427,7 @@ WarpX::AverageAndPackFields ( Vector<std::string>& varnames, {Bfield_aux[lev][0].get(), Bfield_aux[lev][1].get(), Bfield_aux[lev][2].get()}, - WarpX::CellSize(lev) ); + WarpX::CellSize(lev) ); } else if (fieldname == "divE"){ if (do_nodal) amrex::Abort("TODO: do_nodal && plot dive"); const BoxArray& ba = amrex::convert(boxArray(lev),IntVect::TheUnitVector()); |