diff options
Diffstat (limited to 'Source/Diagnostics/Diagnostics.cpp')
| -rw-r--r-- | Source/Diagnostics/Diagnostics.cpp | 85 |
1 files changed, 75 insertions, 10 deletions
diff --git a/Source/Diagnostics/Diagnostics.cpp b/Source/Diagnostics/Diagnostics.cpp index fb41bebf1..b36011c1c 100644 --- a/Source/Diagnostics/Diagnostics.cpp +++ b/Source/Diagnostics/Diagnostics.cpp @@ -56,27 +56,27 @@ Diagnostics::BaseReadParameters () pp_diag_name.query("dump_last_timestep", m_dump_last_timestep); // Query list of grid fields to write to output - bool varnames_specified = pp_diag_name.queryarr("fields_to_plot", m_varnames); + bool varnames_specified = pp_diag_name.queryarr("fields_to_plot", m_varnames_fields); if (!varnames_specified){ - m_varnames = {"Ex", "Ey", "Ez", "Bx", "By", "Bz", "jx", "jy", "jz"}; + m_varnames_fields = {"Ex", "Ey", "Ez", "Bx", "By", "Bz", "jx", "jy", "jz"}; } // Sanity check if user requests to plot phi - if (WarpXUtilStr::is_in(m_varnames, "phi")){ + if (WarpXUtilStr::is_in(m_varnames_fields, "phi")){ WARPX_ALWAYS_ASSERT_WITH_MESSAGE( warpx.do_electrostatic==ElectrostaticSolverAlgo::LabFrame, "plot phi only works if do_electrostatic = labframe"); } // Sanity check if user requests to plot F - if (WarpXUtilStr::is_in(m_varnames, "F")){ + if (WarpXUtilStr::is_in(m_varnames_fields, "F")){ WARPX_ALWAYS_ASSERT_WITH_MESSAGE( warpx.do_dive_cleaning, "plot F only works if warpx.do_dive_cleaning = 1"); } // G can be written to file only if WarpX::do_divb_cleaning = 1 - if (WarpXUtilStr::is_in(m_varnames, "G")) + if (WarpXUtilStr::is_in(m_varnames_fields, "G")) { WARPX_ALWAYS_ASSERT_WITH_MESSAGE( warpx.do_divb_cleaning, "G can be written to file only if warpx.do_divb_cleaning = 1"); @@ -85,9 +85,74 @@ Diagnostics::BaseReadParameters () // If user requests to plot proc_number for a serial run, // delete proc_number from fields_to_plot if (amrex::ParallelDescriptor::NProcs() == 1){ - m_varnames.erase( - std::remove(m_varnames.begin(), m_varnames.end(), "proc_number"), - m_varnames.end()); + m_varnames_fields.erase( + std::remove(m_varnames_fields.begin(), m_varnames_fields.end(), "proc_number"), + m_varnames_fields.end()); + } + + // Get names of particle quantities to average at each grid point + const bool pfield_varnames_specified = pp_diag_name.queryarr("particle_fields_to_plot", m_pfield_varnames); + if (!pfield_varnames_specified){ + m_pfield_varnames = {}; + } +#ifdef WARPX_DIM_RZ + if (m_pfield_varnames.size() != 0) { + amrex::Abort("Input error: cannot use particle_fields_to_plot not implemented for RZ"); + } +#endif + + + // Get parser strings for particle fields and generate map of parsers + std::string parser_str; + amrex::ParmParse pp_diag_pfield(m_diag_name + ".particle_fields"); + for (const auto& var : m_pfield_varnames) { + Store_parserString(pp_diag_pfield, (var + "(x,y,z,ux,uy,uz)").c_str(), parser_str); + if (parser_str != "") { + m_pfield_strings.insert({var, parser_str}); + } + else { + amrex::Abort("Input error: cannot find parser string for " + var + "." + + m_diag_name + ".particle_fields." + var + " in file"); + } + } + + // Names of all species in the simulation + m_all_species_names = warpx.GetPartContainer().GetSpeciesNames(); + + // Get names of species to average at each grid point + const bool pfield_species_specified = pp_diag_name.queryarr("particle_fields_species", m_pfield_species); + if (!pfield_species_specified){ + m_pfield_species = m_all_species_names; + } + + // Check that species names specified in m_pfield_species are valid + bool p_species_name_is_wrong; + // Loop over all species specified above + for (const auto& species : m_pfield_species) { + // Boolean used to check if species name was misspelled + p_species_name_is_wrong = true; + // Loop over all species + for (int i = 0, n = int(m_all_species_names.size()); i < n; i++) { + if (species == m_all_species_names[i]) { + // Store species index: will be used in ParticleReductionFunctor to calculate + // averages for this species + m_pfield_species_index.push_back(i); + p_species_name_is_wrong = false; + } + } + // If species name was misspelled, abort with error message + if (p_species_name_is_wrong) { + amrex::Abort("Input error: string " + species + " in " + m_diag_name + + ".particle_fields_species does not match any species"); + } + } + + m_varnames = m_varnames_fields; + // Generate names of averaged particle fields and append to m_varnames + for (int ivar=0; ivar<m_pfield_varnames.size(); ivar++) { + for (int ispec=0; ispec < int(m_pfield_species.size()); ispec++) { + m_varnames.push_back(m_pfield_varnames[ivar] + '_' + m_pfield_species[ispec]); + } } // Read user-defined physical extents for the output and store in m_lo and m_hi. @@ -139,8 +204,6 @@ Diagnostics::BaseReadParameters () // Names of species to write to output bool species_specified = pp_diag_name.queryarr("species", m_output_species_names); - // Names of all species in the simulation - m_all_species_names = warpx.GetPartContainer().GetSpeciesNames(); // Auxiliary variables std::string species; @@ -175,6 +238,8 @@ Diagnostics::BaseReadParameters () bool checkpoint_compatibility = false; if (m_format == "checkpoint"){ if ( varnames_specified == false && + pfield_varnames_specified == false && + pfield_species_specified == false && lo_specified == false && hi_specified == false && cr_specified == false && |