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Checkpoint and Plotfile tools: coarsen mesh and CSV output (#885)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,4 @@ | ||
| add_subdirectory(refine-chkpt) | ||
| add_subdirectory(coarsen-chkpt) | ||
| add_subdirectory(CheckpointToCSV) | ||
| add_subdirectory(PlotfileToCSV) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| set(tool_exe_name CheckpointToCSV) | ||
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| add_executable(${tool_exe_name}) | ||
| target_sources(${tool_exe_name} | ||
| PRIVATE | ||
| CheckpointToCSV.cpp | ||
| CheckpointFileUtil.cpp) | ||
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| target_include_directories(${tool_exe_name} PRIVATE | ||
| $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>) | ||
| target_link_libraries(${tool_exe_name} PUBLIC ${amr_wind_lib_name} AMReX-Hydro::amrex_hydro_api) | ||
| set_cuda_build_properties(${tool_exe_name}) | ||
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| install(TARGETS ${tool_exe_name} | ||
| RUNTIME DESTINATION bin | ||
| ARCHIVE DESTINATION lib | ||
| LIBRARY DESTINATION lib) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,108 @@ | ||
| #ifndef CHECKPOINTFILEUTIL_H_ | ||
| #define CHECKPOINTFILEUTIL_H_ | ||
| #include <AMReX_Config.H> | ||
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| #include <AMReX_Geometry.H> | ||
| #include <AMReX_MultiFab.H> | ||
| #include <AMReX_VisMF.H> | ||
| #include <string> | ||
| #include <memory> | ||
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| using namespace amrex; | ||
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| // Adapted from amrex/Src/Base/AMReX_PlotFileDataImpl.H | ||
| // not inherited because constructor needed to be rewritten | ||
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| class CheckpointFileDataImpl | ||
| { | ||
| public: | ||
| explicit CheckpointFileDataImpl( | ||
| std::string const& chkptfile_name, | ||
| Vector<std::string> addl_field_names = {}); | ||
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| [[nodiscard]] int spaceDim() const noexcept { return m_spacedim; } | ||
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| [[nodiscard]] Real time() const noexcept { return m_time; } | ||
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| [[nodiscard]] int finestLevel() const noexcept { return m_finest_level; } | ||
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| [[nodiscard]] const BoxArray& boxArray(int level) const noexcept | ||
| { | ||
| return m_ba[level]; | ||
| } | ||
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| [[nodiscard]] const DistributionMapping& | ||
| DistributionMap(int level) const noexcept | ||
| { | ||
| return m_dmap[level]; | ||
| } | ||
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| void syncDistributionMap(CheckpointFileDataImpl const& src) noexcept; | ||
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| void | ||
| syncDistributionMap(int level, CheckpointFileDataImpl const& src) noexcept; | ||
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| [[nodiscard]] Box probDomain(int level) const noexcept | ||
| { | ||
| return m_prob_domain[level]; | ||
| } | ||
| [[nodiscard]] Array<Real, AMREX_SPACEDIM> probLo() const noexcept | ||
| { | ||
| return m_prob_lo; | ||
| } | ||
| [[nodiscard]] Array<Real, AMREX_SPACEDIM> probHi() const noexcept | ||
| { | ||
| return m_prob_hi; | ||
| } | ||
| [[nodiscard]] Array<Real, AMREX_SPACEDIM> cellSize(int level) const noexcept | ||
| { | ||
| return m_cell_size[level]; | ||
| } | ||
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| [[nodiscard]] const Vector<std::string>& varNames() const noexcept | ||
| { | ||
| return m_var_names; | ||
| } | ||
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| [[nodiscard]] const Vector<std::string>& varNamesComponents() const noexcept | ||
| { | ||
| return m_var_names_full; | ||
| } | ||
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| [[nodiscard]] int nComp() const noexcept { return m_ncomp; } | ||
| [[nodiscard]] IntVect nGrowVect(int level) const noexcept | ||
| { | ||
| return m_ngrow[level]; | ||
| } | ||
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| MultiFab get(int level) noexcept; | ||
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| private: | ||
| std::string m_chkptfile_name; | ||
| int m_ncomp{8}; | ||
| int m_nfields{4}; | ||
| Vector<std::string> m_var_names = {"density", "gp", "p", "velocity"}; | ||
| Vector<std::string> m_var_names_full = { | ||
| "density", "gpx", "gpy", "gpz", | ||
| "p", "velocityx", "velocityy", "velocityz"}; | ||
| Vector<int> m_var_ncomp = {1, 3, 1, 3}; | ||
| const int m_spacedim{3}; | ||
| Real m_time; | ||
| Real m_dt_restart; | ||
| Real m_dt_nm1; | ||
| Real m_dt_nm2; | ||
| int m_finest_level, m_nlevels; | ||
| Array<Real, AMREX_SPACEDIM> m_prob_lo{{AMREX_D_DECL(0., 0., 0.)}}; | ||
| Array<Real, AMREX_SPACEDIM> m_prob_hi{{AMREX_D_DECL(1., 1., 1.)}}; | ||
| Vector<int> m_ref_ratio; | ||
| Vector<Box> m_prob_domain; | ||
| int m_nstep; | ||
| Vector<Array<Real, AMREX_SPACEDIM>> m_cell_size; | ||
| Vector<std::string> m_mf_name; | ||
| Vector<std::unique_ptr<VisMF>> m_vismf; | ||
| Vector<BoxArray> m_ba; | ||
| Vector<DistributionMapping> m_dmap; | ||
| Vector<IntVect> m_ngrow; | ||
| }; | ||
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| #endif |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,172 @@ | ||
| #include "CheckpointFileUtil.H" | ||
| #include <AMReX_AsyncOut.H> | ||
| #include <AMReX_PlotFileUtil.H> | ||
| #include <AMReX_FPC.H> | ||
| #include <AMReX_FabArrayUtility.H> | ||
| #include <AMReX_ParallelDescriptor.H> | ||
| #include <algorithm> | ||
| #include <fstream> | ||
| #include <iomanip> | ||
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| using namespace amrex; | ||
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| namespace { | ||
| void GotoNextLine(std::istream& is) | ||
| { | ||
| constexpr std::streamsize bl_ignore_max{100000}; | ||
| is.ignore(bl_ignore_max, '\n'); | ||
| } | ||
| } // namespace | ||
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| CheckpointFileDataImpl::CheckpointFileDataImpl( | ||
| std::string const& chkptfile_name, Vector<std::string> addl_field_names) | ||
| : m_chkptfile_name(chkptfile_name) | ||
| { | ||
| // Add field names from input | ||
| const int naf = addl_field_names.size(); | ||
| for (int n = 0; n < naf; ++n) { | ||
| m_var_names.push_back(addl_field_names[n]); | ||
| m_var_names_full.push_back(addl_field_names[n]); | ||
| m_var_ncomp.push_back(1); | ||
| } | ||
| // Total number of components, assume addl fields are one component | ||
| m_ncomp += naf; | ||
| // Total number of fields | ||
| m_nfields += naf; | ||
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| // Header | ||
| std::string File(chkptfile_name + "/Header"); | ||
| Vector<char> fileCharPtr; | ||
| ParallelDescriptor::ReadAndBcastFile(File, fileCharPtr); | ||
| std::istringstream is( | ||
| std::string(fileCharPtr.dataPtr()), std::istringstream::in); | ||
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| std::string line, word; | ||
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| // !! -- Start reading from checkpoint file -- !! | ||
| // Title line | ||
| std::getline(is, line); | ||
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| // Finest level | ||
| is >> m_finest_level; | ||
| GotoNextLine(is); | ||
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| // Step count | ||
| is >> m_nstep; | ||
| GotoNextLine(is); | ||
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| // Current time | ||
| is >> m_time; | ||
| GotoNextLine(is); | ||
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| // Time step size | ||
| is >> m_dt_restart; | ||
| GotoNextLine(is); | ||
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| is >> m_dt_nm1; | ||
| GotoNextLine(is); | ||
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| is >> m_dt_nm2; | ||
| GotoNextLine(is); | ||
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| // Low coordinates of domain bounding box | ||
| std::getline(is, line); | ||
| { | ||
| std::istringstream lis(line); | ||
| int i = 0; | ||
| while (lis >> word) { | ||
| m_prob_lo[i++] = std::stod(word); | ||
| } | ||
| } | ||
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| // High coordinates of domain bounding box | ||
| std::getline(is, line); | ||
| { | ||
| std::istringstream lis(line); | ||
| int i = 0; | ||
| while (lis >> word) { | ||
| m_prob_hi[i++] = std::stod(word); | ||
| } | ||
| } | ||
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| // Read in box array to get domain box | ||
| m_nlevels = m_finest_level + 1; | ||
| m_ba.resize(m_nlevels); | ||
| m_dmap.resize(m_nlevels); | ||
| m_ngrow.resize(m_nlevels); | ||
| m_prob_domain.resize(m_nlevels); | ||
| m_cell_size.resize( | ||
| m_nlevels, Array<Real, AMREX_SPACEDIM>{{AMREX_D_DECL(1., 1., 1.)}}); | ||
| for (int lev = 0; lev <= m_finest_level; ++lev) { | ||
| // read in level 'lev' BoxArray from Header | ||
| m_ba[lev].readFrom(is); | ||
| GotoNextLine(is); | ||
| // get minimal box from box array for prob domain | ||
| m_prob_domain[lev] = m_ba[lev].minimalBox(); | ||
| // make distribution map | ||
| m_dmap[lev].define(m_ba[lev], ParallelDescriptor::NProcs()); | ||
| // ngrow is set to 0, don't know how to find it properly | ||
| m_ngrow[lev] = {0, 0, 0}; | ||
| } | ||
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| // Calculate cell size for lowest level | ||
| for (int idim = 0; idim < m_spacedim; ++idim) { | ||
| m_cell_size[0][idim] = (m_prob_hi[idim] - m_prob_lo[idim]) / | ||
| (m_prob_domain[0].bigEnd(idim) - | ||
| m_prob_domain[0].smallEnd(idim) + 1); | ||
| } | ||
| // Do the higher levels using refratio, assume 2 | ||
| for (int lev = 1; lev <= m_finest_level; ++lev) { | ||
| for (int idim = 0; idim < m_spacedim; ++idim) { | ||
| m_cell_size[lev][idim] = m_cell_size[lev - 1][idim]; | ||
| } | ||
| } | ||
|
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| AMREX_ASSERT(m_nlevels > 0 && m_nlevels <= 1000); | ||
| } | ||
|
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| void CheckpointFileDataImpl::syncDistributionMap( | ||
| CheckpointFileDataImpl const& src) noexcept | ||
| { | ||
| int nlevs_min = std::min(m_nlevels, src.m_nlevels); | ||
| for (int ilev = 0; ilev < nlevs_min; ++ilev) { | ||
| syncDistributionMap(ilev, src); | ||
| } | ||
| } | ||
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| void CheckpointFileDataImpl::syncDistributionMap( | ||
| int level, CheckpointFileDataImpl const& src) noexcept | ||
| { | ||
| if (level <= src.finestLevel() && | ||
| m_dmap[level].size() == src.DistributionMap(level).size()) { | ||
| m_dmap[level] = src.DistributionMap(level); | ||
| } | ||
| } | ||
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| MultiFab CheckpointFileDataImpl::get(int level) noexcept | ||
| { | ||
| const std::string level_prefix{"Level_"}; | ||
| MultiFab mf(m_ba[level], m_dmap[level], m_ncomp, m_ngrow[level]); | ||
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| // Do checkpoint reading, which is a field at a time | ||
| for (int lev = 0; lev < m_nlevels; ++lev) { | ||
| int icomp = 0; | ||
| for (int nf = 0; nf < m_nfields; ++nf) { | ||
| MultiFab tmp_mfab( | ||
| m_ba[level], m_dmap[level], m_var_ncomp[nf], m_ngrow[level]); | ||
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| // Read current field into temporary fab | ||
| amrex::VisMF::Read( | ||
| tmp_mfab, | ||
| amrex::MultiFabFileFullPrefix( | ||
| lev, m_chkptfile_name, level_prefix, m_var_names[nf])); | ||
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| // Copy from tmp fab to bigger fab | ||
| amrex::MultiFab::Copy( | ||
| mf, tmp_mfab, 0, icomp, m_var_ncomp[nf], m_ngrow[lev]); | ||
| // Advance index among total components | ||
| icomp += m_var_ncomp[nf]; | ||
| } | ||
| } | ||
| return mf; | ||
| } |
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