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Added output format that might just work for Gadget-4
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glatterf42
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1 changed files with 855 additions and 0 deletions
855
plugins/output_gadget_hdf5.cc
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855
plugins/output_gadget_hdf5.cc
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/*
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* output_arepo.cc - This file is part of MUSIC -
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* a code to generate multi-scale initial conditions
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* for cosmological simulations
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*
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* Copyright (C) 2010 Oliver Hahn
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*
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* Plugin: Dylan Nelson (dnelson@cfa.harvard.edu)
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*/
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#ifdef HAVE_HDF5
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#define GAS_PARTTYPE 2
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#define HIGHRES_DM_PARTTYPE 0 //This is only true for PBH simulations b/c we hijacked the usual gastype!
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#define COARSE_DM_DEFAULT_PARTTYPE 1
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#define STAR_PARTTYPE 4
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#define NTYPES 6
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#include "HDF_IO.hh"
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#include "output.hh"
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#include <algorithm>
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#include <sstream>
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#include <string>
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class gadget_hdf5_output_plugin : public output_plugin {
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protected:
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// header/config
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std::vector<std::vector<unsigned int>> nPart;
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std::vector<long long> nPartTotal;
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std::vector<double> massTable;
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double time, redshift, boxSize;
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unsigned int numFiles, coarsePartType;
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double omega0, omega_L, hubbleParam;
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// configuration
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double UnitLength_in_cm, UnitMass_in_g, UnitVelocity_in_cm_per_s;
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double omega_b, rhoCrit;
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double posFac, velFac;
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long long nPartTotAllTypes;
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bool doBaryons, useLongIDs, doublePrec;
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size_t npfine, npart, npcoarse;
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std::vector<size_t> levelcounts;
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// parameter file hints
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int pmgrid, gridboost;
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float softening, Tini;
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double gamma, YHe, Tcmb0; //for gas properties
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using output_plugin::cf_;
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// Nx1 vector (e.g. masses,particleids)
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template <typename T> void writeHDF5_a(std::string fieldName, int partTypeNum, const std::vector<T> &data) {
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hid_t HDF_FileID, HDF_GroupID, HDF_DatasetID, HDF_DataspaceID, HDF_Type;
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hsize_t HDF_Dims, offset = 0;
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std::stringstream GrpName;
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GrpName << "PartType" << partTypeNum;
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for (unsigned i = 0; i < numFiles; i++) {
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std::string filename = fname_;
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HDF_Dims = data.size();
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// modify local filename and write size
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if (numFiles > 1) {
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std::stringstream s;
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s << "." << i << ".hdf5";
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filename.replace(filename.find(".hdf5"), 5, s.str());
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HDF_Dims = ceil(data.size() / numFiles);
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if (i == numFiles - 1)
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HDF_Dims = data.size() - offset;
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}
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HDF_FileID = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
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HDF_GroupID = H5Gopen(HDF_FileID, GrpName.str().c_str());
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HDF_Type = GetDataType<T>();
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HDF_DataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
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HDF_DatasetID = H5Dcreate(HDF_GroupID, fieldName.c_str(), HDF_Type, HDF_DataspaceID, H5P_DEFAULT);
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// write and close
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H5Dwrite(HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data[offset]);
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H5Dclose(HDF_DatasetID);
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H5Sclose(HDF_DataspaceID);
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H5Gclose(HDF_GroupID);
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H5Fclose(HDF_FileID);
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offset += HDF_Dims;
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}
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}
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// Nx3 vector (e.g. pos,vel), where coord = index of the second dimension (written one at a time)
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template <typename T>
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void writeHDF5_b(std::string fieldName, int coord, int partTypeNum, std::vector<T> &data, bool readFlag = false) {
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hid_t HDF_FileID, HDF_GroupID, HDF_DatasetID, HDF_DataspaceID, HDF_Type;
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hsize_t HDF_Dims[2], HDF_DimsMem[2], w_offset = 0;
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std::stringstream GrpName;
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GrpName << "PartType" << partTypeNum;
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for (unsigned i = 0; i < numFiles; i++) {
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std::string filename = fname_;
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HDF_Dims[0] = data.size();
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// modify local filename and write size
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if (numFiles > 1) {
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std::stringstream s;
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s << "." << i << ".hdf5";
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filename.replace(filename.find(".hdf5"), 5, s.str());
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HDF_Dims[0] = ceil(data.size() / numFiles);
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if (i == numFiles - 1)
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HDF_Dims[0] = data.size() - w_offset;
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}
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HDF_FileID = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
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HDF_GroupID = H5Gopen(HDF_FileID, GrpName.str().c_str());
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HDF_Type = GetDataType<T>();
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HDF_Dims[1] = 3;
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// if dataset does not yet exist, create it (on first coord call)
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if (!(H5Lexists(HDF_GroupID, fieldName.c_str(), H5P_DEFAULT))) {
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HDF_DataspaceID = H5Screate_simple(2, HDF_Dims, NULL);
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HDF_DatasetID = H5Dcreate(HDF_GroupID, fieldName.c_str(), HDF_Type, HDF_DataspaceID, H5P_DEFAULT);
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H5Sclose(HDF_DataspaceID);
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H5Dclose(HDF_DatasetID);
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}
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// make memory space (just indicates the size/shape of data)
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HDF_DimsMem[0] = HDF_Dims[0];
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HDF_DimsMem[1] = 1;
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hid_t HDF_MemoryspaceID = H5Screate_simple(2, HDF_DimsMem, NULL);
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// open hyperslab
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hsize_t count[2] = {1, 1}, stride[2] = {1, 1}, offset[2] = {0, 0};
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offset[1] = coord; // set where in the second dimension to write
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count[0] = HDF_Dims[0]; // set size in the first dimension (num particles of this type)
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HDF_DatasetID = H5Dopen(HDF_GroupID, fieldName.c_str());
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HDF_DataspaceID = H5Dget_space(HDF_DatasetID);
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H5Sselect_hyperslab(HDF_DataspaceID, H5S_SELECT_SET, offset, stride, count, NULL);
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// write (or read) and close
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if (readFlag)
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H5Dread(HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT, &data[w_offset]);
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else
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H5Dwrite(HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT, &data[w_offset]);
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H5Dclose(HDF_DatasetID);
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H5Gclose(HDF_GroupID);
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H5Fclose(HDF_FileID);
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w_offset += HDF_Dims[0];
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}
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}
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// called from finalize()
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void generateAndWriteIDs(void) {
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long long offset = 1; // don't use ID==0
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nPartTotAllTypes = 0;
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for (size_t i = 0; i < nPartTotal.size(); i++) {
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if (!nPartTotal[i])
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continue;
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nPartTotAllTypes += nPartTotal[i];
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if (!useLongIDs) {
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std::vector<int> ids = std::vector<int>(nPartTotal[i]);
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for (int j = 0; j < nPartTotal[i]; j++)
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ids[j] = offset + j;
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writeHDF5_a("ParticleIDs", i, ids);
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} else {
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std::vector<long long> ids = std::vector<long long>(nPartTotal[i]);
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for (long long j = 0; j < nPartTotal[i]; j++)
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ids[j] = offset + j;
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writeHDF5_a("ParticleIDs", i, ids);
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}
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// make IDs of all particle types sequential (unique) = unnecessary, but consistent with gadget output format
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offset += nPartTotal[i];
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}
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}
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void countLeafCells(const grid_hierarchy &gh) {
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npfine = 0;
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npart = 0;
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npcoarse = 0;
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npfine = gh.count_leaf_cells(gh.levelmax(), gh.levelmax());
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npart = gh.count_leaf_cells(gh.levelmin(), gh.levelmax());
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if (levelmax_ != levelmin_) // multimass
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npcoarse = gh.count_leaf_cells(gh.levelmin(), gh.levelmax() - 1);
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}
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template <typename T> void __write_dm_mass(const grid_hierarchy &gh) {
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countLeafCells(gh);
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// FINE: collect velocities and convert to correct units
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int ilevel = gh.levelmax();
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std::vector<T> data(npfine);
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size_t count = 0;
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for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
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for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
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for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
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if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) {
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if (!doBaryons)
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data[count++] = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_);
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else
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data[count++] = (omega0 - omega_b) * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_);
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}
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writeHDF5_a("Masses", HIGHRES_DM_PARTTYPE, data); // write fine DM
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if (count != npfine)
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throw std::runtime_error("Internal consistency error while writing fine DM masses");
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// fill levelcount for header
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levelcounts = std::vector<size_t>(levelmax_ - levelmin_ + 1);
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for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel)
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levelcounts[gh.levelmax() - ilevel] = gh.count_leaf_cells(ilevel, ilevel);
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if (levelmax_ > levelmin_ + 1) // morethan2bnd
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{
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// DM particles will have variable masses
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size_t count = 0;
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std::vector<T> data(npcoarse);
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for (int ilevel = gh.levelmax() - 1; ilevel >= (int)gh.levelmin(); --ilevel) {
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// baryon particles live only on finest grid, these particles here are total matter particles
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T pmass = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * ilevel);
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for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
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for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
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for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
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if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) {
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data[count++] = pmass;
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}
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}
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if (count != npcoarse)
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throw std::runtime_error("Internal consistency error while writing masses");
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writeHDF5_a("Masses", coarsePartType, data); // write DM
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} else {
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// DM particles will all have the same mass, just write to massTable
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if (levelmax_ != levelmin_) // multimass
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massTable[coarsePartType] = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmin_);
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}
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}
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template <typename T> void __write_dm_position(int coord, const grid_hierarchy &gh) {
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countLeafCells(gh);
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// update header
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hsize_t offset_fine = 0, offset_coarse = 0;
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for (unsigned i = 0; i < numFiles; i++) {
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hsize_t dims_fine = ceil(npfine / numFiles);
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hsize_t dims_coarse = ceil(npcoarse / numFiles);
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if (i == numFiles - 1) {
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dims_fine = npfine - offset_fine;
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dims_coarse = npcoarse - offset_coarse;
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}
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nPart[i][HIGHRES_DM_PARTTYPE] = dims_fine;
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nPart[i][coarsePartType] = dims_coarse;
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offset_fine += dims_fine;
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offset_coarse += dims_coarse;
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}
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nPartTotal[HIGHRES_DM_PARTTYPE] = npfine;
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nPartTotal[coarsePartType] = npcoarse;
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// FINE: collect displacements and convert to absolute coordinates with correct units
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int ilevel = gh.levelmax();
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std::vector<T> data(npfine);
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size_t count = 0;
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for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
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for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
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for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
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if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) {
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double xx[3];
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gh.cell_pos(ilevel, i, j, k, xx);
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xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i, j, k)) * boxSize;
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xx[coord] = fmod(xx[coord] + boxSize, boxSize); //added fmod here (see below), otherwise only takes latter value
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data[count++] = (T)(xx[coord] * posFac);
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}
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writeHDF5_b("Coordinates", coord, HIGHRES_DM_PARTTYPE, data); // write fine DM
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if (count != npfine)
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throw std::runtime_error("Internal consistency error while writing fine DM pos");
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// COARSE: collect displacements and convert to absolute coordinates with correct units
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if (levelmax_ != levelmin_) // multimass
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{
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data = std::vector<T>(npcoarse, 0.0);
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count = 0;
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for (int ilevel = gh.levelmax() - 1; ilevel >= (int)gh.levelmin(); --ilevel)
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for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
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for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
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for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
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if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) {
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double xx[3];
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gh.cell_pos(ilevel, i, j, k, xx);
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xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i, j, k)) * boxSize;
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if (!doBaryons) // if so, we will handle the mod in write_gas_position
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xx[coord] = fmod(xx[coord] + boxSize, boxSize) * posFac;
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data[count++] = (T)xx[coord];
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}
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if (count != npcoarse)
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throw std::runtime_error("Internal consistency error while writing coarse DM pos");
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writeHDF5_b("Coordinates", coord, coarsePartType, data); // write coarse DM
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}
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}
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template <typename T> void __write_dm_velocity(int coord, const grid_hierarchy &gh) {
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countLeafCells(gh);
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// FINE: collect velocities and convert to correct units
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int ilevel = gh.levelmax();
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std::vector<T> data(npfine);
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size_t count = 0;
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for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
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for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
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for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
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if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) {
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data[count++] = (T)(*gh.get_grid(ilevel))(i, j, k) * velFac;
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}
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writeHDF5_b("Velocities", coord, HIGHRES_DM_PARTTYPE, data); // write fine DM
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if (count != npfine)
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throw std::runtime_error("Internal consistency error while writing fine DM pos");
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// COARSE: collect velocities and convert to correct units
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if (levelmax_ != levelmin_) // multimass
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{
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data = std::vector<T>(npcoarse, 0.0);
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count = 0;
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for (int ilevel = gh.levelmax() - 1; ilevel >= (int)gh.levelmin(); --ilevel)
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for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
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for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
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for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
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if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) {
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data[count++] = (T)(*gh.get_grid(ilevel))(i, j, k) * velFac;
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}
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if (count != npcoarse)
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throw std::runtime_error("Internal consistency error while writing coarse DM pos");
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writeHDF5_b("Velocities", coord, coarsePartType, data); // write coarse DM
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}
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}
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template <typename T> void __write_gas_velocity(int coord, const grid_hierarchy &gh) {
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countLeafCells(gh);
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std::vector<T> gas_data(npart); // read/write gas at all levels from the gh
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size_t count = 0;
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for (int ilevel = levelmax_; ilevel >= (int)levelmin_; --ilevel)
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for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
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for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
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for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
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if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) {
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gas_data[count++] = (T)(*gh.get_grid(ilevel))(i, j, k) * velFac;
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}
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if (count != npart)
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throw std::runtime_error("Internal consistency error while writing GAS pos");
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// calculate modified DM velocities if: multimass and baryons present
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if (doBaryons && npcoarse) {
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double facb = omega_b / omega0;
|
||||
double facc = (omega0 - omega_b) / omega0;
|
||||
|
||||
std::vector<T> dm_data(npcoarse);
|
||||
|
||||
writeHDF5_b("Velocities", coord, coarsePartType, dm_data, true); // read coarse DM vels
|
||||
|
||||
// overwrite
|
||||
for (size_t i = 0; i < npcoarse; i++)
|
||||
dm_data[i] = facc * dm_data[i] + facb * gas_data[npfine + i];
|
||||
|
||||
writeHDF5_b("Velocities", coord, coarsePartType, dm_data); // overwrite coarse DM vels
|
||||
} // dm_data deallocated
|
||||
|
||||
// restrict gas_data to fine only and request write
|
||||
std::vector<T> data(gas_data.begin() + 0, gas_data.begin() + npfine);
|
||||
|
||||
std::vector<T>().swap(gas_data); // deallocate
|
||||
|
||||
writeHDF5_b("Velocities", coord, GAS_PARTTYPE, data); // write highres gas
|
||||
}
|
||||
|
||||
template <typename T> void __write_gas_position(int coord, const grid_hierarchy &gh) {
|
||||
countLeafCells(gh);
|
||||
|
||||
// update header (will actually write only gas at levelmax)
|
||||
hsize_t offset = 0;
|
||||
|
||||
for (unsigned i = 0; i < numFiles; i++) {
|
||||
hsize_t dims = ceil(npfine / numFiles);
|
||||
if (i == numFiles - 1)
|
||||
dims = npfine - offset;
|
||||
|
||||
nPart[i][GAS_PARTTYPE] = dims;
|
||||
offset += dims;
|
||||
}
|
||||
|
||||
nPartTotal[GAS_PARTTYPE] = npfine;
|
||||
|
||||
std::vector<double> gas_data(npart); // read/write gas at all levels from the gh
|
||||
size_t count = 0;
|
||||
|
||||
double h = 1.0 / (1ul << gh.levelmax());
|
||||
|
||||
for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel)
|
||||
for (unsigned i = 0; i < gh.get_grid(ilevel)->size(0); ++i)
|
||||
for (unsigned j = 0; j < gh.get_grid(ilevel)->size(1); ++j)
|
||||
for (unsigned k = 0; k < gh.get_grid(ilevel)->size(2); ++k)
|
||||
if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) {
|
||||
double xx[3];
|
||||
gh.cell_pos(ilevel, i, j, k, xx);
|
||||
|
||||
// shift particle positions (this has to be done as the same shift
|
||||
// is used when computing the convolution kernel for SPH baryons)
|
||||
xx[coord] += 0.5 * h;
|
||||
|
||||
xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i, j, k)) * boxSize;
|
||||
|
||||
gas_data[count++] = xx[coord];
|
||||
}
|
||||
|
||||
if (count != npart)
|
||||
throw std::runtime_error("Internal consistency error while writing coarse DM pos");
|
||||
|
||||
// calculate modified DM coordinates if: multimass and baryons present
|
||||
if (doBaryons && npcoarse) {
|
||||
double facb = omega_b / omega0;
|
||||
double facc = (omega0 - omega_b) / omega0;
|
||||
|
||||
std::vector<T> dm_data(npcoarse);
|
||||
|
||||
writeHDF5_b("Coordinates", coord, coarsePartType, dm_data, true); // read coarse DM vels
|
||||
|
||||
// overwrite
|
||||
for (size_t i = 0; i < npcoarse; i++) {
|
||||
dm_data[i] = facc * dm_data[i] + facb * gas_data[npfine + i];
|
||||
dm_data[i] = fmod(dm_data[i] + boxSize, boxSize) * posFac;
|
||||
}
|
||||
|
||||
writeHDF5_b("Coordinates", coord, coarsePartType, dm_data); // overwrite coarse DM vels
|
||||
}
|
||||
|
||||
// restrict gas_data to fine only and request write
|
||||
// std::vector<float> data( gas_data.begin() + 0, gas_data.begin() + npfine );
|
||||
|
||||
std::vector<T> data(npfine);
|
||||
|
||||
for (size_t i = 0; i < npfine; i++)
|
||||
data[i] = (T)(fmod(gas_data[i] + boxSize, boxSize) * posFac);
|
||||
|
||||
std::vector<double>().swap(gas_data); // deallocate
|
||||
|
||||
writeHDF5_b("Coordinates", coord, GAS_PARTTYPE, data); // write highres gas
|
||||
}
|
||||
|
||||
template <typename T> void __write_gas_properties(const grid_hierarchy &gh) {
|
||||
countLeafCells(gh);
|
||||
|
||||
std::vector<T> masses(npfine);
|
||||
std::vector<T> smoothing_lengths(npfine);
|
||||
std::vector<T> internal_energies(npfine);
|
||||
|
||||
T gas_mass = omega_b * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_);
|
||||
T smoothing_length = boxSize / hubbleParam / pow(2, levelmax_);
|
||||
|
||||
// calculate internal energy for gas
|
||||
double npol = (fabs(1.0 - gamma) > 1e-7) ? 1.0 / (gamma - 1.) : 1.0;
|
||||
double astart = 1.0 / (1.0 + redshift);
|
||||
double h2 = hubbleParam * hubbleParam;
|
||||
double adec = 1.0 / (160.0 * pow(omega_b * h2 / 0.022, 2.0 / 5.0));
|
||||
|
||||
Tini = astart < adec ? Tcmb0 / astart : Tcmb0 / astart / astart * adec;
|
||||
|
||||
const double mu = (Tini > 1.e4) ? 4.0 / (8. - 5. * YHe) : 4.0 / (1. + 3. * (1. - YHe));
|
||||
T internal_energy = 1.3806e-16 / 1.6726e-24 * Tini * npol / mu / UnitVelocity_in_cm_per_s / UnitVelocity_in_cm_per_s;
|
||||
|
||||
for (size_t i = 0; i < npfine; i++){
|
||||
masses[i] = gas_mass;
|
||||
smoothing_lengths[i] = smoothing_length;
|
||||
internal_energies[i] = internal_energy;
|
||||
}
|
||||
|
||||
writeHDF5_a("Masses", GAS_PARTTYPE, masses); // write gas masses and other data
|
||||
writeHDF5_a("SmoothingLength", GAS_PARTTYPE, smoothing_lengths);
|
||||
writeHDF5_a("InternalEnergy", GAS_PARTTYPE, internal_energies);
|
||||
}
|
||||
|
||||
public:
|
||||
gadget_hdf5_output_plugin(config_file &cf) : output_plugin(cf) {
|
||||
// ensure that everyone knows we want to do SPH, implies: bsph=1, bbshift=1, decic_baryons=1
|
||||
// -> instead of just writing gas densities (which are here ignored), the gas displacements are also written
|
||||
cf.insertValue("setup", "do_SPH", "yes");
|
||||
|
||||
// init header and config parameters
|
||||
nPartTotal = std::vector<long long>(NTYPES, 0);
|
||||
massTable = std::vector<double>(NTYPES, 0.0);
|
||||
|
||||
hubbleParam = cf.getValue<double>("cosmology", "H0") / 100.0;
|
||||
|
||||
coarsePartType = cf.getValueSafe<unsigned>("output", "gadget_hdf5_coarsetype", COARSE_DM_DEFAULT_PARTTYPE);
|
||||
UnitLength_in_cm = cf.getValueSafe<double>("output", "gadget_hdf5_unitlength", 3.085678e24); // 1.0 Mpc
|
||||
UnitMass_in_g = cf.getValueSafe<double>("output", "gadget_hdf5_unitmass", 1.989e43); // 1.0e10 solar masses
|
||||
UnitVelocity_in_cm_per_s = cf.getValueSafe<double>("output", "gadget_hdf5_unitvel", 1e5); // 1 km/sec
|
||||
|
||||
omega0 = cf.getValue<double>("cosmology", "Omega_m");
|
||||
omega_b = cf.getValue<double>("cosmology", "Omega_b");
|
||||
omega_L = cf.getValue<double>("cosmology", "Omega_L");
|
||||
redshift = cf.getValue<double>("setup", "zstart");
|
||||
boxSize = cf.getValue<double>("setup", "boxlength");
|
||||
doBaryons = cf.getValueSafe<bool>("setup", "baryons", false);
|
||||
useLongIDs = cf.getValueSafe<bool>("output", "gadget_hdf5_longids", false);
|
||||
numFiles = cf.getValueSafe<unsigned>("output", "gadget_hdf5_num_files", 1);
|
||||
doublePrec = cf.getValueSafe<bool>("output", "gadget_hdf5_doubleprec", 0);
|
||||
|
||||
for (unsigned i = 0; i < numFiles; i++)
|
||||
nPart.push_back(std::vector<unsigned int>(NTYPES, 0));
|
||||
|
||||
// factors which multiply positions and velocities
|
||||
time = 1.0 / (1.0 + redshift);
|
||||
posFac = 3.085678e24 / UnitLength_in_cm; // MUSIC uses Mpc internally, i.e. posFac=1e3 for kpc output
|
||||
velFac = boxSize / std::sqrt(time);
|
||||
|
||||
// critical density
|
||||
rhoCrit = 27.7519737; // in h^2 1e10 M_sol / Mpc^3
|
||||
rhoCrit *= pow(UnitLength_in_cm / (3.085678e24), 3.0);
|
||||
rhoCrit *= (1.989e43 / UnitMass_in_g);
|
||||
|
||||
// calculate PMGRID suggestion
|
||||
pmgrid = pow(2, levelmin_) * 2; // unigrid
|
||||
gridboost = 1;
|
||||
|
||||
if (levelmin_ != levelmax_) {
|
||||
double lxref[3], x0ref[3], x1ref[3];
|
||||
double pmgrid_new;
|
||||
|
||||
the_region_generator->get_AABB(x0ref, x1ref, levelmax_); // generalized beyond box
|
||||
for (int i = 0; i < 3; i++)
|
||||
lxref[i] = x1ref[i] - x0ref[i];
|
||||
|
||||
// fraction box length of the zoom region
|
||||
lxref[0] = pow((lxref[0] * lxref[1] * lxref[2]), 0.333);
|
||||
|
||||
pmgrid_new = pow(2, levelmax_) * 2; // to cover entire box at highest resolution
|
||||
pmgrid_new *= lxref[0]; // only need to cover a fraction
|
||||
|
||||
if ((gridboost = round(pmgrid_new / pmgrid)) > 1)
|
||||
gridboost = pow(2, ceil(log(gridboost) / log(2.0))); // round to nearest, higher power of 2
|
||||
if (gridboost == 0)
|
||||
gridboost = 1;
|
||||
}
|
||||
|
||||
// calculate Tini for gas
|
||||
Tcmb0 = cf.getValueSafe<double>("cosmology", "Tcmb0", 2.7255); //from monofonIC Planck2018EE+BAO+SN
|
||||
gamma = cf.getValueSafe<double>("cosmology", "gamma", 5.0 / 3.0);
|
||||
YHe = cf.getValueSafe<double>("cosmology", "YHe", 0.245421); //from monofonIC Planck2018EE+BAO+SN
|
||||
|
||||
double astart = 1.0 / (1.0 + redshift);
|
||||
double h2 = hubbleParam * hubbleParam;
|
||||
double adec = 1.0 / (160.0 * pow(omega_b * h2 / 0.022, 2.0 / 5.0));
|
||||
|
||||
Tini = astart < adec ? Tcmb0 / astart : Tcmb0 / astart / astart * adec;
|
||||
|
||||
// calculate softening suggestion
|
||||
softening = (boxSize * posFac) / pow(2, levelmax_) / 40.0;
|
||||
|
||||
// header and sanity checks
|
||||
if (!doBaryons)
|
||||
massTable[HIGHRES_DM_PARTTYPE] = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_);
|
||||
else
|
||||
massTable[HIGHRES_DM_PARTTYPE] =
|
||||
(omega0 - omega_b) * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_);
|
||||
|
||||
if (coarsePartType == GAS_PARTTYPE || coarsePartType == HIGHRES_DM_PARTTYPE)
|
||||
throw std::runtime_error("Error: Specified illegal Gadget particle type for coarse particles.");
|
||||
if (coarsePartType == STAR_PARTTYPE)
|
||||
LOGWARN("WARNING: Specified coarse particle type will collide with stars if USE_SFR enabled.");
|
||||
|
||||
// create file(s)
|
||||
for (unsigned i = 0; i < numFiles; i++) {
|
||||
std::string filename = fname_;
|
||||
if (numFiles > 1) {
|
||||
size_t pos = filename.find(".hdf5");
|
||||
if (pos != filename.length() - 5)
|
||||
throw std::runtime_error("Error: Unexpected output filename (doesn't end in .hdf5).");
|
||||
|
||||
std::stringstream s;
|
||||
s << "." << i << ".hdf5";
|
||||
filename.replace(pos, 5, s.str());
|
||||
}
|
||||
|
||||
HDFCreateFile(filename);
|
||||
|
||||
// create particle type groups
|
||||
std::stringstream GrpName;
|
||||
GrpName << "PartType" << HIGHRES_DM_PARTTYPE;
|
||||
|
||||
HDFCreateGroup(filename, GrpName.str().c_str()); // highres or unigrid DM
|
||||
|
||||
if (doBaryons) {
|
||||
GrpName.str("");
|
||||
GrpName << "PartType" << GAS_PARTTYPE;
|
||||
HDFCreateGroup(filename, GrpName.str().c_str()); // gas
|
||||
}
|
||||
|
||||
if (levelmax_ != levelmin_) // multimass
|
||||
{
|
||||
GrpName.str("");
|
||||
GrpName << "PartType" << coarsePartType;
|
||||
HDFCreateGroup(filename, GrpName.str().c_str()); // coarse DM
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
~gadget_hdf5_output_plugin() {}
|
||||
|
||||
/* ------------------------------------------------------------------------------- */
|
||||
void write_dm_mass(const grid_hierarchy &gh) {
|
||||
if (!doublePrec)
|
||||
__write_dm_mass<float>(gh);
|
||||
else
|
||||
__write_dm_mass<double>(gh);
|
||||
}
|
||||
|
||||
void write_dm_position(int coord, const grid_hierarchy &gh) {
|
||||
if (!doublePrec)
|
||||
__write_dm_position<float>(coord, gh);
|
||||
else
|
||||
__write_dm_position<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_dm_velocity(int coord, const grid_hierarchy &gh) {
|
||||
if (!doublePrec)
|
||||
__write_dm_velocity<float>(coord, gh);
|
||||
else
|
||||
__write_dm_velocity<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_dm_density(const grid_hierarchy &gh) { /* skip */
|
||||
}
|
||||
|
||||
void write_dm_potential(const grid_hierarchy &gh) { /* skip */
|
||||
}
|
||||
|
||||
/* ------------------------------------------------------------------------------- */
|
||||
void write_gas_velocity(int coord, const grid_hierarchy &gh) {
|
||||
if (!doublePrec)
|
||||
__write_gas_velocity<float>(coord, gh);
|
||||
else
|
||||
__write_gas_velocity<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_gas_position(int coord, const grid_hierarchy &gh) {
|
||||
if (!doublePrec)
|
||||
__write_gas_position<float>(coord, gh);
|
||||
else
|
||||
__write_gas_position<double>(coord, gh);
|
||||
}
|
||||
|
||||
void write_gas_properties(const grid_hierarchy &gh) {
|
||||
if (!doublePrec)
|
||||
__write_gas_properties<float>(gh);
|
||||
else
|
||||
__write_gas_properties<double>(gh);
|
||||
}
|
||||
|
||||
void write_gas_density(const grid_hierarchy &gh) {
|
||||
// if only saving highres gas, then all gas cells have the same initial mass
|
||||
// do not write out densities as we write out displacements
|
||||
if (doBaryons)
|
||||
massTable[GAS_PARTTYPE] = omega_b * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_);
|
||||
}
|
||||
|
||||
void write_gas_potential(const grid_hierarchy &gh) { /* skip */
|
||||
}
|
||||
|
||||
void finalize(void) {
|
||||
// generate and add contiguous IDs for each particle type we have written
|
||||
generateAndWriteIDs();
|
||||
|
||||
std::vector<unsigned int> nPartTotalLW(nPartTotal.size());
|
||||
std::vector<unsigned int> nPartTotalHW(nPartTotal.size());
|
||||
for (size_t i = 0; i < nPartTotalHW.size(); i++) {
|
||||
nPartTotalHW[i] = (unsigned)((size_t)nPartTotal[i] >> 32);
|
||||
nPartTotalLW[i] = (unsigned int)((size_t)nPartTotal[i]);
|
||||
}
|
||||
|
||||
// output particle counts
|
||||
std::cout << " - GADGET HDF5 : wrote " << nPartTotAllTypes << " particles..." << std::endl;
|
||||
for (size_t i = 0; i < nPartTotal.size(); i++)
|
||||
std::cout << " type [" << i << "] : " << std::setw(12) << nPartTotal[i] << std::endl;
|
||||
std::cout << std::endl;
|
||||
|
||||
// write final header (some of these fields are required, others are extra info)
|
||||
for (unsigned i = 0; i < numFiles; i++) {
|
||||
std::string filename = fname_;
|
||||
if (numFiles > 1) {
|
||||
std::stringstream s;
|
||||
s << "." << i << ".hdf5";
|
||||
filename.replace(filename.find(".hdf5"), 5, s.str());
|
||||
|
||||
std::cout << " " << filename;
|
||||
for (size_t j = 0; j < nPart[i].size(); j++)
|
||||
std::cout << " " << std::setw(10) << nPart[i][j];
|
||||
std::cout << std::endl;
|
||||
}
|
||||
|
||||
// Write UNITS header using the physical constants assumed internally by Gadget(4)
|
||||
HDFCreateGroup(filename, "Units");
|
||||
HDFWriteGroupAttribute(filename, "Units", "Unit mass in cgs (U_M)", 1.98841e43); // 10^10 Msun in grams
|
||||
HDFWriteGroupAttribute(filename, "Units", "Unit length in cgs (U_L)", 3.08567758149e24); // 1 Mpc in cm
|
||||
HDFWriteGroupAttribute(filename, "Units", "Unit time in cgs (U_t)", 3.08567758149e19); // so that unit vel is 1 km/s
|
||||
HDFWriteGroupAttribute(filename, "Units", "Unit current in cgs (U_I)", 1.0); // 1 Ampere
|
||||
HDFWriteGroupAttribute(filename, "Units", "Unit temperature in cgs (U_T)", 1.0); // 1 Kelvin
|
||||
|
||||
HDFCreateGroup(filename, "Header");
|
||||
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPart_ThisFile", nPart[i]);
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPart_Total", nPartTotalLW);
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPart_Total_HighWord", nPartTotalHW);
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumPartTypes", massTable.size());
|
||||
HDFWriteGroupAttribute(filename, "Header", "MassTable", massTable);
|
||||
HDFWriteGroupAttribute(filename, "Header", "InitialMassTable", massTable);
|
||||
HDFWriteGroupAttribute(filename, "Header", "BoxSize", boxSize);
|
||||
HDFWriteGroupAttribute(filename, "Header", "NumFilesPerSnapshot", numFiles);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Dimension", 3);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Time", time);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Redshift", redshift);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Scale-factor", redshift);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Omega0", omega0); //this might be CDM plus baryons
|
||||
HDFWriteGroupAttribute(filename, "Header", "OmegaLambda", omega_L);
|
||||
HDFWriteGroupAttribute(filename, "Header", "OmegaBaryon", omega_b);
|
||||
HDFWriteGroupAttribute(filename, "Header", "HubbleParam", hubbleParam);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Sfr", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Cooling", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_StellarAge", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Metals", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Feedback", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_DoublePrecision", (int)doublePrec);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Music_levelmin", levelmin_);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Music_levelmax", levelmax_);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Music_levelcounts", levelcounts);
|
||||
HDFWriteGroupAttribute(filename, "Header", "longIDs", (int)useLongIDs);
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_pmgrid", pmgrid);
|
||||
// HDFWriteGroupAttribute(filename, "Header", "suggested_gridboost", gridboost);
|
||||
HDFWriteGroupAttribute(filename, "Header", "suggested_highressoft", softening);
|
||||
// HDFWriteGroupAttribute(filename, "Header", "suggested_gas_Tinit", Tini);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Flag_Entropy_ICs", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "Virtual", 0);
|
||||
HDFWriteGroupAttribute(filename, "Header", "ThisFile", i);
|
||||
HDFWriteGroupAttribute(filename, "Header", "TimeBase_dloga", 3.20238316e-17); // copied this from first snapshot of swift agora sim
|
||||
HDFWriteGroupAttribute(filename, "Header", "TimeBase_dt", 5.91490951e-20); // same as above
|
||||
|
||||
HDFCreateGroup(filename, "ICs_parameters");
|
||||
HDFWriteGroupAttribute(filename, "ICs_parameters", "Code", std::string("MUSIC-Panphasia"));
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Git Revision", std::string(GIT_REV));
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Git Tag", std::string(GIT_TAG));
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Git Branch", std::string(GIT_BRANCH));
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Precision", std::string(CMAKE_PRECISION_STR));
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Convolutions", std::string(CMAKE_CONVOLVER_STR));
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "PLT", std::string(CMAKE_PLT_STR));
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "LPT Order", order);
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Particle Load", load);
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Transfer Function", tf);
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Cosmology Parameter Set", cosmo_set);
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Random Generator", rng);
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Mode Fixing", do_fixing);
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Mode inversion", do_invert);
|
||||
HDFWriteGroupAttribute(filename, "ICs_parameters", "Baryons", (int)doBaryons);
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Baryons Relative Velocity", do_baryonsVrel);
|
||||
// HDFWriteGroupAttribute(fname_, "ICs_parameters", "Grid Resolution", L);
|
||||
|
||||
HDFCreateGroup(filename, "Cosmology");
|
||||
HDFWriteGroupAttribute(filename, "Cosmology", "Omega_b", omega_b);
|
||||
HDFWriteGroupAttribute(filename, "Cosmology", "Omega_cdm", omega0 - omega_b); //since omega0 + omega_L = 1
|
||||
HDFWriteGroupAttribute(filename, "Cosmology", "Omega_lambda", omega_L);
|
||||
HDFWriteGroupAttribute(filename, "Cosmology", "h", hubbleParam);
|
||||
|
||||
}
|
||||
|
||||
// give config/parameter file hints
|
||||
if (useLongIDs)
|
||||
std::cout << " - GADGET HDF5: Wrote 64bit IDs, enable LONGIDS." << std::endl;
|
||||
if (doublePrec)
|
||||
std::cout << " - GADGET HDF5: Double precision ICs, set INPUT_IN_DOUBLEPRECISION." << std::endl;
|
||||
if (NTYPES != 6)
|
||||
std::cout << " - GADGET HDF5: Using [" << NTYPES << "] particle types, set NTYPES to match." << std::endl;
|
||||
if (doBaryons)
|
||||
std::cout << " - GADGET HDF5: Wrote high-res gas (only), set REFINEMENT_HIGH_RES_GAS and GENERATE_GAS_IN_ICS with "
|
||||
<< "SPLIT_PARTICLE_TYPE=" << pow(2, coarsePartType) << "." << std::endl;
|
||||
if (levelmax_ != levelmin_)
|
||||
std::cout << " - GADGET HDF5: Have zoom type ICs, set PLACEHIGHRESREGION=" << pow(2, HIGHRES_DM_PARTTYPE)
|
||||
<< " (suggest PMGRID=" << pmgrid << " with GRIDBOOST=" << gridboost << ")." << std::endl;
|
||||
else
|
||||
std::cout << " - GADGET HDF5: Have unigrid type ICs (suggest PMGRID=" << pmgrid << ")." << std::endl;
|
||||
if (levelmax_ > levelmin_ + 1)
|
||||
std::cout << " - GADGET HDF5: More than one coarse DM mass using same type, set INDIVIDUAL_GRAVITY_SOFTENING="
|
||||
<< pow(2, coarsePartType) << " (+" << pow(2, STAR_PARTTYPE) << " if including stars)." << std::endl;
|
||||
if (doBaryons)
|
||||
std::cout << " - GADGET HDF5: Set initial gas temperature to " << std::fixed << std::setprecision(3) << Tini << " K."
|
||||
<< std::endl;
|
||||
std::cout << " - GADGET HDF5: Suggest grav softening = " << std::setprecision(3) << softening << " for high res DM."
|
||||
<< std::endl;
|
||||
}
|
||||
};
|
||||
|
||||
namespace {
|
||||
output_plugin_creator_concrete<gadget_hdf5_output_plugin> creator("gadget_hdf5");
|
||||
}
|
||||
|
||||
#endif // HAVE_HDF5
|
||||
Loading…
Reference in a new issue