From 47c253a22b79fd47b36e5d326dd20a53ecefa818 Mon Sep 17 00:00:00 2001 From: Oliver Hahn Date: Fri, 23 Feb 2024 09:35:22 +0100 Subject: [PATCH] added SWIFT output plugin --- src/plugins/output_swift.cc | 380 ++++++++++++++++++++---------------- 1 file changed, 214 insertions(+), 166 deletions(-) diff --git a/src/plugins/output_swift.cc b/src/plugins/output_swift.cc index f629ebf..d23622b 100644 --- a/src/plugins/output_swift.cc +++ b/src/plugins/output_swift.cc @@ -1,10 +1,10 @@ /* * output_arepo.cc - This file is part of MUSIC - - * a code to generate multi-scale initial conditions + * a code to generate multi-scale initial conditions * for cosmological simulations - * + * * Copyright (C) 2010 Oliver Hahn - * + * * Plugin: Dylan Nelson (dnelson@cfa.harvard.edu) */ @@ -16,14 +16,13 @@ #define STAR_PARTTYPE 4 #define NTYPES 6 +#include "HDF_IO.hh" +#include "output.hh" +#include #include #include -#include -#include "output.hh" -#include "HDF_IO.hh" -class arepo_output_plugin : public output_plugin -{ +class swift_output_plugin : public output_plugin { protected: // header/config std::vector> nPart; @@ -47,27 +46,24 @@ protected: // parameter file hints int pmgrid, gridboost; float softening, Tini; + double gamma, YHe, Tcmb0; //for gas properties using output_plugin::cf_; // Nx1 vector (e.g. masses,particleids) - template - void writeHDF5_a(std::string fieldName, int partTypeNum, const std::vector &data) - { + template void writeHDF5_a(std::string fieldName, int partTypeNum, const std::vector &data) { hid_t HDF_FileID, HDF_GroupID, HDF_DatasetID, HDF_DataspaceID, HDF_Type; hsize_t HDF_Dims, offset = 0; std::stringstream GrpName; GrpName << "PartType" << partTypeNum; - for (unsigned i = 0; i < numFiles; i++) - { + for (unsigned i = 0; i < numFiles; i++) { std::string filename = fname_; HDF_Dims = data.size(); // modify local filename and write size - if (numFiles > 1) - { + if (numFiles > 1) { std::stringstream s; s << "." << i << ".hdf5"; filename.replace(filename.find(".hdf5"), 5, s.str()); @@ -99,22 +95,19 @@ protected: // Nx3 vector (e.g. pos,vel), where coord = index of the second dimension (written one at a time) template - void writeHDF5_b(std::string fieldName, int coord, int partTypeNum, std::vector &data, bool readFlag = false) - { + void writeHDF5_b(std::string fieldName, int coord, int partTypeNum, std::vector &data, bool readFlag = false) { hid_t HDF_FileID, HDF_GroupID, HDF_DatasetID, HDF_DataspaceID, HDF_Type; hsize_t HDF_Dims[2], HDF_DimsMem[2], w_offset = 0; std::stringstream GrpName; GrpName << "PartType" << partTypeNum; - for (unsigned i = 0; i < numFiles; i++) - { + for (unsigned i = 0; i < numFiles; i++) { std::string filename = fname_; HDF_Dims[0] = data.size(); // modify local filename and write size - if (numFiles > 1) - { + if (numFiles > 1) { std::stringstream s; s << "." << i << ".hdf5"; filename.replace(filename.find(".hdf5"), 5, s.str()); @@ -131,8 +124,7 @@ protected: HDF_Dims[1] = 3; // if dataset does not yet exist, create it (on first coord call) - if (!(H5Lexists(HDF_GroupID, fieldName.c_str(), H5P_DEFAULT))) - { + if (!(H5Lexists(HDF_GroupID, fieldName.c_str(), H5P_DEFAULT))) { HDF_DataspaceID = H5Screate_simple(2, HDF_Dims, NULL); HDF_DatasetID = H5Dcreate(HDF_GroupID, fieldName.c_str(), HDF_Type, HDF_DataspaceID, H5P_DEFAULT); @@ -158,11 +150,9 @@ protected: // write (or read) and close if (readFlag) - H5Dread(HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT, - &data[w_offset]); + H5Dread(HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT, &data[w_offset]); else - H5Dwrite(HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT, - &data[w_offset]); + H5Dwrite(HDF_DatasetID, HDF_Type, HDF_MemoryspaceID, HDF_DataspaceID, H5P_DEFAULT, &data[w_offset]); H5Dclose(HDF_DatasetID); H5Gclose(HDF_GroupID); @@ -173,28 +163,23 @@ protected: } // called from finalize() - void generateAndWriteIDs(void) - { + void generateAndWriteIDs(void) { long long offset = 1; // don't use ID==0 nPartTotAllTypes = 0; - for (size_t i = 0; i < nPartTotal.size(); i++) - { + for (size_t i = 0; i < nPartTotal.size(); i++) { if (!nPartTotal[i]) continue; nPartTotAllTypes += nPartTotal[i]; - if (!useLongIDs) - { + if (!useLongIDs) { std::vector ids = std::vector(nPartTotal[i]); for (int j = 0; j < nPartTotal[i]; j++) ids[j] = offset + j; writeHDF5_a("ParticleIDs", i, ids); - } - else - { + } else { std::vector ids = std::vector(nPartTotal[i]); for (long long j = 0; j < nPartTotal[i]; j++) ids[j] = offset + j; @@ -207,8 +192,7 @@ protected: } } - void countLeafCells(const grid_hierarchy &gh) - { + void countLeafCells(const grid_hierarchy &gh) { npfine = 0; npart = 0; npcoarse = 0; @@ -220,11 +204,30 @@ protected: npcoarse = gh.count_leaf_cells(gh.levelmin(), gh.levelmax() - 1); } - template - void __write_dm_mass(const grid_hierarchy &gh) - { + template void __write_dm_mass(const grid_hierarchy &gh) { countLeafCells(gh); + // FINE: collect velocities and convert to correct units + int ilevel = gh.levelmax(); + + std::vector data(npfine); + size_t count = 0; + + 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)) { + if (!doBaryons) + data[count++] = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_); + else + data[count++] = (omega0 - omega_b) * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmax_); + } + + writeHDF5_a("Masses", HIGHRES_DM_PARTTYPE, data); // write fine DM + + if (count != npfine) + throw std::runtime_error("Internal consistency error while writing fine DM masses"); + // fill levelcount for header levelcounts = std::vector(levelmax_ - levelmin_ + 1); for (int ilevel = gh.levelmax(); ilevel >= (int)gh.levelmin(); --ilevel) @@ -237,16 +240,14 @@ protected: std::vector data(npcoarse); - for (int ilevel = gh.levelmax() - 1; ilevel >= (int)gh.levelmin(); --ilevel) - { + for (int ilevel = gh.levelmax() - 1; ilevel >= (int)gh.levelmin(); --ilevel) { // baryon particles live only on finest grid, these particles here are total matter particles T pmass = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * 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)) - { + if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) { data[count++] = pmass; } } @@ -255,30 +256,25 @@ protected: throw std::runtime_error("Internal consistency error while writing masses"); writeHDF5_a("Masses", coarsePartType, data); // write DM - } - else - { + + } else { // DM particles will all have the same mass, just write to massTable if (levelmax_ != levelmin_) // multimass massTable[coarsePartType] = omega0 * rhoCrit * pow(boxSize * posFac, 3.0) / pow(2, 3 * levelmin_); } } - template - void __write_dm_position(int coord, const grid_hierarchy &gh) - { + template void __write_dm_position(int coord, const grid_hierarchy &gh) { countLeafCells(gh); // update header hsize_t offset_fine = 0, offset_coarse = 0; - for (unsigned i = 0; i < numFiles; i++) - { + for (unsigned i = 0; i < numFiles; i++) { hsize_t dims_fine = ceil(npfine / numFiles); hsize_t dims_coarse = ceil(npcoarse / numFiles); - if (i == numFiles - 1) - { + if (i == numFiles - 1) { dims_fine = npfine - offset_fine; dims_coarse = npcoarse - offset_coarse; } @@ -302,13 +298,12 @@ protected: 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)) - { + 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); xx[coord] = (xx[coord] + (*gh.get_grid(ilevel))(i, j, k)) * boxSize; - xx[coord] = fmod(xx[coord] + boxSize, boxSize); + xx[coord] = fmod(xx[coord] + boxSize, boxSize); //added fmod here (see below), otherwise only takes latter value data[count++] = (T)(xx[coord] * posFac); } @@ -328,8 +323,7 @@ protected: 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)) - { + 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); @@ -348,9 +342,7 @@ protected: } } - template - void __write_dm_velocity(int coord, const grid_hierarchy &gh) - { + template void __write_dm_velocity(int coord, const grid_hierarchy &gh) { countLeafCells(gh); // FINE: collect velocities and convert to correct units @@ -362,8 +354,7 @@ protected: 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)) - { + if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) { data[count++] = (T)(*gh.get_grid(ilevel))(i, j, k) * velFac; } @@ -382,8 +373,7 @@ protected: 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)) - { + if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) { data[count++] = (T)(*gh.get_grid(ilevel))(i, j, k) * velFac; } @@ -394,9 +384,7 @@ protected: } } - template - void __write_gas_velocity(int coord, const grid_hierarchy &gh) - { + template void __write_gas_velocity(int coord, const grid_hierarchy &gh) { countLeafCells(gh); std::vector gas_data(npart); // read/write gas at all levels from the gh @@ -406,8 +394,7 @@ protected: 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)) - { + if (gh.is_in_mask(ilevel, i, j, k) && !gh.is_refined(ilevel, i, j, k)) { gas_data[count++] = (T)(*gh.get_grid(ilevel))(i, j, k) * velFac; } @@ -415,8 +402,7 @@ protected: throw std::runtime_error("Internal consistency error while writing GAS pos"); // calculate modified DM velocities if: multimass and baryons present - if (doBaryons && npcoarse) - { + if (doBaryons && npcoarse) { double facb = omega_b / omega0; double facc = (omega0 - omega_b) / omega0; @@ -439,16 +425,13 @@ protected: writeHDF5_b("Velocities", coord, GAS_PARTTYPE, data); // write highres gas } - template - void __write_gas_position(int coord, const grid_hierarchy &gh) - { + template 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++) - { + for (unsigned i = 0; i < numFiles; i++) { hsize_t dims = ceil(npfine / numFiles); if (i == numFiles - 1) dims = npfine - offset; @@ -468,8 +451,7 @@ protected: 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)) - { + 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); @@ -486,8 +468,7 @@ protected: throw std::runtime_error("Internal consistency error while writing coarse DM pos"); // calculate modified DM coordinates if: multimass and baryons present - if (doBaryons && npcoarse) - { + if (doBaryons && npcoarse) { double facb = omega_b / omega0; double facc = (omega0 - omega_b) / omega0; @@ -496,8 +477,7 @@ protected: writeHDF5_b("Coordinates", coord, coarsePartType, dm_data, true); // read coarse DM vels // overwrite - for (size_t i = 0; i < npcoarse; i++) - { + 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; } @@ -506,7 +486,7 @@ protected: } // restrict gas_data to fine only and request write - //std::vector data( gas_data.begin() + 0, gas_data.begin() + npfine ); + // std::vector data( gas_data.begin() + 0, gas_data.begin() + npfine ); std::vector data(npfine); @@ -518,31 +498,62 @@ protected: writeHDF5_b("Coordinates", coord, GAS_PARTTYPE, data); // write highres gas } + template void __write_gas_properties(const grid_hierarchy &gh) { + countLeafCells(gh); + + std::vector masses(npfine); + std::vector smoothing_lengths(npfine); + std::vector 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: - arepo_output_plugin(config_file &cf) : output_plugin(cf) - { + swift_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.insert_value("setup", "do_SPH", "yes"); + cf.insertValue("setup", "do_SPH", "yes"); // init header and config parameters nPartTotal = std::vector(NTYPES, 0); massTable = std::vector(NTYPES, 0.0); - coarsePartType = cf.get_value_safe("output", "arepo_coarsetype", COARSE_DM_DEFAULT_PARTTYPE); - UnitLength_in_cm = cf.get_value_safe("output", "arepo_unitlength", 3.085678e21); // 1.0 kpc - UnitMass_in_g = cf.get_value_safe("output", "arepo_unitmass", 1.989e43); // 1.0e10 solar masses - UnitVelocity_in_cm_per_s = cf.get_value_safe("output", "arepo_unitvel", 1e5); // 1 km/sec + coarsePartType = cf.getValueSafe("output", "swift_coarsetype", COARSE_DM_DEFAULT_PARTTYPE); + UnitLength_in_cm = cf.getValueSafe("output", "swift_unitlength", 3.085678e24); // 1.0 Mpc + UnitMass_in_g = cf.getValueSafe("output", "swift_unitmass", 1.989e43); // 1.0e10 solar masses + UnitVelocity_in_cm_per_s = cf.getValueSafe("output", "swift_unitvel", 1e5); // 1 km/sec - omega0 = cf.get_value("cosmology", "Omega_m"); - omega_b = cf.get_value("cosmology", "Omega_b"); - omega_L = cf.get_value("cosmology", "Omega_L"); - redshift = cf.get_value("setup", "zstart"); - boxSize = cf.get_value("setup", "boxlength"); - doBaryons = cf.get_value_safe("setup", "baryons", false); - useLongIDs = cf.get_value_safe("output", "arepo_longids", false); - numFiles = cf.get_value_safe("output", "arepo_num_files", 1); - doublePrec = cf.get_value_safe("output", "arepo_doubleprec", 0); + omega0 = cf.getValue("cosmology", "Omega_m"); + omega_b = cf.getValue("cosmology", "Omega_b"); + omega_L = cf.getValue("cosmology", "Omega_L"); + redshift = cf.getValue("setup", "zstart"); + boxSize = cf.getValue("setup", "boxlength"); + doBaryons = cf.getValueSafe("setup", "baryons", false); + useLongIDs = cf.getValueSafe("output", "swift_longids", false); + numFiles = cf.getValueSafe("output", "swift_num_files", 1); + doublePrec = cf.getValueSafe("output", "swift_doubleprec", 0); for (unsigned i = 0; i < numFiles; i++) nPart.push_back(std::vector(NTYPES, 0)); @@ -550,20 +561,19 @@ public: // 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 = (1.0f / sqrt(time)) * boxSize; + velFac = boxSize; // critical density - rhoCrit = 27.7519737e-9; // in h^2 1e10 M_sol / kpc^3 - rhoCrit *= pow(UnitLength_in_cm / 3.085678e21, 3.0); + 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_) - { - vec3_t lxref, x0ref, x1ref; + if (levelmin_ != levelmax_) { + double lxref[3], x0ref[3], x1ref[3]; double pmgrid_new; the_region_generator->get_AABB(x0ref, x1ref, levelmax_); // generalized beyond box @@ -583,12 +593,17 @@ public: } // calculate Tini for gas - hubbleParam = cf.get_value("cosmology", "H0") / 100.0; + hubbleParam = cf.getValue("cosmology", "H0") / 100.0; + Tcmb0 = cf.getValueSafe("cosmology", "Tcmb0", 2.7255); //from monofonIC Planck2018EE+BAO+SN + gamma = cf.getValueSafe("cosmology", "gamma", 5.0 / 3.0); + YHe = cf.getValueSafe("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)); - double Tcmb0 = 2.726; + + rhoCrit *= h2; + posFac /= hubbleParam; Tini = astart < adec ? Tcmb0 / astart : Tcmb0 / astart / astart * adec; @@ -599,19 +614,18 @@ public: 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_); + 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 Arepo particle type for coarse particles."); + throw std::runtime_error("Error: Specified illegal Swift particle type for coarse particles."); if (coarsePartType == STAR_PARTTYPE) - music::wlog.Print("WARNING: Specified coarse particle type will collide with stars if USE_SFR enabled."); + LOGWARN("WARNING: Specified coarse particle type will collide with stars if USE_SFR enabled."); // create file(s) - for (unsigned i = 0; i < numFiles; i++) - { + for (unsigned i = 0; i < numFiles; i++) { std::string filename = fname_; - if (numFiles > 1) - { + 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)."); @@ -629,8 +643,7 @@ public: HDFCreateGroup(filename, GrpName.str().c_str()); // highres or unigrid DM - if (doBaryons) - { + if (doBaryons) { GrpName.str(""); GrpName << "PartType" << GAS_PARTTYPE; HDFCreateGroup(filename, GrpName.str().c_str()); // gas @@ -645,97 +658,89 @@ public: } } - ~arepo_output_plugin() - { - } + ~swift_output_plugin() {} /* ------------------------------------------------------------------------------- */ - void write_dm_mass(const grid_hierarchy &gh) - { + void write_dm_mass(const grid_hierarchy &gh) { if (!doublePrec) __write_dm_mass(gh); else __write_dm_mass(gh); } - void write_dm_position(int coord, const grid_hierarchy &gh) - { + void write_dm_position(int coord, const grid_hierarchy &gh) { if (!doublePrec) __write_dm_position(coord, gh); else __write_dm_position(coord, gh); } - void write_dm_velocity(int coord, const grid_hierarchy &gh) - { + void write_dm_velocity(int coord, const grid_hierarchy &gh) { if (!doublePrec) __write_dm_velocity(coord, gh); else __write_dm_velocity(coord, gh); } - void write_dm_density(const grid_hierarchy &gh) - { /* skip */ + void write_dm_density(const grid_hierarchy &gh) { /* skip */ } - void write_dm_potential(const grid_hierarchy &gh) - { /* skip */ + void write_dm_potential(const grid_hierarchy &gh) { /* skip */ } /* ------------------------------------------------------------------------------- */ - void write_gas_velocity(int coord, const grid_hierarchy &gh) - { + void write_gas_velocity(int coord, const grid_hierarchy &gh) { if (!doublePrec) __write_gas_velocity(coord, gh); else __write_gas_velocity(coord, gh); } - void write_gas_position(int coord, const grid_hierarchy &gh) - { + void write_gas_position(int coord, const grid_hierarchy &gh) { if (!doublePrec) __write_gas_position(coord, gh); else __write_gas_position(coord, gh); } - void write_gas_density(const grid_hierarchy &gh) - { + void write_gas_properties(const grid_hierarchy &gh) { + if (!doublePrec) + __write_gas_properties(gh); + else + __write_gas_properties(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 write_gas_potential(const grid_hierarchy &gh) { /* skip */ } - void finalize(void) - { + void finalize(void) { // generate and add contiguous IDs for each particle type we have written generateAndWriteIDs(); std::vector nPartTotalLW(nPartTotal.size()); std::vector nPartTotalHW(nPartTotal.size()); - for (size_t i = 0; i < nPartTotalHW.size(); i++) - { + 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 << " - Arepo : wrote " << nPartTotAllTypes << " particles..." << std::endl; + std::cout << " - Swift : 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++) - { + for (unsigned i = 0; i < numFiles; i++) { std::string filename = fname_; - if (numFiles > 1) - { + if (numFiles > 1) { std::stringstream s; s << "." << i << ".hdf5"; filename.replace(filename.find(".hdf5"), 5, s.str()); @@ -746,17 +751,29 @@ public: std::cout << std::endl; } + // Write UNITS header using the physical constants assumed internally by SWIFT + 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", "BoxSize", boxSize * posFac); + HDFWriteGroupAttribute(filename, "Header", "InitialMassTable", massTable); + HDFWriteGroupAttribute(filename, "Header", "BoxSize", boxSize / hubbleParam); //might prefer / hubble_param OR have Swift deal with h factors HDFWriteGroupAttribute(filename, "Header", "NumFilesPerSnapshot", numFiles); + HDFWriteGroupAttribute(filename, "Header", "Dimension", 3); HDFWriteGroupAttribute(filename, "Header", "Time", time); HDFWriteGroupAttribute(filename, "Header", "Redshift", redshift); - HDFWriteGroupAttribute(filename, "Header", "Omega0", omega0); + 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); @@ -769,41 +786,72 @@ public: HDFWriteGroupAttribute(filename, "Header", "Music_levelmin", levelmin_); HDFWriteGroupAttribute(filename, "Header", "Music_levelmax", levelmax_); HDFWriteGroupAttribute(filename, "Header", "Music_levelcounts", levelcounts); - HDFWriteGroupAttribute(filename, "Header", "haveBaryons", (int)doBaryons); HDFWriteGroupAttribute(filename, "Header", "longIDs", (int)useLongIDs); HDFWriteGroupAttribute(filename, "Header", "suggested_pmgrid", pmgrid); - HDFWriteGroupAttribute(filename, "Header", "suggested_gridboost", gridboost); + // HDFWriteGroupAttribute(filename, "Header", "suggested_gridboost", gridboost); HDFWriteGroupAttribute(filename, "Header", "suggested_highressoft", softening); - HDFWriteGroupAttribute(filename, "Header", "suggested_gas_Tinit", Tini); + // 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 << " - Arepo: Wrote 64bit IDs, enable LONGIDS." << std::endl; + std::cout << " - Swift: Wrote 64bit IDs, enable LONGIDS." << std::endl; if (doublePrec) - std::cout << " - Arepo: Double precision ICs, set INPUT_IN_DOUBLEPRECISION." << std::endl; + std::cout << " - Swift: Double precision ICs, set INPUT_IN_DOUBLEPRECISION." << std::endl; if (NTYPES != 6) - std::cout << " - Arepo: Using [" << NTYPES << "] particle types, set NTYPES to match." << std::endl; + std::cout << " - Swift: Using [" << NTYPES << "] particle types, set NTYPES to match." << std::endl; if (doBaryons) - std::cout << " - Arepo: Wrote high-res gas (only), set REFINEMENT_HIGH_RES_GAS and GENERATE_GAS_IN_ICS with " + std::cout << " - Swift: 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 << " - Arepo: Have zoom type ICs, set PLACEHIGHRESREGION=" << pow(2, HIGHRES_DM_PARTTYPE) + std::cout << " - Swift: Have zoom type ICs, set PLACEHIGHRESREGION=" << pow(2, HIGHRES_DM_PARTTYPE) << " (suggest PMGRID=" << pmgrid << " with GRIDBOOST=" << gridboost << ")." << std::endl; else - std::cout << " - Arepo: Have unigrid type ICs (suggest PMGRID=" << pmgrid << ")." << std::endl; + std::cout << " - Swift: Have unigrid type ICs (suggest PMGRID=" << pmgrid << ")." << std::endl; if (levelmax_ > levelmin_ + 1) - std::cout << " - Arepo: More than one coarse DM mass using same type, set INDIVIDUAL_GRAVITY_SOFTENING=" + std::cout << " - Swift: 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 << " - Arepo: Set initial gas temperature to " << std::fixed << std::setprecision(3) << Tini << " K." << std::endl; - std::cout << " - Arepo: Suggest grav softening = " << std::setprecision(3) << softening << " for high res DM." << std::endl; + std::cout << " - Swift: Set initial gas temperature to " << std::fixed << std::setprecision(3) << Tini << " K." + << std::endl; + std::cout << " - Swift: Suggest grav softening = " << std::setprecision(3) << softening << " for high res DM." + << std::endl; } }; -namespace -{ -output_plugin_creator_concrete creator("arepo"); +namespace { +output_plugin_creator_concrete creator("swift"); } #endif // HAVE_HDF5