/*******************************************************************************
* This file is part of SWIFT.
* Copyright (c) 2020 Matthieu Schaller (schaller@strw.leidenuniv.nl)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program. If not, see .
*
******************************************************************************/
/* Config parameters. */
#include
#ifdef HAVE_HDF5
/* Some standard headers. */
#include
/* Local headers */
#include "engine.h"
#include "fof.h"
#include "hydro_io.h"
#include "tools.h"
#include "version.h"
void write_fof_hdf5_header(hid_t h_file, const struct engine* e,
const long long num_groups_total,
const long long num_groups_this_file,
const struct fof_props* props,
const int virtual_file) {
/* Open header to write simulation properties */
hid_t h_grp =
H5Gcreate(h_file, "/Header", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating file header\n");
/* Convert basic output information to snapshot units */
const double factor_time = units_conversion_factor(
e->internal_units, e->snapshot_units, UNIT_CONV_TIME);
const double factor_length = units_conversion_factor(
e->internal_units, e->snapshot_units, UNIT_CONV_LENGTH);
const double dblTime = e->time * factor_time;
const double dim[3] = {e->s->dim[0] * factor_length,
e->s->dim[1] * factor_length,
e->s->dim[2] * factor_length};
io_write_attribute(h_grp, "BoxSize", DOUBLE, dim, 3);
io_write_attribute_d(h_grp, "Time", dblTime);
io_write_attribute_d(h_grp, "Dimension", (int)hydro_dimension);
io_write_attribute_d(h_grp, "Redshift", e->cosmology->z);
io_write_attribute_d(h_grp, "Scale-factor", e->cosmology->a);
io_write_attribute_s(h_grp, "Code", "SWIFT");
io_write_attribute_s(h_grp, "RunName", e->run_name);
/* We write rank 0's hostname so that it is uniform across all files. */
char systemname[256] = {0};
if (e->nodeID == 0) sprintf(systemname, "%s", hostname());
io_write_attribute_s(h_grp, "System", systemname);
io_write_attribute(h_grp, "Shift", DOUBLE, e->s->initial_shift, 3);
/* Write out the particle types */
io_write_part_type_names(h_grp);
/* Write out the time-base */
if (e->policy & engine_policy_cosmology) {
io_write_attribute_d(h_grp, "TimeBase_dloga", e->time_base);
const double delta_t = cosmology_get_timebase(e->cosmology, e->ti_current);
io_write_attribute_d(h_grp, "TimeBase_dt", delta_t);
} else {
io_write_attribute_d(h_grp, "TimeBase_dloga", 0);
io_write_attribute_d(h_grp, "TimeBase_dt", e->time_base);
}
/* Store the time at which the snapshot was written */
time_t tm = time(NULL);
struct tm* timeinfo = localtime(&tm);
char snapshot_date[64];
strftime(snapshot_date, 64, "%T %F %Z", timeinfo);
io_write_attribute_s(h_grp, "SnapshotDate", snapshot_date);
/* GADGET-2 legacy values */
/* Number of particles of each type */
long long N_total[swift_type_count] = {0};
unsigned int numParticles[swift_type_count] = {0};
unsigned int numParticlesHighWord[swift_type_count] = {0};
for (int ptype = 0; ptype < swift_type_count; ++ptype) {
numParticles[ptype] = (unsigned int)N_total[ptype];
numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
}
io_write_attribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
swift_type_count);
io_write_attribute(h_grp, "NumPart_Total", UINT, numParticles,
swift_type_count);
io_write_attribute(h_grp, "NumPart_Total_HighWord", UINT,
numParticlesHighWord, swift_type_count);
io_write_attribute(h_grp, "TotalNumberOfParticles", LONGLONG, N_total,
swift_type_count);
double MassTable[swift_type_count] = {0};
io_write_attribute(h_grp, "MassTable", DOUBLE, MassTable, swift_type_count);
io_write_attribute(h_grp, "InitialMassTable", DOUBLE,
e->s->initial_mean_mass_particles, swift_type_count);
unsigned int flagEntropy[swift_type_count] = {0};
flagEntropy[0] = writeEntropyFlag();
io_write_attribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
swift_type_count);
io_write_attribute_i(h_grp, "NumFilesPerSnapshot", 1);
io_write_attribute_i(h_grp, "ThisFile", 0);
io_write_attribute_s(h_grp, "SelectOutput", "Default");
io_write_attribute_i(h_grp, "Virtual", virtual_file);
const int to_write[swift_type_count] = {0};
io_write_attribute(h_grp, "CanHaveTypes", INT, to_write, swift_type_count);
io_write_attribute_i(h_grp, "ZoomIn", e->s->with_zoom_region);
io_write_attribute_s(h_grp, "OutputType", "FOF");
/* FOF-specific counters */
io_write_attribute_ll(h_grp, "NumGroups_Total", num_groups_total);
io_write_attribute_ll(h_grp, "NumGroups_ThisFile", num_groups_this_file);
/* Close group */
H5Gclose(h_grp);
/* Copy metadata from ICs to the file */
ic_info_write_hdf5(e->ics_metadata, h_file);
/* Write all the meta-data */
io_write_meta_data(h_file, e, e->internal_units, e->snapshot_units,
/*fof=*/1);
}
void write_fof_hdf5_array(
const struct engine* e, hid_t grp, const char* fileName,
const char* partTypeGroupName, const struct io_props props, const size_t N,
const enum lossy_compression_schemes lossy_compression,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units) {
const size_t typeSize = io_sizeof_type(props.type);
const size_t num_elements = N * props.dimension;
/* message("Writing '%s' array...", props.name); */
/* Allocate temporary buffer */
void* temp = NULL;
if (swift_memalign("writebuff", (void**)&temp, IO_BUFFER_ALIGNMENT,
num_elements * typeSize) != 0)
error("Unable to allocate temporary i/o buffer");
/* Copy the particle data to the temporary buffer */
io_copy_temp_buffer(temp, e, props, N, internal_units, snapshot_units);
/* Create data space */
hid_t h_space;
if (N > 0)
h_space = H5Screate(H5S_SIMPLE);
else
h_space = H5Screate(H5S_NULL);
if (h_space < 0)
error("Error while creating data space for field '%s'.", props.name);
/* Decide what chunk size to use based on compression */
int log2_chunk_size = 20;
int rank;
hsize_t shape[2];
hsize_t chunk_shape[2];
if (props.dimension > 1) {
rank = 2;
shape[0] = N;
shape[1] = props.dimension;
chunk_shape[0] = 1 << log2_chunk_size;
chunk_shape[1] = props.dimension;
} else {
rank = 1;
shape[0] = N;
shape[1] = 0;
chunk_shape[0] = 1 << log2_chunk_size;
chunk_shape[1] = 0;
}
/* Make sure the chunks are not larger than the dataset */
if (chunk_shape[0] > N) chunk_shape[0] = N;
/* Change shape of data space */
hid_t h_err = H5Sset_extent_simple(h_space, rank, shape, shape);
if (h_err < 0)
error("Error while changing data space shape for field '%s'.", props.name);
/* Dataset type */
hid_t h_type = H5Tcopy(io_hdf5_type(props.type));
/* Dataset properties */
hid_t h_prop = H5Pcreate(H5P_DATASET_CREATE);
/* Create filters and set compression level if we have something to write */
char comp_buffer[32] = "None";
if (N > 0) {
/* Set chunk size */
h_err = H5Pset_chunk(h_prop, rank, chunk_shape);
if (h_err < 0)
error("Error while setting chunk size (%llu, %llu) for field '%s'.",
(unsigned long long)chunk_shape[0],
(unsigned long long)chunk_shape[1], props.name);
/* Are we imposing some form of lossy compression filter? */
if (lossy_compression != compression_write_lossless)
set_hdf5_lossy_compression(&h_prop, &h_type, lossy_compression,
props.name, comp_buffer);
/* Impose GZIP data compression */
if (e->snapshot_compression > 0) {
h_err = H5Pset_shuffle(h_prop);
if (h_err < 0)
error("Error while setting shuffling options for field '%s'.",
props.name);
h_err = H5Pset_deflate(h_prop, e->snapshot_compression);
if (h_err < 0)
error("Error while setting compression options for field '%s'.",
props.name);
}
/* Impose check-sum to verify data corruption */
h_err = H5Pset_fletcher32(h_prop);
if (h_err < 0)
error("Error while setting checksum options for field '%s'.", props.name);
}
/* Create dataset */
const hid_t h_data = H5Dcreate(grp, props.name, h_type, h_space, H5P_DEFAULT,
h_prop, H5P_DEFAULT);
if (h_data < 0) error("Error while creating dataspace '%s'.", props.name);
/* Write temporary buffer to HDF5 dataspace */
h_err = H5Dwrite(h_data, io_hdf5_type(props.type), h_space, H5S_ALL,
H5P_DEFAULT, temp);
if (h_err < 0) error("Error while writing data array '%s'.", props.name);
/* Write unit conversion factors for this data set */
char buffer[FIELD_BUFFER_SIZE] = {0};
units_cgs_conversion_string(buffer, snapshot_units, props.units,
props.scale_factor_exponent);
float baseUnitsExp[5];
units_get_base_unit_exponents_array(baseUnitsExp, props.units);
io_write_attribute_f(h_data, "U_M exponent", baseUnitsExp[UNIT_MASS]);
io_write_attribute_f(h_data, "U_L exponent", baseUnitsExp[UNIT_LENGTH]);
io_write_attribute_f(h_data, "U_t exponent", baseUnitsExp[UNIT_TIME]);
io_write_attribute_f(h_data, "U_I exponent", baseUnitsExp[UNIT_CURRENT]);
io_write_attribute_f(h_data, "U_T exponent", baseUnitsExp[UNIT_TEMPERATURE]);
io_write_attribute_f(h_data, "h-scale exponent", 0.f);
io_write_attribute_f(h_data, "a-scale exponent", props.scale_factor_exponent);
io_write_attribute_s(h_data, "Expression for physical CGS units", buffer);
io_write_attribute_s(h_data, "Lossy compression filter", comp_buffer);
io_write_attribute_b(h_data, "Value stored as physical", props.is_physical);
io_write_attribute_b(h_data, "Property can be converted to comoving",
props.is_convertible_to_comoving);
/* Write the actual number this conversion factor corresponds to */
const double factor =
units_cgs_conversion_factor(snapshot_units, props.units);
io_write_attribute_d(
h_data,
"Conversion factor to CGS (not including cosmological corrections)",
factor);
io_write_attribute_d(
h_data,
"Conversion factor to physical CGS (including cosmological corrections)",
factor * pow(e->cosmology->a, props.scale_factor_exponent));
#ifdef SWIFT_DEBUG_CHECKS
if (strlen(props.description) == 0)
error("Invalid (empty) description of the field '%s'", props.name);
#endif
/* Write the full description */
io_write_attribute_s(h_data, "Description", props.description);
/* Free and close everything */
swift_free("writebuff", temp);
H5Tclose(h_type);
H5Pclose(h_prop);
H5Dclose(h_data);
H5Sclose(h_space);
}
void write_fof_hdf5_catalogue(const struct fof_props* props,
const struct engine* e) {
char file_name[512];
sprintf(file_name, "%s_%04i.hdf5", props->base_name,
e->snapshot_output_count);
/* Set the minimal API version to avoid issues with advanced features */
hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
HDF5_HIGHEST_FILE_FORMAT_VERSION);
if (err < 0) error("Error setting the hdf5 API version");
hid_t h_file = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
if (h_file < 0) error("Error while opening file '%s'.", file_name);
/* Compute the number of groups */
long long num_groups_local = props->num_groups;
long long num_groups_total = props->num_groups;
/* Start by writing the header */
write_fof_hdf5_header(h_file, e, num_groups_total, num_groups_local, props,
/*virtual_file=*/0);
hid_t h_grp =
H5Gcreate(h_file, "/Groups", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating groups group.\n");
struct io_props output_prop;
output_prop = io_make_output_field_("Masses", DOUBLE, 1, UNIT_CONV_MASS, 0.f,
(char*)props->group_mass, sizeof(double),
"FOF group masses", /*physical=*/0,
/*convertible_to_comoving=*/1);
write_fof_hdf5_array(e, h_grp, file_name, "Groups", output_prop,
num_groups_local, compression_write_lossless,
e->internal_units, e->snapshot_units);
output_prop =
io_make_output_field_("Centres", DOUBLE, 3, UNIT_CONV_LENGTH, 1.f,
(char*)props->group_centre_of_mass,
3 * sizeof(double), "FOF group centres of mass",
/*physical=*/0, /*convertible_to_comoving=*/1);
write_fof_hdf5_array(e, h_grp, file_name, "Groups", output_prop,
num_groups_local, compression_write_lossless,
e->internal_units, e->snapshot_units);
output_prop = io_make_output_field_(
"Radii", FLOAT, 1, UNIT_CONV_LENGTH, 1.f, (char*)props->group_radii,
sizeof(float), "Distance to the particle furthest from the centre",
/*physical=*/0, /*convertible_to_comoving=*/1);
write_fof_hdf5_array(e, h_grp, file_name, "Groups", output_prop,
num_groups_local, compression_write_lossless,
e->internal_units, e->snapshot_units);
output_prop =
io_make_output_field_("GroupIDs", LONGLONG, 1, UNIT_CONV_NO_UNITS, 0.f,
(char*)props->final_group_index, sizeof(long long),
"FOF group IDs", /*physical=*/1,
/*convertible_to_comoving=*/0);
write_fof_hdf5_array(e, h_grp, file_name, "Groups", output_prop,
num_groups_local, compression_write_lossless,
e->internal_units, e->snapshot_units);
output_prop =
io_make_output_field_("Sizes", LONGLONG, 1, UNIT_CONV_NO_UNITS, 0.f,
(char*)props->final_group_size, sizeof(long long),
"FOF group length (number of particles)",
/*physical=*/1, /*convertible_to_comoving=*/0);
write_fof_hdf5_array(e, h_grp, file_name, "Groups", output_prop,
num_groups_local, compression_write_lossless,
e->internal_units, e->snapshot_units);
/* Close everything */
H5Gclose(h_grp);
H5Fclose(h_file);
H5Pclose(h_props);
}
#endif /* HAVE_HDF5 */