-
Matthieu Schaller authoredMatthieu Schaller authored
single_io.c 44.33 KiB
/*******************************************************************************
* This file is part of SWIFT.
* Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
* Matthieu Schaller (matthieu.schaller@durham.ac.uk).
*
* 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 <http://www.gnu.org/licenses/>.
*
******************************************************************************/
/* Config parameters. */
#include "../config.h"
#if defined(HAVE_HDF5) && !defined(WITH_MPI)
/* Some standard headers. */
#include <hdf5.h>
#include <math.h>
#include <stddef.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
/* This object's header. */
#include "single_io.h"
/* Local includes. */
#include "black_holes_io.h"
#include "chemistry_io.h"
#include "common_io.h"
#include "cooling_io.h"
#include "dimension.h"
#include "engine.h"
#include "entropy_floor.h"
#include "error.h"
#include "gravity_io.h"
#include "gravity_properties.h"
#include "hydro_io.h"
#include "hydro_properties.h"
#include "io_properties.h"
#include "kernel_hydro.h"
#include "memuse.h"
#include "part.h"
#include "part_type.h"
#include "star_formation_io.h"
#include "stars_io.h"
#include "tracers_io.h"
#include "units.h"
#include "velociraptor_io.h"
#include "xmf.h"
/**
* @brief Reads a data array from a given HDF5 group.
*
* @param h_grp The group from which to read.
* @param prop The #io_props of the field to read
* @param N The number of particles.
* @param internal_units The #unit_system used internally
* @param ic_units The #unit_system used in the ICs * @param cleanup_h Are we removing h-factors from the ICs?
* @param cleanup_sqrt_a Are we cleaning-up the sqrt(a) factors in the Gadget
* IC velocities?
* @param h The value of the reduced Hubble constant.
* @param a The current value of the scale-factor.
*
* @todo A better version using HDF5 hyper-slabs to read the file directly into
* the part array will be written once the structures have been stabilized.
*/
void readArray(hid_t h_grp, const struct io_props props, size_t N,
const struct unit_system* internal_units,
const struct unit_system* ic_units, int cleanup_h,
int cleanup_sqrt_a, double h, double a) {
const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
/* Check whether the dataspace exists or not */
const htri_t exist = H5Lexists(h_grp, props.name, 0);
if (exist < 0) {
error("Error while checking the existence of data set '%s'.", props.name);
} else if (exist == 0) {
if (props.importance == COMPULSORY) {
error("Compulsory data set '%s' not present in the file.", props.name);
} else {
/* message("Optional data set '%s' not present. Zeroing this particle
* props...", name); */
for (size_t i = 0; i < N; ++i)
memset(props.field + i * props.partSize, 0, copySize);
return;
}
}
/* message("Reading %s '%s' array...", */
/* props.importance == COMPULSORY ? "compulsory" : "optional ", */
/* props.name); */
/* Open data space */
const hid_t h_data = H5Dopen(h_grp, props.name, H5P_DEFAULT);
if (h_data < 0) error("Error while opening data space '%s'.", props.name);
/* Allocate temporary buffer */
void* temp = malloc(num_elements * typeSize);
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Read HDF5 dataspace in temporary buffer */
/* Dirty version that happens to work for vectors but should be improved */
/* Using HDF5 dataspaces would be better */
const hid_t h_err = H5Dread(h_data, io_hdf5_type(props.type), H5S_ALL,
H5S_ALL, H5P_DEFAULT, temp);
if (h_err < 0) error("Error while reading data array '%s'.", props.name);
/* Unit conversion if necessary */
const double unit_factor =
units_conversion_factor(ic_units, internal_units, props.units);
if (unit_factor != 1. && exist != 0) {
/* message("Converting ! factor=%e", factor); */
if (io_is_double_precision(props.type)) {
double* temp_d = (double*)temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= unit_factor;
} else {
float* temp_f = (float*)temp;
#ifdef SWIFT_DEBUG_CHECKS float maximum = 0.f;
float minimum = FLT_MAX;
#endif
/* Loop that converts the Units */
for (size_t i = 0; i < num_elements; ++i) {
#ifdef SWIFT_DEBUG_CHECKS
/* Find the absolute minimum and maximum values */
const float abstemp_f = fabsf(temp_f[i]);
if (abstemp_f != 0.f) {
maximum = max(maximum, abstemp_f);
minimum = min(minimum, abstemp_f);
}
#endif
/* Convert the float units */
temp_f[i] *= unit_factor;
}
#ifdef SWIFT_DEBUG_CHECKS
/* The two possible errors: larger than float or smaller
* than float precision. */
if (unit_factor * maximum > FLT_MAX) {
error("Unit conversion results in numbers larger than floats");
} else if (unit_factor * minimum < FLT_MIN) {
error("Numbers smaller than float precision");
}
#endif
}
}
/* Clean-up h if necessary */
const float h_factor_exp = units_h_factor(internal_units, props.units);
if (cleanup_h && h_factor_exp != 0.f && exist != 0) {
/* message("Multipltying '%s' by h^%f=%f", props.name, h_factor_exp,
* h_factor); */
if (io_is_double_precision(props.type)) {
double* temp_d = (double*)temp;
const double h_factor = pow(h, h_factor_exp);
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= h_factor;
} else {
float* temp_f = (float*)temp;
const float h_factor = pow(h, h_factor_exp);
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= h_factor;
}
}
/* Clean-up a if necessary */
if (cleanup_sqrt_a && a != 1. && (strcmp(props.name, "Velocities") == 0)) {
if (io_is_double_precision(props.type)) {
double* temp_d = (double*)temp;
const double vel_factor = sqrt(a);
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= vel_factor;
} else {
float* temp_f = (float*)temp;
const float vel_factor = sqrt(a);
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= vel_factor;
}
}
/* Copy temporary buffer to particle data */
char* temp_c = (char*)temp;
for (size_t i = 0; i < N; ++i)
memcpy(props.field + i * props.partSize, &temp_c[i * copySize], copySize);
/* Free and close everything */ free(temp);
H5Dclose(h_data);
}
/**
* @brief Writes a data array in given HDF5 group.
*
* @param e The #engine we are writing from.
* @param grp The group in which to write.
* @param fileName The name of the file in which the data is written
* @param xmfFile The FILE used to write the XMF description
* @param partTypeGroupName The name of the group containing the particles in
* the HDF5 file.
* @param props The #io_props of the field to read
* @param N The number of particles to write.
* @param internal_units The #unit_system used internally
* @param snapshot_units The #unit_system used in the snapshots
*
* @todo A better version using HDF5 hyper-slabs to write the file directly from
* the part array will be written once the structures have been stabilized.
*/
void writeArray(const struct engine* e, hid_t grp, char* fileName,
FILE* xmfFile, char* partTypeGroupName,
const struct io_props props, size_t N,
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 */
const hid_t h_space = H5Screate(H5S_SIMPLE);
if (h_space < 0)
error("Error while creating data space for field '%s'.", props.name);
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 << 20; /* Just a guess...*/
chunk_shape[1] = props.dimension;
} else {
rank = 1;
shape[0] = N;
shape[1] = 0;
chunk_shape[0] = 1 << 20; /* Just a guess...*/
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 properties */
const hid_t h_prop = H5Pcreate(H5P_DATASET_CREATE);
/* 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'.",
chunk_shape[0], chunk_shape[1], 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);
/* Impose 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);
}
/* Create dataset */
const hid_t h_data = H5Dcreate(grp, props.name, io_hdf5_type(props.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 XMF description for this data set */
if (xmfFile != NULL)
xmf_write_line(xmfFile, fileName, partTypeGroupName, props.name, N,
props.dimension, props.type);
/* Write unit conversion factors for this data set */
char buffer[FIELD_BUFFER_SIZE];
units_cgs_conversion_string(buffer, snapshot_units, props.units);
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);
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);
/* 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 phyical CGS (including cosmological corrections)",
factor * pow(e->cosmology->a, props.scale_factor_exponent));
if (strlen(props.description) != 0) {
/* Write the full description */
io_write_attribute_s(h_data, "Description", props.description);
}
/* Free and close everything */
swift_free("writebuff", temp);
H5Pclose(h_prop);
H5Dclose(h_data);
H5Sclose(h_space);
}
/**
* @brief Reads an HDF5 initial condition file (GADGET-3 type)
*
* @param fileName The file to read.
* @param internal_units The system units used internally
* @param dim (output) The dimension of the volume.
* @param parts (output) Array of #part particles.
* @param gparts (output) Array of #gpart particles.
* @param sparts (output) Array of #spart particles.
* @param bparts (output) Array of #bpart particles.
* @param Ngas (output) number of Gas particles read.
* @param Ngparts (output) The number of #gpart read.
* @param Nstars (output) The number of #spart read.
* @param Nblackholes (output) The number of #bpart read.
* @param flag_entropy (output) 1 if the ICs contained Entropy in the
* InternalEnergy field
* @param with_hydro Are we reading gas particles ?
* @param with_gravity Are we reading/creating #gpart arrays ?
* @param with_stars Are we reading star particles ?
* @param with_black_hole Are we reading black hole particles ?
* @param cleanup_h Are we cleaning-up h-factors from the quantities we read?
* @param cleanup_sqrt_a Are we cleaning-up the sqrt(a) factors in the Gadget
* IC velocities?
* @param h The value of the reduced Hubble constant to use for correction.
* @param a The current value of the scale-factor.
* @prarm n_threads The number of threads to use for the temporary threadpool.
* @param dry_run If 1, don't read the particle. Only allocates the arrays.
*
* Opens the HDF5 file fileName and reads the particles contained
* in the parts array. N is the returned number of particles found
* in the file.
*
* @warning Can not read snapshot distributed over more than 1 file !!!
* @todo Read snapshots distributed in more than one file.
*/
void read_ic_single(const char* fileName,
const struct unit_system* internal_units, double dim[3],
struct part** parts, struct gpart** gparts,
struct spart** sparts, struct bpart** bparts, size_t* Ngas,
size_t* Ngparts, size_t* Nstars, size_t* Nblackholes,
int* flag_entropy, int with_hydro, int with_gravity,
int with_stars, int with_black_holes, int cleanup_h,
int cleanup_sqrt_a, double h, double a, int n_threads,
int dry_run) {
hid_t h_file = 0, h_grp = 0;
/* GADGET has only cubic boxes (in cosmological mode) */
double boxSize[3] = {0.0, -1.0, -1.0};
/* GADGET has 6 particle types. We only keep the type 0 & 1 for now...*/
long long numParticles[swift_type_count] = {0};
long long numParticles_highWord[swift_type_count] = {0};
size_t N[swift_type_count] = {0};
int dimension = 3; /* Assume 3D if nothing is specified */
size_t Ndm = 0;
/* Initialise counters */
*Ngas = 0, *Ngparts = 0, *Nstars = 0, *Nblackholes = 0;
/* Open file */
/* message("Opening file '%s' as IC.", fileName); */
h_file = H5Fopen(fileName, H5F_ACC_RDONLY, H5P_DEFAULT);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
/* Open header to read simulation properties */
/* message("Reading file header..."); */
h_grp = H5Gopen(h_file, "/Header", H5P_DEFAULT);
if (h_grp < 0) error("Error while opening file header\n");
/* Check the dimensionality of the ICs (if the info exists) */
const hid_t hid_dim = H5Aexists(h_grp, "Dimension");
if (hid_dim < 0)
error("Error while testing existance of 'Dimension' attribute");
if (hid_dim > 0) io_read_attribute(h_grp, "Dimension", INT, &dimension);
if (dimension != hydro_dimension)
error("ICs dimensionality (%dD) does not match code dimensionality (%dD)",
dimension, (int)hydro_dimension);
/* Check whether the number of files is specified (if the info exists) */
const hid_t hid_files = H5Aexists(h_grp, "NumFilesPerSnapshot");
int num_files = 1;
if (hid_files < 0)
error(
"Error while testing the existance of 'NumFilesPerSnapshot' attribute");
if (hid_files > 0)
io_read_attribute(h_grp, "NumFilesPerSnapshot", INT, &num_files);
if (num_files != 1)
error(
"ICs are split over multiples files (%d). SWIFT cannot handle this "
"case. The script /tools/combine_ics.py is availalbe in the repository "
"to combine files into a valid input file.",
num_files);
/* Read the relevant information and print status */
int flag_entropy_temp[6];
io_read_attribute(h_grp, "Flag_Entropy_ICs", INT, flag_entropy_temp);
*flag_entropy = flag_entropy_temp[0];
io_read_attribute(h_grp, "BoxSize", DOUBLE, boxSize);
io_read_attribute(h_grp, "NumPart_Total", LONGLONG, numParticles);
io_read_attribute(h_grp, "NumPart_Total_HighWord", LONGLONG,
numParticles_highWord);
for (int ptype = 0; ptype < swift_type_count; ++ptype)
N[ptype] = (numParticles[ptype]) + (numParticles_highWord[ptype] << 32);
/* Get the box size if not cubic */
dim[0] = boxSize[0];
dim[1] = (boxSize[1] < 0) ? boxSize[0] : boxSize[1];
dim[2] = (boxSize[2] < 0) ? boxSize[0] : boxSize[2];
/* Change box size in the 1D and 2D case */
if (hydro_dimension == 2)
dim[2] = min(dim[0], dim[1]);
else if (hydro_dimension == 1)
dim[2] = dim[1] = dim[0];
/* Convert the box size if we want to clean-up h-factors */
if (cleanup_h) {
dim[0] /= h;
dim[1] /= h;
dim[2] /= h;
}
/* message("Found %d particles in a %speriodic box of size [%f %f %f].", */
/* *N, (periodic ? "": "non-"), dim[0], dim[1], dim[2]); */
/* Close header */
H5Gclose(h_grp);
/* Read the unit system used in the ICs */
struct unit_system* ic_units =
(struct unit_system*)malloc(sizeof(struct unit_system));
if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
io_read_unit_system(h_file, ic_units, internal_units, 0);
/* Tell the user if a conversion will be needed */
if (units_are_equal(ic_units, internal_units)) {
message("IC and internal units match. No conversion needed.");
} else {
message("Conversion needed from:");
message("(ICs) Unit system: U_M = %e g.", ic_units->UnitMass_in_cgs);
message("(ICs) Unit system: U_L = %e cm.",
ic_units->UnitLength_in_cgs);
message("(ICs) Unit system: U_t = %e s.", ic_units->UnitTime_in_cgs);
message("(ICs) Unit system: U_I = %e A.",
ic_units->UnitCurrent_in_cgs);
message("(ICs) Unit system: U_T = %e K.",
ic_units->UnitTemperature_in_cgs);
message("to:");
message("(internal) Unit system: U_M = %e g.",
internal_units->UnitMass_in_cgs);
message("(internal) Unit system: U_L = %e cm.",
internal_units->UnitLength_in_cgs);
message("(internal) Unit system: U_t = %e s.",
internal_units->UnitTime_in_cgs);
message("(internal) Unit system: U_I = %e A.",
internal_units->UnitCurrent_in_cgs);
message("(internal) Unit system: U_T = %e K.",
internal_units->UnitTemperature_in_cgs);
}
/* Convert the dimensions of the box */
for (int j = 0; j < 3; j++)
dim[j] *=
units_conversion_factor(ic_units, internal_units, UNIT_CONV_LENGTH);
/* Allocate memory to store SPH particles */
if (with_hydro) {
*Ngas = N[swift_type_gas];
if (swift_memalign("parts", (void**)parts, part_align,
*Ngas * sizeof(struct part)) != 0)
error("Error while allocating memory for SPH particles");
bzero(*parts, *Ngas * sizeof(struct part));
}
/* Allocate memory to store star particles */
if (with_stars) {
*Nstars = N[swift_type_stars];
if (swift_memalign("sparts", (void**)sparts, spart_align,
*Nstars * sizeof(struct spart)) != 0)
error("Error while allocating memory for stars particles");
bzero(*sparts, *Nstars * sizeof(struct spart));
}
/* Allocate memory to store black hole particles */
if (with_black_holes) {
*Nblackholes = N[swift_type_black_hole];
if (swift_memalign("bparts", (void**)bparts, bpart_align,
*Nblackholes * sizeof(struct bpart)) != 0)
error("Error while allocating memory for stars particles");
bzero(*bparts, *Nblackholes * sizeof(struct bpart));
}
/* Allocate memory to store all gravity particles */
if (with_gravity) { Ndm = N[swift_type_dark_matter];
*Ngparts = (with_hydro ? N[swift_type_gas] : 0) +
N[swift_type_dark_matter] +
(with_stars ? N[swift_type_stars] : 0) +
(with_black_holes ? N[swift_type_black_hole] : 0);
if (swift_memalign("gparts", (void**)gparts, gpart_align,
*Ngparts * sizeof(struct gpart)) != 0)
error("Error while allocating memory for gravity particles");
bzero(*gparts, *Ngparts * sizeof(struct gpart));
}
/* message("Allocated %8.2f MB for particles.", *N * sizeof(struct part) /
* (1024.*1024.)); */
/* message("BoxSize = %lf", dim[0]); */
/* message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm, *Ngparts); */
/* Loop over all particle types */
for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (N[ptype] == 0) continue;
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
ptype);
h_grp = H5Gopen(h_file, partTypeGroupName, H5P_DEFAULT);
if (h_grp < 0)
error("Error while opening particle group %s.", partTypeGroupName);
int num_fields = 0;
struct io_props list[100];
size_t Nparticles = 0;
/* Read particle fields into the structure */
switch (ptype) {
case swift_type_gas:
if (with_hydro) {
Nparticles = *Ngas;
hydro_read_particles(*parts, list, &num_fields);
num_fields += chemistry_read_particles(*parts, list + num_fields);
}
break;
case swift_type_dark_matter:
if (with_gravity) {
Nparticles = Ndm;
darkmatter_read_particles(*gparts, list, &num_fields);
}
break;
case swift_type_stars:
if (with_stars) {
Nparticles = *Nstars;
stars_read_particles(*sparts, list, &num_fields);
}
break;
case swift_type_black_hole:
if (with_black_holes) {
Nparticles = *Nblackholes;
black_holes_read_particles(*bparts, list, &num_fields);
}
break;
default:
message("Particle Type %d not yet supported. Particles ignored", ptype);
}
/* Read everything */
if (!dry_run)
for (int i = 0; i < num_fields; ++i)
readArray(h_grp, list[i], Nparticles, internal_units, ic_units,
cleanup_h, cleanup_sqrt_a, h, a);
/* Close particle group */
H5Gclose(h_grp);
}
/* Duplicate the parts for gravity */
if (!dry_run && with_gravity) {
/* Let's initialise a bit of thread parallelism here */
struct threadpool tp;
threadpool_init(&tp, n_threads);
/* Prepare the DM particles */
io_prepare_dm_gparts(&tp, *gparts, Ndm);
/* Duplicate the hydro particles into gparts */
if (with_hydro) io_duplicate_hydro_gparts(&tp, *parts, *gparts, *Ngas, Ndm);
/* Duplicate the star particles into gparts */
if (with_stars)
io_duplicate_stars_gparts(&tp, *sparts, *gparts, *Nstars, Ndm + *Ngas);
/* Duplicate the black hole particles into gparts */
if (with_black_holes)
io_duplicate_black_holes_gparts(&tp, *bparts, *gparts, *Nblackholes,
Ndm + *Ngas + *Nstars);
threadpool_clean(&tp);
}
/* message("Done Reading particles..."); */
/* Clean up */
free(ic_units);
/* Close file */
H5Fclose(h_file);
}
/**
* @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor
*
* @param e The engine containing all the system.
* @param baseName The common part of the snapshot file name.
* @param internal_units The #unit_system used internally
* @param snapshot_units The #unit_system used in the snapshots
*
* Creates an HDF5 output file and writes the particles contained
* in the engine. If such a file already exists, it is erased and replaced
* by the new one.
* The companion XMF file is also updated accordingly.
*
* Calls #error() if an error occurs.
*
*/
void write_output_single(struct engine* e, const char* baseName,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units) {
hid_t h_file = 0, h_grp = 0;
int numFiles = 1;
const struct part* parts = e->s->parts;
const struct xpart* xparts = e->s->xparts;
const struct gpart* gparts = e->s->gparts; const struct spart* sparts = e->s->sparts;
const struct bpart* bparts = e->s->bparts;
struct swift_params* params = e->parameter_file;
const int with_cosmology = e->policy & engine_policy_cosmology;
const int with_cooling = e->policy & engine_policy_cooling;
const int with_temperature = e->policy & engine_policy_temperature;
#ifdef HAVE_VELOCIRAPTOR
const int with_stf = (e->policy & engine_policy_structure_finding) &&
(e->s->gpart_group_data != NULL);
#else
const int with_stf = 0;
#endif
/* Number of particles currently in the arrays */
const size_t Ntot = e->s->nr_gparts;
const size_t Ngas = e->s->nr_parts;
const size_t Nstars = e->s->nr_sparts;
const size_t Nblackholes = e->s->nr_bparts;
// const size_t Nbaryons = Ngas + Nstars;
// const size_t Ndm = Ntot > 0 ? Ntot - Nbaryons : 0;
/* Number of particles that we will write */
const size_t Ntot_written =
e->s->nr_gparts - e->s->nr_inhibited_gparts - e->s->nr_extra_gparts;
const size_t Ngas_written =
e->s->nr_parts - e->s->nr_inhibited_parts - e->s->nr_extra_parts;
const size_t Nstars_written =
e->s->nr_sparts - e->s->nr_inhibited_sparts - e->s->nr_extra_sparts;
const size_t Nblackholes_written =
e->s->nr_bparts - e->s->nr_inhibited_bparts - e->s->nr_extra_bparts;
const size_t Nbaryons_written =
Ngas_written + Nstars_written + Nblackholes_written;
const size_t Ndm_written =
Ntot_written > 0 ? Ntot_written - Nbaryons_written : 0;
/* Format things in a Gadget-friendly array */
long long N_total[swift_type_count] = {
(long long)Ngas_written, (long long)Ndm_written, 0, 0,
(long long)Nstars_written, (long long)Nblackholes_written};
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
if (e->snapshot_int_time_label_on)
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%06i.hdf5", baseName,
(int)round(e->time));
else
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.hdf5", baseName,
e->snapshot_output_count);
/* First time, we need to create the XMF file */
if (e->snapshot_output_count == 0) xmf_create_file(baseName);
/* Prepare the XMF file for the new entry */
FILE* xmfFile = 0;
xmfFile = xmf_prepare_file(baseName);
/* Write the part corresponding to this specific output */
xmf_write_outputheader(xmfFile, fileName, e->time);
/* Open file */
/* message("Opening file '%s'.", fileName); */
h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
/* Open header to write simulation properties */
/* message("Writing file header..."); */
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(internal_units, snapshot_units, UNIT_CONV_TIME);
const double factor_length =
units_conversion_factor(internal_units, 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};
/* Print the relevant information and print status */
io_write_attribute(h_grp, "BoxSize", DOUBLE, dim, 3);
io_write_attribute(h_grp, "Time", DOUBLE, &dblTime, 1);
const int dimension = (int)hydro_dimension;
io_write_attribute(h_grp, "Dimension", INT, &dimension, 1);
io_write_attribute(h_grp, "Redshift", DOUBLE, &e->cosmology->z, 1);
io_write_attribute(h_grp, "Scale-factor", DOUBLE, &e->cosmology->a, 1);
io_write_attribute_s(h_grp, "Code", "SWIFT");
time_t tm = time(NULL);
io_write_attribute_s(h_grp, "Snapshot date", ctime(&tm));
io_write_attribute_s(h_grp, "RunName", e->run_name);
/* GADGET-2 legacy values */
/* Number of particles of each type */
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);
double MassTable[swift_type_count] = {0};
io_write_attribute(h_grp, "MassTable", DOUBLE, MassTable, 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(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
/* Close header */
H5Gclose(h_grp);
/* Print the code version */
io_write_code_description(h_file);
/* Print the run's policy */
io_write_engine_policy(h_file, e);
/* Print the SPH parameters */
if (e->policy & engine_policy_hydro) {
h_grp = H5Gcreate(h_file, "/HydroScheme", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating SPH group");
hydro_props_print_snapshot(h_grp, e->hydro_properties);
hydro_write_flavour(h_grp);
H5Gclose(h_grp);
}
/* Print the subgrid parameters */
h_grp = H5Gcreate(h_file, "/SubgridScheme", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating subgrid group");
entropy_floor_write_flavour(h_grp);
cooling_write_flavour(h_grp, e->cooling_func);
chemistry_write_flavour(h_grp);
tracers_write_flavour(h_grp); H5Gclose(h_grp);
/* Print the gravity parameters */
if (e->policy & engine_policy_self_gravity) {
h_grp = H5Gcreate(h_file, "/GravityScheme", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating gravity group");
gravity_props_print_snapshot(h_grp, e->gravity_properties);
H5Gclose(h_grp);
}
/* Print the stellar parameters */
if (e->policy & engine_policy_stars) {
h_grp = H5Gcreate(h_file, "/StarsScheme", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating stars group");
stars_props_print_snapshot(h_grp, e->stars_properties);
H5Gclose(h_grp);
}
/* Print the cosmological model */
h_grp =
H5Gcreate(h_file, "/Cosmology", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating cosmology group");
if (e->policy & engine_policy_cosmology)
io_write_attribute_i(h_grp, "Cosmological run", 1);
else
io_write_attribute_i(h_grp, "Cosmological run", 0);
cosmology_write_model(h_grp, e->cosmology);
H5Gclose(h_grp);
/* Print the runtime parameters */
h_grp =
H5Gcreate(h_file, "/Parameters", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating parameters group");
parser_write_params_to_hdf5(e->parameter_file, h_grp, 1);
H5Gclose(h_grp);
/* Print the runtime unused parameters */
h_grp = H5Gcreate(h_file, "/UnusedParameters", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating parameters group");
parser_write_params_to_hdf5(e->parameter_file, h_grp, 0);
H5Gclose(h_grp);
/* Print the system of Units used in the spashot */
io_write_unit_system(h_file, snapshot_units, "Units");
/* Print the system of Units used internally */
io_write_unit_system(h_file, internal_units, "InternalCodeUnits");
/* Now write the top-level cell structure */
long long global_offsets[swift_type_count] = {0};
h_grp = H5Gcreate(h_file, "/Cells", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating cells group");
/* Write the location of the particles in the arrays */
io_write_cell_offsets(h_grp, e->s->cdim, e->s->cells_top, e->s->nr_cells,
e->s->width, e->nodeID, N_total, global_offsets,
internal_units, snapshot_units);
H5Gclose(h_grp);
/* Tell the user if a conversion will be needed */
if (e->verbose) {
if (units_are_equal(snapshot_units, internal_units)) {
message("Snapshot and internal units match. No conversion needed.");
} else {
message("Conversion needed from:");
message("(Snapshot) Unit system: U_M = %e g.",
snapshot_units->UnitMass_in_cgs);
message("(Snapshot) Unit system: U_L = %e cm.",
snapshot_units->UnitLength_in_cgs);
message("(Snapshot) Unit system: U_t = %e s.",
snapshot_units->UnitTime_in_cgs);
message("(Snapshot) Unit system: U_I = %e A.",
snapshot_units->UnitCurrent_in_cgs);
message("(Snapshot) Unit system: U_T = %e K.",
snapshot_units->UnitTemperature_in_cgs);
message("to:");
message("(internal) Unit system: U_M = %e g.",
internal_units->UnitMass_in_cgs);
message("(internal) Unit system: U_L = %e cm.",
internal_units->UnitLength_in_cgs);
message("(internal) Unit system: U_t = %e s.",
internal_units->UnitTime_in_cgs);
message("(internal) Unit system: U_I = %e A.",
internal_units->UnitCurrent_in_cgs);
message("(internal) Unit system: U_T = %e K.",
internal_units->UnitTemperature_in_cgs);
}
}
/* Loop over all particle types */
for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (numParticles[ptype] == 0) continue;
/* Add the global information for that particle type to the XMF meta-file */
xmf_write_groupheader(xmfFile, fileName, numParticles[ptype],
(enum part_type)ptype);
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
ptype);
h_grp = H5Gcreate(h_file, partTypeGroupName, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating particle group.\n");
int num_fields = 0;
struct io_props list[100];
size_t N = 0;
struct part* parts_written = NULL;
struct xpart* xparts_written = NULL;
struct gpart* gparts_written = NULL;
struct velociraptor_gpart_data* gpart_group_data_written = NULL;
struct spart* sparts_written = NULL;
struct bpart* bparts_written = NULL;
/* Write particle fields from the particle structure */
switch (ptype) {
case swift_type_gas: {
if (Ngas == Ngas_written) {
/* No inhibted particles: easy case */
N = Ngas;
hydro_write_particles(parts, xparts, list, &num_fields);
num_fields += chemistry_write_particles(parts, list + num_fields);
if (with_cooling || with_temperature) {
num_fields += cooling_write_particles(
parts, xparts, list + num_fields, e->cooling_func);
}
if (with_stf) {
num_fields += velociraptor_write_parts(parts, xparts, list + num_fields);
}
num_fields += tracers_write_particles(
parts, xparts, list + num_fields, with_cosmology);
num_fields +=
star_formation_write_particles(parts, xparts, list + num_fields);
} else {
/* Ok, we need to fish out the particles we want */
N = Ngas_written;
/* Allocate temporary arrays */
if (swift_memalign("parts_written", (void**)&parts_written,
part_align,
Ngas_written * sizeof(struct part)) != 0)
error("Error while allocating temporart memory for parts");
if (swift_memalign("xparts_written", (void**)&xparts_written,
xpart_align,
Ngas_written * sizeof(struct xpart)) != 0)
error("Error while allocating temporart memory for xparts");
/* Collect the particles we want to write */
io_collect_parts_to_write(parts, xparts, parts_written,
xparts_written, Ngas, Ngas_written);
/* Select the fields to write */
hydro_write_particles(parts_written, xparts_written, list,
&num_fields);
num_fields +=
chemistry_write_particles(parts_written, list + num_fields);
if (with_cooling || with_temperature) {
num_fields +=
cooling_write_particles(parts_written, xparts_written,
list + num_fields, e->cooling_func);
}
if (with_stf) {
num_fields += velociraptor_write_parts(
parts_written, xparts_written, list + num_fields);
}
num_fields += tracers_write_particles(
parts_written, xparts_written, list + num_fields, with_cosmology);
num_fields += star_formation_write_particles(
parts_written, xparts_written, list + num_fields);
}
} break;
case swift_type_dark_matter: {
if (Ntot == Ndm_written) {
/* This is a DM-only run without inhibited particles */
N = Ntot;
darkmatter_write_particles(gparts, list, &num_fields);
if (with_stf) {
num_fields += velociraptor_write_gparts(e->s->gpart_group_data,
list + num_fields);
}
} else {
/* Ok, we need to fish out the particles we want */
N = Ndm_written;
/* Allocate temporary array */
if (swift_memalign("gparts_written", (void**)&gparts_written,
gpart_align,
Ndm_written * sizeof(struct gpart)) != 0)
error("Error while allocating temporart memory for gparts");
if (with_stf) {
if (swift_memalign( "gpart_group_written", (void**)&gpart_group_data_written,
gpart_align,
Ndm_written * sizeof(struct velociraptor_gpart_data)) != 0)
error(
"Error while allocating temporart memory for gparts STF "
"data");
}
/* Collect the non-inhibited DM particles from gpart */
io_collect_gparts_to_write(gparts, e->s->gpart_group_data,
gparts_written, gpart_group_data_written,
Ntot, Ndm_written, with_stf);
/* Select the fields to write */
darkmatter_write_particles(gparts_written, list, &num_fields);
if (with_stf) {
num_fields += velociraptor_write_gparts(gpart_group_data_written,
list + num_fields);
}
}
} break;
case swift_type_stars: {
if (Nstars == Nstars_written) {
/* No inhibted particles: easy case */
N = Nstars;
stars_write_particles(sparts, list, &num_fields);
num_fields += chemistry_write_sparticles(sparts, list + num_fields);
num_fields += tracers_write_sparticles(sparts, list + num_fields,
with_cosmology);
if (with_stf) {
num_fields += velociraptor_write_sparts(sparts, list + num_fields);
}
} else {
/* Ok, we need to fish out the particles we want */
N = Nstars_written;
/* Allocate temporary arrays */
if (swift_memalign("sparts_written", (void**)&sparts_written,
spart_align,
Nstars_written * sizeof(struct spart)) != 0)
error("Error while allocating temporart memory for sparts");
/* Collect the particles we want to write */
io_collect_sparts_to_write(sparts, sparts_written, Nstars,
Nstars_written);
/* Select the fields to write */
stars_write_particles(sparts_written, list, &num_fields);
num_fields +=
chemistry_write_sparticles(sparts_written, list + num_fields);
num_fields += tracers_write_sparticles(
sparts_written, list + num_fields, with_cosmology);
if (with_stf) {
num_fields +=
velociraptor_write_sparts(sparts_written, list + num_fields);
}
}
} break;
case swift_type_black_hole: {
if (Nblackholes == Nblackholes_written) {
/* No inhibted particles: easy case */
N = Nblackholes;
black_holes_write_particles(bparts, list, &num_fields);
if (with_stf) {
num_fields += velociraptor_write_bparts(bparts, list + num_fields); }
} else {
/* Ok, we need to fish out the particles we want */
N = Nblackholes_written;
/* Allocate temporary arrays */
if (swift_memalign("bparts_written", (void**)&bparts_written,
bpart_align,
Nblackholes_written * sizeof(struct bpart)) != 0)
error("Error while allocating temporart memory for bparts");
/* Collect the particles we want to write */
io_collect_bparts_to_write(bparts, bparts_written, Nblackholes,
Nblackholes_written);
/* Select the fields to write */
black_holes_write_particles(bparts_written, list, &num_fields);
if (with_stf) {
num_fields +=
velociraptor_write_bparts(bparts_written, list + num_fields);
}
}
} break;
default:
error("Particle Type %d not yet supported. Aborting", ptype);
}
/* Write everything that is not cancelled */
for (int i = 0; i < num_fields; ++i) {
/* Did the user cancel this field? */
char field[PARSER_MAX_LINE_SIZE];
sprintf(field, "SelectOutput:%s_%s", list[i].name,
part_type_names[ptype]);
int should_write = parser_get_opt_param_int(params, field, 1);
if (should_write)
writeArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i], N,
internal_units, snapshot_units);
}
/* Free temporary arrays */
if (parts_written) swift_free("parts_written", parts_written);
if (xparts_written) swift_free("xparts_written", xparts_written);
if (gparts_written) swift_free("gparts_written", gparts_written);
if (gpart_group_data_written)
swift_free("gpart_group_written", gpart_group_data_written);
if (sparts_written) swift_free("sparts_written", sparts_written);
if (bparts_written) swift_free("bparts_written", bparts_written);
/* Close particle group */
H5Gclose(h_grp);
/* Close this particle group in the XMF file as well */
xmf_write_groupfooter(xmfFile, (enum part_type)ptype);
}
/* Write LXMF file descriptor */
xmf_write_outputfooter(xmfFile, e->snapshot_output_count, e->time);
/* message("Done writing particles..."); */
/* Close file */
H5Fclose(h_file);
e->snapshot_output_count++;
}
#endif /* HAVE_HDF5 */