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Matthieu Schaller authoredMatthieu Schaller authored
common_io.c 29.72 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"
/* This object's header. */
#include "common_io.h"
/* Local includes. */
#include "chemistry_io.h"
#include "engine.h"
#include "error.h"
#include "gravity_io.h"
#include "hydro.h"
#include "hydro_io.h"
#include "io_properties.h"
#include "kernel_hydro.h"
#include "part.h"
#include "part_type.h"
#include "stars_io.h"
#include "threadpool.h"
#include "units.h"
#include "version.h"
/* Some standard headers. */
#include <math.h>
#include <stddef.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#if defined(HAVE_HDF5)
#include <hdf5.h>
/* MPI headers. */
#ifdef WITH_MPI
#include <mpi.h>
#endif
/**
* @brief Converts a C data type to the HDF5 equivalent.
*
* This function is a trivial wrapper around the HDF5 types but allows
* to change the exact storage types matching the code types in a transparent
*way.
*/
hid_t io_hdf5_type(enum IO_DATA_TYPE type) {
switch (type) {
case INT:
return H5T_NATIVE_INT; case UINT:
return H5T_NATIVE_UINT;
case LONG:
return H5T_NATIVE_LONG;
case ULONG:
return H5T_NATIVE_ULONG;
case LONGLONG:
return H5T_NATIVE_LLONG;
case ULONGLONG:
return H5T_NATIVE_ULLONG;
case FLOAT:
return H5T_NATIVE_FLOAT;
case DOUBLE:
return H5T_NATIVE_DOUBLE;
case CHAR:
return H5T_NATIVE_CHAR;
default:
error("Unknown type");
return 0;
}
}
/**
* @brief Return 1 if the type has double precision
*
* Returns an error if the type is not FLOAT or DOUBLE
*/
int io_is_double_precision(enum IO_DATA_TYPE type) {
switch (type) {
case FLOAT:
return 0;
case DOUBLE:
return 1;
default:
error("Invalid type");
return 0;
}
}
/**
* @brief Reads an attribute from a given HDF5 group.
*
* @param grp The group from which to read.
* @param name The name of the attribute to read.
* @param type The #IO_DATA_TYPE of the attribute.
* @param data (output) The attribute read from the HDF5 group.
*
* Calls #error() if an error occurs.
*/
void io_read_attribute(hid_t grp, const char* name, enum IO_DATA_TYPE type,
void* data) {
const hid_t h_attr = H5Aopen(grp, name, H5P_DEFAULT);
if (h_attr < 0) error("Error while opening attribute '%s'", name);
const hid_t h_err = H5Aread(h_attr, io_hdf5_type(type), data);
if (h_err < 0) error("Error while reading attribute '%s'", name);
H5Aclose(h_attr);
}
/**
* @brief Write an attribute to a given HDF5 group.
*
* @param grp The group in which to write.
* @param name The name of the attribute to write.
* @param type The #IO_DATA_TYPE of the attribute.
* @param data The attribute to write.
* @param num The number of elements to write *
* Calls #error() if an error occurs.
*/
void io_write_attribute(hid_t grp, const char* name, enum IO_DATA_TYPE type,
void* data, int num) {
const hid_t h_space = H5Screate(H5S_SIMPLE);
if (h_space < 0)
error("Error while creating dataspace for attribute '%s'.", name);
hsize_t dim[1] = {(hsize_t)num};
const hid_t h_err = H5Sset_extent_simple(h_space, 1, dim, NULL);
if (h_err < 0)
error("Error while changing dataspace shape for attribute '%s'.", name);
const hid_t h_attr =
H5Acreate1(grp, name, io_hdf5_type(type), h_space, H5P_DEFAULT);
if (h_attr < 0) error("Error while creating attribute '%s'.", name);
const hid_t h_err2 = H5Awrite(h_attr, io_hdf5_type(type), data);
if (h_err2 < 0) error("Error while reading attribute '%s'.", name);
H5Sclose(h_space);
H5Aclose(h_attr);
}
/**
* @brief Write a string as an attribute to a given HDF5 group.
*
* @param grp The group in which to write.
* @param name The name of the attribute to write.
* @param str The string to write.
* @param length The length of the string
*
* Calls #error() if an error occurs.
*/
void io_writeStringAttribute(hid_t grp, const char* name, const char* str,
int length) {
const hid_t h_space = H5Screate(H5S_SCALAR);
if (h_space < 0)
error("Error while creating dataspace for attribute '%s'.", name);
const hid_t h_type = H5Tcopy(H5T_C_S1);
if (h_type < 0) error("Error while copying datatype 'H5T_C_S1'.");
const hid_t h_err = H5Tset_size(h_type, length);
if (h_err < 0) error("Error while resizing attribute type to '%i'.", length);
const hid_t h_attr = H5Acreate1(grp, name, h_type, h_space, H5P_DEFAULT);
if (h_attr < 0) error("Error while creating attribute '%s'.", name);
const hid_t h_err2 = H5Awrite(h_attr, h_type, str);
if (h_err2 < 0) error("Error while reading attribute '%s'.", name);
H5Tclose(h_type);
H5Sclose(h_space);
H5Aclose(h_attr);
}
/**
* @brief Writes a double value as an attribute
* @param grp The group in which to write
* @param name The name of the attribute
* @param data The value to write
*/
void io_write_attribute_d(hid_t grp, const char* name, double data) {
io_write_attribute(grp, name, DOUBLE, &data, 1);
}
/**
* @brief Writes a float value as an attribute
* @param grp The group in which to write
* @param name The name of the attribute
* @param data The value to write
*/
void io_write_attribute_f(hid_t grp, const char* name, float data) {
io_write_attribute(grp, name, FLOAT, &data, 1);
}
/**
* @brief Writes an int value as an attribute
* @param grp The group in which to write
* @param name The name of the attribute
* @param data The value to write
*/
void io_write_attribute_i(hid_t grp, const char* name, int data) {
io_write_attribute(grp, name, INT, &data, 1);
}
/**
* @brief Writes a long value as an attribute
* @param grp The group in which to write
* @param name The name of the attribute
* @param data The value to write
*/
void io_write_attribute_l(hid_t grp, const char* name, long data) {
io_write_attribute(grp, name, LONG, &data, 1);
}
/**
* @brief Writes a string value as an attribute
* @param grp The group in which to write
* @param name The name of the attribute
* @param str The string to write
*/
void io_write_attribute_s(hid_t grp, const char* name, const char* str) {
io_writeStringAttribute(grp, name, str, strlen(str));
}
/**
* @brief Reads the Unit System from an IC file.
* @param h_file The (opened) HDF5 file from which to read.
* @param us The unit_system to fill.
* @param mpi_rank The MPI rank we are on.
*
* If the 'Units' group does not exist in the ICs, cgs units will be assumed
*/
void io_read_unit_system(hid_t h_file, struct unit_system* us, int mpi_rank) {
/* First check if it exists as this is *not* required. */
const htri_t exists = H5Lexists(h_file, "/Units", H5P_DEFAULT);
if (exists == 0) {
if (mpi_rank == 0)
message("'Units' group not found in ICs. Assuming CGS unit system.");
/* Default to CGS */
us->UnitMass_in_cgs = 1.;
us->UnitLength_in_cgs = 1.;
us->UnitTime_in_cgs = 1.;
us->UnitCurrent_in_cgs = 1.;
us->UnitTemperature_in_cgs = 1.;
return;
} else if (exists < 0) {
error("Serious problem with 'Units' group in ICs. H5Lexists gives %d",
exists);
}
if (mpi_rank == 0) message("Reading IC units from ICs.");
hid_t h_grp = H5Gopen(h_file, "/Units", H5P_DEFAULT);
/* Ok, Read the damn thing */
io_read_attribute(h_grp, "Unit length in cgs (U_L)", DOUBLE,
&us->UnitLength_in_cgs);
io_read_attribute(h_grp, "Unit mass in cgs (U_M)", DOUBLE,
&us->UnitMass_in_cgs);
io_read_attribute(h_grp, "Unit time in cgs (U_t)", DOUBLE,
&us->UnitTime_in_cgs);
io_read_attribute(h_grp, "Unit current in cgs (U_I)", DOUBLE,
&us->UnitCurrent_in_cgs);
io_read_attribute(h_grp, "Unit temperature in cgs (U_T)", DOUBLE,
&us->UnitTemperature_in_cgs);
/* Clean up */
H5Gclose(h_grp);
}
/**
* @brief Writes the current Unit System
* @param h_file The (opened) HDF5 file in which to write
* @param us The unit_system to dump
* @param groupName The name of the HDF5 group to write to
*/
void io_write_unit_system(hid_t h_file, const struct unit_system* us,
const char* groupName) {
const hid_t h_grpunit = H5Gcreate1(h_file, groupName, 0);
if (h_grpunit < 0) error("Error while creating Unit System group");
io_write_attribute_d(h_grpunit, "Unit mass in cgs (U_M)",
units_get_base_unit(us, UNIT_MASS));
io_write_attribute_d(h_grpunit, "Unit length in cgs (U_L)",
units_get_base_unit(us, UNIT_LENGTH));
io_write_attribute_d(h_grpunit, "Unit time in cgs (U_t)",
units_get_base_unit(us, UNIT_TIME));
io_write_attribute_d(h_grpunit, "Unit current in cgs (U_I)",
units_get_base_unit(us, UNIT_CURRENT));
io_write_attribute_d(h_grpunit, "Unit temperature in cgs (U_T)",
units_get_base_unit(us, UNIT_TEMPERATURE));
H5Gclose(h_grpunit);
}
/**
* @brief Writes the code version to the file
* @param h_file The (opened) HDF5 file in which to write
*/
void io_write_code_description(hid_t h_file) {
const hid_t h_grpcode = H5Gcreate1(h_file, "/Code", 0);
if (h_grpcode < 0) error("Error while creating code group");
io_write_attribute_s(h_grpcode, "Code", "SWIFT");
io_write_attribute_s(h_grpcode, "Code Version", package_version());
io_write_attribute_s(h_grpcode, "Compiler Name", compiler_name());
io_write_attribute_s(h_grpcode, "Compiler Version", compiler_version());
io_write_attribute_s(h_grpcode, "Git Branch", git_branch());
io_write_attribute_s(h_grpcode, "Git Revision", git_revision());
io_write_attribute_s(h_grpcode, "Git Date", git_date());
io_write_attribute_s(h_grpcode, "Configuration options",
configuration_options());
io_write_attribute_s(h_grpcode, "CFLAGS", compilation_cflags());
io_write_attribute_s(h_grpcode, "HDF5 library version", hdf5_version());
io_write_attribute_s(h_grpcode, "Thread barriers", thread_barrier_version());
io_write_attribute_s(h_grpcode, "Allocators", allocator_version());
#ifdef HAVE_FFTW
io_write_attribute_s(h_grpcode, "FFTW library version", fftw3_version());#endif
#ifdef HAVE_LIBGSL
io_write_attribute_s(h_grpcode, "GSL library version", libgsl_version());
#endif
#ifdef WITH_MPI
io_write_attribute_s(h_grpcode, "MPI library", mpi_version());
#ifdef HAVE_METIS
io_write_attribute_s(h_grpcode, "METIS library version", metis_version());
#endif
#else
io_write_attribute_s(h_grpcode, "MPI library", "Non-MPI version of SWIFT");
#endif
H5Gclose(h_grpcode);
}
/**
* @brief Write the #engine policy to the file.
* @param h_file File to write to.
* @param e The #engine to read the policy from.
*/
void io_write_engine_policy(hid_t h_file, const struct engine* e) {
const hid_t h_grp = H5Gcreate1(h_file, "/Policy", 0);
if (h_grp < 0) error("Error while creating policy group");
for (int i = 1; i <= engine_maxpolicy; ++i)
if (e->policy & (1 << i))
io_write_attribute_i(h_grp, engine_policy_names[i + 1], 1);
else
io_write_attribute_i(h_grp, engine_policy_names[i + 1], 0);
H5Gclose(h_grp);
}
#endif /* HAVE_HDF5 */
/**
* @brief Returns the memory size of the data type
*/
size_t io_sizeof_type(enum IO_DATA_TYPE type) {
switch (type) {
case INT:
return sizeof(int);
case UINT:
return sizeof(unsigned int);
case LONG:
return sizeof(long);
case ULONG:
return sizeof(unsigned long);
case LONGLONG:
return sizeof(long long);
case ULONGLONG:
return sizeof(unsigned long long);
case FLOAT:
return sizeof(float);
case DOUBLE:
return sizeof(double);
case CHAR:
return sizeof(char);
default:
error("Unknown type");
return 0;
}
}
/**
* @brief Mapper function to copy #part or #gpart fields into a buffer.
*/
void io_copy_mapper(void* restrict temp, int N, void* restrict extra_data) {
const struct io_props props = *((const struct io_props*)extra_data);
const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
/* How far are we with this chunk? */
char* restrict temp_c = (char*)temp;
const ptrdiff_t delta = (temp_c - props.start_temp_c) / copySize;
for (int k = 0; k < N; k++) {
memcpy(&temp_c[k * copySize], props.field + (delta + k) * props.partSize,
copySize);
}
}
/**
* @brief Mapper function to copy #part into a buffer of floats using a
* conversion function.
*/
void io_convert_part_f_mapper(void* restrict temp, int N,
void* restrict extra_data) {
const struct io_props props = *((const struct io_props*)extra_data);
const struct part* restrict parts = props.parts;
const struct xpart* restrict xparts = props.xparts;
const struct engine* e = props.e;
const size_t dim = props.dimension;
/* How far are we with this chunk? */
float* restrict temp_f = (float*)temp;
const ptrdiff_t delta = (temp_f - props.start_temp_f) / dim;
for (int i = 0; i < N; i++)
props.convert_part_f(e, parts + delta + i, xparts + delta + i,
&temp_f[i * dim]);
}
/**
* @brief Mapper function to copy #part into a buffer of doubles using a
* conversion function.
*/
void io_convert_part_d_mapper(void* restrict temp, int N,
void* restrict extra_data) {
const struct io_props props = *((const struct io_props*)extra_data);
const struct part* restrict parts = props.parts;
const struct xpart* restrict xparts = props.xparts;
const struct engine* e = props.e;
const size_t dim = props.dimension;
/* How far are we with this chunk? */
double* restrict temp_d = (double*)temp;
const ptrdiff_t delta = (temp_d - props.start_temp_d) / dim;
for (int i = 0; i < N; i++)
props.convert_part_d(e, parts + delta + i, xparts + delta + i,
&temp_d[i * dim]);
}
/**
* @brief Mapper function to copy #gpart into a buffer of floats using a
* conversion function.
*/
void io_convert_gpart_f_mapper(void* restrict temp, int N,
void* restrict extra_data) {
const struct io_props props = *((const struct io_props*)extra_data);
const struct gpart* restrict gparts = props.gparts;
const struct engine* e = props.e;
const size_t dim = props.dimension;
/* How far are we with this chunk? */
float* restrict temp_f = (float*)temp;
const ptrdiff_t delta = (temp_f - props.start_temp_f) / dim;
for (int i = 0; i < N; i++)
props.convert_gpart_f(e, gparts + delta + i, &temp_f[i * dim]);
}
/**
* @brief Mapper function to copy #gpart into a buffer of doubles using a
* conversion function.
*/
void io_convert_gpart_d_mapper(void* restrict temp, int N,
void* restrict extra_data) {
const struct io_props props = *((const struct io_props*)extra_data);
const struct gpart* restrict gparts = props.gparts;
const struct engine* e = props.e;
const size_t dim = props.dimension;
/* How far are we with this chunk? */
double* restrict temp_d = (double*)temp;
const ptrdiff_t delta = (temp_d - props.start_temp_d) / dim;
for (int i = 0; i < N; i++)
props.convert_gpart_d(e, gparts + delta + i, &temp_d[i * dim]);
}
/**
* @brief Copy the particle data into a temporary buffer ready for i/o.
*
* @param temp The buffer to be filled. Must be allocated and aligned properly.
* @param e The #engine.
* @param props The #io_props corresponding to the particle field we are
* copying.
* @param N The number of particles to copy
* @param internal_units The system of units used internally.
* @param snapshot_units The system of units used for the snapshots.
*/
void io_copy_temp_buffer(void* temp, const struct engine* e,
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 copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
/* Copy particle data to temporary buffer */
if (props.conversion == 0) { /* No conversion */
/* Prepare some parameters */
char* temp_c = (char*)temp;
props.start_temp_c = temp_c;
/* Copy the whole thing into a buffer */
threadpool_map((struct threadpool*)&e->threadpool, io_copy_mapper, temp_c,
N, copySize, 0, (void*)&props);
} else { /* Converting particle to data */
if (props.convert_part_f != NULL) {
/* Prepare some parameters */
float* temp_f = (float*)temp;
props.start_temp_f = (float*)temp;
props.e = e;
/* Copy the whole thing into a buffer */ threadpool_map((struct threadpool*)&e->threadpool,
io_convert_part_f_mapper, temp_f, N, copySize, 0,
(void*)&props);
} else if (props.convert_part_d != NULL) {
/* Prepare some parameters */
double* temp_d = (double*)temp;
props.start_temp_d = (double*)temp;
props.e = e;
/* Copy the whole thing into a buffer */
threadpool_map((struct threadpool*)&e->threadpool,
io_convert_part_d_mapper, temp_d, N, copySize, 0,
(void*)&props);
} else if (props.convert_gpart_f != NULL) {
/* Prepare some parameters */
float* temp_f = (float*)temp;
props.start_temp_f = (float*)temp;
props.e = e;
/* Copy the whole thing into a buffer */
threadpool_map((struct threadpool*)&e->threadpool,
io_convert_gpart_f_mapper, temp_f, N, copySize, 0,
(void*)&props);
} else if (props.convert_gpart_d != NULL) {
/* Prepare some parameters */
double* temp_d = (double*)temp;
props.start_temp_d = (double*)temp;
props.e = e;
/* Copy the whole thing into a buffer */
threadpool_map((struct threadpool*)&e->threadpool,
io_convert_gpart_d_mapper, temp_d, N, copySize, 0,
(void*)&props);
} else {
error("Missing conversion function");
}
}
/* Unit conversion if necessary */
const double factor =
units_conversion_factor(internal_units, snapshot_units, props.units);
if (factor != 1.) {
/* message("Converting ! factor=%e", factor); */
if (io_is_double_precision(props.type)) {
swift_declare_aligned_ptr(double, temp_d, (double*)temp,
IO_BUFFER_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
swift_declare_aligned_ptr(float, temp_f, (float*)temp,
IO_BUFFER_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
}
}
}
void io_prepare_dm_gparts_mapper(void* restrict data, int Ndm, void* dummy) {
struct gpart* restrict gparts = (struct gpart*)data;
/* Let's give all these gparts a negative id */
for (int i = 0; i < Ndm; ++i) {
/* 0 or negative ids are not allowed */
if (gparts[i].id_or_neg_offset <= 0)
error("0 or negative ID for DM particle %i: ID=%lld", i,
gparts[i].id_or_neg_offset);
/* Set gpart type */
gparts[i].type = swift_type_dark_matter;
}
}
/**
* @brief Prepare the DM particles (in gparts) read in for the addition of the
* other particle types
*
* This function assumes that the DM particles are all at the start of the
* gparts array
*
* @param tp The current #threadpool.
* @param gparts The array of #gpart freshly read in.
* @param Ndm The number of DM particles read in.
*/
void io_prepare_dm_gparts(struct threadpool* tp, struct gpart* const gparts,
size_t Ndm) {
threadpool_map(tp, io_prepare_dm_gparts_mapper, gparts, Ndm,
sizeof(struct gpart), 0, NULL);
}
struct duplication_data {
struct part* parts;
struct gpart* gparts;
struct spart* sparts;
int Ndm;
int Ngas;
int Nstars;
};
void io_duplicate_hydro_gparts_mapper(void* restrict data, int Ngas,
void* restrict extra_data) {
struct duplication_data* temp = (struct duplication_data*)extra_data;
const int Ndm = temp->Ndm;
struct part* parts = (struct part*)data;
const ptrdiff_t offset = parts - temp->parts;
struct gpart* gparts = temp->gparts + offset;
for (int i = 0; i < Ngas; ++i) {
/* Duplicate the crucial information */
gparts[i + Ndm].x[0] = parts[i].x[0];
gparts[i + Ndm].x[1] = parts[i].x[1];
gparts[i + Ndm].x[2] = parts[i].x[2];
gparts[i + Ndm].v_full[0] = parts[i].v[0];
gparts[i + Ndm].v_full[1] = parts[i].v[1];
gparts[i + Ndm].v_full[2] = parts[i].v[2];
gparts[i + Ndm].mass = hydro_get_mass(&parts[i]);
/* Set gpart type */
gparts[i + Ndm].type = swift_type_gas;
/* Link the particles */
gparts[i + Ndm].id_or_neg_offset = -(long long)(offset + i);
parts[i].gpart = &gparts[i + Ndm];
}
}
/**
* @brief Copy every #part into the corresponding #gpart and link them.
*
* This function assumes that the DM particles are all at the start of the
* gparts array and adds the hydro particles afterwards
*
* @param tp The current #threadpool.
* @param parts The array of #part freshly read in.
* @param gparts The array of #gpart freshly read in with all the DM particles
* at the start
* @param Ngas The number of gas particles read in.
* @param Ndm The number of DM particles read in.
*/
void io_duplicate_hydro_gparts(struct threadpool* tp, struct part* const parts,
struct gpart* const gparts, size_t Ngas,
size_t Ndm) {
struct duplication_data data;
data.parts = parts;
data.gparts = gparts;
data.Ndm = Ndm;
threadpool_map(tp, io_duplicate_hydro_gparts_mapper, parts, Ngas,
sizeof(struct part), 0, &data);
}
void io_duplicate_hydro_sparts_mapper(void* restrict data, int Nstars,
void* restrict extra_data) {
struct duplication_data* temp = (struct duplication_data*)extra_data;
const int Ndm = temp->Ndm;
struct spart* sparts = (struct spart*)data;
const ptrdiff_t offset = sparts - temp->sparts;
struct gpart* gparts = temp->gparts + offset;
for (int i = 0; i < Nstars; ++i) {
/* Duplicate the crucial information */
gparts[i + Ndm].x[0] = sparts[i].x[0];
gparts[i + Ndm].x[1] = sparts[i].x[1];
gparts[i + Ndm].x[2] = sparts[i].x[2];
gparts[i + Ndm].v_full[0] = sparts[i].v[0];
gparts[i + Ndm].v_full[1] = sparts[i].v[1];
gparts[i + Ndm].v_full[2] = sparts[i].v[2];
gparts[i + Ndm].mass = sparts[i].mass;
/* Set gpart type */
gparts[i + Ndm].type = swift_type_star;
/* Link the particles */
gparts[i + Ndm].id_or_neg_offset = -(long long)(offset + i);
sparts[i].gpart = &gparts[i + Ndm];
}
}
/**
* @brief Copy every #spart into the corresponding #gpart and link them.
*
* This function assumes that the DM particles and gas particles are all at
* the start of the gparts array and adds the star particles afterwards
*
* @param tp The current #threadpool.
* @param sparts The array of #spart freshly read in.
* @param gparts The array of #gpart freshly read in with all the DM and gas
* particles at the start.
* @param Nstars The number of stars particles read in.
* @param Ndm The number of DM and gas particles read in.
*/
void io_duplicate_star_gparts(struct threadpool* tp, struct spart* const sparts, struct gpart* const gparts, size_t Nstars,
size_t Ndm) {
struct duplication_data data;
data.gparts = gparts;
data.sparts = sparts;
data.Ndm = Ndm;
threadpool_map(tp, io_duplicate_hydro_sparts_mapper, sparts, Nstars,
sizeof(struct spart), 0, &data);
}
/**
* @brief Copy every DM #gpart into the dmparts array.
*
* @param gparts The array of #gpart containing all particles.
* @param Ntot The number of #gpart.
* @param dmparts The array of #gpart containg DM particles to be filled.
* @param Ndm The number of DM particles.
*/
void io_collect_dm_gparts(const struct gpart* const gparts, size_t Ntot,
struct gpart* const dmparts, size_t Ndm) {
size_t count = 0;
/* Loop over all gparts */
for (size_t i = 0; i < Ntot; ++i) {
/* message("i=%zd count=%zd id=%lld part=%p", i, count, gparts[i].id,
* gparts[i].part); */
/* And collect the DM ones */
if (gparts[i].type == swift_type_dark_matter) {
dmparts[count] = gparts[i];
count++;
}
}
/* Check that everything is fine */
if (count != Ndm)
error("Collected the wrong number of dm particles (%zu vs. %zu expected)",
count, Ndm);
}
/**
* @brief Verify the io parameter file
*
* @param params The #swift_params
* @param N_total The total number of each particle type.
*/
void io_check_output_fields(const struct swift_params* params,
const long long N_total[3]) {
/* Create some fake particles as arguments for the writing routines */
struct part p;
struct xpart xp;
struct spart sp;
struct gpart gp;
/* Copy N_total to array with length == 6 */
const long long nr_total[swift_type_count] = {N_total[0], N_total[1], 0,
0, N_total[2], 0};
/* Loop over all particle types to check the fields */
for (int ptype = 0; ptype < swift_type_count; ptype++) {
int num_fields = 0;
struct io_props list[100];
/* Don't do anything if no particle of this kind */ if (nr_total[ptype] == 0) continue;
/* Gather particle fields from the particle structures */
switch (ptype) {
case swift_type_gas:
hydro_write_particles(&p, &xp, list, &num_fields);
num_fields += chemistry_write_particles(&p, list + num_fields);
break;
case swift_type_dark_matter:
darkmatter_write_particles(&gp, list, &num_fields);
break;
case swift_type_star:
star_write_particles(&sp, list, &num_fields);
break;
default:
error("Particle Type %d not yet supported. Aborting", ptype);
}
/* loop over each parameter */
for (int param_id = 0; param_id < params->paramCount; param_id++) {
const char* param_name = params->data[param_id].name;
char section_name[PARSER_MAX_LINE_SIZE];
/* Skip if wrong section */
sprintf(section_name, "SelectOutput:");
if (strstr(param_name, section_name) == NULL) continue;
/* Skip if wrong particle type */
sprintf(section_name, "_%s", part_type_names[ptype]);
if (strstr(param_name, section_name) == NULL) continue;
int found = 0;
/* loop over each possible output field */
for (int field_id = 0; field_id < num_fields; field_id++) {
char field_name[PARSER_MAX_LINE_SIZE];
sprintf(field_name, "SelectOutput:%s_%s", list[field_id].name,
part_type_names[ptype]);
if (strcmp(param_name, field_name) == 0) {
found = 1;
/* check if correct input */
int retParam = 0;
char str[PARSER_MAX_LINE_SIZE];
sscanf(params->data[param_id].value, "%d%s", &retParam, str);
/* Check that we have a 0 or 1 */
if (retParam != 0 && retParam != 1)
message(
"WARNING: Unexpected input for %s. Received %i but expect 0 or "
"1. ",
field_name, retParam);
/* Found it, so move to the next one. */
break;
}
}
if (!found)
message(
"WARNING: Trying to dump particle field '%s' (read from '%s') that "
"does not exist.",
param_name, params->fileName);
}
}
}
/**
* @brief Write the output field parameters file
*
* @param filename The file to write
*/
void io_write_output_field_parameter(const char* filename) {
FILE* file = fopen(filename, "w");
if (file == NULL) error("Error opening file '%s'", filename);
/* Loop over all particle types */
fprintf(file, "SelectOutput:\n");
for (int ptype = 0; ptype < swift_type_count; ptype++) {
int num_fields = 0;
struct io_props list[100];
/* Write particle fields from the particle structure */
switch (ptype) {
case swift_type_gas:
hydro_write_particles(NULL, NULL, list, &num_fields);
num_fields += chemistry_write_particles(NULL, list + num_fields);
break;
case swift_type_dark_matter:
darkmatter_write_particles(NULL, list, &num_fields);
break;
case swift_type_star:
star_write_particles(NULL, list, &num_fields);
break;
default:
break;
}
if (num_fields == 0) continue;
/* Output a header for that particle type */
fprintf(file, " # Particle Type %s\n", part_type_names[ptype]);
/* Write all the fields of this particle type */
for (int i = 0; i < num_fields; ++i)
fprintf(file, " %s_%s: 1\n", list[i].name, part_type_names[ptype]);
fprintf(file, "\n");
}
fclose(file);
printf(
"List of valid ouput fields for the particle in snapshots dumped in "
"'%s'.\n",
filename);
}