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Matthieu Schaller authoredMatthieu Schaller authored
common_io.c 17.68 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)
/* Some standard headers. */
#include <hdf5.h>
#include <math.h>
#include <stddef.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/* MPI headers. */
#ifdef WITH_MPI
#include <mpi.h>
#endif
/* This object's header. */
#include "common_io.h"
/* Local includes. */
#include "const.h"
#include "error.h"
#include "kernel_hydro.h"
#include "version.h"
const char* particle_type_names[NUM_PARTICLE_TYPES] = {
"Gas", "DM", "Boundary", "Dummy", "Star", "BH"};
/**
* @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 hdf5Type(enum 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_C_S1;
default:
error("Unknown type");
return 0;
}
}
/**
* @brief Returns the memory size of the data type
*/
size_t sizeOfType(enum 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 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 #DATA_TYPE of the attribute.
* @param data (output) The attribute read from the HDF5 group.
*
* Calls #error() if an error occurs.
*/
void readAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data) {
hid_t h_attr = 0, h_err = 0;
h_attr = H5Aopen(grp, name, H5P_DEFAULT);
if (h_attr < 0) {
error("Error while opening attribute '%s'", name);
}
h_err = H5Aread(h_attr, hdf5Type(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 #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 writeAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data,
int num) {
hid_t h_space = 0, h_attr = 0, h_err = 0;
hsize_t dim[1] = {num};
h_space = H5Screate(H5S_SIMPLE);
if (h_space < 0) {
error("Error while creating dataspace for attribute '%s'.", name);
}
h_err = H5Sset_extent_simple(h_space, 1, dim, NULL);
if (h_err < 0) {
error("Error while changing dataspace shape for attribute '%s'.", name);
}
h_attr = H5Acreate1(grp, name, hdf5Type(type), h_space, H5P_DEFAULT);
if (h_attr < 0) {
error("Error while creating attribute '%s'.", name);
}
h_err = H5Awrite(h_attr, hdf5Type(type), data);
if (h_err < 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 writeStringAttribute(hid_t grp, char* name, const char* str, int length) {
hid_t h_space = 0, h_attr = 0, h_err = 0, h_type = 0;
h_space = H5Screate(H5S_SCALAR);
if (h_space < 0) {
error("Error while creating dataspace for attribute '%s'.", name);
}
h_type = H5Tcopy(H5T_C_S1);
if (h_type < 0) {
error("Error while copying datatype 'H5T_C_S1'.");
}
h_err = H5Tset_size(h_type, length);
if (h_err < 0) {
error("Error while resizing attribute type to '%i'.", length);
}
h_attr = H5Acreate1(grp, name, h_type, h_space, H5P_DEFAULT);
if (h_attr < 0) {
error("Error while creating attribute '%s'.", name);
}
h_err = H5Awrite(h_attr, h_type, str);
if (h_err < 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 writeAttribute_d(hid_t grp, char* name, double data) {
writeAttribute(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 writeAttribute_f(hid_t grp, char* name, float data) {
writeAttribute(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 writeAttribute_i(hid_t grp, char* name, int data) {
writeAttribute(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 writeAttribute_l(hid_t grp, char* name, long data) {
writeAttribute(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 writeAttribute_s(hid_t grp, char* name, const char* str) {
writeStringAttribute(grp, name, str, strlen(str));
}
/**
* @brief Writes the current Unit System
* @param h_file The (opened) HDF5 file in which to write
* @param us The UnitSystem used in the run
*/
void writeUnitSystem(hid_t h_file, struct UnitSystem* us) {
hid_t h_grpunit = 0;
h_grpunit = H5Gcreate1(h_file, "/Units", 0);
if (h_grpunit < 0) error("Error while creating Unit System group");
writeAttribute_d(h_grpunit, "Unit mass in cgs (U_M)",
units_get_base_unit(us, UNIT_MASS));
writeAttribute_d(h_grpunit, "Unit length in cgs (U_L)",
units_get_base_unit(us, UNIT_LENGTH));
writeAttribute_d(h_grpunit, "Unit time in cgs (U_t)",
units_get_base_unit(us, UNIT_TIME));
writeAttribute_d(h_grpunit, "Unit current in cgs (U_I)",
units_get_base_unit(us, UNIT_CURRENT));
writeAttribute_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 writeCodeDescription(hid_t h_file) {
hid_t h_grpcode = 0;
h_grpcode = H5Gcreate1(h_file, "/Code", 0);
if (h_grpcode < 0) error("Error while creating code group");
writeAttribute_s(h_grpcode, "Code Version", package_version());
writeAttribute_s(h_grpcode, "Compiler Name", compiler_name());
writeAttribute_s(h_grpcode, "Compiler Version", compiler_version());
writeAttribute_s(h_grpcode, "Git Branch", git_branch());
writeAttribute_s(h_grpcode, "Git Revision", git_revision());
writeAttribute_s(h_grpcode, "HDF5 library version", hdf5_version());
#ifdef WITH_MPI
writeAttribute_s(h_grpcode, "MPI library", mpi_version());
#ifdef HAVE_METIS
writeAttribute_s(h_grpcode, "METIS library version", metis_version());
#endif
#else
writeAttribute_s(h_grpcode, "MPI library", "Non-MPI version of SWIFT");
#endif
H5Gclose(h_grpcode);
}
/* ------------------------------------------------------------------------------------------------
* This part writes the XMF file descriptor enabling a visualisation through
* ParaView
* ------------------------------------------------------------------------------------------------
*/
/**
* @brief Prepares the XMF file for the new entry
*
* Creates a temporary file on the disk in order to copy the right lines.
*
* @todo Use a proper XML library to avoid stupid copies.
*/
FILE* prepareXMFfile(const char* baseName) {
char buffer[1024];
char fileName[FILENAME_BUFFER_SIZE];
char tempFileName[FILENAME_BUFFER_SIZE];
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s.xmf", baseName);
snprintf(tempFileName, FILENAME_BUFFER_SIZE, "%s_temp.xmf", baseName);
FILE* xmfFile = fopen(fileName, "r");
FILE* tempFile = fopen(tempFileName, "w");
if (xmfFile == NULL) error("Unable to open current XMF file.");
if (tempFile == NULL) error("Unable to open temporary file.");
/* First we make a temporary copy of the XMF file and count the lines */
int counter = 0;
while (fgets(buffer, 1024, xmfFile) != NULL) {
counter++;
fprintf(tempFile, "%s", buffer);
}
fclose(tempFile);
fclose(xmfFile);
/* We then copy the XMF file back up to the closing lines */
xmfFile = fopen(fileName, "w");
tempFile = fopen(tempFileName, "r");
if (xmfFile == NULL) error("Unable to open current XMF file.");
if (tempFile == NULL) error("Unable to open temporary file.");
int i = 0;
while (fgets(buffer, 1024, tempFile) != NULL && i < counter - 3) {
i++;
fprintf(xmfFile, "%s", buffer);
}
fprintf(xmfFile, "\n");
fclose(tempFile);
remove(tempFileName);
return xmfFile;
}
/**
* @brief Writes the begin of the XMF file
*
* @todo Exploit the XML nature of the XMF format to write a proper XML writer
*and simplify all the XMF-related stuff.
*/
void createXMFfile(const char* baseName) {
char fileName[FILENAME_BUFFER_SIZE];
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s.xmf", baseName);
FILE* xmfFile = fopen(fileName, "w");
fprintf(xmfFile, "<?xml version=\"1.0\" ?> \n");
fprintf(xmfFile, "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []> \n");
fprintf(
xmfFile,
"<Xdmf xmlns:xi=\"http://www.w3.org/2003/XInclude\" Version=\"2.1\">\n");
fprintf(xmfFile, "<Domain>\n");
fprintf(xmfFile,
"<Grid Name=\"TimeSeries\" GridType=\"Collection\" "
"CollectionType=\"Temporal\">\n\n");
fprintf(xmfFile, "</Grid>\n");
fprintf(xmfFile, "</Domain>\n");
fprintf(xmfFile, "</Xdmf>\n");
fclose(xmfFile);
}
/**
* @brief Writes the part of the XMF entry presenting the geometry of the
*snapshot
*
* @param xmfFile The file to write in.
* @param hdfFileName The name of the HDF5 file corresponding to this output.
* @param time The current simulation time.
*/
void writeXMFoutputheader(FILE* xmfFile, char* hdfFileName, float time) {
/* Write end of file */
fprintf(xmfFile, "<!-- XMF description for file: %s -->\n", hdfFileName);
fprintf(xmfFile,
"<Grid GridType=\"Collection\" CollectionType=\"Spatial\">\n");
fprintf(xmfFile, "<Time Type=\"Single\" Value=\"%f\"/>\n", time);
}
/**
* @brief Writes the end of the XMF file (closes all open markups)
*
* @param xmfFile The file to write in.
* @param output The number of this output.
* @param time The current simulation time.
*/
void writeXMFoutputfooter(FILE* xmfFile, int output, float time) {
/* Write end of the section of this time step */
fprintf(xmfFile,
"\n</Grid> <!-- End of meta-data for output=%03i, time=%f -->\n",
output, time);
fprintf(xmfFile, "\n</Grid> <!-- timeSeries -->\n");
fprintf(xmfFile, "</Domain>\n");
fprintf(xmfFile, "</Xdmf>\n");
fclose(xmfFile);
}
void writeXMFgroupheader(FILE* xmfFile, char* hdfFileName, size_t N,
enum PARTICLE_TYPE ptype) {
fprintf(xmfFile, "\n<Grid Name=\"%s\" GridType=\"Uniform\">\n",
particle_type_names[ptype]);
fprintf(xmfFile,
"<Topology TopologyType=\"Polyvertex\" Dimensions=\"%zi\"/>\n", N);
fprintf(xmfFile, "<Geometry GeometryType=\"XYZ\">\n");
fprintf(xmfFile,
"<DataItem Dimensions=\"%zi 3\" NumberType=\"Double\" "
"Precision=\"8\" "
"Format=\"HDF\">%s:/PartType%d/Coordinates</DataItem>\n",
N, hdfFileName, ptype);
fprintf(xmfFile,
"</Geometry>\n <!-- Done geometry for %s, start of particle fields "
"list -->\n",
particle_type_names[ptype]);
}
void writeXMFgroupfooter(FILE* xmfFile, enum PARTICLE_TYPE ptype) {
fprintf(xmfFile, "</Grid> <!-- End of meta-data for parttype=%s -->\n",
particle_type_names[ptype]);
}
/**
* @brief Writes the lines corresponding to an array of the HDF5 output
*
* @param xmfFile The file in which to write
* @param fileName The name of the HDF5 file associated to this XMF descriptor.
* @param partTypeGroupName The name of the group containing the particles in
*the HDF5 file.
* @param name The name of the array in the HDF5 file.
* @param N The number of particles.
* @param dim The dimension of the quantity (1 for scalars, 3 for vectors).
* @param type The type of the data to write.
*
* @todo Treat the types in a better way.
*/
void writeXMFline(FILE* xmfFile, char* fileName, char* partTypeGroupName,
char* name, size_t N, int dim, enum DATA_TYPE type) {
fprintf(xmfFile,
"<Attribute Name=\"%s\" AttributeType=\"%s\" Center=\"Node\">\n",
name, dim == 1 ? "Scalar" : "Vector");
if (dim == 1)
fprintf(xmfFile, "<DataItem Dimensions=\"%zi\" NumberType=\"Double\" "
"Precision=\"%d\" Format=\"HDF\">%s:%s/%s</DataItem>\n",
N, type == FLOAT ? 4 : 8, fileName, partTypeGroupName, name);
else
fprintf(xmfFile,
"<DataItem Dimensions=\"%zi %d\" NumberType=\"Double\" "
"Precision=\"%d\" Format=\"HDF\">%s:%s/%s</DataItem>\n",
N, dim, type == FLOAT ? 4 : 8, fileName, partTypeGroupName, name);
fprintf(xmfFile, "</Attribute>\n");
}
/**
* @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 gparts The array of #gpart freshly read in.
* @param Ndm The number of DM particles read in.
*/
void prepare_dm_gparts(struct gpart* const gparts, size_t Ndm) {
/* Let's give all these gparts a negative id */
for (size_t i = 0; i < Ndm; ++i) {
/* 0 or negative ids are not allowed */
if (gparts[i].id <= 0)
error("0 or negative ID for DM particle %zd: ID=%lld", i, gparts[i].id);
gparts[i].id = -gparts[i].id;
}
}
/**
* @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 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 duplicate_hydro_gparts(struct part* const parts,
struct gpart* const gparts, size_t Ngas,
size_t Ndm) {
for (size_t 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 = parts[i].mass;
/* Link the particles */
gparts[i + Ndm].part = &parts[i];
parts[i].gpart = &gparts[i + Ndm];
}
}
/** * @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 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].id < 0LL) {
memcpy(&dmparts[count], &gparts[i], sizeof(struct gpart));
dmparts[count].id = -dmparts[count].id;
count++;
}
}
/* Check that everything is fine */
if (count != Ndm)
error("Collected the wrong number of dm particles (%zd vs. %zd expected)",
count, Ndm);
}
#endif