diff --git a/src/single_io.c b/src/single_io.c new file mode 100644 index 0000000000000000000000000000000000000000..485cb60aa51140682ef868d0323b31f00ce4ed9e --- /dev/null +++ b/src/single_io.c @@ -0,0 +1,503 @@ +/******************************************************************************* + * This file is part of SWIFT. + * Coypright (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 <stdio.h> +#include <stdlib.h> +#include <string.h> +#include <stddef.h> +#include <hdf5.h> +#include <math.h> + +#include "const.h" +#include "cycle.h" +#include "lock.h" +#include "task.h" +#include "part.h" +#include "space.h" +#include "scheduler.h" +#include "engine.h" +#include "error.h" +#include "kernel.h" +#include "common_io.h" + + + +/*----------------------------------------------------------------------------- + * Routines reading an IC file + *-----------------------------------------------------------------------------*/ + +/** + * @brief Reads a data array from a given HDF5 group. + * + * @param grp The group from which to read. + * @param name The name of the array to read. + * @param type The #DATA_TYPE of the attribute. + * @param N The number of particles. + * @param dim The dimension of the data (1 for scalar, 3 for vector) + * @param part_c A (char*) pointer on the first occurence of the field of interest in the parts array + * @param importance If COMPULSORY, the data must be present in the IC file. If OPTIONAL, the array will be zeroed when the data is not present. + * + * @todo A better version using HDF5 hyperslabs to read the file directly into the part array + * will be written once the strucutres have been stabilized. + * + * Calls #error() if an error occurs. + */ +void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N, int dim, char* part_c, enum DATA_IMPORTANCE importance) +{ + hid_t h_data=0, h_err=0, h_type=0; + htri_t exist=0; + void* temp; + int i=0; + const size_t typeSize = sizeOfType(type); + const size_t copySize = typeSize * dim; + const size_t partSize = sizeof(struct part); + char* temp_c = 0; + + /* Check whether the dataspace exists or not */ + exist = H5Lexists(grp, name, 0); + if(exist < 0) + { + error( "Error while checking the existence of data set '%s'." , name ); + } + else if(exist == 0) + { + if(importance == COMPULSORY) + { + error( "Compulsory data set '%s' not present in the file." , name ); + } + else + { + /* message("Optional data set '%s' not present. Zeroing this particle field...", name); */ + + for(i=0; i<N; ++i) + memset(part_c+i*partSize, 0, copySize); + + return; + } + } + + /* message( "Reading %s '%s' array...", importance == COMPULSORY ? "compulsory": "optional ", name); */ + + /* Open data space */ + h_data = H5Dopen1(grp, name); + if(h_data < 0) + { + error( "Error while opening data space '%s'." , name ); + } + + /* Check data type */ + h_type = H5Dget_type(h_data); + if(h_type < 0) + error("Unable to retrieve data type from the file"); + if(!H5Tequal(h_type, hdf5Type(type))) + error("Non-matching types between the code and the file"); + + /* Allocate temporary buffer */ + temp = malloc(N * dim * sizeOfType(type)); + 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 */ + h_err = H5Dread(h_data, hdf5Type(type), H5S_ALL, H5S_ALL, H5P_DEFAULT, temp); + if(h_err < 0) + { + error( "Error while reading data array '%s'." , name ); + } + + /* Copy temporary buffer to particle data */ + temp_c = temp; + for(i=0; i<N; ++i) + memcpy(part_c+i*partSize, &temp_c[i*copySize], copySize); + + /* Free and close everything */ + free(temp); + H5Tclose(h_type); + H5Dclose(h_data); +} + +/** + * @brief A helper macro to call the readArrayBackEnd function more easily. + * + * @param grp The group from which to read. + * @param name The name of the array to read. + * @param type The #DATA_TYPE of the attribute. + * @param N The number of particles. + * @param dim The dimension of the data (1 for scalar, 3 for vector) + * @param part The array of particles to fill + * @param field The name of the field (C code name as defined in part.h) to fill + * @param importance Is the data compulsory or not + * + */ +#define readArray(grp, name, type, N, dim, part, field, importance) readArrayBackEnd(grp, name, type, N, dim, (char*)(&(part[0]).field), importance) + +/** + * @brief Reads an HDF5 initial condition file (GADGET-3 type) + * + * @param fileName The file to read. + * @param dim (output) The dimension of the volume read from the file. + * @param parts (output) The array of #part read from the file. + * @param N (output) The number of particles read from the file. + * @param periodic (output) 1 if the volume is periodic, 0 if not. + * + * 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 snaphsots distributed in more than one file. + * + * Calls #error() if an error occurs. + * + */ +void read_ic_single ( char* fileName, double dim[3], struct part **parts, int* N, int* periodic) +{ + hid_t h_file=0, h_grp=0; + double boxSize[3]={0.0,-1.0,-1.0}; /* GADGET has only cubic boxes (in cosmological mode) */ + int numParticles[6]={0}; /* GADGET has 6 particle types. We only keep the type 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 runtime parameters..."); */ + h_grp = H5Gopen1(h_file, "/RuntimePars"); + if(h_grp < 0) + error("Error while opening runtime parameters\n"); + + /* Read the relevant information */ + readAttribute(h_grp, "PeriodicBoundariesOn", INT, periodic); + + /* Close runtime parameters */ + H5Gclose(h_grp); + + /* Open header to read simulation properties */ + /* message("Reading file header..."); */ + h_grp = H5Gopen1(h_file, "/Header"); + if(h_grp < 0) + error("Error while opening file header\n"); + + /* Read the relevant information and print status */ + readAttribute(h_grp, "BoxSize", DOUBLE, boxSize); + readAttribute(h_grp, "NumPart_Total", UINT, numParticles); + + *N = numParticles[0]; + dim[0] = boxSize[0]; + dim[1] = ( boxSize[1] < 0 ) ? boxSize[0] : boxSize[1]; + dim[2] = ( boxSize[2] < 0 ) ? boxSize[0] : boxSize[2]; + + /* 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); + + /* Allocate memory to store particles */ + if(posix_memalign( (void*)parts , part_align , *N * sizeof(struct part)) != 0) + error("Error while allocating memory for particles"); + bzero( *parts , *N * sizeof(struct part) ); + + /* message("Allocated %8.2f MB for particles.", *N * sizeof(struct part) / (1024.*1024.)); */ + + /* Open SPH particles group */ + /* message("Reading particle arrays..."); */ + h_grp = H5Gopen1(h_file, "/PartType0"); + if(h_grp < 0) + error( "Error while opening particle group.\n"); + + /* Read arrays */ + readArray(h_grp, "Coordinates", DOUBLE, *N, 3, *parts, x, COMPULSORY); + readArray(h_grp, "Velocities", FLOAT, *N, 3, *parts, v, COMPULSORY); + readArray(h_grp, "Masses", FLOAT, *N, 1, *parts, mass, COMPULSORY); + readArray(h_grp, "SmoothingLength", FLOAT, *N, 1, *parts, h, COMPULSORY); + readArray(h_grp, "InternalEnergy", FLOAT, *N, 1, *parts, u, COMPULSORY); + readArray(h_grp, "ParticleIDs", ULONGLONG, *N, 1, *parts, id, COMPULSORY); + readArray(h_grp, "TimeStep", FLOAT, *N, 1, *parts, dt, OPTIONAL); + readArray(h_grp, "Acceleration", FLOAT, *N, 3, *parts, a, OPTIONAL); + readArray(h_grp, "Density", FLOAT, *N, 1, *parts, rho, OPTIONAL ); + + /* Close particle group */ + H5Gclose(h_grp); + + /* message("Done Reading particles..."); */ + + /* Close file */ + H5Fclose(h_file); +} + + +/*----------------------------------------------------------------------------- + * Routines writing an output file + *-----------------------------------------------------------------------------*/ + +/** + * @brief Writes a data array in given HDF5 group. + * + * @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 name The name of the array to write. + * @param type The #DATA_TYPE of the array. + * @param N The number of particles to write. + * @param dim The dimension of the data (1 for scalar, 3 for vector) + * @param part_c A (char*) pointer on the first occurence of the field of interest in the parts array + * @param us The UnitSystem currently in use + * @param convFactor The UnitConversionFactor for this array + * + * @todo A better version using HDF5 hyperslabs to write the file directly from the part array + * will be written once the strucutres have been stabilized. + * + * Calls #error() if an error occurs. + */ +void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name, enum DATA_TYPE type, int N, int dim, char* part_c, struct UnitSystem* us, enum UnitConversionFactor convFactor) +{ + hid_t h_data=0, h_err=0, h_space=0; + void* temp = 0; + int i=0, rank=0; + const size_t typeSize = sizeOfType(type); + const size_t copySize = typeSize * dim; + const size_t partSize = sizeof(struct part); + char* temp_c = 0; + hsize_t shape[2]; + char buffer[150]; + + /* message("Writing '%s' array...", name); */ + + /* Allocate temporary buffer */ + temp = malloc(N * dim * sizeOfType(type)); + if(temp == NULL) + error("Unable to allocate memory for temporary buffer"); + + /* Copy particle data to temporary buffer */ + temp_c = temp; + for(i=0; i<N; ++i) + memcpy(&temp_c[i*copySize], part_c+i*partSize, copySize); + + /* Create data space */ + h_space = H5Screate(H5S_SIMPLE); + if(h_space < 0) + { + error( "Error while creating data space for field '%s'." , name ); + } + + if(dim > 1) + { + rank = 2; + shape[0] = N; shape[1] = dim; + } + else + { + rank = 1; + shape[0] = N; shape[1] = 0; + } + + /* Change shape of data space */ + h_err = H5Sset_extent_simple(h_space, rank, shape, NULL); + if(h_err < 0) + { + error( "Error while changing data space shape for field '%s'." , name ); + } + + /* Create dataset */ + h_data = H5Dcreate1(grp, name, hdf5Type(type), h_space, H5P_DEFAULT); + if(h_data < 0) + { + error( "Error while creating dataspace '%s'." , name ); + } + + /* Write temporary buffer to HDF5 dataspace */ + h_err = H5Dwrite(h_data, hdf5Type(type), h_space, H5S_ALL, H5P_DEFAULT, temp); + if(h_err < 0) + { + error( "Error while writing data array '%s'." , name ); + } + + /* Write XMF description for this data set */ + writeXMFline(xmfFile, fileName, name, N, dim, type); + + /* Write unit conversion factors for this data set */ + conversionString( buffer, us, convFactor ); + writeAttribute_d( h_data, "CGS conversion factor", conversionFactor( us, convFactor ) ); + writeAttribute_f( h_data, "h-scale exponant", hFactor( us, convFactor ) ); + writeAttribute_f( h_data, "a-scale exponant", aFactor( us, convFactor ) ); + writeAttribute_s( h_data, "Conversion factor", buffer ); + + /* Free and close everything */ + free(temp); + H5Dclose(h_data); + H5Sclose(h_space); +} + +/** + * @brief A helper macro to call the readArrayBackEnd function more easily. + * + * @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 name The name of the array to write. + * @param type The #DATA_TYPE of the array. + * @param N The number of particles to write. + * @param dim The dimension of the data (1 for scalar, 3 for vector) + * @param part A (char*) pointer on the first occurence of the field of interest in the parts array + * @param field The name (code name) of the field to read from. + * @param us The UnitSystem currently in use + * @param convFactor The UnitConversionFactor for this array + * + */ +#define writeArray(grp, fileName, xmfFile, name, type, N, dim, part, field, us, convFactor) writeArrayBackEnd(grp, fileName, xmfFile, name, type, N, dim, (char*)(&(part[0]).field), us, convFactor) + +/** + * @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor + * + * @param e The engine containing all the system. + * @param us The UnitSystem used for the conversion of units in the output + * + * 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, struct UnitSystem* us) +{ + + hid_t h_file=0, h_grp=0; + int N = e->s->nr_parts; + int periodic = e->s->periodic; + int numParticles[6]={N,0}; + int numParticlesHighWord[6]={0}; + int numFiles = 1; + struct part* parts = e->s->parts; + FILE* xmfFile = 0; + static int outputCount = 0; + + /* File name */ + char fileName[200]; + sprintf(fileName, "output_%03i.hdf5", outputCount); + + /* First time, we need to create the XMF file */ + if(outputCount == 0) + createXMFfile(); + + /* Prepare the XMF file for the new entry */ + xmfFile = prepareXMFfile(); + + /* Write the part corresponding to this specific output */ + writeXMFheader(xmfFile, N, 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 runtime parameters..."); */ + h_grp = H5Gcreate1(h_file, "/RuntimePars", 0); + if(h_grp < 0) + error("Error while creating runtime parameters group\n"); + + /* Write the relevant information */ + writeAttribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1); + + /* Close runtime parameters */ + H5Gclose(h_grp); + + /* Open header to write simulation properties */ + /* message("Writing file header..."); */ + h_grp = H5Gcreate1(h_file, "/Header", 0); + if(h_grp < 0) + error("Error while creating file header\n"); + + /* Print the relevant information and print status */ + writeAttribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3); + writeAttribute(h_grp, "NumPart_ThisFile", UINT, numParticles, 6); + writeAttribute(h_grp, "Time", DOUBLE, &e->time, 1); + + /* GADGET-2 legacy values */ + writeAttribute(h_grp, "NumPart_Total", UINT, numParticles, 6); + writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord, 6); + double MassTable[6] = {0., 0., 0., 0., 0., 0.}; + writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, 6); + writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, numParticlesHighWord, 6); + writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1); + + /* Close header */ + H5Gclose(h_grp); + + /* Print the SPH parameters */ + writeSPHflavour(h_file); + + /* Print the system of Units */ + writeUnitSystem(h_file, us); + + /* Create SPH particles group */ + /* message("Writing particle arrays..."); */ + h_grp = H5Gcreate1(h_file, "/PartType0", 0); + if(h_grp < 0) + error( "Error while creating particle group.\n"); + + /* Write arrays */ + writeArray(h_grp, fileName, xmfFile, "Coordinates", DOUBLE, N, 3, parts, x, us, UNIT_CONV_LENGTH); + writeArray(h_grp, fileName, xmfFile, "Velocities", FLOAT, N, 3, parts, v, us, UNIT_CONV_SPEED); + writeArray(h_grp, fileName, xmfFile, "Masses", FLOAT, N, 1, parts, mass, us, UNIT_CONV_MASS); + writeArray(h_grp, fileName, xmfFile, "SmoothingLength", FLOAT, N, 1, parts, h, us, UNIT_CONV_LENGTH); + writeArray(h_grp, fileName, xmfFile, "InternalEnergy", FLOAT, N, 1, parts, u, us, UNIT_CONV_ENERGY_PER_UNIT_MASS); + writeArray(h_grp, fileName, xmfFile, "ParticleIDs", ULONGLONG, N, 1, parts, id, us, UNIT_CONV_NO_UNITS); + writeArray(h_grp, fileName, xmfFile, "TimeStep", FLOAT, N, 1, parts, dt, us, UNIT_CONV_TIME); + writeArray(h_grp, fileName, xmfFile, "Acceleration", FLOAT, N, 3, parts, a, us, UNIT_CONV_ACCELERATION); + writeArray(h_grp, fileName, xmfFile, "Density", FLOAT, N, 1, parts, rho, us, UNIT_CONV_DENSITY); + + /* Close particle group */ + H5Gclose(h_grp); + + /* Write LXMF file descriptor */ + writeXMFfooter(xmfFile); + + /* message("Done writing particles..."); */ + + /* Close file */ + H5Fclose(h_file); + + ++outputCount; +} + + +#endif /* HAVE_HDF5 */ + + diff --git a/src/single_io.h b/src/single_io.h new file mode 100644 index 0000000000000000000000000000000000000000..3cc58a46cc5398affd63e5d7e22b317ae79db3f5 --- /dev/null +++ b/src/single_io.h @@ -0,0 +1,28 @@ +/******************************************************************************* + * This file is part of SWIFT. + * Coypright (c) 2012 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/>. + * + ******************************************************************************/ + + +#if defined(HAVE_HDF5) && !defined(WITH_MPI) + +void read_ic_single ( char* fileName, double dim[3], struct part **parts, int* N, int* periodic); + +void write_output_single ( struct engine* e, struct UnitSystem* us ); + +#endif +