serial_io.c

/*******************************************************************************
 * 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 ( 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 (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 */