/*******************************************************************************
 * 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) && !defined(HAVE_PARALLEL_HDF5)

/* Some standard headers. */
#include <hdf5.h>
#include <math.h>
#include <mpi.h>
#include <stddef.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>

/* This object's header. */
#include "serial_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 "error.h"
#include "fof_io.h"
#include "gravity_io.h"
#include "gravity_properties.h"
#include "hydro_io.h"
#include "hydro_properties.h"
#include "io_properties.h"
#include "memuse.h"
#include "output_list.h"
#include "output_options.h"
#include "part.h"
#include "part_type.h"
#include "rt_io.h"
#include "sink_io.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 grp The group from which to read.
 * @param props The #io_props of the field to read
 * @param N The number of particles to read on this rank.
 * @param N_total The total number of particles on all ranks.
 * @param offset The offset position where this rank starts reading.
 * @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 to use for cleaning.
 * @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 read_array_serial(hid_t grp, const struct io_props props, size_t N,
                       long long N_total, long long offset,
                       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(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 {
      for (size_t i = 0; i < N; ++i)
        memset(props.field + i * props.partSize, 0, copySize);
      return;
    }
  }

  /* message( "Reading %s '%s' array...", importance == COMPULSORY ? */
  /* 	   "compulsory": "optional  ", name); */
  /* fflush(stdout); */

  /* Open data space */
  const hid_t h_data = H5Dopen(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");

  /* Prepare information for hyper-slab */
  hsize_t shape[2], offsets[2];
  int rank;
  if (props.dimension > 1) {
    rank = 2;
    shape[0] = N;
    shape[1] = props.dimension;
    offsets[0] = offset;
    offsets[1] = 0;
  } else {
    rank = 2;
    shape[0] = N;
    shape[1] = 1;
    offsets[0] = offset;
    offsets[1] = 0;
  }

  /* Create data space in memory */
  const hid_t h_memspace = H5Screate_simple(rank, shape, NULL);

  /* Select hyper-slab in file */
  const hid_t h_filespace = H5Dget_space(h_data);
  H5Sselect_hyperslab(h_filespace, H5S_SELECT_SET, offsets, NULL, shape, NULL);

  /* 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), h_memspace,
                              h_filespace, H5P_DEFAULT, temp);
  if (h_err < 0) error("Error while reading data array '%s'.", props.name);

  /* Unit conversion if necessary */
  const double factor =
      units_conversion_factor(ic_units, internal_units, props.units);
  if (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] *= 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] *= factor;
      }

#ifdef SWIFT_DEBUG_CHECKS
      /* The two possible errors: larger than float or smaller
       * than float precision. */
      if (factor * maximum > FLT_MAX) {
        error("Unit conversion results in numbers larger than floats");
      } else if (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);
  H5Sclose(h_filespace);
  H5Sclose(h_memspace);
  H5Dclose(h_data);
}

void prepare_array_serial(
    const struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
    char* partTypeGroupName, const struct io_props props,
    unsigned long long N_total,
    const enum lossy_compression_schemes lossy_compression,
    const struct unit_system* internal_units,
    const struct unit_system* 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);

  /* Decide what chunk size to use based on compression */
  int log2_chunk_size = 20;

  int rank = 0;
  hsize_t shape[2];
  hsize_t chunk_shape[2];
  if (props.dimension > 1) {
    rank = 2;
    shape[0] = N_total;
    shape[1] = props.dimension;
    chunk_shape[0] = 1 << log2_chunk_size;
    chunk_shape[1] = props.dimension;
  } else {
    rank = 1;
    shape[0] = N_total;
    shape[1] = 0;
    chunk_shape[0] = 1 << log2_chunk_size;
    chunk_shape[1] = 0;
  }

  /* Make sure the chunks are not larger than the dataset */
  if (chunk_shape[0] > N_total) chunk_shape[0] = N_total;

  /* 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 type */
  hid_t h_type = H5Tcopy(io_hdf5_type(props.type));

  /* Dataset properties */
  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);

  /* Are we imposing some form of lossy compression filter? */
  if (lossy_compression != compression_write_lossless)
    set_hdf5_lossy_compression(&h_prop, &h_type, lossy_compression, 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);
  }

  /* 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);

  /* Create dataset */
  const hid_t h_data = H5Dcreate(grp, props.name, h_type, h_space, H5P_DEFAULT,
                                 h_prop, H5P_DEFAULT);
  if (h_data < 0) error("Error while creating dataspace '%s'.", props.name);

  /* Write XMF description for this data set */
  if (xmfFile != NULL)
    xmf_write_line(xmfFile, fileName, partTypeGroupName, props.name, N_total,
                   props.dimension, props.type);

  /* Write unit conversion factors for this data set */
  char buffer[FIELD_BUFFER_SIZE] = {0};
  units_cgs_conversion_string(buffer, snapshot_units, props.units,
                              props.scale_factor_exponent);
  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.f);
  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 physical CGS (including cosmological corrections)",
      factor * pow(e->cosmology->a, props.scale_factor_exponent));

#ifdef SWIFT_DEBUG_CHECKS
  if (strlen(props.description) == 0)
    error("Invalid (empty) description of the field '%s'", props.name);
#endif

  /* Write the full description */
  io_write_attribute_s(h_data, "Description", props.description);

  /* Close everything */
  H5Tclose(h_type);
  H5Pclose(h_prop);
  H5Dclose(h_data);
  H5Sclose(h_space);
}

/**
 * @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 N_total The total number of particles on all ranks.
 * @param offset The offset position where this rank starts writing.
 * @param lossy_compression Lossy compression filter to apply.
 * @param mpi_rank The MPI rank of this node
 * @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 write_array_serial(const struct engine* e, hid_t grp, char* fileName,
                        FILE* xmfFile, char* partTypeGroupName,
                        const struct io_props props, size_t N,
                        long long N_total, int mpi_rank, long long offset,
                        const enum lossy_compression_schemes lossy_compression,
                        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); */

  /* Prepare the arrays in the file */
  if (mpi_rank == 0)
    prepare_array_serial(e, grp, fileName, xmfFile, partTypeGroupName, props,
                         N_total, lossy_compression, internal_units,
                         snapshot_units);

  /* 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);

  /* Construct information for the hyper-slab */
  int rank;
  hsize_t shape[2];
  hsize_t offsets[2];
  if (props.dimension > 1) {
    rank = 2;
    shape[0] = N;
    shape[1] = props.dimension;
    offsets[0] = offset;
    offsets[1] = 0;
  } else {
    rank = 1;
    shape[0] = N;
    shape[1] = 0;
    offsets[0] = offset;
    offsets[1] = 0;
  }

  /* Create data space in memory */
  const hid_t h_memspace = H5Screate(H5S_SIMPLE);
  if (h_memspace < 0)
    error("Error while creating data space (memory) for field '%s'.",
          props.name);

  /* Change shape of memory data space */
  hid_t h_err = H5Sset_extent_simple(h_memspace, rank, shape, NULL);
  if (h_err < 0)
    error("Error while changing data space (memory) shape for field '%s'.",
          props.name);

  /* Open pre-existing data set */
  const hid_t h_data = H5Dopen(grp, props.name, H5P_DEFAULT);
  if (h_data < 0) error("Error while opening dataset '%s'.", props.name);

  /* Select data space in that data set */
  const hid_t h_filespace = H5Dget_space(h_data);
  H5Sselect_hyperslab(h_filespace, H5S_SELECT_SET, offsets, NULL, shape, NULL);

  /* Write temporary buffer to HDF5 dataspace */
  h_err = H5Dwrite(h_data, io_hdf5_type(props.type), h_memspace, h_filespace,
                   H5P_DEFAULT, temp);
  if (h_err < 0) error("Error while writing data array '%s'.", props.name);

  /* Free and close everything */
  swift_free("writebuff", temp);
  H5Dclose(h_data);
  H5Sclose(h_memspace);
  H5Sclose(h_filespace);
}

/**
 * @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 read from the file.
 * @param parts (output) The array of #part (gas particles) read from the file.
 * @param gparts (output) The array of #gpart read from the file.
 * @param sinks (output) Array of #sink particles.
 * @param sparts (output) Array of #spart particles.
 * @param bparts (output) Array of #bpart particles.
 * @param Ngas (output) The number of #part read from the file on that node.
 * @param Ngparts (output) The number of #gpart read from the file on that node.
 * @param Ngparts_background (output) The number of background #gpart (type 2)
 * read from the file on that node.
 * @param Nsinks (output) The number of #sink read from the file on that node.
 * @param Nstars (output) The number of #spart read from the file on that node.
 * @param Nblackholes (output) The number of #bpart read from the file on that
 * node.
 * @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_sink Are we reading sink particles ?
 * @param with_stars Are we reading star particles ?
 * @param with_black_holes Are we reading black hole particles ?
 * @param with_cosmology Are we running with cosmology ?
 * @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.
 * @param mpi_rank The MPI rank of this node
 * @param mpi_size The number of MPI ranks
 * @param comm The MPI communicator
 * @param info The MPI information object
 * @param n_threads The number of threads to use for local operations.
 * @param dry_run If 1, don't read the particle. Only allocates the arrays.
 * @param remap_ids Are we ignoring the ICs' IDs and remapping them to [1, N[ ?
 *
 * 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_serial(char* fileName, const struct unit_system* internal_units,
                    double dim[3], struct part** parts, struct gpart** gparts,
                    struct sink** sinks, struct spart** sparts,
                    struct bpart** bparts, size_t* Ngas, size_t* Ngparts,
                    size_t* Ngparts_background, size_t* Nsinks, size_t* Nstars,
                    size_t* Nblackholes, int* flag_entropy, int with_hydro,
                    int with_gravity, int with_sink, int with_stars,
                    int with_black_holes, int with_cosmology, int cleanup_h,
                    int cleanup_sqrt_a, double h, double a, int mpi_rank,
                    int mpi_size, MPI_Comm comm, MPI_Info info, int n_threads,
                    int dry_run, int remap_ids) {

  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};
  long long N_total[swift_type_count] = {0};
  long long offset[swift_type_count] = {0};
  int dimension = 3; /* Assume 3D if nothing is specified */
  size_t Ndm = 0;
  size_t Ndm_background = 0;
  struct unit_system* ic_units =
      (struct unit_system*)malloc(sizeof(struct unit_system));

  /* Initialise counters */
  *Ngas = 0, *Ngparts = 0, *Ngparts_background = 0, *Nstars = 0,
  *Nblackholes = 0, *Nsinks = 0;

  /* First read some information about the content */
  if (mpi_rank == 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' for initial read.", 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);

    /* Check that the user is not doing something silly when they e.g. restart
     * from a snapshot by asserting that the current scale-factor (from
     * parameter file) and the redshift in the header are consistent */
    if (with_cosmology) {
      io_assert_valid_header_cosmology(h_grp, a);
    }

    for (int ptype = 0; ptype < swift_type_count; ++ptype)
      N_total[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 %lld particles in a %speriodic box of size [%f %f %f].",
       N_total, (periodic ? "": "non-"), dim[0], dim[1], dim[2]); */

    /* Close header */
    H5Gclose(h_grp);

    /* Read the unit system used in the ICs */
    if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
    io_read_unit_system(h_file, ic_units, internal_units, mpi_rank);

    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);
    }

    /* Close file */
    H5Fclose(h_file);
  }

  /* 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);

  /* Now need to broadcast that information to all ranks. */
  MPI_Bcast(flag_entropy, 1, MPI_INT, 0, comm);
  MPI_Bcast(N_total, swift_type_count, MPI_LONG_LONG_INT, 0, comm);
  MPI_Bcast(dim, 3, MPI_DOUBLE, 0, comm);
  MPI_Bcast(ic_units, sizeof(struct unit_system), MPI_BYTE, 0, comm);

  /* Divide the particles among the tasks. */
  for (int ptype = 0; ptype < swift_type_count; ++ptype) {
    offset[ptype] = mpi_rank * N_total[ptype] / mpi_size;
    N[ptype] = (mpi_rank + 1) * N_total[ptype] / mpi_size - offset[ptype];
  }

  /* Allocate memory to store SPH particles */
  if (with_hydro) {
    *Ngas = N[0];
    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 sinks particles */
  if (with_sink) {
    *Nsinks = N[swift_type_sink];
    if (swift_memalign("sinks", (void**)sinks, sink_align,
                       *Nsinks * sizeof(struct sink)) != 0)
      error("Error while allocating memory for sink particles");
    bzero(*sinks, *Nsinks * sizeof(struct sink));
  }

  /* Allocate memory to store stars 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 stars 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 black hole particles");
    bzero(*bparts, *Nblackholes * sizeof(struct bpart));
  }

  /* Allocate memory to store all gravity  particles */
  if (with_gravity) {
    Ndm = N[swift_type_dark_matter];
    Ndm_background = N[swift_type_dark_matter_background];
    *Ngparts = (with_hydro ? N[swift_type_gas] : 0) +
               N[swift_type_dark_matter] +
               N[swift_type_dark_matter_background] +
               (with_sink ? N[swift_type_sink] : 0) +
               (with_stars ? N[swift_type_stars] : 0) +
               (with_black_holes ? N[swift_type_black_hole] : 0);
    *Ngparts_background = Ndm_background;
    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); */

  /* For dry runs, only need to do this on rank 0 */
  if (dry_run) mpi_size = 1;

  /* Now loop over ranks and read the data */
  for (int rank = 0; rank < mpi_size; ++rank) {

    /* Is it this rank's turn to read ? */
    if (rank == mpi_rank) {

      h_file = H5Fopen(fileName, H5F_ACC_RDONLY, H5P_DEFAULT);
      if (h_file < 0)
        error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);

      /* 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 particle 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_dark_matter_background:
            if (with_gravity) {
              Nparticles = Ndm_background;
              darkmatter_read_particles(*gparts + Ndm, list, &num_fields);
            }
            break;

          case swift_type_sink:
            if (with_sink) {
              Nparticles = *Nsinks;
              sink_read_particles(*sinks, list, &num_fields);
            }
            break;

          case swift_type_stars:
            if (with_stars) {
              Nparticles = *Nstars;
              stars_read_particles(*sparts, list, &num_fields);
              num_fields +=
                  star_formation_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:
            if (mpi_rank == 0)
              message("Particle Type %d not yet supported. Particles ignored",
                      ptype);
        }

        /* Read everything */
        if (!dry_run)
          for (int i = 0; i < num_fields; ++i) {
            /* If we are remapping ParticleIDs later, don't need to read them.
             */
            if (remap_ids && strcmp(list[i].name, "ParticleIDs") == 0) continue;

            /* Read array. */
            read_array_serial(h_grp, list[i], Nparticles, N_total[ptype],
                              offset[ptype], internal_units, ic_units,
                              cleanup_h, cleanup_sqrt_a, h, a);
          }

        /* Close particle group */
        H5Gclose(h_grp);
      }

      /* Close file */
      H5Fclose(h_file);
    }

    /* Wait for the read of the reading to complete */
    MPI_Barrier(comm);
  }

  /* If we are remapping ParticleIDs later, start by setting them to 1. */
  if (remap_ids) io_set_ids_to_one(*gparts, *Ngparts);

  /* 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);

    /* Prepare the DM background particles */
    io_prepare_dm_background_gparts(&tp, *gparts + Ndm, Ndm_background);

    /* Duplicate the hydro particles into gparts */
    if (with_hydro)
      io_duplicate_hydro_gparts(&tp, *parts, *gparts, *Ngas,
                                Ndm + Ndm_background);

    /* Duplicate the sink particles into gparts */
    if (with_sink)
      io_duplicate_sinks_gparts(&tp, *sinks, *gparts, *Nsinks,
                                Ndm + Ndm_background + *Ngas);

    /* Duplicate the stars particles into gparts */
    if (with_stars)
      io_duplicate_stars_gparts(&tp, *sparts, *gparts, *Nstars,
                                Ndm + Ndm_background + *Ngas + *Nsinks);

    /* Duplicate the black holes particles into gparts */
    if (with_black_holes)
      io_duplicate_black_holes_gparts(
          &tp, *bparts, *gparts, *Nblackholes,
          Ndm + Ndm_background + *Ngas + *Nsinks + *Nstars);

    threadpool_clean(&tp);
  }

  /* message("Done Reading particles..."); */

  /* Clean up */
  free(ic_units);
}

/**
 * @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor
 *
 * @param e The engine containing all the system.
 * @param internal_units The #unit_system used internally
 * @param snapshot_units The #unit_system used in the snapshots
 * @param mpi_rank The MPI rank of this node.
 * @param mpi_size The number of MPI ranks.
 * @param comm The MPI communicator.
 * @param info The MPI information object
 *
 * 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_serial(struct engine* e,
                         const struct unit_system* internal_units,
                         const struct unit_system* snapshot_units, int mpi_rank,
                         int mpi_size, MPI_Comm comm, MPI_Info info) {

  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;
  const struct sink* sinks = e->s->sinks;
  struct output_options* output_options = e->output_options;
  struct output_list* output_list = e->output_list_snapshots;
  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;
  const int with_fof = e->policy & engine_policy_fof;
  const int with_DM_background = e->s->with_DM_background;
#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
  const int with_rt = e->policy & engine_policy_rt;

  FILE* xmfFile = 0;

  /* 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 Nsinks = e->s->nr_sinks;
  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;

  size_t Ndm_background = 0;
  if (with_DM_background) {
    Ndm_background = io_count_dm_background_gparts(gparts, Ntot);
  }

  /* Number of particles that we will write
   * Recall that background particles are never inhibited and have no extras */
  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 Nsinks_written =
      e->s->nr_sinks - e->s->nr_inhibited_sinks - e->s->nr_extra_sinks;
  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 + Nsinks_written;
  const size_t Ndm_written =
      Ntot_written > 0 ? Ntot_written - Nbaryons_written - Ndm_background : 0;

  /* File name */
  char fileName[FILENAME_BUFFER_SIZE];
  char xmfFileName[FILENAME_BUFFER_SIZE];
  io_get_snapshot_filename(fileName, xmfFileName, e->snapshot_int_time_label_on,
                           e->snapshot_invoke_stf, e->time, e->stf_output_count,
                           e->snapshot_output_count, e->snapshot_subdir,
                           e->snapshot_base_name);

  /* Determine if we are writing a reduced snapshot, and if so which
   * output selection type to use. Can just create a copy of this on
   * each rank. */
  char current_selection_name[FIELD_BUFFER_SIZE] =
      select_output_header_default_name;
  if (output_list) {
    /* Users could have specified a different Select Output scheme for each
     * snapshot. */
    output_list_get_current_select_output(output_list, current_selection_name);
  }

  /* Total number of fields to write per ptype */
  int numFields[swift_type_count] = {0};
  for (int ptype = 0; ptype < swift_type_count; ++ptype) {
    numFields[ptype] = output_options_get_num_fields_to_write(
        output_options, current_selection_name, ptype);
  }

  /* Compute offset in the file and total number of particles */
  size_t N[swift_type_count] = {Ngas_written,   Ndm_written,
                                Ndm_background, Nsinks_written,
                                Nstars_written, Nblackholes_written};
  long long N_total[swift_type_count] = {0};
  long long offset[swift_type_count] = {0};
  MPI_Exscan(N, offset, swift_type_count, MPI_LONG_LONG_INT, MPI_SUM, comm);
  for (int ptype = 0; ptype < swift_type_count; ++ptype)
    N_total[ptype] = offset[ptype] + N[ptype];

  /* The last rank now has the correct N_total. Let's broadcast from there */
  MPI_Bcast(N_total, 6, MPI_LONG_LONG_INT, mpi_size - 1, comm);

  /* Now everybody knows its offset and the total number of particles of each
   * type */

  /* Do common stuff first */
  if (mpi_rank == 0) {

    /* First time, we need to create the XMF file */
    if (e->snapshot_output_count == 0) xmf_create_file(xmfFileName);

    /* Prepare the XMF file for the new entry */
    xmfFile = xmf_prepare_file(xmfFileName);

    /* 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");
    io_write_attribute_s(h_grp, "RunName", e->run_name);

    /* Write out the time-base */
    if (with_cosmology) {
      io_write_attribute_d(h_grp, "TimeBase_dloga", e->time_base);
      const double delta_t =
          cosmology_get_timebase(e->cosmology, e->ti_current);
      io_write_attribute_d(h_grp, "TimeBase_dt", delta_t);
    } else {
      io_write_attribute_d(h_grp, "TimeBase_dloga", 0);
      io_write_attribute_d(h_grp, "TimeBase_dt", e->time_base);
    }

    /* Store the time at which the snapshot was written */
    time_t tm = time(NULL);
    struct tm* timeinfo = localtime(&tm);
    char snapshot_date[64];
    strftime(snapshot_date, 64, "%T %F %Z", timeinfo);
    io_write_attribute_s(h_grp, "Snapshot date", snapshot_date);

    /* 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[6] = {0., 0., 0., 0., 0., 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);
    io_write_attribute_i(h_grp, "ThisFile", 0);
    io_write_attribute_s(h_grp, "OutputType", "FullVolume");
    io_write_attribute_s(h_grp, "SelectOutput", current_selection_name);

    /* Close header */
    H5Gclose(h_grp);

    /* Write all the meta-data */
    io_write_meta_data(h_file, e, internal_units, snapshot_units);

    /* Loop over all particle types */
    for (int ptype = 0; ptype < swift_type_count; ptype++) {

      /* Don't do anything if there are (a) no particles of this kind, or (b)
       * if we have disabled every field of this particle type. */
      if (N_total[ptype] == 0 || numFields[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 = H5Gcreate(h_file, partTypeGroupName, H5P_DEFAULT, H5P_DEFAULT,
                        H5P_DEFAULT);
      if (h_grp < 0) error("Error while creating particle group.\n");

      /* Add an alias name for convenience */
      char aliasName[PARTICLE_GROUP_BUFFER_SIZE];
      snprintf(aliasName, PARTICLE_GROUP_BUFFER_SIZE, "/%sParticles",
               part_type_names[ptype]);
      hid_t h_err = H5Lcreate_soft(partTypeGroupName, h_grp, aliasName,
                                   H5P_DEFAULT, H5P_DEFAULT);
      if (h_err < 0) error("Error while creating alias for particle group.\n");

      /* Write the number of particles as an attribute */
      io_write_attribute_l(h_grp, "NumberOfParticles", N_total[ptype]);

      /* Close particle group */
      H5Gclose(h_grp);
    }

    /* Close file */
    H5Fclose(h_file);
  }

  /* Now write the top-level cell structure */
  hid_t h_file_cells = 0, h_grp_cells = 0;
  if (mpi_rank == 0) {

    /* Open the snapshot on rank 0 */
    h_file_cells = H5Fopen(fileName, H5F_ACC_RDWR, H5P_DEFAULT);
    if (h_file_cells < 0)
      error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);

    /* Create the group we want in the file */
    h_grp_cells = H5Gcreate(h_file_cells, "/Cells", H5P_DEFAULT, H5P_DEFAULT,
                            H5P_DEFAULT);
    if (h_grp_cells < 0) error("Error while creating cells group");
  }

  /* Write the location of the particles in the arrays */
  io_write_cell_offsets(h_grp_cells, e->s->cdim, e->s->dim, e->s->cells_top,
                        e->s->nr_cells, e->s->width, mpi_rank,
                        /*distributed=*/0, N_total, offset, numFields,
                        internal_units, snapshot_units);

  /* Close everything */
  if (mpi_rank == 0) {
    H5Gclose(h_grp_cells);
    H5Fclose(h_file_cells);
  }

  /* Now loop over ranks and write the data */
  for (int rank = 0; rank < mpi_size; ++rank) {

    /* Is it this rank's turn to write ? */
    if (rank == mpi_rank) {

      h_file = H5Fopen(fileName, H5F_ACC_RDWR, H5P_DEFAULT);
      if (h_file < 0)
        error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);

      /* Loop over all particle types */
      for (int ptype = 0; ptype < swift_type_count; ptype++) {

        /* Don't do anything if there are (a) no particles of this kind, or (b)
         * if we have disabled every field of this particle type. */
        if (N_total[ptype] == 0 || numFields[ptype] == 0) continue;

        /* Add the global information for that particle type to the XMF
         * meta-file */
        if (mpi_rank == 0)
          xmf_write_groupheader(xmfFile, fileName, N_total[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 = 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;

        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;
        struct sink* sinks_written = NULL;

        /* Write particle fields from the particle structure */
        switch (ptype) {

          case swift_type_gas: {
            if (Ngas == Ngas_written) {

              /* No inhibted particles: easy case */
              Nparticles = Ngas;
              hydro_write_particles(parts, xparts, list, &num_fields);
              num_fields += chemistry_write_particles(
                  parts, xparts, list + num_fields, with_cosmology);
              if (with_cooling || with_temperature) {
                num_fields += cooling_write_particles(
                    parts, xparts, list + num_fields, e->cooling_func);
              }
              if (with_fof) {
                num_fields += fof_write_parts(parts, xparts, list + num_fields);
              }
              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);
              if (with_rt) {
                num_fields += rt_write_particles(parts, list + num_fields);
              }

            } else {

              /* Ok, we need to fish out the particles we want */
              Nparticles = 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 temporary memory for parts");
              if (swift_memalign("xparts_written", (void**)&xparts_written,
                                 xpart_align,
                                 Ngas_written * sizeof(struct xpart)) != 0)
                error("Error while allocating temporary 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, xparts_written,
                                            list + num_fields, with_cosmology);
              if (with_cooling || with_temperature) {
                num_fields +=
                    cooling_write_particles(parts_written, xparts_written,
                                            list + num_fields, e->cooling_func);
              }
              if (with_fof) {
                num_fields += fof_write_parts(parts_written, xparts_written,
                                              list + num_fields);
              }
              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);
              if (with_rt) {
                num_fields +=
                    rt_write_particles(parts_written, list + num_fields);
              }
            }
          } break;

          case swift_type_dark_matter: {
            if (Ntot == Ndm_written) {

              /* This is a DM-only run without background or inhibited particles
               */
              Nparticles = Ntot;
              darkmatter_write_particles(gparts, list, &num_fields);
              if (with_fof) {
                num_fields +=
                    fof_write_gparts(gparts_written, 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 */
              Nparticles = 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 temporary 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 temporary 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_fof) {
                num_fields +=
                    fof_write_gparts(gparts_written, list + num_fields);
              }
              if (with_stf) {
                num_fields += velociraptor_write_gparts(
                    gpart_group_data_written, list + num_fields);
              }
            }
          } break;

          case swift_type_dark_matter_background: {

            /* Ok, we need to fish out the particles we want */
            Nparticles = Ndm_background;

            /* Allocate temporary array */
            if (swift_memalign("gparts_written", (void**)&gparts_written,
                               gpart_align,
                               Ndm_background * 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_background *
                                     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_background_to_write(
                gparts, e->s->gpart_group_data, gparts_written,
                gpart_group_data_written, Ntot, Ndm_background, with_stf);

            /* Select the fields to write */
            darkmatter_write_particles(gparts_written, list, &num_fields);
            if (with_fof) {
              num_fields += fof_write_gparts(gparts_written, list + num_fields);
            }
            if (with_stf) {
              num_fields += velociraptor_write_gparts(gpart_group_data_written,
                                                      list + num_fields);
            }

          } break;

          case swift_type_sink: {
            if (Nsinks == Nsinks_written) {

              /* No inhibted particles: easy case */
              Nparticles = Nsinks;
              sink_write_particles(sinks, list, &num_fields, with_cosmology);
            } else {

              /* Ok, we need to fish out the particles we want */
              Nparticles = Nsinks_written;

              /* Allocate temporary arrays */
              if (swift_memalign("sinks_written", (void**)&sinks_written,
                                 sink_align,
                                 Nsinks_written * sizeof(struct sink)) != 0)
                error("Error while allocating temporary memory for sinks");

              /* Collect the particles we want to write */
              io_collect_sinks_to_write(sinks, sinks_written, Nsinks,
                                        Nsinks_written);

              /* Select the fields to write */
              sink_write_particles(sinks_written, list, &num_fields,
                                   with_cosmology);
            }
          } break;

          case swift_type_stars: {
            if (Nstars == Nstars_written) {

              /* No inhibted particles: easy case */
              Nparticles = Nstars;
              stars_write_particles(sparts, list, &num_fields, with_cosmology);
              num_fields +=
                  chemistry_write_sparticles(sparts, list + num_fields);
              num_fields += tracers_write_sparticles(sparts, list + num_fields,
                                                     with_cosmology);
              num_fields +=
                  star_formation_write_sparticles(sparts, list + num_fields);
              if (with_fof) {
                num_fields += fof_write_sparts(sparts, list + num_fields);
              }
              if (with_stf) {
                num_fields +=
                    velociraptor_write_sparts(sparts, list + num_fields);
              }
              if (with_rt) {
                num_fields += rt_write_stars(sparts, list + num_fields);
              }
            } else {

              /* Ok, we need to fish out the particles we want */
              Nparticles = 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 temporary 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,
                                    with_cosmology);
              num_fields +=
                  chemistry_write_sparticles(sparts_written, list + num_fields);
              num_fields += tracers_write_sparticles(
                  sparts_written, list + num_fields, with_cosmology);
              num_fields += star_formation_write_sparticles(sparts_written,
                                                            list + num_fields);
              if (with_fof) {
                num_fields +=
                    fof_write_sparts(sparts_written, list + num_fields);
              }
              if (with_stf) {
                num_fields += velociraptor_write_sparts(sparts_written,
                                                        list + num_fields);
              }
              if (with_rt) {
                num_fields += rt_write_stars(sparts_written, list + num_fields);
              }
            }
          } break;

          case swift_type_black_hole: {
            if (Nblackholes == Nblackholes_written) {

              /* No inhibted particles: easy case */
              Nparticles = Nblackholes;
              black_holes_write_particles(bparts, list, &num_fields,
                                          with_cosmology);
              num_fields +=
                  chemistry_write_bparticles(bparts, list + num_fields);
              if (with_fof) {
                num_fields += fof_write_bparts(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 */
              Nparticles = 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 temporary 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,
                                          with_cosmology);
              num_fields +=
                  chemistry_write_bparticles(bparts, list + num_fields);
              if (with_fof) {
                num_fields +=
                    fof_write_bparts(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);
        }

        /* Did the user specify a non-standard default for the entire particle
         * type? */
        const enum lossy_compression_schemes compression_level_current_default =
            output_options_get_ptype_default_compression(
                output_options->select_output, current_selection_name,
                (enum part_type)ptype);

        /* Write everything that is not cancelled */
        int num_fields_written = 0;
        for (int i = 0; i < num_fields; ++i) {

          /* Did the user cancel this field? */
          const enum lossy_compression_schemes compression_level =
              output_options_get_field_compression(
                  output_options, current_selection_name, list[i].name,
                  (enum part_type)ptype, compression_level_current_default);

          if (compression_level != compression_do_not_write) {
            write_array_serial(e, h_grp, fileName, xmfFile, partTypeGroupName,
                               list[i], Nparticles, N_total[ptype], mpi_rank,
                               offset[ptype], compression_level, internal_units,
                               snapshot_units);
            num_fields_written++;
          }
        }

        if (mpi_rank == 0) {
          /* Only write this now that we know exactly how many fields there are.
           */
          io_write_attribute_i(h_grp, "NumberOfFields", num_fields_written);
        }

        /* Free temporary array */
        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", sparts_written);
        if (sinks_written) swift_free("sinks_written", sinks_written);

        /* Close particle group */
        H5Gclose(h_grp);

        /* Close this particle group in the XMF file as well */
        if (mpi_rank == 0)
          xmf_write_groupfooter(xmfFile, (enum part_type)ptype);
      }

      /* Close file */
      H5Fclose(h_file);
    }

    /* Wait for the read of the reading to complete */
    MPI_Barrier(comm);
  }

  /* Write footer of LXMF file descriptor */
  if (mpi_rank == 0)
    xmf_write_outputfooter(xmfFile, e->snapshot_output_count, e->time);

  /* message("Done writing particles..."); */
  e->snapshot_output_count++;
  if (e->snapshot_invoke_stf) e->stf_output_count++;
}

#endif /* HAVE_HDF5 && HAVE_MPI */
