/*******************************************************************************
 * This file is part of SWIFT.
 * Copyright (c) 2016 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/>.
 *
 ******************************************************************************/
#ifndef SWIFT_COOLING_CHIMES_IO_H
#define SWIFT_COOLING_CHIMES_IO_H

/* Config parameters. */
#include <config.h>

/* Local includes */
#include "cooling.h"
#include "engine.h"
#include "io_properties.h"

#ifdef HAVE_HDF5

/**
 * @brief Writes the current model of SPH to the file
 * @param h_grp The HDF5 group in which to write
 * @param h_grp_columns The HDF5 group containing named columns
 * @param cooling the parameters of the cooling function.
 */
__attribute__((always_inline)) INLINE static void cooling_write_flavour(
    hid_t h_grp, hid_t h_grp_columns,
    const struct cooling_function_data* cooling) {

  io_write_attribute_s(h_grp, "Cooling Model", "CHIMES");

  /* Add the species names to the named columns */
  hsize_t dims[1] = {CHIMES_NETWORK_SIZE};
  hid_t type = H5Tcopy(H5T_C_S1);
  H5Tset_size(type, CHIMES_NAME_STR_LENGTH);
  hid_t space = H5Screate_simple(1, dims, NULL);
  hid_t dset = H5Dcreate(h_grp_columns, "SpeciesFractions", type, space,
                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  H5Dwrite(dset, type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
           cooling->chimes_species_names_reduced[0]);
  H5Dclose(dset);

  /* Let's construct the names from the raw full CHIMES list */
  char chimes_species_names_snipshots[4][CHIMES_NAME_STR_LENGTH] = {0};
  strcpy(chimes_species_names_snipshots[0], chimes_species_names[1]); /* HI */
  strcpy(chimes_species_names_snipshots[1], chimes_species_names[4]); /* HeI */
  strcpy(chimes_species_names_snipshots[2], chimes_species_names[5]); /* HeII */
  strcpy(chimes_species_names_snipshots[3],
         chimes_species_names[137]); /* H_2 */

  /* Same for the reduced arrays in snipshots */
  dims[0] = 4;
  space = H5Screate_simple(1, dims, NULL);
  dset = H5Dcreate(h_grp_columns, "ReducedSpeciesFractions", type, space,
                   H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  H5Dwrite(dset, type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
           chimes_species_names_snipshots[0]);
  H5Dclose(dset);

  H5Tclose(type);
  H5Sclose(space);
}
#endif

INLINE static void convert_part_T(const struct engine* e, const struct part* p,
                                  const struct xpart* xp, float* ret) {

  ret[0] = cooling_get_snapshot_temperature(
      e->physical_constants, e->hydro_properties, e->entropy_floor,
      e->internal_units, e->cosmology, e->cooling_func, p, xp);
}

INLINE static void convert_part_sub_T(const struct engine* e,
                                      const struct part* p,
                                      const struct xpart* xp, float* ret) {

  ret[0] = cooling_get_subgrid_temperature(
      e->internal_units, e->physical_constants, e->cosmology,
      e->hydro_properties, e->entropy_floor, e->cooling_func, p, xp);
}

INLINE static void convert_part_sub_rho(const struct engine* e,
                                        const struct part* p,
                                        const struct xpart* xp, float* ret) {

  ret[0] = cooling_get_subgrid_density(
      e->internal_units, e->physical_constants, e->cosmology,
      e->hydro_properties, e->entropy_floor, e->cooling_func, p, xp);
}

INLINE static void convert_part_chimes_abundances(const struct engine* e,
                                                  const struct part* p,
                                                  const struct xpart* xp,
                                                  float* ret) {

  /* Create dummy part and xpart structures that we can use to
   * temporarily update the CHIMES abundance array for the snapshot. */
  struct part dummy_p = *p;
  struct xpart dummy_xp = *xp;

  /* Update abundance array for particles on the EOS. */
  cooling_set_subgrid_properties(e->physical_constants, e->internal_units,
                                 e->cosmology, e->hydro_properties,
                                 e->entropy_floor, e->cooling_func, e->dustevo,
                                 &dummy_p, &dummy_xp);

  for (int i = 0; i < CHIMES_NETWORK_SIZE; i++)
    ret[i] = (float)dummy_xp.cooling_data.chimes_abundances[i];
}

INLINE static void convert_part_reduced_chimes_abundances(
    const struct engine* e, const struct part* p, const struct xpart* xp,
    float* ret) {

  /* Create dummy part and xpart structures that we can use to
   * temporarily update the CHIMES abundance array for the snapshot. */
  struct part dummy_p = *p;
  struct xpart dummy_xp = *xp;

  const struct cooling_function_data* cooling = e->cooling_func;

  /* Update abundance array for particles on the EOS. */
  cooling_set_subgrid_properties(e->physical_constants, e->internal_units,
                                 e->cosmology, e->hydro_properties,
                                 e->entropy_floor, cooling, e->dustevo,
                                 &dummy_p, &dummy_xp);

  const int HI_ind = cooling->ChimesGlobalVars.speciesIndices[sp_HI];
  const int HeI_ind = cooling->ChimesGlobalVars.speciesIndices[sp_HeI];
  const int HeII_ind = cooling->ChimesGlobalVars.speciesIndices[sp_HeII];
  const int H2_ind = cooling->ChimesGlobalVars.speciesIndices[sp_H2];
  ret[0] = (float)dummy_xp.cooling_data.chimes_abundances[HI_ind];   /* HI */
  ret[1] = (float)dummy_xp.cooling_data.chimes_abundances[HeI_ind];  /* HeI */
  ret[2] = (float)dummy_xp.cooling_data.chimes_abundances[HeII_ind]; /* HeII */
  ret[3] = (float)dummy_xp.cooling_data.chimes_abundances[H2_ind];   /* H_2 */
}

INLINE static void convert_part_HI_mass(const struct engine* e,
                                        const struct part* p,
                                        const struct xpart* xp, float* ret) {

  const float X_H =
      chemistry_get_metal_mass_fraction_for_cooling(p)[chemistry_element_H];

  const float HI_frac = cooling_get_particle_subgrid_HI_fraction(
      e->internal_units, e->physical_constants, e->cosmology,
      e->hydro_properties, e->entropy_floor, e->cooling_func, p, xp);

  *ret = hydro_get_mass(p) * X_H * HI_frac;
}

INLINE static void convert_part_H2_mass(const struct engine* e,
                                        const struct part* p,
                                        const struct xpart* xp, float* ret) {

  const float X_H =
      chemistry_get_metal_mass_fraction_for_cooling(p)[chemistry_element_H];

  const float H2_frac = cooling_get_particle_subgrid_H2_fraction(
      e->internal_units, e->physical_constants, e->cosmology,
      e->hydro_properties, e->entropy_floor, e->cooling_func, p, xp);

  *ret = hydro_get_mass(p) * X_H * H2_frac * 2.f;
}

INLINE static void convert_part_e_density(const struct engine* e,
                                          const struct part* p,
                                          const struct xpart* xp, double* ret) {

  *ret = cooling_get_electron_density(
      e->physical_constants, e->hydro_properties, e->entropy_floor,
      e->internal_units, e->cosmology, e->cooling_func, e->dustevo, p, xp);
}

INLINE static void convert_part_y_compton(const struct engine* e,
                                          const struct part* p,
                                          const struct xpart* xp, double* ret) {

  *ret = cooling_get_ycompton(e->physical_constants, e->hydro_properties,
                              e->entropy_floor, e->internal_units, e->cosmology,
                              e->cooling_func, e->dustevo, p, xp);
}

/**
 * @brief Specifies which particle fields to write to a dataset
 *
 * @param parts The particle array.
 * @param xparts The extended particle array.
 * @param list The list of i/o properties to write.
 * @param cooling The #cooling_function_data
 *
 * @return Returns the number of fields to write.
 */
__attribute__((always_inline)) INLINE static int cooling_write_particles(
    const struct part* parts, const struct xpart* xparts,
    struct io_props* list) {

  list[0] = io_make_output_field_convert_part(
      "SpeciesFractions", FLOAT, CHIMES_NETWORK_SIZE, UNIT_CONV_NO_UNITS, 0.f,
      parts, xparts, convert_part_chimes_abundances,
      "Species fractions array for all ions and molecules in the CHIMES "
      "network. The fraction of species i is defined in terms "
      "of its number density relative to hydrogen, i.e. n_i / n_H_tot.");

  list[1] = io_make_output_field_convert_part(
      "ReducedSpeciesFractions", FLOAT, 4, UNIT_CONV_NO_UNITS, 0.f, parts,
      xparts, convert_part_reduced_chimes_abundances,
      "Species fractions array for a reduced set of ions and molecules in the "
      "CHIMES network. The fraction of species i is defined in terms of its "
      "number density relative to hydrogen, i.e. n_i / n_H_tot.");

  list[2] = io_make_output_field_convert_part(
      "Temperatures", FLOAT, 1, UNIT_CONV_TEMPERATURE, 0.f, parts, xparts,
      convert_part_T, "Temperature of the particles");

  list[3] = io_make_output_field_convert_part(
      "SubgridTemperatures", FLOAT, 1, UNIT_CONV_TEMPERATURE, 0.f, parts,
      xparts, convert_part_sub_T,
      "The subgrid temperatures if the particles are within deltaT of the "
      "entropy floor the subgrid temperature is calculated assuming a "
      "pressure equilibrium on the entropy floor, if the particles are "
      "above deltaT of the entropy floor the subgrid temperature is "
      "identical to the SPH temperature.");

  list[4] = io_make_physical_output_field_convert_part(
      "SubgridPhysicalDensities", FLOAT, 1, UNIT_CONV_DENSITY, -3.f, parts,
      xparts, /*can convert to comoving=*/1, convert_part_sub_rho,
      "The subgrid physical density if the particles are within deltaT of the "
      "entropy floor the subgrid density is calculated assuming a pressure "
      "equilibrium on the entropy floor, if the particles are above deltaT "
      "of the entropy floor the subgrid density is identical to the "
      "physical SPH density.");

  list[5] = io_make_output_field_convert_part(
      "AtomicHydrogenMasses", FLOAT, 1, UNIT_CONV_MASS, 0.f, parts, xparts,
      convert_part_HI_mass,
      "Atomic hydrogen masses containted in the particles. This quantity is "
      "obtained from the cooling tables and, if the particle is on the entropy "
      "floor, by extrapolating to the equilibrium curve assuming constant "
      "pressure.");

  list[6] = io_make_output_field_convert_part(
      "MolecularHydrogenMasses", FLOAT, 1, UNIT_CONV_MASS, 0.f, parts, xparts,
      convert_part_H2_mass,
      "Molecular hydrogen masses containted in the particles. This quantity is "
      "obtained from the cooling tables and, if the particle is on the entropy "
      "floor, by extrapolating to the equilibrium curve assuming constant "
      "pressure.");

  list[7] = io_make_physical_output_field(
      "NetCoolingRates", FLOAT, 1, UNIT_CONV_ENERGY_PER_UNIT_MASS_PER_UNIT_TIME,
      0.f, xparts, cooling_data.net_cooling_rate, /*can convert to comoving=*/0,
      "Net cooling rate of the particle, i.e. energy per unit mass per unit "
      "time. Positive values indicate net cooling, negative values indicate "
      "net heating.");

  list[8] = io_make_physical_output_field_convert_part(
      "TotalElectronNumberDensities", DOUBLE, 1, UNIT_CONV_NUMBER_DENSITY, 0.f,
      parts, xparts, /*can convert to comoving=*/0, convert_part_e_density,
      "Total electron number densities in the physical frame computed as the "
      "sum of the electron number densities from the elements evolved with "
      "the non-equilibrium network CHIMES and the electron number densities "
      "from the other elements based on the equilibrium cooling tables.");

  list[9] = io_make_physical_output_field_convert_part(
      "ComptonYParameters", DOUBLE, 1, UNIT_CONV_AREA, 0.f, parts, xparts,
      /*can convert to comoving=*/0, convert_part_y_compton,
      "Compton y parameters in the physical frame computed based on the "
      "cooling tables. This is 0 for star-forming particles.");

  return 10;
}

#endif /* SWIFT_COOLING_CHIMES_IO_H */