Merge branch 'chemistry' into 'master'

Add chemistry in part

See merge request !486

configure.ac

@@ -932,6 +932,29 @@ case "$with_cooling" in
    ;;
 esac
 
+#  chemistry function
+AC_ARG_WITH([chemistry],
+   [AS_HELP_STRING([--with-chemistry=<function>],
+      [chemistry function @<:@none, gear, EAGLE default: none@:>@]
+   )],
+   [with_chemistry="$withval"],
+   [with_chemistry="none"]
+)
+case "$with_chemistry" in
+   none)
+      AC_DEFINE([CHEMISTRY_NONE], [1], [No chemistry function])
+   ;; 
+   gear)
+      AC_DEFINE([CHEMISTRY_GEAR], [1], [Chemistry taken from the GEAR model])
+   ;; 
+   EAGLE)
+      AC_DEFINE([CHEMISTRY_EAGLE], [1], [Chemistry taken from the EAGLE model])
+   ;; 
+   *)
+      AC_MSG_ERROR([Unknown chemistry function: $with_chemistry])
+   ;;
+esac
+
 #  External potential
 AC_ARG_WITH([ext-potential],
    [AS_HELP_STRING([--with-ext-potential=<pot>],
@@ -1031,6 +1054,7 @@ AC_MSG_RESULT([
    Adiabatic index    : $with_gamma
    Riemann solver     : $with_riemann
    Cooling function   : $with_cooling
+   Chemistry          : $with_chemistry
    
    External potential  : $with_potential
    Multipole order     : $with_multipole_order

doc/Doxyfile.in

@@ -765,7 +765,8 @@ INPUT		       += @top_srcdir@/src/gravity/Default
 INPUT		       += @top_srcdir@/src/stars/Default
 INPUT		       += @top_srcdir@/src/riemann
 INPUT		       += @top_srcdir@/src/potential/point_mass
-INPUT		       += @top_srcdir@/src/cooling/const_du
+INPUT		       += @top_srcdir@/src/cooling/none
+INPUT		       += @top_srcdir@/src/chemistry/none
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

examples/CoolingBox/coolingBox.yml

@@ -46,3 +46,17 @@ GrackleCooling:
   UVbackground: 0 # Enable or not the UV background
   GrackleRedshift: 0 # Redshift to use (-1 means time based redshift)
   GrackleHSShieldingDensityThreshold: 1.1708e-26 # self shielding threshold in internal system of units
+
+EAGLEChemistry:
+  InitMetallicity:         0.
+  InitAbundance_Hydrogen:  0.752
+  InitAbundance_Helium:    0.248
+  InitAbundance_Carbon:    0.000
+  InitAbundance_Nitrogen:  0.000
+  InitAbundance_Oxygen:    0.000
+  InitAbundance_Neon:      0.000
+  InitAbundance_Magnesium: 0.000
+  InitAbundance_Silicon:   0.000
+  InitAbundance_Iron:      0.000
+  CalciumOverSilicon:      0.0941736
+  SulphurOverSilicon:      0.6054160

examples/main.c

@@ -612,6 +612,11 @@ int main(int argc, char *argv[]) {
   if (with_cooling) cooling_init(params, &us, &prog_const, &cooling_func);
   if (with_cooling && myrank == 0) cooling_print(&cooling_func);
 
+  /* Initialise the chemistry */
+  struct chemistry_data chemistry;
+  chemistry_init(params, &us, &prog_const, &chemistry);
+  if (myrank == 0) chemistry_print(&chemistry);
+
   /* Initialise the feedback properties */
   struct sourceterms sourceterms;
   if (with_sourceterms) sourceterms_init(params, &us, &sourceterms);
@@ -636,7 +641,7 @@ int main(int argc, char *argv[]) {
   engine_init(&e, &s, params, nr_nodes, myrank, nr_threads, N_total[0],
               N_total[1], with_aff, engine_policies, talking, &reparttype, &us,
               &prog_const, &hydro_properties, &gravity_properties, &potential,
-              &cooling_func, &sourceterms);
+              &cooling_func, &chemistry, &sourceterms);
   if (myrank == 0) {
     clocks_gettime(&toc);
     message("engine_init took %.3f %s.", clocks_diff(&tic, &toc),

examples/parameter_example.yml

@@ -151,3 +151,21 @@ GrackleCooling:
   UVbackground: 1 # Enable or not the UV background
   GrackleRedshift: 0 # Redshift to use (-1 means time based redshift)
   GrackleHSShieldingDensityThreshold: 1.1708e-26 # self shielding threshold in internal system of units
+
+# Parameters related to chemistry models  -----------------------------------------------
+
+# EAGLE model
+EAGLEChemistry:
+  InitMetallicity:         0.           # Inital fraction of particle mass in *all* metals
+  InitAbundance_Hydrogen:  0.752        # Inital fraction of particle mass in Hydrogen
+  InitAbundance_Helium:    0.248        # Inital fraction of particle mass in Helium
+  InitAbundance_Carbon:    0.000        # Inital fraction of particle mass in Carbon
+  InitAbundance_Nitrogen:  0.000        # Inital fraction of particle mass in Nitrogen
+  InitAbundance_Oxygen:    0.000        # Inital fraction of particle mass in Oxygen
+  InitAbundance_Neon:      0.000        # Inital fraction of particle mass in Neon
+  InitAbundance_Magnesium: 0.000        # Inital fraction of particle mass in Magnesium
+  InitAbundance_Silicon:   0.000        # Inital fraction of particle mass in Silicon
+  InitAbundance_Iron:      0.000        # Inital fraction of particle mass in Iron
+  CalciumOverSilicon:      0.0941736    # Constant ratio of Calcium over Silicon abundance
+  SulphurOverSilicon:      0.6054160    # Constant ratio of Sulphur over Silicon abundance
+

src/Makefile.am

@@ -46,7 +46,8 @@ include_HEADERS = space.h runner.h queue.h task.h lock.h cell.h part.h const.h \
     hydro_properties.h riemann.h threadpool.h cooling.h cooling_struct.h sourceterms.h \
     sourceterms_struct.h statistics.h memswap.h cache.h runner_doiact_vec.h profiler.h \
     dump.h logger.h active.h timeline.h xmf.h gravity_properties.h gravity_derivatives.h \
-    gravity_softened_derivatives.h vector_power.h collectgroup.h hydro_space.h sort_part.h
+    gravity_softened_derivatives.h vector_power.h collectgroup.h hydro_space.h sort_part.h \
+    chemistry.h chemistry_io.h chemistry_struct.h
 
 # Common source files
 AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
@@ -57,7 +58,8 @@ AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
     runner_doiact_fft.c threadpool.c cooling.c sourceterms.c \
     statistics.c runner_doiact_vec.c profiler.c dump.c logger.c \
     part_type.c xmf.c gravity_properties.c gravity.c \
-    collectgroup.c hydro_space.c equation_of_state.c
+    collectgroup.c hydro_space.c equation_of_state.c \
+    chemistry.c
 
 
 # Include files for distribution, not installation.
@@ -117,7 +119,16 @@ nobase_noinst_HEADERS = align.h approx_math.h atomic.h barrier.h cycle.h error.h
 	         cooling/const_du/cooling.h cooling/const_du/cooling_struct.h \
                  cooling/const_lambda/cooling.h cooling/const_lambda/cooling_struct.h \
                  cooling/grackle/cooling.h cooling/grackle/cooling_struct.h \
-                 memswap.h dump.h logger.h
+                 memswap.h dump.h logger.h \
+                 chemistry/none/chemistry.h \
+		 chemistry/none/chemistry_io.h \
+		 chemistry/none/chemistry_struct.h \
+                 chemistry/gear/chemistry.h \
+		 chemistry/gear/chemistry_io.h \
+		 chemistry/gear/chemistry_struct.h \
+                 chemistry/EAGLE/chemistry.h \
+		 chemistry/EAGLE/chemistry_io.h \
+		 chemistry/EAGLE/chemistry_struct.h
 
 
 # Sources and flags for regular library

src/chemistry.c

+/*******************************************************************************
+ * 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/>.
+ *
+ ******************************************************************************/
+
+/* Config parameters. */
+#include "../config.h"
+
+/* This object's header. */
+#include "chemistry.h"
+
+/**
+ * @brief Initialises the chemistry properties.
+ *
+ * Calls chemistry_init_backend for the chosen chemistry function.
+ *
+ * @param parameter_file The parsed parameter file.
+ * @param us The current internal system of units.
+ * @param phys_const The physical constants in internal units.
+ * @param data The properties to initialise.
+ */
+void chemistry_init(const struct swift_params* parameter_file,
+                    const struct unit_system* us,
+                    const struct phys_const* phys_const,
+                    struct chemistry_data* data) {
+
+  chemistry_init_backend(parameter_file, us, phys_const, data);
+}
+
+/**
+ * @brief Prints the properties of the chemistry model to stdout.
+ *
+ * Calls chemistry_print_backend for the chosen chemistry model.
+ *
+ * @brief The #chemistry_data containing information about the current model.
+ */
+void chemistry_print(const struct chemistry_data* data) {
+  chemistry_print_backend(data);
+}

src/chemistry.h

+/*******************************************************************************
+ * 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_CHEMISTRY_H
+#define SWIFT_CHEMISTRY_H
+
+/**
+ * @file src/chemistry.h
+ * @brief Branches between the different chemistry functions.
+ */
+
+/* Config parameters. */
+#include "../config.h"
+#include "chemistry_struct.h"
+
+/* Import the right chemistry definition */
+#if defined(CHEMISTRY_NONE)
+#include "./chemistry/none/chemistry.h"
+#elif defined(CHEMISTRY_GEAR)
+#include "./chemistry/gear/chemistry.h"
+#elif defined(CHEMISTRY_EAGLE)
+#include "./chemistry/EAGLE/chemistry.h"
+#else
+#error "Invalid choice of chemistry function."
+#endif
+
+/* Common functions */
+void chemistry_init(const struct swift_params* parameter_file,
+                    const struct unit_system* us,
+                    const struct phys_const* phys_const,
+                    struct chemistry_data* data);
+
+void chemistry_print(const struct chemistry_data* data);
+
+#endif /* SWIFT_CHEMISTRY_H */

src/chemistry/EAGLE/chemistry.h

+/*******************************************************************************
+ * 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_CHEMISTRY_EAGLE_H
+#define SWIFT_CHEMISTRY_EAGLE_H
+
+/**
+ * @file src/chemistry/gear/chemistry.h
+ * @brief Empty infrastructure for the cases without chemistry function
+ */
+
+/* Some standard headers. */
+#include <float.h>
+#include <math.h>
+
+/* Local includes. */
+#include "chemistry_struct.h"
+#include "error.h"
+#include "hydro.h"
+#include "parser.h"
+#include "part.h"
+#include "physical_constants.h"
+#include "units.h"
+
+/**
+ * @brief Return a string containing the name of a given #chemistry_element.
+ */
+__attribute__((always_inline)) INLINE static const char*
+chemistry_get_element_name(enum chemistry_element elem) {
+
+  static const char* chemistry_element_names[chemistry_element_count] = {
+      "Hydrogen", "Helium",    "Carbon",  "Nitrogen", "Oxygen",
+      "Neon",     "Magnesium", "Silicon", "Iron"};
+
+  return chemistry_element_names[elem];
+}
+
+/**
+ * @brief Sets the chemistry properties of the (x-)particles to a valid start
+ * state.
+ *
+ * @param p Pointer to the particle data.
+ * @param xp Pointer to the extended particle data.
+ * @param data The global chemistry information.
+ */
+__attribute__((always_inline)) INLINE static void chemistry_first_init_part(
+    struct part* restrict p, struct xpart* restrict xp,
+    const struct chemistry_data* data) {
+
+  p->chemistry_data.metal_mass_fraction_total =
+      data->initial_metal_mass_fraction_total;
+  for (int elem = 0; elem < chemistry_element_count; ++elem)
+    p->chemistry_data.metal_mass_fraction[elem] =
+        data->initial_metal_mass_fraction[elem];
+}
+
+/**
+ * @brief Initialises the chemistry properties.
+ *
+ * @param parameter_file The parsed parameter file.
+ * @param us The current internal system of units.
+ * @param phys_const The physical constants in internal units.
+ * @param data The properties to initialise.
+ */
+static INLINE void chemistry_init_backend(
+    const struct swift_params* parameter_file, const struct unit_system* us,
+    const struct phys_const* phys_const, struct chemistry_data* data) {
+
+  /* Read the total metallicity */
+  data->initial_metal_mass_fraction_total =
+      parser_get_param_float(parameter_file, "EAGLEChemistry:InitMetallicity");
+
+  /* Read the individual mass fractions */
+  for (int elem = 0; elem < chemistry_element_count; ++elem) {
+    char buffer[50];
+    sprintf(buffer, "EAGLEChemistry:InitAbundance_%s",
+            chemistry_get_element_name(elem));
+
+    data->initial_metal_mass_fraction[elem] =
+        parser_get_param_float(parameter_file, buffer);
+  }
+
+  /* Read the constant ratios */
+  data->calcium_over_silicon_ratio = parser_get_param_float(
+      parameter_file, "EAGLEChemistry:CalciumOverSilicon");
+  data->sulphur_over_silicon_ratio = parser_get_param_float(
+      parameter_file, "EAGLEChemistry:SulphurOverSilicon");
+}
+
+/**
+ * @brief Prints the properties of the chemistry model to stdout.
+ *
+ * @brief The #chemistry_data containing information about the current model.
+ */
+static INLINE void chemistry_print_backend(const struct chemistry_data* data) {
+
+  message("Chemistry model is 'EAGLE' tracking %d elements.",
+          chemistry_element_count);
+}
+
+#endif /* SWIFT_CHEMISTRY_EAGLE_H */

src/chemistry/EAGLE/chemistry_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (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_CHEMISTRY_IO_EAGLE_H
+#define SWIFT_CHEMISTRY_IO_EAGLE_H
+
+#include "chemistry.h"
+#include "io_properties.h"
+
+/**
+ * @brief Specifies which particle fields to read from a dataset
+ *
+ * @param parts The particle array.
+ * @param list The list of i/o properties to read.
+ *
+ * @return Returns the number of fields to read.
+ */
+int chemistry_read_particles(struct part* parts, struct io_props* list) {
+
+  /* Nothing to read */
+  return 0;
+}
+
+/**
+ * @brief Specifies which particle fields to write to a dataset
+ *
+ * @param parts The particle array.
+ * @param list The list of i/o properties to write.
+ *
+ * @return Returns the number of fields to write.
+ */
+int chemistry_write_particles(const struct part* parts, struct io_props* list) {
+
+  /* List what we want to write */
+  list[0] = io_make_output_field("ElementAbundance", FLOAT,
+                                 chemistry_element_count, UNIT_CONV_NO_UNITS,
+                                 parts, chemistry_data.metal_mass_fraction);
+
+  list[1] = io_make_output_field(
+      "SmoothedElementAbundance", FLOAT, chemistry_element_count,
+      UNIT_CONV_NO_UNITS, parts, chemistry_data.smoothed_metal_mass_fraction);
+
+  list[2] =
+      io_make_output_field("Metallicity", FLOAT, 1, UNIT_CONV_NO_UNITS, parts,
+                           chemistry_data.metal_mass_fraction_total);
+
+  list[3] = io_make_output_field(
+      "SmoothedMetallicity", FLOAT, 1, UNIT_CONV_NO_UNITS, parts,
+      chemistry_data.smoothed_metal_mass_fraction_total);
+
+  list[4] = io_make_output_field("TotalMassFromSNIa", FLOAT, 1, UNIT_CONV_MASS,
+                                 parts, chemistry_data.mass_from_SNIa);
+
+  list[5] = io_make_output_field("MetalMassFracFromSNIa", FLOAT, 1,
+                                 UNIT_CONV_NO_UNITS, parts,
+                                 chemistry_data.metal_mass_fraction_from_SNIa);
+
+  list[6] = io_make_output_field("TotalMassFromAGB", FLOAT, 1, UNIT_CONV_MASS,
+                                 parts, chemistry_data.mass_from_AGB);
+
+  list[7] =
+      io_make_output_field("MetalMassFracFromAGB", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                           parts, chemistry_data.metal_mass_fraction_from_AGB);
+
+  list[8] = io_make_output_field("TotalMassFromSNII", FLOAT, 1, UNIT_CONV_MASS,
+                                 parts, chemistry_data.mass_from_SNII);
+
+  list[9] = io_make_output_field("MetalMassFracFromSNII", FLOAT, 1,
+                                 UNIT_CONV_NO_UNITS, parts,
+                                 chemistry_data.metal_mass_fraction_from_SNII);
+
+  list[10] =
+      io_make_output_field("IronMassFracFromSNIa", FLOAT, 1, UNIT_CONV_NO_UNITS,
+                           parts, chemistry_data.iron_mass_fraction_from_SNIa);
+
+  list[11] = io_make_output_field(
+      "SmoothedIronMassFracFromSNIa", FLOAT, 1, UNIT_CONV_NO_UNITS, parts,
+      chemistry_data.smoothed_iron_mass_fraction_from_SNIa);
+
+  return 12;
+}
+
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_grpsph The HDF5 group in which to write
+ */
+void chemistry_write_flavour(hid_t h_grp) {
+
+  io_write_attribute_s(h_grp, "Chemistry Model", "EAGLE");
+  for (int elem = 0; elem < chemistry_element_count; ++elem) {
+    char buffer[20];
+    sprintf(buffer, "Element %d", elem);
+    io_write_attribute_s(h_grp, buffer, chemistry_get_element_name(elem));
+  }
+}
+
+#endif /* SWIFT_CHEMISTRY_IO_EAGLE_H */

src/chemistry/EAGLE/chemistry_struct.h

+/*******************************************************************************
+ * 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_CHEMISTRY_STRUCT_EAGLE_H
+#define SWIFT_CHEMISTRY_STRUCT_EAGLE_H
+
+/**
+ * @brief The individual elements traced in the EAGLE model.
+ */
+enum chemistry_element {
+  chemistry_element_H = 0,
+  chemistry_element_He,
+  chemistry_element_C,
+  chemistry_element_N,
+  chemistry_element_O,
+  chemistry_element_Ne,
+  chemistry_element_Mg,
+  chemistry_element_Si,
+  chemistry_element_Fe,
+  chemistry_element_count
+};
+
+/**
+ * @brief Global chemical abundance information in the EAGLE model.
+ */
+struct chemistry_data {
+
+  /*! Fraction of the particle mass in given elements at the start of the run */
+  float initial_metal_mass_fraction[chemistry_element_count];
+
+  /*! Fraction of the particle mass in *all* metals at the start of the run */
+  float initial_metal_mass_fraction_total;
+
+  /*! Constant ratio of Calcium over Silicium */
+  float calcium_over_silicon_ratio;
+
+  /*! Constant ratio of Calcium over Silicium */
+  float sulphur_over_silicon_ratio;
+};
+
+/**
+ * @brief Chemical abundances traced by the #part in the EAGLE model.
+ */
+struct chemistry_part_data {
+
+  /*! Fraction of the particle mass in a given element */
+  float metal_mass_fraction[chemistry_element_count];
+
+  /*! Fraction of the particle mass in *all* metals */
+  float metal_mass_fraction_total;
+
+  /*! Smoothed fraction of the particle mass in a given element */
+  float smoothed_metal_mass_fraction[chemistry_element_count];
+
+  /*! Smoothed fraction of the particle mass in *all* metals */
+  float smoothed_metal_mass_fraction_total;
+
+  /*! Mass coming from SNIa */
+  float mass_from_SNIa;
+
+  /*! Fraction of total gas mass in metals coming from SNIa */
+  float metal_mass_fraction_from_SNIa;
+
+  /*! Mass coming from AGB */
+  float mass_from_AGB;
+
+  /*! Fraction of total gas mass in metals coming from AGB */
+  float metal_mass_fraction_from_AGB;
+
+  /*! Mass coming from SNII */
+  float mass_from_SNII;
+
+  /*! Fraction of total gas mass in metals coming from SNII */
+  float metal_mass_fraction_from_SNII;
+
+  /*! Fraction of total gas mass in Iron coming from SNIa */
+  float iron_mass_fraction_from_SNIa;
+
+  /*! Smoothed fraction of total gas mass in Iron coming from SNIa */
+  float smoothed_iron_mass_fraction_from_SNIa;
+};
+
+#endif /* SWIFT_CHEMISTRY_STRUCT_EAGLE_H */

src/chemistry/gear/chemistry.h

+/*******************************************************************************
+ * 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_CHEMISTRY_GEAR_H
+#define SWIFT_CHEMISTRY_GEAR_H
+
+/**
+ * @file src/chemistry/gear/chemistry.h
+ * @brief Empty infrastructure for the cases without chemistry function
+ */
+
+/* Some standard headers. */
+#include <float.h>
+#include <math.h>
+
+/* Local includes. */
+#include "chemistry_struct.h"
+#include "error.h"
+#include "hydro.h"
+#include "parser.h"
+#include "part.h"
+#include "physical_constants.h"
+#include "units.h"
+
+/**
+ * @brief Sets the chemistry properties of the (x-)particles to a valid start
+ * state.
+ *
+ * Nothing to do here.
+ *
+ * @param p Pointer to the particle data.
+ * @param xp Pointer to the extended particle data.
+ * @param data The global chemistry information.
+ */
+__attribute__((always_inline)) INLINE static void chemistry_first_init_part(
+    const struct part* restrict p, struct xpart* restrict xp,
+    const struct chemistry_data* data) {}
+
+/**
+ * @brief Initialises the chemistry properties.
+ *
+ * Nothing to do here.
+ *
+ * @param parameter_file The parsed parameter file.
+ * @param us The current internal system of units.
+ * @param phys_const The physical constants in internal units.
+ * @param data The properties to initialise.
+ */
+static INLINE void chemistry_init_backend(
+    const struct swift_params* parameter_file, const struct unit_system* us,
+    const struct phys_const* phys_const, struct chemistry_data* data) {}
+
+/**
+ * @brief Prints the properties of the chemistry model to stdout.
+ *
+ * @brief The #chemistry_data containing information about the current model.
+ */
+static INLINE void chemistry_print_backend(const struct chemistry_data* data) {
+
+  message("Chemistry function is 'gear'.");
+}
+
+#endif /* SWIFT_CHEMISTRY_GEAR_H */

src/chemistry/gear/chemistry_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (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_CHEMISTRY_IO_GEAR_H
+#define SWIFT_CHEMISTRY_IO_GEAR_H
+
+#include "io_properties.h"
+
+/**
+ * @brief Specifies which particle fields to read from a dataset
+ *
+ * @param parts The particle array.
+ * @param list The list of i/o properties to read.
+ *
+ * @return Returns the number of fields to read.
+ */
+int chemistry_read_particles(struct part* parts, struct io_props* list) {
+
+  /* List what we want to read */
+  list[0] =
+      io_make_input_field("HeDensity", FLOAT, 1, COMPULSORY, UNIT_CONV_DENSITY,
+                          parts, chemistry_data.he_density);
+
+  return 1;
+}
+
+/**
+ * @brief Specifies which particle fields to write to a dataset
+ *
+ * @param parts The particle array.
+ * @param list The list of i/o properties to write.
+ *
+ * @return Returns the number of fields to write.
+ */
+int chemistry_write_particles(const struct part* parts, struct io_props* list) {
+
+  /* List what we want to write */
+  list[0] = io_make_output_field("HeDensity", FLOAT, 1, UNIT_CONV_DENSITY,
+                                 parts, chemistry_data.he_density);
+
+  return 1;
+}
+
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_grpsph The HDF5 group in which to write
+ */
+void chemistry_write_flavour(hid_t h_grpsph) {
+
+  io_write_attribute_s(h_grpsph, "Chemistry Model", "GEAR");
+}
+
+#endif /* SWIFT_CHEMISTRY_IO_GEAR_H */

src/chemistry/gear/chemistry_struct.h

+/*******************************************************************************
+ * 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_CHEMISTRY_STRUCT_GEAR_H
+#define SWIFT_CHEMISTRY_STRUCT_GEAR_H
+
+/**
+ * @brief The individual elements traced in the model.
+ */
+enum chemistry_element { chemistry_element_count = 0 };
+
+/**
+ * @brief Global chemical abundance information.
+ */
+struct chemistry_data {};
+
+/**
+ * @brief Properties of the chemistry function.
+ */
+struct chemistry_part_data {
+  float he_density;
+};
+
+#endif /* SWIFT_CHEMISTRY_STRUCT_GEAR_H */

src/chemistry/none/chemistry.h

+/*******************************************************************************
+ * 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_CHEMISTRY_NONE_H
+#define SWIFT_CHEMISTRY_NONE_H
+
+/**
+ * @file src/chemistry/none/chemistry.h
+ * @brief Empty infrastructure for the cases without chemistry function
+ */
+
+/* Some standard headers. */
+#include <float.h>
+#include <math.h>
+
+/* Local includes. */
+#include "chemistry_struct.h"
+#include "error.h"
+#include "hydro.h"
+#include "parser.h"
+#include "part.h"
+#include "physical_constants.h"
+#include "units.h"
+
+/**
+ * @brief Sets the chemistry properties of the (x-)particles to a valid start
+ * state.
+ *
+ * Nothing to do here.
+ *
+ * @param p Pointer to the particle data.
+ * @param xp Pointer to the extended particle data.
+ * @param data The global chemistry information used for this run.
+ */
+__attribute__((always_inline)) INLINE static void chemistry_first_init_part(
+    const struct part* restrict p, struct xpart* restrict xp,
+    const struct chemistry_data* data) {}
+
+/**
+ * @brief Initialises the chemistry properties.
+ *
+ * Nothing to do here.
+ *
+ * @param parameter_file The parsed parameter file.
+ * @param us The current internal system of units.
+ * @param phys_const The physical constants in internal units.
+ * @param data The global chemistry information (to be filled).
+ */
+static INLINE void chemistry_init_backend(
+    const struct swift_params* parameter_file, const struct unit_system* us,
+    const struct phys_const* phys_const, struct chemistry_data* data) {}
+
+/**
+ * @brief Prints the properties of the chemistry model to stdout.
+ *
+ * @brief The #chemistry_data containing information about the current model.
+ */
+static INLINE void chemistry_print_backend(const struct chemistry_data* data) {
+
+  message("Chemistry function is 'No chemistry'.");
+}
+
+#endif /* SWIFT_CHEMISTRY_NONE_H */

src/chemistry/none/chemistry_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (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_CHEMISTRY_IO_NONE_H
+#define SWIFT_CHEMISTRY_IO_NONE_H
+
+#include "io_properties.h"
+
+/**
+ * @brief Specifies which particle fields to read from a dataset
+ *
+ * @param parts The particle array.
+ * @param list The list of i/o properties to read.
+ *
+ * @return Returns the number of fields to write.
+ */
+int chemistry_read_particles(struct part* parts, struct io_props* list) {
+
+  /* update list according to hydro_io */
+
+  /* Return the number of fields to read */
+  return 0;
+}
+
+/**
+ * @brief Specifies which particle fields to write to a dataset
+ *
+ * @param parts The particle array.
+ * @param list The list of i/o properties to write.
+ *
+ * @return Returns the number of fields to write.
+ */
+int chemistry_write_particles(const struct part* parts, struct io_props* list) {
+
+  /* update list according to hydro_io */
+
+  /* Return the number of fields to write */
+  return 0;
+}
+
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_grpsph The HDF5 group in which to write
+ */
+void chemistry_write_flavour(hid_t h_grpsph) {
+
+  io_write_attribute_s(h_grpsph, "Chemistry Model", "None");
+}
+
+#endif /* SWIFT_CHEMISTRY_IO_NONE_H */

src/chemistry/none/chemistry_struct.h

+/*******************************************************************************
+ * 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_CHEMISTRY_STRUCT_NONE_H
+#define SWIFT_CHEMISTRY_STRUCT_NONE_H
+
+/**
+ * @file src/chemistry/none/chemistry_struct.h
+ * @brief Empty infrastructure for the cases without chemistry function
+ */
+
+/**
+ * @brief The individual elements traced in the model.
+ */
+enum chemistry_element { chemistry_element_count = 0 };
+
+/**
+ * @brief Global chemical abundance information.
+ *
+ * Nothing here.
+ */
+struct chemistry_data {};
+
+/**
+ * @brief Chemistry properties carried by the #part.
+ *
+ * Nothing here.
+ */
+struct chemistry_part_data {};
+
+#endif /* SWIFT_CHEMISTRY_STRUCT_NONE_H */

src/chemistry_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Coypright (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_CHEMISTRY_IO_H
+#define SWIFT_CHEMISTRY_IO_H
+
+/* Config parameters. */
+#include "../config.h"
+
+/* Import the right functions */
+#if defined(CHEMISTRY_NONE)
+#include "./chemistry/none/chemistry_io.h"
+#elif defined(CHEMISTRY_GEAR)
+#include "./chemistry/gear/chemistry_io.h"
+#elif defined(CHEMISTRY_EAGLE)
+#include "./chemistry/EAGLE/chemistry_io.h"
+#else
+#error "Invalid choice of chemistry function."
+#endif
+
+#endif /* SWIFT_CHEMISTRY_IO_H */

src/chemistry_struct.h

+/*******************************************************************************
+ * 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_CHEMISTRY_STRUCT_H
+#define SWIFT_CHEMISTRY_STRUCT_H
+
+/**
+ * @file src/chemistry_struct.h
+ * @brief Branches between the different chemistry functions.
+ */
+
+/* Config parameters. */
+#include "../config.h"
+
+/* Import the right chemistry definition */
+#if defined(CHEMISTRY_NONE)
+#include "./chemistry/none/chemistry_struct.h"
+#elif defined(CHEMISTRY_GEAR)
+#include "./chemistry/gear/chemistry_struct.h"
+#elif defined(CHEMISTRY_EAGLE)
+#include "./chemistry/EAGLE/chemistry_struct.h"
+#else
+#error "Invalid choice of chemistry function."
+#endif
+
+#endif /* SWIFT_CHEMISTRY_STRUCT_H */

src/cooling/const_du/cooling.h

@@ -38,11 +38,22 @@
 #include "cooling_struct.h"
 #include "error.h"
 #include "hydro.h"
+#include "io_properties.h"
 #include "parser.h"
 #include "part.h"
 #include "physical_constants.h"
 #include "units.h"
 
+/**
+ * @brief Writes the current model of SPH to the file
+ * @param h_grpsph The HDF5 group in which to write
+ */
+__attribute__((always_inline)) INLINE static void cooling_write_flavour(
+    hid_t h_grpsph) {
+
+  io_write_attribute_s(h_grpsph, "Cooling Model", "Constant du/dt");
+}
+
 /**
  * @brief Apply the cooling function to a particle.
  *
@@ -120,9 +131,11 @@ __attribute__((always_inline)) INLINE static float cooling_timestep(
  *
  * @param p Pointer to the particle data.
  * @param xp Pointer to the extended particle data.
+ * @param cooling The properties of the cooling function.
  */
-__attribute__((always_inline)) INLINE static void cooling_init_part(
-    const struct part* restrict p, struct xpart* restrict xp) {
+__attribute__((always_inline)) INLINE static void cooling_first_init_part(
+    const struct part* restrict p, struct xpart* restrict xp,
+    const struct cooling_function_data* cooling) {
 
   xp->cooling_data.radiated_energy = 0.f;
 }