Merge branch 'improved_grackle' into 'master'

Add support for Grackle 3.0.

See merge request swift/swiftsim!499

configure.ac

@@ -962,7 +962,7 @@ esac
 #  Cooling function
 AC_ARG_WITH([cooling],
    [AS_HELP_STRING([--with-cooling=<function>],
-      [cooling function @<:@none, const-du, const-lambda, grackle default: none@:>@]
+      [cooling function @<:@none, const-du, const-lambda, EAGLE, grackle, grackle1, grackle2, grackle3 default: none@:>@]
    )],
    [with_cooling="$withval"],
    [with_cooling="none"]
@@ -979,7 +979,20 @@ case "$with_cooling" in
    ;;
    grackle)
       AC_DEFINE([COOLING_GRACKLE], [1], [Cooling via the grackle library])
+      AC_DEFINE([COOLING_GRACKLE_MODE], [0], [Grackle chemistry network, mode 0])
+   ;; 
+   grackle1)
+      AC_DEFINE([COOLING_GRACKLE], [1], [Cooling via the grackle library])
+      AC_DEFINE([COOLING_GRACKLE_MODE], [1], [Grackle chemistry network, mode 1])
    ;;
+   grackle2)
+      AC_DEFINE([COOLING_GRACKLE], [1], [Cooling via the grackle library])
+      AC_DEFINE([COOLING_GRACKLE_MODE], [2], [Grackle chemistry network, mode 2])
+   ;; 
+   grackle3)
+      AC_DEFINE([COOLING_GRACKLE], [1], [Cooling via the grackle library])
+      AC_DEFINE([COOLING_GRACKLE_MODE], [3], [Grackle chemistry network, mode 3])
+   ;; 
    EAGLE)
       AC_DEFINE([COOLING_EAGLE], [1], [Cooling following the EAGLE model])
    ;;

examples/CoolingBox/coolingBox.yml

@@ -42,11 +42,17 @@ LambdaCooling:
 
 # Cooling with Grackle 2.0
 GrackleCooling:
-  GrackleCloudyTable: ../CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
-  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
-
+  CloudyTable: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
+  WithUVbackground: 0 # Enable or not the UV background
+  Redshift: 0 # Redshift to use (-1 means time based redshift)
+  WithMetalCooling: 1 # Enable or not the metal cooling
+  ProvideVolumetricHeatingRates: 0 # User provide volumetric heating rates
+  ProvideSpecificHeatingRates: 0 # User provide specific heating rates
+  SelfShieldingMethod: 0 # Grackle (<= 3) or Gear self shielding method
+  OutputMode: 1 # Write in output corresponding primordial chemistry mode
+  MaxSteps: 1000
+  ConvergenceLimit: 1e-2
+  
 EAGLEChemistry:
   InitMetallicity:         0.
   InitAbundance_Hydrogen:  0.752
@@ -60,3 +66,6 @@ EAGLEChemistry:
   InitAbundance_Iron:      0.000
   CalciumOverSilicon:      0.0941736
   SulphurOverSilicon:      0.6054160
+
+GearChemistry:
+  InitialMetallicity: 0.01295

examples/main.c

@@ -124,7 +124,7 @@ int main(int argc, char *argv[]) {
 
   /* Structs used by the engine. Declare now to make sure these are always in
    * scope.  */
-  struct chemistry_data chemistry;
+  struct chemistry_global_data chemistry;
   struct cooling_function_data cooling_func;
   struct cosmology cosmo;
   struct external_potential potential;

examples/parameter_example.yml

@@ -179,12 +179,18 @@ LambdaCooling:
   hydrogen_mass_abundance:     0.75  # Hydrogen mass abundance (dimensionless)
   cooling_tstep_mult:          1.0   # Dimensionless pre-factor for the time-step condition
 
-# Cooling with Grackle 2.0
+# Cooling with Grackle 3.0
 GrackleCooling:
-  GrackleCloudyTable: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
-  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
+  CloudyTable: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
+  WithUVbackground: 1                   # Enable or not the UV background
+  Redshift: 0                           # Redshift to use (-1 means time based redshift)
+  WithMetalCooling: 1                   # Enable or not the metal cooling
+  ProvideVolumetricHeatingRates: 0      # (optional) User provide volumetric heating rates
+  ProvideSpecificHeatingRates: 0        # (optional) User provide specific heating rates
+  SelfShieldingMethod: 0                # (optional) Grackle (<= 3) or Gear self shielding method
+  OutputMode: 0                         # (optional) Write in output corresponding primordial chemistry mode
+  MaxSteps: 10000                       # (optional) Max number of step when computing the initial composition
+  ConvergenceLimit: 1e-2                # (optional) Convergence threshold (relative) for initial composition
 
 # Parameters related to chemistry models  -----------------------------------------------
 

src/Makefile.am

@@ -43,8 +43,8 @@ include_HEADERS = space.h runner.h queue.h task.h lock.h cell.h part.h const.h \
     engine.h swift.h serial_io.h timers.h debug.h scheduler.h proxy.h parallel_io.h \
     common_io.h single_io.h multipole.h map.h tools.h partition.h clocks.h parser.h \
     physical_constants.h physical_constants_cgs.h potential.h version.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 \
+    hydro_properties.h riemann.h threadpool.h cooling_io.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 \
     chemistry.h chemistry_io.h chemistry_struct.h cosmology.h restart.h
@@ -118,10 +118,15 @@ nobase_noinst_HEADERS = align.h approx_math.h atomic.h barrier.h cycle.h error.h
                  potential/isothermal/potential.h potential/disc_patch/potential.h \
                  potential/sine_wave/potential.h \
 		 cooling/none/cooling.h cooling/none/cooling_struct.h \
+                 cooling/none/cooling_io.h \
 	         cooling/const_du/cooling.h cooling/const_du/cooling_struct.h \
+                 cooling/const_du/cooling_io.h \
                  cooling/const_lambda/cooling.h cooling/const_lambda/cooling_struct.h \
+                 cooling/const_lambda/cooling_io.h \
                  cooling/grackle/cooling.h cooling/grackle/cooling_struct.h \
+                 cooling/grackle/cooling_io.h \
 		 cooling/EAGLE/cooling.h cooling/EAGLE/cooling_struct.h \
+                 cooling/EAGLE/cooling_io.h \
                  chemistry/none/chemistry.h \
 		 chemistry/none/chemistry_io.h \
 		 chemistry/none/chemistry_struct.h \

src/chemistry.c

@@ -36,7 +36,7 @@
 void chemistry_init(const struct swift_params* parameter_file,
                     const struct unit_system* us,
                     const struct phys_const* phys_const,
-                    struct chemistry_data* data) {
+                    struct chemistry_global_data* data) {
 
   chemistry_init_backend(parameter_file, us, phys_const, data);
 }
@@ -46,9 +46,10 @@ void chemistry_init(const struct swift_params* parameter_file,
  *
  * Calls chemistry_print_backend for the chosen chemistry model.
  *
- * @brief The #chemistry_data containing information about the current model.
+ * @brief The #chemistry_global_data containing information about the current
+ * model.
  */
-void chemistry_print(const struct chemistry_data* data) {
+void chemistry_print(const struct chemistry_global_data* data) {
   chemistry_print_backend(data);
 }
 
@@ -58,10 +59,10 @@ void chemistry_print(const struct chemistry_data* data) {
  * @param chemistry the struct
  * @param stream the file stream
  */
-void chemistry_struct_dump(const struct chemistry_data* chemistry,
+void chemistry_struct_dump(const struct chemistry_global_data* chemistry,
                            FILE* stream) {
-  restart_write_blocks((void*)chemistry, sizeof(struct chemistry_data), 1,
-                       stream, "chemistry", "chemistry function");
+  restart_write_blocks((void*)chemistry, sizeof(struct chemistry_global_data),
+                       1, stream, "chemistry", "chemistry function");
 }
 
 /**
@@ -71,8 +72,8 @@ void chemistry_struct_dump(const struct chemistry_data* chemistry,
  * @param chemistry the struct
  * @param stream the file stream
  */
-void chemistry_struct_restore(const struct chemistry_data* chemistry,
+void chemistry_struct_restore(const struct chemistry_global_data* chemistry,
                               FILE* stream) {
-  restart_read_blocks((void*)chemistry, sizeof(struct chemistry_data), 1,
+  restart_read_blocks((void*)chemistry, sizeof(struct chemistry_global_data), 1,
                       stream, NULL, "chemistry function");
 }

src/chemistry.h

@@ -46,14 +46,14 @@
 void chemistry_init(const struct swift_params* parameter_file,
                     const struct unit_system* us,
                     const struct phys_const* phys_const,
-                    struct chemistry_data* data);
+                    struct chemistry_global_data* data);
 
-void chemistry_print(const struct chemistry_data* data);
+void chemistry_print(const struct chemistry_global_data* data);
 
 /* Dump/restore. */
-void chemistry_struct_dump(const struct chemistry_data* chemistry,
+void chemistry_struct_dump(const struct chemistry_global_data* chemistry,
                            FILE* stream);
-void chemistry_struct_restore(const struct chemistry_data* chemistry,
+void chemistry_struct_restore(const struct chemistry_global_data* chemistry,
                               FILE* stream);
 
 #endif /* SWIFT_CHEMISTRY_H */

src/chemistry/EAGLE/chemistry.h

@@ -57,10 +57,10 @@ chemistry_get_element_name(enum chemistry_element elem) {
  * the various smooth metallicity tasks
  *
  * @param p The particle to act upon
- * @param cd #chemistry_data containing chemistry informations.
+ * @param cd #chemistry_global_data containing chemistry informations.
  */
 __attribute__((always_inline)) INLINE static void chemistry_init_part(
-    struct part* restrict p, const struct chemistry_data* cd) {}
+    struct part* restrict p, const struct chemistry_global_data* cd) {}
 
 /**
  * @brief Finishes the smooth metal calculation.
@@ -71,11 +71,11 @@ __attribute__((always_inline)) INLINE static void chemistry_init_part(
  * This function requires the #hydro_end_density to have been called.
  *
  * @param p The particle to act upon.
- * @param cd #chemistry_data containing chemistry informations.
+ * @param cd #chemistry_global_data containing chemistry informations.
  * @param cosmo The current cosmological model.
  */
 __attribute__((always_inline)) INLINE static void chemistry_end_density(
-    struct part* restrict p, const struct chemistry_data* cd,
+    struct part* restrict p, const struct chemistry_global_data* cd,
     const struct cosmology* cosmo) {}
 
 /**
@@ -87,8 +87,11 @@ __attribute__((always_inline)) INLINE static void chemistry_end_density(
  * @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) {
+    const struct phys_const* restrict phys_const,
+    const struct unit_system* restrict us,
+    const struct cosmology* restrict cosmo,
+    const struct chemistry_global_data* data, struct part* restrict p,
+    struct xpart* restrict xp) {
 
   p->chemistry_data.metal_mass_fraction_total =
       data->initial_metal_mass_fraction_total;
@@ -107,7 +110,7 @@ __attribute__((always_inline)) INLINE static void chemistry_first_init_part(
  */
 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) {
+    const struct phys_const* phys_const, struct chemistry_global_data* data) {
 
   /* Read the total metallicity */
   data->initial_metal_mass_fraction_total =
@@ -133,9 +136,11 @@ static INLINE void chemistry_init_backend(
 /**
  * @brief Prints the properties of the chemistry model to stdout.
  *
- * @brief The #chemistry_data containing information about the current model.
+ * @brief The #chemistry_global_data containing information about the current
+ * model.
  */
-static INLINE void chemistry_print_backend(const struct chemistry_data* data) {
+static INLINE void chemistry_print_backend(
+    const struct chemistry_global_data* data) {
 
   message("Chemistry model is 'EAGLE' tracking %d elements.",
           chemistry_element_count);

src/chemistry/EAGLE/chemistry_struct.h

@@ -38,7 +38,7 @@ enum chemistry_element {
 /**
  * @brief Global chemical abundance information in the EAGLE model.
  */
-struct chemistry_data {
+struct chemistry_global_data {
 
   /*! Fraction of the particle mass in given elements at the start of the run */
   float initial_metal_mass_fraction[chemistry_element_count];

src/chemistry/gear/chemistry.h

@@ -29,6 +29,7 @@
 #include <math.h>
 
 /* Local includes. */
+#include "chemistry_io.h"
 #include "chemistry_struct.h"
 #include "error.h"
 #include "hydro.h"
@@ -38,16 +39,16 @@
 #include "units.h"
 
 /**
- * @brief Return a string containing the name of a given #chemistry_element.
+ * @brief Compute the metal mass fraction
+ *
+ * @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 const char*
-chemistry_get_element_name(enum chemistry_element elem) {
-
-  static const char* chemistry_element_names[chemistry_element_count] = {
-      "Oxygen",    "Magnesium", "Sulfur", "Iron",    "Zinc",
-      "Strontium", "Yttrium",   "Barium", "Europium"};
-
-  return chemistry_element_names[elem];
+__attribute__((always_inline)) INLINE static float
+chemistry_metal_mass_fraction(const struct part* restrict p,
+                              const struct xpart* restrict xp) {
+  return p->chemistry_data.Z;
 }
 
 /**
@@ -62,16 +63,10 @@ chemistry_get_element_name(enum chemistry_element elem) {
  */
 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) {}
+    const struct phys_const* phys_const, struct chemistry_global_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'.");
+  /* read parameters */
+  chemistry_read_parameters(parameter_file, us, phys_const, data);
 }
 
 /**
@@ -81,10 +76,10 @@ static INLINE void chemistry_print_backend(const struct chemistry_data* data) {
  * the various smooth metallicity tasks
  *
  * @param p The particle to act upon
- * @param cd #chemistry_data containing chemistry informations.
+ * @param cd #chemistry_global_data containing chemistry informations.
  */
 __attribute__((always_inline)) INLINE static void chemistry_init_part(
-    struct part* restrict p, const struct chemistry_data* cd) {
+    struct part* restrict p, const struct chemistry_global_data* cd) {
 
   struct chemistry_part_data* cpd = &p->chemistry_data;
 
@@ -102,11 +97,11 @@ __attribute__((always_inline)) INLINE static void chemistry_init_part(
  * This function requires the #hydro_end_density to have been called.
  *
  * @param p The particle to act upon.
- * @param cd #chemistry_data containing chemistry informations.
+ * @param cd #chemistry_global_data containing chemistry informations.
  * @param cosmo The current cosmological model.
  */
 __attribute__((always_inline)) INLINE static void chemistry_end_density(
-    struct part* restrict p, const struct chemistry_data* cd,
+    struct part* restrict p, const struct chemistry_global_data* cd,
     const struct cosmology* cosmo) {
 
   /* Some smoothing length multiples. */
@@ -138,8 +133,13 @@ __attribute__((always_inline)) INLINE static void chemistry_end_density(
  * @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) {
+    const struct phys_const* restrict phys_const,
+    const struct unit_system* restrict us,
+    const struct cosmology* restrict cosmo,
+    const struct chemistry_global_data* data, struct part* restrict p,
+    struct xpart* restrict xp) {
+
+  p->chemistry_data.Z = data->initial_metallicity;
   chemistry_init_part(p, data);
 }
 

src/chemistry/gear/chemistry_io.h

@@ -19,9 +19,38 @@
 #ifndef SWIFT_CHEMISTRY_IO_GEAR_H
 #define SWIFT_CHEMISTRY_IO_GEAR_H
 
-#include "chemistry.h"
 #include "chemistry_struct.h"
+#include "error.h"
 #include "io_properties.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] = {
+      "Oxygen",    "Magnesium", "Sulfur", "Iron",    "Zinc",
+      "Strontium", "Yttrium",   "Barium", "Europium"};
+
+  return chemistry_element_names[elem];
+}
+
+/**
+ * @brief Prints the properties of the chemistry model to stdout.
+ *
+ * @brief The #chemistry_global_data containing information about the current
+ * model.
+ */
+static INLINE void chemistry_print_backend(
+    const struct chemistry_global_data* data) {
+
+  message("Chemistry function is 'Gear'.");
+}
 
 /**
  * @brief Specifies which particle fields to read from a dataset
@@ -31,13 +60,25 @@
  *
  * @return Returns the number of fields to read.
  */
-int chemistry_read_particles(struct part* parts, struct io_props* list) {
+__attribute__((always_inline)) INLINE static int chemistry_read_particles(
+    struct part* parts, struct io_props* list) {
 
   /* List what we want to read */
   list[0] = io_make_input_field(
       "ElementAbundance", FLOAT, chemistry_element_count, OPTIONAL,
       UNIT_CONV_NO_UNITS, parts, chemistry_data.metal_mass_fraction);
-  return 1;
+  list[1] = io_make_input_field("Z", FLOAT, 1, OPTIONAL, UNIT_CONV_NO_UNITS,
+                                parts, chemistry_data.Z);
+
+  return 2;
+}
+
+__attribute__((always_inline)) INLINE static void chemistry_read_parameters(
+    const struct swift_params* parameter_file, const struct unit_system* us,
+    const struct phys_const* phys_const, struct chemistry_global_data* data) {
+
+  data->initial_metallicity = parser_get_opt_param_float(
+      parameter_file, "GearChemistry:InitialMetallicity", -1);
 }
 
 /**
@@ -48,18 +89,21 @@ int chemistry_read_particles(struct part* parts, struct io_props* list) {
  *
  * @return Returns the number of fields to write.
  */
-int chemistry_write_particles(const struct part* parts, struct io_props* list) {
+__attribute__((always_inline)) INLINE static int chemistry_write_particles(
+    const struct part* parts, struct io_props* list) {
 
   /* List what we want to write */
   list[0] = io_make_output_field(
       "SmoothedElementAbundance", FLOAT, chemistry_element_count,
       UNIT_CONV_NO_UNITS, parts, chemistry_data.smoothed_metal_mass_fraction);
+  list[1] = io_make_output_field("Z", FLOAT, 1, UNIT_CONV_NO_UNITS, parts,
+                                 chemistry_data.Z);
 
-  list[1] = io_make_output_field("ElementAbundance", FLOAT,
+  list[2] = io_make_output_field("ElementAbundance", FLOAT,
                                  chemistry_element_count, UNIT_CONV_NO_UNITS,
                                  parts, chemistry_data.metal_mass_fraction);
 
-  return 2;
+  return 3;
 }
 
 #ifdef HAVE_HDF5
@@ -68,7 +112,8 @@ int chemistry_write_particles(const struct part* parts, struct io_props* list) {
  * @brief Writes the current model of SPH to the file
  * @param h_grp The HDF5 group in which to write
  */
-void chemistry_write_flavour(hid_t h_grp) {
+__attribute__((always_inline)) INLINE static void chemistry_write_flavour(
+    hid_t h_grp) {
 
   io_write_attribute_s(h_grp, "Chemistry Model", "GEAR");
   for (enum chemistry_element i = chemistry_element_O;

src/chemistry/gear/chemistry_struct.h

@@ -38,7 +38,11 @@ enum chemistry_element {
 /**
  * @brief Global chemical abundance information.
  */
-struct chemistry_data {};
+struct chemistry_global_data {
+
+  /* Initial metallicity Z */
+  float initial_metallicity;
+};
 
 /**
  * @brief Properties of the chemistry function.
@@ -50,6 +54,8 @@ struct chemistry_part_data {
 
   /*! Smoothed fraction of the particle mass in a given element */
   float smoothed_metal_mass_fraction[chemistry_element_count];
+
+  float Z;
 };
 
 #endif /* SWIFT_CHEMISTRY_STRUCT_GEAR_H */

src/chemistry/none/chemistry.h

@@ -61,14 +61,16 @@ chemistry_get_element_name(enum chemistry_element elem) {
  */
 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) {}
+    const struct phys_const* phys_const, struct chemistry_global_data* data) {}
 
 /**
  * @brief Prints the properties of the chemistry model to stdout.
  *
- * @brief The #chemistry_data containing information about the current model.
+ * @brief The #chemistry_global_data containing information about the current
+ * model.
  */
-static INLINE void chemistry_print_backend(const struct chemistry_data* data) {
+static INLINE void chemistry_print_backend(
+    const struct chemistry_global_data* data) {
 
   message("Chemistry function is 'No chemistry'.");
 }
@@ -81,7 +83,7 @@ static INLINE void chemistry_print_backend(const struct chemistry_data* data) {
  * @param cosmo The current cosmological model.
  */
 __attribute__((always_inline)) INLINE static void chemistry_end_density(
-    struct part* restrict p, const struct chemistry_data* cd,
+    struct part* restrict p, const struct chemistry_global_data* cd,
     const struct cosmology* cosmo) {}
 
 /**
@@ -90,13 +92,19 @@ __attribute__((always_inline)) INLINE static void chemistry_end_density(
  *
  * Nothing to do here.
  *
+ * @param phys_const The physical constant in internal units.
+ * @param us The unit system.
+ * @param cosmo The current cosmological model.
+ * @param data The global chemistry information used for this run.
  * @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) {}
+    const struct phys_const* restrict phys_const,
+    const struct unit_system* restrict us,
+    const struct cosmology* restrict cosmo,
+    const struct chemistry_global_data* data, const struct part* restrict p,
+    struct xpart* restrict xp) {}
 
 /**
  * @brief Sets the chemistry properties of the (x-)particles to a valid start
@@ -108,6 +116,6 @@ __attribute__((always_inline)) INLINE static void chemistry_first_init_part(
  * @param data The global chemistry information.
  */
 __attribute__((always_inline)) INLINE static void chemistry_init_part(
-    struct part* restrict p, const struct chemistry_data* data) {}
+    struct part* restrict p, const struct chemistry_global_data* data) {}
 
 #endif /* SWIFT_CHEMISTRY_NONE_H */

src/chemistry/none/chemistry_struct.h

@@ -34,7 +34,7 @@ enum chemistry_element { chemistry_element_count = 0 };
  *
  * Nothing here.
  */
-struct chemistry_data {};
+struct chemistry_global_data {};
 
 /**
  * @brief Chemistry properties carried by the #part.

src/cooling/EAGLE/cooling.h

@@ -20,10 +20,13 @@
 #define SWIFT_COOLING_EAGLE_H
 
 /**
- * @file src/cooling/none/cooling.h
- * @brief Empty infrastructure for the cases without cooling function
+ * @file src/cooling/EAGLE/cooling.h
+ * @brief EAGLE cooling function
  */
 
+/* Config parameters. */
+#include "../config.h"
+
 /* Some standard headers. */
 #include <float.h>
 #include <math.h>
@@ -31,25 +34,11 @@
 /* Local includes. */
 #include "error.h"
 #include "hydro.h"
-#include "io_properties.h"
 #include "parser.h"
 #include "part.h"
 #include "physical_constants.h"
 #include "units.h"
 
-#ifdef HAVE_HDF5
-
-/**
- * @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", "EAGLE");
-}
-#endif
-
 /**
  * @brief Apply the cooling function to a particle.
  *
@@ -95,8 +84,11 @@ __attribute__((always_inline)) INLINE static float cooling_timestep(
  * @param cooling The properties of the cooling function.
  */
 __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) {}
+    const struct phys_const* restrict phys_const,
+    const struct unit_system* restrict us,
+    const struct cosmology* restrict cosmo,
+    const struct cooling_function_data* restrict cooling,
+    const struct part* restrict p, struct xpart* restrict xp) {}
 
 /**
  * @brief Returns the total radiated energy by this particle.

src/cooling/EAGLE/cooling_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2017 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_EAGLE_IO_H
+#define SWIFT_COOLING_EAGLE_IO_H
+
+/* Config parameters. */
+#include "../config.h"
+
+/* Local includes */
+#include "io_properties.h"
+
+#ifdef HAVE_HDF5
+
+/**
+ * @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", "EAGLE");
+}
+#endif
+
+/**
+ * @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.
+ * @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 xpart* xparts, struct io_props* list,
+    const struct cooling_function_data* cooling) {
+  return 0;
+}
+
+#endif /* SWIFT_COOLING_EAGLE_IO_H */

src/cooling/const_du/cooling.h

@@ -30,33 +30,21 @@
  * realistic functions.
  */
 
+/* Config parameters. */
+#include "../config.h"
+
 /* Some standard headers. */
 #include <math.h>
 
 /* Local includes. */
 #include "const.h"
-#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"
 
-#ifdef HAVE_HDF5
-
-/**
- * @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");
-}
-#endif
-
 /**
  * @brief Apply the cooling function to a particle.
  *
@@ -141,8 +129,11 @@ __attribute__((always_inline)) INLINE static float cooling_timestep(
  * @param cooling The properties of the cooling function.
  */
 __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) {
+    const struct phys_const* restrict phys_const,
+    const struct unit_system* restrict us,
+    const struct cosmology* restrict cosmo,
+    const struct cooling_function_data* restrict cooling,
+    const struct part* restrict p, struct xpart* restrict xp) {
 
   xp->cooling_data.radiated_energy = 0.f;
 }

src/cooling/const_du/cooling_io.h

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ *                    Richard Bower (r.g.bower@durham.ac.uk)
+ *                    Stefan Arridge  (stefan.arridge@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.
+ *