diff --git a/configure.ac b/configure.ac
index e730619ea17ce87df7b5c62225094e1d7d0e34db..58f25b1eedbab44f9e3f0ecbf157f6c394674f78 100644
--- a/configure.ac
+++ b/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])
;;
diff --git a/examples/CoolingBox/coolingBox.yml b/examples/CoolingBox/coolingBox.yml
index c2ada783a316a08ee729907ba69e9a66aebe6910..2bd2f19f6d78388ae638521f590255d410bc8697 100644
--- a/examples/CoolingBox/coolingBox.yml
+++ b/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
diff --git a/examples/main.c b/examples/main.c
index ca91c9e718cca9f7f8d82fce2f5d237f9f5b98e4..39177560981c8d292ff4e69d871db7515645431c 100644
--- a/examples/main.c
+++ b/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;
diff --git a/examples/parameter_example.yml b/examples/parameter_example.yml
index 0a81716a3e34bbb305916b1148a9d8199b84fa5a..edf1afe51a1169c672eedc6fc629e044dda0d966 100644
--- a/examples/parameter_example.yml
+++ b/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 -----------------------------------------------
diff --git a/src/Makefile.am b/src/Makefile.am
index 1bd80b669396d4b4597f6149acafe6b1a4165f43..e21cb6539d2b7ae360ea07c92c426e99342bc2ec 100644
--- a/src/Makefile.am
+++ b/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 \
diff --git a/src/chemistry.c b/src/chemistry.c
index 091a0b363d16507894f3dcbba2ca79860f3cbaa9..44cbea1361d96c4cf1d4d3d21c3c91e5225640a5 100644
--- a/src/chemistry.c
+++ b/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");
}
diff --git a/src/chemistry.h b/src/chemistry.h
index a5cbd77efbaab99e98ca5f031512e7e5bef0a613..77b8d5b5fa5314d692fb8f46c8e6229b57119a6c 100644
--- a/src/chemistry.h
+++ b/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 */
diff --git a/src/chemistry/EAGLE/chemistry.h b/src/chemistry/EAGLE/chemistry.h
index ae333252426f5fb79cc1fd1cee818754483214f8..fa63c8cc877861d443d6cdb3cc1c8f0c94befefe 100644
--- a/src/chemistry/EAGLE/chemistry.h
+++ b/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);
diff --git a/src/chemistry/EAGLE/chemistry_struct.h b/src/chemistry/EAGLE/chemistry_struct.h
index e76e082d9b92bcde800b084feea44515b9579dc8..9093709e62d0af638ae485bd1154a4537791e84a 100644
--- a/src/chemistry/EAGLE/chemistry_struct.h
+++ b/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];
diff --git a/src/chemistry/gear/chemistry.h b/src/chemistry/gear/chemistry.h
index e9d3d00febe2438c52728f94d0136fb72ff8dc3b..9653e7eb05005977c39bca20eab961af83f40b5f 100644
--- a/src/chemistry/gear/chemistry.h
+++ b/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);
}
diff --git a/src/chemistry/gear/chemistry_io.h b/src/chemistry/gear/chemistry_io.h
index 9b0852fa2d23c8dd3e4d36406b55f4353d23b807..2343b6ba18ada5d04825a12d53a6f9cc7e984ef2 100644
--- a/src/chemistry/gear/chemistry_io.h
+++ b/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;
diff --git a/src/chemistry/gear/chemistry_struct.h b/src/chemistry/gear/chemistry_struct.h
index b0ddee2b37c2d1126523ff7a4283f5c18ae3a7b4..c3443126cf0ac72c76774d9000fe218378cc6663 100644
--- a/src/chemistry/gear/chemistry_struct.h
+++ b/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 */
diff --git a/src/chemistry/none/chemistry.h b/src/chemistry/none/chemistry.h
index 7fb83339bed6fc2db007e58a5b8372f003186db5..3ca51660ddfeead2b7ad0010979b719e59c4934e 100644
--- a/src/chemistry/none/chemistry.h
+++ b/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 */
diff --git a/src/chemistry/none/chemistry_struct.h b/src/chemistry/none/chemistry_struct.h
index 8ac5f6924c6893717033cd5f144fe873f6f17e24..a80699d66cccd2e290555006d45216ff53d9c99c 100644
--- a/src/chemistry/none/chemistry_struct.h
+++ b/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.
diff --git a/src/cooling/EAGLE/cooling.h b/src/cooling/EAGLE/cooling.h
index 62d1cc9b72681fe96c901185a10efe5523b206e3..bdf3801887256cb97ae1d5b6a3095250764aa822 100644
--- a/src/cooling/EAGLE/cooling.h
+++ b/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.
diff --git a/src/cooling/EAGLE/cooling_io.h b/src/cooling/EAGLE/cooling_io.h
new file mode 100644
index 0000000000000000000000000000000000000000..d6ed4f122863be7b591b095b11803a3d2729f694
--- /dev/null
+++ b/src/cooling/EAGLE/cooling_io.h
@@ -0,0 +1,56 @@
+/*******************************************************************************
+ * 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 */
diff --git a/src/cooling/const_du/cooling.h b/src/cooling/const_du/cooling.h
index 25aa974e47b277d0dfcc21077e5041a49e8168c8..ba8211174919419c37856dc1fcbdaa73b23e319e 100644
--- a/src/cooling/const_du/cooling.h
+++ b/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;
}
diff --git a/src/cooling/const_du/cooling_io.h b/src/cooling/const_du/cooling_io.h
new file mode 100644
index 0000000000000000000000000000000000000000..52a943aca86e51665fd1841d7bcb8a100b046ed8
--- /dev/null
+++ b/src/cooling/const_du/cooling_io.h
@@ -0,0 +1,58 @@
+/*******************************************************************************
+ * 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.
+ *
+ * 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_CONST_DU_IO_H
+#define SWIFT_COOLING_CONST_DU_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", "Constant du/dt");
+}
+#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_CONST_DU_IO_H */
diff --git a/src/cooling/const_lambda/cooling.h b/src/cooling/const_lambda/cooling.h
index a402b749300e64ef79253764c402d41f5a214d82..43ca7ab75b0bce370d7405e52cea9b54335ae73c 100644
--- a/src/cooling/const_lambda/cooling.h
+++ b/src/cooling/const_lambda/cooling.h
@@ -23,6 +23,9 @@
#ifndef SWIFT_COOLING_CONST_LAMBDA_H
#define SWIFT_COOLING_CONST_LAMBDA_H
+/* Config parameters. */
+#include "../config.h"
+
/* Some standard headers. */
#include <float.h>
#include <math.h>
@@ -31,25 +34,11 @@
#include "const.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 Lambda");
-}
-#endif
-
/**
* @brief Calculates du/dt in code units for a particle.
*
@@ -154,8 +143,11 @@ __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;
}
diff --git a/src/cooling/const_lambda/cooling_io.h b/src/cooling/const_lambda/cooling_io.h
new file mode 100644
index 0000000000000000000000000000000000000000..89c9471a291a4a6a5740a8c6c816913cbc6316a0
--- /dev/null
+++ b/src/cooling/const_lambda/cooling_io.h
@@ -0,0 +1,59 @@
+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2016 Tom Theuns (tom.theuns@durham.ac.uk)
+ * 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.
+ *
+ * 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_CONST_LAMBDA_IO_H
+#define SWIFT_COOLING_CONST_LAMBDA_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", "Constant Lambda");
+}
+#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_CONST_LAMBDA_IO_H */
diff --git a/src/cooling/grackle/cooling.h b/src/cooling/grackle/cooling.h
index d1da52300121ca56feea4114d74322120bd501ce..dd59e9af1431681a8c5bdc1e5cb0c22053063651 100644
--- a/src/cooling/grackle/cooling.h
+++ b/src/cooling/grackle/cooling.h
@@ -20,19 +20,24 @@
#define SWIFT_COOLING_GRACKLE_H
/**
- * @file src/cooling/none/cooling.h
- * @brief Empty infrastructure for the cases without cooling function
+ * @file src/cooling/grackle/cooling.h
+ * @brief Cooling using the GRACKLE 3.0 library.
*/
+/* Config parameters. */
+#include "../config.h"
+
/* Some standard headers. */
#include <float.h>
-#include <grackle.h>
#include <math.h>
+/* The grackle library itself */
+#include <grackle.h>
+
/* Local includes. */
+#include "chemistry.h"
#include "error.h"
#include "hydro.h"
-#include "io_properties.h"
#include "parser.h"
#include "part.h"
#include "physical_constants.h"
@@ -42,18 +47,147 @@
#define GRACKLE_NPART 1
#define GRACKLE_RANK 3
-#ifdef HAVE_HDF5
+/* prototypes */
+static gr_float cooling_time(
+ 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);
+
+static double cooling_rate(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, double dt);
/**
- * @brief Writes the current model of SPH to the file
- * @param h_grpsph The HDF5 group in which to write
+ * @brief Print the chemical network
+ *
+ * @param xp The #xpart to print
*/
-__attribute__((always_inline)) INLINE static void cooling_write_flavour(
- hid_t h_grpsph) {
+__attribute__((always_inline)) INLINE static void cooling_print_fractions(
+ const struct xpart* restrict xp) {
+
+ const struct cooling_xpart_data tmp = xp->cooling_data;
+#if COOLING_GRACKLE_MODE > 0
+ message("HI %g, HII %g, HeI %g, HeII %g, HeIII %g, e %g", tmp.HI_frac,
+ tmp.HII_frac, tmp.HeI_frac, tmp.HeII_frac, tmp.HeIII_frac,
+ tmp.e_frac);
+#endif
- io_write_attribute_s(h_grpsph, "Cooling Model", "Grackle");
+#if COOLING_GRACKLE_MODE > 1
+ message("HM %g, H2I %g, H2II %g", tmp.HM_frac, tmp.H2I_frac, tmp.H2II_frac);
+#endif
+
+#if COOLING_GRACKLE_MODE > 2
+ message("DI %g, DII %g, HDI %g", tmp.DI_frac, tmp.DII_frac, tmp.HDI_frac);
+#endif
+ message("Metal: %g", tmp.metal_frac);
}
+
+/**
+ * @brief Check if the difference of a given field is lower than limit
+ *
+ * @param xp First #xpart
+ * @param old Second #xpart
+ * @param field The field to check
+ * @param limit Difference limit
+ *
+ * @return 0 if diff > limit
+ */
+#define cooling_check_field(xp, old, field, limit) \
+ ({ \
+ float tmp = xp->cooling_data.field - old->cooling_data.field; \
+ tmp = fabs(tmp) / xp->cooling_data.field; \
+ if (tmp > limit) return 0; \
+ })
+
+/**
+ * @brief Check if difference between two particles is lower than a given value
+ *
+ * @param xp One of the #xpart
+ * @param old The other #xpart
+ * @param limit The difference limit
+ */
+__attribute__((always_inline)) INLINE static int cooling_converged(
+ const struct xpart* restrict xp, const struct xpart* restrict old,
+ const float limit) {
+
+#if COOLING_GRACKLE_MODE > 0
+ cooling_check_field(xp, old, HI_frac, limit);
+ cooling_check_field(xp, old, HII_frac, limit);
+ cooling_check_field(xp, old, HeI_frac, limit);
+ cooling_check_field(xp, old, HeII_frac, limit);
+ cooling_check_field(xp, old, HeIII_frac, limit);
+ cooling_check_field(xp, old, e_frac, limit);
#endif
+#if COOLING_GRACKLE_MODE > 1
+ cooling_check_field(xp, old, HM_frac, limit);
+ cooling_check_field(xp, old, H2I_frac, limit);
+ cooling_check_field(xp, old, H2II_frac, limit);
+#endif
+
+#if COOLING_GRACKLE_MODE > 2
+ cooling_check_field(xp, old, DI_frac, limit);
+ cooling_check_field(xp, old, DII_frac, limit);
+ cooling_check_field(xp, old, HDI_frac, limit);
+#endif
+
+ return 1;
+}
+
+/**
+ * @brief Compute equilibrium fraction
+ *
+ * @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_compute_equilibrium(
+ 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) {
+
+ /* get temporary data */
+ struct part p_tmp = *p;
+ struct cooling_function_data cooling_tmp = *cooling;
+ cooling_tmp.chemistry.with_radiative_cooling = 0;
+ /* need density for computation, therefore quick estimate */
+ p_tmp.rho = 0.2387 * p_tmp.mass / pow(p_tmp.h, 3);
+
+ /* compute time step */
+ const double alpha = 0.01;
+ double dt =
+ fabs(cooling_time(phys_const, us, cosmo, &cooling_tmp, &p_tmp, xp));
+ cooling_rate(phys_const, us, cosmo, &cooling_tmp, &p_tmp, xp, dt);
+ dt = alpha *
+ fabs(cooling_time(phys_const, us, cosmo, &cooling_tmp, &p_tmp, xp));
+
+ /* init simple variables */
+ int step = 0;
+ const int max_step = cooling_tmp.max_step;
+ const float conv_limit = cooling_tmp.convergence_limit;
+ struct xpart old;
+
+ do {
+ /* update variables */
+ step += 1;
+ old = *xp;
+
+ /* update chemistry */
+ cooling_rate(phys_const, us, cosmo, &cooling_tmp, &p_tmp, xp, dt);
+ } while (step < max_step && !cooling_converged(xp, &old, conv_limit));
+
+ if (step == max_step)
+ error(
+ "A particle element fraction failed to converge."
+ "You can change 'GrackleCooling:MaxSteps' or "
+ "'GrackleCooling:ConvergenceLimit' to avoid this problem");
+}
/**
* @brief Sets the cooling properties of the (x-)particles to a valid start
@@ -64,10 +198,46 @@ __attribute__((always_inline)) INLINE static void cooling_write_flavour(
* @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* cooling, const struct part* restrict p,
+ struct xpart* restrict xp) {
xp->cooling_data.radiated_energy = 0.f;
+
+#if COOLING_GRACKLE_MODE >= 1
+ gr_float zero = 1.e-20;
+
+ /* primordial chemistry >= 1 */
+ xp->cooling_data.HI_frac = zero;
+ xp->cooling_data.HII_frac = grackle_data->HydrogenFractionByMass;
+ xp->cooling_data.HeI_frac = 1. - grackle_data->HydrogenFractionByMass;
+ xp->cooling_data.HeII_frac = zero;
+ xp->cooling_data.HeIII_frac = zero;
+ xp->cooling_data.e_frac = xp->cooling_data.HII_frac +
+ 0.25 * xp->cooling_data.HeII_frac +
+ 0.5 * xp->cooling_data.HeIII_frac;
+#endif // MODE >= 1
+
+#if COOLING_GRACKLE_MODE >= 2
+ /* primordial chemistry >= 2 */
+ xp->cooling_data.HM_frac = zero;
+ xp->cooling_data.H2I_frac = zero;
+ xp->cooling_data.H2II_frac = zero;
+#endif // MODE >= 2
+
+#if COOLING_GRACKLE_MODE >= 3
+ /* primordial chemistry >= 3 */
+ xp->cooling_data.DI_frac = grackle_data->DeuteriumToHydrogenRatio *
+ grackle_data->HydrogenFractionByMass;
+ xp->cooling_data.DII_frac = zero;
+ xp->cooling_data.HDI_frac = zero;
+#endif // MODE >= 3
+
+#if COOLING_GRACKLE_MODE > 0
+ cooling_compute_equilibrium(phys_const, us, cosmo, cooling, p, xp);
+#endif
}
/**
@@ -90,17 +260,17 @@ __attribute__((always_inline)) INLINE static void cooling_print_backend(
const struct cooling_function_data* cooling) {
message("Cooling function is 'Grackle'.");
- message("Using Grackle = %i", cooling->chemistry.use_grackle);
- message("Chemical network = %i",
- cooling->chemistry.primordial_chemistry);
- message("Radiative cooling = %i",
- cooling->chemistry.with_radiative_cooling);
- message("Metal cooling = %i", cooling->chemistry.metal_cooling);
-
- message("CloudyTable = %s", cooling->cloudy_table);
- message("UVbackground = %d", cooling->uv_background);
- message("Redshift = %g", cooling->redshift);
- message("Density Self Shielding = %g", cooling->density_self_shielding);
+ message("Using Grackle = %i", cooling->chemistry.use_grackle);
+ message("Chemical network = %i", cooling->chemistry.primordial_chemistry);
+ message("CloudyTable = %s", cooling->cloudy_table);
+ message("Redshift = %g", cooling->redshift);
+ message("UV background = %d", cooling->with_uv_background);
+ message("Metal cooling = %i", cooling->chemistry.metal_cooling);
+ message("Self Shielding = %i", cooling->self_shielding_method);
+ message("Specific Heating Rates = %i",
+ cooling->provide_specific_heating_rates);
+ message("Volumetric Heating Rates = %i",
+ cooling->provide_volumetric_heating_rates);
message("Units:");
message("\tComoving = %i", cooling->units.comoving_coordinates);
message("\tLength = %g", cooling->units.length_units);
@@ -110,29 +280,221 @@ __attribute__((always_inline)) INLINE static void cooling_print_backend(
}
/**
- * @brief Compute the cooling rate
+ * @brief copy a single field from the grackle data to a #xpart
+ *
+ * @param data The #grackle_field_data
+ * @param xp The #xpart
+ * @param rho Particle density
+ * @param field The field to copy
+ */
+#define cooling_copy_field_from_grackle(data, xp, rho, field) \
+ xp->cooling_data.field##_frac = *data.field##_density / rho;
+
+/**
+ * @brief copy a single field from a #xpart to the grackle data
+ *
+ * @param data The #grackle_field_data
+ * @param xp The #xpart
+ * @param rho Particle density
+ * @param field The field to copy
+ */
+#define cooling_copy_field_to_grackle(data, xp, rho, field) \
+ gr_float grackle_##field = xp->cooling_data.field##_frac * rho; \
+ data.field##_density = &grackle_##field;
+
+/**
+ * @brief copy a #xpart to the grackle data
+ *
+ * Warning this function creates some variable, therefore the grackle call
+ * should be in a block that still has the variables.
+ *
+ * @param data The #grackle_field_data
+ * @param p The #part
+ * @param xp The #xpart
+ * @param rho Particle density
+ */
+#if COOLING_GRACKLE_MODE > 0
+#define cooling_copy_to_grackle1(data, p, xp, rho) \
+ cooling_copy_field_to_grackle(data, xp, rho, HI); \
+ cooling_copy_field_to_grackle(data, xp, rho, HII); \
+ cooling_copy_field_to_grackle(data, xp, rho, HeI); \
+ cooling_copy_field_to_grackle(data, xp, rho, HeII); \
+ cooling_copy_field_to_grackle(data, xp, rho, HeIII); \
+ cooling_copy_field_to_grackle(data, xp, rho, e);
+#else
+#define cooling_copy_to_grackle1(data, p, xp, rho) \
+ data.HI_density = NULL; \
+ data.HII_density = NULL; \
+ data.HeI_density = NULL; \
+ data.HeII_density = NULL; \
+ data.HeIII_density = NULL; \
+ data.e_density = NULL;
+#endif
+
+/**
+ * @brief copy a #xpart to the grackle data
+ *
+ * Warning this function creates some variable, therefore the grackle call
+ * should be in a block that still has the variables.
+ *
+ * @param data The #grackle_field_data
+ * @param p The #part
+ * @param xp The #xpart
+ * @param rho Particle density
+ */
+#if COOLING_GRACKLE_MODE > 1
+#define cooling_copy_to_grackle2(data, p, xp, rho) \
+ cooling_copy_field_to_grackle(data, xp, rho, HM); \
+ cooling_copy_field_to_grackle(data, xp, rho, H2I); \
+ cooling_copy_field_to_grackle(data, xp, rho, H2II);
+#else
+#define cooling_copy_to_grackle2(data, p, xp, rho) \
+ data.HM_density = NULL; \
+ data.H2I_density = NULL; \
+ data.H2II_density = NULL;
+#endif
+
+/**
+ * @brief copy a #xpart to the grackle data
+ *
+ * Warning this function creates some variable, therefore the grackle call
+ * should be in a block that still has the variables.
+ *
+ * @param data The #grackle_field_data
+ * @param p The #part
+ * @param xp The #xpart
+ * @param rho Particle density
+ */
+#if COOLING_GRACKLE_MODE > 2
+#define cooling_copy_to_grackle3(data, p, xp, rho) \
+ cooling_copy_field_to_grackle(data, xp, rho, DI); \
+ cooling_copy_field_to_grackle(data, xp, rho, DII); \
+ cooling_copy_field_to_grackle(data, xp, rho, HDI);
+#else
+#define cooling_copy_to_grackle3(data, p, xp, rho) \
+ data.DI_density = NULL; \
+ data.DII_density = NULL; \
+ data.HDI_density = NULL;
+#endif
+
+/**
+ * @brief copy the grackle data to a #xpart
+ *
+ * @param data The #grackle_field_data
+ * @param p The #part
+ * @param xp The #xpart
+ * @param rho Particle density
+ */
+#if COOLING_GRACKLE_MODE > 0
+#define cooling_copy_from_grackle1(data, p, xp, rho) \
+ cooling_copy_field_from_grackle(data, xp, rho, HI); \
+ cooling_copy_field_from_grackle(data, xp, rho, HII); \
+ cooling_copy_field_from_grackle(data, xp, rho, HeI); \
+ cooling_copy_field_from_grackle(data, xp, rho, HeII); \
+ cooling_copy_field_from_grackle(data, xp, rho, HeIII); \
+ cooling_copy_field_from_grackle(data, xp, rho, e);
+#else
+#define cooling_copy_from_grackle1(data, p, xp, rho)
+#endif
+
+/**
+ * @brief copy the grackle data to a #xpart
+ *
+ * @param data The #grackle_field_data
+ * @param p The #part
+ * @param xp The #xpart
+ * @param rho Particle density
+ */
+#if COOLING_GRACKLE_MODE > 1
+#define cooling_copy_from_grackle2(data, p, xp, rho) \
+ cooling_copy_field_from_grackle(data, xp, rho, HM); \
+ cooling_copy_field_from_grackle(data, xp, rho, H2I); \
+ cooling_copy_field_from_grackle(data, xp, rho, H2II);
+#else
+#define cooling_copy_from_grackle2(data, p, xp, rho)
+#endif
+
+/**
+ * @brief copy the grackle data to a #xpart
+ *
+ * @param data The #grackle_field_data
+ * @param p The #part
+ * @param xp The #xpart
+ * @param rho Particle density
+ */
+#if COOLING_GRACKLE_MODE > 2
+#define cooling_copy_from_grackle3(data, p, xp, rho) \
+ cooling_copy_field_from_grackle(data, xp, rho, DI); \
+ cooling_copy_field_from_grackle(data, xp, rho, DII); \
+ cooling_copy_field_from_grackle(data, xp, rho, HDI);
+#else
+#define cooling_copy_from_grackle3(data, p, xp, rho)
+#endif
+
+/**
+ * @brief copy a #xpart to the grackle data
+ *
+ * Warning this function creates some variable, therefore the grackle call
+ * should be in a block that still has the variables.
+ *
+ * @param data The #grackle_field_data
+ * @param p The #part
+ * @param xp The #xpart
+ * @param rho Particle density
+ */
+#define cooling_copy_to_grackle(data, p, xp, rho) \
+ cooling_copy_to_grackle1(data, p, xp, rho); \
+ cooling_copy_to_grackle2(data, p, xp, rho); \
+ cooling_copy_to_grackle3(data, p, xp, rho); \
+ data.volumetric_heating_rate = NULL; \
+ data.specific_heating_rate = NULL; \
+ data.RT_heating_rate = NULL; \
+ data.RT_HI_ionization_rate = NULL; \
+ data.RT_HeI_ionization_rate = NULL; \
+ data.RT_HeII_ionization_rate = NULL; \
+ data.RT_H2_dissociation_rate = NULL; \
+ gr_float metal_density = chemistry_metal_mass_fraction(p, xp) * rho; \
+ data.metal_density = &metal_density;
+
+/**
+ * @brief copy a #xpart to the grackle data
+ *
+ * Warning this function creates some variable, therefore the grackle call
+ * should be in a block that still has the variables.
+ *
+ * @param data The #grackle_field_data
+ * @param p The #part
+ * @param xp The #xpart
+ * @param rho Particle density
+ */
+#define cooling_copy_from_grackle(data, p, xp, rho) \
+ cooling_copy_from_grackle1(data, p, xp, rho); \
+ cooling_copy_from_grackle2(data, p, xp, rho); \
+ cooling_copy_from_grackle3(data, p, xp, rho);
+
+/**
+ * @brief Compute the cooling rate and update the particle chemistry data
*
* @param phys_const The physical constants in internal units.
* @param us The internal system of units.
* @param cooling The #cooling_function_data used in the run.
* @param p Pointer to the particle data.
+ * @param xp Pointer to the particle extra data
* @param dt The time-step of this particle.
*
* @return du / dt
*/
-__attribute__((always_inline)) INLINE static double cooling_rate(
+__attribute__((always_inline)) INLINE static gr_float cooling_rate(
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,
- struct part* restrict p, float dt) {
-
- if (cooling->chemistry.primordial_chemistry > 1) error("Not implemented");
+ const struct part* restrict p, struct xpart* restrict xp, double dt) {
/* set current time */
code_units units = cooling->units;
if (cooling->redshift == -1)
- error("TODO time dependant redshift");
+ units.a_value = cosmo->a;
else
units.a_value = 1. / (1. + cooling->redshift);
@@ -145,6 +507,7 @@ __attribute__((always_inline)) INLINE static double cooling_rate(
int grid_start[GRACKLE_RANK] = {0, 0, 0};
int grid_end[GRACKLE_RANK] = {GRACKLE_NPART - 1, 0, 0};
+ data.grid_dx = 0.;
data.grid_rank = GRACKLE_RANK;
data.grid_dimension = grid_dimension;
data.grid_start = grid_start;
@@ -154,70 +517,114 @@ __attribute__((always_inline)) INLINE static double cooling_rate(
gr_float density = hydro_get_physical_density(p, cosmo);
const double energy_before = hydro_get_physical_internal_energy(p, cosmo);
gr_float energy = energy_before;
- gr_float vx = 0;
- gr_float vy = 0;
- gr_float vz = 0;
+ /* initialize density */
data.density = &density;
+
+ /* initialize energy */
data.internal_energy = &energy;
- data.x_velocity = &vx;
- data.y_velocity = &vy;
- data.z_velocity = &vz;
-
- /* /\* primordial chemistry >= 1 *\/ */
- /* gr_float HI_density = density; */
- /* gr_float HII_density = 0.; */
- /* gr_float HeI_density = 0.; */
- /* gr_float HeII_density = 0.; */
- /* gr_float HeIII_density = 0.; */
- /* gr_float e_density = 0.; */
-
- /* data.HI_density = &HI_density; */
- /* data.HII_density = &HII_density; */
- /* data.HeI_density = &HeI_density; */
- /* data.HeII_density = &HeII_density; */
- /* data.HeIII_density = &HeIII_density; */
- /* data.e_density = &e_density; */
-
- /* /\* primordial chemistry >= 2 *\/ */
- /* gr_float HM_density = 0.; */
- /* gr_float H2I_density = 0.; */
- /* gr_float H2II_density = 0.; */
-
- /* data.HM_density = &HM_density; */
- /* data.H2I_density = &H2I_density; */
- /* data.H2II_density = &H2II_density; */
-
- /* /\* primordial chemistry >= 3 *\/ */
- /* gr_float DI_density = 0.; */
- /* gr_float DII_density = 0.; */
- /* gr_float HDI_density = 0.; */
-
- /* data.DI_density = &DI_density; */
- /* data.DII_density = &DII_density; */
- /* data.HDI_density = &HDI_density; */
-
- /* metal cooling = 1 */
- gr_float metal_density = density * grackle_data->SolarMetalFractionByMass;
- data.metal_density = &metal_density;
+ /* grackle 3.0 doc: "Currently not used" */
+ data.x_velocity = NULL;
+ data.y_velocity = NULL;
+ data.z_velocity = NULL;
+
+ /* copy to grackle structure */
+ cooling_copy_to_grackle(data, p, xp, density);
+
+ /* solve chemistry */
+ chemistry_data chemistry_grackle = cooling->chemistry;
+ chemistry_data_storage my_rates = grackle_rates;
+ int error_code = _solve_chemistry(
+ &chemistry_grackle, &my_rates, &units, dt, data.grid_dx, data.grid_rank,
+ data.grid_dimension, data.grid_start, data.grid_end, data.density,
+ data.internal_energy, data.x_velocity, data.y_velocity, data.z_velocity,
+ data.HI_density, data.HII_density, data.HM_density, data.HeI_density,
+ data.HeII_density, data.HeIII_density, data.H2I_density,
+ data.H2II_density, data.DI_density, data.DII_density, data.HDI_density,
+ data.e_density, data.metal_density, data.volumetric_heating_rate,
+ data.specific_heating_rate, data.RT_heating_rate,
+ data.RT_HI_ionization_rate, data.RT_HeI_ionization_rate,
+ data.RT_HeII_ionization_rate, data.RT_H2_dissociation_rate, NULL);
+ if (error_code == 0) error("Error in solve_chemistry.");
+ // if (solve_chemistry(&units, &data, dt) == 0) {
+ // error("Error in solve_chemistry.");
+ //}
+
+ /* copy from grackle data to particle */
+ cooling_copy_from_grackle(data, p, xp, density);
+
+ /* compute rate */
+ return (energy - energy_before) / dt;
+}
- /* /\* volumetric heating rate *\/ */
- /* gr_float volumetric_heating_rate = 0.; */
+/**
+ * @brief Compute the cooling time
+ *
+ * @param cooling The #cooling_function_data used in the run.
+ * @param p Pointer to the particle data.
+ * @param xp Pointer to the particle extra data
+ *
+ * @return cooling time
+ */
+__attribute__((always_inline)) INLINE static gr_float cooling_time(
+ 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) {
- /* data.volumetric_heating_rate = &volumetric_heating_rate; */
+ /* set current time */
+ code_units units = cooling->units;
+ if (cooling->redshift == -1)
+ error("TODO time dependant redshift");
+ else
+ units.a_value = 1. / (1. + cooling->redshift);
- /* /\* specific heating rate *\/ */
- /* gr_float specific_heating_rate = 0.; */
+ /* initialize data */
+ grackle_field_data data;
+
+ /* set values */
+ /* grid */
+ int grid_dimension[GRACKLE_RANK] = {GRACKLE_NPART, 1, 1};
+ int grid_start[GRACKLE_RANK] = {0, 0, 0};
+ int grid_end[GRACKLE_RANK] = {GRACKLE_NPART - 1, 0, 0};
+
+ data.grid_rank = GRACKLE_RANK;
+ data.grid_dimension = grid_dimension;
+ data.grid_start = grid_start;
+ data.grid_end = grid_end;
- /* data.specific_heating_rate = &specific_heating_rate; */
+ /* general particle data */
+ const gr_float energy_before = hydro_get_physical_internal_energy(p, cosmo);
+ gr_float density = hydro_get_physical_density(p, cosmo);
+ gr_float energy = energy_before;
+
+ /* initialize density */
+ data.density = &density;
+
+ /* initialize energy */
+ data.internal_energy = &energy;
+
+ /* grackle 3.0 doc: "Currently not used" */
+ data.x_velocity = NULL;
+ data.y_velocity = NULL;
+ data.z_velocity = NULL;
+
+ /* copy data from particle to grackle data */
+ cooling_copy_to_grackle(data, p, xp, density);
- /* solve chemistry with table */
- if (solve_chemistry(&units, &data, dt) == 0) {
- error("Error in solve_chemistry.");
+ /* Compute cooling time */
+ gr_float cooling_time;
+ if (calculate_cooling_time(&units, &data, &cooling_time) == 0) {
+ error("Error in calculate_cooling_time.");
}
- return (energy - energy_before) / dt;
+ /* copy from grackle data to particle */
+ cooling_copy_from_grackle(data, p, xp, density);
+
+ /* compute rate */
+ return cooling_time;
}
/**
@@ -235,7 +642,7 @@ __attribute__((always_inline)) INLINE static void cooling_cool_part(
const struct unit_system* restrict us,
const struct cosmology* restrict cosmo,
const struct cooling_function_data* restrict cooling,
- struct part* restrict p, struct xpart* restrict xp, float dt) {
+ struct part* restrict p, struct xpart* restrict xp, double dt) {
if (dt == 0.) return;
@@ -243,7 +650,7 @@ __attribute__((always_inline)) INLINE static void cooling_cool_part(
const float hydro_du_dt = hydro_get_internal_energy_dt(p);
/* compute cooling rate */
- const float du_dt = cooling_rate(phys_const, us, cosmo, cooling, p, dt);
+ const float du_dt = cooling_rate(phys_const, us, cosmo, cooling, p, xp, dt);
/* record energy lost */
xp->cooling_data.radiated_energy += -du_dt * dt * hydro_get_mass(p);
@@ -273,37 +680,15 @@ __attribute__((always_inline)) INLINE static float cooling_timestep(
}
/**
- * @brief Initialises the cooling properties.
+ * @brief Initialises the cooling unit system.
*
- * @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 cooling The cooling properties to initialize
*/
-__attribute__((always_inline)) INLINE static void cooling_init_backend(
- const struct swift_params* parameter_file, const struct unit_system* us,
- const struct phys_const* phys_const,
- struct cooling_function_data* cooling) {
-
- /* read parameters */
- parser_get_param_string(parameter_file, "GrackleCooling:GrackleCloudyTable",
- cooling->cloudy_table);
- cooling->uv_background =
- parser_get_param_int(parameter_file, "GrackleCooling:UVbackground");
-
- cooling->redshift =
- parser_get_param_double(parameter_file, "GrackleCooling:GrackleRedshift");
-
- cooling->density_self_shielding = parser_get_param_double(
- parameter_file, "GrackleCooling:GrackleHSShieldingDensityThreshold");
-
-#ifdef SWIFT_DEBUG_CHECKS
- /* enable verbose for grackle */
- grackle_verbose = 1;
-#endif
+__attribute__((always_inline)) INLINE static void cooling_init_units(
+ const struct unit_system* us, struct cooling_function_data* cooling) {
- /* Set up the units system.
- These are conversions from code units to cgs. */
+ /* These are conversions from code units to cgs. */
/* first cosmo */
cooling->units.a_units = 1.0; // units for the expansion factor (1/1+zi)
@@ -321,6 +706,20 @@ __attribute__((always_inline)) INLINE static void cooling_init_backend(
cooling->units.velocity_units = cooling->units.a_units *
cooling->units.length_units /
cooling->units.time_units;
+}
+
+/**
+ * @brief Initialises Grackle.
+ *
+ * @param cooling The cooling properties to initialize
+ */
+__attribute__((always_inline)) INLINE static void cooling_init_grackle(
+ struct cooling_function_data* cooling) {
+
+#ifdef SWIFT_DEBUG_CHECKS
+ /* enable verbose for grackle */
+ grackle_verbose = 1;
+#endif
chemistry_data* chemistry = &cooling->chemistry;
@@ -332,38 +731,60 @@ __attribute__((always_inline)) INLINE static void cooling_init_backend(
// Set parameter values for chemistry.
chemistry->use_grackle = 1;
chemistry->with_radiative_cooling = 1;
+
/* molecular network with H, He, D
From Cloudy table */
- chemistry->primordial_chemistry = 0;
- chemistry->metal_cooling = 1; // metal cooling on
- chemistry->UVbackground = cooling->uv_background;
+ chemistry->primordial_chemistry = COOLING_GRACKLE_MODE;
+ chemistry->metal_cooling = cooling->with_metal_cooling;
+ chemistry->UVbackground = cooling->with_uv_background;
chemistry->grackle_data_file = cooling->cloudy_table;
- chemistry->use_radiative_transfer = 0;
- chemistry->use_volumetric_heating_rate = 0;
- chemistry->use_specific_heating_rate = 0;
+
+ /* radiative transfer */
+ chemistry->use_radiative_transfer = cooling->provide_specific_heating_rates ||
+ cooling->provide_volumetric_heating_rates;
+ chemistry->use_volumetric_heating_rate =
+ cooling->provide_volumetric_heating_rates;
+ chemistry->use_specific_heating_rate =
+ cooling->provide_specific_heating_rates;
+
+ if (cooling->provide_specific_heating_rates &&
+ cooling->provide_volumetric_heating_rates)
+ message(
+ "WARNING: You should specified either the specific or the volumetric "
+ "heating rates, not both");
+
+ /* self shielding */
+ chemistry->self_shielding_method = cooling->self_shielding_method;
/* Initialize the chemistry object. */
if (initialize_chemistry_data(&cooling->units) == 0) {
error("Error in initialize_chemistry_data.");
}
+}
+
+/**
+ * @brief Initialises the cooling 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 cooling The cooling properties to initialize
+ */
+__attribute__((always_inline)) INLINE static void cooling_init_backend(
+ const struct swift_params* parameter_file, const struct unit_system* us,
+ const struct phys_const* phys_const,
+ struct cooling_function_data* cooling) {
-#ifdef SWIFT_DEBUG_CHECKS
if (GRACKLE_NPART != 1)
error("Grackle with multiple particles not implemented");
- float threshold = cooling->density_self_shielding;
- threshold /= phys_const->const_proton_mass;
- threshold /= pow(us->UnitLength_in_cgs, 3);
+ /* read parameters */
+ cooling_read_parameters(parameter_file, cooling);
- message("***************************************");
- message("initializing grackle cooling function");
- message("");
- cooling_print_backend(cooling);
- message("Density Self Shielding = %g atom/cm3", threshold);
+ /* Set up the units system. */
+ cooling_init_units(us, cooling);
- message("");
- message("***************************************");
-#endif
+ cooling_init_grackle(cooling);
}
#endif /* SWIFT_COOLING_GRACKLE_H */
diff --git a/src/cooling/grackle/cooling_io.h b/src/cooling/grackle/cooling_io.h
new file mode 100644
index 0000000000000000000000000000000000000000..5a6edb8f1c559a7b495351e256559f251b97c1cf
--- /dev/null
+++ b/src/cooling/grackle/cooling_io.h
@@ -0,0 +1,169 @@
+/*******************************************************************************
+ * 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_GRACKLE_IO_H
+#define SWIFT_COOLING_GRACKLE_IO_H
+
+/* Config parameters. */
+#include "../config.h"
+
+/* Local includes */
+#include "cooling_struct.h"
+#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) {
+
+#if COOLING_GRACKLE_MODE == 0
+ io_write_attribute_s(h_grpsph, "Cooling Model", "Grackle");
+#elif COOLING_GRACKLE_MODE == 1
+ io_write_attribute_s(h_grpsph, "Cooling Model", "Grackle1");
+#elif COOLING_GRACKLE_MODE == 2
+ io_write_attribute_s(h_grpsph, "Cooling Model", "Grackle2");
+#elif COOLING_GRACKLE_MODE == 3
+ io_write_attribute_s(h_grpsph, "Cooling Model", "Grackle3");
+#else
+ error("This function should be called only with one of the Grackle cooling.");
+#endif
+}
+#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) {
+
+ int num = 0;
+
+ if (cooling->output_mode == 0) return num;
+
+#if COOLING_GRACKLE_MODE >= 1
+ /* List what we want to write */
+ list[0] = io_make_output_field("HI", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.HI_frac);
+
+ list[1] = io_make_output_field("HII", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.HII_frac);
+
+ list[2] = io_make_output_field("HeI", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.HeI_frac);
+
+ list[3] = io_make_output_field("HeII", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.HeII_frac);
+
+ list[4] = io_make_output_field("HeIII", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.HeIII_frac);
+
+ list[5] = io_make_output_field("e", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.e_frac);
+
+ num += 6;
+#endif
+
+ if (cooling->output_mode == 1) return num;
+
+#if COOLING_GRACKLE_MODE >= 2
+ list += num;
+
+ list[0] = io_make_output_field("HM", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.HM_frac);
+
+ list[1] = io_make_output_field("H2I", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.H2I_frac);
+
+ list[2] = io_make_output_field("H2II", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.H2II_frac);
+
+ num += 3;
+#endif
+
+ if (cooling->output_mode == 2) return num;
+
+#if COOLING_GRACKLE_MODE >= 3
+ list += num;
+
+ list[0] = io_make_output_field("DI", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.DI_frac);
+
+ list[1] = io_make_output_field("DII", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.DII_frac);
+
+ list[2] = io_make_output_field("HDI", FLOAT, 1, UNIT_CONV_NO_UNITS, xparts,
+ cooling_data.HDI_frac);
+
+ num += 3;
+#endif
+
+ return num;
+}
+
+/**
+ * @brief Parser the parameter file and initialize the #cooling_function_data
+ *
+ * @param parameter_file The parser parameter file
+ * @param cooling The cooling properties to initialize
+ */
+__attribute__((always_inline)) INLINE static void cooling_read_parameters(
+ const struct swift_params* parameter_file,
+ struct cooling_function_data* cooling) {
+
+ parser_get_param_string(parameter_file, "GrackleCooling:CloudyTable",
+ cooling->cloudy_table);
+ cooling->with_uv_background =
+ parser_get_param_int(parameter_file, "GrackleCooling:WithUVbackground");
+
+ cooling->redshift =
+ parser_get_param_double(parameter_file, "GrackleCooling:Redshift");
+
+ cooling->with_metal_cooling =
+ parser_get_param_int(parameter_file, "GrackleCooling:WithMetalCooling");
+
+ cooling->provide_volumetric_heating_rates = parser_get_opt_param_int(
+ parameter_file, "GrackleCooling:ProvideVolumetricHeatingRates", 0);
+
+ cooling->provide_specific_heating_rates = parser_get_opt_param_int(
+ parameter_file, "GrackleCooling:ProvideSpecificHeatingRates", 0);
+
+ cooling->self_shielding_method = parser_get_opt_param_int(
+ parameter_file, "GrackleCooling:SelfShieldingMethod", 0);
+
+ cooling->output_mode =
+ parser_get_opt_param_int(parameter_file, "GrackleCooling:OutputMode", 0);
+
+ cooling->max_step = parser_get_opt_param_int(
+ parameter_file, "GrackleCooling:MaxSteps", 10000);
+
+ cooling->convergence_limit = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:ConvergenceLimit", 1e-2);
+}
+
+#endif /* SWIFT_COOLING_GRACKLE_IO_H */
diff --git a/src/cooling/grackle/cooling_struct.h b/src/cooling/grackle/cooling_struct.h
index 9ad1470922fdcbf892014f988389eccc1a4e9014..b714690ce4688268723748b29506e458cccc4be9 100644
--- a/src/cooling/grackle/cooling_struct.h
+++ b/src/cooling/grackle/cooling_struct.h
@@ -22,6 +22,8 @@
/* include grackle */
#include <grackle.h>
+#include "../config.h"
+
/**
* @file src/cooling/none/cooling_struct.h
* @brief Empty infrastructure for the cases without cooling function
@@ -36,19 +38,40 @@ struct cooling_function_data {
char cloudy_table[200];
/* Enable/Disable UV backgroud */
- int uv_background;
+ int with_uv_background;
/* Redshift to use for the UV backgroud (-1 to use cosmological one) */
double redshift;
- /* Density Threshold for the shielding */
- double density_self_shielding;
-
/* unit system */
code_units units;
/* grackle chemistry data */
chemistry_data chemistry;
+
+ /* Enable/Disable metal cooling */
+ int with_metal_cooling;
+
+ /* User provide volumetric heating rates */
+ int provide_volumetric_heating_rates;
+
+ /* User provide specific heating rates */
+ int provide_specific_heating_rates;
+
+ /* Self shielding method (<= 3) means grackle modes */
+ int self_shielding_method;
+
+ /* Output mode (correspond to primordial chemistry mode */
+ int output_mode;
+
+ /* convergence limit for first init */
+ float convergence_limit;
+
+ /* number of step max for first init */
+ int max_step;
+
+ /* over relaxation parameter */
+ float omega;
};
/**
@@ -58,6 +81,36 @@ struct cooling_xpart_data {
/*! Energy radiated away by this particle since the start of the run */
float radiated_energy;
+
+/* here all fractions are mass fraction */
+#if COOLING_GRACKLE_MODE >= 1
+ /* primordial chemistry >= 1 */
+ float HI_frac;
+ float HII_frac;
+ float HeI_frac;
+ float HeII_frac;
+ float HeIII_frac;
+ float e_frac;
+
+#if COOLING_GRACKLE_MODE >= 2
+ /* primordial chemistry >= 2 */
+ float HM_frac;
+ float H2I_frac;
+ float H2II_frac;
+
+#if COOLING_GRACKLE_MODE >= 3
+ /* primordial chemistry >= 3 */
+ float DI_frac;
+ float DII_frac;
+ float HDI_frac;
+#endif // MODE >= 3
+
+#endif // MODE >= 2
+
+#endif // MODE >= 1
+
+ /* metal cooling = 1 */
+ float metal_frac;
};
#endif /* SWIFT_COOLING_STRUCT_NONE_H */
diff --git a/src/cooling/none/cooling.h b/src/cooling/none/cooling.h
index a1cc6491115a38d6971a57603fef413c35b52027..5081c7cbe6c4b5168da082ead80687226f9d0c16 100644
--- a/src/cooling/none/cooling.h
+++ b/src/cooling/none/cooling.h
@@ -31,25 +31,11 @@
/* 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", "None");
-}
-#endif
-
/**
* @brief Apply the cooling function to a particle.
*
@@ -96,13 +82,19 @@ __attribute__((always_inline)) INLINE static float cooling_timestep(
*
* 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 properties of the cooling function.
* @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_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* data, const struct part* restrict p,
+ struct xpart* restrict xp) {}
/**
* @brief Returns the total radiated energy by this particle.
diff --git a/src/cooling/none/cooling_io.h b/src/cooling/none/cooling_io.h
new file mode 100644
index 0000000000000000000000000000000000000000..e4c84f506bcd31ff95ededb5be889fbf9a27261b
--- /dev/null
+++ b/src/cooling/none/cooling_io.h
@@ -0,0 +1,56 @@
+/*******************************************************************************
+ * 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_NONE_IO_H
+#define SWIFT_COOLING_NONE_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", "None");
+}
+#endif
+
+/**
+ * @brief Specifies which particle fields to write to a dataset
+ *
+ * @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 xpart* xparts, struct io_props* list,
+ const struct cooling_function_data* cooling) {
+ return 0;
+}
+
+#endif /* SWIFT_COOLING_NONE_IO_H */
diff --git a/src/cooling_io.h b/src/cooling_io.h
new file mode 100644
index 0000000000000000000000000000000000000000..88eeae2cabdaa8a0909977b84a7dbcf03145d988
--- /dev/null
+++ b/src/cooling_io.h
@@ -0,0 +1,40 @@
+/*******************************************************************************
+ * 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_COOLING_IO_H
+#define SWIFT_COOLING_IO_H
+
+/* Config parameters. */
+#include "../config.h"
+
+/* Import the i/o routines of the right cooling definition */
+#if defined(COOLING_NONE)
+#include "./cooling/none/cooling_io.h"
+#elif defined(COOLING_CONST_DU)
+#include "./cooling/const_du/cooling_io.h"
+#elif defined(COOLING_CONST_LAMBDA)
+#include "./cooling/const_lambda/cooling_io.h"
+#elif defined(COOLING_GRACKLE)
+#include "./cooling/grackle/cooling_io.h"
+#elif defined(COOLING_EAGLE)
+#include "./cooling/EAGLE/cooling_io.h"
+#else
+#error "Invalid choice of cooling function."
+#endif
+
+#endif /* SWIFT_COOLING_IO_H */
diff --git a/src/engine.c b/src/engine.c
index 6f8c0e9937ee40912964b88a3be69cacf060a0ae..2bdad767aeb198d3c4c9d0dc6113a7580445022e 100644
--- a/src/engine.c
+++ b/src/engine.c
@@ -5202,15 +5202,18 @@ void engine_unpin() {
* @param chemistry The chemistry information.
* @param sourceterms The properties of the source terms function.
*/
-void engine_init(
- struct engine *e, struct space *s, const struct swift_params *params,
- long long Ngas, long long Ndm, int policy, int verbose,
- struct repartition *reparttype, const struct unit_system *internal_units,
- const struct phys_const *physical_constants, struct cosmology *cosmo,
- const struct hydro_props *hydro, struct gravity_props *gravity,
- const struct external_potential *potential,
- const struct cooling_function_data *cooling_func,
- const struct chemistry_data *chemistry, struct sourceterms *sourceterms) {
+void engine_init(struct engine *e, struct space *s,
+ const struct swift_params *params, long long Ngas,
+ long long Ndm, int policy, int verbose,
+ struct repartition *reparttype,
+ const struct unit_system *internal_units,
+ const struct phys_const *physical_constants,
+ struct cosmology *cosmo, const struct hydro_props *hydro,
+ struct gravity_props *gravity,
+ const struct external_potential *potential,
+ const struct cooling_function_data *cooling_func,
+ const struct chemistry_global_data *chemistry,
+ struct sourceterms *sourceterms) {
/* Clean-up everything */
bzero(e, sizeof(struct engine));
@@ -5973,8 +5976,9 @@ void engine_struct_restore(struct engine *e, FILE *stream) {
cooling_struct_restore(cooling_func, stream);
e->cooling_func = cooling_func;
- struct chemistry_data *chemistry =
- (struct chemistry_data *)malloc(sizeof(struct chemistry_data));
+ struct chemistry_global_data *chemistry =
+ (struct chemistry_global_data *)malloc(
+ sizeof(struct chemistry_global_data));
chemistry_struct_restore(chemistry, stream);
e->chemistry = chemistry;
diff --git a/src/engine.h b/src/engine.h
index 4c37aab593fdffc5f68ea16cb83b29ad782debf0..29a064876317d7e1a7ff1cba5e3cb740b6e171a9 100644
--- a/src/engine.h
+++ b/src/engine.h
@@ -287,7 +287,7 @@ struct engine {
const struct cooling_function_data *cooling_func;
/* Properties of the chemistry model */
- const struct chemistry_data *chemistry;
+ const struct chemistry_global_data *chemistry;
/* Properties of source terms */
struct sourceterms *sourceterms;
@@ -330,15 +330,18 @@ void engine_drift_top_multipoles(struct engine *e);
void engine_reconstruct_multipoles(struct engine *e);
void engine_print_stats(struct engine *e);
void engine_dump_snapshot(struct engine *e);
-void engine_init(
- struct engine *e, struct space *s, const struct swift_params *params,
- long long Ngas, long long Ndm, int policy, int verbose,
- struct repartition *reparttype, const struct unit_system *internal_units,
- const struct phys_const *physical_constants, struct cosmology *cosmo,
- const struct hydro_props *hydro, struct gravity_props *gravity,
- const struct external_potential *potential,
- const struct cooling_function_data *cooling_func,
- const struct chemistry_data *chemistry, struct sourceterms *sourceterms);
+void engine_init(struct engine *e, struct space *s,
+ const struct swift_params *params, long long Ngas,
+ long long Ndm, int policy, int verbose,
+ struct repartition *reparttype,
+ const struct unit_system *internal_units,
+ const struct phys_const *physical_constants,
+ struct cosmology *cosmo, const struct hydro_props *hydro,
+ struct gravity_props *gravity,
+ const struct external_potential *potential,
+ const struct cooling_function_data *cooling_func,
+ const struct chemistry_global_data *chemistry,
+ struct sourceterms *sourceterms);
void engine_config(int restart, struct engine *e,
const struct swift_params *params, int nr_nodes, int nodeID,
int nr_threads, int with_aff, int verbose,
diff --git a/src/io_properties.h b/src/io_properties.h
index 55e128e890b75db2d01911bd3c3b46388b0c6597..d0005531afa3a0cf4de0302e86dd362e0abc11ab 100644
--- a/src/io_properties.h
+++ b/src/io_properties.h
@@ -26,6 +26,9 @@
#include "common_io.h"
#include "inline.h"
+/* Standard includes. */
+#include <string.h>
+
/**
* @brief The two sorts of data present in the GADGET IC files: compulsory to
* start a run or optional.
diff --git a/src/parallel_io.c b/src/parallel_io.c
index 51c88e95396eb6af1ab7f7eb2d1ed48eada59e0d..b5741fb747a0cd8a2dd9ff1645d4a22ffa780869 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -38,7 +38,7 @@
/* Local includes. */
#include "chemistry_io.h"
#include "common_io.h"
-#include "cooling.h"
+#include "cooling_io.h"
#include "dimension.h"
#include "engine.h"
#include "error.h"
@@ -860,6 +860,8 @@ void prepare_file(struct engine* e, const char* baseName, long long N_total[6],
int periodic = e->s->periodic;
int numFiles = 1;
+ const struct cooling_function_data* cooling = e->cooling_func;
+
/* First time, we need to create the XMF file */
if (e->snapshotOutputCount == 0) xmf_create_file(baseName);
@@ -1243,6 +1245,8 @@ void write_output_parallel(struct engine* e, const char* baseName,
Nparticles = Ngas;
hydro_write_particles(parts, xparts, list, &num_fields);
num_fields += chemistry_write_particles(parts, list + num_fields);
+ num_fields +=
+ cooling_write_particles(xparts, list + num_fields, cooling);
break;
case swift_type_dark_matter:
diff --git a/src/runner.c b/src/runner.c
index 35996a3ba9a760d5f019ede35abc207bbdcbe1b3..51801a779481a8ce0500d8c5f3f0b20d7ed79faf 100644
--- a/src/runner.c
+++ b/src/runner.c
@@ -656,7 +656,7 @@ void runner_do_ghost(struct runner *r, struct cell *c, int timer) {
const struct space *s = e->s;
const struct hydro_space *hs = &s->hs;
const struct cosmology *cosmo = e->cosmology;
- const struct chemistry_data *chemistry = e->chemistry;
+ const struct chemistry_global_data *chemistry = e->chemistry;
const float hydro_h_max = e->hydro_properties->h_max;
const float eps = e->hydro_properties->h_tolerance;
const float hydro_eta_dim =
diff --git a/src/serial_io.c b/src/serial_io.c
index dd623f946ce6ec32415586e5048979de3adb58fa..fa48d0ac96e58f9dfc4e9d8c513197b6e91800e4 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -38,7 +38,7 @@
/* Local includes. */
#include "chemistry_io.h"
#include "common_io.h"
-#include "cooling.h"
+#include "cooling_io.h"
#include "dimension.h"
#include "engine.h"
#include "error.h"
@@ -744,6 +744,7 @@ void write_output_serial(struct engine* e, const char* baseName,
const struct gpart* gparts = e->s->gparts;
struct gpart* dmparts = NULL;
const struct spart* sparts = e->s->sparts;
+ const struct cooling_function_data* cooling = e->cooling_func;
FILE* xmfFile = 0;
/* Number of unassociated gparts */
@@ -992,6 +993,8 @@ void write_output_serial(struct engine* e, const char* baseName,
Nparticles = Ngas;
hydro_write_particles(parts, xparts, list, &num_fields);
num_fields += chemistry_write_particles(parts, list + num_fields);
+ num_fields +=
+ cooling_write_particles(xparts, list + num_fields, cooling);
break;
case swift_type_dark_matter:
diff --git a/src/single_io.c b/src/single_io.c
index 2170bcffc4ce3ab21f1edd168d1dc37b2b4af963..73c7f5d946544ed61ebfae01a6ccd4708a8a5f3c 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -37,7 +37,7 @@
/* Local includes. */
#include "chemistry_io.h"
#include "common_io.h"
-#include "cooling.h"
+#include "cooling_io.h"
#include "dimension.h"
#include "engine.h"
#include "error.h"
@@ -612,6 +612,7 @@ void write_output_single(struct engine* e, const char* baseName,
const struct gpart* gparts = e->s->gparts;
struct gpart* dmparts = NULL;
const struct spart* sparts = e->s->sparts;
+ const struct cooling_function_data* cooling = e->cooling_func;
/* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;
@@ -811,6 +812,8 @@ void write_output_single(struct engine* e, const char* baseName,
N = Ngas;
hydro_write_particles(parts, xparts, list, &num_fields);
num_fields += chemistry_write_particles(parts, list + num_fields);
+ num_fields +=
+ cooling_write_particles(xparts, list + num_fields, cooling);
break;
case swift_type_dark_matter:
diff --git a/src/space.c b/src/space.c
index 4f2213793b270cde1c29281bbf411fcfd97c1b4c..b6aef6ea7db1b7bfe0ecbe6a39157f9be5994b50 100644
--- a/src/space.c
+++ b/src/space.c
@@ -2317,7 +2317,7 @@ void space_synchronize_particle_positions(struct space *s) {
* Calls chemistry_first_init_part() on all the particles
*/
void space_first_init_parts(struct space *s,
- const struct chemistry_data *chemistry,
+ const struct chemistry_global_data *chemistry,
const struct cooling_function_data *cool_func) {
const size_t nr_parts = s->nr_parts;
@@ -2325,6 +2325,8 @@ void space_first_init_parts(struct space *s,
struct xpart *restrict xp = s->xparts;
const struct cosmology *cosmo = s->e->cosmology;
+ const struct phys_const *phys_const = s->e->physical_constants;
+ const struct unit_system *us = s->e->internal_units;
const float a_factor_vel = cosmo->a * cosmo->a;
const struct hydro_props *hydro_props = s->e->hydro_properties;
@@ -2355,10 +2357,10 @@ void space_first_init_parts(struct space *s,
if (u_min > 0.f) hydro_set_init_internal_energy(&p[i], u_min);
/* Also initialise the chemistry */
- chemistry_first_init_part(&p[i], &xp[i], chemistry);
+ chemistry_first_init_part(phys_const, us, cosmo, chemistry, &p[i], &xp[i]);
/* And the cooling */
- cooling_first_init_part(&p[i], &xp[i], cool_func);
+ cooling_first_init_part(phys_const, us, cosmo, cool_func, &p[i], &xp[i]);
/* Check part->gpart->part linkeage. */
if (p[i].gpart) p[i].gpart->id_or_neg_offset = -i;
diff --git a/src/space.h b/src/space.h
index 571b595eda8758c510a014bc784ae4bde85abaea..db9c9edad3d7435ea619e72814e2c97094344090 100644
--- a/src/space.h
+++ b/src/space.h
@@ -222,7 +222,7 @@ void space_do_parts_sort();
void space_do_gparts_sort();
void space_do_sparts_sort();
void space_first_init_parts(struct space *s,
- const struct chemistry_data *chemistry,
+ const struct chemistry_global_data *chemistry,
const struct cooling_function_data *cool_func);
void space_first_init_gparts(struct space *s,
const struct gravity_props *grav_props);