Gear: Change chemistry_data -> chemistry_global_data + minor changes

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"
@@ -62,14 +63,18 @@ 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) {
+
+  /* read parameters */
+  chemistry_read_parameters(parameter_file, us, phys_const, 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 'Gear'.");
 }
@@ -81,10 +86,10 @@ 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 +107,11 @@ __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. */
@@ -139,7 +144,7 @@ __attribute__((always_inline)) INLINE static void chemistry_end_density(
  */
 __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 chemistry_global_data* data) {
   chemistry_init_part(p, data);
 }
 

src/chemistry/gear/chemistry_io.h

@@ -22,6 +22,10 @@
 #include "chemistry.h"
 #include "chemistry_struct.h"
 #include "io_properties.h"
+#include "parser.h"
+#include "part.h"
+#include "physical_constants.h"
+#include "units.h"
 
 /**
  * @brief Specifies which particle fields to read from a dataset
@@ -31,15 +35,30 @@
  *
  * @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);
 }
 
+
 /**
  * @brief Specifies which particle fields to write to a dataset
  *
@@ -48,18 +67,21 @@ 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 +90,8 @@ 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_grpsph) {
 
   io_write_attribute_s(h_grp, "Chemistry Model", "GEAR");
   for (enum chemistry_element i = chemistry_element_O;
@@ -80,4 +103,5 @@ void chemistry_write_flavour(hid_t h_grp) {
 }
 #endif
 
+
 #endif /* SWIFT_CHEMISTRY_IO_GEAR_H */

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/cooling/grackle/cooling.h

@@ -810,7 +810,7 @@ __attribute__((always_inline)) INLINE static void cooling_init_backend(
     error("Grackle with multiple particles not implemented");
 
   /* read parameters */
-  cooling_parse_arguments(parameter_file, cooling);
+  cooling_read_parameters(parameter_file, cooling);
 
   /* Set up the units system. */
   cooling_init_units(us, cooling);

src/cooling/grackle/cooling_io.h

@@ -119,10 +119,11 @@ __attribute__((always_inline)) INLINE static int cooling_write_particles(
 
 /**
  * @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_parse_arguments(
+__attribute__((always_inline)) INLINE static void cooling_read_parameters(
     const struct swift_params* parameter_file,
     struct cooling_function_data* cooling) {
 
@@ -146,7 +147,6 @@ __attribute__((always_inline)) INLINE static void cooling_parse_arguments(
   cooling->self_shielding_method =
     parser_get_opt_param_int(parameter_file, "GrackleCooling:SelfShieldingMethod", 0);
 
-#if COOLING_GRACKLE_MODE > 0
   cooling->output_mode =
     parser_get_opt_param_int(parameter_file, "GrackleCooling:OutputMode", 0);
 
@@ -158,7 +158,6 @@ __attribute__((always_inline)) INLINE static void cooling_parse_arguments(
 
   cooling->omega =
     parser_get_opt_param_double(parameter_file, "GrackleCooling:Omega", 0.8);
-#endif
 }