Rebasing corrections

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;

src/chemistry.c

@@ -58,9 +58,9 @@ void chemistry_print(const struct chemistry_global_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,
+  restart_write_blocks((void*)chemistry, sizeof(struct chemistry_global_data), 1,
                        stream, "chemistry", "chemistry function");
 }
 
@@ -71,8 +71,8 @@ void chemistry_struct_dump(const struct chemistry_data* chemistry,
  * @param chemistry the struct
  * @param stream the file stream
  */
-void chemistry_struct_restore(const struct chemistry_data* chemistry,
+void chemistry_struct_restore(const struct chemistry_global_data* chemistry,
                               FILE* stream) {
-  restart_read_blocks((void*)chemistry, sizeof(struct chemistry_data), 1,
+  restart_read_blocks((void*)chemistry, sizeof(struct chemistry_global_data), 1,
                       stream, NULL, "chemistry function");
 }

src/chemistry.h

@@ -51,9 +51,9 @@ void chemistry_init(const struct swift_params* parameter_file,
 void chemistry_print(const struct chemistry_global_data* data);
 
 /* Dump/restore. */
-void chemistry_struct_dump(const struct chemistry_data* chemistry,
+void chemistry_struct_dump(const struct chemistry_global_data* chemistry,
                            FILE* stream);
-void chemistry_struct_restore(const struct chemistry_data* chemistry,
+void chemistry_struct_restore(const struct chemistry_global_data* chemistry,
                               FILE* stream);
 
 #endif /* SWIFT_CHEMISTRY_H */

src/chemistry/gear/chemistry.h

@@ -38,18 +38,6 @@
 #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 Compute the metal mass fraction
@@ -81,16 +69,6 @@ static INLINE void chemistry_init_backend(
   chemistry_read_parameters(parameter_file, us, phys_const, data);
 }
 
-/**
- * @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 Prepares a particle for the smooth metal calculation.
  *
@@ -155,8 +133,11 @@ __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_global_data* data) {
+    const struct phys_const* restrict phys_const,
+    const struct unit_system* restrict us,
+    const struct cosmology* restrict cosmo,
+    const struct chemistry_global_data* data,
+    struct part* restrict p, struct xpart* restrict xp) {
 
   p->chemistry_data.Z = data->initial_metallicity;
   chemistry_init_part(p, data);

src/chemistry/gear/chemistry_io.h

@@ -19,14 +19,37 @@
 #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
  *
@@ -91,7 +114,7 @@ __attribute__((always_inline)) INLINE static int chemistry_write_particles(
  * @param h_grp The HDF5 group in which to write
  */
 __attribute__((always_inline)) INLINE static void chemistry_write_flavour(
-    hid_t h_grpsph) {
+    hid_t h_grp) {
 
   io_write_attribute_s(h_grp, "Chemistry Model", "GEAR");
   for (enum chemistry_element i = chemistry_element_O;

src/cooling/grackle/cooling.h

@@ -47,12 +47,16 @@
 
 /* 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);
 
@@ -144,9 +148,12 @@ __attribute__((always_inline)) INLINE static int cooling_converged(
  * @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,
-    const struct cooling_function_data* cooling) {
+    struct xpart* restrict xp) {
 
   /* get temporary data */
   struct part p_tmp = *p;
@@ -157,9 +164,9 @@ __attribute__((always_inline)) INLINE static void cooling_compute_equilibrium(
 
   /* compute time step */
   const double alpha = 0.01;
-  double dt = fabs(cooling_time(&cooling_tmp, &p_tmp, xp));
-  cooling_rate(NULL, NULL, &cooling_tmp, &p_tmp, xp, dt);
-  dt = alpha * fabs(cooling_time(&cooling_tmp, &p_tmp, xp));
+  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;
@@ -173,7 +180,7 @@ __attribute__((always_inline)) INLINE static void cooling_compute_equilibrium(
     old = *xp;
 
     /* update chemistry */
-    cooling_rate(NULL, NULL, &cooling_tmp, &p_tmp, xp, dt);
+    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)
@@ -191,8 +198,11 @@ __attribute__((always_inline)) INLINE static void cooling_compute_equilibrium(
  * @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;
 
@@ -226,7 +236,7 @@ __attribute__((always_inline)) INLINE static void cooling_first_init_part(
 #endif  // MODE >= 3
 
 #if COOLING_GRACKLE_MODE > 0
-  cooling_compute_equilibrium(p, xp, cooling);
+  cooling_compute_equilibrium(phys_const, us, cosmo, p, xp, cooling);
 #endif
 }
 
@@ -567,6 +577,9 @@ __attribute__((always_inline)) INLINE static gr_float cooling_rate(
  * @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) {
 
@@ -592,8 +605,8 @@ __attribute__((always_inline)) INLINE static gr_float cooling_time(
   data.grid_end = grid_end;
 
   /* general particle data */
-  const gr_float energy_before = hydro_get_internal_energy(p);
-  gr_float density = hydro_get_density(p);
+  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 */
@@ -646,7 +659,7 @@ __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);

src/engine.c

@@ -5965,8 +5965,8 @@ 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;
 

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 =

src/space.c

@@ -2648,6 +2648,8 @@ 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;
@@ -2678,10 +2680,10 @@ 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]);
 
 #ifdef SWIFT_DEBUG_CHECKS
     p[i].ti_drift = 0;