From 80ec719d01bea8c2ffad38663ce25231f21ec63c Mon Sep 17 00:00:00 2001
From: lhausamm <loic_hausammann@hotmail.com>
Date: Wed, 18 Apr 2018 14:09:52 +0200
Subject: [PATCH] Rebasing corrections
---
examples/main.c | 2 +-
src/chemistry.c | 8 +++----
src/chemistry.h | 4 ++--
src/chemistry/gear/chemistry.h | 29 +++++-------------------
src/chemistry/gear/chemistry_io.h | 27 ++++++++++++++++++++--
src/cooling/grackle/cooling.h | 37 +++++++++++++++++++++----------
src/engine.c | 4 ++--
src/runner.c | 2 +-
src/space.c | 6 +++--
9 files changed, 69 insertions(+), 50 deletions(-)
diff --git a/examples/main.c b/examples/main.c
index ca91c9e718..3917756098 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/src/chemistry.c b/src/chemistry.c
index fb327a5ede..d9e36448bb 100644
--- a/src/chemistry.c
+++ b/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");
}
diff --git a/src/chemistry.h b/src/chemistry.h
index d54c0c4801..77b8d5b5fa 100644
--- a/src/chemistry.h
+++ b/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 */
diff --git a/src/chemistry/gear/chemistry.h b/src/chemistry/gear/chemistry.h
index a73125e0a1..ba5e9ace83 100644
--- a/src/chemistry/gear/chemistry.h
+++ b/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);
diff --git a/src/chemistry/gear/chemistry_io.h b/src/chemistry/gear/chemistry_io.h
index 33a099cb6f..8a084db25b 100644
--- a/src/chemistry/gear/chemistry_io.h
+++ b/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;
diff --git a/src/cooling/grackle/cooling.h b/src/cooling/grackle/cooling.h
index 9760499bee..d1e7c30c9c 100644
--- a/src/cooling/grackle/cooling.h
+++ b/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);
diff --git a/src/engine.c b/src/engine.c
index b5c9c848db..d74a44b5cf 100644
--- a/src/engine.c
+++ b/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;
diff --git a/src/runner.c b/src/runner.c
index 35996a3ba9..51801a7794 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/space.c b/src/space.c
index 05a0719224..b1d25fb85f 100644
--- a/src/space.c
+++ b/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;
--
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