Merge branch 'gear_cleanup' into 'master'

Small GEAR merge fixes

See merge request !1011

examples/parameter_example.yml

@@ -292,6 +292,7 @@ SineWavePotential:
   timestep_limit:   1.      # Time-step dimensionless pre-factor.
   growth_time:      0.      # (Optional) Time for the potential to grow to its final size.
 
+
 # Parameters related to entropy floors    ----------------------------------------------
 
 EAGLEEntropyFloor:
@@ -303,12 +304,14 @@ EAGLEEntropyFloor:
   Cool_over_density_threshold:     10.       # Overdensity above which the EAGLE Cool limiter entropy floor can kick in.
   Cool_temperature_norm_K:         8000      # Temperature of the EAGLE Cool limiter entropy floor at the density threshold expressed in Kelvin.
   Cool_gamma_effective:            1.        # Slope the of the EAGLE Cool limiter entropy floor
-  
+
+
 # Parameters related to pressure floors    ----------------------------------------------
 
 GEARPressureFloor:
   jeans_factor: 10.       # Number of particles required to suppose a resolved clump and avoid the pressure floor.
 
+
 # Parameters related to cooling function  ----------------------------------------------
 
 # Constant du/dt cooling function
@@ -326,6 +329,7 @@ LambdaCooling:
 EAGLECooling:
   dir_name:                  ./coolingtables/  # Location of the Wiersma+08 cooling tables
   H_reion_z:                 8.5               # Redshift of Hydrogen re-ionization
+  H_reion_eV_p_H:            2.0               # Energy inject by Hydrogen re-ionization in electron-volt per Hydrogen atom
   He_reion_z_centre:         3.5               # Redshift of the centre of the Helium re-ionization Gaussian
   He_reion_z_sigma:          0.5               # Spread in redshift of the  Helium re-ionization Gaussian
   He_reion_eV_p_H:           2.0               # Energy inject by Helium re-ionization in electron-volt per Hydrogen atom
@@ -336,16 +340,17 @@ EAGLECooling:
 # Cooling with Grackle 3.0
 GrackleCooling:
   cloudy_table: CloudyData_UVB=HM2012.h5       # Name of the Cloudy Table (available on the grackle bitbucket repository)
-  with_UV_background: 1                         # Enable or not the UV background
-  redshift: 0                                 # Redshift to use (-1 means time based redshift)
-  with_metal_cooling: 1                         # Enable or not the metal cooling
-  provide_volumetric_heating_rates: 0            # (optional) User provide volumetric heating rates
-  provide_specific_heating_rates: 0              # (optional) User provide specific heating rates
+  with_UV_background: 1                        # Enable or not the UV background
+  redshift: 0                                  # Redshift to use (-1 means time based redshift)
+  with_metal_cooling: 1                        # Enable or not the metal cooling
+  provide_volumetric_heating_rates: 0          # (optional) User provide volumetric heating rates
+  provide_specific_heating_rates: 0            # (optional) User provide specific heating rates
   max_steps: 10000                             # (optional) Max number of step when computing the initial composition
   convergence_limit: 1e-2                      # (optional) Convergence threshold (relative) for initial composition
   thermal_time_myr: 5                          # (optional) Time (in Myr) for adiabatic cooling after a feedback event.
-  self_shielding_method: -1                     # (optional) Grackle (1->3 for Grackle's ones, 0 for none and -1 for GEAR)
-  self_shielding_threshold_atom_per_cm3: 0.007  # Required only with GEAR's self shielding. Density threshold of the self shielding
+  self_shielding_method: -1                    # (optional) Grackle (1->3 for Grackle's ones, 0 for none and -1 for GEAR)
+  self_shielding_threshold_atom_per_cm3: 0.007 # Required only with GEAR's self shielding. Density threshold of the self shielding
+
 
 # Parameters related to chemistry models  -----------------------------------------------
 
@@ -365,16 +370,11 @@ EAGLEChemistry:
 # GEAR chemistry model (Revaz and Jablonka 2018)
 GEARChemistry:
   initial_metallicity: 1         # Initial metallicity of the gas (mass fraction)
-  scale_initial_metallicity: 1    # Should we scale the initial metallicity with the solar one?
+  scale_initial_metallicity: 1   # Should we scale the initial metallicity with the solar one?
 
 
 # Parameters related to star formation models  -----------------------------------------------
 
-# GEAR star formation model (Revaz and Jablonka 2018)
-GEARStarFormation:
-  star_formation_efficiency: 0.01   # star formation efficiency (c_*)
-  maximal_temperature:  3e4         # Upper limit to the temperature of a star forming particle
-
 # EAGLE star formation model (Schaye and Dalla Vecchia 2008)
 EAGLEStarFormation:
   EOS_density_norm_H_p_cm3:          0.1       # Physical density used for the normalisation of the EOS assumed for the star-forming gas in Hydrogen atoms per cm^3.
@@ -392,7 +392,13 @@ EAGLEStarFormation:
   threshold_Z0:                      0.002     # Reference metallicity (metal mass fraction) for the metal-dependant threshold for star formation.
   threshold_slope:                   -0.64     # Slope of the metal-dependant star formation threshold
   threshold_max_density_H_p_cm3:     10.0      # Maximal density of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.  
-  
+
+# GEAR star formation model (Revaz and Jablonka 2018)
+GEARStarFormation:
+  star_formation_efficiency: 0.01   # star formation efficiency (c_*)
+  maximal_temperature:  3e4         # Upper limit to the temperature of a star forming particle
+
+
 # Parameters related to feedback models  -----------------------------------------------
 
 # EAGLE feedback model
@@ -438,9 +444,10 @@ EAGLEFeedback:
 
 # GEAR feedback model
 GEARFeedback:
-  supernovae_energy_erg: 0.1e51                      # Energy released by a single supernovae.
+  supernovae_energy_erg: 0.1e51                            # Energy released by a single supernovae.
   yields_table: chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5  # Table containing the yields.
-  discrete_yields: 0                                 # Should we use discrete yields or the IMF integrated one?
+  discrete_yields: 0                                       # Should we use discrete yields or the IMF integrated one?
+
 
 # Parameters related to AGN models  -----------------------------------------------
   

src/Makefile.am

@@ -77,7 +77,7 @@ if HAVEGRACKLECOOLING
 GRACKLE_COOLING_SOURCES += cooling/grackle/cooling.c
 endif
 
-# source files for GRACKLE cooling
+# source files for GEAR feedback
 GEAR_FEEDBACK_SOURCES =
 if HAVEGEARFEEDBACK
 GEAR_FEEDBACK_SOURCES += feedback/GEAR/stellar_evolution.c feedback/GEAR/feedback.c \
@@ -102,8 +102,8 @@ AM_SOURCES = space.c runner_main.c runner_doiact_hydro.c runner_doiact_limiter.c
     chemistry.c cosmology.c restart.c mesh_gravity.c velociraptor_interface.c \
     outputlist.c velociraptor_dummy.c logger_io.c memuse.c mpiuse.c memuse_rnodes.c fof.c \
     hashmap.c pressure_floor.c \
-    $(EAGLE_COOLING_SOURCES) $(EAGLE_FEEDBACK_SOURCES) $(GRACKLE_COOLING_SOURCES) \
-		$(GEAR_FEEDBACK_SOURCES)
+    $(EAGLE_COOLING_SOURCES) $(EAGLE_FEEDBACK_SOURCES) \
+    $(GRACKLE_COOLING_SOURCES) $(GEAR_FEEDBACK_SOURCES)
 
 # Include files for distribution, not installation.
 nobase_noinst_HEADERS = align.h approx_math.h atomic.h barrier.h cycle.h error.h inline.h kernel_hydro.h kernel_gravity.h \

src/cooling/Compton/cooling.h

@@ -136,9 +136,10 @@ __attribute__((always_inline)) INLINE static double Compton_cooling_rate_cgs(
  * @param cooling The #cooling_function_data used in the run.
  * @param p Pointer to the particle data.
  * @param xp Pointer to the particle' extended data.
- * @param time The current time.
  * @param dt The time-step of this particle.
  * @param dt_therm The time-step operator used for thermal quantities.
+ * @param time Time since Big Bang (or start of the simulation) in internal
+ * units.
  */
 __attribute__((always_inline)) INLINE static void cooling_cool_part(
     const struct phys_const* restrict phys_const,
@@ -147,8 +148,8 @@ __attribute__((always_inline)) INLINE static void cooling_cool_part(
     const struct hydro_props* hydro_props,
     const struct entropy_floor_properties* floor_props,
     const struct cooling_function_data* restrict cooling,
-    struct part* restrict p, struct xpart* restrict xp, const double time,
-    const float dt, const float dt_therm) {
+    struct part* restrict p, struct xpart* restrict xp, const float dt,
+    const float dt_therm, const double time) {
 
   /* Nothing to do here? */
   if (dt == 0.) return;

src/cooling/EAGLE/cooling.c

@@ -372,10 +372,10 @@ INLINE static double bisection_iter(
  * @param cooling The #cooling_function_data used in the run.
  * @param p Pointer to the particle data.
  * @param xp Pointer to the extended particle data.
- * @param time The current time (since the Big Bang or start of the run) in
- * internal units.
  * @param dt The cooling time-step of this particle.
  * @param dt_therm The hydro time-step of this particle.
+ * @param time The current time (since the Big Bang or start of the run) in
+ * internal units.
  */
 void cooling_cool_part(const struct phys_const *phys_const,
                        const struct unit_system *us,
@@ -384,8 +384,8 @@ void cooling_cool_part(const struct phys_const *phys_const,
                        const struct entropy_floor_properties *floor_props,
                        const struct cooling_function_data *cooling,
                        struct part *restrict p, struct xpart *restrict xp,
-                       const double time, const float dt,
-                       const float dt_therm) {
+                       const float dt, const float dt_therm,
+                       const double time) {
 
   /* No cooling happens over zero time */
   if (dt == 0.) return;

src/cooling/EAGLE/cooling.h

@@ -44,7 +44,7 @@ void cooling_cool_part(const struct phys_const *phys_const,
                        const struct entropy_floor_properties *floor_props,
                        const struct cooling_function_data *cooling,
                        struct part *restrict p, struct xpart *restrict xp,
-                       const double time, const float dt, const float dt_therm);
+                       const float dt, const float dt_therm, const double time);
 
 float cooling_timestep(const struct cooling_function_data *restrict cooling,
                        const struct phys_const *restrict phys_const,

src/cooling/const_du/cooling.h

@@ -76,9 +76,10 @@ INLINE static void cooling_update(const struct cosmology* cosmo,
  * @param cooling The #cooling_function_data used in the run.
  * @param p Pointer to the particle data.
  * @param xp Pointer to the extended particle data.
- * @param time The current time.
  * @param dt The time-step of this particle.
  * @param dt_therm The time-step operator used for thermal quantities.
+ * @param time Time since Big Bang (or start of the simulation) in internal
+ * units.
  */
 __attribute__((always_inline)) INLINE static void cooling_cool_part(
     const struct phys_const* restrict phys_const,
@@ -87,8 +88,8 @@ __attribute__((always_inline)) INLINE static void cooling_cool_part(
     const struct hydro_props* hydro_props,
     const struct entropy_floor_properties* floor_props,
     const struct cooling_function_data* restrict cooling,
-    struct part* restrict p, struct xpart* restrict xp, const double time,
-    const float dt, const float dt_therm) {
+    struct part* restrict p, struct xpart* restrict xp, const float dt,
+    const float dt_therm, const double time) {
 
   /* Internal energy floor */
   const float u_floor = cooling->min_energy;

src/cooling/const_lambda/cooling.h

@@ -106,9 +106,10 @@ __attribute__((always_inline)) INLINE static double cooling_rate_cgs(
  * @param cooling The #cooling_function_data used in the run.
  * @param p Pointer to the particle data.
  * @param xp Pointer to the particle' extended data.
- * @param time The current time.
  * @param dt The time-step of this particle.
  * @param dt_therm The time-step operator used for thermal quantities.
+ * @param time Time since Big Bang (or start of the simulation) in internal
+ * units.
  */
 __attribute__((always_inline)) INLINE static void cooling_cool_part(
     const struct phys_const* restrict phys_const,
@@ -117,8 +118,8 @@ __attribute__((always_inline)) INLINE static void cooling_cool_part(
     const struct hydro_props* hydro_props,
     const struct entropy_floor_properties* floor_props,
     const struct cooling_function_data* restrict cooling,
-    struct part* restrict p, struct xpart* restrict xp, const double time,
-    const float dt, const float dt_therm) {
+    struct part* restrict p, struct xpart* restrict xp, const float dt,
+    const float dt_therm, const double time) {
 
   /* Nothing to do here? */
   if (dt == 0.) return;

src/cooling/grackle/cooling.c

@@ -748,9 +748,10 @@ void cooling_apply(struct part* restrict p, struct xpart* restrict xp,
  * @param cooling The #cooling_function_data used in the run.
  * @param p Pointer to the particle data.
  * @param xp Pointer to the particle' extended data.
- * @param time The current time.
  * @param dt The time-step of this particle.
  * @param dt_therm The time-step operator used for thermal quantities.
+ * @param time The current time (since the Big Bang or start of the run) in
+ * internal units.
  */
 void cooling_cool_part(const struct phys_const* restrict phys_const,
                        const struct unit_system* restrict us,
@@ -759,8 +760,8 @@ void cooling_cool_part(const struct phys_const* restrict phys_const,
                        const struct entropy_floor_properties* floor_props,
                        const struct cooling_function_data* restrict cooling,
                        struct part* restrict p, struct xpart* restrict xp,
-                       const double time, const double dt,
-                       const double dt_therm) {
+                       const double dt, const double dt_therm,
+                       const double time) {
 
   /* Nothing to do here? */
   if (dt == 0.) return;

src/cooling/grackle/cooling.h

@@ -115,8 +115,8 @@ void cooling_cool_part(const struct phys_const* restrict phys_const,
                        const struct entropy_floor_properties* floor_props,
                        const struct cooling_function_data* restrict cooling,
                        struct part* restrict p, struct xpart* restrict xp,
-                       const double time, const double dt,
-                       const double dt_therm);
+                       const double dt, const double dt_therm,
+                       const double time);
 
 float cooling_get_temperature(
     const struct phys_const* restrict phys_const,

src/cooling/none/cooling.h

@@ -63,9 +63,10 @@ INLINE static void cooling_update(const struct cosmology* cosmo,
  * @param cooling The #cooling_function_data used in the run.
  * @param p Pointer to the particle data.
  * @param xp Pointer to the extended particle data.
- * @param time The current time.
  * @param dt The time-step of this particle.
  * @param dt_therm The time-step operator used for thermal quantities.
+ * @param time The current time (since the Big Bang or start of the run) in
+ * internal units.
  */
 __attribute__((always_inline)) INLINE static void cooling_cool_part(
     const struct phys_const* restrict phys_const,
@@ -74,8 +75,8 @@ __attribute__((always_inline)) INLINE static void cooling_cool_part(
     const struct hydro_props* hydro_props,
     const struct entropy_floor_properties* floor_props,
     const struct cooling_function_data* restrict cooling,
-    struct part* restrict p, struct xpart* restrict xp, const double time,
-    const float dt, const float dt_therm) {}
+    struct part* restrict p, struct xpart* restrict xp, const float dt,
+    const float dt_therm, const double time) {}
 
 /**
  * @brief Computes the cooling time-step.

src/runner_others.c

@@ -145,6 +145,7 @@ void runner_do_grav_mesh(struct runner *r, struct cell *c, int timer) {
  * @param timer 1 if the time is to be recorded.
  */
 void runner_do_cooling(struct runner *r, struct cell *c, int timer) {
+
   const struct engine *e = r->e;
   const struct cosmology *cosmo = e->cosmology;
   const int with_cosmology = (e->policy & engine_policy_cosmology);
@@ -202,8 +203,8 @@ void runner_do_cooling(struct runner *r, struct cell *c, int timer) {
 
         /* Let's cool ! */
         cooling_cool_part(constants, us, cosmo, hydro_props,
-                          entropy_floor_props, cooling_func, p, xp, time,
-                          dt_cool, dt_therm);
+                          entropy_floor_props, cooling_func, p, xp, dt_cool,
+                          dt_therm, time);
 
         /* Apply the effects of feedback on this particle
          * (Note: Only used in schemes that have a delayed feedback mechanism