Naming convention improvements in the EAGLE cooling section of the YAML file. Code formatting.

doc/RTD/source/SubgridModels/EAGLE/index.rst

@@ -98,32 +98,30 @@ In the snapshots, we output for each gas and star particle:
 |                                  | | smoothed over SPH neighbours      |           |                             |
 +----------------------------------+-------------------------------------+-----------+-----------------------------+
 
-The stars will lose mass over their lifetime (up to ~45%). The
-fractions will remain unchanged but if one is interested in computing
-an absolute metal mass (say) for a star, the ``InitialMass`` (see
-below) of the star must be used.
-
-The chemistry model only requires a small number of parameters to be
-specified in the `EAGLEChemistry` section of the YAML file. These are
-the initial values of the metallicity and element mass
-fractions. These are then applied at the start of a simulation to
-*all* the *gas* particles. All 9 elements have to be specified An
-example section, for primordial abundances (typical for a cosmological
-run), is:
+The stars will lose mass over their lifetime (up to ~45%). The fractions will
+remain unchanged but if one is interested in computing an absolute metal mass
+(say) for a star, the ``InitialMass`` (see below) of the star must be used.
+
+The chemistry model only requires a small number of parameters to be specified
+in the `EAGLEChemistry` section of the YAML file. These are the initial values
+of the metallicity and element mass fractions. These are then applied at the
+start of a simulation to *all* the *gas* particles. All 9 traced elements have
+to be specified An example section, for primordial abundances (typical for a
+cosmological run), is:
 
 .. code:: YAML
 
    EAGLEChemistry:
-     Metallicity:                0.    # Mass fraction in all metals
-     InitAbundance_Hydrogen:     0.755 # Mass fraction in Hydrogen
-     InitAbundance_Helium:       0.245 # Mass fraction in Helium
-     InitAbundance_Carbon:       0.    # Mass fraction in Carbon
-     InitAbundance_Nitrogen:     0.    # Mass fraction in Nitrogen
-     InitAbundance_Oxygen:       0.    # Mass fraction in Oxygen
-     InitAbundance_Neon:         0.    # Mass fraction in Neon
-     InitAbundance_Magnesium:    0.    # Mass fraction in Magnesium
-     InitAbundance_Silicon:      0.    # Mass fraction in Silicon
-     InitAbundance_Iron:         0.    # Mass fraction in Iron
+     init_abundance_metal:        0.    # Mass fraction in *all* metals
+     init_abundance_Hydrogen:     0.755 # Mass fraction in Hydrogen
+     init_abundance_Helium:       0.245 # Mass fraction in Helium
+     init_abundance_Carbon:       0.    # Mass fraction in Carbon
+     init_abundance_Nitrogen:     0.    # Mass fraction in Nitrogen
+     init_abundance_Oxygen:       0.    # Mass fraction in Oxygen
+     init_abundance_Neon:         0.    # Mass fraction in Neon
+     init_abundance_Magnesium:    0.    # Mass fraction in Magnesium
+     init_abundance_Silicon:      0.    # Mass fraction in Silicon
+     init_abundance_Iron:         0.    # Mass fraction in Iron
 
 Whilst one would use the following values for solar abundances
 (typical for an idealised low-redshift run):
@@ -131,16 +129,16 @@ Whilst one would use the following values for solar abundances
 .. code:: YAML
 
    EAGLEChemistry:
-     Metallicity:                0.014        # Mass fraction in all metals
-     InitAbundance_Hydrogen:     0.70649785   # Mass fraction in Hydrogen
-     InitAbundance_Helium:       0.28055534   # Mass fraction in Helium
-     InitAbundance_Carbon:       2.0665436e-3 # Mass fraction in Carbon
-     InitAbundance_Nitrogen:     8.3562563e-4 # Mass fraction in Nitrogen
-     InitAbundance_Oxygen:       5.4926244e-3 # Mass fraction in Oxygen
-     InitAbundance_Neon:         1.4144605e-3 # Mass fraction in Neon
-     InitAbundance_Magnesium:    5.907064e-4  # Mass fraction in Magnesium
-     InitAbundance_Silicon:      6.825874e-4  # Mass fraction in Silicon
-     InitAbundance_Iron:         1.1032152e-3 # Mass fraction in Iron
+     init_abundance_metal:        0.014        # Mass fraction in *all* metals
+     init_abundance_Hydrogen:     0.70649785   # Mass fraction in Hydrogen
+     init_abundance_Helium:       0.28055534   # Mass fraction in Helium
+     init_abundance_Carbon:       2.0665436e-3 # Mass fraction in Carbon
+     init_abundance_Nitrogen:     8.3562563e-4 # Mass fraction in Nitrogen
+     init_abundance_Oxygen:       5.4926244e-3 # Mass fraction in Oxygen
+     init_abundance_Neon:         1.4144605e-3 # Mass fraction in Neon
+     init_abundance_Magnesium:    5.907064e-4  # Mass fraction in Magnesium
+     init_abundance_Silicon:      6.825874e-4  # Mass fraction in Silicon
+     init_abundance_Iron:         1.1032152e-3 # Mass fraction in Iron
 
 
      

examples/CoolingBox/coolingBox.yml

@@ -59,17 +59,17 @@ EAGLECooling:
   He_reion_z_sigma:        0.5
   He_reion_eV_p_H:         2.0
 
-EAGLEChemistry:
-  InitMetallicity:         0.014
-  InitAbundance_Hydrogen:  0.70649785
-  InitAbundance_Helium:    0.28055534
-  InitAbundance_Carbon:    2.0665436e-3
-  InitAbundance_Nitrogen:  8.3562563e-4
-  InitAbundance_Oxygen:    5.4926244e-3
-  InitAbundance_Neon:      1.4144605e-3
-  InitAbundance_Magnesium: 5.907064e-4
-  InitAbundance_Silicon:   6.825874e-4
-  InitAbundance_Iron:      1.1032152e-3
+EAGLEChemistry:             # Solar abundances
+  init_abundance_metal:     0.014
+  init_abundance_Hydrogen:  0.70649785
+  init_abundance_Helium:    0.28055534
+  init_abundance_Carbon:    2.0665436e-3
+  init_abundance_Nitrogen:  8.3562563e-4
+  init_abundance_Oxygen:    5.4926244e-3
+  init_abundance_Neon:      1.4144605e-3
+  init_abundance_Magnesium: 5.907064e-4
+  init_abundance_Silicon:   6.825874e-4
+  init_abundance_Iron:      1.1032152e-3
 
 GearChemistry:
   InitialMetallicity: 0.01295

examples/CoolingRates/cooling_rates.yml

@@ -16,16 +16,16 @@ Cosmology:
   Omega_b:        0.0455        # Baryon density parameter
 
 EAGLEChemistry:
-  InitMetallicity:         0.014
-  InitAbundance_Hydrogen:  0.70649785
-  InitAbundance_Helium:    0.28055534
-  InitAbundance_Carbon:    2.0665436e-3
-  InitAbundance_Nitrogen:  8.3562563e-4
-  InitAbundance_Oxygen:    5.4926244e-3
-  InitAbundance_Neon:      1.4144605e-3
-  InitAbundance_Magnesium: 5.907064e-4
-  InitAbundance_Silicon:   6.825874e-4
-  InitAbundance_Iron:      1.1032152e-3
+  init_abundance_metal:     0.014
+  init_abundance_Hydrogen:  0.70649785
+  init_abundance_Helium:    0.28055534
+  init_abundance_Carbon:    2.0665436e-3
+  init_abundance_Nitrogen:  8.3562563e-4
+  init_abundance_Oxygen:    5.4926244e-3
+  init_abundance_Neon:      1.4144605e-3
+  init_abundance_Magnesium: 5.907064e-4
+  init_abundance_Silicon:   6.825874e-4
+  init_abundance_Iron:      1.1032152e-3
 
 EAGLECooling:
   dir_name:                ./coolingtables/

examples/EAGLE_12/eagle_12.yml

@@ -57,17 +57,17 @@ InitialConditions:
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 
-EAGLEChemistry: 	    # Solar abundances
-  InitMetallicity:          0.014
-  InitAbundance_Hydrogen:   0.70649785
-  InitAbundance_Helium:     0.28055534
-  InitAbundance_Carbon:     2.0665436e-3
-  InitAbundance_Nitrogen:   8.3562563e-4
-  InitAbundance_Oxygen:     5.4926244e-3
-  InitAbundance_Neon:       1.4144605e-3
-  InitAbundance_Magnesium:  5.907064e-4
-  InitAbundance_Silicon:    6.825874e-4
-  InitAbundance_Iron:       1.1032152e-3
+EAGLEChemistry: 	     # Solar abundances
+  init_abundance_metal:      0.014
+  init_abundance_Hydrogen:   0.70649785
+  init_abundance_Helium:     0.28055534
+  init_abundance_Carbon:     2.0665436e-3
+  init_abundance_Nitrogen:   8.3562563e-4
+  init_abundance_Oxygen:     5.4926244e-3
+  init_abundance_Neon:       1.4144605e-3
+  init_abundance_Magnesium:  5.907064e-4
+  init_abundance_Silicon:    6.825874e-4
+  init_abundance_Iron:       1.1032152e-3
 
 EAGLECooling:
   dir_name:                ./coolingtables/

examples/EAGLE_25/eagle_25.yml

@@ -66,18 +66,18 @@ InitialConditions:
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 
-EAGLEChemistry: 	    # Solar abundances
-  InitMetallicity:          0.014
-  InitAbundance_Hydrogen:   0.70649785
-  InitAbundance_Helium:     0.28055534
-  InitAbundance_Carbon:     2.0665436e-3
-  InitAbundance_Nitrogen:   8.3562563e-4
-  InitAbundance_Oxygen:     5.4926244e-3
-  InitAbundance_Neon:       1.4144605e-3
-  InitAbundance_Magnesium:  5.907064e-4
-  InitAbundance_Silicon:    6.825874e-4
-  InitAbundance_Iron:       1.1032152e-3
-
+EAGLEChemistry: 	     # Solar abundances
+  init_abundance_metal:      0.014
+  init_abundance_Hydrogen:   0.70649785
+  init_abundance_Helium:     0.28055534
+  init_abundance_Carbon:     2.0665436e-3
+  init_abundance_Nitrogen:   8.3562563e-4
+  init_abundance_Oxygen:     5.4926244e-3
+  init_abundance_Neon:       1.4144605e-3
+  init_abundance_Magnesium:  5.907064e-4
+  init_abundance_Silicon:    6.825874e-4
+  init_abundance_Iron:       1.1032152e-3
+  
 EAGLECooling:
   dir_name:                ./coolingtables/
   H_reion_z:               11.5 

examples/EAGLE_50/eagle_50.yml

@@ -59,18 +59,18 @@ InitialConditions:
   cleanup_h_factors: 1                # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1         # Remove the sqrt(a) factor in the velocities inherited from Gadget
 
-EAGLEChemistry: 	    # Solar abundances
-  InitMetallicity:          0.014
-  InitAbundance_Hydrogen:   0.70649785
-  InitAbundance_Helium:     0.28055534
-  InitAbundance_Carbon:     2.0665436e-3
-  InitAbundance_Nitrogen:   8.3562563e-4
-  InitAbundance_Oxygen:     5.4926244e-3
-  InitAbundance_Neon:       1.4144605e-3
-  InitAbundance_Magnesium:  5.907064e-4
-  InitAbundance_Silicon:    6.825874e-4
-  InitAbundance_Iron:       1.1032152e-3
-
+EAGLEChemistry: 	     # Solar abundances
+  init_abundance_metal:      0.014
+  init_abundance_Hydrogen:   0.70649785
+  init_abundance_Helium:     0.28055534
+  init_abundance_Carbon:     2.0665436e-3
+  init_abundance_Nitrogen:   8.3562563e-4
+  init_abundance_Oxygen:     5.4926244e-3
+  init_abundance_Neon:       1.4144605e-3
+  init_abundance_Magnesium:  5.907064e-4
+  init_abundance_Silicon:    6.825874e-4
+  init_abundance_Iron:       1.1032152e-3
+  
 EAGLECooling:
   dir_name:                ./coolingtables/
   H_reion_z:               11.5 

examples/EAGLE_6/eagle_6.yml

@@ -70,17 +70,17 @@ InitialConditions:
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 
-EAGLEChemistry: 	    # Solar abundances
-  InitMetallicity:          0.014
-  InitAbundance_Hydrogen:   0.70649785
-  InitAbundance_Helium:     0.28055534
-  InitAbundance_Carbon:     2.0665436e-3
-  InitAbundance_Nitrogen:   8.3562563e-4
-  InitAbundance_Oxygen:     5.4926244e-3
-  InitAbundance_Neon:       1.4144605e-3
-  InitAbundance_Magnesium:  5.907064e-4
-  InitAbundance_Silicon:    6.825874e-4
-  InitAbundance_Iron:       1.1032152e-3
+EAGLEChemistry: 	     # Solar abundances
+  init_abundance_metal:      0.014
+  init_abundance_Hydrogen:   0.70649785
+  init_abundance_Helium:     0.28055534
+  init_abundance_Carbon:     2.0665436e-3
+  init_abundance_Nitrogen:   8.3562563e-4
+  init_abundance_Oxygen:     5.4926244e-3
+  init_abundance_Neon:       1.4144605e-3
+  init_abundance_Magnesium:  5.907064e-4
+  init_abundance_Silicon:    6.825874e-4
+  init_abundance_Iron:       1.1032152e-3
 
 EAGLECooling:
   dir_name:                ./coolingtables/

examples/SantaBarbara/santa_barbara.yml

@@ -59,17 +59,18 @@ InitialConditions:
   generate_gas_in_ics: 1            # Generate gas particles from the DM-only ICs
   cleanup_smoothing_lengths: 1      # Since we generate gas, make use of the (expensive) cleaning-up procedure.
 
+# Impose primoridal metallicity
 EAGLEChemistry:
-  InitMetallicity:         0.0
-  InitAbundance_Hydrogen:  0.752
-  InitAbundance_Helium:    0.248
-  InitAbundance_Carbon:    0.0
-  InitAbundance_Nitrogen:  0.0
-  InitAbundance_Oxygen:    0.0
-  InitAbundance_Neon:      0.0
-  InitAbundance_Magnesium: 0.0
-  InitAbundance_Silicon:   0.0
-  InitAbundance_Iron:      0.0
+  init_abundance_metal:     0.0
+  init_abundance_Hydrogen:  0.752
+  init_abundance_Helium:    0.248
+  init_abundance_Carbon:    0.0
+  init_abundance_Nitrogen:  0.0
+  init_abundance_Oxygen:    0.0
+  init_abundance_Neon:      0.0
+  init_abundance_Magnesium: 0.0
+  init_abundance_Silicon:   0.0
+  init_abundance_Iron:      0.0
 
 EAGLECooling:
   dir_name:                ./coolingtables/

examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml

@@ -72,13 +72,13 @@ EAGLECooling:
 
 # Impose primoridal metallicity
 EAGLEChemistry:
-  InitMetallicity: 0.0
-  InitAbundance_Hydrogen: 0.755
-  InitAbundance_Helium: 0.245
-  InitAbundance_Carbon: 0.
-  InitAbundance_Nitrogen: 0.
-  InitAbundance_Oxygen: 0.
-  InitAbundance_Neon: 0.
-  InitAbundance_Magnesium:  0.
-  InitAbundance_Silicon: 0.
-  InitAbundance_Iron: 0.
+  init_abundance_metal:     0.0
+  init_abundance_Hydrogen:  0.752
+  init_abundance_Helium:    0.248
+  init_abundance_Carbon:    0.0
+  init_abundance_Nitrogen:  0.0
+  init_abundance_Oxygen:    0.0
+  init_abundance_Neon:      0.0
+  init_abundance_Magnesium: 0.0
+  init_abundance_Silicon:   0.0
+  init_abundance_Iron:      0.0

examples/parameter_example.yml

@@ -276,16 +276,16 @@ GrackleCooling:
 
 # EAGLE model
 EAGLEChemistry:
-  InitMetallicity:         0.           # Inital fraction of particle mass in *all* metals
-  InitAbundance_Hydrogen:  0.752        # Inital fraction of particle mass in Hydrogen
-  InitAbundance_Helium:    0.248        # Inital fraction of particle mass in Helium
-  InitAbundance_Carbon:    0.000        # Inital fraction of particle mass in Carbon
-  InitAbundance_Nitrogen:  0.000        # Inital fraction of particle mass in Nitrogen
-  InitAbundance_Oxygen:    0.000        # Inital fraction of particle mass in Oxygen
-  InitAbundance_Neon:      0.000        # Inital fraction of particle mass in Neon
-  InitAbundance_Magnesium: 0.000        # Inital fraction of particle mass in Magnesium
-  InitAbundance_Silicon:   0.000        # Inital fraction of particle mass in Silicon
-  InitAbundance_Iron:      0.000        # Inital fraction of particle mass in Iron
+  init_abundance_metal:     0.           # Inital fraction of particle mass in *all* metals
+  init_abundance_Hydrogen:  0.752        # Inital fraction of particle mass in Hydrogen
+  init_abundance_Helium:    0.248        # Inital fraction of particle mass in Helium
+  init_abundance_Carbon:    0.000        # Inital fraction of particle mass in Carbon
+  init_abundance_Nitrogen:  0.000        # Inital fraction of particle mass in Nitrogen
+  init_abundance_Oxygen:    0.000        # Inital fraction of particle mass in Oxygen
+  init_abundance_Neon:      0.000        # Inital fraction of particle mass in Neon
+  init_abundance_Magnesium: 0.000        # Inital fraction of particle mass in Magnesium
+  init_abundance_Silicon:   0.000        # Inital fraction of particle mass in Silicon
+  init_abundance_Iron:      0.000        # Inital fraction of particle mass in Iron
 
 # Structure finding options (requires velociraptor)
 StructureFinding:

src/chemistry/EAGLE/chemistry.h

@@ -154,6 +154,7 @@ __attribute__((always_inline)) INLINE static void chemistry_first_init_part(
   if (data->initial_metal_mass_fraction_total != -1) {
     p->chemistry_data.metal_mass_fraction_total =
         data->initial_metal_mass_fraction_total;
+
     for (int elem = 0; elem < chemistry_element_count; ++elem)
       p->chemistry_data.metal_mass_fraction[elem] =
           data->initial_metal_mass_fraction[elem];
@@ -176,13 +177,13 @@ static INLINE void chemistry_init_backend(struct swift_params* parameter_file,
 
   /* Read the total metallicity */
   data->initial_metal_mass_fraction_total = parser_get_opt_param_float(
-      parameter_file, "EAGLEChemistry:InitMetallicity", -1);
+      parameter_file, "EAGLEChemistry:init_abundance_metal", -1);
 
   if (data->initial_metal_mass_fraction_total != -1) {
     /* Read the individual mass fractions */
     for (int elem = 0; elem < chemistry_element_count; ++elem) {
       char buffer[50];
-      sprintf(buffer, "EAGLEChemistry:InitAbundance_%s",
+      sprintf(buffer, "EAGLEChemistry:init_abundance_%s",
               chemistry_get_element_name((enum chemistry_element)elem));
 
       data->initial_metal_mass_fraction[elem] =

src/cooling/EAGLE/cooling.c

@@ -740,8 +740,8 @@ void cooling_init_backend(struct swift_params *parameter_file,
   /* read some parameters */
   parser_get_param_string(parameter_file, "EAGLECooling:dir_name",
                           cooling->cooling_table_path);
-  cooling->H_reion_z = parser_get_param_float(
-      parameter_file, "EAGLECooling:H_reion_z");
+  cooling->H_reion_z =
+      parser_get_param_float(parameter_file, "EAGLECooling:H_reion_z");
   cooling->He_reion_z_centre =
       parser_get_param_float(parameter_file, "EAGLECooling:He_reion_z_centre");
   cooling->He_reion_z_sigma =
@@ -754,7 +754,7 @@ void cooling_init_backend(struct swift_params *parameter_file,
       parameter_file, "EAGLECooling:Ca_over_Si_in_solar", 1.f);
   cooling->S_over_Si_ratio_in_solar = parser_get_opt_param_float(
       parameter_file, "EAGLECooling:S_over_Si_in_solar", 1.f);
-  
+
   /* convert to cgs */
   cooling->He_reion_heat_cgs *=
       phys_const->const_electron_volt *