From 903f845a7fc0a8735e35c45c6a8d28b70a48a484 Mon Sep 17 00:00:00 2001
From: Matthieu Schaller <schaller@strw.leidenuniv.nl>
Date: Thu, 3 Jan 2019 15:10:06 +0100
Subject: [PATCH] Naming convention improvements in the EAGLE cooling section
of the YAML file. Code formatting.
---
doc/RTD/source/SubgridModels/EAGLE/index.rst | 62 +++++++++----------
examples/CoolingBox/coolingBox.yml | 22 +++----
examples/CoolingRates/cooling_rates.yml | 20 +++---
examples/EAGLE_12/eagle_12.yml | 22 +++----
examples/EAGLE_25/eagle_25.yml | 24 +++----
examples/EAGLE_50/eagle_50.yml | 24 +++----
examples/EAGLE_6/eagle_6.yml | 22 +++----
examples/SantaBarbara/santa_barbara.yml | 21 ++++---
.../small_cosmo_volume.yml | 20 +++---
examples/parameter_example.yml | 20 +++---
src/chemistry/EAGLE/chemistry.h | 5 +-
src/cooling/EAGLE/cooling.c | 6 +-
12 files changed, 134 insertions(+), 134 deletions(-)
diff --git a/doc/RTD/source/SubgridModels/EAGLE/index.rst b/doc/RTD/source/SubgridModels/EAGLE/index.rst
index a5687efb8a..6388f7d3d4 100644
--- a/doc/RTD/source/SubgridModels/EAGLE/index.rst
+++ b/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
diff --git a/examples/CoolingBox/coolingBox.yml b/examples/CoolingBox/coolingBox.yml
index 785f699bf0..97b452e5ea 100644
--- a/examples/CoolingBox/coolingBox.yml
+++ b/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
diff --git a/examples/CoolingRates/cooling_rates.yml b/examples/CoolingRates/cooling_rates.yml
index 343c24d320..1d67ad0af7 100644
--- a/examples/CoolingRates/cooling_rates.yml
+++ b/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/
diff --git a/examples/EAGLE_12/eagle_12.yml b/examples/EAGLE_12/eagle_12.yml
index 062870a23b..367c5f7697 100644
--- a/examples/EAGLE_12/eagle_12.yml
+++ b/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/
diff --git a/examples/EAGLE_25/eagle_25.yml b/examples/EAGLE_25/eagle_25.yml
index 0edc8bfa1d..0aec970db4 100644
--- a/examples/EAGLE_25/eagle_25.yml
+++ b/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
diff --git a/examples/EAGLE_50/eagle_50.yml b/examples/EAGLE_50/eagle_50.yml
index 56b945a06a..35f7c85993 100644
--- a/examples/EAGLE_50/eagle_50.yml
+++ b/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
diff --git a/examples/EAGLE_6/eagle_6.yml b/examples/EAGLE_6/eagle_6.yml
index af533f5d84..7c64c1cded 100644
--- a/examples/EAGLE_6/eagle_6.yml
+++ b/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/
diff --git a/examples/SantaBarbara/santa_barbara.yml b/examples/SantaBarbara/santa_barbara.yml
index 08cb71d0ce..eb20030e00 100644
--- a/examples/SantaBarbara/santa_barbara.yml
+++ b/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/
diff --git a/examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml b/examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml
index 47511f6b40..2d2dec8408 100644
--- a/examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml
+++ b/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
diff --git a/examples/parameter_example.yml b/examples/parameter_example.yml
index 2b20909b9d..9fdfc993c3 100644
--- a/examples/parameter_example.yml
+++ b/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:
diff --git a/src/chemistry/EAGLE/chemistry.h b/src/chemistry/EAGLE/chemistry.h
index 9e9dc3b323..b8a50f237a 100644
--- a/src/chemistry/EAGLE/chemistry.h
+++ b/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] =
diff --git a/src/cooling/EAGLE/cooling.c b/src/cooling/EAGLE/cooling.c
index bf3d2ace16..8345109a4e 100644
--- a/src/cooling/EAGLE/cooling.c
+++ b/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 *
--
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