diff --git a/examples/Cooling/CoolingWithPrimordialElements/CoolingWithPrimordialElements.yml b/examples/Cooling/CoolingWithPrimordialElements/CoolingWithPrimordialElements.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a65f3e40b7a3301b48f844c2c8d072afa630b78e
--- /dev/null
+++ b/examples/Cooling/CoolingWithPrimordialElements/CoolingWithPrimordialElements.yml
@@ -0,0 +1,108 @@
+# Define some meta-data about the simulation
+MetaData:
+ run_name: CosmoBox00
+
+# Define the system of units to use internally.
+InternalUnitSystem:
+ UnitMass_in_cgs: 1.98841e43 # 10^10 M_sun in grams
+ UnitLength_in_cgs: 3.08567758e24 # Mpc in centimeters
+ UnitVelocity_in_cgs: 1e5 # km/s in centimeters per second
+ UnitCurrent_in_cgs: 1 # Amperes
+ UnitTemp_in_cgs: 1 # Kelvin
+
+
+# Cosmological parameters
+Cosmology:
+ h: 0.67321 # Reduced qHubble constant
+ a_begin: 0.01282051 # Initial scale-factor of the simulation (z=77)
+ a_end: 1.0 # Final scale factor of the simulation
+ Omega_cdm: 0.26641139 # Cold Dark Matter density parameter (value without neutrinos : 0.26499)
+ Omega_lambda: 0.6842 # Dark-energy density parameter
+ Omega_b: 0.049389 # Baryon density parameter
+
+# Parameters governing the time integration
+TimeIntegration:
+ dt_min: 1e-10 # The minimal time-step size of the simulation (in internal units).
+ dt_max: 1e-2 # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+ basename: snap/snapshot # Common part of the name of output files
+ output_list_on: 1
+ output_list: ./output_list.txt
+ compression: 4
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1.01
+ scale_factor_first: 0.02
+
+# Parameters for the self-gravity scheme
+Gravity:
+ eta: 0.025 # Constant dimensionless multiplier for time integration.
+ MAC: adaptive # Use the geometric opening angle condition
+ theta_cr: 0.7 # Opening angle (Multipole acceptance criterion)
+ epsilon_fmm: 0.001 # Adaptive opening angle
+ mesh_side_length: 256
+ comoving_DM_softening: 0.0066 # Comoving softening for DM
+ max_physical_DM_softening: 0.00174 # Physical softening for DM
+ comoving_baryon_softening: 0.0066 # Comoving softening for DM
+ max_physical_baryon_softening: 0.00174 # Physical softening for DM
+
+
+# Parameters for the hydrodynamics scheme
+SPH:
+ resolution_eta: 1.2348 # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
+ h_min_ratio: 0.01 # Minimal smoothing length in units of softening.
+ h_max: 0.5 # Maximal smoothing length in co-moving internal units.
+ CFL_condition: 0.2 # Courant-Friedrich-Levy condition for time integration.
+ minimal_temperature: 10.0 # (internal units)
+
+# 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: 0 # Enable or not the UV background
+ redshift: -1 # Redshift to use (-1 means time based redshift)
+ with_metal_cooling: 0 # Enable or not the metal cooling
+ 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: 0 # (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
+ HydrogenFractionByMass : 0.76 # Hydrogen fraction by mass (default is 0.76)
+ use_radiative_transfer : 0 # Arrays of ionization and heating rates are provided
+ H2_three_body_rate : 1 # (optional) H2 formation three body rate (see grackle documentation)
+ H2_cie_cooling : 0 # Enable/disable H2 collision-induced emission cooling from Ripamonti & Abel (2004)
+ cmb_temperature_floor : 1 # Enable/disable an effective CMB temperature floor
+ initial_nHII_to_nH_ratio: 2.393761E-004 # initial nHII to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHeI_to_nH_ratio: 7.900000E-002 # initial nHeI to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHeII_to_nH_ratio: 5.692753E-020 # initial nHeII to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHeIII_to_nH_ratio: 0 # initial nHeIII to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nDI_to_nH_ratio: 2.529538E-005 # initial nDI to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nDII_to_nH_ratio: 4.284496E-009 # initial nDII to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHM_to_nH_ratio: 6.509693E-012 # initial nHM to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nH2I_to_nH_ratio: 1.891128E-006 # initial nH2I to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nH2II_to_nH_ratio: 4.153181E-014 # initial nH2II to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHDI_to_nH_ratio: 3.356904E-010 # initial nHDI to nH ratio (number density ratio). Value is ignored if set to -1.
+
+
+
+
+Scheduler:
+ max_top_level_cells: 12
+ #cell_split_size: 200
+
+Restarts:
+ onexit: 1
+ delta_hours: 6.0
+ max_run_time: 71.5 # Three days minus fergie time
+ #resubmit_on_exit: 1
+ #resubmit_command: ./resub.sh
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: homogeneousCube_32.hdf5
+ periodic: 1
+ cleanup_h_factors: 0 # Remove the h-factors inherited from Gadget
+ cleanup_velocity_factors: 0 # Remove the sqrt(a) factor in the velocities inherited from Gadget
+
diff --git a/examples/Cooling/CoolingWithPrimordialElements/README b/examples/Cooling/CoolingWithPrimordialElements/README
new file mode 100644
index 0000000000000000000000000000000000000000..248a64c11dc7df99263d677100d0502111c06512
--- /dev/null
+++ b/examples/Cooling/CoolingWithPrimordialElements/README
@@ -0,0 +1,11 @@
+Runs a uniform cosmological box with imposed abundances for a set of
+elements entering the Grackle cooling.
+The simulation is run with the Grackle thermochemistry, down to redhift 0
+where the resulting abundances are compared with predictions.
+
+To run, configure swift with:
+ ./configure --with-cooling=grackle_3 --with-grackle=$GRACKLE_ROOT
+
+
+Note : the script getPrimordialAbundances.py helps in the setting of the
+initial abundances.
diff --git a/examples/Cooling/CoolingWithPrimordialElements/faure2024.dat b/examples/Cooling/CoolingWithPrimordialElements/faure2024.dat
new file mode 100644
index 0000000000000000000000000000000000000000..9e0427ad507dcaf4b3b2f63c3d894e3a65d81a6a
--- /dev/null
+++ b/examples/Cooling/CoolingWithPrimordialElements/faure2024.dat
@@ -0,0 +1,193 @@
+! Fractional density (n(X)/nH)
+! 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
+ Redshift ctime Trad Tn nb nH e- H He D H2 HD D2 H+ D+ He+ H2+ HD+ D2+ HeH+ H3+ H2D+ HD2+ D3+ H-
+ 3.401000E+003 0.000000E+000 9.269426E+003 9.269426E+003 8.151816E+003 7.547801E+003 1.080025E+000 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.000000E+000 2.530000E-005 8.000000E-002 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000
+ 3.400876E+003 3.168879E+000 9.269089E+003 9.269088E+003 8.150927E+003 7.546978E+003 1.080024E+000 1.796857E-010 1.705857E-006 4.546047E-015 6.941758E-036 3.211260E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.554308E-028 0.000000E+000 0.000000E+000 1.268827E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.306460E-028
+ 3.400867E+003 3.485767E+000 9.269064E+003 9.269063E+003 8.150861E+003 7.546917E+003 1.080024E+000 1.796933E-010 1.705992E-006 4.546240E-015 6.942382E-036 3.211549E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.554494E-028 0.000000E+000 0.000000E+000 1.268924E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.306636E-028
+ 3.400858E+003 3.834344E+000 9.269039E+003 9.269038E+003 8.150795E+003 7.546856E+003 1.080024E+000 1.797009E-010 1.706126E-006 4.546433E-015 6.943006E-036 3.211838E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.554679E-028 0.000000E+000 0.000000E+000 1.269021E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.306812E-028
+ 3.400842E+003 4.217778E+000 9.268995E+003 9.268994E+003 8.150680E+003 7.546749E+003 1.080024E+000 1.797142E-010 1.706362E-006 4.546770E-015 6.944097E-036 3.212344E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.555003E-028 0.000000E+000 0.000000E+000 1.269191E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.307120E-028
+ 3.400825E+003 4.639556E+000 9.268948E+003 9.268947E+003 8.150556E+003 7.546635E+003 1.080024E+000 1.797285E-010 1.706613E-006 4.547131E-015 6.945265E-036 3.212885E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.555350E-028 0.000000E+000 0.000000E+000 1.269372E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.307450E-028
+ 3.400808E+003 5.103511E+000 9.268902E+003 9.268901E+003 8.150433E+003 7.546521E+003 1.080024E+000 1.797427E-010 1.706865E-006 4.547491E-015 6.946434E-036 3.213426E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.555697E-028 0.000000E+000 0.000000E+000 1.269554E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.307780E-028
+ 3.400790E+003 5.613863E+000 9.268855E+003 9.268854E+003 8.150310E+003 7.546406E+003 1.080024E+000 1.797570E-010 1.707117E-006 4.547852E-015 6.947602E-036 3.213968E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.556044E-028 0.000000E+000 0.000000E+000 1.269735E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.308109E-028
+ 3.400771E+003 6.175249E+000 9.268802E+003 9.268801E+003 8.150170E+003 7.546277E+003 1.080024E+000 1.797732E-010 1.707403E-006 4.548261E-015 6.948928E-036 3.214582E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.556437E-028 0.000000E+000 0.000000E+000 1.269941E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.308483E-028
+ 3.400745E+003 6.792774E+000 9.268730E+003 9.268729E+003 8.149981E+003 7.546102E+003 1.080024E+000 1.797950E-010 1.707789E-006 4.548813E-015 6.950717E-036 3.215410E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.556968E-028 0.000000E+000 0.000000E+000 1.270219E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.308988E-028
+ 3.400723E+003 7.472051E+000 9.268670E+003 9.268669E+003 8.149822E+003 7.545955E+003 1.080024E+000 1.798133E-010 1.708113E-006 4.549277E-015 6.952221E-036 3.216107E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.557414E-028 0.000000E+000 0.000000E+000 1.270453E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.309412E-028
+ 3.400696E+003 8.219256E+000 9.268598E+003 9.268597E+003 8.149633E+003 7.545779E+003 1.080024E+000 1.798353E-010 1.708500E-006 4.549832E-015 6.954020E-036 3.216940E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.557948E-028 0.000000E+000 0.000000E+000 1.270732E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.309919E-028
+ 3.400664E+003 9.041182E+000 9.268511E+003 9.268510E+003 8.149402E+003 7.545566E+003 1.080024E+000 1.798620E-010 1.708972E-006 4.550508E-015 6.956208E-036 3.217954E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.558597E-028 0.000000E+000 0.000000E+000 1.271072E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.310537E-028
+ 3.400633E+003 9.945300E+000 9.268424E+003 9.268423E+003 8.149174E+003 7.545355E+003 1.080024E+000 1.798883E-010 1.709437E-006 4.551174E-015 6.958368E-036 3.218954E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.559238E-028 0.000000E+000 0.000000E+000 1.271407E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.311145E-028
+ 3.400592E+003 1.093983E+001 9.268314E+003 9.268313E+003 8.148882E+003 7.545084E+003 1.080024E+000 1.799221E-010 1.710035E-006 4.552029E-015 6.961143E-036 3.220240E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.560060E-028 0.000000E+000 0.000000E+000 1.271838E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.311927E-028
+ 3.400549E+003 1.203381E+001 9.268196E+003 9.268195E+003 8.148573E+003 7.544798E+003 1.080024E+000 1.799579E-010 1.710668E-006 4.552934E-015 6.964078E-036 3.221599E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.560931E-028 0.000000E+000 0.000000E+000 1.272294E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.312755E-028
+ 3.400507E+003 1.323719E+001 9.268081E+003 9.268080E+003 8.148268E+003 7.544516E+003 1.080024E+000 1.799931E-010 1.711291E-006 4.553826E-015 6.966971E-036 3.222939E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.561788E-028 0.000000E+000 0.000000E+000 1.272743E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.313570E-028
+ 3.400462E+003 1.456091E+001 9.267959E+003 9.267958E+003 8.147946E+003 7.544218E+003 1.080024E+000 1.800305E-010 1.711952E-006 4.554771E-015 6.970036E-036 3.224359E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.562696E-028 0.000000E+000 0.000000E+000 1.273219E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.314433E-028
+ 3.400409E+003 1.601701E+001 9.267814E+003 9.267813E+003 8.147565E+003 7.543865E+003 1.080024E+000 1.800746E-010 1.712733E-006 4.555888E-015 6.973662E-036 3.226039E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.563771E-028 0.000000E+000 0.000000E+000 1.273782E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.315454E-028
+ 3.400349E+003 1.761871E+001 9.267652E+003 9.267651E+003 8.147137E+003 7.543469E+003 1.080024E+000 1.801242E-010 1.713610E-006 4.557142E-015 6.977733E-036 3.227925E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.564977E-028 0.000000E+000 0.000000E+000 1.274414E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.316600E-028
+ 3.400284E+003 1.938058E+001 9.267475E+003 9.267474E+003 8.146670E+003 7.543036E+003 1.080024E+000 1.801783E-010 1.714568E-006 4.558511E-015 6.982181E-036 3.229985E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999829E-002 4.566294E-028 0.000000E+000 0.000000E+000 1.275105E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.317852E-028
+ 3.400213E+003 2.131863E+001 9.267281E+003 9.267280E+003 8.146160E+003 7.542564E+003 1.080024E+000 1.802375E-010 1.715616E-006 4.560008E-015 6.987044E-036 3.232237E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999828E-002 4.567733E-028 0.000000E+000 0.000000E+000 1.275859E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.319220E-028
+ 3.400135E+003 2.345050E+001 9.267068E+003 9.267067E+003 8.145596E+003 7.542042E+003 1.080024E+000 1.803029E-010 1.716774E-006 4.561662E-015 6.992421E-036 3.234728E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999828E-002 4.569323E-028 0.000000E+000 0.000000E+000 1.276694E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.320732E-028
+ 3.400048E+003 2.579555E+001 9.266831E+003 9.266830E+003 8.144972E+003 7.541464E+003 1.080024E+000 1.803753E-010 1.718057E-006 4.563495E-015 6.998379E-036 3.237488E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999828E-002 4.571085E-028 0.000000E+000 0.000000E+000 1.277618E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.322407E-028
+ 3.399950E+003 2.837510E+001 9.266563E+003 9.266562E+003 8.144265E+003 7.540809E+003 1.080024E+000 1.804574E-010 1.719512E-006 4.565571E-015 7.005134E-036 3.240617E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999828E-002 4.573082E-028 0.000000E+000 0.000000E+000 1.278666E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.324304E-028
+ 3.399845E+003 3.121261E+001 9.266278E+003 9.266277E+003 8.143515E+003 7.540115E+003 1.080024E+000 1.805445E-010 1.721057E-006 4.567777E-015 7.012313E-036 3.243942E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999828E-002 4.575203E-028 0.000000E+000 0.000000E+000 1.279780E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.326320E-028
+ 3.399730E+003 3.433387E+001 9.265964E+003 9.265964E+003 8.142687E+003 7.539349E+003 1.080024E+000 1.806407E-010 1.722763E-006 4.570210E-015 7.020235E-036 3.247612E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999828E-002 4.577542E-028 0.000000E+000 0.000000E+000 1.281009E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.328543E-028
+ 3.399586E+003 3.776726E+001 9.265571E+003 9.265570E+003 8.141651E+003 7.538389E+003 1.080024E+000 1.807613E-010 1.724903E-006 4.573260E-015 7.030175E-036 3.252216E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999828E-002 4.580475E-028 0.000000E+000 0.000000E+000 1.282550E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.331331E-028
+ 3.399460E+003 4.154399E+001 9.265230E+003 9.265229E+003 8.140750E+003 7.537555E+003 1.080024E+000 1.808661E-010 1.726765E-006 4.575913E-015 7.038829E-036 3.256225E-040 0.000000E+000 1.000000E+000 2.530000E-005 7.999827E-002 4.583026E-028 0.000000E+000 0.000000E+000 1.283892E-024 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 4.333756E-028
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+ 5.810253E+001 3.793629E+007 1.583585E+002 7.315137E+001 4.064608E-002 3.763446E-002 2.289569E-004 9.997661E-001 8.000000E-002 2.529614E-005 2.497607E-006 6.385807E-010 0.000000E+000 2.289537E-004 3.218247E-009 5.634519E-020 1.885758E-014 0.000000E+000 0.000000E+000 7.860068E-015 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 3.638098E-012
+ 5.463936E+001 4.172992E+007 1.489196E+002 6.574776E+001 3.380262E-002 3.129806E-002 2.271399E-004 9.997677E-001 8.000000E-002 2.529633E-005 2.561867E-006 6.846069E-010 0.000000E+000 2.271369E-004 2.988244E-009 5.624736E-020 1.645156E-014 0.000000E+000 0.000000E+000 8.537545E-015 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 3.256642E-012
+ 5.130393E+001 4.590291E+007 1.398289E+002 5.888496E+001 2.798242E-002 2.590910E-002 2.253428E-004 9.997694E-001 8.000000E-002 2.529653E-005 2.616166E-006 7.258462E-010 0.000000E+000 2.253400E-004 2.747058E-009 5.615181E-020 1.442451E-014 0.000000E+000 0.000000E+000 9.320518E-015 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 2.912471E-012
+ 4.821007E+001 5.049320E+007 1.313965E+002 5.276826E+001 2.321917E-002 2.149878E-002 2.236289E-004 9.997711E-001 8.000000E-002 2.529673E-005 2.660290E-006 7.607670E-010 0.000000E+000 2.236263E-004 2.504933E-009 5.606187E-020 1.278221E-014 0.000000E+000 0.000000E+000 1.019681E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 2.614047E-012
+ 4.522805E+001 5.554252E+007 1.232691E+002 4.711226E+001 1.917154E-002 1.775105E-002 2.219285E-004 9.997727E-001 8.000000E-002 2.529695E-005 2.697497E-006 7.909465E-010 0.000000E+000 2.219263E-004 2.254244E-009 5.597383E-020 1.140009E-014 0.000000E+000 0.000000E+000 1.122239E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 2.345813E-012
+ 4.251272E+001 6.109677E+007 1.158684E+002 4.217719E+001 1.592172E-002 1.474202E-002 2.203335E-004 9.997742E-001 8.000000E-002 2.529717E-005 2.727125E-006 8.151859E-010 0.000000E+000 2.203315E-004 2.011385E-009 5.589237E-020 1.029823E-014 0.000000E+000 0.000000E+000 1.236195E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 2.118536E-012
+ 3.986658E+001 6.720645E+007 1.086564E+002 3.757461E+001 1.312986E-002 1.215703E-002 2.187309E-004 9.997758E-001 8.000000E-002 2.529740E-005 2.752354E-006 8.356743E-010 0.000000E+000 2.187291E-004 1.762374E-009 5.581165E-020 9.353267E-015 0.000000E+000 0.000000E+000 1.372642E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.913042E-012
+ 3.747910E+001 7.392709E+007 1.021493E+002 3.360472E+001 1.090940E-002 1.010109E-002 2.172388E-004 9.997772E-001 8.000000E-002 2.529762E-005 2.772234E-006 8.514375E-010 0.000000E+000 2.172373E-004 1.529050E-009 5.573755E-020 8.596120E-015 0.000000E+000 0.000000E+000 1.524847E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.741611E-012
+ 3.517334E+001 8.131980E+007 9.586494E+001 2.994199E+001 9.017251E-003 8.349132E-003 2.157511E-004 9.997787E-001 8.000000E-002 2.529784E-005 2.789008E-006 8.642026E-010 0.000000E+000 2.157498E-004 1.298583E-009 5.566472E-020 7.937007E-015 0.000000E+000 0.000000E+000 1.707692E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.589122E-012
+ 3.302470E+001 8.945178E+007 9.000884E+001 2.668604E+001 7.463631E-003 6.910626E-003 2.143184E-004 9.997801E-001 8.000000E-002 2.529804E-005 2.802639E-006 8.739627E-010 0.000000E+000 2.143173E-004 1.082663E-009 5.559560E-020 7.373232E-015 0.000000E+000 0.000000E+000 1.921788E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.459148E-012
+ 3.100436E+001 9.839696E+007 8.450238E+001 2.376766E+001 6.175918E-003 5.718324E-003 2.129253E-004 9.997814E-001 8.000000E-002 2.529824E-005 2.813813E-006 8.813342E-010 0.000000E+000 2.129244E-004 8.825753E-010 5.552938E-020 6.873859E-015 0.000000E+000 0.000000E+000 2.176804E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.348265E-012
+ 2.913074E+001 1.082367E+008 7.939585E+001 2.118924E+001 5.122572E-003 4.743024E-003 2.115888E-004 9.997828E-001 8.000000E-002 2.529841E-005 2.822848E-006 8.867003E-010 0.000000E+000 2.115881E-004 7.037638E-010 5.546679E-020 6.424560E-015 0.000000E+000 0.000000E+000 2.478812E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.256027E-012
+ 2.734339E+001 1.190603E+008 7.452442E+001 1.884777E+001 4.236338E-003 3.922453E-003 2.102690E-004 9.997841E-001 8.000000E-002 2.529857E-005 2.830358E-006 8.906108E-010 0.000000E+000 2.102685E-004 5.435595E-010 5.540591E-020 5.995520E-015 0.000000E+000 0.000000E+000 2.850692E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.178497E-012
+ 2.568486E+001 1.309664E+008 7.000409E+001 1.678121E+001 3.511277E-003 3.251114E-003 2.090005E-004 9.997853E-001 8.000000E-002 2.529870E-005 2.836422E-006 8.932981E-010 0.000000E+000 2.090001E-004 4.079754E-010 5.534829E-020 5.584660E-015 0.000000E+000 0.000000E+000 3.301291E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.116866E-012
+ 2.411109E+001 1.440630E+008 6.571478E+001 1.491720E+001 2.904584E-003 2.689374E-003 2.077532E-004 9.997866E-001 8.000000E-002 2.529881E-005 2.841425E-006 8.951240E-010 0.000000E+000 2.077529E-004 2.944540E-010 5.529250E-020 5.173227E-015 0.000000E+000 0.000000E+000 3.866340E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.069046E-012
+ 2.262709E+001 1.584693E+008 6.167012E+001 1.324807E+001 2.400597E-003 2.222729E-003 2.065333E-004 9.997878E-001 8.000000E-002 2.529890E-005 2.845519E-006 8.963068E-010 0.000000E+000 2.065331E-004 2.036036E-010 5.523878E-020 4.754201E-015 0.000000E+000 0.000000E+000 4.581304E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.035351E-012
+ 2.122592E+001 1.743162E+008 5.785125E+001 1.175282E+001 1.981678E-003 1.834848E-003 2.053381E-004 9.997890E-001 8.000000E-002 2.529897E-005 2.848865E-006 8.970395E-010 0.000000E+000 2.053379E-004 1.339654E-010 5.518699E-020 4.322880E-015 0.000000E+000 0.000000E+000 5.501588E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.016136E-012
+ 1.995168E+001 1.917478E+008 5.437831E+001 1.046252E+001 1.645780E-003 1.523839E-003 2.042100E-004 9.997901E-001 8.000000E-002 2.529902E-005 2.851499E-006 8.974576E-010 0.000000E+000 2.042099E-004 8.486382E-011 5.513888E-020 3.894012E-015 0.000000E+000 0.000000E+000 6.654599E-014 0.000000E+000 0.000000E+000 0.000000E+000 0.000000E+000 1.012244E-012
diff --git a/examples/Cooling/CoolingWithPrimordialElements/getICs.sh b/examples/Cooling/CoolingWithPrimordialElements/getICs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1d641db93bce61580301b14c634552df6f368671
--- /dev/null
+++ b/examples/Cooling/CoolingWithPrimordialElements/getICs.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/homogeneousCube_32.hdf5
diff --git a/examples/Cooling/CoolingWithPrimordialElements/getPrimordialAbundances.py b/examples/Cooling/CoolingWithPrimordialElements/getPrimordialAbundances.py
new file mode 100755
index 0000000000000000000000000000000000000000..278dd20496648eb7fdc7946fda5bb1ca1fd3c980
--- /dev/null
+++ b/examples/Cooling/CoolingWithPrimordialElements/getPrimordialAbundances.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+"""
+This script is an example of how to compute the
+fractional abundances of different elements with
+respect to Hydrogen.
+
+For comparison, see
+for example Dalgarno 2005
+"""
+
+# some parameters (Planck 2018)
+Omega0 = 0.315
+Omega_b = 0.049
+h0 = 0.674
+T0 = 2.73
+fH = 0.76
+z0 = 300
+
+z = 77
+
+# Temperature
+T = T0 / (1 + 200) * (1 + z) ** 2 # Anninos & Norman 1996 eq.11
+
+# all abundances per unit of nH
+nHII = 1.2e-5 * Omega0 ** 0.5 / (h0 * Omega_b) # Anninos & Norman 1996 eq. 9
+
+nHeI = (1 - fH) / fH / 4
+nHeII = 0 # assume neutral He
+nHeIII = 0 # assume neutral He
+
+nHM = 2e-11 * (1 + z) ** (1.76) * nHII # Anninos & Norman 1996 eq. 12
+
+nH2I = (
+ 2e-20 * fH * Omega0 ** (3 / 2.0) / (h0 * Omega_b) * (1 + z0) ** (5.1)
+) # Anninos & Norman 1996 eq. 15
+nH2II = 1e-17 * (1 + z) ** (3.6) * nHII # Anninos & Norman 1996 eq. 13
+
+nDI = 4e-5 # Bromm 20002 from Galli & Palla 1998
+nDII = 1e-8 # Bromm 20002
+
+nHDI = 1e-3 * nH2I # Bromm 20002
+
+
+print("T : %g K" % T)
+
+print("initial_nHII_to_nH_ratio : %g" % nHII)
+
+print("initial_nHeI_to_nH_ratio : %g" % nHeI)
+print("initial_nHeII_to_nH_ratio : %g" % nHeII)
+print("initial_nHeIII_to_nH_ratio : %g" % nHeIII)
+
+print("initial_nDI_to_nH_ratio : %g" % nDI)
+print("initial_nDII_to_nH_ratio : %g" % nDII)
+
+print("initial_nHM_to_nH_ratio : %g" % nHM)
+
+print("initial_nH2I_to_nH_ratio : %g" % nH2I)
+print("initial_nH2II_to_nH_ratio : %g" % nH2II)
+
+
+print("initial_nHDI_to_nH_ratio : %g" % nHDI)
diff --git a/examples/Cooling/CoolingWithPrimordialElements/local.mplstyle b/examples/Cooling/CoolingWithPrimordialElements/local.mplstyle
new file mode 100644
index 0000000000000000000000000000000000000000..f0a096801d2065ef70102d0f6c9256b0bb057f27
--- /dev/null
+++ b/examples/Cooling/CoolingWithPrimordialElements/local.mplstyle
@@ -0,0 +1,28 @@
+# Line Properties
+lines.linewidth: 2
+
+# Font options
+font.size: 8
+font.family: STIXGeneral
+mathtext.fontset: stix
+
+# LaTeX options
+text.usetex: False
+
+# Legend options
+#legend.frameon: False
+#legend.fontsize: 8
+
+# Figure options for publications
+figure.dpi: 300
+figure.figsize: 3.321, 3.0 # Correct width for MNRAS
+
+# Histogram options
+hist.bins: auto
+
+# Ticks inside plots; more space devoted to plot.
+xtick.direction: in
+ytick.direction: in
+# Always plot ticks on top of data
+axes.axisbelow: False
+
diff --git a/examples/Cooling/CoolingWithPrimordialElements/output_list.txt b/examples/Cooling/CoolingWithPrimordialElements/output_list.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47d7c037b0d3d86dcc0217a5ed48cf6a4282c21a
--- /dev/null
+++ b/examples/Cooling/CoolingWithPrimordialElements/output_list.txt
@@ -0,0 +1,28 @@
+# Redshift
+77
+70
+60
+50
+40
+30
+20
+19
+18
+17
+16
+15
+14
+13
+12
+11
+10
+9
+8
+7
+6
+5
+4
+3
+2
+1
+0
diff --git a/examples/Cooling/CoolingWithPrimordialElements/plotAbundances.py b/examples/Cooling/CoolingWithPrimordialElements/plotAbundances.py
new file mode 100755
index 0000000000000000000000000000000000000000..f920172e9f7bd21a207be39f7b632ae9e73fdad1
--- /dev/null
+++ b/examples/Cooling/CoolingWithPrimordialElements/plotAbundances.py
@@ -0,0 +1,185 @@
+#!/usr/bin/env python3
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2023 Yves Revaz (yves.revaz@epfl.ch)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published
+# by the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+##############################################################################
+
+import matplotlib.pyplot as plt
+
+plt.style.use("local.mplstyle")
+
+import numpy as np
+from glob import glob
+import h5py
+import sys
+
+filenames = sys.argv[1:]
+
+n = len(filenames)
+
+
+rs = np.zeros(n)
+nHIs = np.zeros(n)
+nHIIs = np.zeros(n)
+nHeIs = np.zeros(n)
+nHeIIs = np.zeros(n)
+nHeIIIs = np.zeros(n)
+nHMs = np.zeros(n)
+nH2Is = np.zeros(n)
+nH2IIs = np.zeros(n)
+nDIs = np.zeros(n)
+nDIIs = np.zeros(n)
+nHDIs = np.zeros(n)
+
+
+for i, filename in enumerate(filenames):
+
+ with h5py.File(filename, "r") as f:
+
+ XHI = f["PartType0/HI"][:]
+ XHII = f["PartType0/HII"][:]
+ XHeI = f["PartType0/HeI"][:]
+ XHeII = f["PartType0/HeII"][:]
+ XHeIII = f["PartType0/HeIII"][:]
+ XHM = f["PartType0/HM"][:]
+ XH2I = f["PartType0/H2I"][:]
+ XH2II = f["PartType0/H2II"][:]
+ XDI = f["PartType0/DI"][:]
+ XDII = f["PartType0/DII"][:]
+ XHDI = f["PartType0/HDI"][:]
+
+ redshift = f["Header"].attrs["Redshift"][0]
+ rs[i] = redshift
+
+ # compute hydrogen mass fraction
+ XH = (
+ XHI.mean()
+ + XHII.mean()
+ + XHM.mean()
+ + XH2I.mean()
+ + XH2II.mean()
+ + XDI.mean()
+ + XDII.mean()
+ + XHDI.mean()
+ )
+
+ # make it equal to the hydrogen number density (do not consider density on purpose)
+ nH = XH
+
+ # all abundances per unit of nH
+
+ nHI = XHI / nH
+ nHII = XHII / nH
+ nHeI = XHeI / nH / 4
+ nHeII = XHeII / nH / 4
+ nHeIII = XHeIII / nH / 4
+ nHM = XHM / nH
+ nH2I = XH2I / nH / 2
+ nH2II = XH2II / nH / 2
+ nDI = XDI / nH / 2
+ nDII = XDII / nH / 2
+ nHDI = XHDI / nH / 3
+
+ nHIs[i] = nHI.mean()
+ nHIIs[i] = nHII.mean()
+ nHeIs[i] = nHeI.mean()
+ nHeIIs[i] = nHeII.mean()
+ nHeIIIs[i] = nHeIII.mean()
+ nHMs[i] = nHM.mean()
+ nH2Is[i] = nH2I.mean()
+ nH2IIs[i] = nH2II.mean()
+ nDIs[i] = nDI.mean()
+ nDIIs[i] = nDII.mean()
+ nHDIs[i] = nHDI.mean()
+
+
+# data from Faure, A., Hily-Blant, Pineau des Forêts, Flower 2024
+# The last lines have been removed on purpose. Their predictions
+# are not reliable below z=20.
+# Note: the "Redshift" field = z+1
+
+with open("faure2024.dat", "r") as f:
+ f.readline()
+ f.readline()
+ header = str.split(f.readline())
+ lines = f.readlines()
+ data = np.array(list(map(str.split, lines)), float)
+ dic = {x: i for i, x in enumerate(header)}
+
+
+##########################################
+# plot
+##########################################
+
+plt.figure()
+plt.subplots_adjust(left=0.17, bottom=0.12, right=0.97, top=0.97)
+
+ax = plt.gca()
+
+rs = rs + 1
+
+pHI = ax.plot(rs, nHIs, ms=2, lw=1, label="HI")
+pHII = ax.plot(rs, nHIIs, ms=2, lw=1, label="HII")
+pHeI = ax.plot(rs, nHeIs, ms=2, lw=1, label="HeI")
+pHeII = ax.plot(rs, nHeIIs, ms=2, lw=1, label="HeII")
+pHeIII = ax.plot(rs, nHeIIIs, ms=2, lw=1, label="HeIII")
+pHM = ax.plot(rs, nHMs, ms=2, lw=1, label="HM")
+pH2I = ax.plot(rs, nH2Is, ms=2, lw=1, label="H2I")
+pH2II = ax.plot(rs, nH2IIs, ms=2, lw=1, label="H2II")
+pDI = ax.plot(rs, nDIs, ms=2, lw=1, label="DI")
+pDII = ax.plot(rs, nDIIs, ms=2, lw=1, label="DII")
+pHDI = ax.plot(rs, nHDIs, ms=2, lw=1, label="HDI")
+
+
+# add data
+ax.plot(data[:, dic["Redshift"]], data[:, dic["H"]], "--", color=pHI[0].get_color())
+ax.plot(
+ data[:, dic["Redshift"]], data[:, dic["H+"]], "--", color=pHII[0].get_color()
+)
+ax.plot(
+ data[:, dic["Redshift"]], data[:, dic["He"]], "--", color=pHeI[0].get_color()
+)
+ax.plot(
+ data[:, dic["Redshift"]], data[:, dic["He+"]], "--", color=pHeII[0].get_color()
+)
+ax.plot(
+ data[:, dic["Redshift"]], data[:, dic["H-"]], "--", color=pHM[0].get_color()
+)
+ax.plot(
+ data[:, dic["Redshift"]], data[:, dic["H2"]], "--", color=pH2I[0].get_color()
+)
+ax.plot(
+ data[:, dic["Redshift"]], data[:, dic["H2+"]], "--", color=pH2II[0].get_color()
+)
+ax.plot(data[:, dic["Redshift"]], data[:, dic["D"]], "--", color=pDI[0].get_color())
+ax.plot(
+ data[:, dic["Redshift"]], data[:, dic["D+"]], "--", color=pDII[0].get_color()
+)
+ax.plot(
+ data[:, dic["Redshift"]], data[:, dic["HD"]], "--", color=pHDI[0].get_color()
+)
+
+
+ax.set_xlabel(r"$\rm{1+z}$")
+ax.set_xlim(100, 0.9)
+ax.set_ylabel(r"$\rm{Fractional abundances}$")
+ax.set_ylim(1e-21, 2)
+
+ax.loglog()
+ax.legend(loc="lower right")
+
+plt.show()
diff --git a/examples/Cooling/CoolingWithPrimordialElements/run.sh b/examples/Cooling/CoolingWithPrimordialElements/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f3d5ffa09a2aec289600f5dad668709b98d21a1d
--- /dev/null
+++ b/examples/Cooling/CoolingWithPrimordialElements/run.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e homogeneousCube_32.hdf5 ]
+then
+ echo "Fetching initial conditions..."
+ ./getICS.sh
+fi
+
+
+# Get the Grackle cooling table
+if [ ! -e CloudyData_UVB=HM2012.h5 ]
+then
+ echo "Fetching the Cloudy tables required by Grackle..."
+ ../getGrackleCoolingTable.sh
+fi
+
+
+# Create output directory
+rm -rf snap
+mkdir snap
+
+# Run SWIFT
+../../../swift --hydro --cooling --cosmology --threads=14 CoolingWithPrimordialElements.yml
+
+# Check energy conservation and cooling rate
+python3 plotAbundances.py snap/snapshot*.hdf5
+
diff --git a/examples/Cooling/getGrackleCoolingTable.sh b/examples/Cooling/getGrackleCoolingTable.sh
index 5f702aef17df41bfb2f56f1cb474fe3762b1b232..1d75bc6ed2eadb1f83c517b7d5a272bb5b5504a1 100755
--- a/examples/Cooling/getGrackleCoolingTable.sh
+++ b/examples/Cooling/getGrackleCoolingTable.sh
@@ -1,3 +1,4 @@
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/CloudyData_UVB=HM2012.h5
-wget https://obswww.unige.ch/~lhausamm/links/CloudyData_UVB=HM2012_shielded.h5
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/CloudyData_UVB=HM2012_shielded.h5
+
diff --git a/examples/parameter_example.yml b/examples/parameter_example.yml
index 5c7869537eb4c60e0a9aa2185ea6c9438aa8c489..dc103dab65a4b8bd24ff9d09e92ca94e285d1f89 100644
--- a/examples/parameter_example.yml
+++ b/examples/parameter_example.yml
@@ -555,6 +555,18 @@ GrackleCooling:
H2_on_dust: 0 # Flag to enable H2 formation on dust grains
local_dust_to_gas_ratio : -1 # The ratio of total dust mass to gas mass in the local Universe (-1 to use the Grackle default value).
cmb_temperature_floor : 1 # Enable/disable an effective CMB temperature floor
+ initial_nHII_to_nH_ratio: -1 # initial nHII to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHeI_to_nH_ratio: -1 # initial nHeI to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHeII_to_nH_ratio: -1 # initial nHeII to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHeIII_to_nH_ratio: -1 # initial nHeIII to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nDI_to_nH_ratio: -1 # initial nDI to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nDII_to_nH_ratio: -1 # initial nDII to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHM_to_nH_ratio: -1 # initial nHM to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nH2I_to_nH_ratio: -1 # initial nH2I to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nH2II_to_nH_ratio: -1 # initial nH2II to nH ratio (number density ratio). Value is ignored if set to -1.
+ initial_nHDI_to_nH_ratio: -1 # initial nHDI to nH ratio (number density ratio). Value is ignored if set to -1.
+
+
diff --git a/src/cooling/grackle/cooling.c b/src/cooling/grackle/cooling.c
index 89784988f6af899965f50fa3eb7ef92a094f6d93..dd75c99b82b89fa96456159c103b14f42ccf4bcf 100644
--- a/src/cooling/grackle/cooling.c
+++ b/src/cooling/grackle/cooling.c
@@ -207,32 +207,157 @@ void cooling_first_init_part(const struct phys_const* phys_const,
#if COOLING_GRACKLE_MODE >= 1
gr_float zero = 1.e-20;
- /* NOTE: at this stage, we assume neutral gas
- * a better determination will be done in cooling_post_init_part */
+ /* NOTE: if the ratio with respect to hydrogen is given, use it. Instead,
+ * we assume neutral gas.
+ * A better determination of the abundances can be done in
+ * cooling_post_init_part */
+
+ /* Compute nH (formally divided by the gas density and assuming the proton
+ * mass to be one) */
+ double nH = grackle_data->HydrogenFractionByMass;
+
+ /* Compute nHe (formally divided by the gas density and assuming the proton
+ * mass to be one) */
+ double nHe = (1.f - grackle_data->HydrogenFractionByMass) / 4.f;
+
+ /* Electron density */
+ double ne = zero;
+
+ /* Sum of mass fraction (to test its consistency) */
+ double Xtot = 0.f;
/* primordial chemistry >= 1 */
- /* assume neutral gas */
- xp->cooling_data.HI_frac = grackle_data->HydrogenFractionByMass;
- xp->cooling_data.HII_frac = zero;
- xp->cooling_data.HeI_frac = 1. - grackle_data->HydrogenFractionByMass;
- xp->cooling_data.HeII_frac = zero;
- xp->cooling_data.HeIII_frac = zero;
- xp->cooling_data.e_frac = zero;
+
+ /* Hydrogen I */
+ if (cooling->initial_nHII_to_nH_ratio >= 0.f)
+ xp->cooling_data.HI_frac = nH * (1.f - cooling->initial_nHII_to_nH_ratio);
+ else
+ xp->cooling_data.HI_frac = nH;
+
+ Xtot += xp->cooling_data.HI_frac;
+
+ /* Hydrogen II */
+ if (cooling->initial_nHII_to_nH_ratio >= 0.f) {
+ double nHII = nH * cooling->initial_nHII_to_nH_ratio;
+ xp->cooling_data.HII_frac = nHII;
+ ne += nHII;
+ } else
+ xp->cooling_data.HII_frac = zero;
+
+ Xtot += xp->cooling_data.HII_frac;
+
+ /* Helium I */
+ if (cooling->initial_nHeI_to_nH_ratio >= 0.f) {
+ double nHeI = nH * cooling->initial_nHeI_to_nH_ratio;
+ xp->cooling_data.HeI_frac = nHeI * 4.f;
+ } else
+ xp->cooling_data.HeI_frac = nHe * 4.f;
+
+ Xtot += xp->cooling_data.HeI_frac;
+
+ /* Helium II */
+ if (cooling->initial_nHeII_to_nH_ratio >= 0.f) {
+ double nHeII = nH * cooling->initial_nHeII_to_nH_ratio;
+ xp->cooling_data.HeII_frac = nHeII * 4.f;
+ ne += nHeII;
+ } else
+ xp->cooling_data.HeII_frac = zero;
+
+ Xtot += xp->cooling_data.HeII_frac;
+
+ /* Helium III */
+ if (cooling->initial_nHeIII_to_nH_ratio >= 0.f) {
+ double nHeIII = nH * cooling->initial_nHeIII_to_nH_ratio;
+ xp->cooling_data.HeIII_frac = nHeIII * 4.f;
+ ne += 2.f * nHeIII;
+ } else
+ xp->cooling_data.HeIII_frac = zero;
+
+ Xtot += xp->cooling_data.HeIII_frac;
+
+ /* electron mass fraction (multiplied by the proton mass (Grackle convention)
+ */
+ xp->cooling_data.e_frac = ne;
+
#endif // MODE >= 1
#if COOLING_GRACKLE_MODE >= 2
/* primordial chemistry >= 2 */
- xp->cooling_data.HM_frac = zero;
- xp->cooling_data.H2I_frac = zero;
- xp->cooling_data.H2II_frac = zero;
+
+ /* Hydrogen- */
+ if (cooling->initial_nHM_to_nH_ratio >= 0.f) {
+ double nHM = nH * cooling->initial_nHM_to_nH_ratio;
+ xp->cooling_data.HM_frac = nHM;
+ ne -= nHM;
+ } else
+ xp->cooling_data.HM_frac = zero;
+
+ Xtot += xp->cooling_data.HM_frac;
+
+ /* H2I */
+ if (cooling->initial_nH2I_to_nH_ratio >= 0.f) {
+ double nH2I = nH * cooling->initial_nH2I_to_nH_ratio;
+ xp->cooling_data.H2I_frac = nH2I * 2.f;
+ } else
+ xp->cooling_data.H2I_frac = zero;
+
+ Xtot += xp->cooling_data.H2I_frac;
+
+ /* H2II */
+ if (cooling->initial_nH2II_to_nH_ratio >= 0.f) {
+ double nH2II = nH * cooling->initial_nH2II_to_nH_ratio;
+ xp->cooling_data.H2II_frac = nH2II * 2.f;
+ ne += nH2II;
+ } else
+ xp->cooling_data.H2II_frac = zero;
+
+ Xtot += xp->cooling_data.H2II_frac;
+
+ /* electron mass fraction (multiplied by the proton mass (Grackle convention)
+ */
+ xp->cooling_data.e_frac = ne;
+
#endif // MODE >= 2
#if COOLING_GRACKLE_MODE >= 3
/* primordial chemistry >= 3 */
- xp->cooling_data.DI_frac = grackle_data->DeuteriumToHydrogenRatio *
- grackle_data->HydrogenFractionByMass;
- xp->cooling_data.DII_frac = zero;
- xp->cooling_data.HDI_frac = zero;
+
+ /* Deuterium I */
+ if (cooling->initial_nDI_to_nH_ratio >= 0.f) {
+ double nDI = nH * cooling->initial_nDI_to_nH_ratio;
+ xp->cooling_data.DI_frac = nDI * 2.f;
+ } else
+ xp->cooling_data.DI_frac = grackle_data->DeuteriumToHydrogenRatio *
+ grackle_data->HydrogenFractionByMass;
+
+ Xtot += xp->cooling_data.DI_frac;
+
+ /* Deuterium II */
+ if (cooling->initial_nDII_to_nH_ratio >= 0.f) {
+ double nDII = nH * cooling->initial_nDII_to_nH_ratio;
+ xp->cooling_data.DII_frac = nDII * 2.f;
+ ne += nDII;
+ } else
+ xp->cooling_data.DII_frac = zero;
+
+ Xtot += xp->cooling_data.DII_frac;
+
+ /* HD I */
+ if (cooling->initial_nHDI_to_nH_ratio >= 0.f) {
+ double nHDI = nH * cooling->initial_nHDI_to_nH_ratio;
+ xp->cooling_data.HDI_frac = nHDI * 3.f;
+ } else
+ xp->cooling_data.HDI_frac = zero;
+
+ Xtot += xp->cooling_data.HDI_frac;
+
+ /* electron mass fraction (multiplied by the proton mass (Grackle convention)
+ */
+ xp->cooling_data.e_frac = ne;
+
+ if (fabs(Xtot - 1.0) > 1e-3)
+ error("Got total mass fraction of gas = %.6g", Xtot);
+
#endif // MODE >= 3
}
@@ -311,7 +436,26 @@ void cooling_print_backend(const struct cooling_function_data* cooling) {
cooling->RT_HeII_ionization_rate);
message("grackle_chemistry_data.RT_H2_dissociation_rate = %g",
cooling->RT_H2_dissociation_rate);
-
+ message("cooling.initial_nHII_to_nH_ratio= %g",
+ cooling->initial_nHII_to_nH_ratio);
+ message("cooling.initial_nHeI_to_nH_ratio= %g",
+ cooling->initial_nHeI_to_nH_ratio);
+ message("cooling.initial_nHeII_to_nH_ratio= %g",
+ cooling->initial_nHeII_to_nH_ratio);
+ message("cooling.initial_nHeIII_to_nH_ratio= %g",
+ cooling->initial_nHeIII_to_nH_ratio);
+ message("cooling.initial_nDI_to_nH_ratio= %g",
+ cooling->initial_nDI_to_nH_ratio);
+ message("cooling.initial_nDII_to_nH_ratio= %g",
+ cooling->initial_nDII_to_nH_ratio);
+ message("cooling.initial_nHM_to_nH_ratio= %g",
+ cooling->initial_nHM_to_nH_ratio);
+ message("cooling.initial_nH2I_to_nH_ratio= %g",
+ cooling->initial_nH2I_to_nH_ratio);
+ message("cooling.initial_nH2II_to_nH_ratio= %g",
+ cooling->initial_nH2II_to_nH_ratio);
+ message("cooling.initial_nHDI_to_nH_ratio= %g",
+ cooling->initial_nHDI_to_nH_ratio);
message("Units:");
message("\tComoving = %i", cooling->units.comoving_coordinates);
message("\tLength = %g", cooling->units.length_units);
diff --git a/src/cooling/grackle/cooling_io.h b/src/cooling/grackle/cooling_io.h
index f3fbb93def7100024d0281a5d03a8ba4f66f5b3d..5d48cb18b5524f34321ed2588f23559a0f30deb3 100644
--- a/src/cooling/grackle/cooling_io.h
+++ b/src/cooling/grackle/cooling_io.h
@@ -207,6 +207,36 @@ __attribute__((always_inline)) INLINE static void cooling_read_parameters(
cooling->HydrogenFractionByMass = parser_get_opt_param_double(
parameter_file, "GrackleCooling:HydrogenFractionByMass", 0.76);
+ cooling->initial_nHII_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nHII_to_nH_ratio", -1);
+
+ cooling->initial_nHeI_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nHeI_to_nH_ratio", -1);
+
+ cooling->initial_nHeII_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nHeII_to_nH_ratio", -1);
+
+ cooling->initial_nHeIII_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nHeIII_to_nH_ratio", -1);
+
+ cooling->initial_nDI_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nDI_to_nH_ratio", -1);
+
+ cooling->initial_nDII_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nDII_to_nH_ratio", -1);
+
+ cooling->initial_nHM_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nHM_to_nH_ratio", -1);
+
+ cooling->initial_nH2I_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nH2I_to_nH_ratio", -1);
+
+ cooling->initial_nH2II_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nH2II_to_nH_ratio", -1);
+
+ cooling->initial_nHDI_to_nH_ratio = parser_get_opt_param_double(
+ parameter_file, "GrackleCooling:initial_nHDI_to_nH_ratio", -1);
+
/* Self shielding */
cooling->self_shielding_method = parser_get_opt_param_int(
parameter_file, "GrackleCooling:self_shielding_method", 0);
@@ -216,9 +246,6 @@ __attribute__((always_inline)) INLINE static void cooling_read_parameters(
parameter_file, "GrackleCooling:self_shielding_threshold_atom_per_cm3");
}
- cooling->HydrogenFractionByMass = parser_get_opt_param_double(
- parameter_file, "GrackleCooling:HydrogenFractionByMass", 0.76);
-
/* Initial step convergence */
cooling->max_step = parser_get_opt_param_int(
parameter_file, "GrackleCooling:max_steps", 10000);
diff --git a/src/cooling/grackle/cooling_properties.h b/src/cooling/grackle/cooling_properties.h
index f7d8dc49ca3a7c630c55529794556dbdc0916316..270cf87c9ee0f9efcbf57bccf9ba5fbf00bd5c6f 100644
--- a/src/cooling/grackle/cooling_properties.h
+++ b/src/cooling/grackle/cooling_properties.h
@@ -103,6 +103,36 @@ struct cooling_function_data {
/*! Hydrogen fraction by mass */
float HydrogenFractionByMass;
+ /*! initial nHII to nH ratio (number density ratio) */
+ float initial_nHII_to_nH_ratio;
+
+ /*! initial nHeI to nH ratio (number density ratio) */
+ float initial_nHeI_to_nH_ratio;
+
+ /*! initial nHeII to nH ratio (number density ratio) */
+ float initial_nHeII_to_nH_ratio;
+
+ /*! initial nHeIII to nH ratio (number density ratio) */
+ float initial_nHeIII_to_nH_ratio;
+
+ /*! initial nDI to nH ratio (number density ratio) */
+ float initial_nDI_to_nH_ratio;
+
+ /*! initial nDII to nH ratio (number density ratio) */
+ float initial_nDII_to_nH_ratio;
+
+ /*! initial nHM to nH ratio (number density ratio) */
+ float initial_nHM_to_nH_ratio;
+
+ /*! initial nH2I to nH ratio (number density ratio) */
+ float initial_nH2I_to_nH_ratio;
+
+ /*! initial nH2II to nH ratio (number density ratio) */
+ float initial_nH2II_to_nH_ratio;
+
+ /*! initial nHDI to nH ratio (number density ratio) */
+ float initial_nHDI_to_nH_ratio;
+
/*! Self shielding method (1 -> 3 for grackle's ones, 0 for none and -1 for
* GEAR) */
int self_shielding_method;