From f287417beb9e955a78a7069bf826a73c10c78e74 Mon Sep 17 00:00:00 2001
From: Sylvia Ploeckinger <sylvia.ploeckinger@univie.ac.at>
Date: Fri, 13 Oct 2023 14:23:39 +0200
Subject: [PATCH] Added fiducial files
---
fiducial_files/fof.yml | 8 ++
fiducial_files/isolated_galaxy.yml | 171 +++++++++++++++++++++++++++++
fiducial_files/resubmit.job | 20 ++++
fiducial_files/resubmit.sh | 3 +
fiducial_files/submit.job | 20 ++++
5 files changed, 222 insertions(+)
create mode 100644 fiducial_files/fof.yml
create mode 100644 fiducial_files/isolated_galaxy.yml
create mode 100644 fiducial_files/resubmit.job
create mode 100755 fiducial_files/resubmit.sh
create mode 100644 fiducial_files/submit.job
diff --git a/fiducial_files/fof.yml b/fiducial_files/fof.yml
new file mode 100644
index 0000000..9b9e477
--- /dev/null
+++ b/fiducial_files/fof.yml
@@ -0,0 +1,8 @@
+# Parameters of the Friends-Of-Friends module
+FOF:
+ basename: fof_output # Filename for the FOF outputs.
+ min_group_size: 18 # The minimum no. of particles required for a group.
+ absolute_linking_length: 0.025 # (Optional) Absolute linking length (in internal units).
+ group_id_default: 2147483647 # (Optional) Sets the group ID of particles in groups below the minimum size.
+ group_id_offset: 0 # (Optional) Sets the offset of group ID labelling. Defaults to 1 if unspecified.
+ seed_black_holes_enabled: 0
diff --git a/fiducial_files/isolated_galaxy.yml b/fiducial_files/isolated_galaxy.yml
new file mode 100644
index 0000000..91710a6
--- /dev/null
+++ b/fiducial_files/isolated_galaxy.yml
@@ -0,0 +1,171 @@
+# Define some meta-data about the simulation
+MetaData:
+ run_name: RUNNAME
+
+# Define the system of units to use internally.
+InternalUnitSystem:
+ UnitMass_in_cgs: 1.98848e43 # 10^10 M_sun in grams
+ UnitLength_in_cgs: 3.08567758e21 # 1 kpc in cm
+ UnitVelocity_in_cgs: 1e5 # 1 km/s in cm/s
+ UnitCurrent_in_cgs: 1 # Amperes
+ UnitTemp_in_cgs: 1 # Kelvin
+
+# Parameters for the self-gravity scheme
+Gravity:
+ eta: 0.025 # Constant dimensionless multiplier for time integration.
+ MAC: geometric
+ theta_cr: 0.7 # Opening angle (Multipole acceptance criterion).
+ use_tree_below_softening: 1
+ max_physical_baryon_softening: SOFTENING # Physical softening length (in internal units).
+
+# Parameters governing the time integration (Set dt_min and dt_max to the same value for a fixed time-step run.)
+TimeIntegration:
+ time_begin: 0. # The starting time of the simulation (in internal units).
+ time_end: 1.2276 # The end time of the simulation (in internal units).
+ dt_min: 1e-9 # 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: output # Common part of the name of output files
+ time_first: 0. # Time of the first output if non-cosmological time-integration (in internal units)
+ delta_time: 0.01023 # Time difference between consecutive outputs (in internal units)
+ compression: 4 # Compress the snapshots
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # Time between statistics output
+ time_first: 0 # (Optional) Time of the first stats output if non-cosmological time-integration (in internal units)
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ../../data/INITIALCONDITIONS.hdf5 # The file to read
+ periodic: 0 # Are we running with periodic ICs?
+ stars_smoothing_length: 0.5
+
+# 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).
+ CFL_condition: 0.1 # Courant-Friedrich-Levy condition for time integration.
+ h_min_ratio: HMINRATIO # Minimal smoothing in units of softening.
+ h_max: 10.
+ minimal_temperature: 10.
+
+# Parameters for the stars neighbour search
+Stars:
+ resolution_eta: 1.1642 # Target smoothing length in units of the mean inter-particle separation
+ h_tolerance: 7e-3
+ overwrite_birth_time: 0 # Make sure the stars in the ICs do not do any feedback
+ birth_time: -1. # by setting all of their birth times to -1
+ timestep_age_threshold_Myr: 10. # Age at which stars switch from young to old (in Mega-years).
+ max_timestep_young_Myr: 0.1 # Maximal time-step length of young stars (in Mega-years).
+ max_timestep_old_Myr: 1.0 # Maximal time-step length of old stars (in Mega-years).
+ luminosity_filename: ../../data/photometry
+
+# COLIBRE cooling parameters
+COLIBRECooling:
+ dir_name: ../../data/UV_dust1_CR1_G1_shield1.hdf5 # Location of the Ploeckinger+20 cooling tables
+ H_reion_z: 7.5 # Redshift of Hydrogen re-ionization (Planck 2018)
+ H_reion_eV_p_H: 2.0
+ 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
+ delta_logTEOS_subgrid_properties: 0.3 # delta log T above the EOS below which the subgrid properties use Teq assumption
+ rapid_cooling_threshold: 0.333333 # Switch to rapid cooling regime for dt / t_cool above this threshold.
+
+EAGLEChemistry:
+ init_abundance_metal: 0.0133714 # Inital fraction of particle mass in *all* metals
+ init_abundance_Hydrogen: 0.73738788833 # Inital fraction of particle mass in Hydrogen
+ init_abundance_Helium: 0.24924186942 # Inital fraction of particle mass in Helium
+ init_abundance_Carbon: 0.0023647215 # Inital fraction of particle mass in Carbon
+ init_abundance_Nitrogen: 0.0006928991 # Inital fraction of particle mass in Nitrogen
+ init_abundance_Oxygen: 0.00573271036 # Inital fraction of particle mass in Oxygen
+ init_abundance_Neon: 0.00125649278 # Inital fraction of particle mass in Neon
+ init_abundance_Magnesium: 0.00070797838 # Inital fraction of particle mass in Magnesium
+ init_abundance_Silicon: 0.00066495154 # Inital fraction of particle mass in Silicon
+ init_abundance_Iron: 0.00129199252 # Inital fraction of particle mass in Iron
+
+# Hernquist potential parameters
+HernquistPotential:
+ useabspos: 0 # 0 -> positions based on centre, 1 -> absolute positions
+ position: [0.,0.,0.] # Location of centre of isothermal potential with respect to centre of the box (if 0) otherwise absolute (if 1) (internal units)
+ idealizeddisk: 1 # Run with an idealized galaxy disk
+ M200: 137.0 # M200 of the galaxy disk
+ h: 0.704 # reduced Hubble constant (value does not specify the used units!)
+ concentration: 9.0 # concentration of the Halo
+ diskfraction: 0.040 # Disk mass fraction
+ bulgefraction: 0.0 # Bulge mass fraction
+ timestep_mult: 0.01 # Dimensionless pre-factor for the time-step condition, basically determines the fraction of the orbital time we use to do the time integration
+ epsilon: 0.4 # Softening size (internal units)
+
+# EAGLE star formation parameters
+EAGLEStarFormation:
+ SF_threshold: Subgrid # Zdep (Schaye 2004) or Subgrid
+ SF_model: SchmidtLaw # PressureLaw (Schaye et al. 2008) or SchmidtLaw
+ star_formation_efficiency: SFEFFICIENCY
+ min_over_density: 100.0 # The over-density above which star-formation is allowed.
+ threshold_temperature1_K: 1000. # When using subgrid-based SF threshold, subgrid temperature below which gas is star-forming.
+ threshold_temperature2_K: 1000. # When using subgrid-based SF threshold, subgrid temperature below which gas is star-forming if also above the density limit.
+ threshold_number_density_H_p_cm3: 0.1 # When using subgrid-based SF threshold, subgrid number density above which gas is star-forming if also below the second temperature limit.
+
+# Parameters for the EAGLE "equation of state"
+EAGLEEntropyFloor:
+ Jeans_density_threshold_H_p_cm3: EOSDENSITY # Physical density above which the EAGLE Jeans limiter entropy floor kicks in expressed in Hydrogen atoms per cm^3.
+ Jeans_over_density_threshold: 10. # Overdensity above which the EAGLE Jeans limiter entropy floor can kick in.
+ Jeans_temperature_norm_K: EOSTEMPERATURE # Temperature of the EAGLE Jeans limiter entropy floor at the density threshold expressed in Kelvin.
+ Jeans_gamma_effective: EOSSLOPE # Slope the of the EAGLE Jeans limiter entropy floor
+ Cool_density_threshold_H_p_cm3: 1e-5 # Physical density above which the EAGLE Cool limiter entropy floor kicks in expressed in Hydrogen atoms per cm^3.
+ Cool_over_density_threshold: 10. # Overdensity above which the EAGLE Cool limiter entropy floor can kick in.
+ Cool_temperature_norm_K: 10. # Temperature of the EAGLE Cool limiter entropy floor at the density threshold expressed in Kelvin. (NOTE: This is below the min T and hence this floor does nothing)
+ Cool_gamma_effective: 1. # Slope the of the EAGLE Cool limiter entropy floor
+
+# EAGLE feedback model with constant feedback energy fraction
+EAGLEFeedback:
+ use_SNII_feedback: 1 # Global switch for SNII thermal (stochastic) feedback.
+ use_SNIa_feedback: 1 # Global switch for SNIa thermal (continuous) feedback.
+ use_AGB_enrichment: 1 # Global switch for enrichement from AGB stars.
+ use_SNII_enrichment: 1 # Global switch for enrichement from SNII stars.
+ use_SNIa_enrichment: 1 # Global switch for enrichement from SNIa stars.
+ filename: ../../data/yieldtables/ # Path to the directory containing the EAGLE yield tables.
+ IMF_min_mass_Msun: 0.1 # Minimal stellar mass considered for the Chabrier IMF in solar masses.
+ IMF_max_mass_Msun: 100.0 # Maximal stellar mass considered for the Chabrier IMF in solar masses.
+ SNII_min_mass_Msun: 8.0 # Minimal mass considered for SNII stars in solar masses.
+ SNII_max_mass_Msun: 100.0 # Maximal mass considered for SNII stars in solar masses.
+ SNII_feedback_model: MinimumDistance # Feedback modes: Random, Isotropic, MinimumDistance, MinimumDensity
+ SNII_sampled_delay: 1 # Sample the SNII lifetimes to do feedback.
+ SNII_delta_T_K: 3.16228e7 # Change in temperature to apply to the gas particle in a SNII thermal feedback event in Kelvin.
+ SNII_energy_erg: 1.0e51 # Energy of one SNII explosion in ergs.
+ SNII_energy_fraction_function: EAGLE # Type of functional form to use for scaling the energy fraction with density and metallicity ('EAGLE', 'Separable', or 'Independent').
+ SNII_energy_fraction_min: 1.0 # Minimal fraction of energy applied in a SNII feedback event.
+ SNII_energy_fraction_max: 1.0 # Maximal fraction of energy applied in a SNII feedback event.
+ SNII_energy_fraction_Z_0: 0.0012663729 # Pivot point for the metallicity dependance of the SNII energy fraction (metal mass fraction).
+ SNII_energy_fraction_n_0_H_p_cm3: 1.4588 # Pivot point for the birth density dependance of the SNII energy fraction in cm^-3.
+ SNII_energy_fraction_n_Z: 0.8686 # Power-law for the metallicity dependance of the SNII energy fraction.
+ SNII_energy_fraction_n_n: 0.8686 # Power-law for the birth density dependance of the SNII energy fraction.
+ SNII_energy_fraction_use_birth_density: 0 # Are we using the density at birth to compute f_E or at feedback time?
+ SNII_energy_fraction_use_birth_metallicity: 0 # Are we using the metallicity at birth to compuote f_E or at feedback time?
+ SNIa_DTD: Exponential # Functional form of the SNIa delay time distribution.
+ SNIa_DTD_delay_Gyr: 0.04 # Stellar age after which SNIa start in Gyr (40 Myr corresponds to stars ~ 8 Msun).
+ SNIa_DTD_exp_timescale_Gyr: 2.0 # Time-scale of the exponential decay of the SNIa rates in Gyr.
+ SNIa_DTD_exp_norm_p_Msun: 0.002 # Normalisation of the SNIa rates in inverse solar masses.
+ SNIa_energy_erg: 1.0e51 # Energy of one SNIa explosion in ergs.
+ AGB_ejecta_velocity_km_p_s: 10.0 # Velocity of the AGB ejectas in km/s.
+ stellar_evolution_age_cut_Gyr: 0.1 # Age in Gyr above which the enrichment is downsampled.
+ stellar_evolution_sampling_rate: 10 # Number of time-steps in-between two enrichment events for a star above the age threshold.
+ SNII_yield_factor_Hydrogen: 1.0 # (Optional) Correction factor to apply to the Hydrogen yield from the SNII channel.
+ SNII_yield_factor_Helium: 1.0 # (Optional) Correction factor to apply to the Helium yield from the SNII channel.
+ SNII_yield_factor_Carbon: 0.5 # (Optional) Correction factor to apply to the Carbon yield from the SNII channel.
+ SNII_yield_factor_Nitrogen: 1.0 # (Optional) Correction factor to apply to the Nitrogen yield from the SNII channel.
+ SNII_yield_factor_Oxygen: 1.0 # (Optional) Correction factor to apply to the Oxygen yield from the SNII channel.
+ SNII_yield_factor_Neon: 1.0 # (Optional) Correction factor to apply to the Neon yield from the SNII channel.
+ SNII_yield_factor_Magnesium: 2.0 # (Optional) Correction factor to apply to the Magnesium yield from the SNII channel.
+ SNII_yield_factor_Silicon: 1.0 # (Optional) Correction factor to apply to the Silicon yield from the SNII channel.
+ SNII_yield_factor_Iron: 0.5 # (Optional) Correction factor to apply to the Iron yield from the SNII channel.
+
+Restarts:
+ delta_hours: 2.0
+ max_run_time: 71.5
+ onexit: 1
+ resubmit_on_exit: 1
+ resubmit_command: ./resubmit.sh
+
diff --git a/fiducial_files/resubmit.job b/fiducial_files/resubmit.job
new file mode 100644
index 0000000..c4de052
--- /dev/null
+++ b/fiducial_files/resubmit.job
@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH -J RUNNAME
+#SBATCH -o output-%j.out
+#SBATCH -e error-%j.err
+#SBATCH -t 4320
+#SBATCH -N 1
+
+module purge
+module load hdf5
+module load fftw
+module load metis
+module load gsl
+module load python
+module load intel
+
+export LD_LIBRARY_PATH=$LIBRARY_PATH
+
+./swift --threads=24 --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --feedback --limiter --sync --restart isolated_galaxy.yml
+
+
diff --git a/fiducial_files/resubmit.sh b/fiducial_files/resubmit.sh
new file mode 100755
index 0000000..122426a
--- /dev/null
+++ b/fiducial_files/resubmit.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+sbatch resubmit.job
diff --git a/fiducial_files/submit.job b/fiducial_files/submit.job
new file mode 100644
index 0000000..bf28cc5
--- /dev/null
+++ b/fiducial_files/submit.job
@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH -J RUNNAME
+#SBATCH -o output-%j.out
+#SBATCH -e error-%j.err
+#SBATCH --time=TIMEINHOURS:00:00
+#SBATCH -N 1
+
+module purge
+module load hdf5
+module load fftw
+module load metis
+module load gsl
+module load python
+module load intel
+
+export LD_LIBRARY_PATH=$LIBRARY_PATH
+
+./swift --threads=24 --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --feedback --limiter --sync isolated_galaxy.yml
+
+
--
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