diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..acae9ebd05d4c57c7135f61e4157a55f3b645ab3
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+*.hdf5
+M*/
+data/__pycache__/
+data/photometry/
+fiducial_files/run.sh
+fiducial_files/swift
diff --git a/data/create_ics_from_snapshot.py b/data/create_ics_from_snapshot.py
new file mode 100644
index 0000000000000000000000000000000000000000..1144d71283a2e57271a4f3b46a754b962e553dc5
--- /dev/null
+++ b/data/create_ics_from_snapshot.py
@@ -0,0 +1,43 @@
+
+import h5py
+import sys
+
+def ics_from_snapshot(inputfile, outputfile):
+ f_input = h5py.File(inputfile, 'r')
+ f_output = h5py.File(outputfile, 'w')
+
+ f_input.copy('Header', f_output)
+ f_input.copy('Units', f_output)
+
+ g_PT0 = f_output.create_group('PartType0')
+ g_PT4 = f_output.create_group('PartType4')
+
+ f_input.copy('PartType0/Coordinates', g_PT0)
+ f_input.copy('PartType0/InternalEnergies', g_PT0) # InternalEnergy
+ f_input.copy('PartType0/Masses', g_PT0)
+ f_input.copy('PartType0/ParticleIDs', g_PT0)
+ f_input.copy('PartType0/SmoothingLengths', g_PT0) # SmoothingLength
+ f_input.copy('PartType0/Velocities', g_PT0)
+
+ f_input.copy('PartType4/Coordinates', g_PT4)
+ f_input.copy('PartType4/Masses', g_PT4)
+ f_input.copy('PartType4/ParticleIDs', g_PT4)
+ f_input.copy('PartType4/BirthTimes', g_PT4) # StellarFormationTime
+ f_input.copy('PartType4/Velocities', g_PT4)
+
+ f_output['PartType4/StellarFormationTime'] = f_output['PartType4/BirthTimes']
+ del f_output['PartType4/BirthTimes']
+
+ f_output['PartType0/SmoothingLength'] = f_output['PartType0/SmoothingLengths']
+ del f_output['PartType0/SmoothingLengths']
+
+ f_output['PartType0/InternalEnergy'] = f_output['PartType0/InternalEnergies']
+ del f_output['PartType0/InternalEnergies']
+
+ grp = f_output.create_group('Info')
+ grp.attrs["Input file"] = inputfile
+
+ f_input.close()
+ f_output.close()
+
+ return
diff --git a/data/getEaglePhotometryTable.sh b/data/getEaglePhotometryTable.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ee9c3b422f19518612416da0913b162fd4a120ff
--- /dev/null
+++ b/data/getEaglePhotometryTable.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/YieldTables/EAGLE/photometry.tar.gz
+tar -xf photometry.tar.gz
diff --git a/data/getICs.sh b/data/getICs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..389953f0fa576044507311fd8d23f65061365dff
--- /dev/null
+++ b/data/getICs.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# from Swift IsolatedGalaxy_feedback example
+
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/IsolatedGalaxies_COLIBRE/M4_disk.hdf5
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/IsolatedGalaxies_COLIBRE/M5_disk.hdf5
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/IsolatedGalaxies_COLIBRE/M6_disk.hdf5
+
diff --git a/data/getPS20CoolingTables.sh b/data/getPS20CoolingTables.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0945dc565a4c8b1723b21e685b03369e782cd3be
--- /dev/null
+++ b/data/getPS20CoolingTables.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/COLIBRE/UV_dust1_CR1_G1_shield1.hdf5
diff --git a/data/getYieldTable.sh b/data/getYieldTable.sh
new file mode 100755
index 0000000000000000000000000000000000000000..40e24ef34ec47db2b5adde08b8c1a39cd44d6452
--- /dev/null
+++ b/data/getYieldTable.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/YieldTables/EAGLE/yieldtables.tar.gz
+tar -xf yieldtables.tar.gz
+
diff --git a/fiducial_files/isolated_galaxy.yml b/fiducial_files/isolated_galaxy.yml
new file mode 100644
index 0000000000000000000000000000000000000000..91710a6d55bf07a027857640f80895dfefd2cc19
--- /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 0000000000000000000000000000000000000000..28eacbadc7a1c6d02d38644faf886ce927cb4dd2
--- /dev/null
+++ b/fiducial_files/resubmit.job
@@ -0,0 +1,19 @@
+#!/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 hdf5/1.12.2-intel-19.1.3.304-eqsfbup
+module load libtool/2.4.7-intel-2021.5.0-uhp7fp3
+module load fftw/3.3.10-intel-19.1.3.304-kcawvtk
+module load metis/5.1.0-intel-2021.5.0-wijrhuu
+module load gsl/2.7.1-gcc-12.2.0-jgxkcb6
+module load python/3.10.6-intel-2021.5.0-mtvbpzb
+module load intel/19.1.3.304
+
+./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 0000000000000000000000000000000000000000..122426a6e0dbb1179b236f19f60fcd58c35b0217
--- /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 0000000000000000000000000000000000000000..2bf295e739d42742c8f140efe400afcb7639ca2f
--- /dev/null
+++ b/fiducial_files/submit.job
@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -J RUNNAME
+#SBATCH -o output-%j.out
+#SBATCH -e error-%j.err
+#SBATCH --time=TIMEINHOURS:00:00
+#SBATCH --partition=skylake_0096
+#SBATCH --qos=skylake_0096
+#SBATCH -N 1
+
+module purge
+module load hdf5/1.12.2-intel-19.1.3.304-eqsfbup
+module load libtool/2.4.7-intel-2021.5.0-uhp7fp3
+module load fftw/3.3.10-intel-19.1.3.304-kcawvtk
+module load metis/5.1.0-intel-2021.5.0-wijrhuu
+module load gsl/2.7.1-gcc-12.2.0-jgxkcb6
+module load python/3.10.6-intel-2021.5.0-mtvbpzb
+module load intel/19.1.3.304
+
+./swift --threads=24 --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --feedback --limiter --sync isolated_galaxy.yml
+
+
diff --git a/setup_reruns.py b/setup_reruns.py
new file mode 100644
index 0000000000000000000000000000000000000000..0ac53ba62d1765ef95335a196c7a11c08f337abc
--- /dev/null
+++ b/setup_reruns.py
@@ -0,0 +1,78 @@
+import os
+from pathlib import Path
+import shutil
+import glob
+import re
+
+from data.create_ics_from_snapshot import ics_from_snapshot
+
+##########################################
+# Select mass resolution and snapshotnumber
+##########################################
+mass_resolution_levels = ["M6"]
+snapshotnumber = 85
+##########################################
+
+
+
+localdir = os.getcwd()
+for mass in mass_resolution_levels:
+ os.chdir(os.path.join(localdir,mass))
+ for runfolder in glob.glob("Galaxy*3/"):
+ ##########################################
+ # setting runfolder name and creating rerunfolder
+ ##########################################
+ runfolder_absolute_path = os.path.join(localdir, mass, runfolder)
+ rerunfolder_absolute_path = os.path.join(localdir, mass+"_reruns_snap%4.4i"%(snapshotnumber), "Rerun"+runfolder)
+ Path(rerunfolder_absolute_path).mkdir(parents=True, exist_ok=True)
+ print (runfolder_absolute_path)
+
+ ##########################################
+ # change working directory to rerunfolder
+ ##########################################
+ os.chdir(rerunfolder_absolute_path)
+
+ ##########################################
+ # copy files into rerunfolder
+ ##########################################
+ shutil.copy2(os.path.join(runfolder_absolute_path, "isolated_galaxy.yml"), "./")
+ shutil.copy2(os.path.join(runfolder_absolute_path, "swift"), "./")
+ shutil.copy2(os.path.join(runfolder_absolute_path, "output_%4.4i.hdf5"%(int(snapshotnumber))), "./")
+
+ ##########################################
+ # create ICs for rerun
+ ##########################################
+ ics_from_snapshot(os.path.join(rerunfolder_absolute_path, "output_%4.4i.hdf5"%(int(snapshotnumber))), \
+ os.path.join(rerunfolder_absolute_path, "ICs.hdf5"))
+
+ ##########################################
+ # update yml file for rerun
+ ##########################################
+ f = open("isolated_galaxy.yml", "rt")
+ data = f.read()
+ data = re.sub(r'^.*disk\.hdf5.*$', ' file_name: ICs.hdf5', data, flags=re.MULTILINE)
+ data = re.sub(r'^.*h_min_ratio.*$', ' h_min_ratio: 0.0001', data, flags=re.MULTILINE)
+ data = re.sub(r'^.*time_end.*$', ' time_end: 0.00001025', data, flags=re.MULTILINE)
+ data = re.sub(r'^.*delta_time\: 0.*$', ' delta_time: 0.00001023', data, flags=re.MULTILINE)
+ data = re.sub(r'^.*dt_max\:.*$', ' dt_max: 1e-8', data, flags=re.MULTILINE)
+
+ f.close()
+ f = open("isolated_galaxy.yml", "wt")
+ f.write(data)
+ f.close()
+
+ ##########################################
+ # start swift for one timestep
+ ##########################################
+
+ os.system("./swift --threads=28 --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --feedback --limiter --sync -n 1 isolated_galaxy.yml")
+
+
+
+
+
+
+
+
+
+