Merge branch 'add_new_cosmo_ics' into 'master'

Add EAGLE_25 LOWRES

Closes #720

See merge request !1220

examples/EAGLE_ICs/EAGLE_25_low_res/README

+Initial conditions corresponding to the 25 Mpc volume
+of the EAGLE suite at 8x lower resolution.
+The ICs only contain DM particles. The gas particles will be generated in SWIFT.
+
+This resolution corresponds to: EAGLE low res. (m_B = 1.45e7 Msol)
+
+MD5 hash:
+62e7ec93a1b0b4c57ff0c63ad0da2028  EAGLE_L0025N0188_ICs.hdf5

examples/EAGLE_ICs/EAGLE_25_low_res/eagle_25.yml

+# Define some meta-data about the simulation
+MetaData:
+  run_name:   EAGLE-L0025N0188-Ref
+
+# 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:              0.6777        # Reduced Hubble constant
+  a_begin:        0.0078125     # Initial scale-factor of the simulation
+  a_end:          1.0           # Final scale factor of the simulation
+  Omega_m:        0.307         # Matter density parameter
+  Omega_lambda:   0.693         # Dark-energy density parameter
+  Omega_b:        0.0482519     # 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:            eagle # Common part of the name of output files
+  output_list_on:      1
+  output_list:         ./output_list.txt
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:           1.01
+  scale_factor_first:   0.01
+
+# Parameters for the self-gravity scheme
+Gravity:
+  eta:                         0.025     # Constant dimensionless multiplier for time integration.
+  MAC:                         geometric # Use the geometric opening angle condition
+  theta_cr:                    0.7       # Opening angle (Multipole acceptance criterion)
+  use_tree_below_softening:    0
+  mesh_side_length:            128
+  comoving_DM_softening:         0.006640 # Comoving softening for DM (6.67 ckpc)
+  max_physical_DM_softening:     0.002600 # Physical softening for DM (2.60 pkpc)
+  comoving_baryon_softening:     0.003580 # Comoving softening for baryons (3.58 ckpc)
+  max_physical_baryon_softening: 0.001400 # Physical softening for baryons (1.40 pkpc)
+
+# 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:                       0.1      # 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:               100.0    # (internal units)
+  initial_temperature:               268.7    # (internal units)
+  particle_splitting:                1        # Particle splitting is ON
+  particle_splitting_mass_threshold: 5.6e-3   # (internal units, i.e. 5.6e7 Msun ~ 4x initial gas particle mass)
+
+# Parameters of the stars neighbour search
+Stars:
+  resolution_eta:        1.1642   # Target smoothing length in units of the mean inter-particle separation
+  h_tolerance:           7e-3
+
+# Parameters for the Friends-Of-Friends algorithm
+FOF:
+  basename:                        fof_output  # Filename for the FOF outputs.
+  min_group_size:                  32         # The minimum no. of particles required for a group.
+  linking_length_ratio:            0.2         # Linking length in units of the main inter-particle separation.
+  black_hole_seed_halo_mass_Msun:  1.0e10      # Minimal halo mass in which to seed a black hole (in solar masses).
+  scale_factor_first:              0.05        # Scale-factor of first FoF black hole seeding calls.
+  delta_time:                      1.00751     # Scale-factor ratio between consecutive FoF black hole seeding calls.
+
+Scheduler:
+  max_top_level_cells:   16
+  cell_split_size:       200
+  
+Restarts:
+  onexit:       1
+  delta_hours:  6.0
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  EAGLE_L0025N0188_ICs.hdf5
+  periodic:   1
+  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
+  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.
+  remap_ids: 1                       # Re-map the IDs to [1, N] to avoid collision problems when splitting
+
+# Parameters of the line-of-sight outputs
+LineOfSight:
+  basename:            eagle_los
+  num_along_x:         0
+  num_along_y:         0
+  num_along_z:         100
+  scale_factor_first:  0.1
+  delta_time:          1.1
+
+# Impose primoridal metallicity
+EAGLEChemistry:
+  init_abundance_metal:     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
+
+# EAGLE cooling parameters
+EAGLECooling:
+  dir_name:                ./coolingtables/
+  H_reion_z:               7.5                 # Planck 2018
+  H_reion_eV_p_H:          2.0
+  He_reion_z_centre:       3.5
+  He_reion_z_sigma:        0.5
+  He_reion_eV_p_H:         2.0
+
+# COLIBRE cooling parameters
+COLIBRECooling:
+  dir_name:                ./UV_dust1_CR1_G1_shield1.hdf5 # Location of the 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.
+
+# EAGLE star formation parameters
+EAGLEStarFormation:
+  SF_model:                          PressureLaw
+  EOS_density_norm_H_p_cm3:          0.1       # Physical density used for the normalisation of the EOS assumed for the star-forming gas in Hydrogen atoms per cm^3.
+  EOS_temperature_norm_K:            8000      # Temperature om the polytropic EOS assumed for star-forming gas at the density normalisation in Kelvin.
+  EOS_gamma_effective:               1.3333333 # Slope the of the polytropic EOS assumed for the star-forming gas.
+  KS_normalisation:                  1.515e-4  # The normalization of the Kennicutt-Schmidt law in Msun / kpc^2 / yr.
+  KS_exponent:                       1.4       # The exponent of the Kennicutt-Schmidt law.
+  min_over_density:                  100.0     # The over-density above which star-formation is allowed.
+  KS_high_density_threshold_H_p_cm3: 1e3       # Hydrogen number density above which the Kennicut-Schmidt law changes slope in Hydrogen atoms per cm^3.
+  KS_high_density_exponent:          2.0       # Slope of the Kennicut-Schmidt law above the high-density threshold.
+  EOS_entropy_margin_dex:            0.3       # Logarithm base 10 of the maximal entropy above the EOS at which stars can form.
+  threshold_norm_H_p_cm3:            0.1       # Normalisation of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
+  threshold_Z0:                      0.002     # Reference metallicity (metal mass fraction) for the metal-dependant threshold for star formation.
+  threshold_slope:                   -0.64     # Slope of the metal-dependant star formation threshold
+  threshold_max_density_H_p_cm3:     10.0      # Maximal density of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
+  
+# Parameters for the EAGLE "equation of state"
+EAGLEEntropyFloor:
+  Jeans_density_threshold_H_p_cm3: 1e-4      # 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:        800       # Temperature of the EAGLE Jeans limiter entropy floor at the density threshold expressed in Kelvin.
+  Jeans_gamma_effective:           1.3333333 # 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
+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:                             ./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_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_min:             0.5             # Minimal fraction of energy applied in a SNII feedback event.
+  SNII_energy_fraction_max:             5.0             # 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             # Stellar age in Gyr above which the enrichment is down-sampled.
+  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.
+
+# EAGLE AGN model
+EAGLEAGN:
+  subgrid_seed_mass_Msun:             1.0e4      # Black hole subgrid mass at creation time in solar masses.
+  multi_phase_bondi:                  0          # Compute Bondi rates per neighbour particle?
+  subgrid_bondi:                      0          # Compute Bondi rates using the subgrid extrapolation of the gas properties around the BH?
+  with_angmom_limiter:                0          # Are we applying the Rosas-Guevara et al. (2015) viscous time-scale reduction term?
+  viscous_alpha:                      1e6        # Normalisation constant of the viscous time-scale in the accretion reduction term
+  with_boost_factor:                  0          # Are we using the model from Booth & Schaye (2009)?
+  boost_alpha:                        1.         # Lowest value for the accretion effeciency for the Booth & Schaye 2009 accretion model.
+  boost_beta:                         2.         # Slope of the power law for the Booth & Schaye 2009 model, set beta to zero for constant alpha models.
+  boost_n_h_star_H_p_cm3:             0.1        # Normalization of the power law for the Booth & Schaye 2009 model in cgs (cm^-3).
+  radiative_efficiency:               0.1        # Fraction of the accreted mass that gets radiated.
+  use_nibbling:                       1          # Continuously transfer small amounts of mass from all gas neighbours to a black hole [1] or stochastically swallow whole gas particles [0]?
+  min_gas_mass_for_nibbling:          7.2e6      # Minimum mass for a gas particle to be nibbled from [M_Sun]. Only used if use_nibbling is 1.
+  max_eddington_fraction:             1.         # Maximal allowed accretion rate in units of the Eddington rate.
+  eddington_fraction_for_recording:   0.1        # Record the last time BHs reached an Eddington ratio above this threshold.
+  coupling_efficiency:                0.1        # Fraction of the radiated energy that couples to the gas in feedback events.
+  use_variable_delta_T:               1          # Switch to enable adaptive calculation of AGN dT [1], rather than using a constant value [0].
+  AGN_with_locally_adaptive_delta_T:  1          # Switch to enable additional dependence of AGN dT on local gas density and temperature (only used if use_variable_delta_T is 1).
+  AGN_delta_T_mass_norm:              3e8        # Normalisation temperature of AGN dT scaling with BH subgrid mass [K] (only used if use_variable_delta_T is 1).
+  AGN_delta_T_mass_reference:         1e8        # BH subgrid mass at which the normalisation temperature set above applies [M_Sun] (only used if use_variable_delta_T is 1).
+  AGN_delta_T_mass_exponent:          0.666667   # Power-law index of AGN dT scaling with BH subgrid mass (only used if use_variable_delta_T is 1).
+  AGN_delta_T_crit_factor:            1.0        # Multiple of critical dT for numerical efficiency (Dalla Vecchia & Schaye 2012) to use as dT floor (only used if use_variable_delta_T and AGN_with_locally_adaptive_delta_T are both 1).
+  AGN_delta_T_background_factor:      0.0        # Multiple of local gas temperature to use as dT floor (only used if use_variable_delta_T and AGN_with_locally_adaptive_delta_T are both 1).
+  AGN_delta_T_min:                    1e7        # Minimum allowed value of AGN dT [K] (only used if use_variable_delta_T is 1).
+  AGN_delta_T_max:                    3e9        # Maximum allowed value of AGN dT [K] (only used if use_variable_delta_T is 1).
+  AGN_delta_T_K:                      3.16228e8  # Change in temperature to apply to the gas particle in an AGN feedback event [K] (used if use_variable_delta_T is 0 or AGN_use_nheat_with_fixed_dT is 1 AND to initialise the BHs).
+  AGN_use_nheat_with_fixed_dT:        0          # Switch to use the constant AGN dT, rather than the adaptive one, for calculating the energy reservoir threshold.
+  AGN_use_adaptive_energy_reservoir_threshold: 0 # Switch to calculate an adaptive AGN energy reservoir threshold.
+  AGN_num_ngb_to_heat:                1.         # Target number of gas neighbours to heat in an AGN feedback event (only used if AGN_use_adaptive_energy_reservoir_threshold is 0).
+  max_reposition_mass:                1e20       # Maximal BH mass considered for BH repositioning in solar masses (large number implies we always reposition).
+  max_reposition_distance_ratio:      3.0        # Maximal distance a BH can be repositioned, in units of the softening length.
+  with_reposition_velocity_threshold: 0          # Should we only reposition to particles that move slowly w.r.t. the black hole?
+  max_reposition_velocity_ratio:      0.5        # Maximal velocity offset of a particle to reposition a BH to, in units of the ambient sound speed of the BH. Only meaningful if with_reposition_velocity_threshold is 1.
+  min_reposition_velocity_threshold: -1.0        # Minimal value of the velocity threshold for repositioning [km/s], set to < 0 for no effect. Only meaningful if with_reposition_velocity_threshold is 1.
+  set_reposition_speed:               0          # Should we reposition black holes with (at most) a prescribed speed towards the potential minimum?
+  threshold_major_merger:             0.333      # Mass ratio threshold to consider a BH merger as 'major'
+  threshold_minor_merger:             0.1        # Mass ratio threshold to consider a BH merger as 'minor'
+  merger_threshold_type:              2          # Type of velocity threshold for BH mergers (0: v_circ at kernel edge, 1: v_esc at actual distance, with softening, 2: v_esc at actual distance, no softening).
+  merger_max_distance_ratio:          3.0        # Maximal distance over which two BHs can merge, in units of the softening length.

examples/EAGLE_ICs/EAGLE_25_low_res/getIC.sh

+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0025N0188_ICs.hdf5

examples/EAGLE_ICs/EAGLE_25_low_res/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e EAGLE_L0025N0188_ICs.hdf5 ]
+then
+    echo "Fetching initial conditions for the EAGLE 25Mpc low-res. example..."
+    ./getIC.sh
+fi
+
+# Grab the cooling and yield tables if they are not present.
+if [ ! -e yieldtables ]
+then
+    echo "Fetching EAGLE yield tables..."
+    ../getEagleYieldTable.sh
+fi
+
+if [ ! -e coolingtables ]
+then
+    echo "Fetching EAGLE cooling tables..."
+    ../getEagleCoolingTable.sh
+fi
+
+# The following run-time options are broken down by line as:
+# Basic run-time options
+# Create and run with stars
+# Radiative options - run with cooling and stellar feedback
+# Run with the time-step limiter required to capture feedback
+# Run with black holes - fof is needed for the seeding
+# Threading options - run with threads and pinning (latter not required but improves performance)
+# The corresponding parameter file for this run
+
+../../swift \
+    --cosmology --eagle \
+    --threads=16 --pin \
+    eagle_25.yml

examples/EAGLE_ICs/EAGLE_25_low_res/vrconfig_3dfof_subhalos_SO_hydro.cfg

+#Configuration file for analysing Hydro
+#runs 6DFOF + substructure algorithm, demands subhalos and FOF halos be self-bound, calculates many properties
+#Units currently set to take in as input, Mpc, 1e10 solar masses, km/s, output in same units
+#To set temporally unique halo ids, alter Snapshot_value=SNAP to appropriate value. Ie: for snapshot 12, change SNAP to 12
+
+################################
+#input options
+#set up to use SWIFT HDF input, load gas, star, bh and dark matter
+################################
+HDF_name_convention=6 #HDF SWIFT naming convention
+Input_includes_dm_particle=1 #include dark matter particles in hydro input
+Input_includes_gas_particle=1 #include gas particles in hydro input
+Input_includes_star_particle=1 #include star particles in hydro input
+Input_includes_bh_particle=1 #include bh particles in hydro input
+Input_includes_wind_particle=0 #include wind particles in hydro input (used by Illustris and moves particle type 0 to particle type 3 when decoupled from hydro forces). Here shown as example
+Input_includes_tracer_particle=0 #include tracer particles in hydro input (used by Illustris). Here shown as example
+Input_includes_extradm_particle=0 #include extra dm particles stored in particle type 2 and type 3, useful for zooms
+
+Particle_type_for_reference_frames=1 #use DM particles to define reference frame
+Halo_core_phase_merge_dist=0.25 #merge substructures if difference in dispersion normalised distance is < this value
+Apply_phase_merge_to_host=1 #merge substructures with background if centrally located and phase-distance is small
+
+#units conversion from input input to desired internal unit
+Length_input_unit_conversion_to_output_unit=1.0 #default code unit,
+Velocity_input_unit_conversion_to_output_unit=1.0 #default velocity unit,
+Mass_input_unit_conversion_to_output_unit=1.0 #default mass unit,
+#assumes input is in 1e10 msun, Mpc and km/s and output units are the same
+Gravity=43.00918 #for 1e10 Msun, km/s and Mpc
+Hubble_unit=100.0 # assuming units are km/s and Mpc, then value of Hubble in km/s/Mpc
+
+#converting hydro quantities
+Stellar_age_input_is_cosmological_scalefactor=1
+Metallicity_input_unit_conversion_to_output_unit=1.0
+Stellar_age_input_unit_conversion_to_output_unit=1.0
+Star_formation_rate_input_unit_conversion_to_output_unit=1.0
+Stellar_age_to_yr=9.778134136e11
+Stellar_age_input_unit_conversion_to_output_unit=1.022690e-12   # year in units of Mpc / (km / s)
+
+#set the units of the output by providing conversion to a defined unit
+#conversion of output length units to kpc
+Length_unit_to_kpc=1000.0
+#conversion of output velocity units to km/s
+Velocity_to_kms=1.0
+#conversion of output mass units to solar masses
+Mass_to_solarmass=1.0e10
+
+Metallicity_to_solarmetallicity=83.33 #1 / 0.012
+Star_formation_rate_to_solarmassperyear=97.78
+Stellar_age_to_yr=1.0
+#ensures that output is physical and not comoving distances per little h
+Comoving_units=0
+
+#sets the total buffer size in bytes used to store temporary particle information
+#of mpi read threads before they are broadcast to the appropriate waiting non-read threads
+#if not set, default value is equivalent to 1e6 particles per mpi process, quite large
+#but significantly minimises the number of send/receives
+#in this example the buffer size is roughly that for a send/receive of 10000 particles
+#for 100 mpi processes
+MPI_particle_total_buf_size=100000000
+
+################################
+#search related options
+################################
+
+#how to search a simulation
+Particle_search_type=1 #search dark matter particles only
+#for baryon search
+Baryon_searchflag=2 #if 1 search for baryons separately using phase-space search when identifying substructures, 2 allows special treatment in field FOF linking and phase-space substructure search, 0 treat the same as dark matter particles
+#for search for substruture
+Search_for_substructure=1 #if 0, end search once field objects are found
+#also useful for zoom simulations or simulations of individual objects, setting this flag means no field structure search is run
+Singlehalo_search=0 #if file is single halo in which one wishes to search for substructure. Here disabled.
+#additional option for field haloes
+Keep_FOF=0 #if field 6DFOF search is done, allows to keep structures found in 3DFOF (can be interpreted as the inter halo stellar mass when only stellar search is used).\n
+
+#minimum size for structures
+Minimum_size=20 #min 20 particles
+Minimum_halo_size=32 #if field halos have different minimum sizes, otherwise set to -1.
+
+#for field fof halo search
+FoF_Field_search_type=5 #5 3DFOF search for field halos, 4 for 6DFOF clean up of field halos, 3 for 6DFOF with velocity scale distinct for each initial 3D FOF candidate
+Halo_3D_linking_length=0.20
+
+#for mean field estimates and local velocity density distribution funciton estimator related quantiites, rarely need to change this
+Local_velocity_density_approximate_calculation=1 #calculates velocity density using approximative (and quicker) near neighbour search
+Cell_fraction = 0.01 #fraction of field fof halo used to determine mean velocity distribution function. Typical values are ~0.005-0.02
+Grid_type=1 #normal entropy based grid, shouldn't have to change
+Nsearch_velocity=32 #number of velocity neighbours used to calculate local velocity distribution function. Typial values are ~32
+Nsearch_physical=256 #numerof physical neighbours from which the nearest velocity neighbour set is based. Typical values are 128-512
+
+#for substructure search, rarely ever need to change this
+FoF_search_type=1 #default phase-space FOF search. Don't really need to change
+Iterative_searchflag=1 #iterative substructure search, for substructure find initial candidate substructures with smaller linking lengths then expand search region
+Outlier_threshold=2.5 #outlier threshold for a particle to be considered residing in substructure, that is how dynamically distinct a particle is. Typical values are >2
+Substructure_physical_linking_length=0.10
+Velocity_ratio=2.0 #ratio of speeds used in phase-space FOF
+Velocity_opening_angle=0.10 #angle between velocities. 18 degrees here, typical values are ~10-30
+Velocity_linking_length=0.20 #where scaled by structure dispersion
+Significance_level=1.0 #how significant a substructure is relative to Poisson noise. Values >= 1 are fine.
+
+#for iterative substructure search, rarely ever need to change this
+Iterative_threshold_factor=1.0 #change in threshold value when using iterative search. Here no increase in threshold if iterative or not
+Iterative_linking_length_factor=2.0 #increase in final linking final iterative substructure search 
+Iterative_Vratio_factor=1.0 #change in Vratio when using iterative search. no change in vratio
+Iterative_ThetaOp_factor=1.0 #change in velocity opening angle. no change in velocity opening angle
+
+#for checking for halo merger remnants, which are defined as large, well separated phase-space density maxima
+Halo_core_search=2 # searches for separate 6dfof cores in field haloes, and then more than just flags halo as merging, assigns particles to each merging "halo". 2 is full separation, 1 is flagging, 0 is off
+#if searching for cores, linking lengths. likely does not need to change much
+Use_adaptive_core_search=0 #calculate dispersions in configuration & vel space to determine linking lengths
+Use_phase_tensor_core_growth=2 #use full stepped phase-space tensor assignment
+Halo_core_ellx_fac=0.7 #how linking lengths are changed when searching for local 6DFOF cores,
+Halo_core_ellv_fac=2.0 #how velocity lengths based on dispersions are changed when searching for local 6DFOF cores
+Halo_core_ncellfac=0.005 #fraction of total halo particle number setting min size of a local 6DFOF core
+Halo_core_num_loops=8 #number of loops to iteratively search for cores
+Halo_core_loop_ellx_fac=0.75 #how much to change the configuration space linking per iteration
+Halo_core_loop_ellv_fac=1.0 #how much to change the velocity space linking per iteration
+Halo_core_loop_elln_fac=1.2 #how much to change the min number of particles per iteration
+Halo_core_phase_significance=5.0 #how significant a core must be in terms of dispersions (sigma) significance
+
+################################
+#Unbinding options (VELOCIraptor is able to accurately identify tidal debris so particles need not be bound to a structure)
+################################
+
+#unbinding related items
+Unbind_flag=1 #run unbinding
+#objects must have particles that meet the allowed kinetic to potential ratio AND also have some total fraction that are completely bound.
+Unbinding_type=0
+#alpha factor used to determine whether particle is "bound" alaph*T+W<0. For standard subhalo catalogues use >0.9 but if interested in tidal debris 0.2-0.5
+Allowed_kinetic_potential_ratio=0.95
+Min_bound_mass_frac=0.65 #minimum bound mass fraction
+#run unbinding of field structures, aka halos. This is useful for sams and 6DFOF halos but may not be useful if interested in 3DFOF mass functions.
+Bound_halos=0
+#don't keep background potential when unbinding
+Keep_background_potential=1
+#use all particles to determine velocity frame for unbinding
+Frac_pot_ref=1.0
+Min_npot_ref=20
+#reference frame only meaningful if calculating velocity frame using subset of particles in object. Can use radially sorted fraction of particles about minimum potential or centre of mass
+Kinetic_reference_frame_type=0
+#extra options in new unbinding optimisation
+Unbinding_max_unbound_removal_fraction_per_iteration=0.5
+Unbinding_max_unbound_fraction=0.95
+Unbinding_max_unbound_fraction_allowed=0.005
+
+################################
+#Calculation of properties related options
+################################
+
+Number_of_overdensities=5
+Overdensity_values_in_critical_density=100,200,500,1000,2500,
+#when calculating properties, for field objects calculate inclusive masses
+Inclusive_halo_masses=3 #calculate inclusive masses for halos using full Spherical overdensity apertures
+#ensures that output is physical and not comoving distances per little h
+Comoving_units=0
+#calculate more (sub)halo properties (like angular momentum in spherical overdensity apertures, both inclusive and exclusive)
+Extensive_halo_properties_output=1
+Extensive_gas_properties_output=1
+Extensive_star_properties_output=1
+#calculate aperture masses
+Calculate_aperture_quantities=1 
+Number_of_apertures=5
+Aperture_values_in_kpc=5,10,30,50,100,
+Number_of_projected_apertures=5
+Projected_aperture_values_in_kpc=5,10,30,50,100,
+#calculate radial profiles
+Calculate_radial_profiles=1
+Number_of_radial_profile_bin_edges=20
+#default radial normalisation log rad bins, normed by R200crit, Integer flag of 0 is log bins and R200crit norm. 
+Radial_profile_norm=0
+Radial_profile_bin_edges=-2.,-1.87379263,-1.74758526,-1.62137789,-1.49517052,-1.36896316,-1.24275579,-1.11654842,-0.99034105,-0.86413368,-0.73792631,-0.61171894,-0.48551157,-0.3593042,-0.23309684,-0.10688947,0.0193179,0.14552527,0.27173264,0.39794001,
+Iterate_cm_flag=0 #do not interate to determine centre-of-mass
+Sort_by_binding_energy=1 #sort particles by binding energy
+Reference_frame_for_properties=2 #use the minimum potential as reference frame about which to calculate properties 
+
+################################
+#Extra fields
+################################
+
+# Also compute the H abundance as well as the HI, HII and H_2 fractions
+Gas_internal_property_names=ElementMassFractions,SpeciesFractions,SpeciesFractions,SpeciesFractions,
+Gas_internal_property_index_in_file=0,0,1,2,
+Gas_internal_property_input_output_unit_conversion_factors=1.0,1.0,1.0,1.0
+Gas_internal_property_calculation_type =averagemassweighted,averagemassweighted,averagemassweighted,averagemassweighted,
+Gas_internal_property_output_units=unitless,unitless,unitless,unitless,
+
+# Collect the BH subgrid masses and compute the max, min, average and total mass in apertures
+BH_internal_property_names=SubgridMasses,SubgridMasses,SubgridMasses,SubgridMasses,
+BH_internal_property_input_output_unit_conversion_factors=1.0e10,1.0e10,1.0e10,1.0e10,
+BH_internal_property_calculation_type=max,min,average,aperture_total,
+BH_internal_property_output_units=solar_mass,solar_mass,solar_mass,solar_mass,
+
+################################
+#output related
+################################
+
+Write_group_array_file=0 #do not write a group array file
+Separate_output_files=0 #do not separate output into field and substructure files similar to subfind
+Binary_output=2 #Use HDF5 output (binary output 1, ascii 0, and HDF 2)
+#output particles residing in the spherical overdensity apertures of halos, only the particles exclusively belonging to halos
+Spherical_overdensity_halo_particle_list_output=1
+
+#halo ids are adjusted by this value * 1000000000000 (or 1000000 if code compiled with the LONGINTS option turned off)
+#to ensure that halo ids are temporally unique. So if you had 100 snapshots, for snap 100 set this to 100 and 100*1000000000000 will
+#be added to the halo id as set for this snapshot, so halo 1 becomes halo 100*1000000000000+1 and halo 1 of snap 0 would just have ID=1
+
+#ALTER THIS as part of a script to get temporally unique ids
+Snapshot_value=SNAP
+
+################################
+#other options
+################################
+Verbose=1 #how talkative do you want the code to be, 0 not much, 1 a lot, 2 chatterbox