Added example with snipshots

examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/README

+Small LCDM cosmological simulation generated by C. Power. Cosmology
+is WMAP9 and the box is 100Mpc/h in size with 64^3 particles.
+We use a softening length of 1/25th of the mean inter-particle separation.
+
+The ICs have been generated to run with Gadget-2 so we need to switch
+on the options to cancel the h-factors and a-factors at reading time.
+We generate gas from the ICs using SWIFT's internal mechanism and set the
+temperature to the expected gas temperature at this redshift.
+
+The 'plotTempEvolution.py' plots the temperature evolution of the gas
+in the simulated volume.
+
+This version uses an output list that has 'snapshots' and 'snipshots'
+as a useful example for this functionality.
+
+MD5 checksum of the ICs:
+08736c3101fd738e22f5159f78e6022b  small_cosmo_volume.hdf5

examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/getIC.sh

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

examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/plotTempEvolution.py

+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+#
+# 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/>.
+#
+################################################################################
+
+# Computes the temperature evolution of the gas in a cosmological box
+
+# Physical constants needed for internal energy to temperature conversion
+k_in_J_K = 1.38064852e-23
+mH_in_kg = 1.6737236e-27
+
+# Number of snapshots generated
+n_snapshots = 200
+
+import matplotlib
+matplotlib.use("Agg")
+from pylab import *
+import h5py
+import os.path
+
+# Plot parameters
+params = {'axes.labelsize': 10,
+'axes.titlesize': 10,
+'font.size': 9,
+'legend.fontsize': 9,
+'xtick.labelsize': 10,
+'ytick.labelsize': 10,
+'text.usetex': True,
+ 'figure.figsize' : (3.15,3.15),
+'figure.subplot.left'    : 0.14,
+'figure.subplot.right'   : 0.99,
+'figure.subplot.bottom'  : 0.12,
+'figure.subplot.top'     : 0.99,
+'figure.subplot.wspace'  : 0.15,
+'figure.subplot.hspace'  : 0.12,
+'lines.markersize' : 6,
+'lines.linewidth' : 2.,
+'text.latex.unicode': True
+}
+rcParams.update(params)
+rc('font',**{'family':'sans-serif','sans-serif':['Times']})
+
+# Read the simulation data
+sim = h5py.File("snap_0000.hdf5", "r")
+boxSize = sim["/Header"].attrs["BoxSize"][0]
+time = sim["/Header"].attrs["Time"][0]
+scheme = sim["/HydroScheme"].attrs["Scheme"][0]
+kernel = sim["/HydroScheme"].attrs["Kernel function"][0]
+neighbours = sim["/HydroScheme"].attrs["Kernel target N_ngb"][0]
+eta = sim["/HydroScheme"].attrs["Kernel eta"][0]
+alpha = sim["/HydroScheme"].attrs["Alpha viscosity"][0]
+H_mass_fraction = sim["/HydroScheme"].attrs["Hydrogen mass fraction"][0]
+H_transition_temp = sim["/HydroScheme"].attrs["Hydrogen ionization transition temperature"][0]
+T_initial = sim["/HydroScheme"].attrs["Initial temperature"][0]
+T_minimal = sim["/HydroScheme"].attrs["Minimal temperature"][0]
+git = sim["Code"].attrs["Git Revision"]
+
+# Cosmological parameters
+H_0 = sim["/Cosmology"].attrs["H0 [internal units]"][0]
+gas_gamma = sim["/HydroScheme"].attrs["Adiabatic index"][0]
+
+unit_length_in_cgs = sim["/Units"].attrs["Unit length in cgs (U_L)"]
+unit_mass_in_cgs = sim["/Units"].attrs["Unit mass in cgs (U_M)"]
+unit_time_in_cgs = sim["/Units"].attrs["Unit time in cgs (U_t)"]
+
+unit_length_in_si = 0.01 * unit_length_in_cgs
+unit_mass_in_si = 0.001 * unit_mass_in_cgs
+unit_time_in_si = unit_time_in_cgs
+
+# Primoridal ean molecular weight as a function of temperature
+def mu(T, H_frac=H_mass_fraction, T_trans=H_transition_temp):
+    if T > T_trans:
+        return 4. / (8. - 5. * (1. - H_frac))
+    else:
+        return 4. / (1. + 3. * H_frac)
+    
+# Temperature of some primoridal gas with a given internal energy
+def T(u, H_frac=H_mass_fraction, T_trans=H_transition_temp):
+    T_over_mu = (gas_gamma - 1.) * u * mH_in_kg / k_in_J_K
+    ret = np.ones(np.size(u)) * T_trans
+
+    # Enough energy to be ionized?
+    mask_ionized = (T_over_mu > (T_trans+1) / mu(T_trans+1, H_frac, T_trans))
+    if np.sum(mask_ionized)  > 0:
+        ret[mask_ionized] = T_over_mu[mask_ionized] * mu(T_trans*10, H_frac, T_trans)
+
+    # Neutral gas?
+    mask_neutral = (T_over_mu < (T_trans-1) / mu((T_trans-1), H_frac, T_trans))
+    if np.sum(mask_neutral)  > 0:
+        ret[mask_neutral] = T_over_mu[mask_neutral] * mu(0, H_frac, T_trans)
+        
+    return ret
+
+
+z = np.zeros(n_snapshots)
+a = np.zeros(n_snapshots)
+T_mean = np.zeros(n_snapshots)
+T_std = np.zeros(n_snapshots)
+T_log_mean = np.zeros(n_snapshots)
+T_log_std = np.zeros(n_snapshots)
+T_median = np.zeros(n_snapshots)
+T_min = np.zeros(n_snapshots)
+T_max = np.zeros(n_snapshots)
+
+# Loop over all the snapshots
+for i in range(n_snapshots):
+    sim = h5py.File("snap_%04d.hdf5"%i, "r")
+
+    z[i] = sim["/Cosmology"].attrs["Redshift"][0]
+    a[i] = sim["/Cosmology"].attrs["Scale-factor"][0]
+
+    u = sim["/PartType0/InternalEnergies"][:]
+
+    # Compute the temperature
+    u *= (unit_length_in_si**2 / unit_time_in_si**2)
+    u /= a[i]**(3 * (gas_gamma - 1.))
+    Temp = T(u)
+
+    # Gather statistics
+    T_median[i] = np.median(Temp)
+    T_mean[i] = Temp.mean()
+    T_std[i] = Temp.std()
+    T_log_mean[i] = np.log10(Temp).mean()
+    T_log_std[i] = np.log10(Temp).std()
+    T_min[i] = Temp.min()
+    T_max[i] = Temp.max()
+
+# CMB evolution
+a_evol = np.logspace(-3, 0, 60)
+T_cmb = (1. / a_evol)**2 * 2.72
+
+# Plot the interesting quantities
+figure()
+subplot(111, xscale="log", yscale="log")
+
+fill_between(a, T_mean-T_std, T_mean+T_std, color='C0', alpha=0.1)
+plot(a, T_max, ls='-.', color='C0', lw=1., label="${\\rm max}~T$")
+plot(a, T_min, ls=':', color='C0', lw=1., label="${\\rm min}~T$")
+plot(a, T_mean, color='C0', label="${\\rm mean}~T$", lw=1.5)
+fill_between(a, 10**(T_log_mean-T_log_std), 10**(T_log_mean+T_log_std), color='C1', alpha=0.1)
+plot(a, 10**T_log_mean, color='C1', label="${\\rm mean}~{\\rm log} T$", lw=1.5)
+plot(a, T_median, color='C2', label="${\\rm median}~T$", lw=1.5)
+
+legend(loc="upper left", frameon=False, handlelength=1.5)
+
+# Expected lines
+plot([1e-10, 1e10], [H_transition_temp, H_transition_temp], 'k--', lw=0.5, alpha=0.7)
+text(2.5e-2, H_transition_temp*1.07, "$T_{\\rm HII\\rightarrow HI}$", va="bottom", alpha=0.7, fontsize=8)
+plot([1e-10, 1e10], [T_minimal, T_minimal], 'k--', lw=0.5, alpha=0.7)
+text(1e-2, T_minimal*0.8, "$T_{\\rm min}$", va="top", alpha=0.7, fontsize=8)
+plot(a_evol, T_cmb, 'k--', lw=0.5, alpha=0.7)
+text(a_evol[20], T_cmb[20]*0.55, "$(1+z)^2\\times T_{\\rm CMB,0}$", rotation=-34, alpha=0.7, fontsize=8, va="top", bbox=dict(facecolor='w', edgecolor='none', pad=1.0, alpha=0.9))
+
+
+redshift_ticks = np.array([0., 1., 2., 5., 10., 20., 50., 100.])
+redshift_labels = ["$0$", "$1$", "$2$", "$5$", "$10$", "$20$", "$50$", "$100$"]
+a_ticks = 1. / (redshift_ticks + 1.)
+
+xticks(a_ticks, redshift_labels)
+minorticks_off()
+
+xlabel("${\\rm Redshift}~z$", labelpad=0)
+ylabel("${\\rm Temperature}~T~[{\\rm K}]$", labelpad=0)
+xlim(9e-3, 1.1)
+ylim(20, 2.5e7)
+
+savefig("Temperature_evolution.png", dpi=200)
+

examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e small_cosmo_volume.hdf5 ]
+then
+    echo "Fetching initial conditions for the small cosmological volume example..."
+    ./getIC.sh
+fi
+
+# Run SWIFT
+../../swift --cosmology --hydro --self-gravity --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
+
+# Plot the temperature evolution
+python plotTempEvolution.py

examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/select_output.yml

+Snapshot:
+  # Particle Type Gas
+  Coordinates_Gas: on  # Co-moving positions of the particles : a U_L  [ cm ]
+  Velocities_Gas: on  # Peculiar velocities of the stars. This is (a * dx/dt) where x is the co-moving positions of the particles : U_L U_t^-1  [ cm s^-1 ]
+  Masses_Gas: on  # Masses of the particles : U_M  [ g ]
+  SmoothingLengths_Gas: on  # Co-moving smoothing lengths (FWHM of the kernel) of the particles : a U_L  [ cm ]
+  Entropies_Gas: on  # Co-moving entropies per unit mass of the particles : U_M^-1.6667 U_L^4 U_t^-2  [ g^-1.6667 cm^4 s^-2 ]
+  ParticleIDs_Gas: on  # Unique IDs of the particles : [ - ] 
+  Densities_Gas: on  # Co-moving mass densities of the particles : a^-3 U_M U_L^-3  [ g cm^-3 ]
+  InternalEnergies_Gas: on  # Co-moving thermal energies per unit mass of the particles : a^-2 U_L^2 U_t^-2  [ cm^2 s^-2 ]
+  Pressures_Gas: on  # Co-moving pressures of the particles : a^-5 U_M U_L^-1 U_t^-2  [ g cm^-1 s^-2 ]
+  Potentials_Gas: on  # Co-moving gravitational potential at position of the particles : a^-1 U_L^2 U_t^-2  [ cm^2 s^-2 ]
+  Temperatures_Gas: on  # Temperature of the particles : U_T  [ K ]
+  VELOCIraptorGroupIDs_Gas: on  # Group IDs of the particles in the VELOCIraptor catalogue : [ - ] 
+
+  # Particle Type DM
+  Coordinates_DM: on  # Co-moving position of the particles : a U_L  [ cm ]
+  Velocities_DM: on  # Peculiar velocities of the stars. This is a * dx/dt where x is the co-moving position of the particles. : U_L U_t^-1  [ cm s^-1 ]
+  Masses_DM: on  # Masses of the particles : U_M  [ g ]
+  ParticleIDs_DM: on  # Unique ID of the particles : [ - ] 
+  Softenings_DM: on  # Co-moving Plummer-equivalent softening lengths of the particles. : a U_L  [ cm ]
+  VELOCIraptorGroupIDs_DM: on  # Group IDs of the particles in the VELOCIraptor catalogue : [ - ] 
+
+
+Snipshot:
+  # Particle Type Gas
+  Coordinates_Gas: on  # Co-moving positions of the particles : a U_L  [ cm ]
+  Velocities_Gas: on  # Peculiar velocities of the stars. This is (a * dx/dt) where x is the co-moving positions of the particles : U_L U_t^-1  [ cm s^-1 ]
+  Masses_Gas: on  # Masses of the particles : U_M  [ g ]
+  SmoothingLengths_Gas: on  # Co-moving smoothing lengths (FWHM of the kernel) of the particles : a U_L  [ cm ]
+  Entropies_Gas: off  # Co-moving entropies per unit mass of the particles : U_M^-1.6667 U_L^4 U_t^-2  [ g^-1.6667 cm^4 s^-2 ]
+  ParticleIDs_Gas: on  # Unique IDs of the particles : [ - ] 
+  Densities_Gas: off  # Co-moving mass densities of the particles : a^-3 U_M U_L^-3  [ g cm^-3 ]
+  InternalEnergies_Gas: off  # Co-moving thermal energies per unit mass of the particles : a^-2 U_L^2 U_t^-2  [ cm^2 s^-2 ]
+  Pressures_Gas: off  # Co-moving pressures of the particles : a^-5 U_M U_L^-1 U_t^-2  [ g cm^-1 s^-2 ]
+  Potentials_Gas: off  # Co-moving gravitational potential at position of the particles : a^-1 U_L^2 U_t^-2  [ cm^2 s^-2 ]
+  Temperatures_Gas: off  # Temperature of the particles : U_T  [ K ]
+  VELOCIraptorGroupIDs_Gas: off  # Group IDs of the particles in the VELOCIraptor catalogue : [ - ] 
+
+  # Particle Type DM
+  Coordinates_DM: on  # Co-moving position of the particles : a U_L  [ cm ]
+  Velocities_DM: on  # Peculiar velocities of the stars. This is a * dx/dt where x is the co-moving position of the particles. : U_L U_t^-1  [ cm s^-1 ]
+  Masses_DM: off  # Masses of the particles : U_M  [ g ]
+  ParticleIDs_DM: on  # Unique ID of the particles : [ - ] 
+  Softenings_DM: off  # Co-moving Plummer-equivalent softening lengths of the particles. : a U_L  [ cm ]
+  VELOCIraptorGroupIDs_DM: off # Group IDs of the particles in the VELOCIraptor catalogue : [ - ] 
+

examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/small_cosmo_volume.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1.98841e43    # 10^10 M_sun
+  UnitLength_in_cgs:   3.08567758e24 # 1 Mpc
+  UnitVelocity_in_cgs: 1e5           # 1 km/s
+  UnitCurrent_in_cgs:  1             # Amperes
+  UnitTemp_in_cgs:     1             # Kelvin
+
+Cosmology:                      # WMAP9 cosmology
+  Omega_m:        0.276
+  Omega_lambda:   0.724
+  Omega_b:        0.0455
+  h:              0.703
+  a_begin:        0.019607843	# z_ini = 50.
+  a_end:          1.0		# z_end = 0.
+
+# Parameters governing the time integration
+TimeIntegration:
+  dt_min:     1e-6 
+  dt_max:     1e-2 
+
+# Parameters for the self-gravity scheme
+Gravity:
+  eta:          0.025         
+  theta:        0.5           
+  comoving_DM_softening:         0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
+  max_physical_DM_softening:     0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
+  comoving_baryon_softening:     0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
+  max_physical_baryon_softening: 0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
+  mesh_side_length:       64
+
+# Parameters of the hydro scheme
+SPH:
+  resolution_eta:      1.2348   # "48 Ngb" with the cubic spline kernel
+  h_min_ratio:         0.1
+  CFL_condition:       0.1
+  initial_temperature: 7075.    # (1 + z_ini)^2 * 2.72K
+  minimal_temperature: 100.
+
+# Parameters governing the snapshots
+Snapshots:
+  basename:            snap
+  delta_time:          1.05
+  scale_factor_first:  0.05
+  compression:         4
+  select_output_on:    1
+  select_output:       select_output.yml
+  output_list_on:      1
+  output_list:         output_list.txt
+  
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:          1.02
+  scale_factor_first:  0.02
+  
+Scheduler:
+  max_top_level_cells: 8
+  cell_split_size:     50
+  
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  small_cosmo_volume.hdf5
+  periodic:                    1
+  cleanup_h_factors:           1    
+  cleanup_velocity_factors:    1  
+  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.
+
+# Parameters for the EAGLE "equation of state"
+EAGLEEntropyFloor:
+  Jeans_density_threshold_H_p_cm3: 0.1       # 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:        8000      # 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:        8000       # Temperature of the EAGLE Cool limiter entropy floor at the density threshold expressed in Kelvin.
+  Cool_gamma_effective:           1.         # Slope the of the EAGLE Cool limiter entropy floor
+

examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/vrconfig_3dfof_subhalos_SO_hydro.cfg

+#Configuration file for analysing Hydro
+#runs 3DFOF + 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
+
+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=43.0211349 #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
+
+#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
+#1 / 0.012
+Metallicity_to_solarmetallicity=83.33
+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=2.0 #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
+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
+################################
+Virial_density=500 #user defined virial overdensity. Note that 200 rho_c, 200 rho_m and BN98 are already calculated.
+#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 
+
+################################
+#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=0 #how talkative do you want the code to be, 0 not much, 1 a lot, 2 chatterbox
+
+