parameter_example.yml 23.7 KB
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# Define the system of units to use internally.
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InternalUnitSystem:
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  UnitMass_in_cgs:     1   # Grams
  UnitLength_in_cgs:   1   # Centimeters
  UnitVelocity_in_cgs: 1   # Centimeters per second
  UnitCurrent_in_cgs:  1   # Amperes
  UnitTemp_in_cgs:     1   # Kelvin
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# Values of some physical constants
PhysicalConstants:
  G:            6.67408e-8 # (Optional) Overwrite the value of Newton's constant used internally by the code.

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# 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:        0.0455        # Baryon density parameter
  Omega_r:        0.            # (Optional) Radiation density parameter
  w_0:            -1.0          # (Optional) Dark-energy equation-of-state parameter at z=0.
  w_a:            0.            # (Optional) Dark-energy equation-of-state time evolution parameter.

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# 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_tolerance:           1e-4     # (Optional) Relative accuracy of the Netwon-Raphson scheme for the smoothing lengths.
  h_max:                 10.      # (Optional) Maximal allowed smoothing length in internal units. Defaults to FLT_MAX if unspecified.
  max_volume_change:     1.4      # (Optional) Maximal allowed change of kernel volume over one time-step.
  max_ghost_iterations:  30       # (Optional) Maximal number of iterations allowed to converge towards the smoothing length.
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  initial_temperature:   0        # (Optional) Initial temperature (in internal units) to set the gas particles at start-up. Value is ignored if set to 0.
  minimal_temperature:   0        # (Optional) Minimal temperature (in internal units) allowed for the gas particles. Value is ignored if set to 0.
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  H_mass_fraction:       0.755    # (Optional) Hydrogen mass fraction used for initial conversion from temp to internal energy. Default value is derived from the physical constants.
  H_ionization_temperature: 1e4   # (Optional) Temperature of the transition from neutral to ionized Hydrogen for primoridal gas.
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  viscosity_alpha:       0.8      # (Optional) Override for the initial value of the artificial viscosity. In schemes that have a fixed AV, this remains as alpha throughout the run.
  viscosity_alpha_max:   2.0      # (Optional) Maximal value for the artificial viscosity in schemes that allow alpha to vary
  viscosity_alpha_min:   0.1      # (Optional) Minimal value for the artificial viscosity in schemes that allow alpha to vary
  viscosity_length:      0.1      # (Optional) Decay length for the artificial viscosity in schemes that allow alpha to vary
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# Parameters for the self-gravity scheme
Gravity:
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  mesh_side_length:       32        # Number of cells along each axis for the periodic gravity mesh.
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  eta:          0.025               # Constant dimensionless multiplier for time integration.
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  theta:        0.7                 # Opening angle (Multipole acceptance criterion).
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  comoving_softening:     0.0026994 # Comoving softening length (in internal units).
  max_physical_softening: 0.0007    # Physical softening length (in internal units).
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  rebuild_frequency:      0.01      # (Optional) Frequency of the gravity-tree rebuild in units of the number of g-particles (this is the default value).
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  a_smooth:     1.25                # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
  r_cut_max:    4.5                 # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
  r_cut_min:    0.1                 # (Optional) Cut-off in number of top-level cells below which no truncation of FMM forces are performed (this is the default value).
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# Parameters for the task scheduling
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Scheduler:
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  nr_queues:                 0         # (Optional) The number of task queues to use. Use 0  to let the system decide.
  cell_max_size:             8000000   # (Optional) Maximal number of interactions per task if we force the split (this is the default value).
  cell_sub_size_pair_hydro:  256000000 # (Optional) Maximal number of interactions per sub-pair hydro task  (this is the default value).
  cell_sub_size_self_hydro:  32000     # (Optional) Maximal number of interactions per sub-self hydro task  (this is the default value).
  cell_sub_size_pair_grav:   256000000 # (Optional) Maximal number of interactions per sub-pair gravity task  (this is the default value).
  cell_sub_size_self_grav:   32000     # (Optional) Maximal number of interactions per sub-self gravity task  (this is the default value).
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  cell_sub_size_pair_stars:  256000000 # (Optional) Maximal number of interactions per sub-pair stars task  (this is the default value).
  cell_sub_size_self_stars:  32000     # (Optional) Maximal number of interactions per sub-self stars task  (this is the default value).
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  cell_split_size:           400       # (Optional) Maximal number of particles per cell (this is the default value).
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  cell_subdepth_diff_grav:   4         # (Optional) Maximal depth difference between leaves and a cell that gravity tasks can be pushed down to (this is the default value).
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  cell_extra_parts:          0         # (Optional) Number of spare parts per top-level allocated at rebuild time for on-the-fly creation.
  cell_extra_gparts:         0         # (Optional) Number of spare gparts per top-level allocated at rebuild time for on-the-fly creation.
  cell_extra_sparts:         400       # (Optional) Number of spare sparts per top-level allocated at rebuild time for on-the-fly creation.
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  max_top_level_cells:       12        # (Optional) Maximal number of top-level cells in any dimension. The number of top-level cells will be the cube of this (this is the default value).
  tasks_per_cell:            0         # (Optional) The average number of tasks per cell. If not large enough the simulation will fail (means guess...).
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  links_per_tasks:           10        # (Optional) The average number of links per tasks (before adding the communication tasks). If not large enough the simulation will fail (means guess...). Defaults to 10.
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  mpi_message_limit:         4096      # (Optional) Maximum MPI task message size to send non-buffered, KB.
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# Parameters governing the time integration (Set dt_min and dt_max to the same value for a fixed time-step run.)
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TimeIntegration:
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  time_begin:        0.    # The starting time of the simulation (in internal units).
  time_end:          1.    # The end time of the simulation (in internal units).
  dt_min:            1e-6  # 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).
  max_dt_RMS_factor: 0.25  # (Optional) Dimensionless factor for the maximal displacement allowed based on the RMS velocities.
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# Parameters governing the snapshots
Snapshots:
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  basename:   output      # Common part of the name of output files
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  scale_factor_first: 0.1 # (Optional) Scale-factor of the first snapshot if cosmological time-integration.
  time_first: 0.          # (Optional) Time of the first output if non-cosmological time-integration (in internal units)
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  delta_time: 0.01        # Time difference between consecutive outputs (in internal units)
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  invoke_stf: 0           # (Optional) Call VELOCIraptor every time a snapshot is written irrespective of the VELOCIraptor output strategy.
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  compression: 0          # (Optional) Set the level of compression of the HDF5 datasets [0-9]. 0 does no compression.
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  int_time_label_on:   0  # (Optional) Enable to label the snapshots using the time rounded to an integer (in internal units)
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  UnitMass_in_cgs:     1  # (Optional) Unit system for the outputs (Grams)
  UnitLength_in_cgs:   1  # (Optional) Unit system for the outputs (Centimeters)
  UnitVelocity_in_cgs: 1  # (Optional) Unit system for the outputs (Centimeters per second)
  UnitCurrent_in_cgs:  1  # (Optional) Unit system for the outputs (Amperes)
  UnitTemp_in_cgs:     1  # (Optional) Unit system for the outputs (Kelvin)
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  output_list_on:      0  # (Optional) Enable the output list
  output_list:         snaplist.txt # (Optional) File containing the output times (see documentation in "Parameter File" section)
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# Parameters governing the logger snapshot system
Logger:
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  delta_step:           10     # Update the particle log every this many updates
  initial_buffer_size:  1      # buffer size in GB
  buffer_scale:		10     # (Optional) When buffer size is too small, update it with required memory times buffer_scale
  basename:             index  # Common part of the filenames
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# Parameters governing the conserved quantities statistics
Statistics:
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  delta_time:           1e-2     # Time between statistics output
  scale_factor_first:     0.1    # (Optional) Scale-factor of the first statistics dump if cosmological time-integration.
  time_first:             0.     # (Optional) Time of the first stats output if non-cosmological time-integration (in internal units)
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  energy_file_name:    energy    # (Optional) File name for energy output
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  timestep_file_name:  timesteps # (Optional) File name for timing information output. Note: No underscores "_" allowed in file name
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  output_list_on:      0   	 # (Optional) Enable the output list
  output_list:         statlist.txt # (Optional) File containing the output times (see documentation in "Parameter File" section)
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# Parameters related to the initial conditions
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InitialConditions:
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  file_name:  SedovBlast/sedov.hdf5 # The file to read
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  periodic:                    1    # Are we running with periodic ICs?
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  generate_gas_in_ics:         0    # (Optional) Generate gas particles from the DM-only ICs (e.g. from panphasia).
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  cleanup_h_factors:           0    # (Optional) Clean up the h-factors used in the ICs (e.g. in Gadget files).
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  cleanup_velocity_factors:    0    # (Optional) Clean up the scale-factors used in the definition of the velocity variable in the ICs (e.g. in Gadget files).
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  cleanup_smoothing_lengths:   0    # (Optional) Clean the values of the smoothing lengths that are read in to remove stupid values. Set to 1 to activate.
  smoothing_length_scaling:    1.   # (Optional) A scaling factor to apply to all smoothing lengths in the ICs.
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  shift:      [0.0,0.0,0.0]         # (Optional) A shift to apply to all particles read from the ICs (in internal units).
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  replicate:  2                     # (Optional) Replicate all particles along each axis a given integer number of times. Default 1.
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# Parameters controlling restarts
Restarts:
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  enable:             1          # (Optional) whether to enable dumping restarts at fixed intervals.
  save:               1          # (Optional) whether to save copies of the previous set of restart files (named .prev)
  onexit:             0          # (Optional) whether to dump restarts on exit (*needs enable*)
  subdir:             restart    # (Optional) name of subdirectory for restart files.
  basename:           swift      # (Optional) prefix used in naming restart files.
  delta_hours:        6.0        # (Optional) decimal hours between dumps of restart files.
  stop_steps:         100        # (Optional) how many steps to process before checking if the <subdir>/stop file exists. When present the application will attempt to exit early, dumping restart files first.
  max_run_time:       24.0       # (optional) Maximal wall-clock time in hours. The application will exit when this limit is reached.
  resubmit_on_exit:   0          # (Optional) whether to run a command when exiting after the time limit has been reached.
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  resubmit_command:   ./resub.sh # (Optional) Command to run when time limit is reached. Compulsory if resubmit_on_exit is switched on. Note potentially unsafe.
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# Parameters governing domain decomposition
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DomainDecomposition:
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  initial_type:     memory    # (Optional) The initial decomposition strategy: "grid",
                              #            "region", "memory", or "vectorized".
  initial_grid: [10,10,10]    # (Optional) Grid sizes if the "grid" strategy is chosen.

  repartition_type: fullcosts # (Optional) The re-decomposition strategy, one of:
                              # "none", "fullcosts", "edgecosts", "memory" or
                              # "timecosts".
  trigger:          0.05      # (Optional) Fractional (<1) CPU time difference between MPI ranks required to trigger a
                              # new decomposition, or number of steps (>1) between decompositions
  minfrac:          0.9       # (Optional) Fractional of all particles that should be updated in previous step when
                              # using CPU time trigger
  usemetis:         0         # Use serial METIS when ParMETIS is also available.
  adaptive:         1         # Use adaptive repartition when ParMETIS is available, otherwise simple refinement.
  itr:              100       # When adaptive defines the ratio of inter node communication time to data redistribution time, in the range 0.00001 to 10000000.0.
                              # Lower values give less data movement during redistributions, at the cost of global balance which may require more communication.
  use_fixed_costs:  1         # If 1 then use any compiled in fixed costs for
                              # task weights in first repartition, if 0 only use task timings, if > 1 only use
                              # fixed costs, unless none are available.
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# Structure finding options (requires velociraptor)
StructureFinding:
  config_file_name:     stf_input.cfg # Name of the STF config file.
  basename:             ./stf         # Common part of the name of output files.
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  scale_factor_first:   0.92          # (Optional) Scale-factor of the first snaphot (cosmological run)
  time_first:           0.01          # (Optional) Time of the first structure finding output (in internal units).
  delta_time:           1.10          # (Optional) Time difference between consecutive structure finding outputs (in internal units) in simulation time intervals.
  output_list_on:       0   	      # (Optional) Enable the output list
  output_list:          stflist.txt   # (Optional) File containing the output times (see documentation in "Parameter File" section)
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# Parameters related to the equation of state ------------------------------------------

EoS:
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  isothermal_internal_energy: 20.26784  # Thermal energy per unit mass for the case of isothermal equation of state (in internal units).

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  planetary_use_Til:    1   # (Optional) Whether to prepare the Tillotson EOS
  planetary_use_HM80:   0   # (Optional) Whether to prepare the Hubbard & MacFarlane (1980) EOS
  planetary_use_ANEOS:  0   # (Optional) Whether to prepare the ANEOS EOS
  planetary_use_SESAME: 0   # (Optional) Whether to prepare the SESAME EOS
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                            # (Optional) Table file paths
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  planetary_HM80_HHe_table_file:        ./equation_of_state/planetary_HM80_HHe.txt
  planetary_HM80_ice_table_file:        ./equation_of_state/planetary_HM80_ice.txt
  planetary_HM80_rock_table_file:       ./equation_of_state/planetary_HM80_rock.txt
  planetary_SESAME_iron_table_file:     ./equation_of_state/planetary_SESAME_iron_2140.txt
  planetary_SESAME_basalt_table_file:   ./equation_of_state/planetary_SESAME_basalt_7530.txt
  planetary_SESAME_water_table_file:    ./equation_of_state/planetary_SESAME_water_7154.txt
  planetary_SS08_water_table_file:      ./equation_of_state/planetary_SS08_water.txt
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# Parameters related to external potentials --------------------------------------------
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# Point mass external potentials
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PointMassPotential:
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  useabspos:       0        # 0 -> positions based on centre, 1 -> absolute positions 
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  position:        [50.,50.0,50.]      # location of external point mass (internal units)
  mass:            1e10                # mass of external point mass (internal units)
  timestep_mult:   0.03                # Dimensionless pre-factor for the time-step condition
  softening:       0.05                # For point-mass-softened option
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# Isothermal potential parameters
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IsothermalPotential:
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  useabspos:       0        # 0 -> positions based on centre, 1 -> absolute positions 
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  position:        [100.,100.,100.]    # Location of centre of isothermal potential with respect to centre of the box (internal units)
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  vrot:            200.     # Rotation speed of isothermal potential (internal units)
  timestep_mult:   0.03     # Dimensionless pre-factor for the time-step condition
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  epsilon:         0.1      # Softening size (internal units)
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# Hernquist potential parameters
HernquistPotential:
  useabspos:       0        # 0 -> positions based on centre, 1 -> absolute positions 
  position:        [100.,100.,100.]    # Location of centre of isothermal potential with respect to centre of the box (if 0) otherwise absolute (if 1) (internal units)
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  idealizeddisk:   0        # (Optional) Whether to run with idealizeddisk or without, 0 used the mass and scalelength as mandatory parameters, while 1 uses more advanced disk dependent paramters
  mass:            1e10     # (Optional 0) default parameter, Mass of the Hernquist potential
  scalelength:     10.0     # (Optional 0) default parameter, Scale length of the potential
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                            # If multiple X200 values are given, only one is used, in the order M200 > V200 > R200.
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  M200:            3e11     # (Optional 1a) M200 of the galaxy+halo (when used V200 and R200 are not used)
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  V200:            100.     # (Optional 1b) V200 of the galaxy+halo (when used M200 and R200 are not used, if M200 is given M200 is used)
  R200:            10.      # (Optional 1c) R200 of the galaxy+halo (when used M200 and V200 are not used, if M200 or V200 are given they are used)
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  h:               0.704    # (Optional 1) reduced Hubble constant
  concentration:   7.1      # (Optional 1) concentration of the Halo
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  diskfraction:              0.0434370991372   # (Optional 1) Disk mass fraction (equal to MD in MakeNewDisk and GalIC)
  bulgefraction:              0.00705852860979  # (Optional 1) Bulge mass fraction (equal to MB in MakeNewDisk and GalIC)
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  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:         0.1      # Softening size (internal units)
 
# Isothermal potential parameters
NFWPotential:
  useabspos:          0
  position:           [0.0,0.0,0.0]      # Location of centre of isothermal potential with respect to centre of the box (internal units) if useabspos=0 otherwise with respect to the 0,0,0, coordinates.
  concentration:      8.       # Concentration of the halo
  M_200:              2.0e+12  # Mass of the halo (M_200 in internal units)
  critical_density:   127.4    # Critical density (internal units).
  timestep_mult:      0.01     # Dimensionless pre-factor for the time-step condition, basically determines fraction of orbital time we need to do an integration step
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# Disk-patch potential parameters
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DiscPatchPotential:
  surface_density: 10.      # Surface density of the disc (internal units)
  scale_height:    100.     # Scale height of the disc (internal units)
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  z_disc:          400.     # Position of the disc along the z-axis (internal units)
  z_trunc:         300.     # (Optional) Distance from the disc along z-axis above which the potential gets truncated.
  z_max:           380.     # (Optional) Distance from the disc along z-axis above which the potential is set to 0.
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  timestep_mult:   0.03     # Dimensionless pre-factor for the time-step condition
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  growth_time:     5.       # (Optional) Time for the disc to grow to its final size (multiple of the dynamical time)
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# Sine Wave potential
SineWavePotential:
  amplitude:        10.     # Amplitude of the sine wave (internal units)
  timestep_limit:   1.      # Time-step dimensionless pre-factor.
  growth_time:      0.      # (Optional) Time for the potential to grow to its final size.
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# Parameters related to cooling function  ----------------------------------------------

# Constant du/dt cooling function
ConstCooling:
  cooling_rate: 1.          # Cooling rate (du/dt) (internal units)
  min_energy:   1.          # Minimal internal energy per unit mass (internal units)
  cooling_tstep_mult: 1.    # Dimensionless pre-factor for the time-step condition

# Constant lambda cooling function
LambdaCooling:
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  lambda_nH2_cgs:              1e-22 # Cooling rate divided by square Hydrogen number density (in cgs units [erg * s^-1 * cm^3])
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  cooling_tstep_mult:          1.0   # (Optional) Dimensionless pre-factor for the time-step condition.
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# Parameters of the EAGLE cooling model (Wiersma+08 cooling tables).
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EAGLECooling:
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  dir_name:                  ./coolingtables/  # Location of the Wiersma+08 cooling tables
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  H_reion_z:                 8.5               # Redshift of Hydrogen re-ionization
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  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
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  He_reion_eV_p_H:           2.0               # Energy inject by Helium re-ionization in electron-volt per Hydrogen atom
  newton_integration:        0                 # (Optional) Set to 1 to use the Newton-Raphson method to solve the xplicit cooling problem.
  Ca_over_Si_in_solar:       1.                # (Optional) Ratio of Ca/Si to use in units of solar. If set to 1, the code uses [Ca/Si] = 0, i.e. Ca/Si = 0.0941736.
  S_over_Si_in_solar:        1.                # (Optional) Ratio of S/Si to use in units of solar. If set to 1, the code uses [S/Si] = 0, i.e. S/Si = 0.6054160.
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# Cooling with Grackle 3.0
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GrackleCooling:
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  CloudyTable: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
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  WithUVbackground: 1                   # Enable or not the UV background
  Redshift: 0                           # Redshift to use (-1 means time based redshift)
  WithMetalCooling: 1                   # Enable or not the metal cooling
  ProvideVolumetricHeatingRates: 0      # (optional) User provide volumetric heating rates
  ProvideSpecificHeatingRates: 0        # (optional) User provide specific heating rates
  SelfShieldingMethod: 0                # (optional) Grackle (<= 3) or Gear self shielding method
  OutputMode: 0                         # (optional) Write in output corresponding primordial chemistry mode
  MaxSteps: 10000                       # (optional) Max number of step when computing the initial composition
  ConvergenceLimit: 1e-2                # (optional) Convergence threshold (relative) for initial composition
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# Parameters related to chemistry models  -----------------------------------------------

# EAGLE model
EAGLEChemistry:
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  init_abundance_metal:     0.           # Inital fraction of particle mass in *all* metals
  init_abundance_Hydrogen:  0.752        # Inital fraction of particle mass in Hydrogen
  init_abundance_Helium:    0.248        # Inital fraction of particle mass in Helium
  init_abundance_Carbon:    0.000        # Inital fraction of particle mass in Carbon
  init_abundance_Nitrogen:  0.000        # Inital fraction of particle mass in Nitrogen
  init_abundance_Oxygen:    0.000        # Inital fraction of particle mass in Oxygen
  init_abundance_Neon:      0.000        # Inital fraction of particle mass in Neon
  init_abundance_Magnesium: 0.000        # Inital fraction of particle mass in Magnesium
  init_abundance_Silicon:   0.000        # Inital fraction of particle mass in Silicon
  init_abundance_Iron:      0.000        # Inital fraction of particle mass in Iron