parameter_example.yml 19.4 KB
Newer Older
1
# Define the system of units to use internally.
2
InternalUnitSystem:
3
4
5
6
7
  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
Matthieu Schaller's avatar
Matthieu Schaller committed
8

9
10
11
12
# Values of some physical constants
PhysicalConstants:
  G:            6.67408e-8 # (Optional) Overwrite the value of Newton's constant used internally by the code.

13
14
15
16
17
18
19
20
21
22
23
24
# 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.

25
26
27
28
29
30
31
32
# 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.
33
34
  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.
35
36
  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.
Josh Borrow's avatar
Josh Borrow committed
37
38
39
40
  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
41

42
43
# Parameters for the self-gravity scheme
Gravity:
44
  mesh_side_length:       32        # Number of cells along each axis for the periodic gravity mesh.
45
  eta:          0.025               # Constant dimensionless multiplier for time integration.
46
  theta:        0.7                 # Opening angle (Multipole acceptance criterion).
47
48
  comoving_softening:     0.0026994 # Comoving softening length (in internal units).
  max_physical_softening: 0.0007    # Physical softening length (in internal units).
49
  rebuild_frequency:      0.01      # (Optional) Frequency of the gravity-tree rebuild in units of the number of g-particles (this is the default value).
50
51
52
  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).
53

54
# Parameters for the task scheduling
Matthieu Schaller's avatar
Matthieu Schaller committed
55
Scheduler:
56
57
58
59
60
61
  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).
62
63
  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).
64
  cell_split_size:           400       # (Optional) Maximal number of particles per cell (this is the default value).
65
  cell_subdepth_grav:        2         # (Optional) Maximal depth the gravity tasks can be pushed down (this is the default value).
66
67
68
  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...).
  mpi_message_limit:         4096      # (Optional) Maximum MPI task message size to send non-buffered, KB.
Matthieu Schaller's avatar
Matthieu Schaller committed
69

70
# Parameters governing the time integration (Set dt_min and dt_max to the same value for a fixed time-step run.)
Matthieu Schaller's avatar
Matthieu Schaller committed
71
TimeIntegration:
72
73
74
75
76
  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.
77

78
79
# Parameters governing the snapshots
Snapshots:
80
  basename:   output      # Common part of the name of output files
81
82
  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)
83
  delta_time: 0.01        # Time difference between consecutive outputs (in internal units)
84
  compression: 0          # (Optional) Set the level of compression of the HDF5 datasets [0-9]. 0 does no compression.
85
  int_time_label_on:   0  # (Optional) Enable to label the snapshots using the time rounded to an integer (in internal units)
86
87
88
89
90
  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)
91
92
  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)
Loikki's avatar
Loikki committed
93
  logger_max_steps:    10 # (Optional) Number of particle steps between two chunk writing if using logger
94

95
96
# Parameters governing the conserved quantities statistics
Statistics:
97
98
99
  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)
Matthieu Schaller's avatar
Matthieu Schaller committed
100
  energy_file_name:    energy    # (Optional) File name for energy output
101
  timestep_file_name:  timesteps # (Optional) File name for timing information output. Note: No underscores "_" allowed in file name
102
103
  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)
104

105
# Parameters related to the initial conditions
Matthieu Schaller's avatar
Matthieu Schaller committed
106
InitialConditions:
107
  file_name:  SedovBlast/sedov.hdf5 # The file to read
Peter W. Draper's avatar
typo    
Peter W. Draper committed
108
  periodic:                    1    # Are we running with periodic ICs?
109
  generate_gas_in_ics:         0    # (Optional) Generate gas particles from the DM-only ICs (e.g. from panphasia).
110
  cleanup_h_factors:           0    # (Optional) Clean up the h-factors used in the ICs (e.g. in Gadget files).
111
  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).
112
113
  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.
114
  shift:      [0.0,0.0,0.0]         # (Optional) A shift to apply to all particles read from the ICs (in internal units).
115
  replicate:  2                     # (Optional) Replicate all particles along each axis a given integer number of times. Default 1.
Matthieu Schaller's avatar
Matthieu Schaller committed
116

117
118
# Parameters controlling restarts
Restarts:
119
120
121
122
123
124
125
126
127
  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.
128
  resubmit_command:   ./resub.sh # (Optional) Command to run when time limit is reached. Compulsory if resubmit_on_exit is switched on. Note potentially unsafe.
129

130
# Parameters governing domain decomposition
Matthieu Schaller's avatar
Matthieu Schaller committed
131
DomainDecomposition:
132
133
  initial_type:     memory  # (Optional) The initial decomposition strategy: "grid",
                            #            "region", "memory", or "vectorized".
134
  initial_grid: [10,10,10]  # (Optional) Grid sizes if the "grid" strategy is chosen.
135
136

  repartition_type: costs/costs # (Optional) The re-decomposition strategy, one of:
137
                            # "none/none", "costs/costs", "none/costs", "costs/none" or "costs/time".
Peter W. Draper's avatar
Peter W. Draper committed
138
139
                            # These are vertex/edge weights with "costs" as task timing
                            # and "time" as the expected time of the next updates
140

141
142
143
144
  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
145
146
147
  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.
148
                            # Lower values give less data movement during redistributions, at the cost of global balance which may require more communication.
149

150
151
152
# Parameters related to the equation of state ------------------------------------------

EoS:
153
154
  isothermal_internal_energy: 20.26784  # Thermal energy per unit mass for the case of isothermal equation of state (in internal units).

155
156
157
158
  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
159
                            # (Optional) Table file paths
160
161
162
163
164
165
166
  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
167

168
# Parameters related to external potentials --------------------------------------------
169

170
# Point mass external potentials
171
PointMassPotential:
172
173
174
175
  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
176

177
# Isothermal potential parameters
178
IsothermalPotential:
179
  position:        [100.,100.,100.]    # Location of centre of isothermal potential with respect to centre of the box (internal units)
180
181
  vrot:            200.     # Rotation speed of isothermal potential (internal units)
  timestep_mult:   0.03     # Dimensionless pre-factor for the time-step condition
182
  epsilon:         0.1      # Softening size (internal units)
183

184
# Disk-patch potential parameters
185
186
187
DiscPatchPotential:
  surface_density: 10.      # Surface density of the disc (internal units)
  scale_height:    100.     # Scale height of the disc (internal units)
188
189
190
  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.
191
  timestep_mult:   0.03     # Dimensionless pre-factor for the time-step condition
192
  growth_time:     5.       # (Optional) Time for the disc to grow to its final size (multiple of the dynamical time)
193

194
195
196
197
198
# 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.
199

200
201
202
203
204
205
206
207
208
209
# 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:
210
  lambda_nH2_cgs:              1e-22 # Cooling rate divided by square Hydrogen number density (in cgs units [erg * s^-1 * cm^3])
211
  cooling_tstep_mult:          1.0   # (Optional) Dimensionless pre-factor for the time-step condition.
212

213
# Cooling with Grackle 3.0
lhausamm's avatar
lhausamm committed
214
GrackleCooling:
215
  CloudyTable: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
Matthieu Schaller's avatar
Matthieu Schaller committed
216
217
218
219
220
221
222
223
224
  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
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242

# Parameters related to chemistry models  -----------------------------------------------

# EAGLE model
EAGLEChemistry:
  InitMetallicity:         0.           # Inital fraction of particle mass in *all* metals
  InitAbundance_Hydrogen:  0.752        # Inital fraction of particle mass in Hydrogen
  InitAbundance_Helium:    0.248        # Inital fraction of particle mass in Helium
  InitAbundance_Carbon:    0.000        # Inital fraction of particle mass in Carbon
  InitAbundance_Nitrogen:  0.000        # Inital fraction of particle mass in Nitrogen
  InitAbundance_Oxygen:    0.000        # Inital fraction of particle mass in Oxygen
  InitAbundance_Neon:      0.000        # Inital fraction of particle mass in Neon
  InitAbundance_Magnesium: 0.000        # Inital fraction of particle mass in Magnesium
  InitAbundance_Silicon:   0.000        # Inital fraction of particle mass in Silicon
  InitAbundance_Iron:      0.000        # Inital fraction of particle mass in Iron
  CalciumOverSilicon:      0.0941736    # Constant ratio of Calcium over Silicon abundance
  SulphurOverSilicon:      0.6054160    # Constant ratio of Sulphur over Silicon abundance

Loic Hausammann's avatar
Loic Hausammann committed
243
244
245
246
247
248
249
250
251
252
253
# 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.
  output_time_format:   0             # Specifies the frequency format of structure finding. 0 for simulation steps (delta_step) and 1 for simulation time intervals (delta_time).
  scale_factor_first:   0.92          # Scale-factor of the first snaphot (cosmological run)
  time_first:           0.01          # Time of the first structure finding output (in internal units).
  delta_step:           1000          # Time difference between consecutive structure finding outputs (in internal units) in simulation steps.
  delta_time:           1.10          # 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)