Parameterfile¶

The parameter-file, often named param.txt, is a file containing run-time options for Arepo. These include things like the input and output directory, maximum runtimes, memory limits and all kinds of freely choosable simulation and model parameters. In general, the code will output an error message if there are either missing parameters for the given configuration Arepo was compiled with, or if there are extraneous parameters. The latter can be deactivated by setting the compile-time flag ALLOWEXTRAPARAMS. Unlike changing Config.sh, changing the parameters does not require a re-compilation of the code.

Initial conditions¶

InitCondFile

The filename of the initial conditions file. Can be a relative or absolute path. The ICs can be distributed in one or more files, as with snapshots. If ICs with multiple files are used, only the basename without the trailing “.n” should be specified here. Similarly, the “.hdf5” extension should be omitted, the code will automatically append it for ICFormat=3.

ICFormat

The file format of the initial conditions. Currently, three different formats are supported, selected by one of the choices “1”, “2”, or “3”. Format “1” is the traditional Fortran-style unformatted binary format familiar from GADGET. Format “2” is a variant of this format, where each block of data is preceded by a 4-character block-identifier. Finally, format “3” selects the HDF-5 format, which is the recommended format.

InitGasTemp

This sets the initial gas temperature (assuming either a mean molecular weight corresponding to full ionization or full neutrality, depending on whether the temperature is above or below 10^4 K) in Kelvin when initial conditions are read. However, the gas temperature is only set to a certain temperature if InitGasTemp>0, and if the temperature of the gas particles in the initial conditions file is zero, otherwise the initial gas temperature is left at the value stored in the IC file.

MinimumDensityOnStartUp

This sets a lower limit to the density of gas cells after reading in the ICs. All cells that have a lower density are set to this value.

MHDSeedDir

MHD_SEEDFIELD

Direction of the uniform B field that is set before starting the simulation. The direction is encoded by sum(2^k), where k is the index of direction (0, 1, 2 for x, y, z, respectively). E.g. 3 is a diagonal field in the xy plane, parallel to the z axis. This allows only orientations along coordinate axes, perpendicular to them, or in diagonal orientations. Note that the equations of ideal MHD do not change if the field direction is reversed.

MHDSeedValue

MHD_SEEDFIELD

Value of the uniform initial magnetic field in comoving Gauss.

TileICsFactor

TILE_ICS

Factor by which the ICs are replicated in each dimension. Should be an integer. This can be useful for weak scaling tests.

GridSize

ADDBACKGROUNDGRID

Initial guess of grid size for ADDBACKGROUNDGRID. The input will be rounded to the nearest power of two.

Output file names and formats¶

OutputDir

Pathname of the output directory of the code. Can be a relative or absolute path. The output directory is created if it doesn’t exist, but the path to it must already exist.

SnapshotFileBase

Basename of snapshot files produced by the code. e.g. snap for output files snap_000.hdf5 etc.

NumFilesPerSnapshot

The number of separate files requested for each snapshot dump. Each file of the snapshot will hold the data of one or several processors, up to all of them. NumFilesPerSnapshot must hence lie between 1 and the number of processors used. Distributing a snapshot onto several files can be done in parallel and may lead to much better I/O performance, depending on the hardware configuration. It can also help to avoid problems due to big files for large simulations. Note that initial conditions may also be distributed into several files, the number of which is automatically recognized by the code and does not have to be equal to NumFilesPerSnapshot (it may also be larger than the number of processors).

OutputListOn

If set to “1”, the code tries to read a list of desired output times from the file given in OutputListFilename. Otherwise, output times are generated equally spaced from the values assigned from TimeOfFirstSnapshot onwards with spacing TimeBetSnapshot.

OutputListFilename

File with a list of the desired output times. Can be specified with a relative or absolute path.

SnapFormat

Similar to ICFormat, this parameter selects the file-format of snapshot dumps produced by the code. 1 and 2 are two binary formats, identical to the ones in GADGET. 3 is an HDF5 output, which is recommended unless there are good reasons not to use it.

NumFilesWrittenInParallel

The number of files the code may read or write simultaneously when writing or reading snapshot/restart files. If the value of this parameter is larger then the number of processors, it is capped by that. Restricting this parameter to something smaller than the number of MPI ranks is only important for quite large runs, where the file-system can be significantly affected and slowed down by too many tasks writing/reading (in particular restart files) at the same time.

AlternativeOutputDir

TOLERATE_WRITE_ERROR

Path name of an alternative output directory which is used in case output to OutputDir fails. Can be useful on flaky filesystems or machines.

Output frequency¶

CpuTimeBetRestartFile

The value specified here gives the time in seconds the code will run before it writes regularly produced restart files. This can be useful to protect against unexpected interruptions (for example due to a hardware problem) of a simulation, particularly if it is run for a long time. It is then possible to resume a simulation from the last restart file, reducing the potential loss to the elapsed CPU-time since this was produced.

TimeBetSnapshot

The time interval in code units between two subsequent snapshot files in case a file with output times is not specified. For cosmological simulations, this is a multiplicative factor applied to the time of the last snapshot, such that the snapshots will have a constant logarithmic spacing in the scale factor. Otherwise, the parameter is an additive constant that gives the linear spacing between snapshot times.

TimeBetStatistics

The code can be asked to measure the total kinetic, thermal, and potential energy in regular intervals, and to write the results to the file given in energy.txt. The time interval between two such measurements is given by this parameter, in an analogous way as with TimeBetSnapshot. Note that the compile time option EVALPOTENTIAL needs to be activated to obtain a measurement of the gravitational potential energy.

TimeOfFirstSnapshot

The time of the first desired snapshot file in code units in case a file with output times is not specified. For cosmological simulations, the value given here is the scale factor of the first desired output.

FlushCpuTimeDiff

Time interval (in seconds) for flush calls on all log-files. In case REDUCE_FLUSH is not set, this is done during every sync-point.

CPU-time limit and restarts¶

TimeLimitCPU

CPU-time limit for the present submission of the code. If 85 percent of this time have been reached at the end of a timestep, the code terminates itself and produces restart files. The extra 15% is used to guarantee that there is enough time to safely finish the current time step and write the restart files. This CPU time refers to the wall-lock time on a single processor only.

ResubmitOn

If set to “1”, the code will try to resubmit itself to the queuing system when an interruption of the run due to the CPU-time limit occurs. The resubmission itself is done by executing the program/script given with ResubmitCommand.

ResubmitCommand

The name of a script file or program that is executed for automatic resubmission of the job to the queuing system. Note that the file given here needs to be executable. Note that a resubmission can also be triggered by a job-script itself, which is often the more convenient alternative.

Memory allocation¶

MaxMemSize

The memory allocated per MPI task, in megabytes. A contiguous memory area of this total size is allocated at startup, and then partitioned internally within Arepo for memory allocation and deallocation requests. Can generally be set up to ~95% of the total physical memory available per task, e.g. memory per node / number of MPI tasks per node, to leave room for operating system tasks and MPI buffers. This value can be changed upon restart to increase the amount of memory available to each task. In case the code runs out of memory, it terminates and reports in detail how much has been alloacted for each array, and where this happened in the code.

Simulated time span and spatial extent¶

BoxSize

The box size for the simulation, in internal code units. All particles and gas cells in the ICs must have coordinates within the range [0,BoxSize] in each dimension. The only exception from this is for collisionless particles in a tree-only gravity mode (no PMGRID) when GRAVITY_NONPERIODIC is set.

PeriodicBoundariesOn

If set to “1”, periodic boundary conditions are assumed, with a cubical box-size of side-length BoxSize. Particle coordinates are expected to be in the range 0 to BoxSize. Can only be set to zero if GRAVITY_NOT_PERIODIC is set. Note: refers to gravity only. Hydrodynamic boundary conditions are handled by REFLECTIVE_X, REFLECTIVE_Y, and REFLECTIVE_Z in Config.sh.

TimeBegin

This sets the starting time of a simulation when the code is started from initial conditions in internal code units. For cosmological integrations, the value specified here is taken as the initial scale factor.

TimeMax

This sets the final time of the simulation. The code normally tries to run until this time is reached. For cosmological integrations, the value given here is the final scale factor.

Cosmological parameters¶

ComovingIntegrationOn

If set to “0”, the code assumes plain Newtonian physics, with time, positions, velocities, and masses measured in the internal system of units. If set to “1”, the code assumes that a cosmological integration in comoving coordinates should be carried out, assuming an expanding universe described by the ‘Cosmological parameters’ below. In a cosmological integration, the time variable is the scale factor.

Omega0

Gives the total matter density in units of the critical density at z=0 for cosmological simulations. Relevant for comoving integration and halo/subhalo finder

OmegaBaryon

Gives the baryon density in units of the critical density at z=0 for cosmological simulations. Relevant for comoving integration, halo/subhalo finder and star formation model.

OmegaLambda

Gives the vacuum energy density (cosmological constant) at z=0 for cosmological simulations. Relevant for comoving integration and halo/subhalo finder

HubbleParam

This gives the Hubble constant (“little h”) at z=0 in units of 100 km/sec/Mpc. Note that this parameter has been basically absorbed into the definition of the internal code units, such that for gravitational dynamics and adiabatic gas dynamics the actual value assigned for HubbleParam is not used by the code. Only used when conversions to proper (i.e. non-comoving) cgs units are required (e.g. for radiative cooling physics). In other cases, use 1.0.

System of units¶

UnitVelocity_in_cm_per_s

This sets the internal velocity unit in cm/s. For example, the choice of 1e5 sets the velocity unit to 1.0 km/s. Note that the specification of UnitLength_in_cm, UnitMass_in_g, and UnitVelocity_in_cm_per_s also determines the internal unit of time.

UnitLength_in_cm

This sets the internal length unit in cm/h, where H_0 = 100 h km/sec/Mpc. For example, the choice of 3.085678e21 sets the length unit to 1.0 kpc/h.

UnitMass_in_g

This sets the internal mass unit in g/h, where H_0 = 100 h km/s/Mpc. For example, the choice of 1.989e43 sets the mass unit to 10^10 Msun/h.

GravityConstantInternal

The numerical value of the gravitational constant G in internal units depends on the system of units you choose. For example, for the choices above, G=43007.1 in internal units. For GravityConstantInternal=0, the code calculates the value corresponding to the physical value of G automatically. However, you might want to set G yourself. For example, by specifying: GravityConstantInternal=1, UnitLength_in_cm=1, UnitMass_in_g=1, and UnitVelocity_in_cm_per_s=1, one obtains a natural system of units. Note that the code will nevertheless try to use the correct physical value of the Hubble constant in this case, so you should not set GravityConstantInternal in cosmological integrations.

Gravitational force accuracy¶

TypeOfOpeningCriterion

This selects the type of cell-opening criterion used in the tree walks. A value of 1 selects the relative opening criterion (normally recommened), whereas a value of 0 uses a simple geometric Barnes & Hut opening criterion.

ErrTolTheta

If the relative opening criterion is used, the first force estimate is computed using the Barnes-Hut opening criterion with this opening angle. The first forces are then recomputed with the relative opening criterion, which is subsequently used. If the geometric criterion is used, all forces are computed with this opening angle.

ErrTolForceAcc

The accuracy parameter for the relative opening criterion for the tree walk. Only used if TypeOfOpeningCriterion equal to 1.

Time integration accuracy¶

TypeOfTimestepCriterion

This parameter can in principle be used to select different kinds of timestep criteria for gravitational dynamics. However, Arepo presently only supports the criterion 0.

ErrTolIntAccuracy

This dimensionless parameter controls the accuracy of the timestep criterion selected by TypeOfTimestepCriterion. It is the variable eta, where the cosmological timestep for collisionless particles scales as dt ~ eta^0.5.

MaxSizeTimestep

This gives the maximum timestep a particle may take. This should be set to a sensible value in order to protect against too large timesteps for particles with very small acceleration. For cosmological simulations, the parameter given here is the maximum allowed step in terms of the logarithm of the expansion factor. For comoving runs, this is in units of dln(a).

MinSizeTimestep

If a particle requests a timestep smaller than the value specified here, the code will normally terminate with a warning message. If compiled with the NOSTOP_WHEN_BELOW_MINTIMESTEP option, the code will instead force the timesteps to be at least as large as MinSizeTimestep.

CourantFac

This sets the value of the Courant parameter used in the determination of the hydrodynamical timestep of gas cells. The hydrodynamical timestep is this value times the Courant–Friedrichs–Lewy (CFL) condition calculated for each cell.

Domain decomposition¶

ActivePartFracForNewDomainDecomp

Fraction of particles that need to be at least active in order to trigger a new domain decomposition at a sync-point. All sync-points where fewer particles are active will not perform a domain decomposition.

MultipleDomains

Number of domains per MPI task. Consequently, the domain decomposition will cut the computational box into a number of chunks equal to MultipleDomains times the number of tasks. Too few of them make it hard to reach good CPU- and memory-load at the same time, too many cause more MPI communication due to a larger surface area of the domain boundaries.

TopNodeFactor

Determines how fine the top-level tree is constructed (1.0: only as far as necessary to split the domain in the required number of chunks). The higher this factor is, the more precise the Peano-Hilbert curve can be cut into equal pieces of cpu and memory load. A higher value, however, increases the size of the top-level tree, which is stored on every MPI task, thus the total memory requirements.

Moving mesh¶

DesNumNgb

This sets the desired number of nearest neighbors for an initial density/size estimate for gas cells during code startup.

MaxNumNgbDeviation

This sets the allowed variation of the number of neighbors around the target value DesNumNgb. A larger tolerance will reduce the number of iterations needed to find the correct radius.

MaxVolumeDiff

REFINEMENT_VOLUME_LIMIT

Maximum tolerated difference in the volume of two neighboring cells. This avoids large cell-size gradients in the mesh which might cause numerical inaccuracies. In case where the volume of a cell exceeds MaxVolumeDiff times the volume of the smallest neighboring cell, the cell is refined, irrespective of other refinement criteria.

MinVolume

REFINEMENT_VOLUME_LIMIT

Global minimum volume a cell is allowed to have, irrespective of other refinement and derefinement criteria.

MaxVolume

REFINEMENT_VOLUME_LIMIT

Global maximum volume a cell is allowed to have, irrespective of other refinement and derefinement criteria.

MeanVolume

NODEREFINE_BACKGROUND_GRID

Mean volume of cells. In case NODEREFINE_BACKGROUND_GRID is activated, cells with more than 10% or this volume will not be derefined. Used for cosmological zoom simulations.

CellMaxAngleFactor

not for VORONOI_STATIC_MESH, requires REGULARIZE_MESH_FACE_ANGLE

Cell “roundness” criterion. The face angle of an interface of a cell is defined as the square root of its area divided by pi, and divided by the distance to the face. The maximum face angle is the maximum of this values for all faces in a given cell. This value is a measure for the “roundness” of a cell. If this value exceeds 1.5 times CellMaxAngleFactor, the cell is not allowed to be refined, i.e. highly elongated cells are not allowed to be refined. In addition to this, if the cell exceeds 0.75 times CellMaxAngleFactor, the movement of the mesh-generating point will deviate from the pure Lagrangian motion to make the cell rounder.

CellShapingFactor

not for VORONOI_STATIC_MESH, not for REGULARIZE_MESH_FACE_ANGLE

Alternative “roundness” criterion. This criterion uses the distance between center of mass and mesh-generating point as a measure for roundness. If this distance exceeds twice the cell radius times CellShapingFactor, the cell will not be refined. If this distance exceeds 0.75 times the cell radius times CellShapingFactor the movement of the mesh-generating point will deviate from pure Lagrangian motion to make the cell rounder.

CellShapingSpeed

not for VORONOI_STATIC_MESH

Determines the speed of the regularization of the mesh. CellShapingSpeed (times a characteristic speed) is the speed by which the mesh is regularized (i.e. speed by which the motion of a mesh-generating point can deviate from Lagrangian motion). Higher values will lead to round cells in fewer timesteps, but will also introduce more numerical noise.

Hydrodynamics¶

LimitUBelowThisDensity

Density threshold for a specific thermal energy lower limit for low density gas.

LimitUBelowCertainDensityToThisValue

Minimum specific thermal energy for low density gas.

MinGasTemp

A minimum temperature floor imposed by the code. This may be set to zero, but it may be desirable to prevent the gas from becoming too cold, e.g. for resolution reasons or because of lower limits in the implemented cooling function. (This value is converted by the code to a minimum thermal energy per unit mass assuming the mean molecular weight of neutral gas).

MinEgySpec

Minimum specific energy allowed in a gas cell. If specific energy is smaller than the value specified here, Arepo will add additional thermal energy in this cell such that it reaches a specific thermal energy of MinEgySpec. This is mainly as a protection against negative specific energies emerging from numerical round-off errors in kinetically or magnetically dominated cells (keep in mind that the thermal energy is recomputed from the total energy in Arepo). In case this parameter is nonzero, it overrides MinGasTemp. If this is zero, internally, MinEgySpec will be calculated via the value of MinGasTemp. In case both MinEgySpec and MinGasTemp are nonzero, MinGasTemp will only set a lower limit to the cooling.

IsoSoundSpeed

ISOTHERM_EQS

Sound speed of gas in runs with isothermal hydrodynamics.

Gravitational softening¶

GasSoftFactor

The gravitational softening length of a gas cell is this value times the cell size, which is calculated as the radius of the volume-equilvalent sphere.

SofteningComovingTypeX

A Plummer equivalent gravitational softening length, to be referenced by one or more specific particle types. For cosmological simulations in comoving coordinates, this is interpreted as a comoving softening length in code length units.

SofteningMaxPhysTypeX

When comoving integration is used, this parameter gives the maximum physical gravitational softening length corresponding to SofteningComovingTypeX (referenced by one or more specific particle types depending on the entries of SofteningTypeOfPartTypeN). Depending on the relative settings of the Comoving and MaxPhys softenings, the code will hence switch from a softening constant in comoving units to one constant in physical units. For example, if the MaxPhys value is exactly half the Comoving value, then particles using this softening type will have comoving softening until z=1 and fixed physical softenings after that point in time. Given in code length units.

SofteningTypeOfPartTypeX

For each particle type in the simulation which is involved in gravitational calculations, a “softening type” must be assigned, i.e. an integer index referring to one of the above SofteningComovingTypeX/SofteningMaxPhysTypeX entry pairs.

MinimumComovingHydroSoftening

for ADAPTIVE_HYDRO_SOFTENING

If this treatment for gas softenings is used, a discrete spectrum of possible softening lengths for gas cells is created at startup. It contains NSOFTTYPES_HYDRO entries, controlled by this ‘minimum’ parameter and the following ‘spacing’ parameter (as a multiplicative factor). Given in code length units.

AdaptiveHydroSofteningSpacing

only for ADAPTIVE_HYDRO_SOFTENING

The logarithmic spacing for the adaptive gas softenings table, as described above. This is the multiplicative factor by which the next discrete softening length larger than the previous one is calculated. Consequently, this must be larger than unity.

Subfind parameters¶

DesLinkNgb

for SUBFIND

The (integer) minimum number of particles/cells, of all types, for Subfind groups. If a Subfind group is identified with fewer than this number of total particles/cells, it is discarded. Note that this means many small friends-of-friends groups (with a nominal minimum number of 32 member particles) may frequently have no sufficiently large Subfind groups, and so will have GroupFirstSub==-1 indicating that that FoF has no central subhalo in addition to no satellite subhalos.

ErrTolThetaSubfind

for SUBFIND

This has the same meaning as the ErrTolTheta parameter, i.e. the tree opening angle used to control the accuracy of the gravity calculation, for use within the Subfind algorithm to compute the gravitational binding potential of halos and substructure candidates.

Cooling and star formation¶

CoolingOn

If set to “1”, gas looses energy through a (optically-thin) radiative cooling model at each timestep. Can only be set to zero if COOLING is not set.

StarformationOn

If set to “1”, gas can be (stochastically) converted into collisionless star particles based on a star formation model. Can only be set to zero if USE_SFR is not set.

TreecoolFile

for COOLING

File path to cooling file. Possible files are available under ./data/.

CritOverDensity

only if USE_SFR is active

The critical (over-)density above which star formation may take place, where the threshold density is then computed as

rho_th = CritOverDensity 3 Omega_b H^2 / (8 pi G)

(redshift independent). Used in place of a critical physical density for comoving integrations.

TemperatureThresh

for USE_SFR

Star formation is prevented for cells which are hotter than the eEOS, and hotter than the TemperatureThresh parameter (in Kelvin). If this parameter is very large (e.g. 1e20), then nothing is changed compared to the base model. If this parameter is small (e.g. 0, 1e4, or 1e5) then star-formation will be prevented in hot halo gas.

CritPhysDensity

for USE_SFR

The critical physical density above which star formation may take place (in cm^-3). Used instead of CritOverDensity for non-comoving runs.

FactorSN

for USE_SFR

The variable giving the mass fraction of massive stars (> 8 Msun) formed for each initial population of stars. This is thus determined by the stellar IMF.

FactorEVP

for USE_SFR

The variable A from the Springel & Hernquist (2003) model, giving the efficiency of the cloud evaporation process.

TempSupernova

for USE_SFR

The “supernova temperature” T_SN of the hot inter-cloud medium in Kelvin, as defined in the above model.

TempClouds

for USE_SFR

The “cold cloud temperature” T_c, in Kelvin, in the Springel & Hernquist (2003) model.

MaxSfrTimescale

for USE_SFR

This is the star-formation timescale t_0 at the threshold density, such that the local star-formation timescale is then calculated as

t_star(rho) = t_0 (rho / rho_th)^-0.5

Sphericaly symmetric simulations¶

CoreRadius

ONEDIMS_SPHERICAL

Inner radius (position of boundary conditions) of 1d spherical simulation.

CoreMass

ONEDIMS_SPHERICAL

Mass enclosed within the inner boundary radius in 1d spherical simulations. Required for gravity calculation.

Parameterfile¶

Initial conditions¶

Output file names and formats¶

Output frequency¶

CPU-time limit and restarts¶

Memory allocation¶

Simulated time span and spatial extent¶

Cosmological parameters¶

System of units¶

Gravitational force accuracy¶

Time integration accuracy¶

Domain decomposition¶

Moving mesh¶

Refinement and derefinement¶

Hydrodynamics¶

Gravitational softening¶

Subfind parameters¶

Cooling and star formation¶

Sphericaly symmetric simulations¶

Arepo

Navigation

Related Topics