Enzo v2.1 documentation

Writing Enzo Parameter Files

Putting together a parameter file for Enzo is possibly the most critical step when setting up a simulation, and is certainly the step which is most fraught with peril. There are over 200 parameters that one can set - see Enzo Parameter List for a complete listing. For the most part, defaults are set to be sane values for cosmological simulations, and most physics packages are turned off by default, so that you have to explicitly turn on modules. All physics packages are compiled into Enzo (unlike codes such as ZEUS-MP 1.0, where you have to recompile the code in order to enable new physics).

It is inadvisable for a novice to put together a parameter file from scratch. Several parameter files are available for download at Sample inits and Enzo parameter files. The simulations include:

  • dark matter-only unigrid and AMR simulations,
  • dark matter + hydro unigrid and AMR simulations,
  • an AMR dm + hydro simulation with multiple nested grids and a limited refinement region.

In order to make the most of this tutorial it is advisable to have one or more of these parameter files open while reading this page. For the purposes of this tutorial we assume that the user is putting together a cosmology simulation and has already generated the initial conditions files using inits.

All parameters are put into a plain text file (one parameter per line), the name of which is fed into Enzo at execution time at the command line. Typically, a parameter is set by writing the parameter name, an equals sign, and then the parameter value or values, like this:

NumberOfBufferZones = 3

You must leave at least one space between the parameter, the equals sign, and the parameter value. It’s fine if you use more than one space - after the first space, whitespace is unimportant. All lines which start with a # (pound sign) are treated as comments and ignored. In addition, you can have inline comments by using the same pound sign, or two forward slashes // after the parameter line.

NumberOfBufferZones = 3 // More may be needed depending on physics used.

Initialization parameters

Complete descriptions of all initialization parameters are given here. The most fundamental initialization parameter you have to set is ProblemType, which specifies the type of problem to be run, and therefore the way that Enzo initiates the data. A cosmology simulation is problem type 30. As started before, for the purposes of this introduction I’m assuming that you are generating a cosmology simulation, so you would put this line in the parameter file:

ProblemType = 30

TopGridRank specifies the spatial dimensionality of your problem (1, 2 or 3 dimensions), and must be set. TopGridDimensions specifies the number of root grid cells along each axis. For a 3D simulation with 128 grid cells along each axis on the root grid, put this in the parameter file:

TopGridRank = 3
TopGridDimensions = 128 128 128

Additionally, you must specify the names of the initial conditions files with contain the baryon density and velocity information and the dark matter particle positions and velocities. These are controlled via the parameters CosmologySimulationDensityName, CosmologySimulationVelocity[123]Name (where 1, 2 and 3 correspond to the x, y and z directions, respectively), CosmologySimulationParticlePositionName and CosmologySimulationParticleVelocityName. Assuming that the baryon velocity information is all in a single file, and that the baryon density and velocity file names are GridDensity and GridVelocities, and that the particle position and velocity files are named ParticlePositions and ParticleVelocities, these parameters would be set as follows:

CosmologySimulationDensityName = GridDensity
CosmologySimulationVelocity1Name = GridVelocities
CosmologySimulationVelocity2Name = GridVelocities
CosmologySimulationVelocity3Name = GridVelocities
CosmologySimulationParticlePositionName = ParticlePositions
CosmologySimulationParticleVelocityName = ParticleVelocities

Some more advanced are parameters in the Initialization Parameters section control domain and boundary value specifications. These should NOT be altered unless you really, really know what you’re doing!

Cosmology

Complete descriptions of all cosmology parameters are given here and here. ComovingCoordinates determines whether comoving coordinates are used or not. In practice, turning this off turns off all of the cosmology machinery, so you want to leave it set to 1 for a cosmology simulation. CosmologyInitialRedshift and CosmologyFinalRedshift control the start and end times of the simulation, respectively. CosmologyHubbleConstantNow sets the Hubble parameter, and is specified at z=0 in units of 100 km/s/Mpc. CosmologyComovingBoxSize sets the size of the box to be simulated (in units of Mpc/h) at z=0. CosmologyOmegaBaryonNow, CosmologyOmegaMatterNow, CosmologyOmegaCDMNow and CosmologyOmegaLambdaNow set the amounts of baryons, total matter, dark matter and vacuum energy (in units of the critical density at z=0). An addition to the standard baryon fields that can be initialized, one can create a metal tracer field by turning on CosmologySimulationUseMetallicityField. This is handy for simulations with star formation and feedback (described below). For example, in a cosmology simulation with box size 100 Mpc/h with approximately the cosmological parameters determined by WMAP, which starts at z=50 and ends at z=2, and has a metal tracer field, we put the following into the parameter file:

ComovingCoordinates = 1
CosmologyInitialRedshift = 50.0
CosmologyFinalRedshift = 2.0
CosmologyHubbleConstantNow = 0.7
CosmologyComovingBoxSize = 100.0
CosmologyOmegaBaryonNow = 0.04
CosmologyOmegaMatterNow = 0.3
CosmologyOmegaCDMNow = 0.26
CosmologyOmegaLambdaNow = 0.7
CosmologySimulationUseMetallicityField = 1

Gravity and Particle Parameters

The parameter list sections on gravity particle positions are here and here, respectively. The significant gravity-related parameters are SelfGravity, which turns gravity on (1) or off (0) and GravitationalConstant, which must be 1 in cosmological simulations. BaryonSelfGravityApproximation controls whether gravity for baryons is determined by a quick and reasonable approximation. It should be left on (1) in most cases. For a cosmological simulation with self gravity, we would put the following parameters into the startup file:

SelfGravity = 1
GravitationalConstant = 1
BaryonSelfGravityApproximation = 1

We discuss some AMR and parallelization-related particle parameters in later sections.

Adiabatic hydrodynamics parameters

The parameter listing section on hydro parameters can be found here. The most fundamental hydro parameter that you can set is HydroMethod, which lets you decide between the Piecewise Parabolic Method (aka PPM; option 0), or the finite-difference method used in the Zeus astrophysics code (option 2). PPM is the more advanced and optimized method. The Zeus method uses an artificial viscosity-based scheme and may not be suited for some types of work. When using PPM in a cosmological simulation, it is important to turn DualEnergyFormalism on (1), which makes total-energy schemes such as PPM stable in a regime where there are hypersonic fluid flows, which is quite common in cosmology. The final parameter that one must set is Gamma, the ratio of specific heats for an ideal gas. If MultiSpecies (discussed later in Radiative Cooling and UV Physics Parameters) is on, this is ignored. For a cosmological simulation where we wish to use PPM and have Gamma = 5/3, we use the following parameters:

HydroMethod = 0
DualEnergyFormalism = 1
Gamma = 1.66667

In addition to these three parameters, there are several others which control more subtle aspects of the two hydro methods. See the parameter file listing of hydro parameters for more information on these.

One final note: If you are interested in performing simulations where the gas has an isothermal equation of state (gamma = 1), this can be approximated without crashing the code by setting the parameter Gamma equal to a number which is reasonably close to one, such as 1.001.

AMR Hierarchy Control Parameters

These parameters can be found in the parameter list page here. They control whether or not the simulation uses adaptive mesh refinement, and if so, the characteristics of the adaptive meshing grid creation and refinement criteria. We’ll concentrate on a simulation with only a single initial grid first, and then discuss multiple levels of initial grids in a subsection.

The most fundamental AMR parameter is StaticHierarchy. When this is on (1), the code is a unigrid code. When it is off (0), adaptive mesh is turned on. RefineBy controls the refinement factor - for example, a value of 2 means that a child grid is twice as highly refined as its parent grid. It is important to set RefineBy to 2 when using cosmology simulations - this is because if you set it to a larger number (say 4), the ratio of particle mass to gas mass in a cell grows by a factor of eight during each refinement, causing extremely unphysical effects. MaximumRefinementLevel determines how many possible levels of refinement a given simulation can attain, and MaximumGravityRefinementLevel defines the maximum level at which gravitational accelerations are computed. More highly refined levels have their gravitational accelerations interpolated from this level, which effectively provides smoothing of the gravitational force on the spatial resolution of the grids at MaximumGravityRefinementLevel. A simulation with AMR turned on, where there are 6 levels of refinement (with gravity being smoothed on level 4) and where each child grid is twice as highly resolved as its parent grid would have these parameters set as follows:

StaticHierarchy = 0
RefineBy = 2
MaximumRefinementLevel = 6
MaximumGravityRefinementLevel = 4

Once the AMR is turned on, you must specify how and where the hierarchy refines. The parameter CellFlaggingMethod controls the method in which cells are flagged, and can be set with multiple values. We find that refining by baryon and dark matter mass (options 2 and 4) are typically useful in cosmological simulations. The parameter MinimumOverDensityForRefinement allows you to control the overdensity at which a given grid is refined, and can is set with multiple values as well. Another very useful parameter is MinimumMassForRefinementLevelExponent, which modifies the cell masses/overdensities used for refining grid cells. See the parameter page for a more detailed explanation. Leaving this with a value of 0.0 ensures that gas mass resolution in dense regions remains more-or-less Lagrangian in nature. Negative values make the refinement super-Lagrangian (ie, each level has less gas mass per cell on average than the coarser level above it) and positive values make the refinement sub-lagrangian. In an AMR simulation where the AMR triggers on baryon and dark matter overdensities in a given cell of 4.0 and 8.0, respectively, where the refinement is slightly super-Lagrangian, these paramaters would be set as follows:

CellFlaggingMethod = 2 4
MinimumOverDensityForRefinement = 4.0 8.0
MinimumMassForRefinementLevelExponent = -0.1

At times it is very useful to constrain your simulation such that only a small region is adaptively refined (the default is to refine over an entire simulation volume). For example, if you wish to study the formation of a particular galaxy in a very large volume, you may wish to only refine in the small region around where that galaxy forms in your simulation in order to save on computational expense and dataset size. Two parameters, RefineRegionLeftEdge and RefineRegionRightEdge allow control of this. For example, if we only want to refine in the inner half of the volume (0.25 - 0.75 along each axis), we would set these parameters as follows:

RefineRegionLeftEdge = 0.25 0.25 0.25
RefineRegionRightEdge = 0.75 0.75 0.75

This pair of parameters can be combined with the use of nested initial grids (discussed in the next subsection) to get simulations with extremely high dark matter mass and spatial resolution in a small volume at reasonable computational cost.

Multiple nested grids

At times it is highly advantageous to use multiple nested grids. This is extremely useful in a situation where you are interested in a relatively small region of space where you need very good dark matter mass resolution and spatial resolution while at the same time still resolving large scale structure in order to preserve gravitational tidal forces. An excellent example of this is formation of the first generation of objects in the universe, where we are interested in a relatively small (106 solar mass) halo which is strongly tidally influenced by the large-scale structure around it. It is important to resolve this halo with a large number of dark matter particles in order to reduce frictional heating, but the substructure of the distant large-scale structure is not necessarily interesting, so it can be resolved by very massive particles. One could avoid the complication of multiple grids by using a single very large grid - however, this would be far more computationally expensive.

Let us assume for the purpose of this example that in addition to the initial root grid grids (having 128 grid cells along each axis) there are two subgrids, each of which is half the size of the one above it in each spatial direction (so subgrid 1 spans from 0.25-0.75 in units of the box size and subgrid 2 goes from 0.375-0.625 in each direction). If each grid is twice as highly refined spatially as the one above it, the dark matter particles on that level are 8 times smaller, so the dark matter mass resolution on grid #2 is 64 times better than on the root grid, while the total number of initial grid cells only increases by a factor of three (since each grid is half the size, but twice as highly refined as the one above it, the total number of grid cells remains the same). Note: See the page on generating initial conditions for more information on creating this sort of set of nested grids.

When a simulation with more than one initial grid is run, the total number of initial grids is specified by setting CosmologySimulationNumberOfInitialGrids. The parameter CosmologySimulationGridDimension[#] is an array of three integers setting the grid dimensions of each nested grid, and CosmologySimulationGridLeftEdge[#] and CosmologySimulationGridRightEdge[#] specify the left and right edges of the grid spatially, in units of the box size. In the last three parameters, “#” is replaced with the grid number. The root grid is grid 0. None of the previous three parameters need to be set for the root grid. For the setup described above, the parameter file would be set as follows:

CosmologySimulationNumberOfInitialGrids = 3
CosmologySimulationGridDimension[1] = 128 128 128
CosmologySimulationGridLeftEdge[1] = 0.25 0.25 0.25
CosmologySimulationGridRightEdge[1] = 0.75 0.75 0.75
CosmologySimulationGridLevel[1] = 1
CosmologySimulationGridDimension[2] = 128 128 128
CosmologySimulationGridLeftEdge[2] = 0.375 0.375 0.375
CosmologySimulationGridRightEdge[2] = 0.625 0.625 0.625
CosmologySimulationGridLevel[2] = 2

Multiple initial grids can be used with or without AMR being turned on. If AMR is used, the parameter MinimumOverDensityForRefinement must be modified as well. It is advisable to carefully read the entry for this parameter in the parameter list (in this section). The minimum overdensity needs to be divided by r(d*l), where r is the refinement factor, d is the dimensionality, and l is the zero-based highest level of the initial grids. So if we wish for the same values for MinimumOverDensityForRefinement used previous to apply on the most highly refined grid, we must divide the set values by 2(3*2) = 64. In addition, one should only refine on the highest level, so we must reset RefineRegionLeftEdge and RefineRegionRightEdge. The parameters would be reset as follows:

RefineRegionLeftEdge = 0.375 0.375 0.375
RefineRegionRightEdge = 0.625 0.625 0.625
MinimumOverDensityForRefinement = 0.0625 0.125

A note: When creating multi-level intial conditions, make sure that the initial conditions files for all levels have the same file name (ie, GridDensity), but that each file has an extension which is an integer corresponding to its level. For example, the root grid GridDensity file would be GridDensity.0, the level 1 file would be GridDensity.1, and so forth. The parameters which describe file names (discussed above in the section on initialization parameters) should only have the file name to the left of the period the period (as in a simulation with a single initial grid), ie,

CosmologySimulationDensityName = GridDensity

Nested Grids and Particles

When initializing a nested grid problem, there can arise an issue of lost particles as a result of running ring. Please see Particles in Nested Grid Cosmology Simulations for more information.

I/O Parameters

These parameters, defined in more detail in Controlling Enzo data output, control all aspects of Enzo’s data output. One can output data in a cosmological simulation in both a time-based and redshift-based manner. To output data regularly in time, one sets dtDataDump to a value greater than zero. The size of this number, which is in units of Enzo’s internal time variable, controls the output frequency. See the Enzo user’s manual section on output format for more information on physical units. Data can be output at specific redshifts as controlled by CosmologyOutputRedshift[#], where # is the number of the output dump (with a maximum of 10,000 zero-based numbers). The name of the time-based output files are controlled by the parameter DataDumpName and the redshift-based output files have filenames controlled by RedshiftDumpName. For example, if we want to output data every time the code advances by dt=2.0 (in code units) with file hierarchiess named time_0000, time_0001, etc., and ALSO output explicitly at redshifts 10, 5, 3 and 1 with file hierarchy names RedshiftOutput0000, RedshiftOutput0001, etc., we would set these parameters as follows:

dtDataDump = 2.0
DataDumpName = time_
RedshiftDumpName = RedshiftOutput
CosmologyOutputRedshift[0] = 10.0
CosmologyOutputRedshift[1] = 5.0
CosmologyOutputRedshift[2] = 3.0
CosmologyOutputRedshift[3] = 1.0

Note that Enzo always outputs outputs data at the end of the simulation, regardless of the settings of dtDataDump and CosmologyOutputRedshift.

Radiative Cooling and UV Physics Parameters

Enzo comes with multiple ways to calculate baryon cooling and a metagalactic UV background, as described in detail here. The parameter RadiativeCooling controls whether or not a radiative cooling module is called for each grid. The cooling is calculated either by assuming equilibrium cooling and reading in a cooling curve, or by computing the cooling directly from the species abundances. The parameter MultiSpecies controls which cooling module is called - if MultiSpecies is off (0) the equilibrium model is assumed, and if it is on (1 or 2) then nonequilibrium cooling is calculated using either 6 or 9 ionization states of hydrogen and helium (corresponding to MultiSpecies = 1 or 2, respectively). The UV background is controlled using the parameter RadiationFieldType. Currently there are roughly a dozen backgrounds to choose from. RadiationFieldType is turned off by default, and can only be used when Multispecies = 1. For example, if we wish to use a nonequilibrium cooling model with a Haardt and Madau background with qalpha= -1.8, we would set these parameters as follows:

RadiativeCooling = 1
MultiSpecies = 1
RadiationFieldType = 2

Star Formation and Feedback Physics Parameters

Enzo has multiple routines for star formation and feedback. Star particle formation and feedback are controlled separately, by the parameters StarParticleCreation and StarParticleFeedback. Multiple types of star formation and feedback can be used, e.g. models for Pop III stars for metal-free gas and models for Pop II stars for metal-enriched gas. These routines are disabled when these parameters are set equal to 0. These parameters are bitwise to allow multiple types of star formation routines can be used in a single simulation. For example if methods 1 and 3 are desired, the user would specify 10 (21+ 23), or if methods 0, 1 and 4 are wanted, this would be 19 (20+ 21+ 24). See Star Formation and Feedback Parameters for more details.

They are turned on when the i-th bit is flagged. The value of 2 is the recommended value. The most commonly used routines (2) are based upon an algorithm by Cen & Ostriker, and there are a number of free parameters. Note that it is possible to turn star particle formation on while leaving feedback off, but not the other way around.

For the star particle creation algorithm, stars are allowed to form only in cells where a minimum overdensity is reached, as defined by StarMakerOverDensityThreshold. Additionally, gas can only turn into stars with an efficiency controlled by StarMakerMassEfficiency and at a rate limited by StarMakerMinimumDynamicalTime, and the minimum mass of any given particle is controlled by the parameter StarMakerMinimumStarMass, which serves to limit the number of star particles. For example, if we wish to use the “standard” star formation scenario where stars can only form in cells which are at least 100 times the mean density, with a minimum dynamical time of 106 years and a minimum mass of 107 solar masses, and where only 10% of the baryon gas in a cell can be converted into stars in any given timestep, we would set these parameters as follows:

StarParticleCreation = 2
StarMakerOverDensityThreshold = 100.0
StarMakerMassEfficiency = 0.1
StarMakerMinimumDynamicalTime = 1.0e6
StarMakerMinimumStarMass = 1.0e7

Star particles can provide feedback into the Inter-Galactic Medium via stellar winds, thermal energy and metal pollution. The parameter StarMassEjectionFraction controls the fraction of the total initial mass of the star particle which is eventually returned to the gas phase. StarMetalYield controls the mass fraction of metals produced by each star particle that forms, and StarEnergyToThermalFeedback controls the fraction of the rest-mass energy of the stars created which is returned to the gas phase as thermal energy. Note that the latter two parameters are somewhat constrained by theory and observation to be somewhere around 0.02 and 1.0e-5, respectively. The ejection fraction is poorly constrained as of right now. Also, metal feedback only takes place if the metallicity field is turned on (CosmologySimulationUseMetallicityField = 1). As an example, if we wish to use the ‘standard’ star feedback where 25% of the total stellar mass is returned to the gas phase, the yield is 0.02 and 10-5 of the rest mass is returned as thermal energy, we set our parameters as follows:

StarParticleFeedback = 2
StarMassEjectionFraction = 0.25
StarMetalYield = 0.02
StarEnergyToThermalFeedback = 1.0e-5
CosmologySimulationUseMetallicityField = 1

When using the star formation and feedback algorithms it is important to consider the regime of validity of our assumptions. Each “star particle” is supposed to represent an ensemble of stars, which we can characterize with the free parameters described above. This purely phenomenological model is only reasonable as long as the typical mass of the star particles is much greater than the mass of the heaviest stars so that the assumption of averaging over a large population is valid. When the typical star particle mass drops to the point where it is comparable to the mass of a large star, these assumptions must be reexamined and our algorithms reformulated.

IO Parallelization Options

One of Enzo’s great strengths is that it is possible to do extremely large simulations on distributed memory machines. For example, it is possible to intialize a 10243 root grid simulation on a linux cluster where any individual node has 1 or 2 GB of memory, which is on the order of 200 times less than the total dataset size! This is possible because the reading of initial conditions and writing out of data dumps is fully parallelized - at startup, when the parameter ParallelRootGridIO is turned on each processor only reads the portion of the root grid which is within its computational domain, and when ParallelParticleIO is turned on each processor only reads in the particles within its domain (though preprocessing is needed - see below). Additionally, the parameter Unigrid should be turned on for simulations without AMR, as it saves roughly a factor of two in memory on startup, allowing the code to perform even larger simulations for a given computer size. If we wish to perform an extremely large unigrid simulation with parallel root grid and particle IO, we would set the following parameters:

ParallelParticleIO = 1
ParallelRootGridIO = 1
Unigrid = 1

AMR simulations can be run with ParallelRootGridIO and ParallelParticleIO on, though you must be careful to turn off the Unigrid parameter. In addition, it is important to note that in the current version of Enzo you must run the program called “ring” on the particle position and velocity files before Enzo is started in order to take advantage of the parallel particle IO. Assuming the particle position and velocity files are named ParticlePositions and ParticleVelocities, respectively, this is done by running:

mpirun -np [N] ring ParticlePositions ParticleVelocities

Where mpirun is the executable responsible for running MPI programs and “-np [N]” tells the machine that there are [N] processors. This number of processors must be the same as the number which Enzo will be run with!

Notes

This page is intended to help novice Enzo users put together parameter files for their first simulation and therefore is not intended to be an exhaustive list of parameters nor a complete description of each parameter mentioned. It would be wise to refer to the Enzo user guide’s Enzo Parameter List for a more-or-less complete list of AMR parameters, some of which may be extremely useful for your specific application.