Running Inits

Setting the parameter file for the inits package The inits program uses one or more ASCII input files to set parameters, including the details of the power spectrum, the grid size, and output file names. Each line of the parameter file is interpreted independently and can contain only a single parameter. Parameters are specified in the form:

 ParameterName = VALUE

Spaces are ignored, and a parameter statement must be contained on a single line. Lines which begin with the pound symbol (#) are assumed to be comments and ignored.

First, set the parameters in the file. There are a large number of parameters, but many don't need to be set since reasonable default values are provided. Modifying a provided example (see the tutorial page containing many [Tutorials/SampleParameterFiles sample parameter files]) is probably the easiest route, but for reference there is a list of the parameters, their meanings, and their default values.

Generating a single grid initialization (for KRONOS and simple Enzo runs) is relatively straightforward. Generating a multi-grid initialization for Enzo is somewhat more complicated, and we only sketch the full procedure here.

Single Grid Initialization

To run a single grid initialization, you must set at least the following parameters: Rank, GridDims, ParticleDims, as well as the appropriate Cosmology and Power Spectrum parameters. A sample parameter file is available, which sets up a small, single grid cosmology simulation (that is, single grid for the initial conditions, once Enzo is used, additional grids will be created).

After creating or modifying a parameter file, and compiling inits, run the code with:

 inits [-d] parameter_file

Where parameter_file is the name of your modified parameter file (the -d turns on a debug option). This will produce a number of HDF files containing the initial grids and particles, which are in the correct units for use in KRONOS or Enzo.

Multiple-grid Initialization

The multi-grid initialization requires running inits once for each grid to be generated. Typically, one uses this option to examine an object that collapses out of a small region of the top-grid, and so you are interested in simulating this small region with higher initial resolution. We will assume here that two grids are to be used, but the extension to a larger number is relatively straightforward.

The most difficult part is finding the region to be refined. This can be done with an iterative approach. Generate a single-grid initialization and run the simulation at relatively low resolution. Once you have identified an object (see the analysis section), you can use the findinit utility, which is part of the analysis package (see the instructions on obtaining Enzo). After setting the MACHINE_NAME macro in the file amr_mpi/anyl/Makefile, (and making enzo itself, which is a pre-requisite), compile with make findinit. This should generate the findinit utility which can be run with:

 findinit enzo_final_output enzo_initial_output object_file

Here, enzo_initial_output and enzo_final_output refer to the initial and final outputs (usually at z=0) of the low resolution enzo run. The position and radius of the object of interest should be in object_file. This file contains just a single line with four numbers, separated by spaces. The first three specify the position of the object, (as floats ranging from 0 to 1) and the fourth is the radius (again in units of the box size). You can find the position of various objects with enzohop, and its radius with enzo_anyl (see the analysis section).

The way findinit works is to extract all the particles within the sphere centered on the object from the final output and then identify them in the initial output. It returns two points which are the two corners of a volume containing all of the particles at the initial time (although this fails if the region wraps around the edge of the box). It also outputs an ascii file which contains the initial positions of all the particles identified.

To generate a subgrid which corresponds to this region, create two new parameter files (by, for example, copying the old one), one each for the top grid and for the subgrid. The cosmology and power spectrum parameters can be left unchanged, but you will have to modify the grid parameters. Assuming that the refinement factor is 2, you will have to set MaxDims to double the original GridDims, set GridRefinement and ParticleRefinement to 2 in the top grid parameter file (and 1 in the subgrid parameter file). Set StartIndex, and GridDims/ParticleDims in the subgrid to cover the region. The output names should also be modified slightly, adding .0 to the end of the topgrids names and .1 to the sub grid names (this convention is assumed by Enzo when reading more than a single grid).

Once the parameter files are prepared, the top grid can be generated with:

 inits [-d] -s SubGridParameterFile TopGridParameterFile

The -s flag provides the name of the sub-grid parameter file, which is required by inits so that the particles are not replicated in the sub-grid region. The sub-grids are made with the usual command line:

 inits [-d] SubGridParameterFile

!Subgrids with MaxDims of 512 or larger will take some time and require a fair amount of memory since the entire region is generated and then the desired section extracted.

A sample parameter file setup with a top grid and one refined grid is available.

Inits Parameter List

Cosmology Parameters

CosmologyOmegaMatterNow

This is the contribution of all non-relativistic matter (including HDM) to the energy density at the current epoch (z=0), relative to the value required to marginally close the universe. It includes dark and baryonic matter. Default: 1.0

CosmologyOmegaLambdaNow

This is the contribution of the cosmological constant to the energy density at the current epoch, in the same units as above. Default: 0.0

CosmologyOmegaWDMNow

This is the contribution due to warm dark matter alone. Ignored unless PowerSpectrumType = 13 or 14. Default: 0.0

CosmologyOmegaHDMNow

This is the contribution due to hot dark matter alone. Default: 0.0

CosmologyOmegaBaryonNow

The baryonic contribution alone. Default: 0.06

CosmologyComovingBoxSize

The size of the volume to be simulated in Mpc/h (at z=0). Default: 64.0

CosmologyHubbleConstantNow

The Hubble constant at z=0, in units of 100 km/s/Mpc. Default: 0.5

CosmologyInitialRedshift

The redshift for which the initial conditions are to be generated. Default: 20.0

Power Spectrum Parameters

PowerSpectrumType

This integer parameter indicates the routine to be used for generating the power spectrum. Default: 1 The following are currently available:

• 1 - CDM approximation from BBKS (Bardeen et al 1986) as modified by Peacock and Dodds (1994), to include, very roughly, the effect of baryons. This should not be used for high baryon universes or for simulations in which precision in the PS is important.
• 2 - CHDM approximate PS from Ma (1996). Roughly good for hot fractions from 0.05 to 0.3.
• 3 - Power-law (scale-free) spectra.
• 4 - Reads in a power-spectrum from a file (not working).
• 5 - CHDM approximate PS from Ma (1996), modified for 2 equal mass neutrinos.
• 6 - A CDM-like Power spectrum with a shape parameter (Gamma), that is specified by the parameter PowerSpectrumGamma. This kind of power spectrum was used in the late 90's to generate a power-spectrum that fit observations without giving up Omega=1 (considered sacrosanct at the time). The spectral shape is the same as the BBKS power spectrum (type 1; Bardeen et al 1986) but with a free parameter (Gamma) that allowed the spectral shape to be modified independently of the cosmological parameters (Gamma was supposed to be roughly Omega * h). It is now only of historical interest.
• 11 - The Eisenstein and Hu fitting functions for low and moderate baryon fraction, including the case of one massive neutrino.
• 12 - The Eisenstein and Hu fitting functions for low and moderate baryon fraction, for the case of two massive neutrinos.
• 13 - A Warm Dark Matter (WDM) power spectrum based on the formulae of Bode et al. (2001 ApJ 556, 93). The WDM equivalent of the Eisenstein & Hu fitting function with one massive neutrino (so a WDM version of #11).
• 14 - A Warm Dark Matter (WDM) power spectrum based on the formulae of Bode et al. (2001 ApJ 556, 93). The WDM equivalent of the CDM BBKS approximation of Bardeen et al 1986 (the WDM version of #1).
• 20 - A transfer function from CMBFast is input for this option, based on the filenames described below.

PowerSpectrumSigma8

The amplitude of the linear power spectrum at z=0 as specified by the rms amplitude of mass-fluctuations in a top-hat sphere of radius 8 Mpc/h. Default: 0.6

PowerSpectrumPrimordialIndex

This is the index of the mass power spectrum before modification by the transfer function. A value of 1 corresponds to the scale-free primordial spectrum. Default: 1.0.

PowerSpectrumRandomSeed

This is the initial seed for all random number generation, which should be negative. The random number generator (Numerical Recipes RAN3) is machine-independent, so the same seed will produce the same results (with other parameters unchanged). Note also that because the spectrum is sampled strictly in order of increasing k-amplitude, the large-scale power will be the same even if you increase or decrease the grid size. Default: -123456789

PowerSpectrumkcutoff

The spectrum is set to zero above this wavenumber (i.e. smaller scales are set to zero), which is in units of 1/Mpc. It only works for power spectrum types 1-6. A value of 0 means no cutoff. Default: 0.0

PowerSpectrumkmin/kmax

These two parameters control the range of the internal lookup table in wavenumber (units 1/Mpc). Reasonably sized grids will not require changes in these parameters. Defaults: kmin = 1e-3, kmax = 1e+4.

PowerSpectrumNumberOfkPoints

This sets the number of points in the PS look-up table that is generated for efficiency purposes. It should not require changing. Default: 10000.

PowerSpectrumFileNameRedshiftZero

For input power spectra, such as those from CMBFAST, two transfer functions are required: one at z=0 to fix the amplitude (via Sigma8) and the other at the initial redshift to give the shape and amplitude relative to z=0. No default.

PowerSpectrumFileNameInitialRedshift

see above.

PowerSpectrumGamma

The shape parameter (Omega*h); ignored unless PowerSpectrumType = 6.

PowerSpectrumWDMParticleMass

The mass of the dark matter particle in KeV for the Bode et al. warm dark matter (WDM) case. Ignored unless PowerSpectrumType = 13 or 14. Default: 1.0.

PowerSpectrumWDMDegreesOfFreedom

The number of degrees of freedom of the warm dark matter particles for the Bode et al. warm dark matter model. Ignored unless PowerSpectrumType = 13 or 14. Default: 1.5.

PowerSpectrumGamma

The shape parameter (Omega*h); ignored unless PowerSpectrumType = 6.

Grid Parameters: Basic

Rank

Dimensionality of the problem, 1 to 3 (warning: not recently tested for Rank !=2). Default: 3

GridDims

This sets the actual dimensions of the baryon grid that is to be created (and so it may be smaller than MaxDims in some cases). Example: 64 64 64 No default.

ParticleDims

Dimensions of the particle grid that is to be created. No default.

InitializeGrids

Flag indicating if the baryon grids should be produced (set to 0 if inits is being run to generate particles only). Default: 1

InitializeParticles

Flag indicating if the particles should be produced (set to 0 if inits is being run to generate baryons only). Default: 1

ParticlePositionName

This is the name of the particle position output file. This HDF file contains one to three Scientific Data Sets (SDS), one for dimensional component. Default: ParticlePositions

ParticleVelocityName

The particle velocity file name, which must(!) be different from the one above, otherwise the order of the SDS's will be incorrect. Default: ParticleVelocities

ParticleMassName

This is the name of the particle mass file, which is generally not needed (enzo generates its own masses if not provided). Default: None

GridDensityName

The name of the HDF which contains the grid density SDS. Default: GridDensity

GridVelocityName

The name of the HDF file which contains the SDS's for the baryonic velocity (may be the same as GridDensityName). Default: GridVelocity

Grid Parameters: Advanced

MaxDims

All dimensions are specified as one to three numbers deliminated by spaces (and for those familiar with the KRONOS or ZEUS method of specifying dimensions, the ones here do not include ghost zones). An example is: 64 64 64. MaxDims are the dimensions of the conceptual high-resolution grid that covers the entire computational domain. For a single-grid initialization this is just the dimension of the grid (or of the particle grid if there are more particles than grid points). For multi-grid initializations, this is the dimensions of the grid that would cover the region at the highest resolution that will be used. It must be identical across all parameter files (for multi-grid initializations). The default is the maximum of GridDims or ParticleDims, whichever is larger (in other words unless you are using a multi-grid initialization, this parameter does not need to be set). Confused yet?

GridRefinement

This integer is the sampling, for the baryon grid, in each dimension, relative to MaxDims. For single-grid initializations, this is generally 1. For multi-grids, it is the refinement factor relative to the finest level. In other words, if the grid covered the entire computational region, then each value in MaxDims would equal GridDims times the GridRefinement factor. Default: 1

ParticleRefinement

Similar function as above, but for the particles. Note that it can also be used to generate fewer particles than grids (i.e. the GridRefinement and ParticleRefinement factors do not have to be the same). Default: 1

StartIndex

For single-grid initializations, this should be the zero vector. For multi-grid initializations it specifies the index (a triplet of integers in 3D) of the left-hand corner of the grid to be generated. It is specified in terms of the finest conceptual grid and so ranges from 0 to MaxDims-1. Note also that for AMR, the start and end of a sub-grid must lie on the cell-boundary of it's parent. That means that this number must be divisible by the Refinement factor. The end of the sub-grid will be at index: StartIndex + GridRefinement*GridDims. The co-ordinate system used by this parameter is always the unshifted one (i.e. it does not change if NewCenter is set). StartIndex may also be set by the next parameter which is in the shifted co-ordinate system. Default: 0 0 0

StartIndexInNewCenterTopGridSystem

This is an alternative mechanism for setting StartIndex (for a multi-grid initialization). It differs in two ways: (1) the index is specified in the root (or top) grid co-ordinate system so that is ranges from zero to GridDims-1 of the root grid; (2) it is in the shifted co-ordinate system, so that setting NewCenter (or NewCenterFloat) changes the meaning of this parameter. Note that in some ways this is easier, since if NewCenter is set, then this parameter is always relative to the center of the root grid (see the multi-grid initialization example above). If set, this over-rides the value of StartIndex. Also, if used, this parameter requires that the next one be set as well as the RootGridDims parameter. Default: none

EndIndexInNewCenterTopGridSystem

This parameter forms a pair with the previous parameter and specifies the ending index (including the final point) of the region to be refined. As before, it is in the shifted top grid co-ordinate system. If set, this over-rides the setting of GridDims. Default: none

RootGridDims

This informative parameter tells inits the value of the root grid dimensions (in a multi-grid initialization). It is required if the parameters StartIndex/EndIndexInNewCenterTopGridSystem or NewCenterFloat are specified. Default: none

NewCenter

In some cases, for multi-grid initializations, the end of the sub-grid (as calculated above) may extend beyond the edge of the computational volume, and be greater than MaxDims-1. This happens when the region of interest wraps around the grid boundary. In this case, it is desirable to shift the volume (which is periodic) so that this no longer occurs. This can be done by specifying a value for NewCenter, which makes this index (specified in terms of the finest conceptual grid, i.e. MaxDims) the new center. It affects all grids, including the top grid. The value of the index+1 must be divisible by the GridRefinement factor of the root grid. Since these rules are somewhat obscure, you can also set NewCenter by specifying a float location (see below). Default: MaxDims/2 - 1

NewCenterFloat

This triplet of float values between 0 and 1 sets the location of the new center of the grid (see above). It is an easier alternative to setting the integer NewCenter parameter itself. The nearest location which meets the new center requirements outlined above will be chosen. Note that if you do specify NewCenterFloat, then the RootGridDims parameter must also be set. Default: none