Analyzing AMR output

1. 2D projections - The code has the built-in ability to make two-dimensional projections, at a specified resolution, of a number of quantities (tailored for cosmology) along any axis of a given three-dimensional region. The resulting 2D HDF SDS's can then be imaged with a number of tools, including IDL.
2. Extractions - A region (generally 3D, but this option also works for 1 and 2-dimensions) can be extracted with a uniform resolution and saved as a single grid. This is useful for other packages developed for single-grid codes. This option is also built into the amr code.
3. Peakfinder - In the analysis package (amr_mpi/anyl), there is a routine which can find peaks in the baryon or dark-matter distribution, subject to a number of qualifications (such as minimum separation).  [Note: enzohop is recommended for most peak finding].
4. Hop halo finder - Also in the analysis package is a version of Eisenstein & Hut's hop halo finder, as applied to the dark matter.
5. Profiles - Radial profile of density and many other quantities can be generated with another analysis routine, given an object's position.
6. Particle representation - The code also has the ability to convert the grid into a set of particle positions and densities, temperatures, etc. This can then be read into a particle-analysis code.

2D projections

enzo -p dim [-l level] [-m] [-b point1] [-f point2] amr_filename

an example might be:

enzo -p 1 -l 6 -b 0.4 0.4 0.4 -f 0.6 0.6 0.6 data0015

The -p option, which specifies the dimension along which the projection is to occur, and the amr output_filename are the only arguments required. The projection dimension (dim) is an integer from 0 to 2, and indicates along which dimension the projection occurs. For example, a projection along axis-0 produces an image with y-z axis.

The -l option specifies the resolution of the image, by indicating a level at which the projection will occur. The integer value level is zero-based so -l 0  produces an image with the same resolution as the root grid. Levels larger than the maximum in the output_filename may be used. The default value is 0.

The -m option smooths the image by doing a linear interpolation between coarse-grid points. If this option is not invoked, the result will be pixelated in regions in which the pixels are smaller than the grid cells (although this may be useful information). This option takes somewhat longer. The default is no smoothing.

Finally, there are two ways to specify the three-dimensional region in which the projection is to occur, one of which is shown in the commend-line above. This uses the -b and -f (begin and finish) flags. These flags each take a triplet (in 3D) of floats which specify the the two corners of the projection volume. The units are those of the problem (set by DomainLeftEdge and DomainRightEdge). For cosmology problems, this means numbers that range from 0 to 1. The default is the entire domain.

The other mechanism for specifying the projection volume is to specify coordinate indexes. This is done with the -s and -e flags, each of which take a triplet of integers. The integers refer to index positions (zero-based) within that level. This means the numbers should range between 0 and n*r^l-1 where n is the size of the top grid, r is the refinement factor and l is the level. The advantage of this method is that the size of the region can be precisely set, the disadvantage is the calculation is a bit more difficult. Although these two methods can be mixed (by specifying one corner with one method and the other corner with the other method), it is undefined to specify one corner twice. Finally, the error checking on these values is not great, and specifying a region with negative volume or one that goes off the edge may result in a core dump rather than an error message.

The result is placed in the file amr.project and consists of 2D scientific data sets (HDF format) of the following quantities (subject to change):

• baryon density (M(solar)/Mpc^3)
• a field proportional to the bolometric free-free emission (but see below)
• dark matter density (M(solar)/Mpc^3)
• temperature (K, weighted by free-free emission)
• maximum level along projection
• the y-parameter of thermal SZ effect
• the DT/T value of the kinematic SZ effect
• The mean density-weighted fractional metallicity of the gas along the line of sight
• The star particle density (M(solar)/Mpc^3)

Extractions

enzo -x  [-l level] [-b point1] [-f point2] amr_filename

The  meaning of the level (-l) and region (-b, -f) flags are the same as for the projection (see above).

The output is a standard grid file and so consists of an HDF file with a number of scientific data sets.  The scientific data sets are named and have dimensional axis.  The units are code units with the exception of temperature, with is in degrees K.  See the file CosmologyGetUnits.C for a definition of code units, or look in the ascii output file (search for lines which start DataCGSConversionFactor = ...).

Peakfinder

make findpeaks

And should produce the executable amr/anyl/findpeaks.  It is run with the command-line:

findpeaks [-n number] [-m min_density] [-s separation] amr_filename peak_filename

The algorithm reads in the amr output file amr_filename and looks for peaks (a density larger than it's 26 neighbours) in the baryon density distribution.  The result is output as a series of locations (float triplets between 0 and 1) to the file peak_filename, sorted by the peak density.

The -n option takes an integer argument and returns the number largest peaks.  Default: 1

The flag -m tells the algorithm to only check peaks width densities larger than the float value min_density which, for cosmology, is in units of the mean density of non-relativistic mass (at the redshift at which the output occurred).  This option is mostly useful for speeding up the algorithm, since a large value for the minimum density can drastically cut down the number of cells that need to be checked.  Default: 1

The last option, -s,  specified the minimum separation between peaks (the lower density peak is discarded), and the float value separation should be in terms of comoving Mpc/h.  Default: 0

This peakfinder really does just find local peaks -- a halo finder (see below) is probably what you're looking for.

Halofinder

enzohop [-b #] [-f #] [-t #] [-g] [-d] amr_filename

The only required argument, amr_filename, is the name of an amr output file.

The optional flags that specify a region to work on (-b for begin and -f for finish) are as described in the projection section.  Default: the whole region

The next flag (-t) takes a float and specifies the most important threshold used in hop (the outer density definition).  Default: 160

The -g flag indicates that baryon grid points should be converted to particles and passed into hop (along with the dark matter).  This is not recommended.  Finally, the -d flag is the usual debugging flag.

The output is placed into a number of files, only one of which is described here (see hop for the others).  HopAnalysis.out contains a list of the results groups, their particle number, mass and the location of the densest particle.

Profiler

enzo_anyl  amr_filename   anyl_parameter_file

The first argument, amr_filename, is the name of an amr output file, and the second argument is the name of an ascii file which contains some parameters for the analysis routine.  An example of this file should be in amr_mpi/anyl/AnalyzeClusterParameterFile.  The format of the parameters is the same as for the enzo code itself.  The parameters are:

• Rinner - The inner edge of the profile in comoving Mpc.  Default: 0.0001 of the ComovingBoxSize
• Router - The outer edge of the profile in comoving Mpc.  This should be well outside the expected virial radius of the object.  Default: 0.1 of the ComovingBoxSize
• CenterPosition - A triplet of floats from 0 to 1 specifying the location of the center.  This parameter is ignored if CenterListName is set.  Default: if left unspecified, the location of the maximum density in the volume is used.
• NumberOfPoints - An integer: the number of points in the profile.  The radial shells are spaced in equal logarithmic intervals in radius (except for the first point)   Default: 16
• VirialDensity - This float indicates the overdensity, relative to the critical (not mean) density, that is to be used to define the virial radius.  Default: 200
• CenterListName - The name of a file containing a list of center positions (each line should contain a triplet of floats, between 0 and 1).  Up to 1000 positions may be specified.  If not set, then the parameter CenterPosition is used to define a single center.  Default: NULL
• MeanVelocityVirialFraction - This is the fraction of the virial radius which is used to determine the mass-weighted mean velocity of the object.  It can be useful to set this significantly less than the 1.0 (i.e. the virial radius) if the center of the object is moving relative to the center-of-motion of the entire object.  Default: 1.0
• XrayLowerCutoffkeV - If this and the next three parameters are specified, then an accurate calculation of the X-ray emissivity is made.  This parameter and the next indicate the X-ray band (in keV at z=0) that is to be used in the calculation. Default: none
• XrayUpperCutoffkeV - The high energy end of the X-ray band in keV.  Default: none
• XrayTableFileName - The name of the ascii file which contains the spectral lookup table.  There is a version computed with a Raymond-Smith code for a low density hot gas with a metallicity of 0.3 relative to solar in the file amr_mpi/exe/lookup_metal0.3.data.gz.
• ComputeDiskInformation - This toggle flag (1 is on, 0 off) controls whether a disk profile and image is generated.  If yes, then the angular momentum vector of the dense gas (see below) is used to define a disk.  Default: 0
• DiskImageSize - The number of pixels on a side in the three disk images (face, and two sides) which are computed if the above flag is turned on.  Default: 100
• DiskRadius - This is the fraction of the virial radius which the disk image comprises (i.e. each pixel is of size r_virial*DiskRadius/DiskImageSize).  Default: 0.2
• LowerDensityCutoff - This is lower density cutoff (in Msolar/Mpc^3) for material to be counted as dense for the calculation of the "dense" angular momentum gas, the cold fraction and the dense fraction.  Default: 1e14
• UpperDensityCutoff - The maximum density (in Msolar/Mpc^3) for gas to be counted in the "dense" angular momentum.  Default: 1e35
• ColdTemperatureCutoff - The highest temperature (in K) for gas to be considered cold.  Used in the calculation of the "dense" angular momentum gas and in the cold fraction.  Can be over-written by the following parameter.  Default: 15000
• ColdTemperatureCutoffVirialFraction - If set, this parameter sets ColdTemperatureCutoff (for each cluster) to this value times the predicted virial temperature (see below).  Default: none
• VirialTemperatureNormalize - The normalization of the predicted virial temperature relation (mass - temperature - redshift relation), relative to that in Bryan & Norman (1998).  If the virial mass is > 1e8 solar masses then mu (the mean mass per particle) is set to 0.6, otherwise mu=1.22.

Each file consists of description information with the pound symbol (i.e. a comment) at the start of the line, and then the profile itself.  The first column is the center of the bin, while the second column is the right edge of the bin, in terms of Mpc (note: not comoving Mpc/h).

Virial information is also included in AnalyzeCluster, (mass, radius, mean velocity within, etc.), and each file contains a line which gives the mean of the profile quantities within the virial radius.

Particle Representation

enzo -o   amr_filename

This will create two HDF files, one called amr.particles.gas and the other amr.particles.dm which contain one-dimension scientific data sets of the "particle" positions, velocities, radii, density, temperature, etc.

This description will be lengthened if interest is expressed in this format.  Note that there is a version which outputs ascii files called dumpgrids (in amr_mpi/anyl).  Again, this is under development and is intended for conversion to other analysis/visualization programs.