Reads particles from stdin in the tipsy binary format.
[-s <nSmooth>]: Default nSmooth = 64
Specifies the number of neighbors to smooth over when finding densities.
[-d <fMinDensity>]: Default fMinDensity = 0.0
This sets the minimum density for dark matter or gas particles which are considered for grouping.
[-t <fMaxTemperature>]: Default fMaxTemperature =
This sets the maximum temperature for gas particles which are considered for grouping.
[-z <fRedShift>]: Default fRedShift = 0.0
The redshift of the input file. This is used to determine physical coordinates from comoving ones. The default of 0.0 specifies that the input file is the state of the simulation at our (the current) epoch.
[-G <fGravConst>]: Default
fGravConst = 1.0
The relevant gravitational constant in the units of the simulation. Most N-body simulations have their units set such that this constant is 1.0.
<fOmega>]: Default fOmega = 1.0
This sets the Omega parameter for the simulation in question. The default value of 1.0 specifies a flat universe.
[-H <fHubble>]: Default fHubble = 0.0
Sets the Hubble constant for the simulation. If the simulation was not performed in comoving coordinates then this can be left at zero. Note that this must be set in the units of the simulation.
[-m <nMinMembers>]: Default nMinMembers
This argument allows the user to specify what the minimum number of members (particles) per group should be. All groups with less than this value will be dicarded.
[-px <xPeriod>]: Default non-periodic in x dimension
Specifies that denmax take into account periodicity in the x-dimension given by the period <xPeriod>.
[-py <yPeriod>] [-pz <zPeriod>]: As above.
Default non-periodic in x,y and z dimensions
Specifies that denmax take into account periodicity in all three dimension given by the period <xyzPeriod>. This can be used in place of the above as a shorthand.
[-cx <xCenter>]: Default box center is 0.0 in x dimension
Specifies the center of the periodic box when denmax takes into account periodicity in the x-dimension. This arguement can be ignored for a non-periodic simulation.
[-cy <yCenter>] [-cz <zCenter>]: As above for y and z dimensions.
[-c <xyzCenter>]: Default box center is 0.0 in x,y and z dimensions
For periodic simulations specifies the center of the box in all three dimensions. This is a shorthand to the above.
[-r]: Causes the denmax.ray output file
to be produced.
By default denmax does not produce the denmax.ray output file. With this argument present it will produce this (tipsy vector format) file.
Disables Unbinding (No Unbinding).
When this flag is specified denmax will bypass the unbinding procedure but still output all the normal group information. This is useful if special unbinding methods are required for a simulation or if unbinding is completely undesired. The user can write a special unbinding program which would read the denmax.grp file.
[-o <Output Name>]: Default Output Name = "denmax".
This allows the user to specify an alternate name for the output files. For example, if the user specifies -o sim5 on the command line, then denmax will by default produce the files sim5.grp and sim5.gtp (and if requested sim5.ray).
Denmax finds gravitationally bound groups in N-body simulations. The general procedure is first to decide which particles should be grouped, these are called the "moving" particles. The particles considered may be of a certain type (there are three types in the tipsy format, dark matter, gas and stars). They may have to satisfy a minimum density criterion and may also (in the case of gas) need to satisfy a maximum temperature criterion. This choice of particles is affected by the type of input file and the users settings for the minimum density and maximum temperature. There are seven possible types of tipsy input files and here is how each is handled.
Dark matter only: density and density gradients are calculated from all the particles (dark), and the moving particles are those meeting the minimum density criterion.
Gas only: density and density gradients are calculated from all the particles (gas), and the moving particles are those meeting both the minimum density and maximum temperature criteria.
Stars only: density gradients are calculated from all the particles (stars), and all the particles are moved.
Gas and dark matter: density and density gradients are calculated from the gas particles only, and the moving particles are the gas particles which meet the density and temperature criteria.
Stars and gas: density gradients are calculated from the star particles only, and the moving particles are all the star particles.
Stars and dark matter: Same as stars and gas case.
Stars and gas and dark matter: density and density gradients are calculated from all the star particles and all the gas particles. The moving particles are then the gas particles meeting the density and temperature criteria and all the star particles.
Once the moving particles have been found they are then moved along the initial density gradients toward regions of higher density. The particles are successively stepped a distance of fEpsilon/4.0 in this manner until they stay within a distance of fEpsilon over 5 steps. This mean that they are oscillating in a local high density region. We then group all the particles in each high density region together using the friends-of-friends method with a linking length of fEpsilon. Note that this also links together high density regions seperated by less than fEpsilon. Once all particles are localized in this way, we proceed to "squish" them together even more to find the high density center. Lastly we discard groups with less than nMinMembers number of particles.
The next stage (if the user has not specified -nu) is to remove particles from a group which are not gravitationally bound to it. We call this phase unbinding and the initial positions are considered here, not the moved positions. There are cases for unbinding, one for dark matter only or star particle only inputs (case I unbinding) and one for the other input types (case II unbinding).
Case I unbinding:
1. Calculate the potential energies of all the particles in the group taking into account the redshift of the simulation to get physical distances (redshift zero applies also to a simulation in physical coordinates).
2. The center of mass and center of mass velocity for the group is found. The velocity relative to the center of mass velocity if found for all the particles in the group. This relative velocity is converted to a physical velocity by taking into account the redshift and adding a term to include the Hubble flow. For a simulation in physical coordinates fHubble must be 0.0. (Note that this is the default!) From this the kinetic energy with respect to the center of mass is found for all particles in the group.
3. The least bound particle is found. If this particle is bound then all particles are bound and we have finished unbinding for this group. Otherwise we must remove it from the group, adjusting the potential energies and kinetic energies (the center of mass changes) of the remaining particles and return to step 3.
Case II unbinding:
Here we include some of the group’s environment to the potential. For example a galaxy depends on its dark matter halo in order to stay together.
1. Calculate the potential energies as per case I, step 1.
1a. Include the potential contribution of all non-grouped mass within a 2*fEpsilon ball about the center of the high density region of the group. In otherwords we want to include some of the mass about the density maximum.
2. Calculate the kinetic energies as per case I, step 2.
3. The least bound particle is found. If this particle is bound then again we are finished with the group. Otherwise we remove it from the group, adjusting the kinetic energies as in case I. Then we go back to step 3. Note that this time we do not subtract the potential energy contribution of this particle from the others in the group. The potential energies remain fixed as any removed particle is still considered to be part of the groups environment.
After unbinding we check once more that all groups have at least nMinMembers number of particles. We discard those that don’t and output the group information.
Denmax produces three different output files, by default a denmax.grp file, and a denmax.gtp file. Optionally also a denmax.ray file.
denmax.grp: This ASCII file is in TIPSY ARRAY format and contains the group number to which each particle in the input file belongs. Group number zero means this particle was not grouped (could have been removed by unbinding). This file can be read in by tipsy or any other analysis tool able to read this format.
denmax.gtp: This file is in TIPSY BINARY format (same as the input file) and contains one star particle to represent each group that denmax finds. Each particle in this file has as its position, the position of the group’s density maximum. As its velocity, the center of mass velocity of the group. Each star particle’s mass is the mass of the entire group and the star_particle.eps field contains the radial size of the group. (The time stamp of the input file is also stored in each star_particle.tform field.) This file can also be read in by tipsy or any tool accepting TIPSY BINARY format.
denmax.ray: This ASCII file is in TIPSY VECTOR format and contains a vector pointing from the initial position of each particle to the localized (moved and squished) position of that particle. For particles not moved the vector stored is null. This file can be read in by tipsy and used to analyse the actions of denmax.
> denmax -e 9e-4 -H 2.8944 -d 170 -p 1 -o dark < dark.bin
This example groups dark matter particles in the file dark.bin. The simulation is periodic with period length of 1.0 in each dimension and box centered on (0,0,0). The Hubble constant in system units in this case is 2.8944 (sqrt(8*Pi/3)) and the redshift defaults to 0 (current epoch). The density cut is made at a density of 170 (mean density is 1 in these units). The files dark.grp and dark.gtp are produced.
> denmax -e 9e-4 -H 2.8944 -d 170 -t 30000 -z 1 -p 1 < all.bin
Here we suppose that dark matter, gas and stars are in the input file. A cut in the gas is made at a density minimum of 170 and temperature maximum of 30000 (cold dense gas) and groups of this gas and all the stars are formed at a redshift of 1. The files denmax.grp and denmax.gtp are created.
> denmax -e 0.5 -d 100 -m 8 -r -nu -o phys < phys.bin
Here denmax processes a dark matter file in physical coordinates which is non-periodic. It makes a density cut at 100 and finds the groups, but does not try to unbind any particles. It does remove groups with less than 8 members. The output files phys.grp, phys.gtp and phys.ray (-r) are produced.
1. Make sure you set fEpsilon to a reasonable size for your simulation. If too small it can take a long time to converge and may not give reasonable groups do to the limited resolution of objects in the simulation. If too large, it will miss the smaller scale objects and may group together many smaller objects to form large associations. For example the desired groups could be galaxies in a gas and dark matter simulation, epsilon should reflect this fact.
2. Do not run denmax with an nSmooth of less than 64 when finding groups in a dark matter only input file. For gas simulations an nSmooth of 32 is acceptable.
3. The unbinding procedure is O(Ngroup^2), this means that for very large simulations and specifically situations where groups larger than a couple of thousand members are found the unbinding procedure could be prohibitive. So far this has not been a real problem, even in a 2.1 million particle simulation, however, future versions of denmax may need to use a tree code for the group pootential energies. (The friends-of-friends is actually also O(Ngroup^2) but this is not such a big problem)
Please report any!
astro-ph/0405445; Fast Identification of Bound Structures in Large N-body Simulations (Weller et al)
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