PkdGrav-snapshot

Input/output of PkdGrav particle snapshots

This Python library reads and writes particle snapshots in the Tipsy format. Files of this type are typically produced by PkdGrav at each time step of a cosmological N-body simulation. The snapshot files contain information such as mass, position, velocity… of gas, dark-matter, and star particles.

Installation

Install the package directly from the Git repo:

❯ pip install git+https://cosmo-gitlab.phys.ethz.ch/john.hennig/PkdGrav-snapshot.git

Usage

To read particle data from a PkdGrav snapshot file:

import pkdsnap
(gas, dm, star, time) = pkdsnap.read('snapshot.tipsy')

This returns gas, dm (dark matter), and star particles as Pandas data frames as well as the simulation time of the snapshot as a number. The data frames correspond to the struct fields of the PkdGrav file format as documented in the section "Tipsy Format" of the PkdGrav documentation.

Note that PkdGrav does not typically use the .tipsy file extension. For a simulation with output name (achOutName) "results", the files would be named like results.00140, wherein 140 is the time step.

Given Pandas data frames of the same column structure as returned by read(), particle data can be written to a PkdGrav snapshot file with:

pkdsnap.write('snapshot.tipsy', gas=gas, dm=dm, star=star, time=0.01)

For example (made-up numbers, not necessarily physical):

from pandas import DataFrame

gas = DataFrame({
    'm':  [  0.00001 ],
    'x':  [ -0.5     ],
    'y':  [ -0.5     ],
    'z':  [ -0.5     ],
    'vx': [ -0.02    ],
    'vy': [ +0.03    ],
    'vz': [ +0.01    ],
    'ρ':  [  0.1     ],
    'T':  [  4.2     ],
    'hs': [  9.5     ],
    'μ':  [  0.1     ],
    'φ':  [  0.1     ],
})

dm = DataFrame({
    'm':  [  0.00002 ,  0.00002 ],
    'x':  [ -0.1     , +0.5     ],
    'y':  [ -0.4     , +0.2     ],
    'z':  [ +0.1     , +0.4     ],
    'vx': [ -0.02    , +0.03    ],
    'vy': [ +0.03    , +0.00    ],
    'vz': [ -0.00    , +0.02    ],
    'ε':  [  0.0006  ,  0.0006  ],
    'φ':  [ -0.053   , -0.053   ],
})

star = DataFrame({
    'm':  [  0.00003 ,  0.00003 ,  0.00003 ],
    'x':  [ -0.4     , +0.3     , +0.5     ],
    'y':  [ +0.5     , +0.1     , -0.2     ],
    'z':  [ -0.5     , +0.2     , -0.1     ],
    'vx': [ -0.02    , +0.03    , +0.04    ],
    'vy': [ +0.01    , +0.02    , -0.01    ],
    'vz': [ +0.03    , -0.01    , -0.04    ],
    'μ':  [  0.1     ,  0.1     ,  0.1     ],
    'tf': [ 12.1     , 12.2     , 12.3     ],
    'ε':  [  0.0006  ,  0.0006  ,  0.0006  ],
    'φ':  [ -0.053   , -0.053   , -0.053   ],
})

Particle data may also be appended to an existing Tipsy file:

pkdsnap.append('snapshot.tipsy', dm=more_dm_particles)

Note, however, that this only works if the existing file contains only particles of the same type as those to be appended.