AtomMSD

Synopsis

This analyzer calculates the mean-squared-displacement vs. time for atoms that occupy a specific site within molecules of a specific species. It properly takes into account the effects of periodic boundary conditions so as to construct continuous trajectories for these atoms.

Parameters

The parameter file format is:

AtomMSD{
  interval           int
  outputFileName     string
  speciesId          int
  atomid             int
  capacity           int
}

with parameters:

interval	number of steps between data samples
outputFileName	name of output file
speciesId	integer index of molecule species
atomId	integer index of atom within molecule
capacity	number of samples in history

Output

The MSD vs. time is output to a file {outputFileName}.dat.

Parameters are echoed to {outputFileName}.prm