rdfaa calculates calculates atomic, partial radial distribution functions between specific atoms of a single species. Contributions from atom pairs in the same species are omitted, unless specifically requested.

Related programs:

  • To calculate centre-of-mass radial distribution functions between species, see rdf.
  • To calculate site-COM partials, see rdfss.
  • To calculate site-site partials dependent on other sites, see rdfdep.

Basic Usage

rdfaa <HISTORYfile> <OUTPUTfile> <sp>

Where:

  • <HISTORYfile> is the name of the DL_POLY HISTORY file
  • <OUTPUTfile> is the name of the DL_POLY OUTPUT file
  • <sp> is the integer index of the target species

Switches

-discard n

Discard n frames at the start of the trajectory.

-intra

Intramolecular (same molecule) contributions to the partial RDFs will be included in the final results.

-frames n

Stop calculating after processing n frames.

-pair i j

Add the atom indices i-j to the list of partial RDFs to calculate for the specified species. The atom indices are local atom indices for the species in question (i.e. range from 1 to the number of atoms in the molecule).

Output

Given an input HISTORY file results.HISu, then output files are as follows: results.rdfaaSP_II_JJ : partial RDF between atom II and JJ in species SP