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.
rdfaa <HISTORYfile> <OUTPUTfile> <sp>
<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
Discard n frames at the start of the trajectory.
Intramolecular (same molecule) contributions to the partial RDFs will be included in the final results.
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).
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