rdfdep allows specific site-site RDFs between two species to be calculated, dependent on the distances of a number of additional specified pairs involving a third species. For instance, in an alcohol/water mixture one may wish to calculate the radial distribution function of those water molecules that are hydrogen bonding directly to the alcohol OH group.

Related programs:

  • To calculate individual atomic partials for one species, see rdfaa.
  • To calculate site-COM partials, see rdfss.
  • To calculate centre-of-mass radial distribution functions between species, see rdf.

Basic Usage

rdfdep <HISTORYfile> <OUTPUTfile> <sp1> <atoms1> <sp2> <atoms2> <depSp>

Where:

  • <HISTORYfile> is the name of the DL_POLY HISTORY file
  • <OUTPUTfile> is the name of the DL_POLY OUTPUT file
  • <sp1> is the integer index of the first species
  • <atoms1> is a comma-separated list of atoms whose average position form the site of interest on sp1
  • <sp2> is the integer index of the second species
  • <atoms2> is a comma-separated list of atoms whose average position form the site of interest on sp2
  • <depSp> is the integer index of the species for which the 'dependent' contacts with sp1 are tested

Switches

-bin width

Specify the histogram bin width to use in the calculation (default = 0.1).

-dep depAtoms sp1atoms minDist maxDist n

Defines a dependent contact that must be fulfilled in order for the RDF to be calculated. depAtoms and sp1atoms are comma-separated lists of local atom indices on the dependent and first species respectively, defining the sites between which the distance will be tested, with minDist and maxDist defining the acceptable limits. n is the number of times this interaction geometry must be matched for a given sp1 centre to contribute to the final RDF.

-discard n

Discard n frames at the start of the trajectory.

-frames n

Stop calculating after processing n frames.

-header file

Read in trajectory header from the specified DL_POLY HIStory file. Useful when the desired target frames are present in a restarted (and not appended) HIStory file.

-or

When multiple dependent interactions are specified, require that only one need be fulfilled.

Output

Given an input HISTORY file results.HISu, then output files are as follows: results.rdfdepNNMM : dependent RDF between species NN and MM