rdf calculates, by default, the centre-of-mass radial distribution functions between all species in the system, although the options allow a point other than the centre-of-mass to be used in the calculation. In addition, for surrounding molecules a different point can be defined to the central molecule.
Related programs:
rdf <HISTORYfile> <OUTPUTfile>Where:
<HISTORYfile> is the name of the DL_POLY HISTORY file<OUTPUTfile> is the name of the DL_POLY OUTPUT file-bin width
Specify the histogram bin width to use in the calculation (default = 0.1).
-compair sp i j
Instead of the centre-of-mass, use the average coordinates of atom indices i and j for species index sp. 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).
-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.
-nonorm
Do not normalise the radial distribution functions to the bulk number density of species.
-otherpair sp i j
Instead of the centre-of-mass (or -compair specification), use the average coordinates of atom indices i and j for species index sp when considering the position of surrounding molecules. 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).
-zminus z
Surrounding molecules will only be accepted if the z-value of it's centre-of-mass (or defined point) is less than that of the central molecule. Mutually exclusive with -zplus.
-zplus z
Surrounding molecules will only be accepted if the z-value of it's centre-of-mass (or defined point) is greater than that of the central molecule. Mutually exclusive with -zminus.
All RDFs are normalised to reflect the number density of the surrounding species, as is standard practice. However, for RDFs where the central molecule species is the same as the surrounding one, the number density is calculated using N-1 molecules.
Given an input HISTORY file results.HISu, then output files are as follows:
results.rdfNNMM : RDF between species NN and MM