cdf calculates the distribution function of molecules from a reference vector - as such, it allows one to calculate the distribution function of species confined within cylindrical geometries, for instance, or at the surface of cylindrical objects. Typically, one may use this to calculate distributions of molecules in cylindrical pores, nanotubes etc.

A vector describing the direction along which the cylinder lays is input, along with a point on which this vector lays. For each molecule the minimum distance (i.e. the perpendicular distance) between its centre-of-mass and the defining vector is calculated and binned in histogram form.

Related programs:

  • To calculate cylindrical orientational distribution functions, see codf.

Basic Usage

cdf <HISTORYfile> <OUTPUTfile> <ox> <oy> <oz> <vx> <vy> <vz>

Where:

  • <HISTORYfile> is the name of the DL_POLY HISTORY file
  • <OUTPUTfile> is the name of the DL_POLY OUTPUT file
  • <ox> <oy> <oz> is a point on which the defining vector lays
  • <vx> <vy> <vz> is the defining vector of the cylindrical object / pore

Switches

-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.

Normalisation

All CDFs are normalised to reflect the number density of the species, as is standard practice. For systems where the distribution of the species is not homogeneous across the simulation box, the normalisation will be incorrect and must be adjusted by hand.

Output

Given an input HISTORY file results.HISu, then output files are as follows: results.cdfNN : Cylindrical distribution function for species NN about the defining vector