clusterab calculates the sizes of clusters (or semi-continuous networks) of molecules in a similar manner to cluster, but focuses specifically on 'A-B' contacts between the various molecules. Thus, rather than giving the cluster size of a group of molecules based on a single common site between them, clusterab allow true networks to be probed. The best example of this is a hydrogen bonding network, where the hydrogen (A) atoms of one molecule donate a hydrogen bond to an oxygen or nitrogen (B) atom on another (possibly different) molecule. Also, multiple A and B sites may be specified for each molecule type involved, allowing diols, for instance, to be treated in the same manner.

Since the present calculated quantity may involve more than one species, the resulting cluster sizes the sum of the involved molecules of both types. One exception to this is the calculation of a cluster size when then surrounding molecules of interest do not include the central species type - in this case, cluster sizes of zero are possible, since the central molecule may not be interacting with any of the other molecule types.

The normal action of clusterab is to allow paths (i.e. A-B interactions) involving as many molecules as possible, and to allow each molecule in the system to belong to exactly one cluster/path. Sometimes this is not the desired quantity - if, for instance, one was interested in the average number of a molecule type that were clustering around an AB site of a (different) central species molecule, then each molecule may be associated (in)directly to more than one species 1 AB site. In these situations, the -individual option may be provided, which has the effect of 'forgetting' the previous path before the next molecule of the central species is considered in the calculation. The allowable path length in either case can be restricted with the -maxpath switch, allowing 'extended' coordination shells to be investigated.

Basic Usage

clusterab <HISTORYfile> <OUTPUTfile> <sp> <othersp> <maxdist>

Where:

  • <HISTORYfile> is the name of the DL_POLY HISTORY file
  • <OUTPUTfile> is the name of the DL_POLY OUTPUT file
  • <sp> is the index of the central species, from which the cluster calculation begins
  • <othersp> is a comma-separated list of species indices that paths/clusters may be formed from
  • <maxdist> is the maximum allowable distance between any A-B site pair for them to be considered 'interacting'.

The provision of <sp> and <othersp> warrant a little explanation. The calculation of paths/clusters always begins from one species type (given as <sp>) and the species defined in <othersp> will determine exactly what the calculation probes. For instance, in a two-component system, setting both <sp> and <othersp> to a value of 1 will return information on clusters formed from molecules of species 1, completely ignoring species 2. Setting <othersp> to 2, on the other hand, will give the cluster size of molecules of species 2 around species 1, where there is at least one A-B contact between the central species 1 molecule and a surrounding species 2 molecule. Setting <othersp> to 1,2 means that the calculation permits clusters formed from both molecule types, beginning from a favourable A-B contact between a molecule of species 1 and either of the other two species.

Switches

-ab sp aAtoms bAtoms

Specify A and B sites for the species index sp. aAtoms and bAtoms are comma-separated lists of local atom indices on the species. The donor or acceptor sites can be assigned to either A or B sites, but you must be consistent across all species.

-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.

-individual

Treat each central species molecule as a separate calculation, allowing any of the other species to be associated to its cluster.

-maxpath n

Sets the maximum number of sequential A-B interactions to allow before stopping the recursive search. A value of zero will allow no clusters to be formed, a value of 1 will restrict to 'immediate' neighbours, etc. The default is to allow paths of any length.

Output

Given an input HISTORY file results.HISu, then output files are as follows: results.clusterabSP : cluster information for species SP