compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ...
compute 1 all rdf 100 compute 1 all rdf 100 1 1 compute 1 all rdf 100 * 3 compute 1 fluid rdf 500 1 1 1 2 2 1 2 2 compute 1 fluid rdf 500 1*3 2 5 *10
Define a computation that calculates the radial distribution function (RDF), also called g(r), and the coordination number for a group of particles. Both are calculated in histogram form by binning pairwise distances into Nbin bins from 0.0 to the maximum force cutoff defined by the pair_style command. The bins are of uniform size in radial distance. Thus a single bin encompasses a thin shell of distances in 3d and a thin ring of distances in 2d.
The itypeN and jtypeN arguments are optional. These arguments must come in pairs. If no pairs are listed, then a single histogram is computed for g(r) between all atom types. If one or more pairs are listed, then a separate histogram is generated for each itype,jtype pair.
The itypeN and jtypeN settings can be specified in one of two ways. An explicit numeric value can be used, as in the 4th example above. Or a wild-card asterisk can be used to specify a range of atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive).
If both itypeN and jtypeN are single values, as in the 4th example above, this means that a g(r) is computed where atoms of type itypeN are the central atom, and atoms of type jtypeN are the distribution atom. If either itypeN and jtypeN represent a range of values via the wild-card asterisk, as in the 5th example above, this means that a g(r) is computed where atoms of any of the range of types represented by itypeN are the central atom, and atoms of any of the range of types represented by jtypeN are the distribution atom.
Pairwise distances are generated by looping over a pairwise neighbor list, just as they would be in a pair_style computation. The distance between two atoms I and J is included in a specific histogram if the following criteria are met:
It is OK if a particular pairwise distance is included in more than one individual histogram, due to the way the itypeN and jtypeN arguments are specified.
The g(r) value for a bin is calculated from the histogram count by scaling it by the idealized number of how many counts there would be if atoms of type jtypeN were uniformly distributed. Thus it involves the count of itypeN atoms, the count of jtypeN atoms, the volume of the entire simulation box, and the volume of the bin's thin shell in 3d (or the area of the bin's thin ring in 2d).
A coordination number coord(r) is also calculated, which is the sum of g(r) values for all bins up to and including the current bin.
The simplest way to output the results of the compute rdf calculation to a file is to use the fix ave/time command, for example:
compute myRDF all rdf 50 fix 1 all ave/time 100 1 100 c_myRDF file tmp.rdf mode vector
This compute calculates a global array with the number of rows = Nbins, and the number of columns = 1 + 2*Npairs, where Npairs is the number of I,J pairings specified. The first column has the bin coordinate (center of the bin), Each successive set of 2 columns has the g(r) and coord(r) values for a specific set of itypeN versus jtypeN interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.
The array values calculated by this compute are all "intensive".
The first column of array values will be in distance units. The g(r) columns of array values are normalized numbers >= 0.0. The coordination number columns of array values are also numbers >= 0.0.
The RDF is not computed for distances longer than the force cutoff, since processors (in parallel) don't know about atom coordinates for atoms further away than that distance. If you want an RDF for larger distances, you can use the rerun command to post-process a dump file.