atomsk --rdf <listfile> <Rmax> <dR> [options]
In this mode Atomsk computes the radial distribution function(s) (RDF) for the systems in <listfile>.
The analysis is performed for all skins [R;R+dR] with R ranging from 0 up to <Rmax>, and averaged over all atoms (i.e. space-averaged). The maximum radius <Rmax> and the width <dR> of the skin (or shell) must be provided (in Å). The maximum radius <Rmax> can be greater than the system size.
The <listfile> must contain a list of files to process, which should be consecutive snapshots of a molecular dynamics run. The final RDF is averaged over all these snapshots, i.e. it is both space- and time-averaged.
If the system contains several atom species then all the partial RDFs are computed. E.g. if atoms A and B exist, then Atomsk will compute the RDF for A atoms around A atoms, B around A, and B around B.
Output consists of the following files (where the <A> and <B> are replaced by the atomic symbols):
If this mode is used with one or several options they will be applied to the system before computing the RDF.
This mode relies on a neighbor search algorithm, which admittedly was not optimized in Atomsk. The time required for neighbor search increases linearly with the volume (i.e. as R3). Therefore it is advised to use a value of Rmax as small as possible, typically between 10 and 20 Å. After that, the time required for computing the RDF itself increases linearly with the step dR and with the number of particles.
atomsk --rdf list.lst 10 0.1
This will compute the radial distribution function for all systems in list.lst, from 0 to 10 Å, using a shell width dR=0.1 Å.