Back to main menu

Mode: radial distribution function

Syntax

atomsk --rdf <file> <Rmax> <dR> [options]

Description

In this mode Atomsk computes the radial distribution function(s) (RDF) for one or several systems.

The analysis is performed for all skins [R;R+dR] with R ranging from 0 up to <R_max>, and averaged over all atoms (i.e. space-averaged). The maximum radius <R_max> and the width <dR> of the skin (or shell) must be provided (in Å). The maximum radius <R_max> can be greater than the system size.

If the <file> contains an atomic system (in one of the formats supported by Atomsk), then the RDF is computed for this system.

If the <file> contains a list of file names, then the RDF is computed for all of these files, and averaged over all these snapshots, i.e. it is both space- and time-averaged. All files should correspond to the same system (for example, snapshots of a molecular dynamics run) for the calculation to make sense.

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):

• *_rdf_<A><B>.dat: files containing the value of the RDF of atoms B around A as a function of distance.

If this mode is used with one or several options they will be applied to the system before computing the RDF.

Performance

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 R_max as small as possible, typically between 10 and 20 Å. To save computational time, the neighbour list is rebuilt only if the maximum displacement of an atom exceeds the value of <dR>. After that, the time required for computing the RDF itself increases linearly with the step dR and with the number of particles.

Examples

• atomsk --rdf aluminium.cfg 10 0.1

  This will compute the radial distribution function for the system aluminium.cfg, from 0 to 10 Å, using a shell width dR=0.1 Å.

• 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.

Back to main menu