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Radial or angular distribution function (RDF, ADF)

RDF

RDF is commonly used to investigate structure of the system, e.g., solid vs liquid, or crystal vs amorphous.

To get the RDF,

python /path/to/nap/nappy/rdf.py [options] dump_0*

then, you get averaged RDF over atoms in out.rdf.

Given atom configuration files, dump_####, are read and average over atoms in those files are taken.

Options are shown below,

Options:
  -h, --help  Show this help message and exit.
  -d DR       Width of the bin. [default: 0.1]
  -r RMAX     Cutoff radius of radial distribution. [default: 5.0]
  --gsmear=SIGMA
              Width of Gaussian smearing, zero means no smearing. [default: 0]
  -o OUT      Output file name. [default: out.rdf]
  --specorder=SPECORDER
              Order of species separated by comma, like, --specorder=W,H. [default: None]
  --skip=NSKIP 
              Skip first NSKIP steps from the statistics. [default: 0]
  --no-average
              Not to take average over files.
  --no-normalize
              Not to normalize by the density.
  --plot      Plot figures. [default: False]

The RDF of each pair of species normalized with the density of the pair.

image

ADF

To get ADF, perform adf.py something like,

python /path/to/nap/nappy/adf.py --triplets=La-F-F,Ba-F-F dump_0*

The triplets consisting angles must be provided via the option --triplets. Note that the 1st species in the triplet is the central atom having bonds to the other two atoms, which maybe counter-intuitive.

image

Here is some options of adf.py,

Options:
  -h, --help  Show this help message and exit.
  -w DEG      Width of the angular degree. [default: 1.0]
  -r RCUT     Cutoff radius of the bonding pair. [default: 3.0]
  --gsmear=SIGMA
              Width of Gaussian smearing, zero means no smearing. [default: 0]
  --triplets=TRIPLETS
              Triplets whose angles are to be computed. Three species should be specified connected by hyphen,
              and separated by comma, e.g.) P-O-O,Li-O-O. [default: None]
  -o OUT      Output file name [default: out.adf]
  --skip=NSKIP 
              Skip first NSKIP steps from the statistics. [default: 0]
  --no-average
              Not to take average over files.
  --plot      Plot figures. [default: False]