rdf's Introduction

RDF

A code to compute the radial distribution function. This branch is initally planned for the undergraduate student's project on machine learning materials properties.

One could load the crystal from

POSCAR
CIF file

To perform RDF calculation, one needs to provide the following info

crystal structure
R_max (default 12 \AA)
step length (defult: 0.08 \AA)
sigma width for Gaussian smearing (default: 0.10 \AA)

Requirement

This code need the installation of Python3, scipy, numpy, pymatgen. The easiest way is to install them via anaconda or miniconda.

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh
$ conda install -c matsci pymatgen

Usage

$ pythonw RDF.py -h
Usage: RDF.py [options]

Options:
  -h, --help            show this help message and exit
  -c STRUCTURE, --crystal=STRUCTURE
                        crystal from file, cif or poscar, REQUIRED
  -r Rmax, --Rmax=Rmax  Rmax, default: 12 A
  -s SIGMA, --sigma=SIGMA
                        sigma width for Gaussian smearing, default: 0.20
  -d DELTA, --delta=DELTA
                        step length, default: 0.08
  -o MSTYLE, --output=MSTYLE
                        matplotlib style, fivethirtyeight, bmh, grayscale,
                        dark_background, ggplot
  -p PLOT, --plot=PLOT  generate the plot to file, default: None

Execution

one just needs to run the followings,

$ python RDF.py -c POSCAR-Ar

It will generate a png file with RDF plot as follows

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rdf's Issues

database

to create a python file to
1, extract the data (geometry, properties) from Aflowlib or materials project,
2, compute RDF based on the geometry, which is X.
3, the target properties would be Y
4, ML on f(x) = Y