Scripts

Standalone scripts to handle file conversions and other utlities.

File Conversion

• lmp2pos

  $ lmp2pos <lmp_file/POSCAR> <POSCAR/lmp_file>
  [DEFAULT OUTPUT] lmp_pos, POSCAR
  

• lmp2con

  $ lmp2con <lmp_file/file.con> <file.con/lmp_file>
  [DEFAULT OUTPUT] lmps_pos, pos.con
  

• soc2pos

  $ soc2pos <crystal/POSCAR> <POSCAR/crystal>
  [DEFAULT OUTPUT] crystal, POSCAR
  

• splitxdat

  Splits XDATCAR files at given segments and outputs POSCAR.trj or multiple POSCARS

  $ splitxdat --help
  

• water_solvate

  Adds water molecules to outside of structure and saves structure in VASP format.

  $ water-solvate --help
  

• mobfil

  Inputs and outputs .con files with a cutoff distance

Analysis Tools

• pdf-make

  Takes a POSCAR, .con, or XDATCAR with options and calculates the radial-distribution function with a spline fit. Outputs pdf.dat with raw data and interprdf.dat containing the spline fit.

  $ pdf-make --help
  

• pdf-plot

  Plots pdf.dat and interprdf.dat in gnuplot. Outputs pdf.eps

  $ pdf-plot
  

• pdf-multiplot

  Plots up to 20 interprdf-i.dat in gnuplot. Outputs pdf.eps

  $ pdf-multiplot
  

• pdfstats

  Calculates number of neighbors, min/max/avg bond distance, and variance with option. Writes to screen and to bonds/dat.

  $ pdfstats --help
  

• neighbors

  Determines nearest neighbors for given file and write to screen.

  $ neighbors <filename>
  

File Visualization

• xyz

  Displays atomic configurations in formats:

  • .con
  • VASP (POSCAR and XDATCAR)
  • lammps (position and dump files)
  • xyz
  • bopfox
  • socorro

  $ xyz <filename>