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>