.. _scripts:

================================
Scripts
================================

Standalone scripts to handle file conversions and other utlities.

File Conversion
===============

- **lmp2pos**
	.. code-block:: sh

		$ lmp2pos <lmp_file/POSCAR> <POSCAR/lmp_file>
		[DEFAULT OUTPUT] lmp_pos, POSCAR
		
- **lmp2con**
        .. code-block:: sh

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

- **soc2pos**
        .. code-block:: sh

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

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

        .. code-block:: sh

                $ splitxdat --help

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

        .. code-block:: sh

                $ 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.
	
        .. code-block:: sh

                $ pdf-make --help
- **pdf-plot**
	Plots ``pdf.dat`` and ``interprdf.dat`` in gnuplot.
	Outputs ``pdf.eps``

        .. code-block:: sh

                $ pdf-plot 

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

        .. code-block:: sh

                $ pdf-multiplot

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

        .. code-block:: sh

                $ pdfstats --help

- **neighbors**
	Determines nearest neighbors for given file and write to screen.
	
        .. code-block:: sh

                $ neighbors <filename>


File Visualization
==================
- **xyz**
	Displays atomic configurations in formats: 
		- .con
		- VASP (POSCAR and XDATCAR)
		- lammps (position and dump files)
		- xyz
		- bopfox
		- socorro

        .. code-block:: sh

                $ xyz <filename>