potfit wiki

open-source force-matching

User Tools

Site Tools


utilities

Utilities


The potfit/util directory contains a number of utility programs for the preparation of potfit input files and the postprocessing of potfit output files.

force2imd
Convert a potfit configuration into an IMD checkpoint file.

force2poscar
Convert a potfit configuration into a VASP POSCAR file.

list_config
Prints a brief list of all configurations in a potfit config file.

makeapot
Create an analytic potential file for potift.

plotapot
Plot an analytic potfit potential using gnuplot.

potfit_setup
Creates a parameter file for potfit from scratch.

vasp2force
Converts vasp output (POSCAR, OUTCAR) to reference configuration data.

awk scripts
A series of awk scripts to handle various tasks with potential files, like combining, appending, creating from analytical functions, generating from scratch, plotting,…


force2imd

Converts a potfit configuration into an IMD checkpoint file.

usage: force2imd [-h] [-n NUMBER] filename

Convert a potfit configuration into an IMD checkpoint file.

positional arguments:
  filename              name of the potfit config file

optional arguments:
  -h, --help            show this help message and exit
  -n NUMBER, --number NUMBER
                        number of the configuration to convert

The IMD checkpoint file is written to standard output.

force2poscar

Convert a potfit configuration into a VASP POSCAR file.

usage: force2poscar [-h] [-n NUMBER] filename

Convert a potfit configuration into a VASP POSCAR file.

positional arguments:
  filename              name of the potfit config file

optional arguments:
  -h, --help            show this help message and exit
  -n NUMBER, --number NUMBER
                        number of the configuration to convert

The VASP POSCAR data is written to standard output.

list_config

Prints a brief list of all configurations in a potfit config file.

usage: list_config [-h] filename

Prints a brief list of all configurations in a potfit config file.

positional arguments:
  filename    name of the potfit config file

optional arguments:
  -h, --help  show this help message and exit

Scans a potfit configuration file and lists all configurations found. This includes the origin (if comment is found), the starting line, number of atoms and weight of the configuration.

makeapot

Generate analytic potential files for potfit from scratch.

usage: makeapot [-h] [-n N] [-co CUTOFF] [-g] [-r] [-i TYPE] [-l] [-cp]
                [-f [FUNCTIONS [FUNCTIONS ...]]]

Create an analytic potential file for potift.

optional arguments:
  -h, --help            show this help message and exit
  -n N                  number of atoms types, runs from 0 to N-1
  -co CUTOFF, --cutoff CUTOFF
                        cutoff radius
  -g                    use global cutoff parameter
  -r, --random          randomize the starting potential
  -i TYPE, --type TYPE  interaction type, e.g. pair, eam, adp, ...
  -l, --list            list options which are available
  -cp                   enable chemical potentials (only for pair)
  -f [FUNCTIONS [FUNCTIONS ...]]
                        name of potential functions, either name or i*name,
                        where i=1,2,3,...

plotapot

This utility plots an analytic potential with gnuplot.

usage: plotapot [-h] [-f] [-p] [-s size] [-t terminal]
                pot_file [pair_dist_file]

Plot an analytic potfit potential using gnuplot.

positional arguments:
  pot_file        potfit potential file
  pair_dist_file  pair distribution file

optional arguments:
  -h, --help      show this help message and exit
  -f              write plotfiles for gnuplot and exit
  -p              only create plots in png format but do not show them
  -s size         window size of the gnuplot window (default: 640x480)
  -t terminal     use this gnuplot terminal (see the 'help terminal' command
                  in gnuplot for details)

potfit_setup

This utility generates a simple parameter file for potfit.

usage: potfit_setup [-h] [-c config file] [-p potential file] [-s prefix]

Create a simple potfit parameter file from scratch.

optional arguments:
  -h, --help         show this help message and exit
  -c config file     name of the potfit configuration file
  -p potential file  name of the potfit potential file
  -s prefix          prefix for all files

The prefix takes precedence over the -c and -p switches.If the <prefix>.pot
and <prefix>.config files are not found, the values of -c and -p are checked.

If the config file is given via the -c or -s option, the number of atom types is automatically determined and adjusted in the output.

vasp2force

Converts VASP output data into potfit reference configurations.

usage: vasp2force [-h] [-c C] [-e E] [-f] [-l] [-r] [-s CONFIGS] [-w WEIGHT]
                  [files [files ...]]

Converts vasp output data into potfit reference configurations.

positional arguments:
  files                 list of OUTCAR files (plain or gzipped)

optional arguments:
  -h, --help            show this help message and exit
  -c C                  list of chemical species to use, e.g. -c Mg=0,Zn=1
  -e E                  file with single atom energies (NYI)
  -f, --final           use only the final configuration from OUTCAR
  -l, --list            list all chemical species and exit
  -r, --recursive       scan recursively for OUTCAR files
  -s CONFIGS, --configs CONFIGS
                        comma separated list of configurations to use
  -w WEIGHT, --weight WEIGHT
                        set configuration weight for all configurations

Reads information from all OUTCAR files in the current directory. <OUTCAR files> is an optional list of files, if not given all files matching OUTCAR* will be scanned (it is possible to read gzipped files ending with .gz). An optional file can be specified, containing the energy of a single free atom calculated by VASP in a single line in the same order as in the OUTCAR file, e.g.:

# Al      Co        Ni
-0.000219 -0.993872 -0.855835

Writes a force file to be used as a potfit reference configuration to standard output. If no options are given, force data is generated from each ionic step.

utilities.txt · Last modified: 2013/08/29 11:22 by daniel