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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.