utilities
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- | ~~NOTOC~~ | ||
- | ====== 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. | ||
- | [[# | ||
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- | [[# | ||
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- | [[# | ||
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- | [[# | ||
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- | [[# | ||
- | Plot an analytic potfit potential using gnuplot. | ||
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- | [[# | ||
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- | [[# | ||
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- | [[Utilities/ | ||
- | A series of awk scripts to handle various tasks with potential files, like combining, appending, creating from analytical functions, generating from scratch, plotting, | ||
- | |||
- | ---- | ||
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- | ==== force2imd | ||
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- | Converts a potfit configuration into an [[http:// | ||
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- | < | ||
- | usage: force2imd [-h] [-n NUMBER] filename | ||
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- | Convert a potfit configuration into an IMD checkpoint file. | ||
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- | positional arguments: | ||
- | filename | ||
- | |||
- | optional arguments: | ||
- | -h, --help | ||
- | -n NUMBER, --number NUMBER | ||
- | number of the configuration to convert | ||
- | </ | ||
- | |||
- | The IMD checkpoint file is written to standard output. | ||
- | |||
- | ==== force2poscar | ||
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- | Convert a potfit configuration into a [[http:// | ||
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- | < | ||
- | usage: force2poscar [-h] [-n NUMBER] filename | ||
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- | Convert a potfit configuration into a VASP POSCAR file. | ||
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- | positional arguments: | ||
- | filename | ||
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- | optional arguments: | ||
- | -h, --help | ||
- | -n NUMBER, --number NUMBER | ||
- | number of the configuration to convert | ||
- | </ | ||
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- | The VASP POSCAR data is written to standard output. | ||
- | |||
- | ==== list_config | ||
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- | Prints a brief list of all configurations in a potfit config file. | ||
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- | < | ||
- | usage: list_config [-h] filename | ||
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- | Prints a brief list of all configurations in a potfit config file. | ||
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- | positional arguments: | ||
- | filename | ||
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- | optional arguments: | ||
- | -h, --help | ||
- | </ | ||
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- | 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 ...]]] | ||
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- | Create an analytic potential file for potift. | ||
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- | optional arguments: | ||
- | -h, --help | ||
- | -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 | ||
- | -i TYPE, --type TYPE interaction type, e.g. pair, eam, adp, ... | ||
- | -l, --list | ||
- | -cp | ||
- | -f [FUNCTIONS [FUNCTIONS ...]] | ||
- | name of potential functions, either name or i*name, | ||
- | where i=1,2,3,... | ||
- | </ | ||
- | |||
- | |||
- | ==== plotapot | ||
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- | This utility plots an analytic potential with gnuplot. | ||
- | |||
- | < | ||
- | usage: plotapot [-h] [-f] [-p] [-s size] [-t terminal] | ||
- | pot_file [pair_dist_file] | ||
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- | Plot an analytic potfit potential using gnuplot. | ||
- | |||
- | positional arguments: | ||
- | pot_file | ||
- | pair_dist_file | ||
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- | optional arguments: | ||
- | -h, --help | ||
- | -f write plotfiles for gnuplot and exit | ||
- | -p only create plots in png format but do not show them | ||
- | -s size | ||
- | -t terminal | ||
- | in gnuplot for details) | ||
- | </ | ||
- | |||
- | ==== potfit_setup | ||
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- | This utility generates a simple parameter file for //potfit//. | ||
- | |||
- | < | ||
- | usage: potfit_setup [-h] [-c config file] [-p potential file] [-s prefix] | ||
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- | Create a simple potfit parameter file from scratch. | ||
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- | optional arguments: | ||
- | -h, --help | ||
- | -c config file name of the potfit configuration file | ||
- | -p potential file name of the potfit potential file | ||
- | -s prefix | ||
- | |||
- | The prefix takes precedence over the -c and -p switches.If the < | ||
- | and < | ||
- | </ | ||
- | |||
- | 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 [[http:// | ||
- | |||
- | < | ||
- | usage: vasp2force [-h] [-c C] [-e E] [-f] [-l] [-r] [-s CONFIGS] [-w WEIGHT] | ||
- | [files [files ...]] | ||
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- | Converts vasp output data into potfit reference configurations. | ||
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- | positional arguments: | ||
- | files list of OUTCAR files (plain or gzipped) | ||
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- | optional arguments: | ||
- | -h, --help | ||
- | -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 | ||
- | -l, --list | ||
- | -r, --recursive | ||
- | -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 [[http:// | ||
- | |||
- | < | ||
- | # Al Co Ni | ||
- | -0.000219 -0.993872 -0.855835 | ||
- | </ | ||
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- | 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. | ||
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- | ==== awk scripts | ||
- | |||
- | The awk scripts are listed on a [[utilities/ |
utilities.1377767669.txt.gz · Last modified: 2013/08/29 11:14 by daniel