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--- utilities [2013/08/29 11:22] – daniel
+++ utilities [2018/01/06 10:44] (current) – removed daniel
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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.
-[[#force2imd|force2imd]]\\
- Convert a potfit configuration into an IMD checkpoint file.
-[[#force2poscar|force2poscar]]\\
- Convert a potfit configuration into a VASP POSCAR file.
-[[#list_config|list_config]]\\
- Prints a brief list of all configurations in a potfit config file.
-[[#makeapot|makeapot]]\\
- Create an analytic potential file for potift.
-[[#plotapot|plotapot]]\\
- Plot an analytic potfit potential using gnuplot.
-[[#potfit_setup|potfit_setup]]\\
- Creates a parameter file for //potfit// from scratch.
-[[#vasp2force|vasp2force]]\\
- Converts vasp output (POSCAR, OUTCAR) to reference configuration data.
-[[Utilities/awk_scripts|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 [[http://imd.itap.physik.uni-stuttgart.de/|IMD]] checkpoint file.
-<code>
-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
-</code>
-The IMD checkpoint file is written to standard output.
-====  force2poscar  ====
-Convert a potfit configuration into a [[http://cms.mpi.univie.ac.at/vasp/|VASP]] POSCAR file.
-<code>
-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
-</code>
-The VASP POSCAR data is written to standard output.
-====  list_config  ====
-Prints a brief list of all configurations in a potfit config file.
-<code>
-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
-</code>
-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.
-<code>
-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,...
-</code>
-====  plotapot  ====
-This utility plots an analytic potential with gnuplot.
-<code>
-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)
-</code>
-====  potfit_setup  ====
-This utility generates a simple parameter file for //potfit//.
-<code>
-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.
-</code>
-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://cms.mpi.univie.ac.at/vasp/|VASP]] output data into potfit reference configurations.
-<code>
-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
-</code>
-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://cms.mpi.univie.ac.at/vasp/|VASP]] in a single line in the same order as in the OUTCAR file, e.g.:
-<code>
-# Al      Co        Ni
--0.000219 -0.993872 -0.855835
-</code>
-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.