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--- utilities [2013/08/21 15:12] – 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/old|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//.
-Usage:
-  potfit_setup [-c config file] [-p potential file] [-s prefix]
-<code>
- -c <config file>       name of the configuration file
- -p <potential file>    name of the potential file
-                        for analytic potentials this can easily be created with
-                        the makeapot script from the awkscripts
- -s <prefix>            prefix for all files, overrides -c and -p
-                        the following files will be checked:
-                        <prefix>.pot and <prefix>.config
-                        if they are not found, -c and -p will be read
-</code>
-====  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.
-====  pottrans  ====
-Converts betweeen various potential models.
-Compilation:  ''make pottrans''
-Usage:
-  pottrans <paramfile>
-required parameters in paramfile (here with example values)
-<code>
-ntypes     2           # number of atom types
-ncols      3           # number of output potentials
-infile     in.pot      # input potential file for pair potentials
-outfile    out.pot     # output potential file
-nsteps     20 20 20    # number of steps for the output potentials
-atomic_e-density_file  rho.pot   # atomic density for EAM potentials
-embedding_energy_file  embed.pot # embedding energy for EAM potentials
-core_potential_file    phi.pot   # pair potential for EAM potentials
-# optional parameters
-reorder     0 1        # permutes order of potentials in final file,
-                       # ntypes parameters necessary
-r_start   1.8 1.8 1.8  # minimal r for each column in output potential
-</code>
-in.pot is converted to out.pot. in.pot can be of IMD potential format 1 or 2, out.pot is of //potfit// potential format. For EAM potentials, specify the appropriate number of columns in ncols and the required IMD format potential files. The order of the different atom types can be changed with the reorder parameter by specifying the desired sequence.
-To convert from //potfit// to IMD use //potfit// with ''opt 0'' in the parameter file.
-====  awk scripts  ====
-The awk scripts are listed on a [[utilities/Awk_scripts|separate page]].