utilities
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- | {{TOC_right}} | + | ~~NOTOC~~ |
- | The potfit/util directory contains a number of utility programs for the preparation of '' | + | ====== 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. | ||
- | ;[[#force2poscar|force2poscar]] | + | [[#force2imd|force2imd]]\\ |
- | :Converts force files (IMD output) to vasp POSCAR files. | + | Convert a potfit |
- | ; | + | |
- | :Converts vasp output (POSCAR, OUTCAR) to reference | + | |
- | ; | + | |
- | :Converts various | + | |
- | ; | + | |
- | :List all configurations in a configuration | + | |
- | ; | + | |
- | :Creates a parameter file for '' | + | |
- | ; | + | |
- | :A series of awk scripts to handle various tasks with potential files, like combining, appending, creating from analytical functions, generating from scratch, plotting, | + | |
- | ; | + | |
- | :Performs gauge transformations of '' | + | |
- | === force2poscar | + | [[#force2poscar|force2poscar]]\\ |
+ | | ||
- | Converts force files produced by [http:// | + | [[# |
+ | | ||
- | Compilation: | + | [[# |
+ | | ||
- | Usage: | + | [[# |
- | force2poscar input.force | + | Plot an analytic potfit potential using gnuplot. |
+ | |||
+ | [[# | ||
+ | | ||
- | The information is always written to a file called | + | [[# |
+ | | ||
- | === vasp2force === | + | [[Utilities/ |
+ | A series of awk scripts to handle various tasks with potential files, like combining, appending, creating from analytical functions, generating from scratch, plotting, | ||
- | Converts [http:// | + | ---- |
- | Compilation: | ||
- | Usage: | + | ==== force2imd |
- | | + | |
- | 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). | + | Converts a potfit configuration into an [[http://imd.itap.physik.uni-stuttgart.de/|IMD]] checkpoint |
- | 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 | + | |
- | # Al Co Ni | + | < |
- | -0.000219 | + | usage: force2imd [-h] [-n NUMBER] filename |
- | Writes | + | Convert |
- | Options: | + | positional arguments: |
+ | filename | ||
- | < | + | optional arguments: |
- | :list of chemical species to use (e.g. " | + | -h, --help show this help message |
- | <tt>-e < | + | -n NUMBER, |
- | :Specify file to read single atom energies from; if not found, " | + | |
- | <tt>-f</ | + | </code> |
- | :Uses only final configuration of multiple ionic steps. | + | |
- | <tt>-l</ | + | |
- | :List all chemical species found in OUTCAR | + | |
- | <tt>-r</ | + | |
- | :Scan recursively for OUTCAR files in every subdirectory. | + | |
- | <tt>-s list</ | + | |
- | :List is a comma separated list of ionic steps to use, e.g. " | + | |
- | < | + | |
- | :Assign this weight to all configurations. | + | |
- | === pottrans === | + | The IMD checkpoint file is written to standard output. |
- | Converts betweeen various potential models. | + | ==== force2poscar |
- | Compilation: < | + | Convert a potfit configuration into a [[http:// |
- | Usage: | + | <code> |
- | | + | usage: force2poscar [-h] [-n NUMBER] filename |
- | required parameters in paramfile (here with example values) | + | Convert a potfit configuration into a VASP POSCAR file. |
- | < | + | positional arguments: |
- | ntypes | + | |
- | ncols 3 # number of output potentials | + | |
- | infile | + | |
- | outfile | + | |
- | nsteps | + | |
- | atomic_e-density_file | + | |
- | embedding_energy_file | + | |
- | core_potential_file | + | |
- | #optional | + | optional |
+ | -h, --help | ||
+ | -n NUMBER, --number NUMBER | ||
+ | number of the configuration to convert | ||
+ | </ | ||
- | reorder | + | The VASP POSCAR data is written to standard output. |
- | # ntypes parameters necessary | + | |
- | r_start | + | |
- | </ | + | |
- | in.pot is converted to out.pot. in.pot can be of IMD potential format 1 or 2, out.pot is of '' | + | ==== list_config |
- | To convert from '' | + | Prints a brief list of all configurations in a potfit |
- | === list_config | + | < |
+ | usage: | ||
- | Lists all configurations in a config file. | + | Prints a brief list of all configurations in a potfit |
- | Compilation: | + | positional arguments: |
+ | filename | ||
- | Usage: | + | optional arguments: |
- | list_config | + | -h, --help |
+ | </code> | ||
- | Scans a '' | + | 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. | ||
- | === potfit_setup | + | ==== makeapot |
- | This utility generates a simple parameter file for '' | + | 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 | ||
+ | -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, | ||
+ | </ | ||
+ | |||
+ | |||
+ | ==== 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 | ||
+ | pair_dist_file | ||
+ | |||
+ | 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 | ||
+ | |||
+ | This utility generates a simple parameter file for //potfit//. | ||
Usage: | Usage: | ||
- | potfit_setup [-c config file] [-p potential file] [-s prefix] | + | |
- | <tt>-c <config file></ | + | <code> |
- | :name of the configuration file | + | -c <config file> |
- | <tt>-p < | + | -p < |
- | :name of the potential file (for analytic potentials this can easily be created with the <tt>makeapot</ | + | |
- | <tt>-s < | + | |
- | :prefix for all files, overrides -c and -p | + | -s < |
- | :the following files will be checked: | + | the following files will be checked: |
+ | | ||
+ | | ||
+ | </ | ||
- | === awk scripts | + | ==== vasp2force |
- | The awk scripts are listed on a [[Utilities/Awk_scripts|separate page]]. | + | Converts |
- | === potscale === | + | < |
- | '''< | + | usage: vasp2force [-h] [-c C] [-e E] [-f] [-l] [-r] [-s CONFIGS] [-w WEIGHT] |
+ | [files [files ...]] | ||
- | potscale performs gauge transformations on EAM potentials. | + | Converts vasp output data into potfit reference configurations. |
- | Compilation: <tt>make potscale</tt> | + | positional arguments: |
+ | files list of OUTCAR files (plain or gzipped) | ||
+ | |||
+ | 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 | ||
+ | </code> | ||
+ | |||
+ | Reads information from all OUTCAR files in the current directory. | ||
+ | An optional file can be specified, containing the energy of a single free atom calculated by [[http:// | ||
+ | |||
+ | <code> | ||
+ | # 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. | ||
+ | |||
+ | ==== pottrans | ||
+ | |||
+ | Converts betweeen various potential models. | ||
+ | |||
+ | Compilation: | ||
Usage: | Usage: | ||
- | | + | pottrans |
+ | |||
+ | required parameters in paramfile (here with example values) | ||
+ | |||
+ | < | ||
+ | ntypes | ||
+ | ncols 3 # number of output potentials | ||
+ | infile | ||
+ | outfile | ||
+ | nsteps | ||
+ | atomic_e-density_file | ||
+ | embedding_energy_file | ||
+ | core_potential_file | ||
+ | |||
+ | # optional parameters | ||
+ | |||
+ | reorder | ||
+ | # ntypes parameters necessary | ||
+ | r_start | ||
+ | </ | ||
+ | |||
+ | 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. | ||
- | Required parameters | + | To convert from //potfit// to IMD use //potfit// with '' |
- | < | ||
- | ntypes # number of atom types (types vary in [0..ntypes-1]) | ||
- | startpot # file name for starting potential (*) | ||
- | endpot # file name for final potential (*) | ||
- | imdpot # file name prefix for imd potential (*) | ||
- | plotfile # file name for plotting potential (*) | ||
- | plotpointfile # | ||
- | imdpotsteps # number of points in each function in imd file | ||
- | dummy_r # Distance, where dummy_rho and dummy_phi are used (ignored) | ||
- | #optional options | ||
- | dummy_rho # dummy value of rho at dummy_r | ||
- | dummy_phi # vector (length ntypes) dummy values of phi_ii at dummy_r | ||
- | </ | ||
- | Prints the values of < | + | ==== awk scripts |
- | If dummy_phi is given, the potential is transformed so that < | + | The awk scripts are listed on a [[utilities/Awk_scripts|separate page]]. |
- | IMD potentials and potential plot files are also written. | ||