utilities
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utilities [2013/03/01 09:53] – daniel | utilities [2013/08/21 15:03] – daniel | ||
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The potfit/util directory contains a number of utility programs for the preparation of //potfit// input files and the postprocessing of //potfit// output files. | The potfit/util directory contains a number of utility programs for the preparation of //potfit// input files and the postprocessing of //potfit// output files. | ||
+ | |||
+ | [[# | ||
+ | | ||
[[# | [[# | ||
- | Converts force files (IMD output) to vasp POSCAR | + | Convert a potfit configuration into a VASP POSCAR |
- | + | ||
- | [[# | + | |
- | Converts vasp output (POSCAR, OUTCAR) to reference configuration data. | + | |
- | + | ||
- | [[# | + | |
- | Converts various IMD and //potfit// potential formats. | + | |
[[# | [[# | ||
- | List all configurations in a configuration | + | |
+ | [[# | ||
+ | | ||
+ | |||
+ | [[# | ||
+ | Plot an analytic potfit potential using gnuplot. | ||
+ | |||
[[# | [[# | ||
- | Creates a parameter file for //potfit// from scratch. | + | Creates a parameter file for //potfit// from scratch. |
- | [[Utilities/ | + | [[# |
+ | | ||
+ | |||
+ | [[Utilities/ | ||
A series of awk scripts to handle various tasks with potential files, like combining, appending, creating from analytical functions, generating from scratch, plotting, | 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 //potfit// EAM potentials. | ||
---- | ---- | ||
+ | |||
+ | |||
+ | ==== force2imd | ||
+ | |||
+ | Converts a potfit configuration into an [[http:// | ||
+ | |||
+ | < | ||
+ | usage: force2imd [-h] [-n NUMBER] filename | ||
+ | |||
+ | Convert a potfit configuration into an IMD checkpoint file. | ||
+ | |||
+ | 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 | ==== force2poscar | ||
- | Converts force files produced by [[http:// | + | Convert a potfit |
- | Compilation: '' | + | < |
+ | usage: force2poscar [-h] [-n NUMBER] filename | ||
- | Usage: | + | Convert a potfit configuration into a VASP POSCAR file. |
- | | + | |
+ | positional arguments: | ||
+ | | ||
+ | |||
+ | optional arguments: | ||
+ | -h, --help | ||
+ | -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 | ||
+ | |||
+ | optional arguments: | ||
+ | -h, --help | ||
+ | </ | ||
- | The information is always written to a file called POSCAR residing in the local directory. Use compile option '' | + | Scans a //potfit// configuration |
+ | This includes | ||
+ | weight of the configuration. | ||
==== vasp2force | ==== vasp2force | ||
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To convert from //potfit// to IMD use //potfit// with '' | To convert from //potfit// to IMD use //potfit// with '' | ||
- | ==== list_config | ||
- | |||
- | Lists all configurations in a config file. | ||
- | |||
- | Compilation: | ||
- | |||
- | Usage: | ||
- | list_config < | ||
- | |||
- | 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 | ==== potfit_setup | ||
Line 136: | Line 179: | ||
The awk scripts are listed on a [[utilities/ | The awk scripts are listed on a [[utilities/ | ||
- | ==== potscale | ||
- | |||
- | < | ||
- | |||
- | potscale performs gauge transformations on EAM potentials. | ||
- | |||
- | Compilation: | ||
- | |||
- | Usage: | ||
- | potscale < | ||
- | |||
- | Required parameters in paramfile: | ||
- | |||
- | < | ||
- | 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 $\rho_0$(dummy_r) and $\Phi_{ii}$(dummy_r). | ||
- | |||
- | If dummy_phi is given, the potential is transformed so that $\rho_0$(dummy_r)=dummy_rho and $\Phi_{ii}$(dummy_r)=dummy_phi_ii. | ||
- | |||
- | IMD potentials and potential plot files are also written. | ||