utilities
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utilities [2013/03/01 09:29] – daniel | utilities [2013/08/21 15:13] – 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. | + | |
- | ==== force2poscar | ||
- | Converts force files produced by [[http:// | + | ==== force2imd |
- | Compilation: | + | Converts a potfit configuration into an [[http:// |
- | Usage: | + | < |
- | | + | usage: force2imd [-h] [-n NUMBER] filename |
- | The information is always written to a file called POSCAR residing in the local directory. Use compile option '' | + | Convert |
- | ==== vasp2force | + | positional arguments: |
+ | filename | ||
- | Converts [[http:// | + | optional arguments: |
+ | -h, --help | ||
+ | -n NUMBER, --number NUMBER | ||
+ | number of the configuration to convert | ||
+ | </code> | ||
- | Compilation: | + | The IMD checkpoint file is written to standard output. |
- | Usage: | + | ==== force2poscar |
- | vasp2force [-c list] [-e file] [-f] [-l] [-r] [-s list] <OUTCAR files> | + | |
- | 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). | + | Convert a potfit configuration into a [[http:// |
- | An optional file can be specified, containing the energy of a single free atom calculated by [[http:// | + | |
< | < | ||
- | # Al Co Ni | + | usage: force2poscar [-h] [-n NUMBER] filename |
- | -0.000219 | + | |
+ | Convert a potfit configuration into a VASP POSCAR file. | ||
+ | |||
+ | positional arguments: | ||
+ | filename | ||
+ | |||
+ | optional arguments: | ||
+ | | ||
+ | -n NUMBER, --number NUMBER | ||
+ | number of the configuration to convert | ||
</ | </ | ||
- | Writes a force file to be used as a //potfit// reference configuration | + | The VASP POSCAR data is written |
- | Options: | + | ==== list_config |
+ | |||
+ | Prints a brief list of all configurations in a potfit config file. | ||
< | < | ||
- | -c < | + | usage: list_config [-h] filename |
- | (eg. " | + | |
- | -e < | + | |
- | if not found, " | + | |
- | | + | |
- | | + | |
- | | + | |
- | -s < | + | |
- | -w < | + | |
- | </ | + | |
- | ==== pottrans | + | Prints a brief list of all configurations in a potfit config file. |
- | Converts betweeen various potential models. | + | positional arguments: |
+ | filename | ||
- | Compilation: | + | optional arguments: |
+ | -h, --help | ||
+ | </ | ||
- | Usage: | + | 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 | ||
- | required parameters in paramfile (here with example values) | + | Generate analytic potential files for //potfit// from scratch. |
< | < | ||
- | ntypes | + | usage: makeapot [-h] [-n N] [-co CUTOFF] [-g] [-r] [-i TYPE] [-l] [-cp] |
- | ncols 3 # number of output potentials | + | [-f [FUNCTIONS [FUNCTIONS |
- | infile | + | |
- | outfile | + | |
- | nsteps | + | |
- | atomic_e-density_file | + | |
- | embedding_energy_file | + | |
- | core_potential_file | + | |
- | # optional parameters | + | Create an analytic potential file for potift. |
- | reorder | + | optional arguments: |
- | # ntypes parameters necessary | + | -h, --help |
- | r_start | + | -n N number of atoms types, runs from 0 to N-1 |
+ | -co CUTOFF, --cutoff CUTOFF | ||
+ | | ||
+ | | ||
+ | -r, --random | ||
+ | -i TYPE, --type TYPE interaction type, e.g. pair, eam, adp, ... | ||
+ | -l, --list | ||
+ | -cp | ||
+ | -f [FUNCTIONS [FUNCTIONS ...]] | ||
+ | name of potential | ||
+ | where i=1,2,3,... | ||
</ | </ | ||
- | 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 '' | + | ==== plotapot |
- | ==== list_config | + | This utility plots an analytic potential with gnuplot. |
- | Lists all configurations in a config file. | + | < |
+ | usage: plotapot [-h] [-f] [-p] [-s size] [-t terminal] | ||
+ | pot_file [pair_dist_file] | ||
- | Compilation: | + | Plot an analytic potfit potential using gnuplot. |
- | Usage: | + | positional arguments: |
- | | + | |
+ | pair_dist_file | ||
- | Scans a //potfit// configuration file and lists all configurations found. This includes | + | 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 | ==== potfit_setup | ||
Line 130: | Line 158: | ||
</ | </ | ||
- | ==== | + | ==== |
- | 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 ...]] | ||
- | < | + | Converts vasp output data into potfit reference configurations. |
- | potscale performs gauge transformations on EAM potentials. | + | positional arguments: |
+ | files list of OUTCAR files (plain or gzipped) | ||
- | Compilation: '' | + | 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 | ||
+ | </ | ||
- | Usage: | + | Reads information from all OUTCAR files in the current directory. |
- | potscale | + | An optional file can be specified, containing the energy of a single free atom calculated by [[http:// |
- | + | ||
- | Required parameters | + | |
< | < | ||
- | ntypes # number of atom types (types vary in [[0..ntypes-1]]) | + | # Al Co Ni |
- | startpot # file name for starting potential (*) | + | -0.000219 -0.993872 |
- | 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). | + | 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. |
- | 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. | + | ==== awk scripts |
+ | The awk scripts are listed on a [[utilities/ |