utilities
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utilities [2013/02/28 13:31] – created daniel | utilities [2013/03/01 09:53] – daniel | ||
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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. | ||
- | ;[[# | + | [[# |
- | :Converts force files (IMD output) to vasp POSCAR files. | + | |
- | ; | + | |
- | :Converts vasp output (POSCAR, OUTCAR) to reference configuration data. | + | |
- | ; | + | |
- | :Converts various IMD and '' | + | |
- | ; | + | |
- | :List all configurations in a configuration file. | + | |
- | ; | + | |
- | :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 === | + | [[# |
+ | Converts vasp output (POSCAR, OUTCAR) to reference configuration data. | ||
- | Converts | + | [[# |
+ | Converts | ||
- | Compilation: | + | [[# |
+ | List all configurations in a configuration file. | ||
+ | |||
+ | [[# | ||
+ | Creates a parameter file for //potfit// from scratch. | ||
+ | |||
+ | [[Utilities/ | ||
+ | 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:// | ||
+ | |||
+ | Compilation: | ||
Usage: | Usage: | ||
- | force2poscar input.force | + | |
- | The information is always written to a file called POSCAR residing in the local directory. Use compile option -DSTRESS if your force file includes stress tensor information. | + | The information is always written to a file called POSCAR residing in the local directory. Use compile option |
- | === vasp2force === | + | ==== |
- | Converts [http:// | + | Converts |
- | Compilation: | + | Compilation: |
Usage: | Usage: | ||
- | 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). | 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:// | + | An optional file can be specified, containing the energy of a single free atom calculated by [[http:// |
- | # Al Co Ni | + | < |
- | | + | # Al Co Ni |
+ | -0.000219 -0.993872 -0.855835 | ||
+ | </ | ||
- | Writes a force file to be used as a '' | + | 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. |
Options: | Options: | ||
- | <tt>-c < | + | <code> |
- | :list of chemical species to use (e.g. " | + | -c < |
- | <tt>-e < | + | |
- | : | + | -e < |
- | <tt>-f</ | + | |
- | :Uses only final configuration | + | |
- | <tt>-l</ | + | |
- | :List all chemical species found in OUTCAR and exit. | + | |
- | <tt>-r</ | + | |
- | :Scan recursively for OUTCAR files in every subdirectory. | + | -w <weight> |
- | <tt>-s list</tt> | + | </ |
- | :List is a comma separated list of ionic steps to use, e.g. " | + | |
- | <tt>-w weight</tt> | + | |
- | :Assign this weight | + | |
- | === pottrans === | + | ==== |
Converts betweeen various potential models. | Converts betweeen various potential models. | ||
- | Compilation: | + | Compilation: |
Usage: | Usage: | ||
- | pottrans < | + | |
required parameters in paramfile (here with example values) | required parameters in paramfile (here with example values) | ||
- | <code><pre> | + | < |
ntypes | ntypes | ||
ncols 3 # number of output potentials | ncols 3 # number of output potentials | ||
Line 83: | Line 92: | ||
core_potential_file | core_potential_file | ||
- | #optional parameters | + | # optional parameters |
reorder | reorder | ||
# ntypes parameters necessary | # ntypes parameters necessary | ||
r_start | r_start | ||
- | </ | + | </ |
- | in.pot is converted to out.pot. in.pot can be of IMD potential format 1 or 2, out.pot is of '' | + | 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 '' | + | To convert from //potfit// to IMD use //potfit// with '' |
- | === list_config === | + | ==== |
Lists all configurations in a config file. | Lists all configurations in a config file. | ||
- | Compilation: | + | Compilation: |
Usage: | Usage: | ||
- | list_config < | + | |
- | 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 === | + | ==== |
- | This utility generates a simple parameter file for '' | + | This utility generates a simple parameter file for //potfit//. |
Usage: | Usage: | ||
- | potfit_setup [-c config file] [-p potential file] [-s prefix] | + | |
+ | |||
+ | < | ||
+ | -c <config file> | ||
+ | -p < | ||
+ | for analytic potentials this can easily be created with | ||
+ | the makeapot script from the awkscripts | ||
+ | -s < | ||
+ | the following files will be checked: | ||
+ | < | ||
+ | if they are not found, -c and -p will be read | ||
+ | </ | ||
- | < | + | ==== awk scripts |
- | :name of the configuration file | + | |
- | < | + | |
- | :name of the potential file (for analytic potentials this can easily be created with the < | + | |
- | < | + | |
- | :prefix for all files, overrides -c and -p | + | |
- | :the following files will be checked: < | + | |
- | === awk scripts | + | The awk scripts |
- | The awk scripts are listed on a [[Utilities/ | + | ==== potscale |
- | === potscale === | + | <html>< |
- | ''' | + | |
potscale performs gauge transformations on EAM potentials. | potscale performs gauge transformations on EAM potentials. | ||
- | Compilation: | + | Compilation: |
Usage: | Usage: | ||
- | potscale < | + | |
Required parameters in paramfile: | Required parameters in paramfile: | ||
- | <code><pre> | + | < |
- | ntypes # number of atom types (types vary in [0..ntypes-1]) | + | ntypes # number of atom types (types vary in [[0..ntypes-1]]) |
startpot # file name for starting potential (*) | startpot # file name for starting potential (*) | ||
endpot # file name for final potential (*) | endpot # file name for final potential (*) | ||
Line 147: | Line 160: | ||
dummy_r # Distance, where dummy_rho and dummy_phi are used (ignored) | dummy_r # Distance, where dummy_rho and dummy_phi are used (ignored) | ||
- | #optional options | + | # optional options |
dummy_rho # dummy value of rho at dummy_r | dummy_rho # dummy value of rho at dummy_r | ||
dummy_phi # vector (length ntypes) dummy values of phi_ii at dummy_r | dummy_phi # vector (length ntypes) dummy values of phi_ii at dummy_r | ||
- | </ | + | </ |
- | Prints the values of < | + | Prints the values of $\rho_0$(dummy_r) and $\Phi_{ii}$(dummy_r). |
- | If dummy_phi is given, the potential is transformed so that < | + | 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. | IMD potentials and potential plot files are also written. | ||