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utilities [2013/03/01 09:29] – danielutilities [2013/08/29 11:22] – 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.
 +
 +[[#force2imd|force2imd]]\\
 + Convert a potfit configuration into an IMD checkpoint file.
  
 [[#force2poscar|force2poscar]]\\ [[#force2poscar|force2poscar]]\\
- Converts force files (IMD output) to vasp POSCAR files. + Convert a potfit configuration into a VASP POSCAR file.
- +
-[[#vasp2force|vasp2force]]\\ +
-Converts vasp output (POSCAR, OUTCAR) to reference configuration data. +
- +
-[[#pottrans|pottrans]]\\ +
-Converts various IMD and //potfit// potential formats.+
  
 [[#list_config|list_config]]\\ [[#list_config|list_config]]\\
-List all configurations in a configuration file.+ 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]]\\ [[#potfit_setup|potfit_setup]]\\
-Creates a parameter file for //potfit// from scratch.+ Creates a parameter file for //potfit// from scratch. 
 + 
 +[[#vasp2force|vasp2force]]\\ 
 + Converts vasp output (POSCAR, OUTCAR) to reference configuration data.
  
-[[Utilities/Awk_scripts|awk scripts]]\\+[[Utilities/awk_scripts|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,... A series of awk scripts to handle various tasks with potential files, like combining, appending, creating from analytical functions, generating from scratch, plotting,...
  
-[[#potscale|potscale]]\\ +----
-Performs gauge transformations of //potfit// EAM potentials.+
  
-====  force2poscar  ==== 
  
-Converts force files produced by [[http://imd.itap.physik.uni-stuttgart.de/|IMD]] and used by //potfit// to [[http://cms.mpi.univie.ac.at/vasp/|VASP]] input file POSCAR.+====  force2imd  ====
  
-Compilation: ''make force2poscar [-DSTRESS]''+Converts a potfit configuration into an [[http://imd.itap.physik.uni-stuttgart.de/|IMD]] checkpoint file.
  
-Usage:  +<code> 
-  force2poscar input.force+usage: force2imd [-h] [-n NUMBER] filename
  
-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.+Convert a potfit configuration into an IMD checkpoint file.
  
-====  vasp2force  ====+positional arguments: 
 +  filename              name of the potfit config file
  
-Converts [[http://cms.mpi.univie.ac.at/vasp/|VASP]] output to force files.+optional arguments: 
 +  -h, --help            show this help message and exit 
 +  -n NUMBER, --number NUMBER 
 +                        number of the configuration to convert 
 +</code>
  
-Compilation: ''make vasp2force''+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://cms.mpi.univie.ac.at/vasp/|VASP]] POSCAR file.
-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> <code>
-# Al      Co        Ni +usage: force2poscar [-h] [-n NUMBER] filename 
--0.000219 -0.993872 -0.855835+ 
 +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> </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.+The VASP POSCAR data is written to standard output.
  
-Options:+====  list_config  ==== 
 + 
 +Prints a brief list of all configurations in a potfit config file.
  
 <code> <code>
- -c <list>              list of chemical species to use +usage: list_config [-h] filename
-                        (eg. "vasp2force.sh -c Al=0,Mn=1,Pd=2") +
- -e <file>              specify file to read single atom energies from +
-                        if not found, "0" will be used for every atom type +
- -f                     only use the final configuration from OUTCAR +
- -l                     list all chemical species found in OUTCAR and exit +
- -r                     scan recursively for OUTCAR files +
- -s <list>              comma separated list of configurations to use +
- -w <weight>            change weight for all configurations to <weight> +
-</code>+
  
-====  pottrans  ====+Prints a brief list of all configurations in a potfit config file.
  
-Converts betweeen various potential models.+positional arguments: 
 +  filename    name of the potfit config file
  
-Compilation:  ''make pottrans''+optional arguments: 
 +  -h, --help  show this help message and exit 
 +</code>
  
-Usage: +Scans a //potfit// configuration file and lists all configurations found.  
-  pottrans <paramfile>+This includes the origin (if comment is found), the starting line, number of atoms and  
 +weight of the configuration.
  
-required parameters in paramfile (here with example values)+====  makeapot  ==== 
 + 
 +Generate analytic potential files for //potfit// from scratch.
  
 <code> <code>
-ntypes     2           # number of atom types +usage: makeapot [-h] [-n N] [-co CUTOFF] [-g] [-r] [-i TYPE] [-l] [-cp] 
-ncols      3           # number of output potentials +                [-f [FUNCTIONS [FUNCTIONS ...]]]
-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+Create an analytic potential file for potift.
  
-reorder     0 1        # permutes order of potentials in final file, +optional arguments: 
-                       # ntypes parameters necessary +  -h, --help            show this help message and exit 
-r_start   1.8 1.8 1.8  # minimal r for each column in output potential+  -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> </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.+====  plotapot  ====
  
-====  list_config  ====+This utility plots an analytic potential with gnuplot.
  
-Lists all configurations in a config file.+<code> 
 +usage: plotapot [-h] [-f] [-p] [-s size] [-t terminal] 
 +                pot_file [pair_dist_file]
  
-Compilation:  ''make list_config''+Plot an analytic potfit potential using gnuplot.
  
-Usage: +positional arguments: 
-  list_config <config_file>+  pot_file        potfit potential file 
 +  pair_dist_file  pair distribution file
  
-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.+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  ==== ====  potfit_setup  ====
  
 This utility generates a simple parameter file for //potfit//. This utility generates a simple parameter file for //potfit//.
- 
-Usage: 
-  potfit_setup [-c config file] [-p potential file] [-s prefix] 
  
 <code> <code>
- -c <config file>       name of the configuration file +usage: potfit_setup [-h] [-c config file] [-p potential file] [-s prefix]
- -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>+
  
-====  awk scripts  ====+Create a simple potfit parameter file from scratch.
  
-The awk scripts are listed on a [[utilities/Awk_scripts|separate page]].+optional arguments: 
 +  -h, --help         show this help message and exit 
 +  -c config file     name of the potfit configuration file 
 +  -p potential file  name of the potfit potential file 
 +  -s prefix          prefix for all files
  
-====  potscale  ====+The prefix takes precedence over the -c and -p switches.If the <prefix>.pot 
 +and <prefix>.config files are not found, the values of -c and -p are checked. 
 +</code>
  
-<html><span style="color:red;font-size:150%;">Not maintained anymore !</span></html>+If the config file is given via the -c or -s option, the number of atom 
 +types is automatically determined and adjusted in the output. 
 +====  vasp2force  ====
  
-potscale performs gauge transformations on EAM potentials.+Converts [[http://cms.mpi.univie.ac.at/vasp/|VASP]] output data into potfit reference configurations.
  
-Compilation: ''make potscale''+<code> 
 +usage: vasp2force [-h] [-c C] [-e E] [-f] [-l] [-r] [-s CONFIGS] [-w WEIGHT] 
 +                  [files [files ...]]
  
-Usage: +Converts vasp output data into potfit reference configurations.
-  potscale <paramfile>+
  
-Required parameters in paramfile:+positional arguments: 
 +  files                 list of OUTCAR files (plain or gzipped)
  
-<code> +optional arguments: 
-ntypes # number of atom types (types vary in [[0..ntypes-1]])  +  -h, --help            show this help message and exit 
-startpot # file name for starting potential (*) +  -c C                  list of chemical species to use, e.g. -c Mg=0,Zn=1 
-endpot # file name for final potential (*) +  -e E                  file with single atom energies (NYI) 
-imdpot # file name prefix for imd potential (*) +  -f, --final           use only the final configuration from OUTCAR 
-plotfile # file name for plotting potential (*) +  -l, --list            list all chemical species and exit 
-plotpointfile # file name for plotting the sampling points (*)+  -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>
  
-imdpotsteps # number of points in each function in imd file +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). 
-dummy_r # Distance, where dummy_rho and dummy_phi are used (ignored)+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.:
  
-# optional options +<code> 
-dummy_rho # dummy value of rho at dummy_r +# Al      Co        Ni 
-dummy_phi # vector (length ntypes) dummy values of phi_ii at dummy_r+-0.000219 -0.993872 -0.855835
 </code> </code>
  
-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. +