potfit wiki

open source force-matching

User Tools

Site Tools

utilities

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
Last revisionBoth sides next revision
utilities [2013/08/21 15:03] – danielutilities [2013/08/29 11:22] – daniel
Line 25: Line 25:
  Converts vasp output (POSCAR, OUTCAR) to reference configuration data.  Converts vasp output (POSCAR, OUTCAR) to reference configuration data.
  
-[[Utilities/old|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,...
  
Line 91: Line 91:
 weight of the configuration. weight of the configuration.
  
-====  vasp2force  ====+====  makeapot  ====
  
-Converts [[http://cms.mpi.univie.ac.at/vasp/|VASP]] output to force files.+Generate analytic potential files for //potfit// from scratch.
  
-Compilation: ''make vasp2force''+<code> 
 +usage: makeapot [-h] [-n N] [-co CUTOFF] [-g] [-r] [-i TYPE] [-l] [-cp] 
 +                [-f [FUNCTIONS [FUNCTIONS ...]]]
  
-Usage:  +Create an analytic potential file for potift.
-  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). +optional arguments: 
-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.: +  -h, --help            show this help message and exit 
- +  -n N                  number of atoms types, runs from 0 to N-1 
-<code> +  -co CUTOFF, --cutoff CUTOFF 
-# Al      Co        Ni +                        cutoff radius 
--0.000219 -0.993872 -0.855835+  -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>
  
-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:+====  plotapot  ==== 
 + 
 +This utility plots an analytic potential with gnuplot.
  
 <code> <code>
- -c <list>              list of chemical species to use +usage: plotapot [-h] [-f] [-p] [-s size] [-t terminal] 
-                        (eg. "vasp2force.sh -c Al=0,Mn=1,Pd=2") +                pot_file [pair_dist_file]
- -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  ====+Plot an analytic potfit potential using gnuplot.
  
-Converts betweeen various potential models.+positional arguments: 
 +  pot_file        potfit potential file 
 +  pair_dist_file  pair distribution file
  
-Compilation:  ''make pottrans''+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>
  
-Usage: +====  potfit_setup  ====
-  pottrans <paramfile>+
  
-required parameters in paramfile (here with example values)+This utility generates a simple parameter file for //potfit//.
  
 <code> <code>
-ntypes     2           # number of atom types +usage: potfit_setup [-h] [-c config file] [-p potential file] [-s prefix]
-ncols      3           # number of output potentials +
-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 a simple potfit parameter file from scratch.
  
-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+  -c config file     name of the potfit configuration file 
 +  -p potential file  name of the potfit potential file 
 +  -s prefix          prefix for all files 
 + 
 +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> </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.+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  ====
  
-To convert from //potfit// to IMD use //potfit// with ''opt 0'' in the parameter file.+Converts [[http://cms.mpi.univie.ac.at/vasp/|VASP]] output data into potfit reference configurations.
  
 +<code>
 +usage: vasp2force [-h] [-c C] [-e E] [-f] [-l] [-r] [-s CONFIGS] [-w WEIGHT]
 +                  [files [files ...]]
  
-====  potfit_setup  ====+Converts vasp output data into potfit reference configurations.
  
-This utility generates a simple parameter file for //potfit//.+positional arguments: 
 +  files                 list of OUTCAR files (plain or gzipped)
  
-Usage: +optional arguments: 
-  potfit_setup [-c config file] [-p potential file] [-s prefix]+  -h, --help            show this help message and exit 
 +  -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           use only the final configuration from OUTCAR 
 +  -l, --list            list all chemical species and exit 
 +  -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> 
 + 
 +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://cms.mpi.univie.ac.at/vasp/|VASP]] in a single line in the same order as in the OUTCAR file, e.g.:
  
 <code> <code>
- -c <config file>       name of the configuration file +# Al      Co        Ni 
- -p <potential file>    name of the potential file +-0.000219 -0.993872 -0.855835
-                        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> </code>
  
-====  awk scripts  ==== +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 awk scripts are listed on a [[utilities/Awk_scripts|separate page]]. +
- +