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utilities [2013/08/21 15:03] – danielutilities [2013/08/21 15:13] – daniel
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 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'' +
- +
-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). +
-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: makeapot [-h] [-n N] [-co CUTOFF] [-g] [-r] [-i TYPE] [-l] [-cp] 
--0.000219 -0.993872 -0.855835 +                [-f [FUNCTIONS [FUNCTIONS ...]]]
-</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.+Create an analytic potential file for potift.
  
-Options: +optional arguments: 
- +  -h, --help            show this help message and exit 
-<code> +  -n N                  number of atoms types, runs from 0 to N-1 
- -c <list>              list of chemical species to use +  -co CUTOFF, --cutoff CUTOFF 
-                        (eg. "vasp2force.sh -c Al=0,Mn=1,Pd=2") +                        cutoff radius 
- -e <file>              specify file to read single atom energies from +  -g                    use global cutoff parameter 
-                        if not found, "0" will be used for every atom type +  -r, --random          randomize the starting potential 
- -f                     only use the final configuration from OUTCAR +  -i TYPE, --type TYPE  interaction type, e.g. pair, eam, adp, ... 
- -l                     list all chemical species found in OUTCAR and exit +  -l, --list            list options which are available 
- -r                     scan recursively for OUTCAR files +  -cp                   enable chemical potentials (only for pair) 
- -s <list>              comma separated list of configurations to use +  -f [FUNCTIONS [FUNCTIONS ...]] 
- -w <weight>            change weight for all configurations to <weight>+                        name of potential functions, either name or i*name, 
 +                        where i=1,2,3,...
 </code> </code>
  
-====  pottrans  ==== 
  
-Converts betweeen various potential models.+====  plotapot  ====
  
-Compilation:  ''make pottrans'' +This utility plots an analytic potential with gnuplot.
- +
-Usage: +
-  pottrans <paramfile> +
- +
-required parameters in paramfile (here with example values)+
  
 <code> <code>
-ntypes     2           # number of atom types +usage: plotapot [-h] [-f] [-p] [-s size] [-t terminal] 
-ncols      3           # number of output potentials +                pot_file [pair_dist_file]
-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+Plot an analytic potfit potential using gnuplot.
  
-reorder     0 1        # permutes order of potentials in final file, +positional arguments: 
-                       # ntypes parameters necessary +  pot_file        potfit potential file 
-r_start   1.8 1.8 1.8  # minimal r for each column in output potential+  pair_dist_file  pair distribution file 
 + 
 +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> </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. 
- 
  
 ====  potfit_setup  ==== ====  potfit_setup  ====
Line 175: Line 158:
 </code> </code>
  
-====  awk scripts  ====+====  vasp2force  ====
  
-The awk scripts are listed on a [[utilities/Awk_scripts|separate page]].+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 ...]]
  
 +Converts vasp output data into potfit reference configurations.
 +
 +positional arguments:
 +  files                 list of OUTCAR files (plain or gzipped)
 +
 +optional arguments:
 +  -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>
 +# Al      Co        Ni
 +-0.000219 -0.993872 -0.855835
 +</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.
 +
 +
 +====  awk scripts  ====
 +
 +The awk scripts are listed on a [[utilities/Awk_scripts|separate page]].