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--- utilities [2013/03/01 09:29] – daniel
+++ utilities [2018/01/06 10:44] (current) – removed daniel
@@ Line 1: / Line 1: @@
-~~NOTOC~~
-====== 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.
-[[#force2poscar|force2poscar]]\\
- Converts force files (IMD output) to vasp POSCAR files.
-[[#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 all configurations in a configuration file.
-[[#potfit_setup|potfit_setup]]\\
-Creates a parameter file for //potfit// from scratch.
-[[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,...
-[[#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.
-Compilation: ''make force2poscar [-DSTRESS]''
-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.
-====  vasp2force  ====
-Converts [[http://cms.mpi.univie.ac.at/vasp/|VASP]] output to force files.
-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>
-# 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.
-Options:
-<code>
- -c <list>              list of chemical species to use
-                        (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  ====
-Converts betweeen various potential models.
-Compilation:  ''make pottrans''
-Usage:
-  pottrans <paramfile>
-required parameters in paramfile (here with example values)
-<code>
-ntypes     2           # number of atom types
-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
-reorder     0 1        # permutes order of potentials in final file,
-                       # ntypes parameters necessary
-r_start   1.8 1.8 1.8  # minimal r for each column in output potential
-</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.
-====  list_config  ====
-Lists all configurations in a config file.
-Compilation:  ''make list_config''
-Usage:
-  list_config <config_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.
-====  potfit_setup  ====
-This utility generates a simple parameter file for //potfit//.
-Usage:
-  potfit_setup [-c config file] [-p potential file] [-s prefix]
-<code>
- -c <config file>       name of the configuration file
- -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  ====
-The awk scripts are listed on a [[utilities/Awk_scripts|separate page]].
-====  potscale  ====
-<html><span style="color:red;font-size:150%;">Not maintained anymore !</span></html>
-potscale performs gauge transformations on EAM potentials.
-Compilation: ''make potscale''
-Usage:
-  potscale <paramfile>
-Required parameters in paramfile:
-<code>
-ntypes		# number of atom types (types vary in [[0..ntypes-1]])
-startpot	# file name for starting potential (*)
-endpot		# file name for final potential (*)
-imdpot		# file name prefix for imd potential (*)
-plotfile	# file name for plotting potential (*)
-plotpointfile	# file name for plotting the sampling points (*)
-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
-</code>
-Prints the values of $\rho_0$(dummy_r) and $\Phi_{ii}$(dummy_r).
-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.