command_line Package

command_line Package

This package contains various command line interfaces to programs used in pymatgen that do not have Python equivalents.

aconvasp_caller Module

Interface with command line aconvasp. http://aflowlib.org/ Only tested on Linux. Inspired by Shyue”s qhull_caller WARNING: you need to have a convasp in your path for this to work

exception AconvaspError(msg)

Bases: exceptions.Exception

Exception class for aconvasp. Raised when the aconvasp gives an error

get_conv_struct(structure)

Get a minkowski reduced structure

get_minkowski_red(structure)

Get a minkowski reduced structure

get_num_division_kpoints(structure, kppa)

Get kpoint divisions for a given k-point density (per reciprocal-atom): kppa and a given structure

get_prim_struct(structure)

Get standard primitive

get_vasp_kpoint_file_sym(structure)

get a kpoint file ready to be ran in VASP along the symmetry lines of the Brillouin Zone

run_aconvasp_command(command, structure)

Helper function for calling aconvasp with different arguments

bader_caller Module

This module implements an interface to the Henkelmann et al.’s excellent Fortran code for calculating a Bader charge analysis.

This module depends on a compiled bader executable available in the path. Please download the library at http://theory.cm.utexas.edu/vasp/bader/ and follow the instructions to compile the executable.

If you use this module, please cite the following:

G. Henkelman, A. Arnaldsson, and H. Jonsson, “A fast and robust algorithm for Bader decomposition of charge density”, Comput. Mater. Sci. 36, 254-360 (2006).

BaderAnalysis(*args, **kwargs)

Bader analysis for a CHGCAR.

enumlib_caller Module

This module implements an interface to enumlib, Gus Hart”s excellent Fortran code for enumerating derivative structures.

This module depends on a compiled enumlib with the executables multienum.x and makestr.x available in the path. Please download the library at http://enum.sourceforge.net/ and follow the instructions in the README to compile these two executables accordingly.

If you use this module, please cite the following:

Gus L. W. Hart and Rodney W. Forcade, “Algorithm for generating derivative structures,” Phys. Rev. B 77 224115 (26 June 2008)

Gus L. W. Hart and Rodney W. Forcade, “Generating derivative structures from multilattices: Application to hcp alloys,” Phys. Rev. B 80 014120 (July 2009)

Gus L. W. Hart, Lance J. Nelson, and Rodney W. Forcade, “Generating derivative structures at a fixed concentration,” Comp. Mat. Sci. 59 101-107 (March 2012)

EnumlibAdaptor(*args, **kwargs)

An adaptor for enumlib.

structures

List of all enumerated structures.