donaldchung-hk/cif2cell

Generating geometries for electronic structure calculations from CIF files.

A tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The code will generate the crystal structure for the primitive cell or the conventional cell.

CURRENTLY SUPPORTS

code	alloy support	output files
ASE	no	positions.py
ATAT	yes	[compoundname].in
VASP	VCA	POSCAR
ABINIT	no	[compoundname].in
Siesta	no	[compoundname].fdf
CPMD	no	[compoundname].inp
CASTEP	VCA	[compoundname].cell
Crystal09	no	[compoundname].d12
quantum espresso	no	[compoundname].in
FHI-aims	no	geometry.in
RSPt	no	symt.inp
Fleur	no	inp_[compoundname]
hutsepot	no	[compoundname].sys
cellgen	no	cellgen.inp
elk	no	GEOMETRY.OUT
exciting	no	input.xml
spacegroup	no	spacegroup.in
ncol	no	[spacegroupname/compoundname].dat
		for bstr.
emto	yes	[spacegroupname/compoundname].dat
		for kstr, bmdl, shape, kgrn and kfcd
		in separate directories.
spr-kkr	yes	[compoundname].sys
xyz	no	[compoundname].xyz
crymol (gnxas)	no	[compoundname]_cry.in

CONTENTS

The repository includes:

• This README file.
• The file LICENSE with the GPLv3 license.
• The python files cif2cell, uctools.py and spacegroupdata.py
• Installation files, setup.py and MANIFEST.
• A manual.
• The directory cifs/ containing a set of example CIF files as well as the crystal structures of the full periodic table from COD, the Crystallography Open Database http://www.crystallography.net and also a few from ICSD (with permission).

INSTALLATION INSTRUCTIONS

Prerequisites

The program requires Python 2.4 or higher and the PyCIFRW python package (which will be installed automatically if not present). Note however that the output may be slightly different (but formally equivalent) with Python 2.4 than with later Python versions.

pip install cif2cell

The installation will also create a directory $PREFIX/lib/cif2cell that contains the manual and sample cif files.

DOCUMENTATION

The setup will install the manual, cif2cell.pdf, into the $PREFIX/lib/cif2cell/docs directory.

RUNNING

Run cif2cell -h to get a listing of the different options. Example:

cif2cell Ni20Mn3P6.cif -p vasp --vasp-cartesian-positions

will generate a POSCAR file for VASP with the positions in cartesian format.

LICENSE INFORMATION

cif2cell is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

cif2cell is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with cif2cell. If not, see http://www.gnu.org/licenses/.

HOW TO CITE

Please use the following citation information:

Torbjorn Bjorkman, "CIF2Cell: Generating geometries for electronic structure programs", Computer Physics Communications 182, 1183-1186 (2011) doi: 10.1016/j.cpc.2011.01.013

My name is rendered in ascii above, bonus points for getting umlauts over both of the o's. See also below for a BibTeX entry for use with LaTeX, which should be readable for most scientific reference handling software.

@article{cif2cell,
title = "CIF2Cell: Generating geometries for electronic structure programs",
journal = "Computer Physics Communications",
volume = "182",
number = "5",
pages = "1183 - 1186",
year = "2011",
issn = "0010-4655",
doi = "10.1016/j.cpc.2011.01.013",
url = "http://www.sciencedirect.com/science/article/pii/S0010465511000336",
author = "Torbj\"orn Bj\"orkman"
}

Happy computing!

Torbjorn Bjorkman https://orcid.org/0000-0002-1154-9846