Copyright 2010, Torbjorn Bjorkman
I have added support for LAMMPS .data files with orthogonal and triclinic boxes. To convert a CIF-file to LAMMPS data file, simply run (in this directory)
./cif2cell /path/to/file.cif --no-reduce -p lammps -o cif_file.data
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.
| code | alloy support | output files |
|---|---|---|
| ASE | no | positions.py |
| 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 |
The distribution 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).
- The file PyCifRW-3.3.tar.gz, containing the PyCifRW package needed for parsing CIF files.
Prerequisites: The program requires Python 2.4 or higher and the PyCIFRW python package (which will be installed automatically if not present, see below for manual installation instructions). Note however that the output may be slightly different (but formally equivalent) with Python 2.4 than with later versions.
To install the program in your systems standard location, simply type: python setup.py install To choose a different location, add --prefix=where/you/want/it to the above line. For help and more options type python setup.py --help
The installation will also create a directory $PREFIX/lib/cif2cell that contains the manual and sample cif files.
The setup will install the manual, cif2cell.pdf, into the $PREFIX/lib/cif2cell/docs directory.
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.
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/.
Happy computing!
Torbjorn Bjorkman COMP, Aaalto University School ofScience and Technology, Department of Applied Physics, Espoo, Finland [email protected]