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Manuscript Title: CIF2Cell: Generating geometries for electronic structure programs
Authors: Torbjörn Björkman
Program title: CIF2Cell
Catalogue identifier: AEIM_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 182(2011)1183
Programming language: Python (versions 2.4-2.7).
Computer: Any computer that can run Python (versions 2.4-2.7).
Operating system: Any operating system that can run Python (versions 2.4-2.7).
Keywords: Electronic structure calculations, Electron density of states and band structure of crystalline solids, Crystallographic databases, Structure of solids and liquids, crystallography.
PACS: 71.15.-m 71.20.-b 61.68.+n 61..
Classification: 7.3, 7.8, 8.

External routines: PyCifRW[1]

Nature of problem:
Generate the geometrical setup of a crystallographic cell for a variety of electronic structure programs from data contained in a CIF file.

Solution method:
The CIF file is parsed using routines contained in the library PyCifRW[1], and crystallographic as well as bibliographic information is extracted. The program then generates the principal cell from symmetry information, crystal parameters, space group number and Wyckoff sites. Reduction to a primitive cell is then performed, and the resulting cell is output to suitably named files along with documentation of the information source generated from any bibliographic information contained in the CIF file. If the space group symmetries is not present in the CIF file the program will fall back on internal tables, so only the minimal input of space group, crystal parameters and Wyckoff positions are required. Additional key features are handling of alloys and supercell generation.

Additional comments:
Currently implements support for the following general purpose electronic structure programs: ABINIT[2,3], CASTEP[4], CPMD[5], Crystal[6], Elk[7], exciting[8], EMTO[9], Fleur[10], RSPt[11], Siesta[12] andVASP[13-16].

Running time:
The examples provided in the distribution take only seconds to run.

References:
[1] J. R. Hester, A validating CIF parser: PyCIFRW, Journal of Applied Crystallography 39 (4) (2006) 621 625. doi:10.1107/S0021889806015627. URL http://dx.doi.org/10.1107/S0021889806015627
[2] X. Gonze, G.-M. Rignanese, M. Verstraete, J.-M. Beuken, Y. Pouillon, R. Caracas, F. Jollet, M. Torrent, G. Zerah, M. Mikami, P. Ghosez, M. Veithen, J.-Y. Raty, V. Olevano, F. Bruneval, L. Reining, R. Godby, G. Onida, D. R. Hamann, D. C. Allan, A brief introduction to the abinit software package, Zeitschrift für Kristallographie 220 (12) (2005) 558 562.
[3] X. Gonze, B. Amadon, P.-M. Anglade, J.-M. Beuken, F. Bottin, P. Boulanger, F. Bruneval, D. Caliste, R. Caracas, M. Ct, T. Deutsch, L. Genovese, P. Ghosez, M. Giantomassi, S. Goedecker, D. Hamann, P. Hermet, F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet, M. Oliveira, G. Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf, M. Torrent, M. Verstraete, G. Zerah, J. Zwanziger, Abinit: First-principles approach to material and nanosystem properties, Computer Physics Communications 180 (12) (2009) 2582 2615, 40 YEARS OF CPC: A celebratory issue focused on quality software for high performance, grid and novel computing architectures. doi:DOI: 10.1016/j.cpc.2009.07.007. URL http://www.sciencedirect.com/science/article/B6TJ5-4WTRSCM- 3/2/20edf8da70cd808f10fe352c45d0c0be
[4] S. J. Clark, M. D. Segall, C. J. Pickard, P. J. Hasnip, M. J. Probert, K. Refson, M. C. Payne, First principles methods using castep, Zeitschrift für Kristallographie 220 (12) (2005) 567 570.
[5] URL http://www.cpmd.org
[6] R. Dovesi, R. Orlando, B. Civalleri, C. Roetti, V. R. Saunders, C. M. Zicovich-Wilson, Crystal: a computational tool for the ab initio study of the electronic properties of crystals, Zeitschrift für Kristallographie 220 (2005) 571 573. URL http://dx.doi.org/10.1524/zkri.220.5.571.65065
[7] URL http://elk.sourceforge.net
[8] URL http://exciting-code.org
[9] L. Vitos, Computational Quantum Mechanics for Materials Engineers; The EMTO Method and Applications, Springer London, 2007. doi:DOI:10.1007/978-1-84628-951-4.
[10] URL http://www.flapw.de
[11] J. M. Wills, O. Eriksson, M. Alouani, D. L. Price, Full-potential LMTO total energy and force calculations, in: H. Dreussé (Ed.), Electronic Structure and Physical Properties of Solids; The Uses of the LMTO Method, Springer, 1996, pp. 148 167.
[12] J. M. Soler, E. Artacho, J. D. Gale, A. García, J. Junquera, P. Ordejón, D. Sánchez-Portal, The siesta method for ab initio order- n materials simulation, Journal of Physics: Condensed Matter 14 (11) (2002) 2745. URL http://stacks.iop.org/0953-8984/14/i=11/a=302
[13] G. Kresse, J. Hafner, Ab initio molecular dynamics for liquid metals, Phys. Rev. B 47 (1) (1993) 558 561. doi:10.1103/PhysRevB.47.558.
[14] G. Kresse, J. Hafner, Ab initio molecular-dynamics simulation of the liquid-metal amorphous-semiconductor transition in germanium, Phys. Rev. B 49 (20) (1994) 14251 14269. doi:10.1103/PhysRevB.49.14251.
[15] G. Kresse, J. Furthmüller, Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set, Computational Materials Science 6 (1) (1996) 15 50. doi:DOI: 10.1016/0927-0256(96)00008-0. URL http://www.sciencedirect.com/science/article/B6TWM-3VRVTBF- 3/2/88689b1eacfe2b5fe57f09d37eff3b74
[16] G. Kresse, J. Furthmüller, Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set, Phys. Rev. B 54 (16) (1996) 11169 11186. doi:10.1103/PhysRevB.54.11169.