CIF2Cell: Generating geometries for electronic structure programs

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• 作者：Torbjö ; rn Bjö ; rkman^a ; ^{torbjorn@cc.hut.fi}
• 关键词：Electronic structure calculations ; Electron density of states and band structure of crystalline solids ; Crystallographic databases ; Structure of solids and liquids ; Crystallography
• 刊名：Computer Physics Communications
• 出版年：2011
• 出版时间：May 2011
• 年：2011
• 卷：182
• 期：5
• 页码：1183-1186
• 全文大小：123 K

文摘

The CIF2Cell program generates the geometrical setup for a number of electronic structure programs based on the crystallographic information in a Crystallographic Information Framework (CIF) file. The program will retrieve the space group number, Wyckoff positions and crystallographic parameters, make a sensible choice for Bravais lattice vectors (primitive or principal cell) and generate all atomic positions. Supercells can be generated and alloys are handled gracefully. The code currently has output interfaces to the electronic structure programs ABINIT, CASTEP, CPMD, Crystal, Elk, Exciting, EMTO, Fleur, RSPt, Siesta and VASP.

Program summary

Program title: CIF2Cell

Catalogue identifier: AEIM_v1_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIM_v1_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: GNU GPL version 3

No. of lines in distributed program, including test data, etc.: 12 691

No. of bytes in distributed program, including test data, etc.: 74 933

Distribution format: tar.gz

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)

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] and VASP [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:10.1016/j.cpc.2009.07.007; 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: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: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.