Supercell program

a combinatorial structure-generation approach for the local-level modeling of atomic substitutions and partial occupancies in crystals.

News


23-05-2019

Supercell v1.2 (perfromance increase).

The new version of supercell program is around 4 times faster, than the pervious one!

09-02-2019

Microsoft Windows support (experimental).

I would like to announce a Microsoft Windows platform support. You can download the binary below. An output structures packing is not supported(-a option). The binary tested on Windows 7 and Windows 10.

24-01-2019

Supercell v1.1: A maximum limit for processing structures has been increased.

The new version of supercell program can process up to 1015 total structures. The value is far beyond a reasonable limit due to calculation time. The average program performance is about 10-100 billion structures per day with standard desktop processor. Feedback is very welcome.


Introduction


supercell program workflow

A supercell approach is very old, universal and theoretically clean method for approximation of materials with point disorder1. But the method mostly applies to some particular cases, like low amount of impurity (one per supercell) or random disorder with special quasirandom structure (SQS) approximation2, because the number of derivative structures is one in these cases. In general, the number of derivative structures is high enough to be generated "by hand". A few programs exist, which can help to generate derivative structures (see review ). We believe that supercell program is one of the best choice, because the software was created to solve most of the technical problems of supercell approximation. The program includes algorithms for structure manipulation, supercell generation, permutations of atoms and vacancies, charge balancing, detecting symmetry-equivalent structures, electrostatic energy calculations and sampling output derivative structures. The software works with CIF files, therefore it is compatible with most of DFT software (VASP , CASTEP , Wien2k etc). It has a powerful command line interface and works out-of-box on Linux OSX and Windows (experimental support) platforms. The correctness of the program were verified by available literature data. The documentation includes open access paper, program interface manual, tutorial and variety of examples.


1Buerger, M. J. (1947). Derivative Crystal Structures. The Journal of Chemical Physics, 15(1), 1–16.
2Zunger, A., Wei, S. H., Ferreira, L. G., & Bernard, J. E. (1990). Special quasirandom structures. Physical Review Letters, 65(3), 353–356.


Getting started


Tutorial

The fastest way to start with supercell program is to look through the tutorial.

Article

You can read an open access article to get a full information about the program algorithms and scientific applications.

Manual

The manual explains all supercell command line options.

Examples

Check CIF files of disordered compounds and scripts for supercell program run.



Publications


Please cite the following paper, if you use supercell program:

Okhotnikov, K., Charpentier, T., & Cadars, S. (2016). Supercell program: a combinatorial structure-generation approach for the local-level modeling of atomic substitutions and partial occupancies in crystals. Journal of Cheminformatics, 8(1), 17. View Article

Papers which use/cite supercell program:

  • Salager, E., Sarou-Kanian, V., Sathiya, M., Tang, M., Leriche, J.-B., Melin, P., … Tarascon, J.-M. (2014). Solid-State NMR of the Family of Positive Electrode Materials Li2Ru1-ySnyO3 for Lithium-Ion Batteries. Chemistry of Materials, 26(24), 7009–7019. View Article
  • Okhotnikov, K. (2016). Comment on “Symmetry and random sampling of symmetry independent configurations for the simulation of disordered solids”, View Article
  • Fischer, M., & Angel, R. J. (2017). Accurate structures and energetics of neutral-framework zeotypes from dispersion-corrected DFT calculations. The Journal of Chemical Physics, 146(17), 174111. View Article
  • Cadars, S., Ahn, N. H., Okhotnikov, K., Shin, J., Vicente, A., Hong, S. B., & Fernandez, C. (2017). Modeling short-range substitution order and disorder in crystals: Application to the Ga/Si distribution in a natrolite zeolite. Solid State Nuclear Magnetic Resonance, 84, 182–195. View Article, View Example
  • Hong, S. U., Singh, S. P., Pyo, M., Park, W. B., & Sohn, K.-S. (2017). Density functional theory calculations for the band gap and formation energy of Pr4−xCaxSi12O3+xN18−x; a highly disordered compound with low symmetry and a large cell size. Phys. Chem. Chem. Phys., 19(25), 16702–16712. View Article
  • Kim, J. (2017). The Role of Auxiliary Alkali Metal Ions on Scheelite Structure Double Molybdate and Tungstate Phosphors. Inorganic Chemistry, 56(14), 8078–8086. View Article
  • Sharma, R. & Maharjan S. (2017). First Principle Calculation of Lattice Constants for Generalised Quasirandom Structures of Ingan Alloy, IJSR, 6(6) 1817, View Article
  • M. Dieb, T., Ju, S., Yoshizoe, K., Hou, Z., Shiomi, J., & Tsuda, K. (2017). MDTS: automatic complex materials design using Monte Carlo tree search. Science and Technology of Advanced Materials, 18(1), 498–503. View Article
  • Fernandez-Carrion, A. J., Al Saghir, K., Veron, E., Becerro, A. I., Porcher, F., Wisniewski, W., … Allix, M. (2017). Local Disorder and Tunable Luminescence in Sr1–x/2Al2–xSixO4 (0.2 ≤ x ≤ 0.5) Transparent Ceramics. Inorganic Chemistry, 56(23), 14446–14458. View Article
  • Rakhmatullin, A., Boča, M., Mlynáriková, J., Hadzimová, E., Vasková, Z., Polovov, I. B., & Mičušík, M. (2018). Solid state NMR and XPS of ternary fluorido-zirconates of various coordination modes. Journal of Fluorine Chemistry, 208, 24–35. View Article
  • Sicolo, S., Kalcher, C., Sedlmaier, S. J., Janek, J., & Albe, K. (2018). Diffusion mechanism in the superionic conductor Li4PS4I studied by first-principles calculations. Solid State Ionics, 319, 83–91. View Article
  • M. Dieb, T., Hou, Z., & Tsuda, K. (2018). Structure prediction of boron-doped graphene by machine learning. The Journal of Chemical Physics, 148(24), 241716. View Article
  • Juarez-Perez, E. J., Ono, L. K., Maeda, M., Jiang, Y., Hawash, Z., & Qi, Y. (2018). Photodecomposition and thermal decomposition in methylammonium halide lead perovskites and inferred design principles to increase photovoltaic device stability. Journal of Materials Chemistry A, 6(20), 9604–9612. View Article
  • Kim, J., Tahara, D., Miura, Y., & Kim, B. G. (2018). First-principle calculations of electronic structures and polar properties of (κ, ε)-Ga2O3. Applied Physics Express, 11(6), 061101. View Article
  • Onuma, T., Ono, M., Ishii, K., Kaneko, K., Yamaguchi, T., Fujita, S., & Honda, T. (2018). Impact of local arrangement of Mg and Zn atoms in rocksalt-structured MgxZn1−xO alloys on bandgap and deep UV cathodoluminescence peak energies. Applied Physics Letters, 113(6), 061903. View Article
  • Lotfi, S., Oliynyk, A. O., & Brgoch, J. (2018). Polyanionic Gold–Tin Bonding and Crystal Structure Preference in REAu1.5Sn0.5 (RE = La, Ce, Pr, Nd). Inorganic Chemistry, 57(17), 10736–10743. View Article
  • Hoedl, M. F., Makagon, E., Lubomirsky, I., Merkle, R., Kotomin, E. A., & Maier, J. (2018). Impact of point defects on the elastic properties of BaZrO3: Comprehensive insight from experiments and ab initio calculations. Acta Materialia, 160, 247–256. View Article
  • Han, U., Park, W. B., Singh, S. P., Pyo, M., & Sohn, K.-S. (2018). Determination of Possible Configurations for Li0.5CoO2 a Delithiated Li-Ion Battery Cathodes via DFT Calculation Coupled with a Multi-Objective Non-Dominated Sorting Genetic Algorithm (NSGA-III). Physical Chemistry Chemical Physics, 20(41), 26405–26413. View Article
  • Loh, J. Y. Y., & Kherani, N. P. (2018). Photodegradation Activity of Sputtered Indium Oxide and Suboxide Thin Films on Rhodamine-B Dye. The Journal of Physical Chemistry C, 122(42), 24120–24128. View Article
  • Naveen, N., Park, W. B., Singh, S. P., Han, S. C., Ahn, D., Sohn, K.-S., & Pyo, M. (2018). KCrS2 Cathode with Considerable Cyclability and High Rate Performance: The First K + Stoichiometric Layered Compound for Potassium-Ion Batteries. Small, 14(49), 1803495. View Article
  • Saleev, V. A., & Shipilova, A. V. (2018). Ab initio modeling of band gaps of cesium lead halide perovskites depending on the dopant amount. Journal of Physics: Conference Series, 1096, 012115. View Article
  • Kim, N., Perry, N. H., & Ertekin, E. (2019). Atomic Modeling and Electronic Structure of Mixed Ionic-Electronic Conductor SrTi1−xFexO3−x/2+δ Considered as a Mixture of SrTiO3 and Sr2Fe2O5. Chemistry of Materials, 31(1), 233–243. View Article
  • Fischer, M. (2019). Local Environment and Dynamic Behavior of Fluoride Anions in Silicogermanate Zeolites: A Computational Study of the AST Framework. The Journal of Physical Chemistry C, 123(3), 1852–1865. View Article
  • Son, S., Newton, A. G., Jo, K., Lee, J., & Kideok, D. (2019). Manganese speciation in Mn-rich CaCO3 : a density functional theory study. Geochimica et Cosmochimica Acta, 248, 231–241. View Article
  • Alvarado, J., Schroeder, M. A., Pollard, T. P., Wang, X., Lee, J. Z., Zhang, M., … Xu, K. (2019). Bisalt ether electrolytes: a pathway towards lithium metal batteries with Ni-rich cathodes. Energy & Environmental Science, 12(2), 780–794. View Article
  • Zolotarev, P., Nekrasova, N., Golov, A., & Eremin, R. (2019). A combined DFT/topological analysis approach for modeling disordered solid electrolytes. EPJ Web of Conferences, 201, 02005. View Article
  • Zolotarev, P., & Eremin, R. (2019). Comparative analysis of DFT-vdW vs. Coulomb energies for configurational space of layered cathode material at different delithiation levels. EPJ Web of Conferences, 201, 02004. View Article
  • Klar, P. B., Etxebarria, I., & Madariaga, G. (2019). Characterizing modulated structures with first-principles calculations: a unified superspace scheme of ordering in mullite. Acta Crystallographica Section A Foundations and Advances, 75(2), 260–272. View Article
  • Watanabe, E., Zhao, W., Sugahara, A., Mortemard de Boisse, B., Lander, L., Asakura, D., … Yamada, A. (2019). Redox-Driven Spin Transition in a Layered Battery Cathode Material. Chemistry of Materials, 31(7), 2358–2365. View Article
  • Loganathan, N., Bowers, G. M., Ngouana Wakou, B. F., Kalinichev, A. G., Kirkpatrick, R. james, & Yazaydin, A. O. (2019). Understanding methane/carbon dioxide partitioning in clay nano- and meso-pores with constant reservoir composition molecular dynamics modeling. Physical Chemistry Chemical Physics, 21(13), 6917–6924. View Article
  • Zhang, F., Wang, H.-W., Tominaga, K., Hayashi, M., & Sasaki, T. (2019). Terahertz Fingerprints of Short-Range Correlations of Disordered Atoms in Diflunisal. The Journal of Physical Chemistry A, 123(21), 4555–4564. View Article
  • Li, W., Asl, H. Y., Xie, Q., & Manthiram, A. (2019). Collapse of LiNi1-x-yCoxMnyO2 Lattice at Deep Charge Irrespective of Nickel Content in Lithium-Ion Batteries. Journal of the American Chemical Society, 141(13), 5097–5101. View Article
  • Dieb, T. M., Ju, S., Shiomi, J., & Tsuda, K. (2019). Monte Carlo tree search for materials design and discovery. MRS Communications, 1–5. View Article
  • De Lile, J. R., Lee, S. Y., Kim, H.-J., Pak, C., & Lee, S. G. (2019). First-principles study of the effect of compressive strain on oxygen adsorption in Pd/Ni/Cu-alloy-core@Pd/Ir-alloy-shell catalysts. New Journal of Chemistry, 43(21), 8195–8203. View Article
  • Moradabadi, A., & Kaghazchi, P. (2019). Defect chemistry in cubic Li6.25Al0.25La3Zr2O12 solid electrolyte: A density functional theory study. Solid State Ionics, 338, 74–79. View Article
  • Wang, T., Qiu, W., Feng, Q., Huang, K., Zhao, X., Bao, Q., … Liu, J. (2019). The critical role of oxygen-evolution kinetics in the electrochemical stability of oxide superionic conductors. Journal of Materials Chemistry A, 7(28), 17008–17013. View Article
  • Hussain, F., Li, P., & Li, Z. (2019). Theoretical Insights into Li-Ion Transport in LiTa2PO8. The Journal of Physical Chemistry C, acs.jpcc.9b03313. View Article
  • Mansouri Tehrani, A., Oliynyk, A. O., Rizvi, Z., Lotfi, S., Parry, M., Sparks, T. D., & Brgoch, J. (2019). Atomic substitution to balance hardness ductility and sustainability in molybdenum tungsten borocabide. Chemistry of Materials, acs.chemmater.9b02596. View Article

Download


Compiled binaries

The easiest way to obtain the program is to download compiled binaries for Linux and Mac platforms. Just download the archive, unpack it and follow the instruction inside. You don't need to install the binaries, therefore you can use it without a root permission.

Source code

Building the program from source code is suggested for advanced users, who need output packing or want to change the program code. I can recommend to use Ubuntu 12.04 or later for compiling the code. You can also install compiled program to your system, if you have administrator rights. The program can be compiled for Windows platfrom also, but I've never tried this. Tutorial and manual sources are also available.




Contact Us

Dr. Kirill Okhotnikov
kirill.okhotnikov@gmail.com

Dr. Sylvian Cadars
sylvian.cadars@cnrs-imn.fr
Institut des Materiaux Jean Rouxel (IMN) - UMR6502
2 rue de la Houssiniere, BP32229
44322 Nantes cdx3, France
Phone: +33 (0)2 40 37 39 34
Fax: +33 (0)2 40 37 39 95

Notes

License

The supercell code is available for everybody without restrictions, which gives a possibility for all users to check the code, improve it and customize the program for their needs, respecting the license. Read more...

Problems report

Please, report all bugs and problems in supercell program to GitHub site, if possible. Otherwise send a mail to Kirill Okhotnikov.

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