The new version of supercell program is around 4 times faster, than the pervious one!
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.
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.
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.
The fastest way to start with supercell program is to look through the tutorial.
You can read an open access article to get a full information about the program algorithms and scientific applications.
The manual explains all supercell command line options.
Check CIF files of disordered compounds and scripts for supercell program run.
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
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
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.
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.
Atomic Simulation Environment is another set of python tool for setting up, manipulating, running, visualizing and analyzing atomistic simulations. Support many calculation software, both classical and ab-initio, including CASTEP and VASP.
Dr. Sylvian Cadars email@example.com
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
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...
Please, report all bugs and problems in supercell program to GitHub site, if possible. Otherwise send a mail to Kirill Okhotnikov.