Supercell program

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



Supercell v1.2 (performance increase).

The new version of supercell program is around 4 times faster, than the previous 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.


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


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

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, 123(32), 19282–19287. 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, 31(18), 7696–7703. View Article
  • Finley, E., Gaultois, M. W., & Brgoch, J. (2019). Unlocking the key to persistent luminescence with X-ray absorption spectroscopy: A local structure investigation of Cr-substituted spinel-type phosphors. Physical Chemistry Chemical Physics, 21(35), 19349–19358. View Article
  • Edalati, K., Fujita, I., Takechi, S., Nakashima, Y., Kumano, K., Razavi-Khosroshahi, H., … Horita, Z. (2019). Photocatalytic activity of aluminum oxide by oxygen vacancy generation using high-pressure torsion straining. Scripta Materialia, 173, 120–124. View Article
  • Qiu, W., Li, Z., Chen, K., Li, C., Liu, J., & Zhang, W. (2019). Stabilizing Low-coordinated O-ions to Operate Cationic and Anionic Redox Chemistry of Li-ion Battery Materials. ACS Applied Materials & Interfaces, 11(41), 37768–37778. View Article
  • Saleev, V., & Shipilova, A. (2019). Ab initio study of optical and bulk properties of cesium lead halide perovskite solid solutions. Modern Physics Letters B, 33(31), 1950386. View Article
  • Papi, H., Favre, V. Y., Ahmadvand, H., Alaei, M., Khondabi, M., Sheptyakov, D., … Rønnow, H. M. (2019). Magnetic and structural properties of Ni-substituted magnetoelectric Co 4 Nb 2 O 9 Physical Review B, 100(13), 134408. View Article
  • Gautam, A., Sadowski, M., Prinz, N., Eickhoff, H., Minafra, N., Ghidiu, M., … Zeier, W. G. (2019). Rapid Crystallization and Kinetic Freezing of Site-Disorder in the Lithium Superionic Argyrodite Li6PS5Br. Chemistry of Materials, 31(24), 10178–10185. View Article, View ChemRxiv
  • Mao, M., Luo, C., Pollard, T. P., Hou, S., Gao, T., Fan, X., … Wang, C. (2019). A Pyrazine-Based Polymer for Fast-Charge Batteries. Angewandte Chemie International Edition, 58(49), 17820–17826. View Article
  • Eremin, R. A., Zolotarev, P. N., Golov, A. A., Nekrasova, N. A., & Leisegang, T. (2019). Ionic Transport in Doped Solid Electrolytes by Means of DFT Modeling and ML Approaches: A Case Study of Ti-Doped KFeO2. The Journal of Physical Chemistry C, 123(49), 29533–29542. View Article
  • Alfaruqi, M. H., Islam, S., Lee, J., Jo, J., Mathew, V., & Kim, J. (2019). First principles calculations study of α-MnO2 as a potential cathode for Al-ion battery application. Journal of Materials Chemistry A, 7(47), 26966–26974. View Article
  • Arjmandi, H. R., & Grieshammer, S. (2019). Defect formation and migration in Nasicon Li1+xAlxTi2−x(PO4)3. Physical Chemistry Chemical Physics, 21(43), 24232–24238. View Article
  • Romaka, V. V., Rogl, G., Grytsiv, A., & Rogl, P. (2020). Determination of structural disorder in Heusler-type phases. Computational Materials Science, 172(July 2019), 109307. View Article
  • Hamaguchi, M., Momida, H., & Oguchi, T. (2020). Significant role of oxygen redox reaction with O2-release in Li-excess cation-disordered rock-salt cathodes Li2+2xMn1−xTi1−xO4: First-principles calculations. Electrochimica Acta, 330, 135286. View Article
  • Solokha, P., Eremin, R. A., Leisegang, T., Proserpio, D. M., Akhmetshina, T., Gurskaya, A., … De Negri, S. (2020). New Quasicrystal Approximant in the Sc–Pd System: From Topological Data Mining to the Bench. Chemistry of Materials, 32(3), 1064–1079. View Article
  • Zhang, Z., Tehrani, A. M., & Brgoch, J. (2020). Tailoring the Mechanical Properties of Earth-Abundant Transition Metal Borides via Bonding Optimization. The Journal of Physical Chemistry C, 124(8), 4430–4437. View Article
  • Yamanaka, K., Raebiger, H., Mukai, K., & Shudo, K. (2020). Modulation of the optical absorption edge of ε- and κ- Ga2O3 due to Co impurities caused by band structure changes: Work function measurements and first-principle calculations. Journal of Applied Physics, 127(6), 065701. View Article
  • Han, Z., Gui, Z., Zhu, Y. B., Qin, P., Zhang, B.-P., Zhang, W., … Liu, W. (2020). The Electronic Transport Channel Protection and Tuning in Real Space to Boost the Thermoelectric Performance of Mg3+δSb2-yBiy near Room Temperature. Research, 2020, 1–12. View Article
  • Smith Pellizzeri, T., Sanjeewa, L. D., Pellizzeri, S., McMillen, C., Garlea, V. O., Ye, F., … Kolis, J. (2020). Single crystal neutron and magnetic measurements of Rb2Mn3(VO4)2CO3 and K2Co3(VO4)2CO3 with mixed honeycomb and triangular magnetic lattices. Dalton Transactions, 49(14), 4323–4335. View Article
  • Zhu, Y., Poplawsky, J. D., Li, S., Unocic, R. R., Bland, L. G., Taylor, C. D., … Frankel, G. S. (2020). Localized corrosion at nm-scale hardening precipitates in Al-Cu-Li alloys. Acta Materialia, 189, 204–213. View Article
  • Lu, P., Qiu, W., Wei, Y., Zhu, C., Shi, X., Chen, L., & Xu, F. (2020). The order–disorder transition in Cu2Se and medium-range ordering in the high-temperature phase. Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials, 76(2), 1–7. View Article
  • Rakhmatullin, A., Šimko, F., Véron, E., Allix, M., Martineau-Corcos, C., Fitch, A., … Bessada, C. (2020). X-ray Diffraction, NMR Studies, and DFT Calculations of the Room and High Temperature Structures of Rubidium Cryolite, Rb3AlF6. Inorganic Chemistry, 59(9), 6308–6318. View Article
  • Wang, S., Wang, J., & Khazaei, M. (2020). Discovery of stable and intrinsic antiferromagnetic iron oxyhalides monolayers. Physical Chemistry Chemical Physics, 19. View Article
  • Mitra, A., Shaw, A., & Chakrabarti, P. K. (2020). Structural transformation induced enhanced multiferroicity in Al3+ and Ti4+ co-doped LaFeO3. Advanced Powder Technology, (April), 1–11. View Article
  • Dai, Z., Yu, J., Liu, J., Liu, R., Sun, Q., Chen, D., & Ciucci, F. (2020). Highly conductive and nonflammable composite polymer electrolytes for rechargeable quasi-solid-state Li-metal batteries. Journal of Power Sources, 464(February), 228182. View Article
  • Wang, M., Li, L., Zhang, K., & Xie, J. (2020). Colossal permittivity Ti1-x(Eu0.5Ta0.5)xO2 ceramics with excellent thermal stability. ACS Applied Electronic Materials, (May), acsaelm.0c00240. View Article
  • Jiang, C., Lu, X., & Cao, D. (2020). First-principles insight into the entanglements between superionic diffusion and Li/Al antisite in Al-doped Li1+xAlxGe2−x(PO4)3 (LAGP). Science China Technological Sciences, 10(13), 10935–10944. View Article
  • Hoedl, M. F., Gryaznov, D., Merkle, R., Kotomin, E. A., & Maier, J. (2020). Interdependence of Oxygenation and Hydration in Mixed Conducting (Ba,Sr)FeO3-δ Perovskites Studied by Density Functional Theory. The Journal of Physical Chemistry C, 124(22), 11780–11789. View Article
  • Lotfi, S., Zhang, Z., Viswanathan, G., Fortenberry, K., Mansouri Tehrani, A., & Brgoch, J. (2020). Targeting Productive Composition Space through Machine-Learning-Directed Inorganic Synthesis. Matter, (2), 1–12. View Article


Compiled binaries

The easiest way to obtain the program is to download compiled binaries for Linux, Mac and Windows 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. NB! Windows version is significantly slower and do not support acrhive output.

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 natively on Windows platfrom also, but I've never tried this. Tutorial and manual sources are also available.

Contact Us

Dr. Kirill Okhotnikov

Dr. Sylvian Cadars
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...

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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