A new version of supercell program with major improvements: performance, portability and new parameters.
Please check changelog and benchmark.
What's new in v2.0
I'm proud to present you a new version of supercell program. This is a major release with several significant changes:
Performance boost: Almost half of the code was changed in the release to achieve a performance improvement. Algorithms for symmetry search, electrostatic calculation, file I/O and, of course, structures enumeration became 4-10 times faster then previously.
Multi threading: Enumeration algorithm can run in parallel on shared memory architectures. No extra programs (like MPI) are needed. In this release, you can gain from parallelization on up to 16 cores. The limit will be overcome with next release.
Additional scenarios: Supercell program can be used now for searching of high symmetry disorder supercell (-n w option). Randomness of output structures can be controlled by random-seed option.
New I/O module: Supercell program doesn't use OpenBabel library for I/O and structures processing anymore. Reading and writing of CIF files now is done internally (thanks to gemmi library for cif parsing and spacegroup information). Such approach allows to increase performance and treat ambiguous spacegroup information and inconsistency in CIF files much better.
New C++ standard: Supercell code were updated to C++14 standard. Support for old compilers has been dropped.
Dependency update: Supercell v1.x code binaries (from the site) can be run successfully on Linux distribution from 2008 year up to now and support all x86_64 processors younger than year 2005. New version is compiled with relatively recent compilers and does not support obsolete Linux. It supports, for example: Ubuntu 14.04 and newer; Debian 8 and newer; CentOS 7 and newer etc. The CPU should be SSE2 compatible.
Windows version improvement: Performance of Windows version is significantly improved by using modern build chains. Archive output is now also supported.
The same benchmark as in supercell paper (the same as fcc in disorder paper). Time in seconds.
"Binaries" are compiled program which is available on this site, "native" program was built to run optimally on the test machine.
The tests were run ones each on such configuration:
KVM Intel® Xeon® 3.1 GHz (8 cores).
Ubuntu 20.04 LTS
"Native" executables were built with default compilers, build-toolchain etc in Ubuntu 20.04. OpenBabel 2.4.x version vere used for v1.2
Test command line: supercell -i PbSnTe2.cif -m -d -s 2x2x2
v1.2 (1 core)
v2.0 (1 core)
v2.0 (8 cores)
Compiled v1.2 shows slower performance due to compatibility with very old platforms.
Surprisingly slower performance of "native" binaries with 8 cores can be most probably explained by another TBB library, which was used for compiling the code.
Some recommendation for optimal supercell performance:
Prefer to run supercell on modern Workstation/Desktop rather than on old HPC.
The example above is a "special" example which is used to compare different enumeration approaches. It does not include practical aspects like sampling. Please, use more real-world scenarios to check supercell code performance. For example supercell -i data/examples/CaAl6Te10/CaAl6Te10.cif -m -q -n r10 -n l10 -v 2 run includes electrostatic calculation and random sampling, which is needed in almost all practical cases. During this run 1011 structures process in 137 and 28 minutes on 1 and 8 threads respectively on Intel® Xeon® Gold 6226R 2.90GHz CPU.
For regular users binaries are a preferable option. Now, with drop of old platforms support, they showed a good performance.
If you would like to install supercell on cluster, try to compile it by yourself with different compilers and options.
Probably Intel compiler can improve the program performance.
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.
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.
NO and NO. Supercell program can work with any supercells. Half of example supercell in the tutorial have a conventional cell, thus such structures are non-diagonal supercells of a primitive cell. Unique internal algorithms calculates symmetry operations using universal math approach, which does not rely on spacegroup information. But you can’t create a non-diagonal supercell with the program CLI. This is a conscious choice to leave program as simple as possible. Are you ready to write down “primitive to fcc” transformation matrix just by memory? I am not. If you would like to use non-diagonal supercells with supercell, create it with, for example, VESTA GUI (video guide) or cif2cell CLI (PDF page 10) and use it in the program.
Don’t worry! You can use excellent programs (see below) like cif2cell, OpenBabel or AiiDA to convert output cif files to any other structures. And you can use the result in VASP, ABINIT, CPMD, CRYSTAL, Quantum espresso, Elk etc
If you are a researcher, it gives you a full freedom for your research. You can use the program in public, private or commercial research without any limitation. I appreciate, of course, if you put a reference to supercell paper in your work. If you would like to use supercell code in your program, please check the license carefully to use it in a legal way. For example, I’ll be not happy if you take the program, change something and start earning money, selling this as your code.
To be honest, nobody has ever asked me the question, but I would like to answer it so much, that I’ve decided to include it here. Now supercell is my hobby. Therefore, unfortunately, I don’t have much time to work with it. That’s why your help is very important for the project to stay alive. If you have anything valuable for other users, please share this. It can be, for example:
well prepared bug report, of course.
benchmark tests and performance suggestions.
any input structures with description from your paper. I can put it to example folder.
fair comparison with other similar programs. For example, share your story of switching to supercell from other program or vice versa.
sharing your negative experience with supercell as well. It will help other users to avoid similar problems.
anything else, that you think will be useful to share.
Please cite the following paper, if you use supercell program:
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Compiled binaries (v2.0)
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. Supercell v1.2 is available here.
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 18.04 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 platform 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.
Open Babel is a chemical toolbox designed to speak many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Over 110 formats are supported.
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.