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USPEX

Universal Structure Predictor: Evolutionary Xtallography

What is USPEX?

USPEX (Universal Structure Predictor: Evolutionary Xtalloraphy...and in Russian "uspekh" means "success" - owing to the high success rate and many useful results produced by this method!) is a method developed jointly by Artem R. Oganov, Andriy O. Lyakhov, Colin W. Glass, Qiang Zhu, and others implemented in the same-name code. The problem of crystal structure prediction is very old and does, in fact, constitute the central problem of theoretical crystal chemistry. In 1988 John Maddox wrote that:

"One of the continuing scandals in the physical sciences is that it remains in general impossible to predict the structure of even the simplest crystalline solids from a knowledge of their chemical composition solids such as crystalline water (ice) are still thought to lie beyond mortals' ken".

USPEX method/code enables crystal structure prediction at arbitrary P-T conditions, given just the chemical composition of the material. Today, USPEX is used by over 1600 researchers worldwide. The popularity of USPEX is due to its extremely high efficiency and reliability. The First Blind Test of Inorganic Crystal Structure Prediction shows that USPEX outperforms other methods in terms of efficiency and reliability. In addition to crystal structure prediction, USPEX can work in other dimensionalities and predict the structure of nanoparticles, polymers, surfaces, interfaces and 2D-crystals. It can very efficiently handle molecular crystals (including those with flexible and very complex molecules) and can predict stable chemical compositions and corresponding crystal structures, given just the names of the chemical elements. In addition to this fully non-empirical search, USPEX allows one to predict also a large set of robust metastable structures and perform several types of simulations using various degrees of prior knowledge.

How USPEX works

USPEX can also be used for finding low-energy metastable phases, as well as stable structures of nanoparticles, surface reconstructions, molecular packings in organic crystals, and for searching for materials with desired physical (mechanical, electronic) properties. The USPEX code is based on an efficient evolutionary algorithm developed by A.R. Oganov's group, but also has options for using alternative methods (random sampling, metadynamics, corrected PSO algorithms). USPEX is interfaced with many DFT or classical codes, such as VASP, SIESTA, GULP, Quantum Espresso, CP2K, CASTEP, LAMMPS, and so on.

Click for movie Click for movie

Test of USPEX: 40-atom cell of MgSiO3 post-perovskite. Left - structure search using local optimisation of random structures, Right - evolutionary search with USPEX. While random search did not produce the correct structure even after 120000 steps, USPEX found the stable structure in fewer than 1000 steps.

 

Analysis and Visualization

USPEX is characterized not only by high efficiency and reliability (witnessed by the recent blind test of inorganic crystal structure prediction, where it has scored the highest success) but also by state-of-the art analysis and visualization tools developed by Mario Valle specifically for the USPEX project and implemented in the STM4 toolkit.

Features of the code

  1. Prediction of the stable and metastable structures knowing only the chemical composition. Simultaneous searches for stable compositions and structures are also possible.

  2. Incorporation of partial structural information is possible

    1. constraining search to fixed experimental cell parameters, or fixed cell shape, or fixed cell volume,
    2. starting structure search from known or hypothetical structures,
    3. assembling crystal structures from predefined molecules, including flexible molecules.

  3. efficient constraint techniques, which eliminate unphysical and redundant regions of the search space. Cell reduction technique (Oganov & Glass, 2008).

  4. niching using fingerprint functions (Oganov & Valle, 2009; Lyakhov, Oganov, Valle, 2010).

  5. initialization using fully random approach, or using space groups and cell splitting techniques (Lyakhov, Oganov, Valle, 2010)

  6. on-the-flight analysis of results - determination of space groups (and output in CIF-format), calculation of the hardness, order parameters, etc.

  7. prediction of the structure of nanoparticles and surface reconstructions

  8. restart facilities, enabling calculations to be continued from any point along the evolutionary trajectory

  9. powerful visualization and analysis techniques implemented in the STM4 code (by M.Valle), fully interfaced with USPEX.

  10. USPEX is interfaced with VASP, SIESTA, GULP, DMACRYS, CP2k, QuantumEspresso codes. Interfacing with other codes is easy. 

  11. submission of jobs from local workstation to remote clusters and supercomputers is possible.

  12. options for structure prediction using the USPEX algorithm (default), random sampling, corrected particle swarm optimization, evolutionary metadynamics, minima hopping-like algorithm. Capabilities to predict phase transition mechanisms using evolutionary metadynamics, variable-cell NEB method, and TSP method.

  13. options to optimize physical properties other than the energy - e.g., hardness (Lyakhov & Oganov, 2011), density (Zhu et al., 2011), and various electronic properties.

  14. many new features are now in progress. to be described later...

Current limitations of USPEX

Because of the high success rate of the method, we have not seen many limitations in practice. It is efficient for systems with up to 100-200 atoms/cell. Difficulties for large systems are due to the increasing cost of ab initio calculations for increasing system sizes, and also due to the rapidly increasing number of energy minima. Our algorithm seems to be very effective in counteracting this effect and will make structure prediction for systems containing many hundreds of atoms affordable in near future. 

How to collaborate on USPEX

USPEX is a free code for academic use. We welcome collaborations with experimentalists finding new interesting phases and wishing to find their structure, however since we have constantly a large number of such suggestions for collaboration we will have to select only those suggestions which are closest to our own interests (high-pressure crystallography). We are also happy to establish collaborations with industrial partners. The best way to enquire about a possible collaboration is to e-mail Prof. A.R. Oganov.

Conditions for becoming a user of USPEX

The USPEX code is public domain, but as for any public code, there are certain conditions that users must sign to -

  1. the code is given to an individual researcher (not a group or institution), users are not allowed to distribute the code,

  2. citations to the original USPEX publications must be present in all papers that used USPEX.

  3. all new features that the users would like to implement will have to be sent to Prof. A.R. Oganov in order to be included in the common version of USPEX, maximally benefiting the user community. Users of USPEX are welcome to participate in the development of USPEX and will then be named as its coauthors, but will refrain from developing any competing codes.

References, where the method was exhaustively described

  1. Oganov A.R., Glass C.W. (2006). Crystal structure prediction using evolutionary algorithms: principles and applications. J. Chem. Phys. 124, art. 244704 (pdf-file).

  2. Glass C.W., Oganov A.R., Hansen N. (2006). USPEX – evolutionary crystal structure prediction. Comp. Phys. Comm. 175, 713-720 (pdf-file).

  3. Oganov A.R., Ma Y., Lyakhov A.O., Valle M., Gatti C. (2010). Evolutionary crystal structure prediction as a method for the discovery of minerals and materials. Rev. Mineral. Geochem. 71, 271-298 (pdf-file).

  4. Lyakhov A.O., Oganov A.R., Valle M. (2010). How to predict very large and complex crystal structures. Comp. Phys. Comm. 181, 1623-1632 (pdf-file).

  5. Oganov A.R., Lyakhov A.O., Valle M. (2011). How evolutionary crystal structure prediction works - and why. Acc. Chem. Res. 44, 227-237 (pdf-file).

  6. Lyakhov A.O., Oganov A.R., Stokes H.T., Zhu Q. (2013). New developments in evolutionary structure prediction algorithm USPEX. Comp. Phys. Comm. 184, 1172-1182 (pdf-file).

Developers

From its initial development in 2005, USPEX proved to be a powerful tool for crystal structure prediction. An increasing number of researchers are using our code. The code is developed mainly by Prof Oganov's research group. The developers circle is also steadily increasing. Here are the list of people paticipating in developing USPEX:

USPEX works together with:



and many other codes.

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