• 1. Features, aims and history of USPEX
  • 1.1. Overview
  • 1.2. Features of USPEX
  • 1.3. Key USPEX papers
  • 1.4. Version history
• 2. Getting started
  • 2.1. How to obtain USPEX
  • 2.2. Necessary citations
  • 2.3. Bug reports
  • 2.4. On which machines USPEX can be run
  • 2.5. Codes that can work with USPEX
  • 2.6. How to install USPEX
  • 2.7. How to run USPEX
• 3. Overview of input and output files
  • 3.1. Input files
  • 3.2. Output files
• 4. Typical use cases
  • 4.1. Crystal structure prediction (3D): fixed-composition
  • 4.2. Crystal structure prediction (3D): variable-composition
  • 4.3. Crystal structure prediction (3D): molecular crystals
  • 4.4. Thin films (2D)
  • 4.5. Surface reconstructions (2D): fixed-composition
  • 4.6. Nanoparticles prediction (0D)
  • 4.7. Machine learning interatomic potentials.
• 5. Input options. The input.uspex file
  • 5.1. The input.uspex file syntax
  • 5.2. General calculation parameters
  • 5.3. Global optimization search
  • 5.4. Model training
  • 5.5. Optimization type
  • 5.6. Crystal structure prediction
  • 5.7. Evolutionary algorithm USPEX
  • 5.8. Details of ab initio calculations sections
  • 5.9. Task manager definition
  • 5.10. Molecules definitions
  • 5.11. Environment definitions
• 6. Online utilities
  • 6.1. Structure characterization
  • 6.2. Properties calculations
  • 6.3. Molecular crystals
  • 6.4. Surfaces
  • 6.5. Miscellaneous
• 7. Appendices
  • 7.1. Block hierarchy
  • 7.2. List of space groups
  • 7.3. List of layer groups
  • 7.4. List of plane groups
  • 7.5. List of point groups
  • 7.6. Table of univalent covalent radii used in USPEX
  • 7.7. Table of default chemical valences used in USPEX
  • 7.8. Table of default goodBonds used in USPEX

Reference

1

J. Maddox. Crystals from first principles. Nature, 335:201, 1988. URL: http://www.nature.com/nature/journal/v335/n6187/pdf/335201a0.pdf, doi:doi:10.1038/335201a0.

2

A.R. Oganov and C.W. Glass. Crystal structure prediction using ab initio evolutionary techniques: principles and applications. The Journal of Chemical Physics, 124:244704, 2006. URL: http://scitation.aip.org/content/aip/journal/jcp/124/24/10.1063/1.2210932, doi:10.1063/1.2210932.

3

C.W. Glass, A.R. Oganov, and N. Hansen. USPEX — evolutionary crystal structure prediction. Comp. Phys. Comm., 175:713–720, 2006. URL: http://www.sciencedirect.com/science/article/pii/S0010465506002931, doi:10.1016/j.cpc.2006.07.020.

4

A.R. Oganov and S. Ono. Theoretical and experimental evidence for a post-perovskite phase of MgSiO3 in Earth's D" layer. Nature, 430(6998):445–448, July 2004. URL: http://dx.doi.org/10.1038/nature02701, doi:10.1038/nature02701.

5

M. Murakami, K. Hirose, K. Kawamura, N. Sata, and Y. Ohishi. Post-perovskite phase transition in MgSiO3. Science, 304(5672):855–858, 2004. URL: http://www.sciencemag.org/content/304/5672/855.abstract, doi:10.1126/science.1095932.

6

A.R. Oganov, J.C. Schon, M. Jansen, S.M. Woodley, W.W. Tipton, and R.G. Hennig. Appendix: First Blind Test of Inorganic Crystal Structure Prediction Methods, pages 223–231. Wiley-VCH Verlag GmbH & Co. KGaA, 2010. URL: http://onlinelibrary.wiley.com/doi/10.1002/9783527632831.app1/summary, doi:10.1002/9783527632831.app1.

7

C.J. Pickard and R.J. Needs. High-pressure phases of silane. Phys. Rev. Lett., 97:045504, Jul 2006. URL: http://link.aps.org/doi/10.1103/PhysRevLett.97.045504, doi:10.1103/PhysRevLett.97.045504.

8

M. Martinez-Canales, A.R. Oganov, Y. Ma, Y. Yan, A.O. Lyakhov, and A. Bergara. Novel structures and superconductivity of silane under pressure. Phys. Rev. Lett., 102:087005, Feb 2009. URL: http://link.aps.org/doi/10.1103/PhysRevLett.102.087005, doi:10.1103/PhysRevLett.102.087005.

9

Y. Ma, A.R. Oganov, Y. Xie, Z. Li, and J. Kotakoski. Novel high pressure structures of polymeric nitrogen. Phys. Rev. Lett., 102:065501, 2009. URL: http://link.aps.org/doi/10.1103/PhysRevLett.102.065501, doi:10.1103/PhysRevLett.102.065501.

10

C.J. Pickard and R.J. Needs. High-pressure phases of nitrogen. Phys. Rev. Lett., 102:125702, Mar 2009. URL: http://link.aps.org/doi/10.1103/PhysRevLett.102.125702, doi:10.1103/PhysRevLett.102.125702.

11

G. Gao, A.R. Oganov, P. Li, Z. Li, H. Wang, T. Cui, Y. Ma, A. Bergara, A.O. Lyakhov, T. Iitaka, and G. Zou. High-pressure crystal structures and superconductivity of stannane (SnH4). Proceedings of the National Academy of Sciences, 107(4):1317–1320, 2010. URL: http://www.pnas.org/content/107/4/1317.abstract, doi:10.1073/pnas.0908342107.

12

C.J. Pickard and R.J. Needs. Structures at high pressure from random searching. physica status solidi (b), 246(3):536–540, 2009. URL: http://dx.doi.org/10.1002/pssb.200880546, doi:10.1002/pssb.200880546.

13

S.T. Call, D.Yu. Zubarev, and A.I. Boldyrev. Global minimum structure searches via particle swarm optimization. Journal of Computational Chemistry, 28(7):1177–1186, 2007. URL: http://dx.doi.org/10.1002/jcc.20621, doi:10.1002/jcc.20621.

14

A.O. Lyakhov, A.R. Oganov, H.T. Stokes, and Q. Zhu. New developments in evolutionary structure prediction algorithm USPEX. Comp. Phys. Comm., 184:1172–1182, 2013. URL: http://www.sciencedirect.com/science/article/pii/S0010465512004055, doi:10.1016/j.cpc.2012.12.009.

15

G.R. Qian, X. Dong, X.-F. Zhou, Y. Tian, A.R. Oganov, and H.-T. Wang. Variable cell nudged elastic band method for studying solid-solid structural phase transitions. Computer Physics Communications, 184(9):2111–2118, 2013. URL: http://www.sciencedirect.com/science/article/pii/S0010465513001392, doi:10.1016/j.cpc.2013.04.004.

16

C. Dellago, P.G. Bolhuis, F.S. Csajka, and D. Chandler. Transition path sampling and the calculation of rate constants. The Journal of Chemical Physics, 108(5):1964–1977, 1998. URL: http://scitation.aip.org/content/aip/journal/jcp/108/5/10.1063/1.475562, doi:10.1063/1.475562.

17

S.E. Boulfelfel, A.R. Oganov, and S. Leoni. Understanding the nature of "superhard graphite'". Scientific Reports, 2(471):1–9, 2012. URL: http://www.nature.com/srep/2012/120628/srep00471/full/srep00471.html, doi:10.1038/srep00471.

18

A.R. Oganov and C.W. Glass. Evolutionary crystal structure prediction as a tool in materials design. Journal of Physics: Condensed Matter, 20(6):064210, 2008. URL: http://stacks.iop.org/0953-8984/20/i=6/a=064210, doi:doi:10.1088/0953-8984/20/6/064210.

19

A.R. Oganov and M. Valle. How to quantify energy landscapes of solids. The Journal of Chemical Physics, 130:104504, 2009. URL: http://scitation.aip.org/content/aip/journal/jcp/130/10/10.1063/1.3079326, doi:10.1063/1.3079326.

20

A.R. Oganov, A.O. Lyakhov, and M. Valle. How evolutionary crystal structure prediction works — and why. Accounts of Chemical Research, 44(3):227–237, 2011. URL: http://pubs.acs.org/doi/abs/10.1021/ar1001318, doi:10.1021/ar1001318.

21

Pavel V. Bushlanov, Vladislav A. Blatov, and Artem R. Oganov. Topology-based crystal structure generator. Computer Physics Communications, 236:1–7, 2019. URL: https://www.sciencedirect.com/science/article/pii/S0010465518303308, doi:https://doi.org/10.1016/j.cpc.2018.09.016.

22

B. Cordero, V. Gomez, A.E. Platero-Prats, M. Reves, J. Echeverria, E. Cremades, F. Barragan, and S. Alvarez. Covalent radii revisited. Dalton Trans., 21:2832–2838, 2008. URL: http://dx.doi.org/10.1039/B801115J, doi:10.1039/B801115J.