Computer Physics Communications, volume 184, issue 4, pages 1172-1182

New developments in evolutionary structure prediction algorithm USPEX

Lyakhov Andriy O. ¹

Oganov Artem R.

Zhu Q. ¹

Stokes Harold T.

Oganov A. R. ²

Stokes Harold T. ³

Hide authors affiliations Show authors affiliations: 3 affiliations

New York Center for Computational Sciences, Stony Brook University, Stony Brook 11794-2100, NY, USA |

Department of Geosciences, Stony Brook University, Stony Brook 11794-2100, NY, USA |

Department of Physics and Astronomy, Brigham Young University, Provo 84602, UT, USA |

Publication type: Journal Article

Publication date: 2013-04-01

Elsevier

Journal: Computer Physics Communications

Quartile SCImago

Quartile WOS

Impact factor: 6.3

ISSN: 00104655

DOI: 10.1016/j.cpc.2012.12.009

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General Physics and Astronomy

Hardware and Architecture

Abstract

We present new developments of the evolutionary algorithm USPEX for crystal structure prediction and its adaptation to cluster structure prediction. We show how to generate randomly symmetric structures, and how to introduce ‘smart’ variation operators, learning about preferable local environments. These and other developments substantially improve the efficiency of the algorithm and allow reliable prediction of structures with up to ∼200 atoms in the unit cell. We show that an advanced version of the Particle Swarm Optimization (PSO) can be created on the basis of our method, but PSO is strongly outperformed by USPEX. We also show how ideas from metadynamics can be used in the context of evolutionary structure prediction for escaping from local minima. Our cluster structure prediction algorithm, using the ideas initially developed for crystals, also shows excellent performance and outperforms other state-of-the-art algorithms.

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Citations by journals

	10 20 30 40 50 60 70 80
Physical Review B	Physical Review B, 75, 7.87% Physical Review B 75 publications, 7.87%
Physical Chemistry Chemical Physics	Physical Chemistry Chemical Physics, 65, 6.82% Physical Chemistry Chemical Physics 65 publications, 6.82%
Journal of Physical Chemistry C	Journal of Physical Chemistry C, 38, 3.99% Journal of Physical Chemistry C 38 publications, 3.99%
Scientific Reports	Scientific Reports, 37, 3.88% Scientific Reports 37 publications, 3.88%
Journal of Chemical Physics	Journal of Chemical Physics, 29, 3.04% Journal of Chemical Physics 29 publications, 3.04%
Computational Materials Science	Computational Materials Science, 26, 2.73% Computational Materials Science 26 publications, 2.73%
Physical Review Materials	Physical Review Materials, 25, 2.62% Physical Review Materials 25 publications, 2.62%
Journal of Physics Condensed Matter	Journal of Physics Condensed Matter, 23, 2.41% Journal of Physics Condensed Matter 23 publications, 2.41%
Journal of Applied Physics	Journal of Applied Physics, 20, 2.1% Journal of Applied Physics 20 publications, 2.1%
RSC Advances	RSC Advances, 19, 1.99% RSC Advances 19 publications, 1.99%
Journal of Physical Chemistry Letters	Journal of Physical Chemistry Letters, 16, 1.68% Journal of Physical Chemistry Letters 16 publications, 1.68%
npj Computational Materials	npj Computational Materials, 16, 1.68% npj Computational Materials 16 publications, 1.68%
Chemistry of Materials	Chemistry of Materials, 14, 1.47% Chemistry of Materials 14 publications, 1.47%
Crystal Growth and Design	Crystal Growth and Design, 14, 1.47% Crystal Growth and Design 14 publications, 1.47%
Inorganic Chemistry	Inorganic Chemistry, 13, 1.36% Inorganic Chemistry 13 publications, 1.36%
Nanoscale	Nanoscale, 12, 1.26% Nanoscale 12 publications, 1.26%
Journal of Alloys and Compounds	Journal of Alloys and Compounds, 11, 1.15% Journal of Alloys and Compounds 11 publications, 1.15%
Journal of the American Chemical Society	Journal of the American Chemical Society, 10, 1.05% Journal of the American Chemical Society 10 publications, 1.05%
Applied Surface Science	Applied Surface Science, 10, 1.05% Applied Surface Science 10 publications, 1.05%
Acta Materialia	Acta Materialia, 9, 0.94% Acta Materialia 9 publications, 0.94%
Chinese Physics B	Chinese Physics B, 9, 0.94% Chinese Physics B 9 publications, 0.94%
Physical Review Letters	Physical Review Letters, 8, 0.84% Physical Review Letters 8 publications, 0.84%
ACS applied materials & interfaces	ACS applied materials & interfaces, 8, 0.84% ACS applied materials & interfaces 8 publications, 0.84%
Nature Communications	Nature Communications, 8, 0.84% Nature Communications 8 publications, 0.84%
Solid State Communications	Solid State Communications, 8, 0.84% Solid State Communications 8 publications, 0.84%
Chemistry - A European Journal	Chemistry - A European Journal, 7, 0.73% Chemistry - A European Journal 7 publications, 0.73%
Journal of Physical Chemistry A	Journal of Physical Chemistry A, 7, 0.73% Journal of Physical Chemistry A 7 publications, 0.73%
ACS Omega	ACS Omega, 7, 0.73% ACS Omega 7 publications, 0.73%
Computer Physics Communications	Computer Physics Communications, 6, 0.63% Computer Physics Communications 6 publications, 0.63%
	10 20 30 40 50 60 70 80

Citations by publishers

	20 40 60 80 100 120 140 160 180
Elsevier	Elsevier, 172, 18.05% Elsevier 172 publications, 18.05%
American Chemical Society (ACS)	American Chemical Society (ACS), 147, 15.42% American Chemical Society (ACS) 147 publications, 15.42%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 131, 13.75% Royal Society of Chemistry (RSC) 131 publications, 13.75%
American Physical Society (APS)	American Physical Society (APS), 112, 11.75% American Physical Society (APS) 112 publications, 11.75%
Springer Nature	Springer Nature, 103, 10.81% Springer Nature 103 publications, 10.81%
Wiley	Wiley, 66, 6.93% Wiley 66 publications, 6.93%
American Institute of Physics (AIP)	American Institute of Physics (AIP), 60, 6.3% American Institute of Physics (AIP) 60 publications, 6.3%
IOP Publishing	IOP Publishing, 50, 5.25% IOP Publishing 50 publications, 5.25%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 23, 2.41% Multidisciplinary Digital Publishing Institute (MDPI) 23 publications, 2.41%
Pleiades Publishing	Pleiades Publishing, 15, 1.57% Pleiades Publishing 15 publications, 1.57%
Taylor & Francis	Taylor & Francis, 8, 0.84% Taylor & Francis 8 publications, 0.84%
International Union of Crystallography (IUCr)	International Union of Crystallography (IUCr), 7, 0.73% International Union of Crystallography (IUCr) 7 publications, 0.73%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 5, 0.52% American Association for the Advancement of Science (AAAS) 5 publications, 0.52%
Chinese Physical Society	Chinese Physical Society, 4, 0.42% Chinese Physical Society 4 publications, 0.42%
Iron and Steel Institute of Japan	Iron and Steel Institute of Japan, 3, 0.31% Iron and Steel Institute of Japan 3 publications, 0.31%
Japan Society of Applied Physics	Japan Society of Applied Physics, 3, 0.31% Japan Society of Applied Physics 3 publications, 0.31%
Hindawi Limited	Hindawi Limited, 3, 0.31% Hindawi Limited 3 publications, 0.31%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 2, 0.21% Proceedings of the National Academy of Sciences (PNAS) 2 publications, 0.21%
Japan Institute of Metals and Materials	Japan Institute of Metals and Materials, 2, 0.21% Japan Institute of Metals and Materials 2 publications, 0.21%
Cambridge University Press	Cambridge University Press, 2, 0.21% Cambridge University Press 2 publications, 0.21%
Oxford University Press	Oxford University Press, 2, 0.21% Oxford University Press 2 publications, 0.21%
Tsinghua University Press	Tsinghua University Press, 1, 0.1% Tsinghua University Press 1 publication, 0.1%
Walter de Gruyter	Walter de Gruyter, 1, 0.1% Walter de Gruyter 1 publication, 0.1%
Uspekhi Fizicheskikh Nauk Journal	Uspekhi Fizicheskikh Nauk Journal, 1, 0.1% Uspekhi Fizicheskikh Nauk Journal 1 publication, 0.1%
World Scientific	World Scientific, 1, 0.1% World Scientific 1 publication, 0.1%
Science in China Press	Science in China Press, 1, 0.1% Science in China Press 1 publication, 0.1%
King Saud University	King Saud University, 1, 0.1% King Saud University 1 publication, 0.1%
IEEE	IEEE, 1, 0.1% IEEE 1 publication, 0.1%
Shanghai Institute of Ceramics	Shanghai Institute of Ceramics, 1, 0.1% Shanghai Institute of Ceramics 1 publication, 0.1%
	20 40 60 80 100 120 140 160 180

We do not take into account publications that without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

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GOST |

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GOST Copy

Lyakhov A. O. et al. New developments in evolutionary structure prediction algorithm USPEX // Computer Physics Communications. 2013. Vol. 184. No. 4. pp. 1172-1182.

GOST all authors (up to 50) Copy

Lyakhov A. O., Stokes H. T., Zhu Q., Oganov A. R., Oganov A. R., Stokes H. T. New developments in evolutionary structure prediction algorithm USPEX // Computer Physics Communications. 2013. Vol. 184. No. 4. pp. 1172-1182.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1016/j.cpc.2012.12.009

UR - https://doi.org/10.1016%2Fj.cpc.2012.12.009

TI - New developments in evolutionary structure prediction algorithm USPEX

T2 - Computer Physics Communications

AU - Lyakhov, Andriy O.

AU - Stokes, Harold T.

AU - Zhu, Q.

AU - Oganov, Artem R.

AU - Oganov, A. R.

AU - Stokes, Harold T.

PY - 2013

DA - 2013/04/01 00:00:00

PB - Elsevier

SP - 1172-1182

IS - 4

VL - 184

SN - 0010-4655

ER -

BibTex |

Cite this

BibTex Copy

@article{2013_Lyakhov,

author = {Andriy O. Lyakhov and Harold T. Stokes and Q. Zhu and Artem R. Oganov and A. R. Oganov and Harold T. Stokes},

title = {New developments in evolutionary structure prediction algorithm USPEX},

journal = {Computer Physics Communications},

year = {2013},

volume = {184},

publisher = {Elsevier},

month = {apr},

url = {https://doi.org/10.1016%2Fj.cpc.2012.12.009},

number = {4},

pages = {1172--1182},

doi = {10.1016/j.cpc.2012.12.009}

}

MLA

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MLA Copy

Lyakhov, Andriy O., et al. “New developments in evolutionary structure prediction algorithm USPEX.” Computer Physics Communications, vol. 184, no. 4, Apr. 2013, pp. 1172-1182. https://doi.org/10.1016%2Fj.cpc.2012.12.009.

Found error?

Publisher

Elsevier

Journal

Computer Physics Communications

Quartile SCImago

Quartile WOS

Impact factor

6.3

ISSN

00104655 (Print)

Labs

Materials Design Laboratory

Profiles

Oganov, Artem R.