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Chin. Phys. B, 2019, Vol. 28(10): 106105    DOI: 10.1088/1674-1056/ab4174
Special Issue: TOPICAL REVIEW — CALYPSO structure prediction methodology and its applications to materials discovery
TOPICAL REVIEW—CALYPSO structure prediction methodology and its applications to materials discovery Prev   Next  

The CALYPSO methodology for structure prediction

Qunchao Tong(童群超), Jian Lv(吕健), Pengyue Gao(高朋越), Yanchao Wang(王彦超)
Innovation Center of Computational Physics Methods and Software, State Key Laboratory of Superhard Materials, College of Physics, Jilin University, Changchun 130012, China
Abstract  Structure prediction methods have been widely used as a state-of-the-art tool for structure searches and materials discovery, leading to many theory-driven breakthroughs on discoveries of new materials. These methods generally involve the exploration of the potential energy surfaces of materials through various structure sampling techniques and optimization algorithms in conjunction with quantum mechanical calculations. By taking advantage of the general feature of materials potential energy surface and swarm-intelligence-based global optimization algorithms, we have developed the CALYPSO method for structure prediction, which has been widely used in fields as diverse as computational physics, chemistry, and materials science. In this review, we provide the basic theory of the CALYPSO method, placing particular emphasis on the principles of its various structure dealing methods. We also survey the current challenges faced by structure prediction methods and include an outlook on the future developments of CALYPSO in the conclusions.
Keywords:  structure prediction      CALYPSO method      crystal structure      potential energy surface  
Received:  30 July 2019      Revised:  28 August 2019      Published:  05 October 2019
PACS:  61.50.Ah (Theory of crystal structure, crystal symmetry; calculations and modeling)  
  31.50.-x (Potential energy surfaces)  
  02.60.Pn (Numerical optimization)  
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11534003 and 11604117), the National Key Research and Development Program of China (Grant No. 2016YFB0201201), the Program for JLU Science and Technology Innovative Research Team (JLUSTIRT) of China, and the Science Challenge Project of China (Grant No. TZ2016001).
Corresponding Authors:  Jian Lv, Yanchao Wang     E-mail:  lvjian@calypso.cn;wyc@calypso.cn

Cite this article: 

Qunchao Tong(童群超), Jian Lv(吕健), Pengyue Gao(高朋越), Yanchao Wang(王彦超) The CALYPSO methodology for structure prediction 2019 Chin. Phys. B 28 106105

[33] Yang L M, Bačić V, Popov I A, Boldyrev A I, Heine T, Frauenheim T and Ganz E 2015 J. Am. Chem. Soc. 137 2757
[1] Wang L S 2016 Int. Rev. Phys. Chem. 35 69
[34] Woodley S M and Catlow R 2008 Nat. Mater. 7 937
[35] Zhao J, Shi R, Sai L, Huang X and Su Y 2016 Mol. Simul. 42 809
[36] Wang H, Wang Y, Lv J, Li Q, Zhang L and Ma Y 2016 Comput. Mater. Sci. 112 406
[2] Oger E, Crawford N R M, Kelting R, Weis P, Kappes M M and Ahlrichs R 2007 Angew. Chem. Int. Ed. 46 8503
[37] Wang Y, Lv J, Zhu L, Lu S, Yin K, Li Q, Wang H, Zhang L and Ma Y 2015 J. Phys. Condens. Matter 27 203203
[3] Zhang L, Wang Y, Lv J and Ma Y 2017 Nat. Rev. Mater. 2 17005
[38] Stillinger F H 1999 Phys. Rev. E 59 48
[4] Maddox J 1988 Nature 335 201
[39] Tsai C J and Jordan K D 1993 J. Phys. Chem. 97 11227
[40] Doye J P K and Wales D J 1995 J. Chem. Phys. 102 9659
[5] Wang Y and Ma Y 2014 J. Chem. Phys. 140 040901
[41] Wales D 2004 Energy Landscapes: Applications to Clusters, Biomolecules and Glasses (Cambridge: Cambridge University Press)
[6] Oganov A R, Pickard C J, Zhu Q and Needs R J 2019 Nat. Rev. Mater. 4 331
[42] Jensen F 2007 Introduction to Computational Chemistry (Wiley)
[7] Kirkpatrick S, Gelatt C D and Vecchi M P 1983 Science 220 671
[43] Roy S, Goedecker S and Hellmann V 2008 Phys. Rev. E 77 56707
[8] Wales D J and Doye J P K 1997 J. Phys. Chem. A 101 5111
[9] Goedecker S 2004 J. Chem. Phys. 120 9911
[44] Wales D J 1998 Chem. Phys. Lett. 285 330
[10] Martoňák R, Laio A and Parrinello M 2003 Phys. Rev. Lett. 90 075503
[45] Wolpert D H and Macready W G 1997 IEEE Trans. Evol. Comput. 1 67
[11] Pickard C J and Needs R J 2011 J. Phys. Condens. Matter 23 053201
[46] Zhang M, Liu H, Li Q, Gao B, Wang Y, Li H, Chen C and Ma Y 2015 Phys. Rev. Lett. 114 15502
[12] Oganov A R and Glass C W 2006 J. Chem. Phys. 124 244704
[47] Chen F, Ju M, Kuang X and Yeung Y 2018 Inorg. Chem. 57 4563
[13] Lonie D C and Zurek E 2011 Comput. Phys. Commun. 182 372
[48] Xie T and Grossman J C 2018 Phys. Rev. Lett. 120 145301
[14] Kolmogorov A N, Shah S, Margine E R, Bialon A F, Hammerschmidt T and Drautz R 2010 Phys. Rev. Lett. 105 217003
[49] Lv J, Wang Y, Zhu L and Ma Y 2012 J. Chem. Phys. 137 084104
[15] Trimarchi G and Zunger A 2007 Phys. Rev. B 75 104113
[50] Oganov A R and Valle M 2009 J. Chem. Phys. 130 104504
[16] Bahmann S and Kortus J 2013 Comput. Phys. Commun. 184 1618
[51] Zhu L, Amsler M, Fuhrer T, Schaefer B, Faraji S, Rostami S, Ghasemi S A, Sadeghi A, Grauzinyte M, Wolverton C and Goedecker S 2016 J. Chem. Phys. 144 034203
[17] Bi W, Meng Y, Kumar R S, Cornelius A L, Tipton W W, Hennig R G, Zhang Y, Chen C and Schilling J S 2011 Phys. Rev. B 83 104106
[52] Sadeghi A, Ghasemi S A, Schaefer B, Mohr S, Lill M A and Goedecker S 2013 J. Chem. Phys. 139 184118
[18] Wang Y, Lv J, Zhu L and Ma Y 2010 Phys. Rev. B 82 094116
[53] Behler J 2011 J. Chem. Phys. 134 074106
[19] Wang Y, Lv J, Zhu L and Ma Y 2012 Comput. Phys. Commun. 183 2063
[54] Bartók A P, Kondor R and Csányi G 2013 Phys. Rev. B 87 184115
[20] Li Y, Wang L, Liu H, Zhang Y, Hao J, Pickard C J, Nelson J R, Needs R J, Li W, Huang Y, Errea I, Calandra M, Mauri F and Ma Y 2016 Phys. Rev. B 93 020103
[55] Todeschini R and Consonni V 2009 Mol. Descriptors For Chemoinformatics: Volume I: Alphabetical Listing/volume Ⅱ: Appendices References Vol 41 (John Wiley & Sons)
[21] Li Y, Hao J, Liu H, Lu S and Tse J S 2015 Phys. Rev. Lett. 115 105502
[56] Steinhardt P J, Nelson D R and Ronchetti M 1983 Phys. Rev. B 28 784
[22] Li Y, Hao J, Liu H, Tse J S, Wang Y and Ma Y 2015 Sci. Rep. 5 9948
[57] Kennedy J and Eberhart R 1995 Proc. ICNN'95-Int. Conf. Neural Netw. 4 1942
[23] Li Y, Wang Y, Pickard C J, Needs R J, Wang Y and Ma Y 2015 Phys. Rev. Lett. 114 125501
[58] Eberhart R and Kennedy J 1995 Proc. Sixth Int. Symp. Micro Mach. Hum. Sci. p. 39
[24] Li Y, Feng X, Liu H, Hao J, Redfern S A T, Lei W, Liu D and Ma Y 2018 Nat. Commun. 9 722
[59] Wang Y, Liu H, Lv J, Zhu L, Wang H and Ma Y 2011 Nat. Commun. 2 563
[25] Li Y, Hao J, Liu H, Li Y and Ma Y 2014 J. Chem. Phys. 140 174712
[60] Wang Y, Miao M, Lv J, Zhu L, Yin K, Liu H and Ma Y 2012 J. Chem. Phys. 137 224108
[26] Duan D, Liu Y, Tian F, Li D, Huang X, Zhao Z, Yu H, Liu B, Tian W and Cui T 2015 Sci. Rep. 4 6968
[61] Lu S, Wang Y, Liu H, Miao M and Ma Y 2014 Nat. Commun. 5 3666
[27] Peng F, Sun Y, Pickard C J, Needs R J, Wu Q and Ma Y 2017 Phys. Rev. Lett. 119 107001
[62] Gao B, Gao P, Lu S, Lv J, Wang Y and Ma Y 2019 Sci. Bull. 64 301
[28] Liu H, Naumov I I, Hoffmann R, Ashcroft N W and Hemley R J 2017 Proc. Natl. Acad. Sci. 114 6990
[63] Gao B, Shao X, Lv J, Wang Y and Ma Y 2015 J. Phys. Chem. C 119 20111
[29] Drozdov A P, Eremets M I, Troyan I A, Ksenofontov V and Shylin S I 2015 Nature 525 73
[64] Gao P, Wang S, Lv J, Wang Y and Ma Y 2017 RSC Adv. 7 39869
[30] Ahart M, Somayazulu M, Meng Y, Struzhkin V V, Baldini M, Mishra A K, Geballe Z M and Hemley R J 2019 Phys. Rev. Lett. 122 27001
[65] Zhang X, Wang Y, Lv J, Zhu C, Li Q, Zhang M, Li Q and Ma Y 2013 J. Chem. Phys. 138 114101
[31] Drozdov A P, Kong P P, Minkov V S, Besedin S P, Kuzovnikov M A, Mozaffari S, Balicas L, Balakirev F F, Graf D E, Prakapenka V B, Greenberg E, Knyazev D A, Tkacz M and Eremets M I 2019 Nature 569 528
[66] Gao P, Tong Q, Lv J, Wang Y and Ma Y 2017 Comput. Phys. Commun. 213 40
[32] Zhang W, Oganov A R, Goncharov A F, Zhu Q, Boulfelfel S E, Lyakhov A O, Stavrou E, Somayazulu M, Prakapenka V B and Konôpková Z 2013 Science 342 1502
[67] Zhang Y, Wang H, Wang Y, Zhang L and Ma Y 2017 Phys. Rev. X 7 011017
[33] Yang L M, Bačić V, Popov I A, Boldyrev A I, Heine T, Frauenheim T and Ganz E 2015 J. Am. Chem. Soc. 137 2757
[68] Su C, Lv J, Li Q, Wang H, Zhang L, Wang Y and Ma Y 2017 J. Phys. Condens. Matter 29 165901
[34] Woodley S M and Catlow R 2008 Nat. Mater. 7 937
[69] Behler J 2016 J. Chem. Phys. 145 170901
[35] Zhao J, Shi R, Sai L, Huang X and Su Y 2016 Mol. Simul. 42 809
[70] Jacobsen T L, Jorgensen M S and Hammer B 2018 Phys. Rev. Lett. 120 026102
[36] Wang H, Wang Y, Lv J, Li Q, Zhang L and Ma Y 2016 Comput. Mater. Sci. 112 406
[71] Deringer V L, Csányi G and Proserpio D M 2017 ChemPhysChem. 18 873
[37] Wang Y, Lv J, Zhu L, Lu S, Yin K, Li Q, Wang H, Zhang L and Ma Y 2015 J. Phys. Condens. Matter 27 203203
[72] Deringer V L, Pickard C J and Csányi G 2018 Phys. Rev. Lett. 120 156001
[38] Stillinger F H 1999 Phys. Rev. E 59 48
[73] Bartók A P, Payne M C, Kondor R and Csányi G 2010 Phys. Rev. Lett. 104 136403
[39] Tsai C J and Jordan K D 1993 J. Phys. Chem. 97 11227
[74] Tong Q, Xue L, Lv J, Wang Y and Ma Y 2018 Faraday Discuss. 211 31
[75] Reilly A M, Cooper R I, Adjiman C S, et al. 2016 Acta Crystallogr. Sect. B 72 439
[40] Doye J P K and Wales D J 1995 J. Chem. Phys. 102 9659
[41] Wales D 2004 Energy Landscapes: Applications to Clusters, Biomolecules and Glasses (Cambridge: Cambridge University Press)
[42] Jensen F 2007 Introduction to Computational Chemistry (Wiley)
[43] Roy S, Goedecker S and Hellmann V 2008 Phys. Rev. E 77 56707
[44] Wales D J 1998 Chem. Phys. Lett. 285 330
[45] Wolpert D H and Macready W G 1997 IEEE Trans. Evol. Comput. 1 67
[46] Zhang M, Liu H, Li Q, Gao B, Wang Y, Li H, Chen C and Ma Y 2015 Phys. Rev. Lett. 114 15502
[47] Chen F, Ju M, Kuang X and Yeung Y 2018 Inorg. Chem. 57 4563
[48] Xie T and Grossman J C 2018 Phys. Rev. Lett. 120 145301
[49] Lv J, Wang Y, Zhu L and Ma Y 2012 J. Chem. Phys. 137 084104
[50] Oganov A R and Valle M 2009 J. Chem. Phys. 130 104504
[51] Zhu L, Amsler M, Fuhrer T, Schaefer B, Faraji S, Rostami S, Ghasemi S A, Sadeghi A, Grauzinyte M, Wolverton C and Goedecker S 2016 J. Chem. Phys. 144 034203
[52] Sadeghi A, Ghasemi S A, Schaefer B, Mohr S, Lill M A and Goedecker S 2013 J. Chem. Phys. 139 184118
[53] Behler J 2011 J. Chem. Phys. 134 074106
[54] Bartók A P, Kondor R and Csányi G 2013 Phys. Rev. B 87 184115
[55] Todeschini R and Consonni V 2009 Mol. Descriptors For Chemoinformatics: Volume I: Alphabetical Listing/volume Ⅱ: Appendices References Vol 41 (John Wiley & Sons)
[56] Steinhardt P J, Nelson D R and Ronchetti M 1983 Phys. Rev. B 28 784
[57] Kennedy J and Eberhart R 1995 Proc. ICNN'95-Int. Conf. Neural Netw. 4 1942
[58] Eberhart R and Kennedy J 1995 Proc. Sixth Int. Symp. Micro Mach. Hum. Sci. p. 39
[59] Wang Y, Liu H, Lv J, Zhu L, Wang H and Ma Y 2011 Nat. Commun. 2 563
[60] Wang Y, Miao M, Lv J, Zhu L, Yin K, Liu H and Ma Y 2012 J. Chem. Phys. 137 224108
[61] Lu S, Wang Y, Liu H, Miao M and Ma Y 2014 Nat. Commun. 5 3666
[62] Gao B, Gao P, Lu S, Lv J, Wang Y and Ma Y 2019 Sci. Bull. 64 301
[63] Gao B, Shao X, Lv J, Wang Y and Ma Y 2015 J. Phys. Chem. C 119 20111
[64] Gao P, Wang S, Lv J, Wang Y and Ma Y 2017 RSC Adv. 7 39869
[65] Zhang X, Wang Y, Lv J, Zhu C, Li Q, Zhang M, Li Q and Ma Y 2013 J. Chem. Phys. 138 114101
[66] Gao P, Tong Q, Lv J, Wang Y and Ma Y 2017 Comput. Phys. Commun. 213 40
[67] Zhang Y, Wang H, Wang Y, Zhang L and Ma Y 2017 Phys. Rev. X 7 011017
[68] Su C, Lv J, Li Q, Wang H, Zhang L, Wang Y and Ma Y 2017 J. Phys. Condens. Matter 29 165901
[69] Behler J 2016 J. Chem. Phys. 145 170901
[70] Jacobsen T L, Jorgensen M S and Hammer B 2018 Phys. Rev. Lett. 120 026102
[71] Deringer V L, Csányi G and Proserpio D M 2017 ChemPhysChem. 18 873
[72] Deringer V L, Pickard C J and Csányi G 2018 Phys. Rev. Lett. 120 156001
[73] Bartók A P, Payne M C, Kondor R and Csányi G 2010 Phys. Rev. Lett. 104 136403
[74] Tong Q, Xue L, Lv J, Wang Y and Ma Y 2018 Faraday Discuss. 211 31
[75] Reilly A M, Cooper R I, Adjiman C S, et al. 2016 Acta Crystallogr. Sect. B 72 439
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