A fingerprint based metric for measuring similarities of crystalline structures

Journal of Chemical Physics

Volumn 144, Issue 3, 2016, Pages

  Zhu, Li ^a   Amsler, Maximilian ^a,b   Fuhrer, Tobias ^a   Schaefer, Bastian ^a   Faraji, Somayeh ^c   Rostami, Samare ^c   Ghasemi, S Alireza ^c   Sadeghi, Ali ^d   Grauzinyte, Migle ^a   Wolverton, Chris ^b   Goedecker, Stefan ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

^b Northwestern University   (United States)

^c INSTITUTE FOR ADVANCED STUDIES IN BASIC SCIENCES IASBS   (Iran)

^d SHAHID BEHESHTI UNIVERSITY   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL INTELLIGENCE; ATOMS; CRYSTALLINE MATERIALS; POTENTIAL ENERGY;

CRYSTALLINE STRUCTURE; ENERGY LANDSCAPE; HIGH THROUGHPUT SCREENING; LOCAL ENVIRONMENTS; MATHEMATICAL PROPERTIES; MEASURING SIMILARITIES; POTENTIAL ENERGY LANDSCAPES; SWARM INTELLIGENCE ALGORITHMS;

CRYSTAL ATOMIC STRUCTURE;

EID: 84957009994     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4940026     Document Type: Article

References (62)

1. D. Morgan, G. Ceder, and S. Curtarolo, Meas. Sci. Technol. 16, 296 (2004). 10.1088/0957-0233/16/1/039
2. J. E. Saal, S. Kirklin, M. Aykol, B. Meredig, and C. Wolverton, JOM 65, 1501 (2013). 10.1007/s11837-013-0755-4
3. S. Curtarolo, W. Setyawan, G. L. W. Hart, M. Jahnatek, R. V. Chepulskii, R. H. Taylor, S. Wang, J. Xue, K. Yang, O. Levy, M. J. Mehl, H. T. Stokes, D. O. Demchenko, and D. Morgan, Comput. Mater. Sci. 58, 218 (2012). 10.1016/j.commatsci.2012.02.005
4. A. Jain, S. P. Ong, G. Hautier, W. Chen, W. D. Richards, S. Dacek, S. Cholia, D. Gunter, D. Skinner, G. Ceder, and K. a. Persson, APL Mater. 1, 011002 (2013). 10.1063/1.4812323
5. M. de Jong, W. Chen, T. Angsten, A. Jain, R. Notestine, A. Gamst, M. Sluiter, C. Krishna Ande, S. van der Zwaag, J. J. Plata, C. Toher, S. Curtarolo, G. Ceder, K. A. Persson, and M. Asta, Sci. Data 2, 150009 (2015). 10.1038/sdata.2015.9
6. X. Qu, A. Jain, N. N. Rajput, L. Cheng, Y. Zhang, S. P. Ong, M. Brafman, E. Maginn, L. A. Curtiss, and K. A. Persson, Comput. Mater. Sci. 103, 56 (2015). 10.1016/j.commatsci.2015.02.050
7. S. Kirklin, J. E. Saal, B. Meredig, A. Thompson, J. W. Doak, M. Aykol, S. Rühl, and C. Wolverton, " The Open Quantum Materials Database (OQMD): Assessing the accuracy of DFT formation energies," npj Comput. Mater. 1, 15010 (2015). 10.1038/npjcompumats.2015.10
8. S. Goedecker, J. Chem. Phys. 120, 9911 (2004). 10.1063/1.1724816
9. M. Amsler and S. Goedecker, J. Chem. Phys. 133, 224104 (2010). 10.1063/1.3512900
10. C. W. Glass, A. Oganov, A. R. Oganov, and N. Hansen, Comput. Phys. Commun. 175, 713 (2006). 10.1016/j.cpc.2006.07.020
11. C. J. Pickard and R. J. Needs, J. Phys.: Condens. Matter 23, 053201 (2011). 10.1088/0953-8984/23/5/053201
12. Y. Wang, J. Lv, L. Zhu, and Y. Ma, Phys. Rev. B 82, 094116 (2010). 10.1103/PhysRevB.82.094116
13. Y. Wang, J. Lv, L. Zhu, and Y. Ma, Comput. Phys. Commun. 183, 2063 (2012). 10.1016/j.cpc.2012.05.008
14. J. C. Schön and M. Jansen, Z. Kristallogr.-Cryst. Mater. 216, 307 (2001). 10.1524/zkri.216.7.361.20362
15. S. M. Woodley, P. D. Battle, J. D. Gale, C. Richard, and A. Catlow, Phys. Chem. Chem. Phys. 1, 2535 (1999). 10.1039/a901227c
16. M. Amsler, J. Flores-Livas, L. Lehtovaara, F. Balima, S. Ghasemi, D. Machon, S. Pailhès, A. Willand, D. Caliste, S. Botti, A. San Miguel, S. Goedecker, and M. Marques, Phys. Rev. Lett. 108, 065501 (2012). 10.1103/PhysRevLett.108.065501
17. M. Amsler, J. A. Flores-Livas, T. D. Huan, S. Botti, M. A. L. Marques, and S. Goedecker, Phys. Rev. Lett. 108, 205505 (2012). 10.1103/PhysRevLett.108.205505
18. M. Amsler, S. Botti, M. A. L. Marques, and S. Goedecker, Phys. Rev. Lett. 111, 136101 (2013). 10.1103/PhysRevLett.111.136101
19. L. Zhu, Z. Wang, Y. Wang, G. Zou, H.-k. Mao, and Y. Ma, Proc. Natl. Acad. Sci. U. S. A 109, 751 (2012). 10.1073/pnas.1119375109
20. L. Zhu, H. Liu, C. J. Pickard, G. Zou, and Y. Ma, Nat. Chem. 6, 644 (2014). 10.1038/nchem.1925
21. W. Zhang, A. Oganov, A. R. Oganov, A. F. Goncharov, Q. Zhu, S. E. Boulfelfel, A. O. Lyakhov, E. Stavrou, M. Somayazulu, V. B. Prakapenka, and Z. Konopkova, Science 342, 1502 (2013). 10.1126/science.1244989
22. D. C. Lonie and E. Zurek, Comput. Phys. Commun. 183, 690 (2012). 10.1016/j.cpc.2011.11.007
23. P. Niggli, Kristallographische und Strukturtheoretische Grundbegriffe, Handbuch der Experimentalphysik Vol. 7 (Akademische Verlagsgesellschaft, 1928).
24. R. W. Grosse-Kunstleve, N. K. Sauter, and P. D. Adams, Acta Crystallogr., Sect. A: Found. Crystallogr. 60, 1 (2004). 10.1107/S010876730302186X
25. K. J. McGill, M. Asadi, M. T. Karakasheva, L. C. Andrews, H. J. Bernstein, and IUCr, J. Appl. Cryst. 47, 360 (2014). 10.1107/S1600576713031014
26. L. C. Andrews and H. J. Bernstein, e-print arXiv:1203.5146 (2012).
27. L. C. Andrews and H. J. Bernstein, J. Appl. Cryst. 47, 346 (2014). 10.1107/S1600576713031002
28. B. P. Van Eijck and J. Kroon, J. Comput. Chem. 18, 1036 (1997). 10.1002/(SICI)1096-987X(199706)18:8<1036::AID-JCC7>3.0.CO;2-U
29. P. Verwer and F. J. J. Leusen, Computer simulation to predict possible crystal polymorphs, Reviews in Computational Chemistry Vol. 12 (John Wiley & Sons, Inc., Hoboken, NJ, USA, 1998).
30. H. R. Karfunkel, B. Rohde, F. J. J. Leusen, R. J. Gdanitz, and G. Rihs, J. Comput. Chem. 14, 1125 (1993). 10.1002/jcc.540141002
31. R. de Gelder, R. Wehrens, and J. A. Hageman, J. Comput. Chem. 22, 273 (2001). 10.1002/1096-987X(200102)22:3<273::AID-JCC1001>3.0.CO;2-0
32. A. R. Oganov and M. Valle, J. Chem. Phys. 130, 104504 (2009). 10.1063/1.3079326
33. Y. Wang, J. Lv, L. Zhu, S. Lu, K. Yin, Q. Li, H. Wang, L. Zhang, and Y. Ma, J. Phys.: Condens. Matter 27, 203203 (2015). 10.1088/0953-8984/27/20/203203
34. P. J. Steinhardt, D. R. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983). 10.1103/PhysRevB.28.784
35. J. A. Chisholm, S. Motherwell, and IUCr, J. Appl. Crystallogr. 38, 228 (2005). 10.1107/S0021889804027074
36. J. Behler, J. Chem. Phys. 134, 074106 (2011). 10.1063/1.3553717
37. A. P. Bartok, R. Kondor, and G. Csanyi, Phys. Rev. B 87, 184115 (2013). 10.1103/PhysRevB.87.184115
38. O. A. von Lilienfeld, Int. J. Quantum Chem. 113, 1676 (2013). 10.1002/qua.24375
39. P. Gasparotto and M. Ceriotti, J. Chem. Phys. 141, 174110 (2014). 10.1063/1.4900655
40. L. Yang, S. Dacek, and G. Ceder, Phys. Rev. B 90, 054102 (2014). 10.1103/PhysRevB.90.054102
41. H. W. Kuhn, Nav. Res. Logist. Q. 2, 83 (1955). 10.1002/nav.3800020109
42. J. M. Vásquez-Pérez, G. U. G. Martínez, A. M. Köster, and P. Calaminici, J. Chem. Phys. 131, 124126 (2009). 10.1063/1.3231134
43. A. Sadeghi, S. A. Ghasemi, B. Schaefer, S. Mohr, M. A. Lill, and S. Goedecker, J. Chem. Phys. 139, 184118 (2013). 10.1063/1.4828704
44. B. Aradi, B. Hourahine, and T. Frauenheim, J. Phys. Chem. A 111, 5678 (2007). 10.1021/jp070186p
45. T. J. Lenosky, J. D. Kress, I. Kwon, A. F. Voter, B. Edwards, D. F. Richards, S. Yang, and J. B. Adams, Phys. Rev. B 55, 1528 (1997). 10.1103/PhysRevB.55.1528
46. P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. D. Corso, S. de Gironcoli, S. Fabris, G. Fratesi, R. Gebauer, U. Gerstmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari, and R. M. Wentzcovitch, J. Phys.: Condens. Matter 21, 395502 (2009). 10.1088/0953-8984/21/39/395502
47. M. Ceriotti, J. More, and D. E. Manolopoulos, Comput. Phys. Commun. 185, 1019 (2014). 10.1016/j.cpc.2013.10.027
48. M. Amsler, S. Botti, M. A. L. Marques, T. J. Lenosky, and S. Goedecker, Phys. Rev. B 92, 014101 (2015). 10.1103/PhysRevB.92.014101
49. P. M. Morse, Phys. Rev. 34, 57 (1929). 10.1103/PhysRev.34.57
50. D. W. Bassett and P. R. Webber, Surf. Sci. 70, 520 (1978). 10.1016/0039-6028(78)90429-6
51. F. H. Allen, Acta Crystallogr., Sect. B 58, 380 (2002). 10.1107/S0108768102003890
52. See https://github.com/materials/mint for Mint (materials interface).
53. G. Kresse and J. Furthmüller, Phys. Rev. B 54, 11169 (1996). 10.1103/PhysRevB.54.11169
54. P. E. Blöchl, Phys. Rev. B 50, 17953 (1994). 10.1103/PhysRevB.50.17953
55. G. Kresse and D. Joubert, Phys. Rev. B 59, 1758 (1999). 10.1103/PhysRevB.59.1758
56. S. A. Hayward, F. D. Morrison, S. A. T. Redfern, E. K. H. Salje, J. F. Scott, K. S. Knight, S. Tarantino, A. M. Glazer, V. Shuvaeva, P. Daniel, M. Zhang, and M. A. Carpenter, Phys. Rev. B 72, 054110 (2005). 10.1103/PhysRevB.72.054110
57. A. Gelman, J. B. Carlin, H. S. Stern, and D. B. Rubin, Bayesian Data Analysis (Taylor & Francis, 2014), Vol. 2.
58. C. Cortes and V. Vapnik, Mach. Learn. 20, 273 (1995). 10.1007/bf00994018
59. W. McCulloch and W. Pitts, Bull. Math. Biophys. 5, 115 (1943). 10.1007/bf02478259
60. J. Behler, Int. J. Quantum Chem. 115, 1032 (2015). 10.1002/qua.24890
61. A. P. Bartók and Gábor Csányi, Int. J. Quant. Chem. 115, 1051-1057 (2015). 10.1002/qua.24927
62. M. Rupp, R. Ramakrishnan, and O. A. von Lilienfeld, J. Phys. Chem. Lett. 6 (16), 3309-3313 (2015). 10.1021/acs.jpclett.5b01456