Identifying molecular structures of water and ice helps reveal the chemical nature of liquid and solid water. Real-space geometrical information on molecular systems can be precisely obtained from molecular simulations, but classifying the resulting structure is a non-trivial task. Order parameters are ordinarily introduced to effectively distinguish different structures. Many order parameters have been developed for various kinds of structures, such as body-centered cubic, face-centered cubic, hexagonal close-packed, and liquid. Order parameters for water have also been suggested but need further study. There has been no thorough investigation of the classification capability of many existing order parameters. In this work, we investigate the capability of 493 order parameters to classify the three structures of ice: Ih, Ic, and liquid. A total of 159 767 496 combinations of the order parameters are also considered. The investigation is automatically and systematically performed by machine learning. We find the best set of two bond-orientational order parameters, Q4 and Q8, to distinguish the three structures with high accuracy and robustness. A set of three order parameters is also suggested for better accuracy.

1.
D.
Eisenberg
,
W.
Kauzmann
, and
W.
Kauzmann
,
The Structure and Properties of Water
(
Oxford University Press on Demand
,
2005
).
2.
S.
Svanberg
,
Atomic and Molecular Spectroscopy: Basic Aspects and Practical Applications
(
Springer Science & Business Media
,
2012
), Vol. 6.
3.
J. D.
Dunitz
,
X-Ray Analysis and the Structure of Organic Molecules
(
Cornell University Press
,
1979
).
4.
M. F. C.
Ladd
,
R. A.
Palmer
, and
R. A.
Palmer
,
Structure Determination by X-Ray Crystallography
(
Springer
,
1977
).
5.
T.
Schlick
,
Molecular Modeling and Simulation: An Interdisciplinary Guide
(
Springer Science & Business Media
,
2010
), Vol. 21.
6.
D.
Frenkel
and
B.
Smit
,
Understanding Molecular Simulation: From Algorithms to Applications
(
Elsevier
,
2001
), Vol. 1.
7.
L.
Onsager
, “
The effects of shape on the interaction of colloidal particles
,”
Ann. N. Y. Acad. Sci.
51
,
627
659
(
1949
).
8.
W. L.
McMillan
, “
Simple molecular model for the smectic A phase of liquid crystals
,”
Phys. Rev. A
4
,
1238
1246
(
1971
).
9.
P. J.
Steinhardt
,
D. R.
Nelson
, and
M.
Ronchetti
, “
Bond-orientational order in liquids and glasses
,”
Phys. Rev. B
28
,
784
805
(
1983
).
10.
W.
Lechner
and
C.
Dellago
, “
Accurate determination of crystal structures based on averaged local bond order parameters
,”
J. Chem. Phys.
129
,
114707
(
2008
); arXiv:0806.3345v1.
11.
G. J.
Ackland
and
A. P.
Jones
, “
Applications of local crystal structure measures in experiment and simulation
,”
Phys. Rev. B
73
,
054104
(
2006
).
12.
C. L.
Kelchner
,
S. J.
Plimpton
, and
J. C.
Hamilton
, “
Dislocation nucleation and defect structure during surface indentation
,”
Phys. Rev. B
58
,
11085
11088
(
1998
).
13.
A.
Stukowski
, “
Structure identification methods for atomistic simulations of crystalline materials
,”
Modell. Simul. Mater. Sci. Eng.
20
,
045021
(
2012
); arXiv:1202.5005.
14.
A. P.
Bartók
,
R.
Kondor
, and
G.
Csányi
, “
On representing chemical environments
,”
Phys. Rev. B
87
,
184115
(
2013
); arXiv:1209.3140.
15.
A.
Seko
,
A.
Togo
, and
I.
Tanaka
, “
Descriptors for machine learning of materials data
,” in
Nanoinformatics
(
Springer Singapore
,
Singapore
,
2018
), pp.
3
23
; arXiv:1709.01666.
16.
A.
Radhi
and
K.
Behdinan
, “
Identification of crystal structures in atomistic simulation by predominant common neighborhood analysis
,”
Comput. Mater. Sci.
126
,
182
190
(
2017
).
17.
H.
Doi
,
K. Z.
Takahashi
,
K.
Tagashira
,
J.-i.
Fukuda
, and
T.
Aoyagi
, “
Machine learning-aided analysis for complex local structure of liquid crystal polymers
,”
Sci. Rep.
9
,
16370
(
2019
).
18.
A.
Reinhardt
,
J. P. K.
Doye
,
E. G.
Noya
, and
C.
Vega
, “
Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water
,”
J. Chem. Phys.
137
,
194504
(
2012
); arXiv:1208.6033.
19.
E.
Sanz
,
C.
Vega
,
J. R.
Espinosa
,
R.
Caballero-Bernal
,
J. L. F.
Abascal
, and
C.
Valeriani
, “
Homogeneous ice nucleation at moderate supercooling from molecular simulation
,”
J. Am. Chem. Soc.
135
,
15008
15017
(
2013
).
20.
M.
Fitzner
,
G. C.
Sosso
,
S. J.
Cox
, and
A.
Michaelides
, “
Ice is born in low-mobility regions of supercooled liquid water
,”
Proc. Natl. Acad. Sci. U. S. A.
116
,
2009
2014
(
2019
).
21.
H.
Doi
,
K. Z.
Takahashi
, and
T.
Aoyagi
, “
Mining of effective local order parameters for classifying crystal structures: A machine learning study
,”
J. Chem. Phys.
152
,
214501
(
2020
).
22.
K. Z.
Takahashi
,
T.
Aoyagi
, and
J.-i.
Fukuda
, “
Multistep nucleation of anisotropic molecules
,”
Nat. Commun.
(submitted).
23.
J.
Carrasquilla
and
R. G.
Melko
, “
Machine learning phases of matter
,”
Nat. Phys.
13
,
431
434
(
2017
).
24.
E. P. L.
van Nieuwenburg
,
Y.-H.
Liu
, and
S. D.
Huber
, “
Learning phase transitions by confusion
,”
Nat. Phys.
13
,
435
439
(
2017
).
25.
J. F.
Rodriguez-Nieva
and
M. S.
Scheurer
, “
Identifying topological order through unsupervised machine learning
,”
Nat. Phys.
15
,
790
(
2019
).
26.
M.
Spellings
and
S. C.
Glotzer
, “
Machine learning for crystal identification and discovery
,”
AIChE J.
64
,
2198
2206
(
2018
); arXiv:1710.09861.
27.
M.
Walters
,
Q.
Wei
, and
J. Z. Y.
Chen
, “
Machine learning topological defects of confined liquid crystals in two dimensions
,”
Phys. Rev. E
99
,
062701
(
2019
).
28.
R. S.
DeFever
,
C.
Targonski
,
S. W.
Hall
,
M. C.
Smith
, and
S.
Sarupria
, “
A generalized deep learning approach for local structure identification in molecular simulations
,”
Chem. Sci.
10
,
7503
7515
(
2019
).
29.
A.
Okabe
,
B.
Boots
,
K.
Sugihara
, and
S. N.
Chiu
,
Spatial Tessellations: Concepts and Applications of Voronoi Diagrams
(
John Wiley & Sons
,
2009
), Vol. 501.
30.
J. A.
van Meel
,
L.
Filion
,
C.
Valeriani
, and
D.
Frenkel
, “
A parameter-free, solid-angle based, nearest-neighbor algorithm
,”
J. Chem. Phys.
136
,
234107
(
2012
).
31.
M.
Matsumoto
,
T.
Yagasaki
, and
H.
Tanaka
, “
GenIce: Hydrogen-disordered ice generator
,”
J. Comput. Chem.
39
,
61
(
2018
).
32.
J. L. F.
Abascal
and
C.
Vega
, “
A general purpose model for the condensed phases of water: TIP4P/2005
,”
J. Chem. Phys.
123
,
234505
(
2005
).
33.
W. C.
Swope
,
H. C.
Andersen
,
P. H.
Berens
, and
K. R.
Wilson
, “
A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters
,”
J. Chem. Phys.
76
,
637
649
(
1982
).
34.
M. J.
Abraham
,
T.
Murtola
,
R.
Schulz
,
S.
Páll
,
J. C.
Smith
,
B.
Hess
, and
E.
Lindahl
, “
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
,”
SoftwareX
1-2
,
19
25
(
2015
).
35.
J. D.
Honeycutt
and
H. C.
Andersen
, “
Molecular dynamics study of melting and freezing of small Lennard-Jones clusters
,”
J. Phys. Chem.
91
,
4950
4963
(
1987
).
36.
E.
Maras
,
O.
Trushin
,
A.
Stukowski
,
T.
Ala-Nissila
, and
H.
Jónsson
, “
Global transition path search for dislocation formation in Ge on Si(001)
,”
Comput. Phys. Commun.
205
,
13
21
(
2016
).
37.
P.-L.
Chau
and
A. J.
Hardwick
, “
A new order parameter for tetrahedral configurations
,”
Mol. Phys.
93
,
511
518
(
1998
).
38.
E.
Duboué-Dijon
and
D.
Laage
, “
Characterization of the local structure in liquid water by various order parameters
,”
J. Phys. Chem. B
119
,
8406
8418
(
2015
).
39.
E. B.
Moore
,
E.
de la Llave
,
K.
Welke
,
D. A.
Scherlis
, and
V.
Molinero
, “
Freezing, melting and structure of ice in a hydrophilic nanopore
,”
Phys. Chem. Chem. Phys.
12
,
4124
4134
(
2010
).
40.
A. H.
Nguyen
and
V.
Molinero
, “
Identification of clathrate hydrates, hexagonal ice, cubic ice, and liquid water in simulations: The CHILL+ algorithm
,”
J. Phys. Chem. B
119
,
9369
9376
(
2015
).
41.
E. D.
Sloan
, Jr.
and
C. A.
Koh
,
Clathrate Hydrates of Natural Gases
(
CRC Press
,
2007
).
42.
W.
Mickel
,
S. C.
Kapfer
,
G. E.
Schröder-Turk
, and
K.
Mecke
, “
Shortcomings of the bond orientational order parameters for the analysis of disordered particulate matter
,”
J. Chem. Phys.
138
,
044501
(
2013
); arXiv:1209.6180.
43.
L.
Breiman
, “
Random forests
,”
Mach. Learn.
45
,
5
32
(
2001
).
44.
F.
Pedregosa
,
G.
Varoquaux
,
A.
Gramfort
,
V.
Michel
,
B.
Thirion
,
O.
Grisel
,
M.
Blondel
,
P.
Prettenhofer
,
R.
Weiss
,
V.
Dubourg
 et al, “
Scikit-learn: Machine learning in python
,”
J. Mach. Learn. Res.
12
,
2825
2830
(
2011
).
45.
Y.
Freund
and
L.
Mason
, “
The alternating decision tree learning algorithm
,” in
International Conference on Machine Learning (ICML)
(
Citeseer
,
1999
), Vol. 99, pp.
124
133
.
46.
S.
Raschka
, Mlxtend,
2016
.
You do not currently have access to this content.