Global optimization is an active area of research in atomistic simulations, and many algorithms have been proposed to date. A prominent example is basin hopping Monte Carlo, which performs a modified Metropolis Monte Carlo search to explore the potential energy surface of the system of interest. These simulations can be very demanding due to the high-dimensional configurational search space. The effective search space can be reduced by utilizing grids for the atomic positions, but at the cost of possibly biasing the results if fixed grids are employed. In this paper, we present a flexible grid algorithm for global optimization that allows us to exploit the efficiency of grids without biasing the simulation outcome. The method is general and applicable to very heterogeneous systems, such as interfaces between two materials of different crystal structures or large clusters supported at surfaces. As a benchmark case, we demonstrate its performance for the well-known global optimization problem of Lennard-Jones clusters containing up to 100 particles. Despite the simplicity of this model potential, Lennard-Jones clusters represent a challenging test case since the global minima for some “magic” numbers of particles exhibit geometries that are very different from those of clusters with only a slightly different size.

1.
M. M.
Lin
and
A. H.
Zewail
, “
Protein folding – simplicity in complexity
,”
Annu. Phys.
524
,
379
391
(
2012
).
2.
J.
Pillardy
,
C.
Czaplewski
,
A.
Liwo
,
J.
Lee
,
D. R.
Ripoll
,
R.
Kaźmierkiewicz
,
S.
Ołdziej
,
W. J.
Wedemeyer
,
K. D.
Gibson
,
Y. A.
Arnautova
,
J.
Saunders
,
Y.-J.
Ye
, and
H. A.
Scheraga
, “
Recent improvements in prediction of protein structure by global optimization of a potential energy function
,”
Proc. Natl. Acad. Sci. U. S. A.
98
,
2329
2333
(
2001
).
3.
D. J.
Wales
and
H. A.
Scheraga
, “
Global optimization of clusters, crystals, and biomolecules
,”
Science
285
,
1368
(
1999
).
4.
C. A.
Floudas
and
C. E.
Gounaris
, “
A review of recent advances in global optimization
,”
J. Global Optim.
45
,
3
38
(
2009
).
5.
B.
Hartke
, “
Global optimization
,”
Wiley Interdiscip. Rev.: Comput. Mol. Sci.
1
,
879
887
(
2011
).
6.
R. G. A.
Bone
and
H. O.
Villar
, “
Exhaustive enumeration of molecular substructures
,”
J. Comput. Chem.
18
,
86
107
(
1997
).
7.
S. J.
Cyvin
,
J.
Wang
,
J.
Brunvoll
,
S.
Cao
,
Y.
Li
,
B. N.
Cyvin
, and
Y.
Wang
, “
Staggered conformers of alkanes: Complete solution of the enumeration problem
,”
J. Mol. Struct. Struct. Chem.
413–414
,
227
239
(
1997
).
8.
X.
Hu
and
B.
Kuhlman
, “
Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences
,”
Proteins: Struct., Funct., Bioinf.
62
,
739
748
(
2006
).
9.
S. N.
Pollock
,
E. A.
Coutsias
,
M. J.
Wester
, and
T. I.
Oprea
, “
Scaffold topologies. 1. Exhaustive enumeration up to eight rings
,”
J. Chem. Inf. Model.
48
,
1304
1310
(
2008
).
10.
J. M.
Rahm
and
P.
Erhart
, “
Beyond magic numbers: Atomic scale equilibrium nanoparticle shapes for any size
,”
Nano Lett.
17
,
5775
5781
(
2017
).
11.
N.
Metropolis
,
A. W.
Rosenbluth
,
M. N.
Rosenbluth
,
A. H.
Teller
, and
E.
Teller
, “
Equation of state calculations by fast computing machines
,”
J. Chem. Phys.
21
,
1087
1092
(
1953
).
12.
D. B.
Laks
,
L. G.
Ferreira
,
S.
Froyen
, and
A.
Zunger
, “
Efficient cluster expansion for substitutional systems
,”
Phys. Rev. B
46
,
12587
(
1992
).
13.
X.
Shao
,
L.
Cheng
, and
W.
Cai
, “
A dynamic lattice searching method for fast optimization of Lennard–Jones clusters
,”
J. Comput. Chem.
25
,
1693
1698
(
2004
).
14.
K.
Yu
,
X.
Wang
,
L.
Chen
, and
L.
Wang
, “
Unbiased fuzzy global optimization of Lennard-Jones clusters for N 1000
,”
J. Chem. Phys.
151
,
214105
(
2019
).
15.
D. J.
Wales
and
J. P. K.
Doye
, “
Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms
,”
J. Phys. Chem. A
101
,
5111
5116
(
1997
).
16.
S.
Kirkpatrick
,
C. D.
Gelatt
, and
M. P.
Vecchi
, “
Optimization by simulated annealing
,”
Science
220
,
671
680
(
1983
).
17.
S.
Goedecker
, “
Minima hopping: An efficient search method for the global minimum of the potential energy surface of complex molecular systems
,”
J. Chem. Phys.
120
,
9911
9917
(
2004
).
18.
S. E.
Schoenborn
,
S.
Goedecker
,
S.
Roy
, and
A. R.
Oganov
, “
The performance of minima hopping and evolutionary algorithms for cluster structure prediction
,”
J. Chem. Phys.
130
,
144108
(
2009
).
19.
C. J. Z.
Michalewicz
, “
Genetic algorithms for numerical optimization
,”
Stat. Comput.
1
,
75
(
1991
).
20.
D. M.
Deaven
and
K. M.
Ho
, “
Molecular geometry optimization with a genetic algorithm
,”
Phys. Rev. Lett.
75
,
288
291
(
1995
).
21.
A. R.
Oganov
and
C. W.
Glass
, “
Crystal structure predicition using ab initio evolutionary techniques: Principles and applications
,”
J. Chem. Phys.
124
,
244704
(
2006
).
22.
L. B.
Vilhelmsen
and
B.
Hammer
, “
Systematic study of Au6 to Au12 gold clusters on MgO(100) F centers using density-functional theory
,”
Phys. Rev. Lett.
108
,
126101
(
2012
).
23.
L. B.
Vilhelmsen
and
B.
Hammer
, “
Identification of the catalytic site at the interface perimeter of Au clusters on rutile TiO2(110)
,”
ACS Catal.
4
,
1626
1631
(
2014
).
24.
P.
Huang
,
Y.
Jiang
,
T.
Liang
,
E.
Wu
,
J.
Li
, and
J.
Hou
, “
Structural exploration of AuxM (M = Si, Ge, Sn; x = 9–12) clusters with a revised genetic algorithm
,”
RSC Adv.
9
,
7432
7439
(
2019
).
25.
F.
Buendía
,
J. A.
Vargas
,
R. L.
Johnston
, and
M. R.
Beltrán
, “
Study of the stability of small AuRh clusters found by a Genetic Algorithm methodology
,”
Comput. Theor. Chem.
1119
,
51
58
(
2017
).
26.
S.
Heydariyan
,
M. R.
Nouri
,
M.
Alaei
,
Z.
Allahyari
, and
T. A.
Niehaus
, “
New candidates for the global minimum of medium-sized silicon clusters: A hybrid DFTB/DFT genetic algorithm applied to Sin, n = 8–80
,”
J. Chem. Phys.
149
,
074313
(
2018
).
27.
E.
Bozkurt
,
M. A. S.
Perez
,
R.
Hovius
,
N. J.
Browning
, and
U.
Rothlisberger
, “
Genetic algorithm based design and experimental characterization of a highly thermostable metalloprotein
,”
J. Am. Chem. Soc.
140
,
4517
4521
(
2018
).
28.
G. G.
Rondina
and
J. L. F.
Da Silva
, “
Revised basin-hopping Monte Carlo algorithm for structure optimization of clusters and nanoparticles
,”
J. Chem. Inf. Mod.
53
,
2282
(
2013
).
29.
J. E.
Jones
and
S.
Chapman
, “
On the determination of molecular fields. —II. From the equation of state of a gas
,”
Proc. R. Soc. London, Ser. A
106
,
463
477
(
1924
).
30.
H.
Eshet
,
F.
Bruneval
, and
M.
Parrinello
, “
New Lennard-Jones metastable phase
,”
J. Chem. Phys.
129
,
026101
(
2008
).
31.
Z.
Li
and
H. A.
Scheraga
, “
Monte Carlo-minimization approach to the multiple-minima problem in protein folding
,”
Proc. Natl. Acad. Sci. U. S. A.
84
,
6611
6615
(
1987
).
32.
D.
Frenkel
and
B.
Smit
,
Understanding Molecular Simulations
(
Academic Press
,
2002
).
33.
H.
Takeuchi
, “
Clever and efficient method for searching optimal geometries of Lennard-Jones clusters
,”
J. Chem. Inf. Model.
46
,
2066
2070
(
2006
).
34.
J. D.
Hunter
, “
Matplotlib A 2d graphics environment
,”
Comput. Sci. Eng.
9
,
90
95
(
2007
).
35.
S.
Müller
and
A.
Zunger
, “
Structure of ordered and disordered α-brass
,”
Phys. Rev. B
63
,
094204
(
2001
).
36.
A.
Stukowski
, “
Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool
,”
Modell. Simul. Mater. Sci. Eng.
18
,
015012
(
2009
).
37.
L. B.
Vilhelmsen
and
B.
Hammer
, “
A genetic algorithm for first principles global structure optimization of supported nano structures
,”
J. Chem. Phys.
141
,
044711
(
2014
).
38.
S.
Plimpton
, “
Fast parallel algorithms for short-range molecular dynamics
,”
J. Comput. Phys.
117
,
1
(
1995
).
40.
See http://www-wales.ch.cam.ac.uk/CCD.html for Cambridge Energy Landscape Database.
41.
A. H.
Larsen
,
J. J.
Mortensen
,
J.
Blomqvist
,
I. E.
Castelli
,
R.
Christensen
,
M.
Dułak
,
J.
Friis
,
M. N.
Groves
,
B.
Hammer
,
C.
Hargus
,
E. D.
Hermes
,
P. C.
Jennings
,
P. B.
Jensen
,
J.
Kermode
,
J. R.
Kitchin
,
E. L.
Kolsbjerg
,
J.
Kubal
,
K.
Kaasbjerg
,
S.
Lysgaard
,
J. B.
Maronsson
,
T.
Maxson
,
T.
Olsen
,
L.
Pastewka
,
A.
Peterson
,
C.
Rostgaard
,
J.
Schiøtz
,
O.
Schütt
,
M.
Strange
,
K. S.
Thygesen
,
T.
Vegge
,
L.
Vilhelmsen
,
M.
Walter
,
Z.
Zeng
, and
K. W.
Jacobsen
, “
The atomic simulation environment—a Python library for working with atoms
,”
J. Phys.: Condens. Matter
29
,
273002
(
2017
).
42.
J.
Behler
, “
Perspective: Machine learning potentials for atomistic simulations
,”
J. Chem. Phys.
145
,
170901
(
2016
).
43.
M.
Iwamatsu
and
Y.
Okabe
, “
Basin hopping with occasional jumping
,”
Chem. Phys. Lett.
399
,
396
400
(
2004
).
44.
P. W.
Voorhees
, “
The theory of Ostwald ripening
,”
J. Stat. Phys.
38
,
231
252
(
1985
).
45.
S.
Lucas
and
P.
Moskovkin
, “
Simulation at high temperature of atomic deposition, islands coalescence, Ostwald and inverse Ostwald ripening with a general simple kinetic Monte Carlo code
,”
Thin Solid Films
518
,
5355
5361
(
2010
).

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