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Copyright © 2004 American Scientific Publishers.

JOURNAL OF
All rights reserved COMPUTATIONAL AND THEORETICAL NANOSCIENCE
Printed in the United States of America
Vol. 1. 117–131, 2004

REVIEW
Genetic Algorithms for the Geometry
Optimization of Atomic and Molecular Clusters
Jijun Zhaoa, * and Rui-Hua Xieb
a
Department of Physics and Astronomy, University of North Carolina at Chapel Hill, North Carolina 27599, USA
b
Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada

Clusters, aggregates of a few to thousands of atoms or molecules, have been intensively studied during
the past 20 years due to their importance Delivered
in physics,by Ingentabiochemistry
chemistry, to: and material science, as well
Rice University,
as their potential applications as building Fondrenand
blocks in nanoscience Library
nanotechnology. Determination of the
IP : 93.80.184.211
ground-state geometries of clusters is a well-known nondeterministic polynomial-time hard problem be-
cause of the numerous structural isomersThu,on11theOct 2012energy
potential 12:09:44
surface. To overcome this difficulty and
to explore the magic number clusters with high stability, genetic algorithms were introduced and developed
in the global optimization of cluster geometry. In this article, we review the methodological developments of
genetic algorithms in cluster science and present their broad applications for the geometry optimization of
atomic and molecular clusters. In detail, benchmark studies on the noble gas clusters modeled by the
Lennard-Jones potential based on different global optimization approaches are summarized and dis-
cussed. Applications of the genetic algorithm to the realistic clusters such as metal clusters, semiconduc-
tor clusters, alloy and compound clusters, and molecular clusters are presented. The virtues, limitation and
future improvement of the genetic algorithm for the geometry optimization of clusters are remarked.

Keywords: Cluster, global optimization, local minimization, genetic algorithm, potential energy surface,
many-body potential, simulated annealing, molecular dynamics, ab initio, DFT, tight-binding,
Lennard-Jones cluster, Monte Carlo, mutation, selection, crossover, semiconductor, metal,
alloy, water, carbon, fullerene, silicon, gold, platinum, rhodium, zirconium, titanium, palladium,
nickel, aluminum, sodium, potassium, cobalt, copper, chromium, vanadium, lanthanum,
cerium, praseodymium.

CONTENTS 4. Application in the Realistic Clusters . . . . . . . . . . . . . . . . . 124


4.1. Metal Clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 4.2. Semiconductor Clusters . . . . . . . . . . . . . . . . . . . . . . 126
2. Genetic Algorithm as Global Optimization Method . . . . . 119 4.3. Alloy and Compound Clusters . . . . . . . . . . . . . . . . . 127
2.1. General Genetic Algorithm: An Overview . . . . . . . . 119 4.4. Molecular Clusters . . . . . . . . . . . . . . . . . . . . . . . . . . 127
2.2. Cluster Geometry Optimization by GA: History 4.5. Applications in Other Related Fields . . . . . . . . . . . . 128
and Development of the Methodologies . . . . . . . . . . 120 5. Summary and Outlook . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
2.3. Implementation of Genetic Algorithm in Cluster Acknowledgment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Geometry Optimization . . . . . . . . . . . . . . . . . . . . . . 121 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
2.4. Other Competitive Global Optimization
Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
3. Noble Gas Lennard-Jones Clusters by Genetic 1. INTRODUCTION
Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
3.1. Small LJ Clusters with n  30 . . . . . . . . . . . . . . . . . 123 Clusters are aggregates of a few to thousands of identical
3.2. Medium-Size LJ Clusters with 30  n  150 . . . . . 123 or different atoms/molecules, and their length scales range
3.3. Large LJ Clusters with n  150 . . . . . . . . . . . . . . . . 124 from a few angstroms to tens of nanometers. In experiments,
they are usually generated from mass-selective cluster
beams and can be isolated in a number of media such as inert
*Author to whom correspondence should be addressed. matrices and colloidal suspensions, or they can be deposited
J. Comput. Theor. Nanosci. Vol. 1, No. 2 2004 © 2004 by American Scientific Publishers 1546-198X/2004/01/117/131/$17.00+.25 doi:10.1166/jctn.2004.010 117
on the surface of substrates. The relative abundance, ioniza- multi-dimension potential energy surface (PES) of the
tion potentials, photoelectron spectra, magnetic moments cluster will become very complicated. For example, it was
and optical adsorption of these clusters in different forms estimated that the total number M of minimal energy struc-
have been measured by various of experimental means. tures for a Lennard-Jones (LJ) cluster scales exponentially
REVIEW

As the intermediate state between microscopic atoms with the cluster size n as given below17
and macroscopic condensed matters, the structures and
physical properties of clusters exhibit many interesting size- M  exp[2.5176  0.3572 n  0.0286 n2]. (1)
dependent phenomena such as “magic number” in the rela-
tive abundance associated with electron or geometry shells, Indeed, the global geometry optimization of LJ clusters
metal-nonmetal transition, enhanced magnetic moments, was proven to be a nondeterministic polynomial-time hard
red- or blue-shift of optical gap, and so on.1–8 From the (NP-hard) problem.18 For the true atomic or molecular
technological point of view, clusters can be considered as clusters other than LJ ones, the realistic potential energy
superatoms9 and serve as building blocks in nanoscience landscape could be even more complicated. Thus, the de-
and nanotechnology such as cluster-deposited film, cluster- termination for the ground-state geometry of clusters is
assembled solid and cluster-based nanoelectronics.10–16 one of the most fundamental and challenging problems in
During the past 20 years, the structures and properties of cluster science. On the other hand, many cluster properties
atomic and molecular clusters have been intensively stud- are difficult to measure directly. Their spectroscopic and
ied from many aspects. In particular, it is fundamentally mass spectrometric data are usually interpreted in terms of
important to understand the evolution behavior of the ma- theoretical models. Hence, theory and computational tools
terials as a function of size from isolated atomsDelivered
or small by Ingenta
play important
to: roles in cluster science. It is also note-
molecules to nanoparticles and to bulk condensed matters. worthy that
Rice University, Fondren Library the ground-state geometries of clusters dis-
Since the physical and chemical properties of clusters cussed
IP : 93.80.184.211 in this paper are all for the zero-temperature case.
sensitively depend on the cluster geometry, it Thu,
is critical to In reality,
11 Oct 2012 12:09:44 the structures of clusters may change because of
know the lowest-energy atomic structures of clusters in the temperatures. If there are several metastable structural
order to further understand the clusters and to design the isomers on the PES with comparable energy, the cluster
cluster-based materials and devices. The determination of structures may fluctuate among these isomers under a finite
ground-state geometry of a cluster with n atoms can be temperature. As the cluster temperature further increases
considered as a global optimization problem in the 3n- and approaches the melting point, the cluster will undergo
dimension configuration space constituted by the atomic phase transition and become liquid-like.
coordinates. As the cluster size n increases, the number of For larger clusters with hundreds to thousands of atoms or
structural isomers will increase, too. Correspondingly, the molecules, ab initio electronic structure calculations are

Dr. Jijun Zhao was born and educated in Jiangsu, China, in 1973. He received his Bachelor degree in
physics from Nanjing University, China in 1992, and also his Ph.D in condensed matter physics from
Nanjing University in 1996. From 1997 to 1998, he was a postdoctoral fellow in International Centre for
Theoretical Physics (ICTP), Italy. From 1998 to 2002, he became a research associate and then a research
assistant professor in Department of Physics and Astronomy, University of North Carolina at Chapel Hill,
USA. He is currently a senior research associate in Institute for Shock Physics, Washington State
University, USA. His major research field is in computational materials science with special interest for
nanostructures (nanotubes, nanowires, etc.), nanoelectronic devices, atomic clusters and cluster-based ma-
terials, high pressure physics, and molecular crystals. He has contributed over 80 refereed journal papers
and two book chapters in this field.

Dr. (John) Rui-Hua Xie is currently working at the National Institute of Standards and Technology
(NIST), Gaithersburg, Maryland. His research interest and expertise include computational nanoscience
(nanoelectronics, nanostructured materials, nanocrystals, and quantum dots), cluster physics, molecular
physics, quantum computing, quantum optics, quantum theory, quantum chemistry, and electronic spec-
troscopy, such as NMR, UV-vis, and Raman. Dr. Xie received his bachelor’s degree in theoretical physics
from Wuhan University, Hubei, China, in 1991 and his Ph.D in theoretical physics from Nanjing
University, Jiangsu, China, in 1996. From 1997 to 1998, he was a postdoctoral fellow at the University of
Toronto, Canada. During the period from 1998 to 2000, he moved to Germany as an Alexander von
Humboldt fellow, working at the Max-Planck-Institut für Strömungsforschung in the beautiful university
town of Göttingen. Before joining the Quantum Process Group at NIST in 2001, he came to the famous
town of Kingston, the first capital of Canada, working at Queen’s University. He has contributed over 80 peer-reviewed journal articles
and several review articles/chapters in journals, books and encyclopedias, and presented over 10 invited seminars/colloquiums.

118 J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004


computationally expensive. This led to the utilization of theory, where only the fittest individual can survive. In
empirical potentials19–27 for interatomic or intermolecular other words, the essential idea of the GA procedure is to
interactions in the simulations of clusters. However, no mat- allow a population of many individual candidates to evolve
ter which method one may use, one of the main objectives in under a given selection rule that maximizes the fitness. The

REVIEW
computational cluster science is to find the lowest-energy GA method was first developed by Holland32 and further
configuration of atoms or molecules or ions for a given clus- generalized by Goldberg.33 Since 1993, there have been
ter size. This corresponds to the lowest potential energy, i.e., several pioneering works on the structures of clusters from
the global minimum on the potential energy hypersurface. the GA optimization.35–39 Even in its early stage, the GA
Thus, the structural relaxation of clusters plays a key role in demonstrated an impressive efficiency in searching the
achieving this goal. Molecular dynamics (MD)28 is one of global minima of different systems ranging from the noble
the most commonly adopted methods. This method is able gas clusters to the semiconductor clusters. An outstanding
to simulate the structural and dynamic properties of clusters. example is the direct location of the global minimum struc-
On the other hand, gradient-driven numerical minimization ture of C60, starting from a random configuration by
methods29 such as steepest descent, quasi-Newton and Deaven and Ho.39 Because of the strong directional bonds
conjugate gradient methods can be employed to directly in carbon clusters and the consequent high energy barriers
determine the local minima on the PES of clusters. How- between different isomers, the standard SA simulation pro-
ever, neither MD nor numerical minimization is a global cedures failed to yield the buckyball structure of C60 from
optimization method. The optimized structures from these unbiased starting configurations.39 Motivated by the suc-
methods critically depend on the choice of starting config- cess of these pioneering works, there have been increasing
urations. If there are a number of local minima on the clus- interests in
Delivered by Ingenta to:the applications of GA in the cluster geometry
ter PES separated by high-energy barriers, it is almost optimization,
Rice University, Fondren Library as well as in developing the GA methodology
impossible to locate the global minimum of clusters. To in nanoscience
IP : 93.80.184.211 and related fields. For example, the number
overcome this difficulty, some global optimization meth- of published
Thu, 11 Oct 2012 12:09:44 research papers on the GA study of clusters in-
ods such as simulated annealing (SA)30, 31 and genetic al- creased from five per year in 1996 to about 20 per year in
gorithm (GA)31–33 have been developed. The philosophies 2002, based on our incomplete search from the Web of
of these methods are to mimic the processes in nature. The Science. Such a rapid expansion of this field encouraged us
SA method models an annealing process, while the GA to write this article for reviewing the recent progress on the
method models a natural selection and evolution process. application of genetic algorithm in clusters, while the field
Both methods have achieved remarkable success in solv- is still in a highly active phase of development. This article
ing many global optimization problems. is organized as follows. In Section 2, we illustrate how to
The SA method, which was first introduced by Kirk- implement the GA procedure into the global optimization
patrick, Gelatt and Vecchi,30 simulates the natural anneal- of cluster geometry, and we review the methodological de-
ing process. A substance is initially heated to a high tem- velopment as well as the other related global optimization
perature above its melting points, and then cooled gradually approaches. Then, the applications of GA, for example, in
to approach its crystalline state, as the global minimum. the noble gas clusters and the other clusters, are reviewed in
Provided that the cooling schedule is slow enough and the Section 3 and 4, respectively. Finally, we end this review,
traveled trajectory in the phase space is long enough, the giving a brief summary and outlook in Section 5.
global minimum of the system can be found. In previous
works, the SA simulations based on either Monte-Carlo34
or MD28 methods have been widely applied to search the 2. GENETIC ALGORITHM AS GLOBAL
lowest-energy structures of small clusters. However, in OPTIMIZATION METHOD
practice, if the cluster size further increases (for example, 2.1. General Genetic Algorithm: An Overview
n  20  50) and/or the PES is described by some realistic
functions (for example, many-body potentials, density Similar to all of the other optimization methods, the ge-
functional or tight-binding Hamiltonian), the PES would netic algorithm first needs to define a finite set of optimiza-
become so complicated that the search procedure would tion parameters {pi} and the cost function f  f [{pi}].
lead to a formidable simulation in order to escape from Then, the genetic algorithm will search for the minimum
those numerous local minima. Moreover, the SA procedure cost on the M-dimensional configuration space, constituted
can hardly overcome energy barriers that are higher than by the optimization parameters {pi}  {p1, p2, . . . , pM}.
the initial kinetic energy of the system. The optimization parameters can be chosen in either binary
For the global optimization of cluster geometry, it is es- or continuous mode, while the latter option is obviously
sential to develop some other optimization methods that applicable to a much wider range of systems and problems.
can sample the PES more efficiently and that can hop from In the practical applications of genetic algorithms, it is crit-
one region of the PES to another region more easily. One ical to define suitable optimization parameters and the cost
promising tool satisfied for such a requirement is the GA function according to the specific characteristics of the sys-
method. This method is inspired by Darwinian evolution tem that one wants to study.
J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004 119
The genetic algorithm procedure starts with an initial tries were binary encoded. This is obviously inconvenient
population that has totally Np individuals. The individuals and hard to use. As a major breakthrough, Zeiri used the
in the initial population are usually generated randomly by real Cartesian coordinates of the atoms as the natural genes
choosing a set of initial values of the optimization parame- and converted the conventionally binary genetic algorithm
REVIEW

ters {pi} for each of them. It is possible to generate a much into continuous genetic algorithm.38
larger number of the initial population members and dis- Two other significant steps toward the broad applica-
card most of the high-cost members via natural selection. tions of GA to cluster optimization have been made by
With the initial population that is created, two individuals Deaven, Ho and co-workers.39, 40 First, Deaven and Ho
(“parents”) from the population are then selected to pro- introduced an efficient “cut and splice” crossover opera-
duce the new offspring (“mating”). A variety of selection tion.39, 40 As shown in Fig. 1, random planes that pass
rule can be used in pairing the individuals in the population, through the center of the two parent clusters are chosen.
for example, random pairing, pairing by the sequence in the Afterward, a new child cluster is assembled from the two
population, weighted pairing by the cost, etc. After the two halves (upper half in A and down half in B) of the parent
parents are chosen, one or more offspring (“child”) can be clusters A, B. This operation allows the child cluster to in-
created in the mating (or crossover) process. If the genetic herit about half of the (geometry) characteristics from its
algorithm optimization is performed in binary mode, the parents, similar to the natural mating process. The second
mating operation can be rather straightforward, e.g., mix- important contribution in their work is the application of a
ing the binary codes of the two parents by some given reg- local gradient-driven minimization to structures of the
ulations. On the other hand, in the continuous genetic al- child cluster right after each crossover. Such a local mini-
gorithm, there is more flexibility in defining Delivered
a mating by Ingenta
mization isto:proven to significantly improve the efficiency
(crossover) operation. We will illustrate a practical way of of the GA
Rice University, Fondren Library global minimization.
mating for cluster geometry optimization in the nextIP part.
: 93.80.184.211 years, several further efforts have been made
In recent
In the practical global optimization, the genetic algo-
Thu, 11 Oct 2012 to improve
12:09:44 the GA and to apply to the clusters with more
rithm can converge very quickly into one region of the complicated potential energy surface. Some noticeable
configuration space of optimization parameters, which achievements in this area include modified deterministic/
may not be the region of global minimum. To avoid being stochastic genetic algorithm by Gregurick et al.,41 space-
trapped in the local minima, we have to introduce some fixed modified genetic algorithm by Niesse and Mayne,42, 43
stochastic variation (“mutation”) in the optimization para- modified genetic algorithm by Wolf and Landman,44 sym-
meters {pi} so that the other areas of the configuration biotic algorithm by Michaelian,45 predictor algorithm by
space can be also reached. However, too much mutation Zacharias et al.,46 phonotype algorithm by Hartke,47 single-
may destroy the existing “good” parameters and lower the parent evolution algorithm by Rate et al.,48 neural network
efficiency of the genetic algorithm. Thus, the mutation is assisted genetic algorithm by Lemes et al.,49 hierarchical
usually restricted by a mutation rate Pmu, that is, only the greedy algorithm by Krivov,50 modified genetic algorithm
Pmu percentage of the optimization parameters will be
changed. Similar to the natural process, mating operation
realizes the inheritance and combination of “genes” from
the parents, while mutation introduces variation in “genes”
to achieve the possible stronger offspring. Both are essen-
tial to the global optimization. After the mating and muta-
tion, the cost function of the offspring in the next genera-
tion is evaluated. Natural selection, based on the value of
cost function, can be applied to both the parents and
the children so that only the fittest individuals can survive
in the population. The procedure of pairing, mating, muta-
tion and selection will be iterated until the convergence is
achieved or a maximum number of iteration is exceeded.

2.2. Cluster Geometry Optimization by GA:


History and Development of the
Methodologies

In those earlier efforts of applying the genetic algorithm to


cluster geometry optimization, for example, Hartke on Figure 1. Illustrations of the “cut and splice” crossover operation intro-
Si4,35 Xiao and Williams on small molecular clusters of duced by Deaven and Ho.39 The two halves of “parent” clusters A and B
benzene, naphthalene and anthracene,37 the cluster geome- are spliced into a new “child” cluster A1-B2.

120 J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004


with two new evolutionary operators (annihilator and his- spective parents (see Fig. 1 for an illustration). This is the
tory operator) by Guimarães et al.,51 improved genetic al- popular “cut and splice” crossover operation introduced by
gorithm with a self-guiding search strategy by Kabrede Deaven and Ho.39 If the generated child does not contain
and Hentschke,52 etc. We will not discuss the details of them the right number of atoms or the resulting bond lengths are

REVIEW
in this article. Some of the progress on genetic algorithm in unacceptably small, the above mating process will be re-
cluster science can be found in recent reviews.53, 54 peated until a proper child is yielded.
At the end of crossover, we can perform a mutation on
this new generated child with certain possibility Pmu. It is
2.3. Implementation of Genetic Algorithm noteworthy that the current mutation rate is for the entire
in Cluster Geometry Optimization cluster instead of the optimization parameters (i.e., Carte-
sian coordinates) as stated in Section 2.1. Such a mutation
Since the GA method is independently developed in clus- operation can be carried out by applying a number of ran-
ter science by a number of groups, the detailed operations dom displacements (e.g., 100 steps per atom with walk
of doing GA simulations may differ from one to the other. length 0.05 Å per step) on the Cartesian coordinates of
Here, we briefly illustrate a practical procedure that is used each atom in the cluster. We found that the mutation stage
in our own works.55–68 The corresponding genetic algo- is crucial to obtain the global minima if the configuration
rithm code developed by us is also available upon request. space is sufficiently complicated.
Basically, it is very close to the scheme introduced by The child cluster generated from crossover and muta-
Deaven and Ho39, 40 and is also similar to those used by tion operations will be locally optimized by either a MD
most other researchers. As shown in Fig. 2, our Delivered
scheme of by Ingenta
quenchingto: or a numeric minimization like BFGS.69 In the
GA optimizations can be, in general, divided RiceintoUniversity,
three es- case of MD
Fondren relaxation, the cluster is quenched from a rel-
Library
sential steps: crossover, mutation and selection. IP : 93.80.184.211 atively high temperature to a low temperature within a rel-
At the first step, an initial population, whichThu, contains a 2012
11 Oct atively small number of MD steps. Both the BFGS mini-
12:09:44
number of different cluster geometries, is generated at ran- mization and MD quenching are expected to relax the
dom. To ensure a global optimization, the number Np of cluster to a reasonable local minimum nearby. This “local”
the individuals in the population typically increases with quenching strategy is able to obtain the lowest energy
the cluster size. Then, two individuals in the population are minima corresponding to a considerable portion of the
selected as parent clusters to generate a new child cluster, PES, such that the system will not be trapped in the near-
which is known as crossover (or mating) operation. The est minima from the starting configuration that might have
possibility of being chosen as a parent is identical for all a high energy. As a consequence, numerous minima struc-
the candidates in population. The crossover operation is tures with relatively higher energies can be skipped in the
composed by cutting each parent via a randomly chosen search process.
plane passing through its mass center and then assembling After a locally stable “child” cluster is obtained, we per-
the child from the upper and down halves of the two re- form the natural selection, during which the child is either
accepted into the population or discarded according to its
energy and geometry. To preserve the diversity of the pop-
initiation ulation, we first compare the coordination numbers of each
atom in the child to all those for the individuals inside the
parent parent parent parent
population. If the child has the same configuration as any
crossover existing individual, it will be either discarded or replace
local optimization mutation this individual according to its energy. If the child has a
(empirical or TB) lower energy than one of its parents, and has geometry dif-
child ferent from all of the existing individuals in the population,
it will replace its high-energy parent and enter the popula-
selection tion. Therefore, the population always contains individuals
weaker stronger
? ? that have different atomic structures. In this scheme, the
GA optimization not only determines the ground state
discard parent structure, but also collects the other locally stable isomers
crossover of the cluster. As we shall discuss below, the availability of
the other structural isomers is very important for an empir-
parent parent parent parent ical/quantum combination study.
In practice, it was found that the efficiency of the GA
optimization sensitively depends on the number Np of indi-
input for DFT minimization viduals in the population and the mutation probability Pmu.
Figure 2. Flow chart for an empirical/quantum combination genetic For example, Fig. 3 presents the convergence of the lowest-
algorithm optimization. energy structures for a Si16 clusters using different Np and
J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004 121
method,77, 78 generalized simulated annealing,79, 80 confor-
mational space annealing,81, 82 basin-hopping,83–86 quan-
tum annealing,87 parallel tempering algorithm,88 smart
walking annealing,89 multicanonical jump walk anneal-
REVIEW

ing,90 quantum thermal annealing,91 random tunneling


algorithm,92 fast annealing evolutionary algorithm,93–95
quantum path minimization,96 etc. Some details can be
found in other review articles.97, 98 Among these achieve-
ments, it is worthy to mention that Wales and Doye intro-
duced a basin-hopping algorithm83 in the sprite of Monte-
Carlo with minimization.75 By transforming the PES into
a collection of interpenetrating staircases,83 the basin-
hopping algorithm is found to be very robust in cluster
geometry optimizations, demonstrating transferability be-
tween atomic and molecular clusters and yielding useful
results for biomolecules. In Table 1, we summarize some
of these previous works that utilized the LJ clusters as
Figure 3. The evolution of lowest-energy of a Si16 cluster within ge-
benchmark systems. The performance on the LJ clusters
netic algorithm optimization with different choices of numbers of parents
between the GA method and some of those competitive ap-
in population Np and mutation probability Pmu. It is clear that Np  8 and
Pmu  0.3 lead to the best optimization efficiency for the current proaches will
Delivered
case. In by
Ingenta to: be compared in the next section.
Rice
the GA optimizations, Menon and Subbaswamy’s nonorthogonal University,
tight- Fondren Library
binding total energy model70 and the limited memory BFGS minimiza-IP : 93.80.184.211
69
tion method are used. The present global minimum structures (shown
Thu, 11 Oct 2012
on the right) found for Si16 within the nonorthogonal tight-binding model
12:09:44GAS LENNARD-JONES
3. NOBLE
is similar to the metastable C2h isomer predicted by Ho.72 CLUSTERS BY GENETIC ALGORITHM
Although the LJ potential is analytically simple, it is still
Pmu. In the GA optimizations, Menon and Subbaswamy’s widely used by researchers in many areas. There has been
nonorthogonal tight-binding total energy model70 and the a vast amount of literature on the clusters of noble gas
limited memory BFGS minimization method69 are used. atoms modeled by the LJ pair potential. Almost every
For a given cluster size, there are some optimal choices for global optimization method in existence has been tested on
Np and Pmu that approach the lowest-energy structures the LJ clusters as benchmark system. In the 6–12 LJ pair
fastest. potential,
In order to improve the accuracy of the geometry global

∑ [(j / r )  (j / r ) ]
optimization, Zhao and coworkers have further proposed 12 6
a GA-based empirical/quantum combination scheme58 and E  4e ij ij (2)
applied it to study a variety of atomic clusters.58–60, 65–67 The i j

essential idea is to use the GA optimization at either empiri-


cal or semiempirical (e.g., tight-binding model57, 70, 71) level the reduced units j  1, e  1 are conventionally used.
for generating a number of structural isomer candidates of Within a LJ pair potential, it is well-known that the geome-
the cluster. Then, accurate density function theory (DFT) tries of the cluster are dominated by the packing effect.
calculations are performed to locally optimize these isomer In general, the LJ cluster tends to adopt the icosahedral
structures and finally determine the lowest-energy structure compact structures, as called “Mackay icosahedron”99 (see
of the cluster at the accuracy level of DFT. A similar empir- Fig. 4), where the multi-shell structures are complete at
ical/quantum combination method was also used by others particular sizes, for example, n  13, 55, 147, 309, etc.
such as Ho et al. for silicon clusters,72 Tang et al. for Si8H8 (so-called geometry magic number). However, for some of
clusters73 and Garzón et al. for gold clusters.74 those clusters with sizes between the complete icosahedra,
nonicosahedral close-packed structures were found.83, 84, 98
2.4. Other Competitive Global Optimization Therefore, such clusters with non-icosahedral global min-
Algorithms ima are more critical to test the performance of the global
optimization methods.
Besides the GA method, many other competitive global Table 1 summarizes the previous studies of LJ clusters
optimization algorithms have also been developed for these using genetic algorithm and other competitive global opti-
NP-hard problems such as cluster geometry optimization mization methods. A complete collection of energies and
or protein folding. Some major achievements in these Cartesian coordinates for those global minima structures
unbiased global optimization methods are Monte-Carlo up to n  150 can be found in the Cambridge Cluster
with minimization,75 J-walking,76 Monte-Carlo growth Database.100
122 J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004
Table 1. Summary of previous works on LJ clusters using genetic algorithm and related global optimization methods.

Size Method Authors

4  10 genetic algorithm Zeiri101


2  29 Gregurick et al.41

REVIEW
deterministic/stochastic genetic algorithm
4  30 genetic algorithm Chaudhury et al.104
4  55 space fixed modified genetic algorithm Niesse and Mayne42
6, 18, 23, 38, 55 symbiotic algorithm based on GA Michaelian45
2  100 genetic algorithm Deaven et al.40
2  100 genetic algorithm Pullan105
10  100 modified genetic algorithm Wolf and Landman44
13  147 genetic algorithm Barron et al.103
10  150 phenotype algorithm Hartke47
148  309 genetic algorithm Romero et al.106
75, 77, 98, 500, 1000 hierarchchical greedy algorithm Krivov50
2  110 basin-hopping algorithm Wales and Doye83, 84
19, 30, 38 significant structures basin hopping White and Mayne85
5  100 self-consistent basin-to-deformed-basis mapping Pillardy86
2  100 random tunneling algorithm Jiang et al.92
2  13 fast annealing evolutionary algorithm Cai and Shao93
2  74 fast annealing evolutionary algorithm Cai et al.94
2  116 parallel fast annealing evolutionary algorithm Cai et al.95
5  30 multocanonical jump walk annealing Xu and Berne90
201 Delivered
conformational by Ingenta to:
space annealing Lee et al.82
11  100 Rice University,
quantum path minimization Fondren Library Liu and Berne96
IP : 93.80.184.211
Thu, 11 Oct 2012 12:09:44
3.1. Small LJ Clusters with n  30 annealing. Similarly, for LJ Arn clusters with n  30, the
deterministic/stochastic genetic algorithm optimization con-
Small LJ clusters have been studied as a benchmark for verges much more quickly to the global minimum than the
GA optimization in those earlier works. Zeiri has studied random search procedures.41 Moreover, Chaudhury and
the lowest energy structures of very small LJ clusters (n  Bhattacharyya demonstrated that GA can locate critical
4  10) using genetic algorithm.101 Excellent agreement points on the multi-dimensional potential energy surface
was obtained between the GA results with exact classical using Arn (n  4  30) clusters as a test system.104
data.102 He has also shown that the genetic algorithm
based method converges to the global minima much more 3.2. Medium-Size LJ Clusters with 30  n  150
rapidly than both the simulated annealing and quantum
The medium-sized LJ clusters with n  30  150 have
been intensively studied by different groups using the GA
method.40, 42, 44, 45, 47, 103 In this size range, non-icosa-
hedral structures (see Fig. 4) were found as global minima
at several specific sizes (n  38, 75  77, 98, 102  104).
Thus, they can be considered as the “hurdles” for those
global optimization methods. As shown in Fig. 4, a fcc
truncated octahedron was found as a global minimum
structure of the 38-atom LJ cluster. It is particularly inter-
esting, as the only small LJ cluster with fcc lowest-energy
structures during the size range of n  30  150. In previ-
ous GA studies, the fcc truncated octahedron was first
found by Deaven et al., and then successfully reproduced
by other workers.42, 44, 45, 47, 103 At n  75  77 and 102 
104, the global minima structures of LJ clusters are based
on Marks decahedra (see Fig. 4). These global minima
were systematically summarized by Wales and Doye in
their basis-hopping study of LJ clusters.83 It is noteworthy
Figure 4. (Upper) Global minima structures of LJ clusters with com- that Deaven’s original GA optimization of LJ clusters
plete Mackay icosahedron: 13-atoms, 55-atoms, 147-atoms. (Lower) failed to produce those decahedra.40 Wolf and Landman
Typical non-icosahedron global minima structures of LJ cluster: 38-
atoms truncated fcc octahedron, 75-atoms Marks decahedron, 98-atoms
improved the methodology of GA and were able to repro-
tetrahedron-based packing. All the structures are taken from Cambridge duce all of these global minima of LJ clusters with up to
Cluster Database.100 100 atoms.44 Later, Hartke47 and Barron et al.103 have per-
J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004 123
formed independent GA global optimization of LJ clusters as metal clusters, semiconductor clusters, ionic compound
with up to 150 atoms, respectively. Both of the studies clusters and molecular clusters. Certainly, the PESs of all
have successfully obtained the global minima for n  75  these clusters would be much more complicated than the
77 and 102  104. However, for the 98-atom LJ cluster, a noble gas clusters modeled by LJ potentials, making the
REVIEW

tetrahedral global minimum was found by Leary and Doye determination of the global minimum structures of clusters
using the basis-hopping method.83 On the PES, this global more challenging. Therefore, most of the current studies
minimum is at the bottom of a narrow tunnel, so that it is are still limited to relatively smaller clusters, i.e., n  50.
difficult to find. Indeed, within the best of our knowledge,
none of the current GA optimizations have produced this
4.1. Metal Clusters
structure. Thus, determination of global minimum of the
98-atom LJ cluster is still a challenge for the genetic algo- Metal clusters have attracted tremendous attention due to
rithm in clusters science. their interesting atomic and electronic structures. Although
Besides the genetic algorithm and the basis-hopping the cohesion in the metal clusters should be dominated by the
methods, it would be interesting to examine the perfor- effect of valence electrons bonding, empirical many-body
mance of other global-optimization approaches in this size potentials in the sprite of “embedded-atom” are still widely
range. Pillard et al. have proposed a self-consistent basin- used to account for the interatomic interactions in the metal
to-deformed-basin mapping method and tested it in the LJ clusters. Among these empirical potentials, the Gupta-like
clusters with up to 100 atoms.86 Although most of the potential19 is the most popular one in previous GA studies:
global minima, including n  38, are reproduced, their
method failed in yielding the global minimumDeliveredfor n  by Ingenta to:    rij 
75  77 and 98, for which the second-to-the-lowest-energy
Rice University, Fondren LibraryE ∑∑
i 
 B exp  p 1 
  r0  
structures were found. Jiang, Cai and Shao have put IP for-
: 93.80.184.211  j ≠i
ward two global optimization methods and applied them to
Thu, 11 Oct 2012 12:09:44 (3)
LJ clusters.92–95 The global optimization using random    rij  
1/2

tunneling algorithm has successfully produced all the  ∑
 j ≠i
A 2 exp 2 q 1  .
  r0   
global minima of LJ clusters with up to 100,92 while an- 
other work done with fast annealing evolutionary algo-
rithm has extended the successful range to n  116.95 Liu The second attraction part of the potential can be associ-
and Berne proposed a quantum path minimization method ated with the tight-binding model within the second mo-
and found that this new method is able to locate all the ment approximation,20 which essentially describes the band
global minima of LJ clusters of size up to n  100, with character of the metallic bond. Other than empirical poten-
exception at n  76, 77, 98.96 Very recently, Lee and co- tials, semiempirical tight-binding models and extended-
workers applied the conformational space annealing method Hückel method have also been incorporated into the GA ap-
to the LJ clusters with up to 201 atoms and reproduced all proach for a global search of lowest-energy structures of the
known global energy minima.82 metal clusters. Moreover, empirical GA simulation has been
used to provide a number of structural isomer candidates,
3.3. Large LJ Clusters with n  150 which are then further optimized by more accurate DFT cal-
culations. In Table 2, we summarize the total energy meth-
So far, there are only few reports on the LJ clusters with ods and the size range of metal clusters reported in previous
more than 150 atoms using genetic algorithm.50, 106 As an works. The detailed descriptions are presented below.
extension of their previous study on LJ clusters with up to
147 atoms,103 Remero and co-workers proposed a genetic
4.1.1. Noble Metal Clusters
algorithm combined with a stochastic search procedure on
icosahedral lattices to perform global optimization of LJ Noble metal clusters, especially gold clusters, have received
clusters with n  148  309.106 Icosahedral and Marks increasing attention as building blocks in the nanoscale
decahedral structures were found, and a new morphology materials and devices. It is particularly interesting to inves-
called FD was predicted. For the larger LJ clusters with up tigate the noble metal clusters at the magic sizes such as
to 500–1000 atoms, a hierarchical greedy algorithm has 38 and 55, where the complete fcc or icosahedral close-
been developed by Krivov and applied to search the global packing structures might form (see Fig. 4 in Section 3). For
minima of the clusters.50 small Aun (n  2  20) clusters, Wang and co-workers
have carried out a comprehensive GA search for their low-
4. APPLICATION IN THE REALISTIC est-energy structures, and have extensively studied the
CLUSTERS electronic properties using the empirical/quantum combi-
nation method.65 Using the same method, they have re-
In this section, we review the current progress on the GA cently investigated the lowest-energy structures of the 20-
works done for the true atomic and molecular cluster such atoms noble metal clusters (Cu20, Ag20 and Au20).66 After
124 J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004
Table 2. Summary of the cluster, size range and total energy methods in previous GA studies of metal clusters. “Gupta
potential  DFT” denotes that first principles calculated result have been further applied to the local stable candidate
structures from GA optimizations based on empirical potentials.

Element Size Total energy method Authors

REVIEW
Au 220 Gupta potential  DFT Wang et al.65
Au 3855 Gupta potential Li et al.56
Au 38, 55, 75 Gupta potential  DFT Garzón et al.74
Au, Ni, Ag 675 Gupta potential Michaelian et al.107
Au 12212 Gupta potential  DFT Garzón et al.108
Cu, Ag, Au 20 Gupta potential Wang et al.66
Ag 221 tight-binding Zhao et al.57
Na, K, Rb, Cs, Pb 356 Gupta potential Lai et al.109
Al 2155 Murrell-Mottram potential Lloyd et al.110
Be 221 Gupta potential  DFT Wang et al.59
Sr 263 Size-dependent Gupta potential Wang et al.112
Cd 221 Gupta potential  DFT Zhao58
Zn 220 Gupta potential  DFT Wang et al.67
Zn, Cd 13147 Gupta potential  DFT Michaelian et al.113
Hg 714 Quantum-empirical hybrid model Hartke et al.114
Cr 13 Gupta potential Luo et al.115
V 319 Gupta potential Sun et al.118
Rh 919 Gupta potential Sun et al.116
Rh 426 Delivered
Guptaby Ingenta to:
potential Granja et al.117
La, Ce, Pr 320Rice University,
Möbius Fondren
inversion pairLibrary
potential Luo and Wang119
Ni 213 IP : extended-Hückel
93.80.184.211 Curotto et al.120
Fe 226 Thu, 11 density
Oct 2012 12:09:44
functional tight-binding Parvanova et al.121

fitting a semiempirical tight-binding model from bulk and 4.1.3. Divalent Metal Clusters
dimer properties of silver, Zhao et al. have studied the
structural and electronic properties of silver clusters up to Size-dependent evolution of metallic behaviors of the diva-
20 atoms.57 lent metal clusters is an interesting issue in cluster science
In the serial works reported by Garzón and co- since the very small clusters are bound by van der Waals
workers,74, 107, 108 the lowest-energy structures of Aun interaction, similar to helium. Zhao and co-workers have
clusters were obtained from the empirical GA optimiza- employed the combination technique of empirical GA
tions using Gupta potentials. These structures were further global search and DFT local minimization to obtain the
confirmed by the DFT relaxation. In general, disordered or lowest-energy structures of Cd,58 Be,59 Zn67 clusters up to
low-symmetry structures were found to be global minima 20 atoms. The size-dependent electronic properties of those
structures, which are different from the LJ clusters. Similar clusters and the nonmetal-metal transitions were then stud-
results were also obtained by Li et al. in their empirical GA ied based on the optimized structures.58, 59, 67 For the larger
simulations.56 Zn and Cd clusters at “magic” sizes of 13, 38, 55, 75 and
147 atoms, disordered structures, or structures of very low
symmetry, were found as the lowest-energy structures from
4.1.2. Simple Metal Clusters empirical GA optimizations using Gupta potentials.113
Hartke and co-workers have studied Hgn (n  7  14)
The structures of monovalent (Na, K, Rb, Cs) and polyva- clusters via a GA global geometry optimization within a
lent (Pb) clusters with the number of atoms up to 56 have quantum mechanical-empirical hybrid model.114
been systematically studied by using Gupta potentials.109
Both the genetic algorithm and the basin-hopping method
have been used in the global minimization, and excellent 4.1.4. Transition Metal Clusters
agreement was found in the global minima from both
schemes.109 Loyd110 used the GA to optimize the geome- As for the transition metal clusters, the size-dependent
try of aluminum clusters with 21  55 atoms bound by the magnetism of small clusters is particularly interesting.
Murrell-Mottram (MM) 2  3 body potential.111 The MM Combined techniques of empirical GA optimization using
potential is based on a many-body expansion of the poten- Gupta potential and spin-polarized calculations within
tial energy truncated up to the three-body term. The poten- tight-binding approximations have been used to investi-
tial parameters in the MM potentials are derived by fitting gate the structures and magnetic moments of Cr13,115 Rhn
experimental data such as phonon frequencies, elastic con- (n  9, 13, 15, 17, 19 in Ref. [116], 4  n  26 in Ref.
stants, vacency energy, etc., for the solid phase. [117]) and Vn (n  3  19)118 clusters. As well as the 3d
J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004 125
and 4d transition metals, Luo and Wang have extended the Above empirical or tight-binding levels, global geom-
GA optimization to the geometries of rare-earth metal etry optimization of small silicon clusters Sin (n  4, 5, 7,
clusters, i.e., Lan, Cen and Prn (n  3  20) using the 10) using DFT calculations has been achieved by
Möbius inversion pair potential.119 Hartke,123 while Bazterra et al. employ the GA method to
REVIEW

Besides empirical potentials, semiempirical extended- produce the local minima of 14 isomers of Si9 and further
Hückel method and tight-binding models have been uti- relax them at the DFT level.126
lized in the GA optimization of transition metal clusters.
For example, Curotto obtained the minima and isomers of
Nin (n  2  13) clusters based on the extended-Hückel 4.2.2. Hydrogenated Silicon Clusters
total energy model.120 DFT-based tight-binding (DFTB)
calculations121 have been performed to search for the The GA global optimization of hydrogenated silicon clus-
ground-state candidate structures of iron clusters up to 26 ters SinHm has been carried out by several groups.73, 127–129
atoms using a single-parent GA procedure.48 Using tight-binding models, Chakraborti et al.127 deter-
mined the ground-state structures of SinH (n  1, 4  8),
and Tang et al. performed a global structural optimization
4.2. Semiconductor Clusters for Si8H8 cluster.73 At semiempirical AM1 level, Ge and
Head performed the global geometry optimization of fully
4.2.1. Silicon Clusters and partially H-passivated Si clusters, Si10Hm (m  4, 8,
Compared to noble gas clusters and metal clusters, semi- 12, 16, 20) and Si10H20.128 Very recently, they have further
conductor clusters might have more complicatedDelivered improved the accuracy of their simulations at the ab initio
PESs due by Ingenta to:
level by reparametrizing AM1 with the aid of the ab initio
to the intrinsic nature of the covalent bonding.
RiceTherefore,
University, Fondren 129Library
silicon clusters up to 20 atoms have been frequently results. As an example of their new strategy, the ab ini-
IPused
: 93.80.184.211
tio global minima for Si6H2 and Si6H6 were determined.
as prototypes of the clusters with rather complicated PES
Thu, 11 Oct 2012 12:09:44
landscape in the GA global optimizations.35, 36, 43, 46, 48, 49,
62, 72, 122–126
In Hartke’s pioneering work, Si435 and Si1036
clusters described by an empirical Bolding-Anderson po- 4.2.3. Germanium Clusters
tential22 were used as model systems for testing the per- Compared to silicon clusters, less work has been done on
formance, strengths and possible limitations of the GA germanium clusters by using the GA procedure. Wang and
method. Niesse and Mayne applied space-fixed modified co-workers have systematically studied the Gen (n  2 
genetic algorithm (SFMGA) approach to search the global 25) clusters60, 61, 68 using the combination technique of the
minima for silicon clusters43 using the same empirical po- GA simulation with a tight-binding model71 and a DFT
tential.22 Later, this SFMGA was modified and used to minimization. Based on the global minima structures ob-
study the lowest-energy structures of Sin with n  15, tained, the melting behaviors of the germanium clusters
where the interatomic interaction was described by empir- are simulated, and their electronic properties such as ion-
ical Stillinger-Weber (SW) type potential21 and a revised ization potentials, energy gaps and polarizabilities as a
form proposed by Gong.23 function of cluster size have been discussed.
For the larger Sin clusters up to n  20, Ho et al. em-
ployed a combined technique of tight-binding GA global
optimization and LDA local minimization to explore the 4.2.4. Carbon Clusters
cluster ground state structures.72 A single-parent evolu-
tion algorithm, similar to the GA, was introduced to op- The structures of carbon clusters are of particular inter-
timize Si clusters, in which the Si-Si bonding was de- est8, 130, 131 because of the discovery of novel cage-like C60
scribed by DFT-based tight-binding method.48 Zacharias and related fullerenes. In a precursory work, using the GA
et al. introduced a novel hybrid approach of GA and SA procedure and a tight-binding total energy model, Deaven
(namely, predictor algorithm) and applied it to study the and Ho have obtained the fullerene cluster structures up to
geometry of Si20 cluster.46 A modified GA optimization C60.39 Later, several other groups have also optimized the
method, called neural-network-assisted genetic algo- carbon cluster geometries132–134 using the Brenner bond-
rithm,49 was tested in determining the ground state order potential.24 Hobday and Smith studied Cn(n  3 
geometries of Sin (n  10  15) based on a tightbinding 60) and predicted a structural transition from planar poly-
total energy method.124 Recently, the same group has cyclic to fullerenes around n  20.132 In contrast, Zhang
extended their study to larger silicon clusters with 16 et al. found bow-like configurations for most Cn (n  20 
to 21 atoms.125 Using a nonorthogonal tight-binding 30) clusters, with exception at C28 (fullerene structure).133
model,70 Wang et al. have obtained the ground state In order to discuss the formation mechanism of odd-num-
structures of medium-sized Sin (n  7  21) clusters bered fullerene-related species, Kong et al. used the GA
and exploited their melting behavior by Monte Carlo optimization to find the lowest-energy structures of odd-
simulations.62 numbered Cn with n  51  59.134
126 J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004
4.3. Alloy and Compound Clusters in the GA global optimization of water clusters.51, 143–145
In an earlier work by Niesse and Mayne,143 the water clusters
4.3.1. Bimetallic Alloy Clusters up to (H2O)13 were globally optimized using a modified
Bimetallic clusters present a number of structures and GA approach. The transferable intermolecular potentials

REVIEW
phases that are different from those of corresponding pure 3 point (TIP3P)25 was employed to model the interaction
metals. The lowest-energy structures of the clusters should between H2O molecules. Later, based on the same TIP3P,
depend both on the cluster size and on the concentration of Guimaraes et al. determined the water clusters (H2O)n with
the micro-alloys. The GA has also been employed in the n  11  13.51 With the aid of two new evolutionary op-
global optimization of alloy (e.g., Co-Cu, Cu-Au, Ni-Al, erators, namely annihilator and history operators, new global
Pt-Pd) clusters, 63, 64, 135–138
while Gupta potentials were minimum energy structures were found for all (H2O)1113
used to model the interatomic interactions in these works. water clusters. As well as TIP3P, another three-center
For instance, Wang et al. optimized the Co-Cu bimetallic model potential, SPC/E was adopted by Qian to explore
clusters with 18–20 atoms and simulated their melting be- the global potential energy minima of water clusters
63
havior. Using the same technique, they have explored the (H 2 O) n up to n  14,144 while the more realistic TIP4P
lowest-energy structures of Co18mCum with all possible (4 points) potentials were used by Hartke.145 Recently,
concentrations (0  m  18), and then calculated the mag- Kabrede and Hentschke have computed apparent global
netic moments of these clusters within a parameterized minimum structures of (H2O)n (n  25) using all three
64
tightbinding Hamiltonian. Recently, Johnston and co- available empirical potentials (SPC/E, TIP3P, TIP4P).146
workers studied the structural properties of a varieties Hartke has performed global geometry optimization of
Delivered
of nanoalloy clusters up to about 55 atoms, including pure neutral
Pt- by Ingenta the size range of n  2  30
to:water clusters in148
135
Pd, Cu-Au, 136, 137
Ni-Al. 138 using the
Rice University, Fondren Library TTM2-F potential. Above the empirical level,
the global
IP : 93.80.184.211 geometry optimization of water pentamer and
hexamer
Thu, 11 Oct 2012 12:09:44 clusters were performed using a NEMO model
4.3.2. Ionic and Covalent Compound Clusters potential and further improved by minimizing the geome-
Using an improved GA with a self-guiding search strat- tries using ab initio local second-order Moller-Plesset per-
egy, Kabrede and Hentschke have searched for the global turbation theory (MP2).147
minima structures of the neutral sodium chloride clusters Ion-containing in H2O clusters can be viewed as a mi-
52
that consist of 2 to 100 ions. The empirical Born-Mayer croscopic model of solvation. Ions of either alkali metals
repulsive potential, plus a long-range electrostatic Coulomb or halogens inside H2O clusters have been studied. TIP4P-
term, were used to account for the interactions between like empirical potentials can still be used to describe the
 
Na and Cl ions. Similar Coulomb  Born-Mayer po- intermolecular interaction and the interaction between H2O
tentials were used for optimizing the geometries of stoi- molecules and alkali-metal/halogen ions. In previous works,
1
chiometric and non-stoichiometric MgO clusters by the global minima structures of Cl (Br1, I1)(H2O)n
Roberts and Johnston.139 Flikkema and Bromley devel- (n  1  6), Na (H2O)n (n  4  25),150 M(H2O)n
149 

oped a new interatomic potential for nanoscale silica140 (n  4  22, M  Na, K, Cs)151 clusters were studied using
and applied it to the GA simulation of (SiO ) clusters. GA optimization.
2 7
By incorporating the GA with DFTB model, the struc-
tural and electronic properties of small titanium carbo- 4.4.2. Clusters of Aromatic Hydrocarbon
hedrene clusters TimCn with m  7, 8 and n  10  14 Molecules
have been investigated.141 Employing a GA-based search
strategy, Tomasulo and Ramakrishna have carried out a In an earlier work by Xiao and Williams, a computer pro-
global search for the lowest-energy structures of small gram GAME (genetic algorithm for minimization of energy)
(AlP)n (n  6) clusters using the DFT with the local den- was developed to obtain the global minimum structures of
sity approximation.142 benzene, naphthalene and anthracene molecular clusters up
to tetramer.37 Later, Pullan determined the global minimum
energy structures of (C6H6)n (n  2  15) clusters.152 Using
4.4. Molecular Clusters the space-fixed modified GA technique, White et al. studied
4.4.1. Water Clusters the benzene (C6H6)n (n  2  13), naphthalene (C10H8)n
(n  2  6) and anthracene (C14H10)n (n  2  6) clus-
In molecular clusters, the constituting molecules (e.g., H2O, ters.153 They found that the GA method is superior to the
C6H6, etc.) are weakly bound by hydrogen bonding and/ SA and comparable to the basis-hopping technique.83
or van der Waals interaction. Among molecular clusters,
water clusters are of particular interest.51, 143–148 Assuming 4.4.3. C60 Clusters
rigid molecules, several intermolecular potentials, such as
the transferable intermolecular potentials (TIP)25 and sim- In addition to the clusters composed by small molecules,
ple point charge/extended (SPC/E) model,26 have been used the structure of (C60)n clusters have been studied up to n 
J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004 127
25 by Luo et al.55 and up to n  57 by Zhang et al.154 Both were used to search for the “super alloy” materials with
works used the Pacheco-Ramalho intermolecular poten- specific properties.163
tial.27 Luo found a crossover from icosahedral to decahe-
dral at n  17 and (C60)13 as a stable magic numbered clus- 5. SUMMARY AND OUTLOOK
REVIEW

ter, while Zhang further found n  38, 55 as the most


stable species for the larger (C60)n clusters. From the above discussions, it is obvious that introducing
the genetic algorithm into cluster science has led to a sig-
4.5. Applications in Other Related Fields nificant breakthrough in the global optimization of clus-
ters. For the global optimization of those relatively simpler
As a robust global minimization method, GA has been ap- systems like LJ clusters, genetic algorithm has proven it-
plied to other related fields of computational materials sci- self to be an efficient way for solving the NP-hard prob-
ence and nanoscience. In this paper, we only intend to pre- lem. However, it is not quite clear whether the genetic al-
sent some highlights on the recent progress in this aspect. gorithm is able to find the global minima of the clusters
with a rather complicated potential energy surface up to
4.5.1. Nanoscience medium and large size. For instance, it is still a challenge
to find out the global minima structures of silicon clusters
The applications of GA to the other problems in compu- with the cluster size over 20–30 atoms. In those clusters,
tational nanoscience include supported clusters,155, 156 clus- the specific operation of encoding, mating and mutation
ter magnetism,157 nanoparticle-assemblies158 and ultrathin should be more carefully considered, according to the
metal nanowires.159 Using the noble gas atoms byDelivered nature of to:
LJ poten- by Ingenta the chemical bonding in the cluster, to further
tials as model systems for both surface andRicesupported clus- improve the
University, Fondren Library efficiency. Although the “cut and splice”
ters, Miyazaki and Inoue simulated the island andIPlayer crossover
: 93.80.184.211 operation introduced by Deaven and Ho has
structures of the deposited atoms.155 Using Thu, the surface- achieved
11 Oct 2012 12:09:44 a great success for LJ clusters, carbon clusters,
embedded-atom method, Zhang et al. have considered a metal clusters, etc., there might be still some other possible
more realistic system by adatom clusters up to 39 atoms on efficient ways of doing crossover. For example, graph the-
fcc (111) surfaces of different metals (Ag, Pt, Pd, Ni, Al).156 ory might be used to define a new way of crossover in the
Oda et al. applied a Monte Carlo method, incorporated with covalent bonding clusters with a network structure.
the GA approach, to simulate the magnetization and suscep- Among other global optimization approaches, it seems
tibility of randomly generated spin clusters and a-HQNN that the basin-hopping method83, 97 is a good alternative of
organic radical crystal within Ising model.157 Stucke and the genetic algorithm. Therefore, it would be more reliable
Crespi used the GA procedure for optimizing the packing if researchers can perform a global optimization by using
density of self-assembled multicomponent crystals of nano- both techniques and compare the computational results ob-
particles and predicted several new crystalline structures.158 tained from them. In addition, fast annealing evolutionary
Wang and coworkers have extended the GA to the struc- algorithm95 and conformational space annealing method82
tural optimization of one-dimensional ultrathin metal nano- also demonstrated impressive success in the optimization
wires.159 In these studies, periodic boundary conditions are of LJ clusters. On the other hand, combining the virtues of
applied along the wire axis, while the mating is modified GA with other global optimization methods like SA might
from the Deaven-Ho “cut and splice” operation for clus- also lead to a good way for further improving the global
ters.39 Helical multi-shell cylindrical structures were found optimization. An example along this direction is the pre-
for Au, Zr, Ti, Rh, Pt metal nanowires, in agreement with dictor algorithm.46
160
experimental observation on Au and Pt nanowires. One advantage of the GA approach is that it is an ideal
algorithm for implementing on a parallel computer.152
4.5.2. Computational Materials Science First, the evolution of total energy and local minimization
of each individual in a population are totally independent
The GA approach was also employed in determination of and can be simultaneously done on different processes. It
crystal structures as well as the computer-aid materials de- is also possible to simultaneously run several genetic algo-
sign. For example, Woodley et al. have used the GA rithms on each parallel processor and allow the migration
method to generate plausible crystal structures of inorganic between the populations of each of the simulations.
crystals, including binary oxides and ternary oxides.161 Up to now, most GA optimizations are based on empiri-
Bazterra et al. developed a new computational scheme to cal potentials. The empirical/quantum combination tech-
model structures of organic crystals using a modified niques58–60, 65–67, 72, 74 used by several research groups are
162
GA. Based on the knowledge of the geometry of the in- significant improvements over the accuracy of computa-
dividual molecules, the crystal structures of benzene, tional simulations. However, it is not guaranteed that the
naphthalene and anthracene were predicted with an empir- empirical potentials or tight-binding model used in the
ical intermolecular potential.162 Recently, DFT-based cal- combination study (usually fitted for the bulk phase prop-
culations, in conjunction with an evolutionary algorithm, erties) can exactly reproduce the true potential energy sur-
128 J. Comput. Theor. Nanosci. Vol. 1. No. 2, 2004
face of clusters dominated by quantum chemical bonding. 25. W. L. Jorgensen, J. Am. Chem. Soc. 103, 335 (1981); W. L.
In particular, for many clusters, there are size-dependent Jorgensen, J. Chandresekhar, J. D. Madura, R. W. Impey, and M. L.
Klein, J. Chem. Phys. 79, 926 (1983).
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