Global optimization of Lennard-Jones clusters by a parallel fast annealing evolutionary algorithm

A parallel fast annealing evolutionary algorithm (PFAEA) was presented and applied to optimize Lennard-Jones (LJ) clusters. All the lowest known minima up to LJ(116) with both icosahedral and nonicosahedral structure, including the truncated octahedron of LJ(38), central fcc tetrahedron of LJ(98), the Marks' decahedron of LJ(75)(-)(77), and LJ(102)(-)(104), were located successfully by the unbiased algorithm. PFAEA is a parallel version of fast annealing evolutionary algorithm (FAEA) that combines the aspect of population in genetic algorithm and annealing algorithm with a very fast annealing schedule. A master-slave paradigm is used to parallelize FAEA to improve the efficiency. The performance of PFAEA is studied, and the scaling of execution time with the cluster size is approximately cubic, which is important for larger scale energy minimization systems.     

Structural transitions and melting in LJ(74-78) Lennard-Jones clusters from adaptive exchange Monte Carlo simulations

Phase changes in Lennard-Jones (LJ) clusters containing between 74 and 78 atoms are investigated by means of exchange Monte Carlo simulations in the canonical ensemble. The replica temperatures are self-adapted to facilitate the convergence. Although the 74- and 78-atom clusters have icosahedral global minima, the clusters with 75-77 atoms have decahedral ground-state structures and they undergo a structural transition to icosahedral minima before melting. The structural transitions are characterized by quenching and by looking at the Q4 and Q6 orientational bond order parameters. The transition temperatures are estimated to be 0.114, 0.065, and 0.074 reduced units for LJ75, LJ76, and LJ77, respectively. These values, their ordering and the associated latent heats are compared with other estimates based on the harmonic superposition approach.     

Chemical identification of icosahedral structure for cobalt and nickel clusters

Reactions of bare and hydrogenated cobalt and nickel clusters with ammonia and with water are used to determine cluster geometrical structure. Saturation measurements determine the total number of ammonia binding sites on cluster surfaces. A pattern of minima in the number of such sites is found to correlate with the sequence of closed shells and subshells expected for icosahedral packing in the 50- to 120-atom size range (50- to 200-atom range for hydrogenated clusters). In many cases there are 12 sites at the minima, the number that would be expected for preferred ammonia binding sites on closed (sub)shells of icosahedral clusters. The equilibrium adsorption of a single water molecule provides a sensitive measure of changes in cluster-water binding energy. A pattern of binding energy maxima is found, once again correlating with icosahedral structure, but for clusters having one metal atom more than the closed (sub)shells. In general, hydrogenation enhances the patterns of minima and maxima. These observations are explained in terms of the expected nature of ammonia and water binding to icosahedral clusters.     

Novel lattice-searching method for modeling the optimal strain-free close-packed isomers of clusters

Small icosahedral, decahedral, and fcc structures have been studied by unbiased global optimization methods or Wulff construction and Northby lattice methods. Strain-free close-packed structures are not much discussed because the structures are very difficult to optimize and there is no common strain-free close-packed lattice. We propose a new strategy to construct such a lattice containing all possible strain-free close-packed isomers, and by searching the lattice with an efficient method the optimal close-packed structures were modeled. Testing with the Morse potential at rho0=14.0 for cluster size 10相似文献   

Monte Carlo temperature basin paving with effective fragment potential: an efficient and fast method for finding low-energy structures of water clusters (H2O)20 and (H2O)25

Determining low-energy structures of large water clusters is a challenge for any optimization algorithm. In this work, we have developed a new Monte Carlo (MC)-based method, temperature basin paving (TBP), which is related to the well-known basin hopping method. In the TBP method, the Boltzmann weight factor used in MC methods is dynamically modified based on the history of the simulation. The states that are visited more are given a lower probability by increasing their temperatures and vice versa. This allows faster escapes from the states frequently visited in the simulation. We have used the TBP method to find a large number of low-energy minima of water clusters of size 20 and 25. We have found structures energetically same to the global minimum structures known for these two clusters. We have compared the efficiency of this method to the basin-hopping method and found that it can locate the minima faster. Statistical efficiency of the new method has been investigated by running a large number of trajectories. The new method can locate low-energy structures of both the clusters faster than some of the reported algorithms for water clusters and can switch between high energy and low-energy structures multiple times in a simulation illustrating its efficiency. The large number of minima obtained from the simulations is used to get both general and specific features of the minima. The distribution of minima for these two clusters based on the similarity of their oxygen frames shows that the (H(2)O)(20) can have different variety of structures, but for (H(2)O)(25), low-energy structures are mostly cagelike. Several (H(2)O)(25) structures are found with similar energy but with different cage architectures. Noncage structures of (H(2)O)(25) are also found but they are 6-7 kcal/mol higher in energy from the global minimum. The TBP method is likely to play an important role for exploring the complex energy landscape of large molecules.     

Predicting the shape and structure of face-centered cubic gold nanocrystals smaller than 3 nm.

Although a number of computational studies have examined the relative stability of icosahedral and decahedral gold clusters from 1 to 3 nm in size, few studies have focussed on the variety of face-centered cubic (fcc) nanoparticles in this size regime. In most cases small fcc gold particles are assumed to adopt the truncated octahedral shape, but in light of the fact that the shape and structure of gold nanoparticles is known to vary, the relative stability of fcc polyhedra may change with size. Presented here are results of first-principles calculations investigating the preferred shape of gold particles less than 3 nm in size. Our results indicate that the equilibrium shape of fcc gold nanoparticles less than 1 nm is the cuboctahedron, but this shape rapidly becomes energetically unstable with respect to the truncated octahedron, octahedron and truncated cube shapes as the size increases.     

H·(H2O)n clusters: microsolvation of the hydrogen atom via molecular ab initio gradient embedded genetic algorithm (GEGA)

A new version of the ab initio gradient embedded genetic algorithm (GEGA) program for finding the global minima on the potential energy surface (PES) of mixed clusters formed by molecules and atoms is reported. The performance of the algorithm is demonstrated on the neutral H·(H(2)O)(n) (n = 1-4) clusters, that is, a radical H atom solvated in 1-4 water molecules. These clusters are of a fundamental interest. The solvated hydrogen atom forms during photochemical events in water, or during scavenging of solvated electrons by acids, and transiently exists in biological systems and possibly in inclusion complexes in the deep ocean and in the ice shield of earth. The processes associated with its existence are intriguingly complex, however, and have been the subject of decades-long debates. Using GEGA, we explicate the apparently extreme structural diversity in the H·(H(2)O)(n) (n = 1-4) clusters. All considered clusters have four basic structural types: type I, where the H radical is weakly coordinated to the oxygen atom of one of the water molecules; type II, where H is weakly coordinated to a H atom of one of the water molecules; type III, consisting of H(2), the OH radical, and n - 1 H(2)O molecules; and type IV, consisting of H(3)O and n - 1 H(2)O. There are myriads of isomers of all four types. The lowest energy species of types I and II are the isoenergetic global minima. H·(H(2)O)(n) clusters appear to be a challenging case for GEGA because they have many shallow minima close in energy some of which are significantly less stable than the global minimum. Additionally, the global minima themselves have high structural degeneracy, they are only weakly bound, and they are prone to dissociation. GEGA performed exceptionally well in finding both the global and the low-energy local minima that were subsequently confirmed at higher levels of theory.     

Size‐guided multi‐seed heuristic method for geometry optimization of clusters: Application to benzene clusters

Since searching for the global minimum on the potential energy surface of a cluster is very difficult, many geometry optimization methods have been proposed, in which initial geometries are randomly generated and subsequently improved with different algorithms. In this study, a size‐guided multi‐seed heuristic method is developed and applied to benzene clusters. It produces initial configurations of the cluster with n molecules from the lowest‐energy configurations of the cluster with n − 1 molecules (seeds). The initial geometries are further optimized with the geometrical perturbations previously used for molecular clusters. These steps are repeated until the size n satisfies a predefined one. The method locates putative global minima of benzene clusters with up to 65 molecules. The performance of the method is discussed using the computational cost, rates to locate the global minima, and energies of initial geometries. © 2018 Wiley Periodicals, Inc.     

Global optimization and the energy landscapes of Dzugutov clusters

The global minima of clusters bound by a Dzugutov potential form non-compact polytetrahedral clusters mainly composed of interpenetrating and face-sharing 13-atom icosahedra. As the size increases, these icosahedral units first form linear arrays, then two-dimensional rings, then three-dimensional networks. Characterization of the energy landscapes of these clusters shows that they are particularly rough and generally exhibit a multiple-funnel topography. These results provide new insights into the structure and dynamics of bulk supercooled Dzugutov liquids and the form of the bulk phase diagram.     

Binding energy of large icosahedral and cuboctahedral Lennard-Jones clusters

It is widely believed that the lowest energy configurations for small rare gas clusters have icosahedral symmetry. This contrasts with the bulk crystal structures which have cuboctahedral fcc symmetry. It is of interest to understand the transition between this finite and bulk behavior. To model this transition in rare gas clusters we have undertaken optimization studies within the Lennard-Jones pair potential model. Using a combination of Monte Carlo and Partan Search optimization methods, the lowest energy relaxed structures of Lennard-Jones clusters having icosahedral and cuboctahedral symmetry were found. Studies were performed for complete shell clusters ranging in size from one shell having 13 atoms to 14 shells having 10,179 atoms. It was found that the icosahedral structures are lower in energy than the cuboctahedral structures for cluster sizes having 13 shells or fewer. Additional studies were performed using the more accurate Aziz-Chen [HFD-C] pair potential parameterized for argon. The conclusions appear to be relatively insensitive to the form of the potential.     

Lowest-energy structures of (C60)nX (X=Li+,Na+,K+,Cl-) and (C60)nYCl (Y=Li,Na,K) clusters for n</=13

Basin-hopping global optimization is used to find likely candidates for the lowest minima on the potential energy surface of (C(60))(n)X (X=Li(+),Na(+),K(+),Cl(-)) and (C(60))(n)YCl (Y=Li,Na,K) clusters with n相似文献   

Melting Behaviour of Shell-symmetric Aluminum Nanoparticles: Molecular Dynamics Simulation

Molecular dynamics simulations with embedded atom method potential were carried out for Al nanoparticles of 561 atoms in three structures: icosahedron, decahedron, and truncated octahedron. The total potential energy and specfic heat capacity were calculated to estimate the melting temperatures. The melting point is 540±10 K for the icosahedral structure,500±10 K for the decahedral structure, and 520±10 K for the truncated octahedral structure.With the results of mean square displacement, the bond order parameters and radius of gyration are consistent with the variation of total potential energy and specific heat capacity. The relaxation time and stretching parameters in the Kohlraush-William-Watts relaxation law were obtained by fitting the mean square displacement. The results show that the relationship between the relaxation time and the temperatures is in agreement with standard Arrhenius relation in the high temperature range.     

A photoelectron spectroscopic and computational study of sodium auride clusters, NanAun- (n = 1-3)

Negatively charged sodium auride clusters, NanAun- (n = 1-3), have been investigated experimentally using photoelectron spectroscopy and ab initio calculations. Well-resolved electronic transitions were observed in the photoelectron spectra of NanAun- (n = 1-3) at several photon energies. Very large band gaps were observed in the photoelectron spectra of the anion clusters, indicating that the corresponding neutral clusters are stable closed-shell species. Calculations show that the global minimum of Na2Au2- is a quasi-linear species with Cs symmetry. A planar isomer of D2h symmetry is found to be 0.137 eV higher in energy. The two lowest energy isomers of Na3Au3- consist of three-dimensional structures of Cs symmetry. The global minimum of Na3Au3- has a bent-flake structure lying 0.077 eV below a more compact structure. The global minima of the sodium auride clusters are confirmed by the good agreement between the calculated electron detachment energies of the anions and the measured photoelectron spectra. The global minima of neutral Na2Au2 and Na3Au3 are found to possess higher symmetries with a planar four-membered ring (D2h) and a six-membered ring (D3h) structure, respectively. The chemical bonding in the sodium auride clusters is found to be highly ionic with Au acting as the electron acceptor.     

Clusters containing open-shell molecules: minimum-energy structures and low-lying isomers of ArnCH (X 2 pi), n = 1 to 15

The size evolution of the equilibrium structures of open-shell ArnCH (X 2 pi) Van der Waals clusters is investigated for n = 1 to 15. We describe a method for combining pair potentials for Ar-CH and Ar-Ar interactions to obtain potential energy surfaces for ArnCH clusters. For each cluster size considered, the global and a few energetically close local minima are calculated using simulated annealing followed by a direct minimization scheme. Ar2CH is found to have an unusually stable planar structure, which persists as a motif in larger ArnCH clusters and has a strong effect on their optimal geometries. The lowest-energy isomers of ArnCH with n = 3 to 11 have all Ar atoms in a shell around CH. The only exception is Ar4CH, where the fully solvated isomer is 3 cm-1 higher in energy than the optimal isomer with CH bound to the surface of the Ar4 tetrahedron. For n = 7 to 11, the minimum-energy structure of ArnCH derives from the global minimum of the Arn + 1 cluster, by replacing the Ar atom at the bottom of the pentagonal bipyramid with CH. The lowest-energy structure of Ar12CH is that of the optimal icosahedral Ar13 cluster, with CH replacing one of the Ar atoms on the cluster surface. This structure supports the proposition based on the spectroscopic data, that for ArnCH clusters with about 10 to 50 Ar atoms CH resides on the surface of Arn.     

First-principles study of the electronic structures of icosahedral TiN (N=13,19,43,55) clusters

We have studied the electronic structures of icosahedral Ti(N) clusters (N=13, 19, 43, and 55) by using a real-space first-principles cluster method with generalized gradient approximation for exchange-correlation potential. The hexagonal close-packed and fcc close-packed clusters have been studied additionally for comparisons. It is found that the icosahedral structures are the most stable ones except for Ti(43), where fcc close-packed structure is favorable in energy. We present and discuss the variation of bond length, the features of the highest occupied molecular orbitals and the lowest unoccupied molecular orbital, the evolution of density of states, and the magnetic moment in detail. The results are in good agreement with the predictions from the collision-induced dissociation and size-selected anion photoelectron spectroscopy experiments.     

Alternative search strategy for minimal energy nanocluster structures: the case of rhodium, palladium, and silver

An alternative strategy to find the minimal energy structure of nanoclusters is presented and implemented. We use it to determine the structure of metallic clusters. It consists in an unbiased search, with a global minimum algorithm: conformational space annealing. First, we find the minima of a many-body phenomenological potential to create a data bank of putative minima. This procedure assures us the generation of a set of cluster configurations of large diversity. Next, the clusters in this data bank are relaxed by ab initio techniques to obtain their energies and geometrical structures. The scheme is successfully applied to magic number 13 atom clusters of rhodium, palladium, and silver. We obtained minimal energy cluster structures not previously reported, which are different from the phenomenological minima. Moreover, they are not always highly symmetric, thus casting some doubt on the customary biased search scheme, which consists in relaxing with density functional theory global minima chosen among high symmetry structures obtained by means of phenomenological potentials.     

Electron affinity of Al13: a correlated electronic structure study

Neutral and anionic 13-atom aluminum clusters are studied with high-level, fully ab initio methods: second-order perturbation theory (MP2) and coupled cluster theory with singles, doubles, and perturbative triples (CCSD(T)). Energies and vibrational frequencies are reported for icosahedral and decahedral isomers, and are compared with density functional theory results. At the MP2 level of theory, with all of the basis sets employed, the icosahedral structure is energetically favored over the decahedral structure for both the neutral and anionic Al(13) clusters. Hessian calculations imply that only the icosahedral structures are potential energy minima. The CCSD(T)/aug-cc-pVTZ adiabatic electron affinity of Al(13) is found to be 3.57 eV, in excellent agreement with experiment.     

Clever and efficient method for searching optimal geometries of lennard-jones clusters

An unbiased algorithm for determining global minima of Lennard-Jones (LJ) clusters is proposed in the present study. In the algorithm, a global minimum is searched by using two operators: one modifies a cluster configuration by moving atoms to the most stable positions on the surface of a cluster and the other gives a perturbation on a cluster configuration by moving atoms near the center of mass of a cluster. The moved atoms are selected by employing contribution of the atoms to the potential energy of a cluster. It was possible to find new global minima for LJ506, LJ521, LJ536, LJ537, LJ538, and LJ541 together with putative global minima of LJ clusters of 10-561 atoms reported in the literature. This indicates that the present method is clever and efficient for cluster geometry optimization.     

Geometry optimization of carbon dioxide clusters (CO2)n for 4 < or = n < or = 40

Geometry optimization of carbon dioxide clusters (CO2)n with the size of 4 < or = n < or = 40 is performed by a heuristic and unbiased method combined with geometrical perturbations. Comparison with the global minima reported in the literature shows that the present method reproduces the global minima for clusters with n = 6, 8, 13, 19, 28, 30, and 32 and yields new global minima for (CO2)23, (CO2)25, and (CO2)35. For the other clusters under investigation, global minima are first reported in this article. Structural features of CO2 clusters and efficiency of the optimization method are discussed.     

Growth and structural properties of Mg(N) (N = 10-56) clusters: density functional theory study

Using the minima hopping global geometry optimization method on density functional potential energy surface, we have studied the structural and electronic properties of magnesium clusters for a size range of Mg(N) where N = 10-56. Our exhaustive search reveals that most of our global minima are nonsymmetric in the size range above N = 20. We elucidate the evolutionary trend of the entire series and present more details about the peculiar growth of the clusters. For N > 20, it is possible to divide the cluster into two regions: the core region and the surface region. It turns out that the growth follows a peculiar cyclic pattern where the core and surface grow alternatively. The surface energy, as a function of number of atoms shows a clear signature as the number of atoms in the core increases by one. We have also carried out stability analysis and the stable sizes(magic numbers) agree very well with the experimental magic numbers reported by Diederich [J. Chem. Phys. 2011, 134, 124302]. We point out the similarities and differences between our results and sodium clusters.