D.G. Papageorgiou

Merlin-3.0 A multidimensional optimization environment

We present an optimization environment for multidimensional continuous functions. Robust and powerful algorithms are used that guarantee its effectiveness. The environment offers programmability and ease of use by providing a specialized operating system and a control language that can be used to create successful optimization strategies. We report on several applications where this software has been successfully used.

MEMPSODE: A global optimization software based on hybridization of population-based algorithms and local searches☆

Article history: We present MEMPSODE, a global optimization software tool that integrates two prominent population- based stochastic algorithms, namely Particle Swarm Optimization and Differential Evolution, with well established efficient local search procedures made available via the Merlin optimization environment. The resulting hybrid algorithms, also referred to as Memetic Algorithms, combine the space exploration advantage of their global part with the efficiency asset of the local search, and as expected they have displayed a highly efficient behavior in solving diverse optimization problems. The proposed software is carefully parametrized so as to offer complete control to fully exploit the algorithmic virtues. It is accompanied by comprehensive examples and a large set of widely used test functions, including tough atomic cluster and protein conformation problems.

Icosahedral order in Cu-Zr amorphous alloys studied by means of X-ray absorption fine structure and molecular dynamics simulations

We have used the X-ray absorption fine structure method and molecular dynamics (MD) simulations to characterize atomic order in Cu-Zr metallic glasses (MGs). The microstructure of these MGs is described in terms of interconnected icosahedral-like clusters (superclusters) which are basic building units reproducing the stoichiometry of the system. The equilibrium MD configurations are used as an input for ab initio calculations of the extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectra. The theoretical EXAFS and XANES spectra are compared with those measured for rapidly quenched glassy Cu-Zr alloys. We demonstrate that the experimental results are well reproduced by EXAFS modeling of the population of the superclusters derived from the MD configuration. The average local structural motif can be approximated by Cu-centered icosahedral-like cluster satisfying the condition of maximal local packing efficiency and approximating the system stoichiometry. The simulated XANES exhibits good agreement with experiment, indicating that the atomic order of the MD configuration is consistent with that of the real alloy structure over distances of about 1 nm.

MERLIN-2.0 — Enhanced and programmable version

Abstract Merlin 2.0 is a new version of the recently published optimization package MERLIN-1.0. Apart from several minor improvements and extensions, this new version offers a very important feature: Programmability. A high level language has been developed, that enables the user to easily write programs that control the new MERLIN-2.0 at run time.

Structure and dynamics of NiO(001) and Ni/NiO(001) surfaces by molecular dynamics simulation

Abstract Using molecular dynamics and a rigid ion potential, we studied the vibrational and structural properties of the NiO(001) surface with and without cationic adatoms. We found that the bulk phonon density of states (DOS) is altered by the presence of the surface and that the adatom introduces new frequency modes. From the relaxed positions of the surface ions, it came out that up to 0.7 T m , the surface is contacted exhibiting rippling with outwards expansion of the cations and inwards contraction of the anions. The effect is detectable in five layers below the surface, while it persists at high temperatures. Strong contraction is found for the cationic adatom, relaxing on top of a surface anion that is lifted by more than 30% from its equilibrium position at high temperatures.

The Merlin control language for strategic optimization

Abstract Mcl is the programming language of the Merlin optimization environment. It can be used for the implementation of efficient optimization strategies, abolishing to a great extend the need for user intervention. The language is simple to learn and its structure is similar to Fortran. We report on successful applications where Mcl played an instrumental role, as for example in molecular physics problems and in the training of neural networks.

A numerical differentiation library exploiting parallel architectures

We present a software library for numerically estimating first and second order partial derivatives of a function by finite differencing. Various truncation schemes are offered resulting in corresponding formulas that are accurate to order O (h), O (h 2 ) ,a ndO (h 4 ), h being the differencing step. The derivatives are calculated via forward, backward and central differences. Care has been taken that only feasible points are used in the case where bound constraints are imposed on the variables. The Hessian may be approximated either from function or from gradient values. There are three versions of the software: a sequential version, an OpenMP version for shared memory architectures and an MPI version for distributed systems (clusters). The parallel versions exploit the multiprocessing capability offered by computer clusters, as well as modern multi-core systems and due to the independent character of the derivative computation, the speedup scales almost linearly with the number of available processors/cores.

Self-diffusion processes of copper adatom on Cu(110) surface by molecular dynamics simulations

Abstract The self-diffusion mechanisms of single adatoms on the Cu(110) surface have been studied using molecular dynamics simulation and a many-body potential within the second-moment approximation of the tight-binding model. From a detail trajectory analysis we found a variety of diffusion mechanisms, the hopping being the favoured one and we deduced the migration energies for the most important among them. At high temperatures, saturation in diffusion frequency for both hopping and exchange mechanisms is observed, indicating that the diffusion proceeds via complicated and concerted movements. In addition, we estimated the formation energy for the spontaneous creation of the vacancy-adatom pair, in good agreement with the experiment. Furthermore, from the temperature dependence of the relaxed adatom positions we found that the adatom exhibits strong contraction compared to the bulk interlayer spacing, attaining −20% at high temperatures.

MCL — Optimization oriented programming language

Abstract MCL is an optimization control language associated with the recently published MERLIN optimization package. It is developed so as to aid in constructing effective minimization strategies. It is very simple and easy to master. Supports Fortran-like operations, conditional and unconditional branching, multidimensional arrays, loops, statement functions, I/O operations and offers quite a few intrinsic functions. MERLIN has been further developed too, so that now it can be driven by the object code produced by the MCL compiler.

How many conformers of the 1, 2, 3-propanetriol triacetate are present in gas phase and in aqueous solution?

Abstract We found 109 rotamers within 3 kcal from the global minimum of the triglyceride in vacuo and only 6 water-solvated rotamers within this range. Hydration restricts triacetins conformational flexibility which is an unusual situation for small polar molecules. The lowest solvated conformation forms a system of three ring-like formations as the three carbonyl oxygens approach the hydrogen of the mid carbon of the glyceride skeleton. The structures of the global minima were subjected to geometry optimization with ab initio methods in order to validate the results.