Ilian T. Todorov

DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism

DL_POLY_3 is a general-purpose massively parallel molecular dynamics simulation package embedding a highly efficient set of methods and algorithms such as: Domain Decomposition (DD), Linked Cells (LC), Daresbury Advanced Fourier Transform (DAFT), Trotter derived Velocity Verlet (VV) integration and RATTLE. Written to support academic research, it has a wide range of applications and can run on a wide range of computers; from single processor workstations to multi-processor computers. The code development has placed particular emphasis on the efficient utilization of multi-processor power by optimised memory workload and distribution, which makes it possible to simulate systems of the order of tens of millions of particles and beyond. In this paper we discuss the new DL_POLY_3 design, and report on the performance, capability and scalability. We also discuss new features implemented to simulate highly non-equilibrium processes of radiation damage and analyse the structural damage during such processes.

A short description of DL_POLY

DL_POLY is a general purpose molecular dynamics simulation package with in-built parallel algorithms. It may be run on a wide selection of distributed memory parallel computers, from national supercomputers with thousands of processors, to single processor workstations and can simulate small systems with order 100 atoms, to systems with millions of atoms. This introduction provides an outline of the features of the package and the underlying methodology.

The nature of high-energy radiation damage in iron

Understanding and predicting a materials performance in response to high-energy radiation damage, as well as designing future materials to be used in intense radiation environments, requires knowledge of the structure, morphology and amount of radiation-induced structural changes. We report the results of molecular dynamics simulations of high-energy radiation damage in iron in the range 0.2-0.5 MeV. We analyze and quantify the nature of collision cascades both at the global and the local scale. We observe three distinct types of damage production and relaxation, including reversible deformation around the cascade due to elastic expansion, irreversible structural damage due to ballistic displacements and smaller reversible deformation due to the shock wave. We find that the structure of high-energy collision cascades becomes increasingly continuous as opposed to showing sub-cascade branching as reported previously. At the local length scale, we find large defect clusters and novel small vacancy and interstitial clusters. These features form the basis for physical models aimed at understanding the effects of high-energy radiation damage in structural materials.

Ab initio calculation of phase diagrams of ceramics and minerals

A range of methods, based on Monte Carlo and lattice dynamics simulations, are presented for the calculation of the thermodynamic properties of solid solutions and phase diagrams. These include Monte Carlo simulations with the explicit interchange of cations, the use of the semigrand-canonical ensemble and configurational bias techniques, hybrid Monte Carlo/molecular dynamics, and a new configurational lattice dynamics technique. It is crucial to take account of relaxation of the local atomic environment and vibrational effects. Examples studied are (i) the enthalpy and entropy of mixing, the phase diagram and the spinodal of MnO/MgO. The available experimental data disagree widely for this system; (ii) the enthalpy of mixing of CaO/MgO, where the size mismatch between the cations is considerably larger than in (i); (iii) the postulated high-pressure orthorhombic to cubic phase transition in (Mg,Mn)SiO3 perovskite, where we show that impurity cations can have a much larger effect than that expected from a mean-field treatment or linear interpolation between end-member compounds.

Simulation of mineral solid solutions at zero and high pressure using lattice statics, lattice dynamics and Monte Carlo methods

We discuss how two techniques, based on (1) lattice statics/lattice dynamics simulations and (2) Monte Carlo methods may be used to calculate the thermodynamic properties of oxide mixtures at zero and high pressure. The lattice statics/lattice dynamics calculations involve a full free energy structural optimization of each of a number of configurations, followed by thermodynamic averaging. Strategies for generating a suitable set of configurations are discussed. We compare results obtained by random generation with those obtained using radial distribution functions or explicit symmetry arguments to obtain approximate or exact weightings respectively for individual configurations. The Monte Carlo simulations include the explicit interchange of cations and use the semigrand canonical ensemble for chemical potential differences. Both methods are readily applied to high pressures and elevated temperatures without the need for any new parametrization. Agreement between the two techniques is better at high pressures where anharmonic terms are smaller. We compare in detail the use of each technique for properties such as enthalpies, entropies, volume and free energies of mixing at zero and high pressure and thus calculation of the phase diagram. We assess the vibrational contributions to these quantities and compare results with those in the dilute limit. The techniques are illustrated throughout using MnO?MgO and should be readily applicable to more complicated systems.

Radiation damage effects and percolation theory

We combine theoretical and experimental results to study percolation-driven transport phenomena in an irradiated material. We show that whereas the first transition takes place at the value of amorphous fraction , the second transition corresponds to the percolation of depleted phase. The knowledge of the radius of depletion sphere of the isolated damaged region allows one to predict the radiation dose at which the second percolation transition takes place, with dramatic increase in transport.

Advanced Potential Energy Surfaces for Molecular Simulation

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

The DL_POLY molecular dynamics package

Abstract The DL_POLY package provides a set of classical molecular dynamics programs that have application over a wide range of atomic and molecular systems. Written for parallel computers they offer capabilities stretching from small systems consisting of a few hundred atoms running on a single processor, up to systems of several million atoms running on massively parallel computers with thousands of processors. In this article we describe the structure of the programs and some applications.

Order–disorder in grossly non-stoichiometric SrFeO2.50— a simulation study

Configurational lattice energy techniques are used to investigate oxygen vacancy ordering and the order–disorder transition in SrFeO2.50. Vacancy disorder is shown to present many new challenges, largely due to the extensive relaxation in such grossly non-stoichiometric systems. With large supercells it is not feasible to optimise each individual configuration. Efficient methods for choosing a small number of representative configurations are discussed. Oxygen vacancy–vacancy interactions are considerable in SrFeO2.50 and lead to the formation of preferred local structural entities. While the low-temperature structure consists of an ordered arrangement of octahedra and tetrahedra, the disordered high-temperature structure may be described as a mixture of tetrahedra, square pyramids and octahedra. Fe atoms with coordination numbers lower than four are negligible. The assumption of an ideal solution of oxygen vacancies in such systems, commonly made in standard thermodynamic treatments, is questionable.

Electronic effects in high-energy radiation damage in iron

Electronic effects have been shown to be important in high-energy radiation damage processes where a high electronic temperature is expected, yet their effects are not currently understood. Here, we perform molecular dynamics simulations of high-energy collision cascades in α-iron using a coupled two-temperature molecular dynamics (2T-MD) model that incorporates both the effects of electronic stopping and electron-phonon interaction. We subsequently compare it with the model employing electronic stopping only, and find several interesting novel insights. The 2T-MD results in both decreased damage production in the thermal spike and faster relaxation of the damage at short times. Notably, the 2T-MD model gives a similar amount of final damage at longer times, which we interpret to be the result of two competing effects: a smaller amount of short-time damage and a shorter time available for damage recovery.