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Comparison between solid- and solution-state intermolecular interactions identify solvent-dependant pathways directing crystallisation into different polymorphic forms.

We report the effects of radiation damage on helium diffusion in zircon using data from molecular dynamics simulations. We observe an increase in activation energy for helium diffusion as a result of radiation damage and increasing structural disorder. The activation energy in a heavily damaged region is smaller than in a completely amorphous system which is correlated with remaining order in the cation sublattices of the damaged structure not present in the fully amorphized system. The increase in activation energy is related to the disappearance of fast diffusion pathways that are present in the crystal. Consistent with the change in activation energy, we observe the accumulation of helium atoms in the damaged structure and discuss the implications of this effect for the formation of helium bubbles and zircon’s performance as an encapsulation material for nuclear waste. Graphic abstract

In the late 1970s, the embryonic UK research community in molecular simulation – physicists and physical chemists – organised itself around CCP5, one of a set of Collaborative Computational Projects in different fields. CCP5 acted to develop and use the software required by an evolving and expanding scientific agenda, to exploit quickly and efficiently the revolution in computing hardware and to educate and nurture the careers of future generations of researchers in the field. This collaboration formally began in 1980, and is still fully active now, 40 years later. Today, molecular simulation techniques, many of them pioneered by CCP5, are now used very widely, including in several other CCPs in the UK’s current family of Collaborative Computational Projects. This article tells the story of molecular simulation in the UK, with CCP5 itself at centre stage, using the written records in the CCP archives. The authors were, or are, all personally involved in this story.

We present a novel approach of mapping dissipative particle dynamics (DPD) into classical molecular dynamics. By introducing the invariant volume element representing the swarm of atoms we show that the interactions between the emerging Brownian quasiparticles arise naturally from its geometric definition and include both conservative repulsion and dissipative drag forces. The quasiparticles, which are composed of atomistic host solvent rather than being simply immersed in it, provide a link between the atomistic and DPD levels and a practical route to extract the DPD parameters as direct statistical averages over the atomistic host system. The method thus provides the molecular foundations for the mesoscopic DPD. It is illustrated on the example of simple monatomic supercritical fluid demonstrating good agreement in thermodynamic and transport properties calculated for the atomistic system and DPD using the obtained parameters., Comment: 13 pages, 5 figures. Contribution to the DL_POLY 25th Anniversary Special Meeting, 3-4 Nov 2017, Chichely Hall, MK16 9JJ, UK

Three separately developed software Molecular Dynamics packages at Daresbury Laboratory, namely DL_FIELD (DL_F), DL_POLY and DL_ANALYSER, have been integrated to form an efficient computational inf...

Pragmatic interoperability between platforms and service-oriented architectures exists whenever there is an agreement on the roles of participants and components as well as minimum standards for good practice. In this work, it is argued that open platforms require pragmatic interoperability, complementing syntactic interoperability (e.g., through common file formats), and semantic interoperability by ontologies that provide agreed definitions for entities and relations. For consistent data management and the provision of services in computational molecular engineering, community-governed agreements on pragmatics need to be established and formalized. For this purpose, if ontology-based semantic interoperability is already present, the same ontologies can be used. This is illustrated here by the role of the “translator” and procedural definitions for the process of “translation” in materials modelling, which refers to mapping industrial research and development problems onto solutions by modelling and simulation. For associated roles and processes, substantial previous standardization efforts have been carried out by the European Materials Modelling Council (EMMC ASBL). In the present work, the Materials Modelling Translation Ontology (MMTO) is introduced, and it is discussed how the MMTO can contribute to formalizing the pragmatic interoperability standards developed by EMMC ASBL.

The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of nonreactive force fields. In this formalism, most of the implemented coupling terms are built using functional forms that depend on spatial coordinates, while parameters are fitted against reference data to model the change of chemistry between the participating nonreactive states. In this work, we demonstrate that the use of such coupling terms precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. Alternatively, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating nonreactive force fields, and derive a general expression for the EVB stress tensor suitable for computation. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in nonreactive water. Mass densities and probability distributions for the values of the energy gaps computed in the NPT ensemble reveal a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating for the first time the validity of approximations based on the canonical NVT ensemble, customarily adopted for EVB simulations. The presented formalism also aims to contribute to future implementations and extensions of the EVB method to research the limit of highly concentrated solutions.

Including the effects of excited electrons in classical simulations, at the level of the two-temperature model, involves the coupling of a grid-based finite-difference solver for a heat diffusion e...

It was my pleasure to organise and celebrate the 25th anniversary of the DL_POLY project as a special event at the Royal Society’s Chicheley Hall in November 2017. This special issue of Molecular S...

We report a study of the absorption of CO2 into a number of zinc imidazolate framework structures, and subsequent desorption, using the molecular dynamics simulation method with force fields partly developed by ourselves. The simulations primarily give results concerning the mechanism of CO2 absorption under conditions likely to be found in industrial waste gas streams. In particular we compare the rate of uptake of CO2 for different ZIFs. We also show that it is possible to observe desorption by reduced pressure and high temperature. These characteristics confirm that ZIFs might be suitable for CO2 absorption within an industrial capture and sequestration process.

The nature of the amorphous state has been notably difficult to ascertain at the microscopic level. In addition to the fundamental importance of understanding the amorphous state, potential changes to amorphous structures as a result of radiation damage have direct implications for the pressing problem of nuclear waste encapsulation. Here, we develop new methods to identify and quantify the damage produced by high-energy collision cascades that are applicable to amorphous structures and perform large-scale molecular dynamics simulations of high-energy collision cascades in a model zircon system. We find that, whereas the averaged probes of order such as pair distribution function do not indicate structural changes, local coordination analysis shows that the amorphous structure substantially evolves due to radiation damage. Our analysis shows a correlation between the local structural changes and enthalpy. Important implications for the long-term storage of nuclear waste follow from our detection of significant local density inhomogeneities. Although we do not reach the point of convergence where the changes of the amorphous structure saturate, our results imply that the nature of this new converged amorphous state will be of substantial interest in future experimental and modelling work., Comment: 11 pages, 15 figures

Large-scale molecular dynamics simulations have been used to study the microstructure in Y-doped ${\mathrm{ZrO}}_{2}$. From simulations performed as a function of composition the dependence of microstructure on composition is quantified, showing how it is formed from two coexisting phases, and the transformation to the stabilized cubic form is observed at higher concentrations of yttrium and higher temperatures. The effect of composition and temperature on oxygen diffusion is also studied, showing strong correlations between microstructure and diffusion.

The accuracy and robustness of new Buckingham potentials for the pyrochlores Gd2Ti2O7 and Gd2Zr2O7 is demonstrated by calculating and comparing values for a selection of point defects with those calculated using a selection of other published potentials and our own ab inito values. Frenkel pair defect formation energies are substantially lowered in the presence of a small amount of local cation disorder. The activation energy for oxygen vacancy migration between adjacent O48f sites is calculated for Ti and Zr pyrochlores with the energy found to be lower for the non-defective Ti than for the Zr pyrochlore by ∼0.1 eV. The effect of local cation disorder on the VO48f → VO48f migration energy is minimal for Gd2Ti2O7, while the migration energy is lowered typically by ∼43 % for Gd2Zr2O7. As the healing mechanisms of these pyrochlores are likely to rely upon the availability of oxygen vacancies, the healing of a defective Zr pyrochlore is predicted to be faster than for the equivalent Ti pyrochlore.

© 2016 American Chemical Society. 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.

Halothane binding to hydrated dimyristoylphosphatidylcholine (DMPC) bilayer membranes has been examined over a wide range of pressures from 105 to 4 × 108 Pa. We show that the solvation of halothane by the membrane and bulk water are both pressure dependent, with an increased pressure driving halothane into the membrane. Analysis of these results shows that this pressure dependence is not the cause of pressure reversal, the process whereby general anaesthetics lose their efficacy at pressures of about 8 × 106 to about 2.5 × 107 Pa.

A suite of application benchmarks, designed to be broadly representative of UK HPC usage, has been developed to stress a broad range of architectural features of large scale parallel HPC resources. A generic methodology to investigate application performance and scaling characteristics has been defined, resulting in a detailed understanding of the performance of these applications. This methodology is transferable to other applications and systems: it is of practical value to developers and users who are aiming for optimal utilisation of HPC resources. An understanding of the performance characteristics of a range of large-scale HPC resources has been obtained using low-level synthetic benchmarks. A relatively simple, qualitative mechanism to assess and predict application performance on current and future architectures using synthetic benchmark results together with application performance analysis results is explored.

A molecular dynamics (MD) study of MgxAlyOz thin films grown by magnetron sputtering is presented using an ionic model and comparing two potential sets with formal and partial charges. The applicability of the model and the reliability of the potential sets for the simulation of thin film growth are discussed. The formal charge potential set was found to reproduce the thin film structure in close agreement with the structure of the experimentally grown thin films. Graphical abstract A molecular dynamics study of growth of MgxAlyOz thin films is presented using an ionic model and comparing two potential sets with formal and partial charges. The simulation results with the formal charge potential set showed a transition in the film from a crystalline to an amorphous structure, when the Mg metal content decreases below 50% in very close agreement with the structure of the experimentally deposited films.

We review the work carried out within the e Minerals project to develop eScience solutions that facilitate a new generation of molecular-scale simulation work. Technological developments include integration of compute and data systems, developing of collaborative frameworks and new researcher-friendly tools for grid job submission, XML data representation, information delivery, metadata harvesting and metadata management. A number of diverse science applications will illustrate how these tools are being used for large parameter-sweep studies, an emerging type of study for which the integration of computing, data and collaboration is essential.

DL_POLY_3 is a general purpose molecular dynamics (MD) simulation package designed to simulate systems of the order of tens of millions of particles and beyond by efficiently harnessing the power of modern computer clusters. Here we discuss the package design, functionality and report on performance and capability limits. We then report the application of DL_POLY_3 to study radiation cascades in Gd2Ti2O7 and Gd2Zr2O7, potential materials for high-level radioactive waste storage and discuss problems associated with the analysis of the cascades. We see little direct amorphisation but rather the start of a transition to the fluorite structure which is more pronounced for the Zr than the Ti compound.

Recently, there has been a concerted effort to implement advanced classical potential energy surfaces by adding higher order multipoles to fixed point charge electrostatics in a bid to increase the accuracy of simulations of condensed phase systems. One major hurdle is the unwieldy nature of the expressions which in part has limited developers mostly to including only dipoles and quadrupoles. In this paper, we present a generalization of the Cartesian formulation of electrostatic multipolar interactions that enables the specification of an arbitrary order of multipoles. Specifically, we derive formulas for arbitrary order implementation of the particle mesh Ewald method and give a closed form formula for the stress tensor in the reciprocal space. In addition, we provide recurrence relations for common electrostatic potentials employed in molecular simulations, which allows for the generalization to arbitrary order and guarantees a computational cost that scales as O(p(3)) for Cartesian multipole interactions of order p.

We discuss how structural disorder and amorphization affects solid-state diffusion, and consider zirconolite as a currently important case study. By performing extensive molecular dynamics simulations, we disentangle the effects of amorphization and density, and show that a profound increase of solid-state diffusion takes place as a result of amorphization. Importantly, this can take place at the same density as in the crystal, representing an interesting general insight regarding solid-state diffusion. We find that decreasing the density in the amorphous system increases pre-factors of diffusion constants, but not decreasing the activation energy. We also find that atomic species in zirconolite are affected differently by amorphization and density change. Our microscopic insights are relevant for understanding how solid-state diffusion changes due to disorder and for building predictive models of operation of materials to be used to encapsulate nuclear waste.

We use the example of a study of the compressibility anomaly in amorphous silica to illustrate how molecular-scale simulations can be performed using grid computing. The potential for running many simulations within a single study requires the use of new data management methods, which are discussed in this paper. The example of silica highlights the advantages of the use of grid computing for studying subtle effects.

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 Smoothed Particle Mesh Ewald method [U. Essmann, L. Perera, M.L. Berkowtz, T. Darden, H. Lee, L.G. Pedersen, J. Chem. Phys. 103 (1995) 8577] for calculating long ranged forces in molecular simulation has been adapted for the parallel molecular dynamics code DL_POLY_3 [I.T. Todorov, W. Smith, Philos. Trans. Roy. Soc. London 362 (2004) 1835], making use of a novel 3D Fast Fourier Transform (DAFT) [I.J. Bush, The Daresbury Advanced Fourier transform, Daresbury Laboratory, 1999] that perfectly matches the Domain Decomposition (DD) parallelisation strategy [W. Smith, Comput. Phys. Comm. 62 (1991) 229; M.R.S. Pinches, D. Tildesley, W. Smith, Mol. Sim. 6 (1991) 51; D. Rapaport, Comput. Phys. Comm. 62 (1991) 217] of the DL_POLY_3 code. In this article we describe software adaptations undertaken to import this functionality and provide a review of its performance.

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 solid solutions and highly disordered systems. The lattice statics/lattice dynamics calculations involve a full free-energy structural optimization of each of a number of configurations, followed by thermodynamic averaging. 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 parameterization; at agreement between the two techniques is better at high pressures where anharmonic terms are smaller. Vibrational contributions to thermodynamic quantities of mixing are examined. A range of examples, including binary oxides, garnets and carbonates, are used to illustrate the methods. Fil: Allan, N. L.. University of Bristol; Reino Unido Fil: Barrera, Gustavo Daniel. Universidad Nacional de la Patagonia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina Fil: Lavrentiev, M. Yu. Culham Science Centre; Reino Unido Fil: Freeman, C. L. University of Bristol; Reino Unido Fil: Todorov, I. T.. CLRC Daresbury Laboratory; Reino Unido Fil: Purton, J. A.. CLRC Daresbury Laboratory; Reino Unido

We report molecular dynamics simulations of the production of radiation cascades in pyrochlores. We consider the apparently similar systems Gd2Ti2O7, Gd2Zr2O7 and Gd2Pb2O7, the first two of which have been put forward as potential materials for high-level radioactive waste storage. The effects of changing the mass of the 'primary knock-on' atom are also examined and we investigate whether the change in behaviour from Ti to Zr to Pb is largely due to the mass or the size difference between the elements. Problems associated with analysing the cascades and the damage created are discussed. There are clear differences between the three compounds. The simulations see no direct amorphization but rather a transition to the fluorite structure which is more pronounced for the Zr and Pb compounds than the Ti system. Underlying chemical trends are examined.

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.

Collaboratories provide an environment where researchers at distant locations work together at tackling important scientific and industrial problems. In this paper we outline the tools and principles used to form the eMinerals collaboratory, and discuss the experience, from within, of working towards establishing the eMinerals project team as a functioning virtual organisation. Much of the emphasis of this paper is on experience with the IT tools. We introduce a new application sharing tool.

The UK environmental e-science initiative supports the development and modification of simulation tools used to study radiation damage effects. We discuss the development and modification to the DL_POLY molecular dynamics (MD) code. Using the newly developed tools, we study the effects of radiation damage related to the safe encapsulation of highly radioactive materials, including nuclear waste. We address the possible differences between the radiation damage in the bulk and at the surface of a material, and perform MD simulations of energetic events in zircon structure. We find that in the case of readily amorphizable material, the formation of a stable alternative covalent network reduces the possible effect of the surface on the damaged structure.

DL_POLY_3 is a general-purpose molecular-dynamics simulation package embedding a highly efficient domain decomposition (DD) parallelization strategy. It was developed at Daresbury Laboratory under the auspices of the Engineering and Physical Sciences Research Council. Written to support academic research, it has a wide range of applications and will run on a wide range of computers; from single-processor workstations to multi-processor computers, with accent on the efficient use of multi-processor power. A new DD adaptation of the smoothed particle mesh Ewald method for calculating long-range forces in molecular simulations, incorporating a novel three-dimensional fast Fourier transform (the Daresbury Advanced Fourier Transform), makes it possible to simulate systems of the order of one million particles and beyond. DL_POLY_3 structure, functionality, performance and availability are described in this feature paper.

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.

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.

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.

The DL_ANALYSER Notation for Atomic Interactions, DANAI, is the notation syntax to describe interactions between molecules. This notation can annotate precisely the detailed atomistic interactions without having to resolve to diagrammatic illustrations, and yet can be interpreted easily by both human users and computational means. By making use of the DL_F Notation, a universal atom typing scheme for molecular simulations, DANAI contains the expression of atomic species in a natural chemical sense. It is implemented within DL_ANALYSER, a general analysis software program for DL_POLY molecular dynamics simulation software. By making references to the molecular dynamics simulations of pure ethanoic acid liquid, it is shown that DL_ANALYSER can identify and distinguish a variety of hydrogen bond and hydrophobic contact networks through the use of the DANAI expression. It was found that the carboxylic groups preferentially orientated in a “head-to-tail” conformation to form hydrogen bonds between the carbonyl oxygen and hydroxyl hydrogen, resulting in a series of linear structures that intertwined with pockets of methyl clusters.

Although the effects of the electronic excitations during high-energy radiation damage processes are not currently understood, it is shown that their role in the interaction of radiation with matter is important. We perform molecular dynamics simulations of high-energy collision cascades in bcc-tungsten using the coupled two-temperature molecular dynamics (2T-MD) model that incorporates both the effects of electronic stopping and electron-phonon interaction. We compare the combination of these effects on the induced damage with only the effect of electronic stopping, and conclude in several novel insights. In the 2T-MD model, the electron-phonon coupling results in less damage production in the molten region and in faster relaxation of the damage at short times. These two effects lead to significantly smaller amount of the final damage at longer times., Comment: 7 pages, 7 figures

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.

We have used a gravimetric technique to measure the rate of evaporation of water from water-in-dodecane microemulsions stabilised by AOT. Evaporation rates were measured under controlled gas flow conditions for a series of different microemulsion drop sizes and concentrations. Even for microemulsion samples where the equilibrium vapour pressure of water is similar to that of pure water, the evaporation rates are slower by more than an order of magnitude. The measured rates for the different microemulsion compositions are found to be approximately consistent with a model in which it is assumed that diffusion of the water microemulsion drops through the microemulsion to the surface is rate limiting. The subsequent processes of transfer of water across the liquid/vapour surface and the stagnant vapour space are not rate limiting.

Understanding and predicting a material's 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.

To remove problematic, high frequency degrees of freedom from a molecular model, modellers often use rigid body dynamics. The method also has additional benefits, for example it allows molecular charge distributions to be conveniently represented by multipolar moments. Rigid bodies are a well established feature within DL_POLY_ Classic formerly known as DL_POLY_2, which employs the replicated data parallelisation methodology. This paper briefly describes the RB formalism and outlines the strategy for its implementation in DL_POLY_4 formerly known as DL_POLY_3, which uses a very different form of parallelism, namely domain decomposition.

Zirconia is viewed as a material of exceptional resistance to amorphization by radiation damage, and consequently proposed as a candidate to immobilize nuclear waste and serve as an inert nuclear fuel matrix. Here, we perform molecular dynamics simulations of radiation damage in zirconia in the range of 0.1-0.5 MeV energies with full account of electronic energy losses. We find that the lack of amorphizability co-exists with a large number of point defects and their clusters. These, importantly, are largely isolated from each other and therefore represent a dilute damage that does not result in the loss of long-range structural coherence and amorphization. We document the nature of these defects in detail, including their sizes, distribution and morphology, and discuss practical implications of using zirconia in intense radiation environments., Comment: 8 pages, 6 figures

Domain decomposition of dissipative particle dynamics is complicated by the use of random pairwise forces as a component of a momentum-conserving thermostat. The conventional use of a pseudorandom number generator for each processor core leads to the need for an additional communication step to correctly assign random forces to particles in boundary halos. To circumvent this communication, the use of a three-seed pseudorandom number generator is proposed to allow multiple processor cores to evaluate the same forces. This kind of pseudorandom number generator will be applied to the general-purpose mesoscale modelling package DL_MESO to improve its parallel scalability for large processor core counts.

Electronic effects are believed to be important in high--energy radiation damage processes where high electronic temperature is expected, yet their effects are not currently understood. Here, we perform molecular dynamics simulations of high-energy collision cascades in $\alpha$-iron using the coupled two-temperature molecular dynamics (2T-MD) model that incorporates both effects of electronic stopping and electron-ion interaction. We subsequently compare it with the model employing the 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 the final damage at longer times, which we interpret to be the result of two competing effects: smaller amount of short-time damage and shorter time available for damage recovery., Comment: 8 pages, 6 figures

We use molecular-dynamics simulations to study processes related to resistance to amorphization by radiation damage. We simulate high-energy radiation events in ${\mathrm{SiO}}_{2}$, ${\mathrm{GeO}}_{2}$, ${\mathrm{TiO}}_{2}$, ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$, and $\mathrm{MgO}$, and find that simulation results match the experiments. We discuss the difference between the damage that the structures along this series can support. We find that for the same material, activation barriers for damage recovery can strongly depend on the degree of structural damage. We observe that the effect of resistance to amorphization is primarily governed by the relaxation processes at the time scales of several picoseconds. On this time scale, we observe two distinct relaxation processes, reversible elastic deformation around the radiation cascade and recovery of the in-cascade damage of high topological disorder. Finally, we discuss how resistance to amorphization is related to interatomic interactions and to the nature of the chemical bond.

A Monte Carlo exchange technique is used to study segregation in thin ceramic films with application to MgO/MnO. The approach is not restricted to the dilute limit. Surface concentrations as a function of temperature and film composition are determined directly from the simulations. For all compositions studied (Mn(chi)Mg(1-chi)O, 0or = chior = 1) the (001) surface is Mn(2+) rich; the occupancy of sites by Mn(2+) decreases rapidly with depth. The ratio of the number of Mn(2+) to Mg(2+) ions at the surface decreases as a function of temperature. The calculated enthalpies of segregation of Mn(2+) for the thin film are strongly dependent on the total Mn(2+) concentration at small Mn(2+) concentrations, with the enthalpy of segregation varying by a factor of two with surface coverage.

We combine simulation, theoretical and experimental results to study radiation damage effects in complex oxides under irradiation. In zircon, we study large density variations in the damaged structure, and show how damage percolation results in the enhanced transport extending to macroscopic lengthscale, and suggest that percolation threshold serve as a benchmark for acceptable waste load in a waste form. In perovskite, we identify common defects in the damaged structure, and relate their stability to chemical bonding. Finally, we formulate the criterion for resistance to amorphization by radiation damage: a material is amorphizable if it is able to form a covalent network.

Ceramic materials play a critical role in the safe long-term immobilisation of nuclear waste and fundamental understanding of both radiation damage and healing processes are required in order to determine the suitability of proposed storage materials, such as pyrochlores. Here, new interatomic potentials are derived for the pyrochlores Gd2Ti2O7 and Gd2Zr2O7. Their accuracy and robustness is demonstrated by calculating and comparing values for a selection of point defects with those calculated using a selection of other published potentials. Frenkel pair defect formation energies are substantially lowered in the presence of a small amount of local cation disorder. The activation energy for oxygen vacancy migration between adjacent O48f sites is calculated for Ti and Zr pyrochlores using an improved tangent nudged elastic band method. This energy is lower for the non-defective Ti than for the Zr pyrochlore by ∼0.1 eV, consistent with the majority of the potentials tested. The effect of local cation disorder on the VO48f → VO48f migration energy is minimal for Gd2Ti2O7, while in contrast the migration energy is lowered typically by ∼43% for Gd2Zr2O7. Since the healing mechanisms of these pyrochlores are likely to rely upon the availability of oxygen vacancies, the healing of a defective Zr pyrochlore is predicted to be faster than for the equivalent Ti pyrochlore.

We propose an explanation for the anomalous compressibility maximum in amorphous silica based on rigidity arguments. The model considers the fact that a network structure will be rigidly compressed in the high-pressure limit, and rigidly taut in the negative pressure limit, but flexible and hence softer at intermediate pressures. We validate the plausibility of this explanation by the analysis of molecular dynamics simulations. In fact this model is quite general, and will apply to any network solid, crystalline or amorphous; there are experimental indications that support this prediction. In contrast to other ideas concerning the compressibility maximum in amorphous silica, the model presented here does not invoke the existence of polyamorphic phase transitions in the glass phase.