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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 e Minerals collaboratory, and discuss the experience, from within, of working towards establishing the e Minerals 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. [ABSTRACT FROM AUTHOR]

This paper describes a prototype grid infrastructure, called the “ e Minerals minigrid”, for molecular simulation scientists. which is based on an integration of shared compute and data resources. We describe the key components, namely the use of Condor pools, Linux/Unix clusters with PBS and IBM's LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condor's DAGman tool for handling workflow, the Storage Resource Broker for handling data, and the CCLRC dataportal and associated tools for both archiving data with metadata and making data available to other workers. [ABSTRACT FROM AUTHOR]

We present the results of simulations, using density functional theory (DFT) with generalized gradient corrections (GGA), on the troilite (FeS), pyrrhotite (Fe1-xS) and MnP phases of FeS. The values obtained for the cell parameters and c / a ratio of troilite accurate to within 1% of those determined by experiment, a significant improvement on previous simulations. Energy–volume curves for FeS in the troilite and MnP structures indicate a pressure-induced transition at 4?GPa (experimentally observed at 3.4?GPa). Comparison of spin-polarised and non-spin-polarised simulations of the troilite structure demonstrate the significance of magnetostructural effects in determining the c / a ratio and shed light on the magnetic and volume collapse of FeS on its transition from the MnP to a monoclinic structure at 6.7?GPa. Simulations of different (001) surface terminations of troilite indicate that stable surfaces are characterised by triangles of iron atoms “capped” with a sulphur atom. [ABSTRACT FROM AUTHOR]

Computer modelling techniques were used to investigate the structures and stabilities of Li–K solid solutions of three different disilicate structures, employing a newly developed program based on symmetry arguments to identify identical configurations and hence eliminate unnecessary duplication of calculations. Even so, the large number of calculations needed to sample the complete set of configurations of a wide range of solid solutions necessitated the use of an extensive Condor pool of PC clusters, which afforded the necessary computing resources for this study. The results of our calculations show that in the wide range of Li–K solid solutions investigated, the mixed-cationic KLiSi2O5 material retains its original structure when the composition was varied, where six-membered rings of silica tetrahedra are linked to form continuous channels throughout the structure. The channel positions are found to be preferentially occupied by the potassium ions rather than by the smaller lithium ions. The original framework of the experimental K2Si2O5 structure, containing 14-membered rings of silica tetrahedra, similarly remains intact with the introduction of smaller lithium atoms into the bigger potassium lattice sites. However, the replacement of potassium ions for lithium ions in the Li2Si2O5 material causes significant distortions of the original structure, which loses its symmetry, although the ring structure remains. [ABSTRACT FROM AUTHOR]

This article describes the techniques and mechanisms that have been used to tackle workflow problems encountered in the e Minerals project. We examine how established tools and technologies can be brought together to specify and deploy a computational process , consisting of a set of jobs and tasks, on our production level mini-grid infrastructure, with respect to a specific problem—the distribution of calculations required to determine, in a systematic way, the mechanisms by which pollutant molecules such as DDT, dioxins and biphenyls, become bound to soil minerals. We also briefly discuss the use of data standards such as the Chemical Mark-up Language (CML) and web-service based grid standards as a means to facilitate workflow specification. [ABSTRACT FROM AUTHOR]