Rp Bruin

Structural and magnetic phase transitions in simple oxides using hybrid functionals

We present the structural as well as elastic properties of the alkaline earth oxides and FeO, calculated using hybrid exchange functionals within DFT. We show that by empirically fitting the amount of Fock-exchange in the hybrid functionals, we can accurately reproduce the pressure-induced phase transitions for MgO, CaO, SrO and BaO. For FeO the hybrid functionals predict an insulator↔metal transition at ca. 150 GPa, associated with an i-B8↔B8 structural phase transition. The structural phase transition is accompanied by a spin transition from a high- to low-spin electron configuration on the Fe2+ ions. Hence, FeO undergoes a magnetic phase transition from an anti-ferromagnetic to non-magnetic structure. We also find that as the ionicity of the polymorphs increases a higher fraction of Fock-exchange is required to reproduce the structural volumes reported from experiments.

Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated compute and data grid

This paper describes a prototype grid infrastructure, called the “eMinerals 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 IBMs LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condors 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.

Development of a FEP database for the geological storage of carbon dioxide

Publisher Summary This chapter illustrates that systems analysis techniques are applied to the geological storage of CO2, and the use of features, events, and processes (FEPs) to describe the storage concept is instrumental to this technique. FEPs are features, events, and processes that are relevant to the behavior of CO2 in the system being assessed. A generic FEP database for the geological storage of CO2 has been developed with the chosen FEPs included for their relevance to the long-term post-operational safety and performance of the storage system. The database is described, and its potential use as a tool in support of the development of system-level assessment models is discussed. The development of the database was funded by the European commission as part of the IEA Weyburn CO2 monitoring project.

The origin of the compressibility anomaly in amorphous silica: a molecular dynamics study

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.

Lessons in scientific data interoperability: XML and the eMinerals project.

A collaborative environmental eScience project produces a broad range of data, notable as much for its diversity, in source and format, as its quantity. We find that extensible markup language (XML) and associated technologies are invaluable in managing this deluge of data. We describe FoX, a toolkit for allowing Fortran codes to read and write XML, thus allowing existing scientific tools to be easily re-used in an XML-centric workflow.

Developing an End-to-End Scientific Workflow:

Grid-based simulation usually involves sequences of activities such as resource discovery, job submission, file transfer, analysis and simulation, and data harvesting. We can use service-oriented workflow to automate task coordination without direct human control, where each task and legacy scientific code can be presented as a Web service and thereby simplifying workflow development and maintenance. Because each service is described using Web Service Description Language, workflow manager works only with the WSDL interface rather than specific implementations.

Integrating computing, data and collaboration grids: the RMCS tool

We describe RMCS as one of the first tools for grid computing that integrates data and metadata management into a single job submission system. The system is easy to use, with client tools that are easy to install. Although the RMCS system was developed as a prototype, it is now in production use and a number of scientific studies have been completed using it.

eScience for molecular-scale simulations and the eMinerals project

We review the work carried out within the eMinerals 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.

Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within the eMinerals escience project

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.

The eMinerals collaboratory: tools and experience

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.