Probing the structure of complex solids using a distributed computing approach—Applications in zeolite science

We demonstrate the viability of distributed computing techniques employing idle desktop computers in investigating complex structural problems in solids. Through the use of a combined Monte Carlo and energy minimisation method, we show how a large parameter space can be effectively scanned. By controlling the generation and running of different configurations through a database engine, we are able to not only analyse the data “on the fly” but also direct the running of jobs and the algorithms for generating further structures.As an exemplar case, we probe the distribution of Al and extra-framework cations in the structure of the zeolite Mordenite. We compare our computed unit cells with experiment and find that whilst there is excellent correlation between computed and experimentally derived unit cell volumes, cation positioning and short-range Al ordering (i.e. near neighbour environment), there remains some discrepancy in the distribution of Al throughout the framework. We also show that stability-structure correlations only become apparent once a sufficiently large sample is used.     

E-science infrastructures for molecular modeling and parametrization

E-science infrastructures are becoming the essential tools for computational scientific research. In this paper, we describe two e-science infrastructures: Science and Engineering Applications Grid (SEAGrid) and molecular modeling and parametrization (ParamChem). The SEAGrid is a virtual organization with a diverse set of hardware and software resources and provides services to access such resources in a routine and transparent manner. These essential services include allocations of computational resources, client-side application interfaces, computational job and data management tools, and consulting activities. ParamChem is another e-science project dedicated for molecular force-field parametrization based on both ab-initio and molecular mechanics calculations on high performance computers (HPCs) driven by scientific workflow middleware services. Both the projects share a similar three-tier computational infrastructure that consists of a front-end client, a middleware web services layer, and a remote HPC computational layer. The client is a Java Swing desktop application with components for pre- and post-data processing, communications with middleware server and local data management. The middleware service is based on Axis2 web service and MySQL relational database, which provides functionalities for user authentication and session control, HPC resource information collections, discovery and matching, job information logging and notification. It can also be integrated with scientific workflow to manage computations on HPC resources. The grid credentials for accessing HPCs are delegated through MyProxy infrastructure. Currently SEAGrid has integrated several popular application software suites such as Gaussian for quantum chemistry, NAMD for molecular dynamics and engineering software such as Abacus for mechanical engineering. ParamChem has integrated CGenFF (CHARMM General Force-Field) for molecular force-field parametrization of drug-like molecules. Long-term storage of user data is handled by tertiary data archival mechanisms. SEAGrid science gateway serves more than 500 users while more than 1000 users use ParamChem services such as atom typing and initial force-field parameter guess at present.