Journal
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS
Volume 26, Issue 4, Pages 347-357Publisher
SAGE PUBLICATIONS LTD
DOI: 10.1177/1094342011431591
Keywords
code optimization; general purpose computation on GPUs; multicore programming; porous materials; screening; zeolites
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Funding
- Office of Advanced Scientific Computing Research, Office of Science, of the U.S. Department of Energy through the Scientific Discovery through Advanced Computing (SciDAC) program's Visualization and Analytics Center for Enabling Technologies (VACET) [DE-AC02-05CH11231]
- Applied Mathematical Science subprogram of the Office of Energy Research, U.S. Department of Energy [DE-AC03-76SF00098]
- Computational Mathematics Program of the National Science Foundation
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Developing computational tools that enable discovery of new materials for energy-related applications is a challenge. Crystalline porous materials are a promising class of materials that can be used for oil refinement, hydrogen or methane storage as well as carbon dioxide capture. Selecting optimal materials for these important applications requires analysis and screening of millions of potential candidates. Recently, we proposed an automatic approach based on the Fast Marching Method (FMM) for performing analysis of void space inside materials, a critical step preceding expensive molecular dynamics simulations. This breakthrough enables unsupervised, high-throughput characterization of large material databases. The algorithm has three steps: (1) calculation of the cost-grid which represents the structure and encodes the occupiable positions within the void space; (2) using FMM to segment out patches of the void space in the grid of (1), and find how they are connected to form either periodic channels or inaccessible pockets; and (3) generating blocking spheres that encapsulate the discovered inaccessible pockets and are used in proceeding molecular simulations. In this work, we expand upon our original approach through (A) replacement of the FMM-based approach with a more computationally efficient flood fill algorithm; and (B) parallelization of all steps in the algorithm, including a GPU implementation of the most computationally expensive step, the cost-grid generation. We report the acceleration achievable in each step and in the complete application, and discuss the implications for high-throughput material screening.
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