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  Semiempirical Quantum Chemistry

Wu, X., Koslowski, A., & Thiel, W. (2016). Semiempirical Quantum Chemistry. In R. C. Walker, & A. W. Goetz (Eds.), Electronic Structure Calculations on Graphics Processing Units: From Quantum Chemistry to Condensed Matter Physics (pp. 239-257). Chichester: John Wiley & Sons. doi:10.1002/9781118670712.ch11.

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[555].pdf (Publisher version), 481KB
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Copyright Date:
2016
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John Wiley & Sons, Ltd
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 Creators:
Wu, Xin1, Author              
Koslowski, Axel1, Author              
Thiel, Walter1, Author              
Affiliations:
1Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society, ou_1445590              

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Free keywords: CPU-GPU hybrid program; CUDA framework; graphics processing units; semiempirical quantum chemistry; symmetric multiprocessing
 Abstract: This chapter demonstrates how graphics processing units (GPUs) can be used to accelerate large-scale semiempirical quantum-chemical calculations on hybrid CPU-GPU platforms. It focuses on the CUDA framework, which allows developers to employ the C programming language, with CUDA-specific extensions, to use a CUDA-capable GPU as coprocessor of the CPU for computations. The chapter examines the computational bottlenecks by performing systematic calculations on a set of eight proteins with up to 3558 atoms and 8727 basis functions. It outlines how the hotspots identified in this manner are ported to a GPU, and how the remaining code is parallelized using CPU only using the symmetric multiprocessing (SMP) capabilities via OpenMP. Finally, as an illustrative application, the authors use the CPU-GPU hybrid program to optimize the geometries of three small proteins, each consisting predominantly of one type of secondary structure, namely α-helix, β-strand, and random coil, employing six different semiempirical methods.

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Language(s): eng - English
 Dates: 2016-02-192016
 Publication Status: Published in print
 Pages: 19
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1002/9781118670712.ch11
 Degree: -

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Title: Electronic Structure Calculations on Graphics Processing Units: From Quantum Chemistry to Condensed Matter Physics
Source Genre: Book
 Creator(s):
Walker, Ross C., Editor
Goetz, Andreas W., Editor
Affiliations:
-
Publ. Info: Chichester : John Wiley & Sons
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 239 - 257 Identifier: ISBN: 978-1-118-66178-9