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Book Chapter

Semiempirical Quantum Chemistry

MPS-Authors
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Wu,  Xin
Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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Koslowski,  Axel
Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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Thiel,  Walter
Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

Fulltext (public)

[555].pdf
(Publisher version), 481KB

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Citation

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.


Cite as: http://hdl.handle.net/11858/00-001M-0000-002A-3A9B-0
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.