John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus Schulten. GPU-accelerated computation and interactive display of molecular orbitals. In Wen-mei Hwu, editor, GPU Computing Gems, chapter 1, pp. 5-18. Morgan Kaufmann Publishers, 2011.

STON2011A In this chapter, we present several GPU algorithms for evaluating molecular orbitals on three-dimensional lattices, as is commonly used for molecular visualization. For each kernel, we describe necessary design trade-offs, applicability to various problem sizes, and performance on different generations of GPU hardware. Further, we demonstrate the appropriate and effective use of fast on-chip GPU memory subsystems for access to key data structures, show several GPU kernel optimization principles, and explore the application of advanced techniques such as dynamic kernel generation and just-in-time (JIT) kernel compilation techniques.


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