Chapter 1. GPU-Accelerated Computation and Interactive Display of Molecular Orbitals
John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort and Klaus Schulten
In this chapter, we present several graphics processing unit (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. We then 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 ...
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