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.
