GPU-accelerated computation and interactive display of molecular orbitals

This chapter presents several graphics processing unit (GPU) algorithms for evaluating molecular orbitals on three-dimensional lattices, as is commonly used for molecular visualization. The GPU kernels described here form the basis for the high-performance molecular orbital display algorithms in VMD, a popular molecular visualization and analysis tool. VMD (visual molecular dynamics) is a software system designed for displaying, animating, and analyzing large biomolecular systems. A motivation for using GPU acceleration in VMD is to make slow batch-mode jobs fast enough for interactive use, thereby drastically improving the productivity of scientific investigations. A molecular orbital (MO) represents a statistical state in which an electron can be found in a molecule, where the MO's spatial distribution is correlated with the associated electron's probability density. Visualization of MOs is an important task for understanding the chemistry of molecular systems. MOs appeal to the chemist's intuition, and inspection of the MOs aids in explaining chemical reactivities. The performance of each of the presented MO algorithms was evaluated on several hardware platforms. The test datasets were selected to be representative of the range of quantum chemistry simulation data that researchers often work with, and to exercise the limits of the algorithms, particularly in the case of the GPU. The development of a range-limited version of the molecular orbital algorithm that uses a distance cutoffto truncate the contributions of atoms that are either far away or that have very rapidly decaying exponential terms can change the molecular orbital computation from a quadratic time complexity algorithm into one with linear time complexity, enabling it to perform significantly faster for display of very large quantum chemistry simulations. © 2011