Person:

Vogt, Leslie Ann

Two new tools for the acceleration of computational chemistry codes using graphical processing units (GPUs) are presented. First, we propose a general black-box approach for the efficient GPU acceleration of matrix−matrix multiplications where the matrix size is too large for the whole computation to be held in the GPU’s onboard memory. Second, we show how to improve the accuracy of matrix multiplications when using only single-precision GPU devices by proposing a heterogeneous computing model, whereby single- and double-precision operations are evaluated in a mixed fashion on the GPU and central processing unit, respectively. The utility of the library is illustrated for quantum chemistry with application to the acceleration of resolution-of-the-identity second-order Møller−Plesset perturbation theory calculations for molecules, which we were previously unable to treat. In particular, for the 168-atom valinomycin molecule in a cc-pVDZ basis set, we observed speedups of 13.8, 7.8, and 10.1 times for single-, double- and mixed-precision general matrix multiply (SGEMM, DGEMM, and MGEMM), respectively. The corresponding errors in the correlation energy were reduced from −10.0 to −1.2 kcal mol(^{-1}) for SGEMM and MGEMM, respectively, while higher accuracy can be easily achieved with a different choice of cutoff parameter.

The modification of a general purpose code for quantum mechanical calculations of molecular properties (Q-Chem) to use a graphical processing unit (GPU) is reported. A 4.3x speedup of the resolution-of-the-identity second-order Møller−Plesset perturbation theory (RI-MP2) execution time is observed in single point energy calculations of linear alkanes. The code modification is accomplished using the compute unified basic linear algebra subprograms (CUBLAS) library for an NVIDIA Quadro FX 5600 graphics card. Furthermore, speedups of other matrix algebra based electronic structure calculations are anticipated as a result of using a similar approach.

Samples from Thai manuscripts dated to the 18th to 20th century were analyzed by Raman spectroscopy and Fourier-transform infrared spectroscopy (FTIR) to determine the pigments used. This suggested a change in palette from the 18th to 20th century, with use of imported pigments in the later manuscripts. In the 18th century, the main green used was an organic copper salt, which was replaced by emerald green and mixtures of Prussian blue with gamboge, chrome yellow and zinc yellow (zinc potassium chromate). Chrome yellow was used in addition to gamboge in one later 19th century manuscript. Similarly, indigo in the 18th century manuscripts was replaced by Prussian blue and then synthetic ultramarine in the 19th century manuscripts. Lead white was the main white pigment in all but one manuscript, which contained huntite, a magnesium calcium carbonate. Huntite also occurred in mixtures with other pigments in two other manuscripts. In all the works studied, red lead, vermilion and red earth were used for red, orange and pink shades and red earth in brown areas. The organic copper salt used in the 18th century gave good FTIR spectra but could not initially be matched with any published compound. X-ray diffraction (XRD) suggested this was a copper citrate phase, and examination of the literature showed that the FTIR spectra matched those published for a hydrated copper citrate. Raman spectra were obtained from this organic copper salt, which showed close agreement with those obtained from synthetic copper citrate. Copper citrate has not been identified previously as an artist’s material, although its use has been postulated on the basis of historical texts. Minor copper formate and/or copper chloride were also identified by XRD and scanning electron microscopy (SEM) in some green samples containing copper citrate.