Roberto Olivares-Amaya

Accelerating Resolution-of-the-Identity Second-Order Møller−Plesset Quantum Chemistry Calculations with Graphical Processing Units†

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.

Lead candidates for high-performance organic photovoltaics from high-throughput quantum chemistry - the Harvard Clean Energy Project

The virtual high-throughput screening framework of the Harvard Clean Energy Project allows for the computational assessment of candidate structures for organic electronic materials – in particular photovoltaics – at an unprecedented scale. We report the most promising compounds that have emerged after studying 2.3 million molecular motifs by means of 150 million density functional theory calculations. Our top candidates are analyzed with respect to their structural makeup in order to identify important building blocks and extract design rules for efficient materials. An online database of the results is made available to the community.

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library

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 GPUs 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.

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units

Graphical processing units are now being used with dramatic effect to accelerate quantum chemistry applications. The authors give a brief introduction to electronic structure methods and describe their efforts to accelerate a correlated quantum chemistry code. They propose and analyze two new tools for accelerating matrix-multiplications where single-precision accuracy is insuffcient.

Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

Time-Dependent Density Functional Theory of Open Quantum Systems in the Linear-Response Regime

Time-dependent density functional theory (TDDFT) has recently been extended to describe many-body open quantum systems evolving under nonunitary dynamics according to a quantum master equation. In the master equation approach, electronic excitation spectra are broadened and shifted due to relaxation and dephasing of the electronic degrees of freedom by the surrounding environment. In this paper, we develop a formulation of TDDFT linear-response theory (LR-TDDFT) for many-body electronic systems evolving under a master equation, yielding broadened excitation spectra. This is done by mapping an interacting open quantum system onto a noninteracting open Kohn-Sham system yielding the correct nonequilibrium density evolution. A pseudoeigenvalue equation analogous to the Casida equations of the usual LR-TDDFT is derived for the Redfield master equation, yielding complex energies and Lamb shifts. As a simple demonstration, we calculate the spectrum of a C(2 +) atom including natural linewidths, by treating the electromagnetic field vacuum as a photon bath. The performance of an adiabatic exchange-correlation kernel is analyzed and a first-order frequency-dependent correction to the bare Kohn-Sham linewidth based on the Görling-Levy perturbation theory is calculated.

Electronic structure calculations in arbitrary electrostatic environments

Modeling of electronic structure of molecules in electrostatic environments is of considerable relevance for surface-enhanced spectroscopy and molecular electronics. We have developed and implemented a novel approach to the molecular electronic structure in arbitrary electrostatic environments that is compatible with standard quantum chemical methods and can be applied to medium-sized and large molecules. The scheme denoted CheESE (chemistry in electrostatic environments) is based on the description of molecular electronic structure subject to a boundary condition on the system/environment interface. Thus, it is particularly suited to study molecules on metallic surfaces. The proposed model is capable of describing both electrostatic effects near nanostructured metallic surfaces and image-charge effects. We present an implementation of the CheESE model as a library module and show example applications to neutral and negatively charged molecules.

Creating a GUI for Zori, a Quantum Monte Carlo Program

Rappture is a new GUI development kit that enables developers to build I/O interfaces for specific applications. In this article,, the authors describe the Rappture toolkits use in generating a GUI for the Zori computer code.

Topological and Electronic Structure of Heterocyclic Compounds Adsorbed on Hydrotreating Catalysts

We studied the electronic structure of the adsorption of S- and N-containing aromatic compounds present in crude oils on MoS2 and WS2 clusters by means of all-electron DFT methods. The aim of this work is to understand results related to the hydrotreating catalyst poisoning by quinoline. We studied the adsorption of the organic compounds by flat (π) and perpendicular (σ) adsorption on each cluster catalyst. The calculated adsorption energies indicated that π-adsorption was more favorable over σ-adsorption. In the σ mode, quinoline presented the largest adsorption energy, which led to understand the poisoning of the catalysts. We performed electron localization function (ELF) studies on the molecules adsorbed on a perpendicular orientation. We showed methyl-substituted compounds had a weaker S-{Mo,W} bond due to steric hindrance. Furthermore, atoms-in-molecules (AIM) calculations at the critical points (i.e. {S,N}-{Mo,W} interfaces) revealed a correlation between electron density and Laplacian of the electron density at this region and the adsorption energy. Ellipticity (ε) studies revealed structural information of binding at these sites, as well as the competition between S- and N-containing compounds. Similarly, ε showed that methyl-containing compounds had a very distinct character than non-substituted ones, thus revealing the importance of steric effects. Analytic tools such as ELF and AIM provide correlations between the experimental observations and properties. We find these studies can be further used to understand other catalytic phenomena.Graphical Abstract.