Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

Ufimtsev, Ivan S.; Martı́nez, Todd J.

doi:10.1021/ct800526s

Cited by 439 publications

(474 citation statements)

References 37 publications

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“…Our test cases comprise typical biomolecules (water clusters, 29 polypeptides, 30 and triglyceride 31 ), a conducting system (buckminsterfullerene 32 ), and a weakly interacting system (helium cluster 33 ). Geometries are described in the references given here.…”

Section: Numerical Resultsmentioning

confidence: 99%

Resolutions of the Coulomb Operator: VII. Evaluation of Long-Range Coulomb and Exchange Matrices

Limpanuparb

Milthorpe

Rendell

et al. 2013

J. Chem. Theory Comput.

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Use of the resolution of Ewald operator method for computing long-range Coulomb and exchange interactions is presented. We show that the accuracy of this method can be controlled by a single parameter in a manner similar to that used by conventional algorithms that compute two-electron integrals. Significant performance advantages over conventional algorithms are observed, particularly for high quality basis sets and globular systems. The approach is directly applicable to hybrid density functional theory.

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Section: Numerical Resultsmentioning

confidence: 99%

Resolutions of the Coulomb Operator: VII. Evaluation of Long-Range Coulomb and Exchange Matrices

Limpanuparb

Milthorpe

Rendell

et al. 2013

J. Chem. Theory Comput.

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“…The flowchart in Figure 2 summarizes our COSMO-SCF implementation. Following our gas phase SCF implementation, 19,48 the COSMO related integrals needed for c and ΔF S are calculated in a direct SCF manner using GPUs. Here each GPU thread calculates integrals corresponding to one fixed primitive pair.…”

Section: Acceleration Strategies 4a Integral Calculation On Gpusmentioning

confidence: 99%

Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models

Liu

Luehr

Kulik

et al. 2015

J. Chem. Theory Comput.

128

138

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Abstract:The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale biomolecular systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. We have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, we extend the use of GPUs to accelerate electronic structure calculations including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. We further propose two strategies to improve the solution of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. We benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, our method evaluates the C-PCM related integrals and their derivatives more than 10X faster than a conventional CPUbased implementation. Our improvements to the linear solver provide a further 3X acceleration. The overall calculations including C-PCM solvation require typically 20-40% more effort than their gas phase counterparts for moderate basis set and molecule surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore description of solvation with this model should be routine. We also discuss applications to the study of the conformational landscape of an amyloid fibril.Liu, Luehr, Kulik, and Martínez -GPU-based PCM Calculations -Page 2 IntroductionModeling the influence of solvent in quantum chemical calculations is of great importance to understanding solvation effects on electronic properties, nuclear distributions, spectroscopic properties, acidity/basicity, and mechanisms of enzymatic and chemical reactions.

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“…Despite these exciting developments in basic theory, fast numerical algorithms, and novel hardware utilization, [1][2][3][4][5] it is not yet possible to routinely simulate such large systems using readily available computer resources. However, emerging nano-scale simulation challenges involving, for example, large biomolecular aggregates or nanotechnology devices are increasing the demand for firstprinciples methods that can deliver this performance.…”

Section: Introductionmentioning

confidence: 99%

Electronic structure calculations in arbitrary electrostatic environments

Watson

Rappoport

Lee

et al. 2012

The Journal of Chemical Physics

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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 mediumsized 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.

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Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

Cited by 439 publications

References 37 publications

Resolutions of the Coulomb Operator: VII. Evaluation of Long-Range Coulomb and Exchange Matrices

Resolutions of the Coulomb Operator: VII. Evaluation of Long-Range Coulomb and Exchange Matrices

Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models

Electronic structure calculations in arbitrary electrostatic environments

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