NWChem: Past, present, and future

Aprà, Edoardo; Bylaska, Eric J.; Jong, Wibe A. de; Govind, Niranjan; Kowalski, Karol; Straatsma, Tjerk P.; Valiev, Marat; Dam, Hubertus J. J. van; Alexeev, Yuri; Anchell, Jonathan S.; Anisimov, Victor M.; Aquino, Fredy W.; Atta‐Fynn, Raymond; Autschbach, Jochen; Bauman, Nicholas P.; Becca, Jeffrey C.; Bernholdt, David E.; Bhaskaran‐Nair, Kiran; Bogatko, Stuart; Borowski, Piotr; Boschen, Jeffery S.; Brabec, Jiří; Bruner, Adam; Cauët, Émilie; Chen, Y.; Chuev, Gennady N.; Cramer, Christopher J.; Daily, Jeff; Deegan, Miles J.O.; Dunning, Thom H.; Dupuis, Michel; Dyall, Kenneth G.; Fann, George I.; Fischer, Sean A.; Fonari, Alexandr; Früchtl, Herbert; Gagliardi, Laura; Garza, Jorge; Gawande, Nitin; Ghosh, Soumen; Glaesemann, Kurt R.; Götz, Andreas W.; Hammond, Jeff R.; Helms, Volkhard; Hermes, Eric D.; Hirao, Kimihiko; Hirata, So; Jacquelin, Mathias; Jensen, Lin Lin; Johnson, Benny G.; Jónsson, Hannes; Kendall, Ricky A.; Klemm, Michael; Kobayashi, Rika; Konkov, Vladimir; Krishnamoorthy, Sriram; Krishnan, M.; Lin, Zhiyang; Lins, Roberto D.; Littlefield, Richard J.; Logsdail, Andrew J.; Lopata, Kenneth A.; Ma, Wei; Marenich, Aleksandr V.; Campo, Jorge M. del; Mejı́a-Rodrı́guez, Daniel; Moore, Johanna; Mullin, Jonathan; Nakajima, Takahito; Nascimento, Daniel R.; Nichols, Jeffrey A.; Nichols, Patrick; Nieplocha, Jarek; Otero-de-la-Roza, Alberto; Palmer, Bruce; Panyala, Ajay; Pirojsirikul, Teerapong; Peng, Bo; Peverati, Roberto; Pittner, Jiřı́; Pollack, L.; Richard, Ryan M.; Sadayappan, P.; Schatz, George C.; Shelton, W. A.; Silverstein, D.; Smith, Dayle M. A.; Soares, Thereza A.; Song, Duo; Swart, Marcel; Taylor, Hamish; Thomas, Greg S.; Tipparaju, Vinod; Truhlar, Donald G.; Tsemekhman, Kiril; Voorhis, Troy Van; Vázquez-Mayagoitia, Álvaro; Verma, Prakash; Villa, Oreste; Vishnu, Abhinav; Vogiatzis, Konstantinos D.; Wang, D.; Weare, John H.; Williamson, Mark J.; Windus, Theresa L.; Woliński, Krzysztof; Wong, Adrian T.; Wu, Qin; Yang, Chao; Yu, Qi; Zacharias, Martin; Zhang, Zhiyong; Zhao, Yanliang; Harrison, Robert J.

doi:10.1063/5.0004997

Cited by 554 publications

(305 citation statements)

References 366 publications

(413 reference statements)

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“…In this section, we examine various performance characteristics of these phases as implemented in the open-source NWChemEx software package (Kowalski et al, 2020). In addition, we compare the performance and scaling of this implementation to that of an analogous scalable CPU implementation in the open-source NWChem software package (Aprà et al, 2020). We have chosen to examine the performance of the purposed method as applied to 4 molecules: Taxol, Valinomycin, Olestra, and Ubiquitin; and 2 basis sets: 6-31G(d) (Ditchfield et al, 1971;Hehre et al, 1972;Hariharan and Pople, 1973;Francl et al, 1982;Gordon et al, 1982) and cc-pVDZ (Dunning, 1989;Woon and Dunning, 1993), to provide a performance characterization for systems with a wide range of size, spacial extent, and basis dimension.…”

Section: Resultsmentioning

confidence: 99%

“…There are many possible choices for both the atomic partitioning scheme (Becke, 1988;Stratmann et al, 1996;Laqua et al, 2018;Aprà et al, 2020) and base quadratures around each atomic center (Becke, 1988;Murray et al, 1993;Treutler and Ahlrichs, 1995;Mura and Knowles, 1996;Gill and Chien, 2003;Aprà et al, 2020). In this work, we will use the following:…”

Section: Numerical Integration Of Molecular Integrandsmentioning

confidence: 99%

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On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters

et al. 2020

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The predominance of Kohn–Sham density functional theory (KS-DFT) for the theoretical treatment of large experimentally relevant systems in molecular chemistry and materials science relies primarily on the existence of efficient software implementations which are capable of leveraging the latest advances in modern high-performance computing (HPC). With recent trends in HPC leading toward increasing reliance on heterogeneous accelerator-based architectures such as graphics processing units (GPU), existing code bases must embrace these architectural advances to maintain the high levels of performance that have come to be expected for these methods. In this work, we purpose a three-level parallelism scheme for the distributed numerical integration of the exchange-correlation (XC) potential in the Gaussian basis set discretization of the Kohn–Sham equations on large computing clusters consisting of multiple GPUs per compute node. In addition, we purpose and demonstrate the efficacy of the use of batched kernels, including batched level-3 BLAS operations, in achieving high levels of performance on the GPU. We demonstrate the performance and scalability of the implementation of the purposed method in the NWChemEx software package by comparing to the existing scalable CPU XC integration in NWChem.

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Section: Resultsmentioning

confidence: 99%

Section: Numerical Integration Of Molecular Integrandsmentioning

confidence: 99%

On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters

et al. 2020

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“…The output from the codes is also returned in a standardized form, which simplifies databases and any software to analyze the outputs of a QC program. Two examples: (a) a Hessian computed with Psi4 30,31 and NWChem 32 can be analyzed with the same software and (b) the geomeTRIC optimization package 33,34 uses QCE ngine as an interface to different QC packages so as to be agnostic the backend program.…”

Section: Infrastructurementioning

confidence: 99%

The MolSSI QCArchive project: An open‐source platform to compute, organize, and share quantum chemistry data

Smith

Altarawy

Burns

et al. 2020

WIREs Comput Mol Sci

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The Molecular Sciences Software Institute's (MolSSI) Quantum Chemistry Archive (QCArchive) project is an umbrella name that covers both a central server hosted by MolSSI for community data and the Python‐based software infrastructure that powers automated computation and storage of quantum chemistry (QC) results. The MolSSI‐hosted central server provides the computational molecular sciences community a location to freely access tens of millions of QC computations for machine learning, methodology assessment, force‐field fitting, and more through a Python interface. Facile, user‐friendly mining of the centrally archived quantum chemical data also can be achieved through web applications found at https://qcarchive.molssi.org. The software infrastructure can be used as a standalone platform to compute, structure, and distribute hundreds of millions of QC computations for individuals or groups of researchers at any scale. The QCArchive Infrastructure is open‐source (BSD‐3C), code repositories can be found at https://github.com/MolSSI, and releases can be downloaded via PyPI and Conda. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry Data Science > Computer Algorithms and Programming

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“…The AMBER force field was used in MM. The NWChem software package 51 was applied to scan fragments of potential energy surface. To model the system in the triplet electronic state, the unrestricted DFT approach was used.…”

Section: Qm/mm Simulationsmentioning

confidence: 99%

Stalling chromophore maturation of the fluorescent protein Venus reveals the molecular basis of the final oxidation step

Auhim

Grigorenko

Harris

et al. 2020

Preprint

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Fluorescent proteins (FPs) have revolutionised the life sciences but the mechanism of chromophore maturation is still not fully understood. Incorporation of a photo-responsive non-canonical amino acid within the chromophore stalls maturation of Venus, a yellow FP, at an intermediate stage; the crystal structure reveals the presence of O2 located above a dehydrated enolate imidazolone (I) ring, close to the strictly conserved Gly67 that occupies a twisted conformation. His148 adopts an open conformation, potentially allowing O2 access to the chromophore. Absorption spectroscopy supported by QM/MM simulations suggest that the first oxidation step involves formation of a hydroperoxyl intermediate in conjunction with dehydrogenation of the methylene bridge. A fully conjugated mature chromophore is formed through release of H2O2 upon irradiation of this intermediate, both in vitro and in vivo. The possibility of interrupting and photochemically restarting chromophore maturation, and the mechanistic insights opens up new approaches for engineering optically controlled fluorescent proteins.

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NWChem: Past, present, and future

Cited by 554 publications

References 366 publications

On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters

On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters

The MolSSI QCArchive project: An open‐source platform to compute, organize, and share quantum chemistry data

Stalling chromophore maturation of the fluorescent protein Venus reveals the molecular basis of the final oxidation step

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