Literature DB >> 32534542

TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units.

Stefan Seritan1, Christoph Bannwarth1, B Scott Fales1, Edward G Hohenstein1, Sara I L Kokkila-Schumacher2, Nathan Luehr3, James W Snyder4, Chenchen Song5, Alexey V Titov6, Ivan S Ufimtsev7, Todd J Martínez1.   

Abstract

Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem's speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. This greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.

Entities:  

Year:  2020        PMID: 32534542      PMCID: PMC7928072          DOI: 10.1063/5.0007615

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  62 in total

1.  Acceleration of Electron Repulsion Integral Evaluation on Graphics Processing Units via Use of Recurrence Relations.

Authors:  Yipu Miao; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2013-01-04       Impact factor: 6.006

2.  Acceleration of the GAMESS-UK electronic structure package on graphical processing units.

Authors:  Karl A Wilkinson; Paul Sherwood; Martyn F Guest; Kevin J Naidoo
Journal:  J Comput Chem       Date:  2011-05-03       Impact factor: 3.376

3.  GFN2-xTB-An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions.

Authors:  Christoph Bannwarth; Sebastian Ehlert; Stefan Grimme
Journal:  J Chem Theory Comput       Date:  2019-02-11       Impact factor: 6.006

4.  The atomic simulation environment-a Python library for working with atoms.

Authors:  Ask Hjorth Larsen; Jens Jørgen Mortensen; Jakob Blomqvist; Ivano E Castelli; Rune Christensen; Marcin Dułak; Jesper Friis; Michael N Groves; Bjørk Hammer; Cory Hargus; Eric D Hermes; Paul C Jennings; Peter Bjerre Jensen; James Kermode; John R Kitchin; Esben Leonhard Kolsbjerg; Joseph Kubal; Kristen Kaasbjerg; Steen Lysgaard; Jón Bergmann Maronsson; Tristan Maxson; Thomas Olsen; Lars Pastewka; Andrew Peterson; Carsten Rostgaard; Jakob Schiøtz; Ole Schütt; Mikkel Strange; Kristian S Thygesen; Tejs Vegge; Lasse Vilhelmsen; Michael Walter; Zhenhua Zeng; Karsten W Jacobsen
Journal:  J Phys Condens Matter       Date:  2017-03-21       Impact factor: 2.333

5.  Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

Authors:  Daniel G A Smith; Lori A Burns; Dominic A Sirianni; Daniel R Nascimento; Ashutosh Kumar; Andrew M James; Jeffrey B Schriber; Tianyuan Zhang; Boyi Zhang; Adam S Abbott; Eric J Berquist; Marvin H Lechner; Leonardo A Cunha; Alexander G Heide; Jonathan M Waldrop; Tyler Y Takeshita; Asem Alenaizan; Daniel Neuhauser; Rollin A King; Andrew C Simmonett; Justin M Turney; Henry F Schaefer; Francesco A Evangelista; A Eugene DePrince; T Daniel Crawford; Konrad Patkowski; C David Sherrill
Journal:  J Chem Theory Comput       Date:  2018-06-11       Impact factor: 6.006

6.  "Balancing" the Block Davidson-Liu Algorithm.

Authors:  Robert M Parrish; Edward G Hohenstein; Todd J Martínez
Journal:  J Chem Theory Comput       Date:  2016-06-09       Impact factor: 6.006

7.  Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method.

Authors:  Daniel Hollas; Lukáš Šištík; Edward G Hohenstein; Todd J Martínez; Petr Slavíček
Journal:  J Chem Theory Comput       Date:  2017-12-22       Impact factor: 6.006

8.  Tensor Hypercontraction Second-Order Møller-Plesset Perturbation Theory: Grid Optimization and Reaction Energies.

Authors:  Sara I L Kokkila Schumacher; Edward G Hohenstein; Robert M Parrish; Lee-Ping Wang; Todd J Martínez
Journal:  J Chem Theory Comput       Date:  2015-07-14       Impact factor: 6.006

9.  Quartic scaling second-order approximate coupled cluster singles and doubles via tensor hypercontraction: THC-CC2.

Authors:  Edward G Hohenstein; Sara I L Kokkila; Robert M Parrish; Todd J Martínez
Journal:  J Chem Phys       Date:  2013-03-28       Impact factor: 3.488

10.  Discovering chemistry with an ab initio nanoreactor.

Authors:  Lee-Ping Wang; Alexey Titov; Robert McGibbon; Fang Liu; Vijay S Pande; Todd J Martínez
Journal:  Nat Chem       Date:  2014-11-02       Impact factor: 24.427

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  10 in total

Review 1.  Coupled- and Independent-Trajectory Approaches Based on the Exact Factorization Using the PyUNIxMD Package.

Authors:  Tae In Kim; Jong-Kwon Ha; Seung Kyu Min
Journal:  Top Curr Chem (Cham)       Date:  2022-01-27

2.  Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.

Authors:  Daniel G A Smith; Annabelle T Lolinco; Zachary L Glick; Jiyoung Lee; Asem Alenaizan; Taylor A Barnes; Carlos H Borca; Roberto Di Remigio; David L Dotson; Sebastian Ehlert; Alexander G Heide; Michael F Herbst; Jan Hermann; Colton B Hicks; Joshua T Horton; Adrian G Hurtado; Peter Kraus; Holger Kruse; Sebastian J R Lee; Jonathon P Misiewicz; Levi N Naden; Farhad Ramezanghorbani; Maximilian Scheurer; Jeffrey B Schriber; Andrew C Simmonett; Johannes Steinmetzer; Jeffrey R Wagner; Logan Ward; Matthew Welborn; Doaa Altarawy; Jamshed Anwar; John D Chodera; Andreas Dreuw; Heather J Kulik; Fang Liu; Todd J Martínez; Devin A Matthews; Henry F Schaefer; Jiří Šponer; Justin M Turney; Lee-Ping Wang; Nuwan De Silva; Rollin A King; John F Stanton; Mark S Gordon; Theresa L Windus; C David Sherrill; Lori A Burns
Journal:  J Chem Phys       Date:  2021-11-28       Impact factor: 3.488

3.  Excited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential.

Authors:  Simon Axelrod; Eugene Shakhnovich; Rafael Gómez-Bombarelli
Journal:  Nat Commun       Date:  2022-06-15       Impact factor: 17.694

4.  Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

Authors:  Qiang Cui; Tanmoy Pal; Luke Xie
Journal:  J Phys Chem B       Date:  2021-01-06       Impact factor: 2.991

5.  Internal conversion of the anionic GFP chromophore: in and out of the I-twisted S1/S0 conical intersection seam.

Authors:  Nanna H List; Chey M Jones; Todd J Martínez
Journal:  Chem Sci       Date:  2021-12-08       Impact factor: 9.825

6.  Calculating Photoabsorption Cross-Sections for Atmospheric Volatile Organic Compounds.

Authors:  Antonio Prlj; Emanuele Marsili; Lewis Hutton; Daniel Hollas; Darya Shchepanovska; David R Glowacki; Petr Slavíček; Basile F E Curchod
Journal:  ACS Earth Space Chem       Date:  2021-12-17       Impact factor: 3.475

7.  Ab Initio Insight into the Interaction of Metal-Decorated Fluorinated Carbon Fullerenes with Anti-COVID Drugs.

Authors:  Konstantin P Katin; Alexey I Kochaev; Savas Kaya; Fadoua El-Hajjaji; Mikhail M Maslov
Journal:  Int J Mol Sci       Date:  2022-02-21       Impact factor: 5.923

8.  Photochemistry of the pyruvate anion produces CO2, CO, CH3-, CH3, and a low energy electron.

Authors:  Connor J Clarke; Jemma A Gibbard; Lewis Hutton; Jan R R Verlet; Basile F E Curchod
Journal:  Nat Commun       Date:  2022-02-17       Impact factor: 14.919

9.  Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry.

Authors:  Jonathan R Church; Gil S Amoyal; Veniamin A Borin; Suliman Adam; Jógvan Magnus Haugaard Olsen; Igor Schapiro
Journal:  Chemistry       Date:  2022-04-05       Impact factor: 5.020

10.  Search for Novel Potent Inhibitors of the SARS-CoV-2 Papain-like Enzyme: A Computational Biochemistry Approach.

Authors:  Manuel I Osorio; Osvaldo Yáñez; Mauricio Gallardo; Matías Zuñiga-Bustos; Jorge Mulia-Rodríguez; Roberto López-Rendón; Olimpo García-Beltrán; Fernando González-Nilo; José M Pérez-Donoso
Journal:  Pharmaceuticals (Basel)       Date:  2022-08-11
  10 in total

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