Implementation of symmetry-adapted perturbation theory based on density functional theory and using hybrid exchange-correlation kernels for dispersion terms.

Autor: Xie Y; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., Smith DGA; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., Sherrill CD; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.

Publikováno v: The Journal of chemical physics [J Chem Phys] 2022 Jul 14; Vol. 157 (2), pp. 024801.

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

Autor: Smith DGA; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Lolinco AT; Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA., Glick ZL; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Lee J; Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA., Alenaizan A; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Barnes TA; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Borca CH; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Di Remigio R; Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway., Dotson DL; Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA., Ehlert S; Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany., Heide AG; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Herbst MF; Applied and Computational Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062 Aachen, Germany., Hermann J; FU Berlin, Department of Mathematics and Computer Science, 14195 Berlin, Germany., Hicks CB; Department of Chemistry, Stanford University, Stanford, California 94305, USA., Horton JT; Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom., Hurtado AG; Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-5250, USA., Kraus P; School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth 6845, WA, Australia., Kruse H; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic., Lee SJR; California Institute of Technology, Pasadena, California 91125, USA., Misiewicz JP; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Naden LN; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Ramezanghorbani F; Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA., Scheurer M; Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany., Schriber JB; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Simmonett AC; Laboratory of Computational Biology, National Institutes of Health-National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA., Steinmetzer J; Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany., Wagner JR; Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA., Ward L; Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, USA., Welborn M; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Altarawy D; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Anwar J; Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA., Dreuw A; Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany., Kulik HJ; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA., Liu F; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA., Martínez TJ; Department of Chemistry, Stanford University, Stanford, California 94305, USA., Matthews DA; The Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, USA., Schaefer HF 3rd; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Šponer J; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic., Turney JM; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Wang LP; Department of Chemistry, University of California Davis, Davis, California 95616, USA., De Silva N; Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA., King RA; Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, USA., Stanton JF; Quantum Theory Project, The University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, USA., Gordon MS; Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA., Windus TL; Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA., Sherrill CD; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA., Burns LA; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.

Publikováno v: The Journal of chemical physics [J Chem Phys] 2021 Nov 28; Vol. 155 (20), pp. 204801.

Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.

Autor: Qiu Y; Chemistry Department, The University of California at Davis, Davis, California 95616, United States., Smith DGA; The Molecular Sciences Software Institute (MolSSI), Blacksburg, Virginia 24060, United States., Boothroyd S; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., Jang H; Chemistry Department, The University of California at Davis, Davis, California 95616, United States., Hahn DF; Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium., Wagner J; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States., Bannan CC; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States.; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States., Gokey T; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States., Lim VT; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States., Stern CD; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., Rizzi A; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.; Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, United States., Tjanaka B; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States., Tresadern G; Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium., Lucas X; F. Hoffmann-La Roche AG, Basel 4070, Switzerland., Shirts MR; Chemical & Biological Engineering Department, The University of Colorado at Boulder, Boulder, Colorado 80309, United States., Gilson MK; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States., Chodera JD; Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., Bayly CI; OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States., Mobley DL; Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States., Wang LP; Chemistry Department, The University of California at Davis, Davis, California 95616, United States.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2021 Oct 12; Vol. 17 (10), pp. 6262-6280. Date of Electronic Publication: 2021 Sep 22.

The CECAM electronic structure library and the modular software development paradigm.

Autor: Oliveira MJT; Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany., Papior N; DTU Computing Center, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark., Pouillon Y; Departamento CITIMAC, Universidad de Cantabria, Santander, Spain., Blum V; Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA., Artacho E; CIC Nanogune BRTA and DIPC, 20018 San Sebastián, Spain., Caliste D; Department of Physics, IRIG, Univ. Grenoble Alpes and CEA, F-38000 Grenoble, France., Corsetti F; Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom., de Gironcoli S; Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy., Elena AM; Scientific Computing Department, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom., García A; Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Bellaterra E-08193, Spain., García-Suárez VM; Departamento de Física, Universidad de Oviedo & CINN, 33007 Oviedo, Spain., Genovese L; Department of Physics, IRIG, Univ. Grenoble Alpes and CEA, F-38000 Grenoble, France., Huhn WP; Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA., Huhs G; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain., Kokott S; Fritz Haber Institut, 14195 Berlin, Germany., Küçükbenli E; Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy., Larsen AH; Simune Atomistics, 20018 San Sebastián, Spain., Lazzaro A; Department of Chemistry, University of Zürich, CH-8057 Zürich, Switzerland., Lebedeva IV; CIC Nanogune BRTA, 20018 San Sebastián, Spain., Li Y; Department of Mathematics, Duke University, Durham, North Carolina 27708-0320, USA., López-Durán D; CIC Nanogune BRTA, 20018 San Sebastián, Spain., López-Tarifa P; Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, 20018 San Sebastián, Spain., Lüders M; Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany., Marques MAL; Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany., Minar J; New Technologies Research Centre, University of West Bohemia, 301 00 Plzen, Czech Republic., Mohr S; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain., Mostofi AA; Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom., O'Cais A; Institute for Advanced Simulation (IAS), Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany., Payne MC; Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom., Ruh T; Institute of Materials Chemistry, TU Wien, 1060 Vienna, Austria., Smith DGA; Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA., Soler JM; Departamento e Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain., Strubbe DA; Department of Physics, University of California, Merced, California 95343, USA., Tancogne-Dejean N; Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany., Tildesley D; School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom., Torrent M; CEA, DAM, DIF, F-91297 Arpajon, France., Yu VW; Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA.

Publikováno v: The Journal of chemical physics [J Chem Phys] 2020 Jul 14; Vol. 153 (2), pp. 024117.

Psi4 1.4: Open-source software for high-throughput quantum chemistry.

Autor: Smith DGA; Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA., Burns LA; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., Simmonett AC; National Institutes of Health - National Heart, Lung and Blood Institute, Laboratory of Computational Biology, Bethesda, Maryland 20892, USA., Parrish RM; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., Schieber MC; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., Galvelis R; Acellera Labs, C/Doctor Trueta 183, 08005 Barcelona, Spain., Kraus P; School of Molecular and Life Sciences, Curtin University, Kent St., Bentley, Perth, Western Australia 6102, Australia., Kruse H; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic., Di Remigio R; Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway., Alenaizan A; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., James AM; Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA., Lehtola S; Department of Chemistry, University of Helsinki, P.O. Box 55 (A. I. Virtasen aukio 1), FI-00014 Helsinki, Finland., Misiewicz JP; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Scheurer M; Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany., Shaw RA; ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3000, Australia., Schriber JB; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., Xie Y; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., Glick ZL; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., Sirianni DA; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., O'Brien JS; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA., Waldrop JM; Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA., Kumar A; Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA., Hohenstein EG; SLAC National Accelerator Laboratory, Stanford PULSE Institute, Menlo Park, California 94025, USA., Pritchard BP; Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA., Brooks BR; National Institutes of Health - National Heart, Lung and Blood Institute, Laboratory of Computational Biology, Bethesda, Maryland 20892, USA., Schaefer HF 3rd; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Sokolov AY; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA., Patkowski K; Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA., DePrince AE 3rd; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, USA., Bozkaya U; Department of Chemistry, Hacettepe University, Ankara 06800, Turkey., King RA; Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, USA., Evangelista FA; Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA., Turney JM; Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA., Crawford TD; Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA., Sherrill CD; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.

Publikováno v: The Journal of chemical physics [J Chem Phys] 2020 May 14; Vol. 152 (18), pp. 184108.