<scp>Psi4</scp> 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability

Journal of Chemical Theory and Computation - Tập 13 Số 7 - Trang 3185-3197 - 2017
Robert M. Parrish1, Lori A. Burns1, Daniel G. A. Smith1, Andrew C. Simmonett2, A. Eugene DePrince3, Edward G. Hohenstein4, Uğur Bozkaya5, Alexander Yu. Sokolov6, Roberto Di Remigio7, Ryan M. Richard1, Jérôme F. Gonthier1, Andrew M. James8, Harley R. McAlexander8, Ashutosh Kumar8, Masaaki Saitow9, Xiao Wang8, Benjamin P. Pritchard1, Prakash Verma10, Henry F. Schaefer11, Konrad Patkowski12, Rollin A. King13, Edward F. Valeev8, Francesco A. Evangelista10, Justin M. Turney11, T. Daniel Crawford8, C. David Sherrill1
1Center 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, United States
2National Institutes of Health - National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
3Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
4Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
5Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
6Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
7Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
8Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
9Department of Chemistry and Research Center for Smart Molecules, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
10Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
11Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
12Department of Chemistry and Biochemistry,#R#Auburn University,#R#Auburn, Alabama 36849, United States
13Department of Chemistry, Bethel University , St. Paul, Minnesota 55112, United States.

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Tài liệu tham khảo

10.1021/cen-09250-ad05

Valeev, E. F.; Fermann, J. T.Libint: A high-perforrmance library for computing Gaussian integrals in quantum mechanics; 2017.https://github.com/evaleev/libint(accessed May 8, 2017).

Kaliman, I. A.; Slipchenko, L. V.libefp;http://libefp.github.io(accessed May 8, 2017) .

10.1002/jcc.23375

Wouters, S.CheMPS2: A Spin-Adapted Implementation of DMRG for ab initio Quantum Chemistry.http://github.com/SebWouters/CheMPS2(accessed May 8, 2017) .

10.1016/j.cpc.2014.01.019

10.1140/epjd/e2014-50500-1

Pritchard, B. P.; Chow, E.Simint.https://github.com/simint-chem.

10.1002/jcc.24483

Marques, M. A. L.; Oliveira, M.; Burnus, T.; Madsen, G.; Andrade, X.; Strubbve, D.; Lehtola, S.Libxc, a library of exchange-correlation functionals for density-functional theory, version 3.0.0; 2016.http://octopus-code.org/wiki/Libxc(accessed May 8, 2017) .

10.1016/j.cpc.2012.05.007

10.1063/1.1515314

10.1063/1.1818681

Di Remigio, R.; Frediani, L.; Mozgawa, K.PCMSolver, an Application Programming Interface for the Polarizable Continuum Model electrostatic problem, v1.1.7.http://pcmsolver.readthedocs.io/(accessed May 8, 2017) .

Di Remigio, R.; Crawford, T. D.; Frediani, L.PCMSolver, An Application Programming Interface for the Polarizable Continuum Model. Proceedings of the SC15 Workshop on Producing High Performance and Sustainable Software for Molecular Simulation; 2016.

DFTD3, a FORTRAN program implementing the DFT-D3 method, version 3.2 Rev. 0; Grimme Research Group: Mulliken Center for Theoretical Chemistry,Universität Bonn, 2016.http://www.thch.uni-bonn.de/tc/index.php?section/downloads&subsection/DFT-D3(accessed May 8, 2017).

Kállay, M.; Rolik, Z.; Csontos, J.; Ladjánski, I.; Szegedy, L.; Ladóczki, B.; Samu, G.; Petrov, K.; Farkas, M.; Nagy, P.; Mester, D.; Hégely, B.MRCC, A Quantum Chemical Program Suite. See:http://www.mrcc.hu.

10.1063/1.4819401

Schmidt, J. R.; Polik, W. F.WebMO 17;WebMO, LLC:Holland, MI, 2016.http://www.webmo.net(accessed May 8, 2017).

Schaftenaar, G.;MOLDEN, version 5.7.http://www.cmbi.ru.nl/molden/(accessed May 8, 2017) .

10.1023/A:1008193805436

VMD: Visual Molecular Dynamics; Theoretical and Computational Biophysics Group;University of Illinois at Urbana-Champaign, 2017.http://www.ks.uiuc.edu/Research/vmd/(accessed May 8, 2017).

10.1016/0263-7855(96)00018-5

GitHub. https://github.com/(accessed May 8, 2017) .

Wang, L.P.; Song, C.GeomeTRIC, a geometry optimization code that includes the TRIC coordinate system; 2017.http://github.com/leeping/geomeTRIC(accessed May 8, 2017).

10.1063/1.4952956

10.1063/1.449486

JANPA, A Freeware Program Package for Performing Natual Population Analysis, version 1.04; 2016.http://janpa.sourceforge.net/(accessed May 8, 2017).

10.1016/j.comptc.2014.10.002

McGibbon, R. T.RESP2, Restrained Electrostatic Potential Fitting forPsi4; 2016.http://github.com/rmcgibbo/resp2(accessed May 8, 2017).

10.1021/j100142a004

10.1021/acs.jctc.6b00049

10.1063/1.1679012

10.1002/qua.560120813

10.1063/1.438728

10.1063/1.465054

10.1016/0009-2614(93)87156-W

10.1016/0009-2614(93)89151-7

10.1063/1.468148

10.1007/s002140050249

10.1039/b204199p

10.1002/qua.560120408

10.1016/0009-2614(86)80099-9

10.1063/1.1578621

10.1063/1.2736701

10.1063/1.3116784

10.1002/wcms.93

10.1002/jcc.20573

Bolton, E. E.; Wang, Y.; Thiessen, P. A.; Bryant, S. H.InAnnual Reports in Computational Chemistry;Wheeler, R. A.; Spellmeyer, D. C., Eds.Elsevier:Amsterdam, 2005; Vol.4; pp217–241.

10.1063/1.1672392

Werner, H.J.; Knowles, P. J.; Manby, F. R.; Schütz, M.; Celani, P.; Knizia, G.; Korona, T.; Lindh, R.; Mitrushenkov, A.; Rauhut, G.; Adler, T. B.; Amos, R. D.; Bernhardsson, A.; Berning, A.; Cooper, D. L.; Deegan, M. J. O.; Dobbyn, A. J.; Eckert, F.; Goll, E.; Hampel, C.; Hesselmann, A.; Hetzer, G.; Hrenar, T.; Jansen, G.; Köppl, C.; Liu, Y.; Lloyd, A. W.; Mata, R. A.; May, A. J.; Tarroni, R.; Thorsteinsson, T.; Wang, M.; Wolf, A.MOLPRO, version 2010.1; 2010.http://www.molpro.net(accessed May 8, 2017).

10.1063/1.456153

10.1063/1.462569

10.1016/S0009-2614(99)00179-7

10.1016/S0009-2614(98)00111-0

10.1080/00268977000101561

10.1016/S0009-2614(97)00689-1

BOOST C++ Libraries.http://www.boost.org(accessed May 8, 2017) .

Jakob, W.; Rhinelander, J.; Moldovan, D.pybind11, Seamless operability between C++11 and Python; 2017.https://github.com/pybind/pybind11(accessed May 8, 2017).

Smith, D. G. A.; Sirianni, D. A.; Burns, L. A.; Patkowski, K.; Sherrill, C. D.psi4/psi4numpy: beta release; 2017.https://doi.org/10.5281/zenodo.293020.

10.1109/MCSE.2011.37

10.1109/MCSE.2007.53

CMake, a cross-platform family of tools designed to buid, test and package software.http://cmake.org(accessed May 8, 2017) .

Anaconda; Continuum IO, 2017.https://www.continuum.io/(accessed May 8, 2017).

Any system libraries not linked statically fall within the purview ofhttps://www.python.org/dev/peps/pep-0513/#external-shared-libraries.

10.1021/acs.jpclett.6b00780

10.1002/jcc.23317

10.1063/1.4927476

10.1016/0301-0104(81)85090-2

10.1021/cr00031a013

10.1021/cr9904009

Mennucci B., 2008, Continuum Solvation Models in Chemical Physics: From Theory to Applications

10.1023/A:1019133611148

10.1063/1.1507579

10.1063/1.1643727

10.1063/1.4812680

10.1063/1.4943782

10.1021/jp002747h

10.1021/jp107557p

10.1002/jcc.21018

10.1063/1.478295

10.1063/1.1449459

10.1063/1.4885815

10.1063/1.4959817

Stone, A. J.GDMA, A Program to Perform Distributed Multipole Analysis, version 2.2.11; 2015.http://www-stone.ch.cam.ac.uk/programs.html(accessed May 8, 2017).

DePrince, A. E.v2rdm-CASSCF, A variational 2-RDM-driven CASSCF plugin toPsi4; 2016.http://github.com/edeprince3/v2rdm_casscf(accessed May 8, 2017) .

10.1021/acs.jctc.6b00190

Turney, J. M.AMBIT, A C++ Library for the Implementation of Tensor Product Calculations through a Clean, Concise User Interaface; 2017.http://github.com/jturney/ambit(accessed May 8, 2017) .

Stanton, J. F.; Gauss, J.; Harding, M. E.; Szalay, P. G.cfour, Coupled-Cluster Techniques for Computational Chemistry. With contributions from Auer, A. A.; Bartlett, R. J.; Benedikt, U.; Berger, C.; Bernholdt, D. E.; Bomble, Y. J.; Cheng, L.; Christiansen, O.; Heckert, M.; Heun, O.; Huber, C.; Jagau, T.C.; Jonsson, D.; Jusélius, J.; Klein, K.; Lauderdale, W. J.; Lipparini, F.; Matthews, D. A.; Metzroth, T.; Mück, L. A.; O’Neill, D. P.; Price, D. R.; Prochnow, E.; Puzzarini, C.; Ruud, K.; Schiffmann, F.; Schwalbach, W.; Simmons, C.; Stopkowicz, S.; Tajti, A.; Vázquez, J.; Wang, F.; Watts, J. D.; and the integral packages MOLECULE (Almlöf, J. and Taylor, P. R.), PROPS (Taylor, P. R.), ABACUS (Helgaker, T.; Aa. Jensen, H. J.; Jørgensen, P.; and Olsen, J.), and ECP routines by Mitin, A. V. and van Wüllen, C.http://www.cfour.de(accessed May 8, 2017) .

Forte, a suite of quantum chemistry methods for strongly correlated electrons; Evangelista Research Group;Emory University,Atlanta, GA, 2016.https://github.com/evangelistalab/forte(accessed May 8, 2017) .

10.1063/1.4890660

10.1021/acs.jctc.5b00134

10.1063/1.4951684

10.1063/1.4947218

10.1063/1.4948308

10.1021/acs.jctc.6b00639

TravisCI.https://travis-ci.org/(accessed May 8, 2017) .

CodeCov.https://codecov.io/(accessed May 8, 2017) .

10.1016/0021-9991(78)90092-X

10.1002/jcc.540040206

10.1063/1.450106

10.1016/0009-2614(73)80060-0

10.1021/cr00031a008

10.1002/wcms.86

10.1002/wcms.84

10.1021/ar3001124

10.1063/1.3426316

10.1063/1.3656681

10.1063/1.3451077

10.1063/1.3479400

10.1063/1.4826520

10.1063/1.4889855

10.1021/ct500724p

10.1039/C5CP07281F

10.1063/1.4927575

10.1021/ct300544e

10.1063/1.4963385

10.1063/1.4758455

10.1063/1.2968556

10.1063/1.443164

10.1016/0009-2614(89)87399-3

10.1007/s002140050250

10.1135/cccc20050837

10.1063/1.3276630

10.1039/B600027D

10.1021/ct300780u

10.1021/ct400250u

10.1063/1.4869686

10.1080/00268976.2013.874599

10.1002/jcc.21318

10.1080/00268976.2014.952696

10.1135/cccc2011048

10.1063/1.4820484

10.1063/1.4902226

10.1002/cphc.200800718

10.1063/1.4903765

10.1063/1.4948318

10.1063/1.4896235

10.1063/1.452468

10.1063/1.2718952

10.1021/ct600292h

10.1021/ct9003299

10.1016/0009-2614(87)85122-9

10.1063/1.477023

10.1016/S0009-2614(01)00709-6

10.1063/1.463762

10.1016/0009-2614(94)00442-0

10.1063/1.3631129

10.1063/1.3665134

10.1063/1.4803662

10.1063/1.4816628

10.1063/1.475961

10.1002/(SICI)1097-461X(1998)70:4/5<601::AID-QUA6>3.3.CO;2-J

10.1063/1.4720382

10.1063/1.4820877

10.1021/ct500231c

10.1021/acs.jctc.5b01128

10.1039/C6CP00164E

10.1063/1.4921956

10.1063/1.2953696

10.1063/1.2387955

10.1063/1.3503657

10.1063/1.4773580

10.1063/1.4833138

10.1063/1.4892946

10.1021/ct5002895

10.1021/acs.jctc.5b00346

10.1063/1.4739423

10.1021/acs.jctc.6b00589

10.1016/j.chemphys.2006.07.015

10.1016/j.cplett.2011.12.063

10.1007/s002140050387

10.1021/j100247a015

10.1016/0009-2614(95)00646-L

10.1002/chem.201502363

10.1063/1.473860

10.1063/1.1413512

10.1016/S0301-0104(97)00240-1

10.1063/1.2137315

10.1080/00268970600662481

10.1063/1.2710258

10.1063/1.3159445

10.1063/1.2436882

10.1063/1.3603454

10.1063/1.3624397

10.1103/PhysRev.78.29

10.1021/jp401323d

10.1021/acs.jctc.5b00817

Psi4Manual.http://psicode.org/psi4manual/master/index.html(accessed May 8, 2017) .

Sphinx, Python Documentation Generator.http://www.sphinx-doc.org/en/1.5.2/index.html(accessed May 8, 2017) .

Psi4YouTube videos.https://www.youtube.com/user/psitutorials(accessed May 8, 2017) .

Psi4User Forum.http://forum.psicode.org(accessed May 8, 2017) .

Psi4Website.http://www.psicode.org(accessed May 8, 2017) .

Psi4Education.http://www.psicode.org/labs.php(accessed May 8, 2017) .

Fortenberry, R. C.; McDonald, A. R.; Shepherd, T. D.; Kennedy, M.; Sherrill, C. D.InThe Promise of Chemical Education: Addressing our Students’ Needs;Daus, K.; Rigsby, R., Eds.American Chemical Society:Washington, D.C., 2015; Vol.1193; pp85–98.