CaltechAUTHORS
  A Caltech Library Service

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

Smith, Daniel G. A. and Lolinco, Annabelle T. and Glick, Zachary L. and Lee, Jiyoung and Alenaizan, Asem and Barnes, Taylor A. and Borca, Carlos H. and Di Remigio, Roberto and Dotson, David L. and Ehlert, Sebastian and Heide, Alexander G. and Herbst, Michael F. and Hermann, Jan and Hicks, Colton B. and Horton, Joshua T. and Hurtado, Adrian G. and Kraus, Peter and Kruse, Holger and Lee, Sebastian J. R. and Misiewicz, Jonathon P. and Naden, Levi N. and Ramezanghorbani, Farhad and Scheurer, Maximilian and Schriber, Jeffrey B. and Simmonett, Andrew C. and Steinmetzer, Johannes and Wagner, Jeffrey R. and Ward, Logan and Welborn, Matthew and Altarawy, Doaa and Anwar, Jamshed and Chodera, John D. and Dreuw, Andreas and Kulik, Heather J. and Liu, Fang and Martínez, Todd J. and Matthews, Devin A. and Schaefer, Henry F. and Šponer, Jiří and Turney, Justin M. and Wang, Lee-Ping and De Silva, Nuwan and King, Rollin A. and Stanton, John F. and Gordon, Mark S. and Windus, Theresa L. and Sherrill, C. David and Burns, Lori A. (2021) Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. Journal of Chemical Physics, 155 (20). Art. No. 204801. ISSN 0021-9606. PMCID PMC8614229. doi:10.1063/5.0059356. https://resolver.caltech.edu/CaltechAUTHORS:20211206-452781343

This is the latest version of this item.

Full text is not posted in this repository. Consult Related URLs below.

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20211206-452781343

Abstract

Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1063/5.0059356DOIArticle
https://github.com/MolSSI/QCElementalRelated ItemQCElemental
https://molssi.github.io/QCElementalRelated ItemQCElemental
https://github.com/MolSSI/QCEngineRelated ItemQCEngine
https://molssi.github.io/QCEngineRelated ItemQCEngine
https://github.com/qcdb/qcdbRelated ItemQCDB
https://qcdb.github.io/qcdbRelated ItemQCDB
http://docs.qcarchive.molssi.orgRelated ItemQCArchive INFRASTRUCTURE
https://github.com/qcdb/qcdb/blob/master/qcdb/tests/test_manuscript.pyRelated ItemQCDB test suite
ORCID:
AuthorORCID
Smith, Daniel G. A.0000-0001-8626-0900
Lolinco, Annabelle T.0000-0002-1686-778X
Glick, Zachary L.0000-0003-0900-2849
Lee, Jiyoung0000-0002-5216-2859
Alenaizan, Asem0000-0002-0871-664X
Barnes, Taylor A.0000-0001-9396-1094
Borca, Carlos H.0000-0003-0683-7613
Di Remigio, Roberto0000-0002-5452-9239
Dotson, David L.0000-0001-5879-2942
Ehlert, Sebastian0000-0001-7809-771X
Heide, Alexander G.0000-0002-9780-8123
Herbst, Michael F.0000-0003-0378-7921
Hermann, Jan0000-0002-2779-0749
Hicks, Colton B.0000-0003-2834-318X
Horton, Joshua T.0000-0001-8694-7200
Hurtado, Adrian G.0000-0002-2460-8059
Kraus, Peter0000-0002-4359-5003
Kruse, Holger0000-0002-0560-1513
Lee, Sebastian J. R.0000-0001-7006-9378
Misiewicz, Jonathon P.0000-0002-6425-9551
Naden, Levi N.0000-0002-3692-5027
Ramezanghorbani, Farhad0000-0002-7545-4416
Scheurer, Maximilian0000-0003-0592-3464
Schriber, Jeffrey B.0000-0001-6906-8191
Simmonett, Andrew C.0000-0002-5921-9272
Steinmetzer, Johannes0000-0003-2493-6893
Wagner, Jeffrey R.0000-0001-6448-0873
Ward, Logan0000-0002-1323-5939
Altarawy, Doaa0000-0002-7795-4422
Anwar, Jamshed0000-0003-1721-0330
Chodera, John D.0000-0003-0542-119X
Dreuw, Andreas0000-0002-5862-5113
Kulik, Heather J.0000-0001-9342-0191
Liu, Fang0000-0003-1322-4997
Martínez, Todd J.0000-0002-4798-8947
Matthews, Devin A.0000-0003-2795-5483
Schaefer, Henry F.0000-0003-0252-2083
Šponer, Jiří0000-0001-6558-6186
Turney, Justin M.0000-0003-3659-0711
Wang, Lee-Ping0000-0003-3072-9946
De Silva, Nuwan0000-0002-1443-5764
King, Rollin A.0000-0002-1173-4187
Stanton, John F.0000-0003-2345-9781
Gordon, Mark S.0000-0003-2371-1318
Windus, Theresa L.0000-0001-6065-3167
Sherrill, C. David0000-0002-5570-7666
Burns, Lori A.0000-0003-2852-5864
Additional Information:© 2021 Author(s). Published under an exclusive license by AIP Publishing. Submitted: 8 June 2021 • Accepted: 1 October 2021 • Published Online: 22 November 2021. Several of the co-authors have been supported in their development of QCDB and QCEngine and affiliated projects by the U.S. National Science Foundation through Grant Nos. ACI-1449723, CHE-1566192, ACI-1609842, ACI-1547580, ACI-1047772, ACI-1450217, ACI-2003931, CHE-1664325, and CHE-2134792, by the Office of Basic Energy Sciences Computational Chemical Sciences (CCS) Research Program (Grant Nos. AL-18-380-057 and DE-SC0018412), and by the Exascale Computing Project (Grant No. 17-SC-20-SC), a collaborative effort of the U.S. Department of Energy (DOE) Office of Science and the National Nuclear Security Administration. The Molecular Sciences Software Institute acknowledges the Advanced Research Computing at Virginia Tech for providing computational resources and technical support. D.G.A.S. also acknowledges the Open Force Field Consortium and Initiative for financial and scientific support. A.G.H. was supported, in part, by the National Science Foundation under Grant No. OAC-1931387 at Stony Brook University and made use of the high-performance SeaWulf computing system, which was made possible by the National Science Foundation (Grant No. 1531492). L.W. was additionally supported by DOE’s Advanced Scientific Research Office (ASCR) under Contract No. DE-AC02-06CH11357. H.J.K. and F.L. were partially supported by Grant No. DE-SC001896. L.-P.W. acknowledges Grant No. ACS-PRF 58158-DNI6 and National Institutes of Health (Grant No. R01GM132386). J.D.C. acknowledges support from NIH Grant No. P30 CA008748, NIH Grant No. R01 GM132386, and the Sloan Kettering Institute. R.D.R. acknowledges support from the European High-Performance Computing Joint Undertaking under Grant Agreement No. 951732 and partial support from the Research Council of Norway through its Centres of Excellence scheme (Project No. 262695) and through its Mobility Grant scheme (Project No. 261873). H. K. and J.Š. acknowledge funding from the Praemium academiae (CAS). M.F.H. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No 810367). T.J.M. and C.B.H. acknowledge support from the Office of Naval Research (Grant Nos. N00014-18-1-2659 and N00014-17-1-2875). This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1656518 for C.B.H. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. The contents of this paper are solely the responsibility of the authors and do not necessarily represent the views of the commercial partners of the Open Force Field Consortium. DATA AVAILABILITY. The data that support the findings of this study are available within the article. EXTERNAL MATERIAL. Software repositories and documentation are available for QCElemental at https://github.com/MolSSI/QCElemental/ and https://molssi.github.io/QCElemental/, for QCEngine at https://github.com/MolSSI/QCEngine/ and https://molssi.github.io/QCEngine/, for QCDB at https://github.com/qcdb/qcdb/ and https://qcdb.github.io/qcdb/, and for general QCArchive INFRASTRUCTURE at http://docs.qcarchive.molssi.org/. These programs remain in active development. Production computations are under way using many features of the software, and test suites are expected to pass. However, users are encouraged to contact the developers as they venture afield of the verified tests. Many snippets from this work, including an abbreviated diatomic fitting, are demonstrated in the test suite: https://github.com/qcdb/qcdb/blob/master/qcdb/tests/test_manuscript.py. DATA AVAILABILITY. The data that support the findings of this study are available within the article. Conflict of Interest. J.D.C. is a current member of the Scientific Advisory Board of OpenEye Scientific Software, Redesign Science, and Interline Therapeutics and has equity interests in Redesign Science and Interline Therapeutics. Conflict of Interest. J.D.C. is a current member of the Scientific Advisory Board of OpenEye Scientific Software, Redesign Science, and Interline Therapeutics and has equity interests in Redesign Science and Interline Therapeutics.
Funders:
Funding AgencyGrant Number
NSFACI-1449723
NSFCHE-1566192
NSFACI-1609842
NSFACI-1547580
NSFACI-1047772
NSFACI-1450217
NSFACI-2003931
NSFCHE-1664325
NSFCHE-2134792
Department of Energy (DOE)AL-18-380-057
Department of Energy (DOE)DE-SC0018412
Department of Energy (DOE)17-SC-20-SC
Open Force Field Consortium and InitiativeUNSPECIFIED
NSFOAC-1531492
NSFOAC-1931387
Department of Energy (DOE)DE-AC02-06CH11357
Department of Energy (DOE)DE-SC001896
American Chemical Society Petroleum Research Fund58158-DNI6
NIHR01GM132386
NIHP30CA008748
Memorial Sloan Kettering Cancer CenterUNSPECIFIED
European High-Performance Computing Joint Undertaking951732
Research Council of Norway262695
Research Council of Norway261873
Czech Academy of SciencesUNSPECIFIED
European Research Council (ERC)810367
Office of Naval Research (ONR)N00014-18-1-2659
Office of Naval Research (ONR)N00014-17-1-2875
NSF Graduate Research FellowshipDGE-1656518
Issue or Number:20
PubMed Central ID:PMC8614229
DOI:10.1063/5.0059356
Record Number:CaltechAUTHORS:20211206-452781343
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20211206-452781343
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:112227
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Dec 2021 10:42
Last Modified:11 Apr 2022 20:11

Available Versions of this Item

  • Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. (deposited 06 Dec 2021 10:42) [Currently Displayed]

Commentary/Response Threads

  • Smith, Daniel G. A. and Lolinco, Annabelle T. and Glick, Zachary L. and Lee, Jiyoung and Alenaizan, Asem and Barnes, Taylor A. and Borca, Carlos H. and Di Remigio, Roberto and Dotson, David L. and Ehlert, Sebastian and Heide, Alexander G. and Herbst, Michael F. and Hermann, Jan and Hicks, Colton B. and Horton, Joshua T. and Hurtado, Adrian G. and Kraus, Peter and Kruse, Holger and Lee, Sebastian J. R. and Misiewicz, Jonathon P. and Naden, Levi N. and Ramezanghorbani, Farhad and Scheurer, Maximilian and Schriber, Jeffrey B. and Simmonett, Andrew C. and Steinmetzer, Johannes and Wagner, Jeffrey R. and Ward, Logan and Welborn, Matthew and Altarawy, Doaa and Anwar, Jamshed and Chodera, John D. and Dreuw, Andreas and Kulik, Heather J. and Liu, Fang and Martínez, Todd J. and Matthews, Devin A. and Schaefer, Henry F. and Šponer, Jiří and Turney, Justin M. and Wang, Lee-Ping and De Silva, Nuwan and King, Rollin A. and Stanton, John F. and Gordon, Mark S. and Windus, Theresa L. and Sherrill, C. David and Burns, Lori A. Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. (deposited 06 Dec 2021 10:42) [Currently Displayed]

Repository Staff Only: item control page