% Copyright 2022 NWChemEx-Project
%
% Licensed under the Apache License, Version 2.0 (the "License");
% you may not use this file except in compliance with the License.
% You may obtain a copy of the License at
%
% http://www.apache.org/licenses/LICENSE-2.0
%
% Unless required by applicable law or agreed to in writing, software
% distributed under the License is distributed on an "AS IS" BASIS,
% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
% See the License for the specific language governing permissions and
% limitations under the License.


% ------------------------------------------------------------------------------
% -- Scientific Research Software Organizations
% ------------------------------------------------------------------------------

@misc{bssw,
    title = {Better Scientific Software},
    howpublished = {\url{https://bssw.io/}},
    note = {Accessed: 12-30-2022}
}

@article{cca,
    title = {
        A Component Architecture for High-Performance Scientific Computing
    },
    author = {Bernholdt, D.~E. and Allan, B.~A. and Armstrong, R. and
              Bertrand, F. and Chiu, K. and Dahlgren, T.~L. and Damevski, K.
              and Elwasif, W.~R. and Epperly, T.~W. and Govindaraju, M.
              and Katz, D.~S. and Kohl, J.~A. and Krishnan, M. and Kumfert, G.
              and Larson, J.~W. and Lefantzi, S. and Lewis, M.~J. and
              Malony, A.~D. and McInnes, L.~C. and Nieplocha, J. and
              Norris, B. and Parker, S.~G. and Ray, J. and Shende, S. and
              Windus, T.~L. and Zhou, S.
    },
    doi = {10.1177/1094342006064488},
    journal = {
        International Journal of High-Performance Computing Applications
    },
    volume = {20},
    number = {2},
    pages = {163 -- 202},
    year = {2006}
}

@misc{derse,
    title = {German Society for Research Software Engineers},
    howpublished = {\url{https://de-rse.org/de/index.html}},
    note = {Accessed: 12-30-2022}
}

@misc{molssi,
    title = {The Molecular Sciences Software Institute},
    howpublished = {\url{https://molssi.org/}},
    note = {Accessed: 12-28-2022}
}

@misc{nrse,
    title = {The Nordic Research Software Engineers Association},
    howpublished = {\url{https://nordic-rse.org/}},
    note = {Accessed: 12-30-2022}
}

@misc{resa,
    title = {Research Software Alliance},
    howpublished = {\url{https://www.researchsoft.org/}},
    note = {Accessed: 12-30-2022}
}

@misc{rsaau,
    title = {The {RSE} Association of Australia and New Zealand},
    howpublished = {\url{https://rse-aunz.github.io/}},
    note = {Accessed: 12-30-2022}
}

@misc{rse,
    title = {The Society of Research Software Engineering},
    howpublished = {\url{https://society-rse.org}},
    note = {Accessed: 12-30-2022}
}

@misc{se4science,
    title = {Software Engineering for Science},
    howpublished = {\url{https://se4science.org/}},
    note = {Accessed: 12-30-2022}
}

@misc{ssi,
    title = {The Software Sustainability Institute},
    howpublished= {\url{https://www.software.ac.uk/}},
    note = {Accessed: 12-30-2022}
}

@misc{usrse,
    title = {
        The United States Research Software Engineer Association
    },
    howpublished = {\url{https://us-rse.org/}},
    note = {Accessed: 12-30-2022}
}

@misc{wssspe,
    title = {
        Working Towards Sustainable Software for Science: Practice and
        Experiencies
    },
    howpublished = {\url{https://wssspe.researchcomputing.org.uk/}},
    note = {Accessed: 12-30-2022}
}

% ------------------------------------------------------------------------------
% -- C++ Inversion of Control Frameworks
% ------------------------------------------------------------------------------

@misc{autowiring,
    title = {Autowiring: A {C}++ inversion of control framework},
    howpublished = {\url{https://github.com/leapmotion/autowiring}},
    note = {Accessed: 12-28-2022}
}

@misc{ioc,
    title = {{ioc}: Inversion of control container {c}++11},
    howpublished = {\url{https://github.com/unixdev0/ioc}},
    note = {Accessed: 12-28-2022}
}

@misc{ioc_cpp,
    title = {
        {ioc-cpp}: Inversion of control/dependency injection container for C++03
    },
    howpublished = {\url{https://github.com/mrts/ioc-cpp}},
    note = {Accessed: 12-28-2022}
}

@misc{pococapsule,
    title = {
        PocoCapsule: An {IoC} and {DSM} framework for {C}/{C}++ applications
    },
    howpublished = {\url{https://code.google.com/archive/p/pococapsule}},
    note = {Accessed: 12-28-2022}
}

% ------------------------------------------------------------------------------
% -- Other QC Packages
% ------------------------------------------------------------------------------

@article{ase,
    doi = {10.1088/1361-648X/aa680e},
    year = {2017},
    volume = {29},
    number = {27},
    pages = {273002},
    author = {
        Larsen, A.~H. and Mortensen, J.~J. and Blomqvist, J.
        and Castelli, I.~E. and Christensen, R. and Dułak, M. and Friis, J.
        and Groves, M.~N. and Hammer, B. and Hargus, C. and Hermes, E.~D.
        and Jennings, P.~C. and Jensen, P.~B. and Kermode, J.
        and Kitchin, J.~R. and Kolsbjerg, E.~L. and Kubal, J.
        and Kaasbjerg, K. and Lysgaard, S. and Maronsson, J.~B. and Maxson, T.
        and Olsen, T. and Pastewka, L. and Peterson, A. and Rostgaard, C.
        and Schiøtz, J. and Schütt, O. and Strange, M. and Thygesen, K.~S.
        and Vegge, T. and Vilhelmsen, L. and Walter, M. and Zeng, Z.
        and Jacobsen, K.~W.
    },
    title = {
        The atomic simulation environment—a Python library for working with
        atoms
    },
    journal = {Journal of Physics: Condensed Matter},
}

@misc{mdi,
    title = {{MolSSI} {D}river {I}nterface ({MDI}) {L}ibrary},
    howpublished = {\url{https://github.com/MolSSI-MDI/MDI_Library}},
    note = {Accessed: 12-30-2022}
}

@inbook{mpqc,
    author = {Janssen, C.~L. and Seidl, E.~T. and Colvin, M.~E.},
    title = {Object-Oriented Implementation of Parallel Ab Initio Programs},
    booktitle = {Parallel Computing in Computational Chemistry},
    publisher = {American Chemical Society},
    chapter = {4},
    pages = {47-61},
    doi = {10.1021/bk-1995-0592.ch004},
    year = {1995}
}

@misc{mpqc4,
    title = {
        The Massively Parallel Quantum Chemistry Program ({MPQC}),
        Version 4.0.0-beta.1
    },
    author = {
        Peng, C. and Lewis, C. and Wang, X. and Clement, M. and
        Pavosevic, F. and Zhang, J. and Rishi, V. and Teke, N. and Pierce, K.
        and Calvin, J. and Kenny, J. and Seidl, E. and Janssen, C. and
        Valeev, E.
    },
    howpublished = {\url{http://github.com/ValeevGroup/mpqc}},
    note = {Accessed: 12-29-2022}
}

@article{psi3,
    author = {
        Crawford, T.~D. and Sherrill, C.~D. and Valeev, E.~F.
        and Fermann, J.~T. and King, R.~A. and Leininger, M.~L. and
        Brown, S.~T. and Janssen, C.~L. and Seidl, E.~T. and Kenny, J.~P.
        and Allen, W.~D.
    },
    title = {{PSI3}: An open-source Ab Initio electronic structure package},
    journal = {Journal of Computational Chemistry},
    volume = {28},
    number = {9},
    pages = {1610-1616},
    doi = {https://doi.org/10.1002/jcc.20573},
    year = {2007}
}

@article{psi4,
    author = {
        Turney, J.~M. and Simmonett, A.~C. and Parrish, R.~M.
        and Hohenstein, E.~G. and Evangelista, F.~A. and Fermann, J.~T.
        and Mintz, B.~J. and Burns, L.~A. and Wilke, J.~J. and Abrams, M.~L.
        and Russ, N.~J. and Leininger, M.~L. and Janssen, C.~L.
        and Seidl, E.~T. and Allen, W.~D. and Schaefer, H.~F. and King, R.~A.
        and Valeev, E.~F. and Sherrill, C.~D. and Crawford, T.~D.
    },
    title = {Psi4: an open-source ab initio electronic structure program},
    journal = {{WIRE}s Computational Molecular Science},
    volume = {2},
    number = {4},
    pages = {556-565},
    doi = {https://doi.org/10.1002/wcms.93},
    year = {2012}
}

@Article{psi4_11,
    author  = {
        Parrish, R.~M. and Burns, L.~A. and Smith, D.~G.~A. and Simmonett, A.~C.
        and DePrince, A.~E.~III and Hohenstein, E.~G. and Bozkaya, U. and
        Sokolov, A.~Y. and Di Remigio, R. and Richard, R.~M. and Gonthier, J.~F.
        and James, A.~M. and McAlexander, H.~R. and Kumar, A. and Saitow, M.
        and Wang, X. and Pritchard, B.~P. and Verma, P. and Schaefer, H.~F.~III
        and Patkowski, K. and King, R.~A. and Valeev, E.~F.
        and Evangelista, F.~A. and Turney, J.~M. and Crawford, T.~D.
        and Sherrill, C.~D.
    },
    journal = {Journal of Chemical Theory and Computation},
    title   = {
        Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing
        Automation, Advanced Libraries, and Interoperability
    },
    year    = {2017},
    number  = {7},
    pages   = {3185-3197},
    volume  = {13},
    doi     = {10.1021/acs.jctc.7b00174},
}

@article{psi4_14,
    author = {
        Smith, D.~G.~A. and Burns, L.~A. and Simmonett, A.~C. and
        Parrish, R.~M. and Schieber, M.~C. and Galvelis, R. and Kraus, P. and
        Kruse, H. and Di Remigio, R. and Alenaizan, A. and James, A.~M. and
        Lehtola, S. and Misiewicz, J.~P.  and Scheurer, M. and Shaw, R.~A.
        and Schriber, J.~B. and Xie, Y. and Glick, Z.~L. and Sirianni, D.~A.
        and O’Brien, J.~S. and Waldrop, J.~M. and Kumar, A. and
        Hohenstein, E.~G. and Pritchard, B.~P. and Brooks, B.~R. and
        Schaefer, H.~F. and Sokolov, A.~Y. and Patkowski, K. and
        DePrince, A.~E.  and Bozkaya, U. and King, R.~A. and Evangelista, F.~A.
        and Turney, J.~M. and Crawford, T.~D. and Sherrill, C.~D.
    },
    title = {
        {PSI}4 1.4: Open-source software for high-throughput quantum chemistry
    },
    journal = {The Journal of Chemical Physics},
    volume = {152},
    number = {18},
    pages = {184108},
    year = {2020},
    doi = {10.1063/5.0006002},
}

@article{pyadf,
    author = {
        Jacob, C.~R. and Beyhan, S.~M. and Bulo, R.~E. and Gomes, A.~S.~P.
        and Götz, A.~W. and Kiewisch, K. and Sikkema, J. and Visscher, L.
    },
    title = {{PyADF} — A scripting framework for multiscale quantum chemistry},
    journal = {Journal of Computational Chemistry},
    volume = {32},
    number = {10},
    pages = {2328-2338},
    doi = {https://doi.org/10.1002/jcc.21810},
    year = {2011}
}

@article{pymatgen,
    title = {
        Python Materials Genomics (pymatgen): A robust, open-source python
        library for materials analysis
    },
    journal = {Computational Materials Science},
    volume = {68},
    pages = {314-319},
    year = {2013},
    doi = {https://doi.org/10.1016/j.commatsci.2012.10.028},
    author = {
        Ong, S.~P. and Richards, W.~D. and Jain, A. and Hautier, G. and
        Kocher, M. and Cholia, S. and Gunter, D. and Chevrier, V.~L. and
        Persson, K.~A. and Ceder, G.
    }
}

@article{pyscf,
    author = {
        Sun, Q. and Berkelbach, T.~C. and Blunt, N.~S. and Booth, G.~H.
        and Guo, S. and Li, Z. and Liu, J. and McClain, J.~D.
        and Sayfutyarova, E.~R. and Sharma, S. and Wouters, S.
        and Chan, G.~K.-L.
    },
    title = {{PySCF}: the Python-based simulations of chemistry framework},
    journal = {{WIRE}s Computational Molecular Science},
    volume = {8},
    number = {1},
    pages = {e1340},
    doi = {https://doi.org/10.1002/wcms.1340},
    year = {2018}
}

@article{qcarchive,
    author = {
        Smith, D.~G.~A. and Altarawy, D. and Burns, L.~A. and Welborn, M.
        and Naden, L.~N. and Ward, L. and Ellis, S. and Pritchard, B.~P.
        and Crawford, T.~D.
    },
    title = {
        The {MolSSI} {QCArchive} project: An open-source platform to compute,
        organize, and share quantum chemistry data
    },
    journal = {WIREs Computational Molecular Science},
    volume = {11},
    number = {2},
    pages = {e1491},
    doi = {https://doi.org/10.1002/wcms.1491},
    year = {2021}
}

@article{qchasm,
    author = {
        Ingman, V.~M. and Schaefer, A.~J. and Andreola, L.~R. and
        Wheeler, S.~E.
    },
    title = {{QChASM}: Quantum chemistry automation and structure manipulation},
    journal = {{WIRE}s Computational Molecular Science},
    volume = {11},
    number = {4},
    pages = {e1510},
    doi = {https://doi.org/10.1002/wcms.1510},
    year = {2021}
}

% ------------------------------------------------------------------------------
% -- Scientific Software Background
% ------------------------------------------------------------------------------

@article{krylov18,
    author = {
        Krylov, A. and Windus,T.~L. and Barnes, T.  and Marin-Rimoldi,E.
        and Nash, J.~A.  and Pritchard, B.  and Smith, D.~G.~A.  and
        Altarawy,D.  and Saxe,P.  and Clementi,C. and Crawford, T.~D. and
        Harrison, R.~J.  and Jha,S.  and Pande,V.~S. and Head-Gordon,T.
    },
    title = {
        Perspective: Computational chemistry software and its advancement as
        illustrated through three grand challenge cases for molecular science
    },
    journal = {The Journal of Chemical Physics},
    volume = {149},
    number = {18},
    pages = {180901},
    year = {2018},
    doi = {10.1063/1.5052551}
}
