Add paper references for packages using s-dftd3 (#66)

dftd3 · Jun 9, 2024 · 8e04a4e · 8e04a4e
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diff --git a/doc/_static/references.bib b/doc/_static/references.bib
@@ -112,3 +112,121 @@ @article{schroeder2015
   url={https://pubs.acs.org/doi/10.1021/acs.jctc.5b00400},
   publisher={ACS Publications}
 }
+
+@software{hubler2020,
+  author       = {Conrad Hübler},
+  title        = {conradhuebler/curcuma: Curcuma},
+  month        = dec,
+  year         = 2020,
+  publisher    = {Zenodo},
+  version      = {0.0.29},
+  doi          = {10.5281/zenodo.4302723},
+  url          = {https://doi.org/10.5281/zenodo.4302723}
+}
+
+@article{motamarri2020,
+title = {DFT-FE – A massively parallel adaptive finite-element code for large-scale density functional theory calculations},
+journal = {Computer Physics Communications},
+volume = {246},
+pages = {106853},
+year = {2020},
+issn = {0010-4655},
+doi = {https://doi.org/10.1016/j.cpc.2019.07.016},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465519302309},
+author = {Phani Motamarri and Sambit Das and Shiva Rudraraju and Krishnendu Ghosh and Denis Davydov and Vikram Gavini},
+keywords = {Electronic structure, Real-space, Spectral finite-elements, Ionic forces, Mixed-precision arithmetic, Pseudopotential, All-electron, Ab-initio molecular dynamics},
+}
+
+
+@article{garcia2020,
+    author = {García, Alberto and Papior, Nick and Akhtar, Arsalan and Artacho, Emilio and Blum, Volker and Bosoni, Emanuele and Brandimarte, Pedro and Brandbyge, Mads and Cerdá, J. I. and Corsetti, Fabiano and Cuadrado, Ramón and Dikan, Vladimir and Ferrer, Jaime and Gale, Julian and García-Fernández, Pablo and García-Suárez, V. M. and García, Sandra and Huhs, Georg and Illera, Sergio and Korytár, Richard and Koval, Peter and Lebedeva, Irina and Lin, Lin and López-Tarifa, Pablo and Mayo, Sara G. and Mohr, Stephan and Ordejón, Pablo and Postnikov, Andrei and Pouillon, Yann and Pruneda, Miguel and Robles, Roberto and Sánchez-Portal, Daniel and Soler, Jose M. and Ullah, Rafi and Yu, Victor Wen-zhe and Junquera, Javier},
+    title = "{Siesta: Recent developments and applications}",
+    journal = {The Journal of Chemical Physics},
+    volume = {152},
+    number = {20},
+    pages = {204108},
+    year = {2020},
+    month = {05},
+    issn = {0021-9606},
+    doi = {10.1063/5.0005077},
+    url = {https://doi.org/10.1063/5.0005077},
+    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0005077/16745439/204108\_1\_online.pdf},
+}
+
+
+
+@article{sun2020,
+    author = {Sun, Qiming and Zhang, Xing and Banerjee, Samragni and Bao, Peng and Barbry, Marc and Blunt, Nick S. and Bogdanov, Nikolay A. and Booth, George H. and Chen, Jia and Cui, Zhi-Hao and Eriksen, Janus J. and Gao, Yang and Guo, Sheng and Hermann, Jan and Hermes, Matthew R. and Koh, Kevin and Koval, Peter and Lehtola, Susi and Li, Zhendong and Liu, Junzi and Mardirossian, Narbe and McClain, James D. and Motta, Mario and Mussard, Bastien and Pham, Hung Q. and Pulkin, Artem and Purwanto, Wirawan and Robinson, Paul J. and Ronca, Enrico and Sayfutyarova, Elvira R. and Scheurer, Maximilian and Schurkus, Henry F. and Smith, James E. T. and Sun, Chong and Sun, Shi-Ning and Upadhyay, Shiv and Wagner, Lucas K. and Wang, Xiao and White, Alec and Whitfield, James Daniel and Williamson, Mark J. and Wouters, Sebastian and Yang, Jun and Yu, Jason M. and Zhu, Tianyu and Berkelbach, Timothy C. and Sharma, Sandeep and Sokolov, Alexander Yu. and Chan, Garnet Kin-Lic},
+    title = "{Recent developments in the PySCF program package}",
+    journal = {The Journal of Chemical Physics},
+    volume = {153},
+    number = {2},
+    pages = {024109},
+    year = {2020},
+    month = {07},
+    issn = {0021-9606},
+    doi = {10.1063/5.0006074},
+    url = {https://doi.org/10.1063/5.0006074},
+    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0006074/16722275/024109\_1\_online.pdf},
+}
+
+
+
+@article{smith2020,
+    author = {Smith, Daniel G. A. and Burns, Lori A. and Simmonett, Andrew C. and Parrish, Robert M. and Schieber, Matthew C. and Galvelis, Raimondas and Kraus, Peter and Kruse, Holger and Di Remigio, Roberto and Alenaizan, Asem and James, Andrew M. and Lehtola, Susi and Misiewicz, Jonathon P. and Scheurer, Maximilian and Shaw, Robert A. and Schriber, Jeffrey B. and Xie, Yi and Glick, Zachary L. and Sirianni, Dominic A. and O’Brien, Joseph Senan and Waldrop, Jonathan M. and Kumar, Ashutosh and Hohenstein, Edward G. and Pritchard, Benjamin P. and Brooks, Bernard R. and Schaefer, Henry F., III and Sokolov, Alexander Yu. and Patkowski, Konrad and DePrince, A. Eugene, III and Bozkaya, Uğur and King, Rollin A. and Evangelista, Francesco A. and Turney, Justin M. and Crawford, T. Daniel and Sherrill, C. David},
+    title = "{PSI4 1.4: Open-source software for high-throughput quantum chemistry}",
+    journal = {The Journal of Chemical Physics},
+    volume = {152},
+    number = {18},
+    pages = {184108},
+    year = {2020},
+    month = {05},
+    issn = {0021-9606},
+    doi = {10.1063/5.0006002},
+    url = {https://doi.org/10.1063/5.0006002},
+    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0006002/16684807/184108\_1\_online.pdf},
+}
+
+
+@article{steffen2023,
+author = {Steffen, Julien},
+title = {Caracal: A Versatile Ring Polymer Molecular Dynamics Simulation Package},
+journal = {Journal of Chemical Theory and Computation},
+volume = {19},
+number = {16},
+pages = {5334-5355},
+year = {2023},
+doi = {10.1021/acs.jctc.3c00568},
+URL = { https://doi.org/10.1021/acs.jctc.3c00568},
+eprint = { https://doi.org/10.1021/acs.jctc.3c00568}
+}
+
+@article{smith2021,
+    author = {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., III 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.},
+    title = "{Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs}",
+    journal = {The Journal of Chemical Physics},
+    volume = {155},
+    number = {20},
+    pages = {204801},
+    year = {2021},
+    month = {11},
+    issn = {0021-9606},
+    doi = {10.1063/5.0059356},
+    url = {https://doi.org/10.1063/5.0059356},
+    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0059356/18280657/204801\_1\_5.0059356.pdf},
+}
+
+@article{hourahine2020,
+    author = {Hourahine, B. and Aradi, B. and Blum, V. and Bonafé, F. and Buccheri, A. and Camacho, C. and Cevallos, C. and Deshaye, M. Y. and Dumitrică, T. and Dominguez, A. and Ehlert, S. and Elstner, M. and van der Heide, T. and Hermann, J. and Irle, S. and Kranz, J. J. and Köhler, C. and Kowalczyk, T. and Kubař, T. and Lee, I. S. and Lutsker, V. and Maurer, R. J. and Min, S. K. and Mitchell, I. and Negre, C. and Niehaus, T. A. and Niklasson, A. M. N. and Page, A. J. and Pecchia, A. and Penazzi, G. and Persson, M. P. and Řezáč, J. and Sánchez, C. G. and Sternberg, M. and Stöhr, M. and Stuckenberg, F. and Tkatchenko, A. and Yu, V. W.-z. and Frauenheim, T.},
+    title = "{DFTB+, a software package for efficient approximate density functional theory based atomistic simulations}",
+    journal = {The Journal of Chemical Physics},
+    volume = {152},
+    number = {12},
+    pages = {124101},
+    year = {2020},
+    month = {03},
+    issn = {0021-9606},
+    doi = {10.1063/1.5143190},
+    url = {https://doi.org/10.1063/1.5143190},
+    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/1.5143190/16711771/124101\_1\_online.pdf},
+}
diff --git a/doc/comparison.rst b/doc/comparison.rst
@@ -48,21 +48,27 @@ A list of projects currently using this DFT-D3 implementation is given here.
 `tblite <https://github.com/tblite/tblite>`_: (since 0.1.0)
   Light-weight tight-binding framework
 `DFTB+ <https://github.com/dftbplus/dftbplus>`_: (since 21.2)
-  General package for performing fast atomistic calculations
+  General package for performing fast atomistic calculations.\ :footcite:`hourahine2020`
 `DFT-FE <https://github.com/dftfeDevelopers/dftfe>`_:
-  Real-space DFT calculations using Finite Elements
+  Real-space DFT calculations using Finite Elements.\ :footcite:`motamarri2020`
 `QCEngine <https://github.com/molssi/qcengine>`_: (since 0.24.0)
-  Quantum chemistry program executor and IO standardizer.
+  Quantum chemistry program executor and IO standardizer.\ :footcite:`smith2021`
 `Siesta <https://gitlab.com/siesta-project/siesta>`_: (since 5.0.0)
-  A first-principles materials simulation code using DFT.
+  A first-principles materials simulation code using DFT.\ :footcite:`garcia2020`
 `Psi4 <https://github.com/psi4/psi4>`_: (since 1.9.0)
-  Open-Source Quantum Chemistry - an electronic structure package in C++ driven by Python.
-`PySCF <https://github.com/pyscf/pyscf>`:
-  Python-based Simulations of Chemistry Framework
+  Open-Source Quantum Chemistry - an electronic structure package in C++ driven by Python.\ :footcite:`smith2020`
+`PySCF <https://github.com/pyscf/pyscf>`_:
+  Python-based Simulations of Chemistry Framework.\ :footcite:`sun2020`
 `Caracal <https://github.com/Trebonius91/Caracal>`_:
-  Ring polymer molecular dynamics and rate constant calculations on black-box potential energy surfaces.
+  Ring polymer molecular dynamics and rate constant calculations on black-box potential energy surfaces.\ :footcite:`steffen2023`
 `Curcuma <https://github.com/conradhuebler/curcuma>`_:
-  Simple small molecular docking and conformation filtering tool.
+  Simple small molecular docking and conformation filtering tool.\ :footcite:`hubler2020`
 
 
 If your project is using *s-dftd3* feel free to add your project to this list.
+
+
+Literature
+----------
+
+.. footbibliography::