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74 changes: 74 additions & 0 deletions doc/_static/references.bib
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Expand Up @@ -225,4 +225,78 @@ @article{golokesh2022
publisher = {The Royal Society of Chemistry},
doi = {10.1039/D2CP03938A},
url = {http://dx.doi.org/10.1039/D2CP03938A},
}

@article{grimme2016,
title={Dispersion-corrected mean-field electronic structure methods},
author={Grimme, Stefan and Hansen, Andreas and Brandenburg, Jan Gerit and Bannwarth, Christoph},
journal={Chem. Rev.},
volume={116},
number={9},
pages={5105--5154},
year={2016},
publisher={ACS Publications},
doi={10.1021/acs.chemrev.5b00533},
url={https://doi.org/10.1021/acs.chemrev.5b00533},
}

@article{kohn1965,
title={Self-consistent equations including exchange and correlation effects},
author={Kohn, Walter and Sham, Lu Jeu},
journal={Phys. Rev.},
volume={140},
number={4A},
pages={A1133},
year={1965},
publisher={APS},
doi={10.1103/PhysRev.140.A1133},
url={https://doi.org/10.1103/PhysRev.140.A1133},
}

@article{caldeweyher2019,
title={A generally applicable atomic-charge dependent London dispersion correction},
author={Caldeweyher, Eike and Ehlert, Sebastian and Hansen, Andreas and Neugebauer, Hagen and Spicher, Sebastian and Bannwarth, Christoph and Grimme, Stefan},
journal={J. Chem. Phys.},
volume={150},
number={15},
year={2019},
publisher={AIP Publishing},
doi={10.1063/1.5090222},
url={https://doi.org/10.1063/1.5090222},
}

@article{kedward2022,
title={The state of Fortran},
author={Kedward, Laurence J and Aradi, Balint and {\v{C}}ert{\'\i}k, Ond{\v{r}}ej and Curcic, Milan and Ehlert, Sebastian and Engel, Philipp and Goswami, Rohit and Hirsch, Michael and Lozada-Blanco, Asdrubal and Magnin, Vincent and Markus, Arjen and Pagone, Emanuele and Pribec, Ivan and Richardson, Brad and Snyder, Harris and Urban, John and Vandenplas, J{\'e}r{\'e}mie},
journal={Comput. Sci. Eng.},
volume={24},
number={2},
pages={63--72},
year={2022},
publisher={IEEE},
doi={10.1109/MCSE.2022.3159862},
url={https://doi.org/10.1109/MCSE.2022.3159862},
}

@article{larsen2017,
title={The atomic simulation environment—a Python library for working with atoms},
author={Larsen, Ask Hjorth and Mortensen, Jens J{\o}rgen and Blomqvist, Jakob and Castelli, Ivano E and Christensen, Rune and Du{\l}ak, Marcin and Friis, Jesper and Groves, Michael N and Hammer, Bj{\o}rk and Hargus, Cory and Hermes, Eric D and Jennings, Paul C and Jensen, Peter Bjerre and Kermode, James and Kitchin, John R and Kolsbjerg, Esben Leonhard and Kubal, Joseph and Kaasbjerg, Kristen and Lysgaard, Steen and Maronsson, J{\'o}n Bergmann and Maxson, Tristan and Olsen, Thomas and Pastewka, Lars and Peterson, Andrew and Rostgaard, Carsten and Schi{\o}tz, Jakob and Sch{\"u}tt, Ole and Strange, Mikkel and Thygesen, Kristian S and Vegge, Tejs and Vilhelmsen, Lasse and Walter, Michael and Zeng, Zhenhua and Jacobsen, Karsten W},
journal={J. Phys.: Condens. Matter},
volume={29},
number={27},
pages={273002},
year={2017},
publisher={IOP Publishing},
doi={10.1088/1361-648X/aa680e},
url={https://doi.org/10.1088/1361-648X/aa680e},
}

@article{wittmann2024,
title={Extension of the D3 and D4 London Dispersion Corrections to the full Actinides Series},
author={Wittmann, Lukas and Gordiy, Igor and Friede, Marvin and Helmich-Paris, Benjamin and Grimme, Stefan and Hansen, Andreas and Bursch, Markus},
journal={Phys. Chem. Chem. Phys.},
year={2024},
publisher={Royal Society of Chemistry},
doi={10.1039/D4CP01514B},
url={https://doi.org/10.1039/D4CP01514B},
}
25 changes: 23 additions & 2 deletions doc/paper.md
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@@ -1,5 +1,5 @@
---
title: 'Simple DFT-D3: reimplementation of the D3 dispersion correction'
title: 'Simple DFT-D3: Library first implementation of the D3 dispersion correction'
tags:
- Fortran
- Python
Expand All @@ -20,8 +20,29 @@ bibliography: _static/references.bib

# Summary

# Statement of need
The simulation of chemical reactions or processes provides a fundamental approach to understanding chemistry.
The application of Kohn-Sham density functional theory (KSDFT) [@kohn1965] has become an indispensable tool for computational modeling.
However, semilocal KS-DFT often fails to accurately describe long-range correlation effects, such as dispersion interactions, in many exchange-correlation functionals [@grimme2016].
Additive dispersion corrections, like the D3 [@grimme2010] or D4 [@caldeweyher2019] methods, effectively account for these effects.

# Statement of Need

The D3 method is one of the most widely used dispersion corrections, however the original implementation [@grimme2010] has been forked and modified many times to include specific adaptations needed for integration as a library in different electronic structure software packages.
Here, we present a reimplementation of the D3 method, focusing on providing a simple, library-first version with APIs defined in Fortran, C, and Python, including the latest parameters for many D3 method variants.

The ``simple-dftd3`` library implements several variants of the D3 method, including the original zero damping D3(0) [@grimme2010], rational damping D3(BJ) [@grimme2011], modified zero damping D3M(0) [@smith2016], and optimized power damping D3(op) [@witte2017].
The main library is written in modern Fortran [@kedward2022], with additional APIs for C via Fortran-C interoperable functions and for Python via the CFFI library.
A command line interface is also available for standalone usage.

# Usage

The ``simple-dftd3`` library has been successfully adopted by several electronic structure software packages, such as DFTB+ (since version 21.2) [@hourahine2020], Psi4 (since version 1.9.0) [@smith2020], and Siesta (since version 5.0.0) [@garcia2020].
Additionally, the Python API provides interfaces for usage in ASE [@larsen2017], PySCF [@sun2020], and QCEngine [@smith2021].
Given the accessibility of the code base, new method improvements, like the recent extension of the D3 method to actinide elements [@wittmann2024], are easily integrated.
With its simplicity and availability, the library is a valuable tool for the community to include dispersion corrections in their electronic structure calculations.

# Acknowledgements

S.E. acknowledges contributions from Robert Cohn, Marvin Friede, Kjell Jorner, Eisuke Kawashima, Qiming Sun, Thijs Vogels, Shirong Wang, and Lukas Wittmann to the project.

# References

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