From 62ed89aef4ce34247275df0aca228c4c72303d25 Mon Sep 17 00:00:00 2001 From: Sebastian Ehlert Date: Sat, 27 Jul 2024 15:03:33 +0200 Subject: [PATCH] Update JOSS paper --- doc/_static/references.bib | 74 ++++++++++++++++++++++++++++++++++++++ doc/paper.md | 27 ++++++++++++-- 2 files changed, 98 insertions(+), 3 deletions(-) diff --git a/doc/_static/references.bib b/doc/_static/references.bib index 789a7c6d..e0482de0 100644 --- a/doc/_static/references.bib +++ b/doc/_static/references.bib @@ -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}, } \ No newline at end of file diff --git a/doc/paper.md b/doc/paper.md index 61047c0f..9126902d 100644 --- a/doc/paper.md +++ b/doc/paper.md @@ -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 @@ -14,14 +14,35 @@ authors: affiliations: - name: Microsoft Research, AI for Science, The Netherlands index: 1 -date: 8 June 2024 +date: 7 July 2024 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