Publications
------------

The main papers describing the code are:

- Genovese, L., Neelov, A., Goedecker, S., Deutsch, T., Ghasemi, S. A., Willand, A., Caliste, D., et al.  
  "Daubechies wavelets as a basis set for density functional pseudopotential calculations." J. Chem. Phys. 129 (1), 2008, 014109.
- Ratcliff, L. E., Dawson, W., Fisicaro, G., Caliste, D., Mohr, S., Degomme, A., Videau, B., et al.  
  "Flexibilities of wavelets as a computational basis set for large-scale electronic structure calculations." J. Chem. Phys. 152 (19), 2020, 194110.

At the heart of BigDFT is its Poisson solver:

- Genovese, L., Deutsch, T., Neelov, A., Goedecker, S., Beylkin, G.  
  "Efficient solution of Poisson’s equation with free boundary conditions." J. Chem. Phys. 125 (7), 2006, 074105.
- Genovese, L., Deutsch, T., Goedecker, S.  
  "Efficient and accurate three-dimensional Poisson solver for surface problems." J. Chem. Phys. 127 (5), 2007, 054704.
- Fisicaro, G., Genovese, L., Andreussi, O., Marzari, N., Goedecker, S.  
  "A generalized Poisson and Poisson–Boltzmann solver for electrostatic environments." J. Chem. Phys. 144 (1), 2016, 014103.
- Fisicaro, G., Genovese, L., Andreussi, O., Mandal, S., Nair, N. N., Marzari, N., Goedecker, S.  
  "Soft-sphere continuum solvation in electronic-structure calculations." J. Chem. Theory Comput. 13 (8), 2017, 3829–3845.

These papers describe important aspects of the code:

- Mohr, S., Ratcliff, L. E., Boulanger, P., Genovese, L., Caliste, D., Deutsch, T., Goedecker, S., et al.  
  "Daubechies wavelets for linear scaling density functional theory." J. Chem. Phys. 140 (20), 2014, 204110.
- Mohr, S., Ratcliff, L. E., Genovese, L., Caliste, D., Boulanger, P., Goedecker, S., Deutsch, T., et al.  
  "Accurate and efficient linear scaling DFT calculations with universal applicability." Phys. Chem. Chem. Phys. 17 (47), 2015, 31360–31370.
- Genovese, L., Deutsch, T.  
  "Multipole-preserving quadratures for the discretization of functions in real-space electronic structure calculations." Phys. Chem. Chem. Phys. 17 (47), 2015, 31582–31591.
- Ratcliff, L. E., Grisanti, L., Genovese, L., Deutsch, T., Neumann, T., Danilov, D., Wenzel, W., et al.  
  "Toward fast and accurate evaluation of charge on-site energies and transfer integrals in supramolecular architectures using linear constrained density functional theory (CDFT)-based methods." J. Chem. Theory Comput. 11 (5), 2015, 2077–2086.
- Ratcliff, L. E., Genovese, L., Mohr, S., Deutsch, T.  
  "Fragment approach to constrained density functional theory calculations using Daubechies wavelets." J. Chem. Phys. 142 (23), 2015, 234105.
- Mohr, S., Dawson, W., Wagner, M., Caliste, D., Nakajima, T., Genovese, L.  
  "Efficient computation of sparse matrix functions for large-scale electronic structure calculations: The CheSS library." J. Chem. Theory Comput. 13 (10), 2017, 4684–4698.
- Dawson, W., Mohr, S., Ratcliff, L. E., Nakajima, T., Genovese, L.  
  "Complexity reduction in density functional theory calculations of large systems: system partitioning and fragment embedding." J. Chem. Theory Comput. 16 (5), 2020, 2952–2964.
- Stella, M., Thapa, K., Genovese, L., Ratcliff, L. E.  
  "Transition-based constrained DFT for the robust and reliable treatment of excitations in supramolecular systems." J. Chem. Theory Comput. 18 (5), 2022, 3027–3038.
- Dawson, W., Beal, L., Ratcliff, L. E., Stella, M., Nakajima, T., Genovese, L.  
  "Exploratory data science on supercomputers for quantum mechanical calculations." Electronic Structure 6 (2), 2024, 027003.

Papers related to GPU acceleration:

- Genovese, L., Ospici, M., Deutsch, T., Méhaut, J.-F., Neelov, A., Goedecker, S.  
  "Density functional theory calculation on many-cores hybrid central processing unit-graphic processing unit architectures." J. Chem. Phys. 131 (3), 2009, 034103.
- Ratcliff, L. E., Degomme, A., Flores-Livas, J. A., Goedecker, S., Genovese, L.  
  "Affordable and accurate large-scale hybrid-functional calculations on GPU-accelerated supercomputers." J. Phys.: Condens. Matter 30 (9), 2018, 095901.
- Bauinger, C., Genovese, L.  
  "Introducing SYCL to accelerate a Fock operator calculation library of the BigDFT electronic structure code." In Proc. Int. Conf. High Perform. Comput., 79–101 (2023).

Some recent papers using BigDFT for scientific applications:

- Zaccaria, M., Genovese, L., Lawhorn, B. E., Dawson, W., Joyal, A. S., Hu, J., Autissier, P., et al.  
  "Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling." J. R. Soc. Interface 21 (211), 2024, 20230614.
- Zaccaria, M., Genovese, L., Dawson, W., Cristiglio, V., Nakajima, T., Johnson, W., Farzan, M., Momeni, B.  
  "Probing the mutational landscape of the SARS-CoV-2 spike protein via quantum mechanical modeling of crystallographic structures." PNAS Nexus 1 (5), 2022, pgac180.

Talks
=====

You can find some conference and workshop slides about BigDFT on our  
`YouTube channel <https://www.youtube.com/@bigdftchannel6374>`_.

There are also many slides describing the BigDFT approach in our  
`BigDFT school repo <https://github.com/BigDFT-group/bigdft-school/tree/main/slides>`_.

Citing BigDFT
=============

The most recent review article about BigDFT can be cited as::

  @article{doi:10.1063/5.0004792,
    author = {Ratcliff,Laura E.  and Dawson,William  and Fisicaro,Giuseppe  and Caliste,Damien  and Mohr,Stephan  and Degomme,Augustin  and Videau,Brice  and Cristiglio,Viviana  and Stella,Martina  and D’Alessandro,Marco  and Goedecker,Stefan  and Nakajima,Takahito  and Deutsch,Thierry  and Genovese,Luigi },
    title = {Flexibilities of wavelets as a computational basis set for large-scale electronic structure calculations},
    journal = {The Journal of Chemical Physics},
    volume = {152},
    number = {19},
    pages = {194110},
    year = {2020},
    doi = {10.1063/5.0004792},
    URL = {https://doi.org/10.1063/5.0004792},
    eprint = {https://doi.org/10.1063/5.0004792}
  }