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.

There are also many slides describing the BigDFT approach in our BigDFT school repo.

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}
}