PElib: The Polarizable Embedding library

The PE library is an implementation of the polarizable embedding (PE) model which is a fully polarizable fragment-based quantum-classical approach, as described in the following works:

• Olsen, J. M. H., Aidas, K., and Kongsted, J., J. Chem. Theory Comput. 6, 2010, pp 3721–3734 (https://doi.org/10.1021/ct100380)

• Olsen, J .M. H. and Kongsted, J., Adv. Quantum Chem. 61, 2011, pp 107-143 (https://doi.org/10.1016/B978-0-12-386013-2.00003-6)

• Olsen, J. M. H., Ph. d. thesis (2012), Department of Physics, Chemistry and Pharmacy, University of Southern Denmark (https://doi.org/10.6084/m9.figshare.156852)

New features in 1.2 include magnetic gradient using GIAOs as described in:

• Steinmann, C., Olsen, J. M. H., Kongsted, J., J. Chem. Theory Comput. 10, 2014, pp 981–988 (https://doi.org/10.1021/ct400880n)

New features in 1.3 include molecular gradient and effective external fields as described in:

• List, N. H., Beerepoot, M. T. P., Olsen, J. M. H., Gao, B., Ruud, K., Jensen, H. J. Aa., Kongsted, J., J. Chem. Phys. 142, 2015, pp 034119 (https://doi.org/10.1063/1.4905909)
• List, N. H., Jensen, H. J. Aa., Kongsted, J., Phys. Chem. Chem. Phys. 18, 2016, pp 10070-10080 (https://doi.org/10.1039/C6CP00669H)

New features in 1.4 include polarizable density embedding (PDE), FixSol solvation model with FIXPVA2 cavity tesselation, and support for AMOEBA potential.

• PDE is described in:
  •  J. M. H. Olsen, C. Steinmann, K. Ruud, and J. Kongsted, J. Phys. Chem. A 119, 2015, pp 5344-5355 (https://doi.org/10.1021/jp510138k)
  • P. Reinholdt, J. Kongsted, and J. M. H. Olsen, J. Phys. Chem. Lett. 8, 2017, pp 5949-5958 (https://doi.org/10.1021/acs.jpclett.7b02788)
• FixSol is decribed in:
  • N. M. Thellamurege and H. Li, J. Chem. Phys. 137, 2012, pp 246101 (https://doi.org/10.1063/1.4773280)
  • M. S. Nørby, C. Steinmann, J. M. H. Olsen, H. Li, and J. Kongsted, J. Chem. Theory Comput. 12, 2016, pp 5050-5057 (https://doi.org/10.1021/acs.jctc.6b00706)

New features in 1.5 include fast multipole method (FMM).

• M. Scheurer, P. Reinholdt, J. M. H. Olsen, A. Dreuw, and J. Kongsted, J. Chem. Theory Comput. 17, 2021, pp 3445-3454 (https://doi.org/10.1021/acs.jctc.1c00225)

New features in 1.6 include new approximate environment couplings.

• P. Reinholdt, J. Kongsted, and F. Lipparini, J. Chem. Theory Comput. 18, 2021, pp 344-356 (https://doi.org/10.1021/acs.jctc.1c01037)

New features in 1.7 include London orbital contributions for PDE.

• F. K. Jørgensen, P. Reinholdt, E. D. Hedegård, and J. Kongsted, J. Chem. Theory Comput. 18, 2022, pp 7384-7393 (https://doi.org/10.1021/acs.jctc.2c00829)

New features in 1.8 include periodic boundary conditions (PBCs) when solving for induced dipoles.

• S. Kvedaraviciute, D. Carrasco-Busturia, K. B. Møller, and J. M. H. Olsen, J. Chem. Theory Comput. 19, 2023, pp 5122-5141 (https://doi.org/10.1021/acs.jctc.3c00434)