Software

Non-adiabatic quantum dynamics

At the heart of ubiquitous electrochemical, photochemical, and enzymatic reactions lies the transfer of quantum-mechanical particles on a manifold of electronic or vibronic states coupled to the motion of heavier atoms and molecules. Investigation of such electronic-nuclear coupled reactions heavily relies on developing mixed quantum-classical dynamics (MQCD) methods [1] capable of tracking non-adiabatic dynamics, i.e., transitions between different electronic and/or vibrational states. Ring polymer surface hopping (RPSH) [2] is one such method that describes the non-adiabatic transitions based on Fewest-Switches Surface-Hopping (FSSH) [3] algorithm and at the same time introduces nuclear quantum effects (NQEs) such as nuclear tunneling and zero-point energy into the molecular dynamics simulations based on Feynman’s imaginary-time path integral formalism [4]. Here, we have RPSH methodology as an open-source non-adiabatic MQCD package coined SHARP pack, short for Surface Hopping and Ring Polymer package. The pilot version of the SHARP pack is available through our GitHub repository.

Molecular dynamics in condensed phases

Shakib Theory Group has modified the open-source DL_POLY classic v1.10 [5] code to DL_POLY quantum v1.0. The details of these modifications are provided in the link above and the code can be downloaded here. Example cases are provided for different systems in the "data" subdirectory including bulk water (TEST42 and TEST45), dry and hydrated 2-dimensional metal-organic framework Cu3(HHTP)2 (TEST43 and TEST46), and zeolitic-imidazolate framework ZIF-8 (TEST44).

Note: The DL_POLY quantum project is ongoing with new implementations underway; a manual will be available in near future. For suggestions, feedbacks and questions please contact Dr. Farnaz Shakib at shakib@njit.edu. 

EC-MOF/Phase I database

The unique structural and electronic properties of pi-stacked layered metal-organic frameworks (MOFs) can be utilized as supercapcitors, field-effect transistors or optimal cathode materials in lithium-sulfur batteries. Progress in these research areas have been hampered by the lack of a comprehensive database of these electrically conductive (EC) MOFs which prevented accelerated materials discovery. Shakib Theory Group has developed EC-MOF/Phase I database which is available here, the details of Crystal Structure Producer (CrySP) are provided in the link above. 

References

[1] Tully, J. C. J. Chem. Phys. 2012, 137, 22A301.

[2] Shakib, F. A.; Huo, P.  J. Phys. Chem. Lett. 2017, 8, 3073.

[3] Tully, J. C. J. Chem. Phys. 1990, 93, 1061.

[4] Feynman, R. Rev. Modern Physics. 1948, 20, 367.

[5] Todorov, I. T.; Smith, W.; Trachenko, K.; Dove, M. T. J. Mater. Chem. 2006, 16, 1911.