Nudged Elastic Band Development
Physical Analytics Pipeline
Simple Molecular Reactive Force Field
Squid Codebase
Nudged Elastic Band Development
Developed by Jónsson et al., the Nudged Elastic Band (NEB) method is a powerful computational tool for uncovering energy barriers and consequently, transition states for reaction mechanisms. By developing a deep understanding of NEB, our group aims to determine the most efficient optimization method and approach for applying NEB to various molecular systems of interest. Accurate results via minimal time and computational resources is the goal – we are building upon the current NEB method to define a transferrable “recipe” that allows researchers to properly uncover their specific reaction mechanisms using the least arduous approach possible.
Researchers: Henry C. Herbol, Andrew W. Ruttinger, Nia Lowery
Related Publications
H. C. Herbol, W. Hu, P. Frazer, P. Clancy, and M. Poloczek, Efficient Search of a Compositional Space for Hybrid Organic-Inorganic Perovskite Candidates via Bayesian Optimization, NPJ Comput. Mater., 4 (1), 51 (2018).
Physical Analytics Pipeline
PAL is a collaborative project geared towards the study of large, expensive cost functions. With Bayesian optimization, alongside a cheap computational ersatz for some desired experimental property, PAL aids researchers in studying previously too large to tackle type problems. Currently, PAL is being applied to Hybrid Organic Inorganic Perovskites (HOIPs) to isolate the best perovskite salt – solvent combination for dissolving HOIP reagents in solution.
Researchers: Henry C. Herbol
Related Publications
H. C. Herbol, W. Hu, P. Frazer, P. Clancy, and M. Poloczek, Efficient Search of a Compositional Space for Hybrid Organic-Inorganic Perovskite Candidates via Bayesian Optimization, NPJ Comput. Mater., 4 (1), 51 (2018).
Simple Molecular Reactive Force Field (SMRFF)
SMRFF, originally developed in 2016 (link), is a novel reactive force field that strives to strike a balance between accuracy and use. By simplifying the expressions of reactions, the number of parameters necessary decreases, allowing for a more readily parameterized force field. Further, by isolating a “Long Range” and “Short Range” component to the force field, with smooth transitioning between the two, the computationally heavy portion (the short range) is minimized as much as possible, allowing for better speeds. Currently, SMRFF is being extended from the original implementation of Morse, Lennard-Jones, and Coulomb to that of a short-ranged Tersoff with long-ranged Lennard-Jones and Coulomb.
Researchers: Henry C. Herbol, Isaiah Chen, Hongyi “Charlie” Guan
Related Publications
J. Andrejevic, J.M. Stevenson, and P. Clancy, Simple Molecular Reactive Force Field for Metal-Organic Synthesis, J. Chem. Theor. Comp., 12(2), 825-838 (2016).
Squid Codebase
Our group uses a diverse range of computational approaches and methods in order to investigate the nature of atoms and molecules. Therefore, we have developed a custom codebase called Squid which supports software including LAMMPS, Orca, and Quantum ESPRESSO. We have also developed scripts for many data post-processing needs (molecular orbital analysis, reaction rate calculations) and computational approaches (Nudged Elastic Band). As we look to tackle more advanced problems, our codebase is constantly updated and improved, further broadening our computational toolbox.
Researchers: Henry C. Herbol, Andrew W. Ruttinger