As part of my PhD dissertation, I am studying the nucleation and dissocitaion of gas clathrates--crystalline inclusion components--under broad ranges of thermodynamics and in presence of various additives. We perform the simulations using the well-known LAMMPS molecular dynamics package under High-Performance Computing (HPC) environment. Utilizing different sets of molecular models, forcefield potentials, and statistical ensembles, we strive at grasping the transient nature of hydartes' formation and dissociation.
Along my PhD work, I have developed numerous pre- and post-processing packages, some of which are listed below:
- A Python package to post-process the myriad number of molecualr simulations for force field developments
- A Python code to merge the multiple LAMMPS-generated simulation boxes with periodic boundary conditions
- A C++ code for identification of cage-like hydrate structures and hydrogen-bonded planes in gas clathrates using geometrical algorithms
- A Python code for calculations of the four-body structural order parameter (F4) in crystalline structural analysis (Github code)
- A Python code for time tracking of the advancing crystal/liquid interface aiding an intelligent machine learning algoithm