Below, I list the compilation of software, libraries, computer tools, and programming languages that I regularly use—or used in the past—for my papers and other research output.
... (Large-scale Atomic/Molecular Massively Parallel Simulator) is a molecular dynamics program, which makes use of Message Passing Interface (MPI) and is free and open-source software.
... (Vienna Ab initio Simulation Package) is a package for performing ab initio quantum mechanical calculations.
... (Chemistry at HARvard Macromolecular Mechanics) is a molecular dynamics simulation and analysis computer software package.
I used CHARMM for our JACS paper on estimating the methane diffusivity in structure-I gas hydrates.
... (Python Materials Genomics) is an open-source Python library for materials analysis.
I used pymatgen in most of my most recent paper: in the PfEFIS paper about electrostatically estimating ion diffusion barriers in transition metal oxides and the like, in the PyCDT paper that introduces a Python tool for generating, analyzing, and plotting charged defects calculations, in the matminer paper introducing a valuable Python library to perform data mining with materials databases, in the zeolite discovery perspective and in the high-throughput zeolite screening paper which leverage the average tetrahedral order parameter of all T-sites to assess the synthesizability and deployability of hypothetical zeolite structures, as well as in the LoStOP paper and in the paper about various use cases of order parameters which facilitate machine learning and automatic analyses of large materials databases such as materials similarity assessments, interstitial finding, and coordination analyses along diffusion pathways of atoms in solids.
... (Visualization Toolkit) is an open-source software system for 3D computer graphics, image processing, and visualization.
... (Visual Molecular Dynamics) is a molecular modelling and visualization computer program, mainly developed to view and analyze the results of molecular dynamics simulations.
... is my favorite plotting program, a command-line program that can generate two- and three-dimensional plots of functions, data, and data fits..