Various artists

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.

I used LAMMPS for our NaCl nucleation papers in JACS and JCP, where we successfully predicted nucleation rates and unraveled an unexpected attachment mechanism.


VASP logo

... (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.



pymatgen logo

... (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.


PyCDT logo

... is a Python toolkit for generating, analyzing, and plotting results of charged defect calculations.


matminer logo

... is a Python library for data mining the properties of materials.



VTK logo

... (Visualization Toolkit) is an open-source software system for 3D computer graphics, image processing, and visualization.


VMD logo

... (Visual Molecular Dynamics) is a molecular modelling and visualization computer program, mainly developed to view and analyze the results of molecular dynamics simulations.


VESTA logo

... is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.


... is my favorite plotting program, a command-line program that can generate two- and three-dimensional plots of functions, data, and data fits..



FFmpeg logo

... is a free and open-source project consisting of a vast software suite of libraries and programs; at its core, FFmpeg is a command-line-based processing of video and audio files..



BASH logo

... is a Unix shell and command line language written as a free software replacement for the Bourne shell.


C++ logoC logo

... is a general-purpose, procedrual computer programming language supporting structured programming, lexical variable space, and recursion, while a static type system prevents unintended operations, and a high-level, general-purpose programming language created as an extension of C ("C with classes")., respectively.

Fortran (90)

... is a general-purpose, compiled imperative programming language that is especially suited to numeric computation and scientific computing.


Java logo

... is a general-purpose programming language that is class-based, object-oriented, and designed to have as few implementation dependencies as possible.


Python logo

... is a interpreted, high-level, general-purpose programming language.