Vienna Ab initio Simulation Package (VASP): The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modeling e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. (VASP website)

VASPKIT: a postprocessing tool for VASP code. It was written by Fortran 90. (VASPKIT website)

Phonopy:  an open source package for phonon calculations at harmonic and quasi-harmonic levels (Phonopy website)

SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms): SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA's efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. A very important feature of the code is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods. (SIESTA website)

GPAW: a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE) (GPAW website)

Quantum ESPRESSO: is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (Quantum ESPRESSO website)

EPW (Electron-phonon Wannier):  an open-source community code for ab initio calculations of electron-phonon interactions using Density-Functional Perturbation Theory and Maximally Localized Wannier Functions. EPW is a core module of the Quantum ESPRESSO materials simulation suite (EPW website)

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator): LAMMPS is a classical molecular dynamics code. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. (LAMMPS website)

Builders from Materials Design:  Surface Builder, Molecular Builder, PolymerBuilder, Nanoparticle and Nanotube Builders, Substitutional Search, Random Substitutions, Special Quasirandom Structures (SQS) (MedeA website)

Atomic Simulation Environment (ASE):  a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations (ASE website)

PyTorch: an open source machine learning framework that accelerates the path from research prototyping to production deployment (PyTorch website)

Python: a programming language that lets you work more quickly and integrate your systems more effectively (python website)

MATLAB: a programming and numeric computing platform used by millions of engineers and scientists to analyze data, develop algorithms, and create models (MATLAB website)