• python
  • Atomic Simulation Environment (ASE) - scripting and manipulating
  • PyMatGen - Constructing and building crystal facets
  • Fireworks - Managing supercomputer workflows and job submission
  • VASP / QE - DFT codes
  • AMP - Machine-learning calculator plugin for ASE
  • HOOMD - GPU accelerated MD code for coarse-grained systems
  • NAMD - MD code for classical interface simulations
  • VMD - visualization of nanoscale structures