Important: The software provided within the course activities can be used only for your personal education within the scope of the course. Copying any part of licensed software from the provided computing resources is strictly forbidden.

Contact person: Dmitry Aksyonov

Any computing cluster account:

• • students should use their university cluster (e.g. firstname.lastname@hostdomain, use helpdesk to open account)
  • for education (only) one can use our Virtual Machine (firstname.lastname@hostdomain, unzip setupVM to your $HOME folder)
  • ask your advisor for additional computing facilities
• Any program for:
  • visualizing isosurfaces in molecules and crystals: Jmol, Vesta
  • classical molecular mechanics: LAMMPS (available on cluster, install also on your computer)
  • quantum chemistry of molecules: MOPAC (academic), Gaussian (commercial, available on cluster)
  • quantum chemistry of crystals: VASP (commercial, available on cluster)
  • advanced regression analysis for materials data science: SISSO (binaries are provided in bin folder of setupVM)
• Any tools for pre- and post-processing:
  • we recommend IPython and support the following packages: ASE, pymatgen, SIMAN, MolMod
  • we also support Maple with MolMod package (many institutions have site license)
  • optionally you can use any molecular builders and graphical interface to solvers: Avogadro, Ascalaph, BALLview, Spartan (Skoltech has educational license)

See also other software, review of free software, eChem project

Notes on using the above software

• Class on Python Tools in CMS: lecture slides, notebook for ASE, notebook for pymatgen, sample .pmgrc.yaml file
• If you do not have IPython, you might find online IPython server for calculations (test files)
• To install SIMAN package on Linux run sudo pip3 install siman
• MolMod for Python can also be downloaded here
• Check this course if needed: Computing Life with Linux
• Sample reports are provided in LaTeX format with these styles