Required sofware

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: Andriy Zhugayevych

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)

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
Attend this course if needed: Computing Life with Linux
Sample reports are provided in LaTeX format with these styles