1. Import the structures

You can download a tar file containing the structures from

$ wget {{ "/assets/2018_EPFL_molsim/mof_structures.tar.gz" | absolute_url }}
$ tar -xf mof_structures.tar.gz
  • Visualize a few structures using jmol:

    $ cd struct/
    $ jmol <structure>.cif

    Can you think of two criteria for a high deliverable methane capacity?

  • Use the CifData class to import the structures into your database, e.g.

    CifData = DataFactory('cif')
    cif = CifData(file='/path/to/file.cif')
  • Use wildcards with the glob and os modules to get the file paths of all structures like so:

    from glob import glob
    from os import path
    all_structure_files = glob(path.abspath("/path/to/struct/*"))
  • Keep track of your structures using groups

    # Use get_or_create to be able to run this multiple times mofs,
    created = Group.get_or_create(name='mofs')
    mofs.add_nodes([cif1, cif2])
  • Finally, you can load your structures from the group using the AiiDA query builder

    qb = QueryBuilder()
    qb.append(Group, filters = { 'name':'mofs' })
    mofs = qb.one()[0]
    for cif in mofs.nodes:
        print cif