Surfaces
It is crucial for many heterogeneous catalysis studies to be
able to model a catalyst surface where the desired reaction
can take place.
autocat.surface
provides tools for generating
low miller index surfaces for mono-element surfaces with a vacuum
in the \(z\)-direction.
The core function of this module is
generate_surface_structures
where multiple slabs can be generated at once.
>>> from autocat.surface import generate_surface_structures
>>> surf_dict = generate_surface_structures(
... ["Li", "Cu"],
... facets={"Li": ["110"]},
... supercell_dim=[5, 5, 4],
... n_fixed_layers=2,
... default_lat_param_lib="beefvdw_fd",
... write_to_disk=True,
... )
Li_bcc110 structure written to ./Li/bcc110/substrate/input.traj
Cu_fcc100 structure written to ./Cu/fcc100/substrate/input.traj
Cu_fcc111 structure written to ./Cu/fcc111/substrate/input.traj
Cu_fcc110 structure written to ./Cu/fcc110/substrate/input.traj
>>> surf_dict
{'Li': {'bcc110': {'structure': Atoms(...),
'traj_file_path': './Li/bcc110/substrate/input.traj'}},
'Cu': {'fcc100': {'structure': Atoms(...),
'traj_file_path': './Cu/fcc100/substrate/input.traj'},
'fcc111': {'structure': Atoms(...),
'traj_file_path': './Cu/fcc111/substrate/input.traj'},
'fcc110': {'structure': Atoms(...),
'traj_file_path': './Cu/fcc110/substrate/input.traj'}}}
- for Li we only need the 110 facet
- generate all default facets for Cu
- fcc/bcc: ["100", "110", "111"]
- hcp: ["0001"]
- the supercell dimensions of the slabs are 5 \(\times\) 5 \(\times\) 4
- the bottom 2 layers are held fixed
- for structures where the lattice parameter is not explicitly specified,
their default values are pulled from the
autocat.data.lattice_parameterslibrary that used a BEEF-vdW XC and finite difference basis set
When using the write_to_disk functionality the structures
will be written into the following directory structure:
.
├── Cu
│ ├── fcc100
│ │ └── substrate
│ │ └── input.traj
│ ├── fcc110
│ │ └── substrate
│ │ └── input.traj
│ └── fcc111
│ └── substrate
│ └── input.traj
├── Li
│ └── bcc110
│ └── substrate
│ └── input.traj