def from_slabs(
cls,
substrate_slab: Slab,
film_slab: Slab,
in_plane_offset: Tuple[float, float] = (0, 0),
gap: float = 1.6,
vacuum_over_film: float = 0.0,
interface_properties: Optional[Dict] = None,
center_slab: bool = True,
) -> "Interface":
"""
Makes an interface structure by merging a substrate and film slabs
The film a- and b-vectors will be forced to be the substrate slab's
a- and b-vectors.
For now, it's suggested to use a factory method that will ensure the
appropriate interface structure is already met.
Args:
sub_slab: slab for the substrate
film_slab: slab for the film
in_plane_offset: fractional shift in plane
for the film with respect to the substrate
gap: gap between substrate and film in Angstroms
vacuum_over_film: vacuum space above the film in Angstroms
structure_properties: dictionary of misc properties for this structure
center_slab: center the slab
"""
interface_properties = interface_properties or {}
# Ensure c-axis is orthogonal to a/b plane
if isinstance(substrate_slab, Slab):
substrate_slab = substrate_slab.get_orthogonal_c_slab()
if isinstance(film_slab, Slab):
film_slab = film_slab.get_orthogonal_c_slab()
assert np.allclose(film_slab.lattice.alpha, 90, 0.1)
assert np.allclose(film_slab.lattice.beta, 90, 0.1)
assert np.allclose(substrate_slab.lattice.alpha, 90, 0.1)
assert np.allclose(substrate_slab.lattice.beta, 90, 0.1)
# Ensure sub is right-handed
# IE sub has surface facing "up"
sub_vecs = substrate_slab.lattice.matrix.copy()
if np.dot(np.cross(*sub_vecs[:2]), sub_vecs[2]) < 0:
sub_vecs[2] *= -1.0
substrate_slab.lattice = Lattice(sub_vecs)
# Find the limits of C-coords
sub_coords = substrate_slab.frac_coords
film_coords = film_slab.frac_coords
sub_min_c = np.min(sub_coords[:, 2]) * substrate_slab.lattice.c
sub_max_c = np.max(sub_coords[:, 2]) * substrate_slab.lattice.c
film_min_c = np.min(film_coords[:, 2]) * film_slab.lattice.c
film_max_c = np.max(film_coords[:, 2]) * film_slab.lattice.c
min_height = np.abs(film_max_c - film_min_c) + np.abs(sub_max_c -
sub_min_c)
# construct new lattice
abc = substrate_slab.lattice.abc[:2] + (min_height + gap +
vacuum_over_film, )
angles = substrate_slab.lattice.angles
lattice = Lattice.from_parameters(*abc, *angles)
# Get the species
species = substrate_slab.species + film_slab.species
# Get the coords
# Shift substrate to bottom in new lattice
sub_coords = np.subtract(sub_coords, [0, 0, np.min(sub_coords[:, 2])])
sub_coords[:, 2] *= substrate_slab.lattice.c / lattice.c
# Flip the film over
film_coords[:, 2] *= -1.0
film_coords[:, 2] *= film_slab.lattice.c / lattice.c
# Shift the film coords to right over the substrate + gap
film_coords = np.subtract(film_coords,
[0, 0, np.min(film_coords[:, 2])])
film_coords = np.add(
film_coords, [0, 0, gap / lattice.c + np.max(sub_coords[:, 2])])
# Build coords
coords = np.concatenate([sub_coords, film_coords])
# Shift coords to center
if center_slab:
coords = np.add(coords, [0, 0, 0.5 - np.average(coords[:, 2])])
# Only merge site properties in both slabs
site_properties = {}
site_props_in_both = set(substrate_slab.site_properties.keys()) & set(
film_slab.site_properties.keys())
for key in site_props_in_both:
site_properties[key] = [
*substrate_slab.site_properties[key],
*film_slab.site_properties[key],
]
site_properties["interface_label"] = ["substrate"] * len(
substrate_slab) + ["film"] * len(film_slab)
iface = cls(
lattice=lattice,
species=species,
coords=coords,
to_unit_cell=False,
coords_are_cartesian=False,
site_properties=site_properties,
validate_proximity=False,
in_plane_offset=in_plane_offset,
gap=gap,
vacuum_over_film=vacuum_over_film,
interface_properties=interface_properties,
)
iface.sort()
return iface
