def surface_hkl(lattice, hkl, layers, vacuum=1.0, center=False, pbc=True):
"""
Use ase.build.surface to build a surface with surface normal (hkl).
Args:
lattice (pyiron_atomistics.atomistics.structure.atoms.Atoms/str): bulk Atoms
instance or str, e.g. "Fe", from which to build the surface
hkl (list): miller indices of surface to be created
layers (int): # of atomic layers in the surface
vacuum (float): vacuum spacing
center (bool): shift all positions to center the surface
in the cell
Returns:
pyiron_atomistics.atomistics.structure.atoms.Atoms instance: Required surface
"""
# https://gitlab.com/ase/ase/blob/master/ase/lattice/surface.py
state.publications.add(publication_ase())
surface = ase_surf(lattice, hkl, layers)
z_max = np.max(surface.positions[:, 2])
surface.cell[2, 2] = z_max + vacuum
if center:
surface.positions += 0.5 * surface.cell[2] - [0, 0, z_max / 2]
surface.pbc = pbc
return ase_to_pyiron(surface)
def surface(
element,
surface_type,
size=(1, 1, 1),
vacuum=1.0,
center=False,
pbc=True,
**kwargs,
):
"""
Generate a surface based on the ase.build.surface module.
Args:
element (str): Element name
surface_type (str): The string specifying the surface type generators available through ase (fcc111,
hcp0001 etc.)
size (tuple): Size of the surface
vacuum (float): Length of vacuum layer added to the surface along the z direction
center (bool): Tells if the surface layers have to be at the center or at one end along the z-direction
pbc (list/numpy.ndarray): List of booleans specifying the periodic boundary conditions along all three
directions.
**kwargs: Additional, arguments you would normally pass to the structure generator like 'a', 'b',
'orthogonal' etc.
Returns:
pyiron_atomistics.atomistics.structure.atoms.Atoms instance: Required surface
"""
# https://gitlab.com/ase/ase/blob/master/ase/lattice/surface.py
if pbc is None:
pbc = True
state.publications.add(publication_ase())
for surface_class in [
add_adsorbate,
add_vacuum,
bcc100,
bcc110,
bcc111,
diamond100,
diamond111,
fcc100,
fcc110,
fcc111,
fcc211,
hcp0001,
hcp10m10,
mx2,
hcp0001_root,
fcc111_root,
bcc111_root,
root_surface,
root_surface_analysis,
ase_surf,
]:
if surface_type == surface_class.__name__:
surface_type = surface_class
break
if isinstance(surface_type, types.FunctionType):
if center:
surface = surface_type(symbol=element,
size=size,
vacuum=vacuum,
**kwargs)
else:
surface = surface_type(symbol=element, size=size, **kwargs)
z_max = np.max(surface.positions[:, 2])
surface.cell[2, 2] = z_max + vacuum
surface.pbc = pbc
return ase_to_pyiron(surface)
else:
raise ValueError(f"Surface type {surface_type} not recognized.")
def wrapper(*args, **kwargs):
state.publications.add(publication_ase())
return func(*args, **kwargs)