def create_slab(self, vacuum=12, thickness=10):
"""
set the vacuum spacing, slab thickness and call sd_flags
for top 2 layers
returns the poscar corresponding to the modified structure
"""
strt_structure = self.input_structure.copy()
if self.from_ase:
slab_struct = get_ase_slab(strt_structure,
hkl=self.system['hkl'],
min_thick=thickness,
min_vac=vacuum)
else:
slab_struct = SlabGenerator(initial_structure=strt_structure,
miller_index=self.system['hkl'],
min_slab_size=thickness,
min_vacuum_size=vacuum,
lll_reduce=False,
center_slab=True,
primitive=False).get_slab()
slab_struct.sort()
sd = self.set_sd_flags(slab_struct)
comment = 'VAC' + str(vacuum) + 'THICK' + str(thickness)
return Poscar(slab_struct, comment=comment, selective_dynamics=sd)
def __init__(self, strt, hkl=[1,1,1], min_thick=10, min_vac=10,
supercell=[1,1,1], name=None, adsorb_on_species=None,
adatom_on_lig=None, ligand=None, displacement=1.0,
surface_coverage=None, scell_nmax=10,
coverage_tol=0.25, solvent=None,
start_from_slab=False, validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=False,
primitive=True, from_ase=False,
x_shift=0, y_shift=0, rot=[0,0,0],
center_slab=True):
self.from_ase = from_ase
vac_extension = 0
if ligand is not None:
vac_extension = ligand.max_dist
if isinstance(strt, Structure) and not isinstance(strt, Slab):
self.min_vac = min_vac + vac_extension
if self.from_ase:
strt = get_ase_slab(strt,
hkl=hkl,
min_thick=min_thick,
min_vac=min_vac + vac_extension,
center_slab=center_slab)
else:
strt = SlabGenerator(strt, hkl, min_thick,
min_vac + vac_extension,
center_slab=center_slab,
primitive = primitive).get_slab()
strt.make_supercell(supercell)
else:
self.min_vac = min_vac
Slab.__init__(self, strt.lattice, strt.species_and_occu,
strt.frac_coords,
miller_index=strt.miller_index,
oriented_unit_cell=strt.oriented_unit_cell,
shift=strt.shift, scale_factor=strt.scale_factor,
validate_proximity=validate_proximity,
to_unit_cell=to_unit_cell,
coords_are_cartesian=coords_are_cartesian,
site_properties=strt.site_properties,
energy=strt.energy )
self.strt= strt
self.name = name
self.hkl = hkl
self.min_thick = min_thick
self.supercell = supercell
self.ligand = ligand
self.slab = strt
self.displacement = displacement
self.solvent = solvent
self.surface_coverage = surface_coverage
self.adsorb_on_species = adsorb_on_species
self.adatom_on_lig = adatom_on_lig
self.scell_nmax = scell_nmax
self.coverage_tol = coverage_tol
self.x_shift = x_shift
self.y_shift = y_shift
self.rot = rot
def create_slab(self, vacuum=12, thickness=10):
"""
set the vacuum spacing, slab thickness and call sd_flags
for top 2 layers
returns the poscar corresponding to the modified structure
"""
strt_structure = self.input_structure.copy()
if self.from_ase:
slab_struct = get_ase_slab(strt_structure, hkl=self.system['hkl'],
min_thick=thickness, min_vac=vacuum)
else:
slab_struct= SlabGenerator(initial_structure= strt_structure,
miller_index= self.system['hkl'],
min_slab_size= thickness,
min_vacuum_size=vacuum,
lll_reduce=False, center_slab=True,
primitive=False).get_slab()
slab_struct.sort()
sd = self.set_sd_flags(slab_struct)
comment = 'VAC'+str(vacuum)+'THICK'+str(thickness)
return Poscar(slab_struct, comment=comment,
selective_dynamics=sd)
def __init__(self,
strt,
hkl=[1, 1, 1],
min_thick=10,
min_vac=10,
supercell=[1, 1, 1],
name=None,
adsorb_on_species=None,
adatom_on_lig=None,
ligand=None,
displacement=1.0,
surface_coverage=None,
scell_nmax=10,
coverage_tol=0.25,
solvent=None,
start_from_slab=False,
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
primitive=True,
from_ase=False,
lll_reduce=False,
center_slab=True,
max_normal_search=None,
force_normalize=False,
x_shift=0,
y_shift=0,
rot=[0, 0, 0]):
self.from_ase = from_ase
vac_extension = 0
if ligand is not None:
vac_extension = ligand.max_dist
if isinstance(strt, Structure) and not isinstance(strt, Slab):
self.min_vac = min_vac + vac_extension
if self.from_ase:
strt = get_ase_slab(strt,
hkl=hkl,
min_thick=min_thick,
min_vac=min_vac + vac_extension)
else:
slab = SlabGenerator(strt,
hkl,
min_thick,
min_vac + vac_extension,
center_slab=center_slab,
lll_reduce=lll_reduce,
max_normal_search=max_normal_search,
primitive=primitive).get_slab()
if force_normalize:
strt = slab.get_orthogonal_c_slab()
else:
strt = slab
strt.make_supercell(supercell)
else:
self.min_vac = min_vac
Slab.__init__(self,
strt.lattice,
strt.species_and_occu,
strt.frac_coords,
miller_index=strt.miller_index,
oriented_unit_cell=strt.oriented_unit_cell,
shift=strt.shift,
scale_factor=strt.scale_factor,
validate_proximity=validate_proximity,
to_unit_cell=to_unit_cell,
coords_are_cartesian=coords_are_cartesian,
site_properties=strt.site_properties,
energy=strt.energy)
self.strt = strt
self.name = name
self.hkl = hkl
self.min_thick = min_thick
self.supercell = supercell
self.ligand = ligand
self.slab = strt
self.displacement = displacement
self.solvent = solvent
self.surface_coverage = surface_coverage
self.adsorb_on_species = adsorb_on_species
self.adatom_on_lig = adatom_on_lig
self.scell_nmax = scell_nmax
self.coverage_tol = coverage_tol
self.x_shift = x_shift
self.y_shift = y_shift
self.rot = rot
