# the subtrate in the substrate's vacuum space.
# So ensure that the substrate vacuum spacing is sufficietly
# large enough to contain the 2d material
substrate = Interface(substrate_bulk,
hkl=[1, 1, 0],
min_thick=10,
min_vac=25,
primitive=False,
from_ase=True)
mat2d = Interface(mat2d_bulk,
hkl=[1, 1, 0],
min_thick=2,
min_vac=0,
primitive=False,
from_ase=True)
substrate.to(fmt='poscar', filename='POSCAR_substrate_initial.vasp')
mat2d.to(fmt='poscar', filename='POSCAR_mat2d_initial.vasp')
# get the matching substrate and 2D material lattices
uv_substrate, uv_mat2d = get_matching_lattices(substrate,
mat2d,
max_area=200,
max_mismatch=0.01,
max_angle_diff=1,
r1r2_tol=0.02)
# map the intial slabs to the newly found matching lattices
substrate_latt = Lattice(
np.array([
uv_substrate[0][:], uv_substrate[1][:],
substrate.lattice.matrix[2, :]
iface = Interface(strt, hkl=hkl,
min_thick=min_thick, min_vac=min_vac,
supercell=supercell, surface_coverage=0.01,
ligand=hydrazine, displacement=displacement,
adatom_on_lig='N', adsorb_on_species='Pb',
primitive=False)
iface.create_interface()
iface.sort()
# extract bare slab
iface_slab = iface.slab
iface_slab.sort()
# set selective dynamics flags as required
true_site = [1, 1, 1]
false_site = [0, 0, 0]
sd_flag_iface = []
sd_flag_slab = []
# selective dynamics flags for the interface
for i in iface.sites:
sd_flag_iface.append(false_site)
# selective dynamics flags for the bare slab
for i in iface_slab.sites:
sd_flag_slab.append(false_site)
interface_poscar = Poscar(iface, selective_dynamics=sd_flag_iface)
slab_poscar = Poscar(iface_slab, selective_dynamics=sd_flag_slab)
# poscars without selective dynamics flag
iface.to('poscar', 'POSCAR_interface.vasp')
iface_slab.to('poscar', 'POSCAR_slab.vasp')
# poscars with selective dynamics flag
interface_poscar.write_file("POSCAR_interface_with_sd.vasp")
slab_poscar.write_file("POSCAR_slab_with_sd.vasp")
surface_coverage=0.01,
ligand=hydrazine,
displacement=displacement,
adatom_on_lig='N',
adsorb_on_species='Pb',
primitive=False)
iface.create_interface()
iface.sort()
# extract bare slab
iface_slab = iface.slab
iface_slab.sort()
# set selective dynamics flags as required
true_site = [1, 1, 1]
false_site = [0, 0, 0]
sd_flag_iface = []
sd_flag_slab = []
# selective dynamics flags for the interface
for i in iface.sites:
sd_flag_iface.append(false_site)
# selective dynamics flags for the bare slab
for i in iface_slab.sites:
sd_flag_slab.append(false_site)
interface_poscar = Poscar(iface, selective_dynamics=sd_flag_iface)
slab_poscar = Poscar(iface_slab, selective_dynamics=sd_flag_slab)
# poscars without selective dynamics flag
iface.to('poscar', 'POSCAR_interface.vasp')
iface_slab.to('poscar', 'POSCAR_slab.vasp')
# poscars with selective dynamics flag
interface_poscar.write_file("POSCAR_interface_with_sd.vasp")
slab_poscar.write_file("POSCAR_slab_with_sd.vasp")
def get_grain_boundary_interface(structure=None, hkl_pair= {'hkl': [[1,0,0],[1,1,0]],\
'thickness':[10,10]}, twist = 0, tilt = 0, separation=0):
"""
Args:
structure: pymatgen structure to create grain boundary in
hkl_pair: dict of {'hkl':thickness}
twist: twist in degrees
tilt: tilt in degrees
"""
structure = get_struct_from_mp(structure, MAPI_KEY="")
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
structure = structure_conventional.copy()
structure.sort()
#creation of lower part of grain boundary
lower= Interface(structure,\
hkl = hkl_pair['hkl'][0],
min_thick = hkl_pair['thickness'][0],
min_vac = separation+hkl_pair['thickness'][1],
primitive = False, from_ase = True, center_slab=False)
lower.to(fmt="poscar", filename="POSCAR_lower.vasp")
#creation of upper part of grain boundary
upper= Interface(structure,\
hkl = hkl_pair['hkl'][1],
min_thick = hkl_pair['thickness'][1],
min_vac = 0,
primitive = False, from_ase = True)
#find top atoms reference of lower part of gb
substrate_top_z = np.max(np.array([site.coords for site in lower])[:, 2])
# define twist and tilt vectors
twist_shift_normal = lower.lattice.matrix[2,:]/\
np.linalg.norm(lower.lattice.matrix[2,:])
tilt_normal = upper.lattice.matrix[1,:]/\
np.linalg.norm(upper.lattice.matrix[2,:])
#define twist operation SymmOp object
twist_op = SymmOp.from_axis_angle_and_translation(axis= twist_shift_normal,\
angle=twist, angle_in_radians=False,translation_vec=(0, 0, 0))
#define tilt operation SymmOp object
tilt_op = SymmOp.from_axis_angle_and_translation(axis= tilt_normal,\
angle=tilt, angle_in_radians=False,translation_vec=(0, 0, 0))
upper.apply_operation(twist_op)
upper.to(fmt="poscar", filename="POSCAR_upper.vasp")
upper.apply_operation(tilt_op)
#define shift separation along twist vector normal to upper plane
shift = -1 * twist_shift_normal / np.linalg.norm(
twist_shift_normal) * separation
#define origin to shift w.r.t top of the lower grain
origin = np.array([0, 0, substrate_top_z])
#shift sites in upper
for site in upper:
new_coords = site.coords - origin + shift
lower.append(site.specie, new_coords, coords_are_cartesian=True)
return lower
def get_grain_boundary_interface(structure=None, hkl_pair= {'hkl': [[1,0,0],[1,1,0]],\
'thickness':[10,10]}, twist = 0, tilt = 0, separation=0):
"""
Args:
structure: pymatgen structure to create grain boundary in
hkl_pair: dict of {'hkl':thickness}
twist: twist in degrees
tilt: tilt in degrees
"""
structure = get_struct_from_mp(structure, MAPI_KEY="")
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
structure = structure_conventional.copy()
structure.sort()
#creation of lower part of grain boundary
lower= Interface(structure,\
hkl = hkl_pair['hkl'][0],
min_thick = hkl_pair['thickness'][0],
min_vac = separation+hkl_pair['thickness'][1],
primitive = False, from_ase = True, center_slab=False)
lower.to(fmt="poscar", filename="POSCAR_lower.vasp")
#creation of upper part of grain boundary
upper= Interface(structure,\
hkl = hkl_pair['hkl'][1],
min_thick = hkl_pair['thickness'][1],
min_vac = 0,
primitive = False, from_ase = True)
#find top atoms reference of lower part of gb
substrate_top_z = np.max(np.array([site.coords for site in lower])[:,2])
# define twist and tilt vectors
twist_shift_normal = lower.lattice.matrix[2,:]/\
np.linalg.norm(lower.lattice.matrix[2,:])
tilt_normal = upper.lattice.matrix[1,:]/\
np.linalg.norm(upper.lattice.matrix[2,:])
#define twist operation SymmOp object
twist_op = SymmOp.from_axis_angle_and_translation(axis= twist_shift_normal,\
angle=twist, angle_in_radians=False,translation_vec=(0, 0, 0))
#define tilt operation SymmOp object
tilt_op = SymmOp.from_axis_angle_and_translation(axis= tilt_normal,\
angle=tilt, angle_in_radians=False,translation_vec=(0, 0, 0))
upper.apply_operation(twist_op)
upper.to(fmt="poscar", filename="POSCAR_upper.vasp")
upper.apply_operation(tilt_op)
#define shift separation along twist vector normal to upper plane
shift = -1*twist_shift_normal/np.linalg.norm(twist_shift_normal) * separation
#define origin to shift w.r.t top of the lower grain
origin = np.array([0,0, substrate_top_z])
#shift sites in upper
for site in upper:
new_coords = site.coords - origin + shift
lower.append(site.specie, new_coords, coords_are_cartesian=True)
return lower
# 2d material vacuum spacing = 0
# keep in mind that the 2d material will be put on top of
# the subtrate in the substrate's vacuum space.
# So ensure that the substrate vacuum spacing is sufficietly
# large enough to contain the 2d material
substrate = Interface(substrate_bulk,
hkl = [1,1,0],
min_thick = 10,
min_vac = 25,
primitive = False, from_ase = True)
mat2d = Interface(mat2d_bulk,
hkl = [1,1,0],
min_thick = 2,
min_vac = 0,
primitive = False, from_ase = True)
substrate.to(fmt='poscar', filename='POSCAR_substrate_initial.vasp')
mat2d.to(fmt='poscar', filename='POSCAR_mat2d_initial.vasp')
# get the matching substrate and 2D material lattices
uv_substrate, uv_mat2d = get_matching_lattices(substrate, mat2d,
max_area = 200,
max_mismatch = 0.01,
max_angle_diff = 1,
r1r2_tol = 0.02)
# map the intial slabs to the newly found matching lattices
substrate_latt = Lattice( np.array(
[ uv_substrate[0][:],
uv_substrate[1][:],
substrate.lattice.matrix[2,:]
] ))
ligand=hydrazine,
displacement=displacement,
adatom_on_lig="N",
adsorb_on_species="Pb",
primitive=False,
)
iface.create_interface()
iface.sort()
# extract bare slab
iface_slab = iface.slab
iface_slab.sort()
# set selective dynamics flags as required
true_site = [1, 1, 1]
false_site = [0, 0, 0]
sd_flag_iface = []
sd_flag_slab = []
# selective dynamics flags for the interface
for i in iface.sites:
sd_flag_iface.append(false_site)
# selective dynamics flags for the bare slab
for i in iface_slab.sites:
sd_flag_slab.append(false_site)
interface_poscar = Poscar(iface, selective_dynamics=sd_flag_iface)
slab_poscar = Poscar(iface_slab, selective_dynamics=sd_flag_slab)
# poscars without selective dynamics flag
iface.to("poscar", "POSCAR_interface.vasp")
iface_slab.to("poscar", "POSCAR_slab.vasp")
# poscars with selective dynamics flag
interface_poscar.write_file("POSCAR_interface_with_sd.vasp")
slab_poscar.write_file("POSCAR_slab_with_sd.vasp")
