mat2d.lattice.matrix[0, :], mat2d.lattice.matrix[1, :],
substrate.lattice.matrix[2, :]
]))
substrate.modify_lattice(lmap)
# put the 2d material on top of the substrate
# seperation between the 2dmaterial and the substrate in angstroms
seperation = 5
substrate_top_z = np.max(
np.array([site.coords for site in substrate])[:, 2])
# shift origin and vector
shift = substrate.lattice.matrix[2, :]
shift = shift / np.linalg.norm(shift) * seperation
origin = np.array([0, 0, substrate_top_z])
for site in mat2d:
new_coords = site.coords - origin + shift
substrate.append(site.specie, new_coords, coords_are_cartesian=True)
substrate.to(fmt='poscar', filename='POSCAR_final.vasp')
# structure from materials project, use your own key
# gaas = get_struct_from_mp('GaAs', MAPI_KEY="")
# sa_gaas = SpacegroupAnalyzer(gaas)
# gaas_cvn = sa_gaas.get_conventional_standard_structure()
# gaas_cvn.to(fmt='poscar', filename='POSCAR_GaAs.vasp')
# cdte = get_struct_from_mp('CdTe', MAPI_KEY="")
# sa_cdte = SpacegroupAnalyzer(cdte)
# cdte_cvn = sa_cdte.get_conventional_standard_structure()
# cdte_cvn.to(fmt='poscar', filename='POSCAR_CdTe.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
mat2d.lattice.matrix[1,:],
substrate.lattice.matrix[2,:]
] ) )
substrate.modify_lattice(lmap)
# put the 2d material on top of the substrate
# seperation between the 2dmaterial and the substrate in angstroms
seperation = 5
substrate_top_z = np.max(np.array([site.coords for site in substrate])[:,2])
# shift origin and vector
shift = substrate.lattice.matrix[2,:]
shift = shift/np.linalg.norm(shift) * seperation
origin = np.array([0,0, substrate_top_z])
for site in mat2d:
new_coords = site.coords - origin + shift
substrate.append(site.specie, new_coords, coords_are_cartesian=True)
substrate.to(fmt='poscar', filename='POSCAR_final.vasp')
#structure from materials project, use your own key
#gaas = get_struct_from_mp('GaAs', MAPI_KEY="")
#sa_gaas = SpacegroupAnalyzer(gaas)
#gaas_cvn = sa_gaas.get_conventional_standard_structure()
#gaas_cvn.to(fmt='poscar', filename='POSCAR_GaAs.vasp')
#cdte = get_struct_from_mp('CdTe', MAPI_KEY="")
#sa_cdte = SpacegroupAnalyzer(cdte)
#cdte_cvn = sa_cdte.get_conventional_standard_structure()
#cdte_cvn.to(fmt='poscar', filename='POSCAR_CdTe.vasp')