def cleave_operation():
struct = readstructure()
if isinstance(Structure, Molecule):
print("cleave operation is only supported for periodic structure")
return
print('your choice ?')
print('{} >>> {}'.format('1', 'cleave surface'))
print('{} >>> {}'.format('2', 'cleave sphere cluster'))
print('{} >>> {}'.format('3', 'cleave shell structure'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
print(
" input the miller index, minimum size in angstroms of layers containing atomssupercell"
)
print(
" and Minimize size in angstroms of layers containing vacuum like this:"
)
print(' 1 0 0 | 5 | 5')
print(' it means miller index is [1,0,0]')
print(" min_slab_size is 5 Ang ")
print(" min_vacum_size is 5 Ang ")
print(" or like this : ")
print(' 2 | 5 | 5')
print(' it will generate all slab with miller index less than 2')
def generate_selected_slab(in_str):
tmp_list = in_str.split('|')
miller_index = [int(x) for x in tmp_list[0].strip().split()]
min_slab_size = float(tmp_list[1])
min_vac_size = float(tmp_list[2])
slab = SlabGenerator(struct,
miller_index,
min_slab_size=min_slab_size,
min_vacuum_size=min_vac_size,
lll_reduce=True)
slab_struct = slab.get_slab()
slab_struct.sort()
miller_str = [str(i) for i in miller_index]
filename = '_'.join(miller_str) + '.vasp'
slab_struct.to(filename=filename, fmt='POSCAR')
def generate_all_slab(in_str):
tmp_list = in_str.split('|')
max_index = int(tmp_list[0])
min_slab_size = float(tmp_list[1])
min_vac_size = float(tmp_list[2])
slabs = generate_all_slabs(struct,
max_index=max_index,
min_slab_size=min_slab_size,
min_vacuum_size=min_vac_size,
lll_reduce=True)
for slab_struct in slabs:
slab_struct.sort()
miller_str = [str(i) for i in slab_struct.miller_index]
filename = '_'.join(miller_str) + '.vasp'
slab_struct.to(filename=filename, fmt='POSCAR')
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
len_para = len(in_str.split('|')[0].split())
#if in_str.strip().startswith('a'):
if len_para == 3:
generate_selected_slab(in_str)
#elif in_str.strip().startswith('b'):
elif len_para == 1:
generate_all_slab(in_str)
else:
print("unknow format")
os._exit()
elif choice == 2:
print(
" input the center atom index, sphere radius and vacuum layer thickness"
)
print(' 1 3.5 15')
print(
' it means the sphere will be selected according to the 1st atom')
print(
" with the radius equals 5Ang, and vacuum layer thickness is 15 Ang"
)
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
para = in_str.split()
center_atom = int(para[0]) - 1
radius = float(para[1])
vacuum = float(para[2])
center_coord = struct[center_atom].coords
sites = struct.get_neighbors_in_shell(center_coord, 0, radius)
coords = [site[0].coords for site in sites]
species = [site[0].specie for site in sites]
mol = Molecule(coords=coords, species=species)
max_dist = np.max(mol.distance_matrix)
a = b = c = max_dist + vacuum
box_struct = mol.get_boxed_structure(a, b, c)
file_name = "sphere.vasp"
box_struct.to(filename=file_name, fmt='poscar')
elif choice == 3:
print(
" input the center atom index, start radius, shell thickness and")
print(" vacuum layer thickness")
print(' 1 5 10 15')
print(
' it means the ball shell will be selected according to the 1st atom'
)
print(" with the 5< r <15Ang, and vacuum layer thickness is 15 Ang")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
para = in_str.split()
center_atom = int(para[0]) - 1
radius = float(para[1])
shell = float(para[2])
vacuum = float(para[3])
center_coord = struct[center_atom].coords
sites = struct.get_neighbors_in_shell(center_coord, radius, shell)
coords = [site[0].coords for site in sites]
species = [site[0].specie for site in sites]
mol = Molecule(coords=coords, species=species)
max_dist = np.max(mol.distance_matrix)
a = b = c = max_dist + vacuum
box_struct = mol.get_boxed_structure(a, b, c)
file_name = "shell.vasp"
box_struct.to(filename=file_name, fmt='poscar')
else:
print("unkown choice")
return
