def create_min_thickness_slab(structure,
index,
num_termination_min,
layerthickness,
layer_subtractions,
tol,
min_thickness=10):
#Find final_slabthickness such that the cleaned slab is a least min_thickness thick after layer_subtractions times the average layerthickness
#Cleaning consists of removing one layer on each side and then ensuring that the number of atomic layers is multiples of the number of unique terminations
slabthickness = min_thickness
final_slabthickness = 0
while final_slabthickness < min_thickness + layerthickness * layer_subtractions:
final_slab = SlabGenerator(structure,
index,
min_slab_size=slabthickness,
min_vacuum_size=5,
primitive=True,
center_slab=True,
in_unit_planes=False,
max_normal_search=7).get_slab()
final_slabthickness = np.max(final_slab.cart_coords[:, 2]) - np.min(
final_slab.cart_coords[:, 2])
slabthickness += 2 #increase slabthickness for potential next iteration
if final_slabthickness > 5: #Ensure that slab is thick enough for subtractions
#"Clean" the two outside surfaces, pymatgen makes weird terminations sometimes
min_value = np.min(final_slab.cart_coords[:, 2])
first_layer_size = len(
np.where(
np.abs(min_value - final_slab.cart_coords[:, 2]) < tol)[0])
for i in range(first_layer_size):
index_to_remove = np.argmin(final_slab.frac_coords[:, 2])
final_slab.remove_sites([index_to_remove])
max_value = np.max(final_slab.cart_coords[:, 2])
first_layer_size = len(
np.where(
np.abs(max_value - final_slab.cart_coords[:, 2]) < tol)[0])
for i in range(first_layer_size):
index_to_remove = np.argmax(final_slab.frac_coords[:, 2])
final_slab.remove_sites([index_to_remove])
nlayers = number_of_atomic_layers(final_slab, tol)
#Delete all layers that are not multiple of num_termination_min (e.g. make ABCABCAB -> ABCABC; important for slabs with mirror symmetry)
n_extra_layers = nlayers % num_termination_min
if n_extra_layers != 0 and n_extra_layers < nlayers:
for layer in range(n_extra_layers):
max_value = np.max(final_slab.cart_coords[:, 2])
first_layer_size = len(
np.where(
np.abs(max_value -
final_slab.cart_coords[:, 2]) < tol)[0])
for i in range(first_layer_size):
index_to_remove = np.argmax(final_slab.frac_coords[:,
2])
final_slab.remove_sites([index_to_remove])
final_slabthickness = np.max(
final_slab.cart_coords[:, 2]) - np.min(
final_slab.cart_coords[:, 2])
while final_slabthickness - 1.3 * num_termination_min * layerthickness > min_thickness + layerthickness * layer_subtractions:
for nterm in range(num_termination_min):
max_value = np.max(final_slab.cart_coords[:, 2])
first_layer_size = len(
np.where(
np.abs(max_value - final_slab.cart_coords[:, 2]) < tol)[0])
for i in range(first_layer_size):
index_to_remove = np.argmax(final_slab.frac_coords[:, 2])
final_slab.remove_sites([index_to_remove])
final_slabthickness = np.max(final_slab.cart_coords[:, 2]) - np.min(
final_slab.cart_coords[:, 2])
return final_slab
