def remove_noncoord_oxygens(
atoms=None,
):
"""
"""
#| - remove_noncoord_oxygens
df_coord_slab_i = get_structure_coord_df(atoms)
# #########################################################
df_i = df_coord_slab_i[df_coord_slab_i.element == "O"]
df_i = df_i[df_i.num_neighbors == 0]
o_atoms_to_remove = df_i.structure_index.tolist()
# #########################################################
o_atoms_to_remove_1 = []
df_j = df_coord_slab_i[df_coord_slab_i.element == "O"]
for j_cnt, row_j in df_j.iterrows():
neighbor_count = row_j.neighbor_count
if neighbor_count.get("Ir", 0) == 0:
if neighbor_count.get("O", 0) == 1:
o_atoms_to_remove_1.append(row_j.structure_index)
o_atoms_to_remove = list(set(o_atoms_to_remove + o_atoms_to_remove_1))
slab_new = remove_atoms(atoms, atoms_to_remove=o_atoms_to_remove)
return(slab_new)
def remove_highest_metal_atoms(
atoms=None,
num_atoms_to_remove=None,
metal_atomic_number=77,
):
"""
"""
#| - remove_highest_metal_atom
slab_m = atoms[atoms.numbers == metal_atomic_number]
positions_cpy = copy.deepcopy(slab_m.positions)
positions_cpy_sorted = positions_cpy[positions_cpy[:,2].argsort()]
indices_to_remove = []
for coord_i in positions_cpy_sorted[-2:]:
for i_cnt, atom in enumerate(atoms):
if all(atom.position == coord_i):
indices_to_remove.append(i_cnt)
slab_new = remove_atoms(
atoms=atoms,
atoms_to_remove=indices_to_remove,
)
return(slab_new)
def remove_nonsaturated_surface_metal_atoms(
atoms=None,
dz=None,
):
"""
"""
#| - remove_nonsaturated_surface_metal_atoms
# #################################################
# #################################################
z_positions = atoms.positions[:,2]
z_max = np.max(z_positions)
z_min = np.min(z_positions)
# #################################################
# #################################################
df_coord_slab_i = get_structure_coord_df(atoms)
# #################################################
metal_atoms_to_remove = []
for atom in atoms:
if atom.symbol == metal_atom_symbol:
z_pos_i = atom.position[2]
if z_pos_i >= z_max - dz or z_pos_i <= z_min + dz:
row_coord = df_coord_slab_i[
df_coord_slab_i.structure_index == atom.index].iloc[0]
num_o_neighbors = row_coord.neighbor_count.get("O", 0)
if num_o_neighbors < 6:
metal_atoms_to_remove.append(atom.index)
slab_new = remove_atoms(atoms=atoms, atoms_to_remove=metal_atoms_to_remove)
return(slab_new)
o_atoms_to_remove = df_i.structure_index.tolist()
# #########################################################
o_atoms_to_remove_1 = []
df_j = df_coord_slab_i[df_coord_slab_i.element == "O"]
for j_cnt, row_j in df_j.iterrows():
neighbor_count = row_j.neighbor_count
if neighbor_count.get("Ir", 0) == 0:
if neighbor_count.get("O", 0) == 1:
o_atoms_to_remove_1.append(row_j.structure_index)
o_atoms_to_remove = list(set(o_atoms_to_remove + o_atoms_to_remove_1))
slab_new = remove_atoms(atoms, atoms_to_remove=o_atoms_to_remove)
# +
# slab_new.write()
slab_new.write("out_data/temp_out/slab_1.cif")
# + active=""
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