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)
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 get_df_coord_local(
name=None,
ads=None,
atoms=None,
append_str=None,
):
"""
"""
# | - get_df_coord_local
directory = os.path.join(os.environ["PROJ_irox_oer"],
"workflow/seoin_irox_data/featurize_data",
"out_data/df_coord")
if append_str is not None:
file_name_i = name + "__" + ads + "__" + append_str + ".pickle"
else:
file_name_i = name + "__" + ads + ".pickle"
path_i = os.path.join(directory, file_name_i)
my_file = Path(path_i)
if my_file.is_file():
with open(path_i, "rb") as fle:
df_coord_i = pickle.load(fle)
else:
# Create df_coord
df_coord_i = get_structure_coord_df(
atoms,
porous_adjustment=True,
)
directory = os.path.join(os.environ["PROJ_irox_oer"],
"workflow/seoin_irox_data/featurize_data",
"out_data/df_coord")
# file_name_i = name + "__o" + ".pickle"
if not os.path.exists(directory):
os.makedirs(directory)
with open(os.path.join(directory, file_name_i), "wb") as fle:
pickle.dump(df_coord_i, fle)
return (df_coord_i)
def create_save_struct_coord_df(
slab_final=None,
slab_id=None,
):
"""
"""
#| - create_save_struct_coord_df
slab_id_i = slab_id
df_coord_slab_final = get_structure_coord_df(slab_final)
file_name_i = slab_id_i + ".pickle"
file_path_i = os.path.join(
os.environ["PROJ_irox_oer"],
"workflow/creating_slabs/out_data/df_coord_files", file_name_i)
my_file = Path(file_path_i)
if not my_file.is_file():
# df_coord_slab_final = get_structure_coord_df(slab_final)
with open(file_path_i, "wb") as fle:
pickle.dump(df_coord_slab_final, fle)
def process_sys(
slab_id=None,
slab=None,
path_pre=None,
mode="new", # 'new' or 'old'
):
"""
"""
#| - process_sys
if mode == "old":
str_append = ""
elif mode == "new":
str_append = "_after_rep"
path_i = os.path.join(
path_pre, slab_id + str_append + ".pickle")
with open(path_i, "rb") as fle:
df_coord_i = pickle.load(fle)
df_matches_slab_i = df_matches_slab(slab, df_coord_i)
df_coord_redone = None
if not df_matches_slab_i:
print("df_coord_" + mode + " is inconsistent with slab")
df_coord_redone = get_structure_coord_df(slab)
# print("path_i:", path_i)
with open(path_i, "wb") as fle:
# print("Writing file")
pickle.dump(df_coord_redone, fle)
# #####################################################
out_dict = dict()
# #####################################################
out_dict["df_matches_slab"] = df_matches_slab_i
out_dict["df_coord_redone"] = df_coord_redone
# #####################################################
return(out_dict)
# -
assert False
# +
slab_0 = io.read(
"out_data/final_slabs_2/zimuby8uzj__fagepuha_94__001.cif"
# "out_data/temp_out/slab_1_2.cif"
)
slab_0.write("out_data/temp_out/slab_0.cif")
atoms = slab_0
# +
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:
str(att_num_i) + \
""
# str(int(active_site_i)) + "__" + \
file_name_i += ".pickle"
directory = os.path.join(os.environ["PROJ_irox_oer"],
"workflow/creating_slabs/maintain_df_coord",
"out_data/df_coord__init_slabs")
path_i = os.path.join(directory, file_name_i)
# #####################################################
my_file = Path(path_i)
if not my_file.is_file():
df_coord_i = get_structure_coord_df(
init_atoms_i,
porous_adjustment=True,
)
if not os.path.exists(directory):
os.makedirs(directory)
with open(path_i, "wb") as fle:
pickle.dump(df_coord_i, fle)
# -
# ### Main Loop
df_slab_i = df_slab_i[df_slab_i.phase > 1]
if False:
iterator = tqdm(df_slab_i.index, desc="1st loop")
for i_cnt, slab_id_i in enumerate(iterator):
failed_to_sort_i = row_atoms_sorted_i.failed_to_sort
# #####################################################
if not failed_to_sort_i:
df_coord_i = get_df_coord(
mode="post-dft", # 'bulk', 'slab', 'post-dft'
post_dft_name_tuple=name_i,
)
if df_coord_i is None:
if verbose:
print("No df_coord found, running")
# #################################################
# Get df_coord for post-dft, sorted slab
df_coord_i = get_structure_coord_df(
atoms_sorted_good_i,
porous_adjustment=True,
)
# Pickling data ###################################
file_name_i = "_".join([str(i)
for i in list(name_new_i)]) + ".pickle"
file_path_i = os.path.join(directory, file_name_i)
print(file_path_i)
with open(file_path_i, "wb") as fle:
pickle.dump(df_coord_i, fle)
# #################################################
if "H" in df_coord_i.element.unique():
# if True:
df_coord_porous_adj_False_i = get_df_coord(
mode="post-dft", # 'bulk', 'slab', 'post-dft'
def constrain_slab(atoms=None, ):
"""Constrain lower portion of slab geometry.
Has a little bit of built in logic which should provide better slabs.
"""
#| - constrain_slab
slab = atoms
positions = slab.positions
z_pos = positions[:, 2]
z_max = np.max(z_pos)
z_min = np.min(z_pos)
# ang_of_slab_to_constrain = (2 / 4) * (z_max - z_min)
ang_of_slab_to_constrain = (z_max - z_min) - 6
# #########################################################
indices_to_constrain = []
for atom in slab:
if atom.symbol == metal_atom_symbol:
if atom.position[2] < (z_min + ang_of_slab_to_constrain):
indices_to_constrain.append(atom.index)
for atom in slab:
if atom.position[2] < (z_min + ang_of_slab_to_constrain - 2):
indices_to_constrain.append(atom.index)
df_coord_slab_i = get_structure_coord_df(slab)
# #########################################################
other_atoms_to_constrain = []
for ind_i in indices_to_constrain:
row_i = df_coord_slab_i[df_coord_slab_i.structure_index == ind_i]
row_i = row_i.iloc[0]
nn_info = row_i.nn_info
for nn_i in nn_info:
ind_j = nn_i["site_index"]
other_atoms_to_constrain.append(ind_j)
# print(len(indices_to_constrain))
indices_to_constrain.extend(other_atoms_to_constrain)
# print(len(indices_to_constrain))
# #########################################################
constrain_bool_mask = []
for atom in slab:
if atom.index in indices_to_constrain:
constrain_bool_mask.append(True)
else:
constrain_bool_mask.append(False)
# #########################################################
slab_cpy = copy.deepcopy(slab)
from ase.constraints import FixAtoms
c = FixAtoms(mask=constrain_bool_mask)
slab_cpy.set_constraint(c)
# slab_cpy.constraints
return (slab_cpy)
slab_final = row_i.slab_final
slab_id = row_i.slab_id
# #####################################################
if verbose_local:
print(40 * "*")
print("slab_id:", slab_id)
file_name_i = slab_id + "_after_rep" + ".pickle"
file_path_i = os.path.join(
os.environ["PROJ_irox_oer"],
"workflow/creating_slabs/out_data/df_coord_files", file_name_i)
my_file = Path(file_path_i)
if not my_file.is_file():
df_coord_slab_final = get_structure_coord_df(slab_final)
with open(file_path_i, "wb") as fle:
pickle.dump(df_coord_slab_final, fle)
else:
if verbose_local:
print("Already computed")
# + active=""
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