三角錐形または平面三角形の多原子イオン抽出スクリプトの取説

スクリプトの実行方法確認

python3 get_trigonal_pyramidal_planar_shape_ion_contained_pos_folder_p_list.py -h

usage: get_trigonal_pyramidal_planar_shape_ion_contained_pos_folder_p_list.py
example: python3 get_trigonal_pyramidal_planar_shape_ion_contained_pos_folder_p_list.py CO3 C O 0.99 1.66 ../get_some_speceis_existed_poscar_path_list/C_O_existed_poscar_folder_path_list.npy

This script takes five arguments: arg1, arg2, arg3, arg4, arg5 and arg6.

positional arguments:
arg1 target_ion_name: CO3
arg2 central_atom_symbol: C
arg3 neighboring_atom_symbol: O
arg4 bond_length_lower_end: 0.99
arg5 bond_length_upper_end: 1.66
arg6 npy_file_path: ../get_some_speceis_existed_poscar_path_list/C_O_existed_poscar_folder_path_list.npy

options:
-h, --help show this help message and exit

CO3（炭酸イオン）

time python3 get_trigonal_pyramidal_planar_shape_ion_contained_pos_folder_p_list.py CO3 C O 0.99 1.66 ../get_some_speceis_existed_poscar_path_list/C_O_existed_poscar_folder_path_list.npy

target_ion_name: CO3
central_atom_symbol: C
neighboring_atom_symbol: O
bond_length_lower_end: 0.99
bond_length_upper_end: 1.66
target_npy_p: ../get_some_speceis_existed_poscar_path_list/C_O_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 205733
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████| 205733/205733 [2:17:51<00:00, 24.87it/s]
len(CO3_contained_poscar_folder_path_list)/len(C_O_existed_poscar_folder_path_list.npy) :1143/205733

IO3（ヨウ化物イオン）

time python3 get_trigonal_pyramidal_planar_shape_ion_contained_pos_folder_p_list.py IO3 I O 1.49 2.35 ../get_some_speceis_existed_poscar_path_list/I_O_existed_poscar_folder_path_list.npy

target_ion_name: IO3
central_atom_symbol: I
neighboring_atom_symbol: O
bond_length_lower_end: 1.49
bond_length_upper_end: 2.35
target_npy_p: ../get_some_speceis_existed_poscar_path_list/I_O_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 5599
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5599/5599 [00:59<00:00, 94.10it/s]
len(IO3_contained_poscar_folder_path_list)/len(I_O_existed_poscar_folder_path_list.npy) :200/5599

real 1m0.899s
user 3m44.632s
sys 0m20.817s

集化物イオン（BrO3）

time python3 get_trigonal_pyramidal_planar_shape_ion_contained_pos_folder_p_list.py BrO3 Br O 1.33 2.12 ../get_some_speceis_existed_poscar_path_list/Br_O_existed_poscar_folder_path_list.npy

target_ion_name: BrO3
central_atom_symbol: Br
neighboring_atom_symbol: O
bond_length_lower_end: 1.33
bond_length_upper_end: 2.12
target_npy_p: ../get_some_speceis_existed_poscar_path_list/Br_O_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 12652
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 12652/12652 [02:33<00:00, 82.49it/s]
len(BrO3_contained_poscar_folder_path_list)/len(Br_O_existed_poscar_folder_path_list.npy) :20/12652

real 2m34.264s
user 9m21.967s
sys 0m54.363s

亜塩素酸イオン（ClO3）

time python3 get_trigonal_pyramidal_planar_shape_ion_contained_pos_folder_p_list.py ClO3 Cl O 1.22 1.94 ../get_some_speceis_existed_poscar_path_list/Cl_O_existed_poscar_folder_path_list.npy

target_ion_name: ClO3
central_atom_symbol: Cl
neighboring_atom_symbol: O
bond_length_lower_end: 1.22
bond_length_upper_end: 1.94
target_npy_p: ../get_some_speceis_existed_poscar_path_list/Cl_O_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 37770
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 37770/37770 [08:35<00:00, 73.21it/s]
len(ClO3_contained_poscar_folder_path_list)/len(Cl_O_existed_poscar_folder_path_list.npy) :95/37770

real 8m38.958s
user 34m18.824s
sys 2m42.441s

NO3（硝酸イオン）

time python3 get_trigonal_pyramidal_planar_shape_ion_contained_pos_folder_p_list.py NO3 N O 0.94 1.61 ../get_some_speceis_existed_poscar_path_list/N_O_existed_poscar_folder_path_list.npy

target_ion_name: NO3
central_atom_symbol: N
neighboring_atom_symbol: O
bond_length_lower_end: 0.94
bond_length_upper_end: 1.61
target_npy_p: ../get_some_speceis_existed_poscar_path_list/N_O_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 160297
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 160297/160297 [40:54<00:00, 65.30it/s]
len(NO3_contained_poscar_folder_path_list)/len(N_O_existed_poscar_folder_path_list.npy) :5242/160297

real 41m4.198s
user 179m10.998s
sys 8m50.313s

real 53m18.345s
user 226m36.427s
sys 12m47.936s