四面体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_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py -h

usage: get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py
example: python3 get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py NH4 N H 0.82 1.24 ../get_some_speceis_existed_poscar_path_list/N_H_existed_poscar_folder_path_list.npy

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

positional arguments:
arg1 target_ion_name: NH4
arg2 central_atom_symbol: N
arg3 neighboring_atom_symbol: H
arg4 bond_length_lower_end: 0.82
arg5 bond_length_upper_end: 1.24
arg6 npy_file_path: ../get_some_speceis_existed_poscar_path_list/N_H_existed_poscar_folder_path_list.npy

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

NH4（アンモニウムイオン）

python3 get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py NH4 N H 0.82 1.24 ../get_some_speceis_existed_poscar_path_list/N_H_existed_poscar_folder_path_list.npy

target_ion_name: NH4
central_atom_symbol: N
neighboring_atom_symbol: H
bond_length_lower_end: 0.82
bond_length_upper_end: 1.24
target_npy_p: ../get_some_speceis_existed_poscar_path_list/N_H_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 210889
62%|█████████████████████████████████████████████████████████████████████▉ | 131793/210889 [30:44<20:47, 63.39it/s]100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 210889/210889 [53:26<00:00, 65.77it/s]
len(NH4_contained_poscar_folder_path_list)/len(N_H_existed_poscar_folder_path_list.npy) :647/210889

real 53m42.853s
user 253m34.894s
sys 13m0.662s

PH4（ホスホニウムイオン）

python3 get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py PH4 P H 1.14 1.72 ../get_some_speceis_existed_poscar_path_list/P_H_existed_poscar_folder_path_list.npy

target_ion_name: PH4
central_atom_symbol: P
neighboring_atom_symbol: H
bond_length_lower_end: 1.14
bond_length_upper_end: 1.72
target_npy_p: ../get_some_speceis_existed_poscar_path_list/P_H_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 39122
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 39122/39122 [10:15<00:00, 63.52it/s]
len(PH4_contained_poscar_folder_path_list)/len(P_H_existed_poscar_folder_path_list.npy) :0/39122

real 10m18.127s
user 46m22.068s
sys 3m29.873s

AlCl4（テトラクロロアルミン酸イオン）

python3 get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py AlCl4 Al Cl 1.80 2.70 ../get_some_speceis_existed_poscar_path_list/Al_Cl_existed_poscar_folder_path_list.npy

target_ion_name: AlCl4
central_atom_symbol: Al
neighboring_atom_symbol: Cl
bond_length_lower_end: 1.80
bond_length_upper_end: 2.70
target_npy_p: ../get_some_speceis_existed_poscar_path_list/Al_Cl_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 577
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 577/577 [00:08<00:00, 67.93it/s]
len(AlCl4_contained_poscar_folder_path_list)/len(Al_Cl_existed_poscar_folder_path_list.npy) :170/577

real 0m9.118s
user 0m39.099s
sys 0m4.254s

BF4（テトラフルオロホウ酸イオン）

python3 get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py BF4 B F 1.19 1.79 ../get_some_speceis_existed_poscar_path_list/B_F_existed_poscar_folder_path_list.npy

target_ion_name: BF4
central_atom_symbol: B
neighboring_atom_symbol: F
bond_length_lower_end: 1.19
bond_length_upper_end: 1.79
target_npy_p: ../get_some_speceis_existed_poscar_path_list/B_F_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 7284
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 7284/7284 [02:23<00:00, 50.63it/s]
len(BF4_contained_poscar_folder_path_list)/len(B_F_existed_poscar_folder_path_list.npy) :2748/7284

real 2m24.918s
user 11m46.057s
sys 0m52.634s

BH4（水素化ホウ素イオン）

python3 get_tetrahedral_shape_ion_contained_pos_folder_p_
list_argparse.py BH4 B H 0.94 1.40 ../get_some_speceis_existed_poscar_path_list/B_H_existed_poscar_folder_path_list.npy

target_ion_name: BH4
central_atom_symbol: B
neighboring_atom_symbol: H
bond_length_lower_end: 0.94
bond_length_upper_end: 1.40
target_npy_p: ../get_some_speceis_existed_poscar_path_list/B_H_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 19044
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 19044/19044 [04:38<00:00, 68.39it/s]
len(BH4_contained_poscar_folder_path_list)/len(B_H_existed_poscar_folder_path_list.npy) :209/19044

real 4m40.383s
user 21m36.656s
sys 1m27.584s

ClO4（過塩素酸イオン）

python3 get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py ClO4 Cl O 1.22 1.94 ../get_some_speceis_existed_poscar_path_list/Cl_O_existed_poscar_folder_path_list.npy

target_ion_name: ClO4
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 [09:05<00:00, 69.24it/s]
len(ClO4_contained_poscar_folder_path_list)/len(Cl_O_existed_poscar_folder_path_list.npy) :4189/37770

real 9m8.364s
user 41m28.240s
sys 2m55.084s

MnO4（マンガン酸イオン）

python3 get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py MnO4 Mn O 1.30 2.18 ../get_some_speceis_existed_poscar_path_list/Mn_O_existed_poscar_folder_path_list.npy

target_ion_name: MnO4
central_atom_symbol: Mn
neighboring_atom_symbol: O
bond_length_lower_end: 1.30
bond_length_upper_end: 2.18
target_npy_p: ../get_some_speceis_existed_poscar_path_list/Mn_O_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 5028
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5028/5028 [00:56<00:00, 89.01it/s]
len(MnO4_contained_poscar_folder_path_list)/len(Mn_O_existed_poscar_folder_path_list.npy) :120/5028

real 0m58.189s
user 3m39.622s
sys 0m17.247s

SO4（硫酸イオン）

python3 get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py SO4 S O 1.21 1.99 ../get_some_speceis_existed_poscar_path_list/S_O_existed_poscar_folder_path_list.npy

target_ion_name: SO4
central_atom_symbol: S
neighboring_atom_symbol: O
bond_length_lower_end: 1.21
bond_length_upper_end: 1.99
target_npy_p: ../get_some_speceis_existed_poscar_path_list/S_O_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 42415
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 42415/42415 [09:54<00:00, 71.34it/s]
len(SO4_contained_poscar_folder_path_list)/len(S_O_existed_poscar_folder_path_list.npy) :1855/42415

real 9m57.118s
user 42m39.867s
sys 3m50.979s

SeO4（セレン酸イオン）

python3 get_tetrahedral_shape_ion_contained_pos_folder_p_list_argparse.py SeO4 Se O 1.31 2.15 ../get_some_speceis_existed_poscar_path_list/Se_O_existed_poscar_folder_path_list.npy

target_ion_name: SeO4
central_atom_symbol: Se
neighboring_atom_symbol: O
bond_length_lower_end: 1.31
bond_length_upper_end: 2.15
target_npy_p: ../get_some_speceis_existed_poscar_path_list/Se_O_existed_poscar_folder_path_list.npy
os.path.exists(target_npy_p): True
len(some_species_existed_poscar_folder_path_list): 2224
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2224/2224 [00:27<00:00, 80.25it/s]
len(SeO4_contained_poscar_folder_path_list)/len(Se_O_existed_poscar_folder_path_list.npy) :159/2224

real 0m28.284s
user 2m1.873s
sys 0m10.405s

real 86m8.918s
user 398m32.125s
sys 24m23.922s