多原子イオンを点置換した新しい結晶構造作成例（四面体形・三角錐形・平面三角形）

現在地

pwd

/mnt/ssd_elecom_c2c_960gb/scripts/mk_polyatomic_ion_replaced_point_poscar

使い方の確認（四面体形）

python3 do_mk_polyatomic_ion_replaced_point_poscar_for_tetrahedral_shape.py -h

usage: do_mk_polyatomic_ion_replaced_point_poscar_for_tetrahedral_shape.py
example: python3 do_mk_polyatomic_ion_replaced_point_poscar_for_tetrahedral_shape.py NH4 N H 0.82 1.24 ../get_some_ion_contained_pos_folder_p_list/NH4_contained_poscar_folder_path_list_ver2.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_ion_contained_pos_folder_p_list/NH4_contained_poscar_folder_path_list_ver2.npy

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

実行（四面体形：ここでは，アンモニウムイオン）

time python3 do_mk_polyatomic_ion_replaced_point_poscar_for_tetrahedra
l_shape.py NH4 N H 0.82 1.24 ../get_some_ion_contained_pos_folder_p_list/NH4_contained_poscar_folder_path_list_ver2.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_ion_contained_pos_folder_p_list/NH4_contained_poscar_folder_path_list_ver2.npy
os.path.exists(target_npy_p): True
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 647/647 [00:17<00:00, 37.57it/s]

real 0m17.812s
user 1m33.671s
sys 0m6.334s

オリジナルのPOSCARファイルとアンモニウムイオンを点で置換したPOSCARファイルを比較

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使い方の確認（三角錐形・平面三角形）

python3 do_mk_polyatomic_ion_replaced_point_poscar_for_trigonal_pyramidal_planar_shape.py -h

usage: do_mk_polyatomic_ion_replaced_point_poscar_for_trigonal_pyramidal_planar_shape.py
example: python3 do_mk_polyatomic_ion_replaced_point_poscar_for_trigonal_pyramidal_planar_shape.py CO3 C O 0.99 1.66 ../get_some_ion_contained_pos_folder_p_list/CO3_contained_poscar_folder_path_list_ver2.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_ion_contained_pos_folder_p_list/CO3_contained_poscar_folder_path_list_ver2.npy

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

実行（三角錐形・平面三角形：ここでは，炭酸イオン）

time python3 do_mk_polyatomic_ion_replaced_point_poscar_for_trigonal_p
yramidal_planar_shape.py CO3 C O 0.99 1.66 ../get_some_ion_contained_pos_folder_p_list/CO3_contained_poscar_folder_path_list_ver2.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_ion_contained_pos_folder_p_list/CO3_contained_poscar_folder_path_list_ver2.npy
os.path.exists(target_npy_p): True
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1143/1143 [00:47<00:00, 23.87it/s]

real 0m48.528s
user 4m8.260s
sys 0m10.425s

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