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
```terminal
pwd
```
/mnt/ssd_elecom_c2c_960gb/scripts/mk_polyatomic_ion_replaced_point_poscar


### 使い方の確認（四面体形）
```terminal
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 <arg1> <arg2> <arg3> <arg4> <arg5> <arg6>
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）
```terminal
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
+ 1000183
![image.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3487151/9464b20d-ca3e-20eb-12b9-81eccdbf0973.png)

+ 1000235
![image.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3487151/2b63981c-b88b-1523-0147-64dbec8c6d1c.png)
![image.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3487151/9359e45d-30e3-8c1b-aeaa-90f32eabedd9.png)



### 使い方の確認（三角錐形・平面三角形）
```terminal
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 <arg1> <arg2> <arg3> <arg4> <arg5> <arg6>
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）
```terminal
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


+ 1000033
![image.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3487151/a54fa9d2-5f00-6635-fab9-627efc55d498.png)


+ 9008283
![image.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3487151/404795b3-1dc6-bd3e-1ae6-e5cd9ecd0de3.png)
![image.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3487151/b87d9adb-a2ac-500d-63b5-66ae70fa47ed.png)


+ 9008272
![image.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3487151/f2c10f39-bd0f-389f-a52f-bd0dadd263fb.png)
![image.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3487151/fc810f82-61b8-72d1-46cd-829d0618e5cd.png)