## Usages

### General commands

| A                                              | B    | C                                                            | D       | E                 |
| ---------------------------------------------- | ---- | ------------------------------------------------------------ | ------- | ----------------- |
| [array2str](./general_commands/array2str.html) |      | [cut_lmp](./general_commands/cut_lmp.html)                   | density | exchange_position |
| [add_atoms](./general_commands/add_atoms.html) |      | [cut_lmp_atoms](./general_commands/cut_lmp_atoms_etc.html)   |         | extract_substring |
| [addH](./general_commands/addH.html)           |      | [cut_lmp_atoms_etc](./general_commands/cut_lmp_atoms_etc.html) |         |                   |
|                                                |      | combine_lmp                                                  |         |                   |
|                                                |      | coord2zero                                                   |         |                   |
|                                                |      | change_lmp_axis                                              |         |                   |
|                                                |      |                                                              |         |                   |
|                                                |      |                                                              |         |                   |

| F    | I    | G    | K    | L             |
| ---- | ---- | ---- | ---- | ------------- |
|      |      |      |      | lmp2xyz       |
|      |      |      |      | lmp2lammpstrj |
|      |      |      |      | lmp2tip4p     |
|      |      |      |      |               |
|      |      |      |      |               |
|      |      |      |      |               |
|      |      |      |      |               |
|      |      |      |      |               |

| M                | N    | O    | P                                                            | Q    |
| ---------------- | ---- | ---- | ------------------------------------------------------------ | ---- |
| msi2clayff       |      |      | pdb2xyz                                                      |      |
| msi2clayff_OH    |      |      | print_version                                                |      |
| modify_header    |      |      | print_line                                                   |      |
| modify_pos       |      |      | [periodic2interface](./general_commands/periodic2interface.html) |      |
| modify_pore_size |      |      |                                                              |      |
| move_boundary    |      |      |                                                              |      |
|                  |      |      |                                                              |      |
|                  |      |      |                                                              |      |

| R                 | S                                              | T    | U    | V    |
| ----------------- | ---------------------------------------------- | ---- | ---- | ---- |
| read_box          | sort_lmp                                       |      |      |      |
| read_data         | sort_tip4p_ele                                 |      |      |      |
| read_data_sub     | [str2array](./general_commands/str2array.html) |      |      |      |
| read_vol          |                                                |      |      |      |
| read_xyz          |                                                |      |      |      |
| read_pdb          |                                                |      |      |      |
| read_charges      |                                                |      |      |      |
| read_atom_info    |                                                |      |      |      |
| read_terms        |                                                |      |      |      |
| read_len          |                                                |      |      |      |
| read_mass         |                                                |      |      |      |
| read_total_mass   |                                                |      |      |      |
| replace_term_info |                                                |      |      |      |
| read_formula      |                                                |      |      |      |
|                   |                                                |      |      |      |
|                   |                                                |      |      |      |

| W    | X    | Y    | Z    |      |
| ---- | ---- | ---- | ---- | ---- |
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