# Amorphous Oxides Structure Analysis 

```bash 
ai2-kit algorithm aosa
```

## Introduction
A set of tools and Python functions to analyze statistic properties of structure in amorphous oxides.

## Usage

### Effective Coordination Number (ECN)

```bash 
ai2-kit algorithm aosa ecn-analysis
```

This command is used to calculate the average bond length and effective coordination number in a given trajectory, and dump results as a new file.

#### Options
| Option | Description | Type | Default | Example |
| --- | --- | --- | --- | --- |
|input_traj|The trajectory you need to input for analysis.|str|(Required)|--input_traj ./in2o3-eq.xyz|
|out_dir|Dump the result of analysis `result (per frame)` and `average (average values)` in a new directory.|str|(Required)|--out_dir ./out|
|center|Reference atom (Central atom), in the format of [MDA select_atoms](https://docs.mdanalysis.org/stable/documentation_pages/selections.html)|str|(Required)|--center 'name In'|
|ligand|Configuration atom (Coordination atom), use the same format of `center` |str|(Required)|--ligand 'name O'|
|cell|Setting the parameters of the cell.|list[float]|(Required)|--cell '[10.2, 10.2, 10.2, 90, 90, 90]'|

#### Examples
We could run this method by the following command:
```bash
ai2-kit algorithm aosa ecn-analysis \
    --input_traj ./in2o3-eq.xyz \
    --out_dir ./out \
    --center 'name In' \
    --ligand 'name O' \
    --cell '[20.238452856, 20.23845286, 20.23845286, 90, 90, 90]' 
```

The output would be written in a new directory : `./out/raw.txt` and `./out/stat.txt`.

In the file `raw.txt`:
```bash
# frame_index   l_av   ECN
    0        2.1778   5.3359
    1        2.1793   5.3555
    2        2.1789   5.3492
    3        2.1771   5.3276
    4        2.1771   5.3290
    ...      ...      ...
```

In the file `stats.txt`:
```bash
l_av = 2.1752
ECN = 5.2832
```

### Counting Polyhedra

```bash 
ai2-kit algorithm aosa count-shared-polyhedra
```

This command is used to count the numbers and fractions of polyhedra linked in different forms, including "Corner-share", "Edge-share" and "Face-share".

#### Options
| Option | Description | Type | Default | Example |
| --- | --- | --- | --- | --- |
|input_traj|The trajectory you need to input for analysis.|str|(Required)|--input_traj ./in2o3-eq.xyz|
|out_dir|Dump the result of analysis `result (per frame)` and `average (average values)` in a new directory.|str|(Required)|--out_dir ./out |
|center|Reference atom (Central atom), in the format of [MDA select_atoms](https://docs.mdanalysis.org/stable/documentation_pages/selections.html)|str|(Required)|--center 'name In'|
|ligand |Configuration atom (Coordination atom), use the same format of `center` |str|(Required)|--ligand 'name O'|
|cell|Setting the parameters of the cell.|list[float]|(Required)|--cell '[10.2, 10.2, 10.2, 90, 90, 90]'
|cutoff|Setting the cutoff distance to define a bond.|float|(Required)|--cutoff 2.36|
|coord_num|Provide the coordination number of polyhedra that you want to count. For example, you could set `6` for $octahedra$. In particular, `-1` corresponds to counting $All\ categories\ of\ the\ polyhedra$.|int| -1 |--coord_num 6|

#### Examples
We could run this method by the following command :
```bash
ai2-kit algorithm aosa count-shared-polyhedra \
    --input_traj ./in2o3-eq.xyz \
    --out_dir ./out \
    --center 'name In' \
    --ligand 'name O' \
    --cell '[20.23845286, 20.23845286, 20.23845286, 90, 90, 90]' \
    --cutoff 2.36 \
    --coord_num 6
```

The output would be written in a new directory : `./out/raw.txt` and `./out/stats.txt`.

In the file `raw.txt`:
```bash
# frame_index   corner   edge   face
    0        1106.0000   290.0000   0.0000
    1        1098.0000   300.0000   0.0000
    2        1134.0000   286.0000   2.0000
    3        1116.0000   288.0000   2.0000
    4        1114.0000   287.0000   2.0000
    ...      ...         ...        ...      
```
In the file `stats.txt`:
```bash
Corner-share = 1096.4817
Edge-share = 285.7608
Face-share = 1.8439
```