aim(aimnet2) + DIAS(distortion interaction analysis)
---
`aimDIAS` is a Python package compatible with IPython that enables SUPER-FAST Distortion Interaction Analysis (or activation strain analysis) using aimnet2 models.
## Colab Tutorials
aimDIAS is currently in ***beta version***. Functions may change depending on the version, so please check the version number.
|notebook| aimDIAS version|description|
|:-:|:-:|:-:|
|[](link) | v. 1.0.1 | basic tutorials |
## Usage
For detail, see `docs/*`, `notebooks/*`
- Draw your molecule
```python
from aimDIAS import draw_xyz
draw_xyz("h2o.xyz", charge=0)
```
- Run calculation
```python
from aimDIAS import aimDIAS_run
fp = {
"frag_1" : (-1, [1, 2]),
"frag_2" : (+1, [3])
}
aimDIAS_run(trajFile="h2o.xyz", fragments_params=fp)
```
- Plot your Result without calculation
```python
from aimDIAS import aimDIAS_run
gp = {"distance" : "1 2"}
fp = {
"frag_1" : (-1, [1, 2]),
"frag_2" : (+1, [3])
}
aimDIAS_run(trajFile="h2o.xyz", fragments_params=fp, mode="plot", axis_type="distance", geo_param=gp)
```
## Install
1. pip
```shell
pip install aimDIAS
```
2. git clone
```shell
# in terminal #
git clone https://github.com/kangmg/aimDIAS
# since `git clone` doesn't directly install git lfs files, it contains metadata only. You'll need to manually remove it. Models will be automatically downloaded.
rm path/to/aimDIAS/aimDIAS/models/*
pip install -q -r path/to/aimDIAS/requirements.txt
```
```python
# in python #
import sys
sys.path.append("path/to/aimDIAS")
```
## Requirements
python >= 3.10.0
## Bug Report
kangmg@korea.ac.kr or [issue in github](https://github.com/kangmg/aimDIAS/issues)
> *I'm always happy to hear feedback and suggestions. Feel free to contact me anytime.*
## TODO
- add auto_fragmentation
- user-friendly fragmentation GUI
- enhance the plot style for publication-quality
- json to table formatter
- more sample data
- fp enables support for string format
- axis validation plot
- add GPU mode
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"description": "\r\n\r\naim(aimnet2) + DIAS(distortion interaction analysis)\r\n---\r\n`aimDIAS` is a Python package compatible with IPython that enables SUPER-FAST Distortion Interaction Analysis (or activation strain analysis) using aimnet2 models.\r\n\r\n## Colab Tutorials\r\naimDIAS is currently in ***beta version***. Functions may change depending on the version, so please check the version number.\r\n\r\n|notebook| aimDIAS version|description|\r\n|:-:|:-:|:-:|\r\n|[](link) | v. 1.0.1 | basic tutorials |\r\n\r\n## Usage\r\nFor detail, see `docs/*`, `notebooks/*`\r\n\r\n- Draw your molecule\r\n```python\r\nfrom aimDIAS import draw_xyz\r\n\r\ndraw_xyz(\"h2o.xyz\", charge=0)\r\n```\r\n \r\n- Run calculation\r\n```python\r\nfrom aimDIAS import aimDIAS_run\r\n\r\nfp = {\r\n \"frag_1\" : (-1, [1, 2]),\r\n \"frag_2\" : (+1, [3])\r\n }\r\n\r\naimDIAS_run(trajFile=\"h2o.xyz\", fragments_params=fp)\r\n```\r\n\r\n- Plot your Result without calculation\r\n```python\r\nfrom aimDIAS import aimDIAS_run\r\n\r\ngp = {\"distance\" : \"1 2\"}\r\n\r\nfp = {\r\n \"frag_1\" : (-1, [1, 2]),\r\n \"frag_2\" : (+1, [3])\r\n }\r\n\r\naimDIAS_run(trajFile=\"h2o.xyz\", fragments_params=fp, mode=\"plot\", axis_type=\"distance\", geo_param=gp)\r\n```\r\n\r\n## Install\r\n1. pip \r\n```shell\r\npip install aimDIAS\r\n```\r\n\r\n2. git clone\r\n```shell\r\n# in terminal #\r\n\r\ngit clone https://github.com/kangmg/aimDIAS\r\n\r\n# since `git clone` doesn't directly install git lfs files, it contains metadata only. You'll need to manually remove it. Models will be automatically downloaded.\r\nrm path/to/aimDIAS/aimDIAS/models/*\r\n\r\npip install -q -r path/to/aimDIAS/requirements.txt\r\n```\r\n```python\r\n# in python #\r\n\r\nimport sys\r\nsys.path.append(\"path/to/aimDIAS\")\r\n```\r\n\r\n## Requirements\r\npython >= 3.10.0\r\n\r\n## Bug Report\r\nkangmg@korea.ac.kr or [issue in github](https://github.com/kangmg/aimDIAS/issues)\r\n\r\n> *I'm always happy to hear feedback and suggestions. Feel free to contact me anytime.*\r\n\r\n## TODO\r\n- add auto_fragmentation\r\n- user-friendly fragmentation GUI\r\n- enhance the plot style for publication-quality\r\n- json to table formatter\r\n- more sample data\r\n- fp enables support for string format\r\n- axis validation plot\r\n- add GPU mode\r\n",
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