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
	v. 1.0	basic tutorials

Basic Usage

For detail, see docs/*, notebooks/*

• Draw your molecule

from aimDIAS import draw_xyz

draw_xyz("h2o.xyz", charge=0)

• Run calculation

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

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)

Gallery

Diels-Alder reaction

Wittig Rection

How to Install

pip

• pip install aimDIAS

git clone

• terminal

  ### terminal ###
  git clone https://github.com/kangmg/aimDIAS
  
  
  pip install -q -r path/to/aimDIAS/requirements.txt

• ipython

  ### python ###
  import sys
  sys.path.append("path/to/aimDIAS")

Requirements

python >= 3.10.0

Share your Data

Share your files and contribute to the community!

By sharing your xyz trajectory files in the Discussion section, you can make them available as sample data for everyone to use. Please refer to this discussion link for more information:

Files posted in the Discussion section will be uploaded to the samples/ directory in the project repository for easy download and utilization with the load_data() function.

Bug Report

kangmg@korea.ac.kr or issue in github

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 multiprocessing mode
• ASE DeprecationWarning : Atoms.set_calculator(calculator) --> Atoms.calc = calculator