asedias

asedias is designed to streamline the activation strain analysis workflow and to provide a flexible calculator interface integrated with ASE (Atomic Simulation Environment). It also includes built-in plotting functionality to automate complex post-processing tasks.

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Installation

You can install the asedias package using either of the following methods:

1. Install directly from GitHub using pip:

pip install git+https://github.com/kangmg/asedias.git

2. Clone the repository and install locally:

git clone https://github.com/kangmg/asedias.git
cd asedias
pip install .
cd ..
rm -r asedias

Example Usage

from aimnet.calculators import AIMNet2ASE
from asedias.core import Fragment, aseDIAS
from ase.io import read

images = read('rxn.traj', index=':')

def attach_aimnet2(atoms, spin, charge):
    """Attach a calculator to the atoms."""
    calc = AIMNet2ASE('aimnet2nse', charge=charge, mult=(spin*2+1))
    atoms.calc = calc

# Define fragments as Fragment objects
frag1 = Fragment(index=[2, 7], charge=0, spin=0, frag_name='HF')
frag2 = Fragment(index=[0, 1, 3, 4, 5, 6], charge=0, spin=0, frag_name='ethane')

analysis = aseDIAS(images=images, fragments=[frag1, frag2], calc_attach=attach_aimnet2)
analysis.run()
plot = analysis.plot()