PyVibLocalizer

visualize atomic mode and genetrate displacement vectors (normal/local mode, arbitary path)

• Documentation

Installation

$ git clone https://github.com/KenHino/PyVibLocalizer

• In WSL2 or Ubuntu,

$ sudo apt install blender

• In Mac,

$ brew install --cask blender

or simply install from homepage.

• First, modify PATH related to blender in CMakeLists.txt in PyVibLocalizer directory. Below is an example of PATH in Mac OS. (In Ubuntu, this may be /usr/bin/blender)

set(BPython "/Applications/Blender.app/Contents/Resources/3.5/python/bin/python3.10")
set(BPythonDir "/Applications/Blender.app/Contents/Resources/3.5/python/")
set(Blender "/Applications/Blender.app/Contents/MacOS/Blender")

• Next, move to test directory and make build directory. And execute cmake.

$ cd test
$ mkdir build
$ cd build
$ cmake ../..

• At last, activate virtual environment and execute a some example file such as work/ch2o.py.

$ source venv/bin/activate
$ blender --python main.py

• And you can also use jupyter notebook in blender.

$ jupyter-lab

In jupyter notebook, you can use blender_kernel to execute blender script.

Local mode

J. Chem. Phys. 130, 084106 (2009)

• Pipek-Mezy metric

$$\xi_{\mathrm{at}}\left(\widetilde{\boldsymbol{Q}}^{\mathrm{sub}}\right)=\sum_{p=1}^{k} \sum_{i=1}^{n}\left(\tilde{C}_{i p}^{\mathrm{sub}}\right)^{2}$$

$$\tilde{C}_{i p}^{\mathrm{sub}}=\sum_{\alpha=x, y, z}\left(\tilde{Q}_{i \alpha, p}^{\mathrm{sub}}\right)^{2}$$

• Boys metric

$$\xi_{\mathrm{dist}}\left(\widetilde{\boldsymbol{Q}}^{\mathrm{sub}}\right)=\sum_{p=1}^{k}\left(\boldsymbol{R}_{p}^{\text {center }}\right)^{2}$$

$$\boldsymbol{R}_{p}^{\text {center }}=\sum_{i=1}^{n} \tilde{C}_{i p}^{\mathrm{sub}} \boldsymbol{R}_{i}$$

To maximize, metrices, this program used scipy.optimized.minimize_scalar, in jacobi sweep method. The choice of unitary rotation mode pair is based on window frequency.: J. Chem. Phys. 145, 124112 (2016) Default window frequency set as 400 cm-1.

Group Localized Coordinate

Group localized coordinate is one of the local mode, which diagonalize subspace mass-weighted hessian whose subspace is defined by your selction of atoms.

Quick Start

• See here
• To run this program, execute python {$mol_name}.py or blender --python {$mol_name}.py (example; mol_name=src/ch2o)