pothos

pothos is a molecular dynamics tool for tracking and clustering polymer chain behavior. It evaluates order parameters such as $\langle P_2 \rangle$, and uses a modified DBSCAN to cluster aligned chain segments. Output data can be colored in a variety of ways in OVITO, such as cluster size, bead vector, average cluster vector, etc.

The current full version of pothos is pure python, however it is being rewritten into c++ to improve performance. For now, pothos++ offers both the legendre and verho alignment functions as a compiled function.

pothos++ will be updated to eventually replace the python version. As of Dec. 15 24, it only supports coarse-grained systems.

Installation Instructions

Prerequesites

For the Python version : Python 3, Scipy, Numpy, Sci-kit Learn, Rich, Numba, Joblib

Installation

The best way to use pothos is through a virtual enviroment

% set up the virtual environment
python -m venv venv
cd venv/bin
source activate

Download the source from github and enter it

% enter directory
cd /path/to/pothos

Install with pip

pip install .

pothos reads lammps dump files in the form

dump 1 all custom ${n} ${print_dir}/filename.dump id mol type x y z ix iy iz

or 

dump 1 all custom ${n} ${print_dir}/filename.dump id mol type x y z xu yu zu