PyUNIxMD: Python-based UNIversal eXcited state Molecular Dynamics

PyUNIxMD is an object-oriented Python program for molecular dynamics simulations involving multiple electronic states. It is mainly for studying the nonadiabatic dynamics of excited molecules.

Citation

When you publish a work using any part of PyUNIxMD code, please cite the following publication:

• PyUNIxMD: A Python-based excited state molecular dynamics package. J. Comp. Chem. 2021, DOI: 10.1002/jcc.26711
• Coupled- and independent-trajectory approaches based on the exact factorization using the PyUNIxMD package. Top. Cur. Chem. 2022, DOI: 10.1007/s41061-021-00361-7

Requirements

• Python 3.6 or later
• Numpy >= 1.20.0
• Cython https://cython.org
• BLAS/LAPACK libraries or Math Kernel Library

You can easily install the latest Numpy and Cython via Python's pip command.

$ pip install --upgrade numpy Cython

Build

You can build PyUNIxMD by the following command.

$ python3 setup.py build_ext -b ./lib/

Examples

Without the aid of external QM programs, you can try the PyUNIxMD package with model systems. The corresponding examples are:

• $PYUNIXMDHOME/examples/qm/SH-Shin_Metiu
• $PYUNIXMDHOME/examples/qm/SHXF-Shin_Metiu

$PYUNIXMDHOME is the top-level directory where this file belongs.

In each directory, you can find the running script named run.py.

Before running example jobs, add the path of the PyUNIxMD package to your Python path.

$ export PYTHONPATH=$PYUNIXMDHOME/src:$PYUNIXMDHOME:$PYTHONPATH

Then execute run.py as follows.

$ python3 run.py >& log

Test

PyUNIxMD provides pytest-based tests in the $PYUNIXMDHOME/tests directory. To run the tests, first set up the Python path and then use pytest.

$ export PYTHONPATH=$PYUNIXMDHOME/src:$PYUNIXMDHOME:$PYTHONPATH
$ cd $PYUNIXMDHOME/tests
$ pytest -v

You can also run specific test categories using markers:

$ pytest -m mqc -v      # Run all MQC tests
$ pytest -m shxf -v     # Run only SHXF tests
$ pytest -m bomd -v     # Run only BOMD tests

Utility scripts

PyUNIxMD provides other Python scripts to analyze results of dynamics calculations. To use the scripts, you need to add the path of the scripts.

$ export PYTHONPATH=$PYUNIXMDHOME/util:$PYTHONPATH

Documentation

If you have Sphinx, you can locally build the manual of PyUNIxMD by the following command.

$ cd docs
$ make html