Welcome to ZENOWrapper’s documentation!
ZENOWrapper
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Summary
ZENO computes hydrodynamic and electronic properties using numerical path integration techniques based on Brownian motion Monte Carlo methods (MCMs). These methods provide stochastic solutions to elliptic partial differential equations (PDEs), which represent the desired material properties or serve as intermediates for their computation. The mathematical framework maps these problems onto the electrostatic capacitance problem, where the stochastic solution corresponds to the probability of a random walk from infinity hitting the material’s surface. ZENO employs the Walk-on-Spheres (WoS) algorithm to efficiently simulate Brownian motion, enabling larger jumps compared to traditional Brownian dynamics techniques, significantly reducing computational cost.
The ZENOWrapper package provides a Python interface to the ZENO computation engine, integrating it seamlessly with MDAnalysis. This integration automates the preparation of ZENO input files, execution of computations, and retrieval of results as Python objects. By accepting MDAnalysis Universe/AtomGroup objects and trajectory frames, ZENOWrapper enables hydrodynamic and transport property analyses to be conducted directly within MDAnalysis workflows, facilitating reproducible research.
Additionally, ZENOWrapper bridges ZENO’s specialized input system with any simulation package supported by MDAnalysis. It also leverages MDAnalysis’ parallelization capabilities and compatibility with interactive molecular dynamics (IMD3), enhancing the efficiency and scalability of hydrodynamic property calculations for macromolecular systems.
ZENOWrapper is bound by a Code of Conduct.
Documentation
Online: NIST Pages
Dependencies
This package is tested for python 3.10+ on all Windows, MacOS, and Linux systems. Scipy must be installed before installation.
Installation
To build ZENOWrapper from source, we highly recommend using virtual environments.
Below we provide instructions for pip.
Install ZENO
Follow the installation instructions for ZENO.
Then set an environmental variable for the path: ZENOPATH='/Your/Path/to/ZENO' containing the cpp and zeno-build directories.
Download
git clone https://github.com/usnistgov/zenowrapper
User Install from Source
To build the package from source, run:
pip install .
If you want to create a development environment, install the dependencies required for tests and docs with:
pip install ".[test,doc]"
Developer Install from Source
To build the package from source in editable mode, run:
pip install -e .
Initialize pre-commit for automatic formatting.
pre-commit install
Copyright
Works of NIST employees are not not subject to copyright protection in the United States
License
The ZENOWrapper source code is hosted at https://github.com/usnistgov/zenowrapper and is available under the NIST LICENSE. The license in this repository is superseded by the most updated language on of the Public Access to NIST Research Copyright, Fair Use, and Licensing Statement for SRD, Data, and Software.
Contact
Jennifer A. Clark, PhD
Derek Juba (derek.juba@nist.gov)
Walid Keyrouz (walid.keyrouz@nist.gov)
Debra J. Audus, PhD (debra.audus@nist.gov)
Jack F. Douglas, PhD
Affilation:
Polymer Analytics Project
Polymer and Complex Fluids Group
Materials Science and Engineering Division
Material Measurement Laboratory
National Institute of Standards and Technology
Citation
Clark, J. A., D. J. Audus, J. F. Douglas. XXX, 2024. https://doi.org/10.18434/mds2-XXXX
Juba, D., W. Keyrouz, M. Mascagni, M.Brady. Procedia Computer Science, 80, 2026. https://doi.org/10.1016/j.procs.2016.05.319
Juba, D., D. J. Audus, M. Mascagni, J. F. Douglas, W. Keyrouz Journal of Research of National Institute of Standards and Technology, 20, 2017. https://doi.org/10.6028/jres.122.020micro
Acknowledgements
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using ZENOWrapper in published work.