Metadata-Version: 2.4
Name: viscosity_step
Version: 2026.10.15.1
Summary: A SEAMM plug-in for Viscosity
Home-page: https://github.com/molssi-seamm/viscosity_step
Author: Paul Saxe
Author-email: psaxe@molssi.org
License: BSD-3-Clause
Keywords: SEAMM,SEAMMplugin,flowchart
Platform: Linux
Platform: Mac OS-X
Platform: Unix
Platform: Windows
Classifier: Environment :: Plugins
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.12
Description-Content-Type: text/x-rst
License-File: LICENSE
License-File: AUTHORS.rst
Requires-Dist: numpy
Requires-Dist: seamm
Requires-Dist: seamm-md-analysis>=2026.10.15.2
Requires-Dist: seamm-util
Requires-Dist: seamm-widgets
Requires-Dist: tabulate
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: keywords
Dynamic: license
Dynamic: license-file
Dynamic: platform
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

=======================
SEAMM Viscosity Plug-in
=======================

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   :target: https://molssi-seamm.github.io/viscosity_step/index.html
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A SEAMM plug-in for the shear viscosity of liquids from equilibrium molecular
dynamics.

* Free software: BSD-3-Clause
* Documentation: https://molssi-seamm.github.io/viscosity_step/index.html
* Code: https://github.com/molssi-seamm/viscosity_step

Features
--------

* The shear viscosity by Green-Kubo and from the Helfand moments, averaging the
  five independent shear components of the pressure tensor.
* Runs its own MD several times, or analyzes MD run earlier in the flowchart or in
  other jobs, from the ``md.h5md`` files the LAMMPS step writes.
* Checks before the job runs that the MD samples the pressure tensor often enough.
* Passes its result to a later Diffusivity step for the Yeh-Hummer correction.

Acknowledgements
----------------

This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
is based on the excellent Cookiecutter_.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin

Developed by the Molecular Sciences Software Institute (MolSSI_),
which receives funding from the `National Science Foundation`_ under
award CHE-2136142.

.. _MolSSI: https://molssi.org
.. _`National Science Foundation`: https://www.nsf.gov


=======
History
=======
2026.10.15.1 -- Internal: a regression test against SPC/E water
    * ``regression/spce`` holds a flowchart computing the viscosity and diffusion
      coefficient of rigid SPC/E water, and a script checking them against published
      values. It is run by hand after changes that could affect the results; the new
      "Regression" page in the developer guide describes it and records its results.

2026.10.15 -- First release: the shear viscosity from MD
    * Calculates the shear viscosity of a liquid from equilibrium MD by Green-Kubo
      and from the Helfand moments, averaging the five independent shear components
      of the pressure tensor.
    * Runs its own MD several times, or analyzes MD run earlier in the flowchart, in
      each iteration of a loop, or in other jobs, from the md.h5md files the LAMMPS
      step writes. A single run is divided into blocks to estimate the errors.
    * Checks before the job runs that the MD samples the pressure tensor at least
      every 5 fs, and turns it on when it runs its own MD.
    * The result is stored as a property, can be saved in variables and tables, and
      is used by a following Diffusivity step for its finite-size correction.

