Metadata-Version: 2.4
Name: liquid_structure_step
Version: 2026.10.16
Summary: A SEAMM plug-in for Liquid Structure
Home-page: https://github.com/molssi-seamm/liquid_structure_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: MDAnalysis>=2.8
Requires-Dist: numpy
Requires-Dist: seamm
Requires-Dist: seamm-md-analysis[structure]>=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
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==============================
SEAMM Liquid Structure Plug-in
==============================

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   :target: https://github.com/molssi-seamm/liquid_structure_step/pulls
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   :target: https://codecov.io/gh/molssi-seamm/liquid_structure_step
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A SEAMM plug-in for the structure of liquids and solutions from molecular dynamics:
radial distribution functions, coordination numbers, ion pairing and solvation shells.

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

Features
--------

* Partial radial distribution functions with errors, their first peaks and minima, and
  coordination numbers, with fixed cutoffs where the minima mislead.
* The pairing of ions: free, solvent-separated (SSIP), contact (CIP) and aggregated
  (AGG) pairs, also for clusters.
* Solvation shells: coordination numbers per solvent, the most common shells, pairing,
  and residence times.
* Runs its own MD or analyzes MD earlier in the flowchart, from SEAMM's H5MD files.

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
=======

2026.10.16 -- First release: the structure of liquids and solutions
    * Radial distribution functions of pairs of sites, with errors, their first peaks
      and minima, and coordination numbers, with fixed cutoffs where the minima
      mislead.
    * The pairing of ions: each cation free, in a solvent-separated (SSIP) or contact
      (CIP) pair, or in an aggregate (AGG).
    * The solvation shells of solutes: the coordination number of each solvent, the
      most common shells, pairing, and residence times.
    * Runs its own MD or analyzes the MD earlier in the flowchart, and checks before
      the job runs that the MD samples the positions often enough.
