Metadata-Version: 2.4
Name: dielectric_constant_step
Version: 2026.10.19
Summary: A SEAMM plug-in for Dielectric Constant
Home-page: https://github.com/molssi-seamm/dielectric_constant_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>=2026.10.17.1
Requires-Dist: seamm-md-analysis[structure]>=2026.10.19
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
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=================================
SEAMM Dielectric Constant Plug-in
=================================

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A SEAMM plug-in for the static dielectric constant of liquids and electrolytes from MD.

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

Features
--------

* The static dielectric constant of liquids, and of the solvent of electrolytes,
  from the fluctuations of the dipole of the cell, with errors from runs or blocks,
  the running estimate and the dipole's correlation time.
* Analyzes the MD run before it in the flowchart -- the runs of a Loop around the MD,
  as independent runs -- or md.h5md files of earlier runs.

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
=======
2026.10.19 -- Scaled ion charges
    * In MD with the charges of the ions scaled (LAMMPS's 'Scale the charges of ions
      by', e.g. 0.8), the ions were taken for molecules with broken charges. They are
      now recognized as ions, and left out of the dipole as before.

2026.10.18 -- Bugfix: fluids without partial charges are skipped
    * For a fluid whose molecules have no partial charges, such as argon, the step
      printed a dielectric constant of 1, a dipole of 0 and a Kirkwood factor of nan,
      with a warning about the electrostatics. It now says there is no dipole and skips
      the analysis, as Ionic Conductivity does without ions, and checking the flowchart
      warns of it once the atoms are typed.

2026.10.17.1 -- Analyze MD run before the step; more results; labelled errors
    * The step analyzes MD run before it in the flowchart -- the runs of a Loop around
      the MD, as independent replicas ("the last MD run of each loop iteration", the
      default) -- or md.h5md files; it no longer runs its own MD in a sub-flowchart.
      Older flowcharts that stored its settings for that can still be read; the check
      before the job runs says what replaces them.
    * The check before the job runs also warns when the analysis is inside the loop
      holding its MD, when the loop changes the temperature or pressure, and when the
      thermostat does not suit the analysis, with fixes; the step warns before the MD
      when the system is small.
    * Errors are the 95% confidence interval, Student's t for the number of runs or
      blocks, and the output says so; stored errors are standard errors.
    * The state of the runs -- temperature, pressure, volume and density with their
      errors, and the equilibrium density where an NPT run before them gives the bulk
      modulus -- is reported and stored. The values of each run or block are in
      step.out.
    * New results: the mean dipole of a molecule, the Kirkwood factor g_K, and the mean
      dipole of the cell, which should be near zero; a statement that the formula
      assumes conducting (tin-foil) Ewald boundaries.
    * For an isotropic run ε is one value, with a check that the diagonal components
      agree; otherwise the components are given too.


2026.10.17 -- First release: the static dielectric constant
    * The static dielectric constant of liquids, and of the solvent of electrolytes,
      from the fluctuations of the dipole of the cell in MD with fixed charges, with
      errors from independent runs or blocks, the running estimate and the
      correlation time of the dipole.
    * 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.
