=========================
SEAMM Diffusivity Plug-in
=========================
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A SEAMM plug-in for Diffusivity
* Free software: BSD-3-Clause
* Documentation: https://molssi-seamm.github.io/diffusivity_step/index.html
* Code: https://github.com/molssi-seamm/diffusivity_step
Features
--------
* Please edit this section!
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
=======
2024.7.30 -- Added optional correction for cell size
* Added an option to use the Yeh-Hummer hydrostatic correction for the effects of
the finite cell size. The viscosity is required as an input, but the correction
eliminates the need to extrapolate to 1/L = 0.
* Added control parameters and timings to the available results.
2024.7.21 -- Significant improvements!
* Simplified error analysis to safe approach of analyzing the diffusion constants
over runs.
* Improved fitting of the curves to focus on the central linear portion. There are
reasonable defaults but the user can adjust as needed.
* Provided a combined average and error bars when both the MSF approach and Helfand
moments are used.
* Capture temperature, pressure, and cell size from the MD step, providing 1/L as a
result since the true diffusion constants are found by extrapolating to 1/L = 0.
* Provided control over the number of steps for the expensive numerical integration
in the Helfand moments, providing a reasonable default of 1000.
2024.7.15 -- Bugfix: Significant error in Helfand Moment approach
* Now fixed and seems to be working.
2024.7.4 -- Improved fitting of curves
* Removed weighting of the fit by the stdev since it is too biased to the beginning
* Added control over the portion of the data to fit in order to avoid the initial
curvature and poor data towards the end.
2024.6.3 -- Bugfix: handling of options for subflowchart
* Fixed a bug where the options for the subflowchart were not being parsed
correctly.
2024.5.26 -- Updated for new task handling
* The new handling of running tasks such as LAMMPS required a small change in the
code.
2023.9.5 -- Changed default to using only MSD
* The Helfand moments approach seems give incorrect results if the sampling time is
too long. It is not dramatic, but gives increasingly incorrect results as the
sampling time is increased. Thus using the Helfand moments is dangerous because
the results may be wrong, but not obviously so.
2023.8.30 -- Initial working version
* A working version that has been tested somewhat. Further testing and documentation
will follow
2023.5.8 -- Initial development version created
* Plug-in created using the SEAMM plug-in cookiecutter.
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