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computing the eigenvalues of gyration tensor & shape parameters #1583

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merged 8 commits into from Jul 30, 2019

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commented Jul 25, 2019

Summary

Computing the eigenvalues of the gyration tensor and three associated shape parameters (https://en.wikipedia.org/wiki/Gyration_tensor)

Related Issues

It is not related to any open GitHub issue .

Author(s)

Evangelos Voyiatzis at Royal DSM (evoyiatzis@gmail.com)

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

Backward Compatibility

It does not break backward compatibility

Implementation Notes

The code is based on the related "compute gyration" and "compute gyration/chunk" commands. The validation step has been a comparison of the results with the computation of the eigenvalues and shape parameters with an external python script. In all test cases, the gyration tensor has been computed with the compute gyration command.

Post Submission Checklist

Please check the fields below as they are completed after the pull request has been submitted. Delete lines that don't apply

  • The feature or features in this pull request is complete
  • Licensing information is complete
  • Corresponding author information is complete
  • The source code follows the LAMMPS formatting guidelines
  • Suitable new documentation files and/or updates to the existing docs are included
  • The added/updated documentation is integrated and tested with the documentation build system
  • The feature has been verified to work with the conventional build system
  • The feature has been verified to work with the CMake based build system
  • A package specific README file has been included or updated
  • One or more example input decks are included

Further Information, Files, and Links

Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)

evoyiatzis added some commits Jul 25, 2019

Add files via upload
tex file with the equations for the shape parameters
Add files via upload
txt file with the documentation of the new compute style
Update README
Adding my e-mail to README
Add files via upload
The actual source code for the new compute
cpp file for the compute command
The right file with the cpp code
Delete compute_gyration.cpp
It is not part of the new compute style

akohlmey added some commits Jul 29, 2019

cleanup of compute gyration/shape code.
- use MathSpecial::square(x) instead of pow(x,2) for improved precision
and handling of small and negative numbers
- remove unused include statements
- no need to refetch the compute in every step. during init() is sufficient

@evoyiatzis evoyiatzis requested a review from rbberger as a code owner Jul 29, 2019

@akohlmey akohlmey merged commit d2c4989 into lammps:master Jul 30, 2019

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@evoyiatzis evoyiatzis deleted the evoyiatzis:gyration_shape branch Jul 30, 2019

@evoyiatzis evoyiatzis restored the evoyiatzis:gyration_shape branch Jul 30, 2019

@evoyiatzis evoyiatzis deleted the evoyiatzis:gyration_shape branch Jul 30, 2019

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