Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Computing the eigenvalues of the gyration tensor and shape parameters… #1739

Merged
merged 12 commits into from Nov 11, 2019

Conversation

@evoyiatzis
Copy link
Collaborator

evoyiatzis commented Oct 22, 2019

… per chunk

Summary

It is an extension of the gyration/shape compute to treat chunks of particles instead of a single group of particles

Related Issues

It is not related to any open 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/chunk" and "compute gyration/shape" commands. The validation step has been a comparison of the results with the computation of the eigenvalues and shape parameters with an external script. In all test cases, the gyration tensor has been computed with the compute gyration/chunk 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
@akohlmey akohlmey self-assigned this Oct 23, 2019
@akohlmey akohlmey requested review from athomps and sjplimp Oct 23, 2019
akohlmey added 2 commits Oct 23, 2019

:line

[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).

This comment has been minimized.

Copy link
@sjplimp

sjplimp Oct 24, 2019

Contributor

The change made on these 2 citations is incorrect in the parent file (compute gyration shape.txt)
and here. The link(Name) tag needs to be listed. And it needs to be listed
somewhere in the text above. Could be as simple as a sentence like: This method is described in
Theodoru and Mattice. (see other examples in the doc pages for the syntax to do this)

Copy link
Contributor

athomps left a comment

I approve, once the citation error identified by @sjplimp is fixed.


:line

:link(Mattice)

This comment has been minimized.

Copy link
@akohlmey

akohlmey Oct 26, 2019

Member

Please note, that :link anchors have to have unique names across the entire documentation. So in this case there should be :link(Mattice1) and :line(Mattice2) and for Theodorou accordingly. This can be seen when running make html in the doc folder, where there should be a list of anchor related problems. This is why I had removed them. Not sure why @sjplimp insists on using those, but he is da man and thus we should keep him happy. ;-)

@akohlmey

This comment has been minimized.

Copy link
Member

akohlmey commented Nov 6, 2019

@sjplimp this PR is currently blocked from merging because of your request for changes, which seemed to have been implemented. Please check it out.

@sjplimp
sjplimp approved these changes Nov 8, 2019
@sjplimp

This comment has been minimized.

Copy link
Contributor

sjplimp commented Nov 8, 2019

Thanks for the changes

@akohlmey

This comment has been minimized.

Copy link
Member

akohlmey commented Nov 8, 2019

@rbberger looks like we need your magic here...

@rbberger

This comment has been minimized.

Copy link
Member

rbberger commented Nov 8, 2019

ok

rbberger added 2 commits Nov 8, 2019
Merge branch 'master' into shape_chunk
@akohlmey akohlmey mentioned this pull request Nov 8, 2019
@rbberger

This comment has been minimized.

Copy link
Member

rbberger commented Nov 8, 2019

@evoyiatzis Axel created the PR on my behalf. For some reason, I can't push into your branch

Documentation update
@evoyiatzis

This comment has been minimized.

Copy link
Collaborator Author

evoyiatzis commented Nov 10, 2019

@rbberger I think I have merged the PR in my fork but there are two errors in building the docs.

@rbberger

This comment has been minimized.

Copy link
Member

rbberger commented Nov 11, 2019

@evoyiatzis for some reason I can't push into this branch or create a PR into your branch (your fork doesn't even show up as an option for me). Since I've done this already a few times, there must be something blocking me from your side. Axel doesn't have this issue. Did you add him explicitly as "collaborator"? Or can you just add the checkmark to this PR ("Allow edits from maintainers")? I pushed the changes into my own fork for now... https://github.com/rbberger/lammps/tree/shape_chunk

@akohlmey akohlmey assigned rbberger and unassigned akohlmey Nov 11, 2019
@evoyiatzis

This comment has been minimized.

Copy link
Collaborator Author

evoyiatzis commented Nov 11, 2019

@rbberger I have checked that the "Allow edits from maintainers" is enabled. I have also added you and Axel as "collaborator" in my fork. Hope now works. If I can do something else please let me know.

@rbberger rbberger mentioned this pull request Nov 11, 2019
@rbberger

This comment has been minimized.

Copy link
Member

rbberger commented Nov 11, 2019

@evoyiatzis still can't push directly, but now I'm able to create a PR into your branch. please merge evoyiatzis#2

Fix documentation
@rbberger rbberger assigned akohlmey and unassigned rbberger Nov 11, 2019
@rbberger

This comment has been minimized.

Copy link
Member

rbberger commented Nov 11, 2019

@akohlmey docs are building. all yours.

@akohlmey akohlmey merged commit 5289417 into lammps:master Nov 11, 2019
8 checks passed
8 checks passed
lammps/pull-requests/build-docs-pr head run ended
Details
lammps/pull-requests/cmake/cmake-kokkos-cuda-pr head run ended
Details
lammps/pull-requests/cmake/cmake-kokkos-omp-pr head run ended
Details
lammps/pull-requests/cmake/cmake-serial-pr head run ended
Details
lammps/pull-requests/kokkos-omp-pr head run ended
Details
lammps/pull-requests/openmpi-pr head run ended
Details
lammps/pull-requests/serial-pr head run ended
Details
lammps/pull-requests/shlib-pr head run ended
Details
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.