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Compute snap #1779

Merged
merged 15 commits into from Dec 1, 2019
Merged

Compute snap #1779

merged 15 commits into from Dec 1, 2019

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@athomps
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athomps commented Nov 19, 2019

Summary

Added a new compute that generates a global array of SNAP bispectrum quantities that are
needed to train SNAP potentials.

Related Issues

None

Author(s)

Aidan Thompson

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

This is a new feature, the old computes sna/atom, snad/atom and snav/atom still work as before.

Implementation Notes

It works in parallel and gives the same results on any processor count. I added documentation to the existing compute_sna_atom.html doc page. I added an example in examples/snap/in.snap.compute that demonstrates all the computes, showing equivalences, for a minimal system with two atom types. I was not able to get Sphinx to compile the html on my computer, so there might be some formatting issues.

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)

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akohlmey commented Nov 25, 2019

@athomps This needs to add the compute snap command to doc/txt/compute.txt and doc/txt/Command_compute.txt and their RST counterparts in doc/src. Please note, if PR #1786 gets merged first, doc/txt/Command_compute.txt will be gone and doc/src/Command_compute.rst will be different (simpler) in how a new compute is added.

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akohlmey commented Nov 25, 2019

@athomps, also there is a typo in the compute sna/atom doc file, where it says "refence" instead of "reference"
https://ci.lammps.org/job/lammps/job/pull-requests/job/build-docs-pr/1363/warnings3Result/

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athomps commented Nov 25, 2019

Addressed issued identified by @akohlmey

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athomps commented Nov 25, 2019

I don't know how to resolve this conflict without making a new PR.

…ompute.rst
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akohlmey commented Nov 26, 2019

I don't know how to resolve this conflict without making a new PR.

Merge conflict should be resolved now.

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akohlmey commented Nov 26, 2019

@rbberger there is something off with the triggering of jenkins tests for this PR. Can you please have a look?

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athomps commented Nov 26, 2019

@akohlmey akohlmey removed their assignment Nov 27, 2019
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akohlmey commented Nov 27, 2019

@rbberger i suggest to merge this PR before your changes to the command tables.

@rbberger rbberger merged commit 3ce020e into lammps:master Dec 1, 2019
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@athomps athomps deleted the athomps:compute-snap branch Dec 2, 2019
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