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Collected small fixes and updates #4599

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@akohlmey akohlmey commented May 21, 2025 •
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Summary

This pull request combines multiple small fixes and corrections.

Related Issue(s)

N/A

Author(s)

Axel Kohlmeyer, Temple U, akohlmey@gmail.com
Jacob Tavenner, NASA Ames Research Center, tavennerjacob@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

N/A

Implementation Notes

The following individual changes are included:

  • let utils::expand_args() stop with a descriptive error message, when a vector-style variable reference is provided with a wildcard without the required upper boundary
  • refactor fix neighbor/swap for improved errors and modernized C++ code
  • fix argument indexing bug in fix neighbor/swap
  • small documentation updates
  • add example inputs for fix neighbor/swap

Post Submission Checklist

  • 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
  • Suitable tests have been added to the unittest tree.
  • A package specific README file has been included or updated
  • One or more example input decks are included

Further Information, Files, and Links

N/A

@akohlmey akohlmey self-assigned this May 21, 2025
@akohlmey akohlmey moved this to In Progress in LAMMPS Pull Requests May 21, 2025
akohlmey added 2 commits May 20, 2025 21:49
@akohlmey
update expand_args() unit tester with new error message
b924143
@akohlmey
refactor fix neighbor/swap
594953e 
- plug memory leak
- modernize access to computes
- tighten checks
- modernize and improve error messages
- better check for known keywords when processing atom types
- support for typelabels
@akohlmey akohlmey requested a review from Copilot May 21, 2025 11:31
Copilot
Copilot AI reviewed May 21, 2025
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Pull Request Overview

This pull request combines multiple small fixes and updates, including improved error handling for vector-style variable expansion, refactoring of the neighbor/swap fix for clearer errors and modernized C++ usage, and minor documentation improvements.

  • Update of error reporting in utils::expand_args() with a descriptive message when a vector variable is missing an upper bound.
  • Refactoring of the neighbor/swap fix (both header and source) to modernize code and improve error messaging.
  • Revision of unit tests and documentation for consistency with these changes.

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file
File Description
unittest/cplusplus/test_advanced_utils.cpp Adjusted expected error messages and argument count in tests
src/utils.cpp Updated error reporting parameters for consistency
src/MC/fix_neighbor_swap.h Minor renaming and removal of unused code/comments
src/MC/fix_neighbor_swap.cpp Enhancements to error messages, parameter validation, and swap probability computation using modern C++ patterns
doc/src/fix_ave_correlate_long.rst Documentation tweaks to clarify wildcard usage in variable expressions
Comments suppressed due to low confidence (2)

unittest/cplusplus/test_advanced_utils.cpp:223

  • Verify that the updated expected argument count of 14 correctly reflects the intended behavior after the modification in upper-bound error handling.
EXPECT_EQ(narg, 14);

doc/src/fix_ave_correlate_long.rst:85

  • [nitpick] Ensure that the updated terminology ('wildcard string') is consistently used throughout the documentation to avoid potential confusion.
evaluation of an equal-style or vector-style variable.  The specified indices can include a wildcard string.

akohlmey
akohlmey commented May 21, 2025
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@jtavenner-dev I had to do some significant refactoring of your contributed code to modernize some parts and have it better aligned with current programming conventions. Also, a couple minor bugs were fixed and I added support for type labels.

Unfortunately, I could not find an example input in the examples tree, so this is currently untested. Can you have a closer look and - ideally - provide some small, simple examples so that I can check as well.

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Thanks for the code modernization updates and clearer error handling. I have fixed a minor bug unrelated to your changes regarding reading the options. I've also tested some short example scripts.

However, I'm not sure how to add to this pull request. I've updated the changes to a branch in sync with this pull, but can't seem to push any changes. Not sure if this is just permissions-related or if I'm missing something else.

@akohlmey
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However, I'm not sure how to add to this pull request. I've updated the changes to a branch in sync with this pull, but can't seem to push any changes. Not sure if this is just permissions-related or if I'm missing something else.

You cannot push because you have no write permission for the LAMMPS repository.
Just push it to your fork and let me know the name of the branch and then I can pull it myself.
or create a diff and attach it here.

@jtavenner-dev
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Sounds good. I was trying to push to one of your forked lammps branches, so permissions make sense. I've synced the changes here and my updates to my lammps fork on the 'develop' branch.

@akohlmey
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Sounds good. I was trying to push to one of your forked lammps branches, so permissions make sense. I've synced the changes here and my updates to my lammps fork on the 'develop' branch.

@jtavenner-dev The changes are now integrated. I also moved and renamed the example folder, trimmed the inputs and make them use a potential that we already have included.

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@jtavenner-dev The changes are now integrated. I also moved and renamed the example folder, trimmed the inputs and make them use a potential that we already have included.

Looks good to me, thanks.

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Copilot code review Copilot Copilot left review comments

@rbberger rbberger Awaiting requested review from rbberger rbberger will be requested when the pull request is marked ready for review rbberger is a code owner

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@akohlmey @jtavenner-dev
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