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Collected small changes and bugfixes for the next patch release #1282

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merged 21 commits into from Jan 31, 2019

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akohlmey commented Jan 9, 2019

Purpose

This pull request collects all kinds or small changes, minor bugfixes, and enhancements that don't justify having a dedicate pull request set up. This will be expanded and considered work in progress until the release is close.

Author(s)

Axel Kohlmeyer (Temple U)

Backward Compatibility

yes.

Implementation Notes

Individual changes contained in the PR are the following:

  • when checking for C++ headers we should now check for cmath instead of math.h since the former is what we are using in the source code now.
  • correctly call error->one() instead of error->all() for cases when the variable evaluation may not be wrong on all ranks and thus will lead to MPI stalling when hitting the MPI_Barrier() for error->all(). This closes #1283
  • use a per target temporary name when creating the lmpinstalledpkgs.h file, so multiple concurrent conventional make invocations (with different targets) will not corrupt the file. This closes #1284
  • fix two bugs in fix bond/react: correct logic for deleting an internal fix and remove code trying to delete a callback to the Atom class that was never registered
  • detect when something wants to unregister a callback to the Atom class that was not registered.
  • fix bug in PyLammps python module. Closes #1294
  • fix return type issue in lammps python module
  • fix memory issue in fix plumed destructor caused by incorrect string copying. fixes bug reported on lammps-users
  • bugfix for region optimization in create_atoms from PR #1279
  • documentation updates

Post Submission Checklist

Please check the fields below as they are completed

  • The feature or features in this pull request is complete
  • Suitable new documentation files and/or updates to the existing docs are included
  • One or more example input decks are included
  • The source code follows the LAMMPS formatting guidelines

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)

akohlmey added some commits Jan 9, 2019

add option to `print_var_error()` function to delegate errors to erro…
…r->one() instead of error->all()

this change is applied to cases that may happen on individual ranks only, e.g. out-of-range access, division by zero, invalid argument.
fix 2 bugs in fix bond/react
- correct logic when deleting internal fix
- remove line attempting to dele a callback to Atom(), that was never added

@akohlmey akohlmey force-pushed the akohlmey:collected-small-changes branch from 604fae9 to cf00346 Jan 10, 2019

@akohlmey akohlmey requested a review from jrgissing Jan 10, 2019

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jrgissing left a comment

looks good! thanks!

@jrgissing jrgissing referenced this pull request Jan 13, 2019

Merged

Bond/react: limit number of reactions #1288

1 of 4 tasks complete

akohlmey added some commits Jan 21, 2019

@akohlmey akohlmey requested a review from stanmoore1 Jan 30, 2019

@akohlmey akohlmey merged commit a9f8b17 into lammps:master Jan 31, 2019

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@akohlmey akohlmey deleted the akohlmey:collected-small-changes branch Feb 1, 2019

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