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Merge updates #34

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Summary

Related Issue(s)

Author(s)

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

Implementation Notes

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

ndtrung81 and others added 30 commits August 25, 2024 16:41
@ndtrung81
cast into PosixPath to str before writing to file
1148f5f
@jrgissing
refactor how reactions are skipped
99153f2 
better treatment of allowing all possible reactions when using 'overlap' keyword of 'create_atoms' feature
@akohlmey
Merge branch 'develop' into plumed-plugin
d1f141c
@akohlmey
Merge pull request #4293 from jrgissing/bond_react_fixes_summ24
dc66929 
Bond/react: fixes and error checking
@rbberger @akohlmey
kokkos: move #endif to correct location
d9a2fd9
@akohlmey
Merge pull request #4290 from lammps/doc-page-ke-tensors
121195d 
Amend doc page explanations of vector outputs from the various compute temp commands
@akohlmey
Merge remote-tracking branch 'github/develop' into collected-small-fixes
4e59050
@akohlmey
whitespace
ac90dca
@akohlmey
Merge pull request #4295 from akohlmey/collected-small-fixes
6e79103 
Updates for LAMMPS-GUI
@ndtrung81
Reduced the timeout for quick reg tests
a59ac7e
@akohlmey
avoid uninitialized data access in case there are no atoms owned by a…
2ebe1f0 
… process
@akohlmey
remove unused variables
5fbdf15
@akohlmey
fix cut-n-paste issue
d8b9679
@akohlmey
add option to set plugin path from the command line
83aab0f
@akohlmey
make handling of plugin path and recent files more consistent
4060de6
@akohlmey
correct define
49d6645
@akohlmey
revise plugin loading logic
c01585e
@akohlmey
sanity check
98b4771
@akohlmey
make plugin path canonical
99e5b06
@akohlmey
must register variant for QList<QString> before using QSettings
932eaf8
@akohlmey
update docs for LAMMPS-GUI plugin changes and document flatpak build
78310bd
@evoyiatzis
include variable definitions in region_plane.h
5c11c5e
@evoyiatzis
Code for variable point definition in region_plane.cpp
40cd704
@evoyiatzis
Update region.rst
709ab8f
@akohlmey
cosmetic
f2102b7
@akohlmey
Merge pull request #4298 from akohlmey/collected-small-fixes
0ad6404 
Collected small fixes for LAMMPS and LAMMPS-GUI for the stable release
@evoyiatzis @akohlmey
Update doc/src/region.rst
e311915 
Co-authored-by: Axel Kohlmeyer <[email protected]>
@ndtrung81
use the log file with 1 proc in serial runs, removed examples/bpm/imp…
f5ffb28 
…act/brokenDump
@akohlmey
Merge branch 'develop' into plumed-plugin
4e8c1f3
@ndtrung81
have a single job definition with matrix strategy, the build and env …
c60e69e 
…do not persist between jobs
@akohlmey
Merge pull request #4299 from evoyiatzis/patch-3
9339da0 
Allow the definition of point in region plane using variables
@akohlmey
Merge pull request #4324 from rbberger/cmake_optional_docenv
2995cb7 
Make CMake Doc build docenv optional
@akohlmey
make certain values for LAMMPS variables are initialized
1adaab8
@akohlmey
fix linking a URL and fix spelling
92bd9fc
@akohlmey
sync author info with LAMMPS home page
fe8611b
@akohlmey
correct indexing when filling lmp_firstneigh array
bdca275
@akohlmey
fix comparison for missing arguments when using wildcards
1587473
@akohlmey
try out concurrency group feature on quick regression as suggested by @…
79fbd46 
…junghans
@akohlmey
add concurrency group feature to unit test workflows, too.
8c4e67c
@akohlmey
relax epsilon or mark unstable based on test results on non-x86 archi…
44d86c3 
…tectures
@akohlmey
make programming style check and doc info check a github action
f8eac87
@akohlmey
fix typo
4a9b7b1
@akohlmey
remove documentation check (for now)
80cd9ac
@akohlmey
improve error message
804aa4e
@akohlmey
add extract method to bond style harmonic/shift
11365e7
@akohlmey
add support for bond style hybrid to fix adapt
5d40a96
@akohlmey
update fix adapt docs
516d988
@akohlmey
update unit test
47bb1a8
@akohlmey
support angle style hybrid with fix adapt
6503f29
@akohlmey
Merge pull request #4326 from akohlmey/collected-small-changes
805c2ae 
Collected small changes and fixes
@akohlmey
add LAPACK functions for matrix inversion via Cholesky decomposition
9f867b5
@akohlmey
replace calls to GSL with calls to LAPACK
b16b683
@akohlmey
update build support for using LAPACK with RHEO instead of GSL
1ac9f08
@akohlmey
update docs for building the RHEO package
d909b20
@akohlmey
add missing line in Install.sh file
42bcc43
@akohlmey
clarify docs
4eb1b1f
@akohlmey
try to work around macOS issue
d23b8aa
@akohlmey
we no longer need to install GSL for workflows with RHEO
3d2a344
@akohlmey
update readme
20f3b5a
@akohlmey
Merge pull request #4330 from akohlmey/rheo-gsl-to-lapack
3c8b846 
Convert RHEO package to use plain LAPACK instead of GSL
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