Collected small changes

[akohlmey]

Summary

This pull request contains collected small changes and fixes

Related Issue(s)

Addresses the problem reported here: https://matsci.org/t/error-building-mpi-shared-lib-liblammps-mpi-so-undefined-reference-to-lammps-ns-connect-param-counts/40793

Addresses the issues reported here: https://matsci.org/t/segmentation-fault-every-time-i-try-to-run-intel-acceleration/40811

Author(s)

Axel Kohlmeyer, Temple U

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

No known issues.

Implementation Notes

The following individual changes are included:

• update the detection of cythonize for the GNU make build system to be compatible with non-bash Bourne shells (like dash)
• be more careful when updating the settings for the ML-IAP package with the GNU make build system and always delete and restore settings to correctly handle detecting cythonize which also depends on the PYTHON package being installed
• let the rerun command bypass the time-dependent fix check when it resets the timestep; otherwise rerun would be rather useless for most analysis uses.
• use consistent naming scheme in force constant caching of the INTEL package. small refactor to avoid memory leaks.
• fix off-by-one bug in dihedral style fourier/intel
• fix bug in pair style lj/long/coul/long that wasn't triggering an intel style neighbor list which is required to have force field buffers allocated
• add support for recently released plumed versions 2.6.6, 2.7.4, and 2.8.0 (default is now 2.7.4)
• some refactoring to use newer and more compact APIs

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

[athomps]

I approve.