Collected fixes and small changes for the next patch release

[akohlmey]

Summary

This pull request collects multiple small changes and bug fixes for the next release.

Related Issue(s)

Fixes #3441

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:

• recover broken non-labelmap behavior for KOKKOS package. Using a labelmap with Kokkos active triggers an error.
• multiple styles in the EXTRA-MOLECULE package require the MOLECULE package to be installed add dependency
• unit test for fix adapt with long-range coulomb was missing a dependency on pppm
• optimize some C++11 style auto loops by using references
• code improvements suggested by clang-tidy
• reformat with clang-format
• silence some compiler warnings
• allow to build fortran module tests with clang/flang
• rename some ambiguous loop variables in nested loops
• add singularity/apptainer container definition for Alma Linux 9

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