Collected small fixes

[akohlmey]

Summary

This pull request contains multiple small fixes and changes

Related Issue(s)

Closes #4921

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).

Artificial Intelligence (AI) Tools Usage

By submitting this pull request, I confirm that I did NOT use any AI tools to generate
all or parts of the code and modifications in this pull request.

Backward Compatibility

N/A

Implementation Notes

The following individual changes are included:

• fix up a few issues with the increased SafeFilePtr class like removing forgotten fclose() or pclose() statements
• address some issues reported by coverity scan
• print a warning when file style and atomfile style variables are deleted at the end of the file as this may lead to unexpected behavior

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