More fine grained monitoring if computes were initialized

[akohlmey]

Summary

This updates and refactors the changes from PR #3771 to handle cases of computes being created after a run.

Author(s)

Axel Kohlmeyer and Steve Plimpton, 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

N/A

Implementation Notes

This introduces a flag inside the Compute class that tracks whether the compute was initialized by a run or minimize or something else that calls Modify::init(). This flag can be queried with a new Compute::is_initialized() method.

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