Improve performance in MD simulations with many barrier particles.

[joaander]

Description

Improve performance in MD simulations with many barrier particles.

Proposed solution

When there are any 0 entries in the r_cut matrix, generate a list of particle indices that have more than 0 neighbors. Adjust the pair force loops to loop over only particles with non-zero numbers of neighbors.

Additional context

Obtain system configurations from users to benchmark the performance benefits.

[github-actions]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions]

This issue has been automatically closed because it has not had recent activity.

[tcmoore3]

Reopening because of the possible performance benefits for systems of rigid body + surface patches, where the rigid body centers don't interact with the constituent particles.