Output individual energies in fix restrain

C++ style header includes and C++ standard conforming code changes in lib folder

Remove Kokkos deprecated code

cmake: remove obsolete BODY/POEMS conflict

More fixes to conform with C++ standards as indicated by Clang

Docs update and journal reference for USER-CGDNA package

Computation of forces/torques on rigid bodies moved to post_force

Group extract

Collected small changes, fixes and updates

Collected changes to restore C++ standard compliance

bond/react final touches

Fix bug in create_bonds single/bond