update AGNI potential for Al, reference runs and output and citation

improve consistency of manual

Fixes for PairAIREBO::bondorderLJ

this closes #386

collected small bugfixes and updates

more neighbor list changes, some new options

Kokkos version of class2 bond, angle, dihedral, and improper from Ray Shan

neighbor_kokkos.cpp: Don't call grow() on neighbor lists that are copies

updated documentation and examples for coreshell

Fixed bugs with pppm/gpu when used with compute group/group

USER-DPD: performance optimizations to ssa_update() in fix_shardlow

Kokkos library update

This corresponds to a bugfix from commit 9161bd98 on neighbor.cpp

Since we compute dvdw as d vdw / d rij, we have to also compute
dslw as d slw / d rij. Currently, we compute -1/r d slw/d rij,
which leads to incorrect results when the two are later combined.
Alternatively, one could also modify dvdw to be -1/r d vdw/d rij,
which would be a more standard way to do LJ calculations, but this
way seems more consistent.

Overall improvements range from 2% to 18% on our benchmarks
1) Newton has to be turned on for SSA, so remove those conditionals
2) Rework the math in ssa_update() to eliminate many ops and temporaries
3) Split ssa_update() into two versions, based on DPD vs. DPDE
4) Reorder code in ssa_update_*() to reduce register pressure