small bug fixes

doc/README.md

doc/html/Section_howto.html

doc/html/compute_omega_chunk.html

doc/html/fix_nve_manifold_rattle.html

doc/html/fix_nvt_manifold_rattle.html

doc/html/searchindex.js

doc/src/compute_omega_chunk.txt

lib/meam/meam_setup_done.F

src/BODY/compute_body_local.h

src/RIGID/compute_rigid_local.h

src/USER-REAXC/compute_spec_atom.h

src/atom.cpp

src/compute_angle_local.cpp

src/compute_angle_local.h

src/compute_bond_local.cpp

src/compute_bond_local.h

src/compute_chunk_atom.cpp

src/compute_cna_atom.cpp

src/compute_dihedral_local.cpp

src/compute_dihedral_local.h