Merge branch 'core_soft' of https://github.com/agiliopadua/lammps into combined-user-fep-soft-updates

Resolved Conflicts:
	doc/src/compute_fep.txt
	doc/src/fix_adapt_fep.txt

Merge branch 'soft_class2_potentials' of https://github.com/evoyiatzis/lammps into combined-user-fep-soft-updates

Fix mistake in mixing rules for mm3/switch3

Add USER-YAFF package for MOF simulations with QuickFF

Bond/react: add reaction constraints support

USER-CGDNA PDF docs update

introduce a distance constraint between any two reaction-site atoms, in order for reaction to occur

rebase

There are several potentials that contain the method extract() but they are not included in the "fix adapt" and "fix adapt/fep"
A small update of the list is attempted here. The same potentials might be added to the documentation of fix_adapt if it is useful.

Optimize Kokkos SNAP energy calculation

Fix bug in virial calculation for impropers fourier and umbrella

bond/react: strict reaction limit and serial compilation bugfix

also, fixes a bug in the 'serial' build introduced in #1099, wherein no reactions could occur in some cases