Merge branch 'master' into github-tutorial-update

doc/src/Manual.txt

doc/src/PDF/colvars-refman-lammps.pdf

doc/src/Section_commands.txt

doc/src/fix_colvars.txt

doc/src/fix_eos_table_rx.txt

doc/src/fix_momentum.txt

doc/src/fix_nvk.txt

doc/src/fixes.txt

doc/src/lammps.book

doc/src/pair_exp6_rx.txt

doc/src/pair_multi_lucy_rx.txt

doc/src/pair_table_rx.txt

examples/USER/dpd/dpde-vv/log.dpde-vv.reference

examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow

...ples/USER/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference

lib/colvars/Makefile.colvars

lib/colvars/colvar.cpp

lib/colvars/colvar.h

lib/colvars/colvaratoms.cpp

lib/colvars/colvaratoms.h