Warn that extraBonds angles are cosine-based and allow harmonic 63/4763/3
authorJim Phillips <jim@ks.uiuc.edu>
Thu, 1 Nov 2018 03:40:58 +0000 (22:40 -0500)
committerDavid Hardy <dhardy@ks.uiuc.edu>
Mon, 5 Nov 2018 23:23:07 +0000 (17:23 -0600)
commitdc1e20c8d759a9f6df2965cdf193f1eafac110b8
tree9e9b86e0d56f9d19c781e757e632226947c4081e
parent1c5a0775074769b76c1b5ab18853ff2c57e8bfc7
Warn that extraBonds angles are cosine-based and allow harmonic

The "normal" flag for extraBonds angles was left uninitialized
when the cosAngles feature was implemented, which tends to
result in extraBonds angles being treated as cosine-based.

Since workflows may unknowingly depend on the current behavior
warn the user and add extraBondsCosAngles option to change it.
Also fix bad comment that reversed meaning of normal flag.

Change-Id: I1a300d6b12654c676c91f15236b135ef3e5fc4e3
src/Molecule.C
src/Parameters.h
src/SimParameters.C
src/SimParameters.h
ug/ug_forcefield.tex