To try to get things moving a bit, here are the first few changes I
plan on submitting for people to make high level comments:
- adding the introduction.dox file
- adding the XYZRDecorator that has been mentioned numerous times (it
now supports setting the radius attribute name)
- Simplify connectivity restraint to only support sets of size 1. You
can using ParticleRefiners if you want larger sets (as in Frank's paper)
- add io support for the model. It is in a header called core/
model_io.h. In contrast to how it was in the introduction, the methods
are just called write/read rather than write_yaml as the yaml bit is
an implementation detail that there is no reason to expose and we may
want to change the format at some point
slightly later
- change the nonbonded list to use the XYZRDecorator radius by default
- add an is_nan function (this probably should go in kernel) so we
don't have the funny looking x != x in places and the intent of the
code is easier to understand.
- rearrange the BondedLists. I think the best idea there is to replace
BondedListScoreState with a simple ParticlePairsContainer (since that
is all it is) and provide a few implementations of that one of which
is equivalent to the BondDecoratorListScoreState.