diff --git a/segmentmodel.py b/segmentmodel.py index 12f7962e180679d2611495a19fc3ad4c19dacc2d..4f17c64f7b4fb1d8dbc4e5b38cf4ac580144117f 100644 --- a/segmentmodel.py +++ b/segmentmodel.py @@ -1264,7 +1264,7 @@ class SegmentModel(ArbdModel): key = (type_, kSpring, d, max_potential) if key not in self._bonded_potential: if type_ == "bond": - self._bonded_potential[key] = HarmonicBond(kSpring,d, rRange=(0,500), max_potential=max_potential) + self._bonded_potential[key] = HarmonicBond(kSpring,d, rRange=(0,1200), max_potential=max_potential) elif type_ == "angle": self._bonded_potential[key] = HarmonicAngle(kSpring,d, max_potential=max_potential) # , resolution = 1, maxForce=0.1) @@ -1526,8 +1526,10 @@ class SegmentModel(ArbdModel): # print("Working on {}".format(c)) ## TODO be more elegant! # if isinstance(s1, DoubleStrandedSegment) and isinstance(s2, DoubleStrandedSegment) and A.on_fwd_strand == False: continue - if isinstance(s1, DoubleStrandedSegment) and isinstance(s2, DoubleStrandedSegment) and A.on_fwd_strand == False: continue + # if isinstance(s1, DoubleStrandedSegment) and isinstance(s2, DoubleStrandedSegment) and A.on_fwd_strand == False: continue ## if A.on_fwd_strand == False: continue # TODO verify this avoids double-counting + ## TODO determine whether any logic is needed to prevent double-counting + assert( A.particle is None ) assert( B.particle is None )