Commit 6f48f441 authored by cmaffeo2's avatar cmaffeo2
Browse files

Made bond potentials longer ranged (120 vs 50 nm), and removed unneeded...

Made bond potentials longer ranged (120 vs 50 nm), and removed unneeded 'continue' statement that was attempting to prevent double-counting when placing initial beads
parent 541789d7
......@@ -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 )
......
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