From 6f48f4413c98e145d6d84b77098af3f744277e1a Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Mon, 13 Aug 2018 16:48:15 -0500
Subject: [PATCH] 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
---
segmentmodel.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/segmentmodel.py b/segmentmodel.py
index 12f7962..4f17c64 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 )
--
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