From 76f781fd80512d0c004c74238858bf8cbf8e393d Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 18 Dec 2018 13:48:36 -0600
Subject: [PATCH] Fixed code adding dihedral angles between adjacent crossovers
---
mrdna/segmentmodel.py | 16 +++++-----------
1 file changed, 5 insertions(+), 11 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 7782a80..a6d5632 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -2317,9 +2317,6 @@ class SegmentModel(ArbdModel):
for crossovers in self.get_consecutive_crossovers():
if local_twist: break
## filter crossovers
- new_cl = []
- lastParticle = None
- crossovers = new_cl
for i in range(len(crossovers)-2):
c1,A1,B1,dir1 = crossovers[i]
c2,A2,B2,dir2 = crossovers[i+1]
@@ -2333,10 +2330,6 @@ class SegmentModel(ArbdModel):
"""
<cos(q)> = exp(-s/Lp) = integrate( cos[x] exp(-A x^2), {x, 0, pi} ) / integrate( exp(-A x^2), {x, 0, pi} )
- Assume A is small
- int[B_] := Normal[Integrate[ Series[Cos[x] Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]/
- Integrate[Series[Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]]
- Actually, without assumptions I get fitFun below
"""
## From http://www.annualreviews.org/doi/pdf/10.1146/annurev.bb.17.060188.001405
@@ -2348,7 +2341,7 @@ class SegmentModel(ArbdModel):
k = opt.leastsq( fitFun, x0=np.exp(-sep/Lp) )
return k[0][0] * 2*kT*0.00030461742
- k = get_spring( max(sep,1.0) )
+ k = get_spring( max(sep,2) )
t0 = sep*s1.twist_per_nt # TODO weighted avg between s1 and s2
# pdb.set_trace()
@@ -2363,9 +2356,10 @@ class SegmentModel(ArbdModel):
# if n2.idx == 0:
# print( n1.idx,n2.idx,n3.idx,n4.idx,k,t0,sep )
- if sep == 0:
- pot = self.get_angle_potential(k,t0)
- self.add_angle( n1,n2,n4, pot )
+ if sep == 0 and n1 is not n4:
+ # pot = self.get_angle_potential(k,t0)
+ # self.add_angle( n1,n2,n4, pot )
+ pass
else:
pot = self.get_dihedral_potential(k,t0)
self.add_dihedral( n1,n2,n3,n4, pot )
--
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