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Fixup pysawsim.test.constant_rate so it passes.
author
W. Trevor King
<wking@drexel.edu>
Fri, 5 Nov 2010 17:43:33 +0000
(10:43 -0700)
committer
W. Trevor King
<wking@drexel.edu>
Fri, 5 Nov 2010 17:43:33 +0000
(10:43 -0700)
pysawsim/test/constant_rate.py
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diff --git
a/pysawsim/test/constant_rate.py
b/pysawsim/test/constant_rate.py
index bccf3f15e2000bd4aff1d938e9f94f7047bd6370..97f755a90c5234759f3e1334460f9340e5f6099e 100755
(executable)
--- a/
pysawsim/test/constant_rate.py
+++ b/
pysawsim/test/constant_rate.py
@@
-111,8
+111,8
@@
class ExponentialModelFitter (HistogramModelFitter):
def constant_rate(sawsim_runner, num_domains=1, unfolding_rate=1,
def constant_rate(sawsim_runner, num_domains=1, unfolding_rate=1,
- spring_constant=1, velocity=1, N=
4
00):
- loading_rate =
spring_constant * velocity
+ spring_constant=1, velocity=1, N=
1
00):
+ loading_rate =
float(spring_constant * velocity)
tau = loading_rate / unfolding_rate
w = 0.1 * tau # calculate bin width (in force)
A = w*num_domains*N / tau
tau = loading_rate / unfolding_rate
w = 0.1 * tau # calculate bin width (in force)
A = w*num_domains*N / tau
@@
-126,10
+126,13
@@
def constant_rate(sawsim_runner, num_domains=1, unfolding_rate=1,
theory.bin_centers, [tau])
theory.analyze()
theory.bin_centers, [tau])
theory.analyze()
+ max_time_step = tau/10.0
+ max_force_step = loading_rate * max_time_step
param_string = (
param_string = (
- '-v %(velocity)s -s cantilever,hooke,%(spring_constant)s -N1 '
- '-s folded,null -N%(num_domains)s -s unfolded,null '
- '-k folded,unfolded,const,%(unfolding_rate)s -q folded '
+ '-d %(max_time_step)g -F %(max_force_step)g -v %(velocity)g '
+ '-s cantilever,hooke,%(spring_constant)g -N1 '
+ '-s folded,null -N%(num_domains)d -s unfolded,null '
+ '-k folded,unfolded,const,%(unfolding_rate)g -q folded '
) % locals()
sim = sawsim_histogram(sawsim_runner, param_string, N=N,
bin_edges=theory.bin_edges)
) % locals()
sim = sawsim_histogram(sawsim_runner, param_string, N=N,
bin_edges=theory.bin_edges)
@@
-143,7
+146,7
@@
def constant_rate(sawsim_runner, num_domains=1, unfolding_rate=1,
def test(num_domains=[1,50], unfolding_rate=[1,2], spring_constant=[1,2],
def test(num_domains=[1,50], unfolding_rate=[1,2], spring_constant=[1,2],
- velocity=[1,2], threshold=0.
3
):
+ velocity=[1,2], threshold=0.
2
):
m = get_manager()()
sr = SawsimRunner(manager=m)
try:
m = get_manager()()
sr = SawsimRunner(manager=m)
try: