author W. Trevor King Fri, 5 Nov 2010 17:43:33 +0000 (10:43 -0700) committer W. Trevor King Fri, 5 Nov 2010 17:43:33 +0000 (10:43 -0700)

index bccf3f1..97f755a 100755 (executable)
@@ -111,8 +111,8 @@ class ExponentialModelFitter (HistogramModelFitter):

def constant_rate(sawsim_runner, num_domains=1, unfolding_rate=1,
-                  spring_constant=1, velocity=1, N=400):
+                  spring_constant=1, velocity=1, N=100):
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()

+    max_time_step = tau/10.0
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)
@@ -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],
-         velocity=[1,2], threshold=0.3):
+         velocity=[1,2], threshold=0.2):
m = get_manager()()
sr = SawsimRunner(manager=m)
try: