init = np.ones(len(prop))
init[0] = 1.
profile = np.dot(prop, init)
return profile
#f = file("out.time.txt","w+")
#f.close()
import sys
import matplotlib.pyplot as plt
filename = sys.argv[1]
F, D, edges = read_F_D_edges(filename)
def extend_vec(F, ):
n = len(F)
newF = np.zeros((3 * n), float)
newF[:n] = F[0]
newF[2 * n:] = F[-1]
newF[n:2 * n] = F
return newF
#F = extend_vec(F)
#D = extend_vec(D)
sink_index = len(F) - 1
def use_initfile(self, initfile, final=True):
if self.model.ncosF > 0:
v_coeff = read_Fcoeffs(initfile, final=True) # unit: v_coeff[0] in kBT
nc = len(v_coeff)
if nc > 0:
print "USING initfile for v_coeff", initfile, nc, "coeffs"
n = min(nc, self.model.ncosF)
self.model.v_coeff[:n] = v_coeff[:n]
self.model.update_v()
else:
F, D, edges = read_F_D_edges(initfile) # unit: F in kBT
nc = len(F)
assert nc == len(self.model.v)
print "USING initfile for v", initfile, nc, "values"
self.model.v = F # unit: always in kBT
if self.model.ncosD > 0:
w_coeff = read_Dcoeffs(initfile, final=True) # unit: w_coeff[0] in angstrom**2/ps
nc = len(w_coeff)
if nc > 0:
print "USING initfile for w_coeff", initfile, nc, "coeffs"
n = min(nc, self.model.ncosD)
self.model.w_coeff[:n] = w_coeff[:n]
self.model.w_coeff[0] -= self.model.wunit
self.model.update_w()
else:
F, D, edges = read_F_D_edges(initfile) # unit: D in angstrom**2/ps
nc = len(D)
assert nc == len(self.model.w)
print "USING initfile for w", initfile, nc, "values"
self.model.w = np.log(D) - self.model.wunit
if self.do_radial:
if self.model.ncosDrad > 0:
coeff = read_Dradcoeffs(initfile, final=True) # unit: wrad_coeff[0] in angstrom**2/ps
nc = len(coeff)
if nc > 0:
print "USING initfile for wrad_coeff", initfile, nc, "coeffs"
n = min(nc, self.model.ncosDrad)
self.model.wrad_coeff[:n] = coeff[:n]
self.model.wrad_coeff[0] -= self.model.wradunit
self.model.update_wrad()
else:
# print self.model.wrad_coeff
coeff = read_Dcoeffs(initfile, final=True) # unit: w_coeff[0] in angstrom**2/ps
nc = len(coeff)
if nc > 0:
print "USING initfile for wrad_coeff", initfile, nc, "coeffs, using w_coeff!"
n = min(nc, self.model.ncosDrad)
self.model.wrad_coeff[:n] = coeff[:n]
self.model.wrad_coeff[0] -= self.model.wradunit
self.model.update_wrad()
# print self.model.wrad_coeff
else:
Drad, redges = read_Drad(initfile) # unit: Drad in angstrom**2/ps
nc = len(Drad)
assert nc == len(self.model.wrad)
print "USING initfile for wrad", initfile, nc, "values"
self.model.wrad = np.log(Drad) - self.model.wradunit
dv, dw = read_dv_dw(initfile, final=True)
def use_initfile(self, initfile, final=True):
if self.model.ncosF > 0:
v_coeff = read_Fcoeffs(initfile,
final=True) # unit: v_coeff[0] in kBT
nc = len(v_coeff)
if nc > 0:
print "USING initfile for v_coeff", initfile, nc, "coeffs"
n = min(nc, self.model.ncosF)
self.model.v_coeff[:n] = v_coeff[:n]
self.model.update_v()
else:
F, D, edges = read_F_D_edges(initfile) # unit: F in kBT
nc = len(F)
assert nc == len(self.model.v)
print "USING initfile for v", initfile, nc, "values"
self.model.v = F # unit: always in kBT
if self.model.ncosD > 0:
w_coeff = read_Dcoeffs(
initfile, final=True) # unit: w_coeff[0] in angstrom**2/ps
nc = len(w_coeff)
if nc > 0:
print "USING initfile for w_coeff", initfile, nc, "coeffs"
n = min(nc, self.model.ncosD)
self.model.w_coeff[:n] = w_coeff[:n]
self.model.w_coeff[0] -= self.model.wunit
self.model.update_w()
else:
F, D, edges = read_F_D_edges(initfile) # unit: D in angstrom**2/ps
nc = len(D)
assert nc == len(self.model.w)
print "USING initfile for w", initfile, nc, "values"
self.model.w = np.log(D) - self.model.wunit
if self.do_radial:
if self.model.ncosDrad > 0:
coeff = read_Dradcoeffs(
initfile,
final=True) # unit: wrad_coeff[0] in angstrom**2/ps
nc = len(coeff)
if nc > 0:
print "USING initfile for wrad_coeff", initfile, nc, "coeffs"
n = min(nc, self.model.ncosDrad)
self.model.wrad_coeff[:n] = coeff[:n]
self.model.wrad_coeff[0] -= self.model.wradunit
self.model.update_wrad()
else:
#print self.model.wrad_coeff
coeff = read_Dcoeffs(
initfile,
final=True) # unit: w_coeff[0] in angstrom**2/ps
nc = len(coeff)
if nc > 0:
print "USING initfile for wrad_coeff", initfile, nc, "coeffs, using w_coeff!"
n = min(nc, self.model.ncosDrad)
self.model.wrad_coeff[:n] = coeff[:n]
self.model.wrad_coeff[0] -= self.model.wradunit
self.model.update_wrad()
#print self.model.wrad_coeff
else:
Drad, redges = read_Drad(
initfile) # unit: Drad in angstrom**2/ps
nc = len(Drad)
assert nc == len(self.model.wrad)
print "USING initfile for wrad", initfile, nc, "values"
self.model.wrad = np.log(Drad) - self.model.wradunit
dv, dw = read_dv_dw(initfile, final=True)
#print prop
init = np.ones(len(prop))
init[0] = 1.
profile = np.dot(prop,init)
return profile
#f = file("out.time.txt","w+")
#f.close()
import sys
import matplotlib.pyplot as plt
filename = sys.argv[1]
F,D,edges = read_F_D_edges(filename)
def extend_vec(F,):
n = len(F)
newF = np.zeros((3*n),float)
newF[:n] = F[0]
newF[2*n:] = F[-1]
newF[n:2*n] = F
return newF
#F = extend_vec(F)
#D = extend_vec(D)
sink_index = len(F)-1
plt.figure()
for time in np.arange(0,1,0.2):