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):