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Merge pull request #307 from AdityaSavara/develop
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made getLogLikelihood_byResponses (which takes variances for uncertainties)
turned off convergence diagnostics during doe
turned off convergence diagnostics during multi-start (except for best run)
Fixed Example 12 and Example 13 to work with newest PEUQSE and dependencies
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@AdityaSavara
AdityaSavara authored Aug 7, 2022
2 parents 7fbd1a2 + 21986fa commit f8443ca
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0 ...Example07e_custom_logLikelihood - Copy.py → ...unfile_Example07e_custom_logLikelihood.py
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4 changes: 3 additions & 1 deletion Examples/Example12NoScaling/processing_function_mem_reactor_km_only.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
k_minus_1 = 1

def cmr(theta,V,k_1,k_minus_1,k_B,T0):

F_A, F_B = theta
F_T = F_A + F_B
C_T0 = P0 / (R * T0)
Expand All @@ -27,7 +28,8 @@ def cmr(theta,V,k_1,k_minus_1,k_B,T0):
return dFdV

def mem_reactor(sample):
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample, T))
#sample should be a list with 1 value.
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample[0], T))
conc_sol_last=sol[-1,:].T
# print('km',sample)
# print('F_A',conc_sol_last[0])
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23 changes: 12 additions & 11 deletions Examples/Example12NoScaling/runfile_Example12_km_only.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

import processing_function_mem_reactor_km_only as fun

UserInput.responses['responses_observed_uncertainties'] = 0.04
UserInput.responses['responses_observed_uncertainties'] = [0.04]

UserInput.simulated_response_plot_settings['x_label'] = r'$reactor outlet$'
UserInput.simulated_response_plot_settings['y_label'] = r'$ln(C_A)i$'
Expand Down Expand Up @@ -69,18 +69,19 @@
conc_sol_last=sol[-1,0].T
flow_rates_a.append(conc_sol_last)

fig = plt.figure(figsize = (5,5))
ax = fig.add_subplot(111, projection='3d')
#fig = plt.figure(figsize = (5,5))
#ax = fig.add_subplot(111, projection='3d')
fig1,ax1 = plt.subplots(figsize=(5,5))
TT, V = np.meshgrid(temperatures, volumes)
flow_rates_a=np.asarray(flow_rates_a)
FRA = flow_rates_a.reshape(TT.shape)
surf = ax.plot_surface(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax.set_xlabel('Temperature')
ax.set_ylabel('Volume')
ax.set_zlabel('Flow Rate')
ax.set_title('Surface Plot of F_A')
fig.colorbar(surf, shrink=0.5, aspect=5)
fig.savefig('synthetic_observables.png',dpi=220)
surf = ax1.pcolor(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax1.set_xlabel('Temperature')
ax1.set_ylabel('Volume')
#ax1.set_zlabel('Flow Rate')
ax1.set_title('Surface Plot of F_A')
fig1.colorbar(surf, shrink=0.5, aspect=5)
fig1.savefig('synthetic_observables.png',dpi=220)

fun.k_1 = 1e2
fun.k_minus_1 = 1
Expand All @@ -92,7 +93,7 @@
sol = odeint(fun.cmr, F0, np.linspace(0,v,50), args=(k_1,k_minus_1,k_m,t))
conc_sol_last=sol[-1,0].T
print('conc_sol_last',conc_sol_last)
UserInput.responses['responses_observed'] = conc_sol_last
UserInput.responses['responses_observed'] = [conc_sol_last]
PE_object_list.append(PEUQSE.parameter_estimation(UserInput))
fun.T = t
fun.volume = v
Expand Down
4 changes: 3 additions & 1 deletion Examples/Example12withScaling1E-3/processing_function_mem_reactor_km_only.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
k_minus_1 = 1

def cmr(theta,V,k_1,k_minus_1,k_B,T0):

F_A, F_B = theta
F_T = F_A + F_B
C_T0 = P0 / (R * T0)
Expand All @@ -27,7 +28,8 @@ def cmr(theta,V,k_1,k_minus_1,k_B,T0):
return dFdV

def mem_reactor(sample):
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample, T))
#sample should be a list with 1 value.
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample[0], T))
conc_sol_last=sol[-1,:].T
# print('km',sample)
# print('F_A',conc_sol_last[0])
Expand Down
23 changes: 12 additions & 11 deletions Examples/Example12withScaling1E-3/runfile_Example12_km_only_fixed_scaling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

import processing_function_mem_reactor_km_only as fun

UserInput.responses['responses_observed_uncertainties'] = 0.04
UserInput.responses['responses_observed_uncertainties'] = [0.04]

UserInput.simulated_response_plot_settings['x_label'] = r'$reactor outlet$'
UserInput.simulated_response_plot_settings['y_label'] = r'$ln(C_A)i$'
Expand Down Expand Up @@ -69,18 +69,19 @@
conc_sol_last=sol[-1,0].T
flow_rates_a.append(conc_sol_last)

fig = plt.figure(figsize = (5,5))
ax = fig.add_subplot(111, projection='3d')
#fig = plt.figure(figsize = (5,5))
#ax = fig.add_subplot(111, projection='3d')
fig1,ax1 = plt.subplots(figsize=(5,5))
TT, V = np.meshgrid(temperatures, volumes)
flow_rates_a=np.asarray(flow_rates_a)
FRA = flow_rates_a.reshape(TT.shape)
surf = ax.plot_surface(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax.set_xlabel('Temperature')
ax.set_ylabel('Volume')
ax.set_zlabel('Flow Rate')
ax.set_title('Surface Plot of F_A')
fig.colorbar(surf, shrink=0.5, aspect=5)
fig.savefig('synthetic_observables.png',dpi=220)
surf = ax1.pcolor(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax1.set_xlabel('Temperature')
ax1.set_ylabel('Volume')
#ax1.set_zlabel('Flow Rate')
ax1.set_title('Surface Plot of F_A')
fig1.colorbar(surf, shrink=0.5, aspect=5)
fig1.savefig('synthetic_observables.png',dpi=220)

fun.k_1 = 1e2
fun.k_minus_1 = 1
Expand All @@ -92,7 +93,7 @@
sol = odeint(fun.cmr, F0, np.linspace(0,v,50), args=(k_1,k_minus_1,k_m,t))
conc_sol_last=sol[-1,0].T
print('conc_sol_last',conc_sol_last)
UserInput.responses['responses_observed'] = conc_sol_last
UserInput.responses['responses_observed'] = [conc_sol_last]
PE_object_list.append(PEUQSE.parameter_estimation(UserInput))
fun.T = t
fun.volume = v
Expand Down
4 changes: 3 additions & 1 deletion Examples/Example12withScaling1E13/processing_function_mem_reactor_km_only.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
k_minus_1 = 1

def cmr(theta,V,k_1,k_minus_1,k_B,T0):

F_A, F_B = theta
F_T = F_A + F_B
C_T0 = P0 / (R * T0)
Expand All @@ -27,7 +28,8 @@ def cmr(theta,V,k_1,k_minus_1,k_B,T0):
return dFdV

def mem_reactor(sample):
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample, T))
#sample should be a list with 1 value.
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample[0], T))
conc_sol_last=sol[-1,:].T
# print('km',sample)
# print('F_A',conc_sol_last[0])
Expand Down
23 changes: 12 additions & 11 deletions Examples/Example12withScaling1E13/runfile_Example12_km_only_fixed_scaling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

import processing_function_mem_reactor_km_only as fun

UserInput.responses['responses_observed_uncertainties'] = 0.04
UserInput.responses['responses_observed_uncertainties'] = [0.04]

UserInput.simulated_response_plot_settings['x_label'] = r'$reactor outlet$'
UserInput.simulated_response_plot_settings['y_label'] = r'$ln(C_A)i$'
Expand Down Expand Up @@ -71,18 +71,19 @@
conc_sol_last=sol[-1,0].T
flow_rates_a.append(conc_sol_last)

fig = plt.figure(figsize = (5,5))
ax = fig.add_subplot(111, projection='3d')
#fig = plt.figure(figsize = (5,5))
#ax = fig.add_subplot(111, projection='3d')
fig1,ax1 = plt.subplots(figsize=(5,5))
TT, V = np.meshgrid(temperatures, volumes)
flow_rates_a=np.asarray(flow_rates_a)
FRA = flow_rates_a.reshape(TT.shape)
surf = ax.plot_surface(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax.set_xlabel('Temperature')
ax.set_ylabel('Volume')
ax.set_zlabel('Flow Rate')
ax.set_title('Surface Plot of F_A')
fig.colorbar(surf, shrink=0.5, aspect=5)
fig.savefig('synthetic_observables.png',dpi=220)
surf = ax1.pcolor(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax1.set_xlabel('Temperature')
ax1.set_ylabel('Volume')
#ax1.set_zlabel('Flow Rate')
ax1.set_title('Surface Plot of F_A')
fig1.colorbar(surf, shrink=0.5, aspect=5)
fig1.savefig('synthetic_observables.png',dpi=220)

fun.k_1 = 1e2
fun.k_minus_1 = 1
Expand All @@ -94,7 +95,7 @@
sol = odeint(fun.cmr, F0, np.linspace(0,v,50), args=(k_1,k_minus_1,k_m,t))
conc_sol_last=sol[-1,0].T
print('conc_sol_last',conc_sol_last)
UserInput.responses['responses_observed'] = conc_sol_last
UserInput.responses['responses_observed'] = [conc_sol_last]
PE_object_list.append(PEUQSE.parameter_estimation(UserInput))
fun.T = t
fun.volume = v
Expand Down
4 changes: 3 additions & 1 deletion Examples/Example12withScaling1E2/processing_function_mem_reactor_km_only.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
k_minus_1 = 1

def cmr(theta,V,k_1,k_minus_1,k_B,T0):

F_A, F_B = theta
F_T = F_A + F_B
C_T0 = P0 / (R * T0)
Expand All @@ -27,7 +28,8 @@ def cmr(theta,V,k_1,k_minus_1,k_B,T0):
return dFdV

def mem_reactor(sample):
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample, T))
#sample should be a list with 1 value.
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample[0], T))
conc_sol_last=sol[-1,:].T
# print('km',sample)
# print('F_A',conc_sol_last[0])
Expand Down
23 changes: 12 additions & 11 deletions Examples/Example12withScaling1E2/runfile_Example12_km_only_fixed_scaling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

import processing_function_mem_reactor_km_only as fun

UserInput.responses['responses_observed_uncertainties'] = 0.04
UserInput.responses['responses_observed_uncertainties'] = [0.04]

UserInput.simulated_response_plot_settings['x_label'] = r'$reactor outlet$'
UserInput.simulated_response_plot_settings['y_label'] = r'$ln(C_A)i$'
Expand Down Expand Up @@ -69,18 +69,19 @@
conc_sol_last=sol[-1,0].T
flow_rates_a.append(conc_sol_last)

fig = plt.figure(figsize = (5,5))
ax = fig.add_subplot(111, projection='3d')
#fig = plt.figure(figsize = (5,5))
#ax = fig.add_subplot(111, projection='3d')
fig1,ax1 = plt.subplots(figsize=(5,5))
TT, V = np.meshgrid(temperatures, volumes)
flow_rates_a=np.asarray(flow_rates_a)
FRA = flow_rates_a.reshape(TT.shape)
surf = ax.plot_surface(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax.set_xlabel('Temperature')
ax.set_ylabel('Volume')
ax.set_zlabel('Flow Rate')
ax.set_title('Surface Plot of F_A')
fig.colorbar(surf, shrink=0.5, aspect=5)
fig.savefig('synthetic_observables.png',dpi=220)
surf = ax1.pcolor(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax1.set_xlabel('Temperature')
ax1.set_ylabel('Volume')
#ax1.set_zlabel('Flow Rate')
ax1.set_title('Surface Plot of F_A')
fig1.colorbar(surf, shrink=0.5, aspect=5)
fig1.savefig('synthetic_observables.png',dpi=220)

fun.k_1 = 1e2
fun.k_minus_1 = 1
Expand All @@ -92,7 +93,7 @@
sol = odeint(fun.cmr, F0, np.linspace(0,v,50), args=(k_1,k_minus_1,k_m,t))
conc_sol_last=sol[-1,0].T
print('conc_sol_last',conc_sol_last)
UserInput.responses['responses_observed'] = conc_sol_last
UserInput.responses['responses_observed'] = [conc_sol_last]
PE_object_list.append(PEUQSE.parameter_estimation(UserInput))
fun.T = t
fun.volume = v
Expand Down
4 changes: 3 additions & 1 deletion Examples/Example12withScaling1E5/processing_function_mem_reactor_km_only.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
k_minus_1 = 1

def cmr(theta,V,k_1,k_minus_1,k_B,T0):

F_A, F_B = theta
F_T = F_A + F_B
C_T0 = P0 / (R * T0)
Expand All @@ -27,7 +28,8 @@ def cmr(theta,V,k_1,k_minus_1,k_B,T0):
return dFdV

def mem_reactor(sample):
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample, T))
#sample should be a list with 1 value.
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample[0], T))
conc_sol_last=sol[-1,:].T
# print('km',sample)
# print('F_A',conc_sol_last[0])
Expand Down
23 changes: 12 additions & 11 deletions Examples/Example12withScaling1E5/runfile_Example12_km_only_fixed_scaling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

import processing_function_mem_reactor_km_only as fun

UserInput.responses['responses_observed_uncertainties'] = 0.04
UserInput.responses['responses_observed_uncertainties'] = [0.04]

UserInput.simulated_response_plot_settings['x_label'] = r'$reactor outlet$'
UserInput.simulated_response_plot_settings['y_label'] = r'$ln(C_A)i$'
Expand Down Expand Up @@ -69,18 +69,19 @@
conc_sol_last=sol[-1,0].T
flow_rates_a.append(conc_sol_last)

fig = plt.figure(figsize = (5,5))
ax = fig.add_subplot(111, projection='3d')
#fig = plt.figure(figsize = (5,5))
#ax = fig.add_subplot(111, projection='3d')
fig1,ax1 = plt.subplots(figsize=(5,5))
TT, V = np.meshgrid(temperatures, volumes)
flow_rates_a=np.asarray(flow_rates_a)
FRA = flow_rates_a.reshape(TT.shape)
surf = ax.plot_surface(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax.set_xlabel('Temperature')
ax.set_ylabel('Volume')
ax.set_zlabel('Flow Rate')
ax.set_title('Surface Plot of F_A')
fig.colorbar(surf, shrink=0.5, aspect=5)
fig.savefig('synthetic_observables.png',dpi=220)
surf = ax1.pcolor(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax1.set_xlabel('Temperature')
ax1.set_ylabel('Volume')
#ax1.set_zlabel('Flow Rate')
ax1.set_title('Surface Plot of F_A')
fig1.colorbar(surf, shrink=0.5, aspect=5)
fig1.savefig('synthetic_observables.png',dpi=220)

fun.k_1 = 1e2
fun.k_minus_1 = 1
Expand All @@ -92,7 +93,7 @@
sol = odeint(fun.cmr, F0, np.linspace(0,v,50), args=(k_1,k_minus_1,k_m,t))
conc_sol_last=sol[-1,0].T
print('conc_sol_last',conc_sol_last)
UserInput.responses['responses_observed'] = conc_sol_last
UserInput.responses['responses_observed'] = [conc_sol_last]
PE_object_list.append(PEUQSE.parameter_estimation(UserInput))
fun.T = t
fun.volume = v
Expand Down
6 changes: 4 additions & 2 deletions Examples/Example12withScaling2E3/processing_function_mem_reactor_km_only.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,18 +16,20 @@
k_minus_1 = 1

def cmr(theta,V,k_1,k_minus_1,k_B,T0):

F_A, F_B = theta
F_T = F_A + F_B
C_T0 = P0 / (R * T0)
C_A = C_T0 * F_A / F_T
C_B = C_T0 * F_B / F_T
r_A = k_1*C_A - k_minus_1*C_B
R_B = np.array(k_B)*np.array(C_B)
R_B = k_B*C_B
dFdV = [-r_A, r_A - R_B]
return dFdV

def mem_reactor(sample):
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample, T))
#sample should be a list with 1 value.
sol = odeint(cmr, F0, np.linspace(0,volume,2), args=(k_1, k_minus_1, sample[0], T))
conc_sol_last=sol[-1,:].T
# print('km',sample)
# print('F_A',conc_sol_last[0])
Expand Down
23 changes: 12 additions & 11 deletions Examples/Example12withScaling2E3/runfile_Example12_km_only_fixed_no_offset.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

import processing_function_mem_reactor_km_only as fun

UserInput.responses['responses_observed_uncertainties'] = 0.04
UserInput.responses['responses_observed_uncertainties'] = [0.04]

UserInput.simulated_response_plot_settings['x_label'] = r'$reactor outlet$'
UserInput.simulated_response_plot_settings['y_label'] = r'$ln(C_A)i$'
Expand Down Expand Up @@ -69,18 +69,19 @@
conc_sol_last=sol[-1,0].T
flow_rates_a.append(conc_sol_last)

fig = plt.figure(figsize = (5,5))
ax = fig.add_subplot(111, projection='3d')
#fig = plt.figure(figsize = (5,5))
#ax = fig.add_subplot(111, projection='3d')
fig1,ax1 = plt.subplots(figsize=(5,5))
TT, V = np.meshgrid(temperatures, volumes)
flow_rates_a=np.asarray(flow_rates_a)
FRA = flow_rates_a.reshape(TT.shape)
surf = ax.plot_surface(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax.set_xlabel('Temperature')
ax.set_ylabel('Volume')
ax.set_zlabel('Flow Rate')
ax.set_title('Surface Plot of F_A')
fig.colorbar(surf, shrink=0.5, aspect=5)
fig.savefig('synthetic_observables.png',dpi=220)
surf = ax1.pcolor(TT,V,FRA,cmap=matplotlib.cm.coolwarm)
ax1.set_xlabel('Temperature')
ax1.set_ylabel('Volume')
#ax1.set_zlabel('Flow Rate')
ax1.set_title('Surface Plot of F_A')
fig1.colorbar(surf, shrink=0.5, aspect=5)
fig1.savefig('synthetic_observables.png',dpi=220)

fun.k_1 = 1e2
fun.k_minus_1 = 1
Expand All @@ -92,7 +93,7 @@
sol = odeint(fun.cmr, F0, np.linspace(0,v,50), args=(k_1,k_minus_1,k_m,t))
conc_sol_last=sol[-1,0].T
print('conc_sol_last',conc_sol_last)
UserInput.responses['responses_observed'] = conc_sol_last
UserInput.responses['responses_observed'] = [conc_sol_last]
PE_object_list.append(PEUQSE.parameter_estimation(UserInput))
fun.T = t
fun.volume = v
Expand Down
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