Develop Reference

Biodiesel Reactor Design with GEKKO on Python

I'm trying to model a biodiesel reactor on python using GEKKO, but I'm not getting obtain the correct temperature profile, the Manipulated Variable doesn't change the value as expected... Here is my code:
import numpy as np
import matplotlib.pyplot as plt
from gekko import GEKKO
m = GEKKO()
nt = 1001
m.time = np.linspace(0,100,nt)
# Parameters
T = m.MV(value=321,ub=338,lb=298)
T.STATUS = 1
T.DCOST = 0.01
T.DMAX = 20
# Variables
CTG = m.Var(value=0.3226)
CDG = m.Var(value=0)
CMG = m.Var(value=0)
CE = m.Var(value=0)
CA = m.Var(value=1.9356)
CG = m.Var(value=0)
p = np.zeros(nt)
p[-1] = 1.0
final = m.Param(value=p)
# Intermediates
k1 = m.Intermediate(3.92e7*m.exp(-6614.83/T))
k2 = m.Intermediate(5.77e5*m.exp(-4997.98/T))
k3 = m.Intermediate(5.88e12*m.exp(-9993.96/T))
k4 = m.Intermediate(0.98e10*m.exp(-7366.64/T))
k5 = m.Intermediate(5.35e3*m.exp(-3231.18/T))
k6 = m.Intermediate(2.15e4*m.exp(-4824.87/T))
# Equations
m.Equation(CTG.dt()== -k1*CTG*CA + k2*CDG*CE)
m.Equation(CDG.dt()== k1*CTG*CA - k2*CDG*CE - k3*CDG*CA + k4*CMG*CE)
m.Equation(CMG.dt()== k3*CDG*CA - k4*CMG*CE - k5*CMG*CA + k6*CG*CE)
m.Equation(CE.dt()== k1*CTG*CA - k2*CDG*CE + k3*CDG*CA - k4*CMG*CE + k5*CMG*CA - k6*CG*CE)
m.Equation(CA.dt()== -CE.dt())
m.Equation(CG.dt()== k5*CMG*CA - k6*CG*CE)
# Objective Function
m.Maximize(CE*final)
m.options.IMODE = 9
m.solve()
print('Objective: ' + str(CE[-1]))
plt.figure(1)
plt.subplot(2,1,1)
plt.plot(m.time,CE.value,'k:',lw=2,label=r'$C_E$')
plt.plot(m.time,CTG.value,'b-',lw=2,label=r'$C_TG$')
plt.plot(m.time,CA.value,'g-',lw=2,label=r'$C_A$')
plt.ylabel('Value')
plt.legend(loc='best')
plt.figure(2)
plt.subplot(2,1,2)
plt.plot(m.time,T.value,'r--',lw=2,label=r'$Temp$')
plt.legend(loc='best')
plt.xlabel('Time')
plt.ylabel('Value')
plt.show()
I need to obtain a temperature profile like this:

A sensitivity study reveals that the optimal solution is to maximize the temperature. The problem with the code in your question is the selection of IMODE=9. Use IMODE=6 with less time points for a more reliable solution. The sequential optimization mode (9) is not as reliable as the simulataneous mode (6).
Here is a simulation at different temperatures with the temperature status off.
T.STATUS = 0
The simulation sensitivity study shows that there is an effect of temperature on the final objective. Using T.STATUS=1 with different initial conditions also reveals that higher temperature gives a more optimal solution. The only effect of the initial condition is that it requires one or two steps to get up to the maximum allowable temperature.
import numpy as np
import matplotlib.pyplot as plt
from gekko import GEKKO
m = GEKKO()
nt = 101
m.time = np.linspace(0,100,nt)
# Parameters
T = m.MV(value=321,ub=338,lb=298)
T.STATUS = 1
T.DCOST = 0 #0.01
T.DMAX = 20
# Variables
CTG = m.Var(value=0.3226)
CDG = m.Var(value=0)
CMG = m.Var(value=0)
CE = m.Var(value=0)
CA = m.Var(value=1.9356)
CG = m.Var(value=0)
p = np.zeros(nt)
p[-1] = 1.0
final = m.Param(value=p)
# Intermediates
k1 = m.Intermediate(3.92e7*m.exp(-6614.83/T))
k2 = m.Intermediate(5.77e5*m.exp(-4997.98/T))
k3 = m.Intermediate(5.88e12*m.exp(-9993.96/T))
k4 = m.Intermediate(0.98e10*m.exp(-7366.64/T))
k5 = m.Intermediate(5.35e3*m.exp(-3231.18/T))
k6 = m.Intermediate(2.15e4*m.exp(-4824.87/T))
# Equations
m.Equation(CTG.dt()== -k1*CTG*CA + k2*CDG*CE)
m.Equation(CDG.dt()== k1*CTG*CA - k2*CDG*CE - k3*CDG*CA + k4*CMG*CE)
m.Equation(CMG.dt()== k3*CDG*CA - k4*CMG*CE - k5*CMG*CA + k6*CG*CE)
m.Equation(CE.dt()== k1*CTG*CA - k2*CDG*CE + k3*CDG*CA - k4*CMG*CE + k5*CMG*CA - k6*CG*CE)
m.Equation(CA.dt()== -CE.dt())
m.Equation(CG.dt()== k5*CMG*CA - k6*CG*CE)
# Objective Function
m.Maximize(CE*final)
m.options.IMODE=6
m.options.NODES=3
m.options.SOLVER=3
plt.figure()
m.options.TIME_SHIFT=0
for Ti in [300,305,310,315,320,325,330,335]:
T.value=Ti
m.solve(disp=False)
plt.subplot(2,1,1)
plt.plot(m.time,CE.value,lw=2,label=r'$C_E$ # $T_0$='+str(Ti))
plt.subplot(2,1,2)
plt.plot(m.time,T.value,lw=2,label=r'$T$ # $T_0$='+str(Ti))
print(Ti,'K Objective: ' + str(CE[-1]))
plt.ylabel('Value')
plt.legend(loc='best')
plt.xlabel('Time')
plt.show()
I would recommend that you feed in the optimal solution that comes from the publication as an initial guess to see if that improves the optimization result. There may be a difference in equations or objective function that gives the different results.

When solving nonlinear regression problem over a long data set, the Objective value comes high? As a result estimation fails

I am trying to minimize the average root mean squared error of the following form in a class file using Gekko:
objective = np.sqrt((np.sum((ym-np.array(y))**2))/N/
(np.sum((ym-np.mean(ym))**2))/N)
Here is the code:
# Code
from math import ceil
import numpy as np
import pandas as pd
import os
from gekko import GEKKO
import sys
from demandlib.tools import add_weekdays2df
import matplotlib.pyplot as plt
class HeatBuilding_Personalized:
def __init__(self, df_index, **kwargs):
self.datapath = kwargs.get(
'datapath', os.path.join(os.path.dirname(__file__), 'bdew_data'))
self.df = pd.DataFrame(index=df_index)
self.df = add_weekdays2df(self.df, holiday_is_sunday=True,
holidays=kwargs.get('holidays'))
self.df['hour'] = self.df.index.hour + 1 # hour of the day
self.temperature = kwargs.get('temperature')
self.annual_heat_demand = kwargs.get('annual_heat_demand')
self.shlp_type = kwargs.get('shlp_type').upper()
self.wind_class = kwargs.get('wind_class')
self.building_class = kwargs.get('building_class', 0)
self.ww_incl = kwargs.get('ww_incl', True)
self.name = kwargs.get('name', self.shlp_type)
self.data_points = kwargs.get('data_points')
self.st_p= kwargs.get('st_p')
self.end= kwargs.get('end')
def get_bdew_profile(self):
""" Calculation of the normalized hourly heat demand
"""
self.df['temperature'] = self.temperature.values
self.df['temperature_geo'] = self.weighted_temperature(how='geometric_series')
sf = self.get_sf_values()
f = self.get_weekday_parameters()
# measurements
self.df['data_points']=self.data_points.values
self.df= self.df[self.st_p:self.end]
self.df=self.df.dropna()
self.annual_heat_demand= self.df['data_points'].sum()
self.temperature= pd.DataFrame(self.df['temperature'])
print(self.df)
ym = pd.DataFrame(self.df['data_points'])
print("amount of nan",str(ym.isnull().sum()))
ymeas_mean = np.mean(ym)
print(ym)
print('ymeas_mean:',ymeas_mean)
x1= np.array(self.df['temperature_geo'])
x2= np.array(self.get_weekday_parameters())
x3= np.int(self.annual_heat_demand)
x4= np.array(self.get_sf_values())
ym= np.array(ym)
# GEKKO model
m = GEKKO(remote=False)
a = m.FV( 3.7,lb=1,ub=4)
a.STATUS=1
b = m.FV(-35.1,lb=-40,ub=-30)
b.STATUS=1
c = m.FV(7.1,lb=5,ub=9)
c.STATUS=1
d = m.FV( 0.9,lb=0.1,ub=1.5)
d.STATUS=1
# variables
T_g= m.Param(value=x1)
f=m.Param(value=x2)
annual_demand=m.Param(value=x3)
sf=m.Param(value=x4)
ymeas = m.Param(value=ym)
N = len(ym)
print('index n:',N)
yest = m.CV(value=0)
yest.FSTATUS=1
# y=m.Var() # I am defining my state variabel
# y = m.Var()
# z.FSTATUS=1
# regression equation
k = m.Intermediate((a / (1 + (b / (T_g - 40)) ** c) + d))
s=m.Intermediate(np.sum(k*f))
kw=m.Intermediate( 1.0 / (s / 24))
m.Equation(yest == (k* kw * f * sf) * annual_demand)
# objectives
# m.Minimize(((yest-ymeas)/ymeas)**2)
m.Obj(m.sqrt((np.sum((ymeas-yest)**2))/N/(np.sum((ymeas-np.mean(ymeas))**2))/N))
# print('Obj init value = ' + str(object_af.value))
# regression mode
m.options.IMODE = 2
m.options.SOLVER = 1 # considering APOPT solver for 1 and IPOPT for 3
# optimize
m.options.MAX_ITER = 20
m.options.OTOL = 1.0e-10
m.options.RTOL = 1.0e-10
m.solve(disp=True)
# print parameters
# print('Obj after value = ' + str(vd.value))
print('Optimized, a = ' + str(a.value[0]))
print('Optimized, b = ' + str(b.value[0]))
print('Optimized, c = ' + str(c.value[0]))
print('Optimized, d = ' + str(d.value[0]))
# print('Optimized, h = ' + str(h.value))
# sys.exit()
print("optimization is ok")
sf = self.get_sf_values()
f = self.get_weekday_parameters()
h = (a.value[0] / (1 + (b.value[0] / (self.df['temperature_geo'] - 40)) ** c.value[0]) + d.value[0])
kw = 1.0 / (sum(h * f) / 24) #1.0 instead of annual heat demand because the #annual heat demand is already multiplied in get_bdew_profile and divide by 24 to get #daily value
y = (kw * h * f * sf) * self.annual_heat_demand
objective= np.sqrt((np.sum((ym-np.array(y))**2))/N/(np.sum((ym-np.mean(ym))**2))/N)
print('objective calculated without Gekko:',objective)
return y
It returns this output:
Outputs: Solver :
APOPT (v1.0) Solution time : 27.2771999999968 sec
Objective : 40884011.5968099
Successful solution --------------------------------------------------
Optimized, a = 3.8708321781 Optimized, b = -31.844822393
Optimized, c = 7.8648564579 Optimized, d = 1.0244814518
The objective value is high. Without Gekko the objective is calculated as 0.01904060781034217. Why is it different?

It is hard to diagnose the problem because it is missing the data to run and verify. Here are a couple things to change:
Set yest as a Variable instead of a CV. It is automatically adding squared error terms when you declare a CV with FSTATUS=1 as described in the Dynamic Optimization course and in the Estimator Tuning Lesson. Because you are defining a custom objective, there is no need to declare a CV.
#yest = m.CV(value=0)
#yest.FSTATUS=1
yest = m.Var(value=0)
For a direct comparison, try declaring Intermediate variables to inspect the parts of the objective. Also, use m.sum() instead of np.sum() for the Gekko version of summation. The den piece is a number so it can be pre-calculated before the objective function is defined with ym.
den = (np.sum((ym-np.mean(ym))**2)
m.Obj(m.sqrt((np.sum((ymeas-yest)**2))/(den*N*N)))
Please post complete minimal, verifiable code for more specific help.

so we corrected the code like said in the previous comment but we get problems when we try to take a sum of a gekko parameter and we don't understand why. s is the variable where we calculate a sum and try to use it in the next equation but it doesn't work. Even with numpy.sum() it doesn't sum it up. We get this error: TypeError: x must be a python list of GEKKO parameters, variables, or expressions
Any idea what we need to change on factor k or f so the sum can be achieved?
x1= np.array(self.df['temperature_geo'])
x2= np.array(self.get_weekday_parameters())
x3= np.int(self.annual_heat_demand)
x4= np.array(self.get_sf_values())
ym= np.array(ym)
# GEKKO model
m = GEKKO(remote=False)
# variables
T_g= m.Param(value=x1)
f=m.Param(value=x2)
annual_demand=m.Param(value=x3)
sf=m.Param(value=x4)
ymeas = m.Param(value=ym)
yest = m.Var(value=0)
# regression equation
k = m.Intermediate((a / (1 + (b / (T_g - 40)) ** c) + d))
s=m.Intermediate(m.sum(k*f))
kw=m.Intermediate( 1.0 / (s / 24))
m.Equation(yest == (k* kw * f * sf) * annual_demand)
den = (m.sum((ymeas-np.mean(ymeas))**2))
ben = m.sum((ymeas-yest)**2)
m.Obj(m.sqrt((ben)/N/(den)/N))
# print('Obj init value = ' + str(object_af.value))
# regression mode
m.options.IMODE = 2
m.options.SOLVER = 1 # considering APOPT solver for 1 and IPOPT for 3
# optimize
m.options.MAX_ITER = 20
m.options.OTOL = 1.0e-10
m.options.RTOL = 1.0e-10
m.solve(disp=True)

Incremental solving of GEKKO dynamic models

I would like to use GEKKO to incrementally solve a dynamic model. I need to insert some parameters at different points in the simulation that are determined stochastically using an external model.
As a simple proof of concept, I tried adjusting the PID control example from the tutorial website to solve in 10 minute increments.
m = GEKKO()
tf = 40
timesteps = np.linspace(0,tf,2*tf+1)
step = np.zeros(2*tf+1)
step[3:40] = 2.0
step[40:] = 5.0
# Controller model
Kc = 15.0 # controller gain
tauI = 2.0 # controller reset time
tauD = 1.0 # derivative constant
OP_0 = m.Const(value=0.0) # OP bias
OP = m.Var(value=0.0) # controller output
PV = m.Var(value=0.0) # process variable
SP = m.Param(value=step) # set point
Intgl = m.Var(value=0.0) # integral of the error
err = m.Intermediate(SP-PV) # set point error
m.Equation(Intgl.dt()==err) # integral of the error
m.Equation(OP == OP_0 + Kc*err + (Kc/tauI)*Intgl - PV.dt())
# Process model
Kp = 0.5 # process gain
tauP = 10.0 # process time constant
m.Equation(tauP*PV.dt() + PV == Kp*OP)
setpoint_final = []
pv_final = []
output_final = []
for i in range(8):
SP.value = step[10*i:10*(i+1)]
m.time = timesteps[10*i:10*(i+1)]
m.options.IMODE=7
m.solve(disp=False)
setpoint_final.append(SP.value)
pv_final.append(PV.value)
output_final.append(OP.value)
plt.figure()
plt.subplot(2,1,1)
plt.plot(timesteps[:-1],np.concatenate(output_final),'b:',label='OP')
plt.ylabel('Output')
plt.legend()
plt.subplot(2,1,2)
plt.plot(timesteps[:-1],np.concatenate(setpoint_final),'k-',label='SP')
plt.plot(timesteps[:-1],np.concatenate(pv_final),'r--',label='PV')
plt.xlabel('Time (sec)')
plt.ylabel('Process')
plt.legend()
plt.show()
I should get something like this:
Instead it seems to reset at each interval:
Is there something I am missing or is this type of simulation not possible in GEKKO?

Try using m.options.TIME_SHIFT=10, m.options.IMODE=4, and change the way the values are stored.
from gekko import GEKKO
import numpy as np
import matplotlib.pyplot as plt
m = GEKKO(remote=False)
tf = 40
timesteps = np.linspace(0,tf,2*tf+1)
step = np.zeros(2*tf+1)
step[3:40] = 2.0
step[40:] = 5.0
# Controller model
Kc = 15.0 # controller gain
tauI = 2.0 # controller reset time
tauD = 1.0 # derivative constant
OP_0 = m.Const(value=0.0) # OP bias
OP = m.Var(value=0.0) # controller output
PV = m.Var(value=0.0) # process variable
SP = m.Param(value=step) # set point
Intgl = m.Var(value=0.0) # integral of the error
err = m.Intermediate(SP-PV) # set point error
m.Equation(Intgl.dt()==err) # integral of the error
m.Equation(OP == OP_0 + Kc*err + (Kc/tauI)*Intgl - PV.dt())
# Process model
Kp = 0.5 # process gain
tauP = 10.0 # process time constant
m.Equation(tauP*PV.dt() + PV == Kp*OP)
setpoint_final = []
pv_final = []
output_final = []
m.options.TIME_SHIFT=10
m.time = timesteps[0:10]
for i in range(8):
SP.value = step[10*i:10*(i+1)]
m.options.IMODE=4
m.solve(disp=False)
setpoint_final = np.concatenate((setpoint_final,SP.value))
pv_final = np.concatenate((pv_final,PV.value))
output_final = np.concatenate((output_final,OP.value))
plt.figure()
plt.subplot(2,1,1)
plt.plot(timesteps[:-1],output_final,'b:',label='OP')
plt.ylabel('Output')
plt.legend()
plt.subplot(2,1,2)
plt.plot(timesteps[:-1],setpoint_final,'k-',label='SP')
plt.plot(timesteps[:-1],pv_final,'r--',label='PV')
plt.xlabel('Time (sec)')
plt.ylabel('Process')
plt.legend()
plt.show()

System of FOPDT equations in GEKKO - use more than one input

I want to use two inputs or more to create a more precise estimation of a variable. I already estimated it using only one input and one FOPDT equation, but when I try to add one more input and the respective k, tau and theta, along with another equation, i get "Solution Not Found" error. Can I create a system of equations this way?
More details about the solver output below. Even though I added more variables than equations to use more than one input, this made my problem have negative degrees of freedom.
--------- APM Model Size ------------
Each time step contains
Objects : 2
Constants : 0
Variables : 15
Intermediates: 0
Connections : 4
Equations : 6
Residuals : 6
Number of state variables: 1918
Number of total equations: - 2151
Number of slack variables: - 0
---------------------------------------
Degrees of freedom : -233
* Warning: DOF <= 0
**********************************************
Dynamic Estimation with Interior Point Solver
**********************************************
Info: Exact Hessian
******************************************************************************
This program contains Ipopt, a library for large-scale nonlinear optimization.
Ipopt is released as open source code under the Eclipse Public License (EPL).
For more information visit http://projects.coin-or.org/Ipopt
******************************************************************************
This is Ipopt version 3.12.10, running with linear solver ma57.
Number of nonzeros in equality constraint Jacobian...: 6451
Number of nonzeros in inequality constraint Jacobian.: 0
Number of nonzeros in Lagrangian Hessian.............: 1673
Exception of type: TOO_FEW_DOF in file "IpIpoptApplication.cpp" at line 891:
Exception message: status != TOO_FEW_DEGREES_OF_FREEDOM evaluated false: Too few degrees of freedom (rethrown)!
EXIT: Problem has too few degrees of freedom.
An error occured.
The error code is -10
---------------------------------------------------
Solver : IPOPT (v3.12)
Solution time : 2.279999999154825E-002 sec
Objective : 0.000000000000000E+000
Unsuccessful with error code 0
---------------------------------------------------
Creating file: infeasibilities.txt
Use command apm_get(server,app,'infeasibilities.txt') to retrieve file
#error: Solution Not Found
And here's the code
from gekko import GEKKO
import numpy as np
import pandas as pd
import plotly.express as px
d19jc = d19jc.dropna()
d19jcSlice = d19jc.loc['2019-10-22 05:30:00':'2019-10-22 09:30:00'] #jc22
d19jcSlice.index = pd.to_datetime(d19jcSlice.index)
d19jcSliceGroupMin = d19jcSlice.groupby(pd.Grouper(freq='T')).mean()
data = d19jcSliceGroupMin.dropna()
xdf1 = data['Cond_PID_SP']
xdf2 = data['Front_PID_SP']
ydf1 = data['Cond_Center_Top_TC']
xms1 = pd.Series(xdf1)
xm1 = np.array(xms1)
xms2 = pd.Series(xdf2)
xm2 = np.array(xms2)
yms = pd.Series(ydf1)
ym = np.array(yms)
xm_r = len(xm1)
tm = np.linspace(0,xm_r-1,xm_r)
m = GEKKO()
m.options.IMODE=5
m.time = tm; time = m.Var(0); m.Equation(time.dt()==1)
k1 = m.FV(lb=0.1,ub=5); k1.STATUS=1
tau1 = m.FV(lb=1,ub=300); tau1.STATUS=1
theta1 = m.FV(lb=0,ub=30); theta1.STATUS=1
k2 = m.FV(lb=0.1,ub=5); k2.STATUS=1
tau2 = m.FV(lb=1,ub=300); tau2.STATUS=1
theta2 = m.FV(lb=0,ub=30); theta2.STATUS=1
# create cubic spline with t versus u
uc1 = m.Var(xm1); tc1 = m.Var(tm); m.Equation(tc1==time-theta1)
m.cspline(tc1,uc1,tm,xm1,bound_x=False)
# create cubic spline with t versus u
uc2 = m.Var(xm2); tc2 = m.Var(tm); m.Equation(tc2==time-theta2)
m.cspline(tc2,uc2,tm,xm2,bound_x=False)
x1 = m.Param(value=xm1)
x2 = m.Param(value=xm2)
y = m.Var(value=ym)
yObj = m.Param(value=ym)
m.Equation(tau1*y.dt()+(y-ym[0])==k1 * (uc1-xm1[0]))
m.Equation(tau2*y.dt()+(y-ym[0])==k2 * (uc2-xm2[0]))
m.Minimize((y-yObj)**2)
m.options.EV_TYPE=2
print('solve start')
m.solve(disp=True)
print('k1: ', k1.value[0])
print('tau1: ', tau1.value[0])
print('theta1: ', theta1.value[0])
print('k2: ', k2.value[0])
print('tau2: ', tau2.value[0])
print('theta2: ', theta2.value[0])
df_plot = pd.DataFrame({'DateTime' : data.index,
'Cond_Center_Top_TC' : np.array(yObj),
'Fit Cond_Center_Top_TC - Train' : np.array(y),
figGekko = px.line(df_plot,
x='DateTime',
y=['Cond_Center_Top_TC','Fit Cond_Center_Top_TC - Train'],
labels={"value": "Degrees Celsius"},
title = "(Cond_PID_SP & Front_PID_SP) -> Cond_Center_Top_TC JC only - Train")
figGekko.update_layout(legend_title_text='')
figGekko.show()

You currently have only one variable and two equations.
y = m.Var(value=ym)
yObj = m.Param(value=ym)
m.Equation(tau1*y.dt()+(y-ym[0])==k1 * (uc1-xm1[0]))
m.Equation(tau2*y.dt()+(y-ym[0])==k2 * (uc2-xm2[0]))
You need to create two separate variables y1 and y2 for the two equations.
y1 = m.Var(value=ym)
y2 = m.Var(value=ym)
yObj = m.Param(value=ym)
m.Equation(tau1*y1.dt()+(y1-ym[0])==k1 * (uc1-xm1[0]))
m.Equation(tau2*y2.dt()+(y2-ym[0])==k2 * (uc2-xm2[0]))
You may also need to create two separate measurement vectors for ym1 and ym2 if you have different data for each.
Edit: Multiple Input, Single Output (MISO) System
For a MISO system, you need to adjust the equation as shown in the Process Dynamics and Control course.
y = m.Var(value=ym)
yObj = m.Param(value=ym)
m.Equation(tau*y.dt()+(y-ym[0])==k1 * (uc1-xm1[0]) + k2 * (uc2-xm2[0]))
There is only one time constant in this form. If they need different time constants, you can also add the two outputs together with:
y1 = m.Var(value=ym[0])
y2 = m.Var(value=ym[0])
y = m.Var(value=ym)
yObj = m.Param(value=ym)
m.Equation(tau1*y1.dt()+(y1-ym[0])==k1 * (uc1-xm1[0]))
m.Equation(tau2*y2.dt()+(y2-ym[0])==k2 * (uc2-xm2[0]))
m.Equation(y==y1+y2)
In this case, y is the variable that has data and y1 and y2 are unmeasured states.

Please see the below example code for a FOPDT model that has two inputs and one output. Both the transfer function models have different FOPDT parameters, including different deadtimes as well.
It is still in a dynamic simulation mode (IMODE=4), but you can start from this modifying a little bit toward the dynamic estimation mode (IMODE=5) and MPC mode (IMODE=6) later.
from gekko import GEKKO
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
tf = 100
npt = 101
t = np.linspace(0,tf,npt)
u1 = np.zeros(npt)
u2 = np.zeros(npt)
u1[10:] = 5
u2[40:] = -5
m = GEKKO(remote=True)
m.time = t
time = m.Var(0)
m.Equation(time.dt()==1)
K1 = m.FV(1,lb=0,ub=1); K1.STATUS=1
tau1 = m.FV(5, lb=1,ub=300); tau1.STATUS=1
theta1 = m.FV(10, lb=2,ub=30); theta1.STATUS=1
K2 = m.FV(0.5,lb=0,ub=1); K2.STATUS=1
tau2 = m.FV(10, lb=1,ub=300); tau2.STATUS=1
theta2 = m.FV(20, lb=2,ub=30); theta2.STATUS=1
uc1 = m.Var(u1)
uc2 = m.Var(u2)
tc1 = m.Var(t)
tc2 = m.Var(t)
m.Equation(tc1==time-theta1)
m.Equation(tc2==time-theta2)
m.cspline(tc1,uc1,t,u1,bound_x=False)
m.cspline(tc2,uc2,t,u2,bound_x=False)
yp = m.Var()
yp1 = m.Var()
yp2 = m.Var()
m.Equation(yp1.dt() == -yp1/tau1 + K1*uc1/tau1)
m.Equation(yp2.dt() == -yp2/tau2 + K2*uc2/tau2)
m.Equation(yp == yp1 + yp2)
m.options.IMODE=4
m.solve()
print('K1: ', K1.value[0])
print('tau1: ', tau1.value[0])
print('theta1: ', theta1.value[0])
print('')
print('K2: ', K2.value[0])
print('tau2: ', tau2.value[0])
print('theta2: ', theta2.value[0])
plt.figure()
plt.subplot(2,1,1)
plt.plot(t,u1)
plt.plot(t,u2)
plt.legend([r'u1', r'u2'])
plt.ylabel('Inputs 1 & 2')
plt.subplot(2,1,2)
plt.plot(t,yp)
plt.legend([r'y1'])
plt.ylabel('Output')
plt.xlabel('Time')
plt.savefig('sysid.png')
plt.show()
K1: 1.0
tau1: 5.0
theta1: 10.0
K2: 0.5
tau2: 10.0
theta2: 20.0

Inaccurate phase portrait result with matplotlib

I am trying to plot the phase potrait for the equation as defined in my sh2 function in the code below. I know the expected phase plot should be [[expected phase plot][1]][1] [1]: https://i.stack.imgur.com/y1T9Y.png.
However this is my result: [[result][1]: https://i.stack.imgur.com/EuSOm.png.
I am using integrate.odeint can anyone suggest what I could change in the could below or if there would be best to use another algorithm that would give me a closer result to th expected.
Please find my code :
import matplotlib.pyplot as plt
import numpy as np
from numpy import sin
import scipy.integrate as integrate
from math import *
g = 9.81
l = 1.6
l_big = 2.0
l_small = 1.6
m = 0.01
alpha = l_big-l_small
k = 10*(10**40)
def sh2(r1,t):
theta1,omega1 = r1
sh2_theta1 = omega1
sh2_omega1 = -g*(l + ((1/2)*alpha*(1-np.tanh(theta1*omega1*k))))*sin(theta1)
return np.array([sh2_theta1, sh2_omega1],float)
init_state = np.radians([30.0,0])
dt = 1/10.0
time = np.arange(0,10.0,dt)
timexo = np.arange(0,10.0,dt)
state2 = integrate.odeint(sh2,init_state,time)
print(len(state2),len(timexo))
state2_plot = np.transpose(state2[0:2500])
plt.plot(timexo[0:2500],state2_plot[1], '--m', label = r'$\theta = \frac{\pi}{6}$')
plt.xlabel('Time t (s) ')
plt.ylabel('Angular Velocity' ' ' r'$\dot{\theta}$')
plt.show()
#code for phase plot
# initial values
x_0 = 0.0 # intial angular position
v_0 = 1.0 # initial angular momentum
t_0 = 0 # initial time
# initial y-vector from initial position and momentum
y0 = np.array([x_0,v_0])
# max value of time and points in time to integrate to
t_max = 10
N_spacing_in_t = 10000
# create vector of time points you want to evaluate
t = np.linspace(t_0,t_max,N_spacing_in_t)
# create vector of positions for those times
y_result = integrate.odeint(sh2, init_state, t)
# get angle and angular momentum
angle = y_result[:,0]
angular_velocity = y_result[:,1]
# plot result
fig = plt.figure()
plt.plot(angle, angular_velocity,'--k',lw=1)
plt.xlabel('Angle' ' ' r'$\theta$')
plt.ylabel(r'Angular Velocity' r' $\dot{\theta}$')
plt.gcf().savefig('pumping.png',dpi=300)
plt.show()
Thank you for tour time