can roadrunner make bifurcation diagram showing Hopf Bifurcation with oscillation showing?

[ZiyiiiLiu]

Hi, I am using the code below to make my bifurcation diagram for many random parameter sets, and I want to know which set can have oscillation, can we do this? Thanks!
auto = Plugin("tel_auto2000")

Setup properties

auto.setProperty("SBML", r.getCurrentSBML())

auto.setProperty("ScanDirection", 'Positive')
auto.setProperty("PrincipalContinuationParameter", "S1")
auto.setProperty("PreSimulation", "True")
auto.setProperty("PreSimulationDuration", 30)
auto.setProperty("RL0", 0)
auto.setProperty("RL1", 5)
auto.setProperty("NMX", 1000)
#auto.setProperty("NDIM", 15)
auto.setProperty("NPR", 3)
auto.setProperty("KeepTempFiles", True)
auto.setProperty("DS", 0.001)
auto.setProperty("DSMIN", 0.0001)
auto.setProperty("DSMAX", 0.1)
auto.execute()
pts1 = auto.BifurcationPoints
if 1:
lbl1 = auto.BifurcationLabels
biData1 = auto.BifurcationData
# Correct call to the plotBifurcationDiagram function
biData1.plotBifurcationDiagram(pts1, lbl1)

[hsauro]

It should indicate in the bifurcation diagram any points which are limit cycles.

[ZiyiiiLiu]

I made a simple model, there is oscillations with the parameter, but nothing in the bifurcation diagram, do you know where I made wrong?

import tellurium as te

# Define the model
model_sclc_2 = """
    # Parameters
    m1 =1; 

    # Equations
    -> x; y
    -> y; m1 * (1 - x^2) * y - x
"""

# Load the model
r = te.loada(model_sclc_2)

# Initial conditions
ics_1 = {'x': 0.01, 'y': 6.1}
for var, val in ics_1.items():
    setattr(r, var, val)

# Parameter changes
pars = { 
    'm1': 1, 
}

# Apply parameter changes
for k in pars:
    setattr(r, k, pars[k])
#print( r.steadyState())
# Simulate the model
m = r.simulate(0, 100, 5000)
# Extract the simulation results
time = m[:, 0]  # Time data
x = m[:, 1]     # 'Y' variable data
y = m[:, 2]     # 'A' variable data

# Plot the results
plt.figure(figsize=(6,3))


plt.plot(time, x, label='x')
plt.plot(time, y, label='y ')

plt.xlabel('Time')
plt.ylabel('Concentration')
plt.title('Simulation Results of SCLC Model')
plt.legend(loc='best')
plt.grid(True)

# Save the plot
plt.savefig('simulation_results.png', dpi=300, bbox_inches='tight')
plt.show()

auto = Plugin("tel_auto2000")              

#print auto.listOfPropertyNames()

#Setup Auto Propertys
auto.setProperty("SBML", r.getCurrentSBML())

#Auto specific properties
auto.setProperty("ScanDirection", "Positive")    
auto.setProperty("PrincipalContinuationParameter", "m1")
auto.setProperty("PCPLowerBound", 0)
auto.setProperty("PCPUpperBound", 1.5)

#Max numberof points
auto.setProperty("NMX", 5000)  
       
#Execute the plugin
auto.execute()
     
# Bifurcation summary
print("Summary: ", auto.BifurcationSummary)

#Plot Bifurcation diagram
pts     = auto.BifurcationPoints
lbls    = auto.BifurcationLabels
biData  = auto.BifurcationData    

biData.plotBifurcationDiagram(pts, lbls)