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Simulating Models

Antimony models can be converted into a RoadRunner instance, which can be used to simulate the model. The function loada converts Antimony into a simulator instance. This example shows how to get the Antimony / SBML representation of the current state of the model. After running a simulation, the concentraions of the state variables will change. You can retrieve the Antimony representation of the current state of the model using getCurrentAntimony on the RoadRunner instance. This example shows the change in the Antimony / SBML representation. The example also shows how to use variable stepping in a simulation.



In [1]:

    
from __future__ import print_function
import tellurium as te
te.setDefaultPlottingEngine("matplotlib")
%matplotlib inline

print('-' * 80)
te.printVersionInfo()
print('-' * 80)

r = te.loada('''
model example
    p1 = 0;
    at time>=10: p1=10;
    at time>=20: p1=0;
end
''')

# convert current state of model back to Antimony / SBML
ant_str_before = r.getCurrentAntimony()
sbml_str_before = r.getCurrentSBML()
# r.exportToSBML('/path/to/test.xml')

# set selections
r.selections=['time', 'p1']
r.integrator.setValue("variable_step_size", False)
r.resetAll()
s1 = r.simulate(0, 40, 40)
r.plot()
# hitting the trigger point directly works
r.resetAll()
s2 = r.simulate(0, 40, 21)
r.plot()

# variable step size also does not work
r.integrator.setValue("variable_step_size", True)
r.resetAll()
s3 = r.simulate(0, 40)
r.plot()


# convert current state of model back to Antimony / SBML
ant_str_after = r.getCurrentAntimony()
sbml_str_after = r.getCurrentSBML()

import difflib
print("Comparing Antimony at time 0 & 40 (expect no differences)")
print('\n'.join(list(difflib.unified_diff(ant_str_before.splitlines(), ant_str_after.splitlines(), fromfile="before.sb", tofile="after.sb"))))

# now simulate up to time 15
r.resetAll()
s4 = r.simulate(0, 15)
r.plot()


# convert current state of model back to Antimony / SBML
ant_str_after2 = r.getCurrentAntimony()
sbml_str_after2 = r.getCurrentSBML()

print("Comparing Antimony at time 0 & 15")
print('\n'.join(list(difflib.unified_diff(ant_str_before.splitlines(), ant_str_after2.splitlines(), fromfile="before.sb", tofile="after.sb"))))









    



--------------------------------------------------------------------------------
tellurium : 2.0.0
roadrunner : 1.4.21; Compiler: gcc 4.8.2, C++ version: 199711; JIT Compiler: LLVM-3.3; Date: Jul  5 2017, 18:38:02; LibSBML Version: 5.14.0
antimony : 2.9.3
libsbml : 5.15.0
libsedml : 402
phrasedml : 1.0.7
--------------------------------------------------------------------------------
Comparing Antimony at time 0 & 40 (expect no differences)

Comparing Antimony at time 0 & 15
--- before.sb

+++ after.sb

@@ -6,7 +6,7 @@

   _E1: at time >= 20: p1 = 0;
 
   // Variable initializations:
-  p1 = 0;
+  p1 = 10;
 
   // Other declarations:
   var p1;



In [2]:

    
r.getSimulationData()









    Out[2]:





           time, p1
 [[           0,  0],
  [ 0.000514839,  0],
  [      5.1489,  0],
  [          10,  0],
  [          10, 10],
  [     10.0002, 10],
  [     12.2588, 10],
  [          15, 10]]



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