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ODE solver fails if propensity_function contains "vol" #675

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briandrawert opened this issue Jan 10, 2022 · 0 comments · Fixed by #674 or #660
Closed

ODE solver fails if propensity_function contains "vol" #675

briandrawert opened this issue Jan 10, 2022 · 0 comments · Fixed by #674 or #660
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@briandrawert
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This works for the ODECSolver, but not the ODESolver.

This is from the "KineticModelForStyrenePolymerization.ipynb" example:

NameError: name 'vol' is not defined

During handling of the above exception, another exception occurred:

SimulationError                           Traceback (most recent call last)
<ipython-input-12-40050f13f8ae> in <module>
      1 from gillespy2 import ODESolver, ODECSolver
----> 2 r1 = model.run(solver=ODESolver)
      3 r2 = model.run(solver=ODECSolver)
      4 #r1.plot()
      5 r2.plot()

~/Desktop/research/GillesPy2/examples/AdvancedFeatures/../../gillespy2/core/model.py in run(self, solver, timeout, t, increment, show_labels, cpp_support, algorithm, **solver_args)
    997                                 " system, to ensure that GillesPy2 C solvers will"
    998                                 " run properly.")
--> 999             raise SimulationError(
   1000                 "argument 'solver={}' to run() failed.  Reason Given: {}".format(solver, e))
   1001 

SimulationError: argument 'solver=<class 'gillespy2.solvers.numpy.ode_solver.ODESolver'>' to run() failed.  Reason Given: name 'vol' is not defined
@briandrawert briandrawert added this to the 1.6.8 milestone Jan 10, 2022
@briandrawert briandrawert linked a pull request Jan 10, 2022 that will close this issue
briandrawert added a commit that referenced this issue Jan 11, 2022
@briandrawert briandrawert modified the milestones: 1.6.8, 1.6.7 Jan 11, 2022
@BryanRumsey BryanRumsey added bug Something isn't working ✔️​ Issue / PR has been resolved labels Jan 11, 2022
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