Merge pull request #674 from StochSS/ode_solver_vol_issue

Ode solver vol issue

gillespy2/solvers/numpy/ode_solver.py

@@ -257,6 +257,8 @@ def __run(self, curr_state, curr_time, timeline, trajectory_base, tmpSpecies, li
 
         for p_name, param in self.model.listOfParameters.items():
             curr_state[0][p_name] = param.value
+        if 'vol' not in curr_state[0]:
+            curr_state[0]['vol'] = 1.0
         rhs = ode(ODESolver.__f).set_integrator(integrator, **integrator_options)
         rhs.set_initial_value(y0, curr_time[0]).set_f_params(curr_state, self.model, c_prop)
 

test/test_ode_solver.py

@@ -17,6 +17,8 @@
 """
 
 import unittest
+import sys
+sys.path.append("..")
 import numpy as np
 import gillespy2
 from example_models import Example, ExampleNoTspan
@@ -77,6 +79,24 @@ def test_run_example__with_tspan_and_increment(self):
             results = ODESolver.run(model=model, increment=0.2)
 
 
+    def test_stoch3(self):
+        class StochTestModel(gillespy2.Model):
+            def __init__(self, parameter_values=None):
+                gillespy2.Model.__init__(self, name='StochTest1')
+                A = gillespy2.Species(name='A', initial_value=10)
+                B = gillespy2.Species(name='B', initial_value=0)
+                self.add_species([A, B])
+                k = gillespy2.Parameter(name='k', expression=10)
+                self.add_parameter([k])
+                r = gillespy2.Reaction(name='r', reactants={A: 1}, products={B:1},
+                    propensity_function="k*A/vol") # testing if 'vol' is a pre-set variable
+                self.add_reaction([r])
+                self.timespan(np.linspace(0, 100, 101))
+        model = StochTestModel()
+        result = model.run(solver=ODESolver)
+        sys.stderr.write(f"\ntest_shoch3(): B={result['B'][-1]}\n\n")
+        self.assertGreater(result['B'][-1], 5)
 
 if __name__ == '__main__':
-    unittest.main()
+    #unittest.main()
+    TestBasicODESolver().test_stoch3()