Add integrator guard to prevent infinite loops

- Limits the number of sequential invalid states from exceeding 1000
  - Prevents "occasionally invalid" output from terminating the simulation
- Allow `tau_tol` to be properly accepted as argument

gillespy2/solvers/cpp/c_base/arg_parser.h

@@ -44,7 +44,7 @@ class ArgParser
     double end = 0.0;
     double increment = 0.0;
     double switch_tol = 0.0;
-    double tau_tol = 0.0;
+    double tau_tol = 0.03;
 
     ArgParser(int argc, char *argv[]);
     ~ArgParser();

gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSimulation.cpp

@@ -35,7 +35,7 @@ int random_seed = 0;
 double end_time = 100.0;
 bool seed_time = true;
 double increment = 0;
-double tau_tol = 0.05;
+double tau_tol = 0.03;
 
 class PropensityFunction : public IPropensityFunction
 {

gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/TauHybridSolver.cpp

@@ -115,8 +115,11 @@ namespace Gillespy::TauHybrid
 			// An invalid simulation state indicates that an unrecoverable error has occurred,
 			//   and the trajectory should terminate early.
 			bool invalid_state = false;
+			// This is a temporary fix. Ideally, invalid state should allow for integrator options change.
+			// For now, a "guard" is put in place to prevent potentially infinite loops from occurring.
+			unsigned int integration_guard = 1000;
 
-			while (!invalid_state && simulation->current_time < simulation->end_time)
+			while (integration_guard > 0 && simulation->current_time < simulation->end_time)
 			{
 				// Compute current propensity values based on existing state.
 				for (int rxn_i = 0; rxn_i < num_reactions; ++rxn_i)
@@ -256,10 +259,9 @@ namespace Gillespy::TauHybrid
 				// Invalid state after the do-while loop implies that an unrecoverable error has occurred.
 				// While prior results are considered usable, the current integration results are not.
 				// Calling `continue` with an invalid state will discard the results and terminate the trajectory.
-				if (invalid_state)
-				{
-					continue;
-				}
+				integration_guard = invalid_state
+					? integration_guard - 1
+					: 1000;
 
 				// Output the results for this time step.
 				sol.refresh_state();
@@ -276,6 +278,14 @@ namespace Gillespy::TauHybrid
 				}
 			}
 
+			if (integration_guard == 0)
+			{
+				std::cerr
+					<< "[Trajectory #" << traj << "] "
+					<< "Integration guard triggered; problem space too stiff at t="
+					<< simulation->current_time << std::endl;
+			}
+
 			// End of trajectory
 			delete[] population_changes;
 		}

gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.cpp

@@ -144,7 +144,10 @@ URNGenerator::URNGenerator()
 
 URNGenerator::URNGenerator(unsigned long long seed)
 	: uniform(0, 1),
-	  rng(seed) {}
+	  rng(seed)
+{
+	this->seed = seed;
+}
 
 
 /* Generate a new random floating-point number on the range [0,1).

gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/integrator.h

@@ -126,6 +126,7 @@ namespace Gillespy::TauHybrid
 	private:
 		std::uniform_real_distribution<double> uniform;
 		std::mt19937_64 rng;
+		unsigned long long seed;
 	public:
 		double next();
 		URNGenerator();