Bug fixes in integrator

- Revert `SimulationState` enum properties to not use bit packing
- Fix incorrect computation of standard deviation, which caused unexpected output
- Fix CVODE error caused by uninitialized time value

gillespy2/solvers/cpp/c_base/tau_hybrid_cpp_solver/HybridModel.cpp

@@ -211,13 +211,13 @@ namespace Gillespy::TauHybrid
 				if (spec_dx < 0) {
 					// Selected species is a reactant.
 					means[spec_i] -= (tau_step * propensity_values[rxn_i] * spec_dx);
-					sd[spec_i] += std::pow((tau_step * propensity_values[rxn_i] * spec_dx), 2);
+					sd[spec_i] += (tau_step * propensity_values[rxn_i] * std::pow(spec_dx, 2));
 				}
 				else if (spec_dx > 0) {
 					// Selected species is a product.
 					HybridSpecies &product = species[spec_i];
 					means[spec_i] += (tau_step * propensity_values[rxn_i] * spec_dx);
-					sd[spec_i] += std::pow((tau_step * propensity_values[rxn_i] * spec_dx), 2);
+					sd[spec_i] += (tau_step * propensity_values[rxn_i] * std::pow(spec_dx, 2));
 				}
 			}
 		}

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

@@ -60,13 +60,13 @@ namespace Gillespy::TauHybrid
 		// CONTINUOUS or DISCRETE
 		// otherwise, mode will be determined by the program (DYNAMIC)
 		// if no choice is made, DYNAMIC will be assumed 
-		SimulationState  user_mode : 2;
+		SimulationState  user_mode;
 
 		// during simulation execution, a species will fall into either of the two categories, CONTINUOUS or DISCRETE
 		// this is pre-determined only if the user_mode specifies CONTINUOUS or DISCRETE.
 		// otherwise, if DYNAMIC is specified, partition_mode will be continually calculated throughout the simulation
 		// according to standard deviation and coefficient of variance.
-		SimulationState partition_mode : 1;
+		SimulationState partition_mode;
 
 		// Tolerance level for considering a dynamic species deterministically, value is compared
 		// to an estimated sd/mean population of a species after a given time step.
@@ -85,7 +85,7 @@ namespace Gillespy::TauHybrid
 	struct HybridReaction
 	{
 		Reaction *base_reaction;
-		SimulationState mode : 1;
+		SimulationState mode;
 
 		HybridReaction();
 

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

@@ -101,9 +101,6 @@ namespace Gillespy::TauHybrid
 				current_populations[spec_i] = species[spec_i].initial_population;
 			}
 
-			// Represents the largest valid index of the output vector(s), y (and y0).
-			int rxn_offset_boundary  = num_species + num_reactions;
-
 			// SIMULATION STEP LOOP
 			int save_idx = 1;
 			double next_time;
@@ -250,7 +247,7 @@ namespace Gillespy::TauHybrid
 						// "Permanently" update the rxn_state and populations.
 						for (int p_i = 0; p_i < num_species; ++p_i) {
 							current_state[p_i] += population_changes[p_i];
-							current_populations[p_i] = current_state[p_i];
+							current_populations[p_i] = (int) current_state[p_i];
 							result.concentrations[p_i] = current_state[p_i];
 						}
 					}

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

@@ -42,6 +42,8 @@ IntegratorData::IntegratorData(HybridSimulation *simulation)
 
 Integrator::Integrator(HybridSimulation *simulation, N_Vector y0, double reltol, double abstol)
 	: y0(y0),
+	  t(0.0f),
+	  t0(0.0f),
 	  y(N_VClone_Serial(y0)),
 	  data(simulation),
 	  num_reactions(simulation->model->number_reactions),
@@ -140,7 +142,7 @@ IntegrationResults Integrator::integrate(double *t)
 URNGenerator::URNGenerator()
 	: uniform(0, 1) {}
 
-URNGenerator::URNGenerator(double seed)
+URNGenerator::URNGenerator(unsigned long long seed)
 	: uniform(0, 1),
 	  rng(seed) {}
 

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

@@ -129,7 +129,7 @@ namespace Gillespy::TauHybrid
 	public:
 		double next();
 		URNGenerator();
-		URNGenerator(double seed);
+		explicit URNGenerator(unsigned long long seed);
 	};
 
 	N_Vector init_model_vector(Model<double> &model, URNGenerator urn);