rebase Solver.cpp and SimulationParameters.cpp, remove redundancy in Model.cpp

Author: ncdorn

src/solve/SimulationParameters.cpp

@@ -186,7 +186,7 @@ SimulationParameters load_simulation_params(const nlohmann::json& config) {
   sim_params.output_mean_only = sim_config.value("output_mean_only", false);
   sim_params.output_derivative = sim_config.value("output_derivative", false);
   sim_params.output_all_cycles = sim_config.value("output_all_cycles", false);
-  sim_params.sim_cardiac_period = sim_config.value("cardiac_period", 0.0);
+  sim_params.sim_cardiac_period = sim_config.value("cardiac_period", -1.0);
   DEBUG_MSG("Finished loading simulation parameters");
   return sim_params;
 }
@@ -402,20 +402,18 @@ void create_external_coupling(
       connections.push_back({coupling_name, connected_block});
     } else if (coupling_loc == "outlet") {
       std::vector<std::string> possible_types = {
-          "ClosedLoopRCR", "ClosedLoopHeartAndPulmonary", "BloodVessel",
-          "BloodVesselCRL", "BloodVessel"};
+          "ClosedLoopRCR", "ClosedLoopHeartAndPulmonary", "BloodVessel"};
       if (std::find(std::begin(possible_types), std::end(possible_types),
                     connected_type) == std::end(possible_types)) {
         throw std::runtime_error(
             "Error: The specified connection type for outlet "
             "external_coupling_block is invalid.");
       }
-      // Add connection only for closedLoopRCR and BloodVessel
-      // Connection to ClosedLoopHeartAndPulmonary will be
-      // handled in ClosedLoopHeartAndPulmonary creation.
+      // Add connection only for closedLoopRCR and BloodVessel. Connection to
+      // ClosedLoopHeartAndPulmonary will be handled in
+      // ClosedLoopHeartAndPulmonary creation.
       if ((connected_type == "ClosedLoopRCR") ||
-          (connected_type == "BloodVessel") ||
-          (connected_type == "BloodVesselA")) {
+          (connected_type == "BloodVessel")) {
         connections.push_back({connected_block, coupling_name});
       }  // connected_type == "ClosedLoopRCR"
     }  // coupling_loc

src/solve/SimulationParameters.h

@@ -37,11 +37,11 @@
 struct SimulationParameters {
   // Negative value indicates this has not
   // been read from config file yet.
-  double sim_time_step_size{0.0};  ///< Simulation time step size
-  double sim_abs_tol{0.0};         ///< Absolute tolerance for simulation
-  double sim_cardiac_period{0.0};  ///< Cardiac period
-  int sim_num_cycles{0};           ///< Number of cardiac cycles to simulate
-  int sim_pts_per_cycle{0};        ///< Number of time steps per cardiac cycle
+  double sim_time_step_size{0.0};   ///< Simulation time step size
+  double sim_abs_tol{0.0};          ///< Absolute tolerance for simulation
+  double sim_cardiac_period{-1.0};  ///< Cardiac period
+  int sim_num_cycles{0};            ///< Number of cardiac cycles to simulate
+  int sim_pts_per_cycle{0};         ///< Number of time steps per cardiac cycle
   bool use_cycle_to_cycle_error{
       false};  ///< If model does not have RCR boundary conditions, simulate
                ///< model to convergence (based on cycle-to-cycle error of last

src/solve/Solver.cpp

@@ -12,7 +12,20 @@ Solver::Solver(const nlohmann::json& config) {
   DEBUG_MSG("Load model");
   this->model = std::shared_ptr<Model>(new Model());
   load_simulation_model(config, *this->model.get());
-  if (simparams.sim_cardiac_period > 0) {
+
+  // If period isn't specified anywhere, set to 1
+  if (simparams.sim_cardiac_period < 0 &&
+      this->model->cardiac_cycle_period < 0) {
+    this->model->cardiac_cycle_period = 1;
+  } else if (this->model->cardiac_cycle_period >= 0) {
+    // Check for inconsistent period definition
+    if (simparams.sim_cardiac_period >= 0 &&
+        (this->model->cardiac_cycle_period != simparams.sim_cardiac_period)) {
+      throw std::runtime_error(
+          "Inconsistent cardiac cycle period defined in parameters");
+    }
+    // If period is only defined in parameters, set value in model
+  } else {
     this->model->cardiac_cycle_period = simparams.sim_cardiac_period;
   }
   DEBUG_MSG("Load initial condition");