Added option to specify cardiac period

.github/workflows/documentation.yml

@@ -27,4 +27,4 @@ jobs:
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs/build/html
+          publish_dir: ./docs/build/html

.github/workflows/test.yml

@@ -161,4 +161,4 @@ jobs:
         with:
           name: ${{ matrix.os }} installer
           path: svZeroDSolver_*
-          if-no-files-found: error
+          if-no-files-found: error

src/model/Model.cpp

@@ -115,7 +115,7 @@ std::string Model::get_block_name(int block_id) const {
 int Model::add_node(const std::vector<Block *> &inlet_eles,
                     const std::vector<Block *> &outlet_eles,
                     const std::string_view &name) {
-  // DEBUG_MSG("Adding node " << name);
+  DEBUG_MSG("Adding node " << name);
   auto node = std::shared_ptr<Node>(
       new Node(node_count, inlet_eles, outlet_eles, this));
   nodes.push_back(node);
@@ -173,10 +173,6 @@ void Model::finalize() {
   for (auto &block : blocks) {
     block->setup_model_dependent_params();
   }
-
-  if (cardiac_cycle_period < 0.0) {
-    cardiac_cycle_period = 1.0;
-  }
 }
 
 int Model::get_num_blocks(bool internal) const {

src/model/OpenLoopCoronaryBC.h

@@ -73,7 +73,7 @@
  * Parameter sequence for constructing this block
  *
  * * `0` Ra: Small artery resistance
- * * `1` Ram: Microvascualar resistance
+ * * `1` Ram: Microvascualr resistance
  * * `2` Rv: Venous resistance
  * * `3` Ca: Small artery capacitance
  * * `4` Cim: Intramyocardial capacitance

src/solve/SimulationParameters.cpp

@@ -169,7 +169,6 @@ SimulationParameters load_simulation_params(const nlohmann::json& config) {
           sim_config.value("sim_cycle_to_cycle_percent_error", 1.0) / 100;
     }
     sim_params.sim_external_step_size = 0.0;
-
   } else {
     sim_params.sim_num_cycles = 1;
     sim_params.sim_num_time_steps = sim_config["number_of_time_pts"];
@@ -187,6 +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", -1.0);
   DEBUG_MSG("Finished loading simulation parameters");
   return sim_params;
 }
@@ -396,7 +396,7 @@ void create_external_coupling(
       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 inlet "
+            "Error: The specified connection type for inlet"
             "external_coupling_block is invalid.");
       }
       connections.push_back({coupling_name, connected_block});
@@ -409,9 +409,9 @@ void create_external_coupling(
             "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")) {
         connections.push_back({connected_block, coupling_name});

src/solve/SimulationParameters.h

@@ -23,11 +23,11 @@
 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
-
-  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

@@ -12,6 +12,22 @@ 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 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");
   initial_state = load_initial_condition(config, *this->model.get());
 

tests/cases/closedLoopHeart_singleVessel_mistmatchPeriod.json

@@ -0,0 +1,99 @@
+{
+    "description": {
+            "description of test case" : "Closed-loop circulation with one vessel (aorta) connected on either side to the heart model."
+    },
+    "simulation_parameters": {
+        "number_of_cardiac_cycles": 1,
+        "number_of_time_pts_per_cardiac_cycle": 10000,
+        "steady_initial": false,
+        "cardiac_period": 0.67
+    },
+    "boundary_conditions": [
+        {
+            "bc_name": "RCR_aorta",
+            "bc_type": "ClosedLoopRCR",
+            "bc_values": {
+                "_comment_": "R_total = 1.570879*0.948914 = 1.490629075",
+                "_comment_": "Rp = 0.09*R_total",
+                "_comment_": "Rd = 0.91*R_total",
+                "Rp": 0.134156617,
+                "Rd": 1.356472458,
+                "_comment_": "C = 0.228215*1.044637",
+                "C": 0.238401833,
+                "closed_loop_outlet": true
+            }
+        }
+    ],
+    "vessels": [
+        {
+            "_comment_": "aorta",
+            "vessel_name": "branch0_seg0",
+            "boundary_conditions": {
+                "outlet": "RCR_aorta"
+            },
+            "vessel_id": 0,
+            "vessel_length": 10.0,
+            "zero_d_element_type": "BloodVessel",
+            "zero_d_element_values": {
+                "_comment_": "R = 4.464119/1333.34",
+                "R_poiseuille": 0.003348073,
+                "_comment_": "L = 5.25/1333.34",
+                "L": 0.004
+            }
+        }
+    ],
+    "closed_loop_blocks": [
+        {
+            "outlet_blocks": [
+                "branch0_seg0"
+            ],
+            "closed_loop_type": "ClosedLoopHeartAndPulmonary",
+            "cardiac_cycle_period": 1.0169, 
+            "parameters": {
+                "Tsa": 0.407420,
+                "tpwave": 8.976868,
+                "Erv_s": 2.125279,
+                "Elv_s": 3.125202,
+                "iml": 0.509365,
+                "imr": 0.806369,
+                "_comment_": "Lrv_a = 0.249155/pConv",
+                "Lrv_a": 0.000186865,
+                "_comment_": "Rrv_a = 0.993637 * this->Rrv_base /pConv",
+                "Rrv_a": 0.035061704,
+                "_comment_": "Lra_v = 0.289378/pConv",
+                "Lra_v": 0.000217032,
+                "_comment_": "Rra_v = 10.516664/pConv",
+                "Rra_v": 0.007887459,
+                "_comment_": "Lla_v = 0.469052/pConv",
+                "Lla_v": 0.000351787,
+                "_comment_": "Rla_v = 7.081136/pConv",
+                "Rla_v": 0.005310825,
+                "_comment_": "Rlv_ao = 0.972624 * this->Rlv_base /pConv",
+                "Rlv_ao": 0.034320234,
+                "_comment_": "Llv_a = 0.147702/pConv",
+                "Llv_a": 0.000110776,
+                "Vrv_u": 9.424629,
+                "Vlv_u": 5.606007,
+                "_comment_": "Rpd = 1.120725 * this->Rpd_base /pConv",
+                "Rpd": 0.098865401,
+                "Cp": 1.090989,
+                "Cpa": 0.556854,
+                "Kxp_ra": 9.222440,
+                "Kxv_ra": 0.004837,
+                "Emax_ra": 0.208858,
+                "Vaso_ra": 4.848742,
+                "Kxp_la": 9.194992,
+                "Kxv_la": 0.008067,
+                "Emax_la": 0.303119,
+                "Vaso_la": 9.355754
+            }
+        }
+    ],
+    "initial_condition": {
+        "V_RA:CLH": 38.43,
+        "V_RV:CLH": 96.07,
+        "V_LA:CLH": 38.43,
+        "V_LV:CLH": 96.07,
+        "P_pul:CLH": 8.0
+    }
+}