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SimVascular · Nov 7, 2023 · 8ba6323 · 8ba6323
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diff --git a/src/algebra/Integrator.cpp b/src/algebra/Integrator.cpp
@@ -59,7 +59,7 @@ Integrator::Integrator(Model* model, double time_step_size, double rho,
   system.reserve(model);
 }
 
-// Must declare default constructord and dedtructor 
+// Must declare default constructord and dedtructor
 // because of Eigen.
 Integrator::Integrator() {}
 Integrator::~Integrator() {}

diff --git a/src/algebra/Integrator.h b/src/algebra/Integrator.h
@@ -137,7 +137,7 @@ class Integrator {
    * @param atol Absolut tolerance for non-linear iteration termination
    * @param max_iter Maximum number of non-linear iterations
    */
-  Integrator(Model *model, double time_step_size, double rho, double atol,
+  Integrator(Model* model, double time_step_size, double rho, double atol,
              int max_iter);
 
   /**

diff --git a/src/interface/interface.cpp b/src/interface/interface.cpp
@@ -72,8 +72,7 @@ extern "C" void run_simulation(int problem_id, const double external_time,
                                std::vector<double>& output_solutions,
                                int& error_code);
 
-extern "C" void update_block_params(int problem_id,
-                                    std::string block_name,
+extern "C" void update_block_params(int problem_id, std::string block_name,
                                     std::vector<double>& params);
 
 extern "C" void read_block_params(int problem_id, std::string block_name,
@@ -82,8 +81,7 @@ extern "C" void read_block_params(int problem_id, std::string block_name,
 extern "C" void get_block_node_IDs(int problem_id, std::string block_name,
                                    std::vector<int>& IDs);
 
-extern "C" void update_state(int problem_id,
-                             std::vector<double> new_state_y,
+extern "C" void update_state(int problem_id, std::vector<double> new_state_y,
                              std::vector<double> new_state_ydot);
 
 extern "C" void return_y(int problem_id, std::vector<double>& ydot);

diff --git a/src/model/Block.cpp b/src/model/Block.cpp
@@ -43,7 +43,7 @@ std::string Block::get_name() { return this->model->get_block_name(this->id); }
 Block::~Block() {}
 
 void Block::setup_dofs_(DOFHandler &dofhandler, int num_equations,
-                        const std::list<std::string>& internal_var_names) {
+                        const std::list<std::string> &internal_var_names) {
   // Collect external DOFs from inlet nodes
   for (auto &inlet_node : inlet_nodes) {
     global_var_ids.push_back(inlet_node->pres_dof);
@@ -92,4 +92,3 @@ void Block::update_gradient(Eigen::SparseMatrix<double> &jacobian,
 }
 
 TripletsContributions Block::get_num_triplets() { return num_triplets; }
-
diff --git a/src/model/Block.h b/src/model/Block.h
@@ -43,14 +43,13 @@
 #include "SparseSystem.h"
 
 /**
- * @brief The number of triplets that the element contributes 
+ * @brief The number of triplets that the element contributes
  * to the global system.
  */
 struct TripletsContributions {
-  TripletsContributions() {};
-  TripletsContributions(int F, int E, int D) : F(F), E(E), D(D) { } ;
-  TripletsContributions operator+=(const TripletsContributions& other)
-  {
+  TripletsContributions(){};
+  TripletsContributions(int F, int E, int D) : F(F), E(E), D(D){};
+  TripletsContributions operator+=(const TripletsContributions &other) {
     F += other.F;
     E += other.E;
     D += other.D;
@@ -157,7 +156,7 @@ class Block {
    */
 
   void setup_dofs_(DOFHandler &dofhandler, int num_equations,
-                   const std::list<std::string>& internal_var_names);
+                   const std::list<std::string> &internal_var_names);
 
   /**
    * @brief Set up the degrees of freedom (DOF) of the block
@@ -231,7 +230,7 @@ class Block {
    * Number of triplets that the element contributes to the global system
    * (relevant for sparse memory reservation)
    */
-   TripletsContributions num_triplets;
+  TripletsContributions num_triplets;
 
   /**
    * @brief Get number of triplets of element

diff --git a/src/model/BloodVessel.cpp b/src/model/BloodVessel.cpp
@@ -42,15 +42,12 @@ void BloodVessel::update_constant(SparseSystem &system,
   double resistance = parameters[global_param_ids[ParamId::RESISTANCE]];
 
   // Set element contributions
-  system.E.coeffRef(global_eqn_ids[0], global_var_ids[3]) =
-      -inductance;
-  system.E.coeffRef(global_eqn_ids[1], global_var_ids[0]) =
-      -capacitance;
+  system.E.coeffRef(global_eqn_ids[0], global_var_ids[3]) = -inductance;
+  system.E.coeffRef(global_eqn_ids[1], global_var_ids[0]) = -capacitance;
   system.E.coeffRef(global_eqn_ids[1], global_var_ids[1]) =
       capacitance * resistance;
   system.F.coeffRef(global_eqn_ids[0], global_var_ids[0]) = 1.0;
-  system.F.coeffRef(global_eqn_ids[0], global_var_ids[1]) =
-      -resistance;
+  system.F.coeffRef(global_eqn_ids[0], global_var_ids[1]) = -resistance;
   system.F.coeffRef(global_eqn_ids[0], global_var_ids[2]) = -1.0;
   system.F.coeffRef(global_eqn_ids[1], global_var_ids[1]) = 1.0;
   system.F.coeffRef(global_eqn_ids[1], global_var_ids[3]) = -1.0;
@@ -70,8 +67,7 @@ void BloodVessel::update_solution(
 
   // Set element contributions
   system.C(global_eqn_ids[0]) = stenosis_resistance * -q_in;
-  system.C(global_eqn_ids[1]) =
-      stenosis_resistance * 2.0 * capacitance * dq_in;
+  system.C(global_eqn_ids[1]) = stenosis_resistance * 2.0 * capacitance * dq_in;
 
   double sgn_q_in = (0.0 < q_in) - (q_in < 0.0);
   system.dC_dy.coeffRef(global_eqn_ids[0], global_var_ids[1]) =
@@ -103,21 +99,18 @@ void BloodVessel::update_gradient(
   double stenosis_coeff = 0.0;
 
   if (global_param_ids.size() > 3) {
-    stenosis_coeff =
-        alpha[global_param_ids[ParamId::STENOSIS_COEFFICIENT]];
+    stenosis_coeff = alpha[global_param_ids[ParamId::STENOSIS_COEFFICIENT]];
   }
   auto stenosis_resistance = stenosis_coeff * fabs(y1);
 
   jacobian.coeffRef(global_eqn_ids[0], global_param_ids[0]) = -y1;
   jacobian.coeffRef(global_eqn_ids[0], global_param_ids[2]) = -dy3;
 
   if (global_param_ids.size() > 3) {
-    jacobian.coeffRef(global_eqn_ids[0], global_param_ids[3]) =
-        -fabs(y1) * y1;
+    jacobian.coeffRef(global_eqn_ids[0], global_param_ids[3]) = -fabs(y1) * y1;
   }
 
-  jacobian.coeffRef(global_eqn_ids[1], global_param_ids[0]) =
-      capacitance * dy1;
+  jacobian.coeffRef(global_eqn_ids[1], global_param_ids[0]) = capacitance * dy1;
   jacobian.coeffRef(global_eqn_ids[1], global_param_ids[1]) =
       -dy0 + (resistance + 2 * stenosis_resistance) * dy1;
 
@@ -132,4 +125,3 @@ void BloodVessel::update_gradient(
       y1 - y3 - capacitance * dy0 +
       capacitance * (resistance + 2.0 * stenosis_resistance) * dy1;
 }
-
diff --git a/src/model/BloodVessel.h b/src/model/BloodVessel.h
@@ -213,8 +213,7 @@ class BloodVessel : public Block {
    * Number of triplets that the element contributes to the global system
    * (relevant for sparse memory reservation)
    */
-  TripletsContributions num_triplets{5,3,2};
-
+  TripletsContributions num_triplets{5, 3, 2};
 };
 
 #endif  // SVZERODSOLVER_MODEL_BLOODVESSEL_HPP_
diff --git a/src/model/BloodVesselJunction.cpp b/src/model/BloodVesselJunction.cpp
@@ -51,17 +51,14 @@ void BloodVesselJunction::update_constant(SparseSystem &system,
   for (size_t i = 0; i < num_outlets; i++) {
     double inductance = parameters[global_param_ids[num_outlets + i]];
     double resistance = parameters[global_param_ids[i]];
-    system.F.coeffRef(global_eqn_ids[0],
-                      global_var_ids[3 + 2 * i]) = -1.0;
-    system.F.coeffRef(global_eqn_ids[i + 1],
-                      global_var_ids[3 + 2 * i]) = -resistance;
-    system.F.coeffRef(global_eqn_ids[i + 1], global_var_ids[0]) =
-        1.0;
-    system.F.coeffRef(global_eqn_ids[i + 1],
-                      global_var_ids[2 + 2 * i]) = -1.0;
+    system.F.coeffRef(global_eqn_ids[0], global_var_ids[3 + 2 * i]) = -1.0;
+    system.F.coeffRef(global_eqn_ids[i + 1], global_var_ids[3 + 2 * i]) =
+        -resistance;
+    system.F.coeffRef(global_eqn_ids[i + 1], global_var_ids[0]) = 1.0;
+    system.F.coeffRef(global_eqn_ids[i + 1], global_var_ids[2 + 2 * i]) = -1.0;
 
-    system.E.coeffRef(global_eqn_ids[i + 1],
-                      global_var_ids[3 + 2 * i]) = -inductance;
+    system.E.coeffRef(global_eqn_ids[i + 1], global_var_ids[3 + 2 * i]) =
+        -inductance;
   }
 }
 
@@ -71,15 +68,13 @@ void BloodVesselJunction::update_solution(
     Eigen::Matrix<double, Eigen::Dynamic, 1> &dy) {
   for (size_t i = 0; i < num_outlets; i++) {
     // Get parameters
-    auto stenosis_coeff =
-        parameters[global_param_ids[2 * num_outlets + i]];
+    auto stenosis_coeff = parameters[global_param_ids[2 * num_outlets + i]];
     auto q_out = y[global_var_ids[3 + 2 * i]];
     auto stenosis_resistance = stenosis_coeff * fabs(q_out);
 
     // Mass conservation
     system.C(global_eqn_ids[i + 1]) = -stenosis_resistance * q_out;
-    system.dC_dy.coeffRef(global_eqn_ids[i + 1],
-                          global_var_ids[3 + 2 * i]) =
+    system.dC_dy.coeffRef(global_eqn_ids[i + 1], global_var_ids[3 + 2 * i]) =
         -2.0 * stenosis_resistance;
   }
 }
@@ -107,8 +102,7 @@ void BloodVesselJunction::update_gradient(
     auto stenosis_resistance = stenosis_coeff * fabs(q_out);
 
     // Resistance
-    jacobian.coeffRef(global_eqn_ids[i + 1], global_param_ids[i]) =
-        -q_out;
+    jacobian.coeffRef(global_eqn_ids[i + 1], global_param_ids[i]) = -q_out;
 
     // Inductance
     jacobian.coeffRef(global_eqn_ids[i + 1],
@@ -127,4 +121,3 @@ void BloodVesselJunction::update_gradient(
         inductance * dq_out;
   }
 }
-
diff --git a/src/model/ClosedLoopCoronaryBC.cpp b/src/model/ClosedLoopCoronaryBC.cpp
@@ -60,24 +60,20 @@ void ClosedLoopCoronaryBC::update_constant(SparseSystem &system,
   auto ca = parameters[global_param_ids[ParamId::CA]];
   auto cim = parameters[global_param_ids[ParamId::CIM]];
 
-  system.E.coeffRef(global_eqn_ids[0], global_var_ids[0]) =
-      -ram * ca;
-  system.E.coeffRef(global_eqn_ids[0], global_var_ids[1]) =
-      ram * ra * ca;
+  system.E.coeffRef(global_eqn_ids[0], global_var_ids[0]) = -ram * ca;
+  system.E.coeffRef(global_eqn_ids[0], global_var_ids[1]) = ram * ra * ca;
   system.E.coeffRef(global_eqn_ids[1], global_var_ids[0]) = -ca;
   system.E.coeffRef(global_eqn_ids[1], global_var_ids[1]) = ca * ra;
   system.E.coeffRef(global_eqn_ids[1], global_var_ids[4]) = -1.0;
 
   system.F.coeffRef(global_eqn_ids[0], global_var_ids[0]) = -1.0;
-  system.F.coeffRef(global_eqn_ids[0], global_var_ids[1]) =
-      (ra + ram);
+  system.F.coeffRef(global_eqn_ids[0], global_var_ids[1]) = (ra + ram);
   system.F.coeffRef(global_eqn_ids[0], global_var_ids[2]) = 1.0;
   system.F.coeffRef(global_eqn_ids[0], global_var_ids[3]) = rv;
   system.F.coeffRef(global_eqn_ids[1], global_var_ids[1]) = 1.0;
   system.F.coeffRef(global_eqn_ids[1], global_var_ids[3]) = -1.0;
   system.F.coeffRef(global_eqn_ids[2], global_var_ids[2]) = cim;
-  system.F.coeffRef(global_eqn_ids[2], global_var_ids[3]) =
-      cim * rv;
+  system.F.coeffRef(global_eqn_ids[2], global_var_ids[3]) = cim * rv;
   system.F.coeffRef(global_eqn_ids[2], global_var_ids[4]) = -1.0;
 }
 
@@ -90,4 +86,3 @@ void ClosedLoopCoronaryBC::update_solution(
   auto pim = im * y[ventricle_var_id];
   system.C(global_eqn_ids[2]) = -cim * pim;
 }
-
diff --git a/src/model/ClosedLoopHeartPulmonary.cpp b/src/model/ClosedLoopHeartPulmonary.cpp
@@ -100,15 +100,13 @@ void ClosedLoopHeartPulmonary::update_solution(
   // DOF 1: Flow into right atrium (no equation)
 
   // DOF 2, Eq 1: Aortic pressure
-  system.F.coeffRef(global_eqn_ids[1], global_var_ids[15]) =
-      -valves[15];
+  system.F.coeffRef(global_eqn_ids[1], global_var_ids[15]) = -valves[15];
   system.F.coeffRef(global_eqn_ids[1], global_var_ids[3]) = 1.0;
 
   // DOF 3: Flow into aorta (no equation)
 
   // DOF 4, Eq 2: Right atrium volume
-  system.F.coeffRef(global_eqn_ids[2], global_var_ids[5]) =
-      1.0 * valves[5];
+  system.F.coeffRef(global_eqn_ids[2], global_var_ids[5]) = 1.0 * valves[5];
   system.F.coeffRef(global_eqn_ids[2], global_var_ids[1]) = -1.0;
 
   // DOF 5, Eq 3: Right atrium outflow
@@ -119,16 +117,13 @@ void ClosedLoopHeartPulmonary::update_solution(
 
   // DOF 6, Eq 4: Right ventricle pressure
   system.F.coeffRef(global_eqn_ids[4], global_var_ids[6]) = 1.0;
-  system.F.coeffRef(global_eqn_ids[4], global_var_ids[7]) =
-      -Erv;
+  system.F.coeffRef(global_eqn_ids[4], global_var_ids[7]) = -Erv;
   system.C(global_eqn_ids[4]) =
       Erv * parameters[global_param_ids[ParamId::VRV_U]];
 
   // DOF 7, Eq 5: Right ventricle volume
-  system.F.coeffRef(global_eqn_ids[5], global_var_ids[5]) =
-      -1.0 * valves[5];
-  system.F.coeffRef(global_eqn_ids[5], global_var_ids[8]) =
-      1.0 * valves[8];
+  system.F.coeffRef(global_eqn_ids[5], global_var_ids[5]) = -1.0 * valves[5];
+  system.F.coeffRef(global_eqn_ids[5], global_var_ids[8]) = 1.0 * valves[8];
 
   // DOF 8, Eq 6: Right ventricle outflow
   system.F.coeffRef(global_eqn_ids[6], global_var_ids[6]) = -1.0;
@@ -137,8 +132,7 @@ void ClosedLoopHeartPulmonary::update_solution(
       parameters[global_param_ids[ParamId::RRV_A]] * valves[8];
 
   // DOF 9, Eq 7: Pulmonary pressure
-  system.F.coeffRef(global_eqn_ids[7], global_var_ids[8]) =
-      -valves[8];
+  system.F.coeffRef(global_eqn_ids[7], global_var_ids[8]) = -valves[8];
   system.F.coeffRef(global_eqn_ids[7], global_var_ids[9]) =
       1.0 / parameters[global_param_ids[ParamId::RPD]];
   system.F.coeffRef(global_eqn_ids[7], global_var_ids[10]) =
@@ -156,10 +150,8 @@ void ClosedLoopHeartPulmonary::update_solution(
       psi_la_derivative * (AA - 1.0);
 
   // DOF 11, Eq 9: Left atrium volume
-  system.F.coeffRef(global_eqn_ids[9], global_var_ids[8]) =
-      -1.0 * valves[8];
-  system.F.coeffRef(global_eqn_ids[9], global_var_ids[12]) =
-      1.0 * valves[12];
+  system.F.coeffRef(global_eqn_ids[9], global_var_ids[8]) = -1.0 * valves[8];
+  system.F.coeffRef(global_eqn_ids[9], global_var_ids[12]) = 1.0 * valves[12];
 
   // DOF 12, Eq 10: Left atrium outflow
   system.F.coeffRef(global_eqn_ids[10], global_var_ids[10]) = -1.0;
@@ -169,16 +161,13 @@ void ClosedLoopHeartPulmonary::update_solution(
 
   // DOF 13, Eq 11: Left ventricle pressure
   system.F.coeffRef(global_eqn_ids[11], global_var_ids[13]) = 1.0;
-  system.F.coeffRef(global_eqn_ids[11], global_var_ids[14]) =
-      -Elv;
+  system.F.coeffRef(global_eqn_ids[11], global_var_ids[14]) = -Elv;
   system.C(global_eqn_ids[11]) =
       Elv * parameters[global_param_ids[ParamId::VLV_U]];
 
   // DOF 14, Eq 12: Left ventricle volume
-  system.F.coeffRef(global_eqn_ids[12], global_var_ids[12]) =
-      -1.0 * valves[12];
-  system.F.coeffRef(global_eqn_ids[12], global_var_ids[15]) =
-      1.0 * valves[15];
+  system.F.coeffRef(global_eqn_ids[12], global_var_ids[12]) = -1.0 * valves[12];
+  system.F.coeffRef(global_eqn_ids[12], global_var_ids[15]) = 1.0 * valves[15];
 
   // DOF 15, Eq 13: Left ventricle outflow
   system.F.coeffRef(global_eqn_ids[13], global_var_ids[13]) = -1.0;
@@ -242,16 +231,14 @@ void ClosedLoopHeartPulmonary::get_psi_ra_la(
     Eigen::Matrix<double, Eigen::Dynamic, 1> &y) {
   auto RA_volume = y[global_var_ids[4]];
   auto LA_volume = y[global_var_ids[11]];
-  psi_ra =
-      parameters[global_param_ids[ParamId::KXP_RA]] *
-      (exp((RA_volume - parameters[global_param_ids[ParamId::VASO_RA]]) *
-           parameters[global_param_ids[ParamId::KXV_RA]]) -
-       1.0);
-  psi_la =
-      parameters[global_param_ids[ParamId::KXP_LA]] *
-      (exp((LA_volume - parameters[global_param_ids[ParamId::VASO_LA]]) *
-           parameters[global_param_ids[ParamId::KXV_LA]]) -
-       1.0);
+  psi_ra = parameters[global_param_ids[ParamId::KXP_RA]] *
+           (exp((RA_volume - parameters[global_param_ids[ParamId::VASO_RA]]) *
+                parameters[global_param_ids[ParamId::KXV_RA]]) -
+            1.0);
+  psi_la = parameters[global_param_ids[ParamId::KXP_LA]] *
+           (exp((LA_volume - parameters[global_param_ids[ParamId::VASO_LA]]) *
+                parameters[global_param_ids[ParamId::KXV_LA]]) -
+            1.0);
 
   psi_ra_derivative =
       parameters[global_param_ids[ParamId::KXP_RA]] *
@@ -303,4 +290,3 @@ void ClosedLoopHeartPulmonary::get_valve_positions(
     y[global_var_ids[15]] = 0.0;
   }
 }
-
diff --git a/src/model/ClosedLoopRCRBC.cpp b/src/model/ClosedLoopRCRBC.cpp
@@ -51,4 +51,3 @@ void ClosedLoopRCRBC::update_constant(SparseSystem &system,
   system.F.coeffRef(global_eqn_ids[2], global_var_ids[3]) =
       -parameters[global_param_ids[ParamId::RD]];
 }
-
diff --git a/src/model/FlowReferenceBC.cpp b/src/model/FlowReferenceBC.cpp
@@ -43,4 +43,3 @@ void FlowReferenceBC::update_time(SparseSystem &system,
                                   std::vector<double> &parameters) {
   system.C(global_eqn_ids[0]) = -parameters[global_param_ids[0]];
 }
-
diff --git a/src/model/FlowReferenceBC.h b/src/model/FlowReferenceBC.h
@@ -120,7 +120,6 @@ class FlowReferenceBC : public Block {
    * (relevant for sparse memory reservation)
    */
   TripletsContributions num_triplets{1, 0, 0};
-
 };
 
 #endif  // SVZERODSOLVER_MODEL_FLOWREFERENCEBC_HPP_
Original file line number	Diff line number	Diff line change
Expand Up		@@ -51,4 +51,3 @@ void ClosedLoopRCRBC::update_constant(SparseSystem &system,
		system.F.coeffRef(global_eqn_ids[2], global_var_ids[3]) =
		-parameters[global_param_ids[ParamId::RD]];
		}
Original file line number	Diff line number	Diff line change
Expand Up		@@ -43,4 +43,3 @@ void FlowReferenceBC::update_time(SparseSystem &system,
		std::vector<double> &parameters) {
		system.C(global_eqn_ids[0]) = -parameters[global_param_ids[0]];
		}