Allow holding parameters constant in calibrator

src/model/BloodVessel.h

@@ -170,7 +170,7 @@ class BloodVessel : public Block {
    * @param dofhandler Degree-of-freedom handler to register variables and
    * equations at
    */
-  void setup_dofs(DOFHandler& dofhandler);
+  void setup_dofs(DOFHandler& dofhandler) override;
 
   /**
    * @brief Update the constant contributions of the element in a sparse
@@ -179,7 +179,8 @@ class BloodVessel : public Block {
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /**
    * @brief Update the solution-dependent contributions of the element in a
@@ -190,9 +191,10 @@ class BloodVessel : public Block {
    * @param y Current solution
    * @param dy Current derivate of the solution
    */
-  void update_solution(SparseSystem& system, std::vector<double>& parameters,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy);
+  void update_solution(
+      SparseSystem& system, std::vector<double>& parameters,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy) override;
 
   /**
    * @brief Set the gradient of the block contributions with respect to the
@@ -207,7 +209,8 @@ class BloodVessel : public Block {
   void update_gradient(Eigen::SparseMatrix<double>& jacobian,
                        Eigen::Matrix<double, Eigen::Dynamic, 1>& residual,
                        Eigen::Matrix<double, Eigen::Dynamic, 1>& alpha,
-                       std::vector<double>& y, std::vector<double>& dy);
+                       std::vector<double>& y,
+                       std::vector<double>& dy) override;
 
   /**
    * @brief Number of triplets of element

src/model/BloodVesselCRL.h

@@ -149,7 +149,7 @@ class BloodVesselCRL : public Block {
    * @param dofhandler Degree-of-freedom handler to register variables and
    * equations at
    */
-  void setup_dofs(DOFHandler& dofhandler);
+  void setup_dofs(DOFHandler& dofhandler) override;
 
   /**
    * @brief Update the constant contributions of the element in a sparse
@@ -158,7 +158,8 @@ class BloodVesselCRL : public Block {
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /**
    * @brief Update the solution-dependent contributions of the element in a
@@ -169,9 +170,10 @@ class BloodVesselCRL : public Block {
    * @param y Current solution
    * @param dy Current derivate of the solution
    */
-  void update_solution(SparseSystem& system, std::vector<double>& parameters,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy);
+  void update_solution(
+      SparseSystem& system, std::vector<double>& parameters,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy) override;
 
   /**
    * @brief Set the gradient of the block contributions with respect to the
@@ -186,7 +188,8 @@ class BloodVesselCRL : public Block {
   void update_gradient(Eigen::SparseMatrix<double>& jacobian,
                        Eigen::Matrix<double, Eigen::Dynamic, 1>& residual,
                        Eigen::Matrix<double, Eigen::Dynamic, 1>& alpha,
-                       std::vector<double>& y, std::vector<double>& dy);
+                       std::vector<double>& y,
+                       std::vector<double>& dy) override;
 
   /**
    * @brief Number of triplets of element

src/model/BloodVesselJunction.h

@@ -179,15 +179,16 @@ class BloodVesselJunction : public Block {
    * @param dofhandler Degree-of-freedom handler to register variables and
    * equations at
    */
-  void setup_dofs(DOFHandler& dofhandler);
+  void setup_dofs(DOFHandler& dofhandler) override;
 
   /**
    * @brief Update the constant contributions of the element in a sparse system
    *
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /**
    * @brief Update the solution-dependent contributions of the element in a
@@ -201,7 +202,7 @@ class BloodVesselJunction : public Block {
   virtual void update_solution(
       SparseSystem& system, std::vector<double>& parameters,
       const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
-      const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy);
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy) override;
 
   /**
    * @brief Set the gradient of the block contributions with respect to the
@@ -216,7 +217,8 @@ class BloodVesselJunction : public Block {
   void update_gradient(Eigen::SparseMatrix<double>& jacobian,
                        Eigen::Matrix<double, Eigen::Dynamic, 1>& residual,
                        Eigen::Matrix<double, Eigen::Dynamic, 1>& alpha,
-                       std::vector<double>& y, std::vector<double>& dy);
+                       std::vector<double>& y,
+                       std::vector<double>& dy) override;
 
   /**
    * @brief Number of triplets of element

src/model/BloodVesselRC.h

@@ -43,8 +43,9 @@ class BloodVesselRC : public Block {
   /// @brief Local IDs of the parameters
   enum ParamId { RPD = 0, CP = 1 };
 
-  void setup_dofs(DOFHandler& dofhandler);
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void setup_dofs(DOFHandler& dofhandler) override;
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /// @brief Number of triplets of element
   TripletsContributions num_triplets{5, 1, 0};

src/model/ChamberElastanceInductorExponential.h

@@ -65,10 +65,12 @@ class ChamberElastanceInductorExponential : public ChamberElastanceInductor {
     VASO = 4,
   };
 
-  void update_time(SparseSystem& system, std::vector<double>& parameters);
-  void update_solution(SparseSystem& system, std::vector<double>& parameters,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy);
+  void update_time(SparseSystem& system,
+                   std::vector<double>& parameters) override;
+  void update_solution(
+      SparseSystem& system, std::vector<double>& parameters,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy) override;
 
   /// @brief Number of triplets of element
   TripletsContributions num_triplets{6, 2, 1};

src/model/ChamberSphere.h

@@ -182,7 +182,7 @@ class ChamberSphere : public Block {
    * @param dofhandler Degree-of-freedom handler to register variables and
    * equations at
    */
-  void setup_dofs(DOFHandler& dofhandler);
+  void setup_dofs(DOFHandler& dofhandler) override;
 
   /**
    * @brief Update the constant contributions of the element in a sparse
@@ -191,7 +191,8 @@ class ChamberSphere : public Block {
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /**
    * @brief Update the time-dependent contributions of the element in a sparse
@@ -200,7 +201,8 @@ class ChamberSphere : public Block {
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_time(SparseSystem& system, std::vector<double>& parameters);
+  void update_time(SparseSystem& system,
+                   std::vector<double>& parameters) override;
 
   /**
    * @brief Update the solution-dependent contributions of the element in a
@@ -211,9 +213,10 @@ class ChamberSphere : public Block {
    * @param y Current solution
    * @param dy Current derivate of the solution
    */
-  void update_solution(SparseSystem& system, std::vector<double>& parameters,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy);
+  void update_solution(
+      SparseSystem& system, std::vector<double>& parameters,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy) override;
 
   /**
    * @brief Update the elastance functions which depend on time

src/model/ClosedLoopCoronaryBC.h

@@ -127,21 +127,22 @@ class ClosedLoopCoronaryBC : public Block {
    * @param dofhandler Degree-of-freedom handler to register variables and
    * equations at
    */
-  void setup_dofs(DOFHandler& dofhandler);
+  void setup_dofs(DOFHandler& dofhandler) override;
 
   /**
    * @brief Setup parameters that depend on the model
    *
    */
-  virtual void setup_model_dependent_params() = 0;
+  virtual void setup_model_dependent_params() override = 0;
 
   /**
    * @brief Update the constant contributions of the element in a sparse system
    *
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /**
    * @brief Update the solution-dependent contributions of the element in a
@@ -152,9 +153,10 @@ class ClosedLoopCoronaryBC : public Block {
    * @param y Current solution
    * @param dy Current derivate of the solution
    */
-  void update_solution(SparseSystem& system, std::vector<double>& parameters,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy);
+  void update_solution(
+      SparseSystem& system, std::vector<double>& parameters,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy) override;
 
   /**
    * @brief Number of triplets of element

src/model/ClosedLoopCoronaryLeftBC.h

@@ -45,7 +45,7 @@ class ClosedLoopCoronaryLeftBC : public ClosedLoopCoronaryBC {
    * @brief Setup parameters that depend on the model
    *
    */
-  void setup_model_dependent_params();
+  void setup_model_dependent_params() override;
 };
 
 #endif  // SVZERODSOLVER_MODEL_CLOSEDLOOPCORONARYLEFTBC_HPP_

src/model/ClosedLoopCoronaryRightBC.h

@@ -45,7 +45,7 @@ class ClosedLoopCoronaryRightBC : public ClosedLoopCoronaryBC {
    * @brief Setup parameters that depend on the model
    *
    */
-  void setup_model_dependent_params();
+  void setup_model_dependent_params() override;
 };
 
 #endif  // SVZERODSOLVER_MODEL_CLOSEDLOOPCORONARYRIGHTBC_HPP_

src/model/ClosedLoopHeartPulmonary.h

@@ -195,7 +195,7 @@ class ClosedLoopHeartPulmonary : public Block {
    * @param dofhandler Degree-of-freedom handler to register variables and
    * equations at
    */
-  void setup_dofs(DOFHandler& dofhandler);
+  void setup_dofs(DOFHandler& dofhandler) override;
 
   /**
    * @brief Update the constant contributions of the element in a sparse
@@ -204,7 +204,8 @@ class ClosedLoopHeartPulmonary : public Block {
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /**
    * @brief Update the time-dependent contributions of the element in a sparse
@@ -213,7 +214,8 @@ class ClosedLoopHeartPulmonary : public Block {
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_time(SparseSystem& system, std::vector<double>& parameters);
+  void update_time(SparseSystem& system,
+                   std::vector<double>& parameters) override;
 
   /**
    * @brief Update the solution-dependent contributions of the element in a
@@ -224,16 +226,17 @@ class ClosedLoopHeartPulmonary : public Block {
    * @param y Current solution
    * @param dy Current derivate of the solution
    */
-  void update_solution(SparseSystem& system, std::vector<double>& parameters,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
-                       const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy);
+  void update_solution(
+      SparseSystem& system, std::vector<double>& parameters,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& y,
+      const Eigen::Matrix<double, Eigen::Dynamic, 1>& dy) override;
 
   /**
    * @brief Modify the solution after solving it
    *
    * @param y Current solution
    */
-  void post_solve(Eigen::Matrix<double, Eigen::Dynamic, 1>& y);
+  void post_solve(Eigen::Matrix<double, Eigen::Dynamic, 1>& y) override;
 
   /**
    * @brief Number of triplets of element

src/model/ClosedLoopRCRBC.h

@@ -141,7 +141,7 @@ class ClosedLoopRCRBC : public Block {
    * @param dofhandler Degree-of-freedom handler to register variables and
    * equations at
    */
-  void setup_dofs(DOFHandler& dofhandler);
+  void setup_dofs(DOFHandler& dofhandler) override;
 
   /**
    * @brief Update the constant contributions of the element in a sparse
@@ -150,7 +150,8 @@ class ClosedLoopRCRBC : public Block {
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /**
    * @brief Number of triplets of element

src/model/FlowReferenceBC.h

@@ -97,15 +97,16 @@ class FlowReferenceBC : public Block {
    * @param dofhandler Degree-of-freedom handler to register variables and
    * equations at
    */
-  void setup_dofs(DOFHandler& dofhandler);
+  void setup_dofs(DOFHandler& dofhandler) override;
 
   /**
    * @brief Update the constant contributions of the element in a sparse system
    *
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /**
    * @brief Update the time-dependent contributions of the element in a sparse
@@ -114,7 +115,8 @@ class FlowReferenceBC : public Block {
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_time(SparseSystem& system, std::vector<double>& parameters);
+  void update_time(SparseSystem& system,
+                   std::vector<double>& parameters) override;
 
   /**
    * @brief Number of triplets of element

src/model/Junction.h

@@ -109,15 +109,16 @@ class Junction : public Block {
    * @param dofhandler Degree-of-freedom handler to register variables and
    * equations at
    */
-  void setup_dofs(DOFHandler& dofhandler);
+  void setup_dofs(DOFHandler& dofhandler) override;
 
   /**
    * @brief Update the constant contributions of the element in a sparse system
    *
    * @param system System to update contributions at
    * @param parameters Parameters of the model
    */
-  void update_constant(SparseSystem& system, std::vector<double>& parameters);
+  void update_constant(SparseSystem& system,
+                       std::vector<double>& parameters) override;
 
   /**
    * @brief Set the gradient of the block contributions with respect to the
@@ -132,7 +133,8 @@ class Junction : public Block {
   void update_gradient(Eigen::SparseMatrix<double>& jacobian,
                        Eigen::Matrix<double, Eigen::Dynamic, 1>& residual,
                        Eigen::Matrix<double, Eigen::Dynamic, 1>& alpha,
-                       std::vector<double>& y, std::vector<double>& dy);
+                       std::vector<double>& y,
+                       std::vector<double>& dy) override;
 
   /**
    * @brief Number of triplets of element