Object-oriented refactoring of active stress

Code/Source/solver/CMakeLists.txt

@@ -228,6 +228,12 @@ set(CSRCS
   ionic_bueno_orovio.cpp
   ionic_fitzhugh_nagumo.cpp
   ionic_ttp.cpp
+
+  active_stress.cpp
+  active_stress_uniform_steady.cpp
+  active_stress_uniform_unsteady.cpp
+  active_stress_ode.cpp
+  active_stress_nash_panfilov.cpp
 
   SPLIT.c
 

Code/Source/solver/CepMod.h

@@ -194,18 +194,27 @@ class cemModelType
     bool cpld = false;
     //bool cpld = .FALSE.
 
-    /// @brief  Whether active stress formulation is employed
-    bool aStress = false;
-    //bool aStress = .FALSE.
-
     /// @brief  Whether active strain formulation is employed
     bool aStrain = false;
     //bool aStrain = .FALSE.
 
-    /// @brief  Local variable integrated in time
-    ///    := activation force for active stress model
-    ///    := fiber stretch for active strain model
-    Vector<double> Ya;
+    /// @brief Activation along fibers.
+    ///
+    /// Corresponds to active tension along fibers if using active stress, and
+    /// to fiber stretch if using active strain.
+    Vector<double> Ya_f;
+
+    /// @brief Activation along sheets.
+    ///
+    /// Only used if using active stress, in which case it represents the active
+    /// tension along sheets.
+    Vector<double> Ya_s;
+
+    /// @brief Activation along sheet normals.
+    ///
+    /// Only used if using active stress, in which case it represents the active
+    /// tension along sheet normals.
+    Vector<double> Ya_n;
 };
 
 class CepMod 
@@ -221,6 +230,9 @@ class CepMod
     /// @brief Unknowns stored at all nodes
     Array<double> Xion;
 
+    /// @brief Calcium vector at all nodes.
+    Vector<double> calcium;
+
     /// @brief Cardiac electromechanics type
     cemModelType cem;
 

Code/Source/solver/ComMod.h

@@ -7,7 +7,7 @@
 // All of the data structures used for the mesh, boundarsy conditions and solver parameters, etc. 
 // are defined here.
 
-#ifndef COMMOD_H 
+#ifndef COMMOD_H
 #define COMMOD_H
 
 #include "Array.h"
@@ -22,6 +22,7 @@
 #include "SolutionStates.h"
 #include "Timer.h"
 #include "Vector.h"
+#include "active_stress.h"
 
 #include "DebugMsg.h"
 
@@ -278,31 +279,6 @@ class bfType
     MBType bm;
 };
 
-// Fiber stress type
-class fibStrsType
-{
-  public:
-
-    // Type of fiber stress
-    int fType = 0;
-
-    // Constant steady value
-    double g = 0.0;
-
-    // Directional stress distribution parameters
-    // Fraction of active stress in fiber direction (default: 1.0)
-    double eta_f = 1.0;
-
-    // Fraction of active stress in sheet direction (default: 0.0)
-    double eta_s = 0.0;
-
-    // Fraction of active stress in sheet-normal direction (default: 0.0)
-    double eta_n = 0.0;
-
-    // Unsteady time-dependent values
-    FourierInterpolation gt;
-};
-
 /// @brief Structural domain type
 //
 class stModelType
@@ -346,9 +322,6 @@ class stModelType
     double b2 = 0.0;
     double mu0 = 0.0;
 
-    // Fiber reinforcement stress
-    fibStrsType Tf;
-
     // CANN Model/UAnisoHyper_inv
     ArtificialNeuralNetMaterial paramTable;
 
@@ -420,6 +393,12 @@ class dmnType
     // Electrophysiology model
     cepModelType cep;
 
+    /// Active stress model name.
+    std::string active_stress_model_name = "";
+
+    /// Active stress model.
+    std::shared_ptr<ActiveStress> active_stress;
+
     // Structure material model
     stModelType stM;