Documented IElasticity and removed unused methods.

src/elasticity/assemble/IElasticity.hpp

@@ -7,7 +7,9 @@
 #include "CardiacData.hpp"
 #include "problem/ElasticityProblem.hpp"
 
-
+/**
+ * Interface to generate different linear and nonlinear assembles.
+ */
 class IElasticity : public INonLinearTimeAssemble, public ICardiacAssemble {
 protected:
   using IAssemble::verbose;
@@ -24,6 +26,7 @@ protected:
   //Prestress
   std::unique_ptr<Vector> Prestress = nullptr;
 
+  /// Calculates the prestress for the corresponding discretization.
   virtual void prestress(const Vector &u_0, Vector &pStress) = 0;
 
   //Active Deformation
@@ -39,8 +42,10 @@ protected:
 public:
   IElasticity(ElasticityProblem &eP);
 
+  /// Gets the corresponding discretization.
   virtual const IDiscretization &GetDisc() const = 0;
 
+  /// Creates a new discretization with a different size.
   virtual std::unique_ptr<IDiscretization> CreateDisc(int size) const = 0;
 
   const char *Name() const override { return "Cardiac Elasticity"; }
@@ -51,10 +56,17 @@ public:
 
   void InitializePrestress(const Vector &u);
 
+  /**
+   * Clears DirichletFlags and generate Dirichlet boundary dependent of the initialize
+   * method in the assemble.
+   * Is called once per time step.
+   */
   virtual void Initialize(const cell &c, Vector &U) const {};
 
+  /// Updates the displacement vector to the next time step.
   void FinishTimeStep(const Vector &u) override;
 
+  /// Calculates iota4 if time step is finished.
   void Finalize(Vectors &vecs);
 
   using IAssemble::Residual;
@@ -68,10 +80,19 @@ public:
     return r.norm();
   }
 
+  /**
+   *   Calculates the stiffness part k_p for the traction boundary q(u,v,n) = k_p * u + c_p * v and
+       stores it in matrix form.
+   */
   virtual void TractionStiffness(Matrix &matrix) const {};
 
+  /**
+    *   Calculates the stiffness part c_p for the traction boundary q(u,v,n) = k_p * u + c_p * v and
+        stores it in matrix form.
+    */
   virtual void TractionViscosity(Matrix &matrix) const {};
 
+  /// Calculates the residual including viscous part.
   virtual double ViscoResidual(const Vector &u, const Vector &v, Vector &defect) const {
     defect = *Prestress;
     TRY {
@@ -83,11 +104,13 @@ public:
     return defect.norm();
   }
 
+  /// Calculates the residual including viscous part for every cell.
   virtual void
   ViscoResidual(const cell &c, const Vector &u, const Vector &v, Vector &defect) const {
     Residual(c, u, defect);
   }
 
+  /// Calculate Jacobi including viscous part.
   virtual void ViscoJacobi(const Vector &u, const Vector &v, Matrix &jacobi) const {
     jacobi = 0;
     TRY {
@@ -97,36 +120,42 @@ public:
     jacobi.ClearDirichletValues();
   }
 
+  /// Calculate Jacobi including viscous part for every cell.
   virtual void ViscoJacobi(const cell &c, const Vector &u, const Vector &v, Matrix &jacobi) const {
     Jacobi(c, u, jacobi);
   }
 
-
-  virtual void GetStress(const Vector &u, Vector &stress) const = 0;
-
+  /// Calculates the invariant iota4.
   virtual void GetInvariant(const Vector &u, Vector &iota4) const = 0;
 
-
-  virtual void PlotFibres(const Vector &u, VtuPlot &plot) const {}
-
   void PlotDisplacement(const Vector &u, int step, const string &varname) const;
 
+  /**
+   *   Creates a new vector with the discretization of target (coarse vector) and projects fine
+       vector on it.
+   */
   Vector Projection(const Vector &target, const Vector &fine) const {
     Vector v(0.0, target);
     Project(fine, v);
     return v;
   }
 
+  /// Project fine vector on coarse vector.
   virtual void Project(const Vector &fine, Vector &u) const {
     Warning("No Projection implemented")
   }
 
+  /**
+   * Creates a new vector with the discretization of the fine vector and interpolates it on the
+   * coarse vector.
+   */
   Vector Interpolation(const Vector &coarse, const Vector &target) const {
     Vector v(target);
     Interpolate(coarse, v);
     return v;
   }
 
+  /// Interpolates the fine vector through the coarse vector.
   virtual void Interpolate(const Vector &coarse, Vector &u) const {
     Warning("No Interpolation implemented")
   }
@@ -193,10 +222,12 @@ public:
     return 0.0;
   }
 
+  /// For coupled system to update the stretch gamma_f.
   virtual void UpdateStretch(const Vector &gamma_f) const {
     Warning("UpdateStretch is not defined")
   };
 
+  /// Sets the displacement for a problem with exact solution.
   virtual void SetDisplacement(Vector &u) const {
     Warning("SetDisplacement is not defined")
   };
@@ -205,7 +236,6 @@ public:
     return eProblem;
   }
 
-
   virtual void PlotBoundary(const Vector &U, const Vector &scal) const {
     Warning("Nothing to Plot")
   };
@@ -214,21 +244,28 @@ public:
 
   void SetInitialValue(Vectors &values);
 
+  /// Every time step will be plotted if we are in the dynamic case.
   void PlotIteration(const Vector &u) const override;
 
   void PlotIteration(const Vectors &u, int step = -1) const;
 
+  /// Every pressure step will be plotted (static).
   void PlotPressureIteration(const Vector &u, int step) const;
 
+  /// Prints some information after every time step.
   void PrintIteration(const Vector &u) const override;
 
+  /// Prints some information after every pressure step.
   void PrintPressureIteration(const Vector &u) const;
 };
 
-
+/**
+ * Is searching for the current discretization and than calls the function CreateFiniteElasticityAssemble
+   to create different assembles.
+ */
 std::unique_ptr<IElasticity>
 CreateFiniteElasticityAssemble(ElasticityProblem &elasticityProblem, int degree, bool isStatic);
-
+/// Creates different ElasticityAssembles, e.g. Lagrange, DG and EG.
 std::unique_ptr<IElasticity>
 CreateFiniteElasticityAssemble(ElasticityProblem &elasticityProblem, const std::string &modelName,
                                int degree, bool isStatic);