cleaning up compute off-diagonal jacobian after idaholab#13609

bylore · Nov 11, 2020 · b4ef239 · b4ef239
1 parent b543657
commit b4ef239
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Showing 116 changed files with 295 additions and 370 deletions.
diff --git a/examples/ex18_scalar_kernel/include/scalarkernels/ImplicitODEx.h b/examples/ex18_scalar_kernel/include/scalarkernels/ImplicitODEx.h
@@ -62,7 +62,7 @@ class ImplicitODEx : public ODEKernel
    * Note that this can be an approximation or linearization.  In this case it's
    * not because the Jacobian of this operator is easy to calculate.
    */
-  virtual Real computeQpOffDiagJacobian(unsigned int jvar) override;
+  virtual Real computeQpOffDiagJacobianScalar(unsigned int jvar) override;
 
   /**
    * Needed for computing off-diagonal terms in Jacobian
@@ -74,4 +74,3 @@ class ImplicitODEx : public ODEKernel
    */
   const VariableValue & _y;
 };
-
diff --git a/examples/ex18_scalar_kernel/include/scalarkernels/ImplicitODEy.h b/examples/ex18_scalar_kernel/include/scalarkernels/ImplicitODEy.h
@@ -61,7 +61,7 @@ class ImplicitODEy : public ODEKernel
    * This is essentially the partial derivative of the residual with respect to
    * the variable that is coupled into this kernel.
    */
-  virtual Real computeQpOffDiagJacobian(unsigned int jvar) override;
+  virtual Real computeQpOffDiagJacobianScalar(unsigned int jvar) override;
 
   /**
    * Needed for computing off-diagonal terms in Jacobian
@@ -73,4 +73,3 @@ class ImplicitODEy : public ODEKernel
    */
   const VariableValue & _x;
 };
-
diff --git a/examples/ex18_scalar_kernel/src/scalarkernels/ImplicitODEx.C b/examples/ex18_scalar_kernel/src/scalarkernels/ImplicitODEx.C
@@ -48,7 +48,7 @@ ImplicitODEx::computeQpJacobian()
 }
 
 Real
-ImplicitODEx::computeQpOffDiagJacobian(unsigned int jvar)
+ImplicitODEx::computeQpOffDiagJacobianScalar(unsigned int jvar)
 {
   if (jvar == _y_var)
     return -2.; // dF/dy

diff --git a/examples/ex18_scalar_kernel/src/scalarkernels/ImplicitODEy.C b/examples/ex18_scalar_kernel/src/scalarkernels/ImplicitODEy.C
@@ -48,7 +48,7 @@ ImplicitODEy::computeQpJacobian()
 }
 
 Real
-ImplicitODEy::computeQpOffDiagJacobian(unsigned int jvar)
+ImplicitODEy::computeQpOffDiagJacobianScalar(unsigned int jvar)
 {
   if (jvar == _x_var)
     return -4.; // dF/dx

diff --git a/framework/include/bcs/ADNodalBC.h b/framework/include/bcs/ADNodalBC.h
@@ -28,7 +28,7 @@ class ADNodalBCTempl : public NodalBCBase, public MooseVariableInterface<T>
 private:
   void computeResidual() override final;
   void computeJacobian() override final;
-  void computeOffDiagJacobian(unsigned int jvar) override final;
+  void computeOffDiagJacobian(MooseVariableFEBase & jvar) override final;
   void computeOffDiagJacobianScalar(unsigned int jvar) override final;
 
 protected:

diff --git a/framework/include/bcs/ArrayNodalBC.h b/framework/include/bcs/ArrayNodalBC.h
@@ -35,7 +35,7 @@ class ArrayNodalBC : public NodalBCBase, public MooseVariableInterface<RealEigen
   virtual const ArrayMooseVariable & variable() const override { return _var; }
   virtual void computeResidual() override;
   virtual void computeJacobian() override;
-  virtual void computeOffDiagJacobian(unsigned int jvar) override;
+  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
 protected:
   ArrayMooseVariable & _var;

diff --git a/framework/include/bcs/IntegratedBC.h b/framework/include/bcs/IntegratedBC.h
@@ -36,10 +36,6 @@ class IntegratedBC : public IntegratedBCBase, public MooseVariableInterface<Real
    * Computes d-ivar-residual / d-jvar...
    */
   virtual void computeJacobianBlock(MooseVariableFEBase & jvar) override;
-  /**
-   * Deprecated method
-   */
-  virtual void computeJacobianBlock(unsigned jvar);
   /**
    * Computes jacobian block with respect to a scalar variable
    * @param jvar The number of the scalar variable
@@ -62,6 +58,11 @@ class IntegratedBC : public IntegratedBCBase, public MooseVariableInterface<Real
    */
   virtual Real computeQpOffDiagJacobian(unsigned int /*jvar*/) { return 0; }
 
+  /**
+   * Method for computing an off-diagonal jacobian component from a scalar var.
+   */
+  virtual Real computeQpOffDiagJacobianScalar(unsigned int /*jvar*/) { return 0; }
+
   MooseVariable & _var;
 
   /// normals at quadrature points

diff --git a/framework/include/bcs/NodalBC.h b/framework/include/bcs/NodalBC.h
@@ -37,7 +37,7 @@ class NodalBC : public NodalBCBase, public MooseVariableInterface<Real>
   virtual const MooseVariable & variable() const override { return _var; }
   virtual void computeResidual() override;
   virtual void computeJacobian() override;
-  virtual void computeOffDiagJacobian(unsigned int jvar) override;
+  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
 protected:
   MooseVariable & _var;

diff --git a/framework/include/bcs/NodalBCBase.h b/framework/include/bcs/NodalBCBase.h
@@ -37,17 +37,6 @@ class NodalBCBase : public BoundaryCondition,
 
   NodalBCBase(const InputParameters & parameters);
 
-  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override
-  {
-    computeOffDiagJacobian(jvar.number());
-  }
-  virtual void computeOffDiagJacobian(unsigned int jvar) = 0;
-
-  /**
-   * Compute the off-diagonal contributions from scalar variables
-   */
-  virtual void computeOffDiagJacobianScalar(unsigned int /*jvar*/) override {}
-
   /**
    * Whether to verify that this object is acting on a nodal variable
    */

diff --git a/framework/include/bcs/NonlocalIntegratedBC.h b/framework/include/bcs/NonlocalIntegratedBC.h
@@ -40,7 +40,6 @@ class NonlocalIntegratedBC : public IntegratedBC
    */
   virtual void computeJacobian() override;
   virtual void computeJacobianBlock(MooseVariableFEBase & jvar) override;
-  using IntegratedBC::computeJacobianBlock;
 
   /**
    * computeNonlocalJacobian and computeNonlocalOffDiagJacobian methods are

diff --git a/framework/include/bcs/OneDEqualValueConstraintBC.h b/framework/include/bcs/OneDEqualValueConstraintBC.h
@@ -32,7 +32,7 @@ class OneDEqualValueConstraintBC : public IntegratedBC
 protected:
   virtual Real computeQpResidual() override;
   virtual Real computeQpJacobian() override;
-  virtual Real computeQpOffDiagJacobian(unsigned jvar) override;
+  virtual Real computeQpOffDiagJacobianScalar(unsigned int jvar) override;
 
   VariableValue & _lambda;
   unsigned int _lambda_var_number;

diff --git a/framework/include/bcs/VectorIntegratedBC.h b/framework/include/bcs/VectorIntegratedBC.h
@@ -58,6 +58,11 @@ class VectorIntegratedBC : public IntegratedBCBase, public MooseVariableInterfac
    */
   virtual Real computeQpOffDiagJacobian(unsigned int /*jvar*/) { return 0; }
 
+  /**
+   * Method for computing an off-diagonal jacobian component from a scalar var.
+   */
+  virtual Real computeQpOffDiagJacobianScalar(unsigned int /*jvar*/) { return 0; }
+
   VectorMooseVariable & _var;
 
   /// normals at quadrature points

diff --git a/framework/include/bcs/VectorNodalBC.h b/framework/include/bcs/VectorNodalBC.h
@@ -35,7 +35,7 @@ class VectorNodalBC : public NodalBCBase, public MooseVariableInterface<RealVect
   virtual const VectorMooseVariable & variable() const override { return _var; }
   virtual void computeResidual() override;
   virtual void computeJacobian() override;
-  virtual void computeOffDiagJacobian(unsigned int jvar) override;
+  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
 protected:
   VectorMooseVariable & _var;

diff --git a/framework/include/constraints/CoupledTiedValueConstraint.h b/framework/include/constraints/CoupledTiedValueConstraint.h
@@ -41,4 +41,3 @@ class CoupledTiedValueConstraint : public NodeFaceConstraint
   const Real _scaling;
   NumericVector<Number> & _residual_copy;
 };
-
diff --git a/framework/include/constraints/EqualValueEmbeddedConstraint.h b/framework/include/constraints/EqualValueEmbeddedConstraint.h
@@ -34,7 +34,7 @@ class EqualValueEmbeddedConstraint : public NodeElemConstraint
   virtual void residualEnd() override{};
 
   virtual void computeJacobian() override;
-  virtual void computeOffDiagJacobian(unsigned int jvar) override;
+  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
   virtual bool addCouplingEntriesToJacobian() override { return true; }
 

diff --git a/framework/include/constraints/NodeElemConstraint.h b/framework/include/constraints/NodeElemConstraint.h
@@ -51,11 +51,7 @@ class NodeElemConstraint : public Constraint,
   virtual void computeJacobian() override;
 
   /// Computes d-residual / d-jvar...
-  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override
-  {
-    computeOffDiagJacobian(jvar.number());
-  }
-  virtual void computeOffDiagJacobian(unsigned int jvar);
+  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
   /// Gets the indices for all dofs connected to the constraint
   virtual void getConnectedDofIndices(unsigned int var_num);

diff --git a/framework/include/constraints/NodeFaceConstraint.h b/framework/include/constraints/NodeFaceConstraint.h
@@ -63,11 +63,7 @@ class NodeFaceConstraint : public Constraint,
   /**
    * Computes d-residual / d-jvar...
    */
-  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override
-  {
-    computeOffDiagJacobian(jvar.number());
-  }
-  virtual void computeOffDiagJacobian(unsigned int jvar);
+  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
   /**
    * Gets the indices for all dofs connected to the constraint

diff --git a/framework/include/dgkernels/ADDGKernel.h b/framework/include/dgkernels/ADDGKernel.h
@@ -24,9 +24,9 @@ class ADDGKernel : public DGKernelBase, public NeighborMooseVariableInterface<Re
   void computeElemNeighResidual(Moose::DGResidualType type) override final;
   void computeElemNeighJacobian(Moose::DGJacobianType type) override final;
   void computeOffDiagElemNeighJacobian(Moose::DGJacobianType type,
-                                       unsigned int jvar) override final;
+                                       MooseVariableFEBase & jvar) override final;
   void computeJacobian() override final;
-  void computeOffDiagJacobian(unsigned int jvar) override final;
+  void computeOffDiagJacobian(MooseVariableFEBase & jvar) override final;
 
 protected:
   const MooseVariableFEBase & variable() const override { return _var; }

diff --git a/framework/include/dgkernels/ArrayDGKernel.h b/framework/include/dgkernels/ArrayDGKernel.h
@@ -54,13 +54,13 @@ class ArrayDGKernel : public DGKernelBase, public NeighborMooseVariableInterface
   /**
    * Computes d-residual / d-jvar...
    */
-  virtual void computeOffDiagJacobian(unsigned int jvar) override;
+  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
   /**
    * Computes the element-element off-diagonal Jacobian
    */
   virtual void computeOffDiagElemNeighJacobian(Moose::DGJacobianType type,
-                                               unsigned int jvar) override;
+                                               MooseVariableFEBase & jvar) override;
 
 protected:
   /**

diff --git a/framework/include/dgkernels/DGKernel.h b/framework/include/dgkernels/DGKernel.h
@@ -53,7 +53,7 @@ class DGKernel : public DGKernelBase, public NeighborMooseVariableInterface<Real
    * Computes the element-element off-diagonal Jacobian
    */
   virtual void computeOffDiagElemNeighJacobian(Moose::DGJacobianType type,
-                                               unsigned int jvar) override;
+                                               MooseVariableFEBase & jvar) override;
 
 protected:
   /**

diff --git a/framework/include/dgkernels/DGKernelBase.h b/framework/include/dgkernels/DGKernelBase.h
@@ -75,16 +75,13 @@ class DGKernelBase : public ResidualObject,
   /**
    * Computes the element-element off-diagonal Jacobian
    */
-  virtual void computeOffDiagElemNeighJacobian(Moose::DGJacobianType type, unsigned int jvar) = 0;
+  virtual void computeOffDiagElemNeighJacobian(Moose::DGJacobianType type,
+                                               MooseVariableFEBase & jvar) = 0;
 
   /**
    * Computes d-residual / d-jvar...
    */
-  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override
-  {
-    computeOffDiagJacobian(jvar.number());
-  }
-  virtual void computeOffDiagJacobian(unsigned int jvar);
+  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
 protected:
   /// Current element

diff --git a/framework/include/dirackernels/DiracKernel.h b/framework/include/dirackernels/DiracKernel.h
@@ -60,11 +60,7 @@ class DiracKernel : public ResidualObject,
   /**
    * Computes the off-diagonal Jacobian for variable jvar.
    */
-  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override
-  {
-    computeOffDiagJacobian(jvar.number());
-  }
-  virtual void computeOffDiagJacobian(unsigned int jvar);
+  virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
   virtual const MooseVariableField<Real> & variable() const override { return _var; }
 

diff --git a/framework/include/kernels/AverageValueConstraint.h b/framework/include/kernels/AverageValueConstraint.h
@@ -34,17 +34,16 @@ class AverageValueConstraint : public ScalarKernel
   static InputParameters validParams();
 
   AverageValueConstraint(const InputParameters & parameters);
-  virtual ~AverageValueConstraint();
 
-  virtual void reinit();
-  virtual void computeResidual();
-  virtual void computeJacobian();
-  virtual void computeOffDiagJacobian(unsigned int jvar);
+  virtual void reinit() override;
+  virtual void computeResidual() override;
+  virtual void computeJacobian() override;
+  virtual void computeOffDiagJacobianScalar(unsigned int jvar) override;
 
 protected:
   virtual Real computeQpResidual();
   virtual Real computeQpJacobian();
-  virtual Real computeQpOffDiagJacobian(unsigned int jvar);
+  virtual Real computeQpOffDiagJacobianScalar(unsigned int jvar);
 
   /// Local index
   unsigned int _i;

diff --git a/framework/include/kernels/CoupledForce.h b/framework/include/kernels/CoupledForce.h
@@ -39,4 +39,3 @@ class CoupledForce : public Kernel
   const VariableValue & _v;
   Real _coef;
 };
-
diff --git a/framework/include/kernels/CoupledTimeDerivative.h b/framework/include/kernels/CoupledTimeDerivative.h
@@ -36,4 +36,3 @@ class CoupledTimeDerivative : public Kernel
   const VariableValue & _dv_dot;
   const unsigned int _v_var;
 };
-
diff --git a/framework/include/kernels/EigenKernel.h b/framework/include/kernels/EigenKernel.h
@@ -38,8 +38,6 @@ class EigenKernel : public Kernel
   EigenKernel(const InputParameters & parameters);
   virtual bool enabled() const override;
 
-  using Kernel::computeOffDiagJacobian;
-
 protected:
   /// flag for as an eigen kernel or a normal kernel
   bool _eigen;
@@ -53,4 +51,3 @@ class EigenKernel : public Kernel
    */
   const Real * _eigenvalue;
 };
-
diff --git a/framework/include/kernels/Kernel.h b/framework/include/kernels/Kernel.h
@@ -33,11 +33,6 @@ class Kernel : public KernelBase, public MooseVariableInterface<Real>
   /// Computes d-residual / d-jvar... storing the result in Ke.
   virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
-  /**
-   * Deprecated method
-   */
-  virtual void computeOffDiagJacobian(unsigned jvar);
-
   /**
    * Computes jacobian block with respect to a scalar variable
    * @param jvar The number of the scalar variable
@@ -58,11 +53,15 @@ class Kernel : public KernelBase, public MooseVariableInterface<Real>
   virtual Real computeQpJacobian() { return 0; }
 
   /**
-   * This is the virtual that derived classes should override for computing an off-diagonal Jacobian
-   * component.
+   * For coupling standard variables
    */
   virtual Real computeQpOffDiagJacobian(unsigned int /*jvar*/) { return 0; }
 
+  /**
+   * For coupling scalar variables
+   */
+  virtual Real computeQpOffDiagJacobianScalar(unsigned int /*jvar*/) { return 0; }
+
   /**
    * For coupling array variables
    */

diff --git a/framework/include/kernels/KernelGrad.h b/framework/include/kernels/KernelGrad.h
@@ -43,8 +43,6 @@ class KernelGrad : public Kernel
 
   virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
-  using Kernel::computeOffDiagJacobian;
-
 protected:
   /**
    * Called before forming the residual for an element
@@ -58,4 +56,3 @@ class KernelGrad : public Kernel
 
   virtual Real computeQpResidual() override;
 };
-
diff --git a/framework/include/kernels/KernelValue.h b/framework/include/kernels/KernelValue.h
@@ -43,8 +43,6 @@ class KernelValue : public Kernel
 
   virtual void computeOffDiagJacobian(MooseVariableFEBase & jvar) override;
 
-  using Kernel::computeOffDiagJacobian;
-
 protected:
   /**
    * Called before forming the residual for an element
@@ -58,4 +56,3 @@ class KernelValue : public Kernel
 
   virtual Real computeQpResidual() final;
 };
-
diff --git a/framework/include/kernels/MatDiffusionBase.h b/framework/include/kernels/MatDiffusionBase.h
@@ -30,12 +30,12 @@ class MatDiffusionBase : public DerivativeMaterialInterface<JvarMapKernelInterfa
 
   MatDiffusionBase(const InputParameters & parameters);
 
-  virtual void initialSetup();
+  virtual void initialSetup() override;
 
 protected:
-  virtual Real computeQpResidual();
-  virtual Real computeQpJacobian();
-  virtual Real computeQpOffDiagJacobian(unsigned int jvar);
+  virtual Real computeQpResidual() override;
+  virtual Real computeQpJacobian() override;
+  virtual Real computeQpOffDiagJacobian(unsigned int jvar) override;
   virtual Real computeQpCJacobian();
 
   /// diffusion coefficient

diff --git a/framework/include/kernels/NodalScalarKernel.h b/framework/include/kernels/NodalScalarKernel.h
@@ -31,12 +31,11 @@ class NodalScalarKernel : public ScalarKernel,
   NodalScalarKernel(const InputParameters & parameters);
 
   virtual void reinit() override;
-  virtual void computeOffDiagJacobian(unsigned int jvar) override;
+  virtual void computeOffDiagJacobianScalar(unsigned int jvar) override;
 
 protected:
   /// List of node IDs
   std::vector<dof_id_type> _node_ids;
   /// List of node boundary names
   std::vector<BoundaryName> _boundary_names;
 };
-
Original file line number	Diff line number	Diff line change
Expand Up		@@ -41,4 +41,3 @@ class CoupledTiedValueConstraint : public NodeFaceConstraint
		const Real _scaling;
		NumericVector<Number> & _residual_copy;
		};
Original file line number	Diff line number	Diff line change
Expand Up		@@ -39,4 +39,3 @@ class CoupledForce : public Kernel
		const VariableValue & _v;
		Real _coef;
		};
Original file line number	Diff line number	Diff line change
Expand Up		@@ -36,4 +36,3 @@ class CoupledTimeDerivative : public Kernel
		const VariableValue & _dv_dot;
		const unsigned int _v_var;
		};