#125, started adding kernel and scalarKernel for offDiagonal terms be…

…tween variable and scalarVariable.

Runs with offdiagjacscalar branch of https://github.com/pou036/moose.git

include/kernels/RedbackOffDiagonalScalarJacobian.h

@@ -0,0 +1,42 @@
+/****************************************************************/
+/*               DO NOT MODIFY THIS HEADER                      */
+/* MOOSE - Multiphysics Object Oriented Simulation Environment  */
+/*                                                              */
+/*           (c) 2010 Battelle Energy Alliance, LLC             */
+/*                   ALL RIGHTS RESERVED                        */
+/*                                                              */
+/*          Prepared by Battelle Energy Alliance, LLC           */
+/*            Under Contract No. DE-AC07-05ID14517              */
+/*            With the U. S. Department of Energy               */
+/*                                                              */
+/*            See COPYRIGHT for full restrictions               */
+/****************************************************************/
+
+#ifndef REDBACKOFFDIAGONALSCALARJACOBIAN_H
+#define REDBACKOFFDIAGONALSCALARJACOBIAN_H
+
+#include "Kernel.h"
+
+class RedbackOffDiagonalScalarJacobian;
+
+template <>
+InputParameters validParams<RedbackOffDiagonalScalarJacobian>();
+
+class RedbackOffDiagonalScalarJacobian : public Kernel
+{
+public:
+  RedbackOffDiagonalScalarJacobian(const InputParameters & parameters);
+  virtual ~RedbackOffDiagonalScalarJacobian();
+
+protected:
+  virtual Real computeQpResidual();
+  virtual Real computeQpJacobian();
+  virtual Real computeQpOffDiagJacobian(unsigned int jvar);
+  unsigned int _sc_var;
+  const VariableValue & _sc;
+  unsigned int _z_var;
+  const VariableValue & _z;
+
+};
+
+#endif /* REDBACKOFFDIAGONALSCALARJACOBIAN_H */

include/scalarkernels/RedbackOffDiagonalNonScalar.h

@@ -0,0 +1,37 @@
+/****************************************************************/
+/*               DO NOT MODIFY THIS HEADER                      */
+/*     REDBACK - Rock mEchanics with Dissipative feedBACKs      */
+/*                                                              */
+/*              (c) 2014 CSIRO and UNSW Australia               */
+/*                   ALL RIGHTS RESERVED                        */
+/*                                                              */
+/*            Prepared by CSIRO and UNSW Australia              */
+/*                                                              */
+/*            See COPYRIGHT for full restrictions               */
+/****************************************************************/
+
+#ifndef REDBACKOFFDIAGONALNONSCALAR_H
+#define REDBACKOFFDIAGONALNONSCALAR_H
+
+#include "ODEKernel.h"
+
+class RedbackOffDiagonalNonScalar;
+
+template <>
+InputParameters validParams<RedbackOffDiagonalNonScalar>();
+
+class RedbackOffDiagonalNonScalar : public ODEKernel
+{
+public:
+  RedbackOffDiagonalNonScalar(const InputParameters & parameters);
+
+protected:
+  const VariableValue & _non_scalar_variable;
+  unsigned int _non_scalar_variable_var;
+
+  virtual Real computeQpResidual();
+  virtual Real computeQpJacobian();
+  virtual Real computeQpOffDiagJacobian(unsigned int jvar);
+};
+
+#endif /* REDBACKOFFDIAGONALNONSCALAR_H */

src/base/RedbackApp.C

@@ -47,6 +47,7 @@
 #include "RedbackMassDiffusion.h"
 #include "RedbackMechDissip.h"
 #include "RedbackNavier.h"
+#include "RedbackOffDiagonalScalarJacobian.h"
 #include "RedbackPoromechanics.h"
 #include "RedbackStressDivergenceTensors.h"
 #include "RedbackThermalConvection.h"
@@ -56,6 +57,7 @@
 
 // Scalar Kernels
 #include "RedbackContinuation.h"
+#include "RedbackOffDiagonalNonScalar.h"
 
 // Dirac Kernels
 #include "FunctionPointSource.h"
@@ -141,6 +143,7 @@ RedbackApp::registerObjects(Factory & factory)
   registerKernel(RedbackMassDiffusion);
   registerKernel(RedbackMechDissip);
   registerKernel(RedbackNavier);
+  registerKernel(RedbackOffDiagonalScalarJacobian);
   registerKernel(RedbackPoromechanics);
   registerKernel(RedbackStressDivergenceTensors);
   registerKernel(RedbackThermalConvection);
@@ -150,6 +153,7 @@ RedbackApp::registerObjects(Factory & factory)
   registerKernel(RedbackVariableEqualsFunction);
 
   registerScalarKernel(RedbackContinuation);
+  registerScalarKernel(RedbackOffDiagonalNonScalar);
 
   registerDiracKernel(FunctionPointSource);
 

src/kernels/RedbackOffDiagonalScalarJacobian.C

@@ -0,0 +1,61 @@
+/****************************************************************/
+/*               DO NOT MODIFY THIS HEADER                      */
+/*     REDBACK - Rock mEchanics with Dissipative feedBACKs      */
+/*                                                              */
+/*              (c) 2014 CSIRO and UNSW Australia               */
+/*                   ALL RIGHTS RESERVED                        */
+/*                                                              */
+/*            Prepared by CSIRO and UNSW Australia              */
+/*                                                              */
+/*            See COPYRIGHT for full restrictions               */
+/****************************************************************/
+
+#include "RedbackOffDiagonalScalarJacobian.h"
+
+template <>
+InputParameters
+validParams<RedbackOffDiagonalScalarJacobian>()
+{
+  InputParameters params = validParams<Kernel>();
+  params.addRequiredCoupledVar("scalar_variable", "Scalar variable coupled into this kernel");
+  params.addCoupledVar("normal_variable", "Normal variable Z coupled into this kernel");
+  return params;
+}
+
+RedbackOffDiagonalScalarJacobian::RedbackOffDiagonalScalarJacobian(const InputParameters & parameters) :
+    Kernel(parameters),
+    _sc_var(coupledScalar("scalar_variable")),
+    _sc(coupledScalarValue("scalar_variable")),
+    _z_var(isCoupled("normal_variable")?coupled("normal_variable"):0),
+    _z(isCoupled("normal_variable")?coupledValue("normal_variable"):_zero)
+{
+  std::cout << "RedbackOffDiagonalScalarJacobian, _sc_var=" << _sc_var << std::endl;
+  //std::cout << "RedbackOffDiagonalScalarJacobian, _z_var=" << _z_var << std::endl;
+}
+
+RedbackOffDiagonalScalarJacobian::~RedbackOffDiagonalScalarJacobian()
+{
+}
+
+Real
+RedbackOffDiagonalScalarJacobian::computeQpResidual()
+{
+  return 0;
+}
+
+Real
+RedbackOffDiagonalScalarJacobian::computeQpJacobian()
+{
+  return 0;
+}
+
+Real
+RedbackOffDiagonalScalarJacobian::computeQpOffDiagJacobian(unsigned int jvar)
+{
+  // This code is only called for the (normal) variables
+  //std::string name = _sys.system().variable_name(jvar); => doens't work :-(
+  Real x = _u[_qp];
+  Real y = _sc[_i];
+  std::cout << "RedbackOffDiagonalScalarJacobian::computeQpOffDiagJacobian, jvar=" << jvar <<", x=" << x << ", y=" << y <<std::endl;
+  return 0;
+}

src/scalarkernels/RedbackOffDiagonalNonScalar.C

@@ -0,0 +1,54 @@
+/****************************************************************/
+/*               DO NOT MODIFY THIS HEADER                      */
+/*     REDBACK - Rock mEchanics with Dissipative feedBACKs      */
+/*                                                              */
+/*              (c) 2014 CSIRO and UNSW Australia               */
+/*                   ALL RIGHTS RESERVED                        */
+/*                                                              */
+/*            Prepared by CSIRO and UNSW Australia              */
+/*                                                              */
+/*            See COPYRIGHT for full restrictions               */
+/****************************************************************/
+
+#include "RedbackOffDiagonalNonScalar.h"
+
+/**
+ * This function defines the valid parameters for
+ * this Kernel and their default values
+ */
+template <>
+InputParameters
+validParams<RedbackOffDiagonalNonScalar>()
+{
+  InputParameters params = validParams<ODEKernel>();
+  params.addRequiredCoupledVar("non_scalar_variable", "The (non scalar) variable to couple");
+  return params;
+}
+
+RedbackOffDiagonalNonScalar::RedbackOffDiagonalNonScalar(const InputParameters & parameters) :
+    ODEKernel(parameters),
+    _non_scalar_variable(coupledValue("non_scalar_variable")),
+    _non_scalar_variable_var(coupled("non_scalar_variable"))
+{
+}
+
+Real
+RedbackOffDiagonalNonScalar::computeQpResidual()
+{
+  return 0.;
+}
+
+Real
+RedbackOffDiagonalNonScalar::computeQpJacobian()
+{
+  return 0.;
+}
+
+Real
+RedbackOffDiagonalNonScalar::computeQpOffDiagJacobian(unsigned int jvar)
+{
+  if (jvar == _non_scalar_variable_var)
+    return 0.;
+  else
+    return 0.;
+}

tests/off_diag_jac_scalar/test_offdiagjacscalar.i

@@ -0,0 +1,96 @@
+[Mesh]
+  type = GeneratedMesh
+  dim = 3
+[]
+
+[Variables]
+  [./diffused]
+    order = FIRST
+    family = LAGRANGE
+  [../]
+  [./z]
+  [../]
+  [./y]
+    family = SCALAR
+    initial_condition = 1.234
+  [../]
+[]
+
+[Functions]
+  [./init_gradient]
+    type = ParsedFunction
+    value = z
+  [../]
+[]
+
+[Kernels]
+  active = 'diff td_z'
+  [./diff]
+    type = Diffusion
+    variable = diffused
+  [../]
+  [./test]
+    type = RedbackOffDiagonalScalarJacobian
+    variable = diffused
+    normal_variable = z
+    scalar_variable = y
+  [../]
+  [./td_z]
+    type = TimeDerivative
+    variable = z
+  [../]
+[]
+
+[BCs]
+  [./bottom]
+    type = DirichletBC
+    variable = diffused
+    boundary = bottom
+    value = 1
+  [../]
+  [./top]
+    type = DirichletBC
+    variable = diffused
+    boundary = top
+    value = 0
+  [../]
+[]
+
+[Preconditioning]
+  [./smp]
+    type = SMP
+    full = true
+  [../]
+[]
+
+[Executioner]
+  type = Transient
+  num_steps = 1
+  solve_type = PJFNK
+[]
+
+[Outputs]
+  execute_on = 'timestep_end initial'
+  exodus = true
+[]
+
+[ICs]
+  [./diffused_init]
+    function = init_gradient
+    variable = diffused
+    type = FunctionIC
+  [../]
+[]
+
+[ScalarKernels]
+  [./td_y]
+    variable = y
+    type = ODETimeDerivative
+  [../]
+  [./offidiag]
+    variable = y
+    type = RedbackOffDiagonalNonScalar
+    non_scalar_variable = diffused
+  [../]
+[]
+