ArrayReaction

Description

This array kernel implements the following piece of a weak form: $var element = document.getElementById("moose-equation-aec9be80-5f7a-4831-adf8-0d942927dd78");katex.render("(\\vec{u}^\\ast, \\mathbf{R} \\vec{u}),", element, {displayMode:true,throwOnError:false});$ where $var element = document.getElementById("moose-equation-0d2ce157-4737-47fb-a1ed-2248db4072bc");katex.render("\\vec{u}^\\ast", element, {displayMode:false,throwOnError:false});$ is the test function, $var element = document.getElementById("moose-equation-80a5a37d-5828-4a1e-a909-86733ba5485b");katex.render("\\vec{u}", element, {displayMode:false,throwOnError:false});$ is the finite element solution and $var element = document.getElementById("moose-equation-037bd6d4-488e-420c-88a6-05083f823cf7");katex.render("\\mathbf{R}", element, {displayMode:false,throwOnError:false});$ is the reaction coefficients.

Similarly as showed in ArrayDiffusion, we can rearrange it into $var element = document.getElementById("moose-equation-46826a2f-d2f3-4f87-990d-c7241a76fa47");katex.render("(\\vec{u}^\\ast, \\mathbf{R} \\vec{u}) = \\sum_{e} \\sum_{i=1}^{N_{\\text{dof}}} \\sum_{\\text{qp}=1}^{N_{qp}} (|J|w)_{\\text{qp}} \\vec{w}_p\\vec{u}_i^\\ast \\underline{\\mathbf{R}_{\\text{qp}} \\vec{u}_{\\text{qp}} b_{i,\\text{qp}}},", element, {displayMode:true,throwOnError:false});$ where the underlined term is the vector provided by ArrayReaction::computeQpResidual. Detailed explanations on the notations can be found in ArrayDiffusion.

In general, the reaction coefficient $var element = document.getElementById("moose-equation-78861443-bd0c-4453-85f1-b61cc0f12b4c");katex.render("\\mathbf{D}", element, {displayMode:false,throwOnError:false});$ is a square matrix with the size of the number of components. When it is a diagonal matrix, it can be represented by a vector. In such a case, the components are not coupled with this array reaction kernel. If all elements of the diffusion coefficient vector are the same, we can use a scalar reaction coefficient. Thus this kernel gives users an option to set the type of diffusion coefficient with a parameter named as reaction_coefficient_type. Users can set it to scalar, array or full corresponding to scalar, diagonal matrix and full matrix respectively. Its default value is array.

The local Jacobian can be found in the following equation: $var element = document.getElementById("moose-equation-c66b5100-a6c8-450d-b5d9-96755760d3ca");katex.render("(\\vec{u}^\\ast, \\mathbf{R} \\vec{u}) = \\sum_{e} \\sum_{i=1}^{N_{\\text{dof}}} \\sum_{j=1}^{N_{\\text{dof}}} \\sum_{\\text{qp}=1}^{N_{qp}} (|J|w)_{\\text{qp}} \\vec{w}_p\\vec{u}_i^\\ast \\underline{\\mathbf{R}_{\\text{qp}} b_{j,\\text{qp}} b_{i,\\text{qp}}} \\vec{u}_j.", element, {displayMode:true,throwOnError:false});$ The underlined part is the local Jacobian evaluated by ArrayReaction::computeQpJacobian and ArrayReaction::computeQpOffDiagJacobian.

Input Parameters

reaction_coefficientThe name of the reactivity, can be scalar, vector, or matrix material property.
C++ Type:MaterialPropertyName
Unit:(no unit assumed)
Controllable:No
Description:The name of the reactivity, can be scalar, vector, or matrix material property.
variableThe name of the variable that this residual object operates on
C++ Type:NonlinearVariableName
Unit:(no unit assumed)
Controllable:No
Description:The name of the variable that this residual object operates on

Required Parameters

blockThe list of blocks (ids or names) that this object will be applied
C++ Type:std::vector<SubdomainName>
Unit:(no unit assumed)
Controllable:No
Description:The list of blocks (ids or names) that this object will be applied
displacementsThe displacements
C++ Type:std::vector<VariableName>
Unit:(no unit assumed)
Controllable:No
Description:The displacements
prop_getter_suffixAn optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
C++ Type:MaterialPropertyName
Unit:(no unit assumed)
Controllable:No
Description:An optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
use_interpolated_stateFalseFor the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.
Default:False
C++ Type:bool
Unit:(no unit assumed)
Controllable:No
Description:For the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.

Optional Parameters

absolute_value_vector_tagsThe tags for the vectors this residual object should fill with the absolute value of the residual contribution
C++ Type:std::vector<TagName>
Unit:(no unit assumed)
Controllable:No
Description:The tags for the vectors this residual object should fill with the absolute value of the residual contribution
extra_matrix_tagsThe extra tags for the matrices this Kernel should fill
C++ Type:std::vector<TagName>
Unit:(no unit assumed)
Controllable:No
Description:The extra tags for the matrices this Kernel should fill
extra_vector_tagsThe extra tags for the vectors this Kernel should fill
C++ Type:std::vector<TagName>
Unit:(no unit assumed)
Controllable:No
Description:The extra tags for the vectors this Kernel should fill
matrix_tagssystemThe tag for the matrices this Kernel should fill
Default:system
C++ Type:MultiMooseEnum
Unit:(no unit assumed)
Options:nontime, system
Controllable:No
Description:The tag for the matrices this Kernel should fill
vector_tagsnontimeThe tag for the vectors this Kernel should fill
Default:nontime
C++ Type:MultiMooseEnum
Unit:(no unit assumed)
Options:nontime, time
Controllable:No
Description:The tag for the vectors this Kernel should fill

Tagging Parameters

control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Unit:(no unit assumed)
Controllable:No
Description:Adds user-defined labels for accessing object parameters via control logic.
diag_save_inThe name of auxiliary variables to save this Kernel's diagonal Jacobian contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)
C++ Type:std::vector<AuxVariableName>
Unit:(no unit assumed)
Controllable:No
Description:The name of auxiliary variables to save this Kernel's diagonal Jacobian contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)
enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Unit:(no unit assumed)
Controllable:Yes
Description:Set the enabled status of the MooseObject.
implicitTrueDetermines whether this object is calculated using an implicit or explicit form
Default:True
C++ Type:bool
Unit:(no unit assumed)
Controllable:No
Description:Determines whether this object is calculated using an implicit or explicit form
save_inThe name of auxiliary variables to save this Kernel's residual contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)
C++ Type:std::vector<AuxVariableName>
Unit:(no unit assumed)
Controllable:No
Description:The name of auxiliary variables to save this Kernel's residual contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)
seed0The seed for the master random number generator
Default:0
C++ Type:unsigned int
Unit:(no unit assumed)
Controllable:No
Description:The seed for the master random number generator
use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Default:False
C++ Type:bool
Unit:(no unit assumed)
Controllable:No
Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.

Advanced Parameters

(moose/framework/src/kernels/ArrayReaction.C)

// This file is part of the MOOSE framework
// https://www.mooseframework.org
//
// All rights reserved, see COPYRIGHT for full restrictions
// https://github.com/idaholab/moose/blob/master/COPYRIGHT
//
// Licensed under LGPL 2.1, please see LICENSE for details
// https://www.gnu.org/licenses/lgpl-2.1.html

#include "ArrayReaction.h"

registerMooseObject("MooseApp", ArrayReaction);

InputParameters
ArrayReaction::validParams()
{
  InputParameters params = ArrayKernel::validParams();
  params.addRequiredParam<MaterialPropertyName>(
      "reaction_coefficient",
      "The name of the reactivity, can be scalar, vector, or matrix material property.");
  params.addClassDescription("The array reaction operator with the weak "
                             "form of $(\\psi_i, u_h)$.");
  return params;
}

ArrayReaction::ArrayReaction(const InputParameters & parameters)
  : ArrayKernel(parameters),
    _r(hasMaterialProperty<Real>("reaction_coefficient")
           ? &getMaterialProperty<Real>("reaction_coefficient")
           : nullptr),
    _r_array(hasMaterialProperty<RealEigenVector>("reaction_coefficient")
                 ? &getMaterialProperty<RealEigenVector>("reaction_coefficient")
                 : nullptr),
    _r_2d_array(hasMaterialProperty<RealEigenMatrix>("reaction_coefficient")
                    ? &getMaterialProperty<RealEigenMatrix>("reaction_coefficient")
                    : nullptr)
{
  if (!_r && !_r_array && !_r_2d_array)
  {
    MaterialPropertyName mat = getParam<MaterialPropertyName>("reaction_coefficient");
    mooseError("Property " + mat + " is of unsupported type for ArrayReaction");
  }
}

void
ArrayReaction::computeQpResidual(RealEigenVector & residual)
{

  if (_r)
    residual = (*_r)[_qp] * _u[_qp] * _test[_i][_qp];

  else if (_r_array)
  {
    mooseAssert((*_r_array)[_qp].size() == _var.count(),
                "reaction_coefficient size is inconsistent with the number of components of array "
                "variable");
    // WARNING: use noalias() syntax with caution. See ArrayDiffusion.C for more details.
    residual.noalias() = (*_r_array)[_qp].asDiagonal() * _u[_qp] * _test[_i][_qp];
  }

  else
  {
    mooseAssert((*_r_2d_array)[_qp].cols() == _var.count(),
                "reaction_coefficient size is inconsistent with the number of components of array "
                "variable");
    mooseAssert((*_r_2d_array)[_qp].rows() == _var.count(),
                "reaction_coefficient size is inconsistent with the number of components of array "
                "variable");
    // WARNING: use noalias() syntax with caution. See ArrayDiffusion.C for more details.
    residual.noalias() = (*_r_2d_array)[_qp] * _u[_qp] * _test[_i][_qp];
  }
}

RealEigenVector
ArrayReaction::computeQpJacobian()
{
  if (_r)
    return RealEigenVector::Constant(_var.count(), _phi[_j][_qp] * _test[_i][_qp] * (*_r)[_qp]);
  else if (_r_array)
    return _phi[_j][_qp] * _test[_i][_qp] * (*_r_array)[_qp];

  else
    return _phi[_j][_qp] * _test[_i][_qp] * (*_r_2d_array)[_qp].diagonal();
}

RealEigenMatrix
ArrayReaction::computeQpOffDiagJacobian(const MooseVariableFEBase & jvar)
{
  if (jvar.number() == _var.number() && _r_2d_array)
    return _phi[_j][_qp] * _test[_i][_qp] * (*_r_2d_array)[_qp];
  else
    return ArrayKernel::computeQpOffDiagJacobian(jvar);
}

(moose/framework/src/kernels/ArrayReaction.C)

// This file is part of the MOOSE framework
// https://www.mooseframework.org
//
// All rights reserved, see COPYRIGHT for full restrictions
// https://github.com/idaholab/moose/blob/master/COPYRIGHT
//
// Licensed under LGPL 2.1, please see LICENSE for details
// https://www.gnu.org/licenses/lgpl-2.1.html

#include "ArrayReaction.h"

registerMooseObject("MooseApp", ArrayReaction);

InputParameters
ArrayReaction::validParams()
{
  InputParameters params = ArrayKernel::validParams();
  params.addRequiredParam<MaterialPropertyName>(
      "reaction_coefficient",
      "The name of the reactivity, can be scalar, vector, or matrix material property.");
  params.addClassDescription("The array reaction operator with the weak "
                             "form of $(\\psi_i, u_h)$.");
  return params;
}

ArrayReaction::ArrayReaction(const InputParameters & parameters)
  : ArrayKernel(parameters),
    _r(hasMaterialProperty<Real>("reaction_coefficient")
           ? &getMaterialProperty<Real>("reaction_coefficient")
           : nullptr),
    _r_array(hasMaterialProperty<RealEigenVector>("reaction_coefficient")
                 ? &getMaterialProperty<RealEigenVector>("reaction_coefficient")
                 : nullptr),
    _r_2d_array(hasMaterialProperty<RealEigenMatrix>("reaction_coefficient")
                    ? &getMaterialProperty<RealEigenMatrix>("reaction_coefficient")
                    : nullptr)
{
  if (!_r && !_r_array && !_r_2d_array)
  {
    MaterialPropertyName mat = getParam<MaterialPropertyName>("reaction_coefficient");
    mooseError("Property " + mat + " is of unsupported type for ArrayReaction");
  }
}

void
ArrayReaction::computeQpResidual(RealEigenVector & residual)
{

  if (_r)
    residual = (*_r)[_qp] * _u[_qp] * _test[_i][_qp];

  else if (_r_array)
  {
    mooseAssert((*_r_array)[_qp].size() == _var.count(),
                "reaction_coefficient size is inconsistent with the number of components of array "
                "variable");
    // WARNING: use noalias() syntax with caution. See ArrayDiffusion.C for more details.
    residual.noalias() = (*_r_array)[_qp].asDiagonal() * _u[_qp] * _test[_i][_qp];
  }

  else
  {
    mooseAssert((*_r_2d_array)[_qp].cols() == _var.count(),
                "reaction_coefficient size is inconsistent with the number of components of array "
                "variable");
    mooseAssert((*_r_2d_array)[_qp].rows() == _var.count(),
                "reaction_coefficient size is inconsistent with the number of components of array "
                "variable");
    // WARNING: use noalias() syntax with caution. See ArrayDiffusion.C for more details.
    residual.noalias() = (*_r_2d_array)[_qp] * _u[_qp] * _test[_i][_qp];
  }
}

RealEigenVector
ArrayReaction::computeQpJacobian()
{
  if (_r)
    return RealEigenVector::Constant(_var.count(), _phi[_j][_qp] * _test[_i][_qp] * (*_r)[_qp]);
  else if (_r_array)
    return _phi[_j][_qp] * _test[_i][_qp] * (*_r_array)[_qp];

  else
    return _phi[_j][_qp] * _test[_i][_qp] * (*_r_2d_array)[_qp].diagonal();
}

RealEigenMatrix
ArrayReaction::computeQpOffDiagJacobian(const MooseVariableFEBase & jvar)
{
  if (jvar.number() == _var.number() && _r_2d_array)
    return _phi[_j][_qp] * _test[_i][_qp] * (*_r_2d_array)[_qp];
  else
    return ArrayKernel::computeQpOffDiagJacobian(jvar);
}

(moose/framework/src/kernels/ArrayReaction.C)

// This file is part of the MOOSE framework
// https://www.mooseframework.org
//
// All rights reserved, see COPYRIGHT for full restrictions
// https://github.com/idaholab/moose/blob/master/COPYRIGHT
//
// Licensed under LGPL 2.1, please see LICENSE for details
// https://www.gnu.org/licenses/lgpl-2.1.html

#include "ArrayReaction.h"

registerMooseObject("MooseApp", ArrayReaction);

InputParameters
ArrayReaction::validParams()
{
  InputParameters params = ArrayKernel::validParams();
  params.addRequiredParam<MaterialPropertyName>(
      "reaction_coefficient",
      "The name of the reactivity, can be scalar, vector, or matrix material property.");
  params.addClassDescription("The array reaction operator with the weak "
                             "form of $(\\psi_i, u_h)$.");
  return params;
}

ArrayReaction::ArrayReaction(const InputParameters & parameters)
  : ArrayKernel(parameters),
    _r(hasMaterialProperty<Real>("reaction_coefficient")
           ? &getMaterialProperty<Real>("reaction_coefficient")
           : nullptr),
    _r_array(hasMaterialProperty<RealEigenVector>("reaction_coefficient")
                 ? &getMaterialProperty<RealEigenVector>("reaction_coefficient")
                 : nullptr),
    _r_2d_array(hasMaterialProperty<RealEigenMatrix>("reaction_coefficient")
                    ? &getMaterialProperty<RealEigenMatrix>("reaction_coefficient")
                    : nullptr)
{
  if (!_r && !_r_array && !_r_2d_array)
  {
    MaterialPropertyName mat = getParam<MaterialPropertyName>("reaction_coefficient");
    mooseError("Property " + mat + " is of unsupported type for ArrayReaction");
  }
}

void
ArrayReaction::computeQpResidual(RealEigenVector & residual)
{

  if (_r)
    residual = (*_r)[_qp] * _u[_qp] * _test[_i][_qp];

  else if (_r_array)
  {
    mooseAssert((*_r_array)[_qp].size() == _var.count(),
                "reaction_coefficient size is inconsistent with the number of components of array "
                "variable");
    // WARNING: use noalias() syntax with caution. See ArrayDiffusion.C for more details.
    residual.noalias() = (*_r_array)[_qp].asDiagonal() * _u[_qp] * _test[_i][_qp];
  }

  else
  {
    mooseAssert((*_r_2d_array)[_qp].cols() == _var.count(),
                "reaction_coefficient size is inconsistent with the number of components of array "
                "variable");
    mooseAssert((*_r_2d_array)[_qp].rows() == _var.count(),
                "reaction_coefficient size is inconsistent with the number of components of array "
                "variable");
    // WARNING: use noalias() syntax with caution. See ArrayDiffusion.C for more details.
    residual.noalias() = (*_r_2d_array)[_qp] * _u[_qp] * _test[_i][_qp];
  }
}

RealEigenVector
ArrayReaction::computeQpJacobian()
{
  if (_r)
    return RealEigenVector::Constant(_var.count(), _phi[_j][_qp] * _test[_i][_qp] * (*_r)[_qp]);
  else if (_r_array)
    return _phi[_j][_qp] * _test[_i][_qp] * (*_r_array)[_qp];

  else
    return _phi[_j][_qp] * _test[_i][_qp] * (*_r_2d_array)[_qp].diagonal();
}

RealEigenMatrix
ArrayReaction::computeQpOffDiagJacobian(const MooseVariableFEBase & jvar)
{
  if (jvar.number() == _var.number() && _r_2d_array)
    return _phi[_j][_qp] * _test[_i][_qp] * (*_r_2d_array)[_qp];
  else
    return ArrayKernel::computeQpOffDiagJacobian(jvar);
}

Description
Input Parameters