DisplacedSystem Class Reference

#include <DisplacedSystem.h>

Inheritance diagram for DisplacedSystem:

Public Member Functions
	DisplacedSystem (DisplacedProblem &problem, SystemBase &undisplaced_system, const std::string &name, Moose::VarKindType var_kind)
virtual	~DisplacedSystem ()
virtual void	init () override
	Initialize the system. More...
virtual NumericVector< Number > &	getVector (TagID tag_id) override
	Get a raw NumericVector. More...
virtual const NumericVector< Number > &	getVector (TagID tag_id) const override
	Get a raw NumericVector. More...
virtual TagID	residualVectorTag () override
virtual TagID	systemMatrixTag () override
	Return the Matrix Tag ID for System. More...
virtual TagID	timeVectorTag () override
	Ideally, we should not need this API. More...
virtual TagID	nonTimeVectorTag () override
virtual void	associateVectorToTag (NumericVector< Number > &vec, TagID tag) override
	Associate a vector for a given tag. More...
virtual void	disassociateVectorFromTag (NumericVector< Number > &vec, TagID tag) override
	Associate a vector for a given tag. More...
virtual void	disassociateAllTaggedVectors () override
	Disassociate all vectors, and then hasVector() will return false. More...
virtual void	associateMatrixToTag (SparseMatrix< Number > &matrix, TagID tag) override
	associate a matirx to a tag More...
virtual void	disassociateMatrixFromTag (SparseMatrix< Number > &matrix, TagID tag) override
	disassociate a matirx from a tag More...
virtual void	disassociateAllTaggedMatrices () override
	Clear all tagged matrices. More...
virtual NumericVector< Number > &	getVector (const std::string &name) override
	Get a raw NumericVector. More...
virtual NumericVector< Number > &	serializedSolution () override
	Returns a reference to a serialized version of the solution vector for this subproblem. More...
const NumericVector< Number > *const &	currentSolution () const override
	The solution vector that is currently being operated on. More...
NumericVector< Number > &	solution () override
NumericVector< Number > &	solutionOld () override
NumericVector< Number > &	solutionOlder () override
NumericVector< Number > *	solutionPreviousNewton () override
const NumericVector< Number > &	solution () const override
const NumericVector< Number > &	solutionOld () const override
const NumericVector< Number > &	solutionOlder () const override
const NumericVector< Number > *	solutionPreviousNewton () const override
NumericVector< Number > *	solutionUDot () override
NumericVector< Number > *	solutionUDotDot () override
NumericVector< Number > *	solutionUDotOld () override
NumericVector< Number > *	solutionUDotDotOld () override
const NumericVector< Number > *	solutionUDot () const override
const NumericVector< Number > *	solutionUDotDot () const override
const NumericVector< Number > *	solutionUDotOld () const override
const NumericVector< Number > *	solutionUDotDotOld () const override
virtual Number &	duDotDu () override
virtual Number &	duDotDotDu () override
virtual const Number &	duDotDu () const override
virtual const Number &	duDotDotDu () const override
virtual NumericVector< Number > &	residualCopy () override
	Return the residual copy from the NonlinearSystem. More...
virtual NumericVector< Number > &	residualGhosted () override
virtual void	augmentSendList (std::vector< dof_id_type > &send_list) override
	Will modify the send_list to add all of the extra ghosted dofs for this system. More...
virtual void	augmentSparsity (SparsityPattern::Graph &, std::vector< dof_id_type > &, std::vector< dof_id_type > &) override
	This is an empty function since the displaced system doesn't have a matrix! All sparsity pattern modification will be taken care of by the undisplaced system directly. More...
virtual void	addVariableToZeroOnResidual (std::string var_name) override
	Adds this variable to the list of variables to be zeroed during each residual evaluation. More...
virtual void	addVariableToZeroOnJacobian (std::string var_name) override
	Adds this variable to the list of variables to be zeroed during each jacobian evaluation. More...
virtual void	zeroVariables (std::vector< std::string > &vars_to_be_zeroed) override
	Zero out the solution for the list of variables passed in. More...
virtual bool	hasVector (TagID tag_id) const override
	Check if the tagged vector exists in the system. More...
virtual bool	hasMatrix (TagID tag_id) const override
	Check if the tagged matrix exists in the system. More...
virtual SparseMatrix< Number > &	getMatrix (TagID tag) override
	Get a raw SparseMatrix. More...
virtual const SparseMatrix< Number > &	getMatrix (TagID tag) const override
	Get a raw SparseMatrix. More...
virtual TransientExplicitSystem &	sys ()
virtual System &	system () override
	Get the reference to the libMesh system. More...
virtual const System &	system () const override
void	addTimeIntegrator (std::shared_ptr< TimeIntegrator > ti) override
virtual void	addTimeIntegrator (const std::string &, const std::string &, InputParameters &)
virtual void	addTimeIntegrator (std::shared_ptr< TimeIntegrator >)
virtual unsigned int	number () const
	Gets the number of this system. More...
virtual MooseMesh &	mesh ()
virtual const MooseMesh &	mesh () const
virtual SubProblem &	subproblem ()
virtual const SubProblem &	subproblem () const
void	applyScalingFactors (const std::vector< Real > &inverse_scaling_factors)
	Applies scaling factors to the system's variables. More...
bool	computingScalingJacobian () const
	Whether we are computing an initial Jacobian for automatic variable scaling. More...
void	computingScalingJacobian (bool computing_scaling_jacobian)
	Setter for whether we're computing the scaling jacobian. More...
bool	computingScalingResidual () const
	Whether we are computing an initial Residual for automatic variable scaling. More...
void	computingScalingResidual (bool computing_scaling_residual)
	Setter for whether we're computing the scaling residual. More...
virtual DofMap &	dofMap ()
	Gets writeable reference to the dof map. More...
virtual const DofMap &	dofMap () const
	Gets const reference to the dof map. More...
virtual void	initializeObjects ()
	Called only once, just before the solve begins so objects can do some precalculations. More...
virtual void	addExtraVectors ()
	Method called during initialSetup to add extra system vector if they are required by the simulation. More...
virtual void	update ()
	Update the system (doing libMesh magic) More...
virtual void	solve ()
	Solve the system (using libMesh magic) More...
virtual void	copyOldSolutions ()
	Shifts the solutions backwards in time. More...
virtual void	restoreSolutions ()
	Restore current solutions (call after your solve failed) More...
virtual void	saveOldSolutions ()
	Save the old and older solutions. More...
virtual void	restoreOldSolutions ()
	Restore the old and older solutions when the saved solutions present. More...
bool	hasVector (const std::string &tag_name) const
	Check if the named vector exists in the system. More...
virtual TagID	timeMatrixTag ()
	Return the Matrix Tag ID for Time. More...
virtual void	activeAllMatrixTags ()
	Make all exsiting matrices ative. More...
virtual void	activeMatrixTag (TagID tag)
	Active a matrix for tag. More...
virtual bool	matrixTagActive (TagID tag) const
	If or not a matrix tag is active. More...
virtual void	deactiveMatrixTag (TagID tag)
	deactive a matrix for tag More...
virtual void	deactiveAllMatrixTags ()
	Make matrices inactive. More...
void	closeTaggedMatrices (const std::set< TagID > &tags)
	Close all matrices associated the tags. More...
virtual void	addVariable (const std::string &var_type, const std::string &var_name, InputParameters &parameters)
	Canonical method for adding a variable. More...
virtual bool	isArrayVariable (const std::string &var_name) const
	If a variable is an array variable. More...
virtual bool	isScalarVariable (unsigned int var_name) const
MooseVariableFEBase &	getVariable (THREAD_ID tid, const std::string &var_name)
	Gets a reference to a variable of with specified name. More...
MooseVariableFEBase &	getVariable (THREAD_ID tid, unsigned int var_number)
	Gets a reference to a variable with specified number. More...
template<typename T >
MooseVariableFE< T > &	getFieldVariable (THREAD_ID tid, const std::string &var_name)
	Gets a reference to a variable of with specified name. More...
template<typename T >
MooseVariableFE< T > &	getFieldVariable (THREAD_ID tid, unsigned int var_number)
	Gets a reference to a variable with specified number. More...
virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, const std::string &var_name)
	Gets a reference to a scalar variable with specified number. More...
virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, unsigned int var_number)
	Gets a reference to a variable with specified number. More...
virtual const std::set< SubdomainID > *	getVariableBlocks (unsigned int var_number)
	Get the block where a variable of this system is defined. More...
virtual unsigned int	nVariables () const
	Get the number of variables in this system. More...
std::size_t	getMaxVarNDofsPerElem () const
	Gets the maximum number of dofs used by any one variable on any one element. More...
std::size_t	getMaxVarNDofsPerNode () const
	Gets the maximum number of dofs used by any one variable on any one node. More...
void	assignMaxVarNDofsPerElem (std::size_t max_dofs)
	assign the maximum element dofs More...
void	assignMaxVarNDofsPerNode (std::size_t max_dofs)
	assign the maximum node dofs More...
virtual void	zeroVariablesForResidual ()
	Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on residual evaluation by a call to addVariableToZeroOnResidual() More...
virtual void	zeroVariablesForJacobian ()
	Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on Jacobian evaluation by a call to addVariableToZeroOnResidual() More...
virtual Order	getMinQuadratureOrder ()
	Get minimal quadrature order needed for integrating variables in this system. More...
virtual void	prepare (THREAD_ID tid)
	Prepare the system for use. More...
virtual void	prepareFace (THREAD_ID tid, bool resize_data)
	Prepare the system for use on sides. More...
virtual void	prepareNeighbor (THREAD_ID tid)
	Prepare the system for use. More...
virtual void	prepareLowerD (THREAD_ID tid)
	Prepare the system for use for lower dimensional elements. More...
virtual void	reinitElem (const Elem *elem, THREAD_ID tid)
	Reinit an element assembly info. More...
virtual void	reinitElemFace (const Elem *elem, unsigned int side, BoundaryID bnd_id, THREAD_ID tid)
	Reinit assembly info for a side of an element. More...
virtual void	reinitNeighborFace (const Elem *elem, unsigned int side, BoundaryID bnd_id, THREAD_ID tid)
	Compute the values of the variables at all the current points. More...
virtual void	reinitNeighbor (const Elem *elem, THREAD_ID tid)
	Compute the values of the variables at all the current points. More...
virtual void	reinitLowerD (THREAD_ID tid)
	Compute the values of the variables on the lower dimensional element. More...
virtual void	reinitNode (const Node *node, THREAD_ID tid)
	Reinit nodal assembly info. More...
virtual void	reinitNodeFace (const Node *node, BoundaryID bnd_id, THREAD_ID tid)
	Reinit nodal assembly info on a face. More...
virtual void	reinitNodes (const std::vector< dof_id_type > &nodes, THREAD_ID tid)
	Reinit variables at a set of nodes. More...
virtual void	reinitNodesNeighbor (const std::vector< dof_id_type > &nodes, THREAD_ID tid)
	Reinit variables at a set of neighbor nodes. More...
virtual void	reinitScalars (THREAD_ID tid, bool reinit_for_derivative_reordering=false)
	Reinit scalar varaibles. More...
virtual void	addVariableToCopy (const std::string &dest_name, const std::string &source_name, const std::string &timestep)
	Add info about variable that will be copied. More...
const std::vector< MooseVariableFEBase * > &	getVariables (THREAD_ID tid)
const std::vector< MooseVariableScalar * > &	getScalarVariables (THREAD_ID tid)
const std::set< SubdomainID > &	getSubdomainsForVar (unsigned int var_number) const
virtual void	removeVector (const std::string &name)
	Remove a vector from the system with the given name. More...
virtual void	removeVector (TagID tag_id)
	Remove a solution length vector from the system with the specified TagID. More...
virtual NumericVector< Number > &	addVector (const std::string &vector_name, const bool project, const ParallelType type)
	Adds a solution length vector to the system. More...
NumericVector< Number > &	addVector (TagID tag, const bool project, const ParallelType type)
	Adds a solution length vector to the system with the specified TagID. More...
virtual void	closeTaggedVectors (const std::set< TagID > &tags)
	Close all vectors for given tags. More...
virtual void	zeroTaggedVectors (const std::set< TagID > &tags)
	Zero all vectors for given tags. More...
virtual SparseMatrix< Number > &	addMatrix (TagID)
	Adds a jacobian sized vector. More...
virtual void	removeMatrix (TagID)
	Removes a jacobian sized vector. More...
virtual const std::string &	name () const
const std::vector< VariableName > &	getVariableNames () const
unsigned int	getMaxVariableNumber () const
	Returns the maximum number of all variables on the system. More...
virtual void	computeVariables (const NumericVector< Number > &)
void	copyVars (ExodusII_IO &io)
virtual void	copySolutionsBackwards ()
	Copy current solution into old and older. More...
virtual void	addTimeIntegrator (const std::string &, const std::string &, InputParameters &)
TimeIntegrator *	getTimeIntegrator ()
const TimeIntegrator *	getTimeIntegrator () const
std::shared_ptr< TimeIntegrator >	getSharedTimeIntegrator ()
virtual bool	hasVariable (const std::string &var_name) const
	Query a system for a variable. More...
virtual bool	hasScalarVariable (const std::string &var_name) const

Protected Attributes
SystemBase &	_undisplaced_system
TransientExplicitSystem &	_sys
SubProblem &	_subproblem
MooseApp &	_app
Factory &	_factory
MooseMesh &	_mesh
std::string	_name
	The name of this system. More...
std::vector< VariableWarehouse >	_vars
	Variable warehouses (one for each thread) More...
std::map< unsigned int, std::set< SubdomainID > >	_var_map
	Map of variables (variable id -> array of subdomains where it lives) More...
unsigned int	_max_var_number
	Maximum variable number. More...
std::vector< std::string >	_vars_to_be_zeroed_on_residual
std::vector< std::string >	_vars_to_be_zeroed_on_jacobian
Real	_du_dot_du
Real	_du_dotdot_du
std::vector< NumericVector< Number > * >	_tagged_vectors
	Tagged vectors (pointer) More...
std::vector< SparseMatrix< Number > * >	_tagged_matrices
	Tagged matrices (pointer) More...
std::vector< bool >	_matrix_tag_active_flags
	Active flags for tagged matrices. More...
NumericVector< Real > *	_saved_old
NumericVector< Real > *	_saved_older
NumericVector< Real > *	_saved_dot_old
NumericVector< Real > *	_saved_dotdot_old
Moose::VarKindType	_var_kind
	default kind of variables in this system More...
std::vector< VarCopyInfo >	_var_to_copy
size_t	_max_var_n_dofs_per_elem
	Maximum number of dofs for any one variable on any one element. More...
size_t	_max_var_n_dofs_per_node
	Maximum number of dofs for any one variable on any one node. More...
std::shared_ptr< TimeIntegrator >	_time_integrator
	Time integrator. More...
std::vector< std::vector< MooseVariableFEBase * > >	_numbered_vars
	Map variable number to its pointer. More...
MooseObjectWarehouseBase< MooseVariableBase >	_variable_warehouse
	Storage for MooseVariable objects. More...
bool	_computing_scaling_jacobian
	Flag used to indicate whether we are computing the scaling Jacobian. More...
bool	_computing_scaling_residual
	Flag used to indicate whether we are computing the scaling Residual. More...

Detailed Description

Definition at line 24 of file DisplacedSystem.h.

Constructor & Destructor Documentation

DisplacedSystem()

DisplacedSystem::DisplacedSystem	(	DisplacedProblem &	problem,
		SystemBase &	undisplaced_system,
		const std::string &	name,
		Moose::VarKindType	var_kind
	)

Definition at line 18 of file DisplacedSystem.C.

  : SystemBase(problem, name, var_kind),
    _undisplaced_system(undisplaced_system),
    _sys(problem.es().add_system<TransientExplicitSystem>(name))
{
  if (!problem.defaultGhosting())
  {
    auto & dof_map = _sys.get_dof_map();
    dof_map.remove_algebraic_ghosting_functor(dof_map.default_algebraic_ghosting());
    dof_map.set_implicit_neighbor_dofs(false);
  }
}

~DisplacedSystem()

DisplacedSystem::~DisplacedSystem ( )

virtual

Definition at line 34 of file DisplacedSystem.C.

{}

Member Function Documentation

activeAllMatrixTags()

void SystemBase::activeAllMatrixTags ( )

virtualinherited

Make all exsiting matrices ative.

Definition at line 944 of file SystemBase.C.

{
  auto num_matrix_tags = _subproblem.numMatrixTags();
 
  _matrix_tag_active_flags.resize(num_matrix_tags);
 
  for (decltype(num_matrix_tags) tag = 0; tag < num_matrix_tags; tag++)
    if (hasMatrix(tag))
      _matrix_tag_active_flags[tag] = true;
    else
      _matrix_tag_active_flags[tag] = false;
}

Referenced by NonlinearSystemBase::computeJacobianInternal(), and NonlinearSystemBase::computeResidualTags().

activeMatrixTag()

void SystemBase::activeMatrixTag ( TagID  tag )

virtualinherited

Active a matrix for tag.

Definition at line 909 of file SystemBase.C.

{
  mooseAssert(_subproblem.matrixTagExists(tag),
              "Cannot active Matrix with matrix_tag : " << tag << "that does not exist");
 
  if (_matrix_tag_active_flags.size() < tag + 1)
    _matrix_tag_active_flags.resize(tag + 1);
 
  _matrix_tag_active_flags[tag] = true;
}

addExtraVectors()

void SystemBase::addExtraVectors ( )

virtualinherited

Method called during initialSetup to add extra system vector if they are required by the simulation.

Reimplemented in NonlinearSystemBase, and AuxiliarySystem.

Definition at line 1062 of file SystemBase.C.

{
}

addMatrix()

virtual SparseMatrix<Number>& SystemBase::addMatrix ( TagID  )

inlinevirtualinherited

Adds a jacobian sized vector.

Parameters

tag_name

The name of the tag

Reimplemented in NonlinearSystem.

Definition at line 722 of file SystemBase.h.

  {
    mooseError("Adding a matrix is not supported for this type of system!");
  }

addTimeIntegrator() [1/4]

virtual void SystemBase::addTimeIntegrator

inline

Definition at line 755 of file SystemBase.h.

  {
  }

addTimeIntegrator() [2/4]

virtual void SystemBase::addTimeIntegrator ( const std::string &  , const std::string &  , InputParameters &    )

inlinevirtualinherited

Reimplemented in NonlinearSystemBase, and AuxiliarySystem.

Definition at line 755 of file SystemBase.h.

  {
  }

addTimeIntegrator() [3/4]

void DisplacedSystem::addTimeIntegrator ( std::shared_ptr< TimeIntegrator >  ti )

overridevirtual

Reimplemented from SystemBase.

Definition at line 51 of file DisplacedSystem.C.

{
  _time_integrator = ti;
}

Referenced by DisplacedProblem::DisplacedProblem().

addTimeIntegrator() [4/4]

virtual void SystemBase::addTimeIntegrator

inline

Definition at line 761 of file SystemBase.h.

{}

addVariable()

void SystemBase::addVariable ( const std::string &  var_type, const std::string &  var_name, InputParameters &  parameters  )

virtualinherited

Canonical method for adding a variable.

Parameters

var_type	the type of the variable, e.g. MooseVariableScalar
var_name	the variable name, e.g. 'u'
params	the InputParameters from which to construct the variable

Reimplemented in AuxiliarySystem.

Definition at line 614 of file SystemBase.C.

{
  _numbered_vars.resize(libMesh::n_threads());
 
  auto components = parameters.get<unsigned int>("components");
 
  // Convert the std::vector parameter provided by the user into a std::set for use by libMesh's
  // System::add_variable method
  std::set<SubdomainID> blocks;
  const auto & block_param = parameters.get<std::vector<SubdomainName>>("block");
  for (const auto & subdomain_name : block_param)
  {
    SubdomainID blk_id = _mesh.getSubdomainID(subdomain_name);
    blocks.insert(blk_id);
  }
 
  auto fe_type = FEType(Utility::string_to_enum<Order>(parameters.get<MooseEnum>("order")),
                        Utility::string_to_enum<FEFamily>(parameters.get<MooseEnum>("family")));
 
  unsigned int var_num;
 
  if (var_type == "ArrayMooseVariable")
  {
    if (fe_type.family == NEDELEC_ONE || fe_type.family == LAGRANGE_VEC ||
        fe_type.family == MONOMIAL_VEC)
      mooseError("Vector family type cannot be used in an array variable");
 
    // Turn off automatic variable group identification so that we can be sure that this variable
    // group will be ordered exactly like it should be
    system().identify_variable_groups(false);
 
    // Build up the variable names
    std::vector<std::string> var_names;
    for (unsigned int i = 0; i < components; i++)
      var_names.push_back(SubProblem::arrayVariableComponent(name, i));
 
    // The number returned by libMesh is the _last_ variable number... we want to hold onto the
    // _first_
    var_num = system().add_variables(var_names, fe_type, &blocks) - (components - 1);
  }
  else
    var_num = system().add_variable(name, fe_type, &blocks);
 
  parameters.set<unsigned int>("_var_num") = var_num;
  parameters.set<SystemBase *>("_system_base") = this;
 
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    parameters.set<THREAD_ID>("tid") = tid;
    std::shared_ptr<MooseVariableBase> var =
        _factory.create<MooseVariableBase>(var_type, name, parameters, tid);
 
    _vars[tid].add(name, var);
 
    if (auto fe_var = dynamic_cast<MooseVariableFEBase *>(var.get()))
    {
      auto required_size = var_num + components;
      if (required_size > _numbered_vars[tid].size())
        _numbered_vars[tid].resize(required_size);
      for (MooseIndex(components) component = 0; component < components; ++component)
        _numbered_vars[tid][var_num + component] = fe_var;
    }
 
    if (var->blockRestricted())
      for (const SubdomainID & id : var->blockIDs())
        for (MooseIndex(components) component = 0; component < components; ++component)
          _var_map[var_num + component].insert(id);
    else
      for (MooseIndex(components) component = 0; component < components; ++component)
        _var_map[var_num + component] = std::set<SubdomainID>();
  }
 
  // getMaxVariableNumber is an API method used in Rattlesnake
  if (var_num > _max_var_number)
    _max_var_number = var_num;
}

Referenced by DisplacedProblem::addAuxVariable(), AuxiliarySystem::addVariable(), and DisplacedProblem::addVariable().

addVariableToCopy()

void SystemBase::addVariableToCopy ( const std::string &  dest_name, const std::string &  source_name, const std::string &  timestep  )

virtualinherited

Add info about variable that will be copied.

Parameters

dest_name	Name of the nodal variable being used for copying into (name is from the exodusII file)
source_name	Name of the nodal variable being used for copying from (name is from the exodusII file)
timestep	Timestep in the file being used

Definition at line 991 of file SystemBase.C.

{
  _var_to_copy.push_back(VarCopyInfo(dest_name, source_name, timestep));
}

addVariableToZeroOnJacobian()

virtual void DisplacedSystem::addVariableToZeroOnJacobian ( std::string  var_name )

inlineoverridevirtual

Adds this variable to the list of variables to be zeroed during each jacobian evaluation.

Parameters

var_name

The name of the variable to be zeroed.

Reimplemented from SystemBase.

Definition at line 180 of file DisplacedSystem.h.

  {
    _undisplaced_system.addVariableToZeroOnJacobian(var_name);
  }

addVariableToZeroOnResidual()

virtual void DisplacedSystem::addVariableToZeroOnResidual ( std::string  var_name )

inlineoverridevirtual

Adds this variable to the list of variables to be zeroed during each residual evaluation.

Parameters

var_name

The name of the variable to be zeroed.

Reimplemented from SystemBase.

Definition at line 171 of file DisplacedSystem.h.

  {
    _undisplaced_system.addVariableToZeroOnResidual(var_name);
  }

addVector() [1/2]

NumericVector< Number > & SystemBase::addVector ( const std::string &  vector_name, const bool  project, const ParallelType  type  )

virtualinherited

Adds a solution length vector to the system.

Parameters

vector_name	The name of the vector.
project	Whether or not to project this vector when doing mesh refinement. If the vector is just going to be recomputed then there is no need to project it.
type	What type of parallel vector. This is usually either PARALLEL or GHOSTED. GHOSTED is needed if you are going to be accessing off-processor entries. The ghosting pattern is the same as the solution vector.

Reimplemented in AuxiliarySystem.

Definition at line 543 of file SystemBase.C.

{
  if (hasVector(vector_name))
    return getVector(vector_name);
 
  NumericVector<Number> & vec = system().add_vector(vector_name, project, type);
  return vec;
}

Referenced by NonlinearSystemBase::addDotVectors(), NonlinearSystemBase::addExtraVectors(), AStableDirk4::AStableDirk4(), MultiApp::createApp(), ExplicitTimeIntegrator::ExplicitTimeIntegrator(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), FEProblemBase::initNullSpaceVectors(), LStableDirk3::LStableDirk3(), LStableDirk4::LStableDirk4(), PicardSolve::PicardSolve(), NonlinearSystemBase::residualGhosted(), and SystemBase::saveOldSolutions().

addVector() [2/2]

NumericVector< Number > & SystemBase::addVector ( TagID  tag, const bool  project, const ParallelType  type  )

inherited

Adds a solution length vector to the system with the specified TagID.

Parameters

tag_name	The name of the tag
project	Whether or not to project this vector when doing mesh refinement. If the vector is just going to be recomputed then there is no need to project it.
type	What type of parallel vector. This is usually either PARALLEL or GHOSTED. GHOSTED is needed if you are going to be accessing off-processor entries. The ghosting pattern is the same as the solution vector.

Definition at line 553 of file SystemBase.C.

{
  if (!_subproblem.vectorTagExists(tag))
    mooseError("Cannot add a tagged vector with vector_tag, ",
               tag,
               ", that tag does not exist in System ",
               name());
 
  if (hasVector(tag))
    return getVector(tag);
 
  auto vector_name = _subproblem.vectorTagName(tag);
 
  NumericVector<Number> & vec = system().add_vector(vector_name, project, type);
 
  if (_tagged_vectors.size() < tag + 1)
    _tagged_vectors.resize(tag + 1);
 
  _tagged_vectors[tag] = &vec;
 
  return vec;
}

applyScalingFactors()

void SystemBase::applyScalingFactors ( const std::vector< Real > &  inverse_scaling_factors )

inherited

Applies scaling factors to the system's variables.

Parameters

inverse_scaling_factors

A vector containing the inverse of each variable's scaling factor, e.g. 1 / scaling_factor

Definition at line 1141 of file SystemBase.C.

{
  for (MooseIndex(_vars) thread = 0; thread < _vars.size(); ++thread)
  {
    auto & field_variables = _vars[thread].fieldVariables();
    for (MooseIndex(field_variables) i = 0; i < field_variables.size(); ++i)
      field_variables[i]->scalingFactor(1. / inverse_scaling_factors[i] *
                                        field_variables[i]->scalingFactor());
 
    auto offset = field_variables.size();
 
    auto & scalar_variables = _vars[thread].scalars();
    for (MooseIndex(scalar_variables) i = 0; i < scalar_variables.size(); ++i)
      scalar_variables[i]->scalingFactor(1. / inverse_scaling_factors[offset + i] *
                                         scalar_variables[i]->scalingFactor());
  }
}

Referenced by NonlinearSystem::computeScaling().

assignMaxVarNDofsPerElem()

void SystemBase::assignMaxVarNDofsPerElem ( std::size_t  max_dofs )

inlineinherited

assign the maximum element dofs

Definition at line 492 of file SystemBase.h.

{ _max_var_n_dofs_per_elem = max_dofs; }

assignMaxVarNDofsPerNode()

void SystemBase::assignMaxVarNDofsPerNode ( std::size_t  max_dofs )

inlineinherited

assign the maximum node dofs

Definition at line 497 of file SystemBase.h.

{ _max_var_n_dofs_per_node = max_dofs; }

associateMatrixToTag()

virtual void DisplacedSystem::associateMatrixToTag ( SparseMatrix< Number > &  matrix, TagID  tag  )

inlineoverridevirtual

associate a matirx to a tag

Reimplemented from SystemBase.

Definition at line 67 of file DisplacedSystem.h.

  {
    _undisplaced_system.associateMatrixToTag(matrix, tag);
  }

associateVectorToTag()

virtual void DisplacedSystem::associateVectorToTag ( NumericVector< Number > &  vec, TagID  tag  )

inlineoverridevirtual

Associate a vector for a given tag.

Reimplemented from SystemBase.

Definition at line 52 of file DisplacedSystem.h.

  {
    _undisplaced_system.associateVectorToTag(vec, tag);
  }

augmentSendList()

virtual void DisplacedSystem::augmentSendList ( std::vector< dof_id_type > &  send_list )

inlineoverridevirtual

Will modify the send_list to add all of the extra ghosted dofs for this system.

Reimplemented from SystemBase.

Definition at line 152 of file DisplacedSystem.h.

  {
    _undisplaced_system.augmentSendList(send_list);
  }

augmentSparsity()

virtual void DisplacedSystem::augmentSparsity ( SparsityPattern::Graph &  , std::vector< dof_id_type > &  , std::vector< dof_id_type > &    )

inlineoverridevirtual

This is an empty function since the displaced system doesn't have a matrix! All sparsity pattern modification will be taken care of by the undisplaced system directly.

Implements SystemBase.

Definition at line 161 of file DisplacedSystem.h.

  {
  }

closeTaggedMatrices()

void SystemBase::closeTaggedMatrices ( const std::set< TagID > &  tags )

inherited

Close all matrices associated the tags.

Definition at line 874 of file SystemBase.C.

{
  for (auto tag : tags)
    if (hasMatrix(tag))
      getMatrix(tag).close();
}

Referenced by NonlinearSystemBase::computeJacobianInternal().

closeTaggedVectors()

void SystemBase::closeTaggedVectors ( const std::set< TagID > &  tags )

virtualinherited

Close all vectors for given tags.

Definition at line 577 of file SystemBase.C.

{
  for (auto & tag : tags)
  {
    mooseAssert(_subproblem.vectorTagExists(tag), "Tag: " << tag << " does not exsit");
    getVector(tag).close();
  }
}

Referenced by NonlinearSystemBase::computeResidualTags().

computeVariables()

virtual void SystemBase::computeVariables ( const NumericVector< Number > &  )

inlinevirtualinherited

Definition at line 746 of file SystemBase.h.

{}

computingScalingJacobian() [1/2]

bool SystemBase::computingScalingJacobian ( ) const

inlineinherited

Whether we are computing an initial Jacobian for automatic variable scaling.

Definition at line 121 of file SystemBase.h.

{ return _computing_scaling_jacobian; }

Referenced by Assembly::addJacobianBlock(), Assembly::addJacobianBlockNonlocal(), Assembly::addJacobianNeighbor(), Assembly::cacheJacobianBlock(), VectorKernel::computeJacobian(), and Kernel::computeJacobian().

computingScalingJacobian() [2/2]

void SystemBase::computingScalingJacobian ( bool  computing_scaling_jacobian )

inlineinherited

Setter for whether we're computing the scaling jacobian.

Definition at line 126 of file SystemBase.h.

  {
    _computing_scaling_jacobian = computing_scaling_jacobian;
  }

computingScalingResidual() [1/2]

bool SystemBase::computingScalingResidual ( ) const

inlineinherited

Whether we are computing an initial Residual for automatic variable scaling.

Definition at line 134 of file SystemBase.h.

{ return _computing_scaling_residual; }

computingScalingResidual() [2/2]

void SystemBase::computingScalingResidual ( bool  computing_scaling_residual )

inlineinherited

Setter for whether we're computing the scaling residual.

Definition at line 139 of file SystemBase.h.

  {
    _computing_scaling_residual = computing_scaling_residual;
  }

copyOldSolutions()

void SystemBase::copyOldSolutions ( )

virtualinherited

Shifts the solutions backwards in time.

Definition at line 1099 of file SystemBase.C.

{
  solutionOlder() = solutionOld();
  solutionOld() = *currentSolution();
  if (solutionUDotOld())
    *solutionUDotOld() = *solutionUDot();
  if (solutionUDotDotOld())
    *solutionUDotDotOld() = *solutionUDotDot();
  if (solutionPreviousNewton())
    *solutionPreviousNewton() = *currentSolution();
}

Referenced by EigenExecutionerBase::inversePowerIteration().

copySolutionsBackwards()

void SystemBase::copySolutionsBackwards ( )

virtualinherited

Copy current solution into old and older.

Definition at line 1082 of file SystemBase.C.

{
  system().update();
  solutionOlder() = *currentSolution();
  solutionOld() = *currentSolution();
  if (solutionUDotOld())
    *solutionUDotOld() = *solutionUDot();
  if (solutionUDotDotOld())
    *solutionUDotDotOld() = *solutionUDotDot();
  if (solutionPreviousNewton())
    *solutionPreviousNewton() = *currentSolution();
}

copyVars()

void SystemBase::copyVars ( ExodusII_IO &  io )

inherited

Definition at line 999 of file SystemBase.C.

{
  int n_steps = io.get_num_time_steps();
 
  bool did_copy = false;
  for (const auto & vci : _var_to_copy)
  {
    int timestep = -1;
 
    if (vci._timestep == "LATEST")
      // Use the last time step in the file from which to retrieve the solution
      timestep = n_steps;
    else
    {
      timestep = MooseUtils::convert<int>(vci._timestep);
      if (timestep > n_steps)
        mooseError("Invalid value passed as \"initial_from_file_timestep\". Expected \"LATEST\" or "
                   "a valid integer between 1 and ",
                   n_steps,
                   " inclusive, received ",
                   vci._timestep);
    }
 
    did_copy = true;
 
    if (hasVariable(vci._dest_name))
    {
      if (getVariable(0, vci._dest_name).isNodal())
        io.copy_nodal_solution(system(), vci._dest_name, vci._source_name, timestep);
 
      else
        io.copy_elemental_solution(system(), vci._dest_name, vci._source_name, timestep);
    }
    else if (hasScalarVariable(vci._dest_name))
    {
      auto rank = comm().rank();
      auto size = comm().size();
 
      // Read solution on rank 0 only and send data to rank "size - 1" where scalar DOFs are
      // stored
      std::vector<Real> global_values;
      if (rank == 0)
      {
        // Read the scalar value then set that value in the current solution
        io.read_global_variable({vci._source_name}, timestep, global_values);
        if (size > 1)
          comm().send(size - 1, global_values);
      }
      if (rank == size - 1)
      {
        if (size > 1)
          comm().receive(0, global_values);
        const unsigned int var_num = system().variable_number(vci._dest_name);
        system().solution->set(var_num, global_values[0]);
      }
    }
  }
 
  if (did_copy)
    solution().close();
}

currentSolution()

const NumericVector<Number>* const & DisplacedSystem::currentSolution ( ) const

inlineoverridevirtual

The solution vector that is currently being operated on.

This is typically a ghosted vector that comes in from the Nonlinear solver.

Implements SystemBase.

Definition at line 89 of file DisplacedSystem.h.

  {
    return _undisplaced_system.currentSolution();
  }

deactiveAllMatrixTags()

void SystemBase::deactiveAllMatrixTags ( )

virtualinherited

Make matrices inactive.

Definition at line 933 of file SystemBase.C.

{
  auto num_matrix_tags = _subproblem.numMatrixTags();
 
  _matrix_tag_active_flags.resize(num_matrix_tags);
 
  for (decltype(num_matrix_tags) tag = 0; tag < num_matrix_tags; tag++)
    _matrix_tag_active_flags[tag] = false;
}

Referenced by NonlinearSystemBase::computeResidualTags(), and NonlinearSystemBase::setInitialSolution().

deactiveMatrixTag()

void SystemBase::deactiveMatrixTag ( TagID  tag )

virtualinherited

deactive a matrix for tag

Definition at line 921 of file SystemBase.C.

{
  mooseAssert(_subproblem.matrixTagExists(tag),
              "Cannot deactivate Matrix with matrix_tag : " << tag << "that does not exist");
 
  if (_matrix_tag_active_flags.size() < tag + 1)
    _matrix_tag_active_flags.resize(tag + 1);
 
  _matrix_tag_active_flags[tag] = false;
}

disassociateAllTaggedMatrices()

virtual void DisplacedSystem::disassociateAllTaggedMatrices ( )

inlineoverridevirtual

Clear all tagged matrices.

Reimplemented from SystemBase.

Definition at line 77 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateAllTaggedMatrices();
  }

disassociateAllTaggedVectors()

virtual void DisplacedSystem::disassociateAllTaggedVectors ( )

inlineoverridevirtual

Disassociate all vectors, and then hasVector() will return false.

Reimplemented from SystemBase.

Definition at line 62 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateAllTaggedVectors();
  }

disassociateMatrixFromTag()

virtual void DisplacedSystem::disassociateMatrixFromTag ( SparseMatrix< Number > &  matrix, TagID  tag  )

inlineoverridevirtual

disassociate a matirx from a tag

Reimplemented from SystemBase.

Definition at line 72 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateMatrixFromTag(matrix, tag);
  }

disassociateVectorFromTag()

virtual void DisplacedSystem::disassociateVectorFromTag ( NumericVector< Number > &  vec, TagID  tag  )

inlineoverridevirtual

Associate a vector for a given tag.

Reimplemented from SystemBase.

Definition at line 57 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateVectorFromTag(vec, tag);
  }

dofMap() [1/2]

DofMap & SystemBase::dofMap ( )

virtualinherited

Gets writeable reference to the dof map.

Definition at line 979 of file SystemBase.C.

{
  return system().get_dof_map();
}

Referenced by AddPeriodicBCAction::act(), SystemBase::augmentSendList(), NonlinearSystemBase::augmentSparsity(), AddPeriodicBCAction::autoTranslationBoundaries(), NonlinearSystem::computeScaling(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), Adaptivity::init(), DisplacedProblem::init(), PNGOutput::makeMeshFunc(), GhostingUserObject::meshChanged(), TableOutput::outputScalarVariables(), Nemesis::outputScalarVariables(), and Exodus::outputScalarVariables().

dofMap() [2/2]

const DofMap & SystemBase::dofMap ( ) const

virtualinherited

Gets const reference to the dof map.

Definition at line 985 of file SystemBase.C.

{
  return system().get_dof_map();
}

duDotDotDu() [1/2]

virtual const Number& DisplacedSystem::duDotDotDu ( ) const

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 137 of file DisplacedSystem.h.

{ return _undisplaced_system.duDotDotDu(); }

duDotDotDu() [2/2]

virtual Number& DisplacedSystem::duDotDotDu ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 135 of file DisplacedSystem.h.

{ return _undisplaced_system.duDotDotDu(); }

duDotDu() [1/2]

virtual const Number& DisplacedSystem::duDotDu ( ) const

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 136 of file DisplacedSystem.h.

{ return _undisplaced_system.duDotDu(); }

duDotDu() [2/2]

virtual Number& DisplacedSystem::duDotDu ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 134 of file DisplacedSystem.h.

{ return _undisplaced_system.duDotDu(); }

getFieldVariable() [1/2]

template<typename T >

MooseVariableFE< T > & SystemBase::getFieldVariable ( THREAD_ID  tid, const std::string &  var_name  )

inherited

Gets a reference to a variable of with specified name.

Parameters

tid	Thread id
var_name	variable name

Returns

reference the variable (class)

Definition at line 129 of file SystemBase.C.

{
  return *_vars[tid].getFieldVariable<T>(var_name);
}

Referenced by Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), Assembly::copyShapes(), DisplacedProblem::getArrayVariable(), Marker::getMarkerValue(), DisplacedProblem::getStandardVariable(), and DisplacedProblem::getVectorVariable().

getFieldVariable() [2/2]

template<typename T >

MooseVariableFE< T > & SystemBase::getFieldVariable ( THREAD_ID  tid, unsigned int  var_number  )

inherited

Gets a reference to a variable with specified number.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns

reference the variable (class)

Definition at line 136 of file SystemBase.C.

{
  return *_vars[tid].getFieldVariable<T>(var_number);
}

getMatrix() [1/2]

virtual const SparseMatrix<Number>& DisplacedSystem::getMatrix ( TagID  tag ) const

inlineoverridevirtual

Get a raw SparseMatrix.

Reimplemented from SystemBase.

Definition at line 207 of file DisplacedSystem.h.

  {
    return _undisplaced_system.getMatrix(tag);
  }

getMatrix() [2/2]

virtual SparseMatrix<Number>& DisplacedSystem::getMatrix ( TagID  tag )

inlineoverridevirtual

Get a raw SparseMatrix.

Reimplemented from SystemBase.

Definition at line 203 of file DisplacedSystem.h.

  {
    return _undisplaced_system.getMatrix(tag);
  }

getMaxVariableNumber()

unsigned int SystemBase::getMaxVariableNumber ( ) const

inlineinherited

Returns the maximum number of all variables on the system.

Definition at line 744 of file SystemBase.h.

{ return _max_var_number; }

getMaxVarNDofsPerElem()

std::size_t SystemBase::getMaxVarNDofsPerElem ( ) const

inlineinherited

Gets the maximum number of dofs used by any one variable on any one element.

Returns

The max

Definition at line 480 of file SystemBase.h.

{ return _max_var_n_dofs_per_elem; }

Referenced by MooseVariableScalar::computeAD(), Assembly::computeAffineMapAD(), Assembly::computeFaceMap(), and Assembly::computeSinglePointMapAD().

getMaxVarNDofsPerNode()

std::size_t SystemBase::getMaxVarNDofsPerNode ( ) const

inlineinherited

Gets the maximum number of dofs used by any one variable on any one node.

Returns

The max

Definition at line 487 of file SystemBase.h.

{ return _max_var_n_dofs_per_node; }

Referenced by MooseVariableScalar::computeAD().

getMinQuadratureOrder()

Order SystemBase::getMinQuadratureOrder ( )

virtualinherited

Get minimal quadrature order needed for integrating variables in this system.

Returns

The minimal order of quadrature

Reimplemented in AuxiliarySystem.

Definition at line 232 of file SystemBase.C.

{
  Order order = CONSTANT;
  const std::vector<MooseVariableFEBase *> & vars = _vars[0].fieldVariables();
  for (const auto & var : vars)
  {
    FEType fe_type = var->feType();
    if (fe_type.default_quadrature_order() > order)
      order = fe_type.default_quadrature_order();
  }
 
  return order;
}

getScalarVariable() [1/2]

MooseVariableScalar & SystemBase::getScalarVariable ( THREAD_ID  tid, const std::string &  var_name  )

virtualinherited

Gets a reference to a scalar variable with specified number.

Parameters

tid	Thread id
var_name	A string which is the name of the variable to get.

Returns

reference the variable (class)

Definition at line 142 of file SystemBase.C.

{
  MooseVariableScalar * var = dynamic_cast<MooseVariableScalar *>(_vars[tid].getVariable(var_name));
  if (!var)
    mooseError("Scalar variable '" + var_name + "' does not exist in this system");
  return *var;
}

Referenced by Assembly::addJacobianOffDiagScalar(), VectorIntegratedBC::computeJacobianBlockScalar(), ArrayIntegratedBC::computeJacobianBlockScalar(), IntegratedBC::computeJacobianBlockScalar(), ODEKernel::computeOffDiagJacobian(), VectorKernel::computeOffDiagJacobianScalar(), ArrayKernel::computeOffDiagJacobianScalar(), Kernel::computeOffDiagJacobianScalar(), DisplacedProblem::getScalarVariable(), Assembly::init(), and ReferenceResidualProblem::initialSetup().

getScalarVariable() [2/2]

MooseVariableScalar & SystemBase::getScalarVariable ( THREAD_ID  tid, unsigned int  var_number  )

virtualinherited

Gets a reference to a variable with specified number.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns

reference the variable (class)

Definition at line 151 of file SystemBase.C.

{
  MooseVariableScalar * var =
      dynamic_cast<MooseVariableScalar *>(_vars[tid].getVariable(var_number));
  if (!var)
    mooseError("variable #" + Moose::stringify(var_number) + " does not exist in this system");
  return *var;
}

getScalarVariables()

const std::vector<MooseVariableScalar *>& SystemBase::getScalarVariables ( THREAD_ID  tid )

inlineinherited

Definition at line 654 of file SystemBase.h.

  {
    return _vars[tid].scalars();
  }

Referenced by Assembly::addResidualScalar(), ComputeFullJacobianThread::computeFaceJacobian(), ComputeFullJacobianThread::computeJacobian(), ODEKernel::computeJacobian(), AuxiliarySystem::computeScalarVars(), Assembly::init(), ComputeJacobianThread::onElement(), Assembly::prepareOffDiagScalar(), and Assembly::prepareScalar().

getSharedTimeIntegrator()

std::shared_ptr<TimeIntegrator> SystemBase::getSharedTimeIntegrator ( )

inlineinherited

Definition at line 766 of file SystemBase.h.

{ return _time_integrator; }

Referenced by DisplacedProblem::DisplacedProblem().

getSubdomainsForVar()

const std::set<SubdomainID>& SystemBase::getSubdomainsForVar ( unsigned int  var_number ) const

inlineinherited

Definition at line 659 of file SystemBase.h.

  {
    return _var_map.at(var_number);
  }

getTimeIntegrator() [1/2]

TimeIntegrator* SystemBase::getTimeIntegrator ( )

inlineinherited

Definition at line 763 of file SystemBase.h.

{ return _time_integrator.get(); }

Referenced by DT2::computeDT(), Transient::endStep(), AB2PredictorCorrector::estimateTimeError(), MooseVariableData< OutputType >::MooseVariableData(), and Transient::preExecute().

getTimeIntegrator() [2/2]

const TimeIntegrator* SystemBase::getTimeIntegrator ( ) const

inlineinherited

Definition at line 764 of file SystemBase.h.

{ return _time_integrator.get(); }

getVariable() [1/2]

MooseVariableFEBase & SystemBase::getVariable ( THREAD_ID  tid, const std::string &  var_name  )

inherited

Gets a reference to a variable of with specified name.

Parameters

tid	Thread id
var_name	variable name

Returns

reference the variable (class)

Definition at line 109 of file SystemBase.C.

{
  MooseVariableFEBase * var = dynamic_cast<MooseVariableFEBase *>(_vars[tid].getVariable(var_name));
  if (!var)
    mooseError("Variable '", var_name, "' does not exist in this system");
  return *var;
}

Referenced by Assembly::addJacobianBlock(), Assembly::addJacobianBlockNonlocal(), Assembly::addJacobianNeighbor(), SystemBase::addVariableToZeroOnJacobian(), SystemBase::addVariableToZeroOnResidual(), VectorIntegratedBC::computeJacobianBlock(), ArrayIntegratedBC::computeJacobianBlock(), NonlocalIntegratedBC::computeJacobianBlock(), NonlocalKernel::computeNonlocalOffDiagJacobian(), NonlocalIntegratedBC::computeNonlocalOffDiagJacobian(), ArrayDGKernel::computeOffDiagElemNeighJacobian(), Kernel::computeOffDiagJacobian(), VectorKernel::computeOffDiagJacobian(), ArrayKernel::computeOffDiagJacobian(), EigenKernel::computeOffDiagJacobian(), ArrayNodalBC::computeOffDiagJacobian(), NonlocalKernel::computeOffDiagJacobian(), KernelGrad::computeOffDiagJacobian(), KernelValue::computeOffDiagJacobian(), NodeFaceConstraint::computeOffDiagJacobian(), Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), Assembly::copyShapes(), SystemBase::copyVars(), FieldSplitPreconditioner::FieldSplitPreconditioner(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), EqualValueEmbeddedConstraint::getConnectedDofIndices(), NodeElemConstraint::getConnectedDofIndices(), NodeFaceConstraint::getConnectedDofIndices(), SystemBase::getScalarVariable(), SubProblem::getVariableHelper(), Assembly::init(), NodalNormalsPreprocessor::initialize(), ReferenceResidualProblem::initialSetup(), Assembly::initNonlocalCoupling(), PNGOutput::makeMeshFunc(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), Assembly::prepareBlock(), Assembly::prepareBlockNonlocal(), AddPeriodicBCAction::setPeriodicVars(), SingleMatrixPreconditioner::SingleMatrixPreconditioner(), and UpdateErrorVectorsThread::UpdateErrorVectorsThread().

getVariable() [2/2]

MooseVariableFEBase & SystemBase::getVariable ( THREAD_ID  tid, unsigned int  var_number  )

inherited

Gets a reference to a variable with specified number.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns

reference the variable (class)

Definition at line 118 of file SystemBase.C.

{
  if (var_number < _numbered_vars[tid].size())
    if (_numbered_vars[tid][var_number])
      return *_numbered_vars[tid][var_number];
 
  mooseError("Variable #", Moose::stringify(var_number), " does not exist in this system");
}

getVariableBlocks()

const std::set< SubdomainID > * SystemBase::getVariableBlocks ( unsigned int  var_number )

virtualinherited

Get the block where a variable of this system is defined.

Parameters

var_number

The number of the variable

Returns

the set of subdomain ids where the variable is active (defined)

Definition at line 161 of file SystemBase.C.

{
  mooseAssert(_var_map.find(var_number) != _var_map.end(), "Variable does not exist.");
  if (_var_map[var_number].empty())
    return nullptr;
  else
    return &_var_map[var_number];
}

Referenced by PhysicsBasedPreconditioner::addSystem().

getVariableNames()

const std::vector<VariableName>& SystemBase::getVariableNames ( ) const

inlineinherited

Definition at line 739 of file SystemBase.h.

{ return _vars[0].names(); }

Referenced by MooseEigenSystem::buildSystemDoFIndices(), NonlinearSystemBase::checkKernelCoverage(), SystemBase::hasVariable(), SystemBase::isArrayVariable(), and AddPeriodicBCAction::setPeriodicVars().

getVariables()

const std::vector<MooseVariableFEBase *>& SystemBase::getVariables ( THREAD_ID  tid )

inlineinherited

Definition at line 649 of file SystemBase.h.

  {
    return _vars[tid].fieldVariables();
  }

Referenced by Assembly::addJacobianOffDiagScalar(), Assembly::addResidual(), Assembly::addResidualNeighbor(), Assembly::cacheResidual(), Assembly::cacheResidualLower(), Assembly::cacheResidualNeighbor(), ComputeFullJacobianThread::computeFaceJacobian(), ComputeFullJacobianThread::computeJacobian(), Assembly::init(), Assembly::initNonlocalCoupling(), Assembly::prepareLowerD(), Assembly::prepareNeighbor(), Assembly::prepareOffDiagScalar(), Assembly::prepareResidual(), Assembly::setResidual(), and Assembly::setResidualNeighbor().

getVector() [1/3]

NumericVector< Number > & DisplacedSystem::getVector ( const std::string &  name )

overridevirtual

Get a raw NumericVector.

Get a raw NumericVector with the given name.

Reimplemented from SystemBase.

Definition at line 42 of file DisplacedSystem.C.

{
  if (_sys.have_vector(name))
    return _sys.get_vector(name);
  else
    return _undisplaced_system.getVector(name);
}

getVector() [2/3]

virtual const NumericVector<Number>& DisplacedSystem::getVector ( TagID  tag ) const

inlineoverridevirtual

Get a raw NumericVector.

Reimplemented from SystemBase.

Definition at line 39 of file DisplacedSystem.h.

  {
    return _undisplaced_system.getVector(tag_id);
  }

getVector() [3/3]

virtual NumericVector<Number>& DisplacedSystem::getVector ( TagID  tag )

inlineoverridevirtual

Get a raw NumericVector.

Reimplemented from SystemBase.

Definition at line 35 of file DisplacedSystem.h.

  {
    return _undisplaced_system.getVector(tag_id);
  }

hasMatrix()

virtual bool DisplacedSystem::hasMatrix ( TagID  tag ) const

inlineoverridevirtual

Check if the tagged matrix exists in the system.

Reimplemented from SystemBase.

Definition at line 198 of file DisplacedSystem.h.

  {
    return _undisplaced_system.hasMatrix(tag_id);
  }

hasScalarVariable()

bool SystemBase::hasScalarVariable ( const std::string &  var_name ) const

virtualinherited

Definition at line 719 of file SystemBase.C.

{
  if (system().has_variable(var_name))
    return system().variable_type(var_name).family == SCALAR;
  else
    return false;
}

Referenced by ComputeFullJacobianThread::computeFaceJacobian(), ComputeFullJacobianThread::computeJacobian(), NonlinearSystemBase::computeJacobianInternal(), SystemBase::copyVars(), DisplacedProblem::getScalarVariable(), DisplacedProblem::hasScalarVariable(), and AddPeriodicBCAction::setPeriodicVars().

hasVariable()

bool SystemBase::hasVariable ( const std::string &  var_name ) const

virtualinherited

Query a system for a variable.

Parameters

var_name

name of the variable

Returns

true if the variable exists

Definition at line 694 of file SystemBase.C.

{
  auto & names = getVariableNames();
  if (system().has_variable(var_name))
    return system().variable_type(var_name).family != SCALAR;
  if (std::find(names.begin(), names.end(), var_name) != names.end())
    // array variable
    return true;
  else
    return false;
}

Referenced by ADDGKernel< compute_stage >::ADDGKernel(), ADKernelTempl< T, compute_stage >::ADKernelTempl(), ArrayDGKernel::ArrayDGKernel(), ArrayKernel::ArrayKernel(), SystemBase::copyVars(), DGKernel::DGKernel(), FEProblemBase::duplicateVariableCheck(), DisplacedProblem::getArrayVariable(), DisplacedProblem::getStandardVariable(), DisplacedProblem::getSystem(), SubProblem::getVariableHelper(), DisplacedProblem::getVectorVariable(), DisplacedProblem::hasVariable(), InterfaceKernelTempl< T >::InterfaceKernelTempl(), Kernel::Kernel(), and PNGOutput::makeMeshFunc().

hasVector() [1/2]

bool SystemBase::hasVector ( const std::string &  tag_name ) const

inherited

Check if the named vector exists in the system.

Definition at line 748 of file SystemBase.C.

{
  return system().have_vector(name);
}

Referenced by Assembly::addCachedResidual(), Assembly::addCachedResiduals(), Assembly::addResidual(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), AuxiliarySystem::addVector(), SystemBase::addVector(), Assembly::cacheResidual(), Assembly::cacheResidualLower(), Assembly::cacheResidualNeighbor(), ArrayNodalBC::computeResidual(), VectorNodalBC::computeResidual(), NodalBC::computeResidual(), NonlinearSystemBase::computeResidualTags(), SystemBase::getVector(), hasVector(), MooseVariableScalar::reinit(), and SystemBase::removeVector().

hasVector() [2/2]

virtual bool DisplacedSystem::hasVector ( TagID  tag_id ) const

inlineoverridevirtual

Check if the tagged vector exists in the system.

Reimplemented from SystemBase.

Definition at line 193 of file DisplacedSystem.h.

  {
    return _undisplaced_system.hasVector(tag_id);
  }

init()

void DisplacedSystem::init ( )

overridevirtual

Initialize the system.

Reimplemented from SystemBase.

Definition at line 37 of file DisplacedSystem.C.

{
}

Referenced by DisplacedProblem::init().

initializeObjects()

virtual void SystemBase::initializeObjects ( )

inlinevirtualinherited

Called only once, just before the solve begins so objects can do some precalculations.

Definition at line 168 of file SystemBase.h.

{};

isArrayVariable()

bool SystemBase::isArrayVariable ( const std::string &  var_name ) const

virtualinherited

If a variable is an array variable.

Definition at line 707 of file SystemBase.C.

{
  auto & names = getVariableNames();
  if (!system().has_variable(var_name) &&
      std::find(names.begin(), names.end(), var_name) != names.end())
    // array variable
    return true;
  else
    return false;
}

isScalarVariable()

bool SystemBase::isScalarVariable ( unsigned int  var_name ) const

virtualinherited

Definition at line 728 of file SystemBase.C.

{
  return (system().variable(var_num).type().family == SCALAR);
}

Referenced by ODEKernel::computeOffDiagJacobian(), Assembly::init(), ReferenceResidualProblem::initialSetup(), and Assembly::initNonlocalCoupling().

matrixTagActive()

bool SystemBase::matrixTagActive ( TagID  tag ) const

virtualinherited

If or not a matrix tag is active.

Definition at line 958 of file SystemBase.C.

{
  mooseAssert(_subproblem.matrixTagExists(tag), "Matrix tag " << tag << " does not exist");
 
  return tag < _matrix_tag_active_flags.size() && _matrix_tag_active_flags[tag];
}

mesh() [1/2]

virtual MooseMesh& SystemBase::mesh ( )

inlinevirtualinherited

Definition at line 106 of file SystemBase.h.

{ return _mesh; }

Referenced by CreateDisplacedProblemAction::addProxyRelationshipManagers(), NonlinearSystem::computeScaling(), DMMooseGetEmbedding_Private(), DMSetUp_Moose_Pre(), MooseVariableData< OutputType >::MooseVariableData(), ComputeNodalKernelsThread::onNode(), and ComputeNodalKernelJacobiansThread::onNode().

mesh() [2/2]

virtual const MooseMesh& SystemBase::mesh ( ) const

inlinevirtualinherited

Definition at line 107 of file SystemBase.h.

{ return _mesh; }

name()

const std::string & SystemBase::name ( ) const

virtualinherited

Definition at line 1135 of file SystemBase.C.

{
  return system().name();
}

Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addConstraint(), NonlinearSystemBase::addDamper(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), NonlinearSystemBase::addInterfaceKernel(), MooseEigenSystem::addKernel(), AuxiliarySystem::addKernel(), NonlinearSystemBase::addKernel(), NonlinearSystem::addMatrix(), NonlinearSystemBase::addNodalKernel(), AuxiliarySystem::addScalarKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), AuxiliarySystem::addTimeIntegrator(), NonlinearSystemBase::addTimeIntegrator(), AuxiliarySystem::addVariable(), SystemBase::addVariable(), SystemBase::addVector(), NonlinearSystemBase::getSplit(), getVector(), SystemBase::getVector(), SystemBase::hasVector(), SystemBase::removeVector(), and NonlinearSystemBase::setInitialSolution().

nonTimeVectorTag()

virtual TagID DisplacedSystem::nonTimeVectorTag ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 50 of file DisplacedSystem.h.

{ return _undisplaced_system.nonTimeVectorTag(); }

Referenced by DisplacedProblem::addCachedResidualDirectly().

number()

unsigned int SystemBase::number ( ) const

virtualinherited

Gets the number of this system.

Returns

The number of this system

Definition at line 973 of file SystemBase.C.

{
  return system().number();
}

Referenced by ArrayNodalBC::computeOffDiagJacobian(), VectorNodalBC::computeOffDiagJacobian(), NodalBC::computeOffDiagJacobian(), NodalKernel::computeOffDiagJacobian(), EqualValueEmbeddedConstraint::computeQpJacobian(), EqualValueEmbeddedConstraint::computeQpOffDiagJacobian(), DebugResidualAux::computeValue(), NearestNodeValueAux::computeValue(), BoundsAux::computeValue(), NodalNormalsEvaluator::execute(), NodalNormalsCorner::execute(), NodalNormalsPreprocessor::execute(), NonlinearSystemBase::getNodeDofs(), EqualValueEmbeddedConstraint::reinitConstraint(), and MultiAppFieldTransfer::transferDofObject().

nVariables()

unsigned int SystemBase::nVariables ( ) const

virtualinherited

Get the number of variables in this system.

Returns

the number of variables

Definition at line 734 of file SystemBase.C.

{
  unsigned int n = 0;
  for (auto & var : _vars[0].fieldVariables())
    n += var->count();
  n += _vars[0].scalars().size();
 
  return n;
}

Referenced by FieldSplitPreconditioner::FieldSplitPreconditioner(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), NonlinearSystemBase::getNodeDofs(), Assembly::init(), MaxVarNDofsPerElem::onElement(), MaxVarNDofsPerNode::onNode(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), and SingleMatrixPreconditioner::SingleMatrixPreconditioner().

prepare()

void SystemBase::prepare ( THREAD_ID  tid )

virtualinherited

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 247 of file SystemBase.C.

{
  if (_subproblem.hasActiveElementalMooseVariables(tid))
  {
    const std::set<MooseVariableFEBase *> & active_elemental_moose_variables =
        _subproblem.getActiveElementalMooseVariables(tid);
    const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
    for (const auto & var : vars)
      var->clearDofIndices();
 
    for (const auto & var : active_elemental_moose_variables)
      if (&(var->sys()) == this)
        var->prepare();
  }
  else
  {
    const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
    for (const auto & var : vars)
      var->prepare();
  }
}

Referenced by DisplacedProblem::prepare(), DisplacedProblem::reinitDirac(), SubProblem::reinitElemFaceRef(), and DisplacedProblem::reinitElemPhys().

prepareFace()

void SystemBase::prepareFace ( THREAD_ID  tid, bool  resize_data  )

virtualinherited

Prepare the system for use on sides.

This will try to reuse the preparation done on the element.

Parameters

tid	ID of the thread
resize_data	Pass True if this system needs to resize residual and jacobian datastructures based on preparing this face

Definition at line 270 of file SystemBase.C.

{
  // We only need to do something if the element prepare was restricted
  if (_subproblem.hasActiveElementalMooseVariables(tid))
  {
    const std::set<MooseVariableFEBase *> & active_elemental_moose_variables =
        _subproblem.getActiveElementalMooseVariables(tid);
 
    std::vector<MooseVariableFEBase *> newly_prepared_vars;
 
    const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
    for (const auto & var : vars)
    {
      // If it wasn't in the active list, we need to prepare it
      if (&(var->sys()) == this && !active_elemental_moose_variables.count(var))
      {
        var->prepare();
        newly_prepared_vars.push_back(var);
      }
    }
 
    // Make sure to resize the residual and jacobian datastructures for all the new variables
    if (resize_data)
      for (const auto var_ptr : newly_prepared_vars)
      {
        _subproblem.assembly(tid).prepareVariable(var_ptr);
        if (_subproblem.checkNonlocalCouplingRequirement())
          _subproblem.assembly(tid).prepareVariableNonlocal(var_ptr);
      }
  }
}

Referenced by DisplacedProblem::prepareFace().

prepareLowerD()

void SystemBase::prepareLowerD ( THREAD_ID  tid )

virtualinherited

Prepare the system for use for lower dimensional elements.

Parameters

tid	ID of the thread

Definition at line 311 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
    var->prepareLowerD();
}

Referenced by SubProblem::reinitLowerDElemRef().

prepareNeighbor()

void SystemBase::prepareNeighbor ( THREAD_ID  tid )

virtualinherited

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 303 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
    var->prepareNeighbor();
}

Referenced by DisplacedProblem::reinitNeighbor(), SubProblem::reinitNeighborFaceRef(), and DisplacedProblem::reinitNeighborPhys().

reinitElem()

void SystemBase::reinitElem ( const Elem *  elem, THREAD_ID  tid  )

virtualinherited

Reinit an element assembly info.

Parameters

elem	Which element we are reinitializing for
tid	ID of the thread

Reimplemented in AuxiliarySystem.

Definition at line 319 of file SystemBase.C.

{
 
  if (_subproblem.hasActiveElementalMooseVariables(tid))
  {
    const std::set<MooseVariableFEBase *> & active_elemental_moose_variables =
        _subproblem.getActiveElementalMooseVariables(tid);
    for (const auto & var : active_elemental_moose_variables)
      if (&(var->sys()) == this)
        var->computeElemValues();
  }
  else
  {
    const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
    for (const auto & var : vars)
      var->computeElemValues();
  }
}

Referenced by DisplacedProblem::reinitElem().

reinitElemFace()

void SystemBase::reinitElemFace ( const Elem *  elem, unsigned int  side, BoundaryID  bnd_id, THREAD_ID  tid  )

virtualinherited

Reinit assembly info for a side of an element.

Parameters

elem	The element
side	Side of of the element
bnd_id	Boundary id on that side
tid	Thread ID

Reimplemented in AuxiliarySystem.

Definition at line 339 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
    var->computeElemValuesFace();
}

Referenced by DisplacedProblem::reinitElemFace(), SubProblem::reinitElemFaceRef(), and DisplacedProblem::reinitNeighbor().

reinitLowerD()

void SystemBase::reinitLowerD ( THREAD_ID  tid )

virtualinherited

Compute the values of the variables on the lower dimensional element.

Definition at line 369 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
    var->computeLowerDValues();
}

Referenced by SubProblem::reinitLowerDElemRef().

reinitNeighbor()

void SystemBase::reinitNeighbor ( const Elem *  elem, THREAD_ID  tid  )

virtualinherited

Compute the values of the variables at all the current points.

Definition at line 361 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
    var->computeNeighborValues();
}

Referenced by DisplacedProblem::reinitNeighborPhys().

reinitNeighborFace()

void SystemBase::reinitNeighborFace ( const Elem *  elem, unsigned int  side, BoundaryID  bnd_id, THREAD_ID  tid  )

virtualinherited

Compute the values of the variables at all the current points.

Definition at line 350 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
    var->computeNeighborValuesFace();
}

Referenced by DisplacedProblem::reinitNeighbor(), SubProblem::reinitNeighborFaceRef(), and DisplacedProblem::reinitNeighborPhys().

reinitNode()

void SystemBase::reinitNode ( const Node *  node, THREAD_ID  tid  )

virtualinherited

Reinit nodal assembly info.

Parameters

node	Node to reinit for
tid	Thread ID

Definition at line 377 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
  {
    var->reinitNode();
    if (var->isNodalDefined())
      var->computeNodalValues();
  }
}

Referenced by DisplacedProblem::reinitNode().

reinitNodeFace()

void SystemBase::reinitNodeFace ( const Node *  node, BoundaryID  bnd_id, THREAD_ID  tid  )

virtualinherited

Reinit nodal assembly info on a face.

Parameters

node	Node to reinit
bnd_id	Boundary ID
tid	Thread ID

Definition at line 389 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
  {
    var->reinitNode();
    if (var->isNodalDefined())
      var->computeNodalValues();
  }
}

Referenced by DisplacedProblem::reinitNodeFace().

reinitNodes()

void SystemBase::reinitNodes ( const std::vector< dof_id_type > &  nodes, THREAD_ID  tid  )

virtualinherited

Reinit variables at a set of nodes.

Parameters

nodes	List of node ids to reinit
tid	Thread ID

Definition at line 401 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
  {
    var->reinitNodes(nodes);
    var->computeNodalValues();
  }
}

Referenced by DisplacedProblem::reinitNodes().

reinitNodesNeighbor()

void SystemBase::reinitNodesNeighbor ( const std::vector< dof_id_type > &  nodes, THREAD_ID  tid  )

virtualinherited

Reinit variables at a set of neighbor nodes.

Parameters

nodes	List of node ids to reinit
tid	Thread ID

Definition at line 412 of file SystemBase.C.

{
  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
  for (const auto & var : vars)
  {
    var->reinitNodesNeighbor(nodes);
    var->computeNodalNeighborValues();
  }
}

Referenced by DisplacedProblem::reinitNodesNeighbor().

reinitScalars()

void SystemBase::reinitScalars ( THREAD_ID  tid, bool  reinit_for_derivative_reordering = false  )

virtualinherited

Reinit scalar varaibles.

Parameters

tid	Thread ID
reinit_for_derivative_reordering	A flag indicating whether we are reinitializing for the purpose of re-ordering derivative information for ADNodalBCs

Definition at line 423 of file SystemBase.C.

{
  const std::vector<MooseVariableScalar *> & vars = _vars[tid].scalars();
  for (const auto & var : vars)
    var->reinit(reinit_for_derivative_reordering);
}

Referenced by DisplacedProblem::reinitScalars().

removeMatrix()

virtual void SystemBase::removeMatrix ( TagID  )

inlinevirtualinherited

Removes a jacobian sized vector.

Parameters

tag_name

The name of the tag

Definition at line 732 of file SystemBase.h.

  {
    mooseError("Removing a matrix is not supported for this type of system!");
  }

removeVector() [1/2]

void SystemBase::removeVector ( const std::string &  name )

virtualinherited

Remove a vector from the system with the given name.

Definition at line 1129 of file SystemBase.C.

{
  system().remove_vector(name);
}

Referenced by SystemBase::restoreOldSolutions().

removeVector() [2/2]

void SystemBase::removeVector ( TagID  tag_id )

virtualinherited

Remove a solution length vector from the system with the specified TagID.

Parameters

tag_id

Tag ID

Definition at line 597 of file SystemBase.C.

{
  if (!_subproblem.vectorTagExists(tag_id))
    mooseError("Cannot remove an unexisting tag or its associated vector, ",
               tag_id,
               ", that tag does not exist in System ",
               name());
 
  if (hasVector(tag_id))
  {
    auto vector_name = _subproblem.vectorTagName(tag_id);
    system().remove_vector(vector_name);
    _tagged_vectors[tag_id] = nullptr;
  }
}

residualCopy()

virtual NumericVector<Number>& DisplacedSystem::residualCopy ( )

inlineoverridevirtual

Return the residual copy from the NonlinearSystem.

Returns

Residual copy

Reimplemented from SystemBase.

Definition at line 143 of file DisplacedSystem.h.

  {
    return _undisplaced_system.residualCopy();
  }

residualGhosted()

virtual NumericVector<Number>& DisplacedSystem::residualGhosted ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 147 of file DisplacedSystem.h.

  {
    return _undisplaced_system.residualGhosted();
  }

residualVectorTag()

virtual TagID DisplacedSystem::residualVectorTag ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 44 of file DisplacedSystem.h.

{ return _undisplaced_system.residualVectorTag(); }

restoreOldSolutions()

void SystemBase::restoreOldSolutions ( )

virtualinherited

Restore the old and older solutions when the saved solutions present.

Definition at line 514 of file SystemBase.C.

{
  if (_saved_old)
  {
    solutionOld() = *_saved_old;
    removeVector("save_solution_old");
    _saved_old = nullptr;
  }
  if (_saved_older)
  {
    solutionOlder() = *_saved_older;
    removeVector("save_solution_older");
    _saved_older = nullptr;
  }
  if (_saved_dot_old && solutionUDotOld())
  {
    *solutionUDotOld() = *_saved_dot_old;
    removeVector("save_solution_dot_old");
    _saved_dot_old = NULL;
  }
  if (_saved_dotdot_old && solutionUDotDotOld())
  {
    *solutionUDotDotOld() = *_saved_dotdot_old;
    removeVector("save_solution_dotdot_old");
    _saved_dotdot_old = NULL;
  }
}

Referenced by DisplacedProblem::restoreOldSolutions().

restoreSolutions()

void SystemBase::restoreSolutions ( )

virtualinherited

Restore current solutions (call after your solve failed)

Reimplemented in NonlinearSystemBase.

Definition at line 1115 of file SystemBase.C.

{
  *(const_cast<NumericVector<Number> *&>(currentSolution())) = solutionOld();
  solution() = solutionOld();
  if (solutionUDotOld())
    *solutionUDot() = *solutionUDotOld();
  if (solutionUDotDotOld())
    *solutionUDotDot() = *solutionUDotDotOld();
  if (solutionPreviousNewton())
    *solutionPreviousNewton() = solutionOld();
  system().update();
}

Referenced by NonlinearSystemBase::restoreSolutions().

saveOldSolutions()

void SystemBase::saveOldSolutions ( )

virtualinherited

Save the old and older solutions.

Definition at line 489 of file SystemBase.C.

{
  if (!_saved_old)
    _saved_old = &addVector("save_solution_old", false, PARALLEL);
  if (!_saved_older)
    _saved_older = &addVector("save_solution_older", false, PARALLEL);
  if (!_saved_dot_old && solutionUDotOld())
    _saved_dot_old = &addVector("save_solution_dot_old", false, PARALLEL);
  if (!_saved_dotdot_old && solutionUDotDotOld())
    _saved_dotdot_old = &addVector("save_solution_dotdot_old", false, PARALLEL);
 
  *_saved_old = solutionOld();
  *_saved_older = solutionOlder();
 
  if (solutionUDotOld())
    *_saved_dot_old = *solutionUDotOld();
 
  if (solutionUDotDotOld())
    *_saved_dotdot_old = *solutionUDotDotOld();
}

Referenced by DisplacedProblem::saveOldSolutions().

serializedSolution()

virtual NumericVector<Number>& DisplacedSystem::serializedSolution ( )

inlineoverridevirtual

Returns a reference to a serialized version of the solution vector for this subproblem.

Implements SystemBase.

Definition at line 84 of file DisplacedSystem.h.

  {
    return _undisplaced_system.serializedSolution();
  }

solution() [1/2]

const NumericVector<Number>& DisplacedSystem::solution ( ) const

inlineoverridevirtual

Implements SystemBase.

Definition at line 99 of file DisplacedSystem.h.

{ return _undisplaced_system.solution(); }

solution() [2/2]

NumericVector<Number>& DisplacedSystem::solution ( )

inlineoverridevirtual

Implements SystemBase.

Definition at line 94 of file DisplacedSystem.h.

{ return _undisplaced_system.solution(); }

solutionOld() [1/2]

const NumericVector< Number > & DisplacedSystem::solutionOld ( ) const

overridevirtual

Implements SystemBase.

Definition at line 69 of file DisplacedSystem.C.

{
  return *_sys.old_local_solution;
}

solutionOld() [2/2]

NumericVector< Number > & DisplacedSystem::solutionOld ( )

overridevirtual

Implements SystemBase.

Definition at line 57 of file DisplacedSystem.C.

{
  return *_sys.old_local_solution;
}

solutionOlder() [1/2]

const NumericVector< Number > & DisplacedSystem::solutionOlder ( ) const

overridevirtual

Implements SystemBase.

Definition at line 75 of file DisplacedSystem.C.

{
  return *_sys.older_local_solution;
}

solutionOlder() [2/2]

NumericVector< Number > & DisplacedSystem::solutionOlder ( )

overridevirtual

Implements SystemBase.

Definition at line 63 of file DisplacedSystem.C.

{
  return *_sys.older_local_solution;
}

solutionPreviousNewton() [1/2]

const NumericVector<Number>* DisplacedSystem::solutionPreviousNewton ( ) const

inlineoverridevirtual

Implements SystemBase.

Definition at line 102 of file DisplacedSystem.h.

{ return NULL; }

solutionPreviousNewton() [2/2]

NumericVector<Number>* DisplacedSystem::solutionPreviousNewton ( )

inlineoverridevirtual

Implements SystemBase.

Definition at line 97 of file DisplacedSystem.h.

{ return NULL; }

solutionUDot() [1/2]

const NumericVector<Number>* DisplacedSystem::solutionUDot ( ) const

inlineoverridevirtual

Implements SystemBase.

Definition at line 117 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDot();
  }

solutionUDot() [2/2]

NumericVector<Number>* DisplacedSystem::solutionUDot ( )

inlineoverridevirtual

Implements SystemBase.

Definition at line 104 of file DisplacedSystem.h.

{ return _undisplaced_system.solutionUDot(); }

solutionUDotDot() [1/2]

const NumericVector<Number>* DisplacedSystem::solutionUDotDot ( ) const

inlineoverridevirtual

Implements SystemBase.

Definition at line 121 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotDot();
  }

solutionUDotDot() [2/2]

NumericVector<Number>* DisplacedSystem::solutionUDotDot ( )

inlineoverridevirtual

Implements SystemBase.

Definition at line 105 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotDot();
  }

solutionUDotDotOld() [1/2]

const NumericVector<Number>* DisplacedSystem::solutionUDotDotOld ( ) const

inlineoverridevirtual

Implements SystemBase.

Definition at line 129 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotDotOld();
  }

solutionUDotDotOld() [2/2]

NumericVector<Number>* DisplacedSystem::solutionUDotDotOld ( )

inlineoverridevirtual

Implements SystemBase.

Definition at line 113 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotDotOld();
  }

solutionUDotOld() [1/2]

const NumericVector<Number>* DisplacedSystem::solutionUDotOld ( ) const

inlineoverridevirtual

Implements SystemBase.

Definition at line 125 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotOld();
  }

solutionUDotOld() [2/2]

NumericVector<Number>* DisplacedSystem::solutionUDotOld ( )

inlineoverridevirtual

Implements SystemBase.

Definition at line 109 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotOld();
  }

solve()

void SystemBase::solve ( )

virtualinherited

Solve the system (using libMesh magic)

Reimplemented in NonlinearSystemBase, NonlinearSystem, NonlinearEigenSystem, and DumpObjectsNonlinearSystem.

Definition at line 1073 of file SystemBase.C.

{
  system().solve();
}

subproblem() [1/2]

virtual SubProblem& SystemBase::subproblem ( )

inlinevirtualinherited

Definition at line 108 of file SystemBase.h.

{ return _subproblem; }

Referenced by CreateDisplacedProblemAction::addProxyRelationshipManagers(), MooseVariableBase::allDofIndices(), MultiAppVariableValueSamplePostprocessorTransfer::execute(), MultiAppVariableValueSampleTransfer::execute(), MooseVariableData< OutputType >::MooseVariableData(), MooseVariableScalar::MooseVariableScalar(), and MooseVariableScalar::reinit().

subproblem() [2/2]

virtual const SubProblem& SystemBase::subproblem ( ) const

inlinevirtualinherited

Definition at line 109 of file SystemBase.h.

{ return _subproblem; }

sys()

virtual TransientExplicitSystem& DisplacedSystem::sys ( )

inlinevirtual

Definition at line 212 of file DisplacedSystem.h.

{ return _sys; }

Referenced by UpdateDisplacedMeshThread::init(), DisplacedProblem::syncSolutions(), and DisplacedProblem::updateMesh().

system() [1/2]

const System & DisplacedSystem::system ( ) const

overridevirtual

Implements SystemBase.

Definition at line 87 of file DisplacedSystem.C.

{
  return _sys;
}

system() [2/2]

System & DisplacedSystem::system ( )

overridevirtual

Get the reference to the libMesh system.

Implements SystemBase.

Definition at line 81 of file DisplacedSystem.C.

{
  return _sys;
}

Referenced by DisplacedProblem::getSystem().

systemMatrixTag()

virtual TagID DisplacedSystem::systemMatrixTag ( )

inlineoverridevirtual

Return the Matrix Tag ID for System.

Reimplemented from SystemBase.

Definition at line 46 of file DisplacedSystem.h.

{ return _undisplaced_system.systemMatrixTag(); }

timeMatrixTag()

TagID SystemBase::timeMatrixTag ( )

virtualinherited

Return the Matrix Tag ID for Time.

Definition at line 761 of file SystemBase.C.

{
  mooseError("Not implemented yet");
  return 0;
}

timeVectorTag()

virtual TagID DisplacedSystem::timeVectorTag ( )

inlineoverridevirtual

Ideally, we should not need this API.

There exists a really bad API "addCachedResidualDirectly " in FEProblem and DisplacedProblem This API should go away once addCachedResidualDirectly is removed in the future Return Tag ID for Time

Reimplemented from SystemBase.

Definition at line 48 of file DisplacedSystem.h.

{ return _undisplaced_system.timeVectorTag(); }

Referenced by DisplacedProblem::addCachedResidualDirectly().

update()

void SystemBase::update ( )

virtualinherited

Update the system (doing libMesh magic)

Definition at line 1067 of file SystemBase.C.

{
  system().update();
}

Referenced by MooseEigenSystem::combineSystemSolution(), NonlinearSystemBase::computeDamping(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeResidualTags(), dataLoad(), MooseEigenSystem::initSystemSolution(), MooseEigenSystem::initSystemSolutionOld(), RestartableDataIO::restartEquationSystemsObject(), MooseEigenSystem::scaleSystemSolution(), NonlinearSystemBase::setConstraintSlaveValues(), NonlinearSystemBase::setInitialSolution(), PicardSolve::solve(), PicardSolve::solveStep(), DisplacedProblem::syncSolutions(), and MultiAppFieldTransfer::transfer().

zeroTaggedVectors()

void SystemBase::zeroTaggedVectors ( const std::set< TagID > &  tags )

virtualinherited

Zero all vectors for given tags.

Definition at line 587 of file SystemBase.C.

{
  for (auto & tag : tags)
  {
    mooseAssert(_subproblem.vectorTagExists(tag), "Tag: " << tag << " does not exsit");
    getVector(tag).zero();
  }
}

Referenced by NonlinearSystemBase::computeResidualTags().

zeroVariables()

virtual void DisplacedSystem::zeroVariables ( std::vector< std::string > &  vars_to_be_zeroed )

inlineoverridevirtual

Zero out the solution for the list of variables passed in.

Reimplemented from SystemBase.

Definition at line 188 of file DisplacedSystem.h.

  {
    _undisplaced_system.zeroVariables(vars_to_be_zeroed);
  }

zeroVariablesForJacobian()

void SystemBase::zeroVariablesForJacobian ( )

virtualinherited

Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on Jacobian evaluation by a call to addVariableToZeroOnResidual()

Definition at line 226 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_jacobian);
}

zeroVariablesForResidual()

void SystemBase::zeroVariablesForResidual ( )

virtualinherited

Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on residual evaluation by a call to addVariableToZeroOnResidual()

Definition at line 220 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_residual);
}

Member Data Documentation

_app

MooseApp& SystemBase::_app

protectedinherited

Definition at line 771 of file SystemBase.h.

Referenced by NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianTags(), and NonlinearSystemBase::computeResidualTags().

_computing_scaling_jacobian

bool SystemBase::_computing_scaling_jacobian

protectedinherited

Flag used to indicate whether we are computing the scaling Jacobian.

Definition at line 827 of file SystemBase.h.

Referenced by NonlinearSystemBase::computeJacobianInternal(), NonlinearSystem::computeScaling(), NonlinearSystemBase::computeTimeDerivatives(), and SystemBase::computingScalingJacobian().

_computing_scaling_residual

bool SystemBase::_computing_scaling_residual

protectedinherited

Flag used to indicate whether we are computing the scaling Residual.

Definition at line 830 of file SystemBase.h.

Referenced by NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTags(), NonlinearSystem::computeScaling(), and SystemBase::computingScalingResidual().

_du_dot_du

Real SystemBase::_du_dot_du

protectedinherited

Definition at line 788 of file SystemBase.h.

Referenced by SystemBase::duDotDu().

_du_dotdot_du

Real SystemBase::_du_dotdot_du

protectedinherited

Definition at line 789 of file SystemBase.h.

Referenced by SystemBase::duDotDotDu().

_factory

Factory& SystemBase::_factory

protectedinherited

Definition at line 772 of file SystemBase.h.

Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addConstraint(), NonlinearSystemBase::addDamper(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), NonlinearSystemBase::addInterfaceKernel(), MooseEigenSystem::addKernel(), AuxiliarySystem::addKernel(), NonlinearSystemBase::addKernel(), NonlinearSystemBase::addNodalKernel(), AuxiliarySystem::addScalarKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), AuxiliarySystem::addTimeIntegrator(), NonlinearSystemBase::addTimeIntegrator(), and SystemBase::addVariable().

_matrix_tag_active_flags

std::vector<bool> SystemBase::_matrix_tag_active_flags

protectedinherited

Active flags for tagged matrices.

Definition at line 796 of file SystemBase.h.

Referenced by SystemBase::activeAllMatrixTags(), SystemBase::activeMatrixTag(), SystemBase::deactiveAllMatrixTags(), SystemBase::deactiveMatrixTag(), and SystemBase::matrixTagActive().

_max_var_n_dofs_per_elem

size_t SystemBase::_max_var_n_dofs_per_elem

protectedinherited

Maximum number of dofs for any one variable on any one element.

Definition at line 812 of file SystemBase.h.

Referenced by SystemBase::assignMaxVarNDofsPerElem(), and SystemBase::getMaxVarNDofsPerElem().

_max_var_n_dofs_per_node

size_t SystemBase::_max_var_n_dofs_per_node

protectedinherited

Maximum number of dofs for any one variable on any one node.

Definition at line 815 of file SystemBase.h.

Referenced by SystemBase::assignMaxVarNDofsPerNode(), and SystemBase::getMaxVarNDofsPerNode().

_max_var_number

unsigned int SystemBase::_max_var_number

protectedinherited

Maximum variable number.

Definition at line 783 of file SystemBase.h.

Referenced by SystemBase::addVariable(), and SystemBase::getMaxVariableNumber().

_mesh

MooseMesh& SystemBase::_mesh

protectedinherited

Definition at line 774 of file SystemBase.h.

Referenced by SystemBase::addVariable(), SystemBase::augmentSendList(), NonlinearSystemBase::computeDamping(), AuxiliarySystem::computeElementalVarsHelper(), NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeNodalBCs(), AuxiliarySystem::computeNodalVarsHelper(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::constraintJacobians(), NonlinearSystemBase::constraintResiduals(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), NonlinearSystemBase::getNodeDofs(), SystemBase::mesh(), NonlinearSystemBase::setConstraintSlaveValues(), NonlinearSystemBase::setInitialSolution(), NonlinearSystemBase::setVariableGlobalDoFs(), and SystemBase::zeroVariables().

_name

std::string SystemBase::_name

protectedinherited

The name of this system.

Definition at line 776 of file SystemBase.h.

_numbered_vars

std::vector<std::vector<MooseVariableFEBase *> > SystemBase::_numbered_vars

protectedinherited

Map variable number to its pointer.

Definition at line 821 of file SystemBase.h.

Referenced by SystemBase::addVariable(), and SystemBase::getVariable().

_saved_dot_old

NumericVector<Real>* SystemBase::_saved_dot_old

protectedinherited

Definition at line 803 of file SystemBase.h.

Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().

_saved_dotdot_old

NumericVector<Real>* SystemBase::_saved_dotdot_old

protectedinherited

Definition at line 804 of file SystemBase.h.

Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().

_saved_old

NumericVector<Real>* SystemBase::_saved_old

protectedinherited

Definition at line 799 of file SystemBase.h.

Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().

_saved_older

NumericVector<Real>* SystemBase::_saved_older

protectedinherited

Definition at line 800 of file SystemBase.h.

Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().

_subproblem

SubProblem& SystemBase::_subproblem

protectedinherited

Definition at line 769 of file SystemBase.h.

Referenced by SystemBase::activeAllMatrixTags(), SystemBase::activeMatrixTag(), NonlinearSystem::addMatrix(), SystemBase::addVariableToZeroOnJacobian(), SystemBase::addVariableToZeroOnResidual(), SystemBase::addVector(), SystemBase::associateMatrixToTag(), SystemBase::associateVectorToTag(), SystemBase::augmentSendList(), SystemBase::closeTaggedVectors(), SystemBase::deactiveAllMatrixTags(), SystemBase::deactiveMatrixTag(), SystemBase::disassociateMatrixFromTag(), SystemBase::disassociateVectorFromTag(), SystemBase::matrixTagActive(), SystemBase::prepare(), SystemBase::prepareFace(), SystemBase::reinitElem(), SystemBase::removeVector(), SystemBase::subproblem(), and SystemBase::zeroTaggedVectors().

_sys

TransientExplicitSystem& DisplacedSystem::_sys

protected

Definition at line 222 of file DisplacedSystem.h.

Referenced by DisplacedSystem(), getVector(), solutionOld(), solutionOlder(), sys(), and system().

_tagged_matrices

std::vector<SparseMatrix<Number> *> SystemBase::_tagged_matrices

protectedinherited

Tagged matrices (pointer)

Definition at line 794 of file SystemBase.h.

Referenced by NonlinearSystem::addMatrix(), SystemBase::associateMatrixToTag(), SystemBase::disassociateAllTaggedMatrices(), SystemBase::disassociateMatrixFromTag(), SystemBase::getMatrix(), and SystemBase::hasMatrix().

_tagged_vectors

std::vector<NumericVector<Number> *> SystemBase::_tagged_vectors

protectedinherited

Tagged vectors (pointer)

Definition at line 792 of file SystemBase.h.

Referenced by SystemBase::addVector(), SystemBase::associateVectorToTag(), SystemBase::disassociateAllTaggedVectors(), SystemBase::disassociateVectorFromTag(), SystemBase::getVector(), SystemBase::hasVector(), and SystemBase::removeVector().

_time_integrator

std::shared_ptr<TimeIntegrator> SystemBase::_time_integrator

protectedinherited

Time integrator.

Definition at line 818 of file SystemBase.h.

Referenced by NonlinearSystemBase::addTimeIntegrator(), addTimeIntegrator(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::computeTimeDerivatives(), SystemBase::getSharedTimeIntegrator(), SystemBase::getTimeIntegrator(), NonlinearSystemBase::onTimestepBegin(), NonlinearEigenSystem::solve(), and NonlinearSystem::solve().

_undisplaced_system

SystemBase& DisplacedSystem::_undisplaced_system

protected

Definition at line 221 of file DisplacedSystem.h.

Referenced by addVariableToZeroOnJacobian(), addVariableToZeroOnResidual(), associateMatrixToTag(), associateVectorToTag(), augmentSendList(), currentSolution(), disassociateAllTaggedMatrices(), disassociateAllTaggedVectors(), disassociateMatrixFromTag(), disassociateVectorFromTag(), duDotDotDu(), duDotDu(), getMatrix(), getVector(), hasMatrix(), hasVector(), nonTimeVectorTag(), residualCopy(), residualGhosted(), residualVectorTag(), serializedSolution(), solution(), solutionUDot(), solutionUDotDot(), solutionUDotDotOld(), solutionUDotOld(), systemMatrixTag(), timeVectorTag(), and zeroVariables().

_var_kind

Moose::VarKindType SystemBase::_var_kind

protectedinherited

default kind of variables in this system

Definition at line 807 of file SystemBase.h.

_var_map

std::map<unsigned int, std::set<SubdomainID> > SystemBase::_var_map

protectedinherited

Map of variables (variable id -> array of subdomains where it lives)

Definition at line 781 of file SystemBase.h.

Referenced by SystemBase::addVariable(), SystemBase::getSubdomainsForVar(), and SystemBase::getVariableBlocks().

_var_to_copy

std::vector<VarCopyInfo> SystemBase::_var_to_copy

protectedinherited

Definition at line 809 of file SystemBase.h.

Referenced by SystemBase::addVariableToCopy(), and SystemBase::copyVars().

_variable_warehouse

MooseObjectWarehouseBase<MooseVariableBase> SystemBase::_variable_warehouse

protectedinherited

Storage for MooseVariable objects.

Definition at line 824 of file SystemBase.h.

_vars

std::vector<VariableWarehouse> SystemBase::_vars

protectedinherited

Variable warehouses (one for each thread)

Definition at line 779 of file SystemBase.h.

Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addInterfaceKernel(), AuxiliarySystem::addVariable(), SystemBase::addVariable(), SystemBase::applyScalingFactors(), AuxiliarySystem::compute(), NonlinearSystem::computeScaling(), SystemBase::getFieldVariable(), AuxiliarySystem::getMinQuadratureOrder(), SystemBase::getMinQuadratureOrder(), SystemBase::getScalarVariable(), SystemBase::getScalarVariables(), SystemBase::getVariable(), SystemBase::getVariableNames(), SystemBase::getVariables(), SystemBase::nVariables(), SystemBase::prepare(), SystemBase::prepareFace(), SystemBase::prepareLowerD(), SystemBase::prepareNeighbor(), SystemBase::reinitElem(), SystemBase::reinitElemFace(), SystemBase::reinitLowerD(), SystemBase::reinitNeighbor(), SystemBase::reinitNeighborFace(), SystemBase::reinitNode(), SystemBase::reinitNodeFace(), SystemBase::reinitNodes(), SystemBase::reinitNodesNeighbor(), and SystemBase::reinitScalars().

_vars_to_be_zeroed_on_jacobian

std::vector<std::string> SystemBase::_vars_to_be_zeroed_on_jacobian

protectedinherited

Definition at line 786 of file SystemBase.h.

Referenced by SystemBase::addVariableToZeroOnJacobian(), and SystemBase::zeroVariablesForJacobian().

_vars_to_be_zeroed_on_residual

std::vector<std::string> SystemBase::_vars_to_be_zeroed_on_residual

protectedinherited

Definition at line 785 of file SystemBase.h.

Referenced by SystemBase::addVariableToZeroOnResidual(), and SystemBase::zeroVariablesForResidual().

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The documentation for this class was generated from the following files:

• include/systems/DisplacedSystem.h
• src/systems/DisplacedSystem.C