DisplacedSystem Class Reference

#include <DisplacedSystem.h>

Inheritance diagram for DisplacedSystem:

Public Member Functions
	DisplacedSystem (DisplacedSystem &&)=delete
DisplacedSystem &	operator= (DisplacedSystem &&)=delete
	DisplacedSystem (DisplacedProblem &problem, FEProblemBase &fe_problem, SystemBase &undisplaced_system, const std::string &name, Moose::VarKindType var_kind)
virtual	~DisplacedSystem ()
virtual NumericVector< Number > &	getVector (TagID tag_id) override
	Get a raw NumericVector by tag. More...
virtual const NumericVector< Number > &	getVector (TagID tag_id) const override
virtual TagID	residualVectorTag () const override
virtual TagID	systemMatrixTag () const override
	Return the Matrix Tag ID for System. More...
virtual TagID	timeVectorTag () const override
	Ideally, we should not need this API. More...
virtual TagID	nonTimeVectorTag () const override
virtual std::set< TagID >	defaultVectorTags () const override
	Get the default vector tags associated with this system. More...
virtual std::set< TagID >	defaultMatrixTags () const override
	Get the default matrix tags associted with this system. More...
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
	Disassociate a given vector from a given tag. More...
virtual void	disassociateVectorFromTag (TagID tag) override
	Disassociate any vector that is associated with a given tag. More...
virtual void	disassociateDefaultVectorTags () override
	Disassociate the vectors associated with the default vector tags of this system. More...
virtual void	associateMatrixToTag (SparseMatrix< Number > &matrix, TagID tag) override
	Associate a matrix to a tag. More...
virtual void	disassociateMatrixFromTag (SparseMatrix< Number > &matrix, TagID tag) override
	Disassociate a matrix from a tag. More...
virtual void	disassociateMatrixFromTag (TagID tag) override
	Disassociate any matrix that is associated with a given tag. More...
virtual void	disassociateDefaultMatrixTags () override
	Disassociate the matrices associated with the default matrix tags of this system. More...
virtual NumericVector< Number > &	getVector (const std::string &name) override
	Get a raw NumericVector by name. More...
virtual const NumericVector< Number > &	getVector (const std::string &name) const override
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 > *	solutionPreviousNewton () 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 void	addDotVectors () override
	Add u_dot, u_dotdot, u_dot_old and u_dotdot_old vectors if requested by the time integrator. More...
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 void	initSolutionState () override
	Initializes the solution state. More...
virtual NumericVector< Number > &	solutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time) override
	Get a state of the solution (0 = current, 1 = old, 2 = older, etc). More...
virtual const NumericVector< Number > &	solutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time) const override
	Get a state of the solution (0 = current, 1 = old, 2 = older, etc). More...
virtual void	needSolutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time) override
	Registers that the solution state state is needed. More...
virtual bool	hasSolutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time) const override
	Whether or not the system has the solution state (0 = current, 1 = old, 2 = older, etc). 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	compute (ExecFlagType) override
	Compute time derivatives, auxiliary variables, etc. More...
virtual void	addTimeIntegrator (const std::string &, const std::string &, InputParameters &)
virtual void	addTimeIntegrator (std::shared_ptr< TimeIntegrator >)
unsigned int	number () const
	Gets the number of this system. More...
MooseMesh &	mesh ()
const MooseMesh &	mesh () const
SubProblem &	subproblem ()
const SubProblem &	subproblem () const
FEProblemBase &	feProblem ()
const FEProblemBase &	feProblem () 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...
bool	automaticScaling () const
	Getter for whether we are performing automatic scaling. More...
void	automaticScaling (bool automatic_scaling)
	Setter for whether we are performing automatic scaling. More...
void	setVerboseFlag (const bool &verbose)
	Sets the verbose flag. 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	init ()
	Initialize the system. More...
virtual void	initializeObjects ()
	Called only once, just before the solve begins so objects can do some precalculations. More...
virtual void	update (bool update_libmesh_system=true)
	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...
NumericVector< Number > &	solution ()
const NumericVector< Number > &	solution () const
NumericVector< Number > &	solutionOld ()
const NumericVector< Number > &	solutionOld () const
NumericVector< Number > &	solutionOlder ()
const NumericVector< Number > &	solutionOlder () const
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 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...
void	flushTaggedMatrices (const std::set< TagID > &tags)
	flushes all matrices associated to 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
MooseVariableFieldBase &	getVariable (THREAD_ID tid, const std::string &var_name) const
	Gets a reference to a variable of with specified name. More...
MooseVariableFieldBase &	getVariable (THREAD_ID tid, unsigned int var_number) const
	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...
template<typename T >
MooseVariableField< T > &	getActualFieldVariable (THREAD_ID tid, const std::string &var_name)
	Returns a field variable pointer - this includes finite volume variables. More...
template<typename T >
MooseVariableField< T > &	getActualFieldVariable (THREAD_ID tid, unsigned int var_number)
	Returns a field variable pointer - this includes finite volume variables. More...
template<typename T >
MooseVariableFV< T > &	getFVVariable (THREAD_ID tid, const std::string &var_name)
	Return a finite volume variable. More...
virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, const std::string &var_name) const
	Gets a reference to a scalar variable with specified number. More...
virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, unsigned int var_number) const
	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...
unsigned int	nFieldVariables () const
	Get the number of field variables in this system. More...
unsigned int	nFVVariables () const
	Get the number of finite volume 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< MooseVariableFieldBase * > &	getVariables (THREAD_ID tid)
const std::vector< MooseVariableScalar * > &	getScalarVariables (THREAD_ID tid)
const std::set< SubdomainID > &	getSubdomainsForVar (unsigned int var_number) const
const std::set< SubdomainID > &	getSubdomainsForVar (const std::string &var_name) const
	Get the block where a variable of this system is defined. More...
void	removeVector (const std::string &name)
	Remove a vector from the system with the given name. More...
void	removeVector (TagID tag_id)
	Remove a solution length vector from the system with the specified TagID. More...
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...
void	closeTaggedVector (const TagID tag)
	Close vector with the given tag. More...
void	closeTaggedVectors (const std::set< TagID > &tags)
	Close all vectors for given tags. More...
void	zeroTaggedVector (const TagID tag)
	Zero vector with the given tag. More...
void	zeroTaggedVectors (const std::set< TagID > &tags)
	Zero all vectors for given tags. More...
void	setVariableGlobalDoFs (const std::string &var_name)
	set all the global dof indices for a variable More...
const std::vector< dof_id_type > &	getVariableGlobalDoFs ()
	Get the global dof indices of a variable, this needs to be called after the indices have been set by setVariableGlobalDoFs More...
SparseMatrix< Number > &	addMatrix (TagID tag)
	Adds a matrix with a given tag. More...
void	removeMatrix (TagID tag)
	Removes a matrix with a given tag. More...
virtual const std::string &	name () const
const std::vector< VariableName > &	getVariableNames () const
void	getStandardFieldVariableNames (std::vector< VariableName > &std_field_variables) 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 ()
bool	hasVarCopy () const
	Whether or not there are variables to be restarted from an Exodus mesh file. More...
void	addScalingVector ()
	Add the scaling factor vector to the system. More...
bool	solutionStatesInitialized () const
	Whether or not the solution states have been initialized via initSolutionState() More...
virtual void	initialSetup ()
	Setup Functions. More...
virtual void	timestepSetup ()
virtual void	customSetup (const ExecFlagType &exec_type)
virtual void	subdomainSetup ()
virtual void	residualSetup ()
virtual void	jacobianSetup ()
void	clearAllDofIndices ()
	Clear all dof indices from moose variables. More...
void	setActiveVariableCoupleableVectorTags (const std::set< TagID > &vtags, THREAD_ID tid)
	Set the active vector tags for the variables. More...
void	setActiveScalarVariableCoupleableVectorTags (const std::set< TagID > &vtags, THREAD_ID tid)
	Set the active vector tags for the scalar variables. More...
Moose::VarKindType	varKind () const
std::vector< std::unique_ptr< NumericVector< Number > > > &	gradientContainer ()
	Reference to the container vector which hold gradients at dofs (if it can be interpreted). More...
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const
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

Public Attributes
const ConsoleStream	_console
	An instance of helper class to write streams to the Console objects. More...

Protected Member Functions
NumericVector< Number > &	solutionInternal () const override
	Internal getter for solution owned by libMesh. More...

Protected Attributes
SystemBase &	_undisplaced_system
TransientExplicitSystem &	_sys
SubProblem &	_subproblem
	The subproblem for whom this class holds variable data, etc; this can either be the governing finite element/volume problem or a subjugate displaced problem. More...
FEProblemBase &	_fe_problem
	the governing finite element/volume problem More...
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
NumericVector< Number > *	_u_dot
	solution vector for u^dot More...
NumericVector< Number > *	_u_dotdot
	solution vector for u^dotdot More...
NumericVector< Number > *	_u_dot_old
	old solution vector for u^dot More...
NumericVector< Number > *	_u_dotdot_old
	old solution vector for u^dotdot More...
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< MooseVariableFieldBase * > >	_numbered_vars
	Map variable number to its pointer. More...
bool	_automatic_scaling
	Whether to automatically scale the variables. More...
bool	_verbose
	True if printing out additional information. More...
bool	_solution_states_initialized
	Whether or not the solution states have been initialized. More...
std::vector< dof_id_type >	_var_all_dof_indices
	Container for the dof indices of a given variable. More...
std::unique_ptr< NumericVector< Number > >	_serialized_solution
	Serialized version of the solution vector, or nullptr if a serialized solution is not needed. More...
std::vector< std::unique_ptr< NumericVector< Number > > >	_raw_grad_container
	A cache for storing gradients at dof locations. More...
const Parallel::Communicator &	_communicator

Detailed Description

Definition at line 24 of file DisplacedSystem.h.

Constructor & Destructor Documentation

DisplacedSystem() [1/2]

DisplacedSystem::DisplacedSystem ( DisplacedSystem &&  )

delete

DisplacedSystem() [2/2]

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

Definition at line 18 of file DisplacedSystem.C.

  : SystemBase(problem, fe_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 35 of file DisplacedSystem.C.

{}

Member Function Documentation

activeAllMatrixTags()

void SystemBase::activeAllMatrixTags ( )

virtualinherited

Make all exsiting matrices ative.

Definition at line 1110 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), NonlinearSystemBase::computeResidualAndJacobianInternal(), and NonlinearSystemBase::computeResidualTags().

{
  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;
}

activeMatrixTag()

void SystemBase::activeMatrixTag ( TagID  tag )

virtualinherited

Active a matrix for tag.

Definition at line 1075 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;
}

addDotVectors()

virtual void DisplacedSystem::addDotVectors ( )

inlineoverridevirtual

Add u_dot, u_dotdot, u_dot_old and u_dotdot_old vectors if requested by the time integrator.

Reimplemented from SystemBase.

Definition at line 157 of file DisplacedSystem.h.

{ _undisplaced_system.addDotVectors(); }

addMatrix()

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

inherited

Adds a matrix with a given tag.

Parameters

tag_name

The name of the tag

Definition at line 566 of file SystemBase.C.

{
  if (!_subproblem.matrixTagExists(tag))
    mooseError("Cannot add tagged matrix with TagID ",
               tag,
               " in system '",
               name(),
               "' because the tag does not exist in the problem");

  if (hasMatrix(tag))
    return getMatrix(tag);

  const auto matrix_name = _subproblem.matrixTagName(tag);
  SparseMatrix<Number> & mat = system().add_matrix(matrix_name);
  associateMatrixToTag(mat, tag);

  return mat;
}

addScalingVector()

void SystemBase::addScalingVector ( )

inherited

Add the scaling factor vector to the system.

Definition at line 1470 of file SystemBase.C.

Referenced by MooseVariableBase::initialSetup().

{
  addVector("scaling_factors", /*project=*/false, libMesh::ParallelType::GHOSTED);
  _subproblem.hasScalingVector(number());
}

addTimeIntegrator() [1/4]

virtual void SystemBase::addTimeIntegrator

inline

Definition at line 871 of file SystemBase.h.

  {
  }

addTimeIntegrator() [2/4]

virtual void SystemBase::addTimeIntegrator

inline

Definition at line 877 of file SystemBase.h.

{}

addTimeIntegrator() [3/4]

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

overridevirtual

Reimplemented from SystemBase.

Definition at line 56 of file DisplacedSystem.C.

{
  _time_integrator = ti;
}

addTimeIntegrator() [4/4]

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

inlinevirtualinherited

Reimplemented in NonlinearSystemBase, AuxiliarySystem, and LinearSystem.

Definition at line 871 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 715 of file SystemBase.C.

Referenced by AuxiliarySystem::addVariable().

{
  _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 || fe_type.family == RAVIART_THOMAS)
      mooseError("Vector family type cannot be used in an array variable");

    // 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);

    // Set as array variable
    if (parameters.isParamSetByUser("array") && !parameters.get<bool>("array"))
      mooseError("Variable '",
                 name,
                 "' is an array variable ('components' > 1) but 'array' is set to false.");
    parameters.set<bool>("array") = true;
  }
  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<MooseVariableFieldBase *>(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 (auto * const functor = dynamic_cast<Moose::FunctorBase<ADReal> *>(fe_var))
        _subproblem.addFunctor(name, *functor, tid);
      else if (auto * const functor = dynamic_cast<Moose::FunctorBase<ADRealVectorValue> *>(fe_var))
        _subproblem.addFunctor(name, *functor, tid);
      else if (auto * const functor = dynamic_cast<Moose::FunctorBase<RealEigenVector> *>(fe_var))
        _subproblem.addFunctor(name, *functor, tid);
      else
        mooseError("This should be a functor");
    }

    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;
}

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 1150 of file SystemBase.C.

Referenced by CopyNodalVarsAction::act(), and PhysicsBase::copyVariablesFromMesh().

{
  _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 200 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 191 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  )

inherited

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.

Definition at line 604 of file SystemBase.C.

Referenced by SystemBase::addDotVectors(), SystemBase::addScalingVector(), SteffensenSolve::allocateStorage(), SecantSolve::allocateStorage(), PicardSolve::allocateStorage(), AStableDirk4::AStableDirk4(), ExplicitTimeIntegrator::ExplicitTimeIntegrator(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), CentralDifference::initialSetup(), LStableDirk3::LStableDirk3(), LStableDirk4::LStableDirk4(), SystemBase::needSolutionState(), NonlinearSystemBase::residualGhosted(), and SystemBase::saveOldSolutions().

{
  if (hasVector(vector_name))
    return getVector(vector_name);

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

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 614 of file SystemBase.C.

{
  if (!_subproblem.vectorTagExists(tag))
    mooseError("Cannot add tagged vector with TagID ",
               tag,
               " in system '",
               name(),
               "' because the tag does not exist in the problem");

  if (hasVector(tag))
  {
    auto & vec = getVector(tag);

    if (type != ParallelType::AUTOMATIC && vec.type() != type)
      mooseError("Cannot add tagged vector '",
                 _subproblem.vectorTagName(tag),
                 "', in system '",
                 name(),
                 "' because a vector with the same name was found with a different parallel type");

    return vec;
  }

  const auto vector_name = _subproblem.vectorTagName(tag);
  NumericVector<Number> & vec = system().add_vector(vector_name, project, type);
  associateVectorToTag(vec, tag);

  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 1420 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeScaling().

{
  for (MooseIndex(_vars) thread = 0; thread < _vars.size(); ++thread)
  {
    auto & field_variables = _vars[thread].fieldVariables();
    for (MooseIndex(field_variables) i = 0, p = 0; i < field_variables.size(); ++i)
    {
      auto factors = field_variables[i]->arrayScalingFactor();
      for (unsigned int j = 0; j < field_variables[i]->count(); ++j, ++p)
        factors[j] /= inverse_scaling_factors[p];

      field_variables[i]->scalingFactor(factors);
    }

    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()});

    if (thread == 0 && _verbose)
    {
      _console << "Automatic scaling factors:\n";
      auto original_flags = _console.flags();
      auto original_precision = _console.precision();
      _console.unsetf(std::ios_base::floatfield);
      _console.precision(6);

      for (const auto & field_variable : field_variables)
      {
        const auto & factors = field_variable->arrayScalingFactor();
        _console << "  " << field_variable->name() << ":";
        for (const auto i : make_range(field_variable->count()))
          _console << " " << factors[i];
        _console << "\n";
      }
      for (const auto & scalar_variable : scalar_variables)
        _console << "  " << scalar_variable->name() << ": " << scalar_variable->scalingFactor()
                 << "\n";
      _console << "\n" << std::endl;

      // restore state
      _console.flags(original_flags);
      _console.precision(original_precision);
    }
  }
}

assignMaxVarNDofsPerElem()

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

inlineinherited

assign the maximum element dofs

Definition at line 585 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 590 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 matrix to a tag.

Reimplemented from SystemBase.

Definition at line 86 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 66 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 172 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 181 of file DisplacedSystem.h.

  {
  }

automaticScaling() [1/2]

bool SystemBase::automaticScaling ( ) const

inlineinherited

Getter for whether we are performing automatic scaling.

Returns

whether we are performing automatic scaling

Definition at line 123 of file SystemBase.h.

Referenced by SubProblem::automaticScaling().

{ return _automatic_scaling; }

automaticScaling() [2/2]

void SystemBase::automaticScaling ( bool  automatic_scaling )

inlineinherited

Setter for whether we are performing automatic scaling.

Parameters

automatic_scaling

A boolean representing whether we are performing automatic scaling

Definition at line 129 of file SystemBase.h.

{ _automatic_scaling = automatic_scaling; }

clearAllDofIndices()

void SystemBase::clearAllDofIndices ( )

inherited

Clear all dof indices from moose variables.

Definition at line 1538 of file SystemBase.C.

Referenced by SubProblem::clearAllDofIndices().

{
  for (auto & var_warehouse : _vars)
    var_warehouse.clearAllDofIndices();
}

closeTaggedMatrices()

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

inherited

Close all matrices associated the tags.

Definition at line 1016 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), and NonlinearSystemBase::computeResidualAndJacobianTags().

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

closeTaggedVector()

void SystemBase::closeTaggedVector ( const TagID  tag )

inherited

Close vector with the given tag.

Definition at line 645 of file SystemBase.C.

Referenced by SystemBase::closeTaggedVectors().

{
  if (!_subproblem.vectorTagExists(tag))
    mooseError("Cannot close vector with TagID ",
               tag,
               " in system '",
               name(),
               "' because that tag does not exist in the problem");
  else if (!hasVector(tag))
    mooseError("Cannot close vector tag with name '",
               _subproblem.vectorTagName(tag),
               "' in system '",
               name(),
               "' because there is no vector associated with that tag");

  getVector(tag).close();
}

closeTaggedVectors()

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

inherited

Close all vectors for given tags.

Definition at line 664 of file SystemBase.C.

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

{
  for (const auto tag : tags)
    closeTaggedVector(tag);
}

compute()

virtual void DisplacedSystem::compute ( ExecFlagType  type )

inlineoverridevirtual

Compute time derivatives, auxiliary variables, etc.

Parameters

type	Our current execution stage

Implements SystemBase.

Definition at line 255 of file DisplacedSystem.h.

{}

computeVariables()

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

inlinevirtualinherited

Definition at line 862 of file SystemBase.h.

{}

computingScalingJacobian()

bool SystemBase::computingScalingJacobian ( ) const

inherited

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

Definition at line 1477 of file SystemBase.C.

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

{
  return _subproblem.computingScalingJacobian();
}

copyOldSolutions()

void SystemBase::copyOldSolutions ( )

virtualinherited

Shifts the solutions backwards in time.

Definition at line 1245 of file SystemBase.C.

Referenced by SystemBase::copySolutionsBackwards(), and EigenExecutionerBase::inversePowerIteration().

{
  // Copying the solutions backward so the current solution will become the old, and the old will
  // become older. The same applies to the nonlinear iterates.
  for (const auto iteration_index : index_range(_solution_states))
  {
    const auto states = _solution_states[iteration_index].size();
    if (states > 1)
      for (unsigned int i = states - 1; i > 0; --i)
        solutionState(i, Moose::SolutionIterationType(iteration_index)) =
            solutionState(i - 1, Moose::SolutionIterationType(iteration_index));
  }

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

copySolutionsBackwards()

void SystemBase::copySolutionsBackwards ( )

virtualinherited

Copy current solution into old and older.

Definition at line 1234 of file SystemBase.C.

{
  system().update();

  copyOldSolutions();
}

copyVars()

void SystemBase::copyVars ( ExodusII_IO &  io )

inherited

Definition at line 1158 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))
    {
      const auto & var = getVariable(0, vci._dest_name);
      if (var.isArray())
      {
        const auto & array_var = getFieldVariable<RealEigenVector>(0, vci._dest_name);
        for (MooseIndex(var.count()) i = 0; i < var.count(); ++i)
        {
          const auto exodus_var = _subproblem.arrayVariableComponent(vci._source_name, i);
          const auto system_var = array_var.componentName(i);
          if (var.isNodal())
            io.copy_nodal_solution(system(), exodus_var, system_var, timestep);
          else
            io.copy_elemental_solution(system(), exodus_var, system_var, timestep);
        }
      }
      else
      {
        if (var.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))
      io.copy_scalar_solution(system(), {vci._dest_name}, {vci._source_name}, timestep);
    else
      mooseError("Unrecognized variable ", vci._dest_name, " in variables to copy.");
  }

  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 114 of file DisplacedSystem.h.

  {
    return _undisplaced_system.currentSolution();
  }

customSetup()

void SystemBase::customSetup ( const ExecFlagType &  exec_type )

virtualinherited

Reimplemented in NonlinearSystemBase, and AuxiliarySystem.

Definition at line 1510 of file SystemBase.C.

Referenced by AuxiliarySystem::customSetup(), and NonlinearSystemBase::customSetup().

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
    _vars[tid].customSetup(exec_type);
}

deactiveAllMatrixTags()

void SystemBase::deactiveAllMatrixTags ( )

virtualinherited

Make matrices inactive.

Definition at line 1099 of file SystemBase.C.

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

{
  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;
}

deactiveMatrixTag()

void SystemBase::deactiveMatrixTag ( TagID  tag )

virtualinherited

deactive a matrix for tag

Definition at line 1087 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;
}

defaultMatrixTags()

virtual std::set<TagID> DisplacedSystem::defaultMatrixTags ( ) const

inlineoverridevirtual

Get the default matrix tags associted with this system.

Reimplemented from SystemBase.

Definition at line 61 of file DisplacedSystem.h.

  {
    return _undisplaced_system.defaultMatrixTags();
  }

defaultVectorTags()

virtual std::set<TagID> DisplacedSystem::defaultVectorTags ( ) const

inlineoverridevirtual

Get the default vector tags associated with this system.

Reimplemented from SystemBase.

Definition at line 57 of file DisplacedSystem.h.

  {
    return _undisplaced_system.defaultVectorTags();
  }

disassociateDefaultMatrixTags()

virtual void DisplacedSystem::disassociateDefaultMatrixTags ( )

inlineoverridevirtual

Disassociate the matrices associated with the default matrix tags of this system.

Reimplemented from SystemBase.

Definition at line 101 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateDefaultMatrixTags();
  }

disassociateDefaultVectorTags()

virtual void DisplacedSystem::disassociateDefaultVectorTags ( )

inlineoverridevirtual

Disassociate the vectors associated with the default vector tags of this system.

Reimplemented from SystemBase.

Definition at line 81 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateDefaultVectorTags();
  }

disassociateMatrixFromTag() [1/2]

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

inlineoverridevirtual

Disassociate a matrix from a tag.

Reimplemented from SystemBase.

Definition at line 91 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateMatrixFromTag(matrix, tag);
  }

disassociateMatrixFromTag() [2/2]

virtual void DisplacedSystem::disassociateMatrixFromTag ( TagID  tag )

inlineoverridevirtual

Disassociate any matrix that is associated with a given tag.

Reimplemented from SystemBase.

Definition at line 96 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateMatrixFromTag(tag);
  }

disassociateVectorFromTag() [1/2]

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

inlineoverridevirtual

Disassociate a given vector from a given tag.

Reimplemented from SystemBase.

Definition at line 71 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateVectorFromTag(vec, tag);
  }

disassociateVectorFromTag() [2/2]

virtual void DisplacedSystem::disassociateVectorFromTag ( TagID  tag )

inlineoverridevirtual

Disassociate any vector that is associated with a given tag.

Reimplemented from SystemBase.

Definition at line 76 of file DisplacedSystem.h.

  {
    _undisplaced_system.disassociateVectorFromTag(tag);
  }

dofMap() [1/2]

DofMap & SystemBase::dofMap ( )

virtualinherited

Gets writeable reference to the dof map.

Definition at line 1138 of file SystemBase.C.

Referenced by NonlinearSystemBase::assembleScalingVector(), MooseApp::attachRelationshipManagers(), SystemBase::augmentSendList(), NonlinearSystemBase::augmentSparsity(), NonlinearSystemBase::computeScaling(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), Adaptivity::init(), ActivateElementsUserObjectBase::initSolutions(), PNGOutput::makeMeshFunc(), GhostingUserObject::meshChanged(), TableOutput::outputScalarVariables(), Nemesis::outputScalarVariables(), Exodus::outputScalarVariables(), and ElementSubdomainModifier::setOldAndOlderSolutionsForMovedNodes().

{
  return system().get_dof_map();
}

dofMap() [2/2]

const DofMap & SystemBase::dofMap ( ) const

virtualinherited

Gets const reference to the dof map.

Definition at line 1144 of file SystemBase.C.

{
  return system().get_dof_map();
}

duDotDotDu() [1/2]

virtual Number& DisplacedSystem::duDotDotDu ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 153 of file DisplacedSystem.h.

{ return _undisplaced_system.duDotDotDu(); }

duDotDotDu() [2/2]

virtual const Number& DisplacedSystem::duDotDotDu ( ) const

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 155 of file DisplacedSystem.h.

{ return _undisplaced_system.duDotDotDu(); }

duDotDu() [1/2]

virtual Number& DisplacedSystem::duDotDu ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 152 of file DisplacedSystem.h.

{ return _undisplaced_system.duDotDu(); }

duDotDu() [2/2]

virtual const Number& DisplacedSystem::duDotDu ( ) const

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 154 of file DisplacedSystem.h.

{ return _undisplaced_system.duDotDu(); }

feProblem() [1/2]

FEProblemBase& SystemBase::feProblem ( )

inlineinherited

Definition at line 104 of file SystemBase.h.

Referenced by DMMooseGetEmbedding_Private(), DMSetFromOptions_Moose(), and DMSetUp_Moose_Pre().

{ return _fe_problem; }

feProblem() [2/2]

const FEProblemBase& SystemBase::feProblem ( ) const

inlineinherited

Definition at line 105 of file SystemBase.h.

{ return _fe_problem; }

flushTaggedMatrices()

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

inherited

flushes all matrices associated to tags.

Flush assembles the matrix but doesn't shrink memory allocation

Definition at line 1024 of file SystemBase.C.

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

getActualFieldVariable() [1/2]

template<typename T >

MooseVariableField< T > & SystemBase::getActualFieldVariable ( THREAD_ID  tid, const std::string &  var_name  )

inherited

Returns a field variable pointer - this includes finite volume variables.

Definition at line 114 of file SystemBase.C.

Referenced by BoundsBase::BoundsBase(), Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), and Assembly::copyShapes().

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

getActualFieldVariable() [2/2]

template<typename T >

MooseVariableField< T > & SystemBase::getActualFieldVariable ( THREAD_ID  tid, unsigned int  var_number  )

inherited

Returns a field variable pointer - this includes finite volume variables.

Definition at line 135 of file SystemBase.C.

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

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.

This excludes and cannot return finite volume variables.

Parameters

tid	Thread id
var_name	variable name

Returns

reference the variable (class)

Definition at line 107 of file SystemBase.C.

Referenced by Marker::getMarkerValue().

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

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.

This excludes and cannot return finite volume variables.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns

reference the variable (class)

Definition at line 128 of file SystemBase.C.

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

getFVVariable()

template<typename T >

template MooseVariableFV< Real > & SystemBase::getFVVariable< Real > ( THREAD_ID  tid, const std::string &  var_name  )

inherited

Return a finite volume variable.

Definition at line 121 of file SystemBase.C.

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

getMatrix() [1/2]

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

inlineoverridevirtual

Get a raw SparseMatrix.

Reimplemented from SystemBase.

Definition at line 238 of file DisplacedSystem.h.

  {
    return _undisplaced_system.getMatrix(tag);
  }

getMatrix() [2/2]

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

inlineoverridevirtual

Get a raw SparseMatrix.

Reimplemented from SystemBase.

Definition at line 242 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 860 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 573 of file SystemBase.h.

Referenced by Moose::globalDofIndexToDerivative().

{ return _max_var_n_dofs_per_elem; }

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 580 of file SystemBase.h.

{ return _max_var_n_dofs_per_node; }

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 237 of file SystemBase.C.

{
  Order order = CONSTANT;
  const std::vector<MooseVariableFieldBase *> & 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  ) const

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 141 of file SystemBase.C.

Referenced by Assembly::addJacobianOffDiagScalar(), ODEKernel::computeOffDiagJacobianScalar(), VectorKernel::computeOffDiagJacobianScalar(), ArrayKernel::computeOffDiagJacobianScalar(), IntegratedBC::computeOffDiagJacobianScalar(), VectorIntegratedBC::computeOffDiagJacobianScalar(), ArrayIntegratedBC::computeOffDiagJacobianScalar(), Kernel::computeOffDiagJacobianScalar(), ScalarLagrangeMultiplier::computeOffDiagJacobianScalar(), MortarScalarBase::computeOffDiagJacobianScalar(), KernelScalarBase::computeOffDiagJacobianScalarLocal(), KernelScalarBase::computeScalarOffDiagJacobianScalar(), MortarScalarBase::computeScalarOffDiagJacobianScalar(), DMMooseSetVariables(), Assembly::init(), ReferenceResidualProblem::initialSetup(), and NonlinearSystemBase::setupScalingData().

{
  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;
}

getScalarVariable() [2/2]

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

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 150 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 747 of file SystemBase.h.

Referenced by Assembly::addResidualScalar(), ODEKernel::computeJacobian(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), AuxiliarySystem::computeScalarVars(), Assembly::init(), SystemBase::initSolutionState(), NonlinearThread::onElement(), Assembly::prepareOffDiagScalar(), and Assembly::prepareScalar().

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

getSharedTimeIntegrator()

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

inlineinherited

Definition at line 882 of file SystemBase.h.

Referenced by DisplacedProblem::DisplacedProblem().

{ return _time_integrator; }

getStandardFieldVariableNames()

void SystemBase::getStandardFieldVariableNames ( std::vector< VariableName > &  std_field_variables ) const

inherited

getSubdomainsForVar() [1/2]

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

inlineinherited

Definition at line 752 of file SystemBase.h.

Referenced by NonlinearSystemBase::checkKernelCoverage(), and SystemBase::getSubdomainsForVar().

  {
    return _var_map.at(var_number);
  }

getSubdomainsForVar() [2/2]

const std::set<SubdomainID>& SystemBase::getSubdomainsForVar ( const std::string &  var_name ) const

inlineinherited

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

Parameters

var_name

The name of the variable

Returns

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

Definition at line 763 of file SystemBase.h.

  {
    return getSubdomainsForVar(getVariable(0, var_name).number());
  }

getTimeIntegrator() [1/2]

TimeIntegrator* SystemBase::getTimeIntegrator ( )

inlineinherited

Definition at line 879 of file SystemBase.h.

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

{ return _time_integrator.get(); }

getTimeIntegrator() [2/2]

const TimeIntegrator* SystemBase::getTimeIntegrator ( ) const

inlineinherited

Definition at line 880 of file SystemBase.h.

{ return _time_integrator.get(); }

getVariable() [1/2]

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

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 86 of file SystemBase.C.

Referenced by AdaptivityAction::act(), Assembly::addJacobianBlock(), Assembly::addJacobianBlockNonlocal(), FEProblemBase::addJacobianBlockTags(), Assembly::addJacobianNeighbor(), NonlocalKernel::computeNonlocalOffDiagJacobian(), NonlocalIntegratedBC::computeNonlocalOffDiagJacobian(), Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), Assembly::copyShapes(), SystemBase::copyVars(), DMMooseSetVariables(), FieldSplitPreconditioner::FieldSplitPreconditioner(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), NodeElemConstraint::getConnectedDofIndices(), NodeFaceConstraint::getConnectedDofIndices(), SystemBase::getSubdomainsForVar(), ResidualObject::getVariable(), SubProblem::getVariableHelper(), Assembly::init(), NodalNormalsPreprocessor::initialize(), ReferenceResidualProblem::initialSetup(), LinearSystem::initialSetup(), Assembly::initNonlocalCoupling(), PNGOutput::makeMeshFunc(), FEProblemBase::prepare(), Assembly::prepareBlock(), Assembly::prepareBlockNonlocal(), AddPeriodicBCAction::setPeriodicVars(), NonlinearSystemBase::setupScalingData(), UpdateErrorVectorsThread::UpdateErrorVectorsThread(), and VariableCondensationPreconditioner::VariableCondensationPreconditioner().

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

getVariable() [2/2]

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

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 96 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 160 of file SystemBase.C.

Referenced by PhysicsBasedPreconditioner::addSystem().

{
  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];
}

getVariableGlobalDoFs()

const std::vector<dof_id_type>& SystemBase::getVariableGlobalDoFs ( )

inlineinherited

Get the global dof indices of a variable, this needs to be called after the indices have been set by setVariableGlobalDoFs

Definition at line 835 of file SystemBase.h.

{ return _var_all_dof_indices; }

getVariableNames()

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

inlineinherited

Definition at line 853 of file SystemBase.h.

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

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

getVariables()

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

inlineinherited

Definition at line 742 of file SystemBase.h.

Referenced by Assembly::addJacobianOffDiagScalar(), Assembly::addResidual(), Assembly::addResidualLower(), Assembly::addResidualNeighbor(), MooseMesh::cacheFaceInfoVariableOwnership(), MooseMesh::cacheFVElementalDoFs(), Assembly::cacheResidual(), Assembly::cacheResidualLower(), Assembly::cacheResidualNeighbor(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), Assembly::init(), Assembly::initNonlocalCoupling(), SystemBase::initSolutionState(), ComputeLinearFVGreenGaussGradientFaceThread::operator()(), Assembly::prepareLowerD(), Assembly::prepareNeighbor(), Assembly::prepareOffDiagScalar(), Assembly::prepareResidual(), Assembly::setResidual(), and Assembly::setResidualNeighbor().

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

getVector() [1/4]

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

inlineoverridevirtual

Get a raw NumericVector by tag.

Reimplemented from SystemBase.

Definition at line 37 of file DisplacedSystem.h.

  {
    return _undisplaced_system.getVector(tag_id);
  }

getVector() [2/4]

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

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 41 of file DisplacedSystem.h.

  {
    return _undisplaced_system.getVector(tag_id);
  }

getVector() [3/4]

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

overridevirtual

Get a raw NumericVector by name.

Get a raw NumericVector with the given name.

Reimplemented from SystemBase.

Definition at line 38 of file DisplacedSystem.C.

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

getVector() [4/4]

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

overridevirtual

Reimplemented from SystemBase.

Definition at line 47 of file DisplacedSystem.C.

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

gradientContainer()

std::vector<std::unique_ptr<NumericVector<Number> > >& SystemBase::gradientContainer ( )

inlineinherited

Reference to the container vector which hold gradients at dofs (if it can be interpreted).

Mainly used for finite volume systems.

Definition at line 932 of file SystemBase.h.

  {
    return _raw_grad_container;
  }

hasMatrix()

virtual bool DisplacedSystem::hasMatrix ( TagID  tag ) const

inlineoverridevirtual

Check if the tagged matrix exists in the system.

Reimplemented from SystemBase.

Definition at line 218 of file DisplacedSystem.h.

  {
    return _undisplaced_system.hasMatrix(tag_id);
  }

hasScalarVariable()

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

virtualinherited

Definition at line 832 of file SystemBase.C.

Referenced by MortarScalarBase::computeJacobian(), NonlinearSystemBase::computeJacobianInternal(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), SystemBase::copyVars(), NonlinearEigenSystem::postAddResidualObject(), AddPeriodicBCAction::setPeriodicVars(), and NonlinearSystemBase::setupScalingData().

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

hasSolutionState()

bool DisplacedSystem::hasSolutionState ( const unsigned int  state, Moose::SolutionIterationType  iteration_type = Moose::SolutionIterationType::Time  ) const

inlineoverridevirtual

Whether or not the system has the solution state (0 = current, 1 = old, 2 = older, etc).

Reimplemented from SystemBase.

Definition at line 295 of file DisplacedSystem.h.

{
  return _undisplaced_system.hasSolutionState(state, iteration_type);
}

hasVarCopy()

bool SystemBase::hasVarCopy ( ) const

inlineinherited

Whether or not there are variables to be restarted from an Exodus mesh file.

Definition at line 885 of file SystemBase.h.

{ return _var_to_copy.size() > 0; }

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 807 of file SystemBase.C.

Referenced by ADDGKernel::ADDGKernel(), ArrayDGKernel::ArrayDGKernel(), SystemBase::copyVars(), DGKernel::DGKernel(), DMMooseSetVariables(), FEProblemBase::duplicateVariableCheck(), SubProblem::getVariableHelper(), InterfaceKernelTempl< T >::InterfaceKernelTempl(), PNGOutput::makeMeshFunc(), MultiAppVariableValueSamplePostprocessorTransfer::MultiAppVariableValueSamplePostprocessorTransfer(), NonlinearSystemBase::setupScalingData(), and Coupleable::writableCoupledValue().

{
  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;
}

hasVector() [1/2]

virtual bool DisplacedSystem::hasVector ( TagID  tag_id ) const

inlineoverridevirtual

Check if the tagged vector exists in the system.

Reimplemented from SystemBase.

Definition at line 213 of file DisplacedSystem.h.

  {
    return _undisplaced_system.hasVector(tag_id);
  }

hasVector() [2/2]

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

inherited

Check if the named vector exists in the system.

Definition at line 880 of file SystemBase.C.

Referenced by FEProblemBase::addCachedResidualDirectly(), Assembly::addCachedResiduals(), Assembly::addResidual(), Assembly::addResidualLower(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), SystemBase::addVector(), NonlinearSystemBase::assembleScalingVector(), Assembly::cacheResidual(), Assembly::cacheResidualLower(), Assembly::cacheResidualNeighbor(), SystemBase::closeTaggedVector(), FEProblemBase::computeBounds(), NonlinearSystemBase::computeResidualTags(), CentralDifference::computeTimeDerivatives(), SystemBase::disassociateVectorFromTag(), SystemBase::getVector(), hasVector(), MooseVariableScalar::reinit(), SystemBase::removeVector(), SubProblem::selectVectorTagsFromSystem(), NonlinearSystemBase::setPreviousNewtonSolution(), TaggingInterface::setResidual(), SystemBase::solutionPreviousNewton(), and SystemBase::zeroTaggedVector().

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

init()

virtual void SystemBase::init ( )

inlinevirtualinherited

Initialize the system.

Reimplemented in NonlinearSystemBase, NonlinearSystem, and SolverSystem.

Definition at line 156 of file SystemBase.h.

Referenced by SolverSystem::init().

{};

initializeObjects()

virtual void SystemBase::initializeObjects ( )

inlinevirtualinherited

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

Definition at line 161 of file SystemBase.h.

{};

initialSetup()

void SystemBase::initialSetup ( )

virtualinherited

Setup Functions.

Reimplemented in NonlinearSystemBase, LinearSystem, and AuxiliarySystem.

Definition at line 1483 of file SystemBase.C.

Referenced by AuxiliarySystem::initialSetup(), LinearSystem::initialSetup(), and NonlinearSystemBase::initialSetup().

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
    _vars[tid].initialSetup();

  // If we need raw gradients, we initialize them here.
  bool gradient_storage_initialized = false;
  for (const auto & field_var : _vars[0].fieldVariables())
    if (!gradient_storage_initialized && field_var->needsGradientVectorStorage())
    {
      _raw_grad_container.clear();
      for (const auto i : make_range(this->_mesh.dimension()))
      {
        libmesh_ignore(i);
        _raw_grad_container.push_back(currentSolution()->zero_clone());
      }
    }
}

initSolutionState()

void DisplacedSystem::initSolutionState ( )

inlineoverridevirtual

Initializes the solution state.

Reimplemented from SystemBase.

Definition at line 268 of file DisplacedSystem.h.

{
  _undisplaced_system.initSolutionState();
}

isArrayVariable()

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

virtualinherited

If a variable is an array variable.

Definition at line 820 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 841 of file SystemBase.C.

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

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

jacobianSetup()

void SystemBase::jacobianSetup ( )

virtualinherited

Reimplemented in NonlinearSystemBase, LinearSystem, and AuxiliarySystem.

Definition at line 1531 of file SystemBase.C.

Referenced by AuxiliarySystem::jacobianSetup(), and NonlinearSystemBase::jacobianSetup().

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
    _vars[tid].jacobianSetup();
}

matrixTagActive()

bool SystemBase::matrixTagActive ( TagID  tag ) const

virtualinherited

If or not a matrix tag is active.

Definition at line 1124 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]

MooseMesh& SystemBase::mesh ( )

inlineinherited

Definition at line 100 of file SystemBase.h.

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

{ return _mesh; }

mesh() [2/2]

const MooseMesh& SystemBase::mesh ( ) const

inlineinherited

Definition at line 101 of file SystemBase.h.

{ return _mesh; }

name()

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

virtualinherited

Definition at line 1293 of file SystemBase.C.

Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addConstraint(), NonlinearSystemBase::addDamper(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), NonlinearSystemBase::addInterfaceKernel(), MooseEigenSystem::addKernel(), AuxiliarySystem::addKernel(), NonlinearSystemBase::addKernel(), SystemBase::addMatrix(), NonlinearSystemBase::addNodalKernel(), AuxiliarySystem::addScalarKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), AuxiliarySystem::addTimeIntegrator(), NonlinearSystemBase::addTimeIntegrator(), AuxiliarySystem::addVariable(), SystemBase::addVariable(), SystemBase::addVector(), SystemBase::closeTaggedVector(), LinearSystem::computeGradients(), LinearSystem::computeLinearSystemInternal(), LinearSystem::computeLinearSystemTags(), DisplacedProblem::DisplacedProblem(), SystemBase::getMatrix(), NonlinearSystemBase::getSplit(), getVector(), SystemBase::getVector(), SystemBase::hasVector(), LinearSystem::initialSetup(), NonlinearEigenSystem::postAddResidualObject(), SystemBase::removeMatrix(), SystemBase::removeVector(), SystemBase::solutionState(), and SystemBase::zeroTaggedVector().

{
  return system().name();
}

needSolutionState()

void DisplacedSystem::needSolutionState ( const unsigned int  state, Moose::SolutionIterationType  iteration_type = Moose::SolutionIterationType::Time  )

inlineoverridevirtual

Registers that the solution state state is needed.

Reimplemented from SystemBase.

Definition at line 288 of file DisplacedSystem.h.

{
  _undisplaced_system.needSolutionState(state, iteration_type);
}

nFieldVariables()

unsigned int SystemBase::nFieldVariables ( ) const

inherited

Get the number of field variables in this system.

Returns

the number of field variables

Definition at line 856 of file SystemBase.C.

Referenced by SystemBase::nVariables().

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

  return n;
}

nFVVariables()

unsigned int SystemBase::nFVVariables ( ) const

inherited

Get the number of finite volume variables in this system.

Returns

the number of finite volume variables

Definition at line 866 of file SystemBase.C.

Referenced by MooseMesh::cacheFVElementalDoFs().

{
  unsigned int n = 0;
  for (auto & var : _vars[0].fieldVariables())
    if (var->isFV())
      n += var->count();

  return n;
}

nonTimeVectorTag()

virtual TagID DisplacedSystem::nonTimeVectorTag ( ) const

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 55 of file DisplacedSystem.h.

{ return _undisplaced_system.nonTimeVectorTag(); }

number()

unsigned int SystemBase::number ( ) const

inherited

Gets the number of this system.

Returns

The number of this system

Definition at line 1132 of file SystemBase.C.

Referenced by FEProblemBase::addCachedResidualDirectly(), FEProblemBase::addJacobian(), FEProblemBase::addJacobianBlockTags(), FEProblemBase::addJacobianLowerD(), FEProblemBase::addJacobianNeighbor(), FEProblemBase::addJacobianNeighborLowerD(), FEProblemBase::addJacobianOffDiagScalar(), FEProblemBase::addJacobianScalar(), LinearFVElementalKernel::addMatrixContribution(), LinearFVFluxKernel::addMatrixContribution(), FEProblemBase::addResidual(), FEProblemBase::addResidualLower(), FEProblemBase::addResidualNeighbor(), FEProblemBase::addResidualScalar(), LinearFVFluxKernel::addRightHandSideContribution(), LinearFVElementalKernel::addRightHandSideContribution(), SystemBase::addScalingVector(), ADKernelTempl< T >::ADKernelTempl(), ArrayKernel::ArrayKernel(), NonlinearSystemBase::assembleScalingVector(), MooseMesh::cacheFaceInfoVariableOwnership(), MooseVariableScalar::computeAD(), FEProblemBase::computeBounds(), Assembly::computeFaceMap(), VectorNodalBC::computeJacobian(), ArrayNodalBC::computeJacobian(), NodalBC::computeJacobian(), FVBoundaryScalarLagrangeMultiplierConstraint::computeJacobian(), FVFluxBC::computeJacobian(), FVFluxKernel::computeJacobian(), FVInterfaceKernel::computeJacobian(), FEProblemBase::computeJacobianBlock(), NonlinearSystemBase::computeJacobianInternal(), FEProblemBase::computeNearNullSpace(), NonlinearSystemBase::computeNodalBCsResidualAndJacobian(), FEProblemBase::computeNullSpace(), VectorNodalBC::computeOffDiagJacobian(), ArrayNodalBC::computeOffDiagJacobian(), NodalBC::computeOffDiagJacobian(), NodalKernel::computeOffDiagJacobian(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), ComputeFullJacobianThread::computeOnInterface(), ComputeFullJacobianThread::computeOnInternalFace(), FEProblemBase::computePostCheck(), EqualValueEmbeddedConstraint::computeQpJacobian(), EqualValueEmbeddedConstraint::computeQpOffDiagJacobian(), FVOrthogonalBoundaryDiffusion::computeQpResidual(), FVBoundaryScalarLagrangeMultiplierConstraint::computeResidual(), FVFluxBC::computeResidual(), FVFluxKernel::computeResidual(), FVInterfaceKernel::computeResidual(), Kernel::computeResidualAndJacobian(), NodalBC::computeResidualAndJacobian(), IntegratedBC::computeResidualAndJacobian(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::computeScaling(), Assembly::computeSinglePointMapAD(), FEProblemBase::computeTransposeNullSpace(), DebugResidualAux::computeValue(), NearestNodeValueAux::computeValue(), NonlinearSystemBase::constraintJacobians(), Coupleable::coupled(), FEProblemBase::currentLinearSysNum(), FEProblemBase::currentNlSysNum(), PseudoTimestep::currentResidualNorm(), ComputeResidualThread::determineObjectWarehouses(), ComputeResidualAndJacobianThread::determineObjectWarehouses(), Moose::doDerivatives(), VariableResidual::execute(), NodalNormalsCorner::execute(), GreaterThanLessThanPostprocessor::execute(), NodalNormalsEvaluator::execute(), NodalNormalsPreprocessor::execute(), ComputeLinearFVElementalThread::fetchSystemContributionObjects(), ComputeLinearFVFaceThread::fetchSystemContributionObjects(), ElementSubdomainModifier::finalize(), NumNonlinearIterations::finalize(), BoundsBase::getDoFIndex(), NonlinearSystemBase::getNodeDofs(), SystemBase::getSubdomainsForVar(), NumLinearIterations::getValue(), Residual::getValue(), NumResidualEvaluations::getValue(), Moose::globalDofIndexToDerivative(), LinearFVFluxKernel::hasFaceSide(), LinearFVBoundaryCondition::hasFaceSide(), FVBoundaryCondition::hasFaceSide(), NonlinearSystemBase::initialSetup(), ActivateElementsUserObjectBase::initSolutions(), EigenExecutionerBase::inversePowerIteration(), Kernel::Kernel(), MooseVariableInterface< Real >::MooseVariableInterface(), EigenExecutionerBase::nonlinearSolve(), ComputeDiracThread::onElement(), ComputeNodalKernelBCJacobiansThread::onNode(), ComputeNodalKernelJacobiansThread::onNode(), PointwiseRenormalizeVector::PointwiseRenormalizeVector(), FEProblemBase::prepare(), FEProblemBase::prepareAssembly(), SystemBase::prepareFace(), FEProblemBase::prepareFaceShapes(), FEProblemBase::prepareNeighborShapes(), FEProblemBase::prepareShapes(), EqualValueEmbeddedConstraint::reinitConstraint(), FEProblemBase::reinitDirac(), FEProblemBase::reinitNeighborPhys(), FEProblemBase::reinitOffDiagScalars(), LinearFVFluxKernel::setCurrentFaceInfo(), FEProblemBase::setResidual(), FEProblemBase::setResidualNeighbor(), PhysicsBasedPreconditioner::setup(), FVInterfaceKernel::setupData(), FEProblemSolve::solve(), ActuallyExplicitEuler::solve(), LStableDirk2::solve(), LStableDirk3::solve(), ImplicitMidpoint::solve(), ExplicitTVDRK2::solve(), AStableDirk4::solve(), LStableDirk4::solve(), ExplicitRK2::solve(), ExplicitSSPRungeKutta::solveStage(), NonlinearThread::subdomainChanged(), UserObject::systemNumber(), MultiAppDofCopyTransfer::transferDofObject(), FVFluxBC::uOnGhost(), FVFluxBC::uOnUSub(), and MortarConstraintBase::zeroInactiveLMDofs().

{
  return system().number();
}

nVariables()

unsigned int SystemBase::nVariables ( ) const

virtualinherited

Get the number of variables in this system.

Returns

the number of variables

Definition at line 847 of file SystemBase.C.

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

{
  unsigned int n = nFieldVariables();
  n += _vars[0].scalars().size();

  return n;
}

operator=()

DisplacedSystem& DisplacedSystem::operator= ( DisplacedSystem &&  )

delete

prepare()

void SystemBase::prepare ( THREAD_ID  tid )

virtualinherited

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 252 of file SystemBase.C.

Referenced by SubProblem::reinitElemFaceRef().

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

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 275 of file SystemBase.C.

{
  // We only need to do something if the element prepare was restricted
  if (_subproblem.hasActiveElementalMooseVariables(tid))
  {
    const std::set<MooseVariableFieldBase *> & active_elemental_moose_variables =
        _subproblem.getActiveElementalMooseVariables(tid);

    std::vector<MooseVariableFieldBase *> newly_prepared_vars;

    const std::vector<MooseVariableFieldBase *> & vars = _vars[tid].fieldVariables();
    for (const auto & var : vars)
    {
      mooseAssert(&var->sys() == this,
                  "I will cry if we store variables in our warehouse that don't belong to us");

      // If it wasn't in the active list, we need to prepare it. This has the potential to duplicate
      // prepare if we have these conditions:
      //
      // 1. We have a displaced problem
      // 2. We are using AD
      // 3. We are not using global AD indexing
      //
      // But I think I would rather risk duplicate prepare than introduce an additional member set
      // variable for tracking prepared variables. Set insertion is slow and some simulations have a
      // ton of variables
      if (!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, number()).prepareVariable(var_ptr);
        if (_subproblem.checkNonlocalCouplingRequirement())
          _subproblem.assembly(tid, number()).prepareVariableNonlocal(var_ptr);
      }
  }
}

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 328 of file SystemBase.C.

Referenced by SubProblem::reinitLowerDElem().

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

prepareNeighbor()

void SystemBase::prepareNeighbor ( THREAD_ID  tid )

virtualinherited

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 320 of file SystemBase.C.

Referenced by SubProblem::reinitNeighborFaceRef().

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

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 336 of file SystemBase.C.

{

  if (_subproblem.hasActiveElementalMooseVariables(tid))
  {
    const std::set<MooseVariableFieldBase *> & 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<MooseVariableFieldBase *> & vars = _vars[tid].fieldVariables();
    for (const auto & var : vars)
      var->computeElemValues();
  }
}

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 356 of file SystemBase.C.

Referenced by SubProblem::reinitElemFaceRef().

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

reinitLowerD()

void SystemBase::reinitLowerD ( THREAD_ID  tid )

virtualinherited

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

Definition at line 386 of file SystemBase.C.

Referenced by SubProblem::reinitLowerDElem().

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

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 378 of file SystemBase.C.

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

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 367 of file SystemBase.C.

Referenced by SubProblem::reinitNeighborFaceRef().

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

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 394 of file SystemBase.C.

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

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 406 of file SystemBase.C.

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

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 418 of file SystemBase.C.

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

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 429 of file SystemBase.C.

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

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 440 of file SystemBase.C.

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

removeMatrix()

void SystemBase::removeMatrix ( TagID  tag )

inherited

Removes a matrix with a given tag.

Parameters

tag_name

The name of the tag

Definition at line 586 of file SystemBase.C.

{
  if (!_subproblem.matrixTagExists(tag_id))
    mooseError("Cannot remove the matrix with TagID ",
               tag_id,
               "\nin system '",
               name(),
               "', because that tag does not exist in the problem");

  if (hasMatrix(tag_id))
  {
    const auto matrix_name = _subproblem.matrixTagName(tag_id);
    system().remove_matrix(matrix_name);
    _tagged_matrices[tag_id] = nullptr;
  }
}

removeVector() [1/2]

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

inherited

Remove a vector from the system with the given name.

Definition at line 1287 of file SystemBase.C.

Referenced by SystemBase::restoreOldSolutions().

{
  system().remove_vector(name);
}

removeVector() [2/2]

void SystemBase::removeVector ( TagID  tag_id )

inherited

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

Parameters

tag_id

Tag ID

Definition at line 697 of file SystemBase.C.

{
  if (!_subproblem.vectorTagExists(tag_id))
    mooseError("Cannot remove the vector with TagID ",
               tag_id,
               "\nin system '",
               name(),
               "', because that tag does not exist in the problem");

  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 163 of file DisplacedSystem.h.

  {
    return _undisplaced_system.residualCopy();
  }

residualGhosted()

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

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 167 of file DisplacedSystem.h.

  {
    return _undisplaced_system.residualGhosted();
  }

residualSetup()

void SystemBase::residualSetup ( )

virtualinherited

Reimplemented in NonlinearSystemBase, LinearSystem, and AuxiliarySystem.

Definition at line 1524 of file SystemBase.C.

Referenced by AuxiliarySystem::residualSetup(), and NonlinearSystemBase::residualSetup().

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
    _vars[tid].residualSetup();
}

residualVectorTag()

virtual TagID DisplacedSystem::residualVectorTag ( ) const

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 46 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 538 of file SystemBase.C.

{
  const auto states =
      _solution_states[static_cast<unsigned short>(Moose::SolutionIterationType::Time)].size();
  if (states > 1)
    for (unsigned int i = 1; i <= states - 1; ++i)
      if (_saved_solution_states[i])
      {
        solutionState(i) = *(_saved_solution_states[i]);
        removeVector("save_solution_state_" + std::to_string(i));
        _saved_solution_states[i] = nullptr;
      }

  if (_saved_dot_old && solutionUDotOld())
  {
    *solutionUDotOld() = *_saved_dot_old;
    removeVector("save_solution_dot_old");
    _saved_dot_old = nullptr;
  }
  if (_saved_dotdot_old && solutionUDotDotOld())
  {
    *solutionUDotDotOld() = *_saved_dotdot_old;
    removeVector("save_solution_dotdot_old");
    _saved_dotdot_old = nullptr;
  }
}

restoreSolutions()

void SystemBase::restoreSolutions ( )

virtualinherited

Restore current solutions (call after your solve failed)

Reimplemented in SolverSystem.

Definition at line 1270 of file SystemBase.C.

Referenced by SolverSystem::restoreSolutions().

{
  if (!hasSolutionState(1))
    mooseError("Cannot restore solutions without old solution");

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

saveOldSolutions()

void SystemBase::saveOldSolutions ( )

virtualinherited

Save the old and older solutions.

Definition at line 506 of file SystemBase.C.

{
  const auto states =
      _solution_states[static_cast<unsigned short>(Moose::SolutionIterationType::Time)].size();
  if (states > 1)
  {
    _saved_solution_states.resize(states);
    for (unsigned int i = 1; i <= states - 1; ++i)
      if (!_saved_solution_states[i])
        _saved_solution_states[i] =
            &addVector("save_solution_state_" + std::to_string(i), false, PARALLEL);

    for (unsigned int i = 1; i <= states - 1; ++i)
      *(_saved_solution_states[i]) = solutionState(i);
  }

  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);

  if (solutionUDotOld())
    *_saved_dot_old = *solutionUDotOld();

  if (solutionUDotDotOld())
    *_saved_dotdot_old = *solutionUDotDotOld();
}

serializedSolution()

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

inlineoverridevirtual

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

Reimplemented from SystemBase.

Definition at line 109 of file DisplacedSystem.h.

  {
    return _undisplaced_system.serializedSolution();
  }

setActiveScalarVariableCoupleableVectorTags()

void SystemBase::setActiveScalarVariableCoupleableVectorTags ( const std::set< TagID > &  vtags, THREAD_ID  tid  )

inherited

Set the active vector tags for the scalar variables.

Definition at line 1551 of file SystemBase.C.

Referenced by SubProblem::setActiveScalarVariableCoupleableVectorTags().

{
  _vars[tid].setActiveScalarVariableCoupleableVectorTags(vtags);
}

setActiveVariableCoupleableVectorTags()

void SystemBase::setActiveVariableCoupleableVectorTags ( const std::set< TagID > &  vtags, THREAD_ID  tid  )

inherited

Set the active vector tags for the variables.

Definition at line 1545 of file SystemBase.C.

Referenced by SubProblem::setActiveFEVariableCoupleableVectorTags().

{
  _vars[tid].setActiveVariableCoupleableVectorTags(vtags);
}

setVariableGlobalDoFs()

void SystemBase::setVariableGlobalDoFs ( const std::string &  var_name )

inherited

set all the global dof indices for a variable

Parameters

var_name

The name of the variable

Definition at line 182 of file SystemBase.C.

{
  AllLocalDofIndicesThread aldit(_subproblem, {var_name});
  ConstElemRange & elem_range = *_mesh.getActiveLocalElementRange();
  Threads::parallel_reduce(elem_range, aldit);

  // Gather the dof indices across procs to get all the dof indices for var_name
  aldit.dofIndicesSetUnion();

  const auto & all_dof_indices = aldit.getDofIndices();
  _var_all_dof_indices.assign(all_dof_indices.begin(), all_dof_indices.end());
}

setVerboseFlag()

void SystemBase::setVerboseFlag ( const bool &  verbose )

inlineinherited

Sets the verbose flag.

Parameters

[in]

verbose

Verbose flag

Definition at line 135 of file SystemBase.h.

Referenced by Executioner::Executioner().

{ _verbose = verbose; }

solution() [1/2]

NumericVector<Number>& SystemBase::solution ( )

inlineinherited

Definition at line 182 of file SystemBase.h.

Referenced by Adaptivity::adaptMesh(), TransientMultiApp::appTransferVector(), MooseEigenSystem::combineSystemSolution(), NonlinearSystemBase::computeDamping(), AuxiliarySystem::computeElementalVarsHelper(), NonlinearSystemBase::computeJacobianInternal(), AuxiliarySystem::computeMortarNodalVars(), NonlinearSystemBase::computeNodalBCs(), AuxiliarySystem::computeNodalVarsHelper(), NonlinearSystemBase::computeResidualTags(), AuxiliarySystem::computeScalarVars(), NonlinearSystemBase::constraintResiduals(), SystemBase::copyVars(), MultiAppPostprocessorToAuxScalarTransfer::execute(), MultiAppScalarToAuxScalarTransfer::execute(), NodalNormalsCorner::execute(), NodalNormalsEvaluator::execute(), MultiAppVariableValueSamplePostprocessorTransfer::execute(), NodalNormalsPreprocessor::execute(), NodalNormalsCorner::finalize(), NodalNormalsEvaluator::finalize(), NodalNormalsPreprocessor::finalize(), NodalNormalsEvaluator::initialize(), NodalNormalsCorner::initialize(), NodalNormalsPreprocessor::initialize(), MooseEigenSystem::initSystemSolution(), ComputeMarkerThread::onElement(), ComputeIndicatorThread::onElement(), ComputeUserObjectsThread::onElement(), ComputeNodalUserObjectsThread::onNode(), FEProblemBase::projectInitialConditionOnCustomRange(), FEProblemBase::projectSolution(), Transient::relativeSolutionDifferenceNorm(), SystemBase::restoreSolutions(), SecantSolve::saveVariableValues(), SteffensenSolve::saveVariableValues(), PicardSolve::saveVariableValues(), MooseEigenSystem::scaleSystemSolution(), AuxiliarySystem::serializeSolution(), NonlinearSystemBase::setConstraintSecondaryValues(), NonlinearSystemBase::setInitialSolution(), solutionInternal(), NonlinearEigenSystem::solve(), MultiAppDofCopyTransfer::transfer(), SteffensenSolve::transformVariables(), SecantSolve::transformVariables(), PicardSolve::transformVariables(), AuxiliarySystem::variableWiseRelativeSolutionDifferenceNorm(), and SystemBase::zeroVariables().

{ return solutionState(0); }

solution() [2/2]

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

inlineinherited

Definition at line 185 of file SystemBase.h.

{ return solutionState(0); }

solutionInternal()

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

inlineoverrideprotectedvirtual

Internal getter for solution owned by libMesh.

Implements SystemBase.

Definition at line 258 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solution();
  }

solutionOld() [1/2]

NumericVector<Number>& SystemBase::solutionOld ( )

inlineinherited

Definition at line 183 of file SystemBase.h.

Referenced by MooseEigenSystem::combineSystemSolution(), CentralDifference::computeTimeDerivatives(), NonlinearSystemBase::constraintResiduals(), ActivateElementsUserObjectBase::initSolutions(), MooseEigenSystem::initSystemSolutionOld(), MooseVariableScalar::reinit(), Transient::relativeSolutionDifferenceNorm(), SystemBase::restoreSolutions(), ElementSubdomainModifier::setOldAndOlderSolutionsForMovedNodes(), ActuallyExplicitEuler::solve(), AdamsPredictor::timestepSetup(), and AuxiliarySystem::variableWiseRelativeSolutionDifferenceNorm().

{ return solutionState(1); }

solutionOld() [2/2]

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

inlineinherited

Definition at line 186 of file SystemBase.h.

{ return solutionState(1); }

solutionOlder() [1/2]

NumericVector<Number>& SystemBase::solutionOlder ( )

inlineinherited

Definition at line 184 of file SystemBase.h.

Referenced by MooseEigenSystem::combineSystemSolution(), CentralDifference::computeTimeDerivatives(), ActivateElementsUserObjectBase::initSolutions(), MooseVariableScalar::reinit(), and ElementSubdomainModifier::setOldAndOlderSolutionsForMovedNodes().

{ return solutionState(2); }

solutionOlder() [2/2]

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

inlineinherited

Definition at line 187 of file SystemBase.h.

{ return solutionState(2); }

solutionPreviousNewton() [1/2]

NumericVector<Number>* DisplacedSystem::solutionPreviousNewton ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 119 of file DisplacedSystem.h.

{ return nullptr; }

solutionPreviousNewton() [2/2]

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

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 120 of file DisplacedSystem.h.

{ return nullptr; }

solutionState() [1/2]

NumericVector< Number > & DisplacedSystem::solutionState ( const unsigned int  state, Moose::SolutionIterationType  iteration_type = Moose::SolutionIterationType::Time  )

inlineoverridevirtual

Get a state of the solution (0 = current, 1 = old, 2 = older, etc).

If the state does not exist, it will be initialized in addition to any newer states before it that have not been initialized.

Reimplemented from SystemBase.

Definition at line 274 of file DisplacedSystem.h.

{
  return _undisplaced_system.solutionState(state, iteration_type);
}

solutionState() [2/2]

const NumericVector< Number > & DisplacedSystem::solutionState ( const unsigned int  state, Moose::SolutionIterationType  iteration_type = Moose::SolutionIterationType::Time  ) const

inlineoverridevirtual

Get a state of the solution (0 = current, 1 = old, 2 = older, etc).

Reimplemented from SystemBase.

Definition at line 281 of file DisplacedSystem.h.

{
  return _undisplaced_system.solutionState(state, iteration_type);
}

solutionStatesInitialized()

bool SystemBase::solutionStatesInitialized ( ) const

inlineinherited

Whether or not the solution states have been initialized via initSolutionState()

After the solution states have been initialized, additional solution states cannot be added.

Definition at line 898 of file SystemBase.h.

Referenced by ScalarKernelBase::uOld(), and AuxScalarKernel::uOld().

{ return _solution_states_initialized; }

solutionUDot() [1/2]

NumericVector<Number>* DisplacedSystem::solutionUDot ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 122 of file DisplacedSystem.h.

{ return _undisplaced_system.solutionUDot(); }

solutionUDot() [2/2]

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

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 135 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDot();
  }

solutionUDotDot() [1/2]

NumericVector<Number>* DisplacedSystem::solutionUDotDot ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 123 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotDot();
  }

solutionUDotDot() [2/2]

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

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 139 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotDot();
  }

solutionUDotDotOld() [1/2]

NumericVector<Number>* DisplacedSystem::solutionUDotDotOld ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 131 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotDotOld();
  }

solutionUDotDotOld() [2/2]

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

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 147 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotDotOld();
  }

solutionUDotOld() [1/2]

NumericVector<Number>* DisplacedSystem::solutionUDotOld ( )

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 127 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotOld();
  }

solutionUDotOld() [2/2]

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

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 143 of file DisplacedSystem.h.

  {
    return _undisplaced_system.solutionUDotOld();
  }

solve()

void SystemBase::solve ( )

virtualinherited

Solve the system (using libMesh magic)

Reimplemented in NonlinearSystemBase, LinearSystem, NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

Definition at line 1225 of file SystemBase.C.

{
  system().solve();
}

subdomainSetup()

void SystemBase::subdomainSetup ( )

virtualinherited

Reimplemented in AuxiliarySystem.

Definition at line 1517 of file SystemBase.C.

Referenced by AuxiliarySystem::subdomainSetup(), and NonlinearSystemBase::subdomainSetup().

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
    _vars[tid].subdomainSetup();
}

subproblem() [1/2]

SubProblem& SystemBase::subproblem ( )

inlineinherited

Definition at line 102 of file SystemBase.h.

Referenced by CreateDisplacedProblemAction::addProxyRelationshipManagers(), MooseVariableBase::allDofIndices(), NonlinearSystemBase::constraintJacobians(), NonlinearSystemBase::constraintResiduals(), Moose::globalDofIndexToDerivative(), NonlinearSystemBase::initialSetup(), MooseVariableScalar::MooseVariableScalar(), NonlinearSystemBase::overwriteNodeFace(), MooseVariableScalar::reinit(), NonlinearSystemBase::reinitNodeFace(), and NonlinearSystemBase::setConstraintSecondaryValues().

{ return _subproblem; }

subproblem() [2/2]

const SubProblem& SystemBase::subproblem ( ) const

inlineinherited

Definition at line 103 of file SystemBase.h.

{ return _subproblem; }

sys()

virtual TransientExplicitSystem& DisplacedSystem::sys ( )

inlinevirtual

Definition at line 247 of file DisplacedSystem.h.

{ return _sys; }

system() [1/2]

System & DisplacedSystem::system ( )

overridevirtual

Get the reference to the libMesh system.

Implements SystemBase.

Definition at line 62 of file DisplacedSystem.C.

{
  return _sys;
}

system() [2/2]

const System & DisplacedSystem::system ( ) const

overridevirtual

Implements SystemBase.

Definition at line 68 of file DisplacedSystem.C.

{
  return _sys;
}

systemMatrixTag()

virtual TagID DisplacedSystem::systemMatrixTag ( ) const

inlineoverridevirtual

Return the Matrix Tag ID for System.

Reimplemented from SystemBase.

Definition at line 51 of file DisplacedSystem.h.

{ return _undisplaced_system.systemMatrixTag(); }

timestepSetup()

void SystemBase::timestepSetup ( )

virtualinherited

Reimplemented in NonlinearSystemBase, and AuxiliarySystem.

Definition at line 1503 of file SystemBase.C.

Referenced by AuxiliarySystem::timestepSetup(), and NonlinearSystemBase::timestepSetup().

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
    _vars[tid].timestepSetup();
}

timeVectorTag()

virtual TagID DisplacedSystem::timeVectorTag ( ) const

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 53 of file DisplacedSystem.h.

{ return _undisplaced_system.timeVectorTag(); }

update()

void SystemBase::update ( bool  update_libmesh_system = true )

virtualinherited

Update the system (doing libMesh magic)

Definition at line 1218 of file SystemBase.C.

Referenced by Adaptivity::adaptMesh(), MooseEigenSystem::combineSystemSolution(), NonlinearSystemBase::computeDamping(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeResidualTags(), EigenProblem::doFreeNonlinearPowerIterations(), PointwiseRenormalizeVector::finalize(), MooseEigenSystem::initSystemSolution(), MooseEigenSystem::initSystemSolutionOld(), MooseEigenSystem::scaleSystemSolution(), NonlinearSystemBase::setConstraintSecondaryValues(), NonlinearSystemBase::setInitialSolution(), EigenProblem::solve(), FEProblemBase::solve(), DisplacedProblem::syncSolutions(), MultiAppDofCopyTransfer::transfer(), SteffensenSolve::transformVariables(), SecantSolve::transformVariables(), and PicardSolve::transformVariables().

{
  if (update_libmesh_system)
    system().update();
}

varKind()

Moose::VarKindType SystemBase::varKind ( ) const

inlineinherited

Returns

the type of variables this system holds, e.g. nonlinear or auxiliary

Definition at line 926 of file SystemBase.h.

Referenced by Coupleable::coupled(), and UserObject::UserObject().

{ return _var_kind; }

zeroTaggedVector()

void SystemBase::zeroTaggedVector ( const TagID  tag )

inherited

Zero vector with the given tag.

Definition at line 671 of file SystemBase.C.

Referenced by SystemBase::zeroTaggedVectors().

{
  if (!_subproblem.vectorTagExists(tag))
    mooseError("Cannot zero vector with TagID ",
               tag,
               " in system '",
               name(),
               "' because that tag does not exist in the problem");
  else if (!hasVector(tag))
    mooseError("Cannot zero vector tag with name '",
               _subproblem.vectorTagName(tag),
               "' in system '",
               name(),
               "' because there is no vector associated with that tag");

  getVector(tag).zero();
}

zeroTaggedVectors()

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

inherited

Zero all vectors for given tags.

Definition at line 690 of file SystemBase.C.

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

{
  for (const auto tag : tags)
    zeroTaggedVector(tag);
}

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 208 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 231 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 225 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_residual);
}

Member Data Documentation

_app

MooseApp& SystemBase::_app

protectedinherited

Definition at line 956 of file SystemBase.h.

Referenced by SolverSystem::checkInvalidSolution(), NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeJacobianTags(), LinearSystem::computeLinearSystemInternal(), LinearSystem::computeLinearSystemTags(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::jacobianSetup(), NonlinearSystemBase::residualSetup(), NonlinearSystemBase::shouldEvaluatePreSMOResidual(), and NonlinearSystem::solve().

_automatic_scaling

bool SystemBase::_automatic_scaling

protectedinherited

Whether to automatically scale the variables.

Definition at line 1019 of file SystemBase.h.

Referenced by SystemBase::automaticScaling(), NonlinearSystem::init(), NonlinearSystemBase::initialSetup(), and NonlinearSystemBase::preSolve().

_console

const ConsoleStream ConsoleStreamInterface::_console

inherited

An instance of helper class to write streams to the Console objects.

Definition at line 31 of file ConsoleStreamInterface.h.

Referenced by IterationAdaptiveDT::acceptStep(), MeshOnlyAction::act(), SetupDebugAction::act(), MaterialOutputAction::act(), Adaptivity::adaptMesh(), FEProblemBase::adaptMesh(), PerfGraph::addToExecutionList(), SimplePredictor::apply(), SystemBase::applyScalingFactors(), MultiApp::backup(), FEProblemBase::backupMultiApps(), CoarsenedPiecewiseLinear::buildCoarsenedGrid(), MeshDiagnosticsGenerator::checkElementOverlap(), MeshDiagnosticsGenerator::checkElementTypes(), MeshDiagnosticsGenerator::checkElementVolumes(), FEProblemBase::checkExceptionAndStopSolve(), SolverSystem::checkInvalidSolution(), MeshDiagnosticsGenerator::checkLocalJacobians(), MeshDiagnosticsGenerator::checkNonConformalMesh(), MeshDiagnosticsGenerator::checkNonConformalMeshFromAdaptivity(), MeshDiagnosticsGenerator::checkNonPlanarSides(), FEProblemBase::checkProblemIntegrity(), ReferenceResidualProblem::checkRelativeConvergence(), MeshDiagnosticsGenerator::checkSidesetsOrientation(), IterationAdaptiveDT::computeAdaptiveDT(), Transient::computeConstrainedDT(), FixedPointSolve::computeCustomConvergencePostprocessor(), NonlinearSystemBase::computeDamping(), IterationAdaptiveDT::computeDT(), IterationAdaptiveDT::computeFailedDT(), IterationAdaptiveDT::computeInitialDT(), IterationAdaptiveDT::computeInterpolationDT(), FEProblemBase::computeLinearSystemTags(), NonlinearSystemBase::computeScaling(), Problem::console(), IterationAdaptiveDT::constrainStep(), TimeStepper::constrainStep(), MultiApp::createApp(), FEProblemBase::execMultiApps(), FEProblemBase::execMultiAppTransfers(), MessageFromInput::execute(), Steady::execute(), Eigenvalue::execute(), ActionWarehouse::executeActionsWithAction(), ActionWarehouse::executeAllActions(), ElementQualityChecker::finalize(), FEProblemBase::finishMultiAppStep(), MeshRepairGenerator::fixOverlappingNodes(), CoarsenBlockGenerator::generate(), MeshGenerator::generateInternal(), VariableCondensationPreconditioner::getDofToCondense(), InversePowerMethod::init(), NonlinearEigen::init(), FEProblemBase::initialAdaptMesh(), EigenExecutionerBase::inversePowerIteration(), FEProblemBase::joinAndFinalize(), Transient::keepGoing(), IterationAdaptiveDT::limitDTByFunction(), IterationAdaptiveDT::limitDTToPostprocessorValue(), FEProblemBase::logAdd(), EigenExecutionerBase::makeBXConsistent(), Console::meshChanged(), MooseBaseErrorInterface::mooseDeprecated(), MooseBaseErrorInterface::mooseInfo(), MooseBaseErrorInterface::mooseWarning(), MooseBaseErrorInterface::mooseWarningNonPrefixed(), ReferenceResidualProblem::nonlinearConvergenceSetup(), ReporterDebugOutput::output(), PerfGraphOutput::output(), MaterialPropertyDebugOutput::output(), DOFMapOutput::output(), VariableResidualNormsDebugOutput::output(), Console::output(), ControlOutput::outputActiveObjects(), ControlOutput::outputChangedControls(), ControlOutput::outputControls(), Console::outputInput(), Console::outputPostprocessors(), PseudoTimestep::outputPseudoTimestep(), Console::outputReporters(), Console::outputScalarVariables(), Console::outputSystemInformation(), FEProblemBase::possiblyRebuildGeomSearchPatches(), EigenExecutionerBase::postExecute(), AB2PredictorCorrector::postSolve(), ActionWarehouse::printActionDependencySets(), SolutionInvalidity::printDebug(), EigenExecutionerBase::printEigenvalue(), SecantSolve::printFixedPointConvergenceHistory(), SteffensenSolve::printFixedPointConvergenceHistory(), PicardSolve::printFixedPointConvergenceHistory(), FixedPointSolve::printFixedPointConvergenceReason(), PerfGraphLivePrint::printLiveMessage(), MaterialPropertyDebugOutput::printMaterialMap(), PerfGraphLivePrint::printStats(), AutomaticMortarGeneration::projectPrimaryNodesSinglePair(), AutomaticMortarGeneration::projectSecondaryNodesSinglePair(), CoarsenBlockGenerator::recursiveCoarsen(), SolutionTimeAdaptiveDT::rejectStep(), MultiApp::restore(), FEProblemBase::restoreMultiApps(), NonlinearSystemBase::setInitialSolution(), Checkpoint::shouldOutput(), SubProblem::showFunctorRequestors(), SubProblem::showFunctors(), FullSolveMultiApp::showStatusMessage(), FEProblemSolve::solve(), FixedPointSolve::solve(), NonlinearSystem::solve(), EigenProblem::solve(), LStableDirk2::solve(), LStableDirk3::solve(), ImplicitMidpoint::solve(), ExplicitTVDRK2::solve(), LStableDirk4::solve(), AStableDirk4::solve(), ExplicitRK2::solve(), TransientMultiApp::solveStep(), FixedPointSolve::solveStep(), PerfGraphLivePrint::start(), AB2PredictorCorrector::step(), NonlinearEigen::takeStep(), Transient::takeStep(), Console::writeTimestepInformation(), Console::writeVariableNorms(), and FEProblemBase::~FEProblemBase().

_du_dot_du

Real SystemBase::_du_dot_du

protectedinherited

Definition at line 983 of file SystemBase.h.

Referenced by SystemBase::duDotDu().

_du_dotdot_du

Real SystemBase::_du_dotdot_du

protectedinherited

Definition at line 984 of file SystemBase.h.

Referenced by SystemBase::duDotDotDu().

_factory

Factory& SystemBase::_factory

protectedinherited

Definition at line 957 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().

_fe_problem

FEProblemBase& SystemBase::_fe_problem

protectedinherited

the governing finite element/volume problem

Definition at line 954 of file SystemBase.h.

Referenced by SystemBase::addDotVectors(), NonlinearSystemBase::assembleScalingVector(), NonlinearSystemBase::augmentSparsity(), AuxiliarySystem::AuxiliarySystem(), SolverSystem::checkInvalidSolution(), NonlinearSystemBase::checkKernelCoverage(), AuxiliarySystem::clearScalarVariableCoupleableTags(), SolverSystem::compute(), AuxiliarySystem::compute(), NonlinearSystemBase::computeDamping(), NonlinearSystemBase::computeDiracContributions(), AuxiliarySystem::computeElementalVarsHelper(), LinearSystem::computeGradients(), NonlinearSystemBase::computeJacobian(), NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), LinearSystem::computeLinearSystemTags(), AuxiliarySystem::computeMortarNodalVars(), NonlinearSystemBase::computeNodalBCs(), NonlinearSystemBase::computeNodalBCsResidualAndJacobian(), AuxiliarySystem::computeNodalVarsHelper(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::computeScalarKernelsJacobians(), AuxiliarySystem::computeScalarVars(), NonlinearSystemBase::computeScaling(), NonlinearSystem::computeScalingJacobian(), NonlinearSystem::computeScalingResidual(), NonlinearSystemBase::constraintJacobians(), NonlinearSystemBase::constraintResiduals(), NonlinearSystem::converged(), NonlinearSystemBase::customSetup(), MooseEigenSystem::eigenKernelOnCurrent(), MooseEigenSystem::eigenKernelOnOld(), NonlinearSystemBase::enforceNodalConstraintsJacobian(), NonlinearSystemBase::enforceNodalConstraintsResidual(), SystemBase::feProblem(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), NonlinearSystemBase::init(), NonlinearSystemBase::initialSetup(), NonlinearSystemBase::jacobianSetup(), LinearSystem::LinearSystem(), NonlinearSystemBase::NonlinearSystemBase(), NonlinearSystemBase::overwriteNodeFace(), NonlinearSystemBase::reinitNodeFace(), NonlinearSystem::residualAndJacobianTogether(), NonlinearSystemBase::residualSetup(), NonlinearSystemBase::setConstraintSecondaryValues(), NonlinearSystemBase::setInitialSolution(), AuxiliarySystem::setScalarVariableCoupleableTags(), NonlinearSystemBase::shouldEvaluatePreSMOResidual(), NonlinearSystem::solve(), and NonlinearSystemBase::timestepSetup().

_matrix_tag_active_flags

std::vector<bool> SystemBase::_matrix_tag_active_flags

protectedinherited

Active flags for tagged matrices.

Definition at line 991 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 1007 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 1010 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 968 of file SystemBase.h.

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

_mesh

MooseMesh& SystemBase::_mesh

protectedinherited

Definition at line 959 of file SystemBase.h.

Referenced by SystemBase::addVariable(), NonlinearSystemBase::assembleScalingVector(), SystemBase::augmentSendList(), NonlinearSystemBase::checkKernelCoverage(), NonlinearSystemBase::computeDamping(), AuxiliarySystem::computeElementalVarsHelper(), NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianInternal(), AuxiliarySystem::computeMortarNodalVars(), NonlinearSystemBase::computeNodalBCs(), NonlinearSystemBase::computeNodalBCsResidualAndJacobian(), AuxiliarySystem::computeNodalVarsHelper(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::constraintJacobians(), NonlinearSystemBase::constraintResiduals(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), NonlinearSystemBase::getNodeDofs(), SystemBase::initialSetup(), SystemBase::mesh(), NonlinearSystemBase::overwriteNodeFace(), NonlinearSystemBase::reinitNodeFace(), NonlinearSystemBase::setConstraintSecondaryValues(), NonlinearSystemBase::setInitialSolution(), SystemBase::setVariableGlobalDoFs(), AuxiliarySystem::variableWiseRelativeSolutionDifferenceNorm(), and SystemBase::zeroVariables().

_name

std::string SystemBase::_name

protectedinherited

The name of this system.

Definition at line 961 of file SystemBase.h.

_numbered_vars

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

protectedinherited

Map variable number to its pointer.

Definition at line 1016 of file SystemBase.h.

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

_raw_grad_container

std::vector<std::unique_ptr<NumericVector<Number> > > SystemBase::_raw_grad_container

protectedinherited

A cache for storing gradients at dof locations.

We store it on the system because we create copies of variables on each thread and that would lead to increased data duplication when using threading-based parallelism.

Definition at line 1037 of file SystemBase.h.

Referenced by LinearSystem::computeGradients(), SystemBase::gradientContainer(), and SystemBase::initialSetup().

_saved_dot_old

NumericVector<Real>* SystemBase::_saved_dot_old

protectedinherited

Definition at line 998 of file SystemBase.h.

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

_saved_dotdot_old

NumericVector<Real>* SystemBase::_saved_dotdot_old

protectedinherited

Definition at line 999 of file SystemBase.h.

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

_saved_old

NumericVector<Real>* SystemBase::_saved_old

protectedinherited

Definition at line 994 of file SystemBase.h.

_saved_older

NumericVector<Real>* SystemBase::_saved_older

protectedinherited

Definition at line 995 of file SystemBase.h.

_serialized_solution

std::unique_ptr<NumericVector<Number> > SystemBase::_serialized_solution

protectedinherited

Serialized version of the solution vector, or nullptr if a serialized solution is not needed.

Definition at line 1032 of file SystemBase.h.

Referenced by AuxiliarySystem::compute(), SolverSystem::init(), SystemBase::serializedSolution(), SolverSystem::serializeSolution(), AuxiliarySystem::serializeSolution(), and SolverSystem::setSolution().

_solution_states_initialized

bool SystemBase::_solution_states_initialized

protectedinherited

Whether or not the solution states have been initialized.

Definition at line 1025 of file SystemBase.h.

Referenced by SystemBase::initSolutionState(), and SystemBase::solutionStatesInitialized().

_subproblem

SubProblem& SystemBase::_subproblem

protectedinherited

The subproblem for whom this class holds variable data, etc; this can either be the governing finite element/volume problem or a subjugate displaced problem.

Definition at line 951 of file SystemBase.h.

Referenced by SystemBase::activeAllMatrixTags(), SystemBase::activeMatrixTag(), SystemBase::addMatrix(), SystemBase::addScalingVector(), SystemBase::addVariable(), SystemBase::addVector(), SystemBase::associateMatrixToTag(), SystemBase::associateVectorToTag(), SystemBase::augmentSendList(), SystemBase::closeTaggedVector(), SystemBase::computingScalingJacobian(), SystemBase::copyVars(), SystemBase::deactiveAllMatrixTags(), SystemBase::deactiveMatrixTag(), SystemBase::disassociateDefaultMatrixTags(), SystemBase::disassociateDefaultVectorTags(), SystemBase::disassociateMatrixFromTag(), SystemBase::disassociateVectorFromTag(), SystemBase::getMatrix(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), SystemBase::getVector(), SystemBase::matrixTagActive(), SystemBase::needSolutionState(), SystemBase::prepare(), SystemBase::prepareFace(), SystemBase::reinitElem(), SystemBase::removeMatrix(), SystemBase::removeVector(), NonlinearSystemBase::residualGhosted(), SolverSystem::setSolution(), SystemBase::setVariableGlobalDoFs(), SystemBase::subproblem(), SystemBase::zeroTaggedVector(), and SystemBase::zeroVariables().

_sys

TransientExplicitSystem& DisplacedSystem::_sys

protected

Definition at line 264 of file DisplacedSystem.h.

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

_tagged_matrices

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

protectedinherited

Tagged matrices (pointer)

Definition at line 989 of file SystemBase.h.

Referenced by SystemBase::associateMatrixToTag(), SystemBase::disassociateMatrixFromTag(), SystemBase::getMatrix(), SystemBase::hasMatrix(), and SystemBase::removeMatrix().

_tagged_vectors

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

protectedinherited

Tagged vectors (pointer)

Definition at line 987 of file SystemBase.h.

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

_time_integrator

std::shared_ptr<TimeIntegrator> SystemBase::_time_integrator

protectedinherited

Time integrator.

Definition at line 1013 of file SystemBase.h.

Referenced by AuxiliarySystem::addTimeIntegrator(), NonlinearSystemBase::addTimeIntegrator(), addTimeIntegrator(), SolverSystem::compute(), AuxiliarySystem::compute(), NonlinearSystemBase::computeResidualAndJacobianTags(), NonlinearSystemBase::computeResidualTags(), SystemBase::getSharedTimeIntegrator(), SystemBase::getTimeIntegrator(), NonlinearSystemBase::onTimestepBegin(), NonlinearSystem::solve(), and NonlinearEigenSystem::solve().

_u_dot

NumericVector<Number>* SystemBase::_u_dot

protectedinherited

solution vector for u^dot

Definition at line 974 of file SystemBase.h.

Referenced by SystemBase::addDotVectors(), NonlinearSystemBase::setSolutionUDot(), and SystemBase::solutionUDot().

_u_dot_old

NumericVector<Number>* SystemBase::_u_dot_old

protectedinherited

old solution vector for u^dot

Definition at line 979 of file SystemBase.h.

Referenced by SystemBase::addDotVectors(), NonlinearSystemBase::setSolutionUDotOld(), and SystemBase::solutionUDotOld().

_u_dotdot

NumericVector<Number>* SystemBase::_u_dotdot

protectedinherited

solution vector for u^dotdot

Definition at line 976 of file SystemBase.h.

Referenced by SystemBase::addDotVectors(), NonlinearSystemBase::setSolutionUDotDot(), and SystemBase::solutionUDotDot().

_u_dotdot_old

NumericVector<Number>* SystemBase::_u_dotdot_old

protectedinherited

old solution vector for u^dotdot

Definition at line 981 of file SystemBase.h.

Referenced by SystemBase::addDotVectors(), NonlinearSystemBase::setSolutionUDotDotOld(), and SystemBase::solutionUDotDotOld().

_undisplaced_system

SystemBase& DisplacedSystem::_undisplaced_system

protected

Definition at line 263 of file DisplacedSystem.h.

Referenced by addDotVectors(), addVariableToZeroOnJacobian(), addVariableToZeroOnResidual(), associateMatrixToTag(), associateVectorToTag(), augmentSendList(), currentSolution(), defaultMatrixTags(), defaultVectorTags(), disassociateDefaultMatrixTags(), disassociateDefaultVectorTags(), disassociateMatrixFromTag(), disassociateVectorFromTag(), duDotDotDu(), duDotDu(), getMatrix(), getVector(), hasMatrix(), hasSolutionState(), hasVector(), initSolutionState(), needSolutionState(), nonTimeVectorTag(), residualCopy(), residualGhosted(), residualVectorTag(), serializedSolution(), solutionInternal(), solutionState(), solutionUDot(), solutionUDotDot(), solutionUDotDotOld(), solutionUDotOld(), systemMatrixTag(), timeVectorTag(), and zeroVariables().

_var_all_dof_indices

std::vector<dof_id_type> SystemBase::_var_all_dof_indices

protectedinherited

Container for the dof indices of a given variable.

Definition at line 1028 of file SystemBase.h.

Referenced by SystemBase::getVariableGlobalDoFs(), and SystemBase::setVariableGlobalDoFs().

_var_kind

Moose::VarKindType SystemBase::_var_kind

protectedinherited

default kind of variables in this system

Definition at line 1002 of file SystemBase.h.

Referenced by SystemBase::varKind().

_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 966 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 1004 of file SystemBase.h.

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

_vars

std::vector<VariableWarehouse> SystemBase::_vars

protectedinherited

Variable warehouses (one for each thread)

Definition at line 964 of file SystemBase.h.

Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addInterfaceKernel(), AuxiliarySystem::addVariable(), SystemBase::addVariable(), SystemBase::applyScalingFactors(), NonlinearSystemBase::assembleScalingVector(), SystemBase::clearAllDofIndices(), AuxiliarySystem::compute(), SystemBase::customSetup(), SystemBase::getActualFieldVariable(), SystemBase::getFieldVariable(), SystemBase::getFVVariable(), AuxiliarySystem::getMinQuadratureOrder(), SystemBase::getMinQuadratureOrder(), SystemBase::getScalarVariable(), SystemBase::getScalarVariables(), SystemBase::getVariable(), SystemBase::getVariableNames(), SystemBase::getVariables(), LinearSystem::initialSetup(), SystemBase::initialSetup(), SystemBase::jacobianSetup(), SystemBase::nFieldVariables(), SystemBase::nFVVariables(), 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(), SystemBase::reinitScalars(), SystemBase::residualSetup(), SystemBase::setActiveScalarVariableCoupleableVectorTags(), SystemBase::setActiveVariableCoupleableVectorTags(), NonlinearSystemBase::setupScalingData(), SystemBase::subdomainSetup(), and SystemBase::timestepSetup().

_vars_to_be_zeroed_on_jacobian

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

protectedinherited

Definition at line 971 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 970 of file SystemBase.h.

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

_verbose

bool SystemBase::_verbose

protectedinherited

True if printing out additional information.

Definition at line 1022 of file SystemBase.h.

Referenced by SystemBase::applyScalingFactors(), and SystemBase::setVerboseFlag().

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

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