SystemBase Class Reference

Base class for a system (of equations) More...

#include <SystemBase.h>

Inheritance diagram for SystemBase:

Public Member Functions
	SystemBase (SubProblem &subproblem, FEProblemBase &fe_problem, const std::string &name, Moose::VarKindType var_kind)
virtual	~SystemBase ()
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 libMesh::DofMap &	dofMap ()
	Gets writeable reference to the dof map. More...
virtual const libMesh::DofMap &	dofMap () const
	Gets const reference to the dof map. More...
virtual libMesh::System &	system ()=0
	Get the reference to the libMesh system. More...
virtual const libMesh::System &	system () const =0
virtual void	preInit ()
	This is called prior to the libMesh system has been init'd. More...
virtual void	postInit ()
virtual void	reinit ()
	Reinitialize the system when the degrees of freedom in this system have changed. More...
virtual void	initializeObjects ()
	Called only once, just before the solve begins so objects can do some precalculations. More...
void	update ()
	Update the system (doing libMesh magic) More...
virtual void	solve ()
	Solve the system (using libMesh magic) More...
virtual void	copyOldSolutions ()
	Shifts the solutions backwards in time. More...
virtual void	copyPreviousNonlinearSolutions ()
	Shifts the solutions backwards in nonlinear iteration history. More...
virtual void	copyPreviousFixedPointSolutions ()
virtual void	restoreSolutions ()
	Restore current solutions (call after your solve failed) More...
virtual const NumericVector< Number > *const &	currentSolution () const =0
	The solution vector that is currently being operated on. More...
NumericVector< Number > &	solution ()
NumericVector< Number > &	solutionOld ()
NumericVector< Number > &	solutionOlder ()
const NumericVector< Number > &	solution () const
const NumericVector< Number > &	solutionOld () const
const NumericVector< Number > &	solutionOlder () const
virtual const NumericVector< Number > *	solutionPreviousNewton () const
virtual NumericVector< Number > *	solutionPreviousNewton ()
virtual void	initSolutionState ()
	Initializes the solution state. More...
virtual NumericVector< Number > &	solutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time)
	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
	Get a state of the solution (0 = current, 1 = old, 2 = older, etc). More...
libMesh::ParallelType	solutionStateParallelType (const unsigned int state, const Moose::SolutionIterationType iteration_type) const
	Returns the parallel type of the given solution state. More...
virtual void	needSolutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time, libMesh::ParallelType parallel_type=GHOSTED)
	Registers that the solution state state is needed. More...
virtual bool	hasSolutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time) const
	Whether or not the system has the solution state (0 = current, 1 = old, 2 = older, etc). More...
virtual void	addDotVectors ()
	Add u_dot, u_dotdot, u_dot_old and u_dotdot_old vectors if requested by the time integrator. More...
virtual std::vector< Number > &	duDotDus ()
virtual Number &	duDotDotDu ()
virtual const Number &	duDotDu (unsigned int var_num=0) const
virtual const Number &	duDotDotDu () const
virtual NumericVector< Number > *	solutionUDot ()
virtual NumericVector< Number > *	solutionUDotDot ()
virtual NumericVector< Number > *	solutionUDotOld ()
virtual NumericVector< Number > *	solutionUDotDotOld ()
virtual const NumericVector< Number > *	solutionUDot () const
virtual const NumericVector< Number > *	solutionUDotDot () const
virtual const NumericVector< Number > *	solutionUDotOld () const
virtual const NumericVector< Number > *	solutionUDotDotOld () 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 bool	hasVector (TagID tag_id) const
	Check if the tagged vector exists in the system. More...
virtual TagID	timeVectorTag () const
	Ideally, we should not need this API. More...
virtual TagID	systemMatrixTag () const
	Return the Matrix Tag ID for System. More...
virtual TagID	nonTimeVectorTag () const
virtual TagID	residualVectorTag () const
virtual std::set< TagID >	defaultVectorTags () const
	Get the default vector tags associated with this system. More...
virtual std::set< TagID >	defaultMatrixTags () const
	Get the default matrix tags associted with this system. More...
virtual void	associateVectorToTag (NumericVector< Number > &vec, TagID tag)
	Associate a vector for a given tag. More...
virtual void	disassociateVectorFromTag (NumericVector< Number > &vec, TagID tag)
	Disassociate a given vector from a given tag. More...
virtual void	disassociateVectorFromTag (TagID tag)
	Disassociate any vector that is associated with a given tag. More...
virtual void	disassociateDefaultVectorTags ()
	Disassociate the vectors associated with the default vector tags of this system. More...
virtual bool	hasMatrix (TagID tag) const
	Check if the tagged matrix exists in the system. More...
virtual libMesh::SparseMatrix< Number > &	getMatrix (TagID tag)
	Get a raw SparseMatrix. More...
virtual const libMesh::SparseMatrix< Number > &	getMatrix (TagID tag) const
	Get a raw SparseMatrix. More...
virtual void	activateAllMatrixTags ()
	Make all existing matrices active. More...
virtual bool	matrixTagActive (TagID tag) const
	If or not a matrix tag is active. More...
virtual void	deactivateAllMatrixTags ()
	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	associateMatrixToTag (libMesh::SparseMatrix< Number > &matrix, TagID tag)
	Associate a matrix to a tag. More...
virtual void	disassociateMatrixFromTag (libMesh::SparseMatrix< Number > &matrix, TagID tag)
	Disassociate a matrix from a tag. More...
virtual void	disassociateMatrixFromTag (TagID tag)
	Disassociate any matrix that is associated with a given tag. More...
virtual void	disassociateDefaultMatrixTags ()
	Disassociate the matrices associated with the default matrix tags of this system. More...
virtual NumericVector< Number > &	serializedSolution ()
	Returns a reference to a serialized version of the solution vector for this subproblem. More...
virtual NumericVector< Number > &	residualCopy ()
virtual NumericVector< Number > &	residualGhosted ()
virtual void	augmentSendList (std::vector< dof_id_type > &send_list)
	Will modify the send_list to add all of the extra ghosted dofs for this system. More...
virtual void	augmentSparsity (libMesh::SparsityPattern::Graph &sparsity, std::vector< dof_id_type > &n_nz, std::vector< dof_id_type > &n_oz)=0
	Will modify the sparsity pattern to add logical geometric connections. 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 >
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 >
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, 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	addVariableToZeroOnResidual (std::string var_name)
	Adds this variable to the list of variables to be zeroed during each residual evaluation. More...
virtual void	addVariableToZeroOnJacobian (std::string var_name)
	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)
	Zero out the solution for the list of variables passed in. 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 libMesh::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, THREAD_ID tid)
	Reinit assembly info for a side of an element. More...
virtual void	reinitNeighborFace (const Elem *elem, unsigned int side, 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...
NumericVector< Number > &	addVector (const std::string &vector_name, const bool project, const libMesh::ParallelType type)
	Adds a solution length vector to the system. More...
NumericVector< Number > &	addVector (TagID tag, const bool project, const libMesh::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	removeVector (TagID tag_id)
	Remove a solution length vector from the system with the specified TagID. 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...
libMesh::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 (libMesh::ExodusII_IO &io)
virtual void	copySolutionsBackwards ()
	Copy current solution into old and older. More...
void	addTimeIntegrator (const std::string &type, const std::string &name, InputParameters &parameters)
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
const std::vector< std::unique_ptr< NumericVector< Number > > > &	gradientContainer () const
	Reference to the container vector which hold gradients at dofs (if it can be interpreted). More...
virtual void	compute (ExecFlagType type)=0
	Compute time derivatives, auxiliary variables, etc. More...
void	copyTimeIntegrators (const SystemBase &other_sys)
	Copy time integrators from another system. More...
const TimeIntegrator &	getTimeIntegrator (const unsigned int var_num) const
	Retrieve the time integrator that integrates the given variable's equation. More...
const TimeIntegrator *	queryTimeIntegrator (const unsigned int var_num) const
	Retrieve the time integrator that integrates the given variable's equation. More...
const std::vector< std::shared_ptr< TimeIntegrator > > &	getTimeIntegrators ()
std::string	prefix () const
void	sizeVariableMatrixData ()
	size the matrix data for each variable for the number of matrix tags we have More...
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const
virtual NumericVector< Number > &	getVector (const std::string &name)
	Get a raw NumericVector by name. More...
virtual const NumericVector< Number > &	getVector (const std::string &name) const
virtual NumericVector< Number > &	getVector (TagID tag)
	Get a raw NumericVector by tag. More...
virtual const NumericVector< Number > &	getVector (TagID tag) 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
virtual NumericVector< Number > &	solutionInternal () const =0
	Internal getter for solution owned by libMesh. More...

Protected Attributes
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...
std::vector< Real >	_du_dot_du
	Derivative of time derivative of u with respect to uj. More...
Real	_du_dotdot_du
std::vector< NumericVector< Number > * >	_tagged_vectors
	Tagged vectors (pointer) More...
std::vector< libMesh::SparseMatrix< Number > * >	_tagged_matrices
	Tagged matrices (pointer) More...
std::unordered_map< TagID, libMesh::SparseMatrix< Number > * >	_active_tagged_matrices
	Active tagged matrices. A matrix is active if its tag-matrix pair is present in the map. We use a map instead of a vector so that users can easily add and remove to this container with calls to (de)activateMatrixTag. 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::vector< std::shared_ptr< TimeIntegrator > >	_time_integrators
	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

Private Member Functions
TagName	oldSolutionStateVectorName (const unsigned int, Moose::SolutionIterationType iteration_type) const
	Gets the vector name used for an old (not current) solution state. More...

Private Attributes
std::array< std::vector< NumericVector< Number > * >, 3 >	_solution_states
	2D array of solution state vector pointers; first index corresponds to SolutionIterationType, second index corresponds to state index (0=current, 1=old, 2=older) More...
std::vector< NumericVector< Number > * >	_saved_solution_states
	The saved solution states (0 = current, 1 = old, 2 = older, etc) More...

Detailed Description

Base class for a system (of equations)

Definition at line 84 of file SystemBase.h.

Constructor & Destructor Documentation

SystemBase()

SystemBase::SystemBase	(	SubProblem &	subproblem,
		FEProblemBase &	fe_problem,
		const std::string &	name,
		Moose::VarKindType	var_kind
	)

Definition at line 57 of file SystemBase.C.

  : libMesh::ParallelObject(subproblem),
    ConsoleStreamInterface(subproblem.getMooseApp()),
    _subproblem(subproblem),
    _fe_problem(fe_problem),
    _app(subproblem.getMooseApp()),
    _factory(_app.getFactory()),
    _mesh(subproblem.mesh()),
    _name(name),
    _vars(libMesh::n_threads()),
    _var_map(),
    _max_var_number(0),
    _u_dot(nullptr),
    _u_dotdot(nullptr),
    _u_dot_old(nullptr),
    _u_dotdot_old(nullptr),
    _saved_old(nullptr),
    _saved_older(nullptr),
    _saved_dot_old(nullptr),
    _saved_dotdot_old(nullptr),
    _var_kind(var_kind),
    _max_var_n_dofs_per_elem(0),
    _max_var_n_dofs_per_node(0),
    _automatic_scaling(false),
    _verbose(false),
    _solution_states_initialized(false)
{
}

~SystemBase()

virtual SystemBase::~SystemBase ( )

inlinevirtual

Definition at line 92 of file SystemBase.h.

{}

Member Function Documentation

activateAllMatrixTags()

void SystemBase::activateAllMatrixTags ( )

virtual

Make all existing matrices active.

Definition at line 1123 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);
  _active_tagged_matrices.clear();

  for (const auto tag : make_range(num_matrix_tags))
    if (hasMatrix(tag))
    {
      _matrix_tag_active_flags[tag] = true;
      _active_tagged_matrices.emplace(tag, &getMatrix(tag));
    }
    else
      _matrix_tag_active_flags[tag] = false;
}

addDotVectors()

void SystemBase::addDotVectors ( )

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1625 of file SystemBase.C.

Referenced by DisplacedSystem::addDotVectors().

{
  if (_fe_problem.uDotRequested())
    _u_dot = &addVector("u_dot", true, GHOSTED);
  if (_fe_problem.uDotOldRequested())
    _u_dot_old = &addVector("u_dot_old", true, GHOSTED);
  if (_fe_problem.uDotDotRequested())
    _u_dotdot = &addVector("u_dotdot", true, GHOSTED);
  if (_fe_problem.uDotDotOldRequested())
    _u_dotdot_old = &addVector("u_dotdot_old", true, GHOSTED);
}

addMatrix()

SparseMatrix< Number > & SystemBase::addMatrix

(

TagID

tag

)

Adds a matrix with a given tag.

Parameters

tag_name

The name of the tag

Definition at line 570 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

(

)

Add the scaling factor vector to the system.

Definition at line 1537 of file SystemBase.C.

Referenced by MooseVariableBase::initialSetup().

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

addTimeIntegrator()

void SystemBase::addTimeIntegrator	(	const std::string &	type,
		const std::string &	name,
		InputParameters &	parameters
	)

Definition at line 1650 of file SystemBase.C.

{
  parameters.set<SystemBase *>("_sys") = this;
  _time_integrators.push_back(_factory.create<TimeIntegrator>(type, name, parameters));
}

addVariable()

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

virtual

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 718 of file SystemBase.C.

Referenced by AuxiliarySystem::addVariable().

{
  _numbered_vars.resize(libMesh::n_threads());

  const 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);
  }

  const auto fe_type =
      FEType(Utility::string_to_enum<Order>(parameters.get<MooseEnum>("order")),
             Utility::string_to_enum<FEFamily>(parameters.get<MooseEnum>("family")));
  const auto fe_field_type = FEInterface::field_type(fe_type);

  unsigned int var_num;

  if (var_type == "ArrayMooseVariable")
  {
    if (fe_field_type == TYPE_VECTOR)
      mooseError("Vector family type cannot be used in an array variable");

    std::vector<std::string> array_var_component_names;
    const bool has_array_names = parameters.isParamValid("array_var_component_names");
    if (has_array_names)
    {
      array_var_component_names =
          parameters.get<std::vector<std::string>>("array_var_component_names");
      if (array_var_component_names.size() != components)
        parameters.paramError("array_var_component_names",
                              "Must be the same size as 'components' (size ",
                              components,
                              ") for array variable '",
                              name,
                              "'");
    }

    // Build up the variable names
    std::vector<std::string> var_names;
    for (unsigned int i = 0; i < components; i++)
    {
      if (!has_array_names)
        array_var_component_names.push_back(std::to_string(i));
      var_names.push_back(name + "_" + array_var_component_names[i]);
    }

    // makes sure there is always a name, either the provided one or '1 2 3 ...'
    parameters.set<std::vector<std::string>>("array_var_component_names") =
        array_var_component_names;

    // 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"))
      parameters.paramError("array",
                            "Must be set to true for variable '",
                            name,
                            "' because 'components' > 1 (is an array variable)");
    parameters.set<bool>("array") = true;
  }
  else
  {
    if (parameters.isParamSetByUser("array_var_component_names"))
      parameters.paramError("array_var_component_names",
                            "Should not be set because this variable (",
                            name,
                            ") is a non-array variable");
    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;
  _du_dot_du.resize(var_num + 1);
}

addVariableToCopy()

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

virtual

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 1167 of file SystemBase.C.

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

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

addVariableToZeroOnJacobian()

void SystemBase::addVariableToZeroOnJacobian ( std::string  var_name )

virtual

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 in DisplacedSystem.

Definition at line 180 of file SystemBase.C.

Referenced by ADDGKernel::ADDGKernel(), DisplacedSystem::addVariableToZeroOnJacobian(), ADIntegratedBCTempl< T >::ADIntegratedBCTempl(), ADKernelTempl< T >::ADKernelTempl(), ArrayDGKernel::ArrayDGKernel(), ArrayIntegratedBC::ArrayIntegratedBC(), ArrayKernel::ArrayKernel(), DGKernel::DGKernel(), IntegratedBC::IntegratedBC(), InterfaceKernelTempl< T >::InterfaceKernelTempl(), Kernel::Kernel(), NodalBC::NodalBC(), and NodalKernel::NodalKernel().

{
  _vars_to_be_zeroed_on_jacobian.push_back(var_name);
}

addVariableToZeroOnResidual()

void SystemBase::addVariableToZeroOnResidual ( std::string  var_name )

virtual

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 in DisplacedSystem.

Definition at line 174 of file SystemBase.C.

Referenced by ADDGKernel::ADDGKernel(), DisplacedSystem::addVariableToZeroOnResidual(), ADIntegratedBCTempl< T >::ADIntegratedBCTempl(), ADKernelTempl< T >::ADKernelTempl(), ArrayDGKernel::ArrayDGKernel(), ArrayIntegratedBC::ArrayIntegratedBC(), ArrayKernel::ArrayKernel(), DGKernel::DGKernel(), IntegratedBC::IntegratedBC(), InterfaceKernelTempl< T >::InterfaceKernelTempl(), Kernel::Kernel(), NodalBC::NodalBC(), and NodalKernel::NodalKernel().

{
  _vars_to_be_zeroed_on_residual.push_back(var_name);
}

addVector() [1/2]

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

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.

Referenced by addDotVectors(), addScalingVector(), NonlinearTimeIntegratorInterface::addVector(), SecantSolve::allocateStorage(), SteffensenSolve::allocateStorage(), PicardSolve::allocateStorage(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), CentralDifference::initialSetup(), needSolutionState(), NonlinearSystemBase::residualGhosted(), and saveOldSolutions().

addVector() [2/2]

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

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.

applyScalingFactors()

void SystemBase::applyScalingFactors

(

const std::vector< Real > &

inverse_scaling_factors

)

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 1487 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 )

inline

assign the maximum element dofs

Definition at line 597 of file SystemBase.h.

{ _max_var_n_dofs_per_elem = max_dofs; }

assignMaxVarNDofsPerNode()

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

inline

assign the maximum node dofs

Definition at line 602 of file SystemBase.h.

{ _max_var_n_dofs_per_node = max_dofs; }

associateMatrixToTag()

void SystemBase::associateMatrixToTag ( libMesh::SparseMatrix< Number > &  matrix, TagID  tag  )

virtual

Associate a matrix to a tag.

Reimplemented in DisplacedSystem.

Definition at line 1068 of file SystemBase.C.

Referenced by addMatrix(), DisplacedSystem::associateMatrixToTag(), NonlinearSystemBase::computeJacobian(), FEProblemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTag(), FEProblemBase::computeLinearSystemSys(), and FEProblemBase::computeResidualAndJacobian().

{
  if (!_subproblem.matrixTagExists(tag))
    mooseError("Cannot associate matrix to tag ", tag, " because that tag does not exist");

  if (_tagged_matrices.size() < tag + 1)
    _tagged_matrices.resize(tag + 1);

  _tagged_matrices[tag] = &matrix;
}

associateVectorToTag()

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

virtual

Associate a vector for a given tag.

Reimplemented in DisplacedSystem.

Definition at line 973 of file SystemBase.C.

Referenced by DisplacedSystem::associateVectorToTag(), FEProblemBase::computeLinearSystemSys(), FEProblemBase::computeResidualAndJacobian(), FEProblemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTag(), FEProblemBase::computeResidualTag(), FEProblemBase::computeResidualType(), LinearSystem::LinearSystem(), and SolverSystem::setSolution().

{
  if (!_subproblem.vectorTagExists(tag))
    mooseError("Cannot associate vector to tag ", tag, " because that tag does not exist");

  if (_tagged_vectors.size() < tag + 1)
    _tagged_vectors.resize(tag + 1);

  _tagged_vectors[tag] = &vec;
}

augmentSendList()

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

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 452 of file SystemBase.C.

Referenced by DisplacedSystem::augmentSendList(), and extraSendList().

{
  std::set<dof_id_type> & ghosted_elems = _subproblem.ghostedElems();

  DofMap & dof_map = dofMap();

  std::vector<dof_id_type> dof_indices;

  System & sys = system();

  unsigned int sys_num = sys.number();

  unsigned int n_vars = sys.n_vars();

  for (const auto & elem_id : ghosted_elems)
  {
    Elem * elem = _mesh.elemPtr(elem_id);

    if (elem->active())
    {
      dof_map.dof_indices(elem, dof_indices);

      // Only need to ghost it if it's actually not on this processor
      for (const auto & dof : dof_indices)
        if (dof < dof_map.first_dof() || dof >= dof_map.end_dof())
          send_list.push_back(dof);

      // Now add the DoFs from all of the nodes.  This is necessary because of block
      // restricted variables.  A variable might not live _on_ this element but it
      // might live on nodes connected to this element.
      for (unsigned int n = 0; n < elem->n_nodes(); n++)
      {
        Node * node = elem->node_ptr(n);

        // Have to get each variable's dofs
        for (unsigned int v = 0; v < n_vars; v++)
        {
          const Variable & var = sys.variable(v);
          unsigned int var_num = var.number();
          unsigned int n_comp = var.n_components();

          // See if this variable has any dofs at this node
          if (node->n_dofs(sys_num, var_num) > 0)
          {
            // Loop over components of the variable
            for (unsigned int c = 0; c < n_comp; c++)
              send_list.push_back(node->dof_number(sys_num, var_num, c));
          }
        }
      }
    }
  }
}

augmentSparsity()

virtual void SystemBase::augmentSparsity ( libMesh::SparsityPattern::Graph &  sparsity, std::vector< dof_id_type > &  n_nz, std::vector< dof_id_type > &  n_oz  )

pure virtual

Will modify the sparsity pattern to add logical geometric connections.

Implemented in NonlinearSystemBase, DisplacedSystem, LinearSystem, and AuxiliarySystem.

Referenced by extraSparsity().

automaticScaling() [1/2]

bool SystemBase::automaticScaling ( ) const

inline

Getter for whether we are performing automatic scaling.

Returns

whether we are performing automatic scaling

Definition at line 122 of file SystemBase.h.

Referenced by SubProblem::automaticScaling().

{ return _automatic_scaling; }

automaticScaling() [2/2]

void SystemBase::automaticScaling ( bool  automatic_scaling )

inline

Setter for whether we are performing automatic scaling.

Parameters

automatic_scaling

A boolean representing whether we are performing automatic scaling

Definition at line 128 of file SystemBase.h.

{ _automatic_scaling = automatic_scaling; }

clearAllDofIndices()

void SystemBase::clearAllDofIndices

(

)

Clear all dof indices from moose variables.

Definition at line 1605 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

)

Close all matrices associated the tags.

Definition at line 1052 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

)

Close vector with the given tag.

Definition at line 649 of file SystemBase.C.

Referenced by 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

)

Close all vectors for given tags.

Definition at line 667 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeResidualAndJacobianTags(), NonlinearSystemBase::computeResidualTags(), NonlinearSystem::stopSolve(), and LinearSystem::stopSolve().

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

compute()

virtual void SystemBase::compute ( ExecFlagType  type )

pure virtual

Compute time derivatives, auxiliary variables, etc.

Parameters

type	Our current execution stage

Implemented in DisplacedSystem, LinearSystem, AuxiliarySystem, and SolverSystem.

computeVariables()

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

inlinevirtual

Definition at line 869 of file SystemBase.h.

{}

computingScalingJacobian()

bool SystemBase::computingScalingJacobian

(

)

const

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

Definition at line 1544 of file SystemBase.C.

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

{
  return _subproblem.computingScalingJacobian();
}

copyOldSolutions()

void SystemBase::copyOldSolutions ( )

virtual

Shifts the solutions backwards in time.

Definition at line 1278 of file SystemBase.C.

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

{
  // copy the solutions backward: current->old, old->older
  const auto states =
      _solution_states[static_cast<unsigned short>(Moose::SolutionIterationType::Time)].size();
  if (states > 1)
    for (unsigned int i = states - 1; i > 0; --i)
      solutionState(i) = solutionState(i - 1);

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

copyPreviousFixedPointSolutions()

void SystemBase::copyPreviousFixedPointSolutions ( )

virtual

Definition at line 1294 of file SystemBase.C.

Referenced by FixedPointSolve::solveStep().

{
  const auto n_states =
      _solution_states[static_cast<unsigned short>(Moose::SolutionIterationType::FixedPoint)]
          .size();
  if (n_states > 1)
    for (unsigned int i = n_states - 1; i > 0; --i)
      solutionState(i, Moose::SolutionIterationType::FixedPoint) =
          solutionState(i - 1, Moose::SolutionIterationType::FixedPoint);
}

copyPreviousNonlinearSolutions()

void SystemBase::copyPreviousNonlinearSolutions ( )

virtual

Shifts the solutions backwards in nonlinear iteration history.

Definition at line 1261 of file SystemBase.C.

Referenced by copySolutionsBackwards().

{
  const auto states =
      _solution_states[static_cast<unsigned short>(Moose::SolutionIterationType::Nonlinear)].size();
  if (states > 1)
    for (unsigned int i = states - 1; i > 0; --i)
      solutionState(i, Moose::SolutionIterationType::Nonlinear) =
          solutionState(i - 1, Moose::SolutionIterationType::Nonlinear);

  if (solutionPreviousNewton())
    *solutionPreviousNewton() = *currentSolution();
}

copySolutionsBackwards()

void SystemBase::copySolutionsBackwards ( )

virtual

Copy current solution into old and older.

Definition at line 1250 of file SystemBase.C.

{
  system().update();
  copyOldSolutions();
  copyPreviousNonlinearSolutions();
}

copyTimeIntegrators()

void SystemBase::copyTimeIntegrators

(

const SystemBase &

other_sys

)

Copy time integrators from another system.

Definition at line 1659 of file SystemBase.C.

{
  _time_integrators = other_sys._time_integrators;
}

copyVars()

void SystemBase::copyVars

(

libMesh::ExodusII_IO &

io

)

Definition at line 1175 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 = var.arrayVariableComponent(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()

virtual const NumericVector<Number>* const& SystemBase::currentSolution ( ) const

pure virtual

The solution vector that is currently being operated on.

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

Implemented in DisplacedSystem, SolverSystem, and AuxiliarySystem.

Referenced by copyPreviousNonlinearSolutions(), DisplacedSystem::currentSolution(), initialSetup(), MooseVariableScalar::reinit(), and restoreSolutions().

customSetup()

void SystemBase::customSetup ( const ExecFlagType &  exec_type )

virtual

Reimplemented in NonlinearSystemBase, and AuxiliarySystem.

Definition at line 1577 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);
}

deactivateAllMatrixTags()

void SystemBase::deactivateAllMatrixTags ( )

virtual

Make matrices inactive.

Definition at line 1111 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;
  _active_tagged_matrices.clear();
}

defaultMatrixTags()

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

inlinevirtual

Get the default matrix tags associted with this system.

Reimplemented in NonlinearEigenSystem, and DisplacedSystem.

Definition at line 319 of file SystemBase.h.

Referenced by DisplacedSystem::defaultMatrixTags(), NonlinearEigenSystem::defaultMatrixTags(), and disassociateDefaultMatrixTags().

{ return {systemMatrixTag()}; }

defaultVectorTags()

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

inlinevirtual

Get the default vector tags associated with this system.

Reimplemented in NonlinearEigenSystem, and DisplacedSystem.

Definition at line 312 of file SystemBase.h.

Referenced by DisplacedSystem::defaultVectorTags(), NonlinearEigenSystem::defaultVectorTags(), and disassociateDefaultVectorTags().

  {
    return {timeVectorTag(), nonTimeVectorTag(), residualVectorTag()};
  }

disassociateDefaultMatrixTags()

void SystemBase::disassociateDefaultMatrixTags ( )

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1102 of file SystemBase.C.

Referenced by DisplacedSystem::disassociateDefaultMatrixTags().

{
  const auto tags = defaultMatrixTags();
  for (const auto tag : tags)
    if (_subproblem.matrixTagExists(tag))
      disassociateMatrixFromTag(tag);
}

disassociateDefaultVectorTags()

void SystemBase::disassociateDefaultVectorTags ( )

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1007 of file SystemBase.C.

Referenced by DisplacedSystem::disassociateDefaultVectorTags().

{
  const auto tags = defaultVectorTags();
  for (const auto tag : tags)
    if (_subproblem.vectorTagExists(tag))
      disassociateVectorFromTag(tag);
}

disassociateMatrixFromTag() [1/2]

void SystemBase::disassociateMatrixFromTag ( libMesh::SparseMatrix< Number > &  matrix, TagID  tag  )

virtual

Disassociate a matrix from a tag.

Reimplemented in DisplacedSystem.

Definition at line 1080 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeJacobian(), FEProblemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTag(), FEProblemBase::computeLinearSystemSys(), FEProblemBase::computeResidualAndJacobian(), disassociateDefaultMatrixTags(), and DisplacedSystem::disassociateMatrixFromTag().

{
  if (!_subproblem.matrixTagExists(tag))
    mooseError("Cannot disassociate matrix from tag ", tag, " because that tag does not exist");
  if (hasMatrix(tag) && &getMatrix(tag) != &matrix)
    mooseError("You can not disassociate a matrix from a tag which it was not associated to");

  disassociateMatrixFromTag(tag);
}

disassociateMatrixFromTag() [2/2]

void SystemBase::disassociateMatrixFromTag ( TagID  tag )

virtual

Disassociate any matrix that is associated with a given tag.

Reimplemented in DisplacedSystem.

Definition at line 1091 of file SystemBase.C.

{
  if (!_subproblem.matrixTagExists(tag))
    mooseError("Cannot disassociate matrix from tag ", tag, " because that tag does not exist");

  if (_tagged_matrices.size() < tag + 1)
    _tagged_matrices.resize(tag + 1);
  _tagged_matrices[tag] = nullptr;
}

disassociateVectorFromTag() [1/2]

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

virtual

Disassociate a given vector from a given tag.

Reimplemented in DisplacedSystem.

Referenced by FEProblemBase::computeLinearSystemSys(), FEProblemBase::computeResidualAndJacobian(), FEProblemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTag(), FEProblemBase::computeResidualTag(), FEProblemBase::computeResidualType(), disassociateDefaultVectorTags(), DisplacedSystem::disassociateVectorFromTag(), and CentralDifference::initialSetup().

disassociateVectorFromTag() [2/2]

void SystemBase::disassociateVectorFromTag ( TagID  tag )

virtual

Disassociate any vector that is associated with a given tag.

Reimplemented in DisplacedSystem.

Definition at line 996 of file SystemBase.C.

{
  if (!_subproblem.vectorTagExists(tag))
    mooseError("Cannot disassociate vector from tag ", tag, " because that tag does not exist");

  if (_tagged_vectors.size() < tag + 1)
    _tagged_vectors.resize(tag + 1);
  _tagged_vectors[tag] = nullptr;
}

dofMap() [1/2]

DofMap & SystemBase::dofMap ( )

virtual

Gets writeable reference to the dof map.

Definition at line 1155 of file SystemBase.C.

Referenced by NonlinearSystemBase::assembleScalingVector(), MooseApp::attachRelationshipManagers(), augmentSendList(), NonlinearSystemBase::augmentSparsity(), NonlinearSystemBase::computeScaling(), FieldSplitPreconditioner::dofMap(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), Adaptivity::init(), NonlinearEigenSystem::initializeCondensedMatrices(), ActivateElementsUserObjectBase::initSolutions(), PNGOutput::makeMeshFunc(), GhostingUserObject::meshChanged(), TableOutput::outputScalarVariables(), Exodus::outputScalarVariables(), and ElementSubdomainModifierBase::setOldAndOlderSolutions().

{
  return system().get_dof_map();
}

dofMap() [2/2]

const DofMap & SystemBase::dofMap ( ) const

virtual

Gets const reference to the dof map.

Definition at line 1161 of file SystemBase.C.

{
  return system().get_dof_map();
}

duDotDotDu() [1/2]

virtual Number& SystemBase::duDotDotDu ( )

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 257 of file SystemBase.h.

Referenced by DisplacedSystem::duDotDotDu(), and MooseVariableScalar::reinit().

{ return _du_dotdot_du; }

duDotDotDu() [2/2]

virtual const Number& SystemBase::duDotDotDu ( ) const

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 259 of file SystemBase.h.

{ return _du_dotdot_du; }

duDotDu()

const Number & SystemBase::duDotDu ( unsigned int  var_num = 0 ) const

virtual

Reimplemented in DisplacedSystem.

Definition at line 1693 of file SystemBase.C.

Referenced by DisplacedSystem::duDotDu(), and MooseVariableScalar::reinit().

{
  return _du_dot_du[var_num];
}

duDotDus()

virtual std::vector<Number>& SystemBase::duDotDus ( )

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 256 of file SystemBase.h.

Referenced by DisplacedSystem::duDotDus().

{ return _du_dot_du; }

feProblem() [1/2]

FEProblemBase& SystemBase::feProblem ( )

inline

Definition at line 103 of file SystemBase.h.

Referenced by DMMooseGetEmbedding_Private(), and DMSetUp_Moose_Pre().

{ return _fe_problem; }

feProblem() [2/2]

const FEProblemBase& SystemBase::feProblem ( ) const

inline

Definition at line 104 of file SystemBase.h.

{ return _fe_problem; }

flushTaggedMatrices()

void SystemBase::flushTaggedMatrices

(

const std::set< TagID > &

tags

)

flushes all matrices associated to tags.

Flush assembles the matrix but doesn't shrink memory allocation

Definition at line 1060 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
	)

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

Definition at line 118 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
	)

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

Definition at line 139 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
	)

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 111 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
	)

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 132 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
	)

Return a finite volume variable.

Definition at line 125 of file SystemBase.C.

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

getMatrix() [1/2]

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

virtual

Get a raw SparseMatrix.

Reimplemented in DisplacedSystem.

Definition at line 1016 of file SystemBase.C.

Referenced by activateAllMatrixTags(), Assembly::addCachedJacobian(), NonlinearSystemBase::addImplicitGeometricCouplingEntries(), Assembly::addJacobianCoupledVarPair(), Assembly::addJacobianLowerD(), Assembly::addJacobianNeighbor(), Assembly::addJacobianNeighborLowerD(), Assembly::addJacobianNonlocal(), addMatrix(), closeTaggedMatrices(), NonlinearSystemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTags(), LinearSystem::computeLinearSystemInternal(), FEProblemBase::computeLinearSystemTags(), FEProblemBase::computeResidualAndJacobian(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::constraintJacobians(), disassociateMatrixFromTag(), NonlinearSystemBase::enforceNodalConstraintsJacobian(), flushTaggedMatrices(), DisplacedSystem::getMatrix(), LinearSystemContributionObject::linkTaggedVectorsAndMatrices(), MooseVariableScalar::reinit(), Assembly::setCachedJacobian(), and Assembly::zeroCachedJacobian().

{
  if (!hasMatrix(tag))
  {
    if (!_subproblem.matrixTagExists(tag))
      mooseError("Cannot retreive matrix with tag ", tag, " because that tag does not exist");
    else
      mooseError("Cannot retreive matrix with tag ",
                 tag,
                 " in system '",
                 name(),
                 "'\nbecause a matrix has not been associated with that tag.");
  }

  return *_tagged_matrices[tag];
}

getMatrix() [2/2]

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

virtual

Get a raw SparseMatrix.

Reimplemented in DisplacedSystem.

Definition at line 1034 of file SystemBase.C.

{
  if (!hasMatrix(tag))
  {
    if (!_subproblem.matrixTagExists(tag))
      mooseError("Cannot retreive matrix with tag ", tag, " because that tag does not exist");
    else
      mooseError("Cannot retreive matrix with tag ",
                 tag,
                 " in system '",
                 name(),
                 "'\nbecause a matrix has not been associated with that tag.");
  }

  return *_tagged_matrices[tag];
}

getMaxVariableNumber()

unsigned int SystemBase::getMaxVariableNumber ( ) const

inline

Returns the maximum number of all variables on the system.

Definition at line 867 of file SystemBase.h.

{ return _max_var_number; }

getMaxVarNDofsPerElem()

std::size_t SystemBase::getMaxVarNDofsPerElem ( ) const

inline

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

Returns

The max

Definition at line 585 of file SystemBase.h.

Referenced by Moose::globalDofIndexToDerivative().

{ return _max_var_n_dofs_per_elem; }

getMaxVarNDofsPerNode()

std::size_t SystemBase::getMaxVarNDofsPerNode ( ) const

inline

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

Returns

The max

Definition at line 592 of file SystemBase.h.

{ return _max_var_n_dofs_per_node; }

getMinQuadratureOrder()

Order SystemBase::getMinQuadratureOrder ( )

virtual

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

Returns

The minimal order of quadrature

Reimplemented in AuxiliarySystem.

Definition at line 241 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

virtual

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 145 of file SystemBase.C.

Referenced by Assembly::addJacobianOffDiagScalar(), ODEKernel::computeOffDiagJacobianScalar(), VectorKernel::computeOffDiagJacobianScalar(), ArrayKernel::computeOffDiagJacobianScalar(), IntegratedBC::computeOffDiagJacobianScalar(), VectorIntegratedBC::computeOffDiagJacobianScalar(), Kernel::computeOffDiagJacobianScalar(), ArrayIntegratedBC::computeOffDiagJacobianScalar(), ScalarLagrangeMultiplier::computeOffDiagJacobianScalar(), MortarScalarBase::computeOffDiagJacobianScalar(), KernelScalarBase::computeOffDiagJacobianScalarLocal(), KernelScalarBase::computeScalarOffDiagJacobianScalar(), MortarScalarBase::computeScalarOffDiagJacobianScalar(), DMMooseSetVariables(), Assembly::init(), ReferenceResidualConvergence::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

virtual

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 154 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 )

inline

Definition at line 756 of file SystemBase.h.

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

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

getStandardFieldVariableNames()

void SystemBase::getStandardFieldVariableNames

(

std::vector< VariableName > &

std_field_variables

)

const

getSubdomainsForVar() [1/2]

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

inline

Definition at line 761 of file SystemBase.h.

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

  {
    return _var_map.at(var_number);
  }

getSubdomainsForVar() [2/2]

const std::set< SubdomainID > & SystemBase::getSubdomainsForVar

(

const std::string &

var_name

)

const

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 1699 of file SystemBase.C.

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

getTimeIntegrator()

const TimeIntegrator & SystemBase::getTimeIntegrator

(

const unsigned int

var_num

)

const

Retrieve the time integrator that integrates the given variable's equation.

Definition at line 1675 of file SystemBase.C.

Referenced by AB2PredictorCorrector::estimateTimeError().

{
  const auto * const ti = queryTimeIntegrator(var_num);

  if (ti)
    return *ti;
  else
    mooseError("No time integrator found that integrates variable number ",
               std::to_string(var_num));
}

getTimeIntegrators()

const std::vector< std::shared_ptr< TimeIntegrator > > & SystemBase::getTimeIntegrators

(

)

Returns

All the time integrators owned by this system

Definition at line 1687 of file SystemBase.C.

{
  return _time_integrators;
}

getVariable() [1/2]

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

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 90 of file SystemBase.C.

Referenced by AdaptivityAction::act(), Assembly::addJacobianBlockNonlocal(), FEProblemBase::addJacobianBlockTags(), NonlocalKernel::computeNonlocalOffDiagJacobian(), NonlocalIntegratedBC::computeNonlocalOffDiagJacobian(), Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), Assembly::copyShapes(), copyVars(), DMMooseSetVariables(), FieldSplitPreconditionerTempl< MoosePreconditioner >::FieldSplitPreconditionerTempl(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), NodeElemConstraint::getConnectedDofIndices(), NodeFaceConstraint::getConnectedDofIndices(), getSubdomainsForVar(), ResidualObject::getVariable(), SubProblem::getVariableHelper(), Assembly::init(), NodalNormalsPreprocessor::initialize(), ExplicitTimeIntegrator::initialSetup(), ReferenceResidualConvergence::initialSetup(), LinearSystem::initialSetup(), Assembly::initNonlocalCoupling(), PNGOutput::makeMeshFunc(), MooseStaticCondensationPreconditioner::MooseStaticCondensationPreconditioner(), UpdateErrorVectorsThread::onElement(), Assembly::prepareBlock(), Assembly::prepareBlockNonlocal(), AddPeriodicBCAction::setPeriodicVars(), NonlinearSystemBase::setupScalingData(), 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

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 100 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 )

virtual

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 164 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 ( )

inline

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

Definition at line 842 of file SystemBase.h.

{ return _var_all_dof_indices; }

getVariableNames()

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

inline

Definition at line 860 of file SystemBase.h.

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

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

getVariables()

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

inline

Definition at line 751 of file SystemBase.h.

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

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

getVector() [1/4]

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

virtual

Get a raw NumericVector by name.

Get a raw NumericVector with the given name.

Reimplemented in DisplacedSystem.

Definition at line 925 of file SystemBase.C.

Referenced by Assembly::addCachedResiduals(), Assembly::addResidual(), Assembly::addResidualLower(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), NonlinearSystemBase::assembleScalingVector(), closeTaggedVector(), FEProblemBase::computeBounds(), FEProblemBase::computeNearNullSpace(), FEProblemBase::computeNullSpace(), NonlinearSystemBase::computeResidualAndJacobianTags(), NonlinearSystemBase::computeResidualTags(), CentralDifference::computeTimeDerivatives(), FEProblemBase::computeTransposeNullSpace(), DisplacedSystem::getVector(), Assembly::hasScalingVector(), LinearSystemContributionObject::linkTaggedVectorsAndMatrices(), needSolutionState(), ReferenceResidualConvergence::ReferenceResidualConvergence(), MooseVariableScalar::reinit(), SecantSolve::saveVariableValues(), SteffensenSolve::saveVariableValues(), PicardSolve::saveVariableValues(), NonlinearSystemBase::setPreviousNewtonSolution(), TaggingInterface::setResidual(), solutionPreviousNewton(), solutionState(), MultiAppDofCopyTransfer::transfer(), SecantSolve::transformVariables(), SteffensenSolve::transformVariables(), PicardSolve::transformVariables(), and zeroTaggedVector().

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

getVector() [2/4]

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

virtual

Reimplemented in DisplacedSystem.

Definition at line 931 of file SystemBase.C.

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

getVector() [3/4]

NumericVector< Number > & SystemBase::getVector ( TagID  tag )

virtual

Get a raw NumericVector by tag.

Reimplemented in DisplacedSystem.

Definition at line 937 of file SystemBase.C.

{
  if (!hasVector(tag))
  {
    if (!_subproblem.vectorTagExists(tag))
      mooseError("Cannot retreive vector with tag ", tag, " because that tag does not exist");
    else
      mooseError("Cannot retreive vector with tag ",
                 tag,
                 " in system '",
                 name(),
                 "'\nbecause a vector has not been associated with that tag.");
  }

  return *_tagged_vectors[tag];
}

getVector() [4/4]

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

virtual

Reimplemented in DisplacedSystem.

Definition at line 955 of file SystemBase.C.

{
  if (!hasVector(tag))
  {
    if (!_subproblem.vectorTagExists(tag))
      mooseError("Cannot retreive vector with tag ", tag, " because that tag does not exist");
    else
      mooseError("Cannot retreive vector with tag ",
                 tag,
                 " in system '",
                 name(),
                 "'\nbecause a vector has not been associated with that tag.");
  }

  return *_tagged_vectors[tag];
}

gradientContainer()

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

inline

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

Mainly used for finite volume systems.

Definition at line 930 of file SystemBase.h.

  {
    return _raw_grad_container;
  }

hasMatrix()

virtual bool SystemBase::hasMatrix ( TagID  tag ) const

inlinevirtual

Check if the tagged matrix exists in the system.

Reimplemented in DisplacedSystem.

Definition at line 360 of file SystemBase.h.

Referenced by activateAllMatrixTags(), Assembly::addCachedJacobian(), NonlinearSystemBase::addImplicitGeometricCouplingEntries(), Assembly::addJacobianCoupledVarPair(), Assembly::addJacobianLowerD(), Assembly::addJacobianNeighbor(), Assembly::addJacobianNeighborLowerD(), Assembly::addJacobianNonlocal(), addMatrix(), Assembly::cacheJacobian(), Assembly::cacheJacobianBlockNonzero(), Assembly::cacheJacobianCoupledVarPair(), Assembly::cacheJacobianMortar(), Assembly::cacheJacobianNeighbor(), Assembly::cacheJacobianNonlocal(), closeTaggedMatrices(), NonlinearSystemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTags(), FEProblemBase::computeResidualAndJacobian(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::constraintJacobians(), disassociateMatrixFromTag(), NonlinearSystemBase::enforceNodalConstraintsJacobian(), flushTaggedMatrices(), getMatrix(), DisplacedSystem::hasMatrix(), MooseVariableScalar::reinit(), removeMatrix(), SubProblem::selectMatrixTagsFromSystem(), Assembly::setCachedJacobian(), and Assembly::zeroCachedJacobian().

  {
    return tag < _tagged_matrices.size() && _tagged_matrices[tag];
  }

hasScalarVariable()

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

virtual

Definition at line 868 of file SystemBase.C.

Referenced by MortarScalarBase::computeJacobian(), NonlinearSystemBase::computeJacobianInternal(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), copyVars(), ExplicitTimeIntegrator::initialSetup(), 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 SystemBase::hasSolutionState ( const unsigned int  state, Moose::SolutionIterationType  iteration_type = Moose::SolutionIterationType::Time  ) const

inlinevirtual

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

Reimplemented in DisplacedSystem.

Definition at line 1090 of file SystemBase.h.

Referenced by PointwiseRenormalizeVector::execute(), PointwiseRenormalizeVector::finalize(), DisplacedSystem::hasSolutionState(), needSolutionState(), restoreSolutions(), ElementSubdomainModifierBase::setOldAndOlderSolutions(), solutionState(), and solutionStateParallelType().

{
  return _solution_states[static_cast<unsigned short>(iteration_type)].size() > state;
}

hasVarCopy()

bool SystemBase::hasVarCopy ( ) const

inline

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

Definition at line 883 of file SystemBase.h.

{ return _var_to_copy.size() > 0; }

hasVariable()

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

virtual

Query a system for a variable.

Parameters

var_name

name of the variable

Returns

true if the variable exists

Definition at line 843 of file SystemBase.C.

Referenced by ADDGKernel::ADDGKernel(), ArrayDGKernel::ArrayDGKernel(), copyVars(), DGKernel::DGKernel(), DMMooseSetVariables(), FEProblemBase::duplicateVariableCheck(), SubProblem::getVariableHelper(), SubProblem::hasAuxiliaryVariable(), ExplicitTimeIntegrator::initialSetup(), 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]

bool SystemBase::hasVector

(

const std::string &

tag_name

)

const

Check if the named vector exists in the system.

Definition at line 916 of file SystemBase.C.

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

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

hasVector() [2/2]

virtual bool SystemBase::hasVector ( TagID  tag_id ) const

inlinevirtual

Check if the tagged vector exists in the system.

Reimplemented in DisplacedSystem.

Definition at line 281 of file SystemBase.h.

  {
    return tag_id < _tagged_vectors.size() && _tagged_vectors[tag_id];
  }

initializeObjects()

virtual void SystemBase::initializeObjects ( )

inlinevirtual

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

Definition at line 173 of file SystemBase.h.

{}

initialSetup()

void SystemBase::initialSetup ( )

virtual

Setup Functions.

Reimplemented in NonlinearSystemBase, LinearSystem, and AuxiliarySystem.

Definition at line 1550 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 SystemBase::initSolutionState ( )

virtual

Initializes the solution state.

Reimplemented in DisplacedSystem.

Definition at line 1356 of file SystemBase.C.

Referenced by DisplacedSystem::initSolutionState().

{
  // Default is the current solution
  unsigned int state = 0;

  // Add additional states as required by the variable states requested
  for (const auto & var : getVariables(/* tid = */ 0))
    state = std::max(state, var->oldestSolutionStateRequested());
  for (const auto & var : getScalarVariables(/* tid = */ 0))
    state = std::max(state, var->oldestSolutionStateRequested());

  needSolutionState(state, Moose::SolutionIterationType::Time);

  _solution_states_initialized = true;
}

isArrayVariable()

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

virtual

If a variable is an array variable.

Definition at line 856 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

virtual

Definition at line 877 of file SystemBase.C.

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

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

jacobianSetup()

void SystemBase::jacobianSetup ( )

virtual

Reimplemented in NonlinearSystemBase, LinearSystem, and AuxiliarySystem.

Definition at line 1598 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

virtual

If or not a matrix tag is active.

Definition at line 1141 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 ( )

inline

Definition at line 99 of file SystemBase.h.

Referenced by CreateDisplacedProblemAction::addProxyRelationshipManagers(), DMMooseGetEmbedding_Private(), DMSetUp_Moose_Pre(), SolutionIC::initialSetup(), ComputeNodalUserObjectsThread::onNode(), ComputeNodalKernelsThread::onNode(), and ComputeNodalKernelJacobiansThread::onNode().

{ return _mesh; }

mesh() [2/2]

const MooseMesh& SystemBase::mesh ( ) const

inline

Definition at line 100 of file SystemBase.h.

{ return _mesh; }

name()

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

virtual

Definition at line 1332 of file SystemBase.C.

Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addConstraint(), NonlinearSystemBase::addDamper(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), NonlinearSystemBase::addHDGKernel(), NonlinearSystemBase::addInterfaceKernel(), MooseEigenSystem::addKernel(), AuxiliarySystem::addKernel(), NonlinearSystemBase::addKernel(), addMatrix(), NonlinearSystemBase::addNodalKernel(), AuxiliarySystem::addScalarKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), addTimeIntegrator(), AuxiliarySystem::addVariable(), addVariable(), DiffusionLHDGAssemblyHelper::checkCoupling(), closeTaggedVector(), LinearSystem::computeGradients(), LinearSystem::computeLinearSystemTags(), DisplacedProblem::DisplacedProblem(), getMatrix(), NonlinearSystemBase::getSplit(), DisplacedSystem::getVector(), getVector(), hasVector(), LinearSystem::initialSetup(), Moose::PetscSupport::petscSetDefaults(), NonlinearEigenSystem::postAddResidualObject(), MooseStaticCondensationPreconditioner::prefix(), removeMatrix(), removeVector(), solutionState(), LinearSystem::solve(), LinearTimeIntegratorInterface::timeDerivativeMatrixContribution(), LinearTimeIntegratorInterface::timeDerivativeRHSContribution(), and zeroTaggedVector().

{
  return system().name();
}

needSolutionState()

void SystemBase::needSolutionState ( const unsigned int  state, Moose::SolutionIterationType  iteration_type = Moose::SolutionIterationType::Time, libMesh::ParallelType  parallel_type = GHOSTED  )

virtual

Registers that the solution state state is needed.

Reimplemented in DisplacedSystem.

Definition at line 1442 of file SystemBase.C.

Referenced by SecantSolve::allocateStorage(), PicardSolve::allocateStorage(), EigenExecutionerBase::EigenExecutionerBase(), initSolutionState(), DisplacedSystem::needSolutionState(), and solutionState().

{
  libmesh_parallel_only(this->comm());
  mooseAssert(!Threads::in_threads,
              "This routine is not thread-safe. Request the solution state before using it in "
              "a threaded region.");

  if (hasSolutionState(state, iteration_type))
    return;

  auto & solution_states = _solution_states[static_cast<unsigned short>(iteration_type)];
  solution_states.resize(state + 1);

  // The 0-th (current) solution state is owned by libMesh
  if (!solution_states[0])
    solution_states[0] = &solutionInternal();
  else
    mooseAssert(solution_states[0] == &solutionInternal(), "Inconsistent current solution");

  // We will manually add all states past current
  for (unsigned int i = 1; i <= state; ++i)
    if (!solution_states[i])
    {
      auto tag = _subproblem.addVectorTag(oldSolutionStateVectorName(i, iteration_type),
                                          Moose::VECTOR_TAG_SOLUTION);
      solution_states[i] = &addVector(tag, true, parallel_type);
    }
    else
    {
      // If the existing parallel type is PARALLEL and GHOSTED is now requested,
      // this would require an upgrade, which is risky if anybody has already
      // stored a pointer to the existing vector, since the upgrade would create
      // a new vector and make that pointer null. If the existing parallel type
      // is GHOSTED and PARALLEL is now requested, we don't need to do anything.
      if (parallel_type == GHOSTED && solutionStateParallelType(i, iteration_type) == PARALLEL)
        mooseError("The solution state has already been declared as PARALLEL");

      mooseAssert(solution_states[i] == &getVector(oldSolutionStateVectorName(i, iteration_type)),
                  "Inconsistent solution state");
    }
}

nFieldVariables()

unsigned int SystemBase::nFieldVariables

(

)

const

Get the number of field variables in this system.

Returns

the number of field variables

Definition at line 892 of file SystemBase.C.

Referenced by nVariables().

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

  return n;
}

nFVVariables()

unsigned int SystemBase::nFVVariables

(

)

const

Get the number of finite volume variables in this system.

Returns

the number of finite volume variables

Definition at line 902 of file SystemBase.C.

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

  return n;
}

nonTimeVectorTag()

virtual TagID SystemBase::nonTimeVectorTag ( ) const

inlinevirtual

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 302 of file SystemBase.h.

Referenced by defaultVectorTags(), and DisplacedSystem::nonTimeVectorTag().

{ mooseError("Not implemented yet"); }

number()

unsigned int SystemBase::number

(

)

const

Gets the number of this system.

Returns

The number of this system

Definition at line 1149 of file SystemBase.C.

Referenced by SetupResidualDebugAction::act(), FEProblemBase::addCachedResidualDirectly(), FEProblemBase::addJacobian(), FEProblemBase::addJacobianBlockTags(), FEProblemBase::addJacobianLowerD(), FEProblemBase::addJacobianNeighbor(), FEProblemBase::addJacobianNeighborLowerD(), FEProblemBase::addJacobianOffDiagScalar(), FEProblemBase::addJacobianScalar(), FEProblemBase::addResidual(), FEProblemBase::addResidualLower(), FEProblemBase::addResidualNeighbor(), FEProblemBase::addResidualScalar(), addScalingVector(), ADKernelTempl< T >::ADKernelTempl(), ElementSubdomainModifierBase::applyIC(), ArrayKernel::ArrayKernel(), NonlinearSystemBase::assembleScalingVector(), NonlinearEigenSystem::attachPreconditioner(), DiffusionLHDGAssemblyHelper::checkCoupling(), SolverSystem::compute(), MooseVariableScalar::computeAD(), FEProblemBase::computeBounds(), Assembly::computeFaceMap(), InternalSideIndicatorBase::computeIndicator(), VectorNodalBC::computeJacobian(), ArrayNodalBC::computeJacobian(), NodalBC::computeJacobian(), FVBoundaryScalarLagrangeMultiplierConstraint::computeJacobian(), FVFluxBC::computeJacobian(), FVFluxKernel::computeJacobian(), FVInterfaceKernel::computeJacobian(), FEProblemBase::computeJacobianBlock(), NonlinearSystemBase::computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), FEProblemBase::computeNearNullSpace(), NonlinearSystemBase::computeNodalBCsResidualAndJacobian(), FEProblemBase::computeNullSpace(), VectorNodalBC::computeOffDiagJacobian(), ArrayNodalBC::computeOffDiagJacobian(), NodalBC::computeOffDiagJacobian(), NodalKernel::computeOffDiagJacobian(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), ComputeFullJacobianThread::computeOnInterface(), ComputeFullJacobianThread::computeOnInternalFace(), FEProblemBase::computePostCheck(), FVBoundaryScalarLagrangeMultiplierConstraint::computeResidual(), FVFluxKernel::computeResidual(), FVInterfaceKernel::computeResidual(), Kernel::computeResidualAndJacobian(), NodalBC::computeResidualAndJacobian(), IntegratedBC::computeResidualAndJacobian(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::computeResidualInternal(), FEProblemBase::computeResidualL2Norm(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::computeScaling(), Assembly::computeSinglePointMapAD(), FEProblemBase::computeTransposeNullSpace(), DebugResidualAux::computeValue(), NearestNodeValueAux::computeValue(), SlepcEigenSolverConfiguration::configure_solver(), NonlinearSystemBase::constraintJacobians(), LinearSystem::containsTimeKernel(), Coupleable::coupled(), FEProblemBase::currentLinearSysNum(), FEProblemBase::currentNlSysNum(), PseudoTimestep::currentResidualNorm(), ComputeResidualThread::determineObjectWarehouses(), ComputeResidualAndJacobianThread::determineObjectWarehouses(), Moose::doDerivatives(), VariableResidual::execute(), NodalNormalsEvaluator::execute(), GreaterThanLessThanPostprocessor::execute(), NodalNormalsCorner::execute(), NodalNormalsPreprocessor::execute(), ExplicitTimeIntegrator::ExplicitTimeIntegrator(), InternalSideIndicatorBase::finalize(), NumNonlinearIterations::finalize(), BoundsBase::getDoFIndex(), NonlinearSystemBase::getNodeDofs(), NonlinearEigenSystem::getSNES(), getSubdomainsForVar(), NumLinearIterations::getValue(), Residual::getValue(), NumResidualEvaluations::getValue(), Moose::globalDofIndexToDerivative(), FVBoundaryCondition::hasFaceSide(), ExplicitTimeIntegrator::init(), ExplicitTimeIntegrator::initialSetup(), NonlinearSystemBase::initialSetup(), ActivateElementsUserObjectBase::initSolutions(), EigenExecutionerBase::inversePowerIteration(), Kernel::Kernel(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionA(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionAB(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionB(), Moose::SlepcSupport::mooseSlepcEigenFormJacobianA(), MooseStaticCondensationPreconditioner::MooseStaticCondensationPreconditioner(), MooseVariableInterface< Real >::MooseVariableInterface(), EigenExecutionerBase::nonlinearSolve(), ComputeDiracThread::onElement(), ComputeNodalKernelBCJacobiansThread::onNode(), ComputeNodalKernelJacobiansThread::onNode(), VariableResidualNormsDebugOutput::output(), Moose::PetscSupport::petscLinearConverged(), Moose::PetscSupport::petscNonlinearConverged(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), PointwiseRenormalizeVector::PointwiseRenormalizeVector(), FEProblemBase::prepareAssembly(), prepareFace(), FEProblemBase::prepareFaceShapes(), FEProblemBase::prepareNeighborShapes(), FEProblemBase::prepareShapes(), FEProblemBase::reinitDirac(), FEProblemBase::reinitOffDiagScalars(), NonlinearSystem::residualAndJacobianTogether(), FEProblemBase::setResidual(), FEProblemBase::setResidualNeighbor(), PhysicsBasedPreconditioner::setup(), FVInterfaceKernel::setupData(), NonlinearSystemBase::shouldEvaluatePreSMOResidual(), ActuallyExplicitEuler::solve(), NonlinearEigenSystem::solve(), LStableDirk2::solve(), LStableDirk3::solve(), ImplicitMidpoint::solve(), ExplicitTVDRK2::solve(), LStableDirk4::solve(), AStableDirk4::solve(), ExplicitRK2::solve(), ExplicitSSPRungeKutta::solveStage(), NonlinearThread::subdomainChanged(), UserObject::systemNumber(), MultiAppDofCopyTransfer::transferDofObject(), FVFluxBC::uOnGhost(), FVFluxBC::uOnUSub(), FVFluxBC::updateCurrentFace(), and MortarConstraintBase::zeroInactiveLMDofs().

{
  return system().number();
}

nVariables()

unsigned int SystemBase::nVariables ( ) const

virtual

Get the number of variables in this system.

Returns

the number of variables

Definition at line 883 of file SystemBase.C.

Referenced by AdaptivityAction::act(), FieldSplitPreconditionerTempl< MoosePreconditioner >::FieldSplitPreconditionerTempl(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), NonlinearSystemBase::getNodeDofs(), Assembly::init(), ExplicitTimeIntegrator::initialSetup(), MaxVarNDofsPerElem::onElement(), MaxVarNDofsPerNode::onNode(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), SingleMatrixPreconditioner::SingleMatrixPreconditioner(), and AuxiliarySystem::variableWiseRelativeSolutionDifferenceNorm().

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

  return n;
}

oldSolutionStateVectorName()

TagName SystemBase::oldSolutionStateVectorName ( const unsigned int  state, Moose::SolutionIterationType  iteration_type  ) const

private

Gets the vector name used for an old (not current) solution state.

Definition at line 1373 of file SystemBase.C.

Referenced by needSolutionState(), and solutionState().

{
  mooseAssert(state != 0, "Not an old state");

  if (iteration_type == Moose::SolutionIterationType::Time)
  {
    if (state == 1)
      return Moose::OLD_SOLUTION_TAG;
    else if (state == 2)
      return Moose::OLDER_SOLUTION_TAG;
  }
  else if (iteration_type == Moose::SolutionIterationType::Nonlinear && state == 1)
    return Moose::PREVIOUS_NL_SOLUTION_TAG;
  else if (iteration_type == Moose::SolutionIterationType::FixedPoint && state == 1)
    return Moose::PREVIOUS_FP_SOLUTION_TAG;

  return "solution_state_" + std::to_string(state) + "_" + Moose::stringify(iteration_type);
}

postInit()

virtual void SystemBase::postInit ( )

inlinevirtual

Reimplemented in NonlinearEigenSystem.

Definition at line 162 of file SystemBase.h.

Referenced by NonlinearEigenSystem::postInit().

{}

prefix()

std::string SystemBase::prefix

(

)

const

Returns

The prefix used for this system for solver settings for PETSc. This prefix is used to prevent collision of solver settings for different systems. Note that this prefix does not have a leading dash so it's appropriate for passage straight to PETSc APIs

Definition at line 1705 of file SystemBase.C.

Referenced by FieldSplitPreconditioner::FieldSplitPreconditioner(), MoosePreconditioner::initialSetup(), and FieldSplitPreconditioner::prefix().

{
  return system().prefix_with_name() ? system().prefix() : "";
}

preInit()

virtual void SystemBase::preInit ( )

inlinevirtual

This is called prior to the libMesh system has been init'd.

MOOSE system wrappers can use this method to add vectors and matrices to the libMesh system

Reimplemented in NonlinearSystemBase, and SolverSystem.

Definition at line 156 of file SystemBase.h.

Referenced by SolverSystem::preInit().

{}

prepare()

void SystemBase::prepare ( THREAD_ID  tid )

virtual

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 256 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  )

virtual

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 279 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 )

virtual

Prepare the system for use for lower dimensional elements.

Parameters

tid	ID of the thread

Definition at line 332 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 )

virtual

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 324 of file SystemBase.C.

Referenced by SubProblem::reinitNeighborFaceRef().

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

queryTimeIntegrator()

const TimeIntegrator * SystemBase::queryTimeIntegrator

(

const unsigned int

var_num

)

const

Retrieve the time integrator that integrates the given variable's equation.

If no suitable time integrator is found (this could happen for instance if we're solving a non-transient problem), then a nullptr will be returned

Definition at line 1665 of file SystemBase.C.

Referenced by getTimeIntegrator(), HDGKernel::HDGKernel(), and MooseVariableData< OutputType >::MooseVariableData().

{
  for (auto & ti : _time_integrators)
    if (ti->integratesVar(var_num))
      return ti.get();

  return nullptr;
}

reinit()

virtual void SystemBase::reinit ( )

inlinevirtual

Reinitialize the system when the degrees of freedom in this system have changed.

This is called after the libMesh system has been reinit'd

Reimplemented in NonlinearEigenSystem.

Definition at line 168 of file SystemBase.h.

Referenced by NonlinearEigenSystem::reinit().

{}

reinitElem()

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

virtual

Reinit an element assembly info.

Parameters

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

Reimplemented in AuxiliarySystem.

Definition at line 340 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();
  }

  if (system().has_static_condensation())
    for (auto & [tag, matrix] : _active_tagged_matrices)
    {
      libmesh_ignore(tag);
      cast_ptr<StaticCondensation *>(matrix)->set_current_elem(*elem);
    }
}

reinitElemFace()

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

virtual

Reinit assembly info for a side of an element.

Parameters

elem	The element
side	Side of of the element
tid	Thread ID

Reimplemented in AuxiliarySystem.

Definition at line 366 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 )

virtual

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

Definition at line 390 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  )

virtual

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

Definition at line 382 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, THREAD_ID  tid  )

virtual

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

Definition at line 374 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  )

virtual

Reinit nodal assembly info.

Parameters

node	Node to reinit for
tid	Thread ID

Definition at line 398 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  )

virtual

Reinit nodal assembly info on a face.

Parameters

node	Node to reinit
bnd_id	Boundary ID
tid	Thread ID

Definition at line 410 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  )

virtual

Reinit variables at a set of nodes.

Parameters

nodes	List of node ids to reinit
tid	Thread ID

Definition at line 422 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  )

virtual

Reinit variables at a set of neighbor nodes.

Parameters

nodes	List of node ids to reinit
tid	Thread ID

Definition at line 433 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  )

virtual

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 444 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

)

Removes a matrix with a given tag.

Parameters

tag_name

The name of the tag

Definition at line 590 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

)

Remove a vector from the system with the given name.

Definition at line 1326 of file SystemBase.C.

Referenced by restoreOldSolutions().

{
  system().remove_vector(name);
}

removeVector() [2/2]

void SystemBase::removeVector

(

TagID

tag_id

)

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

Parameters

tag_id

Tag ID

Definition at line 700 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>& SystemBase::residualCopy ( )

inlinevirtual

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 426 of file SystemBase.h.

Referenced by DisplacedSystem::residualCopy().

  {
    mooseError("This system does not support getting a copy of the residual");
  }

residualGhosted()

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

inlinevirtual

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 430 of file SystemBase.h.

Referenced by DisplacedSystem::residualGhosted().

  {
    mooseError("This system does not support getting a ghosted copy of the residual");
  }

residualSetup()

void SystemBase::residualSetup ( )

virtual

Reimplemented in NonlinearSystemBase, LinearSystem, and AuxiliarySystem.

Definition at line 1591 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 SystemBase::residualVectorTag ( ) const

inlinevirtual

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 307 of file SystemBase.h.

Referenced by defaultVectorTags(), and DisplacedSystem::residualVectorTag().

{ mooseError("Not implemented yet"); }

restoreOldSolutions()

void SystemBase::restoreOldSolutions ( )

virtual

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

Definition at line 542 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 ( )

virtual

Restore current solutions (call after your solve failed)

Reimplemented in SolverSystem.

Definition at line 1309 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 ( )

virtual

Save the old and older solutions.

Definition at line 510 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()

NumericVector< Number > & SystemBase::serializedSolution ( )

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1638 of file SystemBase.C.

Referenced by PNGOutput::calculateRescalingValues(), PNGOutput::makeMeshFunc(), and DisplacedSystem::serializedSolution().

{
  if (!_serialized_solution.get())
  {
    _serialized_solution = NumericVector<Number>::build(_communicator);
    _serialized_solution->init(system().n_dofs(), false, SERIAL);
  }

  return *_serialized_solution;
}

setActiveScalarVariableCoupleableVectorTags()

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

Set the active vector tags for the scalar variables.

Definition at line 1618 of file SystemBase.C.

Referenced by SubProblem::setActiveScalarVariableCoupleableVectorTags().

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

setActiveVariableCoupleableVectorTags()

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

Set the active vector tags for the variables.

Definition at line 1612 of file SystemBase.C.

Referenced by SubProblem::setActiveFEVariableCoupleableVectorTags().

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

setVariableGlobalDoFs()

void SystemBase::setVariableGlobalDoFs

(

const std::string &

var_name

)

set all the global dof indices for a variable

Parameters

var_name

The name of the variable

Definition at line 186 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 )

inline

Sets the verbose flag.

Parameters

[in]

verbose

Verbose flag

Definition at line 134 of file SystemBase.h.

Referenced by Executioner::Executioner().

{ _verbose = verbose; }

sizeVariableMatrixData()

void SystemBase::sizeVariableMatrixData

(

)

size the matrix data for each variable for the number of matrix tags we have

Definition at line 1711 of file SystemBase.C.

{
  for (const auto & warehouse : _vars)
    for (const auto & [var_num, var_ptr] : warehouse.numberToVariableMap())
      var_ptr->sizeMatrixTagData();
}

solution() [1/2]

NumericVector<Number>& SystemBase::solution ( )

inline

Definition at line 196 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(), 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(), MultiApp::restore(), restoreSolutions(), SecantSolve::saveVariableValues(), SteffensenSolve::saveVariableValues(), PicardSolve::saveVariableValues(), MooseEigenSystem::scaleSystemSolution(), AuxiliarySystem::serializeSolution(), NonlinearSystemBase::setConstraintSecondaryValues(), NonlinearSystemBase::setInitialSolution(), DisplacedSystem::solutionInternal(), NonlinearEigenSystem::solve(), MultiAppDofCopyTransfer::transfer(), SecantSolve::transformVariables(), SteffensenSolve::transformVariables(), PicardSolve::transformVariables(), AuxiliarySystem::variableWiseRelativeSolutionDifferenceNorm(), and zeroVariables().

{ return solutionState(0); }

solution() [2/2]

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

inline

Definition at line 199 of file SystemBase.h.

{ return solutionState(0); }

solutionInternal()

virtual NumericVector<Number>& SystemBase::solutionInternal ( ) const

protectedpure virtual

Internal getter for solution owned by libMesh.

Implemented in DisplacedSystem, AuxiliarySystem, and SolverSystem.

Referenced by needSolutionState(), and solutionState().

solutionOld() [1/2]

NumericVector<Number>& SystemBase::solutionOld ( )

inline

Definition at line 197 of file SystemBase.h.

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

{ return solutionState(1); }

solutionOld() [2/2]

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

inline

Definition at line 200 of file SystemBase.h.

{ return solutionState(1); }

solutionOlder() [1/2]

NumericVector<Number>& SystemBase::solutionOlder ( )

inline

Definition at line 198 of file SystemBase.h.

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

{ return solutionState(2); }

solutionOlder() [2/2]

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

inline

Definition at line 201 of file SystemBase.h.

{ return solutionState(2); }

solutionPreviousNewton() [1/2]

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

virtual

Reimplemented in DisplacedSystem.

Definition at line 1347 of file SystemBase.C.

Referenced by AuxiliarySystem::copyCurrentIntoPreviousNL(), copyPreviousNonlinearSolutions(), and restoreSolutions().

{
  if (hasVector(Moose::PREVIOUS_NL_SOLUTION_TAG))
    return &getVector(Moose::PREVIOUS_NL_SOLUTION_TAG);
  else
    return nullptr;
}

solutionPreviousNewton() [2/2]

NumericVector< Number > * SystemBase::solutionPreviousNewton ( )

virtual

Reimplemented in DisplacedSystem.

Definition at line 1338 of file SystemBase.C.

{
  if (hasVector(Moose::PREVIOUS_NL_SOLUTION_TAG))
    return &getVector(Moose::PREVIOUS_NL_SOLUTION_TAG);
  else
    return nullptr;
}

solutionState() [1/2]

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

virtual

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 in DisplacedSystem.

Definition at line 1423 of file SystemBase.C.

Referenced by copyOldSolutions(), copyPreviousFixedPointSolutions(), copyPreviousNonlinearSolutions(), PointwiseRenormalizeVector::execute(), PointwiseRenormalizeVector::finalize(), restoreOldSolutions(), saveOldSolutions(), solution(), solutionOld(), solutionOlder(), and DisplacedSystem::solutionState().

{
  if (!hasSolutionState(state, iteration_type))
    needSolutionState(state, iteration_type);
  return *_solution_states[static_cast<unsigned short>(iteration_type)][state];
}

solutionState() [2/2]

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

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1394 of file SystemBase.C.

{
  if (!hasSolutionState(state, iteration_type))
    mooseError("For iteration type '",
               Moose::stringify(iteration_type),
               "': solution state ",
               state,
               " was requested in ",
               name(),
               " but only up to state ",
               (_solution_states[static_cast<unsigned short>(iteration_type)].size() == 0)
                   ? 0
                   : _solution_states[static_cast<unsigned short>(iteration_type)].size() - 1,
               " is available.");

  const auto & solution_states = _solution_states[static_cast<unsigned short>(iteration_type)];

  if (state == 0)
    mooseAssert(solution_states[0] == &solutionInternal(), "Inconsistent current solution");
  else
    mooseAssert(solution_states[state] ==
                    &getVector(oldSolutionStateVectorName(state, iteration_type)),
                "Inconsistent solution state");

  return *solution_states[state];
}

solutionStateParallelType()

libMesh::ParallelType SystemBase::solutionStateParallelType	(	const unsigned int	state,
		const Moose::SolutionIterationType	iteration_type
	)		const

Returns the parallel type of the given solution state.

Definition at line 1432 of file SystemBase.C.

Referenced by needSolutionState().

{
  if (!hasSolutionState(state, iteration_type))
    mooseError("solutionStateParallelType() may only be called if the solution state exists.");

  return _solution_states[static_cast<unsigned short>(iteration_type)][state]->type();
}

solutionStatesInitialized()

bool SystemBase::solutionStatesInitialized ( ) const

inline

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 896 of file SystemBase.h.

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

{ return _solution_states_initialized; }

solutionUDot() [1/2]

virtual NumericVector<Number>* SystemBase::solutionUDot ( )

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 261 of file SystemBase.h.

Referenced by MooseVariableScalar::adUDot(), ActuallyExplicitEuler::computeTimeDerivatives(), ImplicitEuler::computeTimeDerivatives(), ExplicitEuler::computeTimeDerivatives(), NewmarkBeta::computeTimeDerivatives(), BDF2::computeTimeDerivatives(), CentralDifference::computeTimeDerivatives(), CrankNicolson::computeTimeDerivatives(), LStableDirk2::computeTimeDerivatives(), LStableDirk3::computeTimeDerivatives(), ImplicitMidpoint::computeTimeDerivatives(), ExplicitTVDRK2::computeTimeDerivatives(), LStableDirk4::computeTimeDerivatives(), AStableDirk4::computeTimeDerivatives(), ExplicitRK2::computeTimeDerivatives(), copyOldSolutions(), CrankNicolson::init(), CentralDifference::initialSetup(), MooseVariableScalar::reinit(), restoreSolutions(), DisplacedSystem::solutionUDot(), and MooseVariableScalar::uDot().

{ return _u_dot; }

solutionUDot() [2/2]

virtual const NumericVector<Number>* SystemBase::solutionUDot ( ) const

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 265 of file SystemBase.h.

{ return _u_dot; }

solutionUDotDot() [1/2]

virtual NumericVector<Number>* SystemBase::solutionUDotDot ( )

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 262 of file SystemBase.h.

Referenced by NewmarkBeta::computeTimeDerivatives(), CentralDifference::computeTimeDerivatives(), copyOldSolutions(), CentralDifference::initialSetup(), MooseVariableScalar::reinit(), restoreSolutions(), DisplacedSystem::solutionUDotDot(), and MooseVariableScalar::uDotDot().

{ return _u_dotdot; }

solutionUDotDot() [2/2]

virtual const NumericVector<Number>* SystemBase::solutionUDotDot ( ) const

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 266 of file SystemBase.h.

{ return _u_dotdot; }

solutionUDotDotOld() [1/2]

virtual NumericVector<Number>* SystemBase::solutionUDotDotOld ( )

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 264 of file SystemBase.h.

Referenced by NewmarkBeta::computeADTimeDerivatives(), NewmarkBeta::computeTimeDerivatives(), copyOldSolutions(), MooseVariableScalar::reinit(), restoreOldSolutions(), restoreSolutions(), saveOldSolutions(), DisplacedSystem::solutionUDotDotOld(), and MooseVariableScalar::uDotDotOld().

{ return _u_dotdot_old; }

solutionUDotDotOld() [2/2]

virtual const NumericVector<Number>* SystemBase::solutionUDotDotOld ( ) const

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 268 of file SystemBase.h.

{ return _u_dotdot_old; }

solutionUDotOld() [1/2]

virtual NumericVector<Number>* SystemBase::solutionUDotOld ( )

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 263 of file SystemBase.h.

Referenced by NewmarkBeta::computeADTimeDerivatives(), NewmarkBeta::computeTimeDerivatives(), copyOldSolutions(), MooseVariableScalar::reinit(), restoreOldSolutions(), restoreSolutions(), saveOldSolutions(), DisplacedSystem::solutionUDotOld(), and MooseVariableScalar::uDotOld().

{ return _u_dot_old; }

solutionUDotOld() [2/2]

virtual const NumericVector<Number>* SystemBase::solutionUDotOld ( ) const

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 267 of file SystemBase.h.

{ return _u_dot_old; }

solve()

void SystemBase::solve ( )

virtual

Solve the system (using libMesh magic)

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

Definition at line 1241 of file SystemBase.C.

{
  system().solve();
}

subdomainSetup()

void SystemBase::subdomainSetup ( )

virtual

Reimplemented in AuxiliarySystem.

Definition at line 1584 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 ( )

inline

Definition at line 101 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(), NonlinearSystemBase::setConstraintSecondaryValues(), and MooseVariableScalar::sizeMatrixTagData().

{ return _subproblem; }

subproblem() [2/2]

const SubProblem& SystemBase::subproblem ( ) const

inline

Definition at line 102 of file SystemBase.h.

{ return _subproblem; }

system() [1/2]

virtual libMesh::System& SystemBase::system ( )

pure virtual

Get the reference to the libMesh system.

Implemented in NonlinearSystemBase, DisplacedSystem, AuxiliarySystem, and LinearSystem.

Referenced by MooseVariableFieldBase::activeOnSubdomain(), MooseVariableFieldBase::activeSubdomains(), SubProblem::addCouplingGhostingFunctor(), addMatrix(), CreateDisplacedProblemAction::addProxyRelationshipManagers(), addVariable(), MultiAppConservativeTransfer::adjustTransferredSolution(), MultiAppConservativeTransfer::adjustTransferredSolutionNearestPoint(), augmentSendList(), MultiAppGeneralFieldNearestLocationTransfer::buildKDTrees(), MultiAppGeneralFieldShapeEvaluationTransfer::buildMeshFunctions(), SubProblem::cloneCouplingGhostingFunctor(), copySolutionsBackwards(), copyVars(), dofMap(), FEProblemBase::duplicateVariableCheck(), EigenProblem::EigenProblem(), PointwiseRenormalizeVector::execute(), MultiAppNearestNodeTransfer::execute(), MultiAppProjectionTransfer::execute(), MultiAppGeometricInterpolationTransfer::execute(), MultiAppUserObjectTransfer::execute(), FEProblem::FEProblem(), MultiAppGeometricInterpolationTransfer::fillSourceInterpolationPoints(), getVector(), Moose::globalDofIndexToDerivative(), hasScalarVariable(), hasVariable(), hasVector(), TimeIntegrator::init(), PointwiseRenormalizeVector::initialize(), MultiAppGeneralFieldNearestLocationTransfer::initialSetup(), MultiAppGeometricInterpolationTransfer::interpolateTargetPoints(), isArrayVariable(), isScalarVariable(), MassMatrix::MassMatrix(), MooseVariableBase::MooseVariableBase(), name(), number(), ConsoleUtils::outputSolverSystemInformation(), PointwiseRenormalizeVector::PointwiseRenormalizeVector(), prefix(), SolverSystem::preInit(), MultiAppProjectionTransfer::projectSolution(), reinitElem(), removeMatrix(), removeVector(), SolverSystem::restoreSolutions(), restoreSolutions(), serializedSolution(), SolverSystem::serializeSolution(), ElementSubdomainModifierBase::setOldAndOlderSolutions(), SolverSystem::solutionInternal(), solve(), MultiAppShapeEvaluationTransfer::transferVariable(), update(), and zeroVariables().

system() [2/2]

virtual const libMesh::System& SystemBase::system ( ) const

pure virtual

Implemented in NonlinearSystemBase, DisplacedSystem, AuxiliarySystem, and LinearSystem.

systemMatrixTag()

virtual TagID SystemBase::systemMatrixTag ( ) const

inlinevirtual

Return the Matrix Tag ID for System.

Reimplemented in NonlinearSystemBase, LinearSystem, and DisplacedSystem.

Definition at line 297 of file SystemBase.h.

Referenced by defaultMatrixTags(), and DisplacedSystem::systemMatrixTag().

{ mooseError("Not implemented yet"); }

timestepSetup()

void SystemBase::timestepSetup ( )

virtual

Reimplemented in NonlinearSystemBase, and AuxiliarySystem.

Definition at line 1570 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 SystemBase::timeVectorTag ( ) const

inlinevirtual

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 in NonlinearSystemBase, and DisplacedSystem.

Definition at line 292 of file SystemBase.h.

Referenced by defaultVectorTags(), and DisplacedSystem::timeVectorTag().

{ mooseError("Not implemented yet"); }

update()

void SystemBase::update

(

)

Update the system (doing libMesh magic)

Definition at line 1235 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(), SecantSolve::transformVariables(), SteffensenSolve::transformVariables(), and PicardSolve::transformVariables().

{
  system().update();
}

varKind()

Moose::VarKindType SystemBase::varKind ( ) const

inline

Returns

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

Definition at line 924 of file SystemBase.h.

Referenced by Coupleable::coupled().

{ return _var_kind; }

zeroTaggedVector()

void SystemBase::zeroTaggedVector

(

const TagID

tag

)

Zero vector with the given tag.

Definition at line 674 of file SystemBase.C.

Referenced by 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");
  if (!_subproblem.vectorTagNotZeroed(tag))
    getVector(tag).zero();
}

zeroTaggedVectors()

void SystemBase::zeroTaggedVectors

(

const std::set< TagID > &

tags

)

Zero all vectors for given tags.

Definition at line 693 of file SystemBase.C.

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

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

zeroVariables()

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

virtual

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

@ param vars_to_be_zeroed The variable names in this vector will have their solutions set to zero after this call

Reimplemented in DisplacedSystem.

Definition at line 200 of file SystemBase.C.

Referenced by DisplacedSystem::zeroVariables(), zeroVariablesForJacobian(), and zeroVariablesForResidual().

{
  if (vars_to_be_zeroed.size() > 0)
  {
    NumericVector<Number> & solution = this->solution();

    auto problem = dynamic_cast<FEProblemBase *>(&_subproblem);
    if (!problem)
      mooseError("System needs to be registered in FEProblemBase for using zeroVariables.");

    AllLocalDofIndicesThread aldit(*problem, vars_to_be_zeroed, true);
    ConstElemRange & elem_range = *_mesh.getActiveLocalElementRange();
    Threads::parallel_reduce(elem_range, aldit);

    const auto & dof_indices_to_zero = aldit.getDofIndices();

    solution.close();

    for (const auto & dof : dof_indices_to_zero)
      solution.set(dof, 0);

    solution.close();

    // Call update to update the current_local_solution for this system
    system().update();
  }
}

zeroVariablesForJacobian()

void SystemBase::zeroVariablesForJacobian ( )

virtual

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 235 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_jacobian);
}

zeroVariablesForResidual()

void SystemBase::zeroVariablesForResidual ( )

virtual

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 229 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_residual);
}

Member Data Documentation

_active_tagged_matrices

std::unordered_map<TagID, libMesh::SparseMatrix<Number> *> SystemBase::_active_tagged_matrices

protected

Active tagged matrices. A matrix is active if its tag-matrix pair is present in the map. We use a map instead of a vector so that users can easily add and remove to this container with calls to (de)activateMatrixTag.

Definition at line 1025 of file SystemBase.h.

Referenced by activateAllMatrixTags(), deactivateAllMatrixTags(), and reinitElem().

_app

MooseApp& SystemBase::_app

protected

Definition at line 988 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

protected

Whether to automatically scale the variables.

Definition at line 1055 of file SystemBase.h.

Referenced by automaticScaling(), 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(), applyScalingFactors(), MultiApp::backup(), FEProblemBase::backupMultiApps(), CoarsenedPiecewiseLinear::buildCoarsenedGrid(), DefaultSteadyStateConvergence::checkConvergence(), MeshDiagnosticsGenerator::checkElementOverlap(), MeshDiagnosticsGenerator::checkElementTypes(), MeshDiagnosticsGenerator::checkElementVolumes(), FEProblemBase::checkExceptionAndStopSolve(), SolverSystem::checkInvalidSolution(), MeshDiagnosticsGenerator::checkLocalJacobians(), MeshDiagnosticsGenerator::checkNonConformalMesh(), MeshDiagnosticsGenerator::checkNonConformalMeshFromAdaptivity(), MeshDiagnosticsGenerator::checkNonMatchingEdges(), MeshDiagnosticsGenerator::checkNonPlanarSides(), FEProblemBase::checkProblemIntegrity(), ReferenceResidualConvergence::checkRelativeConvergence(), MeshDiagnosticsGenerator::checkSidesetsOrientation(), MeshDiagnosticsGenerator::checkWatertightNodesets(), MeshDiagnosticsGenerator::checkWatertightSidesets(), IterationAdaptiveDT::computeAdaptiveDT(), TransientBase::computeConstrainedDT(), DefaultMultiAppFixedPointConvergence::computeCustomConvergencePostprocessor(), NonlinearSystemBase::computeDamping(), FixedPointIterationAdaptiveDT::computeDT(), IterationAdaptiveDT::computeDT(), IterationAdaptiveDT::computeFailedDT(), IterationAdaptiveDT::computeInitialDT(), IterationAdaptiveDT::computeInterpolationDT(), LinearSystem::computeLinearSystemTags(), FEProblemBase::computeLinearSystemTags(), NonlinearSystemBase::computeScaling(), Problem::console(), IterationAdaptiveDT::constrainStep(), TimeStepper::constrainStep(), MultiApp::createApp(), FEProblemBase::execMultiApps(), FEProblemBase::execMultiAppTransfers(), MFEMSteady::execute(), MessageFromInput::execute(), SteadyBase::execute(), Eigenvalue::execute(), ActionWarehouse::executeActionsWithAction(), ActionWarehouse::executeAllActions(), MeshGeneratorSystem::executeMeshGenerators(), ElementQualityChecker::finalize(), SidesetAroundSubdomainUpdater::finalize(), FEProblemBase::finishMultiAppStep(), MeshRepairGenerator::fixOverlappingNodes(), CoarsenBlockGenerator::generate(), MeshGenerator::generateInternal(), VariableCondensationPreconditioner::getDofToCondense(), InversePowerMethod::init(), NonlinearEigen::init(), FEProblemBase::initialAdaptMesh(), DefaultMultiAppFixedPointConvergence::initialize(), EigenExecutionerBase::inversePowerIteration(), FEProblemBase::joinAndFinalize(), TransientBase::keepGoing(), IterationAdaptiveDT::limitDTByFunction(), IterationAdaptiveDT::limitDTToPostprocessorValue(), FEProblemBase::logAdd(), EigenExecutionerBase::makeBXConsistent(), Console::meshChanged(), MooseBase::mooseDeprecated(), MooseBase::mooseInfo(), MooseBase::mooseWarning(), MooseBase::mooseWarningNonPrefixed(), ReferenceResidualConvergence::nonlinearConvergenceSetup(), ReporterDebugOutput::output(), PerfGraphOutput::output(), SolutionInvalidityOutput::output(), MaterialPropertyDebugOutput::output(), DOFMapOutput::output(), VariableResidualNormsDebugOutput::output(), Console::output(), ControlOutput::outputActiveObjects(), ControlOutput::outputChangedControls(), ControlOutput::outputControls(), Console::outputInput(), Console::outputPostprocessors(), PseudoTimestep::outputPseudoTimestep(), Console::outputReporters(), DefaultMultiAppFixedPointConvergence::outputResidualNorm(), Console::outputScalarVariables(), Console::outputSystemInformation(), FEProblemBase::possiblyRebuildGeomSearchPatches(), EigenExecutionerBase::postExecute(), AB2PredictorCorrector::postSolve(), ActionWarehouse::printActionDependencySets(), BlockRestrictionDebugOutput::printBlockRestrictionMap(), SolutionInvalidity::printDebug(), EigenExecutionerBase::printEigenvalue(), SecantSolve::printFixedPointConvergenceHistory(), SteffensenSolve::printFixedPointConvergenceHistory(), PicardSolve::printFixedPointConvergenceHistory(), FixedPointSolve::printFixedPointConvergenceReason(), PerfGraphLivePrint::printLiveMessage(), MaterialPropertyDebugOutput::printMaterialMap(), PerfGraphLivePrint::printStats(), NEML2Action::printSummary(), AutomaticMortarGeneration::projectPrimaryNodesSinglePair(), AutomaticMortarGeneration::projectSecondaryNodesSinglePair(), CoarsenBlockGenerator::recursiveCoarsen(), SolutionTimeAdaptiveDT::rejectStep(), MultiApp::restore(), FEProblemBase::restoreMultiApps(), FEProblemBase::restoreSolutions(), NonlinearSystemBase::setInitialSolution(), MooseApp::setupOptions(), Checkpoint::shouldOutput(), SubProblem::showFunctorRequestors(), SubProblem::showFunctors(), FullSolveMultiApp::showStatusMessage(), EigenProblem::solve(), FEProblemSolve::solve(), NonlinearSystem::solve(), FixedPointSolve::solve(), LinearSystem::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(), MFEMTransient::takeStep(), TransientBase::takeStep(), TerminateChainControl::terminate(), Convergence::verboseOutput(), Console::writeTimestepInformation(), Console::writeVariableNorms(), and FEProblemBase::~FEProblemBase().

_du_dot_du

std::vector<Real> SystemBase::_du_dot_du

protected

Derivative of time derivative of u with respect to uj.

This depends on the time integration scheme

Definition at line 1017 of file SystemBase.h.

Referenced by addVariable(), duDotDu(), and duDotDus().

_du_dotdot_du

Real SystemBase::_du_dotdot_du

protected

Definition at line 1018 of file SystemBase.h.

Referenced by duDotDotDu().

_factory

Factory& SystemBase::_factory

protected

Definition at line 989 of file SystemBase.h.

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

_fe_problem

FEProblemBase& SystemBase::_fe_problem

protected

the governing finite element/volume problem

Definition at line 986 of file SystemBase.h.

Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), addDotVectors(), NonlinearSystemBase::addHDGKernel(), NonlinearSystemBase::addInterfaceKernel(), NonlinearSystemBase::addKernel(), NonlinearSystemBase::addNodalKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), 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(), LinearSystem::containsTimeKernel(), NonlinearSystem::converged(), NonlinearSystemBase::customSetup(), MooseEigenSystem::eigenKernelOnCurrent(), MooseEigenSystem::eigenKernelOnOld(), NonlinearSystemBase::enforceNodalConstraintsJacobian(), NonlinearSystemBase::enforceNodalConstraintsResidual(), feProblem(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), LinearSystem::initialSetup(), NonlinearSystemBase::initialSetup(), NonlinearSystemBase::jacobianSetup(), LinearSystem::LinearSystem(), NonlinearSystemBase::NonlinearSystemBase(), NonlinearSystemBase::overwriteNodeFace(), NonlinearSystem::potentiallySetupFiniteDifferencing(), NonlinearSystemBase::preInit(), 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

protected

Active flags for tagged matrices.

Definition at line 1027 of file SystemBase.h.

Referenced by activateAllMatrixTags(), deactivateAllMatrixTags(), and matrixTagActive().

_max_var_n_dofs_per_elem

size_t SystemBase::_max_var_n_dofs_per_elem

protected

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

Definition at line 1043 of file SystemBase.h.

Referenced by assignMaxVarNDofsPerElem(), and getMaxVarNDofsPerElem().

_max_var_n_dofs_per_node

size_t SystemBase::_max_var_n_dofs_per_node

protected

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

Definition at line 1046 of file SystemBase.h.

Referenced by assignMaxVarNDofsPerNode(), and getMaxVarNDofsPerNode().

_max_var_number

unsigned int SystemBase::_max_var_number

protected

Maximum variable number.

Definition at line 1000 of file SystemBase.h.

Referenced by addVariable(), and getMaxVariableNumber().

_mesh

MooseMesh& SystemBase::_mesh

protected

Definition at line 991 of file SystemBase.h.

Referenced by addVariable(), NonlinearSystemBase::assembleScalingVector(), augmentSendList(), NonlinearSystemBase::checkKernelCoverage(), AuxiliarySystem::computeElementalVarsHelper(), NonlinearSystemBase::computeJacobianInternal(), AuxiliarySystem::computeMortarNodalVars(), AuxiliarySystem::computeNodalVarsHelper(), NonlinearSystemBase::constraintJacobians(), NonlinearSystemBase::constraintResiduals(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), NonlinearSystemBase::getNodeDofs(), initialSetup(), mesh(), NonlinearSystemBase::overwriteNodeFace(), NonlinearSystemBase::reinitNodeFace(), NonlinearSystemBase::setConstraintSecondaryValues(), setVariableGlobalDoFs(), AuxiliarySystem::variableWiseRelativeSolutionDifferenceNorm(), and zeroVariables().

_name

std::string SystemBase::_name

protected

The name of this system.

Definition at line 993 of file SystemBase.h.

_numbered_vars

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

protected

Map variable number to its pointer.

Definition at line 1052 of file SystemBase.h.

Referenced by addVariable(), and getVariable().

_raw_grad_container

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

protected

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 1073 of file SystemBase.h.

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

_saved_dot_old

NumericVector<Real>* SystemBase::_saved_dot_old

protected

Definition at line 1034 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

_saved_dotdot_old

NumericVector<Real>* SystemBase::_saved_dotdot_old

protected

Definition at line 1035 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

_saved_old

NumericVector<Real>* SystemBase::_saved_old

protected

Definition at line 1030 of file SystemBase.h.

_saved_older

NumericVector<Real>* SystemBase::_saved_older

protected

Definition at line 1031 of file SystemBase.h.

_saved_solution_states

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

private

The saved solution states (0 = current, 1 = old, 2 = older, etc)

Definition at line 1086 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

_serialized_solution

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

protected

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

Definition at line 1068 of file SystemBase.h.

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

_solution_states

std::array<std::vector<NumericVector<Number> *>, 3> SystemBase::_solution_states

private

2D array of solution state vector pointers; first index corresponds to SolutionIterationType, second index corresponds to state index (0=current, 1=old, 2=older)

Definition at line 1084 of file SystemBase.h.

Referenced by copyOldSolutions(), copyPreviousFixedPointSolutions(), copyPreviousNonlinearSolutions(), hasSolutionState(), needSolutionState(), restoreOldSolutions(), saveOldSolutions(), solutionState(), and solutionStateParallelType().

_solution_states_initialized

bool SystemBase::_solution_states_initialized

protected

Whether or not the solution states have been initialized.

Definition at line 1061 of file SystemBase.h.

Referenced by initSolutionState(), and solutionStatesInitialized().

_subproblem

SubProblem& SystemBase::_subproblem

protected

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 983 of file SystemBase.h.

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

_tagged_matrices

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

protected

Tagged matrices (pointer)

Definition at line 1023 of file SystemBase.h.

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

_tagged_vectors

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

protected

Tagged vectors (pointer)

Definition at line 1021 of file SystemBase.h.

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

_time_integrators

std::vector<std::shared_ptr<TimeIntegrator> > SystemBase::_time_integrators

protected

Time integrator.

Definition at line 1049 of file SystemBase.h.

Referenced by addTimeIntegrator(), SolverSystem::compute(), AuxiliarySystem::compute(), NonlinearSystemBase::computeResidualAndJacobianTags(), NonlinearSystemBase::computeResidualTags(), copyTimeIntegrators(), getTimeIntegrators(), NonlinearSystemBase::onTimestepBegin(), queryTimeIntegrator(), NonlinearSystem::solve(), and NonlinearEigenSystem::solve().

_u_dot

NumericVector<Number>* SystemBase::_u_dot

protected

solution vector for u^dot

Definition at line 1006 of file SystemBase.h.

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

_u_dot_old

NumericVector<Number>* SystemBase::_u_dot_old

protected

old solution vector for u^dot

Definition at line 1011 of file SystemBase.h.

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

_u_dotdot

NumericVector<Number>* SystemBase::_u_dotdot

protected

solution vector for u^dotdot

Definition at line 1008 of file SystemBase.h.

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

_u_dotdot_old

NumericVector<Number>* SystemBase::_u_dotdot_old

protected

old solution vector for u^dotdot

Definition at line 1013 of file SystemBase.h.

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

_var_all_dof_indices

std::vector<dof_id_type> SystemBase::_var_all_dof_indices

protected

Container for the dof indices of a given variable.

Definition at line 1064 of file SystemBase.h.

Referenced by getVariableGlobalDoFs(), and setVariableGlobalDoFs().

_var_kind

Moose::VarKindType SystemBase::_var_kind

protected

default kind of variables in this system

Definition at line 1038 of file SystemBase.h.

Referenced by varKind().

_var_map

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

protected

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

Definition at line 998 of file SystemBase.h.

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

_var_to_copy

std::vector<VarCopyInfo> SystemBase::_var_to_copy

protected

Definition at line 1040 of file SystemBase.h.

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

_vars

std::vector<VariableWarehouse> SystemBase::_vars

protected

Variable warehouses (one for each thread)

Definition at line 996 of file SystemBase.h.

Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addInterfaceKernel(), AuxiliarySystem::addVariable(), addVariable(), applyScalingFactors(), NonlinearSystemBase::assembleScalingVector(), clearAllDofIndices(), AuxiliarySystem::compute(), customSetup(), getActualFieldVariable(), getFieldVariable(), getFVVariable(), AuxiliarySystem::getMinQuadratureOrder(), getMinQuadratureOrder(), getScalarVariable(), getScalarVariables(), getVariable(), getVariableNames(), getVariables(), LinearSystem::initialSetup(), initialSetup(), jacobianSetup(), nFieldVariables(), nFVVariables(), nVariables(), prepare(), prepareFace(), prepareLowerD(), prepareNeighbor(), reinitElem(), reinitElemFace(), reinitLowerD(), reinitNeighbor(), reinitNeighborFace(), reinitNode(), reinitNodeFace(), reinitNodes(), reinitNodesNeighbor(), reinitScalars(), residualSetup(), setActiveScalarVariableCoupleableVectorTags(), setActiveVariableCoupleableVectorTags(), NonlinearSystemBase::setupScalingData(), sizeVariableMatrixData(), subdomainSetup(), and timestepSetup().

_vars_to_be_zeroed_on_jacobian

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

protected

Definition at line 1003 of file SystemBase.h.

Referenced by addVariableToZeroOnJacobian(), and zeroVariablesForJacobian().

_vars_to_be_zeroed_on_residual

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

protected

Definition at line 1002 of file SystemBase.h.

Referenced by addVariableToZeroOnResidual(), and zeroVariablesForResidual().

_verbose

bool SystemBase::_verbose

protected

True if printing out additional information.

Definition at line 1058 of file SystemBase.h.

Referenced by applyScalingFactors(), and setVerboseFlag().

---

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

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