AuxiliarySystem Class Reference

A system that holds auxiliary variables. More...

#include <AuxiliarySystem.h>

Inheritance diagram for AuxiliarySystem:

Public Member Functions
	AuxiliarySystem (FEProblemBase &subproblem, const std::string &name)
virtual	~AuxiliarySystem ()
virtual void	initialSetup () override
	Setup Functions. More...
virtual void	reinit () override
	Reinitialize the system when the degrees of freedom in this system have changed. More...
virtual void	timestepSetup () override
virtual void	customSetup (const ExecFlagType &exec_type) override
virtual void	subdomainSetup () override
virtual void	residualSetup () override
virtual void	jacobianSetup () override
virtual void	updateActive (THREAD_ID tid)
virtual void	addVariable (const std::string &var_type, const std::string &name, InputParameters &parameters) override
	Canonical method for adding a variable. More...
void	addKernel (const std::string &kernel_name, const std::string &name, InputParameters &parameters)
	Adds an auxiliary kernel. More...
void	addKokkosKernel (const std::string &kernel_name, const std::string &name, InputParameters &parameters)
void	addScalarKernel (const std::string &kernel_name, const std::string &name, InputParameters &parameters)
	Adds a scalar kernel. More...
virtual void	reinitElem (const Elem *elem, THREAD_ID tid) override
	Reinit an element assembly info. More...
virtual void	reinitElemFace (const Elem *elem, unsigned int side, THREAD_ID tid) override
	Reinit assembly info for a side of an element. More...
const NumericVector< Number > *const &	currentSolution () const override
	The solution vector that is currently being operated on. More...
virtual void	serializeSolution ()
virtual void	augmentSparsity (libMesh::SparsityPattern::Graph &, std::vector< dof_id_type > &, std::vector< dof_id_type > &) override
	Will modify the sparsity pattern to add logical geometric connections. More...
virtual void	compute (ExecFlagType type) override
	Compute auxiliary variables. More...
void	kokkosCompute (ExecFlagType type)
std::set< std::string >	getDependObjects (ExecFlagType type)
	Get a list of dependent UserObjects for this exec type. More...
std::set< std::string >	getDependObjects ()
virtual libMesh::Order	getMinQuadratureOrder () override
	Get the minimum quadrature order for evaluating elemental auxiliary variables. More...
bool	needMaterialOnSide (BoundaryID bnd_id)
	Indicated whether this system needs material properties on boundaries. More...
virtual libMesh::System &	sys ()
virtual libMesh::System &	system () override
	Get the reference to the libMesh system. More...
virtual const libMesh::System &	system () const override
virtual void	copyCurrentIntoPreviousNL ()
	Copies the current solution into the previous nonlinear iteration solution. More...
void	setScalarVariableCoupleableTags (ExecFlagType type)
void	clearScalarVariableCoupleableTags ()
const ExecuteMooseObjectWarehouse< AuxKernel > &	nodalAuxWarehouse () const
const ExecuteMooseObjectWarehouse< VectorAuxKernel > &	nodalVectorAuxWarehouse () const
const ExecuteMooseObjectWarehouse< ArrayAuxKernel > &	nodalArrayAuxWarehouse () const
const ExecuteMooseObjectWarehouse< AuxKernel > &	elemAuxWarehouse () const
const ExecuteMooseObjectWarehouse< VectorAuxKernel > &	elemVectorAuxWarehouse () const
const ExecuteMooseObjectWarehouse< ArrayAuxKernel > &	elemArrayAuxWarehouse () const
const ExecuteMooseObjectWarehouse< AuxKernelBase > &	kokkosNodalAuxWarehouse () const
const ExecuteMooseObjectWarehouse< AuxKernelBase > &	kokkosElemAuxWarehouse () const
void	variableWiseRelativeSolutionDifferenceNorm (std::vector< Number > &var_diffs) const
	Computes and stores ||current - old|| / ||current|| for each variable in the given vector. More...
const std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > > &	linearFVLimitedGradientContainer (const Moose::FV::GradientLimiterType limiter_type) const
	Access the stored raw or limited cell-centered gradient components. More...
void	requestLinearFVLimitedGradients (const Moose::FV::GradientLimiterType limiter_type, unsigned int variable_number)
	Request storage and assembly of limiter-specific cell gradients. More...
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 void	preInit ()
	This is called prior to the libMesh system has been init'd. More...
virtual void	postInit ()
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...
NumericVector< Number > &	solution ()
const NumericVector< Number > &	solution () const
NumericVector< Number > &	solutionOld ()
const NumericVector< Number > &	solutionOld () const
NumericVector< Number > &	solutionOlder ()
const NumericVector< Number > &	solutionOlder () const
virtual 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 &	duDotDotDu () const
virtual const Number &	duDotDu (unsigned int var_num=0) const
virtual NumericVector< Number > *	solutionUDot ()
virtual const NumericVector< Number > *	solutionUDot () const
virtual NumericVector< Number > *	solutionUDotDot ()
virtual const NumericVector< Number > *	solutionUDotDot () const
virtual NumericVector< Number > *	solutionUDotOld ()
virtual const NumericVector< Number > *	solutionUDotOld () const
virtual NumericVector< Number > *	solutionUDotDotOld ()
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 bool	isArrayVariable (const std::string &var_name) const
	If a variable is an array variable. More...
virtual bool	isScalarVariable (unsigned int var_name) const
MooseVariableFieldBase &	getVariable (THREAD_ID tid, const std::string &var_name) const
	Gets a reference to a variable of with specified name. More...
MooseVariableFieldBase &	getVariable (THREAD_ID tid, unsigned int var_number) const
	Gets a reference to a variable with specified number. More...
template<typename T >
MooseVariableFE< T > &	getFieldVariable (THREAD_ID tid, const std::string &var_name)
	Gets a reference to a variable of with specified name. More...
template<typename T >
MooseVariableFE< T > &	getFieldVariable (THREAD_ID tid, unsigned int var_number)
	Gets a reference to a variable with specified number. More...
template<typename T >
MooseVariableField< T > &	getActualFieldVariable (THREAD_ID tid, const std::string &var_name)
	Returns a field variable pointer - this includes finite volume variables. More...
template<typename T >
MooseVariableField< T > &	getActualFieldVariable (THREAD_ID tid, unsigned int var_number)
	Returns a field variable pointer - this includes finite volume variables. More...
template<typename T >
MooseVariableFV< T > &	getFVVariable (THREAD_ID tid, const std::string &var_name)
	Return a finite volume variable. More...
virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, const std::string &var_name) const
	Gets a reference to a scalar variable with specified number. More...
virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, unsigned int var_number) const
	Gets a reference to a variable with specified number. More...
virtual const std::set< SubdomainID > *	getVariableBlocks (unsigned int var_number)
	Get the block where a variable of this system is defined. More...
virtual unsigned int	nVariables () const
	Get the number of variables in this system. More...
unsigned int	nFieldVariables () const
	Get the number of field variables in this system. More...
unsigned int	nFVVariables () const
	Get the number of finite volume variables in this system. More...
std::size_t	getMaxVarNDofsPerElem () const
	Gets the maximum number of dofs used by any one variable on any one element. More...
std::size_t	getMaxVarNDofsPerNode () const
	Gets the maximum number of dofs used by any one variable on any one node. More...
void	assignMaxVarNDofsPerElem (std::size_t max_dofs)
	assign the maximum element dofs More...
void	assignMaxVarNDofsPerNode (std::size_t max_dofs)
	assign the maximum node dofs More...
virtual void	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 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	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 VariableWarehouse &	variableWarehouse (THREAD_ID tid=0) const
const std::vector< MooseVariableScalar * > &	getScalarVariables (THREAD_ID tid)
const std::set< SubdomainID > &	getSubdomainsForVar (unsigned int var_number) const
const std::set< SubdomainID > &	getSubdomainsForVar (const std::string &var_name) const
	Get the block where a variable of this system is defined. More...
void	removeVector (const std::string &name)
	Remove a vector from the system with the given name. More...
void	removeVector (TagID tag_id)
	Remove a solution length vector from the system with the specified TagID. More...
NumericVector< Number > &	addVector (const std::string &vector_name, const bool project, const 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	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...
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
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...
void	skipNextSolutionToOldCopy ()
	Skip the next copy from the solution vector to the old solution vector old -> older is still performed. More...
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const
PerfGraph &	perfGraph ()
	Get the PerfGraph. More...
const std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > > &	linearFVGradientContainer () const
	Access the stored raw cell-centered gradient components. More...
void	requestLinearFVLimitedGradients (const Moose::FV::GradientLimiterType limiter_type, unsigned int variable_number)
	Request storage and assembly of limiter-specific cell gradients. More...
const std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > > &	linearFVLimitedGradientContainer (const Moose::FV::GradientLimiterType limiter_type) const
	Access the stored raw or limited cell-centered gradient components. More...
const std::unordered_set< Moose::FV::GradientLimiterType > &	requestedLinearFVLimitedGradientTypes () const
	Access the limiter types requested for this system. More...
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

Static Public Member Functions
static InputParameters	validParams ()

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

Protected Member Functions
void	computeScalarVars (ExecFlagType type)
void	computeNodalVars (ExecFlagType type)
void	computeMortarNodalVars (ExecFlagType type)
void	computeNodalVecVars (ExecFlagType type)
void	computeNodalArrayVars (ExecFlagType type)
void	computeElementalVars (ExecFlagType type)
void	computeElementalVecVars (ExecFlagType type)
void	computeElementalArrayVars (ExecFlagType type)
template<typename AuxKernelType >
void	computeElementalVarsHelper (const MooseObjectWarehouse< AuxKernelType > &warehouse)
template<typename AuxKernelType >
void	computeNodalVarsHelper (const MooseObjectWarehouse< AuxKernelType > &warehouse)
NumericVector< Number > &	solutionInternal () const override
	Internal getter for solution owned by libMesh. More...
PerfID	registerTimedSection (const std::string &section_name, const unsigned int level) const
	Call to register a named section for timing. More...
PerfID	registerTimedSection (const std::string &section_name, const unsigned int level, const std::string &live_message, const bool print_dots=true) const
	Call to register a named section for timing. More...
std::string	timedSectionName (const std::string &section_name) const
void	computeGradients ()
	Compute and store raw and requested limited Green-Gauss gradients for linear FV variables. More...
void	rebuildLinearFVGradientStorage ()
	Rebuild persistent raw and temporary gradient storage after mesh/DOF changes. More...
std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > > &	temporaryLinearFVGradientContainer ()
	Return temporary storage for gradients during gradient assembly. More...
std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > > &	temporaryLinearFVLimitedGradientContainer (const Moose::FV::GradientLimiterType limiter_type)
	Return temporary storage for limited gradients during gradient assembly. More...
std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > > &	rawLinearFVLimitedGradientContainer (const Moose::FV::GradientLimiterType limiter_type)
	Access the persisted limited-gradient storage for a specific limiter. More...
const std::unordered_set< unsigned int > &	requestedLinearFVLimitedGradientVariables (const Moose::FV::GradientLimiterType limiter_type) const
	Access the variable numbers that requested limited gradients for a specific limiter. More...
bool	needsLinearFVGradientStorage () const
void	initializeContainer (std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number >>> &container) const

Protected Attributes
libMesh::System &	_sys
const NumericVector< Number > *	_current_solution
	solution vector from nonlinear solver More...
std::vector< NumericVector< Number > * >	_solution_state
	The current states of the solution (0 = current, 1 = old, etc) More...
std::vector< std::vector< MooseVariableFEBase * > >	_nodal_vars
ExecuteMooseObjectWarehouse< AuxScalarKernel >	_aux_scalar_storage
ExecuteMooseObjectWarehouse< AuxKernel >	_nodal_aux_storage
ExecuteMooseObjectWarehouse< AuxKernel >	_mortar_nodal_aux_storage
ExecuteMooseObjectWarehouse< AuxKernel >	_elemental_aux_storage
ExecuteMooseObjectWarehouse< VectorAuxKernel >	_nodal_vec_aux_storage
ExecuteMooseObjectWarehouse< VectorAuxKernel >	_elemental_vec_aux_storage
ExecuteMooseObjectWarehouse< ArrayAuxKernel >	_nodal_array_aux_storage
ExecuteMooseObjectWarehouse< ArrayAuxKernel >	_elemental_array_aux_storage
ExecuteMooseObjectWarehouse< AuxKernelBase >	_kokkos_nodal_aux_storage
ExecuteMooseObjectWarehouse< AuxKernelBase >	_kokkos_elemental_aux_storage
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...
const Parallel::Communicator &	_communicator
MooseApp &	_pg_moose_app
	The MooseApp that owns the PerfGraph. More...
const std::string	_prefix
	A prefix to use for all sections. More...
std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > >	_temporary_gradient
	Scratch storage for raw gradients assembled during the current compute pass. More...
std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > >	_raw_grad_container
	Persisted raw cell-centered gradient components keyed by spatial direction. More...
std::unordered_set< Moose::FV::GradientLimiterType >	_requested_limited_gradient_types
	Set of requested limiter types for which limited gradients should be computed. More...
std::unordered_map< Moose::FV::GradientLimiterType, std::unordered_set< unsigned int > >	_requested_limited_gradient_variables
	Variable numbers requesting limited gradients, keyed by limiter type. More...
std::unordered_map< Moose::FV::GradientLimiterType, std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > > >	_raw_limited_grad_containers
	Persisted limited gradient components keyed by limiter type. More...
std::unordered_map< Moose::FV::GradientLimiterType, std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number > > > >	_temporary_limited_gradient
	Scratch storage for limited gradients assembled during the current compute pass. More...
std::vector< std::vector< MooseVariableFieldBase * > >	_elem_vars
	Elemental variables. More...

Friends
class	ComputeIndicatorThread
class	ComputeMarkerThread
class	FlagElementsThread
class	ComputeNodalKernelsThread
class	ComputeNodalKernelBcsThread
class	ComputeNodalKernelJacobiansThread
class	ComputeNodalKernelBCJacobiansThread

Detailed Description

A system that holds auxiliary variables.

Definition at line 43 of file AuxiliarySystem.h.

Constructor & Destructor Documentation

AuxiliarySystem()

AuxiliarySystem::AuxiliarySystem	(	FEProblemBase &	subproblem,
		const std::string &	name
	)

Definition at line 75 of file AuxiliarySystem.C.

{
  TIME_SECTION("initialSetup", 3, "Initializing Auxiliary System");

  SystemBase::initialSetup();
  _current_solution = _sys.current_local_solution.get();
  LinearFVGradientInterface::rebuildLinearFVGradientStorage();

  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _aux_scalar_storage.sort(tid);
    _aux_scalar_storage.initialSetup(tid);

    _nodal_aux_storage.sort(tid);
    _nodal_aux_storage.initialSetup(tid);

    _mortar_nodal_aux_storage.sort(tid);
    _mortar_nodal_aux_storage.initialSetup(tid);

    _nodal_vec_aux_storage.sort(tid);
    _nodal_vec_aux_storage.initialSetup(tid);

    _nodal_array_aux_storage.sort(tid);
    _nodal_array_aux_storage.initialSetup(tid);

    _elemental_aux_storage.sort(tid);
    _elemental_aux_storage.initialSetup(tid);

    _elemental_vec_aux_storage.sort(tid);
    _elemental_vec_aux_storage.initialSetup(tid);

    _elemental_array_aux_storage.sort(tid);
    _elemental_array_aux_storage.initialSetup(tid);
  }

#ifdef MOOSE_KOKKOS_ENABLED
  _kokkos_nodal_aux_storage.sort(/*tid=*/0);
  _kokkos_nodal_aux_storage.initialSetup(/*tid=*/0);

  _kokkos_elemental_aux_storage.sort(/*tid=*/0);
  _kokkos_elemental_aux_storage.initialSetup(/*tid=*/0);
#endif
}

~AuxiliarySystem()

virtual AuxiliarySystem::~AuxiliarySystem ( )

virtual

Member Function Documentation

activateAllMatrixTags()

void SystemBase::activateAllMatrixTags ( )

virtualinherited

Make all existing matrices active.

Definition at line 1132 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 ( )

virtualinherited

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 1622 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);
}

addKernel()

void AuxiliarySystem::addKernel	(	const std::string &	kernel_name,
		const std::string &	name,
		InputParameters &	parameters
	)

Adds an auxiliary kernel.

Parameters

kernel_name	The type of the kernel
name	The name of the kernel
parameters	Parameters for this kernel

Definition at line 312 of file AuxiliarySystem.C.

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    const auto & base = parameters.getBase();
    if (base == "AuxKernel" || base == "Bounds")
    {
      std::shared_ptr<AuxKernel> kernel =
          _factory.create<AuxKernel>(kernel_name, name, parameters, tid);
      if (kernel->isNodal())
      {
        if (kernel->isMortar())
          _mortar_nodal_aux_storage.addObject(kernel, tid);
        else
          _nodal_aux_storage.addObject(kernel, tid);
      }
      else
        _elemental_aux_storage.addObject(kernel, tid);
    }

    else if (base == "VectorAuxKernel")
    {
      std::shared_ptr<VectorAuxKernel> kernel =
          _factory.create<VectorAuxKernel>(kernel_name, name, parameters, tid);
      if (kernel->isNodal())
      {
        if (kernel->isMortar())
          mooseError("Vector mortar aux kernels not yet implemented");
        _nodal_vec_aux_storage.addObject(kernel, tid);
      }
      else
        _elemental_vec_aux_storage.addObject(kernel, tid);
    }

    else if (base == "ArrayAuxKernel")
    {
      std::shared_ptr<ArrayAuxKernel> kernel =
          _factory.create<ArrayAuxKernel>(kernel_name, name, parameters, tid);
      if (kernel->isNodal())
      {
        if (kernel->isMortar())
          mooseError("Vector mortar aux kernels not yet implemented");
        _nodal_array_aux_storage.addObject(kernel, tid);
      }
      else
        _elemental_array_aux_storage.addObject(kernel, tid);
    }
    else
      mooseAssert(false,
                  "Attempting to add AuxKernel of type '" + kernel_name + "' and name '" + name +
                      "' to the auxiliary system with invalid _moose_base: " + base);
  }
}

addKokkosKernel()

void AuxiliarySystem::addKokkosKernel	(	const std::string &	kernel_name,
		const std::string &	name,
		InputParameters &	parameters
	)

addMatrix()

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

inherited

Adds a matrix with a given tag.

Parameters

tag_name

The name of the tag

Definition at line 571 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;
}

addScalarKernel()

void AuxiliarySystem::addScalarKernel	(	const std::string &	kernel_name,
		const std::string &	name,
		InputParameters &	parameters
	)

Adds a scalar kernel.

Parameters

kernel_name	The type of the kernel
name	The name of the kernel
parameters	Kernel parameters

Definition at line 369 of file AuxiliarySystem.C.

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    std::shared_ptr<AuxScalarKernel> kernel =
        _factory.create<AuxScalarKernel>(kernel_name, name, parameters, tid);
    _aux_scalar_storage.addObject(kernel, tid);
  }
}

addScalingVector()

void SystemBase::addScalingVector ( )

inherited

Add the scaling factor vector to the system.

Definition at line 1547 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  )

inherited

Definition at line 1647 of file SystemBase.C.

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

addVariable()

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

overridevirtual

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 from SystemBase.

Definition at line 258 of file AuxiliarySystem.C.

{
  SystemBase::addVariable(var_type, name, parameters);

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

  if (var_type == "MooseVariableScalar")
    return;

  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    if (FEInterface::field_type(fe_type) == TYPE_VECTOR)
    {
      auto * var = _vars[tid].getActualFieldVariable<RealVectorValue>(name);
      if (var)
      {
        if (var->feType().family == LAGRANGE_VEC)
          _nodal_vars[tid].push_back(var);
        else
          _elem_vars[tid].push_back(var);
      }
    }

    else
    {
      MooseVariableBase * var_base = _vars[tid].getVariable(name);

      auto * const var = dynamic_cast<MooseVariableField<Real> *>(var_base);

      if (var)
      {
        if (var->feType().family == LAGRANGE)
          _nodal_vars[tid].push_back(var);
        else
          _elem_vars[tid].push_back(var);
      }

      auto * const avar = dynamic_cast<MooseVariableField<RealEigenVector> *>(var_base);

      if (avar)
      {
        if (avar->feType().family == LAGRANGE)
          _nodal_vars[tid].push_back(avar);
        else
          _elem_vars[tid].push_back(avar);
      }
    }
  }
}

addVariableToCopy()

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

virtualinherited

Add info about variable that will be copied.

Parameters

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

Definition at line 1176 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 )

virtualinherited

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 181 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 )

virtualinherited

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 175 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  )

inherited

Adds a solution length vector to the system.

Parameters

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

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

addVector() [2/2]

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

inherited

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

Parameters

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

applyScalingFactors()

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

inherited

Applies scaling factors to the system's variables.

Parameters

inverse_scaling_factors

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

Definition at line 1497 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeScaling().

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

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

    auto offset = field_variables.size();

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

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

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

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

assignMaxVarNDofsPerElem()

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

inlineinherited

assign the maximum element dofs

Definition at line 598 of file SystemBase.h.

{ _max_var_n_dofs_per_elem = max_dofs; }

assignMaxVarNDofsPerNode()

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

inlineinherited

assign the maximum node dofs

Definition at line 603 of file SystemBase.h.

{ _max_var_n_dofs_per_node = max_dofs; }

associateMatrixToTag()

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

virtualinherited

Associate a matrix to a tag.

Reimplemented in DisplacedSystem.

Definition at line 1077 of file SystemBase.C.

Referenced by SystemBase::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  )

virtualinherited

Associate a vector for a given tag.

Reimplemented in DisplacedSystem.

Definition at line 982 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 )

virtualinherited

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

Reimplemented in DisplacedSystem.

Definition at line 453 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()

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

overridevirtual

Will modify the sparsity pattern to add logical geometric connections.

Implements SystemBase.

Definition at line 875 of file AuxiliarySystem.C.

{
}

automaticScaling() [1/2]

bool SystemBase::automaticScaling ( ) const

inlineinherited

Getter for whether we are performing automatic scaling.

Returns

whether we are performing automatic scaling

Definition at line 123 of file SystemBase.h.

Referenced by SubProblem::automaticScaling().

{ return _automatic_scaling; }

automaticScaling() [2/2]

void SystemBase::automaticScaling ( bool  automatic_scaling )

inlineinherited

Setter for whether we are performing automatic scaling.

Parameters

automatic_scaling

A boolean representing whether we are performing automatic scaling

Definition at line 129 of file SystemBase.h.

{ _automatic_scaling = automatic_scaling; }

clearAllDofIndices()

void SystemBase::clearAllDofIndices ( )

inherited

Clear all dof indices from moose variables.

Definition at line 1602 of file SystemBase.C.

Referenced by SubProblem::clearAllDofIndices().

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

clearScalarVariableCoupleableTags()

void AuxiliarySystem::clearScalarVariableCoupleableTags

(

)

Definition at line 719 of file AuxiliarySystem.C.

Referenced by computeScalarVars().

{
  _fe_problem.clearActiveScalarVariableCoupleableMatrixTags(0);
  _fe_problem.clearActiveScalarVariableCoupleableVectorTags(0);
}

closeTaggedMatrices()

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

inherited

Close all matrices associated the tags.

Definition at line 1061 of file SystemBase.C.

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

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

closeTaggedVector()

void SystemBase::closeTaggedVector ( const TagID  tag )

inherited

Close vector with the given tag.

Definition at line 650 of file SystemBase.C.

Referenced by SystemBase::closeTaggedVectors().

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

closeTaggedVectors()

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

inherited

Close all vectors for given tags.

Definition at line 668 of file SystemBase.C.

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

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

compute()

void AuxiliarySystem::compute ( ExecFlagType  type )

overridevirtual

Compute auxiliary variables.

Parameters

type	Time flag of which variables should be computed

Implements SystemBase.

Definition at line 425 of file AuxiliarySystem.C.

{
  // avoid division by dt which might be zero.
  if (_fe_problem.dt() > 0.)
    for (auto & ti : _time_integrators)
      ti->preStep();

  // We need to compute time derivatives every time each kind of the variables is finished, because:
  //
  //  a) the user might want to use the aux variable value somewhere, thus we need to provide the
  //  up-to-date value
  //  b) time integration system works with the whole vectors of solutions, thus we cannot update
  //  only a part of the vector
  //

  if (_vars[0].scalars().size() > 0)
  {
    computeScalarVars(type);
    // compute time derivatives of scalar aux variables _after_ the values were updated
    if (_fe_problem.dt() > 0.)
      for (auto & ti : _time_integrators)
        ti->computeTimeDerivatives();
  }

  if (_vars[0].fieldVariables().size() > 0)
  {
    computeNodalArrayVars(type);
    computeNodalVecVars(type);
    computeNodalVars(type);
    computeMortarNodalVars(type);
    computeElementalArrayVars(type);
    computeElementalVecVars(type);
    computeElementalVars(type);

#ifdef MOOSE_KOKKOS_ENABLED
    kokkosCompute(type);
#endif

    if (!_raw_grad_container.empty())
    {
      solution().close();
      _sys.update();
      computeGradients();
    }

    // compute time derivatives of nodal aux variables _after_ the values were updated
    if (_fe_problem.dt() > 0.)
      for (auto & ti : _time_integrators)
        ti->computeTimeDerivatives();
  }

  if (_serialized_solution.get())
    serializeSolution();
}

computeElementalArrayVars()

void AuxiliarySystem::computeElementalArrayVars ( ExecFlagType  type )

protected

Definition at line 868 of file AuxiliarySystem.C.

Referenced by compute().

{
  const MooseObjectWarehouse<ArrayAuxKernel> & elemental = _elemental_array_aux_storage[type];
  computeElementalVarsHelper<ArrayAuxKernel>(elemental);
}

computeElementalVars()

void AuxiliarySystem::computeElementalVars ( ExecFlagType  type )

protected

Definition at line 850 of file AuxiliarySystem.C.

Referenced by compute().

{
  TIME_SECTION("computeElementalVars", 3);

  const MooseObjectWarehouse<AuxKernel> & elemental = _elemental_aux_storage[type];
  computeElementalVarsHelper<AuxKernel>(elemental);
}

computeElementalVarsHelper()

template<typename AuxKernelType >

template void AuxiliarySystem::computeElementalVarsHelper< VectorAuxKernel > ( const MooseObjectWarehouse< AuxKernelType > &  warehouse )

protected

Definition at line 916 of file AuxiliarySystem.C.

{
  if (warehouse.hasActiveBlockObjects())
  {
    // Block Elemental AuxKernels
    PARALLEL_TRY
    {
      ConstElemRange & range = *_mesh.getActiveLocalElementRange();
      ComputeElemAuxVarsThread<AuxKernelType> eavt(_fe_problem, warehouse, true);
      try
      {
        Threads::parallel_reduce(range, eavt);
      }
      catch (MooseException & e)
      {
        _fe_problem.setException("The following MooseException was raised during elemental "
                                 "Auxiliary variable computation:\n" +
                                 std::string(e.what()));
      }
    }
    PARALLEL_CATCH;

    // We need to make sure we propagate exceptions to all processes before trying to close
    // here, which is a parallel operation
    solution().close();
    _sys.update();
  }

  // Boundary Elemental AuxKernels
  if (warehouse.hasActiveBoundaryObjects())
  {
    TIME_SECTION("computeElementalVecVars", 3);

    PARALLEL_TRY
    {
      ConstBndElemRange & bnd_elems = *_mesh.getBoundaryElementRange();
      ComputeElemAuxBcsThread<AuxKernelType> eabt(_fe_problem, warehouse, true);
      try
      {
        Threads::parallel_reduce(bnd_elems, eabt);
      }
      catch (MooseException & e)
      {
        _fe_problem.setException("The following MooseException was raised during boundary "
                                 "elemental Auxiliary variable computation:\n" +
                                 std::string(e.what()));
      }
    }
    PARALLEL_CATCH;

    // We need to make sure we propagate exceptions to all processes before trying to close
    // here, which is a parallel operation
    solution().close();
    _sys.update();
  }
}

computeElementalVecVars()

void AuxiliarySystem::computeElementalVecVars ( ExecFlagType  type )

protected

Definition at line 859 of file AuxiliarySystem.C.

Referenced by compute().

{
  TIME_SECTION("computeElementalVecVars", 3);

  const MooseObjectWarehouse<VectorAuxKernel> & elemental = _elemental_vec_aux_storage[type];
  computeElementalVarsHelper<VectorAuxKernel>(elemental);
}

computeGradients()

void LinearFVGradientInterface::computeGradients ( )

protectedinherited

Compute and store raw and requested limited Green-Gauss gradients for linear FV variables.

Definition at line 27 of file LinearFVGradientInterface.C.

Referenced by compute(), and LinearSystem::computeLinearSystemInternal().

{
  // No gradients have been requested, by now we should have set up the
  // containers to receive the gradients. Time to early return.
  if (_raw_grad_container.empty())
    return;

  auto & temporary_gradient = temporaryLinearFVGradientContainer();
  mooseAssert(temporary_gradient.size() == _raw_grad_container.size(),
              "Temporary and raw gradient containers must have the same size.");
  for (auto & vec : temporary_gradient)
    vec->zero();

  auto & fe_problem = _sys.feProblem();
  auto * const perf_graph_interface = dynamic_cast<PerfGraphInterface *>(&_sys);
  mooseAssert(perf_graph_interface,
              "LinearFVGradientInterface requires its owning system to implement "
              "PerfGraphInterface.");
  const auto perf_id = perf_graph_interface->registerTimedSection("LinearVariableFV_Gradients", 3);
  mooseAssert(!Threads::in_threads, "PerfGraph timing cannot be used within threaded sections");
  PerfGuard time_guard(perf_graph_interface->perfGraph(), perf_id);

  PARALLEL_TRY
  {
    using FaceInfoRange = StoredRange<MooseMesh::const_face_info_iterator, const FaceInfo *>;
    FaceInfoRange face_info_range(fe_problem.mesh().ownedFaceInfoBegin(),
                                  fe_problem.mesh().ownedFaceInfoEnd());

    ComputeLinearFVGreenGaussGradientFaceThread gradient_face_thread(
        fe_problem, _sys, temporary_gradient);
    Threads::parallel_reduce(face_info_range, gradient_face_thread);
  }
  fe_problem.checkExceptionAndStopSolve();

  for (auto & vec : temporary_gradient)
    vec->close();

  PARALLEL_TRY
  {
    using ElemInfoRange = StoredRange<MooseMesh::const_elem_info_iterator, const ElemInfo *>;
    ElemInfoRange elem_info_range(fe_problem.mesh().ownedElemInfoBegin(),
                                  fe_problem.mesh().ownedElemInfoEnd());

    ComputeLinearFVGreenGaussGradientVolumeThread gradient_volume_thread(
        fe_problem, _sys, temporary_gradient);
    Threads::parallel_reduce(elem_info_range, gradient_volume_thread);
  }
  fe_problem.checkExceptionAndStopSolve();

  for (const auto i : index_range(_raw_grad_container))
    temporary_gradient[i]->close();

  _raw_grad_container.swap(temporary_gradient);

  if (!requestedLinearFVLimitedGradientTypes().empty())
  {
    using ElemInfoRange = StoredRange<MooseMesh::const_elem_info_iterator, const ElemInfo *>;
    ElemInfoRange elem_info_range(fe_problem.mesh().ownedElemInfoBegin(),
                                  fe_problem.mesh().ownedElemInfoEnd());

    for (const auto limiter_type : requestedLinearFVLimitedGradientTypes())
    {
      if (limiter_type == Moose::FV::GradientLimiterType::None)
        continue;

      auto & raw_container = rawLinearFVLimitedGradientContainer(limiter_type);
      auto & temporary_container = temporaryLinearFVLimitedGradientContainer(limiter_type);
      mooseAssert(temporary_container.size() == raw_container.size(),
                  "Temporary and raw limited gradient containers must have the same size.");
      for (auto & vec : temporary_container)
        vec->zero();

      PARALLEL_TRY
      {
        ComputeLinearFVLimitedGradientThread limited_gradient_thread(
            fe_problem,
            _sys,
            _raw_grad_container,
            temporary_container,
            limiter_type,
            requestedLinearFVLimitedGradientVariables(limiter_type));
        Threads::parallel_reduce(elem_info_range, limited_gradient_thread);
      }
      fe_problem.checkExceptionAndStopSolve();

      for (auto & vec : temporary_container)
        vec->close();

      raw_container.swap(temporary_container);
    }
  }
}

computeMortarNodalVars()

void AuxiliarySystem::computeMortarNodalVars ( ExecFlagType  type )

protected

Definition at line 792 of file AuxiliarySystem.C.

Referenced by compute().

{
  TIME_SECTION("computeMortarNodalVars", 3);

  const MooseObjectWarehouse<AuxKernel> & mortar_nodal_warehouse = _mortar_nodal_aux_storage[type];

  mooseAssert(!mortar_nodal_warehouse.hasActiveBlockObjects(),
              "We don't allow creation of block restricted mortar nodal aux kernels.");

  if (mortar_nodal_warehouse.hasActiveBoundaryObjects())
  {
    ConstBndNodeRange & bnd_nodes = *_mesh.getBoundaryNodeRange();
    for (const auto & [bnd_id, mortar_nodal_auxes] :
         mortar_nodal_warehouse.getActiveBoundaryObjects())
      for (const auto index : index_range(mortar_nodal_auxes))
      {
        PARALLEL_TRY
        {
          try
          {
            ComputeMortarNodalAuxBndThread<AuxKernel> mnabt(
                _fe_problem, mortar_nodal_warehouse, bnd_id, index);
            Threads::parallel_reduce(bnd_nodes, mnabt);
          }
          catch (MooseException & e)
          {
            _fe_problem.setException("The following MooseException was raised during mortar nodal "
                                     "Auxiliary variable computation:\n" +
                                     std::string(e.what()));
          }
          catch (MetaPhysicL::LogicError & e)
          {
            moose::translateMetaPhysicLError(e);
          }
          catch (std::exception & e)
          {
            // Continue if we find a libMesh degenerate map exception, but
            // just re-throw for any real error
            if (!strstr(e.what(), "Jacobian") && !strstr(e.what(), "singular") &&
                !strstr(e.what(), "det != 0"))
              throw;

            _fe_problem.setException("We caught a libMesh degeneracy exception during mortar "
                                     "nodal Auxiliary variable computation:\n" +
                                     std::string(e.what()));
          }
        }
        PARALLEL_CATCH;

        // We need to make sure we propagate exceptions to all processes before trying to close
        // here, which is a parallel operation
        solution().close();
        _sys.update();
      }
  }
}

computeNodalArrayVars()

void AuxiliarySystem::computeNodalArrayVars ( ExecFlagType  type )

protected

Definition at line 785 of file AuxiliarySystem.C.

Referenced by compute().

{
  const MooseObjectWarehouse<ArrayAuxKernel> & nodal = _nodal_array_aux_storage[type];
  computeNodalVarsHelper<ArrayAuxKernel>(nodal);
}

computeNodalVars()

void AuxiliarySystem::computeNodalVars ( ExecFlagType  type )

protected

Definition at line 767 of file AuxiliarySystem.C.

Referenced by compute().

{
  TIME_SECTION("computeNodalVars", 3);

  const MooseObjectWarehouse<AuxKernel> & nodal = _nodal_aux_storage[type];
  computeNodalVarsHelper<AuxKernel>(nodal);
}

computeNodalVarsHelper()

template<typename AuxKernelType >

template void AuxiliarySystem::computeNodalVarsHelper< VectorAuxKernel > ( const MooseObjectWarehouse< AuxKernelType > &  warehouse )

protected

Definition at line 975 of file AuxiliarySystem.C.

{
  if (warehouse.hasActiveBlockObjects())
  {
    // Block Nodal AuxKernels
    PARALLEL_TRY
    {
      ConstNodeRange & range = *_mesh.getLocalNodeRange();
      ComputeNodalAuxVarsThread<AuxKernelType> navt(_fe_problem, warehouse);
      Threads::parallel_reduce(range, navt);

      solution().close();
      _sys.update();
    }
    PARALLEL_CATCH;
  }

  if (warehouse.hasActiveBoundaryObjects())
  {
    TIME_SECTION("computeBoundaryObjects", 3);

    // Boundary Nodal AuxKernels
    PARALLEL_TRY
    {
      ConstBndNodeRange & bnd_nodes = *_mesh.getBoundaryNodeRange();
      ComputeNodalAuxBcsThread<AuxKernelType> nabt(_fe_problem, warehouse);
      Threads::parallel_reduce(bnd_nodes, nabt);

      solution().close();
      _sys.update();
    }
    PARALLEL_CATCH;
  }
}

computeNodalVecVars()

void AuxiliarySystem::computeNodalVecVars ( ExecFlagType  type )

protected

Definition at line 776 of file AuxiliarySystem.C.

Referenced by compute().

{
  TIME_SECTION("computeNodalVecVars", 3);

  const MooseObjectWarehouse<VectorAuxKernel> & nodal = _nodal_vec_aux_storage[type];
  computeNodalVarsHelper<VectorAuxKernel>(nodal);
}

computeScalarVars()

void AuxiliarySystem::computeScalarVars ( ExecFlagType  type )

protected

Definition at line 726 of file AuxiliarySystem.C.

Referenced by compute().

{
  setScalarVariableCoupleableTags(type);

  // Reference to the current storage container
  const MooseObjectWarehouse<AuxScalarKernel> & storage = _aux_scalar_storage[type];

  if (storage.hasActiveObjects())
  {
    TIME_SECTION("computeScalarVars", 1);

    PARALLEL_TRY
    {
      // FIXME: run multi-threaded
      THREAD_ID tid = 0;
      if (storage.hasActiveObjects())
      {
        _fe_problem.reinitScalars(tid);

        const std::vector<std::shared_ptr<AuxScalarKernel>> & objects =
            storage.getActiveObjects(tid);

        // Call compute() method on all active AuxScalarKernel objects
        for (const auto & obj : objects)
          obj->compute();

        const std::vector<MooseVariableScalar *> & scalar_vars = getScalarVariables(tid);
        for (const auto & var : scalar_vars)
          var->insert(solution());
      }
    }
    PARALLEL_CATCH;

    solution().close();
    _sys.update();
  }

  clearScalarVariableCoupleableTags();
}

computeVariables()

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

inlinevirtualinherited

Definition at line 872 of file SystemBase.h.

{}

computingScalingJacobian()

bool SystemBase::computingScalingJacobian ( ) const

inherited

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

Definition at line 1554 of file SystemBase.C.

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

{
  return _subproblem.computingScalingJacobian();
}

copyCurrentIntoPreviousNL()

void AuxiliarySystem::copyCurrentIntoPreviousNL ( )

virtual

Copies the current solution into the previous nonlinear iteration solution.

Definition at line 908 of file AuxiliarySystem.C.

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

copyOldSolutions()

void SystemBase::copyOldSolutions ( )

virtualinherited

Shifts the solutions backwards in time.

Definition at line 1287 of file SystemBase.C.

Referenced by SystemBase::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 > uint(_skip_next_solution_to_old_copy); --i)
      solutionState(i) = solutionState(i - 1);
  _skip_next_solution_to_old_copy = false;

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

copyPreviousFixedPointSolutions()

void SystemBase::copyPreviousFixedPointSolutions ( )

virtualinherited

Definition at line 1304 of file SystemBase.C.

{
  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 ( )

virtualinherited

Shifts the solutions backwards in nonlinear iteration history.

Definition at line 1270 of file SystemBase.C.

Referenced by SystemBase::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 ( )

virtualinherited

Copy current solution into old and older.

Definition at line 1259 of file SystemBase.C.

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

copyTimeIntegrators()

void SystemBase::copyTimeIntegrators ( const SystemBase &  other_sys )

inherited

Copy time integrators from another system.

Definition at line 1656 of file SystemBase.C.

{
  _time_integrators = other_sys._time_integrators;
}

copyVars()

void SystemBase::copyVars ( libMesh::ExodusII_IO &  io )

inherited

Definition at line 1184 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()

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

inlineoverridevirtual

The solution vector that is currently being operated on.

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

Implements SystemBase.

Definition at line 93 of file AuxiliarySystem.h.

Referenced by copyCurrentIntoPreviousNL(), FlagElementsThread::onElement(), AB2PredictorCorrector::step(), and DisplacedProblem::syncSolutions().

  {
    return _current_solution;
  }

customSetup()

void AuxiliarySystem::customSetup ( const ExecFlagType &  exec_type )

overridevirtual

Reimplemented from SystemBase.

Definition at line 150 of file AuxiliarySystem.C.

{
  SystemBase::customSetup(exec_type);

  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _aux_scalar_storage.customSetup(exec_type, tid);
    _nodal_aux_storage.customSetup(exec_type, tid);
    _mortar_nodal_aux_storage.customSetup(exec_type, tid);
    _nodal_vec_aux_storage.customSetup(exec_type, tid);
    _nodal_array_aux_storage.customSetup(exec_type, tid);
    _elemental_aux_storage.customSetup(exec_type, tid);
    _elemental_vec_aux_storage.customSetup(exec_type, tid);
    _elemental_array_aux_storage.customSetup(exec_type, tid);
  }

#ifdef MOOSE_KOKKOS_ENABLED
  _kokkos_nodal_aux_storage.customSetup(exec_type, /*tid=*/0);
  _kokkos_elemental_aux_storage.customSetup(exec_type, /*tid=*/0);
#endif
}

deactivateAllMatrixTags()

void SystemBase::deactivateAllMatrixTags ( )

virtualinherited

Make matrices inactive.

Definition at line 1120 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

inlinevirtualinherited

Get the default matrix tags associted with this system.

Reimplemented in NonlinearEigenSystem, and DisplacedSystem.

Definition at line 320 of file SystemBase.h.

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

{ return {systemMatrixTag()}; }

defaultVectorTags()

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

inlinevirtualinherited

Get the default vector tags associated with this system.

Reimplemented in NonlinearEigenSystem, and DisplacedSystem.

Definition at line 313 of file SystemBase.h.

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

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

disassociateDefaultMatrixTags()

void SystemBase::disassociateDefaultMatrixTags ( )

virtualinherited

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

Reimplemented in DisplacedSystem.

Definition at line 1111 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 ( )

virtualinherited

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

Reimplemented in DisplacedSystem.

Definition at line 1016 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  )

virtualinherited

Disassociate a matrix from a tag.

Reimplemented in DisplacedSystem.

Definition at line 1089 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeJacobian(), FEProblemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTag(), FEProblemBase::computeLinearSystemSys(), FEProblemBase::computeResidualAndJacobian(), SystemBase::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 )

virtualinherited

Disassociate any matrix that is associated with a given tag.

Reimplemented in DisplacedSystem.

Definition at line 1100 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  )

virtualinherited

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(), SystemBase::disassociateDefaultVectorTags(), DisplacedSystem::disassociateVectorFromTag(), and CentralDifference::initialSetup().

disassociateVectorFromTag() [2/2]

void SystemBase::disassociateVectorFromTag ( TagID  tag )

virtualinherited

Disassociate any vector that is associated with a given tag.

Reimplemented in DisplacedSystem.

Definition at line 1005 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 ( )

virtualinherited

Gets writeable reference to the dof map.

Definition at line 1164 of file SystemBase.C.

Referenced by NonlinearSystemBase::assembleScalingVector(), MooseApp::attachRelationshipManagers(), SystemBase::augmentSendList(), NonlinearSystemBase::augmentSparsity(), NonlinearSystemBase::computeScaling(), FieldSplitPreconditioner::dofMap(), NEML2FEInterpolation::execute(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), Moose::Kokkos::System::getDofMap(), Adaptivity::init(), NonlinearEigenSystem::initializeCondensedMatrices(), ActivateElementsUserObjectBase::initSolutions(), PNGOutput::makeMeshFunc(), GhostingUserObject::meshChanged(), TableOutput::outputScalarVariables(), Nemesis::outputScalarVariables(), Exodus::outputScalarVariables(), and ElementSubdomainModifierBase::setOldAndOlderSolutions().

{
  return system().get_dof_map();
}

dofMap() [2/2]

const DofMap & SystemBase::dofMap ( ) const

virtualinherited

Gets const reference to the dof map.

Definition at line 1170 of file SystemBase.C.

{
  return system().get_dof_map();
}

duDotDotDu() [1/2]

virtual Number& SystemBase::duDotDotDu ( )

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 258 of file SystemBase.h.

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

{ return _du_dotdot_du; }

duDotDotDu() [2/2]

virtual const Number& SystemBase::duDotDotDu ( ) const

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 260 of file SystemBase.h.

{ return _du_dotdot_du; }

duDotDu()

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

virtualinherited

Reimplemented in DisplacedSystem.

Definition at line 1690 of file SystemBase.C.

Referenced by DisplacedSystem::duDotDu(), MooseVariableScalar::reinit(), Moose::Kokkos::VariableGradientTempl< is_ad >::VariableGradientTempl(), and Moose::Kokkos::VariableValueTempl< is_ad >::VariableValueTempl().

{
  return _du_dot_du[var_num];
}

duDotDus()

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 257 of file SystemBase.h.

Referenced by DisplacedSystem::duDotDus().

{ return _du_dot_du; }

elemArrayAuxWarehouse()

const ExecuteMooseObjectWarehouse< ArrayAuxKernel > & AuxiliarySystem::elemArrayAuxWarehouse ( ) const

inline

Definition at line 264 of file AuxiliarySystem.h.

{
  return _elemental_array_aux_storage;
}

elemAuxWarehouse()

const ExecuteMooseObjectWarehouse< AuxKernel > & AuxiliarySystem::elemAuxWarehouse ( ) const

inline

Definition at line 252 of file AuxiliarySystem.h.

{
  return _elemental_aux_storage;
}

elemVectorAuxWarehouse()

const ExecuteMooseObjectWarehouse< VectorAuxKernel > & AuxiliarySystem::elemVectorAuxWarehouse ( ) const

inline

Definition at line 258 of file AuxiliarySystem.h.

{
  return _elemental_vec_aux_storage;
}

feProblem() [1/2]

FEProblemBase& SystemBase::feProblem ( )

inlineinherited

Definition at line 104 of file SystemBase.h.

Referenced by DMMooseGetEmbedding_Private(), and DMSetUp_Moose_Pre().

{ return _fe_problem; }

feProblem() [2/2]

const FEProblemBase& SystemBase::feProblem ( ) const

inlineinherited

Definition at line 105 of file SystemBase.h.

{ return _fe_problem; }

flushTaggedMatrices()

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

inherited

flushes all matrices associated to tags.

Flush assembles the matrix but doesn't shrink memory allocation

Definition at line 1069 of file SystemBase.C.

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

getActualFieldVariable() [1/2]

template<typename T >

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

inherited

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

Definition at line 119 of file SystemBase.C.

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

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

getActualFieldVariable() [2/2]

template<typename T >

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

inherited

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

Definition at line 140 of file SystemBase.C.

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

getDependObjects() [1/2]

std::set< std::string > AuxiliarySystem::getDependObjects

(

ExecFlagType

type

)

Get a list of dependent UserObjects for this exec type.

Parameters

type	Execution flag type

Returns

a set of dependent user objects

Definition at line 481 of file AuxiliarySystem.C.

Referenced by groupUserObjects().

{
  std::set<std::string> depend_objects;

  // Elemental AuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernel>> & auxs =
        _elemental_aux_storage[type].getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Elemental VectorAuxKernels
  {
    const std::vector<std::shared_ptr<VectorAuxKernel>> & auxs =
        _elemental_vec_aux_storage[type].getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Elemental ArrayAuxKernels
  {
    const std::vector<std::shared_ptr<ArrayAuxKernel>> & auxs =
        _elemental_array_aux_storage[type].getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Nodal AuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernel>> & auxs =
        _nodal_aux_storage[type].getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Mortar Nodal AuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernel>> & auxs =
        _mortar_nodal_aux_storage[type].getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Nodal VectorAuxKernels
  {
    const std::vector<std::shared_ptr<VectorAuxKernel>> & auxs =
        _nodal_vec_aux_storage[type].getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Nodal ArrayAuxKernels
  {
    const std::vector<std::shared_ptr<ArrayAuxKernel>> & auxs =
        _nodal_array_aux_storage[type].getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

#ifdef MOOSE_KOKKOS_ENABLED
  // Kokkos NodalAuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernelBase>> & auxs =
        _kokkos_nodal_aux_storage[type].getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Kokkos ElementalAuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernelBase>> & auxs =
        _kokkos_elemental_aux_storage[type].getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }
#endif

  return depend_objects;
}

getDependObjects() [2/2]

std::set< std::string > AuxiliarySystem::getDependObjects

(

)

Definition at line 590 of file AuxiliarySystem.C.

{
  std::set<std::string> depend_objects;

  // Elemental AuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernel>> & auxs =
        _elemental_aux_storage.getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Elemental VectorAuxKernels
  {
    const std::vector<std::shared_ptr<VectorAuxKernel>> & auxs =
        _elemental_vec_aux_storage.getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Elemental ArrayAuxKernels
  {
    const std::vector<std::shared_ptr<ArrayAuxKernel>> & auxs =
        _elemental_array_aux_storage.getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Nodal AuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernel>> & auxs = _nodal_aux_storage.getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Mortar Nodal AuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernel>> & auxs =
        _mortar_nodal_aux_storage.getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Nodal VectorAuxKernels
  {
    const std::vector<std::shared_ptr<VectorAuxKernel>> & auxs =
        _nodal_vec_aux_storage.getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Nodal ArrayAuxKernels
  {
    const std::vector<std::shared_ptr<ArrayAuxKernel>> & auxs =
        _nodal_array_aux_storage.getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

#ifdef MOOSE_KOKKOS_ENABLED
  // Nodal KokkosAuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernelBase>> & auxs =
        _kokkos_nodal_aux_storage.getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }

  // Elemental KokkosAuxKernels
  {
    const std::vector<std::shared_ptr<AuxKernelBase>> & auxs =
        _kokkos_elemental_aux_storage.getActiveObjects();
    for (const auto & aux : auxs)
    {
      const std::set<UserObjectName> & uo = aux->getDependObjects();
      depend_objects.insert(uo.begin(), uo.end());
    }
  }
#endif

  return depend_objects;
}

getFieldVariable() [1/2]

template<typename T >

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

inherited

Gets a reference to a variable of with specified name.

This excludes and cannot return finite volume variables.

Parameters

tid	Thread id
var_name	variable name

Returns

reference the variable (class)

Definition at line 112 of file SystemBase.C.

Referenced by Marker::getMarkerValue().

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

getFieldVariable() [2/2]

template<typename T >

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

inherited

Gets a reference to a variable with specified number.

This excludes and cannot return finite volume variables.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns

reference the variable (class)

Definition at line 133 of file SystemBase.C.

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

getFVVariable()

template<typename T >

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

inherited

Return a finite volume variable.

Definition at line 126 of file SystemBase.C.

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

getMatrix() [1/2]

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

virtualinherited

Get a raw SparseMatrix.

Reimplemented in DisplacedSystem.

Definition at line 1025 of file SystemBase.C.

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

{
  if (!hasMatrix(tag))
  {
    if (!_subproblem.matrixTagExists(tag))
      mooseError("Cannot retrieve matrix with tag ", tag, " because that tag does not exist");
    else
      mooseError("Cannot retrieve 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

virtualinherited

Get a raw SparseMatrix.

Reimplemented in DisplacedSystem.

Definition at line 1043 of file SystemBase.C.

{
  if (!hasMatrix(tag))
  {
    if (!_subproblem.matrixTagExists(tag))
      mooseError("Cannot retrieve matrix with tag ", tag, " because that tag does not exist");
    else
      mooseError("Cannot retrieve 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

inlineinherited

Returns the maximum number of all variables on the system.

Definition at line 870 of file SystemBase.h.

{ return _max_var_number; }

getMaxVarNDofsPerElem()

std::size_t SystemBase::getMaxVarNDofsPerElem ( ) const

inlineinherited

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

Returns

The max

Definition at line 586 of file SystemBase.h.

Referenced by Moose::globalDofIndexToDerivative().

{ return _max_var_n_dofs_per_elem; }

getMaxVarNDofsPerNode()

std::size_t SystemBase::getMaxVarNDofsPerNode ( ) const

inlineinherited

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

Returns

The max

Definition at line 593 of file SystemBase.h.

{ return _max_var_n_dofs_per_node; }

getMinQuadratureOrder()

Order AuxiliarySystem::getMinQuadratureOrder ( )

overridevirtual

Get the minimum quadrature order for evaluating elemental auxiliary variables.

Reimplemented from SystemBase.

Definition at line 883 of file AuxiliarySystem.C.

{
  Order order = CONSTANT;
  std::vector<MooseVariableFEBase *> vars = _vars[0].fieldVariables();
  for (const auto & var : vars)
  {
    if (!var->isNodal()) // nodal aux variables do not need quadrature
    {
      FEType fe_type = var->feType();
      if (fe_type.default_quadrature_order() > order)
        order = fe_type.default_quadrature_order();
    }
  }

  return order;
}

getScalarVariable() [1/2]

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

virtualinherited

Gets a reference to a scalar variable with specified number.

Parameters

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

Returns

reference the variable (class)

Definition at line 146 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

virtualinherited

Gets a reference to a variable with specified number.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns

reference the variable (class)

Definition at line 155 of file SystemBase.C.

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

getScalarVariables()

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

inlineinherited

Definition at line 759 of file SystemBase.h.

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

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

getStandardFieldVariableNames()

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

inherited

getSubdomainsForVar() [1/2]

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

inlineinherited

Definition at line 764 of file SystemBase.h.

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

  {
    return _var_map.at(var_number);
  }

getSubdomainsForVar() [2/2]

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

inherited

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 1696 of file SystemBase.C.

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

getTimeIntegrator()

const TimeIntegrator & SystemBase::getTimeIntegrator ( const unsigned int  var_num ) const

inherited

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

Definition at line 1672 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 ( )

inherited

Returns

All the time integrators owned by this system

Definition at line 1684 of file SystemBase.C.

{
  return _time_integrators;
}

getVariable() [1/2]

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

inherited

Gets a reference to a variable of with specified name.

Parameters

tid	Thread id
var_name	variable name

Returns

reference the variable (class)

Definition at line 91 of file SystemBase.C.

Referenced by AdaptivityAction::act(), Assembly::addJacobianBlockNonlocal(), FEProblemBase::addJacobianBlockTags(), NonlocalIntegratedBC::computeNonlocalOffDiagJacobian(), NonlocalKernel::computeNonlocalOffDiagJacobian(), Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), Assembly::copyShapes(), SystemBase::copyVars(), DMMooseSetVariables(), FieldSplitPreconditionerTempl< MoosePreconditioner >::FieldSplitPreconditionerTempl(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), NodeElemConstraint::getConnectedDofIndices(), NodeFaceConstraint::getConnectedDofIndices(), SystemBase::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(), 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

inherited

Gets a reference to a variable with specified number.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns

reference the variable (class)

Definition at line 101 of file SystemBase.C.

{
  if (var_number < _numbered_vars[tid].size())
    if (_numbered_vars[tid][var_number])
      return *_numbered_vars[tid][var_number];

  mooseError("Variable #", Moose::stringify(var_number), " does not exist in this system");
}

getVariableBlocks()

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

virtualinherited

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

Parameters

var_number

The number of the variable

Returns

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

Definition at line 165 of file SystemBase.C.

Referenced by PhysicsBasedPreconditioner::addSystem().

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

getVariableGlobalDoFs()

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

inlineinherited

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

Definition at line 845 of file SystemBase.h.

{ return _var_all_dof_indices; }

getVariableNames()

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

inlineinherited

Definition at line 863 of file SystemBase.h.

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

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

getVariables()

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

inlineinherited

Definition at line 752 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(), SystemBase::initSolutionState(), ComputeLinearFVGreenGaussGradientFaceThread::operator()(), ComputeLinearFVGreenGaussGradientVolumeThread::operator()(), ComputeLinearFVLimitedGradientThread::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 )

virtualinherited

Get a raw NumericVector by name.

Get a raw NumericVector with the given name.

Reimplemented in DisplacedSystem.

Definition at line 934 of file SystemBase.C.

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

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

getVector() [2/4]

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

virtualinherited

Reimplemented in DisplacedSystem.

Definition at line 940 of file SystemBase.C.

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

getVector() [3/4]

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

virtualinherited

Get a raw NumericVector by tag.

Reimplemented in DisplacedSystem.

Definition at line 946 of file SystemBase.C.

{
  if (!hasVector(tag))
  {
    if (!_subproblem.vectorTagExists(tag))
      mooseError("Cannot retrieve vector with tag ", tag, " because that tag does not exist");
    else
      mooseError("Cannot retrieve 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

virtualinherited

Reimplemented in DisplacedSystem.

Definition at line 964 of file SystemBase.C.

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

  return *_tagged_vectors[tag];
}

hasMatrix()

virtual bool SystemBase::hasMatrix ( TagID  tag ) const

inlinevirtualinherited

Check if the tagged matrix exists in the system.

Reimplemented in DisplacedSystem.

Definition at line 361 of file SystemBase.h.

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

virtualinherited

Definition at line 877 of file SystemBase.C.

Referenced by MortarScalarBase::computeJacobian(), NonlinearSystemBase::computeNodalBCsJacobian(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), SystemBase::copyVars(), ExplicitTimeIntegrator::initialSetup(), NonlinearEigenSystem::postAddResidualObject(), 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

inlinevirtualinherited

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

Reimplemented in DisplacedSystem.

Definition at line 1087 of file SystemBase.h.

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

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

hasVarCopy()

bool SystemBase::hasVarCopy ( ) const

inlineinherited

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

Definition at line 886 of file SystemBase.h.

{ return _var_to_copy.size() > 0; }

hasVariable()

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

virtualinherited

Query a system for a variable.

Parameters

var_name

name of the variable

Returns

true if the variable exists

Definition at line 852 of file SystemBase.C.

Referenced by ADDGKernel::ADDGKernel(), ArrayDGKernel::ArrayDGKernel(), SystemBase::copyVars(), DGKernel::DGKernel(), DMMooseSetVariables(), FEProblemBase::duplicateVariableCheck(), FixedPointSolve::findTransformedSystem(), SubProblem::getVariableHelper(), SubProblem::hasAuxiliaryVariable(), ExplicitTimeIntegrator::initialSetup(), ElementSubdomainModifierBase::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

inherited

Check if the named vector exists in the system.

Definition at line 925 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(), SystemBase::closeTaggedVector(), FEProblemBase::computeBounds(), NonlinearSystemBase::computeResidualTags(), CentralDifference::computeTimeDerivatives(), SystemBase::getVector(), DisplacedSystem::hasVector(), MooseVariableScalar::reinit(), SystemBase::removeVector(), SubProblem::selectVectorTagsFromSystem(), NonlinearSystemBase::setPreviousNewtonSolution(), TaggingInterface::setResidual(), SystemBase::solutionPreviousNewton(), and SystemBase::zeroTaggedVector().

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

hasVector() [2/2]

virtual bool SystemBase::hasVector ( TagID  tag_id ) const

inlinevirtualinherited

Check if the tagged vector exists in the system.

Reimplemented in DisplacedSystem.

Definition at line 282 of file SystemBase.h.

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

initializeContainer()

void LinearFVGradientInterface::initializeContainer ( std::vector< std::unique_ptr< libMesh::NumericVector< libMesh::Number >>> &  container ) const

protectedinherited

Definition at line 131 of file LinearFVGradientInterface.C.

{
  container.clear();
  mooseAssert(_sys.currentSolution(),
              "Current solution must exist before building FV gradient storage.");
  for (unsigned int i = 0; i < _sys.mesh().dimension(); ++i)
    container.push_back(_sys.currentSolution()->zero_clone());
}

initializeObjects()

virtual void SystemBase::initializeObjects ( )

inlinevirtualinherited

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

Definition at line 174 of file SystemBase.h.

{}

initialSetup()

virtual void AuxiliarySystem::initialSetup ( )

overridevirtual

Setup Functions.

Reimplemented from SystemBase.

initSolutionState()

void SystemBase::initSolutionState ( )

virtualinherited

Initializes the solution state.

Reimplemented in DisplacedSystem.

Definition at line 1366 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

virtualinherited

If a variable is an array variable.

Definition at line 865 of file SystemBase.C.

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

isScalarVariable()

bool SystemBase::isScalarVariable ( unsigned int  var_name ) const

virtualinherited

Definition at line 886 of file SystemBase.C.

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

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

jacobianSetup()

void AuxiliarySystem::jacobianSetup ( )

overridevirtual

Reimplemented from SystemBase.

Definition at line 191 of file AuxiliarySystem.C.

{
  SystemBase::jacobianSetup();

  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _aux_scalar_storage.jacobianSetup(tid);
    _nodal_aux_storage.jacobianSetup(tid);
    _mortar_nodal_aux_storage.jacobianSetup(tid);
    _nodal_vec_aux_storage.jacobianSetup(tid);
    _nodal_array_aux_storage.jacobianSetup(tid);
    _elemental_aux_storage.jacobianSetup(tid);
    _elemental_vec_aux_storage.jacobianSetup(tid);
    _elemental_array_aux_storage.jacobianSetup(tid);
  }

#ifdef MOOSE_KOKKOS_ENABLED
  _kokkos_nodal_aux_storage.jacobianSetup(/*tid=*/0);
  _kokkos_elemental_aux_storage.jacobianSetup(/*tid=*/0);
#endif
}

kokkosCompute()

void AuxiliarySystem::kokkosCompute

(

ExecFlagType

type

)

Referenced by compute().

kokkosElemAuxWarehouse()

const ExecuteMooseObjectWarehouse< AuxKernelBase > & AuxiliarySystem::kokkosElemAuxWarehouse ( ) const

inline

Definition at line 277 of file AuxiliarySystem.h.

{
  return _kokkos_elemental_aux_storage;
}

kokkosNodalAuxWarehouse()

const ExecuteMooseObjectWarehouse< AuxKernelBase > & AuxiliarySystem::kokkosNodalAuxWarehouse ( ) const

inline

Definition at line 271 of file AuxiliarySystem.h.

{
  return _kokkos_nodal_aux_storage;
}

linearFVGradientContainer()

const std::vector<std::unique_ptr<libMesh::NumericVector<libMesh::Number> > >& LinearFVGradientInterface::linearFVGradientContainer ( ) const

inlineinherited

Access the stored raw cell-centered gradient components.

Returns

Raw cell-centered gradient vectors keyed by spatial direction.

Definition at line 45 of file LinearFVGradientInterface.h.

  {
    return _raw_grad_container;
  }

linearFVLimitedGradientContainer() [1/2]

const std::vector< std::unique_ptr< NumericVector< Number > > > & LinearFVGradientInterface::linearFVLimitedGradientContainer ( const Moose::FV::GradientLimiterType  limiter_type ) const

inherited

Access the stored raw or limited cell-centered gradient components.

Parameters

limiter_type

The limiter type whose gradient container is being requested.

Returns

The requested raw or limited gradient vectors ordered by spatial direction.

Definition at line 198 of file LinearFVGradientInterface.C.

{
  if (limiter_type == Moose::FV::GradientLimiterType::None)
    return _raw_grad_container;

  const auto it = _raw_limited_grad_containers.find(limiter_type);
  if (it == _raw_limited_grad_containers.end())
    mooseError("Limited gradient container was requested but not initialized on system '",
               _sys.name(),
               "'.");

  return it->second;
}

linearFVLimitedGradientContainer() [2/2]

const std::vector< std::unique_ptr< NumericVector< Number > > > & LinearFVGradientInterface::linearFVLimitedGradientContainer

Access the stored raw or limited cell-centered gradient components.

Parameters

limiter_type

The limiter type whose gradient container is being requested.

Returns

The requested raw or limited gradient vectors ordered by spatial direction.

Definition at line 198 of file LinearFVGradientInterface.C.

{
  if (limiter_type == Moose::FV::GradientLimiterType::None)
    return _raw_grad_container;

  const auto it = _raw_limited_grad_containers.find(limiter_type);
  if (it == _raw_limited_grad_containers.end())
    mooseError("Limited gradient container was requested but not initialized on system '",
               _sys.name(),
               "'.");

  return it->second;
}

matrixTagActive()

bool SystemBase::matrixTagActive ( TagID  tag ) const

virtualinherited

If or not a matrix tag is active.

Definition at line 1150 of file SystemBase.C.

{
  mooseAssert(_subproblem.matrixTagExists(tag), "Matrix tag " << tag << " does not exist");

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

mesh() [1/2]

MooseMesh& SystemBase::mesh ( )

inlineinherited

Definition at line 100 of file SystemBase.h.

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

{ return _mesh; }

mesh() [2/2]

const MooseMesh& SystemBase::mesh ( ) const

inlineinherited

Definition at line 101 of file SystemBase.h.

{ return _mesh; }

name()

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

virtualinherited

Definition at line 1342 of file SystemBase.C.

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

{
  return system().name();
}

needMaterialOnSide()

bool AuxiliarySystem::needMaterialOnSide

(

BoundaryID

bnd_id

)

Indicated whether this system needs material properties on boundaries.

Returns

Boolean if IntegratedBCs are active

Definition at line 901 of file AuxiliarySystem.C.

{
  return _elemental_aux_storage.hasActiveBoundaryObjects(bnd_id) ||
         _elemental_vec_aux_storage.hasActiveBoundaryObjects(bnd_id);
}

needsLinearFVGradientStorage()

bool LinearFVGradientInterface::needsLinearFVGradientStorage ( ) const

protectedinherited

Definition at line 121 of file LinearFVGradientInterface.C.

{
  for (const auto * const field_var : _sys.variableWarehouse().fieldVariables())
    if (field_var->needsGradientVectorStorage())
      return true;

  return false;
}

needSolutionState()

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

virtualinherited

Registers that the solution state state is needed.

Reimplemented in DisplacedSystem.

Definition at line 1452 of file SystemBase.C.

Referenced by SecantSolve::allocateStorage(), PicardSolve::allocateStorage(), EigenExecutionerBase::EigenExecutionerBase(), SystemBase::initSolutionState(), DisplacedSystem::needSolutionState(), SolverSystem::saveOldSolutionForFixedPointRelaxation(), and SystemBase::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

inherited

Get the number of field variables in this system.

Returns

the number of field variables

Definition at line 901 of file SystemBase.C.

Referenced by SystemBase::nVariables().

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

  return n;
}

nFVVariables()

unsigned int SystemBase::nFVVariables ( ) const

inherited

Get the number of finite volume variables in this system.

Returns

the number of finite volume variables

Definition at line 911 of file SystemBase.C.

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

  return n;
}

nodalArrayAuxWarehouse()

const ExecuteMooseObjectWarehouse< ArrayAuxKernel > & AuxiliarySystem::nodalArrayAuxWarehouse ( ) const

inline

Definition at line 246 of file AuxiliarySystem.h.

{
  return _nodal_array_aux_storage;
}

nodalAuxWarehouse()

const ExecuteMooseObjectWarehouse< AuxKernel > & AuxiliarySystem::nodalAuxWarehouse ( ) const

inline

Definition at line 234 of file AuxiliarySystem.h.

{
  return _nodal_aux_storage;
}

nodalVectorAuxWarehouse()

const ExecuteMooseObjectWarehouse< VectorAuxKernel > & AuxiliarySystem::nodalVectorAuxWarehouse ( ) const

inline

Definition at line 240 of file AuxiliarySystem.h.

{
  return _nodal_vec_aux_storage;
}

nonTimeVectorTag()

virtual TagID SystemBase::nonTimeVectorTag ( ) const

inlinevirtualinherited

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 303 of file SystemBase.h.

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

{ mooseError("Not implemented yet"); }

number()

unsigned int SystemBase::number ( ) const

inherited

Gets the number of this system.

Returns

The number of this system

Definition at line 1158 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::addObjectParamsHelper(), FEProblemBase::addResidual(), FEProblemBase::addResidualLower(), FEProblemBase::addResidualNeighbor(), FEProblemBase::addResidualScalar(), SystemBase::addScalingVector(), ADKernelTempl< T >::ADKernelTempl(), ElementSubdomainModifierBase::applyIC(), ArrayKernel::ArrayKernel(), NonlinearSystemBase::assembleScalingVector(), NonlinearEigenSystem::attachPreconditioner(), MooseMesh::cacheFaceInfoVariableOwnership(), DiffusionLHDGAssemblyHelper::checkCoupling(), SolverSystem::compute(), MooseVariableScalar::computeAD(), FEProblemBase::computeBounds(), Assembly::computeFaceMap(), InternalSideIndicatorBase::computeIndicator(), ArrayNodalBC::computeJacobian(), VectorNodalBC::computeJacobian(), NodalBC::computeJacobian(), FVBoundaryScalarLagrangeMultiplierConstraint::computeJacobian(), FVFluxBC::computeJacobian(), FVFluxKernel::computeJacobian(), FVInterfaceKernel::computeJacobian(), FEProblemBase::computeJacobianBlock(), NonlinearSystemBase::computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), FEProblemBase::computeNearNullSpace(), NonlinearSystemBase::computeNodalBCsJacobian(), NonlinearSystemBase::computeNodalBCsResidualAndJacobian(), FEProblemBase::computeNullSpace(), ArrayNodalBC::computeOffDiagJacobian(), VectorNodalBC::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(), NodalNormalsCorner::execute(), NodalNormalsEvaluator::execute(), GreaterThanLessThanPostprocessor::execute(), NodalNormalsPreprocessor::execute(), ExplicitTimeIntegrator::ExplicitTimeIntegrator(), InternalSideIndicatorBase::finalize(), NumNonlinearIterations::finalize(), NonlinearEigenSystem::finalNonlinearResidual(), BoundsBase::getDoFIndex(), NonlinearSystemBase::getNodeDofs(), NonlinearEigenSystem::getSNES(), SystemBase::getSubdomainsForVar(), NumLinearIterations::getValue(), Residual::getValue(), NumResidualEvaluations::getValue(), Moose::globalDofIndexToDerivative(), FVBoundaryCondition::hasFaceSide(), ExplicitTimeIntegrator::init(), ExplicitTimeIntegrator::initialSetup(), AuxKernelBase::initialSetup(), NonlinearSystemBase::initialSetup(), ActivateElementsUserObjectBase::initSolutions(), EigenExecutionerBase::inversePowerIteration(), MooseMesh::isTranslatedPeriodic(), Kernel::Kernel(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionA(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionAB(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionB(), Moose::SlepcSupport::mooseSlepcEigenFormJacobianA(), MooseStaticCondensationPreconditioner::MooseStaticCondensationPreconditioner(), MooseVariableInterface< Real >::MooseVariableInterface(), NonlinearEigenSystem::nLinearIterations(), NonlinearEigenSystem::nNonlinearIterations(), EigenExecutionerBase::nonlinearSolve(), ComputeDiracThread::onElement(), ComputeNodalKernelBCJacobiansThread::onNode(), ComputeNodalKernelJacobiansThread::onNode(), VariableResidualNormsDebugOutput::output(), Moose::PetscSupport::petscLinearConverged(), Moose::PetscSupport::petscNonlinearConverged(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), PointwiseRenormalizeVector::PointwiseRenormalizeVector(), FEProblemBase::prepareAssembly(), SystemBase::prepareFace(), FEProblemBase::prepareFaceShapes(), FEProblemBase::prepareNeighborShapes(), FEProblemBase::prepareShapes(), MooseMesh::queryPeriodicDimensions(), 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(), UserObjectBase::systemNumber(), MultiAppDofCopyTransfer::transferDofObject(), FVFluxBC::uOnGhost(), FVFluxBC::uOnUSub(), FVFluxBC::updateCurrentFace(), NodalDamper::variableDefinedOnNode(), and MortarConstraintBase::zeroInactiveLMDofs().

{
  return system().number();
}

nVariables()

unsigned int SystemBase::nVariables ( ) const

virtualinherited

Get the number of variables in this system.

Returns

the number of variables

Definition at line 892 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 variableWiseRelativeSolutionDifferenceNorm().

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

  return n;
}

perfGraph()

PerfGraph & PerfGraphInterface::perfGraph ( )

inherited

Get the PerfGraph.

Definition at line 86 of file PerfGraphInterface.C.

Referenced by CommonOutputAction::act(), PerfGraphData::finalize(), PerfGraphReporter::finalize(), and PerfGraphOutput::output().

{
  return _pg_moose_app.perfGraph();
}

postInit()

virtual void SystemBase::postInit ( )

inlinevirtualinherited

Reimplemented in NonlinearEigenSystem.

Definition at line 163 of file SystemBase.h.

Referenced by NonlinearEigenSystem::postInit().

{}

prefix()

std::string SystemBase::prefix ( ) const

inherited

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 1702 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 ( )

inlinevirtualinherited

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 157 of file SystemBase.h.

Referenced by SolverSystem::preInit().

{}

prepare()

void SystemBase::prepare ( THREAD_ID  tid )

virtualinherited

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 257 of file SystemBase.C.

Referenced by SubProblem::reinitElemFaceRef().

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

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

prepareFace()

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

virtualinherited

Prepare the system for use on sides.

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

Parameters

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

Definition at line 280 of file SystemBase.C.

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

    std::vector<MooseVariableFieldBase *> newly_prepared_vars;

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

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

    // Make sure to resize the residual and jacobian datastructures for all the new variables
    if (resize_data)
      for (const auto var_ptr : newly_prepared_vars)
      {
        _subproblem.assembly(tid, number()).prepareVariable(var_ptr);
        if (_subproblem.checkNonlocalCouplingRequirement())
          _subproblem.assembly(tid, number()).prepareVariableNonlocal(var_ptr);
      }
  }
}

prepareLowerD()

void SystemBase::prepareLowerD ( THREAD_ID  tid )

virtualinherited

Prepare the system for use for lower dimensional elements.

Parameters

tid	ID of the thread

Definition at line 333 of file SystemBase.C.

Referenced by SubProblem::reinitLowerDElem().

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

prepareNeighbor()

void SystemBase::prepareNeighbor ( THREAD_ID  tid )

virtualinherited

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 325 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

inherited

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 1662 of file SystemBase.C.

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

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

  return nullptr;
}

rawLinearFVLimitedGradientContainer()

std::vector<std::unique_ptr<libMesh::NumericVector<libMesh::Number> > >& LinearFVGradientInterface::rawLinearFVLimitedGradientContainer ( const Moose::FV::GradientLimiterType  limiter_type )

inlineprotectedinherited

Access the persisted limited-gradient storage for a specific limiter.

Parameters

limiter_type

The limiter type whose persisted storage is being accessed.

Returns

The persisted limited-gradient vectors keyed by spatial direction.

Definition at line 117 of file LinearFVGradientInterface.h.

  {
    return _raw_limited_grad_containers[limiter_type];
  }

rebuildLinearFVGradientStorage()

void LinearFVGradientInterface::rebuildLinearFVGradientStorage ( )

protectedinherited

Rebuild persistent raw and temporary gradient storage after mesh/DOF changes.

Definition at line 142 of file LinearFVGradientInterface.C.

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

{
  _raw_grad_container.clear();
  _temporary_gradient.clear();
  _raw_limited_grad_containers.clear();
  _temporary_limited_gradient.clear();

  if (!needsLinearFVGradientStorage())
    return;

  initializeContainer(_raw_grad_container);
  initializeContainer(_temporary_gradient);

  for (const auto limiter_type : _requested_limited_gradient_types)
  {
    if (limiter_type == Moose::FV::GradientLimiterType::None)
      continue;

    initializeContainer(_raw_limited_grad_containers[limiter_type]);
    initializeContainer(_temporary_limited_gradient[limiter_type]);
  }
}

registerTimedSection() [1/2]

PerfID PerfGraphInterface::registerTimedSection ( const std::string &  section_name, const unsigned int  level  ) const

protectedinherited

Call to register a named section for timing.

Parameters

section_name	The name of the code section to be timed
level	The importance of the timer - lower is more important (0 will always come out)

Returns

The ID of the section - use when starting timing

Definition at line 61 of file PerfGraphInterface.C.

{
  const auto timed_section_name = timedSectionName(section_name);
  if (!moose::internal::getPerfGraphRegistry().sectionExists(timed_section_name))
    return moose::internal::getPerfGraphRegistry().registerSection(timed_section_name, level);
  else
    return moose::internal::getPerfGraphRegistry().sectionID(timed_section_name);
}

registerTimedSection() [2/2]

PerfID PerfGraphInterface::registerTimedSection ( const std::string &  section_name, const unsigned int  level, const std::string &  live_message, const bool  print_dots = true  ) const

protectedinherited

Call to register a named section for timing.

Parameters

section_name	The name of the code section to be timed
level	The importance of the timer - lower is more important (0 will always come out)
live_message	The message to be printed to the screen during execution
print_dots	Whether or not progress dots should be printed for this section

Returns

The ID of the section - use when starting timing

Definition at line 72 of file PerfGraphInterface.C.

{
  const auto timed_section_name = timedSectionName(section_name);
  if (!moose::internal::getPerfGraphRegistry().sectionExists(timed_section_name))
    return moose::internal::getPerfGraphRegistry().registerSection(
        timedSectionName(section_name), level, live_message, print_dots);
  else
    return moose::internal::getPerfGraphRegistry().sectionID(timed_section_name);
}

reinit()

void AuxiliarySystem::reinit ( )

overridevirtual

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 from SystemBase.

Definition at line 120 of file AuxiliarySystem.C.

{
  _current_solution = _sys.current_local_solution.get();
  LinearFVGradientInterface::rebuildLinearFVGradientStorage();
}

reinitElem()

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

overridevirtual

Reinit an element assembly info.

Parameters

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

Reimplemented from SystemBase.

Definition at line 382 of file AuxiliarySystem.C.

{
  for (auto * var : _nodal_vars[tid])
    var->computeElemValues();

  for (auto * var : _elem_vars[tid])
  {
    var->reinitAux();
    var->computeElemValues();
  }
}

reinitElemFace()

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

overridevirtual

Reinit assembly info for a side of an element.

Parameters

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

Reimplemented from SystemBase.

Definition at line 395 of file AuxiliarySystem.C.

{
  for (auto * var : _nodal_vars[tid])
    var->computeElemValuesFace();

  for (auto * var : _elem_vars[tid])
  {
    var->reinitAux();
    var->reinitAuxNeighbor();
    var->computeElemValuesFace();
  }
}

reinitLowerD()

void SystemBase::reinitLowerD ( THREAD_ID  tid )

virtualinherited

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

Definition at line 391 of file SystemBase.C.

Referenced by SubProblem::reinitLowerDElem().

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

reinitNeighbor()

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

virtualinherited

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

Definition at line 383 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  )

virtualinherited

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

Definition at line 375 of file SystemBase.C.

Referenced by SubProblem::reinitNeighborFaceRef().

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

reinitNode()

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

virtualinherited

Reinit nodal assembly info.

Parameters

node	Node to reinit for
tid	Thread ID

Definition at line 399 of file SystemBase.C.

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

reinitNodeFace()

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

virtualinherited

Reinit nodal assembly info on a face.

Parameters

node	Node to reinit
bnd_id	Boundary ID
tid	Thread ID

Definition at line 411 of file SystemBase.C.

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

reinitNodes()

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

virtualinherited

Reinit variables at a set of nodes.

Parameters

nodes	List of node ids to reinit
tid	Thread ID

Definition at line 423 of file SystemBase.C.

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

reinitNodesNeighbor()

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

virtualinherited

Reinit variables at a set of neighbor nodes.

Parameters

nodes	List of node ids to reinit
tid	Thread ID

Definition at line 434 of file SystemBase.C.

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

reinitScalars()

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

virtualinherited

Reinit scalar varaibles.

Parameters

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

Definition at line 445 of file SystemBase.C.

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

removeMatrix()

void SystemBase::removeMatrix ( TagID  tag )

inherited

Removes a matrix with a given tag.

Parameters

tag_name

The name of the tag

Definition at line 591 of file SystemBase.C.

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

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

removeVector() [1/2]

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

inherited

Remove a vector from the system with the given name.

Definition at line 1336 of file SystemBase.C.

Referenced by SystemBase::restoreOldSolutions().

{
  system().remove_vector(name);
}

removeVector() [2/2]

void SystemBase::removeVector ( TagID  tag_id )

inherited

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

Parameters

tag_id

Tag ID

Definition at line 701 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;
  }
}

requestedLinearFVLimitedGradientTypes()

const std::unordered_set<Moose::FV::GradientLimiterType>& LinearFVGradientInterface::requestedLinearFVLimitedGradientTypes ( ) const

inlineinherited

Access the limiter types requested for this system.

Returns

The set of limiter types whose limited gradients should be assembled. They are only assembled for the variable(s) for which they were requested not all of them

Definition at line 72 of file LinearFVGradientInterface.h.

  {
    return _requested_limited_gradient_types;
  }

requestedLinearFVLimitedGradientVariables()

const std::unordered_set<unsigned int>& LinearFVGradientInterface::requestedLinearFVLimitedGradientVariables ( const Moose::FV::GradientLimiterType  limiter_type ) const

inlineprotectedinherited

Access the variable numbers that requested limited gradients for a specific limiter.

Parameters

limiter_type

The limiter type whose request set is being accessed.

Returns

The set of variable numbers that requested the limiter.

Definition at line 128 of file LinearFVGradientInterface.h.

  {
    return libmesh_map_find(_requested_limited_gradient_variables, limiter_type);
  }

requestLinearFVLimitedGradients() [1/2]

void LinearFVGradientInterface::requestLinearFVLimitedGradients ( const Moose::FV::GradientLimiterType  limiter_type, unsigned int  variable_number  )

inherited

Request storage and assembly of limiter-specific cell gradients.

Parameters

limiter_type	The limiter whose gradient storage should be made available.
variable_number	The libMesh variable number requesting the limited gradients.

Definition at line 166 of file LinearFVGradientInterface.C.

{
  if (limiter_type == Moose::FV::GradientLimiterType::None)
    return;

  auto * const variable =
      dynamic_cast<MooseVariableFieldBase *>(_sys.variableWarehouse().getVariable(variable_number));
  if (!variable)
    mooseError("Limited gradients were requested for variable number ",
               variable_number,
               " on system '",
               _sys.name(),
               "', but no field variable with that number exists on the system.");

  if (!variable->needsGradientVectorStorage())
    mooseError("Limited gradients were requested for variable '",
               variable->name(),
               "' on system '",
               _sys.name(),
               "', but regular gradients were not requested for that variable.");

  _requested_limited_gradient_variables[limiter_type].insert(variable_number);

  if (_requested_limited_gradient_types.insert(limiter_type).second && !_raw_grad_container.empty())
  {
    initializeContainer(_raw_limited_grad_containers[limiter_type]);
    initializeContainer(_temporary_limited_gradient[limiter_type]);
  }
}

requestLinearFVLimitedGradients() [2/2]

void LinearFVGradientInterface::requestLinearFVLimitedGradients

Request storage and assembly of limiter-specific cell gradients.

Parameters

limiter_type	The limiter whose gradient storage should be made available.
variable_number	The libMesh variable number requesting the limited gradients.

Definition at line 166 of file LinearFVGradientInterface.C.

{
  if (limiter_type == Moose::FV::GradientLimiterType::None)
    return;

  auto * const variable =
      dynamic_cast<MooseVariableFieldBase *>(_sys.variableWarehouse().getVariable(variable_number));
  if (!variable)
    mooseError("Limited gradients were requested for variable number ",
               variable_number,
               " on system '",
               _sys.name(),
               "', but no field variable with that number exists on the system.");

  if (!variable->needsGradientVectorStorage())
    mooseError("Limited gradients were requested for variable '",
               variable->name(),
               "' on system '",
               _sys.name(),
               "', but regular gradients were not requested for that variable.");

  _requested_limited_gradient_variables[limiter_type].insert(variable_number);

  if (_requested_limited_gradient_types.insert(limiter_type).second && !_raw_grad_container.empty())
  {
    initializeContainer(_raw_limited_grad_containers[limiter_type]);
    initializeContainer(_temporary_limited_gradient[limiter_type]);
  }
}

residualCopy()

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

inlinevirtualinherited

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 427 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 ( )

inlinevirtualinherited

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 431 of file SystemBase.h.

Referenced by DisplacedSystem::residualGhosted().

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

residualSetup()

void AuxiliarySystem::residualSetup ( )

overridevirtual

Reimplemented from SystemBase.

Definition at line 214 of file AuxiliarySystem.C.

{
  SystemBase::residualSetup();

  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _aux_scalar_storage.residualSetup(tid);
    _nodal_aux_storage.residualSetup(tid);
    _mortar_nodal_aux_storage.residualSetup(tid);
    _nodal_vec_aux_storage.residualSetup(tid);
    _nodal_array_aux_storage.residualSetup(tid);
    _elemental_aux_storage.residualSetup(tid);
    _elemental_vec_aux_storage.residualSetup(tid);
    _elemental_array_aux_storage.residualSetup(tid);
  }

#ifdef MOOSE_KOKKOS_ENABLED
  _kokkos_nodal_aux_storage.residualSetup(/*tid=*/0);
  _kokkos_elemental_aux_storage.residualSetup(/*tid=*/0);
#endif
}

residualVectorTag()

virtual TagID SystemBase::residualVectorTag ( ) const

inlinevirtualinherited

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 308 of file SystemBase.h.

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

{ mooseError("Not implemented yet"); }

restoreOldSolutions()

void SystemBase::restoreOldSolutions ( )

virtualinherited

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

Definition at line 543 of file SystemBase.C.

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

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

restoreSolutions()

void SystemBase::restoreSolutions ( )

virtualinherited

Restore current solutions (call after your solve failed)

Reimplemented in SolverSystem.

Definition at line 1319 of file SystemBase.C.

Referenced by SolverSystem::restoreSolutions().

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

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

saveOldSolutions()

void SystemBase::saveOldSolutions ( )

virtualinherited

Save the old and older solutions.

Definition at line 511 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 ( )

virtualinherited

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

Reimplemented in DisplacedSystem.

Definition at line 1635 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;
}

serializeSolution()

void AuxiliarySystem::serializeSolution ( )

virtual

Definition at line 409 of file AuxiliarySystem.C.

Referenced by compute().

{
  if (_serialized_solution.get() &&
      _sys.n_dofs() > 0) // libMesh does not like serializing of empty vectors
  {
    if (!_serialized_solution->initialized() || _serialized_solution->size() != _sys.n_dofs())
    {
      _serialized_solution->clear();
      _serialized_solution->init(_sys.n_dofs(), false, SERIAL);
    }

    solution().localize(*_serialized_solution);
  }
}

setActiveScalarVariableCoupleableVectorTags()

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

inherited

Set the active vector tags for the scalar variables.

Definition at line 1615 of file SystemBase.C.

Referenced by SubProblem::setActiveScalarVariableCoupleableVectorTags().

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

setActiveVariableCoupleableVectorTags()

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

inherited

Set the active vector tags for the variables.

Definition at line 1609 of file SystemBase.C.

Referenced by SubProblem::setActiveFEVariableCoupleableVectorTags().

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

setScalarVariableCoupleableTags()

void AuxiliarySystem::setScalarVariableCoupleableTags

(

ExecFlagType

type

)

Definition at line 698 of file AuxiliarySystem.C.

Referenced by computeScalarVars().

{
  const MooseObjectWarehouse<AuxScalarKernel> & storage = _aux_scalar_storage[type];
  const std::vector<std::shared_ptr<AuxScalarKernel>> & objects = storage.getActiveObjects(0);

  std::set<TagID> needed_sc_var_matrix_tags;
  std::set<TagID> needed_sc_var_vector_tags;
  for (const auto & obj : objects)
  {
    auto & sc_var_coup_vtags = obj->getScalarVariableCoupleableVectorTags();
    needed_sc_var_vector_tags.insert(sc_var_coup_vtags.begin(), sc_var_coup_vtags.end());

    auto & sc_var_coup_mtags = obj->getScalarVariableCoupleableMatrixTags();
    needed_sc_var_matrix_tags.insert(sc_var_coup_mtags.begin(), sc_var_coup_mtags.end());
  }

  _fe_problem.setActiveScalarVariableCoupleableMatrixTags(needed_sc_var_matrix_tags, 0);
  _fe_problem.setActiveScalarVariableCoupleableVectorTags(needed_sc_var_vector_tags, 0);
}

setVariableGlobalDoFs()

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

inherited

set all the global dof indices for a variable

Parameters

var_name

The name of the variable

Definition at line 187 of file SystemBase.C.

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

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

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

setVerboseFlag()

void SystemBase::setVerboseFlag ( const bool &  verbose )

inlineinherited

Sets the verbose flag.

Parameters

[in]

verbose

Verbose flag

Definition at line 135 of file SystemBase.h.

Referenced by Executioner::Executioner().

{ _verbose = verbose; }

sizeVariableMatrixData()

void SystemBase::sizeVariableMatrixData ( )

inherited

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

Definition at line 1708 of file SystemBase.C.

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

skipNextSolutionToOldCopy()

void SystemBase::skipNextSolutionToOldCopy ( )

inlineinherited

Skip the next copy from the solution vector to the old solution vector old -> older is still performed.

Definition at line 973 of file SystemBase.h.

{ _skip_next_solution_to_old_copy = true; }

solution() [1/2]

NumericVector<Number>& SystemBase::solution ( )

inlineinherited

Definition at line 197 of file SystemBase.h.

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

{ return solutionState(0); }

solution() [2/2]

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

inlineinherited

Definition at line 200 of file SystemBase.h.

{ return solutionState(0); }

solutionInternal()

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

inlineoverrideprotectedvirtual

Internal getter for solution owned by libMesh.

Implements SystemBase.

Definition at line 230 of file AuxiliarySystem.h.

{ return *_sys.solution; }

solutionOld() [1/2]

NumericVector<Number>& SystemBase::solutionOld ( )

inlineinherited

Definition at line 198 of file SystemBase.h.

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

{ return solutionState(1); }

solutionOld() [2/2]

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

inlineinherited

Definition at line 201 of file SystemBase.h.

{ return solutionState(1); }

solutionOlder() [1/2]

NumericVector<Number>& SystemBase::solutionOlder ( )

inlineinherited

Definition at line 199 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

inlineinherited

Definition at line 202 of file SystemBase.h.

{ return solutionState(2); }

solutionPreviousNewton() [1/2]

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

virtualinherited

Reimplemented in DisplacedSystem.

Definition at line 1357 of file SystemBase.C.

Referenced by copyCurrentIntoPreviousNL(), SystemBase::copyPreviousNonlinearSolutions(), and SystemBase::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 ( )

virtualinherited

Reimplemented in DisplacedSystem.

Definition at line 1348 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  )

virtualinherited

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 1433 of file SystemBase.C.

Referenced by SolverSystem::applyFixedPointRelaxation(), SystemBase::copyOldSolutions(), SystemBase::copyPreviousFixedPointSolutions(), SystemBase::copyPreviousNonlinearSolutions(), PointwiseRenormalizeVector::execute(), PointwiseRenormalizeVector::finalize(), MooseVariableBase::getSolution(), SystemBase::restoreOldSolutions(), SolverSystem::saveOldSolutionForFixedPointRelaxation(), SystemBase::saveOldSolutions(), SystemBase::solution(), SystemBase::solutionOld(), SystemBase::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

virtualinherited

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

Reimplemented in DisplacedSystem.

Definition at line 1404 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

inherited

Returns the parallel type of the given solution state.

Definition at line 1442 of file SystemBase.C.

Referenced by SolverSystem::applyFixedPointRelaxation(), SystemBase::needSolutionState(), and SolverSystem::saveOldSolutionForFixedPointRelaxation().

{
  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

inlineinherited

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

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

Definition at line 899 of file SystemBase.h.

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

{ return _solution_states_initialized; }

solutionUDot() [1/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 262 of file SystemBase.h.

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

{ return _u_dot; }

solutionUDot() [2/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 266 of file SystemBase.h.

{ return _u_dot; }

solutionUDotDot() [1/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 263 of file SystemBase.h.

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

{ return _u_dotdot; }

solutionUDotDot() [2/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 267 of file SystemBase.h.

{ return _u_dotdot; }

solutionUDotDotOld() [1/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 265 of file SystemBase.h.

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

{ return _u_dotdot_old; }

solutionUDotDotOld() [2/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 269 of file SystemBase.h.

{ return _u_dotdot_old; }

solutionUDotOld() [1/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 264 of file SystemBase.h.

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

{ return _u_dot_old; }

solutionUDotOld() [2/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 268 of file SystemBase.h.

{ return _u_dot_old; }

solve()

void SystemBase::solve ( )

virtualinherited

Solve the system (using libMesh magic)

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

Definition at line 1250 of file SystemBase.C.

{
  system().solve();
}

subdomainSetup()

void AuxiliarySystem::subdomainSetup ( )

overridevirtual

Reimplemented from SystemBase.

Definition at line 173 of file AuxiliarySystem.C.

{
  SystemBase::subdomainSetup();

  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _aux_scalar_storage.subdomainSetup(tid);
    _nodal_aux_storage.subdomainSetup(tid);
    _mortar_nodal_aux_storage.subdomainSetup(tid);
    _nodal_vec_aux_storage.subdomainSetup(tid);
    _nodal_array_aux_storage.subdomainSetup(tid);
    _elemental_aux_storage.subdomainSetup(tid);
    _elemental_vec_aux_storage.subdomainSetup(tid);
    _elemental_array_aux_storage.subdomainSetup(tid);
  }
}

subproblem() [1/2]

SubProblem& SystemBase::subproblem ( )

inlineinherited

Definition at line 102 of file SystemBase.h.

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

{ return _subproblem; }

subproblem() [2/2]

const SubProblem& SystemBase::subproblem ( ) const

inlineinherited

Definition at line 103 of file SystemBase.h.

{ return _subproblem; }

sys()

virtual libMesh::System& AuxiliarySystem::sys ( )

inlinevirtual

Definition at line 134 of file AuxiliarySystem.h.

Referenced by ReferenceResidualConvergence::initialSetup(), and ReferenceResidualConvergence::updateReferenceResidual().

{ return _sys; }

system() [1/2]

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

inlineoverridevirtual

Get the reference to the libMesh system.

Implements SystemBase.

Definition at line 136 of file AuxiliarySystem.h.

Referenced by TransientMultiApp::appTransferVector(), NonlinearSystemBase::constraintResiduals(), NodalNormalsPreprocessor::initialize(), ActivateElementsUserObjectBase::initSolutions(), ConsoleUtils::outputAuxiliarySystemInformation(), TransientMultiApp::setupApp(), and TransientMultiApp::solveStep().

{ return _sys; }

system() [2/2]

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

inlineoverridevirtual

Implements SystemBase.

Definition at line 137 of file AuxiliarySystem.h.

{ return _sys; }

systemMatrixTag()

virtual TagID SystemBase::systemMatrixTag ( ) const

inlinevirtualinherited

Return the Matrix Tag ID for System.

Reimplemented in NonlinearSystemBase, LinearSystem, and DisplacedSystem.

Definition at line 298 of file SystemBase.h.

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

{ mooseError("Not implemented yet"); }

temporaryLinearFVGradientContainer()

std::vector<std::unique_ptr<libMesh::NumericVector<libMesh::Number> > >& LinearFVGradientInterface::temporaryLinearFVGradientContainer ( )

inlineprotectedinherited

Return temporary storage for gradients during gradient assembly.

The returned vectors are persistent scratch storage reused across calls and swapped with the final gradient container before gradient assembly returns.

Definition at line 94 of file LinearFVGradientInterface.h.

  {
    return _temporary_gradient;
  }

temporaryLinearFVLimitedGradientContainer()

std::vector<std::unique_ptr<libMesh::NumericVector<libMesh::Number> > >& LinearFVGradientInterface::temporaryLinearFVLimitedGradientContainer ( const Moose::FV::GradientLimiterType  limiter_type )

inlineprotectedinherited

Return temporary storage for limited gradients during gradient assembly.

The returned vectors are persistent scratch storage reused across calls and swapped with the final limited-gradient container before gradient assembly returns.

Parameters

limiter_type

The limiter type whose temporary storage is being accessed.

Definition at line 106 of file LinearFVGradientInterface.h.

  {
    return _temporary_limited_gradient[limiter_type];
  }

timedSectionName()

std::string PerfGraphInterface::timedSectionName ( const std::string &  section_name ) const

protectedinherited

Returns

The name of the timed section with the name section_name.

Optionally adds a prefix if one is defined.

Definition at line 55 of file PerfGraphInterface.C.

Referenced by PerfGraphInterface::registerTimedSection().

{
  return _prefix.empty() ? "" : (_prefix + "::") + section_name;
}

timestepSetup()

void AuxiliarySystem::timestepSetup ( )

overridevirtual

Reimplemented from SystemBase.

Definition at line 127 of file AuxiliarySystem.C.

{
  SystemBase::timestepSetup();

  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _aux_scalar_storage.timestepSetup(tid);
    _nodal_aux_storage.timestepSetup(tid);
    _mortar_nodal_aux_storage.timestepSetup(tid);
    _nodal_vec_aux_storage.timestepSetup(tid);
    _nodal_array_aux_storage.timestepSetup(tid);
    _elemental_aux_storage.timestepSetup(tid);
    _elemental_vec_aux_storage.timestepSetup(tid);
    _elemental_array_aux_storage.timestepSetup(tid);
  }

#ifdef MOOSE_KOKKOS_ENABLED
  _kokkos_nodal_aux_storage.timestepSetup(/*tid=*/0);
  _kokkos_elemental_aux_storage.timestepSetup(/*tid=*/0);
#endif
}

timeVectorTag()

virtual TagID SystemBase::timeVectorTag ( ) const

inlinevirtualinherited

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 293 of file SystemBase.h.

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

{ mooseError("Not implemented yet"); }

update()

void SystemBase::update ( )

inherited

Update the system (doing libMesh magic)

Definition at line 1244 of file SystemBase.C.

Referenced by Adaptivity::adaptMesh(), SolverSystem::applyFixedPointRelaxation(), 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();
}

updateActive()

void AuxiliarySystem::updateActive ( THREAD_ID  tid )

virtual

Definition at line 237 of file AuxiliarySystem.C.

{
  _aux_scalar_storage.updateActive(tid);
  _nodal_aux_storage.updateActive(tid);
  _mortar_nodal_aux_storage.updateActive(tid);
  _nodal_vec_aux_storage.updateActive(tid);
  _nodal_array_aux_storage.updateActive(tid);
  _elemental_aux_storage.updateActive(tid);
  _elemental_vec_aux_storage.updateActive(tid);
  _elemental_array_aux_storage.updateActive(tid);

#ifdef MOOSE_KOKKOS_ENABLED
  if (tid == 0)
  {
    _kokkos_nodal_aux_storage.updateActive(/*tid=*/0);
    _kokkos_elemental_aux_storage.updateActive(/*tid=*/0);
  }
#endif
}

validParams()

InputParameters PerfGraphInterface::validParams ( )

staticinherited

Definition at line 16 of file PerfGraphInterface.C.

Referenced by Convergence::validParams().

{
  InputParameters params = emptyInputParameters();
  return params;
}

variableWarehouse()

const VariableWarehouse& SystemBase::variableWarehouse ( THREAD_ID  tid = 0 ) const

inlineinherited

Definition at line 757 of file SystemBase.h.

{ return _vars[tid]; }

variableWiseRelativeSolutionDifferenceNorm()

void AuxiliarySystem::variableWiseRelativeSolutionDifferenceNorm

(

std::vector< Number > &

var_diffs

)

const

Computes and stores ||current - old|| / ||current|| for each variable in the given vector.

Parameters

var_diffs

a vector being filled with the L2 norm of the solution difference

Definition at line 1011 of file AuxiliarySystem.C.

Referenced by DefaultSteadyStateConvergence::checkConvergence().

{
  rel_diff_norms.resize(nVariables(), 0);
  // Get dof map from system
  const auto & dof_map = _sys.get_dof_map();

  for (const auto n : make_range(nVariables()))
  {
    // Get local indices from dof map for each variable
    std::vector<dof_id_type> local_indices_n;
    dof_map.local_variable_indices(local_indices_n, _mesh, n);
    Number diff_norm_n = 0;
    Number norm_n = 0;
    // Get values from system, update norm
    for (const auto local_index : local_indices_n)
    {
      const Number & value = solution()(local_index);
      const Number & value_old = solutionOld()(local_index);
      diff_norm_n += Utility::pow<2, Number>(value - value_old);
      norm_n += Utility::pow<2, Number>(value);
    }
    // Aggregate norm over proceccors
    _communicator.sum(diff_norm_n);
    _communicator.sum(norm_n);
    diff_norm_n = sqrt(diff_norm_n);
    norm_n = sqrt(norm_n);
    rel_diff_norms[n] = diff_norm_n > 0 ? diff_norm_n / norm_n : 0.0;
  }
}

varKind()

Moose::VarKindType SystemBase::varKind ( ) const

inlineinherited

Returns

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

Definition at line 927 of file SystemBase.h.

Referenced by Coupleable::coupled().

{ return _var_kind; }

zeroTaggedVector()

void SystemBase::zeroTaggedVector ( const TagID  tag )

inherited

Zero vector with the given tag.

Definition at line 675 of file SystemBase.C.

Referenced by SystemBase::zeroTaggedVectors().

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

zeroTaggedVectors()

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

inherited

Zero all vectors for given tags.

Definition at line 694 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 )

virtualinherited

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 201 of file SystemBase.C.

Referenced by DisplacedSystem::zeroVariables(), SystemBase::zeroVariablesForJacobian(), and SystemBase::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 ( )

virtualinherited

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

Definition at line 236 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_jacobian);
}

zeroVariablesForResidual()

void SystemBase::zeroVariablesForResidual ( )

virtualinherited

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

Definition at line 230 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_residual);
}

Friends And Related Function Documentation

ComputeIndicatorThread

friend class ComputeIndicatorThread

friend

Definition at line 222 of file AuxiliarySystem.h.

ComputeMarkerThread

friend class ComputeMarkerThread

friend

Definition at line 223 of file AuxiliarySystem.h.

ComputeNodalKernelBCJacobiansThread

friend class ComputeNodalKernelBCJacobiansThread

friend

Definition at line 228 of file AuxiliarySystem.h.

ComputeNodalKernelBcsThread

friend class ComputeNodalKernelBcsThread

friend

Definition at line 226 of file AuxiliarySystem.h.

ComputeNodalKernelJacobiansThread

friend class ComputeNodalKernelJacobiansThread

friend

Definition at line 227 of file AuxiliarySystem.h.

ComputeNodalKernelsThread

friend class ComputeNodalKernelsThread

friend

Definition at line 225 of file AuxiliarySystem.h.

FlagElementsThread

friend class FlagElementsThread

friend

Definition at line 224 of file AuxiliarySystem.h.

Member Data Documentation

_active_tagged_matrices

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

protectedinherited

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 SystemBase::activateAllMatrixTags(), SystemBase::deactivateAllMatrixTags(), and SystemBase::reinitElem().

_app

MooseApp& SystemBase::_app

protectedinherited

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(), NonlinearSystem::converged(), and NonlinearSystemBase::shouldEvaluatePreSMOResidual().

_automatic_scaling

bool SystemBase::_automatic_scaling

protectedinherited

Whether to automatically scale the variables.

Definition at line 1055 of file SystemBase.h.

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

_aux_scalar_storage

ExecuteMooseObjectWarehouse<AuxScalarKernel> AuxiliarySystem::_aux_scalar_storage

protected

Definition at line 201 of file AuxiliarySystem.h.

Referenced by addScalarKernel(), AuxiliarySystem(), computeScalarVars(), customSetup(), jacobianSetup(), residualSetup(), setScalarVariableCoupleableTags(), subdomainSetup(), timestepSetup(), and updateActive().

_console

const ConsoleStream ConsoleStreamInterface::_console

inherited

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

Definition at line 31 of file ConsoleStreamInterface.h.

Referenced by IterationAdaptiveDT::acceptStep(), MeshOnlyAction::act(), SetupDebugAction::act(), MaterialOutputAction::act(), Adaptivity::adaptMesh(), FEProblemBase::adaptMesh(), PerfGraph::addToExecutionList(), SimplePredictor::apply(), SystemBase::applyScalingFactors(), MultiApp::backup(), FEProblemBase::backupMultiApps(), CoarsenedPiecewiseLinear::buildCoarsenedGrid(), DefaultSteadyStateConvergence::checkConvergence(), MeshDiagnosticsGenerator::checkElementOverlap(), MeshDiagnosticsGenerator::checkElementTypes(), MeshDiagnosticsGenerator::checkElementVolumes(), FEProblemBase::checkExceptionAndStopSolve(), SolverSystem::checkInvalidSolution(), MeshDiagnosticsGenerator::checkLocalJacobians(), MeshDiagnosticsGenerator::checkNonConformalMesh(), MeshDiagnosticsGenerator::checkNonConformalMeshFromAdaptivity(), MeshDiagnosticsGenerator::checkNonMatchingEdges(), MeshDiagnosticsGenerator::checkNonPlanarSides(), MeshDiagnosticsGenerator::checkPolygons(), 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(), SurfaceSubdomainsDelaunayRemesher::General2DDelaunay(), OrientSurfaceMeshGenerator::generate(), CoarsenBlockGenerator::generate(), PolyLineMeshFollowingNodeSetGenerator::generate(), MeshGenerator::generateInternal(), VariableCondensationPreconditioner::getDofToCondense(), InversePowerMethod::init(), NonlinearEigen::init(), FEProblemBase::initialAdaptMesh(), DefaultMultiAppFixedPointConvergence::initialize(), SubProblem::initialSetup(), EigenExecutionerBase::inversePowerIteration(), FEProblemBase::joinAndFinalize(), TransientBase::keepGoing(), IterationAdaptiveDT::limitDTByFunction(), IterationAdaptiveDT::limitDTToPostprocessorValue(), FEProblemBase::logAdd(), EigenExecutionerBase::makeBXConsistent(), Console::meshChanged(), SurfaceDelaunayGeneratorBase::meshNormalDeviation2D(), MooseBase::mooseDeprecated(), MooseBase::mooseDeprecatedNoTrace(), 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(), WebServerControl::outputMessage(), 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(), FixedPointSolve::solve(), NonlinearSystem::solve(), LinearSystem::solve(), LStableDirk2::solve(), LStableDirk3::solve(), ImplicitMidpoint::solve(), ExplicitTVDRK2::solve(), AStableDirk4::solve(), LStableDirk4::solve(), ExplicitRK2::solve(), TransientMultiApp::solveStep(), FixedPointSolve::solveStep(), MeshRepairGenerator::splitNonConvexPolygons(), PerfGraphLivePrint::start(), WebServerControl::startServer(), AB2PredictorCorrector::step(), NonlinearEigen::takeStep(), MFEMTransient::takeStep(), TransientBase::takeStep(), TerminateChainControl::terminate(), SubProblem::timestepSetup(), FEProblemBase::updateMeshXFEM(), Convergence::verboseOutput(), Console::writeTimestepInformation(), Console::writeVariableNorms(), and FEProblemBase::~FEProblemBase().

_current_solution

const NumericVector<Number>* AuxiliarySystem::_current_solution

protected

solution vector from nonlinear solver

Definition at line 185 of file AuxiliarySystem.h.

Referenced by AuxiliarySystem(), currentSolution(), and reinit().

_du_dot_du

std::vector<Real> SystemBase::_du_dot_du

protectedinherited

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 SystemBase::addVariable(), SystemBase::duDotDu(), and SystemBase::duDotDus().

_du_dotdot_du

Real SystemBase::_du_dotdot_du

protectedinherited

Definition at line 1018 of file SystemBase.h.

Referenced by SystemBase::duDotDotDu().

_elem_vars

std::vector<std::vector<MooseVariableFieldBase *> > AuxiliarySystem::_elem_vars

protected

Elemental variables.

These may be either finite element or finite volume variables

Definition at line 197 of file AuxiliarySystem.h.

Referenced by addVariable(), ComputeMarkerThread::onElement(), ComputeIndicatorThread::onElement(), ComputeIndicatorThread::onInternalSide(), reinitElem(), reinitElemFace(), and ComputeMarkerThread::subdomainChanged().

_elemental_array_aux_storage

ExecuteMooseObjectWarehouse<ArrayAuxKernel> AuxiliarySystem::_elemental_array_aux_storage

protected

Definition at line 214 of file AuxiliarySystem.h.

Referenced by addKernel(), AuxiliarySystem(), computeElementalArrayVars(), customSetup(), elemArrayAuxWarehouse(), getDependObjects(), jacobianSetup(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_elemental_aux_storage

ExecuteMooseObjectWarehouse<AuxKernel> AuxiliarySystem::_elemental_aux_storage

protected

Definition at line 206 of file AuxiliarySystem.h.

Referenced by addKernel(), AuxiliarySystem(), computeElementalVars(), customSetup(), elemAuxWarehouse(), getDependObjects(), jacobianSetup(), needMaterialOnSide(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_elemental_vec_aux_storage

ExecuteMooseObjectWarehouse<VectorAuxKernel> AuxiliarySystem::_elemental_vec_aux_storage

protected

Definition at line 210 of file AuxiliarySystem.h.

Referenced by addKernel(), AuxiliarySystem(), computeElementalVecVars(), customSetup(), elemVectorAuxWarehouse(), getDependObjects(), jacobianSetup(), needMaterialOnSide(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_factory

Factory& SystemBase::_factory

protectedinherited

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(), addKernel(), NonlinearSystemBase::addKernel(), NonlinearSystemBase::addNodalKernel(), addScalarKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), SystemBase::addTimeIntegrator(), and SystemBase::addVariable().

_fe_problem

FEProblemBase& SystemBase::_fe_problem

protectedinherited

the governing finite element/volume problem

Definition at line 986 of file SystemBase.h.

Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addConstraint(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), SystemBase::addDotVectors(), NonlinearSystemBase::addHDGKernel(), NonlinearSystemBase::addInterfaceKernel(), NonlinearSystemBase::addKernel(), NonlinearSystemBase::addNodalKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), NonlinearSystemBase::assembleScalingVector(), NonlinearSystemBase::augmentSparsity(), SolverSystem::checkInvalidSolution(), NonlinearSystemBase::checkKernelCoverage(), clearScalarVariableCoupleableTags(), SolverSystem::compute(), compute(), LinearSystem::compute(), NonlinearSystemBase::computeDamping(), NonlinearSystemBase::computeDiracContributions(), computeElementalVarsHelper(), NonlinearSystemBase::computeJacobian(), NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), LinearSystem::computeLinearSystemTags(), computeMortarNodalVars(), NonlinearSystemBase::computeNodalBCsJacobian(), NonlinearSystemBase::computeNodalBCsResidual(), NonlinearSystemBase::computeNodalBCsResidualAndJacobian(), computeNodalVarsHelper(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::computeScalarKernelsJacobians(), 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(), SystemBase::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(), setScalarVariableCoupleableTags(), NonlinearSystemBase::shouldEvaluatePreSMOResidual(), NonlinearSystem::solve(), and NonlinearSystemBase::timestepSetup().

_kokkos_elemental_aux_storage

ExecuteMooseObjectWarehouse<AuxKernelBase> AuxiliarySystem::_kokkos_elemental_aux_storage

protected

Definition at line 219 of file AuxiliarySystem.h.

Referenced by AuxiliarySystem(), customSetup(), getDependObjects(), jacobianSetup(), kokkosElemAuxWarehouse(), residualSetup(), timestepSetup(), and updateActive().

_kokkos_nodal_aux_storage

ExecuteMooseObjectWarehouse<AuxKernelBase> AuxiliarySystem::_kokkos_nodal_aux_storage

protected

Definition at line 218 of file AuxiliarySystem.h.

Referenced by AuxiliarySystem(), customSetup(), getDependObjects(), jacobianSetup(), kokkosNodalAuxWarehouse(), residualSetup(), timestepSetup(), and updateActive().

_matrix_tag_active_flags

std::vector<bool> SystemBase::_matrix_tag_active_flags

protectedinherited

Active flags for tagged matrices.

Definition at line 1027 of file SystemBase.h.

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

_max_var_n_dofs_per_elem

size_t SystemBase::_max_var_n_dofs_per_elem

protectedinherited

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

Definition at line 1043 of file SystemBase.h.

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

_max_var_n_dofs_per_node

size_t SystemBase::_max_var_n_dofs_per_node

protectedinherited

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

Definition at line 1046 of file SystemBase.h.

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

_max_var_number

unsigned int SystemBase::_max_var_number

protectedinherited

Maximum variable number.

Definition at line 1000 of file SystemBase.h.

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

_mesh

MooseMesh& SystemBase::_mesh

protectedinherited

Definition at line 991 of file SystemBase.h.

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

_mortar_nodal_aux_storage

ExecuteMooseObjectWarehouse<AuxKernel> AuxiliarySystem::_mortar_nodal_aux_storage

protected

Definition at line 205 of file AuxiliarySystem.h.

Referenced by addKernel(), AuxiliarySystem(), computeMortarNodalVars(), customSetup(), getDependObjects(), jacobianSetup(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_name

std::string SystemBase::_name

protectedinherited

The name of this system.

Definition at line 993 of file SystemBase.h.

_nodal_array_aux_storage

ExecuteMooseObjectWarehouse<ArrayAuxKernel> AuxiliarySystem::_nodal_array_aux_storage

protected

Definition at line 213 of file AuxiliarySystem.h.

Referenced by addKernel(), AuxiliarySystem(), computeNodalArrayVars(), customSetup(), getDependObjects(), jacobianSetup(), nodalArrayAuxWarehouse(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_nodal_aux_storage

ExecuteMooseObjectWarehouse<AuxKernel> AuxiliarySystem::_nodal_aux_storage

protected

Definition at line 204 of file AuxiliarySystem.h.

Referenced by addKernel(), AuxiliarySystem(), computeNodalVars(), customSetup(), getDependObjects(), jacobianSetup(), nodalAuxWarehouse(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_nodal_vars

std::vector<std::vector<MooseVariableFEBase *> > AuxiliarySystem::_nodal_vars

protected

Definition at line 191 of file AuxiliarySystem.h.

Referenced by addVariable(), ComputeNodalKernelBcsThread::onNode(), ComputeNodalKernelsThread::onNode(), ComputeNodalKernelBCJacobiansThread::onNode(), ComputeNodalKernelJacobiansThread::onNode(), reinitElem(), and reinitElemFace().

_nodal_vec_aux_storage

ExecuteMooseObjectWarehouse<VectorAuxKernel> AuxiliarySystem::_nodal_vec_aux_storage

protected

Definition at line 209 of file AuxiliarySystem.h.

Referenced by addKernel(), AuxiliarySystem(), computeNodalVecVars(), customSetup(), getDependObjects(), jacobianSetup(), nodalVectorAuxWarehouse(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_numbered_vars

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

protectedinherited

Map variable number to its pointer.

Definition at line 1052 of file SystemBase.h.

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

_pg_moose_app

MooseApp& PerfGraphInterface::_pg_moose_app

protectedinherited

The MooseApp that owns the PerfGraph.

Definition at line 135 of file PerfGraphInterface.h.

Referenced by PerfGraphInterface::perfGraph().

_prefix

const std::string PerfGraphInterface::_prefix

protectedinherited

A prefix to use for all sections.

Definition at line 138 of file PerfGraphInterface.h.

Referenced by PerfGraphInterface::timedSectionName().

_raw_grad_container

std::vector<std::unique_ptr<libMesh::NumericVector<libMesh::Number> > > LinearFVGradientInterface::_raw_grad_container

protectedinherited

Persisted raw cell-centered gradient components keyed by spatial direction.

Definition at line 145 of file LinearFVGradientInterface.h.

Referenced by compute(), and LinearFVGradientInterface::linearFVGradientContainer().

_raw_limited_grad_containers

std::unordered_map<Moose::FV::GradientLimiterType, std::vector<std::unique_ptr<libMesh::NumericVector<libMesh::Number> > > > LinearFVGradientInterface::_raw_limited_grad_containers

protectedinherited

Persisted limited gradient components keyed by limiter type.

Definition at line 157 of file LinearFVGradientInterface.h.

Referenced by LinearFVGradientInterface::rawLinearFVLimitedGradientContainer().

_requested_limited_gradient_types

std::unordered_set<Moose::FV::GradientLimiterType> LinearFVGradientInterface::_requested_limited_gradient_types

protectedinherited

Set of requested limiter types for which limited gradients should be computed.

Definition at line 148 of file LinearFVGradientInterface.h.

Referenced by LinearFVGradientInterface::requestedLinearFVLimitedGradientTypes().

_requested_limited_gradient_variables

std::unordered_map<Moose::FV::GradientLimiterType, std::unordered_set<unsigned int> > LinearFVGradientInterface::_requested_limited_gradient_variables

protectedinherited

Variable numbers requesting limited gradients, keyed by limiter type.

Definition at line 152 of file LinearFVGradientInterface.h.

Referenced by LinearFVGradientInterface::requestedLinearFVLimitedGradientVariables().

_saved_dot_old

NumericVector<Real>* SystemBase::_saved_dot_old

protectedinherited

Definition at line 1034 of file SystemBase.h.

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

_saved_dotdot_old

NumericVector<Real>* SystemBase::_saved_dotdot_old

protectedinherited

Definition at line 1035 of file SystemBase.h.

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

_saved_old

NumericVector<Real>* SystemBase::_saved_old

protectedinherited

Definition at line 1030 of file SystemBase.h.

_saved_older

NumericVector<Real>* SystemBase::_saved_older

protectedinherited

Definition at line 1031 of file SystemBase.h.

_serialized_solution

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

protectedinherited

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

Definition at line 1068 of file SystemBase.h.

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

_solution_state

std::vector<NumericVector<Number> *> AuxiliarySystem::_solution_state

protected

The current states of the solution (0 = current, 1 = old, etc)

Definition at line 188 of file AuxiliarySystem.h.

_solution_states_initialized

bool SystemBase::_solution_states_initialized

protectedinherited

Whether or not the solution states have been initialized.

Definition at line 1061 of file SystemBase.h.

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

_subproblem

SubProblem& SystemBase::_subproblem

protectedinherited

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

Definition at line 983 of file SystemBase.h.

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

_sys

libMesh::System& AuxiliarySystem::_sys

protected

Definition at line 182 of file AuxiliarySystem.h.

Referenced by AuxiliarySystem(), compute(), computeElementalVarsHelper(), computeMortarNodalVars(), computeNodalVarsHelper(), computeScalarVars(), reinit(), serializeSolution(), solutionInternal(), sys(), system(), and variableWiseRelativeSolutionDifferenceNorm().

_tagged_matrices

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

protectedinherited

Tagged matrices (pointer)

Definition at line 1023 of file SystemBase.h.

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

_tagged_vectors

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

protectedinherited

Tagged vectors (pointer)

Definition at line 1021 of file SystemBase.h.

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

_temporary_gradient

std::vector<std::unique_ptr<libMesh::NumericVector<libMesh::Number> > > LinearFVGradientInterface::_temporary_gradient

protectedinherited

Scratch storage for raw gradients assembled during the current compute pass.

Definition at line 142 of file LinearFVGradientInterface.h.

Referenced by LinearFVGradientInterface::temporaryLinearFVGradientContainer().

_temporary_limited_gradient

std::unordered_map<Moose::FV::GradientLimiterType, std::vector<std::unique_ptr<libMesh::NumericVector<libMesh::Number> > > > LinearFVGradientInterface::_temporary_limited_gradient

protectedinherited

Scratch storage for limited gradients assembled during the current compute pass.

Definition at line 162 of file LinearFVGradientInterface.h.

Referenced by LinearFVGradientInterface::temporaryLinearFVLimitedGradientContainer().

_time_integrators

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

protectedinherited

Time integrator.

Definition at line 1049 of file SystemBase.h.

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

_u_dot

NumericVector<Number>* SystemBase::_u_dot

protectedinherited

solution vector for u^dot

Definition at line 1006 of file SystemBase.h.

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

_u_dot_old

NumericVector<Number>* SystemBase::_u_dot_old

protectedinherited

old solution vector for u^dot

Definition at line 1011 of file SystemBase.h.

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

_u_dotdot

NumericVector<Number>* SystemBase::_u_dotdot

protectedinherited

solution vector for u^dotdot

Definition at line 1008 of file SystemBase.h.

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

_u_dotdot_old

NumericVector<Number>* SystemBase::_u_dotdot_old

protectedinherited

old solution vector for u^dotdot

Definition at line 1013 of file SystemBase.h.

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

_var_all_dof_indices

std::vector<dof_id_type> SystemBase::_var_all_dof_indices

protectedinherited

Container for the dof indices of a given variable.

Definition at line 1064 of file SystemBase.h.

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

_var_kind

Moose::VarKindType SystemBase::_var_kind

protectedinherited

default kind of variables in this system

Definition at line 1038 of file SystemBase.h.

Referenced by SystemBase::varKind().

_var_map

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

protectedinherited

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

Definition at line 998 of file SystemBase.h.

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

_var_to_copy

std::vector<VarCopyInfo> SystemBase::_var_to_copy

protectedinherited

Definition at line 1040 of file SystemBase.h.

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

_vars

std::vector<VariableWarehouse> SystemBase::_vars

protectedinherited

Variable warehouses (one for each thread)

Definition at line 996 of file SystemBase.h.

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

_vars_to_be_zeroed_on_jacobian

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

protectedinherited

Definition at line 1003 of file SystemBase.h.

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

_vars_to_be_zeroed_on_residual

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

protectedinherited

Definition at line 1002 of file SystemBase.h.

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

_verbose

bool SystemBase::_verbose

protectedinherited

True if printing out additional information.

Definition at line 1058 of file SystemBase.h.

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

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

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