NonlinearSystemBase Class Reference

Nonlinear system to be solved. More...

#include <NonlinearSystemBase.h>

Inheritance diagram for NonlinearSystemBase:

Public Member Functions
	NonlinearSystemBase (FEProblemBase &problem, libMesh::System &sys, const std::string &name)
virtual	~NonlinearSystemBase ()
virtual void	preInit () override
	This is called prior to the libMesh system has been init'd. More...
bool	computedScalingJacobian () const
virtual void	turnOffJacobian ()
	Turn off the Jacobian (must be called before equation system initialization) More...
virtual void	solve () override=0
	Solve the system (using libMesh magic) More...
virtual libMesh::NonlinearSolver< Number > *	nonlinearSolver ()=0
virtual SNES	getSNES ()=0
virtual unsigned int	getCurrentNonlinearIterationNumber ()=0
bool	computingPreSMOResidual ()
	Returns true if this system is currently computing the pre-SMO residual for a solve. More...
virtual void	initialSetup () override
	Setup Functions. More...
virtual void	timestepSetup () override
virtual void	customSetup (const ExecFlagType &exec_type) override
virtual void	residualSetup () override
virtual void	jacobianSetup () override
virtual void	setupFiniteDifferencedPreconditioner ()=0
void	setupFieldDecomposition ()
bool	haveFiniteDifferencedPreconditioner () const
bool	haveFieldSplitPreconditioner () const
virtual void	addKernel (const std::string &kernel_name, const std::string &name, InputParameters &parameters)
	Adds a kernel. More...
virtual void	addHDGKernel (const std::string &kernel_name, const std::string &name, InputParameters &parameters)
	Adds a hybridized discontinuous Galerkin (HDG) kernel. More...
virtual void	addNodalKernel (const std::string &kernel_name, const std::string &name, InputParameters &parameters)
	Adds a NodalKernel. More...
void	addScalarKernel (const std::string &kernel_name, const std::string &name, InputParameters &parameters)
	Adds a scalar kernel. More...
void	addBoundaryCondition (const std::string &bc_name, const std::string &name, InputParameters &parameters)
	Adds a boundary condition. More...
void	addConstraint (const std::string &c_name, const std::string &name, InputParameters &parameters)
	Adds a Constraint. More...
void	addDiracKernel (const std::string &kernel_name, const std::string &name, InputParameters &parameters)
	Adds a Dirac kernel. More...
void	addDGKernel (std::string dg_kernel_name, const std::string &name, InputParameters &parameters)
	Adds a DG kernel. More...
void	addInterfaceKernel (std::string interface_kernel_name, const std::string &name, InputParameters &parameters)
	Adds an interface kernel. More...
void	addDamper (const std::string &damper_name, const std::string &name, InputParameters &parameters)
	Adds a damper. More...
void	addSplit (const std::string &split_name, const std::string &name, InputParameters &parameters)
	Adds a split. More...
std::shared_ptr< Split >	getSplit (const std::string &name)
	Retrieves a split by name. More...
MooseObjectWarehouseBase< Split > &	getSplits ()
	Retrieves all splits. More...
bool	shouldEvaluatePreSMOResidual () const
	We offer the option to check convergence against the pre-SMO residual. More...
void	setPreSMOResidual (bool use)
	Set whether to evaluate the pre-SMO residual and use it in the subsequent relative convergence checks. More...
const bool &	usePreSMOResidual () const
	Whether we are using pre-SMO residual in relative convergence checks. More...
Real	referenceResidual () const
	The reference residual used in relative convergence check. More...
Real	preSMOResidual () const
	The pre-SMO residual. More...
Real	initialResidual () const
	The initial residual. More...
void	setInitialResidual (Real r)
	Record the initial residual (for later relative convergence check) More...
void	zeroVectorForResidual (const std::string &vector_name)
void	setInitialSolution ()
void	setConstraintSecondaryValues (NumericVector< Number > &solution, bool displaced)
	Sets the value of constrained variables in the solution vector. More...
void	constraintResiduals (NumericVector< Number > &residual, bool displaced)
	Add residual contributions from Constraints. More...
void	computeResidualTag (NumericVector< Number > &residual, TagID tag_id)
	Computes residual for a given tag. More...
void	computeResidualTags (const std::set< TagID > &tags)
	Form multiple tag-associated residual vectors for all the given tags. More...
void	computeResidualAndJacobianTags (const std::set< TagID > &vector_tags, const std::set< TagID > &matrix_tags)
	Form possibly multiple tag-associated vectors and matrices. More...
void	computeResidualAndJacobianInternal (const std::set< TagID > &vector_tags, const std::set< TagID > &matrix_tags)
	Compute residual and Jacobian from contributions not related to constraints, such as nodal boundary conditions. More...
void	computeResidual (NumericVector< Number > &residual, TagID tag_id)
	Form a residual vector for a given tag. More...
void	addImplicitGeometricCouplingEntries (GeometricSearchData &geom_search_data)
	Adds entries to the Jacobian in the correct positions for couplings coming from dofs being coupled that are related geometrically (i.e. More...
void	constraintJacobians (const SparseMatrix< Number > &jacobian_to_view, bool displaced)
	Add jacobian contributions from Constraints. More...
void	computeJacobianTags (const std::set< TagID > &tags)
	Computes multiple (tag associated) Jacobian matricese. More...
bool	computeScaling ()
	Method used to obtain scaling factors for variables. More...
void	computeJacobian (libMesh::SparseMatrix< Number > &jacobian, const std::set< TagID > &tags)
	Associate jacobian to systemMatrixTag, and then form a matrix for all the tags. More...
void	computeJacobian (libMesh::SparseMatrix< Number > &jacobian)
	Take all tags in the system, and form a matrix for all tags in the system. More...
void	computeJacobianBlocks (std::vector< JacobianBlock *> &blocks)
	Computes several Jacobian blocks simultaneously, summing their contributions into smaller preconditioning matrices. More...
void	computeJacobianBlocks (std::vector< JacobianBlock *> &blocks, const std::set< TagID > &tags)
Real	computeDamping (const NumericVector< Number > &solution, const NumericVector< Number > &update)
	Compute damping. More...
void	onTimestepBegin ()
	Called at the beginning of the time step. More...
virtual void	subdomainSetup (SubdomainID subdomain, THREAD_ID tid)
	Called from assembling when we hit a new subdomain. More...
void	overwriteNodeFace (NumericVector< Number > &soln)
	Called from explicit time stepping to overwrite boundary positions (explicit dynamics). More...
void	updateActive (THREAD_ID tid)
	Update active objects of Warehouses owned by NonlinearSystemBase. More...
virtual void	setSolutionUDot (const NumericVector< Number > &udot)
	Set transient term used by residual and Jacobian evaluation. More...
virtual void	setSolutionUDotDot (const NumericVector< Number > &udotdot)
	Set transient term used by residual and Jacobian evaluation. More...
NumericVector< Number > &	getResidualTimeVector ()
	Return a numeric vector that is associated with the time tag. More...
NumericVector< Number > &	getResidualNonTimeVector ()
	Return a numeric vector that is associated with the nontime tag. More...
NumericVector< Number > &	residualVector (TagID tag)
	Return a residual vector that is associated with the residual tag. More...
virtual NumericVector< Number > &	residualCopy () override
virtual NumericVector< Number > &	residualGhosted () override
virtual NumericVector< Number > &	RHS ()=0
virtual void	augmentSparsity (libMesh::SparsityPattern::Graph &sparsity, std::vector< dof_id_type > &n_nz, std::vector< dof_id_type > &n_oz) override
	Will modify the sparsity pattern to add logical geometric connections. More...
void	setPreconditioner (std::shared_ptr< MoosePreconditioner > pc)
	Sets a preconditioner. More...
MoosePreconditioner const *	getPreconditioner () const
void	useFiniteDifferencedPreconditioner (bool use=true)
	If called with true this system will use a finite differenced form of the Jacobian as the preconditioner. More...
void	setDecomposition (const std::vector< std::string > &decomposition)
	If called with a single string, it is used as the name of a the top-level decomposition split. More...
void	useFieldSplitPreconditioner (bool use=true)
	If called with true this system will use a field split preconditioner matrix. More...
void	addImplicitGeometricCouplingEntriesToJacobian (bool add=true)
	If called with true this will add entries into the jacobian to link together degrees of freedom that are found to be related through the geometric search system. More...
void	assembleConstraintsSeparately (bool separately=true)
	Indicates whether to assemble residual and Jacobian after each constraint application. More...
virtual void	attachPreconditioner (libMesh::Preconditioner< Number > *preconditioner)=0
	Attach a customized preconditioner that requires physics knowledge. More...
void	setupDampers ()
	Setup damping stuff (called before we actually start) More...
void	reinitIncrementAtQpsForDampers (THREAD_ID tid, const std::set< MooseVariable *> &damped_vars)
	Compute the incremental change in variables at QPs for dampers. More...
void	reinitIncrementAtNodeForDampers (THREAD_ID tid, const std::set< MooseVariable *> &damped_vars)
	Compute the incremental change in variables at nodes for dampers. More...
unsigned int	nNonlinearIterations () const
	Return the number of non-linear iterations. More...
unsigned int	nLinearIterations () const
	Return the number of linear iterations. More...
unsigned int	nResidualEvaluations () const
	Return the total number of residual evaluations done so far in this calculation. More...
Real	finalNonlinearResidual () const
	Return the final nonlinear residual. More...
Real	nonlinearNorm () const
	Return the last nonlinear norm. More...
void	printAllVariableNorms (bool state)
	Force the printing of all variable norms after each solve. More...
void	debuggingResiduals (bool state)
void	setPredictor (std::shared_ptr< Predictor > predictor)
Predictor *	getPredictor ()
bool	needBoundaryMaterialOnSide (BoundaryID bnd_id, THREAD_ID tid) const
	Indicated whether this system needs material properties on boundaries. More...
bool	needInterfaceMaterialOnSide (BoundaryID bnd_id, THREAD_ID tid) const
	Indicated whether this system needs material properties on interfaces. More...
bool	needSubdomainMaterialOnSide (SubdomainID subdomain_id, THREAD_ID tid) const
	Indicates whether this system needs material properties on internal sides. More...
bool	doingDG () const
	Getter for _doing_dg. More...
bool	hasSaveIn () const
	Weather or not the nonlinear system has save-ins. More...
bool	hasDiagSaveIn () const
	Weather or not the nonlinear system has diagonal Jacobian save-ins. More...
virtual libMesh::System &	system () override
	Get the reference to the libMesh system. More...
virtual const libMesh::System &	system () const override
virtual void	setSolutionUDotOld (const NumericVector< Number > &u_dot_old)
virtual void	setSolutionUDotDotOld (const NumericVector< Number > &u_dotdot_old)
virtual void	setPreviousNewtonSolution (const NumericVector< Number > &soln)
TagID	timeVectorTag () const override
	Ideally, we should not need this API. More...
TagID	nonTimeVectorTag () const override
TagID	residualVectorTag () const override
TagID	systemMatrixTag () const override
	Return the Matrix Tag ID for System. More...
virtual void	residualAndJacobianTogether ()=0
	Call this method if you want the residual and Jacobian to be computed simultaneously. More...
bool	computeScalingOnce () const
void	computeScalingOnce (bool compute_scaling_once)
void	autoScalingParam (Real resid_vs_jac_scaling_param)
	Sets the param that indicates the weighting of the residual vs the Jacobian in determining variable scaling parameters. More...
void	scalingGroupVariables (const std::vector< std::vector< std::string >> &scaling_group_variables)
void	ignoreVariablesForAutoscaling (const std::vector< std::string > &ignore_variables_for_autoscaling)
bool	offDiagonalsInAutoScaling () const
void	offDiagonalsInAutoScaling (bool off_diagonals_in_auto_scaling)
void	setupDM ()
	Setup the PETSc DM object (when appropriate) More...
virtual void	potentiallySetupFiniteDifferencing ()
	Create finite differencing contexts for assembly of the Jacobian and/or approximating the action of the Jacobian on vectors (e.g. More...
void	destroyColoring ()
	Destroy the coloring object if it exists. More...
virtual void	subdomainSetup ()
virtual void	reinitNodeFace (const Node *node, BoundaryID bnd_id, THREAD_ID tid)
	Reinit nodal assembly info on a face. More...
virtual void	restoreSolutions () override final
	Restore current solutions (call after your solve failed) More...
void	serializeSolution ()
virtual void	stopSolve (const ExecFlagType &exec_flag, const std::set< TagID > &vector_tags_to_close)=0
	Quit the current solve as soon as possible. More...
virtual bool	converged ()=0
	Returns the convergence state. More...
void	setSolution (const NumericVector< Number > &soln)
	Set the solution to a given vector. More...
void	setPCSide (MooseEnum pcs)
	Set the side on which the preconditioner is applied to. More...
Moose::PCSideType	getPCSide ()
	Get the current preconditioner side. More...
void	setMooseKSPNormType (MooseEnum kspnorm)
	Set the norm in which the linear convergence will be measured. More...
Moose::MooseKSPNormType	getMooseKSPNormType ()
	Get the norm in which the linear convergence is measured. More...
virtual const NumericVector< Number > *const &	currentSolution () const override final
	The solution vector that is currently being operated on. More...
virtual void	compute (ExecFlagType type) override
	Compute time derivatives, auxiliary variables, etc. 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	postInit ()
virtual void	reinit ()
	Reinitialize the system when the degrees of freedom in this system have changed. More...
virtual void	initializeObjects ()
	Called only once, just before the solve begins so objects can do some precalculations. More...
void	update ()
	Update the system (doing libMesh magic) More...
virtual void	copyOldSolutions ()
	Shifts the solutions backwards in time. More...
virtual void	copyPreviousNonlinearSolutions ()
	Shifts the solutions backwards in nonlinear iteration history. 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...
virtual void	needSolutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time)
	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 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	activeAllMatrixTags ()
	Make all exsiting matrices ative. More...
virtual void	activeMatrixTag (TagID tag)
	Active a matrix for tag. More...
virtual bool	matrixTagActive (TagID tag) const
	If or not a matrix tag is active. More...
virtual void	deactiveMatrixTag (TagID tag)
	deactive a matrix for tag More...
virtual void	deactiveAllMatrixTags ()
	Make matrices inactive. More...
void	closeTaggedMatrices (const std::set< TagID > &tags)
	Close all matrices associated the tags. More...
void	flushTaggedMatrices (const std::set< TagID > &tags)
	flushes all matrices associated to tags. More...
virtual void	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 void	augmentSendList (std::vector< dof_id_type > &send_list)
	Will modify the send_list to add all of the extra ghosted dofs for this system. More...
virtual void	addVariable (const std::string &var_type, const std::string &var_name, InputParameters &parameters)
	Canonical method for adding a variable. More...
virtual bool	isArrayVariable (const std::string &var_name) const
	If a variable is an array variable. More...
virtual bool	isScalarVariable (unsigned int var_name) const
MooseVariableFieldBase &	getVariable (THREAD_ID tid, const std::string &var_name) const
	Gets a reference to a variable of with specified name. More...
MooseVariableFieldBase &	getVariable (THREAD_ID tid, unsigned int var_number) const
	Gets a reference to a variable with specified number. More...
template<typename T >
MooseVariableFE< T > &	getFieldVariable (THREAD_ID tid, const std::string &var_name)
	Gets a reference to a variable of with specified name. More...
template<typename T >
MooseVariableFE< T > &	getFieldVariable (THREAD_ID tid, unsigned int var_number)
	Gets a reference to a variable with specified number. More...
template<typename T >
MooseVariableField< T > &	getActualFieldVariable (THREAD_ID tid, const std::string &var_name)
	Returns a field variable pointer - this includes finite volume variables. More...
template<typename T >
MooseVariableField< T > &	getActualFieldVariable (THREAD_ID tid, unsigned int var_number)
	Returns a field variable pointer - this includes finite volume variables. More...
template<typename T >
MooseVariableFV< T > &	getFVVariable (THREAD_ID tid, const std::string &var_name)
	Return a finite volume variable. More...
virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, const std::string &var_name) const
	Gets a reference to a scalar variable with specified number. More...
virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, unsigned int var_number) const
	Gets a reference to a variable with specified number. More...
virtual const std::set< SubdomainID > *	getVariableBlocks (unsigned int var_number)
	Get the block where a variable of this system is defined. More...
virtual unsigned int	nVariables () const
	Get the number of variables in this system. More...
unsigned int	nFieldVariables () const
	Get the number of field variables in this system. More...
unsigned int	nFVVariables () const
	Get the number of finite volume variables in this system. More...
std::size_t	getMaxVarNDofsPerElem () const
	Gets the maximum number of dofs used by any one variable on any one element. More...
std::size_t	getMaxVarNDofsPerNode () const
	Gets the maximum number of dofs used by any one variable on any one node. More...
void	assignMaxVarNDofsPerElem (std::size_t max_dofs)
	assign the maximum element dofs More...
void	assignMaxVarNDofsPerNode (std::size_t max_dofs)
	assign the maximum node dofs More...
virtual void	addVariableToZeroOnResidual (std::string var_name)
	Adds this variable to the list of variables to be zeroed during each residual evaluation. More...
virtual void	addVariableToZeroOnJacobian (std::string var_name)
	Adds this variable to the list of variables to be zeroed during each Jacobian evaluation. More...
virtual void	zeroVariables (std::vector< std::string > &vars_to_be_zeroed)
	Zero out the solution for the list of variables passed in. More...
virtual void	zeroVariablesForResidual ()
	Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on residual evaluation by a call to addVariableToZeroOnResidual() More...
virtual void	zeroVariablesForJacobian ()
	Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on Jacobian evaluation by a call to addVariableToZeroOnResidual() More...
virtual libMesh::Order	getMinQuadratureOrder ()
	Get minimal quadrature order needed for integrating variables in this system. More...
virtual void	prepare (THREAD_ID tid)
	Prepare the system for use. More...
virtual void	prepareFace (THREAD_ID tid, bool resize_data)
	Prepare the system for use on sides. More...
virtual void	prepareNeighbor (THREAD_ID tid)
	Prepare the system for use. More...
virtual void	prepareLowerD (THREAD_ID tid)
	Prepare the system for use for lower dimensional elements. More...
virtual void	reinitElem (const Elem *elem, THREAD_ID tid)
	Reinit an element assembly info. More...
virtual void	reinitElemFace (const Elem *elem, unsigned int side, THREAD_ID tid)
	Reinit assembly info for a side of an element. More...
virtual void	reinitNeighborFace (const Elem *elem, unsigned int side, THREAD_ID tid)
	Compute the values of the variables at all the current points. More...
virtual void	reinitNeighbor (const Elem *elem, THREAD_ID tid)
	Compute the values of the variables at all the current points. More...
virtual void	reinitLowerD (THREAD_ID tid)
	Compute the values of the variables on the lower dimensional element. More...
virtual void	reinitNode (const Node *node, THREAD_ID tid)
	Reinit nodal assembly info. More...
virtual void	reinitNodeFace (const Node *node, BoundaryID bnd_id, THREAD_ID tid)
	Reinit nodal assembly info on a face. More...
virtual void	reinitNodes (const std::vector< dof_id_type > &nodes, THREAD_ID tid)
	Reinit variables at a set of nodes. More...
virtual void	reinitNodesNeighbor (const std::vector< dof_id_type > &nodes, THREAD_ID tid)
	Reinit variables at a set of neighbor nodes. More...
virtual void	reinitScalars (THREAD_ID tid, bool reinit_for_derivative_reordering=false)
	Reinit scalar varaibles. More...
virtual void	addVariableToCopy (const std::string &dest_name, const std::string &source_name, const std::string &timestep)
	Add info about variable that will be copied. More...
const std::vector< MooseVariableFieldBase * > &	getVariables (THREAD_ID tid)
const std::vector< MooseVariableScalar * > &	getScalarVariables (THREAD_ID tid)
const std::set< SubdomainID > &	getSubdomainsForVar (unsigned int var_number) const
const std::set< SubdomainID > &	getSubdomainsForVar (const std::string &var_name) const
	Get the block where a variable of this system is defined. More...
void	removeVector (const std::string &name)
	Remove a vector from the system with the given name. More...
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...
virtual void	subdomainSetup ()
void	clearAllDofIndices ()
	Clear all dof indices from moose variables. More...
void	setActiveVariableCoupleableVectorTags (const std::set< TagID > &vtags, THREAD_ID tid)
	Set the active vector tags for the variables. More...
void	setActiveScalarVariableCoupleableVectorTags (const std::set< TagID > &vtags, THREAD_ID tid)
	Set the active vector tags for the scalar variables. More...
Moose::VarKindType	varKind () const
const std::vector< std::unique_ptr< NumericVector< Number > > > &	gradientContainer () const
	Reference to the container vector which hold gradients at dofs (if it can be interpreted). More...
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
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const
PerfGraph &	perfGraph ()
	Get the PerfGraph. More...
void	checkKernelCoverage (const std::set< SubdomainID > &mesh_subdomains) const
virtual bool	containsTimeKernel () override
	If the system has a kernel that corresponds to a time derivative. More...
virtual std::vector< std::string >	timeKernelVariableNames () override
	Returns the names of the variables that have time derivative kernels in the system. More...
MooseObjectTagWarehouse< KernelBase > &	getKernelWarehouse ()
	Access functions to Warehouses from outside NonlinearSystemBase. More...
const MooseObjectTagWarehouse< KernelBase > &	getKernelWarehouse () const
MooseObjectTagWarehouse< DGKernelBase > &	getDGKernelWarehouse ()
MooseObjectTagWarehouse< InterfaceKernelBase > &	getInterfaceKernelWarehouse ()
MooseObjectTagWarehouse< DiracKernelBase > &	getDiracKernelWarehouse ()
MooseObjectTagWarehouse< IntegratedBCBase > &	getIntegratedBCWarehouse ()
const MooseObjectTagWarehouse< ScalarKernelBase > &	getScalarKernelWarehouse () const
const MooseObjectTagWarehouse< NodalKernelBase > &	getNodalKernelWarehouse () const
MooseObjectTagWarehouse< HDGKernel > &	getHDGKernelWarehouse ()
const MooseObjectWarehouse< ElementDamper > &	getElementDamperWarehouse () const
const MooseObjectWarehouse< NodalDamper > &	getNodalDamperWarehouse () const
const ConstraintWarehouse &	getConstraintWarehouse () const
const MooseObjectTagWarehouse< NodalBCBase > &	getNodalBCWarehouse () const
	Return the NodalBCBase warehouse. More...
const MooseObjectTagWarehouse< IntegratedBCBase > &	getIntegratedBCWarehouse () const
	Return the IntegratedBCBase warehouse. 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
unsigned int	_num_residual_evaluations
libMesh::System &	_sys
Real	_last_nl_rnorm
std::vector< unsigned int >	_current_l_its
unsigned int	_current_nl_its
const ConsoleStream	_console
	An instance of helper class to write streams to the Console objects. More...

Protected Member Functions
void	computeResidualInternal (const std::set< TagID > &tags)
	Compute the residual for a given tag. More...
void	computeNodalBCs (NumericVector< Number > &residual)
	Enforces nodal boundary conditions. More...
void	computeNodalBCs (NumericVector< Number > &residual, const std::set< TagID > &tags)
	Form a residual for BCs that at least has one of the given tags. More...
void	computeNodalBCs (const std::set< TagID > &tags)
	Form multiple tag-associated residual vectors for the given tags. More...
void	computeNodalBCsResidualAndJacobian ()
	compute the residual and Jacobian for nodal boundary conditions More...
void	computeJacobianInternal (const std::set< TagID > &tags)
	Form multiple matrices for all the tags. More...
void	computeDiracContributions (const std::set< TagID > &tags, bool is_jacobian)
void	computeScalarKernelsJacobians (const std::set< TagID > &tags)
void	enforceNodalConstraintsResidual (NumericVector< Number > &residual)
	Enforce nodal constraints. More...
void	enforceNodalConstraintsJacobian ()
void	mortarConstraints (Moose::ComputeType compute_type, const std::set< TagID > &vector_tags, const std::set< TagID > &matrix_tags)
	Do mortar constraint residual/jacobian computations. More...
virtual void	computeScalingJacobian ()=0
	Compute a "Jacobian" for automatic scaling purposes. More...
virtual void	computeScalingResidual ()=0
	Compute a "residual" for automatic scaling purposes. More...
void	assembleScalingVector ()
	Assemble the numeric vector of scaling factors such that it can be used during assembly of the system matrix. More...
virtual void	postAddResidualObject (ResidualObject &)
	Called after any ResidualObject-derived objects are added to the system. More...
void	reinitNodeFace (const Node &secondary_node, const BoundaryID secondary_boundary, const PenetrationInfo &info, const bool displaced)
	Reinitialize quantities such as variables, residuals, Jacobians, materials for node-face constraints. More...
bool	preSolve ()
	Perform some steps to get ready for the solver. More...
void	getNodeDofs (dof_id_type node_id, std::vector< dof_id_type > &dofs)
void	checkInvalidSolution ()
virtual NumericVector< Number > &	solutionInternal () const override final
	Internal getter for solution owned by libMesh. More...
virtual bool	matrixFromColoring () const
	Whether a system matrix is formed from coloring. 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

Protected Attributes
NumericVector< Number > *	_residual_ghosted
	ghosted form of the residual More...
std::unique_ptr< NumericVector< Number > >	_residual_copy
	Copy of the residual vector, or nullptr if a copy is not needed. More...
Number	_du_dot_du
	\( {du^dot}\over{du} \) More...
Number	_du_dotdot_du
	\( {du^dotdot}\over{du} \) More...
TagID	_Re_time_tag
	Tag for time contribution residual. More...
std::set< TagID >	_nl_vector_tags
	Vector tags to temporarily store all tags associated with the current system. More...
std::set< TagID >	_nl_matrix_tags
	Matrix tags to temporarily store all tags associated with the current system. More...
NumericVector< Number > *	_Re_time
	residual vector for time contributions More...
TagID	_Re_non_time_tag
	Tag for non-time contribution residual. More...
NumericVector< Number > *	_Re_non_time
	residual vector for non-time contributions More...
TagID	_Re_tag
	Used for the residual vector from PETSc. More...
TagID	_Ke_non_time_tag
	Tag for non-time contribution Jacobian. More...
TagID	_Ke_system_tag
	Tag for system contribution Jacobian. More...
MooseObjectTagWarehouse< DiracKernelBase >	_dirac_kernels
	Dirac Kernel storage for each thread. More...
MooseObjectWarehouse< ElementDamper >	_element_dampers
	Element Dampers for each thread. More...
MooseObjectWarehouse< NodalDamper >	_nodal_dampers
	Nodal Dampers for each thread. More...
MooseObjectWarehouse< GeneralDamper >	_general_dampers
	General Dampers. More...
MooseObjectTagWarehouse< NodalKernelBase >	_nodal_kernels
	NodalKernels for each thread. More...
MooseObjectWarehouseBase< Split >	_splits
	Decomposition splits. More...
ConstraintWarehouse	_constraints
	Constraints storage object. More...
NumericVector< Number > *	_increment_vec
	increment vector More...
std::shared_ptr< MoosePreconditioner >	_preconditioner
	Preconditioner. More...
bool	_use_finite_differenced_preconditioner
	Whether or not to use a finite differenced preconditioner. More...
MatFDColoring	_fdcoloring
bool	_have_decomposition
	Whether or not the system can be decomposed into splits. More...
std::string	_decomposition_split
	Name of the top-level split of the decomposition. More...
bool	_use_field_split_preconditioner
	Whether or not to use a FieldSplitPreconditioner matrix based on the decomposition. More...
bool	_add_implicit_geometric_coupling_entries_to_jacobian
	Whether or not to add implicit geometric couplings to the Jacobian for FDP. More...
bool	_assemble_constraints_separately
	Whether or not to assemble the residual and Jacobian after the application of each constraint. More...
bool	_need_residual_ghosted
	Whether or not a ghosted copy of the residual needs to be made. More...
bool	_debugging_residuals
	true if debugging residuals More...
bool	_doing_dg
	true if DG is active (optimization reasons) More...
std::vector< std::string >	_vecs_to_zero_for_residual
	vectors that will be zeroed before a residual computation More...
unsigned int	_n_iters
unsigned int	_n_linear_iters
unsigned int	_n_residual_evaluations
	Total number of residual evaluations that have been performed. More...
Real	_final_residual
std::shared_ptr< Predictor >	_predictor
	If predictor is active, this is non-NULL. More...
bool	_computing_pre_smo_residual
Real	_pre_smo_residual
	The pre-SMO residual, see setPreSMOResidual for a detailed explanation. More...
Real	_initial_residual
	The initial (i.e., 0th nonlinear iteration) residual, see setPreSMOResidual for a detailed explanation. More...
bool	_use_pre_smo_residual
	Whether to use the pre-SMO initial residual in the relative convergence check. More...
bool	_print_all_var_norms
bool	_has_save_in
	If there is any Kernel or IntegratedBC having save_in. More...
bool	_has_diag_save_in
	If there is any Kernel or IntegratedBC having diag_save_in. More...
bool	_has_nodalbc_save_in
	If there is a nodal BC having save_in. More...
bool	_has_nodalbc_diag_save_in
	If there is a nodal BC having diag_save_in. More...
bool	_computed_scaling
	Flag used to indicate whether we have already computed the scaling Jacobian. More...
bool	_compute_scaling_once
	Whether the scaling factors should only be computed once at the beginning of the simulation through an extra Jacobian evaluation. More...
Real	_resid_vs_jac_scaling_param
	The param that indicates the weighting of the residual vs the Jacobian in determining variable scaling parameters. More...
std::vector< std::vector< std::string > >	_scaling_group_variables
	A container of variable groupings that can be used in scaling calculations. More...
std::vector< bool >	_variable_autoscaled
	Container to hold flag if variable is to participate in autoscaling. More...
std::vector< std::string >	_ignore_variables_for_autoscaling
	A container for variables that do not partipate in autoscaling. More...
bool	_off_diagonals_in_auto_scaling
	Whether to include off diagonals when determining automatic scaling factors. More...
std::unique_ptr< libMesh::DiagonalMatrix< Number > >	_scaling_matrix
	A diagonal matrix used for computing scaling. More...
const NumericVector< Number > *	_current_solution
	solution vector from solver More...
Moose::PCSideType	_pc_side
	Preconditioning side. More...
Moose::MooseKSPNormType	_ksp_norm
	KSP norm type. More...
bool	_solution_is_invalid
	Boolean to see if solution is invalid. More...
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< NumericVector< Number > * >	_tagged_vectors
	Tagged vectors (pointer) More...
std::vector< libMesh::SparseMatrix< Number > * >	_tagged_matrices
	Tagged matrices (pointer) More...
std::vector< bool >	_matrix_tag_active_flags
	Active flags for tagged matrices. More...
NumericVector< Real > *	_saved_old
NumericVector< Real > *	_saved_older
NumericVector< Real > *	_saved_dot_old
NumericVector< Real > *	_saved_dotdot_old
Moose::VarKindType	_var_kind
	default kind of variables in this system More...
std::vector< VarCopyInfo >	_var_to_copy
size_t	_max_var_n_dofs_per_elem
	Maximum number of dofs for any one variable on any one element. More...
size_t	_max_var_n_dofs_per_node
	Maximum number of dofs for any one variable on any one node. More...
std::vector< std::shared_ptr< TimeIntegrator > >	_time_integrators
	Time integrator. More...
std::vector< std::vector< MooseVariableFieldBase * > >	_numbered_vars
	Map variable number to its pointer. More...
bool	_automatic_scaling
	Whether to automatically scale the variables. More...
bool	_verbose
	True if printing out additional information. More...
bool	_solution_states_initialized
	Whether or not the solution states have been initialized. More...
std::vector< dof_id_type >	_var_all_dof_indices
	Container for the dof indices of a given variable. More...
std::unique_ptr< NumericVector< Number > >	_serialized_solution
	Serialized version of the solution vector, or nullptr if a serialized solution is not needed. More...
std::vector< std::unique_ptr< NumericVector< Number > > >	_raw_grad_container
	A cache for storing gradients at dof locations. More...
const Parallel::Communicator &	_communicator
MooseApp &	_pg_moose_app
	The MooseApp that owns the PerfGraph. More...
const std::string	_prefix
	A prefix to use for all sections. More...
MooseObjectTagWarehouse< KernelBase >	_kernels
MooseObjectTagWarehouse< HDGKernel >	_hybridized_kernels
MooseObjectTagWarehouse< ScalarKernelBase >	_scalar_kernels
MooseObjectTagWarehouse< DGKernelBase >	_dg_kernels
MooseObjectTagWarehouse< InterfaceKernelBase >	_interface_kernels
MooseObjectTagWarehouse< IntegratedBCBase >	_integrated_bcs
MooseObjectTagWarehouse< NodalBCBase >	_nodal_bcs
MooseObjectWarehouse< DirichletBCBase >	_preset_nodal_bcs
MooseObjectWarehouse< ADDirichletBCBase >	_ad_preset_nodal_bcs

Private Member Functions
void	findImplicitGeometricCouplingEntries (GeometricSearchData &geom_search_data, std::unordered_map< dof_id_type, std::vector< dof_id_type >> &graph)
	Finds the implicit sparsity graph between geometrically related dofs. More...
void	setupScalingData ()
	Setup group scaling containers. More...

Private Attributes
std::unordered_map< std::pair< BoundaryID, BoundaryID >, ComputeMortarFunctor >	_undisplaced_mortar_functors
	Functors for computing undisplaced mortar constraints. More...
std::unordered_map< std::pair< BoundaryID, BoundaryID >, ComputeMortarFunctor >	_displaced_mortar_functors
	Functors for computing displaced mortar constraints. More...
std::vector< NumericVector< Number > * >	_solution_state
	The current states of the solution (0 = current, 1 = old, etc) More...
bool	_auto_scaling_initd
	Whether we've initialized the automatic scaling data structures. More...
std::unordered_map< unsigned int, unsigned int >	_var_to_group_var
	A map from variable index to group variable index and it's associated (inverse) scaling factor. More...
std::size_t	_num_scaling_groups
	The number of scaling groups. More...

Detailed Description

Nonlinear system to be solved.

It is a part of FEProblemBase ;-)

Definition at line 66 of file NonlinearSystemBase.h.

Constructor & Destructor Documentation

NonlinearSystemBase()

NonlinearSystemBase::NonlinearSystemBase	(	FEProblemBase &	problem,
		libMesh::System &	sys,
		const std::string &	name
	)

Definition at line 113 of file NonlinearSystemBase.C.

  : SolverSystem(fe_problem, fe_problem, name, Moose::VAR_SOLVER),
    PerfGraphInterface(fe_problem.getMooseApp().perfGraph(), "NonlinearSystemBase"),
    _sys(sys),
    _last_nl_rnorm(0.),
    _current_nl_its(0),
    _residual_ghosted(NULL),
    _Re_time_tag(-1),
    _Re_time(NULL),
    _Re_non_time_tag(-1),
    _Re_non_time(NULL),
    _scalar_kernels(/*threaded=*/false),
    _nodal_bcs(/*threaded=*/false),
    _preset_nodal_bcs(/*threaded=*/false),
    _ad_preset_nodal_bcs(/*threaded=*/false),
    _splits(/*threaded=*/false),
    _increment_vec(NULL),
    _use_finite_differenced_preconditioner(false),
    _fdcoloring(nullptr),
    _have_decomposition(false),
    _use_field_split_preconditioner(false),
    _add_implicit_geometric_coupling_entries_to_jacobian(false),
    _assemble_constraints_separately(false),
    _need_residual_ghosted(false),
    _debugging_residuals(false),
    _doing_dg(false),
    _n_iters(0),
    _n_linear_iters(0),
    _n_residual_evaluations(0),
    _final_residual(0.),
    _computing_pre_smo_residual(false),
    _pre_smo_residual(0),
    _initial_residual(0),
    _use_pre_smo_residual(false),
    _print_all_var_norms(false),
    _has_save_in(false),
    _has_diag_save_in(false),
    _has_nodalbc_save_in(false),
    _has_nodalbc_diag_save_in(false),
    _computed_scaling(false),
    _compute_scaling_once(true),
    _resid_vs_jac_scaling_param(0),
    _off_diagonals_in_auto_scaling(false),
    _auto_scaling_initd(false)
{
  getResidualNonTimeVector();
  // Don't need to add the matrix - it already exists (for now)
  _Ke_system_tag = _fe_problem.addMatrixTag("SYSTEM");

  // The time matrix tag is not normally used - but must be added to the system
  // in case it is so that objects can have 'time' in their matrix tags by default
  _fe_problem.addMatrixTag("TIME");

  _Re_tag = _fe_problem.addVectorTag("RESIDUAL");

  _sys.identify_variable_groups(_fe_problem.identifyVariableGroupsInNL());

  if (!_fe_problem.defaultGhosting())
  {
    auto & dof_map = _sys.get_dof_map();
    dof_map.remove_algebraic_ghosting_functor(dof_map.default_algebraic_ghosting());
    dof_map.set_implicit_neighbor_dofs(false);
  }
}

~NonlinearSystemBase()

NonlinearSystemBase::~NonlinearSystemBase ( )

virtualdefault

Member Function Documentation

activeAllMatrixTags()

void SystemBase::activeAllMatrixTags ( )

virtualinherited

Make all exsiting matrices ative.

Definition at line 1137 of file SystemBase.C.

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

{
  auto num_matrix_tags = _subproblem.numMatrixTags();

  _matrix_tag_active_flags.resize(num_matrix_tags);

  for (decltype(num_matrix_tags) tag = 0; tag < num_matrix_tags; tag++)
    if (hasMatrix(tag))
      _matrix_tag_active_flags[tag] = true;
    else
      _matrix_tag_active_flags[tag] = false;
}

activeMatrixTag()

void SystemBase::activeMatrixTag ( TagID  tag )

virtualinherited

Active a matrix for tag.

Definition at line 1102 of file SystemBase.C.

{
  mooseAssert(_subproblem.matrixTagExists(tag),
              "Cannot active Matrix with matrix_tag : " << tag << "that does not exist");

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

  _matrix_tag_active_flags[tag] = true;
}

addBoundaryCondition()

void NonlinearSystemBase::addBoundaryCondition	(	const std::string &	bc_name,
		const std::string &	name,
		InputParameters &	parameters
	)

Adds a boundary condition.

Parameters

bc_name	The type of the boundary condition
name	The name of the boundary condition
parameters	Boundary condition parameters

Definition at line 521 of file NonlinearSystemBase.C.

{
  // ThreadID
  THREAD_ID tid = 0;

  // Create the object
  std::shared_ptr<BoundaryCondition> bc =
      _factory.create<BoundaryCondition>(bc_name, name, parameters, tid);
  postAddResidualObject(*bc);

  // Active BoundaryIDs for the object
  const std::set<BoundaryID> & boundary_ids = bc->boundaryIDs();
  auto bc_var = dynamic_cast<const MooseVariableFieldBase *>(&bc->variable());
  _vars[tid].addBoundaryVar(boundary_ids, bc_var);

  // Cast to the various types of BCs
  std::shared_ptr<NodalBCBase> nbc = std::dynamic_pointer_cast<NodalBCBase>(bc);
  std::shared_ptr<IntegratedBCBase> ibc = std::dynamic_pointer_cast<IntegratedBCBase>(bc);

  // NodalBCBase
  if (nbc)
  {
    if (nbc->checkNodalVar() && !nbc->variable().isNodal())
      mooseError("Trying to use nodal boundary condition '",
                 nbc->name(),
                 "' on a non-nodal variable '",
                 nbc->variable().name(),
                 "'.");

    _nodal_bcs.addObject(nbc);
    // Add to theWarehouse, a centralized storage for all moose objects
    _fe_problem.theWarehouse().add(nbc);
    _vars[tid].addBoundaryVars(boundary_ids, nbc->getCoupledVars());

    if (parameters.get<std::vector<AuxVariableName>>("save_in").size() > 0)
      _has_nodalbc_save_in = true;
    if (parameters.get<std::vector<AuxVariableName>>("diag_save_in").size() > 0)
      _has_nodalbc_diag_save_in = true;

    // DirichletBCs that are preset
    std::shared_ptr<DirichletBCBase> dbc = std::dynamic_pointer_cast<DirichletBCBase>(bc);
    if (dbc && dbc->preset())
      _preset_nodal_bcs.addObject(dbc);

    std::shared_ptr<ADDirichletBCBase> addbc = std::dynamic_pointer_cast<ADDirichletBCBase>(bc);
    if (addbc && addbc->preset())
      _ad_preset_nodal_bcs.addObject(addbc);
  }

  // IntegratedBCBase
  else if (ibc)
  {
    _integrated_bcs.addObject(ibc, tid);
    // Add to theWarehouse, a centralized storage for all moose objects
    _fe_problem.theWarehouse().add(ibc);
    _vars[tid].addBoundaryVars(boundary_ids, ibc->getCoupledVars());

    if (parameters.get<std::vector<AuxVariableName>>("save_in").size() > 0)
      _has_save_in = true;
    if (parameters.get<std::vector<AuxVariableName>>("diag_save_in").size() > 0)
      _has_diag_save_in = true;

    for (tid = 1; tid < libMesh::n_threads(); tid++)
    {
      // Create the object
      bc = _factory.create<BoundaryCondition>(bc_name, name, parameters, tid);

      // Give users opportunity to set some parameters
      postAddResidualObject(*bc);

      // Active BoundaryIDs for the object
      const std::set<BoundaryID> & boundary_ids = bc->boundaryIDs();
      _vars[tid].addBoundaryVar(boundary_ids, bc_var);

      ibc = std::static_pointer_cast<IntegratedBCBase>(bc);

      _integrated_bcs.addObject(ibc, tid);
      _vars[tid].addBoundaryVars(boundary_ids, ibc->getCoupledVars());
    }
  }

  else
    mooseError("Unknown BoundaryCondition type for object named ", bc->name());
}

addConstraint()

void NonlinearSystemBase::addConstraint	(	const std::string &	c_name,
		const std::string &	name,
		InputParameters &	parameters
	)

Adds a Constraint.

Parameters

c_name	The type of the constraint
name	The name of the constraint
parameters	Constraint parameters

Definition at line 609 of file NonlinearSystemBase.C.

{
  std::shared_ptr<Constraint> constraint = _factory.create<Constraint>(c_name, name, parameters);
  _constraints.addObject(constraint);
  postAddResidualObject(*constraint);

  if (constraint && constraint->addCouplingEntriesToJacobian())
    addImplicitGeometricCouplingEntriesToJacobian(true);
}

addDamper()

void NonlinearSystemBase::addDamper	(	const std::string &	damper_name,
		const std::string &	name,
		InputParameters &	parameters
	)

Adds a damper.

Parameters

damper_name	The type of the damper
name	The name of the damper
parameters	Damper parameters

Definition at line 682 of file NonlinearSystemBase.C.

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); ++tid)
  {
    std::shared_ptr<Damper> damper = _factory.create<Damper>(damper_name, name, parameters, tid);

    // Attempt to cast to the damper types
    std::shared_ptr<ElementDamper> ed = std::dynamic_pointer_cast<ElementDamper>(damper);
    std::shared_ptr<NodalDamper> nd = std::dynamic_pointer_cast<NodalDamper>(damper);
    std::shared_ptr<GeneralDamper> gd = std::dynamic_pointer_cast<GeneralDamper>(damper);

    if (gd)
    {
      _general_dampers.addObject(gd);
      break; // not threaded
    }
    else if (ed)
      _element_dampers.addObject(ed, tid);
    else if (nd)
      _nodal_dampers.addObject(nd, tid);
    else
      mooseError("Invalid damper type");
  }
}

addDGKernel()

void NonlinearSystemBase::addDGKernel	(	std::string	dg_kernel_name,
		const std::string &	name,
		InputParameters &	parameters
	)

Adds a DG kernel.

Parameters

dg_kernel_name	The type of the DG kernel
name	The name of the DG kernel
parameters	DG kernel parameters

Definition at line 638 of file NonlinearSystemBase.C.

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); ++tid)
  {
    auto dg_kernel = _factory.create<DGKernelBase>(dg_kernel_name, name, parameters, tid);
    _dg_kernels.addObject(dg_kernel, tid);
    // Add to theWarehouse, a centralized storage for all moose objects
    _fe_problem.theWarehouse().add(dg_kernel);
    postAddResidualObject(*dg_kernel);
  }

  _doing_dg = true;

  if (parameters.get<std::vector<AuxVariableName>>("save_in").size() > 0)
    _has_save_in = true;
  if (parameters.get<std::vector<AuxVariableName>>("diag_save_in").size() > 0)
    _has_diag_save_in = true;
}

addDiracKernel()

void NonlinearSystemBase::addDiracKernel	(	const std::string &	kernel_name,
		const std::string &	name,
		InputParameters &	parameters
	)

Adds a Dirac kernel.

Parameters

kernel_name	The type of the dirac kernel
name	The name of the Dirac kernel
parameters	Dirac kernel parameters

Definition at line 622 of file NonlinearSystemBase.C.

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    std::shared_ptr<DiracKernelBase> kernel =
        _factory.create<DiracKernelBase>(kernel_name, name, parameters, tid);
    postAddResidualObject(*kernel);
    _dirac_kernels.addObject(kernel, tid);
    // Add to theWarehouse, a centralized storage for all moose objects
    _fe_problem.theWarehouse().add(kernel);
  }
}

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 1600 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);
}

addHDGKernel()

void NonlinearSystemBase::addHDGKernel ( const std::string &  kernel_name, const std::string &  name, InputParameters &  parameters  )

virtual

Adds a hybridized discontinuous Galerkin (HDG) kernel.

Parameters

kernel_name	The type of the hybridized kernel
name	The name of the hybridized kernel
parameters	HDG kernel parameters

Definition at line 469 of file NonlinearSystemBase.C.

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    // Create the kernel object via the factory and add to warehouse
    auto kernel = _factory.create<HDGKernel>(kernel_name, name, parameters, tid);
    _kernels.addObject(kernel, tid);
    _hybridized_kernels.addObject(kernel, tid);
    // Add to theWarehouse, a centralized storage for all moose objects
    _fe_problem.theWarehouse().add(kernel);
    postAddResidualObject(*kernel);
  }
}

addImplicitGeometricCouplingEntries()

void NonlinearSystemBase::addImplicitGeometricCouplingEntries

(

GeometricSearchData &

geom_search_data

)

Adds entries to the Jacobian in the correct positions for couplings coming from dofs being coupled that are related geometrically (i.e.

near each other across a gap).

Definition at line 2278 of file NonlinearSystemBase.C.

Referenced by computeJacobianInternal().

{
  if (!hasMatrix(systemMatrixTag()))
    mooseError("Need a system matrix ");

  // At this point, have no idea how to make
  // this work with tag system
  auto & jacobian = getMatrix(systemMatrixTag());

  std::unordered_map<dof_id_type, std::vector<dof_id_type>> graph;

  findImplicitGeometricCouplingEntries(geom_search_data, graph);

  for (const auto & it : graph)
  {
    dof_id_type dof = it.first;
    const auto & row = it.second;

    for (const auto & coupled_dof : row)
      jacobian.add(dof, coupled_dof, 0);
  }
}

addImplicitGeometricCouplingEntriesToJacobian()

void NonlinearSystemBase::addImplicitGeometricCouplingEntriesToJacobian ( bool  add = true )

inline

If called with true this will add entries into the jacobian to link together degrees of freedom that are found to be related through the geometric search system.

These entries are really only used by the Finite Difference Preconditioner and the constraint system right now.

Definition at line 472 of file NonlinearSystemBase.h.

Referenced by addConstraint(), and FiniteDifferencePreconditioner::FiniteDifferencePreconditioner().

  {
    _add_implicit_geometric_coupling_entries_to_jacobian = add;
  }

addInterfaceKernel()

void NonlinearSystemBase::addInterfaceKernel	(	std::string	interface_kernel_name,
		const std::string &	name,
		InputParameters &	parameters
	)

Adds an interface kernel.

Parameters

interface_kernel_name	The type of the interface kernel
name	The name of the interface kernel
parameters	interface kernel parameters

Definition at line 660 of file NonlinearSystemBase.C.

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); ++tid)
  {
    std::shared_ptr<InterfaceKernelBase> interface_kernel =
        _factory.create<InterfaceKernelBase>(interface_kernel_name, name, parameters, tid);
    postAddResidualObject(*interface_kernel);

    const std::set<BoundaryID> & boundary_ids = interface_kernel->boundaryIDs();
    auto ik_var = dynamic_cast<const MooseVariableFieldBase *>(&interface_kernel->variable());
    _vars[tid].addBoundaryVar(boundary_ids, ik_var);

    _interface_kernels.addObject(interface_kernel, tid);
    // Add to theWarehouse, a centralized storage for all moose objects
    _fe_problem.theWarehouse().add(interface_kernel);
    _vars[tid].addBoundaryVars(boundary_ids, interface_kernel->getCoupledVars());
  }
}

addKernel()

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

virtual

Adds a kernel.

Parameters

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

Reimplemented in MooseEigenSystem.

Definition at line 447 of file NonlinearSystemBase.C.

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    // Create the kernel object via the factory and add to warehouse
    std::shared_ptr<KernelBase> kernel =
        _factory.create<KernelBase>(kernel_name, name, parameters, tid);
    _kernels.addObject(kernel, tid);
    postAddResidualObject(*kernel);
    // Add to theWarehouse, a centralized storage for all moose objects
    _fe_problem.theWarehouse().add(kernel);
  }

  if (parameters.get<std::vector<AuxVariableName>>("save_in").size() > 0)
    _has_save_in = true;
  if (parameters.get<std::vector<AuxVariableName>>("diag_save_in").size() > 0)
    _has_diag_save_in = true;
}

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 562 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;
}

addNodalKernel()

void NonlinearSystemBase::addNodalKernel ( const std::string &  kernel_name, const std::string &  name, InputParameters &  parameters  )

virtual

Adds a NodalKernel.

Parameters

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

Definition at line 486 of file NonlinearSystemBase.C.

{
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    // Create the kernel object via the factory and add to the warehouse
    std::shared_ptr<NodalKernelBase> kernel =
        _factory.create<NodalKernelBase>(kernel_name, name, parameters, tid);
    _nodal_kernels.addObject(kernel, tid);
    // Add to theWarehouse, a centralized storage for all moose objects
    _fe_problem.theWarehouse().add(kernel);
    postAddResidualObject(*kernel);
  }

  if (parameters.get<std::vector<AuxVariableName>>("save_in").size() > 0)
    _has_save_in = true;
  if (parameters.get<std::vector<AuxVariableName>>("diag_save_in").size() > 0)
    _has_diag_save_in = true;
}

addScalarKernel()

void NonlinearSystemBase::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 508 of file NonlinearSystemBase.C.

{
  std::shared_ptr<ScalarKernelBase> kernel =
      _factory.create<ScalarKernelBase>(kernel_name, name, parameters);
  postAddResidualObject(*kernel);
  // Add to theWarehouse, a centralized storage for all moose objects
  _fe_problem.theWarehouse().add(kernel);
  _scalar_kernels.addObject(kernel);
}

addScalingVector()

void SystemBase::addScalingVector ( )

inherited

Add the scaling factor vector to the system.

Definition at line 1512 of file SystemBase.C.

Referenced by MooseVariableBase::initialSetup().

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

addSplit()

void NonlinearSystemBase::addSplit	(	const std::string &	split_name,
		const std::string &	name,
		InputParameters &	parameters
	)

Adds a split.

Parameters

split_name	The type of the split
name	The name of the split
parameters	Split parameters

Definition at line 710 of file NonlinearSystemBase.C.

{
  std::shared_ptr<Split> split = _factory.create<Split>(split_name, name, parameters);
  _splits.addObject(split);
  // Add to theWarehouse, a centralized storage for all moose objects
  _fe_problem.theWarehouse().add(split);
}

addTimeIntegrator()

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

inherited

Definition at line 1625 of file SystemBase.C.

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

addVariable()

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

virtualinherited

Canonical method for adding a variable.

Parameters

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

Reimplemented in AuxiliarySystem.

Definition at line 710 of file SystemBase.C.

Referenced by AuxiliarySystem::addVariable().

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

  auto components = parameters.get<unsigned int>("components");

  // Convert the std::vector parameter provided by the user into a std::set for use by libMesh's
  // System::add_variable method
  std::set<SubdomainID> blocks;
  const auto & block_param = parameters.get<std::vector<SubdomainName>>("block");
  for (const auto & subdomain_name : block_param)
  {
    SubdomainID blk_id = _mesh.getSubdomainID(subdomain_name);
    blocks.insert(blk_id);
  }

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

  unsigned int var_num;

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

    std::vector<std::string> array_var_component_names;
    const bool has_array_names = parameters.isParamValid("array_var_component_names");
    if (has_array_names)
    {
      array_var_component_names =
          parameters.get<std::vector<std::string>>("array_var_component_names");
      if (array_var_component_names.size() != components)
        mooseError("For variable ",
                   name,
                   ", parameter 'array_var_component_names' has ",
                   array_var_component_names.size(),
                   " name(s), but there are ",
                   components,
                   " array variable component(s).");
    }

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

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

    // The number returned by libMesh is the _last_ variable number... we want to hold onto the
    // _first_
    var_num = system().add_variables(var_names, fe_type, &blocks) - (components - 1);

    // Set as array variable
    if (parameters.isParamSetByUser("array") && !parameters.get<bool>("array"))
      mooseError("Variable '",
                 name,
                 "' is an array variable ('components' > 1) but 'array' is set to false.");
    parameters.set<bool>("array") = true;
  }
  else
  {
    if (parameters.isParamSetByUser("array_var_component_names"))
      mooseError("Variable '",
                 name,
                 "' is a regular variable. 'array_var_component_names' should not be set.");
    var_num = system().add_variable(name, fe_type, &blocks);
  }

  parameters.set<unsigned int>("_var_num") = var_num;
  parameters.set<SystemBase *>("_system_base") = this;

  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    parameters.set<THREAD_ID>("tid") = tid;
    std::shared_ptr<MooseVariableBase> var =
        _factory.create<MooseVariableBase>(var_type, name, parameters, tid);

    _vars[tid].add(name, var);

    if (auto fe_var = dynamic_cast<MooseVariableFieldBase *>(var.get()))
    {
      auto required_size = var_num + components;
      if (required_size > _numbered_vars[tid].size())
        _numbered_vars[tid].resize(required_size);
      for (MooseIndex(components) component = 0; component < components; ++component)
        _numbered_vars[tid][var_num + component] = fe_var;

      if (auto * const functor = dynamic_cast<Moose::FunctorBase<ADReal> *>(fe_var))
        _subproblem.addFunctor(name, *functor, tid);
      else if (auto * const functor = dynamic_cast<Moose::FunctorBase<ADRealVectorValue> *>(fe_var))
        _subproblem.addFunctor(name, *functor, tid);
      else if (auto * const functor = dynamic_cast<Moose::FunctorBase<RealEigenVector> *>(fe_var))
        _subproblem.addFunctor(name, *functor, tid);
      else
        mooseError("This should be a functor");
    }

    if (var->blockRestricted())
      for (const SubdomainID & id : var->blockIDs())
        for (MooseIndex(components) component = 0; component < components; ++component)
          _var_map[var_num + component].insert(id);
    else
      for (MooseIndex(components) component = 0; component < components; ++component)
        _var_map[var_num + component] = std::set<SubdomainID>();
  }

  // getMaxVariableNumber is an API method used in Rattlesnake
  if (var_num > _max_var_number)
    _max_var_number = var_num;
  _du_dot_du.resize(var_num + 1);
}

addVariableToCopy()

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

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 1177 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 179 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 173 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(), getResidualNonTimeVector(), getResidualTimeVector(), CentralDifference::initialSetup(), SystemBase::needSolutionState(), 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 1462 of file SystemBase.C.

Referenced by 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);
    }
  }
}

assembleConstraintsSeparately()

void NonlinearSystemBase::assembleConstraintsSeparately ( bool  separately = true )

inline

Indicates whether to assemble residual and Jacobian after each constraint application.

When true, enables "transitive" constraint application: subsequent constraints can use prior constraints' results.

Definition at line 482 of file NonlinearSystemBase.h.

  {
    _assemble_constraints_separately = separately;
  }

assembleScalingVector()

void NonlinearSystemBase::assembleScalingVector ( )

protected

Assemble the numeric vector of scaling factors such that it can be used during assembly of the system matrix.

Definition at line 4047 of file NonlinearSystemBase.C.

Referenced by computeScaling(), and preSolve().

{
  if (!hasVector("scaling_factors"))
    // No variables have indicated they need scaling
    return;

  auto & scaling_vector = getVector("scaling_factors");

  const auto & lm_mesh = _mesh.getMesh();
  const auto & dof_map = dofMap();

  const auto & field_variables = _vars[0].fieldVariables();
  const auto & scalar_variables = _vars[0].scalars();

  std::vector<dof_id_type> dof_indices;

  for (const Elem * const elem :
       as_range(lm_mesh.active_local_elements_begin(), lm_mesh.active_local_elements_end()))
    for (const auto * const field_var : field_variables)
    {
      const auto & factors = field_var->arrayScalingFactor();
      for (const auto i : make_range(field_var->count()))
      {
        dof_map.dof_indices(elem, dof_indices, field_var->number() + i);
        for (const auto dof : dof_indices)
          scaling_vector.set(dof, factors[i]);
      }
    }

  for (const auto * const scalar_var : scalar_variables)
  {
    mooseAssert(scalar_var->count() == 1,
                "Scalar variables should always have only one component.");
    dof_map.SCALAR_dof_indices(dof_indices, scalar_var->number());
    for (const auto dof : dof_indices)
      scaling_vector.set(dof, scalar_var->scalingFactor());
  }

  // Parallel assemble
  scaling_vector.close();

  if (auto * displaced_problem = _fe_problem.getDisplacedProblem().get())
    // copy into the corresponding displaced system vector because they should be the exact same
    displaced_problem->systemBaseNonlinear(number()).getVector("scaling_factors") = scaling_vector;
}

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 1059 of file SystemBase.C.

Referenced by SystemBase::addMatrix(), DisplacedSystem::associateMatrixToTag(), 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 964 of file SystemBase.C.

Referenced by DisplacedSystem::associateVectorToTag(), FEProblemBase::computeLinearSystemSys(), FEProblemBase::computeResidualAndJacobian(), FEProblemBase::computeResidualInternal(), 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;
}

attachPreconditioner()

virtual void NonlinearSystemBase::attachPreconditioner ( libMesh::Preconditioner< Number > *  preconditioner )

pure virtual

Attach a customized preconditioner that requires physics knowledge.

Generic preconditioners should be implemented in PETSc, instead.

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

Referenced by PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), and VariableCondensationPreconditioner::VariableCondensationPreconditioner().

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 444 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 NonlinearSystemBase::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 3468 of file NonlinearSystemBase.C.

{
  if (_add_implicit_geometric_coupling_entries_to_jacobian)
  {
    _fe_problem.updateGeomSearch();

    std::unordered_map<dof_id_type, std::vector<dof_id_type>> graph;

    findImplicitGeometricCouplingEntries(_fe_problem.geomSearchData(), graph);

    if (_fe_problem.getDisplacedProblem())
      findImplicitGeometricCouplingEntries(_fe_problem.getDisplacedProblem()->geomSearchData(),
                                           graph);

    const dof_id_type first_dof_on_proc = dofMap().first_dof(processor_id());
    const dof_id_type end_dof_on_proc = dofMap().end_dof(processor_id());

    // The total number of dofs on and off processor
    const dof_id_type n_dofs_on_proc = dofMap().n_local_dofs();
    const dof_id_type n_dofs_not_on_proc = dofMap().n_dofs() - dofMap().n_local_dofs();

    for (const auto & git : graph)
    {
      dof_id_type dof = git.first;
      dof_id_type local_dof = dof - first_dof_on_proc;

      if (dof < first_dof_on_proc || dof >= end_dof_on_proc)
        continue;

      const auto & row = git.second;

      SparsityPattern::Row & sparsity_row = sparsity[local_dof];

      unsigned int original_row_length = sparsity_row.size();

      sparsity_row.insert(sparsity_row.end(), row.begin(), row.end());

      SparsityPattern::sort_row(
          sparsity_row.begin(), sparsity_row.begin() + original_row_length, sparsity_row.end());

      // Fix up nonzero arrays
      for (const auto & coupled_dof : row)
      {
        if (coupled_dof < first_dof_on_proc || coupled_dof >= end_dof_on_proc)
        {
          if (n_oz[local_dof] < n_dofs_not_on_proc)
            n_oz[local_dof]++;
        }
        else
        {
          if (n_nz[local_dof] < n_dofs_on_proc)
            n_nz[local_dof]++;
        }
      }
    }
  }
}

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 122 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 128 of file SystemBase.h.

{ _automatic_scaling = automatic_scaling; }

autoScalingParam()

void NonlinearSystemBase::autoScalingParam ( Real  resid_vs_jac_scaling_param )

inline

Sets the param that indicates the weighting of the residual vs the Jacobian in determining variable scaling parameters.

A value of 1 indicates pure residual-based scaling. A value of 0 indicates pure Jacobian-based scaling

Definition at line 668 of file NonlinearSystemBase.h.

  {
    _resid_vs_jac_scaling_param = resid_vs_jac_scaling_param;
  }

checkInvalidSolution()

void SolverSystem::checkInvalidSolution ( )

protectedinherited

Definition at line 111 of file SolverSystem.C.

Referenced by NonlinearSystem::solve(), and LinearSystem::solve().

{
  auto & solution_invalidity = _app.solutionInvalidity();

  // sync all solution invalid counts to rank 0 process
  solution_invalidity.syncIteration();

  if (solution_invalidity.hasInvalidSolution())
  {
    if (_fe_problem.acceptInvalidSolution())
      if (_fe_problem.showInvalidSolutionConsole())
        solution_invalidity.print(_console);
      else
        mooseWarning("The Solution Invalidity warnings are detected but silenced! "
                     "Use Problem/show_invalid_solution_console=true to show solution counts");
    else
      // output the occurrence of solution invalid in a summary table
      if (_fe_problem.showInvalidSolutionConsole())
        solution_invalidity.print(_console);
  }
}

checkKernelCoverage()

void NonlinearSystemBase::checkKernelCoverage

(

const std::set< SubdomainID > &

mesh_subdomains

)

const

System Integrity Checks

Definition at line 3590 of file NonlinearSystemBase.C.

{
  // Obtain all blocks and variables covered by all kernels
  std::set<SubdomainID> input_subdomains;
  std::set<std::string> kernel_variables;

  bool global_kernels_exist = false;
  global_kernels_exist |= _scalar_kernels.hasActiveObjects();
  global_kernels_exist |= _nodal_kernels.hasActiveObjects();

  _kernels.subdomainsCovered(input_subdomains, kernel_variables);
  _dg_kernels.subdomainsCovered(input_subdomains, kernel_variables);
  _nodal_kernels.subdomainsCovered(input_subdomains, kernel_variables);
  _scalar_kernels.subdomainsCovered(input_subdomains, kernel_variables);
  _constraints.subdomainsCovered(input_subdomains, kernel_variables);

  if (_fe_problem.haveFV())
  {
    std::vector<FVElementalKernel *> fv_elemental_kernels;
    _fe_problem.theWarehouse()
        .query()
        .template condition<AttribSystem>("FVElementalKernel")
        .queryInto(fv_elemental_kernels);

    for (auto fv_kernel : fv_elemental_kernels)
    {
      if (fv_kernel->blockRestricted())
        for (auto block_id : fv_kernel->blockIDs())
          input_subdomains.insert(block_id);
      else
        global_kernels_exist = true;
      kernel_variables.insert(fv_kernel->variable().name());

      // Check for lagrange multiplier
      if (dynamic_cast<FVScalarLagrangeMultiplierConstraint *>(fv_kernel))
        kernel_variables.insert(dynamic_cast<FVScalarLagrangeMultiplierConstraint *>(fv_kernel)
                                    ->lambdaVariable()
                                    .name());
    }

    std::vector<FVFluxKernel *> fv_flux_kernels;
    _fe_problem.theWarehouse()
        .query()
        .template condition<AttribSystem>("FVFluxKernel")
        .queryInto(fv_flux_kernels);

    for (auto fv_kernel : fv_flux_kernels)
    {
      if (fv_kernel->blockRestricted())
        for (auto block_id : fv_kernel->blockIDs())
          input_subdomains.insert(block_id);
      else
        global_kernels_exist = true;
      kernel_variables.insert(fv_kernel->variable().name());
    }

    std::vector<FVInterfaceKernel *> fv_interface_kernels;
    _fe_problem.theWarehouse()
        .query()
        .template condition<AttribSystem>("FVInterfaceKernel")
        .queryInto(fv_interface_kernels);

    for (auto fvik : fv_interface_kernels)
      if (auto scalar_fvik = dynamic_cast<FVScalarLagrangeMultiplierInterface *>(fvik))
        kernel_variables.insert(scalar_fvik->lambdaVariable().name());

    std::vector<FVFluxBC *> fv_flux_bcs;
    _fe_problem.theWarehouse()
        .query()
        .template condition<AttribSystem>("FVFluxBC")
        .queryInto(fv_flux_bcs);

    for (auto fvbc : fv_flux_bcs)
      if (auto scalar_fvbc = dynamic_cast<FVBoundaryScalarLagrangeMultiplierConstraint *>(fvbc))
        kernel_variables.insert(scalar_fvbc->lambdaVariable().name());
  }

  // Check kernel coverage of subdomains (blocks) in your mesh
  if (!global_kernels_exist)
  {
    std::set<SubdomainID> difference;
    std::set_difference(mesh_subdomains.begin(),
                        mesh_subdomains.end(),
                        input_subdomains.begin(),
                        input_subdomains.end(),
                        std::inserter(difference, difference.end()));

    // there supposed to be no kernels on this lower-dimensional subdomain
    for (const auto & id : _mesh.interiorLowerDBlocks())
      difference.erase(id);
    for (const auto & id : _mesh.boundaryLowerDBlocks())
      difference.erase(id);

    if (!difference.empty())
    {
      std::vector<SubdomainID> difference_vec =
          std::vector<SubdomainID>(difference.begin(), difference.end());
      std::vector<SubdomainName> difference_names = _mesh.getSubdomainNames(difference_vec);
      std::stringstream missing_block_names;
      std::copy(difference_names.begin(),
                difference_names.end(),
                std::ostream_iterator<std::string>(missing_block_names, " "));
      std::stringstream missing_block_ids;
      std::copy(difference.begin(),
                difference.end(),
                std::ostream_iterator<unsigned int>(missing_block_ids, " "));

      mooseError("Each subdomain must contain at least one Kernel.\nThe following block(s) lack an "
                 "active kernel: " +
                     missing_block_names.str(),
                 " (ids: ",
                 missing_block_ids.str(),
                 ")");
    }
  }

  // Check kernel use of variables
  std::set<VariableName> variables(getVariableNames().begin(), getVariableNames().end());

  std::set<VariableName> difference;
  std::set_difference(variables.begin(),
                      variables.end(),
                      kernel_variables.begin(),
                      kernel_variables.end(),
                      std::inserter(difference, difference.end()));

  // skip checks for varaibles defined on lower-dimensional subdomain
  std::set<VariableName> vars(difference);
  for (auto & var_name : vars)
  {
    auto blks = getSubdomainsForVar(var_name);
    for (const auto & id : blks)
      if (_mesh.interiorLowerDBlocks().count(id) > 0 || _mesh.boundaryLowerDBlocks().count(id) > 0)
        difference.erase(var_name);
  }

  if (!difference.empty())
  {
    std::stringstream missing_kernel_vars;
    std::copy(difference.begin(),
              difference.end(),
              std::ostream_iterator<std::string>(missing_kernel_vars, " "));
    mooseError("Each variable must be referenced by at least one active Kernel.\nThe following "
               "variable(s) lack an active kernel: " +
               missing_kernel_vars.str());
  }
}

clearAllDofIndices()

void SystemBase::clearAllDofIndices ( )

inherited

Clear all dof indices from moose variables.

Definition at line 1580 of file SystemBase.C.

Referenced by SubProblem::clearAllDofIndices().

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

closeTaggedMatrices()

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

inherited

Close all matrices associated the tags.

Definition at line 1043 of file SystemBase.C.

Referenced by computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), and 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 641 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 659 of file SystemBase.C.

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

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

compute()

void SolverSystem::compute ( ExecFlagType  type )

overridevirtualinherited

Compute time derivatives, auxiliary variables, etc.

Parameters

type	Our current execution stage

Implements SystemBase.

Reimplemented in LinearSystem.

Definition at line 134 of file SolverSystem.C.

{
  // Let's try not to overcompute
  bool compute_tds = false;
  if (type == EXEC_LINEAR)
    compute_tds = true;
  else if (type == EXEC_NONLINEAR)
  {
    if (_fe_problem.computingScalingJacobian() || matrixFromColoring())
      compute_tds = true;
  }
  else if ((type == EXEC_TIMESTEP_END) || (type == EXEC_FINAL))
  {
    if (_fe_problem.solverParams(number())._type == Moose::ST_LINEAR)
      // We likely don't have a final residual evaluation upon which we compute the time derivatives
      // so we need to do so now
      compute_tds = true;
  }

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

computeDamping()

Real NonlinearSystemBase::computeDamping	(	const NumericVector< Number > &	solution,
		const NumericVector< Number > &	update
	)

Compute damping.

Parameters

solution	The trail solution vector
update	The incremental update to the solution vector

Returns

returns The damping factor

Definition at line 3316 of file NonlinearSystemBase.C.

Referenced by FEProblemBase::computeDamping().

{
  // Default to no damping
  Real damping = 1.0;
  bool has_active_dampers = false;

  try
  {
    if (_element_dampers.hasActiveObjects())
    {
      PARALLEL_TRY
      {
        TIME_SECTION("computeDampers", 3, "Computing Dampers");
        has_active_dampers = true;
        *_increment_vec = update;
        ComputeElemDampingThread cid(_fe_problem, *this);
        Threads::parallel_reduce(_fe_problem.getCurrentAlgebraicElementRange(), cid);
        damping = std::min(cid.damping(), damping);
      }
      PARALLEL_CATCH;
    }

    if (_nodal_dampers.hasActiveObjects())
    {
      PARALLEL_TRY
      {
        TIME_SECTION("computeDamping::element", 3, "Computing Element Damping");

        has_active_dampers = true;
        *_increment_vec = update;
        ComputeNodalDampingThread cndt(_fe_problem, *this);
        Threads::parallel_reduce(_fe_problem.getCurrentAlgebraicNodeRange(), cndt);
        damping = std::min(cndt.damping(), damping);
      }
      PARALLEL_CATCH;
    }

    if (_general_dampers.hasActiveObjects())
    {
      PARALLEL_TRY
      {
        TIME_SECTION("computeDamping::general", 3, "Computing General Damping");

        has_active_dampers = true;
        const auto & gdampers = _general_dampers.getActiveObjects();
        for (const auto & damper : gdampers)
        {
          Real gd_damping = damper->computeDamping(solution, update);
          try
          {
            damper->checkMinDamping(gd_damping);
          }
          catch (MooseException & e)
          {
            _fe_problem.setException(e.what());
          }
          damping = std::min(gd_damping, damping);
        }
      }
      PARALLEL_CATCH;
    }
  }
  catch (MooseException & e)
  {
    // The buck stops here, we have already handled the exception by
    // calling stopSolve(), it is now up to PETSc to return a
    // "diverged" reason during the next solve.
  }

  _communicator.min(damping);

  if (has_active_dampers && damping < 1.0)
    _console << " Damping factor: " << damping << std::endl;

  return damping;
}

computeDiracContributions()

void NonlinearSystemBase::computeDiracContributions ( const std::set< TagID > &  tags, bool  is_jacobian  )

protected

Definition at line 3395 of file NonlinearSystemBase.C.

Referenced by computeJacobianInternal(), and computeResidualInternal().

{
  _fe_problem.clearDiracInfo();

  std::set<const Elem *> dirac_elements;

  if (_dirac_kernels.hasActiveObjects())
  {
    TIME_SECTION("computeDirac", 3, "Computing DiracKernels");

    // TODO: Need a threading fix... but it's complicated!
    for (THREAD_ID tid = 0; tid < libMesh::n_threads(); ++tid)
    {
      const auto & dkernels = _dirac_kernels.getActiveObjects(tid);
      for (const auto & dkernel : dkernels)
      {
        dkernel->clearPoints();
        dkernel->addPoints();
      }
    }

    ComputeDiracThread cd(_fe_problem, tags, is_jacobian);

    _fe_problem.getDiracElements(dirac_elements);

    DistElemRange range(dirac_elements.begin(), dirac_elements.end(), 1);
    // TODO: Make Dirac work thread!
    // Threads::parallel_reduce(range, cd);

    cd(range);
  }
}

computedScalingJacobian()

bool NonlinearSystemBase::computedScalingJacobian ( ) const

inline

Definition at line 74 of file NonlinearSystemBase.h.

{ return _computed_scaling; }

computeJacobian() [1/2]

void NonlinearSystemBase::computeJacobian	(	libMesh::SparseMatrix< Number > &	jacobian,
		const std::set< TagID > &	tags
	)

Associate jacobian to systemMatrixTag, and then form a matrix for all the tags.

Definition at line 3166 of file NonlinearSystemBase.C.

Referenced by computeJacobian().

{
  associateMatrixToTag(jacobian, systemMatrixTag());

  computeJacobianTags(tags);

  disassociateMatrixFromTag(jacobian, systemMatrixTag());
}

computeJacobian() [2/2]

void NonlinearSystemBase::computeJacobian

(

libMesh::SparseMatrix< Number > &

jacobian

)

Take all tags in the system, and form a matrix for all tags in the system.

Definition at line 3153 of file NonlinearSystemBase.C.

{
  _nl_matrix_tags.clear();

  auto & tags = _fe_problem.getMatrixTags();

  for (auto & tag : tags)
    _nl_matrix_tags.insert(tag.second);

  computeJacobian(jacobian, _nl_matrix_tags);
}

computeJacobianBlocks() [1/2]

void NonlinearSystemBase::computeJacobianBlocks

(

std::vector< JacobianBlock *> &

blocks

)

Computes several Jacobian blocks simultaneously, summing their contributions into smaller preconditioning matrices.

Used by Physics-based preconditioning

Parameters

blocks

The blocks to fill in (JacobianBlock is defined in ComputeJacobianBlocksThread)

Definition at line 3195 of file NonlinearSystemBase.C.

Referenced by EigenProblem::computeJacobianBlocks(), and FEProblemBase::computeJacobianBlocks().

{
  _nl_matrix_tags.clear();

  auto & tags = _fe_problem.getMatrixTags();
  for (auto & tag : tags)
    _nl_matrix_tags.insert(tag.second);

  computeJacobianBlocks(blocks, _nl_matrix_tags);
}

computeJacobianBlocks() [2/2]

void NonlinearSystemBase::computeJacobianBlocks	(	std::vector< JacobianBlock *> &	blocks,
		const std::set< TagID > &	tags
	)

Definition at line 3207 of file NonlinearSystemBase.C.

{
  TIME_SECTION("computeJacobianBlocks", 3);
  FloatingPointExceptionGuard fpe_guard(_app);

  for (unsigned int i = 0; i < blocks.size(); i++)
  {
    SparseMatrix<Number> & jacobian = blocks[i]->_jacobian;

    LibmeshPetscCall(MatSetOption(static_cast<PetscMatrix<Number> &>(jacobian).mat(),
                                  MAT_KEEP_NONZERO_PATTERN, // This is changed in 3.1
                                  PETSC_TRUE));
    if (!_fe_problem.errorOnJacobianNonzeroReallocation())
      LibmeshPetscCall(MatSetOption(static_cast<PetscMatrix<Number> &>(jacobian).mat(),
                                    MAT_NEW_NONZERO_ALLOCATION_ERR,
                                    PETSC_TRUE));

    jacobian.zero();
  }

  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
    _fe_problem.reinitScalars(tid);

  PARALLEL_TRY
  {
    const ConstElemRange & elem_range = _fe_problem.getCurrentAlgebraicElementRange();
    ComputeJacobianBlocksThread cjb(_fe_problem, blocks, tags);
    Threads::parallel_reduce(elem_range, cjb);
  }
  PARALLEL_CATCH;

  for (unsigned int i = 0; i < blocks.size(); i++)
    blocks[i]->_jacobian.close();

  for (unsigned int i = 0; i < blocks.size(); i++)
  {
    libMesh::System & precond_system = blocks[i]->_precond_system;
    SparseMatrix<Number> & jacobian = blocks[i]->_jacobian;

    unsigned int ivar = blocks[i]->_ivar;
    unsigned int jvar = blocks[i]->_jvar;

    // Dirichlet BCs
    std::vector<numeric_index_type> zero_rows;
    PARALLEL_TRY
    {
      const ConstBndNodeRange & bnd_nodes = _fe_problem.getCurrentAlgebraicBndNodeRange();
      for (const auto & bnode : bnd_nodes)
      {
        BoundaryID boundary_id = bnode->_bnd_id;
        Node * node = bnode->_node;

        if (_nodal_bcs.hasActiveBoundaryObjects(boundary_id))
        {
          const auto & bcs = _nodal_bcs.getActiveBoundaryObjects(boundary_id);

          if (node->processor_id() == processor_id())
          {
            _fe_problem.reinitNodeFace(node, boundary_id, 0);

            for (const auto & bc : bcs)
              if (bc->variable().number() == ivar && bc->shouldApply())
              {
                // The first zero is for the variable number... there is only one variable in
                // each mini-system The second zero only works with Lagrange elements!
                zero_rows.push_back(node->dof_number(precond_system.number(), 0, 0));
              }
          }
        }
      }
    }
    PARALLEL_CATCH;

    jacobian.close();

    // This zeroes the rows corresponding to Dirichlet BCs and puts a 1.0 on the diagonal
    if (ivar == jvar)
      jacobian.zero_rows(zero_rows, 1.0);
    else
      jacobian.zero_rows(zero_rows, 0.0);

    jacobian.close();
  }
}

computeJacobianInternal()

void NonlinearSystemBase::computeJacobianInternal ( const std::set< TagID > &  tags )

protected

Form multiple matrices for all the tags.

Users should not call this func directly.

Definition at line 2787 of file NonlinearSystemBase.C.

Referenced by computeJacobianTags().

{
  TIME_SECTION("computeJacobianInternal", 3);

  _fe_problem.setCurrentNonlinearSystem(number());

  // Make matrix ready to use
  activeAllMatrixTags();

  for (auto tag : tags)
  {
    if (!hasMatrix(tag))
      continue;

    auto & jacobian = getMatrix(tag);
    // Necessary for speed
    if (auto petsc_matrix = dynamic_cast<PetscMatrix<Number> *>(&jacobian))
    {
      LibmeshPetscCall(MatSetOption(petsc_matrix->mat(),
                                    MAT_KEEP_NONZERO_PATTERN, // This is changed in 3.1
                                    PETSC_TRUE));
      if (!_fe_problem.errorOnJacobianNonzeroReallocation())
        LibmeshPetscCall(
            MatSetOption(petsc_matrix->mat(), MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE));
      if (_fe_problem.ignoreZerosInJacobian())
        LibmeshPetscCall(MatSetOption(static_cast<PetscMatrix<Number> &>(jacobian).mat(),
                                      MAT_IGNORE_ZERO_ENTRIES,
                                      PETSC_TRUE));
    }
  }

  jacobianSetup();

  // Jacobian contributions from UOs - for now this is used for ray tracing
  // and ray kernels that contribute to the Jacobian (think line sources)
  std::vector<UserObject *> uos;
  _fe_problem.theWarehouse()
      .query()
      .condition<AttribSystem>("UserObject")
      .condition<AttribExecOns>(EXEC_PRE_KERNELS)
      .queryInto(uos);
  for (auto & uo : uos)
    uo->jacobianSetup();
  for (auto & uo : uos)
  {
    uo->initialize();
    uo->execute();
    uo->finalize();
  }

  // reinit scalar variables
  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
    _fe_problem.reinitScalars(tid);

  PARALLEL_TRY
  {
    // We would like to compute ScalarKernels, block NodalKernels, FVFluxKernels, and mortar objects
    // up front because we want these included whether we are computing an ordinary Jacobian or a
    // Jacobian for determining variable scaling factors
    computeScalarKernelsJacobians(tags);

    // Block restricted Nodal Kernels
    if (_nodal_kernels.hasActiveBlockObjects())
    {
      ComputeNodalKernelJacobiansThread cnkjt(_fe_problem, *this, _nodal_kernels, tags);
      const ConstNodeRange & range = _fe_problem.getCurrentAlgebraicNodeRange();
      Threads::parallel_reduce(range, cnkjt);

      unsigned int n_threads = libMesh::n_threads();
      for (unsigned int i = 0; i < n_threads;
           i++) // Add any cached jacobians that might be hanging around
        _fe_problem.assembly(i, number()).addCachedJacobian(Assembly::GlobalDataKey{});
    }

    using FVRange = StoredRange<MooseMesh::const_face_info_iterator, const FaceInfo *>;
    if (_fe_problem.haveFV())
    {
      // the same loop works for both residual and jacobians because it keys
      // off of FEProblem's _currently_computing_jacobian parameter
      ComputeFVFluxJacobianThread<FVRange> fvj(
          _fe_problem, this->number(), tags, /*on_displaced=*/false);
      FVRange faces(_fe_problem.mesh().ownedFaceInfoBegin(), _fe_problem.mesh().ownedFaceInfoEnd());
      Threads::parallel_reduce(faces, fvj);
    }
    if (auto displaced_problem = _fe_problem.getDisplacedProblem();
        displaced_problem && displaced_problem->haveFV())
    {
      ComputeFVFluxJacobianThread<FVRange> fvr(
          _fe_problem, this->number(), tags, /*on_displaced=*/true);
      FVRange faces(displaced_problem->mesh().ownedFaceInfoBegin(),
                    displaced_problem->mesh().ownedFaceInfoEnd());
      Threads::parallel_reduce(faces, fvr);
    }

    mortarConstraints(Moose::ComputeType::Jacobian, {}, tags);

    // Get our element range for looping over
    const ConstElemRange & elem_range = _fe_problem.getCurrentAlgebraicElementRange();

    if (_fe_problem.computingScalingJacobian())
    {
      // Only compute Jacobians corresponding to the diagonals of volumetric compute objects
      // because this typically gives us a good representation of the physics. NodalBCs and
      // Constraints can introduce dramatically different scales (often order unity).
      // IntegratedBCs and/or InterfaceKernels may use penalty factors. DGKernels may be ok, but
      // they are almost always used in conjunction with Kernels
      ComputeJacobianForScalingThread cj(_fe_problem, tags);
      Threads::parallel_reduce(elem_range, cj);
      unsigned int n_threads = libMesh::n_threads();
      for (unsigned int i = 0; i < n_threads;
           i++) // Add any Jacobian contributions still hanging around
        _fe_problem.addCachedJacobian(i);

      // Check whether any exceptions were thrown and propagate this information for parallel
      // consistency before
      // 1) we do parallel communication when closing tagged matrices
      // 2) early returning before reaching our PARALLEL_CATCH below
      _fe_problem.checkExceptionAndStopSolve();

      closeTaggedMatrices(tags);

      return;
    }

    switch (_fe_problem.coupling())
    {
      case Moose::COUPLING_DIAG:
      {
        ComputeJacobianThread cj(_fe_problem, tags);
        Threads::parallel_reduce(elem_range, cj);

        unsigned int n_threads = libMesh::n_threads();
        for (unsigned int i = 0; i < n_threads;
             i++) // Add any Jacobian contributions still hanging around
          _fe_problem.addCachedJacobian(i);

        // Boundary restricted Nodal Kernels
        if (_nodal_kernels.hasActiveBoundaryObjects())
        {
          ComputeNodalKernelBCJacobiansThread cnkjt(_fe_problem, *this, _nodal_kernels, tags);
          const ConstBndNodeRange & bnd_range = _fe_problem.getCurrentAlgebraicBndNodeRange();

          Threads::parallel_reduce(bnd_range, cnkjt);
          unsigned int n_threads = libMesh::n_threads();
          for (unsigned int i = 0; i < n_threads;
               i++) // Add any cached jacobians that might be hanging around
            _fe_problem.assembly(i, number()).addCachedJacobian(Assembly::GlobalDataKey{});
        }
      }
      break;

      default:
      case Moose::COUPLING_CUSTOM:
      {
        ComputeFullJacobianThread cj(_fe_problem, tags);
        Threads::parallel_reduce(elem_range, cj);
        unsigned int n_threads = libMesh::n_threads();

        for (unsigned int i = 0; i < n_threads; i++)
          _fe_problem.addCachedJacobian(i);

        // Boundary restricted Nodal Kernels
        if (_nodal_kernels.hasActiveBoundaryObjects())
        {
          ComputeNodalKernelBCJacobiansThread cnkjt(_fe_problem, *this, _nodal_kernels, tags);
          const ConstBndNodeRange & bnd_range = _fe_problem.getCurrentAlgebraicBndNodeRange();

          Threads::parallel_reduce(bnd_range, cnkjt);
          unsigned int n_threads = libMesh::n_threads();
          for (unsigned int i = 0; i < n_threads;
               i++) // Add any cached jacobians that might be hanging around
            _fe_problem.assembly(i, number()).addCachedJacobian(Assembly::GlobalDataKey{});
        }
      }
      break;
    }

    computeDiracContributions(tags, true);

    static bool first = true;

    // This adds zeroes into geometric coupling entries to ensure they stay in the matrix
    if ((_fe_problem.restoreOriginalNonzeroPattern() || first) &&
        _add_implicit_geometric_coupling_entries_to_jacobian)
    {
      first = false;
      addImplicitGeometricCouplingEntries(_fe_problem.geomSearchData());

      if (_fe_problem.getDisplacedProblem())
        addImplicitGeometricCouplingEntries(_fe_problem.getDisplacedProblem()->geomSearchData());
    }
  }
  PARALLEL_CATCH;

  // Have no idea how to have constraints work
  // with the tag system
  PARALLEL_TRY
  {
    // Add in Jacobian contributions from other Constraints
    if (_fe_problem._has_constraints && tags.count(systemMatrixTag()))
    {
      // Some constraints need to be able to read values from the Jacobian, which requires that it
      // be closed/assembled
      auto & system_matrix = getMatrix(systemMatrixTag());
#if PETSC_RELEASE_GREATER_EQUALS(3, 23, 0)
      SparseMatrix<Number> * view_jac_ptr;
      std::unique_ptr<SparseMatrix<Number>> hash_copy;
      if (system_matrix.use_hash_table())
      {
        hash_copy = libMesh::cast_ref<PetscMatrix<Number> &>(system_matrix).copy_from_hash();
        view_jac_ptr = hash_copy.get();
      }
      else
        view_jac_ptr = &system_matrix;
      auto & jacobian_to_view = *view_jac_ptr;
#else
      auto & jacobian_to_view = system_matrix;
#endif
      if (&jacobian_to_view == &system_matrix)
        system_matrix.close();

      // Nodal Constraints
      enforceNodalConstraintsJacobian();

      // Undisplaced Constraints
      constraintJacobians(jacobian_to_view, false);

      // Displaced Constraints
      if (_fe_problem.getDisplacedProblem())
        constraintJacobians(jacobian_to_view, true);
    }
  }
  PARALLEL_CATCH;

  // We need to close the save_in variables on the aux system before NodalBCBases clear the dofs
  // on boundary nodes
  if (_has_diag_save_in)
    _fe_problem.getAuxiliarySystem().solution().close();

  PARALLEL_TRY
  {
    MooseObjectWarehouse<NodalBCBase> * nbc_warehouse;
    // Select nodal kernels
    if (tags.size() == _fe_problem.numMatrixTags() || !tags.size())
      nbc_warehouse = &_nodal_bcs;
    else if (tags.size() == 1)
      nbc_warehouse = &(_nodal_bcs.getMatrixTagObjectWarehouse(*(tags.begin()), 0));
    else
      nbc_warehouse = &(_nodal_bcs.getMatrixTagsObjectWarehouse(tags, 0));

    if (nbc_warehouse->hasActiveObjects())
    {
      // We may be switching from add to set. Moreover, we rely on a call to MatZeroRows to enforce
      // the nodal boundary condition constraints which requires that the matrix be truly assembled
      // as opposed to just flushed. Consequently we can't do the following despite any desire to
      // keep our initial sparsity pattern honored (see https://gitlab.com/petsc/petsc/-/issues/852)
      //
      // flushTaggedMatrices(tags);
      closeTaggedMatrices(tags);

      // Cache the information about which BCs are coupled to which
      // variables, so we don't have to figure it out for each node.
      std::map<std::string, std::set<unsigned int>> bc_involved_vars;
      const std::set<BoundaryID> & all_boundary_ids = _mesh.getBoundaryIDs();
      for (const auto & bid : all_boundary_ids)
      {
        // Get reference to all the NodalBCs for this ID.  This is only
        // safe if there are NodalBCBases there to be gotten...
        if (nbc_warehouse->hasActiveBoundaryObjects(bid))
        {
          const auto & bcs = nbc_warehouse->getActiveBoundaryObjects(bid);
          for (const auto & bc : bcs)
          {
            const std::vector<MooseVariableFEBase *> & coupled_moose_vars =
                bc->getCoupledMooseVars();

            // Create the set of "involved" MOOSE nonlinear vars, which includes all coupled vars
            // and the BC's own variable
            std::set<unsigned int> & var_set = bc_involved_vars[bc->name()];
            for (const auto & coupled_var : coupled_moose_vars)
              if (coupled_var->kind() == Moose::VAR_SOLVER)
                var_set.insert(coupled_var->number());

            var_set.insert(bc->variable().number());
          }
        }
      }

      // reinit scalar variables again. This reinit does not re-fill any of the scalar variable
      // solution arrays because that was done above. It only will reorder the derivative
      // information for AD calculations to be suitable for NodalBC calculations
      for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
        _fe_problem.reinitScalars(tid, true);

      // Get variable coupling list.  We do all the NodalBCBase stuff on
      // thread 0...  The couplingEntries() data structure determines
      // which variables are "coupled" as far as the preconditioner is
      // concerned, not what variables a boundary condition specifically
      // depends on.
      auto & coupling_entries = _fe_problem.couplingEntries(/*_tid=*/0, this->number());

      // Compute Jacobians for NodalBCBases
      const ConstBndNodeRange & bnd_nodes = _fe_problem.getCurrentAlgebraicBndNodeRange();
      for (const auto & bnode : bnd_nodes)
      {
        BoundaryID boundary_id = bnode->_bnd_id;
        Node * node = bnode->_node;

        if (nbc_warehouse->hasActiveBoundaryObjects(boundary_id) &&
            node->processor_id() == processor_id())
        {
          _fe_problem.reinitNodeFace(node, boundary_id, 0);

          const auto & bcs = nbc_warehouse->getActiveBoundaryObjects(boundary_id);
          for (const auto & bc : bcs)
          {
            // Get the set of involved MOOSE vars for this BC
            std::set<unsigned int> & var_set = bc_involved_vars[bc->name()];

            // Loop over all the variables whose Jacobian blocks are
            // actually being computed, call computeOffDiagJacobian()
            // for each one which is actually coupled (otherwise the
            // value is zero.)
            for (const auto & it : coupling_entries)
            {
              unsigned int ivar = it.first->number(), jvar = it.second->number();

              // We are only going to call computeOffDiagJacobian() if:
              // 1.) the BC's variable is ivar
              // 2.) jvar is "involved" with the BC (including jvar==ivar), and
              // 3.) the BC should apply.
              if ((bc->variable().number() == ivar) && var_set.count(jvar) && bc->shouldApply())
                bc->computeOffDiagJacobian(jvar);
            }

            const auto & coupled_scalar_vars = bc->getCoupledMooseScalarVars();
            for (const auto & jvariable : coupled_scalar_vars)
              if (hasScalarVariable(jvariable->name()))
                bc->computeOffDiagJacobianScalar(jvariable->number());
          }
        }
      } // end loop over boundary nodes

      // Set the cached NodalBCBase values in the Jacobian matrix
      _fe_problem.assembly(0, number()).setCachedJacobian(Assembly::GlobalDataKey{});
    }
  }
  PARALLEL_CATCH;

  closeTaggedMatrices(tags);

  // We need to close the save_in variables on the aux system before NodalBCBases clear the dofs
  // on boundary nodes
  if (_has_nodalbc_diag_save_in)
    _fe_problem.getAuxiliarySystem().solution().close();

  if (hasDiagSaveIn())
    _fe_problem.getAuxiliarySystem().update();

  // Accumulate the occurrence of solution invalid warnings for the current iteration cumulative
  // counters
  _app.solutionInvalidity().syncIteration();
  _app.solutionInvalidity().solutionInvalidAccumulation();
}

computeJacobianTags()

void NonlinearSystemBase::computeJacobianTags

(

const std::set< TagID > &

tags

)

Computes multiple (tag associated) Jacobian matricese.

Definition at line 3176 of file NonlinearSystemBase.C.

Referenced by computeJacobian(), and FEProblemBase::computeJacobianTags().

{
  TIME_SECTION("computeJacobianTags", 5);

  FloatingPointExceptionGuard fpe_guard(_app);

  try
  {
    computeJacobianInternal(tags);
  }
  catch (MooseException & e)
  {
    // The buck stops here, we have already handled the exception by
    // calling stopSolve(), it is now up to PETSc to return a
    // "diverged" reason during the next solve.
  }
}

computeNodalBCs() [1/3]

void NonlinearSystemBase::computeNodalBCs ( NumericVector< Number > &  residual )

protected

Enforces nodal boundary conditions.

The boundary condition will be implemented in the residual using all the tags in the system.

Referenced by computeResidualTags().

computeNodalBCs() [2/3]

void NonlinearSystemBase::computeNodalBCs ( NumericVector< Number > &  residual, const std::set< TagID > &  tags  )

protected

Form a residual for BCs that at least has one of the given tags.

computeNodalBCs() [3/3]

void NonlinearSystemBase::computeNodalBCs ( const std::set< TagID > &  tags )

protected

Form multiple tag-associated residual vectors for the given tags.

Definition at line 2063 of file NonlinearSystemBase.C.

{
  // We need to close the diag_save_in variables on the aux system before NodalBCBases clear the
  // dofs on boundary nodes
  if (_has_save_in)
    _fe_problem.getAuxiliarySystem().solution().close();

  // Select nodal kernels
  MooseObjectWarehouse<NodalBCBase> * nbc_warehouse;

  if (tags.size() == _fe_problem.numVectorTags(Moose::VECTOR_TAG_RESIDUAL) || !tags.size())
    nbc_warehouse = &_nodal_bcs;
  else if (tags.size() == 1)
    nbc_warehouse = &(_nodal_bcs.getVectorTagObjectWarehouse(*(tags.begin()), 0));
  else
    nbc_warehouse = &(_nodal_bcs.getVectorTagsObjectWarehouse(tags, 0));

  // Return early if there is no nodal kernel
  if (!nbc_warehouse->size())
    return;

  PARALLEL_TRY
  {
    const ConstBndNodeRange & bnd_nodes = _fe_problem.getCurrentAlgebraicBndNodeRange();

    if (!bnd_nodes.empty())
    {
      TIME_SECTION("NodalBCs", 3 /*, "Computing NodalBCs"*/);

      for (const auto & bnode : bnd_nodes)
      {
        BoundaryID boundary_id = bnode->_bnd_id;
        Node * node = bnode->_node;

        if (node->processor_id() == processor_id() &&
            nbc_warehouse->hasActiveBoundaryObjects(boundary_id))
        {
          // reinit variables in nodes
          _fe_problem.reinitNodeFace(node, boundary_id, 0);

          const auto & bcs = nbc_warehouse->getActiveBoundaryObjects(boundary_id);
          for (const auto & nbc : bcs)
            if (nbc->shouldApply())
              nbc->computeResidual();
        }
      }
    }
  }
  PARALLEL_CATCH;

  if (_Re_time)
    _Re_time->close();
  _Re_non_time->close();
}

computeNodalBCsResidualAndJacobian()

void NonlinearSystemBase::computeNodalBCsResidualAndJacobian ( )

protected

compute the residual and Jacobian for nodal boundary conditions

Definition at line 2119 of file NonlinearSystemBase.C.

Referenced by computeResidualAndJacobianTags().

{
  PARALLEL_TRY
  {
    const ConstBndNodeRange & bnd_nodes = _fe_problem.getCurrentAlgebraicBndNodeRange();

    if (!bnd_nodes.empty())
    {
      TIME_SECTION("NodalBCs", 3 /*, "Computing NodalBCs"*/);

      for (const auto & bnode : bnd_nodes)
      {
        BoundaryID boundary_id = bnode->_bnd_id;
        Node * node = bnode->_node;

        if (node->processor_id() == processor_id())
        {
          // reinit variables in nodes
          _fe_problem.reinitNodeFace(node, boundary_id, 0);
          if (_nodal_bcs.hasActiveBoundaryObjects(boundary_id))
          {
            const auto & bcs = _nodal_bcs.getActiveBoundaryObjects(boundary_id);
            for (const auto & nbc : bcs)
              if (nbc->shouldApply())
                nbc->computeResidualAndJacobian();
          }
        }
      }
    }
  }
  PARALLEL_CATCH;

  // Set the cached NodalBCBase values in the Jacobian matrix
  _fe_problem.assembly(0, number()).setCachedJacobian(Assembly::GlobalDataKey{});
}

computeResidual()

void NonlinearSystemBase::computeResidual	(	NumericVector< Number > &	residual,
		TagID	tag_id
	)

Form a residual vector for a given tag.

Definition at line 796 of file NonlinearSystemBase.C.

{
  mooseDeprecated(" Please use computeResidualTag");

  computeResidualTag(residual, tag_id);
}

computeResidualAndJacobianInternal()

void NonlinearSystemBase::computeResidualAndJacobianInternal	(	const std::set< TagID > &	vector_tags,
		const std::set< TagID > &	matrix_tags
	)

Compute residual and Jacobian from contributions not related to constraints, such as nodal boundary conditions.

Definition at line 1944 of file NonlinearSystemBase.C.

Referenced by computeResidualAndJacobianTags().

{
  TIME_SECTION("computeResidualAndJacobianInternal", 3);

  // Make matrix ready to use
  activeAllMatrixTags();

  for (auto tag : matrix_tags)
  {
    if (!hasMatrix(tag))
      continue;

    auto & jacobian = getMatrix(tag);
    // Necessary for speed
    if (auto petsc_matrix = dynamic_cast<PetscMatrix<Number> *>(&jacobian))
    {
      LibmeshPetscCall(MatSetOption(petsc_matrix->mat(),
                                    MAT_KEEP_NONZERO_PATTERN, // This is changed in 3.1
                                    PETSC_TRUE));
      if (!_fe_problem.errorOnJacobianNonzeroReallocation())
        LibmeshPetscCall(
            MatSetOption(petsc_matrix->mat(), MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE));
      if (_fe_problem.ignoreZerosInJacobian())
        LibmeshPetscCall(MatSetOption(static_cast<PetscMatrix<Number> &>(jacobian).mat(),
                                      MAT_IGNORE_ZERO_ENTRIES,
                                      PETSC_TRUE));
    }
  }

  residualSetup();

  // Residual contributions from UOs - for now this is used for ray tracing
  // and ray kernels that contribute to the residual (think line sources)
  std::vector<UserObject *> uos;
  _fe_problem.theWarehouse()
      .query()
      .condition<AttribSystem>("UserObject")
      .condition<AttribExecOns>(EXEC_PRE_KERNELS)
      .queryInto(uos);
  for (auto & uo : uos)
    uo->residualSetup();
  for (auto & uo : uos)
  {
    uo->initialize();
    uo->execute();
    uo->finalize();
  }

  // reinit scalar variables
  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
    _fe_problem.reinitScalars(tid);

  // residual contributions from the domain
  PARALLEL_TRY
  {
    TIME_SECTION("Kernels", 3 /*, "Computing Kernels"*/);

    const ConstElemRange & elem_range = _fe_problem.getCurrentAlgebraicElementRange();

    ComputeResidualAndJacobianThread crj(_fe_problem, vector_tags, matrix_tags);
    Threads::parallel_reduce(elem_range, crj);

    using FVRange = StoredRange<MooseMesh::const_face_info_iterator, const FaceInfo *>;
    if (_fe_problem.haveFV())
    {
      ComputeFVFluxRJThread<FVRange> fvrj(
          _fe_problem, this->number(), vector_tags, matrix_tags, /*on_displaced=*/false);
      FVRange faces(_fe_problem.mesh().ownedFaceInfoBegin(), _fe_problem.mesh().ownedFaceInfoEnd());
      Threads::parallel_reduce(faces, fvrj);
    }
    if (auto displaced_problem = _fe_problem.getDisplacedProblem();
        displaced_problem && displaced_problem->haveFV())
    {
      ComputeFVFluxRJThread<FVRange> fvr(
          _fe_problem, this->number(), vector_tags, matrix_tags, /*on_displaced=*/true);
      FVRange faces(displaced_problem->mesh().ownedFaceInfoBegin(),
                    displaced_problem->mesh().ownedFaceInfoEnd());
      Threads::parallel_reduce(faces, fvr);
    }

    mortarConstraints(Moose::ComputeType::ResidualAndJacobian, vector_tags, matrix_tags);

    unsigned int n_threads = libMesh::n_threads();
    for (unsigned int i = 0; i < n_threads;
         i++) // Add any cached residuals that might be hanging around
    {
      _fe_problem.addCachedResidual(i);
      _fe_problem.addCachedJacobian(i);
    }
  }
  PARALLEL_CATCH;
}

computeResidualAndJacobianTags()

void NonlinearSystemBase::computeResidualAndJacobianTags	(	const std::set< TagID > &	vector_tags,
		const std::set< TagID > &	matrix_tags
	)

Form possibly multiple tag-associated vectors and matrices.

Definition at line 884 of file NonlinearSystemBase.C.

Referenced by FEProblemBase::computeResidualAndJacobian().

{
  const bool required_residual =
      vector_tags.find(residualVectorTag()) == vector_tags.end() ? false : true;

  try
  {
    zeroTaggedVectors(vector_tags);
    computeResidualAndJacobianInternal(vector_tags, matrix_tags);
    closeTaggedVectors(vector_tags);
    closeTaggedMatrices(matrix_tags);

    if (required_residual)
    {
      auto & residual = getVector(residualVectorTag());
      if (!_time_integrators.empty())
      {
        for (auto & ti : _time_integrators)
          ti->postResidual(residual);
      }
      else
        residual += *_Re_non_time;
      residual.close();
    }

    computeNodalBCsResidualAndJacobian();
    closeTaggedVectors(vector_tags);
    closeTaggedMatrices(matrix_tags);
  }
  catch (MooseException & e)
  {
    // The buck stops here, we have already handled the exception by
    // calling stopSolve(), it is now up to PETSc to return a
    // "diverged" reason during the next solve.
  }
}

computeResidualInternal()

void NonlinearSystemBase::computeResidualInternal ( const std::set< TagID > &  tags )

protected

Compute the residual for a given tag.

Parameters

tags	The tags of kernels for which the residual is to be computed.

Definition at line 1724 of file NonlinearSystemBase.C.

Referenced by computeResidualTags().

{
  parallel_object_only();

  TIME_SECTION("computeResidualInternal", 3);

  residualSetup();

  const auto vector_tag_data = _fe_problem.getVectorTags(tags);

  // Residual contributions from UOs - for now this is used for ray tracing
  // and ray kernels that contribute to the residual (think line sources)
  std::vector<UserObject *> uos;
  _fe_problem.theWarehouse()
      .query()
      .condition<AttribSystem>("UserObject")
      .condition<AttribExecOns>(EXEC_PRE_KERNELS)
      .queryInto(uos);
  for (auto & uo : uos)
    uo->residualSetup();
  for (auto & uo : uos)
  {
    uo->initialize();
    uo->execute();
    uo->finalize();
  }

  // reinit scalar variables
  for (unsigned int tid = 0; tid < libMesh::n_threads(); tid++)
    _fe_problem.reinitScalars(tid);

  // residual contributions from the domain
  PARALLEL_TRY
  {
    TIME_SECTION("Kernels", 3 /*, "Computing Kernels"*/);

    const ConstElemRange & elem_range = _fe_problem.getCurrentAlgebraicElementRange();

    ComputeResidualThread cr(_fe_problem, tags);
    Threads::parallel_reduce(elem_range, cr);

    // We pass face information directly to FV residual objects for their evaluation. Consequently
    // we must make sure to do separate threaded loops for 1) undisplaced face information objects
    // and undisplaced residual objects and 2) displaced face information objects and displaced
    // residual objects
    using FVRange = StoredRange<MooseMesh::const_face_info_iterator, const FaceInfo *>;
    if (_fe_problem.haveFV())
    {
      ComputeFVFluxResidualThread<FVRange> fvr(
          _fe_problem, this->number(), tags, /*on_displaced=*/false);
      FVRange faces(_fe_problem.mesh().ownedFaceInfoBegin(), _fe_problem.mesh().ownedFaceInfoEnd());
      Threads::parallel_reduce(faces, fvr);
    }
    if (auto displaced_problem = _fe_problem.getDisplacedProblem();
        displaced_problem && displaced_problem->haveFV())
    {
      ComputeFVFluxResidualThread<FVRange> fvr(
          _fe_problem, this->number(), tags, /*on_displaced=*/true);
      FVRange faces(displaced_problem->mesh().ownedFaceInfoBegin(),
                    displaced_problem->mesh().ownedFaceInfoEnd());
      Threads::parallel_reduce(faces, fvr);
    }

    unsigned int n_threads = libMesh::n_threads();
    for (unsigned int i = 0; i < n_threads;
         i++) // Add any cached residuals that might be hanging around
      _fe_problem.addCachedResidual(i);
  }
  PARALLEL_CATCH;

  // residual contributions from the scalar kernels
  PARALLEL_TRY
  {
    // do scalar kernels (not sure how to thread this)
    if (_scalar_kernels.hasActiveObjects())
    {
      TIME_SECTION("ScalarKernels", 3 /*, "Computing ScalarKernels"*/);

      MooseObjectWarehouse<ScalarKernelBase> * scalar_kernel_warehouse;
      // This code should be refactored once we can do tags for scalar
      // kernels
      // Should redo this based on Warehouse
      if (!tags.size() || tags.size() == _fe_problem.numVectorTags(Moose::VECTOR_TAG_RESIDUAL))
        scalar_kernel_warehouse = &_scalar_kernels;
      else if (tags.size() == 1)
        scalar_kernel_warehouse =
            &(_scalar_kernels.getVectorTagObjectWarehouse(*(tags.begin()), 0));
      else
        // scalar_kernels is not threading
        scalar_kernel_warehouse = &(_scalar_kernels.getVectorTagsObjectWarehouse(tags, 0));

      bool have_scalar_contributions = false;
      const auto & scalars = scalar_kernel_warehouse->getActiveObjects();
      for (const auto & scalar_kernel : scalars)
      {
        scalar_kernel->reinit();
        const std::vector<dof_id_type> & dof_indices = scalar_kernel->variable().dofIndices();
        const DofMap & dof_map = scalar_kernel->variable().dofMap();
        const dof_id_type first_dof = dof_map.first_dof();
        const dof_id_type end_dof = dof_map.end_dof();
        for (dof_id_type dof : dof_indices)
        {
          if (dof >= first_dof && dof < end_dof)
          {
            scalar_kernel->computeResidual();
            have_scalar_contributions = true;
            break;
          }
        }
      }
      if (have_scalar_contributions)
        _fe_problem.addResidualScalar();
    }
  }
  PARALLEL_CATCH;

  // residual contributions from Block NodalKernels
  PARALLEL_TRY
  {
    if (_nodal_kernels.hasActiveBlockObjects())
    {
      TIME_SECTION("NodalKernels", 3 /*, "Computing NodalKernels"*/);

      ComputeNodalKernelsThread cnk(_fe_problem, _nodal_kernels, tags);

      const ConstNodeRange & range = _fe_problem.getCurrentAlgebraicNodeRange();

      if (range.begin() != range.end())
      {
        _fe_problem.reinitNode(*range.begin(), 0);

        Threads::parallel_reduce(range, cnk);

        unsigned int n_threads = libMesh::n_threads();
        for (unsigned int i = 0; i < n_threads;
             i++) // Add any cached residuals that might be hanging around
          _fe_problem.addCachedResidual(i);
      }
    }
  }
  PARALLEL_CATCH;

  if (_fe_problem.computingScalingResidual())
    // We computed the volumetric objects. We can return now before we get into
    // any strongly enforced constraint conditions or penalty-type objects
    // (DGKernels, IntegratedBCs, InterfaceKernels, Constraints)
    return;

  // residual contributions from boundary NodalKernels
  PARALLEL_TRY
  {
    if (_nodal_kernels.hasActiveBoundaryObjects())
    {
      TIME_SECTION("NodalKernelBCs", 3 /*, "Computing NodalKernelBCs"*/);

      ComputeNodalKernelBcsThread cnk(_fe_problem, _nodal_kernels, tags);

      const ConstBndNodeRange & bnd_node_range = _fe_problem.getCurrentAlgebraicBndNodeRange();

      Threads::parallel_reduce(bnd_node_range, cnk);

      unsigned int n_threads = libMesh::n_threads();
      for (unsigned int i = 0; i < n_threads;
           i++) // Add any cached residuals that might be hanging around
        _fe_problem.addCachedResidual(i);
    }
  }
  PARALLEL_CATCH;

  mortarConstraints(Moose::ComputeType::Residual, tags, {});

  if (_residual_copy.get())
  {
    _Re_non_time->close();
    _Re_non_time->localize(*_residual_copy);
  }

  if (_need_residual_ghosted)
  {
    _Re_non_time->close();
    *_residual_ghosted = *_Re_non_time;
    _residual_ghosted->close();
  }

  PARALLEL_TRY { computeDiracContributions(tags, false); }
  PARALLEL_CATCH;

  if (_fe_problem._has_constraints)
  {
    PARALLEL_TRY { enforceNodalConstraintsResidual(*_Re_non_time); }
    PARALLEL_CATCH;
    _Re_non_time->close();
  }

  // Add in Residual contributions from other Constraints
  if (_fe_problem._has_constraints)
  {
    PARALLEL_TRY
    {
      // Undisplaced Constraints
      constraintResiduals(*_Re_non_time, false);

      // Displaced Constraints
      if (_fe_problem.getDisplacedProblem())
        constraintResiduals(*_Re_non_time, true);

      if (_fe_problem.computingNonlinearResid())
        _constraints.residualEnd();
    }
    PARALLEL_CATCH;
    _Re_non_time->close();
  }

  // Accumulate the occurrence of solution invalid warnings for the current iteration cumulative
  // counters
  _app.solutionInvalidity().syncIteration();
  _app.solutionInvalidity().solutionInvalidAccumulation();
}

computeResidualTag()

void NonlinearSystemBase::computeResidualTag	(	NumericVector< Number > &	residual,
		TagID	tag_id
	)

Computes residual for a given tag.

Parameters

residual	Residual is formed in here
the	tag of kernels for which the residual is to be computed.

Definition at line 782 of file NonlinearSystemBase.C.

Referenced by computeResidual(), and CrankNicolson::init().

{
  _nl_vector_tags.clear();
  _nl_vector_tags.insert(tag_id);
  _nl_vector_tags.insert(residualVectorTag());

  associateVectorToTag(residual, residualVectorTag());

  computeResidualTags(_nl_vector_tags);

  disassociateVectorFromTag(residual, residualVectorTag());
}

computeResidualTags()

void NonlinearSystemBase::computeResidualTags

(

const std::set< TagID > &

tags

)

Form multiple tag-associated residual vectors for all the given tags.

Definition at line 804 of file NonlinearSystemBase.C.

Referenced by computeResidualTag(), and FEProblemBase::computeResidualTags().

{
  parallel_object_only();

  TIME_SECTION("nl::computeResidualTags", 5);

  _fe_problem.setCurrentNonlinearSystem(number());
  _fe_problem.setCurrentlyComputingResidual(true);

  bool required_residual = tags.find(residualVectorTag()) == tags.end() ? false : true;

  _n_residual_evaluations++;

  // not suppose to do anythin on matrix
  deactiveAllMatrixTags();

  FloatingPointExceptionGuard fpe_guard(_app);

  for (const auto & numeric_vec : _vecs_to_zero_for_residual)
    if (hasVector(numeric_vec))
    {
      NumericVector<Number> & vec = getVector(numeric_vec);
      vec.close();
      vec.zero();
    }

  try
  {
    zeroTaggedVectors(tags);
    computeResidualInternal(tags);
    closeTaggedVectors(tags);

    if (required_residual)
    {
      auto & residual = getVector(residualVectorTag());
      if (!_time_integrators.empty())
      {
        for (auto & ti : _time_integrators)
          ti->postResidual(residual);
      }
      else
        residual += *_Re_non_time;
      residual.close();
    }
    if (_fe_problem.computingScalingResidual())
      // We don't want to do nodal bcs or anything else
      return;

    computeNodalBCs(tags);
    closeTaggedVectors(tags);

    // If we are debugging residuals we need one more assignment to have the ghosted copy up to
    // date
    if (_need_residual_ghosted && _debugging_residuals && required_residual)
    {
      auto & residual = getVector(residualVectorTag());

      *_residual_ghosted = residual;
      _residual_ghosted->close();
    }
    // Need to close and update the aux system in case residuals were saved to it.
    if (_has_nodalbc_save_in)
      _fe_problem.getAuxiliarySystem().solution().close();
    if (hasSaveIn())
      _fe_problem.getAuxiliarySystem().update();
  }
  catch (MooseException & e)
  {
    // The buck stops here, we have already handled the exception by
    // calling stopSolve(), it is now up to PETSc to return a
    // "diverged" reason during the next solve.
  }

  // not supposed to do anything on matrix
  activeAllMatrixTags();

  _fe_problem.setCurrentlyComputingResidual(false);
}

computeScalarKernelsJacobians()

void NonlinearSystemBase::computeScalarKernelsJacobians ( const std::set< TagID > &  tags )

protected

Definition at line 2713 of file NonlinearSystemBase.C.

Referenced by computeJacobianInternal().

{
  MooseObjectWarehouse<ScalarKernelBase> * scalar_kernel_warehouse;

  if (!tags.size() || tags.size() == _fe_problem.numMatrixTags())
    scalar_kernel_warehouse = &_scalar_kernels;
  else if (tags.size() == 1)
    scalar_kernel_warehouse = &(_scalar_kernels.getMatrixTagObjectWarehouse(*(tags.begin()), 0));
  else
    scalar_kernel_warehouse = &(_scalar_kernels.getMatrixTagsObjectWarehouse(tags, 0));

  // Compute the diagonal block for scalar variables
  if (scalar_kernel_warehouse->hasActiveObjects())
  {
    const auto & scalars = scalar_kernel_warehouse->getActiveObjects();

    _fe_problem.reinitScalars(/*tid=*/0);

    _fe_problem.reinitOffDiagScalars(/*_tid*/ 0);

    bool have_scalar_contributions = false;
    for (const auto & kernel : scalars)
    {
      kernel->reinit();
      const std::vector<dof_id_type> & dof_indices = kernel->variable().dofIndices();
      const DofMap & dof_map = kernel->variable().dofMap();
      const dof_id_type first_dof = dof_map.first_dof();
      const dof_id_type end_dof = dof_map.end_dof();
      for (dof_id_type dof : dof_indices)
      {
        if (dof >= first_dof && dof < end_dof)
        {
          kernel->computeJacobian();
          _fe_problem.addJacobianOffDiagScalar(kernel->variable().number());
          have_scalar_contributions = true;
          break;
        }
      }
    }

    if (have_scalar_contributions)
      _fe_problem.addJacobianScalar();
  }
}

computeScaling()

bool NonlinearSystemBase::computeScaling

(

)

Method used to obtain scaling factors for variables.

Returns

whether this method ran without exceptions

Definition at line 3886 of file NonlinearSystemBase.C.

Referenced by preSolve().

{
  if (_compute_scaling_once && _computed_scaling)
    return true;

  _console << "\nPerforming automatic scaling calculation\n" << std::endl;

  TIME_SECTION("computeScaling", 3, "Computing Automatic Scaling");

  // It's funny but we need to assemble our vector of scaling factors here otherwise we will be
  // applying scaling factors of 0 during Assembly of our scaling Jacobian
  assembleScalingVector();

  // container for repeated access of element global dof indices
  std::vector<dof_id_type> dof_indices;

  if (!_auto_scaling_initd)
    setupScalingData();

  std::vector<Real> inverse_scaling_factors(_num_scaling_groups, 0);
  std::vector<Real> resid_inverse_scaling_factors(_num_scaling_groups, 0);
  std::vector<Real> jac_inverse_scaling_factors(_num_scaling_groups, 0);
  auto & dof_map = dofMap();

  // what types of scaling do we want?
  bool jac_scaling = _resid_vs_jac_scaling_param < 1. - TOLERANCE;
  bool resid_scaling = _resid_vs_jac_scaling_param > TOLERANCE;

  const NumericVector<Number> & scaling_residual = RHS();

  if (jac_scaling)
  {
    // if (!_auto_scaling_initd)
    // We need to reinit this when the number of dofs changes
    // but there is no good way to track that
    // In theory, it is the job of libmesh system to track this,
    // but this special matrix is not owned by libMesh system
    // Let us reinit eveytime since it is not expensive
    {
      auto init_vector = NumericVector<Number>::build(this->comm());
      init_vector->init(system().n_dofs(), system().n_local_dofs(), /*fast=*/false, PARALLEL);

      _scaling_matrix->clear();
      _scaling_matrix->init(*init_vector);
    }

    _fe_problem.computingScalingJacobian(true);
    // Dispatch to derived classes to ensure that we use the correct matrix tag
    computeScalingJacobian();
    _fe_problem.computingScalingJacobian(false);
  }

  if (resid_scaling)
  {
    _fe_problem.computingScalingResidual(true);
    _fe_problem.computingNonlinearResid(true);
    // Dispatch to derived classes to ensure that we use the correct vector tag
    computeScalingResidual();
    _fe_problem.computingNonlinearResid(false);
    _fe_problem.computingScalingResidual(false);
  }

  // Did something bad happen during residual/Jacobian scaling computation?
  if (_fe_problem.getFailNextNonlinearConvergenceCheck())
    return false;

  auto examine_dof_indices = [this,
                              jac_scaling,
                              resid_scaling,
                              &dof_map,
                              &jac_inverse_scaling_factors,
                              &resid_inverse_scaling_factors,
                              &scaling_residual](const auto & dof_indices, const auto var_number)
  {
    for (auto dof_index : dof_indices)
      if (dof_map.local_index(dof_index))
      {
        if (jac_scaling)
        {
          // For now we will use the diagonal for determining scaling
          auto mat_value = (*_scaling_matrix)(dof_index, dof_index);
          auto & factor = jac_inverse_scaling_factors[_var_to_group_var[var_number]];
          factor = std::max(factor, std::abs(mat_value));
        }
        if (resid_scaling)
        {
          auto vec_value = scaling_residual(dof_index);
          auto & factor = resid_inverse_scaling_factors[_var_to_group_var[var_number]];
          factor = std::max(factor, std::abs(vec_value));
        }
      }
  };

  // Compute our scaling factors for the spatial field variables
  for (const auto & elem : _fe_problem.getCurrentAlgebraicElementRange())
    for (const auto i : make_range(system().n_vars()))
      if (_variable_autoscaled[i] && system().variable_type(i).family != SCALAR)
      {
        dof_map.dof_indices(elem, dof_indices, i);
        examine_dof_indices(dof_indices, i);
      }

  for (const auto i : make_range(system().n_vars()))
    if (_variable_autoscaled[i] && system().variable_type(i).family == SCALAR)
    {
      dof_map.SCALAR_dof_indices(dof_indices, i);
      examine_dof_indices(dof_indices, i);
    }

  if (resid_scaling)
    _communicator.max(resid_inverse_scaling_factors);
  if (jac_scaling)
    _communicator.max(jac_inverse_scaling_factors);

  if (jac_scaling && resid_scaling)
    for (MooseIndex(inverse_scaling_factors) i = 0; i < inverse_scaling_factors.size(); ++i)
    {
      // Be careful not to take log(0)
      if (!resid_inverse_scaling_factors[i])
      {
        if (!jac_inverse_scaling_factors[i])
          inverse_scaling_factors[i] = 1;
        else
          inverse_scaling_factors[i] = jac_inverse_scaling_factors[i];
      }
      else if (!jac_inverse_scaling_factors[i])
        // We know the resid is not zero
        inverse_scaling_factors[i] = resid_inverse_scaling_factors[i];
      else
        inverse_scaling_factors[i] =
            std::exp(_resid_vs_jac_scaling_param * std::log(resid_inverse_scaling_factors[i]) +
                     (1 - _resid_vs_jac_scaling_param) * std::log(jac_inverse_scaling_factors[i]));
    }
  else if (jac_scaling)
    inverse_scaling_factors = jac_inverse_scaling_factors;
  else if (resid_scaling)
    inverse_scaling_factors = resid_inverse_scaling_factors;
  else
    mooseError("We shouldn't be calling this routine if we're not performing any scaling");

  // We have to make sure that our scaling values are not zero
  for (auto & scaling_factor : inverse_scaling_factors)
    if (scaling_factor == 0)
      scaling_factor = 1;

  // Now flatten the group scaling factors to the individual variable scaling factors
  std::vector<Real> flattened_inverse_scaling_factors(system().n_vars());
  for (const auto i : index_range(flattened_inverse_scaling_factors))
    flattened_inverse_scaling_factors[i] = inverse_scaling_factors[_var_to_group_var[i]];

  // Now set the scaling factors for the variables
  applyScalingFactors(flattened_inverse_scaling_factors);
  if (auto displaced_problem = _fe_problem.getDisplacedProblem().get())
    displaced_problem->systemBaseNonlinear(number()).applyScalingFactors(
        flattened_inverse_scaling_factors);

  _computed_scaling = true;
  return true;
}

computeScalingJacobian()

virtual void NonlinearSystemBase::computeScalingJacobian ( )

protectedpure virtual

Compute a "Jacobian" for automatic scaling purposes.

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

Referenced by computeScaling().

computeScalingOnce() [1/2]

bool NonlinearSystemBase::computeScalingOnce ( ) const

inline

Definition at line 657 of file NonlinearSystemBase.h.

{ return _compute_scaling_once; }

computeScalingOnce() [2/2]

void NonlinearSystemBase::computeScalingOnce ( bool  compute_scaling_once )

inline

Definition at line 658 of file NonlinearSystemBase.h.

  {
    _compute_scaling_once = compute_scaling_once;
  }

computeScalingResidual()

virtual void NonlinearSystemBase::computeScalingResidual ( )

protectedpure virtual

Compute a "residual" for automatic scaling purposes.

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

Referenced by computeScaling().

computeVariables()

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

inlinevirtualinherited

Definition at line 870 of file SystemBase.h.

{}

computingPreSMOResidual()

bool NonlinearSystemBase::computingPreSMOResidual ( )

inline

Returns true if this system is currently computing the pre-SMO residual for a solve.

Returns

Whether or not we are currently computing the pre-SMO residual.

Definition at line 93 of file NonlinearSystemBase.h.

{ return _computing_pre_smo_residual; }

computingScalingJacobian()

bool SystemBase::computingScalingJacobian ( ) const

inherited

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

Definition at line 1519 of file SystemBase.C.

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

{
  return _subproblem.computingScalingJacobian();
}

constraintJacobians()

void NonlinearSystemBase::constraintJacobians	(	const SparseMatrix< Number > &	jacobian_to_view,
		bool	displaced
	)

Add jacobian contributions from Constraints.

Parameters

jacobian	reference to a read-only view of the Jacobian matrix
displaced	Controls whether to do the displaced Constraints or non-displaced

Definition at line 2302 of file NonlinearSystemBase.C.

Referenced by computeJacobianInternal().

{
  if (!hasMatrix(systemMatrixTag()))
    mooseError("A system matrix is required");

  auto & jacobian = getMatrix(systemMatrixTag());

  if (!_fe_problem.errorOnJacobianNonzeroReallocation())
    LibmeshPetscCall(MatSetOption(static_cast<PetscMatrix<Number> &>(jacobian).mat(),
                                  MAT_NEW_NONZERO_ALLOCATION_ERR,
                                  PETSC_FALSE));
  if (_fe_problem.ignoreZerosInJacobian())
    LibmeshPetscCall(MatSetOption(
        static_cast<PetscMatrix<Number> &>(jacobian).mat(), MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));

  std::vector<numeric_index_type> zero_rows;

  if (displaced)
    mooseAssert(_fe_problem.getDisplacedProblem(),
                "If we're calling this method with displaced = true, then we better well have a "
                "displaced problem");
  auto & subproblem = displaced ? static_cast<SubProblem &>(*_fe_problem.getDisplacedProblem())
                                : static_cast<SubProblem &>(_fe_problem);
  const auto & penetration_locators = subproblem.geomSearchData()._penetration_locators;

  bool constraints_applied;
  if (!_assemble_constraints_separately)
    constraints_applied = false;
  for (const auto & it : penetration_locators)
  {
    if (_assemble_constraints_separately)
    {
      // Reset the constraint_applied flag before each new constraint, as they need to be
      // assembled separately
      constraints_applied = false;
    }
    PenetrationLocator & pen_loc = *(it.second);

    std::vector<dof_id_type> & secondary_nodes = pen_loc._nearest_node._secondary_nodes;

    BoundaryID secondary_boundary = pen_loc._secondary_boundary;
    BoundaryID primary_boundary = pen_loc._primary_boundary;

    zero_rows.clear();
    if (_constraints.hasActiveNodeFaceConstraints(secondary_boundary, displaced))
    {
      const auto & constraints =
          _constraints.getActiveNodeFaceConstraints(secondary_boundary, displaced);

      for (const auto & secondary_node_num : secondary_nodes)
      {
        Node & secondary_node = _mesh.nodeRef(secondary_node_num);

        if (secondary_node.processor_id() == processor_id())
        {
          if (pen_loc._penetration_info[secondary_node_num])
          {
            PenetrationInfo & info = *pen_loc._penetration_info[secondary_node_num];

            reinitNodeFace(secondary_node, secondary_boundary, info, displaced);
            _fe_problem.reinitOffDiagScalars(0);

            for (const auto & nfc : constraints)
            {
              if (nfc->isExplicitConstraint())
                continue;
              // Return if this constraint does not correspond to the primary-secondary pair
              // prepared by the outer loops.
              // This continue statement is required when, e.g. one secondary surface constrains
              // more than one primary surface.
              if (nfc->secondaryBoundary() != secondary_boundary ||
                  nfc->primaryBoundary() != primary_boundary)
                continue;

              nfc->_jacobian = &jacobian_to_view;

              if (nfc->shouldApply())
              {
                constraints_applied = true;

                nfc->prepareShapes(nfc->variable().number());
                nfc->prepareNeighborShapes(nfc->variable().number());

                nfc->computeJacobian();

                if (nfc->overwriteSecondaryJacobian())
                {
                  // Add this variable's dof's row to be zeroed
                  zero_rows.push_back(nfc->variable().nodalDofIndex());
                }

                std::vector<dof_id_type> secondary_dofs(1, nfc->variable().nodalDofIndex());

                // Assume that if the user is overwriting the secondary Jacobian, then they are
                // supplying Jacobians that do not correspond to their other physics
                // (e.g. Kernels), hence we should not apply a scalingFactor that is normally
                // based on the order of their other physics (e.g. Kernels)
                Real scaling_factor =
                    nfc->overwriteSecondaryJacobian() ? 1. : nfc->variable().scalingFactor();

                // Cache the jacobian block for the secondary side
                nfc->addJacobian(_fe_problem.assembly(0, number()),
                                 nfc->_Kee,
                                 secondary_dofs,
                                 nfc->_connected_dof_indices,
                                 scaling_factor);

                // Cache Ken, Kne, Knn
                if (nfc->addCouplingEntriesToJacobian())
                {
                  // Make sure we use a proper scaling factor (e.g. don't use an interior scaling
                  // factor when we're overwriting secondary stuff)
                  nfc->addJacobian(_fe_problem.assembly(0, number()),
                                   nfc->_Ken,
                                   secondary_dofs,
                                   nfc->primaryVariable().dofIndicesNeighbor(),
                                   scaling_factor);

                  // Use _connected_dof_indices to get all the correct columns
                  nfc->addJacobian(_fe_problem.assembly(0, number()),
                                   nfc->_Kne,
                                   nfc->primaryVariable().dofIndicesNeighbor(),
                                   nfc->_connected_dof_indices,
                                   nfc->primaryVariable().scalingFactor());

                  // We've handled Ken and Kne, finally handle Knn
                  _fe_problem.cacheJacobianNeighbor(0);
                }

                // Do the off-diagonals next
                const std::vector<MooseVariableFEBase *> coupled_vars = nfc->getCoupledMooseVars();
                for (const auto & jvar : coupled_vars)
                {
                  // Only compute jacobians for nonlinear variables
                  if (jvar->kind() != Moose::VAR_SOLVER)
                    continue;

                  // Only compute Jacobian entries if this coupling is being used by the
                  // preconditioner
                  if (nfc->variable().number() == jvar->number() ||
                      !_fe_problem.areCoupled(
                          nfc->variable().number(), jvar->number(), this->number()))
                    continue;

                  // Need to zero out the matrices first
                  _fe_problem.prepareAssembly(0);

                  nfc->prepareShapes(nfc->variable().number());
                  nfc->prepareNeighborShapes(jvar->number());

                  nfc->computeOffDiagJacobian(jvar->number());

                  // Cache the jacobian block for the secondary side
                  nfc->addJacobian(_fe_problem.assembly(0, number()),
                                   nfc->_Kee,
                                   secondary_dofs,
                                   nfc->_connected_dof_indices,
                                   scaling_factor);

                  // Cache Ken, Kne, Knn
                  if (nfc->addCouplingEntriesToJacobian())
                  {
                    // Make sure we use a proper scaling factor (e.g. don't use an interior scaling
                    // factor when we're overwriting secondary stuff)
                    nfc->addJacobian(_fe_problem.assembly(0, number()),
                                     nfc->_Ken,
                                     secondary_dofs,
                                     jvar->dofIndicesNeighbor(),
                                     scaling_factor);

                    // Use _connected_dof_indices to get all the correct columns
                    nfc->addJacobian(_fe_problem.assembly(0, number()),
                                     nfc->_Kne,
                                     nfc->variable().dofIndicesNeighbor(),
                                     nfc->_connected_dof_indices,
                                     nfc->variable().scalingFactor());

                    // We've handled Ken and Kne, finally handle Knn
                    _fe_problem.cacheJacobianNeighbor(0);
                  }
                }
              }
            }
          }
        }
      }
    }
    if (_assemble_constraints_separately)
    {
      // See if constraints were applied anywhere
      _communicator.max(constraints_applied);

      if (constraints_applied)
      {
        LibmeshPetscCall(MatSetOption(static_cast<PetscMatrix<Number> &>(jacobian).mat(),
                                      MAT_KEEP_NONZERO_PATTERN, // This is changed in 3.1
                                      PETSC_TRUE));

        jacobian.close();
        jacobian.zero_rows(zero_rows, 0.0);
        jacobian.close();
        _fe_problem.addCachedJacobian(0);
        jacobian.close();
      }
    }
  }
  if (!_assemble_constraints_separately)
  {
    // See if constraints were applied anywhere
    _communicator.max(constraints_applied);

    if (constraints_applied)
    {
      LibmeshPetscCall(MatSetOption(static_cast<PetscMatrix<Number> &>(jacobian).mat(),
                                    MAT_KEEP_NONZERO_PATTERN, // This is changed in 3.1
                                    PETSC_TRUE));

      jacobian.close();
      jacobian.zero_rows(zero_rows, 0.0);
      jacobian.close();
      _fe_problem.addCachedJacobian(0);
      jacobian.close();
    }
  }

  THREAD_ID tid = 0;
  // go over element-element constraint interface
  const auto & element_pair_locators = subproblem.geomSearchData()._element_pair_locators;
  for (const auto & it : element_pair_locators)
  {
    ElementPairLocator & elem_pair_loc = *(it.second);

    if (_constraints.hasActiveElemElemConstraints(it.first, displaced))
    {
      // ElemElemConstraint objects
      const auto & _element_constraints =
          _constraints.getActiveElemElemConstraints(it.first, displaced);

      // go over pair elements
      const std::list<std::pair<const Elem *, const Elem *>> & elem_pairs =
          elem_pair_loc.getElemPairs();
      for (const auto & pr : elem_pairs)
      {
        const Elem * elem1 = pr.first;
        const Elem * elem2 = pr.second;

        if (elem1->processor_id() != processor_id())
          continue;

        const ElementPairInfo & info = elem_pair_loc.getElemPairInfo(pr);

        // for each element process constraints on the
        for (const auto & ec : _element_constraints)
        {
          _fe_problem.setCurrentSubdomainID(elem1, tid);
          subproblem.reinitElemPhys(elem1, info._elem1_constraint_q_point, tid);
          _fe_problem.setNeighborSubdomainID(elem2, tid);
          subproblem.reinitNeighborPhys(elem2, info._elem2_constraint_q_point, tid);

          ec->prepareShapes(ec->variable().number());
          ec->prepareNeighborShapes(ec->variable().number());

          ec->reinit(info);
          ec->computeJacobian();
          _fe_problem.cacheJacobian(tid);
          _fe_problem.cacheJacobianNeighbor(tid);
        }
        _fe_problem.addCachedJacobian(tid);
      }
    }
  }

  // go over NodeElemConstraints
  std::set<dof_id_type> unique_secondary_node_ids;
  constraints_applied = false;
  for (const auto & secondary_id : _mesh.meshSubdomains())
  {
    for (const auto & primary_id : _mesh.meshSubdomains())
    {
      if (_constraints.hasActiveNodeElemConstraints(secondary_id, primary_id, displaced))
      {
        const auto & constraints =
            _constraints.getActiveNodeElemConstraints(secondary_id, primary_id, displaced);

        // get unique set of ids of all nodes on current block
        unique_secondary_node_ids.clear();
        const MeshBase & meshhelper = _mesh.getMesh();
        for (const auto & elem : as_range(meshhelper.active_subdomain_elements_begin(secondary_id),
                                          meshhelper.active_subdomain_elements_end(secondary_id)))
        {
          for (auto & n : elem->node_ref_range())
            unique_secondary_node_ids.insert(n.id());
        }

        for (auto secondary_node_id : unique_secondary_node_ids)
        {
          const Node & secondary_node = _mesh.nodeRef(secondary_node_id);
          // check if secondary node is on current processor
          if (secondary_node.processor_id() == processor_id())
          {
            // This reinits the variables that exist on the secondary node
            _fe_problem.reinitNodeFace(&secondary_node, secondary_id, 0);

            // This will set aside residual and jacobian space for the variables that have dofs
            // on the secondary node
            _fe_problem.prepareAssembly(0);
            _fe_problem.reinitOffDiagScalars(0);

            for (const auto & nec : constraints)
            {
              if (nec->shouldApply())
              {
                constraints_applied = true;

                nec->_jacobian = &jacobian_to_view;
                nec->prepareShapes(nec->variable().number());
                nec->prepareNeighborShapes(nec->variable().number());

                nec->computeJacobian();

                if (nec->overwriteSecondaryJacobian())
                {
                  // Add this variable's dof's row to be zeroed
                  zero_rows.push_back(nec->variable().nodalDofIndex());
                }

                std::vector<dof_id_type> secondary_dofs(1, nec->variable().nodalDofIndex());

                // Cache the jacobian block for the secondary side
                nec->addJacobian(_fe_problem.assembly(0, number()),
                                 nec->_Kee,
                                 secondary_dofs,
                                 nec->_connected_dof_indices,
                                 nec->variable().scalingFactor());

                // Cache the jacobian block for the primary side
                nec->addJacobian(_fe_problem.assembly(0, number()),
                                 nec->_Kne,
                                 nec->primaryVariable().dofIndicesNeighbor(),
                                 nec->_connected_dof_indices,
                                 nec->primaryVariable().scalingFactor());

                _fe_problem.cacheJacobian(0);
                _fe_problem.cacheJacobianNeighbor(0);

                // Do the off-diagonals next
                const std::vector<MooseVariableFEBase *> coupled_vars = nec->getCoupledMooseVars();
                for (const auto & jvar : coupled_vars)
                {
                  // Only compute jacobians for nonlinear variables
                  if (jvar->kind() != Moose::VAR_SOLVER)
                    continue;

                  // Only compute Jacobian entries if this coupling is being used by the
                  // preconditioner
                  if (nec->variable().number() == jvar->number() ||
                      !_fe_problem.areCoupled(
                          nec->variable().number(), jvar->number(), this->number()))
                    continue;

                  // Need to zero out the matrices first
                  _fe_problem.prepareAssembly(0);

                  nec->prepareShapes(nec->variable().number());
                  nec->prepareNeighborShapes(jvar->number());

                  nec->computeOffDiagJacobian(jvar->number());

                  // Cache the jacobian block for the secondary side
                  nec->addJacobian(_fe_problem.assembly(0, number()),
                                   nec->_Kee,
                                   secondary_dofs,
                                   nec->_connected_dof_indices,
                                   nec->variable().scalingFactor());

                  // Cache the jacobian block for the primary side
                  nec->addJacobian(_fe_problem.assembly(0, number()),
                                   nec->_Kne,
                                   nec->variable().dofIndicesNeighbor(),
                                   nec->_connected_dof_indices,
                                   nec->variable().scalingFactor());

                  _fe_problem.cacheJacobian(0);
                  _fe_problem.cacheJacobianNeighbor(0);
                }
              }
            }
          }
        }
      }
    }
  }
  // See if constraints were applied anywhere
  _communicator.max(constraints_applied);

  if (constraints_applied)
  {
    LibmeshPetscCall(MatSetOption(static_cast<PetscMatrix<Number> &>(jacobian).mat(),
                                  MAT_KEEP_NONZERO_PATTERN, // This is changed in 3.1
                                  PETSC_TRUE));

    jacobian.close();
    jacobian.zero_rows(zero_rows, 0.0);
    jacobian.close();
    _fe_problem.addCachedJacobian(0);
    jacobian.close();
  }
}

constraintResiduals()

void NonlinearSystemBase::constraintResiduals	(	NumericVector< Number > &	residual,
		bool	displaced
	)

Add residual contributions from Constraints.

Parameters

residual	- reference to the residual vector where constraint contributions will be computed
displaced	Controls whether to do the displaced Constraints or non-displaced

Definition at line 1329 of file NonlinearSystemBase.C.

Referenced by computeResidualInternal().

{
  // Make sure the residual is in a good state
  residual.close();

  if (displaced)
    mooseAssert(_fe_problem.getDisplacedProblem(),
                "If we're calling this method with displaced = true, then we better well have a "
                "displaced problem");
  auto & subproblem = displaced ? static_cast<SubProblem &>(*_fe_problem.getDisplacedProblem())
                                : static_cast<SubProblem &>(_fe_problem);
  const auto & penetration_locators = subproblem.geomSearchData()._penetration_locators;

  bool constraints_applied;
  bool residual_has_inserted_values = false;
  if (!_assemble_constraints_separately)
    constraints_applied = false;
  for (const auto & it : penetration_locators)
  {
    if (_assemble_constraints_separately)
    {
      // Reset the constraint_applied flag before each new constraint, as they need to be
      // assembled separately
      constraints_applied = false;
    }
    PenetrationLocator & pen_loc = *(it.second);

    std::vector<dof_id_type> & secondary_nodes = pen_loc._nearest_node._secondary_nodes;

    BoundaryID secondary_boundary = pen_loc._secondary_boundary;
    BoundaryID primary_boundary = pen_loc._primary_boundary;

    bool has_writable_variables(false);

    if (_constraints.hasActiveNodeFaceConstraints(secondary_boundary, displaced))
    {
      const auto & constraints =
          _constraints.getActiveNodeFaceConstraints(secondary_boundary, displaced);

      for (unsigned int i = 0; i < secondary_nodes.size(); i++)
      {
        dof_id_type secondary_node_num = secondary_nodes[i];
        Node & secondary_node = _mesh.nodeRef(secondary_node_num);

        if (secondary_node.processor_id() == processor_id())
        {
          if (pen_loc._penetration_info[secondary_node_num])
          {
            PenetrationInfo & info = *pen_loc._penetration_info[secondary_node_num];

            reinitNodeFace(secondary_node, secondary_boundary, info, displaced);

            for (const auto & nfc : constraints)
            {
              // Return if this constraint does not correspond to the primary-secondary pair
              // prepared by the outer loops.
              // This continue statement is required when, e.g. one secondary surface constrains
              // more than one primary surface.
              if (nfc->secondaryBoundary() != secondary_boundary ||
                  nfc->primaryBoundary() != primary_boundary)
                continue;

              if (nfc->shouldApply())
              {
                constraints_applied = true;
                nfc->computeResidual();

                if (nfc->overwriteSecondaryResidual())
                {
                  // The below will actually overwrite the residual for every single dof that
                  // lives on the node. We definitely don't want to do that!
                  // _fe_problem.setResidual(residual, 0);

                  const auto & secondary_var = nfc->variable();
                  const auto & secondary_dofs = secondary_var.dofIndices();
                  mooseAssert(secondary_dofs.size() == secondary_var.count(),
                              "We are on a node so there should only be one dof per variable (for "
                              "an ArrayVariable we should have a number of dofs equal to the "
                              "number of components");

                  // Assume that if the user is overwriting the secondary residual, then they are
                  // supplying residuals that do not correspond to their other physics
                  // (e.g. Kernels), hence we should not apply a scalingFactor that is normally
                  // based on the order of their other physics (e.g. Kernels)
                  std::vector<Number> values = {nfc->secondaryResidual()};
                  residual.insert(values, secondary_dofs);
                  residual_has_inserted_values = true;
                }
                else
                  _fe_problem.cacheResidual(0);
                _fe_problem.cacheResidualNeighbor(0);
              }
              if (nfc->hasWritableCoupledVariables())
              {
                Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
                has_writable_variables = true;
                for (auto * var : nfc->getWritableCoupledVariables())
                {
                  if (var->isNodalDefined())
                    var->insert(_fe_problem.getAuxiliarySystem().solution());
                }
              }
            }
          }
        }
      }
    }
    _communicator.max(has_writable_variables);

    if (has_writable_variables)
    {
      // Explicit contact dynamic constraints write to auxiliary variables and update the old
      // displacement solution on the constraint boundaries. Close solutions and update system
      // accordingly.
      _fe_problem.getAuxiliarySystem().solution().close();
      _fe_problem.getAuxiliarySystem().system().update();
      solutionOld().close();
    }

    if (_assemble_constraints_separately)
    {
      // Make sure that secondary contribution to primary are assembled, and ghosts have been
      // exchanged, as current primaries might become secondaries on next iteration and will need to
      // contribute their former secondaries' contributions to the future primaries. See if
      // constraints were applied anywhere
      _communicator.max(constraints_applied);

      if (constraints_applied)
      {
        // If any of the above constraints inserted values in the residual, it needs to be
        // assembled before adding the cached residuals below.
        _communicator.max(residual_has_inserted_values);
        if (residual_has_inserted_values)
        {
          residual.close();
          residual_has_inserted_values = false;
        }
        _fe_problem.addCachedResidualDirectly(residual, 0);
        residual.close();

        if (_need_residual_ghosted)
          *_residual_ghosted = residual;
      }
    }
  }
  if (!_assemble_constraints_separately)
  {
    _communicator.max(constraints_applied);

    if (constraints_applied)
    {
      // If any of the above constraints inserted values in the residual, it needs to be assembled
      // before adding the cached residuals below.
      _communicator.max(residual_has_inserted_values);
      if (residual_has_inserted_values)
        residual.close();

      _fe_problem.addCachedResidualDirectly(residual, 0);
      residual.close();

      if (_need_residual_ghosted)
        *_residual_ghosted = residual;
    }
  }

  // go over element-element constraint interface
  THREAD_ID tid = 0;
  const auto & element_pair_locators = subproblem.geomSearchData()._element_pair_locators;
  for (const auto & it : element_pair_locators)
  {
    ElementPairLocator & elem_pair_loc = *(it.second);

    if (_constraints.hasActiveElemElemConstraints(it.first, displaced))
    {
      // ElemElemConstraint objects
      const auto & _element_constraints =
          _constraints.getActiveElemElemConstraints(it.first, displaced);

      // go over pair elements
      const std::list<std::pair<const Elem *, const Elem *>> & elem_pairs =
          elem_pair_loc.getElemPairs();
      for (const auto & pr : elem_pairs)
      {
        const Elem * elem1 = pr.first;
        const Elem * elem2 = pr.second;

        if (elem1->processor_id() != processor_id())
          continue;

        const ElementPairInfo & info = elem_pair_loc.getElemPairInfo(pr);

        // for each element process constraints on the
        for (const auto & ec : _element_constraints)
        {
          _fe_problem.setCurrentSubdomainID(elem1, tid);
          subproblem.reinitElemPhys(elem1, info._elem1_constraint_q_point, tid);
          _fe_problem.setNeighborSubdomainID(elem2, tid);
          subproblem.reinitNeighborPhys(elem2, info._elem2_constraint_q_point, tid);

          ec->prepareShapes(ec->variable().number());
          ec->prepareNeighborShapes(ec->variable().number());

          ec->reinit(info);
          ec->computeResidual();
          _fe_problem.cacheResidual(tid);
          _fe_problem.cacheResidualNeighbor(tid);
        }
        _fe_problem.addCachedResidual(tid);
      }
    }
  }

  // go over NodeElemConstraints
  std::set<dof_id_type> unique_secondary_node_ids;

  constraints_applied = false;
  residual_has_inserted_values = false;
  bool has_writable_variables = false;
  for (const auto & secondary_id : _mesh.meshSubdomains())
  {
    for (const auto & primary_id : _mesh.meshSubdomains())
    {
      if (_constraints.hasActiveNodeElemConstraints(secondary_id, primary_id, displaced))
      {
        const auto & constraints =
            _constraints.getActiveNodeElemConstraints(secondary_id, primary_id, displaced);

        // get unique set of ids of all nodes on current block
        unique_secondary_node_ids.clear();
        const MeshBase & meshhelper = _mesh.getMesh();
        for (const auto & elem : as_range(meshhelper.active_subdomain_elements_begin(secondary_id),
                                          meshhelper.active_subdomain_elements_end(secondary_id)))
        {
          for (auto & n : elem->node_ref_range())
            unique_secondary_node_ids.insert(n.id());
        }

        for (auto secondary_node_id : unique_secondary_node_ids)
        {
          Node & secondary_node = _mesh.nodeRef(secondary_node_id);
          // check if secondary node is on current processor
          if (secondary_node.processor_id() == processor_id())
          {
            // This reinits the variables that exist on the secondary node
            _fe_problem.reinitNodeFace(&secondary_node, secondary_id, 0);

            // This will set aside residual and jacobian space for the variables that have dofs
            // on the secondary node
            _fe_problem.prepareAssembly(0);

            for (const auto & nec : constraints)
            {
              if (nec->shouldApply())
              {
                constraints_applied = true;
                nec->computeResidual();

                if (nec->overwriteSecondaryResidual())
                {
                  _fe_problem.setResidual(residual, 0);
                  residual_has_inserted_values = true;
                }
                else
                  _fe_problem.cacheResidual(0);
                _fe_problem.cacheResidualNeighbor(0);
              }
              if (nec->hasWritableCoupledVariables())
              {
                Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
                has_writable_variables = true;
                for (auto * var : nec->getWritableCoupledVariables())
                {
                  if (var->isNodalDefined())
                    var->insert(_fe_problem.getAuxiliarySystem().solution());
                }
              }
            }
            _fe_problem.addCachedResidual(0);
          }
        }
      }
    }
  }
  _communicator.max(constraints_applied);

  if (constraints_applied)
  {
    // If any of the above constraints inserted values in the residual, it needs to be assembled
    // before adding the cached residuals below.
    _communicator.max(residual_has_inserted_values);
    if (residual_has_inserted_values)
      residual.close();

    _fe_problem.addCachedResidualDirectly(residual, 0);
    residual.close();

    if (_need_residual_ghosted)
      *_residual_ghosted = residual;
  }
  _communicator.max(has_writable_variables);

  if (has_writable_variables)
  {
    // Explicit contact dynamic constraints write to auxiliary variables and update the old
    // displacement solution on the constraint boundaries. Close solutions and update system
    // accordingly.
    _fe_problem.getAuxiliarySystem().solution().close();
    _fe_problem.getAuxiliarySystem().system().update();
    solutionOld().close();
  }

  // We may have additional tagged vectors that also need to be accumulated
  _fe_problem.addCachedResidual(0);
}

containsTimeKernel()

bool NonlinearSystemBase::containsTimeKernel ( )

overridevirtual

If the system has a kernel that corresponds to a time derivative.

Implements SolverSystem.

Definition at line 3739 of file NonlinearSystemBase.C.

Referenced by EigenExecutionerBase::checkIntegrity(), and Eigenvalue::checkIntegrity().

{
  auto & time_kernels = _kernels.getVectorTagObjectWarehouse(timeVectorTag(), 0);

  return time_kernels.hasActiveObjects();
}

converged()

virtual bool SolverSystem::converged ( )

pure virtualinherited

Returns the convergence state.

Returns

true if converged, otherwise false

Implemented in NonlinearEigenSystem, NonlinearEigenSystem, NonlinearSystem, LinearSystem, DumpObjectsLinearSystem, and DumpObjectsNonlinearSystem.

copyOldSolutions()

void SystemBase::copyOldSolutions ( )

virtualinherited

Shifts the solutions backwards in time.

Definition at line 1288 of file SystemBase.C.

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

{
  // Copying the solutions backward so the current solution will become the old, and the old will
  // become older. 0 index is for time, 1 would be nonlinear iteration.
  const auto states = _solution_states[0].size();
  if (states > 1)
    for (unsigned int i = states - 1; i > 0; --i)
      solutionState(i) = solutionState(i - 1);

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

copyPreviousNonlinearSolutions()

void SystemBase::copyPreviousNonlinearSolutions ( )

virtualinherited

Shifts the solutions backwards in nonlinear iteration history.

Definition at line 1271 of file SystemBase.C.

Referenced by SystemBase::copySolutionsBackwards().

{
  // 1 is for nonlinear, 0 is for time, we do this for nonlinear only here
  const auto states = _solution_states[1].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 1260 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 1634 of file SystemBase.C.

{
  _time_integrators = other_sys._time_integrators;
}

copyVars()

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

inherited

Definition at line 1185 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 & SolverSystem::currentSolution ( ) const

inlinefinaloverridevirtualinherited

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 117 of file SolverSystem.h.

Referenced by FEProblemBase::computeDamping(), FEProblemBase::computeLinearSystemSys(), FEProblemBase::computeResidualL2Norm(), and AB2PredictorCorrector::step().

{
  return _current_solution;
}

customSetup()

void NonlinearSystemBase::customSetup ( const ExecFlagType &  exec_type )

overridevirtual

Reimplemented from SystemBase.

Definition at line 360 of file NonlinearSystemBase.C.

{
  SolverSystem::customSetup(exec_type);

  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _kernels.customSetup(exec_type, tid);
    _nodal_kernels.customSetup(exec_type, tid);
    _dirac_kernels.customSetup(exec_type, tid);
    if (_doing_dg)
      _dg_kernels.customSetup(exec_type, tid);
    _interface_kernels.customSetup(exec_type, tid);
    _element_dampers.customSetup(exec_type, tid);
    _nodal_dampers.customSetup(exec_type, tid);
    _integrated_bcs.customSetup(exec_type, tid);

    if (_fe_problem.haveFV())
    {
      std::vector<FVFluxBC *> bcs;
      _fe_problem.theWarehouse()
          .query()
          .template condition<AttribSystem>("FVFluxBC")
          .template condition<AttribThread>(tid)
          .queryInto(bcs);

      std::vector<FVInterfaceKernel *> iks;
      _fe_problem.theWarehouse()
          .query()
          .template condition<AttribSystem>("FVInterfaceKernel")
          .template condition<AttribThread>(tid)
          .queryInto(iks);

      std::vector<FVFluxKernel *> kernels;
      _fe_problem.theWarehouse()
          .query()
          .template condition<AttribSystem>("FVFluxKernel")
          .template condition<AttribThread>(tid)
          .queryInto(kernels);

      for (auto * bc : bcs)
        bc->customSetup(exec_type);
      for (auto * ik : iks)
        ik->customSetup(exec_type);
      for (auto * kernel : kernels)
        kernel->customSetup(exec_type);
    }
  }
  _scalar_kernels.customSetup(exec_type);
  _constraints.customSetup(exec_type);
  _general_dampers.customSetup(exec_type);
  _nodal_bcs.customSetup(exec_type);
}

deactiveAllMatrixTags()

void SystemBase::deactiveAllMatrixTags ( )

virtualinherited

Make matrices inactive.

Definition at line 1126 of file SystemBase.C.

Referenced by computeResidualTags(), and setInitialSolution().

{
  auto num_matrix_tags = _subproblem.numMatrixTags();

  _matrix_tag_active_flags.resize(num_matrix_tags);

  for (decltype(num_matrix_tags) tag = 0; tag < num_matrix_tags; tag++)
    _matrix_tag_active_flags[tag] = false;
}

deactiveMatrixTag()

void SystemBase::deactiveMatrixTag ( TagID  tag )

virtualinherited

deactive a matrix for tag

Definition at line 1114 of file SystemBase.C.

{
  mooseAssert(_subproblem.matrixTagExists(tag),
              "Cannot deactivate Matrix with matrix_tag : " << tag << "that does not exist");

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

  _matrix_tag_active_flags[tag] = false;
}

debuggingResiduals()

void NonlinearSystemBase::debuggingResiduals ( bool  state )

inline

Definition at line 551 of file NonlinearSystemBase.h.

{ _debugging_residuals = state; }

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 310 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 303 of file SystemBase.h.

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

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

destroyColoring()

void NonlinearSystemBase::destroyColoring

(

)

Destroy the coloring object if it exists.

Definition at line 4120 of file NonlinearSystemBase.C.

Referenced by LStableDirk2::solve(), LStableDirk3::solve(), and LStableDirk4::solve().

{
  if (matrixFromColoring())
    LibmeshPetscCall(MatFDColoringDestroy(&_fdcoloring));
}

disassociateDefaultMatrixTags()

void SystemBase::disassociateDefaultMatrixTags ( )

virtualinherited

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

Reimplemented in DisplacedSystem.

Definition at line 1093 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 998 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 1071 of file SystemBase.C.

Referenced by 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 1082 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(), 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 987 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 1165 of file SystemBase.C.

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

{
  return system().get_dof_map();
}

dofMap() [2/2]

const DofMap & SystemBase::dofMap ( ) const

virtualinherited

Gets const reference to the dof map.

Definition at line 1171 of file SystemBase.C.

{
  return system().get_dof_map();
}

doingDG()

bool NonlinearSystemBase::doingDG

(

)

const

Getter for _doing_dg.

Definition at line 3778 of file NonlinearSystemBase.C.

{
  return _doing_dg;
}

duDotDotDu() [1/2]

virtual Number& SystemBase::duDotDotDu ( )

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 248 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 250 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 1668 of file SystemBase.C.

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

{
  return _du_dot_du[var_num];
}

duDotDus()

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 247 of file SystemBase.h.

Referenced by DisplacedSystem::duDotDus().

{ return _du_dot_du; }

enforceNodalConstraintsJacobian()

void NonlinearSystemBase::enforceNodalConstraintsJacobian ( )

protected

Definition at line 1097 of file NonlinearSystemBase.C.

Referenced by computeJacobianInternal().

{
  if (!hasMatrix(systemMatrixTag()))
    mooseError(" A system matrix is required");

  auto & jacobian = getMatrix(systemMatrixTag());
  THREAD_ID tid = 0; // constraints are going to be done single-threaded

  if (_constraints.hasActiveNodalConstraints())
  {
    const auto & ncs = _constraints.getActiveNodalConstraints();
    for (const auto & nc : ncs)
    {
      std::vector<dof_id_type> & secondary_node_ids = nc->getSecondaryNodeId();
      std::vector<dof_id_type> & primary_node_ids = nc->getPrimaryNodeId();

      if ((secondary_node_ids.size() > 0) && (primary_node_ids.size() > 0))
      {
        _fe_problem.reinitNodes(primary_node_ids, tid);
        _fe_problem.reinitNodesNeighbor(secondary_node_ids, tid);
        nc->computeJacobian(jacobian);
      }
    }
    _fe_problem.addCachedJacobian(tid);
  }
}

enforceNodalConstraintsResidual()

void NonlinearSystemBase::enforceNodalConstraintsResidual ( NumericVector< Number > &  residual )

protected

Enforce nodal constraints.

Definition at line 1072 of file NonlinearSystemBase.C.

Referenced by computeResidualInternal().

{
  THREAD_ID tid = 0; // constraints are going to be done single-threaded
  residual.close();
  if (_constraints.hasActiveNodalConstraints())
  {
    const auto & ncs = _constraints.getActiveNodalConstraints();
    for (const auto & nc : ncs)
    {
      std::vector<dof_id_type> & secondary_node_ids = nc->getSecondaryNodeId();
      std::vector<dof_id_type> & primary_node_ids = nc->getPrimaryNodeId();

      if ((secondary_node_ids.size() > 0) && (primary_node_ids.size() > 0))
      {
        _fe_problem.reinitNodes(primary_node_ids, tid);
        _fe_problem.reinitNodesNeighbor(secondary_node_ids, tid);
        nc->computeResidual(residual);
      }
    }
    _fe_problem.addCachedResidualDirectly(residual, tid);
    residual.close();
  }
}

feProblem() [1/2]

FEProblemBase& SystemBase::feProblem ( )

inlineinherited

Definition at line 103 of file SystemBase.h.

Referenced by DMMooseGetEmbedding_Private(), and DMSetUp_Moose_Pre().

{ return _fe_problem; }

feProblem() [2/2]

const FEProblemBase& SystemBase::feProblem ( ) const

inlineinherited

Definition at line 104 of file SystemBase.h.

{ return _fe_problem; }

finalNonlinearResidual()

Real NonlinearSystemBase::finalNonlinearResidual ( ) const

inline

Return the final nonlinear residual.

Definition at line 537 of file NonlinearSystemBase.h.

{ return _final_residual; }

findImplicitGeometricCouplingEntries()

void NonlinearSystemBase::findImplicitGeometricCouplingEntries ( GeometricSearchData &  geom_search_data, std::unordered_map< dof_id_type, std::vector< dof_id_type >> &  graph  )

private

Finds the implicit sparsity graph between geometrically related dofs.

Definition at line 2169 of file NonlinearSystemBase.C.

Referenced by addImplicitGeometricCouplingEntries(), and augmentSparsity().

{
  const auto & node_to_elem_map = _mesh.nodeToElemMap();
  const auto & nearest_node_locators = geom_search_data._nearest_node_locators;
  for (const auto & it : nearest_node_locators)
  {
    std::vector<dof_id_type> & secondary_nodes = it.second->_secondary_nodes;

    for (const auto & secondary_node : secondary_nodes)
    {
      std::set<dof_id_type> unique_secondary_indices;
      std::set<dof_id_type> unique_primary_indices;

      auto node_to_elem_pair = node_to_elem_map.find(secondary_node);
      if (node_to_elem_pair != node_to_elem_map.end())
      {
        const std::vector<dof_id_type> & elems = node_to_elem_pair->second;

        // Get the dof indices from each elem connected to the node
        for (const auto & cur_elem : elems)
        {
          std::vector<dof_id_type> dof_indices;
          dofMap().dof_indices(_mesh.elemPtr(cur_elem), dof_indices);

          for (const auto & dof : dof_indices)
            unique_secondary_indices.insert(dof);
        }
      }

      std::vector<dof_id_type> primary_nodes = it.second->_neighbor_nodes[secondary_node];

      for (const auto & primary_node : primary_nodes)
      {
        auto primary_node_to_elem_pair = node_to_elem_map.find(primary_node);
        mooseAssert(primary_node_to_elem_pair != node_to_elem_map.end(),
                    "Missing entry in node to elem map");
        const std::vector<dof_id_type> & primary_node_elems = primary_node_to_elem_pair->second;

        // Get the dof indices from each elem connected to the node
        for (const auto & cur_elem : primary_node_elems)
        {
          std::vector<dof_id_type> dof_indices;
          dofMap().dof_indices(_mesh.elemPtr(cur_elem), dof_indices);

          for (const auto & dof : dof_indices)
            unique_primary_indices.insert(dof);
        }
      }

      for (const auto & secondary_id : unique_secondary_indices)
        for (const auto & primary_id : unique_primary_indices)
        {
          graph[secondary_id].push_back(primary_id);
          graph[primary_id].push_back(secondary_id);
        }
    }
  }

  // handle node-to-node constraints
  const auto & ncs = _constraints.getActiveNodalConstraints();
  for (const auto & nc : ncs)
  {
    std::vector<dof_id_type> primary_dofs;
    std::vector<dof_id_type> & primary_node_ids = nc->getPrimaryNodeId();
    for (const auto & node_id : primary_node_ids)
    {
      Node * node = _mesh.queryNodePtr(node_id);
      if (node && node->processor_id() == this->processor_id())
      {
        getNodeDofs(node_id, primary_dofs);
      }
    }

    _communicator.allgather(primary_dofs);

    std::vector<dof_id_type> secondary_dofs;
    std::vector<dof_id_type> & secondary_node_ids = nc->getSecondaryNodeId();
    for (const auto & node_id : secondary_node_ids)
    {
      Node * node = _mesh.queryNodePtr(node_id);
      if (node && node->processor_id() == this->processor_id())
      {
        getNodeDofs(node_id, secondary_dofs);
      }
    }

    _communicator.allgather(secondary_dofs);

    for (const auto & primary_id : primary_dofs)
      for (const auto & secondary_id : secondary_dofs)
      {
        graph[primary_id].push_back(secondary_id);
        graph[secondary_id].push_back(primary_id);
      }
  }

  // Make every entry sorted and unique
  for (auto & it : graph)
  {
    std::vector<dof_id_type> & row = it.second;
    std::sort(row.begin(), row.end());
    std::vector<dof_id_type>::iterator uit = std::unique(row.begin(), row.end());
    row.resize(uit - row.begin());
  }
}

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 1051 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 117 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 138 of file SystemBase.C.

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

getConstraintWarehouse()

const ConstraintWarehouse& NonlinearSystemBase::getConstraintWarehouse ( ) const

inline

Definition at line 611 of file NonlinearSystemBase.h.

{ return _constraints; }

getCurrentNonlinearIterationNumber()

virtual unsigned int NonlinearSystemBase::getCurrentNonlinearIterationNumber ( )

pure virtual

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

getDGKernelWarehouse()

MooseObjectTagWarehouse<DGKernelBase>& NonlinearSystemBase::getDGKernelWarehouse ( )

inline

Definition at line 587 of file NonlinearSystemBase.h.

Referenced by ExplicitTimeIntegrator::initialSetup().

{ return _dg_kernels; }

getDiracKernelWarehouse()

MooseObjectTagWarehouse<DiracKernelBase>& NonlinearSystemBase::getDiracKernelWarehouse ( )

inline

Definition at line 592 of file NonlinearSystemBase.h.

{ return _dirac_kernels; }

getElementDamperWarehouse()

const MooseObjectWarehouse<ElementDamper>& NonlinearSystemBase::getElementDamperWarehouse ( ) const

inline

Definition at line 603 of file NonlinearSystemBase.h.

Referenced by ComputeElemDampingThread::onElement(), and ComputeElemDampingThread::printGeneralExecutionInformation().

  {
    return _element_dampers;
  }

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 110 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 131 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 124 of file SystemBase.C.

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

getHDGKernelWarehouse()

MooseObjectTagWarehouse<HDGKernel>& NonlinearSystemBase::getHDGKernelWarehouse ( )

inline

Definition at line 602 of file NonlinearSystemBase.h.

{ return _hybridized_kernels; }

getIntegratedBCWarehouse() [1/2]

MooseObjectTagWarehouse<IntegratedBCBase>& NonlinearSystemBase::getIntegratedBCWarehouse ( )

inline

Definition at line 593 of file NonlinearSystemBase.h.

Referenced by BoundaryElemIntegrityCheckThread::operator()().

{ return _integrated_bcs; }

getIntegratedBCWarehouse() [2/2]

const MooseObjectTagWarehouse<IntegratedBCBase>& NonlinearSystemBase::getIntegratedBCWarehouse ( ) const

inline

Return the IntegratedBCBase warehouse.

Definition at line 621 of file NonlinearSystemBase.h.

  {
    return _integrated_bcs;
  }

getInterfaceKernelWarehouse()

MooseObjectTagWarehouse<InterfaceKernelBase>& NonlinearSystemBase::getInterfaceKernelWarehouse ( )

inline

Definition at line 588 of file NonlinearSystemBase.h.

  {
    return _interface_kernels;
  }

getKernelWarehouse() [1/2]

MooseObjectTagWarehouse<KernelBase>& NonlinearSystemBase::getKernelWarehouse ( )

inline

Access functions to Warehouses from outside NonlinearSystemBase.

Definition at line 585 of file NonlinearSystemBase.h.

Referenced by ExplicitTimeIntegrator::initialSetup(), DOFMapOutput::output(), and BlockRestrictionDebugOutput::printBlockRestrictionMap().

{ return _kernels; }

getKernelWarehouse() [2/2]

const MooseObjectTagWarehouse<KernelBase>& NonlinearSystemBase::getKernelWarehouse ( ) const

inline

Definition at line 586 of file NonlinearSystemBase.h.

{ return _kernels; }

getMatrix() [1/2]

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

virtualinherited

Get a raw SparseMatrix.

Reimplemented in DisplacedSystem.

Definition at line 1007 of file SystemBase.C.

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

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

  return *_tagged_matrices[tag];
}

getMatrix() [2/2]

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

virtualinherited

Get a raw SparseMatrix.

Reimplemented in DisplacedSystem.

Definition at line 1025 of file SystemBase.C.

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

  return *_tagged_matrices[tag];
}

getMaxVariableNumber()

unsigned int SystemBase::getMaxVariableNumber ( ) const

inlineinherited

Returns the maximum number of all variables on the system.

Definition at line 868 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 SystemBase::getMinQuadratureOrder ( )

virtualinherited

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

Returns

The minimal order of quadrature

Reimplemented in AuxiliarySystem.

Definition at line 240 of file SystemBase.C.

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

  return order;
}

getMooseKSPNormType()

Moose::MooseKSPNormType SolverSystem::getMooseKSPNormType ( )

inlineinherited

Get the norm in which the linear convergence is measured.

Definition at line 87 of file SolverSystem.h.

Referenced by Moose::PetscSupport::petscSetDefaultKSPNormType().

{ return _ksp_norm; }

getNodalBCWarehouse()

const MooseObjectTagWarehouse<NodalBCBase>& NonlinearSystemBase::getNodalBCWarehouse ( ) const

inline

Return the NodalBCBase warehouse.

Definition at line 616 of file NonlinearSystemBase.h.

{ return _nodal_bcs; }

getNodalDamperWarehouse()

const MooseObjectWarehouse<NodalDamper>& NonlinearSystemBase::getNodalDamperWarehouse ( ) const

inline

Definition at line 607 of file NonlinearSystemBase.h.

Referenced by ComputeNodalDampingThread::onNode(), and ComputeNodalDampingThread::printGeneralExecutionInformation().

  {
    return _nodal_dampers;
  }

getNodalKernelWarehouse()

const MooseObjectTagWarehouse<NodalKernelBase>& NonlinearSystemBase::getNodalKernelWarehouse ( ) const

inline

Definition at line 598 of file NonlinearSystemBase.h.

Referenced by ExplicitTimeIntegrator::initialSetup().

  {
    return _nodal_kernels;
  }

getNodeDofs()

void NonlinearSystemBase::getNodeDofs ( dof_id_type  node_id, std::vector< dof_id_type > &  dofs  )

protected

Definition at line 2156 of file NonlinearSystemBase.C.

Referenced by findImplicitGeometricCouplingEntries().

{
  const Node & node = _mesh.nodeRef(node_id);
  unsigned int s = number();
  if (node.has_dofs(s))
  {
    for (unsigned int v = 0; v < nVariables(); v++)
      for (unsigned int c = 0; c < node.n_comp(s, v); c++)
        dofs.push_back(node.dof_number(s, v, c));
  }
}

getPCSide()

Moose::PCSideType SolverSystem::getPCSide ( )

inlineinherited

Get the current preconditioner side.

Definition at line 76 of file SolverSystem.h.

Referenced by Moose::PetscSupport::petscSetDefaultPCSide().

{ return _pc_side; }

getPreconditioner()

MoosePreconditioner const * NonlinearSystemBase::getPreconditioner

(

)

const

Definition at line 3562 of file NonlinearSystemBase.C.

Referenced by ConsoleUtils::outputExecutionInformation().

{
  return _preconditioner.get();
}

getPredictor()

Predictor* NonlinearSystemBase::getPredictor ( )

inline

Definition at line 556 of file NonlinearSystemBase.h.

Referenced by AB2PredictorCorrector::estimateTimeError().

{ return _predictor.get(); }

getResidualNonTimeVector()

NumericVector< Number > & NonlinearSystemBase::getResidualNonTimeVector

(

)

Return a numeric vector that is associated with the nontime tag.

Definition at line 1032 of file NonlinearSystemBase.C.

Referenced by PseudoTimestep::currentResidualNorm(), NonlinearSystemBase(), and residualVector().

{
  if (!_Re_non_time)
  {
    _Re_non_time_tag = _fe_problem.addVectorTag("NONTIME");

    // Most applications don't need the expense of ghosting
    ParallelType ptype = _need_residual_ghosted ? GHOSTED : PARALLEL;
    _Re_non_time = &addVector(_Re_non_time_tag, false, ptype);
  }
  else if (_need_residual_ghosted && _Re_non_time->type() == PARALLEL)
  {
    const auto vector_name = _subproblem.vectorTagName(_Re_non_time_tag);

    // If an application changes its mind, the libMesh API lets us
    // change the vector.
    _Re_non_time = &system().add_vector(vector_name, false, GHOSTED);
  }

  return *_Re_non_time;
}

getResidualTimeVector()

NumericVector< Number > & NonlinearSystemBase::getResidualTimeVector

(

)

Return a numeric vector that is associated with the time tag.

Definition at line 1009 of file NonlinearSystemBase.C.

Referenced by residualVector().

{
  if (!_Re_time)
  {
    _Re_time_tag = _fe_problem.addVectorTag("TIME");

    // Most applications don't need the expense of ghosting
    ParallelType ptype = _need_residual_ghosted ? GHOSTED : PARALLEL;
    _Re_time = &addVector(_Re_time_tag, false, ptype);
  }
  else if (_need_residual_ghosted && _Re_time->type() == PARALLEL)
  {
    const auto vector_name = _subproblem.vectorTagName(_Re_time_tag);

    // If an application changes its mind, the libMesh API lets us
    // change the vector.
    _Re_time = &system().add_vector(vector_name, false, GHOSTED);
  }

  return *_Re_time;
}

getScalarKernelWarehouse()

const MooseObjectTagWarehouse<ScalarKernelBase>& NonlinearSystemBase::getScalarKernelWarehouse ( ) const

inline

Definition at line 594 of file NonlinearSystemBase.h.

Referenced by ExplicitTimeIntegrator::initialSetup().

  {
    return _scalar_kernels;
  }

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 144 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 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 153 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 757 of file SystemBase.h.

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

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

getSNES()

virtual SNES NonlinearSystemBase::getSNES ( )

pure virtual

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

Referenced by DefaultNonlinearConvergence::checkConvergence(), and PetscOutput::solveSetup().

getSplit()

std::shared_ptr< Split > NonlinearSystemBase::getSplit

(

const std::string &

name

)

Retrieves a split by name.

Parameters

name	The name of the split

Definition at line 721 of file NonlinearSystemBase.C.

Referenced by Split::setup(), and setupFieldDecomposition().

{
  return _splits.getActiveObject(name);
}

getSplits()

MooseObjectWarehouseBase<Split>& NonlinearSystemBase::getSplits ( )

inline

Retrieves all splits.

Definition at line 227 of file NonlinearSystemBase.h.

Referenced by ConsoleUtils::outputExecutionInformation().

{ return _splits; }

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 762 of file SystemBase.h.

Referenced by 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 1674 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 1650 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 1662 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 89 of file SystemBase.C.

Referenced by AdaptivityAction::act(), Assembly::addJacobianBlockNonlocal(), FEProblemBase::addJacobianBlockTags(), NonlocalKernel::computeNonlocalOffDiagJacobian(), NonlocalIntegratedBC::computeNonlocalOffDiagJacobian(), Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), Assembly::copyShapes(), SystemBase::copyVars(), DMMooseSetVariables(), FieldSplitPreconditioner::FieldSplitPreconditioner(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), NodeElemConstraint::getConnectedDofIndices(), NodeFaceConstraint::getConnectedDofIndices(), SystemBase::getSubdomainsForVar(), ResidualObject::getVariable(), SubProblem::getVariableHelper(), Assembly::init(), NodalNormalsPreprocessor::initialize(), ExplicitTimeIntegrator::initialSetup(), ReferenceResidualConvergence::initialSetup(), LinearSystem::initialSetup(), Assembly::initNonlocalCoupling(), PNGOutput::makeMeshFunc(), MooseStaticCondensationPreconditioner::MooseStaticCondensationPreconditioner(), UpdateErrorVectorsThread::onElement(), Assembly::prepareBlock(), Assembly::prepareBlockNonlocal(), AddPeriodicBCAction::setPeriodicVars(), 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 99 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 163 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 843 of file SystemBase.h.

{ return _var_all_dof_indices; }

getVariableNames()

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

inlineinherited

Definition at line 861 of file SystemBase.h.

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

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

getVariables()

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

inlineinherited

Definition at line 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()(), 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 916 of file SystemBase.C.

Referenced by Assembly::addCachedResiduals(), Assembly::addResidual(), Assembly::addResidualLower(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), assembleScalingVector(), SystemBase::closeTaggedVector(), FEProblemBase::computeBounds(), FEProblemBase::computeNearNullSpace(), FEProblemBase::computeNullSpace(), computeResidualAndJacobianTags(), computeResidualTags(), CentralDifference::computeTimeDerivatives(), FEProblemBase::computeTransposeNullSpace(), DisplacedSystem::getVector(), Assembly::hasScalingVector(), LinearSystemContributionObject::linkTaggedVectorsAndMatrices(), SystemBase::needSolutionState(), ReferenceResidualConvergence::ReferenceResidualConvergence(), MooseVariableScalar::reinit(), SecantSolve::saveVariableValues(), SteffensenSolve::saveVariableValues(), PicardSolve::saveVariableValues(), 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 922 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 928 of file SystemBase.C.

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

  return *_tagged_vectors[tag];
}

getVector() [4/4]

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

virtualinherited

Reimplemented in DisplacedSystem.

Definition at line 946 of file SystemBase.C.

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

  return *_tagged_vectors[tag];
}

gradientContainer()

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

inlineinherited

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

Mainly used for finite volume systems.

Definition at line 931 of file SystemBase.h.

  {
    return _raw_grad_container;
  }

hasDiagSaveIn()

bool NonlinearSystemBase::hasDiagSaveIn ( ) const

inline

Weather or not the nonlinear system has diagonal Jacobian save-ins.

Definition at line 636 of file NonlinearSystemBase.h.

Referenced by computeJacobianInternal().

{ return _has_diag_save_in || _has_nodalbc_diag_save_in; }

hasMatrix()

virtual bool SystemBase::hasMatrix ( TagID  tag ) const

inlinevirtualinherited

Check if the tagged matrix exists in the system.

Reimplemented in DisplacedSystem.

Definition at line 351 of file SystemBase.h.

Referenced by SystemBase::activeAllMatrixTags(), Assembly::addCachedJacobian(), 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(), computeJacobianInternal(), FEProblemBase::computeJacobianTags(), FEProblemBase::computeResidualAndJacobian(), computeResidualAndJacobianInternal(), constraintJacobians(), SystemBase::disassociateMatrixFromTag(), 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];
  }

hasSaveIn()

bool NonlinearSystemBase::hasSaveIn ( ) const

inline

Weather or not the nonlinear system has save-ins.

Definition at line 631 of file NonlinearSystemBase.h.

Referenced by computeResidualTags().

{ return _has_save_in || _has_nodalbc_save_in; }

hasScalarVariable()

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

virtualinherited

Definition at line 859 of file SystemBase.C.

Referenced by MortarScalarBase::computeJacobian(), computeJacobianInternal(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), SystemBase::copyVars(), ExplicitTimeIntegrator::initialSetup(), NonlinearEigenSystem::postAddResidualObject(), AddPeriodicBCAction::setPeriodicVars(), and 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 1081 of file SystemBase.h.

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

{
  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 884 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 834 of file SystemBase.C.

Referenced by ADDGKernel::ADDGKernel(), ArrayDGKernel::ArrayDGKernel(), SystemBase::copyVars(), DGKernel::DGKernel(), DMMooseSetVariables(), FEProblemBase::duplicateVariableCheck(), SubProblem::getVariableHelper(), SubProblem::hasAuxiliaryVariable(), ExplicitTimeIntegrator::initialSetup(), InterfaceKernelTempl< T >::InterfaceKernelTempl(), PNGOutput::makeMeshFunc(), MultiAppVariableValueSamplePostprocessorTransfer::MultiAppVariableValueSamplePostprocessorTransfer(), 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 907 of file SystemBase.C.

Referenced by FEProblemBase::addCachedResidualDirectly(), Assembly::addCachedResiduals(), Assembly::addResidual(), Assembly::addResidualLower(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), assembleScalingVector(), Assembly::cacheResidual(), Assembly::cacheResidualLower(), Assembly::cacheResidualNeighbor(), SystemBase::closeTaggedVector(), FEProblemBase::computeBounds(), computeResidualTags(), CentralDifference::computeTimeDerivatives(), SystemBase::getVector(), DisplacedSystem::hasVector(), MooseVariableScalar::reinit(), SystemBase::removeVector(), SubProblem::selectVectorTagsFromSystem(), 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 272 of file SystemBase.h.

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

haveFieldSplitPreconditioner()

bool NonlinearSystemBase::haveFieldSplitPreconditioner ( ) const

inline

Definition at line 109 of file NonlinearSystemBase.h.

Referenced by setupDM().

{ return _use_field_split_preconditioner; }

haveFiniteDifferencedPreconditioner()

bool NonlinearSystemBase::haveFiniteDifferencedPreconditioner ( ) const

inline

Definition at line 105 of file NonlinearSystemBase.h.

  {
    return _use_finite_differenced_preconditioner;
  }

ignoreVariablesForAutoscaling()

void NonlinearSystemBase::ignoreVariablesForAutoscaling ( const std::vector< std::string > &  ignore_variables_for_autoscaling )

inline

Definition at line 679 of file NonlinearSystemBase.h.

  {
    _ignore_variables_for_autoscaling = ignore_variables_for_autoscaling;
  }

initializeObjects()

virtual void SystemBase::initializeObjects ( )

inlinevirtualinherited

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

Definition at line 173 of file SystemBase.h.

{}

initialResidual()

Real NonlinearSystemBase::initialResidual

(

)

const

The initial residual.

Definition at line 760 of file NonlinearSystemBase.C.

Referenced by referenceResidual().

{
  return _initial_residual;
}

initialSetup()

void NonlinearSystemBase::initialSetup ( )

overridevirtual

Setup Functions.

Reimplemented from SystemBase.

Definition at line 202 of file NonlinearSystemBase.C.

{
  TIME_SECTION("nlInitialSetup", 2, "Setting Up Nonlinear System");

  SolverSystem::initialSetup();

  {
    TIME_SECTION("kernelsInitialSetup", 2, "Setting Up Kernels/BCs/Constraints");

    for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
    {
      _kernels.initialSetup(tid);
      _nodal_kernels.initialSetup(tid);
      _dirac_kernels.initialSetup(tid);
      if (_doing_dg)
        _dg_kernels.initialSetup(tid);
      _interface_kernels.initialSetup(tid);

      _element_dampers.initialSetup(tid);
      _nodal_dampers.initialSetup(tid);
      _integrated_bcs.initialSetup(tid);

      if (_fe_problem.haveFV())
      {
        std::vector<FVElementalKernel *> fv_elemental_kernels;
        _fe_problem.theWarehouse()
            .query()
            .template condition<AttribSystem>("FVElementalKernel")
            .template condition<AttribThread>(tid)
            .queryInto(fv_elemental_kernels);

        for (auto * fv_kernel : fv_elemental_kernels)
          fv_kernel->initialSetup();

        std::vector<FVFluxKernel *> fv_flux_kernels;
        _fe_problem.theWarehouse()
            .query()
            .template condition<AttribSystem>("FVFluxKernel")
            .template condition<AttribThread>(tid)
            .queryInto(fv_flux_kernels);

        for (auto * fv_kernel : fv_flux_kernels)
          fv_kernel->initialSetup();
      }
    }

    _scalar_kernels.initialSetup();
    _constraints.initialSetup();
    _general_dampers.initialSetup();
    _nodal_bcs.initialSetup();
  }

  {
    TIME_SECTION("mortarSetup", 2, "Initializing Mortar Interfaces");

    auto create_mortar_functors = [this](const bool displaced)
    {
      // go over mortar interfaces and construct functors
      const auto & mortar_interfaces = _fe_problem.getMortarInterfaces(displaced);
      for (const auto & mortar_interface : mortar_interfaces)
      {
        const auto primary_secondary_boundary_pair = mortar_interface.first;
        if (!_constraints.hasActiveMortarConstraints(primary_secondary_boundary_pair, displaced))
          continue;

        const auto & mortar_generation_object = mortar_interface.second;

        auto & mortar_constraints =
            _constraints.getActiveMortarConstraints(primary_secondary_boundary_pair, displaced);

        auto & subproblem = displaced
                                ? static_cast<SubProblem &>(*_fe_problem.getDisplacedProblem())
                                : static_cast<SubProblem &>(_fe_problem);

        auto & mortar_functors =
            displaced ? _displaced_mortar_functors : _undisplaced_mortar_functors;

        mortar_functors.emplace(primary_secondary_boundary_pair,
                                ComputeMortarFunctor(mortar_constraints,
                                                     mortar_generation_object,
                                                     subproblem,
                                                     _fe_problem,
                                                     displaced,
                                                     subproblem.assembly(0, number())));
      }
    };

    create_mortar_functors(false);
    create_mortar_functors(true);
  }

  if (_automatic_scaling)
  {
    if (_off_diagonals_in_auto_scaling)
      _scaling_matrix = std::make_unique<OffDiagonalScalingMatrix<Number>>(_communicator);
    else
      _scaling_matrix = std::make_unique<DiagonalMatrix<Number>>(_communicator);
  }

  if (_preconditioner)
    _preconditioner->initialSetup();
}

initSolutionState()

void SystemBase::initSolutionState ( )

virtualinherited

Initializes the solution state.

Reimplemented in DisplacedSystem.

Definition at line 1354 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 847 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 868 of file SystemBase.C.

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

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

jacobianSetup()

void NonlinearSystemBase::jacobianSetup ( )

overridevirtual

Reimplemented from SystemBase.

Definition at line 2759 of file NonlinearSystemBase.C.

Referenced by computeJacobianInternal().

{
  SolverSystem::jacobianSetup();

  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _kernels.jacobianSetup(tid);
    _nodal_kernels.jacobianSetup(tid);
    _dirac_kernels.jacobianSetup(tid);
    if (_doing_dg)
      _dg_kernels.jacobianSetup(tid);
    _interface_kernels.jacobianSetup(tid);
    _element_dampers.jacobianSetup(tid);
    _nodal_dampers.jacobianSetup(tid);
    _integrated_bcs.jacobianSetup(tid);
  }
  _scalar_kernels.jacobianSetup();
  _constraints.jacobianSetup();
  _general_dampers.jacobianSetup();
  _nodal_bcs.jacobianSetup();

  // Avoid recursion
  if (this == &_fe_problem.currentNonlinearSystem())
    _fe_problem.jacobianSetup();
  _app.solutionInvalidity().resetSolutionInvalidCurrentIteration();
}

matrixFromColoring()

virtual bool SolverSystem::matrixFromColoring ( ) const

inlineprotectedvirtualinherited

Whether a system matrix is formed from coloring.

This influences things like when to compute time derivatives

Reimplemented in NonlinearSystem.

Definition at line 102 of file SolverSystem.h.

Referenced by SolverSystem::compute(), and destroyColoring().

{ return false; }

matrixTagActive()

bool SystemBase::matrixTagActive ( TagID  tag ) const

virtualinherited

If or not a matrix tag is active.

Definition at line 1151 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 99 of file SystemBase.h.

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

{ return _mesh; }

mesh() [2/2]

const MooseMesh& SystemBase::mesh ( ) const

inlineinherited

Definition at line 100 of file SystemBase.h.

{ return _mesh; }

mortarConstraints()

void NonlinearSystemBase::mortarConstraints ( Moose::ComputeType  compute_type, const std::set< TagID > &  vector_tags, const std::set< TagID > &  matrix_tags  )

protected

Do mortar constraint residual/jacobian computations.

Definition at line 3791 of file NonlinearSystemBase.C.

Referenced by computeJacobianInternal(), computeResidualAndJacobianInternal(), and computeResidualInternal().

{
  parallel_object_only();

  try
  {
    for (auto & map_pr : _undisplaced_mortar_functors)
      map_pr.second(compute_type, vector_tags, matrix_tags);

    for (auto & map_pr : _displaced_mortar_functors)
      map_pr.second(compute_type, vector_tags, matrix_tags);
  }
  catch (MetaPhysicL::LogicError &)
  {
    mooseError(
        "We caught a MetaPhysicL error in NonlinearSystemBase::mortarConstraints. This is very "
        "likely due to AD not having a sufficiently large derivative container size. Please run "
        "MOOSE configure with the '--with-derivative-size=<n>' option");
  }
}

name()

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

virtualinherited

Definition at line 1330 of file SystemBase.C.

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

{
  return system().name();
}

needBoundaryMaterialOnSide()

bool NonlinearSystemBase::needBoundaryMaterialOnSide	(	BoundaryID	bnd_id,
		THREAD_ID	tid
	)		const

Indicated whether this system needs material properties on boundaries.

Returns

Boolean if IntegratedBCs are active

Definition at line 3759 of file NonlinearSystemBase.C.

{
  return _integrated_bcs.hasActiveBoundaryObjects(bnd_id, tid);
}

needInterfaceMaterialOnSide()

bool NonlinearSystemBase::needInterfaceMaterialOnSide	(	BoundaryID	bnd_id,
		THREAD_ID	tid
	)		const

Indicated whether this system needs material properties on interfaces.

Returns

Boolean if IntegratedBCs are active

Definition at line 3765 of file NonlinearSystemBase.C.

{
  return _interface_kernels.hasActiveBoundaryObjects(bnd_id, tid);
}

needSolutionState()

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

virtualinherited

Registers that the solution state state is needed.

Reimplemented in DisplacedSystem.

Definition at line 1428 of file SystemBase.C.

Referenced by EigenExecutionerBase::EigenExecutionerBase(), SystemBase::initSolutionState(), DisplacedSystem::needSolutionState(), 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, GHOSTED);
    }
    else
      mooseAssert(solution_states[i] == &getVector(oldSolutionStateVectorName(i, iteration_type)),
                  "Inconsistent solution state");
}

needSubdomainMaterialOnSide()

bool NonlinearSystemBase::needSubdomainMaterialOnSide	(	SubdomainID	subdomain_id,
		THREAD_ID	tid
	)		const

Indicates whether this system needs material properties on internal sides.

Returns

Boolean if DGKernels are active

Definition at line 3771 of file NonlinearSystemBase.C.

{
  return _doing_dg;
}

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 883 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 893 of file SystemBase.C.

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

  return n;
}

nLinearIterations()

unsigned int NonlinearSystemBase::nLinearIterations ( ) const

inline

Return the number of linear iterations.

Definition at line 527 of file NonlinearSystemBase.h.

Referenced by IterationAdaptiveDT::acceptStep().

{ return _n_linear_iters; }

nNonlinearIterations()

unsigned int NonlinearSystemBase::nNonlinearIterations ( ) const

inline

Return the number of non-linear iterations.

Definition at line 522 of file NonlinearSystemBase.h.

Referenced by IterationAdaptiveDT::acceptStep().

{ return _n_iters; }

nonlinearNorm()

Real NonlinearSystemBase::nonlinearNorm ( ) const

inline

Return the last nonlinear norm.

Returns

A Real containing the last computed residual norm

Definition at line 543 of file NonlinearSystemBase.h.

Referenced by Console::writeVariableNorms().

{ return _last_nl_rnorm; }

nonlinearSolver()

virtual libMesh::NonlinearSolver<Number>* NonlinearSystemBase::nonlinearSolver ( )

pure virtual

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

Referenced by DMCreateFieldDecomposition_Moose(), DMMooseFunction(), DMMooseJacobian(), DMSetUp_Moose(), DMVariableBounds_Moose(), MatrixSymmetryCheck::execute(), Moose::PetscSupport::petscSetDefaults(), Moose::PetscSupport::petscSetupDM(), and turnOffJacobian().

nonTimeVectorTag()

TagID NonlinearSystemBase::nonTimeVectorTag ( ) const

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 648 of file NonlinearSystemBase.h.

Referenced by FEProblemBase::addCachedResidualDirectly(), and CrankNicolson::init().

{ return _Re_non_time_tag; }

nResidualEvaluations()

unsigned int NonlinearSystemBase::nResidualEvaluations ( ) const

inline

Return the total number of residual evaluations done so far in this calculation.

Definition at line 532 of file NonlinearSystemBase.h.

{ return _n_residual_evaluations; }

number()

unsigned int SystemBase::number ( ) const

inherited

Gets the number of this system.

Returns

The number of this system

Definition at line 1159 of file SystemBase.C.

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

{
  return system().number();
}

nVariables()

unsigned int SystemBase::nVariables ( ) const

virtualinherited

Get the number of variables in this system.

Returns

the number of variables

Definition at line 874 of file SystemBase.C.

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

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

  return n;
}

offDiagonalsInAutoScaling() [1/2]

bool NonlinearSystemBase::offDiagonalsInAutoScaling ( ) const

inline

Definition at line 684 of file NonlinearSystemBase.h.

Referenced by ComputeJacobianForScalingThread::computeOnElement().

{ return _off_diagonals_in_auto_scaling; }

offDiagonalsInAutoScaling() [2/2]

void NonlinearSystemBase::offDiagonalsInAutoScaling ( bool  off_diagonals_in_auto_scaling )

inline

Definition at line 685 of file NonlinearSystemBase.h.

  {
    _off_diagonals_in_auto_scaling = off_diagonals_in_auto_scaling;
  }

onTimestepBegin()

void NonlinearSystemBase::onTimestepBegin

(

)

Called at the beginning of the time step.

Definition at line 923 of file NonlinearSystemBase.C.

{
  for (auto & ti : _time_integrators)
    ti->preSolve();
  if (_predictor.get())
    _predictor->timestepSetup();
}

overwriteNodeFace()

void NonlinearSystemBase::overwriteNodeFace

(

NumericVector< Number > &

soln

)

Called from explicit time stepping to overwrite boundary positions (explicit dynamics).

This will close/assemble the passed-in soln after overwrite

Definition at line 1645 of file NonlinearSystemBase.C.

Referenced by ActuallyExplicitEuler::solve().

{
  // Overwrite results from integrator in case we have explicit dynamics contact constraints
  auto & subproblem = _fe_problem.getDisplacedProblem()
                          ? static_cast<SubProblem &>(*_fe_problem.getDisplacedProblem())
                          : static_cast<SubProblem &>(_fe_problem);
  const auto & penetration_locators = subproblem.geomSearchData()._penetration_locators;

  for (const auto & it : penetration_locators)
  {
    PenetrationLocator & pen_loc = *(it.second);

    const auto & secondary_nodes = pen_loc._nearest_node._secondary_nodes;
    const BoundaryID secondary_boundary = pen_loc._secondary_boundary;
    const BoundaryID primary_boundary = pen_loc._primary_boundary;

    if (_constraints.hasActiveNodeFaceConstraints(secondary_boundary, true))
    {
      const auto & constraints =
          _constraints.getActiveNodeFaceConstraints(secondary_boundary, true);
      for (const auto i : index_range(secondary_nodes))
      {
        const auto secondary_node_num = secondary_nodes[i];
        const Node & secondary_node = _mesh.nodeRef(secondary_node_num);

        if (secondary_node.processor_id() == processor_id())
          if (pen_loc._penetration_info[secondary_node_num])
            for (const auto & nfc : constraints)
            {
              if (!nfc->isExplicitConstraint())
                continue;

              // Return if this constraint does not correspond to the primary-secondary pair
              // prepared by the outer loops.
              // This continue statement is required when, e.g. one secondary surface constrains
              // more than one primary surface.
              if (nfc->secondaryBoundary() != secondary_boundary ||
                  nfc->primaryBoundary() != primary_boundary)
                continue;

              nfc->overwriteBoundaryVariables(soln, secondary_node);
            }
      }
    }
  }
  soln.close();
}

perfGraph()

PerfGraph & PerfGraphInterface::perfGraph ( )

inherited

Get the PerfGraph.

Definition at line 78 of file PerfGraphInterface.C.

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

{
  return _pg_moose_app.perfGraph();
}

postAddResidualObject()

virtual void NonlinearSystemBase::postAddResidualObject ( ResidualObject &  )

inlineprotectedvirtual

Called after any ResidualObject-derived objects are added to the system.

Reimplemented in NonlinearEigenSystem.

Definition at line 784 of file NonlinearSystemBase.h.

Referenced by addBoundaryCondition(), addConstraint(), addDGKernel(), addDiracKernel(), addHDGKernel(), addInterfaceKernel(), addKernel(), addNodalKernel(), and addScalarKernel().

{}

postInit()

virtual void SystemBase::postInit ( )

inlinevirtualinherited

Reimplemented in NonlinearEigenSystem.

Definition at line 162 of file SystemBase.h.

Referenced by NonlinearEigenSystem::postInit().

{}

potentiallySetupFiniteDifferencing()

virtual void NonlinearSystemBase::potentiallySetupFiniteDifferencing ( )

inlinevirtual

Create finite differencing contexts for assembly of the Jacobian and/or approximating the action of the Jacobian on vectors (e.g.

FD and/or MFFD respectively)

Reimplemented in NonlinearSystem.

Definition at line 707 of file NonlinearSystemBase.h.

Referenced by LStableDirk2::solve(), LStableDirk3::solve(), and LStableDirk4::solve().

{}

prefix()

std::string SystemBase::prefix ( ) const

inherited

Returns

A prefix for solvers

Definition at line 1680 of file SystemBase.C.

Referenced by MoosePreconditioner::initialSetup().

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

preInit()

void NonlinearSystemBase::preInit ( )

overridevirtual

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 from SolverSystem.

Definition at line 183 of file NonlinearSystemBase.C.

{
  SolverSystem::preInit();

  if (_fe_problem.hasDampers())
    setupDampers();

  if (_residual_copy.get())
    _residual_copy->init(_sys.n_dofs(), false, SERIAL);
}

prepare()

void SystemBase::prepare ( THREAD_ID  tid )

virtualinherited

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 255 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 278 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 331 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 323 of file SystemBase.C.

Referenced by SubProblem::reinitNeighborFaceRef().

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

preSMOResidual()

Real NonlinearSystemBase::preSMOResidual

(

)

const

The pre-SMO residual.

Definition at line 751 of file NonlinearSystemBase.C.

Referenced by Residual::getValue(), and referenceResidual().

{
  if (!shouldEvaluatePreSMOResidual())
    mooseError("pre-SMO residual is requested but not evaluated.");

  return _pre_smo_residual;
}

preSolve()

bool NonlinearSystemBase::preSolve ( )

protected

Perform some steps to get ready for the solver.

These include

• zeroing iteration counters
• setting initial solutions
• possibly performing automatic scaling
• forming a scaling vector which, at least at some point, was required when AD objects were used with non-unity scaling factors for nonlinear variables

  Returns

  Whether any exceptions were raised while running this method

Definition at line 4094 of file NonlinearSystemBase.C.

Referenced by NonlinearSystem::solve(), and NonlinearEigenSystem::solve().

{
  // Clear the iteration counters
  _current_l_its.clear();
  _current_nl_its = 0;

  // Initialize the solution vector using a predictor and known values from nodal bcs
  setInitialSolution();

  // Now that the initial solution has ben set, potentially perform a residual/Jacobian evaluation
  // to determine variable scaling factors
  if (_automatic_scaling)
  {
    const bool scaling_succeeded = computeScaling();
    if (!scaling_succeeded)
      return false;
  }

  // We do not know a priori what variable a global degree of freedom corresponds to, so we need a
  // map from global dof to scaling factor. We just use a ghosted NumericVector for that mapping
  assembleScalingVector();

  return true;
}

printAllVariableNorms()

void NonlinearSystemBase::printAllVariableNorms ( bool  state )

inline

Force the printing of all variable norms after each solve.

Todo:

{Remove after output update

Definition at line 549 of file NonlinearSystemBase.h.

{ _print_all_var_norms = state; }

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 1640 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;
}

referenceResidual()

Real NonlinearSystemBase::referenceResidual

(

)

const

The reference residual used in relative convergence check.

Definition at line 745 of file NonlinearSystemBase.C.

Referenced by DefaultNonlinearConvergence::checkConvergence(), and EigenExecutionerBase::inversePowerIteration().

{
  return usePreSMOResidual() ? preSMOResidual() : initialResidual();
}

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 53 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 64 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()

virtual void SystemBase::reinit ( )

inlinevirtualinherited

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

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

Reimplemented in NonlinearEigenSystem.

Definition at line 168 of file SystemBase.h.

Referenced by NonlinearEigenSystem::reinit().

{}

reinitElem()

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

virtualinherited

Reinit an element assembly info.

Parameters

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

Reimplemented in AuxiliarySystem.

Definition at line 339 of file SystemBase.C.

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

reinitElemFace()

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

virtualinherited

Reinit assembly info for a side of an element.

Parameters

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

Reimplemented in AuxiliarySystem.

Definition at line 358 of file SystemBase.C.

Referenced by SubProblem::reinitElemFaceRef().

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

reinitIncrementAtNodeForDampers()

void NonlinearSystemBase::reinitIncrementAtNodeForDampers	(	THREAD_ID	tid,
		const std::set< MooseVariable *> &	damped_vars
	)

Compute the incremental change in variables at nodes for dampers.

Called before we use damping

Parameters

tid	Thread ID
damped_vars	Set of variables for which increment is to be computed

Definition at line 3582 of file NonlinearSystemBase.C.

Referenced by ComputeNodalDampingThread::onNode().

{
  for (const auto & var : damped_vars)
    var->computeIncrementAtNode(*_increment_vec);
}

reinitIncrementAtQpsForDampers()

void NonlinearSystemBase::reinitIncrementAtQpsForDampers	(	THREAD_ID	tid,
		const std::set< MooseVariable *> &	damped_vars
	)

Compute the incremental change in variables at QPs for dampers.

Called before we use damping

Parameters

tid	Thread ID
damped_vars	Set of variables for which increment is to be computed

Definition at line 3574 of file NonlinearSystemBase.C.

Referenced by ComputeElemDampingThread::onElement().

{
  for (const auto & var : damped_vars)
    var->computeIncrementAtQps(*_increment_vec);
}

reinitLowerD()

void SystemBase::reinitLowerD ( THREAD_ID  tid )

virtualinherited

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

Definition at line 382 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 374 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 366 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 390 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() [1/3]

void SystemBase::reinitNodeFace

Reinit nodal assembly info on a face.

Parameters

node	Node to reinit
bnd_id	Boundary ID
tid	Thread ID

Definition at line 402 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() [2/3]

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 402 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() [3/3]

void NonlinearSystemBase::reinitNodeFace ( const Node &  secondary_node, const BoundaryID  secondary_boundary, const PenetrationInfo &  info, const bool  displaced  )

protected

Reinitialize quantities such as variables, residuals, Jacobians, materials for node-face constraints.

Definition at line 1125 of file NonlinearSystemBase.C.

Referenced by constraintJacobians(), constraintResiduals(), and setConstraintSecondaryValues().

{
  auto & subproblem = displaced ? static_cast<SubProblem &>(*_fe_problem.getDisplacedProblem())
                                : static_cast<SubProblem &>(_fe_problem);

  const Elem * primary_elem = info._elem;
  unsigned int primary_side = info._side_num;
  std::vector<Point> points;
  points.push_back(info._closest_point);

  // *These next steps MUST be done in this order!*
  // ADL: This is a Chesterton's fence situation. I don't know which calls exactly the above comment
  // is referring to. If I had to guess I would guess just the reinitNodeFace and prepareAssembly
  // calls since the former will size the variable's dof indices and then the latter will resize the
  // residual/Jacobian based off the variable's cached dof indices size

  // This reinits the variables that exist on the secondary node
  _fe_problem.reinitNodeFace(&secondary_node, secondary_boundary, 0);

  // This will set aside residual and jacobian space for the variables that have dofs on
  // the secondary node
  _fe_problem.prepareAssembly(0);

  _fe_problem.setNeighborSubdomainID(primary_elem, 0);

  //
  // Reinit material on undisplaced mesh
  //

  const Elem * const undisplaced_primary_elem =
      displaced ? _mesh.elemPtr(primary_elem->id()) : primary_elem;
  const Point undisplaced_primary_physical_point =
      [&points, displaced, primary_elem, undisplaced_primary_elem]()
  {
    if (displaced)
    {
      const Point reference_point =
          FEMap::inverse_map(primary_elem->dim(), primary_elem, points[0]);
      return FEMap::map(primary_elem->dim(), undisplaced_primary_elem, reference_point);
    }
    else
      // If our penetration locator is on the reference mesh, then our undisplaced
      // physical point is simply the point coming from the penetration locator
      return points[0];
  }();

  _fe_problem.reinitNeighborPhys(
      undisplaced_primary_elem, primary_side, {undisplaced_primary_physical_point}, 0);
  // Stateful material properties are only initialized for neighbor material data for internal faces
  // for discontinuous Galerkin methods or for conforming interfaces for interface kernels. We don't
  // have either of those use cases here where we likely have disconnected meshes
  _fe_problem.reinitMaterialsNeighbor(primary_elem->subdomain_id(), 0, /*swap_stateful=*/false);

  // Reinit points for constraint enforcement
  if (displaced)
    subproblem.reinitNeighborPhys(primary_elem, primary_side, points, 0);
}

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 414 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 425 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 436 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 582 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 1324 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 692 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;
  }
}

residualAndJacobianTogether()

virtual void NonlinearSystemBase::residualAndJacobianTogether ( )

pure virtual

Call this method if you want the residual and Jacobian to be computed simultaneously.

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

residualCopy()

NumericVector< Number > & NonlinearSystemBase::residualCopy ( )

overridevirtual

Reimplemented from SystemBase.

Definition at line 3429 of file NonlinearSystemBase.C.

{
  if (!_residual_copy.get())
    _residual_copy = NumericVector<Number>::build(_communicator);

  return *_residual_copy;
}

residualGhosted()

NumericVector< Number > & NonlinearSystemBase::residualGhosted ( )

overridevirtual

Reimplemented from SystemBase.

Definition at line 3438 of file NonlinearSystemBase.C.

{
  _need_residual_ghosted = true;
  if (!_residual_ghosted)
  {
    // The first time we realize we need a ghosted residual vector,
    // we add it.
    _residual_ghosted = &addVector("residual_ghosted", false, GHOSTED);

    // If we've already realized we need time and/or non-time
    // residual vectors, but we haven't yet realized they need to be
    // ghosted, fix that now.
    //
    // If an application changes its mind, the libMesh API lets us
    // change the vector.
    if (_Re_time)
    {
      const auto vector_name = _subproblem.vectorTagName(_Re_time_tag);
      _Re_time = &system().add_vector(vector_name, false, GHOSTED);
    }
    if (_Re_non_time)
    {
      const auto vector_name = _subproblem.vectorTagName(_Re_non_time_tag);
      _Re_non_time = &system().add_vector(vector_name, false, GHOSTED);
    }
  }
  return *_residual_ghosted;
}

residualSetup()

void NonlinearSystemBase::residualSetup ( )

overridevirtual

Reimplemented from SystemBase.

Definition at line 1694 of file NonlinearSystemBase.C.

Referenced by computeResidualAndJacobianInternal(), and computeResidualInternal().

{
  TIME_SECTION("residualSetup", 3);

  SolverSystem::residualSetup();

  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _kernels.residualSetup(tid);
    _nodal_kernels.residualSetup(tid);
    _dirac_kernels.residualSetup(tid);
    if (_doing_dg)
      _dg_kernels.residualSetup(tid);
    _interface_kernels.residualSetup(tid);
    _element_dampers.residualSetup(tid);
    _nodal_dampers.residualSetup(tid);
    _integrated_bcs.residualSetup(tid);
  }
  _scalar_kernels.residualSetup();
  _constraints.residualSetup();
  _general_dampers.residualSetup();
  _nodal_bcs.residualSetup();

  // Avoid recursion
  if (this == &_fe_problem.currentNonlinearSystem())
    _fe_problem.residualSetup();
  _app.solutionInvalidity().resetSolutionInvalidCurrentIteration();
}

residualVector()

NumericVector< Number > & NonlinearSystemBase::residualVector

(

TagID

tag

)

Return a residual vector that is associated with the residual tag.

Definition at line 1055 of file NonlinearSystemBase.C.

{
  mooseDeprecated("Please use getVector()");
  switch (tag)
  {
    case 0:
      return getResidualNonTimeVector();

    case 1:
      return getResidualTimeVector();

    default:
      mooseError("The required residual vector is not available");
  }
}

residualVectorTag()

TagID NonlinearSystemBase::residualVectorTag ( ) const

inlineoverridevirtual

Reimplemented from SystemBase.

Definition at line 649 of file NonlinearSystemBase.h.

Referenced by FEProblemBase::computeResidualAndJacobian(), computeResidualAndJacobianTags(), FEProblemBase::computeResidualInternal(), computeResidualTag(), computeResidualTags(), FEProblemBase::computeResidualType(), and FEProblemBase::setResidualNeighbor().

{ return _Re_tag; }

restoreOldSolutions()

void SystemBase::restoreOldSolutions ( )

virtualinherited

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

Definition at line 534 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 SolverSystem::restoreSolutions ( )

finaloverridevirtualinherited

Restore current solutions (call after your solve failed)

Reimplemented from SystemBase.

Definition at line 43 of file SolverSystem.C.

{
  // call parent
  SystemBase::restoreSolutions();
  // and update _current_solution
  _current_solution = system().current_local_solution.get();
}

RHS()

virtual NumericVector<Number>& NonlinearSystemBase::RHS ( )

pure virtual

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

Referenced by FEProblemBase::computeResidualL2Norm(), computeScaling(), VariableResidual::execute(), CrankNicolson::init(), VariableResidualNormsDebugOutput::output(), TopResidualDebugOutput::output(), ReferenceResidualConvergence::updateReferenceResidual(), and Console::writeVariableNorms().

saveOldSolutions()

void SystemBase::saveOldSolutions ( )

virtualinherited

Save the old and older solutions.

Definition at line 502 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();
}

scalingGroupVariables()

void NonlinearSystemBase::scalingGroupVariables ( const std::vector< std::vector< std::string >> &  scaling_group_variables )

inline

Definition at line 673 of file NonlinearSystemBase.h.

  {
    _scaling_group_variables = scaling_group_variables;
  }

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 1613 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 SolverSystem::serializeSolution ( )

inherited

Definition at line 52 of file SolverSystem.C.

Referenced by SolverSystem::setSolution().

{
  if (_serialized_solution.get())
  {
    if (!_serialized_solution->initialized() || _serialized_solution->size() != system().n_dofs())
    {
      _serialized_solution->clear();
      _serialized_solution->init(system().n_dofs(), false, SERIAL);
    }

    _current_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 1593 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 1587 of file SystemBase.C.

Referenced by SubProblem::setActiveFEVariableCoupleableVectorTags().

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

setConstraintSecondaryValues()

void NonlinearSystemBase::setConstraintSecondaryValues	(	NumericVector< Number > &	solution,
		bool	displaced
	)

Sets the value of constrained variables in the solution vector.

Definition at line 1187 of file NonlinearSystemBase.C.

Referenced by setInitialSolution().

{

  if (displaced)
    mooseAssert(_fe_problem.getDisplacedProblem(),
                "If we're calling this method with displaced = true, then we better well have a "
                "displaced problem");
  auto & subproblem = displaced ? static_cast<SubProblem &>(*_fe_problem.getDisplacedProblem())
                                : static_cast<SubProblem &>(_fe_problem);
  const auto & penetration_locators = subproblem.geomSearchData()._penetration_locators;

  bool constraints_applied = false;

  for (const auto & it : penetration_locators)
  {
    PenetrationLocator & pen_loc = *(it.second);

    std::vector<dof_id_type> & secondary_nodes = pen_loc._nearest_node._secondary_nodes;

    BoundaryID secondary_boundary = pen_loc._secondary_boundary;
    BoundaryID primary_boundary = pen_loc._primary_boundary;

    if (_constraints.hasActiveNodeFaceConstraints(secondary_boundary, displaced))
    {
      const auto & constraints =
          _constraints.getActiveNodeFaceConstraints(secondary_boundary, displaced);
      std::unordered_set<unsigned int> needed_mat_props;
      for (const auto & constraint : constraints)
      {
        const auto & mp_deps = constraint->getMatPropDependencies();
        needed_mat_props.insert(mp_deps.begin(), mp_deps.end());
      }
      _fe_problem.setActiveMaterialProperties(needed_mat_props, /*tid=*/0);

      for (unsigned int i = 0; i < secondary_nodes.size(); i++)
      {
        dof_id_type secondary_node_num = secondary_nodes[i];
        Node & secondary_node = _mesh.nodeRef(secondary_node_num);

        if (secondary_node.processor_id() == processor_id())
        {
          if (pen_loc._penetration_info[secondary_node_num])
          {
            PenetrationInfo & info = *pen_loc._penetration_info[secondary_node_num];

            reinitNodeFace(secondary_node, secondary_boundary, info, displaced);

            for (const auto & nfc : constraints)
            {
              if (nfc->isExplicitConstraint())
                continue;
              // Return if this constraint does not correspond to the primary-secondary pair
              // prepared by the outer loops.
              // This continue statement is required when, e.g. one secondary surface constrains
              // more than one primary surface.
              if (nfc->secondaryBoundary() != secondary_boundary ||
                  nfc->primaryBoundary() != primary_boundary)
                continue;

              if (nfc->shouldApply())
              {
                constraints_applied = true;
                nfc->computeSecondaryValue(solution);
              }

              if (nfc->hasWritableCoupledVariables())
              {
                Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
                for (auto * var : nfc->getWritableCoupledVariables())
                {
                  if (var->isNodalDefined())
                    var->insert(_fe_problem.getAuxiliarySystem().solution());
                }
              }
            }
          }
        }
      }
    }
  }

  // go over NodeELemConstraints
  std::set<dof_id_type> unique_secondary_node_ids;

  for (const auto & secondary_id : _mesh.meshSubdomains())
  {
    for (const auto & primary_id : _mesh.meshSubdomains())
    {
      if (_constraints.hasActiveNodeElemConstraints(secondary_id, primary_id, displaced))
      {
        const auto & constraints =
            _constraints.getActiveNodeElemConstraints(secondary_id, primary_id, displaced);

        // get unique set of ids of all nodes on current block
        unique_secondary_node_ids.clear();
        const MeshBase & meshhelper = _mesh.getMesh();
        for (const auto & elem : as_range(meshhelper.active_subdomain_elements_begin(secondary_id),
                                          meshhelper.active_subdomain_elements_end(secondary_id)))
        {
          for (auto & n : elem->node_ref_range())
            unique_secondary_node_ids.insert(n.id());
        }

        for (auto secondary_node_id : unique_secondary_node_ids)
        {
          Node & secondary_node = _mesh.nodeRef(secondary_node_id);

          // check if secondary node is on current processor
          if (secondary_node.processor_id() == processor_id())
          {
            // This reinits the variables that exist on the secondary node
            _fe_problem.reinitNodeFace(&secondary_node, secondary_id, 0);

            // This will set aside residual and jacobian space for the variables that have dofs
            // on the secondary node
            _fe_problem.prepareAssembly(0);

            for (const auto & nec : constraints)
            {
              if (nec->shouldApply())
              {
                constraints_applied = true;
                nec->computeSecondaryValue(solution);
              }
            }
          }
        }
      }
    }
  }

  // See if constraints were applied anywhere
  _communicator.max(constraints_applied);

  if (constraints_applied)
  {
    solution.close();
    update();
  }
}

setDecomposition()

void NonlinearSystemBase::setDecomposition

(

const std::vector< std::string > &

decomposition

)

If called with a single string, it is used as the name of a the top-level decomposition split.

If the array is empty, no decomposition is used. In all other cases an error occurs.

Although a single top-level split is allowed in Problem, treat it as a list of splits for conformity with the Split input syntax.

Definition at line 421 of file NonlinearSystemBase.C.

Referenced by FieldSplitPreconditioner::FieldSplitPreconditioner().

{
  if (splits.size() && splits.size() != 1)
    mooseError("Only a single top-level split is allowed in a Problem's decomposition.");

  if (splits.size())
  {
    _decomposition_split = splits[0];
    _have_decomposition = true;
  }
  else
    _have_decomposition = false;
}

setInitialResidual()

void NonlinearSystemBase::setInitialResidual

(

Real

r

)

Record the initial residual (for later relative convergence check)

Definition at line 766 of file NonlinearSystemBase.C.

Referenced by DefaultNonlinearConvergence::checkConvergence().

{
  _initial_residual = r;
}

setInitialSolution()

void NonlinearSystemBase::setInitialSolution

(

)

Definition at line 932 of file NonlinearSystemBase.C.

Referenced by preSolve().

{
  deactiveAllMatrixTags();

  NumericVector<Number> & initial_solution(solution());
  if (_predictor.get())
  {
    if (_predictor->shouldApply())
    {
      TIME_SECTION("applyPredictor", 2, "Applying Predictor");

      _predictor->apply(initial_solution);
      _fe_problem.predictorCleanup(initial_solution);
    }
    else
      _console << " Skipping predictor this step" << std::endl;
  }

  // do nodal BC
  {
    TIME_SECTION("initialBCs", 2, "Applying BCs To Initial Condition");

    const ConstBndNodeRange & bnd_nodes = _fe_problem.getCurrentAlgebraicBndNodeRange();
    for (const auto & bnode : bnd_nodes)
    {
      BoundaryID boundary_id = bnode->_bnd_id;
      Node * node = bnode->_node;

      if (node->processor_id() == processor_id())
      {
        // reinit variables in nodes
        _fe_problem.reinitNodeFace(node, boundary_id, 0);

        if (_preset_nodal_bcs.hasActiveBoundaryObjects(boundary_id))
        {
          const auto & preset_bcs = _preset_nodal_bcs.getActiveBoundaryObjects(boundary_id);
          for (const auto & preset_bc : preset_bcs)
            preset_bc->computeValue(initial_solution);
        }
        if (_ad_preset_nodal_bcs.hasActiveBoundaryObjects(boundary_id))
        {
          const auto & preset_bcs_res = _ad_preset_nodal_bcs.getActiveBoundaryObjects(boundary_id);
          for (const auto & preset_bc : preset_bcs_res)
            preset_bc->computeValue(initial_solution);
        }
      }
    }
  }

  _sys.solution->close();
  update();

  // Set constraint secondary values
  setConstraintSecondaryValues(initial_solution, false);

  if (_fe_problem.getDisplacedProblem())
    setConstraintSecondaryValues(initial_solution, true);
}

setMooseKSPNormType()

void SolverSystem::setMooseKSPNormType ( MooseEnum  kspnorm )

inherited

Set the norm in which the linear convergence will be measured.

Parameters

kspnorm

The required norm

Definition at line 94 of file SolverSystem.C.

Referenced by MoosePreconditioner::MoosePreconditioner().

{
  if (kspnorm == "none")
    _ksp_norm = Moose::KSPN_NONE;
  else if (kspnorm == "preconditioned")
    _ksp_norm = Moose::KSPN_PRECONDITIONED;
  else if (kspnorm == "unpreconditioned")
    _ksp_norm = Moose::KSPN_UNPRECONDITIONED;
  else if (kspnorm == "natural")
    _ksp_norm = Moose::KSPN_NATURAL;
  else if (kspnorm == "default")
    _ksp_norm = Moose::KSPN_DEFAULT;
  else
    mooseError("Unknown ksp norm type specified.");
}

setPCSide()

void SolverSystem::setPCSide ( MooseEnum  pcs )

inherited

Set the side on which the preconditioner is applied to.

Parameters

pcs	The required preconditioning side

Definition at line 79 of file SolverSystem.C.

Referenced by MoosePreconditioner::MoosePreconditioner().

{
  if (pcs == "left")
    _pc_side = Moose::PCS_LEFT;
  else if (pcs == "right")
    _pc_side = Moose::PCS_RIGHT;
  else if (pcs == "symmetric")
    _pc_side = Moose::PCS_SYMMETRIC;
  else if (pcs == "default")
    _pc_side = Moose::PCS_DEFAULT;
  else
    mooseError("Unknown PC side specified.");
}

setPreconditioner()

void NonlinearSystemBase::setPreconditioner

(

std::shared_ptr< MoosePreconditioner >

pc

)

Sets a preconditioner.

Parameters

pc	The preconditioner to be set

Definition at line 3553 of file NonlinearSystemBase.C.

Referenced by SetupPreconditionerAction::act().

{
  if (_preconditioner.get() != nullptr)
    mooseError("More than one active Preconditioner detected");

  _preconditioner = pc;
}

setPredictor()

void NonlinearSystemBase::setPredictor

(

std::shared_ptr< Predictor >

predictor

)

Definition at line 992 of file NonlinearSystemBase.C.

Referenced by SetupPredictorAction::act().

{
  _predictor = predictor;
}

setPreSMOResidual()

void NonlinearSystemBase::setPreSMOResidual ( bool  use )

inline

Set whether to evaluate the pre-SMO residual and use it in the subsequent relative convergence checks.

If set to true, an additional residual evaluation is performed before any solution-modifying object is executed, and before the initial (0-th nonlinear iteration) residual evaluation. Such residual is referred to as the pre-SMO residual. If the pre-SMO residual is evaluated, it is used in the subsequent relative convergence checks.

If set to false, no residual evaluation takes place before the initial residual evaluation, and the initial residual is used in the subsequent relative convergence checks. This mode is recommended for performance-critical code as it avoids the additional pre-SMO residual evaluation.

Definition at line 251 of file NonlinearSystemBase.h.

Referenced by FEProblemSolve::FEProblemSolve().

{ _use_pre_smo_residual = use; }

setPreviousNewtonSolution()

void NonlinearSystemBase::setPreviousNewtonSolution ( const NumericVector< Number > &  soln )

virtual

Definition at line 3784 of file NonlinearSystemBase.C.

Referenced by FEProblemBase::computePostCheck().

{
  if (hasVector(Moose::PREVIOUS_NL_SOLUTION_TAG))
    getVector(Moose::PREVIOUS_NL_SOLUTION_TAG) = soln;
}

setSolution()

void SolverSystem::setSolution ( const NumericVector< Number > &  soln )

inherited

Set the solution to a given vector.

Parameters

soln	The vector which should be treated as the solution.

Definition at line 67 of file SolverSystem.C.

Referenced by FEProblemBase::computeDamping(), FEProblemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTag(), FEProblemBase::computeLinearSystemTags(), FEProblemBase::computeResidualAndJacobian(), FEProblemBase::computeResidualInternal(), FEProblemBase::computeResidualTag(), FEProblemBase::computeResidualType(), ActuallyExplicitEuler::solve(), and ExplicitSSPRungeKutta::solveStage().

{
  _current_solution = &soln;

  auto tag = _subproblem.getVectorTagID(Moose::SOLUTION_TAG);
  associateVectorToTag(const_cast<NumericVector<Number> &>(soln), tag);

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

setSolutionUDot()

void NonlinearSystemBase::setSolutionUDot ( const NumericVector< Number > &  udot )

virtual

Set transient term used by residual and Jacobian evaluation.

Parameters

udot	transient term

Note

If the calling sequence for residual evaluation was changed, this could become an explicit argument.

Definition at line 3529 of file NonlinearSystemBase.C.

{
  *_u_dot = u_dot;
}

setSolutionUDotDot()

void NonlinearSystemBase::setSolutionUDotDot ( const NumericVector< Number > &  udotdot )

virtual

Set transient term used by residual and Jacobian evaluation.

Parameters

udotdot

transient term

Note

If the calling sequence for residual evaluation was changed, this could become an explicit argument.

Definition at line 3535 of file NonlinearSystemBase.C.

{
  *_u_dotdot = u_dotdot;
}

setSolutionUDotDotOld()

void NonlinearSystemBase::setSolutionUDotDotOld ( const NumericVector< Number > &  u_dotdot_old )

virtual

Definition at line 3547 of file NonlinearSystemBase.C.

{
  *_u_dotdot_old = u_dotdot_old;
}

setSolutionUDotOld()

void NonlinearSystemBase::setSolutionUDotOld ( const NumericVector< Number > &  u_dot_old )

virtual

Definition at line 3541 of file NonlinearSystemBase.C.

{
  *_u_dot_old = u_dot_old;
}

setupDampers()

void NonlinearSystemBase::setupDampers

(

)

Setup damping stuff (called before we actually start)

Definition at line 3568 of file NonlinearSystemBase.C.

Referenced by preInit().

{
  _increment_vec = &_sys.add_vector("u_increment", true, GHOSTED);
}

setupDM()

void NonlinearSystemBase::setupDM

(

)

Setup the PETSc DM object (when appropriate)

Definition at line 414 of file NonlinearSystemBase.C.

Referenced by FEProblemBase::solve().

{
  if (haveFieldSplitPreconditioner())
    Moose::PetscSupport::petscSetupDM(*this, _decomposition_split);
}

setupFieldDecomposition()

void NonlinearSystemBase::setupFieldDecomposition

(

)

Definition at line 437 of file NonlinearSystemBase.C.

Referenced by FieldSplitPreconditioner::FieldSplitPreconditioner().

{
  if (!_have_decomposition)
    return;

  std::shared_ptr<Split> top_split = getSplit(_decomposition_split);
  top_split->setup(*this);
}

setupFiniteDifferencedPreconditioner()

virtual void NonlinearSystemBase::setupFiniteDifferencedPreconditioner ( )

pure virtual

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

setupScalingData()

void NonlinearSystemBase::setupScalingData ( )

private

Setup group scaling containers.

Definition at line 3815 of file NonlinearSystemBase.C.

Referenced by computeScaling().

{
  if (_auto_scaling_initd)
    return;

  // Want the libMesh count of variables, not MOOSE, e.g. I don't care about array variable counts
  const auto n_vars = system().n_vars();

  if (_scaling_group_variables.empty())
  {
    _var_to_group_var.reserve(n_vars);
    _num_scaling_groups = n_vars;

    for (const auto var_number : make_range(n_vars))
      _var_to_group_var.emplace(var_number, var_number);
  }
  else
  {
    std::set<unsigned int> var_numbers, var_numbers_covered, var_numbers_not_covered;
    for (const auto var_number : make_range(n_vars))
      var_numbers.insert(var_number);

    _num_scaling_groups = _scaling_group_variables.size();

    for (const auto group_index : index_range(_scaling_group_variables))
      for (const auto & var_name : _scaling_group_variables[group_index])
      {
        if (!hasVariable(var_name) && !hasScalarVariable(var_name))
          mooseError("'",
                     var_name,
                     "', provided to the 'scaling_group_variables' parameter, does not exist in "
                     "the nonlinear system.");

        const MooseVariableBase & var =
            hasVariable(var_name)
                ? static_cast<MooseVariableBase &>(getVariable(0, var_name))
                : static_cast<MooseVariableBase &>(getScalarVariable(0, var_name));
        auto map_pair = _var_to_group_var.emplace(var.number(), group_index);
        if (!map_pair.second)
          mooseError("Variable ", var_name, " is contained in multiple scaling grouplings");
        var_numbers_covered.insert(var.number());
      }

    std::set_difference(var_numbers.begin(),
                        var_numbers.end(),
                        var_numbers_covered.begin(),
                        var_numbers_covered.end(),
                        std::inserter(var_numbers_not_covered, var_numbers_not_covered.begin()));

    _num_scaling_groups = _scaling_group_variables.size() + var_numbers_not_covered.size();

    auto index = static_cast<unsigned int>(_scaling_group_variables.size());
    for (auto var_number : var_numbers_not_covered)
      _var_to_group_var.emplace(var_number, index++);
  }

  _variable_autoscaled.resize(n_vars, true);
  const auto & number_to_var_map = _vars[0].numberToVariableMap();

  if (_ignore_variables_for_autoscaling.size())
    for (const auto i : index_range(_variable_autoscaled))
      if (std::find(_ignore_variables_for_autoscaling.begin(),
                    _ignore_variables_for_autoscaling.end(),
                    libmesh_map_find(number_to_var_map, i)->name()) !=
          _ignore_variables_for_autoscaling.end())
        _variable_autoscaled[i] = false;

  _auto_scaling_initd = true;
}

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 185 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 134 of file SystemBase.h.

Referenced by Executioner::Executioner().

{ _verbose = verbose; }

shouldEvaluatePreSMOResidual()

bool NonlinearSystemBase::shouldEvaluatePreSMOResidual

(

)

const

We offer the option to check convergence against the pre-SMO residual.

This method handles the logic as to whether we should perform such residual evaluation.

Returns

A boolean indicating whether we should evaluate the pre-SMO residual.

Definition at line 727 of file NonlinearSystemBase.C.

Referenced by preSMOResidual(), and NonlinearSystem::solve().

{
  if (_fe_problem.solverParams(number())._type == Moose::ST_LINEAR)
    return false;

  // The legacy behavior (#10464) _always_ performs the pre-SMO residual evaluation
  // regardless of whether it is needed.
  //
  // This is not ideal and has been fixed by #23472. This legacy option ensures a smooth transition
  // to the new behavior. Modules and Apps that want to migrate to the new behavior should set this
  // parameter to false.
  if (_app.parameters().get<bool>("use_legacy_initial_residual_evaluation_behavior"))
    return true;

  return _use_pre_smo_residual;
}

solution() [1/2]

NumericVector<Number>& SystemBase::solution ( )

inlineinherited

Definition at line 195 of file SystemBase.h.

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

{ return solutionState(0); }

solution() [2/2]

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

inlineinherited

Definition at line 198 of file SystemBase.h.

{ return solutionState(0); }

solutionInternal()

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

inlinefinaloverrideprotectedvirtualinherited

Internal getter for solution owned by libMesh.

Implements SystemBase.

Definition at line 123 of file SolverSystem.h.

{
  return *system().solution;
}

solutionOld() [1/2]

NumericVector<Number>& SystemBase::solutionOld ( )

inlineinherited

Definition at line 196 of file SystemBase.h.

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

{ return solutionState(1); }

solutionOld() [2/2]

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

inlineinherited

Definition at line 199 of file SystemBase.h.

{ return solutionState(1); }

solutionOlder() [1/2]

NumericVector<Number>& SystemBase::solutionOlder ( )

inlineinherited

Definition at line 197 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 200 of file SystemBase.h.

{ return solutionState(2); }

solutionPreviousNewton() [1/2]

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

virtualinherited

Reimplemented in DisplacedSystem.

Definition at line 1345 of file SystemBase.C.

Referenced by AuxiliarySystem::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 1336 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 1419 of file SystemBase.C.

Referenced by SystemBase::copyOldSolutions(), SystemBase::copyPreviousNonlinearSolutions(), PointwiseRenormalizeVector::execute(), PointwiseRenormalizeVector::finalize(), SystemBase::restoreOldSolutions(), 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 1390 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];
}

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 897 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 252 of file SystemBase.h.

Referenced by MooseVariableScalar::adUDot(), ActuallyExplicitEuler::computeTimeDerivatives(), ImplicitEuler::computeTimeDerivatives(), ExplicitEuler::computeTimeDerivatives(), NewmarkBeta::computeTimeDerivatives(), BDF2::computeTimeDerivatives(), CentralDifference::computeTimeDerivatives(), CrankNicolson::computeTimeDerivatives(), LStableDirk2::computeTimeDerivatives(), LStableDirk3::computeTimeDerivatives(), ImplicitMidpoint::computeTimeDerivatives(), ExplicitTVDRK2::computeTimeDerivatives(), LStableDirk4::computeTimeDerivatives(), AStableDirk4::computeTimeDerivatives(), ExplicitRK2::computeTimeDerivatives(), 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 256 of file SystemBase.h.

{ return _u_dot; }

solutionUDotDot() [1/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 253 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 257 of file SystemBase.h.

{ return _u_dotdot; }

solutionUDotDotOld() [1/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 255 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 259 of file SystemBase.h.

{ return _u_dotdot_old; }

solutionUDotOld() [1/2]

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

inlinevirtualinherited

Reimplemented in DisplacedSystem.

Definition at line 254 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 258 of file SystemBase.h.

{ return _u_dot_old; }

solve()

virtual void NonlinearSystemBase::solve ( )

overridepure virtual

Solve the system (using libMesh magic)

Reimplemented from SystemBase.

Implemented in NonlinearEigenSystem, NonlinearSystem, and DumpObjectsNonlinearSystem.

Referenced by EigenProblem::doFreeNonlinearPowerIterations(), EigenProblem::solve(), and FEProblemBase::solve().

stopSolve()

virtual void SolverSystem::stopSolve ( const ExecFlagType &  exec_flag, const std::set< TagID > &  vector_tags_to_close  )

pure virtualinherited

Quit the current solve as soon as possible.

Implemented in LinearSystem, NonlinearEigenSystem, NonlinearSystem, DumpObjectsLinearSystem, and DumpObjectsNonlinearSystem.

Referenced by FEProblemBase::checkExceptionAndStopSolve().

subdomainSetup() [1/3]

void SystemBase::subdomainSetup

Definition at line 1559 of file SystemBase.C.

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

subdomainSetup() [2/3]

void NonlinearSystemBase::subdomainSetup ( SubdomainID  subdomain, THREAD_ID  tid  )

virtual

Called from assembling when we hit a new subdomain.

Parameters

subdomain	ID of the new subdomain
tid	Thread ID

Definition at line 998 of file NonlinearSystemBase.C.

{
  SolverSystem::subdomainSetup();

  _kernels.subdomainSetup(subdomain, tid);
  _nodal_kernels.subdomainSetup(subdomain, tid);
  _element_dampers.subdomainSetup(subdomain, tid);
  _nodal_dampers.subdomainSetup(subdomain, tid);
}

subdomainSetup() [3/3]

void SystemBase::subdomainSetup ( )

virtualinherited

Reimplemented in AuxiliarySystem.

Definition at line 1559 of file SystemBase.C.

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

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

subproblem() [1/2]

SubProblem& SystemBase::subproblem ( )

inlineinherited

Definition at line 101 of file SystemBase.h.

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

{ return _subproblem; }

subproblem() [2/2]

const SubProblem& SystemBase::subproblem ( ) const

inlineinherited

Definition at line 102 of file SystemBase.h.

{ return _subproblem; }

system() [1/2]

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

inlineoverridevirtual

Get the reference to the libMesh system.

Implements SystemBase.

Definition at line 638 of file NonlinearSystemBase.h.

Referenced by Adaptivity::adaptMesh(), PhysicsBasedPreconditioner::addSystem(), PhysicsBasedPreconditioner::apply(), computeScaling(), PseudoTimestep::currentResidualNorm(), DMCreateGlobalVector_Moose(), DMCreateMatrix_Moose(), DMMooseFunction(), DMMooseGetEmbedding_Private(), DMMooseGetMeshBlocks_Private(), DMMooseJacobian(), DMSetUp_Moose_Pre(), VariableResidual::execute(), getResidualNonTimeVector(), getResidualTimeVector(), NonlinearSystem::getSNES(), ExplicitTimeIntegrator::initialSetup(), ReferenceResidualConvergence::initialSetup(), MooseStaticCondensationPreconditioner::MooseStaticCondensationPreconditioner(), Moose::PetscSupport::petscSetDefaults(), Moose::PetscSupport::petscSetupDM(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), residualGhosted(), Moose::PetscSupport::setLineSearchFromParams(), PhysicsBasedPreconditioner::setup(), setupScalingData(), SingleMatrixPreconditioner::SingleMatrixPreconditioner(), NonlinearSystem::solve(), NonlinearEigenSystem::solve(), LStableDirk2::solve(), LStableDirk3::solve(), ImplicitMidpoint::solve(), ExplicitTVDRK2::solve(), LStableDirk4::solve(), AStableDirk4::solve(), ExplicitRK2::solve(), turnOffJacobian(), ReferenceResidualConvergence::updateReferenceResidual(), VariableCondensationPreconditioner::VariableCondensationPreconditioner(), and Console::writeVariableNorms().

{ return _sys; }

system() [2/2]

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

inlineoverridevirtual

Implements SystemBase.

Definition at line 639 of file NonlinearSystemBase.h.

{ return _sys; }

systemMatrixTag()

TagID NonlinearSystemBase::systemMatrixTag ( ) const

inlineoverridevirtual

Return the Matrix Tag ID for System.

Reimplemented from SystemBase.

Definition at line 650 of file NonlinearSystemBase.h.

Referenced by addImplicitGeometricCouplingEntries(), computeJacobian(), computeJacobianInternal(), FEProblemBase::computeJacobianInternal(), FEProblemBase::computeResidualAndJacobian(), constraintJacobians(), and enforceNodalConstraintsJacobian().

{ return _Ke_system_tag; }

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 47 of file PerfGraphInterface.C.

Referenced by PerfGraphInterface::registerTimedSection().

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

timeKernelVariableNames()

std::vector< std::string > NonlinearSystemBase::timeKernelVariableNames ( )

overridevirtual

Returns the names of the variables that have time derivative kernels in the system.

Implements SolverSystem.

Definition at line 3747 of file NonlinearSystemBase.C.

{
  std::vector<std::string> variable_names;
  const auto & time_kernels = _kernels.getVectorTagObjectWarehouse(timeVectorTag(), 0);
  if (time_kernels.hasActiveObjects())
    for (const auto & kernel : time_kernels.getObjects())
      variable_names.push_back(kernel->variable().name());

  return variable_names;
}

timestepSetup()

void NonlinearSystemBase::timestepSetup ( )

overridevirtual

Reimplemented from SystemBase.

Definition at line 306 of file NonlinearSystemBase.C.

{
  SolverSystem::timestepSetup();

  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    _kernels.timestepSetup(tid);
    _nodal_kernels.timestepSetup(tid);
    _dirac_kernels.timestepSetup(tid);
    if (_doing_dg)
      _dg_kernels.timestepSetup(tid);
    _interface_kernels.timestepSetup(tid);
    _element_dampers.timestepSetup(tid);
    _nodal_dampers.timestepSetup(tid);
    _integrated_bcs.timestepSetup(tid);

    if (_fe_problem.haveFV())
    {
      std::vector<FVFluxBC *> bcs;
      _fe_problem.theWarehouse()
          .query()
          .template condition<AttribSystem>("FVFluxBC")
          .template condition<AttribThread>(tid)
          .queryInto(bcs);

      std::vector<FVInterfaceKernel *> iks;
      _fe_problem.theWarehouse()
          .query()
          .template condition<AttribSystem>("FVInterfaceKernel")
          .template condition<AttribThread>(tid)
          .queryInto(iks);

      std::vector<FVFluxKernel *> kernels;
      _fe_problem.theWarehouse()
          .query()
          .template condition<AttribSystem>("FVFluxKernel")
          .template condition<AttribThread>(tid)
          .queryInto(kernels);

      for (auto * bc : bcs)
        bc->timestepSetup();
      for (auto * ik : iks)
        ik->timestepSetup();
      for (auto * kernel : kernels)
        kernel->timestepSetup();
    }
  }
  _scalar_kernels.timestepSetup();
  _constraints.timestepSetup();
  _general_dampers.timestepSetup();
  _nodal_bcs.timestepSetup();
}

timeVectorTag()

TagID NonlinearSystemBase::timeVectorTag ( ) const

inlineoverridevirtual

Ideally, we should not need this API.

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

Reimplemented from SystemBase.

Definition at line 647 of file NonlinearSystemBase.h.

Referenced by FEProblemBase::addCachedResidualDirectly(), containsTimeKernel(), and timeKernelVariableNames().

{ return _Re_time_tag; }

turnOffJacobian()

void NonlinearSystemBase::turnOffJacobian ( )

virtual

Turn off the Jacobian (must be called before equation system initialization)

Reimplemented in NonlinearEigenSystem.

Definition at line 195 of file NonlinearSystemBase.C.

{
  system().set_basic_system_only();
  nonlinearSolver()->jacobian = NULL;
}

update()

void SystemBase::update ( )

inherited

Update the system (doing libMesh magic)

Definition at line 1245 of file SystemBase.C.

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

{
  system().update();
}

updateActive()

void NonlinearSystemBase::updateActive

(

THREAD_ID

tid

)

Update active objects of Warehouses owned by NonlinearSystemBase.

Definition at line 3294 of file NonlinearSystemBase.C.

{
  _element_dampers.updateActive(tid);
  _nodal_dampers.updateActive(tid);
  _integrated_bcs.updateActive(tid);
  _dg_kernels.updateActive(tid);
  _interface_kernels.updateActive(tid);
  _dirac_kernels.updateActive(tid);
  _kernels.updateActive(tid);
  _nodal_kernels.updateActive(tid);
  if (tid == 0)
  {
    _general_dampers.updateActive();
    _nodal_bcs.updateActive();
    _preset_nodal_bcs.updateActive();
    _ad_preset_nodal_bcs.updateActive();
    _constraints.updateActive();
    _scalar_kernels.updateActive();
  }
}

useFieldSplitPreconditioner()

void NonlinearSystemBase::useFieldSplitPreconditioner ( bool  use = true )

inline

If called with true this system will use a field split preconditioner matrix.

Definition at line 462 of file NonlinearSystemBase.h.

Referenced by FieldSplitPreconditioner::FieldSplitPreconditioner().

{ _use_field_split_preconditioner = use; }

useFiniteDifferencedPreconditioner()

void NonlinearSystemBase::useFiniteDifferencedPreconditioner ( bool  use = true )

inline

If called with true this system will use a finite differenced form of the Jacobian as the preconditioner.

Definition at line 447 of file NonlinearSystemBase.h.

Referenced by FiniteDifferencePreconditioner::FiniteDifferencePreconditioner().

  {
    _use_finite_differenced_preconditioner = use;
  }

usePreSMOResidual()

const bool& NonlinearSystemBase::usePreSMOResidual ( ) const

inline

Whether we are using pre-SMO residual in relative convergence checks.

Definition at line 254 of file NonlinearSystemBase.h.

Referenced by Console::outputSystemInformation(), and referenceResidual().

{ return _use_pre_smo_residual; }

validParams()

InputParameters PerfGraphInterface::validParams ( )

staticinherited

Definition at line 16 of file PerfGraphInterface.C.

Referenced by Convergence::validParams().

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

varKind()

Moose::VarKindType SystemBase::varKind ( ) const

inlineinherited

Returns

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

Definition at line 925 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 666 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 685 of file SystemBase.C.

Referenced by computeResidualAndJacobianTags(), and 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 199 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 234 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 228 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_residual);
}

zeroVectorForResidual()

void NonlinearSystemBase::zeroVectorForResidual

(

const std::string &

vector_name

)

Definition at line 772 of file NonlinearSystemBase.C.

{
  for (unsigned int i = 0; i < _vecs_to_zero_for_residual.size(); ++i)
    if (vector_name == _vecs_to_zero_for_residual[i])
      return;

  _vecs_to_zero_for_residual.push_back(vector_name);
}

Member Data Documentation

_ad_preset_nodal_bcs

MooseObjectWarehouse<ADDirichletBCBase> NonlinearSystemBase::_ad_preset_nodal_bcs

protected

Definition at line 858 of file NonlinearSystemBase.h.

Referenced by addBoundaryCondition(), setInitialSolution(), and updateActive().

_add_implicit_geometric_coupling_entries_to_jacobian

bool NonlinearSystemBase::_add_implicit_geometric_coupling_entries_to_jacobian

protected

Whether or not to add implicit geometric couplings to the Jacobian for FDP.

Definition at line 900 of file NonlinearSystemBase.h.

Referenced by addImplicitGeometricCouplingEntriesToJacobian(), augmentSparsity(), and computeJacobianInternal().

_app

MooseApp& SystemBase::_app

protectedinherited

Definition at line 982 of file SystemBase.h.

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

_assemble_constraints_separately

bool NonlinearSystemBase::_assemble_constraints_separately

protected

Whether or not to assemble the residual and Jacobian after the application of each constraint.

Definition at line 903 of file NonlinearSystemBase.h.

Referenced by assembleConstraintsSeparately(), constraintJacobians(), and constraintResiduals().

_auto_scaling_initd

bool NonlinearSystemBase::_auto_scaling_initd

private

Whether we've initialized the automatic scaling data structures.

Definition at line 1007 of file NonlinearSystemBase.h.

Referenced by computeScaling(), and setupScalingData().

_automatic_scaling

bool SystemBase::_automatic_scaling

protectedinherited

Whether to automatically scale the variables.

Definition at line 1047 of file SystemBase.h.

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

_compute_scaling_once

bool NonlinearSystemBase::_compute_scaling_once

protected

Whether the scaling factors should only be computed once at the beginning of the simulation through an extra Jacobian evaluation.

If this is set to false, then the scaling factors will be computed during an extra Jacobian evaluation at the beginning of every time step.

Definition at line 958 of file NonlinearSystemBase.h.

Referenced by computeScaling(), and computeScalingOnce().

_computed_scaling

bool NonlinearSystemBase::_computed_scaling

protected

Flag used to indicate whether we have already computed the scaling Jacobian.

Definition at line 953 of file NonlinearSystemBase.h.

Referenced by computedScalingJacobian(), and computeScaling().

_computing_pre_smo_residual

bool NonlinearSystemBase::_computing_pre_smo_residual

protected

Definition at line 927 of file NonlinearSystemBase.h.

Referenced by computingPreSMOResidual(), and NonlinearSystem::solve().

_console

const ConsoleStream ConsoleStreamInterface::_console

inherited

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

Definition at line 31 of file ConsoleStreamInterface.h.

Referenced by IterationAdaptiveDT::acceptStep(), MeshOnlyAction::act(), SetupDebugAction::act(), MaterialOutputAction::act(), Adaptivity::adaptMesh(), FEProblemBase::adaptMesh(), PerfGraph::addToExecutionList(), SimplePredictor::apply(), SystemBase::applyScalingFactors(), MultiApp::backup(), FEProblemBase::backupMultiApps(), CoarsenedPiecewiseLinear::buildCoarsenedGrid(), MeshDiagnosticsGenerator::checkElementOverlap(), MeshDiagnosticsGenerator::checkElementTypes(), MeshDiagnosticsGenerator::checkElementVolumes(), FEProblemBase::checkExceptionAndStopSolve(), SolverSystem::checkInvalidSolution(), MeshDiagnosticsGenerator::checkLocalJacobians(), MeshDiagnosticsGenerator::checkNonConformalMesh(), MeshDiagnosticsGenerator::checkNonConformalMeshFromAdaptivity(), MeshDiagnosticsGenerator::checkNonMatchingEdges(), MeshDiagnosticsGenerator::checkNonPlanarSides(), FEProblemBase::checkProblemIntegrity(), ReferenceResidualConvergence::checkRelativeConvergence(), MeshDiagnosticsGenerator::checkSidesetsOrientation(), MeshDiagnosticsGenerator::checkWatertightNodesets(), MeshDiagnosticsGenerator::checkWatertightSidesets(), IterationAdaptiveDT::computeAdaptiveDT(), TransientBase::computeConstrainedDT(), DefaultMultiAppFixedPointConvergence::computeCustomConvergencePostprocessor(), computeDamping(), FixedPointIterationAdaptiveDT::computeDT(), IterationAdaptiveDT::computeDT(), IterationAdaptiveDT::computeFailedDT(), IterationAdaptiveDT::computeInitialDT(), IterationAdaptiveDT::computeInterpolationDT(), LinearSystem::computeLinearSystemTags(), FEProblemBase::computeLinearSystemTags(), 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(), FEProblemBase::finishMultiAppStep(), MeshRepairGenerator::fixOverlappingNodes(), CoarsenBlockGenerator::generate(), MeshGenerator::generateInternal(), VariableCondensationPreconditioner::getDofToCondense(), InversePowerMethod::init(), NonlinearEigen::init(), FEProblemBase::initialAdaptMesh(), DefaultMultiAppFixedPointConvergence::initialize(), EigenExecutionerBase::inversePowerIteration(), FEProblemBase::joinAndFinalize(), TransientBase::keepGoing(), IterationAdaptiveDT::limitDTByFunction(), IterationAdaptiveDT::limitDTToPostprocessorValue(), FEProblemBase::logAdd(), EigenExecutionerBase::makeBXConsistent(), Console::meshChanged(), MooseBaseErrorInterface::mooseDeprecated(), MooseBaseErrorInterface::mooseInfo(), MooseBaseErrorInterface::mooseWarning(), MooseBaseErrorInterface::mooseWarningNonPrefixed(), ReferenceResidualConvergence::nonlinearConvergenceSetup(), ReporterDebugOutput::output(), PerfGraphOutput::output(), SolutionInvalidityOutput::output(), MaterialPropertyDebugOutput::output(), DOFMapOutput::output(), VariableResidualNormsDebugOutput::output(), Console::output(), ControlOutput::outputActiveObjects(), ControlOutput::outputChangedControls(), ControlOutput::outputControls(), Console::outputInput(), Console::outputPostprocessors(), PseudoTimestep::outputPseudoTimestep(), Console::outputReporters(), DefaultMultiAppFixedPointConvergence::outputResidualNorm(), Console::outputScalarVariables(), Console::outputSystemInformation(), FEProblemBase::possiblyRebuildGeomSearchPatches(), EigenExecutionerBase::postExecute(), AB2PredictorCorrector::postSolve(), ActionWarehouse::printActionDependencySets(), BlockRestrictionDebugOutput::printBlockRestrictionMap(), SolutionInvalidity::printDebug(), EigenExecutionerBase::printEigenvalue(), SecantSolve::printFixedPointConvergenceHistory(), SteffensenSolve::printFixedPointConvergenceHistory(), PicardSolve::printFixedPointConvergenceHistory(), FixedPointSolve::printFixedPointConvergenceReason(), PerfGraphLivePrint::printLiveMessage(), MaterialPropertyDebugOutput::printMaterialMap(), PerfGraphLivePrint::printStats(), NEML2Action::printSummary(), AutomaticMortarGeneration::projectPrimaryNodesSinglePair(), AutomaticMortarGeneration::projectSecondaryNodesSinglePair(), CoarsenBlockGenerator::recursiveCoarsen(), SolutionTimeAdaptiveDT::rejectStep(), MultiApp::restore(), FEProblemBase::restoreMultiApps(), FEProblemBase::restoreSolutions(), setInitialSolution(), MooseApp::setupOptions(), Checkpoint::shouldOutput(), SubProblem::showFunctorRequestors(), SubProblem::showFunctors(), FullSolveMultiApp::showStatusMessage(), FEProblemSolve::solve(), FixedPointSolve::solve(), EigenProblem::solve(), NonlinearSystem::solve(), LinearSystem::solve(), LStableDirk2::solve(), LStableDirk3::solve(), ImplicitMidpoint::solve(), ExplicitTVDRK2::solve(), AStableDirk4::solve(), LStableDirk4::solve(), ExplicitRK2::solve(), TransientMultiApp::solveStep(), FixedPointSolve::solveStep(), PerfGraphLivePrint::start(), AB2PredictorCorrector::step(), NonlinearEigen::takeStep(), TransientBase::takeStep(), TerminateChainControl::terminate(), Convergence::verboseOutput(), Console::writeTimestepInformation(), Console::writeVariableNorms(), and FEProblemBase::~FEProblemBase().

_constraints

ConstraintWarehouse NonlinearSystemBase::_constraints

protected

Constraints storage object.

Definition at line 880 of file NonlinearSystemBase.h.

Referenced by addConstraint(), checkKernelCoverage(), computeResidualInternal(), constraintJacobians(), constraintResiduals(), customSetup(), enforceNodalConstraintsJacobian(), enforceNodalConstraintsResidual(), findImplicitGeometricCouplingEntries(), getConstraintWarehouse(), initialSetup(), jacobianSetup(), overwriteNodeFace(), residualSetup(), setConstraintSecondaryValues(), timestepSetup(), and updateActive().

_current_l_its

std::vector<unsigned int> NonlinearSystemBase::_current_l_its

Definition at line 693 of file NonlinearSystemBase.h.

Referenced by SolutionHistory::output(), and preSolve().

_current_nl_its

unsigned int NonlinearSystemBase::_current_nl_its

Definition at line 694 of file NonlinearSystemBase.h.

Referenced by DefaultNonlinearConvergence::checkConvergence(), SolutionHistory::output(), and preSolve().

_current_solution

const NumericVector<Number>* SolverSystem::_current_solution

protectedinherited

solution vector from solver

Definition at line 105 of file SolverSystem.h.

Referenced by NonlinearSystem::computeScalingJacobian(), NonlinearEigenSystem::computeScalingJacobian(), NonlinearSystem::computeScalingResidual(), NonlinearEigenSystem::computeScalingResidual(), SolverSystem::currentSolution(), SolverSystem::preInit(), SolverSystem::restoreSolutions(), SolverSystem::serializeSolution(), SolverSystem::setSolution(), and NonlinearSystem::solve().

_debugging_residuals

bool NonlinearSystemBase::_debugging_residuals

protected

true if debugging residuals

Definition at line 908 of file NonlinearSystemBase.h.

Referenced by computeResidualTags(), and debuggingResiduals().

_decomposition_split

std::string NonlinearSystemBase::_decomposition_split

protected

Name of the top-level split of the decomposition.

Definition at line 895 of file NonlinearSystemBase.h.

Referenced by setDecomposition(), setupDM(), and setupFieldDecomposition().

_dg_kernels

MooseObjectTagWarehouse<DGKernelBase> NonlinearSystemBase::_dg_kernels

protected

Definition at line 848 of file NonlinearSystemBase.h.

Referenced by addDGKernel(), checkKernelCoverage(), customSetup(), getDGKernelWarehouse(), initialSetup(), jacobianSetup(), residualSetup(), timestepSetup(), and updateActive().

_dirac_kernels

MooseObjectTagWarehouse<DiracKernelBase> NonlinearSystemBase::_dirac_kernels

protected

Dirac Kernel storage for each thread.

Definition at line 862 of file NonlinearSystemBase.h.

Referenced by addDiracKernel(), computeDiracContributions(), customSetup(), getDiracKernelWarehouse(), initialSetup(), jacobianSetup(), residualSetup(), timestepSetup(), and updateActive().

_displaced_mortar_functors

std::unordered_map<std::pair<BoundaryID, BoundaryID>, ComputeMortarFunctor> NonlinearSystemBase::_displaced_mortar_functors

private

Functors for computing displaced mortar constraints.

Definition at line 1001 of file NonlinearSystemBase.h.

Referenced by initialSetup(), and mortarConstraints().

_doing_dg

bool NonlinearSystemBase::_doing_dg

protected

true if DG is active (optimization reasons)

Definition at line 911 of file NonlinearSystemBase.h.

Referenced by addDGKernel(), customSetup(), doingDG(), initialSetup(), jacobianSetup(), needSubdomainMaterialOnSide(), residualSetup(), and timestepSetup().

_du_dot_du

Number NonlinearSystemBase::_du_dot_du

protected

\( {du^dot}\over{du} \)

Definition at line 813 of file NonlinearSystemBase.h.

_du_dotdot_du

Number NonlinearSystemBase::_du_dotdot_du

protected

\( {du^dotdot}\over{du} \)

Definition at line 815 of file NonlinearSystemBase.h.

_element_dampers

MooseObjectWarehouse<ElementDamper> NonlinearSystemBase::_element_dampers

protected

Element Dampers for each thread.

Definition at line 865 of file NonlinearSystemBase.h.

Referenced by addDamper(), computeDamping(), customSetup(), getElementDamperWarehouse(), initialSetup(), jacobianSetup(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_factory

Factory& SystemBase::_factory

protectedinherited

Definition at line 983 of file SystemBase.h.

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

_fdcoloring

MatFDColoring NonlinearSystemBase::_fdcoloring

protected

Definition at line 890 of file NonlinearSystemBase.h.

Referenced by destroyColoring(), NonlinearSystem::setupColoringFiniteDifferencedPreconditioner(), and NonlinearSystem::solve().

_fe_problem

FEProblemBase& SystemBase::_fe_problem

protectedinherited

the governing finite element/volume problem

Definition at line 980 of file SystemBase.h.

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

_final_residual

Real NonlinearSystemBase::_final_residual

protected

Definition at line 922 of file NonlinearSystemBase.h.

Referenced by finalNonlinearResidual(), and NonlinearSystem::solve().

_general_dampers

MooseObjectWarehouse<GeneralDamper> NonlinearSystemBase::_general_dampers

protected

General Dampers.

Definition at line 871 of file NonlinearSystemBase.h.

Referenced by addDamper(), computeDamping(), customSetup(), initialSetup(), jacobianSetup(), residualSetup(), timestepSetup(), and updateActive().

_has_diag_save_in

bool NonlinearSystemBase::_has_diag_save_in

protected

If there is any Kernel or IntegratedBC having diag_save_in.

Definition at line 942 of file NonlinearSystemBase.h.

Referenced by addBoundaryCondition(), addDGKernel(), MooseEigenSystem::addKernel(), addKernel(), addNodalKernel(), computeJacobianInternal(), and hasDiagSaveIn().

_has_nodalbc_diag_save_in

bool NonlinearSystemBase::_has_nodalbc_diag_save_in

protected

If there is a nodal BC having diag_save_in.

Definition at line 948 of file NonlinearSystemBase.h.

Referenced by addBoundaryCondition(), computeJacobianInternal(), and hasDiagSaveIn().

_has_nodalbc_save_in

bool NonlinearSystemBase::_has_nodalbc_save_in

protected

If there is a nodal BC having save_in.

Definition at line 945 of file NonlinearSystemBase.h.

Referenced by addBoundaryCondition(), computeResidualTags(), and hasSaveIn().

_has_save_in

bool NonlinearSystemBase::_has_save_in

protected

If there is any Kernel or IntegratedBC having save_in.

Definition at line 939 of file NonlinearSystemBase.h.

Referenced by addBoundaryCondition(), addDGKernel(), MooseEigenSystem::addKernel(), addKernel(), addNodalKernel(), computeNodalBCs(), and hasSaveIn().

_have_decomposition

bool NonlinearSystemBase::_have_decomposition

protected

Whether or not the system can be decomposed into splits.

Definition at line 893 of file NonlinearSystemBase.h.

Referenced by setDecomposition(), and setupFieldDecomposition().

_hybridized_kernels

MooseObjectTagWarehouse<HDGKernel> NonlinearSystemBase::_hybridized_kernels

protected

Definition at line 846 of file NonlinearSystemBase.h.

Referenced by addHDGKernel(), and getHDGKernelWarehouse().

_ignore_variables_for_autoscaling

std::vector<std::string> NonlinearSystemBase::_ignore_variables_for_autoscaling

protected

A container for variables that do not partipate in autoscaling.

Definition at line 974 of file NonlinearSystemBase.h.

Referenced by ignoreVariablesForAutoscaling(), and setupScalingData().

_increment_vec

NumericVector<Number>* NonlinearSystemBase::_increment_vec

protected

increment vector

Definition at line 883 of file NonlinearSystemBase.h.

Referenced by computeDamping(), reinitIncrementAtNodeForDampers(), reinitIncrementAtQpsForDampers(), and setupDampers().

_initial_residual

Real NonlinearSystemBase::_initial_residual

protected

The initial (i.e., 0th nonlinear iteration) residual, see setPreSMOResidual for a detailed explanation.

Definition at line 932 of file NonlinearSystemBase.h.

Referenced by initialResidual(), and setInitialResidual().

_integrated_bcs

MooseObjectTagWarehouse<IntegratedBCBase> NonlinearSystemBase::_integrated_bcs

protected

BoundaryCondition Warhouses

Definition at line 855 of file NonlinearSystemBase.h.

Referenced by addBoundaryCondition(), customSetup(), getIntegratedBCWarehouse(), initialSetup(), jacobianSetup(), needBoundaryMaterialOnSide(), residualSetup(), timestepSetup(), and updateActive().

_interface_kernels

MooseObjectTagWarehouse<InterfaceKernelBase> NonlinearSystemBase::_interface_kernels

protected

Definition at line 849 of file NonlinearSystemBase.h.

Referenced by addInterfaceKernel(), customSetup(), getInterfaceKernelWarehouse(), initialSetup(), jacobianSetup(), needInterfaceMaterialOnSide(), residualSetup(), timestepSetup(), and updateActive().

_Ke_non_time_tag

TagID NonlinearSystemBase::_Ke_non_time_tag

protected

Tag for non-time contribution Jacobian.

Definition at line 838 of file NonlinearSystemBase.h.

_Ke_system_tag

TagID NonlinearSystemBase::_Ke_system_tag

protected

Tag for system contribution Jacobian.

Definition at line 841 of file NonlinearSystemBase.h.

Referenced by NonlinearSystemBase(), and systemMatrixTag().

_kernels

MooseObjectTagWarehouse<KernelBase> NonlinearSystemBase::_kernels

protected

Kernel Storage

Definition at line 845 of file NonlinearSystemBase.h.

Referenced by addHDGKernel(), MooseEigenSystem::addKernel(), addKernel(), checkKernelCoverage(), containsTimeKernel(), customSetup(), getKernelWarehouse(), initialSetup(), jacobianSetup(), residualSetup(), subdomainSetup(), timeKernelVariableNames(), timestepSetup(), and updateActive().

_ksp_norm

Moose::MooseKSPNormType SolverSystem::_ksp_norm

protectedinherited

KSP norm type.

Definition at line 110 of file SolverSystem.h.

Referenced by SolverSystem::getMooseKSPNormType(), and SolverSystem::setMooseKSPNormType().

_last_nl_rnorm

Real NonlinearSystemBase::_last_nl_rnorm

Definition at line 692 of file NonlinearSystemBase.h.

Referenced by DefaultNonlinearConvergence::checkConvergence(), and nonlinearNorm().

_matrix_tag_active_flags

std::vector<bool> SystemBase::_matrix_tag_active_flags

protectedinherited

Active flags for tagged matrices.

Definition at line 1019 of file SystemBase.h.

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

_max_var_n_dofs_per_elem

size_t SystemBase::_max_var_n_dofs_per_elem

protectedinherited

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

Definition at line 1035 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 1038 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 994 of file SystemBase.h.

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

_mesh

MooseMesh& SystemBase::_mesh

protectedinherited

Definition at line 985 of file SystemBase.h.

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

_n_iters

unsigned int NonlinearSystemBase::_n_iters

protected

Definition at line 916 of file NonlinearSystemBase.h.

Referenced by nNonlinearIterations(), and NonlinearSystem::solve().

_n_linear_iters

unsigned int NonlinearSystemBase::_n_linear_iters

protected

Definition at line 917 of file NonlinearSystemBase.h.

Referenced by nLinearIterations(), and NonlinearSystem::solve().

_n_residual_evaluations

unsigned int NonlinearSystemBase::_n_residual_evaluations

protected

Total number of residual evaluations that have been performed.

Definition at line 920 of file NonlinearSystemBase.h.

Referenced by computeResidualTags(), and nResidualEvaluations().

_name

std::string SystemBase::_name

protectedinherited

The name of this system.

Definition at line 987 of file SystemBase.h.

_need_residual_ghosted

bool NonlinearSystemBase::_need_residual_ghosted

protected

Whether or not a ghosted copy of the residual needs to be made.

Definition at line 906 of file NonlinearSystemBase.h.

Referenced by computeResidualInternal(), computeResidualTags(), constraintResiduals(), getResidualNonTimeVector(), getResidualTimeVector(), and residualGhosted().

_nl_matrix_tags

std::set<TagID> NonlinearSystemBase::_nl_matrix_tags

protected

Matrix tags to temporarily store all tags associated with the current system.

Definition at line 824 of file NonlinearSystemBase.h.

Referenced by computeJacobian(), and computeJacobianBlocks().

_nl_vector_tags

std::set<TagID> NonlinearSystemBase::_nl_vector_tags

protected

Vector tags to temporarily store all tags associated with the current system.

Definition at line 821 of file NonlinearSystemBase.h.

Referenced by computeResidualTag().

_nodal_bcs

MooseObjectTagWarehouse<NodalBCBase> NonlinearSystemBase::_nodal_bcs

protected

Definition at line 856 of file NonlinearSystemBase.h.

Referenced by addBoundaryCondition(), NonlinearEigenSystem::checkIntegrity(), computeJacobianBlocks(), computeJacobianInternal(), computeNodalBCs(), computeNodalBCsResidualAndJacobian(), customSetup(), getNodalBCWarehouse(), initialSetup(), jacobianSetup(), residualSetup(), timestepSetup(), and updateActive().

_nodal_dampers

MooseObjectWarehouse<NodalDamper> NonlinearSystemBase::_nodal_dampers

protected

Nodal Dampers for each thread.

Definition at line 868 of file NonlinearSystemBase.h.

Referenced by addDamper(), computeDamping(), customSetup(), getNodalDamperWarehouse(), initialSetup(), jacobianSetup(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_nodal_kernels

MooseObjectTagWarehouse<NodalKernelBase> NonlinearSystemBase::_nodal_kernels

protected

NodalKernels for each thread.

Definition at line 874 of file NonlinearSystemBase.h.

Referenced by addNodalKernel(), checkKernelCoverage(), computeJacobianInternal(), computeResidualInternal(), customSetup(), getNodalKernelWarehouse(), initialSetup(), jacobianSetup(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().

_num_residual_evaluations

unsigned int NonlinearSystemBase::_num_residual_evaluations

Definition at line 553 of file NonlinearSystemBase.h.

_num_scaling_groups

std::size_t NonlinearSystemBase::_num_scaling_groups

private

The number of scaling groups.

Definition at line 1013 of file NonlinearSystemBase.h.

Referenced by computeScaling(), and setupScalingData().

_numbered_vars

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

protectedinherited

Map variable number to its pointer.

Definition at line 1044 of file SystemBase.h.

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

_off_diagonals_in_auto_scaling

bool NonlinearSystemBase::_off_diagonals_in_auto_scaling

protected

Whether to include off diagonals when determining automatic scaling factors.

Definition at line 977 of file NonlinearSystemBase.h.

Referenced by initialSetup(), and offDiagonalsInAutoScaling().

_pc_side

Moose::PCSideType SolverSystem::_pc_side

protectedinherited

Preconditioning side.

Definition at line 108 of file SolverSystem.h.

Referenced by SolverSystem::getPCSide(), and SolverSystem::setPCSide().

_pg_moose_app

MooseApp& PerfGraphInterface::_pg_moose_app

protectedinherited

The MooseApp that owns the PerfGraph.

Definition at line 124 of file PerfGraphInterface.h.

Referenced by PerfGraphInterface::perfGraph().

_pre_smo_residual

Real NonlinearSystemBase::_pre_smo_residual

protected

The pre-SMO residual, see setPreSMOResidual for a detailed explanation.

Definition at line 930 of file NonlinearSystemBase.h.

Referenced by preSMOResidual(), and NonlinearSystem::solve().

_preconditioner

std::shared_ptr<MoosePreconditioner> NonlinearSystemBase::_preconditioner

protected

Preconditioner.

Definition at line 885 of file NonlinearSystemBase.h.

Referenced by getPreconditioner(), initialSetup(), setPreconditioner(), and NonlinearSystem::setupFiniteDifferencedPreconditioner().

_predictor

std::shared_ptr<Predictor> NonlinearSystemBase::_predictor

protected

If predictor is active, this is non-NULL.

Definition at line 925 of file NonlinearSystemBase.h.

Referenced by getPredictor(), onTimestepBegin(), setInitialSolution(), and setPredictor().

_prefix

const std::string PerfGraphInterface::_prefix

protectedinherited

A prefix to use for all sections.

Definition at line 127 of file PerfGraphInterface.h.

Referenced by PerfGraphInterface::timedSectionName().

_preset_nodal_bcs

MooseObjectWarehouse<DirichletBCBase> NonlinearSystemBase::_preset_nodal_bcs

protected

Definition at line 857 of file NonlinearSystemBase.h.

Referenced by addBoundaryCondition(), setInitialSolution(), and updateActive().

_print_all_var_norms

bool NonlinearSystemBase::_print_all_var_norms

protected

Definition at line 936 of file NonlinearSystemBase.h.

Referenced by printAllVariableNorms().

_raw_grad_container

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

protectedinherited

A cache for storing gradients at dof locations.

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

Definition at line 1065 of file SystemBase.h.

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

_Re_non_time

NumericVector<Number>* NonlinearSystemBase::_Re_non_time

protected

residual vector for non-time contributions

Definition at line 832 of file NonlinearSystemBase.h.

Referenced by computeNodalBCs(), computeResidualAndJacobianTags(), computeResidualInternal(), computeResidualTags(), getResidualNonTimeVector(), and residualGhosted().

_Re_non_time_tag

TagID NonlinearSystemBase::_Re_non_time_tag

protected

Tag for non-time contribution residual.

Definition at line 830 of file NonlinearSystemBase.h.

Referenced by getResidualNonTimeVector(), nonTimeVectorTag(), and residualGhosted().

_Re_tag

TagID NonlinearSystemBase::_Re_tag

protected

Used for the residual vector from PETSc.

Definition at line 835 of file NonlinearSystemBase.h.

Referenced by NonlinearSystemBase(), and residualVectorTag().

_Re_time

NumericVector<Number>* NonlinearSystemBase::_Re_time

protected

residual vector for time contributions

Definition at line 827 of file NonlinearSystemBase.h.

Referenced by computeNodalBCs(), getResidualTimeVector(), and residualGhosted().

_Re_time_tag

TagID NonlinearSystemBase::_Re_time_tag

protected

Tag for time contribution residual.

Definition at line 818 of file NonlinearSystemBase.h.

Referenced by getResidualTimeVector(), residualGhosted(), and timeVectorTag().

_resid_vs_jac_scaling_param

Real NonlinearSystemBase::_resid_vs_jac_scaling_param

protected

The param that indicates the weighting of the residual vs the Jacobian in determining variable scaling parameters.

A value of 1 indicates pure residual-based scaling. A value of 0 indicates pure Jacobian-based scaling

Definition at line 963 of file NonlinearSystemBase.h.

Referenced by autoScalingParam(), and computeScaling().

_residual_copy

std::unique_ptr<NumericVector<Number> > NonlinearSystemBase::_residual_copy

protected

Copy of the residual vector, or nullptr if a copy is not needed.

Definition at line 810 of file NonlinearSystemBase.h.

Referenced by computeResidualInternal(), preInit(), and residualCopy().

_residual_ghosted

NumericVector<Number>* NonlinearSystemBase::_residual_ghosted

protected

ghosted form of the residual

Definition at line 807 of file NonlinearSystemBase.h.

Referenced by computeResidualInternal(), computeResidualTags(), constraintResiduals(), and residualGhosted().

_saved_dot_old

NumericVector<Real>* SystemBase::_saved_dot_old

protectedinherited

Definition at line 1026 of file SystemBase.h.

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

_saved_dotdot_old

NumericVector<Real>* SystemBase::_saved_dotdot_old

protectedinherited

Definition at line 1027 of file SystemBase.h.

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

_saved_old

NumericVector<Real>* SystemBase::_saved_old

protectedinherited

Definition at line 1022 of file SystemBase.h.

_saved_older

NumericVector<Real>* SystemBase::_saved_older

protectedinherited

Definition at line 1023 of file SystemBase.h.

_scalar_kernels

MooseObjectTagWarehouse<ScalarKernelBase> NonlinearSystemBase::_scalar_kernels

protected

Definition at line 847 of file NonlinearSystemBase.h.

Referenced by addScalarKernel(), checkKernelCoverage(), computeResidualInternal(), computeScalarKernelsJacobians(), customSetup(), getScalarKernelWarehouse(), initialSetup(), jacobianSetup(), residualSetup(), timestepSetup(), and updateActive().

_scaling_group_variables

std::vector<std::vector<std::string> > NonlinearSystemBase::_scaling_group_variables

protected

A container of variable groupings that can be used in scaling calculations.

This can be useful for simulations in which vector-like variables are split into invidual scalar-field components like for solid/fluid mechanics

Definition at line 968 of file NonlinearSystemBase.h.

Referenced by scalingGroupVariables(), and setupScalingData().

_scaling_matrix

std::unique_ptr<libMesh::DiagonalMatrix<Number> > NonlinearSystemBase::_scaling_matrix

protected

A diagonal matrix used for computing scaling.

Definition at line 980 of file NonlinearSystemBase.h.

Referenced by computeScaling(), NonlinearSystem::computeScalingJacobian(), NonlinearEigenSystem::computeScalingJacobian(), and initialSetup().

_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 1060 of file SystemBase.h.

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

_solution_is_invalid

bool SolverSystem::_solution_is_invalid

protectedinherited

Boolean to see if solution is invalid.

Definition at line 113 of file SolverSystem.h.

_solution_state

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

private

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

Definition at line 1004 of file NonlinearSystemBase.h.

_solution_states_initialized

bool SystemBase::_solution_states_initialized

protectedinherited

Whether or not the solution states have been initialized.

Definition at line 1053 of file SystemBase.h.

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

_splits

MooseObjectWarehouseBase<Split> NonlinearSystemBase::_splits

protected

Decomposition splits.

Definition at line 877 of file NonlinearSystemBase.h.

Referenced by addSplit(), getSplit(), and getSplits().

_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 977 of file SystemBase.h.

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

_sys

libMesh::System& NonlinearSystemBase::_sys

Definition at line 690 of file NonlinearSystemBase.h.

Referenced by NonlinearSystemBase(), preInit(), setInitialSolution(), setupDampers(), and system().

_tagged_matrices

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

protectedinherited

Tagged matrices (pointer)

Definition at line 1017 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 1015 of file SystemBase.h.

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

_time_integrators

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

protectedinherited

Time integrator.

Definition at line 1041 of file SystemBase.h.

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

_u_dot

NumericVector<Number>* SystemBase::_u_dot

protectedinherited

solution vector for u^dot

Definition at line 1000 of file SystemBase.h.

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

_u_dot_old

NumericVector<Number>* SystemBase::_u_dot_old

protectedinherited

old solution vector for u^dot

Definition at line 1005 of file SystemBase.h.

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

_u_dotdot

NumericVector<Number>* SystemBase::_u_dotdot

protectedinherited

solution vector for u^dotdot

Definition at line 1002 of file SystemBase.h.

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

_u_dotdot_old

NumericVector<Number>* SystemBase::_u_dotdot_old

protectedinherited

old solution vector for u^dotdot

Definition at line 1007 of file SystemBase.h.

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

_undisplaced_mortar_functors

std::unordered_map<std::pair<BoundaryID, BoundaryID>, ComputeMortarFunctor> NonlinearSystemBase::_undisplaced_mortar_functors

private

Functors for computing undisplaced mortar constraints.

Definition at line 997 of file NonlinearSystemBase.h.

Referenced by initialSetup(), and mortarConstraints().

_use_field_split_preconditioner

bool NonlinearSystemBase::_use_field_split_preconditioner

protected

Whether or not to use a FieldSplitPreconditioner matrix based on the decomposition.

Definition at line 897 of file NonlinearSystemBase.h.

Referenced by haveFieldSplitPreconditioner(), and useFieldSplitPreconditioner().

_use_finite_differenced_preconditioner

bool NonlinearSystemBase::_use_finite_differenced_preconditioner

protected

Whether or not to use a finite differenced preconditioner.

Definition at line 888 of file NonlinearSystemBase.h.

Referenced by haveFiniteDifferencedPreconditioner(), NonlinearSystem::potentiallySetupFiniteDifferencing(), and useFiniteDifferencedPreconditioner().

_use_pre_smo_residual

bool NonlinearSystemBase::_use_pre_smo_residual

protected

Whether to use the pre-SMO initial residual in the relative convergence check.

Definition at line 934 of file NonlinearSystemBase.h.

Referenced by setPreSMOResidual(), shouldEvaluatePreSMOResidual(), and usePreSMOResidual().

_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 1056 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 1030 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 992 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 1032 of file SystemBase.h.

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

_var_to_group_var

std::unordered_map<unsigned int, unsigned int> NonlinearSystemBase::_var_to_group_var

private

A map from variable index to group variable index and it's associated (inverse) scaling factor.

Definition at line 1010 of file NonlinearSystemBase.h.

Referenced by computeScaling(), and setupScalingData().

_variable_autoscaled

std::vector<bool> NonlinearSystemBase::_variable_autoscaled

protected

Container to hold flag if variable is to participate in autoscaling.

Definition at line 971 of file NonlinearSystemBase.h.

Referenced by computeScaling(), and setupScalingData().

_vars

std::vector<VariableWarehouse> SystemBase::_vars

protectedinherited

Variable warehouses (one for each thread)

Definition at line 990 of file SystemBase.h.

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

_vars_to_be_zeroed_on_jacobian

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

protectedinherited

Definition at line 997 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 996 of file SystemBase.h.

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

_vecs_to_zero_for_residual

std::vector<std::string> NonlinearSystemBase::_vecs_to_zero_for_residual

protected

vectors that will be zeroed before a residual computation

Definition at line 914 of file NonlinearSystemBase.h.

Referenced by computeResidualTags(), and zeroVectorForResidual().

_verbose

bool SystemBase::_verbose

protectedinherited

True if printing out additional information.

Definition at line 1050 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/NonlinearSystemBase.h
• src/systems/NonlinearSystemBase.C