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

#include <SystemBase.h>

Inheritance diagram for SystemBase:

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

virtual	~SystemBase ()

unsigned int	number () const
	Gets the number of this system.

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.

bool	computingScalingJacobian () const
	Whether we are computing an initial Jacobian for automatic variable scaling.

bool	automaticScaling () const
	Getter for whether we are performing automatic scaling.

void	automaticScaling (bool automatic_scaling)
	Setter for whether we are performing automatic scaling.

void	setVerboseFlag (const bool &verbose)
	Sets the verbose flag.

virtual libMesh::DofMap &	dofMap ()
	Gets writeable reference to the dof map.

virtual const libMesh::DofMap &	dofMap () const
	Gets const reference to the dof map.

virtual libMesh::System &	system ()=0
	Get the reference to the libMesh system.

virtual const libMesh::System &	system () const =0

virtual void	preInit ()
	This is called prior to the libMesh system has been init'd.

virtual void	postInit ()

virtual void	reinit ()
	Reinitialize the system when the degrees of freedom in this system have changed.

virtual void	initializeObjects ()
	Called only once, just before the solve begins so objects can do some precalculations.

void	update ()
	Update the system (doing libMesh magic)

virtual void	solve ()
	Solve the system (using libMesh magic)

void	copyOldSolutions ()
	Copy the solution back in time (older -> old, etc).

void	copyPreviousSolutions (const Moose::SolutionIterationType iteration_type)
	Copy a specific type of solution back in time (older -> old, etc).

virtual void	restoreSolutions ()
	Restore current solutions (call after your solve failed)

virtual const NumericVector< Number > *const &	currentSolution () const =0
	The solution vector that is currently being operated on.

NumericVector< Number > &	solution ()

NumericVector< Number > &	solutionOld ()

NumericVector< Number > &	solutionOlder ()

const NumericVector< Number > &	solution () const

const NumericVector< Number > &	solutionOld () const

const NumericVector< Number > &	solutionOlder () const

virtual const NumericVector< Number > *	solutionPreviousNewton () const

virtual NumericVector< Number > *	solutionPreviousNewton ()

virtual void	initSolutionState ()
	Initializes the solution state.

const std::vector< NumericVector< Number > * > &	getSolutionStates (const Moose::SolutionIterationType iteration_type) const
	Get all of the solution states (current, old, ...) for the given iteration type.

std::size_t	getNumSolutionStates (const Moose::SolutionIterationType iteration_type) const
	Get the number of solution states (0 = current, 1 = current + old, ...) for the given iteration type.

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).

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).

libMesh::ParallelType	solutionStateParallelType (const unsigned int state, const Moose::SolutionIterationType iteration_type) const
	Returns the parallel type of the given solution state.

virtual void	needSolutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time, libMesh::ParallelType parallel_type=GHOSTED)
	Registers that the solution state `state` is needed.

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).

virtual void	addDotVectors ()
	Add u_dot, u_dotdot, u_dot_old and u_dotdot_old vectors if requested by the time integrator.

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

virtual Number &	duDotDotDu ()

virtual const Number &	duDotDu (unsigned int var_num=0) const

virtual const Number &	duDotDotDu () const

virtual NumericVector< Number > *	solutionUDot ()

virtual NumericVector< Number > *	solutionUDotDot ()

virtual NumericVector< Number > *	solutionUDotOld ()

virtual NumericVector< Number > *	solutionUDotDotOld ()

virtual const NumericVector< Number > *	solutionUDot () const

virtual const NumericVector< Number > *	solutionUDotDot () const

virtual const NumericVector< Number > *	solutionUDotOld () const

virtual const NumericVector< Number > *	solutionUDotDotOld () const

virtual void	saveOldSolutions ()
	Save the old and older solutions.

virtual void	restoreOldSolutions ()
	Restore the old and older solutions when the saved solutions present.

bool	hasVector (const std::string &tag_name) const
	Check if the named vector exists in the system.

virtual bool	hasVector (TagID tag_id) const
	Check if the tagged vector exists in the system.

virtual TagID	timeVectorTag () const
	Ideally, we should not need this API.

virtual TagID	systemMatrixTag () const
	Return the Matrix Tag ID for System.

virtual TagID	nonTimeVectorTag () const

virtual TagID	residualVectorTag () const

virtual std::set< TagID >	defaultVectorTags () const
	Get the default vector tags associated with this system.

virtual std::set< TagID >	defaultMatrixTags () const
	Get the default matrix tags associted with this system.

virtual void	associateVectorToTag (NumericVector< Number > &vec, TagID tag)
	Associate a vector for a given tag.

virtual void	disassociateVectorFromTag (NumericVector< Number > &vec, TagID tag)
	Disassociate a given vector from a given tag.

virtual void	disassociateVectorFromTag (TagID tag)
	Disassociate any vector that is associated with a given tag.

virtual void	disassociateDefaultVectorTags ()
	Disassociate the vectors associated with the default vector tags of this system.

virtual bool	hasMatrix (TagID tag) const
	Check if the tagged matrix exists in the system.

virtual libMesh::SparseMatrix< Number > &	getMatrix (TagID tag)
	Get a raw SparseMatrix.

virtual const libMesh::SparseMatrix< Number > &	getMatrix (TagID tag) const
	Get a raw SparseMatrix.

virtual void	activateAllMatrixTags ()
	Make all existing matrices active.

virtual bool	matrixTagActive (TagID tag) const
	If or not a matrix tag is active.

virtual void	deactivateAllMatrixTags ()
	Make matrices inactive.

void	closeTaggedMatrices (const std::set< TagID > &tags)
	Close all matrices associated the tags.

void	flushTaggedMatrices (const std::set< TagID > &tags)
	flushes all matrices associated to tags.

virtual void	associateMatrixToTag (libMesh::SparseMatrix< Number > &matrix, TagID tag)
	Associate a matrix to a tag.

virtual void	disassociateMatrixFromTag (libMesh::SparseMatrix< Number > &matrix, TagID tag)
	Disassociate a matrix from a tag.

virtual void	disassociateMatrixFromTag (TagID tag)
	Disassociate any matrix that is associated with a given tag.

virtual void	disassociateDefaultMatrixTags ()
	Disassociate the matrices associated with the default matrix tags of this system.

virtual NumericVector< Number > &	serializedSolution ()
	Returns a reference to a serialized version of the solution vector for this subproblem.

virtual NumericVector< Number > &	residualCopy ()

virtual NumericVector< Number > &	residualGhosted ()

virtual void	augmentSendList (std::vector< dof_id_type > &send_list)
	Will modify the send_list to add all of the extra ghosted dofs for this system.

virtual void	augmentSparsity (libMesh::SparsityPattern::Graph &sparsity, std::vector< dof_id_type > &n_nz, std::vector< dof_id_type > &n_oz)=0
	Will modify the sparsity pattern to add logical geometric connections.

virtual void	addVariable (const std::string &var_type, const std::string &var_name, InputParameters &parameters)
	Canonical method for adding a variable.

virtual bool	isArrayVariable (const std::string &var_name) const
	If a variable is an array variable.

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.

MooseVariableFieldBase &	getVariable (THREAD_ID tid, unsigned int var_number) const
	Gets a reference to a variable with specified number.

template<typename T >
MooseVariableFE< T > &	getFieldVariable (THREAD_ID tid, const std::string &var_name)
	Gets a reference to a variable of with specified name.

template<typename T >
MooseVariableField< T > &	getActualFieldVariable (THREAD_ID tid, const std::string &var_name)
	Returns a field variable pointer - this includes finite volume variables.

template<typename T >
MooseVariableFE< T > &	getFieldVariable (THREAD_ID tid, unsigned int var_number)
	Gets a reference to a variable with specified number.

template<typename T >
MooseVariableField< T > &	getActualFieldVariable (THREAD_ID tid, unsigned int var_number)
	Returns a field variable pointer - this includes finite volume variables.

template<typename T >
MooseVariableFV< T > &	getFVVariable (THREAD_ID tid, const std::string &var_name)
	Return a finite volume variable.

virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, const std::string &var_name) const
	Gets a reference to a scalar variable with specified number.

virtual MooseVariableScalar &	getScalarVariable (THREAD_ID tid, unsigned int var_number) const
	Gets a reference to a variable with specified number.

virtual const std::set< SubdomainID > *	getVariableBlocks (unsigned int var_number)
	Get the block where a variable of this system is defined.

virtual unsigned int	nVariables () const
	Get the number of variables in this system.

unsigned int	nFieldVariables () const
	Get the number of field variables in this system.

unsigned int	nFVVariables () const
	Get the number of finite volume variables in this system.

std::size_t	getMaxVarNDofsPerElem () const
	Gets the maximum number of dofs used by any one variable on any one element.

std::size_t	getMaxVarNDofsPerNode () const
	Gets the maximum number of dofs used by any one variable on any one node.

void	assignMaxVarNDofsPerElem (std::size_t max_dofs)
	assign the maximum element dofs

void	assignMaxVarNDofsPerNode (std::size_t max_dofs)
	assign the maximum node dofs

virtual void	addVariableToZeroOnResidual (std::string var_name)
	Adds this variable to the list of variables to be zeroed during each residual evaluation.

virtual void	addVariableToZeroOnJacobian (std::string var_name)
	Adds this variable to the list of variables to be zeroed during each Jacobian evaluation.

virtual void	zeroVariables (std::vector< std::string > &vars_to_be_zeroed)
	Zero out the solution for the list of variables passed in.

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()

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()

virtual libMesh::Order	getMinQuadratureOrder ()
	Get minimal quadrature order needed for integrating variables in this system.

virtual void	prepare (THREAD_ID tid)
	Prepare the system for use.

virtual void	prepareFace (THREAD_ID tid, bool resize_data)
	Prepare the system for use on sides.

virtual void	prepareNeighbor (THREAD_ID tid)
	Prepare the system for use.

virtual void	prepareLowerD (THREAD_ID tid)
	Prepare the system for use for lower dimensional elements.

virtual void	reinitElem (const Elem *elem, THREAD_ID tid)
	Reinit an element assembly info.

virtual void	reinitElemFace (const Elem *elem, unsigned int side, THREAD_ID tid)
	Reinit assembly info for a side of an element.

virtual void	reinitNeighborFace (const Elem *elem, unsigned int side, THREAD_ID tid)
	Compute the values of the variables at all the current points.

virtual void	reinitNeighbor (const Elem *elem, THREAD_ID tid)
	Compute the values of the variables at all the current points.

virtual void	reinitLowerD (THREAD_ID tid)
	Compute the values of the variables on the lower dimensional element.

virtual void	reinitNode (const Node *node, THREAD_ID tid)
	Reinit nodal assembly info.

virtual void	reinitNodeFace (const Node *node, BoundaryID bnd_id, THREAD_ID tid)
	Reinit nodal assembly info on a face.

virtual void	reinitNodes (const std::vector< dof_id_type > &nodes, THREAD_ID tid)
	Reinit variables at a set of nodes.

virtual void	reinitNodesNeighbor (const std::vector< dof_id_type > &nodes, THREAD_ID tid)
	Reinit variables at a set of neighbor nodes.

virtual void	reinitScalars (THREAD_ID tid, bool reinit_for_derivative_reordering=false)
	Reinit scalar varaibles.

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.

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

const VariableWarehouse &	variableWarehouse (THREAD_ID tid=0) const

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

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

const std::set< SubdomainID > &	getSubdomainsForVar (const std::string &var_name) const
	Get the block where a variable of this system is defined.

void	removeVector (const std::string &name)
	Remove a vector from the system with the given name.

NumericVector< Number > &	addVector (const std::string &vector_name, const bool project, const libMesh::ParallelType type)
	Adds a solution length vector to the system.

NumericVector< Number > &	addVector (TagID tag, const bool project, const libMesh::ParallelType type)
	Adds a solution length vector to the system with the specified TagID.

void	closeTaggedVector (const TagID tag)
	Close vector with the given tag.

void	closeTaggedVectors (const std::set< TagID > &tags)
	Close all vectors for given tags.

void	zeroTaggedVector (const TagID tag)
	Zero vector with the given tag.

void	zeroTaggedVectors (const std::set< TagID > &tags)
	Zero all vectors for given tags.

void	removeVector (TagID tag_id)
	Remove a solution length vector from the system with the specified TagID.

void	setVariableGlobalDoFs (const std::string &var_name)
	set all the global dof indices for a variable

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`

libMesh::SparseMatrix< Number > &	addMatrix (TagID tag)
	Adds a matrix with a given tag.

void	removeMatrix (TagID tag)
	Removes a matrix with a given tag.

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.

virtual void	computeVariables (const NumericVector< Number > &)

void	copyVars (libMesh::ExodusII_IO &io)

virtual void	copySolutionsBackwards ()
	Copy current solution into old and older.

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.

void	addScalingVector ()
	Add the scaling factor vector to the system.

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

virtual void	initialSetup ()
	Setup Functions.

virtual void	timestepSetup ()

virtual void	customSetup (const ExecFlagType &exec_type)

virtual void	subdomainSetup ()

virtual void	residualSetup ()

virtual void	jacobianSetup ()

void	clearAllDofIndices ()
	Clear all dof indices from moose variables.

void	setActiveVariableCoupleableVectorTags (const std::set< TagID > &vtags, THREAD_ID tid)
	Set the active vector tags for the variables.

void	setActiveScalarVariableCoupleableVectorTags (const std::set< TagID > &vtags, THREAD_ID tid)
	Set the active vector tags for the scalar variables.

Moose::VarKindType	varKind () const

virtual void	compute (ExecFlagType type)=0
	Compute time derivatives, auxiliary variables, etc.

void	copyTimeIntegrators (const SystemBase &other_sys)
	Copy time integrators from another system.

const TimeIntegrator &	getTimeIntegrator (const unsigned int var_num) const
	Retrieve the time integrator that integrates the given variable's equation.

const TimeIntegrator *	queryTimeIntegrator (const unsigned int var_num) const
	Retrieve the time integrator that integrates the given variable's equation.

const std::vector< std::shared_ptr< TimeIntegrator > > &	getTimeIntegrators ()

std::string	prefix () const

void	sizeVariableMatrixData ()
	size the matrix data for each variable for the number of matrix tags we have

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

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const


virtual NumericVector< Number > &	getVector (const std::string &name)
	Get a raw NumericVector by name.

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


virtual NumericVector< Number > &	getVector (TagID tag)
	Get a raw NumericVector by tag.

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


virtual bool	hasVariable (const std::string &var_name) const
	Query a system for a variable.

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

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

Protected Member Functions
virtual NumericVector< Number > &	solutionInternal () const =0
	Internal getter for solution owned by libMesh.

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

FEProblemBase &	_fe_problem
	the governing finite element/volume problem

MooseApp &	_app

Factory &	_factory

MooseMesh &	_mesh

std::string	_name
	The name of this system.

std::vector< VariableWarehouse >	_vars
	Variable warehouses (one for each thread)

std::map< unsigned int, std::set< SubdomainID > >	_var_map
	Map of variables (variable id -> array of subdomains where it lives)

unsigned int	_max_var_number
	Maximum variable number.

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

NumericVector< Number > *	_u_dotdot
	solution vector for u^dotdot

NumericVector< Number > *	_u_dot_old
	old solution vector for u^dot

NumericVector< Number > *	_u_dotdot_old
	old solution vector for u^dotdot

std::vector< Real >	_du_dot_du
	Derivative of time derivative of u with respect to uj.

Real	_du_dotdot_du

std::vector< NumericVector< Number > * >	_tagged_vectors
	Tagged vectors (pointer)

std::vector< libMesh::SparseMatrix< Number > * >	_tagged_matrices
	Tagged matrices (pointer)

std::unordered_map< TagID, libMesh::SparseMatrix< Number > * >	_active_tagged_matrices
	Active tagged matrices. A matrix is active if its tag-matrix pair is present in the map. We use a map instead of a vector so that users can easily add and remove to this container with calls to (de)activateMatrixTag.

std::vector< bool >	_matrix_tag_active_flags
	Active flags for tagged matrices.

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

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.

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

std::vector< std::shared_ptr< TimeIntegrator > >	_time_integrators
	Time integrator.

std::vector< std::vector< MooseVariableFieldBase * > >	_numbered_vars
	Map variable number to its pointer.

bool	_automatic_scaling
	Whether to automatically scale the variables.

bool	_verbose
	True if printing out additional information.

bool	_solution_states_initialized
	Whether or not the solution states have been initialized.

std::vector< dof_id_type >	_var_all_dof_indices
	Container for the dof indices of a given variable.

std::unique_ptr< NumericVector< Number > >	_serialized_solution
	Serialized version of the solution vector, or nullptr if a serialized solution is not needed.

const Parallel::Communicator &	_communicator

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

std::vector< NumericVector< Number > * > &	getSolutionStates (const Moose::SolutionIterationType iteration_type)
	Get all of the solution states (current, old, ...) for the given iteration type.

Private Attributes
std::array< std::vector< NumericVector< Number > * >, static_cast< size_t >(Moose::SolutionIterationType::Count)>	_solution_states
	2D array of solution state vector pointers.

std::vector< NumericVector< Number > * >	_saved_solution_states
	The saved solution states (0 = current, 1 = old, 2 = older, etc)

bool	_skip_next_solution_to_old_copy
	Whether to skip the next copy from the solution to the old vector.

Detailed Description

Base class for a system (of equations)

Definition at line 85 of file SystemBase.h.

Constructor & Destructor Documentation

◆ SystemBase()

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

Definition at line 55 of file SystemBase.C.

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

◆ ~SystemBase()

virtual SystemBase::~SystemBase ( )

inlinevirtual

Definition at line 93 of file SystemBase.h.

93{}

Member Function Documentation

◆ activateAllMatrixTags()

void SystemBase::activateAllMatrixTags ( )

virtual

Make all existing matrices active.

Definition at line 1130 of file SystemBase.C.

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

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

◆ addDotVectors()

void SystemBase::addDotVectors ( )

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1632 of file SystemBase.C.

{
  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);
}

Referenced by DisplacedSystem::addDotVectors().

◆ addMatrix()

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

Adds a matrix with a given tag.

Parameters

tag_name The name of the tag

Definition at line 567 of file SystemBase.C.

{
  if (!_subproblem.matrixTagExists(tag))
    mooseError("Cannot add tagged matrix with TagID ",
               tag,
               " in system '",
               name(),
               "' because the tag does not exist in the problem");
 
  if (hasMatrix(tag))
    return getMatrix(tag);
 
  const auto matrix_name = _subproblem.matrixTagName(tag);
  SparseMatrix<Number> & mat = system().add_matrix(matrix_name);
  associateMatrixToTag(mat, tag);
 
  return mat;
}

◆ addScalingVector()

void SystemBase::addScalingVector ( )

Add the scaling factor vector to the system.

Definition at line 1557 of file SystemBase.C.

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

Referenced by MooseVariableBase::initialSetup().

◆ addTimeIntegrator()

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

Definition at line 1657 of file SystemBase.C.

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

◆ addVariable()

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

virtual

Canonical method for adding a variable.

Parameters

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

Reimplemented in AuxiliarySystem.

Definition at line 717 of file SystemBase.C.

{
  _numbered_vars.resize(libMesh::n_threads());
 
  const auto components = parameters.get<unsigned int>("components");
 
  // Convert the std::vector parameter provided by the user into a std::set for use by libMesh's
  // System::add_variable method
  std::set<SubdomainID> blocks;
  const auto & block_param = parameters.get<std::vector<SubdomainName>>("block");
  for (const auto & subdomain_name : block_param)
  {
    SubdomainID blk_id = _mesh.getSubdomainID(subdomain_name);
    blocks.insert(blk_id);
  }
 
  const auto fe_type =
      FEType(Utility::string_to_enum<Order>(parameters.get<MooseEnum>("order")),
             Utility::string_to_enum<FEFamily>(parameters.get<MooseEnum>("family")));
  const auto fe_field_type = FEInterface::field_type(fe_type);
 
  unsigned int var_num;
 
  if (var_type == "ArrayMooseVariable")
  {
    if (fe_field_type == libMesh::TYPE_VECTOR)
      mooseError("Vector family type cannot be used in an array variable");
 
    std::vector<std::string> array_var_component_names;
    const bool has_array_names = parameters.isParamValid("array_var_component_names");
    if (has_array_names)
    {
      array_var_component_names =
          parameters.get<std::vector<std::string>>("array_var_component_names");
      if (array_var_component_names.size() != components)
        parameters.paramError("array_var_component_names",
                              "Must be the same size as 'components' (size ",
                              components,
                              ") for array variable '",
                              name,
                              "'");
    }
 
    // Build up the variable names
    std::vector<std::string> var_names;
    for (unsigned int i = 0; i < components; i++)
    {
      if (!has_array_names)
        array_var_component_names.push_back(std::to_string(i));
      var_names.push_back(name + "_" + array_var_component_names[i]);
    }
 
    // makes sure there is always a name, either the provided one or '1 2 3 ...'
    parameters.set<std::vector<std::string>>("array_var_component_names") =
        array_var_component_names;
 
    // The number returned by libMesh is the _last_ variable number... we want to hold onto the
    // _first_
    var_num = system().add_variable_array(var_names, fe_type, &blocks) - (components - 1);
 
    // Set as array variable
    if (parameters.isParamSetByUser("array") && !parameters.get<bool>("array"))
      parameters.paramError("array",
                            "Must be set to true for variable '",
                            name,
                            "' because 'components' > 1 (is an array variable)");
    parameters.set<bool>("array") = true;
  }
  else
  {
    if (parameters.isParamSetByUser("array_var_component_names"))
      parameters.paramError("array_var_component_names",
                            "Should not be set because this variable (",
                            name,
                            ") is a non-array variable");
    var_num = system().add_variable(name, fe_type, &blocks);
  }
 
  parameters.set<unsigned int>("_var_num") = var_num;
  parameters.set<SystemBase *>("_system_base") = this;
 
  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
  {
    parameters.set<THREAD_ID>("tid") = tid;
    std::shared_ptr<MooseVariableBase> var =
        _factory.create<MooseVariableBase>(var_type, name, parameters, tid);
 
    _vars[tid].add(name, var);
 
    if (auto fe_var = dynamic_cast<MooseVariableFieldBase *>(var.get()))
    {
      auto required_size = var_num + components;
      if (required_size > _numbered_vars[tid].size())
        _numbered_vars[tid].resize(required_size);
      for (MooseIndex(components) component = 0; component < components; ++component)
        _numbered_vars[tid][var_num + component] = fe_var;
 
      if (auto * const functor = dynamic_cast<Moose::FunctorBase<ADReal> *>(fe_var))
        _subproblem.addFunctor(name, *functor, tid);
      else if (auto * const functor = dynamic_cast<Moose::FunctorBase<ADRealVectorValue> *>(fe_var))
        _subproblem.addFunctor(name, *functor, tid);
      else if (auto * const functor = dynamic_cast<Moose::FunctorBase<ADRealEigenVector> *>(fe_var))
        _subproblem.addFunctor(name, *functor, tid);
      else
        mooseError("This should be a functor");
    }
 
    if (auto scalar_var = dynamic_cast<MooseVariableScalar *>(var.get()))
    {
      if (auto * const functor = dynamic_cast<Moose::FunctorBase<ADReal> *>(scalar_var))
        _subproblem.addFunctor(name, *functor, tid);
      else
        mooseError("Scalar variables should be functors");
    }
 
    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);
}

Referenced by AuxiliarySystem::addVariable().

◆ addVariableToCopy()

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

virtual

Add info about variable that will be copied.

Parameters

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

Definition at line 1174 of file SystemBase.C.

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

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

◆ addVariableToZeroOnJacobian()

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

virtual

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

Parameters

var_name The name of the variable to be zeroed.

Reimplemented in DisplacedSystem.

Definition at line 179 of file SystemBase.C.

{
  _vars_to_be_zeroed_on_jacobian.push_back(var_name);
}

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().

◆ addVariableToZeroOnResidual()

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

virtual

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

Parameters

var_name The name of the variable to be zeroed.

Reimplemented in DisplacedSystem.

Definition at line 173 of file SystemBase.C.

{
  _vars_to_be_zeroed_on_residual.push_back(var_name);
}

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().

◆ addVector() [1/2]

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

Adds a solution length vector to the system.

Parameters

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

Definition at line 605 of file SystemBase.C.

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

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

◆ addVector() [2/2]

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

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

Parameters

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

Definition at line 617 of file SystemBase.C.

{
  if (!_subproblem.vectorTagExists(tag))
    mooseError("Cannot add tagged vector with TagID ",
               tag,
               " in system '",
               name(),
               "' because the tag does not exist in the problem");
 
  if (hasVector(tag))
  {
    auto & vec = getVector(tag);
 
    if (type != AUTOMATIC && vec.type() != type)
      mooseError("Cannot add tagged vector '",
                 _subproblem.vectorTagName(tag),
                 "', in system '",
                 name(),
                 "' because a vector with the same name was found with a different parallel type");
 
    return vec;
  }
 
  const auto vector_name = _subproblem.vectorTagName(tag);
  NumericVector<Number> & vec = system().add_vector(vector_name, project, type);
  associateVectorToTag(vec, tag);
 
  return vec;
}

◆ applyScalingFactors()

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

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 1507 of file SystemBase.C.

{
  for (MooseIndex(_vars) thread = 0; thread < _vars.size(); ++thread)
  {
    auto & field_variables = _vars[thread].fieldVariables();
    for (MooseIndex(field_variables) i = 0, 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);
    }
  }
}

Referenced by NonlinearSystemBase::computeScaling().

◆ assignMaxVarNDofsPerElem()

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

inline

assign the maximum element dofs

Definition at line 616 of file SystemBase.h.

616{ _max_var_n_dofs_per_elem = max_dofs; }

◆ assignMaxVarNDofsPerNode()

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

inline

assign the maximum node dofs

Definition at line 621 of file SystemBase.h.

621{ _max_var_n_dofs_per_node = max_dofs; }

◆ associateMatrixToTag()

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

virtual

Associate a matrix to a tag.

Reimplemented in DisplacedSystem.

Definition at line 1075 of file SystemBase.C.

{
  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;
}

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

◆ associateVectorToTag()

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

virtual

Associate a vector for a given tag.

Reimplemented in DisplacedSystem.

Definition at line 980 of file SystemBase.C.

{
  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;
}

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

◆ augmentSendList()

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

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 451 of file SystemBase.C.

{
  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 libMesh::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));
          }
        }
      }
    }
  }
}

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

◆ augmentSparsity()

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

pure virtual

Will modify the sparsity pattern to add logical geometric connections.

Implemented in AuxiliarySystem, DisplacedSystem, NonlinearSystemBase, and LinearSystem.

Referenced by extraSparsity().

◆ automaticScaling() [1/2]

bool SystemBase::automaticScaling ( ) const

inline

Getter for whether we are performing automatic scaling.

Returns: whether we are performing automatic scaling

Definition at line 123 of file SystemBase.h.

123{ return _automatic_scaling; }

Referenced by SubProblem::automaticScaling(), and SubProblem::automaticScaling().

◆ automaticScaling() [2/2]

void SystemBase::automaticScaling ( bool automatic_scaling )

inline

Setter for whether we are performing automatic scaling.

Parameters

automatic_scaling A boolean representing whether we are performing automatic scaling

Definition at line 129 of file SystemBase.h.

129{ _automatic_scaling = automatic_scaling; }

◆ clearAllDofIndices()

void SystemBase::clearAllDofIndices ( )

Clear all dof indices from moose variables.

Definition at line 1612 of file SystemBase.C.

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

Referenced by SubProblem::clearAllDofIndices().

◆ closeTaggedMatrices()

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

Close all matrices associated the tags.

Definition at line 1059 of file SystemBase.C.

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

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

◆ closeTaggedVector()

void SystemBase::closeTaggedVector ( const TagID tag )

Close vector with the given tag.

Definition at line 648 of file SystemBase.C.

{
  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();
}

Referenced by closeTaggedVectors().

◆ closeTaggedVectors()

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

Close all vectors for given tags.

Definition at line 666 of file SystemBase.C.

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

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

◆ compute()

virtual void SystemBase::compute ( ExecFlagType type )

pure virtual

Compute time derivatives, auxiliary variables, etc.

Parameters

type	Our current execution stage

Implemented in AuxiliarySystem, LinearSystem, SolverSystem, and DisplacedSystem.

◆ computeVariables()

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

inlinevirtual

Definition at line 890 of file SystemBase.h.

890{}

◆ computingScalingJacobian()

bool SystemBase::computingScalingJacobian ( ) const

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

Definition at line 1564 of file SystemBase.C.

{
  return _subproblem.computingScalingJacobian();
}

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

◆ copyOldSolutions()

void SystemBase::copyOldSolutions ( )

Copy the solution back in time (older -> old, etc).

Shifts the solutions backwards in time.

Definition at line 1305 of file SystemBase.C.

{
  copyPreviousSolutions(Moose::SolutionIterationType::Time);
}

Referenced by EigenExecutionerBase::inversePowerIteration().

◆ copyPreviousSolutions()

void SystemBase::copyPreviousSolutions ( const Moose::SolutionIterationType iteration_type )

Copy a specific type of solution back in time (older -> old, etc).

Definition at line 1265 of file SystemBase.C.

{
  const auto num_states = getNumSolutionStates(iteration_type);
  if (num_states > 1)
  {
    // Normally copy through old (index 1). For Time, optionally stop at older
    // and leave old unchanged.
    const bool skip_old =
        iteration_type == Moose::SolutionIterationType::Time && _skip_next_solution_to_old_copy;
 
    const std::size_t stop = skip_old ? 1 : 0;
    for (std::size_t i = num_states - 1; i > stop; --i)
      solutionState(i, iteration_type) = solutionState(i - 1, iteration_type);
  }
 
  // Custom logic for changing state based on iteration type
  switch (iteration_type)
  {
    case Moose::SolutionIterationType::Time:
      _skip_next_solution_to_old_copy = false;
      if (solutionUDotOld())
        *solutionUDotOld() = *solutionUDot();
      if (solutionUDotDotOld())
        *solutionUDotDotOld() = *solutionUDotDot();
      break;
    case Moose::SolutionIterationType::Nonlinear:
      if (solutionPreviousNewton())
        *solutionPreviousNewton() = *currentSolution();
      break;
    case Moose::SolutionIterationType::MultiAppFixedPoint:
    case Moose::SolutionIterationType::MultiSystemFixedPoint:
    case Moose::SolutionIterationType::Count:
      break;
  }
}

Referenced by copyOldSolutions(), and copySolutionsBackwards().

◆ copySolutionsBackwards()

void SystemBase::copySolutionsBackwards ( )

virtual

Copy current solution into old and older.

Definition at line 1257 of file SystemBase.C.

{
  system().update();
  copyPreviousSolutions(Moose::SolutionIterationType::Time);
  copyPreviousSolutions(Moose::SolutionIterationType::Nonlinear);
}

◆ copyTimeIntegrators()

void SystemBase::copyTimeIntegrators ( const SystemBase & other_sys )

Copy time integrators from another system.

Definition at line 1666 of file SystemBase.C.

{
  _time_integrators = other_sys._time_integrators;
}

◆ copyVars()

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

Definition at line 1182 of file SystemBase.C.

{
  int n_steps = io.get_num_time_steps();
 
  bool did_copy = false;
  for (const auto & vci : _var_to_copy)
  {
    int timestep = -1;
 
    if (vci._timestep == "LATEST")
      // Use the last time step in the file from which to retrieve the solution
      timestep = n_steps;
    else
    {
      timestep = MooseUtils::convert<int>(vci._timestep);
      if (timestep > n_steps)
        mooseError("Invalid value passed as \"initial_from_file_timestep\". Expected \"LATEST\" or "
                   "a valid integer between 1 and ",
                   n_steps,
                   " inclusive, received ",
                   vci._timestep);
    }
 
    did_copy = true;
 
    if (hasVariable(vci._dest_name))
    {
      const auto & var = getVariable(0, vci._dest_name);
      if (var.isArray())
      {
        const auto & array_var = getFieldVariable<RealEigenVector>(0, vci._dest_name);
        for (MooseIndex(var.count()) i = 0; i < var.count(); ++i)
        {
          const auto & exodus_var = var.arrayVariableComponent(i);
          const auto & system_var = array_var.componentName(i);
          if (var.isNodal())
            io.copy_nodal_solution(system(), exodus_var, system_var, timestep);
          else
            io.copy_elemental_solution(system(), exodus_var, system_var, timestep);
        }
      }
      else
      {
        if (var.isNodal())
          io.copy_nodal_solution(system(), vci._dest_name, vci._source_name, timestep);
        else
          io.copy_elemental_solution(system(), vci._dest_name, vci._source_name, timestep);
      }
    }
    else if (hasScalarVariable(vci._dest_name))
      io.copy_scalar_solution(system(), {vci._dest_name}, {vci._source_name}, timestep);
    else
      mooseError("Unrecognized variable ", vci._dest_name, " in variables to copy.");
  }
 
  if (did_copy)
    solution().close();
}

◆ currentSolution()

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

pure virtual

The solution vector that is currently being operated on.

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

Implemented in AuxiliarySystem, DisplacedSystem, and SolverSystem.

Referenced by copyPreviousSolutions(), DisplacedSystem::currentSolution(), MooseVariableBase::getSolution(), LinearFVGradientInterface::initializeContainer(), NEML2FEInterpolation::initialSetup(), MooseVariableScalar::reinit(), and restoreSolutions().

◆ customSetup()

void SystemBase::customSetup ( const ExecFlagType & exec_type )

virtual

Reimplemented in AuxiliarySystem, and NonlinearSystemBase.

Definition at line 1584 of file SystemBase.C.

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

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

◆ deactivateAllMatrixTags()

void SystemBase::deactivateAllMatrixTags ( )

virtual

Make matrices inactive.

Definition at line 1118 of file SystemBase.C.

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

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

◆ defaultMatrixTags()

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

inlinevirtual

Get the default matrix tags associted with this system.

Reimplemented in DisplacedSystem, and NonlinearEigenSystem.

Definition at line 338 of file SystemBase.h.

338{ return {systemMatrixTag()}; }

SystemBase::systemMatrixTag

virtual TagID systemMatrixTag() const

Return the Matrix Tag ID for System.

Definition SystemBase.h:316

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

◆ defaultVectorTags()

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

inlinevirtual

Get the default vector tags associated with this system.

Reimplemented in DisplacedSystem, and NonlinearEigenSystem.

Definition at line 331 of file SystemBase.h.

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

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

◆ disassociateDefaultMatrixTags()

void SystemBase::disassociateDefaultMatrixTags ( )

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1109 of file SystemBase.C.

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

Referenced by DisplacedSystem::disassociateDefaultMatrixTags().

◆ disassociateDefaultVectorTags()

void SystemBase::disassociateDefaultVectorTags ( )

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1014 of file SystemBase.C.

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

Referenced by DisplacedSystem::disassociateDefaultVectorTags().

◆ disassociateMatrixFromTag() [1/2]

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

virtual

Disassociate a matrix from a tag.

Reimplemented in DisplacedSystem.

Definition at line 1087 of file SystemBase.C.

{
  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);
}

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

◆ disassociateMatrixFromTag() [2/2]

void SystemBase::disassociateMatrixFromTag ( TagID tag )

virtual

Disassociate any matrix that is associated with a given tag.

Reimplemented in DisplacedSystem.

Definition at line 1098 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]

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

virtual

Disassociate a given vector from a given tag.

Reimplemented in DisplacedSystem.

Definition at line 992 of file SystemBase.C.

{
  if (!_subproblem.vectorTagExists(tag))
    mooseError("Cannot disassociate vector from tag ", tag, " because that tag does not exist");
  if (hasVector(tag) && &getVector(tag) != &vec)
    mooseError("You can not disassociate a vector from a tag which it was not associated to");
 
  disassociateVectorFromTag(tag);
}

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

◆ disassociateVectorFromTag() [2/2]

void SystemBase::disassociateVectorFromTag ( TagID tag )

virtual

Disassociate any vector that is associated with a given tag.

Reimplemented in DisplacedSystem.

Definition at line 1003 of file SystemBase.C.

{
  if (!_subproblem.vectorTagExists(tag))
    mooseError("Cannot disassociate vector from tag ", tag, " because that tag does not exist");
 
  if (_tagged_vectors.size() < tag + 1)
    _tagged_vectors.resize(tag + 1);
  _tagged_vectors[tag] = nullptr;
}

◆ dofMap() [1/2]

DofMap & SystemBase::dofMap ( )

virtual

Gets writeable reference to the dof map.

Definition at line 1162 of file SystemBase.C.

{
  return system().get_dof_map();
}

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

◆ dofMap() [2/2]

const DofMap & SystemBase::dofMap ( ) const

virtual

Gets const reference to the dof map.

Definition at line 1168 of file SystemBase.C.

{
  return system().get_dof_map();
}

◆ duDotDotDu() [1/2]

virtual Number & SystemBase::duDotDotDu ( )

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 276 of file SystemBase.h.

276{ return _du_dotdot_du; }

SystemBase::_du_dotdot_du

Real _du_dotdot_du

Definition SystemBase.h:1036

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

◆ duDotDotDu() [2/2]

virtual const Number & SystemBase::duDotDotDu ( ) const

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 278 of file SystemBase.h.

278{ return _du_dotdot_du; }

◆ duDotDu()

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

virtual

Reimplemented in DisplacedSystem.

Definition at line 1700 of file SystemBase.C.

{
  return _du_dot_du[var_num];
}

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

◆ duDotDus()

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

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 275 of file SystemBase.h.

275{ return _du_dot_du; }

Referenced by DisplacedSystem::duDotDus().

◆ feProblem() [1/2]

FEProblemBase & SystemBase::feProblem ( )

inline

Definition at line 104 of file SystemBase.h.

104{ return _fe_problem; }

Referenced by FVGradientMethod::computeGradient(), FVGreenGaussGradient::computeGradientWithoutLimiter(), DMMooseGetEmbedding_Private(), DMSetUp_Moose_Pre(), and LinearFVGradientInterface::resolveFVGradientMethod().

◆ feProblem() [2/2]

const FEProblemBase & SystemBase::feProblem ( ) const

inline

Definition at line 105 of file SystemBase.h.

105{ return _fe_problem; }

◆ flushTaggedMatrices()

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

flushes all matrices associated to tags.

Flush assembles the matrix but doesn't shrink memory allocation

Definition at line 1067 of file SystemBase.C.

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

◆ getActualFieldVariable() [1/2]

template<typename T >

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

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

Definition at line 117 of file SystemBase.C.

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

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

◆ getActualFieldVariable() [2/2]

template<typename T >

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

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);
}

◆ getFieldVariable() [1/2]

template<typename T >

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

Gets a reference to a variable of with specified name.

This excludes and cannot return finite volume variables.

Parameters

tid	Thread id
var_name	variable name

Returns: reference the variable (class)

Definition at line 110 of file SystemBase.C.

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

Referenced by Marker::getMarkerValue().

◆ getFieldVariable() [2/2]

template<typename T >

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

Gets a reference to a variable with specified number.

This excludes and cannot return finite volume variables.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns: reference the variable (class)

Definition at line 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
	)

Return a finite volume variable.

Definition at line 124 of file SystemBase.C.

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

◆ getMatrix() [1/2]

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

virtual

Get a raw SparseMatrix.

Reimplemented in DisplacedSystem.

Definition at line 1023 of file SystemBase.C.

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

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

◆ getMatrix() [2/2]

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

virtual

Get a raw SparseMatrix.

Reimplemented in DisplacedSystem.

Definition at line 1041 of file SystemBase.C.

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

◆ getMaxVariableNumber()

unsigned int SystemBase::getMaxVariableNumber ( ) const

inline

Returns the maximum number of all variables on the system.

Definition at line 888 of file SystemBase.h.

888{ return _max_var_number; }

◆ getMaxVarNDofsPerElem()

std::size_t SystemBase::getMaxVarNDofsPerElem ( ) const

inline

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

Returns: The max

Definition at line 604 of file SystemBase.h.

604{ return _max_var_n_dofs_per_elem; }

Referenced by Moose::globalDofIndexToDerivative().

◆ getMaxVarNDofsPerNode()

std::size_t SystemBase::getMaxVarNDofsPerNode ( ) const

inline

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

Returns: The max

Definition at line 611 of file SystemBase.h.

611{ return _max_var_n_dofs_per_node; }

◆ getMinQuadratureOrder()

Order SystemBase::getMinQuadratureOrder ( )

virtual

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

Returns: The minimal order of quadrature

Reimplemented in AuxiliarySystem.

Definition at line 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;
}

◆ getNumSolutionStates()

std::size_t SystemBase::getNumSolutionStates ( const Moose::SolutionIterationType iteration_type ) const

inline

Get the number of solution states (0 = current, 1 = current + old, ...) for the given iteration type.

Definition at line 1134 of file SystemBase.h.

{
  return getSolutionStates(iteration_type).size();
}

Referenced by copyPreviousSolutions(), hasSolutionState(), restoreOldSolutions(), saveOldSolutions(), and solutionState().

◆ getScalarVariable() [1/2]

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

virtual

Gets a reference to a scalar variable with specified number.

Parameters

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

Returns: reference the variable (class)

Definition at line 144 of file SystemBase.C.

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

◆ getScalarVariable() [2/2]

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

virtual

Gets a reference to a variable with specified number.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns: reference the variable (class)

Definition at line 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 )

inline

Definition at line 777 of file SystemBase.h.

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

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

◆ getSolutionStates() [1/2]

std::vector< NumericVector< Number > * > & SystemBase::getSolutionStates ( const Moose::SolutionIterationType iteration_type )

inlineprivate

Get all of the solution states (current, old, ...) for the given iteration type.

Definition at line 1099 of file SystemBase.h.

  {
    return const_cast<std::vector<NumericVector<Number> *> &>(
        cast_ptr<const SystemBase *>(this)->getSolutionStates(iteration_type));
  }

◆ getSolutionStates() [2/2]

const std::vector< NumericVector< Number > * > & SystemBase::getSolutionStates ( const Moose::SolutionIterationType iteration_type ) const

inline

Get all of the solution states (current, old, ...) for the given iteration type.

Definition at line 1124 of file SystemBase.h.

{
  const auto iteration_type_index = static_cast<std::size_t>(iteration_type);
  mooseAssert(iteration_type_index < static_cast<std::size_t>(Moose::SolutionIterationType::Count),
              "Invalid solution iteration type");
  mooseAssert(iteration_type_index < _solution_states.size(), "_solution_states sized incorrectly");
  return _solution_states[iteration_type_index];
}

Referenced by getNumSolutionStates(), needSolutionState(), solutionState(), solutionState(), and solutionStateParallelType().

◆ getStandardFieldVariableNames()

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

◆ getSubdomainsForVar() [1/2]

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

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

Parameters

var_name The name of the variable

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

Definition at line 1706 of file SystemBase.C.

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

◆ getSubdomainsForVar() [2/2]

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

inline

Definition at line 782 of file SystemBase.h.

  {
    return _var_map.at(var_number);
  }

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

◆ getTimeIntegrator()

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

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

Definition at line 1682 of file SystemBase.C.

{
  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));
}

Referenced by AB2PredictorCorrector::estimateTimeError().

◆ getTimeIntegrators()

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

Returns: All the time integrators owned by this system

Definition at line 1694 of file SystemBase.C.

{
  return _time_integrators;
}

◆ getVariable() [1/2]

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

Gets a reference to a variable of with specified name.

Parameters

tid	Thread id
var_name	variable name

Returns: reference the variable (class)

Definition at line 89 of file SystemBase.C.

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

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

◆ getVariable() [2/2]

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

Gets a reference to a variable with specified number.

Parameters

tid	Thread id
var_number	libMesh variable number

Returns: reference the variable (class)

Definition at line 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 )

virtual

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

Parameters

var_number The number of the variable

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

Definition at line 163 of file SystemBase.C.

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

Referenced by PhysicsBasedPreconditioner::addSystem().

◆ getVariableGlobalDoFs()

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

inline

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

Definition at line 863 of file SystemBase.h.

863{ return _var_all_dof_indices; }

SystemBase::_var_all_dof_indices

std::vector< dof_id_type > _var_all_dof_indices

Container for the dof indices of a given variable.

Definition SystemBase.h:1082

◆ getVariableNames()

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

inline

Definition at line 881 of file SystemBase.h.

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

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

◆ getVariables()

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

inline

Definition at line 770 of file SystemBase.h.

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

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

◆ getVector() [1/4]

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

virtual

Get a raw NumericVector by name.

Get a raw NumericVector with the given name.

Reimplemented in DisplacedSystem.

Definition at line 932 of file SystemBase.C.

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

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

◆ getVector() [2/4]

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

virtual

Reimplemented in DisplacedSystem.

Definition at line 938 of file SystemBase.C.

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

◆ getVector() [3/4]

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

virtual

Get a raw NumericVector by tag.

Reimplemented in DisplacedSystem.

Definition at line 944 of file SystemBase.C.

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

◆ getVector() [4/4]

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

virtual

Reimplemented in DisplacedSystem.

Definition at line 962 of file SystemBase.C.

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

◆ hasMatrix()

virtual bool SystemBase::hasMatrix ( TagID tag ) const

inlinevirtual

Check if the tagged matrix exists in the system.

Reimplemented in DisplacedSystem.

Definition at line 379 of file SystemBase.h.

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

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

◆ hasScalarVariable()

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

virtual

Definition at line 875 of file SystemBase.C.

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

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

◆ hasSolutionState()

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

inlinevirtual

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

Reimplemented in DisplacedSystem.

Definition at line 1140 of file SystemBase.h.

{
  return getNumSolutionStates(iteration_type) > state;
}

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

◆ hasVarCopy()

bool SystemBase::hasVarCopy ( ) const

inline

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

Definition at line 904 of file SystemBase.h.

904{ return _var_to_copy.size() > 0; }

◆ hasVariable()

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

virtual

Query a system for a variable.

Parameters

var_name name of the variable

Returns: true if the variable exists

Definition at line 850 of file SystemBase.C.

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

Referenced by ADDGKernel::ADDGKernel(), ADKernelTempl< T >::ADKernelTempl(), ArrayDGKernel::ArrayDGKernel(), ArrayKernel::ArrayKernel(), copyVars(), DGKernel::DGKernel(), DMMooseSetVariables(), FEProblemBase::duplicateVariableCheck(), FixedPointSolve::findTransformedSystem(), SubProblem::getVariableHelper(), SubProblem::hasAuxiliaryVariable(), SubProblem::hasLinearVariable(), ElementSubdomainModifierBase::initialSetup(), ExplicitTimeIntegrator::initialSetup(), InterfaceKernelTempl< T >::InterfaceKernelTempl(), Kernel::Kernel(), PNGOutput::makeMeshFunc(), MultiAppVariableValueSamplePostprocessorTransfer::MultiAppVariableValueSamplePostprocessorTransfer(), NonlinearSystemBase::setupScalingData(), and Coupleable::writableCoupledValue().

◆ hasVector() [1/2]

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

Check if the named vector exists in the system.

Definition at line 923 of file SystemBase.C.

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

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

◆ hasVector() [2/2]

virtual bool SystemBase::hasVector ( TagID tag_id ) const

inlinevirtual

Check if the tagged vector exists in the system.

Reimplemented in DisplacedSystem.

Definition at line 300 of file SystemBase.h.

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

◆ initializeObjects()

virtual void SystemBase::initializeObjects ( )

inlinevirtual

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

Definition at line 174 of file SystemBase.h.

174{}

◆ initialSetup()

void SystemBase::initialSetup ( )

virtual

Setup Functions.

Reimplemented in AuxiliarySystem, LinearSystem, and NonlinearSystemBase.

Definition at line 1570 of file SystemBase.C.

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

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

◆ initSolutionState()

void SystemBase::initSolutionState ( )

virtual

Initializes the solution state.

Reimplemented in DisplacedSystem.

Definition at line 1361 of file SystemBase.C.

{
  // 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;
}

Referenced by DisplacedSystem::initSolutionState().

◆ isArrayVariable()

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

virtual

If a variable is an array variable.

Definition at line 863 of file SystemBase.C.

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

◆ isScalarVariable()

bool SystemBase::isScalarVariable ( unsigned int var_name ) const

virtual

Definition at line 884 of file SystemBase.C.

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

Referenced by Assembly::initNonlocalCoupling().

◆ jacobianSetup()

void SystemBase::jacobianSetup ( )

virtual

Reimplemented in AuxiliarySystem, LinearSystem, and NonlinearSystemBase.

Definition at line 1605 of file SystemBase.C.

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

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

◆ matrixTagActive()

bool SystemBase::matrixTagActive ( TagID tag ) const

virtual

If or not a matrix tag is active.

Definition at line 1148 of file SystemBase.C.

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

◆ mesh() [1/2]

MooseMesh & SystemBase::mesh ( )

inline

Definition at line 100 of file SystemBase.h.

100{ return _mesh; }

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

◆ mesh() [2/2]

const MooseMesh & SystemBase::mesh ( ) const

inline

Definition at line 101 of file SystemBase.h.

101{ return _mesh; }

◆ name()

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

virtual

Definition at line 1337 of file SystemBase.C.

{
  return system().name();
}

◆ needSolutionState()

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

virtual

Registers that the solution state state is needed.

Reimplemented in DisplacedSystem.

Definition at line 1462 of file SystemBase.C.

{
  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 = getSolutionStates(iteration_type);
  solution_states.resize(state + 1);
 
  // The 0-th (current) solution state is owned by libMesh
  if (!solution_states[0])
    solution_states[0] = &solutionInternal();
  else
    mooseAssert(solution_states[0] == &solutionInternal(), "Inconsistent current solution");
 
  // We will manually add all states past current
  for (unsigned int i = 1; i <= state; ++i)
    if (!solution_states[i])
    {
      auto tag = _subproblem.addVectorTag(oldSolutionStateVectorName(i, iteration_type),
                                          Moose::VECTOR_TAG_SOLUTION);
      solution_states[i] = &addVector(tag, true, parallel_type);
    }
    else
    {
      // If the existing parallel type is PARALLEL and GHOSTED is now requested,
      // this would require an upgrade, which is risky if anybody has already
      // stored a pointer to the existing vector, since the upgrade would create
      // a new vector and make that pointer null. If the existing parallel type
      // is GHOSTED and PARALLEL is now requested, we don't need to do anything.
      if (parallel_type == GHOSTED && solutionStateParallelType(i, iteration_type) == PARALLEL)
        mooseError("The solution state has already been declared as PARALLEL");
 
      mooseAssert(solution_states[i] == &getVector(oldSolutionStateVectorName(i, iteration_type)),
                  "Inconsistent solution state");
    }
}

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

◆ nFieldVariables()

unsigned int SystemBase::nFieldVariables ( ) const

Get the number of field variables in this system.

Returns: the number of field variables

Definition at line 899 of file SystemBase.C.

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

Referenced by nVariables().

◆ nFVVariables()

unsigned int SystemBase::nFVVariables ( ) const

Get the number of finite volume variables in this system.

Returns: the number of finite volume variables

Definition at line 909 of file SystemBase.C.

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

◆ nonTimeVectorTag()

virtual TagID SystemBase::nonTimeVectorTag ( ) const

inlinevirtual

Reimplemented in DisplacedSystem, and NonlinearSystemBase.

Definition at line 321 of file SystemBase.h.

321{ mooseError("Not implemented yet"); }

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

◆ number()

unsigned int SystemBase::number ( ) const

Gets the number of this system.

Returns: The number of this system

Definition at line 1156 of file SystemBase.C.

{
  return system().number();
}

◆ nVariables()

unsigned int SystemBase::nVariables ( ) const

virtual

Get the number of variables in this system.

Returns: the number of variables

Definition at line 890 of file SystemBase.C.

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

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

◆ oldSolutionStateVectorName()

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

private

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

Definition at line 1378 of file SystemBase.C.

{
  mooseAssert(state != 0, "Not an old state");
  mooseAssert(static_cast<unsigned short>(iteration_type) <
                  static_cast<unsigned short>(Moose::SolutionIterationType::Count),
              "Invalid iteration_type");
 
  switch (iteration_type)
  {
    case Moose::SolutionIterationType::Time:
      if (state == 1)
        return Moose::OLD_SOLUTION_TAG;
      else if (state == 2)
        return Moose::OLDER_SOLUTION_TAG;
      break;
    case Moose::SolutionIterationType::Nonlinear:
      if (state == 1)
        return Moose::PREVIOUS_NL_SOLUTION_TAG;
      break;
    case Moose::SolutionIterationType::MultiAppFixedPoint:
      if (state == 1)
        return Moose::PREVIOUS_MULTIAPP_FP_SOLUTION_TAG;
      break;
    case Moose::SolutionIterationType::MultiSystemFixedPoint:
      if (state == 1)
        return Moose::PREVIOUS_MULTISYSTEM_FP_SOLUTION_TAG;
      break;
    case Moose::SolutionIterationType::Count:
      break;
  }
 
  return "solution_state_" + std::to_string(state) + "_" + Moose::stringify(iteration_type);
}

Referenced by needSolutionState(), and solutionState().

◆ postInit()

virtual void SystemBase::postInit ( )

inlinevirtual

Reimplemented in NonlinearEigenSystem.

Definition at line 163 of file SystemBase.h.

163{}

Referenced by NonlinearEigenSystem::postInit().

◆ prefix()

std::string SystemBase::prefix ( ) const

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

Definition at line 1712 of file SystemBase.C.

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

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

◆ preInit()

virtual void SystemBase::preInit ( )

inlinevirtual

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

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

Reimplemented in LinearSystem, NonlinearSystemBase, and SolverSystem.

Definition at line 157 of file SystemBase.h.

157{}

Referenced by SolverSystem::preInit().

◆ prepare()

void SystemBase::prepare ( THREAD_ID tid )

virtual

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 255 of file SystemBase.C.

{
  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();
  }
}

Referenced by SubProblem::reinitElemFaceRef().

◆ prepareFace()

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

virtual

Prepare the system for use on sides.

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

Parameters

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

Definition at line 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 )

virtual

Prepare the system for use for lower dimensional elements.

Parameters

tid	ID of the thread

Definition at line 331 of file SystemBase.C.

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

Referenced by SubProblem::reinitLowerDElem().

◆ prepareNeighbor()

void SystemBase::prepareNeighbor ( THREAD_ID tid )

virtual

Prepare the system for use.

Parameters

tid	ID of the thread

Definition at line 323 of file SystemBase.C.

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

Referenced by SubProblem::reinitNeighborFaceRef().

◆ queryTimeIntegrator()

const TimeIntegrator * SystemBase::queryTimeIntegrator ( const unsigned int var_num ) const

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

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

Definition at line 1672 of file SystemBase.C.

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

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

◆ reinit()

virtual void SystemBase::reinit ( )

inlinevirtual

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

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

Reimplemented in AuxiliarySystem, LinearSystem, and NonlinearEigenSystem.

Definition at line 169 of file SystemBase.h.

169{}

Referenced by NonlinearEigenSystem::reinit().

◆ reinitElem()

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

virtual

Reinit an element assembly info.

Parameters

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

Reimplemented in AuxiliarySystem.

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

◆ reinitElemFace()

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

virtual

Reinit assembly info for a side of an element.

Parameters

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

Reimplemented in AuxiliarySystem.

Definition at line 365 of file SystemBase.C.

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

Referenced by SubProblem::reinitElemFaceRef().

◆ reinitLowerD()

void SystemBase::reinitLowerD ( THREAD_ID tid )

virtual

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

Definition at line 389 of file SystemBase.C.

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

Referenced by SubProblem::reinitLowerDElem().

◆ reinitNeighbor()

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

virtual

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

Definition at line 381 of file SystemBase.C.

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

◆ reinitNeighborFace()

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

virtual

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

Definition at line 373 of file SystemBase.C.

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

Referenced by SubProblem::reinitNeighborFaceRef().

◆ reinitNode()

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

virtual

Reinit nodal assembly info.

Parameters

node	Node to reinit for
tid	Thread ID

Definition at line 397 of file SystemBase.C.

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

◆ reinitNodeFace()

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

virtual

Reinit nodal assembly info on a face.

Parameters

node	Node to reinit
bnd_id	Boundary ID
tid	Thread ID

Reimplemented in NonlinearSystemBase.

Definition at line 409 of file SystemBase.C.

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

◆ reinitNodes()

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

virtual

Reinit variables at a set of nodes.

Parameters

nodes	List of node ids to reinit
tid	Thread ID

Definition at line 421 of file SystemBase.C.

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

Referenced by SubProblem::reinitNodes().

◆ reinitNodesNeighbor()

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

virtual

Reinit variables at a set of neighbor nodes.

Parameters

nodes	List of node ids to reinit
tid	Thread ID

Definition at line 432 of file SystemBase.C.

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

Referenced by SubProblem::reinitNodesNeighbor().

◆ reinitScalars()

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

virtual

Reinit scalar varaibles.

Parameters

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

Definition at line 443 of file SystemBase.C.

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

◆ removeMatrix()

void SystemBase::removeMatrix ( TagID tag )

Removes a matrix with a given tag.

Parameters

tag_name The name of the tag

Definition at line 587 of file SystemBase.C.

{
  if (!_subproblem.matrixTagExists(tag_id))
    mooseError("Cannot remove the matrix with TagID ",
               tag_id,
               "\nin system '",
               name(),
               "', because that tag does not exist in the problem");
 
  if (hasMatrix(tag_id))
  {
    const auto matrix_name = _subproblem.matrixTagName(tag_id);
    system().remove_matrix(matrix_name);
    _tagged_matrices[tag_id] = nullptr;
  }
}

◆ removeVector() [1/2]

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

Remove a vector from the system with the given name.

Definition at line 1331 of file SystemBase.C.

{
  system().remove_vector(name);
}

Referenced by restoreOldSolutions().

◆ removeVector() [2/2]

void SystemBase::removeVector ( TagID tag_id )

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

Parameters

tag_id Tag ID

Definition at line 699 of file SystemBase.C.

{
  if (!_subproblem.vectorTagExists(tag_id))
    mooseError("Cannot remove the vector with TagID ",
               tag_id,
               "\nin system '",
               name(),
               "', because that tag does not exist in the problem");
 
  if (hasVector(tag_id))
  {
    auto vector_name = _subproblem.vectorTagName(tag_id);
    system().remove_vector(vector_name);
    _tagged_vectors[tag_id] = nullptr;
  }
}

◆ residualCopy()

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

inlinevirtual

Reimplemented in DisplacedSystem, and NonlinearSystemBase.

Definition at line 445 of file SystemBase.h.

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

Referenced by DisplacedSystem::residualCopy().

◆ residualGhosted()

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

inlinevirtual

Reimplemented in DisplacedSystem, and NonlinearSystemBase.

Definition at line 449 of file SystemBase.h.

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

Referenced by DisplacedSystem::residualGhosted().

◆ residualSetup()

void SystemBase::residualSetup ( )

virtual

Reimplemented in AuxiliarySystem, LinearSystem, and NonlinearSystemBase.

Definition at line 1598 of file SystemBase.C.

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

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

◆ residualVectorTag()

virtual TagID SystemBase::residualVectorTag ( ) const

inlinevirtual

Reimplemented in DisplacedSystem, and NonlinearSystemBase.

Definition at line 326 of file SystemBase.h.

326{ mooseError("Not implemented yet"); }

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

◆ restoreOldSolutions()

void SystemBase::restoreOldSolutions ( )

virtual

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

Definition at line 540 of file SystemBase.C.

{
  const auto num_states = getNumSolutionStates(Moose::SolutionIterationType::Time);
  if (num_states > 1)
    for (unsigned int i = 1; i <= num_states - 1; ++i)
      if (_saved_solution_states[i])
      {
        solutionState(i) = *(_saved_solution_states[i]);
        removeVector("save_solution_state_" + std::to_string(i));
        _saved_solution_states[i] = nullptr;
      }
 
  if (_saved_dot_old && solutionUDotOld())
  {
    *solutionUDotOld() = *_saved_dot_old;
    removeVector("save_solution_dot_old");
    _saved_dot_old = nullptr;
  }
  if (_saved_dotdot_old && solutionUDotDotOld())
  {
    *solutionUDotDotOld() = *_saved_dotdot_old;
    removeVector("save_solution_dotdot_old");
    _saved_dotdot_old = nullptr;
  }
}

◆ restoreSolutions()

void SystemBase::restoreSolutions ( )

virtual

Restore current solutions (call after your solve failed)

Reimplemented in SolverSystem.

Definition at line 1314 of file SystemBase.C.

{
  if (!hasSolutionState(1))
    mooseError("Cannot restore solutions without old solution");
 
  *(const_cast<NumericVector<Number> *&>(currentSolution())) = solutionOld();
  solution() = solutionOld();
  if (solutionUDotOld())
    *solutionUDot() = *solutionUDotOld();
  if (solutionUDotDotOld())
    *solutionUDotDot() = *solutionUDotDotOld();
  if (solutionPreviousNewton())
    *solutionPreviousNewton() = solutionOld();
  system().update();
}

Referenced by SolverSystem::restoreSolutions().

◆ saveOldSolutions()

void SystemBase::saveOldSolutions ( )

virtual

Save the old and older solutions.

Definition at line 509 of file SystemBase.C.

{
  const auto num_states = getNumSolutionStates(Moose::SolutionIterationType::Time);
  if (num_states > 1)
  {
    _saved_solution_states.resize(num_states);
    for (unsigned int i = 1; i <= num_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 <= num_states - 1; ++i)
      *(_saved_solution_states[i]) = solutionState(i);
  }
 
  if (!_saved_dot_old && solutionUDotOld())
    _saved_dot_old = &addVector("save_solution_dot_old", false, PARALLEL);
  if (!_saved_dotdot_old && solutionUDotDotOld())
    _saved_dotdot_old = &addVector("save_solution_dotdot_old", false, PARALLEL);
 
  if (solutionUDotOld())
    *_saved_dot_old = *solutionUDotOld();
 
  if (solutionUDotDotOld())
    *_saved_dotdot_old = *solutionUDotDotOld();
}

◆ serializedSolution()

NumericVector< Number > & SystemBase::serializedSolution ( )

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1645 of file SystemBase.C.

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

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

◆ setActiveScalarVariableCoupleableVectorTags()

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

Set the active vector tags for the scalar variables.

Definition at line 1625 of file SystemBase.C.

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

Referenced by SubProblem::setActiveScalarVariableCoupleableVectorTags().

◆ setActiveVariableCoupleableVectorTags()

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

Set the active vector tags for the variables.

Definition at line 1619 of file SystemBase.C.

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

Referenced by SubProblem::setActiveFEVariableCoupleableVectorTags().

◆ setVariableGlobalDoFs()

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

set all the global dof indices for a variable

Parameters

var_name The name of the variable

Definition at line 185 of file SystemBase.C.

{
  AllLocalDofIndicesThread aldit(_subproblem, {var_name});
  const ConstElemRange & elem_range = *_mesh.getActiveLocalElementRange();
  Threads::parallel_reduce(elem_range, aldit);
 
  // Gather the dof indices across procs to get all the dof indices for var_name
  aldit.dofIndicesSetUnion();
 
  const auto & all_dof_indices = aldit.getDofIndices();
  _var_all_dof_indices.assign(all_dof_indices.begin(), all_dof_indices.end());
}

◆ setVerboseFlag()

void SystemBase::setVerboseFlag ( const bool & verbose )

inline

Sets the verbose flag.

Parameters

[in] verbose Verbose flag

Definition at line 135 of file SystemBase.h.

135{ _verbose = verbose; }

Referenced by Executioner::Executioner().

◆ sizeVariableMatrixData()

void SystemBase::sizeVariableMatrixData ( )

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

Definition at line 1718 of file SystemBase.C.

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

◆ skipNextSolutionToOldCopy()

void SystemBase::skipNextSolutionToOldCopy ( )

inline

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

Definition at line 991 of file SystemBase.h.

991{ _skip_next_solution_to_old_copy = true; }

◆ solution() [1/2]

NumericVector< Number > & SystemBase::solution ( )

inline

Definition at line 203 of file SystemBase.h.

203{ return solutionState(0); }

◆ solution() [2/2]

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

inline

Definition at line 206 of file SystemBase.h.

206{ return solutionState(0); }

◆ solutionInternal()

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

protectedpure virtual

Internal getter for solution owned by libMesh.

Implemented in AuxiliarySystem, DisplacedSystem, and SolverSystem.

Referenced by needSolutionState(), and solutionState().

◆ solutionOld() [1/2]

NumericVector< Number > & SystemBase::solutionOld ( )

inline

Definition at line 204 of file SystemBase.h.

204{ return solutionState(1); }

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

◆ solutionOld() [2/2]

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

inline

Definition at line 207 of file SystemBase.h.

207{ return solutionState(1); }

◆ solutionOlder() [1/2]

NumericVector< Number > & SystemBase::solutionOlder ( )

inline

Definition at line 205 of file SystemBase.h.

205{ return solutionState(2); }

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

◆ solutionOlder() [2/2]

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

inline

Definition at line 208 of file SystemBase.h.

208{ return solutionState(2); }

◆ solutionPreviousNewton() [1/2]

NumericVector< Number > * SystemBase::solutionPreviousNewton ( )

virtual

Reimplemented in DisplacedSystem.

Definition at line 1343 of file SystemBase.C.

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

◆ solutionPreviousNewton() [2/2]

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

virtual

Reimplemented in DisplacedSystem.

Definition at line 1352 of file SystemBase.C.

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

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

◆ solutionState() [1/2]

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

virtual

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

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

Reimplemented in DisplacedSystem.

Definition at line 1444 of file SystemBase.C.

{
  if (!hasSolutionState(state, iteration_type))
    needSolutionState(state, iteration_type);
  return *getSolutionStates(iteration_type)[state];
}

Referenced by SolverSystem::applyFixedPointRelaxation(), copyPreviousSolutions(), FunctorNodalCorrector::execute(), PointwiseRenormalizeVector::execute(), PointwiseRenormalizeVector::finalize(), MooseVariableBase::getSolution(), restoreOldSolutions(), saveOldSolutions(), solution(), solution(), solutionOld(), solutionOld(), solutionOlder(), solutionOlder(), DisplacedSystem::solutionState(), and DisplacedSystem::solutionState().

◆ solutionState() [2/2]

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

virtual

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

Reimplemented in DisplacedSystem.

Definition at line 1414 of file SystemBase.C.

{
  if (!hasSolutionState(state, iteration_type))
  {
    const auto num_states = getNumSolutionStates(iteration_type);
    mooseError("For iteration type '",
               Moose::stringify(iteration_type),
               "': solution state ",
               state,
               " was requested in ",
               name(),
               " but only up to state ",
               (num_states == 0) ? 0 : num_states - 1,
               " is available.");
  }
 
  const auto & solution_states = getSolutionStates(iteration_type);
 
  if (state == 0)
    mooseAssert(solution_states[0] == &solutionInternal(), "Inconsistent current solution");
  else
    mooseAssert(solution_states[state] ==
                    &getVector(oldSolutionStateVectorName(state, iteration_type)),
                "Inconsistent solution state");
 
  return *solution_states[state];
}

◆ solutionStateParallelType()

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

Returns the parallel type of the given solution state.

Definition at line 1453 of file SystemBase.C.

{
  if (!hasSolutionState(state, iteration_type))
    mooseError("solutionStateParallelType() may only be called if the solution state exists.");
  return getSolutionStates(iteration_type)[state]->type();
}

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

◆ solutionStatesInitialized()

bool SystemBase::solutionStatesInitialized ( ) const

inline

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

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

Definition at line 917 of file SystemBase.h.

917{ return _solution_states_initialized; }

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

◆ solutionUDot() [1/2]

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

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 280 of file SystemBase.h.

280{ return _u_dot; }

◆ solutionUDot() [2/2]

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

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 284 of file SystemBase.h.

284{ return _u_dot; }

◆ solutionUDotDot() [1/2]

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

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 281 of file SystemBase.h.

281{ return _u_dotdot; }

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

◆ solutionUDotDot() [2/2]

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

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 285 of file SystemBase.h.

285{ return _u_dotdot; }

◆ solutionUDotDotOld() [1/2]

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

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 283 of file SystemBase.h.

283{ return _u_dotdot_old; }

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

◆ solutionUDotDotOld() [2/2]

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

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 287 of file SystemBase.h.

287{ return _u_dotdot_old; }

◆ solutionUDotOld() [1/2]

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

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 282 of file SystemBase.h.

282{ return _u_dot_old; }

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

◆ solutionUDotOld() [2/2]

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

inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 286 of file SystemBase.h.

286{ return _u_dot_old; }

◆ solve()

void SystemBase::solve ( )

virtual

Solve the system (using libMesh magic)

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

Definition at line 1248 of file SystemBase.C.

{
  system().solve();
}

◆ subdomainSetup()

void SystemBase::subdomainSetup ( )

virtual

Reimplemented in NonlinearSystemBase, and AuxiliarySystem.

Definition at line 1591 of file SystemBase.C.

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

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

◆ subproblem() [1/2]

SubProblem & SystemBase::subproblem ( )

inline

Definition at line 102 of file SystemBase.h.

102{ return _subproblem; }

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

◆ subproblem() [2/2]

const SubProblem & SystemBase::subproblem ( ) const

inline

Definition at line 103 of file SystemBase.h.

103{ return _subproblem; }

◆ system() [1/2]

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

pure virtual

Implemented in AuxiliarySystem, DisplacedSystem, LinearSystem, and NonlinearSystemBase.

◆ system() [2/2]

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

pure virtual

Get the reference to the libMesh system.

Implemented in AuxiliarySystem, DisplacedSystem, LinearSystem, and NonlinearSystemBase.

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

◆ systemMatrixTag()

virtual TagID SystemBase::systemMatrixTag ( ) const

inlinevirtual

Return the Matrix Tag ID for System.

Reimplemented in DisplacedSystem, LinearSystem, and NonlinearSystemBase.

Definition at line 316 of file SystemBase.h.

316{ mooseError("Not implemented yet"); }

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

◆ timestepSetup()

void SystemBase::timestepSetup ( )

virtual

Reimplemented in AuxiliarySystem, and NonlinearSystemBase.

Definition at line 1577 of file SystemBase.C.

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

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

◆ timeVectorTag()

virtual TagID SystemBase::timeVectorTag ( ) const

inlinevirtual

Ideally, we should not need this API.

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

Reimplemented in DisplacedSystem, and NonlinearSystemBase.

Definition at line 311 of file SystemBase.h.

311{ mooseError("Not implemented yet"); }

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

◆ update()

void SystemBase::update ( )

Update the system (doing libMesh magic)

Definition at line 1242 of file SystemBase.C.

{
  system().update();
}

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

◆ variableWarehouse()

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

inline

Definition at line 775 of file SystemBase.h.

775{ return _vars[tid]; }

Referenced by LinearFVGradientInterface::registerFVGradient().

◆ varKind()

Moose::VarKindType SystemBase::varKind ( ) const

inline

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

Definition at line 945 of file SystemBase.h.

945{ return _var_kind; }

Referenced by Coupleable::coupled().

◆ zeroTaggedVector()

void SystemBase::zeroTaggedVector ( const TagID tag )

Zero vector with the given tag.

Definition at line 673 of file SystemBase.C.

{
  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();
}

Referenced by zeroTaggedVectors().

◆ zeroTaggedVectors()

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

Zero all vectors for given tags.

Definition at line 692 of file SystemBase.C.

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

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

◆ zeroVariables()

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

virtual

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

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

Reimplemented in DisplacedSystem.

Definition at line 199 of file SystemBase.C.

{
  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);
    const 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();
  }
}

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

◆ zeroVariablesForJacobian()

void SystemBase::zeroVariablesForJacobian ( )

virtual

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

Definition at line 234 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_jacobian);
}

◆ zeroVariablesForResidual()

void SystemBase::zeroVariablesForResidual ( )

virtual

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

Definition at line 228 of file SystemBase.C.

{
  zeroVariables(_vars_to_be_zeroed_on_residual);
}

Member Data Documentation

◆ _active_tagged_matrices

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

protected

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

Definition at line 1043 of file SystemBase.h.

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

◆ _app

MooseApp& SystemBase::_app

protected

Definition at line 1006 of file SystemBase.h.

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

◆ _automatic_scaling

bool SystemBase::_automatic_scaling

protected

Whether to automatically scale the variables.

Definition at line 1073 of file SystemBase.h.

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

◆ _console

const ConsoleStream ConsoleStreamInterface::_console

inherited

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

Definition at line 31 of file ConsoleStreamInterface.h.

◆ _du_dot_du

std::vector<Real> SystemBase::_du_dot_du

protected

Derivative of time derivative of u with respect to uj.

This depends on the time integration scheme

Definition at line 1035 of file SystemBase.h.

Referenced by duDotDu(), and duDotDus().

◆ _du_dotdot_du

Real SystemBase::_du_dotdot_du

protected

Definition at line 1036 of file SystemBase.h.

Referenced by duDotDotDu(), and duDotDotDu().

◆ _factory

Factory& SystemBase::_factory

protected

Definition at line 1007 of file SystemBase.h.

◆ _fe_problem

FEProblemBase& SystemBase::_fe_problem

protected

the governing finite element/volume problem

Definition at line 1004 of file SystemBase.h.

◆ _matrix_tag_active_flags

std::vector<bool> SystemBase::_matrix_tag_active_flags

protected

Active flags for tagged matrices.

Definition at line 1045 of file SystemBase.h.

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

◆ _max_var_n_dofs_per_elem

size_t SystemBase::_max_var_n_dofs_per_elem

protected

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

Definition at line 1061 of file SystemBase.h.

Referenced by assignMaxVarNDofsPerElem(), and getMaxVarNDofsPerElem().

◆ _max_var_n_dofs_per_node

size_t SystemBase::_max_var_n_dofs_per_node

protected

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

Definition at line 1064 of file SystemBase.h.

Referenced by assignMaxVarNDofsPerNode(), and getMaxVarNDofsPerNode().

◆ _max_var_number

unsigned int SystemBase::_max_var_number

protected

Maximum variable number.

Definition at line 1018 of file SystemBase.h.

Referenced by getMaxVariableNumber().

◆ _mesh

MooseMesh& SystemBase::_mesh

protected

◆ _name

std::string SystemBase::_name

protected

The name of this system.

Definition at line 1011 of file SystemBase.h.

◆ _numbered_vars

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

protected

Map variable number to its pointer.

Definition at line 1070 of file SystemBase.h.

Referenced by addVariable(), and getVariable().

◆ _saved_dot_old

NumericVector<Real>* SystemBase::_saved_dot_old

protected

Definition at line 1052 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

◆ _saved_dotdot_old

NumericVector<Real>* SystemBase::_saved_dotdot_old

protected

Definition at line 1053 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

◆ _saved_old

NumericVector<Real>* SystemBase::_saved_old

protected

Definition at line 1048 of file SystemBase.h.

◆ _saved_older

NumericVector<Real>* SystemBase::_saved_older

protected

Definition at line 1049 of file SystemBase.h.

◆ _saved_solution_states

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

private

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

Definition at line 1118 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

◆ _serialized_solution

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

protected

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

Definition at line 1086 of file SystemBase.h.

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

◆ _skip_next_solution_to_old_copy

bool SystemBase::_skip_next_solution_to_old_copy

private

Whether to skip the next copy from the solution to the old vector.

Definition at line 1120 of file SystemBase.h.

Referenced by copyPreviousSolutions(), and skipNextSolutionToOldCopy().

◆ _solution_states

std::array<std::vector<NumericVector<Number> *>, static_cast<size_t>(Moose::SolutionIterationType::Count)> SystemBase::_solution_states

private

2D array of solution state vector pointers.

Outer (array) index: SolutionIterationType (Time, Nonlinear, ...) Inner (vector) index: State (0=current, 1=old, ...)

Should only be accessed through getSolutionStates() when possible for bounds checking.

Definition at line 1116 of file SystemBase.h.

Referenced by getSolutionStates().

◆ _solution_states_initialized

bool SystemBase::_solution_states_initialized

protected

Whether or not the solution states have been initialized.

Definition at line 1079 of file SystemBase.h.

Referenced by initSolutionState(), and solutionStatesInitialized().

◆ _subproblem

SubProblem& SystemBase::_subproblem

protected

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

Definition at line 1001 of file SystemBase.h.

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

◆ _tagged_matrices

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

protected

Tagged matrices (pointer)

Definition at line 1041 of file SystemBase.h.

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

◆ _tagged_vectors

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

protected

Tagged vectors (pointer)

Definition at line 1039 of file SystemBase.h.

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

◆ _time_integrators

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

protected

Time integrator.

Definition at line 1067 of file SystemBase.h.

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

◆ _u_dot

NumericVector<Number>* SystemBase::_u_dot

protected

solution vector for u^dot

Definition at line 1024 of file SystemBase.h.

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

◆ _u_dot_old

NumericVector<Number>* SystemBase::_u_dot_old

protected

old solution vector for u^dot

Definition at line 1029 of file SystemBase.h.

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

◆ _u_dotdot

NumericVector<Number>* SystemBase::_u_dotdot

protected

solution vector for u^dotdot

Definition at line 1026 of file SystemBase.h.

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

◆ _u_dotdot_old

NumericVector<Number>* SystemBase::_u_dotdot_old

protected

old solution vector for u^dotdot

Definition at line 1031 of file SystemBase.h.

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

◆ _var_all_dof_indices

std::vector<dof_id_type> SystemBase::_var_all_dof_indices

protected

Container for the dof indices of a given variable.

Definition at line 1082 of file SystemBase.h.

Referenced by getVariableGlobalDoFs(), and setVariableGlobalDoFs().

◆ _var_kind

Moose::VarKindType SystemBase::_var_kind

protected

default kind of variables in this system

Definition at line 1056 of file SystemBase.h.

Referenced by varKind().

◆ _var_map

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

protected

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

Definition at line 1016 of file SystemBase.h.

Referenced by getSubdomainsForVar(), and getVariableBlocks().

◆ _var_to_copy

std::vector<VarCopyInfo> SystemBase::_var_to_copy

protected

Definition at line 1058 of file SystemBase.h.

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

◆ _vars

std::vector<VariableWarehouse> SystemBase::_vars

protected

Variable warehouses (one for each thread)

Definition at line 1014 of file SystemBase.h.

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

◆ _vars_to_be_zeroed_on_jacobian

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

protected

Definition at line 1021 of file SystemBase.h.

Referenced by addVariableToZeroOnJacobian(), and zeroVariablesForJacobian().

◆ _vars_to_be_zeroed_on_residual

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

protected

Definition at line 1020 of file SystemBase.h.

Referenced by addVariableToZeroOnResidual(), and zeroVariablesForResidual().

◆ _verbose

bool SystemBase::_verbose

protected

True if printing out additional information.

Definition at line 1076 of file SystemBase.h.

Referenced by applyScalingFactors(), and setVerboseFlag().

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

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

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SystemBase()

◆ ~SystemBase()

Member Function Documentation

◆ activateAllMatrixTags()

◆ addDotVectors()

◆ addMatrix()

◆ addScalingVector()

◆ addTimeIntegrator()

◆ addVariable()

◆ addVariableToCopy()

◆ addVariableToZeroOnJacobian()

◆ addVariableToZeroOnResidual()

◆ addVector() [1/2]

◆ addVector() [2/2]

◆ applyScalingFactors()

◆ assignMaxVarNDofsPerElem()

◆ assignMaxVarNDofsPerNode()

◆ associateMatrixToTag()

◆ associateVectorToTag()

◆ augmentSendList()

◆ augmentSparsity()

◆ automaticScaling() [1/2]

◆ automaticScaling() [2/2]

◆ clearAllDofIndices()

◆ closeTaggedMatrices()

◆ closeTaggedVector()

◆ closeTaggedVectors()

◆ compute()

◆ computeVariables()

◆ computingScalingJacobian()

◆ copyOldSolutions()

◆ copyPreviousSolutions()

◆ copySolutionsBackwards()

◆ copyTimeIntegrators()

◆ copyVars()

◆ currentSolution()

◆ customSetup()

◆ deactivateAllMatrixTags()

◆ defaultMatrixTags()

◆ defaultVectorTags()

◆ disassociateDefaultMatrixTags()

◆ disassociateDefaultVectorTags()

◆ disassociateMatrixFromTag() [1/2]

◆ disassociateMatrixFromTag() [2/2]

◆ disassociateVectorFromTag() [1/2]

◆ disassociateVectorFromTag() [2/2]

◆ dofMap() [1/2]

◆ dofMap() [2/2]

◆ duDotDotDu() [1/2]

◆ duDotDotDu() [2/2]

◆ duDotDu()

◆ duDotDus()

◆ feProblem() [1/2]

◆ feProblem() [2/2]

◆ flushTaggedMatrices()

◆ getActualFieldVariable() [1/2]

◆ getActualFieldVariable() [2/2]

◆ getFieldVariable() [1/2]

◆ getFieldVariable() [2/2]

◆ getFVVariable()

◆ getMatrix() [1/2]

◆ getMatrix() [2/2]

◆ getMaxVariableNumber()

◆ getMaxVarNDofsPerElem()

◆ getMaxVarNDofsPerNode()

◆ getMinQuadratureOrder()

◆ getNumSolutionStates()

◆ getScalarVariable() [1/2]

◆ getScalarVariable() [2/2]

◆ getScalarVariables()

◆ getSolutionStates() [1/2]

◆ getSolutionStates() [2/2]