www.mooseframework.org
Public Member Functions | Protected Attributes | List of all members
SystemBase Class Referenceabstract

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

#include <SystemBase.h>

Inheritance diagram for SystemBase:
[legend]

Public Member Functions

 SystemBase (SubProblem &subproblem, const std::string &name, Moose::VarKindType var_kind)
 
virtual ~SystemBase ()
 
virtual unsigned int number () const
 Gets the number of this system. More...
 
virtual MooseMeshmesh ()
 
virtual SubProblemsubproblem ()
 
virtual DofMap & dofMap ()
 Gets the dof map. More...
 
virtual System & system ()=0
 Get the reference to the libMesh system. More...
 
virtual const System & system () const =0
 
virtual void init ()
 Initialize the system. More...
 
virtual void initializeObjects ()
 Called only once, just before the solve begins so objects can do some precalculations. More...
 
virtual void addExtraVectors ()
 Method called during initialSetup to add extra system vector if they are required by the simulation. More...
 
virtual void update ()
 Update the system (doing libMesh magic) More...
 
virtual void solve ()
 Solve the system (using libMesh magic) More...
 
virtual void copyOldSolutions ()
 Shifts the solutions backwards in time. More...
 
virtual void restoreSolutions ()
 Restore current solutions (call after your solve failed) More...
 
virtual const NumericVector< Number > *& currentSolution ()=0
 The solution vector that is currently being operated on. More...
 
virtual NumericVector< Number > & solution ()=0
 
virtual NumericVector< Number > & solutionOld ()=0
 
virtual NumericVector< Number > & solutionOlder ()=0
 
virtual NumericVector< Number > * solutionPreviousNewton ()=0
 
virtual Number & duDotDu ()
 
virtual Number & duDotDotDu ()
 
virtual NumericVector< Number > * solutionUDot ()=0
 
virtual NumericVector< Number > * solutionUDotOld ()=0
 
virtual NumericVector< Number > * solutionUDotDot ()=0
 
virtual NumericVector< Number > * solutionUDotDotOld ()=0
 
virtual void saveOldSolutions ()
 Save the old and older solutions. More...
 
virtual void restoreOldSolutions ()
 Restore the old and older solutions when the saved solutions present. More...
 
bool hasVector (const std::string &tag_name) const
 Check if the named vector exists in the system. More...
 
virtual bool hasVector (TagID tag_id)
 Check if the tagged vector exists in the system. More...
 
virtual TagID timeVectorTag ()
 Ideally, we should not need this API. More...
 
virtual TagID timeMatrixTag ()
 Return the Matrix Tag ID for Time. More...
 
virtual TagID systemMatrixTag ()
 Return the Matrix Tag ID for System. More...
 
virtual TagID nonTimeVectorTag ()
 
virtual TagID residualVectorTag ()
 
virtual NumericVector< Number > & getVector (const std::string &name)
 Get a raw NumericVector. More...
 
virtual NumericVector< Number > & getVector (TagID tag)
 Get a raw NumericVector. More...
 
virtual void associateVectorToTag (NumericVector< Number > &vec, TagID tag)
 Associate a vector for a given tag. More...
 
virtual void disassociateVectorFromTag (NumericVector< Number > &vec, TagID tag)
 Associate a vector for a given tag. More...
 
virtual void disassociateAllTaggedVectors ()
 Disassociate all vectors, and then hasVector() will return false. More...
 
virtual bool hasMatrix (TagID tag)
 Check if the tagged matrix exists in the system. More...
 
virtual SparseMatrix< Number > & getMatrix (TagID tag)
 Get a raw SparseMatrix. More...
 
virtual void activeAllMatrixTags ()
 Make all exsiting matrices ative. More...
 
virtual void activeMatrixTag (TagID tag)
 Active a matrix for tag. More...
 
virtual bool matrixTagActive (TagID tag)
 If or not a matrix tag is active. More...
 
virtual void deactiveMatrixTag (TagID tag)
 deactive a matrix for tag More...
 
virtual void deactiveAllMatrixTags ()
 Make matrices inactive. More...
 
void closeTaggedMatrices (const std::set< TagID > &tags)
 Close all matrices associated the tags. More...
 
virtual void associateMatrixToTag (SparseMatrix< Number > &matrix, TagID tag)
 associate a matirx to a tag More...
 
virtual void disassociateMatrixFromTag (SparseMatrix< Number > &matrix, TagID tag)
 disassociate a matirx from a tag More...
 
virtual void disassociateAllTaggedMatrices ()
 Clear all tagged matrices. More...
 
virtual NumericVector< Number > & serializedSolution ()=0
 Returns a reference to a serialized version of the solution vector for this subproblem. More...
 
virtual NumericVector< Number > & residualCopy ()
 
virtual NumericVector< Number > & residualGhosted ()
 
virtual void augmentSendList (std::vector< dof_id_type > &send_list)
 Will modify the send_list to add all of the extra ghosted dofs for this system. More...
 
virtual void augmentSparsity (SparsityPattern::Graph &sparsity, std::vector< dof_id_type > &n_nz, std::vector< dof_id_type > &n_oz)=0
 Will modify the sparsity pattern to add logical geometric connections. More...
 
virtual void addVariable (const std::string &var_name, const FEType &type, Real scale_factor, const std::set< SubdomainID > *const active_subdomains=NULL)
 Adds a variable to the system. More...
 
virtual bool isScalarVariable (unsigned int var_name) const
 
MooseVariableFEBasegetVariable (THREAD_ID tid, const std::string &var_name)
 Gets a reference to a variable of with specified name. More...
 
MooseVariableFEBasegetVariable (THREAD_ID tid, unsigned int var_number)
 Gets a reference to a variable with specified number. More...
 
template<typename T >
MooseVariableFE< T > & getFieldVariable (THREAD_ID tid, const std::string &var_name)
 Gets a reference to a variable of with specified name. More...
 
template<typename T >
MooseVariableFE< T > & getFieldVariable (THREAD_ID tid, unsigned int var_number)
 Gets a reference to a variable with specified number. More...
 
virtual MooseVariableScalargetScalarVariable (THREAD_ID tid, const std::string &var_name)
 Gets a reference to a scalar variable with specified number. More...
 
virtual MooseVariableScalargetScalarVariable (THREAD_ID tid, unsigned int var_number)
 Gets a reference to a variable with specified number. More...
 
virtual const std::set< SubdomainID > * getVariableBlocks (unsigned int var_number)
 Get the block where a variable of this system is defined. More...
 
virtual unsigned int nVariables () const
 Get the number of variables in this system. More...
 
size_t getMaxVarNDofsPerElem ()
 Gets the maximum number of dofs used by any one variable on any one element. More...
 
size_t getMaxVarNDofsPerNode ()
 Gets the maximum number of dofs used by any one variable on any one node. More...
 
void assignMaxVarNDofsPerElem (const size_t &max_dofs)
 assign the maximum element dofs More...
 
void assignMaxVarNDofsPerNode (const size_t &max_dofs)
 assign the maximum node dofs More...
 
virtual void addVariableToZeroOnResidual (std::string var_name)
 Adds this variable to the list of variables to be zeroed during each residual evaluation. More...
 
virtual void addVariableToZeroOnJacobian (std::string var_name)
 Adds this variable to the list of variables to be zeroed during each Jacobian evaluation. More...
 
virtual void zeroVariables (std::vector< std::string > &vars_to_be_zeroed)
 Zero out the solution for the list of variables passed in. More...
 
virtual void zeroVariablesForResidual ()
 Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on residual evaluation by a call to addVariableToZeroOnResidual() More...
 
virtual void zeroVariablesForJacobian ()
 Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on Jacobian evaluation by a call to addVariableToZeroOnResidual() More...
 
virtual Order getMinQuadratureOrder ()
 Get minimal quadrature order needed for integrating variables in this system. More...
 
virtual void prepare (THREAD_ID tid)
 Prepare the system for use. More...
 
virtual void prepareFace (THREAD_ID tid, bool resize_data)
 Prepare the system for use on sides. More...
 
virtual void prepareNeighbor (THREAD_ID tid)
 Prepare the system for use. More...
 
virtual void reinitElem (const Elem *elem, THREAD_ID tid)
 Reinit an element assembly info. More...
 
virtual void reinitElemFace (const Elem *elem, unsigned int side, BoundaryID bnd_id, THREAD_ID tid)
 Reinit assembly info for a side of an element. More...
 
virtual void reinitNeighborFace (const Elem *elem, unsigned int side, BoundaryID bnd_id, THREAD_ID tid)
 Compute the values of the variables at all the current points. More...
 
virtual void reinitNeighbor (const Elem *elem, THREAD_ID tid)
 Compute the values of the variables at all the current points. More...
 
virtual void reinitNode (const Node *node, THREAD_ID tid)
 Reinit nodal assembly info. More...
 
virtual void reinitNodeFace (const Node *node, BoundaryID bnd_id, THREAD_ID tid)
 Reinit nodal assembly info on a face. More...
 
virtual void reinitNodes (const std::vector< dof_id_type > &nodes, THREAD_ID tid)
 Reinit variables at a set of nodes. More...
 
virtual void reinitNodesNeighbor (const std::vector< dof_id_type > &nodes, THREAD_ID tid)
 Reinit variables at a set of neighbor nodes. More...
 
virtual void reinitScalars (THREAD_ID tid)
 Reinit scalar varaibles. More...
 
virtual void addVariableToCopy (const std::string &dest_name, const std::string &source_name, const std::string &timestep)
 Add info about variable that will be copied. More...
 
const std::vector< MooseVariableFEBase * > & getVariables (THREAD_ID tid)
 
const std::vector< MooseVariableScalar * > & getScalarVariables (THREAD_ID tid)
 
const std::set< SubdomainID > & getSubdomainsForVar (unsigned int var_number) const
 
virtual void removeVector (const std::string &name)
 Remove a vector from the system with the given name. More...
 
virtual NumericVector< Number > & addVector (const std::string &vector_name, const bool project, const ParallelType type)
 Adds a solution length vector to the system. More...
 
NumericVector< Number > & addVector (TagID tag, const bool project, const ParallelType type)
 Adds a solution length vector to the system with the specified TagID. More...
 
virtual void closeTaggedVectors (const std::set< TagID > &tags)
 Close all vectors for given tags. More...
 
virtual void zeroTaggedVectors (const std::set< TagID > &tags)
 Zero all vectors for given tags. More...
 
virtual void removeVector (TagID tag_id)
 Remove a solution length vector from the system with the specified TagID. More...
 
virtual SparseMatrix< Number > & addMatrix (TagID)
 Adds a jacobian sized vector. More...
 
virtual void removeMatrix (TagID)
 Removes a jacobian sized vector. More...
 
virtual const std::string & name () const
 
virtual void addScalarVariable (const std::string &var_name, Order order, Real scale_factor, const std::set< SubdomainID > *const active_subdomains=NULL)
 Adds a scalar variable. More...
 
const std::vector< VariableName > & getVariableNames () const
 
virtual void computeVariables (const NumericVector< Number > &)
 
void copyVars (ExodusII_IO &io)
 
virtual void copySolutionsBackwards ()
 Copy current solution into old and older. More...
 
virtual void addTimeIntegrator (const std::string &, const std::string &, InputParameters)
 
virtual void addTimeIntegrator (std::shared_ptr< TimeIntegrator >)
 
TimeIntegratorgetTimeIntegrator ()
 
std::shared_ptr< TimeIntegratorgetSharedTimeIntegrator ()
 
virtual bool hasVariable (const std::string &var_name) const
 Query a system for a variable. More...
 
virtual bool hasScalarVariable (const std::string &var_name) const
 

Protected Attributes

SubProblem_subproblem
 
MooseApp_app
 
Factory_factory
 
MooseMesh_mesh
 
std::string _name
 The name of this system. More...
 
std::vector< VariableWarehouse_vars
 Variable warehouses (one for each thread) More...
 
std::map< unsigned int, std::set< SubdomainID > > _var_map
 Map of variables (variable id -> array of subdomains where it lives) More...
 
std::vector< std::string > _vars_to_be_zeroed_on_residual
 
std::vector< std::string > _vars_to_be_zeroed_on_jacobian
 
Real _du_dot_du
 
Real _du_dotdot_du
 
std::vector< NumericVector< Number > * > _tagged_vectors
 Tagged vectors (pointer) More...
 
std::vector< SparseMatrix< Number > * > _tagged_matrices
 Tagged matrices (pointer) More...
 
std::vector< bool > _matrix_tag_active_flags
 Active flags for tagged matrices. More...
 
NumericVector< Real > * _saved_old
 
NumericVector< Real > * _saved_older
 
NumericVector< Real > * _saved_dot_old
 
NumericVector< Real > * _saved_dotdot_old
 
Moose::VarKindType _var_kind
 default kind of variables in this system More...
 
std::vector< VarCopyInfo_var_to_copy
 
size_t _max_var_n_dofs_per_elem
 Maximum number of dofs for any one variable on any one element. More...
 
size_t _max_var_n_dofs_per_node
 Maximum number of dofs for any one variable on any one node. More...
 
std::shared_ptr< TimeIntegrator_time_integrator
 Time integrator. More...
 

Detailed Description

Base class for a system (of equations)

Definition at line 93 of file SystemBase.h.

Constructor & Destructor Documentation

◆ SystemBase()

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

Definition at line 82 of file SystemBase.C.

85  : libMesh::ParallelObject(subproblem),
90  _name(name),
91  _vars(libMesh::n_threads()),
92  _var_map(),
93  _saved_old(NULL),
94  _saved_older(NULL),
95  _saved_dot_old(NULL),
96  _saved_dotdot_old(NULL),
97  _var_kind(var_kind),
100  _time_integrator(nullptr)
101 {
102 }
virtual MooseMesh & mesh()=0
size_t _max_var_n_dofs_per_node
Maximum number of dofs for any one variable on any one node.
Definition: SystemBase.h:738
Factory & _factory
Definition: SystemBase.h:697
size_t _max_var_n_dofs_per_elem
Maximum number of dofs for any one variable on any one element.
Definition: SystemBase.h:735
NumericVector< Real > * _saved_older
Definition: SystemBase.h:723
Factory & getFactory()
Retrieve the Factory associated with this App.
Definition: MooseApp.h:280
virtual const std::string & name() const
Definition: SystemBase.C:1022
SubProblem & _subproblem
Definition: SystemBase.h:694
Moose::VarKindType _var_kind
default kind of variables in this system
Definition: SystemBase.h:730
NumericVector< Real > * _saved_dot_old
Definition: SystemBase.h:726
virtual SubProblem & subproblem()
Definition: SystemBase.h:105
std::map< unsigned int, std::set< SubdomainID > > _var_map
Map of variables (variable id -> array of subdomains where it lives)
Definition: SystemBase.h:706
std::string _name
The name of this system.
Definition: SystemBase.h:701
MooseApp & _app
Definition: SystemBase.h:696
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704
MooseMesh & _mesh
Definition: SystemBase.h:699
std::shared_ptr< TimeIntegrator > _time_integrator
Time integrator.
Definition: SystemBase.h:741
NumericVector< Real > * _saved_old
Definition: SystemBase.h:722
NumericVector< Real > * _saved_dotdot_old
Definition: SystemBase.h:727
MooseApp & getMooseApp() const
Get the MooseApp this object is associated with.
Definition: MooseObject.h:91

◆ ~SystemBase()

virtual SystemBase::~SystemBase ( )
inlinevirtual

Definition at line 97 of file SystemBase.h.

97 {}

Member Function Documentation

◆ activeAllMatrixTags()

void SystemBase::activeAllMatrixTags ( )
virtual

Make all exsiting matrices ative.

Definition at line 865 of file SystemBase.C.

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

866 {
867  auto num_matrix_tags = _subproblem.numMatrixTags();
868 
869  _matrix_tag_active_flags.resize(num_matrix_tags);
870 
871  for (decltype(num_matrix_tags) tag = 0; tag < num_matrix_tags; tag++)
872  if (hasMatrix(tag))
873  _matrix_tag_active_flags[tag] = true;
874  else
875  _matrix_tag_active_flags[tag] = false;
876 }
virtual bool hasMatrix(TagID tag)
Check if the tagged matrix exists in the system.
Definition: SystemBase.C:781
std::vector< bool > _matrix_tag_active_flags
Active flags for tagged matrices.
Definition: SystemBase.h:719
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual unsigned int numMatrixTags()
The total number of tags.
Definition: SubProblem.h:152

◆ activeMatrixTag()

void SystemBase::activeMatrixTag ( TagID  tag)
virtual

Active a matrix for tag.

Definition at line 830 of file SystemBase.C.

831 {
832  mooseAssert(_subproblem.matrixTagExists(tag),
833  "Cannot active Matrix with matrix_tag : " << tag << "that does not exist");
834 
835  if (_matrix_tag_active_flags.size() < tag + 1)
836  _matrix_tag_active_flags.resize(tag + 1);
837 
838  _matrix_tag_active_flags[tag] = true;
839 }
virtual bool matrixTagExists(const TagName &tag_name)
Check to see if a particular Tag exists.
Definition: SubProblem.C:119
std::vector< bool > _matrix_tag_active_flags
Active flags for tagged matrices.
Definition: SystemBase.h:719
SubProblem & _subproblem
Definition: SystemBase.h:694

◆ addExtraVectors()

void SystemBase::addExtraVectors ( )
virtual

Method called during initialSetup to add extra system vector if they are required by the simulation.

Reimplemented in NonlinearSystemBase, and AuxiliarySystem.

Definition at line 949 of file SystemBase.C.

950 {
951 }

◆ addMatrix()

virtual SparseMatrix<Number>& SystemBase::addMatrix ( TagID  )
inlinevirtual

Adds a jacobian sized vector.

Parameters
tag_nameThe name of the tag

Reimplemented in NonlinearSystem.

Definition at line 642 of file SystemBase.h.

643  {
644  mooseError("Adding a matrix is not supported for this type of system!");
645  }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208

◆ addScalarVariable()

void SystemBase::addScalarVariable ( const std::string &  var_name,
Order  order,
Real  scale_factor,
const std::set< SubdomainID > *const  active_subdomains = NULL 
)
virtual

Adds a scalar variable.

Parameters
var_nameThe name of the variable
orderThe order of the variable
scale_factorThe scaling factor to be used with this scalar variable

Definition at line 628 of file SystemBase.C.

Referenced by DisplacedProblem::addAuxScalarVariable(), and DisplacedProblem::addScalarVariable().

632 {
633  FEType type(order, SCALAR);
634  unsigned int var_num = system().add_variable(var_name, type, active_subdomains);
635  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
636  {
637  // FIXME: we cannot refer fetype in libMesh at this point, so we will just make a copy in
638  // MooseVariableBase.
639  MooseVariableScalar * var =
640  new MooseVariableScalar(var_num, type, *this, _subproblem.assembly(tid), _var_kind, tid);
641  var->scalingFactor(scale_factor);
642  _vars[tid].add(var_name, var);
643  }
644  if (active_subdomains == nullptr)
645  _var_map[var_num] = std::set<SubdomainID>();
646  else
647  for (const auto subdomain_id : *active_subdomains)
648  _var_map[var_num].insert(subdomain_id);
649 }
virtual Assembly & assembly(THREAD_ID tid)=0
SubProblem & _subproblem
Definition: SystemBase.h:694
Moose::VarKindType _var_kind
default kind of variables in this system
Definition: SystemBase.h:730
virtual System & system()=0
Get the reference to the libMesh system.
std::map< unsigned int, std::set< SubdomainID > > _var_map
Map of variables (variable id -> array of subdomains where it lives)
Definition: SystemBase.h:706
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704
MatType type
Class for scalar variables (they are different).
unsigned int THREAD_ID
Definition: MooseTypes.h:126
void scalingFactor(Real factor)
Set the scaling factor for this variable.

◆ addTimeIntegrator() [1/2]

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

Reimplemented in NonlinearSystemBase, and AuxiliarySystem.

Definition at line 681 of file SystemBase.h.

684  {
685  }

◆ addTimeIntegrator() [2/2]

virtual void SystemBase::addTimeIntegrator ( std::shared_ptr< TimeIntegrator )
inlinevirtual

Reimplemented in DisplacedSystem.

Definition at line 687 of file SystemBase.h.

687 {}

◆ addVariable()

void SystemBase::addVariable ( const std::string &  var_name,
const FEType &  type,
Real  scale_factor,
const std::set< SubdomainID > *const  active_subdomains = NULL 
)
virtual

Adds a variable to the system.

Parameters
var_namename of the variable
typeFE type of the variable
scale_factorthe scaling factor for the variable
active_subdomainsa list of subdomain ids this variable is active on

Reimplemented in AuxiliarySystem.

Definition at line 597 of file SystemBase.C.

Referenced by DisplacedProblem::addAuxVariable(), AuxiliarySystem::addVariable(), and DisplacedProblem::addVariable().

601 {
602  unsigned int var_num = system().add_variable(var_name, type, active_subdomains);
603  for (THREAD_ID tid = 0; tid < libMesh::n_threads(); tid++)
604  {
605  // FIXME: we cannot refer fetype in libMesh at this point, so we will just make a copy in
606  // MooseVariableBase.
607  MooseVariableBase * var;
608  if (type == FEType(0, MONOMIAL))
609  var = new MooseVariableConstMonomial(
610  var_num, type, *this, _subproblem.assembly(tid), _var_kind, tid);
611  else if (type == FEType(FIRST, NEDELEC_ONE) || type.family == LAGRANGE_VEC)
612  var =
613  new VectorMooseVariable(var_num, type, *this, _subproblem.assembly(tid), _var_kind, tid);
614  else
615  var = new MooseVariable(var_num, type, *this, _subproblem.assembly(tid), _var_kind, tid);
616 
617  var->scalingFactor(scale_factor);
618  _vars[tid].add(var_name, var);
619  }
620  if (active_subdomains == nullptr)
621  _var_map[var_num] = std::set<SubdomainID>();
622  else
623  for (const auto subdomain_id : *active_subdomains)
624  _var_map[var_num].insert(subdomain_id);
625 }
virtual Assembly & assembly(THREAD_ID tid)=0
MooseVariableFE< Real > MooseVariable
Definition: Adaptivity.h:30
SubProblem & _subproblem
Definition: SystemBase.h:694
Moose::VarKindType _var_kind
default kind of variables in this system
Definition: SystemBase.h:730
virtual System & system()=0
Get the reference to the libMesh system.
std::map< unsigned int, std::set< SubdomainID > > _var_map
Map of variables (variable id -> array of subdomains where it lives)
Definition: SystemBase.h:706
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704
MatType type
MooseVariableFE< VectorValue< Real > > VectorMooseVariable
Definition: Adaptivity.h:32
unsigned int THREAD_ID
Definition: MooseTypes.h:126
void scalingFactor(Real factor)
Set the scaling factor for this variable.

◆ 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_nameName of the nodal variable being used for copying into (name is from the exodusII file)
source_nameName of the nodal variable being used for copying from (name is from the exodusII file)
timestepTimestep in the file being used

Definition at line 906 of file SystemBase.C.

909 {
910  _var_to_copy.push_back(VarCopyInfo(dest_name, source_name, timestep));
911 }
std::vector< VarCopyInfo > _var_to_copy
Definition: SystemBase.h:732
Information about variables that will be copied.
Definition: SystemBase.h:75

◆ 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_nameThe name of the variable to be zeroed.

Reimplemented in DisplacedSystem.

Definition at line 184 of file SystemBase.C.

Referenced by DisplacedSystem::addVariableToZeroOnJacobian(), ADIntegratedBCTempl< T, compute_stage >::ADIntegratedBCTempl(), ADKernelTempl< T, compute_stage >::ADKernelTempl(), DGKernel::DGKernel(), IntegratedBC::IntegratedBC(), InterfaceKernel::InterfaceKernel(), Kernel::Kernel(), NodalBC::NodalBC(), and NodalKernel::NodalKernel().

185 {
186  _vars_to_be_zeroed_on_jacobian.push_back(var_name);
187 }
std::vector< std::string > _vars_to_be_zeroed_on_jacobian
Definition: SystemBase.h:709

◆ 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_nameThe name of the variable to be zeroed.

Reimplemented in DisplacedSystem.

Definition at line 178 of file SystemBase.C.

Referenced by DisplacedSystem::addVariableToZeroOnResidual(), ADIntegratedBCTempl< T, compute_stage >::ADIntegratedBCTempl(), ADKernelTempl< T, compute_stage >::ADKernelTempl(), DGKernel::DGKernel(), IntegratedBC::IntegratedBC(), InterfaceKernel::InterfaceKernel(), Kernel::Kernel(), NodalBC::NodalBC(), and NodalKernel::NodalKernel().

179 {
180  _vars_to_be_zeroed_on_residual.push_back(var_name);
181 }
std::vector< std::string > _vars_to_be_zeroed_on_residual
Definition: SystemBase.h:708

◆ addVector() [1/2]

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

Adds a solution length vector to the system.

Parameters
vector_nameThe name of the vector.
projectWhether 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.
typeWhat 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.

Reimplemented in AuxiliarySystem.

Definition at line 526 of file SystemBase.C.

Referenced by ActuallyExplicitEuler::ActuallyExplicitEuler(), NonlinearSystemBase::addDotVectors(), NonlinearSystemBase::addExtraVectors(), AStableDirk4::AStableDirk4(), MultiApp::createApp(), Executioner::Executioner(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), FEProblemBase::initNullSpaceVectors(), LStableDirk3::LStableDirk3(), LStableDirk4::LStableDirk4(), NonlinearSystemBase::residualGhosted(), and saveOldSolutions().

527 {
528  if (hasVector(vector_name))
529  return getVector(vector_name);
530 
531  NumericVector<Number> & vec = system().add_vector(vector_name, project, type);
532  return vec;
533 }
bool hasVector(const std::string &tag_name) const
Check if the named vector exists in the system.
Definition: SystemBase.C:685
virtual System & system()=0
Get the reference to the libMesh system.
MatType type
virtual NumericVector< Number > & getVector(const std::string &name)
Get a raw NumericVector.
Definition: SystemBase.C:735

◆ addVector() [2/2]

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

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

Parameters
tag_nameThe name of the tag
projectWhether 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.
typeWhat 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 536 of file SystemBase.C.

537 {
538  if (!_subproblem.vectorTagExists(tag))
539  mooseError("Cannot add a tagged vector with vector_tag, ",
540  tag,
541  ", that tag does not exist in System ",
542  name());
543 
544  if (hasVector(tag))
545  return getVector(tag);
546 
547  auto vector_name = _subproblem.vectorTagName(tag);
548 
549  NumericVector<Number> & vec = system().add_vector(vector_name, project, type);
550 
551  if (_tagged_vectors.size() < tag + 1)
552  _tagged_vectors.resize(tag + 1);
553 
554  _tagged_vectors[tag] = &vec;
555 
556  return vec;
557 }
virtual TagName vectorTagName(TagID tag)
Retrieve the name associated with a TagID.
Definition: SubProblem.C:96
bool hasVector(const std::string &tag_name) const
Check if the named vector exists in the system.
Definition: SystemBase.C:685
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208
virtual const std::string & name() const
Definition: SystemBase.C:1022
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual bool vectorTagExists(TagID tag)
Check to see if a particular Tag exists.
Definition: SubProblem.h:107
virtual System & system()=0
Get the reference to the libMesh system.
MatType type
std::vector< NumericVector< Number > * > _tagged_vectors
Tagged vectors (pointer)
Definition: SystemBase.h:715
virtual NumericVector< Number > & getVector(const std::string &name)
Get a raw NumericVector.
Definition: SystemBase.C:735

◆ assignMaxVarNDofsPerElem()

void SystemBase::assignMaxVarNDofsPerElem ( const size_t &  max_dofs)
inline

assign the maximum element dofs

Definition at line 425 of file SystemBase.h.

425 { _max_var_n_dofs_per_elem = max_dofs; }
size_t _max_var_n_dofs_per_elem
Maximum number of dofs for any one variable on any one element.
Definition: SystemBase.h:735

◆ assignMaxVarNDofsPerNode()

void SystemBase::assignMaxVarNDofsPerNode ( const size_t &  max_dofs)
inline

assign the maximum node dofs

Definition at line 430 of file SystemBase.h.

430 { _max_var_n_dofs_per_node = max_dofs; }
size_t _max_var_n_dofs_per_node
Maximum number of dofs for any one variable on any one node.
Definition: SystemBase.h:738

◆ associateMatrixToTag()

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

associate a matirx to a tag

Reimplemented in DisplacedSystem.

Definition at line 803 of file SystemBase.C.

Referenced by DisplacedSystem::associateMatrixToTag(), and NonlinearSystemBase::computeJacobian().

804 {
805  mooseAssert(_subproblem.matrixTagExists(tag),
806  "Cannot associate Matrix with matrix_tag : " << tag << "that does not exist");
807 
808  if (_tagged_matrices.size() < tag + 1)
809  _tagged_matrices.resize(tag + 1);
810 
811  _tagged_matrices[tag] = &matrix;
812 }
std::vector< SparseMatrix< Number > * > _tagged_matrices
Tagged matrices (pointer)
Definition: SystemBase.h:717
virtual bool matrixTagExists(const TagName &tag_name)
Check to see if a particular Tag exists.
Definition: SubProblem.C:119
SubProblem & _subproblem
Definition: SystemBase.h:694

◆ associateVectorToTag()

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

Associate a vector for a given tag.

Reimplemented in DisplacedSystem.

Definition at line 749 of file SystemBase.C.

Referenced by DisplacedSystem::associateVectorToTag(), NonlinearSystemBase::computeNodalBCs(), and NonlinearSystemBase::computeResidualTag().

750 {
751  mooseAssert(_subproblem.vectorTagExists(tag),
752  "You can't associate a tag that does not exist " << tag);
753  if (_tagged_vectors.size() < tag + 1)
754  _tagged_vectors.resize(tag + 1);
755 
756  _tagged_vectors[tag] = &vec;
757 }
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual bool vectorTagExists(TagID tag)
Check to see if a particular Tag exists.
Definition: SubProblem.h:107
std::vector< NumericVector< Number > * > _tagged_vectors
Tagged vectors (pointer)
Definition: SystemBase.h:715

◆ 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 414 of file SystemBase.C.

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

415 {
416  std::set<dof_id_type> & ghosted_elems = _subproblem.ghostedElems();
417 
418  DofMap & dof_map = dofMap();
419 
420  std::vector<dof_id_type> dof_indices;
421 
422  System & sys = system();
423 
424  unsigned int sys_num = sys.number();
425 
426  unsigned int n_vars = sys.n_vars();
427 
428  for (const auto & elem_id : ghosted_elems)
429  {
430  Elem * elem = _mesh.elemPtr(elem_id);
431 
432  if (elem->active())
433  {
434  dof_map.dof_indices(elem, dof_indices);
435 
436  // Only need to ghost it if it's actually not on this processor
437  for (const auto & dof : dof_indices)
438  if (dof < dof_map.first_dof() || dof >= dof_map.end_dof())
439  send_list.push_back(dof);
440 
441  // Now add the DoFs from all of the nodes. This is necessary because of block
442  // restricted variables. A variable might not live _on_ this element but it
443  // might live on nodes connected to this element.
444  for (unsigned int n = 0; n < elem->n_nodes(); n++)
445  {
446  Node * node = elem->node_ptr(n);
447 
448  // Have to get each variable's dofs
449  for (unsigned int v = 0; v < n_vars; v++)
450  {
451  const Variable & var = sys.variable(v);
452  unsigned int var_num = var.number();
453  unsigned int n_comp = var.n_components();
454 
455  // See if this variable has any dofs at this node
456  if (node->n_dofs(sys_num, var_num) > 0)
457  {
458  // Loop over components of the variable
459  for (unsigned int c = 0; c < n_comp; c++)
460  send_list.push_back(node->dof_number(sys_num, var_num, c));
461  }
462  }
463  }
464  }
465  }
466 }
virtual Elem * elemPtr(const dof_id_type i)
Definition: MooseMesh.C:2262
virtual DofMap & dofMap()
Gets the dof map.
Definition: SystemBase.C:900
DofMap & dof_map
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual std::set< dof_id_type > & ghostedElems()
Return the list of elements that should have their DoFs ghosted to this processor.
Definition: SubProblem.h:500
virtual System & system()=0
Get the reference to the libMesh system.
MooseMesh & _mesh
Definition: SystemBase.h:699
PetscInt n

◆ augmentSparsity()

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

Will modify the sparsity pattern to add logical geometric connections.

Implemented in NonlinearSystemBase, DisplacedSystem, and AuxiliarySystem.

Referenced by extraSparsity().

◆ closeTaggedMatrices()

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

Close all matrices associated the tags.

Definition at line 795 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeJacobianInternal().

796 {
797  for (auto tag : tags)
798  if (hasMatrix(tag))
799  getMatrix(tag).close();
800 }
virtual bool hasMatrix(TagID tag)
Check if the tagged matrix exists in the system.
Definition: SystemBase.C:781
virtual SparseMatrix< Number > & getMatrix(TagID tag)
Get a raw SparseMatrix.
Definition: SystemBase.C:787

◆ closeTaggedVectors()

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

Close all vectors for given tags.

Definition at line 560 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeResidualTags().

561 {
562  for (auto & tag : tags)
563  {
564  mooseAssert(_subproblem.vectorTagExists(tag), "Tag: " << tag << " does not exsit");
565  getVector(tag).close();
566  }
567 }
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual bool vectorTagExists(TagID tag)
Check to see if a particular Tag exists.
Definition: SubProblem.h:107
virtual NumericVector< Number > & getVector(const std::string &name)
Get a raw NumericVector.
Definition: SystemBase.C:735

◆ computeVariables()

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

Definition at line 672 of file SystemBase.h.

672 {}

◆ copyOldSolutions()

void SystemBase::copyOldSolutions ( )
virtual

Shifts the solutions backwards in time.

Definition at line 986 of file SystemBase.C.

Referenced by EigenExecutionerBase::inversePowerIteration().

987 {
990  if (solutionUDotOld())
992  if (solutionUDotDotOld())
996 }
virtual NumericVector< Number > * solutionUDot()=0
virtual NumericVector< Number > & solutionOld()=0
virtual NumericVector< Number > * solutionUDotDotOld()=0
virtual NumericVector< Number > * solutionPreviousNewton()=0
virtual NumericVector< Number > & solutionOlder()=0
virtual NumericVector< Number > * solutionUDotOld()=0
virtual NumericVector< Number > * solutionUDotDot()=0
virtual const NumericVector< Number > *& currentSolution()=0
The solution vector that is currently being operated on.

◆ copySolutionsBackwards()

void SystemBase::copySolutionsBackwards ( )
virtual

Copy current solution into old and older.

Definition at line 969 of file SystemBase.C.

970 {
971  system().update();
974  if (solutionUDotOld())
976  if (solutionUDotDotOld())
980 }
virtual NumericVector< Number > * solutionUDot()=0
virtual NumericVector< Number > & solutionOld()=0
virtual NumericVector< Number > * solutionUDotDotOld()=0
virtual NumericVector< Number > * solutionPreviousNewton()=0
virtual System & system()=0
Get the reference to the libMesh system.
virtual NumericVector< Number > & solutionOlder()=0
virtual NumericVector< Number > * solutionUDotOld()=0
virtual NumericVector< Number > * solutionUDotDot()=0
virtual const NumericVector< Number > *& currentSolution()=0
The solution vector that is currently being operated on.

◆ copyVars()

void SystemBase::copyVars ( ExodusII_IO &  io)

Definition at line 914 of file SystemBase.C.

915 {
916  int n_steps = io.get_num_time_steps();
917 
918  bool did_copy = false;
919  for (const auto & vci : _var_to_copy)
920  {
921  int timestep = -1;
922 
923  if (vci._timestep == "LATEST")
924  // Use the last time step in the file from which to retrieve the solution
925  timestep = n_steps;
926  else
927  {
928  timestep = MooseUtils::convert<int>(vci._timestep);
929  if (timestep > n_steps)
930  mooseError("Invalid value passed as \"initial_from_file_timestep\". Expected \"LATEST\" or "
931  "a valid integer between 1 and ",
932  n_steps,
933  " inclusive, received ",
934  vci._timestep);
935  }
936 
937  did_copy = true;
938  if (getVariable(0, vci._dest_name).isNodal())
939  io.copy_nodal_solution(system(), vci._dest_name, vci._source_name, timestep);
940  else
941  io.copy_elemental_solution(system(), vci._dest_name, vci._source_name, timestep);
942  }
943 
944  if (did_copy)
945  solution().close();
946 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208
MooseVariableFEBase & getVariable(THREAD_ID tid, const std::string &var_name)
Gets a reference to a variable of with specified name.
Definition: SystemBase.C:105
virtual bool isNodal() const =0
Is this variable nodal.
std::vector< VarCopyInfo > _var_to_copy
Definition: SystemBase.h:732
int convert< int >(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:656
virtual System & system()=0
Get the reference to the libMesh system.
virtual NumericVector< Number > & solution()=0

◆ currentSolution()

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

◆ deactiveAllMatrixTags()

void SystemBase::deactiveAllMatrixTags ( )
virtual

Make matrices inactive.

Definition at line 854 of file SystemBase.C.

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

855 {
856  auto num_matrix_tags = _subproblem.numMatrixTags();
857 
858  _matrix_tag_active_flags.resize(num_matrix_tags);
859 
860  for (decltype(num_matrix_tags) tag = 0; tag < num_matrix_tags; tag++)
861  _matrix_tag_active_flags[tag] = false;
862 }
std::vector< bool > _matrix_tag_active_flags
Active flags for tagged matrices.
Definition: SystemBase.h:719
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual unsigned int numMatrixTags()
The total number of tags.
Definition: SubProblem.h:152

◆ deactiveMatrixTag()

void SystemBase::deactiveMatrixTag ( TagID  tag)
virtual

deactive a matrix for tag

Definition at line 842 of file SystemBase.C.

843 {
844  mooseAssert(_subproblem.matrixTagExists(tag),
845  "Cannot deactivate Matrix with matrix_tag : " << tag << "that does not exist");
846 
847  if (_matrix_tag_active_flags.size() < tag + 1)
848  _matrix_tag_active_flags.resize(tag + 1);
849 
850  _matrix_tag_active_flags[tag] = false;
851 }
virtual bool matrixTagExists(const TagName &tag_name)
Check to see if a particular Tag exists.
Definition: SubProblem.C:119
std::vector< bool > _matrix_tag_active_flags
Active flags for tagged matrices.
Definition: SystemBase.h:719
SubProblem & _subproblem
Definition: SystemBase.h:694

◆ disassociateAllTaggedMatrices()

void SystemBase::disassociateAllTaggedMatrices ( )
virtual

Clear all tagged matrices.

Reimplemented in DisplacedSystem.

Definition at line 887 of file SystemBase.C.

Referenced by DisplacedSystem::disassociateAllTaggedMatrices().

888 {
889  for (auto & matrix : _tagged_matrices)
890  matrix = nullptr;
891 }
std::vector< SparseMatrix< Number > * > _tagged_matrices
Tagged matrices (pointer)
Definition: SystemBase.h:717

◆ disassociateAllTaggedVectors()

void SystemBase::disassociateAllTaggedVectors ( )
virtual

Disassociate all vectors, and then hasVector() will return false.

Reimplemented in DisplacedSystem.

Definition at line 774 of file SystemBase.C.

Referenced by DisplacedSystem::disassociateAllTaggedVectors().

775 {
776  for (auto & tagged_vector : _tagged_vectors)
777  tagged_vector = nullptr;
778 }
std::vector< NumericVector< Number > * > _tagged_vectors
Tagged vectors (pointer)
Definition: SystemBase.h:715

◆ disassociateMatrixFromTag()

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

disassociate a matirx from a tag

Reimplemented in DisplacedSystem.

Definition at line 815 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeJacobian(), and DisplacedSystem::disassociateMatrixFromTag().

816 {
817  mooseAssert(_subproblem.matrixTagExists(tag),
818  "Cannot disassociate Matrix with matrix_tag : " << tag << "that does not exist");
819 
820  if (_tagged_matrices.size() < tag + 1)
821  _tagged_matrices.resize(tag + 1);
822 
823  if (_tagged_matrices[tag] != &matrix)
824  mooseError("You can not disassociate a matrix from a tag which it was not associated to");
825 
826  _tagged_matrices[tag] = nullptr;
827 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208
std::vector< SparseMatrix< Number > * > _tagged_matrices
Tagged matrices (pointer)
Definition: SystemBase.h:717
virtual bool matrixTagExists(const TagName &tag_name)
Check to see if a particular Tag exists.
Definition: SubProblem.C:119
SubProblem & _subproblem
Definition: SystemBase.h:694

◆ disassociateVectorFromTag()

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

Associate a vector for a given tag.

Reimplemented in DisplacedSystem.

Definition at line 760 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeNodalBCs(), NonlinearSystemBase::computeResidualTag(), and DisplacedSystem::disassociateVectorFromTag().

761 {
762  mooseAssert(_subproblem.vectorTagExists(tag),
763  "You can't associate a tag that does not exist " << tag);
764  if (_tagged_vectors.size() < tag + 1)
765  _tagged_vectors.resize(tag + 1);
766 
767  if (_tagged_vectors[tag] != &vec)
768  mooseError("You can not disassociate a vector from a tag which it was not associated to");
769 
770  _tagged_vectors[tag] = nullptr;
771 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual bool vectorTagExists(TagID tag)
Check to see if a particular Tag exists.
Definition: SubProblem.h:107
std::vector< NumericVector< Number > * > _tagged_vectors
Tagged vectors (pointer)
Definition: SystemBase.h:715

◆ dofMap()

DofMap & SystemBase::dofMap ( )
virtual

◆ duDotDotDu()

virtual Number& SystemBase::duDotDotDu ( )
inlinevirtual

◆ duDotDu()

virtual Number& SystemBase::duDotDu ( )
inlinevirtual

◆ getFieldVariable() [1/2]

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

Gets a reference to a variable of with specified name.

Parameters
tidThread id
var_namevariable name
Returns
reference the variable (class)

Definition at line 136 of file SystemBase.C.

Referenced by Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), Assembly::copyShapes(), DisplacedProblem::getStandardVariable(), and DisplacedProblem::getVectorVariable().

137 {
138  return *_vars[tid].getFieldVariable<T>(var_name);
139 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ getFieldVariable() [2/2]

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

Gets a reference to a variable with specified number.

Parameters
tidThread id
var_numberlibMesh variable number
Returns
reference the variable (class)

Definition at line 143 of file SystemBase.C.

144 {
145  return *_vars[tid].getFieldVariable<T>(var_number);
146 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ getMatrix()

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

◆ getMaxVarNDofsPerElem()

size_t SystemBase::getMaxVarNDofsPerElem ( )
inline

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

Returns
The max

Definition at line 413 of file SystemBase.h.

Referenced by Assembly::computeAffineMapAD(), Assembly::computeFaceMap(), and Assembly::computeSinglePointMapAD().

413 { return _max_var_n_dofs_per_elem; }
size_t _max_var_n_dofs_per_elem
Maximum number of dofs for any one variable on any one element.
Definition: SystemBase.h:735

◆ getMaxVarNDofsPerNode()

size_t SystemBase::getMaxVarNDofsPerNode ( )
inline

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

Returns
The max

Definition at line 420 of file SystemBase.h.

420 { return _max_var_n_dofs_per_node; }
size_t _max_var_n_dofs_per_node
Maximum number of dofs for any one variable on any one node.
Definition: SystemBase.h:738

◆ 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 227 of file SystemBase.C.

228 {
229  Order order = CONSTANT;
230  const std::vector<MooseVariableFEBase *> & vars = _vars[0].fieldVariables();
231  for (const auto & var : vars)
232  {
233  FEType fe_type = var->feType();
234  if (fe_type.default_quadrature_order() > order)
235  order = fe_type.default_quadrature_order();
236  }
237 
238  return order;
239 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ getScalarVariable() [1/2]

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

Gets a reference to a scalar variable with specified number.

Parameters
tidThread id
var_nameA string which is the name of the variable to get.
Returns
reference the variable (class)

Definition at line 149 of file SystemBase.C.

Referenced by Assembly::addJacobianOffDiagScalar(), IntegratedBC::computeJacobianBlockScalar(), VectorIntegratedBC::computeJacobianBlockScalar(), ODEKernel::computeOffDiagJacobian(), VectorKernel::computeOffDiagJacobianScalar(), Kernel::computeOffDiagJacobianScalar(), DisplacedProblem::getScalarVariable(), and Assembly::init().

150 {
151  MooseVariableScalar * var = dynamic_cast<MooseVariableScalar *>(_vars[tid].getVariable(var_name));
152  if (!var)
153  mooseError("Scalar variable '" + var_name + "' does not exist in this system");
154  return *var;
155 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704
Class for scalar variables (they are different).

◆ getScalarVariable() [2/2]

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

Gets a reference to a variable with specified number.

Parameters
tidThread id
var_numberlibMesh variable number
Returns
reference the variable (class)

Definition at line 158 of file SystemBase.C.

159 {
160  MooseVariableScalar * var =
161  dynamic_cast<MooseVariableScalar *>(_vars[tid].getVariable(var_number));
162  if (!var)
163  mooseError("variable #" + Moose::stringify(var_number) + " does not exist in this system");
164  return *var;
165 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208
std::string stringify(const T &t)
conversion to string
Definition: Conversion.h:61
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704
Class for scalar variables (they are different).

◆ getScalarVariables()

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

◆ getSharedTimeIntegrator()

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

Definition at line 691 of file SystemBase.h.

Referenced by DisplacedProblem::DisplacedProblem().

691 { return _time_integrator; }
std::shared_ptr< TimeIntegrator > _time_integrator
Time integrator.
Definition: SystemBase.h:741

◆ getSubdomainsForVar()

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

Definition at line 579 of file SystemBase.h.

580  {
581  return _var_map.at(var_number);
582  }
std::map< unsigned int, std::set< SubdomainID > > _var_map
Map of variables (variable id -> array of subdomains where it lives)
Definition: SystemBase.h:706

◆ getTimeIntegrator()

TimeIntegrator* SystemBase::getTimeIntegrator ( )
inline

Definition at line 689 of file SystemBase.h.

Referenced by DT2::computeDT(), Transient::endStep(), AB2PredictorCorrector::estimateTimeError(), Transient::init(), and MooseVariableFE< Real >::MooseVariableFE().

689 { return _time_integrator.get(); }
std::shared_ptr< TimeIntegrator > _time_integrator
Time integrator.
Definition: SystemBase.h:741

◆ getVariable() [1/2]

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

Gets a reference to a variable of with specified name.

Parameters
tidThread id
var_namevariable name
Returns
reference the variable (class)

Definition at line 105 of file SystemBase.C.

Referenced by Assembly::addJacobianBlock(), Assembly::addJacobianBlockNonlocal(), Assembly::addJacobianNeighbor(), NonlocalIntegratedBC::computeJacobianBlock(), NonlocalIntegratedBC::computeNonlocalOffDiagJacobian(), NonlocalKernel::computeNonlocalOffDiagJacobian(), copyVars(), FieldSplitPreconditioner::FieldSplitPreconditioner(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), EqualValueEmbeddedConstraint::getConnectedDofIndices(), NodeElemConstraint::getConnectedDofIndices(), NodeFaceConstraint::getConnectedDofIndices(), Marker::getMarkerValue(), SubProblem::getVariableHelper(), Assembly::init(), NodalNormalsPreprocessor::initialize(), Assembly::initNonlocalCoupling(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), AddPeriodicBCAction::setPeriodicVars(), SingleMatrixPreconditioner::SingleMatrixPreconditioner(), and UpdateErrorVectorsThread::UpdateErrorVectorsThread().

106 {
107  MooseVariableFEBase * var = dynamic_cast<MooseVariableFEBase *>(_vars[tid].getVariable(var_name));
108  if (!var)
109  {
110  std::stringstream errMsg;
111  errMsg << "Variable '" << var_name << "' does not exist in this system" << std::endl;
112  throw std::runtime_error(errMsg.str().c_str());
113  // mooseError("Variable '" + var_name + "' does not exist in this system");
114  }
115  return *var;
116 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ getVariable() [2/2]

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

Gets a reference to a variable with specified number.

Parameters
tidThread id
var_numberlibMesh variable number
Returns
reference the variable (class)

Definition at line 119 of file SystemBase.C.

120 {
121  MooseVariableFEBase * var =
122  dynamic_cast<MooseVariableFEBase *>(_vars[tid].getVariable(var_number));
123  if (!var)
124  {
125  std::stringstream errMsg;
126  errMsg << "Variable '" << Moose::stringify(var_number) << "' does not exist in this system"
127  << std::endl;
128  throw std::runtime_error(errMsg.str().c_str());
129  // mooseError("variable #" + Moose::stringify(var_number) + " does not exist in this system");
130  }
131  return *var;
132 }
std::string stringify(const T &t)
conversion to string
Definition: Conversion.h:61
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ 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_numberThe number of the variable
Returns
the set of subdomain ids where the variable is active (defined)

Definition at line 168 of file SystemBase.C.

Referenced by PhysicsBasedPreconditioner::addSystem().

169 {
170  mooseAssert(_var_map.find(var_number) != _var_map.end(), "Variable does not exist.");
171  if (_var_map[var_number].empty())
172  return nullptr;
173  else
174  return &_var_map[var_number];
175 }
std::map< unsigned int, std::set< SubdomainID > > _var_map
Map of variables (variable id -> array of subdomains where it lives)
Definition: SystemBase.h:706

◆ getVariableNames()

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

Definition at line 670 of file SystemBase.h.

Referenced by MooseEigenSystem::buildSystemDoFIndices(), NonlinearSystemBase::checkKernelCoverage(), and AddPeriodicBCAction::setPeriodicVars().

670 { return _vars[0].names(); }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ getVariables()

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

◆ getVector() [1/2]

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

Get a raw NumericVector.

Get a raw NumericVector with the given name.

Reimplemented in DisplacedSystem.

Definition at line 735 of file SystemBase.C.

Referenced by Assembly::addCachedResiduals(), Assembly::addResidual(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), AuxiliarySystem::addVector(), addVector(), closeTaggedVectors(), VectorNodalBC::computeResidual(), NodalBC::computeResidual(), NonlinearSystemBase::computeResidualTags(), DisplacedSystem::getVector(), MooseVariableScalar::reinit(), PicardSolve::solve(), PicardSolve::solveStep(), and zeroTaggedVectors().

736 {
737  return system().get_vector(name);
738 }
virtual const std::string & name() const
Definition: SystemBase.C:1022
virtual System & system()=0
Get the reference to the libMesh system.

◆ getVector() [2/2]

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

Get a raw NumericVector.

Reimplemented in DisplacedSystem.

Definition at line 741 of file SystemBase.C.

742 {
743  mooseAssert(hasVector(tag), "Cannot retrieve vector with residual_tag: " << tag);
744 
745  return *_tagged_vectors[tag];
746 }
bool hasVector(const std::string &tag_name) const
Check if the named vector exists in the system.
Definition: SystemBase.C:685
std::vector< NumericVector< Number > * > _tagged_vectors
Tagged vectors (pointer)
Definition: SystemBase.h:715

◆ hasMatrix()

bool SystemBase::hasMatrix ( TagID  tag)
virtual

◆ hasScalarVariable()

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

Definition at line 661 of file SystemBase.C.

Referenced by ComputeFullJacobianThread::computeFaceJacobian(), ComputeFullJacobianThread::computeJacobian(), DisplacedProblem::getScalarVariable(), DisplacedProblem::hasScalarVariable(), and AddPeriodicBCAction::setPeriodicVars().

662 {
663  if (system().has_variable(var_name))
664  return system().variable_type(var_name).family == SCALAR;
665  else
666  return false;
667 }
virtual System & system()=0
Get the reference to the libMesh system.

◆ hasVariable()

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

Query a system for a variable.

Parameters
var_namename of the variable
Returns
true if the variable exists

Definition at line 652 of file SystemBase.C.

Referenced by ADKernelTempl< T, compute_stage >::ADKernelTempl(), DGKernel::DGKernel(), FEProblemBase::duplicateVariableCheck(), DisplacedProblem::getStandardVariable(), DisplacedProblem::getSystem(), SubProblem::getVariableHelper(), DisplacedProblem::getVectorVariable(), DisplacedProblem::hasVariable(), InterfaceKernel::InterfaceKernel(), and Kernel::Kernel().

653 {
654  if (system().has_variable(var_name))
655  return system().variable_type(var_name).family != SCALAR;
656  else
657  return false;
658 }
virtual System & system()=0
Get the reference to the libMesh system.

◆ hasVector() [1/2]

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

◆ hasVector() [2/2]

bool SystemBase::hasVector ( TagID  tag_id)
virtual

Check if the tagged vector exists in the system.

Reimplemented in DisplacedSystem.

Definition at line 726 of file SystemBase.C.

727 {
728  return tag < _tagged_vectors.size() && _tagged_vectors[tag];
729 }
std::vector< NumericVector< Number > * > _tagged_vectors
Tagged vectors (pointer)
Definition: SystemBase.h:715

◆ init()

virtual void SystemBase::init ( )
inlinevirtual

Initialize the system.

Reimplemented in NonlinearSystemBase, AuxiliarySystem, and DisplacedSystem.

Definition at line 121 of file SystemBase.h.

121 {};

◆ initializeObjects()

virtual void SystemBase::initializeObjects ( )
inlinevirtual

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

Definition at line 126 of file SystemBase.h.

126 {};

◆ isScalarVariable()

bool SystemBase::isScalarVariable ( unsigned int  var_name) const
virtual

Definition at line 670 of file SystemBase.C.

Referenced by ODEKernel::computeOffDiagJacobian(), Assembly::init(), and Assembly::initNonlocalCoupling().

671 {
672  return (system().variable(var_num).type().family == SCALAR);
673 }
virtual System & system()=0
Get the reference to the libMesh system.
MatType type

◆ matrixTagActive()

bool SystemBase::matrixTagActive ( TagID  tag)
virtual

If or not a matrix tag is active.

Definition at line 879 of file SystemBase.C.

880 {
881  mooseAssert(_subproblem.matrixTagExists(tag), "Matrix tag " << tag << " does not exist");
882 
883  return tag < _matrix_tag_active_flags.size() && _matrix_tag_active_flags[tag];
884 }
virtual bool matrixTagExists(const TagName &tag_name)
Check to see if a particular Tag exists.
Definition: SubProblem.C:119
std::vector< bool > _matrix_tag_active_flags
Active flags for tagged matrices.
Definition: SystemBase.h:719
SubProblem & _subproblem
Definition: SystemBase.h:694

◆ mesh()

virtual MooseMesh& SystemBase::mesh ( )
inlinevirtual

◆ name()

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

◆ nonTimeVectorTag()

TagID SystemBase::nonTimeVectorTag ( )
virtual

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 712 of file SystemBase.C.

Referenced by DisplacedSystem::nonTimeVectorTag().

713 {
714  mooseError("Not implemented yet");
715  return 0;
716 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208

◆ number()

unsigned int SystemBase::number ( ) const
virtual

◆ nVariables()

unsigned int SystemBase::nVariables ( ) const
virtual

Get the number of variables in this system.

Returns
the number of variables

Definition at line 676 of file SystemBase.C.

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

677 {
678  return _vars[0].names().size();
679 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ prepare()

void SystemBase::prepare ( THREAD_ID  tid)
virtual

Prepare the system for use.

Parameters
tidID of the thread

Definition at line 242 of file SystemBase.C.

Referenced by DisplacedProblem::prepare(), DisplacedProblem::reinitDirac(), and DisplacedProblem::reinitElemPhys().

243 {
245  {
246  const std::set<MooseVariableFEBase *> & active_elemental_moose_variables =
248  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
249  for (const auto & var : vars)
250  var->clearDofIndices();
251 
252  for (const auto & var : active_elemental_moose_variables)
253  if (&(var->sys()) == this)
254  var->prepare();
255  }
256  else
257  {
258  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
259  for (const auto & var : vars)
260  var->prepare();
261  }
262 }
virtual bool hasActiveElementalMooseVariables(THREAD_ID tid) const
Whether or not a list of active elemental moose variables has been set.
Definition: SubProblem.C:243
virtual const std::set< MooseVariableFEBase * > & getActiveElementalMooseVariables(THREAD_ID tid) const
Get the MOOSE variables to be reinited on each element.
Definition: SubProblem.C:237
SubProblem & _subproblem
Definition: SystemBase.h:694
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ 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
tidID of the thread
resize_dataPass True if this system needs to resize residual and jacobian datastructures based on preparing this face

Definition at line 265 of file SystemBase.C.

Referenced by DisplacedProblem::prepareFace().

266 {
267  // We only need to do something if the element prepare was restricted
269  {
270  const std::set<MooseVariableFEBase *> & active_elemental_moose_variables =
272 
273  std::vector<MooseVariableFEBase *> newly_prepared_vars;
274 
275  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
276  for (const auto & var : vars)
277  {
278  // If it wasn't in the active list, we need to prepare it
279  if (&(var->sys()) == this && !active_elemental_moose_variables.count(var))
280  {
281  var->prepare();
282  newly_prepared_vars.push_back(var);
283  }
284  }
285 
286  // Make sure to resize the residual and jacobian datastructures for all the new variables
287  if (resize_data)
288  for (const auto var_ptr : newly_prepared_vars)
289  {
290  _subproblem.assembly(tid).prepareVariable(var_ptr);
293  }
294  }
295 }
virtual bool hasActiveElementalMooseVariables(THREAD_ID tid) const
Whether or not a list of active elemental moose variables has been set.
Definition: SubProblem.C:243
virtual Assembly & assembly(THREAD_ID tid)=0
virtual const std::set< MooseVariableFEBase * > & getActiveElementalMooseVariables(THREAD_ID tid) const
Get the MOOSE variables to be reinited on each element.
Definition: SubProblem.C:237
void prepareVariableNonlocal(MooseVariableFEBase *var)
Definition: Assembly.C:2004
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual bool checkNonlocalCouplingRequirement()
Definition: SubProblem.h:69
void prepareVariable(MooseVariableFEBase *var)
Used for preparing the dense residual and jacobian blocks for one particular variable.
Definition: Assembly.C:1975
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ prepareNeighbor()

void SystemBase::prepareNeighbor ( THREAD_ID  tid)
virtual

Prepare the system for use.

Parameters
tidID of the thread

Definition at line 298 of file SystemBase.C.

Referenced by DisplacedProblem::reinitNeighbor(), and DisplacedProblem::reinitNeighborPhys().

299 {
300  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
301  for (const auto & var : vars)
302  var->prepareNeighbor();
303 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ reinitElem()

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

Reinit an element assembly info.

Parameters
elemWhich element we are reinitializing for
tidID of the thread

Reimplemented in AuxiliarySystem.

Definition at line 306 of file SystemBase.C.

Referenced by DisplacedProblem::reinitElem().

307 {
308 
310  {
311  const std::set<MooseVariableFEBase *> & active_elemental_moose_variables =
313  for (const auto & var : active_elemental_moose_variables)
314  if (&(var->sys()) == this)
315  var->computeElemValues();
316  }
317  else
318  {
319  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
320  for (const auto & var : vars)
321  var->computeElemValues();
322  }
323 }
virtual bool hasActiveElementalMooseVariables(THREAD_ID tid) const
Whether or not a list of active elemental moose variables has been set.
Definition: SubProblem.C:243
virtual const std::set< MooseVariableFEBase * > & getActiveElementalMooseVariables(THREAD_ID tid) const
Get the MOOSE variables to be reinited on each element.
Definition: SubProblem.C:237
SubProblem & _subproblem
Definition: SystemBase.h:694
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ reinitElemFace()

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

Reinit assembly info for a side of an element.

Parameters
elemThe element
sideSide of of the element
bnd_idBoundary id on that side
tidThread ID

Reimplemented in AuxiliarySystem.

Definition at line 326 of file SystemBase.C.

Referenced by DisplacedProblem::reinitElemFace(), and DisplacedProblem::reinitNeighbor().

330 {
331  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
332  for (const auto & var : vars)
333  var->computeElemValuesFace();
334 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ 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 348 of file SystemBase.C.

Referenced by DisplacedProblem::reinitNeighborPhys().

349 {
350  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
351  for (const auto & var : vars)
352  var->computeNeighborValues();
353 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ reinitNeighborFace()

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

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

Definition at line 337 of file SystemBase.C.

Referenced by DisplacedProblem::reinitNeighbor(), and DisplacedProblem::reinitNeighborPhys().

341 {
342  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
343  for (const auto & var : vars)
344  var->computeNeighborValuesFace();
345 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ reinitNode()

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

Reinit nodal assembly info.

Parameters
nodeNode to reinit for
tidThread ID

Definition at line 356 of file SystemBase.C.

Referenced by DisplacedProblem::reinitNode().

357 {
358  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
359  for (const auto & var : vars)
360  {
361  if (var->isNodal())
362  {
363  var->reinitNode();
364  var->computeNodalValues();
365  }
366  }
367 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ reinitNodeFace()

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

Reinit nodal assembly info on a face.

Parameters
nodeNode to reinit
bnd_idBoundary ID
tidThread ID

Definition at line 370 of file SystemBase.C.

Referenced by DisplacedProblem::reinitNodeFace().

371 {
372  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
373  for (const auto & var : vars)
374  {
375  if (var->isNodal())
376  {
377  var->reinitNode();
378  var->computeNodalValues();
379  }
380  }
381 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ reinitNodes()

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

Reinit variables at a set of nodes.

Parameters
nodesList of node ids to reinit
tidThread ID

Definition at line 384 of file SystemBase.C.

Referenced by DisplacedProblem::reinitNodes().

385 {
386  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
387  for (const auto & var : vars)
388  {
389  var->reinitNodes(nodes);
390  var->computeNodalValues();
391  }
392 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ reinitNodesNeighbor()

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

Reinit variables at a set of neighbor nodes.

Parameters
nodesList of node ids to reinit
tidThread ID

Definition at line 395 of file SystemBase.C.

Referenced by DisplacedProblem::reinitNodesNeighbor().

396 {
397  const std::vector<MooseVariableFEBase *> & vars = _vars[tid].fieldVariables();
398  for (const auto & var : vars)
399  {
400  var->reinitNodesNeighbor(nodes);
401  var->computeNodalNeighborValues();
402  }
403 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ reinitScalars()

void SystemBase::reinitScalars ( THREAD_ID  tid)
virtual

Reinit scalar varaibles.

Parameters
tidThread ID

Definition at line 406 of file SystemBase.C.

Referenced by DisplacedProblem::reinitScalars().

407 {
408  const std::vector<MooseVariableScalar *> & vars = _vars[tid].scalars();
409  for (const auto & var : vars)
410  var->reinit();
411 }
std::vector< VariableWarehouse > _vars
Variable warehouses (one for each thread)
Definition: SystemBase.h:704

◆ removeMatrix()

virtual void SystemBase::removeMatrix ( TagID  )
inlinevirtual

Removes a jacobian sized vector.

Parameters
tag_nameThe name of the tag

Definition at line 652 of file SystemBase.h.

653  {
654  mooseError("Removing a matrix is not supported for this type of system!");
655  }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208

◆ removeVector() [1/2]

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

Remove a vector from the system with the given name.

Definition at line 1016 of file SystemBase.C.

Referenced by restoreOldSolutions().

1017 {
1018  system().remove_vector(name);
1019 }
virtual const std::string & name() const
Definition: SystemBase.C:1022
virtual System & system()=0
Get the reference to the libMesh system.

◆ removeVector() [2/2]

void SystemBase::removeVector ( TagID  tag_id)
virtual

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

Parameters
tag_idTag ID

Definition at line 580 of file SystemBase.C.

581 {
582  if (!_subproblem.vectorTagExists(tag_id))
583  mooseError("Cannot remove an unexisting tag or its associated vector, ",
584  tag_id,
585  ", that tag does not exist in System ",
586  name());
587 
588  if (hasVector(tag_id))
589  {
590  auto vector_name = _subproblem.vectorTagName(tag_id);
591  system().remove_vector(vector_name);
592  _tagged_vectors[tag_id] = nullptr;
593  }
594 }
virtual TagName vectorTagName(TagID tag)
Retrieve the name associated with a TagID.
Definition: SubProblem.C:96
bool hasVector(const std::string &tag_name) const
Check if the named vector exists in the system.
Definition: SystemBase.C:685
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208
virtual const std::string & name() const
Definition: SystemBase.C:1022
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual bool vectorTagExists(TagID tag)
Check to see if a particular Tag exists.
Definition: SubProblem.h:107
virtual System & system()=0
Get the reference to the libMesh system.
std::vector< NumericVector< Number > * > _tagged_vectors
Tagged vectors (pointer)
Definition: SystemBase.h:715

◆ residualCopy()

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

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 291 of file SystemBase.h.

Referenced by DisplacedSystem::residualCopy().

292  {
293  mooseError("This system does not support getting a copy of the residual");
294  }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208

◆ residualGhosted()

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

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 295 of file SystemBase.h.

Referenced by DisplacedSystem::residualGhosted().

296  {
297  mooseError("This system does not support getting a ghosted copy of the residual");
298  }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208

◆ residualVectorTag()

TagID SystemBase::residualVectorTag ( )
virtual

Reimplemented in NonlinearSystemBase.

Definition at line 719 of file SystemBase.C.

720 {
721  mooseError("Not implemented yet");
722  return 0;
723 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208

◆ restoreOldSolutions()

void SystemBase::restoreOldSolutions ( )
virtual

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

Definition at line 497 of file SystemBase.C.

Referenced by DisplacedProblem::restoreOldSolutions().

498 {
499  if (_saved_old)
500  {
501  solutionOld() = *_saved_old;
502  removeVector("save_solution_old");
503  _saved_old = nullptr;
504  }
505  if (_saved_older)
506  {
508  removeVector("save_solution_older");
509  _saved_older = nullptr;
510  }
512  {
514  removeVector("save_solution_dot_old");
515  _saved_dot_old = NULL;
516  }
518  {
520  removeVector("save_solution_dotdot_old");
521  _saved_dotdot_old = NULL;
522  }
523 }
virtual NumericVector< Number > & solutionOld()=0
virtual NumericVector< Number > * solutionUDotDotOld()=0
NumericVector< Real > * _saved_older
Definition: SystemBase.h:723
NumericVector< Real > * _saved_dot_old
Definition: SystemBase.h:726
virtual void removeVector(const std::string &name)
Remove a vector from the system with the given name.
Definition: SystemBase.C:1016
NumericVector< Real > * _saved_old
Definition: SystemBase.h:722
virtual NumericVector< Number > & solutionOlder()=0
NumericVector< Real > * _saved_dotdot_old
Definition: SystemBase.h:727
virtual NumericVector< Number > * solutionUDotOld()=0

◆ restoreSolutions()

void SystemBase::restoreSolutions ( )
virtual

Restore current solutions (call after your solve failed)

Reimplemented in NonlinearSystemBase.

Definition at line 1002 of file SystemBase.C.

Referenced by NonlinearSystemBase::restoreSolutions().

1003 {
1004  *(const_cast<NumericVector<Number> *&>(currentSolution())) = solutionOld();
1005  solution() = solutionOld();
1006  if (solutionUDotOld())
1007  *solutionUDot() = *solutionUDotOld();
1008  if (solutionUDotDotOld())
1010  if (solutionPreviousNewton())
1012  system().update();
1013 }
virtual NumericVector< Number > * solutionUDot()=0
virtual NumericVector< Number > & solutionOld()=0
virtual NumericVector< Number > * solutionUDotDotOld()=0
virtual NumericVector< Number > * solutionPreviousNewton()=0
virtual System & system()=0
Get the reference to the libMesh system.
virtual NumericVector< Number > & solution()=0
virtual NumericVector< Number > * solutionUDotOld()=0
virtual NumericVector< Number > * solutionUDotDot()=0
virtual const NumericVector< Number > *& currentSolution()=0
The solution vector that is currently being operated on.

◆ saveOldSolutions()

void SystemBase::saveOldSolutions ( )
virtual

Save the old and older solutions.

Definition at line 472 of file SystemBase.C.

Referenced by DisplacedProblem::saveOldSolutions().

473 {
474  if (!_saved_old)
475  _saved_old = &addVector("save_solution_old", false, PARALLEL);
476  if (!_saved_older)
477  _saved_older = &addVector("save_solution_older", false, PARALLEL);
479  _saved_dot_old = &addVector("save_solution_dot_old", false, PARALLEL);
481  _saved_dotdot_old = &addVector("save_solution_dotdot_old", false, PARALLEL);
482 
483  *_saved_old = solutionOld();
485 
486  if (solutionUDotOld())
488 
489  if (solutionUDotDotOld())
491 }
virtual NumericVector< Number > & addVector(const std::string &vector_name, const bool project, const ParallelType type)
Adds a solution length vector to the system.
Definition: SystemBase.C:526
virtual NumericVector< Number > & solutionOld()=0
virtual NumericVector< Number > * solutionUDotDotOld()=0
NumericVector< Real > * _saved_older
Definition: SystemBase.h:723
NumericVector< Real > * _saved_dot_old
Definition: SystemBase.h:726
NumericVector< Real > * _saved_old
Definition: SystemBase.h:722
virtual NumericVector< Number > & solutionOlder()=0
NumericVector< Real > * _saved_dotdot_old
Definition: SystemBase.h:727
virtual NumericVector< Number > * solutionUDotOld()=0

◆ serializedSolution()

virtual NumericVector<Number>& SystemBase::serializedSolution ( )
pure virtual

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

Implemented in NonlinearSystemBase, AuxiliarySystem, and DisplacedSystem.

Referenced by DisplacedSystem::serializedSolution().

◆ solution()

virtual NumericVector<Number>& SystemBase::solution ( )
pure virtual

◆ solutionOld()

virtual NumericVector<Number>& SystemBase::solutionOld ( )
pure virtual

◆ solutionOlder()

virtual NumericVector<Number>& SystemBase::solutionOlder ( )
pure virtual

◆ solutionPreviousNewton()

virtual NumericVector<Number>* SystemBase::solutionPreviousNewton ( )
pure virtual

◆ solutionUDot()

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

◆ solutionUDotDot()

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

◆ solutionUDotDotOld()

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

◆ solutionUDotOld()

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

◆ solve()

void SystemBase::solve ( )
virtual

Solve the system (using libMesh magic)

Reimplemented in NonlinearSystemBase, NonlinearEigenSystem, DumpObjectsNonlinearSystem, and NonlinearSystem.

Definition at line 960 of file SystemBase.C.

961 {
962  system().solve();
963 }
virtual System & system()=0
Get the reference to the libMesh system.

◆ subproblem()

virtual SubProblem& SystemBase::subproblem ( )
inlinevirtual

◆ system() [1/2]

virtual System& SystemBase::system ( )
pure virtual

◆ system() [2/2]

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

◆ systemMatrixTag()

TagID SystemBase::systemMatrixTag ( )
virtual

Return the Matrix Tag ID for System.

Reimplemented in NonlinearSystemBase.

Definition at line 705 of file SystemBase.C.

706 {
707  mooseError("Not implemented yet");
708  return 0;
709 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208

◆ timeMatrixTag()

TagID SystemBase::timeMatrixTag ( )
virtual

Return the Matrix Tag ID for Time.

Definition at line 698 of file SystemBase.C.

699 {
700  mooseError("Not implemented yet");
701  return 0;
702 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208

◆ timeVectorTag()

TagID SystemBase::timeVectorTag ( )
virtual

Ideally, we should not need this API.

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

Reimplemented in NonlinearSystemBase, and DisplacedSystem.

Definition at line 691 of file SystemBase.C.

Referenced by DisplacedSystem::timeVectorTag().

692 {
693  mooseError("Not implemented yet");
694  return 0;
695 }
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:208

◆ update()

void SystemBase::update ( )
virtual

◆ zeroTaggedVectors()

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

Zero all vectors for given tags.

Definition at line 570 of file SystemBase.C.

Referenced by NonlinearSystemBase::computeResidualTags().

571 {
572  for (auto & tag : tags)
573  {
574  mooseAssert(_subproblem.vectorTagExists(tag), "Tag: " << tag << " does not exsit");
575  getVector(tag).zero();
576  }
577 }
SubProblem & _subproblem
Definition: SystemBase.h:694
virtual bool vectorTagExists(TagID tag)
Check to see if a particular Tag exists.
Definition: SubProblem.h:107
virtual NumericVector< Number > & getVector(const std::string &name)
Get a raw NumericVector.
Definition: SystemBase.C:735

◆ 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 190 of file SystemBase.C.

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

191 {
192  if (vars_to_be_zeroed.size() > 0)
193  {
194  NumericVector<Number> & solution = this->solution();
195 
196  AllLocalDofIndicesThread aldit(system(), vars_to_be_zeroed);
197  ConstElemRange & elem_range = *_mesh.getActiveLocalElementRange();
198  Threads::parallel_reduce(elem_range, aldit);
199 
200  const std::set<dof_id_type> & dof_indices_to_zero = aldit._all_dof_indices;
201 
202  solution.close();
203 
204  for (const auto & dof : dof_indices_to_zero)
205  solution.set(dof, 0);
206 
207  solution.close();
208 
209  // Call update to update the current_local_solution for this system
210  system().update();
211  }
212 }
ConstElemRange * getActiveLocalElementRange()
Return pointers to range objects for various types of ranges (local nodes, boundary elems...
Definition: MooseMesh.C:738
Grab all the local dof indices for the variables passed in, in the system passed in.
virtual System & system()=0
Get the reference to the libMesh system.
MooseMesh & _mesh
Definition: SystemBase.h:699
virtual NumericVector< Number > & solution()=0

◆ 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 221 of file SystemBase.C.

222 {
224 }
std::vector< std::string > _vars_to_be_zeroed_on_jacobian
Definition: SystemBase.h:709
virtual void zeroVariables(std::vector< std::string > &vars_to_be_zeroed)
Zero out the solution for the list of variables passed in.
Definition: SystemBase.C:190

◆ 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 215 of file SystemBase.C.

216 {
218 }
std::vector< std::string > _vars_to_be_zeroed_on_residual
Definition: SystemBase.h:708
virtual void zeroVariables(std::vector< std::string > &vars_to_be_zeroed)
Zero out the solution for the list of variables passed in.
Definition: SystemBase.C:190

Member Data Documentation

◆ _app

MooseApp& SystemBase::_app
protected

◆ _du_dot_du

Real SystemBase::_du_dot_du
protected

Definition at line 711 of file SystemBase.h.

Referenced by duDotDu().

◆ _du_dotdot_du

Real SystemBase::_du_dotdot_du
protected

Definition at line 712 of file SystemBase.h.

Referenced by duDotDotDu().

◆ _factory

Factory& SystemBase::_factory
protected

◆ _matrix_tag_active_flags

std::vector<bool> SystemBase::_matrix_tag_active_flags
protected

Active flags for tagged matrices.

Definition at line 719 of file SystemBase.h.

Referenced by activeAllMatrixTags(), activeMatrixTag(), deactiveAllMatrixTags(), deactiveMatrixTag(), 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 735 of file SystemBase.h.

Referenced by assignMaxVarNDofsPerElem(), getMaxVarNDofsPerElem(), and NonlinearSystemBase::init().

◆ _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 738 of file SystemBase.h.

Referenced by assignMaxVarNDofsPerNode(), getMaxVarNDofsPerNode(), and NonlinearSystemBase::init().

◆ _mesh

MooseMesh& SystemBase::_mesh
protected

◆ _name

std::string SystemBase::_name
protected

The name of this system.

Definition at line 701 of file SystemBase.h.

◆ _saved_dot_old

NumericVector<Real>* SystemBase::_saved_dot_old
protected

Definition at line 726 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

◆ _saved_dotdot_old

NumericVector<Real>* SystemBase::_saved_dotdot_old
protected

Definition at line 727 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

◆ _saved_old

NumericVector<Real>* SystemBase::_saved_old
protected

Definition at line 722 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

◆ _saved_older

NumericVector<Real>* SystemBase::_saved_older
protected

Definition at line 723 of file SystemBase.h.

Referenced by restoreOldSolutions(), and saveOldSolutions().

◆ _subproblem

SubProblem& SystemBase::_subproblem
protected

◆ _tagged_matrices

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

◆ _tagged_vectors

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

◆ _time_integrator

std::shared_ptr<TimeIntegrator> SystemBase::_time_integrator
protected

◆ _var_kind

Moose::VarKindType SystemBase::_var_kind
protected

default kind of variables in this system

Definition at line 730 of file SystemBase.h.

Referenced by addScalarVariable(), and addVariable().

◆ _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 706 of file SystemBase.h.

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

◆ _var_to_copy

std::vector<VarCopyInfo> SystemBase::_var_to_copy
protected

Definition at line 732 of file SystemBase.h.

Referenced by addVariableToCopy(), and copyVars().

◆ _vars

std::vector<VariableWarehouse> SystemBase::_vars
protected

◆ _vars_to_be_zeroed_on_jacobian

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

Definition at line 709 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 708 of file SystemBase.h.

Referenced by addVariableToZeroOnResidual(), and zeroVariablesForResidual().


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