#include <DisplacedSystem.h>
Public Member Functions | |
DisplacedSystem (DisplacedProblem &problem, SystemBase &undisplaced_system, const std::string &name, Moose::VarKindType var_kind) | |
virtual | ~DisplacedSystem () |
virtual void | init () override |
Initialize the system. More... | |
virtual NumericVector< Number > & | getVector (TagID tag_id) override |
Get a raw NumericVector. More... | |
virtual TagID | timeVectorTag () override |
Ideally, we should not need this API. More... | |
virtual TagID | nonTimeVectorTag () override |
virtual void | associateVectorToTag (NumericVector< Number > &vec, TagID tag) override |
Associate a vector for a given tag. More... | |
virtual void | disassociateVectorFromTag (NumericVector< Number > &vec, TagID tag) override |
Associate a vector for a given tag. More... | |
virtual void | disassociateAllTaggedVectors () override |
Disassociate all vectors, and then hasVector() will return false. More... | |
virtual void | associateMatrixToTag (SparseMatrix< Number > &matrix, TagID tag) override |
associate a matirx to a tag More... | |
virtual void | disassociateMatrixFromTag (SparseMatrix< Number > &matrix, TagID tag) override |
disassociate a matirx from a tag More... | |
virtual void | disassociateAllTaggedMatrices () override |
Clear all tagged matrices. More... | |
virtual NumericVector< Number > & | getVector (const std::string &name) override |
Get a raw NumericVector. More... | |
virtual NumericVector< Number > & | serializedSolution () override |
Returns a reference to a serialized version of the solution vector for this subproblem. More... | |
virtual const NumericVector< Number > *& | currentSolution () override |
The solution vector that is currently being operated on. More... | |
virtual NumericVector< Number > & | solution () override |
virtual NumericVector< Number > * | solutionUDot () override |
virtual NumericVector< Number > * | solutionUDotDot () override |
virtual Number & | duDotDu () override |
virtual Number & | duDotDotDu () override |
virtual NumericVector< Number > & | residualCopy () override |
Return the residual copy from the NonlinearSystem. More... | |
virtual NumericVector< Number > & | residualGhosted () override |
virtual void | augmentSendList (std::vector< dof_id_type > &send_list) override |
Will modify the send_list to add all of the extra ghosted dofs for this system. More... | |
virtual void | augmentSparsity (SparsityPattern::Graph &, std::vector< dof_id_type > &, std::vector< dof_id_type > &) override |
This is an empty function since the displaced system doesn't have a matrix! All sparsity pattern modification will be taken care of by the undisplaced system directly. More... | |
virtual void | addVariableToZeroOnResidual (std::string var_name) override |
Adds this variable to the list of variables to be zeroed during each residual evaluation. More... | |
virtual void | addVariableToZeroOnJacobian (std::string var_name) override |
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) override |
Zero out the solution for the list of variables passed in. More... | |
virtual bool | hasVector (TagID tag_id) override |
Check if the tagged vector exists in the system. More... | |
virtual bool | hasMatrix (TagID tag_id) override |
Check if the tagged matrix exists in the system. More... | |
virtual SparseMatrix< Number > & | getMatrix (TagID tag) override |
Get a raw SparseMatrix. More... | |
virtual NumericVector< Number > & | solutionOld () override |
virtual NumericVector< Number > & | solutionOlder () override |
virtual NumericVector< Number > * | solutionUDotOld () override |
virtual NumericVector< Number > * | solutionUDotDotOld () override |
virtual NumericVector< Number > * | solutionPreviousNewton () override |
virtual TransientExplicitSystem & | sys () |
virtual System & | system () override |
Get the reference to the libMesh system. More... | |
virtual const System & | system () const override |
void | addTimeIntegrator (std::shared_ptr< TimeIntegrator > ti) override |
virtual void | addTimeIntegrator (const std::string &, const std::string &, InputParameters) |
virtual void | addTimeIntegrator (std::shared_ptr< TimeIntegrator >) |
virtual unsigned int | number () const |
Gets the number of this system. More... | |
virtual MooseMesh & | mesh () |
virtual SubProblem & | subproblem () |
virtual DofMap & | dofMap () |
Gets the dof map. 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 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 TagID | timeMatrixTag () |
Return the Matrix Tag ID for Time. More... | |
virtual TagID | systemMatrixTag () |
Return the Matrix Tag ID for System. More... | |
virtual TagID | residualVectorTag () |
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 | 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 |
MooseVariableFEBase & | getVariable (THREAD_ID tid, const std::string &var_name) |
Gets a reference to a variable of with specified name. More... | |
MooseVariableFEBase & | getVariable (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 MooseVariableScalar & | getScalarVariable (THREAD_ID tid, const std::string &var_name) |
Gets a reference to a scalar variable with specified number. More... | |
virtual MooseVariableScalar & | getScalarVariable (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 | 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 ×tep) |
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 void | removeVector (TagID tag_id) |
Remove a solution length vector from the system with the specified TagID. 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 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) |
TimeIntegrator * | getTimeIntegrator () |
std::shared_ptr< TimeIntegrator > | getSharedTimeIntegrator () |
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 | |
SystemBase & | _undisplaced_system |
TransientExplicitSystem & | _sys |
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... | |
Definition at line 25 of file DisplacedSystem.h.
DisplacedSystem::DisplacedSystem | ( | DisplacedProblem & | problem, |
SystemBase & | undisplaced_system, | ||
const std::string & | name, | ||
Moose::VarKindType | var_kind | ||
) |
Definition at line 16 of file DisplacedSystem.C.
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virtual |
Definition at line 26 of file DisplacedSystem.C.
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virtualinherited |
Make all exsiting matrices ative.
Definition at line 865 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeJacobianInternal(), and NonlinearSystemBase::computeResidualTags().
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virtualinherited |
Active a matrix for tag.
Definition at line 830 of file SystemBase.C.
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virtualinherited |
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.
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inlinevirtualinherited |
Adds a jacobian sized vector.
tag_name | The name of the tag |
Reimplemented in NonlinearSystem.
Definition at line 642 of file SystemBase.h.
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virtualinherited |
Adds a scalar variable.
var_name | The name of the variable |
order | The order of the variable |
scale_factor | The scaling factor to be used with this scalar variable |
Definition at line 628 of file SystemBase.C.
Referenced by DisplacedProblem::addAuxScalarVariable(), and DisplacedProblem::addScalarVariable().
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inline |
Definition at line 681 of file SystemBase.h.
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inline |
Definition at line 687 of file SystemBase.h.
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overridevirtual |
Reimplemented from SystemBase.
Definition at line 43 of file DisplacedSystem.C.
Referenced by DisplacedProblem::DisplacedProblem().
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inlinevirtualinherited |
Reimplemented in NonlinearSystemBase, and AuxiliarySystem.
Definition at line 681 of file SystemBase.h.
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virtualinherited |
Adds a variable to the system.
var_name | name of the variable |
type | FE type of the variable |
scale_factor | the scaling factor for the variable |
active_subdomains | a 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().
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virtualinherited |
Add info about variable that will be copied.
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 906 of file SystemBase.C.
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inlineoverridevirtual |
Adds this variable to the list of variables to be zeroed during each jacobian evaluation.
var_name | The name of the variable to be zeroed. |
Reimplemented from SystemBase.
Definition at line 143 of file DisplacedSystem.h.
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inlineoverridevirtual |
Adds this variable to the list of variables to be zeroed during each residual evaluation.
var_name | The name of the variable to be zeroed. |
Reimplemented from SystemBase.
Definition at line 134 of file DisplacedSystem.h.
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virtualinherited |
Adds a solution length vector to the system.
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. |
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 SystemBase::saveOldSolutions().
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inherited |
Adds a solution length vector to the system with the specified TagID.
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 536 of file SystemBase.C.
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inlineinherited |
assign the maximum element dofs
Definition at line 425 of file SystemBase.h.
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inlineinherited |
assign the maximum node dofs
Definition at line 430 of file SystemBase.h.
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inlineoverridevirtual |
associate a matirx to a tag
Reimplemented from SystemBase.
Definition at line 60 of file DisplacedSystem.h.
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inlineoverridevirtual |
Associate a vector for a given tag.
Reimplemented from SystemBase.
Definition at line 45 of file DisplacedSystem.h.
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inlineoverridevirtual |
Will modify the send_list to add all of the extra ghosted dofs for this system.
Reimplemented from SystemBase.
Definition at line 115 of file DisplacedSystem.h.
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inlineoverridevirtual |
This is an empty function since the displaced system doesn't have a matrix! All sparsity pattern modification will be taken care of by the undisplaced system directly.
Implements SystemBase.
Definition at line 124 of file DisplacedSystem.h.
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inherited |
Close all matrices associated the tags.
Definition at line 795 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeJacobianInternal().
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virtualinherited |
Close all vectors for given tags.
Definition at line 560 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeResidualTags().
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inlinevirtualinherited |
Definition at line 672 of file SystemBase.h.
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virtualinherited |
Shifts the solutions backwards in time.
Definition at line 986 of file SystemBase.C.
Referenced by EigenExecutionerBase::inversePowerIteration().
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virtualinherited |
Copy current solution into old and older.
Definition at line 969 of file SystemBase.C.
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inherited |
Definition at line 914 of file SystemBase.C.
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inlineoverridevirtual |
The solution vector that is currently being operated on.
This is typically a ghosted vector that comes in from the Nonlinear solver.
Implements SystemBase.
Definition at line 82 of file DisplacedSystem.h.
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virtualinherited |
Make matrices inactive.
Definition at line 854 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeResidualTags(), and NonlinearSystemBase::setInitialSolution().
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virtualinherited |
deactive a matrix for tag
Definition at line 842 of file SystemBase.C.
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inlineoverridevirtual |
Clear all tagged matrices.
Reimplemented from SystemBase.
Definition at line 70 of file DisplacedSystem.h.
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inlineoverridevirtual |
Disassociate all vectors, and then hasVector() will return false.
Reimplemented from SystemBase.
Definition at line 55 of file DisplacedSystem.h.
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inlineoverridevirtual |
disassociate a matirx from a tag
Reimplemented from SystemBase.
Definition at line 65 of file DisplacedSystem.h.
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inlineoverridevirtual |
Associate a vector for a given tag.
Reimplemented from SystemBase.
Definition at line 50 of file DisplacedSystem.h.
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virtualinherited |
Gets the dof map.
Definition at line 900 of file SystemBase.C.
Referenced by AddPeriodicBCAction::act(), AlgebraicRelationshipManager::attachAlgebraicFunctorHelper(), SystemBase::augmentSendList(), NonlinearSystemBase::augmentSparsity(), AddPeriodicBCAction::autoTranslationBoundaries(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), DisplacedProblem::init(), Adaptivity::init(), TableOutput::outputScalarVariables(), Nemesis::outputScalarVariables(), and Exodus::outputScalarVariables().
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inlineoverridevirtual |
Reimplemented from SystemBase.
Definition at line 100 of file DisplacedSystem.h.
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inlineoverridevirtual |
Reimplemented from SystemBase.
Definition at line 99 of file DisplacedSystem.h.
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inherited |
Gets a reference to a variable of with specified name.
tid | Thread id |
var_name | variable name |
Definition at line 136 of file SystemBase.C.
Referenced by Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), Assembly::copyShapes(), DisplacedProblem::getStandardVariable(), and DisplacedProblem::getVectorVariable().
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inherited |
Gets a reference to a variable with specified number.
tid | Thread id |
var_number | libMesh variable number |
Definition at line 143 of file SystemBase.C.
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inlineoverridevirtual |
Get a raw SparseMatrix.
Reimplemented from SystemBase.
Definition at line 160 of file DisplacedSystem.h.
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inlineinherited |
Gets the maximum number of dofs used by any one variable on any one element.
Definition at line 413 of file SystemBase.h.
Referenced by Assembly::computeAffineMapAD(), Assembly::computeFaceMap(), and Assembly::computeSinglePointMapAD().
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inlineinherited |
Gets the maximum number of dofs used by any one variable on any one node.
Definition at line 420 of file SystemBase.h.
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virtualinherited |
Get minimal quadrature order needed for integrating variables in this system.
Reimplemented in AuxiliarySystem.
Definition at line 227 of file SystemBase.C.
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virtualinherited |
Gets a reference to a scalar variable with specified number.
tid | Thread id |
var_name | A string which is the name of the variable to get. |
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().
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virtualinherited |
Gets a reference to a variable with specified number.
tid | Thread id |
var_number | libMesh variable number |
Definition at line 158 of file SystemBase.C.
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inlineinherited |
Definition at line 574 of file SystemBase.h.
Referenced by Assembly::addResidualScalar(), ComputeFullJacobianThread::computeFaceJacobian(), ODEKernel::computeJacobian(), ComputeFullJacobianThread::computeJacobian(), AuxiliarySystem::computeScalarVars(), Assembly::init(), ComputeJacobianThread::onElement(), Assembly::prepareOffDiagScalar(), and Assembly::prepareScalar().
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inlineinherited |
Definition at line 691 of file SystemBase.h.
Referenced by DisplacedProblem::DisplacedProblem().
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inlineinherited |
Definition at line 579 of file SystemBase.h.
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inlineinherited |
Definition at line 689 of file SystemBase.h.
Referenced by DT2::computeDT(), Transient::endStep(), AB2PredictorCorrector::estimateTimeError(), MooseVariableFE< Real >::MooseVariableFE(), and Transient::preExecute().
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inherited |
Gets a reference to a variable of with specified name.
tid | Thread id |
var_name | variable name |
Definition at line 105 of file SystemBase.C.
Referenced by Assembly::addJacobianBlock(), Assembly::addJacobianBlockNonlocal(), Assembly::addJacobianNeighbor(), NonlocalIntegratedBC::computeJacobianBlock(), NonlocalIntegratedBC::computeNonlocalOffDiagJacobian(), NonlocalKernel::computeNonlocalOffDiagJacobian(), SystemBase::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().
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inherited |
Gets a reference to a variable with specified number.
tid | Thread id |
var_number | libMesh variable number |
Definition at line 119 of file SystemBase.C.
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virtualinherited |
Get the block where a variable of this system is defined.
var_number | The number of the variable |
Definition at line 168 of file SystemBase.C.
Referenced by PhysicsBasedPreconditioner::addSystem().
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inlineinherited |
Definition at line 670 of file SystemBase.h.
Referenced by MooseEigenSystem::buildSystemDoFIndices(), NonlinearSystemBase::checkKernelCoverage(), and AddPeriodicBCAction::setPeriodicVars().
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inlineinherited |
Definition at line 569 of file SystemBase.h.
Referenced by Assembly::addJacobianOffDiagScalar(), Assembly::addResidual(), Assembly::addResidualNeighbor(), Assembly::cacheResidual(), Assembly::cacheResidualNeighbor(), ComputeFullJacobianThread::computeFaceJacobian(), ComputeFullJacobianThread::computeJacobian(), Assembly::init(), Assembly::initNonlocalCoupling(), Assembly::prepareNeighbor(), Assembly::prepareOffDiagScalar(), Assembly::prepareResidual(), Assembly::setResidual(), and Assembly::setResidualNeighbor().
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inlineoverridevirtual |
Get a raw NumericVector.
Reimplemented from SystemBase.
Definition at line 36 of file DisplacedSystem.h.
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overridevirtual |
Get a raw NumericVector.
Get a raw NumericVector with the given name.
Reimplemented from SystemBase.
Definition at line 34 of file DisplacedSystem.C.
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inlineoverridevirtual |
Check if the tagged matrix exists in the system.
Reimplemented from SystemBase.
Definition at line 158 of file DisplacedSystem.h.
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virtualinherited |
Definition at line 661 of file SystemBase.C.
Referenced by ComputeFullJacobianThread::computeFaceJacobian(), ComputeFullJacobianThread::computeJacobian(), DisplacedProblem::getScalarVariable(), DisplacedProblem::hasScalarVariable(), and AddPeriodicBCAction::setPeriodicVars().
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virtualinherited |
Query a system for a variable.
var_name | name of the variable |
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().
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inlineoverridevirtual |
Check if the tagged vector exists in the system.
Reimplemented from SystemBase.
Definition at line 156 of file DisplacedSystem.h.
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inherited |
Check if the named vector exists in the system.
Definition at line 685 of file SystemBase.C.
Referenced by Assembly::addCachedResidual(), Assembly::addCachedResiduals(), Assembly::addResidual(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), AuxiliarySystem::addVector(), SystemBase::addVector(), Assembly::cacheResidual(), Assembly::cacheResidualNeighbor(), VectorNodalBC::computeResidual(), NodalBC::computeResidual(), NonlinearSystemBase::computeResidualTags(), SystemBase::getVector(), hasVector(), MooseVariableScalar::reinit(), and SystemBase::removeVector().
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overridevirtual |
Initialize the system.
Reimplemented from SystemBase.
Definition at line 29 of file DisplacedSystem.C.
Referenced by DisplacedProblem::init().
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inlinevirtualinherited |
Called only once, just before the solve begins so objects can do some precalculations.
Definition at line 126 of file SystemBase.h.
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virtualinherited |
Definition at line 670 of file SystemBase.C.
Referenced by ODEKernel::computeOffDiagJacobian(), Assembly::init(), and Assembly::initNonlocalCoupling().
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virtualinherited |
If or not a matrix tag is active.
Definition at line 879 of file SystemBase.C.
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inlinevirtualinherited |
Definition at line 104 of file SystemBase.h.
Referenced by DMMooseGetEmbedding_Private(), DMSetUp_Moose_Pre(), MooseVariableFE< Real >::MooseVariableFE(), ComputeNodalAuxVarsThread::onNode(), ComputeNodalKernelsThread::onNode(), and ComputeNodalKernelJacobiansThread::onNode().
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virtualinherited |
Definition at line 1022 of file SystemBase.C.
Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addConstraint(), NonlinearSystemBase::addDamper(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), NonlinearSystemBase::addInterfaceKernel(), MooseEigenSystem::addKernel(), AuxiliarySystem::addKernel(), NonlinearSystemBase::addKernel(), NonlinearSystem::addMatrix(), NonlinearSystemBase::addNodalKernel(), AuxiliarySystem::addScalarKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), AuxiliarySystem::addTimeIntegrator(), NonlinearSystemBase::addTimeIntegrator(), SystemBase::addVector(), NonlinearSystemBase::getSplit(), getVector(), SystemBase::getVector(), SystemBase::hasVector(), and SystemBase::removeVector().
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inlineoverridevirtual |
Reimplemented from SystemBase.
Definition at line 43 of file DisplacedSystem.h.
Referenced by DisplacedProblem::addCachedResidualDirectly().
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virtualinherited |
Gets the number of this system.
Definition at line 894 of file SystemBase.C.
Referenced by VectorNodalBC::computeOffDiagJacobian(), NodalBC::computeOffDiagJacobian(), NodalKernel::computeOffDiagJacobian(), EqualValueEmbeddedConstraint::computeQpJacobian(), EqualValueEmbeddedConstraint::computeQpOffDiagJacobian(), DebugResidualAux::computeValue(), NearestNodeValueAux::computeValue(), BoundsAux::computeValue(), NodalNormalsEvaluator::execute(), NodalNormalsCorner::execute(), NodalNormalsPreprocessor::execute(), NonlinearSystemBase::getNodeDofs(), EqualValueEmbeddedConstraint::reinitConstraint(), and MultiAppCopyTransfer::transferDofObject().
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virtualinherited |
Get the number of variables in this system.
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().
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virtualinherited |
Prepare the system for use.
tid | ID of the thread |
Definition at line 242 of file SystemBase.C.
Referenced by DisplacedProblem::prepare(), DisplacedProblem::reinitDirac(), and DisplacedProblem::reinitElemPhys().
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virtualinherited |
Prepare the system for use on sides.
This will try to reuse the preparation done on the element.
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 265 of file SystemBase.C.
Referenced by DisplacedProblem::prepareFace().
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virtualinherited |
Prepare the system for use.
tid | ID of the thread |
Definition at line 298 of file SystemBase.C.
Referenced by DisplacedProblem::reinitNeighbor(), and DisplacedProblem::reinitNeighborPhys().
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virtualinherited |
Reinit an element assembly info.
elem | Which element we are reinitializing for |
tid | ID of the thread |
Reimplemented in AuxiliarySystem.
Definition at line 306 of file SystemBase.C.
Referenced by DisplacedProblem::reinitElem().
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virtualinherited |
Reinit assembly info for a side of an element.
elem | The element |
side | Side of of the element |
bnd_id | Boundary id on that side |
tid | Thread ID |
Reimplemented in AuxiliarySystem.
Definition at line 326 of file SystemBase.C.
Referenced by DisplacedProblem::reinitElemFace(), and DisplacedProblem::reinitNeighbor().
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virtualinherited |
Compute the values of the variables at all the current points.
Definition at line 348 of file SystemBase.C.
Referenced by DisplacedProblem::reinitNeighborPhys().
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virtualinherited |
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().
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virtualinherited |
Reinit nodal assembly info.
node | Node to reinit for |
tid | Thread ID |
Definition at line 356 of file SystemBase.C.
Referenced by DisplacedProblem::reinitNode().
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virtualinherited |
Reinit nodal assembly info on a face.
node | Node to reinit |
bnd_id | Boundary ID |
tid | Thread ID |
Definition at line 370 of file SystemBase.C.
Referenced by DisplacedProblem::reinitNodeFace().
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virtualinherited |
Reinit variables at a set of nodes.
nodes | List of node ids to reinit |
tid | Thread ID |
Definition at line 384 of file SystemBase.C.
Referenced by DisplacedProblem::reinitNodes().
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virtualinherited |
Reinit variables at a set of neighbor nodes.
nodes | List of node ids to reinit |
tid | Thread ID |
Definition at line 395 of file SystemBase.C.
Referenced by DisplacedProblem::reinitNodesNeighbor().
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virtualinherited |
Reinit scalar varaibles.
tid | Thread ID |
Definition at line 406 of file SystemBase.C.
Referenced by DisplacedProblem::reinitScalars().
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inlinevirtualinherited |
Removes a jacobian sized vector.
tag_name | The name of the tag |
Definition at line 652 of file SystemBase.h.
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virtualinherited |
Remove a vector from the system with the given name.
Definition at line 1016 of file SystemBase.C.
Referenced by SystemBase::restoreOldSolutions().
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virtualinherited |
Remove a solution length vector from the system with the specified TagID.
tag_id | Tag ID |
Definition at line 580 of file SystemBase.C.
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inlineoverridevirtual |
Return the residual copy from the NonlinearSystem.
Reimplemented from SystemBase.
Definition at line 106 of file DisplacedSystem.h.
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inlineoverridevirtual |
Reimplemented from SystemBase.
Definition at line 110 of file DisplacedSystem.h.
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virtualinherited |
Reimplemented in NonlinearSystemBase.
Definition at line 719 of file SystemBase.C.
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virtualinherited |
Restore the old and older solutions when the saved solutions present.
Definition at line 497 of file SystemBase.C.
Referenced by DisplacedProblem::restoreOldSolutions().
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virtualinherited |
Restore current solutions (call after your solve failed)
Reimplemented in NonlinearSystemBase.
Definition at line 1002 of file SystemBase.C.
Referenced by NonlinearSystemBase::restoreSolutions().
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virtualinherited |
Save the old and older solutions.
Definition at line 472 of file SystemBase.C.
Referenced by DisplacedProblem::saveOldSolutions().
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inlineoverridevirtual |
Returns a reference to a serialized version of the solution vector for this subproblem.
Implements SystemBase.
Definition at line 77 of file DisplacedSystem.h.
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inlineoverridevirtual |
Implements SystemBase.
Definition at line 87 of file DisplacedSystem.h.
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overridevirtual |
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overridevirtual |
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inlineoverridevirtual |
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inlineoverridevirtual |
Implements SystemBase.
Definition at line 89 of file DisplacedSystem.h.
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inlineoverridevirtual |
Implements SystemBase.
Definition at line 94 of file DisplacedSystem.h.
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inlineoverridevirtual |
Implements SystemBase.
Definition at line 174 of file DisplacedSystem.h.
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inlineoverridevirtual |
Implements SystemBase.
Definition at line 169 of file DisplacedSystem.h.
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virtualinherited |
Solve the system (using libMesh magic)
Reimplemented in NonlinearSystemBase, NonlinearEigenSystem, DumpObjectsNonlinearSystem, and NonlinearSystem.
Definition at line 960 of file SystemBase.C.
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inlinevirtualinherited |
Definition at line 105 of file SystemBase.h.
Referenced by MooseVariableBase::allDofIndices(), MultiAppVariableValueSamplePostprocessorTransfer::execute(), MultiAppVariableValueSampleTransfer::execute(), MooseVariableFE< Real >::MooseVariableFE(), MooseVariableScalar::MooseVariableScalar(), and MooseVariableScalar::reinit().
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inlinevirtual |
Definition at line 181 of file DisplacedSystem.h.
Referenced by UpdateDisplacedMeshThread::init(), and DisplacedProblem::syncSolutions().
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overridevirtual |
Get the reference to the libMesh system.
Implements SystemBase.
Definition at line 61 of file DisplacedSystem.C.
Referenced by DisplacedProblem::getSystem().
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overridevirtual |
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virtualinherited |
Return the Matrix Tag ID for System.
Reimplemented in NonlinearSystemBase.
Definition at line 705 of file SystemBase.C.
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virtualinherited |
Return the Matrix Tag ID for Time.
Definition at line 698 of file SystemBase.C.
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inlineoverridevirtual |
Ideally, we should not need this API.
There exists a really bad API "addCachedResidualDirectly " in FEProblem and DisplacedProblem This API should go away once addCachedResidualDirectly is removed in the future Return Tag ID for Time
Reimplemented from SystemBase.
Definition at line 41 of file DisplacedSystem.h.
Referenced by DisplacedProblem::addCachedResidualDirectly().
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virtualinherited |
Update the system (doing libMesh magic)
Definition at line 954 of file SystemBase.C.
Referenced by MooseEigenSystem::combineSystemSolution(), NonlinearSystemBase::computeDamping(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeResidualTags(), dataLoad(), MooseEigenSystem::initSystemSolution(), MooseEigenSystem::initSystemSolutionOld(), Resurrector::restartFromFile(), MooseEigenSystem::scaleSystemSolution(), NonlinearSystemBase::setConstraintSlaveValues(), NonlinearSystemBase::setInitialSolution(), PicardSolve::solve(), PicardSolve::solveStep(), DisplacedProblem::syncSolutions(), and MultiAppCopyTransfer::transfer().
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virtualinherited |
Zero all vectors for given tags.
Definition at line 570 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeResidualTags().
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inlineoverridevirtual |
Zero out the solution for the list of variables passed in.
Reimplemented from SystemBase.
Definition at line 151 of file DisplacedSystem.h.
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virtualinherited |
Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on Jacobian evaluation by a call to addVariableToZeroOnResidual()
Definition at line 221 of file SystemBase.C.
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virtualinherited |
Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on residual evaluation by a call to addVariableToZeroOnResidual()
Definition at line 215 of file SystemBase.C.
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protectedinherited |
Definition at line 696 of file SystemBase.h.
Referenced by NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianTags(), and NonlinearSystemBase::computeResidualTags().
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protectedinherited |
Definition at line 711 of file SystemBase.h.
Referenced by SystemBase::duDotDu().
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protectedinherited |
Definition at line 712 of file SystemBase.h.
Referenced by SystemBase::duDotDotDu().
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protectedinherited |
Definition at line 697 of file SystemBase.h.
Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addConstraint(), NonlinearSystemBase::addDamper(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), NonlinearSystemBase::addInterfaceKernel(), MooseEigenSystem::addKernel(), AuxiliarySystem::addKernel(), NonlinearSystemBase::addKernel(), NonlinearSystemBase::addNodalKernel(), AuxiliarySystem::addScalarKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), AuxiliarySystem::addTimeIntegrator(), and NonlinearSystemBase::addTimeIntegrator().
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protectedinherited |
Active flags for tagged matrices.
Definition at line 719 of file SystemBase.h.
Referenced by SystemBase::activeAllMatrixTags(), SystemBase::activeMatrixTag(), SystemBase::deactiveAllMatrixTags(), SystemBase::deactiveMatrixTag(), and SystemBase::matrixTagActive().
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protectedinherited |
Maximum number of dofs for any one variable on any one element.
Definition at line 735 of file SystemBase.h.
Referenced by SystemBase::assignMaxVarNDofsPerElem(), SystemBase::getMaxVarNDofsPerElem(), and NonlinearSystemBase::init().
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protectedinherited |
Maximum number of dofs for any one variable on any one node.
Definition at line 738 of file SystemBase.h.
Referenced by SystemBase::assignMaxVarNDofsPerNode(), SystemBase::getMaxVarNDofsPerNode(), and NonlinearSystemBase::init().
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protectedinherited |
Definition at line 699 of file SystemBase.h.
Referenced by SystemBase::augmentSendList(), NonlinearSystemBase::computeDamping(), AuxiliarySystem::computeElementalVars(), NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeNodalBCs(), AuxiliarySystem::computeNodalVars(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::constraintJacobians(), NonlinearSystemBase::constraintResiduals(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), NonlinearSystemBase::getNodeDofs(), NonlinearSystemBase::init(), SystemBase::mesh(), NonlinearSystemBase::setConstraintSlaveValues(), NonlinearSystemBase::setInitialSolution(), NonlinearSystemBase::setVariableGlobalDoFs(), and SystemBase::zeroVariables().
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protectedinherited |
The name of this system.
Definition at line 701 of file SystemBase.h.
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protectedinherited |
Definition at line 726 of file SystemBase.h.
Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().
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protectedinherited |
Definition at line 727 of file SystemBase.h.
Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().
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protectedinherited |
Definition at line 722 of file SystemBase.h.
Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().
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protectedinherited |
Definition at line 723 of file SystemBase.h.
Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().
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protectedinherited |
Definition at line 694 of file SystemBase.h.
Referenced by SystemBase::activeAllMatrixTags(), SystemBase::activeMatrixTag(), NonlinearSystem::addMatrix(), SystemBase::addScalarVariable(), SystemBase::addVariable(), SystemBase::addVector(), SystemBase::associateMatrixToTag(), SystemBase::associateVectorToTag(), SystemBase::augmentSendList(), SystemBase::closeTaggedVectors(), SystemBase::deactiveAllMatrixTags(), SystemBase::deactiveMatrixTag(), SystemBase::disassociateMatrixFromTag(), SystemBase::disassociateVectorFromTag(), SystemBase::matrixTagActive(), SystemBase::prepare(), SystemBase::prepareFace(), SystemBase::reinitElem(), SystemBase::removeVector(), SystemBase::subproblem(), and SystemBase::zeroTaggedVectors().
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protected |
Definition at line 191 of file DisplacedSystem.h.
Referenced by getVector(), solutionOld(), solutionOlder(), sys(), and system().
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protectedinherited |
Tagged matrices (pointer)
Definition at line 717 of file SystemBase.h.
Referenced by NonlinearSystem::addMatrix(), SystemBase::associateMatrixToTag(), SystemBase::disassociateAllTaggedMatrices(), SystemBase::disassociateMatrixFromTag(), SystemBase::getMatrix(), and SystemBase::hasMatrix().
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protectedinherited |
Tagged vectors (pointer)
Definition at line 715 of file SystemBase.h.
Referenced by SystemBase::addVector(), SystemBase::associateVectorToTag(), SystemBase::disassociateAllTaggedVectors(), SystemBase::disassociateVectorFromTag(), SystemBase::getVector(), SystemBase::hasVector(), and SystemBase::removeVector().
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protectedinherited |
Time integrator.
Definition at line 741 of file SystemBase.h.
Referenced by NonlinearSystemBase::addTimeIntegrator(), addTimeIntegrator(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::computeTimeDerivatives(), SystemBase::getSharedTimeIntegrator(), SystemBase::getTimeIntegrator(), NonlinearSystemBase::onTimestepBegin(), NonlinearSystem::solve(), and NonlinearEigenSystem::solve().
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protected |
Definition at line 190 of file DisplacedSystem.h.
Referenced by addVariableToZeroOnJacobian(), addVariableToZeroOnResidual(), associateMatrixToTag(), associateVectorToTag(), augmentSendList(), currentSolution(), disassociateAllTaggedMatrices(), disassociateAllTaggedVectors(), disassociateMatrixFromTag(), disassociateVectorFromTag(), duDotDotDu(), duDotDu(), getMatrix(), getVector(), hasMatrix(), hasVector(), nonTimeVectorTag(), residualCopy(), residualGhosted(), serializedSolution(), solution(), solutionUDot(), solutionUDotDot(), solutionUDotDotOld(), solutionUDotOld(), timeVectorTag(), and zeroVariables().
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protectedinherited |
default kind of variables in this system
Definition at line 730 of file SystemBase.h.
Referenced by SystemBase::addScalarVariable(), and SystemBase::addVariable().
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protectedinherited |
Map of variables (variable id -> array of subdomains where it lives)
Definition at line 706 of file SystemBase.h.
Referenced by SystemBase::addScalarVariable(), SystemBase::addVariable(), SystemBase::getSubdomainsForVar(), and SystemBase::getVariableBlocks().
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protectedinherited |
Definition at line 732 of file SystemBase.h.
Referenced by SystemBase::addVariableToCopy(), and SystemBase::copyVars().
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protectedinherited |
Variable warehouses (one for each thread)
Definition at line 704 of file SystemBase.h.
Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addInterfaceKernel(), SystemBase::addScalarVariable(), AuxiliarySystem::addVariable(), SystemBase::addVariable(), AuxiliarySystem::compute(), SystemBase::getFieldVariable(), AuxiliarySystem::getMinQuadratureOrder(), SystemBase::getMinQuadratureOrder(), SystemBase::getScalarVariable(), SystemBase::getScalarVariables(), SystemBase::getVariable(), SystemBase::getVariableNames(), SystemBase::getVariables(), SystemBase::nVariables(), SystemBase::prepare(), SystemBase::prepareFace(), SystemBase::prepareNeighbor(), SystemBase::reinitElem(), SystemBase::reinitElemFace(), SystemBase::reinitNeighbor(), SystemBase::reinitNeighborFace(), SystemBase::reinitNode(), SystemBase::reinitNodeFace(), SystemBase::reinitNodes(), SystemBase::reinitNodesNeighbor(), and SystemBase::reinitScalars().
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protectedinherited |
Definition at line 709 of file SystemBase.h.
Referenced by SystemBase::addVariableToZeroOnJacobian(), and SystemBase::zeroVariablesForJacobian().
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protectedinherited |
Definition at line 708 of file SystemBase.h.
Referenced by SystemBase::addVariableToZeroOnResidual(), and SystemBase::zeroVariablesForResidual().