A system that holds auxiliary variables. More...
#include <AuxiliarySystem.h>
Public Member Functions | |
AuxiliarySystem (FEProblemBase &subproblem, const std::string &name) | |
virtual | ~AuxiliarySystem () |
virtual void | initialSetup () override |
Setup Functions. More... | |
virtual void | timestepSetup () override |
virtual void | customSetup (const ExecFlagType &exec_type) override |
virtual void | subdomainSetup () override |
virtual void | residualSetup () override |
virtual void | jacobianSetup () override |
virtual void | updateActive (THREAD_ID tid) |
virtual void | addVariable (const std::string &var_type, const std::string &name, InputParameters ¶meters) override |
Canonical method for adding a variable. More... | |
void | addKernel (const std::string &kernel_name, const std::string &name, InputParameters ¶meters) |
Adds an auxiliary kernel. More... | |
void | addScalarKernel (const std::string &kernel_name, const std::string &name, InputParameters ¶meters) |
Adds a scalar kernel. More... | |
virtual void | reinitElem (const Elem *elem, THREAD_ID tid) override |
Reinit an element assembly info. More... | |
virtual void | reinitElemFace (const Elem *elem, unsigned int side, THREAD_ID tid) override |
Reinit assembly info for a side of an element. More... | |
const NumericVector< Number > *const & | currentSolution () const override |
The solution vector that is currently being operated on. More... | |
virtual void | serializeSolution () |
virtual void | augmentSparsity (libMesh::SparsityPattern::Graph &, std::vector< dof_id_type > &, std::vector< dof_id_type > &) override |
Will modify the sparsity pattern to add logical geometric connections. More... | |
virtual void | compute (ExecFlagType type) override |
Compute auxiliary variables. More... | |
std::set< std::string > | getDependObjects (ExecFlagType type) |
Get a list of dependent UserObjects for this exec type. More... | |
std::set< std::string > | getDependObjects () |
virtual libMesh::Order | getMinQuadratureOrder () override |
Get the minimum quadrature order for evaluating elemental auxiliary variables. More... | |
bool | needMaterialOnSide (BoundaryID bnd_id) |
Indicated whether this system needs material properties on boundaries. More... | |
virtual libMesh::System & | sys () |
virtual libMesh::System & | system () override |
Get the reference to the libMesh system. More... | |
virtual const libMesh::System & | system () const override |
virtual void | copyCurrentIntoPreviousNL () |
Copies the current solution into the previous nonlinear iteration solution. More... | |
void | setScalarVariableCoupleableTags (ExecFlagType type) |
void | clearScalarVariableCoupleableTags () |
const ExecuteMooseObjectWarehouse< AuxKernel > & | nodalAuxWarehouse () const |
const ExecuteMooseObjectWarehouse< VectorAuxKernel > & | nodalVectorAuxWarehouse () const |
const ExecuteMooseObjectWarehouse< ArrayAuxKernel > & | nodalArrayAuxWarehouse () const |
const ExecuteMooseObjectWarehouse< AuxKernel > & | elemAuxWarehouse () const |
const ExecuteMooseObjectWarehouse< VectorAuxKernel > & | elemVectorAuxWarehouse () const |
const ExecuteMooseObjectWarehouse< ArrayAuxKernel > & | elemArrayAuxWarehouse () const |
void | variableWiseRelativeSolutionDifferenceNorm (std::vector< Number > &var_diffs) const |
Computes and stores ||current - old|| / ||current|| for each variable in the given vector. More... | |
unsigned int | number () const |
Gets the number of this system. More... | |
MooseMesh & | mesh () |
const MooseMesh & | mesh () const |
SubProblem & | subproblem () |
const SubProblem & | subproblem () const |
FEProblemBase & | feProblem () |
const FEProblemBase & | feProblem () const |
void | applyScalingFactors (const std::vector< Real > &inverse_scaling_factors) |
Applies scaling factors to the system's variables. More... | |
bool | computingScalingJacobian () const |
Whether we are computing an initial Jacobian for automatic variable scaling. More... | |
bool | automaticScaling () const |
Getter for whether we are performing automatic scaling. More... | |
void | automaticScaling (bool automatic_scaling) |
Setter for whether we are performing automatic scaling. More... | |
void | setVerboseFlag (const bool &verbose) |
Sets the verbose flag. More... | |
virtual libMesh::DofMap & | dofMap () |
Gets writeable reference to the dof map. More... | |
virtual const libMesh::DofMap & | dofMap () const |
Gets const reference to the dof map. More... | |
virtual void | preInit () |
This is called prior to the libMesh system has been init'd. More... | |
virtual void | postInit () |
virtual void | reinit () |
Reinitialize the system when the degrees of freedom in this system have changed. More... | |
virtual void | initializeObjects () |
Called only once, just before the solve begins so objects can do some precalculations. More... | |
void | update () |
Update the system (doing libMesh magic) More... | |
virtual void | solve () |
Solve the system (using libMesh magic) More... | |
virtual void | copyOldSolutions () |
Shifts the solutions backwards in time. More... | |
virtual void | copyPreviousNonlinearSolutions () |
Shifts the solutions backwards in nonlinear iteration history. More... | |
virtual void | restoreSolutions () |
Restore current solutions (call after your solve failed) More... | |
NumericVector< Number > & | solution () |
const NumericVector< Number > & | solution () const |
NumericVector< Number > & | solutionOld () |
const NumericVector< Number > & | solutionOld () const |
NumericVector< Number > & | solutionOlder () |
const NumericVector< Number > & | solutionOlder () const |
virtual const NumericVector< Number > * | solutionPreviousNewton () const |
virtual NumericVector< Number > * | solutionPreviousNewton () |
virtual void | initSolutionState () |
Initializes the solution state. More... | |
virtual NumericVector< Number > & | solutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time) |
Get a state of the solution (0 = current, 1 = old, 2 = older, etc). More... | |
virtual const NumericVector< Number > & | solutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time) const |
Get a state of the solution (0 = current, 1 = old, 2 = older, etc). More... | |
virtual void | needSolutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time) |
Registers that the solution state state is needed. More... | |
virtual bool | hasSolutionState (const unsigned int state, Moose::SolutionIterationType iteration_type=Moose::SolutionIterationType::Time) const |
Whether or not the system has the solution state (0 = current, 1 = old, 2 = older, etc). More... | |
virtual void | addDotVectors () |
Add u_dot, u_dotdot, u_dot_old and u_dotdot_old vectors if requested by the time integrator. More... | |
virtual std::vector< Number > & | duDotDus () |
virtual Number & | duDotDotDu () |
virtual const Number & | duDotDotDu () const |
virtual const Number & | duDotDu (unsigned int var_num=0) const |
virtual NumericVector< Number > * | solutionUDot () |
virtual const NumericVector< Number > * | solutionUDot () const |
virtual NumericVector< Number > * | solutionUDotDot () |
virtual const NumericVector< Number > * | solutionUDotDot () const |
virtual NumericVector< Number > * | solutionUDotOld () |
virtual const NumericVector< Number > * | solutionUDotOld () const |
virtual NumericVector< Number > * | solutionUDotDotOld () |
virtual const NumericVector< Number > * | solutionUDotDotOld () const |
virtual void | saveOldSolutions () |
Save the old and older solutions. More... | |
virtual void | restoreOldSolutions () |
Restore the old and older solutions when the saved solutions present. More... | |
bool | hasVector (const std::string &tag_name) const |
Check if the named vector exists in the system. More... | |
virtual bool | hasVector (TagID tag_id) const |
Check if the tagged vector exists in the system. More... | |
virtual TagID | timeVectorTag () const |
Ideally, we should not need this API. More... | |
virtual TagID | systemMatrixTag () const |
Return the Matrix Tag ID for System. More... | |
virtual TagID | nonTimeVectorTag () const |
virtual TagID | residualVectorTag () const |
virtual std::set< TagID > | defaultVectorTags () const |
Get the default vector tags associated with this system. More... | |
virtual std::set< TagID > | defaultMatrixTags () const |
Get the default matrix tags associted with this system. More... | |
virtual void | associateVectorToTag (NumericVector< Number > &vec, TagID tag) |
Associate a vector for a given tag. More... | |
virtual void | disassociateVectorFromTag (NumericVector< Number > &vec, TagID tag) |
Disassociate a given vector from a given tag. More... | |
virtual void | disassociateVectorFromTag (TagID tag) |
Disassociate any vector that is associated with a given tag. More... | |
virtual void | disassociateDefaultVectorTags () |
Disassociate the vectors associated with the default vector tags of this system. More... | |
virtual bool | hasMatrix (TagID tag) const |
Check if the tagged matrix exists in the system. More... | |
virtual libMesh::SparseMatrix< Number > & | getMatrix (TagID tag) |
Get a raw SparseMatrix. More... | |
virtual const libMesh::SparseMatrix< Number > & | getMatrix (TagID tag) const |
Get a raw SparseMatrix. More... | |
virtual void | activeAllMatrixTags () |
Make all exsiting matrices ative. More... | |
virtual void | activeMatrixTag (TagID tag) |
Active a matrix for tag. More... | |
virtual bool | matrixTagActive (TagID tag) const |
If or not a matrix tag is active. More... | |
virtual void | deactiveMatrixTag (TagID tag) |
deactive a matrix for tag More... | |
virtual void | deactiveAllMatrixTags () |
Make matrices inactive. More... | |
void | closeTaggedMatrices (const std::set< TagID > &tags) |
Close all matrices associated the tags. More... | |
void | flushTaggedMatrices (const std::set< TagID > &tags) |
flushes all matrices associated to tags. More... | |
virtual void | associateMatrixToTag (libMesh::SparseMatrix< Number > &matrix, TagID tag) |
Associate a matrix to a tag. More... | |
virtual void | disassociateMatrixFromTag (libMesh::SparseMatrix< Number > &matrix, TagID tag) |
Disassociate a matrix from a tag. More... | |
virtual void | disassociateMatrixFromTag (TagID tag) |
Disassociate any matrix that is associated with a given tag. More... | |
virtual void | disassociateDefaultMatrixTags () |
Disassociate the matrices associated with the default matrix tags of this system. More... | |
virtual NumericVector< Number > & | serializedSolution () |
Returns a reference to a serialized version of the solution vector for this subproblem. More... | |
virtual NumericVector< Number > & | residualCopy () |
virtual NumericVector< Number > & | residualGhosted () |
virtual void | augmentSendList (std::vector< dof_id_type > &send_list) |
Will modify the send_list to add all of the extra ghosted dofs for this system. More... | |
virtual bool | isArrayVariable (const std::string &var_name) const |
If a variable is an array variable. More... | |
virtual bool | isScalarVariable (unsigned int var_name) const |
MooseVariableFieldBase & | getVariable (THREAD_ID tid, const std::string &var_name) const |
Gets a reference to a variable of with specified name. More... | |
MooseVariableFieldBase & | getVariable (THREAD_ID tid, unsigned int var_number) const |
Gets a reference to a variable with specified number. More... | |
template<typename T > | |
MooseVariableFE< T > & | getFieldVariable (THREAD_ID tid, const std::string &var_name) |
Gets a reference to a variable of with specified name. More... | |
template<typename T > | |
MooseVariableFE< T > & | getFieldVariable (THREAD_ID tid, unsigned int var_number) |
Gets a reference to a variable with specified number. More... | |
template<typename T > | |
MooseVariableField< T > & | getActualFieldVariable (THREAD_ID tid, const std::string &var_name) |
Returns a field variable pointer - this includes finite volume variables. More... | |
template<typename T > | |
MooseVariableField< T > & | getActualFieldVariable (THREAD_ID tid, unsigned int var_number) |
Returns a field variable pointer - this includes finite volume variables. More... | |
template<typename T > | |
MooseVariableFV< T > & | getFVVariable (THREAD_ID tid, const std::string &var_name) |
Return a finite volume variable. More... | |
virtual MooseVariableScalar & | getScalarVariable (THREAD_ID tid, const std::string &var_name) const |
Gets a reference to a scalar variable with specified number. More... | |
virtual MooseVariableScalar & | getScalarVariable (THREAD_ID tid, unsigned int var_number) const |
Gets a reference to a variable with specified number. More... | |
virtual const std::set< SubdomainID > * | getVariableBlocks (unsigned int var_number) |
Get the block where a variable of this system is defined. More... | |
virtual unsigned int | nVariables () const |
Get the number of variables in this system. More... | |
unsigned int | nFieldVariables () const |
Get the number of field variables in this system. More... | |
unsigned int | nFVVariables () const |
Get the number of finite volume variables in this system. More... | |
std::size_t | getMaxVarNDofsPerElem () const |
Gets the maximum number of dofs used by any one variable on any one element. More... | |
std::size_t | getMaxVarNDofsPerNode () const |
Gets the maximum number of dofs used by any one variable on any one node. More... | |
void | assignMaxVarNDofsPerElem (std::size_t max_dofs) |
assign the maximum element dofs More... | |
void | assignMaxVarNDofsPerNode (std::size_t max_dofs) |
assign the maximum node dofs More... | |
virtual void | addVariableToZeroOnResidual (std::string var_name) |
Adds this variable to the list of variables to be zeroed during each residual evaluation. More... | |
virtual void | addVariableToZeroOnJacobian (std::string var_name) |
Adds this variable to the list of variables to be zeroed during each Jacobian evaluation. More... | |
virtual void | zeroVariables (std::vector< std::string > &vars_to_be_zeroed) |
Zero out the solution for the list of variables passed in. More... | |
virtual void | zeroVariablesForResidual () |
Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on residual evaluation by a call to addVariableToZeroOnResidual() More... | |
virtual void | zeroVariablesForJacobian () |
Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on Jacobian evaluation by a call to addVariableToZeroOnResidual() More... | |
virtual void | prepare (THREAD_ID tid) |
Prepare the system for use. More... | |
virtual void | prepareFace (THREAD_ID tid, bool resize_data) |
Prepare the system for use on sides. More... | |
virtual void | prepareNeighbor (THREAD_ID tid) |
Prepare the system for use. More... | |
virtual void | prepareLowerD (THREAD_ID tid) |
Prepare the system for use for lower dimensional elements. More... | |
virtual void | reinitNeighborFace (const Elem *elem, unsigned int side, THREAD_ID tid) |
Compute the values of the variables at all the current points. More... | |
virtual void | reinitNeighbor (const Elem *elem, THREAD_ID tid) |
Compute the values of the variables at all the current points. More... | |
virtual void | reinitLowerD (THREAD_ID tid) |
Compute the values of the variables on the lower dimensional element. More... | |
virtual void | reinitNode (const Node *node, THREAD_ID tid) |
Reinit nodal assembly info. More... | |
virtual void | reinitNodeFace (const Node *node, BoundaryID bnd_id, THREAD_ID tid) |
Reinit nodal assembly info on a face. More... | |
virtual void | reinitNodes (const std::vector< dof_id_type > &nodes, THREAD_ID tid) |
Reinit variables at a set of nodes. More... | |
virtual void | reinitNodesNeighbor (const std::vector< dof_id_type > &nodes, THREAD_ID tid) |
Reinit variables at a set of neighbor nodes. More... | |
virtual void | reinitScalars (THREAD_ID tid, bool reinit_for_derivative_reordering=false) |
Reinit scalar varaibles. More... | |
virtual void | addVariableToCopy (const std::string &dest_name, const std::string &source_name, const std::string ×tep) |
Add info about variable that will be copied. More... | |
const std::vector< MooseVariableFieldBase * > & | getVariables (THREAD_ID tid) |
const std::vector< MooseVariableScalar * > & | getScalarVariables (THREAD_ID tid) |
const std::set< SubdomainID > & | getSubdomainsForVar (unsigned int var_number) const |
const std::set< SubdomainID > & | getSubdomainsForVar (const std::string &var_name) const |
Get the block where a variable of this system is defined. More... | |
void | removeVector (const std::string &name) |
Remove a vector from the system with the given name. More... | |
void | removeVector (TagID tag_id) |
Remove a solution length vector from the system with the specified TagID. More... | |
NumericVector< Number > & | addVector (const std::string &vector_name, const bool project, const libMesh::ParallelType type) |
Adds a solution length vector to the system. More... | |
NumericVector< Number > & | addVector (TagID tag, const bool project, const libMesh::ParallelType type) |
Adds a solution length vector to the system with the specified TagID. More... | |
void | closeTaggedVector (const TagID tag) |
Close vector with the given tag. More... | |
void | closeTaggedVectors (const std::set< TagID > &tags) |
Close all vectors for given tags. More... | |
void | zeroTaggedVector (const TagID tag) |
Zero vector with the given tag. More... | |
void | zeroTaggedVectors (const std::set< TagID > &tags) |
Zero all vectors for given tags. More... | |
void | setVariableGlobalDoFs (const std::string &var_name) |
set all the global dof indices for a variable More... | |
const std::vector< dof_id_type > & | getVariableGlobalDoFs () |
Get the global dof indices of a variable, this needs to be called after the indices have been set by setVariableGlobalDoFs More... | |
libMesh::SparseMatrix< Number > & | addMatrix (TagID tag) |
Adds a matrix with a given tag. More... | |
void | removeMatrix (TagID tag) |
Removes a matrix with a given tag. More... | |
virtual const std::string & | name () const |
const std::vector< VariableName > & | getVariableNames () const |
void | getStandardFieldVariableNames (std::vector< VariableName > &std_field_variables) const |
unsigned int | getMaxVariableNumber () const |
Returns the maximum number of all variables on the system. More... | |
virtual void | computeVariables (const NumericVector< Number > &) |
void | copyVars (libMesh::ExodusII_IO &io) |
virtual void | copySolutionsBackwards () |
Copy current solution into old and older. More... | |
void | addTimeIntegrator (const std::string &type, const std::string &name, InputParameters ¶meters) |
bool | hasVarCopy () const |
Whether or not there are variables to be restarted from an Exodus mesh file. More... | |
void | addScalingVector () |
Add the scaling factor vector to the system. More... | |
bool | solutionStatesInitialized () const |
Whether or not the solution states have been initialized via initSolutionState() More... | |
void | clearAllDofIndices () |
Clear all dof indices from moose variables. More... | |
void | setActiveVariableCoupleableVectorTags (const std::set< TagID > &vtags, THREAD_ID tid) |
Set the active vector tags for the variables. More... | |
void | setActiveScalarVariableCoupleableVectorTags (const std::set< TagID > &vtags, THREAD_ID tid) |
Set the active vector tags for the scalar variables. More... | |
Moose::VarKindType | varKind () const |
const std::vector< std::unique_ptr< NumericVector< Number > > > & | gradientContainer () const |
Reference to the container vector which hold gradients at dofs (if it can be interpreted). More... | |
void | copyTimeIntegrators (const SystemBase &other_sys) |
Copy time integrators from another system. More... | |
const TimeIntegrator & | getTimeIntegrator (const unsigned int var_num) const |
Retrieve the time integrator that integrates the given variable's equation. More... | |
const TimeIntegrator * | queryTimeIntegrator (const unsigned int var_num) const |
Retrieve the time integrator that integrates the given variable's equation. More... | |
const std::vector< std::shared_ptr< TimeIntegrator > > & | getTimeIntegrators () |
std::string | prefix () const |
const Parallel::Communicator & | comm () const |
processor_id_type | n_processors () const |
processor_id_type | processor_id () const |
PerfGraph & | perfGraph () |
Get the PerfGraph. More... | |
virtual NumericVector< Number > & | getVector (const std::string &name) |
Get a raw NumericVector by name. More... | |
virtual const NumericVector< Number > & | getVector (const std::string &name) const |
virtual NumericVector< Number > & | getVector (TagID tag) |
Get a raw NumericVector by tag. More... | |
virtual const NumericVector< Number > & | getVector (TagID tag) const |
virtual bool | hasVariable (const std::string &var_name) const |
Query a system for a variable. More... | |
virtual bool | hasScalarVariable (const std::string &var_name) const |
Static Public Member Functions | |
static InputParameters | validParams () |
Public Attributes | |
const ConsoleStream | _console |
An instance of helper class to write streams to the Console objects. More... | |
Protected Member Functions | |
void | computeScalarVars (ExecFlagType type) |
void | computeNodalVars (ExecFlagType type) |
void | computeMortarNodalVars (ExecFlagType type) |
void | computeNodalVecVars (ExecFlagType type) |
void | computeNodalArrayVars (ExecFlagType type) |
void | computeElementalVars (ExecFlagType type) |
void | computeElementalVecVars (ExecFlagType type) |
void | computeElementalArrayVars (ExecFlagType type) |
template<typename AuxKernelType > | |
void | computeElementalVarsHelper (const MooseObjectWarehouse< AuxKernelType > &warehouse) |
template<typename AuxKernelType > | |
void | computeNodalVarsHelper (const MooseObjectWarehouse< AuxKernelType > &warehouse) |
NumericVector< Number > & | solutionInternal () const override |
Internal getter for solution owned by libMesh. More... | |
PerfID | registerTimedSection (const std::string §ion_name, const unsigned int level) const |
Call to register a named section for timing. More... | |
PerfID | registerTimedSection (const std::string §ion_name, const unsigned int level, const std::string &live_message, const bool print_dots=true) const |
Call to register a named section for timing. More... | |
std::string | timedSectionName (const std::string §ion_name) const |
Protected Attributes | |
libMesh::System & | _sys |
const NumericVector< Number > * | _current_solution |
solution vector from nonlinear solver More... | |
std::vector< NumericVector< Number > * > | _solution_state |
The current states of the solution (0 = current, 1 = old, etc) More... | |
std::vector< std::vector< MooseVariableFEBase * > > | _nodal_vars |
ExecuteMooseObjectWarehouse< AuxScalarKernel > | _aux_scalar_storage |
ExecuteMooseObjectWarehouse< AuxKernel > | _nodal_aux_storage |
ExecuteMooseObjectWarehouse< AuxKernel > | _mortar_nodal_aux_storage |
ExecuteMooseObjectWarehouse< AuxKernel > | _elemental_aux_storage |
ExecuteMooseObjectWarehouse< VectorAuxKernel > | _nodal_vec_aux_storage |
ExecuteMooseObjectWarehouse< VectorAuxKernel > | _elemental_vec_aux_storage |
ExecuteMooseObjectWarehouse< ArrayAuxKernel > | _nodal_array_aux_storage |
ExecuteMooseObjectWarehouse< ArrayAuxKernel > | _elemental_array_aux_storage |
SubProblem & | _subproblem |
The subproblem for whom this class holds variable data, etc; this can either be the governing finite element/volume problem or a subjugate displaced problem. More... | |
FEProblemBase & | _fe_problem |
the governing finite element/volume problem More... | |
MooseApp & | _app |
Factory & | _factory |
MooseMesh & | _mesh |
std::string | _name |
The name of this system. More... | |
std::vector< VariableWarehouse > | _vars |
Variable warehouses (one for each thread) More... | |
std::map< unsigned int, std::set< SubdomainID > > | _var_map |
Map of variables (variable id -> array of subdomains where it lives) More... | |
unsigned int | _max_var_number |
Maximum variable number. More... | |
std::vector< std::string > | _vars_to_be_zeroed_on_residual |
std::vector< std::string > | _vars_to_be_zeroed_on_jacobian |
NumericVector< Number > * | _u_dot |
solution vector for u^dot More... | |
NumericVector< Number > * | _u_dotdot |
solution vector for u^dotdot More... | |
NumericVector< Number > * | _u_dot_old |
old solution vector for u^dot More... | |
NumericVector< Number > * | _u_dotdot_old |
old solution vector for u^dotdot More... | |
std::vector< Real > | _du_dot_du |
Derivative of time derivative of u with respect to uj. More... | |
Real | _du_dotdot_du |
std::vector< NumericVector< Number > * > | _tagged_vectors |
Tagged vectors (pointer) More... | |
std::vector< libMesh::SparseMatrix< Number > * > | _tagged_matrices |
Tagged matrices (pointer) More... | |
std::vector< bool > | _matrix_tag_active_flags |
Active flags for tagged matrices. More... | |
NumericVector< Real > * | _saved_old |
NumericVector< Real > * | _saved_older |
NumericVector< Real > * | _saved_dot_old |
NumericVector< Real > * | _saved_dotdot_old |
Moose::VarKindType | _var_kind |
default kind of variables in this system More... | |
std::vector< VarCopyInfo > | _var_to_copy |
size_t | _max_var_n_dofs_per_elem |
Maximum number of dofs for any one variable on any one element. More... | |
size_t | _max_var_n_dofs_per_node |
Maximum number of dofs for any one variable on any one node. More... | |
std::vector< std::shared_ptr< TimeIntegrator > > | _time_integrators |
Time integrator. More... | |
std::vector< std::vector< MooseVariableFieldBase * > > | _numbered_vars |
Map variable number to its pointer. More... | |
bool | _automatic_scaling |
Whether to automatically scale the variables. More... | |
bool | _verbose |
True if printing out additional information. More... | |
bool | _solution_states_initialized |
Whether or not the solution states have been initialized. More... | |
std::vector< dof_id_type > | _var_all_dof_indices |
Container for the dof indices of a given variable. More... | |
std::unique_ptr< NumericVector< Number > > | _serialized_solution |
Serialized version of the solution vector, or nullptr if a serialized solution is not needed. More... | |
std::vector< std::unique_ptr< NumericVector< Number > > > | _raw_grad_container |
A cache for storing gradients at dof locations. More... | |
const Parallel::Communicator & | _communicator |
MooseApp & | _pg_moose_app |
The MooseApp that owns the PerfGraph. More... | |
const std::string | _prefix |
A prefix to use for all sections. More... | |
std::vector< std::vector< MooseVariableFieldBase * > > | _elem_vars |
Elemental variables. More... | |
Friends | |
class | ComputeIndicatorThread |
class | ComputeMarkerThread |
class | FlagElementsThread |
class | ComputeNodalKernelsThread |
class | ComputeNodalKernelBcsThread |
class | ComputeNodalKernelJacobiansThread |
class | ComputeNodalKernelBCJacobiansThread |
A system that holds auxiliary variables.
Definition at line 41 of file AuxiliarySystem.h.
AuxiliarySystem::AuxiliarySystem | ( | FEProblemBase & | subproblem, |
const std::string & | name | ||
) |
Definition at line 38 of file AuxiliarySystem.C.
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virtualdefault |
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virtualinherited |
Make all exsiting matrices ative.
Definition at line 1137 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), NonlinearSystemBase::computeResidualAndJacobianInternal(), and NonlinearSystemBase::computeResidualTags().
Active a matrix for tag.
Definition at line 1102 of file SystemBase.C.
|
virtualinherited |
Add u_dot, u_dotdot, u_dot_old and u_dotdot_old vectors if requested by the time integrator.
Reimplemented in DisplacedSystem.
Definition at line 1600 of file SystemBase.C.
Referenced by DisplacedSystem::addDotVectors().
void AuxiliarySystem::addKernel | ( | const std::string & | kernel_name, |
const std::string & | name, | ||
InputParameters & | parameters | ||
) |
Adds an auxiliary kernel.
kernel_name | The type of the kernel |
name | The name of the kernel |
parameters | Parameters for this kernel |
Definition at line 258 of file AuxiliarySystem.C.
|
inherited |
Adds a matrix with a given tag.
tag_name | The name of the tag |
Definition at line 562 of file SystemBase.C.
void AuxiliarySystem::addScalarKernel | ( | const std::string & | kernel_name, |
const std::string & | name, | ||
InputParameters & | parameters | ||
) |
Adds a scalar kernel.
kernel_name | The type of the kernel |
name | The name of the kernel |
parameters | Kernel parameters |
Definition at line 316 of file AuxiliarySystem.C.
|
inherited |
Add the scaling factor vector to the system.
Definition at line 1512 of file SystemBase.C.
Referenced by MooseVariableBase::initialSetup().
|
inherited |
Definition at line 1625 of file SystemBase.C.
|
overridevirtual |
Canonical method for adding a variable.
var_type | the type of the variable, e.g. MooseVariableScalar |
var_name | the variable name, e.g. 'u' |
params | the InputParameters from which to construct the variable |
Reimplemented from SystemBase.
Definition at line 204 of file AuxiliarySystem.C.
|
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 1177 of file SystemBase.C.
Referenced by CopyNodalVarsAction::act(), and PhysicsBase::copyVariablesFromMesh().
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virtualinherited |
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 in DisplacedSystem.
Definition at line 179 of file SystemBase.C.
Referenced by ADDGKernel::ADDGKernel(), DisplacedSystem::addVariableToZeroOnJacobian(), ADIntegratedBCTempl< T >::ADIntegratedBCTempl(), ADKernelTempl< T >::ADKernelTempl(), ArrayDGKernel::ArrayDGKernel(), ArrayIntegratedBC::ArrayIntegratedBC(), ArrayKernel::ArrayKernel(), DGKernel::DGKernel(), IntegratedBC::IntegratedBC(), InterfaceKernelTempl< T >::InterfaceKernelTempl(), Kernel::Kernel(), NodalBC::NodalBC(), and NodalKernel::NodalKernel().
|
virtualinherited |
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 in DisplacedSystem.
Definition at line 173 of file SystemBase.C.
Referenced by ADDGKernel::ADDGKernel(), DisplacedSystem::addVariableToZeroOnResidual(), ADIntegratedBCTempl< T >::ADIntegratedBCTempl(), ADKernelTempl< T >::ADKernelTempl(), ArrayDGKernel::ArrayDGKernel(), ArrayIntegratedBC::ArrayIntegratedBC(), ArrayKernel::ArrayKernel(), DGKernel::DGKernel(), IntegratedBC::IntegratedBC(), InterfaceKernelTempl< T >::InterfaceKernelTempl(), Kernel::Kernel(), NodalBC::NodalBC(), and NodalKernel::NodalKernel().
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inherited |
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. |
Referenced by SystemBase::addDotVectors(), SystemBase::addScalingVector(), NonlinearTimeIntegratorInterface::addVector(), SecantSolve::allocateStorage(), SteffensenSolve::allocateStorage(), PicardSolve::allocateStorage(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), CentralDifference::initialSetup(), SystemBase::needSolutionState(), NonlinearSystemBase::residualGhosted(), and SystemBase::saveOldSolutions().
|
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. |
|
inherited |
Applies scaling factors to the system's variables.
inverse_scaling_factors | A vector containing the inverse of each variable's scaling factor, e.g. 1 / scaling_factor |
Definition at line 1462 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeScaling().
|
inlineinherited |
assign the maximum element dofs
Definition at line 598 of file SystemBase.h.
|
inlineinherited |
assign the maximum node dofs
Definition at line 603 of file SystemBase.h.
|
virtualinherited |
Associate a matrix to a tag.
Reimplemented in DisplacedSystem.
Definition at line 1059 of file SystemBase.C.
Referenced by SystemBase::addMatrix(), DisplacedSystem::associateMatrixToTag(), NonlinearSystemBase::computeJacobian(), FEProblemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTag(), FEProblemBase::computeLinearSystemSys(), and FEProblemBase::computeResidualAndJacobian().
|
virtualinherited |
Associate a vector for a given tag.
Reimplemented in DisplacedSystem.
Definition at line 964 of file SystemBase.C.
Referenced by DisplacedSystem::associateVectorToTag(), FEProblemBase::computeLinearSystemSys(), FEProblemBase::computeResidualAndJacobian(), FEProblemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTag(), FEProblemBase::computeResidualTag(), FEProblemBase::computeResidualType(), LinearSystem::LinearSystem(), and SolverSystem::setSolution().
|
virtualinherited |
Will modify the send_list to add all of the extra ghosted dofs for this system.
Reimplemented in DisplacedSystem.
Definition at line 444 of file SystemBase.C.
Referenced by DisplacedSystem::augmentSendList(), and extraSendList().
|
overridevirtual |
Will modify the sparsity pattern to add logical geometric connections.
Implements SystemBase.
Definition at line 757 of file AuxiliarySystem.C.
|
inlineinherited |
Getter for whether we are performing automatic scaling.
Definition at line 122 of file SystemBase.h.
Referenced by SubProblem::automaticScaling().
|
inlineinherited |
Setter for whether we are performing automatic scaling.
automatic_scaling | A boolean representing whether we are performing automatic scaling |
Definition at line 128 of file SystemBase.h.
|
inherited |
Clear all dof indices from moose variables.
Definition at line 1580 of file SystemBase.C.
Referenced by SubProblem::clearAllDofIndices().
void AuxiliarySystem::clearScalarVariableCoupleableTags | ( | ) |
Definition at line 607 of file AuxiliarySystem.C.
Referenced by computeScalarVars().
Close all matrices associated the tags.
Definition at line 1043 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), and NonlinearSystemBase::computeResidualAndJacobianTags().
Close vector with the given tag.
Definition at line 641 of file SystemBase.C.
Referenced by SystemBase::closeTaggedVectors().
Close all vectors for given tags.
Definition at line 659 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeResidualAndJacobianTags(), NonlinearSystemBase::computeResidualTags(), NonlinearSystem::stopSolve(), and LinearSystem::stopSolve().
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overridevirtual |
Compute auxiliary variables.
type | Time flag of which variables should be computed |
Implements SystemBase.
Definition at line 372 of file AuxiliarySystem.C.
|
protected |
Definition at line 750 of file AuxiliarySystem.C.
Referenced by compute().
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protected |
Definition at line 732 of file AuxiliarySystem.C.
Referenced by compute().
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protected |
Definition at line 798 of file AuxiliarySystem.C.
|
protected |
Definition at line 741 of file AuxiliarySystem.C.
Referenced by compute().
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protected |
Definition at line 680 of file AuxiliarySystem.C.
Referenced by compute().
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protected |
Definition at line 673 of file AuxiliarySystem.C.
Referenced by compute().
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protected |
Definition at line 655 of file AuxiliarySystem.C.
Referenced by compute().
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protected |
Definition at line 857 of file AuxiliarySystem.C.
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protected |
Definition at line 664 of file AuxiliarySystem.C.
Referenced by compute().
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protected |
Definition at line 614 of file AuxiliarySystem.C.
Referenced by compute().
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inlinevirtualinherited |
Definition at line 870 of file SystemBase.h.
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inherited |
Whether we are computing an initial Jacobian for automatic variable scaling.
Definition at line 1519 of file SystemBase.C.
Referenced by Assembly::addJacobianBlock(), Assembly::addJacobianBlockNonlocal(), VectorKernel::computeJacobian(), Kernel::computeJacobian(), EigenKernel::computeJacobian(), and FEProblemBase::computeJacobianTags().
|
virtual |
Copies the current solution into the previous nonlinear iteration solution.
Definition at line 790 of file AuxiliarySystem.C.
|
virtualinherited |
Shifts the solutions backwards in time.
Definition at line 1288 of file SystemBase.C.
Referenced by SystemBase::copySolutionsBackwards(), and EigenExecutionerBase::inversePowerIteration().
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virtualinherited |
Shifts the solutions backwards in nonlinear iteration history.
Definition at line 1271 of file SystemBase.C.
Referenced by SystemBase::copySolutionsBackwards().
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virtualinherited |
Copy current solution into old and older.
Definition at line 1260 of file SystemBase.C.
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inherited |
Copy time integrators from another system.
Definition at line 1634 of file SystemBase.C.
|
inherited |
Definition at line 1185 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 AuxiliarySystem.h.
Referenced by copyCurrentIntoPreviousNL(), FlagElementsThread::onElement(), AB2PredictorCorrector::step(), and DisplacedProblem::syncSolutions().
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overridevirtual |
Reimplemented from SystemBase.
Definition at line 119 of file AuxiliarySystem.C.
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virtualinherited |
Make matrices inactive.
Definition at line 1126 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeResidualTags(), and NonlinearSystemBase::setInitialSolution().
deactive a matrix for tag
Definition at line 1114 of file SystemBase.C.
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inlinevirtualinherited |
Get the default matrix tags associted with this system.
Reimplemented in NonlinearEigenSystem, and DisplacedSystem.
Definition at line 310 of file SystemBase.h.
Referenced by DisplacedSystem::defaultMatrixTags(), NonlinearEigenSystem::defaultMatrixTags(), and SystemBase::disassociateDefaultMatrixTags().
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inlinevirtualinherited |
Get the default vector tags associated with this system.
Reimplemented in NonlinearEigenSystem, and DisplacedSystem.
Definition at line 303 of file SystemBase.h.
Referenced by DisplacedSystem::defaultVectorTags(), NonlinearEigenSystem::defaultVectorTags(), and SystemBase::disassociateDefaultVectorTags().
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virtualinherited |
Disassociate the matrices associated with the default matrix tags of this system.
Reimplemented in DisplacedSystem.
Definition at line 1093 of file SystemBase.C.
Referenced by DisplacedSystem::disassociateDefaultMatrixTags().
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virtualinherited |
Disassociate the vectors associated with the default vector tags of this system.
Reimplemented in DisplacedSystem.
Definition at line 998 of file SystemBase.C.
Referenced by DisplacedSystem::disassociateDefaultVectorTags().
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virtualinherited |
Disassociate a matrix from a tag.
Reimplemented in DisplacedSystem.
Definition at line 1071 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeJacobian(), FEProblemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTag(), FEProblemBase::computeLinearSystemSys(), FEProblemBase::computeResidualAndJacobian(), SystemBase::disassociateDefaultMatrixTags(), and DisplacedSystem::disassociateMatrixFromTag().
Disassociate any matrix that is associated with a given tag.
Reimplemented in DisplacedSystem.
Definition at line 1082 of file SystemBase.C.
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virtualinherited |
Disassociate a given vector from a given tag.
Reimplemented in DisplacedSystem.
Referenced by FEProblemBase::computeLinearSystemSys(), FEProblemBase::computeResidualAndJacobian(), FEProblemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTag(), FEProblemBase::computeResidualTag(), FEProblemBase::computeResidualType(), SystemBase::disassociateDefaultVectorTags(), DisplacedSystem::disassociateVectorFromTag(), and CentralDifference::initialSetup().
Disassociate any vector that is associated with a given tag.
Reimplemented in DisplacedSystem.
Definition at line 987 of file SystemBase.C.
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virtualinherited |
Gets writeable reference to the dof map.
Definition at line 1165 of file SystemBase.C.
Referenced by NonlinearSystemBase::assembleScalingVector(), MooseApp::attachRelationshipManagers(), SystemBase::augmentSendList(), NonlinearSystemBase::augmentSparsity(), NonlinearSystemBase::computeScaling(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), Adaptivity::init(), NonlinearEigenSystem::initializeCondensedMatrices(), ActivateElementsUserObjectBase::initSolutions(), PNGOutput::makeMeshFunc(), GhostingUserObject::meshChanged(), TableOutput::outputScalarVariables(), Exodus::outputScalarVariables(), and ElementSubdomainModifierBase::setOldAndOlderSolutions().
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virtualinherited |
Gets const reference to the dof map.
Definition at line 1171 of file SystemBase.C.
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 248 of file SystemBase.h.
Referenced by DisplacedSystem::duDotDotDu(), and MooseVariableScalar::reinit().
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 1668 of file SystemBase.C.
Referenced by DisplacedSystem::duDotDu(), and MooseVariableScalar::reinit().
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 247 of file SystemBase.h.
Referenced by DisplacedSystem::duDotDus().
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inline |
Definition at line 235 of file AuxiliarySystem.h.
|
inline |
Definition at line 223 of file AuxiliarySystem.h.
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inline |
Definition at line 229 of file AuxiliarySystem.h.
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inlineinherited |
Definition at line 103 of file SystemBase.h.
Referenced by DMMooseGetEmbedding_Private(), and DMSetUp_Moose_Pre().
|
inlineinherited |
Definition at line 104 of file SystemBase.h.
flushes all matrices associated to tags.
Flush assembles the matrix but doesn't shrink memory allocation
Definition at line 1051 of file SystemBase.C.
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inherited |
Returns a field variable pointer - this includes finite volume variables.
Definition at line 117 of file SystemBase.C.
Referenced by BoundsBase::BoundsBase(), Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), and Assembly::copyShapes().
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inherited |
Returns a field variable pointer - this includes finite volume variables.
Definition at line 138 of file SystemBase.C.
std::set< std::string > AuxiliarySystem::getDependObjects | ( | ExecFlagType | type | ) |
Get a list of dependent UserObjects for this exec type.
type | Execution flag type |
Definition at line 417 of file AuxiliarySystem.C.
Referenced by groupUserObjects().
std::set< std::string > AuxiliarySystem::getDependObjects | ( | ) |
Definition at line 502 of file AuxiliarySystem.C.
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inherited |
Gets a reference to a variable of with specified name.
This excludes and cannot return finite volume variables.
tid | Thread id |
var_name | variable name |
Definition at line 110 of file SystemBase.C.
Referenced by Marker::getMarkerValue().
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inherited |
Gets a reference to a variable with specified number.
This excludes and cannot return finite volume variables.
tid | Thread id |
var_number | libMesh variable number |
Definition at line 131 of file SystemBase.C.
|
inherited |
Return a finite volume variable.
Definition at line 124 of file SystemBase.C.
|
virtualinherited |
Get a raw SparseMatrix.
Reimplemented in DisplacedSystem.
Definition at line 1007 of file SystemBase.C.
Referenced by Assembly::addCachedJacobian(), NonlinearSystemBase::addImplicitGeometricCouplingEntries(), Assembly::addJacobianCoupledVarPair(), Assembly::addJacobianLowerD(), Assembly::addJacobianNeighbor(), Assembly::addJacobianNeighborLowerD(), Assembly::addJacobianNonlocal(), SystemBase::addMatrix(), SystemBase::closeTaggedMatrices(), NonlinearSystemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTags(), LinearSystem::computeLinearSystemInternal(), FEProblemBase::computeLinearSystemTags(), FEProblemBase::computeResidualAndJacobian(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::constraintJacobians(), SystemBase::disassociateMatrixFromTag(), NonlinearSystemBase::enforceNodalConstraintsJacobian(), SystemBase::flushTaggedMatrices(), DisplacedSystem::getMatrix(), LinearSystemContributionObject::linkTaggedVectorsAndMatrices(), MooseVariableScalar::reinit(), Assembly::setCachedJacobian(), and Assembly::zeroCachedJacobian().
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virtualinherited |
Get a raw SparseMatrix.
Reimplemented in DisplacedSystem.
Definition at line 1025 of file SystemBase.C.
|
inlineinherited |
Returns the maximum number of all variables on the system.
Definition at line 868 of file SystemBase.h.
|
inlineinherited |
Gets the maximum number of dofs used by any one variable on any one element.
Definition at line 586 of file SystemBase.h.
Referenced by Moose::globalDofIndexToDerivative().
|
inlineinherited |
Gets the maximum number of dofs used by any one variable on any one node.
Definition at line 593 of file SystemBase.h.
|
overridevirtual |
Get the minimum quadrature order for evaluating elemental auxiliary variables.
Reimplemented from SystemBase.
Definition at line 765 of file AuxiliarySystem.C.
|
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 144 of file SystemBase.C.
Referenced by Assembly::addJacobianOffDiagScalar(), ODEKernel::computeOffDiagJacobianScalar(), VectorKernel::computeOffDiagJacobianScalar(), ArrayKernel::computeOffDiagJacobianScalar(), IntegratedBC::computeOffDiagJacobianScalar(), VectorIntegratedBC::computeOffDiagJacobianScalar(), Kernel::computeOffDiagJacobianScalar(), ArrayIntegratedBC::computeOffDiagJacobianScalar(), ScalarLagrangeMultiplier::computeOffDiagJacobianScalar(), MortarScalarBase::computeOffDiagJacobianScalar(), KernelScalarBase::computeOffDiagJacobianScalarLocal(), KernelScalarBase::computeScalarOffDiagJacobianScalar(), MortarScalarBase::computeScalarOffDiagJacobianScalar(), DMMooseSetVariables(), Assembly::init(), ReferenceResidualConvergence::initialSetup(), and NonlinearSystemBase::setupScalingData().
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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 153 of file SystemBase.C.
|
inlineinherited |
Definition at line 757 of file SystemBase.h.
Referenced by Assembly::addResidualScalar(), ODEKernel::computeJacobian(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), computeScalarVars(), Assembly::init(), SystemBase::initSolutionState(), NonlinearThread::onElement(), Assembly::prepareOffDiagScalar(), and Assembly::prepareScalar().
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inherited |
|
inlineinherited |
Definition at line 762 of file SystemBase.h.
Referenced by NonlinearSystemBase::checkKernelCoverage(), and SystemBase::getSubdomainsForVar().
|
inherited |
Get the block where a variable of this system is defined.
var_name | The name of the variable |
Definition at line 1674 of file SystemBase.C.
|
inherited |
Retrieve the time integrator that integrates the given variable's equation.
Definition at line 1650 of file SystemBase.C.
Referenced by AB2PredictorCorrector::estimateTimeError().
|
inherited |
Definition at line 1662 of file SystemBase.C.
|
inherited |
Gets a reference to a variable of with specified name.
tid | Thread id |
var_name | variable name |
Definition at line 89 of file SystemBase.C.
Referenced by AdaptivityAction::act(), Assembly::addJacobianBlockNonlocal(), FEProblemBase::addJacobianBlockTags(), NonlocalKernel::computeNonlocalOffDiagJacobian(), NonlocalIntegratedBC::computeNonlocalOffDiagJacobian(), Assembly::copyFaceShapes(), Assembly::copyNeighborShapes(), Assembly::copyShapes(), SystemBase::copyVars(), DMMooseSetVariables(), FieldSplitPreconditioner::FieldSplitPreconditioner(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), NodeElemConstraint::getConnectedDofIndices(), NodeFaceConstraint::getConnectedDofIndices(), SystemBase::getSubdomainsForVar(), ResidualObject::getVariable(), SubProblem::getVariableHelper(), Assembly::init(), NodalNormalsPreprocessor::initialize(), ExplicitTimeIntegrator::initialSetup(), ReferenceResidualConvergence::initialSetup(), LinearSystem::initialSetup(), Assembly::initNonlocalCoupling(), PNGOutput::makeMeshFunc(), MooseStaticCondensationPreconditioner::MooseStaticCondensationPreconditioner(), UpdateErrorVectorsThread::onElement(), Assembly::prepareBlock(), Assembly::prepareBlockNonlocal(), AddPeriodicBCAction::setPeriodicVars(), NonlinearSystemBase::setupScalingData(), and VariableCondensationPreconditioner::VariableCondensationPreconditioner().
|
inherited |
Gets a reference to a variable with specified number.
tid | Thread id |
var_number | libMesh variable number |
Definition at line 99 of file SystemBase.C.
|
virtualinherited |
Get the block where a variable of this system is defined.
var_number | The number of the variable |
Definition at line 163 of file SystemBase.C.
Referenced by PhysicsBasedPreconditioner::addSystem().
|
inlineinherited |
Get the global dof indices of a variable, this needs to be called after the indices have been set by setVariableGlobalDoFs
Definition at line 843 of file SystemBase.h.
|
inlineinherited |
Definition at line 861 of file SystemBase.h.
Referenced by MooseEigenSystem::buildSystemDoFIndices(), NonlinearSystemBase::checkKernelCoverage(), MFEMProblem::getAuxVariableNames(), SystemBase::hasVariable(), SystemBase::isArrayVariable(), AddPeriodicBCAction::setPeriodicVars(), and SingleMatrixPreconditioner::SingleMatrixPreconditioner().
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inlineinherited |
Definition at line 752 of file SystemBase.h.
Referenced by Assembly::addJacobianOffDiagScalar(), Assembly::addResidual(), Assembly::addResidualLower(), Assembly::addResidualNeighbor(), Assembly::cacheResidual(), Assembly::cacheResidualLower(), Assembly::cacheResidualNeighbor(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), Assembly::init(), Assembly::initNonlocalCoupling(), SystemBase::initSolutionState(), ComputeLinearFVGreenGaussGradientFaceThread::operator()(), Assembly::prepareLowerD(), Assembly::prepareNeighbor(), Assembly::prepareOffDiagScalar(), Assembly::prepareResidual(), Assembly::setResidual(), and Assembly::setResidualNeighbor().
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virtualinherited |
Get a raw NumericVector by name.
Get a raw NumericVector with the given name.
Reimplemented in DisplacedSystem.
Definition at line 916 of file SystemBase.C.
Referenced by Assembly::addCachedResiduals(), Assembly::addResidual(), Assembly::addResidualLower(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), NonlinearSystemBase::assembleScalingVector(), SystemBase::closeTaggedVector(), FEProblemBase::computeBounds(), FEProblemBase::computeNearNullSpace(), FEProblemBase::computeNullSpace(), NonlinearSystemBase::computeResidualAndJacobianTags(), NonlinearSystemBase::computeResidualTags(), CentralDifference::computeTimeDerivatives(), FEProblemBase::computeTransposeNullSpace(), DisplacedSystem::getVector(), Assembly::hasScalingVector(), LinearSystemContributionObject::linkTaggedVectorsAndMatrices(), SystemBase::needSolutionState(), ReferenceResidualConvergence::ReferenceResidualConvergence(), MooseVariableScalar::reinit(), SecantSolve::saveVariableValues(), SteffensenSolve::saveVariableValues(), PicardSolve::saveVariableValues(), NonlinearSystemBase::setPreviousNewtonSolution(), TaggingInterface::setResidual(), SystemBase::solutionPreviousNewton(), SystemBase::solutionState(), MultiAppDofCopyTransfer::transfer(), SecantSolve::transformVariables(), SteffensenSolve::transformVariables(), PicardSolve::transformVariables(), and SystemBase::zeroTaggedVector().
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virtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 922 of file SystemBase.C.
|
virtualinherited |
Get a raw NumericVector by tag.
Reimplemented in DisplacedSystem.
Definition at line 928 of file SystemBase.C.
|
virtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 946 of file SystemBase.C.
|
inlineinherited |
Reference to the container vector which hold gradients at dofs (if it can be interpreted).
Mainly used for finite volume systems.
Definition at line 931 of file SystemBase.h.
|
inlinevirtualinherited |
Check if the tagged matrix exists in the system.
Reimplemented in DisplacedSystem.
Definition at line 351 of file SystemBase.h.
Referenced by SystemBase::activeAllMatrixTags(), Assembly::addCachedJacobian(), NonlinearSystemBase::addImplicitGeometricCouplingEntries(), Assembly::addJacobianCoupledVarPair(), Assembly::addJacobianLowerD(), Assembly::addJacobianNeighbor(), Assembly::addJacobianNeighborLowerD(), Assembly::addJacobianNonlocal(), SystemBase::addMatrix(), Assembly::cacheJacobian(), Assembly::cacheJacobianBlockNonzero(), Assembly::cacheJacobianCoupledVarPair(), Assembly::cacheJacobianMortar(), Assembly::cacheJacobianNeighbor(), Assembly::cacheJacobianNonlocal(), SystemBase::closeTaggedMatrices(), NonlinearSystemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTags(), FEProblemBase::computeResidualAndJacobian(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::constraintJacobians(), SystemBase::disassociateMatrixFromTag(), NonlinearSystemBase::enforceNodalConstraintsJacobian(), SystemBase::flushTaggedMatrices(), SystemBase::getMatrix(), DisplacedSystem::hasMatrix(), MooseVariableScalar::reinit(), SystemBase::removeMatrix(), SubProblem::selectMatrixTagsFromSystem(), Assembly::setCachedJacobian(), and Assembly::zeroCachedJacobian().
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virtualinherited |
Definition at line 859 of file SystemBase.C.
Referenced by MortarScalarBase::computeJacobian(), NonlinearSystemBase::computeJacobianInternal(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), SystemBase::copyVars(), ExplicitTimeIntegrator::initialSetup(), NonlinearEigenSystem::postAddResidualObject(), AddPeriodicBCAction::setPeriodicVars(), and NonlinearSystemBase::setupScalingData().
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inlinevirtualinherited |
Whether or not the system has the solution state (0 = current, 1 = old, 2 = older, etc).
Reimplemented in DisplacedSystem.
Definition at line 1081 of file SystemBase.h.
Referenced by PointwiseRenormalizeVector::execute(), PointwiseRenormalizeVector::finalize(), DisplacedSystem::hasSolutionState(), SystemBase::needSolutionState(), SystemBase::restoreSolutions(), ElementSubdomainModifierBase::setOldAndOlderSolutions(), and SystemBase::solutionState().
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inlineinherited |
Whether or not there are variables to be restarted from an Exodus mesh file.
Definition at line 884 of file SystemBase.h.
|
virtualinherited |
Query a system for a variable.
var_name | name of the variable |
Definition at line 834 of file SystemBase.C.
Referenced by ADDGKernel::ADDGKernel(), ArrayDGKernel::ArrayDGKernel(), SystemBase::copyVars(), DGKernel::DGKernel(), DMMooseSetVariables(), FEProblemBase::duplicateVariableCheck(), SubProblem::getVariableHelper(), SubProblem::hasAuxiliaryVariable(), ExplicitTimeIntegrator::initialSetup(), InterfaceKernelTempl< T >::InterfaceKernelTempl(), PNGOutput::makeMeshFunc(), MultiAppVariableValueSamplePostprocessorTransfer::MultiAppVariableValueSamplePostprocessorTransfer(), NonlinearSystemBase::setupScalingData(), and Coupleable::writableCoupledValue().
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inherited |
Check if the named vector exists in the system.
Definition at line 907 of file SystemBase.C.
Referenced by FEProblemBase::addCachedResidualDirectly(), Assembly::addCachedResiduals(), Assembly::addResidual(), Assembly::addResidualLower(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), NonlinearSystemBase::assembleScalingVector(), Assembly::cacheResidual(), Assembly::cacheResidualLower(), Assembly::cacheResidualNeighbor(), SystemBase::closeTaggedVector(), FEProblemBase::computeBounds(), NonlinearSystemBase::computeResidualTags(), CentralDifference::computeTimeDerivatives(), SystemBase::getVector(), DisplacedSystem::hasVector(), MooseVariableScalar::reinit(), SystemBase::removeVector(), SubProblem::selectVectorTagsFromSystem(), NonlinearSystemBase::setPreviousNewtonSolution(), TaggingInterface::setResidual(), SystemBase::solutionPreviousNewton(), and SystemBase::zeroTaggedVector().
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inlinevirtualinherited |
Check if the tagged vector exists in the system.
Reimplemented in DisplacedSystem.
Definition at line 272 of file SystemBase.h.
|
inlinevirtualinherited |
Called only once, just before the solve begins so objects can do some precalculations.
Definition at line 173 of file SystemBase.h.
|
overridevirtual |
Setup Functions.
Reimplemented from SystemBase.
Definition at line 66 of file AuxiliarySystem.C.
|
virtualinherited |
Initializes the solution state.
Reimplemented in DisplacedSystem.
Definition at line 1354 of file SystemBase.C.
Referenced by DisplacedSystem::initSolutionState().
|
virtualinherited |
If a variable is an array variable.
Definition at line 847 of file SystemBase.C.
|
virtualinherited |
Definition at line 868 of file SystemBase.C.
Referenced by Assembly::init(), ReferenceResidualConvergence::initialSetup(), and Assembly::initNonlocalCoupling().
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overridevirtual |
Reimplemented from SystemBase.
Definition at line 155 of file AuxiliarySystem.C.
|
virtualinherited |
If or not a matrix tag is active.
Definition at line 1151 of file SystemBase.C.
|
inlineinherited |
Definition at line 99 of file SystemBase.h.
Referenced by CreateDisplacedProblemAction::addProxyRelationshipManagers(), DMMooseGetEmbedding_Private(), DMSetUp_Moose_Pre(), SolutionIC::initialSetup(), ComputeNodalUserObjectsThread::onNode(), ComputeNodalKernelsThread::onNode(), and ComputeNodalKernelJacobiansThread::onNode().
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inlineinherited |
Definition at line 100 of file SystemBase.h.
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virtualinherited |
Definition at line 1330 of file SystemBase.C.
Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addConstraint(), NonlinearSystemBase::addDamper(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), NonlinearSystemBase::addHDGKernel(), NonlinearSystemBase::addInterfaceKernel(), MooseEigenSystem::addKernel(), addKernel(), NonlinearSystemBase::addKernel(), SystemBase::addMatrix(), NonlinearSystemBase::addNodalKernel(), addScalarKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), SystemBase::addTimeIntegrator(), addVariable(), SystemBase::addVariable(), DiffusionLHDGAssemblyHelper::checkCoupling(), SystemBase::closeTaggedVector(), LinearSystem::computeGradients(), LinearSystem::computeLinearSystemTags(), DisplacedProblem::DisplacedProblem(), SystemBase::getMatrix(), NonlinearSystemBase::getSplit(), DisplacedSystem::getVector(), SystemBase::getVector(), SystemBase::hasVector(), MooseStaticCondensationPreconditioner::initialSetup(), LinearSystem::initialSetup(), Moose::PetscSupport::petscSetDefaults(), NonlinearEigenSystem::postAddResidualObject(), SystemBase::removeMatrix(), SystemBase::removeVector(), SystemBase::solutionState(), LinearSystem::solve(), LinearTimeIntegratorInterface::timeDerivativeMatrixContribution(), LinearTimeIntegratorInterface::timeDerivativeRHSContribution(), and SystemBase::zeroTaggedVector().
bool AuxiliarySystem::needMaterialOnSide | ( | BoundaryID | bnd_id | ) |
Indicated whether this system needs material properties on boundaries.
Definition at line 783 of file AuxiliarySystem.C.
|
virtualinherited |
Registers that the solution state state
is needed.
Reimplemented in DisplacedSystem.
Definition at line 1428 of file SystemBase.C.
Referenced by EigenExecutionerBase::EigenExecutionerBase(), SystemBase::initSolutionState(), DisplacedSystem::needSolutionState(), and SystemBase::solutionState().
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inherited |
Get the number of field variables in this system.
Definition at line 883 of file SystemBase.C.
Referenced by SystemBase::nVariables().
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inherited |
Get the number of finite volume variables in this system.
Definition at line 893 of file SystemBase.C.
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inline |
Definition at line 217 of file AuxiliarySystem.h.
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inline |
Definition at line 205 of file AuxiliarySystem.h.
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inline |
Definition at line 211 of file AuxiliarySystem.h.
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inlinevirtualinherited |
Reimplemented in NonlinearSystemBase, and DisplacedSystem.
Definition at line 293 of file SystemBase.h.
Referenced by SystemBase::defaultVectorTags(), and DisplacedSystem::nonTimeVectorTag().
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inherited |
Gets the number of this system.
Definition at line 1159 of file SystemBase.C.
Referenced by SetupResidualDebugAction::act(), FEProblemBase::addCachedResidualDirectly(), FEProblemBase::addJacobian(), FEProblemBase::addJacobianBlockTags(), FEProblemBase::addJacobianLowerD(), FEProblemBase::addJacobianNeighbor(), FEProblemBase::addJacobianNeighborLowerD(), FEProblemBase::addJacobianOffDiagScalar(), FEProblemBase::addJacobianScalar(), FEProblemBase::addResidual(), FEProblemBase::addResidualLower(), FEProblemBase::addResidualNeighbor(), FEProblemBase::addResidualScalar(), SystemBase::addScalingVector(), ADKernelTempl< T >::ADKernelTempl(), ElementSubdomainModifierBase::applyIC(), ArrayKernel::ArrayKernel(), NonlinearSystemBase::assembleScalingVector(), NonlinearEigenSystem::attachPreconditioner(), DiffusionLHDGAssemblyHelper::checkCoupling(), SolverSystem::compute(), MooseVariableScalar::computeAD(), FEProblemBase::computeBounds(), Assembly::computeFaceMap(), InternalSideIndicatorBase::computeIndicator(), ArrayNodalBC::computeJacobian(), VectorNodalBC::computeJacobian(), NodalBC::computeJacobian(), FVBoundaryScalarLagrangeMultiplierConstraint::computeJacobian(), FVFluxBC::computeJacobian(), FVFluxKernel::computeJacobian(), FVInterfaceKernel::computeJacobian(), FEProblemBase::computeJacobianBlock(), NonlinearSystemBase::computeJacobianInternal(), FEProblemBase::computeJacobianTags(), LinearSystem::computeLinearSystemInternal(), FEProblemBase::computeNearNullSpace(), NonlinearSystemBase::computeNodalBCsResidualAndJacobian(), FEProblemBase::computeNullSpace(), VectorNodalBC::computeOffDiagJacobian(), ArrayNodalBC::computeOffDiagJacobian(), NodalBC::computeOffDiagJacobian(), NodalKernel::computeOffDiagJacobian(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), ComputeFullJacobianThread::computeOnInterface(), ComputeFullJacobianThread::computeOnInternalFace(), FEProblemBase::computePostCheck(), FVOrthogonalBoundaryDiffusion::computeQpResidual(), FVBoundaryScalarLagrangeMultiplierConstraint::computeResidual(), FVFluxKernel::computeResidual(), FVInterfaceKernel::computeResidual(), Kernel::computeResidualAndJacobian(), NodalBC::computeResidualAndJacobian(), IntegratedBC::computeResidualAndJacobian(), FEProblemBase::computeResidualAndJacobian(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::computeResidualInternal(), FEProblemBase::computeResidualL2Norm(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::computeScaling(), Assembly::computeSinglePointMapAD(), FEProblemBase::computeTransposeNullSpace(), DebugResidualAux::computeValue(), NearestNodeValueAux::computeValue(), SlepcEigenSolverConfiguration::configure_solver(), NonlinearSystemBase::constraintJacobians(), LinearSystem::containsTimeKernel(), Coupleable::coupled(), FEProblemBase::currentLinearSysNum(), FEProblemBase::currentNlSysNum(), PseudoTimestep::currentResidualNorm(), ComputeResidualThread::determineObjectWarehouses(), ComputeResidualAndJacobianThread::determineObjectWarehouses(), Moose::doDerivatives(), VariableResidual::execute(), NodalNormalsCorner::execute(), NodalNormalsEvaluator::execute(), GreaterThanLessThanPostprocessor::execute(), NodalNormalsPreprocessor::execute(), ExplicitTimeIntegrator::ExplicitTimeIntegrator(), InternalSideIndicatorBase::finalize(), NumNonlinearIterations::finalize(), BoundsBase::getDoFIndex(), NonlinearSystemBase::getNodeDofs(), NonlinearEigenSystem::getSNES(), SystemBase::getSubdomainsForVar(), NumLinearIterations::getValue(), NumResidualEvaluations::getValue(), Residual::getValue(), Moose::globalDofIndexToDerivative(), FVBoundaryCondition::hasFaceSide(), ExplicitTimeIntegrator::init(), ExplicitTimeIntegrator::initialSetup(), NonlinearSystemBase::initialSetup(), ActivateElementsUserObjectBase::initSolutions(), EigenExecutionerBase::inversePowerIteration(), Kernel::Kernel(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionA(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionAB(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionB(), Moose::SlepcSupport::mooseSlepcEigenFormJacobianA(), MooseStaticCondensationPreconditioner::MooseStaticCondensationPreconditioner(), MooseVariableInterface< Real >::MooseVariableInterface(), EigenExecutionerBase::nonlinearSolve(), ComputeDiracThread::onElement(), ComputeNodalKernelBCJacobiansThread::onNode(), ComputeNodalKernelJacobiansThread::onNode(), VariableResidualNormsDebugOutput::output(), Moose::PetscSupport::petscLinearConverged(), Moose::PetscSupport::petscNonlinearConverged(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), PointwiseRenormalizeVector::PointwiseRenormalizeVector(), ComputeJacobianThread::postElement(), FEProblemBase::prepareAssembly(), SystemBase::prepareFace(), FEProblemBase::prepareFaceShapes(), FEProblemBase::prepareNeighborShapes(), FEProblemBase::prepareShapes(), FEProblemBase::reinitDirac(), FEProblemBase::reinitOffDiagScalars(), NonlinearSystem::residualAndJacobianTogether(), FEProblemBase::setResidual(), FEProblemBase::setResidualNeighbor(), PhysicsBasedPreconditioner::setup(), FVInterfaceKernel::setupData(), NonlinearSystemBase::shouldEvaluatePreSMOResidual(), ActuallyExplicitEuler::solve(), NonlinearEigenSystem::solve(), LStableDirk2::solve(), LStableDirk3::solve(), ImplicitMidpoint::solve(), ExplicitTVDRK2::solve(), LStableDirk4::solve(), AStableDirk4::solve(), ExplicitRK2::solve(), ExplicitSSPRungeKutta::solveStage(), NonlinearThread::subdomainChanged(), UserObject::systemNumber(), MultiAppDofCopyTransfer::transferDofObject(), FVFluxBC::uOnGhost(), FVFluxBC::uOnUSub(), FVFluxBC::updateCurrentFace(), and MortarConstraintBase::zeroInactiveLMDofs().
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virtualinherited |
Get the number of variables in this system.
Definition at line 874 of file SystemBase.C.
Referenced by AdaptivityAction::act(), FieldSplitPreconditioner::FieldSplitPreconditioner(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), NonlinearSystemBase::getNodeDofs(), Assembly::init(), ExplicitTimeIntegrator::initialSetup(), MaxVarNDofsPerElem::onElement(), MaxVarNDofsPerNode::onNode(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), SingleMatrixPreconditioner::SingleMatrixPreconditioner(), and variableWiseRelativeSolutionDifferenceNorm().
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inherited |
Get the PerfGraph.
Definition at line 78 of file PerfGraphInterface.C.
Referenced by CommonOutputAction::act(), PerfGraphData::finalize(), and PerfGraphOutput::output().
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inlinevirtualinherited |
Reimplemented in NonlinearEigenSystem.
Definition at line 162 of file SystemBase.h.
Referenced by NonlinearEigenSystem::postInit().
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inherited |
Definition at line 1680 of file SystemBase.C.
Referenced by MoosePreconditioner::initialSetup().
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inlinevirtualinherited |
This is called prior to the libMesh system has been init'd.
MOOSE system wrappers can use this method to add vectors and matrices to the libMesh system
Reimplemented in NonlinearSystemBase, and SolverSystem.
Definition at line 156 of file SystemBase.h.
Referenced by SolverSystem::preInit().
Prepare the system for use.
tid | ID of the thread |
Definition at line 255 of file SystemBase.C.
Referenced by SubProblem::reinitElemFaceRef().
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 278 of file SystemBase.C.
Prepare the system for use for lower dimensional elements.
tid | ID of the thread |
Definition at line 331 of file SystemBase.C.
Referenced by SubProblem::reinitLowerDElem().
Prepare the system for use.
tid | ID of the thread |
Definition at line 323 of file SystemBase.C.
Referenced by SubProblem::reinitNeighborFaceRef().
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inherited |
Retrieve the time integrator that integrates the given variable's equation.
If no suitable time integrator is found (this could happen for instance if we're solving a non-transient problem), then a nullptr will be returned
Definition at line 1640 of file SystemBase.C.
Referenced by SystemBase::getTimeIntegrator(), HDGKernel::HDGKernel(), and MooseVariableData< OutputType >::MooseVariableData().
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protectedinherited |
Call to register a named section for timing.
section_name | The name of the code section to be timed |
level | The importance of the timer - lower is more important (0 will always come out) |
Definition at line 53 of file PerfGraphInterface.C.
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protectedinherited |
Call to register a named section for timing.
section_name | The name of the code section to be timed |
level | The importance of the timer - lower is more important (0 will always come out) |
live_message | The message to be printed to the screen during execution |
print_dots | Whether or not progress dots should be printed for this section |
Definition at line 64 of file PerfGraphInterface.C.
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inlinevirtualinherited |
Reinitialize the system when the degrees of freedom in this system have changed.
This is called after the libMesh system has been reinit'd
Reimplemented in NonlinearEigenSystem.
Definition at line 168 of file SystemBase.h.
Referenced by NonlinearEigenSystem::reinit().
Reinit an element assembly info.
elem | Which element we are reinitializing for |
tid | ID of the thread |
Reimplemented from SystemBase.
Definition at line 329 of file AuxiliarySystem.C.
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overridevirtual |
Reinit assembly info for a side of an element.
elem | The element |
side | Side of of the element |
tid | Thread ID |
Reimplemented from SystemBase.
Definition at line 342 of file AuxiliarySystem.C.
Compute the values of the variables on the lower dimensional element.
Definition at line 382 of file SystemBase.C.
Referenced by SubProblem::reinitLowerDElem().
Compute the values of the variables at all the current points.
Definition at line 374 of file SystemBase.C.
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virtualinherited |
Compute the values of the variables at all the current points.
Definition at line 366 of file SystemBase.C.
Referenced by SubProblem::reinitNeighborFaceRef().
Reinit nodal assembly info.
node | Node to reinit for |
tid | Thread ID |
Definition at line 390 of file SystemBase.C.
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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 402 of file SystemBase.C.
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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 414 of file SystemBase.C.
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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 425 of file SystemBase.C.
|
virtualinherited |
Reinit scalar varaibles.
tid | Thread ID |
reinit_for_derivative_reordering | A flag indicating whether we are reinitializing for the purpose of re-ordering derivative information for ADNodalBCs |
Definition at line 436 of file SystemBase.C.
Removes a matrix with a given tag.
tag_name | The name of the tag |
Definition at line 582 of file SystemBase.C.
|
inherited |
Remove a vector from the system with the given name.
Definition at line 1324 of file SystemBase.C.
Referenced by SystemBase::restoreOldSolutions().
Remove a solution length vector from the system with the specified TagID.
tag_id | Tag ID |
Definition at line 692 of file SystemBase.C.
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inlinevirtualinherited |
Reimplemented in NonlinearSystemBase, and DisplacedSystem.
Definition at line 427 of file SystemBase.h.
Referenced by DisplacedSystem::residualCopy().
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inlinevirtualinherited |
Reimplemented in NonlinearSystemBase, and DisplacedSystem.
Definition at line 431 of file SystemBase.h.
Referenced by DisplacedSystem::residualGhosted().
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overridevirtual |
Reimplemented from SystemBase.
Definition at line 173 of file AuxiliarySystem.C.
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inlinevirtualinherited |
Reimplemented in NonlinearSystemBase, and DisplacedSystem.
Definition at line 298 of file SystemBase.h.
Referenced by SystemBase::defaultVectorTags(), and DisplacedSystem::residualVectorTag().
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virtualinherited |
Restore the old and older solutions when the saved solutions present.
Definition at line 534 of file SystemBase.C.
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virtualinherited |
Restore current solutions (call after your solve failed)
Reimplemented in SolverSystem.
Definition at line 1307 of file SystemBase.C.
Referenced by SolverSystem::restoreSolutions().
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virtualinherited |
Save the old and older solutions.
Definition at line 502 of file SystemBase.C.
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virtualinherited |
Returns a reference to a serialized version of the solution vector for this subproblem.
Reimplemented in DisplacedSystem.
Definition at line 1613 of file SystemBase.C.
Referenced by PNGOutput::calculateRescalingValues(), PNGOutput::makeMeshFunc(), and DisplacedSystem::serializedSolution().
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virtual |
Definition at line 356 of file AuxiliarySystem.C.
Referenced by compute().
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inherited |
Set the active vector tags for the scalar variables.
Definition at line 1593 of file SystemBase.C.
Referenced by SubProblem::setActiveScalarVariableCoupleableVectorTags().
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inherited |
Set the active vector tags for the variables.
Definition at line 1587 of file SystemBase.C.
Referenced by SubProblem::setActiveFEVariableCoupleableVectorTags().
void AuxiliarySystem::setScalarVariableCoupleableTags | ( | ExecFlagType | type | ) |
Definition at line 586 of file AuxiliarySystem.C.
Referenced by computeScalarVars().
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inherited |
set all the global dof indices for a variable
var_name | The name of the variable |
Definition at line 185 of file SystemBase.C.
|
inlineinherited |
Sets the verbose flag.
[in] | verbose | Verbose flag |
Definition at line 134 of file SystemBase.h.
Referenced by Executioner::Executioner().
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inlineinherited |
Definition at line 195 of file SystemBase.h.
Referenced by Adaptivity::adaptMesh(), TransientMultiApp::appTransferVector(), MooseEigenSystem::combineSystemSolution(), NonlinearSystemBase::computeDamping(), computeElementalVarsHelper(), NonlinearSystemBase::computeJacobianInternal(), computeMortarNodalVars(), NonlinearSystemBase::computeNodalBCs(), computeNodalVarsHelper(), NonlinearSystemBase::computeResidualTags(), computeScalarVars(), NonlinearSystemBase::constraintResiduals(), SystemBase::copyVars(), MultiAppPostprocessorToAuxScalarTransfer::execute(), MultiAppScalarToAuxScalarTransfer::execute(), NodalNormalsCorner::execute(), NodalNormalsEvaluator::execute(), MultiAppVariableValueSamplePostprocessorTransfer::execute(), NodalNormalsPreprocessor::execute(), NodalNormalsCorner::finalize(), NodalNormalsEvaluator::finalize(), NodalNormalsPreprocessor::finalize(), NodalNormalsEvaluator::initialize(), NodalNormalsCorner::initialize(), NodalNormalsPreprocessor::initialize(), MooseEigenSystem::initSystemSolution(), ComputeMarkerThread::onElement(), ComputeIndicatorThread::onElement(), ComputeUserObjectsThread::onElement(), ComputeNodalUserObjectsThread::onNode(), FEProblemBase::projectInitialConditionOnCustomRange(), FEProblemBase::projectSolution(), Transient::relativeSolutionDifferenceNorm(), MultiApp::restore(), SystemBase::restoreSolutions(), SecantSolve::saveVariableValues(), SteffensenSolve::saveVariableValues(), PicardSolve::saveVariableValues(), MooseEigenSystem::scaleSystemSolution(), serializeSolution(), NonlinearSystemBase::setConstraintSecondaryValues(), NonlinearSystemBase::setInitialSolution(), DisplacedSystem::solutionInternal(), NonlinearEigenSystem::solve(), MultiAppDofCopyTransfer::transfer(), SecantSolve::transformVariables(), SteffensenSolve::transformVariables(), PicardSolve::transformVariables(), variableWiseRelativeSolutionDifferenceNorm(), and SystemBase::zeroVariables().
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inlineinherited |
Definition at line 198 of file SystemBase.h.
|
inlineoverrideprotectedvirtual |
Internal getter for solution owned by libMesh.
Implements SystemBase.
Definition at line 201 of file AuxiliarySystem.h.
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inlineinherited |
Definition at line 196 of file SystemBase.h.
Referenced by MooseEigenSystem::combineSystemSolution(), CentralDifference::computeTimeDerivatives(), NonlinearSystemBase::constraintResiduals(), ActivateElementsUserObjectBase::initSolutions(), MooseEigenSystem::initSystemSolutionOld(), MooseVariableScalar::reinit(), Transient::relativeSolutionDifferenceNorm(), SystemBase::restoreSolutions(), ElementSubdomainModifierBase::setOldAndOlderSolutions(), ActuallyExplicitEuler::solve(), AdamsPredictor::timestepSetup(), and variableWiseRelativeSolutionDifferenceNorm().
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inlineinherited |
Definition at line 199 of file SystemBase.h.
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inlineinherited |
Definition at line 197 of file SystemBase.h.
Referenced by MooseEigenSystem::combineSystemSolution(), CentralDifference::computeTimeDerivatives(), ActivateElementsUserObjectBase::initSolutions(), MooseVariableScalar::reinit(), and ElementSubdomainModifierBase::setOldAndOlderSolutions().
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inlineinherited |
Definition at line 200 of file SystemBase.h.
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virtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 1345 of file SystemBase.C.
Referenced by copyCurrentIntoPreviousNL(), SystemBase::copyPreviousNonlinearSolutions(), and SystemBase::restoreSolutions().
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virtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 1336 of file SystemBase.C.
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virtualinherited |
Get a state of the solution (0 = current, 1 = old, 2 = older, etc).
If the state does not exist, it will be initialized in addition to any newer states before it that have not been initialized.
Reimplemented in DisplacedSystem.
Definition at line 1419 of file SystemBase.C.
Referenced by SystemBase::copyOldSolutions(), SystemBase::copyPreviousNonlinearSolutions(), PointwiseRenormalizeVector::execute(), PointwiseRenormalizeVector::finalize(), SystemBase::restoreOldSolutions(), SystemBase::saveOldSolutions(), SystemBase::solution(), SystemBase::solutionOld(), SystemBase::solutionOlder(), and DisplacedSystem::solutionState().
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virtualinherited |
Get a state of the solution (0 = current, 1 = old, 2 = older, etc).
Reimplemented in DisplacedSystem.
Definition at line 1390 of file SystemBase.C.
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inlineinherited |
Whether or not the solution states have been initialized via initSolutionState()
After the solution states have been initialized, additional solution states cannot be added.
Definition at line 897 of file SystemBase.h.
Referenced by ScalarKernelBase::uOld(), and AuxScalarKernel::uOld().
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 252 of file SystemBase.h.
Referenced by MooseVariableScalar::adUDot(), ActuallyExplicitEuler::computeTimeDerivatives(), ExplicitEuler::computeTimeDerivatives(), ImplicitEuler::computeTimeDerivatives(), NewmarkBeta::computeTimeDerivatives(), BDF2::computeTimeDerivatives(), CentralDifference::computeTimeDerivatives(), CrankNicolson::computeTimeDerivatives(), LStableDirk2::computeTimeDerivatives(), LStableDirk3::computeTimeDerivatives(), ImplicitMidpoint::computeTimeDerivatives(), ExplicitTVDRK2::computeTimeDerivatives(), LStableDirk4::computeTimeDerivatives(), AStableDirk4::computeTimeDerivatives(), ExplicitRK2::computeTimeDerivatives(), SystemBase::copyOldSolutions(), CrankNicolson::init(), CentralDifference::initialSetup(), MooseVariableScalar::reinit(), SystemBase::restoreSolutions(), DisplacedSystem::solutionUDot(), and MooseVariableScalar::uDot().
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 256 of file SystemBase.h.
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 253 of file SystemBase.h.
Referenced by NewmarkBeta::computeTimeDerivatives(), CentralDifference::computeTimeDerivatives(), SystemBase::copyOldSolutions(), CentralDifference::initialSetup(), MooseVariableScalar::reinit(), SystemBase::restoreSolutions(), DisplacedSystem::solutionUDotDot(), and MooseVariableScalar::uDotDot().
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 257 of file SystemBase.h.
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 255 of file SystemBase.h.
Referenced by NewmarkBeta::computeADTimeDerivatives(), NewmarkBeta::computeTimeDerivatives(), SystemBase::copyOldSolutions(), MooseVariableScalar::reinit(), SystemBase::restoreOldSolutions(), SystemBase::restoreSolutions(), SystemBase::saveOldSolutions(), DisplacedSystem::solutionUDotDotOld(), and MooseVariableScalar::uDotDotOld().
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 259 of file SystemBase.h.
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 254 of file SystemBase.h.
Referenced by NewmarkBeta::computeADTimeDerivatives(), NewmarkBeta::computeTimeDerivatives(), SystemBase::copyOldSolutions(), MooseVariableScalar::reinit(), SystemBase::restoreOldSolutions(), SystemBase::restoreSolutions(), SystemBase::saveOldSolutions(), DisplacedSystem::solutionUDotOld(), and MooseVariableScalar::uDotOld().
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inlinevirtualinherited |
Reimplemented in DisplacedSystem.
Definition at line 258 of file SystemBase.h.
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virtualinherited |
Solve the system (using libMesh magic)
Reimplemented in NonlinearSystemBase, LinearSystem, NonlinearEigenSystem, NonlinearSystem, DumpObjectsLinearSystem, and DumpObjectsNonlinearSystem.
Definition at line 1251 of file SystemBase.C.
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overridevirtual |
Reimplemented from SystemBase.
Definition at line 137 of file AuxiliarySystem.C.
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inlineinherited |
Definition at line 101 of file SystemBase.h.
Referenced by CreateDisplacedProblemAction::addProxyRelationshipManagers(), MooseVariableBase::allDofIndices(), NonlinearSystemBase::constraintJacobians(), NonlinearSystemBase::constraintResiduals(), Moose::globalDofIndexToDerivative(), NonlinearSystemBase::initialSetup(), MooseVariableScalar::MooseVariableScalar(), NonlinearSystemBase::overwriteNodeFace(), MooseVariableScalar::reinit(), NonlinearSystemBase::reinitNodeFace(), and NonlinearSystemBase::setConstraintSecondaryValues().
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inlineinherited |
Definition at line 102 of file SystemBase.h.
|
inlinevirtual |
Definition at line 119 of file AuxiliarySystem.h.
Referenced by ReferenceResidualConvergence::initialSetup(), and ReferenceResidualConvergence::updateReferenceResidual().
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inlineoverridevirtual |
Get the reference to the libMesh system.
Implements SystemBase.
Definition at line 121 of file AuxiliarySystem.h.
Referenced by TransientMultiApp::appTransferVector(), NonlinearSystemBase::constraintResiduals(), NodalNormalsPreprocessor::initialize(), ActivateElementsUserObjectBase::initSolutions(), ConsoleUtils::outputAuxiliarySystemInformation(), TransientMultiApp::setupApp(), and TransientMultiApp::solveStep().
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inlineoverridevirtual |
|
inlinevirtualinherited |
Return the Matrix Tag ID for System.
Reimplemented in NonlinearSystemBase, LinearSystem, and DisplacedSystem.
Definition at line 288 of file SystemBase.h.
Referenced by SystemBase::defaultMatrixTags(), and DisplacedSystem::systemMatrixTag().
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protectedinherited |
section_name
.Optionally adds a prefix if one is defined.
Definition at line 47 of file PerfGraphInterface.C.
Referenced by PerfGraphInterface::registerTimedSection().
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overridevirtual |
Reimplemented from SystemBase.
Definition at line 101 of file AuxiliarySystem.C.
|
inlinevirtualinherited |
Ideally, we should not need this API.
There exists a really bad API "addCachedResidualDirectly " in FEProblem and DisplacedProblem This API should go away once addCachedResidualDirectly is removed in the future Return Tag ID for Time
Reimplemented in NonlinearSystemBase, and DisplacedSystem.
Definition at line 283 of file SystemBase.h.
Referenced by SystemBase::defaultVectorTags(), and DisplacedSystem::timeVectorTag().
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inherited |
Update the system (doing libMesh magic)
Definition at line 1245 of file SystemBase.C.
Referenced by Adaptivity::adaptMesh(), MooseEigenSystem::combineSystemSolution(), NonlinearSystemBase::computeDamping(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeResidualTags(), EigenProblem::doFreeNonlinearPowerIterations(), PointwiseRenormalizeVector::finalize(), MooseEigenSystem::initSystemSolution(), MooseEigenSystem::initSystemSolutionOld(), MooseEigenSystem::scaleSystemSolution(), NonlinearSystemBase::setConstraintSecondaryValues(), NonlinearSystemBase::setInitialSolution(), EigenProblem::solve(), FEProblemBase::solve(), DisplacedProblem::syncSolutions(), MultiAppDofCopyTransfer::transfer(), SecantSolve::transformVariables(), SteffensenSolve::transformVariables(), and PicardSolve::transformVariables().
Definition at line 191 of file AuxiliarySystem.C.
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staticinherited |
Definition at line 16 of file PerfGraphInterface.C.
Referenced by Convergence::validParams().
void AuxiliarySystem::variableWiseRelativeSolutionDifferenceNorm | ( | std::vector< Number > & | var_diffs | ) | const |
Computes and stores ||current - old|| / ||current|| for each variable in the given vector.
var_diffs | a vector being filled with the L2 norm of the solution difference |
Definition at line 893 of file AuxiliarySystem.C.
Referenced by TransientBase::convergedToSteadyState().
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Definition at line 925 of file SystemBase.h.
Referenced by Coupleable::coupled().
Zero vector with the given tag.
Definition at line 666 of file SystemBase.C.
Referenced by SystemBase::zeroTaggedVectors().
Zero all vectors for given tags.
Definition at line 685 of file SystemBase.C.
Referenced by NonlinearSystemBase::computeResidualAndJacobianTags(), and NonlinearSystemBase::computeResidualTags().
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Zero out the solution for the list of variables passed in.
@ param vars_to_be_zeroed The variable names in this vector will have their solutions set to zero after this call
Reimplemented in DisplacedSystem.
Definition at line 199 of file SystemBase.C.
Referenced by DisplacedSystem::zeroVariables(), SystemBase::zeroVariablesForJacobian(), and SystemBase::zeroVariablesForResidual().
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Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on Jacobian evaluation by a call to addVariableToZeroOnResidual()
Definition at line 234 of file SystemBase.C.
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Zero out the solution for the variables that were registered as needing to have their solutions zeroed on out on residual evaluation by a call to addVariableToZeroOnResidual()
Definition at line 228 of file SystemBase.C.
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Definition at line 193 of file AuxiliarySystem.h.
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friend |
Definition at line 194 of file AuxiliarySystem.h.
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friend |
Definition at line 199 of file AuxiliarySystem.h.
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friend |
Definition at line 197 of file AuxiliarySystem.h.
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friend |
Definition at line 198 of file AuxiliarySystem.h.
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friend |
Definition at line 196 of file AuxiliarySystem.h.
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friend |
Definition at line 195 of file AuxiliarySystem.h.
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Definition at line 982 of file SystemBase.h.
Referenced by SolverSystem::checkInvalidSolution(), NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeJacobianTags(), LinearSystem::computeLinearSystemInternal(), LinearSystem::computeLinearSystemTags(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::jacobianSetup(), NonlinearSystemBase::residualSetup(), NonlinearSystemBase::shouldEvaluatePreSMOResidual(), and NonlinearSystem::solve().
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Whether to automatically scale the variables.
Definition at line 1047 of file SystemBase.h.
Referenced by SystemBase::automaticScaling(), NonlinearSystemBase::initialSetup(), and NonlinearSystemBase::preSolve().
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Definition at line 178 of file AuxiliarySystem.h.
Referenced by addScalarKernel(), computeScalarVars(), customSetup(), initialSetup(), jacobianSetup(), residualSetup(), setScalarVariableCoupleableTags(), subdomainSetup(), timestepSetup(), and updateActive().
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An instance of helper class to write streams to the Console objects.
Definition at line 31 of file ConsoleStreamInterface.h.
Referenced by IterationAdaptiveDT::acceptStep(), MeshOnlyAction::act(), SetupDebugAction::act(), MaterialOutputAction::act(), Adaptivity::adaptMesh(), FEProblemBase::adaptMesh(), PerfGraph::addToExecutionList(), SimplePredictor::apply(), SystemBase::applyScalingFactors(), MultiApp::backup(), FEProblemBase::backupMultiApps(), CoarsenedPiecewiseLinear::buildCoarsenedGrid(), MeshDiagnosticsGenerator::checkElementOverlap(), MeshDiagnosticsGenerator::checkElementTypes(), MeshDiagnosticsGenerator::checkElementVolumes(), FEProblemBase::checkExceptionAndStopSolve(), SolverSystem::checkInvalidSolution(), MeshDiagnosticsGenerator::checkLocalJacobians(), MeshDiagnosticsGenerator::checkNonConformalMesh(), MeshDiagnosticsGenerator::checkNonConformalMeshFromAdaptivity(), MeshDiagnosticsGenerator::checkNonMatchingEdges(), MeshDiagnosticsGenerator::checkNonPlanarSides(), FEProblemBase::checkProblemIntegrity(), ReferenceResidualConvergence::checkRelativeConvergence(), MeshDiagnosticsGenerator::checkSidesetsOrientation(), MeshDiagnosticsGenerator::checkWatertightNodesets(), MeshDiagnosticsGenerator::checkWatertightSidesets(), IterationAdaptiveDT::computeAdaptiveDT(), TransientBase::computeConstrainedDT(), DefaultMultiAppFixedPointConvergence::computeCustomConvergencePostprocessor(), NonlinearSystemBase::computeDamping(), FixedPointIterationAdaptiveDT::computeDT(), IterationAdaptiveDT::computeDT(), IterationAdaptiveDT::computeFailedDT(), IterationAdaptiveDT::computeInitialDT(), IterationAdaptiveDT::computeInterpolationDT(), LinearSystem::computeLinearSystemTags(), FEProblemBase::computeLinearSystemTags(), NonlinearSystemBase::computeScaling(), Problem::console(), IterationAdaptiveDT::constrainStep(), TimeStepper::constrainStep(), MultiApp::createApp(), FEProblemBase::execMultiApps(), FEProblemBase::execMultiAppTransfers(), MFEMSteady::execute(), MessageFromInput::execute(), SteadyBase::execute(), Eigenvalue::execute(), ActionWarehouse::executeActionsWithAction(), ActionWarehouse::executeAllActions(), MeshGeneratorSystem::executeMeshGenerators(), ElementQualityChecker::finalize(), FEProblemBase::finishMultiAppStep(), MeshRepairGenerator::fixOverlappingNodes(), CoarsenBlockGenerator::generate(), MeshGenerator::generateInternal(), VariableCondensationPreconditioner::getDofToCondense(), InversePowerMethod::init(), NonlinearEigen::init(), FEProblemBase::initialAdaptMesh(), DefaultMultiAppFixedPointConvergence::initialize(), EigenExecutionerBase::inversePowerIteration(), FEProblemBase::joinAndFinalize(), TransientBase::keepGoing(), IterationAdaptiveDT::limitDTByFunction(), IterationAdaptiveDT::limitDTToPostprocessorValue(), FEProblemBase::logAdd(), EigenExecutionerBase::makeBXConsistent(), Console::meshChanged(), MooseBaseErrorInterface::mooseDeprecated(), MooseBaseErrorInterface::mooseInfo(), MooseBaseErrorInterface::mooseWarning(), MooseBaseErrorInterface::mooseWarningNonPrefixed(), ReferenceResidualConvergence::nonlinearConvergenceSetup(), ReporterDebugOutput::output(), PerfGraphOutput::output(), SolutionInvalidityOutput::output(), MaterialPropertyDebugOutput::output(), DOFMapOutput::output(), VariableResidualNormsDebugOutput::output(), Console::output(), ControlOutput::outputActiveObjects(), ControlOutput::outputChangedControls(), ControlOutput::outputControls(), Console::outputInput(), Console::outputPostprocessors(), PseudoTimestep::outputPseudoTimestep(), Console::outputReporters(), DefaultMultiAppFixedPointConvergence::outputResidualNorm(), Console::outputScalarVariables(), Console::outputSystemInformation(), FEProblemBase::possiblyRebuildGeomSearchPatches(), EigenExecutionerBase::postExecute(), AB2PredictorCorrector::postSolve(), ActionWarehouse::printActionDependencySets(), BlockRestrictionDebugOutput::printBlockRestrictionMap(), SolutionInvalidity::printDebug(), EigenExecutionerBase::printEigenvalue(), SecantSolve::printFixedPointConvergenceHistory(), SteffensenSolve::printFixedPointConvergenceHistory(), PicardSolve::printFixedPointConvergenceHistory(), FixedPointSolve::printFixedPointConvergenceReason(), PerfGraphLivePrint::printLiveMessage(), MaterialPropertyDebugOutput::printMaterialMap(), PerfGraphLivePrint::printStats(), NEML2Action::printSummary(), AutomaticMortarGeneration::projectPrimaryNodesSinglePair(), AutomaticMortarGeneration::projectSecondaryNodesSinglePair(), CoarsenBlockGenerator::recursiveCoarsen(), SolutionTimeAdaptiveDT::rejectStep(), MultiApp::restore(), FEProblemBase::restoreMultiApps(), FEProblemBase::restoreSolutions(), NonlinearSystemBase::setInitialSolution(), MooseApp::setupOptions(), Checkpoint::shouldOutput(), SubProblem::showFunctorRequestors(), SubProblem::showFunctors(), FullSolveMultiApp::showStatusMessage(), FEProblemSolve::solve(), FixedPointSolve::solve(), EigenProblem::solve(), NonlinearSystem::solve(), LinearSystem::solve(), LStableDirk2::solve(), LStableDirk3::solve(), ImplicitMidpoint::solve(), ExplicitTVDRK2::solve(), AStableDirk4::solve(), LStableDirk4::solve(), ExplicitRK2::solve(), TransientMultiApp::solveStep(), FixedPointSolve::solveStep(), PerfGraphLivePrint::start(), AB2PredictorCorrector::step(), NonlinearEigen::takeStep(), TransientBase::takeStep(), TerminateChainControl::terminate(), Convergence::verboseOutput(), Console::writeTimestepInformation(), Console::writeVariableNorms(), and FEProblemBase::~FEProblemBase().
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solution vector from nonlinear solver
Definition at line 162 of file AuxiliarySystem.h.
Referenced by currentSolution().
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Derivative of time derivative of u with respect to uj.
This depends on the time integration scheme
Definition at line 1011 of file SystemBase.h.
Referenced by SystemBase::addVariable(), SystemBase::duDotDu(), and SystemBase::duDotDus().
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Definition at line 1012 of file SystemBase.h.
Referenced by SystemBase::duDotDotDu().
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Elemental variables.
These may be either finite element or finite volume variables
Definition at line 174 of file AuxiliarySystem.h.
Referenced by addVariable(), AuxiliarySystem(), ComputeMarkerThread::onElement(), ComputeIndicatorThread::onElement(), ComputeIndicatorThread::onInternalSide(), reinitElem(), reinitElemFace(), and ComputeMarkerThread::subdomainChanged().
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Definition at line 191 of file AuxiliarySystem.h.
Referenced by addKernel(), computeElementalArrayVars(), customSetup(), elemArrayAuxWarehouse(), getDependObjects(), initialSetup(), jacobianSetup(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().
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Definition at line 183 of file AuxiliarySystem.h.
Referenced by addKernel(), computeElementalVars(), customSetup(), elemAuxWarehouse(), getDependObjects(), initialSetup(), jacobianSetup(), needMaterialOnSide(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().
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Definition at line 187 of file AuxiliarySystem.h.
Referenced by addKernel(), computeElementalVecVars(), customSetup(), elemVectorAuxWarehouse(), getDependObjects(), initialSetup(), jacobianSetup(), needMaterialOnSide(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().
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Definition at line 983 of file SystemBase.h.
Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addConstraint(), NonlinearSystemBase::addDamper(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), NonlinearSystemBase::addHDGKernel(), NonlinearSystemBase::addInterfaceKernel(), MooseEigenSystem::addKernel(), addKernel(), NonlinearSystemBase::addKernel(), NonlinearSystemBase::addNodalKernel(), addScalarKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), SystemBase::addTimeIntegrator(), and SystemBase::addVariable().
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the governing finite element/volume problem
Definition at line 980 of file SystemBase.h.
Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addDGKernel(), NonlinearSystemBase::addDiracKernel(), SystemBase::addDotVectors(), NonlinearSystemBase::addHDGKernel(), NonlinearSystemBase::addInterfaceKernel(), NonlinearSystemBase::addKernel(), NonlinearSystemBase::addNodalKernel(), NonlinearSystemBase::addScalarKernel(), NonlinearSystemBase::addSplit(), NonlinearSystemBase::assembleScalingVector(), NonlinearSystemBase::augmentSparsity(), AuxiliarySystem(), SolverSystem::checkInvalidSolution(), NonlinearSystemBase::checkKernelCoverage(), clearScalarVariableCoupleableTags(), SolverSystem::compute(), compute(), NonlinearSystemBase::computeDamping(), NonlinearSystemBase::computeDiracContributions(), computeElementalVarsHelper(), LinearSystem::computeGradients(), NonlinearSystemBase::computeJacobian(), NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianInternal(), LinearSystem::computeLinearSystemInternal(), LinearSystem::computeLinearSystemTags(), computeMortarNodalVars(), NonlinearSystemBase::computeNodalBCs(), NonlinearSystemBase::computeNodalBCsResidualAndJacobian(), computeNodalVarsHelper(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::computeResidualTags(), NonlinearSystemBase::computeScalarKernelsJacobians(), computeScalarVars(), NonlinearSystemBase::computeScaling(), NonlinearSystem::computeScalingJacobian(), NonlinearSystem::computeScalingResidual(), NonlinearSystemBase::constraintJacobians(), NonlinearSystemBase::constraintResiduals(), LinearSystem::containsTimeKernel(), NonlinearSystem::converged(), NonlinearSystemBase::customSetup(), MooseEigenSystem::eigenKernelOnCurrent(), MooseEigenSystem::eigenKernelOnOld(), NonlinearSystemBase::enforceNodalConstraintsJacobian(), NonlinearSystemBase::enforceNodalConstraintsResidual(), SystemBase::feProblem(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), NonlinearSystemBase::initialSetup(), NonlinearSystemBase::jacobianSetup(), LinearSystem::LinearSystem(), NonlinearSystemBase::NonlinearSystemBase(), NonlinearSystemBase::overwriteNodeFace(), NonlinearSystem::potentiallySetupFiniteDifferencing(), NonlinearSystemBase::preInit(), NonlinearSystemBase::reinitNodeFace(), NonlinearSystem::residualAndJacobianTogether(), NonlinearSystemBase::residualSetup(), NonlinearSystemBase::setConstraintSecondaryValues(), NonlinearSystemBase::setInitialSolution(), setScalarVariableCoupleableTags(), NonlinearSystemBase::shouldEvaluatePreSMOResidual(), NonlinearSystem::solve(), and NonlinearSystemBase::timestepSetup().
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Active flags for tagged matrices.
Definition at line 1019 of file SystemBase.h.
Referenced by SystemBase::activeAllMatrixTags(), SystemBase::activeMatrixTag(), SystemBase::deactiveAllMatrixTags(), SystemBase::deactiveMatrixTag(), and SystemBase::matrixTagActive().
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Maximum number of dofs for any one variable on any one element.
Definition at line 1035 of file SystemBase.h.
Referenced by SystemBase::assignMaxVarNDofsPerElem(), and SystemBase::getMaxVarNDofsPerElem().
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Maximum number of dofs for any one variable on any one node.
Definition at line 1038 of file SystemBase.h.
Referenced by SystemBase::assignMaxVarNDofsPerNode(), and SystemBase::getMaxVarNDofsPerNode().
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Maximum variable number.
Definition at line 994 of file SystemBase.h.
Referenced by SystemBase::addVariable(), and SystemBase::getMaxVariableNumber().
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Definition at line 985 of file SystemBase.h.
Referenced by SystemBase::addVariable(), NonlinearSystemBase::assembleScalingVector(), SystemBase::augmentSendList(), NonlinearSystemBase::checkKernelCoverage(), computeElementalVarsHelper(), NonlinearSystemBase::computeJacobianInternal(), computeMortarNodalVars(), computeNodalVarsHelper(), NonlinearSystemBase::constraintJacobians(), NonlinearSystemBase::constraintResiduals(), NonlinearSystemBase::findImplicitGeometricCouplingEntries(), NonlinearSystemBase::getNodeDofs(), SystemBase::initialSetup(), SystemBase::mesh(), NonlinearSystemBase::overwriteNodeFace(), NonlinearSystemBase::reinitNodeFace(), NonlinearSystemBase::setConstraintSecondaryValues(), SystemBase::setVariableGlobalDoFs(), variableWiseRelativeSolutionDifferenceNorm(), and SystemBase::zeroVariables().
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Definition at line 182 of file AuxiliarySystem.h.
Referenced by addKernel(), computeMortarNodalVars(), customSetup(), getDependObjects(), initialSetup(), jacobianSetup(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().
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The name of this system.
Definition at line 987 of file SystemBase.h.
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Definition at line 190 of file AuxiliarySystem.h.
Referenced by addKernel(), computeNodalArrayVars(), customSetup(), getDependObjects(), initialSetup(), jacobianSetup(), nodalArrayAuxWarehouse(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().
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Definition at line 181 of file AuxiliarySystem.h.
Referenced by addKernel(), computeNodalVars(), customSetup(), getDependObjects(), initialSetup(), jacobianSetup(), nodalAuxWarehouse(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().
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Definition at line 168 of file AuxiliarySystem.h.
Referenced by addVariable(), AuxiliarySystem(), ComputeNodalKernelBcsThread::onNode(), ComputeNodalKernelsThread::onNode(), ComputeNodalKernelBCJacobiansThread::onNode(), ComputeNodalKernelJacobiansThread::onNode(), reinitElem(), and reinitElemFace().
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Definition at line 186 of file AuxiliarySystem.h.
Referenced by addKernel(), computeNodalVecVars(), customSetup(), getDependObjects(), initialSetup(), jacobianSetup(), nodalVectorAuxWarehouse(), residualSetup(), subdomainSetup(), timestepSetup(), and updateActive().
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protectedinherited |
Map variable number to its pointer.
Definition at line 1044 of file SystemBase.h.
Referenced by SystemBase::addVariable(), and SystemBase::getVariable().
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The MooseApp that owns the PerfGraph.
Definition at line 124 of file PerfGraphInterface.h.
Referenced by PerfGraphInterface::perfGraph().
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protectedinherited |
A prefix to use for all sections.
Definition at line 127 of file PerfGraphInterface.h.
Referenced by PerfGraphInterface::timedSectionName().
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A cache for storing gradients at dof locations.
We store it on the system because we create copies of variables on each thread and that would lead to increased data duplication when using threading-based parallelism.
Definition at line 1065 of file SystemBase.h.
Referenced by LinearSystem::computeGradients(), SystemBase::gradientContainer(), and SystemBase::initialSetup().
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Definition at line 1026 of file SystemBase.h.
Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().
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protectedinherited |
Definition at line 1027 of file SystemBase.h.
Referenced by SystemBase::restoreOldSolutions(), and SystemBase::saveOldSolutions().
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Definition at line 1022 of file SystemBase.h.
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Definition at line 1023 of file SystemBase.h.
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Serialized version of the solution vector, or nullptr if a serialized solution is not needed.
Definition at line 1060 of file SystemBase.h.
Referenced by compute(), SolverSystem::preInit(), SystemBase::serializedSolution(), SolverSystem::serializeSolution(), serializeSolution(), and SolverSystem::setSolution().
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The current states of the solution (0 = current, 1 = old, etc)
Definition at line 165 of file AuxiliarySystem.h.
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Whether or not the solution states have been initialized.
Definition at line 1053 of file SystemBase.h.
Referenced by SystemBase::initSolutionState(), and SystemBase::solutionStatesInitialized().
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The subproblem for whom this class holds variable data, etc; this can either be the governing finite element/volume problem or a subjugate displaced problem.
Definition at line 977 of file SystemBase.h.
Referenced by SystemBase::activeAllMatrixTags(), SystemBase::activeMatrixTag(), SystemBase::addMatrix(), SystemBase::addScalingVector(), SystemBase::addVariable(), SystemBase::associateMatrixToTag(), SystemBase::associateVectorToTag(), SystemBase::augmentSendList(), SystemBase::closeTaggedVector(), SystemBase::computingScalingJacobian(), SystemBase::deactiveAllMatrixTags(), SystemBase::deactiveMatrixTag(), SystemBase::disassociateDefaultMatrixTags(), SystemBase::disassociateDefaultVectorTags(), SystemBase::disassociateMatrixFromTag(), SystemBase::disassociateVectorFromTag(), SystemBase::getMatrix(), NonlinearSystemBase::getResidualNonTimeVector(), NonlinearSystemBase::getResidualTimeVector(), SystemBase::getVector(), SystemBase::matrixTagActive(), SystemBase::needSolutionState(), SystemBase::prepare(), SystemBase::prepareFace(), SystemBase::reinitElem(), SystemBase::removeMatrix(), SystemBase::removeVector(), NonlinearSystemBase::residualGhosted(), SolverSystem::setSolution(), SystemBase::setVariableGlobalDoFs(), SystemBase::subproblem(), SystemBase::zeroTaggedVector(), and SystemBase::zeroVariables().
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Definition at line 159 of file AuxiliarySystem.h.
Referenced by AuxiliarySystem(), computeElementalVarsHelper(), computeMortarNodalVars(), computeNodalVarsHelper(), computeScalarVars(), serializeSolution(), solutionInternal(), sys(), system(), and variableWiseRelativeSolutionDifferenceNorm().
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protectedinherited |
Tagged matrices (pointer)
Definition at line 1017 of file SystemBase.h.
Referenced by SystemBase::associateMatrixToTag(), SystemBase::disassociateMatrixFromTag(), SystemBase::getMatrix(), SystemBase::hasMatrix(), and SystemBase::removeMatrix().
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Tagged vectors (pointer)
Definition at line 1015 of file SystemBase.h.
Referenced by SystemBase::associateVectorToTag(), SystemBase::disassociateVectorFromTag(), SystemBase::getVector(), SystemBase::hasVector(), and SystemBase::removeVector().
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protectedinherited |
Time integrator.
Definition at line 1041 of file SystemBase.h.
Referenced by SystemBase::addTimeIntegrator(), SolverSystem::compute(), compute(), NonlinearSystemBase::computeResidualAndJacobianTags(), NonlinearSystemBase::computeResidualTags(), SystemBase::copyTimeIntegrators(), SystemBase::getTimeIntegrators(), NonlinearSystemBase::onTimestepBegin(), SystemBase::queryTimeIntegrator(), NonlinearSystem::solve(), and NonlinearEigenSystem::solve().
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protectedinherited |
solution vector for u^dot
Definition at line 1000 of file SystemBase.h.
Referenced by SystemBase::addDotVectors(), NonlinearSystemBase::setSolutionUDot(), and SystemBase::solutionUDot().
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protectedinherited |
old solution vector for u^dot
Definition at line 1005 of file SystemBase.h.
Referenced by SystemBase::addDotVectors(), NonlinearSystemBase::setSolutionUDotOld(), and SystemBase::solutionUDotOld().
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protectedinherited |
solution vector for u^dotdot
Definition at line 1002 of file SystemBase.h.
Referenced by SystemBase::addDotVectors(), NonlinearSystemBase::setSolutionUDotDot(), and SystemBase::solutionUDotDot().
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protectedinherited |
old solution vector for u^dotdot
Definition at line 1007 of file SystemBase.h.
Referenced by SystemBase::addDotVectors(), NonlinearSystemBase::setSolutionUDotDotOld(), and SystemBase::solutionUDotDotOld().
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protectedinherited |
Container for the dof indices of a given variable.
Definition at line 1056 of file SystemBase.h.
Referenced by SystemBase::getVariableGlobalDoFs(), and SystemBase::setVariableGlobalDoFs().
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protectedinherited |
default kind of variables in this system
Definition at line 1030 of file SystemBase.h.
Referenced by SystemBase::varKind().
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protectedinherited |
Map of variables (variable id -> array of subdomains where it lives)
Definition at line 992 of file SystemBase.h.
Referenced by SystemBase::addVariable(), SystemBase::getSubdomainsForVar(), and SystemBase::getVariableBlocks().
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protectedinherited |
Definition at line 1032 of file SystemBase.h.
Referenced by SystemBase::addVariableToCopy(), SystemBase::copyVars(), and SystemBase::hasVarCopy().
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protectedinherited |
Variable warehouses (one for each thread)
Definition at line 990 of file SystemBase.h.
Referenced by NonlinearSystemBase::addBoundaryCondition(), NonlinearSystemBase::addInterfaceKernel(), addVariable(), SystemBase::addVariable(), SystemBase::applyScalingFactors(), NonlinearSystemBase::assembleScalingVector(), SystemBase::clearAllDofIndices(), compute(), SystemBase::customSetup(), SystemBase::getActualFieldVariable(), SystemBase::getFieldVariable(), SystemBase::getFVVariable(), getMinQuadratureOrder(), SystemBase::getMinQuadratureOrder(), SystemBase::getScalarVariable(), SystemBase::getScalarVariables(), SystemBase::getVariable(), SystemBase::getVariableNames(), SystemBase::getVariables(), LinearSystem::initialSetup(), SystemBase::initialSetup(), SystemBase::jacobianSetup(), SystemBase::nFieldVariables(), SystemBase::nFVVariables(), SystemBase::nVariables(), SystemBase::prepare(), SystemBase::prepareFace(), SystemBase::prepareLowerD(), SystemBase::prepareNeighbor(), SystemBase::reinitElem(), SystemBase::reinitElemFace(), SystemBase::reinitLowerD(), SystemBase::reinitNeighbor(), SystemBase::reinitNeighborFace(), SystemBase::reinitNode(), SystemBase::reinitNodeFace(), SystemBase::reinitNodes(), SystemBase::reinitNodesNeighbor(), SystemBase::reinitScalars(), SystemBase::residualSetup(), SystemBase::setActiveScalarVariableCoupleableVectorTags(), SystemBase::setActiveVariableCoupleableVectorTags(), NonlinearSystemBase::setupScalingData(), SystemBase::subdomainSetup(), and SystemBase::timestepSetup().
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protectedinherited |
Definition at line 997 of file SystemBase.h.
Referenced by SystemBase::addVariableToZeroOnJacobian(), and SystemBase::zeroVariablesForJacobian().
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protectedinherited |
Definition at line 996 of file SystemBase.h.
Referenced by SystemBase::addVariableToZeroOnResidual(), and SystemBase::zeroVariablesForResidual().
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True if printing out additional information.
Definition at line 1050 of file SystemBase.h.
Referenced by SystemBase::applyScalingFactors(), and SystemBase::setVerboseFlag().