libMesh
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The Biharmonic class encapsulates most of the data structures necessary to calculate the biharmonic residual and Jacobian, auxiliary quantities, to take a timestep, and to output the state – biharmonic solution and vectors of auxiliary quantities. More...
#include <biharmonic.h>
Classes | |
class | JR |
Biharmonic's friend class definition. More... | |
Public Types | |
enum | InitialStateEnum { STRIP = 0, ROD = 1, BALL = 2 } |
enum | FreeEnergyEnum { DOUBLE_WELL = 1, DOUBLE_OBSTACLE = 2, LOG_DOUBLE_WELL = 3, LOG_DOUBLE_OBSTACLE = 4 } |
enum | ReadFlags { READ_HEADER = 1, READ_DATA = 2, READ_ADDITIONAL_DATA = 4, READ_LEGACY_FORMAT = 8, TRY_READ_IFEMS = 16, READ_BASIC_ONLY = 32 } |
Define enumeration to set properties in EquationSystems::read() More... | |
enum | WriteFlags { WRITE_DATA = 1, WRITE_ADDITIONAL_DATA = 2, WRITE_PARALLEL_FILES = 4, WRITE_SERIAL_FILES = 8 } |
Define enumeration to set properties in EquationSystems::write() More... | |
Public Member Functions | |
Biharmonic (ReplicatedMesh &mesh) | |
Constructor retrieves command-line options, setting defaults, if necessary. More... | |
~Biharmonic () | |
Destructor. More... | |
bool | verbose () |
Real | dt0 () |
Real | dt () |
void | viewParameters () |
void | init () |
Initialize all the systems. More... | |
void | step (const Real &dt=-1.0) |
void | output (int timestep, const Real &t, Real &o_t, bool force=false) |
void | run () |
virtual void | clear () |
Restores the data structure to a pristine state. More... | |
virtual void | reinit () |
Handle any mesh changes and reinitialize all the systems on the updated mesh. More... | |
virtual void | reinit_mesh () |
Handle the association of a completely new mesh with the EquationSystem and all the Systems assigned to it. More... | |
virtual void | enable_default_ghosting (bool enable) |
Enable or disable default ghosting functors on the Mesh and on all Systems. More... | |
void | update () |
Updates local values for all the systems. More... | |
unsigned int | n_systems () const |
bool | has_system (std::string_view name) const |
template<typename T_sys > | |
const T_sys & | get_system (std::string_view name) const |
template<typename T_sys > | |
T_sys & | get_system (std::string_view name) |
template<typename T_sys > | |
const T_sys & | get_system (const unsigned int num) const |
template<typename T_sys > | |
T_sys & | get_system (const unsigned int num) |
const System & | get_system (std::string_view name) const |
System & | get_system (std::string_view name) |
const System & | get_system (const unsigned int num) const |
System & | get_system (const unsigned int num) |
virtual System & | add_system (std::string_view system_type, std::string_view name) |
Add the system of type system_type named name to the systems array. More... | |
template<typename T_sys > | |
T_sys & | add_system (std::string_view name) |
Add the system named name to the systems array. More... | |
unsigned int | n_vars () const |
std::size_t | n_dofs () const |
std::size_t | n_active_dofs () const |
virtual void | solve () |
Call solve on all the individual equation systems. More... | |
virtual void | adjoint_solve (const QoISet &qoi_indices=QoISet()) |
Call adjoint_solve on all the individual equation systems. More... | |
virtual void | sensitivity_solve (const ParameterVector ¶meters) |
Call sensitivity_solve on all the individual equation systems. More... | |
void | build_variable_names (std::vector< std::string > &var_names, const FEType *type=nullptr, const std::set< std::string > *system_names=nullptr) const |
Fill the input vector var_names with the names of the variables for each system. More... | |
void | build_solution_vector (std::vector< Number > &soln, std::string_view system_name, std::string_view variable_name="all_vars") const |
Fill the input vector soln with the solution values for the system named name . More... | |
void | build_solution_vector (std::vector< Number > &soln, const std::set< std::string > *system_names=nullptr, bool add_sides=false) const |
Fill the input vector soln with solution values. More... | |
std::unique_ptr< NumericVector< Number > > | build_parallel_solution_vector (const std::set< std::string > *system_names=nullptr, bool add_sides=false) const |
A version of build_solution_vector which is appropriate for "parallel" output formats like Nemesis. More... | |
void | get_vars_active_subdomains (const std::vector< std::string > &names, std::vector< std::set< subdomain_id_type >> &vars_active_subdomains) const |
Retrieve vars_active_subdomains , which indicates the active subdomains for each variable in names . More... | |
void | get_solution (std::vector< Number > &soln, std::vector< std::string > &names) const |
Retrieve the solution data for CONSTANT MONOMIALs and/or components of CONSTANT MONOMIAL_VECs. More... | |
void | build_elemental_solution_vector (std::vector< Number > &soln, std::vector< std::string > &names) const |
Retrieve the solution data for CONSTANT MONOMIALs and/or components of CONSTANT MONOMIAL_VECs. More... | |
std::vector< std::pair< unsigned int, unsigned int > > | find_variable_numbers (std::vector< std::string > &names, const FEType *type=nullptr, const std::vector< FEType > *types=nullptr) const |
Finds system and variable numbers for any variables of 'type' or of 'types' corresponding to the entries in the input 'names' vector. More... | |
std::unique_ptr< NumericVector< Number > > | build_parallel_elemental_solution_vector (std::vector< std::string > &names) const |
Builds a parallel vector of CONSTANT MONOMIAL and/or components of CONSTANT MONOMIAL_VEC solution values corresponding to the entries in the input 'names' vector. More... | |
void | build_discontinuous_solution_vector (std::vector< Number > &soln, const std::set< std::string > *system_names=nullptr, const std::vector< std::string > *var_names=nullptr, bool vertices_only=false, bool add_sides=false) const |
Fill the input vector soln with solution values. More... | |
template<typename InValType = Number> | |
void | read (std::string_view name, const XdrMODE, const unsigned int read_flags=(READ_HEADER|READ_DATA), bool partition_agnostic=true) |
Read & initialize the systems from disk using the XDR data format. More... | |
template<typename InValType = Number> | |
void | read (std::string_view name, const unsigned int read_flags=(READ_HEADER|READ_DATA), bool partition_agnostic=true) |
template<typename InValType = Number> | |
void | read (Xdr &io, std::function< std::unique_ptr< Xdr >()> &local_io_functor, const unsigned int read_flags=(READ_HEADER|READ_DATA), bool partition_agnostic=true) |
void | write (std::string_view name, const XdrMODE, const unsigned int write_flags=(WRITE_DATA), bool partition_agnostic=true) const |
Write the systems to disk using the XDR data format. More... | |
void | write (std::string_view name, const unsigned int write_flags=(WRITE_DATA), bool partition_agnostic=true) const |
void | write (std::ostream name, const unsigned int write_flags=(WRITE_DATA), bool partition_agnostic=true) const |
void | write (Xdr &io, const unsigned int write_flags=(WRITE_DATA), bool partition_agnostic=true, Xdr *const local_io=nullptr) const |
virtual bool | compare (const EquationSystems &other_es, const Real threshold, const bool verbose) const |
virtual std::string | get_info () const |
void | print_info (std::ostream &os=libMesh::out) const |
Prints information about the equation systems, by default to libMesh::out. More... | |
const MeshBase & | get_mesh () const |
MeshBase & | get_mesh () |
void | allgather () |
Serializes a distributed mesh and its associated degree of freedom numbering for all systems. More... | |
void | enable_refine_in_reinit () |
Calls to reinit() will also do two-step coarsen-then-refine. More... | |
void | disable_refine_in_reinit () |
Calls to reinit() will not try to coarsen or refine the mesh. More... | |
bool | refine_in_reinit_flag () |
bool | reinit_solutions () |
Handle any mesh changes and project any solutions onto the updated mesh. More... | |
virtual void | reinit_systems () |
Reinitialize all systems on the current mesh. More... | |
const Parallel::Communicator & | comm () const |
processor_id_type | n_processors () const |
processor_id_type | processor_id () const |
Static Public Member Functions | |
static bool | redundant_added_side (const Elem &elem, unsigned int side) |
static std::string | get_info () |
Gets a string containing the reference information. More... | |
static void | print_info (std::ostream &out_stream=libMesh::out) |
Prints the reference information, by default to libMesh::out . More... | |
static unsigned int | n_objects () |
Prints the number of outstanding (created, but not yet destroyed) objects. More... | |
static void | enable_print_counter_info () |
Methods to enable/disable the reference counter output from print_info() More... | |
static void | disable_print_counter_info () |
Public Attributes | |
Parameters | parameters |
Data structure holding arbitrary parameters. More... | |
Protected Types | |
typedef std::map< std::string, std::pair< unsigned int, unsigned int > > | Counts |
Data structure to log the information. More... | |
Protected Member Functions | |
void | increment_constructor_count (const std::string &name) noexcept |
Increments the construction counter. More... | |
void | increment_destructor_count (const std::string &name) noexcept |
Increments the destruction counter. More... | |
Protected Attributes | |
std::map< std::string, std::unique_ptr< System >, std::less<> > | _systems |
Data structure holding the systems. More... | |
bool | _refine_in_reinit |
Flag for whether to call coarsen/refine in reinit(). More... | |
bool | _enable_default_ghosting |
Flag for whether to enable default ghosting on newly added Systems. More... | |
const Parallel::Communicator & | _communicator |
Static Protected Attributes | |
static Counts | _counts |
Actually holds the data. More... | |
static Threads::atomic< unsigned int > | _n_objects |
The number of objects. More... | |
static Threads::spin_mutex | _mutex |
Mutual exclusion object to enable thread-safe reference counting. More... | |
static bool | _enable_print_counter = true |
Flag to control whether reference count information is printed when print_info is called. More... | |
Private Attributes | |
unsigned int | _dim |
unsigned int | _N |
Real | _kappa |
Real | _theta |
Real | _theta_c |
Real | _tol |
bool | _growth |
bool | _degenerate |
bool | _cahn_hillard |
bool | _netforce |
FreeEnergyEnum | _energy |
int | _log_truncation |
bool | _verbose |
InitialStateEnum | _initialState |
Point | _initialCenter |
Real | _initialWidth |
Real | _dt0 |
Real | _dt |
Real | _t0 |
Real | _T |
Real | _t1 |
Real | _cnWeight |
std::string | _ofile_base |
std::string | _ofile |
std::unique_ptr< ExodusII_IO > | _exio |
Real | _o_dt |
int | _o_count |
ReplicatedMesh & | _mesh |
JR * | _jr |
Friends | |
class | JR |
The Biharmonic class encapsulates most of the data structures necessary to calculate the biharmonic residual and Jacobian, auxiliary quantities, to take a timestep, and to output the state – biharmonic solution and vectors of auxiliary quantities.
The main reason for this design is to have a data structure that has all of the necessary data in one place, where all of the calculation subroutines can access these data. Currently these data are split up among several interdependent objects with no clear hierarchy between them: mesh, equation system, equation system bundle, residual/Jacobian calculator.
Since no object contains all others and the data are distributed among many objects, the natural control and data flow resides outside of these objects and is typically implemented in main(). We, however, would like to split the calculation into natural chunks – subroutines – while retaining these subroutines access to the common necessary data – biharmonic parameters, mesh and time interval sizes, etc. Thus, class Biharmonic. Finally, making Biharmonic inherit from EquationSystems makes it possible to include it in the most common callbacks that do not pass back a user context, but only an EquationSystems object.
Definition at line 45 of file biharmonic.h.
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protectedinherited |
Data structure to log the information.
The log is identified by the class name.
Definition at line 119 of file reference_counter.h.
Enumerator | |
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DOUBLE_WELL | |
DOUBLE_OBSTACLE | |
LOG_DOUBLE_WELL | |
LOG_DOUBLE_OBSTACLE |
Definition at line 54 of file biharmonic.h.
Enumerator | |
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STRIP | |
ROD | |
BALL |
Definition at line 49 of file biharmonic.h.
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inherited |
Define enumeration to set properties in EquationSystems::read()
Enumerator | |
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READ_HEADER | |
READ_DATA | |
READ_ADDITIONAL_DATA | |
READ_LEGACY_FORMAT | |
TRY_READ_IFEMS | |
READ_BASIC_ONLY |
Definition at line 77 of file equation_systems.h.
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inherited |
Define enumeration to set properties in EquationSystems::write()
Enumerator | |
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WRITE_DATA | |
WRITE_ADDITIONAL_DATA | |
WRITE_PARALLEL_FILES | |
WRITE_SERIAL_FILES |
Definition at line 87 of file equation_systems.h.
Biharmonic::Biharmonic | ( | ReplicatedMesh & | mesh | ) |
Constructor retrieves command-line options, setting defaults, if necessary.
It then builds the mesh using these options, then the equations systems around it, and, finally, sets up the output. We recommend that this be used through the factory Create function, which allocates the mesh. In that case don't forget to call Destroy at the end, to free the mesh up.
Definition at line 16 of file biharmonic.C.
References _cahn_hillard, _cnWeight, _degenerate, _dim, _dt0, _energy, _exio, _growth, _initialCenter, _initialState, _initialWidth, _kappa, _log_truncation, _mesh, _N, _netforce, _o_dt, _ofile, _ofile_base, _T, _t0, _t1, _theta, _theta_c, _tol, _verbose, BALL, libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_line(), libMesh::MeshTools::Generation::build_square(), libMesh::command_line_value(), libMesh::command_line_vector(), DOUBLE_OBSTACLE, DOUBLE_WELL, libMesh::EDGE2, libMesh::HEX8, LOG_DOUBLE_OBSTACLE, LOG_DOUBLE_WELL, libMesh::on_command_line(), libMesh::out, libMesh::QUAD4, ROD, and STRIP.
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inline |
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virtualinherited |
Add the system of type system_type
named name
to the systems array.
Definition at line 338 of file equation_systems.C.
References libMesh::EquationSystems::_systems, libMesh::EquationSystems::get_system(), and libMesh::Quality::name().
Referenced by assemble_and_solve(), build_system(), main(), libMesh::ErrorVector::plot_error(), libMesh::EquationSystems::read(), libMesh::StaticCondensationDofMap::reinit(), TimeSolverTestImplementation< NewmarkSolver >::run_test_with_exact_soln(), setup(), WriteVecAndScalar::setupTests(), SystemsTest::simpleSetup(), libMesh::VariationalMeshSmoother::smooth(), MultiEvaluablePredTest::test(), SystemsTest::test100KVariables(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), SystemsTest::test2DProjectVectorFE(), SystemsTest::test3DProjectVectorFE(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), MeshFunctionTest::test_subdomain_id_sets(), EquationSystemsTest::testAddSystem(), SystemsTest::testAssemblyWithDgFemContext(), DofMapTest::testBadElemFECombo(), EquationSystemsTest::testBadVarNames(), SystemsTest::testBlockRestrictedVarNDofs(), SystemsTest::testBoundaryProjectCube(), DofMapTest::testConstraintLoopDetection(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyElementVectorImpl(), MeshInputTest::testCopyNodalSolutionImpl(), ConstraintOperatorTest::testCoreform(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), EquationSystemsTest::testDisableDefaultGhosting(), SystemsTest::testDofCouplingWithVarGroups(), MixedDimensionMeshTest::testDofOrdering(), MixedDimensionRefinedMeshTest::testDofOrdering(), MixedDimensionNonUniformRefinement::testDofOrdering(), MixedDimensionNonUniformRefinementTriangle::testDofOrdering(), MixedDimensionNonUniformRefinement3D::testDofOrdering(), DofMapTest::testDofOwner(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), EquationSystemsTest::testInit(), MeshAssignTest::testMeshMoveAssign(), PeriodicBCTest::testPeriodicBC(), EquationSystemsTest::testPostInitAddElem(), EquationSystemsTest::testPostInitAddRealSystem(), EquationSystemsTest::testPostInitAddSystem(), SystemsTest::testProjectCube(), SystemsTest::testProjectCubeWithMeshFunction(), MeshInputTest::testProjectionRegression(), SystemsTest::testProjectLine(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), SystemsTest::testProjectSquare(), InfFERadialTest::testRefinement(), EquationSystemsTest::testRefineThenReinitPreserveFlags(), EquationSystemsTest::testReinitWithNodeElem(), EquationSystemsTest::testRepartitionThenReinit(), EquationSystemsTest::testSelectivePRefine(), SystemsTest::testSetSystemParameterOverEquationSystem(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testWriteExodus(), and WriteVecAndScalar::testWriteNemesis().
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inlineinherited |
Add the system named name
to the systems array.
Definition at line 671 of file equation_systems.h.
References libMesh::EquationSystems::_add_system_to_nodes_and_elems(), libMesh::EquationSystems::_enable_default_ghosting, libMesh::EquationSystems::_remove_default_ghosting(), libMesh::EquationSystems::_systems, libMesh::EquationSystems::n_systems(), and libMesh::Quality::name().
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virtualinherited |
Call adjoint_solve
on all the individual equation systems.
By default this function solves each system's adjoint once, in the reverse order from that in which they were added. For more sophisticated decoupled problems the user may with to override this behavior in a derived class.
Definition at line 440 of file equation_systems.C.
References libMesh::EquationSystems::get_system(), libMesh::libmesh_assert(), and libMesh::EquationSystems::n_systems().
Referenced by libMesh::UniformRefinementEstimator::_estimate_error().
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inherited |
Serializes a distributed mesh and its associated degree of freedom numbering for all systems.
Definition at line 265 of file equation_systems.C.
References libMesh::EquationSystems::_mesh, libMesh::MeshBase::allgather(), libMesh::DofMap::distribute_dofs(), libMesh::System::get_dof_map(), libMesh::EquationSystems::get_system(), libMesh::MeshBase::is_serial(), libMesh::make_range(), libMesh::EquationSystems::n_systems(), and libMesh::System::reinit_constraints().
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inherited |
Fill the input vector soln
with solution values.
The entries will be in variable-major format (corresponding to the names from build_variable_names()
).
If systems_names!=nullptr, only include data from the specified systems.
If vertices_only == true, then for higher-order elements only the solution at the vertices is computed. This can be useful when plotting discontinuous solutions on higher-order elements and only a lower-order representation is required.
If add_sides == true, append data for plotting on "side elements" too.
Definition at line 1262 of file equation_systems.C.
References libMesh::Variable::active_on_subdomain(), libMesh::DISCONTINUOUS, libMesh::FEInterface::get_continuity(), libMesh::H_CURL, libMesh::H_DIV, libMesh::index_range(), libMesh::Elem::level(), libMesh::libmesh_assert(), libMesh::make_range(), libMesh::FEInterface::n_vec_dim(), libMesh::Elem::neighbor_ptr(), libMesh::FEInterface::nodal_soln(), libMesh::Elem::node_ptr(), libMesh::Elem::nodes_on_side(), libMesh::FEInterface::side_nodal_soln(), libMesh::Elem::subdomain_id(), and libMesh::Elem::which_neighbor_am_i().
Referenced by libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems(), libMesh::ExodusII_IO::write_discontinuous_exodusII(), libMesh::GMVIO::write_discontinuous_gmv(), and libMesh::ExodusII_IO::write_element_data_from_discontinuous_nodal_data().
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inherited |
Retrieve the solution data for CONSTANT MONOMIALs and/or components of CONSTANT MONOMIAL_VECs.
If 'names' is populated, only the variables corresponding to those names will be retrieved. This can be used to filter which variables are retrieved.
This is the more appropriately-named replacement for the get_solution() function defined above.
Definition at line 1027 of file equation_systems.C.
References libMesh::EquationSystems::build_parallel_elemental_solution_vector().
Referenced by libMesh::EquationSystems::get_solution(), and libMesh::ExodusII_IO::write_element_data().
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inherited |
Builds a parallel vector of CONSTANT MONOMIAL and/or components of CONSTANT MONOMIAL_VEC solution values corresponding to the entries in the input 'names' vector.
This vector is approximately uniformly distributed across all of the available processors.
The related function build_elemental_solution_vector() is implemented by calling this function and then calling localize_to_one() on the resulting vector.
Returns a nullptr if no CONSTANT, MONOMIAL/MONOMIAL_VEC variables exist in the 'names' vector (if it is empty, then it will return all variables in the system of this type if any) or a std::unique_ptr to a var-major numeric vector of total length n_elem * n_vars, where n_vars includes all components of vectors, ordered according to: [u0, u1, ... uN, v0, v1, ... vN, w0, w1, ... wN] for constant monomial variables (u, v, w) on a mesh with N elements.
Definition at line 1151 of file equation_systems.C.
References libMesh::ParallelObject::_communicator, libMesh::EquationSystems::_mesh, libMesh::Variable::active_on_subdomain(), libMesh::NumericVector< T >::build(), libMesh::NumericVector< T >::close(), libMesh::ParallelObject::comm(), libMesh::CONSTANT, libMesh::System::current_local_solution, libMesh::DofMap::dof_indices(), libMesh::EquationSystems::find_variable_numbers(), libMesh::System::get_dof_map(), libMesh::EquationSystems::get_system(), libMesh::index_range(), libMesh::NumericVector< T >::init(), libMesh::libmesh_assert(), libMesh::MeshBase::max_elem_id(), libMesh::MONOMIAL, libMesh::MONOMIAL_VEC, libMesh::MeshBase::n_elem(), libMesh::ParallelObject::n_processors(), libMesh::PARALLEL, libMesh::ParallelObject::processor_id(), libMesh::NumericVector< T >::set(), libMesh::System::solution, libMesh::MeshBase::spatial_dimension(), libMesh::System::update(), libMesh::System::variable(), and libMesh::System::variable_type().
Referenced by libMesh::EquationSystems::build_elemental_solution_vector().
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inherited |
A version of build_solution_vector which is appropriate for "parallel" output formats like Nemesis.
Definition at line 581 of file equation_systems.C.
References libMesh::ParallelObject::_communicator, libMesh::EquationSystems::_mesh, libMesh::EquationSystems::_systems, libMesh::Variable::active_on_subdomain(), libMesh::NumericVector< T >::add(), TIMPI::Communicator::allgather(), libMesh::NumericVector< T >::build(), libMesh::NumericVector< T >::close(), libMesh::ParallelObject::comm(), libMesh::System::current_local_solution, dim, distance(), libMesh::DofMap::dof_indices(), libMesh::FEInterface::field_type(), libMesh::NumericVector< T >::first_local_index(), libMesh::NumericVector< T >::get(), libMesh::System::get_dof_map(), libMesh::DofObject::id(), libMesh::index_range(), libMesh::NumericVector< T >::init(), libMesh::NumericVector< T >::last_local_index(), libMesh::libmesh_assert(), libMesh::make_range(), libMesh::MeshBase::max_node_id(), libMesh::DofObject::n_dofs(), libMesh::System::n_vars(), libMesh::FEInterface::n_vec_dim(), libMesh::FEInterface::nodal_soln(), libMesh::System::number(), libMesh::PARALLEL, libMesh::ParallelObject::processor_id(), TIMPI::Communicator::rank(), libMesh::EquationSystems::redundant_added_side(), libMesh::NumericVector< T >::set(), libMesh::DofMap::should_p_refine(), libMesh::FEInterface::side_nodal_soln(), TIMPI::Communicator::size(), libMesh::System::solution, libMesh::MeshBase::spatial_dimension(), TIMPI::Communicator::sum(), libMesh::TOLERANCE, libMesh::TYPE_VECTOR, libMesh::System::update(), libMesh::DofMap::var_group_from_var_number(), libMesh::System::variable(), and libMesh::System::variable_type().
Referenced by libMesh::EquationSystems::build_solution_vector(), and libMesh::MeshOutput< MeshBase >::write_nodal_data().
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inherited |
Fill the input vector soln
with the solution values for the system named name
.
soln
will only be assembled on processor 0, so this method is only applicable to outputting plot files from processor 0. Definition at line 569 of file equation_systems.C.
Referenced by libMesh::MeshOutput< MeshBase >::write_equation_systems().
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inherited |
Fill the input vector soln
with solution values.
The entries will be in variable-major format (corresponding to the names from build_variable_names()
).
If systems_names!=nullptr, only include data from the specified systems.
If add_sides
is true, append data for plotting on "side
elements" too.
Definition at line 973 of file equation_systems.C.
References libMesh::EquationSystems::build_parallel_solution_vector().
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inherited |
Fill the input vector var_names
with the names of the variables for each system.
If type
is passed, only variables of the specified type will be populated. If systems_names!=nullptr, only include names from the specified systems.
Definition at line 450 of file equation_systems.C.
References libMesh::EquationSystems::_systems, dim, libMesh::FEInterface::field_type(), libMesh::EquationSystems::get_mesh(), libMesh::make_range(), libMesh::EquationSystems::n_vars(), libMesh::FEInterface::n_vec_dim(), libMesh::MeshBase::spatial_dimension(), and libMesh::TYPE_VECTOR.
Referenced by main(), EquationSystemsTest::testBadVarNames(), libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems(), libMesh::ExodusII_IO::write_discontinuous_exodusII(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::Nemesis_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data_from_discontinuous_nodal_data(), libMesh::MeshOutput< MeshBase >::write_equation_systems(), libMesh::Nemesis_IO::write_nodal_data(), and libMesh::MeshOutput< MeshBase >::write_nodal_data().
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virtualinherited |
Restores the data structure to a pristine state.
Definition at line 69 of file equation_systems.C.
References libMesh::EquationSystems::_systems, libMesh::Parameters::clear(), and libMesh::EquationSystems::parameters.
Referenced by main().
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inlineinherited |
Parallel::Communicator
object used by this mesh. Definition at line 97 of file parallel_object.h.
References libMesh::ParallelObject::_communicator.
Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult_add(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::DofMap::add_constraints_to_send_list(), add_cube_convex_hull_to_mesh(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::RBEIMEvaluation::add_interpolation_data(), libMesh::CondensedEigenSystem::add_matrices(), libMesh::EigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::System::add_vector(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::AdvectionSystem::assemble_claw_rhs(), libMesh::FEMSystem::assemble_qoi(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::MeshCommunication::assign_global_indices(), libMesh::Partitioner::assign_partitioning(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::Partitioner::build_graph(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::PetscDMWrapper::build_sf(), libMesh::MeshBase::cache_elem_data(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::RBSCMConstruction::compute_SCM_bounds_on_training_set(), libMesh::DofMap::computed_sparsity_already(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ContinuationSystem::ContinuationSystem(), libMesh::MeshBase::copy_constraint_rows(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::MeshTools::create_subdomain_bounding_box(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), create_wrapped_function(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::RBEIMEvaluation::distribute_bfs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::DTKSolutionTransfer::DTKSolutionTransfer(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_interiors(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_nodes(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_sides(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::EpetraVector< T >::EpetraVector(), AssembleOptimization::equality_constraints(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_error_tolerance(), libMesh::MeshRefinement::flag_elements_by_mean_stddev(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::DofMap::gather_constraints(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::RBEIMEvaluation::get_eim_basis_function_node_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_side_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_value(), libMesh::MeshBase::get_info(), libMesh::System::get_info(), libMesh::DofMap::get_info(), libMesh::RBEIMEvaluation::get_interior_basis_functions_as_vecs(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::RBEIMConstruction::get_max_abs_value(), libMesh::RBEIMConstruction::get_node_max_abs_value(), libMesh::RBEIMEvaluation::get_parametrized_function_node_value(), libMesh::RBEIMEvaluation::get_parametrized_function_side_value(), libMesh::RBEIMEvaluation::get_parametrized_function_value(), libMesh::RBEIMConstruction::get_random_point(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::StaticCondensation::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::AdvectionSystem::init_data(), libMesh::ClawSystem::init_data(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_parametrized_functions_in_training_set(), libMesh::RBEIMConstruction::inner_product(), integrate_function(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_equal_connectivity(), libMesh::MeshTools::libmesh_assert_equal_points(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_constraint_rows(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::libmesh_petsc_linesearch_shellfunc(), libMesh::libmesh_petsc_preconditioner_apply(), libMesh::libmesh_petsc_recalculate_monitor(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_interface(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_precheck(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), libMesh::LinearImplicitSystem::LinearImplicitSystem(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_elems_parallel_consistent(), libMesh::MeshRefinement::make_flags_parallel_consistent(), libMesh::MeshCommunication::make_new_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_new_nodes_parallel_consistent(), libMesh::MeshCommunication::make_node_bcids_parallel_consistent(), libMesh::MeshCommunication::make_node_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_unique_ids_parallel_consistent(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::FEMSystem::mesh_position_set(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::MeshTools::n_connected_components(), libMesh::DofMap::n_constrained_dofs(), libMesh::MeshBase::n_constraint_rows(), libMesh::DofMap::n_dofs(), libMesh::DofMap::n_dofs_per_processor(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), MixedOrderTest::n_neighbor_links(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::SparsityPattern::Build::n_nonzeros(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_distribute_bfs(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::RBEIMConstruction::node_inner_product(), libMesh::MeshBase::operator==(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::MeshTools::paranoid_n_levels(), libMesh::Partitioner::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::prepare_for_use(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Partitioner::processor_pairs_to_interface_nodes(), libMesh::InterMeshProjection::project_system_vectors(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::RBEIMEvaluation::read_in_interior_basis_functions(), libMesh::RBEIMEvaluation::read_in_node_basis_functions(), libMesh::RBEIMEvaluation::read_in_side_basis_functions(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::SimplexRefiner::refine_via_edges(), libMesh::StaticCondensationDofMap::reinit(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), scale_mesh_and_plot(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::send_and_insert_dof_values(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::Partitioner::set_interface_node_processor_ids_BFS(), libMesh::Partitioner::set_interface_node_processor_ids_linear(), libMesh::Partitioner::set_interface_node_processor_ids_petscpartitioner(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::RBEIMEvaluation::side_distribute_bfs(), libMesh::RBEIMEvaluation::side_gather_bfs(), libMesh::RBEIMConstruction::side_inner_product(), libMesh::Partitioner::single_partition(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::VariationalMeshSmoother::smooth(), libMesh::ClawSystem::solve_conservation_law(), libMesh::split_mesh(), libMesh::RBEIMConstruction::store_eim_solutions_for_training_set(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), libMesh::MeshRefinement::test_unflagged(), DofMapTest::testBadElemFECombo(), SystemsTest::testBlockRestrictedVarNDofs(), BoundaryInfoTest::testBoundaryOnChildrenErrors(), VolumeTest::testC0PolygonMethods(), VolumeTest::testC0PolyhedronMethods(), ConstraintOperatorTest::testCoreform(), ConnectedComponentsTest::testEdge(), MeshInputTest::testExodusIGASidesets(), MeshTriangulationTest::testFoundCenters(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), PointLocatorTest::testPlanar(), MeshTriangulationTest::testPoly2TriRefinementBase(), SystemsTest::testProjectCubeWithMeshFunction(), BoundaryInfoTest::testRenumber(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), MeshTriangulationTest::testTriangulatorInterp(), MeshTriangulationTest::testTriangulatorMeshedHoles(), MeshTriangulationTest::testTriangulatorRoundHole(), libMesh::MeshTools::total_weight(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::Poly2TriTriangulator::triangulate(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), update_current_local_solution(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::MeshTools::volume(), libMesh::STLIO::write(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::VTKIO::write_nodal_data(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), libMesh::RBEvaluation::write_out_vectors(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::RBDataSerialization::RBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::TransientRBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::RBEIMEvaluationSerialization::write_to_file(), and libMesh::RBDataSerialization::RBSCMEvaluationSerialization::write_to_file().
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true
when this equation system contains identical data, up to the given threshold. Delegates most of the comparisons to perform to the responsible systems Definition at line 1602 of file equation_systems.C.
References libMesh::EquationSystems::_systems, libMesh::EquationSystems::get_system(), libMesh::EquationSystems::n_systems(), and libMesh::out.
Referenced by do_compare().
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Definition at line 100 of file reference_counter.C.
References libMesh::ReferenceCounter::_enable_print_counter.
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Calls to reinit() will not try to coarsen or refine the mesh.
Definition at line 574 of file equation_systems.h.
References libMesh::EquationSystems::_refine_in_reinit.
Referenced by EquationSystemsTest::testRefineThenReinitPreserveFlags(), and EquationSystemsTest::testSelectivePRefine().
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Enable or disable default ghosting functors on the Mesh and on all Systems.
Standard ghosting is enabled by default. If disabled, default ghosting will also be disabled on any later added systems.
Unless other equivalent ghosting functors have been added, removing the default coupling functor is only safe for explicit solves, and removing the default algebraic ghosting functor is only safe for codes where no evaluations on neighbor cells (e.g. no jump error estimators) are done.
Definition at line 305 of file equation_systems.C.
References libMesh::EquationSystems::_enable_default_ghosting, libMesh::DofMap::add_default_ghosting(), libMesh::EquationSystems::get_mesh(), libMesh::EquationSystems::get_system(), libMesh::make_range(), mesh, libMesh::EquationSystems::n_systems(), and libMesh::DofMap::remove_default_ghosting().
Referenced by EquationSystemsTest::testDisableDefaultGhosting().
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Methods to enable/disable the reference counter output from print_info()
Definition at line 94 of file reference_counter.C.
References libMesh::ReferenceCounter::_enable_print_counter.
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Calls to reinit() will also do two-step coarsen-then-refine.
Definition at line 569 of file equation_systems.h.
References libMesh::EquationSystems::_refine_in_reinit.
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Finds system and variable numbers for any variables of 'type' or of 'types' corresponding to the entries in the input 'names' vector.
If 'names' is empty, this returns all variables of the type. The names of vector variables are decomposed into individual ones suffixed with their cartesian component, but there will still be a single pair of system numbers for such vector variables. Thus, the size of the 'names' vector modified by this function may not be equal to that of the returned vector of pairs. Nevertheless, both should be sorted in accordance with ExodusII format, and so the developer just needs to know to separate dof_indices when accessing the system solution for vector variables.
This function is designed to work for either a single type or a vector of types, but not both. This is because it can't simply be called a second time with another type as it filters (deletes) the names of those on the first call that used a different type. Thus, the 'types' argument is for the case where variables of multiple types are allowed to pass through.
TODO: find a more generic way to handle this whole procedure.
Definition at line 1046 of file equation_systems.C.
References dim, libMesh::FEInterface::field_type(), libMesh::index_range(), libMesh::Utility::iota(), libMesh::libmesh_assert(), libMesh::make_range(), libMesh::System::n_vars(), libMesh::Quality::name(), libMesh::System::number(), libMesh::TYPE_VECTOR, libMesh::System::variable_name(), and libMesh::System::variable_type().
Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::Nemesis_IO::write_element_data(), and libMesh::Nemesis_IO::write_nodal_data().
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Gets a string containing the reference information.
Definition at line 47 of file reference_counter.C.
References libMesh::ReferenceCounter::_counts, and libMesh::Quality::name().
Referenced by libMesh::ReferenceCounter::print_info().
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Definition at line 1657 of file equation_systems.C.
References libMesh::EquationSystems::_systems, and libMesh::EquationSystems::n_systems().
Referenced by libMesh::EquationSystems::print_info().
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Definition at line 646 of file equation_systems.h.
References libMesh::EquationSystems::_mesh.
Referenced by libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), alternative_fe_assembly(), assemble(), LinearElasticity::assemble(), assemble_1D(), assemble_biharmonic(), assemble_cd(), assemble_divgrad(), assemble_elasticity(), assemble_ellipticdg(), assemble_func(), assemble_graddiv(), assemble_helmholtz(), assemble_laplace(), assemble_mass(), assemble_matrices(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_SchroedingerEquation(), assemble_shell(), assemble_stokes(), assemble_wave(), assembly_with_dg_fem_context(), libMesh::EquationSystems::build_variable_names(), compute_stresses(), LinearElasticity::compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::EquationSystems::enable_default_ghosting(), libMesh::AdjointRefinementEstimator::estimate_error(), fe_assembly(), fill_dirichlet_bc(), libMesh::MeshFunction::init(), LaplaceYoung::jacobian(), LargeDeformationElasticity::jacobian(), periodic_bc_test_poisson(), libMesh::EquationSystems::read(), libMesh::EquationSystems::reinit_solutions(), LaplaceYoung::residual(), LargeDeformationElasticity::residual(), run_timestepping(), scale_mesh_and_plot(), libMesh::DirectSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::DTKSolutionTransfer::transfer(), transform_mesh_and_plot(), libMesh::EquationSystems::write(), libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems(), libMesh::MeshOutput< MeshBase >::write_equation_systems(), libMesh::Nemesis_IO_Helper::write_nodal_solution(), write_output(), and write_output_solvedata().
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Definition at line 654 of file equation_systems.h.
References libMesh::EquationSystems::_mesh.
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Retrieve the solution data for CONSTANT MONOMIALs and/or components of CONSTANT MONOMIAL_VECs.
If 'names' is populated, only the variables corresponding to those names will be retrieved. This can be used to filter which variables are retrieved.
Definition at line 1016 of file equation_systems.C.
References libMesh::EquationSystems::build_elemental_solution_vector().
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name
. The template argument defines the return type. For example, const SteadySystem & sys = eq.get_system<SteadySystem> ("sys"); is an example of how the method might be used Definition at line 757 of file equation_systems.h.
References libMesh::EquationSystems::_systems, and libMesh::Quality::name().
Referenced by libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::EquationSystems::_remove_default_ghosting(), add_M_C_K_helmholtz(), libMesh::EnsightIO::add_scalar(), libMesh::RBSCMConstruction::add_scaled_symm_Aq(), libMesh::EquationSystems::add_system(), libMesh::EnsightIO::add_vector(), libMesh::EquationSystems::adjoint_solve(), libMesh::EquationSystems::allgather(), alternative_fe_assembly(), apply_initial(), assemble(), LinearElasticity::assemble(), assemble_1D(), assemble_biharmonic(), assemble_cd(), assemble_divgrad(), assemble_elasticity(), assemble_ellipticdg(), assemble_func(), assemble_graddiv(), assemble_helmholtz(), assemble_laplace(), assemble_mass(), assemble_matrices(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_SchroedingerEquation(), assemble_shell(), assemble_stokes(), assemble_wave(), assembly_with_dg_fem_context(), libMesh::ExactSolution::attach_exact_deriv(), libMesh::ExactSolution::attach_exact_hessian(), libMesh::ExactSolution::attach_exact_value(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::compare(), libMesh::ExactSolution::compute_error(), compute_stresses(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::GMVIO::copy_nodal_solution(), SolidSystem::element_time_derivative(), libMesh::EquationSystems::enable_default_ghosting(), libMesh::ExactSolution::error_norm(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ErrorEstimator::estimate_errors(), libMesh::ExactSolution::ExactSolution(), fe_assembly(), fill_dirichlet_bc(), libMesh::DTKAdapter::find_sys(), form_functionA(), form_functionB(), form_matrixA(), libMesh::EquationSystems::init(), init_cd(), SolidSystem::init_data(), init_sys(), initialize(), LaplaceYoung::jacobian(), LargeDeformationElasticity::jacobian(), line_print(), libMesh::RBSCMConstruction::load_matrix_B(), main(), libMesh::RBSCMConstruction::perform_SCM_greedy(), periodic_bc_test_poisson(), libMesh::EquationSystems::read(), libMesh::EquationSystems::reinit_mesh(), libMesh::EquationSystems::reinit_solutions(), libMesh::EquationSystems::reinit_systems(), LaplaceYoung::residual(), LargeDeformationElasticity::residual(), run_timestepping(), SolidSystem::save_initial_mesh(), libMesh::EquationSystems::sensitivity_solve(), set_initial_condition(), SolidSystem::side_time_derivative(), libMesh::EquationSystems::solve(), MixedDimensionMeshTest::testDofOrdering(), MixedDimensionRefinedMeshTest::testDofOrdering(), MixedDimensionNonUniformRefinement::testDofOrdering(), MixedDimensionNonUniformRefinementTriangle::testDofOrdering(), MixedDimensionNonUniformRefinement3D::testDofOrdering(), SlitMeshRefinedSystemTest::testRestart(), libMesh::EquationSystems::update(), libMesh::Nemesis_IO_Helper::write_element_values(), libMesh::Nemesis_IO_Helper::write_nodal_solution(), libMesh::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().
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name
. The template argument defines the return type. For example, const SteadySystem & sys = eq.get_system<SteadySystem> ("sys"); is an example of how the method might be used Definition at line 776 of file equation_systems.h.
References libMesh::EquationSystems::_systems, and libMesh::Quality::name().
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num
. The template argument defines the return type. For example, const SteadySystem & sys = eq.get_system<SteadySystem> (0); is an example of how the method might be used Definition at line 716 of file equation_systems.h.
References libMesh::EquationSystems::_systems, and libMesh::EquationSystems::n_systems().
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inlineinherited |
num
. The template argument defines the return type. For example, const SteadySystem & sys = eq.get_system<SteadySystem> (0); is an example of how the method might be used Definition at line 735 of file equation_systems.h.
References libMesh::EquationSystems::_systems, and libMesh::EquationSystems::n_systems().
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inlineinherited |
name
. Definition at line 795 of file equation_systems.h.
References libMesh::Quality::name().
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inlineinherited |
name
. Definition at line 803 of file equation_systems.h.
References libMesh::Quality::name().
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inlineinherited |
num
. Definition at line 811 of file equation_systems.h.
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inlineinherited |
num
. Definition at line 819 of file equation_systems.h.
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inherited |
Retrieve vars_active_subdomains
, which indicates the active subdomains for each variable in names
.
Definition at line 989 of file equation_systems.C.
References libMesh::EquationSystems::_systems, libMesh::Variable::active_subdomains(), distance(), and libMesh::make_range().
Referenced by libMesh::Nemesis_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data(), and libMesh::ExodusII_IO::write_element_data_from_discontinuous_nodal_data().
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inlineinherited |
true
if the system named name
exists within this EquationSystems object. Definition at line 704 of file equation_systems.h.
References libMesh::EquationSystems::_systems, and libMesh::Quality::name().
Referenced by libMesh::EnsightIO::add_scalar(), libMesh::EnsightIO::add_vector(), libMesh::ExactSolution::compute_error(), libMesh::ExactSolution::error_norm(), and main().
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inlineprotectednoexceptinherited |
Increments the construction counter.
Should be called in the constructor of any derived class that will be reference counted.
Definition at line 183 of file reference_counter.h.
References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.
Referenced by libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().
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inlineprotectednoexceptinherited |
Increments the destruction counter.
Should be called in the destructor of any derived class that will be reference counted.
Definition at line 207 of file reference_counter.h.
References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.
Referenced by libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().
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virtual |
Initialize all the systems.
Reimplemented from libMesh::EquationSystems.
Definition at line 212 of file biharmonic.C.
References _dt, _jr, _o_count, _verbose, libMesh::TriangleWrapper::init(), and libMesh::out.
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inherited |
Definition at line 1732 of file equation_systems.C.
References libMesh::EquationSystems::_systems.
Referenced by main(), and write_output_solvedata().
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inherited |
Definition at line 1719 of file equation_systems.C.
References libMesh::EquationSystems::_systems.
Referenced by Biharmonic::JR::bounds(), and Biharmonic::JR::residual_and_jacobian().
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inlinestaticinherited |
Prints the number of outstanding (created, but not yet destroyed) objects.
Definition at line 85 of file reference_counter.h.
References libMesh::ReferenceCounter::_n_objects.
Referenced by libMesh::LibMeshInit::~LibMeshInit().
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inlineinherited |
Definition at line 103 of file parallel_object.h.
References libMesh::ParallelObject::_communicator, libMesh::libmesh_assert(), and TIMPI::Communicator::size().
Referenced by libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::DofMap::add_constraints_to_send_list(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::System::add_vector(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::Partitioner::build_graph(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::EnsightIO::EnsightIO(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::MeshBase::get_info(), libMesh::StaticCondensation::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::Nemesis_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::DistributedMesh::insert_elem(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_elem_on_proc(), libMesh::DofMap::n_dofs_per_processor(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::Partitioner::partition(), libMesh::MeshBase::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::prepare_send_list(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_header(), libMesh::CheckpointIO::read_nodes(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::Partitioner::repartition(), OverlappingFunctorTest::run_partitioner_test(), libMesh::DofMap::scatter_constraints(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), WriteVecAndScalar::setupTests(), libMesh::RBEIMEvaluation::side_gather_bfs(), DistributedMeshTest::testRemoteElemError(), CheckpointIOTest::testSplitter(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().
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inlineinherited |
Definition at line 661 of file equation_systems.h.
References libMesh::EquationSystems::_systems.
Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::EquationSystems::add_system(), libMesh::EquationSystems::adjoint_solve(), libMesh::EquationSystems::allgather(), libMesh::ExactSolution::attach_exact_deriv(), libMesh::ExactSolution::attach_exact_hessian(), libMesh::ExactSolution::attach_exact_value(), libMesh::EquationSystems::compare(), libMesh::GMVIO::copy_nodal_solution(), libMesh::EquationSystems::enable_default_ghosting(), libMesh::ErrorEstimator::estimate_errors(), libMesh::ExactSolution::ExactSolution(), libMesh::DTKAdapter::find_sys(), libMesh::EquationSystems::get_info(), libMesh::EquationSystems::get_system(), libMesh::EquationSystems::init(), main(), libMesh::EquationSystems::reinit_mesh(), libMesh::EquationSystems::reinit_solutions(), libMesh::EquationSystems::reinit_systems(), libMesh::EquationSystems::sensitivity_solve(), libMesh::EquationSystems::solve(), and libMesh::EquationSystems::update().
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inherited |
Definition at line 1707 of file equation_systems.C.
References libMesh::EquationSystems::_systems.
Referenced by libMesh::EquationSystems::build_variable_names().
void Biharmonic::output | ( | int | timestep, |
const Real & | t, | ||
Real & | o_t, | ||
bool | force = false |
||
) |
Definition at line 253 of file biharmonic.C.
References _exio, _o_count, _o_dt, _ofile, _verbose, and libMesh::out.
Referenced by run().
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staticinherited |
Prints the reference information, by default to libMesh::out
.
Definition at line 81 of file reference_counter.C.
References libMesh::ReferenceCounter::_enable_print_counter, and libMesh::ReferenceCounter::get_info().
Referenced by libMesh::LibMeshInit::~LibMeshInit().
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inherited |
Prints information about the equation systems, by default to libMesh::out.
Definition at line 1690 of file equation_systems.C.
References libMesh::EquationSystems::get_info().
Referenced by assemble_and_solve(), do_compare(), main(), and libMesh::operator<<().
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inlineinherited |
Definition at line 114 of file parallel_object.h.
References libMesh::ParallelObject::_communicator, and TIMPI::Communicator::rank().
Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::Partitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::MeshFunction::check_found_elem(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::ExodusII_IO_Helper::close(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::compute_communication_map_parameters(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_node_communication_maps(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMapBase::end_dof(), libMesh::DofMapBase::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMapBase::first_dof(), libMesh::DofMapBase::first_old_dof(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::Nemesis_IO_Helper::get_cmap_params(), libMesh::Nemesis_IO_Helper::get_eb_info_global(), libMesh::Nemesis_IO_Helper::get_elem_cmap(), libMesh::Nemesis_IO_Helper::get_elem_map(), libMesh::MeshBase::get_info(), libMesh::DofMap::get_info(), libMesh::Nemesis_IO_Helper::get_init_global(), libMesh::Nemesis_IO_Helper::get_init_info(), libMesh::RBEIMEvaluation::get_interior_basis_functions_as_vecs(), libMesh::Nemesis_IO_Helper::get_loadbal_param(), libMesh::DofMap::get_local_constraints(), libMesh::MeshBase::get_local_constraints(), libMesh::Nemesis_IO_Helper::get_node_cmap(), libMesh::Nemesis_IO_Helper::get_node_map(), libMesh::Nemesis_IO_Helper::get_ns_param_global(), libMesh::Nemesis_IO_Helper::get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::LaplaceMeshSmoother::init(), libMesh::SystemSubsetBySubdomain::init(), HeatSystem::init_data(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::DistributedMesh::insert_elem(), libMesh::DofMap::is_evaluable(), libMesh::SparsityPattern::Build::join(), libMesh::TransientRBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBSCMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEvaluation::legacy_write_offline_data_to_files(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DofMap::local_variable_indices(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), AugmentSparsityOnInterface::mesh_reinit(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::MeshTools::n_connected_components(), libMesh::MeshBase::n_constraint_rows(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMapBase::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::DistributedMesh::own_node(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Nemesis_IO_Helper::put_cmap_params(), libMesh::Nemesis_IO_Helper::put_elem_cmap(), libMesh::Nemesis_IO_Helper::put_elem_map(), libMesh::Nemesis_IO_Helper::put_loadbal_param(), libMesh::Nemesis_IO_Helper::put_node_cmap(), libMesh::Nemesis_IO_Helper::put_node_map(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::DynaIO::read_mesh(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::System::read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::System::read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), libMesh::SimplexRefiner::refine_via_edges(), libMesh::StaticCondensationDofMap::reinit(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::RBEIMEvaluation::side_gather_bfs(), ExodusTest< elem_type >::test_read_gold(), ExodusTest< elem_type >::test_write(), MeshInputTest::testAbaqusRead(), MeshInputTest::testBadGmsh(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyElementVectorImpl(), MeshInputTest::testCopyNodalSolutionImpl(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testDynaFileMappings(), MeshInputTest::testDynaNoSplines(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusFileMappings(), MeshInputTest::testExodusIGASidesets(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), MeshInputTest::testGmshBCIDOverlap(), MeshInputTest::testGoodGmsh(), MeshInputTest::testGoodSTL(), MeshInputTest::testGoodSTLBinary(), MeshInputTest::testLowOrderEdgeBlocks(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testSolution(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), libMesh::MeshTools::total_weight(), libMesh::NetGenMeshInterface::triangulate(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::DTKAdapter::update_variable_values(), libMesh::MeshTools::volume(), libMesh::STLIO::write(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::EquationSystems::write(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_elemsets(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::System::write_header(), libMesh::ExodusII_IO::write_information_records(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), write_output_solvedata(), libMesh::System::write_parallel_data(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::System::write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), libMesh::ExodusII_IO_Helper::write_sideset_data(), libMesh::Nemesis_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO::write_timestep(), libMesh::ExodusII_IO_Helper::write_timestep(), and libMesh::ExodusII_IO::write_timestep_discontinuous().
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inherited |
Read & initialize the systems from disk using the XDR data format.
This format allows for machine-independent binary output.
Set which sections of the file to read by bitwise OR'ing the EquationSystems::ReadFlags enumeration together. For example, to read all sections of the file, set read_flags to: (READ_HEADER | READ_DATA | READ_ADDITIONAL_DATA)
If XdrMODE is omitted, it will be inferred as READ for filenames containing .xda or as DECODE for filenames containing .xdr
name | Name of the file to be read. |
read_flags | Single flag created by bitwise-OR'ing several flags together. |
mode | Controls whether reading is done in binary or ascii mode. |
partition_agnostic | If true then the mesh and degrees of freedom will be temporarily renumbered in a partition agnostic way so that files written using "n" mpi processes can be re-read on "m" mpi processes. This renumbering is not compatible with meshes that have two nodes in exactly the same position! |
Definition at line 89 of file equation_systems_io.C.
References libMesh::Quality::name(), and libMesh::ParallelObject::processor_id().
Referenced by main(), libMesh::EquationSystems::read(), libMesh::FileHistoryData::retrieve_adjoint_solution(), libMesh::FileHistoryData::retrieve_primal_solution(), and SlitMeshRefinedSystemTest::testRestart().
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inherited |
Definition at line 76 of file equation_systems_io.C.
References libMesh::DECODE, libMesh::Quality::name(), libMesh::READ, and libMesh::EquationSystems::read().
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inherited |
This program implements the output of an EquationSystems object. This warrants some documentation. The output file essentially consists of 11 sections:
1.) A version header (for non-'legacy' formats, libMesh-0.7.0 and greater). 2.) The number of individual equation systems (unsigned int) for each system 3.) The name of the system (string) 4.) The type of the system (string) handled through System::read(): +-------------------------------------------------------------+ | 5.) The number of variables in the system (unsigned int) | | | | for each variable in the system | | | | 6.) The name of the variable (string) | | | | 7.) Combined in an FEType: | | - The approximation order(s) of the variable (Order | | Enum, cast to int/s) | | - The finite element family/ies of the variable | | (FEFamily Enum, cast to int/s) | | | | end variable loop | | | | 8.) The number of additional vectors (unsigned int), | | | | for each additional vector in the equation system object | | | | 9.) the name of the additional vector (string) | +-------------------------------------------------------------+ end system loop for each system, handled through System::read_{serialized,parallel}_data(): +--------------------------------------------------------------+ | 10.) The global solution vector, re-ordered to be node-major | | (More on this later.) | | | | for each additional vector in the equation system object | | | | 11.) The global additional vector, re-ordered to be | | node-major (More on this later.) | +--------------------------------------------------------------+ end system loop
Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.
Definition at line 108 of file equation_systems_io.C.
References libMesh::EquationSystems::_mesh, libMesh::EquationSystems::add_system(), TIMPI::Communicator::broadcast(), libMesh::MeshRefinement::clean_refinement_flags(), libMesh::Xdr::close(), libMesh::ParallelObject::comm(), libMesh::Xdr::data(), libMesh::MeshBase::fix_broken_node_and_element_numbering(), libMesh::EquationSystems::get_mesh(), libMesh::EquationSystems::get_system(), libMesh::MeshTools::Private::globally_renumber_nodes_and_elements(), libMesh::EquationSystems::init(), libMesh::libmesh_assert(), mesh, libMesh::ParallelObject::processor_id(), libMesh::EquationSystems::read(), libMesh::EquationSystems::READ_ADDITIONAL_DATA, libMesh::EquationSystems::READ_BASIC_ONLY, libMesh::EquationSystems::READ_DATA, libMesh::EquationSystems::READ_HEADER, libMesh::System::read_header(), libMesh::EquationSystems::READ_LEGACY_FORMAT, libMesh::Xdr::reading(), libMesh::System::set_basic_system_only(), libMesh::Xdr::set_version(), libMesh::EquationSystems::TRY_READ_IFEMS, and libMesh::EquationSystems::update().
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staticinherited |
Definition at line 1577 of file equation_systems.C.
References libMesh::Elem::active(), libMesh::DofObject::id(), libMesh::libmesh_assert(), libMesh::Elem::neighbor_ptr(), and libMesh::remote_elem.
Referenced by libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), and libMesh::ExodusII_IO::write_nodal_data().
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inlineinherited |
Definition at line 579 of file equation_systems.h.
References libMesh::EquationSystems::_refine_in_reinit.
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virtualinherited |
Handle any mesh changes and reinitialize all the systems on the updated mesh.
Definition at line 92 of file equation_systems.C.
References libMesh::EquationSystems::reinit_solutions(), and libMesh::EquationSystems::reinit_systems().
Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), assemble_and_solve(), libMesh::AdjointRefinementEstimator::estimate_error(), main(), run_timestepping(), SystemsTest::test2DProjectVectorFE(), SystemsTest::test3DProjectVectorFE(), EquationSystemsTest::testBadVarNames(), MeshAssignTest::testMeshMoveAssign(), EquationSystemsTest::testPostInitAddElem(), EquationSystemsTest::testPostInitAddRealSystem(), EquationSystemsTest::testPostInitAddSystem(), SystemsTest::testProjectCube(), SystemsTest::testProjectLine(), SystemsTest::testProjectSquare(), InfFERadialTest::testRefinement(), EquationSystemsTest::testRefineThenReinitPreserveFlags(), EquationSystemsTest::testReinitWithNodeElem(), EquationSystemsTest::testRepartitionThenReinit(), and EquationSystemsTest::testSelectivePRefine().
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Handle the association of a completely new mesh with the EquationSystem and all the Systems assigned to it.
Definition at line 102 of file equation_systems.C.
References libMesh::EquationSystems::_mesh, libMesh::MeshRefinement::clean_refinement_flags(), libMesh::EquationSystems::get_system(), libMesh::make_range(), and libMesh::EquationSystems::n_systems().
Referenced by libMesh::EquationSystems::init(), and MeshAssignTest::testMeshMoveAssign().
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Handle any mesh changes and project any solutions onto the updated mesh.
Definition at line 131 of file equation_systems.C.
References libMesh::EquationSystems::_mesh, libMesh::EquationSystems::_refine_in_reinit, libMesh::MeshRefinement::coarsen_elements(), libMesh::MeshBase::contract(), libMesh::DofMap::distribute_dofs(), libMesh::MeshRefinement::face_level_mismatch_limit(), libMesh::System::get_dof_map(), libMesh::EquationSystems::get_mesh(), libMesh::EquationSystems::get_system(), libMesh::make_range(), libMesh::EquationSystems::n_systems(), libMesh::MeshRefinement::overrefined_boundary_limit(), libMesh::System::prolong_vectors(), libMesh::MeshRefinement::refine_elements(), libMesh::System::reinit_constraints(), libMesh::System::restrict_vectors(), and libMesh::MeshRefinement::underrefined_boundary_limit().
Referenced by libMesh::EquationSystems::reinit().
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Reinitialize all systems on the current mesh.
Definition at line 257 of file equation_systems.C.
References libMesh::EquationSystems::get_system(), libMesh::make_range(), and libMesh::EquationSystems::n_systems().
Referenced by libMesh::EquationSystems::reinit().
void Biharmonic::run | ( | ) |
Definition at line 289 of file biharmonic.C.
References _dt, _t0, _t1, _verbose, libMesh::out, output(), libMesh::Real, and step().
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Call sensitivity_solve
on all the individual equation systems.
By default this function solves each sensitivity system once, in the order in which in which they were added. For more sophisticated decoupled problems the user may with to override this behavior in a derived class.
Definition at line 430 of file equation_systems.C.
References libMesh::EquationSystems::get_system(), libMesh::libmesh_assert(), libMesh::make_range(), and libMesh::EquationSystems::n_systems().
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Call solve
on all the individual equation systems.
By default this function solves each equation system once, in the order they were added. For more sophisticated decoupled problems the user may with to override this behavior in a derived class.
Definition at line 420 of file equation_systems.C.
References libMesh::EquationSystems::get_system(), libMesh::libmesh_assert(), libMesh::make_range(), and libMesh::EquationSystems::n_systems().
Referenced by libMesh::UniformRefinementEstimator::_estimate_error().
void Biharmonic::step | ( | const Real & | dt = -1.0 | ) |
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Updates local values for all the systems.
Definition at line 327 of file equation_systems.C.
References libMesh::EquationSystems::get_system(), libMesh::make_range(), and libMesh::EquationSystems::n_systems().
Referenced by main(), and libMesh::EquationSystems::read().
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void Biharmonic::viewParameters | ( | ) |
Definition at line 165 of file biharmonic.C.
References _cahn_hillard, _cnWeight, _degenerate, _dim, _dt0, _energy, _growth, _initialCenter, _initialState, _initialWidth, _kappa, _log_truncation, _N, _netforce, _o_dt, _ofile_base, _T, _t0, _t1, _theta, _theta_c, _tol, _verbose, BALL, int, libMesh::out, ROD, and STRIP.
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Write the systems to disk using the XDR data format.
This format allows for machine-independent binary output.
Set the writing properties using the EquationSystems::WriteFlags enumeration. Set which sections to write out by bitwise OR'ing the enumeration values. Write everything by setting write_flags to: (WRITE_DATA | WRITE_ADDITIONAL_DATA)
If XdrMODE is omitted, it will be inferred as WRITE for filenames containing .xda or as ENCODE for filenames containing .xdr
name | Name of the file to be read. |
write_flags | Single flag created by bitwise-OR'ing several flags together. |
mode | Controls whether reading is done in binary or ascii mode. |
partition_agnostic | If true then the mesh and degrees of freedom will be temporarily renumbered in a partition agnostic way so that files written using "n" mpi processes can be re-read on "m" mpi processes. This renumbering is not compatible with meshes that have two nodes in exactly the same position! |
Definition at line 350 of file equation_systems_io.C.
References libMesh::Quality::name(), libMesh::ParallelObject::processor_id(), libMesh::EquationSystems::WRITE_DATA, and libMesh::EquationSystems::WRITE_PARALLEL_FILES.
Referenced by main(), libMesh::ErrorVector::plot_error(), libMesh::FileHistoryData::rewrite_stored_solution(), libMesh::FileHistoryData::store_adjoint_solution(), libMesh::FileHistoryData::store_initial_solution(), libMesh::FileHistoryData::store_primal_solution(), libMesh::EquationSystems::write(), libMesh::NameBasedIO::write_equation_systems(), and write_output().
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Definition at line 338 of file equation_systems_io.C.
References libMesh::ENCODE, libMesh::Quality::name(), libMesh::WRITE, and libMesh::EquationSystems::write().
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This program implements the output of an EquationSystems object. This warrants some documentation. The output file essentially consists of 11 sections:
1.) The version header. 2.) The number of individual equation systems (unsigned int) for each system 3.) The name of the system (string) 4.) The type of the system (string) handled through System::read(): +-------------------------------------------------------------+ | 5.) The number of variables in the system (unsigned int) | | | | for each variable in the system | | | | 6.) The name of the variable (string) | | | | 7.) Combined in an FEType: | | - The approximation order(s) of the variable (Order | | Enum, cast to int/s) | | - The finite element family/ies of the variable | | (FEFamily Enum, cast to int/s) | | | | end variable loop | | | | 8.) The number of additional vectors (unsigned int), | | | | for each additional vector in the equation system object | | | | 9.) the name of the additional vector (string) | +-------------------------------------------------------------+ end system loop for each system, handled through System::write_{serialized,parallel}_data(): +--------------------------------------------------------------+ | 10.) The global solution vector, re-ordered to be node-major | | (More on this later.) | | | | for each additional vector in the equation system object | | | | 11.) The global additional vector, re-ordered to be | | node-major (More on this later.) | +--------------------------------------------------------------+ end system loop
Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will write XDR or ASCII files with no changes.
Definition at line 367 of file equation_systems_io.C.
References libMesh::EquationSystems::_mesh, libMesh::EquationSystems::_systems, libMesh::Xdr::close(), libMesh::Xdr::data(), libMesh::get_io_compatibility_version(), libMesh::EquationSystems::get_mesh(), libMesh::MeshTools::Private::globally_renumber_nodes_and_elements(), libMesh::libmesh_assert(), mesh, libMesh::ParallelObject::processor_id(), libMesh::Xdr::set_version(), libMesh::EquationSystems::WRITE_ADDITIONAL_DATA, libMesh::EquationSystems::WRITE_DATA, libMesh::EquationSystems::WRITE_PARALLEL_FILES, and libMesh::Xdr::writing().
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Definition at line 110 of file biharmonic.h.
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Definition at line 95 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 103 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 120 of file parallel_object.h.
Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::StaticCondensation::close(), libMesh::ParallelObject::comm(), libMesh::CondensedEigenSystem::initialize_condensed_matrices(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), libMesh::ParallelObject::processor_id(), libMesh::BoundaryInfo::regenerate_id_sets(), and libMesh::StaticCondensationDofMap::reinit().
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Actually holds the data.
Definition at line 124 of file reference_counter.h.
Referenced by libMesh::ReferenceCounter::get_info().
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Definition at line 95 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 92 of file biharmonic.h.
Referenced by Biharmonic(), Biharmonic::JR::JR(), and viewParameters().
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Definition at line 102 of file biharmonic.h.
Referenced by Biharmonic(), dt0(), step(), and viewParameters().
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Flag for whether to enable default ghosting on newly added Systems.
Default value: true
Definition at line 623 of file equation_systems.h.
Referenced by libMesh::EquationSystems::add_system(), and libMesh::EquationSystems::enable_default_ghosting().
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Flag to control whether reference count information is printed when print_info is called.
Definition at line 143 of file reference_counter.h.
Referenced by libMesh::ReferenceCounter::disable_print_counter_info(), libMesh::ReferenceCounter::enable_print_counter_info(), and libMesh::ReferenceCounter::print_info().
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Definition at line 96 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 106 of file biharmonic.h.
Referenced by Biharmonic(), and output().
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Definition at line 95 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 100 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 99 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 101 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 113 of file biharmonic.h.
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Definition at line 93 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 97 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 111 of file biharmonic.h.
Referenced by Biharmonic().
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Mutual exclusion object to enable thread-safe reference counting.
Definition at line 137 of file reference_counter.h.
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Definition at line 92 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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The number of objects.
Print the reference count information when the number returns to 0.
Definition at line 132 of file reference_counter.h.
Referenced by libMesh::ReferenceCounter::n_objects(), libMesh::ReferenceCounter::ReferenceCounter(), and libMesh::ReferenceCounter::~ReferenceCounter().
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Definition at line 95 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 108 of file biharmonic.h.
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Definition at line 107 of file biharmonic.h.
Referenced by Biharmonic(), output(), and viewParameters().
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Definition at line 105 of file biharmonic.h.
Referenced by Biharmonic(), and output().
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Definition at line 105 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Flag for whether to call coarsen/refine in reinit().
Default value: true
Definition at line 617 of file equation_systems.h.
Referenced by libMesh::EquationSystems::disable_refine_in_reinit(), libMesh::EquationSystems::enable_refine_in_reinit(), libMesh::EquationSystems::refine_in_reinit_flag(), and libMesh::EquationSystems::reinit_solutions().
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Data structure holding the systems.
Definition at line 611 of file equation_systems.h.
Referenced by libMesh::EquationSystems::add_system(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::EquationSystems::build_variable_names(), libMesh::EquationSystems::clear(), libMesh::EquationSystems::compare(), libMesh::EquationSystems::get_info(), libMesh::EquationSystems::get_system(), libMesh::EquationSystems::get_vars_active_subdomains(), libMesh::EquationSystems::has_system(), libMesh::EquationSystems::n_active_dofs(), libMesh::EquationSystems::n_dofs(), libMesh::EquationSystems::n_systems(), libMesh::EquationSystems::n_vars(), and libMesh::EquationSystems::write().
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Definition at line 102 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 102 of file biharmonic.h.
Referenced by Biharmonic(), run(), and viewParameters().
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Definition at line 102 of file biharmonic.h.
Referenced by Biharmonic(), run(), and viewParameters().
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Definition at line 93 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 93 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 94 of file biharmonic.h.
Referenced by Biharmonic(), and viewParameters().
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Definition at line 98 of file biharmonic.h.
Referenced by Biharmonic(), init(), output(), run(), verbose(), and viewParameters().
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Data structure holding arbitrary parameters.
Definition at line 597 of file equation_systems.h.
Referenced by add_M_C_K_helmholtz(), assemble_biharmonic(), assemble_cd(), assemble_divgrad(), assemble_ellipticdg(), assemble_func(), assemble_helmholtz(), assemble_poisson(), assemble_SchroedingerEquation(), assemble_shell(), assemble_stokes(), assemble_wave(), libMesh::ExactSolution::attach_exact_deriv(), libMesh::ExactSolution::attach_exact_hessian(), libMesh::ExactSolution::attach_exact_value(), libMesh::NewmarkSystem::clear(), libMesh::EquationSystems::clear(), libMesh::FrequencySystem::clear_all(), compute_jacobian(), compute_residual(), LinearElasticityWithContact::compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::EquationSystems::EquationSystems(), fe_assembly(), fill_dirichlet_bc(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::ImplicitSystem::get_linear_solve_parameters(), libMesh::FEComputeData::init(), init_cd(), HeatSystem::init_data(), libMesh::FrequencySystem::init_data(), init_sys(), initialize(), LargeDeformationElasticity::jacobian(), line_print(), main(), libMesh::FrequencySystem::n_frequencies(), libMesh::NewmarkSystem::NewmarkSystem(), libMesh::NonlinearImplicitSystem::NonlinearImplicitSystem(), LargeDeformationElasticity::residual(), LinearElasticityWithContact::residual_and_jacobian(), run_timestepping(), libMesh::FrequencySystem::set_current_frequency(), libMesh::FrequencySystem::set_frequencies(), libMesh::FrequencySystem::set_frequencies_by_range(), libMesh::FrequencySystem::set_frequencies_by_steps(), set_initial_condition(), libMesh::NewmarkSystem::set_newmark_parameters(), libMesh::NonlinearImplicitSystem::set_solver_parameters(), setup(), SolidSystem::side_time_derivative(), libMesh::RBConstruction::solve_for_matrix_and_rhs(), libMesh::EigenSystem::solve_helper(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), MeshFunctionTest::test_subdomain_id_sets(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyNodalSolutionImpl(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), SystemsTest::testProjectCube(), SystemsTest::testProjectCubeWithMeshFunction(), MeshInputTest::testProjectionRegression(), SystemsTest::testProjectLine(), SystemsTest::testProjectSquare(), EquationSystemsTest::testRepartitionThenReinit(), SystemsTest::testSetSystemParameterOverEquationSystem(), MeshInputTest::testSingleElementImpl(), and libMesh::WrappedFunction< Output >::WrappedFunction().