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>

Inheritance diagram for Biharmonic:

[legend]

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	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 (const std::string &name) const

template<typename T_sys >
const T_sys &	get_system (const std::string &name) const

template<typename T_sys >
T_sys &	get_system (const std::string &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 (const std::string &name) const

System &	get_system (const std::string &name)

const System &	get_system (const unsigned int num) const

System &	get_system (const unsigned int num)

virtual System &	add_system (const std::string &system_type, const std::string &name)
	Add the system of type `system_type` named `name` to the systems array. More...

template<typename T_sys >
T_sys &	add_system (const std::string &name)
	Add the system named `name` to the systems array. More...

void	delete_system (const std::string &name)
	Remove the system named `name` from 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 &parameters)
	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, const std::string &system_name, const std::string &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) 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) 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. More...

void	build_elemental_solution_vector (std::vector< Number > &soln, std::vector< std::string > &names) const
	Retrieve the solution data for CONSTANT MONOMIALs. More...

std::unique_ptr< NumericVector< Number > >	build_parallel_elemental_solution_vector (std::vector< std::string > &names) const
	Builds a parallel vector of CONSTANT MONOMIAL 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
	Fill the input vector `soln` with solution values. More...

template<typename InValType >
void	read (const std::string &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...

void	read (const std::string &name, const XdrMODE mode, const unsigned int read_flags=(READ_HEADER\|READ_DATA), bool partition_agnostic=true)

template<typename InValType >
void	read (const std::string &name, const unsigned int read_flags=(READ_HEADER\|READ_DATA), bool partition_agnostic=true)

void	read (const std::string &name, const unsigned int read_flags=(READ_HEADER\|READ_DATA), bool partition_agnostic=true)

void	write (const std::string &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 (const std::string &name, const unsigned int write_flags=(WRITE_DATA), bool partition_agnostic=true) 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 std::string	get_info ()
	Gets a string containing the reference information. More...

static void	print_info (std::ostream &out=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, System * >::iterator	system_iterator
	Typedef for system iterators. More...

typedef std::map< std::string, System * >::const_iterator	const_system_iterator
	Typedef for constant system iterators. More...

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)
	Increments the construction counter. More...

void	increment_destructor_count (const std::string &name)
	Increments the destruction counter. More...

Protected Attributes
std::map< std::string, System * >	_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
	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

Detailed Description

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.

Member Typedef Documentation

◆ const_system_iterator

typedef std::map<std::string, System *>::const_iterator libMesh::EquationSystems::const_system_iterator

protectedinherited

Typedef for constant system iterators.

Definition at line 566 of file equation_systems.h.

◆ Counts

typedef std::map<std::string, std::pair<unsigned int, unsigned int> > libMesh::ReferenceCounter::Counts

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 117 of file reference_counter.h.

◆ system_iterator

typedef std::map<std::string, System *>::iterator libMesh::EquationSystems::system_iterator

protectedinherited

Typedef for system iterators.

Definition at line 561 of file equation_systems.h.

Member Enumeration Documentation

◆ FreeEnergyEnum

enum Biharmonic::FreeEnergyEnum

Enumerator
DOUBLE_WELL
DOUBLE_OBSTACLE
LOG_DOUBLE_WELL
LOG_DOUBLE_OBSTACLE

Definition at line 54 of file biharmonic.h.

                       {DOUBLE_WELL         = 1,
                        DOUBLE_OBSTACLE     = 2,
                        LOG_DOUBLE_WELL     = 3,
                        LOG_DOUBLE_OBSTACLE = 4};

◆ InitialStateEnum

enum Biharmonic::InitialStateEnum

Enumerator
STRIP
ROD
BALL

Definition at line 49 of file biharmonic.h.

                         {STRIP = 0,
                          ROD   = 1,
                          BALL  = 2};

◆ ReadFlags

enum libMesh::EquationSystems::ReadFlags

inherited

Define enumeration to set properties in EquationSystems::read()

Enumerator
READ_HEADER
READ_DATA
READ_ADDITIONAL_DATA
READ_LEGACY_FORMAT
TRY_READ_IFEMS
READ_BASIC_ONLY

Definition at line 83 of file equation_systems.h.

                  { READ_HEADER           = 1,
                    READ_DATA             = 2,
                    READ_ADDITIONAL_DATA  = 4,
                    READ_LEGACY_FORMAT    = 8,
                    TRY_READ_IFEMS        = 16,
                    READ_BASIC_ONLY       = 32 };

◆ WriteFlags

enum libMesh::EquationSystems::WriteFlags

inherited

Define enumeration to set properties in EquationSystems::write()

Enumerator
WRITE_DATA
WRITE_ADDITIONAL_DATA
WRITE_PARALLEL_FILES
WRITE_SERIAL_FILES

Definition at line 93 of file equation_systems.h.

                   { WRITE_DATA             = 1,
                     WRITE_ADDITIONAL_DATA  = 2,
                     WRITE_PARALLEL_FILES   = 4,
                     WRITE_SERIAL_FILES     = 8 };

Constructor & Destructor Documentation

◆ Biharmonic()

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.

◆ ~Biharmonic()

Biharmonic::~Biharmonic ( )

Destructor.

Definition at line 72 of file biharmonic.h.

   {
     // delete _meshRefinement;
   }

Member Function Documentation

◆ add_system() [1/2]

virtual System& libMesh::EquationSystems::add_system	(	const std::string &	system_type,
		const std::string &	name
	)

virtualinherited

Add the system of type system_type named name to the systems array.

Referenced by build_system(), TimeSolverTestImplementation< TimeSolverType >::run_test_with_exact_soln(), and FETest< order, family, elem_type >::setUp().

◆ add_system() [2/2]

template<typename T_sys >

T_sys & libMesh::EquationSystems::add_system ( const std::string & name )

inherited

Add the system named name to the systems array.

Definition at line 647 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().

 {
   T_sys * ptr = nullptr;
 
   if (!_systems.count(name))
     {
       const unsigned int sys_num = this->n_systems();
       ptr = new T_sys(*this, name, sys_num);
 
       _systems.insert (std::make_pair(name, ptr));
 
       if (!_enable_default_ghosting)
         this->_remove_default_ghosting(sys_num);
 
       // Tell all the \p DofObject entities to add a system.
       this->_add_system_to_nodes_and_elems();
     }
   else
     {
       // We now allow redundant add_system calls, to make it
       // easier to load data from files for user-derived system
       // subclasses
       ptr = &(this->get_system<T_sys>(name));
     }
 
   // Return a dynamically casted reference to the newly added System.
   return *ptr;
 }

◆ adjoint_solve()

virtual void libMesh::EquationSystems::adjoint_solve ( const QoISet & qoi_indices = QoISet() )

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.

◆ allgather()

void libMesh::EquationSystems::allgather ( )

inherited

Serializes a distributed mesh and its associated degree of freedom numbering for all systems.

◆ build_discontinuous_solution_vector()

void libMesh::EquationSystems::build_discontinuous_solution_vector	(	std::vector< Number > &	soln,
		const std::set< std::string > *	system_names = `nullptr`
	)		const

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.

◆ build_elemental_solution_vector()

void libMesh::EquationSystems::build_elemental_solution_vector	(	std::vector< Number > &	soln,
		std::vector< std::string > &	names
	)		const

inherited

Retrieve the solution data for CONSTANT MONOMIALs.

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.

◆ build_parallel_elemental_solution_vector()

std::unique_ptr<NumericVector<Number> > libMesh::EquationSystems::build_parallel_elemental_solution_vector ( std::vector< std::string > & names ) const

inherited

Builds a parallel vector of CONSTANT MONOMIAL 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 variables exist on the system) or a std::unique_ptr to a var-major numeric vector of total length n_elem * n_vars 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.

◆ build_parallel_solution_vector()

std::unique_ptr<NumericVector<Number> > libMesh::EquationSystems::build_parallel_solution_vector ( const std::set< std::string > * system_names = nullptr ) const

inherited

A version of build_solution_vector which is appropriate for "parallel" output formats like Nemesis.

Returns: A std::unique_ptr to a node-major NumericVector of total length n_nodes*n_vars that various I/O classes can then use to get the local values they need to write on each processor.

◆ build_solution_vector() [1/2]

void libMesh::EquationSystems::build_solution_vector	(	std::vector< Number > &	soln,
		const std::string &	system_name,
		const std::string &	variable_name = `"all_vars"`
	)		const

inherited

Fill the input vector soln with the solution values for the system named name.

Note: The input vector soln will only be assembled on processor 0, so this method is only applicable to outputting plot files from processor 0.

◆ build_solution_vector() [2/2]

void libMesh::EquationSystems::build_solution_vector	(	std::vector< Number > &	soln,
		const std::set< std::string > *	system_names = `nullptr`
	)		const

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.

◆ build_variable_names()

void libMesh::EquationSystems::build_variable_names	(	std::vector< std::string > &	var_names,
		const FEType *	type = `nullptr`,
		const std::set< std::string > *	system_names = `nullptr`
	)		const

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.

◆ clear()

virtual void libMesh::EquationSystems::clear ( )

virtualinherited

Restores the data structure to a pristine state.

◆ comm()

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const

inherited

Returns: A reference to the Parallel::Communicator object used by this mesh.

Definition at line 87 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::EpetraVector< T >::EpetraVector(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), and libMesh::Parallel::sync_node_data_by_element_id_once().

88 { return _communicator; }

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:105

◆ compare()

virtual bool libMesh::EquationSystems::compare	(	const EquationSystems &	other_es,
		const Real	threshold,
		const bool	verbose
	)		const

virtualinherited

Returns: true when this equation system contains identical data, up to the given threshold. Delegates most of the comparisons to perform to the responsible systems

◆ delete_system()

void libMesh::EquationSystems::delete_system ( const std::string & name )

inherited

Remove the system named name from the systems array.

Deprecated:: This function may not work as intended and has not been actively tested over the years. If you need the ability to delete a System from an EquationSystems object, it could probably be added.

◆ disable_print_counter_info()

static void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

◆ disable_refine_in_reinit()

void libMesh::EquationSystems::disable_refine_in_reinit ( )

inherited

Calls to reinit() will not try to coarsen or refine the mesh.

Definition at line 519 of file equation_systems.h.

References libMesh::EquationSystems::_refine_in_reinit.

519 { this->_refine_in_reinit = false; }

libMesh::EquationSystems::_refine_in_reinit

bool _refine_in_reinit

Flag for whether to call coarsen/refine in reinit().

Definition: equation_systems.h:572

◆ dt()

Real Biharmonic::dt ( )

Definition at line 81 of file biharmonic.h.

References _dt.

81 { return _dt; }

Biharmonic::_dt

Real _dt

Definition: biharmonic.h:102

◆ dt0()

Real Biharmonic::dt0 ( )

Definition at line 80 of file biharmonic.h.

References _dt0.

80 { return _dt0; }

Biharmonic::_dt0

Real _dt0

Definition: biharmonic.h:102

◆ enable_default_ghosting()

virtual void libMesh::EquationSystems::enable_default_ghosting ( bool enable )

virtualinherited

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.

◆ enable_print_counter_info()

static void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

Methods to enable/disable the reference counter output from print_info()

◆ enable_refine_in_reinit()

void libMesh::EquationSystems::enable_refine_in_reinit ( )

inherited

Calls to reinit() will also do two-step coarsen-then-refine.

Definition at line 514 of file equation_systems.h.

References libMesh::EquationSystems::_refine_in_reinit.

514 { this->_refine_in_reinit = true; }

libMesh::EquationSystems::_refine_in_reinit

bool _refine_in_reinit

Flag for whether to call coarsen/refine in reinit().

Definition: equation_systems.h:572

◆ get_info() [1/2]

static std::string libMesh::ReferenceCounter::get_info ( )

staticinherited

Gets a string containing the reference information.

◆ get_info() [2/2]

virtual std::string libMesh::EquationSystems::get_info ( ) const

virtualinherited

Returns: A string containing information about the systems, flags, and parameters.

◆ get_mesh() [1/2]

const MeshBase & libMesh::EquationSystems::get_mesh ( ) const

inherited

Returns: A constant reference to the mesh

Definition at line 622 of file equation_systems.h.

References libMesh::EquationSystems::_mesh.

 {
   return _mesh;
 }

◆ get_mesh() [2/2]

MeshBase & libMesh::EquationSystems::get_mesh ( )

inherited

Returns: A reference to the mesh

Definition at line 630 of file equation_systems.h.

References libMesh::EquationSystems::_mesh.

 {
   return _mesh;
 }

◆ get_solution()

void libMesh::EquationSystems::get_solution	(	std::vector< Number > &	soln,
		std::vector< std::string > &	names
	)		const

inherited

Retrieve the solution data for CONSTANT MONOMIALs.

If names is populated, only the variables corresponding to those names will be retrieved. This can be used to filter which variables are retrieved.

Deprecated:: Call the more appropriately-named build_elemental_solution_vector() instead.

◆ get_system() [1/8]

template<typename T_sys >

const T_sys & libMesh::EquationSystems::get_system ( const std::string & name ) const

inherited

Returns: A constant reference to the system named 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 742 of file equation_systems.h.

References libMesh::EquationSystems::_systems, and libMesh::Quality::name().

 {
   const_system_iterator pos = _systems.find(name);
 
   // Check for errors
   if (pos == _systems.end())
     libmesh_error_msg("ERROR: no system named \"" << name << "\" found!");
 
   // Attempt dynamic cast
   return *cast_ptr<T_sys *>(pos->second);
 }

◆ get_system() [2/8]

template<typename T_sys >

T_sys & libMesh::EquationSystems::get_system ( const std::string & name )

inherited

Returns: A writable reference to the system named 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 761 of file equation_systems.h.

References libMesh::EquationSystems::_systems, and libMesh::Quality::name().

 {
   system_iterator pos = _systems.find(name);
 
   // Check for errors
   if (pos == _systems.end())
     libmesh_error_msg("ERROR: no system named " << name << " found!");
 
   // Attempt dynamic cast
   return *cast_ptr<T_sys *>(pos->second);
 }

◆ get_system() [3/8]

template<typename T_sys >

const T_sys & libMesh::EquationSystems::get_system ( const unsigned int num ) const

inherited

Returns: A constant reference to system number 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 691 of file equation_systems.h.

References libMesh::EquationSystems::_systems, end, and libMesh::EquationSystems::n_systems().

 {
   libmesh_assert_less (num, this->n_systems());
 
 
   const_system_iterator       pos = _systems.begin();
   const const_system_iterator end = _systems.end();
 
   for (; pos != end; ++pos)
     if (pos->second->number() == num)
       break;
 
   // Check for errors
   if (pos == end)
     libmesh_error_msg("ERROR: no system number " << num << " found!");
 
   // Attempt dynamic cast
   return *cast_ptr<T_sys *>(pos->second);
 }

◆ get_system() [4/8]

template<typename T_sys >

T_sys & libMesh::EquationSystems::get_system ( const unsigned int num )

inherited

Returns: A writable reference to the system number 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, end, and libMesh::EquationSystems::n_systems().

 {
   libmesh_assert_less (num, this->n_systems());
 
   const_system_iterator       pos = _systems.begin();
   const const_system_iterator end = _systems.end();
 
   for (; pos != end; ++pos)
     if (pos->second->number() == num)
       break;
 
   // Check for errors
   if (pos == end)
     libmesh_error_msg("ERROR: no system number " << num << " found!");
 
   // Attempt dynamic cast
   return *cast_ptr<T_sys *>(pos->second);
 }

◆ get_system() [5/8]

const System & libMesh::EquationSystems::get_system ( const std::string & name ) const

inherited

Returns: A constant reference to the system named name.

Definition at line 780 of file equation_systems.h.

References libMesh::Quality::name().

 {
   return this->get_system<System>(name);
 }

◆ get_system() [6/8]

System & libMesh::EquationSystems::get_system ( const std::string & name )

inherited

Returns: A writable reference to the system named name.

Definition at line 788 of file equation_systems.h.

References libMesh::Quality::name().

 {
   return this->get_system<System>(name);
 }

◆ get_system() [7/8]

const System & libMesh::EquationSystems::get_system ( const unsigned int num ) const

inherited

Returns: A constant reference to system number num.

Definition at line 796 of file equation_systems.h.

 {
   return this->get_system<System>(num);
 }

◆ get_system() [8/8]

System & libMesh::EquationSystems::get_system ( const unsigned int num )

inherited

Returns: A writable reference to the system number num.

Definition at line 804 of file equation_systems.h.

 {
   return this->get_system<System>(num);
 }

◆ get_vars_active_subdomains()

void libMesh::EquationSystems::get_vars_active_subdomains	(	const std::vector< std::string > &	names,
		std::vector< std::set< subdomain_id_type >> &	vars_active_subdomains
	)		const

inherited

Retrieve vars_active_subdomains, which indicates the active subdomains for each variable in names.

◆ has_system()

bool libMesh::EquationSystems::has_system ( const std::string & name ) const

inherited

Returns: true if the system named name exists within this EquationSystems object.

Definition at line 679 of file equation_systems.h.

References libMesh::EquationSystems::_systems, and libMesh::Quality::name().

 {
   if (_systems.find(name) == _systems.end())
     return false;
   return true;
 }

◆ increment_constructor_count()

void libMesh::ReferenceCounter::increment_constructor_count ( const std::string & name )

protectedinherited

Increments the construction counter.

Should be called in the constructor of any derived class that will be reference counted.

Definition at line 181 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().

 {
   Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
   std::pair<unsigned int, unsigned int> & p = _counts[name];
 
   p.first++;
 }

◆ increment_destructor_count()

void libMesh::ReferenceCounter::increment_destructor_count ( const std::string & name )

protectedinherited

Increments the destruction counter.

Should be called in the destructor of any derived class that will be reference counted.

Definition at line 194 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().

 {
   Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
   std::pair<unsigned int, unsigned int> & p = _counts[name];
 
   p.second++;
 }

◆ init()

void Biharmonic::init ( )

virtual

Initialize all the systems.

Reimplemented from libMesh::EquationSystems.

◆ n_active_dofs()

std::size_t libMesh::EquationSystems::n_active_dofs ( ) const

inherited

Returns: The number of active degrees of freedom for the EquationSystems object.

◆ n_dofs()

std::size_t libMesh::EquationSystems::n_dofs ( ) const

inherited

Returns: The total number of degrees of freedom in all systems.

◆ n_objects()

static unsigned int libMesh::ReferenceCounter::n_objects ( )

staticinherited

Prints the number of outstanding (created, but not yet destroyed) objects.

Definition at line 83 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

84 { return _n_objects; }

libMesh::ReferenceCounter::_n_objects

static Threads::atomic< unsigned int > _n_objects

The number of objects.

Definition: reference_counter.h:130

◆ n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inherited

Returns: The number of processors in the group.

Definition at line 93 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and libMesh::Parallel::Communicator::size().

Referenced by libMesh::MeshBase::partition().

94 { return cast_int<processor_id_type>(_communicator.size()); }

libMesh::Parallel::Communicator::size

processor_id_type size() const

Definition: communicator.h:175

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:105

◆ n_systems()

unsigned int libMesh::EquationSystems::n_systems ( ) const

inherited

Returns: The number of equation systems.

Definition at line 637 of file equation_systems.h.

References libMesh::EquationSystems::_systems.

Referenced by libMesh::EquationSystems::add_system(), and libMesh::EquationSystems::get_system().

 {
   return cast_int<unsigned int>(_systems.size());
 }

◆ n_vars()

unsigned int libMesh::EquationSystems::n_vars ( ) const

inherited

Returns: The total number of variables in all systems.

◆ output()

void Biharmonic::output	(	int	timestep,
		const Real &	t,
		Real &	o_t,
		bool	force = `false`
	)

◆ print_info() [1/2]

static void libMesh::ReferenceCounter::print_info ( std::ostream & out = libMesh::out )

staticinherited

Prints the reference information, by default to libMesh::out.

◆ print_info() [2/2]

void libMesh::EquationSystems::print_info ( std::ostream & os = libMesh::out ) const

inherited

Prints information about the equation systems, by default to libMesh::out.

◆ processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inherited

Returns: The rank of this processor in the group.

Definition at line 99 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and libMesh::Parallel::Communicator::rank().

Referenced by libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), libMesh::DofMap::last_dof(), libMesh::MeshBase::n_active_local_elem(), libMesh::DofMap::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), and libMesh::MeshTools::weight().

100 { return cast_int<processor_id_type>(_communicator.rank()); }

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:105

libMesh::Parallel::Communicator::rank

processor_id_type rank() const

Definition: communicator.h:173

◆ read() [1/4]

template<typename InValType >

void libMesh::EquationSystems::read	(	const std::string &	name,
		const XdrMODE	,
		const unsigned int	read_flags = `(READ_HEADER\|READ_DATA)`,
		bool	partition_agnostic = `true`
	)

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)

Note: The equation system can be defined without initializing the data vectors to any solution values. This can be done by omitting READ_DATA in the read_flags parameter.

If XdrMODE is omitted, it will be inferred as READ for filenames containing .xda or as DECODE for filenames containing .xdr

Parameters

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!

◆ read() [2/4]

void libMesh::EquationSystems::read	(	const std::string &	name,
		const XdrMODE	mode,
		const unsigned int	read_flags = `(READ_HEADER \| READ_DATA)`,
		bool	partition_agnostic = `true`
	)

inherited

Definition at line 417 of file equation_systems.h.

References libMesh::Quality::name().

421 { read<Number>(name, mode, read_flags, partition_agnostic); }

libMesh::Quality::name

std::string name(const ElemQuality q)

◆ read() [3/4]

template<typename InValType >

void libMesh::EquationSystems::read	(	const std::string &	name,
		const unsigned int	read_flags = `(READ_HEADER\|READ_DATA)`,
		bool	partition_agnostic = `true`
	)

inherited

◆ read() [4/4]

void libMesh::EquationSystems::read	(	const std::string &	name,
		const unsigned int	read_flags = `(READ_HEADER \| READ_DATA)`,
		bool	partition_agnostic = `true`
	)

inherited

Definition at line 428 of file equation_systems.h.

References libMesh::Quality::name().

431 { read<Number>(name, read_flags, partition_agnostic); }

libMesh::Quality::name

std::string name(const ElemQuality q)

◆ refine_in_reinit_flag()

bool libMesh::EquationSystems::refine_in_reinit_flag ( )

inherited

Returns: Whether or not calls to reinit() will try to coarsen/refine the mesh

Definition at line 524 of file equation_systems.h.

References libMesh::EquationSystems::_refine_in_reinit.

524 { return this->_refine_in_reinit; }

libMesh::EquationSystems::_refine_in_reinit

bool _refine_in_reinit

Flag for whether to call coarsen/refine in reinit().

Definition: equation_systems.h:572

◆ reinit()

virtual void libMesh::EquationSystems::reinit ( )

virtualinherited

Handle any mesh changes and reinitialize all the systems on the updated mesh.

◆ reinit_solutions()

bool libMesh::EquationSystems::reinit_solutions ( )

inherited

Handle any mesh changes and project any solutions onto the updated mesh.

Returns: Whether or not the mesh may have changed.

◆ reinit_systems()

virtual void libMesh::EquationSystems::reinit_systems ( )

virtualinherited

Reinitialize all systems on the current mesh.

◆ run()

void Biharmonic::run ( )

◆ sensitivity_solve()

virtual void libMesh::EquationSystems::sensitivity_solve ( const ParameterVector & parameters )

virtualinherited

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.

◆ solve()

virtual void libMesh::EquationSystems::solve ( )

virtualinherited

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.

◆ step()

void Biharmonic::step ( const Real & dt = -1.0 )

◆ update()

void libMesh::EquationSystems::update ( )

inherited

Updates local values for all the systems.

◆ verbose()

bool Biharmonic::verbose ( )

Definition at line 79 of file biharmonic.h.

References _verbose.

79 { return _verbose; }

Biharmonic::_verbose

bool _verbose

Definition: biharmonic.h:98

◆ viewParameters()

void Biharmonic::viewParameters ( )

◆ write() [1/2]

void libMesh::EquationSystems::write	(	const std::string &	name,
		const XdrMODE	,
		const unsigned int	write_flags = `(WRITE_DATA)`,
		bool	partition_agnostic = `true`
	)		const

inherited

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)

Note: The solution data can be omitted by calling this routine with WRITE_DATA omitted in the write_flags argument.

If XdrMODE is omitted, it will be inferred as WRITE for filenames containing .xda or as ENCODE for filenames containing .xdr

Parameters

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!

◆ write() [2/2]

void libMesh::EquationSystems::write	(	const std::string &	name,
		const unsigned int	write_flags = `(WRITE_DATA)`,
		bool	partition_agnostic = `true`
	)		const

inherited

Friends And Related Function Documentation

◆ JR

friend class JR

friend

Definition at line 110 of file biharmonic.h.

Member Data Documentation

◆ _cahn_hillard

bool Biharmonic::_cahn_hillard

private

Definition at line 95 of file biharmonic.h.

◆ _cnWeight

Real Biharmonic::_cnWeight

private

Definition at line 103 of file biharmonic.h.

◆ _communicator

const Parallel::Communicator& libMesh::ParallelObject::_communicator

protectedinherited

Definition at line 105 of file parallel_object.h.

Referenced by libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), and libMesh::ParallelObject::processor_id().

◆ _counts

Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 122 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::increment_constructor_count(), and libMesh::ReferenceCounter::increment_destructor_count().

◆ _degenerate

bool Biharmonic::_degenerate

private

Definition at line 95 of file biharmonic.h.

◆ _dim

unsigned int Biharmonic::_dim

private

Definition at line 92 of file biharmonic.h.

◆ _dt

Real Biharmonic::_dt

private

Definition at line 102 of file biharmonic.h.

Referenced by dt().

◆ _dt0

Real Biharmonic::_dt0

private

Definition at line 102 of file biharmonic.h.

Referenced by dt0().

◆ _enable_default_ghosting

bool libMesh::EquationSystems::_enable_default_ghosting

protectedinherited

Flag for whether to enable default ghosting on newly added Systems.

Default value: true

Definition at line 578 of file equation_systems.h.

Referenced by libMesh::EquationSystems::add_system().

◆ _enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter

staticprotectedinherited

Flag to control whether reference count information is printed when print_info is called.

Definition at line 141 of file reference_counter.h.

◆ _energy

FreeEnergyEnum Biharmonic::_energy

private

Definition at line 96 of file biharmonic.h.

◆ _exio

std::unique_ptr<ExodusII_IO> Biharmonic::_exio

private

Definition at line 106 of file biharmonic.h.

◆ _growth

bool Biharmonic::_growth

private

Definition at line 95 of file biharmonic.h.

◆ _initialCenter

Point Biharmonic::_initialCenter

private

Definition at line 100 of file biharmonic.h.

◆ _initialState

InitialStateEnum Biharmonic::_initialState

private

Definition at line 99 of file biharmonic.h.

◆ _initialWidth

Real Biharmonic::_initialWidth

private

Definition at line 101 of file biharmonic.h.

◆ _jr

JR* Biharmonic::_jr

private

Definition at line 113 of file biharmonic.h.

◆ _kappa

Real Biharmonic::_kappa

private

Definition at line 93 of file biharmonic.h.

◆ _log_truncation

int Biharmonic::_log_truncation

private

Definition at line 97 of file biharmonic.h.

◆ _mesh

ReplicatedMesh& Biharmonic::_mesh

private

Definition at line 111 of file biharmonic.h.

◆ _mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 135 of file reference_counter.h.

◆ _N

unsigned int Biharmonic::_N

private

Definition at line 92 of file biharmonic.h.

◆ _n_objects

Threads::atomic<unsigned int> libMesh::ReferenceCounter::_n_objects

staticprotectedinherited

The number of objects.

Print the reference count information when the number returns to 0.

Definition at line 130 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::n_objects(), libMesh::ReferenceCounter::ReferenceCounter(), and libMesh::ReferenceCounter::~ReferenceCounter().

◆ _netforce

bool Biharmonic::_netforce

private

Definition at line 95 of file biharmonic.h.

◆ _o_count

int Biharmonic::_o_count

private

Definition at line 108 of file biharmonic.h.

◆ _o_dt

Real Biharmonic::_o_dt

private

Definition at line 107 of file biharmonic.h.

◆ _ofile

std::string Biharmonic::_ofile

private

Definition at line 105 of file biharmonic.h.

◆ _ofile_base

std::string Biharmonic::_ofile_base

private

Definition at line 105 of file biharmonic.h.

◆ _refine_in_reinit

bool libMesh::EquationSystems::_refine_in_reinit

protectedinherited

Flag for whether to call coarsen/refine in reinit().

Default value: true

Definition at line 572 of file equation_systems.h.

Referenced by libMesh::EquationSystems::disable_refine_in_reinit(), libMesh::EquationSystems::enable_refine_in_reinit(), and libMesh::EquationSystems::refine_in_reinit_flag().

◆ _systems

std::map<std::string, System *> libMesh::EquationSystems::_systems

protectedinherited

Data structure holding the systems.

Definition at line 556 of file equation_systems.h.

Referenced by libMesh::EquationSystems::add_system(), libMesh::EquationSystems::get_system(), libMesh::EquationSystems::has_system(), and libMesh::EquationSystems::n_systems().

◆ _T

Real Biharmonic::_T

private

Definition at line 102 of file biharmonic.h.

◆ _t0

Real Biharmonic::_t0

private

Definition at line 102 of file biharmonic.h.

◆ _t1

Real Biharmonic::_t1

private

Definition at line 102 of file biharmonic.h.

◆ _theta

Real Biharmonic::_theta

private

Definition at line 93 of file biharmonic.h.

◆ _theta_c

Real Biharmonic::_theta_c

private

Definition at line 93 of file biharmonic.h.

◆ _tol

Real Biharmonic::_tol

private

Definition at line 94 of file biharmonic.h.

◆ _verbose

bool Biharmonic::_verbose

private

Definition at line 98 of file biharmonic.h.

Referenced by verbose().

◆ parameters

Parameters libMesh::EquationSystems::parameters

inherited

Data structure holding arbitrary parameters.

Definition at line 542 of file equation_systems.h.

Referenced by FETest< order, family, elem_type >::setUp(), and libMesh::WrappedFunction< Output >::WrappedFunction().

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

examples/miscellaneous/miscellaneous_ex7/biharmonic.h

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ const_system_iterator

◆ Counts

◆ system_iterator

Member Enumeration Documentation

◆ FreeEnergyEnum

◆ InitialStateEnum

◆ ReadFlags

◆ WriteFlags

Constructor & Destructor Documentation

◆ Biharmonic()

◆ ~Biharmonic()

Member Function Documentation

◆ add_system() [1/2]

◆ add_system() [2/2]

◆ adjoint_solve()

◆ allgather()

◆ build_discontinuous_solution_vector()

◆ build_elemental_solution_vector()

◆ build_parallel_elemental_solution_vector()

◆ build_parallel_solution_vector()

◆ build_solution_vector() [1/2]

◆ build_solution_vector() [2/2]

◆ build_variable_names()

◆ clear()

◆ comm()

◆ compare()

◆ delete_system()

◆ disable_print_counter_info()

◆ disable_refine_in_reinit()

◆ dt()

◆ dt0()

◆ enable_default_ghosting()

◆ enable_print_counter_info()

◆ enable_refine_in_reinit()

◆ get_info() [1/2]

◆ get_info() [2/2]

◆ get_mesh() [1/2]

◆ get_mesh() [2/2]

◆ get_solution()

◆ get_system() [1/8]

◆ get_system() [2/8]

◆ get_system() [3/8]

◆ get_system() [4/8]

◆ get_system() [5/8]

◆ get_system() [6/8]

◆ get_system() [7/8]

◆ get_system() [8/8]

◆ get_vars_active_subdomains()

◆ has_system()

◆ increment_constructor_count()

◆ increment_destructor_count()

◆ init()

◆ n_active_dofs()

◆ n_dofs()

◆ n_objects()

◆ n_processors()

◆ n_systems()

◆ n_vars()

◆ output()

◆ print_info() [1/2]

◆ print_info() [2/2]

◆ processor_id()

◆ read() [1/4]

◆ read() [2/4]

◆ read() [3/4]

◆ read() [4/4]

◆ refine_in_reinit_flag()