A two dimensional Hermite bicubic element quadrilateral mesh for a topologically rectangular domain. The geometry of the problem must be prescribed using the TopologicallyRectangularDomain. Non uniform node spacing can be prescribed using a function pointer. More...

#include <hermite_element_quad_mesh.template.h>

Inheritance diagram for oomph::HermiteQuadMesh< ELEMENT >:

Public Types
typedef void(*	MeshSpacingFnPtr) (const Vector< double > &m_uniform_spacing, Vector< double > &m_non_uniform_spacing)
	Mesh Spacing Function Pointer - an optional function pointer to prescibe the node spacing in a non-uniformly spaced mesh - takes the position of a node (in macro element coordinates) in the uniformly spaced mesh and return the position in the non-uniformly spaced mesh. More...

Public Types inherited from oomph::Mesh
typedef void(FiniteElement::*	SteadyExactSolutionFctPt) (const Vector< double > &x, Vector< double > &soln)
	Typedef for function pointer to function that computes steady exact solution. More...

typedef void(FiniteElement::*	UnsteadyExactSolutionFctPt) (const double &time, const Vector< double > &x, Vector< double > &soln)
	Typedef for function pointer to function that computes unsteady exact solution. More...

Public Member Functions
	HermiteQuadMesh (const unsigned &nx, const unsigned &ny, TopologicallyRectangularDomain domain, const bool &periodic_in_x=false, TimeStepper time_stepper_pt=&Mesh::Default_TimeStepper)
	Mesh Constructor (for a uniformly spaced mesh). Takes the following arguments : nx : number of elements in x direction; ny : number of elements in y direction; domain : topologically rectangular domain; periodic_in_x : flag specifying if the mesh is periodic in the x direction (default = false); time_stepper_pt : pointer to the time stepper (default = no timestepper);. More...

	HermiteQuadMesh (const unsigned &nx, const unsigned &ny, TopologicallyRectangularDomain domain, const MeshSpacingFnPtr spacing_fn, const bool &periodic_in_x=false, TimeStepper time_stepper_pt=&Mesh::Default_TimeStepper)
	Mesh Constructor (for a non-uniformly spaced mesh). Takes the following arguments : nx : number of elements in x direction; ny : number of elements in y direction; domain : topologically rectangular domain; spacing_fn : spacing function prescribing a non-uniformly spaced mesh periodic_in_x : flag specifying if the mesh is periodic in the x direction (default = false); time_stepper_pt : pointer to the time stepper (default = notimestepper);. More...

	~HermiteQuadMesh ()
	Destructor - does nothing - handled in mesh base class. More...

unsigned &	nelement_in_dim (const unsigned &d)
	Access function for number of elements in mesh in each dimension. More...

Public Member Functions inherited from oomph::Mesh
void	resize_halo_nodes ()
	Helper function that resizes halo nodes to the same size as their non-halo counterparts if required. (A discrepancy can arise if a FaceElement that introduces additional unknowns are attached to a bulk element that shares a node with a haloed element. In that case the joint node between haloed and non-haloed element is resized on that processor but not on the one that holds the halo counterpart (because no FaceElement is attached to the halo element) More...

	Mesh ()
	Default constructor. More...

	Mesh (const Vector< Mesh * > &sub_mesh_pt)
	Constructor builds combined mesh from the meshes specified. Note: This simply merges the meshes' elements and nodes (ignoring duplicates; no boundary information etc. is created). More...

void	merge_meshes (const Vector< Mesh * > &sub_mesh_pt)
	Merge meshes. Note: This simply merges the meshes' elements and nodes (ignoring duplicates; no boundary information etc. is created). More...

virtual void	reset_boundary_element_info (Vector< unsigned > &ntmp_boundary_elements, Vector< Vector< unsigned >> &ntmp_boundary_elements_in_region, Vector< FiniteElement * > &deleted_elements)
	Virtual function to perform the reset boundary elements info rutines. More...

template<class BULK_ELEMENT >
void	doc_boundary_coordinates (const unsigned &b, std::ofstream &the_file)
	Output boundary coordinates on boundary b – template argument specifies the bulk element type (needed to create FaceElement of appropriate type on mesh boundary). More...

virtual void	scale_mesh (const double &factor)
	Scale all nodal coordinates by given factor. Virtual so it can be overloaded in SolidMesh class where it also re-assigns the Lagrangian coordinates. More...

	Mesh (const Mesh &dummy)=delete
	Broken copy constructor. More...

void	operator= (const Mesh &)=delete
	Broken assignment operator. More...

virtual	~Mesh ()
	Virtual Destructor to clean up all memory. More...

void	flush_element_and_node_storage ()
	Flush storage for elements and nodes by emptying the vectors that store the pointers to them. This is useful if a particular mesh is only built to generate a small part of a bigger mesh. Once the elements and nodes have been created, they are typically copied into the new mesh and the auxiliary mesh can be deleted. However, if we simply call the destructor of the auxiliary mesh, it will also wipe out the nodes and elements, because it still "thinks" it's in charge of these... More...

void	flush_element_storage ()
	Flush storage for elements (only) by emptying the vectors that store the pointers to them. This is useful if a particular mesh is only built to generate a small part of a bigger mesh. Once the elements and nodes have been created, they are typically copied into the new mesh and the auxiliary mesh can be deleted. However, if we simply call the destructor of the auxiliary mesh, it will also wipe out the nodes and elements, because it still "thinks" it's in charge of these... More...

void	flush_node_storage ()
	Flush storage for nodes (only) by emptying the vectors that store the pointers to them. More...

Node *&	node_pt (const unsigned long &n)
	Return pointer to global node n. More...

Node *	node_pt (const unsigned long &n) const
	Return pointer to global node n (const version) More...

GeneralisedElement *&	element_pt (const unsigned long &e)
	Return pointer to element e. More...

GeneralisedElement *	element_pt (const unsigned long &e) const
	Return pointer to element e (const version) More...

const Vector< GeneralisedElement * > &	element_pt () const
	Return reference to the Vector of elements. More...

Vector< GeneralisedElement * > &	element_pt ()
	Return reference to the Vector of elements. More...

FiniteElement *	finite_element_pt (const unsigned &e) const
	Upcast (downcast?) to FiniteElement (needed to access FiniteElement member functions). More...

Node *&	boundary_node_pt (const unsigned &b, const unsigned &n)
	Return pointer to node n on boundary b. More...

Node *	boundary_node_pt (const unsigned &b, const unsigned &n) const
	Return pointer to node n on boundary b. More...

void	set_nboundary (const unsigned &nbound)
	Set the number of boundaries in the mesh. More...

void	remove_boundary_nodes ()
	Clear all pointers to boundary nodes. More...

void	remove_boundary_nodes (const unsigned &b)
	Remove all information about nodes stored on the b-th boundary of the mesh. More...

void	remove_boundary_node (const unsigned &b, Node *const &node_pt)
	Remove a node from the boundary b. More...

void	add_boundary_node (const unsigned &b, Node *const &node_pt)
	Add a (pointer to) a node to the b-th boundary. More...

void	copy_boundary_node_data_from_nodes ()
	Replace existing boundary node lookup schemes with new schemes created using the boundary data stored in the nodes. More...

bool	boundary_coordinate_exists (const unsigned &i) const
	Indicate whether the i-th boundary has an intrinsic coordinate. More...

unsigned long	nelement () const
	Return number of elements in the mesh. More...

unsigned long	nnode () const
	Return number of nodes in the mesh. More...

unsigned	ndof_types () const
	Return number of dof types in mesh. More...

unsigned	elemental_dimension () const
	Return number of elemental dimension in mesh. More...

unsigned	nodal_dimension () const
	Return number of nodal dimension in mesh. More...

void	add_node_pt (Node *const &node_pt)
	Add a (pointer to a) node to the mesh. More...

void	add_element_pt (GeneralisedElement *const &element_pt)
	Add a (pointer to) an element to the mesh. More...

virtual void	node_update (const bool &update_all_solid_nodes=false)
	Update nodal positions in response to changes in the domain shape. Uses the FiniteElement::get_x(...) function for FiniteElements and doesn't do anything for other element types. If a MacroElement pointer has been set for a FiniteElement, the MacroElement representation is used to update the nodal positions; if not get_x(...) uses the FE interpolation and thus leaves the nodal positions unchanged. Virtual, so it can be overloaded by specific meshes, such as AlgebraicMeshes or SpineMeshes. Generally, this function updates the position of all nodes in response to changes in the boundary position. However, we ignore all SolidNodes since their position is computed as part of the solution – unless the bool flag is set to true. Such calls are typically made when the initial mesh is created and/or after a mesh has been refined repeatedly before the start of the computation. More...

virtual void	reorder_nodes (const bool &use_old_ordering=true)
	Re-order nodes in the order in which they appear in elements – can be overloaded for more efficient re-ordering. More...

virtual void	get_node_reordering (Vector< Node * > &reordering, const bool &use_old_ordering=true) const
	Get a reordering of the nodes in the order in which they appear in elements – can be overloaded for more efficient re-ordering. More...

template<class BULK_ELEMENT , template< class > class FACE_ELEMENT>
void	build_face_mesh (const unsigned &b, Mesh *const &face_mesh_pt)
	Constuct a Mesh of FACE_ELEMENTs along the b-th boundary of the mesh (which contains elements of type BULK_ELEMENT) More...

unsigned	self_test ()
	Self-test: Check elements and nodes. Return 0 for OK. More...

void	max_and_min_element_size (double &max_size, double &min_size)
	Determine max and min area for all FiniteElements in the mesh (non-FiniteElements are ignored) More...

double	total_size ()
	Determine the sum of all "sizes" of the FiniteElements in the mesh (non-FiniteElements are ignored). This gives the length/area/volume occupied by the mesh. More...

void	check_inverted_elements (bool &mesh_has_inverted_elements, std::ofstream &inverted_element_file)
	Check for inverted elements and report outcome in boolean variable. This visits all elements at their integration points and checks if the Jacobian of the mapping between local and global coordinates is positive – using the same test that would be carried out (but only in PARANOID mode) during the assembly of the elements' Jacobian matrices. Inverted elements are output in inverted_element_file (if the stream is open). More...

void	check_inverted_elements (bool &mesh_has_inverted_elements)
	Check for inverted elements and report outcome in boolean variable. This visits all elements at their integration points and checks if the Jacobian of the mapping between local and global coordinates is positive – using the same test that would be carried out (but only in PARANOID mode) during the assembly of the elements' Jacobian matrices. More...

unsigned	check_for_repeated_nodes (const double &epsilon=1.0e-12)
	Check for repeated nodes within a given spatial tolerance. Return (0/1) for (pass/fail). More...

Vector< Node * >	prune_dead_nodes ()
	Prune nodes. Nodes that have been marked as obsolete are removed from the mesh (and its boundary-node scheme). Returns vector of pointers to deleted nodes. More...

unsigned	nboundary () const
	Return number of boundaries. More...

unsigned long	nboundary_node (const unsigned &ibound) const
	Return number of nodes on a particular boundary. More...

FiniteElement *	boundary_element_pt (const unsigned &b, const unsigned &e) const
	Return pointer to e-th finite element on boundary b. More...

Node *	get_some_non_boundary_node () const
	Find a node not on any boundary in mesh_pt (useful for pinning a single node in a purely Neumann problem so that it is fully determined). More...

unsigned	nboundary_element (const unsigned &b) const
	Return number of finite elements that are adjacent to boundary b. More...

int	face_index_at_boundary (const unsigned &b, const unsigned &e) const
	For the e-th finite element on boundary b, return int to indicate the face_index of the face adjacent to the boundary. This is consistent with input required during the generation of FaceElements. More...

virtual void	dump (std::ofstream &dump_file, const bool &use_old_ordering=true) const
	Dump the data in the mesh into a file for restart. More...

void	dump (const std::string &dump_file_name, const bool &use_old_ordering=true) const
	Dump the data in the mesh into a file for restart. More...

virtual void	read (std::ifstream &restart_file)
	Read solution from restart file. More...

void	output_paraview (std::ofstream &file_out, const unsigned &nplot) const
	Output in paraview format into specified file. Breaks up each element into sub-elements for plotting purposes. We assume that all elements are of the same type (fct will break break (in paranoid mode) if paraview output fcts of the elements are inconsistent). More...

void	output_fct_paraview (std::ofstream &file_out, const unsigned &nplot, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt) const
	Output in paraview format into specified file. Breaks up each element into sub-elements for plotting purposes. We assume that all elements are of the same type (fct will break break (in paranoid mode) if paraview output fcts of the elements are inconsistent). More...

void	output_fct_paraview (std::ofstream &file_out, const unsigned &nplot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt) const
	Output in paraview format into specified file. Breaks up each element into sub-elements for plotting purposes. We assume that all elements are of the same type (fct will break break (in paranoid mode) if paraview output fcts of the elements are inconsistent). More...

void	output (std::ostream &outfile)
	Output for all elements. More...

void	output (std::ostream &outfile, const unsigned &n_plot)
	Output at f(n_plot) points in each element. More...

void	output (FILE *file_pt)
	Output for all elements (C-style output) More...

void	output (FILE *file_pt, const unsigned &nplot)
	Output at f(n_plot) points in each element (C-style output) More...

void	output (const std::string &output_filename)
	Output for all elements. More...

void	output (const std::string &output_filename, const unsigned &n_plot)
	Output at f(n_plot) points in each element. More...

void	output_fct (std::ostream &outfile, const unsigned &n_plot, FiniteElement::SteadyExactSolutionFctPt)
	Output a given Vector function at f(n_plot) points in each element. More...

void	output_fct (std::ostream &outfile, const unsigned &n_plot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt)
	Output a given time-dep. Vector function at f(n_plot) points in each element. More...

void	output_boundaries (std::ostream &outfile)
	Output the nodes on the boundaries (into separate tecplot zones) More...

void	output_boundaries (const std::string &output_filename)
	Output the nodes on the boundaries (into separate tecplot zones). Specify filename. More...

void	assign_initial_values_impulsive ()
	Assign initial values for an impulsive start. More...

void	shift_time_values ()
	Shift time-dependent data along for next timestep: Deal with nodal Data/positions and the element's internal Data. More...

void	calculate_predictions ()
	Calculate predictions for all Data and positions associated with the mesh, usually used in adaptive time-stepping. More...

void	set_nodal_and_elemental_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data)
	Set the timestepper associated with all nodal and elemental data stored in the mesh. More...

virtual void	set_mesh_level_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data)
	Function that can be used to set any additional timestepper data stored at the Mesh (as opposed to nodal and elemental) levels. This is virtual so that it can be overloaded in the appropriate Meshes. Examples include the SpineMeshes and adaptive triangle and tet meshes. More...

void	set_consistent_pinned_values_for_continuation (ContinuationStorageScheme *const &continuation_stepper_pt)
	Set consistent values for pinned data in continuation. More...

bool	does_pointer_correspond_to_mesh_data (double *const &parameter_pt)
	Does the double pointer correspond to any mesh data. More...

void	set_nodal_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data)
	Set the timestepper associated with the nodal data in the mesh. More...

void	set_elemental_internal_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data)
	Set the timestepper associated with the internal data stored within elements in the meah. More...

virtual void	compute_norm (double &norm)
	Compute norm of solution by summing contributions of compute_norm(...) for all constituent elements in the mesh. What that norm means depends on what's defined in the element's function; may need to take the square root afterwards if the elements compute the square of the L2 norm, say. More...

virtual void	compute_norm (Vector< double > &norm)
	Compute norm of solution by summing contributions of compute_norm(...) for all constituent elements in the mesh. What that norm means depends on what's defined in the element's function; may need to take the square root afterwards if the elements compute the square of the L2 norm, say. More...

virtual void	compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm)
	Plot error when compared against a given exact solution. Also returns the norm of the error and that of the exact solution. More...

virtual void	compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm)
	Plot error when compared against a given time-depdendent exact solution. Also returns the norm of the error and that of the exact solution. More...

virtual void	compute_error (FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm)
	Plot error when compared against a given time-dependent exact solution. Also returns the norm of the error and that of the exact solution. More...

virtual void	compute_error (FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, Vector< double > &error, Vector< double > &norm)
	Plot error when compared against a given time-dependent exact solution. Also returns the norm of the error and that of the exact solution. More...

virtual void	compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, Vector< double > &error, Vector< double > &norm)
	Plot error when compared against a given time-depdendent exact solution. Also returns the norm of the error and that of the exact solution. Version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More...

virtual void	compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, Vector< double > &error, Vector< double > &norm)
	Plot error when compared against a given time-depdendent exact solution. Also returns the norm of the error and that of the exact solution. Version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More...

virtual void	compute_error (FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm)
	Returns the norm of the error and that of the exact solution. More...

virtual void	compute_error (FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, Vector< double > &error, Vector< double > &norm)
	Returns the norm of the error and that of the exact solution. Version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More...

bool	is_mesh_distributed () const
	Boolean to indicate if Mesh has been distributed. More...

OomphCommunicator *	communicator_pt () const
	Read-only access fct to communicator (Null if mesh is not distributed, i.e. if we don't have mpi). More...

void	set_communicator_pt (OomphCommunicator *comm_pt)
	Function to set communicator (mesh is assumed to be distributed if the communicator pointer is non-null). Only defined if mpi is enabled becaus Comm_pt itself is only defined when mpi is enabled. More...

void	set_keep_all_elements_as_halos ()
	Call this function to keep all the elements as halo elements. More...

void	unset_keep_all_elements_as_halos ()
	Calll this function to unset the flag that keeps all elements in the mesh as halo elements. More...

virtual void	distribute (OomphCommunicator comm_pt, const Vector< unsigned > &element_domain, Vector< GeneralisedElement > &deleted_element_pt, DocInfo &doc_info, const bool &report_stats, const bool &overrule_keep_as_halo_element_status)
	Distribute the problem and doc; make this virtual to allow overloading for particular meshes where further work is required. Add to vector of pointers to deleted elements. More...

void	distribute (OomphCommunicator comm_pt, const Vector< unsigned > &element_domain, Vector< GeneralisedElement > &deleted_element_pt, const bool &report_stats=false)
	Distribute the problem Add to vector of pointers to deleted elements. More...

void	prune_halo_elements_and_nodes (Vector< GeneralisedElement * > &deleted_element_pt, const bool &report_stats=false)
	(Irreversibly) prune halo(ed) elements and nodes, usually after another round of refinement, to get rid of excessively wide halo layers. Note that the current mesh will be now regarded as the base mesh and no unrefinement relative to it will be possible once this function has been called. More...

void	prune_halo_elements_and_nodes (Vector< GeneralisedElement * > &deleted_element_pt, DocInfo &doc_info, const bool &report_stats)
	(Irreversibly) prune halo(ed) elements and nodes, usually after another round of refinement, to get rid of excessively wide halo layers. Note that the current mesh will be now regarded as the base mesh and no unrefinement relative to it will be possible once this function has been called. More...

void	get_efficiency_of_mesh_distribution (double &av_efficiency, double &max_efficiency, double &min_efficiency)
	Get efficiency of mesh distribution: In an ideal distribution without halo overhead, each processor would only hold its own elements. Efficieny per processor = (number of non-halo elements)/ (total number of elements). More...

void	doc_mesh_distribution (DocInfo &doc_info)
	Doc the mesh distribution, to be processed with tecplot macros. More...

void	check_halo_schemes (DocInfo &doc_info, double &max_permitted_error_for_halo_check)
	Check halo and shared schemes on the mesh. More...

virtual void	classify_halo_and_haloed_nodes (DocInfo &doc_info, const bool &report_stats)
	Classify the halo and haloed nodes in the mesh. Virtual so it can be overloaded to perform additional functionality (such as synchronising hanging nodes) in refineable meshes, say. More...

virtual void	classify_halo_and_haloed_nodes (const bool &report_stats=false)
	Classify the halo and haloed nodes in the mesh. Virtual so it can be overloaded to perform additional functionality (such as synchronising hanging nodes) in refineable meshes, say. More...

void	synchronise_shared_nodes (const bool &report_stats)
	Synchronise shared node lookup schemes to cater for the the case where: (1) a certain node on the current processor is halo with proc p (i.e. its non-halo counterpart lives on processor p) (2) that node is also exists (also as a halo) on another processor (q, say) where its non-halo counter part is also known to be on processor p. However, without calling this function the current processor does not necessarily know that it shares a node with processor q. This information can be required, e.g. when synchronising hanging node schemes over all processors. More...

void	get_all_halo_data (std::map< unsigned, double * > &map_of_halo_data)
	Get all the halo data stored in the mesh and add pointers to the data to the map, indexed by global equation number. More...

Vector< GeneralisedElement * >	halo_element_pt (const unsigned &p)
	Return vector of halo elements in this Mesh whose non-halo counterpart is held on processor p. More...

Vector< GeneralisedElement * >	haloed_element_pt (const unsigned &p)
	Return vector of haloed elements in this Mesh whose haloing counterpart is held on processor p. More...

unsigned	nnon_halo_element ()
	Total number of non-halo elements in this mesh (Costly call computes result on the fly) More...

unsigned	nroot_halo_element ()
	Total number of root halo elements in this Mesh. More...

unsigned	nroot_halo_element (const unsigned &p)
	Number of root halo elements in this Mesh whose non-halo counterpart is held on processor p. More...

Vector< GeneralisedElement * >	root_halo_element_pt (const unsigned &p)
	Vector of pointers to root halo elements in this Mesh whose non-halo counterpart is held on processor p. More...

GeneralisedElement *&	root_halo_element_pt (const unsigned &p, const unsigned &e)
	Access fct to the e-th root halo element in this Mesh whose non-halo counterpart is held on processor p. More...

void	add_root_halo_element_pt (const unsigned &p, GeneralisedElement *&el_pt)
	Add root halo element whose non-halo counterpart is held on processor p to this Mesh. More...

unsigned	nhalo_node ()
	Total number of halo nodes in this Mesh. More...

unsigned	nhalo_node (const unsigned &p)
	Number of halo nodes in this Mesh whose non-halo counterpart is held on processor p. More...

void	add_halo_node_pt (const unsigned &p, Node *&nod_pt)
	Add halo node whose non-halo counterpart is held on processor p to the storage scheme for halo nodes. More...

Node *	halo_node_pt (const unsigned &p, const unsigned &j)
	Access fct to the j-th halo node in this Mesh whose non-halo counterpart is held on processor p. More...

unsigned	nroot_haloed_element ()
	Total number of root haloed elements in this Mesh. More...

unsigned	nroot_haloed_element (const unsigned &p)
	Number of root haloed elements in this Mesh whose non-halo counterpart is held on processor p. More...

Vector< GeneralisedElement * >	root_haloed_element_pt (const unsigned &p)
	Vector of pointers to root haloed elements in this Mesh whose non-halo counterpart is held on processor p. More...

GeneralisedElement *&	root_haloed_element_pt (const unsigned &p, const unsigned &e)
	Access fct to the e-th root haloed element in this Mesh whose non-halo counterpart is held on processor p. More...

void	add_root_haloed_element_pt (const unsigned &p, GeneralisedElement *&el_pt)
	Add root haloed element whose non-halo counterpart is held on processor p to the storage scheme for haloed elements. Note: This does not add the element to the storage scheme for elements as it's understood to naturally live on this processor anyway! More...

unsigned	nhaloed_node ()
	Total number of haloed nodes in this Mesh. More...

unsigned	nhaloed_node (const unsigned &p)
	Number of haloed nodes in this Mesh whose haloed counterpart is held on processor p. More...

Node *	haloed_node_pt (const unsigned &p, const unsigned &j)
	Access fct to the j-th haloed node in this Mesh whose halo counterpart is held on processor p. More...

void	add_haloed_node_pt (const unsigned &p, Node *&nod_pt)
	Add haloed node whose halo counterpart is held on processor p to the storage scheme for haloed nodes. More...

void	disable_resizing_of_halo_nodes ()
	Function to suppress resizing of halo nodes – optmisation but call it at your own risk! More...

void	enable_resizing_of_halo_nodes ()
	Function to (re-)enable resizing of halo nodes – this returns things to the default behaviour. More...

void	disable_output_of_halo_elements ()
	Function to disable halo element output. More...

void	enable_output_of_halo_elements ()
	Function to enable halo element output. More...

unsigned	nshared_node ()
	Total number of shared nodes in this Mesh. More...

void	doc_shared_nodes ()
	Doc shared nodes. More...

unsigned	nshared_node (const unsigned &p)
	Number of shared nodes in this Mesh who have a counterpart on processor p. More...

Node *	shared_node_pt (const unsigned &p, const unsigned &j)
	Access fct to the j-th shared node in this Mesh who has a counterpart on processor p. More...

void	get_shared_node_pt (const unsigned &p, Vector< Node * > &shared_node_pt)
	Get vector of pointers to shared nodes with processor p. Required for faster search in Missing_masters_functions::add_external_haloed_node_helper() and Missing_masters_functions::add_external_haloed_master_node_helper() More...

void	add_shared_node_pt (const unsigned &p, Node *&nod_pt)
	Add shared node whose counterpart is held on processor p to the storage scheme for shared nodes. (NB: ensure that this routine is called twice, once for each process) More...

void	get_halo_node_stats (double &av_number, unsigned &max_number, unsigned &min_number)
	Get halo node stats for this distributed mesh: Average/max/min number of halo nodes over all processors. Careful: Involves MPI Broadcasts and must therefore be called on all processors! More...

void	get_haloed_node_stats (double &av_number, unsigned &max_number, unsigned &min_number)
	Get haloed node stats for this distributed mesh: Average/max/min number of haloed nodes over all processors. Careful: Involves MPI Broadcasts and must therefore be called on all processors! More...

void	output_external_halo_elements (std::ostream &outfile, const unsigned &n_plot=5)
	Output all external halo elements. More...

void	output_external_halo_elements (const unsigned &p, std::ostream &outfile, const unsigned &n_plot=5)
	Output all external halo elements with processor p. More...

void	output_external_haloed_elements (std::ostream &outfile, const unsigned &n_plot=5)
	Output all external haloed elements. More...

void	output_external_haloed_elements (const unsigned &p, std::ostream &outfile, const unsigned &n_plot=5)
	Output all external haloed elements with processor p. More...

unsigned	nexternal_halo_element ()
	Total number of external halo elements in this Mesh. More...

unsigned	nexternal_halo_element (const unsigned &p)
	Number of external halo elements in this Mesh whose non-halo counterpart is held on processor p. More...

GeneralisedElement *&	external_halo_element_pt (const unsigned &p, const unsigned &e)
	Access fct to the e-th external halo element in this Mesh whose non-halo counterpart is held on processor p. More...

void	add_external_halo_element_pt (const unsigned &p, GeneralisedElement *&el_pt)
	Add external halo element whose non-halo counterpart is held on processor p to this Mesh. More...

unsigned	nexternal_haloed_element ()
	Total number of external haloed elements in this Mesh. More...

unsigned	nexternal_haloed_element (const unsigned &p)
	Number of external haloed elements in this Mesh whose non-halo counterpart is held on processor p. More...

GeneralisedElement *&	external_haloed_element_pt (const unsigned &p, const unsigned &e)
	Access fct to the e-th external haloed element in this Mesh whose non-halo counterpart is held on processor p. More...

unsigned	add_external_haloed_element_pt (const unsigned &p, GeneralisedElement *&el_pt)
	Add external haloed element whose non-halo counterpart is held on processor p to the storage scheme for haloed elements. More...

unsigned	nexternal_halo_node ()
	Total number of external halo nodes in this Mesh. More...

void	get_external_halo_node_pt (Vector< Node * > &external_halo_node_pt)
	Get vector of pointers to all external halo nodes. More...

unsigned	nexternal_halo_node (const unsigned &p)
	Number of external halo nodes in this Mesh whose non-halo (external) counterpart is held on processor p. More...

void	add_external_halo_node_pt (const unsigned &p, Node *&nod_pt)
	Add external halo node whose non-halo (external) counterpart is held on processor p to the storage scheme for halo nodes. More...

Node *&	external_halo_node_pt (const unsigned &p, const unsigned &j)
	Access fct to the j-th external halo node in this Mesh whose non-halo external counterpart is held on processor p. More...

Vector< Node * >	external_halo_node_pt (const unsigned &p)
	Access fct to vector of external halo node in this Mesh whose non-halo external counterpart is held on processor p. (read only) More...

void	set_external_halo_node_pt (const unsigned &p, const Vector< Node * > &external_halo_node_pt)
	Set vector of external halo node in this Mesh whose non-halo external counterpart is held on processor p. More...

void	null_external_halo_node (const unsigned &p, Node *nod_pt)
	Null out specified external halo node (used when deleting duplicates) More...

void	remove_null_pointers_from_external_halo_node_storage ()
	Consolidate external halo node storage by removing nulled out pointes in external halo and haloed schemes. More...

unsigned	nexternal_haloed_node ()
	Total number of external haloed nodes in this Mesh. More...

unsigned	nexternal_haloed_node (const unsigned &p)
	Number of external haloed nodes in this Mesh whose halo (external) counterpart is held on processor p. More...

Node *&	external_haloed_node_pt (const unsigned &p, const unsigned &j)
	Access fct to the j-th external haloed node in this Mesh whose halo external counterpart is held on processor p. More...

unsigned	add_external_haloed_node_pt (const unsigned &p, Node *&nod_pt)
	Add external haloed node whose halo (external) counterpart is held on processor p to the storage scheme for haloed nodes. More...

Vector< Node * >	external_haloed_node_pt (const unsigned &p)
	Access fct to vector of external haloed node in this Mesh whose halo external counterpart is held on processor p. (read only) More...

void	set_external_haloed_node_pt (const unsigned &p, const Vector< Node * > &external_haloed_node_pt)
	Set vector of external haloed node in this Mesh whose halo external counterpart is held on processor p. More...

std::set< int >	external_halo_proc ()
	Return the set of processors that hold external halo nodes. This is required to avoid having to pass a communicator into the node_update functions for Algebraic-based and MacroElement-based Meshes. More...

virtual void	create_shared_boundaries (OomphCommunicator comm_pt, const Vector< unsigned > &element_domain, const Vector< GeneralisedElement > &backed_up_el_pt, const Vector< FiniteElement * > &backed_up_f_el_pt, std::map< Data *, std::set< unsigned >> &processors_associated_with_data, const bool &overrule_keep_as_halo_element_status)
	Creates the shared boundaries, only used in unstructured meshes In this case with the "TriangleMesh" class. More...

virtual unsigned	try_to_add_root_haloed_element_pt (const unsigned &p, GeneralisedElement *&el_pt)

virtual unsigned	try_to_add_haloed_node_pt (const unsigned &p, Node *&nod_pt)

void	delete_all_external_storage ()
	Wipe the storage for all externally-based elements. More...

Private Member Functions
void	macro_coordinate_position (const unsigned &node_num_x, const unsigned &node_num_y, Vector< double > &macro_element_position)
	returns the macro element position of the node that is the x-th node along from the LHS and the y-th node up from the lower edge More...

void	set_position_of_node (const unsigned &node_num_x, const unsigned &node_num_y, Node *node_pt)
	sets the generalised position of the node (i.e. - x_i, dx_i/ds_0, dx_i/ds_1 & d2x_i/ds_0ds_1 for i = 1,2). Takes the x,y coordinates of the node from which its position can be determined. More...

void	set_position_of_boundary_node (const unsigned &node_num_x, const unsigned &node_num_y, BoundaryNode< Node > *node_pt)
	sets the generalised position of the node (i.e. - x_i, dx_i/ds_0, dx_i/ds_1 & d2x_i/ds_0ds_1 for i = 1,2). Takes the x,y coordinates of the node from which its position can be determined. Also sets coordinates on boundary vector for the node to be the generalised position of the node in macro element coordinates More...

void	generalised_macro_element_position_of_node (const unsigned &node_num_x, const unsigned &node_num_y, DenseMatrix< double > &m_gen)
	computes the generalised position of the node at position (node_num_x, node_num_y) in the macro element coordinate scheme. index 0 of m_gen : 0 - m_i 1 - dm_i/ds_0 2 - dm_i/ds_1 3 - d2m_i/ds_0ds_1 (where i is index 1 of m_gen) More...

virtual void	build_mesh (TimeStepper *time_stepper_pt)
	Generic mesh construction function to build the mesh. More...

virtual void	setup_boundary_element_info ()
	Setup lookup schemes which establish whic elements are located next to mesh's boundaries (wrapper to suppress doc). Specific version for HermiteQuadMesh to ensure that the order of the elements in Boundary_element_pt matches the actual order along the boundary. This is required when hijacking the BiharmonicElement to apply the BiharmonicFluidBoundaryElement in BiharmonicFluidProblem::impose_traction_free_edge(...) More...

virtual void	setup_boundary_element_info (std::ostream &outfile)
	Setup lookup schemes which establish which elements are located next to which boundaries (Doc to outfile if it's open). Specific version for HermiteQuadMesh to ensure that the order of the elements in Boundary_element_pt matches the actual order along the boundary. This is required when hijacking the BiharmonicElement to apply the BiharmonicFluidBoundaryElement in BiharmonicFluidProblem::impose_traction_free_edge(...) More...

Private Attributes
Vector< unsigned >	Nelement
	number of elements in each coordinate direction More...

bool	Xperiodic
	boolean variable to determine whether the mesh is periodic in the x-direction More...

TopologicallyRectangularDomain *	Domain_pt
	Pointer to the topologically rectangular domain which prescribes the problem domain. More...

MeshSpacingFnPtr	Node_spacing_fn
	non uniform mesh spacing function pointer More...

Additional Inherited Members
Public Attributes inherited from oomph::Mesh
bool	Output_halo_elements
	Bool for output of halo elements. More...

Static Public Attributes inherited from oomph::Mesh
static Steady< 0 >	Default_TimeStepper
	Default Steady Timestepper, to be used in default arguments to Mesh constructors. More...

static bool	Suppress_warning_about_empty_mesh_level_time_stepper_function
	Boolean used to control warning about empty mesh level timestepper function. More...

Protected Member Functions inherited from oomph::Mesh
void	setup_shared_node_scheme ()
	Setup shared node scheme. More...

unsigned long	assign_global_eqn_numbers (Vector< double * > &Dof_pt)
	Assign the global equation numbers in the Data stored at the nodes and also internal element Data. Also, build (via push_back) the Vector of pointers to the dofs (variables). More...

void	describe_dofs (std::ostream &out, const std::string &current_string) const
	Function to describe the dofs of the Mesh. The ostream specifies the output stream to which the description is written; the string stores the currently assembled output that is ultimately written to the output stream by Data::describe_dofs(...); it is typically built up incrementally as we descend through the call hierarchy of this function when called from Problem::describe_dofs(...) More...

void	describe_local_dofs (std::ostream &out, const std::string &current_string) const
	Function to describe the local dofs of the elements. The ostream specifies the output stream to which the description is written; the string stores the currently assembled output that is ultimately written to the output stream by Data::describe_dofs(...); it is typically built up incrementally as we descend through the call hierarchy of this function when called from Problem::describe_dofs(...) More...

void	assign_local_eqn_numbers (const bool &store_local_dof_pt)
	Assign the local equation numbers in all elements If the boolean argument is true then also store pointers to dofs. More...

void	convert_to_boundary_node (Node &node_pt, const Vector< FiniteElement > &finite_element_pt)
	A function that upgrades an ordinary node to a boundary node We shouldn't ever really use this, but it does make life that bit easier for the lazy mesh writer. The pointer to the node is replaced by a pointer to the new boundary node in all element look-up schemes and in the mesh's Node_pt vector. The new node is also addressed by node_pt on return from the function. More...

void	convert_to_boundary_node (Node *&node_pt)
	A function that upgrades an ordinary node to a boundary node. All pointers to the node from the mesh's elements are found. and replaced by pointers to the new boundary node. If the node is present in the mesh's list of nodes, that pointer is also replaced. Finally, the pointer argument node_pt addresses the new node on return from the function. We shouldn't ever really use this, but it does make life that bit easier for the lazy mesh writer. More...

Protected Attributes inherited from oomph::Mesh
Vector< Vector< Node * > >	Boundary_node_pt
	Vector of Vector of pointers to nodes on the boundaries: Boundary_node_pt(b,n). Note that this is private to force the use of the add_boundary_node() function, which ensures that the reverse look-up schemes for the nodes are set up. More...

bool	Lookup_for_elements_next_boundary_is_setup
	Flag to indicate that the lookup schemes for elements that are adjacent to the boundaries has been set up. More...

Vector< Vector< FiniteElement * > >	Boundary_element_pt
	Vector of Vector of pointers to elements on the boundaries: Boundary_element_pt(b,e) More...

Vector< Vector< int > >	Face_index_at_boundary
	For the e-th finite element on boundary b, this is the index of the face that lies along that boundary. More...

std::map< unsigned, Vector< GeneralisedElement * > >	Root_halo_element_pt
	Map of vectors holding the pointers to the root halo elements. More...

std::map< unsigned, Vector< GeneralisedElement * > >	Root_haloed_element_pt
	Map of vectors holding the pointers to the root haloed elements. More...

std::map< unsigned, Vector< Node * > >	Halo_node_pt
	Map of vectors holding the pointers to the halo nodes. More...

std::map< unsigned, Vector< Node * > >	Haloed_node_pt
	Map of vectors holding the pointers to the haloed nodes. More...

std::map< unsigned, Vector< Node * > >	Shared_node_pt
	Map of vectors holding the pointers to the shared nodes. These are all the nodes that are on two "neighbouring" processes (the halo(ed) lookup scheme depends upon which processor is in charge. More...

OomphCommunicator *	Comm_pt
	Pointer to communicator – set to NULL if mesh is not distributed. More...

std::map< unsigned, Vector< GeneralisedElement * > >	External_halo_element_pt
	External halo(ed) elements are created as and when they are needed to act as source elements for the particular process's mesh. The storage is wiped and rebuilt every time the mesh is refined. More...

std::map< unsigned, Vector< GeneralisedElement * > >	External_haloed_element_pt
	Map of vectors holding the pointers to the external haloed elements. More...

std::map< unsigned, Vector< Node * > >	External_halo_node_pt
	Map of vectors holding the pointers to the external halo nodes. More...

std::map< unsigned, Vector< Node * > >	External_haloed_node_pt
	Map of vectors holding the pointers to the external haloed nodes. More...

bool	Keep_all_elements_as_halos
	bool to indicate whether to keep all elements in a mesh as halos or not More...

bool	Resize_halo_nodes_not_required
	Set this to true to suppress resizing of halo nodes (at your own risk!) More...

Vector< Node * >	Node_pt
	Vector of pointers to nodes. More...

Vector< GeneralisedElement * >	Element_pt
	Vector of pointers to generalised elements. More...

std::vector< bool >	Boundary_coordinate_exists
	Vector of boolean data that indicates whether the boundary coordinates have been set for the boundary. More...

Detailed Description

template<class ELEMENT>
class oomph::HermiteQuadMesh< ELEMENT >

A two dimensional Hermite bicubic element quadrilateral mesh for a topologically rectangular domain. The geometry of the problem must be prescribed using the TopologicallyRectangularDomain. Non uniform node spacing can be prescribed using a function pointer.

Definition at line 52 of file hermite_element_quad_mesh.template.h.

Member Typedef Documentation

◆ MeshSpacingFnPtr

template<class ELEMENT >

typedef void(* oomph::HermiteQuadMesh< ELEMENT >::MeshSpacingFnPtr) (const Vector< double > &m_uniform_spacing, Vector< double > &m_non_uniform_spacing)

Mesh Spacing Function Pointer - an optional function pointer to prescibe the node spacing in a non-uniformly spaced mesh - takes the position of a node (in macro element coordinates) in the uniformly spaced mesh and return the position in the non-uniformly spaced mesh.

Definition at line 59 of file hermite_element_quad_mesh.template.h.

Constructor & Destructor Documentation

◆ HermiteQuadMesh() [1/2]

template<class ELEMENT >

oomph::HermiteQuadMesh< ELEMENT >::HermiteQuadMesh	(	const unsigned &	nx,
		const unsigned &	ny,
		TopologicallyRectangularDomain *	domain,
		const bool &	periodic_in_x = `false`,
		TimeStepper *	time_stepper_pt = `&Mesh::Default_TimeStepper`
	)

inline

Mesh Constructor (for a uniformly spaced mesh). Takes the following arguments : nx : number of elements in x direction; ny : number of elements in y direction; domain : topologically rectangular domain; periodic_in_x : flag specifying if the mesh is periodic in the x direction (default = false); time_stepper_pt : pointer to the time stepper (default = no timestepper);.

Definition at line 73 of file hermite_element_quad_mesh.template.h.

References oomph::HermiteQuadMesh< ELEMENT >::build_mesh(), oomph::HermiteQuadMesh< ELEMENT >::Domain_pt, oomph::HermiteQuadMesh< ELEMENT >::Nelement, oomph::HermiteQuadMesh< ELEMENT >::Node_spacing_fn, and oomph::HermiteQuadMesh< ELEMENT >::Xperiodic.

◆ HermiteQuadMesh() [2/2]

template<class ELEMENT >

oomph::HermiteQuadMesh< ELEMENT >::HermiteQuadMesh	(	const unsigned &	nx,
		const unsigned &	ny,
		TopologicallyRectangularDomain *	domain,
		const MeshSpacingFnPtr	spacing_fn,
		const bool &	periodic_in_x = `false`,
		TimeStepper *	time_stepper_pt = `&Mesh::Default_TimeStepper`
	)

inline

Mesh Constructor (for a non-uniformly spaced mesh). Takes the following arguments : nx : number of elements in x direction; ny : number of elements in y direction; domain : topologically rectangular domain; spacing_fn : spacing function prescribing a non-uniformly spaced mesh periodic_in_x : flag specifying if the mesh is periodic in the x direction (default = false); time_stepper_pt : pointer to the time stepper (default = notimestepper);.

build the mesh

Definition at line 114 of file hermite_element_quad_mesh.template.h.

References oomph::HermiteQuadMesh< ELEMENT >::build_mesh(), oomph::HermiteQuadMesh< ELEMENT >::Domain_pt, oomph::HermiteQuadMesh< ELEMENT >::Nelement, oomph::HermiteQuadMesh< ELEMENT >::Node_spacing_fn, and oomph::HermiteQuadMesh< ELEMENT >::Xperiodic.

◆ ~HermiteQuadMesh()

template<class ELEMENT >

oomph::HermiteQuadMesh< ELEMENT >::~HermiteQuadMesh ( )

inline

Destructor - does nothing - handled in mesh base class.

Definition at line 144 of file hermite_element_quad_mesh.template.h.

Member Function Documentation

◆ build_mesh()

template<class ELEMENT >

void oomph::HermiteQuadMesh< ELEMENT >::build_mesh ( TimeStepper * time_stepper_pt )

privatevirtual

Generic mesh construction function to build the mesh.

Definition at line 603 of file hermite_element_quad_mesh.template.cc.

References i.

Referenced by oomph::HermiteQuadMesh< ELEMENT >::HermiteQuadMesh().

◆ generalised_macro_element_position_of_node()

template<class ELEMENT >

void oomph::HermiteQuadMesh< ELEMENT >::generalised_macro_element_position_of_node	(	const unsigned &	node_num_x,
		const unsigned &	node_num_y,
		DenseMatrix< double > &	m_gen
	)

private

computes the generalised position of the node at position (node_num_x, node_num_y) in the macro element coordinate scheme. index 0 of m_gen : 0 - m_i 1 - dm_i/ds_0 2 - dm_i/ds_1 3 - d2m_i/ds_0ds_1 (where i is index 1 of m_gen)

Definition at line 200 of file hermite_element_quad_mesh.template.cc.

◆ macro_coordinate_position()

template<class ELEMENT >

void oomph::HermiteQuadMesh< ELEMENT >::macro_coordinate_position	(	const unsigned &	node_num_x,
		const unsigned &	node_num_y,
		Vector< double > &	macro_element_position
	)

inlineprivate

returns the macro element position of the node that is the x-th node along from the LHS and the y-th node up from the lower edge

Definition at line 157 of file hermite_element_quad_mesh.template.h.

References oomph::HermiteQuadMesh< ELEMENT >::Nelement, and oomph::HermiteQuadMesh< ELEMENT >::Node_spacing_fn.

◆ nelement_in_dim()

template<class ELEMENT >

unsigned& oomph::HermiteQuadMesh< ELEMENT >::nelement_in_dim ( const unsigned & d )

inline

Access function for number of elements in mesh in each dimension.

Definition at line 148 of file hermite_element_quad_mesh.template.h.

References oomph::HermiteQuadMesh< ELEMENT >::Nelement.

◆ set_position_of_boundary_node()

template<class ELEMENT >

void oomph::HermiteQuadMesh< ELEMENT >::set_position_of_boundary_node	(	const unsigned &	node_num_x,
		const unsigned &	node_num_y,
		BoundaryNode< Node > *	node_pt
	)

private

sets the generalised position of the node (i.e. - x_i, dx_i/ds_0, dx_i/ds_1 & d2x_i/ds_0ds_1 for i = 1,2). Takes the x,y coordinates of the node from which its position can be determined. Also sets coordinates on boundary vector for the node to be the generalised position of the node in macro element coordinates

Definition at line 116 of file hermite_element_quad_mesh.template.cc.

References i, oomph::BoundaryNode< NODE_TYPE >::is_on_boundary(), and oomph::BoundaryNode< NODE_TYPE >::set_coordinates_on_boundary().

◆ set_position_of_node()

template<class ELEMENT >

void oomph::HermiteQuadMesh< ELEMENT >::set_position_of_node	(	const unsigned &	node_num_x,
		const unsigned &	node_num_y,
		Node *	node_pt
	)

private

sets the generalised position of the node (i.e. - x_i, dx_i/ds_0, dx_i/ds_1 & d2x_i/ds_0ds_1 for i = 1,2). Takes the x,y coordinates of the node from which its position can be determined.

Definition at line 48 of file hermite_element_quad_mesh.template.cc.

References i, and oomph::Node::x_gen().

◆ setup_boundary_element_info() [1/2]

template<class ELEMENT >

virtual void oomph::HermiteQuadMesh< ELEMENT >::setup_boundary_element_info ( )

inlineprivatevirtual

Setup lookup schemes which establish whic elements are located next to mesh's boundaries (wrapper to suppress doc). Specific version for HermiteQuadMesh to ensure that the order of the elements in Boundary_element_pt matches the actual order along the boundary. This is required when hijacking the BiharmonicElement to apply the BiharmonicFluidBoundaryElement in BiharmonicFluidProblem::impose_traction_free_edge(...)

Reimplemented from oomph::Mesh.

Definition at line 215 of file hermite_element_quad_mesh.template.h.

◆ setup_boundary_element_info() [2/2]

template<class ELEMENT >

void oomph::HermiteQuadMesh< ELEMENT >::setup_boundary_element_info ( std::ostream & outfile )

privatevirtual

Setup lookup schemes which establish which elements are located next to which boundaries (Doc to outfile if it's open). Specific version for HermiteQuadMesh to ensure that the order of the elements in Boundary_element_pt matches the actual order along the boundary. This is required when hijacking the BiharmonicElement to apply the BiharmonicFluidBoundaryElement in BiharmonicFluidProblem::impose_traction_free_edge(...)

Reimplemented from oomph::Mesh.

Definition at line 1271 of file hermite_element_quad_mesh.template.cc.

References oomph::FiniteElement::dim(), oomph::LeakCheckNames::doc(), e, oomph::Node::get_boundaries_pt(), i, oomph::FiniteElement::nnode_1d(), oomph::FiniteElement::node_pt(), and oomph::Global_string_for_annotation::string().