Base class for refineable tet meshes. More...

#include <refineable_mesh.h>

Inheritance diagram for oomph::RefineableTetMeshBase:

Public Member Functions
double &	max_element_size ()
	Max element size allowed during adaptation. More...

double &	min_element_size ()
	Min element size allowed during adaptation. More...

double &	max_permitted_edge_ratio ()
	Min edge ratio before remesh gets triggered. More...

void	doc_adaptivity_targets (std::ostream &outfile)
	Doc the targets for mesh adaptation. More...

double	compute_volume_target (const Vector< double > &elem_error, Vector< double > &target_volume)

Public Member Functions inherited from oomph::RefineableMeshBase
bool	adapt_flag ()

	RefineableMeshBase ()

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

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

virtual	~RefineableMeshBase ()
	Empty Destructor: More...

unsigned	nrefined ()
	Access fct for number of elements that were refined. More...

unsigned	nunrefined ()
	Access fct for number of elements that were unrefined. More...

unsigned &	nrefinement_overruled ()

unsigned &	max_keep_unrefined ()

ErrorEstimator *&	spatial_error_estimator_pt ()
	Access to spatial error estimator. More...

ErrorEstimator *	spatial_error_estimator_pt () const
	Access to spatial error estimator (const version. More...

double &	min_permitted_error ()

double &	max_permitted_error ()

double &	min_error ()

double &	max_error ()

DocInfo *&	doc_info_pt ()
	Access fct for pointer to DocInfo. More...

void	enable_adaptation ()
	Enable adaptation. More...

void	disable_adaptation ()
	Disable adaptation. More...

void	enable_p_adaptation ()
	Enable adaptation. More...

void	disable_p_adaptation ()
	Disable adaptation. More...

void	enable_additional_synchronisation_of_hanging_nodes ()
	Enable additional synchronisation of hanging nodes. More...

void	disable_additional_synchronisation_of_hanging_nodes ()
	Disable additional synchronisation of hanging nodes. More...

bool	is_adaptation_enabled () const
	Return whether the mesh is to be adapted. More...

bool	is_p_adaptation_enabled () const
	Return whether the mesh is to be adapted. More...

bool	is_additional_synchronisation_of_hanging_nodes_disabled () const
	Return whether additional synchronisation is enabled. More...

DocInfo	doc_info ()
	Access fct for DocInfo. More...

virtual void	adapt (const Vector< double > &elemental_error)=0

virtual void	p_adapt (const Vector< double > &elemental_error)

virtual void	refine_uniformly (DocInfo &doc_info)=0
	Refine mesh uniformly and doc process. More...

virtual void	refine_uniformly ()
	Refine mesh uniformly. More...

virtual void	p_refine_uniformly (DocInfo &doc_info)
	p-refine mesh uniformly and doc process More...

virtual void	p_refine_uniformly ()
	p-refine mesh uniformly More...

virtual unsigned	unrefine_uniformly ()=0

void	p_unrefine_uniformly (DocInfo &doc_info)
	p-unrefine mesh uniformly More...

Public Member Functions inherited from oomph::Mesh
	Mesh ()
	Default constructor. More...

	Mesh (const Vector< Mesh * > &sub_mesh_pt)

void	merge_meshes (const Vector< Mesh * > &sub_mesh_pt)

virtual void	setup_boundary_element_info ()

virtual void	setup_boundary_element_info (std::ostream &outfile)

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)

virtual void	scale_mesh (const double &factor)

	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 ()

void	flush_element_storage ()

void	flush_node_storage ()

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

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)

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 ()

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)

virtual void	reorder_nodes (const bool &use_old_ordering=true)

virtual void	get_node_reordering (Vector< Node * > &reordering, const bool &use_old_ordering=true) const

template<class BULK_ELEMENT , template< class > class FACE_ELEMENT>
void	build_face_mesh (const unsigned &b, Mesh *const &face_mesh_pt)

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)

double	total_size ()

void	check_inverted_elements (bool &mesh_has_inverted_elements, std::ofstream &inverted_element_file)

void	check_inverted_elements (bool &mesh_has_inverted_elements)

unsigned	check_for_repeated_nodes (const double &epsilon=1.0e-12)

Vector< Node * >	prune_dead_nodes ()

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

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

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

void	output_fct_paraview (std::ofstream &file_out, const unsigned &nplot, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt) const

void	output_fct_paraview (std::ofstream &file_out, const unsigned &nplot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt) const

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)

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)

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

void	shift_time_values ()

void	calculate_predictions ()

void	set_nodal_and_elemental_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data)

virtual void	set_mesh_level_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data)

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)

virtual void	compute_norm (double &norm)

virtual void	compute_norm (Vector< double > &norm)

virtual void	compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm)

virtual void	compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm)

virtual void	compute_error (FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm)

virtual void	compute_error (FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, Vector< double > &error, Vector< double > &norm)

virtual void	compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, Vector< double > &error, Vector< double > &norm)

virtual void	compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, Vector< double > &error, Vector< double > &norm)

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)

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

OomphCommunicator *	communicator_pt () const

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

Public Attributes
double	Max_element_size
	Max permitted element size. More...

double	Min_element_size
	Min permitted element size. More...

double	Max_permitted_edge_ratio
	Max edge ratio before remesh gets triggered. More...

Additional Inherited Members
Public Types inherited from oomph::Mesh
typedef void(FiniteElement::*	SteadyExactSolutionFctPt) (const Vector< double > &x, Vector< double > &soln)

typedef void(FiniteElement::*	UnsteadyExactSolutionFctPt) (const double &time, const Vector< double > &x, Vector< double > &soln)

Static Public Attributes inherited from oomph::Mesh
static Steady< 0 >	Default_TimeStepper
	The Steady Timestepper. More...

static bool	Suppress_warning_about_empty_mesh_level_time_stepper_function
	Static boolean flag to control warning about mesh level timesteppers. More...

Protected Member Functions inherited from oomph::Mesh
unsigned long	assign_global_eqn_numbers (Vector< double * > &Dof_pt)
	Assign (global) equation numbers to the nodes. More...

void	describe_dofs (std::ostream &out, const std::string &current_string) const

void	describe_local_dofs (std::ostream &out, const std::string &current_string) const

void	assign_local_eqn_numbers (const bool &store_local_dof_pt)
	Assign local equation numbers in all elements. More...

void	convert_to_boundary_node (Node &node_pt, const Vector< FiniteElement > &finite_element_pt)

void	convert_to_boundary_node (Node *&node_pt)

Protected Attributes inherited from oomph::RefineableMeshBase
ErrorEstimator *	Spatial_error_estimator_pt
	Pointer to spatial error estimator. More...

double	Max_permitted_error
	Max. error (i.e. split elements if their error is larger) More...

double	Min_permitted_error
	Min. error (i.e. (try to) merge elements if their error is smaller) More...

double	Min_error
	Min.actual error. More...

double	Max_error
	Max. actual error. More...

unsigned	Nrefined
	Stats: Number of elements that were refined. More...

unsigned	Nunrefined
	Stats: Number of elements that were unrefined. More...

bool	Adapt_flag
	Flag that requests adaptation. More...

bool	P_adapt_flag
	Flag that requests p-adaptation. More...

bool	Additional_synchronisation_of_hanging_nodes_not_required
	Flag that disables additional synchronisation of hanging nodes. More...

DocInfo *	Doc_info_pt
	Pointer to DocInfo. More...

unsigned	Max_keep_unrefined

unsigned	Nrefinement_overruled

Protected Attributes inherited from oomph::Mesh
Vector< Vector< Node * > >	Boundary_node_pt

bool	Lookup_for_elements_next_boundary_is_setup

Vector< Vector< FiniteElement * > >	Boundary_element_pt

Vector< Vector< int > >	Face_index_at_boundary

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

Detailed Description

Base class for refineable tet meshes.

///////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////

Member Function Documentation

◆ compute_volume_target()

double oomph::RefineableTetMeshBase::compute_volume_target	(	const Vector< double > &	elem_error,
		Vector< double > &	target_volume
	)

inline

Compute target volume based on the elements' error and the error target; return max edge ratio

     {
       double max_edge_ratio = 0.0;
       unsigned count_unrefined = 0;
       unsigned count_refined = 0;
       this->Nrefinement_overruled = 0;
  
       unsigned nel = this->nelement();
       for (unsigned e = 0; e < nel; e++)
       {
         // Get element
         FiniteElement* el_pt = this->finite_element_pt(e);
  
         // Calculate the volume of the element
         double volume = el_pt->size();
  
         // Find the vertex coordinates
         // (vertices are enumerated first)
         double vertex[4][3];
         for (unsigned n = 0; n < 4; ++n)
         {
           for (unsigned i = 0; i < 3; ++i)
           {
             vertex[n][i] = el_pt->node_pt(n)->x(i);
           }
         }
  
         // Compute the radius of the circumsphere of the tetrahedron
         // Algorithm stolen from tetgen for consistency
         DenseDoubleMatrix A(3);
         for (unsigned i = 0; i < 3; ++i)
         {
           A(0, i) = vertex[1][i] - vertex[0][i];
           A(1, i) = vertex[2][i] - vertex[0][i];
           A(2, i) = vertex[3][i] - vertex[0][i];
         }
  
         Vector<double> rhs(3);
         // Compute the right hand side vector b (3x1).
         for (unsigned i = 0; i < 3; ++i)
         {
           rhs[i] = 0.0;
           for (unsigned k = 0; k < 3; ++k)
           {
             rhs[i] += A(i, k) * A(i, k);
           }
           rhs[i] *= 0.5;
         }
  
         // Solve the linear system, in which the rhs is over-written with
         // the solution
         A.solve(rhs);
  
         // Calculate the circum-radius
         double circum_radius =
           sqrt(rhs[0] * rhs[0] + rhs[1] * rhs[1] + rhs[2] * rhs[2]);
  
         // Now find the shortest edge length
         Vector<double> edge(3);
         double min_length = DBL_MAX;
         for (unsigned start = 0; start < 4; ++start)
         {
           for (unsigned end = start + 1; end < 4; ++end)
           {
             for (unsigned i = 0; i < 3; ++i)
             {
               edge[i] = vertex[start][i] - vertex[end][i];
             }
             double length =
               sqrt(edge[0] * edge[0] + edge[1] * edge[1] + edge[2] * edge[2]);
             if (length < min_length)
             {
               min_length = length;
             }
           }
         }
  
         // Now calculate the minimum edge ratio for this element
         double local_max_edge_ratio = circum_radius / min_length;
         if (local_max_edge_ratio > max_edge_ratio)
         {
           max_edge_ratio = local_max_edge_ratio;
         }
  
         // Mimick refinement in tree-based procedure: Target volumes
         // for elements that exceed permitted error is 1/4 of their
         // current volume, corresponding to a uniform sub-division.
         if (elem_error[e] > this->max_permitted_error())
         {
           target_volume[e] = std::max(volume / 4.0, Min_element_size);
           if (target_volume[e] != Min_element_size)
           {
             count_refined++;
           }
           else
           {
             this->Nrefinement_overruled++;
           }
         }
         else if (elem_error[e] < this->min_permitted_error())
         {
           target_volume[e] = std::min(4.0 * volume, Max_element_size);
           if (target_volume[e] != Max_element_size)
           {
             count_unrefined++;
           }
         }
         else
         {
           // Leave it alone
           target_volume[e] = std::max(volume, Min_element_size);
         }
  
       } // End of loop over elements
  
       // Tell everybody
       this->Nrefined = count_refined;
       this->Nunrefined = count_unrefined;
  
       return max_edge_ratio;
     }

References e(), Eigen::placeholders::end, oomph::Mesh::finite_element_pt(), i, k, max, Max_element_size, oomph::RefineableMeshBase::max_permitted_error(), min, Min_element_size, oomph::RefineableMeshBase::min_permitted_error(), n, oomph::Mesh::nelement(), oomph::FiniteElement::node_pt(), oomph::RefineableMeshBase::Nrefined, oomph::RefineableMeshBase::Nrefinement_overruled, oomph::RefineableMeshBase::Nunrefined, oomph::FiniteElement::size(), sqrt(), oomph::CumulativeTimings::start(), and oomph::Node::x().

◆ doc_adaptivity_targets()

void oomph::RefineableTetMeshBase::doc_adaptivity_targets ( std::ostream & outfile )

inlinevirtual

Doc the targets for mesh adaptation.

Reimplemented from oomph::RefineableMeshBase.

     {
       outfile << std::endl;
       outfile << "Targets for mesh adaptation: " << std::endl;
       outfile << "---------------------------- " << std::endl;
       outfile << "Target for max. error: " << Max_permitted_error << std::endl;
       outfile << "Target for min. error: " << Min_permitted_error << std::endl;
       outfile << "Target max edge ratio: " << Max_permitted_edge_ratio
               << std::endl;
       outfile << "Min. allowed element size: " << Min_element_size << std::endl;
       outfile << "Max. allowed element size: " << Max_element_size << std::endl;
       outfile << "Don't unrefine if less than " << Max_keep_unrefined
               << " elements need unrefinement." << std::endl;
       outfile << std::endl;
     }

References Max_element_size, oomph::RefineableMeshBase::Max_keep_unrefined, Max_permitted_edge_ratio, oomph::RefineableMeshBase::Max_permitted_error, Min_element_size, and oomph::RefineableMeshBase::Min_permitted_error.

◆ max_element_size()

double& oomph::RefineableTetMeshBase::max_element_size ( )

inline

Max element size allowed during adaptation.

     {
       return Max_element_size;
     }

References Max_element_size.

◆ max_permitted_edge_ratio()

double& oomph::RefineableTetMeshBase::max_permitted_edge_ratio ( )

inline

Min edge ratio before remesh gets triggered.

     {
       return Max_permitted_edge_ratio;
     }

References Max_permitted_edge_ratio.

◆ min_element_size()

double& oomph::RefineableTetMeshBase::min_element_size ( )

inline

Min element size allowed during adaptation.

     {
       return Min_element_size;
     }

References Min_element_size.

Member Data Documentation

◆ Max_element_size

double oomph::RefineableTetMeshBase::Max_element_size

Max permitted element size.

Referenced by compute_volume_target(), doc_adaptivity_targets(), oomph::RefineableGmshTetMesh< ELEMENT >::initialise_adaptation_data(), and max_element_size().

◆ Max_permitted_edge_ratio

double oomph::RefineableTetMeshBase::Max_permitted_edge_ratio

Max edge ratio before remesh gets triggered.

Referenced by doc_adaptivity_targets(), oomph::RefineableGmshTetMesh< ELEMENT >::initialise_adaptation_data(), and max_permitted_edge_ratio().

◆ Min_element_size

double oomph::RefineableTetMeshBase::Min_element_size

Min permitted element size.

Referenced by compute_volume_target(), doc_adaptivity_targets(), oomph::RefineableGmshTetMesh< ELEMENT >::initialise_adaptation_data(), and min_element_size().

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

refineable_mesh.h

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ compute_volume_target()

◆ doc_adaptivity_targets()

◆ max_element_size()

◆ max_permitted_edge_ratio()

◆ min_element_size()

Member Data Documentation

◆ Max_element_size

◆ Max_permitted_edge_ratio

◆ Min_element_size