#include <gmsh_tet_mesh.template.h>

Inheritance diagram for oomph::RefineableGmshTetMesh< ELEMENT >:

Public Member Functions
	RefineableGmshTetMesh (GmshParameters gmsh_parameters_pt, const bool &use_mesh_grading_from_file, TimeStepper time_stepper_pt=&Mesh::Default_TimeStepper)

	RefineableGmshTetMesh (GmshParameters gmsh_parameters_pt, TimeStepper time_stepper_pt=&Mesh::Default_TimeStepper)
	Constructor. More...

void	adapt (const Vector< double > &elem_error)
	Adapt mesh, based on elemental error provided. More...

unsigned	unrefine_uniformly ()
	Refine uniformly. More...

void	refine_uniformly (DocInfo &doc_info)
	Unrefine uniformly. More...

Public Member Functions inherited from oomph::GmshTetMesh< ELEMENT >
	GmshTetMesh (GmshParameters gmsh_parameters_pt, TimeStepper time_stepper_pt=&Mesh::Default_TimeStepper)
	Constructor. More...

	GmshTetMesh (GmshParameters gmsh_parameters_pt, const bool &use_mesh_grading_from_file, TimeStepper time_stepper_pt=&Mesh::Default_TimeStepper)

Public Member Functions inherited from oomph::TetMeshBase
	TetMeshBase ()
	Constructor. More...

	TetMeshBase (const TetMeshBase &node)=delete
	Broken copy constructor. More...

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

virtual	~TetMeshBase ()
	Destructor (empty) More...

void	assess_mesh_quality (std::ofstream &some_file)

template<class ELEMENT >
void	setup_boundary_coordinates (const unsigned &b)

template<class ELEMENT >
void	setup_boundary_coordinates (const unsigned &b, const bool &switch_normal)

template<class ELEMENT >
void	setup_boundary_coordinates (const unsigned &b, const bool &switch_normal, std::ofstream &outfile)

template<class ELEMENT >
void	setup_boundary_coordinates (const unsigned &b, std::ofstream &outfile)

unsigned	nboundary_element_in_region (const unsigned &b, const unsigned &r) const
	Return the number of elements adjacent to boundary b in region r. More...

FiniteElement *	boundary_element_in_region_pt (const unsigned &b, const unsigned &r, const unsigned &e) const
	Return pointer to the e-th element adjacent to boundary b in region r. More...

int	face_index_at_boundary_in_region (const unsigned &b, const unsigned &r, const unsigned &e) const
	Return face index of the e-th element adjacent to boundary b in region r. More...

unsigned	nregion ()
	Return the number of regions specified by attributes. More...

unsigned	nregion_element (const unsigned &r)
	Return the number of elements in region r. More...

double	region_attribute (const unsigned &i)

FiniteElement *	region_element_pt (const unsigned &r, const unsigned &e)
	Return the e-th element in the r-th region. More...

template<class ELEMENT >
void	snap_to_quadratic_surface (const Vector< unsigned > &boundary_id, const std::string &quadratic_surface_file_name, const bool &switch_normal, DocInfo &doc_info)

template<class ELEMENT >
void	snap_to_quadratic_surface (const Vector< unsigned > &boundary_id, const std::string &quadratic_surface_file_name, const bool &switch_normal)

void	snap_nodes_onto_geometric_objects ()

template<class ELEMENT >
void	split_elements_in_corners (TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper)

void	setup_boundary_element_info ()

void	setup_boundary_element_info (std::ostream &outfile)

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	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 Member Functions inherited from oomph::RefineableTetMeshBase
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	p_adapt (const Vector< double > &elemental_error)

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...

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

Protected Member Functions
void	initialise_adaptation_data ()
	Helper function to initialise data associated with adaptation. 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)

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)

Public Attributes inherited from oomph::RefineableTetMeshBase
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...

Static Public Attributes inherited from oomph::TetMeshBase
static double	Tolerance_for_boundary_finding = 1.0e-5

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 Attributes inherited from oomph::GmshTetMesh< ELEMENT >
GmshParameters *	Gmsh_parameters_pt
	Parameters. More...

Protected Attributes inherited from oomph::TetMeshBase
Vector< Vector< FiniteElement * > >	Region_element_pt

Vector< double >	Region_attribute

Vector< std::map< unsigned, Vector< FiniteElement * > > >	Boundary_region_element_pt
	Storage for elements adjacent to a boundary in a particular region. More...

Vector< std::map< unsigned, Vector< int > > >	Face_index_region_at_boundary

TetMeshFacetedClosedSurface *	Outer_boundary_pt
	Faceted surface that defines outer boundaries. More...

Vector< TetMeshFacetedSurface * >	Internal_surface_pt
	Vector to faceted surfaces that define internal boundaries. More...

std::map< unsigned, TetMeshFacetedSurface * >	Tet_mesh_faceted_surface_pt

std::map< unsigned, TetMeshFacet * >	Tet_mesh_facet_pt

std::map< unsigned, Vector< Vector< double > > >	Triangular_facet_vertex_boundary_coordinate

TimeStepper *	Time_stepper_pt
	Timestepper used to build nodes. More...

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

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

Detailed Description

template<class ELEMENT>
class oomph::RefineableGmshTetMesh< ELEMENT >

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

Constructor & Destructor Documentation

◆ RefineableGmshTetMesh() [1/2]

template<class ELEMENT >

oomph::RefineableGmshTetMesh< ELEMENT >::RefineableGmshTetMesh	(	GmshParameters *	gmsh_parameters_pt,
		const bool &	use_mesh_grading_from_file,
		TimeStepper *	time_stepper_pt = `&Mesh::Default_TimeStepper`
	)

inline

Constructor. If boolean is set to true, the target element sizes are read from file (used during adaptation; otherwise uniform target size is used).

       : GmshTetMesh<ELEMENT>(
           gmsh_parameters_pt, use_mesh_grading_from_file, time_stepper_pt)
     {
       initialise_adaptation_data();
     }

References oomph::RefineableGmshTetMesh< ELEMENT >::initialise_adaptation_data().

◆ RefineableGmshTetMesh() [2/2]

template<class ELEMENT >

oomph::RefineableGmshTetMesh< ELEMENT >::RefineableGmshTetMesh	(	GmshParameters *	gmsh_parameters_pt,
		TimeStepper *	time_stepper_pt = `&Mesh::Default_TimeStepper`
	)

inline

Constructor.

       : GmshTetMesh<ELEMENT>(gmsh_parameters_pt,
                              false, // Don't read mesh size data from file
                                     // unless explicitly requested.
                              time_stepper_pt)
     {
       initialise_adaptation_data();
     }

References oomph::RefineableGmshTetMesh< ELEMENT >::initialise_adaptation_data().

Member Function Documentation

◆ adapt()

template<class ELEMENT >

void oomph::RefineableGmshTetMesh< ELEMENT >::adapt ( const Vector< double > & elem_error )

virtual

Adapt mesh, based on elemental error provided.

Adapt problem based on specified elemental error estimates.

Implements oomph::RefineableMeshBase.

   {
     double t_start = 0.0;
  
     //###################################
     t_start = TimingHelpers::timer();
     //###################################
  
     // Get refinement targets
     Vector<double> target_size(elem_error.size());
     double max_edge_ratio =
       this->compute_volume_target(elem_error, target_size);
     // Get maximum target volume
     unsigned n = target_size.size();
     double max_size = 0.0;
     double min_size = DBL_MAX;
     for (unsigned e = 0; e < n; e++)
     {
       if (target_size[e] > max_size) max_size = target_size[e];
       if (target_size[e] < min_size) min_size = target_size[e];
     }
  
     oomph_info << "Maximum target size: " << max_size << std::endl;
     oomph_info << "Minimum target size: " << min_size << std::endl;
     oomph_info << "Number of elements to be refined " << this->Nrefined
                << std::endl;
     oomph_info << "Number of elements to be unrefined " << this->Nunrefined
                << std::endl;
     oomph_info << "Max edge ratio " << max_edge_ratio << std::endl;
  
     double orig_max_size, orig_min_size;
     this->max_and_min_element_size(orig_max_size, orig_min_size);
     oomph_info << "Max/min element size in original mesh: " << orig_max_size
                << " " << orig_min_size << std::endl;
  
     //##################################################################
     oomph_info
       << "adapt: Time for getting volume targets                      : "
       << TimingHelpers::timer() - t_start << " sec " << std::endl;
     //##################################################################
  
     // Should we bother to adapt?
     if ((Nrefined > 0) || (Nunrefined > this->max_keep_unrefined()) ||
         (max_edge_ratio > this->max_permitted_edge_ratio()))
     {
       if (!((Nrefined > 0) || (Nunrefined > max_keep_unrefined())))
       {
         oomph_info << "Mesh regeneration triggered by edge ratio criterion\n";
       }
  
  
       // Are we dealing with a solid mesh?
       SolidMesh* solid_mesh_pt = dynamic_cast<SolidMesh*>(this);
  
  
       // If the mesh is a solid mesh then do the mapping based on the
       // Eulerian coordinates
       bool use_eulerian_coords = false;
       if (solid_mesh_pt != 0)
       {
         use_eulerian_coords = true;
       }
  
       MeshAsGeomObject* mesh_geom_obj_pt = 0;
  
 #ifdef OOMPH_HAS_CGAL
  
       // Make cgal-based bin
       CGALSamplePointContainerParameters cgal_params(this);
       if (use_eulerian_coords)
       {
         cgal_params.enable_use_eulerian_coordinates_during_setup();
       }
       mesh_geom_obj_pt = new MeshAsGeomObject(&cgal_params);
  
 #else
  
       std::ostringstream error_message;
       error_message << "Non-CGAL-based target size transfer not implemented.\n";
       throw OomphLibError(
         error_message.str(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
  
       // Do something here...
  
 #endif
  
       // Set up a map from pointer to element to its number
       // in the mesh
       std::map<GeneralisedElement*, unsigned> element_number;
       unsigned nelem = this->nelement();
       for (unsigned e = 0; e < nelem; e++)
       {
         element_number[this->element_pt(e)] = e;
       }
  
       // Get min/max coordinates
       Vector<std::pair<double, double>> min_and_max_coordinates =
         mesh_geom_obj_pt->sample_point_container_pt()
           ->min_and_max_coordinates();
  
       // Setup grid dimensions for size transfer
       double dx =
         (min_and_max_coordinates[0].second - min_and_max_coordinates[0].first);
       double dy =
         (min_and_max_coordinates[1].second - min_and_max_coordinates[1].first);
       double dz =
         (min_and_max_coordinates[2].second - min_and_max_coordinates[2].first);
  
       double dx_target =
         this->Gmsh_parameters_pt->dx_for_target_size_transfer();
       unsigned nx = unsigned(dx / dx_target);
       unsigned ny = unsigned(dy / dx_target);
       unsigned nz = unsigned(dz / dx_target);
  
       dx /= double(nx);
       dy /= double(ny);
       dz /= double(nz);
  
  
       // Size transfer via hard disk -- yikes...
       std::string target_size_file_name =
         this->Gmsh_parameters_pt->target_size_file_name();
  
       std::ofstream target_size_file;
       target_size_file.open(target_size_file_name.c_str());
       target_size_file << min_and_max_coordinates[0].first << " "
                        << min_and_max_coordinates[1].first << " "
                        << min_and_max_coordinates[2].first << " " << std::endl;
       target_size_file << dx << " " << dy << " " << dz << std::endl;
       target_size_file << nx + 1 << " " << ny + 1 << " " << nz + 1 << std::endl;
  
  
       // Doc target areas
       int counter =
         this->Gmsh_parameters_pt->counter_for_filename_gmsh_size_transfer();
       std::string stem =
         this->Gmsh_parameters_pt->stem_for_filename_gmsh_size_transfer();
       std::ofstream latest_sizes_file;
       bool doc_target_areas = false;
       if ((stem != "") && (counter >= 0))
       {
         doc_target_areas = true;
         std::string filename =
           stem + oomph::StringConversion::to_string(counter) + ".dat";
         latest_sizes_file.open(filename.c_str());
         latest_sizes_file << "ZONE I=" << nx + 1 << ", J=" << ny + 1
                           << ", K=" << nz + 1 << std::endl;
         this->Gmsh_parameters_pt->counter_for_filename_gmsh_size_transfer()++;
       }
  
  
       Vector<double> x(3);
       for (unsigned i = 0; i <= nx; i++)
       {
         x[0] = min_and_max_coordinates[0].first + double(i) * dx;
         for (unsigned j = 0; j <= ny; j++)
         {
           x[1] = min_and_max_coordinates[1].first + double(j) * dy;
           for (unsigned k = 0; k <= nz; k++)
           {
             x[2] = min_and_max_coordinates[2].first + double(k) * dz;
  
             // Try the specified number of nearest sample points for Newton
             // search then just settle on the nearest one
             Vector<double> s(3);
             GeomObject* geom_obj_pt = 0;
             unsigned max_sample_points =
               this->Gmsh_parameters_pt
                 ->max_sample_points_for_limited_locate_zeta_during_target_size_transfer();
  
 #ifdef OOMPH_HAS_CGAL
  
             dynamic_cast<CGALSamplePointContainer*>(
               mesh_geom_obj_pt->sample_point_container_pt())
               ->limited_locate_zeta(x, max_sample_points, geom_obj_pt, s);
  
 #else
  
             std::ostringstream error_message;
             error_message
               << "Non-CGAL-based target size transfer not implemented.\n";
             throw OomphLibError(error_message.str(),
                                 OOMPH_CURRENT_FUNCTION,
                                 OOMPH_EXCEPTION_LOCATION);
  
             // Do something here...
  
 #endif
  
  
 #ifdef PARANOID
             if (geom_obj_pt == 0)
             {
               std::stringstream error_message;
               error_message << "Limited locate zeta failed for zeta = [ "
                             << x[0] << " " << x[1] << " " << x[2]
                             << " ]. Makes no sense!\n";
               throw OomphLibError(error_message.str(),
                                   OOMPH_CURRENT_FUNCTION,
                                   OOMPH_EXCEPTION_LOCATION);
             }
             else
             {
 #endif
  
               FiniteElement* fe_pt = dynamic_cast<FiniteElement*>(geom_obj_pt);
  
 #ifdef PARANOID
               if (fe_pt == 0)
               {
                 std::stringstream error_message;
                 error_message
                   << "Cast to FE for GeomObject returned by limited "
                   << "locate zeta failed for zeta = [ " << x[0] << " " << x[1]
                   << " " << x[2] << " ]. Makes no sense!\n";
                 throw OomphLibError(error_message.str(),
                                     OOMPH_CURRENT_FUNCTION,
                                     OOMPH_EXCEPTION_LOCATION);
               }
               else
               {
 #endif
  
                 // What's the target size of the element that contains this
                 // point
                 double tg_size =
                   pow(target_size[element_number[fe_pt]], 1.0 / 3.0);
                 target_size_file << tg_size << " ";
  
                 // Doc?
                 if (doc_target_areas)
                 {
                   latest_sizes_file << x[0] << " " << x[1] << " " << x[2] << " "
                                     << tg_size << std::endl;
                 }
  
 #ifdef PARANOID
               }
             }
 #endif
           }
           target_size_file << std::endl;
         }
       }
       target_size_file.close();
  
       if (doc_target_areas)
       {
         latest_sizes_file.close();
       }
  
       // Build new mesh, reading area information from file
       bool use_mesh_grading_from_file = true;
       RefineableGmshTetMesh<ELEMENT>* new_mesh_pt =
         new RefineableGmshTetMesh<ELEMENT>(this->Gmsh_parameters_pt,
                                            use_mesh_grading_from_file,
                                            this->Time_stepper_pt);
  
       /* // keep around for debugging */
       /* unsigned nplot=5; */
       /* ofstream vtu_file; */
       /* vtu_file.open("new_mesh.vtu"); */
       /* new_mesh_pt->output_paraview(vtu_file,nplot); */
       /* vtu_file.close(); */
  
       //###################################
       t_start = TimingHelpers::timer();
       //###################################
  
       ProjectionProblem<ELEMENT>* project_problem_pt = 0;
  
       // Check that the projection step is not disabled
       if (!this->Gmsh_parameters_pt->projection_is_disabled())
       {
         // Project current solution onto new mesh
         //---------------------------------------
         project_problem_pt = new ProjectionProblem<ELEMENT>;
         project_problem_pt->mesh_pt() = new_mesh_pt;
         project_problem_pt->project(this);
  
         oomph_info
           << "adapt: Time for project soln onto new mesh                : "
           << TimingHelpers::timer() - t_start << " sec " << std::endl;
       }
       //###################################
       t_start = TimingHelpers::timer();
       //###################################
  
       // Flush the old mesh
       unsigned nnod = nnode();
       for (unsigned j = nnod; j > 0; j--)
       {
         delete Node_pt[j - 1];
         Node_pt[j - 1] = 0;
       }
       unsigned nel = nelement();
       for (unsigned e = nel; e > 0; e--)
       {
         delete Element_pt[e - 1];
         Element_pt[e - 1] = 0;
       }
  
       // Now copy back to current mesh
       //------------------------------
       nnod = new_mesh_pt->nnode();
       Node_pt.resize(nnod);
       nel = new_mesh_pt->nelement();
       Element_pt.resize(nel);
       for (unsigned j = 0; j < nnod; j++)
       {
         Node_pt[j] = new_mesh_pt->node_pt(j);
       }
       for (unsigned e = 0; e < nel; e++)
       {
         Element_pt[e] = new_mesh_pt->element_pt(e);
       }
  
       // Copy the boundary schemes
       unsigned nbound = new_mesh_pt->nboundary();
       Boundary_element_pt.resize(nbound);
       Face_index_at_boundary.resize(nbound);
       Boundary_node_pt.resize(nbound);
       for (unsigned b = 0; b < nbound; b++)
       {
         unsigned nel = new_mesh_pt->nboundary_element(b);
         Boundary_element_pt[b].resize(nel);
         Face_index_at_boundary[b].resize(nel);
         for (unsigned e = 0; e < nel; e++)
         {
           Boundary_element_pt[b][e] = new_mesh_pt->boundary_element_pt(b, e);
           Face_index_at_boundary[b][e] =
             new_mesh_pt->face_index_at_boundary(b, e);
         }
         unsigned nnod = new_mesh_pt->nboundary_node(b);
         Boundary_node_pt[b].resize(nnod);
         for (unsigned j = 0; j < nnod; j++)
         {
           Boundary_node_pt[b][j] = new_mesh_pt->boundary_node_pt(b, j);
         }
       }
  
       // Also copy over the new boundary and region information
       unsigned n_region = new_mesh_pt->nregion();
  
       // Only bother if we have regions
       if (n_region > 1)
       {
         // Deal with the region information first
         this->Region_element_pt.resize(n_region);
         this->Region_attribute.resize(n_region);
         for (unsigned i = 0; i < n_region; i++)
         {
           // Copy across region attributes (region ids!)
           this->Region_attribute[i] = new_mesh_pt->region_attribute(i);
  
           // Find the number of elements in the region
           unsigned r = this->Region_attribute[i];
           unsigned n_region_element = new_mesh_pt->nregion_element(r);
           this->Region_element_pt[i].resize(n_region_element);
           for (unsigned e = 0; e < n_region_element; e++)
           {
             this->Region_element_pt[i][e] =
               new_mesh_pt->region_element_pt(r, e);
           }
         }
  
         // Now the boundary region information
         this->Boundary_region_element_pt.resize(nbound);
         this->Face_index_region_at_boundary.resize(nbound);
  
         // Now loop over the boundaries
         for (unsigned b = 0; b < nbound; ++b)
         {
           // Loop over the regions
           for (unsigned i = 0; i < n_region; ++i)
           {
             unsigned r = this->Region_attribute[i];
  
             unsigned n_boundary_el_in_region =
               new_mesh_pt->nboundary_element_in_region(b, r);
             if (n_boundary_el_in_region > 0)
             {
               // Allocate storage in the map
               this->Boundary_region_element_pt[b][r].resize(
                 n_boundary_el_in_region);
               this->Face_index_region_at_boundary[b][r].resize(
                 n_boundary_el_in_region);
  
               // Copy over the information
               for (unsigned e = 0; e < n_boundary_el_in_region; ++e)
               {
                 this->Boundary_region_element_pt[b][r][e] =
                   new_mesh_pt->boundary_element_in_region_pt(b, r, e);
                 this->Face_index_region_at_boundary[b][r][e] =
                   new_mesh_pt->face_index_at_boundary_in_region(b, r, e);
               }
             }
           }
         } // End of loop over boundaries
  
       } // End of case when more than one region
  
  
       // Flush the mesh
       new_mesh_pt->flush_element_and_node_storage();
  
       // Delete the mesh and the problem
       delete new_mesh_pt;
       delete project_problem_pt;
  
       //##################################################################
       oomph_info
         << "adapt: Time for moving nodes etc. to actual mesh          : "
         << TimingHelpers::timer() - t_start << " sec " << std::endl;
       //##################################################################
  
  
       // Solid mesh?
       if (solid_mesh_pt != 0)
       {
         // Warning
         std::stringstream error_message;
         error_message
           << "Lagrangian coordinates are currently not projected but are\n"
           << "are re-set during adaptation. This is not appropriate for\n"
           << "real solid mechanics problems!\n";
         OomphLibWarning(error_message.str(),
                         OOMPH_CURRENT_FUNCTION,
                         OOMPH_EXCEPTION_LOCATION);
  
         // Reset Lagrangian coordinates
         dynamic_cast<SolidMesh*>(this)->set_lagrangian_nodal_coordinates();
       }
  
       double max_area;
       double min_area;
       this->max_and_min_element_size(max_area, min_area);
       oomph_info << "Max/min element size in adapted mesh: " << max_area << " "
                  << min_area << std::endl;
     }
     else
     {
       oomph_info << "Not enough benefit in adaptation.\n";
       Nrefined = 0;
       Nunrefined = 0;
     }
   }

References b, oomph::TetMeshBase::boundary_element_in_region_pt(), oomph::Mesh::boundary_element_pt(), oomph::Mesh::boundary_node_pt(), e(), oomph::Mesh::element_pt(), oomph::Mesh::face_index_at_boundary(), oomph::TetMeshBase::face_index_at_boundary_in_region(), MergeRestartFiles::filename, oomph::Mesh::flush_element_and_node_storage(), i, j, k, oomph::Problem::mesh_pt(), SamplePointContainer::min_and_max_coordinates(), n, oomph::Mesh::nboundary(), oomph::Mesh::nboundary_element(), oomph::TetMeshBase::nboundary_element_in_region(), oomph::Mesh::nboundary_node(), oomph::Mesh::nelement(), oomph::Mesh::nnode(), oomph::Mesh::node_pt(), oomph::TetMeshBase::nregion(), oomph::TetMeshBase::nregion_element(), Mesh_Parameters::nx, Mesh_Parameters::ny, Mesh_Parameters::nz, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, oomph::oomph_info, Eigen::bfloat16_impl::pow(), oomph::ProjectionProblem< PROJECTABLE_ELEMENT >::project(), UniformPSDSelfTest::r, oomph::TetMeshBase::region_attribute(), oomph::TetMeshBase::region_element_pt(), s, oomph::MeshAsGeomObject::sample_point_container_pt(), oomph::Global_string_for_annotation::string(), oomph::TimingHelpers::timer(), oomph::StringConversion::to_string(), and plotDoE::x.

◆ initialise_adaptation_data()

template<class ELEMENT >

void oomph::RefineableGmshTetMesh< ELEMENT >::initialise_adaptation_data ( )

inlineprotected

Helper function to initialise data associated with adaptation.

     {
       // Set max and min targets for adaptation
       this->Max_element_size = this->Gmsh_parameters_pt->max_element_size();
       this->Min_element_size = this->Gmsh_parameters_pt->min_element_size();
       this->Max_permitted_edge_ratio =
         this->Gmsh_parameters_pt->max_permitted_edge_ratio();
     }

References oomph::GmshTetMesh< ELEMENT >::Gmsh_parameters_pt, oomph::RefineableTetMeshBase::Max_element_size, oomph::GmshParameters::max_element_size(), oomph::RefineableTetMeshBase::Max_permitted_edge_ratio, oomph::GmshParameters::max_permitted_edge_ratio(), oomph::RefineableTetMeshBase::Min_element_size, and oomph::GmshParameters::min_element_size().

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

◆ refine_uniformly()

template<class ELEMENT >

void oomph::RefineableGmshTetMesh< ELEMENT >::refine_uniformly ( DocInfo & doc_info )

inlinevirtual

Unrefine uniformly.

Implements oomph::RefineableMeshBase.

     {
       // hierher do it!
       std::string error_msg("Not written yet...");
       throw OomphLibError(
         error_msg, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
     }

References OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, and oomph::Global_string_for_annotation::string().

◆ unrefine_uniformly()

template<class ELEMENT >

unsigned oomph::RefineableGmshTetMesh< ELEMENT >::unrefine_uniformly ( )

inlinevirtual

Refine uniformly.

Implements oomph::RefineableMeshBase.

     {
       // hierher do it!
       std::string error_msg("Not written yet...");
       throw OomphLibError(
         error_msg, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
     }

References OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, and oomph::Global_string_for_annotation::string().

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

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

template<class ELEMENT> class oomph::RefineableGmshTetMesh< ELEMENT >

Constructor & Destructor Documentation

◆ RefineableGmshTetMesh() [1/2]

◆ RefineableGmshTetMesh() [2/2]

Member Function Documentation

◆ adapt()

◆ initialise_adaptation_data()

◆ refine_uniformly()

◆ unrefine_uniformly()

template<class ELEMENT>
class oomph::RefineableGmshTetMesh< ELEMENT >