#include <comb_tip_spine_mesh.h>

Inheritance diagram for CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >:

Public Member Functions
	CombTipSpineMesh (const unsigned int &nel, const double &alpha, const double &length, const double &height, const double &radius, const unsigned &flag, TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper)

FiniteElement *&	interface_element_pt (const unsigned long &i)
	Access functions for pointers to interface elements. More...

unsigned long	ninterface_element () const
	Number of elements on interface. More...

FiniteElement *&	bulk_element_pt (const unsigned long &i)
	Access functions for pointers to elements in bulk. More...

unsigned long	nbulk () const
	Number of elements in bulk. More...

void	flush_spine_element_and_node_storage ()

virtual void	spine_node_update (SpineNode *spine_node_pt)

Public Member Functions inherited from oomph::SpineMesh
virtual	~SpineMesh ()
	Destructor to clean up the memory allocated to the spines. More...

Spine *&	spine_pt (const unsigned long &i)
	Return the i-th spine in the mesh. More...

const Spine *	spine_pt (const unsigned long &i) const
	Return the i-th spine in the mesh (const version) More...

unsigned long	nspine () const
	Return the number of spines in the mesh. More...

void	add_spine_pt (Spine *const &spine_pt)
	Add a spine to the mesh. More...

SpineNode *	node_pt (const unsigned long &n)
	Return a pointer to the n-th global SpineNode. More...

SpineNode *	element_node_pt (const unsigned long &e, const unsigned &n)

unsigned long	assign_global_spine_eqn_numbers (Vector< double * > &Dof_pt)
	Assign spines to Spine_pt vector of element. More...

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

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

void	set_spine_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data)
	Assign time stepper to spines data. More...

void	set_consistent_pinned_spine_values_for_continuation (ContinuationStorageScheme *const &continuation_stepper_pt)

bool	does_pointer_correspond_to_spine_data (double *const &parameter_pt)

void	node_update (const bool &update_all_solid_nodes=false)

void	dump (std::ofstream &dump_file) const
	Overload the dump function so that the spine data is dumped. More...

void	read (std::ifstream &restart_file)
	Overload the read function so that the spine data is also read. 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	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...

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)

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...

Protected Member Functions
void	rotate_90_zeq1_xeq0 (SpineMesh *rot_mesh_pt)

void	rotate_90_zeq1_yeq0 (SpineMesh *rot_mesh_pt)

virtual void	build_single_layer_mesh (TimeStepper *time_stepper_pt)

void	add_side_spinemesh (unsigned int bound1, MyTipMesh< ELEMENT, INTERFACE_ELEMENT > addmesh_pt, int addmesh_map_boundary, int total_boundaries, unsigned flag)

void	change_boundaries (Mesh *pt_mesh, unsigned int oldbound, unsigned int newbound, unsigned int total_boundaries)

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
unsigned int	Nel

double	Alpha
	Aspect ratio, lengt, heighth and radius. More...

double	Length

double	Height

double	Radius

unsigned	Flag

double	Xax
	Axis of Symmetry. More...

double	Yax

double	Zax

Vector< FiniteElement * >	Bulk_element_pt
	Vector of pointers to element in the fluid layer. More...

Vector< FiniteElement * >	Interface_element_pt
	Vector of pointers to interface elements. More...

Protected Attributes inherited from oomph::SpineMesh
Vector< Spine * >	Spine_pt
	A Spine mesh contains a Vector of pointers to spines. 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

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...

Detailed Description

template<class ELEMENT, class INTERFACE_ELEMENT>
class CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >

Single-layer spine mesh class derived from standard cubic 3D mesh. The mesh contains a layer of spinified fluid elements (of type ELEMENT; e.g SpineElement<CrozierRaviartElement<2>) of type INTERFACE_ELEMENT, e.g. SpineSurfaceNavierStokesInterfaceElement<ELEMENT> for 3D planar problems.

This mesh has been carefully desihned so that the numeration of the nodes on the boundaries 0 and 5 (bottom and top) coincides with the numeration of the spines

Constructor & Destructor Documentation

◆ CombTipSpineMesh()

template<class ELEMENT , class INTERFACE_ELEMENT >

CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::CombTipSpineMesh	(	const unsigned int &	nel,
		const double &	alpha,
		const double &	length,
		const double &	height,
		const double &	radius,
		const unsigned &	flag,
		TimeStepper *	time_stepper_pt = `&Mesh::Default_TimeStepper`
	)

Constructor: Pass number of elements in x-direction, number of The composed mesh is too complicated for giving xmin,xmax etc.. Nevertheless we keep nx, ny, nz making reference

Constructor for spine 3D mesh:

The mesh contains a layer of spinified fluid elements (of type ELEMENT; e.g SpineElement<CrozierRaviartElement<2>)

                                                                                                                  : 
  Nel(nel), Alpha(alpha), Length(length), Height(height), Radius(radius), Flag(flag)
 {
  // We've called the "generic" constructor for the RectangularQuadMesh
  // which doesn't do much...
  // Now set up the parameters that characterise the mesh geometry
  // then call the constructor
  
  
  // Periodic?
 //  MySimpleCubicQuadMesh<ELEMENT >::Xperiodic = false;
  
  // Now build the mesh: 
  
  
  build_single_layer_mesh(time_stepper_pt);
  
 }

References CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::build_single_layer_mesh().

Member Function Documentation

◆ add_side_spinemesh()

template<class ELEMENT , class INTERFACE_ELEMENT >

void CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::add_side_spinemesh	(	unsigned int	bound1,
		MyTipMesh< ELEMENT, INTERFACE_ELEMENT > *	addmesh_pt,
		int *	addmesh_map_boundary,
		int	total_boundaries,
		unsigned	flag
	)

protected

 {   
  
  
  //Call the generic function
  MeshHelper::merge_spine_meshes(this,bound1,addmesh_pt,addmesh_map_boundary,
                                 total_boundaries,spine_flag);
    
 // add the bulk elements to the mesh
   for(unsigned i = 0; i< addmesh_pt->nbulk(); i++)
   {
     this->Bulk_element_pt.push_back(addmesh_pt->bulk_element_pt(i));
   }
  
    // add the interface elements to the mesh
 for(unsigned i = 0; i< addmesh_pt->ninterface_element(); i++)
   {
     this->Interface_element_pt.push_back(addmesh_pt->interface_element_pt(i));
   }
 }

References MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::bulk_element_pt(), i, MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::interface_element_pt(), oomph::MeshHelper::merge_spine_meshes(), MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::nbulk(), and MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::ninterface_element().

◆ build_single_layer_mesh()

template<class ELEMENT , class INTERFACE_ELEMENT >

void CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::build_single_layer_mesh ( TimeStepper * time_stepper_pt )

protectedvirtual

Helper function to actually build the single-layer spine mesh (called from various constructors)

Helper function that actually builds the single-layer spine mesh based on the parameters set in the various constructors

 {
  
  
 // Axis pf simmetry
  Xax = 0.0;
  Yax = 0.0;
  Zax = 1.0;
  
  unsigned n_x = Nel;
  unsigned n_y = Nel;
  unsigned n_z = Nel;
  
  // Build the first canion mesh: 
 MyTipMesh<ELEMENT,INTERFACE_ELEMENT >* mesh1_pt = new MyTipMesh<ELEMENT,INTERFACE_ELEMENT > (n_x,n_y,n_z,0.0,1.0,-1.0,0.0,0.0,1.0,Radius,0,time_stepper_pt);
  
  mesh1_pt->node_update();
  
  //mesh1_pt->output("tip1.dat");
 // We copy this mesh to our problem mesh 
  
  
 // add the nodes to the mesh
 //we reasign the spine_nodes to point to the ptoblem mesh
  for(unsigned i = 0; i< mesh1_pt->nnode(); i++)
   {
    //Set spine update flag equal to Flag for the nodes of this function
     mesh1_pt->node_pt(i)->node_update_fct_id() = Flag;
     mesh1_pt->node_pt(i)->spine_mesh_pt() = this;
     this->add_node_pt(mesh1_pt->node_pt(i));
   }
  
    // add the bulk elements to the mesh
  for(unsigned i = 0; i< mesh1_pt->nbulk(); i++)
   {
     Bulk_element_pt.push_back(mesh1_pt->bulk_element_pt(i));
   }
  
    // add the interface elements to the mesh
 for(unsigned i = 0; i< mesh1_pt->ninterface_element(); i++)
   {
     Interface_element_pt.push_back(mesh1_pt->interface_element_pt(i));
   }
  
 // add all the elements to the mesh
 for(unsigned i = 0; i< mesh1_pt->nelement(); i++)
   {
     Element_pt.push_back(mesh1_pt->element_pt(i));
   }
  
  
    // add the spines  to the mesh
 for(unsigned i = 0; i< mesh1_pt->nspine(); i++)
   {
     Spine_pt.push_back(mesh1_pt->spine_pt(i));
   }
  
 //add the boundaries
  set_nboundary( mesh1_pt->nboundary()); 
  
 for(unsigned b =0; b< mesh1_pt->nboundary(); b++)
   {
    for(unsigned i = 0; i<mesh1_pt->nboundary_node(b); i++)
     {
      // We remove the node from the old boundary mesh ( This is not necessary and it is mainly wrotten for avoiding the warning message) 
      Node* node_pt =  mesh1_pt->boundary_node_pt(b,i );
      node_pt->remove_from_boundary(b);
      this->add_boundary_node( b , node_pt);
     }
   }
  
  
  
 //We create a second mesh
  MyTipMesh<ELEMENT,INTERFACE_ELEMENT >* mesh2_pt = new MyTipMesh<ELEMENT,INTERFACE_ELEMENT > (n_x,n_y,n_z,0.0,1.0,-1.0,0.0,0.0,1.0,Radius,1,time_stepper_pt);
  
  //mesh2_pt->output("tip2.dat");
  
 //Resignation pointer for the boundary conditions of the second mesh
   int addmesh_map_boundary[6];  
  
   for(unsigned int i =0;i<6;i++)
    {
     addmesh_map_boundary[i] = i;
    }
  
    addmesh_map_boundary[2] = 6; 
    addmesh_map_boundary[0] = 2; 
    addmesh_map_boundary[4] = -1; 
  
   add_side_spinemesh(2, mesh2_pt ,addmesh_map_boundary, 7,Flag);
 //  cout<<"After adding 2 the mesh has "<<nbulk()<<" bulk elements"<<endl;
  
  
  
 //We create a third mesh
  MyTipMesh<ELEMENT,INTERFACE_ELEMENT >* mesh3_pt = new MyTipMesh<ELEMENT,INTERFACE_ELEMENT > (n_x,n_y,n_z,0.0,1.0,-1.0,0.0,0.0,1.0,Radius,2,time_stepper_pt);
  
  //mesh3_pt->output("tip3.dat");
  
  change_boundaries( mesh3_pt,2,3,6);
  
  //std::cout<<"After change the boundary 2 have "
  //        <<mesh3_pt->nboundary_node(2)<<" nodes"<<std::endl;
  
  
 //Resignation pointer for the boundary conditions of the third mesh
  
   for(unsigned int i =0;i<6;i++)
    {
     addmesh_map_boundary[i] = i;
    }
    addmesh_map_boundary[1] = 7;  
    addmesh_map_boundary[0] = 1;
    addmesh_map_boundary[3] = -1; 
  
   add_side_spinemesh(1, mesh3_pt ,addmesh_map_boundary, 8,Flag);
  
 // cout<<"After adding 3 the mesh has "<<nbulk()<<" bulk elements"<<endl;
  
  
 //We create a fourth  mesh
  MyTipMesh<ELEMENT,INTERFACE_ELEMENT >* mesh4_pt = new MyTipMesh<ELEMENT,INTERFACE_ELEMENT > (n_x,n_y,n_z,0.0,1.0,-1.0,0.0,0.0,1.0,Radius,0,time_stepper_pt);
  
  
 // We miror the mesh twice
   rotate_90_zeq1_xeq0(mesh4_pt);
  
   // mesh4_pt->output("tip4.dat");
 //Resignation pointer for the boundary conditions of the fifth mesh
  
   for(unsigned int i =0;i<6;i++)
    {
     addmesh_map_boundary[i] = i;
    }
  addmesh_map_boundary[0] = 2;
    addmesh_map_boundary[1] =7 ;
    addmesh_map_boundary[2] = 6; 
   addmesh_map_boundary[4] = -1; 
 //cout<<"Before adding 4 the mesh has "<<nnode()<<" nodes "<<endl;
  
  add_side_spinemesh(6, mesh4_pt ,addmesh_map_boundary, 8,Flag);
  
  
  
  
 //cout<<"After adding 4 the mesh has "<<nnode()<<" nodes "<<endl;
 //We create a fourth mesh
   MyTipMesh<ELEMENT,INTERFACE_ELEMENT >* mesh5_pt = new MyTipMesh<ELEMENT,INTERFACE_ELEMENT > (n_x,n_y,n_z,0.0,1.0,-1.0,0.0,0.0,1.0,Radius,0,time_stepper_pt);
  
 // We miror the mesh twice
    rotate_90_zeq1_yeq0(mesh5_pt);
  
    //mesh5_pt->output("tip5.dat");
  
   change_boundaries( mesh5_pt,2,3,6);
  
 //Resignation pointer for the boundary conditions of the fourth mesh
  
   for(unsigned int i =0;i<6;i++)
    {
     addmesh_map_boundary[i] = i;
    }
  addmesh_map_boundary[0] = 1;  
    addmesh_map_boundary[1] = 6; 
   addmesh_map_boundary[3] = -1; 
  
 // Add to the general mesh
  add_side_spinemesh(7, mesh5_pt ,addmesh_map_boundary, 8,Flag);
  
 // cout<<"After adding 5 in  the tip mesh the boundary 1 has"<<this->nboundary_node(1)<<"nodes"<<endl;
  
 // cout<<"After adding 5 the mesh has "<<nbulk()<<" bulk elements"<<endl;
  
  
  
  
 // We create the last mesh
  MyTipMesh<ELEMENT,INTERFACE_ELEMENT >* mesh6_pt = new MyTipMesh<ELEMENT,INTERFACE_ELEMENT > (n_x,n_y,n_z,0.0,1.0,-1.0,0.0,0.0,1.0,Radius,1,time_stepper_pt);
  
    rotate_90_zeq1_xeq0(mesh6_pt);
  
    // mesh6_pt->output("tip6.dat");
  
  change_boundaries( mesh6_pt,4,1,6);
  
   for(unsigned int i =0;i<6;i++)
    {
     addmesh_map_boundary[i] = i;
    }
    addmesh_map_boundary[0] = 6;  
    addmesh_map_boundary[1] = -1; 
    addmesh_map_boundary[2] = 4; 
  
 // Add to the general mesh
   add_side_spinemesh(6, mesh6_pt ,addmesh_map_boundary, 7,Flag);
  
   std::cout<<"The tip mesh consists of  "
            <<nbulk()<<" bulk elements and "<<ninterface_element()
            << " interface elements."<<std::endl;
  
 // At the end we destroy the block meshes in two steps
  
 // 1. We disconect the meshesh from the nodes and elements (if not we delete them at the time we delete the meshes)
   mesh1_pt->flush_spine_element_and_node_storage();
   mesh2_pt->flush_spine_element_and_node_storage();
   mesh3_pt->flush_spine_element_and_node_storage();
   mesh4_pt->flush_spine_element_and_node_storage();
   mesh5_pt->flush_spine_element_and_node_storage();
   mesh6_pt->flush_spine_element_and_node_storage();
  
 //2. Simply delete (this function can give a segmentation fault error when there are spines still attached to the old update functions written in the constructor)
   delete mesh1_pt;
   delete mesh2_pt;
   delete mesh3_pt;
   delete mesh4_pt;
   delete mesh5_pt;
   delete mesh6_pt; 
  
  
  
  
 // until now we have just worked with a square channel
 // introduce the aspect ratio and different lenght (there is a factor 2 becasue 1 = halve height= b/2)
   int ncount;
   ncount = this->nnode();
   for(int i = 0; i< ncount; i++)
    {
      Node* node_pt =  this->node_pt(i);
      node_pt->x(0) =  node_pt->x(0) * Alpha/2;
      node_pt->x(1) =  node_pt->x(1) * Length;
      node_pt->x(2) =   node_pt->x(2) * Height/2;
    }
 // Update also the origin of the spines
  unsigned long nspines = this->nspine();
  for(unsigned long i = 0; i<nspines;i++)
     {
       Spine* spine_pt = this->spine_pt(i);
       double x_spine = spine_pt->geom_parameter(0);
       double y_spine = spine_pt->geom_parameter(1);
       double z_spine = spine_pt->geom_parameter(2);
       spine_pt->geom_parameter(0) = x_spine *Alpha/2.0;
       spine_pt->geom_parameter(1) = y_spine * Length;
       spine_pt->geom_parameter(2) = z_spine * Height/2.0;
     }
  
  
 // Update the axis of simmetry
   Zax = Zax *  Height/2.0;
  
 // Update the spines heigth according to the new geometry
   ncount = this->nboundary_node(5);
   
   for(int i = 0; i< ncount; i++)
    {
      SpineNode* spine_node_pt =  dynamic_cast<SpineNode*>(this->boundary_node_pt(5,i));
      Spine* spine_pt = spine_node_pt->spine_pt();
       double x_spine = spine_pt->geom_parameter(0);
       double y_spine = spine_pt->geom_parameter(1);
       double z_spine = spine_pt->geom_parameter(2);
     
       double  dorg = sqrt( (spine_node_pt->x(0) -  x_spine )*(spine_node_pt->x(0) -  x_spine )+
                  (spine_node_pt->x(1) -  y_spine)*(spine_node_pt->x(1) -  y_spine)+ 
                (spine_node_pt->x(2) -  z_spine)*(spine_node_pt->x(2) -  z_spine) );
      spine_node_pt->h() = dorg;
      
    }
  
  
 }

References TanhSolnForAdvectionDiffusion::Alpha, b, oomph::Mesh::boundary_node_pt(), MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::bulk_element_pt(), oomph::Mesh::element_pt(), oomph::PressureAdvectionDiffusionValidation::Flag, MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::flush_spine_element_and_node_storage(), oomph::Spine::geom_parameter(), oomph::SpineNode::h(), GlobalParameters::Height, i, MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::interface_element_pt(), Global_Physical_Variables::Length, oomph::Mesh::nboundary(), oomph::Mesh::nboundary_node(), MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::nbulk(), oomph::Mesh::nelement(), MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::ninterface_element(), oomph::Mesh::nnode(), oomph::SpineMesh::node_pt(), oomph::SpineMesh::node_update(), oomph::SpineNode::node_update_fct_id(), oomph::SpineMesh::nspine(), Global_Physical_Variables::Radius, oomph::Node::remove_from_boundary(), oomph::SpineNode::spine_mesh_pt(), oomph::SpineNode::spine_pt(), oomph::SpineMesh::spine_pt(), sqrt(), and oomph::Node::x().

Referenced by CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::CombTipSpineMesh().

◆ bulk_element_pt()

template<class ELEMENT , class INTERFACE_ELEMENT >

FiniteElement* & CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::bulk_element_pt ( const unsigned long & i )

inline

Access functions for pointers to elements in bulk.

85 {return Bulk_element_pt[i];}

References i.

Referenced by STSpineMesh< ELEMENT, INTERFACE_ELEMENT >::add_side_spinemesh().

◆ change_boundaries()

template<class ELEMENT , class INTERFACE_ELEMENT >

void CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::change_boundaries	(	Mesh *	pt_mesh,
		unsigned int	oldbound,
		unsigned int	newbound,
		unsigned int	total_boundaries
	)

protected

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

 {  
  
  for(unsigned int i = 0; i<pt_mesh->nboundary_node(oldbound);i++)
   {
    if( !(pt_mesh->boundary_node_pt(oldbound,i)->is_on_boundary(newbound)) )     //Do not add the nodes which were before on the boundary
      pt_mesh->add_boundary_node(newbound, pt_mesh->boundary_node_pt(oldbound,i) );
   }
    pt_mesh->remove_boundary_nodes(oldbound);
    pt_mesh->set_nboundary(total_boundaries);
  
 }

References oomph::Mesh::add_boundary_node(), oomph::Mesh::boundary_node_pt(), i, oomph::Node::is_on_boundary(), oomph::Mesh::nboundary_node(), oomph::Mesh::remove_boundary_nodes(), and oomph::Mesh::set_nboundary().

◆ flush_spine_element_and_node_storage()

template<class ELEMENT , class INTERFACE_ELEMENT >

void CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::flush_spine_element_and_node_storage ( )

inline

   { 
     //Clear vectors of pointers to the nodes and elements
     Node_pt.clear();
     Bulk_element_pt.clear();
     Interface_element_pt.clear();
     Element_pt.clear();
     Spine_pt.clear();
   }

Referenced by STSpineMesh< ELEMENT, INTERFACE_ELEMENT >::build_single_layer_mesh().

◆ interface_element_pt()

template<class ELEMENT , class INTERFACE_ELEMENT >

FiniteElement* & CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::interface_element_pt ( const unsigned long & i )

inline

Access functions for pointers to interface elements.

77 {return Interface_element_pt[i];}

References i.

Referenced by STSpineMesh< ELEMENT, INTERFACE_ELEMENT >::add_side_spinemesh().

◆ nbulk()

template<class ELEMENT , class INTERFACE_ELEMENT >

unsigned long CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::nbulk ( ) const

inline

Number of elements in bulk.

89 {return Bulk_element_pt.size();}

Referenced by STSpineMesh< ELEMENT, INTERFACE_ELEMENT >::add_side_spinemesh().

◆ ninterface_element()

template<class ELEMENT , class INTERFACE_ELEMENT >

unsigned long CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::ninterface_element ( ) const

inline

Number of elements on interface.

81 {return Interface_element_pt.size();}

Referenced by STSpineMesh< ELEMENT, INTERFACE_ELEMENT >::add_side_spinemesh().

◆ rotate_90_zeq1_xeq0()

template<class ELEMENT , class INTERFACE_ELEMENT >

void CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::rotate_90_zeq1_xeq0 ( SpineMesh * rot_mesh_pt )

inlineprotected

   {
    unsigned long nnode = rot_mesh_pt->nnode();
    for(unsigned long i = 0; i<nnode;i++)
     {
       Node* node_pt = rot_mesh_pt->node_pt(i);
       double x_node = node_pt->x(0);
       double z_node = node_pt->x(2);
       node_pt->x(0) = 1.0 - z_node;
       node_pt->x(2) = 1.0 + x_node;
     }
    
  
 // We rotate as well the geometric parameters which were originally set as the coordinate of the node at the origin of the spine
  unsigned long nspines = rot_mesh_pt->nspine();
   for(unsigned long i = 0; i<nspines;i++)
     {
       Spine* spine_pt = rot_mesh_pt->spine_pt(i);
       double x_spine = spine_pt->geom_parameter(0);
       double z_spine = spine_pt->geom_parameter(2);
       spine_pt->geom_parameter(0) = 1.0 - z_spine;
       spine_pt->geom_parameter(2) = 1.0 + x_spine;
     }
  
    //we update again the nodes
     rot_mesh_pt->node_update();
   } 

References oomph::Spine::geom_parameter(), i, oomph::Mesh::nnode(), oomph::SpineMesh::node_pt(), oomph::SpineMesh::node_update(), oomph::SpineMesh::nspine(), oomph::SpineMesh::spine_pt(), and oomph::Node::x().

◆ rotate_90_zeq1_yeq0()

template<class ELEMENT , class INTERFACE_ELEMENT >

void CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::rotate_90_zeq1_yeq0 ( SpineMesh * rot_mesh_pt )

inlineprotected

   {
    unsigned long nnode = rot_mesh_pt->nnode();
    for(unsigned long i = 0; i<nnode;i++)
     {
       Node* node_pt = rot_mesh_pt->node_pt(i);
       double y_node = node_pt->x(1);
       double z_node = node_pt->x(2);
       node_pt->x(1) =  -1.0 + z_node;
       node_pt->x(2) = 1.0 - y_node;
     }
  
   // We rotate as well the geometric parameters which were originally set as the coordinate of the node at the origin of the spine
  
  unsigned long nspines = rot_mesh_pt->nspine();
  for(unsigned long i = 0; i<nspines;i++)
     {
       Spine* spine_pt = rot_mesh_pt->spine_pt(i);
       double y_spine = spine_pt->geom_parameter(1);
       double z_spine = spine_pt->geom_parameter(2);
       spine_pt->geom_parameter(1) = -1.0 + z_spine;
       spine_pt->geom_parameter(2) = 1.0 - y_spine;
     }
  
    //we update again the nodes
     rot_mesh_pt->node_update();
   } 

References oomph::Spine::geom_parameter(), i, oomph::Mesh::nnode(), oomph::SpineMesh::node_pt(), oomph::SpineMesh::node_update(), oomph::SpineMesh::nspine(), oomph::SpineMesh::spine_pt(), and oomph::Node::x().

◆ spine_node_update()

template<class ELEMENT , class INTERFACE_ELEMENT >

virtual void CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::spine_node_update ( SpineNode * spine_node_pt )

inlinevirtual

General node update function implements pure virtual function defined in SpineMesh base class and performs specific node update actions: along vertical spines

Implements oomph::SpineMesh.

   {
  //Get fraction along the spine
    double W = spine_node_pt->fraction();
    //Get spine height
    double H = spine_node_pt->h();
    //Get the position of the node at the origin
    // SpineNode* origin_pt = dynamic_cast<SpineNode*>(spine_node_pt->spine_pt()->geom_data_pt(0));
    Vector<double> origin_pt(3);
    origin_pt[0] = spine_node_pt->spine_pt()->geom_parameter(0); 
    origin_pt[1] = spine_node_pt->spine_pt()->geom_parameter(1); 
    origin_pt[2] = spine_node_pt->spine_pt()->geom_parameter(2); 
  
    //set scale norm vector
    double norm = sqrt( (Xax -  origin_pt[0] ) *  (Xax -  origin_pt[0] )+ (Yax -  origin_pt[1] ) *  (Yax -  origin_pt[1] ) + 
                        (Zax -  origin_pt[2] ) *  (Zax -  origin_pt[2])  );
  
    //Set the x coordinate
    spine_node_pt->x(0) = origin_pt[0] + H*W* (Xax -  origin_pt[0] )/norm;
    
    //Set the y coordinate
    spine_node_pt->x(1) = origin_pt[1] + H*W* (Yax -  origin_pt[1] )/norm;
    
    //Set the value of z
    spine_node_pt->x(2) = origin_pt[2] + H*W* (Zax -  origin_pt[2] )/norm;
  
    
   }

References oomph::SpineNode::fraction(), oomph::Spine::geom_parameter(), H, oomph::SpineNode::h(), oomph::SpineNode::spine_pt(), sqrt(), oomph::QuadTreeNames::W, and oomph::Node::x().

Member Data Documentation

◆ Alpha

template<class ELEMENT , class INTERFACE_ELEMENT >

double CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Alpha

protected

Aspect ratio, lengt, heighth and radius.

◆ Bulk_element_pt

template<class ELEMENT , class INTERFACE_ELEMENT >

Vector<FiniteElement *> CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Bulk_element_pt

protected

Vector of pointers to element in the fluid layer.

◆ Flag

template<class ELEMENT , class INTERFACE_ELEMENT >

unsigned CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Flag

protected

◆ Height

template<class ELEMENT , class INTERFACE_ELEMENT >

double CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Height

protected

◆ Interface_element_pt

template<class ELEMENT , class INTERFACE_ELEMENT >

Vector<FiniteElement *> CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Interface_element_pt

protected

Vector of pointers to interface elements.

◆ Length

template<class ELEMENT , class INTERFACE_ELEMENT >

double CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Length

protected

◆ Nel

template<class ELEMENT , class INTERFACE_ELEMENT >

unsigned int CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Nel

protected

◆ Radius

template<class ELEMENT , class INTERFACE_ELEMENT >

double CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Radius

protected

◆ Xax

template<class ELEMENT , class INTERFACE_ELEMENT >

double CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Xax

protected

Axis of Symmetry.

◆ Yax

template<class ELEMENT , class INTERFACE_ELEMENT >

double CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Yax

protected

◆ Zax

template<class ELEMENT , class INTERFACE_ELEMENT >

double CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >::Zax

protected

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

comb_tip_spine_mesh.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

template<class ELEMENT, class INTERFACE_ELEMENT> class CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >

Constructor & Destructor Documentation

◆ CombTipSpineMesh()

Member Function Documentation

◆ add_side_spinemesh()

◆ build_single_layer_mesh()

◆ bulk_element_pt()

◆ change_boundaries()

◆ flush_spine_element_and_node_storage()

◆ interface_element_pt()

◆ nbulk()

◆ ninterface_element()

◆ rotate_90_zeq1_xeq0()

◆ rotate_90_zeq1_yeq0()

◆ spine_node_update()

Member Data Documentation

◆ Alpha

◆ Bulk_element_pt

◆ Flag

◆ Height

◆ Interface_element_pt

◆ Length

◆ Nel

◆ Radius

◆ Xax

◆ Yax

◆ Zax

template<class ELEMENT, class INTERFACE_ELEMENT>
class CombTipSpineMesh< ELEMENT, INTERFACE_ELEMENT >