coincides with the numeration of the spines More...

#include <tip_spine_mesh.h>

Inheritance diagram for MyTipMesh< ELEMENT, INTERFACE_ELEMENT >:

Public Member Functions
	MyTipMesh (const unsigned &nx, const unsigned &ny, const unsigned &nz, const double &x_min, const double &x_max, const double &y_min, const double &y_max, const double &z_min, const double &z_max, const double &R, const unsigned &rotation_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...

double	radius ()

void	change_radius (double R)

virtual void	spine_node_update (SpineNode *spine_node_pt)

double	init_spine_height (SpineNode *spine_node_pt)

void	flush_spine_element_and_node_storage ()

Public Member Functions inherited from oomph::SimpleCubicMesh< ELEMENT >
	SimpleCubicMesh (const unsigned &nx, const unsigned &ny, const unsigned &nz, const double &lx, const double &ly, const double &lz, TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper)

	SimpleCubicMesh (const unsigned &nx, const unsigned &ny, const unsigned &nz, const double &xmin, const double &xmax, const double &ymin, const double &ymax, const double &zmin, const double &zmax, TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper)

const unsigned &	nx () const
	Access function for number of elements in x directions. More...

const unsigned &	ny () const
	Access function for number of elements in y directions. More...

const unsigned &	nz () const
	Access function for number of elements in y directions. More...

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

	BrickMeshBase (const BrickMeshBase &)=delete
	Broken copy constructor. More...

virtual	~BrickMeshBase ()
	Broken assignment operator. More...

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	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...

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...

Protected Member Functions
virtual void	build_single_layer_mesh (TimeStepper *time_stepper_pt)

Protected Member Functions inherited from oomph::SimpleCubicMesh< ELEMENT >
void	build_mesh (TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper)
	Generic mesh construction function: contains all the hard work. 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
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...

double	Radius
	Sacled radius of the canyon (must be between 0 and one. More...

double	Xax

double	Yax

double	Zax

unsigned	Rotation_flag

Protected Attributes inherited from oomph::SimpleCubicMesh< ELEMENT >
unsigned	Nx
	Number of elements in x direction. More...

unsigned	Ny
	Number of elements in y direction. More...

unsigned	Nz
	Number of elements in y direction. More...

double	Xmin
	Minimum value of x coordinate. More...

double	Xmax
	Maximum value of x coordinate. More...

double	Ymin
	Minimum value of y coordinate. More...

double	Ymax
	Minimum value of y coordinate. More...

double	Zmin
	Minimum value of z coordinate. More...

double	Zmax
	Maximum value of z coordinate. 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::SpineMesh
Vector< Spine * >	Spine_pt
	A Spine mesh contains a Vector of pointers to spines. 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...

Detailed Description

template<class ELEMENT, class INTERFACE_ELEMENT>
class MyTipMesh< ELEMENT, INTERFACE_ELEMENT >

coincides with the numeration of the spines

Quater of a canieon mesh Mesh with outer part cubic and inner part cilindric The outer face is given by the plane z = zmin The cilinder axis is given by the line x = xmin, z = zmax

Constructor & Destructor Documentation

◆ MyTipMesh()

template<class ELEMENT , class INTERFACE_ELEMENT >

MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::MyTipMesh	(	const unsigned &	nx,
		const unsigned &	ny,
		const unsigned &	nz,
		const double &	x_min,
		const double &	x_max,
		const double &	y_min,
		const double &	y_max,
		const double &	z_min,
		const double &	z_max,
		const double &	R,
		const unsigned &	rotation_flag,
		TimeStepper *	time_stepper_pt = `&Mesh::Default_TimeStepper`
	)

Constructor: Pass number of elements in x-direction, number of elements in y-direction, axial length, height of layer, and pointer to timestepper (defaults to Steady timestepper)

Constructor for spine 3D mesh: Pass number of elements in x-direction, number of elements in y-direction, number elements in z-direction, axial length, deep and height of layer, and pointer to timestepper (defaults to Static timestepper).

The mesh contains a layer of spinified fluid elements (of type ELEMENT; e.g SpineElement<CrozierRaviartElement<2>) and a surface layer of corresponding Spine interface elements of type INTERFACE_ELEMENT, e.g. SpineLineNavierStokesInterfaceElement<ELEMENT> for 2D planar problems.

                                                                                                                                               :
   SimpleCubicMesh<ELEMENT >(nx,ny,nz,x_min,x_max,y_min,y_max,z_min,z_max,
                             time_stepper_pt)
 {
 // Point to which all spines point
   this->Xax = 0.0;
  
   this->Yax = 0.0; 
  
   this->Zax = 1.0;
  
   this->Rotation_flag = rotation_flag;
  
  
    change_radius(R);
  
  
  // Periodic?
 //  MySimpleCubicQuadMesh<ELEMENT >::Xperiodic = false;
  
  // Now build the mesh: 
  build_single_layer_mesh(time_stepper_pt);
 }

References MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::build_single_layer_mesh(), MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::change_radius(), R, MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::Rotation_flag, MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::Xax, MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::Yax, and MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::Zax.

Member Function Documentation

◆ build_single_layer_mesh()

template<class ELEMENT , class INTERFACE_ELEMENT >

void MyTipMesh< 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

 {
  
 // Set rotation
  if(Rotation_flag == 1)  //rotation around y--axis
    for(unsigned i = 0;i< this->nnode();i++)
     { 
       double x_node = this->node_pt(i)->x(0);
       double z_node = this->node_pt(i)->x(2);
       this->node_pt(i)->x(0) = -z_node +1.0;
       this->node_pt(i)->x(2) = x_node;
     }
  
  if(Rotation_flag == 2)  //rotation around y--axis
    for(unsigned i = 0;i< this->nnode();i++)
     { 
       double y_node = this->node_pt(i)->x(1);
       double z_node = this->node_pt(i)->x(2);
       this->node_pt(i)->x(1) = z_node - 1.0;
       this->node_pt(i)->x(2) = -y_node;
     }
  
 //Read out the number of elements in the x-direction
  unsigned n_x = this->Nx;
  unsigned n_y = this->Ny;
  unsigned n_z = this->Nz;
  
  
  
  //Set up the pointers to elements in the bulk
  unsigned nbulk=nelement();
  Bulk_element_pt.reserve(nbulk);
  for(unsigned e=0;e<nbulk;e++)
   {
    Bulk_element_pt.push_back(this->finite_element_pt(e));
   }
  
  //Allocate memory for the spines and fractions along spines
  //---------------------------------------------------------
  
  //Read out number of linear points in the element
  unsigned n_p = dynamic_cast<ELEMENT*>(finite_element_pt(0))->nnode_1d();
  
  //Allocate store for the spines: (different in the case of periodic meshes !!)
    Spine_pt.reserve(((n_p-1)*n_x+1)*((n_p-1)*n_y+1));
   
  
 // NOW WE GO THROUH ALL THE ELEMENTS OF THE LOWER LAYERS AND ATTACHING THE SPINES
  
 // FIRST ELEMENT: Element 0
  
   
  
 for(unsigned l1=0;l1<n_p;l1++) //y loop over the nodes
 {
  for(unsigned l2=0;l2<n_p;l2++)  //x loop over the nodes
   {
  
    //Node j + i*np
 // Vector to the origin node, it will be passed as argument for the a later update of the spine
    Vector<double> origin_node(3);
    origin_node[0] = element_node_pt(0,l2+l1*n_p)->x(0);
    origin_node[1] = element_node_pt(0,l2+l1*n_p)->x(1);
    origin_node[2] = element_node_pt(0,l2+l1*n_p)->x(2);
  
    double hinit  = init_spine_height( element_node_pt(0,l2+l1*n_p) );
    //Assign the new spine within the cilinder
 //   Spine* new_spine_pt=new Spine( hinit,origin_node );
   Spine* new_spine_pt=new Spine(hinit);          
   new_spine_pt->set_geom_parameter(origin_node);
   Spine_pt.push_back(new_spine_pt);
  
    // Get pointer to node
    SpineNode* nod_pt=element_node_pt(0,l2+l1*n_p); // Element 0; node j + i*n_p
    //Set the pointer to the spine
    nod_pt->spine_pt() = new_spine_pt;
    //Set the fraction
    nod_pt->fraction() = 0.0;
    // Pointer to the mesh that implements the update fct
    nod_pt->spine_mesh_pt() = this; 
  
   //Loop vertically along the spine
    //Loop over the elements 
    for(unsigned long k=0;k<n_z;k++)
    {
       //Add bottom spine to element (equal to the one defined before the for structure (for k=0) or the top of the last one)
       //dynamic_cast<ELEMENT*>(Element_pt[k*n_x*n_y])->add_spine(new_spine_pt);
  
      //Loop over the vertical nodes, apart from the first
      for(unsigned l3=1;l3<n_p;l3++)
       {
        // Get pointer to node
        SpineNode* nod_pt=element_node_pt(k*n_x*n_y,l3*n_p*n_p+l2+l1*n_p);
        //Set the pointer to the spine
        nod_pt->spine_pt() = new_spine_pt;
        //Set the fraction
        nod_pt->fraction()=(double(k)+double(l3)/double(n_p-1))/double(n_z);
        // Pointer to the mesh that implements the update fct
        nod_pt->spine_mesh_pt() = this; 
       }
     }
  
  
   }
 }
  
  
  
  //LOOP OVER OTHER ELEMENTS IN THE FIRST ROW
  //-----------------------------------------
  
 // The procedure is the same but we have to identify the before defined spines for not defining them two times
  
 for(unsigned j=1;j<n_x;j++) //loop over the elements in the first row
 {
  
   for(unsigned l1=0;l1<n_p;l1++) //y loop over the nodes
   {
     
  
    // First we copy the last row of nodes into the first row of the new element (and extend to the third dimension)
    /*for(unsigned k=0;k<n_z;k++)
     {
          //Recover the Spine of the before defined element
          Spine* old_spine = dynamic_cast<ELEMENT*>(Element_pt[k*n_x*n_y+j-1])->spine_pt(l1*n_p+n_p-1);
          //Add before defined  spine to element 
          dynamic_cast<ELEMENT*>(Element_pt[k*n_x*n_y+j])->add_spine(old_spine);
          }*/
  
  
    for(unsigned l2=1;l2<n_p;l2++)  //x loop over the nodes
     {
  
      //Node j + i*np
     Vector<double> origin_node(3);
     origin_node[0] = element_node_pt(j,l2+l1*n_p)->x(0);
     origin_node[1] = element_node_pt(j,l2+l1*n_p)->x(1);
     origin_node[2] = element_node_pt(j,l2+l1*n_p)->x(2);
  
     double hinit  = init_spine_height( element_node_pt(j,l2+l1*n_p) ); 
    //Assign the new spine
     Spine* new_spine_pt=new Spine( hinit);   
     new_spine_pt->set_geom_parameter(origin_node);
  
      Spine_pt.push_back(new_spine_pt);
  
  
      // Get pointer to node
      SpineNode* nod_pt=element_node_pt(j,l2+l1*n_p); // Element j; node l2 + l1*n_p
      //Set the pointer to the spine
      nod_pt->spine_pt() = new_spine_pt;
      //Set the fraction
      nod_pt->fraction() = 0.0;
      // Pointer to the mesh that implements the update fct
      nod_pt->spine_mesh_pt() = this; 
  
     //Loop vertically along the spine
      //Loop over the elements 
      for(unsigned long k=0;k<n_z;k++)
      {
         //Add bottom spine to element (equal to the one defined before the for structure (for k=0) or the top of the last one)
       //dynamic_cast<ELEMENT*>(Element_pt[j+k*n_x*n_y])->add_spine(new_spine_pt);
        //Loop over the vertical nodes, apart from the first
        for(unsigned l3=1;l3<n_p;l3++)
         {
          // Get pointer to node
          SpineNode* nod_pt=element_node_pt(j+k*n_x*n_y,l3*n_p*n_p+l2+l1*n_p);
          //Set the pointer to the spine
          nod_pt->spine_pt() = new_spine_pt;
          //Set the fraction
          nod_pt->fraction()=(double(k)+double(l3)/double(n_p-1))/double(n_z);
          // Pointer to the mesh that implements the update fct
          nod_pt->spine_mesh_pt() = this; 
         }
       }
  
  
     }
   }
 }
  
 //REST OF THE ELEMENTS
 // Now we loop over the rest of the elements. We will separe the first of each row being al the rest equal
  
  
  
 for(unsigned long i=1;i<n_y;i++)
 {
 //FIRST ELEMENT OF THE ROW
    
  //First line of nodes is copied from the element of the bottom
   
 /*  for(unsigned l2=0;l2<n_p;l2++)
   {
  
     for(unsigned long k=0;k<n_z;k++)
     {
          //Recover the Spine of the before defined element
          Spine* old_spine = dynamic_cast<ELEMENT*>(Element_pt[k*n_x*n_y+(i-1)*n_x])->spine_pt(n_p*(n_p-1)+l2);
          //Add before defined  spine to element 
          dynamic_cast<ELEMENT*>(Element_pt[i*n_x+k*n_x*n_y])->add_spine(old_spine);
     }
  
     }*/
  
  
  
   for(unsigned l1=1;l1<n_p;l1++) //y loop over the nodes
   {
    
    for(unsigned l2=0;l2<n_p;l2++)  //x loop over the nodes
     {
  
      //Node j + i*np
     Vector<double> origin_node(3); 
     origin_node[0] = element_node_pt(i*n_x,l2+l1*n_p)->x(0);
     origin_node[1] = element_node_pt(i*n_x,l2+l1*n_p)->x(1);
     origin_node[2] = element_node_pt(i*n_x,l2+l1*n_p)->x(2);
  
      double hinit  = init_spine_height( element_node_pt(i*n_x,l2+l1*n_p) );   
     //Assign the new spine 
     Spine* new_spine_pt= new Spine( hinit);
     new_spine_pt->set_geom_parameter(origin_node);
  
  
      Spine_pt.push_back(new_spine_pt);
  
  
      // Get pointer to node
      SpineNode* nod_pt=element_node_pt(i*n_x,l2+l1*n_p); // Element i*n_x; node l2 + l1*n_p
      //Set the pointer to the spine
      nod_pt->spine_pt() = new_spine_pt;
      //Set the fraction
      nod_pt->fraction() = 0.0;
      // Pointer to the mesh that implements the update fct
      nod_pt->spine_mesh_pt() = this; 
  
     //Loop vertically along the spine
      //Loop over the elements 
      for(unsigned long k=0;k<n_z;k++)
      {
         //Add bottom spine to element (equal to the one defined before the for structure (for k=0) or the top of the last one)
       // dynamic_cast<ELEMENT*>(Element_pt[i*n_x+k*n_x*n_y])->add_spine(new_spine_pt);
        //Loop over the vertical nodes, apart from the first
        for(unsigned l3=1;l3<n_p;l3++)
         {
          // Get pointer to node
          SpineNode* nod_pt=element_node_pt(i*n_x+k*n_x*n_y,l3*n_p*n_p+l2+l1*n_p);
          //Set the pointer to the spine
          nod_pt->spine_pt() = new_spine_pt;
          //Set the fraction
          nod_pt->fraction()=(double(k)+double(l3)/double(n_p-1))/double(n_z);
          // Pointer to the mesh that implements the update fct
          nod_pt->spine_mesh_pt() = this; 
         }
       }
  
  
     }
   }
  
  
  
  
  
   // REST OF THE ELEMENTS OF THE ROW
  for(unsigned j=1;j<n_x;j++)
   {
  
  
 //First line of nodes is copied from the element of the bottom
 /*    for(unsigned l2=0;l2<n_p;l2++)
     {
  
       for(unsigned long k=0;k<n_z;k++)
       {
            //Recover the Spine of the before defined element
            Spine* old_spine = dynamic_cast<ELEMENT*>(Element_pt[k*n_x*n_y+(i-1)*n_x+j])->spine_pt(n_p*(n_p-1)+l2);
            //Add before defined  spine to element 
            dynamic_cast<ELEMENT*>(Element_pt[i*n_x+k*n_x*n_y+j])->add_spine(old_spine);
       }
  
       }*/
  
  
  
     for(unsigned l1=1;l1<n_p;l1++) //y loop over the nodes
     {
  
       // First we copy the last row of nodes into the first row of the new element (and extend to the third dimension)
      /*    for(unsigned long k=0;k<n_z;k++)
       {
          //Recover the Spine of the before defined element
          Spine* old_spine = dynamic_cast<ELEMENT*>(Element_pt[k*n_x*n_y+(j-1)+i*n_x])->spine_pt(l1*n_p+n_p-1);
          //Add before defined  spine to element 
          dynamic_cast<ELEMENT*>(Element_pt[k*n_x*n_y+j+i*n_x])->add_spine(old_spine);
          }*/
    
      for(unsigned l2=1;l2<n_p;l2++)  //x loop over the nodes
       {
  
        //Node j + i*np
         Vector<double> origin_node(3);
         origin_node[0] = element_node_pt(j+i*n_x,l2+l1*n_p)->x(0);
         origin_node[1] = element_node_pt(j+i*n_x,l2+l1*n_p)->x(1);
         origin_node[2] = element_node_pt(j+i*n_x,l2+l1*n_p)->x(2);
          double hinit  = init_spine_height( element_node_pt(j+i*n_x,l2+l1*n_p) );   
         
      //Assign the new spine with radius as unit length
         Spine* new_spine_pt=new Spine( hinit);
         new_spine_pt->set_geom_parameter(origin_node);
  
  
        Spine_pt.push_back(new_spine_pt);
  
  
        // Get pointer to node
        SpineNode* nod_pt=element_node_pt(j+i*n_x,l2+l1*n_p); // Element j + i*n_x; node l2 + l1*n_p
        //Set the pointer to the spine
        nod_pt->spine_pt() = new_spine_pt;
        //Set the fraction
        nod_pt->fraction() = 0.0;
        // Pointer to the mesh that implements the update fct
        nod_pt->spine_mesh_pt() = this; 
  
       //Loop vertically along the spine
        //Loop over the elements 
        for(unsigned long k=0;k<n_z;k++)
        {
           //Add bottom spine to element (equal to the one defined before the for structure (for k=0) or the top of the last one)
         //dynamic_cast<ELEMENT*>(Element_pt[j+i*n_x+k*n_x*n_y])->add_spine(new_spine_pt);
          //Loop over the vertical nodes, apart from the first
          for(unsigned l3=1;l3<n_p;l3++)
           {
            // Get pointer to node
            SpineNode* nod_pt=element_node_pt(j+i*n_x+k*n_x*n_y,l3*n_p*n_p+l2+l1*n_p);
            //Set the pointer to the spine
            nod_pt->spine_pt() = new_spine_pt;
            //Set the fraction
            nod_pt->fraction()=(double(k)+double(l3)/double(n_p-1))/double(n_z);
            // Pointer to the mesh that implements the update fct
            nod_pt->spine_mesh_pt() = this; 
           }
         }
  
  
       }
     }
  
   }
  
  
 }
  
  
  
  
  
  
  //Assign the 2D Line elements
  //---------------------------
  
  //Get the present number of elements
  unsigned long element_count = Element_pt.size();
  
  //Loop over the elements on the plane
  for(unsigned l1=0;l1<n_y;l1++)
    for(unsigned l2=0;l2<n_x;l2++)
  {
   {
   //Construct a new 2D surface element on the face on which the local
   //coordinate 2 is fixed at its max. value (1)
    FiniteElement *interface_element_element_pt =
     new INTERFACE_ELEMENT(finite_element_pt(n_x*n_y*(n_z-1)+l2+l1*n_x),3);
  
  
    //Push it back onto the stack
    Element_pt.push_back(interface_element_element_pt); 
  
    //Push it back onto the stack of interface elements
    Interface_element_pt.push_back(interface_element_element_pt);
  
    //Now assign the spines to the elements
    /*for(unsigned i=0;i<n_p;i++)  // y coordinate loop
     { 
       for(unsigned j=0;j<n_p;j++)         // x coordinate loop
       {
        //Push the spines back onto the stack
        dynamic_cast<INTERFACE_ELEMENT*>
         (Element_pt[element_count])->
         add_spine(element_node_pt(n_x*n_y*(n_z-1)+l2+l1*n_x,n_p*n_p*(n_p-1)+j+i*n_p)->spine_pt());
       }
       }*/ 
    element_count++;
    }
   }
  
 // We update all nodes
 this->node_update();
  
 }

References e(), oomph::SpineNode::fraction(), i, j, k, GlobalParameters::Nx, GlobalParameters::Ny, Global_Parameters::Nz, oomph::Spine::set_geom_parameter(), oomph::SpineNode::spine_mesh_pt(), and oomph::SpineNode::spine_pt().

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

◆ bulk_element_pt()

template<class ELEMENT , class INTERFACE_ELEMENT >

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

inline

Access functions for pointers to elements in bulk.

83 {return Bulk_element_pt[i];}

References i.

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

◆ change_radius()

template<class ELEMENT , class INTERFACE_ELEMENT >

void MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::change_radius ( double R )

inline

   {
    double scaled_R = R/(this->Zmax - this->Zmin);
    if ( (scaled_R<0.95) && (scaled_R>0.05) )
     Radius = R;
    else
     {
      std::ostringstream error_stream;
      error_stream 
       <<
       "We can not constract so small elements so close to the origin\n"
       <<"Choose a different radius (actual scaled radius = "<<scaled_R<<"\n";
  
      throw OomphLibError(error_stream.str(),
                          OOMPH_CURRENT_FUNCTION,
                          OOMPH_EXCEPTION_LOCATION);
     }
   }

References OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, R, Global_Physical_Variables::Radius, Global_Parameters::Zmax, and Global_Parameters::Zmin.

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

◆ flush_spine_element_and_node_storage()

template<class ELEMENT , class INTERFACE_ELEMENT >

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

inline

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

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

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

◆ init_spine_height()

template<class ELEMENT , class INTERFACE_ELEMENT >

double MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::init_spine_height ( SpineNode * spine_node_pt )

inline

   {
  
    //set distance to the axis
    double daxis = sqrt( (this->Xax -  spine_node_pt->x(0) ) *(this->Xax - spine_node_pt->x(0) )+(this->Yax -  spine_node_pt->x(1) ) *  (this->Yax -  spine_node_pt->x(1))
   + (this->Zax -  spine_node_pt->x(2) ) *  (this->Zax -  spine_node_pt->x(2)) );
    double init_h = ( daxis - radius() ) ; 
    return init_h;
   
   }

References UniformPSDSelfTest::radius, sqrt(), and oomph::Node::x().

◆ interface_element_pt()

template<class ELEMENT , class INTERFACE_ELEMENT >

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

inline

Access functions for pointers to interface elements.

76 {return Interface_element_pt[i];}

References i.

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

◆ nbulk()

template<class ELEMENT , class INTERFACE_ELEMENT >

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

inline

Number of elements in bulk.

86 {return Bulk_element_pt.size();}

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

◆ ninterface_element()

template<class ELEMENT , class INTERFACE_ELEMENT >

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

inline

Number of elements on interface.

79 {return Interface_element_pt.size();}

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

◆ radius()

template<class ELEMENT , class INTERFACE_ELEMENT >

double MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::radius ( )

inline

89 {return Radius;}

References Global_Physical_Variables::Radius.

◆ spine_node_update()

template<class ELEMENT , class INTERFACE_ELEMENT >

virtual void MyTipMesh< 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

◆ Bulk_element_pt

template<class ELEMENT , class INTERFACE_ELEMENT >

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

protected

Vector of pointers to element in the fluid layer.

◆ Interface_element_pt

template<class ELEMENT , class INTERFACE_ELEMENT >

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

protected

Vector of pointers to interface elements.

◆ Radius

template<class ELEMENT , class INTERFACE_ELEMENT >

double MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::Radius

protected

Sacled radius of the canyon (must be between 0 and one.

◆ Rotation_flag

template<class ELEMENT , class INTERFACE_ELEMENT >

unsigned MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::Rotation_flag

protected

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

◆ Xax

template<class ELEMENT , class INTERFACE_ELEMENT >

double MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::Xax

protected

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

◆ Yax

template<class ELEMENT , class INTERFACE_ELEMENT >

double MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::Yax

protected

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

◆ Zax

template<class ELEMENT , class INTERFACE_ELEMENT >

double MyTipMesh< ELEMENT, INTERFACE_ELEMENT >::Zax

protected

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

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

tip_spine_mesh.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

template<class ELEMENT, class INTERFACE_ELEMENT> class MyTipMesh< ELEMENT, INTERFACE_ELEMENT >

Constructor & Destructor Documentation

◆ MyTipMesh()

Member Function Documentation

◆ build_single_layer_mesh()

◆ bulk_element_pt()

◆ change_radius()

◆ flush_spine_element_and_node_storage()

◆ init_spine_height()

◆ interface_element_pt()

◆ nbulk()

◆ ninterface_element()

◆ radius()

◆ spine_node_update()

Member Data Documentation

◆ Bulk_element_pt

◆ Interface_element_pt

◆ Radius

◆ Rotation_flag

◆ Xax

◆ Yax

◆ Zax

template<class ELEMENT, class INTERFACE_ELEMENT>
class MyTipMesh< ELEMENT, INTERFACE_ELEMENT >