Collapsible channel mesh with algebraic node update. More...

#include <my_alg_channel_mesh.h>

Inheritance diagram for oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >:

Public Member Functions
	MyAlgebraicCollapsibleChannelMesh (const unsigned &nup, const unsigned &ncollapsible, const unsigned &ndown, const unsigned &ny, const double &lup, const double &lcollapsible, const double &ldown, const double &ly, GeomObject wall_pt, TimeStepper time_stepper_pt=&Mesh::Default_TimeStepper)

	MyAlgebraicCollapsibleChannelMesh (const unsigned &nup, const unsigned &ncollapsible, const unsigned &ndown, const unsigned &ny, const double &lup, const double &lcollapsible, const double &ldown, const double &ly, GeomObject wall_pt, CollapsibleChannelDomain::BLSquashFctPt bl_squash_function_pt, TimeStepper time_stepper_pt=&Mesh::Default_TimeStepper)

virtual	~MyAlgebraicCollapsibleChannelMesh ()
	Destructor: empty. More...

CollapsibleChannelDomain::BLSquashFctPt &	bl_squash_fct_pt ()

void	algebraic_node_update (const unsigned &t, AlgebraicNode *&node_pt)

void	update_node_update (AlgebraicNode *&node_pt)

Public Member Functions inherited from oomph::AlgebraicMesh
	AlgebraicMesh ()

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

	~AlgebraicMesh ()
	Broken assignment operator. More...

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

void	node_update (const bool &update_all_solid_nodes=false)

unsigned	self_test ()
	Self test: check consistentency of multiple node updates. More...

void	add_geom_object_list_pt (GeomObject *geom_object_pt)

unsigned	ngeom_object_list_pt ()
	Return number of geometric objects associated with AlgebraicMesh. More...

GeomObject *	geom_object_list_pt (const unsigned &i)
	Access function to the ith GeomObject. 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	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...

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::CollapsibleChannelMesh< ELEMENT >
	CollapsibleChannelMesh (const unsigned &nup, const unsigned &ncollapsible, const unsigned &ndown, const unsigned &ny, const double &lup, const double &lcollapsible, const double &ldown, const double &ly, GeomObject wall_pt, TimeStepper time_stepper_pt=&Mesh::Default_TimeStepper)

	~CollapsibleChannelMesh ()
	destructor More...

GeomObject *&	wall_pt ()
	Access function to GeomObject representing wall. More...

CollapsibleChannelDomain *	domain_pt ()
	Access function to domain. More...

CollapsibleChannelDomain::BLSquashFctPt	bl_squash_fct_pt () const

virtual CollapsibleChannelDomain::AxialSpacingFctPt &	axial_spacing_fct_pt ()

virtual CollapsibleChannelDomain::AxialSpacingFctPt &	axial_spacing_fct_pt () const

Public Member Functions inherited from oomph::SimpleRectangularQuadMesh< ELEMENT >
	SimpleRectangularQuadMesh (const unsigned &Nx, const unsigned &Ny, const double &Lx, const double &Ly, 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...

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

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

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

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

void	setup_boundary_element_info ()

void	setup_boundary_element_info (std::ostream &outfile)

Protected Member Functions
void	setup_algebraic_node_update ()
	Function to setup the algebraic node update. 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
CollapsibleChannelDomain::BLSquashFctPt	Dummy_fct_pt
	Dummy function pointer. 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::CollapsibleChannelMesh< ELEMENT >
CollapsibleChannelDomain *	Domain_pt
	Pointer to domain. More...

unsigned	Nup
	Number of element columns in upstream part. More...

unsigned	Ncollapsible
	Number of element columns in collapsible part. More...

unsigned	Ndown
	Number of element columns in downstream part. More...

unsigned	Ny
	Number of element rows across channel. More...

GeomObject *	Wall_pt
	Pointer to geometric object that represents the moving wall. 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 oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >

Collapsible channel mesh with algebraic node update.

Constructor & Destructor Documentation

◆ MyAlgebraicCollapsibleChannelMesh() [1/2]

template<class ELEMENT >

oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >::MyAlgebraicCollapsibleChannelMesh	(	const unsigned &	nup,
		const unsigned &	ncollapsible,
		const unsigned &	ndown,
		const unsigned &	ny,
		const double &	lup,
		const double &	lcollapsible,
		const double &	ldown,
		const double &	ly,
		GeomObject *	wall_pt,
		TimeStepper *	time_stepper_pt = `&Mesh::Default_TimeStepper`
	)

inline

Constructor: Pass number of elements in upstream/collapsible/ downstream segment and across the channel; lengths of upstream/ collapsible/downstream segments and width of channel, pointer to GeomObject that defines the collapsible segment, and pointer to TimeStepper (defaults to the default timestepper, Steady).

                                                              :
   CollapsibleChannelMesh<ELEMENT>(nup, ncollapsible, ndown, ny,
                                   lup, lcollapsible, ldown, ly,
                                   wall_pt,
                                   time_stepper_pt)
   {
    // Setup algebraic node update operations
    setup_algebraic_node_update();
   }

References oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >::setup_algebraic_node_update().

◆ MyAlgebraicCollapsibleChannelMesh() [2/2]

template<class ELEMENT >

oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >::MyAlgebraicCollapsibleChannelMesh	(	const unsigned &	nup,
		const unsigned &	ncollapsible,
		const unsigned &	ndown,
		const unsigned &	ny,
		const double &	lup,
		const double &	lcollapsible,
		const double &	ldown,
		const double &	ly,
		GeomObject *	wall_pt,
		CollapsibleChannelDomain::BLSquashFctPt	bl_squash_function_pt,
		TimeStepper *	time_stepper_pt = `&Mesh::Default_TimeStepper`
	)

inline

Constructor: Pass number of elements in upstream/collapsible/ downstream segment and across the channel; lengths of upstream/ collapsible/downstream segments and width of channel, pointer to GeomObject that defines the collapsible segment, function pointer to "boundary layer squash function", and pointer to TimeStepper (defaults to the default timestepper, Steady).

                             :
   CollapsibleChannelMesh<ELEMENT>(nup, ncollapsible, ndown, ny,
                                   lup, lcollapsible, ldown, ly,
                                   wall_pt,
                                   time_stepper_pt)
   {
    // Set boundary layer squash function
    this->Domain_pt->bl_squash_fct_pt()=bl_squash_function_pt;
  
    // Do MacroElement-based node update
    CollapsibleChannelMesh<ELEMENT>::node_update();
  
    // Setup algebraic node update operations
    setup_algebraic_node_update();
   }

References oomph::CollapsibleChannelDomain::bl_squash_fct_pt(), oomph::CollapsibleChannelMesh< ELEMENT >::Domain_pt, oomph::Mesh::node_update(), and oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >::setup_algebraic_node_update().

◆ ~MyAlgebraicCollapsibleChannelMesh()

template<class ELEMENT >

virtual oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >::~MyAlgebraicCollapsibleChannelMesh ( )

inlinevirtual

Destructor: empty.

118 {}

Member Function Documentation

◆ algebraic_node_update()

template<class ELEMENT >

void oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >::algebraic_node_update	(	const unsigned &	t,
		AlgebraicNode *&	node_pt
	)

virtual

Update nodal position at time level t (t=0: present; t>0: previous)

Perform algebraic mesh update at time level t (t=0: present; t>0: previous)

Implements oomph::AlgebraicMesh.

 {
  
  // Extract reference values for update by copy construction
  Vector<double> ref_value(node_pt->vector_ref_value());
  
  // Extract geometric objects for update by copy construction
  Vector<GeomObject*> geom_object_pt(node_pt->vector_geom_object_pt());
  
  // First reference value: Original x-position 
  double x_bottom=ref_value[0];
  
  // Second reference value: Fractional position along 
  // straight line from the bottom (at the original x-position)
  // to the point on the wall
  double fract=ref_value[1];
  
  // Third reference value: Zeta coordinate on wall
  Vector<double> zeta(1);
  zeta[0]=ref_value[2];
      
  // Pointer to wall geom object
  GeomObject* wall_pt=geom_object_pt[0];
  
  // Get position vector to wall at previous timestep t
  Vector<double> r_wall(2);
  wall_pt->position(t,zeta,r_wall);
  
  // Assign new nodal coordinates
  node_pt->x(t,0)=x_bottom+fract*(r_wall[0]-x_bottom);
  node_pt->x(t,1)=         fract* r_wall[1];
  
 }

References oomph::GeomObject::position(), plotPSD::t, oomph::AlgebraicNode::vector_geom_object_pt(), oomph::AlgebraicNode::vector_ref_value(), oomph::Node::x(), and Eigen::zeta().

◆ bl_squash_fct_pt()

template<class ELEMENT >

CollapsibleChannelDomain::BLSquashFctPt& oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >::bl_squash_fct_pt ( )

inlinevirtual

Function pointer for function that squashes the mesh near the walls. Default trivial mapping (the identity) leaves vertical nodal positions unchanged. Mapping is used in underlying CollapsibleChannelDomain. This (deliberately broken) function overloads the one in the CollapsibleChannelMesh base class.

Reimplemented from oomph::CollapsibleChannelMesh< ELEMENT >.

   {
    std::ostringstream error_message;
    error_message 
     << "It does not make sense to set the bl_squash_fct_pt \n"
     << "outside the constructor as it's only used to set up the \n"
     << "algebraic remesh data when the algebraic mesh is first built. \n";
     std::string function_name =
     "MyAlgebraicCollapsibleChannelMesh::bl_squash_fct_pt()\n";
    
    throw OomphLibError(error_message.str(),
                        OOMPH_CURRENT_FUNCTION,
                        OOMPH_EXCEPTION_LOCATION);
  
    // Dummy return
    return Dummy_fct_pt;
   }

References oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >::Dummy_fct_pt, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, and oomph::Global_string_for_annotation::string().

◆ setup_algebraic_node_update()

template<class ELEMENT >

void oomph::MyAlgebraicCollapsibleChannelMesh< ELEMENT >::setup_algebraic_node_update

protected

Function to setup the algebraic node update.

Setup algebraic mesh update – assumes that mesh has initially been set up with the wall in its undeformed position.

 {
  
  // Extract some reference lengths from the CollapsibleChannelDomain. 
  double l_up=this->domain_pt()->l_up();
  double l_collapsible=this->domain_pt()->l_collapsible();
  
  // Loop over all nodes in mesh
  unsigned nnod=this->nnode();
  for (unsigned j=0;j<nnod;j++)
   {
    // Get pointer to node
    AlgebraicNode* nod_pt=node_pt(j);
  
    // Get coordinates
    double x=nod_pt->x(0);
    double y=nod_pt->x(1);
  
    // Check if the node is in the collapsible part:
    if ( (x>=l_up) && (x<=(l_up+l_collapsible)) )
     {
  
      // Get zeta coordinate on the undeformed wall
      Vector<double> zeta(1);
      zeta[0]=x-l_up;
  
      // Get position vector to wall:
      Vector<double> r_wall(2);
      this->Wall_pt->position(zeta,r_wall);
  
  
      // Sanity check: Confirm that the wall is in its undeformed position
 #ifdef PARANOID
      if ((std::abs(r_wall[0]-x)>1.0e-15)&&(std::abs(r_wall[1]-y)>1.0e-15))
       {
        std::ostringstream error_stream;
        error_stream 
         << "Wall must be in its undeformed position when\n"
         << "algebraic node update information is set up!\n "
         << "x-discrepancy: " << std::abs(r_wall[0]-x) << std::endl
         << "y-discrepancy: " << std::abs(r_wall[1]-y) << std::endl;
        
        throw OomphLibError(
         error_stream.str(),
         OOMPH_CURRENT_FUNCTION,
         OOMPH_EXCEPTION_LOCATION);
       }
 #endif       
  
      // Only a single geometric object is involved in the node update operation
      Vector<GeomObject*> geom_object_pt(1);
  
      // The wall geometric object
      geom_object_pt[0]=this->Wall_pt;
      
      // The update function requires three parameters:
      Vector<double> ref_value(3);
      
      // First reference value: Original x-position on the lower wall 
      ref_value[0]=r_wall[0];
      
      // Second reference value: Fractional position along 
      // straight line from the bottom (at the original x-position)
      // to the point on the wall
      ref_value[1]=y/r_wall[1];
      
      // Third reference value: Zeta coordinate on wall
      ref_value[2]=zeta[0];   
  
      // Setup algebraic update for node: Pass update information
      // to AlgebraicNode:
      nod_pt->add_node_update_info(
       this,               // mesh
       geom_object_pt,     // vector of geom objects
       ref_value);         // vector of ref. values
     }
    
   }
  
 } //end of setup_algebraic_node_update