PML mesh class. Policy class for 2D PML meshes. More...

#include <pml_meshes.h>

Inheritance diagram for oomph::PMLQuadMeshBase< ELEMENT >:

Public Member Functions
	PMLQuadMeshBase (const unsigned &n_pml_x, const unsigned &n_pml_y, const double &x_pml_start, const double &x_pml_end, const double &y_pml_start, const double &y_pml_end, TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper)
	Constructor: Create the underlying rectangular quad mesh. More...

void	pml_locate_zeta (const Vector< double > &x, FiniteElement *&coarse_mesh_el_pt)

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

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

	RectangularQuadMesh (const unsigned &nx, const unsigned &ny, const double &lx, const double &ly, const bool &periodic_in_x, TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper)

	RectangularQuadMesh (const unsigned &nx, const unsigned &ny, const double &xmin, const double &xmax, const double &ymin, const double &ymax, const bool &periodic_in_x, TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper)

const unsigned &	nx () const
	Return number of elements in x direction. More...

const unsigned &	ny () const
	Return number of elements in y direction. More...

const double	x_min () const
	Return the minimum value of x coordinate. More...

const double	x_max () const
	Return the maximum value of x coordinate. More...

const double	y_min () const
	Return the minimum value of y coordinate. More...

const double	y_max () const
	Return the maximum value of y coordinate. More...

virtual void	element_reorder ()

virtual double	x_spacing_function (unsigned xelement, unsigned xnode, unsigned yelement, unsigned ynode)

virtual double	y_spacing_function (unsigned xelement, unsigned xnode, unsigned yelement, unsigned ynode)

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)

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

	Mesh (const Vector< Mesh * > &sub_mesh_pt)

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

virtual void	reset_boundary_element_info (Vector< unsigned > &ntmp_boundary_elements, Vector< Vector< unsigned >> &ntmp_boundary_elements_in_region, Vector< FiniteElement * > &deleted_elements)
	Virtual function to perform the reset boundary elements info rutines. More...

template<class BULK_ELEMENT >
void	doc_boundary_coordinates (const unsigned &b, std::ofstream &the_file)

virtual void	scale_mesh (const double &factor)

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

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

virtual	~Mesh ()
	Virtual Destructor to clean up all memory. More...

void	flush_element_and_node_storage ()

void	flush_element_storage ()

void	flush_node_storage ()

Node *&	node_pt (const unsigned long &n)
	Return pointer to global node n. More...

Node *	node_pt (const unsigned long &n) const
	Return pointer to global node n (const version) More...

GeneralisedElement *&	element_pt (const unsigned long &e)
	Return pointer to element e. More...

GeneralisedElement *	element_pt (const unsigned long &e) const
	Return pointer to element e (const version) More...

const Vector< GeneralisedElement * > &	element_pt () const
	Return reference to the Vector of elements. More...

Vector< GeneralisedElement * > &	element_pt ()
	Return reference to the Vector of elements. More...

FiniteElement *	finite_element_pt (const unsigned &e) const

Node *&	boundary_node_pt (const unsigned &b, const unsigned &n)
	Return pointer to node n on boundary b. More...

Node *	boundary_node_pt (const unsigned &b, const unsigned &n) const
	Return pointer to node n on boundary b. More...

void	set_nboundary (const unsigned &nbound)
	Set the number of boundaries in the mesh. More...

void	remove_boundary_nodes ()
	Clear all pointers to boundary nodes. More...

void	remove_boundary_nodes (const unsigned &b)

void	remove_boundary_node (const unsigned &b, Node *const &node_pt)
	Remove a node from the boundary b. More...

void	add_boundary_node (const unsigned &b, Node *const &node_pt)
	Add a (pointer to) a node to the b-th boundary. More...

void	copy_boundary_node_data_from_nodes ()

bool	boundary_coordinate_exists (const unsigned &i) const
	Indicate whether the i-th boundary has an intrinsic coordinate. More...

unsigned long	nelement () const
	Return number of elements in the mesh. More...

unsigned long	nnode () const
	Return number of nodes in the mesh. More...

unsigned	ndof_types () const
	Return number of dof types in mesh. More...

unsigned	elemental_dimension () const
	Return number of elemental dimension in mesh. More...

unsigned	nodal_dimension () const
	Return number of nodal dimension in mesh. More...

void	add_node_pt (Node *const &node_pt)
	Add a (pointer to a) node to the mesh. More...

void	add_element_pt (GeneralisedElement *const &element_pt)
	Add a (pointer to) an element to the mesh. More...

virtual void	node_update (const bool &update_all_solid_nodes=false)

virtual void	reorder_nodes (const bool &use_old_ordering=true)

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

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

unsigned	self_test ()
	Self-test: Check elements and nodes. Return 0 for OK. More...

void	max_and_min_element_size (double &max_size, double &min_size)

double	total_size ()

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

void	check_inverted_elements (bool &mesh_has_inverted_elements)

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

Vector< Node * >	prune_dead_nodes ()

unsigned	nboundary () const
	Return number of boundaries. More...

unsigned long	nboundary_node (const unsigned &ibound) const
	Return number of nodes on a particular boundary. More...

FiniteElement *	boundary_element_pt (const unsigned &b, const unsigned &e) const
	Return pointer to e-th finite element on boundary b. More...

Node *	get_some_non_boundary_node () const

unsigned	nboundary_element (const unsigned &b) const
	Return number of finite elements that are adjacent to boundary b. More...

int	face_index_at_boundary (const unsigned &b, const unsigned &e) const

virtual void	dump (std::ofstream &dump_file, const bool &use_old_ordering=true) const
	Dump the data in the mesh into a file for restart. More...

void	dump (const std::string &dump_file_name, const bool &use_old_ordering=true) const
	Dump the data in the mesh into a file for restart. More...

virtual void	read (std::ifstream &restart_file)
	Read solution from restart file. More...

void	output_paraview (std::ofstream &file_out, const unsigned &nplot) const

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

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

void	output (std::ostream &outfile)
	Output for all elements. More...

void	output (std::ostream &outfile, const unsigned &n_plot)
	Output at f(n_plot) points in each element. More...

void	output (FILE *file_pt)
	Output for all elements (C-style output) More...

void	output (FILE *file_pt, const unsigned &nplot)
	Output at f(n_plot) points in each element (C-style output) More...

void	output (const std::string &output_filename)
	Output for all elements. More...

void	output (const std::string &output_filename, const unsigned &n_plot)
	Output at f(n_plot) points in each element. More...

void	output_fct (std::ostream &outfile, const unsigned &n_plot, FiniteElement::SteadyExactSolutionFctPt)
	Output a given Vector function at f(n_plot) points in each element. More...

void	output_fct (std::ostream &outfile, const unsigned &n_plot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt)

void	output_boundaries (std::ostream &outfile)
	Output the nodes on the boundaries (into separate tecplot zones) More...

void	output_boundaries (const std::string &output_filename)

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

void	shift_time_values ()

void	calculate_predictions ()

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

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

void	set_consistent_pinned_values_for_continuation (ContinuationStorageScheme *const &continuation_stepper_pt)
	Set consistent values for pinned data in continuation. More...

bool	does_pointer_correspond_to_mesh_data (double *const &parameter_pt)
	Does the double pointer correspond to any mesh data. More...

void	set_nodal_time_stepper (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data)
	Set the timestepper associated with the nodal data in the mesh. More...

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

virtual void	compute_norm (double &norm)

virtual void	compute_norm (Vector< double > &norm)

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

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

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

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

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

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

virtual void	compute_error (FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm)
	Returns the norm of the error and that of the exact solution. More...

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

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

OomphCommunicator *	communicator_pt () const

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

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

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

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

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

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

	RectangularQuadMesh (const unsigned &nx, const unsigned &ny, const double &xmin, const double &xmax, const double &ymin, const double &ymax, const bool &periodic_in_x, const bool &build, TimeStepper *time_stepper_pt=&Mesh::Default_TimeStepper)

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

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

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

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

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

void	convert_to_boundary_node (Node *&node_pt)

Protected Attributes inherited from oomph::RectangularQuadMesh< ELEMENT >
unsigned	Nx
	Nx: number of elements in x-direction. More...

unsigned	Ny
	Ny: number of elements in y-direction. More...

unsigned	Np
	Np: number of (linear) points in the element. 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
	Maximum value of y coordinate. More...

bool	Xperiodic

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

bool	Lookup_for_elements_next_boundary_is_setup

Vector< Vector< FiniteElement * > >	Boundary_element_pt

Vector< Vector< int > >	Face_index_at_boundary

Vector< Node * >	Node_pt
	Vector of pointers to nodes. More...

Vector< GeneralisedElement * >	Element_pt
	Vector of pointers to generalised elements. More...

std::vector< bool >	Boundary_coordinate_exists

Detailed Description

template<class ELEMENT>
class oomph::PMLQuadMeshBase< ELEMENT >

PML mesh class. Policy class for 2D PML meshes.

Constructor & Destructor Documentation

◆ PMLQuadMeshBase()

template<class ELEMENT >

oomph::PMLQuadMeshBase< ELEMENT >::PMLQuadMeshBase	(	const unsigned &	n_pml_x,
		const unsigned &	n_pml_y,
		const double &	x_pml_start,
		const double &	x_pml_end,
		const double &	y_pml_start,
		const double &	y_pml_end,
		TimeStepper *	time_stepper_pt = `&Mesh::Default_TimeStepper`
	)

inline

Constructor: Create the underlying rectangular quad mesh.

       : RectangularQuadMesh<ELEMENT>(n_pml_x,
                                      n_pml_y,
                                      x_pml_start,
                                      x_pml_end,
                                      y_pml_start,
                                      y_pml_end,
                                      time_stepper_pt)
     {
     }

Member Function Documentation

◆ pml_locate_zeta()

template<class ELEMENT >

void oomph::PMLQuadMeshBase< ELEMENT >::pml_locate_zeta	(	const Vector< double > &	x,
		FiniteElement *&	coarse_mesh_el_pt
	)

inlinevirtual

Overloaded function to allow the user to locate an element in mesh given the (Eulerian) position of a point. Note, the result may be nonunique if the given point lies on the boundary of two elements in the mesh. Additionally, we assume that the PML mesh is axis aligned when deciding if the given point lies inside the mesh

Implements oomph::PMLMeshBase.

     {
       //------------------------------------------
       // Make sure the point lies inside the mesh:
       //------------------------------------------
       // Get the lower x limit of the mesh
       const double x_min = this->x_min();
  
       // Get the upper x limit of the mesh
       const double x_max = this->x_max();
  
       // Get the lower y limit of the mesh
       const double y_min = this->y_min();
  
       // Get the upper y limit of the mesh
       const double y_max = this->y_max();
  
       // Due to roundoff error we will choose a small tolerance which will be
       // used to determine whether or not the point lies in the mesh
       double tol = 1.0e-12;
  
       // Assuming the mesh is axis-aligned we merely need to check if the
       // x-coordinate of the input lies in the range [x_min,x_max] and the
       // y-coordinate of the input lies in the range [y_min,y_max]
       if ((x[0] < x_min - tol) || (x[0] > x_max + tol) ||
           (x[1] < y_min - tol) || (x[1] > y_max + tol))
       {
         // Open an output string stream
         std::ostringstream error_message_stream;
  
         // Create an error message
         error_message_stream << "Point does not lie in the mesh." << std::endl;
  
         // Throw the error message
         throw OomphLibError(error_message_stream.str(),
                             OOMPH_CURRENT_FUNCTION,
                             OOMPH_EXCEPTION_LOCATION);
       }
  
       //-----------------------------------------
       // Collect some information about the mesh:
       //-----------------------------------------
       // Find out how many elements there are in the x-direction
       const unsigned nx = this->nx();
  
       // Find out how many elements there are in the y-direction
       const unsigned ny = this->ny();
  
       // Find out how many nodes there are in one direction in each element
       unsigned nnode_1d = this->finite_element_pt(0)->nnode_1d();
  
       // Find out how many nodes there are in each element
       unsigned nnode = this->finite_element_pt(0)->nnode();
  
       // Create a pointer to store the element pointer as a FiniteElement
       FiniteElement* el_pt = 0;
  
       // Vector to store the coordinate of each element corner node which
       // lies on the bottom boundary of the mesh and varies, i.e. if we're
       // on the bottom boundary of the PML mesh then the y-coordinate will
       // be fixed therefore we need only store the x-coordinates of the
       // corner nodes of each element attached to this boundary
       Vector<double> bottom_boundary_x_coordinates(nx + 1, 0.0);
  
       // Vector to store the coordinate of each element corner node which lies
       // on the right boundary of the mesh and varies
       Vector<double> right_boundary_y_coordinates(ny + 1, 0.0);
  
       // Recall, we already know the start and end coordinates of the mesh
       // in the x-direction so we can assign these entries straight away.
       // Note, these values are exactly the same as those had we instead
       // considered the upper boundary so it is only necessary to store
       // the information of the one of these boundaries. A similar argument
       // holds for the left and right boundaries.
  
       // The first entry of bottom_boundary_x_coordinates is:
       bottom_boundary_x_coordinates[0] = x_min;
  
       // The last entry is:
       bottom_boundary_x_coordinates[nx] = x_max;
  
       // The first entry of right_boundary_y_coordinates is:
       right_boundary_y_coordinates[0] = y_min;
  
       // The last entry is:
       right_boundary_y_coordinates[ny] = y_max;
  
       // To collect the remaining entries we need to loop over all of the
       // elements on the bottom boundary and collect the x-coordinate of
       // the bottom right node in the element. To avoid assigning the
       // last entry twice we ignore the last element.
  
       // Store the lower boundary ID
       unsigned lower_boundary_id = 0;
  
       // Store the right boundary ID
       unsigned right_boundary_id = 1;
  
       // Loop over the elements on the bottom boundary
       for (unsigned i = 0; i < nx; i++)
       {
         // Assign the element pointer
         el_pt = this->boundary_element_pt(lower_boundary_id, i);
  
         // Store the x-coordinate of the bottom right node in this element
         bottom_boundary_x_coordinates[i + 1] =
           el_pt->node_pt(nnode_1d - 1)->x(0);
       }
  
       // To collect the remaining entries we need to loop over all of the
       // elements on the right boundary and collect the y-coordinate of
       // the top right node in the element. To avoid assigning the
       // last entry twice we ignore the last element.
  
       // Loop over the elements on the bottom boundary
       for (unsigned i = 0; i < ny; i++)
       {
         // Assign the element pointer
         el_pt = this->boundary_element_pt(right_boundary_id, i);
  
         // Store the y-coordinate of the top right node in this element
         right_boundary_y_coordinates[i + 1] = el_pt->node_pt(nnode - 1)->x(1);
       }
  
       //---------------------------
       // Find the matching element:
       //---------------------------
       // Boolean variable to indicate that the ID of the element in the
       // x-direction has been found. Note, the value of this ID must lie
       // in the range [0,nx]
       bool element_x_id_has_been_found = false;
  
       // Boolean variable to indicate that the ID of the element in the
       // y-direction has been found. Note, the value of this ID must lie
       // in the range [0,ny]
       bool element_y_id_has_been_found = false;
  
       // Initialise the ID of the element in the x-direction
       unsigned element_x_id = 0;
  
       // Initialise the ID of the element in the y-direction
       unsigned element_y_id = 0;
  
       // Loop over all of the entries in bottom_boundary_x_coordinates
       for (unsigned i = 0; i < nx; i++)
       {
         // Check if the x-coordinate of the input lies in this interval
         if ((x[0] >= bottom_boundary_x_coordinates[i]) &&
             (x[0] <= bottom_boundary_x_coordinates[i + 1]))
         {
           // The point lies in the i-th interval so the element ID is i
           element_x_id = i;
  
           // Indicate that the element ID has been found
           element_x_id_has_been_found = true;
         }
       } // for (unsigned i=0;i<nx;i++)
  
       // If the element ID hasn't been found
       if (!element_x_id_has_been_found)
       {
         // Open an output string stream
         std::ostringstream error_message_stream;
  
         // Create an error message
         error_message_stream << "The ID of the element in the x-direction "
                              << "has not been found." << std::endl;
  
         // Throw the error message
         throw OomphLibError(error_message_stream.str(),
                             OOMPH_CURRENT_FUNCTION,
                             OOMPH_EXCEPTION_LOCATION);
       }
  
       // Loop over all of the entries in right_boundary_y_coordinates
       for (unsigned i = 0; i < ny; i++)
       {
         // Check if the y-coordinate of the input lies in this interval
         if ((x[1] >= right_boundary_y_coordinates[i]) &&
             (x[1] <= right_boundary_y_coordinates[i + 1]))
         {
           // The point lies in the i-th interval so the element ID is i
           element_y_id = i;
  
           // Indicate that the element ID has been found
           element_y_id_has_been_found = true;
         }
       } // for (unsigned i=0;i<ny;i++)
  
       // If the element ID hasn't been found
       if (!element_y_id_has_been_found)
       {
         // Open an output string stream
         std::ostringstream error_message_stream;
  
         // Create an error message
         error_message_stream << "The ID of the element in the y-direction "
                              << "has not been found." << std::endl;
  
         // Throw the error message
         throw OomphLibError(error_message_stream.str(),
                             OOMPH_CURRENT_FUNCTION,
                             OOMPH_EXCEPTION_LOCATION);
       }
  
       // Calculate the element number in the mesh
       unsigned el_id = element_y_id * nx + element_x_id;
  
       // Set the pointer to this element
       coarse_mesh_el_pt = dynamic_cast<FiniteElement*>(this->element_pt(el_id));
     } // End of pml_locate_zeta

References oomph::Mesh::boundary_element_pt(), oomph::Mesh::element_pt(), oomph::Mesh::finite_element_pt(), i, oomph::FiniteElement::nnode(), oomph::Mesh::nnode(), oomph::FiniteElement::nnode_1d(), oomph::FiniteElement::node_pt(), oomph::RectangularQuadMesh< ELEMENT >::nx(), oomph::RectangularQuadMesh< ELEMENT >::ny(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, plotDoE::x, oomph::Node::x(), oomph::RectangularQuadMesh< ELEMENT >::x_max(), oomph::RectangularQuadMesh< ELEMENT >::x_min(), oomph::RectangularQuadMesh< ELEMENT >::y_max(), and oomph::RectangularQuadMesh< ELEMENT >::y_min().

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

pml_meshes.h

Public Member Functions