oomph::QuadMeshBase Class Reference

Base class for quad meshes (meshes made of 2D quad elements). More...

#include <quad_mesh.h>

Inheritance diagram for oomph::QuadMeshBase:

Public Member Functions
	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::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::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

Base class for quad meshes (meshes made of 2D quad elements).

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

Constructor & Destructor Documentation

QuadMeshBase() [1/2]

oomph::QuadMeshBase::QuadMeshBase ( )

inline

Constructor (empty)

{}

QuadMeshBase() [2/2]

oomph::QuadMeshBase::QuadMeshBase ( const QuadMeshBase &  node )

delete

Broken copy constructor.

~QuadMeshBase()

virtual oomph::QuadMeshBase::~QuadMeshBase ( )

inlinevirtual

Destructor (empty)

{}

Member Function Documentation

operator=()

void oomph::QuadMeshBase::operator= ( const QuadMeshBase &  )

delete

Broken assignment operator.

setup_boundary_element_info() [1/2]

void oomph::QuadMeshBase::setup_boundary_element_info ( )

inlinevirtual

Setup lookup schemes which establish whic elements are located next to mesh's boundaries (wrapper to suppress doc).

Reimplemented from oomph::Mesh.

    {
      std::ofstream outfile;
      setup_boundary_element_info(outfile);
    }

Referenced by oomph::ChannelWithLeafletMesh< ELEMENT >::ChannelWithLeafletMesh(), oomph::CollapsibleChannelMesh< ELEMENT >::CollapsibleChannelMesh(), oomph::FSIDrivenCavityMesh< ELEMENT >::FSIDrivenCavityMesh(), oomph::FullCircleMesh< ELEMENT >::FullCircleMesh(), and oomph::QuarterCircleSectorMesh< ELEMENT >::QuarterCircleSectorMesh().

setup_boundary_element_info() [2/2]

void oomph::QuadMeshBase::setup_boundary_element_info ( std::ostream &  outfile )

virtual

Setup lookup schemes which establish whic elements are located next to mesh's boundaries. Doc in outfile (if it's open).

Setup lookup schemes which establish which elements are located next to which boundaries (Doc to outfile if it's open).

Reimplemented from oomph::Mesh.

  {
    bool doc = false;
    if (outfile) doc = true;
 
    // Number of boundaries
    unsigned nbound = nboundary();
 
    // Wipe/allocate storage for arrays
    Boundary_element_pt.clear();
    Face_index_at_boundary.clear();
    Boundary_element_pt.resize(nbound);
    Face_index_at_boundary.resize(nbound);
 
    // Temporary vector of vectors to pointers to elements on the boundaries:
    // This is not a set to ensure UNIQUE ordering
    Vector<Vector<FiniteElement*>> vector_of_boundary_element_pt;
    vector_of_boundary_element_pt.resize(nbound);
 
    // Matrix map for working out the fixed local coord for elements on boundary
    MapMatrixMixed<unsigned, FiniteElement*, Vector<int>*> boundary_identifier;
 
 
    // Loop over elements
    //-------------------
    unsigned nel = nelement();
    for (unsigned e = 0; e < nel; e++)
    {
      // Get pointer to element
      FiniteElement* fe_pt = finite_element_pt(e);
 
      if (doc) outfile << "Element: " << e << " " << fe_pt << std::endl;
 
      // Only include 2D elements! Some meshes contain interface elements too.
      if (fe_pt->dim() == 2)
      {
        // Loop over the element's nodes and find out which boundaries they're
        // on
        // ----------------------------------------------------------------------
        unsigned nnode_1d = fe_pt->nnode_1d();
 
        // Loop over nodes in order
        for (unsigned i0 = 0; i0 < nnode_1d; i0++)
        {
          for (unsigned i1 = 0; i1 < nnode_1d; i1++)
          {
            // Local node number
            unsigned j = i0 + i1 * nnode_1d;
 
            // Get pointer to vector of boundaries that this
            // node lives on
            std::set<unsigned>* boundaries_pt = 0;
            fe_pt->node_pt(j)->get_boundaries_pt(boundaries_pt);
 
            // If the node lives on some boundaries....
            if (boundaries_pt != 0)
            {
              // Loop over boundaries
              // unsigned nbound=(*boundaries_pt).size();
              for (std::set<unsigned>::iterator it = boundaries_pt->begin();
                   it != boundaries_pt->end();
                   ++it)
              {
                // Add pointer to finite element to vector for the appropriate
                // boundary
 
                // Does the pointer already exits in the vector
                Vector<FiniteElement*>::iterator b_el_it =
                  std::find(vector_of_boundary_element_pt[*it].begin(),
                            vector_of_boundary_element_pt[*it].end(),
                            fe_pt);
                // Only insert if we have not found it (i.e. got to the end)
                if (b_el_it == vector_of_boundary_element_pt[*it].end())
                {
                  vector_of_boundary_element_pt[*it].push_back(fe_pt);
                }
 
                // For the current element/boundary combination, create
                // a vector that stores an indicator which element boundaries
                // the node is located (boundary_identifier=-/+1 for nodes
                // on the left/right boundary; boundary_identifier=-/+2 for
                // nodes on the lower/upper boundary. We determine these indices
                // for all corner nodes of the element and add them to a vector
                // to a vector. This allows us to decide which face of the
                // element coincides with the boundary since the (quad!) element
                // must have exactly two corner nodes on the boundary.
                if (boundary_identifier(*it, fe_pt) == 0)
                {
                  boundary_identifier(*it, fe_pt) = new Vector<int>;
                }
 
                // Are we at a corner node?
                if (((i0 == 0) || (i0 == nnode_1d - 1)) &&
                    ((i1 == 0) || (i1 == nnode_1d - 1)))
                {
                  // Create index to represent position relative to s_0
                  (*boundary_identifier(*it, fe_pt))
                    .push_back(1 * (2 * i0 / (nnode_1d - 1) - 1));
 
                  // Create index to represent position relative to s_1
                  (*boundary_identifier(*it, fe_pt))
                    .push_back(2 * (2 * i1 / (nnode_1d - 1) - 1));
                }
              }
            }
            // else
            // {
            //  oomph_info << "...does not live on any boundaries " <<
            //  std::endl;
            // }
          }
        }
      }
      // else
      //{
      // oomph_info << "Element " << e << " does not qualify" << std::endl;
      //}
    }
 
    // Now copy everything across into permanent arrays
    //-------------------------------------------------
 
    // Note: vector_of_boundary_element_pt contains all elements
    // that have (at least) one corner node on a boundary -- can't copy
    // them across into Boundary_element_pt
    // yet because some of them might have only one node on the
    // the boundary in which case they don't qualify as
    // boundary elements!
 
    // Loop over boundaries
    //---------------------
    for (unsigned i = 0; i < nbound; i++)
    {
      // Number of elements on this boundary
      // nel is unused, so I've commented it out - RWhite.
      //   unsigned nel=vector_of_boundary_element_pt[i].size();
 
      // Allocate storage for the face identifiers
      // Face_index_at_boundary[i].resize(nel);
 
      // Loop over elements that have at least one corner node on this boundary
      //-----------------------------------------------------------------------
      // unsigned e_count=0;
      typedef Vector<FiniteElement*>::iterator IT;
      for (IT it = vector_of_boundary_element_pt[i].begin();
           it != vector_of_boundary_element_pt[i].end();
           it++)
      {
        // Recover pointer to element
        FiniteElement* fe_pt = *it;
 
        // Initialise count for boundary identiers (-2,-1,1,2)
        std::map<int, unsigned> count;
 
        // Loop over coordinates
        for (unsigned ii = 0; ii < 2; ii++)
        {
          // Loop over upper/lower end of coordinates
          for (int sign = -1; sign < 3; sign += 2)
          {
            count[(ii + 1) * sign] = 0;
          }
        }
 
        // Loop over boundary indicators for this element/boundary
        unsigned n_indicators = (*boundary_identifier(i, fe_pt)).size();
        for (unsigned j = 0; j < n_indicators; j++)
        {
          count[(*boundary_identifier(i, fe_pt))[j]]++;
        }
        delete boundary_identifier(i, fe_pt);
 
        // Determine the correct boundary indicator by checking that it
        // occurs twice (since two corner nodes of the element's boundary
        // need to be located on the domain boundary
        int indicator = -10;
 
        // Check that we're finding exactly one boundary indicator
        // bool found=false;
 
        // Loop over coordinates
        for (unsigned ii = 0; ii < 2; ii++)
        {
          // Loop over upper/lower end of coordinates
          for (int sign = -1; sign < 3; sign += 2)
          {
            // If an index occurs twice then that face is on the boundary
            // But we can have multiple faces on the same boundary id, so just
            // add all the ones that we have
            if (count[(ii + 1) * sign] == 2)
            {
              // Check that we haven't found multiple boundaries
              /*if (found)
               {
                std::string error_message=
                 "Trouble: Multiple boundary identifiers!\n";
                error_message +=
                 "Elements should only have at most 2 corner ";
                error_message +=
                 "nodes on any one boundary.\n";
 
                throw OomphLibError(
                 error_message,
                 OOMPH_CURRENT_FUNCTION,
                 OOMPH_EXCEPTION_LOCATION);
               }
               found=true;*/
              indicator = (ii + 1) * sign;
 
              // Copy into the data structure
              Boundary_element_pt[i].push_back(*it);
              Face_index_at_boundary[i].push_back(indicator);
            }
          }
        }
 
        // Element has exactly two corner nodes on boundary
        /*if (found)
         {
          // Add to permanent storage
          Boundary_element_pt[i].push_back(fe_pt);
 
          // Now convert boundary indicator into information required
          // for FaceElements
          switch (indicator)
           {
            //South face
           case -2:
 
            // s_1 is fixed at -1.0:
            Face_index_at_boundary[i][e_count] = -2;
            break;
 
            //West face
           case -1:
 
            // s_0 is fixed at -1.0:
            Face_index_at_boundary[i][e_count] = -1;
            break;
 
            //East face
           case 1:
 
            // s_0 is fixed at 1.0:
            Face_index_at_boundary[i][e_count] = 1;
            break;
 
            //North face
           case 2:
 
            // s_1 is fixed at 1.0:
            Face_index_at_boundary[i][e_count] = 2;
            break;
 
           default:
 
            throw OomphLibError("Never get here",
                                OOMPH_CURRENT_FUNCTION,
                                OOMPH_EXCEPTION_LOCATION);
                                }
 
          // Increment counter
          e_count++;
          }*/
      }
    }
 
 
    // Doc?
    //-----
    if (doc)
    {
      // Loop over boundaries
      for (unsigned i = 0; i < nbound; i++)
      {
        unsigned nel = Boundary_element_pt[i].size();
        outfile << "Boundary: " << i << " is adjacent to " << nel << " elements"
                << std::endl;
 
        // Loop over elements on given boundary
        for (unsigned e = 0; e < nel; e++)
        {
          FiniteElement* fe_pt = Boundary_element_pt[i][e];
          outfile << "Boundary element:" << fe_pt
                  << " Face index on boundary is "
                  << Face_index_at_boundary[i][e] << std::endl;
        }
      }
    }
 
 
    // Lookup scheme has now been setup
    Lookup_for_elements_next_boundary_is_setup = true;
  }

References oomph::Mesh::Boundary_element_pt, oomph::FiniteElement::dim(), e(), Eigen::placeholders::end, oomph::Mesh::Face_index_at_boundary, oomph::Mesh::finite_element_pt(), oomph::Node::get_boundaries_pt(), i, j, oomph::Mesh::Lookup_for_elements_next_boundary_is_setup, oomph::Mesh::nboundary(), oomph::Mesh::nelement(), oomph::FiniteElement::nnode_1d(), oomph::FiniteElement::node_pt(), SYCL::sign(), and size.

---

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

• quad_mesh.h
• quad_mesh.cc