oomph::GeompackQuadScaffoldMesh Class Reference

#include <geompack_scaffold_mesh.h>

Inheritance diagram for oomph::GeompackQuadScaffoldMesh:

Public Member Functions
	GeompackQuadScaffoldMesh ()
	Empty constructor. More...
	GeompackQuadScaffoldMesh (const std::string &mesh_file_name, const std::string &curve_file_name)
	Constructor: Pass the filename of the mesh files. More...
	GeompackQuadScaffoldMesh (const GeompackQuadScaffoldMesh &)=delete
	Broken copy constructor. More...
void	operator= (const GeompackQuadScaffoldMesh &)=delete
	Broken assignment operator. More...
	~GeompackQuadScaffoldMesh ()
	Empty destructor. More...
Public Member Functions inherited from oomph::Mesh
	Mesh ()
	Default constructor. More...
	Mesh (const Vector< Mesh * > &sub_mesh_pt)
void	merge_meshes (const Vector< Mesh * > &sub_mesh_pt)
virtual void	setup_boundary_element_info ()
virtual void	setup_boundary_element_info (std::ostream &outfile)
virtual void	reset_boundary_element_info (Vector< unsigned > &ntmp_boundary_elements, Vector< Vector< unsigned >> &ntmp_boundary_elements_in_region, Vector< FiniteElement * > &deleted_elements)
	Virtual function to perform the reset boundary elements info rutines. More...
template<class BULK_ELEMENT >
void	doc_boundary_coordinates (const unsigned &b, std::ofstream &the_file)
virtual void	scale_mesh (const double &factor)
	Mesh (const Mesh &dummy)=delete
	Broken copy constructor. More...
void	operator= (const Mesh &)=delete
	Broken assignment operator. More...
virtual	~Mesh ()
	Virtual Destructor to clean up all memory. More...
void	flush_element_and_node_storage ()
void	flush_element_storage ()
void	flush_node_storage ()
Node *&	node_pt (const unsigned long &n)
	Return pointer to global node n. More...
Node *	node_pt (const unsigned long &n) const
	Return pointer to global node n (const version) More...
GeneralisedElement *&	element_pt (const unsigned long &e)
	Return pointer to element e. More...
GeneralisedElement *	element_pt (const unsigned long &e) const
	Return pointer to element e (const version) More...
const Vector< GeneralisedElement * > &	element_pt () const
	Return reference to the Vector of elements. More...
Vector< GeneralisedElement * > &	element_pt ()
	Return reference to the Vector of elements. More...
FiniteElement *	finite_element_pt (const unsigned &e) const
Node *&	boundary_node_pt (const unsigned &b, const unsigned &n)
	Return pointer to node n on boundary b. More...
Node *	boundary_node_pt (const unsigned &b, const unsigned &n) const
	Return pointer to node n on boundary b. More...
void	set_nboundary (const unsigned &nbound)
	Set the number of boundaries in the mesh. More...
void	remove_boundary_nodes ()
	Clear all pointers to boundary nodes. More...
void	remove_boundary_nodes (const unsigned &b)
void	remove_boundary_node (const unsigned &b, Node *const &node_pt)
	Remove a node from the boundary b. More...
void	add_boundary_node (const unsigned &b, Node *const &node_pt)
	Add a (pointer to) a node to the b-th boundary. More...
void	copy_boundary_node_data_from_nodes ()
bool	boundary_coordinate_exists (const unsigned &i) const
	Indicate whether the i-th boundary has an intrinsic coordinate. More...
unsigned long	nelement () const
	Return number of elements in the mesh. More...
unsigned long	nnode () const
	Return number of nodes in the mesh. More...
unsigned	ndof_types () const
	Return number of dof types in mesh. More...
unsigned	elemental_dimension () const
	Return number of elemental dimension in mesh. More...
unsigned	nodal_dimension () const
	Return number of nodal dimension in mesh. More...
void	add_node_pt (Node *const &node_pt)
	Add a (pointer to a) node to the mesh. More...
void	add_element_pt (GeneralisedElement *const &element_pt)
	Add a (pointer to) an element to the mesh. More...
virtual void	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

Mesh that is based on input files generated by the quadrilateral mesh generator Geompack.

Constructor & Destructor Documentation

GeompackQuadScaffoldMesh() [1/3]

oomph::GeompackQuadScaffoldMesh::GeompackQuadScaffoldMesh ( )

inline

Empty constructor.

{}

GeompackQuadScaffoldMesh() [2/3]

oomph::GeompackQuadScaffoldMesh::GeompackQuadScaffoldMesh	(	const std::string &	mesh_file_name,
		const std::string &	curve_file_name
	)

Constructor: Pass the filename of the mesh files.

  {
    // Read the output mesh file to find informations about the nodes
    // and elements of the mesh
 
    // Process mesh file
    //---------------------
    std::ifstream mesh_file(mesh_file_name.c_str(), std::ios_base::in);
 
    // Number of nodes
    unsigned n_node;
    mesh_file >> n_node;
 
    // Coordinates of nodes and extra information index
    Vector<double> x_node(n_node);
    Vector<double> y_node(n_node);
    Vector<int> vertinfo(n_node);
    for (unsigned i = 0; i < n_node; i++)
    {
      mesh_file >> x_node[i];
      mesh_file >> y_node[i];
      mesh_file >> vertinfo[i];
    }
 
    // Extra information (nodes lying on a curve)
    unsigned n_vx;
    mesh_file >> n_vx;
 
    // Dummy storage for the node code
    int dummy_node_code;
 
    // Storage for the curve indice
    Vector<int> icurv(n_vx); // it's negative if not used
 
    // Dummy storage for the location of the point on the curve
    double dummy_ucurv;
 
    for (unsigned i = 0; i < n_vx; i++)
    {
      mesh_file >> dummy_node_code;
      mesh_file >> icurv[i];
      mesh_file >> dummy_ucurv;
    }
 
    // Number of local nodes per element
    unsigned n_local_node;
    mesh_file >> n_local_node;
 
    // Number of elements
    unsigned n_element;
    mesh_file >> n_element;
 
    // Storage for global node numbers for all elements
    Vector<unsigned> global_node(n_local_node * n_element);
 
    // Storage for edge information
    // (needed for a possible construction of midside node
    // in the following build from scaffold function)
    Vector<int> edgeinfo(n_local_node * n_element);
 
    // Initialize counter
    unsigned k = 0;
 
    // Read global node numbers for all elements
    for (unsigned i = 0; i < n_element; i++)
    {
      for (unsigned j = 0; j < n_local_node; j++)
      {
        mesh_file >> global_node[k];
        k++;
      }
    }
 
    // Initialize counter
    unsigned l = 0;
 
    // Read the edge information
    for (unsigned i = 0; i < n_element; i++)
    {
      for (unsigned j = 0; j < n_local_node; j++)
      {
        mesh_file >> edgeinfo[l];
        l++;
      }
    }
 
    mesh_file.close();
 
    // Create a vector of boolean so as not to create the same node twice
    std::vector<bool> done(n_node);
    for (unsigned i = 0; i < n_node; i++)
    {
      done[i] = false;
    }
 
    // Resize the Node vector
    Node_pt.resize(n_node, 0);
 
    // Resize the Element vector
    Element_pt.resize(n_element);
 
 
    // Process curve file to extract information about boundaries
    // ----------------------------------------------------------
 
    // Important: the input file must NOT have NURBS curve
    std::ifstream curve_file(curve_file_name.c_str(), std::ios_base::in);
 
    // Number of curves
    unsigned n_curv;
    curve_file >> n_curv;
 
    // Storage of several information for each curve
    Vector<Vector<int>> curv;
 
    // Resize to n_curv rows
    curv.resize(n_curv);
 
    // Curve type
    unsigned type;
 
    // Loop over the curves to extract information
    for (unsigned i = 0; i < n_curv; i++)
    {
      curve_file >> type;
      if (type == 1)
      {
        curv[i].resize(4);
        curv[i][0] = type;
        for (unsigned j = 1; j < 4; j++)
        {
          curve_file >> curv[i][j];
        }
      }
      else if (type == 2)
      {
        curv[i].resize(5);
        curv[i][0] = type;
        for (unsigned j = 1; j < 5; j++)
        {
          curve_file >> curv[i][j];
        }
      }
      else
      {
        std::ostringstream error_stream;
        error_stream << "Current we can only process curves of\n"
                     << "type 1 (straight lines) and 2 (circular arcs\n"
                     << "You've specified: type " << type << std::endl;
 
        throw OomphLibError(
          error_stream.str(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
      }
    }
 
    curve_file.close();
 
    // Searching the number of boundaries
    int d = 0;
    for (unsigned i = 0; i < n_curv; i++)
    {
      if (d < curv[i][1])
      {
        d = curv[i][1]; // the boundary code is the 2nd value of each curve
      }
    }
    oomph_info << "The number of boundaries is " << d << std::endl;
 
    // Set number of boundaries
    if (d > 0)
    {
      set_nboundary(d);
    }
 
    // Search the boundary number of node located on a boundary
    // If after this, boundary_of_node[j][0] is -1 then node j
    // is not located on any boundary.
    // If boundary_of_node[j][0] is positive, the node is located
    // on the boundary indicated by that number.
    // If boundary_of_node[j][1] is also positive, the node is also
    // located on that boundary. Note: We're ignoring the (remote)
    // possibility that node is located on 3 or more boundaries
    // as one of them would have to be an internal boundary which
    // would be odd...
    Vector<Vector<int>> boundary_of_node;
    boundary_of_node.resize(n_node);
    unsigned n;
    for (unsigned i = 0; i < n_node; i++)
    {
      n = 0;
      boundary_of_node[i].resize(2);
      boundary_of_node[i][0] = -1;
      boundary_of_node[i][1] = -1;
      if (vertinfo[i] == 2) // it's an endpoint
      {
        for (unsigned j = 0; j < n_curv; j++)
        {
          for (unsigned m = 2; m < curv[j].size(); m++)
          {
            if (curv[j][m] ==
                static_cast<int>(i + 1)) // node number begins at 1
            { // in the mesh file !!!
              boundary_of_node[i][n] = curv[j][1];
              n++;
            }
          }
        }
      }
      if (vertinfo[i] > 20)
      {
        int a = 0;
        a = (vertinfo[i]) / 20;
        int b;
        b = icurv[a - 1]; // 1st value of vector at [0] !!
        boundary_of_node[i][0] =
          curv[b - 1][1]; // 1st value of vector at [0] !!
      }
    }
 
 
    // Create the elements
    //--------------------
 
    unsigned count = 0;
    unsigned c;
    for (unsigned e = 0; e < n_element; e++)
    {
      // Build simplex four node quad in the scaffold mesh
      Element_pt[e] = new QElement<2, 2>;
 
      // Construction of the two first nodes of the element
      for (unsigned j = 0; j < 2; j++)
      {
        c = global_node[count];
        if (done[c - 1] == false) // c-1 because node number begins
        // at 1 in the mesh file
        {
          // If the node is located on a boundary construct a boundary node
          if ((d > 0) && ((boundary_of_node[c - 1][0] > 0) ||
                          (boundary_of_node[c - 1][1] > 0)))
          {
            // Construct a boundary node
            Node_pt[c - 1] = finite_element_pt(e)->construct_boundary_node(j);
            // Add to the look=up schemes
            if (boundary_of_node[c - 1][0] > 0)
            {
              add_boundary_node(boundary_of_node[c - 1][0] - 1, Node_pt[c - 1]);
            }
            if (boundary_of_node[c - 1][1] > 0)
            {
              add_boundary_node(boundary_of_node[c - 1][1] - 1, Node_pt[c - 1]);
            }
          }
          // Otherwise construct a normal node
          else
          {
            Node_pt[c - 1] = finite_element_pt(e)->construct_node(j);
          }
          done[c - 1] = true;
          Node_pt[c - 1]->x(0) = x_node[c - 1];
          Node_pt[c - 1]->x(1) = y_node[c - 1];
        }
        else
        {
          finite_element_pt(e)->node_pt(j) = Node_pt[c - 1];
        }
        count++;
      }
 
      // Construction of the third node not in anticlockwise order
      c = global_node[count + 1];
      if (done[c - 1] ==
          false) // c-1 because node number begins at 1 in the mesh file
      {
        // If the node is on a boundary, construct a boundary node
        if ((d > 0) && ((boundary_of_node[c - 1][0] > 0) ||
                        (boundary_of_node[c - 1][1] > 0)))
        {
          // Construct the node
          Node_pt[c - 1] = finite_element_pt(e)->construct_boundary_node(2);
          // Add to the look-up schemes
          if (boundary_of_node[c - 1][0] > 0)
          {
            add_boundary_node(boundary_of_node[c - 1][0] - 1, Node_pt[c - 1]);
          }
          if (boundary_of_node[c - 1][1] > 0)
          {
            add_boundary_node(boundary_of_node[c - 1][1] - 1, Node_pt[c - 1]);
          }
        }
        // otherwise construct a normal node
        else
        {
          Node_pt[c - 1] = finite_element_pt(e)->construct_node(2);
        }
        done[c - 1] = true;
        Node_pt[c - 1]->x(0) = x_node[c - 1];
        Node_pt[c - 1]->x(1) = y_node[c - 1];
      }
      else
      {
        finite_element_pt(e)->node_pt(2) = Node_pt[c - 1];
      }
 
      count++;
 
      // Construction of the fourth node
      c = global_node[count - 1];
      if (done[c - 1] ==
          false) // c-1 because node number begins at 1 in the mesh file
      {
        // If the node is on a boundary, constuct a boundary node
        if ((d > 0) && ((boundary_of_node[c - 1][0] > 0) ||
                        (boundary_of_node[c - 1][1] > 0)))
        {
          // Construct the boundary node
          Node_pt[c - 1] = finite_element_pt(e)->construct_boundary_node(3);
          // Add to the look-up schemes
          if (boundary_of_node[c - 1][0] > 0)
          {
            add_boundary_node(boundary_of_node[c - 1][0] - 1, Node_pt[c - 1]);
          }
          if (boundary_of_node[c - 1][1] > 0)
          {
            add_boundary_node(boundary_of_node[c - 1][1] - 1, Node_pt[c - 1]);
          }
        }
        // Otherwise construct a normal node
        else
        {
          Node_pt[c - 1] = finite_element_pt(e)->construct_node(3);
        }
        done[c - 1] = true;
        Node_pt[c - 1]->x(0) = x_node[c - 1];
        Node_pt[c - 1]->x(1) = y_node[c - 1];
      }
      else
      {
        finite_element_pt(e)->node_pt(3) = Node_pt[c - 1];
      }
 
      count++;
    }
  }

References a, oomph::Mesh::add_boundary_node(), b, calibrate::c, oomph::FiniteElement::construct_boundary_node(), oomph::FiniteElement::construct_node(), e(), oomph::Mesh::Element_pt, oomph::Mesh::finite_element_pt(), i, j, k, m, n, oomph::FiniteElement::node_pt(), oomph::Mesh::Node_pt, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, oomph::oomph_info, oomph::Mesh::set_nboundary(), and compute_granudrum_aor::type.

GeompackQuadScaffoldMesh() [3/3]

oomph::GeompackQuadScaffoldMesh::GeompackQuadScaffoldMesh ( const GeompackQuadScaffoldMesh &  )

delete

Broken copy constructor.

~GeompackQuadScaffoldMesh()

oomph::GeompackQuadScaffoldMesh::~GeompackQuadScaffoldMesh ( )

inline

Empty destructor.

{}

Member Function Documentation

operator=()

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

delete

Broken assignment operator.

---

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

• geompack_scaffold_mesh.h
• geompack_scaffold_mesh.cc