#include <perturbed_spines.h>

Inheritance diagram for oomph::PerturbedSpineMesh:

Public Member Functions
virtual	~PerturbedSpineMesh ()
	Destructor to clean up the memory allocated to the perturbed spines. More...

PerturbedSpine *const &	perturbed_spine_pt (const unsigned long &i) const
	Return the i-th perturbed spine in the mesh. More...

unsigned long	nspine () const
	Return the number of perturbed spines in the mesh. More...

void	add_perturbed_spine_pt (PerturbedSpine *const &spine_pt)
	Add a perturbed spine to the mesh. More...

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

PerturbedSpineNode *	element_node_pt (const unsigned long &e, const unsigned &n)

unsigned long	assign_global_eqn_numbers (Vector< double * > &Dof_pt)
	Assign equation numbers for perturbed spines. More...

void	node_update (const bool &update_all_solid_nodes=false)

virtual void	perturbed_spine_node_update (PerturbedSpineNode *spine_node_pt)=0

void	dump (std::ofstream &dump_file, const bool &use_old_ordering=true) const
	Overload the dump function so that the spine data is dumped. More...

void	read (std::ifstream &restart_file)
	Overload the read function so that the spine data is also read. More...

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	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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	output_boundaries (const std::string &output_filename)

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

void	shift_time_values ()

void	calculate_predictions ()

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

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...

Protected Attributes
Vector< PerturbedSpine * >	PerturbedSpine_pt
	A PerturbedSpine mesh contains a Vector of pointers to perturbed spines. 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

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)

Detailed Description

/////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////// General PerturbedSpineMesh class.

Derived from Mesh with virtual so that perturbed spine meshes can be derived from general meshes, without multiple copies of Mesh objects.

Constructor & Destructor Documentation

◆ ~PerturbedSpineMesh()

virtual oomph::PerturbedSpineMesh::~PerturbedSpineMesh ( )

inlinevirtual

Destructor to clean up the memory allocated to the perturbed spines.

   {
    // Set the range of PerturbedSpine_pt
    unsigned long PerturbedSpine_pt_range = PerturbedSpine_pt.size();
  
    // Loop over the entries in reverse and free memory
    for(unsigned long i=PerturbedSpine_pt_range;i>0;i--)
     {
      delete PerturbedSpine_pt[i-1]; PerturbedSpine_pt[i-1] = 0;
     }
   }

References i, and PerturbedSpine_pt.

Member Function Documentation

◆ add_perturbed_spine_pt()

void oomph::PerturbedSpineMesh::add_perturbed_spine_pt ( PerturbedSpine *const & spine_pt )

inline

Add a perturbed spine to the mesh.

  {
   PerturbedSpine_pt.push_back(spine_pt);
  }

References PerturbedSpine_pt.

◆ assign_global_eqn_numbers()

unsigned long oomph::PerturbedSpineMesh::assign_global_eqn_numbers ( Vector< double * > & Dof_pt )

Assign equation numbers for perturbed spines.

Assign (global) equation numbers to spines, nodes and elements.

 {
  // First call the general mesh assign_eqn_numbers
  unsigned long equation_number = Mesh::assign_global_eqn_numbers(Dof_pt);
  
  // Loop over spines and set global equation numbers for the spine heights
  // (they are the only Data items whose global eqn numbers are assigned
  // here)
  unsigned long PerturbedSpine_pt_range = PerturbedSpine_pt.size();
  for(unsigned long i=0;i<PerturbedSpine_pt_range;i++)
   {
    PerturbedSpine_pt[i]->height_pt()->assign_eqn_numbers(equation_number,
                                                          Dof_pt);
   }
  
  // Return total number of equations
  return(equation_number);
 }

References oomph::Mesh::assign_global_eqn_numbers(), i, and PerturbedSpine_pt.

◆ dump()

void oomph::PerturbedSpineMesh::dump	(	std::ofstream &	dump_file,
		const bool &	use_old_ordering = `true`
	)		const

virtual

Overload the dump function so that the spine data is dumped.

Overload the dump function so that the spine data is also dumped.

Reimplemented from oomph::Mesh.

 {
  // Call the standard mesh dump function
   Mesh::dump(dump_file,use_old_ordering);
  
  // Now loop over the spine data and dump the spine height data
  // The ASSUMPTION is that the geometric data is stored elsewhere and will
  // be dumped elsewhere
  
  // Find the number of perturbed spines
  const unsigned long n_spine = nspine();
  
  // Doc number of spines
  dump_file << n_spine << " # number of spines " << std::endl;
  
  // Loop over the perturbed spines
  for(unsigned long s=0;s<n_spine;s++)
   {
    perturbed_spine_pt(s)->height_pt()->dump(dump_file);
   }
 }

References oomph::Mesh::dump(), oomph::Data::dump(), oomph::PerturbedSpine::height_pt(), nspine(), perturbed_spine_pt(), and s.

◆ element_node_pt()

PerturbedSpineNode* oomph::PerturbedSpineMesh::element_node_pt	(	const unsigned long &	e,
		const unsigned &	n
	)

inline

Return the n-th local PerturbedSpineNode in element e. This is required to cast the nodes in a spine mesh to be PerturbedSpineNodes and therefore allow access to the extra PerturbedSpineNode data.

   {
 #ifdef PARANOID
    // Try to cast to FiniteElement
    FiniteElement* el_pt=dynamic_cast<FiniteElement*>(Element_pt[e]);
    if (el_pt==0)
     {
      throw OomphLibError(
       "Can't execute element_node_pt(...) for non FiniteElements",
       "PerturbedSpineMesh::element_node_pt()",
       OOMPH_EXCEPTION_LOCATION);
     }
    if(!dynamic_cast<PerturbedSpineNode*>(el_pt->node_pt(n)))
     {
      std::ostringstream error_message;
      error_message << "Node " << n << "is a "
                    << typeid(el_pt->node_pt(n)).name() 
                    << ", not a PerturbedSpineNode" << std::endl;
      
      throw OomphLibError(error_message.str(),
                          "PerturbedSpineMesh::node_pt()",
                          OOMPH_EXCEPTION_LOCATION);
     }
 #endif
    // Return a cast to the node pointer
    return(dynamic_cast<PerturbedSpineNode*>(
            dynamic_cast<FiniteElement*>(Element_pt[e])->node_pt(n)));
   }

References e(), oomph::Mesh::Element_pt, n, plotDoE::name, oomph::FiniteElement::node_pt(), node_pt(), and OOMPH_EXCEPTION_LOCATION.

◆ node_pt()

PerturbedSpineNode* oomph::PerturbedSpineMesh::node_pt ( const unsigned long & n )

inline

Return a pointer to the n-th global PerturbedSpineNode.

   {
 #ifdef PARANOID
    if(!dynamic_cast<PerturbedSpineNode*>(Node_pt[n]))
     {
      std::ostringstream error_message;
      error_message << "Node " << n << "is a "
                    << typeid(Node_pt[n]).name() 
                    << ", not a PerturbedSpineNode" << std::endl;
      
      throw OomphLibError(error_message.str(),
                          "PerturbedSpineMesh::node_pt()",
                          OOMPH_EXCEPTION_LOCATION);
     } 
 #endif
  
    // Return a cast to the pointer to the node
    return (dynamic_cast<PerturbedSpineNode*>(Node_pt[n]));
   }

References n, plotDoE::name, oomph::Mesh::Node_pt, and OOMPH_EXCEPTION_LOCATION.

Referenced by element_node_pt(), and PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ node_update()

void oomph::PerturbedSpineMesh::node_update ( const bool & update_all_solid_nodes = false )

virtual

Update function to update all nodes of mesh [Doesn't make sense to use this mesh with SolidElements anyway, so we buffer the case if update_all_solid_nodes is set to true.]

////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// Update function to update all nodes of mesh. [Doesn't make sense to use this mesh with SolidElements anyway, so we buffer the case if update_all_solid_nodes (which defaults to false) is set to true.]

Reimplemented from oomph::Mesh.

 {
 #ifdef PARANOID
  if (update_all_solid_nodes)
   {
    std::string error_message =
     "Doesn't make sense to use an PerturbedSpineMesh with\n";
    error_message +=
     "SolidElements so specifying update_all_solid_nodes=true\n";
    error_message += "doesn't make sense either\n";
    
    throw OomphLibError(error_message,
                        "PerturbedSpineMesh::node_update()",
                        OOMPH_EXCEPTION_LOCATION);
   }
 #endif
  
  // Loop over all the nodes
  unsigned long Node_pt_range = Node_pt.size();
  for(unsigned long l=0;l<Node_pt_range;l++)
   {
 #ifdef PARANOID
    if(!dynamic_cast<PerturbedSpineNode*>(Node_pt[l]))
     {
      std::ostringstream error_stream;
      error_stream  
       << "Error: Node " << l << "is a " << typeid(Node_pt[l]).name() 
       << ", not a PerturbedSpineNode" << std::endl;
      throw OomphLibError(error_stream.str(),
                          "PerturbedSpineMesh::node_update()",
                          OOMPH_EXCEPTION_LOCATION);
     } 
 #endif
    
    // Need to cast to spine node to get to update function
    dynamic_cast<PerturbedSpineNode*>(Node_pt[l])->node_update();
   }
 }

References plotDoE::name, oomph::Mesh::Node_pt, OOMPH_EXCEPTION_LOCATION, and oomph::Global_string_for_annotation::string().

◆ nspine()

unsigned long oomph::PerturbedSpineMesh::nspine ( ) const

inline

Return the number of perturbed spines in the mesh.

581 { return PerturbedSpine_pt.size(); }

References PerturbedSpine_pt.

Referenced by dump(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem(), and read().

◆ perturbed_spine_node_update()

virtual void oomph::PerturbedSpineMesh::perturbed_spine_node_update ( PerturbedSpineNode * spine_node_pt )

pure virtual

Update function for given spine node – this must be implemented by all specific PerturbedSpineMeshes.

Implemented in oomph::TwoLayerPerturbedSpineMesh< ELEMENT >, and oomph::TwoLayerPerturbedSpineMesh< PERTURBED_ELEMENT >.

Referenced by oomph::PerturbedSpineNode::node_update().

◆ perturbed_spine_pt()

PerturbedSpine* const& oomph::PerturbedSpineMesh::perturbed_spine_pt ( const unsigned long & i ) const

inline

Return the i-th perturbed spine in the mesh.

   {
    return PerturbedSpine_pt[i];
   }

References i, and PerturbedSpine_pt.

Referenced by dump(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem(), and read().

◆ read()

void oomph::PerturbedSpineMesh::read ( std::ifstream & restart_file )

virtual

Overload the read function so that the spine data is also read.

Overload the read function so that the spine data is read from the restart file

Reimplemented from oomph::Mesh.

 {
  // Call the standard mesh read function
  Mesh::read(restart_file);
  
  // Now loop over the spine data and dump the spine height data
  // The ASSUMPTION is that the geometric data is stored elsewhere and will
  // be dumped elsewhere
  
  // Get the number of perturbed spines
  const unsigned long n_spine = nspine();
  
  std::string input_string;
  // Read line up to termination sign
  getline(restart_file,input_string,'#');
  // Ignore the restr of the line
  restart_file.ignore(80,'\n');
  
  // Check the number of spines
  const unsigned long check_n_spine = atoi(input_string.c_str());
  
  if(check_n_spine != n_spine)
   {
    std::ostringstream error_stream;
     error_stream 
      << "Number of spines in the restart file, " << check_n_spine 
      << std::endl << "does not equal the number of spines in the mesh " 
      << n_spine << std::endl;
  
     throw OomphLibError(error_stream.str(),
                         "PerturbedSpineMesh::read()",
                         OOMPH_EXCEPTION_LOCATION);
   }
  
  // Loop over the spines and read the data
  for(unsigned long s=0;s<n_spine;s++)
   {
    perturbed_spine_pt(s)->height_pt()->read(restart_file);
   }
 }

References oomph::PerturbedSpine::height_pt(), nspine(), OOMPH_EXCEPTION_LOCATION, perturbed_spine_pt(), oomph::Mesh::read(), oomph::Data::read(), s, and oomph::Global_string_for_annotation::string().

Member Data Documentation

◆ PerturbedSpine_pt

Vector<PerturbedSpine*> oomph::PerturbedSpineMesh::PerturbedSpine_pt

protected

A PerturbedSpine mesh contains a Vector of pointers to perturbed spines.

Referenced by add_perturbed_spine_pt(), assign_global_eqn_numbers(), nspine(), perturbed_spine_pt(), and ~PerturbedSpineMesh().

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

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~PerturbedSpineMesh()

Member Function Documentation

◆ add_perturbed_spine_pt()

◆ assign_global_eqn_numbers()

◆ dump()

◆ element_node_pt()

◆ node_pt()

◆ node_update()

◆ nspine()

◆ perturbed_spine_node_update()

◆ perturbed_spine_pt()

◆ read()

Member Data Documentation

◆ PerturbedSpine_pt