Class to adapt the mesh. More...

#include <MeshAdaptor.hpp>

Public Member Functions
	MeshAdaptor (mesh::Mesh &mesh)
	Constructor. More...

virtual	~MeshAdaptor ()
	Destructor. More...

void	prepare ()
	Prepare the mesh adaptor for changes. More...

void	finish ()
	Apply the changes the mesh adaptor for changes and fix inconsistent state. More...

Elementary operations, should not be called usually
void	add_element (const PackedElement &packed_element)
	Add element to the mesh. More...

void	remove_element (const PackedElement &packed_element)
	Remove element from the mesh. More...

void	remove_element (const Uint entities_idx, const Uint elem_loc_idx)
	Remove element from the mesh. More...

void	flush_elements ()
	Apply all changes to elements. More...

void	add_node (const PackedNode &packed_node)
	Add node from the mesh. More...

void	remove_node (const PackedNode &packed_node)
	Remove node from the mesh. More...

void	remove_node (const Uint dict_idx, const Uint node_loc_idx)
	Remove node from the mesh. More...

void	flush_nodes ()
	Apply all changes to nodes. More...

Fine Level functions, should not be called usually
void	create_element_buffers ()
	Creates buffers for element changes. More...

void	create_node_buffers ()
	Creates buffers for node changes. More...

void	clear_element_buffers ()
	Creates buffers for element changes. More...

void	clear_node_buffers ()
	Creates buffers for node changes. More...

void	make_element_node_connectivity_global ()
	Element-node connectivity is replaced with global indices. More...

void	restore_element_node_connectivity ()
	Element-node connectivity is restored with local indices. More...

void	rebuild_node_glb_to_loc_map ()
	rebuild dictionary.glb_to_loc() map with flushed nodes included More...

void	rebuild_node_to_element_connectivity ()
	rebuild dictionary.connectivity() map with flushed nodes and elements included More...

High-level API
void	move_elements (const std::vector< std::vector< std::vector< Uint > > > &exported_elements_loc_id)
	Move elements and attached nodes between processors, according to an elements_changeset. More...

void	grow_overlap ()
	Create an additional cell-layer of overlap between pid's. More...

void	combine_mesh (const Mesh &other_mesh)
	Add another mesh to this mesh. More...

void	remove_duplicate_elements_and_nodes ()
	Add another mesh to this mesh. More...

Low-level API
void	find_nodes_to_export (const std::vector< std::vector< std::vector< Uint > > > &exported_elements_loc_id, std::vector< std::vector< std::vector< Uint > > > &exported_nodes_loc_id)
	Assemble a change-set of nodes to be sent together with elements. More...

void	send_elements (const std::vector< std::vector< std::vector< Uint > > > &exported_elements_loc_id, std::vector< std::vector< std::vector< boost::uint64_t > > > &imported_elements_glb_id)
	Send/Receive elements according to an elements-changeset. More...

void	send_nodes (const std::vector< std::vector< std::vector< Uint > > > &exported_nodes_loc_id, std::vector< std::vector< std::vector< boost::uint64_t > > > &imported_nodes_glb_id)
	Send/Receive nodes according to an nodes-changeset. More...

void	fix_node_ranks ()
	Correct ranks of nodes to be unique in all pid's. More...

void	assign_global_numbering_and_rank_to_unknown_elems ()
	Exactly what it says new elements have a rank and glb_idx to be Uint::max or std::numeric_limits<boost::uint64_t>::max() More...

void	remove_ghost_nodes ()
	remove ghost nodes More...

void	remove_ghost_elements ()
	remove ghost elements More...

void	assign_partition_agnostic_global_indices_to_dict (Dictionary &dict)

Private Attributes
Handle< Mesh >	m_mesh
	Handle to the mesh. More...

bool	is_node_connectivity_global
	boolean that says if mesh has element-node connectivities with global node-indices More...

std::vector< boost::shared_ptr< common::List< Uint >::Buffer > >	element_glb_idx
	Element buffers for global index. More...

std::vector< boost::shared_ptr< common::List< Uint >::Buffer > >	element_rank
	Element buffers for rank. More...

std::vector< std::vector< boost::shared_ptr< common::Table< Uint >::Buffer > > >	element_connected_nodes
	Element buffers for element-node connectivity. More...

std::vector< boost::shared_ptr< common::List< Uint >::Buffer > >	node_glb_idx
	Node buffers for global index. More...

std::vector< boost::shared_ptr< common::List< Uint >::Buffer > >	node_rank
	Node buffers for rank. More...

std::vector< std::vector< boost::shared_ptr< common::Table< Real >::Buffer > > >	node_field_values
	Node buffers for field values. More...

bool	node_glb_to_loc_needs_rebuild
	flag if dictionary.glb_to_loc() must be rebuilt More...

bool	node_elem_connectivity_needs_rebuild
	flag if dictionary.connectivity() must be rebuilt More...

bool	elem_flush_required
	flag if there are still elements that need to be flush More...

bool	node_flush_required
	flag if there are still nodes that need to be flush More...

std::vector< std::set< boost::uint64_t > >	added_elements
	bookkeeping of added and removed elements More...

std::vector< std::set< boost::uint64_t > >	added_nodes
	bookkeeping of added and removed nodes More...

bool	has_element_buffers

bool	has_node_buffers

Detailed Description

Class to adapt the mesh.

First call prepare(). This puts mesh in inconsistent state, but allows it to be changed more easily. Then indicate all the changes with functions like

add_element()
remove_element()
add_node()
remove_node() The changes are NOT applied until finally the function finish() is called. This also puts the mesh back in a consistent state, and updates mesh statistics
Author
Willem Deconinck

Definition at line 45 of file MeshAdaptor.hpp.

Constructor & Destructor Documentation

MeshAdaptor ( mesh::Mesh & mesh )

Constructor.

Definition at line 171 of file MeshAdaptor.cpp.

~MeshAdaptor ( )

virtual

Destructor.

Definition at line 186 of file MeshAdaptor.cpp.

Member Function Documentation

void add_element ( const PackedElement & packed_element )

Add element to the mesh.

Note: Changes are only applied after flush_elements() or finish() is called

Precondition: make_element_node_connectivity_global() must be called; create_element_buffers() must have been called before

Definition at line 372 of file MeshAdaptor.cpp.

void add_node ( const PackedNode & packed_node )

Add node from the mesh.

Note: Changes are only applied after flush_nodes() or finish() is called

Precondition: make_element_node_connectivity_global() must be called; create_node_buffers() must have been called before

Definition at line 421 of file MeshAdaptor.cpp.

void assign_global_numbering_and_rank_to_unknown_elems ( )

Exactly what it says new elements have a rank and glb_idx to be Uint::max or std::numeric_limits<boost::uint64_t>::max()

Definition at line 1803 of file MeshAdaptor.cpp.

void assign_partition_agnostic_global_indices_to_dict ( Dictionary & dict )

Nodes found on pid 0 will be numbered from 0 to nb_nodes(pid0) NEW nodes found on pid 1 will be numbered from nb_nodes(pid0) to nb_nodes(pid0+pid1) NEW nodes found on pid 2 will be numbered from nb_nodes(pid0+pid1) to nb_nodes(pid0+pid1+pid2) ... Any ownership is not claimed! It is still possible that a node with glb_idx between nb_nodes(pid0) and nb_nodes(pid0+pid1) is owned by pid0 or pid1 or pid2. Only when a call to fix_node_ranks() is done, will ownership be claimed by the proc that found the node, with the lowest pid.

Definition at line 1696 of file MeshAdaptor.cpp.

void clear_element_buffers ( )

Creates buffers for element changes.

Definition at line 247 of file MeshAdaptor.cpp.

void clear_node_buffers ( )

Creates buffers for node changes.

Definition at line 292 of file MeshAdaptor.cpp.

void combine_mesh ( const Mesh & other_mesh )

Add another mesh to this mesh.

Definition at line 1330 of file MeshAdaptor.cpp.

void create_element_buffers ( )

Creates buffers for element changes.

Definition at line 222 of file MeshAdaptor.cpp.

void create_node_buffers ( )

Creates buffers for node changes.

Definition at line 267 of file MeshAdaptor.cpp.

void find_nodes_to_export	(	const std::vector< std::vector< std::vector< Uint > > > &	exported_elements_loc_id,
		std::vector< std::vector< std::vector< Uint > > > &	exported_nodes_loc_id
	)

Assemble a change-set of nodes to be sent together with elements.

Parameters

[in]	exported_elements_loc_id	A set with 3 indices: send_element[to_pid][from_entities_idx][local_elem_idx]
[out]	exported_nodes_loc_id	A set with 3 indices: send_node[to_pid][from_dict_idx][local_node_idx]

Definition at line 549 of file MeshAdaptor.cpp.

void finish ( )

Apply the changes the mesh adaptor for changes and fix inconsistent state.

Postcondition: Mesh is back in consistent state!

Definition at line 205 of file MeshAdaptor.cpp.

void fix_node_ranks ( )

Correct ranks of nodes to be unique in all pid's.

Definition at line 1044 of file MeshAdaptor.cpp.

void flush_elements ( )

Apply all changes to elements.

Definition at line 467 of file MeshAdaptor.cpp.

void flush_nodes ( )

Apply all changes to nodes.

Definition at line 492 of file MeshAdaptor.cpp.

void grow_overlap ( )

Create an additional cell-layer of overlap between pid's.

Postcondition: nodes and elements are flushed, and node-ranks are uniquely defined in all pid's. Call finish() to notify the mesh of updates.

Definition at line 1178 of file MeshAdaptor.cpp.

void make_element_node_connectivity_global ( )

Element-node connectivity is replaced with global indices.

This is to allow elements from other ranks to be added, in which case local indices are meaningless

Postcondition: Mesh is in inconsistent state! Call restore_element_node_connectivity() to fix it, after element modifications are done.

Definition at line 312 of file MeshAdaptor.cpp.

void move_elements ( const std::vector< std::vector< std::vector< Uint > > > & exported_elements_loc_id )

Move elements and attached nodes between processors, according to an elements_changeset.

Parameters

[in] exported_elements_loc_id A set with 3 indices: move_element[to_pid][from_entities_idx][local_elem_idx]

Postcondition: nodes and elements are flushed, and node-ranks are uniquely defined in all pid's. Call finish() to notify the mesh of updates.

Definition at line 844 of file MeshAdaptor.cpp.

void prepare ( )

Prepare the mesh adaptor for changes.

Prepare the mesh adaptor for changes to add/remove nodes and elements The element-node connectivity tables are replaced with global node indices instead of local indices, so that elements from other processes can be added.

Note: All changes that are given (remove_node(), add_element(), ...) are not applied until finish() or flush_nodes() and/or flush_elements() is called.

Postcondition: Mesh is in inconsistent state after this! Call finish() to fix it, after modifications

Definition at line 192 of file MeshAdaptor.cpp.

void rebuild_node_glb_to_loc_map ( )

rebuild dictionary.glb_to_loc() map with flushed nodes included

Definition at line 811 of file MeshAdaptor.cpp.

void rebuild_node_to_element_connectivity ( )

rebuild dictionary.connectivity() map with flushed nodes and elements included

Definition at line 827 of file MeshAdaptor.cpp.

void remove_duplicate_elements_and_nodes ( )

Add another mesh to this mesh.

Definition at line 1537 of file MeshAdaptor.cpp.

void remove_element ( const PackedElement & packed_element )

Remove element from the mesh.

Note: Changes are only applied after flush_elements() or finish() is called

Precondition: create_element_buffers() must have been called before

Definition at line 395 of file MeshAdaptor.cpp.

void remove_element	(	const Uint	entities_idx,
		const Uint	elem_loc_idx
	)

Remove element from the mesh.

Note: Changes are only applied after flush_elements() or finish() is called

Precondition: create_element_buffers() must have been called before

Definition at line 402 of file MeshAdaptor.cpp.

void remove_ghost_elements ( )

remove ghost elements

Postcondition: Elements are not flushed yet, so additional operations can be performed

Definition at line 518 of file MeshAdaptor.cpp.

void remove_ghost_nodes ( )

remove ghost nodes

Postcondition: Nodes are not flushed yet, so additional operations can be performed

Definition at line 534 of file MeshAdaptor.cpp.

void remove_node ( const PackedNode & packed_node )

Remove node from the mesh.

Note: Changes are only applied after flush_nodes() or finish() is called

Precondition: create_node_buffers() must have been called before

Definition at line 444 of file MeshAdaptor.cpp.

void remove_node	(	const Uint	dict_idx,
		const Uint	node_loc_idx
	)

Remove node from the mesh.

Note: Changes are only applied after flush_nodes() or finish() is called

Precondition: create_node_buffers() must have been called before

Definition at line 451 of file MeshAdaptor.cpp.

void restore_element_node_connectivity ( )

Element-node connectivity is restored with local indices.

Postcondition: Mesh is in inconsistent state! Call restore_element_node_connectivity() to fix it, after element modifications are done.

Definition at line 341 of file MeshAdaptor.cpp.

void send_elements	(	const std::vector< std::vector< std::vector< Uint > > > &	exported_elements_loc_id,
		std::vector< std::vector< std::vector< boost::uint64_t > > > &	imported_elements_glb_id
	)

Send/Receive elements according to an elements-changeset.

Parameters

[in]	exported_elements_loc_id	A set with 3 indices: send_element[to_pid][from_entities_idx][local_elem_idx]
[out]	imported_elements_glb_id	A set with 3 indices: received_element[from_pid][from_entities_idx][glb_elem_idx]

Postcondition: Elements are not flushed yet, so additional operations can be performed

Definition at line 620 of file MeshAdaptor.cpp.

void send_nodes	(	const std::vector< std::vector< std::vector< Uint > > > &	exported_nodes_loc_id,
		std::vector< std::vector< std::vector< boost::uint64_t > > > &	imported_nodes_glb_id
	)

Send/Receive nodes according to an nodes-changeset.

Parameters

[in]	exported_nodes_loc_id	A set with 3 indices: send_node[to_pid][from_dict_idx][local_node_idx]
[out]	imported_nodes_glb_id	A set with 3 indices: received_node[from_pid][from_dict_idx][glb_node_idx]

Postcondition: Nodes are not flushed yet, so additional operations can be performed

Definition at line 726 of file MeshAdaptor.cpp.

Member Data Documentation

std::vector< std::set<boost::uint64_t> > added_elements

private

bookkeeping of added and removed elements

Definition at line 256 of file MeshAdaptor.hpp.

std::vector< std::set<boost::uint64_t> > added_nodes

private

bookkeeping of added and removed nodes

Definition at line 259 of file MeshAdaptor.hpp.

bool elem_flush_required

private

flag if there are still elements that need to be flush

Definition at line 250 of file MeshAdaptor.hpp.

std::vector< std::vector< boost::shared_ptr<common::Table<Uint>::Buffer> > > element_connected_nodes

private

Element buffers for element-node connectivity.

Definition at line 232 of file MeshAdaptor.hpp.

std::vector< boost::shared_ptr<common::List<Uint>::Buffer> > element_glb_idx

private

Element buffers for global index.

Definition at line 226 of file MeshAdaptor.hpp.

std::vector< boost::shared_ptr<common::List<Uint>::Buffer> > element_rank

private

Element buffers for rank.

Definition at line 229 of file MeshAdaptor.hpp.

bool has_element_buffers

private

Definition at line 261 of file MeshAdaptor.hpp.

bool has_node_buffers

private

Definition at line 263 of file MeshAdaptor.hpp.

bool is_node_connectivity_global

private

boolean that says if mesh has element-node connectivities with global node-indices

Definition at line 223 of file MeshAdaptor.hpp.

Handle<Mesh> m_mesh

private

Handle to the mesh.

Definition at line 220 of file MeshAdaptor.hpp.

bool node_elem_connectivity_needs_rebuild

private

flag if dictionary.connectivity() must be rebuilt

Definition at line 247 of file MeshAdaptor.hpp.

std::vector< std::vector< boost::shared_ptr<common::Table<Real>::Buffer> > > node_field_values

private

Node buffers for field values.

Definition at line 241 of file MeshAdaptor.hpp.

bool node_flush_required

private

flag if there are still nodes that need to be flush

Definition at line 253 of file MeshAdaptor.hpp.

std::vector< boost::shared_ptr<common::List<Uint>::Buffer> > node_glb_idx

private

Node buffers for global index.

Definition at line 235 of file MeshAdaptor.hpp.

bool node_glb_to_loc_needs_rebuild

private

flag if dictionary.glb_to_loc() must be rebuilt

Definition at line 244 of file MeshAdaptor.hpp.

std::vector< boost::shared_ptr<common::List<Uint>::Buffer> > node_rank

private

Node buffers for rank.

Definition at line 238 of file MeshAdaptor.hpp.

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

cf3/mesh/MeshAdaptor.hpp
cf3/mesh/MeshAdaptor.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation