mesh.hh
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mesh.hh
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	/**
	* @file mesh.hh
	*
	* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
	* @author Marco Vocialta <marco.vocialta@epfl.ch>
	* @author Nicolas Richart <nicolas.richart@epfl.ch>
	*
	* @date Fri Jun 18 11:47:19 2010
	*
	* @brief the class representing the meshes
	*
	* @section LICENSE
	*
	* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
	* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
	*
	* Akantu is free software: you can redistribute it and/or modify it under the
	* terms of the GNU Lesser General Public License as published by the Free
	* Software Foundation, either version 3 of the License, or (at your option) any
	* later version.
	*
	* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
	* details.
	*
	* You should have received a copy of the GNU Lesser General Public License
	* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
	*
	*/

	/* -------------------------------------------------------------------------- */
	#ifndef __AKANTU_MESH_HH__
	#define __AKANTU_MESH_HH__

	/* -------------------------------------------------------------------------- */
	#include "aka_common.hh"
	#include "aka_memory.hh"
	#include "aka_vector.hh"
	#include "element_class.hh"
	#include "by_element_type.hh"
	#include "aka_event_handler.hh"

	/* -------------------------------------------------------------------------- */
	#include <set>
	/* -------------------------------------------------------------------------- */

	__BEGIN_AKANTU__

	/* -------------------------------------------------------------------------- */
	/* Element */
	/* -------------------------------------------------------------------------- */
	class Element {
	public:
	Element(ElementType type = _not_defined, UInt element = 0,
	GhostType ghost_type = _not_ghost, ElementKind kind = _ek_regular) :
	type(type), element(element),
	ghost_type(ghost_type), kind(kind) {};

	Element(const Element & element) {
	this->type = element.type;
	this->element = element.element;
	this->ghost_type = element.ghost_type;
	this->kind = element.kind;
	}

	inline bool operator==(const Element & elem) const {
	return ((element == elem.element)
	&& (type == elem.type)
	&& (ghost_type == elem.ghost_type)
	&& (kind == elem.kind));
	}

	inline bool operator!=(const Element & elem) const {
	return ((element != elem.element)
	\|\| (type != elem.type)
	\|\| (ghost_type != elem.ghost_type)
	\|\| (kind != elem.kind));
	}

	bool operator<(const Element& rhs) const {
	bool res = ((this->kind < rhs.kind) \|\|
	((this->kind == rhs.kind) &&
	((this->ghost_type < rhs.ghost_type) \|\|
	((this->ghost_type == rhs.ghost_type) &&
	((this->type < rhs.type) \|\|
	((this->type == rhs.type) &&
	(this->element < rhs.element)))))));
	return res;
	}

	virtual ~Element() {};

	/// function to print the containt of the class
	virtual void printself(std::ostream & stream, int indent = 0) const;
	public:
	ElementType type;
	UInt element;
	GhostType ghost_type;
	ElementKind kind;
	};

	struct CompElementLess {
	bool operator() (const Element& lhs, const Element& rhs) const {
	return lhs < rhs;
	}
	};

	extern const Element ElementNull;



	/* -------------------------------------------------------------------------- */
	/* -------------------------------------------------------------------------- */
	/* Mesh modifications events */
	/* -------------------------------------------------------------------------- */
	template<class Entity>
	class MeshEvent {
	public:
	virtual ~MeshEvent() {}
	const Vector<Entity> & getList() const { return list; }
	Vector<Entity> & getList() { return list; }
	protected:
	Vector<Entity> list;
	};



	class Mesh;

	class NewNodesEvent : public MeshEvent<UInt> { };
	class RemovedNodesEvent : public MeshEvent<UInt> {
	public:
	inline RemovedNodesEvent(const Mesh & mesh);
	AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering, Vector<UInt> &);
	AKANTU_GET_MACRO(NewNumbering, new_numbering, const Vector<UInt> &);
	private:
	Vector<UInt> new_numbering;
	};

	class NewElementsEvent : public MeshEvent<Element> { };
	class RemovedElementsEvent : public MeshEvent<Element> {
	public:
	inline RemovedElementsEvent(const Mesh & mesh);
	AKANTU_GET_MACRO(NewNumbering, new_numbering, const ByElementTypeUInt &);
	AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering, ByElementTypeUInt &);
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE(NewNumbering, new_numbering, UInt);
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(NewNumbering, new_numbering, UInt);
	protected:
	ByElementTypeUInt new_numbering;
	};

	/* -------------------------------------------------------------------------- */

	class MeshEventHandler {
	public:
	virtual ~MeshEventHandler() {};
	/* ------------------------------------------------------------------------ */
	/* Internal code */
	/* ------------------------------------------------------------------------ */
	protected:
	inline void sendEvent(const NewNodesEvent & event) { onNodesAdded (event.getList()); }
	inline void sendEvent(const RemovedNodesEvent & event) { onNodesRemoved(event.getList(),
	event.getNewNumbering()); }

	inline void sendEvent(const NewElementsEvent & event) { onElementsAdded (event.getList()); }
	inline void sendEvent(const RemovedElementsEvent & event) { onElementsRemoved(event.getList(),
	event.getNewNumbering()); }

	template<class EventHandler>
	friend class EventHandlerManager;

	/* ------------------------------------------------------------------------ */
	/* Interface */
	/* ------------------------------------------------------------------------ */
	public:
	virtual void onNodesAdded (__attribute__((unused)) const Vector<UInt> & nodes_list) { }
	virtual void onNodesRemoved(__attribute__((unused)) const Vector<UInt> & nodes_list,
	__attribute__((unused)) const Vector<UInt> & new_numbering) { }


	virtual void onElementsAdded (__attribute__((unused)) const Vector<Element> & elements_list) { }
	virtual void onElementsRemoved(__attribute__((unused)) const Vector<Element> & elements_list,
	__attribute__((unused)) const ByElementTypeUInt & new_numbering) { }
	};

	/* -------------------------------------------------------------------------- */
	/* Mesh */
	/* -------------------------------------------------------------------------- */

	/**
	* @class Mesh this contain the coordinates of the nodes in the Mesh.nodes
	* Vector, and the connectivity. The connectivity are stored in by element
	* types.
	*
	* To know all the element types present in a mesh you can get the
	* Mesh::ConnectivityTypeList
	*
	* In order to loop on all element you have to loop on all types like this :
	* @code
	Mesh::type_iterator it = mesh.firstType(dim, ghost_type);
	Mesh::type_iterator end = mesh.lastType(dim, ghost_type);

	for(; it != end; ++it) {
	UInt nb_element = mesh.getNbElement(*it);
	const Vector<UInt> & conn = mesh.getConnectivity(*it);

	for(UInt e = 0; e < nb_element; ++e) {
	...
	}
	}
	@endcode
	*/
	class Mesh : protected Memory, public EventHandlerManager<MeshEventHandler> {
	/* ------------------------------------------------------------------------ */
	/* Constructors/Destructors */
	/* ------------------------------------------------------------------------ */
	public:

	/// constructor that create nodes coordinates array
	Mesh(UInt spatial_dimension,
	const ID & id = "mesh",
	const MemoryID & memory_id = 0);

	/// constructor that use an existing nodes coordinates array, by knowing its ID
	Mesh(UInt spatial_dimension,
	const ID & nodes_id,
	const ID & id = "mesh",
	const MemoryID & memory_id = 0);

	/**
	* constructor that use an existing nodes coordinates
	* array, by getting the vector of coordinates
	*/
	Mesh(UInt spatial_dimension,
	Vector<Real> & nodes,
	const ID & id = "mesh",
	const MemoryID & memory_id = 0);


	virtual ~Mesh();

	/// @typedef ConnectivityTypeList list of the types present in a Mesh
	typedef std::set<ElementType> ConnectivityTypeList;

	/// read the mesh from a file
	void read (const std::string & filename, const MeshIOType & mesh_io_type = _miot_auto);
	/// write the mesh to a file
	void write(const std::string & filename, const MeshIOType & mesh_io_type = _miot_auto);


	private:
	/// initialize the connectivity to NULL and other stuff
	void init();

	/* ------------------------------------------------------------------------ */
	/* Methods */
	/* ------------------------------------------------------------------------ */
	public:

	/// function to print the containt of the class
	virtual void printself(std::ostream & stream, int indent = 0) const;

	/// function that computes the bounding box (fills xmin, xmax)
	void computeBoundingBox();

	/// init a by-element-type real vector with provided ids
	template<typename T>
	void initByElementTypeVector(ByElementTypeVector<T> & v,
	UInt nb_component,
	UInt spatial_dimension,
	const bool & flag_nb_node_per_elem_multiply = false,
	ElementKind element_kind = _ek_regular,
	bool size_to_nb_element = false) const; /// @todo: think about nicer way to do it

	/// extract coordinates of nodes from an element
	template<typename T>
	inline void extractNodalValuesFromElement(const Vector<T> & nodal_values,
	T * elemental_values,
	UInt * connectivity,
	UInt n_nodes,
	UInt nb_degree_of_freedom) const;

	/// extract coordinates of nodes from a reversed element
	inline void extractNodalCoordinatesFromPBCElement(Real * local_coords,
	UInt * connectivity,
	UInt n_nodes);

	/// convert a element to a linearized element
	inline UInt elementToLinearized(const Element & elem) const;

	/// convert a linearized element to an element
	inline Element linearizedToElement (UInt linearized_element) const;

	/// update the types offsets array for the conversions
	inline void updateTypesOffsets(const GhostType & ghost_type);

	/// add a Vector of connectivity for the type <type>.
	inline void addConnectivityType(const ElementType & type);

	/* ------------------------------------------------------------------------ */
	template <class Event>
	inline void sendEvent(Event & event) {
	if(event.getList().getSize() != 0)
	EventHandlerManager<MeshEventHandler>::sendEvent<Event>(event);
	}

	/* ------------------------------------------------------------------------ */
	template<typename T>
	inline void removeNodesFromVector(Vector<T> & vect, const Vector<UInt> & new_numbering);


	/* ------------------------------------------------------------------------ */
	/* Accessors */
	/* ------------------------------------------------------------------------ */
	public:
	AKANTU_GET_MACRO(ID, id, const ID &);

	/// get the spatial dimension of the mesh = number of component of the coordinates
	AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);

	/// get the nodes Vector aka coordinates
	AKANTU_GET_MACRO(Nodes, *nodes, const Vector<Real> &);
	AKANTU_GET_MACRO_NOT_CONST(Nodes, *nodes, Vector<Real> &);

	/// get the number of nodes
	AKANTU_GET_MACRO(NbNodes, nodes->getSize(), UInt);

	/// get the Vector of global ids of the nodes (only used in parallel)
	AKANTU_GET_MACRO(GlobalNodesIds, *nodes_global_ids, const Vector<UInt> &);

	/// get the global id of a node
	inline UInt getNodeGlobalId(UInt local_id) const;

	/// get the global number of nodes
	inline UInt getNbGlobalNodes() const;

	/// get the nodes type Vector
	AKANTU_GET_MACRO(NodesType, *nodes_type, const Vector<Int> &);
	inline Int getNodeType(UInt local_id) const;

	/// say if a node is a pure ghost node
	inline bool isPureGhostNode(UInt n) const;

	/// say if a node is pur local or master node
	inline bool isLocalOrMasterNode(UInt n) const;

	inline bool isLocalNode(UInt n) const;
	inline bool isMasterNode(UInt n) const;
	inline bool isSlaveNode(UInt n) const;

	AKANTU_GET_MACRO(XMin, lower_bounds[0], Real);
	AKANTU_GET_MACRO(YMin, lower_bounds[1], Real);
	AKANTU_GET_MACRO(ZMin, lower_bounds[2], Real);
	AKANTU_GET_MACRO(XMax, upper_bounds[0], Real);
	AKANTU_GET_MACRO(YMax, upper_bounds[1], Real);
	AKANTU_GET_MACRO(ZMax, upper_bounds[2], Real);

	inline void getLowerBounds(Real * lower) const;
	inline void getUpperBounds(Real * upper) const;

	inline void getLocalLowerBounds(Real * lower) const;
	inline void getLocalUpperBounds(Real * upper) const;

	/// get the number of surfaces
	AKANTU_GET_MACRO(NbSurfaces, nb_surfaces, UInt);

	/// get the connectivity Vector for a given type
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Connectivity, connectivities, UInt);
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Connectivity, connectivities, UInt);
	AKANTU_GET_MACRO(Connectivities, connectivities, const ByElementTypeVector<UInt> &);

	/// @todo take out this set, if mesh can read surface id
	/// set the number of surfaces
	AKANTU_SET_MACRO(NbSurfaces, nb_surfaces, UInt);

	/// get the number of element of a type in the mesh
	inline UInt getNbElement(const ElementType & type, const GhostType & ghost_type = _not_ghost) const;

	// /// get the number of ghost element of a type in the mesh
	// inline UInt getNbGhostElement(const ElementType & type) const;

	/// get the connectivity list either for the elements or the ghost elements
	inline const ConnectivityTypeList & getConnectivityTypeList(const GhostType & ghost_type = _not_ghost) const;

	/// compute the barycenter of a given element
	inline void getBarycenter(UInt element, const ElementType & type, Real * barycenter,
	GhostType ghost_type = _not_ghost) const;

	/// get the element connected to a subelement
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ElementToSubelement, element_to_subelement, Vector<Element>);
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE(ElementToSubelement, element_to_subelement, Vector<Element>);

	/// get the subelement connected to an element
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(SubelementToElement, subelement_to_element, Element);
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE(SubelementToElement, subelement_to_element, Element);

	/// get the surface values of facets
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(SurfaceID, surface_id, UInt);
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE(SurfaceID, surface_id, UInt);

	/// set the int data to the surface id vectors
	void setSurfaceIDsFromIntData(const std::string & data_name);

	inline const Vector<UInt> & getUIntData(const ElementType & el_type,
	const std::string & data_name,
	const GhostType & ghost_type = _not_ghost) const;

	/// get the facet to cohesive element vector
	AKANTU_GET_MACRO(FacetsToCohesiveEl, facets_to_cohesive_el, const Vector<UInt> &);
	AKANTU_GET_MACRO_NOT_CONST(FacetsToCohesiveEl, facets_to_cohesive_el, Vector<UInt> &);

	/* ------------------------------------------------------------------------ */
	/* Wrappers on ElementClass functions */
	/* ------------------------------------------------------------------------ */
	public:
	/// get the number of nodes per element for a given element type
	static inline UInt getNbNodesPerElement(const ElementType & type);

	/// get the number of nodes per element for a given element type considered as
	/// a first order element
	static inline ElementType getP1ElementType(const ElementType & type);

	/// get the kind of the element type
	static inline ElementKind getKind(const ElementType & type);

	/// get spatial dimension of a type of element
	static inline UInt getSpatialDimension(const ElementType & type);

	/// get number of facets of a given element type
	static inline UInt getNbFacetsPerElement(const ElementType & type);

	/// get local connectivity of a facet for a given facet type
	static inline UInt ** getFacetLocalConnectivity(const ElementType & type);

	/// get the type of the surface element associated to a given element
	static inline ElementType getFacetElementType(const ElementType & type);

	/// get the pointer to the list of elements for a given type
	inline Vector<UInt> * getReversedElementsPBCPointer(const ElementType & type);


	/* ------------------------------------------------------------------------ */
	/* Element type Iterator */
	/* ------------------------------------------------------------------------ */
	typedef ByElementTypeUInt::type_iterator type_iterator;

	inline type_iterator firstType(UInt dim = 0,
	GhostType ghost_type = _not_ghost,
	ElementKind kind = _ek_regular) const {
	return connectivities.firstType(dim, ghost_type, kind);
	}

	inline type_iterator lastType(UInt dim = 0,
	GhostType ghost_type = _not_ghost,
	ElementKind kind = _ek_regular) const {
	return connectivities.lastType(dim, ghost_type, kind);
	}

	/* ------------------------------------------------------------------------ */
	/* Private methods for friends */
	/* ------------------------------------------------------------------------ */
	private:
	friend class MeshIOMSH;
	friend class MeshIOMSHStruct;
	friend class MeshIODiana;
	friend class MeshUtils;
	friend class DistributedSynchronizer;

	AKANTU_GET_MACRO(NodesPointer, nodes, Vector<Real> *);

	/// get a pointer to the nodes_global_ids Vector<UInt> and create it if necessary
	inline Vector<UInt> * getNodesGlobalIdsPointer();

	/// get a pointer to the nodes_type Vector<Int> and create it if necessary
	inline Vector<Int> * getNodesTypePointer();

	/// get a pointer to the connectivity Vector for the given type and create it if necessary
	inline Vector<UInt> * getConnectivityPointer(const ElementType & type,
	const GhostType & ghost_type = _not_ghost);

	// inline Vector<Real> * getNormalsPointer(ElementType type) const;

	/// get a pointer to the surface_id Vector for the given type and create it if necessary
	inline Vector<UInt> * getSurfaceIDPointer(const ElementType & type, const GhostType & ghost_type = _not_ghost);

	/// get the UIntDataMap for a given ElementType
	inline UIntDataMap & getUIntDataMap(const ElementType & el_type,
	const GhostType & ghost_type = _not_ghost);

	/// get the IntDataMap pointer (modifyable) for a given ElementType
	inline Vector<UInt> * getUIntDataPointer(const ElementType & el_type,
	const std::string & data_name,
	const GhostType & ghost_type = _not_ghost);

	/// get a pointer to the element_to_subelement Vector for the given type and create it if necessary
	inline Vector<Vector<Element> > * getElementToSubelementPointer(const ElementType & type,
	const GhostType & ghost_type = _not_ghost);

	/// get a pointer to the subelement_to_element Vector for the given type and create it if necessary
	inline Vector<Element > * getSubelementToElementPointer(const ElementType & type,
	const GhostType & ghost_type = _not_ghost);

	/* ------------------------------------------------------------------------ */
	/* Class Members */
	/* ------------------------------------------------------------------------ */
	private:

	/// id of the mesh
	ID id;

	/// array of the nodes coordinates
	Vector<Real> * nodes;

	/// global node ids
	Vector<UInt> * nodes_global_ids;

	/// node type, -3 pure ghost, -2 master for the node, -1 normal node, i in
	/// [0-N] slave node and master is proc i
	Vector<Int> * nodes_type;

	/// global number of nodes;
	UInt nb_global_nodes;

	/// boolean to know if the nodes have to be deleted with the mesh or not
	bool created_nodes;

	/// all class of elements present in this mesh (for heterogenous meshes)
	ByElementTypeUInt connectivities;

	/// map to normals for all class of elements present in this mesh
	ByElementTypeReal normals;

	/// list of all existing types in the mesh
	ConnectivityTypeList type_set;

	/// the spatial dimension of this mesh
	UInt spatial_dimension;

	/// types offsets
	Vector<UInt> types_offsets;

	/// list of all existing types in the mesh
	ConnectivityTypeList ghost_type_set;
	/// ghost types offsets
	Vector<UInt> ghost_types_offsets;

	/// number of surfaces present in this mesh
	UInt nb_surfaces;

	/// surface id of the surface elements in this mesh
	ByElementTypeUInt surface_id;

	/// min of coordinates
	Real lower_bounds[3];
	/// max of coordinates
	Real upper_bounds[3];
	/// size covered by the mesh on each direction
	Real size[3];

	/// local min of coordinates
	Real local_lower_bounds[3];
	/// local max of coordinates
	Real local_upper_bounds[3];

	/// List of elements connected to subelements
	ByElementTypeVector<Vector<Element> > element_to_subelement;

	/// List of subelements connected to elements
	ByElementTypeVector<Element > subelement_to_element;

	/// list of facets connected to each cohesive element
	Vector<UInt> facets_to_cohesive_el;

	// /// list of elements that are reversed due to pbc
	// ByElementTypeUInt reversed_elements_pbc;
	// /// direction in which pbc are to be applied
	// UInt pbc_directions[3];

	/// list of the vectors corresponding to tags in the mesh
	ByElementTypeUIntDataMap uint_data;

	};

	/* -------------------------------------------------------------------------- */
	/* Inline functions */
	/* -------------------------------------------------------------------------- */

	/// standard output stream operator
	inline std::ostream & operator <<(std::ostream & stream, const Element & _this)
	{
	_this.printself(stream);
	return stream;
	}

	#if defined (AKANTU_INCLUDE_INLINE_IMPL)
	# include "mesh_inline_impl.cc"
	#endif

	#include "by_element_type_tmpl.hh"


	/// standard output stream operator
	inline std::ostream & operator <<(std::ostream & stream, const Mesh & _this)
	{
	_this.printself(stream);
	return stream;
	}


	__END_AKANTU__


	#endif /* __AKANTU_MESH_HH__ */

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