mesh.hh
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mesh.hh
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	/**
	* @file mesh.hh
	*
	* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
	* @author Dana Christen <dana.christen@epfl.ch>
	* @author David Simon Kammer <david.kammer@epfl.ch>
	* @author Nicolas Richart <nicolas.richart@epfl.ch>
	* @author Marco Vocialta <marco.vocialta@epfl.ch>
	*
	* @date creation: Fri Jun 18 2010
	* @date last modification: Thu Jan 14 2016
	*
	* @brief the class representing the meshes
	*
	* @section LICENSE
	*
	* Copyright (©) 2010-2012, 2014, 2015 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_config.hh"
	#include "aka_common.hh"
	#include "aka_memory.hh"
	#include "aka_array.hh"
	#include "element_class.hh"
	#include "element_type_map.hh"
	#include "aka_event_handler_manager.hh"
	#include "group_manager.hh"
	#include "element.hh"
	/* -------------------------------------------------------------------------- */
	#include <set>
	/* -------------------------------------------------------------------------- */
	#include "mesh_data.hh"
	#include "dumpable.hh"

	__BEGIN_AKANTU__

	/* -------------------------------------------------------------------------- */
	/* Mesh modifications events */
	/* -------------------------------------------------------------------------- */
	#include "mesh_events.hh"


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

	/**
	* @class Mesh this contain the coordinates of the nodes in the Mesh.nodes
	* Array, 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{.cpp}
	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 Array<UInt> & conn = mesh.getConnectivity(*it);
	for(UInt e = 0; e < nb_element; ++e) {
	...
	}
	}
	@endcode
	*/
	class Mesh : protected Memory,
	public EventHandlerManager<MeshEventHandler>,
	public GroupManager,
	public Dumpable {
	/* ------------------------------------------------------------------------ */
	/* 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,
	const MemoryID & memory_id = 0);

	/**
	* constructor that use an existing nodes coordinates
	* array, by getting the vector of coordinates
	*/
	Mesh(UInt spatial_dimension,
	Array<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();

	#ifdef AKANTU_CORE_CXX11
	/// translate the mesh by the given amount in x[, y[, z]] directions
	template <typename... Args> void translate(Args... params);
	#endif

	/// init a by-element-type real vector with provided ids
	template<typename T>
	void initElementTypeMapArray(ElementTypeMapArray<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
	template<typename T>
	void initElementTypeMapArray(ElementTypeMapArray<T> & v,
	UInt nb_component,
	UInt spatial_dimension,
	GhostType ghost_type,
	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

	template<typename T>
	void initElementTypeMapArray(ElementTypeMapArray<T> & v,
	UInt nb_component,
	UInt spatial_dimension,
	GhostType ghost_type,
	const T & default_value,
	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 Array<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 Array of connectivity for the type <type>.
	inline void addConnectivityType(const ElementType & type,
	const GhostType & ghost_type = _not_ghost);

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

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

	/// initialize normals
	void initNormals();

	/// init facets' mesh
	Mesh & initMeshFacets(const ID & id = "mesh_facets");

	/// define parent mesh
	void defineMeshParent(const Mesh & mesh);

	/// get global connectivity array
	void getGlobalConnectivity(ElementTypeMapArray<UInt> & global_connectivity,
	UInt dimension,
	GhostType ghost_type);

	/* ------------------------------------------------------------------------ */
	/* Accessors */
	/* ------------------------------------------------------------------------ */
	public:
	/// get the id of the mesh
	AKANTU_GET_MACRO(ID, Memory::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 Array aka coordinates
	AKANTU_GET_MACRO(Nodes, *nodes, const Array<Real> &);
	AKANTU_GET_MACRO_NOT_CONST(Nodes, *nodes, Array<Real> &);

	/// get the normals for the elements
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Normals, normals, Real);

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

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

	protected:
	AKANTU_GET_MACRO_NOT_CONST(NodesType, nodes_type, Array<Int> &);
	public:
	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(LowerBounds, lower_bounds, const Vector<Real> &);
	AKANTU_GET_MACRO(UpperBounds, upper_bounds, const Vector<Real> &);
	AKANTU_GET_MACRO(LocalLowerBounds, local_lower_bounds, const Vector<Real> &);
	AKANTU_GET_MACRO(LocalUpperBounds, local_upper_bounds, const Vector<Real> &);

	/// get the connectivity Array 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 ElementTypeMapArray<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 element for a given ghost_type and a given dimension
	inline UInt getNbElement(const UInt spatial_dimension = _all_dimensions,
	const GhostType & ghost_type = _not_ghost,
	const ElementKind & kind = _ek_not_defined) 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;
	inline void getBarycenter(const Element & element, Vector<Real> & barycenter) const;

	/// get the element connected to a subelement
	const Array< std::vector<Element> > & getElementToSubelement(const ElementType & el_type,
	const GhostType & ghost_type = _not_ghost) const;
	/// get the element connected to a subelement
	Array< std::vector<Element> > & getElementToSubelement(const ElementType & el_type,
	const GhostType & ghost_type = _not_ghost);

	/// get the subelement connected to an element
	const Array<Element> & getSubelementToElement(const ElementType & el_type,
	const GhostType & ghost_type = _not_ghost) const;
	/// get the subelement connected to an element
	Array<Element> & getSubelementToElement(const ElementType & el_type,
	const GhostType & ghost_type = _not_ghost);

	/// get a name field associated to the mesh
	template<typename T>
	inline const Array<T> & getData(const std::string & data_name,
	const ElementType & el_type,
	const GhostType & ghost_type = _not_ghost) const;

	/// get a name field associated to the mesh
	template<typename T>
	inline Array<T> & getData(const std::string & data_name,
	const ElementType & el_type,
	const GhostType & ghost_type = _not_ghost);

	/// register a new ElementalTypeMap in the MeshData
	template<typename T>
	inline ElementTypeMapArray<T> & registerData(const std::string & data_name);

	/// get a name field associated to the mesh
	template<typename T>
	inline const ElementTypeMapArray<T> & getData(const std::string & data_name) const;

	/// get a name field associated to the mesh
	template<typename T>
	inline ElementTypeMapArray<T> & getData(const std::string & data_name);


	template <typename T>
	ElementTypeMap<UInt> getNbDataPerElem(ElementTypeMapArray<T> & array,
	const ElementKind & element_kind);

	template <typename T>
	dumper::Field * createFieldFromAttachedData(const std::string & field_id,
	const std::string & group_name,
	const ElementKind & element_kind);

	/// templated getter returning the pointer to data in MeshData (modifiable)
	template<typename T>
	inline Array<T> * getDataPointer(const std::string & data_name,
	const ElementType & el_type,
	const GhostType & ghost_type = _not_ghost,
	UInt nb_component = 1,
	bool size_to_nb_element = true,
	bool resize_with_parent = false);

	/// Facets mesh accessor
	AKANTU_GET_MACRO(MeshFacets, *mesh_facets, const Mesh &);
	AKANTU_GET_MACRO_NOT_CONST(MeshFacets, *mesh_facets, Mesh &);

	/// Parent mesh accessor
	AKANTU_GET_MACRO(MeshParent, *mesh_parent, const Mesh &);

	inline bool isMeshFacets() const { return this->is_mesh_facets; }

	/// defines is the mesh is distributed or not
	inline bool isDistributed() const { return this->is_distributed; }

	#ifndef SWIG
	/// return the dumper from a group and and a dumper name
	DumperIOHelper & getGroupDumper(const std::string & dumper_name,
	const std::string & group_name);
	#endif
	/* ------------------------------------------------------------------------ */
	/* 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 number of facets of a given element type
	static inline UInt getNbFacetsPerElement(const ElementType & type, UInt t);

	/// get local connectivity of a facet for a given facet type
	static inline MatrixProxy<UInt> getFacetLocalConnectivity(const ElementType & type, UInt t = 0);

	/// get connectivity of facets for a given element
	inline Matrix<UInt> getFacetConnectivity(const Element & element, UInt t = 0) const;

	/// get the number of type of the surface element associated to a given element type
	static inline UInt getNbFacetTypes(const ElementType & type, UInt t = 0);

	/// get the type of the surface element associated to a given element
	static inline ElementType getFacetType(const ElementType & type, UInt t = 0);

	/// get all the type of the surface element associated to a given element
	static inline VectorProxy<ElementType> getAllFacetTypes(const ElementType & type);

	/// get the number of nodes in the given element list
	static inline UInt getNbNodesPerElementList(const Array<Element> & elements);

	/* ------------------------------------------------------------------------ */
	/* Element type Iterator */
	/* ------------------------------------------------------------------------ */
	typedef ElementTypeMapArray<UInt, ElementType>::type_iterator type_iterator;

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

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

	/* ------------------------------------------------------------------------ */
	/* Private methods for friends */
	/* ------------------------------------------------------------------------ */
	private:
	friend class MeshAccessor;

	friend class MeshIOMSH;
	friend class MeshIOMSHStruct;
	friend class MeshIODiana;
	friend class MeshUtils;
	friend class DistributedSynchronizer;
	template<class T> friend class SpatialGrid;

	#if defined(AKANTU_COHESIVE_ELEMENT)
	friend class CohesiveElementInserter;
	#endif

	#if defined(AKANTU_IGFEM)
	template<UInt dim> friend class MeshIgfemSphericalGrowingGel;
	#endif

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

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

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

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



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

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

	AKANTU_GET_MACRO_NOT_CONST(MeshData, mesh_data, MeshData &);

	/* ------------------------------------------------------------------------ */
	/* Class Members */
	/* ------------------------------------------------------------------------ */
	private:
	/// array of the nodes coordinates
	Array<Real> * nodes;

	/// global node ids
	Array<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
	Array<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)
	ElementTypeMapArray<UInt> connectivities;

	/// map to normals for all class of elements present in this mesh
	ElementTypeMapArray<Real> normals;

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

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

	/// types offsets
	Array<UInt> types_offsets;

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

	/// min of coordinates
	Vector<Real> lower_bounds;
	/// max of coordinates
	Vector<Real> upper_bounds;
	/// size covered by the mesh on each direction
	Vector<Real> size;

	/// local min of coordinates
	Vector<Real> local_lower_bounds;
	/// local max of coordinates
	Vector<Real> local_upper_bounds;

	/// Extra data loaded from the mesh file
	MeshData mesh_data;

	/// facets' mesh
	Mesh * mesh_facets;

	/// parent mesh (this is set for mesh_facets meshes)
	const Mesh * mesh_parent;

	/// defines if current mesh is mesh_facets or not
	bool is_mesh_facets;

	/// defines if the mesh is centralized or distributed
	bool is_distributed;
	};


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


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

	__END_AKANTU__


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

	#include "mesh_inline_impl.cc"
	#include "element_type_map_tmpl.hh"
	//#include "group_manager_inline_impl.cc"
	//#include "element_group_inline_impl.cc"

	#endif /* __AKANTU_MESH_HH__ */

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