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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_array.hh"
			#include "aka_event_handler_manager.hh"
			#include "aka_memory.hh"
			#include "dumpable.hh"
			#include "element.hh"
			#include "element_class.hh"
			#include "element_type_map.hh"
			#include "group_manager.hh"
			#include "mesh_data.hh"
			#include "mesh_events.hh"
			/* -------------------------------------------------------------------------- */
			#include <set>
			/* -------------------------------------------------------------------------- */

			namespace akantu {
			class StaticCommunicator;
			class ElementSynchronizer;
			class NodeSynchronizer;
			} // akantu

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			/* 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.
			*
			* 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 */
			/* ------------------------------------------------------------------------ */
			private:
			/// default constructor used for chaining, the last parameter is just to
			/// differentiate constructors
			Mesh(UInt spatial_dimension, const ID & id,
			const MemoryID & memory_id, StaticCommunicator & communicator);

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

			/// mesh not distributed and not using the default communicator
			Mesh(UInt spatial_dimension, StaticCommunicator & communicator,
			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:
			/// patitionate the mesh among the processors involved in their computation
			virtual void distribute(StaticCommunicator & communicator);
			virtual void distribute();

			/// 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 id of the mesh
			AKANTU_GET_MACRO(MemoryID, Memory::memory_id, const MemoryID &);

			/// 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 id of a node
			inline UInt getNodeLocalId(UInt global_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<NodeType> &);

			protected:
			AKANTU_GET_MACRO_NOT_CONST(NodesType, nodes_type, Array<NodeType> &);

			public:
			inline NodeType 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
			inline const Mesh & getMeshFacets() const;
			inline Mesh & getMeshFacets();

			/// Parent mesh accessor
			inline const Mesh & getMeshParent() const;

			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);
			}

			AKANTU_GET_MACRO(ElementSynchronizer, *element_synchronizer,
			const ElementSynchronizer &);
			AKANTU_GET_MACRO(NodeSynchronizer, *node_synchronizer,
			const NodeSynchronizer &);

			//AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, StaticCommunicator &);
			AKANTU_GET_MACRO(Communicator, *communicator, const StaticCommunicator &);
			/* ------------------------------------------------------------------------ */
			/* Private methods for friends */
			/* ------------------------------------------------------------------------ */
			private:
			friend class MeshAccessor;

			//#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<NodeType> * 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<NodeType> 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;

			/// Communicator on which mesh is distributed
			StaticCommunicator * communicator;

			/// Element synchronizer
			ElementSynchronizer * element_synchronizer;

			/// Node synchronizer
			NodeSynchronizer * node_synchronizer;
			};

			/// 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;
			}

			} // akantu

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

			#include "element_type_map_tmpl.hh"
			#include "mesh_inline_impl.cc"

			#endif /* __AKANTU_MESH_HH__ */

rAKA/src/mesh/mesh.hh0035fcd74950bugfixes/39-the-python…

mesh.hhView Options

rAKA/src/mesh/mesh.hh
0035fcd74950bugfixes/39-the-python…

mesh.hh
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