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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;
} // namespace 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, std::shared_ptr<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();
/// function that computes the bounding box (fills xmin, xmax)
void computeBoundingBox();
/* ------------------------------------------------------------------------ */
/* 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;
/// 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().size() != 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);
public:
void getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements);
private:
/// fills the nodes_to_elements structure
void fillNodesToElements();
/* ------------------------------------------------------------------------ */
/* 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->size(), 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 */
/* ------------------------------------------------------------------------ */
using type_iterator = ElementTypeMapArray<UInt, ElementType>::type_iterator;
using ElementTypesIteratorHelper =
ElementTypeMapArray<UInt, ElementType>::ElementTypesIteratorHelper;
inline ElementTypesIteratorHelper
elementTypes(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.elementTypes(dim, ghost_type, kind);
}
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_NOT_CONST(ElementSynchronizer, *element_synchronizer,
ElementSynchronizer &);
AKANTU_GET_MACRO(NodeSynchronizer, *node_synchronizer,
const NodeSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(NodeSynchronizer, *node_synchronizer,
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
std::shared_ptr<Array<Real>> nodes;
/// global node ids
std::unique_ptr<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{0};
/// 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{0};
/// 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
std::unique_ptr<Mesh> mesh_facets;
/// parent mesh (this is set for mesh_facets meshes)
const Mesh * mesh_parent{nullptr};
/// defines if current mesh is mesh_facets or not
bool is_mesh_facets{false};
/// defines if the mesh is centralized or distributed
bool is_distributed{false};
/// Communicator on which mesh is distributed
const StaticCommunicator * communicator;
/// Element synchronizer
std::unique_ptr<ElementSynchronizer> element_synchronizer;
/// Node synchronizer
std::unique_ptr<NodeSynchronizer> node_synchronizer;
using NodesToElements = std::vector<std::unique_ptr<std::set<Element>>>;
/// This info is stored to simplify the dynamic changes
NodesToElements nodes_to_elements;
};
/// 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;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
#include "element_type_map_tmpl.hh"
#include "mesh_inline_impl.cc"
#endif /* __AKANTU_MESH_HH__ */
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