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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 Nov 12 2020
*
* @brief the class representing the meshes
*
*
* @section LICENSE
*
* Copyright (©) 2010-2021 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_bbox.hh"
#include "aka_event_handler_manager.hh"
#include "communicator.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 <functional>
#include <set>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer;
class NodeSynchronizer;
class PeriodicNodeSynchronizer;
class MeshGlobalDataUpdater;
} // namespace akantu
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(communicator);
DECLARE_NAMED_ARGUMENT(edge_weight_function);
DECLARE_NAMED_ARGUMENT(vertex_weight_function);
} // namespace
/* -------------------------------------------------------------------------- */
/* Mesh */
/* -------------------------------------------------------------------------- */
/**
* @class Mesh mesh.hh
*
* This class contaisn the coordinates of the nodes in the Mesh.nodes
* akant::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}
for(auto & type : mesh.elementTypes()) {
Int nb_element = mesh.getNbElement(type);
const auto & conn = mesh.getConnectivity(type);
for(Int e = 0; e < nb_element; ++e) {
...
}
}
or
for_each_element(mesh, [](Element & element) {
std::cout << element << std::endl
});
@endcode
*/
class Mesh : public EventHandlerManager<MeshEventHandler>,
public GroupManager,
public MeshData,
public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
/// default constructor used for chaining, the last parameter is just to
/// differentiate constructors
Mesh(Int spatial_dimension, const ID & id, Communicator & communicator);
public:
/// constructor that create nodes coordinates array
Mesh(Int spatial_dimension, const ID & id = "mesh");
/// mesh not distributed and not using the default communicator
Mesh(Int spatial_dimension, Communicator & communicator,
const ID & id = "mesh");
/**
* constructor that use an existing nodes coordinates
* array, by getting the vector of coordinates
*/
Mesh(Int spatial_dimension, const std::shared_ptr<Array<Real>> & nodes,
const ID & id = "mesh");
~Mesh() override;
/// 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);
protected:
void makeReady();
private:
/// initialize the connectivity to NULL and other stuff
void init();
/// function that computes the bounding box (fills xmin, xmax)
void computeBoundingBox();
/* ------------------------------------------------------------------------ */
/* Distributed memory methods and accessors */
/* ------------------------------------------------------------------------ */
public:
protected:
/// patitionate the mesh among the processors involved in their computation
virtual void distributeImpl(
Communicator & communicator,
const std::function<Int(const Element &, const Element &)> &
edge_weight_function,
const std::function<Int(const Element &)> & vertex_weight_function);
public:
/// with the arguments to pass to the partitionner
template <typename... pack>
std::enable_if_t<are_named_argument<pack...>::value>
distribute(pack &&... _pack) {
distributeImpl(
OPTIONAL_NAMED_ARG(communicator, Communicator::getStaticCommunicator()),
OPTIONAL_NAMED_ARG(edge_weight_function,
[](auto &&, auto &&) { return 1; }),
OPTIONAL_NAMED_ARG(vertex_weight_function, [](auto &&) { return 1; }));
}
/// defines is the mesh is distributed or not
inline bool isDistributed() const { return this->is_distributed; }
/* ------------------------------------------------------------------------ */
/* Periodicity methods and accessors */
/* ------------------------------------------------------------------------ */
public:
/// set the periodicity in a given direction
void makePeriodic(const SpatialDirection & direction);
void makePeriodic(const SpatialDirection & direction, const ID & list_1,
const ID & list_2);
protected:
void makePeriodic(const SpatialDirection & direction,
const Array<Idx> & list_1, const Array<Idx> & list_2);
/// Removes the face that the mesh is periodic
void wipePeriodicInfo();
inline void addPeriodicSlave(Idx slave, Idx master);
template <typename T>
void synchronizePeriodicSlaveDataWithMaster(Array<T> & data);
// update the periodic synchronizer (creates it if it does not exists)
void updatePeriodicSynchronizer();
public:
/// defines if the mesh is periodic or not
inline bool isPeriodic() const { return this->is_periodic; }
inline bool isPeriodic(const SpatialDirection & /*direction*/) const {
return this->is_periodic;
}
class PeriodicSlaves;
/// get the master node for a given slave nodes, except if node not a slave
inline Idx getPeriodicMaster(Idx slave) const;
/// get an iterable list of slaves for a given master node
inline decltype(auto) getPeriodicSlaves(Idx master) const;
/* ------------------------------------------------------------------------ */
/* General Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// extract coordinates of nodes from an element
template <typename T>
inline void extractNodalValuesFromElement(const Array<T> & nodal_values,
T * elemental_values,
Idx * connectivity, Int n_nodes,
Int nb_degree_of_freedom) const;
/// add a Array of connectivity for the given ElementType and GhostType .
inline void addConnectivityType(ElementType type,
GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
template <class Event> inline void sendEvent(Event & event) {
// if(event.getList().size() != 0)
EventHandlerManager<MeshEventHandler>::sendEvent<Event>(event);
}
/// prepare the event to remove the elements listed
void eraseElements(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
template <typename T>
inline void removeNodesFromArray(Array<T> & vect,
const Array<Int> & new_numbering);
/// 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<Int> & global_connectivity);
public:
void getAssociatedElements(const Array<Int> & node_list,
Array<Element> & elements);
void getAssociatedElements(const Idx & node, Array<Element> & elements) const;
public:
/// fills the nodes_to_elements for given dimension elements
void fillNodesToElements(Int dimension = _all_dimensions);
private:
/// update the global ids, nodes type, ...
std::tuple<Int, Int> updateGlobalData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event);
void registerGlobalDataUpdater(
std::unique_ptr<MeshGlobalDataUpdater> && global_data_updater);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the id of the mesh
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, Int);
/// 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 number of nodes
auto getNbNodes() const { return nodes->size(); }
/// get the Array of global ids of the nodes (only used in parallel)
AKANTU_GET_MACRO_AUTO(GlobalNodesIds, *nodes_global_ids);
// AKANTU_GET_MACRO_NOT_CONST(GlobalNodesIds, *nodes_global_ids, Array<UInt>
// &);
/// get the global id of a node
inline auto getNodeGlobalId(Idx local_id) const;
/// get the global id of a node
inline auto getNodeLocalId(Idx global_id) const;
/// get the global number of nodes
inline auto getNbGlobalNodes() const;
/// get the nodes type Array
AKANTU_GET_MACRO(NodesFlags, *nodes_flags, const Array<NodeFlag> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(NodesFlags, *nodes_flags, Array<NodeFlag> &);
public:
inline NodeFlag getNodeFlag(Idx local_id) const;
inline auto getNodePrank(Idx local_id) const;
/// say if a node is a pure ghost node
inline bool isPureGhostNode(Idx n) const;
/// say if a node is pur local or master node
inline bool isLocalOrMasterNode(Idx n) const;
inline bool isLocalNode(Idx n) const;
inline bool isMasterNode(Idx n) const;
inline bool isSlaveNode(Idx n) const;
inline bool isPeriodicSlave(Idx n) const;
inline bool isPeriodicMaster(Idx n) const;
const Vector<Real> & getLowerBounds() const { return bbox.getLowerBounds(); }
const Vector<Real> & getUpperBounds() const { return bbox.getUpperBounds(); }
AKANTU_GET_MACRO(BBox, bbox, const BBox &);
const Vector<Real> & getLocalLowerBounds() const {
return bbox_local.getLowerBounds();
}
const Vector<Real> & getLocalUpperBounds() const {
return bbox_local.getUpperBounds();
}
AKANTU_GET_MACRO(LocalBBox, bbox_local, const BBox &);
/// get the connectivity Array for a given type
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Connectivity, connectivities, Idx);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Connectivity, connectivities, Idx);
AKANTU_GET_MACRO(Connectivities, connectivities,
const ElementTypeMapArray<Idx> &);
/// get the number of element of a type in the mesh
inline auto getNbElement(ElementType type,
GhostType ghost_type = _not_ghost) const;
/// get the number of element for a given ghost_type and a given dimension
inline auto getNbElement(const Int spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
/// compute the barycenter of a given element
template <class D, std::enable_if_t<aka::is_vector<D>::value> * = nullptr>
inline void getBarycenter(const Element & element,
Eigen::MatrixBase<D> & barycenter) const;
void getBarycenters(Array<Real> & barycenter, ElementType type,
GhostType ghost_type) const;
/// get the element connected to a subelement (element of lower dimension)
decltype(auto) getElementToSubelement() const;
/// get the element connected to a subelement
const auto & getElementToSubelement(ElementType el_type,
GhostType ghost_type = _not_ghost) const;
/// get the elements connected to a subelement
decltype(auto) getElementToSubelement(const Element & element) const;
/// get the subelement (element of lower dimension) connected to a element
decltype(auto) getSubelementToElement() const;
/// get the subelement connected to an element
const auto & getSubelementToElement(ElementType el_type,
GhostType ghost_type = _not_ghost) const;
/// get the subelement (element of lower dimension) connected to a element
decltype(auto) getSubelementToElement(const Element & element) const;
/// get connectivity of a given element
inline decltype(auto) getConnectivity(const Element & element) const;
inline decltype(auto)
getConnectivityWithPeriodicity(const Element & element) const;
protected:
/// get the element connected to a subelement (element of lower dimension)
auto & getElementToSubelementNC();
auto & getSubelementToElementNC();
inline auto & getElementToSubelementNC(const Element & element);
inline decltype(auto) getSubelementToElementNC(const Element & element) const;
/// get the element connected to a subelement
auto & getElementToSubelementNC(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// get the subelement connected to an element
auto & getSubelementToElementNC(ElementType el_type,
GhostType ghost_type = _not_ghost);
inline decltype(auto) getConnectivityNC(const Element & element);
public:
/// get a name field associated to the mesh
template <typename T>
inline decltype(auto) getData(const ID & data_name, ElementType el_type,
GhostType ghost_type = _not_ghost) const;
/// get a name field associated to the mesh
template <typename T>
inline decltype(auto) getData(const ID & data_name, ElementType el_type,
GhostType ghost_type = _not_ghost);
/// get a name field associated to the mesh
template <typename T>
inline decltype(auto) getData(const ID & data_name) const;
/// get a name field associated to the mesh
template <typename T> inline decltype(auto) getData(const ID & data_name);
template <typename T>
auto getNbDataPerElem(ElementTypeMapArray<T> & array) -> ElementTypeMap<Int>;
template <typename T>
std::shared_ptr<dumpers::Field>
createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
ElementKind element_kind);
/// templated getter returning the pointer to data in MeshData (modifiable)
template <typename T>
inline decltype(auto)
getDataPointer(const std::string & data_name, ElementType el_type,
GhostType ghost_type = _not_ghost, Int nb_component = 1,
bool size_to_nb_element = true,
bool resize_with_parent = false);
template <typename T>
inline decltype(auto)
getDataPointer(const ID & data_name, ElementType el_type,
GhostType ghost_type, Int nb_component,
bool size_to_nb_element, bool resize_with_parent,
const T & defaul_);
/// Facets mesh accessor
inline auto getMeshFacets() const -> const Mesh &;
inline auto getMeshFacets() -> Mesh &;
inline auto hasMeshFacets() const { return mesh_facets != nullptr; }
/// Parent mesh accessor
inline auto getMeshParent() const -> const Mesh &;
inline auto isMeshFacets() const { return this->is_mesh_facets; }
/// return the dumper from a group and and a dumper name
auto getGroupDumper(const std::string & dumper_name,
const std::string & group_name) -> DumperIOHelper &;
/* ------------------------------------------------------------------------ */
/* Wrappers on ElementClass functions */
/* ------------------------------------------------------------------------ */
public:
/// get the number of nodes per element for a given element type
static inline constexpr auto getNbNodesPerElement(ElementType type) -> Int;
/// get the number of nodes per element for a given element type considered as
/// a first order element
static inline constexpr auto getP1ElementType(ElementType type)
-> ElementType;
/// get the kind of the element type
static inline constexpr auto getKind(ElementType type) -> ElementKind;
/// get spatial dimension of a type of element
static inline constexpr auto getSpatialDimension(ElementType type) -> Int;
/// get the natural space dimension of a type of element
static inline constexpr auto getNaturalSpaceDimension(ElementType type)
-> Int;
/// get number of facets of a given element type
static inline constexpr auto getNbFacetsPerElement(ElementType type) -> Int;
/// get number of facets of a given element type
static inline constexpr auto getNbFacetsPerElement(ElementType type, Idx t)
-> Int;
/// get local connectivity of a facet for a given facet type
static inline decltype(auto) getFacetLocalConnectivity(ElementType type,
Idx t = 0);
/// get connectivity of facets for a given element
inline auto getFacetConnectivity(const Element & element, Idx t = 0) const
-> Matrix<Idx>;
/// get the number of type of the surface element associated to a given
/// element type
static inline constexpr auto getNbFacetTypes(ElementType type, Idx t = 0)
-> Int;
/// get the type of the surface element associated to a given element
static inline constexpr auto getFacetType(ElementType type, Idx t = 0)
-> ElementType;
/// get all the type of the surface element associated to a given element
static inline decltype(auto) getAllFacetTypes(ElementType type);
/// get the number of nodes in the given element list
static inline auto getNbNodesPerElementList(const Array<Element> & elements)
-> Int;
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
using type_iterator [[deprecated]] =
ElementTypeMapArray<Idx, ElementType>::type_iterator;
using ElementTypesIteratorHelper =
ElementTypeMapArray<Idx, ElementType>::ElementTypesIteratorHelper;
template <typename... pack>
auto elementTypes(pack &&... _pack) const -> ElementTypesIteratorHelper;
[[deprecated("Use elementTypes instead")]] inline decltype(auto)
firstType(Int dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.elementTypes(dim, ghost_type, kind).begin();
}
[[deprecated("Use elementTypes instead")]] inline decltype(auto)
lastType(Int dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.elementTypes(dim, ghost_type, kind).end();
}
AKANTU_GET_MACRO_DEREF_PTR(ElementSynchronizer, element_synchronizer);
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(ElementSynchronizer,
element_synchronizer);
AKANTU_GET_MACRO_DEREF_PTR(NodeSynchronizer, node_synchronizer);
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(NodeSynchronizer, node_synchronizer);
AKANTU_GET_MACRO_DEREF_PTR(PeriodicNodeSynchronizer,
periodic_node_synchronizer);
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(PeriodicNodeSynchronizer,
periodic_node_synchronizer);
// AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, StaticCommunicator
// &);
AKANTU_GET_MACRO_DEREF_PTR(Communicator, communicator);
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Communicator, communicator);
AKANTU_GET_MACRO_AUTO(PeriodicMasterSlaves, periodic_master_slave);
/* ------------------------------------------------------------------------ */
/* Private methods for friends */
/* ------------------------------------------------------------------------ */
private:
friend class MeshAccessor;
friend class MeshUtils;
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(NodesPointer, nodes);
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline auto getNodesGlobalIdsPointer() -> Array<Idx> &;
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline auto getNodesFlagsPointer() -> Array<NodeFlag> &;
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
inline auto getConnectivityPointer(ElementType type,
GhostType ghost_type = _not_ghost)
-> Array<Idx> &;
/// get the ghost element counter
inline auto getGhostsCounters(ElementType type, GhostType ghost_type = _ghost)
-> Array<Idx> & {
AKANTU_DEBUG_ASSERT(ghost_type != _not_ghost,
"No ghost counter for _not_ghost elements");
return ghosts_counters(type, ghost_type);
}
/// get a pointer to the element_to_subelement Array for the given type and
/// create it if necessary
inline decltype(auto)
getElementToSubelementPointer(ElementType type,
GhostType ghost_type = _not_ghost);
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
inline decltype(auto)
getSubelementToElementPointer(ElementType type,
GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
ID id;
/// array of the nodes coordinates
std::shared_ptr<Array<Real>> nodes;
/// global node ids
std::shared_ptr<Array<Idx>> nodes_global_ids;
/// node flags (shared/periodic/...)
std::shared_ptr<Array<NodeFlag>> nodes_flags;
/// processor handling the node when not local or master
std::unordered_map<Idx, Int> nodes_prank;
/// global number of nodes;
Int nb_global_nodes{0};
/// all class of elements present in this mesh (for heterogenous meshes)
ElementTypeMapArray<Idx> connectivities;
/// count the references on ghost elements
ElementTypeMapArray<Idx> ghosts_counters;
/// the spatial dimension of this mesh
Idx spatial_dimension{0};
/// size covered by the mesh on each direction
Vector<Real> size;
/// global bounding box
BBox bbox;
/// local bounding box
BBox bbox_local;
/// 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};
/// defines if the mesh is periodic
bool is_periodic{false};
/// Communicator on which mesh is distributed
Communicator * communicator;
/// Element synchronizer
std::unique_ptr<ElementSynchronizer> element_synchronizer;
/// Node synchronizer
std::unique_ptr<NodeSynchronizer> node_synchronizer;
/// Node synchronizer for periodic nodes
std::unique_ptr<PeriodicNodeSynchronizer> periodic_node_synchronizer;
using NodesToElements = std::vector<std::unique_ptr<std::set<Element>>>;
/// class to update global data using external knowledge
std::unique_ptr<MeshGlobalDataUpdater> global_data_updater;
/// This info is stored to simplify the dynamic changes
NodesToElements nodes_to_elements;
/// periodicity local info
std::unordered_map<Idx, Idx> periodic_slave_master;
std::unordered_multimap<Idx, Idx> periodic_master_slave;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Mesh & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
inline constexpr auto Mesh::getNbNodesPerElement(ElementType type) -> Int {
Int nb_nodes_per_element = 0;
#define GET_NB_NODES_PER_ELEMENT(type) \
nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH_CONSTEXPR(GET_NB_NODES_PER_ELEMENT);
#undef GET_NB_NODES_PER_ELEMENT
return nb_nodes_per_element;
}
/* -------------------------------------------------------------------------- */
inline auto Mesh::getNbElement(ElementType type, GhostType ghost_type) const {
try {
const auto & conn = connectivities(type, ghost_type);
return conn.size();
} catch (...) {
return 0;
}
}
/* -------------------------------------------------------------------------- */
inline auto Mesh::getNbElement(const Int spatial_dimension,
GhostType ghost_type, ElementKind kind) const {
AKANTU_DEBUG_ASSERT(spatial_dimension <= 3 || spatial_dimension == Int(-1),
"spatial_dimension is " << spatial_dimension
<< " and is greater than 3 !");
Int nb_element = 0;
for (auto type : elementTypes(spatial_dimension, ghost_type, kind))
nb_element += getNbElement(type, ghost_type);
return nb_element;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
#include "element_type_map_tmpl.hh"
#include "mesh_inline_impl.hh"
#endif /* AKANTU_MESH_HH_ */
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