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mesh_inline_impl.cc
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/**
* @file mesh_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jul 15 2010
* @date last modification: Thu Jan 21 2016
*
* @brief Implementation of the inline functions of the mesh class
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "cohesive_element.hh"
#endif
#ifndef __AKANTU_MESH_INLINE_IMPL_CC__
#define __AKANTU_MESH_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline RemovedNodesEvent::RemovedNodesEvent(const Mesh & mesh)
: new_numbering(mesh.getNbNodes(), 1, "new_numbering") {}
/* -------------------------------------------------------------------------- */
inline RemovedElementsEvent::RemovedElementsEvent(const Mesh & mesh,
ID new_numbering_id)
: new_numbering(new_numbering_id, mesh.getID(), mesh.getMemoryID()) {}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<NewElementsEvent>(NewElementsEvent & event) {
this->nodes_to_elements.resize(nodes->size());
for (const auto & elem : event.getList()) {
const Array<UInt> & conn = connectivities(elem.type, elem.ghost_type);
UInt nb_nodes_per_elem = this->getNbNodesPerElement(elem.type);
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = conn(elem.element, n);
if (not nodes_to_elements[node])
nodes_to_elements[node] = std::make_unique<std::set<Element>>();
nodes_to_elements[node]->insert(elem);
}
}
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <> inline void Mesh::sendEvent<NewNodesEvent>(NewNodesEvent & event) {
this->computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
Mesh::sendEvent<RemovedElementsEvent>(RemovedElementsEvent & event) {
this->connectivities.onElementsRemoved(event.getNewNumbering());
this->fillNodesToElements();
this->computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<RemovedNodesEvent>(RemovedNodesEvent & event) {
const auto & new_numbering = event.getNewNumbering();
this->removeNodesFromArray(*nodes, new_numbering);
if (nodes_global_ids)
this->removeNodesFromArray(*nodes_global_ids, new_numbering);
if (nodes_type.size() != 0)
this->removeNodesFromArray(nodes_type, new_numbering);
if (not nodes_to_elements.empty()) {
std::vector<std::unique_ptr<std::set<Element>>> tmp(
nodes_to_elements.size());
auto it = nodes_to_elements.begin();
UInt new_nb_nodes = 0;
for (auto new_i : new_numbering) {
if (new_i != UInt(-1)) {
tmp[new_i] = std::move(*it);
++new_nb_nodes;
}
++it;
}
tmp.resize(new_nb_nodes);
std::move(tmp.begin(), tmp.end(), nodes_to_elements.begin());
}
computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering) {
Array<T> tmp(vect.size(), vect.getNbComponent());
UInt nb_component = vect.getNbComponent();
UInt new_nb_nodes = 0;
for (UInt i = 0; i < new_numbering.size(); ++i) {
UInt new_i = new_numbering(i);
if (new_i != UInt(-1)) {
T * to_copy = vect.storage() + i * nb_component;
std::uninitialized_copy(to_copy, to_copy + nb_component,
tmp.storage() + new_i * nb_component);
++new_nb_nodes;
}
}
tmp.resize(new_nb_nodes);
vect.copy(tmp);
}
/* -------------------------------------------------------------------------- */
// inline UInt Mesh::elementToLinearized(const Element & elem) const {
// AKANTU_DEBUG_ASSERT(elem.type < _max_element_type &&
// elem.element < types_offsets.storage()[elem.type +
// 1],
// "The element " << elem << "does not exists in the mesh
// "
// << getID());
// return types_offsets.storage()[elem.type] + elem.element;
// }
// /* --------------------------------------------------------------------------
// */ inline Element Mesh::linearizedToElement(UInt linearized_element) const {
// UInt t;
// for (t = _not_defined;
// t != _max_element_type && linearized_element >= types_offsets(t); ++t)
// ;
// AKANTU_DEBUG_ASSERT(linearized_element < types_offsets(t),
// "The linearized element "
// << linearized_element
// << "does not exists in the mesh " << getID());
// --t;
// ElementType type = ElementType(t);
// return Element(type, linearized_element - types_offsets.storage()[t],
// _not_ghost, getKind(type));
// }
// /* --------------------------------------------------------------------------
// */ inline void Mesh::updateTypesOffsets(const GhostType & ghost_type) {
// Array<UInt> * types_offsets_ptr = &this->types_offsets;
// if (ghost_type == _ghost)
// types_offsets_ptr = &this->ghost_types_offsets;
// Array<UInt> & types_offsets = *types_offsets_ptr;
// types_offsets.clear();
// for (auto type : elementTypes(_all_dimensions, ghost_type,
// _ek_not_defined))
// types_offsets(type) = connectivities(type, ghost_type).size();
// for (UInt t = _not_defined + 1; t < _max_element_type; ++t)
// types_offsets(t) += types_offsets(t - 1);
// for (UInt t = _max_element_type; t > _not_defined; --t)
// types_offsets(t) = types_offsets(t - 1);
// types_offsets(0) = 0;
// }
// /* --------------------------------------------------------------------------
// */ inline const Mesh::ConnectivityTypeList &
// Mesh::getConnectivityTypeList(const GhostType & ghost_type) const {
// if (ghost_type == _not_ghost)
// return type_set;
// else
// return ghost_type_set;
// }
/* -------------------------------------------------------------------------- */
inline Array<UInt> & Mesh::getNodesGlobalIdsPointer() {
AKANTU_DEBUG_IN();
if (not nodes_global_ids) {
nodes_global_ids = std::make_unique<Array<UInt>>(
nodes->size(), 1, getID() + ":nodes_global_ids");
for (auto && global_ids : counting(*nodes_global_ids)) {
std::get<1>(global_ids) = std::get<0>(global_ids);
}
}
AKANTU_DEBUG_OUT();
return *nodes_global_ids;
}
/* -------------------------------------------------------------------------- */
inline Array<NodeType> & Mesh::getNodesTypePointer() {
AKANTU_DEBUG_IN();
if (nodes_type.size() == 0) {
nodes_type.resize(nodes->size());
nodes_type.set(_nt_normal);
}
AKANTU_DEBUG_OUT();
return nodes_type;
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> &
Mesh::getConnectivityPointer(const ElementType & type,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> * tmp;
if (!connectivities.exists(type, ghost_type)) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
tmp = &(connectivities.alloc(0, nb_nodes_per_element, type, ghost_type));
AKANTU_DEBUG_INFO("The connectivity vector for the type " << type
<< " created");
// if (ghost_type == _not_ghost)
// type_set.insert(type);
// else
// ghost_type_set.insert(type);
// updateTypesOffsets(ghost_type);
} else {
tmp = &connectivities(type, ghost_type);
}
AKANTU_DEBUG_OUT();
return *tmp;
}
/* -------------------------------------------------------------------------- */
inline Array<std::vector<Element>> &
Mesh::getElementToSubelementPointer(const ElementType & type,
const GhostType & ghost_type) {
return getDataPointer<std::vector<Element>>("element_to_subelement", type,
ghost_type, 1, true);
}
/* -------------------------------------------------------------------------- */
inline Array<Element> &
Mesh::getSubelementToElementPointer(const ElementType & type,
const GhostType & ghost_type) {
return getDataPointer<Element>("subelement_to_element", type, ghost_type,
getNbFacetsPerElement(type), true,
is_mesh_facets);
}
/* -------------------------------------------------------------------------- */
inline const Array<std::vector<Element>> &
Mesh::getElementToSubelement(const ElementType & type,
const GhostType & ghost_type) const {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<std::vector<Element>> &
Mesh::getElementToSubelement(const ElementType & type,
const GhostType & ghost_type) {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const Array<Element> &
Mesh::getSubelementToElement(const ElementType & type,
const GhostType & ghost_type) const {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<Element> &
Mesh::getSubelementToElement(const ElementType & type,
const GhostType & ghost_type) {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> &
Mesh::getDataPointer(const std::string & data_name, const ElementType & el_type,
const GhostType & ghost_type, UInt nb_component,
bool size_to_nb_element, bool resize_with_parent) {
Array<T> & tmp = mesh_data.getElementalDataArrayAlloc<T>(
data_name, el_type, ghost_type, nb_component);
if (size_to_nb_element) {
if (resize_with_parent)
tmp.resize(mesh_parent->getNbElement(el_type, ghost_type));
else
tmp.resize(this->getNbElement(el_type, ghost_type));
} else {
tmp.resize(0);
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const Array<T> & Mesh::getData(const std::string & data_name,
const ElementType & el_type,
const GhostType & ghost_type) const {
return mesh_data.getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> & Mesh::getData(const std::string & data_name,
const ElementType & el_type,
const GhostType & ghost_type) {
return mesh_data.getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const ElementTypeMapArray<T> &
Mesh::getData(const std::string & data_name) const {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> & Mesh::getData(const std::string & data_name) {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> &
Mesh::registerData(const std::string & data_name) {
this->mesh_data.registerElementalData<T>(data_name);
return this->getData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const ElementType & type,
const GhostType & ghost_type) const {
try {
const Array<UInt> & conn = connectivities(type, ghost_type);
return conn.size();
} catch (...) {
return 0;
}
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & kind) const {
AKANTU_DEBUG_ASSERT(spatial_dimension <= 3 || spatial_dimension == UInt(-1),
"spatial_dimension is " << spatial_dimension
<< " and is greater than 3 !");
UInt nb_element = 0;
for (auto type : elementTypes(spatial_dimension, ghost_type, kind))
nb_element += getNbElement(type, ghost_type);
return nb_element;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(UInt element, const ElementType & type,
Real * barycenter, GhostType ghost_type) const {
UInt * conn_val = getConnectivity(type, ghost_type).storage();
UInt nb_nodes_per_element = getNbNodesPerElement(type);
Real * local_coord = new Real[spatial_dimension * nb_nodes_per_element];
UInt offset = element * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
memcpy(local_coord + n * spatial_dimension,
nodes->storage() + conn_val[offset + n] * spatial_dimension,
spatial_dimension * sizeof(Real));
}
Math::barycenter(local_coord, nb_nodes_per_element, spatial_dimension,
barycenter);
delete[] local_coord;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(const Element & element,
Vector<Real> & barycenter) const {
getBarycenter(element.element, element.type, barycenter.storage(),
element.ghost_type);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElement(const ElementType & type) {
UInt nb_nodes_per_element = 0;
#define GET_NB_NODES_PER_ELEMENT(type) \
nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_NODES_PER_ELEMENT);
#undef GET_NB_NODES_PER_ELEMENT
return nb_nodes_per_element;
}
/* -------------------------------------------------------------------------- */
inline ElementType Mesh::getP1ElementType(const ElementType & type) {
ElementType p1_type = _not_defined;
#define GET_P1_TYPE(type) p1_type = ElementClass<type>::getP1ElementType()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_P1_TYPE);
#undef GET_P1_TYPE
return p1_type;
}
/* -------------------------------------------------------------------------- */
inline ElementKind Mesh::getKind(const ElementType & type) {
ElementKind kind = _ek_not_defined;
#define GET_KIND(type) kind = ElementClass<type>::getKind()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_KIND);
#undef GET_KIND
return kind;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getSpatialDimension(const ElementType & type) {
UInt spatial_dimension = 0;
#define GET_SPATIAL_DIMENSION(type) \
spatial_dimension = ElementClass<type>::getSpatialDimension()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SPATIAL_DIMENSION);
#undef GET_SPATIAL_DIMENSION
return spatial_dimension;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetTypes(const ElementType & type,
__attribute__((unused)) UInt t) {
UInt nb = 0;
#define GET_NB_FACET_TYPE(type) nb = ElementClass<type>::getNbFacetTypes()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET_TYPE);
#undef GET_NB_FACET_TYPE
return nb;
}
/* -------------------------------------------------------------------------- */
inline ElementType Mesh::getFacetType(const ElementType & type, UInt t) {
ElementType surface_type = _not_defined;
#define GET_FACET_TYPE(type) surface_type = ElementClass<type>::getFacetType(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_TYPE);
#undef GET_FACET_TYPE
return surface_type;
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<ElementType>
Mesh::getAllFacetTypes(const ElementType & type) {
#define GET_FACET_TYPE(type) \
UInt nb = ElementClass<type>::getNbFacetTypes(); \
ElementType * elt_ptr = \
const_cast<ElementType *>(ElementClass<type>::getFacetTypeInternal()); \
return VectorProxy<ElementType>(elt_ptr, nb);
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_TYPE);
#undef GET_FACET_TYPE
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(const ElementType & type) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) n_facet = ElementClass<type>::getNbFacetsPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(const ElementType & type, UInt t) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) \
n_facet = ElementClass<type>::getNbFacetsPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline MatrixProxy<UInt>
Mesh::getFacetLocalConnectivity(const ElementType & type, UInt t) {
AKANTU_DEBUG_IN();
#define GET_FACET_CON(type) \
AKANTU_DEBUG_OUT(); \
return ElementClass<type>::getFacetLocalConnectivityPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_CON);
#undef GET_FACET_CON
AKANTU_DEBUG_OUT();
return MatrixProxy<UInt>(
nullptr, 0, 0); // This avoid a compilation warning but will certainly
// also cause a segfault if reached
}
/* -------------------------------------------------------------------------- */
inline Matrix<UInt> Mesh::getFacetConnectivity(const Element & element,
UInt t) const {
AKANTU_DEBUG_IN();
Matrix<UInt> local_facets(getFacetLocalConnectivity(element.type, t), false);
Matrix<UInt> facets(local_facets.rows(), local_facets.cols());
const Array<UInt> & conn = connectivities(element.type, element.ghost_type);
for (UInt f = 0; f < facets.rows(); ++f) {
for (UInt n = 0; n < facets.cols(); ++n) {
facets(f, n) = conn(element.element, local_facets(f, n));
}
}
AKANTU_DEBUG_OUT();
return facets;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::extractNodalValuesFromElement(
const Array<T> & nodal_values, T * local_coord, UInt * connectivity,
UInt n_nodes, UInt nb_degree_of_freedom) const {
for (UInt n = 0; n < n_nodes; ++n) {
memcpy(local_coord + n * nb_degree_of_freedom,
nodal_values.storage() + connectivity[n] * nb_degree_of_freedom,
nb_degree_of_freedom * sizeof(T));
}
}
/* -------------------------------------------------------------------------- */
inline void Mesh::addConnectivityType(const ElementType & type,
const GhostType & ghost_type) {
getConnectivityPointer(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPureGhostNode(UInt n) const {
return nodes_type.size() ? (nodes_type(n) == _nt_pure_gost) : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalOrMasterNode(UInt n) const {
return nodes_type.size()
? (nodes_type(n) == _nt_master) || (nodes_type(n) == _nt_normal)
: true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalNode(UInt n) const {
return nodes_type.size() ? nodes_type(n) == _nt_normal : true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isMasterNode(UInt n) const {
return nodes_type.size() ? nodes_type(n) == _nt_master : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isSlaveNode(UInt n) const {
return nodes_type.size() ? nodes_type(n) >= 0 : false;
}
/* -------------------------------------------------------------------------- */
inline NodeType Mesh::getNodeType(UInt local_id) const {
return nodes_type.size() ? nodes_type(local_id) : _nt_normal;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeGlobalId(UInt local_id) const {
return nodes_global_ids ? (*nodes_global_ids)(local_id) : local_id;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeLocalId(UInt global_id) const {
AKANTU_DEBUG_ASSERT(nodes_global_ids != NULL, "The global ids are note set.");
return nodes_global_ids->find(global_id);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbGlobalNodes() const {
return nodes_global_ids ? nb_global_nodes : nodes->size();
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElementList(const Array<Element> & elements) {
UInt nb_nodes_per_element = 0;
UInt nb_nodes = 0;
ElementType current_element_type = _not_defined;
Array<Element>::const_iterator<Element> el_it = elements.begin();
Array<Element>::const_iterator<Element> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
const Element & el = *el_it;
if (el.type != current_element_type) {
current_element_type = el.type;
nb_nodes_per_element = Mesh::getNbNodesPerElement(current_element_type);
}
nb_nodes += nb_nodes_per_element;
}
return nb_nodes;
}
/* -------------------------------------------------------------------------- */
inline Mesh & Mesh::getMeshFacets() {
if (!this->mesh_facets)
AKANTU_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshFacets() const {
if (!this->mesh_facets)
AKANTU_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshParent() const {
if (!this->mesh_parent)
AKANTU_EXCEPTION(
"No parent mesh is defined! This is only valid in a mesh_facets");
return *this->mesh_parent;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_MESH_INLINE_IMPL_CC__ */
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