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mesh.cc
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/**
* @file mesh.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Mohit Pundir <mohit.pundir@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: Tue Feb 09 2021
*
* @brief class handling 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "group_manager_inline_impl.hh"
#include "mesh.hh"
#include "mesh_global_data_updater.hh"
#include "mesh_io.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "facet_synchronizer.hh"
#include "mesh_utils_distribution.hh"
#include "node_synchronizer.hh"
#include "periodic_node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
#include "dumper_field.hh"
#include "dumper_internal_material_field.hh"
/* -------------------------------------------------------------------------- */
#include <limits>
#include <sstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, Communicator & communicator)
: GroupManager(*this, id + ":group_manager"), MeshData("mesh_data", id),
id(id), connectivities("connectivities", id),
ghosts_counters("ghosts_counters", id), normals("normals", id),
spatial_dimension(spatial_dimension), size(spatial_dimension, 0.),
bbox(spatial_dimension), bbox_local(spatial_dimension),
communicator(&communicator) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, Communicator & communicator, const ID & id)
: Mesh(spatial_dimension, id, communicator) {
AKANTU_DEBUG_IN();
this->nodes =
std::make_shared<Array<Real>>(0, spatial_dimension, id + ":coordinates");
this->nodes_flags = std::make_shared<Array<NodeFlag>>(0, 1, NodeFlag::_normal,
id + ":nodes_flags");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id)
: Mesh(spatial_dimension, Communicator::getStaticCommunicator(), id) {}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const std::shared_ptr<Array<Real>> & nodes,
const ID & id)
: Mesh(spatial_dimension, id, Communicator::getStaticCommunicator()) {
this->nodes = nodes;
this->nb_global_nodes = this->nodes->size();
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
void Mesh::getBarycenters(Array<Real> & barycenter, ElementType type,
GhostType ghost_type) const {
barycenter.resize(getNbElement(type, ghost_type));
for (auto && data : enumerate(make_view(barycenter, spatial_dimension))) {
getBarycenter(Element{type, UInt(std::get<0>(data)), ghost_type},
std::get<1>(data));
}
}
class FacetGlobalConnectivityAccessor : public DataAccessor<Element> {
public:
FacetGlobalConnectivityAccessor(Mesh & mesh)
: global_connectivity("global_connectivity",
"facet_connectivity_synchronizer") {
global_connectivity.initialize(
mesh, _spatial_dimension = _all_dimensions, _with_nb_element = true,
_with_nb_nodes_per_element = true, _element_kind = _ek_regular);
mesh.getGlobalConnectivity(global_connectivity);
}
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override {
UInt size = 0;
if (tag == SynchronizationTag::_smmc_facets_conn) {
UInt nb_nodes = Mesh::getNbNodesPerElementList(elements);
size += nb_nodes * sizeof(UInt);
}
return size;
}
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_smmc_facets_conn) {
for (const auto & element : elements) {
const auto & conns =
global_connectivity(element.type, element.ghost_type);
for (auto n : arange(conns.getNbComponent())) {
buffer << conns(element.element, n);
}
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override {
if (tag == SynchronizationTag::_smmc_facets_conn) {
for (const auto & element : elements) {
auto & conns = global_connectivity(element.type, element.ghost_type);
for (auto n : arange(conns.getNbComponent())) {
buffer >> conns(element.element, n);
}
}
}
}
AKANTU_GET_MACRO(GlobalConnectivity, (global_connectivity), decltype(auto));
protected:
ElementTypeMapArray<UInt> global_connectivity;
};
/* -------------------------------------------------------------------------- */
Mesh & Mesh::initMeshFacets(const ID & id) {
AKANTU_DEBUG_IN();
if (mesh_facets) {
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
mesh_facets = std::make_unique<Mesh>(spatial_dimension, this->nodes,
getID() + ":" + id);
mesh_facets->mesh_parent = this;
mesh_facets->is_mesh_facets = true;
mesh_facets->nodes_flags = this->nodes_flags;
mesh_facets->nodes_global_ids = this->nodes_global_ids;
MeshUtils::buildAllFacets(*this, *mesh_facets, 0);
if (mesh.isDistributed()) {
mesh_facets->is_distributed = true;
mesh_facets->element_synchronizer = std::make_unique<FacetSynchronizer>(
*mesh_facets, mesh.getElementSynchronizer());
FacetGlobalConnectivityAccessor data_accessor(*mesh_facets);
/// communicate
mesh_facets->element_synchronizer->synchronizeOnce(
data_accessor, SynchronizationTag::_smmc_facets_conn);
/// flip facets
MeshUtils::flipFacets(*mesh_facets, data_accessor.getGlobalConnectivity(),
_ghost);
}
/// transfers the the mesh physical names to the mesh facets
if (not this->hasData("physical_names")) {
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
auto & mesh_phys_data = this->getData<std::string>("physical_names");
auto & phys_data = mesh_facets->getData<std::string>("physical_names");
phys_data.initialize(*mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
ElementTypeMapArray<Real> barycenters(getID(), "temporary_barycenters");
barycenters.initialize(*mesh_facets, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
for (auto && ghost_type : ghost_types) {
for (auto && type :
barycenters.elementTypes(spatial_dimension - 1, ghost_type)) {
mesh_facets->getBarycenters(barycenters(type, ghost_type), type,
ghost_type);
}
}
for_each_element(
mesh,
[&](auto && element) {
Vector<Real> barycenter(spatial_dimension);
mesh.getBarycenter(element, barycenter);
auto norm_barycenter = barycenter.norm();
auto tolerance = Math::getTolerance();
if (norm_barycenter > tolerance) {
tolerance *= norm_barycenter;
}
Vector<Real> barycenter_facet(spatial_dimension);
auto range = enumerate(make_view(
barycenters(element.type, element.ghost_type), spatial_dimension));
#ifndef AKANTU_NDEBUG
auto min_dist = std::numeric_limits<Real>::max();
#endif
// this is a spacial search coded the most inefficient way.
auto facet =
std::find_if(range.begin(), range.end(), [&](auto && data) {
auto norm_distance = barycenter.distance(std::get<1>(data));
#ifndef AKANTU_NDEBUG
min_dist = std::min(min_dist, norm_distance);
#endif
return (norm_distance < tolerance);
});
if (facet == range.end()) {
AKANTU_DEBUG_INFO("The element "
<< element
<< " did not find its associated facet in the "
"mesh_facets! Try to decrease math tolerance. "
"The closest element was at a distance of "
<< min_dist);
return;
}
// set physical name
auto && facet_element = Element{element.type, UInt(std::get<0>(*facet)),
element.ghost_type};
phys_data(facet_element) = mesh_phys_data(element);
},
_spatial_dimension = spatial_dimension - 1);
mesh_facets->createGroupsFromMeshData<std::string>("physical_names");
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
/* -------------------------------------------------------------------------- */
void Mesh::defineMeshParent(const Mesh & mesh) {
AKANTU_DEBUG_IN();
this->mesh_parent = &mesh;
this->is_mesh_facets = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::~Mesh() = default;
/* -------------------------------------------------------------------------- */
void Mesh::read(const std::string & filename, const MeshIOType & mesh_io_type) {
AKANTU_DEBUG_ASSERT(not is_distributed,
"You cannot read a mesh that is already distributed");
MeshIO::read(filename, *this, mesh_io_type);
auto types =
this->elementTypes(spatial_dimension, _not_ghost, _ek_not_defined);
auto it = types.begin();
auto last = types.end();
if (it == last) {
AKANTU_DEBUG_WARNING(
"The mesh contained in the file "
<< filename << " does not seem to be of the good dimension."
<< " No element of dimension " << spatial_dimension << " were read.");
}
this->makeReady();
}
/* -------------------------------------------------------------------------- */
void Mesh::write(const std::string & filename,
const MeshIOType & mesh_io_type) {
MeshIO::write(filename, *this, mesh_io_type);
}
/* -------------------------------------------------------------------------- */
void Mesh::makeReady() {
this->nb_global_nodes = this->nodes->size();
this->computeBoundingBox();
this->nodes_flags->resize(nodes->size(), NodeFlag::_normal);
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
}
/* -------------------------------------------------------------------------- */
void Mesh::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Mesh [" << std::endl;
stream << space << " + id : " << getID() << std::endl;
stream << space << " + spatial dimension : " << this->spatial_dimension
<< std::endl;
stream << space << " + nodes [" << std::endl;
nodes->printself(stream, indent + 2);
stream << space << " + connectivities [" << std::endl;
connectivities.printself(stream, indent + 2);
stream << space << " ]" << std::endl;
GroupManager::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void Mesh::computeBoundingBox() {
AKANTU_DEBUG_IN();
bbox_local.reset();
for (auto & pos : make_view(*nodes, spatial_dimension)) {
// if(!isPureGhostNode(i))
bbox_local += pos;
}
if (this->is_distributed) {
bbox = bbox_local.allSum(*communicator);
} else {
bbox = bbox_local;
}
size = bbox.size();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Mesh::initNormals() {
normals.initialize(*this, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_element_kind = _ek_not_defined);
}
/* -------------------------------------------------------------------------- */
void Mesh::getGlobalConnectivity(
ElementTypeMapArray<UInt> & global_connectivity) {
AKANTU_DEBUG_IN();
for (auto && ghost_type : ghost_types) {
for (auto type :
global_connectivity.elementTypes(_spatial_dimension = _all_dimensions,
_element_kind = _ek_not_defined, _ghost_type = ghost_type)) {
if (not connectivities.exists(type, ghost_type)) {
continue;
}
auto & local_conn = connectivities(type, ghost_type);
auto & g_connectivity = global_connectivity(type, ghost_type);
UInt nb_nodes = local_conn.size() * local_conn.getNbComponent();
std::transform(local_conn.begin_reinterpret(nb_nodes),
local_conn.end_reinterpret(nb_nodes),
g_connectivity.begin_reinterpret(nb_nodes),
[&](UInt l) -> UInt { return this->getNodeGlobalId(l); });
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Mesh::getGroupDumper(const std::string & dumper_name,
const std::string & group_name) {
if (group_name == "all") {
return this->getDumper(dumper_name);
}
return element_groups[group_name]->getDumper(dumper_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementTypeMap<UInt> Mesh::getNbDataPerElem(ElementTypeMapArray<T> & arrays) {
ElementTypeMap<UInt> nb_data_per_elem;
for (auto type : arrays.elementTypes(_element_kind = _ek_not_defined)) {
UInt nb_elements = this->getNbElement(type);
auto & array = arrays(type);
nb_data_per_elem(type) = array.getNbComponent() * array.size();
nb_data_per_elem(type) /= nb_elements;
}
return nb_data_per_elem;
}
/* -------------------------------------------------------------------------- */
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<Real> & array);
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<UInt> & array);
/* -------------------------------------------------------------------------- */
template <typename T>
std::shared_ptr<dumpers::Field>
Mesh::createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
ElementKind element_kind) {
std::shared_ptr<dumpers::Field> field;
ElementTypeMapArray<T> * internal = nullptr;
try {
internal = &(this->getData<T>(field_id));
} catch (...) {
return nullptr;
}
ElementTypeMap<UInt> nb_data_per_elem = this->getNbDataPerElem(*internal);
field = this->createElementalField<T, dumpers::InternalMaterialField>(
*internal, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
return field;
}
template std::shared_ptr<dumpers::Field>
Mesh::createFieldFromAttachedData<Real>(const std::string & field_id,
const std::string & group_name,
ElementKind element_kind);
template std::shared_ptr<dumpers::Field>
Mesh::createFieldFromAttachedData<UInt>(const std::string & field_id,
const std::string & group_name,
ElementKind element_kind);
/* -------------------------------------------------------------------------- */
void Mesh::distributeImpl(
Communicator & communicator,
const std::function<Int(const Element &, const Element &)> &
edge_weight_function [[gnu::unused]],
const std::function<Int(const Element &)> & vertex_weight_function
[[gnu::unused]]) {
AKANTU_DEBUG_ASSERT(is_distributed == false,
"This mesh is already distribute");
this->communicator = &communicator;
this->element_synchronizer = std::make_unique<ElementSynchronizer>(
*this, this->getID() + ":element_synchronizer", true);
this->node_synchronizer = std::make_unique<NodeSynchronizer>(
*this, this->getID() + ":node_synchronizer", true);
Int psize = this->communicator->getNbProc();
if (psize > 1) {
#ifdef AKANTU_USE_SCOTCH
Int prank = this->communicator->whoAmI();
if (prank == 0) {
MeshPartitionScotch partition(*this, spatial_dimension);
partition.partitionate(psize, edge_weight_function,
vertex_weight_function);
MeshUtilsDistribution::distributeMeshCentralized(*this, 0, partition);
} else {
MeshUtilsDistribution::distributeMeshCentralized(*this, 0);
}
#else
if (psize > 1) {
AKANTU_ERROR("Cannot distribute a mesh without a partitioning tool");
}
#endif
}
// if (psize > 1)
this->is_distributed = true;
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
void Mesh::getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements) const {
for (const auto & node : node_list) {
for (const auto & element : *nodes_to_elements[node]) {
elements.push_back(element);
}
}
}
/* -------------------------------------------------------------------------- */
void Mesh::getAssociatedElements(const UInt & node,
Array<Element> & elements) const {
for (const auto & element : *nodes_to_elements[node]) {
elements.push_back(element);
}
}
/* -------------------------------------------------------------------------- */
void Mesh::fillNodesToElements(UInt dimension) {
Element e;
UInt nb_nodes = nodes->size();
this->nodes_to_elements.resize(nb_nodes);
for (UInt n = 0; n < nb_nodes; ++n) {
if (this->nodes_to_elements[n]) {
this->nodes_to_elements[n]->clear();
} else {
this->nodes_to_elements[n] = std::make_unique<std::set<Element>>();
}
}
for (auto ghost_type : ghost_types) {
e.ghost_type = ghost_type;
for (const auto & type :
elementTypes(dimension, ghost_type, _ek_not_defined)) {
e.type = type;
UInt nb_element = this->getNbElement(type, ghost_type);
auto connectivity = connectivities(type, ghost_type);
auto conn_it = connectivity.begin(connectivity.getNbComponent());
for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
e.element = el;
const Vector<UInt> & conn = *conn_it;
for (auto node : conn) {
nodes_to_elements[node]->insert(e);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt>
Mesh::updateGlobalData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event) {
if (global_data_updater) {
return this->global_data_updater->updateData(nodes_event, elements_event);
}
return std::make_tuple(nodes_event.getList().size(),
elements_event.getList().size());
}
/* -------------------------------------------------------------------------- */
void Mesh::registerGlobalDataUpdater(
std::unique_ptr<MeshGlobalDataUpdater> && global_data_updater) {
this->global_data_updater = std::move(global_data_updater);
}
/* -------------------------------------------------------------------------- */
void Mesh::eraseElements(const Array<Element> & elements) {
ElementTypeMap<UInt> last_element;
RemovedElementsEvent event(*this, "new_numbering", AKANTU_CURRENT_FUNCTION);
auto & remove_list = event.getList();
auto & new_numbering = event.getNewNumbering();
for (auto && el : elements) {
if (el.ghost_type != _not_ghost) {
auto & count = ghosts_counters(el);
--count;
if (count > 0) {
continue;
}
}
remove_list.push_back(el);
if (not new_numbering.exists(el.type, el.ghost_type)) {
auto nb_element = mesh.getNbElement(el.type, el.ghost_type);
auto & numbering =
new_numbering.alloc(nb_element, 1, el.type, el.ghost_type);
for (auto && pair : enumerate(numbering)) {
std::get<1>(pair) = std::get<0>(pair);
}
}
new_numbering(el) = UInt(-1);
}
auto find_last_not_deleted = [](auto && array, Int start) -> Int {
do {
--start;
} while (start >= 0 and array[start] == UInt(-1));
return start;
};
auto find_first_deleted = [](auto && array, Int start) -> Int {
auto begin = array.begin();
auto it = std::find_if(begin + start, array.end(),
[](auto & el) { return el == UInt(-1); });
return Int(it - begin);
};
for (auto ghost_type : ghost_types) {
for (auto type : new_numbering.elementTypes(_ghost_type = ghost_type)) {
auto & numbering = new_numbering(type, ghost_type);
auto last_not_delete = find_last_not_deleted(numbering, numbering.size());
if (last_not_delete < 0) {
continue;
}
auto pos = find_first_deleted(numbering, 0);
while (pos < last_not_delete) {
std::swap(numbering[pos], numbering[last_not_delete]);
last_not_delete = find_last_not_deleted(numbering, last_not_delete);
pos = find_first_deleted(numbering, pos + 1);
}
}
}
this->sendEvent(event);
}
} // namespace akantu
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