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rAKA/src/mesh/mesh.cc
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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 Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Jan 22 2016
*
* @brief class handling 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "group_manager_inline_impl.cc"
#include "mesh.hh"
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "mesh_utils_distribution.hh"
#include "node_synchronizer.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_field.hh"
#include "dumper_internal_material_field.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
const Element ElementNull(_not_defined, 0);
/* -------------------------------------------------------------------------- */
void Element::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Element [" << type << ", " << element << ", "
<< ghost_type << "]";
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id,
StaticCommunicator & communicator)
: Memory(id, memory_id),
GroupManager(*this, id + ":group_manager", memory_id), nodes(NULL),
nodes_global_ids(nullptr), nodes_type(0, 1, id + ":nodes_type"),
nb_global_nodes(0), created_nodes(true),
connectivities("connectivities", id, memory_id),
normals("normals", id, memory_id), spatial_dimension(spatial_dimension),
types_offsets(Array<UInt>((UInt)_max_element_type + 1, 1)),
ghost_types_offsets(Array<UInt>((UInt)_max_element_type + 1, 1)),
lower_bounds(spatial_dimension, 0.), upper_bounds(spatial_dimension, 0.),
size(spatial_dimension, 0.), local_lower_bounds(spatial_dimension, 0.),
local_upper_bounds(spatial_dimension, 0.),
mesh_data("mesh_data", id, memory_id), mesh_facets(nullptr),
mesh_parent(nullptr), is_mesh_facets(false), is_distributed(false),
communicator(&communicator), element_synchronizer(nullptr),
node_synchronizer(nullptr) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, StaticCommunicator & communicator,
const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id, communicator) {
AKANTU_DEBUG_IN();
this->nodes =
&(alloc<Real>(id + ":coordinates", memory_id, spatial_dimension));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, StaticCommunicator::getStaticCommunicator(), id,
memory_id) {}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & nodes_id, const ID & id,
const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id,
StaticCommunicator::getStaticCommunicator()) {
this->nodes = &(this->getArray<Real>(nodes_id));
this->nb_global_nodes = this->nodes->getSize();
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, Array<Real> & nodes, const ID & id,
const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id,
StaticCommunicator::getStaticCommunicator()) {
this->nodes = &nodes;
this->nb_global_nodes = this->nodes->getSize();
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
Mesh & Mesh::initMeshFacets(const ID & id) {
AKANTU_DEBUG_IN();
if (!mesh_facets) {
mesh_facets = new Mesh(spatial_dimension, *(this->nodes),
getID() + ":" + id, getMemoryID());
mesh_facets->mesh_parent = this;
mesh_facets->is_mesh_facets = true;
}
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() {
AKANTU_DEBUG_IN();
delete mesh_facets;
delete element_synchronizer;
delete node_synchronizer;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Mesh::read(const std::string & filename, const MeshIOType & mesh_io_type) {
MeshIO mesh_io;
mesh_io.read(filename, *this, mesh_io_type);
type_iterator it =
this->firstType(spatial_dimension, _not_ghost, _ek_not_defined);
type_iterator last =
this->lastType(spatial_dimension, _not_ghost, _ek_not_defined);
if (it == last)
AKANTU_EXCEPTION(
"The mesh contained in the file "
<< filename << " does not seem to be of the good dimension."
<< " No element of dimension " << spatial_dimension << " where read.");
}
/* -------------------------------------------------------------------------- */
void Mesh::write(const std::string & filename,
const MeshIOType & mesh_io_type) {
MeshIO mesh_io;
mesh_io.write(filename, *this, mesh_io_type);
}
/* -------------------------------------------------------------------------- */
void Mesh::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += 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();
for (UInt k = 0; k < spatial_dimension; ++k) {
local_lower_bounds(k) = std::numeric_limits<double>::max();
local_upper_bounds(k) = -std::numeric_limits<double>::max();
}
for (UInt i = 0; i < nodes->getSize(); ++i) {
// if(!isPureGhostNode(i))
for (UInt k = 0; k < spatial_dimension; ++k) {
local_lower_bounds(k) = std::min(local_lower_bounds[k], (*nodes)(i, k));
local_upper_bounds(k) = std::max(local_upper_bounds[k], (*nodes)(i, k));
}
}
if (this->is_distributed) {
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Matrix<Real> reduce_bounds(spatial_dimension, 2);
for (UInt k = 0; k < spatial_dimension; ++k) {
reduce_bounds(k, 0) = local_lower_bounds(k);
reduce_bounds(k, 1) = -local_upper_bounds(k);
}
comm.allReduce(reduce_bounds, _so_min);
for (UInt k = 0; k < spatial_dimension; ++k) {
lower_bounds(k) = reduce_bounds(k, 0);
upper_bounds(k) = -reduce_bounds(k, 1);
}
} else {
this->lower_bounds = this->local_lower_bounds;
this->upper_bounds = this->local_upper_bounds;
}
size = upper_bounds - lower_bounds;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Mesh::initElementTypeMapArray(ElementTypeMapArray<T> & vect,
UInt nb_component, UInt dim,
const bool & flag_nb_node_per_elem_multiply,
ElementKind element_kind,
bool size_to_nb_element) const {
AKANTU_DEBUG_IN();
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
this->initElementTypeMapArray(vect, nb_component, dim, gt,
flag_nb_node_per_elem_multiply, element_kind,
size_to_nb_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Mesh::initElementTypeMapArray(ElementTypeMapArray<T> & vect,
UInt nb_component, UInt dim, GhostType gt,
const bool & flag_nb_node_per_elem_multiply,
ElementKind element_kind,
bool size_to_nb_element) const {
AKANTU_DEBUG_IN();
this->initElementTypeMapArray(vect, nb_component, dim, gt, T(),
flag_nb_node_per_elem_multiply, element_kind,
size_to_nb_element);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Mesh::initElementTypeMapArray(ElementTypeMapArray<T> & vect,
UInt nb_component, UInt dim, GhostType gt,
const T & default_value,
const bool & flag_nb_node_per_elem_multiply,
ElementKind element_kind,
bool size_to_nb_element) const {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = firstType(dim, gt, element_kind);
Mesh::type_iterator end = lastType(dim, gt, element_kind);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_comp = nb_component;
if (flag_nb_node_per_elem_multiply)
nb_comp *= Mesh::getNbNodesPerElement(*it);
UInt size = 0;
if (size_to_nb_element)
size = this->getNbElement(type, gt);
vect.alloc(size, nb_comp, type, gt, default_value);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Mesh::initNormals() {
this->initElementTypeMapArray(normals, spatial_dimension, spatial_dimension,
false, _ek_not_defined);
}
/* -------------------------------------------------------------------------- */
void Mesh::getGlobalConnectivity(
ElementTypeMapArray<UInt> & global_connectivity, UInt dimension,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = firstType(dimension, ghost_type);
Mesh::type_iterator end = lastType(dimension, ghost_type);
for (; it != end; ++it) {
ElementType type = *it;
Array<UInt> & local_conn = connectivities(type, ghost_type);
Array<UInt> & g_connectivity = global_connectivity(type, ghost_type);
if (!nodes_global_ids)
nodes_global_ids = mesh_parent->nodes_global_ids;
UInt * local_c = local_conn.storage();
UInt * global_c = g_connectivity.storage();
UInt nb_terms = local_conn.getSize() * local_conn.getNbComponent();
for (UInt i = 0; i < nb_terms; ++i, ++local_c, ++global_c)
*global_c = (*nodes_global_ids)(*local_c);
}
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);
else
return element_groups[group_name]->getDumper(dumper_name);
}
/* -------------------------------------------------------------------------- */
#define AKANTU_INSTANTIATE_INIT(type) \
template void Mesh::initElementTypeMapArray<type>( \
ElementTypeMapArray<type> & vect, UInt nb_component, UInt dim, \
const bool & flag_nb_elem_multiply, ElementKind element_kind, \
bool size_to_nb_element) const; \
template void Mesh::initElementTypeMapArray<type>( \
ElementTypeMapArray<type> & vect, UInt nb_component, UInt dim, \
GhostType gt, const bool & flag_nb_elem_multiply, \
ElementKind element_kind, bool size_to_nb_element) const; \
template void Mesh::initElementTypeMapArray<type>( \
ElementTypeMapArray<type> & vect, UInt nb_component, UInt dim, \
GhostType gt, const type & default_value, \
const bool & flag_nb_elem_multiply, ElementKind element_kind, \
bool size_to_nb_element) const
AKANTU_INSTANTIATE_INIT(Real);
AKANTU_INSTANTIATE_INIT(UInt);
AKANTU_INSTANTIATE_INIT(Int);
AKANTU_INSTANTIATE_INIT(bool);
/* -------------------------------------------------------------------------- */
template <typename T>
ElementTypeMap<UInt> Mesh::getNbDataPerElem(ElementTypeMapArray<T> & array,
const ElementKind & element_kind) {
ElementTypeMap<UInt> nb_data_per_elem;
typename ElementTypeMapArray<T>::type_iterator it =
array.firstType(spatial_dimension, _not_ghost, element_kind);
typename ElementTypeMapArray<T>::type_iterator last_type =
array.lastType(spatial_dimension, _not_ghost, element_kind);
for (; it != last_type; ++it) {
UInt nb_elements = this->getNbElement(*it);
nb_data_per_elem(*it) = array(*it).getNbComponent() * array(*it).getSize();
nb_data_per_elem(*it) /= nb_elements;
}
return nb_data_per_elem;
}
/* -------------------------------------------------------------------------- */
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<Real> & array,
const ElementKind & element_kind);
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<UInt> & array,
const ElementKind & element_kind);
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
template <typename T>
dumper::Field *
Mesh::createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind) {
dumper::Field * field = nullptr;
ElementTypeMapArray<T> * internal = nullptr;
try {
internal = &(this->getData<T>(field_id));
} catch (...) {
return nullptr;
}
ElementTypeMap<UInt> nb_data_per_elem =
this->getNbDataPerElem(*internal, element_kind);
field = this->createElementalField<T, dumper::InternalMaterialField>(
*internal, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
return field;
}
template dumper::Field *
Mesh::createFieldFromAttachedData<Real>(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
template dumper::Field *
Mesh::createFieldFromAttachedData<UInt>(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
#endif
/* -------------------------------------------------------------------------- */
void Mesh::distribute() {
this->distribute(StaticCommunicator::getStaticCommunicator());
}
/* -------------------------------------------------------------------------- */
void Mesh::distribute(StaticCommunicator & communicator) {
AKANTU_DEBUG_ASSERT(is_distributed == false,
"This mesh is already distribute");
this->communicator = &communicator;
this->element_synchronizer =
new ElementSynchronizer(*this, this->getID() + ":element_synchronizer",
this->getMemoryID(), true, communicator);
this->node_synchronizer =
new NodeSynchronizer(*this, this->getID() + ":node_synchronizer",
this->getMemoryID(), true, communicator);
Int psize = this->communicator->getNbProc();
#ifdef AKANTU_USE_SCOTCH
Int prank = this->communicator->whoAmI();
if (prank == 0) {
MeshPartitionScotch partition(*this, spatial_dimension);
partition.partitionate(psize);
MeshUtilsDistribution::distributeMeshCentralized(*this, 0, partition);
} else {
MeshUtilsDistribution::distributeMeshCentralized(*this, 0);
}
#else
if(!(psize == 1)) {
AKANTU_DEBUG_ERROR(
"Cannot distribute a mesh without a partitioning tool");
}
#endif
this->is_distributed = true;
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
} // akantu
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