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neighborhood_base.cc
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neighborhood_base.cc
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/**
* @file neighborhood_base.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Wed Nov 25 2015
*
* @brief Implementation of generic neighborhood base
*
* @section LICENSE
*
* Copyright (©) 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 "neighborhood_base.hh"
#include "grid_synchronizer.hh"
#include "mesh_accessor.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NeighborhoodBase::NeighborhoodBase(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), model(model), neighborhood_radius(0.),
spatial_grid(nullptr), is_creating_grid(false),
grid_synchronizer(nullptr), quad_coordinates(quad_coordinates),
spatial_dimension(this->model.getMesh().getSpatialDimension()) {
AKANTU_DEBUG_IN();
this->registerDataAccessor(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NeighborhoodBase::~NeighborhoodBase() = default;
/* -------------------------------------------------------------------------- */
// void NeighborhoodBase::createSynchronizerRegistry(
// DataAccessor<Element> * data_accessor) {
// this->synch_registry = new SynchronizerRegistry(*data_accessor);
// }
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::initNeighborhood() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Creating the grid");
this->createGrid();
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------- */
void NeighborhoodBase::createGrid() {
AKANTU_DEBUG_IN();
const Real safety_factor = 1.2; // for the cell grid spacing
Mesh & mesh = this->model.getMesh();
const auto & lower_bounds = mesh.getLocalLowerBounds();
const auto & upper_bounds = mesh.getLocalUpperBounds();
Vector<Real> center = 0.5 * (upper_bounds + lower_bounds);
Vector<Real> spacing(spatial_dimension,
this->neighborhood_radius * safety_factor);
spatial_grid = std::make_unique<SpatialGrid<IntegrationPoint>>(
spatial_dimension, spacing, center);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::updatePairList() {
AKANTU_DEBUG_IN();
//// loop over all quads -> all cells
for (auto && cell_id : *spatial_grid) {
AKANTU_DEBUG_INFO("Looping on next cell");
for (auto && q1 : spatial_grid->getCell(cell_id)) {
if (q1.ghost_type == _ghost)
break;
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
auto q1_coords = Vector<Real>(coords_type_1_it[q1.global_num]);
AKANTU_DEBUG_INFO("Current quadrature point in this cell: " << q1);
auto cell_id = spatial_grid->getCellID(q1_coords);
/// loop over all the neighboring cells of the current quad
for (auto && neighbor_cell : cell_id.neighbors()) {
// loop over the quadrature point in the current neighboring cell
for (auto && q2 : spatial_grid->getCell(neighbor_cell)) {
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
auto q2_coords = Vector<Real>(coords_type_2_it[q2.global_num]);
Real distance = q1_coords.distance(q2_coords);
if (distance <= this->neighborhood_radius + Math::getTolerance() &&
(q2.ghost_type == _ghost ||
(q2.ghost_type == _not_ghost &&
q1.global_num <= q2.global_num))) { // storing only half lists
pair_list[q2.ghost_type].push_back(std::make_pair(q1, q2));
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::savePairs(const std::string & filename) const {
std::stringstream sstr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
std::ofstream pout;
pout.open(sstr.str().c_str());
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
const auto & q1 = pair.first;
const auto & q2 = pair.second;
pout << q1 << " " << q2 << " " << std::endl;
}
}
pout.close();
if (comm.getNbProc() != 1)
return;
Mesh mesh_out(spatial_dimension);
MeshAccessor mesh_accessor(mesh_out);
auto & connectivity = mesh_accessor.getConnectivity(_segment_2);
auto & tag = mesh_accessor.getData<UInt>("tag_1", _segment_2);
auto & nodes = mesh_accessor.getNodes();
std::map<IntegrationPoint, UInt> quad_to_nodes;
UInt node = 0;
IntegrationPoint q1, q2;
bool inserted;
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
std::tie(q1, q2) = pair;
auto add_node = [&](auto && q) {
std::tie(std::ignore, inserted) =
quad_to_nodes.insert(std::make_pair(q, node));
if (not inserted)
return;
auto coords_it = this->quad_coordinates(q.type, q.ghost_type)
.begin(spatial_dimension);
auto && coords = Vector<Real>(coords_it[q.global_num]);
nodes.push_back(coords);
++node;
};
add_node(q1);
add_node(q2);
}
}
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
std::tie(q1, q2) = pair;
UInt node1 = quad_to_nodes[q1];
UInt node2 = quad_to_nodes[q2];
connectivity.push_back(Vector<UInt>{node1, node2});
tag.push_back(node1 + 1);
if (node1 != node2) {
connectivity.push_back(Vector<UInt>{node2, node1});
tag.push_back(node2 + 1);
}
}
}
mesh_out.write(filename + ".msh");
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::saveNeighborCoords(const std::string & filename) const {
// this function is not optimized and only used for tests on small meshes
// @todo maybe optimize this function for better performance?
IntegrationPoint q2;
std::stringstream sstr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
std::ofstream pout;
pout.open(sstr.str().c_str());
/// loop over all the quads and write the position of their neighbors
for (auto && cell_id : *spatial_grid) {
for (auto && q1 : spatial_grid->getCell(cell_id)) {
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
auto && q1_coords = Vector<Real>(coords_type_1_it[q1.global_num]);
pout << "#neighbors for quad " << q1.global_num << std::endl;
pout << q1_coords << std::endl;
for (auto && ghost_type2 : ghost_types) {
for (auto && pair : pair_list[ghost_type2]) {
if (q1 == pair.first && pair.second != q1) {
q2 = pair.second;
} else if (q1 == pair.second && pair.first != q1) {
q2 = pair.first;
} else {
continue;
}
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
auto && q2_coords = Vector<Real>(coords_type_2_it[q2.global_num]);
pout << q2_coords << std::endl;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = 0;
// Change the pairs in new global numbering
for (auto ghost_type2 : ghost_types) {
for (auto && pair : pair_list[ghost_type2]) {
auto cleanPoint = [&](auto && q) {
if (new_numbering.exists(q.type, q.ghost_type)) {
UInt q_new_el = new_numbering(q.type, q.ghost_type)(q.element);
AKANTU_DEBUG_ASSERT(q_new_el != UInt(-1),
"A local quadrature_point "
"as been removed instead of "
"just being renumbered");
q.element = q_new_el;
nb_quad = fem.getNbIntegrationPoints(q.type, q.ghost_type);
q.global_num = nb_quad * q.element + q.num_point;
}
};
cleanPoint(pair.first);
cleanPoint(pair.second);
}
}
this->grid_synchronizer->onElementsRemoved(element_list, new_numbering,
event);
AKANTU_DEBUG_OUT();
}
} // namespace akantu

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