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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 "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();
mesh.computeBoundingBox();
const Vector<Real> & lower_bounds = mesh.getLocalLowerBounds();
const Vector<Real> & 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
SpatialGrid<IntegrationPoint>::cells_iterator cell_it =
spatial_grid->beginCells();
SpatialGrid<IntegrationPoint>::cells_iterator cell_end =
spatial_grid->endCells();
Vector<Real> q1_coords(spatial_dimension);
Vector<Real> q2_coords(spatial_dimension);
IntegrationPoint q1;
IntegrationPoint q2;
UInt counter = 0;
for (; cell_it != cell_end; ++cell_it) {
AKANTU_DEBUG_INFO("Looping on next cell");
SpatialGrid<IntegrationPoint>::Cell::iterator first_quad =
spatial_grid->beginCell(*cell_it);
SpatialGrid<IntegrationPoint>::Cell::iterator last_quad =
spatial_grid->endCell(*cell_it);
for (; first_quad != last_quad; ++first_quad, ++counter) {
q1 = *first_quad;
if (q1.ghost_type == _ghost)
break;
Array<Real>::const_vector_iterator coords_type_1_it =
this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
q1_coords = coords_type_1_it[q1.global_num];
AKANTU_DEBUG_INFO("Current quadrature point in this cell: " << q1);
SpatialGrid<IntegrationPoint>::CellID cell_id =
spatial_grid->getCellID(q1_coords);
/// loop over all the neighbouring cells of the current quad
SpatialGrid<IntegrationPoint>::neighbor_cells_iterator first_neigh_cell =
spatial_grid->beginNeighborCells(cell_id);
SpatialGrid<IntegrationPoint>::neighbor_cells_iterator last_neigh_cell =
spatial_grid->endNeighborCells(cell_id);
for (; first_neigh_cell != last_neigh_cell; ++first_neigh_cell) {
SpatialGrid<IntegrationPoint>::Cell::iterator first_neigh_quad =
spatial_grid->beginCell(*first_neigh_cell);
SpatialGrid<IntegrationPoint>::Cell::iterator last_neigh_quad =
spatial_grid->endCell(*first_neigh_cell);
// loop over the quadrature point in the current neighboring cell
for (; first_neigh_quad != last_neigh_quad; ++first_neigh_quad) {
q2 = *first_neigh_quad;
Array<Real>::const_vector_iterator coords_type_2_it =
this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
q2_coords = 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::ofstream pout;
std::stringstream sstr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
pout.open(sstr.str().c_str());
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType)gt;
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
for (; first_pair != last_pair; ++first_pair) {
const IntegrationPoint & q1 = first_pair->first;
const IntegrationPoint & q2 = first_pair->second;
pout << q1 << " " << q2 << " " << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::saveNeighborCoords(const std::string & filename) const {
/// this function is not optimazed and only used for tests on small meshes
/// @todo maybe optimize this function for better performance?
Vector<Real> q1_coords(spatial_dimension);
Vector<Real> q2_coords(spatial_dimension);
IntegrationPoint q1;
IntegrationPoint q2;
std::ofstream pout;
std::stringstream sstr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
pout.open(sstr.str().c_str());
/// loop over all the quads and write the position of their neighbors
SpatialGrid<IntegrationPoint>::cells_iterator cell_it =
spatial_grid->beginCells();
SpatialGrid<IntegrationPoint>::cells_iterator cell_end =
spatial_grid->endCells();
for (; cell_it != cell_end; ++cell_it) {
SpatialGrid<IntegrationPoint>::Cell::iterator first_quad =
spatial_grid->beginCell(*cell_it);
SpatialGrid<IntegrationPoint>::Cell::iterator last_quad =
spatial_grid->endCell(*cell_it);
for (; first_quad != last_quad; ++first_quad) {
q1 = *first_quad;
Array<Real>::const_vector_iterator coords_type_1_it =
this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
q1_coords = coords_type_1_it[q1.global_num];
pout << "#neighbors for quad " << q1.global_num << std::endl;
pout << q1_coords << std::endl;
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType)gt;
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
for (; first_pair != last_pair; ++first_pair) {
if (q1 == first_pair->first && first_pair->second != q1) {
q2 = first_pair->second;
Array<Real>::const_vector_iterator coords_type_2_it =
this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
q2_coords = coords_type_2_it[q2.global_num];
pout << q2_coords << std::endl;
}
if (q1 == first_pair->second && first_pair->first != q1) {
q2 = first_pair->first;
Array<Real>::const_vector_iterator coords_type_2_it =
this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
q2_coords = 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) {
auto first_pair = pair_list[ghost_type2].begin();
auto last_pair = pair_list[ghost_type2].end();
for (; first_pair != last_pair; ++first_pair) {
IntegrationPoint & q1 = first_pair->first;
if (new_numbering.exists(q1.type, q1.ghost_type)) {
UInt q1_new_el = new_numbering(q1.type, q1.ghost_type)(q1.element);
AKANTU_DEBUG_ASSERT(q1_new_el != UInt(-1), "A local quadrature_point "
"as been removed instead of "
"just being renumbered");
q1.element = q1_new_el;
nb_quad = fem.getNbIntegrationPoints(q1.type, q1.ghost_type);
q1.global_num = nb_quad * q1.element + q1.num_point;
}
IntegrationPoint & q2 = first_pair->second;
if (new_numbering.exists(q2.type, q2.ghost_type)) {
UInt q2_new_el = new_numbering(q2.type, q2.ghost_type)(q2.element);
AKANTU_DEBUG_ASSERT(q2_new_el != UInt(-1), "A local quadrature_point "
"as been removed instead of "
"just being renumbered");
q2.element = q2_new_el;
nb_quad = fem.getNbIntegrationPoints(q2.type, q2.ghost_type);
q2.global_num = nb_quad * q2.element + q2.num_point;
}
}
}
this->grid_synchronizer->onElementsRemoved(element_list, new_numbering,
event);
AKANTU_DEBUG_OUT();
}
} // namespace akantu

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