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mesh_periodic.cc
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mesh_periodic.cc
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/**
* @file mesh_pbc.cc
*
* @author Nicolas Richart
*
* @date creation Sat Feb 10 2018
*
* @brief Implementation of the perdiodicity capabilities in the mesh
*
* @section LICENSE
*
* Copyright (©) 2010-2011 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 "communicator.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void Mesh::makePeriodic(const SpatialDirection & direction) {
const auto & lower_bound = this->getLowerBounds();
const auto & upper_bound = this->getUpperBounds();
Array<UInt> list_1;
Array<UInt> list_2;
const auto & positions = *nodes;
for (auto && data : enumerate(make_view(positions, spatial_dimension))) {
UInt node = std::get<0>(data);
const auto & pos = std::get<1>(data);
if (Math::are_float_equal(pos(direction), lower_bound(direction))) {
list_1.push_back(node);
}
if (Math::are_float_equal(pos(direction), upper_bound(direction))) {
list_2.push_back(node);
}
}
this->makePeriodic(direction, list_1, list_2);
}
namespace {
struct NodeInfo {
NodeInfo() {}
NodeInfo(UInt node, const Vector<Real> & position,
const Vector<Real> & lower_node,
const SpatialDirection & direction)
: node(node), position(position) {
direction_position = position(direction);
this->position(direction) = 0.;
this->distance = this->position.distance(lower_node);
}
NodeInfo(const NodeInfo & other)
: node(other.node), distance(other.distance), position(other.position),
direction_position(other.direction_position) {}
UInt node{0};
Real distance{-1.};
Vector<Real> position;
Real direction_position{0.};
};
// std::ostream & operator<<(std::ostream & stream, const NodeInfo & info) {
// stream << info.node << " " << info.position << " " << info.distance;
// return stream;
// }
}
class BBox {
public:
BBox(UInt spatial_dimension)
: dim(spatial_dimension),
lower_bounds(spatial_dimension, std::numeric_limits<Real>::max()),
upper_bounds(spatial_dimension, -std::numeric_limits<Real>::max()) {}
BBox(const BBox & other)
: dim(other.dim), lower_bounds(other.lower_bounds),
upper_bounds(other.upper_bounds) {}
BBox & operator=(const BBox & other) {
if (this != &other) {
this->dim = dim;
this->lower_bounds = other.lower_bounds;
this->upper_bounds = other.upper_bounds;
}
return *this;
}
BBox & operator+=(const Vector<Real> & position) {
for (auto s : arange(dim)) {
lower_bounds(s) = std::min(lower_bounds(s), position(s));
upper_bounds(s) = std::min(upper_bounds(s), position(s));
}
return *this;
}
const Vector<Real> & getLowerBounds() const { return lower_bounds; }
const Vector<Real> & getUpperBounds() const { return upper_bounds; }
Vector<Real> & getLowerBounds() { return lower_bounds; }
Vector<Real> & getUpperBounds() { return upper_bounds; }
void reset() {
lower_bounds.set(std::numeric_limits<Real>::max());
upper_bounds.set(-std::numeric_limits<Real>::max());
}
protected:
UInt dim;
Vector<Real> lower_bounds;
Vector<Real> upper_bounds;
};
/* -------------------------------------------------------------------------- */
void Mesh::makePeriodic(const SpatialDirection & direction,
const Array<UInt> & list_1,
const Array<UInt> & list_2) {
Real tolerance = Math::getTolerance();
const auto & positions = *nodes;
auto lower_bound = this->getLowerBounds();
auto upper_bound = this->getUpperBounds();
auto length = upper_bound(direction) - lower_bound(direction);
lower_bound(direction) = 0;
upper_bound(direction) = 0;
std::vector<NodeInfo> nodes_1(list_1.size());
std::vector<NodeInfo> nodes_2(list_2.size());
BBox bbox(spatial_dimension);
auto to_position = [&](UInt node) {
Vector<Real> pos(spatial_dimension);
for (UInt s : arange(spatial_dimension)) {
pos(s) = direction == s ? 0 : positions(node, s);
}
bbox += pos;
return NodeInfo(node, pos, lower_bound, direction);
};
std::transform(list_1.begin(), list_1.end(), nodes_1.begin(), to_position);
BBox bbox1 = bbox;
bbox.reset();
std::transform(list_2.begin(), list_2.end(), nodes_2.begin(), to_position);
BBox bbox2 = bbox;
if (is_distributed) {
auto prank = communicator->whoAmI();
auto nb_proc = communicator->getNbProc();
Array<Real> bboxes(nb_proc, spatial_dimension * 4);
auto * base = bboxes.storage() + prank * 4 * spatial_dimension;
Vector<Real>(base + spatial_dimension * 0, spatial_dimension) =
bbox1.getLowerBounds();
Vector<Real>(base + spatial_dimension * 1, spatial_dimension) =
bbox1.getUpperBounds();
Vector<Real>(base + spatial_dimension * 2, spatial_dimension) =
bbox2.getLowerBounds();
Vector<Real>(base + spatial_dimension * 3, spatial_dimension) =
bbox2.getUpperBounds();
communicator->allGather(bboxes);
for (auto p : arange(nb_proc)) {
if (p == prank)
continue;
}
}
auto to_sort = [&](auto && info1, auto && info2) -> bool {
return info1.distance < info2.distance;
};
std::sort(nodes_1.begin(), nodes_1.end(), to_sort);
std::sort(nodes_2.begin(), nodes_2.end(), to_sort);
auto it = nodes_2.begin();
for (auto && info1 : nodes_1) {
auto & pos1 = info1.position;
auto it_cur = it;
bool found = false;
for (; it_cur != nodes_2.end(); ++it_cur) {
auto & info2 = *it_cur;
auto & pos2 = info2.position;
auto dist = pos1.distance(pos2) / length;
if (dist < tolerance) {
found = true;
it = it_cur;
break;
}
}
if (found) {
auto node1 = info1.node;
auto node2 = it_cur->node;
if (info1.direction_position < it_cur->direction_position) {
std::swap(node1, node2);
}
periodic_pairs.emplace(node1, std::make_pair(node2, direction));
std::cout << "master: " << node1 << " - slave: " << node2 << std::endl;
}
}
std::cout << periodic_pairs.size() << std::endl;
this->is_periodic |= 1 < direction;
}
} // akantu

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