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rAKA/src/mesh_utils/mesh_utils_pbc.cc
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mesh_utils_pbc.cc
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/**
* @file mesh_utils_pbc.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Wed Feb 09 2011
* @date last modification: Tue Feb 20 2018
*
* @brief periodic boundary condition connectivity tweak
*
*
* Copyright (©) 2010-2018 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 <map>
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/// class that sorts a set of nodes of same coordinates in 'dir' direction
class CoordinatesComparison {
public:
CoordinatesComparison(const UInt dimension, const UInt dir_1,
const UInt dir_2, Real normalization, Real tolerance,
const Array<Real> & coords)
: dim(dimension), dir_1(dir_1), dir_2(dir_2),
normalization(normalization), tolerance(tolerance),
coords_it(coords.begin(dim)) {}
// answers the question whether n2 is larger or equal to n1
bool operator()(const UInt n1, const UInt n2) {
Vector<Real> coords_n1 = coords_it[n1];
Vector<Real> coords_n2 = coords_it[n2];
return this->operator()(coords_n1, coords_n2);
}
bool operator()(const Vector<Real> & coords_n1,
const Vector<Real> & coords_n2) const {
Real diff = coords_n1(dir_1) - coords_n2(dir_1);
;
if (dim == 2 || std::abs(diff) / normalization > tolerance) {
return (diff <= 0.);
}
if (dim > 2) {
diff = coords_n1(dir_2) - coords_n2(dir_2);
return (diff <= 0);
}
return true;
}
private:
UInt dim;
UInt dir_1;
UInt dir_2;
Real normalization;
Real tolerance;
const Array<Real>::const_vector_iterator coords_it;
};
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh, const UInt dir,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_left;
Array<UInt> selected_right;
const UInt dim = mesh.getSpatialDimension();
auto it = mesh.getNodes().begin(dim);
auto end = mesh.getNodes().end(dim);
if (dim <= dir) {
return;
}
const Vector<Real> & lower_bounds = mesh.getLowerBounds();
const Vector<Real> & upper_bounds = mesh.getUpperBounds();
AKANTU_DEBUG_INFO("min " << lower_bounds(dir));
AKANTU_DEBUG_INFO("max " << upper_bounds(dir));
for (UInt node = 0; it != end; ++it, ++node) {
const Vector<Real> & coords = *it;
AKANTU_DEBUG_TRACE("treating " << coords(dir));
if (Math::are_float_equal(coords(dir), lower_bounds(dir))) {
AKANTU_DEBUG_TRACE("pushing node " << node << " on the left side");
selected_left.push_back(node);
} else if (Math::are_float_equal(coords(dir), upper_bounds(dir))) {
selected_right.push_back(node);
AKANTU_DEBUG_TRACE("pushing node " << node << " on the right side");
}
}
AKANTU_DEBUG_INFO("found "
<< selected_left.size() << " and " << selected_right.size()
<< " nodes at each boundary for direction " << dir);
// match pairs
MeshUtils::matchPBCPairs(mesh, dir, selected_left, selected_right, pbc_pair);
}
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh,
const std::pair<ID, ID> & surface_pair,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_first;
Array<UInt> selected_second;
// find nodes on surfaces
const ElementGroup & first_surf = mesh.getElementGroup(surface_pair.first);
const ElementGroup & second_surf = mesh.getElementGroup(surface_pair.second);
// if this surface pair is not on this proc
if (first_surf.getNbNodes() == 0 || second_surf.getNbNodes() == 0) {
AKANTU_DEBUG_WARNING("computePBCMap has at least one surface without any "
"nodes. I will ignore it.");
return;
}
// copy nodes from element group
selected_first.copy(first_surf.getNodeGroup().getNodes());
selected_second.copy(second_surf.getNodeGroup().getNodes());
// coordinates
const Array<Real> & coords = mesh.getNodes();
const UInt dim = mesh.getSpatialDimension();
// variables to find min and max of surfaces
Real first_max[3];
Real first_min[3];
Real second_max[3];
Real second_min[3];
for (UInt i = 0; i < dim; ++i) {
first_min[i] = std::numeric_limits<Real>::max();
second_min[i] = std::numeric_limits<Real>::max();
first_max[i] = -std::numeric_limits<Real>::max();
second_max[i] = -std::numeric_limits<Real>::max();
}
// find min and max of surface nodes
for (auto it = selected_first.begin(); it != selected_first.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
if (first_min[i] > coords(*it, i)) {
first_min[i] = coords(*it, i);
}
if (first_max[i] < coords(*it, i)) {
first_max[i] = coords(*it, i);
}
}
}
for (auto it = selected_second.begin(); it != selected_second.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
if (second_min[i] > coords(*it, i)) {
second_min[i] = coords(*it, i);
}
if (second_max[i] < coords(*it, i)) {
second_max[i] = coords(*it, i);
}
}
}
// find direction of pbc
Int first_dir = -1;
#ifndef AKANTU_NDEBUG
Int second_dir = -2;
#endif
for (UInt i = 0; i < dim; ++i) {
if (Math::are_float_equal(first_min[i], first_max[i])) {
first_dir = i;
}
#ifndef AKANTU_NDEBUG
if (Math::are_float_equal(second_min[i], second_max[i])) {
second_dir = i;
}
#endif
}
AKANTU_DEBUG_ASSERT(first_dir == second_dir,
"Surface pair has not same direction. Surface "
<< surface_pair.first << " dir=" << first_dir
<< " ; Surface " << surface_pair.second
<< " dir=" << second_dir);
UInt dir = first_dir;
// match pairs
if (first_min[dir] < second_min[dir]) {
MeshUtils::matchPBCPairs(mesh, dir, selected_first, selected_second,
pbc_pair);
} else {
MeshUtils::matchPBCPairs(mesh, dir, selected_second, selected_first,
pbc_pair);
}
}
/* -------------------------------------------------------------------------- */
void MeshUtils::matchPBCPairs(const Mesh & mesh, const UInt dir,
Array<UInt> & selected_left,
Array<UInt> & selected_right,
std::map<UInt, UInt> & pbc_pair) {
// tolerance is that large because most meshers generate points coordinates
// with single precision only (it is the case of GMSH for instance)
Real tolerance = 1e-7;
const UInt dim = mesh.getSpatialDimension();
Real normalization = mesh.getUpperBounds()(dir) - mesh.getLowerBounds()(dir);
AKANTU_DEBUG_ASSERT(std::abs(normalization) > Math::getTolerance(),
"In matchPBCPairs: The normalization is zero. "
<< "Did you compute the bounding box of the mesh?");
auto odir_1 = UInt(-1);
auto odir_2 = UInt(-1);
if (dim == 3) {
if (dir == _x) {
odir_1 = _y;
odir_2 = _z;
} else if (dir == _y) {
odir_1 = _x;
odir_2 = _z;
} else if (dir == _z) {
odir_1 = _x;
odir_2 = _y;
}
} else if (dim == 2) {
if (dir == _x) {
odir_1 = _y;
} else if (dir == _y) {
odir_1 = _x;
}
}
CoordinatesComparison compare_nodes(dim, odir_1, odir_2, normalization,
tolerance, mesh.getNodes());
std::sort(selected_left.begin(), selected_left.end(), compare_nodes);
std::sort(selected_right.begin(), selected_right.end(), compare_nodes);
auto it_left = selected_left.begin();
auto end_left = selected_left.end();
auto it_right = selected_right.begin();
auto end_right = selected_right.end();
auto nit = mesh.getNodes().begin(dim);
while ((it_left != end_left) && (it_right != end_right)) {
UInt i1 = *it_left;
UInt i2 = *it_right;
Vector<Real> coords1 = nit[i1];
Vector<Real> coords2 = nit[i2];
AKANTU_DEBUG_TRACE("do I pair? " << i1 << "(" << coords1 << ") with" << i2
<< "(" << coords2 << ") in direction "
<< dir);
Real dx = 0.0;
Real dy = 0.0;
if (dim >= 2) {
dx = coords1(odir_1) - coords2(odir_1);
}
if (dim == 3) {
dy = coords1(odir_2) - coords2(odir_2);
}
if (std::abs(dx * dx + dy * dy) / normalization < tolerance) {
// then i match these pairs
if (pbc_pair.count(i2) != 0U) {
i2 = pbc_pair[i2];
}
pbc_pair[i1] = i2;
AKANTU_DEBUG_TRACE("pairing " << i1 << "(" << coords1 << ") with" << i2
<< "(" << coords2 << ") in direction "
<< dir);
++it_left;
++it_right;
} else if (compare_nodes(coords1, coords2)) {
++it_left;
} else {
++it_right;
}
}
AKANTU_DEBUG_INFO("found " << pbc_pair.size() << " pairs for direction "
<< dir);
}
} // namespace akantu
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