bridging.cc
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bridging.cc
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	/**
	* @file bridging.cc
	*
	* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
	*
	* @date Fri Jul 11 15:47:44 2014
	*
	* @brief Bridging object between atomistic and finite elements
	*
	* @section LICENSE
	*
	* Copyright INRIA and CEA
	*
	* The LibMultiScale is a C++ parallel framework for the multiscale
	* coupling methods dedicated to material simulations. This framework
	* provides an API which makes it possible to program coupled simulations
	* and integration of already existing codes.
	*
	* This Project was initiated in a collaboration between INRIA Futurs Bordeaux
	* within ScAlApplix team and CEA/DPTA Ile de France.
	* The project is now continued at the Ecole Polytechnique Fédérale de Lausanne
	* within the LSMS/ENAC laboratory.
	*
	* This software is governed by the CeCILL-C license under French law and
	* abiding by the rules of distribution of free software. You can use,
	* modify and/ or redistribute the software under the terms of the CeCILL-C
	* license as circulated by CEA, CNRS and INRIA at the following URL
	* "http://www.cecill.info".
	*
	* As a counterpart to the access to the source code and rights to copy,
	* modify and redistribute granted by the license, users are provided only
	* with a limited warranty and the software's author, the holder of the
	* economic rights, and the successive licensors have only limited
	* liability.
	*
	* In this respect, the user's attention is drawn to the risks associated
	* with loading, using, modifying and/or developing or reproducing the
	* software by the user in light of its specific status of free software,
	* that may mean that it is complicated to manipulate, and that also
	* therefore means that it is reserved for developers and experienced
	* professionals having in-depth computer knowledge. Users are therefore
	* encouraged to load and test the software's suitability as regards their
	* requirements in conditions enabling the security of their systems and/or
	* data to be ensured and, more generally, to use and operate it in the
	* same conditions as regards security.
	*
	* The fact that you are presently reading this means that you have had
	* knowledge of the CeCILL-C license and that you accept its terms.
	*
	*/

	//#define TIMER
	/* -------------------------------------------------------------------------- */
	#include "bridging.hh"
	#include "compute_extract.hh"
	#include "factory_multiscale.hh"
	#include "filter_geometry.hh"
	#include "geometry_manager.hh"
	#include "lib_bridging.hh"
	#include "lm_common.hh"
	#include "trace_atom.hh"
	/* -------------------------------------------------------------------------- */
	__BEGIN_LIBMULTISCALE__

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	Bridging<ContainerPoints, ContainerMesh, Dim>::Bridging(const std::string &name,
	ContainerPoints &cP,
	ContainerMesh &cM)
	: LMObject(name), DofAssociation<ContainerPoints, ContainerMesh, Dim>(
	name, cP, cM),
	unmatchedPointList("unmatched-point-" + name),
	pointList("matched-point-" + name),
	unmatchedMeshList("unmatched-fe-" + name), meshList("matched-fe-" + name),
	node_shape("node_shape-" + name), contPoints(cP), contMesh(cM) {
	assoc_found = 0;
	smatrix = NULL;

	/* registering computes for outer world */
	FilterManager::getManager().addObject(unmatchedMeshList);
	FilterManager::getManager().addObject(unmatchedPointList);
	FilterManager::getManager().addObject(pointList);
	FilterManager::getManager().addObject(meshList);
	}
	/* -------------------------------------------------------------------------- */
	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	Bridging<ContainerPoints, ContainerMesh, Dim>::~Bridging() {
	if (smatrix)
	delete smatrix;
	smatrix = NULL;
	}

	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::init() {

	DUMPBYPROC("selecting DOFs in bridging zone", DBG_INFO_STARTUP, 0);
	if (this->in_group_A) {
	this->buildPointList();
	this->buildPositions(unmatchedPointList);
	}
	if (this->in_group_B)
	this->buildContinuumDOFsList();

	DUMP(this->getID() << " : Generating Communication Scheme", DBG_INFO_STARTUP);
	MPI_Barrier(MPI_COMM_WORLD);
	DUMP(this->getID() << " : exchange coarse geometries", DBG_MESSAGE);
	this->exchangeGeometries(this->unmatchedPointList, this->unmatchedMeshList);
	MPI_Barrier(MPI_COMM_WORLD);

	DUMP(this->getID() << " : exchange points positions", DBG_MESSAGE);
	this->exchangePositions();
	MPI_Barrier(MPI_COMM_WORLD);

	DUMP(this->getID() << " : build shape matrix", DBG_MESSAGE);
	if (this->in_group_B) {
	DUMP(this->getID() << " : build shape matrix (parsing "
	<< this->local_points << " points by position)",
	DBG_INFO);
	this->buildShapeMatrix(this->local_points);
	this->local_points = this->assoc_found;
	DUMP(this->getID() << " : I will manage " << this->local_points << " atoms",
	DBG_INFO);
	}

	MPI_Barrier(MPI_COMM_WORLD);

	DUMP(this->getID() << " : ExchangeAssociation", DBG_MESSAGE);
	std::vector<UInt> managed;
	this->exchangeAssociationInformation(managed);

	if (this->in_group_A)
	for (UInt i = 0; i < this->nb_zone_B; ++i)
	DUMP("second test Do I communicate with " << i << " : "
	<< this->com_with[i],
	DBG_INFO);

	if (this->in_group_B)
	for (UInt i = 0; i < this->nb_zone_A; ++i)
	DUMP("second test Do I communicate with " << i << " : "
	<< this->com_with[i],
	DBG_INFO);

	MPI_Barrier(MPI_COMM_WORLD);

	DUMP(this->getID()
	<< " : generate duo vector and detect double atom assignement",
	DBG_MESSAGE);
	std::vector<std::vector<UInt>> unassociated;
	if (this->in_group_A)
	this->createDuoVectorA("Atom", managed, unassociated);

	DUMP(this->getID() << " : doing exchange rejected", DBG_MESSAGE);
	this->exchangeRejectedContinuumOwners(unassociated);

	MPI_Barrier(MPI_COMM_WORLD);

	DUMP(this->getID() << " : doing filter rejected", DBG_MESSAGE);
	this->filterRejectedContinuumOwners(unassociated);

	MPI_Barrier(MPI_COMM_WORLD);

	DUMP(this->getID() << " : filtering position & association vector",
	DBG_MESSAGE);

	if (this->in_group_A) {
	this->filterPointListForUnmatched();
	}

	if (this->in_group_B) {
	this->filterArray(this->positions, Dim);
	this->filterAssoc();
	this->buildNodeShape();
	}

	this->deleteGrid();

	DUMP(this->getID() << " : all done for scheme generation", DBG_MESSAGE);

	MPI_Barrier(MPI_COMM_WORLD);
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::buildContinuumDOFsList() {

	unmatchedMeshList.setParam("GEOMETRY", this->geomID);
	unmatchedMeshList.buildManual(contMesh);

	DUMP("we have found " << unmatchedMeshList->getContainerElems().size()
	<< " concerned elements",
	DBG_INFO_STARTUP);

	STARTTIMER("Filling spatial-grid");

	auto contElems = unmatchedMeshList->getContainerElems();
	auto contNodes = unmatchedMeshList->getContainerNodes();

	std::vector<UInt> nodes;
	Geometry &geom = *GeometryManager::getManager().getGeometry(this->geomID);
	Cube cube = geom.getBoundingBox();
	DUMP("geometry of the grid => \n" << cube, DBG_INFO_STARTUP);
	if (this->grid)
	this->deleteGrid();
	this->grid = new SpatialGridElem<UInt, Dim>(cube, this->grid_division);

	UInt nb_elem = 0;
	for (auto &&el : contElems) {
	std::vector<Real> node_coords;
	auto &&nodes = el.globalIndexes();
	UInt nb = nodes.size();

	for (UInt i = 0; i < nb; ++i) {
	RefNode nd = el.getNode(i);
	#ifndef LM_OPTIMIZED
	Real mass_node = nd.mass();
	#endif
	LM_ASSERT(mass_node > 0, "invalid mass" << nodes[i] << " " << mass_node);

	auto X = nd.position0();
	for (UInt i = 0; i < Dim; ++i)
	node_coords.push_back(X[i]);
	}

	this->grid->addFiniteElement(nb_elem, node_coords);
	++nb_elem;
	}
	STOPTIMER("Filling spatial-grid");

	DUMP("we have found " << nb_elem << " concerned elements", DBG_INFO_STARTUP);
	DUMP("in average " << this->grid->getAverageEltByBlock()
	<< " elements par block",
	DBG_INFO_STARTUP);
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>

	void Bridging<ContainerPoints, ContainerMesh, Dim>::buildNodeList() {

	meshList.computeAlteredConnectivity(contMesh.getContainerNodes());
	UInt nb = meshList.size();
	if (!nb) {
	DUMP("We found no nodes in bridging zone", DBG_INFO_STARTUP);
	return;
	}

	DUMP("We found " << nb << " nodes concerned into "
	<< meshList.getContainerElems().size() << " elements",
	DBG_INFO_STARTUP);
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::buildPointList() {

	unmatchedPointList.setParam("GEOMETRY", this->geomID);
	unmatchedPointList.buildManual(contPoints);
	this->local_points = unmatchedPointList->size();

	if (!this->local_points)
	DUMP("We found no atom in the bridging zone", DBG_INFO);

	DUMP("We found " << this->local_points << " atom in the bridging zone",
	DBG_INFO_STARTUP);
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::buildShapeMatrix(
	UInt nb_atoms) {

	this->assoc.assign(nb_atoms, UINT_MAX);

	if (unmatchedMeshList->getContainerElems().size() == 0) {
	DUMP("elem_rec is empty!", DBG_WARNING);
	// delete grid;
	return;
	}

	std::vector<UInt> nb_atoms_per_element;
	nb_atoms_per_element.resize(unmatchedMeshList->getContainerElems().size());

	/* construction du array d'assoc atoms elem */

	STARTTIMER("Construction association");

	for (UInt i = 0; i < nb_atoms; ++i) {

	#ifndef TIMER
	if (i % 100000 == 0)
	DUMP("construction de l'association - atome " << i << "/" << nb_atoms,
	DBG_INFO);
	#endif

	LM_ASSERT(i * Dim < this->positions.size(), "overflow detected");

	Vector<Dim> x;
	for (UInt k = 0; k < Dim; ++k)
	x[k] = this->positions[i * Dim + k];

	std::vector<UInt> &subset_elts = this->grid->findSet(x);
	std::vector<UInt>::iterator it = subset_elts.begin();

	for (it = subset_elts.begin(); it != subset_elts.end(); ++it) {

	RefElem el = unmatchedMeshList->getContainerElems().get(*it);
	UInt j = *it;

	DUMP("is atom " << i << " within element " << j << "?", DBG_ALL);

	if (el.contains(x)) {
	LM_ASSERT(this->assoc[i] == UINT_MAX,
	"this should not happen. "
	<< "I found twice the same atom while filtering");
	DUMP("associating atom " << i << " and element " << j, DBG_ALL);
	this->assoc[i] = j;
	++assoc_found;
	break;
	}
	}

	if (it == subset_elts.end()) {
	this->assoc[i] = UINT_MAX;
	}
	}

	STOPTIMER("Construction association");

	/* build number of atoms per element */
	for (UInt i = 0; i < nb_atoms; ++i) {
	if (this->assoc[i] != UINT_MAX)
	++nb_atoms_per_element[this->assoc[i]];
	}

	/* filter element list and node list for the unassociated node and elements */
	filterContainerElems(nb_atoms_per_element);
	buildNodeList();

	smatrix = new ShapeMatrix<Dim>(meshList.getContainerElems().size());

	UInt i = 0;
	for (auto &&el : meshList.getContainerElems()) {
	DUMP("declare sub matrix number " << i << " which will be of size "
	<< nb_atoms_per_element[i] << "x"
	<< el.nNodes(),
	DBG_ALL);
	LM_ASSERT(nb_atoms_per_element[i] > 0, "this should not happen any more");
	// if (nb_atoms_per_element[i]>0)
	smatrix->setSub(i, nb_atoms_per_element[i], el.nNodes());
	++i;
	}
	// Allocate the shapematrix structure (contiguous)
	smatrix->allocate();

	/* set the indirection (alloc tab) plus the shapes */
	std::vector<Real> shapes;

	UInt atom_index = 0;

	for (i = 0; i < nb_atoms; ++i) {
	if (this->assoc[i] == UINT_MAX)
	continue;

	Real X[3] = {0.0, 0.0, 0.0};
	for (UInt k = 0; k < Dim; ++k)
	X[k] = this->positions[i * Dim + k];

	auto el = meshList.getContainerElems().get(this->assoc[i]);
	el.computeShapes(shapes, X);
	auto &&nodes = el.globalIndexes();

	IF_TRACED(X, "checking for atom in trouble");

	for (UInt j = 0; j < shapes.size(); ++j)
	smatrix->fill(atom_index, nodes[j], meshList.subIndex2Index(nodes[j]),
	this->assoc[i], shapes[j]);
	++atom_index;
	}
	}
	/* -------------------------------------------------------------------------- */
	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::buildLocalPBCPairs() {

	UInt npairs = pbc_pairs.size();
	for (UInt pair = 0; pair < npairs; ++pair) {
	UInt ind1 = pbc_pairs[pair].first;
	UInt ind2 = pbc_pairs[pair].second;
	UInt i1 = meshList.subIndex2Index(ind1);
	UInt i2 = meshList.subIndex2Index(ind2);
	if (i1 == UINT_MAX \|\| i2 == UINT_MAX)
	continue;

	std::pair<UInt, UInt> p((UInt)(i1), (UInt)(i2));
	local_pbc_pairs.push_back(p);
	}
	DUMP("Detected " << local_pbc_pairs.size() << " local pairs", DBG_MESSAGE);
	smatrix->alterMatrixIndexesForPBC(local_pbc_pairs);
	}
	/* -------------------------------------------------------------------------- */
	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::buildNodeShape() {

	if (this->local_points == 0)
	return;

	UInt nb_coupled_nodes = meshList.size();
	node_shape.assign(nb_coupled_nodes, 0);

	LM_ASSERT(smatrix,
	"shapematrix object was not allocated "
	<< " eventhough local atoms were detected");
	smatrix->buildNodeShape(node_shape);

	buildLocalPBCPairs();
	cumulPBC(node_shape);

	#ifndef LM_OPTIMIZED

	for (UInt i = 0; i < nb_coupled_nodes; ++i) {
	if (node_shape[i] <= 1e-1) {
	DUMP(i << " " << node_shape[i], DBG_MESSAGE);
	LM_FATAL("Please check your geometry:"
	<< " one or more nodes has zero nodal shape values."
	<< " Changing the FE element size may resolve this issue!"
	<< std::endl);
	}
	}

	#endif // LM_OPTIMIZED

	FilterManager::getManager().addObject(node_shape);
	}
	/* -------------------------------------------------------------------------- */
	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::filterContainerElems(
	std::vector<UInt> &nb_atome_par_element) {

	typename ContainerMeshSubset::ContainerElems new_t(this->getID() + ":elems");
	std::vector<int> new_index;

	for (UInt i = 0; i < nb_atome_par_element.size(); ++i) {
	DUMP("filtering old index element " << i, DBG_ALL);
	if (nb_atome_par_element[i] > 0) {

	DUMP("for container, elem " << i << " becomes " << new_t.size(), DBG_ALL);
	new_index.push_back(new_t.size());

	DUMP("maintenant nb_atome_par_element["
	<< new_t.size() << "]= " << nb_atome_par_element[i]
	<< " (i=" << i << ")",
	DBG_ALL);
	nb_atome_par_element[new_t.size()] = nb_atome_par_element[i];
	new_t.add(unmatchedMeshList->getContainerElems().get(i));
	} else
	new_index.push_back(new_t.size());
	}
	nb_atome_par_element.resize(new_t.size());
	meshList.clear();

	// rebuild the element container
	for (UInt i = 0; i < new_t.size(); ++i)
	meshList.getContainerElems().add(new_t.get(i));
	// rebuild the association list
	for (UInt i = 0; i < this->assoc.size(); ++i) {
	if (this->assoc[i] != UINT_MAX) {
	this->assoc[i] = new_index[this->assoc[i]];
	}
	}
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh,
	Dim>::filterPointListForUnmatched() {

	pointList.clear();

	for (UInt i = 0; i < this->assoc.size(); ++i)
	if (this->assoc[i] != UINT_MAX) {
	DUMP("for container, atom " << i << " becomes " << pointList.size(),
	DBG_ALL);
	pointList.add(unmatchedPointList->get(i));
	} else {
	DUMP("atom filtered " << i << " " << unmatchedPointList->get(i),
	DBG_DETAIL);
	}
	pointList.copyContainerInfo(unmatchedPointList);
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::filterArray(
	std::vector<Real> &array, UInt stride) {
	UInt index = 0;

	for (UInt i = 0; i < this->assoc.size(); ++i)
	if (this->assoc[i] != UINT_MAX) {
	DUMP("for container, atom " << i << " becomes " << index, DBG_ALL);
	LM_ASSERT(i < array.size() && index < array.size(),
	"overflow detected: nmax = " << array.size() << " , index = "
	<< index << " and i = " << i);

	for (UInt k = 0; k < stride; ++k)
	array[stride * index + k] = array[stride * i + k];
	++index;
	}
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::allocateBuffer(
	UInt size, UInt stride) {

	if (size > buffer.size()) {
	buffer.assign(stride * size, 0);
	DUMP("allocating buffer of size " << size * stride, DBG_INFO);
	}
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::interpolatePointData(
	std::vector<Real> &data_atom, std::vector<Real> &data_node, UInt stride) {

	if (this->local_points == 0) {
	DUMP("Warning : atomic container is empty:"
	<< " cannot interpolate mesh fields on control points (check "
	"geometries ?!)",
	DBG_WARNING);
	return;
	}
	smatrix->interpolate(data_atom, data_node, stride);
	}

	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::cumulPBC(
	std::vector<Real> &data, UInt stride) {

	UInt npairs = local_pbc_pairs.size();
	DUMP("Detected " << npairs << " local pairs", DBG_INFO);
	for (UInt pair = 0; pair < npairs; ++pair) {
	UInt i1 = local_pbc_pairs[pair].first;
	UInt i2 = local_pbc_pairs[pair].second;

	for (UInt k = 0; k < stride; ++k) {
	data[i2 * stride + k] += data[stride * i1 + k];
	DUMP("cumul pbc : [" << i2 * stride + k << "] = " << data[i2 * stride + k]
	<< " += [" << i2 * stride + k
	<< "] = " << data[stride * i1 + k] << " := "
	<< data[stride * i1 + k] + data[stride * i2 + k],
	DBG_DETAIL);
	}
	}
	for (UInt pair = 0; pair < npairs; ++pair) {
	UInt i1 = local_pbc_pairs[pair].first;
	UInt i2 = local_pbc_pairs[pair].second;
	for (UInt k = 0; k < stride; ++k)
	data[stride * i1 + k] = data[stride * i2 + k];
	}
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::leastSquarePointData(
	std::vector<Real> &v_out, std::vector<Real> &data_atom, UInt stride,
	UInt nmax) {
	LM_TOIMPLEMENT;
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::solveLeastSquare(
	std::vector<Real> &mesh_data, std::vector<Real> &atomic_data, UInt stride) {

	// build right hand side of leastsquare system
	mesh_data.assign(stride * meshList.size(), 0);
	smatrix->buildLeastSquareRHS(mesh_data, atomic_data, stride);
	cumulPBC(mesh_data, stride);

	LM_ASSERT(node_shape.size() != 0,
	"node_shape is empty this should not happen, check geometry");
	// solve least square system
	for (UInt i = 0; i < meshList.size(); ++i)
	for (UInt k = 0; k < stride; ++k) {
	DUMP(mesh_data[i * stride + k]
	<< " / " << node_shape[i] << " = "
	<< mesh_data[i * stride + k] / node_shape[i],
	DBG_DETAIL);
	mesh_data[i * stride + k] /= node_shape[i];
	}
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::averageOnElements(
	std::vector<Real> &data_atomic, std::vector<Real> &data_mesh, UInt stride) {

	data_mesh.assign(stride * meshList.getContainerElems().size(), 0);
	smatrix->averageOnElements(data_atomic, data_mesh, stride);
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::clearAll() {
	if (smatrix)
	delete smatrix;
	smatrix = NULL;
	meshList.getContainerElems().clear();
	// nodeList.clear();
	assoc_found = 0;
	this->assoc.clear();
	pointList.clear();
	}

	/* -------------------------------------------------------------------------- */
	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::buildLeastSquareMatrix(
	math::Matrix &mat) {
	smatrix->buildLeastSquareMatrix(&mat);
	cumulPBC(mat);
	}

	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::cumulPBC(
	math::Matrix &mat) {

	UInt npairs = local_pbc_pairs.size();

	for (UInt pair = 0; pair < npairs; ++pair) {
	UInt i1 = local_pbc_pairs[pair].first;
	UInt i2 = local_pbc_pairs[pair].second;
	for (UInt j = 0; j < mat.n(); ++j) {
	mat(i2, j) += mat(i1, j);
	}
	}

	for (UInt pair = 0; pair < npairs; ++pair) {
	UInt i1 = local_pbc_pairs[pair].first;
	for (UInt j = 0; j < mat.n(); ++j) {
	if (i1 == j)
	mat(i1, j) = 1.;
	else
	mat(i1, j) = 0.;
	}
	}
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::copySlaveValues(
	std::vector<Real> &v, UInt stride) {

	UInt npairs = local_pbc_pairs.size();

	for (UInt pair = 0; pair < npairs; ++pair) {
	UInt i1 = local_pbc_pairs[pair].first;
	UInt i2 = local_pbc_pairs[pair].second;
	for (UInt k = 0; k < stride; ++k) {
	v[i1 * stride + k] = v[i2 * stride + k];
	}
	}
	}

	/* -------------------------------------------------------------------------- */
	template <typename ContainerPoints, typename ContainerMesh, UInt Dim>
	void Bridging<ContainerPoints, ContainerMesh, Dim>::extractShapeMatrix(
	math::Matrix &mat) {
	smatrix->extractShapeMatrix(&mat);
	}

	/* -------------------------------------------------------------------------- */
	/* Parallel Methods */
	/* -------------------------------------------------------------------------- */

	template <typename DomainA, typename DomainC, UInt Dim>
	void Bridging<DomainA, DomainC, Dim>::communicateBufferAtom2Continuum(
	UInt stride, std::vector<Real> &buf) {

	if (this->local_points != 0) {
	this->distributeVectorA2B("communicate buffer", buf, stride);
	}
	}
	/* -------------------------------------------------------------------------- */

	template <typename DomainA, typename DomainC, UInt Dim>
	void Bridging<DomainA, DomainC, Dim>::communicateBufferContinuum2Atom(
	UInt stride, std::vector<Real> &buf) {

	if (this->local_points != 0) {
	this->distributeVectorB2A("communicate buffer", buf, stride);
	}
	}
	/* -------------------------------------------------------------------------- */

	template <typename DomainA, typename DomainC, UInt Dim>
	void Bridging<DomainA, DomainC, Dim>::synchSumBuffer(UInt stride,
	std::vector<Real> &buf) {

	if (this->local_points != 0) {
	this->synchronizeVectorBySum("synchsumvector", buf, stride);
	}
	}
	/* -------------------------------------------------------------------------- */

	template <typename ContainerA, typename ContainerB, UInt Dim>
	void Bridging<ContainerA, ContainerB, Dim>::filterRejectedContinuumOwners(
	std::vector<std::vector<UInt>> &unassociated_atoms) {

	if (this->comm_group_A == this->comm_group_B)
	return;

	if (this->in_group_B) {
	DUMP("local points", DBG_MESSAGE);
	if (this->local_points == 0)
	return;

	UInt offset = 0;
	// recompute indexes of continuum atoms
	std::vector<int> current_indexes(this->assoc.size());
	{
	UInt indirection = 0;
	for (UInt at = 0; at < this->assoc.size(); ++at) {
	current_indexes[at] = -1;
	if (this->assoc[at] == UINT_MAX)
	continue;
	current_indexes[at] = indirection;
	++indirection;
	}
	LM_ASSERT(indirection == this->local_points,
	"this should not happend " << indirection << " "
	<< this->local_points);
	}
	// remove unassociated atoms
	{
	offset = 0;
	UInt cpt = 0;
	for (UInt i = 0; i < this->nb_zone_A; ++i) {
	if (this->com_with[i]) {
	DUMP("atomic processor " << i << " unassociated "
	<< unassociated_atoms[i].size() << " atoms ",
	DBG_INFO_STARTUP);
	UInt size = unassociated_atoms[i].size();
	for (UInt j = 0; j < size; ++j) {
	// get element that owned the atom
	UInt at_index = offset + unassociated_atoms[i][j];
	LM_ASSERT(this->assoc[at_index] != UINT_MAX,
	"this should not happend !! " << at_index);
	LM_ASSERT(current_indexes[at_index] != -1,
	"this should not happend !! " << at_index);

	UInt el = this->assoc[at_index];
	this->smatrix->removeAtom(current_indexes[at_index], el);
	this->assoc[at_index] = UINT_MAX;
	++cpt;
	DUMP("unassociated atom at position "
	<< at_index << " whereas offset = " << offset
	<< " next offset is "
	<< offset + this->nb_points_per_proc[i],
	DBG_INFO_STARTUP);
	}
	offset += this->nb_points_per_proc[i];
	}
	}
	if (cpt) {
	DUMP("removed " << cpt
	<< " atoms from unassociation. Now local atoms is "
	<< this->local_points,
	DBG_MESSAGE);
	this->local_points -= cpt;
	DUMP("and becomes " << this->local_points, DBG_MESSAGE);
	}
	}
	// little check
	{
	UInt cpt_tmp = 0;
	for (UInt i = 0; i < this->assoc.size(); ++i)
	if (this->assoc[i] != UINT_MAX)
	cpt_tmp++;

	if (cpt_tmp != this->local_points)
	LM_FATAL("biip this should not happend " << cpt_tmp << " "
	<< this->local_points);
	}
	// now renumber indirection in shapematrix
	{
	UInt indirection = 0;
	for (UInt at = 0; at < this->assoc.size(); ++at) {
	if (this->assoc[at] == UINT_MAX)
	continue;
	LM_ASSERT(current_indexes[at] != -1, "This should not happend");
	this->smatrix->changeAtomIndirection(this->assoc[at],
	current_indexes[at], indirection);
	++indirection;
	}
	this->smatrix->swapAtomIndirections();
	}
	// //now i set the duo vector
	this->createDuoVectorB("FE");
	// std::stringstream sstr;
	// sstr << "duoFE-" << this->getID();
	// DuoDistributedVector & duo =
	// this->createDuoVector(this->local_points,this->total_points);

	// UInt counter = 0;
	// offset = 0;
	// for (UInt i = 0 ; i < this->nb_zone_A ; ++i)
	// if (this->com_with[i]){
	// for (UInt j = 0 ; j < this->nb_points_per_proc[i] ; ++j)
	// if (this->assoc[j+offset] != UINT_MAX){
	// duo.setDuoProc(counter,i);
	// ++counter;
	// }
	// DUMP("compteur is " << counter << " after treating atoms from " << i
	// << " offset is " << offset,DBG_INFO_STARTUP);
	// offset += this->nb_points_per_proc[i];
	// }
	}
	}

	/* -------------------------------------------------------------------------- */

	template <typename DomainA, typename DomainC, UInt Dim>
	void Bridging<DomainA, DomainC, Dim>::updateForMigration() {

	DUMPBYPROC("update migration for " << this->getID(), DBG_INFO, 0);

	STARTTIMER("syncMigration resize");
	// update local number of atoms in atomic part
	if (this->in_group_A) {
	this->local_points = this->pointList.size();
	this->positions.resize(Dim * this->local_points);
	}
	STOPTIMER("syncMigration resize");

	STARTTIMER("syncMigration duo");
	this->synchronizeMigration(this->comm_group_A, this->comm_group_B);
	STOPTIMER("syncMigration duo");

	// pointList.setRelease(this->contA.getRelease());
	// meshList.setRelease(this->contB.getRelease());
	}
	/* -------------------------------------------------------------------------- */

	/* LMDESC Bridging
	This class implements a bridging zone where
	point and elements are associated. \\ \\

	For debugging pruposes, several set of DOf are registered to the central
	system:

	\begin{itemize}
	\item unmatched-fe-\${couplerID} : the set of nodes and elements
	that are contained in the geometry provided by GEOMETRY keyword.
	\item unmatched-point-\${couplerID} : the set of points
	that are contained in the geometry provided by GEOMETRY keyword.
	\item matched-fe-\${couplerID} : the set of nodes and elements
	that are containing at least one point of unmatched-point-\${couplerID}.
	\item matched-point-\${couplerID} : the set of points
	that are contained in at least one element of unmatched-fe-\${couplerID}.
	\end{itemize}
	*/

	/* LMHERITANCE filter_geometry dof_association */

	template <typename ContainerA, typename ContainerB, UInt Dim>
	void Bridging<ContainerA, ContainerB, Dim>::declareParams() {

	this->addSubParsableObject(unmatchedMeshList);

	DofAssociation<ContainerA, ContainerB, Dim>::declareParams();
	}
	/* -------------------------------------------------------------------------- */

	DECLARE_BRIDGING_ATOMIC_CONTINUUM_TEMPLATE(Bridging)
	DECLARE_BRIDGING_DD_CONTINUUM_TEMPLATE(Bridging)

	__END_LIBMULTISCALE__

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