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mesh_sphere_intersector_tmpl.hh
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			/**
			* @file mesh_sphere_intersector_tmpl.hh
			*
			* @author Clément Roux-Langlois <clement.roux@epfl.ch>
			*
			* @date creation: Wed june 10 2015
			* @date last modification: Wed June 17 2015
			*
			* @brief Computation of mesh intersection with spheres
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2015 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/>.
			*
			*/

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

			#ifndef __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__
			#define __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__

			#include "aka_common.hh"
			#include "mesh_geom_common.hh"
			#include "tree_type_helper.hh"
			#include "mesh_sphere_intersector.hh"
			#include "static_communicator.hh"

			__BEGIN_AKANTU__

			template<UInt dim, ElementType type>
			MeshSphereIntersector<dim, type>::MeshSphereIntersector(Mesh & mesh,
			const ID & id,
			const MemoryID & memory_id):
			parent_type(mesh, id, memory_id),
			tol_intersection_on_node(1e-10),
			nb_nodes_fem(mesh.getNodes().getSize()),
			nb_prim_by_el(0)
			{
			this->intersection_points = new Array<Real>(0,dim);

			for(Mesh::type_iterator it = mesh.firstType(dim); it != mesh.lastType(dim); ++it){
			#if defined(AKANTU_IGFEM)
			if(*it == _triangle_3){
			// Addition of the igfem types in the mesh
			this->mesh.addConnectivityType(_igfem_triangle_4, _not_ghost);
			this->mesh.addConnectivityType(_igfem_triangle_4, _ghost);
			this->mesh.addConnectivityType(_igfem_triangle_5, _not_ghost);
			this->mesh.addConnectivityType(_igfem_triangle_5, _ghost);
			}

			else if( (it != _triangle_3) && (it != _igfem_triangle_4) && (*it != _igfem_triangle_5) ) {
			AKANTU_DEBUG_ERROR("Not ready for mesh type " << *it);
			}

			if( (type == _triangle_3) \|\| (type == _igfem_triangle_4) \|\| (type == _igfem_triangle_5) ){
			this->nb_prim_by_el = 3;
			const_cast<UInt &>(this->nb_seg_by_el) = 3;
			} else {
			AKANTU_DEBUG_ERROR("Not ready for mesh type " << type);
			}
			#else
			if( (*it != _triangle_3) )
			AKANTU_DEBUG_ERROR("Not ready for mesh type " << *it);
			this->nb_prim_by_el = 3;
			#endif
			}

			for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
			GhostType ghost_type = *gt;
			UInt nb_comp = 1 + nb_prim_by_el * 2;
			this->new_node_per_elem.alloc(0, nb_comp, type, ghost_type, 0);
			// std::cout << "new_node_per_elem size = " << this->new_node_per_elem(type,ghost_type).getSize() << " (type = " << type << ", ghost_type = " << ghost_type << ")" << std::endl;
			}

			this->constructData();
			}

			template<UInt dim, ElementType type>
			MeshSphereIntersector<dim, type>::~MeshSphereIntersector()
			{}

			template<UInt dim, ElementType type>
			void MeshSphereIntersector<dim, type>::constructData() {

			for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
			GhostType ghost_type = *gt;
			this->new_node_per_elem(type, ghost_type).resize(this->mesh.getNbElement(type, ghost_type));
			this->new_node_per_elem(type, ghost_type).clear();
			}

			MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK>::constructData();
			}

			template<UInt dim, ElementType type>
			void MeshSphereIntersector<dim, type>::computeIntersectionQuery(const SK::Sphere_3 & query) {
			AKANTU_DEBUG_IN();

			Array<Real> & nodes = this->mesh.getNodes();
			UInt nb_node = nodes.getSize();
			UInt nb_not_ghost_elements = this->mesh.getNbElement(type);

			// Tolerance for proximity checks should be defined by user
			Math::setTolerance(tol_intersection_on_node);
			typedef boost::variant<pair_type> sk_inter_res;

			TreeTypeHelper<Line_arc<Spherical>, Spherical>::const_iterator
			it = this->factory.getPrimitiveList().begin(),
			end= this->factory.getPrimitiveList().end();

			#if defined(AKANTU_IGFEM)
			NewIGFEMNodesEvent new_nodes;
			#else
			NewNodesEvent new_nodes;
			#endif

			for (; it != end ; ++it) {
			std::list<sk_inter_res> s_results;
			CGAL::intersection(*it, query, std::back_inserter(s_results));

			if (s_results.size() == 1) { // just one point
			if (pair_type * pair = boost::get<pair_type>(&s_results.front())) {
			if (pair->second == 1) { // not a point tangent to the sphere
			// Addition of the new node
			Vector<Real> new_node(dim, 0.0);
			Cartesian::Point_3 point(CGAL::to_double(pair->first.x()),
			CGAL::to_double(pair->first.y()),
			CGAL::to_double(pair->first.z()));

			for (UInt i = 0 ; i < dim ; i++) {
			new_node(i) = point[i];
			}

			bool is_on_mesh = false, is_new = true;
			// check if we already compute this intersection for a neighboor element
			UInt n = nb_nodes_fem-1;
			for (; n < nb_node ; ++n) {
			Array<Real>::vector_iterator existing_node = nodes.begin(dim) + n;
			if (Math::are_vector_equal(dim, new_node.storage(), existing_node->storage())) {
			is_new = false;
			break;
			}
			}

			Cartesian::Point_3 source_cgal(CGAL::to_double(it->source().x()),
			CGAL::to_double(it->source().y()),
			CGAL::to_double(it->source().z()));
			Cartesian::Point_3 target_cgal(CGAL::to_double(it->target().x()),
			CGAL::to_double(it->target().y()),
			CGAL::to_double(it->target().z()));

			Vector<Real> source(dim), target(dim);
			for (UInt i = 0 ; i < dim ; i++) {
			source(i) = source_cgal[i];
			target(i) = target_cgal[i];
			}

			// Check if we are close from a node of the segment
			if (Math::are_vector_equal(dim, source.storage(), new_node.storage()) \|\|
			Math::are_vector_equal(dim, target.storage(), new_node.storage())) {
			is_on_mesh = true;
			is_new = false;
			}

			if (is_new) {
			nodes.push_back(new_node);
			new_nodes.getList().push_back(nb_node);
			nb_node++;
			}

			// deduce ghost type and element id
			UInt element_id = it->id();
			GhostType ghost_type = _not_ghost;
			if (element_id >= nb_not_ghost_elements) {
			element_id -= nb_not_ghost_elements;
			ghost_type = _ghost;
			}

			Array<UInt> & new_node_per_elem_array = this->new_node_per_elem(type, ghost_type);

			if (!is_on_mesh) {
			new_node_per_elem_array(element_id, 0) += 1;
			new_node_per_elem_array(element_id, (2 * new_node_per_elem_array(element_id, 0)) - 1) = n;
			new_node_per_elem_array(element_id, 2 * new_node_per_elem_array(element_id, 0)) = it->segId();
			} else {
			// if intersection is at a node, write node number (in el) in pennultimate position
			if (Math::are_vector_equal(dim, source.storage(), new_node.storage())) {
			new_node_per_elem_array(element_id, (new_node_per_elem_array.getNbComponent() - 2)) = it->segId() - 1;
			} else {
			new_node_per_elem_array(element_id, (new_node_per_elem_array.getNbComponent() - 2)) =
			it->segId() % this->nb_prim_by_el;
			}
			}
			}
			}
			}
			}

			if(new_nodes.getList().getSize()) {
			#if defined(AKANTU_IGFEM)
			new_nodes.setNewNodePerElem(this->new_node_per_elem);
			new_nodes.setType(type);
			#endif
			this->mesh.sendEvent(new_nodes);
			}

			AKANTU_DEBUG_OUT();
			}

			template<UInt dim, ElementType type>
			void MeshSphereIntersector<dim, type>:: computeMeshQueryIntersectionPoint(const SK::Sphere_3 & query) {
			/// function to replace computeIntersectionQuery in a more generic geometry module version
			// The newNodeEvent is not send from this method who only compute the intersection points
			AKANTU_DEBUG_IN();

			Array<Real> & nodes = this->mesh.getNodes();
			UInt nb_node = nodes.getSize() + this->intersection_points->getSize();
			UInt nb_not_ghost_elements = this->mesh.getNbElement(type);

			// Tolerance for proximity checks should be defined by user
			Math::setTolerance(tol_intersection_on_node);
			typedef boost::variant<pair_type> sk_inter_res;

			TreeTypeHelper<Line_arc<Spherical>, Spherical>::const_iterator
			it = this->factory.getPrimitiveList().begin(),
			end= this->factory.getPrimitiveList().end();

			for (; it != end ; ++it) {
			std::list<sk_inter_res> s_results;
			CGAL::intersection(*it, query, std::back_inserter(s_results));

			if (s_results.size() == 1) { // just one point
			if (pair_type * pair = boost::get<pair_type>(&s_results.front())) {
			if (pair->second == 1) { // not a point tangent to the sphere
			// Addition of the new node
			Vector<Real> new_node(dim, 0.0);
			Cartesian::Point_3 point(CGAL::to_double(pair->first.x()),
			CGAL::to_double(pair->first.y()),
			CGAL::to_double(pair->first.z()));

			for (UInt i = 0 ; i < dim ; i++) {
			new_node(i) = point[i];
			}

			bool is_on_mesh = false, is_new = true;
			// check if we already compute this intersection for a neighboor element
			UInt n = nb_nodes_fem;
			Array<Real>::vector_iterator existing_node = nodes.begin(dim);
			for (; n < nodes.getSize() ; ++n) {
			if (Math::are_vector_equal(dim, new_node.storage(), existing_node[n].storage())) {
			is_new = false;
			break;
			}
			}
			if(is_new){
			Array<Real>::vector_iterator intersection_points_it = this->intersection_points->begin(dim);
			Array<Real>::vector_iterator intersection_points_end = this->intersection_points->end(dim);
			for (; intersection_points_it != intersection_points_end ; ++intersection_points_it, ++n) {
			if (Math::are_vector_equal(dim, new_node.storage(), intersection_points_it->storage())) {
			is_new = false;
			break;
			}
			}
			}

			Cartesian::Point_3 source_cgal(CGAL::to_double(it->source().x()),
			CGAL::to_double(it->source().y()),
			CGAL::to_double(it->source().z()));
			Cartesian::Point_3 target_cgal(CGAL::to_double(it->target().x()),
			CGAL::to_double(it->target().y()),
			CGAL::to_double(it->target().z()));

			Vector<Real> source(dim), target(dim);
			for (UInt i = 0 ; i < dim ; i++) {
			source(i) = source_cgal[i];
			target(i) = target_cgal[i];
			}

			// Check if we are close from a node of the segment
			if (Math::are_vector_equal(dim, source.storage(), new_node.storage()) \|\|
			Math::are_vector_equal(dim, target.storage(), new_node.storage())) {
			is_on_mesh = true;
			is_new = false;
			}

			if (is_new) {
			this->intersection_points->push_back(new_node);
			nb_node++;
			}

			// deduce ghost type and element id
			UInt element_id = it->id();
			GhostType ghost_type = _not_ghost;
			if (element_id >= nb_not_ghost_elements) {
			element_id -= nb_not_ghost_elements;
			ghost_type = _ghost;
			}

			Array<UInt> & new_node_per_elem_array = this->new_node_per_elem(type, ghost_type);

			if (!is_on_mesh) {
			new_node_per_elem_array(element_id, 0) += 1;
			new_node_per_elem_array(element_id, (2 * new_node_per_elem_array(element_id, 0)) - 1) = n;
			new_node_per_elem_array(element_id, 2 * new_node_per_elem_array(element_id, 0)) = it->segId();
			} else {
			// if intersection is at a node, write node number (in el) in pennultimate position
			if (Math::are_vector_equal(dim, source.storage(), new_node.storage())) {
			new_node_per_elem_array(element_id, (new_node_per_elem_array.getNbComponent() - 2)) = it->segId() - 1;
			} else {
			new_node_per_elem_array(element_id, (new_node_per_elem_array.getNbComponent() - 2)) =
			it->segId() % this->nb_prim_by_el;
			}
			}
			}
			}
			}
			}

			AKANTU_DEBUG_OUT();
			}

			template<UInt dim, ElementType type>
			void MeshSphereIntersector<dim, type>::removeAdditionnalNodes() {
			AKANTU_DEBUG_IN();

			RemovedNodesEvent remove_nodes(this->mesh);
			Array<UInt> & nodes_removed = remove_nodes.getList();
			Array<UInt> & new_numbering = remove_nodes.getNewNumbering();

			for(UInt i = 0 ; i < nb_nodes_fem ; ++i){
			new_numbering(i) = i;
			}

			for(UInt i = nb_nodes_fem ; i < this->mesh.getNodes().getSize(); ++i){
			new_numbering(i) = UInt(-1) ;
			nodes_removed.push_back(i);
			}

			this->mesh.sendEvent(remove_nodes);
			AKANTU_DEBUG_OUT();
			}


			#if defined(AKANTU_IGFEM)

			template<UInt dim, ElementType type>
			void MeshSphereIntersector<dim, type>::buildResultFromQueryList(const std::list<SK::Sphere_3> & query_list) {
			AKANTU_DEBUG_IN();

			this->computeIntersectionQueryList(query_list);

			NewIGFEMElementsEvent new_elements;
			UInt total_new_elements = 0;
			Array<Element> & new_elements_list = new_elements.getList();
			Array<Element> & old_elements_list = new_elements.getOldElementsList();
			RemovedElementsEvent remove_elem(this->mesh);
			Int nb_proc = StaticCommunicator::getStaticCommunicator().getNbProc();

			for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
			GhostType ghost_type = *gt;

			if (nb_proc == 1 && ghost_type == _ghost) continue;
			if (!this->mesh.getConnectivities().exists(type, ghost_type)) continue;
			UInt n_new_el = 0;
			Array<UInt> & connec_type_tmpl = this->mesh.getConnectivity(type, ghost_type);

			Array<UInt>
			& connec_igfem_tri4 = this->mesh.getConnectivity(_igfem_triangle_4, ghost_type),
			& connec_igfem_tri5 = this->mesh.getConnectivity(_igfem_triangle_5, ghost_type),
			& connec_tri3 = this->mesh.getConnectivity(_triangle_3, ghost_type);

			Element element_tri3(_triangle_3, 0, ghost_type, _ek_regular);
			Element element_tri4(_igfem_triangle_4, 0, ghost_type, _ek_igfem);
			Element element_tri5(_igfem_triangle_5, 0, ghost_type, _ek_igfem);


			remove_elem.getNewNumbering().alloc(connec_type_tmpl.getSize(), 1, type, ghost_type);
			Array<UInt> & new_numbering = remove_elem.getNewNumbering(type, ghost_type);
			UInt new_nb_type_tmpl = 0; // Meter of the number of element (type) will we loop on elements
			Array<UInt> & new_node_per_elem_array = this->new_node_per_elem(type, ghost_type);

			for (UInt nel = 0 ; nel != new_node_per_elem_array.getSize(); ++nel) {
			if( (type != _triangle_3)
			&& ( (new_node_per_elem_array(nel,0)==0)
			\|\| ( (new_node_per_elem_array(nel,0) == 1)
			&& ( ( (new_node_per_elem_array(nel,2)+1) % this->nb_prim_by_el )
			!= new_node_per_elem_array(nel, new_node_per_elem_array.getNbComponent() - 2) ) ) ) ){
			Element element_type_tmpl(type, 0, ghost_type, Mesh::getKind(type));
			new_elements_list.resize(n_new_el+1);
			old_elements_list.resize(n_new_el+1);
			Vector<UInt> ctri3(3);
			ctri3(0) = connec_type_tmpl(nel,0);
			ctri3(1) = connec_type_tmpl(nel,1);
			ctri3(2) = connec_type_tmpl(nel,2);
			/// add the new element in the mesh
			UInt nb_tri3 = connec_tri3.getSize();
			connec_tri3.push_back(ctri3);
			element_tri3.element = nb_tri3;
			new_elements_list(n_new_el) = element_tri3;
			/// the number of the old element in the mesh
			element_type_tmpl.element = nel;
			old_elements_list(n_new_el) = element_type_tmpl;
			new_numbering(nel) = UInt(-1);
			++n_new_el;

			remove_elem.getList().push_back(element_type_tmpl);

			}
			else if( (new_node_per_elem_array(nel,0)!=0)
			&& !( (new_node_per_elem_array(nel,0) == 1)
			&& ( ( (new_node_per_elem_array(nel,2)+1) % this->nb_prim_by_el )
			!= new_node_per_elem_array(nel, new_node_per_elem_array.getNbComponent() - 2) ) ) ){
			Element element_type_tmpl(type, 0, ghost_type);
			element_type_tmpl.kind = Mesh::getKind(type);
			new_elements_list.resize(n_new_el+1);
			old_elements_list.resize(n_new_el+1);
			switch(new_node_per_elem_array(nel,0)){
			case 1 :{
			Vector<UInt> ctri4(4);
			switch(new_node_per_elem_array(nel,2)){
			case 1 :
			ctri4(0) = connec_type_tmpl(nel,2);
			ctri4(1) = connec_type_tmpl(nel,0);
			ctri4(2) = connec_type_tmpl(nel,1);
			break;
			case 2 :
			ctri4(0) = connec_type_tmpl(nel,0);
			ctri4(1) = connec_type_tmpl(nel,1);
			ctri4(2) = connec_type_tmpl(nel,2);
			break;
			case 3 :
			ctri4(0) = connec_type_tmpl(nel,1);
			ctri4(1) = connec_type_tmpl(nel,2);
			ctri4(2) = connec_type_tmpl(nel,0);
			break;
			default :
			AKANTU_DEBUG_ERROR("A triangle have only 3 segments not "<< new_node_per_elem_array(nel,2));
			break;
			}
			ctri4(3) = new_node_per_elem_array(nel,1);
			UInt nb_tri4 = connec_igfem_tri4.getSize();
			connec_igfem_tri4.push_back(ctri4);
			element_tri4.element = nb_tri4;
			//new_elements.getList().push_back(element_tri4);
			new_elements_list(n_new_el) = element_tri4;
			if(type == _igfem_triangle_4)
			new_numbering.push_back(connec_igfem_tri4.getSize()-2);
			break;
			}
			case 2 :{
			Vector<UInt> ctri5(5);
			if( (new_node_per_elem_array(nel,2)==1) && (new_node_per_elem_array(nel,4)==2) ){
			ctri5(0) = connec_type_tmpl(nel,1);
			ctri5(1) = connec_type_tmpl(nel,2);
			ctri5(2) = connec_type_tmpl(nel,0);
			ctri5(3) = new_node_per_elem_array(nel,3);
			ctri5(4) = new_node_per_elem_array(nel,1);
			}
			else if((new_node_per_elem_array(nel,2)==1) && (new_node_per_elem_array(nel,4)==3)){
			ctri5(0) = connec_type_tmpl(nel,0);
			ctri5(1) = connec_type_tmpl(nel,1);
			ctri5(2) = connec_type_tmpl(nel,2);
			ctri5(3) = new_node_per_elem_array(nel,1);
			ctri5(4) = new_node_per_elem_array(nel,3);
			}
			else if((new_node_per_elem_array(nel,2)==2) && (new_node_per_elem_array(nel,4)==3)){
			ctri5(0) = connec_type_tmpl(nel,2);
			ctri5(1) = connec_type_tmpl(nel,0);
			ctri5(2) = connec_type_tmpl(nel,1);
			ctri5(3) = new_node_per_elem_array(nel,3);
			ctri5(4) = new_node_per_elem_array(nel,1);
			}
			else if((new_node_per_elem_array(nel,2)==2) && (new_node_per_elem_array(nel,4)==1)){
			ctri5(0) = connec_type_tmpl(nel,1);
			ctri5(1) = connec_type_tmpl(nel,2);
			ctri5(2) = connec_type_tmpl(nel,0);
			ctri5(3) = new_node_per_elem_array(nel,1);
			ctri5(4) = new_node_per_elem_array(nel,3);
			}
			else if((new_node_per_elem_array(nel,2)==3) && (new_node_per_elem_array(nel,4)==1)){
			ctri5(0) = connec_type_tmpl(nel,0);
			ctri5(1) = connec_type_tmpl(nel,1);
			ctri5(2) = connec_type_tmpl(nel,2);
			ctri5(3) = new_node_per_elem_array(nel,3);
			ctri5(4) = new_node_per_elem_array(nel,1);
			}
			else if((new_node_per_elem_array(nel,2)==3) && (new_node_per_elem_array(nel,4)==2)){
			ctri5(0) = connec_type_tmpl(nel,2);
			ctri5(1) = connec_type_tmpl(nel,0);
			ctri5(2) = connec_type_tmpl(nel,1);
			ctri5(3) = new_node_per_elem_array(nel,1);
			ctri5(4) = new_node_per_elem_array(nel,3);
			}
			else{
			AKANTU_DEBUG_ERROR("A triangle have only 3 segments not "<< new_node_per_elem_array(nel,2) << "and" << new_node_per_elem_array(nel,4));
			}
			UInt nb_tri5 = connec_igfem_tri5.getSize();
			connec_igfem_tri5.push_back(ctri5);
			element_tri5.element = nb_tri5;
			//new_elements.getList().push_back(element_tri5);
			new_elements_list(n_new_el) = element_tri5;
			if(type == _igfem_triangle_5){
			new_numbering.push_back(new_nb_type_tmpl);
			++new_nb_type_tmpl;
			}
			break;
			}
			default:
			AKANTU_DEBUG_ERROR("Igfem cannot add "<< new_node_per_elem_array(nel,0) << " nodes to triangles");
			break;
			}
			element_type_tmpl.element = nel;
			old_elements_list(n_new_el) = element_type_tmpl;
			remove_elem.getList().push_back(element_type_tmpl);
			new_numbering(nel) = UInt(-1);
			++n_new_el;
			}
			else{
			new_numbering(nel) = new_nb_type_tmpl;
			++new_nb_type_tmpl;
			}
			}

			// for(UInt nel=new_node_per_elem_array.getSize(); nel < this->mesh.getNbElement(type); ++nel) {
			// new_numbering(nel) = new_nb_type_tmpl;
			// ++new_nb_type_tmpl;
			// }

			UInt el_index = 0;
			for (UInt e = 0; e < this->mesh.getNbElement(type, ghost_type); ++e) {
			if (new_numbering(e) != UInt(-1)) {
			new_numbering(e) = el_index;
			++el_index;
			}
			}

			total_new_elements += n_new_el;
			}

			if(total_new_elements > 0){
			this->mesh.sendEvent(new_elements);
			this->mesh.sendEvent(remove_elem);
			}

			AKANTU_DEBUG_OUT();
			}

			#else

			template<UInt dim, ElementType type>
			void MeshSphereIntersector<dim, type>::buildResultFromQueryList(const std::list<SK::Sphere_3> & query_list) {
			AKANTU_DEBUG_TO_IMPLEMENT();
			}


			#endif

			__END_AKANTU__

			#endif // __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__

rAKA/src/geometry/mesh_sphere_intersector_tmpl.hhde3be14b9a19bugfixes/project_metada…

mesh_sphere_intersector_tmpl.hhView Options

rAKA/src/geometry/mesh_sphere_intersector_tmpl.hh
de3be14b9a19bugfixes/project_metada…

mesh_sphere_intersector_tmpl.hh
View Options