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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__
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