void Foam::cellShapeControlMesh::barycentricCoords
(
const Foam::point& pt,
barycentric& bary,
Cell_handle& ch
) const
{
// Use the previous cell handle as a hint on where to start searching
// Giving a hint causes strange errors...
ch = locate(toPoint(pt));
if (dimension() > 2 && !is_infinite(ch))
{
oldCellHandle_ = ch;
tetPointRef tet
(
topoint(ch->vertex(0)->point()),
topoint(ch->vertex(1)->point()),
topoint(ch->vertex(2)->point()),
topoint(ch->vertex(3)->point())
);
bary = tet.pointToBarycentric(pt);
}
}
double operator() (const AdvancingFront& adv, Cell_handle& c,
const int& index) const
{
// bound == 0 is better than bound < infinity
// as it avoids the distance computations
if(bound == 0){
return adv.smallest_radius_delaunay_sphere (c, index);
}
// If perimeter > bound, return infinity so that facet is not used
double d = 0;
d = sqrt(squared_distance(c->vertex((index+1)%4)->point(),
c->vertex((index+2)%4)->point()));
if(d>bound) return adv.infinity();
d += sqrt(squared_distance(c->vertex((index+2)%4)->point(),
c->vertex((index+3)%4)->point()));
if(d>bound) return adv.infinity();
d += sqrt(squared_distance(c->vertex((index+1)%4)->point(),
c->vertex((index+3)%4)->point()));
if(d>bound) return adv.infinity();
// Otherwise, return usual priority value: smallest radius of
// delaunay sphere
return adv.smallest_radius_delaunay_sphere (c, index);
}
// Returns whether the facet facet is attached to the cell
// that is used to represent facet
bool edge_attached_to(const DT_3& dt, const Edge& edge, const Facet& facet) {
if(dt.is_infinite(facet)) {
return false;
}
Vertex_handle v1 = edge.first->vertex(edge.second);
Vertex_handle v2 = edge.first->vertex(edge.third);
Cell_handle cell = facet.first;
int i1 = facet.second;
int i2 = cell->index(v1);
int i3 = cell->index(v2);
CGAL_assertion(i1!=i2);
CGAL_assertion(i1!=i3);
CGAL_assertion(i2!=i3);
int j = 0;
while(j==i1 || j==i2 || j==i3) {
j++;
}
// j is the index of the third point of the facet
Vertex_handle w = cell->vertex(j);
return CGAL::side_of_bounded_sphere(v1->point(),v2->point(),w->point())==CGAL::ON_BOUNDED_SIDE;
}
void draw_facets(Delaunay &Tr,std::vector<Facet> &facets,PointColor pcolors,CGAL::Geomview_stream &gv) {
if(! gv_on) return;
CGAL::Color colors[] = {CGAL::BLUE,CGAL::GREEN,CGAL::YELLOW,CGAL::DEEPBLUE,
CGAL::PURPLE,CGAL::VIOLET,CGAL::ORANGE,CGAL::RED};
if(pcolors.size() == 0)
return draw_facets(Tr,facets,gv);
// draw with color interpolation
for (std::vector<Facet>::iterator it = facets.begin();it != facets.end();it++) {
Facet f = *it;
Cell_handle c = f.first;
int j = f.second;
CGAL::Color vcolors[3];
int k = 0;
for(int i = 0;i < 4;i++)
if(i != j)
vcolors[k++] = pcolors[c->vertex(i)->info()];
int r = (vcolors[0].red() + vcolors[1].red() + vcolors[2].red()) / 3;
int g = (vcolors[0].green() + vcolors[1].green() + vcolors[2].green()) / 3;
int b = (vcolors[0].blue() + vcolors[1].blue() + vcolors[2].blue()) / 3;
gv << CGAL::Color(r,g,b);
// std::cout << "RGB " << r << " " << g << " " << b <<std::endl;
Triangle t = Tr.triangle(f);
gv << t;
}
}
AlphaSimplex3D::
AlphaSimplex3D(const Delaunay3D::Edge& e)
{
Cell_handle c = e.first;
Parent::add(c->vertex(e.second));
Parent::add(c->vertex(e.third));
}
AlphaSimplex3D::
AlphaSimplex3D(const Delaunay3D::Facet& f)
{
Cell_handle c = f.first;
for (int i = 0; i < 4; ++i)
if (i != f.second)
Parent::add(c->vertex(i));
}
double
cell_volume(const Cell_handle& c)
{
Tetrahedron t = Tetrahedron(c->vertex(0)->point(),
c->vertex(1)->point(),
c->vertex(2)->point(),
c->vertex(3)->point());
return ( CGAL::to_double(CGAL::abs(t.volume()) ) );
}
Point
circumcenter(const Facet& f)
{
Cell_handle c = f.first;
int id = f.second;
Point p[3];
for(int i = 0; i < 3; i ++)
p[i] = c->vertex((id + (i+1))%4)->point();
return cc_tr_3(p[0], p[1], p[2]);
}
void Foam::cellShapeControlMesh::writeTriangulation()
{
OFstream str
(
"refinementTriangulation_"
+ name(Pstream::myProcNo())
+ ".obj"
);
label count = 0;
Info<< "Write refinementTriangulation" << endl;
for
(
CellSizeDelaunay::Finite_edges_iterator e = finite_edges_begin();
e != finite_edges_end();
++e
)
{
Cell_handle c = e->first;
Vertex_handle vA = c->vertex(e->second);
Vertex_handle vB = c->vertex(e->third);
// Don't write far edges
if (vA->farPoint() || vB->farPoint())
{
continue;
}
// Don't write unowned edges
if (vA->referred() && vB->referred())
{
continue;
}
pointFromPoint p1 = topoint(vA->point());
pointFromPoint p2 = topoint(vB->point());
meshTools::writeOBJ(str, p1, p2, count);
}
if (is_valid())
{
Info<< " Triangulation is valid" << endl;
}
else
{
FatalErrorIn
(
"Foam::triangulatedMesh::writeRefinementTriangulation()"
) << "Triangulation is not valid"
<< abort(FatalError);
}
}
static void printCell(const Cell_handle &cell, const Vertex_handle &infinity)
{
DEBUG_START;
unsigned infinityIndex = cell->index(infinity);
for (unsigned i = 0; i < NUM_CELL_VERTICES; ++i)
if (i != infinityIndex)
std::cout << cell->vertex(i)->info()
<< " ";
std::cout << std::endl;
DEBUG_END;
}
/**
* Gets the material for the given point
* @param p The point to get the material for
* @return The material at the given point
*/
Contents StoneWeatherer::getContents( const Point & p ) const {
// Get a handle to the cell that contains the given point
Cell_handle ch = newDT->locate( p );
if ( newDT->is_infinite( ch ) ) {
return AIR;
}
else {
return ch->info();
}
}
// Calculates void volume and spheres area (only for own four spheres) of regular triangulation cell.
// Doesn't consider extraneous atoms from neighbor cells! True volume can be obtained only for cluster of cells comprising one connected void.
// S. Sastry, D.S. Corti, P.G. Debenedetti, F.H. Stillinger, "Statistical geometry of particle packings. I. Algorithm for exact determination of connectivity,
// volume, and surface areas of void space in monodisperse and polydisperse sphere packings", Phys. Rev. E, V.56, N5, p. 5524, 1997. doi:10.1103/PhysRevE.56.5524
double cell_void_volume(Cell_handle c, double &out_surf, Array_double_4 &out_atom_surf)
{
const Point *pts[4] = { &((c->vertex(0)->point()).point()),
&((c->vertex(1)->point()).point()),
&((c->vertex(2)->point()).point()),
&((c->vertex(3)->point()).point()) };
const Point &V = c->weighted_circumcenter().point(); // Voronoi vertex V
double volume = 0.0, surface = 0.0;
Array_double_4 per_atom_surface;
std::fill(per_atom_surface.begin(), per_atom_surface.end(), 0.0);
// General idea: consider 24 subsimplexes with three orthogonal edges
// by constructing normals from weighted circumcenter to the faces and then to the edges
for (int i = 0; i < 4; i++) { // iteration over cell facets
const Point *p_vertex_i = pts[i];
pts[i] = &V; // replace vertex(i) in array by weighted circumcenter of cell
CGAL::Sign sV = orientation(*pts[0], *pts[1], *pts[2], *pts[3]); // do V and vertex(i) on the same side of facet?
const int a[3] = { (i+1)%4, (i+2)%4, (i+3)%4 }; // indicies of atoms of face opposite to cell vertex i
const Point E = K::Plane_3(*pts[a[0]], *pts[a[1]], *pts[a[2]]).projection(V); // projection of Voronoi vertex to facet
const double z0 = sqrt((V-E).squared_length()); // length of normal to facet
for (int j = 0; j < 3; j++) { // iteration over facet edges
const int e[2] = { a[(j+1)%3], a[(j+2)%3] }; // indices of two edge atoms
const Weighted_point WA[2] = { c->vertex(e[0])->point(), c->vertex(e[1])->point() };
const Point A[2] = { WA[0].point(), WA[1].point() };
const CGAL::Sign sE = coplanar_orientation(A[0], A[1], *pts[a[j]], E);
const Point B = K::Line_3(A[0], A[1]).projection(E); // projection of E to edge
const double y0 = sqrt((E-B).squared_length());
for (int k = 0; k < 2; k++) { // iteration over edge ends (two atoms)
CGAL::Sign sB = CGAL::sign((B - A[k])*(A[(k+1)%2] - A[k])); // negative if point B is in other direction than opposite A[(k+1)%2] looking from A[k]
CGAL::Sign sF = sV * sE * sB; // final subsimplex sign
double x0 = sqrt((B-A[k]).squared_length());
double area;
volume += sF * subsimplex_void_volume(x0, y0, z0, WA[k].weight(), &area); // sum signed volume contribution from subsimplexes
surface += sF * area;
per_atom_surface[e[k]] += sF * area;
}
}
pts[i] = p_vertex_i; // place vertex(i) back to array
}
out_atom_surf = per_atom_surface;
out_surf = surface;
return volume;
}
// Returns whether the facet facet is attached to the cell
// that is used to represent facet
bool triangle_attached_to(const DT_3& dt, const Facet& facet) {
Cell_handle cell = facet.first;
int index = facet.second;
if(dt.is_infinite(cell)) {
return false;
}
Vertex_handle v1 = cell->vertex((index+1)%4);
Vertex_handle v2 = cell->vertex((index+2)%4);
Vertex_handle v3 = cell->vertex((index+3)%4);
Vertex_handle w = cell->vertex(facet.second);
return CGAL::side_of_bounded_sphere(v1->point(),v2->point(),v3->point(),w->point())==CGAL::ON_BOUNDED_SIDE;
}
void draw_line_tetra(Delaunay &Tr,std::vector<Cell_handle> &cells,CGAL::Geomview_stream &gv) {
if(! gv_on) return;
CGAL::Color colors[] = {CGAL::BLUE,CGAL::GREEN,CGAL::YELLOW,CGAL::DEEPBLUE,
CGAL::PURPLE,CGAL::VIOLET,CGAL::ORANGE,CGAL::RED};
int k = 0;
for (std::vector<Cell_handle>::iterator it = cells.begin();it != cells.end();it++,k++) {
Cell_handle c = *it;
gv << colors[k % 8];
Segment segs[4];
for(int i = 0;i < 4;i++) {
for(int j = i + 1;j < 4;j++) {
Segment s = Segment(c->vertex(i)->point(),c->vertex(j)->point());
gv << s;
}
}
}
}
void print(const Cell_handle c, const std::string& name) const
{
std::cerr << name << ":[" ;
for ( int i=0; i<4 ; ++i )
std::cerr << "[" << c->vertex(i)->point() << "]";
std::cerr << "] ";
}
Vertex_list fromCell(const Cell_handle& ch)
{
Vertex_list the_list;
for (auto i = 0; i < 4; i++)
{
the_list.push_back(ch->vertex(i));
}
return the_list;
}
bool
is_p_inside_cell(const Point& p, const Cell_handle& c, bool& is_degenerate)
{
is_degenerate = false;
for(int id = 0; id < 4; id ++)
{
Tetrahedron t1 (c->vertex((id+1)%4)->point(),
c->vertex((id+2)%4)->point(),
c->vertex((id+3)%4)->point(),
p);
Tetrahedron t2 (c->vertex((id+1)%4)->point(),
c->vertex((id+2)%4)->point(),
c->vertex((id+3)%4)->point(),
c->vertex(id)->point());
if( CGAL::is_negative(t1.volume()*t2.volume()) ) return false;
if( ! CGAL::is_positive(t1.volume()*t2.volume()) ) is_degenerate = true;
}
return true;
}
static std::vector<unsigned> calculateActiveGroup(const Cell_handle &cell,
unsigned iNearest,
const std::vector<SupportItem> &items)
{
DEBUG_START;
Vector_3 xOld = cell->info().point - CGAL::Origin();
std::vector<unsigned> activeGroup;
unsigned numUnresolvedCurrent = 0;
bool nearestFound = false;
for (unsigned iPlane : cell->info().associations)
{
const SupportItem &item = items[iPlane];
double delta = item.direction * xOld - item.value;
std::cout << " delta for plane #" << iPlane << "= " << delta
<< "; resolved: " << item.resolved << std::endl;
if (!item.resolved)
{
++numUnresolvedCurrent;
if (iPlane == iNearest)
{
activeGroup.push_back(iPlane);
nearestFound = true;
}
}
else
activeGroup.push_back(iPlane);
}
std::cout << " Number of current unresolved items: "
<< numUnresolvedCurrent << std::endl;
if (numUnresolvedCurrent == 0)
{
DEBUG_END;
return std::vector<unsigned>();
}
ASSERT(numUnresolvedCurrent > 0 && "Nothing to be resolved");
ASSERT(nearestFound && "Failed to find nearest point inside given "
"cell");
ASSERT(activeGroup.size() > NUM_FACET_VERTICES && "Not enough planes");
DEBUG_END;
return activeGroup;
}
AlphaSimplex3D::
AlphaSimplex3D(const Delaunay3D::Edge& e, const SimplexSet& simplices, const Delaunay3D& Dt, Facet_circulator facet_bg)
{
Cell_handle c = e.first;
Parent::add(c->vertex(e.second));
Parent::add(c->vertex(e.third));
Facet_circulator cur = facet_bg;
while (Dt.is_infinite(*cur)) ++cur;
SimplexSet::const_iterator cur_iter = simplices.find(AlphaSimplex3D(*cur));
RealValue min = cur_iter->alpha();
const VertexSet& vertices = static_cast<const Parent*>(this)->vertices();
VertexSet::const_iterator v = vertices.begin();
const DPoint& p1 = (*v++)->point();
const DPoint& p2 = (*v)->point();
attached_ = false;
if (facet_bg != 0) do
{
VertexSet::const_iterator v = vertices.begin();
int i0 = (*cur).first->index(*v++);
int i1 = (*cur).first->index(*v);
int i = 6 - i0 - i1 - (*cur).second;
if (Dt.is_infinite(cur->first->vertex(i))) { ++cur; continue; }
DPoint p3 = (*cur).first->vertex(i)->point();
cur_iter = simplices.find(AlphaSimplex3D(*cur));
if (CGAL::side_of_bounded_sphere(p1, p2, p3) == CGAL::ON_BOUNDED_SIDE)
attached_ = true;
RealValue val = cur_iter->alpha();
if (val < min)
min = val;
++cur;
} while (cur != facet_bg);
if (attached_)
alpha_ = min;
else
alpha_ = CGAL::squared_radius(p1, p2);
}
/**
* Computes the circumcenters of the given cell
* @param cell The cell to compute the circumcenters for
* @param result Stores the circumcenter
* @return TRUE always
*/
bool computeCircumcenter( const Cell_handle & cell, Point & result ) {
// The four vertices of the cell (tetrahedron)
const Point & p = cell->vertex( 0 )->point();
const Point & q = cell->vertex( 1 )->point();
const Point & r = cell->vertex( 2 )->point();
const Point & s = cell->vertex( 3 )->point();
// Translate p to the origin to simplify the expression
double qpx = q.x() - p.x();
double qpy = q.y() - p.y();
double qpz = q.z() - p.z();
double qp2 = square( qpx ) + square( qpy ) + square( qpz );
double rpx = r.x() - p.x();
double rpy = r.y() - p.y();
double rpz = r.z() - p.z();
double rp2 = square( rpx ) + square( rpy ) + square( rpz );
double spx = s.x() - p.x();
double spy = s.y() - p.y();
double spz = s.z() - p.z();
double sp2 = square( spx ) + square( spy ) + square( spz );
double determinant = CGAL::determinant( qpx, qpy, qpz, rpx, rpy, rpz, spx, spy, spz );
if ( determinant == 0 ) {
result = CGAL::ORIGIN + ( ( p - CGAL::ORIGIN ) * 0.25 + ( q - CGAL::ORIGIN ) * 0.25 + ( r - CGAL::ORIGIN ) * 0.25 + ( s - CGAL::ORIGIN ) * 0.25 );
return true;
}
double numX = CGAL::determinant( qpy, qpz, qp2, rpy, rpz, rp2, spy, spz, sp2 );
double numY = CGAL::determinant( qpx, qpz, qp2, rpx, rpz, rp2, spx, spz, sp2 );
double numZ = CGAL::determinant( qpx, qpy, qp2, rpx, rpy, rp2, spx, spy, sp2 );
double inverse = 1.0 / ( 2.0 * determinant );
result = Point( p.x() + numX * inverse, p.y() - numY * inverse, p.z() + numZ * inverse );
return true;
}
static Cell_handle findBestCell(const Vector_3 &direction,
const Vertex_handle &infinity,
const Cell_handle &startingCell)
{
DEBUG_START;
/* FIXME: Maybe some hint will be useful here */
ASSERT(startingCell->has_vertex(infinity) && "Wrong input");
Cell_handle bestCell = startingCell;
Cell_handle nextCell = bestCell;
double maxProduct = calculateProduct(direction, bestCell, infinity);
unsigned numIterations = 0;
do
{
++numIterations;
bestCell = nextCell;
ASSERT(bestCell->has_vertex(infinity) && "Wrong iteration");
int infinityIndex = bestCell->index(infinity);
for (int i = 0; i < NUM_CELL_VERTICES; ++i)
{
if (i == infinityIndex)
continue;
Cell_handle neighbor = bestCell->neighbor(i);
double product = calculateProduct(direction,
neighbor, infinity);
if (product > maxProduct)
{
nextCell = neighbor;
maxProduct = product;
}
}
} while (nextCell != bestCell);
ASSERT(bestCell->has_vertex(infinity) && "Wrong result");
DEBUG_END;
return bestCell;
}
static unsigned getNearestOuterItemID(const Cell_handle &cell,
const std::vector<SupportItem> &items,
const Vertex_handle &infinity)
{
DEBUG_START;
Plane_3 plane = getOppositeFacetPlane(cell, infinity);
Point_3 point = dual(plane);
cell->info().point = point;
double distanceMin = MINIMIZATION_STARTING_VALUE;
unsigned iNearest = 0;
const auto &associations = cell->info().associations;
unsigned numUnresolved = 0;
for (unsigned iPlane : associations)
{
SupportItem item = items[iPlane];
Vector_3 u = item.direction;
double value = item.value;
double distance = value - u * (point - CGAL::Origin());
if (!item.resolved)
{
ASSERT(distance > 0. && "Incorrect resolved flag");
if (distance < distanceMin)
{
iNearest = iPlane;
distanceMin = distance;
}
++numUnresolved;
}
}
if (numUnresolved > 0)
ASSERT(distanceMin < MINIMIZATION_STARTING_VALUE
&& "Failed to find");
cell->info().distance = distanceMin;
DEBUG_END;
return iNearest;
}
/**
* Finds a circumcenter in the grid and labels its associated cell
* @param point The location of the circumcenter
* @param cell The cell to label
* @param midpoint Stores the weighted midpoint of non-air cells
* @param volume Accumulates the volume of non-air cells
*/
void UniformGrid::locateAndLabel( const Point & point, Cell_handle & cell, double * midpoint, double & volume ) const {
Point3D p( point.x(), point.y(), point.z() );
unsigned int x = ( unsigned int ) ( ( p.x - xmin ) * inv_Xsize );
unsigned int y = ( unsigned int ) ( ( p.y - ymin ) * inv_Ysize );
unsigned int z = ( unsigned int ) ( ( p.z - zmin ) * inv_Zsize );
unsigned int i = ( ( ( My * z ) + y ) * Mx ) + x;
unsigned int start = grid[ i ];
unsigned int end = grid[ i + 1 ];
double tetrahedronVolume = 0.0;
for ( i = start; i < end; ++i ) {
if ( tetrahedrons[ L[ i ] ]->contains( p ) ) {
cell->info() = tetrahedrons[ L[ i ] ]->cell->info();
if ( cell->info() > AIR ) {
tetrahedronVolume = Tetrahedron::volume( cell );
#pragma omp critical(updateVolume)
{
volume += tetrahedronVolume;
midpoint[ 0 ] += p.x * tetrahedronVolume;
midpoint[ 1 ] += p.y * tetrahedronVolume;
midpoint[ 2 ] += p.z * tetrahedronVolume;
}
}
return;
}
}
cell->info() = AIR;
}
AlphaSimplex3D::
AlphaSimplex3D(const Delaunay3D::Facet& f, const SimplexSet& simplices, const Delaunay3D& Dt)
{
Cell_handle c = f.first;
for (int i = 0; i < 4; ++i)
if (i != f.second)
Parent::add(c->vertex(i));
Cell_handle o = c->neighbor(f.second);
int oi = o->index(c);
VertexSet::const_iterator v = static_cast<const Parent*>(this)->vertices().begin();
const DPoint& p1 = (*v++)->point();
const DPoint& p2 = (*v++)->point();
const DPoint& p3 = (*v)->point();
attached_ = false;
if (!Dt.is_infinite(c->vertex(f.second)) &&
CGAL::side_of_bounded_sphere(p1, p2, p3,
c->vertex(f.second)->point()) == CGAL::ON_BOUNDED_SIDE)
attached_ = true;
else if (!Dt.is_infinite(o->vertex(oi)) &&
CGAL::side_of_bounded_sphere(p1, p2, p3,
o->vertex(oi)->point()) == CGAL::ON_BOUNDED_SIDE)
attached_ = true;
else
alpha_ = CGAL::squared_radius(p1, p2, p3);
if (attached_)
{
if (Dt.is_infinite(c))
alpha_ = simplices.find(AlphaSimplex3D(*o))->alpha();
else if (Dt.is_infinite(o))
alpha_ = simplices.find(AlphaSimplex3D(*c))->alpha();
else
alpha_ = std::min(simplices.find(AlphaSimplex3D(*c))->alpha(),
simplices.find(AlphaSimplex3D(*o))->alpha());
}
}
bool
is_p_outside(const Point& q, const Triangulation& triang,
const Cell_handle& start_cell,
Cell_handle& c, int& u, int& v)
{
Triangulation::Locate_type lt;
u = -1; v = -1;
c = triang.locate(q, lt, u, v, start_cell);
if( lt == Triangulation::OUTSIDE_AFFINE_HULL )
{
cerr << "Point " << q << " is outside the affine hull." << endl;
return true;
}
else if( lt == Triangulation::OUTSIDE_CONVEX_HULL )
return true;
else
{
if( lt == Triangulation::CELL )
{
if( c->outside )
return true;
else
return false;
}
else if( lt == Triangulation::FACET )
{
Cell_handle _c = c->neighbor(u);
if( c->outside && _c->outside )
return true;
else
return false;
}
else if( lt == Triangulation::EDGE )
{
if( is_outside_VF(triang, Edge(c, u, v)) )
return true;
else
return false;
}
else
{
CGAL_assertion( lt == Triangulation::VERTEX );
return false;
}
}
}
/**
* Adds a new tetrahedron to the hierarchy
* @param cell The cell associated with the tetrahedron
*/
void UniformGrid::add( Cell_handle cell ) {
Point3D v0( cell->vertex( 0 )->point().x(), cell->vertex( 0 )->point().y(), cell->vertex( 0 )->point().z() );
Point3D v1( cell->vertex( 1 )->point().x(), cell->vertex( 1 )->point().y(), cell->vertex( 1 )->point().z() );
Point3D v2( cell->vertex( 2 )->point().x(), cell->vertex( 2 )->point().y(), cell->vertex( 2 )->point().z() );
Point3D v3( cell->vertex( 3 )->point().x(), cell->vertex( 3 )->point().y(), cell->vertex( 3 )->point().z() );
tetrahedrons.push_back( new Tetrahedron( v0, v1, v2, v3, cell ) );
xmin = MIN( xmin, MIN( MIN( v0.x, v1.x ), MIN( v2.x, v3.x ) ) );
ymin = MIN( ymin, MIN( MIN( v0.y, v1.y ), MIN( v2.y, v3.y ) ) );
zmin = MIN( zmin, MIN( MIN( v0.z, v1.z ), MIN( v2.z, v3.z ) ) );
xmax = MAX( xmax, MAX( MAX( v0.x, v1.x ), MAX( v2.x, v3.x ) ) );
ymax = MAX( ymax, MAX( MAX( v0.y, v1.y ), MAX( v2.y, v3.y ) ) );
zmax = MAX( zmax, MAX( MAX( v0.z, v1.z ), MAX( v2.z, v3.z ) ) );
}
void DualPolyhedron_3::associateVertex(const Vertex_handle &vertex)
{
DEBUG_START;
int iPlane = vertex->info();
if (isOuterVertex(vertex))
{
Cell_handle cell;
int iVertex, iInfinity;
bool result = is_edge(vertex, infinite_vertex(), cell,
iVertex, iInfinity);
ASSERT(result && "Wrong set");
TDelaunay_3::Edge edge(cell, iVertex, iInfinity);
auto circulator = incident_cells(edge);
auto end = circulator;
do
{
Cell_handle currentCell = circulator;
ASSERT(currentCell->has_vertex(vertex));
ASSERT(currentCell->has_vertex(infinite_vertex()));
currentCell->info().associations.insert(iPlane);
items[iPlane].associations.insert(currentCell);
items[iPlane].resolved = true;
++circulator;
} while (circulator != end);
}
else
{
Vector_3 direction = items[iPlane].direction;
Cell_handle bestCell = findBestCell(direction,
infinite_vertex(), infinite_cell());
bestCell->info().associations.insert(iPlane);
/* FIXME: Maybe the association for a plane is singular? */
items[iPlane].associations.insert(bestCell);
}
DEBUG_END;
}
bool is_degenerate_VF(const Triangulation& triang, const Cell_handle& c, const int& fid, const int& uid, const int& vid, const Point& d, const char* prefix)
{
char degen_op_filename[200];
strcat(strcpy(degen_op_filename, prefix), ".degen_VF");
// an extra check - probably not needed.
if (triang.is_infinite(c) || triang.is_infinite(c->neighbor(fid)) || triang.is_infinite(c->neighbor(6 - fid - uid - vid)))
{
return true;
}
vector<Cell_handle> VF;
Facet_circulator fcirc = triang.incident_facets(Edge(c,uid,vid));
Facet_circulator begin = fcirc;
do
{
if (triang.is_infinite((*fcirc).first))
{
cerr << "< Inf VF >";
return true; // by check-1 it is degenerate.
}
Cell_handle cur_c = (*fcirc).first;
int cur_fid = (*fcirc).second;
// check if cur_c and its cur_fid neighbors are cospherical.
if (is_cospherical_pair(triang, Facet(cur_c,cur_fid)))
{
cerr << "< Cosph VF >";
return true; // by check-2 it is degenerate.
}
fcirc ++;
}
while (fcirc != begin);
// check-3
Point vv[3];
vv[0] = c->voronoi();
vv[1] = c->neighbor(fid)->voronoi();
vv[2] = c->neighbor(6 - fid - uid - vid)->voronoi();
Vector v[3];
v[0] = vv[0] - d;
v[1] = vv[1] - d;
v[2] = vv[2] - d;
Vector v1xv0 = CGAL::cross_product(v[1], v[0]);
Vector v0xv2 = CGAL::cross_product(v[0], v[2]);
if (CGAL::to_double(v1xv0 * v0xv2) < 0)
{
ofstream fout;
fout.open(degen_op_filename, ofstream::app);
fout << "# prob : v1xv0 * v0xv2 = " <<
CGAL::to_double(v1xv0 * v0xv2) << endl;
fout << "{LIST " << endl;
fout << "# VF - color yellow " << endl;
draw_VF(triang, Edge(c, uid, vid), 1, 1, 0, 1, fout);
fout << "# v0 : segment(driver, voronoi(c)) - color red " << endl;
draw_segment(Segment(d, vv[0]), 1, 0, 0, 1, fout);
fout << "# v1 : segment(driver, voronoi(c->neighbor1)) - color green " << endl;
draw_segment(Segment(d, vv[1]), 0, 1, 0, 1, fout);
fout << "# v2 : segment(driver, voronoi(c->neighbor2)) - color blue " << endl;
draw_segment(Segment(d, vv[2]), 0, 0, 1, 1, fout);
fout << "}" << endl;
fout.close();
cerr << "< - v1xv0 * v0xv2 < 0 - >";
return true;
}
return false;
}
bool DualPolyhedron_3::lift(Cell_handle cell, unsigned iNearest)
{
DEBUG_START;
Vector_3 xOld = cell->info().point - CGAL::Origin();
std::cout << "Old tangient point: " << xOld << std::endl;
const auto activeGroup = calculateActiveGroup(cell, iNearest, items);
if (activeGroup.empty())
{
DEBUG_END;
return false;
}
Vector_3 xNew = leastSquaresPoint(activeGroup, items);
std::cout << "New tangient point: " << xNew << std::endl;
ASSERT(cell->has_vertex(infinite_vertex()));
unsigned infinityIndex = cell->index(infinite_vertex());
std::vector<Vertex_handle> vertices;
Vertex_handle dominator;
double alphaMax = 0.;
double alphaMax2 = 0.;
for (unsigned i = 0; i < NUM_CELL_VERTICES; ++i)
{
if (i == infinityIndex)
continue;
vertices.push_back(cell->vertex(i));
Vertex_handle vertex = mirror_vertex(cell, i);
Plane_3 plane = ::dual(vertex->point());
double alpha;
bool succeeded;
std::tie(succeeded, alpha) = calculateAlpha(xOld, xNew, plane);
if (!succeeded)
return false;
std::cout << "Alpha #" << i << ": " << alpha << std::endl;
ASSERT(alpha <= 1. && "Wrongly computed alpha");
if (alpha > alphaMax)
{
alphaMax2 = alphaMax;
alphaMax = alpha;
dominator = vertex;
}
}
std::cout << "Maximal alpha: " << alphaMax << std::endl;
std::cout << "Maximal alpha 2nd: " << alphaMax2 << std::endl;
ASSERT(alphaMax < 1. && "What to do then?");
if (alphaMax > 0.)
{
std::cout << "Full move is impossible, performing partial move"
<< std::endl;
partiallyMove(xOld, xNew, vertices, dominator, alphaMax,
alphaMax2);
}
else
{
std::cout << "Performing full move" << std::endl;
if (!fullyMove(vertices, xNew, activeGroup))
{
DEBUG_END;
return false;
}
}
DEBUG_END;
return true;
}
// Constructs regular triangulation of weighted points.
// Builds graph of cells with voids. Finds connected components of this graph (voids as clusters of cells).
// For each component calculates total void volume and area.
// Excludes roughs on the surface (components, connected to the infinite cell).
bool regular_triangulation_voids(const Wpi_container& points, Voids_result &res)
{
typedef typename boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, Cell_handle> CellGraph;
typedef typename boost::graph_traits<CellGraph>::vertex_descriptor GVertex;
typedef typename boost::graph_traits<CellGraph>::vertex_iterator GVertex_iterator;
Rt T; // regular triangulation
CellGraph G; // Voronoi subgraph where cells_sqr_r > 0 and edges_sqr_r > 0 (cells and edges with voids)
GVertex_iterator vi, vi_end;
res.out_log << "Number of input points for RT : " << points.size() << std::endl;
T.insert(points.begin(), points.end()); // insert all points in a row (this is faster than one insert() at a time).
T.infinite_vertex()->info().atom_id = -1; // set special atom_id for dummy infinite triangulation vertex
assert(T.dimension() == 3);
/*res.out_log << "Is valid : " << T.is_valid() << std::endl;*/
res.out_log << "Number of vertices in RT : " << T.number_of_vertices() << std::endl;
res.out_log << "Number of cells : " << T.number_of_cells() << std::endl;
res.out_log << "Number of finite cells : " << T.number_of_finite_cells() << std::endl;
/*res.out_log << "Inf. vert. atom id : " << T.infinite_vertex()->info().atom_id << std::endl;*/
// Add finite cells having sqr_r > 0 as graph verticies
Finite_cells_iterator cit, cit_end = T.finite_cells_end();
for (cit = T.finite_cells_begin(); cit != cit_end; cit++) {
if (cit->weighted_circumcenter().weight() > 0) // cached weighted circumcenter computation
cit->id() = add_vertex(Cell_handle(cit), G); // store corresponding graph vertex descriptor in cell's id()
}
// store one of infinite cells in graph: it will represent all of them. It should be the last vertex in graph with maximal vertex_descriptor.
const GVertex inf_graph_v = add_vertex(T.infinite_cell(), G);
res.out_log << "inf_graph_v descriptor : " << inf_graph_v << std::endl;
// Add graph edges connecting cells with void
for (boost::tie(vi, vi_end) = vertices(G); vi != vi_end; ++vi) {
const GVertex v1 = *vi; // current graph vertex
if (v1 != inf_graph_v) { // check edges only from finite cells
const Cell_handle c1 = G[v1]; // current cell
for (int i = 0; i < 4; i++) { // for each of four neighbor cells
const Cell_handle c2 = c1->neighbor(i);
bool ends_in_void = false; // do both corresponding Voronoi verticies lie in void space?
bool on_same_side = false; // do both ends lie on the same side of corresponding cell facet?
const Weighted_point &p1 = c1->vertex((i+1)&3)->point(); // weighted points of common facet between c and c2 cells
const Weighted_point &p2 = c1->vertex((i+2)&3)->point();
const Weighted_point &p3 = c1->vertex((i+3)&3)->point();
const Point &wcc = c1->weighted_circumcenter().point();
GVertex v2; // neighbor vertex in graph to construct edge to
if (c2->id() != -1) { // neighbor cell is finite and in graph: id()=vertex_descriptor
v2 = c2->id();
ends_in_void = true;
on_same_side = (orientation(p1.point(), p2.point(), p3.point(), wcc) ==
orientation(p1.point(), p2.point(), p3.point(), c2->weighted_circumcenter().point()));
} else if (T.is_infinite(c2)) {
v2 = inf_graph_v; // use our infinite graph vertex as destination if neighbor cell is infinite
ends_in_void = true;
on_same_side = (orientation(p1.point(), p2.point(), p3.point(), wcc) !=
orientation(p1.point(), p2.point(), p3.point(), c1->vertex(i)->point().point())); // same side with infinite vertex = different sides with cell vertex
}
typename K::Compute_squared_radius_smallest_orthogonal_sphere_3 r_mouth; // facet bottleneck squared radius (facet closed if < 0)
if (ends_in_void && (v2 > v1) && (on_same_side || r_mouth(p1, p2, p3) > 0))
add_edge(v1, v2, G); // use ordering v2>v1 to rule out most of the parallel edges: rely on v_inf>v1 for all finite vertices
}
}
}
res.out_log << "Number of vertices in G : " << num_vertices(G) << std::endl;
res.out_log << "Number of edges in G : " << num_edges(G) << std::endl;
// Find connected components on this Voronoi subnetwork
std::vector<int> component(num_vertices(G));
int num_components = boost::connected_components(G, &component[0]);
const int inf_comp_id = component[inf_graph_v]; // component of infinite vertex
res.out_log << "Number of connected components : " << num_components << std::endl;
res.out_log << "Component id of infinite vertex : " << inf_comp_id << std::endl;
// Reserve storage for results
res.voids.resize(num_components);
std::fill(res.atom_surf.begin(), res.atom_surf.end(), 0.0L);
// Calculate total volume of each finite component
for (boost::tie(vi, vi_end) = vertices(G); vi != vi_end; ++vi) {
const int comp_id = component[*vi];
if (comp_id != inf_comp_id) { // skip infinite component
Cell_handle cell = G[*vi]; // current cell
double Vc, Sc; // cell volume and surface
Array_double_4 Sa; // per atom surface in cell
Vc = cell_void_volume(cell, Sc, Sa); // void volume of cell and its surface area
res.voids[comp_id].volume += Vc; // add to volume of component
res.voids[comp_id].surface += Sc;
for (int k = 0; k < 4; k++) { // process four cell atoms
int atom_id = cell->vertex(k)->info().atom_id;
res.atom_surf[atom_id] += Sa[k]; // atom exposed surface
res.voids[comp_id].atoms.insert(atom_id); // add to set of cavity atoms
}
}
}
// Remove skipped infinite component with zero values
res.voids.erase(res.voids.begin() + inf_comp_id);
// Sort cavities by volume
std::sort(res.voids.begin(), res.voids.end(), void_greater);
return true;
}