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/*************************************************************************
* Copyright (C) 2008 by Bruno Chareyre *
* bruno.chareyre@grenoble-inp.fr *
* *
* This program is free software; it is licensed under the terms of the *
* GNU General Public License v2 or later. See file LICENSE for details. *
*************************************************************************/
#ifdef YADE_CGAL
#include "TesselationWrapper.hpp"
#include <lib/high-precision/Constants.hpp>
#include <preprocessing/dem/Shop.hpp>
#include <preprocessing/dem/SpherePack.hpp>
#ifdef YADE_OPENGL
#include <lib/opengl/GLUtils.hpp>
#include <lib/opengl/OpenGLWrapper.hpp>
#include <pkg/common/GLDrawFunctors.hpp>
#include <chrono>
#include <thread>
#endif
namespace yade { // Cannot have #include directive inside.
using math::max;
using math::min; // using inside .cpp file is ok.
YADE_PLUGIN((TesselationWrapper));
CREATE_LOGGER(TesselationWrapper);
// helper macro do assign Matrix3r values to subarrays
#define TENSOR_TO_MATRIX3R(mat, arr) \
{ \
arr(0, 0) = mat(1, 1); \
arr(0, 1) = mat(1, 2); \
arr(0, 2) = mat(1, 3); \
arr(1, 0) = mat(2, 1); \
arr(1, 1) = mat(2, 2); \
arr(1, 2) = mat(2, 3); \
arr(2, 0) = mat(3, 1); \
arr(2, 1) = mat(3, 2); \
arr(2, 2) = mat(3, 3); \
}
//spatial sort traits to use with a pair of CGAL::sphere pointers and integer.
//template<class _Triangulation>
struct RTraits_for_spatial_sort : public CGT::SimpleTriangulationTypes::RTriangulation::Geom_traits {
typedef CGT::SimpleTriangulationTypes::RTriangulation::Geom_traits Gt;
typedef std::pair<const CGT::Sphere*, Body::id_t> Point_3;
struct Less_x_3 {
bool operator()(const Point_3& p, const Point_3& q) const { return Gt::Less_x_3()(p.first->point(), q.first->point()); }
};
struct Less_y_3 {
bool operator()(const Point_3& p, const Point_3& q) const { return Gt::Less_y_3()(p.first->point(), q.first->point()); }
};
struct Less_z_3 {
bool operator()(const Point_3& p, const Point_3& q) const { return Gt::Less_z_3()(p.first->point(), q.first->point()); }
};
Less_x_3 less_x_3_object() const { return Less_x_3(); }
Less_y_3 less_y_3_object() const { return Less_y_3(); }
Less_z_3 less_z_3_object() const { return Less_z_3(); }
};
//function inserting points into a triangulation (where YADE::Sphere is converted to CGT::Sphere)
//and setting the info field to the bodies id.
//Possible improvements : use bodies pointers to avoid one copy, use aabb's lists to replace the shuffle/sort part
// template <class Triangulation>
void build_triangulation_with_ids(const shared_ptr<BodyContainer>& bodies, TesselationWrapper& TW, bool reset = true)
{
if (reset) TW.clear();
typedef SimpleTesselation::RTriangulation RTriangulation;
SimpleTesselation& Tes = *(TW.Tes);
RTriangulation& T = Tes.Triangulation();
std::vector<CGT::Sphere> spheres;
std::vector<std::pair<const CGT::Sphere*, Body::id_t>> pointsPtrs;
spheres.reserve(bodies->size());
pointsPtrs.reserve(bodies->size());
Tes.vertexHandles.clear();
Tes.vertexHandles.resize(bodies->size() + 6, NULL); //+6 extra slots in case boundaries will be added latter as additional vertices
Body::id_t Ng = 0;
Body::id_t& MaxId = Tes.maxId;
TW.mean_radius = 0;
int nonSpheres = 0;
shared_ptr<Sphere> sph(new Sphere);
int Sph_Index = sph->getClassIndexStatic();
Scene* scene = Omega::instance().getScene().get();
for (const auto& bi : *bodies) {
if (bi and bi->shape->getClassIndex() == Sph_Index and bi->maskOk(TW.groupMask)) {
const Sphere* s = YADE_CAST<Sphere*>(bi->shape.get());
//FIXME: is the scene periodicity verification useful in the next line ? Tesselation seems to work in both periodic and non-periodic conditions with "scene->cell->wrapShearedPt(bi->state->pos)". I keep the verification to be consistent with all other uses of "wrapShearedPt" function.
const Vector3r& pos = scene->isPeriodic ? scene->cell->wrapShearedPt(bi->state->pos) : bi->state->pos;
const Real rad = s->radius;
CGT::Sphere sp(CGT::Point(pos[0], pos[1], pos[2]), rad * rad);
spheres.push_back(sp);
pointsPtrs.push_back(std::make_pair(&(spheres[Ng] /*.point()*/), bi->getId()));
TW.Pmin = CGT::Point(min(TW.Pmin.x(), pos.x() - rad), min(TW.Pmin.y(), pos.y() - rad), min(TW.Pmin.z(), pos.z() - rad));
TW.Pmax = CGT::Point(max(TW.Pmax.x(), pos.x() + rad), max(TW.Pmax.y(), pos.y() + rad), max(TW.Pmax.z(), pos.z() + rad));
Ng++;
TW.mean_radius += rad;
MaxId = max(MaxId, bi->getId());
} else
++nonSpheres;
}
TW.mean_radius /= Ng;
TW.rad_divided = true;
spheres.resize(Ng);
pointsPtrs.resize(Ng);
// random shuffling here is suggested in CGAL examples but it is probably not very helpful in yade since the positions are _usually_ random already.
// We skip it to avoid unnecessary indeterminacy
// std::random_shuffle(pointsPtrs.begin(), pointsPtrs.end());
spatial_sort(pointsPtrs.begin(), pointsPtrs.end(), RTraits_for_spatial_sort() /*, CGT::RTriangulation::Weighted_point*/);
RTriangulation::Cell_handle hint;
TW.n_spheres = 0;
for (std::vector<std::pair<const CGT::Sphere*, Body::id_t>>::const_iterator p = pointsPtrs.begin(); p != pointsPtrs.end(); ++p) {
RTriangulation::Locate_type lt;
RTriangulation::Cell_handle c;
int li, lj;
c = T.locate(*(p->first), lt, li, lj, hint);
RTriangulation::Vertex_handle v = T.insert(*(p->first), lt, c, li, lj);
if (v == RTriangulation::Vertex_handle()) hint = c;
else {
v->info().setId((unsigned int)p->second);
//Vh->info().isFictious = false;//false is the default
Tes.maxId = math::max(Tes.maxId, (int)p->second);
Tes.vertexHandles[p->second] = v;
hint = v->cell();
++TW.n_spheres;
}
}
}
Real thickness = 0;
TesselationWrapper::~TesselationWrapper() { }
void TesselationWrapper::clear(void)
{
Tes->Clear();
Pmin = CGT::Point(inf, inf, inf);
Pmax = CGT::Point(-inf, -inf, -inf);
mean_radius = 0;
n_spheres = 0;
rad_divided = false;
bounded = false;
Tes->vertexHandles.clear();
}
void TesselationWrapper::insertSceneSpheres(bool reset) { build_triangulation_with_ids(scene->bodies, *this, reset); }
Real TesselationWrapper::Volume(unsigned int id) { return ((unsigned int)Tes->Max_id() >= id and Tes->vertex(id) != NULL) ? Tes->Volume(id) : 0; }
bool TesselationWrapper::insert(Real x, Real y, Real z, Real rad, unsigned int id)
{
checkMinMax(x, y, z, rad);
mean_radius += rad;
++n_spheres;
return (Tes->insert(x, y, z, rad, id) != NULL);
}
void TesselationWrapper::checkMinMax(Real x, Real y, Real z, Real rad)
{
Pmin = CGT::Point(min(Pmin.x(), x - rad), min(Pmin.y(), y - rad), min(Pmin.z(), z - rad));
Pmax = CGT::Point(max(Pmax.x(), x + rad), max(Pmax.y(), y + rad), max(Pmax.z(), z + rad));
}
bool TesselationWrapper::move(Real x, Real y, Real z, Real rad, unsigned int id)
{
checkMinMax(x, y, z, rad);
if (Tes->move(x, y, z, rad, id) != NULL) return true;
else {
std::cerr << "Tes->move(x,y,z,rad,id)==NULL" << std::endl;
return false;
}
}
void TesselationWrapper::computeTesselation(void)
{
if (not(Tes->vertexHandles.size() > 0)) insertSceneSpheres();
addBoundingPlanes();
if (!rad_divided) {
mean_radius /= n_spheres;
rad_divided = true;
}
Tes->compute();
}
void TesselationWrapper::computeTesselation(Real pminx, Real pmaxx, Real pminy, Real pmaxy, Real pminz, Real pmaxz)
{
if (not(Tes->vertexHandles.size() > 0)) insertSceneSpheres();
addBoundingPlanes(pminx, pmaxx, pminy, pmaxy, pminz, pmaxz);
computeTesselation();
}
void TesselationWrapper::computeVolumes(void)
{
computeTesselation();
Tes->computeVolumes();
}
int TesselationWrapper::addBoundingPlane(short axis, bool positive)
{
Vector3r cornerMin = Vector3r(Pmin.x(), Pmin.y(), Pmin.z());
Vector3r cornerMax = Vector3r(Pmax.x(), Pmax.y(), Pmax.z());
Vector3r halfSize = 0.5 * (cornerMax - cornerMin);
Vector3r centerPoint = 0.5 * (cornerMin + cornerMax);
// shift by half-size + a large radius
Vector3r shift = Vector3r::Zero();
shift[axis] = positive ? 1 : -1;
shift *= far * (cornerMax - cornerMin).norm();
shift[axis] += positive ? halfSize[axis] : -halfSize[axis];
centerPoint += shift;
//find a free id
int freeId = 0;
while (Tes->vertexHandles[freeId] != NULL)
++freeId;
// we don't want to count this virtual sphere's radius in the average, so compute it before inserting
if (!rad_divided) {
mean_radius /= n_spheres;
rad_divided = true;
}
// now insert
Tes->vertexHandles[freeId] = Tes->insert(centerPoint[0], centerPoint[1], centerPoint[2], far * (cornerMax - cornerMin).norm(), freeId, false);
return freeId;
}
void TesselationWrapper::addBoundingPlanes(Real pminx, Real pmaxx, Real pminy, Real pmaxy, Real pminz, Real pmaxz)
{
if (!bounded) {
if (!rad_divided) {
mean_radius /= n_spheres;
rad_divided = true;
}
// Insert the 6 additional vertices in the right place (usually they will be ids 0 to 5 when walls/facets/boxes are used, but not always)
// append them at the end if the initial list is full
int freeIds[6];
int i = 0;
for (int k = 0; k < 6; k++) {
while (Tes->vertexHandles[i] != NULL)
++i;
freeIds[k] = i++;
}
// now insert
Tes->vertexHandles[freeIds[0]] = Tes->insert(
pminx - far * (pmaxy - pminy), 0.5 * (pmaxy + pminy), 0.5 * (pmaxz + pminz), far * (pmaxy - pminy) + thickness, freeIds[0], true);
Tes->vertexHandles[freeIds[1]] = Tes->insert(
pmaxx + far * (pmaxy - pminy), 0.5 * (pmaxy + pminy), 0.5 * (pmaxz + pminz), far * (pmaxy - pminy) + thickness, freeIds[1], true);
Tes->vertexHandles[freeIds[2]] = Tes->insert(
0.5 * (pminx + pmaxx), pminy - far * (pmaxx - pminx), 0.5 * (pmaxz + pminz), far * (pmaxx - pminx) + thickness, freeIds[2], true);
Tes->vertexHandles[freeIds[3]] = Tes->insert(
0.5 * (pminx + pmaxx), pmaxy + far * (pmaxx - pminx), 0.5 * (pmaxz + pminz), far * (pmaxx - pminx) + thickness, freeIds[3], true);
Tes->vertexHandles[freeIds[4]] = Tes->insert(
0.5 * (pminx + pmaxx), 0.5 * (pmaxy + pminy), pminz - far * (pmaxy - pminy), far * (pmaxy - pminy) + thickness, freeIds[4], true);
Tes->vertexHandles[freeIds[5]] = Tes->insert(
0.5 * (pminx + pmaxx), 0.5 * (pmaxy + pminy), pmaxz + far * (pmaxy - pminy), far * (pmaxy - pminy) + thickness, freeIds[5], true);
bounded = true;
}
}
void TesselationWrapper::addBoundingPlanes(void) { addBoundingPlanes(Pmin.x(), Pmax.x(), Pmin.y(), Pmax.y(), Pmin.z(), Pmax.z()); }
void TesselationWrapper::setState(bool state) { mma->setState(state ? 2 : 1, false, false, groupMask); }
void TesselationWrapper::loadState(string filename, bool stateNumber, bool bz2)
{
CGT::TriaxialState& TS = stateNumber ? *(mma->analyser->TS1) : *(mma->analyser->TS0);
TS.from_file(filename.c_str(), bz2);
}
void TesselationWrapper::saveState(string filename, bool stateNumber, bool bz2)
{
CGT::TriaxialState& TS = stateNumber ? *(mma->analyser->TS1) : *(mma->analyser->TS0);
TS.to_file(filename.c_str(), bz2);
}
void TesselationWrapper::defToVtkFromStates(string inputFile1, string inputFile2, string outputFile, bool bz2)
{
mma->analyser->DefToFile(inputFile1.c_str(), inputFile2.c_str(), outputFile.c_str(), bz2);
}
void createSphere(shared_ptr<Body>& body, Vector3r position, Real radius, bool /*big*/, bool /*dynamic*/)
{
body = shared_ptr<Body>(new Body);
body->groupMask = 2;
shared_ptr<Sphere> iSphere(new Sphere);
body->state->blockedDOFs = State::DOF_NONE;
body->state->pos = position;
iSphere->radius = radius;
body->shape = iSphere;
}
void TesselationWrapper::defToVtkFromPositions(string inputFile1, string inputFile2, string outputFile, bool /*bz2*/)
{
SpherePack sp1, sp2;
sp1.fromFile(inputFile1);
sp2.fromFile(inputFile2);
size_t imax = sp1.pack.size();
if (imax != sp2.pack.size()) LOG_ERROR("The files have different numbers of spheres");
shared_ptr<Body> body;
scene->bodies->clear();
for (size_t i = 0; i < imax; i++) {
const SpherePack::Sph& sp(sp1.pack[i]);
LOG_DEBUG("sphere (" << sp.c << " " << sp.r << ")");
createSphere(body, sp.c, sp.r, false, true);
scene->bodies->insert(body);
}
mma->setState(1);
scene->bodies->clear();
for (size_t i = 0; i < imax; i++) {
const SpherePack::Sph& sp(sp2.pack[i]);
LOG_DEBUG("sphere (" << sp.c << " " << sp.r << ")");
createSphere(body, sp.c, sp.r, false, true);
scene->bodies->insert(body);
}
mma->setState(2);
mma->analyser->DefToFile(outputFile.c_str());
}
void TesselationWrapper::defToVtk(string outputFile) { mma->analyser->DefToFile(outputFile.c_str()); }
boost::python::dict TesselationWrapper::calcVolPoroDef(bool deformation)
{
CGT::TriaxialState* ts;
bounded = true; // TriaxialState already has bounding planes together with the actual spheres, no need to bound again.
if (deformation) mma->analyser->computeParticlesDeformation();
Tes = &mma->analyser->TS0->tesselation(); //no reason to use the final state if we don't want to compute deformations, keep using the initial
ts = mma->analyser->TS0;
computeVolumes();
RTriangulation& Tri = Tes->Triangulation();
Pmin = ts->box.base;
Pmax = ts->box.sommet;
int bodiesDim = Tes->Max_id() + 1; //=scene->bodies->size();
vector<Real> vol_(bodiesDim, 0);
vector<Real> poro_(bodiesDim, 0);
vector<Matrix3r> def_(bodiesDim, Matrix3r::Zero());
boost::python::list vol;
boost::python::list poro;
boost::python::list def;
for (RTriangulation::Finite_vertices_iterator V_it = Tri.finite_vertices_begin(); V_it != Tri.finite_vertices_end(); V_it++) {
const Body::id_t id = V_it->info().id();
if (id < 0 or V_it->info().v() == 0 or V_it->info().isFictious) continue;
Real sphereVol = 4.188790 * math::pow((V_it->point().weight()), 1.5); // 4/3*PI*R³ = 4.188...*R³
vol_[id] = V_it->info().v();
poro_[id] = (V_it->info().v() - sphereVol) / V_it->info().v();
if (deformation) TENSOR_TO_MATRIX3R(mma->analyser->ParticleDeformation[id], def_[id]);
}
for (auto& v : vol_)
vol.append(v);
for (auto& v : poro_)
poro.append(v);
if (deformation)
for (auto& v : def_)
def.append(v);
boost::python::dict ret;
ret["vol"] = vol;
ret["poro"] = poro;
if (deformation) ret["def"] = def;
return ret;
}
boost::python::list TesselationWrapper::getAlphaFaces(Real alpha)
{
vector<AlphaFace> faces;
Tes->setAlphaFaces(faces, alpha);
boost::python::list ret;
for (auto f = faces.begin(); f != faces.end(); f++)
ret.append(boost::python::make_tuple(Vector3i(f->ids[0], f->ids[1], f->ids[2]), makeVector3r(f->normal)));
return ret;
}
boost::python::list TesselationWrapper::getAlphaCaps(Real alpha, Real shrinkedAlpha, bool fixedAlpha)
{
vector<AlphaCap> caps;
Tes->setExtendedAlphaCaps(caps, alpha, shrinkedAlpha, fixedAlpha);
bounded = true;
boost::python::list ret;
for (auto f = caps.begin(); f != caps.end(); f++)
ret.append(boost::python::make_tuple(f->id, makeVector3r(f->normal), makeVector3r(f->centroid)));
return ret;
}
void TesselationWrapper::applyAlphaForces(Matrix3r stress, Real alpha, Real shrinkedAlpha, bool fixedAlpha, bool reset)
{
if ((Tes->Triangulation().number_of_vertices() == 0) or reset) insertSceneSpheres(true);
vector<AlphaCap> caps;
Tes->setExtendedAlphaCaps(caps, alpha, shrinkedAlpha, fixedAlpha);
bounded = true;
for (const auto& b : *scene->bodies)
scene->forces.setPermForce(b->id, Vector3r::Zero());
for (auto f = caps.begin(); f != caps.end(); f++) {
if (not scene->bodies->exists(f->id)) continue; // FIXME: probably not needed
scene->forces.setPermForce(f->id, stress * makeVector3r(f->normal));
}
}
void TesselationWrapper::applyAlphaVel(Matrix3r velGrad, Real alpha, Real shrinkedAlpha, bool fixedAlpha)
{
build_triangulation_with_ids(scene->bodies, *this, true); //triangulation needed
vector<AlphaCap> caps;
Tes->setExtendedAlphaCaps(caps, alpha, shrinkedAlpha, fixedAlpha);
bounded = true;
for (const auto& b : *scene->bodies)
b->state->blockedDOFs = State::DOF_NONE;
const auto aabb = Shop::aabbExtrema();
Vector3r bbCenter = 0.5 * (aabb.first + aabb.second);
for (auto f = caps.begin(); f != caps.end(); f++) {
Body* b = Body::byId(f->id, scene).get();
b->state->blockedDOFs = State::DOF_ALL;
b->state->vel = velGrad * (makeVector3r(f->centroid) - bbCenter);
b->state->angVel = Vector3r::Zero();
}
}
Matrix3r TesselationWrapper::calcAlphaStress(Real alpha, Real shrinkedAlpha, bool fixedAlpha)
{
build_triangulation_with_ids(scene->bodies, *this, true); //triangulation needed
vector<AlphaCap> caps;
Tes->setExtendedAlphaCaps(caps, alpha, shrinkedAlpha, fixedAlpha);
bounded = true;
Matrix3r cauchyLWS(Matrix3r::Zero());
scene->forces.sync(); // needed to make resultants predictable
alphaCapsVol = 0.;
for (auto f = caps.begin(); f != caps.end(); f++) {
Vector3r areaV = makeVector3r(f->normal);
Vector3r resultant = scene->forces.getPermForce(f->id) - scene->forces.getForce(f->id);
Vector3r centroid = makeVector3r(f->centroid);
cauchyLWS += resultant * (centroid.transpose());
alphaCapsVol += areaV.norm() / 3. * centroid.dot(areaV.normalized());
}
cauchyLWS /= alphaCapsVol;
return cauchyLWS;
}
boost::python::list TesselationWrapper::getAlphaGraph(Real alpha, Real shrinkedAlpha, bool fixedAlpha)
{
if (Tes->Triangulation().number_of_vertices() == 0) insertSceneSpheres(true);
segments = Tes->getExtendedAlphaGraph(alpha, shrinkedAlpha, fixedAlpha);
bounded = true;
boost::python::list ret;
for (auto f = segments.begin(); f != segments.end(); f++)
ret.append(*f);
return ret;
}
boost::python::list TesselationWrapper::getAlphaVertices(Real alpha)
{
vector<int> vertices = Tes->getAlphaVertices(alpha);
boost::python::list ret;
for (auto f = vertices.begin(); f != vertices.end(); f++)
ret.append(*f);
return ret;
}
#ifdef YADE_OPENGL
YADE_PLUGIN((GlExtra_AlphaGraph))
GLUquadric* GlExtra_AlphaGraph::gluQuadric = NULL;
int GlExtra_AlphaGraph::glCylinderList = -1;
int GlExtra_AlphaGraph::oneCylinder = -1;
void GlExtra_AlphaGraph::render()
{
if (not tesselationWrapper) tesselationWrapper = shared_ptr<TesselationWrapper>(new TesselationWrapper);
if (tesselationWrapper->Tes->Triangulation().number_of_vertices() == 0) tesselationWrapper->insertSceneSpheres(true);
if (tesselationWrapper->segments.size() == 0 or reset) {
#ifdef BREAK_OPENGL
segments =
#endif
tesselationWrapper->segments = tesselationWrapper->Tes->getExtendedAlphaGraph(alpha, shrinkedAlpha, fixedAlpha);
reset = true;
}
#ifdef BREAK_OPENGL
else
segments = tesselationWrapper->segments;
#endif
if ((reset or refreshDisplay) and not wire) {
rots.clear();
lengths.clear();
}
const vector<Vector3r>& segments_ = tesselationWrapper->segments;
unsigned maxI = segments_.size() - 1;
glLineWidth(lineWidth);
glColor3v(color);
if (lighting) glEnable(GL_LIGHTING);
else
glDisable(GL_LIGHTING);
glDisable(GL_CULL_FACE);
if ((rots.size() == 0 or reset or refreshDisplay) and not wire) {
Real radiusTemp = 0;
unsigned i = 0;
while (i < maxI) {
const Vector3r& p1 = segments_[i];
const Vector3r& p2 = segments_[i + 1];
Vector3r relPos = p2 - p1;
Real length = relPos.norm();
lengths.push_back(length);
rots.push_back(Eigen::Transform<Real, 3, Eigen::Affine>(Quaternionr().setFromTwoVectors(Vector3r(0, 0, 1), relPos / length)));
radiusTemp += length;
i += 2;
}
if (radius == 0) radius = radiusTemp / Real(i * 3);
reset = false;
}
if (glCylinderList < 0) // will always be true unless the glGenLists() below is commented in (not sure it helps, should be tested)
{
unsigned i = 0, jj = 0;
if (!gluQuadric) {
gluQuadric = gluNewQuadric();
if (!gluQuadric) throw runtime_error("Gl1_NormPhys::go unable to allocate new GLUquadric object (out of memory?).");
}
while (i < maxI) {
const Vector3r& p1 = segments_[i];
const Vector3r& p2 = segments_[i + 1];
if (wire) {
glBegin(GL_LINES)
;
glVertex3v(p1);
glVertex3v(p2);
glEnd();
} else {
glPushMatrix();
glTranslatev(p1);
glMultMatrix(rots[jj].data());
gluCylinder(gluQuadric, radius, radius, lengths[jj], 4, 1);
glPopMatrix();
}
i += 2;
++jj;
}
}
}
#endif /*OPENGL*/
} // namespace yade
#endif /* YADE_CGAL */
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