bool Mesh::bndDistAndGradients(int iEl, double &f , std::vector<double> &gradF, double eps)
{
MElement *element = _el[iEl];
f = 0.;
// dommage ;-)
if (element->getDim() != 2)
return false;
int currentId = 0;
std::vector<int> vertex2param(element->getNumVertices());
for (size_t i = 0; i < element->getNumVertices(); ++i) {
if (_el2FV[iEl][i] >= 0) {
vertex2param[i] = currentId;
currentId += _nPCFV[_el2FV[iEl][i]];
}
else
vertex2param[i] = -1;
}
gradF.clear();
gradF.resize(currentId, 0.);
const nodalBasis &elbasis = *element->getFunctionSpace();
bool edgeFound = false;
for (int iEdge = 0; iEdge < element->getNumEdges(); ++iEdge) {
int clId = elbasis.getClosureId(iEdge, 1);
const std::vector<int> &closure = elbasis.closures[clId];
std::vector<MVertex *> vertices;
GEdge *edge = NULL;
for (size_t i = 0; i < closure.size(); ++i) {
MVertex *v = element->getVertex(closure[i]);
vertices.push_back(v);
// only valid in 2D
if ((int)i >= 2 && v->onWhat() && v->onWhat()->dim() == 1) {
edge = v->onWhat()->cast2Edge();
}
}
if (edge) {
edgeFound = true;
std::vector<double> localgrad;
std::vector<SPoint3> nodes(closure.size());
std::vector<double> params(closure.size());
std::vector<bool> onedge(closure.size());
for (size_t i = 0; i < closure.size(); ++i) {
nodes[i] = _xyz[_el2V[iEl][closure[i]]];
onedge[i] = element->getVertex(closure[i])->onWhat() == edge && _el2FV[iEl][closure[i]] >= 0;
if (onedge[i]) {
params[i] = _uvw[_el2FV[iEl][closure[i]]].x();
}else
reparamMeshVertexOnEdge(element->getVertex(closure[i]), edge, params[i]);
}
f += computeBndDistAndGradient(edge, params, vertices, *BasisFactory::getNodalBasis(elbasis.getClosureType(clId)), nodes, onedge, localgrad, eps);
for (size_t i = 0; i < closure.size(); ++i) {
if (onedge[i])
gradF[vertex2param[closure[i]]] += localgrad[i];
}
}
}
return edgeFound;
}
double elasticitySolver::computeDisplacementError(simpleFunction<double> *f0,
simpleFunction<double> *f1,
simpleFunction<double> *f2)
{
std::cout << "compute displacement error" << std::endl;
double err = 0.;
std::set<MVertex *> v;
std::map<MVertex *, MElement *> vCut;
for(std::size_t i = 0; i < elasticFields.size(); ++i) {
if(elasticFields[i]._e == 0.) continue;
for(groupOfElements::elementContainer::const_iterator it =
elasticFields[i].g->begin();
it != elasticFields[i].g->end(); ++it) {
MElement *e = *it;
if(e->getParent()) {
for(std::size_t j = 0; j < e->getNumVertices(); ++j) {
if(vCut.find(e->getVertex(j)) == vCut.end())
vCut[e->getVertex(j)] = e->getParent();
}
}
else {
for(std::size_t j = 0; j < e->getNumVertices(); ++j)
v.insert(e->getVertex(j));
}
}
}
SolverField<SVector3> Field(pAssembler, LagSpace);
for(std::set<MVertex *>::iterator it = v.begin(); it != v.end(); ++it) {
SVector3 val;
MPoint p(*it);
Field.f(&p, 0, 0, 0, val);
SVector3 sol((*f0)((*it)->x(), (*it)->y(), (*it)->z()),
(*f1)((*it)->x(), (*it)->y(), (*it)->z()),
(*f2)((*it)->x(), (*it)->y(), (*it)->z()));
double diff = normSq(sol - val);
err += diff;
}
for(std::map<MVertex *, MElement *>::iterator it = vCut.begin();
it != vCut.end(); ++it) {
SVector3 val;
double uvw[3];
double xyz[3] = {it->first->x(), it->first->y(), it->first->z()};
it->second->xyz2uvw(xyz, uvw);
Field.f(it->second, uvw[0], uvw[1], uvw[2], val);
SVector3 sol((*f0)(xyz[0], xyz[1], xyz[2]), (*f1)(xyz[0], xyz[1], xyz[2]),
(*f2)(xyz[0], xyz[1], xyz[2]));
double diff = normSq(sol - val);
err += diff;
}
printf("Displacement Error = %g\n", sqrt(err));
return sqrt(err);
}
PView *elasticitySolver::buildDisplacementView(const std::string postFileName)
{
std::cout << "build Displacement View" << std::endl;
std::set<MVertex *> v;
std::map<MVertex *, MElement *> vCut;
for(std::size_t i = 0; i < elasticFields.size(); ++i) {
if(elasticFields[i]._e == 0.) continue;
for(groupOfElements::elementContainer::const_iterator it =
elasticFields[i].g->begin();
it != elasticFields[i].g->end(); ++it) {
MElement *e = *it;
if(e->getParent()) {
for(std::size_t j = 0; j < e->getNumVertices(); ++j) {
if(vCut.find(e->getVertex(j)) == vCut.end())
vCut[e->getVertex(j)] = e->getParent();
}
}
else {
for(std::size_t j = 0; j < e->getNumVertices(); ++j)
v.insert(e->getVertex(j));
}
}
}
std::map<int, std::vector<double> > data;
SolverField<SVector3> Field(pAssembler, LagSpace);
for(std::set<MVertex *>::iterator it = v.begin(); it != v.end(); ++it) {
SVector3 val;
MPoint p(*it);
Field.f(&p, 0, 0, 0, val);
std::vector<double> vec(3);
vec[0] = val(0);
vec[1] = val(1);
vec[2] = val(2);
data[(*it)->getNum()] = vec;
}
for(std::map<MVertex *, MElement *>::iterator it = vCut.begin();
it != vCut.end(); ++it) {
SVector3 val;
double uvw[3];
double xyz[3] = {it->first->x(), it->first->y(), it->first->z()};
it->second->xyz2uvw(xyz, uvw);
Field.f(it->second, uvw[0], uvw[1], uvw[2], val);
std::vector<double> vec(3);
vec[0] = val(0);
vec[1] = val(1);
vec[2] = val(2);
data[it->first->getNum()] = vec;
}
PView *pv = new PView(postFileName, "NodeData", pModel, data, 0.0);
return pv;
}
PView* elasticitySolver::buildLagrangeMultiplierView (const std::string postFileName)
{
std::cout << "build Lagrange Multiplier View"<< std::endl;
if(!LagrangeMultiplierSpace) return new PView();
std::set<MVertex*> v;
for (unsigned int i = 0; i < LagrangeMultiplierFields.size(); ++i)
{
for(groupOfElements::elementContainer::const_iterator it =
LagrangeMultiplierFields[i].g->begin();
it != LagrangeMultiplierFields[i].g->end(); ++it)
{
MElement *e = *it;
for (int j = 0; j < e->getNumVertices(); ++j) v.insert(e->getVertex(j));
}
}
std::map<int, std::vector<double> > data;
SolverField<double> Field(pAssembler, LagrangeMultiplierSpace);
for(std::set<MVertex*>::iterator it = v.begin(); it != v.end(); ++it)
{
double val;
MPoint p(*it);
Field.f(&p, 0, 0, 0, val);
std::vector<double> vec;
vec.push_back(val);
data[(*it)->getNum()] = vec;
}
PView *pv = new PView (postFileName, "NodeData", pModel, data, 0.0);
return pv;
}
PView *thermicSolver::buildTemperatureView(const std::string postFileName)
{
std::cout << "build Temperature View" << std::endl;
std::set<MVertex *> v;
std::map<MVertex *, MElement *> vCut;
for(std::size_t i = 0; i < thermicFields.size(); ++i) {
for(groupOfElements::elementContainer::const_iterator it =
thermicFields[i].g->begin();
it != thermicFields[i].g->end(); ++it) {
MElement *e = *it;
if(e->getParent()) {
for(std::size_t j = 0; j < e->getNumVertices(); ++j) {
if(vCut.find(e->getVertex(j)) == vCut.end())
vCut[e->getVertex(j)] = e->getParent();
}
}
else {
for(std::size_t j = 0; j < e->getNumVertices(); ++j)
v.insert(e->getVertex(j));
}
}
}
std::map<int, std::vector<double> > data;
SolverField<double> Field(pAssembler, LagSpace);
for(std::set<MVertex *>::iterator it = v.begin(); it != v.end(); ++it) {
double val;
MPoint p(*it);
Field.f(&p, 0, 0, 0, val); // printf("valv=%g\n",val);
std::vector<double> vec;
vec.push_back(val);
data[(*it)->getNum()] = vec;
}
for(std::map<MVertex *, MElement *>::iterator it = vCut.begin();
it != vCut.end(); ++it) {
double val;
double uvw[3];
double xyz[3] = {it->first->x(), it->first->y(), it->first->z()};
it->second->xyz2uvw(xyz, uvw);
Field.f(it->second, uvw[0], uvw[1], uvw[2],
val); // printf("valvc=%g\n",val);
std::vector<double> vec;
vec.push_back(val);
data[it->first->getNum()] = vec;
}
PView *pv = new PView(postFileName, "NodeData", pModel, data, 0.0, 1);
return pv;
}
double frameFieldBackgroundMesh2D::angle(double u, double v)
{
MElement *e = const_cast<MElement*>(findElement(u, v));
if (!e) return -1000.0;
std::vector<double> val = get_nodal_values(e,angles);
std::vector<double> element_uvw = get_element_uvw_from_xyz(e,u,v,0.);
std::vector<double> cosvalues(e->getNumVertices()), sinvalues(e->getNumVertices());
for (int i=0; i<e->getNumVertices(); i++) {
cosvalues[i]=cos(4*val[i]);
sinvalues[i]=sin(4*val[i]);
}
double cos4 = e->interpolate(&cosvalues[0], element_uvw[0], element_uvw[1], element_uvw[2], 1, order);
double sin4 = e->interpolate(&sinvalues[0], element_uvw[0], element_uvw[1], element_uvw[2], 1, order);
double a = atan2(sin4,cos4)/4.0;
normalizeAngle (a);
return a;
}
void elasticitySolver::computeEffectiveStiffness(std::vector<double> stiff)
{
double st[6] = {0., 0., 0., 0., 0., 0.};
double volTot = 0.;
for(std::size_t i = 0; i < elasticFields.size(); ++i) {
double E = elasticFields[i]._e;
double nu = elasticFields[i]._nu;
SolverField<SVector3> Field(pAssembler, LagSpace);
for(groupOfElements::elementContainer::const_iterator it =
elasticFields[i].g->begin();
it != elasticFields[i].g->end(); ++it) {
MElement *e = *it;
double vol = e->getVolume() * e->getVolumeSign();
int nbVertex = e->getNumVertices();
std::vector<SVector3> val(nbVertex);
double valx[256];
double valy[256];
double valz[256];
for(int k = 0; k < nbVertex; k++) {
MVertex *v = e->getVertex(k);
MPoint p(v);
Field.f(&p, 0, 0, 0, val[k]);
valx[k] = val[k](0);
valy[k] = val[k](1);
valz[k] = val[k](2);
}
double gradux[3];
double graduy[3];
double graduz[3];
SPoint3 center = e->barycenterUVW();
double u = center.x(), v = center.y(), w = center.z();
e->interpolateGrad(valx, u, v, w, gradux);
e->interpolateGrad(valy, u, v, w, graduy);
e->interpolateGrad(valz, u, v, w, graduz);
double eps[6] = {gradux[0],
graduy[1],
graduz[2],
0.5 * (gradux[1] + graduy[0]),
0.5 * (gradux[2] + graduz[0]),
0.5 * (graduy[2] + graduz[1])};
double A = E / (1. + nu);
double B = A * (nu / (1. - 2 * nu));
double trace = eps[0] + eps[1] + eps[2];
st[0] += (A * eps[0] + B * trace) * vol;
st[1] += (A * eps[1] + B * trace) * vol;
st[2] += (A * eps[2] + B * trace) * vol;
st[3] += (A * eps[3]) * vol;
st[4] += (A * eps[4]) * vol;
st[5] += (A * eps[5]) * vol;
volTot += vol;
}
}
for(int i = 0; i < 6; i++) stiff[i] = st[i] / volTot;
}
void frameFieldBackgroundMesh2D::computeSmoothness()
{
smoothness.clear();
// build vertex -> neighbors table
std::multimap<MVertex*,MVertex*> vertex2vertex;
for (std::vector<MElement*>::iterator it = beginelements(); it!=endelements(); it++) {
MElement *e = *it;
for (int i=0; i<e->getNumVertices(); i++) {
MVertex *current = e->getVertex(i);
for (int j=0; j<e->getNumVertices(); j++) {
if (i==j) continue;
MVertex *neighbor = e->getVertex(j);
vertex2vertex.insert(make_pair(current,neighbor));
}
}
}
// compute smoothness
for (std::vector<MVertex*>::iterator it = beginvertices(); it!=endvertices(); it++) {
MVertex *v = *it;
double angle_current = angle(v);
// compare to all neighbors...
std::pair<std::multimap<MVertex*,MVertex*>::iterator, std::multimap<MVertex*,MVertex*>::iterator> range = vertex2vertex.equal_range(v);
double minangle,totalangle=0.;
int N=0;
for (std::multimap<MVertex*,MVertex*>::iterator itneighbor = range.first; itneighbor!=range.second; itneighbor++) {
N++;
minangle=M_PI/2;
MVertex *v_nb = itneighbor->second;
double angle_nb = angle(v_nb);
// angle comparison...
minangle = std::min(minangle, fabs(angle_current-angle_nb));
minangle = std::min(minangle, fabs(angle_current-(angle_nb+M_PI/2.)));
minangle = std::min(minangle, fabs(angle_current-(angle_nb-M_PI/2.)));
totalangle += minangle;
}
totalangle /= N;
smoothness[v] = 1. - (totalangle/M_PI*2);
}
}
std::set<MVertex *> BGMBase::get_vertices_of_maximum_dim(int dim)
{
std::set<MVertex *> bnd_vertices;
for(unsigned int i = 0; i < gf->getNumMeshElements(); i++) {
MElement *element = gf->getMeshElement(i);
for(std::size_t j = 0; j < element->getNumVertices(); j++) {
MVertex *vertex = element->getVertex(j);
if(vertex->onWhat()->dim() <= dim) bnd_vertices.insert(vertex);
}
}
return bnd_vertices;
}
double BGMBase::get_field_value(double u, double v, double w,
const DoubleStorageType &data)
{
// TODO C++11 Remove const_cast
MElement *e = const_cast<MElement *>(findElement(u, v, w));
if(!e) return -1000.;
std::vector<double> val = get_nodal_values(e, data);
std::vector<double> element_uvw = get_element_uvw_from_xyz(e, u, v, w);
std::vector<double> values(e->getNumVertices());
for(std::size_t i = 0; i < e->getNumVertices(); i++) values[i] = val[i];
return e->interpolate(&values[0], element_uvw[0], element_uvw[1],
element_uvw[2], 1, order);
}
std::vector<double> BGMBase::get_field_value(double u, double v, double w,
const VectorStorageType &data)
{
// TODO C++11 remove const_cast and enforce const-correctness otherwise
MElement *e = const_cast<MElement *>(findElement(u, v, w));
if(!e) return std::vector<double>(3, -1000.);
std::vector<std::vector<double> > val = get_nodal_values(e, data);
std::vector<double> element_uvw = get_element_uvw_from_xyz(e, u, v, w);
std::vector<double> res(3);
for(int j = 0; j < 3; j++) {
std::vector<double> values(e->getNumVertices());
for(std::size_t i = 0; i < e->getNumVertices(); i++) {
values[i] = val[i][j];
}
res[j] = e->interpolate(&values[0], element_uvw[0], element_uvw[1],
element_uvw[2], 1, order);
}
return res;
}
PView *elasticitySolver::buildStrainView(const std::string postFileName)
{
std::cout << "build strain view" << std::endl;
std::map<int, std::vector<double> > data;
for(std::size_t i = 0; i < elasticFields.size(); ++i) {
SolverField<SVector3> Field(pAssembler, LagSpace);
for(groupOfElements::elementContainer::const_iterator it =
elasticFields[i].g->begin();
it != elasticFields[i].g->end(); ++it) {
MElement *e = *it;
int nbVertex = e->getNumVertices();
std::vector<SVector3> val(nbVertex);
double valx[256];
double valy[256];
double valz[256];
for(int k = 0; k < nbVertex; k++) {
MVertex *v = e->getVertex(k);
MPoint p(v);
Field.f(&p, 0, 0, 0, val[k]);
valx[k] = val[k](0);
valy[k] = val[k](1);
valz[k] = val[k](2);
}
double gradux[3];
double graduy[3];
double graduz[3];
double u = 0.33, v = 0.33, w = 0.0;
e->interpolateGrad(valx, u, v, w, gradux);
e->interpolateGrad(valy, u, v, w, graduy);
e->interpolateGrad(valz, u, v, w, graduz);
std::vector<double> vec(9);
vec[0] = gradux[0];
vec[4] = graduy[1];
vec[8] = graduy[2];
vec[1] = vec[3] = 0.5 * (gradux[0] + graduy[1]);
vec[2] = vec[6] = 0.5 * (gradux[0] + graduz[2]);
vec[5] = vec[7] = 0.5 * (gradux[1] + graduz[2]);
data[e->getNum()] = vec;
}
}
PView *pv = new PView(postFileName, "ElementData", pModel, data, 0.0);
return pv;
}
static int getGenus (std::vector<MElement *> &elements,
std::vector<std::vector<MEdge> > &boundaries)
{
//We suppose MElements are simply connected
std::set<MEdge, Less_Edge> es;
std::set<MVertex*> vs;
int N = 0;
for(unsigned int i = 0; i < elements.size(); i++){
N++;
MElement *e = elements[i];
for(int j = 0; j < e->getNumVertices(); j++){
vs.insert(e->getVertex(j));
}
for(int j = 0; j < e->getNumEdges(); j++){
es.insert(e->getEdge(j));
}
}
int poincare = vs.size() - es.size() + N;
//compute connected boundaries
int nbBounds = 0;
std::vector<MEdge> bEdges;
for(unsigned int i = 0; i < elements.size(); i++){
for(int j = 0; j < elements[i]->getNumEdges(); j++){
MEdge me = elements[i]->getEdge(j);
if(std::find(bEdges.begin(), bEdges.end(), me) == bEdges.end())
bEdges.push_back(me);
else
bEdges.erase(std::find(bEdges.begin(), bEdges.end(),me));
}
}
nbBounds = connected_bounds(bEdges, boundaries);
int genus = (int)(-poincare + 2 - nbBounds)/2;
//printf("************** partition has %d boundaries and genus =%d \n", nbBounds, genus);
return genus;
}
static void drawVerticesPerElement(drawContext *ctx, GEntity *e,
std::vector<T*> &elements)
{
for(unsigned int i = 0; i < elements.size(); i++){
MElement *ele = elements[i];
for(int j = 0; j < ele->getNumVertices(); j++){
MVertex *v = ele->getVertex(j);
// FIXME isElementVisible() can be slow: we should also use a
// vertex array for drawing vertices...
if(isElementVisible(ele) && v->getVisibility()){
if(CTX::instance()->mesh.points) {
if(CTX::instance()->mesh.colorCarousel == 0 ||
CTX::instance()->mesh.volumesFaces ||
CTX::instance()->mesh.surfacesFaces){ // by element type
if(v->getPolynomialOrder() > 1)
glColor4ubv((GLubyte *) & CTX::instance()->color.mesh.vertexSup);
else
glColor4ubv((GLubyte *) & CTX::instance()->color.mesh.vertex);
}
else{
unsigned int col = getColorByEntity(e);
glColor4ubv((GLubyte *) & col);
}
if(CTX::instance()->mesh.pointType)
ctx->drawSphere(CTX::instance()->mesh.pointSize, v->x(), v->y(), v->z(),
CTX::instance()->mesh.light);
else{
glBegin(GL_POINTS);
glVertex3d(v->x(), v->y(), v->z());
glEnd();
}
}
if(CTX::instance()->mesh.pointsNum)
drawVertexLabel(ctx, v->onWhat() ? v->onWhat() : e, v);
}
}
}
}
PView *GMSH_DistancePlugin::execute(PView *v)
{
int id_pt = (int) DistanceOptions_Number[0].def;
int id_line = (int) DistanceOptions_Number[1].def;
int id_face = (int) DistanceOptions_Number[2].def;
double type = (double) DistanceOptions_Number[3].def;
int ortho = (int) DistanceOptions_Number[6].def;
PView *view = new PView();
_data = getDataList(view);
#if defined(HAVE_SOLVER)
#if defined(HAVE_TAUCS)
linearSystemCSRTaucs<double> *lsys = new linearSystemCSRTaucs<double>;
#else
linearSystemCSRGmm<double> *lsys = new linearSystemCSRGmm<double>;
lsys->setNoisy(1);
lsys->setGmres(1);
lsys->setPrec(5.e-8);
#endif
dofManager<double> * dofView = new dofManager<double>(lsys);
#endif
std::vector<GEntity*> _entities;
GModel::current()->getEntities(_entities);
if (!_entities.size() || !_entities[_entities.size()-1]->getMeshElement(0)) {
Msg::Error("This plugin needs a mesh !");
return view;
}
GEntity* ge = _entities[_entities.size()-1];
int integrationPointTetra[2] = {0,0};
int numnodes = 0;
for (unsigned int i = 0; i < _entities.size()-1; i++)
numnodes += _entities[i]->mesh_vertices.size();
int totNodes = numnodes + _entities[_entities.size()-1]->mesh_vertices.size();
int order = ge->getMeshElement(0)->getPolynomialOrder();
int totNumNodes = totNodes + ge->getNumMeshElements()*integrationPointTetra[order-1];
std::vector<SPoint3> pts;
std::vector<double> distances;
std::vector<MVertex* > pt2Vertex;
pts.clear();
distances.clear();
pt2Vertex.clear();
pts.reserve(totNumNodes);
distances.reserve(totNumNodes);
pt2Vertex.reserve(totNumNodes);
std::map<MVertex*,double> _distanceE_map;
std::map<MVertex*,int> _isInYarn_map;
std::vector<int> index;
std::vector<double> distancesE;
std::vector<double> distances2;
std::vector<double> distancesE2;
std::vector<int> isInYarn;
std::vector<int> isInYarn2;
std::vector<SPoint3> closePts;
std::vector<SPoint3> closePts2;
for (int i=0; i<totNumNodes; i++) {
distances.push_back(1.e22);
}
int k = 0;
for (unsigned int i=0; i<_entities.size(); i++){
GEntity* ge = _entities[i];
_maxDim = std::max(_maxDim, ge->dim());
for (unsigned int j=0; j<ge->mesh_vertices.size(); j++) {
MVertex *v = ge->mesh_vertices[j];
pts.push_back(SPoint3(v->x(), v->y(), v->z()));
_distance_map.insert(std::make_pair(v, 0.0));
/* TO DO (by AM)
SPoint3 p_empty();
_closePts_map.insert(std::make_pair(v, p_empty));
*/
pt2Vertex[k] = v;
k++;
}
}
// Compute geometrical distance to mesh boundaries
//------------------------------------------------------
if (type < 0.0 ) {
bool existEntity = false;
for (unsigned int i=0; i<_entities.size(); i++) {
GEntity* g2 = _entities[i];
int gDim = g2->dim();
std::vector<int> phys = g2->getPhysicalEntities();
bool computeForEntity = false;
for(unsigned int k = 0; k<phys.size(); k++) {
int tagp = phys[k];
if (id_pt == 0 && id_line == 0 && id_face == 0 && gDim == _maxDim - 1)
computeForEntity = true;
else if ((tagp == id_pt && gDim == 0) || (tagp == id_line && gDim == 1) ||
(tagp == id_face && gDim == 2))
computeForEntity = true;
}
if (computeForEntity) {
existEntity = true;
for (unsigned int k = 0; k < g2->getNumMeshElements(); k++) {
std::vector<double> iDistances;
std::vector<SPoint3> iClosePts;
std::vector<double> iDistancesE;
std::vector<int> iIsInYarn;
MElement *e = g2->getMeshElement(k);
MVertex *v1 = e->getVertex(0);
MVertex *v2 = e->getVertex(1);
SPoint3 p1(v1->x(), v1->y(), v1->z());
SPoint3 p2(v2->x(), v2->y(), v2->z());
if ((e->getNumVertices() == 2 && order == 1) ||
(e->getNumVertices() == 3 && order == 2)) {
signedDistancesPointsLine(iDistances, iClosePts, pts, p1, p2);
}
else if ((e->getNumVertices() == 3 && order == 1) ||
(e->getNumVertices() == 6 && order == 2)) {
MVertex *v3 = e->getVertex(2);
SPoint3 p3 (v3->x(),v3->y(),v3->z());
signedDistancesPointsTriangle(iDistances, iClosePts, pts, p1, p2, p3);
}
for (unsigned int kk=0; kk<pts.size(); kk++) {
if (std::abs(iDistances[kk]) < distances[kk]) {
distances[kk] = std::abs(iDistances[kk]);
MVertex *v = pt2Vertex[kk];
_distance_map[v] = distances[kk];
/* TO DO (by AM)
_closePts_map[v] = iClosePts[kk];
*/
}
}
}
}
}
if (!existEntity){
if (id_pt != 0) Msg::Error("The Physical Point does not exist !");
if (id_line != 0) Msg::Error("The Physical Line does not exist !");
if (id_face != 0) Msg::Error("The Physical Surface does not exist !");
return view;
}
printView(_entities, _distance_map);
/* TO DO (by AM)
printView(_entities, _closePts_map);
*/
}
// Compute PDE for distance function
//-----------------------------------
else if (type > 0.0) {
#if defined(HAVE_SOLVER)
bool existEntity = false;
SBoundingBox3d bbox;
for(unsigned int i = 0; i < _entities.size(); i++){
GEntity* ge = _entities[i];
int gDim = ge->dim();
bool fixForEntity = false;
std::vector<int> phys = ge->getPhysicalEntities();
for(unsigned int k = 0; k < phys.size(); k++) {
int tagp = phys[k];
if (id_pt == 0 && id_line == 0 && id_face == 0 && gDim == _maxDim - 1)
fixForEntity = true;
else if ((tagp == id_pt && gDim == 0) || (tagp == id_line && gDim == 1) ||
(tagp == id_face && gDim == 2) )
fixForEntity = true;
}
if (fixForEntity) {
existEntity = true;
for (unsigned int i = 0; i < ge->getNumMeshElements(); ++i) {
MElement *t = ge->getMeshElement(i);
for (int k=0; k<t->getNumVertices(); k++) {
MVertex *v = t->getVertex(k);
dofView->fixVertex(v, 0, 1, 0.);
bbox += SPoint3(v->x(), v->y(), v->z());
}
}
}
}
if (!existEntity){
if (id_pt != 0) Msg::Error("The Physical Point does not exist !");
if (id_line != 0) Msg::Error("The Physical Line does not exist !");
if (id_face != 0) Msg::Error("The Physical Surface does not exist !");
return view;
}
std::vector<MElement *> allElems;
for(unsigned int ii = 0; ii < _entities.size(); ii++){
if(_entities[ii]->dim() == _maxDim) {
GEntity *ge = _entities[ii];
for(unsigned int i = 0; i < ge->getNumMeshElements(); ++i) {
MElement *t = ge->getMeshElement(i);
allElems.push_back(t);
for (int k = 0; k < t->getNumVertices(); k++)
dofView->numberVertex(t->getVertex(k), 0, 1);
}
}
}
double L = norm(SVector3(bbox.max(), bbox.min()));
double mu = type*L;
simpleFunction<double> DIFF(mu*mu), ONE(1.0);
distanceTerm distance(GModel::current(), 1, &DIFF, &ONE);
for (std::vector<MElement* >::iterator it = allElems.begin();
it != allElems.end(); it++){
SElement se((*it));
distance.addToMatrix(*dofView, &se);
}
groupOfElements gr(allElems);
distance.addToRightHandSide(*dofView, gr);
Msg::Info("Distance Computation: Assembly done");
lsys->systemSolve();
Msg::Info("Distance Computation: System solved");
for (std::map<MVertex*,double >::iterator itv = _distance_map.begin();
itv != _distance_map.end() ; ++itv) {
MVertex *v = itv->first;
double value;
dofView->getDofValue(v, 0, 1, value);
value = std::min(0.9999, value);
double dist = -mu * log(1. - value);
itv->second = dist;
}
printView(_entities, _distance_map);
#endif
}
_data->setName("distance");
_data->Time.push_back(0);
_data->setFileName(_fileName.c_str());
_data->finalize();
// compute also orthogonal vector to distance field
// A Uortho = -C DIST
//------------------------------------------------
if (ortho > 0) {
#if defined(HAVE_SOLVER)
#ifdef HAVE_TAUCS
linearSystemCSRTaucs<double> *lsys2 = new linearSystemCSRTaucs<double>;
#else
linearSystemCSRGmm<double> *lsys2 = new linearSystemCSRGmm<double>;
lsys->setNoisy(1);
lsys->setGmres(1);
lsys->setPrec(5.e-8);
#endif
dofManager<double> myAssembler(lsys2);
simpleFunction<double> ONE(1.0);
double dMax = 1.0; //EMI TO CHANGE
std::vector<MElement *> allElems;
for(unsigned int ii = 0; ii < _entities.size(); ii++){
if (_entities[ii]->dim() == _maxDim) {
GEntity *ge = _entities[ii];
for (unsigned int i=0; i<ge->getNumMeshElements(); ++i) {
MElement *t = ge->getMeshElement(i);
double vMean = 0.0;
for (int k = 0; k < t->getNumVertices(); k++) {
std::map<MVertex*, double>::iterator it = _distance_map.find(t->getVertex(k));
vMean += it->second;
}
vMean /= t->getNumVertices();
if (vMean < dMax)
allElems.push_back(ge->getMeshElement(i));
}
}
}
int mid = (int)floor(allElems.size() / 2.);
MElement *e = allElems[mid];
MVertex *vFIX = e->getVertex(0);
myAssembler.fixVertex(vFIX, 0, 1, 0.0);
for (std::vector<MElement* >::iterator it = allElems.begin();
it != allElems.end(); it++){
MElement *t = *it;
for(int k = 0; k < t->getNumVertices(); k++)
myAssembler.numberVertex(t->getVertex(k), 0, 1);
}
orthogonalTerm *ortho;
ortho = new orthogonalTerm(GModel::current(), 1, &ONE, &_distance_map);
// if (type < 0)
// ortho = new orthogonalTerm(GModel::current(), 1, &ONE, view);
// else
// ortho = new orthogonalTerm(GModel::current(), 1, &ONE, dofView);
for (std::vector<MElement* >::iterator it = allElems.begin();
it != allElems.end(); it++){
SElement se((*it));
ortho->addToMatrix(myAssembler, &se);
}
groupOfElements gr(allElems);
ortho->addToRightHandSide(myAssembler, gr);
Msg::Info("Orthogonal Computation: Assembly done");
lsys2->systemSolve();
Msg::Info("Orthogonal Computation: System solved");
PView *view2 = new PView();
PViewDataList *data2 = getDataList(view2);
data2->setName("ortogonal field");
Msg::Info("Writing orthogonal.pos");
FILE * f5 = Fopen("orthogonal.pos","w");
fprintf(f5,"View \"orthogonal\"{\n");
for (std::vector<MElement* >::iterator it = allElems.begin();
it != allElems.end(); it++){
MElement *e = *it;
int numNodes = e->getNumVertices();
if (e->getType() == TYPE_POLYG)
numNodes = e->getNumChildren() * e->getChild(0)->getNumVertices();
std::vector<double> x(numNodes), y(numNodes), z(numNodes);
std::vector<double> *out2 = data2->incrementList(1, e->getType(), numNodes);
std::vector<MVertex*> nods;
std::vector<double> orth;
if(!e->getNumChildren())
for(int i=0; i<numNodes; i++)
nods.push_back(e->getVertex(i));
else
for(int i = 0; i < e->getNumChildren(); i++)
for(int j = 0; j < e->getChild(i)->getNumVertices(); j++)
nods.push_back(e->getChild(i)->getVertex(j));
for(int nod = 0; nod < numNodes; nod++) out2->push_back((nods[nod])->x());
for(int nod = 0; nod < numNodes; nod++) out2->push_back((nods[nod])->y());
for(int nod = 0; nod < numNodes; nod++) out2->push_back((nods[nod])->z());
if (_maxDim == 2)
switch (numNodes) {
case 2: fprintf(f5,"SL("); break;
case 3: fprintf(f5,"ST("); break;
case 4: fprintf(f5,"SQ("); break;
default: Msg::Fatal("Error in Plugin 'Distance' (numNodes=%g).",numNodes); break;
}
else if (_maxDim == 3)
switch (numNodes) {
case 4: fprintf(f5,"SS("); break;
case 8: fprintf(f5,"SH("); break;
case 6: fprintf(f5,"SI("); break;
case 5: fprintf(f5,"SY("); break;
default: Msg::Fatal("Error in Plugin 'Distance' (numNodes=%g).",numNodes); break;
}
for (int j=0; j<numNodes; j++) {
MVertex *v = nods[j];
if (j)
fprintf(f5, ",%g,%g,%g", v->x(), v->y(), v->z());
else
fprintf(f5, "%g,%g,%g", v->x(), v->y(), v->z());
double value;
myAssembler.getDofValue(v, 0, 1, value);
orth.push_back(value);
}
fprintf(f5,"){");
for (unsigned int i=0; i<orth.size(); i++) {
out2->push_back(orth[i]);
if (i)
fprintf(f5,",%g", orth[i]);
else
fprintf(f5,"%g", orth[i]);
}
fprintf(f5,"};\n");
}
fprintf(f5,"};\n");
fclose(f5);
lsys->clear();
lsys2->clear();
data2->Time.push_back(0);
data2->setFileName("orthogonal.pos");
data2->finalize();
#endif
}
return view;
}
void GMSH_DistancePlugin::printView(std::vector<GEntity*> _entities,
std::map<MVertex*, double > _distance_map)
{
_fileName = DistanceOptions_String[0].def;
_minScale = (double) DistanceOptions_Number[4].def;
_maxScale = (double) DistanceOptions_Number[5].def;
double minDist=1.e4;
double maxDist=0.0;
for (std::map<MVertex*,double >::iterator itv=_distance_map.begin();
itv != _distance_map.end(); ++itv){
double dist = itv->second;
if (dist>maxDist) maxDist = dist;
if (dist<minDist) minDist = dist;
itv->second = dist;
}
Msg::Info("Writing %s", _fileName.c_str());
FILE *fName = Fopen(_fileName.c_str(),"w");
fprintf(fName, "View \"distance \"{\n");
for (unsigned int ii=0; ii<_entities.size(); ii++) {
if (_entities[ii]->dim() == _maxDim) {
for (unsigned int i=0; i<_entities[ii]->getNumMeshElements(); i++) {
MElement *e = _entities[ii]->getMeshElement(i);
int numNodes = e->getNumVertices();
if (e->getNumChildren())
numNodes = e->getNumChildren() * e->getChild(0)->getNumVertices();
std::vector<double> x(numNodes), y(numNodes), z(numNodes);
std::vector<double> *out = _data->incrementList(1, e->getType(), numNodes);
std::vector<MVertex*> nods;
if (!e->getNumChildren())
for(int i = 0; i < numNodes; i++)
nods.push_back(e->getVertex(i));
else
for(int i = 0; i < e->getNumChildren(); i++)
for(int j = 0; j < e->getChild(i)->getNumVertices(); j++)
nods.push_back(e->getChild(i)->getVertex(j));
for (int nod = 0; nod < numNodes; nod++) out->push_back((nods[nod])->x());
for (int nod = 0; nod < numNodes; nod++) out->push_back((nods[nod])->y());
for (int nod = 0; nod < numNodes; nod++) out->push_back((nods[nod])->z());
if (_maxDim == 2)
switch (numNodes) {
case 2: fprintf(fName,"SL("); break;
case 3: fprintf(fName,"ST("); break;
case 4: fprintf(fName,"SQ("); break;
default: Msg::Error("Error in Plugin 'Distance' (numNodes=%d)",
numNodes); break;
}
else if (_maxDim == 3)
switch (numNodes) {
case 4: fprintf(fName,"SS("); break;
case 8: fprintf(fName,"SH("); break;
case 6: fprintf(fName,"SI("); break;
case 5: fprintf(fName,"SY("); break;
default: Msg::Error("Error in Plugin 'Distance' (numNodes=%d)",
numNodes); break;
}
std::vector<double> dist;
for (int j=0; j<numNodes; j++) {
MVertex *v = nods[j];
if (j)
fprintf(fName, ",%.16g,%.16g,%.16g", v->x(), v->y(), v->z());
else
fprintf(fName, "%.16g,%.16g,%.16g", v->x(), v->y(), v->z());
std::map<MVertex*, double>::iterator it = _distance_map.find(v);
dist.push_back(it->second);
}
fprintf(fName,"){");
for (unsigned int i=0; i<dist.size(); i++) {
if (_minScale>0 && _maxScale>0)
dist[i] = _minScale + ((dist[i] - minDist) / (maxDist - minDist)) *
(_maxScale - _minScale);
else if (_minScale>0 && _maxScale<0)
dist[i] = _minScale + dist[i];
out->push_back(dist[i]);
if (i)
fprintf(fName, ",%.16g", dist[i]);
else
fprintf(fName, "%.16g", dist[i]);
}
fprintf(fName,"};\n");
}
}
}
fprintf(fName,"};\n");
fclose(fName);
}
PView *elasticitySolver::buildStressesView(const std::string postFileName)
{
double sti[6] = {0., 0., 0., 0., 0., 0.};
double str[6] = {0., 0., 0., 0., 0., 0.};
double volTot = 0.;
std::cout << "build stresses view" << std::endl;
std::map<int, std::vector<double> > data;
for(std::size_t i = 0; i < elasticFields.size(); ++i) {
double E = elasticFields[i]._e;
double nu = elasticFields[i]._nu;
SolverField<SVector3> Field(pAssembler, LagSpace);
for(groupOfElements::elementContainer::const_iterator it =
elasticFields[i].g->begin();
it != elasticFields[i].g->end(); ++it) {
MElement *e = *it;
double vol = e->getVolume() * e->getVolumeSign();
int nbVertex = e->getNumVertices();
std::vector<SVector3> val(nbVertex);
double valx[256];
double valy[256];
double valz[256];
for(int k = 0; k < nbVertex; k++) {
MVertex *v = e->getVertex(k);
MPoint p(v);
Field.f(&p, 0, 0, 0, val[k]);
valx[k] = val[k](0);
valy[k] = val[k](1);
valz[k] = val[k](2);
}
double gradux[3];
double graduy[3];
double graduz[3];
SPoint3 center = e->barycenterUVW();
double u = center.x(), v = center.y(), w = center.z();
e->interpolateGrad(valx, u, v, w, gradux);
e->interpolateGrad(valy, u, v, w, graduy);
e->interpolateGrad(valz, u, v, w, graduz);
double eps[6] = {gradux[0],
graduy[1],
graduz[2],
0.5 * (gradux[1] + graduy[0]),
0.5 * (gradux[2] + graduz[0]),
0.5 * (graduy[2] + graduz[1])};
double A = E / (1. + nu);
double B = A * (nu / (1. - 2 * nu));
double trace = eps[0] + eps[1] + eps[2];
double sxx = A * eps[0] + B * trace;
double syy = A * eps[1] + B * trace;
double szz = A * eps[2] + B * trace;
double sxy = A * eps[3];
double sxz = A * eps[4];
double syz = A * eps[5];
std::vector<double> vec(9);
vec[0] = sxx;
vec[1] = sxy;
vec[2] = sxz;
vec[3] = sxy;
vec[4] = syy;
vec[5] = syz;
vec[6] = sxz;
vec[7] = syz;
vec[8] = szz;
data[e->getNum()] = vec;
for(int k = 0; k < 6; k++) str[k] += eps[k] * vol;
sti[0] += sxx * vol;
sti[1] += syy * vol;
sti[2] += szz * vol;
sti[3] += sxy * vol;
sti[4] += sxz * vol;
sti[5] += syz * vol;
volTot += vol;
}
}
for(int i = 0; i < 6; i++) {
str[i] = str[i] / volTot;
sti[i] = sti[i] / volTot;
}
printf("effective stiffn = ");
for(int i = 0; i < 6; i++) printf("%g ", sti[i]);
printf("\n");
printf("effective strain = ");
for(int i = 0; i < 6; i++) printf("%g ", str[i]);
printf("\n");
PView *pv = new PView(postFileName, "ElementData", pModel, data, 0.0);
return pv;
}
static int getAspectRatio(std::vector<MElement *> &elements,
std::vector<std::vector<MEdge> > &boundaries)
{
double area3D = 0.0;
for(unsigned int i = 0; i <elements.size(); ++i){
MElement *t = elements[i];
std::vector<MVertex *> v(3);
for(int k = 0; k < 3; k++) v[k] = t->getVertex(k);
double p0[3] = {v[0]->x(), v[0]->y(), v[0]->z()};
double p1[3] = {v[1]->x(), v[1]->y(), v[1]->z()};
double p2[3] = {v[2]->x(), v[2]->y(), v[2]->z()};
double a_3D = fabs(triangle_area(p0, p1, p2));
area3D += a_3D;
}
double tot_length = 0.0;
for(unsigned int i = 0; i <boundaries.size(); ++i){
std::vector<MEdge> iBound = boundaries[i];
double iLength = 0.0;
for( unsigned int j = 0; j <iBound.size(); ++j){
MVertex *v0 = iBound[j].getVertex(0);
MVertex *v1 = iBound[j].getVertex(1);
const double length = sqrt((v0->x() - v1->x()) * (v0->x() - v1->x()) +
(v0->y() - v1->y()) * (v0->y() - v1->y()) +
(v0->z() - v1->z()) * (v0->z() - v1->z()));
iLength += length;
}
tot_length += iLength;
}
int AR = 1;
if (boundaries.size() > 0){
tot_length /= boundaries.size();
AR = (int) ceil(2*3.14*area3D/(tot_length*tot_length));
}
//compute AR also with Bounding box
std::set<MVertex*> vs;
for(unsigned int i = 0; i < elements.size(); i++){
MElement *e = elements[i];
for(int j = 0; j < e->getNumVertices(); j++){
vs.insert(e->getVertex(j));
}
}
SBoundingBox3d bb;
std::vector<SPoint3> vertices;
for (std::set<MVertex* >::iterator it = vs.begin(); it != vs.end(); it++){
SPoint3 pt((*it)->x(),(*it)->y(), (*it)->z());
vertices.push_back(pt);
bb += pt;
}
double H = norm(SVector3(bb.max(), bb.min()));
//SOrientedBoundingBox obbox = SOrientedBoundingBox::buildOBB(vertices);
//double H = obbox.getMaxSize();
double D = H;
if (boundaries.size() > 0 ) D = 10e4;
for (unsigned int i = 0; i < boundaries.size(); i++){
std::set<MVertex*> vb;
std::vector<MEdge> iBound = boundaries[i];
for (unsigned int j = 0; j < iBound.size(); j++){
MEdge e = iBound[j];
vb.insert(e.getVertex(0));
vb.insert(e.getVertex(1));
}
std::vector<SPoint3> vBounds;
SBoundingBox3d bb;
for (std::set<MVertex* >::iterator it = vb.begin(); it != vb.end(); it++){
SPoint3 pt((*it)->x(),(*it)->y(), (*it)->z());
vBounds.push_back(pt);
bb +=pt;
}
double iD = norm(SVector3(bb.max(), bb.min()));
D = std::min(D, iD);
//SOrientedBoundingBox obboxD = SOrientedBoundingBox::buildOBB(vBounds);
//D = std::max(D, obboxD.getMaxSize());
}
int AR2 = (int)ceil(H/D);
return std::max(AR, AR2);
}
double highOrderTools::smooth_metric_(std::vector<MElement*> & v,
GFace *gf,
dofManager<double> &myAssembler,
std::set<MVertex*> &verticesToMove,
elasticityTerm &El)
{
std::set<MVertex*>::iterator it;
double dx = 0.0;
if (myAssembler.sizeOfR()){
// while convergence
for (unsigned int i = 0; i < v.size(); i++){
MElement *e = v[i];
int nbNodes = e->getNumVertices();
const int n2 = 2 * nbNodes;
const int n3 = 3 * nbNodes;
fullMatrix<double> K33(n3, n3);
fullMatrix<double> K22(n2, n2);
fullMatrix<double> J32(n3, n2);
fullMatrix<double> J23(n2, n3);
fullVector<double> D3(n3);
fullVector<double> R2(n2);
fullMatrix<double> J23K33(n2, n3);
K33.setAll(0.0);
SElement se(e);
El.elementMatrix(&se, K33);
computeMetricInfo(gf, e, J32, J23, D3);
J23K33.gemm(J23, K33, 1, 0);
K22.gemm(J23K33, J32, 1, 0);
J23K33.mult(D3, R2);
for (int j = 0; j < n2; j++){
Dof RDOF = El.getLocalDofR(&se, j);
myAssembler.assemble(RDOF, -R2(j));
for (int k = 0; k < n2; k++){
Dof CDOF = El.getLocalDofC(&se, k);
myAssembler.assemble(RDOF, CDOF, K22(j, k));
}
}
}
myAssembler.systemSolve();
// for all element, compute detJ at integration points --> material law end
// while convergence
for (it = verticesToMove.begin(); it != verticesToMove.end(); ++it){
if ((*it)->onWhat()->dim() == 2){
SPoint2 param;
reparamMeshVertexOnFace((*it), gf, param);
SPoint2 dparam;
myAssembler.getDofValue((*it), 0, _tag, dparam[0]);
myAssembler.getDofValue((*it), 1, _tag, dparam[1]);
SPoint2 newp = param+dparam;
dx += newp.x() * newp.x() + newp.y() * newp.y();
(*it)->setParameter(0, newp.x());
(*it)->setParameter(1, newp.y());
}
}
myAssembler.systemClear();
}
return dx;
}
int GModel::writeINP(const std::string &name, bool saveAll, bool saveGroupsOfNodes,
double scalingFactor)
{
FILE *fp = Fopen(name.c_str(), "w");
if(!fp){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
if(noPhysicalGroups()) saveAll = true;
indexMeshVertices(saveAll);
std::vector<GEntity*> entities;
getEntities(entities);
fprintf(fp, "*Heading\n");
fprintf(fp, " %s\n", name.c_str());
fprintf(fp, "*Node\n");
for(unsigned int i = 0; i < entities.size(); i++)
for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++)
entities[i]->mesh_vertices[j]->writeINP(fp, scalingFactor);
for(viter it = firstVertex(); it != lastVertex(); ++it){
writeElementsINP(fp, *it, (*it)->points, saveAll);
}
for(eiter it = firstEdge(); it != lastEdge(); ++it){
writeElementsINP(fp, *it, (*it)->lines, saveAll);
}
for(fiter it = firstFace(); it != lastFace(); ++it){
writeElementsINP(fp, *it, (*it)->triangles, saveAll);
writeElementsINP(fp, *it, (*it)->quadrangles, saveAll);
}
for(riter it = firstRegion(); it != lastRegion(); ++it){
writeElementsINP(fp, *it, (*it)->tetrahedra, saveAll);
writeElementsINP(fp, *it, (*it)->hexahedra, saveAll);
writeElementsINP(fp, *it, (*it)->prisms, saveAll);
writeElementsINP(fp, *it, (*it)->pyramids, saveAll);
}
std::map<int, std::vector<GEntity*> > groups[4];
getPhysicalGroups(groups);
// save elements sets for each physical group
for(int dim = 0; dim <= 3; dim++){
for(std::map<int, std::vector<GEntity*> >::iterator it = groups[dim].begin();
it != groups[dim].end(); it++){
std::vector<GEntity *> &entities = it->second;
fprintf(fp, "*ELSET,ELSET=%s\n", physicalName(this, dim, it->first).c_str());
int n = 0;
for(unsigned int i = 0; i < entities.size(); i++){
for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
MElement *e = entities[i]->getMeshElement(j);
if(n && !(n % 10)) fprintf(fp, "\n");
fprintf(fp, "%d, ", e->getNum());
n++;
}
}
fprintf(fp, "\n");
}
}
// save node sets for each physical group
if(saveGroupsOfNodes){
for(int dim = 1; dim <= 3; dim++){
for(std::map<int, std::vector<GEntity*> >::iterator it = groups[dim].begin();
it != groups[dim].end(); it++){
std::set<MVertex*> nodes;
std::vector<GEntity *> &entities = it->second;
for(unsigned int i = 0; i < entities.size(); i++){
for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
MElement *e = entities[i]->getMeshElement(j);
for (int k = 0; k < e->getNumVertices(); k++)
nodes.insert(e->getVertex(k));
}
}
fprintf(fp, "*NSET,NSET=%s\n", physicalName(this, dim, it->first).c_str());
int n = 0;
for(std::set<MVertex*>::iterator it2 = nodes.begin(); it2 != nodes.end(); it2++){
if(n && !(n % 10)) fprintf(fp, "\n");
fprintf(fp, "%d, ", (*it2)->getIndex());
n++;
}
fprintf(fp, "\n");
}
}
}
fclose(fp);
return 1;
}
int GModel::writeDIFF(const std::string &name, bool binary, bool saveAll,
double scalingFactor)
{
if(binary){
Msg::Error("Binary DIFF output is not implemented");
return 0;
}
FILE *fp = Fopen(name.c_str(), binary ? "wb" : "w");
if(!fp){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
if(noPhysicalGroups()) saveAll = true;
// get the number of vertices and index the vertices in a continuous
// sequence
int numVertices = indexMeshVertices(saveAll);
// tag the vertices according to which surface they belong to (Note
// that we use a brute force approach here, so that we can deal with
// models with incomplete topology. For example, when we merge 2 STL
// triangulations we don't have the boundary information between the
// faces, and the vertices would end up categorized on either one.)
std::vector<std::list<int> > vertexTags(numVertices);
std::list<int> boundaryIndicators;
for(riter it = firstRegion(); it != lastRegion(); it++){
std::list<GFace*> faces = (*it)->faces();
for(std::list<GFace*>::iterator itf = faces.begin(); itf != faces.end(); itf++){
GFace *gf = *itf;
boundaryIndicators.push_back(gf->tag());
for(unsigned int i = 0; i < gf->getNumMeshElements(); i++){
MElement *e = gf->getMeshElement(i);
for(int j = 0; j < e->getNumVertices(); j++){
MVertex *v = e->getVertex(j);
if(v->getIndex() > 0)
vertexTags[v->getIndex() - 1].push_back(gf->tag());
}
}
}
}
boundaryIndicators.sort();
boundaryIndicators.unique();
for(int i = 0; i < numVertices; i++){
vertexTags[i].sort();
vertexTags[i].unique();
}
// get all the entities in the model
std::vector<GEntity*> entities;
getEntities(entities);
// find max dimension of mesh elements we need to save
int dim = 0;
for(unsigned int i = 0; i < entities.size(); i++)
if(entities[i]->physicals.size() || saveAll)
for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++)
dim = std::max(dim, entities[i]->getMeshElement(j)->getDim());
// loop over all elements we need to save
int numElements = 0, maxNumNodesPerElement = 0;
for(unsigned int i = 0; i < entities.size(); i++){
if(entities[i]->physicals.size() || saveAll){
for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
MElement *e = entities[i]->getMeshElement(j);
if(e->getStringForDIFF() && e->getDim() == dim){
numElements++;
maxNumNodesPerElement = std::max(maxNumNodesPerElement, e->getNumVertices());
}
}
}
}
fprintf(fp, "\n\n");
fprintf(fp, " Finite element mesh (GridFE):\n\n");
fprintf(fp, " Number of space dim. = 3\n");
fprintf(fp, " Number of elements = %d\n", numElements);
fprintf(fp, " Number of nodes = %d\n\n", numVertices);
fprintf(fp, " All elements are of the same type : dpTRUE\n");
fprintf(fp, " Max number of nodes in an element: %d \n", maxNumNodesPerElement);
fprintf(fp, " Only one subdomain : dpFALSE\n");
fprintf(fp, " Lattice data ? 0\n\n\n\n");
fprintf(fp, " %d Boundary indicators: ", (int)boundaryIndicators.size());
for(std::list<int>::iterator it = boundaryIndicators.begin();
it != boundaryIndicators.end(); it++)
fprintf(fp, " %d", *it);
fprintf(fp, "\n\n\n");
fprintf(fp," Nodal coordinates and nodal boundary indicators,\n");
fprintf(fp," the columns contain:\n");
fprintf(fp," - node number\n");
fprintf(fp," - coordinates\n");
fprintf(fp," - no of boundary indicators that are set (ON)\n");
fprintf(fp," - the boundary indicators that are set (ON) if any.\n");
fprintf(fp,"#\n");
// write mesh vertices
for(unsigned int i = 0; i < entities.size(); i++){
for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++){
MVertex *v = entities[i]->mesh_vertices[j];
if(v->getIndex() > 0){
v->writeDIFF(fp, binary, scalingFactor);
fprintf(fp, " [%d] ", (int)vertexTags[v->getIndex() - 1].size());
for(std::list<int>::iterator it = vertexTags[v->getIndex() - 1].begin();
it != vertexTags[v->getIndex() - 1].end(); it++)
fprintf(fp," %d ", *it);
fprintf(fp,"\n");
}
}
}
fprintf(fp, "\n");
fprintf(fp, "\n");
fprintf(fp, " Element types and connectivity\n");
fprintf(fp, " the columns contain:\n");
fprintf(fp, " - element number\n");
fprintf(fp, " - element type\n");
fprintf(fp, " - subdomain number \n");
fprintf(fp, " - the global node numbers of the nodes in the element.\n");
fprintf(fp, "#\n");
// write mesh elements
int num = 0;
for(unsigned int i = 0; i < entities.size(); i++){
if(entities[i]->physicals.size() || saveAll){
for(unsigned int j = 0; j < entities[i]->getNumMeshElements(); j++){
MElement *e = entities[i]->getMeshElement(j);
if(e->getStringForDIFF() && e->getDim() == dim)
e->writeDIFF(fp, ++num, binary, entities[i]->tag());
}
}
}
fprintf(fp, "\n");
fclose(fp);
return 1;
}
// This function meshes the top surface of a QuadToTri extrusion. It returns 0 if it is given a
// non-quadToTri extrusion or if it fails.
// Args:
// 'GFace *to' is the top surface to mesh, 'from' is the source surface, 'pos' is a std::set
// of vertex positions for the top surface.
int MeshQuadToTriTopSurface( GFace *from, GFace *to, std::set<MVertex*,
MVertexLessThanLexicographic> &pos )
{
if( !to->meshAttributes.extrude || !to->meshAttributes.extrude->mesh.QuadToTri )
return 0;
// if the source is all triangles, then just let this function is not needed. Return 1.
if( from->triangles.size() && !from->quadrangles.size() )
return 1;
// in weird case of NO quads and NO tri
if( !from->triangles.size() && !from->quadrangles.size() )
return 0;
ExtrudeParams *ep = to->meshAttributes.extrude;
if( !ep || !ep->mesh.ExtrudeMesh || !(ep->geo.Mode == COPIED_ENTITY) ){
Msg::Error("In MeshQuadToTriTopSurface(), incomplete or no "
"extrude information for top face %d.", to->tag() );
return 0;
}
// is this a quadtri extrusion with added vertices?
bool is_addverts = false;
if( ep && (ep->mesh.QuadToTri == QUADTRI_ADDVERTS_1 || ep->mesh.QuadToTri == QUADTRI_ADDVERTS_1_RECOMB) )
is_addverts = true;
// execute this section if
// IF this is a 'no new vertices' quadToTri, mesh the surfaces according to this modified
// least point value method: if a 3 boundary point quad, draw diagonals from middle corner toward
// interior. If a a 2- or 1- point boundary quad, draw toward lowest pointer number NOT on boundary.
// All interior quad, draw diagonal to vertex with lowest pointer number.
if( !is_addverts ){
std::set<MVertex*, MVertexLessThanLexicographic> pos_src_edge;
QuadToTriInsertFaceEdgeVertices(from, pos_src_edge);
std::set<MVertex*, MVertexLessThanLexicographic>::iterator itp;
// loop through each element source quadrangle and extrude
for(unsigned int i = 0; i < from->quadrangles.size(); i++){
std::vector<MVertex*> verts;
for(int j = 0; j < from->quadrangles[i]->getNumVertices(); j++){
MVertex *v = from->quadrangles[i]->getVertex(j);
MVertex tmp(v->x(), v->y(), v->z(), 0, -1);
ExtrudeParams *ep = to->meshAttributes.extrude;
ep->Extrude(ep->mesh.NbLayer - 1, ep->mesh.NbElmLayer[ep->mesh.NbLayer - 1],
tmp.x(), tmp.y(), tmp.z());
itp = pos.find(&tmp);
if(itp == pos.end()){ // FIXME: workaround
Msg::Info("Linear search for (%.16g, %.16g, %.16g)", tmp.x(), tmp.y(), tmp.z());
itp = tmp.linearSearch(pos);
}
if(itp == pos.end()) {
Msg::Error("In MeshQuadToTriTopSurface(), Could not find "
"extruded vertex (%.16g, %.16g, %.16g) in surface %d",
tmp.x(), tmp.y(), tmp.z(), to->tag());
to->triangles.reserve(to->triangles.size()+1);
return 0;
}
verts.push_back(*itp);
}
if( verts.size() != 4 ){
Msg::Error("During mesh of QuadToTri surface %d, %d vertices found "
"in quad of source surface %d.", to->tag(), verts.size(),
from->tag() );
return 0;
}
// make the element
MElement *element = from->quadrangles[i];
// count vertices that are on a boundary edge
int edge_verts_count = 0;
//int skip_index = 0;
int bnd_indices[4];
for( int p = 0; p < element->getNumVertices(); p++ ){
if( pos_src_edge.find( element->getVertex(p) ) != pos_src_edge.end() ){
edge_verts_count++;
bnd_indices[p] = 1;
}
else{
//skip_index = p;
bnd_indices[p] = 0;
}
}
// Apply modified lowest vertex pointer diagonalization
int low_index = -1;
if( edge_verts_count == 3 || edge_verts_count == 2 || edge_verts_count == 1 ){
for( int p = 0; p < 4; p++ ){
if( !bnd_indices[p] && verts[p] != element->getVertex(p) ){
if( low_index < 0 )
low_index = p;
else if( verts[p] < verts[low_index] )
low_index = p;
}
}
if( low_index < 0 ) // what if they are all degenerate? Avoid the out-of-bounds error.
low_index = 0;
}
// lowest possible vertex pointer, regardless of if on edge or not
else if( edge_verts_count == 4 || edge_verts_count == 0 )
low_index = getIndexForLowestVertexPointer(verts);
addTriangle( verts[low_index],verts[(low_index+1)%verts.size()],
verts[(low_index+2)%verts.size()],to);
addTriangle( verts[low_index],verts[(low_index+2)%verts.size()],
verts[(low_index+3)%verts.size()],to);
}
return 1;
}
// AFTER THIS POINT IN FUNCTION, CODE IS ALL FOR 'ADD INTERNAL VERTEX' EXTRUSIONS (Less restrictive).
// if source face is unstructured, can try to make the top mesh a little neater
GFace *root_source = findRootSourceFaceForFace( from );
ExtrudeParams *ep_src = root_source->meshAttributes.extrude;
bool struct_root = false;
if( root_source &&
( (ep_src && ep_src->mesh.ExtrudeMesh && ep_src->geo.Mode == EXTRUDED_ENTITY) ||
root_source->meshAttributes.method == MESH_TRANSFINITE ) )
struct_root = true;
if( !struct_root && MeshQuadToTriTopUnstructured(from, to, pos) )
return 1;
// And top surface for the 'added internal vertex' method can be meshed quite easily
else{
std::set<MVertex *, MVertexLessThanLexicographic >::iterator itp;
// loop through each element source quadrangle and extrude
for(unsigned int i = 0; i < from->quadrangles.size(); i++){
std::vector<MVertex*> verts;
for(int j = 0; j < from->quadrangles[i]->getNumVertices(); j++){
MVertex *v = from->quadrangles[i]->getVertex(j);
MVertex tmp(v->x(), v->y(), v->z(), 0, -1);
ExtrudeParams *ep = to->meshAttributes.extrude;
ep->Extrude(ep->mesh.NbLayer - 1, ep->mesh.NbElmLayer[ep->mesh.NbLayer - 1],
tmp.x(), tmp.y(), tmp.z());
itp = pos.find(&tmp);
if(itp == pos.end()){ // FIXME: workaround
Msg::Info("Linear search for (%.16g, %.16g, %.16g)", tmp.x(), tmp.y(), tmp.z());
itp = tmp.linearSearch(pos);
}
if(itp == pos.end()) {
Msg::Error("In MeshQuadToTriTopSurface(), Could not find "
"extruded vertex (%.16g, %.16g, %.16g) in surface %d",
tmp.x(), tmp.y(), tmp.z(), to->tag());
to->triangles.reserve(to->triangles.size()+1);
return 0;
}
verts.push_back(*itp);
}
if( verts.size() != 4 ){
Msg::Error("During mesh of QuadToTri surface %d, %d vertices found "
"in quad of source surface %d.", to->tag(), verts.size(),
from->tag() );
return 0;
}
// make the elements
addTriangle( verts[0],verts[2], verts[3],to);
addTriangle( verts[0],verts[1], verts[2],to);
}
return 1;
}
return 0;
}
void Filler::treat_region(GRegion* gr){
int NumSmooth = CTX::instance()->mesh.smoothCrossField;
std::cout << "NumSmooth = " << NumSmooth << std::endl ;
if(NumSmooth && (gr->dim() == 3)){
double scale = gr->bounds().diag()*1e-2;
Frame_field::initRegion(gr,NumSmooth);
Frame_field::saveCrossField("cross0.pos",scale);
Frame_field::smoothRegion(gr,NumSmooth);
Frame_field::saveCrossField("cross1.pos",scale);
}
#if defined(HAVE_RTREE)
unsigned int i;
int j;
int count;
int limit;
bool ok2;
double x,y,z;
SPoint3 point;
Node *node,*individual,*parent;
MVertex* vertex;
MElement* element;
MElementOctree* octree;
deMeshGRegion deleter;
Wrapper wrapper;
GFace* gf;
std::queue<Node*> fifo;
std::vector<Node*> spawns;
std::vector<Node*> garbage;
std::vector<MVertex*> boundary_vertices;
std::set<MVertex*> temp;
std::list<GFace*> faces;
std::map<MVertex*,int> limits;
std::set<MVertex*>::iterator it;
std::list<GFace*>::iterator it2;
std::map<MVertex*,int>::iterator it3;
RTree<Node*,double,3,double> rtree;
Frame_field::init_region(gr);
Size_field::init_region(gr);
Size_field::solve(gr);
octree = new MElementOctree(gr->model());
garbage.clear();
boundary_vertices.clear();
temp.clear();
new_vertices.clear();
faces.clear();
limits.clear();
faces = gr->faces();
for(it2=faces.begin();it2!=faces.end();it2++){
gf = *it2;
limit = code(gf->tag());
for(i=0;i<gf->getNumMeshElements();i++){
element = gf->getMeshElement(i);
for(j=0;j<element->getNumVertices();j++){
vertex = element->getVertex(j);
temp.insert(vertex);
limits.insert(std::pair<MVertex*,int>(vertex,limit));
}
}
}
/*for(i=0;i<gr->getNumMeshElements();i++){
element = gr->getMeshElement(i);
for(j=0;j<element->getNumVertices();j++){
vertex = element->getVertex(j);
temp.insert(vertex);
}
}*/
for(it=temp.begin();it!=temp.end();it++){
if((*it)->onWhat()->dim()==0){
boundary_vertices.push_back(*it);
}
}
for(it=temp.begin();it!=temp.end();it++){
if((*it)->onWhat()->dim()==1){
boundary_vertices.push_back(*it);
}
}
for(it=temp.begin();it!=temp.end();it++){
if((*it)->onWhat()->dim()==2){
boundary_vertices.push_back(*it);
}
}
/*for(it=temp.begin();it!=temp.end();it++){
if((*it)->onWhat()->dim()<3){
boundary_vertices.push_back(*it);
}
}*/
//std::ofstream file("nodes.pos");
//file << "View \"test\" {\n";
for(i=0;i<boundary_vertices.size();i++){
x = boundary_vertices[i]->x();
y = boundary_vertices[i]->y();
z = boundary_vertices[i]->z();
node = new Node(SPoint3(x,y,z));
compute_parameters(node,gr);
node->set_layer(0);
it3 = limits.find(boundary_vertices[i]);
node->set_limit(it3->second);
rtree.Insert(node->min,node->max,node);
fifo.push(node);
//print_node(node,file);
}
count = 1;
while(!fifo.empty()){
parent = fifo.front();
fifo.pop();
garbage.push_back(parent);
if(parent->get_limit()!=-1 && parent->get_layer()>=parent->get_limit()){
continue;
}
spawns.clear();
spawns.resize(6);
for(i=0;i<6;i++){
spawns[i] = new Node();
}
create_spawns(gr,octree,parent,spawns);
for(i=0;i<6;i++){
ok2 = 0;
individual = spawns[i];
point = individual->get_point();
x = point.x();
y = point.y();
z = point.z();
if(inside_domain(octree,x,y,z)){
compute_parameters(individual,gr);
individual->set_layer(parent->get_layer()+1);
individual->set_limit(parent->get_limit());
if(far_from_boundary(octree,individual)){
wrapper.set_ok(1);
wrapper.set_individual(individual);
wrapper.set_parent(parent);
rtree.Search(individual->min,individual->max,rtree_callback,&wrapper);
if(wrapper.get_ok()){
fifo.push(individual);
rtree.Insert(individual->min,individual->max,individual);
vertex = new MVertex(x,y,z,gr,0);
new_vertices.push_back(vertex);
ok2 = 1;
//print_segment(individual->get_point(),parent->get_point(),file);
}
}
}
if(!ok2) delete individual;
}
if(count%100==0){
printf("%d\n",count);
}
count++;
}
//file << "};\n";
int option = CTX::instance()->mesh.algo3d;
CTX::instance()->mesh.algo3d = ALGO_3D_DELAUNAY;
deleter(gr);
std::vector<GRegion*> regions;
regions.push_back(gr);
meshGRegion mesher(regions); //?
mesher(gr); //?
MeshDelaunayVolume(regions);
CTX::instance()->mesh.algo3d = option;
for(i=0;i<garbage.size();i++) delete garbage[i];
for(i=0;i<new_vertices.size();i++) delete new_vertices[i];
new_vertices.clear();
delete octree;
rtree.RemoveAll();
Size_field::clear();
Frame_field::clear();
#endif
}
int GModel::readPLY(const std::string &name)
{
// this is crazy!?
replaceCommaByDot(name);
FILE *fp = Fopen(name.c_str(), "r");
if(!fp){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
std::vector<MVertex*> vertexVector;
std::map<int, std::vector<MElement*> > elements[5];
std::map<int, std::vector<double> > properties;
char buffer[256], str[256], str2[256], str3[256];
std::string s1;
int elementary = getMaxElementaryNumber(-1) + 1;
int nbv = 0, nbf = 0;
int nbprop = 0;
int nbView = 0;
std::vector<std::string> propName;
while(!feof(fp)) {
if(!fgets(buffer, sizeof(buffer), fp)) break;
if(buffer[0] != '#'){ // skip comments
sscanf(buffer, "%s %s", str, str2);
if(!strcmp(str, "element") && !strcmp(str2, "vertex")){
sscanf(buffer, "%s %s %d", str, str2, &nbv);
}
if(!strcmp(str, "format") && strcmp(str2, "ascii")){
Msg::Error("Only reading of ascii PLY files implemented");
fclose(fp);
return 0;
}
if(!strcmp(str, "property") && strcmp(str2, "list")){
nbprop++;
sscanf(buffer, "%s %s %s", str, str2, str3);
if (nbprop > 3) propName.push_back(s1+str3);
}
if(!strcmp(str, "element") && !strcmp(str2, "face")){
sscanf(buffer, "%s %s %d", str, str2, &nbf);
}
if(!strcmp(str, "end_header")){
nbView = nbprop -3;
Msg::Info("%d elements", nbv);
Msg::Info("%d triangles", nbf);
Msg::Info("%d properties", nbView);
vertexVector.resize(nbv);
for(int i = 0; i < nbv; i++) {
double x,y,z;
char line[10000], *pEnd, *pEnd2, *pEnd3;
if(!fgets(line, sizeof(line), fp)){ fclose(fp); return 0; }
x = strtod(line, &pEnd);
y = strtod(pEnd, &pEnd2);
z = strtod(pEnd2, &pEnd3);
vertexVector[i] = new MVertex(x, y, z);
pEnd = pEnd3;
std::vector<double> prop(nbView);
for (int k = 0; k < nbView; k++){
prop[k]=strtod(pEnd, &pEnd2);
pEnd = pEnd2;
properties[k].push_back(prop[k]);
}
}
for(int i = 0; i < nbf; i++) {
if(!fgets(buffer, sizeof(buffer), fp)) break;
int n[3], nbe;
sscanf(buffer, "%d %d %d %d", &nbe, &n[0], &n[1], &n[2]);
std::vector<MVertex*> vertices;
if(!getVertices(3, n, vertexVector, vertices)){ fclose(fp); return 0; }
elements[0][elementary].push_back(new MTriangle(vertices));
}
}
}
}
for(int i = 0; i < (int)(sizeof(elements) / sizeof(elements[0])); i++)
_storeElementsInEntities(elements[i]);
_associateEntityWithMeshVertices();
_storeVerticesInEntities(vertexVector);
#if defined(HAVE_POST)
// create PViews here
std::vector<GEntity*> _entities;
getEntities(_entities);
for (int iV=0; iV< nbView; iV++){
PView *view = new PView();
PViewDataList *data = dynamic_cast<PViewDataList*>(view->getData());
for(unsigned int ii = 0; ii < _entities.size(); ii++){
for(unsigned int i = 0; i < _entities[ii]->getNumMeshElements(); i++){
MElement *e = _entities[ii]->getMeshElement(i);
int numNodes = e->getNumVertices();
std::vector<double> x(numNodes), y(numNodes), z(numNodes);
std::vector<double> *out = data->incrementList(1, e->getType());
for(int nod = 0; nod < numNodes; nod++) out->push_back((e->getVertex(nod))->x());
for(int nod = 0; nod < numNodes; nod++) out->push_back((e->getVertex(nod))->y());
for(int nod = 0; nod < numNodes; nod++) out->push_back((e->getVertex(nod))->z());
std::vector<double> props;
int n[3];
n[0] = e->getVertex(0)->getNum()-1;
n[1] = e->getVertex(1)->getNum()-1;
n[2] = e->getVertex(2)->getNum()-1;
if(!getProperties(3, n, properties[iV], props)){ fclose(fp); return 0; }
for(int nod = 0; nod < numNodes; nod++) out->push_back(props[nod]);
}
}
data->setName(propName[iV]);
data->Time.push_back(0);
data->setFileName("property.pos");
data->finalize();
}
#endif
fclose(fp);
return 1;
}
bool Filler3D::treat_region(GRegion *gr)
{
BGMManager::set_use_cross_field(true);
bool use_vectorial_smoothness;
bool use_fifo;
string algo;
// readValue("param.dat","SMOOTHNESSALGO",algo);
algo.assign("SCALAR");
if (!algo.compare("SCALAR")){
use_vectorial_smoothness = false;
use_fifo = false;
}
else if (!algo.compare("FIFO")){
use_vectorial_smoothness = false;
use_fifo = true;
}
else{
cout << "unknown SMOOTHNESSALGO !" << endl;
throw;
}
const bool debug=false;
const bool export_stuff=true;
double a;
cout << "ENTERING POINTINSERTION3D" << endl;
// acquire background mesh
cout << "pointInsertion3D: recover BGM" << endl;
a = Cpu();
frameFieldBackgroundMesh3D *bgm =
dynamic_cast<frameFieldBackgroundMesh3D*>(BGMManager::get(gr));
time_smoothing += (Cpu() - a);
if (!bgm){
cout << "pointInsertion3D:: BGM dynamic cast failed ! " << endl;
throw;
}
// export BGM fields
if(export_stuff){
cout << "pointInsertion3D: export size field " << endl;
stringstream ss;
ss << "bg3D_sizefield_" << gr->tag() << ".pos";
bgm->exportSizeField(ss.str());
cout << "pointInsertion3D : export crossfield " << endl;
stringstream sscf;
sscf << "bg3D_crossfield_" << gr->tag() << ".pos";
bgm->exportCrossField(sscf.str());
cout << "pointInsertion3D : export smoothness " << endl;
stringstream sss;
sss << "bg3D_smoothness_" << gr->tag() << ".pos";
bgm->exportSmoothness(sss.str());
if (use_vectorial_smoothness){
cout << "pointInsertion3D : export vectorial smoothness " << endl;
stringstream ssvs;
ssvs << "bg3D_vectorial_smoothness_" << gr->tag() << ".pos";
bgm->exportVectorialSmoothness(ssvs.str());
}
}
// ---------------- START FILLING NEW POINTS ----------------
cout << "pointInsertion3D : inserting points in region " << gr->tag() << endl;
//ProfilerStart("/home/bernard/profile");
a = Cpu();
// ----- initialize fifo list -----
RTree<MVertex*,double,3,double> rtree;
listOfPoints *fifo;
if (use_fifo)
fifo = new listOfPointsFifo();
else if (use_vectorial_smoothness)
fifo = new listOfPointsVectorialSmoothness();
else
fifo = new listOfPointsScalarSmoothness();
set<MVertex*> temp;
vector<MVertex*> boundary_vertices;
map<MVertex*,int> vert_priority;
map<MVertex*,double> smoothness_forplot;
MElement *element;
MVertex *vertex;
list<GFace*> faces = gr->faces();
for(list<GFace*>::iterator it=faces.begin();it!=faces.end();it++){// for all faces
GFace *gf = *it;
// int limit = code_kesskessai(gf->tag());
for(unsigned int i=0;i<gf->getNumMeshElements();i++){
element = gf->getMeshElement(i);
for(int j=0;j<element->getNumVertices();j++){// for all vertices
vertex = element->getVertex(j);
temp.insert(vertex);
// limits.insert(make_pair(vertex,limit));
}
}
}
int geodim;
for(set<MVertex*>::iterator it=temp.begin();it!=temp.end();it++){
geodim = (*it)->onWhat()->dim();
if ((geodim==0) || (geodim==1) || (geodim==2)) boundary_vertices.push_back(*it);
}
double min[3],max[3],x,y,z,h;
for(unsigned int i=0;i<boundary_vertices.size();i++){
x = boundary_vertices[i]->x();
y = boundary_vertices[i]->y();
z = boundary_vertices[i]->z();
// "on boundary since working on boundary_vertices ...
MVertex *closest = bgm->get_nearest_neighbor_on_boundary(boundary_vertices[i]);
h = bgm->size(closest);// get approximate size, closest vertex, faster ?!
fill_min_max(x,y,z,h,min,max);
rtree.Insert(min,max,boundary_vertices[i]);
if (!use_vectorial_smoothness){
smoothness_vertex_pair *svp = new smoothness_vertex_pair();
svp->v = boundary_vertices[i];
svp->rank = bgm->get_smoothness(x,y,z);
svp->dir = 0;
svp->layer = 0;
svp->size = h;
bgm->eval_approximate_crossfield(closest, svp->cf);
fifo->insert(svp);
if (debug){
smoothness_forplot[svp->v] = svp->rank;
}
}
else{
STensor3 temp;
bgm->eval_approximate_crossfield(closest, temp);
for (int idir=0;idir<3;idir++){
smoothness_vertex_pair *svp = new smoothness_vertex_pair();
svp->v = boundary_vertices[i];
svp->rank = bgm->get_vectorial_smoothness(idir,x,y,z);
svp->dir = idir;
svp->layer = 0;
svp->size = h;
svp->cf = temp;
for (int k=0;k<3;k++) svp->direction(k) = temp(k,idir);
// cout << "fifo size=" << fifo->size() << " inserting " ;
fifo->insert(svp);
// cout << " -> fifo size=" << fifo->size() << endl;
}
}
}
// TODO: si fifo était list of *PTR -> pas de copies, gain temps ?
Wrapper3D wrapper;
wrapper.set_bgm(bgm);
MVertex *parent,*individual;
new_vertices.clear();
bool spawn_created;
int priority_counter=0;
STensor3 crossfield;
int parent_layer;
while(!fifo->empty()){
parent = fifo->get_first_vertex();
// parent_limit = fifo->get_first_limit();
parent_layer = fifo->get_first_layer();
// if(parent_limit!=-1 && parent_layer>=parent_limit()){
// continue;
// }
vector<MVertex*> spawns;
if (!use_vectorial_smoothness){
spawns.resize(6);
computeSixNeighbors(bgm,parent,spawns,fifo->get_first_crossfield(),
fifo->get_first_size());
}
else{
spawns.resize(2);
computeTwoNeighbors(bgm,parent,spawns,fifo->get_first_direction(),
fifo->get_first_size());
}
fifo->erase_first();
// cout << "while, fifo->size()=" << fifo->size() << " parent=(" <<
// parent->x() << "," << parent->y() << "," << parent->z() << ")" <<
// endl;
for(unsigned int i=0;i<spawns.size();i++){
spawn_created = false;
individual = spawns[i];
x = individual->x();
y = individual->y();
z = individual->z();
// cout << " working on candidate " << "(" << individual->x() << ","
// << individual->y() << "," << individual->z() << ")" << endl;
if(bgm->inDomain(x,y,z)){
// cout << " spawn " << i << " in domain" << endl;
MVertex *closest = bgm->get_nearest_neighbor(individual);
h = bgm->size(closest);// get approximate size, closest vertex, faster ?!
if(far_from_boundary_3D(bgm,individual,h)){
// cout << " spawn " << i << " far from bnd" << endl;
bgm->eval_approximate_crossfield(closest, crossfield);
wrapper.set_ok(true);
wrapper.set_individual(individual);
wrapper.set_parent(parent);
wrapper.set_size(&h);
wrapper.set_crossfield(&crossfield);
fill_min_max(x,y,z,h,min,max);
rtree.Search(min,max,rtree_callback_3D,&wrapper);
if(wrapper.get_ok()){
// cout << " spawn " << i << " wrapper OK" << endl;
if (!use_vectorial_smoothness){
smoothness_vertex_pair *svp = new smoothness_vertex_pair();
svp->v = individual;
svp->rank=bgm->get_smoothness(individual->x(),individual->y(),individual->z());
svp->dir = 0;
svp->layer = parent_layer+1;
svp->size = h;
svp->cf = crossfield;
fifo->insert(svp);
if (debug){
smoothness_forplot[svp->v] = svp->rank;
vert_priority[individual] = priority_counter++;
}
}
else{
if (debug) vert_priority[individual] = priority_counter++;
for (int idir=0;idir<3;idir++){
smoothness_vertex_pair *svp = new smoothness_vertex_pair();
svp->v = individual;
svp->rank = bgm->get_vectorial_smoothness(idir,x,y,z);
svp->dir = idir;
svp->layer = parent_layer+1;
svp->size = h;
for (int k=0;k<3;k++) svp->direction(k) = crossfield(k,idir);
svp->cf = crossfield;
fifo->insert(svp);
}
}
rtree.Insert(min,max,individual);
new_vertices.push_back(individual);
spawn_created = true;
}
}
}
if(!spawn_created){
delete individual;
}
}// end loop on spawns
}
//ProfilerStop();
time_insert_points += (Cpu() - a);
// --- output ---
if (debug){
stringstream ss;
ss << "priority_3D_" << gr->tag() << ".pos";
print_nodal_info(ss.str().c_str(),vert_priority);
ss.clear();
stringstream sss;
sss << "smoothness_3D_" << gr->tag() << ".pos";
print_nodal_info(sss.str().c_str(),smoothness_forplot);
sss.clear();
}
// ------- meshing using new points
cout << "tets in gr before= " << gr->tetrahedra.size() << endl;
cout << "nb new vertices= " << new_vertices.size() << endl;
a=Cpu();
int option = CTX::instance()->mesh.algo3d;
CTX::instance()->mesh.algo3d = ALGO_3D_DELAUNAY;
deMeshGRegion deleter;
deleter(gr);
std::vector<GRegion*> regions;
regions.push_back(gr);
meshGRegion mesher(regions); //?
mesher(gr); //?
MeshDelaunayVolume(regions);
time_meshing += (Cpu() - a);
cout << "tets in gr after= " << gr->tetrahedra.size() << endl;
cout << "gr tag=" << gr->tag() << endl;
CTX::instance()->mesh.algo3d = option;
delete fifo;
for(unsigned int i=0;i<new_vertices.size();i++) delete new_vertices[i];
new_vertices.clear();
rtree.RemoveAll();
return true;
}
int GModel::writeKEY(const std::string &name, int saveAll,
int saveGroupsOfNodes, double scalingFactor)
{
FILE *fp = Fopen(name.c_str(), "w");
if(!fp) {
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
if(noPhysicalGroups()) saveAll = 0x51;
indexMeshVertices(saveAll & 0x51);
std::vector<GEntity *> entities;
getEntities(entities);
fprintf(fp, "$# LS-DYNA Keyword file created by Gmsh\n*KEYWORD\n*TITLE\n");
fprintf(fp, " %s\n", name.c_str());
fprintf(fp, "*NODE\n");
for(std::size_t i = 0; i < entities.size(); i++)
for(std::size_t j = 0; j < entities[i]->mesh_vertices.size(); j++)
entities[i]->mesh_vertices[j]->writeKEY(fp, scalingFactor);
if(!(saveAll & 0x2)) // save or ignore Vertex, not in GUI
for(viter it = firstVertex(); it != lastVertex(); ++it) {
writeElementsKEY(fp, *it, (*it)->points, saveAll & 0x1);
}
if(!(saveAll & 0x8)) // save or ignore line
for(eiter it = firstEdge(); it != lastEdge(); ++it) {
writeElementsKEY(fp, *it, (*it)->lines, saveAll & 0x4);
}
if(!(saveAll & 0x20)) // save or ignore surface
for(fiter it = firstFace(); it != lastFace(); ++it) {
writeElementsKEY(fp, *it, (*it)->triangles, saveAll & 0x10);
writeElementsKEY(fp, *it, (*it)->quadrangles, saveAll & 0x10);
}
if(!(saveAll & 0x80)) // save or ignore surface
for(riter it = firstRegion(); it != lastRegion(); ++it) {
writeElementsKEY(fp, *it, (*it)->tetrahedra, saveAll & 0x40);
writeElementsKEY(fp, *it, (*it)->hexahedra, saveAll & 0x40);
writeElementsKEY(fp, *it, (*it)->prisms, saveAll & 0x40);
writeElementsKEY(fp, *it, (*it)->pyramids, saveAll & 0x40);
}
std::map<int, std::vector<GEntity *> > groups[4];
getPhysicalGroups(groups);
int setid = 0;
// save elements sets for each physical group
if(saveGroupsOfNodes & 0x2) {
for(int dim = 0; dim <= 3; dim++) {
if(saveAll & (0x2 << (2 * dim))) continue; // elements are ignored
for(std::map<int, std::vector<GEntity *> >::iterator it =
groups[dim].begin();
it != groups[dim].end(); it++) {
std::vector<GEntity *> &entities = it->second;
int n = 0;
for(std::size_t i = 0; i < entities.size(); i++) {
for(std::size_t j = 0; j < entities[i]->getNumMeshElements(); j++) {
MElement *e = entities[i]->getMeshElement(j);
if(!n) {
const char *str = (e->getDim() == 3) ?
"SOLID" :
(e->getDim() == 2) ?
"SHELL" :
(e->getDim() == 1) ? "BEAM" : "NODE";
fprintf(fp, "*SET_%s_LIST\n$# %s\n%d", str,
physicalName(this, dim, it->first).c_str(), ++setid);
}
if(!(n % 8))
fprintf(fp, "\n%lu", e->getNum());
else
fprintf(fp, ", %lu", e->getNum());
n++;
}
}
if(n) fprintf(fp, "\n");
}
}
}
// save node sets for each physical group, for easier load/b.c.
if(saveGroupsOfNodes & 0x1) {
for(int dim = 1; dim <= 3; dim++) {
for(std::map<int, std::vector<GEntity *> >::iterator it =
groups[dim].begin();
it != groups[dim].end(); it++) {
std::set<MVertex *> nodes;
std::vector<GEntity *> &entities = it->second;
for(std::size_t i = 0; i < entities.size(); i++) {
for(std::size_t j = 0; j < entities[i]->getNumMeshElements(); j++) {
MElement *e = entities[i]->getMeshElement(j);
for(std::size_t k = 0; k < e->getNumVertices(); k++)
nodes.insert(e->getVertex(k));
}
}
fprintf(fp, "*SET_NODE_LIST\n$# %s\n%d",
physicalName(this, dim, it->first).c_str(), ++setid);
int n = 0;
for(std::set<MVertex *>::iterator it2 = nodes.begin();
it2 != nodes.end(); it2++) {
if(!(n % 8))
fprintf(fp, "\n%ld", (*it2)->getIndex());
else
fprintf(fp, ", %ld", (*it2)->getIndex());
n++;
}
if(n) fprintf(fp, "\n");
}
}
}
fprintf(fp, "*END\n");
fclose(fp);
return 1;
}
void Mesh::approximationErrorAndGradients(int iEl, double &f, std::vector<double> &gradF, double eps,
simpleFunction<double> &fct)
{
std::vector<SPoint3> _xyz_temp;
for (int iV = 0; iV < nVert(); iV++){
_xyz_temp.push_back(SPoint3( _vert[iV]->x(), _vert[iV]->y(), _vert[iV]->z()));
_vert[iV]->setXYZ(_xyz[iV].x(),_xyz[iV].y(),_xyz[iV].z());
}
MElement *element = _el[iEl];
f = approximationError (fct, element);
// FIME
// if (iEl < 1)printf("approx error elem %d = %g\n",iEl,f);
int currentId = 0;
// compute the size of the gradient
// depends on how many dofs exist per vertex (0,1,2 or 3)
for (size_t i = 0; i < element->getNumVertices(); ++i) {
if (_el2FV[iEl][i] >= 0) {// some free coordinates
currentId += _nPCFV[_el2FV[iEl][i]];
}
}
gradF.clear();
gradF.resize(currentId, 0.);
currentId = 0;
for (size_t i = 0; i < element->getNumVertices(); ++i) {
if (_el2FV[iEl][i] >= 0) {// some free coordinates
MVertex *v = element->getVertex(i);
// vertex classified on a model edge
if (_nPCFV[_el2FV[iEl][i]] == 1){
double t = _uvw[_el2FV[iEl][i]].x();
GEdge *ge = (GEdge*)v->onWhat();
SPoint3 p (v->x(),v->y(),v->z());
GPoint d = ge->point(t+eps);
v->setXYZ(d.x(),d.y(),d.z());
double f_d = approximationError (fct, element);
gradF[currentId++] = (f_d-f)/eps;
if (iEl < 1)printf("df = %g\n",(f_d-f)/eps);
v->setXYZ(p.x(),p.y(),p.z());
}
else if (_nPCFV[_el2FV[iEl][i]] == 2){
double uu = _uvw[_el2FV[iEl][i]].x();
double vv = _uvw[_el2FV[iEl][i]].y();
GFace *gf = (GFace*)v->onWhat();
SPoint3 p (v->x(),v->y(),v->z());
GPoint d = gf->point(uu+eps,vv);
v->setXYZ(d.x(),d.y(),d.z());
double f_u = approximationError (fct, element);
gradF[currentId++] = (f_u-f)/eps;
d = gf->point(uu,vv+eps);
v->setXYZ(d.x(),d.y(),d.z());
double f_v = approximationError (fct, element);
gradF[currentId++] = (f_v-f)/eps;
v->setXYZ(p.x(),p.y(),p.z());
// if (iEl < 1)printf("df = %g %g\n",(f_u-f)/eps,(f_v-f)/eps);
}
}
}
for (int iV = 0; iV < nVert(); iV++)
_vert[iV]->setXYZ(_xyz_temp[iV].x(),_xyz_temp[iV].y(),_xyz_temp[iV].z());
}