void GMSH_CutPlanePlugin::draw(void *context)
{
#if defined(HAVE_OPENGL)
int num = (int)CutPlaneOptions_Number[7].def;
drawContext *ctx = (drawContext *)context;
if(num < 0) num = iview;
if(num >= 0 && num < (int)PView::list.size()) {
glColor4ubv((GLubyte *)&CTX::instance()->color.fg);
glLineWidth((float)CTX::instance()->lineWidth);
SBoundingBox3d bb = PView::list[num]->getData()->getBoundingBox();
ctx->drawPlaneInBoundingBox(
bb.min().x(), bb.min().y(), bb.min().z(), bb.max().x(), bb.max().y(),
bb.max().z(), CutPlaneOptions_Number[0].def,
CutPlaneOptions_Number[1].def, CutPlaneOptions_Number[2].def,
CutPlaneOptions_Number[3].def);
}
#endif
}
int GModel::readSTL(const std::string &name, double tolerance)
{
FILE *fp = Fopen(name.c_str(), "rb");
if(!fp){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
// store triplets of points for each solid found in the file
std::vector<std::vector<SPoint3> > points;
SBoundingBox3d bbox;
// "solid", or binary data header
char buffer[256];
if(!fgets(buffer, sizeof(buffer), fp)){ fclose(fp); return 0; }
bool binary = strncmp(buffer, "solid", 5) && strncmp(buffer, "SOLID", 5);
// ASCII STL
if(!binary){
points.resize(1);
while(!feof(fp)) {
// "facet normal x y z" or "endsolid"
if(!fgets(buffer, sizeof(buffer), fp)) break;
if(!strncmp(buffer, "endsolid", 8) ||
!strncmp(buffer, "ENDSOLID", 8)){
// "solid"
if(!fgets(buffer, sizeof(buffer), fp)) break;
if(!strncmp(buffer, "solid", 5) ||
!strncmp(buffer, "SOLID", 5)){
points.resize(points.size() + 1);
// "facet normal x y z"
if(!fgets(buffer, sizeof(buffer), fp)) break;
}
}
// "outer loop"
if(!fgets(buffer, sizeof(buffer), fp)) break;
// "vertex x y z"
for(int i = 0; i < 3; i++){
if(!fgets(buffer, sizeof(buffer), fp)) break;
char s1[256];
double x, y, z;
if(sscanf(buffer, "%s %lf %lf %lf", s1, &x, &y, &z) != 4) break;
SPoint3 p(x, y, z);
points.back().push_back(p);
bbox += p;
}
// "endloop"
if(!fgets(buffer, sizeof(buffer), fp)) break;
// "endfacet"
if(!fgets(buffer, sizeof(buffer), fp)) break;
}
}
// check if we could parse something
bool empty = true;
for(unsigned int i = 0; i < points.size(); i++){
if(points[i].size()){
empty = false;
break;
}
}
if(empty) points.clear();
// binary STL (we also try to read in binary mode if the header told
// us the format was ASCII but we could not read any vertices)
if(binary || empty){
if(binary)
Msg::Info("Mesh is in binary format");
else
Msg::Info("Wrong ASCII header or empty file: trying binary read");
rewind(fp);
while(!feof(fp)) {
char header[80];
if(!fread(header, sizeof(char), 80, fp)) break;
unsigned int nfacets = 0;
size_t ret = fread(&nfacets, sizeof(unsigned int), 1, fp);
bool swap = false;
if(nfacets > 100000000){
Msg::Info("Swapping bytes from binary file");
swap = true;
SwapBytes((char*)&nfacets, sizeof(unsigned int), 1);
}
if(ret && nfacets){
points.resize(points.size() + 1);
char *data = new char[nfacets * 50 * sizeof(char)];
ret = fread(data, sizeof(char), nfacets * 50, fp);
if(ret == nfacets * 50){
for(unsigned int i = 0; i < nfacets; i++) {
float *xyz = (float *)&data[i * 50 * sizeof(char)];
if(swap) SwapBytes((char*)xyz, sizeof(float), 12);
for(int j = 0; j < 3; j++){
SPoint3 p(xyz[3 + 3 * j], xyz[3 + 3 * j + 1], xyz[3 + 3 * j + 2]);
points.back().push_back(p);
bbox += p;
}
}
}
delete [] data;
}
}
}
std::vector<GFace*> faces;
for(unsigned int i = 0; i < points.size(); i++){
if(points[i].empty()){
Msg::Error("No facets found in STL file for solid %d", i);
fclose(fp);
return 0;
}
if(points[i].size() % 3){
Msg::Error("Wrong number of points (%d) in STL file for solid %d",
points[i].size(), i);
fclose(fp);
return 0;
}
Msg::Info("%d facets in solid %d", points[i].size() / 3, i);
// create face
GFace *face = new discreteFace(this, getMaxElementaryNumber(2) + 1);
faces.push_back(face);
add(face);
}
// create triangles using unique vertices
double eps = norm(SVector3(bbox.max(), bbox.min())) * tolerance;
std::vector<MVertex*> vertices;
for(unsigned int i = 0; i < points.size(); i++)
for(unsigned int j = 0; j < points[i].size(); j++)
vertices.push_back(new MVertex(points[i][j].x(), points[i][j].y(),
points[i][j].z()));
MVertexPositionSet pos(vertices);
std::set<MFace,Less_Face> unique;
int nbDuplic = 0;
for(unsigned int i = 0; i < points.size(); i ++){
for(unsigned int j = 0; j < points[i].size(); j += 3){
MVertex *v[3];
for(int k = 0; k < 3; k++){
double x = points[i][j + k].x();
double y = points[i][j + k].y();
double z = points[i][j + k].z();
v[k] = pos.find(x, y, z, eps);
}
MFace mf (v[0], v[1], v[2]);
if (unique.find(mf) == unique.end()){
faces[i]->triangles.push_back(new MTriangle(v[0], v[1], v[2]));
unique.insert(mf);
}
else{
nbDuplic++;
}
}
}
if (nbDuplic)
Msg::Warning("%d duplicate triangles in STL file", nbDuplic);
_associateEntityWithMeshVertices();
_storeVerticesInEntities(vertices); // will delete unused vertices
fclose(fp);
return 1;
}
void GMSH_SimplePartitionPlugin::run()
{
#if defined(HAVE_MESH)
int numSlicesX = (int)SimplePartitionOptions_Number[0].def;
int numSlicesY = (int)SimplePartitionOptions_Number[1].def;
int numSlicesZ = (int)SimplePartitionOptions_Number[2].def;
int createTopology = (int)SimplePartitionOptions_Number[3].def;
std::vector<std::string> exprX(1), exprY(1), exprZ(1);
exprX[0] = SimplePartitionOptions_String[0].def;
exprY[0] = SimplePartitionOptions_String[1].def;
exprZ[0] = SimplePartitionOptions_String[2].def;
GModel *m = GModel::current();
if(!m->getNumMeshElements()){
Msg::Error("Plugin(SimplePartition) requires a mesh");
return;
}
if(numSlicesX < 1 || numSlicesY < 1 || numSlicesZ < 1){
Msg::Error("Number of slices should be strictly positive");
return;
}
m->unpartitionMesh();
SBoundingBox3d bbox = m->bounds();
double pminX = bbox.min()[0], pmaxX = bbox.max()[0];
double pminY = bbox.min()[1], pmaxY = bbox.max()[1];
double pminZ = bbox.min()[2], pmaxZ = bbox.max()[2];
std::vector<double> ppX(numSlicesX + 1);
std::vector<double> ppY(numSlicesY + 1);
std::vector<double> ppZ(numSlicesZ + 1);
std::vector<std::string> variables(1, "t");
std::vector<double> values(1), res(1);
{
mathEvaluator f(exprX, variables);
for(int p = 0; p <= numSlicesX; p++) {
double t = values[0] = (double)p / (double)numSlicesX;
if(f.eval(values, res)) t = res[0];
ppX[p] = pminX + t * (pmaxX - pminX);
}
}
bool emptyX = (ppX[0] == ppX[numSlicesX]);
{
mathEvaluator f(exprY, variables);
for(int p = 0; p <= numSlicesY; p++) {
double t = values[0] = (double)p / (double)numSlicesY;
if(f.eval(values, res)) t = res[0];
ppY[p] = pminY + t * (pmaxY - pminY);
}
}
bool emptyY = (ppY[0] == ppY[numSlicesY]);
{
mathEvaluator f(exprZ, variables);
for(int p = 0; p <= numSlicesZ; p++) {
double t = values[0] = (double)p / (double)numSlicesZ;
if(f.eval(values, res)) t = res[0];
ppZ[p] = pminZ + t * (pmaxZ - pminZ);
}
}
bool emptyZ = (ppZ[0] == ppZ[numSlicesZ]);
std::vector<GEntity *> entities;
m->getEntities(entities);
hashmap<MElement *, unsigned int> elmToPartition;
for(std::size_t i = 0; i < entities.size(); i++) {
GEntity *ge = entities[i];
for(std::size_t j = 0; j < ge->getNumMeshElements(); j++) {
MElement *e = ge->getMeshElement(j);
SPoint3 point = e->barycenter();
int part = 0;
for(int kx = 0; kx < numSlicesX; kx++) {
if(part) break;
for(int ky = 0; ky < numSlicesY; ky++) {
if(part) break;
for(int kz = 0; kz < numSlicesZ; kz++) {
if(part) break;
if((emptyX || (kx == 0 && ppX[0] == point[0]) ||
(ppX[kx] < point[0] && point[0] <= ppX[kx + 1])) &&
(emptyY || (ky == 0 && ppY[0] == point[1]) ||
(ppY[ky] < point[1] && point[1] <= ppY[ky + 1])) &&
(emptyZ || (kz == 0 && ppZ[0] == point[2]) ||
(ppZ[kz] < point[2] && point[2] <= ppZ[kz + 1]))){
part = kx * numSlicesY * numSlicesZ + ky * numSlicesZ + kz + 1;
elmToPartition.insert(std::pair<MElement *, unsigned int>(e, part));
e->setPartition(part); // this will be removed
}
}
}
}
}
}
opt_mesh_partition_create_topology(0, GMSH_SET | GMSH_GUI, createTopology);
int ier = PartitionUsingThisSplit(m, numSlicesX * numSlicesY * numSlicesZ,
elmToPartition);
if(!ier) {
opt_mesh_color_carousel(0, GMSH_SET | GMSH_GUI, 3.);
CTX::instance()->mesh.changed = ENT_ALL;
}
#else
Msg::Error("Gmsh must be compiled with Mesh support to partition meshes");
#endif
}
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;
}
int main(int argc,char *argv[])
{
if(argc < 6){
printf("Usage: %s file lx ly lz rmax [levels=1] [refcs=1]\n", argv[0]);
printf("where\n");
printf(" 'file' contains a CAD model\n");
printf(" 'lx', 'ly' and 'lz' are the sizes of the elements along the"
" x-, y- and z-axis at the coarsest level\n");
printf(" 'rmax' is the radius of the largest sphere that can be inscribed"
" in the structure\n");
printf(" 'levels' sets the number of levels in the grid\n");
printf(" 'refcs' selects if curved surfaces should be refined\n");
return -1;
}
GmshInitialize();
GmshSetOption("General", "Terminal", 1.);
GmshMergeFile(argv[1]);
double lx = atof(argv[2]), ly = atof(argv[3]), lz = atof(argv[4]);
double rmax = atof(argv[5]);
int levels = (argc > 6) ? atof(argv[6]) : 1;
int refineCurvedSurfaces = (argc > 7) ? atof(argv[7]) : 1;
// minimum distance between points in the cloud at the coarsest
// level
double sampling = std::min(rmax, std::min(lx, std::min(ly, lz)));
// radius of the "tube" created around parts to refine at the
// coarsest level
double rtube = std::max(lx, std::max(ly, lz)) * 2.;
GModel *gm = GModel::current();
std::vector<SPoint3> points;
Msg::Info("Filling coarse point cloud on surfaces");
for (GModel::fiter fit = gm->firstFace(); fit != gm->lastFace(); fit++)
(*fit)->fillPointCloud(sampling, &points);
Msg::Info(" %d points in the surface cloud", (int)points.size());
std::vector<SPoint3> refinePoints;
if(levels > 1){
double s = sampling / pow(2., levels - 1);
Msg::Info("Filling refined point cloud on curves and curved surfaces");
for (GModel::eiter eit = gm->firstEdge(); eit != gm->lastEdge(); eit++)
fillPointCloud(*eit, s, refinePoints);
// FIXME: refine this by computing e.g. "mean" curvature
if(refineCurvedSurfaces){
for (GModel::fiter fit = gm->firstFace(); fit != gm->lastFace(); fit++)
if((*fit)->geomType() != GEntity::Plane)
(*fit)->fillPointCloud(2 * s, &refinePoints);
}
Msg::Info(" %d points in the refined cloud", (int)refinePoints.size());
}
SBoundingBox3d bb;
for(unsigned int i = 0; i < points.size(); i++) bb += points[i];
for(unsigned int i = 0; i < refinePoints.size(); i++) bb += refinePoints[i];
bb.scale(1.21, 1.21, 1.21);
SVector3 range = bb.max() - bb.min();
int NX = range.x() / lx;
int NY = range.y() / ly;
int NZ = range.z() / lz;
if(NX < 2) NX = 2;
if(NY < 2) NY = 2;
if(NZ < 2) NZ = 2;
Msg::Info(" bounding box min: %g %g %g -- max: %g %g %g",
bb.min().x(), bb.min().y(), bb.min().z(),
bb.max().x(), bb.max().y(), bb.max().z());
Msg::Info(" Nx=%d Ny=%d Nz=%d", NX, NY, NZ);
cartesianBox<double> box(bb.min().x(), bb.min().y(), bb.min().z(),
SVector3(range.x(), 0, 0),
SVector3(0, range.y(), 0),
SVector3(0, 0, range.z()),
NX, NY, NZ, levels);
Msg::Info("Inserting active cells in the cartesian grid");
Msg::Info(" level %d", box.getLevel());
for (unsigned int i = 0; i < points.size(); i++)
insertActiveCells(points[i].x(), points[i].y(), points[i].z(), rmax, box);
cartesianBox<double> *parent = &box, *child;
while((child = parent->getChildBox())){
Msg::Info(" level %d", child->getLevel());
for(unsigned int i = 0; i < refinePoints.size(); i++)
insertActiveCells(refinePoints[i].x(), refinePoints[i].y(), refinePoints[i].z(),
rtube / pow(2., (levels - child->getLevel())), *child);
parent = child;
}
// remove child cells that do not entirely fill parent cell or for
// which there is no parent neighbor; then remove parent cells that
// have children
Msg::Info("Removing cells to match X-FEM mesh topology constraints");
removeBadChildCells(&box);
removeParentCellsWithChildren(&box);
// we generate duplicate nodes at this point so we can easily access
// cell values at each level; we will clean up by renumbering after
// filtering
Msg::Info("Initializing nodal values in the cartesian grid");
box.createNodalValues();
Msg::Info("Computing levelset on the cartesian grid");
computeLevelset(gm, box);
Msg::Info("Removing cells outside the structure");
removeOutsideCells(&box);
Msg::Info("Renumbering mesh vertices across levels");
box.renumberNodes();
bool decomposeInSimplex = false;
box.writeMSH("yeah.msh", decomposeInSimplex);
Msg::Info("Done!");
GmshFinalize();
}
PView *GMSH_BubblesPlugin::execute(PView *v)
{
double shrink = (double)BubblesOptions_Number[0].def;
std::string fileName = BubblesOptions_String[0].def;
FILE *fp = Fopen(fileName.c_str(), "w");
if(!fp){
Msg::Error("Could not open output file '%s'", fileName.c_str());
return v;
}
GModel *m = GModel::current();
int p = m->getMaxElementaryNumber(0) + 1;
int l = m->getMaxElementaryNumber(1) + 1;
int s = m->getMaxElementaryNumber(2) + 1;
int ll = s, ps = 1;
SBoundingBox3d bbox = m->bounds();
double lc = norm(SVector3(bbox.max(), bbox.min())) / 100;
fprintf(fp, "lc = %g;\n", lc);
for(GModel::viter vit = m->firstVertex(); vit != m->lastVertex(); vit++)
(*vit)->writeGEO(fp, "lc");
for(GModel::eiter eit = m->firstEdge(); eit != m->lastEdge(); eit++)
(*eit)->writeGEO(fp);
for(GModel::fiter fit = m->firstFace(); fit != m->lastFace(); fit++){
(*fit)->writeGEO(fp);
fprintf(fp, "Delete { Surface {%d}; }\n", (*fit)->tag());
int sbeg = s;
int llbeg = ll;
// compute vertex-to-triangle_barycenter map
std::map<MVertex*, std::vector<SPoint3> > v2t;
for(unsigned int i = 0; i < (*fit)->triangles.size(); i++)
for(int j = 0; j < 3; j++)
v2t[(*fit)->triangles[i]->getVertex(j)].push_back((*fit)->triangles[i]->barycenter());
// add boundary vertices in map to get cells "closer" to the boundary
for(std::map<MVertex*, std::vector<SPoint3> >::iterator it = v2t.begin();
it != v2t.end(); it++){
MVertex *v = it->first;
if(v->onWhat() && v->onWhat()->dim() < 2)
it->second.push_back(SPoint3(it->first->x(), it->first->y(), it->first->z()));
}
for(std::map<MVertex*, std::vector<SPoint3> >::iterator it = v2t.begin();
it != v2t.end(); it++){
if(it->second.size() > 2){
// get barycenter of cell boundary points and order them
SPoint3 bc;
for(unsigned int i = 0; i < it->second.size(); i++)
bc += it->second[i];
bc *= 1. / (double)it->second.size();
compareAngle comp(bc);
std::sort(it->second.begin(), it->second.end(), comp);
// shrink cells
if(shrink){
for(unsigned int i = 0; i < it->second.size(); i++){
double dir[3] = {it->second[i].x() - bc.x(),
it->second[i].y() - bc.y(),
it->second[i].z() - bc.z()};
it->second[i][0] -= shrink * dir[0];
it->second[i][1] -= shrink * dir[1];
it->second[i][2] -= shrink * dir[2];
}
}
// create b-spline bounded surface for each cell
int nump = it->second.size();
for(int i = 0; i < nump; i++){
SPoint3 &b(it->second[i]);
fprintf(fp, "Point(%d) = {%.16g, %.16g, %.16g, lc};\n", p++, b.x(), b.y(), b.z());
}
fprintf(fp, "BSpline(%d) = {", l++);
for(int i = nump - 1; i >= 0; i--)
fprintf(fp, "%d,", p - i - 1);
fprintf(fp, "%d};\n", p - nump);
fprintf(fp, "Line Loop(%d) = {%d};\n", ll++, l - 1);
fprintf(fp, "Plane Surface(%d) = {%d};\n", s++, ll - 1);
}
}
fprintf(fp, "Physical Surface(%d) = {%d:%d};\n", ps++, sbeg, s - 1);
fprintf(fp, "Plane Surface(%d) = {%d, %d:%d};\n", s++, (*fit)->tag(), llbeg, ll - 1);
fprintf(fp, "Physical Surface(%d) = {%d};\n", ps++, s - 1);
}
fclose(fp);
return v;
}
void GMSH_ProbePlugin::draw(void *context)
{
#if defined(HAVE_OPENGL)
int num = (int)ProbeOptions_Number[3].def;
if(num < 0) num = iview;
if(num >= 0 && num < (int)PView::list.size()){
double x = ProbeOptions_Number[0].def;
double y = ProbeOptions_Number[1].def;
double z = ProbeOptions_Number[2].def;
drawContext *ctx = (drawContext*)context;
glColor4ubv((GLubyte *) & CTX::instance()->color.fg);
glLineWidth((float)CTX::instance()->lineWidth);
SBoundingBox3d bb = PView::list[num]->getData()->getBoundingBox();
if(x >= bb.min().x() && x <= bb.max().x() &&
y >= bb.min().y() && y <= bb.max().y() &&
z >= bb.min().z() && z <= bb.max().z()){
// we're inside the bounding box: draw a large cross
glBegin(GL_LINES);
glVertex3d(bb.min().x(), y, z); glVertex3d(bb.max().x(), y, z);
glVertex3d(x, bb.min().y(), z); glVertex3d(x, bb.max().y(), z);
glVertex3d(x, y, bb.min().z()); glVertex3d(x, y, bb.max().z());
glEnd();
}
else{
// draw 10-pixel marker
double d = 10 * ctx->pixel_equiv_x / ctx->s[0];
glBegin(GL_LINES);
glVertex3d(x - d, y, z); glVertex3d(x + d, y, z);
glVertex3d(x, y - d, z); glVertex3d(x, y + d, z);
glVertex3d(x, y, z - d); glVertex3d(x, y, z + d);
glEnd();
}
ctx->drawSphere(CTX::instance()->pointSize, x, y, z, 1);
}
#endif
}
PView *GMSH_TriangulatePlugin::execute(PView *v)
{
int iView = (int)TriangulateOptions_Number[0].def;
PView *v1 = getView(iView, v);
if(!v1) return v;
PViewData *data1 = v1->getData();
if(data1->hasMultipleMeshes()){
Msg::Error("Triangulate plugin cannot be applied to multi-mesh views");
return v1;
}
// create list of points with associated data
std::vector<MVertex*> points;
int numSteps = data1->getNumTimeSteps();
for(int ent = 0; ent < data1->getNumEntities(0); ent++){
for(int ele = 0; ele < data1->getNumElements(0, ent); ele++){
if(data1->skipElement(0, ent, ele)) continue;
if(data1->getNumNodes(0, ent, ele) != 1) continue;
int numComp = data1->getNumComponents(0, ent, ele);
double x, y, z;
data1->getNode(0, ent, ele, 0, x, y, z);
PointData *p = new PointData(x, y, z, numComp * numSteps);
for(int step = 0; step < numSteps; step++)
for(int comp = 0; comp < numComp; comp++)
data1->getValue(step, ent, ele, 0, comp, p->v[3 + numComp * step + comp]);
points.push_back(p);
}
}
if(points.size() < 3){
Msg::Error("Need at least 3 points to triangulate");
for(unsigned int i = 0; i < points.size(); i++)
delete points[i];
return v1;
}
// project points onto plane
discreteFace *s = new discreteFace
(GModel::current(), GModel::current()->getNumFaces() + 1);
s->computeMeanPlane(points);
double plan[3][3];
s->getMeanPlaneData(plan);
for(unsigned int i = 0; i < points.size(); i++) project(points[i], plan);
delete s;
// get lc
SBoundingBox3d bbox;
for(unsigned int i = 0; i < points.size(); i++) bbox += points[i]->point();
double lc = norm(SVector3(bbox.max(), bbox.min()));
// build a point record structure for the divide and conquer algorithm
DocRecord doc(points.size());
for(unsigned int i = 0; i < points.size(); i++){
double XX = CTX::instance()->mesh.randFactor * lc * (double)rand() / (double)RAND_MAX;
double YY = CTX::instance()->mesh.randFactor * lc * (double)rand() / (double)RAND_MAX;
doc.points[i].where.h = points[i]->x() + XX;
doc.points[i].where.v = points[i]->y() + YY;
doc.points[i].adjacent = NULL;
doc.points[i].data = (void*)points[i];
}
// triangulate
doc.MakeMeshWithPoints();
// create output (using unperturbed data)
PView *v2 = new PView();
PViewDataList *data2 = getDataList(v2);
for(int i = 0; i < doc.numTriangles; i++){
PointData *p[3];
p[0] = (PointData*)doc.points[doc.triangles[i].a].data;
p[1] = (PointData*)doc.points[doc.triangles[i].b].data;
p[2] = (PointData*)doc.points[doc.triangles[i].c].data;
int numComp = 0;
std::vector<double> *vec = 0;
if((int)p[0]->v.size() == 3 + 9 * numSteps &&
(int)p[1]->v.size() == 3 + 9 * numSteps &&
(int)p[2]->v.size() == 3 + 9 * numSteps){
numComp = 9; data2->NbTT++; vec = &data2->TT;
}
else if((int)p[0]->v.size() == 3 + 3 * numSteps &&
(int)p[1]->v.size() == 3 + 3 * numSteps &&
(int)p[2]->v.size() == 3 + 3 * numSteps){
numComp = 3; data2->NbVT++; vec = &data2->VT;
}
else{
numComp = 1; data2->NbST++; vec = &data2->ST;
}
for(int nod = 0; nod < 3; nod++) vec->push_back(p[nod]->v[0]);
for(int nod = 0; nod < 3; nod++) vec->push_back(p[nod]->v[1]);
for(int nod = 0; nod < 3; nod++) vec->push_back(p[nod]->v[2]);
for(int step = 0; step < numSteps; step++)
for(int nod = 0; nod < 3; nod++)
for(int comp = 0; comp < numComp; comp++)
vec->push_back(p[nod]->v[3 + numComp * step + comp]);
}
for(unsigned int i = 0; i < points.size(); i++)
delete points[i];
for(int i = 0; i < data1->getNumTimeSteps(); i++)
data2->Time.push_back(data1->getTime(i));
data2->setName(data1->getName() + "_Triangulate");
data2->setFileName(data1->getName() + "_Triangulate.pos");
data2->finalize();
return v2;
}
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);
}
