// sets the entity m from which the mesh will be copied
void GEntity::setMeshMaster(int m_signed)
{
if(m_signed == tag()){ _meshMaster = m_signed; return; }
GEntity *gMaster = 0;
int m = abs(m_signed);
switch(dim()){
case 0 : gMaster = model()->getVertexByTag(m); break;
case 1 : gMaster = model()->getEdgeByTag(m); break;
case 2 : gMaster = model()->getFaceByTag(m); break;
case 3 : gMaster = model()->getRegionByTag(m); break;
}
if (!gMaster){
Msg::Error("Model entity %d of dimension %d cannot be the mesh master of entity %d",
m, dim(), tag());
return;
}
int masterOfMaster = gMaster->meshMaster();
if (masterOfMaster == gMaster->tag()){
_meshMaster = m_signed;
}
else {
setMeshMaster ( masterOfMaster * ((m_signed > 0) ? 1 : -1));
}
}
int main(int argc, char **argv)
{
GmshInitialize(argc, argv);
GmshSetOption("Mesh", "Algorithm", 5.);
GmshSetOption("General", "Terminal", 1.);
GModel *m = new GModel();
m->readMSH("bunny.msh");
m->fillVertexArrays();
std::vector<GEntity*> entities;
m->getEntities(entities);
for(unsigned int i = 0; i < entities.size(); i++){
GEntity *ge = entities[i];
printf("coucou entite %d (dimension %d)\n", ge->tag(), ge->dim());
if(ge->va_triangles)
printf(" j'ai un va de triangles: %d vertex\n", ge->va_triangles->getNumVertices());
if(ge->va_lines)
printf(" j'ai un va de lignes: %d vertex\n", ge->va_lines->getNumVertices());
}
delete m;
GmshFinalize();
}
static void getBoundaryFromMesh(GModel *m, int visible)
{
int dim = m->getDim();
std::vector<GEntity*> entities;
m->getEntities(entities);
std::set<MFace, Less_Face> bndFaces;
std::set<MEdge, Less_Edge> bndEdges;
for(unsigned int i = 0; i < entities.size(); i++){
GEntity *ge = entities[i];
if(ge->dim() != dim) continue;
if(visible && !ge->getVisibility()) continue;
for(unsigned int j = 0; j < ge->getNumMeshElements(); j++){
MElement *e = ge->getMeshElement(j);
if(dim == 2){
for(int i = 0; i < e->getNumEdges(); i++){
MEdge f = e->getEdge(i);
if(bndEdges.find(f) == bndEdges.end())
bndEdges.insert(f);
else
bndEdges.erase(f);
}
}
else if(dim == 3){
for(int i = 0; i < e->getNumFaces(); i++){
MFace f = e->getFace(i);
if(bndFaces.find(f) == bndFaces.end())
bndFaces.insert(f);
else
bndFaces.erase(f);
}
}
}
}
if(dim == 2){
discreteEdge *e = new discreteEdge(m, m->getMaxElementaryNumber(1) + 1, 0, 0);
m->add(e);
for(std::set<MEdge, Less_Edge>::iterator it = bndEdges.begin();
it != bndEdges.end(); it++){
e->lines.push_back(new MLine(it->getVertex(0), it->getVertex(1)));
}
}
else if(dim == 3){
discreteFace *f = new discreteFace(m, m->getMaxElementaryNumber(2) + 1);
m->add(f);
for(std::set<MFace, Less_Face>::iterator it = bndFaces.begin();
it != bndFaces.end(); it++){
if(it->getNumVertices() == 3)
f->triangles.push_back(new MTriangle(it->getVertex(0), it->getVertex(1),
it->getVertex(2)));
else if(it->getNumVertices() == 4)
f->quadrangles.push_back(new MQuadrangle(it->getVertex(0), it->getVertex(1),
it->getVertex(2), it->getVertex(3)));
}
}
}
void Mesh::calcScaledNormalEl2D(const std::map<MElement*,GEntity*> &element2entity, int iEl)
{
const JacobianBasis *jac = _el[iEl]->getJacobianFuncSpace();
fullMatrix<double> primNodesXYZ(jac->getNumPrimMapNodes(),3);
SVector3 geoNorm(0.,0.,0.);
std::map<MElement*,GEntity*>::const_iterator itEl2ent = element2entity.find(_el[iEl]);
GEntity *ge = (itEl2ent == element2entity.end()) ? 0 : itEl2ent->second;
const bool hasGeoNorm = ge && (ge->dim() == 2) && ge->haveParametrization();
for (int i=0; i<jac->getNumPrimMapNodes(); i++) {
const int &iV = _el2V[iEl][i];
primNodesXYZ(i,0) = _xyz[iV].x();
primNodesXYZ(i,1) = _xyz[iV].y();
primNodesXYZ(i,2) = _xyz[iV].z();
if (hasGeoNorm && (_vert[iV]->onWhat() == ge)) {
double u, v;
_vert[iV]->getParameter(0,u);
_vert[iV]->getParameter(1,v);
geoNorm += ((GFace*)ge)->normal(SPoint2(u,v));
}
}
if (hasGeoNorm && (geoNorm.normSq() == 0.)) {
SPoint2 param = ((GFace*)ge)->parFromPoint(_el[iEl]->barycenter(true),false);
geoNorm = ((GFace*)ge)->normal(param);
}
fullMatrix<double> &elNorm = _scaledNormEl[iEl];
elNorm.resize(1,3);
const double norm = jac->getPrimNormal2D(primNodesXYZ,elNorm);
double factor = 1./norm;
if (hasGeoNorm) {
const double scal = geoNorm(0)*elNorm(0,0)+geoNorm(1)*elNorm(0,1)+geoNorm(2)*elNorm(0,2);
if (scal < 0.) factor = -factor;
}
elNorm.scale(factor); // Re-scaling normal here is faster than an extra scaling operation on the Jacobian
}
// gets the entity from which the mesh will be copied
int GEntity::meshMaster() const
{
if (_meshMaster == tag()) return tag();
GEntity *gMaster = 0;
switch(dim()){
case 0 : gMaster = model()->getVertexByTag(abs(_meshMaster)); break;
case 1 : gMaster = model()->getEdgeByTag(abs(_meshMaster)); break;
case 2 : gMaster = model()->getFaceByTag(abs(_meshMaster)); break;
case 3 : gMaster = model()->getRegionByTag(abs(_meshMaster)); break;
}
if (!gMaster){
Msg::Error("Could not find mesh master entity %d",_meshMaster);
return tag();
}
int masterOfMaster = gMaster->meshMaster();
if (masterOfMaster == gMaster->tag()){
return _meshMaster ;
}
else {
return gMaster->meshMaster() * ((_meshMaster > 0) ? 1 : -1);
}
}
void updateBoVec<3, MFace>(
const int normalSource, const MVertex *const vertex, const int zoneIndex,
const int vertIndex,
const CCon::FaceVector<MZoneBoundary<3>::GlobalVertexData<MFace>::FaceDataB>
&faces,
ZoneBoVec &zoneBoVec, BCPatchIndex &patch, bool &warnNormFromElem)
{
GEntity *ent;
if(normalSource == NormalSourceElement) goto getNormalFromElements;
ent = vertex->onWhat();
if(ent == 0) {
goto getNormalFromElements;
// No entity: try to find a normal from the faces
}
else {
switch(ent->dim()) {
case 0:
case 1:
/*--------------------------------------------------------------------*
* In this case, there are possibly multiple GFaces from this zone
* connected to the vertex. One patch for each GFace will be written.
*--------------------------------------------------------------------*/
{
//--Get a list of face entities connected to 'ent'
std::list<GFace *> gFaceList;
switch(ent->dim()) {
case 0: {
std::vector<GEdge *> gEdgeList = ent->edges();
std::list<GFace *> gFaceList;
for(std::vector<GEdge *>::const_iterator gEIt = gEdgeList.begin();
gEIt != gEdgeList.end(); ++gEIt) {
std::vector<GFace *> alist = (*gEIt)->faces();
gFaceList.insert(gFaceList.end(), alist.begin(), alist.end());
}
// Remove duplicates
gFaceList.sort();
gFaceList.unique();
} break;
case 1: {
std::vector<GFace *> fac = ent->faces();
gFaceList.insert(gFaceList.end(), fac.begin(), fac.end());
} break;
}
//--Get a list of face entities connected to the 'vertex' that are also
// in the
//--zone
std::list<const GFace *> useGFace;
std::vector<GEdge *> gEdgeList;
const int nFace = faces.size();
for(int iFace = 0; iFace != nFace; ++iFace) {
if(zoneIndex == faces[iFace].zoneIndex) {
bool matchedFace = false;
MFace mFace =
faces[iFace].parentElement->getFace(faces[iFace].parentFace);
const int nVOnF = mFace.getNumVertices();
int vertexOnF = 0; // The index of 'vertex' in the face
for(int iVOnF = 0; iVOnF != nVOnF; ++iVOnF) {
const MVertex *const vertex2 = mFace.getVertex(iVOnF);
if(vertex == vertex2)
vertexOnF = iVOnF;
else {
const GEntity *const ent2 = vertex2->onWhat();
if(ent2->dim() == 2) {
matchedFace = true;
useGFace.push_back(static_cast<const GFace *>(ent2));
break;
}
}
}
// Triangle MElements are a total P.I.T.A.:
// - If the original 'ent' is a vertex, one MVertex can be on the
// GVertex, and the other two on GEdges, and then the MElement is
// still on the GFace.
// - If the original 'ent' is an edge, one MVertex can be on the
// original GEdge, another on a GVertex, and the final on another
// GEdge, and then the MElement is still on the GFace. There is
// also the unlikely case where the two other MVertex are both on
// edges ... and the MElement is still on the GFace.
if(!matchedFace && (3 == nVOnF)) {
const MVertex *vertex2 = 0;
const MVertex *vertex3 = 0;
switch(vertexOnF) {
case 0:
vertex2 = mFace.getVertex(1);
vertex3 = mFace.getVertex(2);
break;
case 1:
vertex2 = mFace.getVertex(0);
vertex3 = mFace.getVertex(2);
break;
case 2:
vertex2 = mFace.getVertex(0);
vertex3 = mFace.getVertex(1);
break;
}
if(vertex2 && vertex3) {
const GEntity *const ent2 = vertex2->onWhat();
const GEntity *const ent3 = vertex3->onWhat();
if(ent2 && ent3) {
if(ent2->dim() == 1 && ent3->dim() == 1) {
// Which GFace is bounded by edges ent2 and ent3?
for(std::list<GFace *>::const_iterator gFIt =
gFaceList.begin();
gFIt != gFaceList.end(); ++gFIt) {
gEdgeList = (*gFIt)->edges();
if((std::find(gEdgeList.begin(), gEdgeList.end(), ent2) !=
gEdgeList.end()) &&
(std::find(gEdgeList.begin(), gEdgeList.end(), ent3) !=
gEdgeList.end())) {
// Edges ent2 and ent3 bound this face
useGFace.push_back(*gFIt);
break;
}
}
}
else if(ent->dim() == 1 && (ent2->dim() + ent3->dim() == 1)) {
const GEntity *entCmp;
if(ent2->dim() == 1)
entCmp = ent2;
else
entCmp = ent3;
// Which GFace is bounded by entCmp
for(std::list<GFace *>::const_iterator gFIt =
gFaceList.begin();
gFIt != gFaceList.end(); ++gFIt) {
gEdgeList = (*gFIt)->edges();
if(std::find(gEdgeList.begin(), gEdgeList.end(),
entCmp) != gEdgeList.end()) {
// Edge entCmp and the original edge bound this face
useGFace.push_back(*gFIt);
break;
}
}
}
}
}
} // Stupid triangles
} // End if face in zone
} // End loop over faces
// Duplicates are a possibility, remove
useGFace.sort();
useGFace.unique();
//--'useGFace' now contains the face entities that connect to vertex. A
// BC
//--patch will be written for each of them.
for(std::list<const GFace *>::const_iterator gFIt = useGFace.begin();
gFIt != useGFace.end(); ++gFIt) {
SPoint2 par;
if(!reparamMeshVertexOnFace(const_cast<MVertex *>(vertex), *gFIt,
par))
goto getNormalFromElements; // :P After all that!
SVector3 boNormal = (*gFIt)->normal(par);
SPoint3 interior(0., 0., 0.);
int cFace = 0;
const int nFace = faces.size();
for(int iFace = 0; iFace != nFace; ++iFace) {
if(faces[iFace].zoneIndex == zoneIndex) {
++cFace;
interior += faces[iFace].parentElement->barycenter();
}
}
interior /= cFace;
if(dot(boNormal, SVector3(vertex->point(), interior)) < 0.)
boNormal.negate();
zoneBoVec.push_back(
VertexBoundary(zoneIndex, (*gFIt)->tag(), boNormal,
const_cast<MVertex *>(vertex), vertIndex));
patch.add((*gFIt)->tag());
}
}
break;
case 2:
/*--------------------------------------------------------------------*
* The vertex exists on a face and belongs to only 1 BC patch.
*--------------------------------------------------------------------*/
{
const GFace *const gFace = static_cast<const GFace *>(ent);
SPoint2 par;
if(!reparamMeshVertexOnFace(const_cast<MVertex *>(vertex), gFace, par))
goto getNormalFromElements;
SVector3 boNormal = static_cast<const GFace *>(ent)->normal(par);
SPoint3 interior(0., 0., 0.);
int cFace = 0;
const int nFace = faces.size();
for(int iFace = 0; iFace != nFace; ++iFace) {
if(faces[iFace].zoneIndex == zoneIndex) {
++cFace;
interior += faces[iFace].parentElement->barycenter();
}
}
interior /= cFace;
if(dot(boNormal, SVector3(vertex->point(), interior)) < 0.)
boNormal.negate();
zoneBoVec.push_back(VertexBoundary(zoneIndex, gFace->tag(), boNormal,
const_cast<MVertex *>(vertex),
vertIndex));
patch.add(gFace->tag());
}
break;
default: goto getNormalFromElements;
}
}
return;
getNormalFromElements:;
/*--------------------------------------------------------------------*
* Geometry information cannot be used - generate normals from the
* elements
*--------------------------------------------------------------------*/
{
if(warnNormFromElem && normalSource == 1) {
Msg::Warning("Some or all boundary normals were determined from mesh "
"elements instead of from the geometry");
warnNormFromElem = false;
}
// Sum the normals from each element connected to the vertex and in the
// zone. Each normal has to be converted independently into an inwards-
// pointing normal.
//**Weight each normal by the area of the boundary element?
SVector3 boNormal(0.);
const int nFace = faces.size();
for(int iFace = 0; iFace != nFace; ++iFace) {
if(faces[iFace].zoneIndex == zoneIndex) {
// Normal to the boundary (unknown direction)
SVector3 bnt =
faces[iFace].parentElement->getFace(faces[iFace].parentFace).normal();
// Inwards normal
const SVector3 inwards(vertex->point(),
faces[iFace].parentElement->barycenter());
if(dot(bnt, inwards) < 0.) bnt.negate();
boNormal += bnt;
}
}
boNormal.normalize();
zoneBoVec.push_back(VertexBoundary(
zoneIndex, 0, boNormal, const_cast<MVertex *>(vertex), vertIndex));
patch.add(0);
}
}
void updateBoVec<2, MEdge>(
const int normalSource, const MVertex *const vertex, const int zoneIndex,
const int vertIndex,
const CCon::FaceVector<MZoneBoundary<2>::GlobalVertexData<MEdge>::FaceDataB>
&faces,
ZoneBoVec &zoneBoVec, BCPatchIndex &patch, bool &warnNormFromElem)
{
GEntity *ent;
if(normalSource == NormalSourceElement) goto getNormalFromElements;
ent = vertex->onWhat();
if(ent == 0) {
goto getNormalFromElements;
// No entity: try to find a normal from the faces
}
else {
switch(ent->dim()) {
case 0:
/*--------------------------------------------------------------------*
* In this case, there are possibly two GEdges from this zone
* connected to the vertex. If the angle between the two edges is
* significant, the BC patch will be split and this vertex will be
* written in both patches with different normals. If the angle is
* small, or only one GEdge belongs to this zone, then the vertex will
* only be written to one patch.
*--------------------------------------------------------------------*/
{
// Find edge entities that are connected to elements in the zone
std::vector<std::pair<GEdge *, int> > useGEdge;
const int nFace = faces.size();
for(int iFace = 0; iFace != nFace; ++iFace) {
if(zoneIndex == faces[iFace].zoneIndex) {
MEdge mEdge =
faces[iFace].parentElement->getEdge(faces[iFace].parentFace);
// Get the other vertex on the mesh edge.
MVertex *vertex2 = mEdge.getMinVertex();
if(vertex2 == vertex) vertex2 = mEdge.getMaxVertex();
// Check if the entity associated with vertex2 is a line and
// is also connected to vertex. If so, add it to the container of
// edge entities that will be used to determine the normal
GEntity *const ent2 = vertex2->onWhat();
if(ent2->dim() == 1) {
useGEdge.push_back(
std::pair<GEdge *, int>(static_cast<GEdge *>(ent2), iFace));
}
}
}
//--'useGEdge' now contains the edge entities that will be used to
// determine
//--the normals
switch(useGEdge.size()) {
case 0:
// goto getNormalFromElements;
// We probably don't want BC data if none of the faces attatched to
// this vertex and in this zone are on the boundary.
break;
case 1: {
const GEdge *const gEdge =
static_cast<const GEdge *>(useGEdge[0].first);
SVector3 boNormal;
if(edge_normal(vertex, zoneIndex, gEdge, faces, boNormal))
goto getNormalFromElements;
zoneBoVec.push_back(VertexBoundary(zoneIndex, gEdge->tag(), boNormal,
const_cast<MVertex *>(vertex),
vertIndex));
patch.add(gEdge->tag());
} break;
case 2: {
// Get the first normal
const GEdge *const gEdge1 =
static_cast<const GEdge *>(useGEdge[0].first);
SVector3 boNormal1;
if(edge_normal(vertex, zoneIndex, gEdge1, faces, boNormal1,
useGEdge[0].second))
goto getNormalFromElements;
// Get the second normal
const GEdge *const gEdge2 =
static_cast<const GEdge *>(useGEdge[1].first);
SVector3 boNormal2;
if(edge_normal(vertex, zoneIndex, gEdge2, faces, boNormal2,
useGEdge[1].second))
goto getNormalFromElements;
if(dot(boNormal1, boNormal2) < 0.98) {
//--Write 2 separate patches
zoneBoVec.push_back(
VertexBoundary(zoneIndex, gEdge1->tag(), boNormal1,
const_cast<MVertex *>(vertex), vertIndex));
patch.add(gEdge1->tag());
zoneBoVec.push_back(
VertexBoundary(zoneIndex, gEdge2->tag(), boNormal2,
const_cast<MVertex *>(vertex), vertIndex));
patch.add(gEdge2->tag());
}
else {
//--Write one patch
boNormal1 += boNormal2;
boNormal1 *= 0.5;
zoneBoVec.push_back(
VertexBoundary(zoneIndex, gEdge1->tag(), boNormal1,
const_cast<MVertex *>(vertex), vertIndex));
patch.addPair(gEdge1->tag(), gEdge2->tag());
}
} break;
default:
Msg::Error("Internal error based on 2-D boundary assumptions (file "
"\'MZoneBoundary.cpp'). Boundary vertices may be "
"incorrect");
break;
}
}
break;
case 1:
/*--------------------------------------------------------------------*
* The vertex exists on an edge and belongs to only 1 BC patch.
*--------------------------------------------------------------------*/
{
SVector3 boNormal;
if(edge_normal(vertex, zoneIndex, static_cast<const GEdge *>(ent),
faces, boNormal))
goto getNormalFromElements;
zoneBoVec.push_back(VertexBoundary(zoneIndex, ent->tag(), boNormal,
const_cast<MVertex *>(vertex),
vertIndex));
patch.add(ent->tag());
}
break;
default: goto getNormalFromElements;
}
}
return;
getNormalFromElements:;
/*--------------------------------------------------------------------*
* Geometry information cannot be used - generate normals from the
* elements
*--------------------------------------------------------------------*/
{
if(warnNormFromElem && normalSource == 1) {
Msg::Warning("Some or all boundary normals were determined from mesh "
"elements instead of from the geometry");
warnNormFromElem = false;
}
// The mesh plane normal is computed from all elements attached to the
// vertex
SVector3 meshPlaneNormal(0.); // This normal is perpendicular to the
// plane of the mesh
const int nFace = faces.size();
for(int iFace = 0; iFace != nFace; ++iFace) {
if(faces[iFace].zoneIndex == zoneIndex) {
// Make sure all the planes go in the same direction
//**Required?
SVector3 mpnt = faces[iFace].parentElement->getFace(0).normal();
if(dot(mpnt, meshPlaneNormal) < 0.) mpnt.negate();
meshPlaneNormal += mpnt;
}
}
// Sum the normals from each element. The tangent is computed from all
// faces in the zone attached to the vertex and is weighted by the length of
// the edge. Each tangent has to be converted independently into an
// inwards-pointing normal.
SVector3 boNormal(0.);
for(int iFace = 0; iFace != nFace; ++iFace) {
if(faces[iFace].zoneIndex == zoneIndex) {
const SVector3 tangent =
faces[iFace]
.parentElement->getEdge(faces[iFace].parentFace)
.tangent();
// Normal to the boundary (unknown direction)
SVector3 bnt = crossprod(tangent, meshPlaneNormal);
// Inwards normal
const SVector3 inwards(vertex->point(),
faces[iFace].parentElement->barycenter());
if(dot(bnt, inwards) < 0.) bnt.negate();
boNormal += bnt;
}
}
boNormal.normalize();
zoneBoVec.push_back(VertexBoundary(
zoneIndex, 0, boNormal, const_cast<MVertex *>(vertex), vertIndex));
patch.add(0);
}
}
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_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
}
int GModel::readMED(const std::string &name)
{
med_idt fid = MEDouvrir((char*)name.c_str(), MED_LECTURE);
if(fid < 0) {
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
med_int v[3], vf[3];
MEDversionDonner(&v[0], &v[1], &v[2]);
MEDversionLire(fid, &vf[0], &vf[1], &vf[2]);
Msg::Info("Reading MED file V%d.%d.%d using MED library V%d.%d.%d",
vf[0], vf[1], vf[2], v[0], v[1], v[2]);
if(vf[0] < 2 || (vf[0] == 2 && vf[1] < 2)){
Msg::Error("Cannot read MED file older than V2.2");
return 0;
}
std::vector<std::string> meshNames;
for(int i = 0; i < MEDnMaa(fid); i++){
char meshName[MED_TAILLE_NOM + 1], meshDesc[MED_TAILLE_DESC + 1];
med_int spaceDim;
med_maillage meshType;
#if (MED_MAJOR_NUM == 3)
med_int meshDim, nStep;
char dtUnit[MED_SNAME_SIZE + 1];
char axisName[3 * MED_SNAME_SIZE + 1], axisUnit[3 * MED_SNAME_SIZE + 1];
med_sorting_type sortingType;
med_axis_type axisType;
if(MEDmeshInfo(fid, i + 1, meshName, &spaceDim, &meshDim, &meshType, meshDesc,
dtUnit, &sortingType, &nStep, &axisType, axisName, axisUnit) < 0){
#else
if(MEDmaaInfo(fid, i + 1, meshName, &spaceDim, &meshType, meshDesc) < 0){
#endif
Msg::Error("Unable to read mesh information");
return 0;
}
meshNames.push_back(meshName);
}
if(MEDfermer(fid) < 0){
Msg::Error("Unable to close file '%s'", (char*)name.c_str());
return 0;
}
int ret = 1;
for(unsigned int i = 0; i < meshNames.size(); i++){
// we use the filename as a kind of "partition" indicator, allowing to
// complete a model part by part (used e.g. in DDM, since MED does not store
// a partition index)
GModel *m = findByName(meshNames[i], name);
if(!m) m = new GModel(meshNames[i]);
ret = m->readMED(name, i);
if(!ret) return 0;
}
return ret;
}
int GModel::readMED(const std::string &name, int meshIndex)
{
med_idt fid = MEDouvrir((char*)name.c_str(), MED_LECTURE);
if(fid < 0){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
int numMeshes = MEDnMaa(fid);
if(meshIndex >= numMeshes){
Msg::Info("Could not find mesh %d in MED file", meshIndex);
return 0;
}
checkPointMaxNumbers();
GModel::setCurrent(this); // make sure we increment max nums in this model
// read mesh info
char meshName[MED_TAILLE_NOM + 1], meshDesc[MED_TAILLE_DESC + 1];
med_int spaceDim, nStep = 1;
med_maillage meshType;
#if (MED_MAJOR_NUM == 3)
med_int meshDim;
char dtUnit[MED_SNAME_SIZE + 1];
char axisName[3 * MED_SNAME_SIZE + 1], axisUnit[3 * MED_SNAME_SIZE + 1];
med_sorting_type sortingType;
med_axis_type axisType;
if(MEDmeshInfo(fid, meshIndex + 1, meshName, &spaceDim, &meshDim, &meshType, meshDesc,
dtUnit, &sortingType, &nStep, &axisType, axisName, axisUnit) < 0){
#else
if(MEDmaaInfo(fid, meshIndex + 1, meshName, &spaceDim, &meshType, meshDesc) < 0){
#endif
Msg::Error("Unable to read mesh information");
return 0;
}
// FIXME: we should support multi-step MED3 meshes (probably by
// storing each mesh as a separate model, with a naming convention
// e.g. meshName_step%d). This way we could also handle multi-mesh
// time sequences in MED3.
if(nStep > 1)
Msg::Warning("Discarding %d last meshes in multi-step MED mesh", nStep - 1);
setName(meshName);
setFileName(name);
if(meshType == MED_NON_STRUCTURE){
Msg::Info("Reading %d-D unstructured mesh <<%s>>", spaceDim, meshName);
}
else{
Msg::Error("Reading structured MED meshes is not supported");
return 0;
}
med_int vf[3];
MEDversionLire(fid, &vf[0], &vf[1], &vf[2]);
// read nodes
#if (MED_MAJOR_NUM == 3)
med_bool changeOfCoord, geoTransform;
med_int numNodes = MEDmeshnEntity(fid, meshName, MED_NO_DT, MED_NO_IT, MED_NODE,
MED_NO_GEOTYPE, MED_COORDINATE, MED_NO_CMODE,
&changeOfCoord, &geoTransform);
#else
med_int numNodes = MEDnEntMaa(fid, meshName, MED_COOR, MED_NOEUD, MED_NONE,
MED_NOD);
#endif
if(numNodes < 0){
Msg::Error("Could not read number of MED nodes");
return 0;
}
if(numNodes == 0){
Msg::Error("No nodes in MED mesh");
return 0;
}
std::vector<MVertex*> verts(numNodes);
std::vector<med_float> coord(spaceDim * numNodes);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshNodeCoordinateRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_FULL_INTERLACE,
&coord[0]) < 0){
#else
std::vector<char> coordName(spaceDim * MED_TAILLE_PNOM + 1);
std::vector<char> coordUnit(spaceDim * MED_TAILLE_PNOM + 1);
med_repere rep;
if(MEDcoordLire(fid, meshName, spaceDim, &coord[0], MED_FULL_INTERLACE,
MED_ALL, 0, 0, &rep, &coordName[0], &coordUnit[0]) < 0){
#endif
Msg::Error("Could not read MED node coordinates");
return 0;
}
std::vector<med_int> nodeTags(numNodes);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshEntityNumberRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_NODE,
MED_NO_GEOTYPE, &nodeTags[0]) < 0)
#else
if(MEDnumLire(fid, meshName, &nodeTags[0], numNodes, MED_NOEUD, MED_NONE) < 0)
#endif
nodeTags.clear();
for(int i = 0; i < numNodes; i++)
verts[i] = new MVertex(coord[spaceDim * i],
(spaceDim > 1) ? coord[spaceDim * i + 1] : 0.,
(spaceDim > 2) ? coord[spaceDim * i + 2] : 0.,
0, nodeTags.empty() ? 0 : nodeTags[i]);
// read elements (loop over all possible MSH element types)
for(int mshType = 0; mshType < MSH_NUM_TYPE; mshType++){
med_geometrie_element type = msh2medElementType(mshType);
if(type == MED_NONE) continue;
#if (MED_MAJOR_NUM == 3)
med_bool changeOfCoord;
med_bool geoTransform;
med_int numEle = MEDmeshnEntity(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, MED_CONNECTIVITY, MED_NODAL, &changeOfCoord,
&geoTransform);
#else
med_int numEle = MEDnEntMaa(fid, meshName, MED_CONN, MED_MAILLE, type, MED_NOD);
#endif
if(numEle <= 0) continue;
int numNodPerEle = type % 100;
std::vector<med_int> conn(numEle * numNodPerEle);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshElementConnectivityRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, MED_NODAL, MED_FULL_INTERLACE, &conn[0]) < 0){
#else
if(MEDconnLire(fid, meshName, spaceDim, &conn[0], MED_FULL_INTERLACE, 0, MED_ALL,
MED_MAILLE, type, MED_NOD) < 0){
#endif
Msg::Error("Could not read MED elements");
return 0;
}
std::vector<med_int> fam(numEle, 0);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshEntityFamilyNumberRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, &fam[0]) < 0){
#else
if(MEDfamLire(fid, meshName, &fam[0], numEle, MED_MAILLE, type) < 0){
#endif
Msg::Info("No family number for elements: using 0 as default family number");
}
std::vector<med_int> eleTags(numEle);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshEntityNumberRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, &eleTags[0]) < 0)
#else
if(MEDnumLire(fid, meshName, &eleTags[0], numEle, MED_MAILLE, type) < 0)
#endif
eleTags.clear();
std::map<int, std::vector<MElement*> > elements;
MElementFactory factory;
for(int j = 0; j < numEle; j++){
std::vector<MVertex*> v(numNodPerEle);
for(int k = 0; k < numNodPerEle; k++)
v[k] = verts[conn[numNodPerEle * j + med2mshNodeIndex(type, k)] - 1];
MElement *e = factory.create(mshType, v, eleTags.empty() ? 0 : eleTags[j]);
if(e) elements[-fam[j]].push_back(e);
}
_storeElementsInEntities(elements);
}
_associateEntityWithMeshVertices();
_storeVerticesInEntities(verts);
// read family info
med_int numFamilies = MEDnFam(fid, meshName);
if(numFamilies < 0){
Msg::Error("Could not read MED families");
return 0;
}
for(int i = 0; i < numFamilies; i++){
#if (MED_MAJOR_NUM == 3)
med_int numAttrib = (vf[0] == 2) ? MEDnFamily23Attribute(fid, meshName, i + 1) : 0;
med_int numGroups = MEDnFamilyGroup(fid, meshName, i + 1);
#else
med_int numAttrib = MEDnAttribut(fid, meshName, i + 1);
med_int numGroups = MEDnGroupe(fid, meshName, i + 1);
#endif
if(numAttrib < 0 || numGroups < 0){
Msg::Error("Could not read MED groups or attributes");
return 0;
}
std::vector<med_int> attribId(numAttrib + 1);
std::vector<med_int> attribVal(numAttrib + 1);
std::vector<char> attribDes(MED_TAILLE_DESC * numAttrib + 1);
std::vector<char> groupNames(MED_TAILLE_LNOM * numGroups + 1);
char familyName[MED_TAILLE_NOM + 1];
med_int familyNum;
#if (MED_MAJOR_NUM == 3)
if(vf[0] == 2){ // MED2 file
if(MEDfamily23Info(fid, meshName, i + 1, familyName, &attribId[0],
&attribVal[0], &attribDes[0], &familyNum,
&groupNames[0]) < 0){
Msg::Error("Could not read info for MED2 family %d", i + 1);
continue;
}
}
else{
if(MEDfamilyInfo(fid, meshName, i + 1, familyName, &familyNum,
&groupNames[0]) < 0){
Msg::Error("Could not read info for MED3 family %d", i + 1);
continue;
}
}
#else
if(MEDfamInfo(fid, meshName, i + 1, familyName, &familyNum, &attribId[0],
&attribVal[0], &attribDes[0], &numAttrib, &groupNames[0],
&numGroups) < 0){
Msg::Error("Could not read info for MED family %d", i + 1);
continue;
}
#endif
// family tags are unique (for all dimensions)
GEntity *ge;
if((ge = getRegionByTag(-familyNum))){}
else if((ge = getFaceByTag(-familyNum))){}
else if((ge = getEdgeByTag(-familyNum))){}
else ge = getVertexByTag(-familyNum);
if(ge){
elementaryNames[std::pair<int, int>(ge->dim(), -familyNum)] = familyName;
if(numGroups > 0){
for(int j = 0; j < numGroups; j++){
char tmp[MED_TAILLE_LNOM + 1];
strncpy(tmp, &groupNames[j * MED_TAILLE_LNOM], MED_TAILLE_LNOM);
tmp[MED_TAILLE_LNOM] = '\0';
// don't use same physical number across dimensions, as e.g. getdp
// does not support this
int pnum = setPhysicalName(tmp, ge->dim(), getMaxPhysicalNumber(-1) + 1);
if(std::find(ge->physicals.begin(), ge->physicals.end(), pnum) ==
ge->physicals.end())
ge->physicals.push_back(pnum);
}
}
}
}
// check if we need to read some post-processing data later
#if (MED_MAJOR_NUM == 3)
bool postpro = (MEDnField(fid) > 0) ? true : false;
#else
bool postpro = (MEDnChamp(fid, 0) > 0) ? true : false;
#endif
if(MEDfermer(fid) < 0){
Msg::Error("Unable to close file '%s'", (char*)name.c_str());
return 0;
}
return postpro ? 2 : 1;
}
template<class T>
static void fillElementsMED(med_int family, std::vector<T*> &elements,
std::vector<med_int> &conn, std::vector<med_int> &fam,
med_geometrie_element &type)
{
if(elements.empty()) return;
type = msh2medElementType(elements[0]->getTypeForMSH());
if(type == MED_NONE){
Msg::Warning("Unsupported element type in MED format");
return;
}
for(unsigned int i = 0; i < elements.size(); i++){
elements[i]->setVolumePositive();
for(int j = 0; j < elements[i]->getNumVertices(); j++)
conn.push_back(elements[i]->getVertex(med2mshNodeIndex(type, j))->getIndex());
fam.push_back(family);
}
}
static void writeElementsMED(med_idt &fid, char *meshName, std::vector<med_int> &conn,
std::vector<med_int> &fam, med_geometrie_element type)
{
if(fam.empty()) return;
#if (MED_MAJOR_NUM == 3)
if(MEDmeshElementWr(fid, meshName, MED_NO_DT, MED_NO_IT, 0., MED_CELL, type,
MED_NODAL, MED_FULL_INTERLACE, (med_int)fam.size(),
&conn[0], MED_FALSE, 0, MED_FALSE, 0, MED_TRUE, &fam[0]) < 0)
#else
if(MEDelementsEcr(fid, meshName, (med_int)3, &conn[0], MED_FULL_INTERLACE,
0, MED_FAUX, 0, MED_FAUX, &fam[0], (med_int)fam.size(),
MED_MAILLE, type, MED_NOD) < 0)
#endif
Msg::Error("Could not write MED elements");
}
int GModel::writeMED(const std::string &name, bool saveAll, double scalingFactor)
{
med_idt fid = MEDouvrir((char*)name.c_str(), MED_CREATION);
if(fid < 0){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
// write header
if(MEDfichDesEcr(fid, (char*)"MED file generated by Gmsh") < 0){
Msg::Error("Unable to write MED descriptor");
return 0;
}
char *meshName = (char*)getName().c_str();
// Gmsh always writes 3D unstructured meshes
#if (MED_MAJOR_NUM == 3)
char dtUnit[MED_SNAME_SIZE + 1] = "";
char axisName[3 * MED_SNAME_SIZE + 1] = "";
char axisUnit[3 * MED_SNAME_SIZE + 1] = "";
if(MEDmeshCr(fid, meshName, 3, 3, MED_UNSTRUCTURED_MESH, "Mesh created with Gmsh",
dtUnit, MED_SORT_DTIT, MED_CARTESIAN, axisName, axisUnit) < 0){
#else
if(MEDmaaCr(fid, meshName, 3, MED_NON_STRUCTURE,
(char*)"Mesh created with Gmsh") < 0){
#endif
Msg::Error("Could not create MED mesh");
return 0;
}
// if there are no physicals we save all the elements
if(noPhysicalGroups()) saveAll = true;
// index the vertices we save in a continuous sequence (MED
// connectivity is given in terms of vertex indices)
indexMeshVertices(saveAll);
// get a vector containing all the geometrical entities in the
// model (the ordering of the entities must be the same as the one
// used during the indexing of the vertices)
std::vector<GEntity*> entities;
getEntities(entities);
std::map<GEntity*, int> families;
// write the families
{
// always create a "0" family, with no groups or attributes
#if (MED_MAJOR_NUM == 3)
if(MEDfamilyCr(fid, meshName, "F_0", 0, 0, "") < 0)
#else
if(MEDfamCr(fid, meshName, (char*)"F_0", 0, 0, 0, 0, 0, 0, 0) < 0)
#endif
Msg::Error("Could not create MED family 0");
// create one family per elementary entity, with one group per
// physical entity and no attributes
for(unsigned int i = 0; i < entities.size(); i++){
if(saveAll || entities[i]->physicals.size()){
int num = - ((int)families.size() + 1);
families[entities[i]] = num;
std::ostringstream fs;
fs << entities[i]->dim() << "D_" << entities[i]->tag();
std::string familyName = "F_" + fs.str();
std::string groupName;
for(unsigned j = 0; j < entities[i]->physicals.size(); j++){
std::string tmp = getPhysicalName
(entities[i]->dim(), entities[i]->physicals[j]);
if(tmp.empty()){ // create unique name
std::ostringstream gs;
gs << entities[i]->dim() << "D_" << entities[i]->physicals[j];
groupName += "G_" + gs.str();
}
else
groupName += tmp;
groupName.resize((j + 1) * MED_TAILLE_LNOM, ' ');
}
#if (MED_MAJOR_NUM == 3)
if(MEDfamilyCr(fid, meshName, familyName.c_str(),
(med_int)num, (med_int)entities[i]->physicals.size(),
groupName.c_str()) < 0)
#else
if(MEDfamCr(fid, meshName, (char*)familyName.c_str(),
(med_int)num, 0, 0, 0, 0, (char*)groupName.c_str(),
(med_int)entities[i]->physicals.size()) < 0)
#endif
Msg::Error("Could not create MED family %d", num);
}
}
}
// write the nodes
{
std::vector<med_float> coord;
std::vector<med_int> fam;
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){
coord.push_back(v->x() * scalingFactor);
coord.push_back(v->y() * scalingFactor);
coord.push_back(v->z() * scalingFactor);
fam.push_back(0); // we never create node families
}
}
}
if(fam.empty()){
Msg::Error("No nodes to write in MED mesh");
return 0;
}
#if (MED_MAJOR_NUM == 3)
if(MEDmeshNodeWr(fid, meshName, MED_NO_DT, MED_NO_IT, 0., MED_FULL_INTERLACE,
(med_int)fam.size(), &coord[0], MED_FALSE, "", MED_FALSE, 0,
MED_TRUE, &fam[0]) < 0)
#else
char coordName[3 * MED_TAILLE_PNOM + 1] =
"x y z ";
char coordUnit[3 * MED_TAILLE_PNOM + 1] =
"unknown unknown unknown ";
if(MEDnoeudsEcr(fid, meshName, (med_int)3, &coord[0], MED_FULL_INTERLACE,
MED_CART, coordName, coordUnit, 0, MED_FAUX, 0, MED_FAUX,
&fam[0], (med_int)fam.size()) < 0)
#endif
Msg::Error("Could not write nodes");
}
// write the elements
{
{ // points
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(viter it = firstVertex(); it != lastVertex(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->points, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // lines
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(eiter it = firstEdge(); it != lastEdge(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->lines, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // triangles
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(fiter it = firstFace(); it != lastFace(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->triangles, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // quads
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(fiter it = firstFace(); it != lastFace(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->quadrangles, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // tets
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(riter it = firstRegion(); it != lastRegion(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->tetrahedra, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // hexas
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(riter it = firstRegion(); it != lastRegion(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->hexahedra, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // prisms
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(riter it = firstRegion(); it != lastRegion(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->prisms, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // pyramids
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(riter it = firstRegion(); it != lastRegion(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->pyramids, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
}
if(MEDfermer(fid) < 0){
Msg::Error("Unable to close file '%s'", (char*)name.c_str());
return 0;
}
return 1;
}
#else
int GModel::readMED(const std::string &name)
{
Msg::Error("Gmsh must be compiled with MED support to read '%s'",
name.c_str());
return 0;
}
Mesh::Mesh(const std::map<MElement*,GEntity*> &element2entity,
const std::set<MElement*> &els, std::set<MVertex*> &toFix,
bool fixBndNodes, bool fastJacEval) :
_fastJacEval(fastJacEval)
{
_dim = (*els.begin())->getDim();
// Initialize elements, vertices, free vertices and element->vertices
// connectivity
const int nElements = els.size();
_nPC = 0;
_el.resize(nElements);
_el2FV.resize(nElements);
_el2V.resize(nElements);
_nBezEl.resize(nElements);
_nNodEl.resize(nElements);
_indPCEl.resize(nElements);
int iEl = 0;
bool nonGeoMove = false;
for(std::set<MElement*>::const_iterator it = els.begin();
it != els.end(); ++it, ++iEl) {
_el[iEl] = *it;
const JacobianBasis *jac = _el[iEl]->getJacobianFuncSpace();
_nBezEl[iEl] = _fastJacEval ? jac->getNumJacNodesFast() : jac->getNumJacNodes();
_nNodEl[iEl] = jac->getNumMapNodes();
for (int iVEl = 0; iVEl < jac->getNumMapNodes(); iVEl++) {
MVertex *vert = _el[iEl]->getVertex(iVEl);
GEntity *ge = vert->onWhat();
const int vDim = ge->dim();
const bool hasParam = ge->haveParametrization();
int iV = addVert(vert);
_el2V[iEl].push_back(iV);
if ((vDim > 0) && (toFix.find(vert) == toFix.end()) && (!fixBndNodes || vDim == _dim)) { // Free vertex?
ParamCoord *param;
if (vDim == 3) param = new ParamCoordPhys3D();
else if (hasParam) param = new ParamCoordParent(vert);
else {
if (vDim == 2) param = new ParamCoordLocalSurf(vert);
else param = new ParamCoordLocalLine(vert);
nonGeoMove = true;
}
int iFV = addFreeVert(vert,iV,vDim,param,toFix);
_el2FV[iEl].push_back(iFV);
for (int i=_startPCFV[iFV]; i<_startPCFV[iFV]+vDim; i++) _indPCEl[iEl].push_back(i);
}
else _el2FV[iEl].push_back(-1);
}
}
if (nonGeoMove) Msg::Info("WARNING: Some vertices will be moved along local lines "
"or planes, they may not remain on the exact geometry");
// Initial coordinates
_ixyz.resize(nVert());
for (int iV = 0; iV < nVert(); iV++) _ixyz[iV] = _vert[iV]->point();
_iuvw.resize(nFV());
for (int iFV = 0; iFV < nFV(); iFV++) _iuvw[iFV] = _paramFV[iFV]->getUvw(_freeVert[iFV]);
// Set current coordinates
_xyz = _ixyz;
_uvw = _iuvw;
// Set normals to 2D elements (with magnitude of inverse Jacobian) or initial
// Jacobians of 3D elements
if (_dim == 2) {
_scaledNormEl.resize(nEl());
for (int iEl = 0; iEl < nEl(); iEl++) calcScaledNormalEl2D(element2entity,iEl);
}
else {
_invStraightJac.resize(nEl(),1.);
double dumJac[3][3];
for (int iEl = 0; iEl < nEl(); iEl++)
_invStraightJac[iEl] = 1. / fabs(_el[iEl]->getPrimaryJacobian(0.,0.,0.,dumJac));
}
}
// Main function for fast curving
void HighOrderMeshFastCurving(GModel *gm, FastCurvingParameters &p)
{
double t1 = Cpu();
Msg::StatusBar(true, "Optimizing high order mesh...");
std::vector<GEntity*> allEntities;
gm->getEntities(allEntities);
// Compute vert. -> elt. connectivity
Msg::Info("Computing connectivity...");
std::map<MVertex*, std::vector<MElement *> > vertex2elements;
for (int iEnt = 0; iEnt < allEntities.size(); ++iEnt)
calcVertex2Elements(p.dim, allEntities[iEnt], vertex2elements);
// Get BL field (if any)
BoundaryLayerField *blf = getBLField(gm);
// Build multimap of each geometric entity to its boundaries
std::multimap<GEntity*,GEntity*> entities;
if (blf) { // BF field?
for (int iEnt = 0; iEnt < allEntities.size(); ++iEnt) {
GEntity* &entity = allEntities[iEnt];
if (entity->dim() == p.dim && (!p.onlyVisible || entity->getVisibility())) // Consider only "domain" entities
if (p.dim == 2) { // "Domain" face?
std::list<GEdge*> edges = entity->edges();
for (std::list<GEdge*>::iterator itEd = edges.begin(); itEd != edges.end(); itEd++) // Loop over model boundary edges
if (blf->isEdgeBL((*itEd)->tag())) // Already skip model edge if no BL there
entities.insert(std::pair<GEntity*,GEntity*>(entity, *itEd));
}
else if (p.dim == 3) { // "Domain" region?
std::list<GFace*> faces = entity->faces();
for (std::list<GFace*>::iterator itF = faces.begin(); itF != faces.end(); itF++) // Loop over model boundary faces
if (blf->isFaceBL((*itF)->tag())) // Already skip model face if no BL there
entities.insert(std::pair<GEntity*,GEntity*>(entity, *itF));
}
}
}
else { // No BL field
for (int iEnt = 0; iEnt < allEntities.size(); ++iEnt) {
GEntity* &entity = allEntities[iEnt];
if (entity->dim() == p.dim-1 && (!p.onlyVisible || entity->getVisibility())) // Consider boundary entities
entities.insert(std::pair<GEntity*,GEntity*>(0, entity));
}
}
// Build normals if necessary
std::map<GEntity*, std::map<MVertex*, SVector3> > normVertEnt; // Normal to each vertex for each geom. entity
if (!blf) {
Msg::Warning("Boundary layer data not found, trying to detect columns");
buildNormals(vertex2elements, entities, p, normVertEnt);
}
// Loop over geometric entities
for (std::multimap<GEntity*,GEntity*>::iterator itBE = entities.begin();
itBE != entities.end(); itBE++) {
GEntity *domEnt = itBE->first, *bndEnt = itBE->second;
BoundaryLayerColumns *blc = 0;
if (blf) {
Msg::Info("Curving elements for entity %d bounding entity %d...",
bndEnt->tag(), domEnt->tag());
if (p.dim == 2)
blc = domEnt->cast2Face()->getColumns();
else if (p.dim == 3)
blc = domEnt->cast2Region()->getColumns();
else
Msg::Error("Fast curving implemented only in dim. 2 and 3");
}
else
Msg::Info("Curving elements for boundary entity %d...", bndEnt->tag());
std::map<MVertex*, SVector3> &normVert = normVertEnt[bndEnt];
curveMeshFromBnd(vertex2elements, normVert, blc, bndEnt, p);
}
double t2 = Cpu();
Msg::StatusBar(true, "Done curving high order mesh (%g s)", t2-t1);
}