void TPZGeoCloneMesh::Write(TPZStream &buf, int withclassid) const
{
TPZGeoMesh::Write(buf,withclassid);
try
{
if(!fGeoReference) {
std::cout << "Cloned geo mesh without geometric mesh from which this mesh is cloned." << std::endl;
DebugStop();
}
TPZPersistenceManager::WritePointer(fGeoReference, &buf);
buf.Write(fMapNodes);
// Maps elements with original elements
std::map<int64_t,int64_t> MappingElements;
TPZGeoEl *gel;
int64_t indexorig, indexcloned;
std::map<TPZGeoEl* , TPZGeoEl* >::const_iterator it;
for(it=fMapElements.begin();it!=fMapElements.end();it++) {
gel = it->first;
indexorig = gel->Index();
gel = it->second;
indexcloned = gel->Index();
MappingElements.insert(std::make_pair(indexorig,indexcloned));
}
buf.Write(MappingElements);
// Writing index of the elements in fReferenceElement
TPZStack<int64_t> RefElements;
int64_t sz = fReferenceElement.size();
for(int64_t ii=0;ii<sz;ii++) {
RefElements.push_back(fReferenceElement[ii]->Index());
}
buf.Write(RefElements);
// Have to save a compact structure of the vector??
// Writing index of the elements in fPatchElement
std::set<int> PatchElements;
std::set<TPZGeoEl* >::iterator itpatch = fPatchElements.begin();
while(itpatch != fPatchElements.end()) {
PatchElements.insert((*itpatch)->Index());
itpatch++;
}
buf.Write(PatchElements);
int64_t rootindex = fGeoRoot->Index();
buf.Write(&rootindex,1);
}
catch(const exception& e)
{
cout << "Exception catched! " << e.what() << std::endl;
cout.flush();
DebugStop();
}
}//method
/// Delete very short fractures
void TPZFracSet::DeleteVeryShortFractures(REAL length)
{
int64_t nel = fgmesh.NElements();
double lmin = 2000.;
for (int64_t el=0; el<nel; el++) {
TPZGeoEl *gel = fgmesh.Element(el);
if (!gel) {
continue;
}
int64_t inode0 = gel->NodeIndex(0);
int64_t inode1 = gel->NodeIndex(1);
if (gel->Neighbour(0).Element() == gel || gel->Neighbour(1).Element() == gel)
{
REAL l = Length(gel);
if (l<lmin) {
lmin = l;
}
if(l < length)
{
std::cout << "Deleting Fracture " << gel->Index() << " length " << l << std::endl;
std::cout << "Index " << gel->NodeIndex(0) << " ";
gel->Node(0).Print();
std::cout << "Index " << gel->NodeIndex(1) << " ";
gel->Node(1).Print();
gel->RemoveConnectivities();
delete gel;
fgmesh.ElementVec()[el] = 0;
gel = 0;
}
}
}
std::cout << "shortest fracture length " << lmin << std::endl;
}
int64_t TPZGeoCloneMesh::CloneElement(TPZGeoEl *orgel){
int64_t i,j;
// int nnod = orgel->NNodes();
// cout << "Original element nodes = " << nnod << endl;
if(HasElement(orgel)) return Index(fMapElements[orgel]);
// Create a cloned element
TPZGeoEl *el = InitializeClone(orgel);
int64_t elindex = Index(el);
// cout << "\nClonned element\n";
// el->Print(cout);
//fill the map
fMapElements[orgel] = el;
if(elindex >= fReferenceElement.NElements()) {
fReferenceElement.Resize(elindex+1,0);
}
fReferenceElement[elindex] = orgel;
//fill the neighbours
for (i=0;i<orgel->NSides();i++){
el->SetSideDefined(i);
TPZGeoElSide neig = orgel->Neighbour(i);
if(!neig.Element()) continue;
// insert all neighbours which have been cloned as neighbours
// THIS IS OVERKILL it would be suficient to insert a single neighbour
while(neig.Element() != orgel) {
// verify if neig.Element has been cloned
if (HasElement((neig.Element()))){
TPZGeoElSide sid(el,i);
// sid.SetConnectivity(sid);
//SetNeighbour(i,neig);
TPZGeoElSide localneig(fMapElements[neig.Element()],neig.Side());
if(!sid.NeighbourExists(localneig)) {
sid.SetConnectivity(localneig);
}
}
neig = neig.Neighbour();
}
}
//loop over the sons
if (orgel->HasSubElement()){
int subel = orgel->NSubElements();
for (j=0;j<subel;j++){
TPZGeoEl *gelson = orgel->SubElement(j);
CloneElement(gelson);
fMapElements[gelson]->SetFather(el);
fMapElements[gelson]->SetFather(el->Index());
el->SetSubElement(j,fMapElements[gelson]);
}
}
// el->Print(cout);
return elindex;
}
void GetElIndexCoarseMesh(TPZAutoPointer<TPZGeoMesh> gmesh, std::set<int64_t> &coarseindex)
{
int nel = gmesh->NElements();
int iel;
int hassubel=0;
int dim = gmesh->Dimension();
int eldim;
for(iel = 0; iel<nel; iel++)
{
TPZGeoEl * gel = gmesh->ElementVec()[iel];
if(!gel) DebugStop();
hassubel = gel->HasSubElement();
eldim = gel->Dimension();
if(!hassubel && eldim ==dim)
{
coarseindex.insert(gel->Index());
}
}
}
/// Merge lines which are parallel
void TPZFracSet::MergeParallelLines()
{
int64_t nel = fgmesh.NElements();
REAL maxcos = 0.;
for (int64_t el = 0; el<nel; el++) {
TPZGeoEl *gel = fgmesh.Element(el);
if(!gel) continue;
TPZManVector<REAL,3> dir1(3);
Direction(gel, dir1);
int nnodes = gel->NCornerNodes();
for(int is = 0; is<nnodes; is++)
{
TPZGeoElSide gelside(gel,is);
TPZGeoElSide neighbour = gelside.Neighbour();
while (neighbour != gelside) {
TPZManVector<REAL,3> dir2(3);
Direction(neighbour.Element(), dir2);
if (neighbour.Side() != is) {
for (int i=0; i<3; i++) {
dir2[i] *= -1.;
}
}
REAL cosangle = 0.;
for (int i=0; i<3; i++) {
cosangle += dir1[i]*dir2[i];
}
if (cosangle> maxcos) {
maxcos = cosangle;
}
if (cosangle > 0.99) {
std::cout << "Fractures " << gel->Index() << " and " << neighbour.Element()->Index() << " are parallel " << cosangle << "\n";
std::cout << "Index " << gel->NodeIndex(0) << " ";
gel->Node(0).Print();
std::cout << "Index " << gel->NodeIndex(1) << " ";
gel->Node(1).Print();
std::cout << "Index " << neighbour.Element()->NodeIndex(0) << " ";
neighbour.Element()->Node(0).Print();
std::cout << "Index " << neighbour.Element()->NodeIndex(1) << " ";
neighbour.Element()->Node(1).Print();
REAL l1 = Length(gel);
REAL l2 = Length(neighbour.Element());
if (l1 < l2) {
gel->RemoveConnectivities();
delete gel;
fgmesh.ElementVec()[el] = 0;
gel = 0;
break;
}
else
{
neighbour.Element()->RemoveConnectivities();
int64_t neighindex = neighbour.Element()->Index();
delete neighbour.Element();
fgmesh.ElementVec()[neighindex] = 0;
neighbour = gelside;
}
}
neighbour = neighbour.Neighbour();
}
if(!gel) break;
}
}
std::cout << "max cosine angle " << maxcos << std::endl;
}
/// Transfer to the geometric mesh
void TPZFracSet::ToGeoMesh()
{
fgmesh.CleanUp();
fgmesh.NodeVec() = fNodeVec;
int64_t nfrac = fFractureVec.NElements();
for (int64_t ifr = 0; ifr < nfrac; ifr++) {
TPZManVector<int64_t,2> nodes(2);
nodes = fFractureVec[ifr].fNodes;
int64_t index;
fgmesh.CreateGeoElement(EOned, nodes, fFractureVec[ifr].fMatId, index);
}
fgmesh.BuildConnectivity();
int64_t nel = fgmesh.NElements();
for (int64_t el=0; el<nel; el++) {
TPZGeoEl *gel = fgmesh.Element(el);
if(!gel) continue;
if (gel->Neighbour(2).Element() != gel) {
std::cout << "gel index " << el << " is overlapping with " << gel->Neighbour(2).Element()->Index() << std::endl;
TPZGeoEl *neigh = gel->Neighbour(2).Element();
int matid = min(gel->MaterialId(),neigh->MaterialId());
if(gel->MaterialId() == neigh->MaterialId())
{
matid = gel->MaterialId();
}
else if(gel->MaterialId() == matid_BC || neigh->MaterialId() == matid_BC)
{
matid = matid_BC;
}
else if((gel->MaterialId() == matid_internal_frac && neigh->MaterialId() == matid_MHM_line) ||
(gel->MaterialId() == matid_MHM_line && neigh->MaterialId() == matid_internal_frac))
{
matid = matid_MHM_frac;
}
else
{
DebugStop();
}
gel->SetMaterialId(matid);
neigh->SetMaterialId(matid);
// remove the element with the lowest index
if (gel->Index() > neigh->Index())
{
// delete neigh
neigh->RemoveConnectivities();
int64_t neighindex = neigh->Index();
delete neigh;
fgmesh.ElementVec()[neighindex] = 0;
std::string matname = fFractureVec[neighindex].fPhysicalName;
fFractureVec[gel->Index()].fPhysicalName = matname + "_MHM";
}
else
{
gel->RemoveConnectivities();
std::string matname = fFractureVec[gel->Index()].fPhysicalName;
fFractureVec[neigh->Index()].fPhysicalName = matname + "_MHM";
delete gel;
fgmesh.ElementVec()[el] = 0;
}
}
}
}
int SubStructure(TPZAutoPointer<TPZCompMesh> cmesh, REAL height)
{
int nelem = cmesh->NElements();
TPZManVector<int> subindex(nelem,-1);
int iel;
int nsub = 0;
for (iel=0; iel<nelem; iel++)
{
TPZCompEl *cel = cmesh->ElementVec()[iel];
if (!cel) {
continue;
}
TPZGeoEl *gel = cel->Reference();
if (!gel) {
continue;
}
int nsides = gel->NSides();
TPZManVector<REAL> center(gel->Dimension(),0.), xco(3,0.);
gel->CenterPoint(nsides-1,center);
gel->X(center,xco);
REAL z = xco[2];
int floor = (int) z/height;
nsub = (floor+1) > nsub ? (floor+1) : nsub;
subindex[iel] = floor;
}
#ifdef DEBUG
{
TPZGeoMesh *gmesh = cmesh->Reference();
int nelgeo = gmesh->NElements();
TPZVec<int> domaincolor(nelgeo,-999);
int cel;
int nel = cmesh->NElements();
for (cel=0; cel<nel; cel++) {
TPZCompEl *compel = cmesh->ElementVec()[cel];
if(!compel) continue;
TPZGeoEl *gel = compel->Reference();
if (!gel) {
continue;
}
domaincolor[gel->Index()] = subindex[cel];
}
ofstream vtkfile("partition.vtk");
TPZVTKGeoMesh::PrintGMeshVTK(gmesh, vtkfile, domaincolor);
}
#endif
int isub;
TPZManVector<TPZSubCompMesh *> submeshes(nsub,0);
for (isub=0; isub<nsub; isub++)
{
int index;
std::cout << '^'; std::cout.flush();
submeshes[isub] = new TPZSubCompMesh(cmesh,index);
if (index < subindex.NElements())
{
subindex[index] = -1;
}
}
for (iel=0; iel<nelem; iel++)
{
int domindex = subindex[iel];
if (domindex >= 0)
{
TPZCompEl *cel = cmesh->ElementVec()[iel];
if (!cel)
{
continue;
}
submeshes[domindex]->TransferElement(cmesh.operator->(),iel);
}
}
cmesh->ComputeNodElCon();
for (isub=0; isub<nsub; isub++)
{
submeshes[isub]->MakeAllInternal();
std::cout << '*'; std::cout.flush();
}
cmesh->ComputeNodElCon();
cmesh->CleanUpUnconnectedNodes();
return nsub;
}