/// 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;
}
void RefinamentoSingular(TPZAutoPointer<TPZGeoMesh> gmesh,int nref)
{
int64_t nnodes = gmesh->NNodes();
int64_t in;
for (in=0; in<nnodes; in++) {
TPZGeoNode *gno = &gmesh->NodeVec()[in];
if (abs(gno->Coord(0))< 1.e-6 && abs(gno->Coord(1)) < 1.e-6) {
break;
}
}
if (in == nnodes) {
DebugStop();
}
TPZGeoElSide gelside;
int64_t nelem = gmesh->NElements();
for (int64_t el = 0; el<nelem; el++) {
TPZGeoEl *gel = gmesh->ElementVec()[el];
int ncorner = gel->NCornerNodes();
for (int ic=0; ic<ncorner; ic++) {
int64_t nodeindex = gel->NodeIndex(ic);
if (nodeindex == in) {
gelside = TPZGeoElSide(gel, ic);
break;
}
}
if (gelside.Element()) {
break;
}
}
if (!gelside.Element()) {
DebugStop();
}
for (int iref = 0; iref <nref; iref++) {
TPZStack<TPZGeoElSide> gelstack;
gelstack.Push(gelside);
TPZGeoElSide neighbour = gelside.Neighbour();
while (neighbour != gelside) {
gelstack.Push(neighbour);
neighbour = neighbour.Neighbour();
}
int64_t nstack = gelstack.size();
for (int64_t ist=0; ist < nstack; ist++) {
if (!gelstack[ist].Element()->HasSubElement()) {
TPZVec<TPZGeoEl *> subel;
gelstack[ist].Element()->Divide(subel);
}
}
}
}
/// Compute the mesh size at the nodes
void TPZFracSet::ComputeMeshSizeAtNodes()
{
REAL minsize = this->fMinElementSize;
REAL normalsize = this->fElementSize;
ToGeoMesh();
fMeshSizeAtNodes.Resize(fNodeVec.NElements(), normalsize);
fMeshSizeAtNodes.Fill(normalsize);
int64_t nel = fgmesh.NElements();
for (int64_t el=0; el<nel; el++) {
TPZGeoEl *gel = fgmesh.Element(el);
if (!gel) {
continue;
}
REAL length = Length(gel);
if (length < normalsize) {
REAL meshsize = length < minsize ? minsize : length;
int64_t inode0 = gel->NodeIndex(0);
int64_t inode1 = gel->NodeIndex(1);
fMeshSizeAtNodes[inode0] = min(fMeshSizeAtNodes[inode0],meshsize);
fMeshSizeAtNodes[inode1] = min(fMeshSizeAtNodes[inode1],meshsize);
}
}
int64_t nnode = fgmesh.NodeVec().NElements();
for (int64_t node = 0; node < nnode; node++) {
TPZManVector<REAL,3> co(3);
fgmesh.NodeVec()[node].GetCoordinates(co);
for (int ico =0; ico < 2; ico++)
{
int mhm = co[ico]/fMHMSpacing[ico];
REAL mhm_min = mhm*fMHMSpacing[ico];
REAL mhm_max = (mhm+1)*fMHMSpacing[ico];
REAL dist = min(co[ico]-mhm_min,mhm_max-co[ico]);
if (dist > 1.e-6 && dist < normalsize) {
dist = max(dist,minsize);
fMeshSizeAtNodes[node] = min(fMeshSizeAtNodes[node],dist);
}
}
}
int64_t nhor = fHorizontalLines.NElements();
for (int64_t hr=0; hr<nhor; hr++) {
for (auto it = fHorizontalLines[hr].begin(); it != fHorizontalLines[hr].end(); it++) {
auto it2 = it;
it2++;
if (it2 == fHorizontalLines[hr].end()) {
continue;
}
int64_t node0 = it->second;
int64_t node1 = it2->second;
REAL length = it2->first - it->first;
if (length > normalsize) {
continue;
}
if (length < minsize) {
length = minsize;
}
fMeshSizeAtNodes[node0] = min(fMeshSizeAtNodes[node0],length);
fMeshSizeAtNodes[node1] = min(fMeshSizeAtNodes[node1],length);
}
}
int64_t nver = fVerticalLines.NElements();
for (int64_t vr=0; vr<nver; vr++) {
for (auto it = fVerticalLines[vr].begin(); it != fVerticalLines[vr].end(); it++) {
auto it2 = it;
it2++;
if (it2 == fVerticalLines[vr].end()) {
continue;
}
int64_t node0 = it->second;
int64_t node1 = it2->second;
REAL length = it2->first - it->first;
if (length > normalsize) {
continue;
}
if (length < minsize) {
length = minsize;
}
fMeshSizeAtNodes[node0] = min(fMeshSizeAtNodes[node0],length);
fMeshSizeAtNodes[node1] = min(fMeshSizeAtNodes[node1],length);
}
}
FromGeoMesh();
}
/// 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;
}
TPZGeoMesh *MalhaCubo()
{
int numnodes=-1;
int numelements=-1;
string FileName, dirname = PZSOURCEDIR;
FileName = dirname + "/Projects/Substruct_Viscoelastic/";
FileName += "cube1.txt";
{
bool countnodes = false;
bool countelements = false;
ifstream read (FileName.c_str());
while(read)
{
char buf[1024];
read.getline(buf, 1024);
std::string str(buf);
if(str == "Coordinates") countnodes = true;
if(str == "end coordinates") countnodes = false;
if(countnodes) numnodes++;
if(str == "Elements") countelements = true;
if(str == "end elements") countelements = false;
if(countelements) numelements++;
}
}
TPZGeoMesh * gMesh = new TPZGeoMesh;
gMesh -> NodeVec().Resize(numnodes);
TPZManVector <int> TopolTetra(4);
const int Qnodes = numnodes;
TPZVec <TPZGeoNode> Node(Qnodes);
//setting nodes coords
int nodeId = 0, elementId = 0, matElId = 1;
ifstream read;
read.open(FileName.c_str());
double nodecoordX , nodecoordY , nodecoordZ ;
char buf[1024];
read.getline(buf, 1024);
read.getline(buf, 1024);
std::string str(buf);
int in;
for(in=0; in<numnodes; in++)
{
read >> nodeId;
read >> nodecoordX;
read >> nodecoordY;
read >> nodecoordZ;
Node[nodeId-1].SetNodeId(nodeId);
Node[nodeId-1].SetCoord(0,nodecoordX);
Node[nodeId-1].SetCoord(1,nodecoordY);
Node[nodeId-1].SetCoord(2,nodecoordZ);
gMesh->NodeVec()[nodeId-1] = Node[nodeId-1];
}
{
read.close();
read.open(FileName.c_str());
int l , m = numnodes+5;
for(l=0; l<m; l++)
{
read.getline(buf, 1024);
}
int el;
int neumann1 = -4, neumann2 = -5;
//std::set<int> ncoordz; //jeitoCaju
for(el=0; el<numelements; el++)
{
read >> elementId;
read >> TopolTetra[0]; //node 1
read >> TopolTetra[1]; //node 2
read >> TopolTetra[2]; //node 3
read >> TopolTetra[3]; //node 4
// O GID comeca com 1 na contagem dos nodes, e nao zero como no PZ, assim o node 1 na verdade é o node 0
TopolTetra[0]--;
TopolTetra[1]--;
TopolTetra[2]--;
TopolTetra[3]--;
int index = el;
TPZGeoEl * tetra = new TPZGeoElRefPattern< pzgeom::TPZGeoTetrahedra> (index, TopolTetra, matElId, *gMesh);
}
gMesh->BuildConnectivity();
// Colocando as condicoes de contorno
for(el=0; el<numelements; el++)
{
TPZManVector <TPZGeoNode,4> Nodefinder(4);
TPZManVector <REAL,3> nodecoord(3);
TPZGeoEl *tetra = gMesh->ElementVec()[el];
// na face x = 1
TPZVec<int> ncoordzVec(0); int sizeOfVec = 0;
for (int i = 0; i < 4; i++)
{
int pos = tetra->NodeIndex(i);
Nodefinder[i] = gMesh->NodeVec()[pos];
Nodefinder[i].GetCoordinates(nodecoord);
if (nodecoord[0] == 1.)
{
sizeOfVec++;
ncoordzVec.Resize(sizeOfVec);
ncoordzVec[sizeOfVec-1] = pos;
}
}
if(ncoordzVec.NElements() == 3)
{
int lado = tetra->WhichSide(ncoordzVec);
TPZGeoElSide tetraSide(tetra, lado);
TPZGeoElBC(tetraSide,neumann1);
}
// Na face x = -1
ncoordzVec.Resize(0);
sizeOfVec = 0;
for (int i = 0; i < 4; i++)
{
int pos = tetra->NodeIndex(i);
Nodefinder[i] = gMesh->NodeVec()[pos];
Nodefinder[i].GetCoordinates(nodecoord);
if (nodecoord[0] == -1.)
{
sizeOfVec++;
ncoordzVec.Resize(sizeOfVec);
ncoordzVec[sizeOfVec-1] = pos;
}
}
if(ncoordzVec.NElements() == 3)
{
int lado = tetra->WhichSide(ncoordzVec);
TPZGeoElSide tetraSide(tetra, lado);
TPZGeoElBC(tetraSide,neumann2);
}
}
TPZVec <REAL> xyz(3,-1.), yz(3,-1.), z(3,1.);
yz[0] = 1.;
z[2] = -1;
int bcidxyz = -1, bcidyz = -2, bcidz = -3;
SetPointBC(gMesh, xyz, bcidxyz);
SetPointBC(gMesh, yz, bcidyz);
SetPointBC(gMesh, z, bcidz);
}
ofstream arg("malhaPZ1BC.txt");
gMesh->Print(arg);
std::ofstream out("Cube.vtk");
TPZVTKGeoMesh::PrintGMeshVTK(gMesh, out, true);
return gMesh;
}
TPZGeoMesh *PyramidalMesh::CreateGMeshCubeWithPyramids(int64_t nelem, int MaterialId)
{
TPZGeoMesh *gmesh = new TPZGeoMesh;
GenerateNodesforPyramidalMesh(gmesh,nelem);
int posicao = 0;
for (int64_t i=0; i<=nelem; i++) {
for (int64_t j=0; j<=nelem; j++) {
for (int64_t k=0; k<=nelem; k++) {
posicao = i*(nelem+1)*(nelem+1)+j*(nelem+1)+k;
}
}
}
for (int64_t i=0; i<nelem; i++) {
for (int64_t j=0; j<nelem; j++) {
for (int64_t k=0; k<nelem; k++) {
TPZManVector<int64_t,9> nodes(9,0);
nodes[0] = k*(nelem+1)*(nelem+1)+j*(nelem+1)+i;
nodes[1] = k*(nelem+1)*(nelem+1)+j*(nelem+1)+i+1;
nodes[2] = k*(nelem+1)*(nelem+1)+(j+1)*(nelem+1)+i+1;
nodes[3] = k*(nelem+1)*(nelem+1)+(j+1)*(nelem+1)+i;
nodes[4] = (k+1)*(nelem+1)*(nelem+1)+j*(nelem+1)+i;
nodes[5] = (k+1)*(nelem+1)*(nelem+1)+j*(nelem+1)+i+1;
nodes[6] = (k+1)*(nelem+1)*(nelem+1)+(j+1)*(nelem+1)+i+1;
nodes[7] = (k+1)*(nelem+1)*(nelem+1)+(j+1)*(nelem+1)+i;
nodes[8] = posicao + (k)*(nelem)*(nelem)+(j)*(nelem)+i+1;
for (int el=0; el<6; el++)
{
TPZManVector<int64_t,5> elnodes(5);
int64_t index;
for (int il=0; il<5; il++) {
elnodes[il] = nodes[piramide_2[el][il]];
}
gmesh->CreateGeoElement(EPiramide, elnodes, MaterialId, index);
}
}
}
}
gmesh->BuildConnectivity();
// Boundary Conditions
const int numelements = gmesh->NElements();
// const int bczMinus = -3, bczplus = -2, bcids = -1;
// const int bczMinus = -1, bczplus = -1, bcids = -1;
for(int el=0; el<numelements; el++)
{
TPZManVector <TPZGeoNode,5> Nodefinder(5);
TPZManVector <REAL,3> nodecoord(3);
TPZGeoEl *piramide = gmesh->ElementVec()[el];
TPZVec<int64_t> ncoordVec(0); int64_t sizeOfVec = 0;
// na face z = 0
for (int i = 0; i < 5; i++)
{
int64_t pos = piramide->NodeIndex(i);
Nodefinder[i] = gmesh->NodeVec()[pos];
Nodefinder[i].GetCoordinates(nodecoord);
if (DoubleComparer(nodecoord[2],0.))
{
sizeOfVec++;
ncoordVec.Resize(sizeOfVec);
ncoordVec[sizeOfVec-1] = pos;
}
}
if(ncoordVec.NElements() == 4)
{
int lado = piramide->WhichSide(ncoordVec);
TPZGeoElSide piramideSide(piramide, lado);
TPZGeoElBC(piramideSide,bc0);
}
ncoordVec.clear();
sizeOfVec = 0;
// na face y = 0
for (int i = 0; i < 5; i++)
{
int64_t pos = piramide->NodeIndex(i);
Nodefinder[i] = gmesh->NodeVec()[pos];
Nodefinder[i].GetCoordinates(nodecoord);
if (DoubleComparer(nodecoord[1],0.))
{
sizeOfVec++;
ncoordVec.Resize(sizeOfVec);
ncoordVec[sizeOfVec-1] = pos;
}
}
if(ncoordVec.NElements() == 4)
{
int lado = piramide->WhichSide(ncoordVec);
TPZGeoElSide piramideSide(piramide, lado);
TPZGeoElBC(piramideSide,bc1);
}
ncoordVec.clear();
sizeOfVec = 0;
// na face x = 1
for (int i = 0; i < 5; i++)
{
int64_t pos = piramide->NodeIndex(i);
Nodefinder[i] = gmesh->NodeVec()[pos];
Nodefinder[i].GetCoordinates(nodecoord);
if (DoubleComparer(nodecoord[0],1.))
{
sizeOfVec++;
ncoordVec.Resize(sizeOfVec);
ncoordVec[sizeOfVec-1] = pos;
}
}
if(ncoordVec.NElements() == 4)
{
int lado = piramide->WhichSide(ncoordVec);
TPZGeoElSide piramideSide(piramide, lado);
TPZGeoElBC(piramideSide,bc2);
}
ncoordVec.clear();
sizeOfVec = 0;
// na face y = 1
for (int i = 0; i < 5; i++)
{
int64_t pos = piramide->NodeIndex(i);
Nodefinder[i] = gmesh->NodeVec()[pos];
Nodefinder[i].GetCoordinates(nodecoord);
if (DoubleComparer(nodecoord[1],1.))
{
sizeOfVec++;
ncoordVec.Resize(sizeOfVec);
ncoordVec[sizeOfVec-1] = pos;
}
}
if(ncoordVec.NElements() == 4)
{
int lado = piramide->WhichSide(ncoordVec);
TPZGeoElSide piramideSide(piramide, lado);
TPZGeoElBC(piramideSide,bc3);
}
ncoordVec.clear();
sizeOfVec = 0;
// na face x = 0
for (int i = 0; i < 5; i++)
{
int64_t pos = piramide->NodeIndex(i);
Nodefinder[i] = gmesh->NodeVec()[pos];
Nodefinder[i].GetCoordinates(nodecoord);
if (DoubleComparer(nodecoord[0],0.))
{
sizeOfVec++;
ncoordVec.Resize(sizeOfVec);
ncoordVec[sizeOfVec-1] = pos;
}
}
if(ncoordVec.NElements() == 4)
{
int lado = piramide->WhichSide(ncoordVec);
TPZGeoElSide piramideSide(piramide, lado);
TPZGeoElBC(piramideSide,bc4);
}
ncoordVec.clear();
sizeOfVec = 0;
// na face z = 1
for (int i = 0; i < 5; i++)
{
int64_t pos = piramide->NodeIndex(i);
Nodefinder[i] = gmesh->NodeVec()[pos];
Nodefinder[i].GetCoordinates(nodecoord);
if (DoubleComparer(nodecoord[2],1.))
{
sizeOfVec++;
ncoordVec.Resize(sizeOfVec);
ncoordVec[sizeOfVec-1] = pos;
}
}
if(ncoordVec.NElements() == 4)
{
int lado = piramide->WhichSide(ncoordVec);
TPZGeoElSide piramideSide(piramide, lado);
TPZGeoElBC(piramideSide,bc5);
}
}
std::ofstream out("CubeWithPyramidswithBcs.vtk");
TPZVTKGeoMesh::PrintGMeshVTK(gmesh, out, true);
return gmesh;
}