const MeshLib::CFEMesh* GridAdapter::toCFEMesh() const
{
MeshLib::CFEMesh* mesh (new MeshLib::CFEMesh());
std::cout << "Converting mesh object ... ";
// set mesh nodes
size_t nNodes = _nodes->size();
for (size_t i = 0; i < nNodes; i++)
mesh->nod_vector.push_back(new MeshLib::CNode(i, (*(*_nodes)[i])[0], (*(*_nodes)[i])[1], (*(*_nodes)[i])[2]));
// set mesh elements
size_t nElems = _elems->size();
for (size_t i = 0; i < nElems; i++)
{
MeshLib::CElem* elem(new MeshLib::CElem());
elem->setElementProperties((*_elems)[i]->type);
elem->SetPatchIndex((*_elems)[i]->material);
size_t nElemNodes = ((*_elems)[i]->nodes).size();
for (size_t j = 0; j < nElemNodes; j++)
elem->SetNodeIndex(j, (*_elems)[i]->nodes[j]);
mesh->ele_vector.push_back(elem);
}
mesh->ConstructGrid();
std::cout << "done." << "\n";
return mesh;
}
void writeOGSMesh(const MeshLib::CFEMesh &mesh, const std::string file_base_name)
{
const string fname = file_base_name + "_mesh_converted_from_GIS_shape_data.msh";
ofstream os(fname.c_str(), ios::trunc);
os.setf(ios::scientific, ios::floatfield);
setw(14);
os.precision(10);
os << "#FEM_MSH \n $PCS_TYPE\n NO_PCS\n $NODES" <<endl;
const size_t nn = mesh.GetNodesNumber(false);
os << nn <<endl;
for(size_t i=0; i<nn; i++)
{
MeshLib::CNode *n_ptr = mesh.nod_vector[i];
const double *xyz_ptr = n_ptr->getData();
os<< n_ptr->GetIndex() <<" "<<xyz_ptr[0] <<" "<<xyz_ptr[1] <<" "<<xyz_ptr[2] <<"\n";
}
os << "$ELEMENTS" <<endl;
const size_t ne = mesh.ele_vector.size();
for(size_t i=0; i<ne; i++)
{
MeshLib::CElem *e_ptr = mesh.ele_vector[i];
e_ptr->WriteIndex(os);
}
os << "#STOP" <<endl;
os.close();
}
void LegacyVtkInterface::WriteVTKCellDataPETSC(PetscViewer viewer) const
{
size_t nelocal = _mesh->ele_vector.size(); // local size
// count overall length of element vector
long numAllPoints = 0;
for (size_t i = 0; i < nelocal; i++)
{
MeshLib::CElem* ele = _mesh->ele_vector[i];
numAllPoints = numAllPoints + (ele->GetNodesNumber(false)) + 1;
}
PetscScalar* ep, *eglobp; // used for pointer
PetscInt low, high, neglob, nn;
int i;
VecScatter ctx;
// get my petsc rank
int myrank;
MPI_Comm_rank(PETSC_COMM_WORLD, &myrank);
// test vtk output
PETSc_Vec e, eglob, x; //
// vector for elements ...contains number of nodes connected to form a
// element in first entry and then the node numbers
VecCreate(PETSC_COMM_WORLD, &e);
VecSetSizes(
e, numAllPoints,
PETSC_DECIDE); // nummAllPoints is local lenght of the vector we need
VecSetFromOptions(e); //
// get range of local variables
VecGetOwnershipRange(e, &low, &high);
VecGetSize(e, &neglob);
// get local part of vector
VecGetArray(e, &ep);
// in order to get a global mesh the node numbers have to be corrected..
// we have to get the position in the global node vector in order to get
// the correct additive value
// is there a simpler way to do it (as below)?
MeshLib::CFEMesh* mesh = fem_msh_vector[0];
// const int nn = mesh->getNumNodesGlobal(); //global number of nodes
// without shadow nodes
const size_t n_linear_pnts(mesh->GetNodesNumber(false));
VecCreate(PETSC_COMM_WORLD, &x);
VecSetSizes(x, n_linear_pnts, PETSC_DECIDE);
VecSetFromOptions(x); //
// get range of local variables
VecGetOwnershipRange(x, &low, &high);
VecGetSize(x, &nn);
// cout << " " << low << " " << high << " \n";
// low is now the first node number
// now we can fill the element vector
size_t anz_elem = 0; // here a local value
for (size_t i = 0; i < nelocal; i++)
{
MeshLib::CElem* ele = _mesh->ele_vector[i];
// cout << ele->GetNodesNumber(false)<< " " ;
switch (ele->GetElementType()) // first entry: type of element as
// defined for vtk ..better than number
// of nodes
{
case MshElemType::LINE:
ep[anz_elem] = 3;
break;
case MshElemType::QUAD:
ep[anz_elem] = 9;
break;
case MshElemType::HEXAHEDRON:
ep[anz_elem] = 12;
break;
case MshElemType::TRIANGLE:
ep[anz_elem] = 5;
break;
case MshElemType::TETRAHEDRON:
ep[anz_elem] = 10;
break;
case MshElemType::PRISM: // VTK_WEDGE
ep[anz_elem] = 13;
break;
case MshElemType::PYRAMID:
ep[anz_elem] = 14;
break;
default:
cerr << "PETSC VTK output::WriteVTKElementData MshElemType not "
"recogniced"
<< "\n";
break;
}
// cout << ele->GetNodesNumber(false)<< " " ;
for (size_t j = 0; j < ele->GetNodesNumber(false); j++)
{
ep[anz_elem + j + 1] =
ele->GetNodeIndeces()[j] + low; // this are the nodes
// cout << "DEBUG " << ele->GetNodeIndeces()[j] << " " ;
}
// cout << " \n";
anz_elem = anz_elem + (ele->GetNodesNumber(false)) + 1;
}
// now scatter the vectors to process rank 0
VecScatterCreateToZero(e, &ctx, &eglob);
VecScatterBegin(ctx, e, eglob, INSERT_VALUES, SCATTER_FORWARD);
VecScatterEnd(ctx, e, eglob, INSERT_VALUES, SCATTER_FORWARD);
// count number of elements
if (myrank == 0)
{
VecGetArray(eglob, &eglobp);
anz_elem = 0; // here this es global number of elements
i = 0;
while (i < neglob)
{
anz_elem += 1; // add one for the element
int mswitch = (int)eglobp[i];
switch (mswitch) // first entry: type of element as defined for vtk
// ..better than number of nodes
{
case 3: // LINE
i += 2 + 1;
break;
case 9: // QUAD
i += 4 + 1;
break;
case 12: // HEXAHEDRON:
i += 6 + 1;
break;
case 5: // TRIANGLE:
i += 3 + 1;
break;
case 10: // TETRAHEDRON:
i += 4 + 1;
break;
case 13: // PRISM: // VTK_WEDGE
i += 6 + 1;
break;
case 14: // PYRAMID:
i += 5 + 1;
break;
default:
cerr << "PETSC VTK Output 1::WriteVTKElementData "
"MshElemType not handled, i. anz_elem. ep[i] type "
<< i << " " << anz_elem << " " << eglobp[i] << "\n";
exit(1);
break;
}
}
// write elements
// vtk_file << "CELLS " << numCells << " " << numAllPoints << "\n";
PetscViewerASCIIPrintf(viewer, "CELLS %d %d\n", anz_elem, neglob);
i = 0;
std::stringstream ss;
while (i < neglob)
{
switch ((int)eglobp[i]) // first entry: type of element as defined
// for vtk ..better than number of nodes
{
case 3: // LINE
ss << " 2 ";
// PetscViewerASCIIPrintf(viewer," 2 ");
for (size_t j = 0; j < 2; j++)
ss << eglobp[i + j + 1] << " ";
// PetscViewerASCIIPrintf(viewer," %d
// ",(long) eglobp[i+j+1]);
i += 2 + 1;
break;
case 9: // QUAD
ss << " 4 ";
// PetscViewerASCIIPrintf(viewer," 4 ");
for (size_t j = 0; j < 4; j++)
ss << eglobp[i + j + 1] << " ";
// PetscViewerASCIIPrintf(viewer," %d
// ",(long) eglobp[i+j+1]);
i += 4 + 1;
break;
case 12: // HEXAHEDRON:
ss << " 6 ";
// PetscViewerASCIIPrintf(viewer," 6 ");
for (size_t j = 0; j < 6; j++)
ss << eglobp[i + j + 1] << " ";
// PetscViewerASCIIPrintf(viewer," %d ",(long)
// eglobp[i+j+1]);
i += 6 + 1;
break;
case 5: // TRIANGLE:
ss << " 3 ";
// PetscViewerASCIIPrintf(viewer," 3 ");
for (size_t j = 0; j < 3; j++)
ss << eglobp[i + j + 1] << " ";
// PetscViewerASCIIPrintf(viewer," %d ",(long)
// eglobp[i+j+1]);
i += 3 + 1;
break;
case 10: // TETRAHEDRON:
ss << " 4 ";
// PetscViewerASCIIPrintf(viewer," 4 ");
for (size_t j = 0; j < 4; j++)
ss << eglobp[i + j + 1] << " ";
// PetscViewerASCIIPrintf(viewer," %d ",(long)
// eglobp[i+j+1]);
i += 4 + 1;
break;
case 13: // PRISM: // VTK_WEDGE
ss << " 6 ";
// PetscViewerASCIIPrintf(viewer," 6 ");
for (size_t j = 0; j < 6; j++)
ss << eglobp[i + j + 1] << " ";
// PetscViewerASCIIPrintf(viewer," %d ",(long)
// eglobp[i+j+1]);
i += 6 + 1;
break;
case 14: // PYRAMID:
ss << " 5 ";
// PetscViewerASCIIPrintf(viewer," 5 ");
for (size_t j = 0; j < 5; j++)
ss << eglobp[i + j + 1] << " ";
// PetscViewerASCIIPrintf(viewer," %d ",(long)
// eglobp[i+j+1]);
i += 5 + 1;
break;
default:
cerr << "PETSC VTK Output 2::WriteVTKElementData "
"MshElemType not handled"
<< "\n";
break;
}
ss << "\n";
// PetscViewerASCIIPrintf(viewer," \n ");
if (i % 1000 == 0)
{
PetscViewerASCIIPrintf(viewer, ss.str().c_str());
ss.str("");
ss.clear();
}
}
if (!ss.str().empty())
{
PetscViewerASCIIPrintf(viewer, ss.str().c_str());
}
ss.str("");
ss.clear();
// write cell types
// vtk_file << "CELL_TYPES " << numCells << "\n";
PetscViewerASCIIPrintf(viewer, "CELL_TYPES %d \n", anz_elem);
i = 0;
while (i < neglob)
{
switch ((int)eglobp[i]) // first entry: type of element as defined
// for vtk ..better than number of nodes
{
case 3: // LINE
ss << " 3 \n";
// PetscViewerASCIIPrintf(viewer," 3 \n");
i += 2 + 1;
break;
case 9: // QUAD
ss << " 9 \n";
// PetscViewerASCIIPrintf(viewer," 9 \n");
i += 4 + 1;
break;
case 12: // HEXAHEDRON:
ss << " 12 \n";
// PetscViewerASCIIPrintf(viewer," 12 \n");
i += 6 + 1;
break;
case 5: // TRIANGLE:
ss << " 5 \n";
// PetscViewerASCIIPrintf(viewer," 5 \n");
i += 3 + 1;
break;
case 10: // TETRAHEDRON:
ss << " 10 \n";
// PetscViewerASCIIPrintf(viewer," 10 \n");
i += 4 + 1;
break;
case 13: // PRISM: // VTK_WEDGE
ss << " 13 \n";
// PetscViewerASCIIPrintf(viewer," 13 \n");
i += 6 + 1;
break;
case 14: // PYRAMID:
ss << " 14 \n";
// PetscViewerASCIIPrintf(viewer," 14 \n");;
i += 5 + 1;
break;
default:
cerr << "COutput::WriteVTKElementData MshElemType not "
"handled"
<< "\n";
break;
}
if (i % 1000 == 0)
{
PetscViewerASCIIPrintf(viewer, ss.str().c_str());
ss.str("");
ss.clear();
}
// PetscViewerASCIIPrintf(viewer," \n ");
}
if (!ss.str().empty())
{
PetscViewerASCIIPrintf(viewer, ss.str().c_str());
}
ss.str("");
ss.clear();
VecRestoreArray(eglob, &eglobp);
} // end myrank == 0
VecRestoreArray(e, &ep);
VecDestroy(&e);
VecDestroy(&eglob);
VecDestroy(&x);
}
void LegacyVtkInterface::WriteVTKPointDataPETSC(PetscViewer viewer) const
{
PetscScalar* xp, *yp, *zp; // used for pointer
PetscInt low, high, nn;
PetscInt count;
int i;
VecScatter ctx;
MeshLib::CFEMesh* mesh = fem_msh_vector[0];
// const int nn = mesh->getNumNodesGlobal(); //global number of nodes
// without shadow nodes
const size_t n_linear_pnts(mesh->GetNodesNumber(false));
// get my petsc rank
int myrank;
MPI_Comm_rank(PETSC_COMM_WORLD, &myrank);
// test vtk output
PETSc_Vec x, y, z, xcoor, ycoor, zcoor; //
VecCreate(PETSC_COMM_WORLD, &x);
VecSetSizes(x, n_linear_pnts, PETSC_DECIDE);
VecSetFromOptions(x); //
// get range of local variables
VecGetOwnershipRange(x, &low, &high);
VecGetLocalSize(x, &count);
VecGetSize(x, &nn);
// first duplicate x vector
VecDuplicate(x, &y);
VecDuplicate(x, &z);
// get local part of vectors
VecGetArray(x, &xp);
VecGetArray(y, &yp);
VecGetArray(z, &zp);
// write coordinates
PetscViewerASCIIPrintf(viewer, "POINTS %d double\n", nn);
const std::vector<MeshLib::CNode*> pointVector = mesh->getNodeVector();
for (size_t i = 0; i < (size_t)count; i++)
{
double const* const coords(pointVector[i]->getData());
// now fill the vectors
// get the pointer to current node;
// copy local coordinates to pointer
xp[i] = coords[0];
yp[i] = coords[1];
zp[i] = coords[2];
}
// create a sequential vector and scatter the coordinates
// to this seq. vector on proc 0
VecScatterCreateToZero(x, &ctx, &xcoor);
VecScatterBegin(ctx, x, xcoor, INSERT_VALUES, SCATTER_FORWARD);
VecScatterEnd(ctx, x, xcoor, INSERT_VALUES, SCATTER_FORWARD);
VecScatterCreateToZero(y, &ctx, &ycoor);
VecScatterBegin(ctx, y, ycoor, INSERT_VALUES, SCATTER_FORWARD);
VecScatterEnd(ctx, y, ycoor, INSERT_VALUES, SCATTER_FORWARD);
VecScatterCreateToZero(z, &ctx, &zcoor);
VecScatterBegin(ctx, z, zcoor, INSERT_VALUES, SCATTER_FORWARD);
VecScatterEnd(ctx, z, zcoor, INSERT_VALUES, SCATTER_FORWARD);
// now we have the global vector on rank 0 and can write
if (myrank == 0)
{
VecGetArray(xcoor, &xp);
VecGetArray(ycoor, &yp);
VecGetArray(zcoor, &zp);
for (i = 0; i < nn; i++)
{
PetscViewerASCIIPrintf(viewer, "%1.13lg %1.13lg %1.13lg \n", xp[i],
yp[i], zp[i]);
}
VecRestoreArray(xcoor, &xp);
VecRestoreArray(ycoor, &yp);
VecRestoreArray(zcoor, &zp);
}
VecDestroy(&x);
VecDestroy(&y);
VecDestroy(&z);
VecDestroy(&xcoor);
VecDestroy(&ycoor);
VecDestroy(&zcoor);
return;
}
