I am trying to visualise in ParaView an (initially structured) unstructured mesh that I have made from my own code, however, when I slice through the middle it displays the edges wrong. It seems to keep the old connectivity? However I know for a fact that those edges are not actually there. This only happens when I try to visualise the mesh in 3D. I have produced similar examples in 2D and it is fine. I am not sure why this is happening or how I can fix it.
It is a moving mesh and I am trying to visualise it at different stages. I have attached below what the mesh looks like (when slicing through the middle of the domain).
I have attached below a code snippet of how I output the unstructured mesh data. The same is used for the structured case, as the mesh initially is structured and then deforms into unstructured.
Side note: I have made a small MATLAB script that lets me plot a very small mesh to view if the connectivity is right and it displays as it should, however, when I view it Paraview it shows like the one above.
void OutputMesh(int ts, std::vector<Node> nodes, std::vector<Tetra> elements)
{
std::stringstream ss;
ss << "results/mesh_" << std::setfill('0') << std::setw(4) << ts + 1 << ".vtu";
std::ofstream out(ss.str());
if (!out.is_open())
{
std::cerr << "Failed to open file " << ss.str() << std::endl;
exit(-1);
}
/*header*/
out << "<?xml version=\"1.0\"?>\n";
out << "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n";
out << "<UnstructuredGrid>\n";
out << "<Piece NumberOfPoints=\"" << nodes.size() << "\" NumberOfVerts=\"0\" NumberOfLines=\"0\" ";
out << "NumberOfStrips=\"0\" NumberOfCells=\"" << elements.size() << "\">\n";
/*points*/
out << "<Points>\n";
out << "<DataArray type=\"Float32\" NumberOfComponents=\"3\" format=\"ascii\">\n";
for (Node &node : nodes)
out << node.pos[0] << " " << node.pos[1] << " " << node.pos[2] << "\n";
out << "</DataArray>\n";
out << "</Points>\n";
/*Cells*/
out << "<Cells>\n";
out << "<DataArray type=\"Int32\" Name=\"connectivity\" format=\"ascii\">\n";
for (Tetra &tetra : elements)
out << tetra.con[0] << " " << tetra.con[1] << " " << tetra.con[2] << " " << tetra.con[3] << "\n";
out << "</DataArray>\n";
out << "<DataArray type=\"Int32\" Name=\"offsets\" format=\"ascii\">\n";
for (size_t e = 0; e < elements.size(); e++)
out << (e + 1) * 4 << " ";
//out << e << " ";
out << "\n";
out << "</DataArray>\n";
out << "<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n";
for (size_t e = 0; e < elements.size(); e++)
out << "10 ";
out << "\n";
out << "</DataArray>\n";
out << "</Cells>\n";
/*save point data*/
out << "<PointData Scalars=\"phi\">\n";
out << "<DataArray type=\"Int32\" Name=\"node_index\" format=\"ascii\">\n";
for (size_t n = 0; n < nodes.size(); n++)
out << n << " ";
out << "\n";
out << "</DataArray>\n";
///*
out << "<DataArray type=\"Int32\" Name=\"node_type\" format=\"ascii\">\n";
for (size_t n = 0; n < nodes.size(); n++)
out << 0 << " ";
out << "\n";
out << "</DataArray>\n";
//*/
out << "<DataArray type=\"Float32\" Name=\"phi\" format=\"ascii\">\n";
for (size_t n = 0; n < nodes.size(); n++)
out << 0 << " ";
out << "\n";
out << "</DataArray>\n";
out << "<DataArray type=\"Float32\" Name=\"ion_den\" format=\"ascii\">\n";
for (size_t n = 0; n < nodes.size(); n++)
out << 0 << " ";
out << "\n";
out << "</DataArray>\n";
out << "</PointData>\n";
/*save cell data*/
out << "<CellData Vectors=\"ef\">\n";
out << "<DataArray type=\"Float32\" NumberOfComponents=\"3\" Name=\"ef\" format=\"ascii\">\n";
for (size_t e = 0; e < elements.size(); e++)
out << 0 << " " << 0 << " " << 0 << " ";
out << "\n";
out << "</DataArray>\n";
out << "<DataArray type=\"Float32\" Name=\"cell_volume\" format=\"ascii\">\n";
for (Tetra &tet : elements)
out << 0 << " ";
out << "\n";
out << "</DataArray>\n";
out << "</CellData>\n";
out << "</Piece>\n";
out << "</UnstructuredGrid>\n";
out << "</VTKFile>\n";
out.close();
}
When I check the initial mesh file in the “SpreadSheet View” the x,y,z coordinate of the nodes are correct, however, when one performs a slice, it modifies the y and z values slightly, which is what I believe is causing the issue. Is there anyway to prevent this? Otherwise, what would you advise to do in order to be able to visualise it?
