void TestMeshWriterWithDeletedNode() throw (Exception)
{
// Create mesh
VertexMeshReader<2,2> mesh_reader("mesh/test/data/TestVertexMesh/honeycomb_vertex_mesh_3_by_3");
MutableVertexMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(mesh.GetNumNodes(), 30u);
TS_ASSERT_EQUALS(mesh.GetNumElements(), 9u);
/*
* Delete element 0. This element contains 3 nodes that are
* not contained in any other element and so will be marked
* as deleted.
*/
mesh.DeleteElementPriorToReMesh(0);
// Write mesh to file
VertexMeshWriter<2,2> mesh_writer("TestMeshWriterWithDeletedNode", "vertex_mesh");
TS_ASSERT_THROWS_NOTHING(mesh_writer.WriteFilesUsingMesh(mesh));
// Read mesh back in from file
std::string output_dir = mesh_writer.GetOutputDirectory();
VertexMeshReader<2,2> mesh_reader2(output_dir + "vertex_mesh");
// We should have one less element and three less nodes
TS_ASSERT_EQUALS(mesh_reader2.GetNumNodes(), 27u);
TS_ASSERT_EQUALS(mesh_reader2.GetNumElements(), 8u);
}
void AbstractContinuumMechanicsSolver<DIM>::CreateVtkOutput(std::string spatialSolutionName)
{
if (this->mOutputDirectory=="")
{
EXCEPTION("No output directory was given so no output was written, cannot convert to VTK format");
}
#ifdef CHASTE_VTK
VtkMeshWriter<DIM, DIM> mesh_writer(this->mOutputDirectory + "/vtk", "solution", true);
mesh_writer.AddPointData(spatialSolutionName, this->rGetSpatialSolution());
if (mCompressibilityType==INCOMPRESSIBLE)
{
mesh_writer.AddPointData("Pressure", rGetPressures());
}
//Output the element attribute as cell data.
std::vector<double> element_attribute;
for(typename QuadraticMesh<DIM>::ElementIterator iter = this->mrQuadMesh.GetElementIteratorBegin();
iter != this->mrQuadMesh.GetElementIteratorEnd();
++iter)
{
element_attribute.push_back(iter->GetAttribute());
}
mesh_writer.AddCellData("Attribute", element_attribute);
mesh_writer.WriteFilesUsingMesh(this->mrQuadMesh);
#endif
}
void TestReadingAndWritingElementAttributes() throw(Exception)
{
// Read in a mesh with element attributes
VertexMeshReader<2,2> mesh_reader("mesh/test/data/TestVertexMeshReader2d/vertex_mesh_with_element_attributes");
TS_ASSERT_EQUALS(mesh_reader.GetNumElements(), 2u);
TS_ASSERT_EQUALS(mesh_reader.GetNumElementAttributes(), 1u);
// Construct the mesh
VertexMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(mesh.GetElement(0)->GetUnsignedAttribute(), 97u);
TS_ASSERT_EQUALS(mesh.GetElement(1)->GetUnsignedAttribute(), 152u);
// Write the mesh to file
// Nested scope so the reader is destroyed before we try writing to the folder again
{
VertexMeshWriter<2,2> mesh_writer("TestReadingAndWritingElementAttributes", "vertex_mesh_with_element_attributes");
mesh_writer.WriteFilesUsingMesh(mesh);
// Now read in the mesh that was written
OutputFileHandler handler("TestReadingAndWritingElementAttributes", false);
VertexMeshReader<2,2> mesh_reader2(handler.GetOutputDirectoryFullPath() + "vertex_mesh_with_element_attributes");
TS_ASSERT_EQUALS(mesh_reader2.GetNumElements(), 2u);
TS_ASSERT_EQUALS(mesh_reader2.GetNumElementAttributes(), 1u);
// Construct the mesh again
VertexMesh<2,2> mesh2;
mesh2.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_EQUALS(mesh2.GetElement(0)->GetUnsignedAttribute(), 97u);
TS_ASSERT_EQUALS(mesh2.GetElement(1)->GetUnsignedAttribute(), 152u);
}
// For coverage, repeat this test for a vertex mesh whose elements have faces
VertexMeshReader<3,3> mesh_reader3d("mesh/test/data/TestVertexMeshWriter/vertex_mesh_3d_with_faces_and_attributes");
TS_ASSERT_EQUALS(mesh_reader3d.GetNumElements(), 1u);
TS_ASSERT_EQUALS(mesh_reader3d.GetNumElementAttributes(), 1u);
// Construct the mesh
VertexMesh<3,3> mesh3d;
mesh3d.ConstructFromMeshReader(mesh_reader3d);
TS_ASSERT_EQUALS(mesh3d.GetElement(0)->GetUnsignedAttribute(), 49u);
// Write the mesh to file
VertexMeshWriter<3,3> mesh_writer3d("TestReadingAndWritingElementAttributes", "vertex_mesh_3d_with_faces_and_attributes");
mesh_writer3d.WriteFilesUsingMesh(mesh3d);
// Now read in the mesh that was written
OutputFileHandler handler3d("TestReadingAndWritingElementAttributes", false);
VertexMeshReader<3,3> mesh_reader3d2(handler3d.GetOutputDirectoryFullPath() + "vertex_mesh_3d_with_faces_and_attributes");
TS_ASSERT_EQUALS(mesh_reader3d2.GetNumElements(), 1u);
TS_ASSERT_EQUALS(mesh_reader3d2.GetNumElementAttributes(), 1u);
// Construct the mesh again
VertexMesh<3,3> mesh3d2;
mesh3d2.ConstructFromMeshReader(mesh_reader3d2);
TS_ASSERT_EQUALS(mesh3d2.GetElement(0)->GetUnsignedAttribute(), 49u);
}
void RunTest(unsigned numStepsInEachDimension)
{
MeshEventHandler::Reset();
unsigned nodes = SmallPow(numStepsInEachDimension+1, 3);
if (PetscTools::AmMaster())
{
std::cout<<"Number steps per dimension = " << std::setw(12) << numStepsInEachDimension<<std::endl;
std::cout<<"Number nodes = " << std::setw(12) << nodes<<std::endl;
}
std::string file_name = "cuboid";
std::stringstream directory_stream;
directory_stream << "TestMeshWritersWeekly/steps_" << std::setw(12) << std::setfill('0')<< numStepsInEachDimension;
std::string directory_name = directory_stream.str();
DistributedTetrahedralMesh<3,3> cuboid_mesh;
cuboid_mesh.ConstructCuboid(numStepsInEachDimension, numStepsInEachDimension, numStepsInEachDimension);
TS_ASSERT_EQUALS(cuboid_mesh.GetNumNodes(), nodes);
MeshEventHandler::BeginEvent(MeshEventHandler::TRIANGLES);
{
TrianglesMeshWriter<3,3> mesh_writer(directory_name, file_name, false);
mesh_writer.WriteFilesUsingMesh(cuboid_mesh);
}
MeshEventHandler::EndEvent(MeshEventHandler::TRIANGLES);
MeshEventHandler::BeginEvent(MeshEventHandler::BINTRI);
{
TrianglesMeshWriter<3,3> bin_mesh_writer(directory_name, file_name+"_bin", false);
bin_mesh_writer.SetWriteFilesAsBinary();
bin_mesh_writer.WriteFilesUsingMesh(cuboid_mesh);
}
MeshEventHandler::EndEvent(MeshEventHandler::BINTRI);
#ifdef CHASTE_VTK
MeshEventHandler::BeginEvent(MeshEventHandler::VTK);
{
VtkMeshWriter<3,3> vtk_writer(directory_name, file_name, false);
vtk_writer.WriteFilesUsingMesh(cuboid_mesh);
}
MeshEventHandler::EndEvent(MeshEventHandler::VTK);
MeshEventHandler::BeginEvent(MeshEventHandler::PVTK);
{
VtkMeshWriter<3,3> parallel_vtk_writer(directory_name, file_name+"par",false);
parallel_vtk_writer.SetParallelFiles(cuboid_mesh);
std::vector<double> dummy_data(cuboid_mesh.GetNumLocalNodes(), PetscTools::GetMyRank());
parallel_vtk_writer.AddPointData("Process", dummy_data);
parallel_vtk_writer.WriteFilesUsingMesh(cuboid_mesh);
}
MeshEventHandler::EndEvent(MeshEventHandler::PVTK);
#endif //CHASTE_VTK
MeshEventHandler::Headings();
MeshEventHandler::Report();
}
void CellBasedPdeHandler<DIM>::OpenResultsFiles(std::string outputDirectory)
{
// If appropriate, make a coarse mesh which exactly overlays the lattice sites of a PottsMesh (used for all OnLattice simulations)
if ((dynamic_cast<MultipleCaBasedCellPopulation<DIM>*>(mpCellPopulation) != NULL) && mpCoarsePdeMesh==NULL)
{
assert(DIM ==2);
ChasteCuboid<DIM> cuboid = mpCellPopulation->rGetMesh().CalculateBoundingBox();
// Currently only works with square meshes
assert(cuboid.GetWidth(0) == cuboid.GetWidth(1));
UseCoarsePdeMesh(1, cuboid, false);
}
// If using a NodeBasedCellPopulation a VertexBasedCellPopulation, a MultipleCABasedCellPopulation or a PottsBasedCellPopulation, mpCoarsePdeMesh must be set up
if (PdeSolveNeedsCoarseMesh() && mpCoarsePdeMesh==NULL)
{
EXCEPTION("Trying to solve a PDE on a cell population that doesn't have a mesh. Try calling UseCoarsePdeMesh().");
}
if (mpCoarsePdeMesh != NULL)
{
InitialiseCellPdeElementMap();
// Write mesh to file
TrianglesMeshWriter<DIM,DIM> mesh_writer(outputDirectory+"/coarse_mesh_output", "coarse_mesh",false);
mesh_writer.WriteFilesUsingMesh(*mpCoarsePdeMesh);
}
if (PetscTools::AmMaster())
{
OutputFileHandler output_file_handler(outputDirectory+"/", false);
if (mpCoarsePdeMesh != NULL)
{
mpVizPdeSolutionResultsFile = output_file_handler.OpenOutputFile("results.vizcoarsepdesolution");
}
else
{
mpVizPdeSolutionResultsFile = output_file_handler.OpenOutputFile("results.vizpdesolution");
}
if (mWriteAverageRadialPdeSolution)
{
mpAverageRadialPdeSolutionResultsFile = output_file_handler.OpenOutputFile("radial_dist.dat");
}
}
mDirPath = outputDirectory; // caching the path to the output directory for VTK
//double current_time = SimulationTime::Instance()->GetTime();
//WritePdeSolution(current_time);
}
void TestWritingCableFilesUsingMeshReader() throw(Exception)
{
std::string mesh_base("mesh/test/data/mixed_dimension_meshes/2D_0_to_1mm_200_elements");
TrianglesMeshReader<2,2> reader(mesh_base);
TrianglesMeshWriter<2,2> mesh_writer("TestMixedDimensionMesh", "CableMeshFromReader");
mesh_writer.WriteFilesUsingMeshReader(reader);
PetscTools::Barrier("TestWritingCableFilesUsingMeshReader");
FileFinder generated("TestMixedDimensionMesh/CableMeshFromReader.cable",RelativeTo::ChasteTestOutput);
FileFinder reference("mesh/test/data/mixed_dimension_meshes/2D_0_to_1mm_200_elements.cable", RelativeTo::ChasteSourceRoot);
FileComparison comparer(generated,reference);
TS_ASSERT(comparer.CompareFiles());
}
void TestWritingCableFiles() throw(Exception)
{
std::string mesh_base("mesh/test/data/mixed_dimension_meshes/2D_0_to_1mm_200_elements");
TrianglesMeshReader<2,2> reader(mesh_base);
MixedDimensionMesh<2,2> mesh(DistributedTetrahedralMeshPartitionType::DUMB);
mesh.ConstructFromMeshReader(reader);
TrianglesMeshWriter<2,2> mesh_writer("TestMixedDimensionMesh", "CableMesh", true);
mesh_writer.WriteFilesUsingMesh(mesh);
FileFinder generated("TestMixedDimensionMesh/CableMesh.cable",RelativeTo::ChasteTestOutput);
FileFinder reference("mesh/test/data/mixed_dimension_meshes/2D_0_to_1mm_200_elements.cable", RelativeTo::ChasteSourceRoot);
FileComparison comparer(generated,reference);
TS_ASSERT(comparer.CompareFiles());
}
/*
* Failing test for ReMesh (see #1275)
*/
void noTestCylindricalReMeshFailingTest() throw (Exception)
{
// Load a problematic mesh
TrianglesMeshReader<2,2> mesh_reader("cell_based/test/data/TestCylindricalMeshBug/mesh");
Cylindrical2dMesh mesh(20);
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_DELTA(mesh.GetWidth(0), 20, 1e-3);
TrianglesMeshWriter<2,2> mesh_writer("TestCylindricalMeshBug", "mesh", false);
mesh_writer.WriteFilesUsingMesh(mesh);
// Use showme to view this mesh
NodeMap map(mesh.GetNumNodes());
mesh.ReMesh(map);
}
void MeshBasedCellPopulationWithGhostNodes<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
if (this->mpVoronoiTessellation != NULL)
{
unsigned num_timesteps = SimulationTime::Instance()->GetTimeStepsElapsed();
std::stringstream time;
time << num_timesteps;
// Create mesh writer for VTK output
VertexMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results", false);
// Iterate over any cell writers that are present
unsigned num_vtk_cells = this->mpVoronoiTessellation->GetNumElements();
for (typename std::vector<boost::shared_ptr<AbstractCellWriter<DIM, DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_vtk_cells);
// Loop over elements of mpVoronoiTessellation
for (typename VertexMesh<DIM, DIM>::VertexElementIterator elem_iter = this->mpVoronoiTessellation->GetElementIteratorBegin();
elem_iter != this->mpVoronoiTessellation->GetElementIteratorEnd();
++elem_iter)
{
// Get the indices of this element and the corresponding node in mrMesh
unsigned elem_index = elem_iter->GetIndex();
unsigned node_index = this->mpVoronoiTessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);
// If this node corresponds to a ghost node, set any "cell" data to be -1.0
if (this->IsGhostNode(node_index))
{
// Populate the vector of VTK cell data
vtk_cell_data[elem_index] = -1.0;
}
else
{
// Get the cell corresponding to this node
CellPtr p_cell = this->GetCellUsingLocationIndex(node_index);
// Populate the vector of VTK cell data
vtk_cell_data[elem_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(p_cell, this);
}
}
mesh_writer.AddCellData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// Next, record which nodes are ghost nodes
// Note that the cell writer hierarchy can not be used to do this as ghost nodes don't have corresponding cells.
std::vector<double> ghosts(num_vtk_cells);
for (typename VertexMesh<DIM, DIM>::VertexElementIterator elem_iter = this->mpVoronoiTessellation->GetElementIteratorBegin();
elem_iter != this->mpVoronoiTessellation->GetElementIteratorEnd();
++elem_iter)
{
unsigned elem_index = elem_iter->GetIndex();
unsigned node_index = this->mpVoronoiTessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);
ghosts[elem_index] = (double) (this->IsGhostNode(node_index));
}
mesh_writer.AddCellData("Non-ghosts", ghosts);
///\todo #1975 - deal with possibility of information stored in CellData
mesh_writer.WriteVtkUsingMesh(*(this->mpVoronoiTessellation), time.str());
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
}
#endif //CHASTE_VTK
}
void TestGeneralConvolution3DWithHomogeneousUblas()
{
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_136_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
TS_ASSERT_DELTA(mesh.GetVolume(), 1.0, 1e-6);
TS_ASSERT_DELTA(mesh.GetSurfaceArea(), 6.0, 1e-6);
// Change coordinates
c_matrix<double, 4, 4> x_rotation_matrix = identity_matrix<double>(4);
c_matrix<double, 4, 4> y_rotation_matrix = identity_matrix<double>(4);
c_matrix<double, 4, 4> z_rotation_matrix = identity_matrix<double>(4);
c_matrix<double, 4, 4> translation_matrix = identity_matrix<double>(4);
double theta = 0.7;
double phi = 0.3;
double psi = 1.4;
x_rotation_matrix(1,1) = cos(theta);
x_rotation_matrix(1,2) = sin(theta);
x_rotation_matrix(2,1) = -sin(theta);
x_rotation_matrix(2,2) = cos(theta);
y_rotation_matrix(0,0) = cos(phi);
y_rotation_matrix(0,2) = -sin(phi);
y_rotation_matrix(2,0) = sin(phi);
y_rotation_matrix(2,2) = cos(phi);
z_rotation_matrix(0,0) = cos(psi);
z_rotation_matrix(0,1) = sin(psi);
z_rotation_matrix(1,0) = -sin(psi);
z_rotation_matrix(1,1) = cos(psi);
translation_matrix(0,3) = 2.3;
translation_matrix(1,3) = 3.1;
translation_matrix(2,3) = 1.7;
/*
Note: because we are using column-major vectors this tranformation:
RotX(theta) . RotY(phi) . RotZ(psi) . Trans(...)
is actually being applied right-to-left
See test below.
*/
c_matrix<double, 4, 4> transformation_matrix = prod (x_rotation_matrix, y_rotation_matrix);
transformation_matrix = prod (transformation_matrix, z_rotation_matrix);
transformation_matrix = prod (transformation_matrix, translation_matrix);
for (unsigned i=0; i<mesh.GetNumNodes(); i++)
{
Node<3>* p_node = mesh.GetNode(i);
ChastePoint<3> point = p_node->GetPoint();
c_vector<double, 4> point_location;
point_location[0] = point[0];
point_location[1] = point[1];
point_location[2] = point[2];
point_location[3] = 1.0;
c_vector<double, 4> new_point_location = prod(transformation_matrix, point_location);
TS_ASSERT_EQUALS(new_point_location[3], 1.0);
point.SetCoordinate(0,new_point_location[0]);
point.SetCoordinate(1,new_point_location[1]);
point.SetCoordinate(2,new_point_location[2]);
p_node->SetPoint(point);
}
mesh.RefreshMesh();
TS_ASSERT_DELTA(mesh.GetVolume(), 1.0, 1e-6);
TS_ASSERT_DELTA(mesh.GetSurfaceArea(), 6.0, 1e-6);
ChastePoint<3> corner_after = mesh.GetNode(6)->GetPoint();
TS_ASSERT_DELTA(corner_after[0], 3.59782, 5e-5);
TS_ASSERT_DELTA(corner_after[1], 0.583418, 5e-5);
TS_ASSERT_DELTA(corner_after[2], 4.65889, 5e-5);
// Write to file
TrianglesMeshWriter<3,3> mesh_writer("","TransformedMesh");
mesh_writer.WriteFilesUsingMesh(mesh);
/*
* Now try
tetview /tmp/chaste/testoutput/TransformedMesh
*/
}
void NodeBasedCellPopulationWithParticles<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
// Store the present time as a string
std::stringstream time;
time << SimulationTime::Instance()->GetTimeStepsElapsed();
// Make sure the nodes are ordered contiguously in memory
NodeMap map(1 + this->mpNodesOnlyMesh->GetMaximumNodeIndex());
this->mpNodesOnlyMesh->ReMesh(map);
// Store the number of cells for which to output data to VTK
unsigned num_nodes = this->GetNumNodes();
std::vector<double> rank(num_nodes);
std::vector<double> particles(num_nodes);
unsigned num_cell_data_items = 0;
std::vector<std::string> cell_data_names;
// We assume that the first cell is representative of all cells
if (num_nodes > 0)
{
num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
cell_data_names = this->Begin()->GetCellData()->GetKeys();
}
std::vector<std::vector<double> > cell_data;
for (unsigned var=0; var<num_cell_data_items; var++)
{
std::vector<double> cell_data_var(num_nodes);
cell_data.push_back(cell_data_var);
}
// Create mesh writer for VTK output
VtkMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results_"+time.str(), false);
mesh_writer.SetParallelFiles(*(this->mpNodesOnlyMesh));
// Iterate over any cell writers that are present
for (typename std::vector<boost::shared_ptr<AbstractCellWriter<DIM, DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_nodes);
// Loop over nodes
for (typename AbstractMesh<DIM,DIM>::NodeIterator node_iter = this->mrMesh.GetNodeIteratorBegin();
node_iter != this->mrMesh.GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
// If this node is a particle (not a cell), then we set the 'dummy' VTK cell data for this to be -2.0...
if (this->IsParticle(node_index))
{
vtk_cell_data[node_index] = -2.0;
}
else
{
// ...otherwise we populate the vector of VTK cell data as usual
CellPtr p_cell = this->GetCellUsingLocationIndex(node_index);
vtk_cell_data[node_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(p_cell, this);
}
}
mesh_writer.AddPointData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// Loop over cells
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
cell_iter != this->End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned global_index = this->GetLocationIndexUsingCell(*cell_iter);
unsigned node_index = this->rGetMesh().SolveNodeMapping(global_index);
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][node_index] = cell_iter->GetCellData()->GetItem(cell_data_names[var]);
}
rank[node_index] = (PetscTools::GetMyRank());
}
mesh_writer.AddPointData("Process rank", rank);
// Loop over nodes
for (typename AbstractMesh<DIM,DIM>::NodeIterator node_iter = this->mrMesh.GetNodeIteratorBegin();
node_iter != this->mrMesh.GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
particles[node_index] = (double) (this->IsParticle(node_index));
}
mesh_writer.AddPointData("Non-particles", particles);
if (num_cell_data_items > 0)
{
for (unsigned var=0; var<cell_data.size(); var++)
{
mesh_writer.AddPointData(cell_data_names[var], cell_data[var]);
}
}
mesh_writer.WriteFilesUsingMesh(*(this->mpNodesOnlyMesh));
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
EXCEPT_IF_NOT(PetscTools::IsSequential());
{
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
}
/* {
// Parallel vtu files .vtu -> .pvtu
*(this->mpVtkMetaFile) << ".pvtu\"/>\n";
}*/
#endif //CHASTE_VTK
}
void MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
// Store the present time as a string
unsigned num_timesteps = SimulationTime::Instance()->GetTimeStepsElapsed();
std::stringstream time;
time << num_timesteps;
// Store the number of cells for which to output data to VTK
unsigned num_cells_from_mesh = GetNumNodes();
if (!mWriteVtkAsPoints && (mpVoronoiTessellation != NULL))
{
num_cells_from_mesh = mpVoronoiTessellation->GetNumElements();
}
// When outputting any CellData, we assume that the first cell is representative of all cells
unsigned num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
std::vector<std::string> cell_data_names = this->Begin()->GetCellData()->GetKeys();
std::vector<std::vector<double> > cell_data;
for (unsigned var=0; var<num_cell_data_items; var++)
{
std::vector<double> cell_data_var(num_cells_from_mesh);
cell_data.push_back(cell_data_var);
}
if (mOutputMeshInVtk)
{
// Create mesh writer for VTK output
VtkMeshWriter<ELEMENT_DIM, SPACE_DIM> mesh_writer(rDirectory, "mesh_"+time.str(), false);
mesh_writer.WriteFilesUsingMesh(rGetMesh());
}
if (mWriteVtkAsPoints)
{
// Create mesh writer for VTK output
VtkMeshWriter<SPACE_DIM, SPACE_DIM> cells_writer(rDirectory, "results_"+time.str(), false);
// Iterate over any cell writers that are present
unsigned num_cells = this->GetNumAllCells();
for (typename std::vector<boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_cells);
// Loop over cells
for (typename AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>::Iterator cell_iter = this->Begin();
cell_iter != this->End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned node_index = this->GetLocationIndexUsingCell(*cell_iter);
// Populate the vector of VTK cell data
vtk_cell_data[node_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(*cell_iter, this);
}
cells_writer.AddPointData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// Loop over cells
for (typename AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>::Iterator cell_iter = this->Begin();
cell_iter != this->End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned node_index = this->GetLocationIndexUsingCell(*cell_iter);
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][node_index] = cell_iter->GetCellData()->GetItem(cell_data_names[var]);
}
}
for (unsigned var=0; var<num_cell_data_items; var++)
{
cells_writer.AddPointData(cell_data_names[var], cell_data[var]);
}
// Make a copy of the nodes in a disposable mesh for writing
{
std::vector<Node<SPACE_DIM>* > nodes;
for (unsigned index=0; index<this->mrMesh.GetNumNodes(); index++)
{
Node<SPACE_DIM>* p_node = this->mrMesh.GetNode(index);
nodes.push_back(p_node);
}
NodesOnlyMesh<SPACE_DIM> mesh;
mesh.ConstructNodesWithoutMesh(nodes, 1.5); // Arbitrary cut off as connectivity not used.
cells_writer.WriteFilesUsingMesh(mesh);
}
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
}
else if (mpVoronoiTessellation != NULL)
{
// Create mesh writer for VTK output
VertexMeshWriter<ELEMENT_DIM, SPACE_DIM> mesh_writer(rDirectory, "results", false);
std::vector<double> cell_volumes(num_cells_from_mesh);
// Iterate over any cell writers that are present
unsigned num_cells = this->GetNumAllCells();
for (typename std::vector<boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_cells);
// Loop over elements of mpVoronoiTessellation
for (typename VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator elem_iter = mpVoronoiTessellation->GetElementIteratorBegin();
elem_iter != mpVoronoiTessellation->GetElementIteratorEnd();
++elem_iter)
{
// Get index of this element in mpVoronoiTessellation
unsigned elem_index = elem_iter->GetIndex();
// Get the cell corresponding to this element, via the index of the corresponding node in mrMesh
unsigned node_index = mpVoronoiTessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);
CellPtr p_cell = this->GetCellUsingLocationIndex(node_index);
// Populate the vector of VTK cell data
vtk_cell_data[elem_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(p_cell, this);
}
mesh_writer.AddCellData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// Loop over elements of mpVoronoiTessellation
for (typename VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator elem_iter = mpVoronoiTessellation->GetElementIteratorBegin();
elem_iter != mpVoronoiTessellation->GetElementIteratorEnd();
++elem_iter)
{
// Get index of this element in mpVoronoiTessellation
unsigned elem_index = elem_iter->GetIndex();
// Get the cell corresponding to this element, via the index of the corresponding node in mrMesh
unsigned node_index = mpVoronoiTessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);
CellPtr p_cell = this->GetCellUsingLocationIndex(node_index);
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][elem_index] = p_cell->GetCellData()->GetItem(cell_data_names[var]);
}
}
for (unsigned var=0; var<cell_data.size(); var++)
{
mesh_writer.AddCellData(cell_data_names[var], cell_data[var]);
}
mesh_writer.WriteVtkUsingMesh(*mpVoronoiTessellation, time.str());
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
}
#endif //CHASTE_VTK
}
void NodeBasedCellPopulation<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
std::stringstream time;
time << SimulationTime::Instance()->GetTimeStepsElapsed();
VtkMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results_"+time.str(), false);
// Make sure the nodes are ordered contiguously in memory.
NodeMap map(1 + this->mpNodesOnlyMesh->GetMaximumNodeIndex());
this->mpNodesOnlyMesh->ReMesh(map);
mesh_writer.SetParallelFiles(*mpNodesOnlyMesh);
unsigned num_nodes = GetNumNodes();
std::vector<double> cell_types(num_nodes);
std::vector<double> cell_ancestors(num_nodes);
std::vector<double> cell_mutation_states(num_nodes);
std::vector<double> cell_ages(num_nodes);
std::vector<double> cell_cycle_phases(num_nodes);
std::vector<double> cell_radii(num_nodes);
std::vector<std::vector<double> > cellwise_data;
std::vector<double> rank(num_nodes);
unsigned num_cell_data_items = 0;
std::vector<std::string> cell_data_names;
// We assume that the first cell is representative of all cells
if (num_nodes > 0)
{
num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
cell_data_names = this->Begin()->GetCellData()->GetKeys();
}
for (unsigned var=0; var<num_cell_data_items; var++)
{
std::vector<double> cellwise_data_var(num_nodes);
cellwise_data.push_back(cellwise_data_var);
}
// Loop over cells
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
cell_iter != this->End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned global_index = this->GetLocationIndexUsingCell(*cell_iter);
Node<DIM>* p_node = this->GetNode(global_index);
unsigned node_index = this->rGetMesh().SolveNodeMapping(global_index);
if (this-> template HasWriter<CellAncestorWriter>())
{
double ancestor_index = (cell_iter->GetAncestor() == UNSIGNED_UNSET) ? (-1.0) : (double)cell_iter->GetAncestor();
cell_ancestors[node_index] = ancestor_index;
}
if (this-> template HasWriter<CellProliferativeTypesWriter>())
{
double cell_type = cell_iter->GetCellProliferativeType()->GetColour();
cell_types[node_index] = cell_type;
}
if (this-> template HasWriter<CellMutationStatesCountWriter>())
{
double mutation_state = cell_iter->GetMutationState()->GetColour();
CellPropertyCollection collection = cell_iter->rGetCellPropertyCollection();
CellPropertyCollection label_collection = collection.GetProperties<CellLabel>();
if (label_collection.GetSize() == 1)
{
boost::shared_ptr<CellLabel> p_label = boost::static_pointer_cast<CellLabel>(label_collection.GetProperty());
mutation_state = p_label->GetColour();
}
cell_mutation_states[node_index] = mutation_state;
}
if (this-> template HasWriter<CellAgesWriter>())
{
double age = cell_iter->GetAge();
cell_ages[node_index] = age;
}
if (this-> template HasWriter<CellProliferativePhasesWriter>())
{
double cycle_phase = cell_iter->GetCellCycleModel()->GetCurrentCellCyclePhase();
cell_cycle_phases[node_index] = cycle_phase;
}
if (this-> template HasWriter<CellVolumesWriter>())
{
double cell_radius = p_node->GetRadius();
cell_radii[node_index] = cell_radius;
}
for (unsigned var=0; var<num_cell_data_items; var++)
{
cellwise_data[var][node_index] = cell_iter->GetCellData()->GetItem(cell_data_names[var]);
}
rank[node_index] = (PetscTools::GetMyRank());
}
mesh_writer.AddPointData("Process rank", rank);
if (this-> template HasWriter<CellProliferativeTypesWriter>())
{
mesh_writer.AddPointData("Cell types", cell_types);
}
if (this-> template HasWriter<CellAncestorWriter>())
{
mesh_writer.AddPointData("Ancestors", cell_ancestors);
}
if (this-> template HasWriter<CellMutationStatesCountWriter>())
{
mesh_writer.AddPointData("Mutation states", cell_mutation_states);
}
if (this-> template HasWriter<CellAgesWriter>())
{
mesh_writer.AddPointData("Ages", cell_ages);
}
if (this-> template HasWriter<CellProliferativePhasesWriter>())
{
mesh_writer.AddPointData("Cycle phases", cell_cycle_phases);
}
if (this-> template HasWriter<CellVolumesWriter>())
{
mesh_writer.AddPointData("Cell radii", cell_radii);
}
if (num_cell_data_items > 0)
{
for (unsigned var=0; var<cellwise_data.size(); var++)
{
mesh_writer.AddPointData(cell_data_names[var], cellwise_data[var]);
}
}
mesh_writer.WriteFilesUsingMesh(*mpNodesOnlyMesh);
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
#endif //CHASTE_VTK
}
void PottsBasedCellPopulation<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
unsigned num_timesteps = SimulationTime::Instance()->GetTimeStepsElapsed();
std::stringstream time;
time << num_timesteps;
// Create mesh writer for VTK output
VtkMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results_"+time.str(), false);
// Iterate over any cell writers that are present
unsigned num_nodes = GetNumNodes();
for (typename std::set<boost::shared_ptr<AbstractCellWriter<DIM, DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_nodes);
// Iterate over nodes in the mesh
for (typename AbstractMesh<DIM,DIM>::NodeIterator iter = mpPottsMesh->GetNodeIteratorBegin();
iter != mpPottsMesh->GetNodeIteratorEnd();
++iter)
{
// Get the index of this node in the mesh and those elements (i.e. cells) that contain this node
unsigned node_index = iter->GetIndex();
std::set<unsigned> element_indices = iter->rGetContainingElementIndices();
// If there are no elements associated with this node, then we set the value of any VTK cell data to be -1 at this node...
if (element_indices.empty())
{
// Populate the vector of VTK cell data
vtk_cell_data[node_index] = -1.0;
}
else
{
// ... otherwise there should be exactly one element (i.e. cell) containing this node
assert(element_indices.size() == 1);
unsigned elem_index = *(element_indices.begin());
CellPtr p_cell = this->GetCellUsingLocationIndex(elem_index);
// Populate the vector of VTK cell data
vtk_cell_data[node_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(p_cell, this);
}
}
mesh_writer.AddPointData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// When outputting any CellData, we assume that the first cell is representative of all cells
unsigned num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
std::vector<std::string> cell_data_names = this->Begin()->GetCellData()->GetKeys();
std::vector<std::vector<double> > cell_data;
for (unsigned var=0; var<num_cell_data_items; var++)
{
std::vector<double> cell_data_var(num_nodes);
cell_data.push_back(cell_data_var);
}
for (typename AbstractMesh<DIM,DIM>::NodeIterator iter = mpPottsMesh->GetNodeIteratorBegin();
iter != mpPottsMesh->GetNodeIteratorEnd();
++iter)
{
// Get the index of this node in the mesh and those elements (i.e. cells) that contain this node
unsigned node_index = iter->GetIndex();
std::set<unsigned> element_indices = iter->rGetContainingElementIndices();
// If there are no elements associated with this node, then we set the value of any VTK cell data to be -1 at this node...
if (element_indices.empty())
{
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][node_index] = -1.0;
}
}
else
{
// ... otherwise there should be exactly one element (i.e. cell) containing this node
assert(element_indices.size() == 1);
unsigned elem_index = *(element_indices.begin());
CellPtr p_cell = this->GetCellUsingLocationIndex(elem_index);
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][node_index] = p_cell->GetCellData()->GetItem(cell_data_names[var]);
}
}
}
for (unsigned var=0; var<cell_data.size(); var++)
{
mesh_writer.AddPointData(cell_data_names[var], cell_data[var]);
}
/*
* The current VTK writer can only write things which inherit from AbstractTetrahedralMeshWriter.
* For now, we do an explicit conversion to NodesOnlyMesh. This can be written to VTK then visualized as glyphs.
*/
NodesOnlyMesh<DIM> temp_mesh;
temp_mesh.ConstructNodesWithoutMesh(*mpPottsMesh, 1.5); // This cut-off is arbitrary, as node connectivity is not used here
mesh_writer.WriteFilesUsingMesh(temp_mesh);
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
#endif //CHASTE_VTK
}
void TestTessellationConstructor() throw (Exception)
{
// Create a simple Cylindrical2dMesh, the Delaunay triangulation
unsigned cells_across = 3;
unsigned cells_up = 3;
unsigned thickness_of_ghost_layer = 0;
CylindricalHoneycombMeshGenerator generator(cells_across, cells_up, thickness_of_ghost_layer);
Cylindrical2dMesh* p_delaunay_mesh = generator.GetCylindricalMesh();
TrianglesMeshWriter<2,2> mesh_writer("TestVertexMeshWriters", "DelaunayMesh", false);
TS_ASSERT_THROWS_NOTHING(mesh_writer.WriteFilesUsingMesh(*p_delaunay_mesh));
TS_ASSERT_EQUALS(p_delaunay_mesh->GetWidth(0), 3u);
TS_ASSERT_EQUALS(p_delaunay_mesh->CheckIsVoronoi(), true);
TS_ASSERT_EQUALS(p_delaunay_mesh->GetNumElements(), 12u);
TS_ASSERT_EQUALS(p_delaunay_mesh->GetNumNodes(), 9u);
// Create a vertex mesh, the Voronoi tessellation, using the tetrahedral mesh
Cylindrical2dVertexMesh voronoi_mesh(*p_delaunay_mesh);
VertexMeshWriter<2,2> vertexmesh_writer("TestVertexMeshWriters", "VertexMesh", false);
TS_ASSERT_THROWS_NOTHING(vertexmesh_writer.WriteFilesUsingMesh(voronoi_mesh));
// Test the Voronoi tessellation has the correct number of nodes and elements
TS_ASSERT_EQUALS(voronoi_mesh.GetWidth(0), 3u);
TS_ASSERT_EQUALS(voronoi_mesh.GetNumElements(), 9u);
TS_ASSERT_EQUALS(voronoi_mesh.GetNumNodes(), 12u);
//
// Test the location of the Voronoi nodes
/* These are ordered from right to left from bottom to top as
* 10 1 0 5 4 6 9 2 3 11 7 8
* Due to the numbering of the elements in the generator.
*/
TS_ASSERT_DELTA(voronoi_mesh.GetNode(10)->rGetLocation()[0], 3.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(10)->rGetLocation()[1], sqrt(3.0)/3.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(1)->rGetLocation()[0], 0.5, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(1)->rGetLocation()[1], sqrt(3.0)/6.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(0)->rGetLocation()[0], 1.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(0)->rGetLocation()[1], sqrt(3.0)/3.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(5)->rGetLocation()[0], 1.5, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(5)->rGetLocation()[1], sqrt(3.0)/6.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(4)->rGetLocation()[0], 2.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(4)->rGetLocation()[1], sqrt(3.0)/3.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(6)->rGetLocation()[0], 2.5, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(6)->rGetLocation()[1], sqrt(3.0)/6.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(9)->rGetLocation()[0], 0.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(9)->rGetLocation()[1], 2.0*sqrt(3.0)/3.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(2)->rGetLocation()[0], 0.5, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(2)->rGetLocation()[1], 5.0*sqrt(3.0)/6.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(3)->rGetLocation()[0], 1.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(3)->rGetLocation()[1], 2.0*sqrt(3.0)/3.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(11)->rGetLocation()[0], 1.5, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(11)->rGetLocation()[1], 5.0*sqrt(3.0)/6.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(7)->rGetLocation()[0], 2.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(7)->rGetLocation()[1], 2.0*sqrt(3.0)/3.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(8)->rGetLocation()[0], 2.5, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetNode(8)->rGetLocation()[1], 5.0*sqrt(3.0)/6.0, 1e-6);
// Test the number of nodes owned by each Voronoi element
TS_ASSERT_EQUALS(voronoi_mesh.GetElement(0)->GetNumNodes(), 3u);
TS_ASSERT_EQUALS(voronoi_mesh.GetElement(1)->GetNumNodes(), 3u);
TS_ASSERT_EQUALS(voronoi_mesh.GetElement(2)->GetNumNodes(), 3u);
TS_ASSERT_EQUALS(voronoi_mesh.GetElement(3)->GetNumNodes(), 6u);
TS_ASSERT_EQUALS(voronoi_mesh.GetElement(4)->GetNumNodes(), 6u);
TS_ASSERT_EQUALS(voronoi_mesh.GetElement(5)->GetNumNodes(), 6u);
TS_ASSERT_EQUALS(voronoi_mesh.GetElement(6)->GetNumNodes(), 3u);
TS_ASSERT_EQUALS(voronoi_mesh.GetElement(7)->GetNumNodes(), 3u);
TS_ASSERT_EQUALS(voronoi_mesh.GetElement(8)->GetNumNodes(), 3u);
// Test element areas
TS_ASSERT_DELTA(voronoi_mesh.GetVolumeOfElement(0), sqrt(3.0)/12.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetVolumeOfElement(1), sqrt(3.0)/12.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetVolumeOfElement(2), sqrt(3.0)/12.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetVolumeOfElement(3), sqrt(3.0)/2.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetVolumeOfElement(4), sqrt(3.0)/2.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetVolumeOfElement(5), sqrt(3.0)/2.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetVolumeOfElement(6), sqrt(3.0)/12.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetVolumeOfElement(7), sqrt(3.0)/12.0, 1e-6);
TS_ASSERT_DELTA(voronoi_mesh.GetVolumeOfElement(8), sqrt(3.0)/12.0, 1e-6);
}
void VtkNonlinearElasticitySolutionWriter<DIM>::Write()
{
if (mpSolver->mOutputDirectory=="")
{
EXCEPTION("No output directory was given to the mechanics solver");
}
#ifdef CHASTE_VTK
VtkMeshWriter<DIM, DIM> mesh_writer(mpSolver->mOutputDirectory + "/vtk", "solution", true);
// write the displacement
std::vector<c_vector<double,DIM> > displacement(mpSolver->mrQuadMesh.GetNumNodes());
std::vector<c_vector<double,DIM> >& r_spatial_solution = mpSolver->rGetSpatialSolution();
for(unsigned i=0; i<mpSolver->mrQuadMesh.GetNumNodes(); i++)
{
for(unsigned j=0; j<DIM; j++)
{
displacement[i](j) = r_spatial_solution[i](j)- mpSolver->mrQuadMesh.GetNode(i)->rGetLocation()[j];
}
}
mesh_writer.AddPointData("Displacement", displacement);
// write pressures
if (mpSolver->mCompressibilityType==INCOMPRESSIBLE)
{
mesh_writer.AddPointData("Pressure", mpSolver->rGetPressures());
}
// write the element attribute as cell data.
std::vector<double> element_attribute;
for(typename QuadraticMesh<DIM>::ElementIterator iter = mpSolver->mrQuadMesh.GetElementIteratorBegin();
iter != mpSolver->mrQuadMesh.GetElementIteratorEnd();
++iter)
{
element_attribute.push_back(iter->GetAttribute());
}
mesh_writer.AddCellData("Attribute", element_attribute);
// write strains if requested
if (mWriteElementWiseStrains)
{
mTensorData.clear();
mTensorData.resize(mpSolver->mrQuadMesh.GetNumElements());
std::string name;
switch(mElementWiseStrainType)
{
case DEFORMATION_GRADIENT_F:
{
name = "deformation_gradient_F";
break;
}
case DEFORMATION_TENSOR_C:
{
name = "deformation_tensor_C";
break;
}
case LAGRANGE_STRAIN_E:
{
name = "Lagrange_strain_E";
break;
}
default:
{
NEVER_REACHED;
}
}
for (typename AbstractTetrahedralMesh<DIM,DIM>::ElementIterator iter = mpSolver->mrQuadMesh.GetElementIteratorBegin();
iter != mpSolver->mrQuadMesh.GetElementIteratorEnd();
++iter)
{
mpSolver->GetElementCentroidStrain(mElementWiseStrainType, *iter, mTensorData[iter->GetIndex()]);
}
mesh_writer.AddTensorCellData(name, mTensorData);
}
//// Future..
// if (mWriteNodeWiseStresses)
// {
// std::vector<c_matrix<double,DIM,DIM> > tensor_data;
// // use recoverer
// mesh_writer.AddTensorCellData("Stress_NAME_ME", tensor_data);
// }
// final write
mesh_writer.WriteFilesUsingMesh(mpSolver->mrQuadMesh);
#endif // CHASTE_VTK
}
void VertexBasedCellPopulation<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
// Create mesh writer for VTK output
VertexMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results", false);
// Iterate over any cell writers that are present
unsigned num_cells = this->GetNumAllCells();
for (typename std::vector<boost::shared_ptr<AbstractCellWriter<DIM, DIM> > >::iterator cell_writer_iter = this->mCellWriters.begin();
cell_writer_iter != this->mCellWriters.end();
++cell_writer_iter)
{
// Create vector to store VTK cell data
std::vector<double> vtk_cell_data(num_cells);
// Iterate over vertex elements ///\todo #2512 - replace with loop over cells
for (typename VertexMesh<DIM,DIM>::VertexElementIterator elem_iter = mpMutableVertexMesh->GetElementIteratorBegin();
elem_iter != mpMutableVertexMesh->GetElementIteratorEnd();
++elem_iter)
{
// Get index of this element in the vertex mesh
unsigned elem_index = elem_iter->GetIndex();
// Get the cell corresponding to this element
CellPtr p_cell = this->GetCellUsingLocationIndex(elem_index);
assert(p_cell);
// Populate the vector of VTK cell data
vtk_cell_data[elem_index] = (*cell_writer_iter)->GetCellDataForVtkOutput(p_cell, this);
}
mesh_writer.AddCellData((*cell_writer_iter)->GetVtkCellDataName(), vtk_cell_data);
}
// When outputting any CellData, we assume that the first cell is representative of all cells
unsigned num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
std::vector<std::string> cell_data_names = this->Begin()->GetCellData()->GetKeys();
std::vector<std::vector<double> > cell_data;
for (unsigned var=0; var<num_cell_data_items; var++)
{
std::vector<double> cell_data_var(num_cells);
cell_data.push_back(cell_data_var);
}
// Loop over vertex elements ///\todo #2512 - replace with loop over cells
for (typename VertexMesh<DIM,DIM>::VertexElementIterator elem_iter = mpMutableVertexMesh->GetElementIteratorBegin();
elem_iter != mpMutableVertexMesh->GetElementIteratorEnd();
++elem_iter)
{
// Get index of this element in the vertex mesh
unsigned elem_index = elem_iter->GetIndex();
// Get the cell corresponding to this element
CellPtr p_cell = this->GetCellUsingLocationIndex(elem_index);
assert(p_cell);
for (unsigned var=0; var<num_cell_data_items; var++)
{
cell_data[var][elem_index] = p_cell->GetCellData()->GetItem(cell_data_names[var]);
}
}
for (unsigned var=0; var<num_cell_data_items; var++)
{
mesh_writer.AddCellData(cell_data_names[var], cell_data[var]);
}
unsigned num_timesteps = SimulationTime::Instance()->GetTimeStepsElapsed();
std::stringstream time;
time << num_timesteps;
mesh_writer.WriteVtkUsingMesh(*mpMutableVertexMesh, time.str());
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << num_timesteps;
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
#endif //CHASTE_VTK
}