void TestMeshGetWidth()
{
// Create mesh
CylindricalHoneycombVertexMeshGenerator generator(4, 4);
Cylindrical2dVertexMesh* p_mesh = generator.GetCylindricalMesh();
// Test CalculateBoundingBox() method
ChasteCuboid<2> bounds = p_mesh->CalculateBoundingBox();
///\todo this should really be 4 as mesh is periodic
TS_ASSERT_DELTA(bounds.rGetUpperCorner()[0], 3.5, 1e-4);
TS_ASSERT_DELTA(bounds.rGetUpperCorner()[1], 13.0*0.5/sqrt(3.0), 1e-4);
TS_ASSERT_DELTA(bounds.rGetLowerCorner()[0], 0.0, 1e-4);
TS_ASSERT_DELTA(bounds.rGetLowerCorner()[1], 0.0, 1e-4);
// Test GetWidth() method
double width = p_mesh->GetWidth(0);
double height = p_mesh->GetWidth(1);
TS_ASSERT_DELTA(width, 4, 1e-4);
TS_ASSERT_DELTA(height, 13.0*0.5/sqrt(3.0), 1e-4);
//Scale mesh and check its updated correctly
p_mesh->Scale(0.5,1.0);
TS_ASSERT_DELTA(p_mesh->GetWidth(0), 2, 1e-4);
}
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 CellBasedPdeHandler<DIM>::UseCoarsePdeMesh(double stepSize, ChasteCuboid<DIM> meshCuboid, bool centreOnCellPopulation)
{
if (mPdeAndBcCollection.empty())
{
EXCEPTION("mPdeAndBcCollection should be populated prior to calling UseCoarsePdeMesh().");
}
// If solving PDEs on a coarse mesh, each PDE must have an averaged source term
for (unsigned pde_index=0; pde_index<mPdeAndBcCollection.size(); pde_index++)
{
if (mPdeAndBcCollection[pde_index]->HasAveragedSourcePde() == false && !dynamic_cast<MultipleCaBasedCellPopulation<DIM>*>(mpCellPopulation))
{
EXCEPTION("UseCoarsePdeMesh() should only be called if averaged-source PDEs are specified.");
}
}
// Create a regular coarse tetrahedral mesh
mpCoarsePdeMesh = new TetrahedralMesh<DIM,DIM>;
switch (DIM)
{
case 1:
mpCoarsePdeMesh->ConstructRegularSlabMesh(stepSize, meshCuboid.GetWidth(0));
break;
case 2:
mpCoarsePdeMesh->ConstructRegularSlabMesh(stepSize, meshCuboid.GetWidth(0), meshCuboid.GetWidth(1));
break;
case 3:
mpCoarsePdeMesh->ConstructRegularSlabMesh(stepSize, meshCuboid.GetWidth(0), meshCuboid.GetWidth(1), meshCuboid.GetWidth(2));
break;
default:
NEVER_REACHED;
}
if (centreOnCellPopulation)
{
// Find the centre of the coarse PDE mesh
c_vector<double,DIM> centre_of_coarse_mesh = zero_vector<double>(DIM);
for (unsigned i=0; i<mpCoarsePdeMesh->GetNumNodes(); i++)
{
centre_of_coarse_mesh += mpCoarsePdeMesh->GetNode(i)->rGetLocation();
}
centre_of_coarse_mesh /= mpCoarsePdeMesh->GetNumNodes();
// Translate the centre of coarse PDE mesh to the centre of the cell population
c_vector<double,DIM> centre_of_cell_population = mpCellPopulation->GetCentroidOfCellPopulation();
mpCoarsePdeMesh->Translate(centre_of_cell_population - centre_of_coarse_mesh);
}
else
{
// Get centroid of meshCuboid
ChastePoint<DIM> upper = meshCuboid.rGetUpperCorner();
ChastePoint<DIM> lower = meshCuboid.rGetLowerCorner();
c_vector<double,DIM> centre_of_cuboid = 0.5*(upper.rGetLocation() + lower.rGetLocation());
// Find the centre of the coarse PDE mesh
c_vector<double,DIM> centre_of_coarse_mesh = zero_vector<double>(DIM);
for (unsigned i=0; i<mpCoarsePdeMesh->GetNumNodes(); i++)
{
centre_of_coarse_mesh += mpCoarsePdeMesh->GetNode(i)->rGetLocation();
}
centre_of_coarse_mesh /= mpCoarsePdeMesh->GetNumNodes();
mpCoarsePdeMesh->Translate(centre_of_cuboid - centre_of_coarse_mesh);
}
}
