def get_cell_function(mesh: df.Mesh) -> df.MeshFunction: """Return a cell function intended for multi cell model.""" mesh_function = df.MeshFunction("size_t", mesh, mesh.geometry().dim()) mesh_function.set_all(1) # df.CompiledSubDomain("x[0] < 0.05").mark(mesh_function, 12) df.CompiledSubDomain("x[0] > 5.0").mark(mesh_function, 12) return mesh_function
def read_fenics_solution(filepath): from dolfin import (Mesh, XDMFFile, MeshValueCollection, cpp, FunctionSpace, Function, HDF5File, MPI) mesh = Mesh() with XDMFFile("%s_triangle.xdmf" % filepath.split('.')[0]) as infile: infile.read(mesh) # read the complete mesh #mvc_subdo = MeshValueCollection("size_t", mesh, mesh.geometric_dimension() - 1) #with XDMFFile("%s_triangle.xdmf" % filepath.split('.')[0]) as infile: # infile.read(mvc_subdo, "subdomains") # read the diferent subdomians #subdomains = cpp.mesh.MeshFunctionSizet(mesh, mvc_subdo) #mvc = MeshValueCollection("size_t", mesh, mesh.geometric_dimension() - 2) #with XDMFFile("%s_line.xdmf" % filepath.split('.')[0]) as infile: # infile.read(mvc, "boundary_conditions") # read the boundary conditions #boundary = cpp.mesh.MeshFunctionSizet(mesh, mvc) # Define function space and basis functions V = FunctionSpace(mesh, "CG", 1) U = Function(V) input_file = HDF5File(MPI.comm_world, filepath.split('.')[0] + "_solution_field.h5", "r") input_file.read(U, "solution") input_file.close() dofs = V.tabulate_dof_coordinates().reshape( V.dim(), mesh.geometry().dim()) # coordinates of nodes U.set_allow_extrapolation(True) return U, mesh, dofs.shape[0]
def mesh_around_1d(mesh, size=1, scale=10, padding=0.05): ''' From a 1d in xd (X > 1) mesh (in XML format) produce a Xd mesh where the 1d structure is embedded. Mesh size close to strucure should be size(given as multiple of hmin(), elsewhere scale * size. Padding controls size of the bounding box. ''' dot = mesh.find('.') root, ext = mesh[:dot], mesh[dot:] assert ext == '.xml' or ext == '.xml.gz', ext mesh = Mesh(mesh) gdim = mesh.geometry().dim() assert gdim > 1 and mesh.topology().dim() == 1 x = mesh.coordinates() mesh.init(1, 0) # Compute fall back mesh size: assert size > 0 size = mesh.hmin() * size # Don't allow zero padding - collision of lines with bdry segfaults # too ofter so we prevent it assert padding > 0 # Finally scale better be positive assert scale > 0 point = (lambda xi: tuple(xi) + (0, ))\ if gdim == 2 else (lambda xi: tuple(xi)) geo = '.'.join([root, 'geo']) with open(geo, 'w') as outfile: # Setup outfile.write('SetFactory("OpenCASCADE");\n') outfile.write('size = %g;\n' % size) outfile.write('SIZE = %g;\n' % (size * scale)) # Points fmt = 'Point(%d) = {%.16f, %.16f, %.16f, size};\n' for i, xi in enumerate(x, 1): outfile.write(fmt % ((i, ) + point(xi))) # Lines fmt = 'Line(%d) = {%d, %d};\n' for i, cell in enumerate(cells(mesh), 1): outfile.write(fmt % ((i, ) + tuple(cell.entities(0) + 1))) # BBox xmin, xmax = x.min(0), x.max(0) padding = (xmax - xmin) * padding / 2. xmin -= padding xmax += padding dx = xmax - xmin if gdim == 2 or dx[-1] < 1E-14: # All points are on a plane rect = 'Rectangle(1) = {%g, %g, %g, %g, %g};\n' % ( xmin[0], xmin[1], 0 if gdim == 2 else xmin[2], dx[0], dx[1]) outfile.write(rect) bbox = 'Surface' else: box = 'Box(1) = {%g, %g, %g, %g, %g, %g};\n' % ( xmin[0], xmin[1], xmin[2], dx[0], dx[1], dx[2]) outfile.write(box) bbox = 'Volume' # Crack for line in xrange(1, mesh.num_cells() + 1): outfile.write('Line{%d} In %s{1};\n' % (line, bbox)) # Add Physical volume/surface outfile.write('Physical %s(1) = {1};\n' % bbox) # Add Physical surface/line lines = ', '.join( map(lambda v: '%d' % v, xrange(1, mesh.num_cells() + 1))) outfile.write('Physical Line(1) = {%s};\n' % lines) return geo, gdim
def run_simulation( filepath, topology_info: int = None, top_bc: int = None, bot_bc: int = None, left_bc: int = None, right_bc: int = None, geometry: dict = None, kappa=3, #only if geometry is None show=True, save_solution=False): from dolfin import (Mesh, XDMFFile, MeshValueCollection, cpp, FunctionSpace, TrialFunction, TestFunction, DirichletBC, Constant, Measure, inner, nabla_grad, Function, solve, plot, File) mesh = Mesh() with XDMFFile("%s_triangle.xdmf" % filepath.split('.')[0]) as infile: infile.read(mesh) # read the complete mesh mvc_subdo = MeshValueCollection("size_t", mesh, mesh.geometric_dimension() - 1) with XDMFFile("%s_triangle.xdmf" % filepath.split('.')[0]) as infile: infile.read(mvc_subdo, "subdomains") # read the diferent subdomians subdomains = cpp.mesh.MeshFunctionSizet(mesh, mvc_subdo) mvc = MeshValueCollection("size_t", mesh, mesh.geometric_dimension() - 2) with XDMFFile("%s_line.xdmf" % filepath.split('.')[0]) as infile: infile.read(mvc, "boundary_conditions") #read the boundary conditions boundary = cpp.mesh.MeshFunctionSizet(mesh, mvc) # Define function space and basis functions V = FunctionSpace(mesh, "CG", 1) u = TrialFunction(V) v = TestFunction(V) # Boundary conditions bcs = [] for bc_id in topology_info.keys(): if bc_id[-2:] == "bc": if bot_bc is not None and bc_id[:3] == "bot": bcs.append( DirichletBC(V, Constant(bot_bc), boundary, topology_info[bc_id])) elif left_bc is not None and bc_id[:4] == "left": bcs.append( DirichletBC(V, Constant(left_bc), boundary, topology_info[bc_id])) elif top_bc is not None and bc_id[:3] == "top": bcs.append( DirichletBC(V, Constant(top_bc), boundary, topology_info[bc_id])) elif right_bc is not None and bc_id[:5] == "right": bcs.append( DirichletBC(V, Constant(right_bc), boundary, topology_info[bc_id])) else: print(bc_id + " Not assigned as boundary condition ") # raise NotImplementedError # Define new measures associated with the interior domains and # exterior boundaries dx = Measure("dx", subdomain_data=subdomains) ds = Measure("ds", subdomain_data=boundary) f = Constant(0) g = Constant(0) if geometry is not None: # run multipatch implementation (Multiple domains) a = [] L = [] for patch_id in geometry.keys(): kappa = geometry[patch_id].get("kappa") a.append( inner(Constant(kappa) * nabla_grad(u), nabla_grad(v)) * dx(topology_info[patch_id])) L.append(f * v * dx(topology_info[patch_id])) a = sum(a) L = sum(L) else: a = inner(Constant(kappa) * nabla_grad(u), nabla_grad(v)) * dx L = f * v * dx ## Redefine u as a function in function space V for the solution u = Function(V) # Solve solve(a == L, u, bcs) u.rename('u', 'Temperature') # Save solution to file in VTK format print(' [+] Output to %s_solution.pvd' % filepath.split('.')[0]) vtkfile = File('%s_solution.pvd' % filepath.split('.')[0]) vtkfile << u if show: import matplotlib matplotlib.use("Qt5Agg") # Plot solution and gradient plot(u, title="Temperature") plt.gca().view_init(azim=-90, elev=90) plt.show() dofs = V.tabulate_dof_coordinates().reshape( V.dim(), mesh.geometry().dim()) #coordinates of nodes vals = u.vector().get_local() #temperature at nodes if save_solution: from dolfin import HDF5File, MPI output_file = HDF5File(MPI.comm_world, filepath.split('.')[0] + "_solution_field.h5", "w") output_file.write(u, "solution") output_file.close() u.set_allow_extrapolation(True) return dofs, vals, mesh, u