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
