f = Function(V)
dt_inv = Constant(1 / dt)
diffusion_source = 1
diffusion_drain = 1
if args.source:
F = dt_inv * (u - u_n) * v * dx - (f - u_ini) * v * dx + diffusion_source * inner(grad(u), grad(v)) * dx
elif args.drain:
F = dt_inv * (u - u_n) * v * dx - (f - u) * v * dx + diffusion_drain * inner(grad(u), grad(v)) * dx
# Time-stepping
u_np1 = Function(V)
if args.source:
u_n.rename("Source-Data", "")
u_np1.rename("Source-Data", "")
elif args.drain:
u_n.rename("Drain-Data", "")
u_np1.rename("Drain-Data", "")
t = 0
mesh_rank = MeshFunction("size_t", mesh, mesh.topology().dim())
if args.source:
mesh_rank.set_all(MPI.rank(MPI.comm_world) + 4)
else:
mesh_rank.set_all(MPI.rank(MPI.comm_world) + 0)
mesh_rank.rename("myRank", "")
# Generating output files
gamma=gamma,
t=0)
F = u * v / dt * dx + dot(grad(u), grad(v)) * dx - (u_n / dt + f) * v * dx
if problem is ProblemType.DIRICHLET:
# apply Dirichlet boundary condition on coupling interface
bcs.append(precice.create_coupling_dirichlet_boundary_condition(V))
if problem is ProblemType.NEUMANN:
# apply Neumann boundary condition on coupling interface, modify weak form correspondingly
F += precice.create_coupling_neumann_boundary_condition(v)
a, L = lhs(F), rhs(F)
# Time-stepping
u_np1 = Function(V)
u_np1.rename("Temperature", "")
t = 0
# reference solution at t=0
u_ref = interpolate(u_D, V)
u_ref.rename("reference", " ")
temperature_out = File("out/%s.pvd" % precice.get_solver_name())
ref_out = File("out/ref%s.pvd" % precice.get_solver_name())
error_out = File("out/error%s.pvd" % precice.get_solver_name())
# output solution and reference solution at t=0, n=0
n = 0
print('output u^%d and u_ref^%d' % (n, n))
temperature_out << u_n
ref_out << u_ref
# mark mesh w.r.t ranks
ranks = File("output/ranks%s.pvd.pvd" % precice.get_participant_name())
mesh_rank = MeshFunction("size_t", mesh, mesh.topology().dim())
mesh_rank.set_all(MPI.rank(MPI.comm_world))
mesh_rank.rename("myRank", "")
ranks << mesh_rank
# Create output file
file_out = File("output/%s.pvd" % precice.get_participant_name())
file_out << u_n
print("output vtk for time = {}".format(float(t)))
n = 0
fluxes = Function(V_g)
fluxes.rename("Fluxes", "")
while precice.is_coupling_ongoing():
if precice.is_action_required(
precice.action_write_iteration_checkpoint()): # write checkpoint
precice.store_checkpoint(u_n, t, n)
read_data = precice.read_data()
# Update the coupling expression with the new read data
precice.update_coupling_expression(coupling_expression, read_data)
dt.assign(np.min([fenics_dt, precice_dt]))
# Compute solution
a_np1 = update_a(du, u_n, v_n, a_n, ufl=True)
v_np1 = update_v(a_np1, u_n, v_n, a_n, ufl=True)
res = m(avg(a_n, a_np1, alpha_m), v) + k(avg(u_n, du, alpha_f), v)
a_form = lhs(res)
L_form = rhs(res)
# parameters for Time-Stepping
t = 0.0
n = 0
E_ext = 0
displacement_out = File("output/u_fsi.pvd")
u_n.rename("Displacement", "")
u_np1.rename("Displacement", "")
displacement_out << u_n
while precice.is_coupling_ongoing():
if precice.is_action_required(
precice.action_write_iteration_checkpoint()): # write checkpoint
precice.store_checkpoint(u_n, t, n)
# read data from preCICE and get a new coupling expression
read_data = precice.read_data()
# Update the point sources on the coupling boundary with the new read data
Forces_x, Forces_y = precice.get_point_sources(read_data)
# Define variational problem
u = TrialFunction(V)
v = TestFunction(V)
F = u * v / dt * dx + alpha * dot(grad(u), grad(v)) * dx - u_n * v / dt * dx
# apply Dirichlet boundary condition on coupling interface
bcs.append(precice.create_coupling_dirichlet_boundary_condition(V))
a, L = lhs(F), rhs(F)
# Time-stepping
u_np1 = Function(V)
F_known_u = u_np1 * v / dt * dx + alpha * dot(grad(u_np1),
grad(v)) * dx - u_n * v / dt * dx
u_np1.rename("T", "")
t = 0
u_D.t = t + precice._precice_tau
assert (dt == precice._precice_tau)
file_out = File("Solid/VTK/%s.pvd" % solver_name)
while precice.is_coupling_ongoing():
# Compute solution
solve(a == L, u_np1, bcs)
# Dirichlet problem obtains flux from solution and sends flux on boundary to Neumann problem
fluxes = fluxes_from_temperature_full_domain(F_known_u, V, k)
is_converged = precice.advance(fluxes, dt)
f = Constant(beta - 2 - 2 * alpha)
F = u * v / dt * dx + dot(grad(u), grad(v)) * dx - (u_n / dt + f) * v * dx
if problem is ProblemType.DIRICHLET:
# apply Dirichlet boundary condition on coupling interface
bcs.append(precice.create_coupling_dirichlet_boundary_condition(V))
if problem is ProblemType.NEUMANN:
# apply Neumann boundary condition on coupling interface, modify weak form correspondingly
F += precice.create_coupling_neumann_boundary_condition(v)
a, L = lhs(F), rhs(F)
# Time-stepping
u_np1 = Function(V)
F_known_u = u_np1 * v / dt * dx + dot(grad(u_np1), grad(v)) * dx - (u_n / dt + f) * v * dx
u_np1.rename("Temperature", "")
t = 0
# reference solution at t=0
u_ref = interpolate(u_D, V)
u_ref.rename("reference", " ")
temperature_out = File("out/%s.pvd" % precice._solver_name)
ref_out = File("out/ref%s.pvd" % precice._solver_name)
error_out = File("out/error%s.pvd" % precice._solver_name)
# output solution and reference solution at t=0, n=0
n = 0
print('output u^%d and u_ref^%d' % (n, n))
temperature_out << u_n
ref_out << u_ref
def compute_conv_diff_reac_video(self, initial_condition=None, video_ref=None, video_size=None):
names = {'Cl', 'K'}
P1 = FiniteElement('P', fe.triangle, 1)
element = fe.MixedElement([P1, P1])
V_single = FunctionSpace(self.mesh, P1)
V = FunctionSpace(self.mesh, element)
self.V_conc = V
# load video
video = VideoData(element=P1)
video.load_video(self.video_filename)
if( video_ref is not None and video_size is not None):
video.set_reference_frame(video_ref, video_size)
print(video)
dt = 0.05
t = 0.
t_end = 20.
u_init = Function(V)
(u_cl, u_k) = TrialFunction(V)
(v_cl, v_k) = TestFunction(V)
#u_na = video
if initial_condition is None:
#initial_condition = Expression(("f*exp(-0.5*((x[0]-a)*(x[0]-a)+(x[1]-b)*(x[1]-b))/var)/(sqrt(2*pi)*var)",
# "0."), a = 80, b= 55, var=10, f=10, pi=fe.pi, element=element)
initial_condition = Expression(("f",
"0."), a=80, b=55, var=0.1, f=0.1, pi=fe.pi, element=element)
u_init = fe.interpolate(initial_condition, V)
u_init_cl = u_init[0]
u_init_k = u_init[1]
u_init_na : VideoData= video
assert (self.flow is not None)
n = fe.FacetNormal(self.mesh)
dx, ds = self.dx, self.ds
flow = 5. * self.flow
f_in = fe.Constant(0.00)
f_in_cl = fe.Constant(-0.05)
D = fe.Constant(0.1)
C_na = fe.Constant(0.1)
k1 = fe.Constant(0.2)
k_1 = fe.Constant(0.00001)
# explicit
F = (
(u_cl - u_init_cl) * v_cl * dx
+ dt * D * inner(grad(u_cl), grad(v_cl)) * dx
+ dt * inner(flow, grad(u_cl)) * v_cl * dx
#+ (u_na - u_init_na) * v_na * dx
#+ dt * D * inner(grad(u_na), grad(v_na)) * dx
#+ dt * inner(flow, grad(u_na)) * v_na * dx
+ (u_k - u_init_k) * v_k * dx
+ dt * D * inner(grad(u_k), grad(v_k)) * dx
+ dt * inner(flow, grad(u_k)) * v_k * dx
+ f_in_cl * v_cl * dx
#+ f_in * v_na * dx
+ f_in * v_k * dx
+ dt * k1 * u_init_cl * C_na * u_init_na * v_cl * dx
#+ dt * k1 * u_init_cl * u_init_na * v_na * dx
- dt * k1 * u_init_cl * C_na * u_init_na * v_k * dx
- dt * k_1 * u_init_k * v_cl * dx
#- dt * k_1 * u_init_k * v_na * dx
+ dt * k_1 * u_init_k * v_k * dx
)
# implicit
F = (
(u_cl - u_init_cl) * v_cl * dx
+ dt * D * inner(grad(u_cl), grad(v_cl)) * dx
+ dt * inner(flow, grad(u_cl)) * v_cl * dx
# + (u_na - u_init_na) * v_na * dx
# + dt * D * inner(grad(u_na), grad(v_na)) * dx
# + dt * inner(flow, grad(u_na)) * v_na * dx
+ (u_k - u_init_k) * v_k * dx
+ dt * D * inner(grad(u_k), grad(v_k)) * dx
+ dt * inner(flow, grad(u_k)) * v_k * dx
+ f_in_cl * v_cl * dx
# + f_in * v_na * dx
+ f_in * v_k * dx
+ dt * k1 * u_cl * C_na * u_init_na * v_cl * dx
# + dt * k1 * u_init_cl * u_init_na * v_na * dx
- dt * k1 * u_cl * C_na * u_init_na * v_k * dx
- dt * k_1 * u_k * v_cl * dx
# - dt * k_1 * u_init_k * v_na * dx
+ dt * k_1 * u_k * v_k * dx
)
self.F = F
a, L = fe.lhs(F), fe.rhs(F)
a_mat = fe.assemble(a)
L_vec = fe.assemble(L)
output1 = fe.File('/tmp/cl_dyn.pvd')
output2 = fe.File('/tmp/na_dyn.pvd')
output3 = fe.File('/tmp/k_dyn.pvd')
output4 = fe.File('/tmp/all_dyn.pvd')
# solve
self.sol = []
u_na = Function(V_single)
u_na = fe.interpolate(u_init_na,V_single)
na_inflow = 0
t_plot = 0.5
t_last_plot = 0
while t < t_end:
t = t + dt
t_last_plot += dt
print(t)
u = Function(V)
u_init_na.set_time(5*t)
a_mat = fe.assemble(a)
L_vec = fe.assemble(L)
fe.solve(a_mat, u.vector(), L_vec)
# NonlinearVariationalProblem(F,u)
u_init.assign(u)
u_cl, u_k = u.split()
# u_init_cl.assign(u_cl)
# u_init_na.assign(u_na)
# u_init_k.assign(u_k)
u_na = fe.interpolate(u_init_na, V_single)
u_cl.rename("cl", "cl")
u_na.rename("na", "na")
u_k.rename("k", "k")
output1 << u_cl, t
output2 << u_na, t
output3 << u_k, t
self.sol.append((u_cl, u_na, u_k))
print( fe.assemble(u_cl*self.dx))
if t_last_plot > t_plot:
t_last_plot = 0
plt.figure(figsize=(8,16))
plt.subplot(211)
fe.plot(u_cl)
plt.subplot(212)
fe.plot(u_k)
plt.show()
self.u_cl = u_cl
#self.u_na = u_na
self.u_k = u_k