def speed(ncells):
mesh = UnitSquareMesh(ncells, ncells)
V = VectorFunctionSpace(mesh, 'CG', 2)
Q = FunctionSpace(mesh, 'CG', 1)
W = [V, Q]
u, p = list(map(TrialFunction, W))
v, q = list(map(TestFunction, W))
a = [[0] * len(W) for _ in range(len(W))]
a[0][0] = inner(grad(u), grad(v)) * dx
a[0][1] = inner(p, div(v)) * dx
a[1][0] = inner(q, div(u)) * dx
x, y = SpatialCoordinate(mesh)
L = [
inner(as_vector((y * x**2, sin(pi * (x + y)))), v) * dx,
inner(x + y, q) * dx
]
A0 = block_assemble(a)
b0 = block_assemble(L)
# First method
bc = DirichletBC(V, Constant((0, 0)), 'on_boundary')
bcs = [[bc], []]
t = Timer('first')
block_bc(bcs, True).apply(A0).apply(b0)
dt0 = t.stop()
dimW = sum(Wi.dim() for Wi in W)
A, b = list(map(block_assemble, (a, L)))
t = Timer('second')
A, b = apply_bc(A, b, bcs)
dt1 = t.stop()
print('>>>', (b - b0).norm())
# First method
A, c = list(map(block_assemble, (a, L)))
block_rhs_bc(bcs, A).apply(c)
print('>>>', (b - c).norm())
return dimW, dt0, dt1, dt0 / dt1
L1 = inner(f, c)*dx
from block import block_assemble, block_bc, block_mat
from block.iterative import MinRes
from block.algebraic.petsc import ML, Cholesky
# lhs
AA = block_assemble([[a00, a01, a02],
[a10, a11, a12],
[a20, a21, 0]])
# rhs
b = block_assemble([L0, L1, 0])
# Collect boundary conditions
bcs = [[bc0, bc1], [], []]
block_bc(bcs, True).apply(AA).apply(b)
b22 = inner(p, q)*dx
B22 = assemble(b22)
# Possible action of preconditioner
BB = block_mat([[ML(AA[0, 0]), 0, 0],
[0, Cholesky(AA[1, 1]), 0],
[0, 0, Cholesky(B22)]])
AAinv = MinRes(AA, precond=BB, tolerance=1E-10, maxiter=500)
U, B, P = AAinv*b
p = Function(Q)
p.vector()[:] = P
# Plot solution
def compute_A_P(domain):
# names of params - all 1
dt, alpha, alpha_BJS, s0, mu_f, mu_p, lbd_f, lbd_p, K, Cp = [float(1)]*10
C_BJS = (mu_f * alpha_BJS) / sqrt(K)
# measures
dxGamma = Measure("dx", domain=domain.interface)
dxDarcy = Measure("dx", domain=domain.porous_domain)
dxStokes = Measure("dx", domain=domain.stokes_domain)
# dsDarcy = Measure("ds", domain=domain.porous_domain,
# subdomain_data=domain.porous_bdy_markers)
# dsStokes = Measure("ds", domain=domain.stokes_domain,
# subdomain_data=domain.stokes_bdy_markers)
# test/trial functions
W = function_spaces(domain)
up, pp, dp, uf, pf, lbd = map(TrialFunction, W)
vp, wp, ep, vf, wf, mu = map(TestFunction, W)
# and their traces
Tdp, Tuf = map(
lambda x: Trace(x, domain.interface), [dp, uf]
)
Tep, Tvf = map(
lambda x: Trace(x, domain.interface), [ep, vf]
)
# normals
n_Gamma_f = OuterNormal(domain.interface,
[0.5] * domain.dimension)
assert n_Gamma_f(Point(0.0, 0.0))[1] == -1
n_Gamma_p = -n_Gamma_f
Tup = Trace(up, domain.interface, restriction="-", normal=n_Gamma_f)
Tvp = Trace(vp, domain.interface, restriction="-", normal=n_Gamma_f)
# a bunch of forms
af = Constant(2 * mu_f) * inner(sym(grad(uf)), sym(grad(vf))) * dxStokes
mpp = pp * wp * dx
adp = Constant(mu_p / K) * inner(up, vp) * dxDarcy
aep = (
Constant(mu_p) * inner(sym(grad(dp)), sym(grad(ep))) * dxDarcy
+ Constant(lbd_p) * inner(div(dp), div(ep)) * dxDarcy
)
bpvp = - inner(div(vp), pp) * dxDarcy
bpvpt = - inner(div(up), wp) * dxDarcy
bpep = - inner(div(ep), pp) * dxDarcy
bpept = - inner(div(dp), wp) * dxDarcy
bf = - inner(div(vf), pf) * dxStokes
bft = - inner(div(uf), wf) * dx
# matrices living on the interface
npvp, npep, nfvf = [
lbd * dot(testfunc, n) * dxGamma
for (testfunc, n) in [(Tvp, n_Gamma_p), (Tep, n_Gamma_p), (Tvf, n_Gamma_f)]
]
npvpt, npept, nfvft = [
mu * dot(trialfunc, n) * dxGamma
for (trialfunc, n) in [(Tup, n_Gamma_p), (Tdp, n_Gamma_p), (Tuf, n_Gamma_f)]
]
# to build sum_j ((a*tau_j), (b*tau_j)) we use a trick - see Thoughts
svfuf, svfdp, sepuf, sepdp = [
Constant(C_BJS) * (
inner(testfunc, trialfunc) * dxGamma
- inner(testfunc, n_Gamma_f) * inner(trialfunc, n_Gamma_f) * dxGamma
)
for (testfunc, trialfunc) in [
(Tvf, Tuf), (Tvf, Tdp), (Tep, Tuf), (Tep, Tdp)
]
]
a = [
[adp, bpvp, 0, 0, 0, npvp],
[bpvpt, -Constant(s0/dt)*mpp, Constant(alpha/dt)*bpept, 0, 0, 0],
[0, Constant(alpha/dt)*bpep, Constant(1/dt) * (aep + sepdp), -Constant(1/dt) * sepuf, 0, Constant(1/dt) * npep],
[0, 0, -Constant(1/dt)*svfdp, af + svfuf, bf, nfvf],
[0, 0, 0, bft, 0, 0],
[npvpt, 0, Constant(1 / dt) * npept, nfvft, 0, 0],
]
# quick sanity check
N_unknowns = 6
assert len(a) == N_unknowns
for row in a:
assert len(row) == N_unknowns
## the below cause A*P to have unbounded eigenvalues
# homogeneous Dirichlet BCs
up_bcs = [
DirichletBC(
W[0], Constant((0, 0)),
domain.porous_bdy_markers, 2
)
]
dp_bcs = [
DirichletBC(
W[2], Constant((0, 0)),
domain.porous_bdy_markers, 2
)
]
uf_bcs = [
DirichletBC(
W[3], Constant((0, 0)),
domain.stokes_bdy_markers, 2
)
]
bcs = [
up_bcs,
[], # pp
dp_bcs,
uf_bcs,
[], # pf
[] # lbd
]
# bcs = [[] for _ in range(6)] # no bcs
AA = ii_assemble(a)
bbcs = block_bc(bcs, symmetric=True)
AA = ii_convert(AA, "")
AA = set_lg_map(AA)
bbcs.apply(
AA
)
AAm = ii_convert(AA)
A = AAm.array()
# block diagonal preconditioner
P_up = inner(up, vp) * dxDarcy + inner(div(up), div(vp)) * dxDarcy # Hdiv
P_pp = inner(pp, wp) * dxDarcy # L2
P_dp = (inner(dp, ep) + inner(grad(dp), grad(ep))) * dxDarcy # H1
P_uf = (inner(uf, vf) + inner(grad(uf), grad(vf))) * dxStokes # H1
P_pf = (inner(pf, wf)) * dxStokes # H1
P_up, P_pp, P_dp, P_uf, P_pf = map(
lambda form: ii_convert(ii_assemble(form)),
[P_up, P_pp, P_dp, P_uf, P_pf]
)
P_lbd = hsmg.HsNorm(W[-1], s=0.5)
P_lbd * Function(W[-1]).vector() # enforces lazy computation
P_lbd = P_lbd.matrix
P = ii_convert(
block_diag_mat([P_up, P_pp, P_dp, P_uf, P_pf, P_lbd]), ""
)
# TODO: should I use the bbcs object returned from the call to bbcs.apply() above here?
# or would that only be for if i wanted to apply to vectors?
bbcs.apply(
P
)
P = ii_convert(P).array()
return A, P
def get_solver(self):
"""Returns an iterator over solution values. Values are returned as a
list of Functions, with the ordering being [up, pp, dp, uf, pf, lbd].
First returned value is initial conditions."""
# names of params
# print("Using dt = {}").format(dt)
dt = self.params["dt"]
# print("Using dt = {}").format(dt)
alpha = self.params["alpha"]
alpha_BJS = self.params["alpha_BJS"]
s0 = self.params["s0"]
mu_f = self.params["mu_f"]
mu_p = self.params["mu_p"]
lbd_p = self.params["lbd_p"]
_K = self.params["K"]
Cp = self.params["Cp"]
C_BJS = (mu_f * alpha_BJS) / sqrt(_K)
# # set permeability to something else on vessel wall
# KM, K0 = 0.1*_K, _K
# D = self.domain.D_tunnel
# w = 1
# wpDh = (w+D)/2
# class Permeability(Expression):
# def eval(self, value, x):
# if x[1] > wpDh or x[1] < -wpDh:
# value[0] = K0
# else:
# value[0] = KM
# K = Permeability(degree=3)
# K = interpolate(K, FunctionSpace(self.domain.porous_domain, "CG", 1)) # performance?
# File("permeability.pvd") << K
# f**k the vessel wall
K = Constant(_K)
self.params["K"] = K
# names of things needed to build matrices
dxGamma = Measure("dx", domain=self.domain.interface)
dxDarcy = Measure("dx", domain=self.domain.porous_domain)
dxStokes = Measure("dx", domain=self.domain.stokes_domain)
dsDarcy = Measure("ds",
domain=self.domain.porous_domain,
subdomain_data=self.domain.porous_bdy_markers)
dsStokes = Measure("ds",
domain=self.domain.stokes_domain,
subdomain_data=self.domain.stokes_bdy_markers)
up, pp, dp, uf, pf, lbd = map(TrialFunction, self.W)
vp, wp, ep, vf, wf, mu = map(TestFunction, self.W)
up_prev, pp_prev, dp_prev, uf_prev, pf_prev, lbd_prev = map(
Function, self.W)
# thank you, Miro!
Tdp, Tuf = map(lambda x: Trace(x, self.domain.interface), [dp, uf])
Tep, Tvf = map(lambda x: Trace(x, self.domain.interface), [ep, vf])
n_Gamma_f = self.domain.interface_normal_f
n_Gamma_p = self.domain.interface_normal_p
# should be removed when not in the MMS domain
# D = self.domain.D_tunnel
# assert n_Gamma_f(Point(0, D/2.))[1] == 1
# assert n_Gamma_f(Point(0, -D/2.))[1] == -1
# # assert n_Gamma_p(Point(0, 1/3.))[1] == -1
# # tau = Constant(((0, -1),
# # (1, 0))) * n_Gamma_f
Tup = Trace(up, self.domain.interface)
Tvp = Trace(vp, self.domain.interface)
# a bunch of forms
af = Constant(2 * mu_f) * inner(sym(grad(uf)), sym(
grad(vf))) * dxStokes
mpp = pp * wp * dx
adp = Constant(mu_f) / K * inner(up, vp) * dxDarcy
aep = (Constant(2 * mu_p) * inner(sym(grad(dp)), sym(grad(ep))) *
dxDarcy + Constant(lbd_p) * inner(div(dp), div(ep)) * dxDarcy)
bpvp = -inner(div(vp), pp) * dxDarcy
bpvpt = -inner(div(up), wp) * dxDarcy
bpep = -inner(div(ep), pp) * dxDarcy
bpept = -inner(div(dp), wp) * dxDarcy
bf = -inner(div(vf), pf) * dxStokes
bft = -inner(div(uf), wf) * dxStokes
# matrices living on the interface
npvp, npep, nfvf = [
lbd * inner(testfunc, n) * dxGamma
for (testfunc,
n) in [(Tvp, n_Gamma_p), (Tep, n_Gamma_p), (Tvf, n_Gamma_f)]
]
npvpt, npept, nfvft = [
mu * inner(trialfunc, n) * dxGamma
for (trialfunc,
n) in [(Tup, n_Gamma_p), (Tdp, n_Gamma_p), (Tuf, n_Gamma_f)]
]
svfuf, svfdp, sepuf, sepdp = [
Constant(C_BJS) * (inner(testfunc, trialfunc) * dxGamma - inner(
testfunc, n_Gamma_f) * inner(trialfunc, n_Gamma_f) * dxGamma)
# Constant(C_BJS) * (
# inner(testfunc, tau) * inner(trialfunc, tau) * dxGamma
# )
for (testfunc,
trialfunc) in [(Tvf, Tuf), (Tvf, Tdp), (Tep, Tuf), (Tep, Tdp)]
]
Co = Constant
a = [
[adp, bpvp, 0, 0, 0, npvp],
[bpvpt, -Co(s0 / dt) * mpp,
Co(alpha / dt) * bpept, 0, 0, 0],
[
0,
Constant(alpha / dt) * bpep,
Co(1 / dt) * (aep + sepdp), -Co(1 / dt) * sepuf, 0,
Co(1 / dt) * npep
],
[0, 0, Co(-1 / dt) * svfdp, af + svfuf, bf, nfvf],
[0, 0, 0, bft, 0, 0],
[npvpt, 0, Co(1 / dt) * npept, nfvft, 0, 0],
]
AA = ii_assemble(a)
def compute_RHS(dp_prev, pp_prev, neumann_bcs, t):
nf = FacetNormal(self.domain.stokes_domain)
np = FacetNormal(self.domain.porous_domain)
Tdp_prev = Trace(dp_prev, self.domain.interface)
s_vp, s_wp, s_ep, s_vf, s_wf = self.get_source_terms()
# update t in source terms
for expr in (s_vp, s_wp, s_ep, s_vf, s_wf):
expr.t = t
# update t in neumann bcs
for prob_name in ["biot", "darcy", "stokes"]:
for expr in neumann_bcs[prob_name].values():
expr.t = t
biot_neumann_terms = sum( # val = sigma_p
(inner(dot(val, np), ep) * dsDarcy(subdomain)
for subdomain, val in neumann_bcs["biot"].items()))
stokes_neumann_terms = sum( # val = sigma_f
(inner(dot(val, nf), vf) * dsStokes(subdomain)
for subdomain, val in neumann_bcs["stokes"].items()))
darcy_neumann_terms = sum( # val = -pp
(dot(val * np, vp) * dsDarcy(subdomain)
for subdomain, val in neumann_bcs["darcy"].items()))
bpp = (Constant(s0 / dt) * pp_prev * wp * dxDarcy +
Constant(alpha / dt) * inner(div(dp_prev), wp) * dxDarcy)
L_Cp_vp = Constant(Cp) * inner(Tvp, n_Gamma_p) * dxGamma
L_Cp_ep = Constant(Cp) * inner(Tep, n_Gamma_p) * dxGamma
L_BJS_vf = -Constant(C_BJS / dt) * (
inner(Tdp_prev, Tvf) * dxGamma -
inner(Tdp_prev, n_Gamma_f) * inner(Tvf, n_Gamma_f) * dxGamma
# inner(Tdp_prev, tau) * inner(Tvf, tau) * dxGamma
)
L_BJS_ep = Constant(C_BJS / dt) * (
inner(Tdp_prev, Tep) * dxGamma -
inner(Tdp_prev, n_Gamma_f) * inner(Tep, n_Gamma_f) * dxGamma
# inner(Tdp_prev, tau) * inner(Tep, tau) * dxGamma
)
L_mult = Constant(1 / dt) * inner(Tdp_prev,
n_Gamma_p) * mu * dxGamma
# source terms
S_vp = (Constant(mu_f) / K) * inner(s_vp, vp) * dxDarcy
S_wp = inner(s_wp, wp) * dxDarcy
S_ep = inner(s_ep, ep) * dxDarcy
S_vf = inner(s_vf, vf) * dxStokes
S_wf = inner(s_wf, wf) * dxStokes
L = [
L_Cp_vp + S_vp + darcy_neumann_terms, -(bpp + S_wp),
Co(1 / dt) * (L_Cp_ep + S_ep + L_BJS_ep + biot_neumann_terms),
S_vf + L_BJS_vf + stokes_neumann_terms, -S_wf, L_mult
]
return L
up_bcs = [
DirichletBC(self.W[0], self._dirichlet_bcs["darcy"][subdomain_num],
self.domain.porous_bdy_markers, subdomain_num)
for subdomain_num in self._dirichlet_bcs["darcy"]
]
dp_bcs = [
DirichletBC(self.W[2], self._dirichlet_bcs["biot"][subdomain_num],
self.domain.porous_bdy_markers, subdomain_num)
for subdomain_num in self._dirichlet_bcs["biot"]
]
uf_bcs = [
DirichletBC(self.W[3],
self._dirichlet_bcs["stokes"][subdomain_num],
self.domain.stokes_bdy_markers, subdomain_num)
for subdomain_num in self._dirichlet_bcs["stokes"]
]
bcs = [
up_bcs,
[], # pp
dp_bcs,
uf_bcs,
[], # pf
[] # lbd
]
def update_t_in_dirichlet_bcs(t):
all_bc_exprs = (self._dirichlet_bcs["darcy"].values() +
self._dirichlet_bcs["biot"].values() +
self._dirichlet_bcs["stokes"].values())
for expr in all_bc_exprs:
expr.t = t
bbcs = block_bc(bcs, symmetric=True)
AA = ii_convert(AA, "")
AA = set_lg_map(AA)
bbcs = bbcs.apply(AA)
AAm = ii_convert(AA)
# assert np.all(AAm.array() == AAm.array())
w = ii_Function(self.W)
solver = LUSolver('default')
solver.set_operator(AAm)
solver.parameters['reuse_factorization'] = True
# alright, we're all set - now set initial conditions and solve
t = 0
initial_conditions = self.get_initial_conditions()
for func, func_0 in zip([up_prev, pp_prev, dp_prev, uf_prev, pf_prev],
initial_conditions):
func_0.t = 0
func.assign(func_0)
yield t, [up_prev, pp_prev, dp_prev, uf_prev, pf_prev, lbd_prev]
while True:
# solve for next time step
t += dt
update_t_in_dirichlet_bcs(t)
L = compute_RHS(dp_prev, pp_prev, self._neumann_bcs, t)
bb = ii_assemble(L)
bbcs.apply(bb)
bbm = ii_convert(bb)
solver.solve(w.vector(), bbm)
for i, func in enumerate(
[up_prev, pp_prev, dp_prev, uf_prev, pf_prev, lbd_prev]):
func.assign(w[i])
yield t, w
AA = ii_convert(ii_assemble(a), "")
# NOTE: some conversion (typically with transpose) will leave
# the matrix in a wrong state from PETSc point of view (why?)
# From the experience the typical fix is setting the local-to-global
# map for the matrix. So we do it here just in case
set_lg_map(AA)
bcs = [
[
DirichletBC(
W[0], Expression(("1", "1"), degree=2), "on_boundary"
)
],
[],
[
DirichletBC(
W[2], Expression(("1", "1"), degree=2), "on_boundary"
)
],
[
DirichletBC(
W[3], Expression(("1", "1"), degree=2), "on_boundary"
)
],
[],
[],
]
bbcs = block_bc(bcs, symmetric=False)
bbcs.apply(AA)
def time_solve(self,
nonlinear_tol=1e-10,
iter_tol=1e-8,
maxNonlinIters=50,
maxLinIters=200,
show=0,
print_norm=True,
save_freq=1,
save_initial=True,
lin_solver="mumps"):
"""
Loop through the time interval using the time step specified
in the MechanicsProblem config dictionary.
Parameters
----------
nonlinear_tol : float (default 1e-10)
Tolerance used to terminate Newton's method.
iter_tol : float (default 1e-8)
Tolerance used to terminate the iterative linear solver.
maxNonlinIters : int (default 50)
Maximum number of iterations for Newton's method.
maxLinIters : int (default 200)
Maximum number of iterations for iterative linear solver.
show : int (default 0)
Amount of information for iterative.LGMRES to show. See
documentation of this class for different log levels.
print_norm : bool (default True)
True if user wishes to see the norm at every linear iteration
and False otherwise.
save_freq : int (default int)
The frequency at which the solution is to be saved if the problem is
unsteady. E.g., save_freq = 10 if the user wishes to save the solution
every 10 time steps.
save_initial : bool (default True)
True if the user wishes to save the initial condition and False otherwise.
lin_solver : str (default "mumps")
Name of the linear solver to be used for steady compressible elastic
problems. See the dolfin.solve documentation for a list of available
linear solvers.
Returns
-------
None
"""
t, tf = self._mp.config['formulation']['time']['interval']
t0 = t
dt = self._mp.config['formulation']['time']['dt']
count = 0 # Used to check if file(s) should be saved.
lhs, rhs = self.ufl_lhs_rhs()
# Need to be more specific here.
bcs = block.block_bc(self._mp.dirichlet_bcs.values(), False)
rank = dlf.MPI.rank(MPI_COMM_WORLD)
p = self._mp.pressure
u = self._mp.displacement
v = self._mp.velocity
f_objs = [self._file_pressure, self._file_disp, self._file_vel]
# Save initial condition
if save_initial:
_write_objects(f_objs, t=t, close=False, u=u, v=v, p=p)
if self._file_hdf5 is not None:
_write_objects(self._file_hdf5, t=t, close=False, u=u, p=p)
if self._file_xdmf is not None:
_write_objects(self._file_xdmf, t=t, close=False, u=u, p=p)
while t < (tf - dt / 10.0):
# Set to the next time step
t += dt
# Update expressions that depend on time
self._mp.update_time(t, t0)
# Print the current time
if not rank:
print('*' * 30)
print('t = %3.5f' % t)
# Solve the nonlinear equation(s) at current time step.
self.nonlinear_solve(lhs,
rhs,
bcs,
nonlinear_tol=nonlinear_tol,
iter_tol=iter_tol,
maxNonlinIters=maxNonlinIters,
maxLinIters=maxLinIters,
show=show,
print_norm=print_norm,
lin_solver=lin_solver)
# Prepare for the next time step
if self._mp.displacement0 != 0:
self._mp.displacement0.assign(self._mp.displacement)
self._mp.velocity0.assign(self._mp.velocity)
t0 = t
count += 1
MPI.COMM_WORLD.Barrier()
if not count % save_freq:
_write_objects(f_objs, t=t, close=False, u=u, v=v, p=p)
if self._file_hdf5 is not None:
_write_objects(self._file_hdf5, t=t, close=False, u=u, p=p)
if self._file_xdmf is not None:
_write_objects(self._file_xdmf, t=t, close=False, u=u, p=p)
return None
AA = ii_convert(ii_assemble(a), "")
# NOTE: some conversion (typically with transpose) will leave
# the matrix in a wrong state from PETSc point of view (why?)
# From the experience the typical fix is setting the local-to-global
# map for the matrix. So we do it here just in case
set_lg_map(AA)
bcs = [
[
DirichletBC(
W[0], Expression(("1", "1"), degree=2), "on_boundary"
)
],
[],
[
DirichletBC(
W[2], Expression(("1", "1"), degree=2), "on_boundary"
)
],
[
DirichletBC(
W[3], Expression(("1", "1"), degree=2), "on_boundary"
)
],
[],
[],
]
bbcs = block_bc(bcs, symmetric=False)
bbcs.apply(AA)
def compute_A_P_BDS(domain, params):
"""Computes A, P for Biot/Darcy/Stokes problem."""
# # names of params - all 1
# dt, alpha, alpha_BJS, s0, mu_f, mu_p, lbd_f, lbd_p, K, Cp = [float(1)]*10
dt = params["dt"]
alpha = params["alpha"]
alpha_BJS = params["alpha_BJS"]
s0 = params["s0"]
mu_f = params["mu_f"]
mu_p = params["mu_p"]
lbd_p = params["lbd_p"]
K = params["K"]
Cp = params["Cp"]
C_BJS = (mu_f * alpha_BJS) / sqrt(K)
# measures
dxGamma = Measure("dx", domain=domain.interface)
dxDarcy = Measure("dx", domain=domain.porous_domain)
dxStokes = Measure("dx", domain=domain.stokes_domain)
dsDarcy = Measure("ds",
domain=domain.porous_domain,
subdomain_data=domain.porous_bdy_markers)
dsStokes = Measure("ds",
domain=domain.stokes_domain,
subdomain_data=domain.stokes_bdy_markers)
# test/trial functions
W = function_spaces(domain)
up, pp, dp, uf, pf, lbd = map(TrialFunction, W)
vp, wp, ep, vf, wf, mu = map(TestFunction, W)
# and their traces
# Tdp, Tuf = map(
# lambda x: Trace(x, domain.interface), [dp, uf]
# )
# Tep, Tvf = map(
# lambda x: Trace(x, domain.interface), [ep, vf]
# )
# # normals
# n_Gamma_f = OuterNormal(domain.interface,
# [0.5] * domain.dimension)
# assert n_Gamma_f(Point(0.0, 0.0))[1] == -1
# n_Gamma_p = -n_Gamma_f
# Tup = Trace(up, domain.interface, restriction="-", normal=n_Gamma_f)
# Tvp = Trace(vp, domain.interface, restriction="-", normal=n_Gamma_f)
# a bunch of forms
# stokes
af = Constant(2 * mu_f) * inner(sym(grad(uf)), sym(grad(vf))) * dxStokes
bf = -inner(div(vf), pf) * dxStokes
bft = -inner(div(uf), wf) * dxStokes
# biot
mpp = pp * wp * dx
adp = Constant(mu_p / K) * inner(up, vp) * dxDarcy
aep = (Constant(mu_p) * inner(sym(grad(dp)), sym(grad(ep))) * dxDarcy +
Constant(lbd_p) * inner(div(dp), div(ep)) * dxDarcy)
bpvp = -inner(div(vp), pp) * dxDarcy
bpvpt = -inner(div(up), wp) * dxDarcy
bpep = -inner(div(ep), pp) * dxDarcy
bpept = -inner(div(dp), wp) * dxDarcy
Co = Constant
# biot
# a = [
# [adp, bpvp, 0],
# [bpvpt, -Co(s0 / dt) * mpp, Co(alpha / dt) * bpept],
# [0, Constant(alpha / dt) * bpep, Co(1 / dt) * aep],
# ]
# biot
# a = [
# [af, bf],
# [bft, 0],
# ]
# both w/o multiplier
a = [
[adp, bpvp, 0, 0, 0],
[bpvpt, -Co(s0 / dt) * mpp,
Co(alpha / dt) * bpept, 0, 0],
[0, Constant(alpha / dt) * bpep,
Co(1 / dt) * aep, 0, 0],
[0, 0, 0, af, bf],
[0, 0, 0, bft, 0],
]
# # with multiplier
# a = [
# [adp, bpvp, 0, 0, 0, 0],
# [bpvpt, -Co(s0 / dt) * mpp, Co(alpha / dt) * bpept, 0, 0, 0],
# [0, Constant(alpha / dt) * bpep, Co(1 / dt) * aep, 0, 0, 0],
# [0, 0, 0, af, bf, 0],
# [0, 0, 0, bft, 0, 0],
# [0, 0, 0, 0, 0, inner(mu, lbd) * dxGamma]
# ]
# homogeneous Dirichlet BCs
up_bcs = [
DirichletBC(W[0], Constant((0, 0)), domain.porous_bdy_markers, i)
for i in [1, 2]
]
dp_bcs = [
DirichletBC(W[2], Constant((0, 0)), domain.porous_bdy_markers, i)
for i in [1, 2]
]
uf_bcs = [
DirichletBC(W[3], Constant((0, 0)), domain.stokes_bdy_markers, i)
for i in [
1
] # if there are dirichlet BCs all over, pressure gets underdetermined
]
bcs = [
up_bcs,
[], # pp
dp_bcs,
uf_bcs,
[], # pf
]
AA = ii_assemble(a)
bbcs = block_bc(bcs, symmetric=True)
AA = ii_convert(AA, "")
# AA = set_lg_map(AA)
bbcs.apply(AA)
A = ii_convert(AA).array()
# A = AAm.array()
# weighted block diagonal preconditioner
P_up = Constant(mu_p / K) * inner(up, vp) * dxDarcy
P_pp = Constant(s0 / dt + 1 /
(mu_p + lbd_p)) * inner(pp, wp) * dxDarcy + Constant(
K / mu_p) * inner(grad(pp), grad(wp)) * dxDarcy
P_dp = (Constant(mu_p / dt) * inner(grad(dp), grad(ep))) * dxDarcy
P_uf = (Constant(mu_f) * inner(grad(uf), grad(vf))) * dxStokes
P_pf = (Constant(1 / mu_f) * inner(pf, wf)) * dxStokes
P_up, P_pp, P_dp, P_uf, P_pf = map(
# P_up, P_pp, P_dp = map(
# P_uf, P_pf = map(
lambda form: ii_convert(ii_assemble(form)),
[P_up, P_pp, P_dp, P_uf, P_pf])
P_lbd = hsmg.HsNorm(W[-1], s=0.5)
P_lbd * Function(W[-1]).vector() # enforces lazy computation
P_lbd = P_lbd.matrix
P = ii_convert(
block_diag_mat([
P_up,
P_pp,
P_dp,
P_uf,
P_pf,
# P_lbd
]),
"")
# TODO: should I use the bbcs object returned from the call to bbcs.apply() above here?
# or would that only be for if i wanted to apply to vectors?
bbcs.apply(P)
P = ii_convert(P).array()
return A, P
def get_solver(self):
"""Returns an iterator over solution values. Values are returned as a
list of Functions, with the ordering being [up, pp, dp, uf, pf, lbd].
First returned value is initial conditions."""
# names of params
dt = self.params["dt"]
alpha = self.params["alpha"]
alpha_BJS = self.params["alpha_BJS"]
s0 = self.params["s0"]
mu_f = self.params["mu_f"]
mu_p = self.params["mu_p"]
lbd_p = self.params["lbd_p"]
K = self.params["K"]
Cp = self.params["Cp"]
C_BJS = (mu_f * alpha_BJS) / sqrt(K)
# names of things needed to build matrices
dxGamma = Measure("dx", domain=self.domain.interface)
dxDarcy = Measure("dx", domain=self.domain.porous_domain)
dxStokes = Measure("dx", domain=self.domain.stokes_domain)
dsDarcy = Measure("ds",
domain=self.domain.porous_domain,
subdomain_data=self.domain.porous_bdy_markers)
dsStokes = Measure("ds",
domain=self.domain.stokes_domain,
subdomain_data=self.domain.stokes_bdy_markers)
up, pp, dp, uf, pf, lbd = map(TrialFunction, self.W)
vp, wp, ep, vf, wf, mu = map(TestFunction, self.W)
up_prev, pp_prev, dp_prev, uf_prev, pf_prev, lbd_prev = map(
Function, self.W)
# thank you, Miro!
Tdp, Tuf = map(lambda x: Trace(x, self.domain.interface), [dp, uf])
Tep, Tvf = map(lambda x: Trace(x, self.domain.interface), [ep, vf])
# last argument is a point in the interior of the
# domain the normal should point outwards from
n_Gamma_f = OuterNormal(self.domain.interface,
[0.5] * self.domain.dimension)
# should be removed when not in the MMS domain
assert n_Gamma_f(Point(0.0, 0.0))[1] == -1
n_Gamma_p = OuterNormal(self.domain.interface,
[-0.5] * self.domain.dimension)
assert n_Gamma_p(Point(0.0, 0.0))[1] == 1
# tau = Constant(((0, -1),
# (1, 0))) * n_Gamma_f
Tup = Trace(up, self.domain.interface)
Tvp = Trace(vp, self.domain.interface)
# a bunch of forms
af = Constant(2 * mu_f) * inner(sym(grad(uf)), sym(
grad(vf))) * dxStokes
mpp = pp * wp * dx
adp = Constant(mu_p / K) * inner(up, vp) * dxDarcy
aep = (Constant(2 * mu_p) * inner(sym(grad(dp)), sym(grad(ep))) *
dxDarcy + Constant(lbd_p) * inner(div(dp), div(ep)) * dxDarcy)
bpvp = -inner(div(vp), pp) * dxDarcy
bpvpt = -inner(div(up), wp) * dxDarcy
bpep = -inner(div(ep), pp) * dxDarcy
bpept = -inner(div(dp), wp) * dxDarcy
bf = -inner(div(vf), pf) * dxStokes
bft = -inner(div(uf), wf) * dxStokes
# matrices living on the interface
npvp, npep, nfvf = [
lbd * inner(testfunc, n) * dxGamma
for (testfunc,
n) in [(Tvp, n_Gamma_p), (Tep, n_Gamma_p), (Tvf, n_Gamma_f)]
]
npvpt, npept, nfvft = [
mu * inner(trialfunc, n) * dxGamma
for (trialfunc,
n) in [(Tup, n_Gamma_p), (Tdp, n_Gamma_p), (Tuf, n_Gamma_f)]
]
svfuf, svfdp, sepuf, sepdp = [
Constant(C_BJS) * (inner(testfunc, trialfunc) * dxGamma - inner(
testfunc, n_Gamma_f) * inner(trialfunc, n_Gamma_f) * dxGamma)
# Constant(C_BJS) * (
# inner(testfunc, tau) * inner(trialfunc, tau) * dxGamma
# )
for (testfunc,
trialfunc) in [(Tvf, Tuf), (Tvf, Tdp), (Tep, Tuf), (Tep, Tdp)]
]
Co = Constant
a = [[0] * len(self.W) for _ in range(len(self.W))]
# [adp, bpvp, 0, 0, 0, npvp],
a[0][0] = adp
a[0][1] = bpvp
a[0][5] = npvp
# [bpvpt, -Co(s0/dt)*mpp, Co(alpha/dt)*bpept, 0, 0, 0],
a[1][0] = bpvpt
a[1][1] = -Co(s0 / dt) * mpp
a[1][2] = Co(alpha / dt) * bpept
# [0, Constant(alpha/dt)*bpep, Co(1/dt)*(aep + Co(1/dt)*sepdp),
# -Co(1/dt)*sepuf, 0, Co(1/dt)*npep],
a[2][1] = Constant(alpha / dt) * bpep
a[2][2] = Co(1 / dt) * (aep + Co(1 / dt) * sepdp)
a[2][3] = -Co(1 / dt) * sepuf
a[2][5] = Co(1 / dt) * npep
# [0, 0, Co(-1/dt)*svfdp, af + svfuf, bf, nfvf],
a[3][2] = Co(-1 / dt) * svfdp
a[3][3] = af + svfuf
a[3][4] = bf
a[3][5] = nfvf
# [0, 0, 0, bft, 0, 0],
a[4][3] = bft
# [npvpt, 0, Co(1/dt)*npept, nfvft, 0, 0],
a[5][0] = npvpt
a[5][2] = Co(1 / dt) * npept
a[5][3] = nfvft
def compute_RHS(dp_prev, pp_prev, neumann_bcs, t):
nf = FacetNormal(self.domain.stokes_domain)
np = FacetNormal(self.domain.porous_domain)
Tdp_prev = Trace(dp_prev, self.domain.interface)
s_vp, s_wp, s_ep, s_vf, s_wf = self.get_source_terms()
# update t in source terms
for expr in (s_vp, s_wp, s_ep, s_vf, s_wf):
expr.t = t
# update t in neumann bcs
for prob_name in ["biot", "darcy", "stokes"]:
for expr in neumann_bcs[prob_name].keys():
expr.t = t
biot_neumann_terms, darcy_neumann_terms, stokes_neumann_terms = (
sum([
inner(testfunc, neumann_bcs[prob_name][subdomain]) *
measure(subdomain) for subdomain in neumann_bcs[prob_name]
]) for prob_name, testfunc, measure in zip(
["biot", "darcy", "stokes"], [ep, vp, vf],
[dsDarcy, dsDarcy, dsStokes]))
L_neumann_darcy = (inner(vp, np) * Constant(0) * dsDarcy +
darcy_neumann_terms)
L_neumann_biot = (Constant(0) * inner(np, ep) * dsDarcy +
biot_neumann_terms)
L_neumann_stokes = (Constant(0) * inner(nf, vf) * dsStokes +
stokes_neumann_terms)
bpp = (Constant(s0 / dt) * pp_prev * wp * dxDarcy +
Constant(alpha / dt) * inner(div(dp_prev), wp) * dxDarcy)
L_Cp_vp = Constant(Cp) * inner(Tvp, n_Gamma_p) * dxGamma
L_Cp_ep = Constant(Cp) * inner(Tep, n_Gamma_p) * dxGamma
L_BJS_vf = -Constant(C_BJS / dt) * (
inner(Tdp_prev, Tvf) * dxGamma -
inner(Tdp_prev, n_Gamma_f) * inner(Tvf, n_Gamma_f) * dxGamma
# inner(Tdp_prev, tau) * inner(Tvf, tau) * dxGamma
)
L_BJS_ep = Constant(C_BJS / dt) * (
inner(Tdp_prev, Tep) * dxGamma -
inner(Tdp_prev, n_Gamma_f) * inner(Tep, n_Gamma_f) * dxGamma
# inner(Tdp_prev, tau) * inner(Tep, tau) * dxGamma
)
L_mult = Constant(1 / dt) * inner(Tdp_prev,
n_Gamma_p) * mu * dxGamma
# source terms
S_vp = inner(s_vp, vp) * dxDarcy
S_wp = inner(s_wp, wp) * dxDarcy
S_ep = inner(s_ep, ep) * dxDarcy
S_vf = inner(s_vf, vf) * dxStokes
S_wf = inner(s_wf, wf) * dxStokes
L = [
L_Cp_vp + Constant(mu_p / K) * S_vp, -(bpp + S_wp),
Co(1 / dt) * (L_Cp_ep + S_ep + L_BJS_ep), S_vf + L_BJS_vf,
-S_wf, L_mult
]
return L
up_bcs = [
DirichletBC(self.W[0], self._dirichlet_bcs["darcy"][subdomain_num],
self.domain.porous_bdy_markers, subdomain_num)
for subdomain_num in self._dirichlet_bcs["darcy"]
]
dp_bcs = [
DirichletBC(self.W[2], self._dirichlet_bcs["biot"][subdomain_num],
self.domain.porous_bdy_markers, subdomain_num)
for subdomain_num in self._dirichlet_bcs["biot"]
]
uf_bcs = [
DirichletBC(self.W[3],
self._dirichlet_bcs["stokes"][subdomain_num],
self.domain.stokes_bdy_markers, subdomain_num)
for subdomain_num in self._dirichlet_bcs["stokes"]
]
bcs = [
up_bcs,
[], # pp
dp_bcs,
uf_bcs,
[], # pf
[] # lbd
]
AA = ii_assemble(a)
def update_t_in_dirichlet_bcs(t):
all_bc_exprs = (self._dirichlet_bcs["darcy"].values() +
self._dirichlet_bcs["biot"].values() +
self._dirichlet_bcs["stokes"].values())
for expr in all_bc_exprs:
expr.t = t
bbcs = block_bc(bcs, symmetric=True)
AA = ii_convert(AA, "")
AA = set_lg_map(AA)
bbcs = bbcs.apply(AA)
AAm = ii_convert(AA)
# assert np.all(AAm.array() == AAm.array())
w = ii_Function(self.W)
solver = LUSolver('default')
solver.set_operator(AAm)
solver.parameters['reuse_factorization'] = True
# alright, we're all set - now set initial conditions and solve
t = 0
initial_conditions = self.get_initial_conditions()
for func, func_0 in zip([up_prev, pp_prev, dp_prev, uf_prev, pf_prev],
initial_conditions):
func_0.t = 0
func.assign(func_0)
yield t, [up_prev, pp_prev, dp_prev, uf_prev, pf_prev, lbd_prev]
while True:
# solve for next time step
t += dt
update_t_in_dirichlet_bcs(t)
L = compute_RHS(dp_prev, pp_prev, self._neumann_bcs, t)
bb = ii_assemble(L)
bbcs.apply(bb)
bbm = ii_convert(bb)
solver.solve(w.vector(), bbm)
for i, func in enumerate(
[up_prev, pp_prev, dp_prev, uf_prev, pf_prev, lbd_prev]):
func.assign(w[i])
yield t, w
def mini_block(n):
'''Just check MMS'''
mesh = UnitSquareMesh(n, n)
# Just approx
f_space = VectorFunctionSpace(mesh, 'DG', 1)
h_space = TensorFunctionSpace(mesh, 'DG', 1)
u_int = interpolate(u_exact, VectorFunctionSpace(mesh, 'CG', 2))
p_int = interpolate(p_exact, FunctionSpace(mesh, 'CG', 2))
f = project(-div(grad(u_int)) + grad(p_int), f_space)
h = project(-p_int * Identity(2) + grad(u_int), h_space)
# ----------------
V = VectorFunctionSpace(mesh, 'Lagrange', 1)
Vb = VectorFunctionSpace(mesh, 'Bubble', 3)
Q = FunctionSpace(mesh, 'Lagrange', 1)
W = [V, Vb, Q]
u, ub, p = list(map(TrialFunction, W))
v, vb, q = list(map(TestFunction, W))
n = FacetNormal(mesh)
a = [[0] * len(W) for _ in range(len(W))]
a[0][0] = inner(grad(u), grad(v)) * dx
a[0][2] = -inner(div(v), p) * dx
a[2][0] = -inner(div(u), q) * dx
a[1][1] = inner(grad(ub), grad(vb)) * dx
a[1][2] = -inner(div(vb), p) * dx
a[2][1] = -inner(div(ub), q) * dx
a[0][1] = inner(grad(v), grad(ub)) * dx
a[1][0] = inner(grad(vb), grad(u)) * dx
# NOTE: bubbles don't contribute to surface
L = [
inner(dot(h, n), v) * ds + inner(f, v) * dx,
inner(f, vb) * dx,
inner(Constant(0), q) * dx
]
# Bubbles don't have bcs on the surface
bcs = [[DirichletBC(W[0], u_exact, 'near(x[0], 0)')], [], []]
AA = block_assemble(a)
bb = block_assemble(L)
block_bc(bcs, True).apply(AA).apply(bb)
# Preconditioner
B0 = AMG(AA[0][0])
H1_Vb = inner(grad(ub), grad(vb)) * dx + inner(ub, vb) * dx
B1 = LumpedInvDiag(assemble(H1_Vb))
L2_Q = assemble(inner(p, q) * dx)
B2 = LumpedInvDiag(L2_Q)
BB = block_mat([[B0, 0, 0], [0, B1, 0], [0, 0, B2]])
x0 = AA.create_vec()
x0.randomize()
AAinv = MinRes(AA,
precond=BB,
tolerance=1e-10,
maxiter=500,
relativeconv=True,
show=2,
initial_guess=x0)
# Compute solution
u, ub, p = AAinv * bb
uh_ = Function(V, u)
uhb = Function(Vb, ub)
ph = Function(Q, p)
uh = Sum([uh_, uhb], degree=1)
return uh, ph, sum(Wi.dim() for Wi in W)
# Rhs components
L0 = inner(f, v) * dx
L1 = inner(f, c) * dx
from block import block_assemble, block_bc, block_mat
from block.iterative import MinRes
from block.algebraic.petsc import ML, Cholesky
# lhs
AA = block_assemble([[a00, a01, a02], [a10, a11, a12], [a20, a21, 0]])
# rhs
b = block_assemble([L0, L1, 0])
# Collect boundary conditions
bcs = [[bc0, bc1], [], []]
block_bc(bcs, True).apply(AA).apply(b)
b22 = inner(p, q) * dx
B22 = assemble(b22)
# Possible action of preconditioner
BB = block_mat([[ML(AA[0, 0]), 0, 0], [0, Cholesky(AA[1, 1]), 0],
[0, 0, Cholesky(B22)]])
AAinv = MinRes(AA, precond=BB, tolerance=1E-10, maxiter=500)
U, B, P = AAinv * b
p = Function(Q)
p.vector()[:] = P
# Plot solution
plot(p)
def mini_block(n):
'''Just check MMS'''
mesh = UnitSquareMesh(n, n)
# Just approx
f_space = VectorFunctionSpace(mesh, 'DG', 1)
h_space = TensorFunctionSpace(mesh, 'DG', 1)
u_int = interpolate(u_exact, VectorFunctionSpace(mesh, 'CG', 2))
p_int = interpolate(p_exact, FunctionSpace(mesh, 'CG', 2))
f = project(-div(grad(u_int)) + grad(p_int), f_space)
h = project(-p_int*Identity(2) + grad(u_int), h_space)
# ----------------
V = VectorFunctionSpace(mesh, 'Lagrange', 1)
Vb = VectorFunctionSpace(mesh, 'Bubble', 3)
Q = FunctionSpace(mesh, 'Lagrange', 1)
W = [V, Vb, Q]
u, ub, p = map(TrialFunction, W)
v, vb, q = map(TestFunction, W)
n = FacetNormal(mesh)
a = [[0]*len(W) for _ in range(len(W))]
a[0][0] = inner(grad(u), grad(v))*dx
a[0][2] = - inner(div(v), p)*dx
a[2][0] = - inner(div(u), q)*dx
a[1][1] = inner(grad(ub), grad(vb))*dx
a[1][2] = - inner(div(vb), p)*dx
a[2][1] = - inner(div(ub), q)*dx
a[0][1] = inner(grad(v), grad(ub))*dx
a[1][0] = inner(grad(vb), grad(u))*dx
# NOTE: bubbles don't contribute to surface
L = [inner(dot(h, n), v)*ds + inner(f, v)*dx,
inner(f, vb)*dx,
inner(Constant(0), q)*dx]
# Bubbles don't have bcs on the surface
bcs = [[DirichletBC(W[0], u_exact, 'near(x[0], 0)')], [], []]
AA = block_assemble(a)
bb = block_assemble(L)
block_bc(bcs, True).apply(AA).apply(bb)
# Preconditioner
B0 = AMG(AA[0][0])
H1_Vb = inner(grad(ub), grad(vb))*dx + inner(ub, vb)*dx
B1 = LumpedInvDiag(assemble(H1_Vb))
L2_Q = assemble(inner(p, q)*dx)
B2 = LumpedInvDiag(L2_Q)
BB = block_mat([[B0, 0, 0],
[0, B1, 0],
[0, 0, B2]])
x0 = AA.create_vec()
x0.randomize()
AAinv = MinRes(AA, precond=BB, tolerance=1e-10, maxiter=500, relativeconv=True, show=2,
initial_guess=x0)
# Compute solution
u, ub, p = AAinv * bb
uh_ = Function(V, u)
uhb = Function(Vb, ub)
ph = Function(Q, p)
uh = Sum([uh_, uhb], degree=1)
return uh, ph, sum(Wi.dim() for Wi in W)