def __missing__(self, key):
assert len(key) == 4
form, bcs, solver_type, preconditioner_type = key
prec = PETScPreconditioner(preconditioner_type)
sol = PETScKrylovSolver(solver_type, prec)
sol.prec = prec
#sol = KrylovSolver(solver_type, preconditioner_type)
#sol.parameters["preconditioner"]["structure"] = "same"
sol.parameters["error_on_nonconvergence"] = False
sol.parameters["monitor_convergence"] = False
sol.parameters["report"] = False
self[key] = sol
return self[key]
def create_solver(solver, preconditioner="default"):
"""Create solver from arguments. Should be flexible to handle
- strings specifying the solver and preconditioner types
- PETScKrylovSolver/PETScPreconditioner objects
- petsc4py.PETSC.KSP/petsc4py.PETSC.pc objects
or any combination of the above
"""
# Create solver
if isinstance(solver, str):
try:
linear_solvers = set(dict(linear_solver_methods()).keys())
krylov_solvers = set(dict(krylov_solver_methods()).keys())
except:
linear_solvers = set(linear_solver_methods())
krylov_solvers = set(krylov_solver_methods())
direct_solvers = linear_solvers - krylov_solvers
if solver in direct_solvers:
s = LinearSolver(solver)
return s
elif solver in krylov_solvers:
s = PETScKrylovSolver(solver)
else:
s = PETScKrylovSolver()
s.ksp().setType(solver)
if s.ksp().getNormType() == petsc4py.PETSc.KSP.NormType.NONE:
s.ksp().setNormType(petsc4py.PETSc.KSP.NormType.PRECONDITIONED)
#raise RuntimeError("Don't know how to handle solver %s" %solver)
elif isinstance(solver, PETScKrylovSolver):
s = solver
elif isinstance(solver, petsc4py.PETSc.KSP):
s = PETScKrylovSolver(solver)
else:
raise ValueError("Unable to create solver from argument of type %s" %
type(solver))
assert isinstance(s, PETScKrylovSolver)
if preconditioner == "default":
return s
# Create preconditioner
if preconditioner in [None, "none", "None"]:
pc = PETScPreconditioner("none")
pc.set(s)
return s
elif isinstance(preconditioner, str):
if preconditioner in krylov_solver_preconditioners():
pc = PETScPreconditioner(preconditioner)
pc.set(s)
return s
elif preconditioner in ["additive_schwarz", "bjacobi", "jacobi"]:
if preconditioner == "additive_schwarz":
pc_type = "asm"
else:
pc_type = preconditioner
ksp = s.ksp()
pc = ksp.pc
pc.setType(pc_type)
return s
elif isinstance(preconditioner, PETScPreconditioner):
pc = preconditioner
pc.set(s)
return s
elif isinstance(preconditioner, petsc4py.PETSc.PC):
ksp = s.ksp()
ksp.setPC(preconditioner)
return s
else:
raise ValueError(
"Unable to create preconditioner from argument of type %s" %
type(solver))
raise RuntimeError(
"Should not reach this code. The solver/preconditioner (%s/%s) failed to return a valid solver."
% (str(solver), str(preconditioner)))
def compute_pressure(
P,
p0,
mu,
ui,
u,
my_dx,
p_bcs=None,
rotational_form=False,
tol=1.0e-10,
verbose=True,
):
"""Solve the pressure Poisson equation
.. math::
\\begin{align}
-\\frac{1}{r} \\div(r \\nabla (p_1-p_0)) =
-\\frac{1}{r} \\div(r u),\\\\
\\text{(with boundary conditions)},
\\end{align}
for :math:`\\nabla p = u`.
The pressure correction is based on the update formula
.. math::
\\frac{\\rho}{dt} (u_{n+1}-u^*)
+ \\begin{pmatrix}
\\text{d}\\phi/\\text{d}r\\\\
\\text{d}\\phi/\\text{d}z\\\\
\\frac{1}{r} \\text{d}\\phi/\\text{d}\\theta
\\end{pmatrix}
= 0
with :math:`\\phi = p_{n+1} - p^*` and
.. math::
\\frac{1}{r} \\frac{\\text{d}}{\\text{d}r} (r u_r^{(n+1)})
+ \\frac{\\text{d}}{\\text{d}z} (u_z^{(n+1)})
+ \\frac{1}{r} \\frac{\\text{d}}{\\text{d}\\theta} (u_{\\theta}^{(n+1)})
= 0
With the assumption that u does not change in the direction
:math:`\\theta`, one derives
.. math::
- \\frac{1}{r} \\div(r \\nabla \\phi) =
\\frac{1}{r} \\frac{\\rho}{dt} \\div(r (u_{n+1} - u^*))\\\\
- \\frac{1}{r} \\langle n, r \\nabla \\phi\\rangle =
\\frac{1}{r} \\frac{\\rho}{dt} \\langle n, r (u_{n+1} - u^*)\\rangle
In its weak form, this is
.. math::
\\int r \\langle\\nabla\\phi, \\nabla q\\rangle \\,2 \\pi =
- \\frac{\\rho}{dt} \\int \\div(r u^*) q \\, 2 \\pi
- \\frac{\\rho}{dt} \\int_{\\Gamma}
\\langle n, r (u_{n+1}-u^*)\\rangle q \\, 2\\pi.
(The terms :math:`1/r` cancel with the volume elements :math:`2\\pi r`.)
If the Dirichlet boundary conditions are applied to both :math:`u^*` and
:math:`u_n` (the latter in the velocity correction step), the boundary
integral vanishes.
If no Dirichlet conditions are given (which is the default case), the
system has no unique solution; one eigenvalue is 0. This however, does not
hurt CG convergence if the system is consistent, cf. :cite:`vdV03`. And
indeed it is consistent if and only if
.. math::
\\int_\\Gamma r \\langle n, u\\rangle = 0.
This condition makes clear that for incompressible Navier-Stokes, one
either needs to make sure that inflow and outflow always add up to 0, or
one has to specify pressure boundary conditions.
Note that, when using a multigrid preconditioner as is done here, the
coarse solver must be chosen such that it preserves the nullspace of the
problem.
"""
W = ui.function_space()
r = SpatialCoordinate(W.mesh())[0]
p = TrialFunction(P)
q = TestFunction(P)
a2 = dot(r * grad(p), grad(q)) * 2 * pi * my_dx
# The boundary conditions
# n.(p1-p0) = 0
# are implicitly included.
#
# L2 = -div(r*u) * q * 2*pi*my_dx
div_u = 1 / r * (r * u[0]).dx(0) + u[1].dx(1)
L2 = -div_u * q * 2 * pi * r * my_dx
if p0:
L2 += r * dot(grad(p0), grad(q)) * 2 * pi * my_dx
# In the Cartesian variant of the rotational form, one makes use of the
# fact that
#
# curl(curl(u)) = grad(div(u)) - div(grad(u)).
#
# The same equation holds true in cylindrical form. Hence, to get the
# rotational form of the splitting scheme, we need to
#
# rotational form
if rotational_form:
# If there is no dependence of the angular coordinate, what is
# div(grad(div(u))) in Cartesian coordinates becomes
#
# 1/r div(r * grad(1/r div(r*u)))
#
# in cylindrical coordinates (div and grad are in cylindrical
# coordinates). Unfortunately, we cannot write it down that
# compactly since u_phi is in the game.
# When using P2 elements, this value will be 0 anyways.
div_ui = 1 / r * (r * ui[0]).dx(0) + ui[1].dx(1)
grad_div_ui = as_vector((div_ui.dx(0), div_ui.dx(1)))
L2 -= r * mu * dot(grad_div_ui, grad(q)) * 2 * pi * my_dx
# div_grad_div_ui = 1/r * (r * grad_div_ui[0]).dx(0) \
# + (grad_div_ui[1]).dx(1)
# L2 += mu * div_grad_div_ui * q * 2*pi*r*dx
# n = FacetNormal(Q.mesh())
# L2 -= mu * (n[0] * grad_div_ui[0] + n[1] * grad_div_ui[1]) \
# * q * 2*pi*r*ds
p1 = Function(P)
if p_bcs:
solve(
a2 == L2,
p1,
bcs=p_bcs,
solver_parameters={
"linear_solver": "iterative",
"symmetric": True,
"preconditioner": "hypre_amg",
"krylov_solver": {
"relative_tolerance": tol,
"absolute_tolerance": 0.0,
"maximum_iterations": 100,
"monitor_convergence": verbose,
},
},
)
else:
# If we're dealing with a pure Neumann problem here (which is the
# default case), this doesn't hurt CG if the system is consistent,
# cf. :cite:`vdV03`. And indeed it is consistent if and only if
#
# \int_\Gamma r n.u = 0.
#
# This makes clear that for incompressible Navier-Stokes, one
# either needs to make sure that inflow and outflow always add up
# to 0, or one has to specify pressure boundary conditions.
#
# If the right-hand side is very small, round-off errors may impair
# the consistency of the system. Make sure the system we are
# solving remains consistent.
A = assemble(a2)
b = assemble(L2)
# Assert that the system is indeed consistent.
e = Function(P)
e.interpolate(Constant(1.0))
evec = e.vector()
evec /= norm(evec)
alpha = b.inner(evec)
normB = norm(b)
# Assume that in every component of the vector, a round-off error
# of the magnitude DOLFIN_EPS is present. This leads to the
# criterion
# |<b,e>| / (||b||*||e||) < DOLFIN_EPS
# as a check whether to consider the system consistent up to
# round-off error.
#
# TODO think about condition here
# if abs(alpha) > normB * DOLFIN_EPS:
if abs(alpha) > normB * 1.0e-12:
# divu = 1 / r * (r * u[0]).dx(0) + u[1].dx(1)
adivu = assemble(((r * u[0]).dx(0) + u[1].dx(1)) * 2 * pi * my_dx)
info("\\int 1/r * div(r*u) * 2*pi*r = {:e}".format(adivu))
n = FacetNormal(P.mesh())
boundary_integral = assemble((n[0] * u[0] + n[1] * u[1]) * 2 * pi * r * ds)
info("\\int_Gamma n.u * 2*pi*r = {:e}".format(boundary_integral))
message = (
"System not consistent! "
"<b,e> = {:g}, ||b|| = {:g}, <b,e>/||b|| = {:e}.".format(
alpha, normB, alpha / normB
)
)
info(message)
# # Plot the stuff, and project it to a finer mesh with linear
# # elements for the purpose.
# plot(divu, title='div(u_tentative)')
# # Vp = FunctionSpace(Q.mesh(), 'CG', 2)
# # Wp = MixedFunctionSpace([Vp, Vp])
# # up = project(u, Wp)
# fine_mesh = Q.mesh()
# for k in range(1):
# fine_mesh = refine(fine_mesh)
# V = FunctionSpace(fine_mesh, 'CG', 1)
# W = V * V
# # uplot = Function(W)
# # uplot.interpolate(u)
# uplot = project(u, W)
# plot(uplot[0], title='u_tentative[0]')
# plot(uplot[1], title='u_tentative[1]')
# # plot(u, title='u_tentative')
# interactive()
# exit()
raise RuntimeError(message)
# Project out the roundoff error.
b -= alpha * evec
#
# In principle, the ILU preconditioner isn't advised here since it
# might destroy the semidefiniteness needed for CG.
#
# The system is consistent, but the matrix has an eigenvalue 0.
# This does not harm the convergence of CG, but when
# preconditioning one has to make sure that the preconditioner
# preserves the kernel. ILU might destroy this (and the
# semidefiniteness). With AMG, the coarse grid solves cannot be LU
# then, so try Jacobi here.
# <http://lists.mcs.anl.gov/pipermail/petsc-users/2012-February/012139.html>
#
prec = PETScPreconditioner("hypre_amg")
from dolfin import PETScOptions
PETScOptions.set("pc_hypre_boomeramg_relax_type_coarse", "jacobi")
solver = PETScKrylovSolver("cg", prec)
solver.parameters["absolute_tolerance"] = 0.0
solver.parameters["relative_tolerance"] = tol
solver.parameters["maximum_iterations"] = 100
solver.parameters["monitor_convergence"] = verbose
# Create solver and solve system
A_petsc = as_backend_type(A)
b_petsc = as_backend_type(b)
p1_petsc = as_backend_type(p1.vector())
solver.set_operator(A_petsc)
solver.solve(p1_petsc, b_petsc)
return p1
def _compute_pressure(p0,
alpha,
rho,
dt,
mu,
div_ui,
p_bcs=None,
p_function_space=None,
rotational_form=False,
tol=1.0e-10,
verbose=True):
'''Solve the pressure Poisson equation
- \\Delta phi = -div(u),
boundary conditions,
for p with
\\nabla p = u.
'''
#
# The following is based on the update formula
#
# rho/dt (u_{n+1}-u*) + \nabla phi = 0
#
# with
#
# phi = (p_{n+1} - p*) + chi*mu*div(u*)
#
# and div(u_{n+1})=0. One derives
#
# - \nabla^2 phi = rho/dt div(u_{n+1} - u*),
# - n.\nabla phi = rho/dt n.(u_{n+1} - u*),
#
# In its weak form, this is
#
# \int \grad(phi).\grad(q)
# = - rho/dt \int div(u*) q - rho/dt \int_Gamma n.(u_{n+1}-u*) q.
#
# If Dirichlet boundary conditions are applied to both u* and u_{n+1} (the
# latter in the final step), the boundary integral vanishes.
#
# Assume that on the boundary
# L2 -= inner(n, rho/k (u_bcs - ui)) * q * ds
# is zero. This requires the boundary conditions to be set for ui as well
# as u_final.
# This creates some problems if the boundary conditions are supposed to
# remain 'free' for the velocity, i.e., no Dirichlet conditions in normal
# direction. In that case, one needs to specify Dirichlet pressure
# conditions.
#
if p0:
P = p0.function_space()
else:
P = p_function_space
p1 = Function(P)
p = TrialFunction(P)
q = TestFunction(P)
a2 = dot(grad(p), grad(q)) * dx
L2 = -alpha * rho / dt * div_ui * q * dx
L2 += dot(grad(p0), grad(q)) * dx
if rotational_form:
L2 -= mu * dot(grad(div_ui), grad(q)) * dx
if p_bcs:
solve(a2 == L2,
p1,
bcs=p_bcs,
solver_parameters={
'linear_solver': 'iterative',
'symmetric': True,
'preconditioner': 'hypre_amg',
'krylov_solver': {
'relative_tolerance': tol,
'absolute_tolerance': 0.0,
'maximum_iterations': 100,
'monitor_convergence': verbose,
'error_on_nonconvergence': True
}
})
else:
# If we're dealing with a pure Neumann problem here (which is the
# default case), this doesn't hurt CG if the system is consistent, cf.
#
# Iterative Krylov methods for large linear systems,
# Henk A. van der Vorst.
#
# And indeed, it is consistent: Note that
#
# <1, rhs> = \sum_i 1 * \int div(u) v_i
# = 1 * \int div(u) \sum_i v_i
# = \int div(u).
#
# With the divergence theorem, we have
#
# \int div(u) = \int_\Gamma n.u.
#
# The latter term is 0 if and only if inflow and outflow are exactly
# the same at any given point in time. This corresponds with the
# incompressibility of the liquid.
#
# Another lesson from this:
# If the mesh has penetration boundaries, you either have to specify
# the normal component of the velocity such that \int(n.u) = 0, or
# specify Dirichlet conditions for the pressure somewhere.
#
A = assemble(a2)
b = assemble(L2)
# If the right hand side is flawed (e.g., by round-off errors), then it
# may have a component b1 in the direction of the null space,
# orthogonal to the image of the operator:
#
# b = b0 + b1.
#
# When starting with initial guess x0=0, the minimal achievable
# relative tolerance is then
#
# min_rel_tol = ||b1|| / ||b||.
#
# If ||b|| is very small, which is the case when ui is almost
# divergence-free, then min_rel_to may be larger than the prescribed
# relative tolerance tol. This happens, for example, when the time
# steps is very small.
# Sanitation of right-hand side is easy with
#
# e = Function(P)
# e.interpolate(Constant(1.0))
# evec = e.vector()
# evec /= norm(evec)
# print(b.inner(evec))
# b -= b.inner(evec) * evec
#
# However it's hard to decide when the right-hand side is inconsistent
# because of round-off errors in previous steps, or because the system
# is actually inconsistent (insufficient boundary conditions or
# something like that). Hence, don't do anything and rather try to
# fight the cause for round-off.
# In principle, the ILU preconditioner isn't advised here since it
# might destroy the semidefiniteness needed for CG.
#
# The system is consistent, but the matrix has an eigenvalue 0. This
# does not harm the convergence of CG, but with preconditioning one has
# to make sure that the preconditioner preserves the kernel. ILU might
# destroy this (and the semidefiniteness). With AMG, the coarse grid
# solves cannot be LU then, so try Jacobi here.
# <http://lists.mcs.anl.gov/pipermail/petsc-users/2012-February/012139.html>
#
# TODO clear everything; possible in FEniCS 2017.1
# <https://fenicsproject.org/qa/12916/clear-petscoptions>
# PETScOptions.clear()
prec = PETScPreconditioner('hypre_amg')
PETScOptions.set('pc_hypre_boomeramg_relax_type_coarse', 'jacobi')
solver = PETScKrylovSolver('cg', prec)
solver.parameters['absolute_tolerance'] = 0.0
solver.parameters['relative_tolerance'] = tol
solver.parameters['maximum_iterations'] = 1000
solver.parameters['monitor_convergence'] = verbose
solver.parameters['error_on_nonconvergence'] = True
# Create solver and solve system
A_petsc = as_backend_type(A)
b_petsc = as_backend_type(b)
p1_petsc = as_backend_type(p1.vector())
solver.set_operator(A_petsc)
solver.solve(p1_petsc, b_petsc)
return p1
