[firedrake] Specify boundary conditions at a corner

[David Ham]

Hi Justin,

Thanks for that, you uncovered a bug in some of how our internal imports
work. I have just merged a fix into Firedrake master so hopefully this
should now work.

Cheers,

David

On Wed, 26 Aug 2015 at 10:29 Justin Chang <jychang48 at gmail.com> wrote:

> David,
>
> I am still getting the same error. Attached the code, can you have a
> look at it and see what's going on? Note that if you comment out the
> point dirichlet stuff and uncomment the nullspace related operations,
> it outputs the correct solution.
>
> Thanks,
> Justin
>
> On Tue, Aug 25, 2015 at 3:03 AM, David Ham <David.Ham at imperial.ac.uk>
> wrote:
> > Hi Justin,
> >
> > The imports in bcs.py are relative imports (which is slightly bad style
> > but...) In order to access correct module from outside you need to use:
> >
> > from firedrake import utils
> >
> > Regards,
> >
> > David
> >
> > On Tue, 25 Aug 2015 at 00:48 Justin Chang <jychang48 at gmail.com> wrote:
> >>
> >> David,
> >>
> >> I get the following error:
> >>
> >> Traceback (most recent call last):
> >>   File "Test_LSAug.py", line 41, in <module>
> >>     class PointDirichletBC(DirichletBC):
> >>   File "Test_LSAug.py", line 42, in PointDirichletBC
> >>     @utils.cached_property
> >> AttributeError: 'module' object has no attribute 'cached_property'
> >>
> >> When I comment out that line, i get a long error. When I try to import
> >> utils and all the other modules that bcs.py imports, i get errors
> >> saying those modules don't exist. Know what's going on?
> >>
> >> Thanks,
> >> Justin
> >>
> >> On Mon, Aug 24, 2015 at 3:14 AM, David Ham <David.Ham at imperial.ac.uk>
> >> wrote:
> >> > Hi Justin,
> >> >
> >> > Having subclassed DirichletBC, what you now have is a new type of
> >> > Dirichlet
> >> > "boundary" object, so you just use it as a Dirichlet condition:
> >> >
> >> > bc3 = PointDirichletBC(W.sub(1), 0, 0)
> >> >
> >> > bc_all = [bc1, bc2, bc3]
> >> >
> >> > However Andrew is right, removing the nullspace is almost certainly a
> >> > better
> >> > solution in this case.
> >> >
> >> > Cheers,
> >> >
> >> > David
> >> >
> >> > On Sun, 23 Aug 2015 at 05:23 Justin Chang <jychang48 at gmail.com>
> wrote:
> >> >>
> >> >> Andrew,
> >> >>
> >> >> That actually did the trick, thank you very much.
> >> >>
> >> >> But I still would like to know the answer to my original question. Or
> >> >> perhaps, instead of a single corner, I would like to set (x=0,y<0.1)
> >> >> and (x<0.1,y=0) to a specific value while everywhere else is set to a
> >> >> different value.
> >> >>
> >> >> Thanks,
> >> >> Justin
> >> >>
> >> >> On Sat, Aug 22, 2015 at 11:58 AM, Andrew McRae
> >> >> <a.mcrae12 at imperial.ac.uk>
> >> >> wrote:
> >> >> > This doesn't answer your main question, but setting an appropriate
> >> >> > nullspace
> >> >> > might be more appropriate than pinning a single value; see
> >> >> > http://www.firedrakeproject.org/solving-interface.html
> >> >> >
> >> >> > [If I'm wrong, I'll let the usual suspects correct my
> misinformation]
> >> >> >
> >> >> > On 22 August 2015 at 18:47, Justin Chang <jychang48 at gmail.com>
> wrote:
> >> >> >>
> >> >> >> David,
> >> >> >>
> >> >> >> How exactly do I use that class in my code? Say I have the
> following
> >> >> >> function spaces/discretization based on the least-squares finite
> >> >> >> element method:
> >> >> >>
> >> >> >> # Mesh
> >> >> >> mesh = UnitSquareMesh(seed,seed)
> >> >> >> V = VectorFunctionSpace(mesh,"CG",1)
> >> >> >> Q = FunctionSpace(mesh,"CG",1)
> >> >> >> W = V*Q
> >> >> >> v,p = TrialFunctions(W)
> >> >> >> w,q = TestFunctions(W)
> >> >> >>
> >> >> >> # Weak form
> >> >> >> g = Function(V)
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> g.interpolate(Expression(("cos(pi*x[0])*sin(pi*x[1])+2*pi*cos(2*pi*x[0])*sin(2*pi*x[1])","-sin(pi*x[0])*cos(pi*x[1])+2*pi*sin(2*pi*x[0])*cos(2*pi*x[1])")))
> >> >> >> a = dot(v+grad(p),w+grad(q))*dx + div(v)*div(w)*dx
> >> >> >> L = dot(w+grad(q),g)*dx
> >> >> >>
> >> >> >> # Boundary conditions
> >> >> >> bc1 = DirichletBC(W.sub(0).sub(0),
> >> >> >> Expression("cos(pi*x[0])*sin(pi*x[1])"), (1,2))
> >> >> >> bc2 = DirichletBC(W.sub(0).sub(1),
> >> >> >> Expression("-sin(pi*x[0])*cos(pi*x[1])"), (3,4))
> >> >> >> bc_all = [bc1,bc2]
> >> >> >>
> >> >> >> # Solve
> >> >> >> cg_parameters = {
> >> >> >>     'ksp_type': 'cg',
> >> >> >>     'pc_type': 'bjacobi'
> >> >> >>     }
> >> >> >> solution = Function(W)
> >> >> >> A = assemble(a,bcs=bc_all)
> >> >> >> b = assemble(L,bcs=bc_all)
> >> >> >> solver =
> >> >> >>
> LinearSolver(A,solver_parameters=cg_parameters,options_prefix="cg_")
> >> >> >> solver.solve(solution,b)
> >> >> >>
> >> >> >> If I run the above code I get an error saying 'LinearSolver failed
> >> >> >> to
> >> >> >> converge after %d iterations with reason: %s', 196,
> >> >> >> 'DIVERGED_INDEFINITE_MAT'. Which I am guessing has to do with the
> >> >> >> lack
> >> >> >> of a boundary condition for the Q space, thus I want to ensure a
> >> >> >> unique solution by prescribing the bottom left constraint to a
> zero
> >> >> >> value.
> >> >> >>
> >> >> >> Thanks,
> >> >> >> Justin
> >> >> >>
> >> >> >>
> >> >> >> On Fri, Aug 21, 2015 at 4:52 AM, David Ham
> >> >> >> <David.Ham at imperial.ac.uk>
> >> >> >> wrote:
> >> >> >> > Hi Justin,
> >> >> >> >
> >> >> >> > The nice way of doing this would require better subdomain
> support
> >> >> >> > than
> >> >> >> > we
> >> >> >> > have right now. However there is a slightly hacky way of doing
> it
> >> >> >> > which
> >> >> >> > I
> >> >> >> > think will cover your case nicely.
> >> >> >> >
> >> >> >> > If you take a look at the DirichletBC class (in bcs.py), you'll
> >> >> >> > notice
> >> >> >> > that
> >> >> >> > the set of nodes at which the BC should be applied is calculated
> >> >> >> > in
> >> >> >> > DirichletBC.nodes . So you could simply subclass DirichletBC and
> >> >> >> > replace
> >> >> >> > nodes with a function which returns the index of the zero node.
> >> >> >> > For
> >> >> >> > example
> >> >> >> > (and I confess this is a sketch code which I haven't tried to
> >> >> >> > run):
> >> >> >> >
> >> >> >> > class PointDirichletBC(DirichletBC):
> >> >> >> >     @utils.cached_property
> >> >> >> >     def nodes(self):
> >> >> >> >         # Find the array of coordinate values.
> >> >> >> >         x = self.function_space().mesh().coordinates.dat.data_ro
> >> >> >> >         # Find the location of the zero rows in that
> >> >> >> >         return np.where(~x.any(axis=1))[0]
> >> >> >> >
> >> >> >> > Does that work for you?
> >> >> >> >
> >> >> >> > Cheers,
> >> >> >> >
> >> >> >> > David
> >> >> >> >
> >> >> >> > On Fri, 21 Aug 2015 at 03:32 Justin Chang <jychang48 at gmail.com>
> >> >> >> > wrote:
> >> >> >> >>
> >> >> >> >> Hi all,
> >> >> >> >>
> >> >> >> >> If I create a mesh using UnitSquareMesh or UnitCubeMesh, is
> there
> >> >> >> >> a
> >> >> >> >> way to subject a single point (as opposed to an entire
> edge/face)
> >> >> >> >> to
> >> >> >> >> a
> >> >> >> >> DirichletBC? I want to subject the the location x=0,y=0 to some
> >> >> >> >> value.
> >> >> >> >>
> >> >> >> >> Thanks,
> >> >> >> >> Justin
> >> >> >> >>
> >> >> >> >> _______________________________________________
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> >> >> >> >
> >> >> >> >
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> >> >> >>
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> >> >> >
> >> >> >
> >> >> >
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