The script as you supplied it had the constraint commented out. You said the
answer doesn't change when you uncomment the constraint, and I'm suggesting
that you need to sweep it because the constraint clearly depends on the
solution.
Beyond that, I don't understand why you're trying to write a no-flux Robin
condition. FiPy is intrinsically no-flux. What is the real problem that you are
trying to solve that FiPy's intrinsic boundary conditions doesn't already do
for you?
> On Aug 29, 2016, at 12:37 PM, Yun Tao <yun...@ucdavis.edu> wrote:
>
> Hi Jonathan,
>
> So if I understand correctly, what you're saying is that my script, as it is
> now (without sweeping), is generating incorrect results even though the
> solution appears conserved?
>
> On Mon, Aug 29, 2016 at 9:55 AM, Guyer, Jonathan E. Dr. (Fed)
> <jonathan.gu...@nist.gov> wrote:
> Every time you solve, you change the value of phi, which changes your
> boundary condition, which will change the solution for phi. You need to sweep.
>
> > On Aug 26, 2016, at 4:32 PM, Yun Tao <yun...@ucdavis.edu> wrote:
> >
> > Thank you, Jonathan, for the insight. Sorry about my confusion -- I'm still
> > slowly teaching myself the fundamentals as a biologist.
> >
> > I've now read more on the topic. Based on your comments:
> >
> > "By constraining var.faceGrad to zero, you are saying that the boundary
> > flux is
> > \phi b \tanh(alpha*r) (pos-den)/r"
> > This is not a conservative boundary condition.
> >
> > it makes more sense why having var.faceGrad.constrain(0,
> > where=m.exteriorFaces) causes the solution to blow up if advection points
> > rightward toward a point-attractor ("den") and to leak if advection points
> > leftward.
> >
> > I think I've now also correctly set up the Robin BC (line 38 in attached
> > script) -- the solution's integral over space ("cell volume") is indeed
> > conserved at 1 throughout the simulation. However, not defining my boundary
> > condition at all appears to give exactly the same results. Is this because
> > FiPy assumes Robin BC if given no specification?
> >
> > Thanks,
> > Yun
> >
> >
> > On Thu, Aug 25, 2016 at 10:52 AM, Guyer, Jonathan E. Dr. (Fed)
> > <jonathan.gu...@nist.gov> wrote:
> > I'm not sure why you conclude from that example that
> >
> > var.faceGrad.constrain(0, where=m.exteriorFaces)
> >
> > only applies to the advection component. Where does it say that?
> >
> >
> > In the code you sent, with
> >
> > eq3 = TransientTerm() == DiffusionTerm(coeff=D)+
> > convection(coeff=faceVelocity)
> >
> > the flux is
> >
> > D \nabla \phi + \phi b \tanh(alpha*r) (pos-den)/r
> >
> > By constraining var.faceGrad to zero, you are saying that the boundary flux
> > is
> >
> > \phi b \tanh(alpha*r) (pos-den)/r
> >
> > This is not a conservative boundary condition.
> >
> > > On Aug 24, 2016, at 8:59 PM, Yun Tao <yun...@ucdavis.edu> wrote:
> > >
> > > Hi Dan,
> > >
> > > Wow. I did not expect that at all, thanks for that important information!
> > > I just tried searching for ways to implement the Robin BCs in FiPy. This
> > > site example
> > > <http://www.ctcms.nist.gov/fipy/examples/convection/generated/examples.convection.robin.html>
> > > appears to show that the var.faceGrad.constrain(0,
> > > where=m.exteriorFaces) command I mentioned earlier handles only the
> > > advection component, while, I presume, the diffusion component is subject
> > > to Neumann BCs by default. If that is so, then it's even more puzzling
> > > why having that line in my code blows up the solution, yet the solution
> > > seems well-behaved under just the Neumann BCs. Am I missing something
> > > else here?
> > >
> > > Thanks,
> > > Yun
> > >
> > > On Wed, Aug 24, 2016 at 8:24 PM, Daniel Farrell <boyfarr...@gmail.com>
> > > wrote:
> > > Hello Yun,
> > >
> > > I just briefly looked at the code. Seems like you are solving something
> > > like an advection diffusion problem. This might not help but just I case
> > > ...
> > >
> > > If you want a closed boundary you need to apply Robin boundary conditions
> > > because by definition the flux contains two components: one related to
> > > the diffusion process and one the advection process.
> > >
> > > For example, http://scicomp.stackexchange.com/a/10576/3691
> > >
> > > Dan
> > >
> > > On 24 Aug 2016, at 22:56, Yun Tao <yun...@ucdavis.edu> wrote:
> > >
> > >> Hi all,
> > >>
> > >> I'm experiencing a bizarre issue when trying to implement zero-flux
> > >> external boundary condition when solving for transient solutions. My
> > >> understanding is that it is the default setting in FiPy 3. Indeed,
> > >> without specifying it, the solutions (attached) remains at unity
> > >> throughout the simulation duration. However, when I manually tried to
> > >> fix the exterior face gradient to zero with var.faceGrad.constrain(0,
> > >> where=m.exteriorFaces), the solution began to blow up (as shown in the
> > >> printed statements). Why does this happen? Is there a hidden conflict in
> > >> conservation settings I should be careful of?
> > >>
> > >> Thanks,
> > >> Yun
> > >>
> > >>
> > >> --
> > >> Yun Tao
> > >> Postdoc
> > >> Center for Infectious Disease Dynamics
> > >> Pennsylvania State University
> > >> State College, PA 16803
> > >> <0flux_bc_fipylistserve.py>
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> > >
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> > >
> > >
> > >
> > >
> > > --
> > > Yun Tao
> > > Postdoc
> > > Center for Infectious Disease Dynamics
> > > Pennsylvania State University
> > > State College, PA 16803
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> >
> >
> > --
> > Yun Tao
> > Postdoc
> > Center for Infectious Disease Dynamics
> > Pennsylvania State University
> > State College, PA 16803
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>
> --
> Yun Tao
> Postdoc
> Center for Infectious Disease Dynamics
> Pennsylvania State University
> State College, PA 16803
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