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
> > _______________________________________________
> > fipy mailing list
> > fipy@nist.gov
> > http://www.ctcms.nist.gov/fipy
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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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