Sweeping is called for when the coefficients of any of the Terms, or the
boundary conditions, depend on the solution variable. As I read your problem,
with default no-flux boundary conditions, I don't think sweeping is necessary.
> On Aug 29, 2016, at 1:19 PM, Yun Tao <yun...@ucdavis.edu> wrote:
>
> P.S. Would you recommend "sweeping" in a time-evolving problem that's as
> simple as the one in my script?
>
> On Mon, Aug 29, 2016 at 12:54 PM, Guyer, Jonathan E. Dr. (Fed)
> <jonathan.gu...@nist.gov> wrote:
> 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>
> > > >> _______________________________________________
> > > >> fipy mailing list
> > > >> fipy@nist.gov
> > > >> http://www.ctcms.nist.gov/fipy
> > > >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
> > > >
> > > > _______________________________________________
> > > > fipy mailing list
> > > > fipy@nist.gov
> > > > http://www.ctcms.nist.gov/fipy
> > > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > 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
> > > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
> > >
> > >
> > > _______________________________________________
> > > fipy mailing list
> > > fipy@nist.gov
> > > http://www.ctcms.nist.gov/fipy
> > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
> > >
> > >
> > >
> > > --
> > > Yun Tao
> > > Postdoc
> > > Center for Infectious Disease Dynamics
> > > Pennsylvania State University
> > > State College, PA 16803
> > > <new_0flux_bc_fipylistserve.py>_______________________________________________
> > > fipy mailing list
> > > fipy@nist.gov
> > > http://www.ctcms.nist.gov/fipy
> > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
> >
> >
> > _______________________________________________
> > fipy mailing list
> > fipy@nist.gov
> > http://www.ctcms.nist.gov/fipy
> > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
> >
> >
> >
> > --
> > 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
> > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
>
>
> _______________________________________________
> fipy mailing list
> fipy@nist.gov
> http://www.ctcms.nist.gov/fipy
> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
>
>
>
> --
> 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
> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
_______________________________________________
fipy mailing list
fipy@nist.gov
http://www.ctcms.nist.gov/fipy
[ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
