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
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