Great, that makes a lot of sense! I've tried to define the current density as a CellVariable with the value J_n = -mu_n * n.harmonicFaceValue * phi.faceGrad + D_n * n.faceGrad as I've seen you describe in the mailing list before. But, I keep encountering the error "ValueError: could not broadcast input array from shape (135) into shape (134)" with my mesh defined as length of 134.

I believe this is caused by the harmonicFaceValue, though I am not sure? Would the following definition for current density also work: J_p.value = -mu_p * p * psi.arithmeticFaceValue.divergence + Dn * p.aritmeticFaceValue.divergence I apologize for the multiple questions and I'm very grateful for your help! Justin On Thu, Jul 25, 2019 at 10:55 AM Guyer, Jonathan E. Dr. (Fed) via fipy < fipy@nist.gov> wrote: > Justin - > > I would define a function that takes an argument x for each of your > analytical expressions, e.g., > > ``` > def y01(x): > """Initial positive ion charge density""" > return > pini*((special.gamma(k1+p1))/(special.gamma(k1)*special.gamma(p1))*((x/l)**(k1-1))*(1-(x/l))**(p1-1))/7.3572 > > def y02(x): > """"Initial negative ion charge density""" > return > nini*((special.gamma(k2+p2))/(special.gamma(k2)*special.gamma(p2))*((x/l)**(k2-1))*(1-(x/l))**(p2-1))/7.3572 > > def y03(x): > """Initial potential""" > return a1*np.sin(b1*x+c1) + a2*np.sin(b2*x+c2) > ``` > > Then you can invoke these functions with either the linspace to generate > plots like you have, or with the mesh positions, to set the initial > conditions: > > ``` > Pion.value = y01(mesh.x) > Nion.value = y02(mesh.x) > potential.value = y03(mesh.x) > ``` > > - Jon > > > On Jul 24, 2019, at 1:23 PM, Justin Pothoof <jpoth...@uw.edu> wrote: > > > > Thank you Jon, > > > > I will try writing it in one equation as you suggested. Regarding the > experimental data, I have an initial potential curve described by a sum of > sines fit as well as initial positive/negative charge density curves > described by a specific equation I'll show in a file. > > > > Thanks for the help! > > Justin > > > > On Wed, Jul 24, 2019 at 6:06 AM Guyer, Jonathan E. Dr. (Fed) via fipy < > fipy@nist.gov> wrote: > > Justin - > > > > What that error means is that if you write 'var=' for any Term, then you > must write 'var=' for every Term. > > > > In your equations: > > > > ``` > > Pion.equation = TransientTerm() + k_rec * Pion * Nion + > ConvectionTerm(coeff=1 / q, var=Jp) == 0 > > Nion.equation = TransientTerm() + k_rec * Pion * Nion + > ConvectionTerm(coeff=-1 / q, var=Jn) == 0 > > potential.equation = DiffusionTerm(1 / q * epsilon) + Pion * Nion == 0 > > Jp.equation = ImplicitSourceTerm() + ConvectionTerm(coeff=-q * mu_p * > Pion, var=potential) + ConvectionTerm(coeff=-q * Dp, var=Pion) == 0 > > Jn.equation = ImplicitSourceTerm() + ConvectionTerm(coeff=-q * mu_n * > Nion, var=potential) + ConvectionTerm(coeff=q * Dn, var=Nion) == 0 > > ``` > > FiPy does not know what Variable TransientTerm() applies to in > Pion.equation and Nion.equation, DiffusionTerm() in potential.equation, nor > ImplicitSourceTerm() in Jp.equation and Jn.equation. > > > > As a further point, you should not solve Pion.equation and Jp.equation > separately nor Nion.equation/Jn.equation. Combine them for a single, second > order PDE each for n and for p. You will want to take care that, e.g., the > equation should not be taking the gradient (\nabla) of a vector (Jn), which > would give you a tensor; rather, the expression should be divergence > (\nabla\cdot) of a vector (Jn), giving a scalar. > > > > As to comparing to your experimental data, I'd need to know what form it > takes to advise further. > > > > - Jon > > > > > On Jul 23, 2019, at 9:09 PM, Justin Pothoof <jpoth...@uw.edu> wrote: > > > > > > Hello, > > > > > > I understand that modeling the drift diffusion equations are very > challenging, but I'm having issues actually writing the equations. I keep > encountering the error: "fipy.terms.ExplicitVariableError: Terms with > explicit Variables cannot mix with Terms with implicit Variables." > > > > > > Additionally, I have fitted experimental data that describes what the > initial conditions for my system should be, but I don't know how to include > that into FiPy. I would appreciate any guidance that you can offer. I > will include a pdf of what the equations I'm trying to write are as well as > the file I have written thus far. > > > > > > Thank you, > > > Justin > > > <FiPy > Testing.py><Equations.pdf>_______________________________________________ > > > 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 ] > > <Fitted Experimental Data.py> > > > _______________________________________________ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >

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