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 <[email protected]> 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
> <[email protected]> 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 <[email protected]> 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
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>
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