ong. Instead, I put comments at the
> top of my scripts to document how I was looking at your code and
> documentation.
>
> Thanks
>
>
> On Fri, Dec 14, 2018 at 8:20 PM Guyer, Jonathan E. Dr. (Fed) via fipy
> wrote:
> Drew -
>
> I had found the same sign
Due to the federal government shutdown, the FiPy developers are unable to
access e-mails. We will respond to your questions in a timely manner once funds
have been appropriated and the shutdown ends. We apologize for any
inconvenience and look forward to assisting you with FiPy once operations
d, and am just going on a hunch.
>
> It also seemed to me that there might be a minus sign missing in the
> RobinCoeff. The solution I get is still pinned at initial condition
> regardless of a minus sign or no minus sign there.
>
> Thanks
>
> On Fri, Dec 7, 2018 at 6:05
ss around a little in IPython seeing if any terms are coming out all zeros.
>
> Again, I put everything at
> https://github.com/cashTangoTangoCash/Convection2DFiPyExample01.
>
> Thanks
>
> On Mon, Dec 3, 2018 at 4:21 PM Guyer, Jonathan E. Dr. (Fed) via fipy
> wrote:
>
Peter -
The semiconductor drift-diffusion equations are notoriously challenging to
solve. As you may well be aware, many people use alternative formulations such
as pseudo-Fermi-levels and Slotboom variables to mitigate some of the
difficulties that arise from the enormous range of
Dario -
- FiPy's DiffusionTerm is implicit, so there is no Fourier limit on your time
step.
- There's no particular advantage to scaling length and time to 1
- Be sure to set dx = dy = dz = 1., a float, not dx = dy = dz = 1, an integer
- Jon
> On Apr 3, 2019, at 11:28 AM, Dario Panada
sing integer for dx etc. Maybe that's why?)
>
> Kind Regards,
> Dario
>
> On Wed, Apr 3, 2019 at 8:48 PM Guyer, Jonathan E. Dr. (Fed) via fipy
> wrote:
> Dario -
>
> - FiPy's DiffusionTerm is implicit, so there is no Fourier limit on your time
> step.
>
>
> On Apr 3, 2019, at 6:36 PM, Dario Panada wrote:
>
> Many thanks, I think that is making more sense now. I assume I could also
> change D to be expressed in terms of 0.042**(2./3) to keep consistency? (It
> would be a bit of a bizarre setup I admit..)
If you choose to scale things on a
Iterating over a mesh with a Python `for` loop is, as you've found, an
incredibly inefficient way to do things. FiPy, like numpy it relies on, is
intended to be used with vectorized operations.
As far as your approach, things that start with `_` in Python are internal
implementation details
I think option 3 is what you want. Before import fipy or anything else, start
your script with
```
import matplotlib
matplotlib.use('backend')
```
> On Mar 13, 2019, at 9:43 AM, Christoph Margenfeld
> wrote:
>
> Hello,
>
> as mentioned in the FiPy FAQ, a different Matplotlib backend has
`time` is a Variable as FiPy understands it, but stepFunc() simply returns an
integer, so eqI is defined with a source that is the integer 0.
I'd try
eqI = fipy.TransientTerm(coeff=1.) == ((time < 0.1) * 0. + (time >= 0.1) * 1.)
> On Feb 1, 2019, at 6:05 AM, Bill Greene wrote:
>
> I am
a manual section you can point me to, that would be great.
>
> (I changed the function to return a floating point number instead of an
> integer but it is still
> being treated as a constant.)
>
> Thanks,
>
> Bill
>
> On Fri, Feb 1, 2019 at 9:40 AM Guyer, Jonathan
> On Apr 8, 2019, at 11:30 AM, Dario Panada wrote:
> I two initial numpy grids (n*n*n) where each value corresponds to a
> source/sink. Eg: Given my source grid and coordinates (1,2,3) having value 5,
> I want to set such value as a source in FiPy.
That wasn't my question. When you publish
I just please confirm what data type sourceGrid is? In the context of
>> defining the equation
>>
>> eq = TransientTerm() == DiffusionTerm(coeff=D) + sourceGrid - sinkGrid
>>
>> Can sourceGrid/sinkGrid just be numpy arrays or even simple python lists? I
> On Apr 8, 2019, at 4:09 PM, Dario Panada wrote:
>
> DP: That would be diffusion of solubles from blood vessels (endothelial
> cells). Specifically, glucose or oxygen. It wouldn't change significantly be
> increasing it to a 40x40x40 grid, you'd just be simulating a larger section
> of
That's not unsurprising.
The scipy solvers are terribly slow *and* the pysparse LU solver is quite fast,
but uses a lot of memory.
From: fipy-boun...@nist.gov on behalf of Dario Panada
Sent: Wednesday, April 17, 2019 12:03 PM
To: FIPY
Subject: A very
the problem is well defined.
> I’ll be happy to share those calculations if needed. I’m using this problem
> as an example to learn more about fipy.
>
>> On Jun 14, 2019, at 9:10 AM, Guyer, Jonathan E. Dr. (Fed) via fipy
>> wrote:
>>
>> I had the same initial thou
t; sulfuric acid. In this case the three species might be copper, protons, and
> sulfate ions.
>
> ☘
>
>> On Jun 14, 2019, at 11:26 AM, Guyer, Jonathan E. Dr. (Fed) via fipy
>> wrote:
>>
>> Phi = 0 is a solution. Are you suggesting that this set of equations has
ary system where both non-depositing ions have zero flux.
>
> Regarding the environment, I’m using python 3.7, fipy 3.2 converted using
> 2to3, and numpy 1.6.3. I apologize that this is taking up a lot of your time.
>
> ☘
>
>
>> On Jun 14, 2019, at 3:39 PM, Guyer,
Scott -
Eq2 appears to have a typo:
-Eq2 = DiffusionTerm(coeff=z2*C1, var=Phi) + DiffusionTerm(coeff=1.0, var=C2)
+Eq2 = DiffusionTerm(coeff=z2*C2, var=Phi) + DiffusionTerm(coeff=1.0, var=C2)
Eq3 has (much) better coupling if written like this:
-Eq3 = DiffusionTerm(coeff=z3*C3, var=Phi) +
We are pleased to announce the release of FiPy 3.3.
http://www.ctcms.nist.gov/fipy
This release brings support for Python 2 and Python 3 from the same source,
without any 2to3 translation. Thanks to @pya and @woodscn for getting things
started.
This transition secures FiPy for the scheduled
We are pleased to announce the release of FiPy 3.2.
http://www.ctcms.nist.gov/fipy
This is predominantly a DevOps release. The focus has been on making
FiPy easier to install with conda. It's also possible to install a
minimal set of prerequisites with pip. Further, FiPy is
automatically
> On Apr 10, 2019, at 11:12 AM, Dario Panada wrote:
>
> In my case, as I just have only one dimension, using sourceGrid.value[i] or
> sourceGrid[...,i] should be equivalent though?
Yes
___
fipy mailing list
fipy@nist.gov
> On Apr 8, 2019, at 6:38 PM, Dario Panada wrote:
> DP: I guess what confuses me here is the [..., i] syntax on the CellVariable
> object thought.
FiPy is built on NumPy. `...` or Ellipsis means "all the indices except for the
one specified". FiPy stores cells in the last index of the
Clara -
- The cause of everything dropping to zero is that T_var.old is initialized to
zero. This isn't a particularly useful initial value, but that's what it is.
Usually, T_var.updateOld() is the first thing called in the time step loop, so
this initial condition doesn't matter, but because
Also, the natural boundary condition for FiPy is no-flux, so there's no need to
do
T_var.faceGrad.constrain(0, where=mesh.facesLeft)
> On Apr 22, 2019, at 1:28 PM, Guyer, Jonathan E. Dr. (Fed) via fipy
> wrote:
>
> Clara -
>
> - The cause of everything dropping to zero
; is the rank of the velocity -1? What does the Face Variable rank indicate?
>
> Thank you,
> Dan
>
> On Thu, Apr 11, 2019 at 8:14 AM Guyer, Jonathan E. Dr. (Fed) via fipy
> wrote:
>
>
> > On Apr 10, 2019, at 4:42 PM, Daniel DeSantis wrote:
> >
> > 1) S
Jiang -
FiPy is no-flux by default, so if you apply no constraints, P should not flow
out. By constraining P to be zero on the exteriorFaces, you guarantee that
there will be a flux in our out of the external boundary.
- Jon
From: fipy-boun...@nist.gov
tly is the
problem. Could you please give me some advice?
thanks a lot
Jiang
On Tue, Aug 13, 2019 at 9:53 AM Guyer, Jonathan E. Dr. (Fed) via fipy
mailto:fipy@nist.gov>> wrote:
Jiang -
FiPy is no-flux by default, so if you apply no constraints, P should not flow
out. By constraining P
-Candidacy PhD Student
Ginger Group
On Fri, Aug 9, 2019 at 1:36 PM Guyer, Jonathan E. Dr. (Fed) via fipy
mailto:fipy@nist.gov>> wrote:
Justin -
A couple of things:
- Charge Density is not Pion + Nion, it's Pion - Nion
- What are the terms `Pion * potential.faceGrad.divergence` in Pion.eq
m on P, rather than a
> DiffusionTerm on V, e.g.
> ConvectionTerm(coeff=V_variable.faceGrad, var=P_variable)
> instead of
> DiffusionTerm(coeff=P_variable, var=V_variable)
>
> Generally, though, I hate the drift-diffusion equations and find them
> challenging to solve.
>
&g
No need to apologize. I'm glad you were able to find the information you were
looking for.
As [noted
here](https://www.ctcms.nist.gov/fipy/examples/diffusion/generated/examples.diffusion.mesh1D.html?highlight=gradient)
the normal component of the boundary gradients are zero by default.
You can
lt.autoscale() #Autoscale axes if necessary
Justin Pothoof
The University of Washington - Department of Chemistry
Pre-Candidacy PhD Student
Ginger Group
On Fri, Jul 26, 2019 at 10:50 AM Guyer, Jonathan E. Dr. (Fed) via fipy
mailto:fipy@nist.gov>> wrote:
A current density or flux
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 +
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
> wrote:
> Justin -
>
> What that error means is tha
teful for your help!
> Justin
>
> On Thu, Jul 25, 2019 at 10:55 AM Guyer, Jonathan E. Dr. (Fed) via fipy
> wrote:
> Justin -
>
> I would define a function that takes an argument x for each of your
> analytical expressions, e.g.,
>
> ```
> def y01(
dx needs to be a float: `dx = 1.`
This doesn't always seem to be true, but it is often enough that we should
figure out how to fix it or raise an error.
https://github.com/usnistgov/fipy/issues/672
> On Sep 26, 2019, at 7:29 PM, Justin Pothoof wrote:
>
> Hello,
>
> I'm trying to set up a 2D
> On Sep 26, 2019, at 7:29 PM, Justin Pothoof wrote:
>
> I noticed that if i print(shape(CellVariable.value)) after defining a
> CellVariable I get the output (2000,) for example.. which isn't a 2D array.
FiPy is designed for unstructured meshes, so there is no internal structure to
the
>
> Nz, Ny, and Nx are the number of cells in the z, y, and x direction
> respectively.
>
> Best wishes,
> Martin
>
>
>
> On 27/09/2019 20:03, Guyer, Jonathan E. Dr. (Fed) via fipy wrote:
>>> On Sep 26, 2019, at 7:29 PM, Justin Pothoof wrote:
>>>
>>
Mohammad -
Welcome to FiPy.
It's not a problem to mix triangles and quadrilaterals. FiPy is designed for
this. The complication is that FiPy constructs cells from faces and faces are
defined by vertices (nodes), so we need to reconstruct the face definitions
from your cell_node_id.
Cribbing
t getting any value higher than 200 but when I use
> the actual Ux and Uy component of velocities, it gives me unrealistic values.
> Could you please help me to fix this.
>
> Attached are my code and one nc file that contains mesh node and element
> information, temperature, and velocity componen
Glad you found a solution, Marcel.
The issue is that a FaceGradVariable doesn't pickle itself properly. It stores
the state for a generic FaceVariable, but then it doesn't know how to rebuild
itself from that.
It either should
- pickle the correct information, which would also involve
> On Feb 23, 2020, at 8:43 AM, A A wrote:
>
> Uncommenting line 7 of the above code reveals that resetting the cell type
> from 41 to 7 of the UniformGrid2D's underlying tvtk object allows the mesh to
> appear in the plotter.
>
> I recall from previous discussions that failure of cell
AbstractMesh is abstract. It makes no assumptions about geometry, topology, or
dimensionality. Forcing it to render as VTK_POLYGON, an intrinsically 2D
object, is not appropriate.
> On Feb 23, 2020, at 8:43 AM, A A wrote:
>
> Dear All,
>
> This question is loosely related to
>
I'm curious. Do the lines remain dashed on successive calls to plot()?
As to the third question, where are you seeing exponent n and subscript i? I'm
not suggesting we don't use them, just that I don't know where.
Is the discussion at
is still block diagonal, so I don't really understand why this
gives a singular matrix, but initializing \rho to something other than zero
seems to solve that problem. Unfortunately, as I said before, it still diverges.
- Jon
> On Feb 25, 2020, at 10:04 AM, Guyer, Jonathan E. Dr. (Fed) via f
Yuranan -
There are a few things going on here.
I've modified your notebook and posted it at
https://github.com/guyer/sharing-github/blob/master/ion-transport-diagnosis.ipynb.
The singular matrix has gone away, but the solution diverges. In general, I
find the drift-diffusion equations pretty
We are pleased to announce the release of FiPy 3.4.
http://www.ctcms.nist.gov/fipy
This release adds support for the PETSc solvers for solving in parallel.
Pulls
-
- Add support for PETSc solvers (#701)
- Assorted fixes while supporting PETSc (#700)
- Fix print statements for Py3k
-
. Serial SciPy lags them all.
See
https://www.ctcms.nist.gov/fipy/documentation/USAGE.html#solving-in-parallel
for discussion.
Until we can sort this out, we won't be (willingly) dropping support for
Python 2.
> On Jan 29, 2020, at 8:51 AM, Guyer, Jonathan E. Dr. (Fed) via fipy
> wrote:
&
o
> single-thread PetSc)! Wouldn't it be nice if Pysparse worked with Py3k?
> Meanwhile, I'll keep a Python 2.7+pysparse environment around somewhere in
> the lab...
>
>
>
>
>
>
> On 29/01/2020 15:01, Guyer, Jonathan E. Dr. (Fed) via fipy wrote:
>> Some notes
.
If there is a resolution I'd be happy to take a look at submitting a pull
request for a pyvista-enabled Viewer class, though I may need some guidance in
order not to break things.
Regards,
Amine
On Wed, Jan 22, 2020 at 6:19 PM Guyer, Jonathan E. Dr. (Fed) via fipy
mailto:fipy@nist.gov
her processing. Actually this is not much an issue, as I can
> simply save phi and later recompute phi.faceGrad, which is also much more
> economic in terms of storage.
>
> Thank you anyway for spending some time on this
>
> Marcel
>
>
>
> El 20/12/19 a les 16:27, Guyer, Jonat
I filed https://github.com/usnistgov/fipy/issues/691 to address this
> On Jan 9, 2020, at 8:34 AM, Guyer, Jonathan E. Dr. (Fed) via fipy
> wrote:
>
> Thank you for the feedback. I'm inclined to agree.
>
> - Jon
>
>> On Jan 9, 2020, at 3:47 AM, Marcel UJI (IMAP)
Amine -
The n is effectively a power, or how many times the operator
$\nabla\cdot\Gamma\nabla$ should be applied. The index i runs from 1..n to
denote that each operator gets its own coefficient.
If n=1, then apply the operator $\nabla\cdot\Gamma_1\nabla$ to the argument
$\phi$ and you get
I've added comments to your https://github.com/usnistgov/fipy/issues/693, but
the short answer is that FiPy's not exporting a VTK cell type that pyvista
understands. FiPy should put out VTK_PIXELs or VTK_QUADs in this case.
> On Jan 22, 2020, at 6:22 AM, A A wrote:
>
> On another note, I've
of CylindricalGrid objects? It
> seems that fipy is working with/using VTK under the hood so it would be nice
> to be able to recover it and take a look at what I'm working with...
>
> Regards,
>
> Amine
>
> On Tue, Jan 21, 2020 at 3:55 PM Guyer, Jonathan E. Dr. (Fed
My guess is that you got the sign of the outward-facing normal wrong somewhere.
I posted my derivation to
https://gist.github.com/guyer/3b77bbf32d90ef314754f0d76a7e04cc.
On Mar 6, 2020, at 4:09 AM, Alexander Tismer
mailto:alexander.tis...@ihs.uni-stuttgart.de>>
wrote:
Dear Users,
my
You're going to have to give us more to work with. What have you tried? Where
are you stuck?
On Mar 11, 2020, at 11:23 AM, Abderrezak BOUZIANE
mailto:a.bouziane@gmail.com>> wrote:
Hi Everyone, I want to use FiPy to solve Darcy's flow equation, can you give me
some support to speed me up
sposal for further
information.
Best regards
Le ven. 13 mars 2020 à 14:56, Guyer, Jonathan E. Dr. (Fed) via fipy
mailto:fipy@nist.gov>> a écrit :
You're going to have to give us more to work with. What have you tried? Where
are you stuck?
On Mar 11, 2020, at 11:23 AM, Abderre
Setting mu_p_1, mu_n_1, Dp_1, and Dn_1 to zero at the faces of the insulating
cells should prevent any flux of charge into those cells. Those coefficients
should be set as FaceVariables and assigned to coeff= in the Terms, rather than
multiplying outside the Term.
> On Mar 30, 2020, at 3:20
Welcome to FiPy, Davide.
The Matplotlib viewers accept a `figaspect` argument, so in your case, you
would write:
viewer = Matplotlib2DViewer(vars=(phi,), figaspect=1.)
On Mar 23, 2020, at 12:26 PM, Davide Cretti
mailto:davide.cre...@gmail.com>> wrote:
Dear developers,
I am new to fipy
side between phi_W and phi(X=0)? The value of phi is
>> known at this position, because it is the boundary condition.
>>
>> Warm regards,
>> Alex
>> Am 06.03.20 um 21:30 schrieb Guyer, Jonathan E. Dr. (Fed) via fipy:
>>> My guess is that you got the sign of the outw
n
>
>
>
>
>
>
>> On Feb 25, 2020, at 10:32 PM, Guyer, Jonathan E. Dr. (Fed) via fipy
>> wrote:
>>
>> Sorry. I never said what the few things were.
>>
>> FiPy has no-flux boundary conditions by default. It's a characteristic of
>>
You might try dividing through by S(h) and applying the chain rule:
(1/S(h)) d/dx(T(h) dh/dx) = d/dx((T(h) / S(h)) dh/dx) + (T(h) / S(h)^2) dh/dx .
dS(h)/dx
The second term on the RHS still doesn’t have very efficient representation in
FiPy, either, but it’s at least not limited to first order
might be coming in the near future. Thanks for your answer and
for developing FiPy!
Best,
Iñaki
From: fipy-boun...@nist.gov<mailto:fipy-boun...@nist.gov>
mailto:fipy-boun...@nist.gov>> On Behalf Of Guyer,
Jonathan E. Dr. (Fed) via fipy
Sent: lauantai 23. toukokuuta 2020 19.08
To: FIPY ma
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