On Jul 10, 2013, at 3:14 PM, Noam Yorav-Raphael wrote:
> In the "numerical schemes" page, in the first paragraph:
>
> aA-Ff>0 should be aA+Ff>0
> Pf=-Ff/Df should be Pf=Ff/Df
>
> At least that's what makes sense to me.
I'll let Wheeler address that. I know we had some sign changes in how we
On Jul 3, 2013, at 12:59 AM, Caleb Hattingh wrote:
> The attached patch was made against the current "develop" branch. The trac
> issue tracker at matforge would not allow me to register in order to create a
> ticket for this ("The page you are looking for is temporarily unavailable"),
> oth
On Jun 26, 2013, at 11:45 AM, Ianis Bernard wrote:
> I noticed that when deleting the boundary conditions, the first element of
> the faceGrad arrays was replaced by a 0. And I don't know how to keep the old
> value.
.faceGrad is a calculated quantity, not stored. In the absence of constraint
On Jun 25, 2013, at 1:18 PM, Raymond Smith wrote:
> I just re-ran it using divergence operators on arithmetic face values of
> displacements to confirm, and with that it works fine.
Glad to hear it.
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On Jun 20, 2013, at 1:22 PM, Ryan Smith wrote:
> I don't understand the result of 18 being the index if the length of each
> component of mesh.cellCenters.value is 16. So, it seems the biggest problem
> here is that I don't fully understand the use of numerix.nearest(). But, if
> numerix.near
On Jun 20, 2013, at 12:23 AM, Rachel Zucker wrote:
> I am really new to FiPy, so perhaps I'm responsible for the problem in some
> way, but I believe that examples/cahnHilliard/mesh2DCoupled.py does not work
> properly. I have gone through many examples without incident, but in this
> case, i
On Jun 15, 2013, at 12:11 PM, Adam Stone wrote:
> At the end of the phase.simple example, the expected velocity is calculated
> from the undercooling and the parameter beta in order to choose a time step
> within the CFL limit. Beta (linear kinetic coefficient) is given a constant
> value in
On Jun 11, 2013, at 2:34 AM, Ryan Smith wrote:
> I would like to use matplotlib's streamplot function to display the fluid
> flow in the stokesCavity example. Furthermore, I would like to extend this
> for my own simulations of fluid flow (following the same code as stokesCavity
> but with dif
You need to be in the base FiPy directory (~/Scrivania/FiPy-3.0) in order to
run that example.
On Jun 4, 2013, at 12:19 PM, Michelangelo Formisano
wrote:
> Hi Daniel.
> Running sphere.py,I obtain:
>
> miky@miky-Inspiron-5521:~/Scrivania/FiPy-3.0/examples/cahnHilliard$ python
> sphere.py
> p
On May 27, 2013, at 8:11 AM, bvspavankumar wrote:
> Could you suggest me the viewer which displays the contour plot of one or
> more 2D Cell Variable objects. In my case the the CellVariables are 'phase
> field variable1' and 'phase field variable2'
examples.phase.anisotropy shows how to ov
On May 19, 2013, at 12:23 PM, Michelangelo Formisano
wrote:
> I'm Michelangelo, an Italian post-doc, and I recently discovered FIPY.
Welcome to FiPy. We hope it's useful to you.
> I would like to develop a 3D thermal/geophysical model of asteroids by using
> FIPY. My idea is to solve simul
On May 16, 2013, at 1:23 PM, Daniel Wheeler wrote:
> I believe the correct diffusion coefficient across the face that approximates
> a thin layer is
>
>D = Kc * (1 / (epsilon + (1 - epsilon) * D_ratio))
>
> where
>
>D_ratio = Kc / 2 * (1 / K1 + 1 / K2)
>
> and
>
>epsilon = dx
On May 16, 2013, at 6:39 AM, Frederic Durodie
wrote:
> So I'm a bit puzzled as to why for X from -L/2 to 0 the temperature is
> 0. : it should increase linearly to 2.5 deg C.
I suspect the problem is that divergence of the flux at the cell just left of
the thermal contact is satisfactorily ze
On May 15, 2013, at 12:43 AM, Chuck Holbert wrote:
> Now that you explain it, this is exactly what I need. I'm not fluent in
> programming so not sure how to implement these suggestions within FiPy. Can
> you point me to an example that I can use to get started? Any help will be
> greatly
On May 13, 2013, at 4:40 PM, Chuck Holbert wrote:
> Yes, now I see this. So, maybe mathematically I have setup the problem
> incorrectly. I would like to allow the concentrations at the interface to
> increase if the rate of back diffusion becomes greater than the rate of decay.
Do you also
On May 13, 2013, at 3:58 PM, Chuck Holbert wrote:
> To estimate back diffusion and an accumulation at the interface (left-most
> boundary), don't I want the precursor of the exponential to change at every
> timestep as phi changes?
>
> Forgive me if this should be evident, but want to make su
On May 10, 2013, at 2:11 AM, Frederic Durodie
wrote:
> could you help me with how to implement a thermal contact, hc
> [W/(m^2.K)], between two regions : so there is like a discontinuity in
> the temperature between the two regions.
I don't know whether the following is the solution you want
On May 12, 2013, at 10:23 PM, Chuck Holbert wrote:
> I'm looking for a bit of assistance in how to organize a FiPy script I am
> trying to write. I am trying to model transient 1D diffusion into and out of
> soil with an exponentially decaying boundary condition. I assuming a
> starting con
On May 2, 2013, at 12:19 PM, Edwin Sze Lun Khoo wrote:
> The original PDE is dC/dt + alpha*d/dx(1/C) = d^2C/dx^2 where C is the
> dependent variable and alpha is a constant. You suggested that:
>
>
>> You can try running the chain rule on it:
>>
>> \alpha\frac{\partial}{\partial x}\frac{1}{C
On Apr 29, 2013, at 5:45 PM, Frederic Durodie
wrote:
> In a simple 2D heat conduction problem I try to impose a power flux on
> part of the outer boundary and a fixed temperature on the remaining
> part.
>
> However the resulting temperature distribution is not what I expect and
> furthermore
On Apr 26, 2013, at 5:30 AM, Kun-Dar Li wrote:
> I use two different methods to define the
> orientation as the following:
> theta=arctan2(phi.getFaceGrad()[1], phi.getFaceGrad()[0])
> theta=arctan(phi.getFaceGrad()[1] / phi.getFaceGrad()[0])
> However, I got a slight different result from abo
On Apr 25, 2013, at 11:04 AM, Bruno Huet wrote:
> it looks like most time is spent within a fipy function:
> fipy.variables.binaryOperatorVariable.binOp.unit
>
> Am I misusing fipy objects ? Could any one advise or has seen this behavior
> before?
I have seen bottlenecks in fipy.variables.
http://article.gmane.org/gmane.comp.python.fipy/2971
and was just fixed a couple of days ago:
> On Mar 22, 2013, at 9:52 AM, Jonathan Guyer wrote:
>
> This issue has been fixed on the `develop` branch. See
> http://matforge.org/fipy/ticket/513 and
> http://matforge.org/fipy/changeset/
On Mar 27, 2013, at 6:11 PM, Kristopher Kuhlman wrote:
> Please pardon my ignorance, but how do I obtain the develop branch?
No ignorance involved. It's been mentioned on the list a couple of times, but
we've never managed to push updated documentation since we switched to git.
> I see a men
On Mar 22, 2013, at 12:38 AM, Edwin Sze Lun Khoo wrote:
> It turns out that my spatial discretization was too fine, so Python ran out
> of memory. After decreasing my spatial discretization and trying the
> PowerLawConvectionTerm that you suggested, I still get the "IndexError: id1
> does not
On Mar 22, 2013, at 9:52 AM, Jonathan Guyer wrote:
>
> On Mar 21, 2013, at 6:38 PM, Kristopher Kuhlman wrote:
>
>> I have no Idea what this actually means for my problem, but I thought I
>> would report it.
>
>
> I have no idea what it means, either, but it
On Mar 25, 2013, at 7:17 PM, Kristopher Kuhlman wrote:
> I am familiar with domain decomposition methods. This seems a quite abstract
> way to tackle the problem. I don't want to artificially introduce iteration
> into a linear diffusion problem. It is really just a mesh-generation issue.
Ar
On Mar 25, 2013, at 9:32 AM, Jonathan Guyer wrote:
>
> On Mar 23, 2013, at 6:00 PM, Serbulent UNSAL wrote:
>
>>> Much more expediently done with
>>>
>>> return tmp.flatten()
>>>
>>
>> No itertools.chain is clearly fastest method
On Mar 23, 2013, at 6:00 PM, Serbulent UNSAL wrote:
>> Much more expediently done with
>>
>>return tmp.flatten()
>>
>
> No itertools.chain is clearly fastest method. It can be seen on
> http://stackoverflow.com/questions/406121/flattening-a-shallow-list-in-python
But that post is about fi
You'll need to tell us more about what you're doing. I just tested Daniel's
scripts, running the one at http://pastebin.com/p5rARUJf with `mpirun -np 2`
and then running the one at http://pastebin.com/P883d0q4 in serial and it works
fine.
On Mar 22, 2013, at 5:12 PM, Adrian Jacobo wrote:
> Hi
On Mar 21, 2013, at 6:38 PM, Kristopher Kuhlman wrote:
> I have no Idea what this actually means for my problem, but I thought I would
> report it.
I have no idea what it means, either, but it's a helpful diagnostic. Thank you.
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On Mar 21, 2013, at 1:51 PM, Raymond Smith wrote:
> I went ahead and re-updated my scipy and matplotlib as well, so a test output
> with
> numpy-1.7.0
> pysparse-1.1.1
> scipy-0.11.0
> matplotlib-1.2.0
> I got 6 errors
> http://pastebin.com/BHadSKBE
>
> A number of them seem to be related to gm
On Mar 20, 2013, at 6:06 PM, Jason Furtney wrote:
> Thanks again for the great software. I have been looking at linear
> advection problems with FiPy and I ran into a couple issues.
>
> The FiPy VanLeerConvectionTerm seems to implement the MinMod slope
> limiter as described in "Finite Volume Me
On Mar 20, 2013, at 4:51 PM, Serbulent UNSAL wrote:
> First I'm sorry for confusion. I should share both versions (slow one
> and mine) but only share last version. But before that explaining
> problem domain might be helpful for smoothing confusion away.
>
> I'm working on tumor modelling. The
On Mar 12, 2013, at 8:19 AM, Jonathan Guyer wrote:
> On Mar 11, 2013, at 5:05 PM, Philippe Baucour wrote:
>
>> I think I found a bug with numpy 1.7.0 and Fipy (latest git).
>> The best example is the circle diffusion problem in which I can't
>> initialize the viewe
On Feb 22, 2013, at 2:27 PM, Raymond Smith wrote:
> So as far as I can tell, you were exactly right, and numpy-1.7.0 was causing
> the issues. If there's anything else I can do that would help clarify what's
> going on or help ease the transition to numpy-1.7.0, let me know.
Can you try again
On Mar 20, 2013, at 11:38 AM, Daniel Wheeler wrote:
> One way to get around the issue, is to pickle the simpler array and string
> objects and then use them to reconstruct the mesh and variable. This is
> hardly a persistent method for data storage, but pickling in general with
> complicated o
On Mar 20, 2013, at 9:51 AM, Daniel Wheeler wrote:
> On Wed, Mar 20, 2013 at 5:57 AM, Serbulent UNSAL wrote:
> Dear Dan and Raymond,
>
> Thanks for your help to both. After your suggestions I review my code.
> But changing X and Y like
>
> X = mesh.x
> Y = mesh.y
>
> makes the code seriousl
On Mar 15, 2013, at 5:08 PM, Edwin Sze Lun Khoo wrote:
> The term I tried was PowerLawConvectionTerm(coeff=(-alpha/C**2, ), var=C) but
> I got an error that said "IndexError: id1 does not have the same size as b".
> The rest of the error log can be found at http://pastebin.com/K4hy0GCh.
The co
On Mar 14, 2013, at 9:33 PM, Edwin Sze Lun Khoo wrote:
> I am having difficulties with trying to put a PDE into a form that FiPy
> accepts. The equation in question is dC/dt + alpha*d/dx(1/C) = d^2C/dx^2
> where C is the dependent variable and alpha is a constant. The first and last
> terms ar
Thanks for the report. I see the same error, but I don't understand it (and
can't seem to debug it).
I created http://matforge.org/fipy/ticket/513 to track the issue.
On Mar 14, 2013, at 1:13 AM, Kristopher Kuhlman wrote:
> Greetings FiPy list,
>
> I am trying to make a 1D transient convect
On Mar 13, 2013, at 3:44 AM, Philippe Baucour wrote:
> Have a look to my previous email about numpy 1.7 bug !!!
Yes, this definitely looks like the same issue. I don't think it has anything
to do with matplotlib, per se, but that for some reason numpy 1.7 is returning
cell or face indices as f
On Mar 11, 2013, at 5:05 PM, Philippe Baucour wrote:
> I think I found a bug with numpy 1.7.0 and Fipy (latest git).
> The best example is the circle diffusion problem in which I can't
> initialize the viewer. I try to debug the problem and is seems to be
> related to numpy.take for which indices
On Mar 8, 2013, at 10:47 AM, Adrian Jacobo wrote:
> As you suspected, I've installed openmpi using macports, and this
> might be the source of the problem. Here I send you the result of 'otool
> -L' for the mpi4py and PyTrilinos libraries.
Interesting. It would be good to figure out why m
On Mar 7, 2013, at 2:53 PM, Adrian Jacobo wrote:
> On a related comment, I'm able to compile your example code using the openmp
> wrapper for gcc:
>
> openmpicc trivialmpi.c -o trivialmpi
>
> and it runs just fine using openmpirun.
This is the macports openmpi you installed? That may be the pr
On Feb 21, 2013, at 7:43 PM, Raymond Smith wrote:
> I've just installed fipy, and I got a number of errors while running the
> test. My output is located at http://pastebin.com/grn7Maki.
> I'm using Arch Linux, 64 bit, with fipy-3.0, and I've installed pysparse
> (1.1.1), gmsh (2.6.1), numpy (1
On Feb 6, 2013, at 10:47 AM, Laurence wrote:
> I've set up a 3D Gmsh such that there is a convenient surface
> at Y==0.
>
> Therefore, in this 3D mesh there are many faces on this
> plane.
>
> At every step in my transient equation, I want to take the values
> on the faces on this plane, an
On Feb 4, 2013, at 11:59 AM, William McFadden wrote:
> From the FAQ, I'm setting it up by defining CellVariables that can be set to
> vary spatially
>
> n_xx = CellVariable(mesh=mesh, value = x)
> n_yx = CellVariable(mesh=mesh,value= x)
>
> then I generate a few diffusion terms.
> the firs
On Jan 23, 2013, at 8:39 PM, John Assael wrote:
> I think it its not a problem of properties as the same values are used in
> COMSOL and they result different values.
> Moreover, I tried small changes like 5-10% and there was no big difference...
If you drop tc0 by a factor of 2, you get pretty
On Jan 23, 2013, at 11:08 PM, Ajay Rawat wrote:
> Why not try using pygment;
> >> pygmentize -O full,style=emacs -o test.tex inputGrid2D.py
Thanks for the suggestion. That does a nice job of rendering the python code,
but it does not deal with the reStructuredText and TeX mathematics that we u
On Jan 24, 2013, at 7:57 AM, Laurence wrote:
> SOLVED!!!
Good!
> I realised I had to create the constants that control my reactions
> into a CellVariable which are therefore localised to the reaction area.
Yes. If the reaction constant is both localized and constant, then the
.setValue() appr
On Jan 22, 2013, at 9:56 AM, John Assael wrote:
> Well I finally did it with some extra points defining the cell size...
> However I keep getting a marked difference from Comsol results
> The charts are here... http://www.ic3man.gr/Tol8_6c.xls
> Is it possible that the calculations are not done r
On Jan 23, 2013, at 3:39 PM, Laurence wrote:
> I'm happy with the mask and how it ascertains to the mesh I've already
> created.
>
> My issue is that I am creating a diffusion field on the mesh, and
> at one place in the mesh, a localised reaction is taking place
> depending on the concentration
On Jan 23, 2013, at 1:30 PM, Laurence wrote:
> I've only started using Fipy and this is my first post.
Welcome.
>
> I would like to take a mesh I have imported from Gmsh, and create a subset
> mesh of certain cells within certain X,Y limits. The mesh imports
> fine, and I have my cells refer
On Jan 21, 2013, at 7:07 PM, Salomon Turgman Cohen wrote:
>I was wondering how to generate a nicely formatted html or pdf file from
> one of the examples, say mesh1D.py.
In addition to what Wheeler offered, I've posted a script to
http://matforge.org/fipy/wiki/FormatExamples that allows th
On Jan 19, 2013, at 6:21 AM, John Assael wrote:
> Perfect I gave Gmsh a try! However is the Gmsh2D background parameter not
> working?
It works for me. Do the tests pass? Background meshes are tested in the
docstring for Gmsh2D and if the tests pass, then background meshes are working.
What h
On Jan 18, 2013, at 12:01 PM, John Assael wrote:
> I have a couple more questions:
> 1) The problem is a quarter symmetry and I am solving the problem in the
> first Quartile how can I specify the symmetry of the experiment?
I'd use a CylindricalGrid1D mesh for the problem you've shown us so fa
On Jan 17, 2013, at 2:30 PM, John Assael wrote:
> Well, the properties are correct.
> I am simulating a real experiment where I have a tantalum wire inside toluene
> with this heat input and what we observe is 3 degrees temp rise on the
> surface of the wire in 1second.
> Why cant I see it with
On Jan 17, 2013, at 12:58 PM, John Assael wrote:
> from fipy import *
> import time
>
> dx = dy = 10
> nx = ny = 100
> L = dx * nx
> mesh = Grid2D(dx=dx, dy=dy, nx=nx, ny=ny)
>
> # Fluid Properties
> tc0=0.141
> den0=867.
> cp0=1717
>
> # Wire Properties
> tcw=57.5
> denw=16690.
> cpw=135.
> Q
On Jan 17, 2013, at 1:02 PM, Maximilian Balandat wrote:
>> I am confused by the above equation. Are the x and t derivatives on the
>> correct terms?
>
> Yes they are. This equation comes from expressing the equation rho_t +
> (g(rho)*rho)_x in terms of the flux u rather the density rho. The fu
On Jan 16, 2013, at 6:35 AM, John Assael wrote:
> Thank you very much for your help!
> Do you know how can I set only a point (a small circle) as the heat source
> and not the whole side?
examples.diffusion.mesh1D, examples.diffusion.electrostatics, and
examples.phase.anisotropy all show how t
On Jan 14, 2013, at 12:10 PM, John Assael wrote:
> Dear Jonathan,
> The problem that ll try to solve next is in 2D so I would prefer to solve
> everything this way.
> Exactly! Could you please provide me an example sample boundary condition for
> my case?
Sample boundary condition for what? Se
On Jan 13, 2013, at 12:30 PM, John Assael wrote:
> I know
> - properties dw,cpw,kw,d,cp,k and I know Q.
> I want to calculate the temperature rise as a function of time
>
> So I create a mesh and set the CellVariable
> dT = CellVariable(name = r'$\Delta T$',
>mesh = mesh
On Dec 10, 2012, at 3:47 PM, Adrian Jacobo wrote:
>> Not for me. If you're seeing something else, then it may come down to either
>> boundary conditions or parameter values. We probably need to see a minimal
>> script that exhibits what you're seeing.
> I send you attached a minimal script
On Dec 10, 2012, at 1:55 PM, Adrian Jacobo wrote:
> And I'm defining the system in this way:
>
> mesh = fp.Grid3D(dx=dx, dy=dy,dz=dz, nx=nx, ny=ny,nz=nz)
> C = fp.CellVariable(name = "Calcium",mesh = mesh, value = 0.)
> B = fp.CellVariable(name = "Buffer",mesh = mesh, value = B_0)
> eqC = fp.Tra
On Dec 7, 2012, at 5:32 PM, dely wrote:
> I am writing to ask how to correctly use setValue with the where argument
> when running fipy in parallel. For example, to set the value of a
> cellVariable in a hemispherical region on the bottom boundary of a mesh, I
> can do the following:
>
> x, y
On Dec 7, 2012, at 10:47 AM, Adam Stone wrote:
> Or is the '2D' solution actually doing something like this?
>
>
Yes.
Thanks to Benny for the diagnosis.
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This is http://matforge.org/fipy/ticket/447, which we haven't resolved yet.
At this point, either do:
X, Y = mesh.cellCenters[0], mesh.cellCenters[1]
or
X, Y = mesh.cellCenters
X = CellVariable(mesh=mesh, value=X)
Y = CellVariable(mesh=mesh, value=Y)
There is no reason to use the get.
On Dec 5, 2012, at 5:55 AM, Tanya Gornak wrote:
>> Tanya, It might be better to use one of the standard grid classes and then
>> use source terms to blank out exterior cells. Seems much easier to me at
>> least to get something working. Worry about optimizing it later.
>
> Thanks, Daniel. Your id
On Dec 3, 2012, at 12:23 PM, Tanya Gornak wrote:
> How can I create a Cartesian mesh for semicircle for FiPy?
I'm not even sure what that means.
You want square cells?
What should the cells look like at the semicircle boundary?
Why do you need a Cartesian mesh? If you want to know the value
On Dec 4, 2012, at 10:08 AM, Daniel Wheeler wrote:
> What I mean is: will all
> variables be updated as they should be after each iteration of sweep &
> updateOld?
>
> All "var.updateOld()" does is update the var's old value. Each CellVariable
> (if "var.hasOld = True") has an "old" attribute,
On Nov 29, 2012, at 10:49 AM, Adrian Jacobo wrote:
> Hi,
>
> Thank you for your answer.
>>> I'm solving an equation in 3d and I need to calculate the integral of the
>>> field. What is the most convenient/fast way of doing this?
>>
>> int = var.cellVolumeAverage * var.mesh.numberOfCells
> Ju
On Nov 28, 2012, at 5:15 PM, Adrian Jacobo wrote:
> I'm solving an equation in 3d and I need to calculate the integral of the
> field. What is the most convenient/fast way of doing this?
int = var.cellVolumeAverage * var.mesh.numberOfCells
> A related question: how can I access individual
On Nov 26, 2012, at 3:48 PM, Kerem Yunus Camsari wrote:
> Since I am using the Fokker-Planck equation, I needed to add the gradient of
> the diffusion term as a convection term separately (middle term below). It
> appears that if I turn this term off , the solution does not blow up.
>
>
> e
On Nov 22, 2012, at 4:07 PM, Kerem Yunus Camsari wrote:
> I have a doubt regarding the solution I obtain from FiPy in a specific
> problem I am attempting.
> I am solving the 1-Dimensional Fokker-Planck Equation Using FiPy.
>
>
>
> G^n(x) is the electron-density in my model. D_2 (x) is the D
oach to account for melting temp,
> undercooling, driving force, moving interface, etc?
>
> Thanks for being so responsive and patient with a phase-field newcomer.
>
> Adam
>
>
> On 11/15/2012 09:00 AM, Jonathan Guyer wrote:
>> On Nov 14, 2012, at 6:25 PM, Adam Ston
On Nov 14, 2012, at 6:25 PM, Adam Stone wrote:
> I'm going through the quaternary phase field example and having some
> difficulty understanding the calculation of standard potentials.
:
:
> But I don't understand how you "cook" these standard potentials:
>
> for Cj in interstitials + substitut
On Nov 9, 2012, at 8:42 PM, Adam Stone wrote:
> I was reviewing the examples.phase.binaryCoupled example at
>
> http://www.ctcms.nist.gov/fipy/examples/phase/generated/examples.phase.binaryCoupled.html
>
> and while trying to understand the implicit treatment of dC/dt, I noticed
> some possib
It appears that you are trying to run a FiPy 3.0 example with an earlier
installation of FiPy. We do not maintain (or even use) the MatForge Live CD and
I don't know how old it is. The FiPyWorkbook wiki was contributed by one of
FiPy's users, Will Gathright, over two years ago, so I would guess
Thanks, Andreas.
I run 2.7.2 on my Mac OS X laptop and we have 2.6.6 on our Debian machines.
FiPy 3.x should run with Python 2.4 or newer, but there is little incentive to
run with anything other than the newest version of Python 2.x readily available
to you. Although FiPy runs under Python 3.x
On Oct 12, 2012, at 5:17 PM, Kris Kuhlman wrote:
> On Fri, Oct 12, 2012 at 9:03 AM, Jonathan Guyer wrote:
>> The script below illustrates the way I would do this.
>>
>> Note that it crashes once h == hs because C is then zero and the
>> DiffusionTerm g
On Oct 12, 2012, at 11:03 AM, I wrote:
> FiPy has know way of knowing you want a dependency on h.
Ouch! FiPy has *no* way of knowing
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On Oct 12, 2012, at 1:33 AM, Kris Kuhlman wrote:
> I am trying to simulate a non-linear problem with piecewise-defined
> parameters, depending on the range of the dependent variable.
>
> What is the best way to specify this? In my example below, I used a
> function and an intermediate CellVaria
On Sep 19, 2012, at 1:46 PM, Allawala, Altan wrote:
> I'm trying to find the steady state solution to the following linear PDE:
>
> \frac{\partial \varphi}{\partial t} = - x * \frac{\partial \varphi}{\partial
> x} - x^2 \varphi
>
> Below is my code to solve this. However, the numerical solutio
I am very sad to pass along this news. It has been my privilege to get to know
John over the past several years at SciPy and SIAM conferences. He has always
been friendly, helpful, and engaged and his development of matplotlib has been
a key to the advancement of FiPy. He will be missed.
Begin
On Aug 28, 2012, at 2:40 PM, Benny Malengier wrote:
> Yes, that is not the problem. I'm actually not even using Trilinos, in 2.x
> series I did not have the required mpi lib installed. This is trunk, on my
> other PC I run trunk from after the 3.x release, and that does not show this
> issue.
OK, I wouldn't worry about the test failures, then.
On Aug 21, 2012, at 9:48 PM, osman buyukisik wrote:
> On 08/21/2012 02:27 PM, Jonathan Guyer wrote:
>> On Aug 20, 2012, at 8:48 PM, osman buyukisik wrote:
>>
>>> On 08/20/2012 08:13 AM, Jonathan Guyer wrote:
>&
On Aug 20, 2012, at 8:56 PM, osman buyukisik wrote:
> ~/SRC/FiPy-3.0/examples/phase$ python polyxtalCoupled.py
> Traceback (most recent call last):
> File "polyxtalCoupled.py", line 374, in
> exec(fipy.tests.doctestPlus._getScript())
> File "", line 291, in
> File "", line 234, in __i
On Aug 20, 2012, at 8:48 PM, osman buyukisik wrote:
> On 08/20/2012 08:13 AM, Jonathan Guyer wrote:
>> what happens if you run `gmsh --version` at the command line?
>>
>>
> osman@osman-AV019AA-ABA-p6228p:~$ gmsh --version
> 2.5.1
That should be fine. What happens i
On Aug 19, 2012, at 12:19 PM, osman buyukisik wrote:
> Also at the end I get
>
> Ran 550 tests in 277.547s
>
> FAILED (failures=4)
> !!!
> Skipped 188 doctest examples because `gmsh` cannot be found on the $PATH
> !
On Aug 19, 2012, at 12:11 PM, osman buyukisik wrote:
> Hello,
> I have just installed the new version (3.0). both regular and developer
> type installs. However, during testing, I am getting failures like :
> FAIL: polyxtalCoupled (examples.phase)
> Doctest: examples.phase.polyxtalCoupled
>
We are pleased to announce the release of FiPy 3.0.
http://www.ctcms.nist.gov/fipy
The bump in major version number reflects more on the substantial increase in
capabilities and ease of use than it does on a break in compatibility with FiPy
2.x. Few, if any, changes to your existing scripts
On Jul 31, 2012, at 11:19 AM, Daniel Wheeler wrote:
> This might be crazy slow if this is done point by point. Might be better to
> create the interpolated phi array beforehand in one shot and then do the
> integral.
Another option is not to interpolate at all and use FiPy's cell-centered val
On Jul 24, 2012, at 8:14 AM, Yun Tao wrote:
> I encountered an interesting problem when I tried to vary the convection
> coefficient as a function of time steps.
:
:
> There must be a better way to varying the coefficient. I've spent days
> testing out dynamics under seasonal convection strengt
scipy-0.10.0 installation.
> No crashes! Thank you.
>
> Best wishes,
> Ferenc
>
> On Wed, 18 Jul 2012 16:58:42 -0400
> Jonathan Guyer wrote:
>
>> Ferenc,
>>
>> I don't think the problem is because you don't have gmsh. If gmsh is absent,
>>
Ferenc,
I don't think the problem is because you don't have gmsh. If gmsh is absent,
then the tests that require it should just fail and move on. I've just
confirmed this with FiPy 2.1.3 on my Mac.
If I had to guess, I suspect the problem may be with your bleeding-edge
versions of NumPy and Sc
On Jul 2, 2012, at 1:08 PM, Daniel Wheeler wrote:
> On Mon, Jul 2, 2012 at 6:56 AM, Yun Tao wrote:
>
> 1. In Equation [1], when I set the coefficient of the ConvectionTerm to a
> function of psi, it returns
>
> TypeError: unsupported operand type(s) for *: 'binOp' and 'unOp'
>
> I gather t
On Jun 20, 2012, at 3:25 PM, Yun Tao wrote:
> Thanks! Huge help! So, does phi.getCellVolumeAverage() * l act just like
> integration under FiPy then?
Yes.
> If so, for 2-D systems, would I simply do phi.getCellVolumeAverage() * l * l ?
phi.getCellVolumeAverage() * mesh.getCellVolumes().sum()
On Jun 20, 2012, at 7:43 AM, Yun Tao wrote:
> However, though the initial distribution integrates to 1 over the finite
> domain, the area under the curve gradually decays as the function converges
> on the origin (see attachment). This can be witnessed from the numerical
> outputs starting at
On Jun 20, 2012, at 11:20 AM, Kendall Boniface wrote:
> I'm a bit confused about the getCellVolumes() function. Since I am using the
> 2D cylindrical grid, I assume it isn't actually giving me "volumes" so to
> speak. I've manually played around with some of my numbers and can't seem to
> figu
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