installation
> and it stopped working altogether.
>
What stopped working? The matplotlib installation or fipy?
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ng for ubuntu :-(
>
> Thanks for the info.
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>
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_
ilures=33)
>
> !!!
> Skipped 83 doctest examples because the `tvtk` package cannot be imported
>
> !!!!!!!
>
> Any idea? Thanks in advance.
>
> Fausto
ext. I'd be very interested to learn why, and in the process, gain a
> greater understanding of how FiPy works.
>
I think the method of lines is a hybrid non-linear, linear solver. It is
probably best to separate the two, choosing a non-linear method (Picard or
Newton) and a linear
licit. The way I wrote the equation above only includes
one derivative that is explicit (in the second to last term). This should
be more stable than just evaluating the last term completely explicitly
(which you could always do with getGrad()).That is basically what you would
do with FD, so you ca
domains maybe using an
analytical estimate as a baseline.
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On Tue, Jul 31, 2012 at 11:16 AM, Daniel Wheeler
wrote:
> On Mon, Jul 30, 2012 at 10:58 PM, Daniel Farrell wrote:
>
>>
>>
> Just use what you have written. Should work as is. Actually, it should be
>
> numpy.exp( -scipy.quad( lambda x: phi([[x]]), 0, x)[0] )
>
&g
is the interpolated
value of the cell variable at the given positions.
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will "copy-n-paste" from the trunkfolder
> work? or do i have to pay attention here on something?
>
Not sure. What exactly are you going to copy and paste? Either use
virtualenv or set the python path to point at the base fipy directory after
you chec
the memory leak that could well be. For some reason, I rarely use
the Pysparse GMRES solver because it has given me problems in the past. Try
using Trilinos's GMRES solver if you can and see if it helps.
Cheers
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=phi.getGrad()[1]
> Traceback (most recent call last):
> File "", line 1, in
> File
> "/home/x_ferta/PYTHON_MODULES/lib/python2.7/site-packages/FiPy-2.1.3-py2.7.egg/fipy/variables/variable.py",
> line 1335, in __getitem__
>
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Daniel Wheeler
__ == '__main__':
> temp_viewer.plot()
>
>
> I just can't seem to figure out how to implement that within my solver.
> Can anyone suggest a way to do this?
>
> Thank you in advance :)
> Kendall
>
>
> ___
very slowly. This could be due
round off in the solver. The np.trapz seems to be very different from the
cell average. Is that calculation taking into account that the values are
cell centered so the end points may not be weighted correctly?
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Daniel Wheeler
other is
preferable, but it would seem to be better for the term to share the
implicit variable with the equation that nominally solves that variable. I
have never tested this issue so I don't really know or have any good
mathematical reasoning, just a hunch.
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t examples. I will be doing some comparisons in the next few weeks and
will keep you posted on my findings.
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ely sure. Try it and see. I would say that
the former is probably better.
>
> Can't say it enough, but thank you again for all your kind and generous
> help.
>
No problem.
Cheers
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to share my approach that seems to work OK. If there
> are suggestions for improvements I certainly don't mind hearing them.
>
Douwe,
The script looks good to me. Good luck with your work.
Cheers
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fi
allows me to understand what I'm doing a little
better. Anyway, good luck with your work.
> The FiPy works in mysterious ways!
>
:-)
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atamin=-1.5, datamax=1.5)
for i in range(5):
res = eqn.sweep()
vi.plot()
print res
raw_input('stopped')
On Mon, Jun 18, 2012 at 11:27 AM, Allawala, Altan
wrote:
> Thanks for your response, Daniel.
>
> On Mon, Jun 18, 2012 at 10:18 AM, Daniel Wheeler <
> dani
Altan, I'm stumped by this right now. I might look into again in the
future. Cheers.
On Mon, Jun 18, 2012 at 11:27 AM, Allawala, Altan
wrote:
> Thanks for your response, Daniel.
>
> On Mon, Jun 18, 2012 at 10:18 AM, Daniel Wheeler <
> daniel.wheel...@gmail.com> wrote:
&g
he code that you
> provided and it made no qualitative.
>
I see a slight difference. The curve for psi does not have multiple changes
in gradient. How does the fipy solution differ from the mathematica
solution? The residual is tiny and the boundary conditions se
2.04532893 2.75243571]
Do you have any idea about what is going on? Thanks.
On Mon, Jun 4, 2012 at 10:35 AM, Daniel Wheeler
wrote:
> On Sun, Jun 3, 2012 at 8:30 PM, Jason Furtney wrote:
>> Daniel,
>>
>> Thanks for your email on this. I guess I never tested this on a
to set the value of $\psi$ at x=0. But since x=0
> is now no longer at the boundary of the mesh, it appears that one would
> somehow need to set a value of Psi right in the middle of the mesh - a
> "non-boundary condition". Can FiPy do this?
You can do this with
On Wed, Jun 13, 2012 at 11:31 AM, Daniel Wheeler
wrote:
> I have reposted the question to the mailing list. In the mean time, I
> will have a look at the code that you created. The equation that I am
> trying to solve for is:
>
> 0=\frac{\partial\phi}{\partial x}+i*\frac{\
-- Forwarded message --
From: Daniel Wheeler
Date: Wed, Jun 13, 2012 at 11:31 AM
Subject: Fwd: Re: FiPy query
To: Daniel Wheeler
Original Message
Subject: Re: FiPy query
Date: Wed, 13 Jun 2012 10:52:04 -0400
From: Allawala, Altan
To: Wheeler
-- Forwarded message --
From: Daniel Wheeler
Date: Wed, Jun 13, 2012 at 11:30 AM
Subject: Fwd: Re: FiPy query
To: Daniel Wheeler
Original Message
Subject: Re: FiPy query
Date: Wed, 13 Jun 2012 10:20:48 -0400
From: Daniel Wheeler
To: Allawala, Altan
On
x / 2))
< right_anchor = 1e+10 * (x > (D - dx / 2))
< I_right.faceGrad.constrain(0, m.facesRight)
< I_left.faceGrad.constrain(0, m.facesLeft)
---
> left_anchor = 1e+10 * (x < dx)
> right_anchor = 1e+10 * (x > D - dx)
Cheers
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Daniel Wheeler
__
-- Forwarded message --
From: Daniel Wheeler
Date: Tue, Jun 5, 2012 at 9:51 AM
Subject: Re: dynamic boundary condition
To: wang yunbo
On Mon, Jun 4, 2012 at 4:05 PM, wang yunbo wrote:
>
> In the example, the boundary condition is written like
> this: metalEq
source terms to set the value of \varphi to zero in these end cells
using a really large implicit source term just for the end cells. This
will avoid all the boundary issues. Try that and see if it helps.
Good luck.
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le with gmsh
directly, independent from fipy or python. Load a geo file into gmsh
with
$ gmsh file.geo
at the command line. It'll throw up the GUI so you can inspect the geometry.
Commenting out sections from the file and loading into gmsh
demonstrated that "Line Loop(23)" has a
rance for recombination. Try rescaling the problem so
the edge lengths are close to 1. Also cut and paste the gmsh commands
into a geo file and run that against gmsh rather than using fipy
making it easier to debug.
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. The extension velocity example is here:
> https://github.com/scikit-fmm/scikit-fmm/blob/master/examples/extension_velocities_example.py
Great. I'll look into that.
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4 #1 SMP Sat May 5 01:12:59 UTC 2012
x86_64 GNU/Linux
and debian version 6.0.5
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I should let you know that I'm presenting a poster at the scipy
conference on my experiences with lsmlib/scikit-fmm and modeling
electrochemical deposition problems.
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gt; http://www.ctcms.nist.gov/fipy
> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
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ot sure what you mean. Do you mean that the flow should all be
going to a point location? You could certainly construct a velocity
that points to a single point. Can you write what you want
mathematically?
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PCG solver work in this case? Thank you.
>
>
> Best,
>
> Yunbo
>
>
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--
ical outputs, although the
> numerical solutions remain the same. Is there then an optimal way to
> illustrate the results?
Doesn't seem to do that for me. This could be caused by your
matplotlib setup. If you plot twice after the solve step do you get
the correct image?
> Thank you all
__version__"
Also do the tests all pass?
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l the libraries
> fipy requires?
>
Where do you set the LD_LIBRARY_PATH currently?
> Can I force fipy to use python RPATH?
>
Never heard of RPATH.
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y/browser/branches/riemann/examples/riemann/rotation.py
>
for some help.
> Would you be interested in bug reports if it's something that's ready
> to be experimented with?
>
Sure. Give me your thoughts on the design as well. It needs cython right
now
a comment in the ticket
or any of your thoughts in general. Don't hesitate looking under the hood
of LSMLIB if you feel that you might be able to debug these sorts of
issues. I am in contact with the LSMLIB author and I also now have commit
privileges to the r
haps based on existing
> gradient functionality? I suppose that there are workarounds using
> the existing API, but if they're part of an equation I suspect that
> might get more complex than desirable.
>
You'll have to wait for vector equations to do this correc
m,
> a original Gaussian function is not preserved over time when given only a
> convection term and no diffusion term.
>
No scheme will perfectly preserve these features, but higher order schemes
+ limiters will do a good enough job for most applications.
Cheers.
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tral Methods in MATLAB" or
"Finite Volume Methods for Hyperbolic Problems" for a better understanding.
Cheers
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l this be possible with the next release?
I think so. Shouldn't be a problem.
> I cannot find and way to
> specify which CellVariable the boundary conditions corresponds to in
> the fipy/boundaryConditions classes.
>
That's cos it's not there. Constraints belong to va
r: array cannot be safely cast to required type
Don't I also need the msh file? I swapped 'twin_ap_3D_X4.msh' for
'twin_ap_3D_X4.geo' in the script and it gave the error above.
Cheers
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oeff = (-40.,)
##eq = TransientTerm() == PowerLawConvectionTerm(coeff=convCoeff)
eq = TransientTerm() == VanLeerConvectionTerm(coeff=convCoeff)
# temporal config
#timeStepDuration = 0.1 * dx ** 2 / (2 * 30) *3
dt = 0.9 * dx / abs(convCoeff[0])
steps = 500
# solve for transient solution
for steps in range(steps):
ou send
the script that you are running and the geo file that generated the mesh.
Cheers.
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llVariable(mesh=m, value=m.getCellCenters()[0])
>>> a = fipy.numerix.array([[2.5]])
>>> a.shape
(1, 1)
>>> v(a)
array([ 2.5])
Cheers
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On Mon, Mar 26, 2012 at 12:12 PM, Daniel Wheeler
wrote:
> On Mon, Mar 26, 2012 at 10:42 AM, Fausto Arinos de A. Barbuto <
> fausto_barb...@yahoo.ca> wrote
>
>> I didn't know that there were a wiki where I might publish my findings.
>> That's (good) news
>
transient
> and 2D problems, once again following V&M's tracks.
>
It's cool. All feedback is welcome.
> I didn't know that there were a wiki where I might publish my findings.
> That's (good) news
> to me.
>
I just not
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> Phone: +49 151 11728439
> Homepage: http://www.hasenkopf2000.net
> GPG Pub Key: http://goo.gl/4mOsM
>
>
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>
>
>
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>
>
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p://www.ctcms.nist.gov/fipy/documentation/FAQ.html#envvar-FIPY_DISPLAY_MATRIX
>
>
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>
"." in it then it might work, but maybe just rename the pylab.py file
to something else assuming it is a file that you created that happens to
have a name clash.
Cheers
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s 4420. V is
a tuple of len 1 and it is multiplied by an integer. This just makes
the tuple longer, which I'm sure is not what you want.
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t process fipy results with gmsh.
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On Wed, Mar 7, 2012 at 2:36 PM, Justin Lazear wrote:
> **
> Switching to DiffusionTermNoCorrection fixed it. Thanks!
>
Excellent!
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[ NIST internal ON
t; 2.1.2
>
> [~]$ uname -r
> 2.6.34.9-69.fc13.x86_64
>
> [~]$ gmsh --version
> 2.5.0
>
> Thanks,
> Justin
>
> ___________
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> [ NIST internal ONLY: htt
-- Forwarded message --
From: Daniel Wheeler
Date: Mon, Mar 5, 2012 at 12:49 PM
Subject: Re: Diffusion model on level set
To: wang yunbo
On Sun, Mar 4, 2012 at 10:00 PM, wang yunbo wrote:
> Hi Dr. Wheeler,
>
> For a classic diffusion model, I would need to calc
alternative is fantastic. I think fipy should have a single interface to
both libraries and that's probably what I'll do after evaluating scikit-fmm.
> Hopefully this module is of interest to the FiPy community. I would
> like to add to th
do it. Try puting "from fipy.tools.numerix import
*" at the top of your scripts and they should work.
Cheers
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is the best way to update distance variable in this situation?
>
That doesn't make much sense to me.
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to build the manual by python setup.py build_docs --pdf and also
> using --html. But I am getting errors from sphinx, so I was wondering if
> there is a manual you could provide me.
>
>
> Best,
>
> Yunbo
>
> On Feb 20, 2012, at 4:43 PM, Daniel Wheeler wrote:
>
>
&
ary
>
> u=0
>
> Then i would like to plot the energie norm of the error,
>
> Any hint?
>
> FKM
>
>
>
>
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x, y = m.getCellCenters()
instead of m.x and m.y and it should work. The changes to get it ti work
with 2.1.3 are trivial so I wouldn't update your version of fipy,
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ine 7, in
>m = Grid2D(nx=N, ny=N, Lx=L, Ly=L)
> TypeError: Grid2D() got an unexpected keyword argument 'Lx'
>
> When we replace them with the standard dx and dy, then circle.py fails
> further down in the script. Which fipy version are you using?
>
> Thanks.
'include_dirs' : np.get_include()
> TypeError: install() got an unexpected keyword argument 'setup_args'
>
>
> It seems the wrappers don't work here, how can I make it work? Is your
> version of lsmlib modified?
> Thanks.
>
> Best,
>
> Yunbo
ll n+1?
>
The upwind convection term does that.
Hope that helps.
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f(u(x, t), x) I
> need to know u, the unknown!
>
You're quite right! What I said doesn't make any sense. As you say, the
right way is to split it an integrate in time, which seems reasonable. It
remains local that way.
--
Daniel Wheeler
dead atm - even browsing to it through the repo
> brings me to an error page. The others work though. I'll try the Riemann
> branch.
>
There is something wrong with the trac site. If you hit reload a few times
it will show. It is really getting annoying.
Good luck!
--
Dani
l not quite in the standard form for FiPy. I'm guessing I'd
> have to write the uxx term as a source term? Is FiPy suited to this
> kind of problem - and if not can you recommend another (preferably open
> source) tool? I'd appreciate any advice.
>
You could also
rds,
>
> Yunbo
> On Feb 10, 2012, at 11:18 AM, Daniel Wheeler wrote:
>
> On Thu, Feb 9, 2012 at 4:56 PM, wang yunbo wrote:
>
>> Hi,
>>
>> 1. when I look at the 'data' file and checked some point which suppose
>> to be at the surface e.g (50
if you wish.
In short I recommend that you give lsmlib a shot and then use the my cython
wrappers to integrate with python.
Cheers.
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eLoader"
Try running the build only again to double check the output
$ python setup.py build
in the fipy directory and then
$ sudo python setup.py install
Does it build okay?
The funny thing is that it seems to have installed fipy and then barfed
dur
d/release/17>
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out why the
"python setup.py install" of fipy is not working. To be clear, when you try
to install fipy you get
$ sudo python setup.py install
...
line 11, in
import numpy.core.numeric as NX
AttributeError: 'module' object has no attribute 'core'
Wh
1, in
> File "fipy/__init__.py", line 41, in
>from solvers import *
> File "fipy/solvers/__init__.py", line 68, in
>raise ImportError, "Could not import any solver package. If you
> are using Trilinos, make sure you have all of the necessary Trilinos
>
he best way to calculate the curvature?
>
var.getFaceGrad().getDivergence()
should be second order accurate.
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-- Forwarded message --
From: Daniel Wheeler
Date: Fri, Feb 3, 2012 at 10:04 AM
Subject: Re: [Pysparse-users] Requesting help with PySparse installation
To: Leland M Barnard
Cc: pysparse-us...@lists.sourceforge.net
I am not sure what the issue is, but it might be better to
od luck with your research!
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t; mentioned.
> I used python-2.7.2.msi with pysparse-1.1.1.win32-py2.7.exe.
>
> Any suggestion?
>
Can you import pysparse at the python command line? Try
>>> from pysparse import itsolvers
Does that work?
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be able to implement one by using a
staggered grid system in 1D just to test it. Actually, for 1D explicit, it
would be easy to do just with numpy alone. No need for FiPy.
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ownloader
>
> What should one then do?
>
> F.
>
>
>
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>
>
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Daniel W
ucting an operator variable that is used as a
convection coefficient. Unfortunately, the FiPy web page doesn't have
enough highlighted convection examples. They seem to be hidden away in the
examples directory.
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rgence
[ 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4.]
Cheers.
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with the boundary conditions provided. It could also be the choice of
solver. That particular example needs to be diagnosed and fixed (we just
don't have time), but the fourth order term itself is fine for most of the
examples.
Cheers
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Daniel Wheeler
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On Wed, Jan 18, 2012 at 2:43 PM, Raymundo Arroyave wrote:
> Do you have a procedure to build fipy+trillinos under ubuntu?
>
It's packaged (python-pytrilinos) for Ubuntu and Debian now.
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On Wed, Jan 18, 2012 at 2:59 PM, Daniel Wheeler
wrote:
> On Wed, Jan 18, 2012 at 2:43 PM, Raymundo Arroyave
> wrote:
>
>> Do you have a procedure to build fipy+trillinos under ubuntu?
>>
>
For FiPy try using the deb at
<http://matforge.org/fipy/downloader/downlo
On Fri, Jan 13, 2012 at 11:40 AM, Daniel Wheeler
wrote:
> On Sat, Jul 7, 2012 at 11:36 AM, Ferenc Tasnadi wrote:
>
>
>
>> However, if I run the examples/cahnHilliard/mesh2D.py parallel; the
>> script runs, but phi with using
>> phi.getGlobalValue()
>> does n
I think there is a problem with the default solver when running this
example. Try switching the solver to LinearLUSolver. Does it evolve now?
Does it also work in parallel after the switch?
$ mpirun -np 2 python examples/cahnHilliard/mesh2D.py --trilinos
Cheers
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Daniel Wheeler
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sient diffusion. Press to proceed...
> True
> True
> Implicit steady-state diffusion. Press to proceed...
> Time-dependent boundary condition. Press to proceed...
> True
> True
> True
> True
> [matter1: diffusion]$
>
>
> Best wishes,
> Ferenc
>
>
>
>
;>
>> A look at the exponential equation supports the condition of mean != 0.
>> So does this mean the default mean for ExponentialNoiseVariable is poorly
>> set and requires manual configuration for all future operations?
>>
>> Thanks!
>>
>>
>>
&g
running:
$ mpirun -np 2 python setup test --trilinos
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On Wed, Jan 4, 2012 at 12:08 PM, Daniel Wheeler
wrote:
> On Wed, Jan 4, 2012 at 11:56 AM, Ferenc Tasnadi wrote:
>
>> Dear Daniel,
>>
>>
>> Thank you for your response.
>>
>> In my script I do not use any viewer.
>>
>
> In your first em
ements.
True
True
True
...
Implicit steady-state diffusion. Press to proceed...
Is that what you get?
Thanks
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t in
> installing trilinos. I use python2.7 and trilinos-10.8.3.
>
As Jon suggested. It is probably the viewer's inability to plot meshes with
0 cell meshes.
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gt; mesh.getCellCenters()[0]. Any insight?
>
Would this do for a uniform mesh (for non-uniform meshes you can use the
the noise variables included above)?
from fipy import Grid1D, CellVariable, numerix, Viewer
m = Grid1D(nx=100)
v = CellVariable(mesh=m)
v[:] = numerix.random.exponential(size
ich we are trying to make variable objects
work with all the meshing routines. However, at the current time we are not
using units very much because of the difficulties we had making them work
pervasively throughout fipy including terms and equations. I'm sure we'll
give it another sta
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