I suppose the normal way adding python=2.7
to the conda arguments was tried and did not work?
2017-11-08 23:01 GMT+01:00 James Pringle :
> Dear all -- (but mainly Daniel Wheeler, I guess)
>
>I am in the midst of finishing up a paper, but am trying to transition
> to a new workstation. I have
2014-08-21 22:17 GMT+02:00 Daniel Wheeler :
> On Wed, Aug 20, 2014 at 6:12 PM, Seufzer, William J. (LARC-D307) <
> bill.seuf...@nasa.gov> wrote:
>
>> Thanks Dan,
>>
>> This works... but I also made the change to nonUniformGrid3D.py as well.
>> I noticed the simple edits, made them by hand, and re-
2014-06-20 16:24 GMT+02:00 Daniel Wheeler :
> On Thu, Jun 19, 2014 at 11:53 AM, Benny Malengier
> wrote:
> > Hi,
> >
> > another question. This time on SourceTerm use. I'm checking an article
> with
> > diffusion and reaction. So some species diffuse
Hi,
another question. This time on SourceTerm use. I'm checking an article with
diffusion and reaction. So some species diffuse, others only react (waiting
for diffused species to start). If there is an example with this floating
on the internet, do point it my way!
You then have a coupled set of
2014-06-19 16:44 GMT+02:00 Daniel Wheeler :
> Benny,
>
> Good to hear from you. Did you try "python setup.py develop"? This
> allows you to develop on an installed version of a python package. No
> need to mess with PYTHONPATH.
>
> Cheers,
>
> Daniel
>
Hi,
If I run from the build directory, I obtain a
File "/home/benny/git/fipy/fipy/viewers/__init__.py", line 133, in Viewer
raise ImportError, "No viewers found. Run `python setup.py egg_info` or
similar."
It seems it is needed to do
python setup.py build egg_info
mv FiPy.egg-info build/l
2013/10/1 Richard Edward Gillilan
> Sorry, this is a basic theory question.
>
> convection-diffusion problem
>
> I have a pipe containing fluid with dissolved protein of concentration
> phi. I have uniform flow and constant diffusion.
> I would like to make one end of the pipe "open" so that prot
2013/3/25 Kristopher Kuhlman
> Hello FiPy list,
>
> I am interested in solving a problem that involves two or more
> overlapping/connected domains. The same governing equations apply to each
> domain, but the properties are different and I am not sure the best way to
> include geometrical effect
Tanya,
For a lid driven cavity example, see
https://gitorious.org/microchanit/microchanit/blobs/master/patch/patchfipyrev5303.diff
and search for
examples/flow/lidDrivenCavity.py
On a rectangular mesh though. In current fipy is it slower than it was
originally though, and result at end is somewha
2012/8/28 Daniel Wheeler
> On Tue, Aug 28, 2012 at 11:00 AM, Benny Malengier <
> benny.maleng...@gmail.com> wrote:
>
>>
>>
>> 2012/8/28 Daniel Wheeler
>>
>>>
>>>
>>> On Tue, Aug 28, 2012 at 8:08 AM, Benny Malengier <
>&g
2012/8/28 Daniel Wheeler
>
>
> On Tue, Aug 28, 2012 at 8:08 AM, Benny Malengier <
> benny.maleng...@gmail.com> wrote:
>
>> Hi,
>>
>> Installed fipy trunk on a new computer and I seem to have a trilinos
>> issue.
>> I found the error also here:
Hi,
Installed fipy trunk on a new computer and I seem to have a trilinos issue.
I found the error also here: http://matforge.org/fipy/wiki/TrilinosMapPuzzle
What I do is open a console, import fipy, then CTRL+D to exit it. I
immediately obtain a warning Teuchos::RCPNode
Any ideas on what is happ
Hi,
I was wondering if fipy is made in such a way I can call _connectFaces
myself on a grid I constructed via concatenation.
So I do in my code
mesh._connectFaces(numerix.nonzero(mesh.facesLeft),
numerix.nonzero(mesh.facesRight))
If I look in PeriodicGrid2D however, I see some
2011/9/1 Jonathan Guyer
>
>
> On Feb 11, 2011, at 9:43 AM, Benny Malengier wrote:
>
> > Hence I conclude I don't understand the code.
> >
> > I rewrote the code to what I can understand myself and to what I think it
> is supposed to do, using the repeat f
2011/6/2 Jonathan Guyer
>
>
> On Jun 1, 2011, at 10:55 AM, Jeremy Laforet wrote:
>
> >
> > I've been looking to use external software to simulate the model of
> > uterine muscle we developed in our team.
> > FiPy really catch my eye for its high level approach.
> > But even after reading the docu
n?
>>
>> for example, this link would be the up to date version ?
>>
>> http://www.matforge.org/fipy/browser/trunk?rev=3488
>>
>> I dowload and then I
>>
>>
>> sudo python setup.py install --install-layout=deb
>>
>> that should be ok ?
>>
&g
2011/3/3 Julien Derr
> He re is what I get :
>
> julien@derr-Precision-T1500:~/Dropbox/diatomes/videos$ python -c 'import
> fipy; print fipy.__version__'
> 2.2-dev
>
If you install via package manager, you install in /usr/, if you install
manual, you install in /usr/local/
So I think it was sug
I am running pysparse on kubuntu 10.10 from subversion (version 1.2a1).
No errors in the tests.
I do have python-dev installed as I use weave in some projects.
Benny
2011/2/24 Jonathan Guyer
>
>
> On Feb 24, 2011, at 11:58 AM, Julien Derr wrote:
>
> > I might be behind a firewall or proxy, at u
2011/2/18 Daniel Wheeler
>
> On Fri, Feb 18, 2011 at 8:39 AM, Jonathan Guyer wrote:
>
> >> By the way, what packages would I need if I attempt to run FiPy on a
> virtual linux system?
> >
> > http://www.ctcms.nist.gov/fipy/INSTALLATION.html
>
> Billy, On a clean Ubuntu install the deb should be
2011/2/11 Jonathan Guyer
>
>
> On Feb 11, 2011, at 9:43 AM, Benny Malengier wrote:
>
> > I did some tests, and I came to the conclusion I have no idea how the add
> mesh code works. I see in this code 'numerix.resize' and 'numerix.newaxis',
> bu
ll meshpoints
to extract the neareast one. If you do one point at the time, this is
doable, if you 10 points also, ..., but not all points in one go.
In a rectangular regular grid, this is also easy, but not in an unstructured
one.
Benny
> Julien
>
>
>
>
>
> On Tue, Feb
You do
... value=phi(mesh.getCellCenters()))
This is what causes the problem. You can probably work around it by creating
value yourself.
Fipy uses some vectorized algorithms, which works great, but have the
disadvantage that there must be enough memory to allocate the required
arrays.
In this ca
2011/1/31 Jonathan Guyer
>
>
> On Jan 31, 2011, at 11:43 AM, Benny Malengier wrote:
>
> > I have a problem with mesh addition. Script in attachment leads to a
> MemoryError in numpy for me if I use nx,ny,nz=10,80,80, and to a very slow
> operation when I use nx,ny,nz=8
Hi,
I have a problem with mesh addition. Script in attachment leads to a
MemoryError in numpy for me if I use nx,ny,nz=10,80,80, and to a very slow
operation when I use nx,ny,nz=80,80,10. So there seems to be some axis
preference?
Error is:
Traceback (most recent call last):
File "src/testgrid
2010/10/19 Jonathan Guyer
>
>
> On Oct 19, 2010, at 2:47 PM, Jonathan Guyer wrote:
>
> > On Oct 19, 2010, at 11:35 AM, Benny Malengier wrote:
> >
> >> I noted the API for pysparse is greatly changed in development, so trunk
> versions of pysparse will not work
2010/10/19 andre van calster
>
> Hi all,
>
> I encountered the same problem with pysparse on windows. I have rebuilt
> pysparse
> using pysparse-1.2-dev203 with mingw for python 2.6.5 and also for python
> 2.5 on
> windows xp. pysparse still crashes in both cases: "from pysparse import
> precon"
2010/10/13 Daniel Wheeler
>
>
> On Tue, Oct 12, 2010 at 5:26 PM, BIN ZHANG wrote:
>
>> Dear Daniel:
>>
>> Thanks a lot for your suggestions. Now I'm actually able to solve the
>> problem with normal boundary conditions. But I still have one extra
>> question, is it possible for me to use complic
Hi,
I would like to know the reasoning behind the rotation tensor.
My problem is the following: I have a domain with holes, and gmsh creates
some sharp triangles between holes. I don't really want to refine to avoid
many unkowns.
Using a normal
self.eq = TransientTerm() == DiffusionTerm(coeff =
2010/9/9 STANLEY, DOUGLAS
>
> For those of you who don't know me by now, my name is Doug Stanley, and
> I work with Laura Bartolo on Matforge.org.
>
> I just signed up for the mailling list, so I wanted to send an
> introduction note (mainly to make sure I successfully subscribed).
>
>
Ok, receiv
y blocked pipe, so should there be remaining issues, I'll send
additional patches.
Greetings,
Benny
> On Mon, Jul 19, 2010 at 6:58 PM, Benny Malengier
> wrote:
> > Hi,
> >
> > I wanted to test the flow code some more (as was said in the other
> thread,
> &g
2010/7/19 Daniel Wheeler
>
> On Sat, Jul 17, 2010 at 5:06 AM, Benny Malengier
> wrote:
> > Hi,
> >
> > I'd like to know the result of the stokesCavity.py test of some other
> > people. Do they also fail?
>
> Not for me at least.
>
> > When I
Hi,
I wanted to test the flow code some more (as was said in the other thread,
difficult to write a good test for the code in viscous limit), and not
having dolphyn, I decided to see how fipy stacks up for the lid driven
cavity, Re=1000, which is a well known example with many literature
compariso
on't change much most of the time, seeing the oscillations does not give
confidence.
All it attached to http://matforge.org/fipy/ticket/305
I attached a before and after of my experiment to show clearly how the
oscillations are removed nicely.
Greetings,
Benny
> On Tue, Jul 6, 2010 at 5:
Hi,
I'd like to know the result of the stokesCavity.py test of some other
people. Do they also fail?
When I run the flow/stokesCavity.py, the test fails. Adding at the bottom of
that file:
Test values in the last cell.
>>> print pressure.getGlobalValue()[...,-1], 145.233883763
0
>>> print xVeloci
2010/7/16 Jonathan Guyer
>
> On Jul 16, 2010, at 5:41 AM, Benny Malengier wrote:
>
> > test file for this bug in attachment.
> > old = True fails with numpy trunk, old=False works
>
> Thanks for your reports on the new NumPy, Benny. There are clearly some
> issues w
2010/7/16 Jonathan Guyer
>
>
> On Jul 16, 2010, at 10:15 AM, Daniel Wheeler wrote:
>
> >
> > Hi Benny, The issue below is caused because mesh getter methods do
> > not, in general, return Variable objects, but simply numpy arrays. The
> > only method that does currently return a Variable is getCe
test file for this bug in attachment.
old = True fails with numpy trunk, old=False works
Benny
2010/7/16 Benny Malengier
>
>
> 2010/7/16 Benny Malengier
>
>>
>>
>> 2010/7/16 Benny Malengier
>>
>>> I hit a much more problematic thing w
2010/7/16 Benny Malengier
>
>
> 2010/7/16 Benny Malengier
>
>> I hit a much more problematic thing with this numpy.
>>
>> The code
>>
>> from fipy.meshes.numMesh.grid2D import Grid2D
>> mesh = Grid2D(dx=0.1, dy=0.1, nx=10, ny=10)
>> ap
2010/7/16 Benny Malengier
> I hit a much more problematic thing with this numpy.
> The code
>
> from fipy.meshes.numMesh.grid2D import Grid2D
> mesh = Grid2D(dx=0.1, dy=0.1, nx=10, ny=10)
> ap = CellVariable(mesh=mesh, value=0.01)
> coeff = mesh._getFaceAreas() * m
athan Guyer
>
>
> On Jul 15, 2010, at 3:02 AM, Benny Malengier wrote:
>
> > It seems ndarray has a dot function now in numpy trunk, updated my numpy
> and fipy crashes like ...
>
> Thanks for the alert
>
>
>
>
Hi,
I obtain a strange resulting figure with Gnuplot2DViewer, which is due to
the line:
self.g('set dgrid3d %i, %i, 2' % (ny, nx))
It is more correct with
self.g('set dgrid3d %i, %i, 16' % (ny, nx))
I find the gnuplot explanation lacking however:
http://www.nada.kth.se/cgi-bin/info?%28gnupl
Hi,
It seems ndarray has a dot function now in numpy trunk, updated my numpy and
fipy crashes like
File "stratifiedmassflowrect.py", line 44, in
mesh1 = Grid2D(dx=dy1strat, nx=nytot, dy=dz, ny=nztot)
File
"/usr/lib/python2.6/dist-packages/FiPy-2.1-py2.6.egg/fipy/meshes/numMesh/grid2D.py"
Hi,
I am doing a flow field calculation like
http://www.ctcms.nist.gov/fipy/examples/flow/generated/examples.flow.stokesCavity.html
However, I obtain spurious oscillations for the pressure solution. Patankar
in his works is very clear that a staggered grid should be used for the
SIMPLE algorithm,
2010/6/29 Jonathan Guyer
>
>
> On Jun 29, 2010, at 9:41 AM, Benny Malengier wrote:
>
> > First, I'd like to mention I'm happy with how fipy is handling the
> problem I'm throwing at it.
> > I just write here to offer some insight from a user using fi
Hi,
First, I'd like to mention I'm happy with how fipy is handling the problem
I'm throwing at it.
I just write here to offer some insight from a user using fipy for the first
time.
I would just like to mention that I do not like the design chosen for the
UniformGrid2D structure.
I have struggle
2010/6/28 Jonathan Guyer
>
> > Note that this mailing list replies with a fake To address of:
> > "Multiple recipients of list "
>
> As opposed to what?
>
As opposed to leaving the To address I give alone.
The reply to address of this list is clearly listed as fipy@nist.gov,
however, mails arri
replies with a fake To address of:
"Multiple recipients of list "
This is highly annoying in eg gmail and other clients. Can this setting not
be changed, this is the first mailing list I am on that behaves like this.
Benny
2010/6/28 Benny Malengier
> This is actually already in the
This is actually already in the bug tracker I notice:
http://matforge.org/fipy/ticket/243
I've hit some other bugs this weekend I'll submit on the tracker.
Benny
2010/6/26 Benny Malengier
> Hello,
>
> From the FAQ and examples it is said to write out variables with
>
Hello,
>From the FAQ and examples it is said to write out variables with dump.write,
and reuse them with dump.read (eg
http://osdir.com/ml/python.fipy/2008-04/msg2.html).
I have made a non-rectangular U-shaped grid by concatenating different
grid2D, but after dump.write/dump.read, the mesh is
rong
directory (was working in example).
Greetings,
Benny
> On Thu, Jun 24, 2010 at 9:35 AM, Benny Malengier
> wrote:
> > Hi,
> >
> > There is a stupid indent error in trunk at the moment:
> >
> > File "testbenny_viscous2.py", line 90, in
> >
ckage. If you are
using Trilinos, make sure you have all of the necessary Trilinos packages
installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and IFPACK."
ImportError: Could not import any solver package. If you are using Trilinos,
make sure you have all of the necessary Trilinos packages installed -
Epetra, EpetraExt, AztecOO, Amesos, ML, and IFPACK.
Greetings,
Benny Malengier
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