stupid error in trunk

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

Re: stupid error in trunk

(was working in example). Greetings, Benny On Thu, Jun 24, 2010 at 9:35 AM, Benny Malengier benny.maleng...@gmail.com wrote: Hi, There is a stupid indent error in trunk at the moment: File testbenny_viscous2.py, line 90, in module from fipy import * File /usr/lib/python2.6

Re: dump.write not writing out correct mesh

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 benny.maleng...@gmail.com Hello, From the FAQ and examples it is said to write out variables

Re: dump.write not writing out correct mesh

replies with a fake To address of: Multiple recipients of list fipy@nist.gov 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 benny.maleng...@gmail.com

Re: dump.write not writing out correct mesh

2010/6/28 Jonathan Guyer gu...@nist.gov Note that this mailing list replies with a fake To address of: Multiple recipients of list fipy@nist.gov 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,

design decision of UniformGrid

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

flow field example, pressure oscillation

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

ndarray has dot function in numpy trunk

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 module mesh1 = Grid2D(dx=dy1strat, nx=nytot, dy=dz, ny=nztot) File

Re: ndarray has dot function in numpy trunk

2010/7/16 Jonathan Guyer gu...@nist.gov 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

Re: ndarray has dot function in numpy trunk

2010/7/16 Jonathan Guyer gu...@nist.gov 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 we need to deal

Re: lid driven cavity example

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 benny.maleng...@gmail.com wrote: Hi, I wanted to test the flow code some more (as was said in the other thread, difficult to write a good test

Re: Hello FiPy community

2010/9/9 STANLEY, DOUGLAS dmsta...@kent.edu 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).

Re: variable convection term

2010/10/13 Daniel Wheeler daniel.wheel...@gmail.com On Tue, Oct 12, 2010 at 5:26 PM, BIN ZHANG zhn...@gmail.com 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

mem error on adding meshes

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

Re: mem error on adding meshes

2011/1/31 Jonathan Guyer gu...@nist.gov 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=80,80,10. Your

Re: memory limit for irregular mesh ?

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

Re: memory limit for irregular mesh ?

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 8, 2011 at 2:47 PM, Benny Malengier benny.maleng...@gmail.com

Re: mem error on adding meshes

2011/2/11 Jonathan Guyer gu...@nist.gov 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', but these just append with 0's and I see those

Re: simpletrenchsystem.py

2011/2/18 Daniel Wheeler daniel.wheel...@gmail.com On Fri, Feb 18, 2011 at 8:39 AM, Jonathan Guyer gu...@nist.gov 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

Re: fipy class.

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 gu...@nist.gov On Feb 24, 2011, at 11:58 AM, Julien Derr wrote: I might be behind a firewall or

Re: fipy class.

2011/3/3 Julien Derr julien.d...@gmail.com 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

Re: fipy class.

://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 ? thanks a lot, Julien On Fri, Mar 4, 2011 at 9:21 AM, Benny Malengier benny.maleng...@gmail.com wrote: 2011/3/3 Julien Derr julien.d

Re: Porting an Electrophisiological model to FiPy

2011/6/2 Jonathan Guyer gu...@nist.gov 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

Re: mem error on adding meshes

2011/9/1 Jonathan Guyer gu...@nist.gov 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 function of fipy, which I think is more

Re: trilinos issue

2012/8/28 Daniel Wheeler daniel.wheel...@gmail.com 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: http://matforge.org/fipy/wiki

Re: trilinos issue

2012/8/28 Daniel Wheeler daniel.wheel...@gmail.com On Tue, Aug 28, 2012 at 11:00 AM, Benny Malengier benny.maleng...@gmail.com wrote: 2012/8/28 Daniel Wheeler daniel.wheel...@gmail.com On Tue, Aug 28, 2012 at 8:08 AM, Benny Malengier benny.maleng...@gmail.com wrote: Hi, Installed

Re: solving navier-stokes equation in semicircle

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

Re: branching grid

2013/3/25 Kristopher Kuhlman kristopher.kuhl...@gmail.com 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

Re: Any such thing as an open boundary condition?

2013/10/1 Richard Edward Gillilan r...@cornell.edu 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

viewers not found

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

Re: viewers not found

AM, Benny Malengier benny.maleng...@gmail.com wrote: 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

question on source term

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

Re: question on source term

2014-06-20 16:24 GMT+02:00 Daniel Wheeler daniel.wheel...@gmail.com: On Thu, Jun 19, 2014 at 11:53 AM, Benny Malengier benny.maleng...@gmail.com wrote: Hi, another question. This time on SourceTerm use. I'm checking an article with diffusion and reaction. So some species diffuse

Re: pickle/dump

2014-08-21 22:17 GMT+02:00 Daniel Wheeler daniel.wheel...@gmail.com: 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

Re: fipy python 2.7

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