Re: error in getGrad()?

2011-12-20 Thread Daniel Wheeler
320. 310. 304.9998] > shouldn't the first and last value be (near) 400. and 300., respectively? > Depends what the boundary conditions are. We assume that the gradient is zero on the edge. This transfers to the natural boundary condition when solving se

Fwd: 3D Level Set Method

2011-12-05 Thread Daniel Wheeler
-- Forwarded message -- From: Daniel Wheeler Date: Fri, Dec 2, 2011 at 2:39 PM Subject: Re: 3D Level Set Method To: David Ely Hi David, No 3D level set and no easy way to make it happen. Truth be told, the level set implementation doesn't really belong as part of fip

Re: 2-D cylindrical Convection-diffusion boundary conditions question

2011-11-09 Thread Daniel Wheeler
On Wed, Nov 9, 2011 at 10:10 AM, Daniel Wheeler wrote: > On Thu, Nov 3, 2011 at 11:47 AM, Douwe Bruinsma wrote: > >> I'm impressed by the FiPy package, but don't understand how to implement >> the convection boundary conditions for my problem. >> > > Hi

Fwd: open virtually the graphics interface ....

2011-11-01 Thread Daniel Wheeler
...and again. -- Forwarded message -- From: Daniel Wheeler Date: Tue, Nov 1, 2011 at 11:12 AM Subject: Re: open virtually the graphics interface To: Julien Derr Julien, Try the script below and see if it works for you. Also comment out this line < http://matforge.

Fwd: Simple 2D Problem

2011-11-01 Thread Daniel Wheeler
Messed up the reply again. -- Forwarded message -- From: Daniel Wheeler Date: Tue, Nov 1, 2011 at 11:18 AM Subject: Re: Simple 2D Problem To: Lorenzo Isella I think Gmsh should be able to do this. Try it. Tale a look at < http://matforge.org/fipy/browser/trunk/examp

Re: cell_interface

2011-10-18 Thread Daniel Wheeler
1 >         return self > > > Interface_Variable = CellVariable(name="InterfacecellvvariableI", > mesh=mesh,value=0.,hasOld=1) > Interface_Variable=classeinterface(phi) An __init__ is needed that calls CellVariable's __init__ and specifies the phi dependence. See

Re: cell_interface

2011-10-17 Thread Daniel Wheeler
variable. Another option is to create a cell variable class with a calcValue method that uses _cellInterfaceFlag to update its own value and also requires phi. It will then update whenever phi changes. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov

Re: sphere in 3D space - how to define the BCs?

2011-10-17 Thread Daniel Wheeler
dle. >     define the BC in the "infinity" using getExteriorFaces() >     the problem: how can i define the robin BC on the inner hole-sphere > surface? Identify the interior faces using (exteriorFaces & r < R) and make a boundary condition. > or is there a better way?

Re: old level set problem in MetalIonSourcevariable.py

2011-10-05 Thread Daniel Wheeler
the > outside boundary of the mesh. Julien, As far as I can tell, you were printing cell indices at face locations so what you are seeing is gobbledygook. Have you checked the values using the correct indices? -- Daniel Wheeler ___ fipy mailing list f

Fwd: [Fwd: Re: fipy boundary conditions]

2011-10-04 Thread Daniel Wheeler
nt of how to implement this idea with the second mesh. I'm not sure I got it. I also have to admit that I'm totally new to FiPy. Thanks in advance, Samo p.s. Next time I'll make sure to post to FiPy mailing list. On Oct 4, 2011, at 4:59 PM, Daniel Wheeler wrote: > Hi Samo, Th

Re: Memory Allocation

2011-09-23 Thread Daniel Wheeler
uld make a CellVariable non-contiguous, since then it wouldn't be a CellVariable. On Wed, Sep 21, 2011 at 4:02 PM, list user wrote: > When constructing a CellVariable from a lxnXm mesh am I guaranteed the data > to be contiguous? > -- Daniel Wheeler

Re: Initial Conditions

2011-09-20 Thread Daniel Wheeler
x27;t seem to find a method to set > a _pulse_ of concentration. You can just index as you would with a numpy array. Hope that helps. Cheers. -- Daniel Wheeler

Re: old level set problem in MetalIonSourcevariable.py

2011-09-19 Thread Daniel Wheeler
!! is there a reason why the end of the mesh would > have the same property as the interface? Don't know off hand. > does the self.distanceVar._cellInterfaceFlag   Flag is also one at the > outside edge of the mesh ?? Print the values and check it. -- Daniel Wheeler

Re: time issues with implicit method

2011-08-11 Thread Daniel Wheeler
t; for explicit method); and in that case, where is my mistake ? You have the right idea. Make sure you initialize the time variables with a float rather than an integer, but I don't think that should be a problem > - or is it something else, and in that case, could someone please put me on > the right track? Post the entire script so that it runs and I'll try and figure it out. -- Daniel Wheeler

Re: System of PDEs

2011-08-08 Thread Daniel Wheeler
ent term coefficient should just be a cell value. So simply use "r**2" for the transient term. -- Daniel Wheeler

Re: System of PDEs

2011-08-05 Thread Daniel Wheeler
=0? It's a regular 1D mesh, not cylindrical. -- Daniel Wheeler

Re: old level set problem in MetalIonSourcevariable.py

2011-07-14 Thread Daniel Wheeler
## mesh.getCellCenters() for older fipy >>> myRegularEqn + ImplicitSourceTerm(1e+20 * (x > 3)) - 1e-20 * (x > 3) * value == 0 This would set the value of the variable to be `value` where x > 3. -- Daniel Wheeler

Re: old level set problem in MetalIonSourcevariable.py

2011-07-13 Thread Daniel Wheeler
bla c \right) + S_P c = 0 where $S_P$ is a large value. -- Daniel Wheeler

Re: Pb with convergence of sweep method: it's coming from my mesh or my Bcs ?

2011-07-12 Thread Daniel Wheeler
DiffusionTermNoCorrection. Mixing DiffusionTermNoCorrection and DiffusionTerm won't help, but I a not sure that there is a problem with the solution anyway. -- Daniel Wheeler

Re: old level set problem in MetalIonSourcevariable.py

2011-07-12 Thread Daniel Wheeler
_p and S_c large and have the correct ratio in a selected region. It's probably best to do this directly in the script by adding to the existing equations rather than messing directly with the internals of FiPy. The above is a for a fixed value. An internal flux is a little different. Hope this helps. -- Daniel Wheeler

Re: Pb with convergence of sweep method: it's coming from my mesh or my Bcs ?

2011-07-11 Thread Daniel Wheeler
/diffusionTermNoCorrection.py> and in the latest release, it's in"fipy.terms.diffusionTerm" <http://matforge.org/fipy/browser/tags/version-2_1_2/fipy/terms/diffusionTerm.py>. I believe you need to import this directly (not auto-imported with "from fipy import *"). Hope this helps. Cheers -- Daniel Wheeler

Re: Error in making a non-uniform Grid1D

2011-06-28 Thread Daniel Wheeler
it on version-2_1 since we are working towards a new release. > Please check attacked file. None of those failures are important. Two are vtk, which you probably don't have and don't need most likely and the others seem to be testing failures that fail in different ways. Probably because your version of numpy is quite new, but nothing to worry about. Cheers -- Daniel Wheeler

Re: ImplicitSourceTerm, CoupledBinaryTerm, and buildMatrix questions.

2011-06-27 Thread Daniel Wheeler
e.cacheMatrix() e.justResidualVector(v) print e.matrix > I would like to formulate the problem in fipy (because later I will use it > for time evolution) but need to solve for the static configurations first. >  (Also, is there a way of not using sparse solvers and just using numpy > arrays?  For debugging small systems this would be very useful...) You can ask for "e.matrix.numpyArray" to get the matrix as a numpy array if you prefer that format. Hope this helps. Cheers. -- Daniel Wheeler

Re: Error in making a non-uniform Grid1D

2011-06-24 Thread Daniel Wheeler
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FiPy-2.1-py2.7.egg/fipy/meshes/numMesh/mesh.py", > line 521, in _calcFaceCellToCellNormals >    orientation = 1 - 2 * (numerix.dot(self.faceNormals, > self.faceCellToCellNormals) < 0) >  File > "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FiPy-2.1-py2.7.egg/fipy/tools/numerix.py", > line 835, in dot >    return a1.dot(a2) > ValueError: matrices are not aligned >>>> > > -- Daniel Wheeler

Re: coupling fipy with scipy.integrate.odeint

2011-06-21 Thread Daniel Wheeler
x". For this you could use justResidualVector. However, this really defeats the purpose of using FiPy as you will no longer be using an implicit scheme, but an explicit scheme. You also might not want the transient term in the FiPy equation definition since odeint deals with this. Not sure how to get around the implicit/explicit issue though. -- Daniel Wheeler

Re: mechanical equilibrium equation

2011-06-20 Thread Daniel Wheeler
On Mon, Jun 20, 2011 at 11:11 AM, Daniel Wheeler wrote: > Hi Rajeev, > > People have asked about this on the list have a given indications that > they are solving the necessary equations sucessfully. However, we > don;t have a ny canned examples for elasticity to get you strat

Re: mechanical equilibrium equation

2011-06-20 Thread Daniel Wheeler
pe memory alloys. As such, I need to solve the > mechanical equilibrium and elasticity equations. I was wondering if the > elasticity equation has been solved before using FiPy. > Thank you! > Sincerely, > Rajeev -- Daniel Wheeler

Re: Integration

2011-06-16 Thread Daniel Wheeler
t; 0.2) integral = (mask * N * mesh.getCellVolumes()).sum() for example. > I would > also like the result be of ndarray type (i.e., representing the > integrated value at each xc). Not sure what you are asking. The integral is obviously independent of location. Hope the above helps. -- Daniel Wheeler

Re: How to extract a specific surface area of a mesh and imposing a BC ?

2011-06-10 Thread Daniel Wheeler
tp://matforge.org/fipy/browser/trunk/fipy/meshes/gmshImport.py#L297> Hence info associated with faces will be lost. Sorry I can't be of more help. -- Daniel Wheeler

Re: 2D Cylindrical Mesh: Cell Volumes

2011-06-06 Thread Daniel Wheeler
tput is: > > [ 0.5  1.5  2.5  3.5  4.5  5.5  6.5  7.5  8.5  9.5] > > Could it be that a factor of pi is missing here? Assuming that the half > cylinder > is modelled... Hi Burak, The assumption is a 1 Rad wedge. For the inner working of FiPy the factor is not important. Hope this helps. -- Daniel Wheeler

Re: Coupled PDE-ODE systems

2011-06-01 Thread Daniel Wheeler
d to the data-structures used in FiPy? > Best, > Biswa -- Daniel Wheeler

Re: DLA : towards the perfection ?

2011-06-01 Thread Daniel Wheeler
ght be worth trying different solvers. Try using the LinearLUSolver for the equations that are throwing the iteration warning or switching to trilinos's gmres solver as an alternative. -- Daniel Wheeler

Re: DLA : towards the perfection ?

2011-05-31 Thread Daniel Wheeler
hed the code, if someone get the courage and the time to look at it > ...or do you have ideas  just like that ? Julien, I tried running the code, but I didn't get any of those warnings with trunk or version-2_1. Version-2_1 failed with an attribute error. Sorry. -- Daniel Wheeler

Re: download link not workin

2011-05-29 Thread Daniel Wheeler
. > > Kind regards, > > Christine > > -- Daniel Wheeler

Re: How to obtain the index of a cell (variable) at a particular position?

2011-05-26 Thread Daniel Wheeler
t; v = CellVariable(mesh=m) >>> r = (2.9, 2.9) >>> v[argmin(sum((r - m.cellCenters)**2))] = 100. >>> print v [ 0.0.0.0.0.0.0.0. 100.] > My question is: is there a function that gives me the index for a given mesh > and position r? No, but argmin allows you to do this fairly easily. -- Daniel Wheeler

Re: Extract 1D profile from 2D or 3D grid

2011-05-20 Thread Daniel Wheeler
wo weeks ago FiPy on the web and I'm trying to use it > for my purposes. I'm currently trying some simple things to understand a > little bit > more how using FiPy. My conclusion is that Fipy is very easy to use and > seems > powerful. >  You really did a great job ! >

Re: Extract 1D profile from 2D or 3D grid

2011-05-19 Thread Daniel Wheeler
ot float64 in both cases !! > May my *.py file help you ? > >  Thanks > >   Marc > > Daniel Wheeler a écrit : > >> >> What do you get if you print numerix.array(S).dtype? >> >> On Thu, May 19, 2011 at 9:13 AM, Marc Saudreau >> wrote: >>>

Re: Extract 1D profile from 2D or 3D grid

2011-05-19 Thread Daniel Wheeler
>  Thanks again for your help and time > >    Marc > > > Daniel Wheeler a écrit : > >> >> Hi Marc, >> >> CellVariable's __call__ method extracts data. So you can do the following: >> >> from fipy import * >> import pylab >> >> L

Re: Extract 1D profile from 2D or 3D grid

2011-05-17 Thread Daniel Wheeler
; Hi everyone, > >  I'm trying to use Fipy to solve a 2D heat transfer problem, and I need to > extract from my 2D grid, some 1D profiles. For instance I need to plot > temperature versus y axis for x given. > I had a look at Fipy examples but I did not find any way to do it. > Thanks a lot for any help. > >  Best regards, > >   Marc > > -- Daniel Wheeler

Re: 1D diffusion using source term with boundary conditions

2011-05-02 Thread Daniel Wheeler
time() <= 20: > for step in range(100): >     time.setValue(time() + dt) >     # for a new boundary condition for source term (#2) >     grad2setValue(BC_Left, where=mesh.getFacesLeft()) >     grad2.setValue(BC_Right, where=mesh.getFacesRight()) >     # solve the equations >     eqX.

Re: 1D diffusion using source term with boundary conditions

2011-04-27 Thread Daniel Wheeler
On Wed, Apr 27, 2011 at 3:50 AM, Gyeong-Geun LEE wrote: > Thanks for your suggestion. > However, it did not work. > The values at boundary were diverged! Post your script and I'll take a look. -- Daniel Wheeler

Re: 1D diffusion using source term with boundary conditions

2011-04-18 Thread Daniel Wheeler
p in range(100): >     time.setValue(time() + dt) >     eqX.solve(var=phi, boundaryConditions=BCs, dt=dt) >     eqX2.solve(var=phi2, dt=dt) >     # for a new boundary condition >     grad.setValue(BC_Left, where=mesh.getFacesLeft()) >     grad.setValue(BC_Right, where=mesh.getFacesRight()) >     if __name__ == '__main__': >         viewer.plot() > > # Final check > print phi[0:3] > print phi2[0:3] > raw_input('Calculation done. Please hit any key...') > > > -- Daniel Wheeler

Re: question about simpletrenchsystem.py

2011-04-01 Thread Daniel Wheeler
to type $ gmsh at the command line and have it launch. That should be enough. The examples you were running all use gmsh for creating their meshes. -- Daniel Wheeler

Re: python version issue

2011-04-01 Thread Daniel Wheeler
On Fri, Apr 1, 2011 at 3:56 AM, Jacek Hoffman wrote: > Package python-mpi4py  ver. 1.2.2-1 is sent to Daniel Thanks! I'll see if it helps. I'll take it down if mpi4py ever gets an up to date deb. -- Daniel Wheeler

Re: question about simpletrenchsystem.py

2011-03-31 Thread Daniel Wheeler
hanks again very much for your very valuable help!!! I'm glad you are making some progress. -- Daniel Wheeler

Re: python version issue

2011-03-31 Thread Daniel Wheeler
On Thu, Mar 31, 2011 at 1:47 PM, Jacek Hoffman wrote: > 4 -- installing package system-wide as root (in such a case there is no > need to worry about PYTHONPATH or LD_LIBRARY_PATH, I fancy): > dpkg -i python-mpi4py_1.2.2-1~pre1_i386.deb Shall we put this on the download page? -

Re: python version issue

2011-03-31 Thread Daniel Wheeler
pi4py" since once there wasn't > "easy_uninstall". > I prefer using package manager so I did it the hard way. Appreciate the effort and thanks for posting the recipe. -- Daniel Wheeler

Re: python version issue

2011-03-30 Thread Daniel Wheeler
had to build it manually. I haven't actually tried for awhile, but I'm planning to leave well alone until we update to sqeeze. Hope this helps in some way. -- Daniel Wheeler

Re: python version issue

2011-03-30 Thread Daniel Wheeler
cript.py --pypsparse")? Ideally, that would never even attempt any Trilinos or mpi4py imports, but I think it does. I think we should change it so it doesn't. It is often the case that Trilinos breaks in some way so even importing in a try-except block breaks things. Cheers -- Daniel Wheeler

Re: question about simpletrenchsystem.py

2011-03-28 Thread Daniel Wheeler
Set/electroChem/metalIonSourceVariable.py#L88> with "return self.distanceVar._cellInterfaceFlag * 1e+20". You probably want to construct the metal equation in your script to avoid editing these files directly. That will make c=0 on the interface (phi=0). > v= \nabla c I think we've already discussed the above condition. -- Daniel Wheeler

Re: question about simpletrenchsystem.py

2011-03-28 Thread Daniel Wheeler
//www.ctcms.nist.gov/fipy/fipy/generated/models.levelSet.electroChem.html#module-fipy.models.levelSet.electroChem.metalIonDiffusionEquation>? In the examples in FiPy there are essentially two conditions at the interface. It seems like both are required. What is going on physically? Is the metal being deposited at the interface? Do you need to conserve mass at the interface? -- Daniel Wheeler

Re: 3D Diffusion Problem and FiPy

2011-03-28 Thread Daniel Wheeler
ing grid type meshes in Gmsh. Removing an interior circular region is certainly possible in Gmsh. I think you just need to define an interior circular region with four circular lines and then define the line loops with the correct ordering and direction. See the Gmsh tutorial for this <http://

Re: question about simpletrenchsystem.py

2011-03-23 Thread Daniel Wheeler
s is the "self.distanceVar.cellInterfaceAreas" field, which gives an approximation for the area of the boundary interface in a given cell. Hope this helps. -- Daniel Wheeler

Re: simpletrenchsystem.py

2011-03-09 Thread Daniel Wheeler
amples at >> >> http://matplotlib.sourceforge.net/  ? >> >> >> >> You might need to experiment with different matplotlib backends: >> >> >> >>  http://matplotlib.sourceforge.net/faq/installing_faq.html#backends >> >> >> >> > > -- Daniel Wheeler

Re: fipy class.

2011-03-07 Thread Daniel Wheeler
ate, not sure why. Also the example is really set up for deposition rather than dissolution so I added the abs(). -- Daniel Wheeler

Re: fipy class.

2011-03-07 Thread Daniel Wheeler
l run it on my machine? > and also my installation of spyparse looks weird because still a problem a > running  test_spmatrix.py If the fipy tests pass then don't worry about it. -- Daniel Wheeler

Re: 3D Diffusion Problem and FiPy

2011-03-07 Thread Daniel Wheeler
a problem, just set a very large source wherever D=0. -- Daniel Wheeler

Re: Sticky boundary conditions

2011-03-04 Thread Daniel Wheeler
can explain that. > case of growth, which means if my equation is in the following form: > \frac{\partial b}{\partial t} = D \frac{\partila ^2 b}{\partial x^2} + > rb(1-b/k) > where r and k are constants. That is a different equation from above. Do you have a problem solving it or posing it in FiPy? -- Daniel Wheeler

Re: fipy class.

2011-03-04 Thread Daniel Wheeler
ry so that you can run $ python examples/levelSet/electroChem/simpleTrenchSystem.py then try $ set PYTHONPATH=. $ python -c 'import fipy; print fipy.__version__' What do you get? Is it different from 2.2-dev? $ python examples/levelSet/electroChem/simpleTrenchSystem.py Does this now work? -- Daniel Wheeler

Re: fipy class.

2011-03-04 Thread Daniel Wheeler
Sorry. On Fri, Mar 4, 2011 at 5:39 PM, Daniel Wheeler wrote: > You can check and see that the example you are trying to run don't not > match your installed version of FIPy by importing the Grid2D instance > and looking at the arguments it takes. You can check and see that the e

Re: Sticky boundary conditions

2011-03-02 Thread Daniel Wheeler
we express that > in terms of boundary conditions? Sorry. Can't really help with that. We need equations and boundary conditions to make progress. -- Daniel Wheeler

Re: fipy class.

2011-03-02 Thread Daniel Wheeler
u are running appear to be more recent than the version of fipy you are using. -- Daniel Wheeler

Re: fipy class.

2011-02-24 Thread Daniel Wheeler
; >>> On Feb 24, 2011, at 8:20 AM, Julien Derr wrote: >>> >>> > which installation of pysparse would  you suggest ? >>> > I have currently 1.1.1 >>> >>> I am successfully running '1.2-dev213' on a Mac OS X Snow Leopard system >>> and '1.2-dev' on a Debian lenny system. >>> >>> I believe in both cases that I just did `easy_install pysparse`. >>> >>> How are you building it? What is your system? >>> >>> >>> >> > > -- Daniel Wheeler

Re: fipy class.

2011-02-23 Thread Daniel Wheeler
ionRateVariable is a scalar quantity. You may want to advect the interface proportinal to the gradient of the metal ion field. To do this you might set, depositionRateVariable = metalVar.getGrad().dot(distanceVar.getGrad()) I think this is probably what you want. > thanks a lot for your help, No problem. Cheers -- Daniel Wheeler

Re:

2011-02-22 Thread Daniel Wheeler
gt; numberOfsteps=10 > cflNumber = 0.2 > for step in range(numberOfsteps): >     viewer.plot() > >     phi.calcDistanceFunction() > >     phi.updateOld() >     c.updateOld() > >     phi.extendVariable(c.getFaceGrad()) > >     dt = cflNumber * cellSize / c.getFaceGrad().max() > >     advectionEquation.solve(phi, dt=dt) > >     ceq.solve(var=c, dt=dt,boundaryConditions=BCs) > > > > > -- Daniel Wheeler

Re: simpletrenchsystem.py

2011-02-18 Thread Daniel Wheeler
hod for installing <http://matforge.org/fipy/downloader/download/release/16>. -- Daniel Wheeler

Re: simpletrenchsystem.py

2011-02-16 Thread Daniel Wheeler
On Wed, Feb 16, 2011 at 9:08 AM, Daniel Wheeler wrote: > You're obviously using the matplotlib viewer and not the mayavi > viewer. FiPy selects one or the other. You can specify this by setting > the "FIPY_VIEWER" environment variable to "matplotlib" or "

Re: simpletrenchsystem.py

2011-02-16 Thread Daniel Wheeler
>>  import matplotlib >>  print matplolib.__version__ >> >> ? >> >> >> You can try editing line 124 of >> C:\Python25\lib\site-packages\fipy\viewers\matplotlibViewer\matplotlib2DGridViewer.py >> from >> >>    self.image.clim(vmax=datamax, vmin=datamin) >> >> to >> >>    self.image.set_clim(vmax=datamax, vmin=datamin) >> >> >> > > -- Daniel Wheeler

Re: boundary condition general question

2011-02-15 Thread Daniel Wheeler
pecify n\dot\vec{J} with the new scheme. > My guess is that phi.faceGrad.constrain(value=mesh._getFaceNormals() * > phi_grad_mag, where=...) would do the trick, but Wheeler may know some > finite-volumy reason for why that's not necessary. > It looks to me like phi.faceGrad.constrain() has only been tested in 1D > cases, where this doesn't matter. Again, Wheeler will be happy to look into > this when he gets back... won't you Wheeler? I'll change the examples to use vector values. -- Daniel Wheeler

Re: remeshing ?

2011-02-04 Thread Daniel Wheeler
3, ny=3) >>> x1, y1 = m1.getCellCenters() >>> v1 = CellVariable(mesh=m1, value=x1 * y1) >>> m0 = Grid2D(nx=2, ny=2) >>> v0 = CellVariable(mesh=m0, value=v1(m0.getCellCenters())) I haven't checked the above, so possible typos. -- Daniel Wheeler

Re: remeshing ?

2011-02-03 Thread Daniel Wheeler
75 0.75 2.25] > when I look at newphi, there are only zeros, it didn't take the values of > oldphi; isn't it supposed to do that with setValue ? What happens when you "print oldphi((xc,yc))"? Is it actually non zero and is it the same length as phi? You should also be able to do newphi.setValue(oldPhi) if they are the same length. -- Daniel Wheeler

Re: remeshing ?

2011-02-03 Thread Daniel Wheeler
there a simple way to get phi(xa,ya) where xa and ya is any arbitrary > value (ie not on a mesh ) ? X and Y can have arbitrary values. They can also be arbitrary array values. -- Daniel Wheeler

Re: mesh geometry with GmshImporter2D

2011-02-02 Thread Daniel Wheeler
ze}; Circle(6) = {2, 1, 3}; > Circle(7) = {3, 1, 4};Circle(8) = {4, 1, 5}; Circle(9) = {5, 1, 2}; Line > Loop(10) = {6, 7, 8, 9};Plane Surface(12) = {10}; \'\'\' % locals() " > > and then define > > mesh = GmshImporter2D(cmdbase) > > > doesn't seem to work ... > > thanks for your help! > > Julien > > -- Daniel Wheeler

Re: Calculating pore surface area

2011-01-05 Thread Daniel Wheeler
   r = 10 >    phase[((x - cx)**2 + (y - cy)**2 + (z - cz)**2) < r**2]= 1 > for i in range(particles): >    cx = random.random()*nx*dx >    cy = random.random()*nx*dx >    cz = random.random()*nx*dx >    r = 10 >    phase[((x - cx)**2 + (y - cy)**2 + (z - cz)**2) < r**2]= 0 > print "pore volume fraction=",phase.getCellVolumeAverage() > - > > -- Daniel Wheeler

Re: MatplotlibViewer

2010-12-17 Thread Daniel Wheeler
gt; The program stops to respond and I am having to forcefully close the entire > application. > > I am running fipy 2.1.1 along with Enthought python distribution 6.3.1 which > comes with python 2.6 on a windows - 64bit machine. > > Any help will be greatly appreciated. > > Thanks > Ram. > -- Daniel Wheeler

Re: Convective Term

2010-12-15 Thread Daniel Wheeler
"equal to" symbol. > > Am I missing something here? > > Thanks > Ram. > -- Daniel Wheeler

Re: Mayavi and fipy

2010-11-16 Thread Daniel Wheeler
t;import enthought" and from "enthought import mayavi" works at the command > line. The commands run without producing errors. But would that make fipy > recognize mayavi when we run "python setup.py test" from the dos prompt? > > Ram. > > On Mon, Nov 15, 2

Re: Mayavi and fipy

2010-11-15 Thread Daniel Wheeler
; been installed. All the modules that fipy identifies are found in > C:\Python26\Lib\site-packages\. I know that EPD comes with mayavi and can be > found in C:\Python26\Lib\site-packages\enthought\. How do I make fipy > recognize mayavi which is in a different folder? > > Thanks > Ram. > -- Daniel Wheeler

Re: pkg_resources doesn't find the viewer modues

2010-11-15 Thread Daniel Wheeler
ase.finalize_options(self) >  File > "/home/lucia/LuciaDocuments2010/Lucia2010/FiniteElementMethod/FiPy-2.1/setuptools-0.6c11-py2.6.egg/setuptools/command/test.py", > line 64, in finalize_options > > AttributeError: Distribution instance has no attribute 'test_suite' > > > Ok, that's all. FiPy is working fine for me now if I run it from its > own directory. I am using version 2.1. I was going to try 2.1.1 > yesterday before sending mail but the site was broken for downloading > :-) > > Thank you very much for your help. > Lucia > > -- Daniel Wheeler

Re: pkg_resources doesn't find the viewer modues

2010-11-12 Thread Daniel Wheeler
spective code and the viewers themselves are installed > (gnuplot, matplotlib and mayavi2). > > I don't know how to have FiPy recognize the viewers. > > Thanks a lot for your help, > Lucia > > -- Daniel Wheeler

Re: PySparse installation problem

2010-11-10 Thread Daniel Wheeler
e throw some light on it. > Your help will be greatly appreciated. See if FiPy works, probably the best way to know. Don't worry about the "tar.gz" if you have already installed with the the ".exe". Cheers -- Daniel Wheeler

Re: FiPy and PySparse for windows xp-64bit and Red Hat Linux

2010-11-09 Thread Daniel Wheeler
bit and Red hat linux platforms. I see the installation files for > windows-32 bit and for Mac-OS but I don't see them for windows - 64bit and > Redhat linux. > > Any help will be appreciated. > > Thanks > > Ram Balachandran > > > Ram Balachandran, PhD > Senior R&D Engineer > Applied Technologies > Boston Scientific > Tel: 763 255 0208 -- Daniel Wheeler

Re: variable convection term

2010-10-13 Thread Daniel Wheeler
ces" > > Is there a way to enforce these complicated boundaries in fipy? > You can't have interior boundary conditions in FiPy. Cast the boundary condition to a volume integral and apply a source term based on location or use Benny's suggestion, which can more accurately capture the boundary. -- Daniel Wheeler

Re: Speeding up an RD system

2010-10-12 Thread Daniel Wheeler
trilinos matrix, which can be improved on, but that will take more time. I will try and merge these changes back to version-2_1 ASAP and maybe do another release. Cheers On Thu, Oct 7, 2010 at 12:55 PM, Daniel Wheeler wrote: > > Erik, FYI <http://matforge.org/fipy/browser/branches/e

Re: variable convection term

2010-10-12 Thread Daniel Wheeler
ooks to me that only, a scalar, or a constant vector is allowed in this > term. Any suggestion? The coeff for ConvectionTerm needs to be a vector. Try, >>> cv = CellVariable(mesh = m, rank=1) >>> __ConvectionTerm(coeff = cv) "rank=1" makes the variable a vector value. -- Daniel Wheeler

Re: variable convection term

2010-10-12 Thread Daniel Wheeler
ion term with a variable coefficient? If so, the answer is yes. The coefficient can be any vector field that changes in space and time, but the term can not be posed to FiPy in the form you gave. Hope the above helps. -- Daniel Wheeler

Re: Speeding up an RD system

2010-10-07 Thread Daniel Wheeler
aptive" > time-stepping loop that I implemented. > > Best, > > Erik > > On Oct 5, 2010, at 3:09 PM, Daniel Wheeler wrote: > >> Hi Erik, I've attached a script that seems to run faster. It took >> 57.60s to do 200 steps as opposed to your original script, which t

Re: Speeding up an RD system

2010-10-05 Thread Daniel Wheeler
initial residual, rather than some arbitrary number. >> >> On Sep 30, 2010, at 12:55 PM, Erik Sherwood wrote: >> >>> >>> Thanks for taking a look at the code. I'm using FiPy 2.1. >>> >>> Erik >>> >>> On Sep 30, 2010, at 11

Re: Speeding up an RD system

2010-09-30 Thread Daniel Wheeler
;    print "Step %d"%(step) [snip] >    # Update the plots >    if __name__ == '__main__': >        Uviewer.plot() >        Vviewer.plot() >        Wviewer.plot() -- Daniel Wheeler

Re: Speeding up an RD system

2010-09-30 Thread Daniel Wheeler
while residual > desiredResidual and sweepcount < 300: >            #print "Sweep %d"%(sweepcount+1) >            residual = eqn.sweep(var=var, dt=dt) >            sweepcount += 1 >        # Bail if residual remains too large >        if residual > desiredResidual: >            print "Unable to reduce residual!" >            break >    if residual > desiredResidual: >        break > >    # Update the plots >    if __name__ == '__main__': >        Uviewer.plot() >        Vviewer.plot() >        Wviewer.plot() > # > toc = clock() > print "Finished in %.3f secs."%(toc-tic) > > > > -- Daniel Wheeler

Re: rotationtensor, reference?

2010-09-10 Thread Daniel Wheeler
ut how fipy handles it. > I see there a reference to > http://www.ctcms.nist.gov/fipy/documentation/refs.bib_cited.html#croftphd, > but don't find access to that from my university. Thanks. I'll delete that. -- Daniel Wheeler

fipy deb

2010-08-12 Thread Daniel Wheeler
itories at some point. Feel free to test it if you have an appropriate platform. Details for building the deb and testing are here <http://matforge.org/fipy/blog/FiPyDeb>. Cheers. -- Daniel Wheeler

Re: lid driven cavity example

2010-08-11 Thread Daniel Wheeler
iscosity) + pressure.getGrad().dot([0.,1.]) > > Would be nice if sombody can tweak it to have matching results with the > literature, but anyway, this test has shown me fipy is adequate for my > purposes. > Obviously I wonder if the fully coupled matrix equation Daniel talks about > would not also solve the problem better, however, that fortran code I refer > to works apparently great without such a coupled solver. > > Benny > -- Daniel Wheeler

Re: Calculating velocity of interface

2010-08-09 Thread Daniel Wheeler
ield based on a velocity. Back solving using the advection equation when you know the evolution of a field can give you the normal component of a velocity (not all the components). > to the velocities already found in examples/phase/simple, so > that I know I am correctly solving for it. Hope this helps. Cheers. -- Daniel Wheeler

Fwd: [Numpy-discussion] ANN: NumPy 1.5.0 beta 1

2010-08-02 Thread Daniel Wheeler
resolved. Building from source with Python 3.1 should work without problems. Enjoy, Ralf ___ NumPy-Discussion mailing list numpy-discuss...@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion -- Daniel Wheeler

Re: Problem Installing Fipy

2010-07-30 Thread Daniel Wheeler
d enthought version. > > Regards, > Adya > > From: fipy@nist.gov [f...@nist.gov] on behalf of Daniel Wheeler > [daniel.wheel...@gmail.com] > Sent: Wednesday, July 28, 2010 9:41 AM > To: Multiple recipients of list > Subject: Re: Problem

Re: Problem Installing Fipy

2010-07-28 Thread Daniel Wheeler
On Wed, Jul 28, 2010 at 10:25 AM, Daniel Wheeler wrote: >  * Try deleting everything under C:\Pythonxy and install Enthough's That should be "C:\Python26". -- Daniel Wheeler

Re: Problem Installing Fipy

2010-07-28 Thread Daniel Wheeler
; 2.When i try to import jdsym from pysparse i got this error > > Traceback (most recent call last): >  File "", line 1, in >    from pysparse import jdsym > ImportError: DLL load failed: %1 is not a valid Win32 application. > > I've been trying to get this w

Re: Problem Installing Fipy

2010-07-26 Thread Daniel Wheeler
ou pleas help me resolve this issue. > > Thanks and Regards, > Adya > -- Daniel Wheeler

Re: lid driven cavity example

2010-07-20 Thread Daniel Wheeler
ously I wonder if the fully coupled matrix equation Daniel talks about > would not also solve the problem better, however, that fortran code I refer > to works apparently great without such a coupled solver. It will be interesting to see when when we have that functionality in fipy. -- Daniel Wheeler

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