, 2012 at 5:02 PM, Daniel Wheeler
daniel.wheel...@gmail.com wrote:
On Wed, Nov 7, 2012 at 1:43 PM, Julien Derr julien.d...@gmail.com wrote:
Hi everyone,
I am using constrain in a syntax like
c.constrain(1., where=facesOutside)
If I want to release the constrain, Is it possible? how can I
Hi everyone,
I am using constrain in a syntax like
c.constrain(1., where=facesOutside)
If I want to release the constrain, Is it possible? how can I do this ?
thanks a lot,
Julien
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Dear all,
I have been playing a lot with different versions of python for
different purposes, and now I have problems to run my old fipy
scripts!
I am going to remove all my pythons installations (I have like 6
folders in my usr/lib !!)
and reinstall things properly. Which version of python do
.
-- Forwarded message --
From: Daniel Wheeler daniel.wheel...@gmail.com
Date: Tue, Nov 1, 2011 at 11:12 AM
Subject: Re: open virtually the graphics interface
To: Julien Derr julien.d...@gmail.com
Julien,
Try the script below and see if it works for you. Also comment out
Hi Everyone,
for now, I am displaying some of the key parameters with Viewer() and save
the images with the instructions savefig()
I would like to be able to run my code by ssh from a remote machine ... ;
but then I rune into displaying problems ... is it possible to virtually
open this graphs
sorry for having bothered you minimum(x1,x2) does the job fine it seems!
On Mon, Oct 24, 2011 at 5:57 PM, Julien Derr julien.d...@gmail.com wrote:
Hi everyone,
and sorry for bothering you again,
Is there a built in function enabling me to get the min of 2 cellvariables
?
something like
Hi everyone,
and sorry for bothering you again,
Is there a built in function enabling me to get the min of 2 cellvariables ?
something like
xmin=min(x1,x2) where x1 and x2 are cell variables ?
thanks a lot
Julien
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Hi Everyone,
I have a diffusive field c2 defined by the equation :
c2eq= TransientTerm() == DiffusionTerm(coeff=D)
the boundary conditions are defined by a source term (value c20 )in a
circular region :
and a null value on the outside,
X, Y = mesh.getFaceCenters()
XX = FaceVariable(mesh=mesh,
return self
Interface_Variable = CellVariable(name=InterfacecellvvariableI,
mesh=mesh,value=0.,hasOld=1)
Interface_Variable=classeinterface(phi)
On Mon, Oct 17, 2011 at 4:43 PM, Daniel Wheeler
daniel.wheel...@gmail.comwrote:
On Fri, Oct 14, 2011 at 10:44 AM, Julien Derr julien.d
Hi everyone,
here is my technical question of the day ...
phi is a DistanceVariable
type(phi)
Out[39]: class
'fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable'
if I define I=phi._cellInterfaceFlag
it gives me an array.
In [41]: I
Out[41]: array([0, 0, 0, ..., 0, 0,
Hi everyone,
I have this script derived in two versions :
noexplicitsource.py is a typical script for growth of an interface thanks to
the levelset method;
explicitsource.py is the same script with an explicit source term in order
to impose a certain value (set to 0.25 arbitrary) at the
term, email from Daniel dated july 12,2011
return self.distanceVar._cellInterfaceFlag * 1e+20 * value
On Thu, Jul 14, 2011 at 5:16 PM, Daniel Wheeler
daniel.wheel...@gmail.comwrote:
On Thu, Jul 14, 2011 at 10:44 AM, Julien Derr julien.d...@gmail.com
wrote:
reoups.. actually, if you
:
AttributeError: '_CUSTOMMetalIonSourceVariable' object has no attribute
'ionvar'
On Wed, Jul 13, 2011 at 8:04 PM, Julien Derr julien.d...@gmail.com wrote:
I think I got the idea, but I have trouble with implementation
in the
class _CUSTOMMetalIonSourceVariable(CellVariable):
I used
...@gmail.comwrote:
On Mon, Jul 11, 2011 at 8:51 AM, Julien Derr julien.d...@gmail.com
wrote:
Hi Everyone,
I remind you what my problem is about, there is a diffusing field c, a
growing interface (defined by the level set parameter phi) and I wanted
an
absorbing boundary at the interface
oh, I see!!! thanks a lot for the nice explanation ... as usual!!
Julien
On Wed, Jul 13, 2011 at 5:31 PM, Daniel Wheeler
daniel.wheel...@gmail.comwrote:
On Wed, Jul 13, 2011 at 11:00 AM, Julien Derr julien.d...@gmail.com
wrote:
D gradient(c) + source term = 0
so why a huge source
Sorry everyone! nevermind my last email
On Wed, Jul 13, 2011 at 8:04 PM, Julien Derr julien.d...@gmail.com wrote:
I think I got the idea, but I have trouble with implementation
in the
class _CUSTOMMetalIonSourceVariable(CellVariable):
I used to write
#return self.distanceVar
Hi Everyone,
I remind you what my problem is about, there is a diffusing field c, a
growing interface (defined by the level set parameter phi) and I wanted an
absorbing boundary at the interface,
With the valuable help of Daniel and Jonathan, I modified this file
(MetalIonSourcevariable.py)
Thanks so much Jonathan !!
On Tue, May 31, 2011 at 7:41 PM, Jonathan Guyer gu...@nist.gov wrote:
On May 31, 2011, at 1:05 PM, Julien Derr wrote:
I am sure this is an easy question, but I cannot make it work :
I have two variable c and c2
c = CellVariable(name=c, mesh=mesh,value=0
Hi everyone,
I am sure this is an easy question, but I cannot make it work :
I have two variable c and c2
c = CellVariable(name=c, mesh=mesh,value=0.,hasOld=1)
c2 = CellVariable(name=c2, mesh=mesh,value=0.,hasOld=1)
and I want to create a thirdh which would be always the updated product of c
Hi all,
thanks to your continuous help, I have now a running code for simulating
typical diffusion limited aggregation with fipy.
to remove anisotropy, I replaced the 2D carthesian grid, with an irregular
mesh. It works great(anisotropy is removed) except I got know an additional
warning (not
, Julien Derr wrote:
I have a program which seems to run fine, but after quite a long time, it
randomly stops with always the same error :
RuntimeError: maximum recursion depth exceeded
WARNING: Failure executing file: levelset.py
what is the meaning of this error ?
Well, the literal
to implement is that the
concentration is always c=0 at the interface.
so the speed of the interface, appears only for the advection equation of
phi,
does that make sense ?
On Mon, May 2, 2011 at 5:39 PM, Jonathan Guyer gu...@nist.gov wrote:
On May 2, 2011, at 9:03 AM, Julien Derr wrote:
Here
of this ? the time step is too big ?
On Fri, Apr 8, 2011 at 3:36 AM, Jonathan Guyer gu...@nist.gov wrote:
On Apr 7, 2011, at 1:57 PM, Julien Derr wrote:
I implemented this :
X, Y = mesh.getFaceCenters()
XX = FaceVariable(mesh=mesh, value=X)
YY = FaceVariable(mesh=mesh, value=Y)
facesOutside
(failures=2)
[jderr@iliadaccess02 electroChem]$
On Thu, Mar 31, 2011 at 10:20 PM, Daniel Wheeler
daniel.wheel...@gmail.comwrote:
On Thu, Mar 31, 2011 at 12:14 PM, Julien Derr julien.d...@gmail.com
wrote:
1. If I understand well, the line you suggested to add, is setting a
infinite (1E20) out
Hi everyone,
here is my question of the day...
I have a 2D grid, but I would like to have the exterior to be in a circular
geometry. with a boundary condition c=1 at the exterior, so on the exterior
circle
Naively I wrote this few lines to set the concentration c=1 everywhere out
of this big
...@gmail.comwrote:
On Mon, Mar 28, 2011 at 1:38 PM, Julien Derr julien.d...@gmail.com
wrote:
Hi Daniel,
I was also thinking about two conditions :
condition 1 : for the boundary of the diffusion of C
instead of a condition on grad(c) like in the example, I was thinking of
a
condition on c
of concentration.
you need another boundary condition (for example the concentration at the
interface is null)
how could I implement that ? do you have any idea ?
Julien
On Wed, Mar 23, 2011 at 4:47 PM, Daniel Wheeler
daniel.wheel...@gmail.comwrote:
On Tue, Mar 22, 2011 at 1:23 PM, Julien Derr
...@gmail.comwrote:
On Mon, Mar 28, 2011 at 5:31 AM, Julien Derr julien.d...@gmail.com
wrote:
Thanks Daniel for the fast answer as always.
I am a bit confused :
if I understood correctly, in this example, the boundary condition is
that
the normal component of the gradient of c is equal
Hi everyone!
I didn't bother you for a long time! I am back!
in the simpletrenchsystem.py example, I have a question about the boundary
condition :
metalEquation.solve(metalVar, dt = dt,
boundaryConditions = metalEquationBCs)
metalequation BCs defines the boundary
Thanks so much, it is working great
On Mon, Mar 7, 2011 at 11:00 PM, Daniel Wheeler
daniel.wheel...@gmail.comwrote:
On Mon, Mar 7, 2011 at 4:14 PM, Julien Derr julien.d...@gmail.com wrote:
depositionRateVariable =
metalVar.getGrad().dot(distanceVar.getGrad())
This should work
Hi Daniel ,
thanks a lot for your help. Yes you are absolutely right, I actually
dowloaded the examplefile .py from a random place on the internet, so I
understand it doesn't match my installation of fipy.
but this is not my real problem. I can just desactivate the parallel option
and it works
)
bulkCatalystEquation.solve(bulkCatalystVar, dt = dt,
boundaryConditions = catalystBCs)
On Mon, Mar 7, 2011 at 9:59 PM, Daniel Wheeler daniel.wheel...@gmail.comwrote:
On Mon, Mar 7, 2011 at 1:21 PM, Julien Derr julien.d...@gmail.com wrote:
the problem is my message dated
I did that, and I still have version 2.2
julien@derr-Precision-T1500:~/Dropbox/levelset$ python -c 'import fipy;
print fipy.__version__'
2.2-dev
is it the up to date version ? because I still get the same runtime error.
Julien
On Fri, Mar 4, 2011 at 10:22 AM, Julien Derr julien.d
He re is what I get :
julien@derr-Precision-T1500:~/Dropbox/diatomes/videos$ python -c 'import
fipy; print fipy.__version__'
2.2-dev
What is the best way to install the up to date version under ubuntu 10.10??
On Thu, Mar 3, 2011 at 1:43 AM, Daniel Wheeler daniel.wheel...@gmail.comwrote
AM, Julien Derr wrote:
the unmodified simpletrenchsystem.py works fine (but it was working fine
also before)
OK, good. I assumed so, but wanted to be sure.
I just had to remove the following line in the definition of the mesh
# parallelModule=serial)
I hope
!!!
julien@derr-Precision-T1500:~/Dropbox/levelset$ python
modified_simpleTrenchSystem.py
sys:1: DeprecationWarning: Get/set methods are deprecated; use the
associated property instead.
step # 0
/usr/local/lib/python2.6/dist-packages/FiPy-2.2_dev-py2.6.egg/fipy/solvers/pysparse/linearLUSolver.py
indeed!
I have a segmentation fault when I run the test!
I am going to reinstall pyspare or maybe another version ??
julien@derr-Precision-T1500:~/Téléchargements/pysparse-1.1.1/Test$ python
testSuperlu.py
TestRelErr Tolnnz(A) nnz(L+U)Fact Solve
named ‘ob_type’
pysparse/sparse/src/spmatrixmodule.c:366: error: ‘PyTypeObject’ has no
member named ‘ob_type’
On Thu, Feb 24, 2011 at 11:48 AM, Julien Derr julien.d...@gmail.com wrote:
indeed!
I have a segmentation fault when I run the test!
I am going to reinstall pyspare or maybe
I might be behind a firewall or proxy, at university.
here is the full error I get : (as I said before there is already something
which looks obviously wrong like missing {} or integer function returning
void ?)
julien@derr-Precision-T1500:~/Téléchargements/pysparse$ sudo python setup.py
Hi everyone,
I guess I understand where is the problem in my last post: I am a little bit
lost in the classes
I am just modifying the simpletrenchSystem.py example file. I would like the
extension velocity to be proportional to the gradient of the metalVar field.
in the example,
:
On Wed, Feb 23, 2011 at 10:01 AM, Julien Derr julien.d...@gmail.com
wrote:
Hi everyone,
I guess I understand where is the problem in my last post: I am a little
bit
lost in the classes
I am just modifying the simpletrenchSystem.py example file. I would like
the
extension velocity
Hi everyone,
I tried to do a simple level set technique : particules (concentration field
c) are diffusing and aggregating to an aggregate (represented by the
interface phi=0)
I used the template of examples.levelSet.electroChem.howToWriteAScript
to write the following few lines attached at the
, Julien Derr wrote:
yes D is fixed, and the value on the polygon is always positive; Indeed,
here is what I do;
I have an old concentration field at one time step OLDC (all
concentration is between 0 and 1). then I update the geometry of the polygon
(it increases its size a little bit)
I
Hi all,
I am still bothering you with my simple diffusion problem between an outer
circle (Boundary condition value=1)
and an inner polygon (Boundary flux=0)
I am getting negative values on the concentration field !!
a simple diffusion process (eq = TransientTerm() ==
DiffusionTerm(coeff=D))
Thanks a lot Daniel,
so if I understand well it is not possible for now, to impose that the
gradient of the concentration field would be normal to the face?
On Tue, Feb 15, 2011 at 6:33 PM, Daniel Wheeler
daniel.wheel...@gmail.comwrote:
On Mon, Feb 14, 2011 at 9:36 AM, Jonathan Guyer
and 4 of the table ?
also, I could use the actual version to write
BCs = (FixedFlux(faces=facesInside, value=phi.getFaceGrad()) )
wouldn't it be correct ?
On Fri, Feb 11, 2011 at 3:58 PM, Jonathan Guyer gu...@nist.gov wrote:
On Feb 11, 2011, at 7:56 AM, Julien Derr wrote
Thanks Jonathan,
looks like the problem with my polygon was that it had sometimes two submits
at the same place (making a null side)
Julien
On Wed, Feb 9, 2011 at 3:28 PM, Jonathan Guyer gu...@nist.gov wrote:
On Feb 9, 2011, at 9:11 AM, Julien Derr wrote:
Thanks a lot, chunking works
Hi everyone,
I am dealing with an irregular mesh done between a big circle and a small
polygone.
looks like I have memory issues when the polygone becomes more than a few
hundreds sides. Is that a typical limitation by fipy ? Is there a way to
deal with big polygonial shapes?
see error bellow,
, but have the
disadvantage that there must be enough memory to allocate the required
arrays.
In this case, by working in chunks to create value, you can work around
this (I believe, did not try anything).
Benny
2011/2/8 Julien Derr julien.d...@gmail.com
Hi everyone,
I am dealing
do you suggest to do something like
for a in xc:
for b in yc:
newphi.setValue(phi ((array([a]),array([b]) )) )
this is horribly slow...
On Tue, Feb 8, 2011 at 3:52 PM, Benny Malengier
benny.maleng...@gmail.comwrote:
2011/2/8 Julien Derr julien.d...@gmail.com
Thanks
On Thu, Feb 3, 2011 at 9:12 PM, Daniel Wheeler daniel.wheel...@gmail.comwrote:
On Thu, Feb 3, 2011 at 1:45 PM, Julien Derr julien.d...@gmail.com wrote:
Thanks Daniel,
Happy to help.
Indeed getting the value of the variable works great for arbitrary
values.
but I am still a little bit lost
it worked perfectly ! thanks !!!
PS i don't really understand though why it didn't work with (xc,yc) but
with m0.getCellCenters()
even if xc,yc =m0.getCellCenters()
On Fri, Feb 4, 2011 at 3:34 PM, Daniel Wheeler daniel.wheel...@gmail.comwrote:
On Fri, Feb 4, 2011 at 7:10 AM, Julien Derr
oups sorry, I missed that . it makes perfect sense ! thanks again
On Fri, Feb 4, 2011 at 9:09 PM, Jonathan Guyer gu...@nist.gov wrote:
On Feb 4, 2011, at 1:48 PM, Julien Derr wrote:
PS i don't really understand though why it didn't work with (xc,yc) but
with m0.getCellCenters
Thnak you so much for your quick reply.
I understand your answer, but I am still confused how many ' or I should
put for the proper syntax.
cmd= ''' Point(1) = {0, 0, 0, 0.05};Point(2) = {-1, 0, 0, 0.05};
Point(3) = {0, 1, 0, 0.05};Point(4) = {1, 0, 0, 0.05};Point(5) = {0,
-1, 0,
ok sorry about my last email, I got it
adding \n between arguments, make it work!
thanks a lot again for your help !!!
fipy is amazing
Julien
On Thu, Feb 3, 2011 at 3:21 PM, Julien Derr julien.d...@gmail.com wrote:
Hi James,
thanks a lot for your answer and the explanation about
Hi everyone,
sorry for abusing the mailing list these days.
I didn't find much information about remeshing a variable;
I found this page:
http://matforge.org/fipy/browser/trunk/fipy/variables/cellVariable.py?rev=745
but no help corresponding to the remesh function. I tried to implement it
:
On Thu, Feb 3, 2011 at 11:36 AM, Julien Derr julien.d...@gmail.com
wrote:
Hi everyone,
sorry for abusing the mailing list these days.
No problem.
I didn't find much information about remeshing a variable;
We probably got rid of it for a reason. There is a
_ReMeshedCellVariable class
hi again,
the other thing I am wondering is if it is possible to automatize the
commandline to get the mesh
something like
cmdbase= \'\'\' cellSize = %(cellSize)g; radius = %(radius)g; rbis =
%(rbis)g; Point(1) = {0, 0, 0, cellSize}; Point(2) = {-radius, 0, 0,
cellSize}; Point(3) = {0, radius,
Thanks a lot
On Wed, Feb 2, 2011 at 5:23 PM, Jonathan Guyer gu...@nist.gov wrote:
On Feb 2, 2011, at 10:17 AM, Julien Derr wrote:
fipy looks absolutely amazing. but so far, I didn't understand how to
extract the coordinates of a face.
do you know how it could be done
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