Thu, Nov 8, 2012 at 5:02 PM, Daniel Wheeler
wrote:
>
>
>
> On Wed, Nov 7, 2012 at 1:43 PM, Julien Derr wrote:
>>
>> Hi everyone,
>>
>>
>> I am using constrain in a syntax like
>> c.constrain(1., where=facesOutside)
>>
>> If I want to rele
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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fipy@nist.gov
http://www.ctcms.nist.gov/fipy
[ N
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 yo
--- 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
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 wi
Hi everyone,
thanks to you and your valuable help my code is now working nicely in 2D. I
thought the fipy structure would allow smooth transition to 3D case, as all
instructions are very general and mesh independant.
Unfortunately, I have kind of a black box error when evaluating phi (which
is t
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 wrote:
> Hi everyone,
>
> and sorry for bothering you again,
>
> Is there a built in function enabling me to get the min of 2 cellvariables
> ?
> somethi
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,
self[i]=1
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
wrote:
> On Fri, Oct 14, 2011 at 10:44 AM, Julien De
Hi everyone,
here is my technical question of the day ...
phi is a DistanceVariable
type(phi)
Out[39]:
if I define I=phi._cellInterfaceFlag
it gives me an array.
In [41]: I
Out[41]: array([0, 0, 0, ..., 0, 0, 0])
In [42]: type(I)
Out[42]:
is it possible to get directly a Cellvariable ?
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 interfa
cit
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
wrote:
>
> On Thu, Jul 14, 2011 at 10:44 AM, Julien Derr
> wrote:
> > reoups.. actually, if you could mind ... I tried t
ror :
AttributeError: '_CUSTOMMetalIonSourceVariable' object has no attribute
'ionvar'
On Wed, Jul 13, 2011 at 8:04 PM, Julien Derr wrote:
> I think I got the idea, but I have trouble with implementation
>
> in the
> class _CUSTOMMetalIonSourceVariable
12,2011
return self.distanceVar._cellInterfaceFlag * 1e+20 * (self.ionvar() -
0.1)
On Wed, Jul 13, 2011 at 7:11 PM, Julien Derr wrote:
> oh, I see!!! thanks a lot for the nice explanation ... as usual!!
>
> Julien
>
>
> On Wed, Jul 13, 2011 at 5:31 PM, Daniel Wheeler > wrote
Sorry everyone! nevermind my last email
On Wed, Jul 13, 2011 at 8:04 PM, Julien Derr wrote:
> I think I got the idea, but I have trouble with implementation
>
> in the
> class _CUSTOMMetalIonSourceVariable(CellVariable):
>
> I used to write
> #re
oh, I see!!! thanks a lot for the nice explanation ... as usual!!
Julien
On Wed, Jul 13, 2011 at 5:31 PM, Daniel Wheeler
wrote:
>
> On Wed, Jul 13, 2011 at 11:00 AM, Julien Derr
> wrote:
>
> > D gradient(c) + source term = 0
> >
> > so why a huge source term w
>
> On Mon, Jul 11, 2011 at 8:51 AM, Julien Derr
> 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
> > abso
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) l
Thanks so much Jonathan !!
On Tue, May 31, 2011 at 7:41 PM, Jonathan Guyer 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 = Cell
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
2011 at 8:27 AM, Julien Derr
> wrote:
> > 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
> irreg
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 rea
set.py", line 65, in _calcValue
return self.distanceVar._cellInterfaceFlag * 1e+20
AttributeError: 'DistanceVariable' object has no attribute
'_cellInterfaceFlag'
On Fri, Apr 1, 2011 at 4:33 PM, Daniel Wheeler wrote:
>
> On Fri, Apr 1, 2011 at 5:57 AM, Julien
Thanks so much, Jonathan, makes a lot of sense
and working fine now !!!
On Mon, May 2, 2011 at 7:44 PM, Jonathan Guyer wrote:
>
>
> On May 2, 2011, at 11:39 AM, I wrote:
>
> > Does it really need to be such a big problem? Does it fail in a 100x100
> mesh?
>
> Answering my own question, I
I am trying 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 wrote:
>
>
> On May 2, 2011, at 9:03 AM, Julien Derr w
1E-18
#with noise
depositionRateVariable = abs(GaussianNoiseVariable(mesh=mesh, mean=1.,
variance=0.02))*( (abs(v0*c.getGrad().dot(phi.getGrad())) +
v0*c.getGrad().dot(phi.getGrad()) ) /2.0 ) + 1E-18
On Mon, May 2, 2011 at 2:46 PM, Jonathan Guyer wrote:
>
>
> On May 2, 2011, at 8:00 A
Dear all,
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:
what is the meaning of this error ?
do you know if there is a general class of problems
time step is too big ?
On Fri, Apr 8, 2011 at 3:36 AM, Jonathan Guyer 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 = FaceVar
as no attribute
'_resetBoundaryConditionApplied'
WARNING: Failure executing file:
humm, any ideas ? thaks a gain,
Julien
On Fri, Apr 1, 2011 at 9:57 PM, Jonathan Guyer wrote:
>
>
> On Apr 1, 2011, at 9:46 AM, Julien Derr wrote:
>
> > I have a 2D grid, but I would
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 circ
-
File
"/n/sw/Python-2.6.2/lib/python2.6/site-packages/FiPy-2.1.1-py2.6.egg/fipy/models/levelSet/electroChem/gapFillMesh.py",
line 214, in gapFillMesh.TrenchMesh
Failed example:
print numerix.sqrt(localErrors[argmax]) < 0.051
Exception raised:
Traceback (m
aniel Wheeler
wrote:
>
> On Mon, Mar 28, 2011 at 1:38 PM, Julien Derr
> 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
>
> On Mon, Mar 28, 2011 at 5:31 AM, Julien Derr
> 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
the gradient
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
wrote:
> On Tue, Mar 22, 2011 at 1:23 PM, Julien Derr
> w
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 co
Thanks so much, it is working great
On Mon, Mar 7, 2011 at 11:00 PM, Daniel Wheeler
wrote:
>
> On Mon, Mar 7, 2011 at 4:14 PM, Julien Derr wrote:
> > depositionRateVariable =
> metalVar.getGrad().dot(distanceVar.getGrad())
>
> This should work better
>
>
extensionVelocityVariable.setValue(depositionRateVariable())
distanceVar.updateOld()
catalystVar.updateOld()
metalVar.updateOld()
bulkCatalystVar.updateOld()
distanceVar.extendVariable(extensionVelocityVariable)
dt = cflNumber * cellSize / extensio
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 f
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 wrote:
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 wrote:
>
> On Wed
I guess it is version 2.2
I think I installed it with the last .deb file for Ubuntu
In the help, I get this :
FILE
/usr/local/lib/python2.6/dist-packages/FiPy-2.2_dev-py2.6.egg/fipy/__init__.py
On Wed, Mar 2, 2011 at 5:09 PM, Jonathan Guyer wrote:
>
>
> On Mar 2, 2011, at 6:33 A
x27;
Julien
On Tue, Mar 1, 2011 at 7:02 PM, Jonathan Guyer wrote:
>
>
> On Mar 1, 2011, at 5:22 AM, Julien Derr wrote:
>
> > I installed python-dev, and now I can compile pysparse.
>
> Good!
>
> > and the tests work better
>
> Good!
>
> > testSup
ave a new error !!!
########"
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/f
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
loaded the trunk tarball, and
runned python setup.py install, and get the same errors as before
Julien
On Thu, Feb 24, 2011 at 4:39 PM, Jonathan Guyer wrote:
>
>
> On Feb 24, 2011, at 9:23 AM, Julien Derr wrote:
>
> > If I use easy_install, it install the version 1.1 on
If I use easy_install, it install the version 1.1 only
julien@derr-Precision-T1500:~$ sudo easy_install pysparse
install_dir /usr/local/lib/python2.6/dist-packages/
Searching for pysparse
Best match: pysparse 1.1
Adding pysparse 1.1 to easy-install.pth file
Using /usr/lib/python2.6/dist
I am running Ubuntu 10.10
I dowloaded the archive from http://pypi.python.org/pypi/pysparse/1.2-dev213
and then simply runned
sudo python setup.py install
On Thu, Feb 24, 2011 at 2:52 PM, Jonathan Guyer wrote:
>
>
> On Feb 24, 2011, at 8:20 AM, Julien Derr wrote:
>
> > whi
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 wrote:
> indeed!
>
> I have a segmentation fault when I run the test!
> I am going to reinstall pyspare or maybe ano
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
Wed, Feb 23, 2011 at 10:01 AM, Julien Derr
> 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
> t
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, depositionRateVar
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
for chunk in range(int(round(len(indices) / chunk_size + 0.5))):
chunk_indices = indices[chunk*chunk_size:(chunk+1)*chunk_size]
newphi[chunk_indices] = phi(c[..., chunk_indices])
#updating phi
phi=newphi
On Tue, Feb 15, 2011 at 7:37 PM, Jonathan Guyer wrote:
>
>
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
wrote:
>
> On Mon, Feb 14, 2011 at 9:36 AM, Jonathan Guyer wrote:
>
> >> I don't really u
On Tue, Feb 15, 2011 at 3:33 PM, Joshua Bush wrote:
> Julien,
>
> Would you mind giving us more information?
> Is D a fixed value? What is the center polygon's initial concentration
> value?
> On Feb 15, 2011 6:29 AM, "Julien Derr" wrote:
> > Hi
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))
> On Feb 11, 2011, at 1:07 PM, Julien Derr wrote:
>
> > I din't express myself well ; I was meaning, is it possible to impose
> that the resulting gradient would be normal to the side ?
>
> The vector boundary conditions are always normal to the side.
>
>
>
een line
2 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 wrote:
>
>
> On Feb 11, 2011, at 7:56 AM, Julien Derr w
Hi everyone,
In a typical diffusion problem, I would like to have the following boundary
condition
the gradient of the concentration field normal to the interface?
is it possible to set that in fipy ?
thanks a lot,
Julien
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 wrote:
>
>
> On Feb 9, 2011, at 9:11 AM, Julien Derr wrote:
>
> > Thanks a lot, ch
again for your very fast efficient help !!! (I really appreciate it
!)
On Tue, Feb 8, 2011 at 6:37 PM, Jonathan Guyer wrote:
>
>
> On Feb 8, 2011, at 11:15 AM, Julien Derr wrote:
>
> > do you suggest to do something like
> >
> > for a
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
wrote:
>
>
> 2011/2/8 Julien Derr
>
>> Thanks very much Benny f
which works great, 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
>
>
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, i
oups sorry, I missed that . it makes perfect sense ! thanks again
On Fri, Feb 4, 2011 at 9:09 PM, Jonathan Guyer 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
> wit
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 wrote:
>
> On Fri, Feb 4, 2011 at 7:10 AM, Julien Derr wrot
Thu, Feb 3, 2011 at 9:12 PM, Daniel Wheeler wrote:
>
> On Thu, Feb 3, 2011 at 1:45 PM, Julien Derr 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 l
> On Thu, Feb 3, 2011 at 11:36 AM, Julien Derr
> 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 rea
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
remesh
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 wrote:
> Hi James,
> thanks a lot for your answer and the explanation about the triple '
t 2:45 PM, James O'Beirne wrote:
> On Thu, Feb 3, 2011 at 4:51 AM, Julien Derr wrote:
>
>>
>> do you know what is the proper syntax ?
>>
>
> Hey, Julien.
>
> A multi-line string in Python is indicated by an opening and closing set of
> three quotes (eithe
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, 0
Thanks a lot
On Wed, Feb 2, 2011 at 5:23 PM, Jonathan Guyer 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 kno
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,
Hi all,
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 ?
thanks a lot,
Julien
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