http://blog.gmane.org/gmane.comp.python.fipy hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.comp.python.fipy/1257 Hello, again, Just to mention a new problem which I found is when I tried to run as example "python examples/flow/stokesCavity.py" I obtained the error: ......<skip>...... pylab.quiver2(X, Y, U, V, 0.15) AttributeError: 'module' object has no attribute 'quiver2' So I needed to replace "quiver2" with "quiver" in fipy/viewers/matplotlibViewer/matplotlibVectorViewer.py in order to work. Cheers, Ionut Ionut Vancea 2008-11-27T17:28:51 http://comments.gmane.org/gmane.comp.python.fipy/1256 Dear all, First I would like to say thank you for "fipy". Now, my problems with it :) I have just installed fipy, because I would need to solve some problems which involve PDE. It seems that something is wrong because some examples are working (CH mesh2d) and some examples not. Here is what I have: OpenSUSE 11: ionut< at >vaio:~/pywork/CURRENT> uname -a Linux vaio 2.6.25.18-0.2-default #1 SMP 2008-10-21 16:30:26 +0200 x86_64 x86_64 x86_64 GNU/Linux ionut< at >vaio:~/pywork/CURRENT> ionut< at >vaio:~/pywork/CURRENT> svn update At revision 2865. ionut< at >vaio:~/pywork/CURRENT> python-2.5.2-26.2 python-matplotlib-0.98.3-2.1 python-gnuplot-1.8-1.5 python-numeric-24.2-162.1 python-scipy-0.6.0-4.2 python-numpy-1.2.1-7.1 pysparse-1.2a1-py2.5.egg-info and here is what I obtain for the examples which I said that are not working: ===== ionut< at >vaio:~/pywork/CURRENT> python examples/cahnHilliard/inputTanh1D.py /usr/local/lib64/python2.5/site-packages/fipy/viewers/matplotlibViewer/__init__.py:35: UserWarning: Matplotlib1DViewe Ionut Vancea 2008-11-27T17:15:17 http://comments.gmane.org/gmane.comp.python.fipy/1253 Hello, I'm using fipy to model heat transport on 2D meshes. I'd like to be able to save the mesh into a standard hdf5 file, so that it can be easily read by non-fipy users to check my simulations, and I'd also like to be able to directly read the saved file back in and create the appropriate fipy mesh. that the key variables for recreating the original mesh are the vertex coordinates, the FaceVertexIDs, and the CellFaceIDs. Which I can easily retrieve from the mesh I generate and then and store in my hdf5 file. However I have a couple of problems making this happen. First, I can't seem to figure out how to import the Mesh class so that I can pass it this information to re-instance the mesh (assuming this is the right approach). Second, while I understand what the vertex coordinates are, the relationships between the coordinates and the face vertex and cell face IDs is opaque to me, and I'm hoping someone would explain these to me. Finally, if this representation is not a standard, generally recognized Angus Hendrick 2008-11-21T22:38:58 http://comments.gmane.org/gmane.comp.python.fipy/1244 Daniel, Jonathan and other fipy users: I've been struggling for quite some time trying to get FiPy to update a rank 1 CellVariable term as it sweeps to a solution. I think I've finally got it working in a reasonable way, but don't understand why the original way I was doing this was so slow and failed to update. The original, apparently incorrect way, involved creating a rank 1 cell variable of permeabilities: kond=CellVariable(name='hyd.cond.',mesh=mesh,rank=1,value=1.e-5) and multiplying this by a 'saturation phase' variables, with the impact from the saturation states being different in the horizontal (cellSatH) and vertical (cellSatV) directions. cellSat=kond*[cellSatH,cellSatH,cellSatV] This single calculation takes up most of the time in the simulation and this variable never changes as cellSatH and cellSatV change. However, when I calculate the cellSat term as: kond*cellSatH+cellSatV*kond*[0,0,1] my computer model zips along quite nicely and seems to work correctly, for the few situations I'v asreeve 2008-11-17T15:18:53 http://comments.gmane.org/gmane.comp.python.fipy/1242 Thanks for all the previous help, I was looking at the MatplotlibVectorViewer.py and am somewhat confused as to how it finds a U and a V from that data to input in the quiver. Could someone help me? Tom Thomas Cool 2008-11-15T20:19:21 http://comments.gmane.org/gmane.comp.python.fipy/1235 Hi all, I am working on a 3D model that requires a very large mesh. When I tried a uniform grid of 80*80*80 cells, I got the following attached memory error. I wonder if there are ways to overcome this limit. Thank you in advance for any advice. Regards, Zhiwen python(12494) malloc: *** mmap(size=73728000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Traceback (most recent call last): File "run_pyramid.py", line 55, in <module> eq_u,eq_v,eq_w=getEquations(u=u,v=v,w=w,c11=c11,c12=c12,c13=c13,c33=c33,c44= c44,beta11=beta11,beta22=beta22,beta33=beta33,cinn=cinn) File "/Volumes/RAID2/Users/liangz/DEV/Elastic/Solve/elasticEquations.py", line 41, in getEquations graduvw_w=Gradc(c13,Zhat)*Gradc(u,Xhat)+Gradc(c44,Xhat)*Gradc(u,Zhat)+Gradc( c13,Zhat)*Gradc(v,Yhat)+Gradc(c44,Yhat)*Gradc(v,Zhat) File "/Volumes/RAID2/Users/liangz/DEV/Elastic/Solve/myGrads.py", line 15, in G radc return _Gradc(var).dot(hat) File "/Volumes/RAID2/usr/local/st Zhiwen Liang 2008-11-13T17:47:40 http://comments.gmane.org/gmane.comp.python.fipy/1232 Hello, I'm trying to use the matplotlib vector viewer for fipy but i'm having problems: could anyone take a look and tell me what's wrong? Tom #!/usr/bin/env python import os os.environ["FIPY_VIEWER"]="matplotlib" from fipy.tools.parser import parse import time start = time.time() numberOfElements = parse('--numberOfElements', action = 'store', type = 'int', default = 6400) numberOfSteps = parse('--numberOfSteps', action = 'store', type = 'int', default = 5000) import fipy.tools.numerix as numerix nx = int(numerix.sqrt(numberOfElements)) ny = int(numerix.sqrt(numberOfElements)) steps = numberOfSteps dx = 1.0/float(nx) dy = 1.0/float(ny) kappa = 1e-4 M = 1.0 from fipy.meshes.grid2D import Grid2D mesh = Grid2D(dx = dx, dy = dy, nx = nx, ny = ny) from fipy.variables.cellVariable import CellVariable from fipy.tools.numerix import random P = 1.0 E = 0.0 var = CellVariable(name = "phase field", mesh = mesh, value = 2.0*P*random.random(nx * ny) - P) ## a = -1.0 Thomas Cool 2008-11-11T13:52:22 http://comments.gmane.org/gmane.comp.python.fipy/1221 Gentlemen, Thanks for all your help so far. I have been using fipy Trunk successfully with the development version of numpy (1.3.0dev5945). I get the occasional warning about deprecated names, but everything seems to work fine. I've also gotten PyTrilinos working and the Aztec00 solver with MultiLevelPreconditioner is very fast. I did a quick comparison using a simple Poisson problem between fipy with Aztec00 and a stock Poisson matrix builder solved with pyamg. The fipy code was only about 5% slower, and given all the flexibility in fipy versus roll-your-own solutions, that's really impressive. The problem I'm having now is that I want to save my simulation results using the h5 file format with pytables. I can extract all the problem related arrays without much difficulty, but the boundary conditions are more vexing since in the forms I can readily access, the locations where each boundary condition is applied live as unresolved union and intersection of boolean arrays buried inside the FixedValue o Angus Hendrick 2008-11-06T19:08:47 http://comments.gmane.org/gmane.comp.python.fipy/1215 I have a 3x3 domain. I want the center of the left face to have a fixed value boundary condition, and the remainder to have a fixed flux condition. In fipy 1.2.1, I could just say bcs = FixedValue(mesh.getFacesLeft()[1], value=0) and it worked. More comprehensive implementation of lazy evaluation to thwarts that approach in the trunk version, and instead I get the complaint: AttributeError: 'unOp' object has no attribute 'getMesh', presumably because the index operator is not resolving? Of course even if it did resolve, it doesn't look like that would work anymore since getFacesLeft returns boolean FaceVariable, instead of a list of faceIDs. Help! Best Regards, Angus Hendrick Angus Hendrick 2008-10-09T23:34:50 http://comments.gmane.org/gmane.comp.python.fipy/1211 Here's what I get when I try to install this: angus< at >chao:~/src/python/fipy-trunk/trunk$ svn update At revision 2745. angus< at >chao:~/src/python/fipy-trunk/trunk$ sudo python setup.py install running install running bdist_egg running egg_info writing FiPy.egg-info/PKG-INFO writing top-level names to FiPy.egg-info/top_level.txt writing dependency_links to FiPy.egg-info/dependency_links.txt Traceback (most recent call last): File "setup.py", line 754, in <module> 'Topic :: Software Development :: Libraries :: Python Modules' File "/usr/lib/python2.5/distutils/core.py", line 151, in setup dist.run_commands() File "/usr/lib/python2.5/distutils/dist.py", line 974, in run_commands self.run_command(cmd) File "/usr/lib/python2.5/distutils/dist.py", line 994, in run_command cmd_obj.run() File "/usr/lib/python2.5/site-packages/setuptools/command/install.py", line 76, in run self.do_egg_install() File "/usr/lib/python2.5/site-packages/setuptools/command/install.py", line 96, in do_egg_insta Angus Hendrick 2008-10-09T20:34:11 http://comments.gmane.org/gmane.comp.python.fipy/1209 First, thanks for all your help over the past couple of days. Next I managed to obtain a working version of fipy 1.2.1 rev 2744 using numpy 1.2.0 by doing the following: 1. svn update (to get from whereever I was to rev 2744) 2. editing line 11 in /fipy/tools/numerix.py from: from numpy.core import ma as MA to: from numpy import ma as MA 3. running setup.py install All seems well... that is, my previously running code runs. However when I run setup.py test, I get (consistently): (many lines of happy test results, and then...) import examples.convection.exponential1DSource.tri2Dinput ... ok import examples.convection.powerLaw1D.tri2Dinput ... ok import examples.convection.advection.inputVanLeerUpwind ... ok import examples.convection.peclet ... ok Doctest: examples.convection.exponential1D.input ... Segmentation fault It then kicks out. End of test. Of course its possible that the newer version of numpy is to blame, but a Doctest seems like a really weird place for numpy to break things. For now I' Angus Hendrick 2008-10-09T18:54:51 http://comments.gmane.org/gmane.comp.python.fipy/1203 Hello, So I went to upgrade my Numpy from 1.0.4 to 1.2.0, and I ran into a problem with fipy. In particular "from numpy.core import ma as MA" was causing problems. I rolled numpy back and now I'm fine again, but it leads me to a couple of questions... 1. What is the most recent version of FiPy, and does it represent a speed improvement over version 1.2.1? What is the svn checkout command I need to run to get it? (I tried getting "current," a few of months ago when I thought there was a 2.0.1a version around, and I got 1.2.1 again, so I'm screwing something up.) 2. What is the latest version of Numpy that the newest version of FiPy works with? What about the 1.2.1 version? Also, on a completely separate note, has anyone looked at the PyAMG<http://code.google.com/p/pyamg/>solvers for use with FiPy? I confess I don't really understand the differences between different solvers, as I'm not a high-powered numerics guy, but they (whoever "they" are) say that multi-grid solvers are among the fastest for Angus Hendrick 2008-10-08T17:54:14 http://comments.gmane.org/gmane.comp.python.fipy/1196 Hello again, I'd like to use a dynamic link library (dll) in a problem I'll solve with FiPy. And not just any DLL. Our chair of research has a license for the excellent REFPROP software by you-know-who. I'm aware of the existence of the ctypes package, and I even read the tutorial. But quite frankly, I didn't understand much. I think there are much prerequisites I'm lacking. The other solution would be a python extension written in C. But I'm not proficient in C and there is no example of using REFPROP in a C program in the documentation. Perhaps this is a very simple problem for one of you? Or would it be better to ask your colleague Mr. Lemmon? Many thanks, Etienne Rivard 2008-09-22T07:12:58 http://comments.gmane.org/gmane.comp.python.fipy/1188 Dear All, How do I set a viewer in fipy? Regards 2008/9/12 Daniel Wheeler <daniel.wheeler2-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> franck kalala 2008-09-20T22:10:04 http://comments.gmane.org/gmane.comp.python.fipy/1183 Hi all, I wonder if a face variable can be used when defining equations. If I run the following lines (they might not be meaningful, just for example): from fipy import * mesh=Grid1D(nx=2) facev=FaceVariable(mesh=mesh,value=0.) eq=0==DiffusionTerm(0.)+facev I will get "TypeError: The coefficient must be a rank-0 CellVariable or a scalar value.". It seems that I could not use FaceTerm directly. Are there any convenient ways to do this? Thank you in advance for any suggestions. Have a nice day! Zhiwen Zhiwen Liang 2008-09-18T21:54:43 http://comments.gmane.org/gmane.comp.python.fipy/1181 Dear all, I am solving an equation of this type phi_t=div(phi**3*div\theta) in the right hand side of this equation phi is to the power 3. in the manual it is explain how to deal with this term when phi is to the power 1. but here I don't know how to represent it in fipy the second hand side, I try this PowerLowerConvectionTerm((phi**3).getArithmeticFaceValue()*theta.getFaceGrad())) but with tha I don't have expected result for my codes. Is there any other better way to represent such term? Regards 2008/9/3 Daniel Wheeler <daniel.wheeler2-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> franck kalala 2008-09-12T11:34:03 http://comments.gmane.org/gmane.comp.python.fipy/1168 Dear FiPy enthusiasts, It is with great pleasure that we introduce to you the Virtual Kinetics of Materials Laboratory, VKML. VKML is a set of simple FiPy examples that simulate basic aspects of kinetics of materials through an interactive Graphical User Interface. The seminal development includes four examples: Polycrystalline Growth and Coarsening: simulates the growth, impingement, and coarsening of a random distribution of crystallographically oriented nuclei. The user can control every aspect of the model such as the nuclei radius, the size of the simulation cell, and whether the grains are homogeneously dispersed or only on one wall of the simulation. https://www.nanohub.org/tools/vkmlpsgg/ Dendritic Growth: simulates the anisotropic solidification of a single solid seed with an N-fold axis of crystallographic symmetry embedded in an undercooled liquid. The user can specify many material aspects of the solidification process, such as the thermal diffusivity and the strengt R. Edwin Garcia 2008-09-03T15:30:42 http://comments.gmane.org/gmane.comp.python.fipy/1159 Dear Fipy developers and users, Thanks again for solving my last problem. This is the most powerful forum I have ever been involved. I do not know if this is an known issue, but I found it very slow to assign fipy variables as elements of the numerix array. Please see below. from fipy import * import fipy.tools.numerix as numerix mesh=Grid3D(nx=10,ny=10,nz=10) Dx=CellVariable(mesh=mesh,value=1.) Dy=CellVariable(mesh=mesh,value=2.) Dz=CellVariable(mesh=mesh,value=3.) zeros=CellVariable(mesh=mesh,value=0.) Ds=numerix.array(((Dx,zeros,zeros),(zeros,Dy,zeros),(zeros,zeros,Dz))) The last line of the above code took 3.5 second while the rest of the code only took 0.002 second, using my laptop. I wonder if it can be improved. Or maybe the way I did it is too clumsy? I define the "Ds" in the code in order to use it as the anisotropic coefficient in the DiffusionTerm. Thank you for any advice. Enjoy the rest of the Labor Day! Regards, Zhiwen Zhiwen Liang 2008-09-01T19:15:04 http://comments.gmane.org/gmane.comp.python.fipy/1139 Hi all I am so sorry to disturb you so much, I am very young in python, in fipy, sure I lent many thing from you since I decided to use fipy, I was this example ************************************************************************************************************** cellSize=0.05 radius=1. lines= ['cellSize = '+str(cellSize) + ';\in', 'radius ='+str(radius) + ';\in', 'point(1)={0, 0, 0, cellSize};\n', 'point(2)={-radius, 0, 0, cellSize};\n', 'point(3)={0, radius, 0, cellSize};\n', 'point(4)={radius, 0, 0, cellSize};\n', 'point(5)={0, -radius, 0, cellSize};\n', 'point(6)={2, 1, 3};\n', 'point(7)={3, 1, 4};\n', 'point(8)={4, 1, 5};\n', 'circle(9)={5, 1, 2};\n', 'Line Loop(10)={6, 7, 8, 9};\n', 'Plane Surface(11)={10};\n', import tempfile (f,geomName)=tempfile.mkstemp('.geo') file=open(geoName, 'w') file.writelines(lines) file.close() import os os.close(f) import sys if sys.platform=='win32': meshName= franck kalala 2008-08-26T11:39:41 http://comments.gmane.org/gmane.comp.python.fipy/1138 Hi all How do I plot this surface z=exp(-(x**2+y**2)) using viewers within fipy, for a given 2D mesh. Regards franck kalala 2008-08-26T00:25:52 http://comments.gmane.org/gmane.comp.python.fipy/1131 Thanks again for your help, but I still have one error message that I cannot understand, this my code ************************************************************************************************** rom __future__ import division L=1. nx=400 dx=L/nx timeStepDuration=0.012 from fipy.meshes.grid1D import Grid1D mesh=Grid1D(dx=dx, nx=nx) from fipy.variables.cellVariable import CellVariable phi=CellVariable(name="saturation", mesh=mesh) p=CellVariable(name="pressure",mesh=mesh) x=mesh.getCellCenters()[...,0] phi.setValue(.9, where=x<.5) phi.setValue(.3, where=x>=.5) p.setValue(1.) pcs=0 qin=40*((x>=.1)&(x<=.3))+20*((x>=.7)&(x<=.9)) qout=60*((x>=.4)&(x<=.6)) sin=.8 pin=0 q1s=sin*qin+phi*qout q2s=(1-sin)*qin+(1-phi)*qout if __name__=='__main__': import fipy.viewers phiviewer=fipy.viewers.make(vars=(phi), limits={'ymin':.2, 'ymax':1.1}) pviewer=fipy.viewers.make(vars=(p), limits={'ymin':.2, 'ymax':1.1}) phiviewer.plot() pviewer.plot() raw_input("initial condition. press <return> to proceed franck kalala 2008-08-24T14:24:07 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.python.fipy