Hi Dr. Wheeler, We were using fipy 2.1.3 and here is the original error I got:
/home/dely/opt/lib/python2.6/site-packages/pyximport/pyximport.py:184: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility mod = imp.load_dynamic(name, so_path) /home/dely/opt/lib/python2.6/site-packages/pyximport/pyximport.py:184: RuntimeWarning: numpy.flatiter size changed, may indicate binary incompatibility mod = imp.load_dynamic(name, so_path) Traceback (most recent call last): File "circle.py", line 7, in <module> m = Grid2D(nx=N, ny=N, Lx=L, Ly=L) TypeError: Grid2D() got an unexpected keyword argument 'Lx' Here is the secondary error I get when I replace Lx with dx and Ly with dy in circle.py /home/dely/opt/lib/python2.6/site-packages/pyximport/pyximport.py:184: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility mod = imp.load_dynamic(name, so_path) /home/dely/opt/lib/python2.6/site-packages/pyximport/pyximport.py:184: RuntimeWarning: numpy.flatiter size changed, may indicate binary incompatibility mod = imp.load_dynamic(name, so_path) Traceback (most recent call last): File "circle.py", line 11, in <module> phi[:] = (m.x - L / 2)**2 + (m.y - L / 2)**2 - 0.25**2 AttributeError: UniformGrid2D instance has no attribute 'x' The unmodified circle.py does work with the trunk. What version of fipy should I use now? I would prefer not to use the trunk because it may be unstable as the website indicates. Thanks very much. Regards, Yunbo On Feb 17, 2012, at 11:05 PM, Daniel Wheeler wrote: > Im using trunk. You shouldn't need it though. What was the secondary error? > > On Feb 17, 2012 10:39 PM, "wang yunbo" <[email protected]> wrote: > Hi Dr. Wheeler, > > We updated the cython and had an other error. > > Traceback (most recent call last): > File "circle.py", line 7, in <module> > m = Grid2D(nx=N, ny=N, Lx=L, Ly=L) > TypeError: Grid2D() got an unexpected keyword argument 'Lx' > > When we replace them with the standard dx and dy, then circle.py fails > further down in the script. Which fipy version are you using? > > Thanks. > > Yunbo > > On Feb 17, 2012, at 4:12 PM, Daniel Wheeler wrote: > >> What version of cython are you using? I'm using 0.15.1. >> >> On Fri, Feb 17, 2012 at 3:09 PM, wang yunbo <[email protected]> wrote: >> Hi Dr. Wheeler, >> >> I installed lsmlib from its official site and then manually grab the entire >> pylsmlib folder from your link. My platform is ubuntu 10.04.4 LTS with >> Python 2.6.5 and GCC 4.4.3. >> >> Then I attempted to run circle.py. Here is the error I got: >> >> pysparse >> Traceback (most recent call last): >> File "circle.py", line 2, in <module> >> from pylsmlib import computeExtensionFields2d >> File "/home/wang1320/lsmlib/lsmlib-1.0.1/pylsmlib/pylsmlib.py", line 6, in >> <module> >> 'include_dirs' : np.get_include() >> TypeError: install() got an unexpected keyword argument 'setup_args' >> >> >> I checked pysparse, it was OK. >> >> Type "help", "copyright", "credits" or "license" for more information. >> >>> import pysparse >> >>> from pylsmlib import computeExtensionFields2D >> Traceback (most recent call last): >> File "<stdin>", line 1, in <module> >> File "pylsmlib.py", line 6, in <module> >> 'include_dirs' : np.get_include() >> TypeError: install() got an unexpected keyword argument 'setup_args' >> >> >> It seems the wrappers don't work here, how can I make it work? Is your >> version of lsmlib modified? >> Thanks. >> >> Best, >> >> Yunbo >> >> >> >> On Feb 10, 2012, at 3:40 PM, Daniel Wheeler wrote: >> >>> Yunbo, >>> >>> The entire lsmlib code in in my research repository >>> >>> <http://matforge.org/wd15/browser/trunk/lsmlib> >>> >>> It's not been modified apart from for debug reasons. The pylsmlib section >>> is in >>> >>> <http://matforge.org/wd15/browser/trunk/lsmlib/pylsmlib> >>> >>> The three cython wrapper functions are here >>> >>> <http://matforge.org/wd15/browser/trunk/lsmlib/pylsmlib/lsmlib.pyx> >>> >>> Good luck! >>> >>> On Fri, Feb 10, 2012 at 2:20 PM, wang yunbo <[email protected]> wrote: >>> Thanks so much. That'll be great. I'm really looking forwards to trying >>> lsmlib with your cython wrappers. >>> >>> Regards, >>> >>> Yunbo >>> On Feb 10, 2012, at 11:18 AM, Daniel Wheeler wrote: >>> >>>> On Thu, Feb 9, 2012 at 4:56 PM, wang yunbo <[email protected]> wrote: >>>> Hi, >>>> >>>> 1. when I look at the 'data' file and checked some point which suppose to >>>> be at the surface e.g (50, 25), (62, 71), the results are like 0.0 or 0.7 >>>> (not 0.04 as expected). That's where I get confused. How can I reach my >>>> expectation? >>>> >>>> I don't think you can with the current implementation in FiPy. The >>>> calcDistanceFunction method is only first order accurate I believe and >>>> hence the difficulties calculating the curvature accurately. The >>>> applications in FiPy don't use higher derivatives so get away with first >>>> order accuracy. The curvature calculation is second order accurate, but >>>> the underlying calculation of the distance function is not. Hence the >>>> issues. Basically, FiPy as it stands is not accurate enough for this. >>>> >>>> 2. The shape of my plot is quite wavy with many wiggles, not concentric >>>> rings as expected. >>>> >>>> I'm moving towards using lsmlib >>>> <http://ktchu.serendipityresearch.org/software/lsmlib/index.html>, which I >>>> believe has second order accuracy for the distance function calculation >>>> and is also way faster than FiPy. At the moment I have cython wrappers for >>>> calcDistanceFunction2d, calcEikonalEquation2d and calcExtensionFields2d, >>>> which seem to work though I haven't tested extensively. My hope is to >>>> replace all the level set functionality in FiPy with the cython lsmlib >>>> calls. I'm happy to share the cython wrappers with you if you wish. >>>> >>>> In short I recommend that you give lsmlib a shot and then use the my >>>> cython wrappers to integrate with python. >>>> >>>> Cheers. >>>> >>>> -- >>>> Daniel Wheeler >>>> _______________________________________________ >>>> fipy mailing list >>>> [email protected] >>>> http://www.ctcms.nist.gov/fipy >>>> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >>> >>> >>> _______________________________________________ >>> fipy mailing list >>> [email protected] >>> http://www.ctcms.nist.gov/fipy >>> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >>> >>> >>> >>> >>> -- >>> Daniel Wheeler >>> _______________________________________________ >>> fipy mailing list >>> [email protected] >>> http://www.ctcms.nist.gov/fipy >>> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >> >> >> >> >> -- >> Daniel Wheeler >
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