Hedge May 2010

hedge@tiker.net

6 participants
32 discussions

Re: [Hedge] Problem running Maxwell 2D example, and question about creating custom operators

by David Powell

Hi Andreas, >> I have finally found some time to come back to hedge and start looking >> at implementing variable epsilon and mu in the Maxwell operator. So >> far I have succeeded in creating a very rough modification to em.py to >> allow the basic functionality (attached along with an modified example >> to run it). However, I'm having a couple of issues: >> >> - I'm unable to get the absorbing boundary conditions to work >> correctly. As far as I can see they should not need to be >> reformulated when varying epsilon and mu, since the internal value is >> always used. The current code looks correct to me, but it causes a >> TypeError exception and I'm not sure how to remedy this. > > This results from silliness in hedge's language that I've fixed a while > ago. If possible, you should use 'operator(argument)' instead of > 'operator * argument' in newly-written operator code. Otherwise, hedge > has to make a guess about how to bind things like 'operator * arg1 / > arg2', and in your case, it made a wrong guess. I introduced the 'op * > arg' syntax to allow cutesy expressions like 'dot(nabla, arg)', but > aside from these cases, I've come to the conclusion that the > parenthesized form is much less ambiguous. I've attached a diff for your > em.py that fixes this, along with a removal of tuple.count(), which is a > Py2.6ism. Hedge is still meant to run fine on Python 2.4. > Thankyou for this, absorbing boundaries now work fine. >> - I haven't been able to test a model where epsilon and mu have >> different values throughout the structure. The >> VariableVelocityStrongWaveOperator just sets velocity based on the >> spatial coordinates. However using this approach it's hard to >> guarantee that the mesh will coincide with the epsilon and mu >> variation, and it would be much more convenient to use tags. I have >> created examples structures in gmsh where I have tagged different >> volumes, however it seems that the material coefficient functions only >> have the "x" and "el" arguments, and neither of these carries tag >> information. Is there a way to do this that I am missing? > > See Mesh.tag_to_elements["my_tag"]. The gmsh reader should be filling > this with the tags read from the gmsh file. > I found this function and managed to get it working by creating element lists(?) corresponding to each tagged region. However I found that testing each element for membership of this list ("if el in region1_list" etc) was extremely slow. I tried an alternative approach by modifying each element to add epsilon and mu information to it, then getting my TimeDependantGivenFunction to use this value. This worked fine until I tried an MPI example, where it seemed that this information did not survive the distribution of the mesh between MPI nodes. Of course I am doing my initial testing without MPI but I don't want to inadvertently break MPI/GPU compatibility. >> - Is there any mechanism for asymmetric treatment or tagging of >> boundaries? In particular, once I have variable material constants >> working, the next thing I would like to implement is total >> field/scattered field incident boundary conditions, which would >> require different boundary flux operators in the total field and >> scattered field regions. > > I'm not quite sure what you're getting at here--are you talking about an > interior boundary between a total-field and a scattered-field region? Yes, this is exactly what I mean. See "Jens Niegemann, Michael Konig, Kai Stannigel, Kurt Busch, 'Higher-order time-domain methods for the analysis of nano-photonic systems', Photonics and Nanostructures – Fundamentals and Applications 7 (2009) 2–11" for an example of this being implemented (though they refer to Taflove's FDTD book for all the gory details of the total field/scattered-field implementation). The features in their DG code correspond to what I would be looking to implement in HEDGE if possible. > I do respect that you don't want to share your code right now. But a) > there's no reason to feel bad about any of it--in particular, it's a > work in progress and not a mess in any way, and b) if we had this > discussion out in the open, others could potentially learn from it. Plus > you're missing out on potentially useful feedback from others. > > Therefore I'd like to encourage you to involve the list in stuff like > this--there's nothing to lose, really. They're nice people. :) I have noticed the recent exchange of emails with Rafael on the list, so as soon as I have something which actually works I will post it to the list. I do have a couple more issues: Firstly, in the "max_eigenvalue" function of the MaxwellOperator, it seems that "discr" is an optional argument. However to turn the epsilon and mu from TimeDependentGivenFunction into arrays which I can multiply and find the maximum, wouldn't I need to interpolate them over "discr"? Can I just rely on it being passed in? Actually I was wondering if getting the user to pass a TimeDependentGivenFunction is really the best way to go about this. >From the user's point of view it would seem easiest to pass in a dictionary of tag names and corresponding (epsilon, mu) values. Secondly, and this isn't really a show stopper, just a nuisance, it seems that the MPI version freezes randomly on the maxwell-2d example when I use 4 or more CPUS (but strangely not 2 or 3). It just seems to stop part way through the time stepping, and doesn't seem repeatable. I'm using Ubuntu x64 9.10, boost 1.40.0, openmpi 1.3.2. I would assume this is some kind of deadlock problem, though of course the problem could be in MPI libraries rather than with HEDGE. I just thought I'd ask if you are able to reproduce this problem, if not then I will try switching to different MPI libraries. regards David

10 years

Regression Check Failed

by Andreas Kloeckner

Hi there, I'm sorry to report that the regression check failed. Details are attached. - Your guilty conscience

10 years, 1 month

Regression Check Failed

by Andreas Kloeckner

Hi there, I'm sorry to report that the regression check failed. Details are attached. - Your guilty conscience

10 years, 1 month

Re: [Hedge] a new error

by Andreas Kloeckner

On Wed, 26 May 2010 17:04:12 -0400, "Field, Scott" <scott_field(a)brown.edu> wrote: > Sorry I've been so bothersome today. I was trying to update HEDGE, and when > I try to build pylo I get > > /users/kloeckner/mach/x86_64/pool/lib/gcc/x86_64-unknown-linux-gnu/4.3.3/include-fixed/features.h:159:1: > warning: this is the location of the previous definition > src/wrapper/wrap_silo.cpp: In function > 'int<unnamed>::silo_typenum_to_numpy_typenum(int)': > src/wrapper/wrap_silo.cpp:479: error: 'DB_LONG_LONG' was not declared in > this scope > error: command 'gcc' failed with exit status 1 > ------------------------------------------------------------------------ > COMMAND develop ON /users/sfield/src/pylo FAILED! > ------------------------------------------------------------------------ Oops. I fixed this in mid-April in pylo rev fb7582aab1f7..., which I apparently forgot to push to the web. It's up there now. Andreas

10 years, 1 month