I fixed my "out of memory" error, and it was indeed the fact that the ArrayLists weren't being garbage collected. :) I switched from ArrayLists (which I used "clone" for my save/restore operation) to regular arrays (for which I had to write an iterator, but could use the same memory and copy the elements manually), and the error went away. :)
Okay... now I can try to find a nice set of test bonds for rigidity transmission... assuming they exist.
I suppose I should test my code on an example where I know transmission exists... that would be logical.
I'm off to generate such an example... lets hope I have something interesting to show by the time I get to Duke for my meeting... ;)
2 comments:
Holy Cow! What in the world are you talking about? This is your secret sock pal here, I couldn't just lurk, because I have to know *what you do* or what the subject of your dissertation really is. After reading about astrophysics on Yarn Harlot today, I just feel so out there! smiles :)
I'm trying to see if transmission of rigidity can possibly explain protein allostery.
Of course, that sentence probably doesn't make any more sense than this post. ;) I'm used to people not having a clue what I'm talking about.
In *very* general terms, I'm trying to see if a mathematical concept can possibly explain a biological process, and am trying to figure out the computer science needed to do so. ;)
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