[this is a response to an earlier message from Bob Hanson...]
On Dec 24, 2007 10:27 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> William,
>
> Ah, great. So you have been busy! I look forward to hearing about what you
> have done.
> Usually what happens is that projects such as yours take a snapshot of Jmol
> at some
> point and then diverge. (Do you know what point that was in your case?)
> That's fine,
> but it of course limits you to that Jmol point, and it makes integration
> harder. Still,
> it's what I would do as well.
In Sage we try as much as possible to get all changes we make, bug fixes, etc.
back upstream. There are very very few cases where this hasn't happened, and
many excellent cases where it has -- one of the main social goals of Sage is
uniting open source projects, and forking doesn't fit well with that.
So forking
is definitely *not* what we plan to do with Jmol. Plus we're
incredibly busy trying
to make Sage as fully functional as we can as quickly as possible, so the more
work other projects do the better :-).
> What we would be interested in doing, if you care to, would be to work as
> much of your adaptations into core Jmol as is reasonable in terms of general
> use, and, if possible set up some Java interfaces that would allow you to keep
> in step with Jmol developments in the future. The way that is done is that we
> start a new branch, work on it, and merge as needed. At some point we are
> both running the same operation, and we are done. Think about it, anyway.
Certainly.
> There may of course be parts of what you are doing that are so remote
> from chemistry that they are just too "out there" -- but then again, maybe
> not.
> I don't see that much that is so different from molecular orbitals and such.
> At least not on the visualization end.
Yep. It's really very cool the way chemists right code for their application,
and it can easily be used for much more general problems.
> If there were ANY possible way for me to go to the Sage workshop, I
> would jump for the opportunity. Even if it could be for a single day, I would
> do it.
> That week, unfortunately, is our first week of class here, so that's probably
> not possible. When's the next one?
The next one will _probably_ be a small-ish workshop
Feb 29 -- March 4, 2008, and it will be hosted by Enthought
(www.enthought.com/) in Austin, Texas. How are those
dates for you? The themes of that workshop will likely be:
numerical computation, 3d visualization, the sage notebook,
and improving collaboration between Sage and
Enthought (which sponsors scipy/numpy).
> Still, short of being there, maybe I can be a virtual participant. I would
> certainly like to learn more about Sage. You can probably guess from my
> recent contributions to Jmol -- mapped isosurfaces, compressed isosurface
> algorithms, molecular orbitals, PovRAY ray interface, navigation mode,
> quaternions -- that one of my primary interests is mathematics in the context
> of chemistry. Sounds like a great opportunity to learn more.
>
> And, yes, the really great thing about Jmol is the interactive capabilities,
> including quite a bit of in-Jmol programmability. So I can see where
> capitalizing on that would suit you well.
>
> The more you can tell me about Sage and how you are using Jmol between now
> and then, the better. I'm downloading the tar files now -- yow, 200 Mb!!! Is
> this on SourceForge?
>
It's hosted at University of Washington and 8 other mirror sites. We
were slashdotted a few
weeks ago (> 5000 downloads in 2 days), and that was pretty harsh.
Did you download
the source or binary tarball? The optimal thing for you to do might
be to download
sage-2.9.1.1.tar and build from source:
http://sagemath.org/dist/src/
If you have any trouble let me know asap.
I set some instruction to jmol-developer a few minutes ago about how
to try jmol 3d
graphics from within Sage.
You could also just go to http://sagenb.com and sign up for an account
then look at
https://sage.math.washington.edu:8101/home/pub/1647/
and click "Edit a copy". It's annoying to use though, because for
some reason (any
ideas?) when using jmol over https (at least as served by Sage's
Twisted web server)
one has to constantly click about some security certificate issues.
> Also, if we really got going on this, I could imagine involving some advanced
> CS/math/chem undergraduates here as well. oh, oh, oh.... Ha, ha. I've got it.
That would be excellent. I have about 7 of them here at UW involved
in Sage :-).
-- William
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