-------- Original Message --------
Subject: Re: [Jmol-developers] [sage-devel] Re: Jmol and
MathematicsVisualization
Date: Tue, 25 Dec 2007 20:07:25 -0700
From: "William Stein" <[EMAIL PROTECTED]>
To: sage-devel@googlegroups.com, [EMAIL PROTECTED]
http://trac.sagemath.org/sage_trac/ticket/1537
involving "triangulation and shadow weirdness" whose fix might involve
having
to actually change jmol.
I'm not sure what that URL is supposed to tell me. Can you be more
specific? If lighting is the issue, realize that Jmol colors the two sides
of a mesh slightly differently. So the order of vertices listed in each
triangle or quadrilateral set is important. Or, if you don't want that
lighting effect, you can add FULLYLIT to the pmesh command. If you are
seeing cris-crossed triagnles, then you are not sending four quadrilateral
corner indices in the right order. I can't think of anything else that
might go wrong in a pmesh.
One thing we haven't implemented in the pmesh command is vertex normal
averaging. We do that with isosurface. I think the smartest thing to do
would be to modify the isosurface oommand to read pmesh files -- this would
allow more flexibility and better shading.
Can you create callbacks like that using the java applet? This would be
great for Sage, I think.
Yes, there are several callback types, and we could certainly add more,
such as hovering over a pmesh point or clicking on a point. Right now the
callbacks are for atoms and draw objects.
> A very interesting capability of Jmol that has arisen in the past year
> is the capability to save and restore the current state of the applet
> - everything. So if you set up a "scene" in the application you can
> just write the state file to disk and open it with the applet, and you
> will be right where you left off. This has been used in a variety of
> contexts to good effect. I've been interested in exploring it in terms
> of collaborative visualization. (I do something, save a state, send it
> to you, you load it and see the exact same thing.) You might be
> interested in that.
Very cool. Sage also uses tachyon3d for ray-traced rendering and
it would be nice to have a way to find out what angle the user selected
from the applet, so we can render the same scene using tachyon.
Also, it would be good that if a user closes the sage notebook then
re-opens it, that all there 3d images are restored to exactly the same
state.
Right -- that's a nice solution -- use Jmol for a front end, and some other
process for the finished product. This is what is used at some sites for
producing JPG images, for example. It's easy to get orientation information
from Jmol.
from JavaScript:
var info = getPropertyAsArray("orientationInfo")
or, at math.htm site by calling up a console from the menu using
right-click (PC) or control-click (Mac) type
getProperty orientationInfo
> http://chemapps.stolaf.edu/jmol/docs/examples-11/math.htm
The Sage notebook is an ajax app, and evaluating a function like this to
have the mesh built in jmol would potentially be very slow:
1. Jmol requests evaluation of a value
2. Javascript notebook code queries the Sage server for the value
of the function
3. The sage notebook server queries a running Sage compute process for
the value of a function.
4. The Sage compute process calls some library function, maybe defined
in PARI or Maxima.
5. The sage notebook server gets the value of the function
6. The javascript notebook gets the value, then returns that two
the Jmol applet.
This would not be good for building a mesh. If the Sage notebook were a
java
app and Sage were written in Java, it would be a different story, but
that's
not
what Sage is.
Not a problem -- what the applet would want would be ALL the values at once
for a specific set of u,v values. No need to work with single values.
Q: what sort of "interactivity" are you interested in? I'm fairly certain
we can set it up for you.
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