Re: [Jmol-users] Examples of students using the export to web function & Sage...

[Jonathan G. <gu...@uw...>]

On Apr 11, 2009, at 9:13 PM, jmo...@li...  
wrote:

> Message: 6
> Date: Sat, 11 Apr 2009 20:43:03 -0500
> From: jas...@cr...
> Subject: Re: [Jmol-users] Examples of students using the export to web
> 	function..
> To: jmo...@li...
> Message-ID: <49E...@cr...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Thanks for posting this.  I also saw that you had a Sage server set up
> (link on the left of the above page).  Over in the Sage camp, we are
> very interested in cool applications of Sage.  Do you mind telling us
> what you used Sage for?  Is there anything that we can do to help  
> it be
> better for you?
I'm using SAGE a number of ways:
1) As a replacement for Maple that the students can access without  
using a limited subset of the computers on our campus.  Primarily it  
is a useful engine for doing symbolic algebra and integration for my  
students.  Some have been using it to plot functions as well.  I  
accept SAGE output as solutions to homework problems.  It has helped  
a number of my students who are sloppy when writing out longer  
solutions.

2) I wrote some python to generate random chemical reactions and  
mechanisms.  I then combined this with the interact function to  
produce drills on how to write the system of differential equations  
that need to be solved to find the time behavior of the species  
concentrations.

3) I also modified the Euler integration interact to demonstrate how  
numerical integration is used to find the time behavior in complex  
systems.  There is a nice Java program called Tenua that implements  
this for chemical systems relatively nicely, so for actual numerical  
calculations we used that.  I am interested in extending my python so  
that these calculations could be done cleanly in SAGE as this would  
remove the "blackbox" aspect of what is being done.

4) I am also interested in seeing if I can help the students learn to  
use SAGE for matrix manipulations so that they could do somewhat more  
sophisticated quantum mechanics than I have them do now.

5) ONE REQUEST: Using version 3.2.3, I've found that assigning values  
to variables after a SAGE function is defined does not translate into  
those values being incorporated into the calculation of the  
function's value.  If I define a pythonic function and include the  
variables in the call, then things behave as I would like.  The  
reason this would be nice is that we often need an analytical  
solution to a problem in terms of constants and measured values that  
we will then stick measured values into.  This can certainly be  
achieved using copy and paste, but that is not very convenient.  It's  
also possible that I am not understanding how to use SAGE.

>
> (to bring this back on-topic): Can you currently invoke jmol in  
> Sage to
> view chemistry-related things?  If not, my guess is that it would be
> fairly easy to make a jmol() function that would take data or a  
> file and
> invoke a jmol instance with that data.  Would that be useful?
It might be useful.  I haven't tried it so don't know whether it is  
possible.  At present, I'm not sure how I'd use it.  However, I've  
worked on integrating some kinetics (diff eq) calculations into SAGE  
and can imagine wanting to show the molecules involved.  I would say  
it should not be a high priority.
>
> Also, there has been interest recently on getting a units calculation
> package into Sage.  Would that be useful?  (I think that effort could
> also use some help from some more interested motivated people.)
I spent a little time looking at the packages built in to  
maxima...They're hard to use.  I've set up some very simple  
definitions that turns everything into SI units, that I've used with  
more success.  If you are interested in the python for that, I can  
send it along.

I had noticed the discussion on the Sage lists, but haven't had time  
to look at the some of the suggested packages.  As people on the Jmol  
project have heard before, I've had trouble getting credit at my  
institution for time spent contributing to Jmol so am trying to be  
very careful about how much time I spend on these kinds of things.   
I'm also stretched thin, as I am overcommitted with teaching and on- 
campus service duties this year.
>
> Thanks,
>
> Jason

                          Dr. Jonathan H. Gutow
Chemistry Department                                 gu...@uw...
UW-Oshkosh                                           Office:920-424-1326
800 Algoma Boulevard                                 FAX:920-424-2042
Oshkosh, WI 54901
                  http://www.uwosh.edu/faculty_staff/gutow/