Re: [Jmol-developers] Adding Molden file format; MO isosurfaces, f basis functions, spherical d functions

[Bob H. <ha...@st...>]

Matthew Zwier wrote:

>Hello all,
>
>I am currently working on adding read support for Molden files, used
>to describe geometries, basis functions and molecular orbitals, and
>frequencies and normal modes.  The basic support is done and tested.
>However, I'd like to be able to use f basis functions (at least
>Cartesian) and (less important) spherical d and f functions in the
>creation of MO isosurfaces.  Given all that,
>
>  
>
wonderful!

>1) Is anyone currently working on this?  If so, I'd be willing to help
>(or just stay out of the way until it's done).  If not, I'm planning
>on working on it myself and submitting patches.
>
>  
>
all yours

>2) So far, I've spent all of my time digging around in the smarter
>model readers and the org.jmol.quantum package.  There don't appear,
>in those neighborhoods, to be any significant architectural barriers
>to adding such support.  (At worst, it looks like tracking whether
>individual MO coefficients are for Cartesian or spherical functions.)
>Are there any subtle larger-scale architectural concerns involved that
>I might be missing?
>
>  
>
none at all. So the two additions would be 5D orbitals and F orbitals? 
That would be great.

I wrote the rest of it, so as you check it in, I'd like to look it over. 
It could be we will have some issues with other MO-enabled readers, so 
you might want to look those over, but as I recall the adapter will read 
5D and F orbitals just fine; it's the MO calculation that catches the 5D 
business. Note that 6D orbitals must be in a certain order; 5D 
presumably would be as well. If you could generate a few of these using 
Gaussian or Gamess to compare, that would be good.

If you run into anything that is problematic, let me know. I realize the 
gaussian basis arrays are a bit obtuse. I've tried to be very efficient 
in the coding of those MO calculations. Would like to keep it that 
way...or improve on it....


>In other news, I'm not exactly an Eclipse guru (big understatement),
>and I can't seem to get the Jmol log messages (at any level) to appear
>in the Eclipse console (where System.out goes anyway).  Are there any
>Eclipse users out there who can offer a hint?
>
>  
>
Hmm. Works for me... I use this command line:

start c:\jmol-dev\eclipse\eclipse.exe -debug

but I don't think the -debug is enabling that.

>Thanks,
>Matt Z.
>
>--
>Matt Zwier
>Research Programmer
>School of Chemical Sciences
>University of Illinois at Urbana-Champaign
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900