Re: [Jmol-developers] Re: [Jmol-users] Isosurface and .cube files

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

I've been in contact with Wavefuntion. They consider the encoded 
orbital format in SMOL files proprietary and aren't releasing a key to 
it. Bummer!

Bob


Einar Coutin wrote:

> Another question Bob, will it suffice with SPARTAN 04 for that isosurfaces
> project you're doin'?
> 
> 2006/5/22, Einar Coutin <ein...@gm...>:
> 
>>
>> Well it'll be great if Miguel added some more comments on this I get some
>> ideas and clues about .cube and surfaces but thats about it, mostly the
>> links posted there give the information, but the code lacks 
>> explanation, i
>> guess I'm a little rusty on Java (been like 3 years since I programmed on
>> it), anyways the code could be more helpful though, Anyway thanks I'm 
>> closer
>> to figuring this out...Maybe using spartan to calculate orbitals would 
>> be a
>> valid possibility then translate it into .cube, but you're right bob,
>> they're humongous files...
>>
>> 2006/5/22, Einar Coutin <ein...@gm...>:
>>
>> > Yes I am in the developers list too.
>> > Thanks btw...
>> >
>> > 2006/5/19, Bob Hanson < ha...@st...>:
>> >
>> > > Einar, look in
>> > >
>> > > 
>> <http://svn.sourceforge.net/viewcvs.cgi/jmol/trunk/Jmol/src/org/jmol/adapter/smarter/CubeReader.java 
>>
>> > > >
>> > > and
>> > > 
>> <http://svn.sourceforge.net/viewcvs.cgi/jmol/trunk/Jmol/src/org/jmol/viewer/Isosurface.java 
>>
>> > > >
>> > >
>> > > It's all explained there nicely by Miguel, and there are several 
>> links
>> > > there.
>> > >
>> > > also see
>> > >
>> > > http://astronomy.swin.edu.au/~pbourke/dataformats/cube/
>> > > <http://astronomy.swin.edu.au/%7Epbourke/dataformats/cube/>
>> > > But I think there is wrong information there.
>> > > (coordinates are not in Angstroms even if atom number is positive)
>> > >
>> > > http://www.molpro.net/info/current//doc/manual/node401.html
>> > >
>> > > I'm just now working on this, too, by the way. Later this afternoon
>> > > I'll release modifications that allow reading of any of the orbitals
>> > > in a file, not just the first one.
>> > >
>> > > Are you on the Jmol-developers list? I'm replying to that list as
>> > > well.
>> > >
>> > > Bob
>> > >
>> > > Einar Coutin wrote:
>> > >
>> > > > Hi again.
>> > > > Can someone please tell me where is the isosurface information
>> > > located
>> > > > within the .cube files, i plan on building my own for use as
>> > > orbitals on
>> > > > other molecules as separate files.
>> > > >
>> > > > I checked some .cube files like ch3cl-density.cub.gz and
>> > > > o2h2_1_04.cube.gz ,
>> > > > all i see are 6 fields, frist in continuum and the following 5 with
>> > > a
>> > > > separatin row each 9 rows.
>> > > > Maybe a tutorial is in order, i'll be glad to contribute.
>> > > > Thank you
>> > > >
>> > >
>> > > --
>> > >
>> > > Robert M. Hanson, ha...@st..., 507-646-3107
>> > > Professor of Chemistry, St. Olaf College
>> > > 1520 St. Olaf Ave., Northfield, MN 55057
>> > > mailto:ha...@st...
>> > > http://www.stolaf.edu/people/hansonr
>> > >
>> > > "Imagination is more important than knowledge."  - Albert Einstein
>> > >
>> > >
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>> > >
>> > > 
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>> >
>> >
>>
> 

-- 

Robert M. Hanson, ha...@st..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:ha...@st...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein