Now to answer your question, from the links you gave me in the case of unformatted mode, I can see that the first line with data (3rd) and from the 7th on it is the atom info, (i don't see where the bond info would be though), lines from 4th to 6th are the voxel information for the surfaces. Now where I have the problem is in the volumetric data. Lines form 4 to 7 make the axes of the coordinate system used (centered in coordinates given by the line 3 vector). Usually after that comes the volumetirc data with one line for every N3 voxel,. Now there are N1*N2 lines meaning that you have a vector of data for each discrete coordinate in the N1*N2 plane, and thats ok.
If I understand right an isosurface is formed by the conection of spacially distributed coordinats (voxels for instance) with data in common, If one does a search of any given number on a line of one of this cube files, (take for instance benzene-homo.cub which only has the Higher Order Molecular Orbital info you wont find repeated data so easily) so wheres the catch for isosurfaces.
Also regarding orbitals if I understand right in the line after the atoms info you could have something like this
1 21
then form what its in Miguels java comments.
http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
its says:
For molecular orbital output, NAtoms will be less than zero, and an additional record follows the data for the final atom (in format 10I5 if the file is formatted):
NMO, (MO(I),I=1,NMO) Number of MOs and their numbers
If NMO orbitals were evaluated, then each record
is NMO*N3 long and has the values for all
orbitals at each point together.
Finally how the heck do you plot the isosurfaces if theres no data in common to link coordinates?
Thank Very much, I'm done for now...
Take care.
2006/5/22, Bob Hanson <[EMAIL PROTECTED]>:
What do you want to know? I think I understand these files pretty well
now.
Bob
Einar Coutin wrote:
> 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 <[EMAIL PROTECTED]>:
>
>>
>> Yes I am in the developers list too.
>> Thanks btw...
>>
>> 2006/5/19, Bob Hanson < [EMAIL PROTECTED]>:
>>
>> > 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, [EMAIL PROTECTED], 507-646-3107
>> > Professor of Chemistry, St. Olaf College
>> > 1520 St. Olaf Ave., Northfield, MN 55057
>> > mailto:[EMAIL PROTECTED]
>> > http://www.stolaf.edu/people/hansonr
>> >
>> > "Imagination is more important than knowledge." - Albert Einstein
>> >
>> >
>> > -------------------------------------------------------
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>> > security?
>> > Get stuff done quickly with pre-integrated technology to make your job
>> > easier
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>> > Geronimo
>> >
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>> > _______________________________________________
>> > Jmol-developers mailing list
>> > [email protected]
>> > https://lists.sourceforge.net/lists/listinfo/jmol-developers
>> >
>>
>>
>
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto: [EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
-------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
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