Otis,
Isn't that interesting!!! I had not noticed that.
Jmol is taking the output geometry, not the input geometry, from the Spartan
file. For example, for benzene in that C6H6.smol file on the website,we
have:
BEGININPUT
OPT HF 3-21G FREQ
benzenevib
0 1
1 0.000000000 0.000000000 -0.020393968
6 0.000000000 0.000000000 1.075605989
6 0.000000000 0.000000000 3.847966909
6 0.000000000 -1.200467944 1.768697023
6 0.000000000 1.200466990 1.768695951
6 0.000000000 1.200467944 3.154876947
6 0.000000000 -1.200466990 3.154876947
1 0.000000000 -2.149631739 1.220696926
1 0.000000000 2.149630785 1.220695972
1 0.000000000 2.149631739 3.702876925
1 0.000000000 -2.149630249 3.702877820
1 0.000000000 0.000000000 4.943966866
ENDCART
...
ENDINPUT
But Jmol skips those and uses instead the final coordinates:
BEGINMOLSTATE
MODEL=3~HYDROGEN=1~LABELS=0
-0.00000004 -0.00000004 1.00000000 0.00000000
-0.99999994 0.00000000 -0.00000004 0.00000000
0.00000000 -0.99999994 -0.00000004 0.00000000
0.00000000 0.00000000 0.00000000 1.00000000
ENDMOLSTATE
BEGINVIBSTATE
ENDVIBSTATE
BEGINCELLS
ENDCELLS
BEGINARCHIVE
External AB INITIO PROGRAM: converted archive file
Jobname.Temp
12 66 30 54 0 1 66 0 RHF 3-21G(d) NOOPT
FREQ
GEOMETRY
1 4.6433727 0.0000000 0.0000000
6 2.6168992 0.0000000 0.0000000
6 -2.6168992 -0.0000000 0.0000000
6 1.3084496 2.2663012 0.0000000
6 1.3084496 -2.2663012 0.0000000
6 -1.3084496 -2.2663012 0.0000000
6 -1.3084496 2.2663012 0.0000000
1 2.3216863 4.0212787 0.0000000
1 2.3216863 -4.0212787 0.0000000
1 -2.3216863 -4.0212787 0.0000000
1 -2.3216863 4.0212787 0.0000000
1 -4.6433727 -0.0000000 0.0000000
(Those are atomic units.) Beats me why they do the coordinate switch. But
Jmol certainly isn't doing that, Spartan is.
Bob
On Thu, Sep 16, 2010 at 12:23 PM, Otis Rothenberger
<[email protected]>wrote:
> Bob,
>
> I may not understand what should be happening here, so I'll be a bit
> more specific.
>
> > It's suppose to load with the same orientation to the viewer that the
> > user left it in when saved with Spartan. Is it not doing that? Rotate
> > the model in Spartan, save it, and load it into Jmol. Doesn't it
> > appear the same as how you saved it? Jmol is supposed to be reading
> > the orientation from the Spartan file and reproducing that.
> >
>
> Using benzene as an example, the Spartan (.spartan) appears to be
> loading the coordinates below which I've copy/pasted from the .spartan
> file via a text reader. The model was recorded in the XZ plane, and Jmol
> is rendering it in the XZ plane. If I do an axes on, the X axis is
> perpendicular to the screen.
>
> If I use Jmol to capture the molfile of this same model (also pasted
> below) and load this molfile, the rendering now has the Z axis
> perpendicular to the screen, but the model is in the YZ plane. There has
> been a coordinate swap.
>
> Both renderings are correct per the data, but the axes have been
> swapped. Is what I've described expected behavior?
>
> Otis
>
>
> SPARTAN PROPERTIES PACKAGE: MAC/P4 build 129c
> Use of molecular symmetry enabled
> Molecular charge: 0
> Spin multiplicity: 1
> Electrons: 30
>
> Cartesian Coordinates (Angstroms)
> Atom X Y Z
> --------- ------------- ------------- -------------
>
> 1 H H1 0.0000000 0.0000000 -2.4946974
> 2 C C1 0.0000000 0.0000000 -1.3950414
> 3 C C4 0.0000000 0.0000000 1.3950414
> 4 C C2 -1.2081412 0.0000000 -0.6975207
> 5 C C6 1.2081412 0.0000000 -0.6975207
> 6 C C5 1.2081412 0.0000000 0.6975207
> 7 C C3 -1.2081412 0.0000000 0.6975207
> 8 H H2 -2.1604714 0.0000000 -1.2473487
> 9 H H6 2.1604714 0.0000000 -1.2473487
> 10 H H5 2.1604714 0.0000000 1.2473487
> 11 H H3 -2.1604714 0.0000000 1.2473487
> 12 H H4 0.0000000 0.0000000 2.4946974
>
>
> http://localhost:8080/meps/benzene.txt
> Jmol version 12.1.11_dev 2010-09-05 20:18
> MODELKIT: ({0:11})
> 12 12 0 0 0
> 0.0 2.494697 0.0 H
> 0.0 1.3950412 0.0 C
> 0.0 -1.395041 0.0 C
> 0.0 0.6975206 -1.208141 C
> 0.0 0.6975206 1.2081412 C
> 0.0 -0.697520 1.2081412 C
> 0.0 -0.697520 -1.208141 C
> 0.0 1.2473484 -2.160471 H
> 0.0 1.2473484 2.1604712 H
> 0.0 -1.247348 2.1604712 H
> 0.0 -1.247348 -2.160471 H
> 0.0 -2.494697 0.0 H
> 1 2 1
> 2 5 6
> 5 6 7
> 3 6 6
> 3 7 7
> 4 7 6
> 2 4 7
> 6 10 1
> 7 11 1
> 3 12 1
> 4 8 1
> 5 9 1
>
>
>
>
>
>
> ------------------------------------------------------------------------------
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
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