Yes. The only thing JmolData does not have is a graphical interface.
On Thu, Jul 5, 2012 at 11:01 AM, Kubasik, Matt <[email protected]>wrote:
> Dear list,
>
> I am seeking guidance on getproperty (and possibly correct atom
> expressions) within JmolData.jar. Will x=getproperty(“atominfo[nnn].xxx”}
> work in JmolData.jar?
>
> I would like to use JmolData.jar to process Gaussian output files
> containing vibrational vectors of atoms in different vibrational modes.
>
> The following sequence works fine in Jmol.jar (invoked via terminal’s
> command-line, e.g." java -jar $Jmol -on $freqfile -s $script"), but it
> prints an empty string in JmolData.jar:
>
> framenumber=258
> frame @framenumber
> c_index=16
> cvibvector=getproperty("atomInfo["+c_index+"].vibVector")
> show cvibvector
>
>
try
print
instead of
show
> Is it that “frame” does not work in JmolData.jar? Do I need a rigorous
> atom expression (for the 16th atom of the 258th frame) for JmolData.jar?
>
> As a work-around, the following syntax for getproperty places the
> vibvector for EVERY 16th atom of EVERY frame in an array in JmolData.jar:
>
> c_index=16
> allcvibes=getproperty("atominfo.vibVector",{atomno=c_index})
>
> Is there a better way to specify a particular atom of a particular
> frame/model in JmolData.jar?
>
> Matt Kubasik
> Department of Chemistry and Biochemistry
> Fairfield University
>
> PS Getproperty "modelinfo" seems to work equally well in either Jmol.jar
> or JmolData.jar. E.g., the following works the same in both:
>
> freq=getproperty("modelinfo.models["+framenum+"].modelProperties.Frequency");
>
>
> Details:
> Jmol Version: 12.3.31 2012-06-16 00:04
> java.vendor: Apple Inc.
> java.version: 1.6.0_31
> os.name: Mac OS X
> Access: ALL
> memory: 11.3/85.0
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
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