Thanks, Bob.
My problem is in combining atom expression syntax and the brackets in the
getproperty command.
Of the two below, the first is empty, and the second returns the correct value.
What is wrong with the first?
nx=getproperty("atomInfo[{(_N)[7]}].x")
print nx
nx=getproperty("atomInfo.x",{(_N)[7]})
print nx
Matt
From: Robert Hanson <[email protected]<mailto:[email protected]>>
Reply-To:
<[email protected]<mailto:[email protected]>>
Date: Fri, 6 Jul 2012 10:27:18 -0500
To: <[email protected]<mailto:[email protected]>>
Subject: Re: [Jmol-users] Jmol .jar vs JmolData.jar: help with getproperty
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]<mailto:[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<http://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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