Thanks, Bob, I will use the syntax you recommend below. On my machine (OS X
with Jmol 12.3.31) , no "" needed for the atom expression.
It seems like
x = getProperty("atominfo.x", {_N}[7])
Show x
Gives x as a the sole element of a vector, whereas the syntax I was trying to
use (x=getproperty(atominfo[10].x) ) offers x as a number (when it offers a
result in Jmol.jar).
I suppose this result makes sense, since x = getProperty("atominfo", {_N}[7])
offers the full array of all atom properties. Excellent!
From: Robert Hanson <[email protected]<mailto:[email protected]>>
Reply-To:
<[email protected]<mailto:[email protected]>>
Date: Sun, 8 Jul 2012 16:19:43 -0500
To: <[email protected]<mailto:[email protected]>>
Subject: Re: [Jmol-users] Jmol .jar vs JmolData.jar: help with getproperty
OK, I know what it is. Good idea to use -onx; ignore the last comment. The
default second parameter is "{visible}" for getProperty("atomInfo"). With
JmolData, it is determining that nothing is visible. Which, of course, it
isn't, but.... So I'll see what I can do about that. In the mean time, use
x = getProperty("atomInfo", "{*}")
or -- here's your opportunity to to that right!
x = getProperty("atominfo", "{_N}[7]")
There we go! Much more efficient!
On Sun, Jul 8, 2012 at 4:03 PM, Robert Hanson
<[email protected]<mailto:[email protected]>> wrote:
I guess there's a difference there with those flags. JmolData doesn't need any
flags because it automatically adds -onx, but there is something odd there. In
any case, with JmolData, just do this:
java -jar $JmolData $freqfile -s $script
On Fri, Jul 6, 2012 at 2:07 PM, Kubasik, Matt
<[email protected]<mailto:[email protected]>> wrote:
Bob,
However, I'm still having difficulty with JmolData.jar and Jmol.jar. In the
following script, Jmol.jar prints values for getproperty, but JmolData.jar does
not print values.
bindex=({_N}[3].atomindex+1)
print bindex
bx=GetProperty("atomInfo["+bindex+"].x");
print bx
(No difference if using "show" or "print")
For a direct comparison, the shell script I'm using invokes Jmol right after
JmolData (Jmol 12.3.31):
java -jar $JmolData -onx $freqfile -s $script
java -jar $Jmol -onx $freqfile -s $script
Any thoughts? Is it some kind of variable typing issue? Could it be something
with my file, which contains 322 models, the last 321 of which contain
vibrational mode info from a Gaussian calc?
The syntax bx=GetProperty("atominfo.x",bindex), where bindex={(* and
1.322)[29]}, seems to work in JmolData.jar (and in Jmol.jar).
Matt
From: Robert Hanson
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>
Reply-To:
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>
Date: Fri, 6 Jul 2012 11:38:30 -0500
To:
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>
Subject: Re: [Jmol-users] Jmol .jar vs JmolData.jar: help with getproperty
Oh, right. You can't do that. The string must contain a simple expression like
atomInfo[3]:
print getProperty("atomInfo[" + ({_N}[7].atomIndex + 1) + "].x")
Sorry about the "+1" but that's because atomIndex is one of the very few
0-based properties.
On Fri, Jul 6, 2012 at 10:58 AM, Kubasik, Matt
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>
wrote:
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]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>>
Reply-To:
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>>
Date: Fri, 6 Jul 2012 10:27:18 -0500
To:
<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[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]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[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><http://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
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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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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--
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
--
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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today's security and threat landscape has changed and how IT managers can
respond. Discussions will include endpoint security, mobile security and the
latest in malware threats.
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