this was a problem with my new method of tracking visibility. It
should be fixed. Only the first model should show.
I've set Jmol to NOT show vectors by default. Is that OK? My reasoning
is that one may be interested in the vectors, but not necessarily, and
then they would be a pain to have to always turn off.
Bob
René Kanters wrote:
Hi,
I checked out and built this morning, so I am pretty sure I am using
the latest.
If the first file I read is the gaussian/H2O.out file, I see the two
Gaussian orientations of the molecules on the screen at the same time.
The AtomSetChooser allows me to easily pick one over the other (or the
rewind button). If I then read a different file it does indeed only
show the first frame, and when I go back to the H2O.out it also shows
the first frame (as it should). Not sure what is going on here, but I
thought I'd report it.
Initially I started this message because of the preview button not
showing previews of the files to be loaded anymore, but it seems now
that that is caused by exceptions thrown in the preview-caused- reading
of the files (before they are 'opened'). Thus I ran into some other
spartan files that seem to cause problems:
spartan/spartan01.txt:
FileManager.openFile(/Users/rkanters/Projects/Eclipse/Jmol-datafiles/
spartan/spartan01.txt)
SmarterJmolAdapter:The Resolver thinks:Spartan
AtomSetCollection.freeze called
openFile(/Users/rkanters/Projects/Eclipse/Jmol-datafiles/spartan/
spartan01.txt) 89 ms
java.lang.ArrayIndexOutOfBoundsException: 16
at
org.jmol.adapter.smarter.AtomSetCollection.getAtomSetAuxiliaryInfo
(AtomSetCollection.java:487)
at
org.jmol.adapter.smarter.SmarterJmolAdapter.getAtomSetAuxiliaryInfo
(SmarterJmolAdapter.java:157)
at org.jmol.viewer.Frame.<init>(Frame.java:142)
at org.jmol.viewer.ModelManager.setClientFile(ModelManager.java:76)....
Then I need to restart Jmol.... because it doesn't load anything else
(I dot get some userAction output in the console...)
spartan/benzenevib.smol
just opening this one gives:
FileManager.openFile(/Users/rkanters/Projects/Eclipse/Jmol-datafiles/
spartan/benzenevib.smol)
SmarterJmolAdapter:The Resolver thinks:SpartanSmol
Reading BEGINARCHIVE GEOMETERY atom records...
Reading PROPARC properties records...
reading VIBFREQ vibration records: freqCount = 30
java.lang.ArrayIndexOutOfBoundsException: 256
at org.jmol.adapter.smarter.SpartanSmolReader.readVibFreqs
(SpartanSmolReader.java:186)
at org.jmol.adapter.smarter.SpartanSmolReader.readProperties
(SpartanSmolReader.java:92)
at org.jmol.adapter.smarter.SpartanSmolReader.readAtomSetCollection
(SpartanSmolReader.java:43)
at org.jmol.adapter.smarter.Resolver.resolve(Resolver.java:59)
at org.jmol.adapter.smarter.SmarterJmolAdapter.openBufferedReader
(SmarterJmolAdapter.java:56)
at org.jmol.viewer.FileManager$FileOpenThread.openReader
(FileManager.java:424)
at org.jmol.viewer.FileManager$FileOpenThread.openInputStream
(FileManager.java:417)
at org.jmol.viewer.FileManager$FileOpenThread.run(FileManager.java:394)
at org.jmol.viewer.FileManager.openFile(FileManager.java:94)
at org.jmol.viewer.Viewer.openFile(Viewer.java:929)
at org.jmol.viewer.Eval.load(Eval.java:1778)
at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:396)
at org.jmol.viewer.Eval.run(Eval.java:335)
at java.lang.Thread.run(Thread.java:552)
AtomSetCollection.freeze called
error opening /Users/rkanters/Projects/Eclipse/Jmol-datafiles/spartan/
benzenevib.smol
Could not read file:java.lang.ArrayIndexOutOfBoundsException: 256
openFile(/Users/rkanters/Projects/Eclipse/Jmol-datafiles/spartan/
benzenevib.smol) 132 ms
ScriptException:Could not read
file:java.lang.ArrayIndexOutOfBoundsException: 256
Script line:load /Users/rkanters/Projects/Eclipse/Jmol-datafiles/
spartan/benzenevib.smol
René
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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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and join the prime developer group breaking into this new coding territory!
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