Hi Robert,
Ok, the documentation is mistaken for trajectories. It explicitly says
to use the "load APPEND TRAJECTORY" command, but it only works without
the TRAJECTORY parameter.
Furthermore, it is not working using a single XYZ file with more than
one molecule within. Then Jmol throws following exception, when
selecting a different frame than the first:
Exception in thread "QueueThread0"
java.lang.ArrayIndexOutOfBoundsException: 1
at org.jmol.bspt.Bspf.validate(Unknown Source)
at org.jmol.modelset.ModelCollection.initializeBspf(Unknown Source)
at org.jmol.modelset.ModelSet.setAtomPositions(Unknown Source)
at org.jmol.modelset.ModelSet.setTrajectory(Unknown Source)
at org.jmol.viewer.Viewer.setTrajectory(Unknown Source)
at org.jmol.viewer.AnimationManager.setCurrentModelIndex(Unknown
Source)
at org.jmol.viewer.Viewer.setCurrentModelIndex(Unknown Source)
at org.jmol.script.ScriptEvaluator.frame(Unknown Source)
at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
Source)
at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown
Source)
at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
Source)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown
Source)
at java.lang.Thread.run(Thread.java:722)
The file is quite simple:
5
methane molecule 1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000
5
methane molecule 2
C 1.000000 1.000000 0.000000
H 1.000000 0.000000 -1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000
Kind regards,
Andreas
Am 06.08.2012 15:24, schrieb Robert Hanson:
Yes, that's fixed. http://chemapps.stolaf.edu/jmol/Jmol-13.zip
Let me know if that solves the problem. I had no problem loading two
simple files and two trajectories all together. Each trajectory gets
its individual model number, such as 1.1 or 1.2.
On Mon, Aug 6, 2012 at 7:24 AM, Andreas Truszkowski
<[email protected] <mailto:[email protected]>> wrote:
Hi,
are there any news concerning the problem?
Best regards,
Andreas
Am 29.07.2012 03:02, schrieb Robert Hanson:
Yes, that's the bug if using append with trajectory. I'll look
into it.
On Fri, Jul 27, 2012 at 4:49 AM, Andreas Truszkowski
<[email protected] <mailto:[email protected]>> wrote:
Hi,
reading about 500 models from a XYZ file with load TRAJECTORY
"file" seems now to work. See output or attached picture:
FileManager.getAtomSetCollectionFromFile(d:\temp\data.xyz.gz)
FileManager opening d:\temp\data.xyz.gz
The Resolver thinks Xyz
openFile(d:\temp\data.xyz.gz): 45664 ms
reading 105861 atoms
ModelSet: haveSymmetry:false haveUnitcells:false
haveFractionalCoord:false
1 models in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
502 trajectory steps read
Default Van der Waals type for model set to Babel
105861 atoms created
ModelSet: not autobonding; use forceAutobond=true to force
automatic bond creation
But it's not possible to jump to specific frame or model
using the popup menu or following scrip snippets:
frame 1.2; display (_H OR _He);
model 1.2; display (_H OR _He);
select 1.2; display (_H OR _He);
Jmol throws always following exception:
Exception in thread "QueueThread0"
java.lang.ArrayIndexOutOfBoundsException: 1
at org.jmol.bspt.Bspf.validate(Unknown Source)
at
org.jmol.modelset.ModelCollection.initializeBspf(Unknown Source)
at org.jmol.modelset.ModelSet.setTrajectory(Unknown Source)
at org.jmol.modelset.ModelSet.getModelNumberIndex(Unknown
Source)
at org.jmol.viewer.Viewer.getModelNumberIndex(Unknown Source)
at
org.jmol.script.ScriptEvaluator.bitSetForModelFileNumber(Unknown
Source)
at org.jmol.script.ScriptEvaluator.atomExpression(Unknown
Source)
at org.jmol.script.ScriptEvaluator.atomExpression(Unknown
Source)
at org.jmol.script.ScriptEvaluator.select(Unknown Source)
at
org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
Source)
at
org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown Source)
at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown
Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown
Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown
Source)
at java.lang.Thread.run(Thread.java:722)
Any ideas?
Kind regards,
Andreas
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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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_______________________________________________
Jmol-users mailing list
[email protected]
<mailto:[email protected]>
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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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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
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