Hi Robert,
I have referenced Jmol version (13.0 RC3 2012-08-04 18:06) from your
link. But I can't reproduce your scripting without an error. I am
accessing Jmol through the API and the script is executed by using the
"SCRIPT" method of the JmolViewer class.
"load TRAJECTORY "d:\temp\data0.xyz";" -> No error. The structure will
be rendered correctly.
"load APPEND trajectory "d:\temp\data1.xyz";" Error:
file ERROR: d:\\ empdata1.xyz
java.io.FileNotFoundException: d:\ empdata1.xyz (Die Syntax für den
Dateinamen, Verzeichnisnamen oder die Datenträgerbezeichnung ist falsch)
FileManager.getAtomSetCollectionFromFile(d: empdata1.xyz)
FileManager opening d:\\ empdata1.xyz
eval ERROR: java.io.FileNotFoundException: d:\ empdata1.xyz (Die
Syntax für den Dateinamen, Verzeichnisnamen oder die
Datenträgerbezeichnung ist falsch)
openFile(d: empdata1.xyz): 0 ms
----
load append "trajectory" >> "d: empdata1.xyz" <<
But using "load APPEND "d:\temp\data1.xyz";" works.
Furthermore, the single file alternative doesn't work either. Jmol
produces the following error when switching the model:
Exception in thread "QueueThread0"
java.lang.ArrayIndexOutOfBoundsException: 2
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)
Allthough the console writes that 502 trajectory steps have been read
and the context menu offers an entry for every model :
FileManager.getAtomSetCollectionFromFile(d:\mfdresults\data.xyz.gz)
FileManager opening d:\mfdresults\data.xyz.gz
The Resolver thinks Xyz
openFile(d:\mfdresults\data.xyz.gz): 46139 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
502 models
Best regards,
Andreas
Am 06.08.2012 17:31, schrieb Robert Hanson:
I don't think so. Check that version. That's certainly what it WAS
doing. Is this the applet or the application? Here are the correct
file sizes:
08/06/2012 06:26 AM 6,809,502 Jmol.jar
08/06/2012 06:26 AM 2,507,621 JmolApplet.jar
08/06/2012 06:26 AM 1,019,501 JmolApplet0.jar
08/06/2012 06:26 AM 2,705,849 JmolAppletSigned.jar
08/06/2012 06:26 AM 1,141,187 JmolAppletSigned0.jar
$ load $caffeine
$ load append trajectory "C:/temp/cyclohexane_movie.xyz"
36 models
Maybe just a snafu in the caching of the applet?
Bob
On Mon, Aug 6, 2012 at 10:19 AM, Andreas Truszkowski
<[email protected] <mailto:[email protected]>> wrote:
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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St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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_______________________________________________
Jmol-users mailing list
[email protected]
<mailto:[email protected]>
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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
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_______________________________________________
Jmol-users mailing list
[email protected]
<mailto:[email protected]>
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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
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