well,that's a different error. You should use forward slashes within quotes:
"d:/temp/data1.xyz"
Sorry about that. There's a special set up for the second parameter of the
LOAD command that allows the backslashes only because of legacy
compatibility.
Bob
On Tue, Aug 7, 2012 at 2:40 AM, Andreas Truszkowski <[email protected]>wrote:
> 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]
> > 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]>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]> 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
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways 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. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> [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
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways 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. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>
>>>
>>>
>>> _______________________________________________
>>> Jmol-users mailing
>>> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways 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. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> _______________________________________________
>>> Jmol-users mailing list
>>> [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
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways 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. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>
>>
>>
>> _______________________________________________
>> Jmol-users mailing
>> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways 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. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Jmol-users mailing list
>> [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
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways 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. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> Jmol-users mailing
> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways 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. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Jmol-users mailing list
> [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
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways 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. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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