Bugs item #957730, was opened at 2004-05-21 00:52
Message generated for change (Comment added) made by michaelthoward
You can respond by visiting:
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Category: File Input/Output
Group: HEAD
Status: Open
Resolution: None
Priority: 5
Submitted By: Ming Hua (minghua)
>Assigned to: Miguel (michaelthoward)
Summary: Can't import some .xyz files
Initial Comment:
Jmol v10 (and CVS) can't import some of the .xyz files
I am using. Attached is a sample .xyz file. Jmol v9
can import and show it without any problem.
The error message I got for CVS HEAD in Jmol console:
--- 8< ---
java.lang.ArrayIndexOutOfBoundsException: 4
at
org.openscience.jmol.viewer.datamodel.Bspt$Leaf.<init>(Bspt.java:439)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.<init>(Bspt.java:362)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.addTuple(Bspt.java:369)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.addTuple(Bspt.java:367)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.addTuple(Bspt.java:367)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.addTuple(Bspt.java:367)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.addTuple(Bspt.java:367)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.addTuple(Bspt.java:373)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.addTuple(Bspt.java:367)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.addTuple(Bspt.java:373)
at
org.openscience.jmol.viewer.datamodel.Bspt$Node.addTuple(Bspt.java:367)
at
org.openscience.jmol.viewer.datamodel.Bspt.addTuple(Bspt.java:94)
at
org.openscience.jmol.viewer.datamodel.Bspf.addTuple(Bspf.java:56)
at
org.openscience.jmol.viewer.datamodel.Frame.initializeBspf(Frame.java:585)
at
org.openscience.jmol.viewer.datamodel.Frame.rebond(Frame.java:692)
at
org.openscience.jmol.viewer.datamodel.Frame.freeze(Frame.java:106)
at
org.openscience.jmol.viewer.datamodel.FrameBuilder.buildFrame(FrameBuilder.java:107)
at
org.openscience.jmol.viewer.managers.ModelManager.setClientFile(ModelManager.java:81)
at
org.openscience.jmol.viewer.JmolViewer.openClientFile(JmolViewer.java:970)
at
org.openscience.jmol.viewer.JmolViewer.getOpenFileError1(JmolViewer.java:954)
at
org.openscience.jmol.viewer.JmolViewer.getOpenFileError(JmolViewer.java:939)
at
org.openscience.jmol.viewer.script.Eval.load(Eval.java:1473)
at
org.openscience.jmol.viewer.script.Eval.instructionDispatchLoop(Eval.java:336)
at
org.openscience.jmol.viewer.script.Eval.run(Eval.java:280)
at java.lang.Thread.run(Thread.java:534)
Model.finalize() called
--- >8 ---
----------------------------------------------------------------------
>Comment By: Miguel (michaelthoward)
Date: 2004-05-21 10:11
Message:
Logged In: YES
user_id=608250
Hmmm ... a good bug
In this particular case, the problem seems to be caused by
the regularity of the file coordinates. You seem to have
uncovered a subtle bug in the Bspt (binary space
partitioning tree) code.
There are (relatively) large numbers of atoms that have the
same coordinates for x, y, and z. That makes sense because
it is a very regular structure.
It seems that the Bspt code is not splitting a leaf properly.
I thought that this same code was used in v9, but I guess
there must be something different.
More later ...
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