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: Closed
Resolution: Fixed
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: 2004-05-22 11:30
Message:
Logged In: YES
user_id=608250
I think the circumstances for this bug to occur were quite
rare. One needed to have the same coordinate value repeated
in more than one dimensions. So, for example, giving all
atoms a z value of 0.0 would not cause the problem.
nanotube uncovered this bug because the structure is so
regular.
----------------------------------------------------------------------
Comment By: Ming Hua (minghua)
Date: 2004-05-21 22:30
Message:
Logged In: YES
user_id=821593
> Q: May I add this .xyz file to our CVS repository in our
> samples/xyz directory?
I noticed that my sample file has a quite cryptic title. If
you are going to include it in CVS, would you please change
the title (the second line of the file) to ``(10,0) CNT, 3
unit cells, hydrogen terminated'' please?
----------------------------------------------------------------------
Comment By: Ming Hua (minghua)
Date: 2004-05-21 22:17
Message:
Logged In: YES
user_id=821593
Thanks for the fast bugfix. I've confirmed that CVS works
for the .xyz file I uploaded.
> Please confirm that you do not have problems with other .xyz
> files.
Hmm, strangely enough, I found out that is the only file
triggering the problem. I've similar structures, but they
are all displayed fine. I was thinking they are not working
because once such an error occured, Jmol would refuse to
import any other .xyz files. But actually if I restart
Jmol, they would work fine.
> Q: May I add this .xyz file to our CVS repository in our
> samples/xyz directory?
Feel free to do so.
----------------------------------------------------------------------
Comment By: Miguel (michaelthoward)
Date: 2004-05-21 11:59
Message:
Logged In: YES
user_id=608250
OK, this problem is fixed.
Please confirm that you do not have problems with other .xyz
files.
Q: May I add this .xyz file to our CVS repository in our
samples/xyz directory?
Thanks,
Miguel
----------------------------------------------------------------------
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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