Miguel, what do you make of this? Robert is loading a page with five
applets, each displaying a differerent isosurface.
I believe we are seeing this now because people are starting to use
multiple applets on a page. The bugs aren't new, but the realization of
their effect is only showing up when certain browsers are taking certain
amounts of time to do the class loading. Is this a "static variable"
problem? I'm betting those two out-of-bound errors are from two
different applets loading simultaneously but being in two slightly
different stages of loading when a THIRD applet trashes some supposedly
static geodesic object.
Bob
-------- Original Message --------
Subject: Re: [Fwd: [Jmol-users] JMOL AND CALCULATED ORBITALS !!!!]
Date: Fri, 09 Jun 2006 06:49:37 -0500
From: Prof. Robert John Lancashire <[EMAIL PROTECTED]>
Organization: UWI, Mona, Kingston 7, JAMAICA
To: Bob Hanson <[EMAIL PROTECTED]>
References: <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> <[EMAIL PROTECTED]>
Bob,
again with Netscape 8.1 on my laptop from the local drive....
==========================================================================
Java Plug-in 1.5.0_06
Using JRE version 1.5.0_06 Java HotSpot(TM) Client VM
User home directory = C:\Documents and Settings\10007802
----------------------------------------------------
c: clear console window
f: finalize objects on finalization queue
g: garbage collect
h: display this help message
l: dump classloader list
m: print memory usage
o: trigger logging
p: reload proxy configuration
q: hide console
r: reload policy configuration
s: dump system and deployment properties
t: dump thread list
v: dump thread stack
x: clear classloader cache
0-5: set trace level to <n>
----------------------------------------------------
WrappedAppletLoader.run(org.jmol.applet.Jmol)
WrappedAppletLoader.run(org.jmol.applet.Jmol)
WrappedAppletLoader.run(org.jmol.applet.Jmol)
WrappedAppletLoader.run(org.jmol.applet.Jmol)
preloading javax.vecmath.Point3f+
preloading javax.vecmath.Point3f+
WrappedAppletLoader.run(org.jmol.applet.Jmol)
preloading javax.vecmath.Point3f+
preloading org.jmol.g3d.Graphics3D
preloading org.jmol.g3d.Graphics3D
preloading org.jmol.adapter.smarter.SmarterJmolAdapter
preloading org.jmol.g3d.Graphics3D
preloading org.jmol.adapter.smarter.SmarterJmolAdapter
preloading javax.vecmath.Point3f+
preloading javax.vecmath.Point3f+
preloading org.jmol.g3d.Graphics3D
preloading org.jmol.g3d.Graphics3D
preloading org.jmol.adapter.smarter.SmarterJmolAdapter
preloading org.jmol.adapter.smarter.SmarterJmolAdapter
preloading org.jmol.adapter.smarter.SmarterJmolAdapter
loadImage:jmol75x29x8.gif
urlImage=jar:file:/C:/WWW/Software/jmolproto/JmolAppletProto.jar!/jmol75x29x8.gif
successfully loaded jmol75x29x8.gif
[EMAIL PROTECTED]
preloading org.jmol.popup.JmolPopup
preloading org.jmol.popup.JmolPopup
preloading org.jmol.popup.JmolPopup
preloading org.jmol.popup.JmolPopup
preloading org.jmol.popup.JmolPopup
preloading javax.vecmath.Vector3f+
preloading javax.vecmath.Vector3f+
preloading javax.vecmath.Vector3f+
preloading javax.vecmath.Vector3f+
preloading javax.vecmath.Vector3f+
preloading javax.vecmath.Matrix3f+
preloading javax.vecmath.Matrix3f+
preloading javax.vecmath.Matrix3f+
preloading javax.vecmath.Matrix3f+
preloading javax.vecmath.Matrix3f+
preloading javax.vecmath.Point3i+
preloading javax.vecmath.Point3i+
preloading javax.vecmath.Point3i+
preloading javax.vecmath.Point3i+
preloading javax.vecmath.Point3i+
preloading org.jmol.g3d.Sphere3D
preloading org.jmol.g3d.Sphere3D
preloading org.jmol.g3d.Sphere3D
preloading org.jmol.g3d.Sphere3D
preloading org.jmol.g3d.Sphere3D
AppletRegistry.checkIn(jmolAppletdx2y2)
AppletRegistry.checkIn(jmolAppletdz2)
AppletRegistry.checkIn(jmolAppletdyz)
AppletRegistry.checkIn(jmolAppletdxy)
AppletRegistry.checkIn(jmolAppletdxz)
preloading org.jmol.g3d.Line3D
preloading org.jmol.g3d.Line3D
preloading org.jmol.g3d.Line3D
preloading org.jmol.g3d.Line3D
preloading org.jmol.g3d.Line3D
preloading org.jmol.g3d.Cylinder3D
preloading org.jmol.g3d.Cylinder3D
preloading org.jmol.g3d.Cylinder3D
preloading org.jmol.g3d.Cylinder3D
preloading org.jmol.g3d.Cylinder3D
2 seconds
loadImage:jmol75x29x8.gif
preloading org.jmol.g3d.Colix
preloading org.jmol.g3d.Colix
preloading org.jmol.g3d.Colix
preloading org.jmol.g3d.Shade3D
preloading org.jmol.g3d.Colix
preloading org.jmol.g3d.Shade3D
preloading org.jmol.adapter.smarter.Atom
preloading org.jmol.g3d.Colix
preloading org.jmol.g3d.Shade3D
preloading org.jmol.g3d.Shade3D
preloading org.jmol.adapter.smarter.Atom
preloading org.jmol.adapter.smarter.Atom
preloading org.jmol.adapter.smarter.Bond
preloading org.jmol.adapter.smarter.Atom
preloading org.jmol.adapter.smarter.Bond
preloading org.jmol.g3d.Shade3D
preloading org.jmol.adapter.smarter.Bond
preloading org.jmol.adapter.smarter.Bond
preloading org.jmol.adapter.smarter.Atom
urlImage=jar:file:/C:/WWW/Software/jmolproto/JmolAppletProto.jar!/jmol75x29x8.gif
preloading org.jmol.adapter.smarter.Bond
successfully loaded jmol75x29x8.gif
[EMAIL PROTECTED]
preloading org.jmol.adapter.smarter.AtomSetCollection
preloading org.jmol.adapter.smarter.AtomSetCollection
preloading org.jmol.adapter.smarter.AtomSetCollection
preloading org.jmol.adapter.smarter.AtomSetCollection
preloading org.jmol.adapter.smarter.AtomSetCollection
2 seconds
2 seconds
loadImage:jmol75x29x8.gif
urlImage=jar:file:/C:/WWW/Software/jmolproto/JmolAppletProto.jar!/jmol75x29x8.gif
preloading org.jmol.adapter.smarter.AtomSetCollectionReader
preloading org.jmol.adapter.smarter.AtomSetCollectionReader
successfully loaded jmol75x29x8.gif
preloading org.jmol.adapter.smarter.AtomSetCollectionReader
preloading org.jmol.adapter.smarter.AtomSetCollectionReader
[EMAIL PROTECTED]
preloading org.jmol.adapter.smarter.AtomSetCollectionReader
2 seconds
2 seconds
loadImage:jmol75x29x8.gif
urlImage=jar:file:/C:/WWW/Software/jmolproto/JmolAppletProto.jar!/jmol75x29x8.gif
successfully loaded jmol75x29x8.gif
[EMAIL PROTECTED]
2 seconds
2 seconds
preloading org.jmol.adapter.smarter.Resolver
preloading org.jmol.adapter.smarter.Resolver
preloading org.jmol.adapter.smarter.Resolver
preloading org.jmol.adapter.smarter.Resolver
preloading org.jmol.adapter.smarter.Resolver
loadImage:jmol75x29x8.gif
urlImage=jar:file:/C:/WWW/Software/jmolproto/JmolAppletProto.jar!/jmol75x29x8.gif
successfully loaded jmol75x29x8.gif
[EMAIL PROTECTED]
2 seconds
2 seconds
2 seconds
2 seconds
(C) 2006 Jmol Development
Jmol Version 10.x.11(branch bob200603) 2006-06-08 10:10
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_06
os.name:Windows XP
(C) 2006 Jmol Development
Jmol Version 10.x.11(branch bob200603) 2006-06-08 10:10
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_06
os.name:Windows XP
(C) 2006 Jmol Development
Jmol Version 10.x.11(branch bob200603) 2006-06-08 10:10
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_06
os.name:Windows XP
(C) 2006 Jmol Development
Jmol Version 10.x.11(branch bob200603) 2006-06-08 10:10
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_06
os.name:Windows XP
(C) 2006 Jmol Development
Jmol Version 10.x.11(branch bob200603) 2006-06-08 10:10
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_06
os.name:Windows XP
jvm11orGreater=true
jvm12orGreater=true
jvm14orGreater=true
jvm11orGreater=true
jvm12orGreater=true
jvm14orGreater=true
jvm11orGreater=true
jvm12orGreater=true
jvm14orGreater=true
jvm11orGreater=true
jvm12orGreater=true
jvm14orGreater=true
jvm11orGreater=true
jvm12orGreater=true
jvm14orGreater=true
Could not instantiate wrappedApplet classorg.jmol.applet.Jmol
java.lang.ArrayIndexOutOfBoundsException: 42
Could not instantiate wrappedApplet classorg.jmol.applet.Jmol
at org.jmol.g3d.Geodesic3D.getVertex(Geodesic3D.java:400)
at org.jmol.g3d.Geodesic3D.quadruple(Geodesic3D.java:285)
at org.jmol.g3d.Geodesic3D.initialize(Geodesic3D.java:207)
at org.jmol.g3d.Geodesic3D.<init>(Geodesic3D.java:177)
at org.jmol.g3d.Graphics3D.<init>(Graphics3D.java:104)
at org.jmol.viewer.Viewer.<init>(Viewer.java:121)
at org.jmol.viewer.Viewer.allocateViewer(Viewer.java:143)
at org.jmol.api.JmolViewer.allocateViewer(JmolViewer.java:51)
at org.jmol.applet.Jmol.initWindows(Jmol.java:156)
at org.jmol.applet.Jmol.init(Jmol.java:144)
at
org.jmol.appletwrapper.WrappedAppletLoader.run(WrappedAppletLoader.java:51)
java.lang.ArrayIndexOutOfBoundsException: 252
org.jmol.applet.Jmol load time = 3 seconds
at org.jmol.g3d.Geodesic3D.addNeighboringVertexes(Geodesic3D.java:364)
at org.jmol.g3d.Geodesic3D.quadruple(Geodesic3D.java:305)
at org.jmol.g3d.Geodesic3D.initialize(Geodesic3D.java:207)
at org.jmol.g3d.Geodesic3D.<init>(Geodesic3D.java:177)
at org.jmol.g3d.Graphics3D.<init>(Graphics3D.java:104)
at org.jmol.viewer.Viewer.<init>(Viewer.java:121)
at org.jmol.viewer.Viewer.allocateViewer(Viewer.java:143)
at org.jmol.api.JmolViewer.allocateViewer(JmolViewer.java:51)
at org.jmol.applet.Jmol.initWindows(Jmol.java:156)
at org.jmol.applet.Jmol.init(Jmol.java:144)
at
org.jmol.appletwrapper.WrappedAppletLoader.run(WrappedAppletLoader.java:51)
org.jmol.applet.Jmol load time = 3 seconds
MouseManager11 implemented
MouseManager14 implemented
MouseManager11 implemented
MouseManager14 implemented
MouseManager11 implemented
MouseManager14 implemented
3 seconds
3 seconds
3 seconds
appletDocumentBase=file:/C:/WWW/Software/jmolproto/ofieldJ.html
appletDocumentBase=file:/C:/WWW/Software/jmolproto/ofieldJ.html
appletDocumentBase=file:/C:/WWW/Software/jmolproto/ofieldJ.html
4 seconds
4 seconds
4 seconds
5 seconds
5 seconds
5 seconds
setting color scheme to:jmol
setting color scheme to:jmol
setting color scheme to:jmol
6 seconds
6 seconds
6 seconds
English: no need for gettext wrapper
7 seconds
7 seconds
7 seconds
7 seconds
7 seconds
7 seconds
8 seconds
8 seconds
8 seconds
9 seconds
9 seconds
9 seconds
10 seconds
10 seconds
10 seconds
org.jmol.applet.Jmol load time = 10 seconds
org.jmol.applet.Jmol load time = 10 seconds
org.jmol.applet.Jmol load time = 10 seconds
FileManager.openFile(octe.pdb,0,0,0,0)
FileManager.openFile(octa.pdb,0,0,0,0)
FileManager.openFile(octd.pdb,0,0,0,0)
SmarterJmolAdapter:The Resolver thinks:Pdb
SmarterJmolAdapter:The Resolver thinks:Pdb
SmarterJmolAdapter:The Resolver thinks:Pdb
AtomSetCollection.freeze; atomCount = 21
openFile(octe.pdb,0,0,0,0)3438 ms
AtomSetCollection.freeze; atomCount = 21
openFile(octd.pdb,0,0,0,0)3438 ms
AtomSetCollection.freeze; atomCount = 21
openFile(octa.pdb,0,0,0,0)3438 ms
frame: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
frame: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
frame: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
sequential bspt order
sequential bspt order
sequential bspt order
makeConnections(0.1,8.5,64,3,{7, 8, 9, 10, 11, 12, 13, 14},{7, 8, 9, 10, 11,
12, 13, 14})
makeConnections(0.1,8.5,64,3,{7, 8, 9, 10, 11, 12, 13, 14},{7, 8, 9, 10, 11,
12, 13, 14})
makeConnections(0.1,4.5,64,3,{7, 8, 9, 10, 11, 12, 13, 14},{7, 8, 9, 10, 11,
12, 13, 14})
==================================================================================================
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