TmoleX2024 - Generate MOs - error

[basiuk]

Dear all,

I started configuring new calculations, and from the beginning found a problem when generating MOs: an error appears saying "Comparison method violates its general contract!"

Nothing like that happens with other projects.

Please could you help?

Thank you very much in advance.
With best wishes,

V. Basiuk
 

[uwe]

Hello,

do you have more details about the error message? If you use the Extras menu and select Preferences, there is an option named "Switch off Java exception warning" which is selected by default.
If you deactivate it, TmoleX will show a small circle as icon in the menu line (above the System memory status). It is usually green, but when a Java exception happens, it turns red.
Then you can click on that red circle to see the full error message.

Best Regards,
Uwe

[basiuk]

Dear Uwe,

Thank you very for your prompt response. I switched off the Java warning, it keeps generating the error.

The last block in the logfile does not have the today's date (20241017), and it looks as follows:

20241016 09:31:47 Exception in thread "AWT-EventQueue-0"
java.lang.ArrayIndexOutOfBoundsException: Index -6 out of bounds for length 6
   at de.cosmologic.tmolex.menus.results.diffJobs.JobResultsTableModel.getValueAt(JobResultsTableModel.java:234)
   at java.desktop/javax.swing.JTable.getValueAt(JTable.java:2763)
   at java.desktop/javax.swing.JTable.prepareRenderer(JTable.java:5795)
   at java.desktop/javax.swing.plaf.synth.SynthTableUI.paintCell(SynthTableUI.java:688)
   at java.desktop/javax.swing.plaf.synth.SynthTableUI.paintCells(SynthTableUI.java:585)
   at java.desktop/javax.swing.plaf.synth.SynthTableUI.paint(SynthTableUI.java:369)
   at java.desktop/javax.swing.plaf.synth.SynthTableUI.update(SynthTableUI.java:282)
   at java.desktop/javax.swing.JComponent.paintComponent(JComponent.java:842)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1119)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JViewport.paint(JViewport.java:736)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JSplitPane.paintChildren(JSplitPane.java:1030)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JLayeredPane.paint(JLayeredPane.java:586)
   at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:952)
   at java.desktop/javax.swing.JComponent.paint(JComponent.java:1128)
   at java.desktop/javax.swing.JComponent.paintToOffscreen(JComponent.java:5311)
   at java.desktop/javax.swing.RepaintManager$PaintManager.paintDoubleBufferedImpl(RepaintManager.java:1657)
   at java.desktop/javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1632)
   at java.desktop/javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1570)
   at java.desktop/javax.swing.RepaintManager.paint(RepaintManager.java:1337)
   at java.desktop/javax.swing.JComponent._paintImmediately(JComponent.java:5259)
   at java.desktop/javax.swing.JComponent.paintImmediately(JComponent.java:5069)
   at java.desktop/javax.swing.RepaintManager$4.run(RepaintManager.java:879)
   at java.desktop/javax.swing.RepaintManager$4.run(RepaintManager.java:862)
   at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
   at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
   at java.desktop/javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:862)
   at java.desktop/javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:835)
   at java.desktop/javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:784)
   at java.desktop/javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1898)
   at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:318)
   at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:773)
   at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
   at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
   at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
   at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
   at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742)
   at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
   at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
   at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
   at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
   at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
   at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Honestly, I understand nothing....

With best wishes,
Vladimir


 

[uwe]

Hi,

there is something wrong with the project itself. I think at some point in time you used the 'Combine Results' feature and the table that was generated tried to access jobs which did not exist (any more?).

I'd recommend to close all projects. They are on disk and can be opened later on, but one of the projects that are open has corrupt data, so the first step would be to close them. Then open a new project and check if TmoleX works again as expected. If it does, you know the root cause. Then, read in the other projects one by one until you hit the one that causes the errors.

If a new project (without any other ones opened) still shows this error, then we need to look somewhere else for the cause...

Best, Uwe

[basiuk]

Dear Uwe,

What I am doing is a simple task: SP and MO calculations of single lanthanide atoms.

I did that for La, Ce, Pr, Nd and Tb...
Then stuck with the above problem with Lu... Abandoned...
Then continued without any problem with Pm-Gd and Yb.

Do you see any logic in that?

[uwe]

Hi,

well, obviously this seems to be a bit weird. The error is a TmoleX one, but it might be caused by an unexpected Turbomole output underneath. Did the single-point energy for Lu work without issues? With or without symmetry? And did you use an all-electron basis set like x2c-TZVPPall ?

As there seems to be no obvious reason for Lu to fail if the other lanthanides worked, it might be a pure coincidence and the cause is more of a technical issue.

Just guessing: If you visualize many many orbitals, TmoleX might run into memory problems. The reason is that by default TmoleX is only allowed to use a small portion of the memory that is available.

You can change that in the Menu Extras -> Preferences -> Processing. In there you can set the amount of memory TmoleX is allowed to use in the field 'Max. memory for TmoleX and 3DViewer', the unit is MB.
The number left to it shows how much total physical memory (RAM) TmoleX found, so you can set something like 75% of that value to avoid that TmoleX fills your memory completely which would make the usage very slow...

Best Regards, Uwe

[basiuk]

Dear Uwe,

It seems I failed to explained well.

I am just starting the project, define the "Atomic attributes" (the element is Lu and the basis set is def2-SPV), go to "Molecular attributes", press the button "Generate MOs" - and get the error message!

NO JOB WHATSOEVER!!! NO CALCULATIONS WHATSOEVER!!! I cannot get to that point!!!

I would think, checking that by yourself would take less time than writing a message... If you wish, of course...

With best wishes,
Vladimir

[uwe]

Hi,

ah, sorry, I misunderstood! Actually if you try an all-electron basis set it will work (at least it does for me, that's also the reason why I thought it did not occur when clicking the big red "Generate MOs" button). 

And yes, now I can reproduce the error. The error message is not printed to the log file, but to the error.log of TmoleX itself. 

It is a Java bug and needs to be fixed by BIOVIA.

Best, Uwe

[basiuk]

Thank you very much Uwe,

So, what can I do? How to contact BIOVIA?

Actually, I purchased the Turbomole license directly from TURBOMOLE GmbH, not from BIOVIA...

With best wishes,
Vladimir

[uwe]

Hi,

I'll put in a ticket for you.

Best, Uwe

[basiuk]

Thank you very much Uwe!