Author Topic: [SOLVED] I can't visualize vibrational frequencies  (Read 2130 times)

Glxblt76

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[SOLVED] I can't visualize vibrational frequencies
« on: March 01, 2016, 11:05:05 am »
EDIT: Problem was erroneous use of sed (a shell scripting function) that doubled some lines in my vibspectrum file! Problem was solved by manually removing the lines that were doubled.

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Original post

Dear TmoleX developers and users,

tl;dr I can't visualize vibrational frequencies in TmoleX.

as described in detail in another topic of this forum >>here <<, for some reason I had to run numerical frequency calculations with Numforce activating RI from non-RI optimized structures. I ran these calculations successfully in a Linux multi-core machine and then imported the results in my windows 7 - 64 bits machine to visualize the results from TmoleX 4.0.1.

To do so, I opened the control file. Then I got this menu:

Then when I clicked on the "Vibrations" button I got this:

As can be seen, no vibrational frequencies are listed. I checked, the file vib_normal_modes exists and is correctly filled.
I tried to unix2dos all files and do the same operation and got the exact same result. This occurs for all molecules, not only a few.

So, if anyone has some track to fix/troubleshoot/solve this problem, this would greatly help me! :D

Thanks in advance!
« Last Edit: March 18, 2016, 02:16:50 pm by Glxblt76 »

uwe

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Re: I can't visualize vibrational frequencies
« Reply #1 on: March 02, 2016, 04:57:03 pm »
Hello,

TmoleX needs the files vib_normal_modes and vibspectrum, and in the control file there should be two lines:

$vibrational spectrum    file=vibspectrum
$vibrational normal modes    file=vib_normal_modes

It seems that TmoleX finds the file vibspectrum, but it seems to be empty (just the header is printed).

Could you post your vib* files or send them to the Turbomole Support.

Regards,

Uwe

Glxblt76

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Re: I can't visualize vibrational frequencies
« Reply #2 on: March 03, 2016, 09:42:03 am »
Dear Uwe,

Thanks for your answer.

I have both files and they are not empty. I attached them in the present forum post for the examplified molecule in the screen captures above. I added a .txt extension so that the forum enables their attachement but of course they do not have extensions in the original folder.

Moreover, the control file does contain the mentioned lines:
Quote
$vibrational spectrum    file=vibspectrum
$vibrational normal modes    file=vib_normal_modes
« Last Edit: March 03, 2016, 12:11:39 pm by Glxblt76 »

Glxblt76

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Re: I can't visualize vibrational frequencies
« Reply #3 on: March 10, 2016, 12:09:33 pm »
Dear uwe,

Did you succeed in reproducing the bug? Do you need other files?

It is still not possible for me to analyze my files. Is there any way to solve the problem?

Any hint would be appreciated!   :D

uwe

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Re: I can't visualize vibrational frequencies
« Reply #4 on: March 11, 2016, 09:42:46 am »
Hello,

I can not reproduce this error. Your files look correct, so TmoleX should work. I ran NumForce on the command line and opened the control file afterwards in TmoleX and was able to visualize the modes.

In your home directory, in ~/COSMOlogicAppData/TmoleX15/  you will find log files of the TmoleX sessions which contain the Java errors. I'd close TmoleX, open it and read in the control file of that job. Visualize the modes and close TmoleX again. Then, check the <date_time>_systemErrorTmoleX.log file if there are any error messages.

I'd recommend to tar the files and send them to the Turbomole support.

Regards,

Uwe

Glxblt76

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Re: I can't visualize vibrational frequencies
« Reply #5 on: March 17, 2016, 10:48:46 am »
OK, I just identified the problem.

Two lines in vibspectrum file were dedoubled, probably due to an erroneous use of sed during scripting.  ::)

Best regards and thanks for your examination of my files!
It seems it's my errors.