AW: QSTEM: Subscription to the mail list and matlab GUI issue

[Christoph Koch]

Dear Samantha Rudinsky,

 

Unfortunately, I do not have a Linux-compiled vesion of this file, but you can simply change the code in the file that calls readCFG_mex to avoid using the mex file.

 

For this you simply need to change the line 22 in file readCFG_qstem from “if (1)” to “if(0)”.

 

With best regards,

Christoph.

 

Von: samantha...@gmail.com [mailto:samantha...@gmail.com] Im Auftrag von Samantha Rudinsky
Gesendet: Mittwoch, 12. Juli 2017 03:16
An: christo...@physik.hu-berlin.de
Betreff: QSTEM: Subscription to the mail list and matlab GUI issue

 

Dear Dr. Koch,

 

I am a PhD student in the department of Materials Engineering at McGill University. I work on time-dependent diffraction modelling and am currently learning QSTEM to compare to my results. I would like to be part of the mailing list as I am having issues running the matlab GUI in Linux (Ubuntu 16.04).

 

When I try to load a cfg file, I get the error that readCFG_mex does not exist. I believe I've narrowed down the problem to the fact that the package contains a windows compiled mex file. Would it be possible to obtain the file compiled in linux? (readCFG_mex.mexa64) or gain access to post on the mailing list? Any help would be much appreciated.

 

Thank you,

Samantha Rudinsky

PhD Candidate

Department of Mining and Materials Engineering

McGill University

[samantha...@gmail.com]

Thank you very much for the answer. I have run in to another problem now however. When I attempt to run TEM simulations, for example tem_gb_Sigma17_4.qsc from the Examples, from the command line, I get the following:

pix range -1.77675 to 2.32575 real,

          -1.93992 to 2.21902 imag

t=62.48A, int.=0.766755 time: 1.03318sec (avgCount=0)

DEBUG: CImageIO::WriteData: filename is gb_Sigma17/wave.img 

Error: No such file or directory

ReadHeader: Could not open file gb_Sigma17/diff.img for reading header.

terminate called after throwing an instance of 'std::runtime_error'

  what():  Could not open file gb_Sigma17/diff.img for reading header.

Aborted (core dumped)

However, the file wave.img exists and is there. On a similar note, for any simulation where I have saved a .qsc file using the matlab GUI, although the program still runs, I get the following:

[...] DEBUG: stemlib::make3Dslices : muls.cfgFile = /home/sam/QSTEM/Examples/Al_t 

Cannot open file Al//home/sam/QSTEM/Examples/Al_t_0.cfg

Will use 81 sampling points per slice, total nz=486 (40) [...]

In this case, the file Al_t_0.cfg does not get created. Thanks again for your help.

Cheers,

Samantha

[Christoph Koch]

Hi Samantha,

 

I assume that you have compiled the Linux version of stem3.cpp. Can you please check if the folder gb_Sigma17 exists? And if not, try creating it and run stem3 again.

 

Best regards

Christoph.

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[Samantha Rudinsky]

Yes, I am running Ubuntu 16.04. The folder is there, it was created when I ran stem3, and its contents are the following: gb_Sigma17_Proj.img,  wave_0.img,  wave_2.img,  wave.img, gb_Sigma17_t.cfg, wave_1.img and wave_3.img.

Cheers,

Samantha

Samantha Rudinsky

PhD Candidate

Department of Mining and Materials Engineering

McGill University

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[samantha...@gmail.com]

Hi,

I was wondering if you had found any solution to this issue? The folder does get created and the file is there but still the job gets aborted.

Thanks,

Samantha

On Wednesday, 12 July 2017 11:57:18 UTC-4, Christoph Koch wrote:

[Christoph Koch]

Hi Samantha,

 

Did you make the change I suggested? You may also send the corrected file, and I can check. What is the exact error message?

 

Best regards,

Christoph.

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[Samantha Rudinsky]

Hi Christopher,

The folder had been created with the program and had all the required wave function files in it. However, I found the solution to the problem. It seems the source code linked to the QSTEM website is an older version. Once I installed the code from https://github.com/robbmcleod/QSTEM, the bug no longer appeared. I believe I was having the similar problem as that in a previous message where doTEM() was not functioning correctly. 

Thank you very much for the help,

Samantha

Samantha Rudinsky

PhD Candidate

Department of Mining and Materials Engineering

McGill University

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