GBMaker Confusion

[Brandon Daniels]

Hello all,

     I am having some trouble running GBMaker.  I know it is a command line tool, and thus needs an input file specified by hand; but for all my efforts, I cannot open the application.  I tried individually opening sample .gbm files included in the software package (such as Au_Al2O3).  I tried dragging those sample .gbm files over to gbmaker.exe.  I also tried reinstalling the program entirely.  Last, taking the advise of Dr. McLeod, I dragged .gbm files into the command prompt of Windows 7 to view the problem, but I do not know how to rectify the situation.  The command prompt (which I have attached) said that when I attempt to open Au_Al2O3.gbm, Al2O3.cfg cannot be found (though it was downloaded with the rest of the package).  I then tried plainly opening gbmaker.exe, and the prompt indicated that it could not open data input file gb.gbm.  The rest of the program runs excellently, so any help with overcoming this small confusion would be greatly appreciated.

Sincerely,

Brandon Daniels

[Christoph Koch]

Hi Brandon,

 

If you run a command line program you need to supply it an input file. If no input file is supplied, it assumes that your input file is named gb.gbm.

So at the command prompt you need to type, for example:

“gbmaker Au_Al2O3.gbm”

For this you need to make sure that your current working directory is the one that contains also the .cfg files Au.cfg and Al2O3.cfg, or whatever crystal structures your .gbm file calls (they should all be in the same directory, unless you specified absolute paths in the .gbm file).

You do this by calling the “cd” command

(http://www.digitalcitizen.life/command-prompt-how-use-basic-commands).

 

I hope this helps.

 

Best regards,

Christoph.

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[Brandon Daniels]

Professor Koch,

     Thank you for the assistance.  I have one more question though.  Following your directions, I am able to consistently run gbmaker.exe, but I am unaware of the method to see the .gbm files as graphical images, like the ones shown here: https://www.physik.hu-berlin.de/en/sem/software/software_gmbmaker.  Also, I am not sure how the user is suppose to modify .gbm files using gbmaker.exe.  I have attached the command prompt showing gbmaker.exe running for Au_Al2O3.gbm. 

Thank you again,

Brandon Daniels

[Christoph Koch]

Hello Brandon,

 

You can visualize the output of gbmaker using the AtomEye Software, or simply qstem (by loading the configuration into qstem and pressing the ‘3D’ button). This latter option procedure will generate images similar to the ones you have seen on the web page you sent a link to.

 

If you want to modify the .gbm file you should use a text editor, such as Wordpad or Notepad++ (I personally prefer the latter – you can download it for free).

 

However, I get the impression that you are more looking for a graphical user interface (GUI) – driven software. For that I recommend to use the QSTEM Model Builder (qmb) that is also provided with the qstem package. There seems to be also another nice piece of software I was recently made aware of: atomsk (http://atomsk.univ-lille1.fr/) by Pierre Hirel. I recommend that you try that as well.

 

With best regards

Christoph.

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[Brandon Daniels]

Hello Professor Koch,

     Thank you so much for your help.  As I mentioned, your software is excellent, so I am grateful to fully understand it now.  I am working in the lab of Professor Philip Batson at Rutgers University, and he sends his warm greetings.  My advisor back at my own university, Cornell, is Professor David Muller (whom I believe you may also know), and I will be sure to recommend qstem to him if he is not already using it.  Thank you again for your prompt response.

Best,

Brandon Daniels