[Ifeffit] Help: Artemis closes without error message when open.cif file

[Daniel Whittaker]

Hi Jiahui,

I have experienced similar issues with cif files - there are so many 
slightly different formats.

I found a solution was to open the file in Mercury: 
http://www.ccdc.cam.ac.uk/free_services/mercury/downloads/
Save it as a .cif from within the program itself and then read it into 
(D)Artemis. If that works then brilliant :) - If not then there are a few 
other issues I have found working on my organic systems:
1) If there is any disorder I find it best to remove it.
2) When running atoms I have found it can produce an error. In this case, if 
you save the file it produces (*.inp) then open this in a text editor and 
remove any duplicate atoms (normally near the bottom of the file) save it 
again and then reopen in Atoms then it should work fine.

I hope this helps troubleshoot your issues for now?

Regards,
Dan

Daniel Whittaker, MChem
Nuclear FiRST DTC PhD Student
Chemistry Building
The University of Manchester
Brunswick Street
Manchester
M13 9PL


-----Original Message----- 
From: Bruce Ravel
Sent: Monday, December 10, 2012 3:48 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Help: Artemis closes without error message when 
open.cif file


Jiahui,

It would be helpful to me to see an example of a CIF file that
triggers this problem.  If you are running on Windows, then I would
also like to see the contents of the %APPDATA%\demeter\dartemis.log
file.  See

  http://bruceravel.github.com/demeter/pods/bugs.pod.html

If you are a linux user, I would need to see the messages sent to the
terminal, which requires running the program from the terminal rather
from some launcher widget.

As I have said many times before on this mailing list, CIF support is
rather weak at this time.  I am using a CIF parsing tool written by
someone else and it has its problems.  That said, as people report
these problems, I am able to build more smarts into Demeter so that it
at least deals gracefully with a CIF file it doesn't understand.

Cheers,
B

On Monday, December 10, 2012 03:42:27 PM jiahui wrote:
> Dear list,
>
> I am having this problem when I try to open the crystal structure file in
> .cif format. I've tried many times already--each time when I try to open 
> the
> crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will
> close by themselves without any error message.
> What can I do to solve this problem and carry on with my work? I am using
> Demeter 0.9.13 version.
>
> Thank you very much for your help,
>
> [jiahui]
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


-- 

Bruce Ravel  ------------------------------------ bravel at bnl.gov

National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973

Homepage:    http://xafs.org/BruceRavel
Software:    https://github.com/bruceravel
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