Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6

10 Dec 2012

      Hi Jiahui,

I have also experienced this problem when saving a cif file from VESTA.
 What I found to work best was to modify the cif file into a different
format.  For example:

title = VO2(M)
space = P 21/c
a =  5.56300    b =  4.89600     c =  5.66300
alpha = 90 beta =  120.47000 gamma = 90
atoms
  V   0.22780     -0.01020      0.01110   V(1)
  O   0.11190      0.21860      0.23340   O(1)
  O   0.39000      0.70240      0.29860   O(2)

And then save it as a .txt file, which can then be imported.

I hope this helps

Peter

Peter Marley
Ph. D. Candidate
Department of Chemistry
405 Natural Sciences Complex
University at Buffalo
The State University of New York
Buffalo, NY 14260-3000

On Mon, Dec 10, 2012 at 1:00 PM,
wrote:
...
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Today's Topics:
1. Help: Artemis closes without error message when open .cif
      file (jiahui)
   2. Re: Help: Artemis closes without error message when open  .cif
      file (Bruce Ravel)
   3. Re: Help: Artemis closes without error message when       open.cif
      file (Daniel Whittaker)
----------------------------------------------------------------------
Message: 1
Date: Mon, 10 Dec 2012 15:42:27 -0000
From: "jiahui" 
To: 
Subject: [Ifeffit] Help: Artemis closes without error message when
        open .cif       file
Message-ID: <50c602e5.424cb40a.0dd5.42e3@mx.google.com>
Content-Type: text/plain;       charset="us-ascii"
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]
------------------------------
Message: 2
Date: Mon, 10 Dec 2012 10:48:21 -0500
From: Bruce Ravel 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Help: Artemis closes without error message when
        open    .cif file
Message-ID: <61620056.C2dlAnbQpv@lachesis.bnl.gov>
Content-Type: text/plain; charset="us-ascii"
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
...
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
On Monday, December 10, 2012 03:42:27 PM jiahui wrote:
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@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--
Bruce Ravel  ------------------------------------ bravel@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
------------------------------
Message: 3
Date: Mon, 10 Dec 2012 16:16:00 -0000
From: "Daniel Whittaker" 
To: "XAFS Analysis using Ifeffit" 
Subject: Re: [Ifeffit] Help: Artemis closes without error message when
        open.cif file
Message-ID: <6229BE20E02F4353A75ACA302F4B84CD@mbdx5dw2PC>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
        reply-type=original
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@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--
Bruce Ravel  ------------------------------------ bravel@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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Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
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End of Ifeffit Digest, Vol 118, Issue 6
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