Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 7

11 Dec 2012

      Hi Peter,

Thank you very much for your suggestion. The problem for me is the .txt file
cannot be imported by the (D)Artemis (an error message came out)....

Best,
jiahui

--
Dr Jiahui Qi
Research Associate
Department of Material
Imperial College London
South Kensington Campus
London SW7 2AZ
Mobile: +44(0)7948387989
Email: j.qi@imperial.ac.uk
www.imperial.ac.uk

-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of
ifeffit-request@millenia.cars.aps.anl.gov
Sent: 10 December 2012 23:16
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 118, Issue 7

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Today's Topics:

   1. Re: Ifeffit Digest, Vol 118, Issue 6 (Peter Marley)
   2. Re: Ifeffit Digest, Vol 118, Issue 6 (jiahui)

----------------------------------------------------------------------

Message: 1
Date: Mon, 10 Dec 2012 15:15:41 -0500
From: Peter Marley 
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

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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or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Ifeffit digest..."
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]
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--
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@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
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