[Ifeffit] Ifeffit Digest, Vol 118, Issue 6
Peter Marley
petermar at buffalo.edu
Mon Dec 10 14:15:41 CST 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,
<ifeffit-request at millenia.cars.aps.anl.gov>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" <qijiahui.uk at gmail.com>
> To: <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] Help: Artemis closes without error message when
> open .cif file
> Message-ID: <50c602e5.424cb40a.0dd5.42e3 at 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 <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Help: Artemis closes without error message when
> open .cif file
> Message-ID: <61620056.C2dlAnbQpv at 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
>
> 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
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 10 Dec 2012 16:16:00 -0000
> From: "Daniel Whittaker" <daniel.whittaker at postgrad.manchester.ac.uk>
> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Help: Artemis closes without error message when
> open.cif file
> Message-ID: <6229BE20E02F4353A75ACA302F4B84CD at 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 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
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
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>
> End of Ifeffit Digest, Vol 118, Issue 6
> ***************************************
>
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