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 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." 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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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)

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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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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

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