[Ifeffit] Ifeffit Digest, Vol 118, Issue 7
jiahui
qijiahui.uk at gmail.com
Tue Dec 11 13:09:24 CST 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 at imperial.ac.uk
www.imperial.ac.uk
-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of
ifeffit-request at millenia.cars.aps.anl.gov
Sent: 10 December 2012 23:16
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 118, Issue 7
Send Ifeffit mailing list submissions to
ifeffit at millenia.cars.aps.anl.gov
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When replying, please edit your Subject line so it is more specific than
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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 <petermar at buffalo.edu>
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6
Message-ID:
<CAE1g5jH_G67ubO6gPXJgM7mHBHk_UEV4XKF+Hd6DuLAYPS4_CQ at mail.gmail.com>
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,
<ifeffit-request at millenia.cars.aps.anl.gov>wrote:
> Send Ifeffit mailing list submissions to
> ifeffit at 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 at millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> ifeffit-owner at 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. 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
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 118, Issue 6
> ***************************************
>
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Message: 2
Date: Mon, 10 Dec 2012 23:16:14 -0000
From: "jiahui" <qijiahui.uk at gmail.com>
To: <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6
Message-ID: <50c66d41.a94bb40a.08c3.ffffb88d at mx.google.com>
Content-Type: text/plain; charset="us-ascii"
Hi Bruce,
I am a windows user. The two log file(Artemis and Atoms) and one of the CIF
files I used are attached to this email. Please let me know if you need more
information,
Hi Dan,
I use Mercury to open the CIF file then save as another CIF file as you
suggested. The new CIF file can be read by (D)Artemis with an warning
message basically says there're some problem with this file and some
possible ways to solve the problem(s).
I actually went to download an old version of IFEFFIT: Ifeffit 1.2.11. This
version can read the CIF files. I ran atoms and FIFF on it. Then save the
file. It could be opened by (D)Artemis without problem.
Thank you very much for your help and solutions,
Jiahui
-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of
ifeffit-request at millenia.cars.aps.anl.gov
Sent: 10 December 2012 18:00
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 118, Issue 6
Send Ifeffit mailing list submissions to
ifeffit at 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 at millenia.cars.aps.anl.gov
You can reach the person managing the list at
ifeffit-owner at 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. 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
Ifeffit at millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
End of Ifeffit Digest, Vol 118, Issue 6
***************************************
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