- Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6
by jiahui 12 Dec '12

12 Dec '12

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(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 10 December 2012 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 6 Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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(a)gmail.com> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Help: Artemis closes without error message when open .cif file Message-ID: <50c602e5.424cb40a.0dd5.42e3(a)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(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Help: Artemis closes without error message when open .cif file Message-ID: <61620056.C2dlAnbQpv(a)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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel ------------------------------------ bravel(a)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(a)postgrad.manchester.ac.uk> To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> 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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel ------------------------------------ bravel(a)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(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 118, Issue 6 ***************************************

2 2

How to do with diffraction peak
by Zhaomo Tian 11 Dec '12

11 Dec '12

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 7
by jiahui 11 Dec '12

11 Dec '12

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(a)imperial.ac.uk www.imperial.ac.uk -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 10 December 2012 23:16 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 7 Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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 <petermar(a)buffalo.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6 Message-ID: <CAE1g5jH_G67ubO6gPXJgM7mHBHk_UEV4XKF+Hd6DuLAYPS4_CQ(a)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(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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(a)gmail.com> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <50c602e5.424cb40a.0dd5.42e3(a)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(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <61620056.C2dlAnbQpv(a)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(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > > Bruce Ravel ------------------------------------ bravel(a)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(a)postgrad.manchester.ac.uk> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > 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(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > > Bruce Ravel ------------------------------------ bravel(a)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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)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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Re: [Ifeffit] Ifeffit Digest, Vol 118, Issue 6
by Peter Marley 10 Dec '12

10 Dec '12

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(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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(a)gmail.com> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <50c602e5.424cb40a.0dd5.42e3(a)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(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help: Artemis closes without error message when > open .cif file > Message-ID: <61620056.C2dlAnbQpv(a)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(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > > Bruce Ravel ------------------------------------ bravel(a)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(a)postgrad.manchester.ac.uk> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > 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(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > > Bruce Ravel ------------------------------------ bravel(a)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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)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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Help: Artemis closes without error message when open .cif file
by jiahui 10 Dec '12

10 Dec '12

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]

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dathena cannot import data
by Huynh Khuong 05 Dec '12

05 Dec '12

Dear Everyone, I am a complete beginner to this field and to this software, so please forgive me if I ask something stupid. I am using Ubuntu 12.10 64 bit. Demeter was built from source following the guidance here: http://bruceravel.github.com/demeter/pods/installation.pod.html Ifeffit was also built from source before the installation of Demeter. I tried to run dathena from a terminal and import a data file download from here: http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/examples/data.html <http://cars9.uchicago.edu/%7Eravel/software/doc/Athena/html/examples/data.h…> Dathena said that the data file is not readable (see the attached screenshot). No output text appeared on the terminal. If I use the old version of Athena installed from the repository of Ubuntu, the data file can be read easily. The data file is also attach. Could you please explain me about this issue ? Thank you very much in advance. Best, Khuong Huynh

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model for iron oleate
by Monson, Todd 05 Dec '12

05 Dec '12

Does anyone know of an atoms model of iron oleate has been created? Todd Monson Sandia National Labs Nanoscale Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

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Demeter plotting problem in 64-bit Windows 7
by Leon Clarke 05 Dec '12

05 Dec '12

I've just installed the latest version of Demeter on my laptop running 64-bit Windows 7. While I can get the programs to start and run, e.g. Athena, no plots are generated. I'm actually sat in the Diamond XAS workshop and Fred M is stumped by this issue. Are there any known conflicts with the latest version of Demeter, specifically plotting data, running on 64-bit Windows 7 and any solutions? Many thanks, Leon ----- Dr Leon J. Clarke Lecturer in Environmental Analytical Chemistry Division of Chemistry and Environmental Sciences School of Science and the Environment Faculty of Science and Engineering Manchester Metropolitan University John Dalton East Oxford Road Manchester M1 5GD E-mail: l.clarke(a)mmu.ac.uk<mailto:l.clarke@mmu.ac.uk> WWW: http://www.sste.mmu.ac.uk/ Tel: +44 (0)161 247 1412 "Before acting on this email or opening any attachments you should read the Manchester Metropolitan University email disclaimer available on its website http://www.mmu.ac.uk/emaildisclaimer "

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Re: [Ifeffit] S02 and k_min
by Morrill, Michael R 03 Dec '12

03 Dec '12

Thank you for your replies, Anatoly and Matt. As suggested, I've attached a zipped folder with 2 fits that differ only in kmin. You'll notice that the fit improves as kmin is increased. I've also attached the raw data in an Athena file in the event that anyone would like to look at that. Thanks again. ----- Original Message ----- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Monday, December 3, 2012 1:00:01 PM Subject: Ifeffit Digest, Vol 118, Issue 2 Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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: S02 and k_min (Anatoly I Frenkel) 2. Re: S02 and k_min (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Sun, 2 Dec 2012 18:13:14 +0000 From: Anatoly I Frenkel <afrenke2(a)yu.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] S02 and k_min Message-ID: <545F89325F51764C902D37B42C9F4D5313625DAE(a)YUWEXCPM12.yuad.uds.yu.edu> Content-Type: text/plain; charset="us-ascii" Michael, If you use the same kmin for the standard and the unknown you will minimize the ambiguity. Anatoly ----- Reply message ----- From: "Michael Morrill" <mike.morrill(a)gatech.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] S02 and k_min Date: Sun, Dec 2, 2012 1:02 PM Hello everyone, I am currently performing a simple curve fit on bulk MoS2 using an atoms file for crystalline MoS2. I've found that increasing k_min on my fit (e.g. from 2 to 4) improves the quality of the fit (R-factor from 0.028 to 0.009), but also increases S02. If I use a large enough k_min (but not so large I run out of data), S02 gets as high as 1.2 +/- 0.05. This trend is observable for single and multiple k-weight fittings. While I understand that S02>1.0 does not necessarily invalidate the fit, I am not sure how to justify which parameter values are the best seeing that "0.8<S02<1.0" is often one of the justifications that everything "is reasonable." Ultimately, I want to assume the S02 is chemically transferrable and use it for curve fits on metal oxide supported MoS2. Any direction on the mater would be greatly appreciated. Thank you, Mike Morrill GaTech CHBE _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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error function in Athena's peak analysis module
by Linda Lim 03 Dec '12

03 Dec '12

Hi every one I am trying to do peak fitting on Athena. Whenever I choose the error function and click "fit" the software crashes, but it works fine when I choose arctangent. Just wondering if anyone encounter the same issue too, and whether I'm missing something during the fitting process. Thanks! Regards Linda

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