- 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 12 Dec '12

12 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 04 Dec '12

04 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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S02 and k_min
by Michael Morrill 02 Dec '12

02 Dec '12

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

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Help to run Demeter on Windows XP (So. Muru)
by Andrei Shiryaev 30 Nov '12

30 Nov '12

Dear All, I have a similar problem running Demeter on Windows 7 64 bit. It simply makes nothing. I remember that several years ago there was a problem to run IFEFFIT on XP windows machines which were operating under non-unicode settings (in those cases it was Brazilian (i.e. Portugese) and Russian versions). Bruce had solved the problem using another compilation of Perl, if I am correct. Is is possible that the same "non-unicode" problem persists in Demeter? All the best, A.Shiryaev

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Help to run Demeter on Windows XP
by So. Muru 28 Nov '12

28 Nov '12

Dear all, greetings from Murugesan, recently I downloaded the latest version of Demeter for windows and installed it on my windows xp (32bit) environment. I try to run the programs by shortcuts in the desktop, but the programs didn't run. what was the problem, kindly give your suggestions to run the Demeter package successfully on windows xp environment. with thanks and regards S Murugesan -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr S Murugesan Kalpakkam, Tamil Nadu India Email : muruges(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [Ifeffit] FOLP
by Joshua Kas 27 Nov '12

27 Nov '12

Hi Enyuan, It is very strange that FOLP 1.3 is causing the code to take longer. There really should be almost no difference in timing between different values of FOLP. This has to be a bug. Would you mind sending your input file? As for the CRITERIA card, this effects the filtering of the path expansion. The path expansion should only be used for EXAFS calculations, which is why the CRITERIA card is greyed out for XANES calculations (which use full multiple scattering). If you really want to run XANES with path expansion, you can still do that using the text based input and running the code from the command line. If you don't know how to do this, I can explain. Just let me know what operating system you are using. Cheers, Josh > > Hi Joshua, > > Thank you for your comment. Like you said, I tried FOLP with value from 1 > to 1.3 and it didn't change the calculated spectrum much. It's very > time-consuming when FOLP reached 1.3, taking more than 3 hours to finish > the calculation on my laptop. On using 0.8 for hydrogen, actually I'm going > to calculated a sample with lots of Li in it. Do you suggest using a > similarly small number of FOLP for Li, in an analogy to H? The other thing > I want to ask is the CRITERIA card in Feff9. It seemed that once I asked > the program to calculate XANES, the CRITERIA card in the software cannot be > checked. It can only be checked if I selected EXAFS calculation mode. Is > there any way to solve this? thanks again for all your answers. > > Enyuan > > > On Mon, Nov 26, 2012 at 5:33 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. Re: FOLP card (Joshua Kas) > > 2. Question on Glitch in FEFF for Ru EXAFS measurements > > (Dooshaye Moonshiram) > > 3. Re: Question on Glitch in FEFF for Ru EXAFS measurements > > (Bruce Ravel) > > 4. Re: Question on Glitch in FEFF for Ru EXAFS measurements > > (Bobrik, Michael) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 26 Nov 2012 10:56:19 -0800 > > From: Joshua Kas <joshua.j.kas(a)gmail.com> > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] FOLP card > > Message-ID: > > < > > CAHuhYRkW5R6iSLjSc03aNnfVRmX+YWvUiNB4HDF7CDEJLNNSjw(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi Enyuan, > > I don't really know a rule of thumb for ionic bond v.s. covalent bond, > but > > by default, the FEFF code will automatically choose reasonable muffin > tins > > in most cases, and most of the time it overlaps them by ~15%, i.e. FOLP > > 1.15. In many cases, the overlap doesn't change the structure in the > XANES > > a lot until you get far from FOLP 1.0. However, there are some special > > cases. For example, we have found that using FOLP 0.8 for hydrogen atoms > > seem's to work reasonably well in the XANES. This is because of the short > > bond lengths of H. In addition, there are cases where one atom is fairly > > isolated from the others, i.e., cage like structures, where FEFF can't > > overlap the potentials, and setting FOLP to something smaller than 1.0 is > > essential to make the code run. I would start by letting the code choose > > the muffin tins automatically, then change them and see how the results > > change. If the changes in the XANES are small, you probably don't have to > > worry about FOLP. Otherwise, this is probably a limitation of the > spherical > > muffin tin potential. The best thing to do in that case, is to compare > the > > DOS (LDOS) with a calculation from a full potential electronic structure > > code, i.e., WIEN2K, ABINIT, QUANTUM ESPRESSO, etc. > > This can give you confidence in the FEFF calculation, or lead you to the > > best values for FOLP. You could also use the FOLP values to get the best > > comparison to experiment, but in some cases you may be fitting many-body > > effects, which can lead you to the wrong conclusions about your system. > > Cheers, > > Josh Kas > > > > On Mon, Nov 26, 2012 at 7:53 AM, > > <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > > > > > Re: > >

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Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 24
by Enyuan Hu 27 Nov '12

27 Nov '12

Hi Joshua, Thank you for your comment. Like you said, I tried FOLP with value from 1 to 1.3 and it didn't change the calculated spectrum much. It's very time-consuming when FOLP reached 1.3, taking more than 3 hours to finish the calculation on my laptop. On using 0.8 for hydrogen, actually I'm going to calculated a sample with lots of Li in it. Do you suggest using a similarly small number of FOLP for Li, in an analogy to H? The other thing I want to ask is the CRITERIA card in Feff9. It seemed that once I asked the program to calculate XANES, the CRITERIA card in the software cannot be checked. It can only be checked if I selected EXAFS calculation mode. Is there any way to solve this? thanks again for all your answers. Enyuan On Mon, Nov 26, 2012 at 5:33 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. Re: FOLP card (Joshua Kas) > 2. Question on Glitch in FEFF for Ru EXAFS measurements > (Dooshaye Moonshiram) > 3. Re: Question on Glitch in FEFF for Ru EXAFS measurements > (Bruce Ravel) > 4. Re: Question on Glitch in FEFF for Ru EXAFS measurements > (Bobrik, Michael) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Nov 2012 10:56:19 -0800 > From: Joshua Kas <joshua.j.kas(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] FOLP card > Message-ID: > < > CAHuhYRkW5R6iSLjSc03aNnfVRmX+YWvUiNB4HDF7CDEJLNNSjw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Enyuan, > I don't really know a rule of thumb for ionic bond v.s. covalent bond, but > by default, the FEFF code will automatically choose reasonable muffin tins > in most cases, and most of the time it overlaps them by ~15%, i.e. FOLP > 1.15. In many cases, the overlap doesn't change the structure in the XANES > a lot until you get far from FOLP 1.0. However, there are some special > cases. For example, we have found that using FOLP 0.8 for hydrogen atoms > seem's to work reasonably well in the XANES. This is because of the short > bond lengths of H. In addition, there are cases where one atom is fairly > isolated from the others, i.e., cage like structures, where FEFF can't > overlap the potentials, and setting FOLP to something smaller than 1.0 is > essential to make the code run. I would start by letting the code choose > the muffin tins automatically, then change them and see how the results > change. If the changes in the XANES are small, you probably don't have to > worry about FOLP. Otherwise, this is probably a limitation of the spherical > muffin tin potential. The best thing to do in that case, is to compare the > DOS (LDOS) with a calculation from a full potential electronic structure > code, i.e., WIEN2K, ABINIT, QUANTUM ESPRESSO, etc. > This can give you confidence in the FEFF calculation, or lead you to the > best values for FOLP. You could also use the FOLP values to get the best > comparison to experiment, but in some cases you may be fitting many-body > effects, which can lead you to the wrong conclusions about your system. > Cheers, > Josh Kas > > On Mon, Nov 26, 2012 at 7:53 AM, > <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > > > Re: >

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Question on Glitch in FEFF for Ru EXAFS measurements
by Dooshaye Moonshiram 27 Nov '12

27 Nov '12

Dear Bruce, I recently collected EXAFS data on the *Tris(bipyridine)ruthenium(II) dichloride Ru 2 compound-photosensitizer in solution form. In order to compare EXAFS data to XRD data, I uploaded the XRD coordinates of this crystal structure from cambridge database in a FEFF calculation page in ARTEMIS. I ran FEFF on the x,y and z coordinates of this standard compound in Artemis and summed all paths to compare with my experimental data(collected in solution form in fluorescence mode)* *I have 2 problems* *1) I found a glitch when running FEFF in ARTEMIS. In order to compare XRD coordinates to EXAFS data, I upload the XRD coordinates in a FEFF calculation page, run FEFF and sum all paths. Now* *a) **f I upload the XRD coordinates in a FEFF calculation page without having the EXAFS artemis file present, I get different fits compared to* *b) if I first upload the EXAFS experimental file and then run FEFF on the XRD cartesian coordinates. It seems that **the sum of all paths from the FEFF calculation page tend to mimic the experimental EXAFS file which has first been uploaded and is not a true presentation of how the FT should be.* * * *-Please let me know if this is unclear and I can send you my EXAFS file as well as the XRD coordinates which I obtained from Cambridge structural databse* * * *2) Another problem which I have with my EXAFS data is that I have a peak at 2.5 Angstrom which does not match XRD coordinates and is not present if I run FEFF on XRD coordinates only(true comparison as I don't add the the experimental file in Artemis). Could this peak be due to the Ru standard somehow? All measurements were done in fluorescence mode (F/Io) at 20 K in cryostat using a germanium detector. I simultaneously collected EXAFS measurements on Ru metal standard between Iref and IT ionization chambers.* * * *Thank you for your help,* *Sincerely* *Best Regards* *Dooshaye Moonshiram*

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Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 13
by Zack Gainsforth 27 Nov '12

27 Nov '12

Kyler, you and Tsu-Chien are terrific! iXAFS is working for me again! Cheers, Zack Gainsforth Space Sciences Laboratory, UC Berkeley 7 Gauss Way Berkeley, CA 94720 510-642-9733 zackg(a)ssl.berkeley.edu On Nov 15, 2012, at 10:00 AM, 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. Re: Launching Athena on Mountain Lion (Mac OS 10.8) (Kyler Carroll) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Nov 2012 09:32:34 -0800 From: Kyler Carroll <kyler.carroll(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8) Message-ID: <CAN+rEib3FNvmTE0x8BPgCBN2TRytRE+1CG2aN6A=mEEWxS6NcA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Help: some operation using Athena and Artemis
by Bingjie Ouyang 26 Nov '12

26 Nov '12

Hi, I just joined the mailing list recommended by a friend, I hear this is a really good place to communicate and learn. So I'm here, actually I need help for some basic questions on Iffeffit software: 1, In Athena, how to make a fourier transform draft? 2, In Artemis, since I was told that each shell in R-space can be fitted separatly, is it OK to fit each shell in the R-range respectively, and then join up the fitted curve and just ignore the not match part in other R-ranges? And can a shell be comprised of several different paths (like Fe-O and Fe-S)? Thank you. Best wishes, Bingjie -- Bingjie Ouyang School of Earth Sciences and Engineering Nanjing University 22nd Hankou Road, Nanjing, Jiangsu, 210093 P. R. China Email: jessicaoy89(a)gmail.com

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Re: [Ifeffit] FOLP card
by Joshua Kas 26 Nov '12

26 Nov '12

Hi Enyuan, I don't really know a rule of thumb for ionic bond v.s. covalent bond, but by default, the FEFF code will automatically choose reasonable muffin tins in most cases, and most of the time it overlaps them by ~15%, i.e. FOLP 1.15. In many cases, the overlap doesn't change the structure in the XANES a lot until you get far from FOLP 1.0. However, there are some special cases. For example, we have found that using FOLP 0.8 for hydrogen atoms seem's to work reasonably well in the XANES. This is because of the short bond lengths of H. In addition, there are cases where one atom is fairly isolated from the others, i.e., cage like structures, where FEFF can't overlap the potentials, and setting FOLP to something smaller than 1.0 is essential to make the code run. I would start by letting the code choose the muffin tins automatically, then change them and see how the results change. If the changes in the XANES are small, you probably don't have to worry about FOLP. Otherwise, this is probably a limitation of the spherical muffin tin potential. The best thing to do in that case, is to compare the DOS (LDOS) with a calculation from a full potential electronic structure code, i.e., WIEN2K, ABINIT, QUANTUM ESPRESSO, etc. This can give you confidence in the FEFF calculation, or lead you to the best values for FOLP. You could also use the FOLP values to get the best comparison to experiment, but in some cases you may be fitting many-body effects, which can lead you to the wrong conclusions about your system. Cheers, Josh Kas On Mon, Nov 26, 2012 at 7:53 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Re:

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Plot multiple fits in (D)Artemis and statistical errors
by Nilmar Camilo 26 Nov '12

26 Nov '12

Dear Bruce, I am new in the list and really don't know if the points raised below were already discussed. In the (D)Artemis (Demeter version 0.9.13) how may I: - Plot different fits with the experimental data (to visually compare the results) - I don't know if this is a (new) bug of the program but when I try to restore a fit the program closes. In the log file the following line is written: "Can't use an undefined value as a HASH reference at C:/Strawberry/perl/site/lib/Demeter/Fit.pm line 1558." Obs.: I am running Demeter in Windows 7 (Pro). Another problem is related to the statistical errors when constraining the S0^2 parameter to float between two limits. The program doesn't return the error for all others parameters (but just zero as the error value) as you can see below: guess parameters: amp = 0.79284158 # +/- 0.00000000 [0.95] enot = 5.29826510 # +/- 0.00000000 [0] delrIn11 = 0.00235278 # +/- 0.00000000 [0] ssIn11 = 0.00155959 # +/- 0.00000000 [0.00300] delrCe1 = -0.00231455 # +/- 0.00000000 [0] ssCe1 = 0.00192778 # +/- 0.00000000 [0.00300] delrIn11In11 = 0.02070081 # +/- 0.00000000 [0] delrIr1 = -0.00435502 # +/- 0.00000000 [0] ssIr1 = 0.00386517 # +/- 0.00000000 [0.00300] delrIn31 = 0.00648507 # +/- 0.00000000 [0] ssIn31 = 0.00669602 # +/- 0.00000000 [0.00300] delrIn12 = 0.00255704 # +/- 0.00000000 [0] ssIn12 = 0.00305432 # +/- 0.00000000 [0.00300] def parameters: b = 0.80000000 # [min(max(0.8,amp),1.0)] Thanks so much in advance. Nilmar

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Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 21
by Enyuan Hu 25 Nov '12

25 Nov '12

Hi Joshua, Thank you for your answer. So you're saying that we can simultaneously define FOLP for each potential type in the way you showed, right? Then is there any rule of thumb on what appropriate numbers should be used, like what are for anions and what are for cations, what are for ionic bond and what are for covalent bond? thanks. best, Enyuan On Sun, Nov 25, 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. error function in Athena's peak analysis module (Linda Lim) > 2. Re: error function in Athena's peak analysis module > (Chris Patridge) > 3. Re: FOLP card (Joshua Kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Nov 2012 12:24:08 -0800 > From: Linda Lim <ywllim(a)stanford.edu> > To: Ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] error function in Athena's peak analysis module > Message-ID: > <CALPaxYDOUGa7_NMkLmDS31gnk6MFR9RRp4wda+Ji3= > xRdHW5hQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > 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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Re: [Ifeffit] FOLP card
by Joshua Kas 25 Nov '12

25 Nov '12

Hi Enyuan, You can define the folp options separately for each unique potential, i.e., FOLP 0 1.0 FOLP 1 0.8 FOLP 2 1.2 Will give you touching muffin tins for the 0 potential (absorber), and an overlap of 0.8 and 1.2 for the atoms with potential types 1 and 2 respectively. Note that the 0 potential will have not necessarily have "touching" muffin tin, since the 2 potential is larger than touching and could overlap the 0 potential. The third number gives the ratio of the muffin tin size to the touching muffin tin size that the cod would use if all FOLP radii were set to 1.0. Cheers, Josh Kas Cheers, Josh Kas On Sat, Nov 24, 2012 at 10:00 AM, <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. FOLP card (Enyuan Hu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Nov 2012 08:55:58 -0500 > From: Enyuan Hu <bearcharge(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] FOLP card > Message-ID: > < > CAJud35MQx-zvbvpPH1zbPitFXaUj9qm8TgoqEWsH9yCnwawRNA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I'm trying to see the impact of using FOLP card on my simulation results in > Feff9. As far as I understand it, FOLP is defining the overlapping of > muffin-tin radii. The first parameter defines the the position where this > card will be used (expressed as potential type), right? so should I do the > simulation for all potentials, that is going from 0 to the last number in > my potential list, or I just do it for some specific positions (potential > types)? thanks. > > Enyuan >

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FOLP card
by Enyuan Hu 24 Nov '12

24 Nov '12

Dear all, I'm trying to see the impact of using FOLP card on my simulation results in Feff9. As far as I understand it, FOLP is defining the overlapping of muffin-tin radii. The first parameter defines the the position where this card will be used (expressed as potential type), right? so should I do the simulation for all potentials, that is going from 0 to the last number in my potential list, or I just do it for some specific positions (potential types)? thanks. Enyuan

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iXAFS on Mountain Lion
by Weng, Tsu-Chien 22 Nov '12

22 Nov '12

Hi, I had problem launching iXAFS on Mountain Lion after the OS upgrade. It seems the path to X11 might be hard wired in the program. Here is my workaround solution by creating a symbolic link to XQuartz. It might be worth sharing the trick. 1. Install XQuartz 2.7.4 from <http://xquartz.macosforge.org/landing/> 2. Launch Terminal.app and issue the following commands: 2.1) cd /Applications/Utilities 2.2) sudo mkdir X11.app 2.3) cd X11.app 2.4) sudo ln -s ../XQuartz.app/Contents 3. Now either double-click on iXAFS.app or command line `open -a ixafs` should work -- Tsu-Chien WENG Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, Mail Stop 69 Menlo Park, CA 94025, USA +1-650-926-4107 (office) +1-650-926-4100 (fax)

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(no subject)
by Pooja Gupta 19 Nov '12

19 Nov '12

-- "A Ship is always safe at the shore - but that is NOT what it is built for" *********************************************** Dr. Pooja Gupta Scientific Officer Material research Lab Raja Ramanna Center for Advanced Technology, Indore-452013. (M.P.) INDIA. Ph. No. (O): +91-731-2442123 (M): +91 8435718320 Fax No. (O): +91 7312442140 E-mail ID: pooja(a)rrcat.gov.in

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