April 2014 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 Dec '14

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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Atoms and Feff for CuFe2O4 structure
by Qasim Imtiaz 04 May '14

04 May '14

Dear all, I am using Atoms to calculate a Feff input file for CuFe2O4 spinel. However running Atoms/Feff results in program crash owing to 'two atoms very close together'. I modified the .cif file before importing (owing to partial occupancy issue) as following: Deleted: Fe2 Fe3+ 8 d 0.5 0.25 0.125 . 0.5 0 Modified: Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 0.5 0 to Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 1 0 After importing the file in Atoms, I also used different shift vectors (e.g. -0.125 -0.125 -0.125) but the issue is not resolved. Can someone help me please to solve this problem? Thanks. Best Regards Qasim

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Possible bug in fitting
by Ditty Dixon 30 Apr '14

30 Apr '14

Hello IFEFFIT users, I am working on LiNi0.5Mn1.5O4 cathode materials, I am pretty sure that some of you already worked on it. On the first look, a multiple edge analysis on both Ni and Mn is interesting; however it’s not that straight forward due to multiple phase and oxidation states. I started doing multiple edge fit, but I gave up briefly. Then I did individual edge analysis and obtained some values. Looking at both edges my Ni fit looks good. So I thought of taking the Ni-Mn bond distance as well as DW factor value to Mn edge and set this value for my Mn-Ni paths. However it seems like this value is further evaluated in the fit and giving a new value. Can someone reproduce this, please see the project file and the Log file attached, Is it a possible bug or am I doing something wrong? Thank you, Ditty -- Ditty Dixon, Anorganische Chemie Karlsruhe Institute of Technology Kaiserstr 12 Karlsruhe, Germany Ph no: 004972160848093

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Re: [Ifeffit] Ifeffit Digest, Vol 134, Issue 20
by Ditty Dixon 30 Apr '14

30 Apr '14

Hello IFEFFIT users, Sorry, I used the wrong values I should have set the delta r value, Sorry again, Ditty On Wed, Apr 30, 2014 at 2:05 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. Possible bug in fitting (Ditty Dixon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 30 Apr 2014 14:05:40 +0200 > From: Ditty Dixon <ditty.dixon(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Possible bug in fitting > Message-ID: > < > CABPBYUdrOG_atNjT9ef454J_ZhLXPmnTin8KXcNvi1ZVTCxOHg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello IFEFFIT users, > > > > I am working on LiNi0.5Mn1.5O4 cathode materials, I am pretty sure that > some of you already worked on it. On the first look, a multiple edge > analysis on both Ni and Mn is interesting; however it?s not that straight > forward due to multiple phase and oxidation states. I started doing > multiple edge fit, but I gave up briefly. Then I did individual edge > analysis and obtained some values. Looking at both edges my Ni fit looks > good. So I thought of taking the Ni-Mn bond distance as well as DW factor > value to Mn edge and set this value for my Mn-Ni paths. However it seems > like this value is further evaluated in the fit and giving a new value. Can > someone reproduce this, please see the project file and the Log file > attached, Is it a possible bug or am I doing something wrong? > > > > Thank you, > > > Ditty > > -- > Ditty Dixon, > Anorganische Chemie > Karlsruhe Institute of Technology > Kaiserstr 12 > Karlsruhe, Germany > Ph no: 004972160848093 >

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Rendering of windows in Artemis and transferring paths from feff calculation
by Alison Tebo 23 Apr '14

23 Apr '14

Hi All, I am running Demeter 0.9.18 installed on a Mac 10.6.8 via the (very helpful!) Macports port. I've had nearly no problems with processing my data, but Artemis appears very strange. Most of the button can't be seen and are black instead (I've attached a screenshot). The bigger problem is that once I run a Feff calculation, I can't seem to transfer the paths from the Feff Window into the Data Window (see second screenshot). The program seems to think it's doing it--there are no error messages in the log and it even makes the little graphic as it 'grabs' the path--but it never transfers it over to the Data Window. I have attached a project file where I get this error, the feff input file that I run the calculation on, and two screenshots of what Artemis looks like for me. I don't think the input and project file matter much since this happens for me even with examples from the various courses Bruce has given. Any advice would be greatly appreciated. Sincerely, Alison

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Re: [Ifeffit] Rendering of windows in Artemis
by Martha W Schaefer 23 Apr '14

23 Apr '14

I am just now going through the tutorials for Artemis (from the 2011 Diamond Light Source course), so I am by no means familiar with Artemis, but I am seeing the same black buttons. I am running Demeter 0.9.18 from MacPorts, on a Mac 10.8.5, and I don't think I have ever played with the color theme. I can't speak about the feff transferring paths issue (yet). (In the ifeffit mailing list digest I can't seem to see Alison's screenshot, but what I see sounds the same.) Martha W. Schaefer Louisiana State University >> >>> On 03/24/2014 03:21 PM, Alison Tebo wrote: >>> >>>> I am running Demeter 0.9.18 installed on a Mac 10.6.8 via the (very >>>> helpful!) Macports port. I've had nearly no problems with processing my >>>> data, but Artemis appears very strange. Most of the button can't be seen >>>> and are black instead (I've attached a screenshot). The bigger problem >>>> is that once I run a Feff calculation, I can't seem to transfer the >>>> paths from the Feff Window into the Data Window (see second screenshot). >>>> The program seems to think it's doing it--there are no error messages in >>>> the log and it even makes the little graphic as it 'grabs' the path--but >>>> it never transfers it over to the Data Window. >>>> >>>> I have attached a project file where I get this error, the feff input >>>> file that I run the calculation on, and two screenshots of what Artemis >>>> looks like for me. I don't think the input and project file matter much >>>> since this happens for me even with examples from the various courses >>>> Bruce has given. >>>> >>>> Any advice would be greatly appreciated. >>>> >>> >>> Hi Alison, >>> >>> First off, I apologize that it has taken me so long to respond to this. >>> Busy time. >>> >>> I don't quite understand the bigger problem. This is certainly not a >>> problem I have on other platforms. Do other Mac users observe the same >>> behavior? >>> >>> As for the lesser problem, looking at the icons across the top in your >>> screenshots, it would seem that you are using some kind of color theme that >>> is different from a Mac out of the box. Is that right? If so, how does >>> the software behave if you change the theme back to the default? >>> >>> Cheers, >>> B >>> >>> >>> -- >>> Bruce Ravel ------------------------------------ bravel(a)bnl.gov >>> >>> National Institute of Standards and Technology >>> Synchrotron Science 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 >> >> >

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Re: [Ifeffit] possible bug in Atoms
by Matt Frith 19 Apr '14

19 Apr '14

Bruce, thanks for taking a look at the problem- the effort is appreciated. Bests, Matt Frith On Thu, Apr 17, 2014 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. Re: Artemis Feature Request (Bruce Ravel) > 2. Re: possible bug in Atoms (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Apr 2014 16:49:26 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Artemis Feature Request > Message-ID: <534EECD6.2090707(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 04/15/2014 01:12 PM, Shelly Kelly wrote: > > Does Artemis have the ability to save the path list information in a > > format similar to the old intrp.dat file to disk? > > Done. Will be in the next release. > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > Homepage: http://xafs.org/BruceRavel > Software: https://github.com/bruceravel > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Apr 2014 08:44:51 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] possible bug in Atoms > Message-ID: <534FCCC3.9010407(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 04/03/2014 02:19 AM, Matt Frith wrote: > > I think I may have found a possible bug with the stand-alone version of > > (D) Atoms. If I generate an inp file in atoms, save it and then try and > > run feff on it later, Atoms crashes without attempting the calculation. > > However, if I load that same input file in (D)Artemis it will run feff > > without crashing. Stand-alone atoms will also fail if I generate the > > input file in Artemis, save it and then try and later open it using > > Atoms. Only Atoms or Artemis is open at a time, > > > > This will be fixed in the next release. Thanks for the bug report. > > > > This problem is occurring on both 32 and 64 bit Windows 7 computers > > running the current (0.9.18.2) package. The problem occurred using > > 0.9.17 also. Any ideas of why I am all of a sudden having this issue > > when it has not been a problem before? > > > > I suspect that it has long been a problem, but it takes a particular > action to trigger the problem. I think that you, like me, never noticed > it before. > > Cheers, > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science 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 > > > End of Ifeffit Digest, Vol 134, Issue 16 > **************************************** >

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D-ARTEMIS
by JOLLIVET Patrick 18 Apr '14

18 Apr '14

Dear Dr Ravel, In the previous version of ARTEMIS, it was possible to separately do FEFF calculations (with FEFF7, FEFF8 or FEFF9) and then to import all paths or one by one in ARTEMIS (theory menu) to fit the experimental data. Is it still possible with the new version D-ARTEMIS ? If yes, how to proceed to do that because I did not manage to do it. Thank you for your answer. Sincerely yours

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possible bug in Atoms
by Matt Frith 17 Apr '14

17 Apr '14

Dear All, I think I may have found a possible bug with the stand-alone version of (D) Atoms. If I generate an inp file in atoms, save it and then try and run feff on it later, Atoms crashes without attempting the calculation. However, if I load that same input file in (D)Artemis it will run feff without crashing. Stand-alone atoms will also fail if I generate the input file in Artemis, save it and then try and later open it using Atoms. Only Atoms or Artemis is open at a time, This problem is occurring on both 32 and 64 bit Windows 7 computers running the current (0.9.18.2) package. The problem occurred using 0.9.17 also. Any ideas of why I am all of a sudden having this issue when it has not been a problem before? The cif file, inp file, and atoms log file are all attached. Sincerely, Matt Frith

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Artemis Feature Request
by Shelly Kelly 16 Apr '14

16 Apr '14

Bruce: Does Artemis have the ability to save the path list information in a format similar to the old intrp.dat file to disk? Seems like this feature could go on the "export" button on the Atoms tab. Or it might also belong on the "Save calc" on the Paths tab. This button gave me a feff.yaml file that I don't know how to open, maybe it is in there? Thank-you for considering this suggestion. Shelly

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