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

Demeter not open in Windows and can't import raw data in Mac
by Mengling Stuckman 12 Feb '14

12 Feb '14

Hi, all, I'm a new user of Demeter and unfortunately I have problems with installing and using Demeter for both operating systems. In Windows 7 enterprise, all of my Demeter programs (updated to version 0.9.18.2) can't open. In the %APPDATA%\Roaming\demeter\dathena.log, the following message showed up if I tried to open Athena: "Can't load 'C:/strawberry/perl/site/lib/auto/Wx/Wx.dll' for module Wx: load_file:The network path was not found at C:/strawberry/perl/lib/DynaLoader.pm line 200. at C:/strawberry/perl/site/lib/Wx/Perl/SplashFast.pm line 60 Compilation failed in require at C:\strawberry\perl\site\bin\dathena.bat line 23. BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dathena.bat line 23." If I tried to open Artemis, the same error message showed up. I did go through the mailing list to search for similar topics, but I can't find any .mru file or .cwd file in folder %APPDATA%\Roaming\demeter\ to delete. Is there anything else I can do to solve this problem? In my mac OS X 10.7.5, I did successfully install Demeter onto my system and was able to open any files in the .prj file in Athena. However, when I tried to import the raw XANES data files, like sample.0001 or sample.0002, Athena would close. At the same time on Terminal, the follow message showed up: "At line 436 of file iff_show.f Fortran runtime error: End of record" The mac version is very new, I don't know if any user has similar issue to not? Thank you very much! Any reply would be highly appreciated! Mengling -- Mengling Stuckman ORISE Research Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA STUCKMAN.MENGLING(a)CONTR.NETL.DOE.GOV Office: 412-386-7387

2 5

Problem opening demeter in Windows 7
by Arjen van Veelen 12 Feb '14

12 Feb '14

Dear Bruce, In October last year (October 22) I reported a problem in Demeter. I couldn't open Artemis or Athena. The only thing happening was two screens popping up quickly before disappearing. You replied that you had never seen this problem before. Since then I have used Demeter in Ubuntu. Now, first I have to be honest. I haven't read all the threads posted about windows problems with Demeter lately, so I do apologize if you have this solution already posted somewhere. I have been looking into this problem today on my computer again as I found it very frustrating switching between two OS. So, I checked my local environment settings and for some reason there was a whole list of crappy paths accumulated under PATHS. Don't ask me why, I have no idea how this happened. I deleted, after uninstalling Demeter first, everything related to strawberry in PATHS. I also deleted strawberry in C:\strawberry. Then I reinstalled Demeter and everything seems to work fine. Maybe this will be helpful for some people experiencing a similar problem. Best wishes, Arjen ir. A. (Arjen) van Veelen | PhD student | University of Manchester | School of Earth, Atmospheric and Environmental Sciences | Oxford Road | Manchester | M13 9PL | United Kingdom | M +44 77 2037 3237 | arjen.vanveelen(a)postgrad.manchester.ac.uk<mailto:arjen.vanveelen@postgrad.manchester.ac.uk> | www.manchester.ac.uk<http://www.manchester.ac.uk>

1 0

Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fit
by Sathish Mayanna 09 Feb '14

09 Feb '14

Dear Dr. Robert Thanks a lot for your information that's very helpful. I checked the ICSD, but unfortunately we don't have access to the crystal data. It would be great, if you or someone has the access to the crystal data to provide me the coordinates, the *collection code: 202727, Author: Post, Year: 1988. * *Please let me know, if someone has the access to the data.* Regards Sathish On Thu, Feb 6, 2014 at 11:05 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. Re: Correct Crystallographic parameters for Todorokite EXAFS > fitting in Artemis (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 06 Feb 2014 16:05:30 -0600 > From: Robert Gordon <ragordon(a)alumni.sfu.ca> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Correct Crystallographic parameters for > Todorokite EXAFS fitting in Artemis > Message-ID: <52F4072A.1070008(a)alumni.sfu.ca> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Satty, > > The crystal data in your inp file came from the paper. I checked the > International > Crystal Structure Database (ICSD) - printout attached. The structure > data in the paper > are not in standard form - atoms might not give the correct results if > the input is bad- and there > are typos for two of the O5 coordinates according to the ICSD warning. > Does your institution have access to the ICSD - Online or on disc? If you > are not familiar with it, try talking to one of your institution's > reference librarians. > > I'm not certain what you mean by the corner-corner Mn. You were choosing > Mn1 > as the core in your inp. When I look at the structure, Mn1 sits in the > middle of > the set of 3 octahedra that make up a side of the tunnel. Where would > the corner-corner > distance be relative to the middle of the chain? You have 4 different Mn > sites. > > Fitting in R-space is common. > > As for learning about crystal structures, try sitting in on a > coordination chemistry > or solid state chemistry course. For a basic learning book, I like > West's "Basic Solid > State Chemistry" or Muller's "Inorganic Structural Chemistry" (again, > try the library > if you don't want to buy a copy). More recent books may be available. > A bit of > googling may reveal some online lessons, like: > http://www.seas.upenn.edu/~chem101/sschem/solidstatechem.html > > > regards, > Robert > > > On 2/6/2014 3:16 AM, Sathish Mayanna wrote: > > Hi > > > > I am having some problem to get the real crystallographic parameters > > for Todorokite (I know there are many literature available) I used the > > parameters from Post et al 1988 (/Rietveld refinement of the > > Todorokite structure/) and others as well (*attached Todorokite.inp > > file*). > > > > I except the corner corner Mn in Todorokite, since its a tunnel > > structure, but the Feff calculations do not provide any corner corner > > Mn, in addition I cannot fit exactly even Mn-O or Mn-Mn. > > > > But If I use Ramsdellite (*attached Ramsdellite.inp file*), which is > > also a tunnel structure, I could get the Corner-Corner Mn and can fit > > perfectly the Mn-O, Mn-Mn, but cannot fit in K space. > > > > It would be really great, if anyone could provide me the model Tunnel > > type-Mn oxide crystallographic parameters to fit the data *(attached > > Mn Spectra.prj)* > > > > p.s: I tried my best to learn and understand the crystallographic > > parameters and miller indices, but still I feel that I am very poor, > > it would be nice, if someone suggest some good and basic source to > > learn more about pure mineralogy (which is crucial to know the basic > > parameters for fitting in Artemis). > > -- > > Satty > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- > Dr. Robert Gordon > Staff Scientist, PNCSRF > APS Sector 20 (PNC/XSD) > 9700 S Cass Ave. 435E > Argonne, IL, USA 60439 > > 630-252-0581 > 630-252-0580 fax > >

2 1

Athena doesn't open anymore
by Kuri, Ulises 07 Feb '14

07 Feb '14

I am having problems opening Athena. Reading the iffefit mailing list I found a similar problem posted by Roberto Rodriguez on 29 May 2013. I tried to delete the .mru file. but still I have same problem dathena.log says: Failed to load YAML document from 'C:\Users\Sof\AppData\Roaming\demeter\athena.cwd' at C:/strawberry/perl/vendor/lib/YAML/Tiny.pm line 593 YAML::Tiny::LoadFile('C:\Users\Sof\AppData\Roaming\demeter\athena.cwd') called at C:/strawberry/perl/site/lib/Demeter/UI/Athena.pm line 81 Demeter::UI::Athena::OnInit('Demeter::UI::Athena=HASH(0x270eb0c)') called at C:/strawberry/perl/site/lib/Wx/App.pm line 36 eval {...} called at C:/strawberry/perl/site/lib/Wx/App.pm line 36 Wx::App::new('Demeter::UI::Athena') called at C:\strawberry\perl\site\bin\dathena.bat line 57 I will appreciate any help. Sorry if the issue is already solved in the mailing list, but I did not find it Ulises

2 2

Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis
by Sathish Mayanna 06 Feb '14

06 Feb '14

Hi I am having some problem to get the real crystallographic parameters for Todorokite (I know there are many literature available) I used the parameters from Post et al 1988 (*Rietveld refinement of the Todorokite structure*) and others as well (*attached Todorokite.inp file*). I except the corner corner Mn in Todorokite, since its a tunnel structure, but the Feff calculations do not provide any corner corner Mn, in addition I cannot fit exactly even Mn-O or Mn-Mn. But If I use Ramsdellite (*attached Ramsdellite.inp file*), which is also a tunnel structure, I could get the Corner-Corner Mn and can fit perfectly the Mn-O, Mn-Mn, but cannot fit in K space. It would be really great, if anyone could provide me the model Tunnel type-Mn oxide crystallographic parameters to fit the data *(attached Mn Spectra.prj)* p.s: I tried my best to learn and understand the crystallographic parameters and miller indices, but still I feel that I am very poor, it would be nice, if someone suggest some good and basic source to learn more about pure mineralogy (which is crucial to know the basic parameters for fitting in Artemis). -- Satty

2 1

EXAFS simulations - peak too high
by Lisa Bovenkamp 03 Feb '14

03 Feb '14

Hello. I am running some EXAFS simulations Au L3 on Au clusters with SR coating. In the outer shell Au sits between 2 S atoms. 4 Au atoms are in the neighborhood up to 3.5 Angström. Expecting two peaks in the chi(R) - one for Au-S and one for Au-Au (here it can be several little ones) I find that for 1 out of 5 sites the Au-Au peak is way too high. Is something in the FEFF code weighing an Au-Au path for this site too much? Does anyone have some ideas on that? Thanks, Lisa

4 3

Re: [Ifeffit] EXAFS simulations - peak too high
by Lisa Bovenkamp 03 Feb '14

03 Feb '14

Dear Anatoly. Yes, I know that paper. In order to expand that study from pure gold to bimetallic clusters I want to be sure and repeat the results that this group found. Thanks for mentioning it. Dear Scott, That was the answer I was looking for. I believe the paths are reinforcing each other. This is now obvious from the Im chi(R). Thanks for the presentation of yours. Now one question remains: Do I discard/disregard this site from my calculations (in the averaging process) or not? Thanks. Lisa

2 1

How can I fit the results obtained from FEFF9 to the experimental data using the ARTEMIS.
by Abhijeet Gaur 03 Feb '14

03 Feb '14

Hi, I have started using FEFF9 recently. I am using it to generate theoretical model for some copper compounds and complexes. As you have mentioned in one of research article' Nuclear Instruments and Methods in Physics Research A 619(2010)28-32' How can I fit the results obtained from FEFF9 to the experimental data using the ARTEMIS. I have tried to search the answer on the ifeffit mailing list but unable to find a satisfactory one. With thanks in advance -- Dr. Abhijeet Gaur

2 1