September 2007 - Ifeffit - millenia.cars.aps.anl.gov

Elise Fox is out of the office.
by Elise.Fox＠srnl.doe.gov 17 Sep '07

17 Sep '07

I will be out of the office starting 09/17/2007 and will not return until 09/24/2007. I will respond to your message when I return.

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Re: [Ifeffit] Linear Combination Fitting in Athena
by Barton, David (DG) 17 Sep '07

17 Sep '07

Skya, Seeing an example Athena file would help, but my guess is that one or more of your standards are being rejected by the fit (i.e. near zero), when this occurs the LCF routine can finish without the sum forced equal to zero. If this is the case you can just rerun the fit excluding the standard that is near zero and the sum should now equal 1. Dave _________________________________ David Barton, -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Skya Fawcett Sent: Monday, September 17, 2007 3:07 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Linear Combination Fitting in Athena I'm trying to do linear combination fitting on a number of samples, and its working well for the most part, with 4 exceptions. There are 4 samples, of 22, that I can't get to sum to 1, despite the fact that I have "sum to 1" checked off before fitting. I've tried reprocessing the data, and tried reinstalling Athena with no luck. Any ideas? Skya Fawcett PhD Candidate Department of Geological Sciences and Geological Engineering Queen's University, Kingston, Canada _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Linear Combination Fitting in Athena
by Skya Fawcett 17 Sep '07

17 Sep '07

I'm trying to do linear combination fitting on a number of samples, and its working well for the most part, with 4 exceptions. There are 4 samples, of 22, that I can't get to sum to 1, despite the fact that I have "sum to 1" checked off before fitting. I've tried reprocessing the data, and tried reinstalling Athena with no luck. Any ideas? Skya Fawcett PhD Candidate Department of Geological Sciences and Geological Engineering Queen's University, Kingston, Canada

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Re: [Ifeffit] Need your help
by Bruce Ravel 17 Sep '07

17 Sep '07

Hi Jin, I am CCing my response to the Ifeffit mailing list: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ If you are not already a member of the mailing list, I encourage you to join. It is a great place to ask questions and learn about XAFS and the Ifeffit-based software. On Sunday 16 September 2007, you wrote: > Dear Ravel: > > I am just a student of Shanghai Applied Physics Institute, CSA. And I > meet some problem by using FEFF process. > > When I know the coordination number and the coordination distance of known > structure macular, how to set the atom inp file or feff inp file? I'm afraid that I am little unsure what you exact question is. If you know the coordination number and distance because your material is a known crystal, then you can just use a CIF file or an atoms.inp file of the sort described here: http://cars9.uchicago.edu/~ravel/software/doc/Atoms/Atoms/node4.html or available for many materials at this database: http://cars9.uchicago.edu/~newville/adb/search.html If you know coordination and distances because you have structural information of the sort that you might find in a protein data bank file or some other molecular format, then you should skip the use of atoms and simply convert the molecular data to a feff.inp file as described on page 36 of this talk I recently gave: http://cars9.uchicago.edu/~ravel/talks/pimst2.pdf It is important to remember that Atoms is a tool for converting crystallographic data into a list of atomic coordinates. That's all it does. If you are doing XAFS on something that is not a crystal, Atoms is of no use. > And another question is how get the usefully muffin tin from the XRD data > in the protein data bank? Feff computes muffin tins. In 99% of all situations, you do not need to modify how Feff does tht nor do you need to specify muffin tin radii. Feff's algorithm for determining muffin tin radii given a list of atomic coordinates is relatively simple, but surprisingly effective and completely automated. > I have tried many time as the handbook shows, but I also don't know how to > do? So I need your help ? Thank you very much You may find it useful to ask explicit questions on the mailing list by posting examples of the problem you are having. For instance, if you are having trouble running Feff, asking a question about the exact thing that is confusing and posting an example of the feff.inp file that is giving you trouble will help the people on the mailing list help you. Good luck and I hope this was helpful, Bruce > Smiling everyday, > > Best wishes, > > Jin Chan -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Double picks on Near Edge region.
by 沛昌蔡 12 Sep '07

12 Sep '07

To whom it may concern, Dear Prof.; Here have some questions about Zn doped LiNbO3 single crsystal EXAFS fitting problem, we did the similar EXAFS absorption spectra as you can see the attach reference paper Fig 7, that shows double picks on Near Edge region, and our questions are, (1) Base on your great knowledge, how comes about these two picks, and is it normal? (2) On Artemis program R-figure display, we can find a great pick appeared in 0~1 angstrom range (k range=1~12), but we find this pick disappeared under (k range=2~12) parameter choosing ,so is it relation to question (1)? (3) If we want to cut near edge contribution, how should we deal with these double picks? choose the rear EXAFS spectrum (aviod these two picks)? Or using Athena background removal it? Thanks for your time and helping. Pei-chang Tsai 2007/09/12 設定安全圖章，保護您的 Yahoo!奇摩帳號不被駭客盜用！

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Creating Athena Projects from Ifeffit command line
by Matthew Ginder-Vogel 11 Sep '07

11 Sep '07

Hi Bruce and list, Has anyone written an Ifeffit wrapper and/or script that can take a series of data files and create an Athena project without actually having to use Athena? If you have, would you be willing to share it? I'm sure it's possible, but I don't want to recreate the wheel if I don't have to. Thanks, Matt -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

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Re: [Ifeffit] Atoms question
by Bruce Ravel 07 Sep '07

07 Sep '07

On Friday 07 September 2007, Saraiya, Neeraj M. wrote: > Hi Bruce, > I am somewhat of a first time user of the Ifeffit software package > and had a question regarding the Atoms package. I am trying to input > x,y,z coordinates for a crystal structure and I realized that the > coordinates are the same for two different elements - i.e. two elements > that can interchange with each other in the structure. How can I > account for the differing ratios of occupancy between the two elements? > Thanks in advance for addressing this question. > > Best, > Neeraj Neeraj, This is a common question, so I am taking the liberty of CCing my answer to the mailing list. Look at the last question ("How do I handle doped materials? Why doesn't Atoms handle doped materials?") on this FAQ page: http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling If you still have questions after reading that, go ahead and post your questions on the mailing list and we'll see what we can do about answering them. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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energy scale when averaging data
by Matthew Ginder-Vogel 07 Sep '07

07 Sep '07

Hello Everyone, I have a very large number of data files (>10,000) that I'm trying to average using Ifeffit. However, I'm having trouble coming up with the energy scale for the averaged file. The energy scale for each individual file is very similar, but not identical, so I'm not sure if it is the best idea to use the energy scale of a single file as the energy scale for the averaged file. I'm sure that I'm not the first person to deal with this problem, so I'm interested to hear how other people deal with this problem. I'm also sure that Bruce has already come up with a clever way of dealing with this problem in Athena, but unfortunately loading 50 files at a time into Athena to average is a too slow a process. So I'd rather do them 50 at a time from the command line. Thanks, Matt ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

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Linear Combination Fitting in Athena
by Skya Fawcett 06 Sep '07

06 Sep '07

A couple questions about linear combination fitting in Athena: 1. There is the option of floating an E0 for the standards, is there any way to restrict how much it floats, ie. constrain it to +/-0.4eV shifts during fitting? 2. If I am fitting normalized u(E), and only care about the XANES region at this point, is perfecting background removal needed? (I have, of course, carefully checked the pre-edge and normalization range). Thank you! Skya Fawcett PhD Candidate Department of Geological Sciences and Geological Engineering Queen's University, Kingston, Canada

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Can't change values in Athena and Artemis on Ubuntu(Feisty)
by Jun Lin 06 Sep '07

06 Sep '07

Hi Carlo Segre, I install Athena and Artemis from your compiled deb package for feisty. When I try to change values in Athena and Artemis, it doesn't work. The only way change the value is click on the plot canvas. I have tried to execute program as root user, but it also doesn't work. Looking forward for you help. Sincerely, Lin Jun -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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