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

in situ liquid cell
by Renato Canha Ambrosio 26 Mar '07

26 Mar '07

Dear Colleagues, I need to perform XAFS measurements microemulsions (liquid). As I do not have a liquid cell for the in situ XAFS measurements, I would like to know more about liquid cells. Could anyone shoot its cell and send me the photo? I am designing a cell where you optimize the edge jump by modifying the optical path. Thank you very much for your kind attention Renato Canha Ambrosio ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Thu, 22 Mar 2007 17:45:00 -0500 Subject: Ifeffit Digest, Vol 49, Issue 14 > 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: EXAFS reference materials (Frenkel, Anatoly) > 2. Re: EXAFS reference materials (Scott Calvin) > 3. Re: EXAFS reference materials (Frenkel, Anatoly) > 4. Some more questions (Shantanu Behera) > 5. Re: Some more questions (Bruce Ravel) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 22 Mar 2007 15:28:55 -0400 > From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> > Subject: Re: [Ifeffit] EXAFS reference materials > To: <rh2rr(a)virginia.edu> > Cc: Ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <0D9ED6BC247DA847A3855B6726D6E34421854C(a)exchangemb1.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Ruoshuang, > > I am cc'ing this email to IFEFFIT mailing list. There are several > reasons (I am listing just a few) you should measure a reference > sample simultaneously with unknown materials. > > 1) to align the unknown sample scans prior to merging. If those data > are noisy, reference sample can be used for the alignment. In > addition, if you want to compare samples before and after some > changes that may affect their energy positions (e.g., oxidation, > reduction, doping, metal-insulator transition, etc.) you want to > align all of their references to reliably analyze these changes. > > For this purpose, it does not matter whether you use a metal or a > metal oxide or any other standard with the same resonant element. > > 2) to find S02 value. It is usually the same in most samples which > have the same resonant element. > > For this purpose, what matters the most is whether you can reliably > find S02 from your standard (and then impose it on your unknown > sample). Thus, some exotic reference which may still be good for 1) > may not be as good for 2) since it may be difficult to refine its > structure and get precise value for S02. The metals would be the > best, but if you have other materials with "open lattices", e.g., > fcc, rock salt, etc., with well defined first shell that you can > fit with the miniumum parameters, they will all work fine. > > 3) to use as a model for your analysis. > > If you analyze an alloy, as in your case, you want to compare EXAFS > results in your alloys against those in relevant pure compounds. For > binary alloys, the best reference will be a pure metal, for ternary - > an intermetallic compound, etc. An oxide would not be so useful for > modeling. For that reason, people often measure more than one > reference, as per 1),2) and 3). > > Hope it helps, > > Anatoly > > ________________________________ > > From: rh2rr(a)virginia.edu [mailto:rh2rr@virginia.edu] > Sent: Thu 3/22/2007 2:54 PM > To: Frenkel, Anatoly > Subject: EXAFS reference materials > > Dear Dr. Frenkel, > > I'll do EXAFS on metallic glass but I am not sure about the reference > materials. [...] > We are trying to study structural relaxation of metallic glass by > EXAFS. My samples are Al-TM-RE (TM=Fe,Co,Ni, RE=Gd,Ce,Y). Because Ce > and Y are easily oxidized in air, some people suggest use cerium > oxide and yttrium oxide as reference materials. My question is: when > I do EXAFS measurement and data analysis, is METAL necessary for > reference materials, or METAL OXIDE is fine as reference? > > Your kind help would be greatly appreciated. > > Ruoshuang Huang > > ------------------- > Ruoshuang Huang > Research Associate > Materials Science and Engineering > University of Virginia > Phone: 434-982-0238 > Fax: 434-982-5799 > > ------------------------------ > > Message: 2 > Date: Thu, 22 Mar 2007 15:48:31 -0400 > From: Scott Calvin <SCalvin(a)slc.edu> > Subject: Re: [Ifeffit] EXAFS reference materials > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <0JFB006RXLO7QHX0(a)mta3.srv.hcvlny.cv.net> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Hi Ruoshuang, > > Following up on Anatoly's excellent post, I would say that I > personally distinguish between a "reference" and a "standard." > > When I talk about a reference, I usually mean something I'm > measuring simultaneously with the sample. The primary purpose is > energy alignment, although it also gives a check on beam quality > issues > (e.g. harmonics). For this purpose, I generally use whatever is > convenient and well known, such as a metal foil. Sometimes I'll > measure the reference by itself, particularly if it's a beamline or > edge that is new to me. > > On the other hand, I think of a standard as a known compound that is > similar to my sample. I often work with nanoparticles, so my > standard might be the corresponding bulk material. Or if I'm working > with a doped compound, the standard might be the undoped version. > The standard is measured under the same conditions as the > sample...in fact, that means that I measure the standard with a > reference in place, if that makes sense. :) > > So I use a reference for Anatoly's purpose (1) and a standard for > Anatoly's purposes (2) and (3). > > I hope that's helpful. > > --Scott Calvin > Sarah Lawrence College > > At 03:28 PM 3/22/2007, you wrote: > >Hi Ruoshuang, > > > >I am cc'ing this email to IFEFFIT mailing list. There are several > >reasons (I am listing just a few) you should measure a reference > >sample simultaneously with unknown materials. > > > >1) to align the unknown sample scans prior to merging. If those data > >are noisy, reference sample can be used for the alignment. In > >addition, if you want to compare samples before and after some > >changes that may affect their energy positions (e.g., oxidation, > >reduction, doping, metal-insulator transition, etc.) you want to > >align all of their references to reliably analyze these changes. > > > >For this purpose, it does not matter whether you use a metal or a > >metal oxide or any other standard with the same resonant element. > > > >2) to find S02 value. It is usually the same in most samples which > >have the same resonant element. > > > >For this purpose, what matters the most is whether you can reliably > >find S02 from your standard (and then impose it on your unknown > >sample). Thus, some exotic reference which may still be good for 1) > >may not be as good for 2) since it may be difficult to refine its > >structure and get precise value for S02. The metals would be the > >best, but if you have other materials with "open lattices", e.g., > >fcc, rock salt, etc., with well defined first shell that you can fit > >with the miniumum parameters, they will all work fine. > > > >3) to use as a model for your analysis. > > > >If you analyze an alloy, as in your case, you want to compare EXAFS > >results in your alloys against those in relevant pure compounds. For > >binary alloys, the best reference will be a pure metal, for ternary > >- an intermetallic compound, etc. An oxide would not be so useful > >for modeling. For that reason, people often measure more than one > >reference, as per 1),2) and 3). > > > > > > ------------------------------ > > Message: 3 > Date: Thu, 22 Mar 2007 16:03:34 -0400 > From: "Frenkel, Anatoly" <frenkel(a)bnl.gov> > Subject: Re: [Ifeffit] EXAFS reference materials > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <0D9ED6BC247DA847A3855B6726D6E34421854F(a)exchangemb1.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks, Scott! - Good point. > A. > > ________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Scott Calvin > Sent: Thu 3/22/2007 3:48 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] EXAFS reference materials > > Hi Ruoshuang, > > Following up on Anatoly's excellent post, I would say that I > personally distinguish between a "reference" and a "standard." > > When I talk about a reference, I usually mean something I'm measuring > simultaneously with the sample. The primary purpose is energy > alignment, although it also gives a check on beam quality issues > (e.g. harmonics). For this purpose, I generally use whatever is > convenient and well known, such as a metal foil. Sometimes I'll > measure the reference by itself, particularly if it's a beamline or > edge that is new to me. > > On the other hand, I think of a standard as a known compound that is > similar to my sample. I often work with nanoparticles, so my standard > might be the corresponding bulk material. Or if I'm working with a > doped compound, the standard might be the undoped version. The > standard is measured under the same conditions as the sample...in > fact, that means that I measure the standard with a reference in > place, if that makes sense. :) > > So I use a reference for Anatoly's purpose (1) and a standard for > Anatoly's purposes (2) and (3). > > I hope that's helpful. > > --Scott Calvin > Sarah Lawrence College > > At 03:28 PM 3/22/2007, you wrote: > >Hi Ruoshuang, > > > >I am cc'ing this email to IFEFFIT mailing list. There are several > >reasons (I am listing just a few) you should measure a reference > >sample simultaneously with unknown materials. > > > >1) to align the unknown sample scans prior to merging. If those data > >are noisy, reference sample can be used for the alignment. In > >addition, if you want to compare samples before and after some > >changes that may affect their energy positions (e.g., oxidation, > >reduction, doping, metal-insulator transition, etc.) you want to > >align all of their references to reliably analyze these changes. > > > >For this purpose, it does not matter whether you use a metal or a > >metal oxide or any other standard with the same resonant element. > > > >2) to find S02 value. It is usually the same in most samples which > >have the same resonant element. > > > >For this purpose, what matters the most is whether you can reliably > >find S02 from your standard (and then impose it on your unknown > >sample). Thus, some exotic reference which may still be good for 1) > >may not be as good for 2) since it may be difficult to refine its > >structure and get precise value for S02. The metals would be the > >best, but if you have other materials with "open lattices", e.g., > >fcc, rock salt, etc., with well defined first shell that you can fit > >with the miniumum parameters, they will all work fine. > > > >3) to use as a model for your analysis. > > > >If you analyze an alloy, as in your case, you want to compare EXAFS > >results in your alloys against those in relevant pure compounds. For > >binary alloys, the best reference will be a pure metal, for ternary > >- an intermetallic compound, etc. An oxide would not be so useful > >for modeling. For that reason, people often measure more than one > >reference, as per 1),2) and 3). > > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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Some more questions
by Shantanu Behera 22 Mar '07

22 Mar '07

Dear Ifeffiters I have some more questions. 1. There is a k-weight button in the background removal column in Athena. How's that used and what's its significance? 2. Assume that I have collected data up to 14k, and I see that the signal beyond 12k is very noisy. I want to use the data up to 12k and within that data range pick a F-filter window of 2-10k or 3-10k. How do I go about this? Can I do that with the spline range (in k or E) options in bkg removal (Athena) column? I have gone through Bruce's documentations and have some sense, but not quite clear. Would appreciate your help. Warm regards. Shan -- ||||||||||||||||||||||||||||||||| Shantanu Behera Center for Advanced Materials and Nanotechnology Lehigh University 5, East Packer Avenue Bethlehem, PA 18015, USA

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Re: [Ifeffit] EXAFS reference materials
by Frenkel, Anatoly 22 Mar '07

22 Mar '07

Hi Ruoshuang, I am cc'ing this email to IFEFFIT mailing list. There are several reasons (I am listing just a few) you should measure a reference sample simultaneously with unknown materials. 1) to align the unknown sample scans prior to merging. If those data are noisy, reference sample can be used for the alignment. In addition, if you want to compare samples before and after some changes that may affect their energy positions (e.g., oxidation, reduction, doping, metal-insulator transition, etc.) you want to align all of their references to reliably analyze these changes. For this purpose, it does not matter whether you use a metal or a metal oxide or any other standard with the same resonant element. 2) to find S02 value. It is usually the same in most samples which have the same resonant element. For this purpose, what matters the most is whether you can reliably find S02 from your standard (and then impose it on your unknown sample). Thus, some exotic reference which may still be good for 1) may not be as good for 2) since it may be difficult to refine its structure and get precise value for S02. The metals would be the best, but if you have other materials with "open lattices", e.g., fcc, rock salt, etc., with well defined first shell that you can fit with the miniumum parameters, they will all work fine. 3) to use as a model for your analysis. If you analyze an alloy, as in your case, you want to compare EXAFS results in your alloys against those in relevant pure compounds. For binary alloys, the best reference will be a pure metal, for ternary - an intermetallic compound, etc. An oxide would not be so useful for modeling. For that reason, people often measure more than one reference, as per 1),2) and 3). Hope it helps, Anatoly ________________________________ From: rh2rr(a)virginia.edu [mailto:rh2rr@virginia.edu] Sent: Thu 3/22/2007 2:54 PM To: Frenkel, Anatoly Subject: EXAFS reference materials Dear Dr. Frenkel, I'll do EXAFS on metallic glass but I am not sure about the reference materials. [...] We are trying to study structural relaxation of metallic glass by EXAFS. My samples are Al-TM-RE (TM=Fe,Co,Ni, RE=Gd,Ce,Y). Because Ce and Y are easily oxidized in air, some people suggest use cerium oxide and yttrium oxide as reference materials. My question is: when I do EXAFS measurement and data analysis, is METAL necessary for reference materials, or METAL OXIDE is fine as reference? Your kind help would be greatly appreciated. Ruoshuang Huang ------------------- Ruoshuang Huang Research Associate Materials Science and Engineering University of Virginia Phone: 434-982-0238 Fax: 434-982-5799

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viewing individual Fourier components with Athena
by Richard Mayes 22 Mar '07

22 Mar '07

Hello all. Is it possible to view the individual Fourier components of a Fourier transformed EXAFS spectrum in Athena? If so, can someone please direct me toward the documentation that explains how I can do this. Thanks! -Richard Mayes Barnes Group 450/452 Buehler Hall Dept. of Chemistry Univ. of Tennessee Knoxville, TN 27996

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Re: [Ifeffit] Ifeffit Digest, Vol 49, Issue 11
by Shantanu Behera 20 Mar '07

20 Mar '07

Hi Scott, Matt and Silvio Thank you all for the tips. Regards Shan

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Re: [Ifeffit] N-idp
by Silvio Levy 19 Mar '07

19 Mar '07

Hi Shan, here's a somewhat different way to reach the same conclusion as Scott. >scan during data collection? As I see Nidp = (2/pi)*(deltak * >deltaR), there is no reference to the scan step. But there is, an implicit one. Your deltaR is limited by (among other things) the scan step. If you halve the scan step, you can in principle look twice as far in R space. The problem is, because of the nature of the EXAFS equation, there isn't any signal beyond (say) R=15 AA that's not completely drowned by noise. So there is a point beyond which it's not useful to sample more finely in k space. Of course, below that point, the step size in k space does matter. Silvio

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N-idp
by Shan Behera 19 Mar '07

19 Mar '07

Hi All Greetings. I have a generic question. Does the Number of independent points in the data set depend on the step size (in k or E) of the scan during data collection? As I see Nidp = (2/pi)*(deltak * deltaR), there is no reference to the scan step. In a scan of small step size, I would expect a lot more data points than a scan with larger step size. But, as per the formula I am left with the same number of idp's irrespective of the scan step. Am I missing something? Regards Shan Shantanu Behera http://www.lehigh.edu/~skb204

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Path Parameter Names
by David Weedon 14 Mar '07

14 Mar '07

Hi, Can anybody tell me where I can get a complete list of path parameter names for Artemis and how to use them? Thanks, Dave Dr Dave Weedon Research Fellow - ACeSSS, (Applied Centre for Structural and Synchrotron Studies) Division of Information Technology, Engineering and the Environment, University of South Australia, Mawson Lakes, Adelaide, South Australia, 5095 Phone: +61 8 8302 3096 Email: david.weedon(a)unisa.edu.au

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Problems with atoms
by Dominik Samuelis 09 Mar '07

09 Mar '07

Hi, we are trying to create a feff.inp file for the octahedral core of the monoclinic beta-Ga2O3 structure. If we enter '12' as space group, there are some atoms missing. However, if we use the symbolic 'c 2/m', everything is fine. This occurs with TkAtoms, as well as with the Atoms implementation in Artemis 0.8.007. I haven't tried Webatoms yet, but I assume it'll be the same. The .cif-file for b-Ga2O3 is included. Any clues ? Cheers, dominik First octahedron with 'c 2/m' as space group index: [...] ATOMS * this list contains 16 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ga2 0.00000 0 -1.93032 0.00000 0.14228 2 O3 1.93556 1 0.06926 1.51855 -1.20114 2 O1 1.93740 2 0.06926 -1.51855 -1.20114 2 O1 1.93740 3 1.99294 0.00000 0.22127 2 O2 2.00519 4 0.17363 1.51855 1.40203 2 O2 2.07409 5 0.17363 -1.51855 1.40203 2 O2 2.07409 6 0.00000 3.03710 0.00000 1 Ga2 3.03710 7 [...] END The same, with '12' as space group index. Please note the missing O2 in the first octahedron. There are also some other missing atoms: [...] ATOMS * this list contains 12 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ga2 0.00000 0 -1.93032 0.00000 0.14228 2 O3 1.93556 1 0.06926 1.51855 -1.20114 2 O1 1.93740 2 0.06926 -1.51855 -1.20114 2 O1 1.93740 3 0.17363 1.51855 1.40203 2 O2 2.07409 4 0.17363 -1.51855 1.40203 2 O2 2.07409 5 0.00000 3.03710 0.00000 1 Ga2 3.03710 6 [...] END -- Dipl.-Ing. Dominik Samuelis samuelis(a)pc.rwth-aachen.de Physikalische Chemie I RWTH Aachen University Phone: +49-241-80-94840 Fax: +49-241-80-92128 Landoltweg 2 52056 Aachen Germany data_83645-ICSD _audit_creation_date 107-01-11 _audit_creation_method 'generated by RETRIEVE 2.0' _database_code_ICSD 83645 _chemical_name_systematic 'Gallium oxide - $-beta' _chemical_formula_structural 'Ga2 O3' _chemical_formula_sum 'Ga2 O3' _publ_section_title 'A reinvestigation of $-beta-gallium oxide' loop_ _publ_author_name 'Ahman, J' 'Svensson, G' 'Albertsson, J' _journal_name_full 'Acta Crystallographica C (39,1983-)' _journal_coden_ASTM ACSCEE _journal_volume 52 _journal_year 1996 _journal_page_first 1336 _journal_page_last 1338 _cell_length_a 12.214(3) _cell_length_b 3.0371(9) _cell_length_c 5.7981(9) _cell_angle_alpha 90 _cell_angle_beta 103.83(2) _cell_angle_gamma 90 _cell_volume 208.8 _cell_formula_units_Z 4 _symmetry_space_group_name_H-M 'C 1 2/m 1' _symmetry_Int_Tables_number 12 _symmetry_cell_setting monoclinic loop_ _symmetry_equiv_pos_as_xyz 'x,y,z' 'x,-y,z' '-x,-y,-z' '-x,y,-z' '1/2+x,1/2+y,z' '1/2+x,1/2-y,z' '1/2-x,1/2-y,-z' '1/2-x,1/2+y,-z' loop_ _atom_type_symbol _atom_type_oxidation_number Ga3+ 3.000 O2- -2.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy _atom_site_attached_hydrogens _atom_site_calc_flag Ga1 Ga3+ 4 i 0.09050(2) 0. 0.79460(5) 1. 0 d Ga2 Ga3+ 4 i 0.15866(2) 0.5 0.31402(5) 1. 0 d O1 O2- 4 i 0.1645(2) 0. 0.1098(3) 1. 0 d O2 O2- 4 i 0.1733(2) 0. 0.5632(4) 1. 0 d O3 O2- 4 i -0.0041(2) 0.5 0.2566(3) 1. 0 d _refine_ls_R_factor_all 0.022

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Re: [Ifeffit] Atoms error message
by Bruce Ravel 08 Mar '07

08 Mar '07

On Wednesday 07 March 2007 08:58, Øystein Prytz wrote: > Hello! > > I recently installed Ifeffit on my WinXp machine in order to run the > Atoms program locally. However, when I try to run it, I get the > following error message: > > M:\>atoms > can't open \share\perl\Xray\space_groups.db: No such file or directory > at /PerlA > pp/Xray/Xtal.pm line 116 > BEGIN failed--compilation aborted at atoms line 44. > > which is weird, since there is a directory > > C:\Program Files\Ifeffit\share\perl\Xray\ > > which contains the space_groups.db file. Do you have any suggestions as > to what might be wrong? Hi Øystein, I am CCing my answer to the Ifeffit mailing list. It's not so weird. The icons and Start menu entries that Ifeffit installs do not point directly at the executables. Rather they point at BAT files that set some environment variables, then run the executables. If you want to run any of the programs from the DOS command line, you need to set those environment variables i some other way. When I build my codes, I start by running a BAT file with these lines: SET IFEFFIT_DIR=C:\Program Files\Ifeffit SET PATH=%PATH%;%IFEFFIT_DIR% SET PGPLOT_DIR=%IFEFFIT_DIR%\bin SET PGPLOT_DEV=/GW Without those set, you will not be able to run the codes successfully from the command line. > PS: it seems the WebAtoms page is malfunctioning, I get a "HTTP 500 > Internal server error". Yup. That was discssed on the Ifeffit mailing list starting here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-January/002858.html and continuing as the first few messages in February: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-February/thread.html See the whole thread for the discussion and work-around. It seems as though the simplest work-around is to delete the stuff in the titles box. Fixing this is on my list of things to do, but it hasn't happened yet. 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/exafs/

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