- 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

1 0

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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Re: [Ifeffit] Ifeffit on Windows Vista
by Bruce Ravel 08 Mar '07

08 Mar '07

On Monday 05 March 2007 12:28, Francesc Sepulcre wrote: > Dear Bruce, > > Is just to know if is possible to install ifeffit (Artemis, Athena,...) on > Windows Vista. If yes, please, let me know how to do this, because Im > trying to install version 1.2.9 but doesnt works. > > Please, excuse me if this is not the correct way to ask about this problem. Hi Francesc, I am forwarding my response to the Ifeffit mailing list (which is the best forum for questions of this sort.) To join, go to: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I am not in a position to comment. I don't have a Vista machine of my own. Nor does Matt, as far as I know. So we certainly have not yet tested the software on Vista. Is anyone on the list using Vista yet? Any hints for Francesc about getting the installer to work? Francesc, perhaps if you could give us some more information about how it fails -- screenshots, transcriptions of error messages, something that gives a clue as to what the problem is -- someone may be able to make a useful suggestion. 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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Using parameters in Artemis
by David Weedon 08 Mar '07

08 Mar '07

Hi All, I am new to Artemis so these questions are very basic - but never-the-less confusing to me. I learnt a lot by using Scott Calvin's ZnO example but ran into trouble when I got to Fit 3. In the Journal entry we are asked to click "Guess, Def, Set", then click "new" and enter DelScale = 0. After I hit the "Guess" button I cannot find the parameter "dr" on the list. Am I correct in assuming that "dr" is some kind of reserved parameter name that should not be used in equations? Which leads me to ask several questions (probably silly questions)??? QUESTIONS: 1 I presume all the parameters like "amp, deg, delr, ss2 and enot" relate to the obvious parameters in the EXAFS eqn. Assigning numerical values makes sense but what is going on when we create mathematical functions?? Is there a list of functions that we can model here? Is it somewhere in the software? 2 What are we doing when we make our own parameters? Are they a mixture of parameters from the EXAFS equation that we wish to evaluate in the fit, and if so why? 3 The parameter "amp" is defined as the relative importance of the path and is assigned a value eg. 100 or 30, is this some form of percentage of this path to the first (major) path? 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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Re: [Ifeffit] Ifeffit on Windows Vista
by Bruce Ravel 07 Mar '07

07 Mar '07

On Monday 05 March 2007 12:28, Francesc Sepulcre wrote: > Dear Bruce, > > Is just to know if is possible to install ifeffit (Artemis, Athena,...) on > Windows Vista. If yes, please, let me know how to do this, because Im > trying to install version 1.2.9 but doesnt works. > > Please, excuse me if this is not the correct way to ask about this problem. Hi Francesc, I am forwarding my response to the Ifeffit mailing list (which is the best forum for questions of this sort.) To join, go to: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I am not in a position to comment. I don't have a Vista machine of my own. Nor does Matt, as far as I know. So we certainly have not yet tested the software on Vista. Is anyone on the list using Vista yet? Any hints for Francesc about getting the installer to work? Francesc, perhaps if you could give us some more information about how it fails -- screenshots, transcriptions of error messages, something that gives a clue as to what the problem is -- someone may be able to make a useful suggestion. 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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EuL3-edge-XANES (from one of Bruce's courses)
by Joel Brugger 05 Mar '07

05 Mar '07

Hi, Looking at the notes from one of Bruce Ravel¹s 2000 EXAFS courses, I noticed that you used EuTiO3 as an example. My understanding is that this is a Eu++ compound; yet the resonance peak in the XANES spectrum occurs spot on where I would expect Eu+++ to be, around 6982 eV. As the table below shows (from Rakovan, J., Newville, M., and Sutton, S. (2001) Evidence of heterovalent europium in zoned Llallagua apatite using wavelength dispersive XANES. American Mineralogist, 86, 697-700), the location of the Eu++ resonance peak does not seem to vary much from compound to compound. I¹m also joining a figure showing the XANES L3 Eu spectra of EuTiO3 together with other compounds. The Std spectra shown for comparison are for mixtures of Eu2O3, W, and WO3 cooked at 1200C in an inert atmosphere, and prepared so that sample StdB has 20% Eu++, and sample stdC 50% Eu++ (the final product is a mixture of EuWO4 and Eu2(WO4)2). The growing peak at 6974 corresponds to Eu++. Any thought about this discrepancy? Where are the data published? Thanks in advance for you help, All the best as ever, JOEL Ps I cc¹d to Bruce Ravel¹s email address as I don¹t think that the list takes attachments or embedded figures... Rakovan, J., Newville, M., and Sutton, S. (2001) Evidence of heterovalent europium in zoned Llallagua apatite using wavelength dispersive XANES. American Mineralogist, 86, 697-700.

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Re: [Ifeffit] Fwd: Re: why ss_2 is negative?
by hw26＠njit.edu 04 Mar '07

04 Mar '07

Dear all, Thanks million for your great advice for my EXAFS modeling! It helps me understand more about EXAFS and I really appreciate it! But I still have some questions to consult you. I took your suggestion and have the amp and e0 the same for each path. In addition, I fixed the number axial U-O as 2. For the equatorial ligand, since the total coordination number is between 4 and 6, I guess the number of U-F as 2(that is n1), and def the number of U-O as (5-n1)(that is n2). Then I did the fit. The result showed the ss_2 is still negative. So I set the ss_2 as 0.003, did the fitting again. I don't know if it is ok to fix the ss_2=0.003. It seems the dr_1 change a lot. In addition, I tried to do fitting in Kw=2 in stead of Kw=3. At this time, the ss_2 is positive, and from my understanding, it seems the modeling is more resonable for dr_1 and dr_2, but the R-factor is 0.023, a little bit larger than 0.02. How can I decide which one I should use, the Kw=3 or Kw=2? Is there anything I can do to improve the modeling? The attached is my modeling. I am sorry to put attachment in the email that my bother you. Best regards! Hao > Hao, > > A few more comments: > > 1. It is well advised for anyone starting to look at uranyl compounds > with XAS to read Shelly's various publications on that topic. > Geochem. Cosmo. Acta, 66(22) 3875-3891, (2002) is particularly > useful. Google scholar can help you locate more of her papers. > > 2. I am the first to admit that Artemis and Ifeffit are difficult > tools for the beginning exafs practitioner. These tools try to > provide a usable face to a difficult problem. Ifeffit was written > with enough flexibility and power to allow the so-called experts > to do the analysis they want to do. That means that Artemis has > enough freedom to allow the unsuspecting user to do ill-advised > things. > > You really need to think about what each of the parameters means. > For example, just because Artemis allows you to float e0 freely > for each path does not mean that doing so is a good idea. There > are situations where it is a very good idea to have more than one > e0 parameter in your fit, but I suspect that yours is not one of > them. Consequently, you should consider constraining all your > paths to have the same e0. > > What do I mean by "constrain"? Well, on the Guess,Def,Set page, > you can define a single e0 parameter as a guess parameter, then > use that parameter on each of the path pages. In that way, you > will have one floating parameter in your fit that is used to > describe the e0 of all your parameters. > > Similarly, you should think hard about the numbers of each kind of > path. A uranyl moiety is unlikely to have more or less than 2 > uranyl ligands. The uranyl bond is very strong, consequently it > is energetically unfavorable in a uranyl for those two bonds to be > over- or under-filled. Consequently, you can consider setting the > number of yl oxygens to 2. Furthermore, the equatorial plane is > likely to have between 4 and 6 oxygens, so you should think of > ways to constrain the total number of equatorial oxygens to be > something reasonable. Since the coordination number is highly > correlated with sigma^2 in a statistical sense, thinking well > about coordination number should help address your original > question. > > 3. Scott has made a very nice Artemis tutorial which can be found at > http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib > It comes in the form of a series of Artemis projects. Newcomers > benefit by working through his tutorial before trying to analyse > their own data with Artemis. > > 4. The Ifeffit web site, my home page, and especialy http://xafs.org > are all filled with useful information for the XAS novice. If you > haven't already looked through the resources on those sites, you > really should budget some time to do so. > > > HTH, > 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/ > > _______________________________________________ > 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] EXAFS analysis with FEFF
by Bruce Ravel 27 Feb '07

27 Feb '07

Hi Gemma, I am not sure that I have the whole answer for you. I too have had trouble at times getting feff8 to run with hydrogen atoms in the cluster. I am CCing my response to the mailing lists for Feff and Ifeffit in hopes that someone else might have some more wisdom for you. The feff.inp file you sent me is appended to the end of this email, in case any of the brains on the mailing lists need to see it. On Tuesday 27 February 2007 11:27, Gemma GUILERA wrote: > I am currently running FEFF8.2 for one of my systems which include some H > atoms (as hydrides). These are actually very important in the structure and > I want to consider them in the run. > For this I used the FOLP function in POT with an overlapping value of 0.8 > for H as suggested in the manual. Also, since I think that the AFOLP card > gets deactivated, I also added these cards for the rest of the potentials > keeping them at 1.15. > I obviously do something completely wrong because the program stops and > appears an error message of the type: > > FOLP for POTENTIAL type 0 is too big. > Reduce overlap using FOLP and rerun. > > I do not understand what I need to do, because the potential 0 is not the > one I am modifying with respect to the default values. > I would really appreciate if you could have a look at the feff.inp file and > tell me what did I do wrongly...and sorry for wasting your time. Well, my understanding is that Feff's various overlapping methods do have effects that are not restricted to the ipots that you are explicitly modifying. That is, if you restrain the size of one muffin tin, other muffin tins can get a bit bigger or smaller to compensate. It depends on the geometry and how the atom you are modifying is represented in the cluster. My first thought is that you need to play around with the FOLP value for the absorber. Try smaller values to see if you can get Feff to run to completion. My second thought is to abandon the FOLP keywords and try using AFOLP. Another thought is that you may need to use a larger cluster. Some atom types -- B for example -- have few representatives in your cluster and so their muffin tin radii might be improperly constrained. Does anyone else have any good suggestions for Gemma? B TITLE FeBH6Fe complex EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * r_scf [ l_scf n_scf ca ] SCF 2.90160 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 FOLP 0 1.15 FOLP 1 0.8 !Use 0.8 muffin-tin radii overlapping factor for H FOLP 2 1.15 FOLP 3 1.15 FOLP 4 1.15 FOLP 5 1.15 EXAFS RPATH 6 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 2.90160 0 * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 26 Fe -1 -1 0 1 1 H -1 -1 6 2 5 B -1 -1 1 3 15 P -1 -1 6 4 6 C -1 -1 46 5 26 Fe -1 -1 2 ATOMS 0.00000 0.00000 0.00000 0 Fe1 0.00000 -0.71680 -1.08741 -0.20797 1 H42 1.31891 -1.33000 0.40717 0.04190 1 H41 1.39156 -0.20933 -0.03121 -1.56977 1 H40 1.58398 -1.50973 -0.47766 -1.07196 2 B1 1.91221 0.07929 -0.26849 2.16349 3 P3 2.18152 0.78129 2.03650 0.10939 3 P2 2.18397 2.03623 -0.76920 -0.20440 3 P1 2.18625 -2.30265 0.13209 -1.93594 1 H42 3.01123 -2.81012 -0.92412 -0.57414 1 H40 3.01338 -1.68946 -1.36249 -2.18581 1 H41 3.08033 3.15055 -0.21476 1.16774 4 C22 3.36686 0.19242 -2.02477 2.69082 4 C25 3.37301 2.87884 -0.31857 -1.75462 4 C13 3.38643 1.52559 0.58481 2.96848 4 C24 3.38840 2.32803 2.20201 1.14003 4 C49 3.40121 -0.35734 3.30346 0.81773 4 C37 3.42188 1.28771 2.89227 -1.43362 4 C43 3.47544 2.68114 0.97735 2.02827 4 C23 3.50109 -1.29194 0.30124 3.24246 4 C31 3.50334 2.42741 -2.57443 -0.17395 4 C1 3.54263 1.08472 2.33572 -2.68697 4 C48 3.72183 -2.31005 1.13130 2.75352 4 C36 3.76803 -3.01946 -0.95533 -2.14391 5 Fe1 3.82441 -0.91239 -2.83347 2.42108 4 C26 3.83701 1.44841 -3.56032 -0.07829 4 C3 3.84446 2.35340 -0.84952 -2.93358 4 C15 3.85565 -1.36594 3.79736 -0.00896 4 C38 4.03557 -0.32880 3.71800 2.14367 4 C42 4.30429 1.32048 -2.62656 3.24943 4 C30 4.38193 3.96885 0.55229 -1.84177 4 C21 4.41009 1.89033 4.15594 -1.34798 4 C44 4.76049 -1.27608 0.01031 4.60350 4 C32 4.77710 3.77855 -2.96794 -0.18652 4 C11 4.80842 3.85573 1.40280 2.91662 4 C50 5.03400 -4.10418 -3.29104 0.54306 4 C48 5.28868 -3.80075 -2.99182 -2.25330 3 P2 5.33611 -3.09875 -0.68684 -4.30740 3 P3 5.35048 -2.10707 1.87815 -4.56499 4 C26 5.36715 -0.70940 -2.08663 -4.89743 4 C36 5.37049 -5.05569 -0.18613 -1.93951 3 P1 5.41815 -5.37286 -0.10580 0.78966 4 C15 5.43161 -1.65351 -4.75268 -2.13495 4 C38 5.46627 -4.46787 2.60499 -2.06562 4 C3 5.56908 -1.72752 -1.25656 -5.38637 4 C31 5.79450 -4.30717 -3.84760 -0.71029 4 C43 5.81895 -2.66211 -4.25879 -2.96164 4 C37 5.83056 -3.21187 1.06944 -4.83473 4 C25 5.90207 -5.89830 -0.63676 -0.38929 4 C13 5.94533 END -- 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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Re: [Ifeffit] Ifeffit Digest, Vol 48, Issue 14
by Roque, J (Josep) 27 Feb '07

27 Feb '07

The statement "Feff 6.02L doesn't work" is false also in Josep's computer. It works correctly.. Thanks. J. -----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: 26 February 2007 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 48, 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: E0 for bulk crystals and nanoparticles (Leandro Araujo) 2. Fwd: Re: E0 for bulk crystals and nanoparticles (Bruce Ravel) 3. FEFF 6L.02 (Roque, J (Josep)) 4. Re: FEFF 6L.02 (Bruce Ravel) 5. Re: FEFF 6L.02 (Anatoly Frenkel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 26 Feb 2007 14:52:10 +1100 From: "Leandro Araujo" <leandrolangie(a)gmail.com> Subject: Re: [Ifeffit] E0 for bulk crystals and nanoparticles To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <5f59b3760702251952y535fae5axb9fd91d63789564f(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anatoly and Scott, thanks for the quick and valuable answers! Sorry I didn't specify the system in more detail; this is a point that Matt always stresses when replying messages in this list (i.e., there is no "one fits all" answer, so a detailed description of the system is needed) and by now I should have assimilated it already... Anyway, I see no changes whatsoever in the XANES spectra of the T-dep measurements, so I think it will be worth the try. Since I'm dealing with Ge NCs buried about 1micron deep into a SiO2 matrix, I reckon effects like hydrogen chemisorption, charge exchange with support, ligand desorption and oxidation will not take place, specially at such low T's. Thanks once more for the help, Leandro ------------------------------ Message: 2 Date: Mon, 26 Feb 2007 09:04:16 -0600 From: Bruce Ravel <bravel(a)anl.gov> Subject: [Ifeffit] Fwd: Re: E0 for bulk crystals and nanoparticles To: XAFS Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200702260904.16718.bravel(a)anl.gov> Content-Type: Text/Plain; charset="iso-8859-15" On Sunday 25 February 2007 20:44, Leandro Araujo wrote: > I don't know if it is just me, but in my short time working with EXAFS > I got the strong impression that it is very easy to fall into the > temptation of sophistry to get to the "expected" results from a fit. That is very well put. I hope everyone reading the list today appreciates your wise words. > In this respect, I consider the mailing list an invaluable resource to > help overcoming such a temptation. That's great -- thanks. Kind words go a long way with those of us who invest time on the mailing list. As for your question -- I really liked Scott's point about looking at the XANES as a clue about whether e0 should be changing in the EXAFS. Use all the information (spectroscopic or otherwise) available to you. 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/ ------------------------------ Message: 3 Date: Mon, 26 Feb 2007 16:29:49 -0000 From: "Roque, J $Josep$" <josep.roque(a)diamond.ac.uk> Subject: [Ifeffit] FEFF 6L.02 To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <DC69C90BD4A39249BF59689B2E06427803B04E42(a)exchange33.fed.cclrc.ac.uk> Content-Type: text/plain; charset="us-ascii" I am trying to run FEFF 6L.02 from version of IFEFFIT 1.2.9 on a Windows platform but it doesn't seems to work.. How can I fix this problem?? Cheers Dr Josep Roque Post Doctoral Research Associate: Microfocus Spectroscopy (I18) Diamond Light Source Ltd Diamond House Chilton Didcot Oxfordshire OX11 0DE Tel: 01235 778735 Email: josep.roque(a)diamond.ac.uk

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FEFF 6L.02
by Roque, J (Josep) 26 Feb '07

26 Feb '07

I am trying to run FEFF 6L.02 from version of IFEFFIT 1.2.9 on a Windows platform but it doesn't seems to work.. How can I fix this problem?? Cheers Dr Josep Roque Post Doctoral Research Associate: Microfocus Spectroscopy (I18) Diamond Light Source Ltd Diamond House Chilton Didcot Oxfordshire OX11 0DE Tel: 01235 778735 Email: josep.roque(a)diamond.ac.uk

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Fwd: Re: E0 for bulk crystals and nanoparticles
by Bruce Ravel 26 Feb '07

26 Feb '07

On Sunday 25 February 2007 20:44, Leandro Araujo wrote: > I don't know if it is just me, but in my short time working with > EXAFS I got the strong impression that it is very easy to fall into > the temptation of sophistry to get to the "expected" results from a > fit. That is very well put. I hope everyone reading the list today appreciates your wise words. > In this respect, I consider the mailing list an invaluable resource > to help overcoming such a temptation. That's great -- thanks. Kind words go a long way with those of us who invest time on the mailing list. As for your question -- I really liked Scott's point about looking at the XANES as a clue about whether e0 should be changing in the EXAFS. Use all the information (spectroscopic or otherwise) available to you. 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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E0 for bulk crystals and nanoparticles
by Leandro Langie Araujo 26 Feb '07

26 Feb '07

Dear all, could you please let me know your thoughts on this question that has been consuming much of my time lately? It goes like this: When we perform first shell analysis of elemental crystals and nanoparticles (like bulk Ge and Ge NPs, or bulk Pt and Pt NPs, for example), should both bulk and NP samples have the same E0 shift relative to the theory (or, fit-wise, the same deltaE0 when fitting in Artemis)? And, even more important to know, why so? I've been reading some papers and I can find people who do set the NPs deltaE0 to be the same as the crystalline foil as well as people who report different deltaE0s for NPs relative to the foil. This confuses me because by setting (or not) deltaE0 we directly change the correlated variables, delR and C3. Intuitively I would think that for Ge, in particular, NPs could have a different deltaE0 from the bulk since they present smaller band gaps and different electronic structure, causing differences in the occupied/unoccupied states (that's why they show some PL while the bulk doesn't). Would you say this is reasonable? I have used Athena to calibrate (maximum of energy derivative = atomic value), align edges, background subtract (with same parameters) and Fourier transform (with same parameters) both bulk and NP spectra (at the same temperature, from same run/measurement conditions), which I then fit in Artemis to the FEFF8-generated crystalline Ge standard. And I do see a significant change in the odd cumulants (delR and C3) when I let deltaE0 run free or when I set it to the bulk value (the difference is between 1 and 2 eV). Would you say this is physically reasonable or more likely to be a fit artifact? Thanks, Leandro

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Ubuntu binary package problem
by M. Rovezzi 25 Feb '07

25 Feb '07

Dear all, I'm sending to the list a question mainly directed to Carlo, anyway. I've installed the ifeffit/horae packages on a Ubuntu 6.10 "Edgy Eft" distribution from Carlo repositories. Here the problems: mauro@stalker3:~$ ifeffit Killed mauro@stalker3:~$ athena Can't load '/usr/lib/perl5/auto/Ifeffit/Ifeffit.so' for module Ifeffit: /usr/lib/perl5/auto/Ifeffit/Ifeffit.so: cannot map zero-fill pages: Cannot allocate memory at /usr/lib/perl/5.8/DynaLoader.pm line 225. at /usr/bin/athena line 66 Compilation failed in require at /usr/bin/athena line 66. BEGIN failed--compilation aborted at /usr/bin/athena line 70. mauro@stalker3:~$ artemis Can't load '/usr/lib/perl5/auto/Ifeffit/Ifeffit.so' for module Ifeffit: /usr/lib/perl5/auto/Ifeffit/Ifeffit.so: cannot map zero-fill pages: Cannot allocate memory at /usr/lib/perl/5.8/DynaLoader.pm line 225. at /usr/bin/artemis line 52 Compilation failed in require at /usr/bin/artemis line 52. BEGIN failed--compilation aborted at /usr/bin/artemis line 56. It seems related to memory allocation and I have to say that I'm having these problems only on low memory machines (192 Mb of RAM). Anyway I don't understand why Ifeffit is killing itself and how to obtain more information on what is happening with the libraries... well, I wait for your interesting answers. Mauro -- Mauro Rovezzi <mauro.rovezzi(a)esrf.fr> PhD Student - GILDA BM08 at ESRF (Grenoble, FR) ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

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Fwd: Re: why ss_2 is negative?
by Bruce Ravel 24 Feb '07

24 Feb '07

On Friday 23 February 2007 21:41, hw26(a)njit.edu wrote: > Yes, I am modeling the uranyl ligand and two equatorial ligands, one of > which is hypothesized as U-F (from BF4 anion), and the other as U-O (from > hydration),because in the uranyl nitrate standard sloution(without > MOEMIMBF4), there is only one peak that represents the U-O equatorial > ligand, but with the MOEMIMBF4, the equatorial peak is split to two peaks. > So I guess the other equatorial U-F formed. Hao, A few more comments: 1. It is well advised for anyone starting to look at uranyl compounds with XAS to read Shelly's various publications on that topic. Geochem. Cosmo. Acta, 66(22) 3875-3891, (2002) is particularly useful. Google scholar can help you locate more of her papers. 2. I am the first to admit that Artemis and Ifeffit are difficult tools for the beginning exafs practitioner. These tools try to provide a usable face to a difficult problem. Ifeffit was written with enough flexibility and power to allow the so-called experts to do the analysis they want to do. That means that Artemis has enough freedom to allow the unsuspecting user to do ill-advised things. You really need to think about what each of the parameters means. For example, just because Artemis allows you to float e0 freely for each path does not mean that doing so is a good idea. There are situations where it is a very good idea to have more than one e0 parameter in your fit, but I suspect that yours is not one of them. Consequently, you should consider constraining all your paths to have the same e0. What do I mean by "constrain"? Well, on the Guess,Def,Set page, you can define a single e0 parameter as a guess parameter, then use that parameter on each of the path pages. In that way, you will have one floating parameter in your fit that is used to describe the e0 of all your parameters. Similarly, you should think hard about the numbers of each kind of path. A uranyl moiety is unlikely to have more or less than 2 uranyl ligands. The uranyl bond is very strong, consequently it is energetically unfavorable in a uranyl for those two bonds to be over- or under-filled. Consequently, you can consider setting the number of yl oxygens to 2. Furthermore, the equatorial plane is likely to have between 4 and 6 oxygens, so you should think of ways to constrain the total number of equatorial oxygens to be something reasonable. Since the coordination number is highly correlated with sigma^2 in a statistical sense, thinking well about coordination number should help address your original question. 3. Scott has made a very nice Artemis tutorial which can be found at http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib It comes in the form of a series of Artemis projects. Newcomers benefit by working through his tutorial before trying to analyse their own data with Artemis. 4. The Ifeffit web site, my home page, and especialy http://xafs.org are all filled with useful information for the XAS novice. If you haven't already looked through the resources on those sites, you really should budget some time to do so. HTH, 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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why ss_2 is negative?
by hw26＠njit.edu 24 Feb '07

24 Feb '07

Dear all, I am doing model fitting using Artemis. My sample is uranium solution with an ionic liquid, 1-methoxyethyl-3-methyl imidazolium tetrafluoroborate (MOEMIMBF4). The Fitting seems ok except that the ss_2 is negative. I don't know how can I fix this problem. Can you get a chance to take a look? My fitting is simple, only three single scattering pathes which were produced by Six Pack. The fitting file is attached. I really appreciate it if you could take a look and give some advice! Best regards! Hao

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Re: [Ifeffit] Hephaestus
by Matt Newville 23 Feb '07

23 Feb '07

Hi Carloine, On 2/21/07, Caroline Peacock <clp(a)noc.soton.ac.uk> wrote: > Have just installed the Ifeffit package > (feffit-1.2.9-Mac10.4_horae64pre_pkg.dmg) on my Intel Mac > (OS X 10.4.8)... Upon double clicking Hephaestus (as instructed in the > readme) i am prompted to choose either X11 graphics or Aquaterm - either way > X11 opens and then nothing...Is this a UNIX based program - from the > screenshots i guessed it wasn't? > > Any ideas why it isn't working? I'm copying this to the Ifeffit mailing list, as I think someone else may have a better answer than I can give. Hephaestus does require X11, but I think the problem is that the Ifeffit-1.2.9 disk installers are all PPC only. That is, I think no one has made an installer for Intel Mac. --Matt

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(no subject)
by Ruwan Wijesundera 15 Feb '07

15 Feb '07

Dear Bruce We have used Athena and Artemis software to analyses the EXAFS. When we do the analysis, we used different S2o for each path for fitting of Cu2O data. I succeeded to obtain good fitting by this way. Documents related to percent EXAFS analysis have been mentioned S2o is one value for all paths. What I want to know is our fittings are correct or not. I am looking forward early response. About 10 years ago we had being using another program made by Tokyo University in Japan. In this program, the refined parameters also included S2oj and Nj to the each cells Thanks Ruwn

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