March 2012 - Ifeffit - millenia.cars.aps.anl.gov

running ifeffit under 64-bit windows7
by Sameh Ibrahim Ahmed 10 Mar '12

10 Mar '12

Hi, I have used ARTEMIS to fit the EXAFS of a simple Cu foil with the two diffrent machines, a 32 bit and 64 bit ones, both running widows7, 32 ans 64 bit respectively. The results obtained are slightly different, I have appended the message with these results. the very low value of R-factor produced with the 64bit system is difficult to interpret. the questions are; 1- how to account for these differences? 2- if I to publish something, which measure of the quality should I present? and how can I interpret it? regards Sameh ============================================================ 32bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 53.001967099 Reduced Chi-square = 8.586301900 R-factor = 0.000163791 !!! Measurement uncertainty (k) = 0.000110566 Measurement uncertainty (R) = 0.057163282 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 0.9907500 +/- 0.0312520 (1.0000) enot = 5.6814210 +/- 0.3815760 (0.0000) delr1 = 0.0016460 +/- 0.0033990 (0.0000) ss1 = 0.0099820 +/- 0.0004090 (0.0030) w1 3rd cumulant = 0.0001710 +/- 0.0000340 (0.0000) p1 4th cumulant = 0.0000240 +/- 0.0000070 (0.0000) ============================================================ 64bit windows 7 Independent points = 12.172851562 Number of variables = 6.000000000 Chi-square = 54.036163164 Reduced Chi-square = 8.753841335 R-factor = 0.309664502E-06 !!! Measurement uncertainty (k) = 0.000097377 Measurement uncertainty (R) = 0.050344538 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 1.0029100 +/- 0.0296670 (1.0000) enot = 5.7522760 +/- 0.4614510 (0.0000) delr1 = 0.0024980 +/- 0.0040190 (0.0000) ss1 = 0.0101430 +/- 0.0003790 (0.0030) w1 3rd cumulant = 0.0001780 +/- 0.0000410 (0.0000) p1 4th cumulant = 0.0000260 +/- 0.0000070 (0.0000) ============================================================

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the 64-bit problem is already fixed
by Sameh Ibrahim Ahmed 10 Mar '12

10 Mar '12

Hi, Today, when I lunched artemis, it asked to download some update and I leted it updates automatically. Then, I tried running the already saved *.apj files saved before with the 32-bit system and, surprisingly, I have found them running normally and giving the same results as the old ones ... !!! Surely these updates are essential to run ifeffit properly under 64-bit systems. I suggest to integrate these updates in a newer version of ifeffit and make it available online as soon as possible. thanks Sameh Ibrahim Ahmed assistant professor of crystallography Ain-Shams University Egypt current institute XAFS beamline, ELETTRA Trieste, Italy.

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Re: [Ifeffit] how to built ATOM to obtian FEFF by using DFT model?
by winejar8324 10 Mar '12

10 Mar '12

Hi everyone! can u please help me? I was so glad that Prof. J F W Mosselmans gave me advice about EXAFS analysis of complex solution system in last time. Here i have an another question about how to bulit ATOM to obtain FEFF by using DFT model. When getting a reasonable zinc complex model caculated by Density Functional Theory, i wish use it to clarify the experimental EXAFS data. But i don't know how to bulit ATOM file using this model. Except for the coordinates in the DFT output file, i don't know how to get the other structure information including space, cell parameter etc. ********************************* title=name space=? a=? b=? c=? alpha=? beta=? gamma=? ( How to get these data? ) rmax = 8.0 core = Zn1 atom Zn 0 -0.25 -0.125 Zn1 1 (I can get the atom coordinates from the DFT output file) ....... ******************************* Is there any other methods to create the corresponding ATOM file? Thank you very much. winejar 2012-03-09 发件人： Takahide Yamaguchi 发送时间： 2012-03-08 16:00:36 收件人： ifeffit 抄送：主题： [Ifeffit] what is the reasonable arc-tan for edge jump Dear all, I was so glad that Bruce and Zajac gave me advice about MS path treatment in last time. Thank you very much. Now, I am working on analysis of Cu K edge by using EDG_FIT, following previous papers. I am wondering if someone gave me comment about current problem for me. And my question about XANES analysis is "what the reasonable arc-tan is as a back ground of XANES." In previous some papers, Cu K edge were deconvoluted by assuming arc-tan edge jump function. But I couldn't found the reasonable mention for the shape of arc-tan. For example of Cu(II), one paper (1), which has interest in the metalloproteins active site, the arc-tan were positioned around 8992 eV with 5 eV hwhm approximatly. 　 But in another paper (2), which reported about high valence Cu(III), the arc-tan for Cu(II) complex looks having narrow hwhm at higher positons (around at 8984 eV). (1) J. Phys. Chem. B 2000, 104,10814-10819 (2) JACS 2000, 122, 5775-5787 Are there any reason which can explain these difference? I hope any comment and advice. Takahide

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Re: [Ifeffit] inquire for the EXAFS of the mixture of species
by Carmelo Prestipino 09 Mar '12

09 Mar '12

Hi Here an another routine for itfa (PCA_GUI executable). http://code.google.com/p/prestopronto/ You can use athena to create the input file (a file with one energy column and the rest of column are spectra). All the best Carmelo > > Message: 1 > Date: Thu, 08 Mar 2012 17:00:15 +0900 > From: Takahide Yamaguchi <11nm023s(a)mcs.ibaraki.ac.jp> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] what is the reasonable arc-tan for edge jump > Message-ID: <4F58670F.5020600(a)mcs.ibaraki.ac.jp> > Content-Type: text/plain; charset="iso-2022-jp" > Message: 2 > Date: Thu, 8 Mar 2012 08:13:08 +0000 > From: <fred.mosselmans(a)diamond.ac.uk> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] inquire for the EXAFS of the mixture of species > Message-ID: > <CF65047C5B0562499EAFF9FBBC542D6426591B88(a)EXCHMBX01.fed.cclrc.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > > Hi Winejia, > > I think your problem may well be harder than an LC approach as suggest by Darius will solve, as it is possible (probable) that the reaction intermediates are not known structurally so you don't have model spectrum of them. Complex solution equilibrium mixtures are about as tough as it gets for soluble EXAFS problems. The methods that tend to work are Principal component analysis (which is available in sixpack and Athena) > This will probably tell you how many species you have in your reactant spectra, and will also tell you by target transformation if a spectrum of a model you have is one of those species. However to identify the unknowns you may need to use a more advanced approach like iterative transformation factor analysis (ITFA) . there is an itfa package available from the RoBL esrf beamline http://www.esrf.eu/UsersAndScience/Experiments/CRG/BM20/Software/ > This should be able to give you the spectra of the separate solution spectra which then you can analyse with Artemis. > > The key things you need to have is more spectra representing in different ratios of the solution species than the total no of solution species, otherwise your problem is underdetermined, preferably quite a lot more. > > Regards > Fred > > Prof. J F W Mosselmans > Principal Beamline Scientist I18 > Diamond Light Source > Diamond House > Harwell Campus > Didcot > Oxon > OX11 ODE > UK > > > > > > -- > > This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. > > Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. > > Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. > > Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > > > > > >

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Crystallographic data for V(CO)6
by Ismael Graff 08 Mar '12

08 Mar '12

Dear XAS fellows: I have to fit EXAFS data of a nanoparticle colloidal suspension. TEM and NMR data indicate that I have nanoparticles of V(CO)_6 (vanadium hexacarbonyl). The system is orthorhombic, space group Pnma (Nr. 62), and I know the nominal values for the lattice parameters. However, I need the different atomic positions/coordinates to enter in ATOMS. Usually I get such information from a CIF (Crystallographic Information File) card. But in this case, I didn´t find it in the open data banks. Is anyone out there that could help me? Cheers, Ismael. PS: A similar structure/material would also help (like Mo(CO)_6)! -- ************************************ * Ismael Leandro Graff * * * * Universidade Federal do Paraná * * Departamento de Física, CP 19044 * * 81531-990, Curitiba, Brazil. * * Tel (office): +55 41 3361 3278 * * Tel (Lab): +55 41 3361 3427 * * Fax: +55 41 3361 3418 * * http://fisica.ufpr.br/graff * ************************************

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Re: [Ifeffit] inquire for the EXAFS of the mixture of species
by fred.mosselmans＠diamond.ac.uk 08 Mar '12

08 Mar '12

Hi Winejia, I think your problem may well be harder than an LC approach as suggest by Darius will solve, as it is possible (probable) that the reaction intermediates are not known structurally so you don't have model spectrum of them. Complex solution equilibrium mixtures are about as tough as it gets for soluble EXAFS problems. The methods that tend to work are Principal component analysis (which is available in sixpack and Athena) This will probably tell you how many species you have in your reactant spectra, and will also tell you by target transformation if a spectrum of a model you have is one of those species. However to identify the unknowns you may need to use a more advanced approach like iterative transformation factor analysis (ITFA) . there is an itfa package available from the RoBL esrf beamline http://www.esrf.eu/UsersAndScience/Experiments/CRG/BM20/Software/ This should be able to give you the spectra of the separate solution spectra which then you can analyse with Artemis. The key things you need to have is more spectra representing in different ratios of the solution species than the total no of solution species, otherwise your problem is underdetermined, preferably quite a lot more. Regards Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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what is the reasonable arc-tan for edge jump
by Takahide Yamaguchi 08 Mar '12

08 Mar '12

Dear all, I was so glad that Bruce and Zajac gave me advice about MS path treatment in last time. Thank you very much. Now, I am working on analysis of Cu K edge by using EDG_FIT, following previous papers. I am wondering if someone gave me comment about current problem for me. And my question about XANES analysis is "what the reasonable arc-tan is as a back ground of XANES." In previous some papers, Cu K edge were deconvoluted by assuming arc-tan edge jump function. But I couldn't found the reasonable mention for the shape of arc-tan. For example of Cu(II), one paper (1), which has interest in the metalloproteins active site, the arc-tan were positioned around 8992 eV with 5 eV hwhm approximatly. 　 But in another paper (2), which reported about high valence Cu(III), the arc-tan for Cu(II) complex looks having narrow hwhm at higher positons (around at 8984 eV). (1) /J. Phys. Chem./ B 2000, 104,10814-10819 (2) /JACS/ 2000, 122, 5775-5787 Are there any reason which can explain these difference? I hope any comment and advice. Takahide

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what is the reasonable arc-tan for edge jump
by Takahide Yamaguchi 08 Mar '12

08 Mar '12

Dear all, I was so glad that Bruce and Zajac gave me advice about MS path treatment in last time. Thank you very much. Now, I am working on analysis of Cu K edge by using EDG_FIT, following previous papers. I am wondering if someone gave me comment about current problem for me. And my question about XANES analysis is "what the reasonable arc-tan is as a back ground of XANES." In previous some papers, Cu K edge were deconvoluted by assuming arc-tan edge jump function. But I couldn't found the reasonable mention for the shape of arc-tan. For example of Cu(II), one paper (1), which has interest in the metalloproteins active site, the arc-tan were positioned around 8992 eV with 5 eV hwhm approximatly. 　 But in another paper (2), which reported about high valence Cu(III), the arc-tan for Cu(II) complex looks having narrow hwhm at higher positons (around at 8984 eV). (1) /J. Phys. Chem./ B 2000, 104,10814-10819 (2) /JACS/ 2000, 122, 5775-5787 Are there any reason which can explain these difference? I hope any comment and advice. Takahide

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Re: [Ifeffit] inquire for the EXAFS of the mixture of species
by winejar8324 08 Mar '12

08 Mar '12

Hello everyone, I have a puzzle during analyzing of my EXAFS data. can someone please help me: I have a set of EXAFS data on solution sample at different pH. I wish to extract the structure information from the EXAFS region to accont for the reaction machanism. However, there are several configurations(as indicated by XANES) and species(as indicated by thermodynamics caculation) in solution due to the metal-Ligand complex balance. How can i obtain the structure information about this complex system from the EXAFS data? Thanks, winejia

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appropriatness of feff model when central atom is not "embedded" (or only 1 layer embedded)
by Andrea L Foster 07 Mar '12

07 Mar '12

Hello All, can someone please help with this: (1) feff requires that the adsorbing atom be "embedded" (that is, surrounded by) other atoms in order to calculate potentials correctly, but how deeply does the atom need to be embedded? For example, if I construct a model of an adsorbate on a mineral surface, where that adsorbate has a full complement of 1st shell coordinating OH, O, and H2O groups as appropriate, but if I do not include all the uncoordinated f water atoms that would be nearby (so that I essentially have a surface in vacuum), will the potentials for my central atom be calculated correctly (or correctly enough for use in IFEFFIT)? a more specific example: the AsO4 tetrahedron bonded to the goethite surface, which is made of octahedrally-coordinated iron. The arsenate bonds to the goethite by sharing 1 edge of the tetrahedron with the apices of 2 adjacent Fe octahedra. a related question that comes to mind: if I just wanted to see the signal from the 2 adjacent Fe atoms, could I create a perfectly "useable" FEFF model (for IFEFFIT) by limiting my calculations to the small cluster of 1 arsenate tetrahedron and 2 Fe octahedra? thanks, andrea ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andrea L. Foster, Ph.D. U.S.G.S. WMESC 345 Middlfield Rd., MS 901 Menlo Park, CA 94025 T: 650-329-5437 F: 650-329-5491

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