January 2006 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

12 22

Artemis- Loading up error
by Zohair Hussain 17 Apr '06

17 Apr '06

Hi! I recently had to install ifeffit software package on our network computer. The first time I ran Artemis I was asked to update which I did. However, Artemis did not start after that. The error message that I got is shown in the attached figures artemis-error1a and 1b. Please note that only Artemis doesn't work, all the other softwares (Athena, Hephaestus, TKAtoms etc.) work fine. I tried running the .bat file from the Ifeffit folder but that didn't work either. I also tried to run the artemis.exe file and received the error shown in figure "artemis-error2". Later I unisntalled and re-installed Ifeffit and chose not to do the updates and Artemis is now running fine. I was wondering if anyone has any idea why this is so or if there is a way around installing the updates and still being able to use Artemis??? Thanks, Zohair

4 5

FEFF8 vrs FEFF6
by Kelly, Shelly D. 06 Feb '06

06 Feb '06

Hello Ifeffit friends, It is my understanding that FEFF6 or equivalently FEFF7 are considered the standard for Extended X-ray Absorption Fine Structure Analysis. In my experience, FEFF8 is a dangerous tool for EXAFS analysis as it has the ability to produce results that differ significantly from FEFF6 or FEFF7. In the review of EXAFS manuscripts where FEFF8 is the tool of choice, what parameters should be reported to give the reader some confidence that the authors have not tweaked the code to cover-up some errors in the model(s). A Big Thanks Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439

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RESTRAINTS IN IFEFFIT
by Renato Canha Ambrosio 25 Jan '06

25 Jan '06

Hi Folks, this is my first message on the list. Perhaps someone could help me. The subject is how to include restraints on exafs refinement. There is just scanty information about this on the ifeffit reference manual. I'm trying to refine the exafs data of a rhombohedral perovskite. The main MS contributions to the signal at about 3.5 A (non phase correct) arise from M O M interactions being M the absorber . We have a significant SS path, a two-legged and a three-legged path. The structural parameters of these three terms are correlated since all refers to the same A-B-C triangle and the A-B and B-C distances must be that found for M-O1 nearest-neighbor configurations. For these reasons we constrained the photo electron path length for three-legged to the M-O nearest-neighbor distance:R(three-leg = 2*RM-O). I'm trying to intoroduce the quantity defined as delta = R(three-legged)-R(two-legged) and thus define the SS half path length as a function of delta R(SS) = R (three-legged) - 2*delta. I think it is a restraint not a constraint. So I defined (def) the delta function on the line above the command FEFFIT also delr for the SS path. I introduced the restraint in the line FEFFIT as restraint = delrSS). The fit produce the same results as obtainde without the definition of delta and delrSS (function of delta). So I need to know how to introduce this restraint in the fit in order to calculate de M - O - M bond angle (this angle should be calculated using simple geometric relationships) - perhaps introduce the bond angle as a restraint. Someone can say me where I introduce the definitions of restraint parameters? Thank you very much for your kind attention Renato Canha Universidade Federal do Rio Grande doNorte Departamento de Quimica Natal - RN - BRAZIL Open WebMail Project (http://openwebmail.org) ---------- Original Message ----------- From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Mon, 23 Jan 2006 12:00:13 -0600 Subject: Ifeffit Digest, Vol 35, 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: Re: I should be able to find this somewhere... (Bruce Ravel) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Jan 2006 16:58:07 -0600 > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] Re: I should be able to find this somewhere... > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200601221658.07513.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > In fact, Artemis and Athena both attempt to deal correctly with input > chi(k) data that is not on the expected grid. Both codes perform a > test to see if the data is on the standard grid and, if not, > front-loads the data with zeros and uses Ifeffit's boxcar rebinning > function to put the data on the expected grid. > > Alas, there was a bug in the rebinning macro used by A&A which caused > it to fail in a particular situation met by the data in Matthew's > example. This bug will be fixed in the next release. > > If you import mu(E) data into Athena and then import data from the > Athena project file into Artemis, you will never see the problem that > Matthew reported. > > B > > On Tuesday 17 January 2006 16:09, Matt Newville wrote: > > Hi Matthew, Bruce, > > > > OK, I think it's a bug. Well, maybe it's just a consequence of a > > "known but not well advertised" problem. > > > > The chi(k) data you have doesn't start at k=0. By itself, this should > > be OK, and the fit seems to be mostly fine. There seems to be a bug > > in Ifeffit that the output fit chi(k) has the same number of data > > points as the input chi(k) data. In this case is incorrect -- it > > should go to the last data point in k. From looking at the code, I'm > > pretty sure this has no effect on the fit and is only an error in the > > output array. But the shortened chi_fit(k) will have an impact on the > > way Bruce is calculating the residual. Even if that were fixed, the > > residual would still be wrong, as the residual in Artemis is > > calculated as > > set(data0_res.k = data0.k) > > set(data0_res.chi = data0.chi - data0_fit.chi) > > > > and then Fourier transforming to R-space. Since the data and fit > > aren't aligned in k-space, the residual is incorrect. It should be > > > > set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi, > > data0.k)) > > > > or some variation on that. > > > > Sorry for the trouble. It's definitely a result of narrow-mindedly > > expecting that all chi(k) data comes from Ifeffit/Athena and will > > always start at k=0. We should get this fixed (it's mostly there!) so > > that data from other sources can be used. Right now, the easiest > > work-around is to pre-pack the chi(k) data with zeros (starting from > > k=0.00) > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- > Bruce Ravel ---------------------------------------------- bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 > > Argonne National Laboratory phone and voice mail: (1) 630 > 252 5033 Argonne IL 60439, USA fax: > (1) 630 252 9793 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/ > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > End of Ifeffit Digest, Vol 35, Issue 14 > *************************************** ------- End of Original Message -------

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RE: [Ifeffit] RESTRAINTS IN IFEFFIT
by Kelly, Shelly D. 25 Jan '06

25 Jan '06

Hi Renato, See below for some comments: > > Hi Folks, this is my first message on the list. Perhaps someone could help > me. The subject is how to include restraints on exafs refinement. There is > just scanty information about this on the ifeffit reference manual. > > I'm trying to refine the exafs data of a rhombohedral perovskite. > > The main MS contributions to the signal at about 3.5 A (non phase correct) > arise from M - O - M interactions being M the absorber . We have a > significant SS path, a two-legged and a three-legged path. The structural > parameters of these three terms are correlated since all refers to the > same > A-B-C triangle and the A-B and B-C distances must be that found for > M-O1 nearest-neighbor configurations. For these reasons > we constrained the photo electron path length for three-legged to the > M-O nearest-neighbor distance:R(three-leg = 2*RM-O). [Kelly, Shelly D.] The three-leg path length is given by half the total path length. Calculated as R = (distance_AB + distance_BC + distance_AC) * 0.5 You know the distance from A-B and the distance from B-C but the distance from A-C is dependent on the angle of the triangle path. You can write an equation to determine the angle A. a^2 = b^2 + c^2 -2bc cos(A) where a=distance_AC, b=distance_AB, c=distance_BC and A is the angle opposite of the AC side of the triangle. Then the four leg path has a path length defined as R = (2*distance_AB + 2*distance_BC)*0.5 The single path from A to B has the distance R = (2*distance_AB)*0.5 The single path from A to C has the distance R = (2*distance_AC)*0.5 Which also depends on the angle A and distance_AB as defined above. So for your case you have one unknown length and one unknown bond angle to describe these path lengths. i.e. distance_AB=distance_BC is unknown and angle A is unknown. HTH Shelly I'm trying to > intoroduce the quantity defined as delta = R(three-legged)-R(two-legged) > and thus define the SS half path length as a function of delta R(SS) = R > (three-legged) - 2*delta. I think it is a restraint not a constraint. > So I defined (def) the delta function on the line above the command FEFFIT > also delr for the SS path. I introduced the restraint in the line FEFFIT > as > restraint = delrSS). The fit produce the same results as obtainde without > the definition of delta and delrSS (function of delta). > So I need to know how to introduce this restraint in the fit in order to > calculate de M - O - M bond angle (this angle should be calculated using > simple geometric relationships) - perhaps introduce the bond angle as a > restraint. > Someone can say me where I introduce the definitions of restraint > parameters? > > Thank you very much for your kind attention > > Renato Canha > > Universidade Federal do Rio Grande doNorte > Departamento de Quimica > Natal - RN - BRAZIL > Open WebMail Project (http://openwebmail.org) > > > ---------- Original Message ----------- > From: ifeffit-request(a)millenia.cars.aps.anl.gov > To: ifeffit(a)millenia.cars.aps.anl.gov > Sent: Mon, 23 Jan 2006 12:00:13 -0600 > Subject: Ifeffit Digest, Vol 35, 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: Re: I should be able to find this somewhere... (Bruce Ravel) > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sun, 22 Jan 2006 16:58:07 -0600 > > From: Bruce Ravel <bravel(a)anl.gov> > > Subject: Re: [Ifeffit] Re: I should be able to find this somewhere... > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Message-ID: <200601221658.07513.bravel(a)anl.gov> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi, > > > > In fact, Artemis and Athena both attempt to deal correctly with input > > chi(k) data that is not on the expected grid. Both codes perform a > > test to see if the data is on the standard grid and, if not, > > front-loads the data with zeros and uses Ifeffit's boxcar rebinning > > function to put the data on the expected grid. > > > > Alas, there was a bug in the rebinning macro used by A&A which caused > > it to fail in a particular situation met by the data in Matthew's > > example. This bug will be fixed in the next release. > > > > If you import mu(E) data into Athena and then import data from the > > Athena project file into Artemis, you will never see the problem that > > Matthew reported. > > > > B > > > > On Tuesday 17 January 2006 16:09, Matt Newville wrote: > > > Hi Matthew, Bruce, > > > > > > OK, I think it's a bug. Well, maybe it's just a consequence of a > > > "known but not well advertised" problem. > > > > > > The chi(k) data you have doesn't start at k=0. By itself, this should > > > be OK, and the fit seems to be mostly fine. There seems to be a bug > > > in Ifeffit that the output fit chi(k) has the same number of data > > > points as the input chi(k) data. In this case is incorrect -- it > > > should go to the last data point in k. From looking at the code, I'm > > > pretty sure this has no effect on the fit and is only an error in the > > > output array. But the shortened chi_fit(k) will have an impact on the > > > way Bruce is calculating the residual. Even if that were fixed, the > > > residual would still be wrong, as the residual in Artemis is > > > calculated as > > > set(data0_res.k = data0.k) > > > set(data0_res.chi = data0.chi - data0_fit.chi) > > > > > > and then Fourier transforming to R-space. Since the data and fit > > > aren't aligned in k-space, the residual is incorrect. It should be > > > > > > set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi, > > > data0.k)) > > > > > > or some variation on that. > > > > > > Sorry for the trouble. It's definitely a result of narrow-mindedly > > > expecting that all chi(k) data comes from Ifeffit/Athena and will > > > always start at k=0. We should get this fixed (it's mostly there!) so > > > that data from other sources can be used. Right now, the easiest > > > work-around is to pre-pack the chi(k) data with zeros (starting from > > > k=0.00) > > > > > > --Matt > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > -- > > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > > > > Molecular Environmental Science Group, Building 203, Room E-165 > > MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 > > > > Argonne National Laboratory phone and voice mail: (1) 630 > > 252 5033 Argonne IL 60439, USA fax: > > (1) 630 252 9793 > > > > My homepage: http://cars9.uchicago.edu/~ravel > > EXAFS software: http://cars9.uchicago.edu/~ravel/software/ > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > End of Ifeffit Digest, Vol 35, Issue 14 > > *************************************** > ------- End of Original Message ------- > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: Possible bug in Artemis. (Bruce Ravel)
by joshua jason kas 25 Jan '06

25 Jan '06

Hi Bruce, Thanks for the tips. I fooled around with the feff.inp and found that artemis somehow has a problem when feff is run with the RMULTIPLIER card. This card is purely for convenience, so I took it out and things work fine. This card was used in feff6 although the code runs very slowly with it for some reason. Anyway, here is the feff.inp file that I was using for feff6 or feff8 (they both have the problem). Thanks, Josh TITLE GeCl4 HOLE 1 1.0 CONTROL 1 1 1 1 1 1 (feff8) CONTROL 1 1 1 1 (feff6) PRINT 1 0 0 0 0 3 EXCHANGE 0 1 1 CORRECTIONS 1.2427845974 0.0041969513 RMAX 10.0 RMULTIPLIER 1.01 POTENTIALS 0 32 Ge -1 -1 1 1 17 Cl -1 -1 4 ATOMS 0.0000000000 0.0000000000 0.0000000000 0 1.1568027 1.1568027 1.1568027 1 Cl 1.1568027 -1.1568027 -1.1568027 1 Cl -1.1568027 1.1568027 -1.1568027 1 Cl -1.1568027 -1.1568027 1.1568027 1 Cl END > From: Bruce Ravel <bravel(a)anl.gov> > Subject: Re: [Ifeffit] Possible bug in Artemis. > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200601231845.59426.bravel(a)anl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Monday 23 January 2006 17:47, joshua jason kas wrote: >> Hi, >> When I import a feff calculation, or run feff, the paths show up in >> artemis, but the description is garbled. What I mean is that the path >> description under Scattering Path which normally looks like >> >> [+] Cl [+] O ... >> >> looks like >> >> [+] <?> [+] <?> ... > > This looks like another version of a bug that has cropped up here and there. > The algorithm for generating the interpretation page parses the feff.inp file > and a couple of feff's output files. Every so often, someone throws a > hand-made feff.inp file at Artemis that works in feff but breaks the rather > crufty parser I wrote. > > If you can send me the feff.inp file that would help. The artemis project > file might help also, so send that along. Even if it is one that makes > Artemis do bad things when you try to read, I can still peak on the inside and > figure out what's going on. > > 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/ > > > > ------------------------------ > > Message: 2 > Date: Mon, 23 Jan 2006 20:18:42 -0500 > From: "TAO, Ye" <yetao(a)chem.uga.edu> > Subject: Re: [Ifeffit] Possible bug in Artemis. > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <00f001c62084$1d8d28c0$3b05c080@RASD800> > Content-Type: text/plain; format=flowed; charset="iso-8859-1"; > reply-type=original > > Josh, > > Have a try to set the absorber coordinate as origin (0 0 0) in feff.inp, > then it should work. > > Ye > ----- Original Message ----- > From: "joshua jason kas" <hebhop(a)u.washington.edu> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Monday, January 23, 2006 6:47 PM > Subject: [Ifeffit] Possible bug in Artemis. > > >> Hi, >> When I import a feff calculation, or run feff, the paths show up in >> artemis, but the description is garbled. What I mean is that the path >> description under Scattering Path which normally looks like >> >> [+] Cl [+] O ... >> >> looks like >> >> [+] <?> [+] <?> ... >> >> and if I save the project file and reopen it, it can't >> I have attached a screenshot. >> Here is some info on my software >> 1) artemis 0.8.004 >> 2) ifeffit 1.2.8 >> 3) perl -e 'use Tk; print $Tk::VERSION,$/' gives 804.027 >> 4) perl v5.8.7 >> >> I tried updating Tk, and that works about as well as it always has on my >> system. Most of the tests passed, a few failed. >> This may be a problem with my version of Linux, or my version of perl/Tk. >> Anyway, any help would be much appreciated. >> Thank you very much, >> Josh Kas > > > -------------------------------------------------------------------------------- > > >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > > ------------------------------ > > Message: 3 > Date: Tue, 24 Jan 2006 11:43:30 -0300 > From: "Renato Canha Ambrosio" <rcanha(a)ccet.ufrn.br> > Subject: [Ifeffit] RESTRAINTS IN IFEFFIT > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <20060124142316.M21887(a)ccet.ufrn.br> > Content-Type: text/plain; charset=iso-8859-1 > > Hi Folks, this is my first message on the list. Perhaps someone could help > me. The subject is how to include restraints on exafs refinement. There is > just scanty information about this on the ifeffit reference manual. > > I'm trying to refine the exafs data of a rhombohedral perovskite. > > The main MS contributions to the signal at about 3.5 A (non phase correct) > arise from M � O � M interactions being M the absorber . We have a > significant SS path, a two-legged and a three-legged path. The structural > parameters of these three terms are correlated since all refers to the same > A-B-C triangle and the A-B and B-C distances must be that found for > M-O1 nearest-neighbor configurations. For these reasons > we constrained the photo electron path length for three-legged to the > M-O nearest-neighbor distance:R(three-leg = 2*RM-O). I'm trying to > intoroduce the quantity defined as delta = R(three-legged)-R(two-legged) > and thus define the SS half path length as a function of delta R(SS) = R > (three-legged) - 2*delta. I think it is a restraint not a constraint. > So I defined (def) the delta function on the line above the command FEFFIT > also delr for the SS path. I introduced the restraint in the line FEFFIT as > restraint = delrSS). The fit produce the same results as obtainde without > the definition of delta and delrSS (function of delta). > So I need to know how to introduce this restraint in the fit in order to > calculate de M - O - M bond angle (this angle should be calculated using > simple geometric relationships) - perhaps introduce the bond angle as a > restraint. > Someone can say me where I introduce the definitions of restraint parameters? > > Thank you very much for your kind attention > > Renato Canha > > Universidade Federal do Rio Grande doNorte > Departamento de Quimica > Natal - RN - BRAZIL > Open WebMail Project (http://openwebmail.org) > > > ---------- Original Message ----------- > From: ifeffit-request(a)millenia.cars.aps.anl.gov > To: ifeffit(a)millenia.cars.aps.anl.gov > Sent: Mon, 23 Jan 2006 12:00:13 -0600 > Subject: Ifeffit Digest, Vol 35, 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: Re: I should be able to find this somewhere... (Bruce Ravel) >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 22 Jan 2006 16:58:07 -0600 >> From: Bruce Ravel <bravel(a)anl.gov> >> Subject: Re: [Ifeffit] Re: I should be able to find this somewhere... >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Message-ID: <200601221658.07513.bravel(a)anl.gov> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi, >> >> In fact, Artemis and Athena both attempt to deal correctly with input >> chi(k) data that is not on the expected grid. Both codes perform a >> test to see if the data is on the standard grid and, if not, >> front-loads the data with zeros and uses Ifeffit's boxcar rebinning >> function to put the data on the expected grid. >> >> Alas, there was a bug in the rebinning macro used by A&A which caused >> it to fail in a particular situation met by the data in Matthew's >> example. This bug will be fixed in the next release. >> >> If you import mu(E) data into Athena and then import data from the >> Athena project file into Artemis, you will never see the problem that >> Matthew reported. >> >> B >> >> On Tuesday 17 January 2006 16:09, Matt Newville wrote: >>> Hi Matthew, Bruce, >>> >>> OK, I think it's a bug. Well, maybe it's just a consequence of a >>> "known but not well advertised" problem. >>> >>> The chi(k) data you have doesn't start at k=0. By itself, this should >>> be OK, and the fit seems to be mostly fine. There seems to be a bug >>> in Ifeffit that the output fit chi(k) has the same number of data >>> points as the input chi(k) data. In this case is incorrect -- it >>> should go to the last data point in k. From looking at the code, I'm >>> pretty sure this has no effect on the fit and is only an error in the >>> output array. But the shortened chi_fit(k) will have an impact on the >>> way Bruce is calculating the residual. Even if that were fixed, the >>> residual would still be wrong, as the residual in Artemis is >>> calculated as >>> set(data0_res.k = data0.k) >>> set(data0_res.chi = data0.chi - data0_fit.chi) >>> >>> and then Fourier transforming to R-space. Since the data and fit >>> aren't aligned in k-space, the residual is incorrect. It should be >>> >>> set(data0_res.chi = data0.chi - interp(data0_fit.k, data0_fit.chi, >>> data0.k)) >>> >>> or some variation on that. >>> >>> Sorry for the trouble. It's definitely a result of narrow-mindedly >>> expecting that all chi(k) data comes from Ifeffit/Athena and will >>> always start at k=0. We should get this fixed (it's mostly there!) so >>> that data from other sources can be used. Right now, the easiest >>> work-around is to pre-pack the chi(k) data with zeros (starting from >>> k=0.00) >>> >>> --Matt >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> -- >> Bruce Ravel ---------------------------------------------- bravel(a)anl.gov >> >> Molecular Environmental Science Group, Building 203, Room E-165 >> MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 >> >> Argonne National Laboratory phone and voice mail: (1) 630 >> 252 5033 Argonne IL 60439, USA fax: >> (1) 630 252 9793 >> >> My homepage: http://cars9.uchicago.edu/~ravel >> EXAFS software: http://cars9.uchicago.edu/~ravel/software/ >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> End of Ifeffit Digest, Vol 35, Issue 14 >> *************************************** > ------- End of Original Message ------- > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 35, Issue 16 > *************************************** >

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Possible bug in Artemis.
by joshua jason kas 24 Jan '06

24 Jan '06

Hi, When I import a feff calculation, or run feff, the paths show up in artemis, but the description is garbled. What I mean is that the path description under Scattering Path which normally looks like [+] Cl [+] O ... looks like [+] <?> [+] <?> ... and if I save the project file and reopen it, it can't I have attached a screenshot. Here is some info on my software 1) artemis 0.8.004 2) ifeffit 1.2.8 3) perl -e 'use Tk; print $Tk::VERSION,$/' gives 804.027 4) perl v5.8.7 I tried updating Tk, and that works about as well as it always has on my system. Most of the tests passed, a few failed. This may be a problem with my version of Linux, or my version of perl/Tk. Anyway, any help would be much appreciated. Thank you very much, Josh Kas

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Re: I should be able to find this somewhere...
by Bruce Ravel 22 Jan '06

22 Jan '06

On Friday 13 January 2006 20:25, you wrote: > By what factor is the residual multiplied when plotted in Artemis? I can't > find that figure quoted. > mam The residual is saved in k-space and Fourier transformed. 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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Re: moving the legend in Athena
by Bruce Ravel 20 Jan '06

20 Jan '06

On Thursday 19 January 2006 14:05, Carlo Segre wrote: > When I plot data using athena, I would like to move the legend. How can I > do this? Go to the preferences, then to the plot branch. key_x and key_y are the xy coordinates of the upper left corner of the legend box. key_dy is the spacing between lines. The answer is the same for Artemis. 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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