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

Installation troubles on OS X
by Bradley Roberts 08 Feb '06

08 Feb '06

I've spent the past few days going through the backlogs of this list and have been able to solve many problems so far. However, I've hit a point where I don't see a record of this problem/solution and am hoping someone can help. I am able to load ifeffit and execute commands, however when I try to load any of the ancillary programs there are failures (see printout below). As per previous posts, I've installed and updated g77 via fink, as well as tk and tk::pod via cpan. I also had to install LWP via cpan before I could get ifeffit to run. From the install notes I see that ifeffit's intall program trashes the LWP directory in perl, so I'm curious if I've caused this problem myself (and if so, how do I fix it?). Secifically, the ifeffit.pm and Tk/Pod.pm files cannot be found anywhere in the @INC directories. Also, running the locate command I cannot find the files on the drive anywhere else. Additionally, I tried to download and re-install ifeffit from the disk image and it cannot install - the error says "you cannot continue. there is nothing to install." My setup is: PB 15" G4 OS X 10.4.4 ifeffit 1.2.8 perl 5.8.6 fink and cpan selfupdated to the latest via cvs epic-glory:~ apple$ athena Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/athena line 54. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 58. epic-glory:~ apple$ artemis Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/artemis line 49. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/artemis line 53. epic-glory:~ apple$ hephaestus Can't locate Tk/Pod.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Library/Perl/5.8.6/darwin-thread-multi-2level/Tk/widgets.pm line 14. at /Applications/Ifeffit/bin/hephaestus line 66 BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/hephaestus line 66. -- Bradley Roberts (br2(a)u.washington.edu) Graduate Student, Department of Materials Science & Engineering Roberts Hall 302 Box 352120 University of Washington Seattle, WA 98195 206-616-7485 lab 206-543-3100 fax

1 0

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

3 2

Again _ for help with Webatoms input_sorry for incomplete information
by Feng Wang 03 Feb '06

03 Feb '06

Hi Everyone, I had a trouble with the input for webatoms in trying to get feff.inp from it. I got the crystal structure information from papers, as attached below, would you please suggest what should I input for the items listed below: Shift: Alpha= Beta= Gamma= The table of Crystallgraphic sites: Would Dr. Ravel or some of you can help with that? Thank you so much in advance. Best regards, Feng Crystal structure information: Iron trifluorine has a ReO3 type structure (hexagonal), with spac group of R- 3C, with two Fe atoms at (0 0 0) and (0.5 0.5 0.5)and 6 fluorines at (x, 0.5- x, 0.25), -(x, 0.5-x, 0.25), (0.5-x,0.25 x),-(0.5-x,0.25 x), (0.25 x, 0.5- x), -(0.25 x, 0.5-x), and with x=-0.164. ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

2 1

for help with Webatoms input
by Feng Wang 03 Feb '06

03 Feb '06

Hi Everyone, I had a trouble with the input for webatoms in trying to get feff.inp from it. I got the crystal structure information from papers, as attached below, would you please suggest what should I input for the items listed below: Shift: Alpha= Beta= Gamma= The table of Crystallgraphic sites: Thank you so much in advance. Best regards, Feng Crystal structure information: Iron trifluorine has a ReO3 type structure (hexagonal), with spac group of R- 3C, with two Fe atoms at (0 0 0) and (0.5 0.5 0.5)and 6 fluorines at (x, 0.5- x, 0.25), -(x, 0.5-x, 0.25), (0.5-x,0.25 x),-(0.5-x,0.25 x), ( ================================== Feng Wang fwang(a)phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta =========================================================

1 0

correlated Einstein model and Debye model
by Renato Canha Ambrosio 02 Feb '06

02 Feb '06

Good afternoon everybody I have questions about the Einstein and Debye correlated models in IFEFFIT. As described in page 80 of the EXAFS ANALYSIS WITH FEFF AND FEFFIT - PART 2: COMMENTARY by Bruce Ravel the eins function is a function evaluated in the context of the current path. So the reduced mass is calculated with the mass of the atoms in the path. Its ok but I have several scans at different temperatures so I would like to refine not only the Theta (Einstein temperature) but also the reduced mass and perhaps the static disorder. Can I do it in the context of the path or I have to perform a non - xafs refinement with the file containing the temperatures and sigma^2. I make the same question for the Debye correlated model. Thank you very much for your kind attention Renato Canha Universidade Federal do Rio Grande do Norte Natal - RN - BRASIL 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: Wed, 1 Feb 2006 12:00:12 -0600 Subject: Ifeffit Digest, Vol 36, Issue 1 > 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: FEFF8 vrs FEFF6 (Matt Newville) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Feb 2006 08:54:22 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] FEFF8 vrs FEFF6 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0602010654j195cf712hf30b878a67bac08e(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > HI Shelly, > > I wouldn't say it's wrong to use Feff8 for EXAFS analysis, just > rarely necessary. > > Feff8 was definitely designed for XANES, and improvements for EXAFS > were not the main goal. But there are a few cases where Feff8 _is_ > known to be better for EXAFS than Feff6. (I'll leave out Feff7 as it > seems no one is using this much). Clusters with H is one, and > transuranic elements is another. I've heard a few people claim that > Feff8 gives "better E0's", which I think means that E0 refines to a > value closer to 0 (that is, to where the it's arbitrarily assigned in > the data processing). Since E0 has to be refined and has little > physical significance, I don't find this to be a compelling advantage > for Feff8. > > Early versions of Feff8 (pre-release? Including 8.00?? I'm not sure) > were much worse for EXAFS.This did get fixed, but I'm not sure when > (I have a hard time understanding Feff8 version numbers and can never > really tell which get released and widely used: I've given up > complaining and live wih the fact that "Feff8" means one snapshot of > 8 years worth of work.). By Feff8.1 for sure, and maybe eralier, there > were essentially no difference between Feff6, 7, and 8 for EXAFS. > That was based on analysis of data on metal foils (Cu, Ag, Au), and > could hardly be called thorough and possibly not even 'highly > relevent to real-world problems', as it doesn't even test changes in > exchange or overlap of metal-oxygen potentials. Better testing and > comparisons would be very good. > > Anyway, I think it's fine to use Feff6, 7, or 8 for EXAFS. > > I don't think anything should change for these versions in the > reporting of how a Feff calculation was done for EXAFS. Most EXAFS > work using Feff give no details about the calculation, and I think > that's mostly OK, as the Feff/Atoms/Artemis default parameters are > generally quite reasonable. If the work discusses comparing > different Feff calculations, then obviously more detail on what was > changing would be needed. > > That's my opinion, anyway. > > --Matt > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > End of Ifeffit Digest, Vol 36, Issue 1 > ************************************** ------- End of Original Message -------

3 2

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 -------

2 1

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

1 0

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 > *************************************** >

2 1

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

3 2

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/

4 9