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

RE: [Ifeffit] question about S02 (passive electron reduction factor)
by Kelly, Shelly D. 27 Feb '04

27 Feb '04

Yu-Chuan, Matt and all, > >> Yu-Chuan wrote: > >> > >> At the beginning of the fitting, the S02(amp) are far away > from 0.9 > >> (just about 0.3). It's much different than Bruce's and Scott's > >> examples. [...] Also, John have said that the S02 value should be > >> around 0.9. That's why I am wondering if there is anything > wrong with > >> my data processing? Does anyone happen to have this kind > of problem? > > > > > > There are several possibilities. One is sample prep. [...] [...] > > Another is normalization.[...] Finally, look at the correlation > > between S02 and sigma2...if it is very high (say 0.95 or > above) it may > > simply be coming up with low estimates for each. > > Yu-Chuan didn't give details of sample prep or data > collection, and I agree with Scott that these are most likely > cause of low S02 factors (Scott mentioned problems with > transmission measurements, and Grant mentioned how > self-absorption can cause similarly low S02 factors for > fluorescence measurements). I also agree with Scott that > poor normalization will affect S02, though S02~0.3 would > indicate an edge step off by a factor of ~3, which is a > pretty big error for normalization. I doubt that is the culprit. > > But: the correlation between S02 and sigma2 is NOT the cause > of a value for S02 being low by a factor of 3. A high > correlation means that a reasonably good fit could also be > found by changing both S02 and sigma2 away from their > best-fit value. This is not at all the same as saying that > either parameter has the wrong best-fit value. In fact, the > correlation between pair of variables says nothing about the > trustworthiness of the best-fit values, only how much the > uncertainties in the best-fit values depend on other variables. > And, just to be clear, the reported uncertainties already > take these correlation into account. > > Yu-Chuan didn't actually say what the reported uncertainties > in S02 were, but it seems that it was small enough so that > S02~=0.3 could be distinguished from S02~=0.9. > > --Matt The degeneracy of the paths included in the fit were not mentioned, and could easily cause the S02 value to be off by a factor of 3. Especially, if you forget that feff has already taken the degeneracy of the path into account, and then you set some N-value to 2 or 3 or 4. I have seen others make this mistake before... Shelly

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Re: [Ifeffit] question about S02 (passive electron reduction factor)
by Grant Bunker 26 Feb '04

26 Feb '04

As a follow-on to Scott's and Bruce's responses, if the samples were measured in fluorescence, the sample self-absorption effects would be a likely explanation for the problem. At the Vanadium edge the absorption length of the sample would probably be short (microns) and you would have to go to some trouble to avoid those problems. There are good correction procedures for that problem (e.g. see papers by Booth and Bridges, Haskell...). grant bunker On Thu, 26 Feb 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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: question about S02 (passive electron reduction factor) > (Scott Calvin) > 2. Re: question about S02 (passive electron reduction factor) > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 25 Feb 2004 13:18:29 -0500 > From: Scott Calvin <scalvin(a)slc.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <3.0.1.32.20040225131829.00acff58(a)mail.slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Yu-Chuan, > > There are several possibilities. One is sample prep. If you have an > extremely uneven sample (lots of pinholes, etc.) in transmission it can > lead to results like you're describing. Another is normalization. If you're > using Athena for background subtraction make sure you look at the pre-edge > line and post-edge curve and see that they look reasonable. Sometimes if > the background has a funny shape to it Athena can create a post-edge curve > that shoots way up at the edge energy; this could also lead to the effect > you're describing. Finally, look at the correlation between S02 and > sigma2...if it is very high (say 0.95 or above) it may simply be coming up > with low estimates for each. There are, of course, other possibilities as > well, but in my experience those are the most common. > > --Scott Calvin > Sarah Lawrence College > > >This is Yu-Chuan. I am now trying to fit my sample, magnesium > orthovanadate. > >I try to follow Bruce's Cu example and Scott's ZnO example steps and I > found a > >problem come to my fitting. At the beginning of the fitting, the S02(amp) > are > >far away from 0.9 (just about 0.3). It's much different than Bruce's and > >Scott's examples. For Cu and ZnO examples, the fitting results of amp are > >close to 0.9 at the beginning even if you set just four parameters > (guess:amp, > >e0, delr, and ss). Also, John have said that the S02 value should be around > >0.9. That's why I am wondering if there is anything wrong with my data > >processing? Does anyone happen to have this kind of problem? Thank you for > >your help. > > > > > ------------------------------ > > Message: 2 > Date: Thu, 26 Feb 2004 10:43:48 -0500 > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200402261043.48841.ravel(a)phys.washington.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, > > Yesterday we had a question about oddly small S02 values. In his > thorough summary of possible explanations, Scott mentioned this: > > On Wednesday 25 February 2004 01:18 pm, Scott Calvin wrote: > > Another is normalization. If you're using Athena for background > > subtraction make sure you look at the pre-edge line and post-edge > > curve and see that they look reasonable. Sometimes if the background > > has a funny shape to it Athena can create a post-edge curve that > > shoots way up at the edge energy; this could also lead to the effect > > you're describing. > > I thought that a word of explanation about why Athena does what she > does might be helpful to folks. In this email I am going to refer to > data taken on an iron foil. To follow along, fire up Athena and > select "Import a demo project" from the Help menu. Select the > `calibrate.prj' file. This contains an iron foil spectrum. > > Set the plotting range in energy to [-200:1500]. Set the upper bound > of the normalization range to 400. Click on the "post-edge line" > button in the plotting options section. This will plot the data, the > background, and the post-edge line. Note that the post-edge line is > U-saped, diverging from the data a bit at low energy and significantly > at high energy. Note also that the edge step is about 3.05. > > Now set the upper bound of the normalization range to 1700 and click > the red E plotting button. Now the post-edge line goes through the > data and the edge step is about 2.86. > > So what's going on? Well, the post-edge line is determined by > regressing a quadratic polynomial to the data in the user-specified > normalization range. When the upper bound was set to 400, the square > term in the polynomial was quite large because *that* was the > regression to the data over that short data range. When the upper > bound was set to 1700, the square term was a lot smaller, the > post-edge line was closer to linear and it was constrained by the > regression to follow the data over the entire data range. > > Setting the upper bound of the normalization range had the effect of > increasing the edge step by about 6%. Remember that the edge step is > the value of the post-edge line extrapolated back to E0 after the > pre-edge line is removed from the data. With the short energy range, > the edge step is too large and the chi(k) is attenuated. In the > subsequent fit, S02 will have to be similarly smaller to compensate. > In this case it was a 6% effect, but if the post-edge line is really > screwy, the attenuation could be much larger. > > So this was the long-winded way of repeating what Scott said -- plot > the post-edge line and make sure the regression was done such that the > post-edge line goes through the entire data in a way that seems > sensible. It is also, as Scott said, prudent to check the pre-edge > line as well. > > B > > > > -- > ********* PLEASE NOTE MY NEW PHONE, FAX, & ROOM NUMBERS ****************** > > Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu > Code 6134, Building 3, Room 405 > Naval Research Laboratory phone: (1) 202 767 2268 > Washington DC 20375, USA fax: (1) 202 767 4642 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 12, Issue 14 > *************************************** >

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choosing k-weight
by Peter Southon 20 Feb '04

20 Feb '04

Dear Ifeffiters, I'm wondering what principles you have to determine the appropriate k-weight to use for FTs. Until now I've used guidelines from a textbook by Teo, based on the Z of the backscattering atoms: Z > 57; kw = 1 57 > Z > 36; kw = 2 Z < 36; n = 3 Of course you can have different backscatterers around your absorber - I've got C, N and Pt! Are there any other rules you follow? Thanks very much in advance! Peter Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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Re: [Ifeffit] choosing k-weight
by SCalvin100＠aol.com 20 Feb '04

20 Feb '04

Peter, Of course, the bottom line is that the k-weight shouldn't affect the values of the parameters Ifeffit finds. If it does, it's a sign that the parameters should not be trusted. Often, this happens when the k-range chosen to fit is inappropriate (extends up into a range where the data is dominated by noise, down into a range where the background is poorly chosen, or across a small edge due to a contaminant, for example). I always test my "final" fits at all three k-weights separately to make sure the values of the parameters stay fairly stable. --Scott Calvin Sarah Lawrence College

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RE: [Ifeffit] choosing k-weight
by Kelly, Shelly D. 20 Feb '04

20 Feb '04

> Dear Ifeffiters, > > I'm wondering what principles you have to determine the appropriate > k-weight to use for FTs. Until now I've used guidelines from > a textbook by > Teo, based on the Z of the backscattering atoms: > Z > 57; kw = 1 > 57 > Z > 36; kw = 2 > Z < 36; n = 3 > > Of course you can have different backscatterers around your > absorber - I've > got C, N and Pt! Are there any other rules you follow? > > Thanks very much in advance! > > Peter Hi Peter, I have found it very useful to use all three kweights, simultaneously. You can really cut down of the correlation between the different EXAFS parameters by doing so. This paper shows a model that was fit to the data with all three kweights. Geo. Cosmo Acta 66(22): pp 3855-3871, November 2002. I have been thinking about putting together an Artemis project file that shows how to do this. If there is interest, I would be willing. Shelly

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Re: IFEFFIT updater problem
by Matt Newville 19 Feb '04

19 Feb '04

Hi Jeff, On Wed, 18 Feb 2004, Jeffrey Catalano wrote: > > The IFEFFIT updater is behaving badly. Everytime I start an IFEFFIT group > program, it wants to download the same two updates. I've installed them > three times now (remembering to run the make bat thingy each time). Any > ideas if the problem is with my computer or with the updater? Other than > that everything works wondefully! Hmm, that seems weird. Here's what is supposed to happen with the updater (and I hope you mind me sending this on to the mailing list -- if the problem happens for you, it will probably happen for someone else, and the updater isn't very well documented), and a way that should be able to work around it -- you can skip to the end if you like ;). When the applications apt, artemis, athena, gifeffit, ifeffit, sixpack, and tkatoms run (from the batch files, desktop icon, or start menu), the updater is run before the main application is run. The updater reads two files: C:\Program Files\Ifeffit\updates\updater.ini C:\Program Files\Ifeffit\updates\updater.dat updater.dat holds the current 'local update level' on your machine, which is just a 3 digit number, like 003 or 005. updater.ini holds the time of the last "real check for updates" and how long to wait until the next update should be done. If the last real check was within the last 24hours, the updater stops right there. Actually, the time to wait until the next real check can be set longer with the 'Do not remind me again until' list in the main updater GUI. If it's past the time to do a "real check for updates", the updater fetches the current 'available update level' from the cars webpage: http://cars9.uchicago.edu/ifeffit/updates/update.dat, which currently reads '005'. If it can't reach this web page and read this file in 15seconds, the updater stops. If the 'local updater level' is equal to the 'available update level', you are up to date and the updater stops. If the 'local updater level' is less than the 'available update level', a GUI pops up, and you are told that there are update(s) to install, and asked if you'd like to install them. If you approve, the updates are downloaded one by one and installed. The update packages are all zip files, named as http://cars9.uchicago.edu/ifeffit/updates/ifup_XXX.zip for update level=XXX. The progress of the download and unpacking should be shown in the updater GUI. These updates are unpacked relative to the main Ifeffit directory, typically C:\Program Files\Ifeffit. Each of the updates includes, the file 'updates\updater.dat' to have the 'current update level'. So, if the update ifup_005.zip was installed, updates\updater.dat should say '005', and the updater shouldn't run again until I set the update level on the web page to 006. OK, that's what is supposed to happen. If that hasn't happened and updates\updater.dat does not say '005', a simple solution should be to edit it (notepad, whatever) to say 005 in the first line. I'd be interested to hear if other people are having this problem. Cheers, --Matt PS: a small problem can occur if the updater.exe program itself needs to be updated, as an executable program currently in use cannot be overwritten. So any new updater.exe is written to the 'updates' directory, and you are told to run make_bats.exe. Then make_bats.exe checks for an updater.exe in the updates directory and moves it to the main Ifeffit directory.

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Ifeffit updater
by Peter Southon 19 Feb '04

19 Feb '04

Hello, I'm a little confused about the role of the Ifeffit updater - does it cover just Ifeffit, or Athena/Artemis as well? It has updated my Ifeffit to v1.2.5 fine, but my version of Artemis is still 0.6.009, when Bruce's web page says that 0.6.010 was released last year. Do we have to update Athena/Artemis separately, and if so is there a way for PC users to do this without downloading the entire Ifeffit package again? Thanks, Peter Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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finding stuff in the archives
by Bruce Ravel 19 Feb '04

19 Feb '04

Hi folks, A while back there was some discussion about indexing the archive of the mailing list. Still a good idea, but I wanted to suggest a user-land solution to the problem. It is possible to find stuff on the archive using Google. This shouldn't be a surprise -- I, for one, cannot imagine how I ever knew anything in the years B.G. (before Google). Try going to http://www.google.com/ and entering this as your search: site:millenia.cars.aps.anl.gov clamp This will return a hit for every entry in the archive that discusses spline clamps. In my last posting to the mailing list, I did this google search: site:millenia.cars.aps.anl.gov imaginary energy The "site:" directive tells google to restrict its search to pages that match that site. I learned about this trick from the book Google Hacks http://www.amazon.com/exec/obidos/ASIN/0596004478/qid=1077200261/sr=2-1/ ref=sr_2_1/002-8270889-0247203 HTH, B -- ********* PLEASE NOTE MY NEW PHONE, FAX, & ROOM NUMBERS ****************** Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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imaginary energy correction
by Stanislav Stoupin 19 Feb '04

19 Feb '04

Hello all, I would appreciate if somebody could explain the meaning of imaginary energy correction (Ei parameter). So far I have not found any description of the parameter. If anyone knows of any example on how to use it, please let me know. Stanislav

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Sourceforge problem
by Peter Southon 19 Feb '04

19 Feb '04

Hello again, I've been having problems using Sourceforge.net to download Ifeffit. I've mainly been trying to use the Flow Australian mirror, but none of them seem to be responding, returning an Error (110) "Connection timed out" message. Have other people been having this problem? (or it might be something funny at my end) Meanwhile I'll just use the cars sever. Cheers, Peter Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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THANKS AGAIN
by doug pease 17 Feb '04

17 Feb '04

Thanks again to Matt for fixing the graphical screen problem. To Matt and Bruce.....this is great!! Cheers, Doug Pease

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Re: merging
by dmc＠pdx.edu 12 Feb '04

12 Feb '04

Bruce, I succeeded in merging the k-plots of several files in Athena, but failed at opening the data and graphing it in Artemis for fitting purposes. Is this merging function purely for use in Athena? You'd made it sound like I could use that data for fitting. If it is possible to export the merge to Artemis for a fit, let me know how. Thanks, Dan

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FT transform
by Li Dangdang 10 Feb '04

10 Feb '04

Hi, i wonder if there is anyone to tell me what is the advantage of using real and imaginary part of transform in data and fit, compared with magnitude plot. Best, DD _________________________________________________________________ 与联机的朋友进行交流，请使用 MSN Messenger: http://messenger.msn.com/cn

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RE: [Ifeffit] Ifeffit 1.2.5a for Windows
by SCHLEGEL Michel 177447 10 Feb '04

10 Feb '04

Hello, Whatever I observed two days ago didn't repeat itself yesterdy night - I must have mixed uninstall and install sequences. Sorry for the false alarm! Anyhow, by removing all of Ifeffit 1.2.5 by Windows uninstall - and the remaining fold by 'hand' - I could install a clean, working Ifeffit 1.2.4 environment. I then un-installled everything again, and I installed Ifeffit 1.2.5a and Ifeffit updater on W2K. Ifeffit 1.2.5a apparently loaded the datafile and printed the data in the plotting window. Thanks, Matt and Bruce! Best regards, Michel Schlegel > At 12:58 PM 2/9/2004 -0500, you wrote: > >On Monday 09 February 2004 12:18 pm, Matt Newville wrote: > >> OK, ifeffit-1.2.5a.exe is available on sourceforge and the main > >> Ifeffit page. This seems to fix the plotting problem -- it worked > >> on the 5 WinXP machines I tried.

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Ifeffit 1.2.5a for Windows
by Matt Newville 09 Feb '04

09 Feb '04

Hi Everyone, OK, ifeffit-1.2.5a.exe is available on sourceforge and the main Ifeffit page. This seems to fix the plotting problem -- it worked on the 5 WinXP machines I tried. An 'update' was also posted (we're now at update #5) that will fix the problem (in the next day or so, depending on when you last ran athena or other Ifeffit applications). If you've installed ifeffit-1.2.5.exe and can't wait that long, you can apply the update by hand by downloading http://cars9.uchicago.edu/ifeffit/updates/ifup_005.zip and unzipping this (following the directory structure!) in the main Ifeffit directory (C:\Program Files\Ifeffit or C:\Ifeffit). If you haven't installed the broken ifeffit-1.2.5, please don't use this shortcut, as this update is not a complete update from 1.2.4!! Sorry for the problem, and thanks to Doug, Scott, and Michel for the reports! --Matt

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RE: [Ifeffit] Trying to get started
by SCHLEGEL Michel 177447 09 Feb '04

09 Feb '04

Hello, > I suspect that something else must be going on for Michel. I've > seen Ifeffit 1.2.4 plus Updater 1.1 work well on many Windows > machines. I haven't heard otherwise until this report. I'll try another bunch of tests tonight (fortunately -if might say so- it is my home computer that got into severe trouble), and keep a complete reccord of messages,etc... (just mentioning that: could it be updater behavior could be altered upon interaction with a firewall?) I downloaded the versions from sourceforge.net, but there is absolutely no reason to believe that these versions are any different from the ones posted at Chicago. So: don't worry for me, just wait tomorrow for more news. Best regards, Michel Schlegel

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Trying to get started
by doug pease 09 Feb '04

09 Feb '04

Hello All, I am trying to get started using Athena/Artemis. But I have the following problem. My computer is nearly brand new, uses XP and I now have 384 MB of RAM to go along with only 2.71 out of 35.54 GB used on the hard drive. But after I import data into Athena, and give the go ahead, the graphic screen just comes up and hangs up blank. It does NOT graph the data. If I try this on my lab computer that uses 98 there is no such problem.....the graphic screen works well. (There I get the well known "out of parameter space" error if I try to get much further. I would prefer to use my home computer, but will also try to fix up the old lab computer to work as recommended.) I am suspicious that this problem of the graphic screen hanging up with the XP computer might have something to do with my new computer having a liquid crystal display monitor???? Any ideas?? Sincerely, Doug Pease

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RE: [Ifeffit] Trying to get started
by SCHLEGEL Michel 177447 09 Feb '04

09 Feb '04

Doug, Scott, > This may be a brand new bug in the Ifeffit 1.2.5 download. > I am also using XP, and it was working fine under 1.2.4. > I downloaded 1.2.5, and when I try to import any data > (even the example files that come with the package) into > either Artemis or Athena, they crash when they try to display > on the graphics screen. To be specific, I can see the data > get read in, but when it gets to the stage of graphing the > data, the main Artemis or Athena screen vanishes, the program > icons go away from the task bar, and the graphics screen remains, > but it is blank. The very same thing happened to me on a Windows 2000 PC. I tried to remove and reinstall completely Ifeffit 1.2.5, but it didn't work. Then I removed Ifeffit 1.2.5 (including erasing the folders by hand once the 'uninstall' software was run), and installed Ifeffit 1.2.4: same trouble. And Ifeffit 1.2.2: bis repetita non placent. Finally, I had to dig out an old Ifeffit 1.0075 version (sigh...) Also, these problems appeared after I once ran the Ifeffit Updater 1.0. I wonder if there is any communication problem between the updater and the Ifeffit package, or if the new Ifeffit packages are writing files that can be neither removed upon uninstall, nor overwritten on re-installation. Best regards, Michel Schlegel

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Re: [Ifeffit] Trying to get started
by SCalvin100＠aol.com 09 Feb '04

09 Feb '04

Hi Doug, This may be a brand new bug in the Ifeffit 1.2.5 download. I am also using XP, and it was working fine under 1.2.4. I downloaded 1.2.5, and when I try to import any data (even the example files that come with the package) into either Artemis or Athena, they crash when they try to display on the graphics screen. To be specific, I can see the data get read in, but when it gets to the stage of graphing the data, the main Artemis or Athena screen vanishes, the program icons go away from the task bar, and the graphics screen remains, but it is blank. I had not yet determined for sure that this was the fault of the new version...I was going to try some things like redownloading it, and checking to see if 1.2.4 still runs, but if you're seeing this too it may be a problem. --Scott Calvin Sarah Lawrence College

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an input data question of Athena
by hsnuboy 05 Feb '04

05 Feb '04

Dear IFEFFIT folks, Hello, I've been on the mailing list for a long time. It's really helpful for the advice from every expert. I have a problem about data input into Athena. When I want to input my experimental data, Athena replied the cord said that: ############################################################ Use of uninitialized value in subtraction (-) at athena line 2828, <F> line 1. Tk::Error: wrong # args: should be ".frame3.frame.canvas bbox tagOrId ?tagOrId .. ...?" at Tk.pm line 228, <F> line 1. Tk callback for .frame3.frame.canvas [\&main::read_file,0] (menu invoke) ############################################################ and I caanot input my data in to Athena. Is there anyone happens to know this problem? Thank you! Good day Yu-Chuan Lin

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W-O ss
by Tamas Varga 05 Feb '04

05 Feb '04

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Ifeffit 1.2.5
by Matt Newville 05 Feb '04

05 Feb '04

Hi Everyone, I've just posted Ifeffit 1.2.5 on the Ifeffit web pages and to Sourceforge.net. Source code, full windows installer, and Mac OS 10.3 installer are available. The automatic update for windows should be posted in the next couple of days. There are several bug fixes / improvements in the base Ifeffit library. Very briefly, the changes are: - improved feff path lists - fixed problems with spline() clamps - fixed problems with restraints in feffit(), - chi_noise() now estimates 'kmax_suggest', approximately the k-value above which the data is dominated by noise. - added random() command to generate arrays of random numbers. - screen messages for autobk/feffit/feff6 are now sent to a *.run file, and any errors cause a *.err file to be written. On Windows and Mac, the 'choose an input file' wrapper for these programs warn if an error happened, and offer to show you the *.run file. A more complete list of changes is below. The Windows installer contains (what I believe are) the latest versions of Athena, Artemis, and SixPack. The Mac version includes the latest versions of Athena and Artemis. Let me know if you have any questions or problems, --Matt * Version 1.2.5: bug fixes, improved feff path lists, fixed problems with spline() clamps, restraints in feffit(), altered screen messages for autobk/feffit/feff6, and added random() command to generate arrays of random numbers. - path lists for feffit(), ff2chi(), erase(), and show() can now range over undefined paths, so that feffit(1-100,...) will use all *currently defined* paths between 1 and 100 (inclusive), even if only paths 2, 8, and 55 are defined. Here are some related changes: o path indices are strictly checked to be in the range 1..9999. o since the maximum path index is 9999, the list '1-9999' means 'all defined paths'. This can be abbreviated as 'all', as in: ff2chi(all,group=ff) which will sum all curently defined paths. o erase(@paths) and erase(@path=all) are now equivalent, both erasing all defined paths. o when erasing a path, the feff data associated with a path will be freed (if it's not in use by another path) so that new feff paths can be used. - added random() command, to generate an array of random numbers, using uniform, gaussian, or normal distributions. syntax is: random(output=my.random, npts=200, dist=normal, sigma=2.) where sigma will be (approximately) the standard deviation of the normal and gaussian distributions, or the scale of the uniform distribution. Sigma is 1 unless explicitly set. You can optionally reset the seed of the random number generator with the seed keyword. The gaussian and normal distribution appear very similar, and can both be used to simulate noise in data. - chi_noise() now generates 'kmax_suggest', an estimate of the maximum usable k-value for the data, based on the estimated noise in the data. In early tests, this appears to be a reasonable estimate for 'noisy data', and a bit pessimistic for clean data. Please use view this value as a guide. - clamps in spline() now try to bring chi() to zero at kmax/emax and kmin/emin instead af last and first data point. - an error in feffit() for how multiple restraints were applied has been fixed. multiple restraints can now be applied and mixed freely with multiple k-weights and multiple data sets. - improved screen messages printed by autobk/feffit/feff6: o replaced all print* statements with 'call echo()' o messages 'echo'ed to the screen are now 'tee'd to the run files autobk/feffit/feff6.run o replace all 'stop' statements with a 'call echo()' and the creation of an error file autobk/feffit/feff6.err. If this file exists after a run of autobk/feffit/feff6, then an error did occur; after successful runs, the error file will not exist.

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combining marked groups
by dmc＠pdx.edu 04 Feb '04

04 Feb '04

Ifeffit Dudes, I've tried to plot several groups together in Athena and then saved them together under "Save Marked Groups---chi(k)." It seems to work fine, but then when I try to open it up in Artemis I can't do anything. If I try to graph something, it closes. I can't do a fit b/c there are no parameters. My question is this: how can I average and then fit several data files? Thanks, Dan

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the exact edge position
by gabriel rosenblum 02 Feb '04

02 Feb '04

Hi I would like to know what is the exact way to find the edge position of a sample, and I wonder If anyone can help. Currently, I analyze few samples with minor changes, and I suspect those changes might affect edge shifts. The different samples are absolutely aligned, and the next step is to find the edge position of each, and compare the shifts with respect to the reference. When using ATHENA, a circle appears approximately where the edge should be, whereas a different result for the edge position appears when analyzing with UWEXAFS package � by viewing the maximum point of the first derivative of mu(E). I would also like to know, what is the correct definition of the edge position. Thanks. Gabi. __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://webhosting.yahoo.com/ps/sb/

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Spine Clamps and Some Fit Results
by dmc＠pdx.edu 29 Jan '04

29 Jan '04

Dear Panel of Feffit Experts, I have two questions for you, with several parts. I am looking at Lithium Cobalt Oxide annealed at 200 C. (1) In Athena what exactly do the varying levels of spine clamps mean? When do I need to use them? I've been ignoring them up to now, but I think that it might help my resulting fit, which brings me to my second part. (2) By looking at my results is there any advice you can give me? Do my reduced chi-squared, R-factor and correlated variables look good? I know that the R-Factor should be below 0.05, but what about red chi-squared (depends on the material)? Also, I am concerened that my amp (SO^2) should be closer to 1. I am using the einstien model and e01 refers to the farther 3 of my 4 paths. What else should I consider? Thanks, Dan Carter Hunter College Results: Independent points = 11.225585938 Number of variables = 5.000000000 Chi-square = 66.894398861 Reduced Chi-square = 10.745076774 R-factor = 0.040027549 Measurement uncertainty (k) = 0.002990761 Measurement uncertainty (R) = 0.069932022 Number of data sets = 1.000000000 Guess parameters +/- uncertainties: e0 = -3.9151859 +/- 2.3534572 delr = -0.0189516 +/- 0.0134287 ampg = 0.9492922 +/- 0.0001603 e01 = -9.3741702 +/- 2.5615506 theta = 415.2229263 +/- 89.8481275 Restraints: amp = 0.7077880 Set parameters: ampt = 0.9500000 scale = 1000.0000000 temp = 300.0000000 Correlations between variables: ampg and theta --> -0.9015 delr and e01 --> 0.8551 e0 and delr --> 0.7809 e0 and e01 --> 0.6858 All other correlations are below 0.25

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