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

RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide
by Kelly, Shelly D. 29 Oct '04

29 Oct '04

Hi Dan, I would suggest using one ezero with three different delr values for these three paths. You are introducting only one more variable. delr and ezero are correlated so by constraining delr you need more ezero values or vise versa. Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Friday, October 29, 2004 10:25 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Fitting Commercial Molybdenum Disulfide > > > Mike & list, > > Where can I find a reasonable model for my delr terms, > if I do assume > that the bond angles are changing/there is no isotropic > expansion? Is there a > description somewhere in the archives that I could look at? > > Creating different sigma squared parameters for each > path did help the R- Factor somewhat, but not the reduced > chi. Here's some data: > > > Fit with seperate sigma's: > > Independent points = 14.312500000 > Number of variables = 6.000000000 > Chi-square = 5778.957783654 > Reduced Chi-square = 695.212966455 > R-factor = 0.029041008 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0_1 = -4.0347670 +/- 2.9998980 > (guessed as -4.072009 > (1.919404)) > ss = 0.0042860 +/- 0.0005990 > (guessed as 0.004636 > (0.000411)) > e0 = 1.6770760 +/- 1.3230290 > (guessed as 1.765958 > (1.154388)) > alpha = 0.0009180 +/- 0.0034050 > (guessed as 0.001090 > (0.002843)) > ss2 = 0.0048160 +/- 0.0006910 (0.0000) > ss3 = 0.0225310 +/- 0.0657250 (0.0000) > Def parameters: > delr_1 = 0.0036440 > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0_1 and alpha --> 0.8542 > e0 and alpha --> 0.8470 > e0_1 and e0 --> 0.7407 > e0_1 and ss3 --> 0.7060 > alpha and ss3 --> 0.4715 > ss2 and ss3 --> -0.4214 > e0_1 and ss2 --> -0.3892 > e0 and ss3 --> 0.3772 > alpha and ss2 --> -0.2680 > All other correlations are below 0.25 > > > > > > > > > Fit without (original): > > > Independent points = 14.312500000 > Number of variables = 4.000000000 > Chi-square = 6562.747150128 > Reduced Chi-square = 636.387602437 > R-factor = 0.032979787 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0_1 = -4.0720130 +/- 1.9194050 > (guessed as -4.072009 > (1.919404)) > ss = 0.0046360 +/- 0.0004110 > (guessed as 0.004636 > (0.000411)) > e0 = 1.7659560 +/- 1.1543880 > (guessed as 1.765958 > (1.154388)) > alpha = 0.0010900 +/- 0.0028430 > (guessed as 0.001090 > (0.002843)) > > Def parameters: > delr_1 = 0.0043250 > > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0_1 and alpha --> 0.8416 > e0 and alpha --> 0.8045 > e0_1 and e0 --> 0.7141 > All other correlations are below 0.25 > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide
by Kelly, Shelly D. 29 Oct '04

29 Oct '04

Hi Dan, Take a look at the fit in q-space with the model below. I suspect that you have left out important Multiple scattering paths that would cause a miss-fit to the data at low k values. To test for this, change the fit range to something like 4.0 1/Anstroms for k-min value, and try again. Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Friday, October 29, 2004 11:03 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide > > > Hi Shelly, > > I seperated the delr's with different alpha terms, but > Mike seems to think > that this is assuming isotropic expansion that isn't there. > Also, the reduced > chi-square has gone up 150 or so. > > delr# define: alpha# * reff > > > Thanks for the help, Dan > > > Results with 1 eO and differing delr's: > > Independent points = 14.312500000 > Number of variables = 7.000000000 > Chi-square = 6186.771083042 > Reduced Chi-square = 846.054165202 > R-factor = 0.031090393 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > ss = 0.0042720 +/- 0.0006590 > (guessed as 0.004636 > (0.000411)) > e0 = 1.3293700 +/- 1.4673640 > (guessed as 1.765958 > (1.154388)) > alpha = -0.0001750 +/- 0.0040010 > (guessed as 0.001090 > (0.002843)) > ss2 = 0.0043180 +/- 0.0007370 (0.0000) > ss3 = 0.0072300 +/- 0.0164390 (0.0000) > alpha2 = 0.0076940 +/- 0.0027880 (0.0000) > alpha3 = -0.0512670 +/- 0.0232140 (0.0000) > > Def parameters: > delr_1 = -0.0006930 > delr_2 = 0.0305320 > delr_3 = -0.2034430 > > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0 and alpha --> 0.8441 > ss3 and alpha2 --> 0.7651 > ss2 and alpha2 --> -0.6441 > e0 and alpha2 --> 0.5682 > ss2 and ss3 --> 0.4871 > alpha and alpha2 --> 0.4785 > ss3 and alpha3 --> 0.3825 > e0 and alpha3 --> -0.2743 > All other correlations are below 0.25 > > > > > > Original (2 e0s): > > > Independent points = 14.312500000 > Number of variables = 6.000000000 > Chi-square = 5778.957783654 > Reduced Chi-square = 695.212966455 > R-factor = 0.029041008 > Measurement uncertainty (k) = 0.000181935 > Measurement uncertainty (R) = 0.004860095 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > e0_1 = -4.0347670 +/- 2.9998980 > (guessed as -4.072009 > (1.919404)) > ss = 0.0042860 +/- 0.0005990 > (guessed as 0.004636 > (0.000411)) > e0 = 1.6770760 +/- 1.3230290 > (guessed as 1.765958 > (1.154388)) > alpha = 0.0009180 +/- 0.0034050 > (guessed as 0.001090 > (0.002843)) > ss2 = 0.0048160 +/- 0.0006910 (0.0000) > ss3 = 0.0225310 +/- 0.0657250 (0.0000) > > Def parameters: > delr_1 = 0.0036440 > > Set parameters: > amp = 0.7 > > > Correlations between variables: > e0_1 and alpha --> 0.8542 > e0 and alpha --> 0.8470 > e0_1 and e0 --> 0.7407 > e0_1 and ss3 --> 0.7060 > alpha and ss3 --> 0.4715 > ss2 and ss3 --> -0.4214 > e0_1 and ss2 --> -0.3892 > e0 and ss3 --> 0.3772 > alpha and ss2 --> -0.2680 > All other correlations are below 0.25 > > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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to Gael Poirier
by Bruce Ravel 27 Oct '04

27 Oct '04

Hi folks, Recently Gael Poirier has been having a problem using Athena with some XANES data. For whatever reason, when I send mail to Gael it gets bounced back. But he seems to receive mail from the mailing list. Go figure. Sorry for filling up people mail boxes, but I am using the list to send this along... B =============================================================== Gael, Thanks for sending the data. It is now clear what went wrong. I recently made a change in how Athena tries to detect xanes data, that is data that does not extend very far into the extended region. The advantage of identifying data that is xanes and not exafs is that Athena then does not have to do a background removal, which saves a little bit of time doing chores like alignment and normalization. Sadly, you have uncovered a bug. That happens. Your bug is that the kmax for the fourier transform gets set to when the data are imported as xanes. Then Athena mistakenly aborts when it sees this, even though no FT will be performed. Oops! Fortunately there is an easy work-around. When you import the data, explicitly import them as mu(E) rather than xanes(E). The only draw-back of doing so is that Athena will do a background removal every time you change the normalization parameters. That's not a big loss. Thanks for pointing this out. I will certainly fix this in the next release. -- 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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citing Artemis and Athena?
by k-kupiecki＠northwestern.edu 27 Oct '04

27 Oct '04

Hi everyone, I'm in the process of writing up my thesis and I've used Athena and Artemis quite a bit for the analysis of my SEXAFS data.... I was wondering what is the appropriate way to give references for this software and it's use? To my knowledge there are journal articles etc. regarding AUTOBK, FEFFIT, etc. Do I cite those? are there additional ways I should cite to give credit for Athena and Artemis too? Thanks for any suggestions you have! -Kristine Witkowski

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Re: Ifeffit Digest, Vol 20, Issue 22
by Michel Jaouen 25 Oct '04

25 Oct '04

>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: Artimis (Matt Newville) > 2. RE: Artimis (Scott Calvin) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sat, 23 Oct 2004 13:46:12 -0500 (CDT) >From: Matt Newville <newville(a)cars.uchicago.edu> >Subject: RE: [Ifeffit] Artimis >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <Pine.LNX.4.44.0410222107350.19561-100000@corvette> >Content-Type: TEXT/PLAIN; charset=US-ASCII > > >> I did encounter that "No absorbing atom (ipot=0) defined" error >> sometimes, but I run Artemis only after I have feff calculations >> done. > >I don't understand whether Feff ran to completion or not. Are you >saying that you made a successful run of Feff (including real >output files) but that Artemis still failed to read this >calculation? That seems pretty strange. > >> By the way, I use FEFF8. > >For Feff8, I believe you need to be much more careful about line >endings. It's not able to use Windows line-endings on unixes, for >example. > >But also: why would you use Feff8 for EXAFS analysis, as with >artemis?? Feff8 is a XANES code. As far as I know, it does not >give any improvements for EXAFS. > >--Matt > > > > > >------------------------------ > >Message: 2 >Date: Sun, 24 Oct 2004 11:23:03 -0400 >From: Scott Calvin <SCalvin(a)slc.edu> >Subject: RE: [Ifeffit] Artimis >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Cc: SCalvin(a)slc.edu >Message-ID: <a06010203bda178b3a7b7(a)[130.132.241.87]> >Content-Type: text/plain; charset="us-ascii" ; format="flowed" > >> >>But also: why would you use Feff8 for EXAFS analysis, as with >>artemis?? Feff8 is a XANES code. As far as I know, it does not >>give any improvements for EXAFS. > > >FEFF8 does give at least one improvement for EXAFS, which I've used >on occasion: the self-consistent field calculation can be used to >give an improved estimate of E0 prior to fitting. > >--Scott Calvin >Sarah Lawrence College > I agree with Scott: SCF calculation gives more reliable estimate of E0 because the Fermi level is more accurate. It makes that, when several atomic species are involved, you only need in principle one E0 for fitting (I have verified this point, at least for the case I'm presently working on). >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 20, Issue 22 >*************************************** -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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Re: Ifeffit Digest, Vol 20, Issue 22
by Michel Jaouen 25 Oct '04

25 Oct '04

Yongsheng, > > I did encounter that "No absorbing atom (ipot=0) defined" error >> sometimes, but I run Artemis only after I have feff calculations >> done. > >I don't understand whether Feff ran to completion or not. Are you >saying that you made a successful run of Feff (including real >output files) but that Artemis still failed to read this >calculation? That seems pretty strange. > >> By the way, I use FEFF8. > >For Feff8, I believe you need to be much more careful about line >endings. It's not able to use Windows line-endings on unixes, for >example. Artemis works fine for me (on a Mac) with feff8: just ask in the menu for Import feff calculation and choose the folder where is your feff8 calculation where you must have: feff.inp feffXXX.dat files files.dat paths.dat BUT ALL files must be Unix! Following Matt's advice, use BBEdit Lite (that's free or if you had some money buy BBEdit (the last vesrion is 8): that is really a very good Editor (the best for me) on Mac. Then open your files, check the option button and select Unix for Line Breaks. Best regards Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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RE: [Ifeffit] Artimis
by Chen, Yongsheng 23 Oct '04

23 Oct '04

Hi Bruce, Thanks for your advices. I did edit my Feff.inp in Word, but did not have any problems with the old version. I tried the cleaned up Feff.inp you sent me, it worked better in the sense that I could close Artemis after the warning appeared again, with my own version, I would have to use ForceQuit. I am a new mac user. I try to understand the message in the artemis.trap, although it's a text file, I do not understand too much. I sort of remember there is a notice about Perl version on some website. I have seen 'Perl' appearing in the trap file in many places, is this relative to the problem? Thanks for your help. Yongsheng > ---------- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Bruce Ravel > Reply To: ravel(a)phys.washington.edu;XAFS Analysis using Ifeffit > Sent: Friday, October 22, 2004 10:49 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artimis > > <<File: feff.inp>><<File: ATT1852209.txt>> > On Friday 22 October 2004 12:30 pm, Chen, Yongsheng wrote: > > I installed the lastest version of Artemis, but met problems when trying to > > import FEFF calculations. The trap file and the feff input file are > > attached. The old version worked fine. I have a mac. > > Yongsheng, > > What is the history of the files you sent? The feff.inp file you > included in your email has a large number of non-printable chatracters > at the beginning of the file and all of the lines are terminated by > Macintosh end-of-line characters (that is, carriage return (ascii 13), > rather than line-feed (ascii 10)). Artemis currently makes no effort > to deal correctly with Mac EOL characters and Feff (as compiled on an > OSX, which is really a version of Unix under the hood) will not do so > either. Some quick tests suggested that is the case. > > So, there seems to be two problems with the feff.inp file you sent me > > 1. The junk characters at the beginning of the file. Those will > certainly confuse feff. > > 2. The end-ol-line characters. > > You can probably fix both by opening up the feff.inp file in any text > editor, stripping out the junk at the top of the file and explicitly > saving the file as a unix text file. I am sure that some of the Mac > users on the list can provide more details should you need it. > > I am suspicious that you might have edited the feff.inp file with a > word processor (such as MS Word). That is a very poor idea because it > can be hgard to avoid the situation where the word processor inserts > additional, not-for-display information in the file that neither > Artemis nor Feff will know how to deal with. If you create your > feff.inp files outside of Artemis, you must be careful not to do so in > a way that inserts additional stuff into the file. > > When I cleaned up the feff.inp file you sent, Artemis had no problem > with it. > > I suppose that another possibility is that the file became > "contaminated" after you tried it in Artemis but before I received > your email. If that is the case, it is really important that you fix > that and try submitting your question again. It is possible that you > are seeing some deeper problem in Artemis, but that I am focussing on > the ways in which the file became contaminated. That's a problem > because I am therefore not addressing the real issue. > > Attached is the cleaned up file, which works for me. > > Regards, > B > > -- > 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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Athena
by Gael Poirier 22 Oct '04

22 Oct '04

Hi Bruce, I have a problem with Athena version 0.8.032. When I select several opened groups as marked groups and plot them in E (using plot marked groups in E), it doesn't work and only the last opened spectrum appears in the graphic window. The program gives an error message:"ERROR:the minimum value of the forward fourier transform range exceeds the maximum value". However, I've tried with Athena 0.8.024 (IFEFFIT 1.2.5) and it worked very well. How can I plot all the groups in the same graphic window using Athena 0.8.032? Thank you very much Gael

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Artimis
by Chen, Yongsheng 22 Oct '04

22 Oct '04

Hi Bruce, I installed the lastest version of Artemis, but met problems when trying to import FEFF calculations. The trap file and the feff input file are attached. The old version worked fine. I have a mac. Thanks a lot. Yongsheng <<ARTEMIS.TRAP>> <<feff.inp>>

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RE : RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 21 Oct '04

21 Oct '04

Hello Thank you very much for your help Matt. Your advice was quite obvious in fact but I followed it to use horae_update properly. Thanks to that, I could see what was my first problem. I had an error about Aquaterm (the installation script couldn't find an Aquaterm library file (aquaterm.1.0.0.dylib I believe). So, I re-installed Aquaterm (the latest version found on SourceForge). And then, the installation was perfect, without any error anymore. And, here is now my second problem. When I open a project file (a '.chi' file) in Artemis, the program takes about 5s to try to open it (with the comment 'plotting in r space' at the bottom of the window), and then crashes down... I'm really sorry! Any other help or any idea? Thank you David > -----Message d'origine----- > De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] De la part de Matt Newville > Envoyé : jeudi 14 octobre 2004 23:54 > À : XAFS Analysis using Ifeffit > Objet : Re: RE : [Ifeffit] Is artemis running on G5 Mac, > > > On Thu, 14 Oct 2004, POGER David 202545 wrote: > > > I fear it doesn't work for me. I have untared the Horae-045.tar > > file in the Ifeffit directory. And when I type 'perl > > Makefile.PL', the installation script crashes and says 'Could > > not open /config/Config.mak file for reading'. The Greek gods > > may not be with me! I'll wait for the next tarball... Thanks a > > lot in adavance! > > This is probably still an issue with permissions, but I'm not sure > what you did exactly. It sounds like you tried to run horae_update > in the Applications/Ifeffit directory. If so, this probably won't > work, as you probably do NOT have write permissions to the > /Applications/Ifeffit directory, and horae_update creates a > folder (horae-045) to build the code it will install. > > Let me be more specific. Sorry if most of this is obvious! > 1. Open a Terminal > 2. move to your home directory: Type 'cd'. > 3. run horae_update with permission to write to the > /Library/Perl and /Applications/Ifeffit. Type > 'sudo horae_update'. When prompted for a password, > type the password for your user account (that is, > the same one you logged in as). > > 4. If you get a message that says 'command not found', then > read the message. > a) if the message begins 'bash: ... command not found' > then type '. /Applications/Ifeffit/bin/iff_init.sh' > Yes, that's a '.' followed by a space. > b) if the message begins 'tcsh: ... command not found' > then type 'source /Applications/Ifeffit/bin/iff_init.csh' > > Then do 'sudo horae_udate' again. > > If you already have the horae-045.tar.gz file, 'sudo horae_update' > is exactly the same as: > tar xvzf horae-045.tar.gz > cd horae-045 > perl Makefile.PL > sudo make install > > Once the installation is successful, you can remove the > 'horae-045' folder. > > --Matt > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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