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

RE: [Ifeffit] Fitting Commercial Molybdenum Disulfide
by Kelly, Shelly D. 05 Nov '04

05 Nov '04

Hi Dan, Sigma2 can not be negative. It is the mean square displacement of the half path length. You can force it to be positive by using abs(ss) on the definition page for each path in the fit. Shelly > -----Original Message----- > From: dmc(a)pdx.edu [mailto:dmc@pdx.edu] > Sent: Thursday, November 04, 2004 10:19 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Fitting Commercial Molybdenum Disulfide > > Hi List, > > Here's my most recent data. I was able to look at the individual > paths > and changed my R-range to 2-4.5 angstroms on the first set of data, I set > the > second set of data to the same range, although 4 works better as a maximum > for > that set. The k-range on the second range had to be truncated though. > > Six paths are used for each fit, same parameters, except for amp (0.7 for > one > ~0.8 for the other). The seperate data sets still have a few parameters > that > are outside of the error bars of the other (ss2,ss3,ss4,alpha, > alpha2,alpha5). > What can I do to get these beamlines to agree? > > delr_# define alpha# * reff > all other parameters guessed. > ss for each path, only one e0 for all > > Thanks for the help, Dan > > > First Data set -- Full k-range works best, Full range used for fit. > Project title : Fitting merge 10_15_04.chi > > Guess parameters +/- uncertainties (initial guess): > e0 = 0.8686930 +/- 1.1038290 (guessed as 0.868694 > (1.103841)) > ss = 0.0041150 +/- 0.0004990 (guessed as 0.004115 > (0.000499)) > ss2 = 0.0044360 +/- 0.0004450 (guessed as 0.004436 > (0.000445)) > ss3 = 0.0243560 +/- 0.0201400 (guessed as 0.024368 > (0.020159)) > ss4 = -0.0065470 +/- 0.0047820 (guessed as -0.006545 > (0.004786)) > ss5 = -0.0016100 +/- 0.0050490 (guessed as -0.001611 > (0.005047)) > ss6 = 0.0059980 +/- 0.0139390 (guessed as 0.005996 > (0.013935)) > alpha = -0.0011360 +/- 0.0029380 (guessed as -0.001136 > (0.002938)) > alpha2 = 0.0071480 +/- 0.0019780 (guessed as 0.007148 > (0.001978)) > alpha3 = -0.0060900 +/- 0.0273580 (guessed as -0.006078 > (0.027378)) > alpha4 = -0.0198570 +/- 0.0154200 (guessed as -0.019851 > (0.015430)) > alpha5 = 0.1399050 +/- 0.0148530 (guessed as 0.139906 > (0.014848)) > alpha6 = 0.0199630 +/- 0.0268690 (guessed as 0.019961 > (0.026862)) > > Def parameters: > delr_1 = -0.0051820 > delr_2 = 0.0326180 > delr_3 = -0.0277930 > delr_4 = -0.0906110 > delr_5 = 0.6384270 > delr_6 = 0.0910950 > > Set parameters: > amp1 = .7 > > > Correlations between variables: > e0 and alpha --> 0.8170 > e0 and alpha2 --> 0.6726 > ss and ss2 --> 0.6591 > alpha and alpha2 --> 0.5516 > alpha5 and alpha6 --> -0.4856 > e0 and alpha3 --> 0.4083 > alpha3 and alpha4 --> 0.3588 > ss5 and ss6 --> -0.3581 > alpha and alpha3 --> 0.3100 > alpha2 and alpha3 --> 0.3045 > ss2 and alpha6 --> 0.2745 > e0 and ss3 --> 0.2649 > ss and ss3 --> 0.2627 > ss2 and ss3 --> 0.2626 > ss6 and alpha5 --> -0.2510 > All other correlations are below 0.25 > > > > > > > > > > > > Second Data Set -- Trucated k-range (2-13.5) > Project title : Fitting merge 10_15_04.chi > > Independent points = 25.270507813 > Number of variables = 14.000000000 > Chi-square = 1202.598221935 > Reduced Chi-square = 106.703108852 > R-factor = 0.057229121 > Measurement uncertainty (k) = 0.000827712 > Measurement uncertainty (R) = 0.022111003 > Number of data sets = 1.000000000 > > > Guess parameters +/- uncertainties (initial guess): > amp = 0.7976070 +/- 0.1361170 (guessed as 0.776348 (0.139898)) > ss = 0.0037770 +/- 0.0015530 (guessed as 0.003589 > (0.001617)) > e0 = 0.5608430 +/- 1.8018380 (guessed as 0.642687 > (1.861307)) > alpha = -0.0061290 +/- 0.0049080 (guessed as -0.005966 > (0.005078)) > ss2 = 0.0029050 +/- 0.0009970 (guessed as 0.002686 > (0.001078)) > ss3 = 0.0075410 +/- 0.0094220 (guessed as 0.005992 > (0.008858)) > ss4 = -0.0110250 +/- 0.0035850 (guessed as -0.011776 > (0.004653)) > ss5 = -0.0042000 +/- 0.0078070 (guessed as -0.007610 > (0.005250)) > alpha2 = 0.0038110 +/- 0.0030450 (guessed as 0.003762 > (0.003187)) > alpha3 = -0.0037820 +/- 0.0145580 (guessed as 0.001200 > (0.015976)) > alpha4 = -0.0212550 +/- 0.0107080 (guessed as -0.011852 > (0.014417)) > alpha5 = 0.1151980 +/- 0.0236640 (guessed as 0.113430 > (0.014973)) > ss6 = 0.0028560 +/- 0.0166050 (guessed as -0.007250 > (0.003624)) > alpha6 = 0.0193530 +/- 0.0299640 (guessed as 0.001791 > (0.008195)) > > Def parameters: > delr_1 = -0.0279670 > delr_2 = 0.0173920 > delr_3 = -0.0172570 > delr_4 = -0.0969910 > delr_5 = 0.5256830 > delr_6 = 0.0883130 > > > Correlations between variables: > amp and ss --> 0.8382 > e0 and alpha --> 0.8048 > amp and ss2 --> 0.7964 > e0 and alpha2 --> 0.7533 > ss3 and alpha5 --> 0.7397 > ss5 and alpha4 --> -0.6999 > ss and ss2 --> 0.6591 > alpha and alpha2 --> 0.6159 > alpha5 and ss6 --> 0.6116 > ss5 and alpha3 --> -0.5790 > ss5 and alpha6 --> -0.5023 > ss3 and ss6 --> 0.4804 > alpha4 and alpha5 --> -0.4375 > e0 and alpha3 --> 0.4083 > ss4 and ss5 --> -0.4047 > ss3 and alpha4 --> -0.3972 > alpha5 and alpha6 --> 0.3827 > alpha3 and alpha6 --> 0.3498 > ss3 and ss5 --> -0.3278 > amp and ss3 --> 0.3209 > ss4 and ss6 --> 0.3181 > alpha and alpha3 --> 0.3100 > alpha2 and alpha3 --> 0.3045 > ss4 and alpha3 --> 0.2948 > amp and ss5 --> 0.2820 > ss2 and alpha6 --> 0.2745 > ss and ss3 --> 0.2627 > ss2 and ss3 --> 0.2626 > amp and alpha6 --> 0.2589 > alpha2 and alpha5 --> 0.2581 > All other correlations are below 0.25 > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Fitting Commercial Molybdenum Disulfide
by dmc＠pdx.edu 04 Nov '04

04 Nov '04

Hi Mailing list, I'm back at fitting commercial Molybdenum Disulfide to a Hexagonal p 63/m m c space group. Although my present fit is reasonable, thanks to the mailing list in August, I was hoping someone might have more suggestions to optimize it. Also, in order to better my fit, I still have seperate e0's, one for the first path, one for the remaining 2 paths. I haven't gotten a satisfactory physical explanation for this and I thought someone might have a good one. Also, the data on the same sample from two different beamlines seems to be somewhat different, namely the Reduced chi-square is very different (75.6 in one, 636.4 in the other). In both cases I use the first 3 single scattering paths. I may have included too much info, but better too much than too little. Thank You, Dan Carter Here are my parameters in both cases, values differ somewhat: Set: Amp = 0.7 guess: eO ~ 1.57 (1.52) (used for first path) guess: eO_1 ~ -4.77 (2.43) (used for remaining 2 paths) guess: ss ~ 0.0027 (0.000427) guess: alpha ~ -0.004 (0.003255) (positive for second fit) delr_1: alpha*reff First Fit: Project title : Fitting merge 10_15_04.chi Comment : Prepared by : Contact : Started : 11:49:36 on 22 October, 2004 This fit at : 11:10:57 on 28 October, 2004 Environment : Artemis 0.7.010 using Windows 2000, perl 5.006001, Tk 800.024, and Ifeffit 1.2.6 ============================================================ Independent points = 14.312500000 Number of variables = 4.000000000 Chi-square = 779.303886008 Reduced Chi-square = 75.568861674 R-factor = 0.041210572 Measurement uncertainty (k) = 0.000827712 Measurement uncertainty (R) = 0.022111003 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0_1 = -4.7737110 +/- 2.4268840 (guessed as -4.773687 (2.426889)) ss = 0.0027360 +/- 0.0004270 (guessed as 0.002736 (0.000427)) e0 = 1.5684690 +/- 1.5209160 (guessed as 1.568507 (1.520918)) alpha = -0.0040060 +/- 0.0032550 (guessed as -0.004006 (0.003255)) Def parameters: delr_1 = -0.0158980 Set parameters: amp = 0.7 Correlations between variables: e0_1 and alpha --> 0.8622 e0 and alpha --> 0.7870 e0_1 and e0 --> 0.7064 All other correlations are below 0.25 Project title : Fitting merge 10_15_04.chi Comment : Prepared by : Contact : Started : 11:49:36 on 22 October, 2004 This fit at : 11:10:57 on 28 October, 2004 Environment : Artemis 0.7.010 using Windows 2000, perl 5.006001, Tk 800.024, and Ifeffit 1.2.6 ============================================================ Independent points = 14.312500000 Number of variables = 4.000000000 Chi-square = 779.303886008 Reduced Chi-square = 75.568861674 R-factor = 0.041210572 Measurement uncertainty (k) = 0.000827712 Measurement uncertainty (R) = 0.022111003 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): e0_1 = -4.7737110 +/- 2.4268840 (guessed as -4.773687 (2.426889)) ss = 0.0027360 +/- 0.0004270 (guessed as 0.002736 (0.000427)) e0 = 1.5684690 +/- 1.5209160 (guessed as 1.568507 (1.520918)) alpha = -0.0040060 +/- 0.0032550 (guessed as -0.004006 (0.003255)) Def parameters: delr_1 = -0.0158980 Set parameters: amp = 0.7 Correlations between variables: e0_1 and alpha --> 0.8622 e0 and alpha --> 0.7870 e0_1 and e0 --> 0.7064 All other correlations are below 0.25 ===== Data set >>merge 6_17_04.chi<< ======================================== file: C:\Ifeffit\horae\stash\artemis.project.3\chi_data\merge 6_17_04.chi title lines: Athena data file -- Athena version 0.8.032 Saving merge 6_17_04 (group=merge) as chi(k) . Element=Mo Edge=K Background parameters . E0=20007.492 Eshift=0.000 Rbkg=1.000 . Standard=None . Kweight=2.0 Edge step=0.749 . Fixed step=no Flatten=yes . Pre-edge range: [ -150.000 : -75.000 ] . Normalization range: [ 150.000 : 895.199 ] . Spline range: [ 0.952 : 995.207 ] Clamps: None/Strong Foreward FT parameters . Kweight=2 Window=kaiser-bessel Phase correction=no . k-range: [ 2.000 : 16.100 ] dk=0.00 Backward FT parameters . R-range: [ 1.000 : 3.000 ] . dR=0.00 Window=kaiser-bessel Plotting parameters . Multiplier=1 Y-offset=0.000 . Merge in k space of: ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.101 (mos2_101) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.102 (mos2_102) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.103 (mos2_103) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.104 (mos2_104) k-range = 2.000 - 13.500 dk = 2.000 k-window = kaiser-bessel k-weight = 2 R-range = 1.000 - 3.000 dR = 0.100 R-window = kaiser-bessel fitting space = R background function = none phase correction = none R-factor for this data set = 0.74613 Second Fit: Project title : Fitting merge 10_15_04.chi Comment : Prepared by : Contact : Started : 11:49:36 on 22 October, 2004 This fit at : 11:23:36 on 28 October, 2004 Environment : Artemis 0.7.010 using Windows 2000, perl 5.006001, Tk 800.024, and Ifeffit 1.2.6 ============================================================ Independent points = 14.312500000 Number of variables = 4.000000000 Chi-square = 6562.747150466 Reduced Chi-square = 636.387602469 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 = -4.0720090 +/- 1.9194040 (guessed as -4.773711 (2.426884)) ss = 0.0046360 +/- 0.0004110 (guessed as 0.002736 (0.000427)) e0 = 1.7659580 +/- 1.1543880 (guessed as 1.568469 (1.520916)) alpha = 0.0010900 +/- 0.0028430 (guessed as -0.004006 (0.003255)) 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 ===== Data set >>merge 10_15_04.chi<< ======================================== file: C:\Ifeffit\horae\stash\artemis.project.3\chi_data\merge 10_15_04.chi title lines: Athena data file -- Athena version 0.8.032 Saving merge 6_17_04 (group=merge) as chi(k) . Element=Mo Edge=K Background parameters . E0=20007.492 Eshift=0.000 Rbkg=1.000 . Standard=None . Kweight=2.0 Edge step=0.749 . Fixed step=no Flatten=yes . Pre-edge range: [ -150.000 : -75.000 ] . Normalization range: [ 150.000 : 895.199 ] . Spline range: [ 0.952 : 995.207 ] Clamps: None/Strong Foreward FT parameters . Kweight=2 Window=kaiser-bessel Phase correction=no . k-range: [ 2.000 : 16.100 ] dk=0.00 Backward FT parameters . R-range: [ 1.000 : 3.000 ] . dR=0.00 Window=kaiser-bessel Plotting parameters . Multiplier=1 Y-offset=0.000 . Merge in k space of: ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.101 (mos2_101) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.102 (mos2_102) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.103 (mos2_103) ** C:/USERS/Dan2/raw data MoS2 6_17_04/MoS2.104 (mos2_104) k-range = 2.000 - 13.500 dk = 2.000 k-window = kaiser-bessel k-weight = 2 R-range = 1.000 - 3.000 dR = 0.100 R-window = kaiser-bessel fitting space = R background function = none phase correction = none R-factor for this data set = 0.71585 Paths used to fit Both Data Sets, degen, s02 the same. other values different: F1 p 63/m m c: feff0001.dat .. feff = C:\Ifeffit\horae\stash\artemis.project.3\data0.feff2\feff0001.dat id = reff= 2.4135, nlegs= 2, path= Mo<->S label = r = 2.416130 degen = 6.000000 s02 = 0.700000 e0 = 1.765958 dr = 0.002630 ss2 = 0.004636 F1 p 63/m m c: feff0002.dat .. feff = C:\Ifeffit\horae\stash\artemis.project.3\data0.feff2\feff0002.dat id = reff= 3.1500, nlegs= 2, path= Mo<->Mo label = r = 3.153433 degen = 6.000000 s02 = 0.700000 e0 = -4.072009 dr = 0.003433 ss2 = 0.004636 F1 p 63/m m c: feff0003.dat .. feff = C:\Ifeffit\horae\stash\artemis.project.3\data0.feff2\feff0003.dat id = reff= 3.9683, nlegs= 2, path= Mo<->S label = r = 3.972625 degen = 6.000000 s02 = 0.700000 e0 = -4.072009 dr = 0.004325 ss2 = 0.004636

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IFEFFIT: Writing more than 16 arrays with write_data()
by Matt Newville 04 Nov '04

04 Nov '04

Hi Norbert, (Replying to the whole group this time....) On Wed, 3 Nov 2004, Norbert Weiher wrote: > Matt, > > I was just discussing with Bruce about exporting more than 15 sets with the > write_data() command. I am doing fits with lots of paths and like to have it > exported to one file... would it be difficult to increase the number of > arrays exportable by this command above 16 in IFEFFIT? It would not be difficult, and the current limit is definitely too low. I think it's a two line fix. But there will still be a finite limit of number of arrays. So: is 100 arrays enough? Do you need a fixed source kit or dll? And how quickly? This doesn't seem like a full release change to me. I haven't made any source changes to the stable distribution since July. So a question for Bruce and everyone else: Are there any other bug reports or suggestions for changes to the core? --Matt

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Problem exporting fit data with ARTEMIS
by Norbert Weiher 02 Nov '04

02 Nov '04

Dear Friends, I did a multi-dataset fit (9 data sets) and had the following problem: When trying to export all the fits to a single file (using save marked groups as), I got an empty file and artemis trapped a warning like the following. For sake of reproducing, I attached the file. My Tk version is the one which we should use (i.e. not the newest one) and saving just the experimental data in just the same fashion works... Any ideas why this happens? Regards, Norbert -- Error message follows -- Tk::Error: Can't call method "dispose" on unblessed reference at /usr/bin/artemi s line 7971. main::save_selected at /usr/bin/artemis line 7971 [\&main::save_selected,k] Tk callback for .menu1.menu.menu7 Tk::__ANON__ at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm li ne 228 Tk::Menu::Invoke at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk/M enu.pm line 530 (command bound to event) main::__ANON__('Tk::Error: Can\'t call method "dispose" on unblessed ref erenc...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) l ine 402 Tk::Error('MainWindow=HASH(0x953f240)','Can\'t call method "dispose" on unblessed reference at /usr/b...','main::save_selected at /usr/bin/artemis line 7971','[\&main::save_selected,k]','Tk callback for .menu1.menu.menu7','Tk::__ANO N__ at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thr...','Tk::Menu::Invoke at /u sr/lib/perl5/site_perl/5.8.0/i586-linux...','(command bound to event)') called a t /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm line 340 eval {...} called at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-mu lti/Tk.pm line 340 Tk::MainLoop() called at /usr/bin/artemis line 1785 -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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RE: [Ifeffit] Artimis
by Chen, Yongsheng 02 Nov '04

02 Nov '04

Hi Matt, I did encounter that "No absorbing atom (ipot=0) defined" error sometimes, but I run Artemis only after I have feff calculations done. By the way, I use FEFF8. Thanks everybody for your kind help. I am afraid I can not do more test now since I am leaving tomorrow for Argonne for more XAFS experiments. Will check back if the problem remains after I have tried what you have suggested. Have a good weekend. Yongsheng > ---------- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Matt Newville > Reply To: XAFS Analysis using Ifeffit > Sent: Friday, October 22, 2004 2:20 PM > To: ravel(a)phys.washington.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artimis > > Hi, > > > On Friday 22 October 2004 4:38 pm, Chen, Yongsheng wrote: > > > Thanks for your advices. I did edit my Feff.inp in Word, but did not have > > > any problems with the old version. > > > > It is certainly possible to do so, but you MUST be careful to save the > > file as text. Because it is so easy to forget and just save in > > whatever format Word decides to use, I always discourage people from > > using Word for that purpose. > > Actually, Feff6 (and ifeffit) handle Unix and Windows line endings > just fine, but do have a harder time with Mac line-endings. I'm > not sure I know how to fix this: As far as I can tell it's at the > level of the fortran's read() statement. Sorry. > > One thing that confuses me is that Feff6 *should* have reported a > Feff 6L.02 > Fatal Error: No absorbing atom (ipot=0) defined > > which could have been used as a clue that something went wrong. > I don't know how artemis checks if a feff run went OK. > > > Hey Mac users! Could someone suggest a simple editor that Yongsheng, > > a new Mac user, should consider for the task of editing the kinds of > > text files that Feff and similar programs work with? > > TextEdit can save file with Unix-style line endings, especially if > you set the default to using 'Plain text' in the Preferences menu. > > BBedit is a popular and very good editor for Mac OS X. > > --Matt > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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Re: [Ifeffit] choosing dk values
by Scott Calvin 01 Nov '04

01 Nov '04

Hi Mike, I would add to Matt's reply that it is sometimes quite important to realize that for a Hanning window and similar windows where there is a "sill" over which the window function goes from 0 to 1, the sill extends from kmin-dk/2 to kmin+dk/2 and from kmax-dk/2 to kmax+dk/2. This means that as you increase dk you actually sample more k-space, albeit in a suppressed way. Why is this important? Suppose you have something really screwy in your data at k=11.9 inverse angstroms...a second edge comes to mind as a possibility. You might then reasonably set kmax to 11 and think you're staying away from the problem. (Well, it might be messing up your background, but that's an issue for another day...) But suppose you make dk = 2. Now you are actually sampling data up to k = 12, which includes the really screwy bit. In some cases that can be a source of problems...it took me a long time to catch on to that particular wrinkle when I was starting out! Of course, with Artemis and Athena this is easy to catch, because you can plot the window function by checking the box marked "Window" (that Bruce is a clever dude). --Scott Calvin Sarah Lawrence College At 01:13 PM 11/1/2004 -0600, you wrote: >Hi Mike, > >On Mon, 1 Nov 2004, Michael A Groves wrote: > >> I'm doing some fitting with Artemis, and I noticed that, for >> different values of dk, I get better or worse fits. The only >> information I've gotten so far about dk was in the IFEFFIT >> documentation, and it basically said, "Don't mess with it." >> Can anyone give me more information on choosing a good dk value? >> Or, should I just stick with the default? >>

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choosing dk values
by Michael A Groves 01 Nov '04

01 Nov '04

Hi all, I'm doing some fitting with Artemis, and I noticed that, for different values of dk, I get better or worse fits. The only information I've gotten so far about dk was in the IFEFFIT documentation, and it basically said, "Don't mess with it." Can anyone give me more information on choosing a good dk value? Or, should I just stick with the default? Thanks, Mike Groves

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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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