Hi all, I read your papers Anatoly. You fixed the value of S02 found in the Pt metal, and the expression in Artemis would be like this: N:1 x S02: amp·N, right?? I have a low value of S02 in the case of platinum (0.53), how can I solve the problem? Bond distances = delR + Reff (with phase correction)? Thank you very much, Best regards, JA
If you mean that your S02 value for platinum foil is 0.53 instead of the expected 0.85 or so, you have to first find out why that happened. There are too many (for a quick list) setup-related and sample-related reasons that can explain why it happened. You should be careful with your NP data analysis, since your foil EXAFS acts up. Anatoly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Juan Antonio Maciá Agulló Sent: Monday, December 04, 2006 2:03 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] CN and bond distances in Artemis Hi all, I read your papers Anatoly. You fixed the value of S02 found in the Pt metal, and the expression in Artemis would be like this: N:1 x S02: amp·N, right?? I have a low value of S02 in the case of platinum (0.53), how can I solve the problem? Bond distances = delR + Reff (with phase correction)? Thank you very much, Best regards, JA
Hi Juan, You're saying you have that low a value of S02 for a bulk platinum standard? Anatoly's right...you'd better figure out why before you continue. But one piece of advice I have: for a simple crystalline standard like platinum, by all means fit more than one coordination shell (with coordination numbers constrained)! That will be very helpful in diagnosing what is going on, and, for certain cases, might even solve the problem. Which brings up the first important question to ask...what is the uncertainty on the S02 of 0.53? --Scott Calvin Sarah Lawrence College At 02:03 PM 12/4/2006, you wrote:
Hi all,
I read your papers Anatoly. You fixed the value of S02 found in the Pt metal, and the expression in Artemis would be like this: N:1 x S02: amp·N, right?? I have a low value of S02 in the case of platinum (0.53), how can I solve the problem? Bond distances = delR + Reff (with phase correction)?
Did you check your data against someone else's? Maybe you have hole effect
or overabsorption.
mam
----- Original Message -----
From: "Scott Calvin"
Hi Juan,
You're saying you have that low a value of S02 for a bulk platinum standard? Anatoly's right...you'd better figure out why before you continue. But one piece of advice I have: for a simple crystalline standard like platinum, by all means fit more than one coordination shell (with coordination numbers constrained)! That will be very helpful in diagnosing what is going on, and, for certain cases, might even solve the problem.
Which brings up the first important question to ask...what is the uncertainty on the S02 of 0.53?
--Scott Calvin Sarah Lawrence College
At 02:03 PM 12/4/2006, you wrote:
Hi all,
I read your papers Anatoly. You fixed the value of S02 found in the Pt metal, and the expression in Artemis would be like this: N:1 x S02: amp·N, right?? I have a low value of S02 in the case of platinum (0.53), how can I solve the problem? Bond distances = delR + Reff (with phase correction)?
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi all, I did a multiple shell fit for platinum foil and the results were similar: S02 = 0.51 and the uncertainty varies from 0.02 to 0.03 depending on the fit. Please find enclosed a file with values of energy, I0 and I of the platinum foil. I include this file if someone has curiosity on raw data and has time, otherwise forget it. Maybe I can suppose a value of 0.85 for S02 and follow with the analysis of the data, then...CN equation proposed in the first e-mail is ok? Thank you very much Best regards, JA 11297.93828 2878 372358 11306.20956 2906 372292 11314.43751 2914 372058 11322.95624 2928 371952 11331.26478 2944 371682 11339.80927 2960 371614 11348.08699 2992 371372 11356.65728 3006 371244 11365.01615 3044 371104 11373.66867 3082 370976 11381.94038 3120 370776 11390.5627 3152 370662 11399.02884 3190 370420 11407.73406 3218 370214 11415.99953 3270 370056 11424.61761 3328 369524 11433.13526 3366 368060 11441.89347 3444 367558 11450.2663 3570 368788 11458.87993 3644 363456 11467.62108 10656 1026572 11468.65034 10738 1030714 11469.27942 11064 1052010 11469.96578 11292 1071180 11470.76663 11450 1079322 11471.45316 11466 1080080 11472.08256 11502 1078352 11472.76926 11576 1081712 11473.51327 11638 1082000 11474.31463 11626 1079298 11475.00159 11692 1078474 11475.80316 11694 1073826 11476.54757 11730 1076298 11477.17754 11728 1072708 11477.92213 11640 1061240 11478.49496 11654 1054028 11479.23973 11748 1055294 11480.0419 11720 1047422 11480.67225 11572 1030644 11481.35999 11586 1028928 11482.10514 11862 1048432 11482.85038 12238 1074564 11483.48105 12450 1089808 11484.05444 12570 1096612 11484.8573 12674 1099990 11485.71762 12760 1101194 11486.40597 12826 1101086 11487.15178 12860 1099050 11487.95507 12864 1091706 11488.6437 12902 1088520 11489.27501 12960 1091260 11489.9064 13108 1097922 11490.71008 13234 1102234 11491.45646 13308 1103140 11492.14551 13402 1103496 11492.83465 13476 1103560 11493.58131 13564 1103510 11494.27062 13622 1103130 11494.90256 13704 1101982 11495.59203 13762 1100862 11496.39652 13848 1101250 11497.14365 13950 1102366 11497.89088 14076 1102820 11498.6382 14154 1102564 11499.44312 14252 1102140 11500.13315 14346 1101342 11500.82326 14426 1099622 11501.45593 14466 1094870 11502.1462 14442 1084690 11503.00916 14442 1076538 11503.64207 14650 1080264 11504.33261 14896 1090874 11505.13834 15128 1099578 11505.82906 15316 1102778 11506.40473 15462 1103656 11507.03802 15548 1103634 11507.90172 15696 1103636 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1100918 11536.82516 27586 1101058 11537.63551 28202 1100970 11538.3302 28932 1100944 11539.02497 29656 1100886 11539.71983 30380 1100882 11540.41477 31206 1100734 11541.10979 32164 1100714 11541.74698 33074 1100598 11542.5001 34036 1100446 11543.36921 35154 1100304 11544.0646 36308 1100154 11544.87599 37486 1099964 11545.62953 38816 1099796 11546.3252 40330 1099748 11547.02095 41866 1099738 11547.6008 43480 1099556 11548.4127 45452 1099332 11549.22471 47438 1099152 11549.8628 49624 1099186 11550.617 52256 1098970 11551.3713 54904 1098916 11552.06767 57896 1098896 11552.64804 61190 1098838 11553.34456 65264 1098862 11554.15728 69526 1098712 11554.91205 74346 1098854 11555.72499 80362 1098758 11556.47997 86768 1098642 11557.23505 94306 1098736 11557.93213 103146 1098598 11558.6293 114598 1098670 11559.26845 127236 1098714 11560.02389 142650 1098682 11560.89569 163064 1098582 11561.53509 186190 1098508 11562.17456 214738 1098638 11562.9304 249650 1098506 11563.68633 295344 1098518 11564.32605 342848 1098482 11564.96583 391768 1098424 11565.83838 439014 1098346 11566.65289 469606 1098328 11567.29293 485060 1098214 11568.10764 487490 1098262 11568.92247 480756 1098044 11569.56277 470524 1098138 11570.20315 459672 1098000 11570.90182 448844 1097946 11571.65881 440328 1097878 11572.47415 433624 1097858 11573.11485 428168 1097892 11573.81388 422572 1097878 11574.57126 418230 1097864 11575.27047 414744 1097808 11575.96976 412272 1097668 11576.61086 411238 1097700 11577.36861 411580 1097562 11578.18476 412934 1097552 11578.94272 415342 1097446 11579.70078 417852 1097482 11580.45894 420508 1097482 11581.2172 422460 1097512 11581.85889 423052 1097368 11582.50065 422400 1097442 11583.25918 420474 1097268 11584.07617 417308 1097152 11584.77655 414140 1096948 11585.41863 411696 1096896 11586.23594 409922 1096674 11586.93658 409178 1096546 11587.57891 409106 1096484 11588.22131 409384 1096376 11589.03901 410036 1096314 11589.85684 411344 1096128 11590.61635 413220 1096236 11591.4344 416198 1096118 11592.19412 419516 1095998 11592.83704 423462 1096044 11593.53849 427360 1095864 11594.24003 431064 1095882 11594.94165 433598 1095716 11595.76032 434834 1095568 11596.46213 434648 1095618 11597.16402 433270 1095280 11597.92451 431106 1095010 11598.62658 428464 1095158 11599.32874 425664 1094714 11599.97247 423308 1094518 11600.73332 421102 1094448 11601.61136 419332 1094362 11602.31389 418196 1094292 11603.07506 417268 1094092 11603.83633 416808 1094052 11604.59771 416208 1094096 11605.24202 415492 1093946 11605.88641 414580 1093862 11606.64806 413432 1093804 11607.46841 412342 1093760 11608.17165 411344 1093674 11608.81638 410764 1093650 11609.63703 410552 1093530 11610.34055 410764 1093428 11610.98551 411534 1093392 11611.63055 412692 1093346 11612.45161 414156 1093426 11613.27279 415772 1093404 11613.97676 417432 1093340 11614.79816 419356 1093448 11615.56099 421052 1093428 11616.20654 422846 1093376 11616.96956 424750 1093322 11617.61528 426576 1093392 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Hi Juan Antonio: It looks like this is fluorescence data. It is likely that you have significant self-absorption if this is a Pt foil. Try to apply an "infinite" sample correction to this data before fitting. That should correct the SO2 somewhat. A much better thing to do is to take this data in transmission. i suspect that if it is a standard foil, it is optimized for transmission and should be measured in that mode. Carlo On Tue, 5 Dec 2006, Juan Antonio Maciá Agulló wrote:
Hi all,
I did a multiple shell fit for platinum foil and the results were similar: S02 = 0.51 and the uncertainty varies from 0.02 to 0.03 depending on the fit. Please find enclosed a file with values of energy, I0 and I of the platinum foil. I include this file if someone has curiosity on raw data and has time, otherwise forget it. Maybe I can suppose a value of 0.85 for S02 and follow with the analysis of the data, then...CN equation proposed in the first e-mail is ok?
Thank you very much
Best regards, JA
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org
On Tuesday 05 December 2006 09:03, Carlo Segre wrote:
It looks like this is fluorescence data. It is likely that you have significant self-absorption if this is a Pt foil. Try to apply an "infinite" sample correction to this data before fitting. That should correct the SO2 somewhat.
I agree with Carlo. I tried correcting your data as he suggested and it more or less doubled the amplitude of chi(k). This does suggest one of the cardinal rules of EXAFS data analysis, which is that good data analysis starts with careful sample preparation. B -- Bruce Ravel ---------------------------------------------- bravel@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/exafs/
Ok, how can I apply an "infinite" sample correction? The other samples are measured also in fluorescence mode, then is it better to measure Ptfoil in the same conditions (fluorescence)? Thanks a lot Best regards, JA
Juan, There are 2 ways to apply the self-absorption correction in Athena. The first way is to pick thicknesses starting with a couple microns and going thicker and thicker until the correction has no effect. I like this method because it gives an idea of the effects that thickness and concentration can have on the fluorescence. The other way is to simply use a thickness that will be in the infinite thickness domain to begin with. Either way, you get the information needed. To do the self-absorption correction in Athena go to Data then self-absorption, pick your algorithm (I suggest reading the Athena document section to see which you should use), plug in the formula for the sample and then either plot the information depth or plot data and correction. Rich Juan Antonio Maciá Agulló wrote:
Ok, how can I apply an "infinite" sample correction? The other samples are measured also in fluorescence mode, then is it better to measure Ptfoil in the same conditions (fluorescence)?
Thanks a lot
Best regards, JA
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On Tue, 5 Dec 2006, Juan Antonio Maciá Agulló wrote:
Ok, how can I apply an "infinite" sample correction? The other samples are measured also in fluorescence mode, then is it better to measure Ptfoil in the same conditions (fluorescence)?
The question about applying the correction has been answered. As to your question about the standard being measured the same way as the samples. yes, it is important to have standards be the same but not if you are compromising the data quality. If the sample is mad efor transmission it is not necessarily the right sample to measure in fluorescence. Perhaps a thin film of Pt would be a better fluorescence sample. Something with signficantly less than an absorption length of thickness. In my experience, mixing modes (transmission and fluorescence) is OK if you are careful about drawing conclusions. For example, a Pt foil is a geed standard because it permits you to see if you can get a consistent amplitude reduction factor which you can then use for your nanoparticles. For this purpose transmission is fine. If you want a Pt standard that is like your samples, then Pt black would be better but you know that it will have a reduced SO2 as well because it is in nanoparticle form. Cheers, Carlo
Thanks a lot
Best regards, JA
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org
Hi all, I did fits with self absorption corrected data (Fluo and Booth algorithms) and the value for S02 is 1.20 (0.30). It seems that I am not very lucky, if I take an average value (1.20 and 0.50), it should be ok (0.85) jeje, I am joking. Then...what can I do now? Thank you very much, Best regards, JA P.S. If I do not answer until Monday do not hate me, I will be on holidays.
I would remeasure Pt foil in transmission, by all means. Anatoly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Juan Antonio Macia Agullo Sent: Tuesday, December 05, 2006 1:32 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] CN and bond distances in Artemis Hi all, I did fits with self absorption corrected data (Fluo and Booth algorithms) and the value for S02 is 1.20 (0.30). It seems that I am not very lucky, if I take an average value (1.20 and 0.50), it should be ok (0.85) jeje, I am joking. Then...what can I do now? Thank you very much, Best regards, JA P.S. If I do not answer until Monday do not hate me, I will be on holidays.
I imagine somebody has done so and would be willing to provide that data. Unfortunately, the Newville database doesn't have it,
and I don't think I do. Anatoly, surely you must have done Pt foil? Yes, I know it's best to measure everything on the same
beamline, but it's
not essential.
mam
----- Original Message -----
From: "Anatoly Frenkel"
I would remeasure Pt foil in transmission, by all means.
Anatoly
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Juan Antonio Macia Agullo Sent: Tuesday, December 05, 2006 1:32 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] CN and bond distances in Artemis
Hi all,
I did fits with self absorption corrected data (Fluo and Booth algorithms) and the value for S02 is 1.20 (0.30). It seems that I am not very lucky, if I take an average value (1.20 and 0.50), it should be ok (0.85) jeje, I am joking.
Then...what can I do now?
Thank you very much,
Best regards, JA
P.S. If I do not answer until Monday do not hate me, I will be on holidays.
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Matthew,
It should be very easy to send to him Pt foil data, especially because,
based on my and others' tests, Pt data collected at different beamlines are
"identical" and thus transferable, but what if the beamline settings
(detuning, slit size, gases, etc.) were not optimized for his experiment? To
make sure everything is tuned up correctly, he should take his own Pt foil
data and compare with theory other other people standards (good idea!).
Alternatively, he will have to operate under assumption that everything was
tuned up correctly and his NP data are perfect, but why to take chances?
Anatoly
-----Original Message-----
From: Matthew Marcus [mailto:mamarcus@lbl.gov]
Sent: Tuesday, December 05, 2006 1:54 PM
To: anatoly.frenkel@yu.edu; XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] CN and bond distances in Artemis
I imagine somebody has done so and would be willing to provide that data.
Unfortunately, the Newville database doesn't have it,
and I don't think I do. Anatoly, surely you must have done Pt foil? Yes, I
know it's best to measure everything on the same
beamline, but it's
not essential.
mam
----- Original Message -----
From: "Anatoly Frenkel"
I would remeasure Pt foil in transmission, by all means.
Anatoly
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Juan Antonio Macia Agullo Sent: Tuesday, December 05, 2006 1:32 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] CN and bond distances in Artemis
Hi all,
I did fits with self absorption corrected data (Fluo and Booth algorithms) and the value for S02 is 1.20 (0.30). It seems that I am not very lucky, if I take an average value (1.20 and 0.50), it should be ok (0.85) jeje, I am joking.
Then...what can I do now?
Thank you very much,
Best regards, JA
P.S. If I do not answer until Monday do not hate me, I will be on holidays.
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Hi JA, I agree with Anatoly that remeasuring in transmission is a good idea, if you have the beam time. But I would also note that the value you have for S02 with the correction is within the realm of possibility, considering the uncertainty: 1.20 - 0.30 = 0.90. And part of the reason for starting with a standard in the first place is to work out some of the other difficulties that may arise; e.g. questions of normalization. If it is not practical for you to remeasure right now, you can try some of the things that can reduce the uncertainty in S02: fitting with multiple k-weights, changing the k-range being fit, fitting multiple coordination shells, etc.. I also just checked a past paper of mine, and see I ended up with an S02 for a set of platinum samples (transmission) of 1.16 +/- 0.05, suggesting that I wasn't doing something quite right (probably not sample preparation or measurement issues, since most of those tend to lower S02). But since that set of samples included a standard, and I was really interested in the differences between samples (including the standard), the fact that I have some systematic error that's causing the S02 to come out a tad large was acceptable, if a bit troubling. The paper is S. Calvin et al., Appl. Phys. Lett. 87, 233102 (2005). --Scott Calvin Sarah Lawrence College P.S. Just as I finished writing this, Matthew Marcus' post came through. I do have Pt foil data in transmission that I can dig up for you, if you'd like. Maybe I'll send it to Matt to put in the database; it's pretty good quality, as I recall (good data out to 20 inverse angstroms or so). At 01:31 PM 12/5/2006, Juan Antonio Maciá Agulló wrote:
Hi all,
I did fits with self absorption corrected data (Fluo and Booth algorithms) and the value for S02 is 1.20 (0.30). It seems that I am not very lucky, if I take an average value (1.20 and 0.50), it should be ok (0.85) jeje, I am joking.
Then...what can I do now?
On Tuesday 05 December 2006 13:02, Scott Calvin wrote:
P.S. Just as I finished writing this, Matthew Marcus' post came through. I do have Pt foil data in transmission that I can dig up for you, if you'd like. Maybe I'll send it to Matt to put in the database; it's pretty good quality, as I recall (good data out to 20 inverse angstroms or so).
A few years ago, when I was commissioning X11b at NSLS, I prepared a some reports on how things were progressing. This one: http://cars9.uchicago.edu/~ravel/misc/X11b/update_sep02.html includes a link to an athena project file containing my measurements there on several foils and filters that we had lying around X11, including a Pt foil. It comes with all the caveats that the others have already discussed. I agree with what others have said -- Juan would be best served by remeasuring the Pt foil in transmission. That's not, however, the most immediately useful advice. Juan has a problem that he needs to solve *now*. It is quite possible that he will not be able to go to a synchrotron for quite some time. Suggesting that he is stuck until he returns to the synchrotron just isn't especially helpful. What I would recommend, Juan, to get you over this road block is to compare your measured data to the data from my project file or to someone else's data (or both!). Work on the self-absorption correction until your fluorescence data most closely resembles the data you are comparing to. Then proceed with your data analysis using the many excellent suggestions you have received so far. The *next* time you go to measure data, think really hard about how best to measure each of your samples and standards. Try to figure out how to measure the best possible data from each sample. Different samples require different experimental protocols. The goal is, of course, to obtain consistently excellent data, so you will need to be resourceful and do what each sample requires. As helpful as it is to have a slew of "experts" (y'know, disreputable sorts like me) telling you what you need to do, you must remember that your education is a process. If you learn from the mistakes you made last time and improve upon them next time, then you are proceeding in the correct direction. B -- Bruce Ravel ---------------------------------------------- bravel@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/exafs/
Konichiwa from Japan, Alas Bruce, not everyone has a unix without training wheels. The darwin OS is case insensitive. Sort of a good thing in many ways. For instance take the example of "atoms" and "Atoms" in the horae-063 directory. This frozzed tar in the unpacking stage and I didn't realize the conflict until today (I was in Italy until last Friday so didn't get a chance to compile horae until today). Can you remove the conflict with uppercase and lowercase "atoms/ Atoms" in the horae directory so this doesn' happen every time. It would also be sort of neat if there were a some sort of "honest" way to compile the ifeffit_wrapper.c source without having to hack the ucky MakeMaker output (a switch perhaps). All this is of course, when you have time. Thanks for the new release. Paul
participants (9)
-
Anatoly Frenkel -
Bruce Ravel -
Carlo Segre -
Juan Antonio Maciá Agulló -
Matthew -
Matthew Marcus
-
Paul Fons -
Richard Mayes -
Scott Calvin