Fwd: Re: FW: [Ifeffit] Undergraduates and EXAFS

2006-07-02 Thread Scott Calvin
, was a high school student! That's my two cents, anyway. :) --Scott Calvin Sarah Lawrence College In short, the referee's argument is of course strong one, but a good planning of undergraduate research can help make use of undergrads. Since these are EXAFS papers, you can definitely use them

Re: [Ifeffit] Re: Ifeffit Digest, Vol 40, Issue 10

2006-08-07 Thread Scott Calvin
/Ch...') called at /PerlApp/Chemistry/Elemenmts.pm line 527 Chemistry:Elements::_is_Z(undef) called at /PerlApp/Chemistry/Elements.pm line 355 Again, only headers are read in. Changing the LF generated by the Mac to a CRLF in all the text files in the folder solves the problem. --Scott Calvin

Re: [Ifeffit] CN and bond distances in Artemis

2006-12-04 Thread Scott Calvin
(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

Re: [Ifeffit] CN and bond distances in Artemis

2006-12-17 Thread Scott Calvin
fewer free parameters. A search of the literature will reveal several articles by each of us detailing how to do this kind of analysis, including the APL I mentioned earlier on platinum nanoparticles and a JACS article of Anatoly's on platinum-ruthenium nanoparticles. --Scott Calvin Sarah

Re: [Ifeffit] Yttrium in alumina GBs

2006-12-20 Thread Scott Calvin
assuming that CN's are what you're after. If finding out whether it's Alumina or Yttria is what you're after, the quality of fit and CN are not distinguishing between the two possibilities. That leaves bond distance as the best EXAFS indicator of which phase is present. --Scott Calvin Sarah

Re: [Ifeffit] CN and bond distances in Artemis

2006-12-21 Thread Scott Calvin
is used at any given time... --Scott Calvin Sarah Lawrence College At 04:42 PM 12/21/2006, you wrote: Hi all, Thank you very much Scott for your not slow answer and sorry for my very slow one. I think my system is a little bit complicated. I have bimetallic catalysts (PtSn) and I did fits

Re: [Ifeffit] R-factor uncertainty

2007-01-05 Thread Scott Calvin
with 0.01, if, for example, the 0.03 reproduces qualitatively all the features in the data but has small errors in the amplitude of the peaks, while the 0.01 fits the first part of the spectrum perfectly but misses some peak altogether. Hope that helps... --Scott Calvin Sarah Lawrence College

[Ifeffit] Re: ZnO Artemis demo - problem with dr parameter

2007-01-09 Thread Scott Calvin
dr, and then can't do the fit! :( --Scott Calvin Sarah Lawrence College At 01:24 AM 1/9/2007, Craig Klauber wrote: Dear Scott, Sorry to bug you on what may be a very trivial issue - but if its a quick fix a bit of guidance would be very much appreciated. I've been working through

Re: [Ifeffit] Is there a physical meaning to a negative SO2

2007-01-09 Thread Scott Calvin
a rough (but spurious) alignment between model and data. In any case, the model needs work; depending on your system and degree of prior knowledge, you might be assuming the wrong species of scattering atom, for example. --Scott Calvin Sarah Lawrence College At 10:41 AM 1/9/2007, Todd Luxton

Re: [Ifeffit] Re: ZnO Artemis demo - problem with dr parameter

2007-01-11 Thread Scott Calvin
Hi Craig, The correct version of the example has now been uploaded to the Ifeffit Wiki: http://cars9.uchicago.edu/iffwiki/HoraeSoftware --Scott Calvin Sarah Lawrence College At 11:09 AM 1/9/2007, Scott Calvin wrote: Hi Craig, I'm cc'ing this to the Ifeffit mailing list, as others may

Re: [Ifeffit] question about Eo and simultaneous fitting

2007-02-14 Thread Scott Calvin
cases, it may require a different E0's, in others, not. Of course, you can try it both ways, and see what the fits think. --Scott Calvin Sarah Lawrence College At 05:04 AM 2/14/2007, you wrote: Hi, first I would like to thank all experienced people answering in this forum!! I have learned really

Re: [Ifeffit] question about Eo and simultaneous fitting

2007-02-14 Thread Scott Calvin
the chi(k) data with each other, when they oscillate at a different frequency? --Scott Calvin Sarah Lawrence College At 10:38 AM 2/14/2007, you wrote: The approach that I like to take, is to vary the choice of E0 in the background subtraction step so that the chi(k) spectra are well aligned

Re: [Ifeffit] (no subject)

2007-02-15 Thread Scott Calvin
of parameters to fit must also be physically justifiable. If you can justify each path having a different coordination number than in your model, you can try different S02's; otherwise, your fit is unconvincing. --Scott Calvin Sarah Lawrence College At 02:31 AM 2/15/2007, you wrote: Dear Bruce We have

Re: [Ifeffit] E0 for bulk crystals and nanoparticles

2007-02-25 Thread Scott Calvin
and 300 K. And that lets you decouple E0 from lattice expansion and the third cumulant, which was your goal. --Scott Calvin Sarah Lawrence College At 10:06 PM 2/25/2007, Anatoly wrote: Leandro - depending on the details of your system and treatment, electronic structure of the nanoparticle may

Re: [Ifeffit] Fwd: Re: why ss_2 is negative?

2007-03-06 Thread Scott Calvin
to 5.48 and proceed. Using the first procedure in a final, published fit is defensible, the second one is not. Hope that helps. --Scott Calvin Sarah Lawrence College At 01:48 PM 2/27/2007, you wrote: I took your suggestion and have the amp and e0 the same for each path. In addition, I fixed

Re: [Ifeffit] viewing individual Fourier components with Athena

2007-03-20 Thread Scott Calvin
, not Athena. But I may have misunderstood your question. --Scott Calvin Sarah Lawrence College At 04:53 PM 3/20/2007, you wrote: Hello all. Is it possible to view the individual Fourier components of a Fourier transformed EXAFS spectrum in Athena? If so, can someone please direct me toward

[Ifeffit] Artemis autoparams bug

2007-03-20 Thread Scott Calvin
be off-putting to newcomers. --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Artemis autoparams bug

2007-03-21 Thread Scott Calvin
Aha! I see how that works now. Thanks; I'll fix the ZnO tutorial and post the new version to the wiki. --Scott Calvin Sarah Lawrence College At 10:08 AM 3/21/2007, you wrote: Scott, I just looked at the most recent update and its artemis.config file is correct. However, the way

Re: [Ifeffit] EXAFS reference materials

2007-03-22 Thread Scott Calvin
...in fact, that means that I measure the standard with a reference in place, if that makes sense. :) So I use a reference for Anatoly's purpose (1) and a standard for Anatoly's purposes (2) and (3). I hope that's helpful. --Scott Calvin Sarah Lawrence College At 03:28 PM 3/22/2007, you wrote: Hi

Re: [Ifeffit] in situ liquid cell

2007-03-25 Thread Scott Calvin
). This article has a design I used, and also references to some other designs. If you don't have access to that journal, let me know, and I'll send you a copy of the article. --Scott Calvin Sarah Lawrence College At 05:49 AM 3/25/2007, you wrote: Dear Colleagues, I need to perform XAFS measurements

Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

2007-03-28 Thread Scott Calvin
questions are you've got a good chance of getting help using Bruce's and Matt's software. --Scott Calvin Sarah Lawrence College At 02:15 PM 3/28/2007, you wrote: Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary=_=_NextPart_001_01C77165.0DE07268 Hi

Re: [Ifeffit] large Eo's and neg. D-W factors

2007-04-28 Thread Scott Calvin
. But since moving a path by more than about 0.1 Angstrom in Ifeffit starts to reduce the accuracy of the FEFF calculation, it's something you do want to try to prevent. One way to do that is with restraints; it shouldn't take much incentive for Ifeffit to refrain from switching the paths. --Scott

Re: [Ifeffit] Using FEFF8 with Artemis

2007-05-24 Thread Scott Calvin
files to have the pc end-of-line termination. :) Does anyone out there have a simple way to btach convert a whole bunch of files from Mac CR line breaks to pc CR/LF line breaks? I'm not part of the linux or unix worlds, but can use either Windows XP or OS X methods. --Scott Calvin Sarah Lawrence

Re: [Ifeffit] Using FEFF8 with Artemis

2007-05-29 Thread Scott Calvin
to try is obvious: obtain a respectable Fortran compiler and make a new executable. That's my task for tomorrow. --Scott Calvin Sarah Lawrence College At 11:08 AM 5/26/2007, you wrote: Scott, are you using one of the older Classic versions of feff8, I am surprised that anything compiled with gcc

Re: [Ifeffit] How to make a hole on feff.inp file

2007-06-07 Thread Scott Calvin
off the feff calculation, though, and removing the lines in the feff.inp file makes sense. --Scott Calvin Sarah Lawrewnce College At 05:01 AM 6/7/2007, Joji Kuniya wrote: Dear members I have been treating with an EXAFS spectra of an oxide crystals. This crystal has some holes (defects

Re: [Ifeffit] EXAFS Divination Dataset

2007-06-25 Thread Scott Calvin
Thanks, Itzok. I'll check it out. --Scott Calvin Sarah Lawrence College At 05:27 AM 6/25/2007, you wrote: Dear Scott, I would just like to mention a similar study of Fe XANES analysis for a particular case of iron gall inks, where linear combination method (implemented in athena) was used

[Ifeffit] Iron(III) carboxylate structures

2007-08-01 Thread Scott Calvin
in the Fe-Fe coordination and distance. --Scott Calvin Sarah Lawrence College P.S. The mailing list's spam filter has decided that when I send messages from home I am actually engaged in something shady and is blocking me. This is the last day I know I'll be at SLC for a while, so I'm likely

[Ifeffit] Fwd: How to fit the XAFS of alloy?

2007-12-28 Thread Scott Calvin
Hi Kefan, I have forwarded your message to the Ifeffit mailing list. If you are not yet a member of that list, you can join at: http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit --Scott Calvin Sarah Lawrence College Begin forwarded message: From: [EMAIL PROTECTED] Date: December

Re: [Ifeffit] Proposal for a U.S. XAFS conference

2008-04-17 Thread Scott Calvin
Hi Carlo, I think this is a great idea! --Scott Calvin Sarah Lawrence College At 02:23 PM 4/17/2008, you wrote: I have been looking into establishing a topical meeting (with the focus changing from year to year) in the United States in years that IXS is not being held

Re: [Ifeffit] Titanium Oxide reference spectra

2008-06-10 Thread Scott Calvin
I also have anatase, although I haven't looked at it yet, so I can't vouch for it. If Benjamin knows his is good, go that route, but if you'd like a confirming spectrum, let me know. --Scott Calvin Sarah Lawrence College On Jun 10, 2008, at 10:31 AM, Carlo Segre wrote: Hi All: I am

[Ifeffit] Windows dll for 1024 path version

2008-06-10 Thread Scott Calvin
Hi Matt, You used to have an ifeffit dll available for Windows that had a maximum of 1024 paths. Is that still the case? --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http

Re: [Ifeffit] quotation of figures

2008-07-16 Thread Scott Calvin
compounds is confusing? (i.e. it kind of looks at first like the slide claims that the mean-free path comes from a reference compound) --Scott Calvin Sarah Lawrence College On Jul 16, 2008, at 12:04 PM, [EMAIL PROTECTED] wrote: Hi, i have a print out of a talk (about XANES, XAFS and multiple

Re: [Ifeffit] quotation of figures

2008-07-16 Thread Scott Calvin
Whoops--it helps if I actually read the formula that the person actually wrote. --Scott Calvin Sarah Lawrence College On Jul 16, 2008, at 3:40 PM, Bruce Ravel wrote: On Wednesday 16 July 2008 15:27:27 Scott Calvin wrote: Bruce--I'm not following your critique of the third panel. Where's

[Ifeffit] Athena bug

2008-07-21 Thread Scott Calvin
). Since I'm at home today, I don't know if this is a Mac only problem or if it also occurs on other platforms. I've attached a simple file that demonstrates this behavior. Go to linear combination fitting with the first group highlighted, and click fit this group to get the crash. --Scott

Re: [Ifeffit] Background Subtraction

2008-08-25 Thread Scott Calvin
is that either the pre-edge or post-edge lines are being poorly chosen. Click on those options under the plotting to see what those lines look like. If necessary change the pre-edge or normalization ranges to get them straightened out. --Scott Calvin Sarah Lawrence College On Aug 25, 2008, at 11:23

Re: [Ifeffit] Comparison of amp between Feff8.40 and feff6 - Curved waves or Plane waves?

2008-08-29 Thread Scott Calvin
, this is just cosmetic; it shouldn't affect the feff path itself. --Scott Calvin Sarah Lawrence College On Aug 29, 2008, at 9:32 AM, Bruce Ravel wrote: On Thursday 28 August 2008 18:42:12 Ying Zou wrote: While I am calculating FEFF path through Feff8.40 using the feff8.inp as attached, I notice

Re: [Ifeffit] Comparison of amp between Feff8.40 and feff6 - Curved waves or Plane waves?

2008-08-29 Thread Scott Calvin
that are numbered the same. --Scott Calvin Sarah Lawrence College On Aug 29, 2008, at 1:54 PM, Ying Zou wrote: Dear all, Nice to get so prompt response from Bruce and Scott, thanks for their effort to make this list vital! Looks like amp is a factor which can be reduced

Re: [Ifeffit] Crytallites AND polycrystalline - Artemis handling?

2008-10-20 Thread Scott Calvin
oxide. --Scott Calvin Sarah Lawrence College On Oct 20, 2008, at 8:46 AM, Joseph Washington wrote: Scott, Thank you very much. I am looking at this file and I understand everything as far as the isotropic expansion terms in the delr and the debye term. Can you clarify the amp math

Re: [Ifeffit] Fit XANES spectra using Athena

2008-10-26 Thread Scott Calvin
of the substances in the sample, but suspect what some of the other contributors are. --Scott Calvin Sarah Lawrence College On Oct 26, 2008, at 1:16 PM, Frenkel, Anatoly wrote: PCA works only if there are series of spectra with change in the makeup of S species, not for a single spectrum

Re: [Ifeffit] Normalization of XANES spectra

2008-10-29 Thread Scott Calvin
to factors other than relative composition would tend to show up as a third significant component in pca.) --Scott Calvin Sarah Lawrence College On Oct 29, 2008, at 10:02 AM, Jens Kruse wrote: Hi everyone, I have a general question: I know Normalizing is something we do so that we can

Re: [Ifeffit] Normalization of XANES spectra

2008-10-29 Thread Scott Calvin
. Hopefully that helps. --Scott Calvin Sarah Lawrence College On Oct 29, 2008, at 2:31 PM, Jens Kruse wrote: Thanks for your replay and sorry for the confusing question. but I think it not getting better. Scott, you are right LCF would be helpful but even with lot of standards it is hard

Re: [Ifeffit] charge transfer

2009-01-02 Thread Scott Calvin
and +3, that FEFF would probably assign a bigger charge transfer to the +3 in most cases. --Scott Calvin Sarah Lawrence College On Jan 2, 2009, at 6:30 AM, Bruce Ravel wrote: On Friday 02 January 2009 09:15:05 am Bruce Ravel wrote: what does charge transfer mean in FEFF? I cant understand

Re: [Ifeffit] plot multiplier in Athena

2009-01-04 Thread Scott Calvin
Hi Gleb, As a workaround, can you check the fix step box and adjust the edge step by hand that way? --Scott Calvin Sarah Lawrence College On Jan 4, 2009, at 2:00 AM, Gleb Pokrovski wrote: Dear Bruce, Since the 2 or 3 latest athena versions, I have noticed a somewhat strange behavior

Re: [Ifeffit] How to keep enot, delr, and ss within acceptable limits

2009-01-09 Thread Scott Calvin
. Once in a while, though, the penalty function will keep you out of a false minimum and put you in the right one. --Scott Calvin Sarah Lawrence College On Jan 9, 2009, at 12:34 PM, Hashem Stietiya wrote: Dear All, I am currently using ARTEMIS to fit Zn-O, Zn-Zn paths to first and second

Re: [Ifeffit] How to get the accurate fittting results from the fit in Artemis

2009-01-12 Thread Scott Calvin
I think you have to give us more information to be able to help you. Fitting using Artemis is a skill, and takes practice, thought, and persistence. What system are you working with? How do you know the bond length is wrong? How are you attempting to do the fit? --Scott Calvin Sarah

Re: [Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Scott Calvin
Hi Kleper, It looks a little to me like you don't actually have any paths included in the fit, or perhaps the path is defective (all zeroed out, or something like that). If you attach the project file, it will probably be easy to tell. --Scott On Jan 13, 2009, at 5:13 PM, Kleper Oliveira

Re: [Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Scott Calvin
.) --Scott Calvin Sarah Lawrence College On Jan 13, 2009, at 5:43 PM, Kleper Oliveira Rocha wrote: But Scott, this data was that I treat in Athena to begin the treatment in Arthemis. I don´t have the Artemis project. 2009/1/13 Scott Calvin scal...@slc.edu That's an Athena project, Kleper. I

Re: [Ifeffit] Trouble with fitting with Arthemis

2009-01-13 Thread Scott Calvin
that leaves the model. Perhaps you don't have platinum metal. After all, the files are named PtAl--if there are a lot of Pt-Al near neighbors, and you're not accounting for them, that could explain why the fit fails. --Scott Calvin Sarah Lawrence College On Jan 13, 2009, at 6:32 PM, Kleper Oliveira

Re: [Ifeffit] distinguishing between actual shells and artifacts

2009-01-14 Thread Scott Calvin
Hi Hashem, I doubt they're artifacts. Much more likely is that they are either due to multiple-scattering paths, or to sidebands of the single- scatterers. During analysis, you don't want to think of the Fourier transform as being literally a radial distribution function; i.e., features in

Re: [Ifeffit] SCF cards in EXAFS and SO2 of CO, Mn and Cu

2009-01-18 Thread Scott Calvin
. The presence of other energies will act to reduce S02 to some extent, but the extent will vary from beam line to beam line, and often from run to run. --Scott Calvin Sarah Lawrence College On Jan 18, 2009, at 12:31 AM, JeongEunSuk wrote: Hello everyone I am using FEFF8.0 for the analysis of EXAFS

Re: [Ifeffit] Cumulant expansion fittings

2009-01-21 Thread Scott Calvin
to the other). In that case, I'd think fitting a fourth cumulant but not a third would be justified. The bottom line is that you should have a good physical reason, having to do with symmetries, for using the fourth without the third. --Scott Calvin Sarah Lawrence College On Jan 21, 2009, at 9

Re: [Ifeffit] Cumulant expansion fittings

2009-01-21 Thread Scott Calvin
the interstitial atoms, and the distribution of the interstitial atoms is symmetric between two lattice atoms in crystallographically identical sites. In that case, the third cumulant may be considered negligible, while the fourth cumulant might not be. --Scott Calvin Sarah Lawrence Collehe

Re: [Ifeffit] Cumulant expansion fittings

2009-01-21 Thread Scott Calvin
that is intrinsically anharmonic (e.g. all coordinated atoms at the same average distance, but the thermal variation about that average distance is not symmetric), then I also use cumulants. I hope that was helpful. --Scott Calvin Sarah Lawrence College On Jan 21, 2009, at 1:27 PM, Matt Newville wrote

Re: [Ifeffit] Cumulant expansion fittings

2009-01-21 Thread Scott Calvin
the potentials are close enough to harmonic that the fourth cumulant makes little difference, or they are so far from harmonic that the fourth cumulant alone is not enough. --Scott Calvin Sarah Lawrence College On Jan 21, 2009, at 10:11 PM, Frenkel, Anatoly wrote: Thus, I am pretty much

Re: [Ifeffit] Fwd: Guessed parameter and Einstien temperature

2009-02-02 Thread Scott Calvin
them but can't figure out how to do it? Or that you're wondering how to set them? --Scott Calvin Sarah Lawrence College On Feb 2, 2009, at 3:32 AM, abhijeet gaur wrote: Hi everyone, I am giving artemis the following parameters: guess amp 1 def delr alpha*reff guess

[Ifeffit] An additional beta tester

2009-02-05 Thread Scott Calvin
Hi Kathy, I just got a late volunteer for beta testing, whom I think will be a good addition: Ryan Hinrichs, professor of Chemistry at Drew University. Knows a little bit about XAFS, partially from collaboration with me, but has never used it himself. E-mail: hinr...@drew.edu (Yes, his

Re: [Ifeffit] Figure conversion - color to b/w

2009-03-16 Thread Scott Calvin
Hi Jenny, It's strongly recommended that you export the data and use some other graphing program to produce publication-quality graphs. Athena is designed to help see your data, not to produce final graphics. --Scott Calvin Sarah Lawrence College On Mar 16, 2009, at 12:21 PM, Jenny Cai

Re: [Ifeffit] Lattice distortion

2009-03-21 Thread Scott Calvin
that? (I'm asking about the EXAFS region; say, more than two inverse angstroms above the edge.) I eagerly await your collective wisdom, knowledge, and humorous anecdotes. --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit

Re: [Ifeffit] About S02

2009-03-27 Thread Scott Calvin
paths, it can help increase your confidence that the low S02 in your fit is appropriate. --Scott Calvin Sarah Lawrence College On Mar 27, 2009, at 9:19 AM, Zuzaan, Damdinsuren wrote: Hello everyone, I am graduate student and doing EXAFS in my research. My question is about S02. From the XAFS

Re: [Ifeffit] Basic questions

2009-04-06 Thread Scott Calvin
, then I might start with rmax at 1.9 angstroms. That sounds strange, because it sounds like I'm not even including the nearest neighbor, but it too will be shifted down and have width, so I actually am including most of it. --Scott Calvin Sarah Lawrence College

Re: [Ifeffit] Linear combination fitting

2009-04-07 Thread Scott Calvin
is doing what it can, the fractions may not be particularly physically meaningful. One piece of evidence that this is going on is if the chi(k) fit is poor, that is, if the fitted chi(k) does not correspond well to the data. --Scott Calvin Sarah Lawrence College On Apr 6, 2009, at 5:31 PM, Guvenc

Re: [Ifeffit] High SO2 value

2009-04-09 Thread Scott Calvin
Hi Abhijeet, There is no reason to fit the S02 separately for all shells. You should use the same S02 parameter for all shells. Ifeffit's job is to adjust the squiggly curve that comes out of the model until it looks like the squiggly curve that comes from the data. That's it. It doesn't

Re: [Ifeffit] High SO2

2009-04-10 Thread Scott Calvin
to the degrees of freedom? I suspect there's some very practical reason why people use this stepwise approach, but I'm not yet seeing it... --Scott Calvin Sarah Lawrence College On Apr 10, 2009, at 11:24 AM, Kropf, Arthur Jeremy wrote: Abhijeet, I'll add to Scott's comments. I typically perform

Re: [Ifeffit] High SO2

2009-04-10 Thread Scott Calvin
into their head in a system for which it was appropriate. As we both know, fitting can be a complicated and somewhat subjective process. Both for my own skills and for my ability to teach others the technique, I would like to understand more about why people use the approaches they do. --Scott Calvin

Re: [Ifeffit] Fitting procedure

2009-04-18 Thread Scott Calvin
, and Matt initially assumed the first; that was responsible for some of the confusion. --Scott Calvin Sarah Lawrence College On Apr 18, 2009, at 1:57 PM, Matt Newville wrote: Hi Adam, I am confused by this thread too! I find the approach of fit the first shell, then fix those parameters

Re: [Ifeffit] problem with E0 (enot) parameters

2009-06-19 Thread Scott Calvin
. If not, then the material is not what you think it is. --Scott Calvin Sarah Lawrence College On Jun 19, 2009, at 7:30 AM, Zajac, Dariusz A. wrote: Hi Calvin, thanks for the email. I have tried to find something on mailing list about E0 but it seems that my searching words were not correct. I found only few

Re: [Ifeffit] problem with E0 (enot) parameters

2009-06-19 Thread Scott Calvin
? Is it still before the white line? If so, it seems to me you don't have a problem. If not, then we have to ponder further. --Scott Calvin Sarah Lawrence College On Jun 19, 2009, at 8:28 AM, Zajac, Dariusz A. wrote: Hi Scott, look also at H and O, but for me and for this fit important are only W

Re: [Ifeffit] ODP: problem with E0 (enot) parameters

2009-06-20 Thread Scott Calvin
often look at/write responses to these emails when I'm not connected to the web and thus can't follow a link. Is that an OK rule of thumb with the rest of you? Under 2 Mb = OK to attach; over 2 Mb use a link? Or would people prefer a lower threshold? --Scott Calvin Sarah Lawrence College

Re: [Ifeffit] edge height proportional to the molar density?

2009-07-24 Thread Scott Calvin
be as accurate as techniques like ICP or XRF, largely because it's hard to normalize XAS spectra consistently between different edges. But you can easily do better than 20% accuracy. --Scott Calvin Sarah Lawrence College On Jul 24, 2009, at 5:16 PM, Haiyan Zhao wrote: I am wondering whether

[Ifeffit] Kapton in glove box

2009-08-05 Thread Scott Calvin
to be hard to find 1 mil Kapton tape with adhesive, but now it's easy. Hephaestus will give you the absorption of Kapton, so you can judge how big an effect it will be at the energies at which you'll work. --Scott Calvin Sarah Lawrence College On Aug 4, 2009, at 2:39 PM, Monson, Todd wrote

Re: [Ifeffit] Kapton in glove box (Todd Monson)

2009-08-06 Thread Scott Calvin
Hi Todd, Kapton is resistant to most solvents, but that's not necessarily true for the adhesive on it! I've had the adhesive completely washed away by samples with a little solvent on them before. So you should test that before preparing your samples. --Scott Calvin Sarah Lawrence College

Re: [Ifeffit] Chi in arthemis

2009-08-18 Thread Scott Calvin
that are of interest to you, then that is indicative of a problem in the fit and should not be swept under the rug. --Scott Calvin Sarah Lawrence College On Aug 18, 2009, at 4:02 PM, Eugenio Otal wrote: Hi all, I see that the reports of the fits a perform in arthemis have Chi really big

Re: [Ifeffit] Chi in arthemis

2009-08-18 Thread Scott Calvin
approaches that can be used to try to reduce the uncertainties, but you shouldn't even think about that until you get the amp (S02) straightened out. --Scott Calvin Sarah Lawrence College On Aug 18, 2009, at 6:18 PM, Eugenio Otal wrote: Hi Scott, here I copy a part of the report: Independent

Re: [Ifeffit] Chi in arthemis

2009-08-18 Thread Scott Calvin
Report the error bars as given; otherwise you're reintroducing the unknown measurement uncertainty factor. Then somewhere in your paper cite ifeffit and make clear that you used that method to determine uncertainties. --Scott Calvin Sarah Lawrence College On Aug 18, 2009, at 7:31 PM

Re: [Ifeffit] limits for second shell

2009-08-21 Thread Scott Calvin
those for the standard, taking into account the error bars (i.e. the values for the standard do not fall within the error bars for the sample for at least one parameter) --are stable with changes in k-weight. --Scott Calvin Sarah Lawrence College On Aug 21, 2009, at 11:35 AM, Eugenio Otal

[Ifeffit] Tenure track position for chemist

2009-10-06 Thread Scott Calvin
methods, and philosophy of education, please see our Web site at: http://www.slc.edu . SLC is an Equal Opportunity Employer committed to achieving a racially and culturally diverse community. --Scott Calvin Sarah Lawrence College___ Ifeffit mailing

Re: [Ifeffit] Cu oxide fitting result

2009-10-10 Thread Scott Calvin
system. --Scott Calvin Sarah Lawrence College On Oct 9, 2009, at 11:47 AM, Bruce Ravel wrote: Abhijeet, I took a quick peak at your project and I find it very confusing. In the most recent fit, you are fitting only from 3.5 to 4.4 -- the area under the *third* peak in the data. I don't

Re: [Ifeffit] Rbkg value

2009-10-23 Thread Scott Calvin
myself again as to what exactly it is doing), so someone else should explain how that can be used to help address your question. --Scott Calvin Sarah Lawrence College On Oct 23, 2009, at 3:51 PM, Chris Patridge wrote: Hello everyone, In removing background, most literature suggests Rbkg value

Re: [Ifeffit] SrSO4 (Celestite) and SrCO3

2009-10-26 Thread Scott Calvin
Hi Peter, I think I have one of SrCO3, but it will take me a couple days to dig it up. --Scott Calvin Sarah Lawrence College On Oct 26, 2009, at 7:10 PM, Peter Nico wrote: Hello All, Would anyone out there have a SrSO4 or SrCO3 standard XANES spectra they would be willing to share

Re: [Ifeffit] Bug in Athena?

2009-11-19 Thread Scott Calvin
of the merged data from the sample. If 2) is a significant problem and 1) is not, then it makes sense to merge the references along with the sample data, because that will make it easier to determine the chemical shift. If both problems are significant, then you've got a headache. --Scott Calvin

Re: [Ifeffit] Bug in Athena?

2009-11-19 Thread Scott Calvin
scans merged as well as the sample scans, in order to get a clean measure of chemical shift. --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Bug in Athena?

2009-11-19 Thread Scott Calvin
accurate chemical shifts, as loss of energy calibration, harmonics, and noise should all become evident by this procedure. I'm not recommending this procedure over others; it's just what I do in some cases. But it doesn't seem like an unreasonable procedure to me. --Scott Calvin Sarah

[Ifeffit] Lattice parameters: EXAFS vs. XRD

2009-12-25 Thread Scott Calvin
distribution function in a real fcc metal. To the degree it's a question about analysis, it's about XRD: In an fcc metal should the expectation value of the nearest-neighbor separation, multiplied by the square root of two, equal the lattice spacing as determined by XRD? --Scott Calvin Sarah

Re: [Ifeffit] Lattice parameters: EXAFS vs. XRD

2009-12-30 Thread Scott Calvin
settled in last week. --Scott Calvin Sarah Lawrence College On Dec 30, 2009, at 8:47 AM, Matt Newville wrote: Hi Scott, I believe we had a conversation about this last January. XAFS is not sensitive to the crystallographic lattice constants. It measures the spacing between atoms. Because

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Scott Calvin
standard is a theoretically simulated spectrum of some structure. Thus, the theoretical standard is not the crystallographic data itself, although that data can serve as a basis for generating a theoretical standard using software such as FEFF. --Scott Calvin Sarah Lawrence College On Jan 4

Re: [Ifeffit] Bruce ayuda, problemas con athena

2010-02-13 Thread Scott Calvin
Primo Latinam linguam aptiorem dicere disce. Tum te laete respondebo. --Scott On Feb 13, 2010, at 7:05 PM, Matt Newville wrote: On Sat, Feb 13, 2010 at 10:59 AM, Scott Calvin scal...@slc.edu wrote: You'll probably get Russian before I get Latin. Quam utor postulo notitia quinymo quam Feff

Re: [Ifeffit] Anharmonic correction

2010-03-26 Thread Scott Calvin
a blank for 3rd, which is the third cumulant in the literature. It is then used like any other path parameter. (Or, of course, you can access it through IFEFFIT scripts, again using 3rd.) --Scott Calvin Sarah Lawrence College On Mar 26, 2010, at 1:13 PM, Aaron Slowey wrote: Dear XAFS community

Re: [Ifeffit] Anharmonic correction (Aaron Slowey)

2010-03-26 Thread Scott Calvin
of parameters, the stability of the fit to small changes in the data ranges, etc.. --Scott Calvin Sarah Lawrence College On Mar 26, 2010, at 4:09 PM, grant bunker wrote: Aaron - There are a couple of things you should watch out for when fitting cumulants. First, you should make sure

Re: [Ifeffit] Measuring particle size of metal oxide

2010-03-28 Thread Scott Calvin
, and the first scattering shell is thus fully populated no matter how small the particles are. --Scott Calvin Sarah Lawrence College On Mar 8, 2010, at 1:45 PM, bill.schwa...@yale.edu wrote: Hi Scott, We met a couple of times at the EXAFS last two EXAFS workshops at BNL, for relative

Re: [Ifeffit] can sigma square ever be less than zero?

2010-06-28 Thread Scott Calvin
different k-weights, or, better yet, several k-weights simultaneously? At any rate, I'd say your fit is a promising preliminary fit. As far as a publication-quality fit, it would be nice to get the nearest- neighbor ss pinned down a bit better. --Scott Calvin Sarah Lawrence College On Jun 28

Re: [Ifeffit] Vanadium center fitting issues

2010-07-10 Thread Scott Calvin
constraints that aren't physically unreasonable, and seeing how the fit responds to them. --Scott Calvin Sarah Lawrence College On Jul 10, 2010, at 11:03 AM, Christopher Allen wrote: Hi, I wanted to get some advice on a vanadium centered material I’ve been trying to fit for quite a while w

Re: [Ifeffit] Case of nonequivalent multiple atomic sites of absorbing atoms

2010-07-28 Thread Scott Calvin
simple constrains (not only E0's and S02's the same, but also sigma2's), and see if you're on the right track. Then look at the effect of relaxing constraints. --Scott Calvin Sarah Lawrence College On Jul 28, 2010, at 4:00 AM, Jatinkumar Rana wrote: Dear Users, Since long, i was trying

Re: [Ifeffit] Large Amplitude Values

2010-07-31 Thread Scott Calvin
mine, warning you by their deviation from known values as to the magnitude of the errors you're looking at. --Scott Calvin Sarah Lawrence College On Jul 31, 2010, at 11:56 AM, Gavin Garside wrote: Scott, Thank you for a quick response. The value I am getting for SO2 in the fit most

Re: [Ifeffit] Stoichiometry from EXAFS data

2010-08-02 Thread Scott Calvin
for linearity with tricks like putting sheets of aluminum foil before I0 can help detect some (but not all) of those kinds of issues. --Scott Calvin Sarah Lawrence College On Aug 2, 2010, at 4:03 AM, Peter Zalden wrote: Dear Feff users, lately, we measured a sample containing Sb and Te

Re: [Ifeffit] Stoichiometry from EXAFS data

2010-08-02 Thread Scott Calvin
be 11.0 or 11.6 mm, in part because of the ability to eyeball it, and in part because of problems with lining up marks using rulers. But unlike with Gaussian statistics, where two- or three-sigma events happen now and then, I'd often be off by 0.2 mm yet never off by 0.6 mm. --Scott Calvin

Re: [Ifeffit] two measurements of the same compound in different beam-lines

2010-08-13 Thread Scott Calvin
different values of delE0 if the data sets are hard to align properly. --Scott Calvin Sarah Lawrence College On Aug 12, 2010, at 8:44 PM, María Elena Montero Cabrera wrote: Hi all! I have performed two independent XAFS measurements of Cr K-edge of the same Fe-Cr sample at two different

[Ifeffit] Haha

2010-08-15 Thread Scott Calvin
Hi all, For a little comic relief, I just came across this graph: http://www.usablemarkets.com/wp-content/uploads/2010/06/fed-rate-3.jpg I have never seen a graph unrelated to XAFS looks more like (noisy) XAFS data... --Scott Calvin Sarah Lawrence College

[Ifeffit] More than 256 paths on Mac OS 10.5?

2010-10-06 Thread Scott Calvin
Hi all, Do any of you have a version of Ifeffit compiled for Mac OS 10.5 that allows more than 256 paths? --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman

Re: [Ifeffit] sigma^2 values for multiple scattering paths

2010-10-06 Thread Scott Calvin
not be particularly sensitive to the details of their path parameters. --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] More than 256 paths on Mac OS 10.5?

2010-10-06 Thread Scott Calvin
Thanks, Matt! --Scott Calvin Sarah Lawrence College On Oct 6, 2010, at 9:08 AM, Matt Newville wrote: Hi Scott, The attached zip file has dynamic libraries (and static program ifeffit) built with 1024 paths and feff files. It contains the files lib/libifeffit.dylib lib/libifeffit.so bin

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