[Ifeffit] Parameters for parent function in wavelet transform analysis

2022-08-05 Thread Scott Calvin
a fundamental misunderstanding of part of the process, and look forward to learning more! Best, Scott Calvin Lehman College of the City University of New York ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman

Re: [Ifeffit] EXAFS Fitting with 2 CIF files

2021-09-04 Thread Scott Calvin
phases (as I implicitly did by writing it with only one S02 variable), or you could use a standard for each (from a sample prepared and measured in a similar way) to fix the S02 for each phase. Best, Scott Calvin Lehman College of the City University of New York > On Sep 4, 2021, at 4:02 PM, Zi

Re: [Ifeffit] EXAFS fitting - noisy data

2021-09-01 Thread Scott Calvin
. Of course, there are other ways to reduce that correlation, such as by measuring a series of spectra at different temperatures. But it does provide a good example of why high-k information is useful when you can get it. Best, Scott Calvin Lehman College of the City University of New York

Re: [Ifeffit] smoothing XAS data

2020-01-22 Thread Scott Calvin
the position of the peak! Best, Scott Calvin Lehman College of the City University of New York > On Jan 22, 2020, at 8:44 PM, Carlo Segre wrote: > > I generally don't like to smooth XANES data since smoothing does tend to > attenuate sharp features such as the ones which exist near th

Re: [Ifeffit] Two analysts, one spectrum, similar outcome?

2019-08-13 Thread Scott Calvin
Best, Scott Calvin Lehman College of the City University of New York On Tue, Aug 13, 2019 at 9:41 PM Mike Massey wrote: > Hi Everyone, > > > I'm curious, has anyone ever tried turning two analysts loose on the same > unknown EXAFS spectrum to see if their fits come out with

Re: [Ifeffit] Advice on using Athena for XANES LCF on spectra with a small edge step?

2019-01-15 Thread Scott Calvin
Hi Mike, Is there a reason the data stops at 2200 eV—e.g., is there another edge just above that? —Scott > On Jan 15, 2019, at 8:02 PM, Mike Massey wrote: > > Thanks Riti and Carlo. > > Riti: will give it a go, thanks! I think the data are salvageable, it's just > a question of how... > >

Re: [Ifeffit] the meaing of "beta=125.264" in path interpretation

2018-10-19 Thread Scott Calvin
You’ve figured it correctly—it’s the scattering angle. Best, Scott Calvin Lehman College > On Oct 19, 2018, at 10:22 AM, woschangqi...@126.com wrote: > > Dear, > > Firstly, i'm very grateful for the useful responses from Bruce Ravel and Matt > Newville on my previous que

Re: [Ifeffit] Constraining values in Artemis fit

2018-08-23 Thread Scott Calvin
, every system, and every problem, is different. But I do think it’s important to think about your system and about what the scientific problem is that you’re trying to solve. Best, Scott Calvin Lehman College of the City University of New York > On Aug 23, 2018, at 12:13 PM, Bruce Ravel wr

Re: [Ifeffit] Fitting Problems in Artemis version 0.9.26

2018-06-29 Thread Scott Calvin
is used in the fit (the “path parameter”) positive. So if, for example, Artemis reports ss1 = -0.002, that means it used +0.002 in the fit. Best, Scott Calvin > On Jun 28, 2018, at 10:03 PM, LIU HUAN wrote: > > Dear Dr. Ravel, > > I want to ask you that when I use the new v

Re: [Ifeffit] Amplitude and sigma square

2018-05-29 Thread Scott Calvin
a physically defensible manner can help reduce the correlations between fitted parameters and lead to smaller uncertainties in the fitted parameters. For example, the mixed-metal ferrite systems I’ve worked with were like this. Best, Scott Calvin Lehman College of the City University

Re: [Ifeffit] boundary issue in artemis

2017-01-17 Thread Scott Calvin
work to do in adjusting the model; you shouldn't just narrow the fitting window and ignore the misfit. Best, Scott Calvin Lehman College of the City University of New York > On Jan 17, 2017, at 4:21 AM, mfehse <marcus.fe...@univ-montp2.fr> wrote: > > Dear all, > > im fitt

Re: [Ifeffit] about sigma2 for exafs fitting

2017-01-08 Thread Scott Calvin
t; www.iae.cas.cn From: Scott Calvin<mailto:scal...@sarahlawrence.edu> Sent: Friday, January 06, 2017 3:34 AM To: XAFS Analysis using Ifeffit<mailto:ifeffit@millenia.cars.aps.anl.gov> Cc: Shaofeng Wang<mailto:wangshaof...@iae.ac.cn> Subject: Re: about sigma2 for exafs fitting Hi Shao

Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 11

2017-01-08 Thread Scott Calvin
find something that works well, hopefully also supporting it with other lines of evidence? That’s not something we’re going to be able to do for you on this list; it’s the heart of the investigation you’re undertaking. Best, Scott Calvin Lehman College of the City University of New York *

Re: [Ifeffit] Problem with large so2: Updated

2017-01-06 Thread Scott Calvin
it to generate identical values to those from your model, it does show much greater splitting between the nearest-neighbor oxygens (at 2.27 A) and the next-nearest (2.56 A). Your model has 2.28 A and 2.39 A. That’s quite different. Are you sure you entered the starting structure right? Best, Scott

Re: [Ifeffit] about sigma2 for exafs fitting

2017-01-05 Thread Scott Calvin
) value, there needs to be more to the argument, in my opinion. Best, Scott Calvin Lehman College of the City University of New York On Jan 5, 2017, at 12:19 AM, Shaofeng Wang <wangshaof...@iae.ac.cn<mailto:wangshaof...@iae.ac.cn>> wrote: Dear Scott, I have learned the Hamilton t

Re: [Ifeffit] Problem with large so2

2017-01-03 Thread Scott Calvin
distances when in reality the compound is more symmetric. In short, no, the high second S02 does not make sense (although it would be good to know the uncertainties). Best, Scott Calvin Lehman College of the City University of New York > On Jan 3, 2017, at 9:38 AM, Raj kumar &l

Re: [Ifeffit] Time reversibility of multiple scattering paths

2016-11-18 Thread Scott Calvin
to the number of instances. If you think about it that way, the answer to your question becomes evident. Best, Scott Calvin Lehman College > On Nov 18, 2016, at 6:03 AM, Inwood D. <d.inw...@soton.ac.uk> wrote: > > Hi All, > > I’ve just been reading the paper with the following ref

Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

2016-08-09 Thread Scott Calvin
Hi Ed, In case it’s not clear, ATOMS is built in to Artemis. (Long, long ago ATOMS was a separate program, so many people still refer to that functionality of Artemis by that name.) —Scott Calvin Sarah Lawrence College > On Aug 9, 2016, at 12:40 PM, Matthew Marcus <mamar...@lbl.gov&

Re: [Ifeffit] Questions about fitting of EXAFS

2016-08-04 Thread Scott Calvin
is highly sensitive to kmax you should investigate to try to determine why. —Scott Calvin Sarah Lawrence College > On Aug 4, 2016, at 11:07 AM, Bruce Ravel <bra...@bnl.gov> wrote: > >> >> 2. The cutting range of Kmax (FT transform parameters) has great effect >>

Re: [Ifeffit] Applicable scope of delr=alpha*reff

2016-08-02 Thread Scott Calvin
licity” under criterion 4. Whether or not it produces a good fit under the other criteria is, of course, something that you have to find out for each system. —Scott Calvin Sarah Lawrence College On Aug 2, 2016, at 6:27 AM, woschangqiang <woschangqi...@126.com<mailto:woschangqi...@126.com&

Re: [Ifeffit] Multiple scattering path parameters

2016-07-28 Thread Scott Calvin
ur fits much. If it doesn’t, and it often doesn’t, then you don’t have to worry! You can also try to leave the smaller MS paths off altogether, and see if that makes a difference. —Scott Calvin Sarah Lawrence College > On Jul 28, 2016, at 5:52 PM, Neil M Schweitzer > <neil.schweit...@no

Re: [Ifeffit] determining reasonable fitting parameters

2016-07-27 Thread Scott Calvin
of that correction wrong? —Scott Calvin Sarah Lawrence College > On Jul 27, 2016, at 5:26 PM, Matthew Marcus <mamar...@lbl.gov> wrote: > > I think that if the wiggliness in the spline is enough to cause trouble by > the mulriplicative effect, then it's probably eating up the wiggles

Re: [Ifeffit] about sigma square

2016-07-26 Thread Scott Calvin
4, would indeed be troubling, and good evidence that something about the model or the data was problematic. —Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifef

Re: [Ifeffit] determining reasonable fitting parameters

2016-07-20 Thread Scott Calvin
a copy of the full book, but you can certainly get it via inter-library loan. —Scott Calvin Sarah Lawrence College On Jul 20, 2016, at 6:59 PM, Neil M Schweitzer <neil.schweit...@northwestern.edu<mailto:neil.schweit...@northwestern.edu>> wrote: Being somewhere between a novice and an ad

Re: [Ifeffit] How to input atoms in solid solution for Artemis

2016-06-23 Thread Scott Calvin
ratio to the results for the standards. —Scott Calvin Sarah Lawrence College > On Jun 23, 2016, at 3:41 PM, Fuxiang Zhang <zhan...@umich.edu> wrote: > > Hi, Matt and Anayoly, > Thank you very much for the help. > > Fuxiang > > On Thu, Jun 23, 2016 at 1:51 PM, Anat

Re: [Ifeffit] doubt on number of variables

2016-05-26 Thread Scott Calvin
Hi Jesus, Yes, that procedure is fine. As long as the final, reported, fit guesses everything which is varied, whatever you do with earlier fits amounts to exploration and diagnostics. On May 26, 2016, at 10:02 AM, Jesús Eduardo Vega Castillo >

Re: [Ifeffit] Collected k-space and fitting range

2016-03-03 Thread Scott Calvin
that it shouldn’t make much difference. —Scott Calvin Sarah Lawrence College On Mar 3, 2016, at 8:33 PM, Taehoon Kim <oxonh...@outlook.com<mailto:oxonh...@outlook.com>> wrote: Hello, I am a bit confused about the range of k-space, which may affect the quality of EXAFS fitting.

Re: [Ifeffit] XANES pre-edge vs. edge features

2016-01-25 Thread Scott Calvin
nd up with the confusing terminology that the edge energy may well be below some of the pre-edge features! That terminology is unfortunate for people new to the field, but rarely causes any actual ambiguity. —Scott Calvin Sarah Lawrence College On Jan 25, 2016, at 9:40 AM, Matt Newville &

Re: [Ifeffit] Regarding calculations for scattering amplitude

2016-01-21 Thread Scott Calvin
technique places different weight on the low and high end of the actual size distribution. —Scott Calvin Sarah Lawrence College On Jan 21, 2016, at 4:01 AM, pushkar shejwalkar <pshejwalkar2...@gmail.com<mailto:pshejwalkar2...@gmail.com>> wrote: Dear All, I sent a related question

Re: [Ifeffit] Most probably a bug or something.

2015-12-02 Thread Scott Calvin
Hi Pushkar, Bruce Ravel replied to your question on November 30: http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05367.html —Scott Calvin Sarah Lawrence College On Dec 2, 2015, at 7:40 PM, pushkar shejwalkar <pshejwalkar2...@gmail.com<mailto:pshejwalkar2...@gmail.com&g

Re: [Ifeffit] a small question

2015-11-04 Thread Scott Calvin
Dear Shaofeng, You really do need to fit to know for sure. Aside from changes in bond length, there are many other effects that can shift a peak. —Scott Calvin Sarah Lawrence College On Nov 4, 2015, at 7:29 AM, Shaofeng Wang <wangshaof...@iae.ac.cn<mailto:wangshaof...@iae.ac.cn>>

Re: [Ifeffit] La2Zr2O7 EXAFS fitting

2015-08-14 Thread Scott Calvin
transform and read off bond lengths. —Scott Calvin Sarah Lawrence College On Aug 14, 2015, at 4:41 AM, herve muguerra herve.mugue...@neel.cnrs.frmailto:herve.mugue...@neel.cnrs.fr wrote: Dear All, First of all, I am still very new in EXAFS analysis, so please excuse me for any misunderstandings

Re: [Ifeffit] Measuring particle size by coordination number

2015-08-03 Thread Scott Calvin
, and sigma2. Even then, it tends to report sizes that are small compared to those provided by other techniques, but compares sizes between different samples quite well. —Scott Calvin Sarah Lawrence College On Aug 3, 2015, at 4:41 AM, Abhijeet Gaur abhijeetga...@gmail.commailto:abhijeetga

Re: [Ifeffit] Measuring particle size by coordination number

2015-08-03 Thread Scott Calvin
Oops—too early in the morning for me! I meant The formula works poorly when it is only applied with one path” —Scott Calvin Sarah Lawrence College On Aug 3, 2015, at 7:11 AM, Scott Calvin scal...@sarahlawrence.edumailto:scal...@sarahlawrence.edu wrote: Hi Abhijeet, The formula looks poorly

Re: [Ifeffit] Plotting chi(k) linear combination fit in energy

2015-07-20 Thread Scott Calvin
to be converted to k. The conversion from E to k is reversible, but the background subtraction is not, since chi(k) is meant to be background independent. You therefore cannot, in principle, plot chi(k) data as norm(E). —Scott Calvin Sarah Lawrence College On Jul 20, 2015, at 7:48 PM, Ellen Daugherty

Re: [Ifeffit] Create Atoms input with just coordinates

2015-06-01 Thread Scott Calvin
Hi Maryline, Use a = b = c = 10, with alpha = beta = gamma = 90. Now enter the coordinates from your simulation in units of angstroms/10 (which happens to be nm). —Scott Calvin Sarah Lawrence College On Jun 1, 2015, at 10:43 AM, M Ferrier mferr...@hotmail.commailto:mferr...@hotmail.com wrote

Re: [Ifeffit] Athena reporting incorrect element on import

2015-04-20 Thread Scott Calvin
), but it does let it do its interpolations to get the data in the format it needs. --Scott Calvin Sarah Lawrence College On Apr 20, 2015, at 2:48 AM, Zimina, Anna (IKFT) anna.zim...@kit.edumailto:anna.zim...@kit.edu wrote: Hi, Ken, try to load your data as raw data and let the Athena normalized your

Re: [Ifeffit] amplitude parameter S02 larger than 1

2015-03-23 Thread Scott Calvin
ignore the magnitude of the chi-square reported by Artemis, but pay close attention to differences in chi square (actually, reduced chi square) for different fits on the same data. --Scott Calvin Sarah Lawrence College On Mar 23, 2015, at 10:18 PM, Anatoly I Frenkel afren...@yu.edu wrote: Hi

Re: [Ifeffit] Breaking down correlationships between parameters

2015-03-22 Thread Scott Calvin
(not “break”) the correlation. In terms of the main question, I agree with Matt: I don’t think there’s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically. —Scott

Re: [Ifeffit] amplitude parameter S02 larger than 1

2015-03-20 Thread Scott Calvin
it. This discussion has generated several suggestions; hopefully one of them is a good lead! --Scott Calvin Sarah Lawrence College On Mar 20, 2015, at 4:30 PM, huyan...@physics.utoronto.ca wrote: Hi Scott, In all situations, 31.2 independent data points and 24 variables were used. In the case

Re: [Ifeffit] amplitude parameter S02 larger than 1

2015-03-20 Thread Scott Calvin
observed correction factor relative to simplistic theories which is indicative both of experimental effects and limitations in the theoretical model. Hope that helps... --Scott Calvin Sarah Lawrence College On Mar 19, 2015, at 6:32 PM, huyan...@physics.utoronto.ca wrote: Hi all, I know

Re: [Ifeffit] amplitude parameter S02 larger than 1

2015-03-20 Thread Scott Calvin
to fit lots of new free parameters. --Scott Calvin Sarah Lawrence College On Mar 20, 2015, at 1:44 PM, huyan...@physics.utoronto.ca wrote: Hi Josh and Anatoly, Thank you for bringing up this point. I agree that P would be 100% correlated with S02 if we assume both sites have the same

Re: [Ifeffit] amplitude parameter S02 larger than 1

2015-03-20 Thread Scott Calvin
, the Hamilton test does show the floated S02 is yielding a statistically significant improvement, I think you have a bigger issue. Looking at, e.g., whether you may have constrained coordination numbers incorrectly becomes more critical. —Scott Calvin Sarah Lawrence College On Mar 20, 2015, at 12:48

Re: [Ifeffit] amplitude parameter S02 larger than 1

2015-03-20 Thread Scott Calvin
be instructive for some of the other people reading this list who are trying to learn EXAFS. --Scott Calvin Sarah Lawrence College On Mar 20, 2015, at 3:46 PM, huyan...@physics.utoronto.ca wrote: Hi Scott, Thank you so much for giving me your thought again. It is very helpful to know how you

Re: [Ifeffit] A small query on constricting mean square displacement in multi-edge EXAFS refinement

2014-12-03 Thread Scott Calvin
in it between two edges is even smaller. —Scott Calvin Sarah Lawrence College On Dec 3, 2014, at 7:54 AM, Badari Rao badari@gmail.com wrote: Dear All, Suppose I have a compound, say AB. I have the EXAFS data from both A-edge as well as B-edge and I am simultaneously refining

Re: [Ifeffit] multiple absorber atoms

2014-10-20 Thread Scott Calvin
Hi Jesus, Just make a path list for each crystallographic site, and then weight S02 for the paths by the fraction of absorbing atoms in the associated site. --Scott Calvin Sarah Lawrence College On Oct 20, 2014, at 10:00 AM, Jesús Eduardo Vega Castillo jeve...@gmail.com wrote: Hello

Re: [Ifeffit] Inconsistency of the amplitude reduction factor

2014-09-18 Thread Scott Calvin
, constraining the S02 to be the same for each. So you're still fitting S02, but forcing all the spectra to use the same value. Second best is to fit one spectrum and allow S02 to vary, and then constrain all the other fits to use that value. --Scott Calvin Sarah Lawrence College On Sep 18, 2014, at 7:06 AM

Re: [Ifeffit] Inconsistency of the amplitude reduction factor

2014-09-18 Thread Scott Calvin
, and then force all of the other fits to use the value 0.77. --Scott Calvin Sarah Lawrence College I'd like to be more specific about my obtained results, At reference state (that means without any applied current), the amplitude reduction factor was 0.77 At 20% charge, it was 0.67 40% charge = 0.66

Re: [Ifeffit] Inconsistency of the amplitude reduction factor

2014-09-18 Thread Scott Calvin
in a consistent manner. That would directly lead to an apparent change in S02. The solution in that case is to adjust the parameters in Athena to assure the edge jump is determined in a consistent fashion. --Scott Calvin Sarah Lawrence College On Sep 18, 2014, at 8:20 AM, HOON Kim scie

Re: [Ifeffit] Questions for Artemis fit

2014-08-20 Thread Scott Calvin
to their questions is readily and clearly available elsewhere first. --Scott Calvin Sarah Lawrence College On Aug 20, 2014, at 1:11 AM, huyan...@physics.utoronto.ca wrote: Hi all, Does Feff take into account of the radius of the each atom when it calculates atom-pair distance? I am wondering

Re: [Ifeffit] Can the degeneracy (N) in Artemis be a variable?

2014-07-28 Thread Scott Calvin
common knowledge or technical detail. S. Calvin, XAFS for Everyone (CRC Press, 2013). The degeneracy S02 correlation issue is most directly discussed in Section 10.1.2. --Scott Calvin Sarah Lawrence College On Jul 28, 2014, at 9:51 AM, Bruce Ravel bra...@bnl.gov wrote: Peng's question is so

Re: [Ifeffit] from Rui Si at SSRF: help needed

2014-07-18 Thread Scott Calvin
in that region of the Fourier transform. --Scott Calvin Sarah Lawrence College On Jul 15, 2014, at 5:25 AM, Bruce Ravel bra...@bnl.gov wrote: (1) Why the second peak (ca. 3 Å) in experimental data is missing in the Co3O4 model? ___ Ifeffit

Re: [Ifeffit] Multiple phases in samples

2014-07-07 Thread Scott Calvin
transforms, to start getting a sense of what's present, and then switch to Artemis once the possibilities have been narrowed down. --Scott Calvin Sarah Lawrence College On Jul 7, 2014, at 1:20 PM, dien...@srs.govmailto:dien...@srs.gov wrote: Hi, All Assuming there are multiple phases in one

Re: [Ifeffit] Demeter-devel MacPorts Athena issues work-around

2014-07-06 Thread Scott Calvin
that not every report of problems is actually a bug report. That said, I think this is a good list. Everyone who contributes to it is a volunteer, and there are interesting and helpful discussions that take place at a wide range of levels. --Scott Calvin Sarah Lawrence College P.S. If we're

Re: [Ifeffit] How to distinguish whether the coordination element is heavy or light

2014-07-04 Thread Scott Calvin
might have bond lengths that are well known. In that case, bond length would not be a free parameter, but would be fixed to the appropriate value for each fit. In a case like that, a change in Z of 1 is often distinguishable; i.e., there is no +/- 5 rule. --Scott Calvin Sarah Lawrence College

Re: [Ifeffit] Use of the 3rd and 4th Parameter

2014-06-16 Thread Scott Calvin
numbers bigger than that, it suggests that a different starting model might be called for, rather than trying to use a cumulant expansion. You certainly should never guess the third cumulant at 0.5--that's way too big! --Scott Calvin Sarah Lawrence College On Jun 16, 2014, at 11:15 AM, Michael Kömm

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Scott Calvin
of the paths used in FEFF, including multiple-scattering paths. And that's the thing that I don't think currently exists. --Scott Calvin Sarah Lawrence College On May 29, 2014, at 9:04 AM, Bruce Ravel bra...@bnl.gov wrote: On 05/28/2014 06:58 PM, Carl Brozek wrote: Dear listhost, I'm using

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Scott Calvin
parameter delc. In the example I just provided the delr of the path in question would be chosen to be 1.4*delc. The second method is, of course, approximate, but for small changes in a parameter such as c can work pretty well, and can be easier to implement than the first. --Scott Calvin Sarah

Re: [Ifeffit] EXAFS simulations - peak too high

2014-02-03 Thread Scott Calvin
). It is invalid to average the magnitudes of chi(R). --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] Absorption-coefficient data repository?

2014-01-27 Thread Scott Calvin
Hi Damon, Hephaestus will calculate that for you. (There are other options, too, but that may be the simplest.) --Scott Calvin Sarah Lawrence College On Jan 27, 2014, at 1:30 PM, Damon Turney dtur...@ccny.cuny.edu wrote: Dear XAFS Community, I'm looking for values of absorption

Re: [Ifeffit] correlating number of nearest neighborst to the particle size

2014-01-09 Thread Scott Calvin
of x-ray diffraction as methods for determining mean sizes of polydisperse nanoparticles,” S. Calvin, S. X. Luo, C. C. Broadbridge, J. K. McGuinness, E. Anderson, A. Lehman, K. H. Wee, S. A. Morrison, and L. K. Kurihara, Appl. Phys. Lett. 87, 233102 (2005). --Scott Calvin Sarah Lawrence

Re: [Ifeffit] Itinerant vs localized XAFS

2013-12-09 Thread Scott Calvin
apart the two parameters. --Scott Calvin Sarah Lawrence College On Dec 9, 2013, at 10:02 AM, Maurits Boeije m.f.j.boe...@tudelft.nlmailto:m.f.j.boe...@tudelft.nl wrote: Dear XAFS specialists, We’ve performed an experiment at the ESRF in Grenoble to find experimental evidence of an electronic

Re: [Ifeffit] fitting a specific k range

2013-12-06 Thread Scott Calvin
to be off. That's not an attack on the software in general, or on the warning feature it includes. It is my opinion, and it seems to me that this mailing list is an appropriate place to express that kind of opinion. --Scott Calvin Sarah Lawrence College On Dec 6, 2013, at 12:29 AM, Matt Newville newvi

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Scott Calvin
--it probably doesn't. To reproduce features at high-R, it IS necessary to have a model (i.e. paths) that cover the high-R contribution, and it sounds like Matt does not have those paths included in his model. But it's not necessary to FIT up to high R. --Scott Calvin Sarah Lawrence College P.S. My least

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Scott Calvin
not even clear what misstep it's trying to prevent. --Scott Calvin Sarah Lawrence College On Dec 5, 2013, at 2:32 PM, fred.mosselm...@diamond.ac.uk fred.mosselm...@diamond.ac.uk wrote: What I find reassuring about Bruce's warnings is they allow you to think properly about what you

Re: [Ifeffit] calculating particle size from coordination numbers

2013-10-29 Thread Scott Calvin
, thus making the procedure useful for at least judging relative sizes. *The procedure is relatively insensitive to the details of the shape of the nanoparticles; you don't have to get much further than raft-like or sphere-like to have it produce useful results. Hopefully that helps! --Scott

Re: [Ifeffit] Artemis Software Issue

2013-10-25 Thread Scott Calvin
and its predecessors, in a way that strives for egalitarian accessibility with low barriers to entry. --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

[Ifeffit] DAthena crashes when reconstructing data from PCA

2013-06-11 Thread Scott Calvin
in Parallels 8 running under OS 10.8.4 on a MacBook Pro. The log file for the latest crash is below. If you'd like a project file too, let me know, but it happens, e.g., with the gold cyanobacteria project file, and with every data set I've tried. --Scott Calvin Sarah Lawrence College

Re: [Ifeffit] L-edge soft X-ray data in Artemis and Athena

2013-04-11 Thread Scott Calvin
for. --Scott Calvin Sarah Lawrence College On Apr 11, 2013, at 10:03 AM, Dr. Dariusz A. Zając ki...@ifj.edu.pl wrote: Hi, in Athena you can still normalize data, plot together, etc, but due to that lines L2 and L3 are very closed you will observe no EXAFS oscillations. In opposite I use

Re: [Ifeffit] S02 question

2013-01-11 Thread Scott Calvin
of the absorption length, then the EXAFS will be suppressed and mimic a smaller S02. If your standard is then a metal foil, the effective S02 for your powder will be smaller than the foil, not because of an intrinsic difference in absorption, but because of the distortion due to grain size. --Scott Calvin

Re: [Ifeffit] Help: some operation using Athena and Artemis

2012-11-26 Thread Scott Calvin
quality of the analysis. I also worry that an interior exclusion would be used in an attempt to minimize the impact of multiple scattering paths on the analysis. That, too, would be a statistics disaster. In short, you should embrace the correlations between the parts of the problem. --Scott Calvin

Re: [Ifeffit] How to fit N number of Neigbors in (D)Artemis?

2012-08-20 Thread Scott Calvin
, but because you've designed your guess/def/set parameters effectively, it's not a problem! Hope that helps... --Scott Calvin Sarah Lawrence College On Aug 20, 2012, at 9:24 AM, Huaming Guo wrote: Thanks. In this case, is the number of neibors equal to N * SO2 in the model result? Regards

Re: [Ifeffit] question for ifeffit mailing list - ATHENA NORMALIZATION

2012-08-08 Thread Scott Calvin
use linear combination analysis at all. --Scott Calvin Sarah Lawrence College On Aug 8, 2012, at 1:17 PM, Marie Zwetsloot wrote: Hi Scott Calvin, Thanks for your help. Yes, this is as far as my pre- and post-edge range go. I realized I should have made them longer; it was my first time

Re: [Ifeffit] [IFEFFIT] question about chemically unordered systems

2012-08-07 Thread Scott Calvin
#SECTION0044 --Scott Calvin Sarah Lawrence College On Aug 7, 2012, at 10:52 AM, Meutzner, Falk wrote: Dear Matt, dear community thank you for your fast reply! I am not sure, if I understand you correctly. I tried what you suggested, but the result is just the same. I

Re: [Ifeffit] question for ifeffit mailing list - ATHENA NORMALIZATION

2012-08-07 Thread Scott Calvin
spectrum to another, looking for changes, and interpreting them qualitatively, I think what you have is fine--in that cases, what's important is that the spectra be normalized similarly, and that does appear to be what you've done. --Scott Calvin Sarah Lawrence College On Aug 7, 2012, at 4:24 PM

Re: [Ifeffit] Athena Request

2012-07-05 Thread Scott Calvin
. Then choose those as your standards and fit marked groups. You could use PCA (newly added to Demeter Athena--yay!) to make this even more robust, by first ascertaining how many constituents are varying between the whole sample set. --Scott Calvin Sarah Lawrence College On Jul 5, 2012, at 12:15 PM

Re: [Ifeffit] Horae examples with Mac distribution

2012-06-16 Thread Scott Calvin
your lectures is particularly helpful to know about. --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] Find R-factor for linear combination sums?

2012-01-08 Thread Scott Calvin
Thanks, Matt, I'll give it a try. --Scott On Jan 8, 2012, at 10:06 PM, Matt Newville wrote: It should be possible to calculate an R-factor or chi-square statistics with a fairly simple ifeffit macro, using the functions vsum() (to sum an array) and npts().

[Ifeffit] Find R-factor for linear combination sums?

2012-01-07 Thread Scott Calvin
something like a Hamilton test to decide if they're actually consistent. If it's not currently a feature, it's one I'd like to see. It's not that high a priority--I can just export the spectra and calculate it in Excel. But it would be nice. --Scott Calvin Sarah Lawrence College

[Ifeffit] Trouble running Demeter 0.9.6 under Parallels

2011-12-26 Thread Scott Calvin
fails to launch. Any ideas? --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] Looking for reviewers for first chapter of new XAFS book

2011-12-17 Thread Scott Calvin
you to notice is that you have sent the chapter, I think inadvertently, to the entire IFEFFIT discussion list. Or I have been included in the list of reviewers since I did one of them? Best regards Maria Elena 2011/12/16 Scott Calvin scal...@sarahlawrence.edumailto:scal...@sarahlawrence.edu

[Ifeffit] Looking for reviewers for first chapter of new XAFS book

2011-12-14 Thread Scott Calvin
and can get feedback to me by 9 January, please contact me directly at scal...@slc.edumailto:scal...@slc.edu . As always, repeat reviewers are welcome! --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http

Re: [Ifeffit] particle size and coordination number in Runanoparticles on carbon

2011-10-11 Thread Scott Calvin
, and thus might (depending on data quality) provide a more reliable estimate of particle size. --Scott Calvin Sarah Lawrence College On Oct 11, 2011, at 8:54 AM, Dreher Marian wrote: Dear Ifeffit Community, I have a question regarding the signal damping I mentioned in my last post (I searched

Re: [Ifeffit] particle size and coordination numberin Runanoparticles on carbon

2011-10-11 Thread Scott Calvin
Yes, Marian, that makes sense. Anatoly Frenkel also has a number of good papers based on this kind of approach. While the approaches differ in detail, they are all based on using the ratio of CNs, and thus avoiding the issue of having to extract S02 from a standard. --Scott Calvin Sarah

Re: [Ifeffit] particle size and coordination number in Ru nanoparticles on carbon

2011-09-20 Thread Scott Calvin
diagnostic of small nanoparticles. (Actually, for reasons too lengthy to get in to at the moment, this method does tend to produce results a bit biased to the small side, so it's best to try the identical fitting model on a bulk standard for comparison.) --Scott Calvin Sarah Lawrence College On Sep

Re: [Ifeffit] Spline range?

2011-09-18 Thread Scott Calvin
Wei, You may not have looked at it yet, but the chapter draft I sent to you has several pages devoted to the topic. --Scott Calvin Sarah Lawrence College On Sep 18, 2011, at 10:10 AM, Wei Li wrote: Dear all, I am wondering about what range should be chosen in Athena? Some literature says

[Ifeffit] Looking for reviewers for data reduction chapter

2011-09-03 Thread Scott Calvin
are interested in reviewing the chapter and can get feedback to me by 29 September, please contact me directly at scal...@slc.edu . As always, repeat reviewers are welcome! --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit

Re: [Ifeffit] asking questions effectively (yes, *you* need to read this email)

2011-08-05 Thread Scott Calvin
needs to be worked out. It's possible, for instance, to use a service such as Dropbox to make the file available without actually attaching it to an email. --Scott Calvin Sarah Lawrence College On Aug 5, 2011, at 3:25 PM, Bruce Ravel wrote: Hi everyone, This has been a particularly troubling

Re: [Ifeffit] Fe K-edge second shell problems

2011-08-03 Thread Scott Calvin
to 4 to reduce correlations--you've said you expect the first shell to be tetrahedral.) Good luck--sounds like a stubborn one! --Scott Calvin Sarah Lawrence College On Aug 3, 2011, at 9:49 AM, Paul A Bingham wrote: Dear Ifeffit users, I have been struggling with this problem on and off

Re: [Ifeffit] Question on GDS values: amp

2011-08-02 Thread Scott Calvin
to achieve better fits on the inner shells (or vice-versa), you lock in distortions and make it difficult to evaluate statistically-related measures such as error bars. Hopefully that helps! --Scott Calvin Sarah Lawrence College___ Ifeffit mailing list

Re: [Ifeffit] Question on GDS values: amp

2011-08-01 Thread Scott Calvin
setting?), or there was serious distortion in the measurement (perhaps a thick, concentrated standard was measured in fluorescence without correction). --Scott Calvin Sarah Lawrence College On Aug 1, 2011, at 12:36 AM, nicholas@csiro.au wrote: Dear All, Just wondering what could I do

Re: [Ifeffit] E0 issues

2011-06-27 Thread Scott Calvin
be 2 eV less. Hope that helps... --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] SS and MS contributions to EXAFS

2011-06-18 Thread Scott Calvin
it takes a stab at how sigma2 might depend on R, which will help with understanding how important the MS paths are to chi(k). --Scott Calvin Sarah Lawrence College On Jun 17, 2011, at 7:21 PM, Matt Newville wrote: Hi Francisco, On Fri, Jun 17, 2011 at 7:34 PM, Francisco Garcia garcia.ff

Re: [Ifeffit] McMaster correction

2011-06-17 Thread Scott Calvin
guess this was first a discussion and then a feature request. :) --Scott Calvin Sarah Lawrence College On Jun 17, 2011, at 4:14 AM, John J. Rehr wrote: Hi Scott et al., Thanks for bringing up this issue. Whether or not McMaster corrections are useful does seem to depend on details

Re: [Ifeffit] McMaster correction

2011-06-17 Thread Scott Calvin
I apologize if I have abused the list while working on my text. I will find a different channel for raising these questions and requests once the current discussion is complete. --Scott On Jun 16, 2011, at 8:11 PM, Matt Newville wrote: Hope that helps.I have to admit I'm a little

[Ifeffit] McMaster correction

2011-06-16 Thread Scott Calvin
) at one of those stages? --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] Question about shift in E0

2011-06-06 Thread Scott Calvin
substantial changes in the amplitudes of XANES features, even if their position doesn't shift much. Is that the case for your data? --Scott Calvin Sarah Lawrence College On Jun 5, 2011, at 11:56 PM, Brandon Reese wrote: Hi all, I am looking at EXAFS of thin film metal oxides. I am varying both

Re: [Ifeffit] Question about transform windows and statistical parameters

2011-05-13 Thread Scott Calvin
Matt,On May 13, 2011, at 8:39 AM, Matt Newville wrote:After all, the epsilon shouldbe different for differentk-ranges, as your signal to noise ratio probably changes as a function of k.Using the same epsilon doesn't reflect that.Without seeing the data in question, this seems like speculation

Re: [Ifeffit] Question about transform windows and statistical parameters

2011-05-12 Thread Scott Calvin
jumps). Hopefully issues like glitches and high-frequency jitter are nearly the same for both samples, which gives you a fighting chance of making reasonable estimates of epsilon. Done with a little care, there may be value in comparing RCS for this kind of case. --Scott Calvin Sarah

Re: [Ifeffit] Athena Artemis

2011-05-12 Thread Scott Calvin
--none of the other data sets look that close. It sort of seems like it imports a version with a different background subtraction (maybe a different background k-weight, for instance) when you import from the larger project. --Scott Calvin Sarah Lawrence College On May 12, 2011, at 11:18 AM

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