Re: [Ifeffit] error in ATOMS

2013-11-13 Thread Matthew Marcus
Shouldn't ATOMS input coordinates be fractional values? I wonder if putting the S 3000A from center might have something to do with it. I'm guessing that this is the metal-sulfer core of a protein, right? mam On 11/13/2013 9:58 AM, Julius Campecino wrote: Hi Chris, Same problem: Ca

Re: [Ifeffit] modeling significant defects and molecules

2013-10-31 Thread Matthew Marcus
YOu could use ATOMS to make a FEFF file for a simple structure, then copy the header from that and replace the atoms list with a set of coordinates. You'd have to write a program which would automatically fill in the correct IPOTs and symbols, but it's not that hard. What's annoying is if you h

Re: [Ifeffit] X-ray natural circular dichroism by FEFF?

2013-09-11 Thread Matthew Marcus
ifeffit-ow...@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. X-ray natural circular dich

[Ifeffit] X-ray natural circular dichroism by FEFF?

2013-09-10 Thread Matthew Marcus
Can FEFF calculate X-ray natural circular dichroism, which is the XCD that comes from structural chirality and not magnetism? I suppose I could simply try it, putting in coordinates for some simple molecule, but I'd like to know if any results would be meaningful. mam __

Re: [Ifeffit] Linear Combination Fitting using ATHENA

2013-08-14 Thread Matthew Marcus
maghemite spectrum is required is required to fit mine. Both pre-edge features match in the sense that they are roughly bound by the same energy values. On 14 August 2013 17:30, Matthew Marcus wrote: That depends on the way you did your calibration. If it really matches, including the

Re: [Ifeffit] Linear Combination Fitting using ATHENA

2013-08-14 Thread Matthew Marcus
e you did) to fit those taken in fluorescence mode (my case)? Teck Kwang On 14 August 2013 01:37, Matthew Marcus wrote: Here are reference spectra. The calibration is defined with the Fe metal edge at 7110.75eV. The maghemite spectrum has been corrected for

Re: [Ifeffit] Linear Combination Fitting using ATHENA

2013-08-14 Thread Matthew Marcus
On 14 August 2013 01:37, Matthew Marcus wrote: Here are reference spectra. The calibration is defined with the Fe metal edge at 7110.75eV. The maghemite spectrum has been corrected for mild overabsorption by reference to magnetite, which is very similar. The magnetite is synthetic Fe3O4

Re: [Ifeffit] Linear Combination Fitting using ATHENA

2013-08-13 Thread Matthew Marcus
h the data I have! Thanks for all your responses! It is greatly appreciated! This forum has been more helpful than I thought! Teck Kwang On 13 August 2013 01:34, Matthew Marcus mailto:mamar...@lbl.gov>> wrote: While it's true that Mossbauer is the gold standard for Fe valenc

Re: [Ifeffit] normalization methods

2013-05-16 Thread Matthew Marcus
#x27;ve never understood why this happens. mam On 5/16/2013 4:47 AM, Matt Newville wrote: Hi Matthew, George, Zach, Thanks for the discussion! On Wed, May 15, 2013 at 5:41 PM, Matthew Marcus wrote: I'm not sure what 'flattening' means. Does that mean dividing by a linear

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus
can be used in quantitative analysis. Is there reason to believe that cannot be the case? Thanks, George On Wed, May 15, 2013 at 3:04 PM, Matthew Marcus mailto:mamar...@lbl.gov>> wrote: OK, I guess I don't know what 'standard normalization' is. It looks from the qu

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus
Hi Matthew, On Wed, May 15, 2013 at 1:20 PM, Matthew Marcus mailto:mamar...@lbl.gov>> wrote: You say that the flipping difference (p - n) is 0 in pre-edge and far post-edge regions, which is as it should be, but then say that the slopes of p- and n- post-edges, considered se

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus
n Wed, May 15, 2013 at 11:41 AM, Matthew Marcus mailto:mamar...@lbl.gov>> wrote: The way I commonly do pre-edge is to fit with some form plus a power-law singularity representing the initial rise of the edge, then subtract out that "some form". Now, that form can be eit

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus
previously described. Thus, there's no distinction made between data above and below E0 in XANES, whereas there is such a distinction in EXAFS. mam On 5/15/2013 8:25 AM, Matt Newville wrote: Hi Matthew, On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus wrote: What I typically

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus
What I typically do for XANES is divide mu-mu_pre_edge_line by a linear function which goes through the post-edge oscillations. This division goes over the whole data range, including pre-edge. If the data has obvious curvature in the post-edge, I'll use a higher-order polynomial. For transmis

Re: [Ifeffit] Possible bug in atoms files generation by Artemis

2013-03-28 Thread Matthew Marcus
hence lifetime broadening and E0? I knbow it affects XANES, but that's a whole other subject not covered by DemLarchTemis discussions. mam mam On 3/27/2013 7:32 PM, Matt Newville wrote: Hi Matthew, Bruce, On Wed, Mar 27, 2013 at 10:33 AM, Matthew Marcus wrote: Some users do hav

Re: [Ifeffit] Possible bug in atoms files generation by Artemis

2013-03-27 Thread Matthew Marcus
n 3/27/2013 5:44 AM, Bruce Ravel wrote: On Tuesday, March 26, 2013 01:21:58 PM Matthew Marcus wrote: Just to put my bit in, I believe that the most significant advantage of higher FEFF versions for EXAFS analysis is that it results in more reasonable values for E0 for high-Z elements. I forge

Re: [Ifeffit] Possible bug in atoms files generation by Artemis

2013-03-27 Thread Matthew Marcus
for instance, define a dopant system in terms of the displacements of the near-neighbors without having to do the geometry by hand, which is difficult, tedious and error-prone. mam On 3/26/2013 9:24 PM, Matt Newville wrote: Hi Matthew, On Tue, 26 Mar 2013, Matthew Marcus wrote: Just to p

Re: [Ifeffit] Possible bug in atoms files generation by Artemis

2013-03-26 Thread Matthew Marcus
Just to put my bit in, I believe that the most significant advantage of higher FEFF versions for EXAFS analysis is that it results in more reasonable values for E0 for high-Z elements. I forget whether the issue is high-Z scatterer or absorber. If you use any of the common prescriptions for de

Re: [Ifeffit] Beryllium and EXAFS

2012-12-18 Thread Matthew Marcus
Just to stir the pot a little more: 1.ALS has some beamlines which can go down as far as Li. Work has been done on Li, but only on concentrated stuff. 2.The sample is probably really dilute in Be. The signal will be pathetic. 3.Radiation damage will be a major issue, especially with

Re: [Ifeffit] How to do with diffraction peak

2012-12-14 Thread Matthew Marcus
On 12/14/2012 4:10 PM, Matt Newville wrote: Hi Matthew, On Thu, Dec 13, 2012 at 11:28 PM, Matthew Marcus wrote: You might argue (I would agree) that with multiple measures of fluorescence you can determine outliers more rigorously. But I would also say that then the best thing to do then

Re: [Ifeffit] How to do with diffraction peak

2012-12-13 Thread Matthew Marcus
You might argue (I would agree) that with multiple measures of fluorescence you can determine outliers more rigorously. But I would also say that then the best thing to do then is to not simply remove outliers but to take the average AND standard deviation of the samples and include both in the

Re: [Ifeffit] How to do with diffraction peak

2012-12-12 Thread Matthew Marcus
On 12/12/2012 8:03 PM, Matt Newville wrote: Hi Matthew, Bruce, All, Sorry for not being able to join this discussion earlier. I agree that having glitch-free data is preferred. But I also think it's OK to simply remove diffraction peaks from XAFS data -- you're just asserting that you know th

Re: [Ifeffit] How to do with diffraction peak

2012-12-12 Thread Matthew Marcus
-electron peaks in ekements like Ce. For those, you just have to subtract the peaks, but fortunately there is literature on how to do that. mam On 12/12/2012 3:06 PM, Bruce Ravel wrote: On Wednesday, December 12, 2012 03:00:41 PM Matthew Marcus wrote: Hmm. Another possible way to do

Re: [Ifeffit] How to do with diffraction peak

2012-12-12 Thread Matthew Marcus
Hmm. Another possible way to do it is to delete the bad data points and then do a "slow" FT, which would be a fit of the data, at the points given with no interpolation, to a sum of sines and cosines. This would have the nice feature of using the data as it is and ignoring the bad stuff. Fil

Re: [Ifeffit] How to do with diffraction peak

2012-12-12 Thread Matthew Marcus
Here's one last trick that I used to use when I used a plastic scintillator at NSLS and didn't have a spinner. WARNING - this is painful! I used to tape a piece of Polaroid film to the face of the detector, run through a scan, develop the film, see where the white spots were, and put Pb tape on

Re: [Ifeffit] {Spam?} {Disarmed} How to do with diffraction peak

2012-12-11 Thread Matthew Marcus
I second that motion about the usefulness of multi-element detectors. Some people suggest that because single-element detectors can now count as fast as multi-element detectors used to and cover solid angle more efficiently, multi-element detectors are obsolete. My EXAFS data reduction softwar

Re: [Ifeffit] Ifeffit Digest, Vol 117, Issue 13

2012-11-26 Thread Matthew Marcus
What's iXAFS? mam On 11/15/2012 11:15 AM, Zack Gainsforth wrote: Kyler, you and Tsu-Chien are terrific! iXAFS is working for me again! Cheers, Zack Gainsforth Space Sciences Laboratory, UC Berkeley 7 Gauss Way Berkeley, CA 94720 510-642-9733 za...@ssl.berkeley.edu On Nov 15, 2012,

Re: [Ifeffit] determining S02 from ZnO vs. Zn foil

2012-10-09 Thread Matthew Marcus
Even if the glass samples are solid, uniform and measured in fluorescence, overabsorption could reduce the amplitude if the Zn content is high. One approach to fitting the EXAFS is to take the first shell to be a mix of tetrahedral (if appropriate) and octahedral, with appropriate Zn-O distances

Re: [Ifeffit] Why different installations of Atoms generate different results?

2012-09-24 Thread Matthew Marcus
The APJ files can be opened by changing their extensions to .zip and using an unzip utility. - Original Message - From: "Tsuei, Ku-Ding" To: ; Cc: Sent: Monday, September 24, 2012 2:21 PM Subject: Re: [Ifeffit] Why different installations of Atoms generate different results? Dear

Re: [Ifeffit] How to write feff.inp file for CO adsorbed Cu?

2012-09-05 Thread Matthew Marcus
I don't know about surface CO, but I do know that in metal carbonyls, you get a very strong scattering from the distal atom, let's say the O in M-C=O, due to the focusing from the intermediate atom. Thus, if you really have a monolayer-selective method for doing EXAFS, e.g. partial Auger yield,

[Ifeffit] CFAVERAGE card in FEFF9

2012-08-13 Thread Matthew Marcus
I'm trying to simulate EXAFS on a nanoparticle of hydrogen-terminated TiO2, whose atomic coordinates were given to me by a theorist. For that, I need to average over all Ti atoms, which seems to me is what the CFAVERAGE card is for. I tried using that per the attached feff.inp file with Jfeff

Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 5 - Mn XANES

2012-08-09 Thread Matthew Marcus
You might also consider the method given in: Manceau, A., Marcus, M. A., Grangeon, S. (2012) "Determination of Mn valence states in mixed-valent magnanates by XANES spectroscopy", American Mineralogist 97,816-827 (not that I'm plugging my own work or anything :-) ) Marcus, M. A. On 8/9/

Re: [Ifeffit] on Tune and Detune

2012-06-21 Thread Matthew Marcus
This is a function of a 2-crystal monochromator. If the Bragg planes of the two crystals are exactly parallel, that's canned being tuned. Let's say you have Si111 crystals. Not only is the 111 allowed, but so are the 333, 444, ... Thus, if you're set for 3keV, you'll also get some at 9keV, 12

Re: [Ifeffit] Sixpack, PCA controll, "IND" column

2012-06-21 Thread Matthew Marcus
That book is out of print and hard to get. You should refer to later papers. The IND function is not necessarily robust. It's not rigorously derived, but is sort of empirical. mam On 6/21/2012 9:20 AM, Baker, Leslie wrote: This is the factor indicator function. Its minimum can be us

Re: [Ifeffit] first "official" relezse of my new software

2012-04-22 Thread Matthew Marcus
I'll second that. All hail Bruce and whoever else contributed. mam On 4/21/2012 5:09 AM, Ismael Graff wrote: Dear Bruce, thanks a lot for this new version and for your engagement in the Free Software cause. Your softwares Athena, Artemis and Atoms have been a corner stone in my researc

Re: [Ifeffit] Large XAFS data sets

2012-04-11 Thread Matthew Marcus
This is where some sort of automatic classifier or dimensional reducer would come in handy. You would first have to have auto-reduction into some standard form like k^n*chi(k) (EXAFS) or pre-edge-subtracted, post-edge nornalized (XANES). After that, you might use PCA or some other such tool to

Re: [Ifeffit] Fe K-Edge in Zirconium alloys and flattening effect

2012-03-01 Thread Matthew Marcus
I haven't looked at the prj file, but I can say a couple of things: 1. There's no reason why metallic Fe should look like the precipitate. The binary Fe-Zr phase disgram shows several compounds, of which the most Zr-rich is Zr3Fe. This is lighter in Fe than your 40 w/o, but it's notorious

Re: [Ifeffit] fitting sulphur using standards by Athena

2012-02-14 Thread Matthew Marcus
To reiterate a point which is often not understood - dilution won't fix overabsorption if the particles of the concentrated material which are mixed in with the diluent are too big. For concentrated S compounds, "too big" is in the low microns. When I run a S standard, I do it in total electron y

Re: [Ifeffit] XAFS for electride

2012-02-06 Thread Matthew Marcus
The obvious difficulty here is that the predicted phases requre TPa of pressure, which is way above what a DAC can provide. Also, for a DAC, you need an edge at a high-enough energy to get through the diamonds or gasket. There exist ambient-pressure-stable electrides in which an alkali atom is

Re: [Ifeffit] lifetime broadening of pre-edge peaks

2011-10-11 Thread Matthew Marcus
How significant are the photoelectron effects in hard X-rays compared with the core-hole effect? What I'm really after is a criterion for determining, at least roughly, how narrow a real, physical feature can be. mam - Original Message - From: vik...@comcast.net To: ifeffit@mi

Re: [Ifeffit] lifetime broadening of pre-edge peaks?

2011-10-10 Thread Matthew Marcus
, Phys. Rev. A 79, (2009) 032514, regards Iztok Matthew Marcus wrote: Is the core-hole lifetime broadening of pre-edge XANES peaks the same as at the main edge? I'm looking into issues of de-noising of XANES epsctra, so need to figure out how narrow real features c

[Ifeffit] lifetime broadening of pre-edge peaks?

2011-10-08 Thread Matthew Marcus
Is the core-hole lifetime broadening of pre-edge XANES peaks the same as at the main edge? I'm looking into issues of de-noising of XANES epsctra, so need to figure out how narrow real features can be. mam ___ Ifeffit mailing list Ifeffit@mille

[Ifeffit] controlling valence state in FEFF9 XANES sims

2011-10-06 Thread Matthew Marcus
I'm involved in a project involving mixed Fe-Cr oxides. There's some evidence that the presence of Fe2+ in these oxides causes distinctive features to appear in the XANES at the Cr K-edge. I would like to simulate this situation to see if a valence effect could really explain it. However, FEF

Re: [Ifeffit] Preparation help with fly ash sample with

2011-09-29 Thread Matthew Marcus
The downside of non-energy resolving detectors in this context is the huge background from elastic, as well as everything else. You would need to have exquisitely good normalization to get decent data after background subtraction on something that dilute. OTOH, Fred M. implies a good point about

[Ifeffit] ATOMS for PC?

2011-09-29 Thread Matthew Marcus
Is ATOMS available as an executable program anymore? I can't seem to find a download for it on the IFEFFIT site. Is the idea to only use the web version? mam ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.a

Re: [Ifeffit] XAFS of poly-metals contaminated soil samples

2011-09-09 Thread Matthew Marcus
If you're using an energy-dispersive detector like a solid-state detector, then the Cu will not cause too much of a problem because only the Kb line will interfere, and that's smaller in intensity than the Zn Ka line and will have little EXAFS on it. As for Fe, you can get considerable reductio

Re: [Ifeffit] how to consider Jahn-Teller distortion?

2011-08-08 Thread Matthew Marcus
Moving the Fe atom off-center as if it were the Ti atom in a perovskite isn't a good way to simulate JT distortion. In Fe3+ compounds such as goethite (I assume Fe3+, not the rare Fe4+), the distortion consists of the two axial distances being shorter than the 4 equatorial. You could simulate t

Re: [Ifeffit] Third cumulant in DWF

2011-04-04 Thread Matthew Marcus
OK, so if you don't add a sigma2 to your FEFF input file, then IFEFFIT will do the correction properly. Another question is whether, if you add a sigma2 to feff.inp, what does FEFF do? mam On 4/4/2011 3:37 PM, Bruce Ravel wrote: On Monday, April 04, 2011 06:01:20 pm Ping, Yuan wrote:

Re: [Ifeffit] Third cumulant in DWF

2011-04-04 Thread Matthew Marcus
The lambda is in the amplitude. I assume FEFF does not integrate over the distribution of distances, which is where the term in question comes from. That is, FEFF calculates A (complex) in chi(k) = Im(A(k)*exp(-lambda*R+2*i*k*R)/R^2) for a single R, but what you want with a non-0 ss (Artemi

Re: [Ifeffit] Purple & Red E Derivatives

2011-02-22 Thread Matthew Marcus
3, 2011 at 8:46 AM, Bruce Ravel wrote: On Tuesday, February 22, 2011 06:19:16 pm Matthew Marcus wrote: > The numerical derivative > is computed as the numerical differential of the mu(E) spectrum > divided by the numerical differential of the energy array. Ã, Smoothing > happens as exp

Re: [Ifeffit] Purple & Red E Derivatives

2011-02-22 Thread Matthew Marcus
The numerical derivative is computed as the numerical differential of the mu(E) spectrum divided by the numerical differential of the energy array. Smoothing happens as explained above. Justw atch the lines that get printed to the buffer when you click the plot buttons. - B. Ravel I wonder if

Re: [Ifeffit] sample preparation for liquid samples

2011-01-11 Thread Matthew Marcus
Charles Supper sells capillaries with 10um wall thickness and ID ranging from 0.3 to 2.5mm, in quartz, borosilicate or regular glass. These make nice sample holders if your beam is small enough. You can either work in transmission, making the thickness and concentration such that the edge jump

Re: [Ifeffit] Distortion of transmission spectra due to particle size

2010-11-22 Thread Matthew Marcus
I think there is a confusion over what is being averaged. As an example, consider a layer of particles which are completely opaque, and let's say that the area fraction is 1/2. If the particles lined up, then the transmission would be 1/2 for any N, whereas if the layers were random, then you'

Re: [Ifeffit] UO2 thin films on STO

2010-11-16 Thread Matthew Marcus
I'm assuming that the desire is to measure the EXAFS of the UO2, not the SrTiO3 substratem right? The ratio of the signal from the SrTiO3 to the UO2 would depend on the thickness of the UO2 and the incidence and takeoff angle (assuming you do fluorescence). There shouldn't be much interference

Re: [Ifeffit] Origin of terminology "self-absorption"

2010-11-16 Thread Matthew Marcus
down. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Nov 16, 2010, at 10:54 AM, Matthew Marcus wrote: It's definitely a misnomer. I use "overabsorption" and encourage others to do so. I suppose to track it down wo

Re: [Ifeffit] Origin of terminology "self-absorption"

2010-11-16 Thread Matthew Marcus
It's definitely a misnomer. I use "overabsorption" and encourage others to do so. I suppose to track it down would require going back over the seminal papers on the subject. mam On 11/16/2010 10:19 AM, Scott Calvin wrote: Hi all, As some of you know, I'm currently working on a textbo

Re: [Ifeffit] LCF analysis

2010-10-25 Thread Matthew Marcus
Another point is that even if the F-test calls out a .1% probability that A appears just due to noise, that's no guarantee that what looks like A isn't something else which is "A-like" enough to turn up in the LCF. It's probably something similar, but need not be exactly A unless you have s

Re: [Ifeffit] Asymmetric error bars in IFeffit

2010-10-23 Thread Matthew Marcus
The idea was that FEFF was not necessarily trustworthy to get the absolute answers, but was good enough to get the difference, say, between Al and Si, and Cu and Zn. In other words, experiment was the "ground truth" and FEFF used to extrapolate it to where it wasn't available. mam - Or

Re: [Ifeffit] Asymmetric error bars in IFeffit

2010-10-22 Thread Matthew Marcus
Another reason, from my point of view, is that FEFF wasn't accurate enough to use on its own without references. Also, it still can be argued that the process of data reduction and filtering produces distortions which aren't captured by using FEFF alone. Further, if one is comparing very simila

Re: [Ifeffit] Asymmetric error bars in IFeffit

2010-10-22 Thread Matthew Marcus
Some quantities, such as effective coordination numbers, are roughly linear in 1/size, so there's an argument for doing the coordinate transformation size->1/size. If you do that, then be sure to make things functions of abs(u) where u==1/size, because u<0 is unphysical. Doing it this way also

Re: [Ifeffit] Haha

2010-08-15 Thread Matthew Marcus
I thought that was the I0 plot. mam - Original Message - From: "Frenkel, Anatoly" To: "XAFS Analysis using Ifeffit" Sent: Sunday, August 15, 2010 2:16 PM Subject: Re: [Ifeffit] Haha And for the red curve, someone forgot the sample... Anatoly From

Re: [Ifeffit] calibrating and aligning samples for LCF

2010-05-24 Thread Matthew Marcus
If you trust that the calibration did not change between when the nanoparticles and the Fe foils were run, then all you need to do is to align the spectra so that the edge for Fe comes out at the same place as it did for the references. The tricky bit is that if you have references from somewhe

Re: [Ifeffit] energy resolution

2010-05-05 Thread Matthew Marcus
The reason I mentioned using transmission is that you could get to a true back-reflection condition that way, thus removing sensitivity to incidence angle. Another possibility for detecting the reflection is to look for a peak in I0, caused by the back-reflecting beam going back into the I0 ch

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Matthew Marcus
I wonder if some kind soul with some programming time to spare (ha ha) could write a program to do that. It would be relatively simple, but does need the knowledge of how to write a FEFF path. It would ask questions like where the phase and amp files are, what k-power was used, what the distan

Re: [Ifeffit] Principle Component Analysis

2009-08-22 Thread Matthew Marcus
A clear explanation can be found in Ressler, T., Wong, J. Roos, J. Smith, I. Env. Sci. Tech 34,950 (2000). There, it's used to analyze Mn XANES in samples of car exhaust particulates. mam On 8/22/2009 12:14 AM, abhijeet gaur wrote: > Hi all, > > I am trying to understand the method of

Re: [Ifeffit] (no subject)

2009-03-11 Thread Matthew Marcus
Wback in the 70s and 80s, Powers, et. al. claimed to observe a Cu-Fe distance of 3.75A, seeing it in both the Cu and Fe edges. However, a bit of Googling shows that this result is in some doubt. I once saw a Cr-Cr distance of 6 or 7A in a Cr-bis(arene) complex at 8K. Sometimes, the contributi

Re: [Ifeffit] Cumulant expansion fittings

2009-01-21 Thread Matthew Marcus
OK, here's my alternative for modeling asymmetric distributions: I use for the effective RDF a Gaussian-broadened exponential tail function. The tail function is defined as: t(r) = (1/|w|)*exp(-r/w) r*sign(w) >0 0 r*sign(w) <= 0 This limits to a delta function for w->0.

Re: [Ifeffit] Brainteaser

2008-04-03 Thread Matthew Marcus
MessageThe most obvious explanation for why the post-edge scans line up and the pre-edges don't is that the transmission chamber current amp or V/F is saturated and reads a fixed value below the edge. As the ring current decays, I0 goes down while It is fixed below the edge, so ln(I0/It) decreas

Re: [Ifeffit] switching to FEFF8 in Artemis

2008-03-11 Thread Matthew Marcus
> > Is "QFS" the quick fist shell theory thingie in the Theory menu? You > are correct -- it does not give you a choice. Using feff6 is > hardwired into it. It seems silly to me to use feff8 for the quick > first shell thing, but for the sake of completeness, it should be > fixed. Yes, it's the

[Ifeffit] switching to FEFF8 in Artemis

2008-03-07 Thread Matthew Marcus
I have FEFF8 and would like to get Artemis to use it for EXAFS calculations. I figured out how to use the Edit Preferences menu to point Artemis to the executable and how to get the ATOMS module to use the FEFF8_EXAFS template to generate feff.inp files which result in the generation of feffNNN

Re: [Ifeffit] Artemis

2008-01-10 Thread Matthew Marcus
Did you check the data range and interpolation as I suggested? mam - Original Message - From: "Alain Manceau" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Cc: Sent: Thursday, January 10, 2008 3:30 AM Subject: Re: [Ifeffit] Artemis > Bruce, > >>I just tried artemis with feff7 and it

Re: [Ifeffit] GaN atoms imput page

2007-11-26 Thread Matthew Marcus
If you know the positional parameter (the 0.375) and the lattice parameters, you can pull up the input file for any other wurzite structure and modify to suit. That's probably the easiest way. mam - Original Message - From: "Bruce Ravel" <[EMAIL PROTECTED]> To: "XAFS Analysis using

Re: [Ifeffit] Self absorption questions

2007-11-07 Thread Matthew Marcus
er one: A. I. Frenkel, D. M. Pease, J. I. Budnick, P. Shanthakumar, T. Huang Application of Glancing Emergent Angle Flourescence for Polarized XAFS Studies of Single Crystals J. Synchrotron Rad. 14, 272-275 (2007) Anatoly -Original Message- From: [EMAIL PROTECTED]

Re: [Ifeffit] Self absorption questions

2007-11-07 Thread Matthew Marcus
You can find a writeup which explains overabsorption in great and gory detail at http://xraysweb.lbl.gov/uxas/Beamline/Operation/Operation.htm . mam - Original Message - From: "Richard Mayes" <[EMAIL PROTECTED]> To: "XAFS Analysis using Ifeffit" Sent: Wednesday, November 07, 2007 7:39

Re: [Ifeffit] help: can I use ifeffit to predict chi?

2007-11-02 Thread Matthew Marcus
I have sent Chen some data on magnetite and maghemite. mam - Original Message - From: "Tai-Yen Chen" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]>; "XAFS Analysis using Ifeffit" Sent: Friday, November 02, 2007 10:53 AM Subject: Re: [Ifeffit] help: can I use ifeffit to predict chi? >

Re: [Ifeffit] Artemis fitting using FEFF paths plusexperimentalreferences

2007-09-25 Thread Matthew Marcus
The particles are ~8nm diameter, and the distances involved are 0.3-0.34nm, so that's only a 6% effect. Also, the fitted Fe-Fe coordinations vary with oxidation temperature, with the biggest deficits at the lowest temps. The particles actually hollow more at the higher temperature, so one would

Re: [Ifeffit] EXAFS Divination Dataset

2007-06-25 Thread Matthew Marcus
Our library doesn't carry that journal. Could someone send me a copy or put it on an FTP site for download? Thanks. mam - Original Message - From: "Scott Calvin" <[EMAIL PROTECTED]> To: "XAFS Analysis using Ifeffit" Sent: Monday, June 25, 2007 4:40 AM Subject: Re: [Ifeffit] EXAFS D

Re: [Ifeffit] convergence of XANES for STO

2007-06-18 Thread Matthew Marcus
How did you pick the values of the various parameters in the feff.inp file such as Vr, Vi and the SCF parameters? I once tried to do the Zn edge of ZnO and didn't come close, then gave up because there were too many parameters to play with. mam - Original Message - From: "Lena Fittin

Re: [Ifeffit] 2007 NSLS XAFS workshop: save the date

2007-05-09 Thread Matthew Marcus
That's great. Even though it will be several years, I'll still want to see the result when it happens. What you describe is exactly what I think is needed. mam - Original Message - From: "Scott Calvin" <[EMAIL PROTECTED]> To: "XAFS Analysis using Ifeffit" Sent: Wednesday, May 09, 2

Re: [Ifeffit] 2007 NSLS XAFS workshop: save the date

2007-05-08 Thread Matthew Marcus
This sounds possibly interesting. I wonder if experience with my own code would suffice instead of experience with Athena, which I never did really learn. Anyway, I looked at yu.edu/scc and found no courses listed there newer than 2006. On another topic, do you know of a good book or review on

Re: [Ifeffit] CN and bond distances in Artemis

2006-12-05 Thread Matthew Marcus
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

Re: [Ifeffit] Re: Novice FEFF question--feel free to post

2006-10-10 Thread Matthew Marcus
As usual, consistency is everything. It seems to me that one should always compare with a model compound, if possible. If you do that and do the model and unknown the same way, then you need only take the ratios of S0^2 or N or whatever. mam - Original Message - From: "Bruce Ravel"

Re: [Ifeffit] Filter window shape for FT?

2006-09-28 Thread Matthew Marcus
This is about going to what you guys call q-space. It's often of interest to be able to display the contributions from specific shells, thus showing off such things as beat-nodes. For instance, in phyllomanganates, the Mn-O first shell is often not of great interest, but the split Mn-Mn second

[Ifeffit] Filter window shape for FT?

2006-09-28 Thread Matthew Marcus
I've always been told that when doing Fourier filtering, the R-space window shouldn't have sharp corners. Artemis, for instance, allows you to vary this, and by default puts shoulders on the window. I have a user who now wants the sharp corners, claiming that it provides the best filtering. H

Re: [Ifeffit] Phase corrected Fourier transforms

2006-09-23 Thread Matthew Marcus
OK, I have to put in my US$0.02/e0.02. The phase correction can't mean much if the scattering atoms are different, which is usually the case. If the scattering atoms are very heavy, then the phase correction has a kink in it which could cause strange shapes if applied to light-atom shells. I'v

Re: [Ifeffit] Attempted XANES calc using FEFF8.1 - what's wrong?

2006-08-14 Thread Matthew Marcus
This all suggests that Ziyi Wu's claims to be able to tell the difference between 4 and 5 waters of hydration in the metal center of a protein just from fitting XANES features may be a bit overblown. I tried again with FEFF8 and still don't see the pre-edge features, nor get the ratios right.

Re: [Ifeffit] Attempted XANES calc using FEFF8.1 - what's wrong?

2006-08-13 Thread Matthew Marcus
With all the playing around one has to do to get a known structure to agree, how can one fit unknown structures? What started this whole thread was the talk I heard by Wu Ziyu who claimed to fit metalloprotein structures based on subtle features of the XANES, while I can't even get the broad fe

[Ifeffit] Attempted XANES calc using FEFF8.1 - what's wrong?

2006-08-11 Thread Matthew Marcus
I tried the XANES calculation on FEFF8.10 with calcite at the Ca K-edge as the object. I had just taken some data on this compound, and I wanted to see how it compares. The attached shows that it doesn't compare all that well. I've also attached the feff.inp file I used, which was made by ATOM

Re: [Ifeffit] Re: XAFS Analysis using Ifeffit

2006-08-03 Thread Matthew Marcus
How do you get those absorption backgrounds, free of EXAFS? I can see it for Kr, but how did you do it for the other, chemically-reactive elements? mam - Original Message - From: "Alojz Kodre" <[EMAIL PROTECTED]> To: "Matt Newville" <[EMAIL PROTECTED]>; "XAFS Analysis using Ifeffit"

Re: [Ifeffit] Other programs than FEFF - GNXAS and MXAN

2006-07-30 Thread Matthew Marcus
Including only bare-bones ASCII in/out is, IMHO, the only way to obtain true portability, and it has worked. I vaguely recall that they use some sort of verifier on their code to screen out system dependencies. I don't understand this. A verifier is a program that inspects programs, lookin

Re: [Ifeffit] Other programs than FEFF - GNXAS and MXAN

2006-07-29 Thread Matthew Marcus
Feff deliberately did not include graphics or analysis, with the hope / expectation that lots of other people would do this. This turned out to be true, and very many analysis programs use Feff. It is perhaps interesting that this has not happened for GNXAS. In contrast, it is uninteresting fo

Re: [Ifeffit] mxan and gnxas

2006-07-29 Thread Matthew Marcus
Thanks. Do you mean that it's available as source-code only? Is there any tutorial material available? If it does background subtraction, does that mean you feed it raw signal-vs-energy files? mam - Original Message - From: "Francesco Giannici" <[EMAIL PROTECTED]> To: "ifeffit"

Re: [Ifeffit] Other programs than FEFF - GNXAS and MXAN

2006-07-27 Thread Matthew Marcus
One reason I can think of for GNXAS to be less popular than FEFF is that it hasn't been compiled for Windows. It exists only for various forms of Unix. The website says that it's fortran, so there's no reason I can see that it couldn't be compiled for Windows, depending on whether it needs som

[Ifeffit] Other programs than FEFF - GNXAS and MXAN

2006-07-27 Thread Matthew Marcus
I heard a talk by Ziyu Wu of Beijing Synchrotron Radiation Facility in which he said that the international community prefers a package called GNAXS to FEFF for EXAFS calculations. He also has his own package called MXAN for XANES fitting. What do other people think of these programs? Would it

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