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] 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

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

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 ifeffit@millenia.cars.aps.anl.gov Sent:

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 quick

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)

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

Re: [Ifeffit] Haha

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

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 u0 is unphysical. Doing it this way also

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

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 -

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

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] 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

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

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] 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

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

2011-09-30 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

[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,

[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

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 can

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:

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

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

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] 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

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

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,

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

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

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

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

Re: [Ifeffit] How to do with diffraction peak

2012-12-12 Thread Matthew Marcus
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 it is to delete

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

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

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 mamar...@lbl.gov 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

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

2013-03-27 Thread Matthew Marcus
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 put my bit in, I believe

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

2013-03-27 Thread Matthew Marcus
: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 forget whether the issue

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

2013-03-28 Thread Matthew Marcus
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 mamar...@lbl.gov wrote: Some users do have FEFFx (x6l) on their own, so

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

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus
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 mamar...@lbl.gov wrote: What I typically do

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus
, George On Wed, May 15, 2013 at 11:41 AM, Matthew Marcus mamar...@lbl.gov 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

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus
, 2013 at 1:20 PM, Matthew Marcus mamar...@lbl.gov 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 separately, are different

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus
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 mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: OK, I guess I don't know what 'standard normalization' is. It looks from the quotient that you'll need

Re: [Ifeffit] normalization methods

2013-05-16 Thread Matthew Marcus
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 mamar...@lbl.gov wrote: I'm not sure what 'flattening' means. Does that mean dividing by a linear or other polynomial function

Re: [Ifeffit] Linear Combination Fitting using ATHENA

2013-08-13 Thread Matthew Marcus
with 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 mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: While it's true that Mossbauer is the gold standard for Fe valence

[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] X-ray natural circular dichroism by FEFF?

2013-09-11 Thread Matthew Marcus
managing the list at 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 dichroism by FEFF? (Matthew Marcus

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

Re: [Ifeffit] error in ATOMS

2013-11-13 Thread Matthew Marcus
13, 2013 at 10:09 AM, Matthew Marcus mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: 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

[Ifeffit] Ti or V on hydrous Fe oxides?

2013-12-03 Thread Matthew Marcus
Anyone have reference data for Ti or V sorbed on or substituted in Fe oxides or oxyhydroxides? I'm having trouble finding anything in the literature. mam ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov

Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Matthew Marcus
It must be a slow day in the EXAFS world. Does the term 'topic drift' mean anything? :-) The Wikipedia entry http://en.wikipedia.org/wiki/Hosanna has some examples of secular use of the word, FWIW, which I admit isn't much. mam On 12/5/2013 2:02 PM, Matt Newville wrote: Hi Anatoly,

Re: [Ifeffit] How to identify Mn Mn Corner edge paths in Artemis

2014-01-07 Thread Matthew Marcus
Corner-sharing octahedra in birnessite-based structure occur either due to interlayer Mn, i.e. Mn which is attached on top of the layer, over a layer vacancy, or octahedra hanging off the edges of sheets. There is a vast litereature on this, notably from people like Manceau, Bargar and Webb.

Re: [Ifeffit] Absorption-coefficient data repository?

2014-01-27 Thread Matthew Marcus
It won't calculate it accurately in the XANES region because it doesn't know about XANES. What could be done is to take the smooth parts from Hepheastus and scale by the XANES data. mam On 1/27/2014 10:43 AM, Scott Calvin wrote: Hi Damon, Hephaestus will calculate that for you.

Re: [Ifeffit] EXAFS with multiple absorbers

2014-02-22 Thread Matthew Marcus
What about the CFAVERAGE card (love that reminder of times gone by)? mam On 2/21/2014 7:23 PM, Kevin Jorissen wrote: Hi Francisco No. If you e.g. want to sum contributions from several scatterers with different environment/fine structure, the right procedure is to do a separate feff

Re: [Ifeffit] Peaks in MCA spectra

2014-03-31 Thread Matthew Marcus
Hmmm. An interesting brain-teaser. Scaling very roughly from the graph, the mystery peak shows up at about 715eV. This is consistent with Fe. Could there be a background from Fe somewhere in the detection systen? The intensity between the O and Co peaks doesn't really look like a peak, but

Re: [Ifeffit] Peaks in MCA spectra

2014-04-01 Thread Matthew Marcus
OK, I think the other Matt has solved it - it's the L1 peak. I was confused by an inaccurate attempt at reading the energy scale. Also, I somehow didn't read correctly the branching ratio from Hephaestus. mam On 3/31/2014 8:57 PM, George Sterbinsky wrote: Hi Matt, Thanks for your

Re: [Ifeffit] Peaks in MCA spectra

2014-04-01 Thread Matthew Marcus
, George On Tue, Apr 1, 2014 at 11:45 AM, Matthew Marcus mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: OK, I think the other Matt has solved it - it's the L1 peak. I was confused by an inaccurate attempt at reading the energy scale. Also, I somehow didn't read correctly the branching ratio

Re: [Ifeffit] XANES + EXAFS for light elements in diluted samples

2014-05-11 Thread Matthew Marcus
It took some clicking to get from the link below to where there's actually such a compilation: http://www.xafs.org/Experiment . Is that the one you meant? mam On 5/11/2014 3:04 PM, Ravel, Bruce wrote: Federico Boschirini's compilation of the world's XAFS beamlines should help:

Re: [Ifeffit] Problems in Energy calibration

2014-05-14 Thread Matthew Marcus
Which edge is this for? I'm guessing MoK since you talk about using a foil for calibration. Could the problem be polarization? Since MoS2 is a highly anisotropic material, you would expect strong dichroism in both XANES and EXAFS regions. It's possible that the resolutions at the two

Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Matthew Marcus
I wonder if what he was asking about is an automated way of mapping the position parameters for a given space group, that is, fractional atomic coordinates as listed in a .cif, onto the various path distances. As it is now, it's impractically hard to do it except for very simple cases. Maybe

[Ifeffit] Data for Cr selenide?

2014-06-04 Thread Matthew Marcus
Does anyone have EXAFS data to at least k=12 for Cr selenide of known phase? I'm working on fitting the EXAFS of Cr doped into Bi2Se3, and using Feff6L, the S02 comes out to 0.65 if I assume a substitutional site, which seems a bit low. mam

Re: [Ifeffit] Scattering paths in XANES calculations

2014-06-12 Thread Matthew Marcus
That sounds like an interesting talk. Is it available? mam On 6/12/2014 7:07 AM, Stefanie Roese wrote: Dear all, I am performing XANES calculations for silver clusters with FEFF. Aditional to my XANES results, I would like to get information about the participating scattering paths

Re: [Ifeffit] Principal Component Analysis (PCA) for XANES

2014-07-02 Thread Matthew Marcus
Athena (IFEFFIT package) does it. So does the ALS Beamline 10.3.2 software package at https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . If you can't get at it there, I can send the executable and manual. mam On 7/1/2014 10:59 PM, Teck Kwang Choo wrote: Hi Everyone, Does

Re: [Ifeffit] problems re-opening Athena project

2014-09-17 Thread Matthew Marcus
There's a combination-fit program on the ALS 10.3.2 website https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . mam On 9/17/2014 9:55 AM, Foster, Andrea wrote: Bruce, thanks for your help...look forward to seeing new version. FYI I especially am interested using the

Re: [Ifeffit] experimental standard

2014-11-18 Thread Matthew Marcus
You didn't say what you're trying to find out or even which edge you're doing this at. That being the case, it's a little hard to know what the best strategy is. A few things come to mind: 1. If you're looking for the environment of the Ga, then obviously, BaO and Ti2O3 aren't terribly

Re: [Ifeffit] experimental standard

2014-11-18 Thread Matthew Marcus
... If isostructural to something more simple, use that known structure to construct FEFF model. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Matthew Marcus [mamar...@lbl.gov] Sent: Tuesday, November 18

[Ifeffit] S XANES question

2014-11-26 Thread Matthew Marcus
A user on ALS 10.3.2 is taking S K-edge XANES and consistently finding a strong peak at 2484eV (calibration: gypsum white line = 2482.75eV). There's a shoulder at the nominal position of the sulfate peak. Now, peaks below sulfate I can understand, but since there's no such thing as heptavalent

Re: [Ifeffit] S XANES question

2014-11-26 Thread Matthew Marcus
. THE VALENCE AND SPECIATION OF SULFUR IN GLASSES BY X-RAY ABSORPTION SPECTROSCOPY The Canadian Mineralogist Vol. 39, pp. 331-339 (2001) -Lyle On Wed, Nov 26, 2014 at 12:39 PM, Matthew Marcus mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: A user on ALS 10.3.2 is taking S K-edge XANES

Re: [Ifeffit] S XANES question

2014-11-26 Thread Matthew Marcus
/Experiments/Imaging/ID21/php/gypsum We often use the spectra from there as references (or when asking: Is this standard what we think it is?) --Matt On Wed, Nov 26, 2014 at 4:23 PM, Matthew Marcus mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: The gypsum spectrum looks nothing like any

Re: [Ifeffit] SSRL-data

2015-02-04 Thread Matthew Marcus
Seems to me that in this era of nigh-infinite disk space, there's no need for binaries for EXAFS files like this. The ASCII is perfectly fine. One question to ask: Is the offset already subtracted from the data count? I assume that it is, because the last column has numbers that are smaller

Re: [Ifeffit] Ca EXAFS with Ge220 or InSb111

2015-05-11 Thread Matthew Marcus
I do it just fine with Si111 (ALS 10.3.2). Do you have some evidence that the energy resolution or flux isn't what it should be? For instance, have you recorded a S XANES spectrum on sulfate? That has a sharp, intense peak. mam On 5/11/2015 8:16 AM, Lisa Bovenkamp wrote: Hello.

Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Matthew Marcus
. For this sample, the 1st derivative of the Fe foil was 7.112 keV. I can also provide individual scans for the database, if needed. Is there any interest in the As K-edge of this sample, too? I have that one as well. Case On Mon, Jul 6, 2015 at 5:48 PM, Matthew Marcus mamar...@lbl.gov mailto:mamar

Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Matthew Marcus
Thanks! May I add it to the ALS 10.3.2 reference collection? What is the standard of energy calibration? Is the Fe metal edge at 7110.75eV, 7112eV or what? mam On 7/6/2015 7:11 AM, Case Van Genuchten wrote: Dear Shaofeng, I am attaching the averaged, raw data and Fe K-edge EXAFS

Re: [Ifeffit] XAFS short course in BNL on Nov 5-7: Save the date

2015-08-07 Thread Matthew Marcus
of Matthew Marcus [mamar...@lbl.gov] Sent: Friday, August 07, 2015 6:23 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] XAFS short course in BNL on Nov 5-7: Save the date What's MCR-ALS? I know and use all the other things you mentioned. mam On 8/7/2015 3:06 PM, Anatoly I Frenkel

Re: [Ifeffit] XAFS short course in BNL on Nov 5-7: Save the date

2015-08-07 Thread Matthew Marcus
What's MCR-ALS? I know and use all the other things you mentioned. mam On 8/7/2015 3:06 PM, Anatoly I Frenkel wrote: Dear IFEFFIT subscribers: Please save the dates, Nov. 5-7, 2015, of the annual XAFS short course in Brookhaven National Laboratory. As many of you may know, we vary

Re: [Ifeffit] Unable to run Demeter on EPA computers

2015-10-22 Thread Matthew Marcus
This is an application for an acronym: SIMWA! Security In My Way Again! mam On 10/22/2015 11:46 AM, Matt Noerpel wrote: Thank you for your time, Bruce. The IT person tried it with and without the AV running (Symantec) and neither worked. Additionally, the AV does run in Safe Mode.

Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)

2015-09-24 Thread Matthew Marcus
). I would doubt the Chantler's L3+.1 number, all other numbers look ok - this is what you can get. jana padeznik gomilsek Message: 3 Date: Wed, 23 Sep 2015 18:02:08 -0700 From: Matthew Marcus<mamar...@lbl.gov> To: XAFS Analysis using Ifeffit<ifeffit@millenia.cars.aps.anl.gov> Subje

Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)

2015-09-24 Thread Matthew Marcus
OK. Now I get it. Why use 50eV? Since lifetime and other broadening is not taken into acocunt in any of these tables, why not use a very small number? mam On 9/24/2015 11:07 AM, Bruce Ravel wrote: On 09/24/2015 01:43 PM, Matthew Marcus wrote: See the attached ppt for the demo. I

Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)

2015-09-24 Thread Matthew Marcus
except that not trusting Chantler's values for these values might be reasonable. On Thu, Sep 24, 2015 at 10:16 AM, Matthew Marcus <mamar...@lbl.gov <mailto:mamar...@lbl.gov>> wrote: I'm not after absolute data, just the edge-jump ratio. This would have to be extracted by peak+ar

[Ifeffit] Problem with Hephaestus at Ca L-edges

2015-09-23 Thread Matthew Marcus
I wanted to work out the edge-jump ratio between the L3 and L2 edges of Ca using Hephaestus. I ran into two problems: 1. The ratio implied by what it says for the unit-edge-step thickness does not agree with that derived by computing the absorption (cm^2/gm) above and below each edge

Re: [Ifeffit] CuO XAS spectrum

2015-12-02 Thread Matthew Marcus
There are two spectra (transmission, probably) in the XAFS Model Compound Library http://cars9.uchicago.edu/cgi-bin/newville/Model-Search.cgi . mam On 12/2/2015 3:32 PM, Enyuan Hu wrote: Dear all, I'm analyzing some Cu compounds spectra and was wondering if anyone has the CuO XAS

[Ifeffit] ISO Calcite + dolomite EXAFS

2016-05-27 Thread Matthew Marcus
Does anyone have Ca K-edge EXAFS data they can share for calcite and dolomite? I took some, but it seems to disagree with FEFF as to the position of the Ca-(Ca,Mg) peak. mam ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov

Re: [Ifeffit] ISO Calcite + dolomite EXAFS

2016-05-27 Thread Matthew Marcus
PM, Matthew Marcus <mamar...@lbl.gov> wrote: Does anyone have Ca K-edge EXAFS data they can share for calcite and dolomite? I took some, but it seems to disagree with FEFF as to the position of the Ca-(Ca,Mg) peak. mam ___ Ifeffit mailin

Re: [Ifeffit] Ifeffit Digest, Vol 156, Issue 4

2016-02-09 Thread Matthew Marcus
I have an SDD and find very little strength in the escape peak or the Si Ka peak. I have seen Si from the sample. I can't speak to how well Si XAS works because my beamline doesn't go down that far. mam On 2/9/2016 10:25 AM, Pierre Lecante wrote: Hi Pinit, here is what you can

Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 3

2016-04-03 Thread Matthew Marcus
It shouldn't be called 'self-absorption'. That's a misnomer, which seems to have come from a 1992 paper (Troger, et. al."Full correction of the self-absorption in soft-fluorescence extended x-ray-absorption fine structure", PRB 46,3283 (1992). The effect was described and analyzed in a 1982

Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 3

2016-04-03 Thread Matthew Marcus
Still, I wouldn't necessarily trust Debye-Waller (ss2) values taken from EXAFS on strongly overabsorbed samples, even with a correction that gets the right coordination number. mam On 4/3/2016 7:04 PM, Matt Newville wrote: Hi Matthew, On Sun, Apr 3, 2016 at 8:13 PM, Matthew Marcus <mam

Re: [Ifeffit] determining reasonable fitting parameters

2016-07-27 Thread Matthew Marcus
I'm not sure I get your point about ion-chamber response. Shouldn't that normalize out in post-edge spline? If the I0 chamber gets less sensitive as a function of energy, then the post-edge background rises by the same amount as the wiggles get bigger, so it divides out. Similarly for

Re: [Ifeffit] determining reasonable fitting parameters

2016-07-27 Thread Matthew Marcus
/2016 04:39 PM, Matthew Marcus wrote: I'm not sure I get your point about ion-chamber response. Shouldn't that normalize out in post-edge spline? Athena edge-step normalizes (i.e. normalizes by a constant) by default. It does not do a functional (or energy dependent) normalization by default

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

2016-08-09 Thread Matthew Marcus
by that name.) —Scott Calvin Sarah Lawrence College On Aug 9, 2016, at 12:40 PM, Matthew Marcus <mamar...@lbl.gov> wrote: There are two different input files which take the extension .inp. One is the feff.inp file, which is the input to FEFF and contains a list of coordinates (Car

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

2016-08-09 Thread Matthew Marcus
Oh, the Demeter menu. I was looking in Artemis itself. Thanks! mam On 8/9/2016 11:07 AM, Bruce Ravel wrote: On 08/09/2016 01:50 PM, Matthew Marcus wrote: This actually results in a bit of inconvenience - if you want to use ATOMS, you have to load some data into Artemis and pretend

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

2016-08-09 Thread Matthew Marcus
There are two different input files which take the extension .inp. One is the feff.inp file, which is the input to FEFF and contains a list of coordinates (Cartesian, not crystallographic) of all atoms surrounding an absorpber atom out to a certain distance. ATOMS produces this. The other is

Re: [Ifeffit] Ifeffit Digest, Vol 162, Issue 17

2016-08-12 Thread Matthew Marcus
Topic 3: Incorrect dark current (offset) is just one of many ways that glitches can escape being normalized out, and one of the few you can correct in software. Others include but are not limited to 1. Any detection-system nonlinearity in I0 or detected channel (F or T). This includes

Re: [Ifeffit] No Reference Foil

2016-07-13 Thread Matthew Marcus
Just a caveat - CeO2 and Ce(OH)4 have XANES which isn't quite the same as other Ce4+. There's a shoulder on the low side, as if it were slightly reduced, and the first peak is at a slightly different position. Of course, you can use LCF with CeO2 as one of the refs if you need to.

[Ifeffit] fitting of S XANES with arctans and gaussians

2016-07-18 Thread Matthew Marcus
I'm trying to fit 37 micro-XANES spectra taken at the S K-edge, using the method discussed in the paper by Manceau and Nagy "Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy", Geochimica et Cosmochimica Acta 99 (2012) 206–223. In this paper,

Re: [Ifeffit] Multi-electron peak in Yb

2016-08-04 Thread Matthew Marcus
not Fe either. mam On 8/4/2016 4:20 PM, Matt Newville wrote: Hi Matthew, On Thu, Aug 4, 2016 at 2:24 PM, Matthew Marcus <mamar...@lbl.gov <mailto:mamar...@lbl.gov>> wrote: Does anyone know of data on multi-electron peaks at the Yb L3 edge? One of the users here was jus

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

2016-08-08 Thread Matthew Marcus
I'm afraid a PDF file of that sort is useless for EXAFS work because it doesn't tell you where the atoms are. It only tells you the size of the unit cell, unless you use it to solve the crystal structure yourself, which I don't recommend :-) You need to search the literature for structures

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

2016-08-08 Thread Matthew Marcus
That's a theoretical paper, so I don't know how reliable those numbers are. It will take Han some care with crystallography to translate the data into something usable by Atoms, i.e. a complete site list. I suggest starting with structures with the same code (e.g. D022) and filling in new

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

2016-08-08 Thread Matthew Marcus
Use ATOMS, which lets you define the structure by filling in a form, then save as an ATOMS .inp file. You don't need the .cif. I forget whether ATOMS can save as .cif. The crystallographic symmetry rules will duplicate the O atom for you. The CIF only shows symmetry-inequivqlent atoms.

Re: [Ifeffit] Peakfitting CeO2 data in Athena

2016-12-08 Thread Matthew Marcus
The usual justification for using gaussians for peaks, aside from "it works" is that there's inhomogeneous broadening over and above the lifetime. The usual justification for using an arctan for the step is exactly the opposite. Instrument broadening is often taken to be gaussian. Net result:

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