Re: [Ifeffit] S02 selection from reviewer

2021-10-02 Thread Matthew Marcus
Since S02 is a parameter in the description of EXAFS and not of the experiment, it's independent of technique. Overabsorption (misnamed 'self-absorption') can reduce the *measured* amplitude, an effect which can be fudged in analysis by reducing S02. If the sample is truly homogeneous (on

Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matthew Marcus
h for your help. Best, Shinhyo ------------ *보낸 사람:* Matthew Marcus mailto:mamar...@lbl.gov>> 대신 Ifeffit mailto:ifeffit-boun...@millenia.cars.aps.anl.gov>> *보낸 날짜:* 2021년 9월 7일 화요일 오후 4:11 *받는 사람:* ifeffit@millenia.cars.aps.anl.gov <mailto:ifeffit@millenia.cars.aps.anl.gov&g

Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matthew Marcus
There are other characters that Windoze doesn't like in filenames: |\/*":<>? mam On 9/7/2021 3:58 PM, Matt Newville wrote: Hi Shinhyo, Liane, On Tue, Sep 7, 2021 at 5:39 PM Bang, Shinhyo > wrote: Thank you for the response. The OS is Windows 10.

Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matthew Marcus
Or maybe save onto a USB drive. mam On 9/7/2021 3:58 PM, Matt Newville wrote: Hi Shinhyo, Liane, On Tue, Sep 7, 2021 at 5:39 PM Bang, Shinhyo > wrote: Thank you for the response. The OS is Windows 10. In addition to the symptom that was

Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matthew Marcus
This may sound like an 'is it plugged in?' sort of suggestion, but I wonder if there's a permissions issue. Perhaps IFEFFIT doesn't have write permission where it's trying to write. It might help people diagnose the problem if you were to specify the OS being used. mam On 9/7/2021

Re: [Ifeffit] EXAFS Fitting with 2 CIF files

2021-09-04 Thread Matthew Marcus
Extending what Scott said, I find it useful to make the coefficients abs(fracoxide) and abs(1-abs(fracoxide)) to avoid false minima with negative S0^2. mam On 9/4/2021 1:21 PM, Scott Calvin wrote: Hi Zihao, Do it by folding the molar ratio in to the amp parameter for each CIF. Of

Re: [Ifeffit] Manuscript comments regarding EXAFS modeling

2021-08-27 Thread Matthew Marcus
Was there a standard measured that's chemically similar to the unknown? If so, S0^2 could be set by requiring that the CN of the standard be what it's known to be. Often, the dσ² is mostly relevant in terms of differences or changes so an error in the absolute value isn't very important. If

Re: [Ifeffit] [Ext] Farrel Lytle database

2021-07-06 Thread Matthew Marcus
As I recall, not only is the FL Dbase not in a standard format, but the format varies according to the vintage of the files. Also, there's no documentation except for the 1-line comment. mam On 7/6/2021 9:11 AM, Carlo Segre wrote: Dear Monica: The Lytle database is not in a current

Re: [Ifeffit] [Ext] Analyzing EXAFS data on Artemis

2021-05-27 Thread Matthew Marcus
If you go beyond first shell, then you'll need to take into account the Se-Se paths in Li2Se. That may be your best way of detecting Li2Se. mam On 5/27/2021 12:03 PM, Carlo Segre wrote: Hi Deltsidis: Using Artemis, you can compare the calculated Fourier Transforms of the Se-Fe and

Re: [Ifeffit] [Ext] Re: XAS question

2020-10-29 Thread Matthew Marcus
It's possible that your data really has a kink in it. Zoom in on that last bit in E space before any background subtraction and see if there's something odd-looking. If there's really an artifactual kink, then there's not much you can do. mam On 10/29/2020 7:47 AM, Carlo Segre

Re: [Ifeffit] Reported W L3-edge and L2-edge energy

2020-05-07 Thread Matthew Marcus
epeatability are very good.  I believe there are equally good moons in existence.   As Matthew Marcus pointed to the Kraft paper (which used an older source but 4-bounce mono to improve resolution), we find that Fe foil is definitely better defined as 7110.75 and Cu foil is between 8980.0 and 8

Re: [Ifeffit] Reported W L3-edge and L2-edge energy

2020-05-05 Thread Matthew Marcus
This paper: Kraft, S., Stümpel, J., Becker, P., & Kuetgens, U. (1996). High resolution x‐ray absorption spectroscopy with absolute energy calibration for the determination of absorption edge energies. Review of Scientific Instruments, 67(3), 681-687. has precision measurements of a bunch of

Re: [Ifeffit] errors in bond lengths

2020-04-12 Thread Matthew Marcus
Something I've done for analyzing DWF on data taken at several temperatures is what I called 'consensus amplitude' fitting. Here, I fitted shells to k^n*chi[i](k) = exp(-2 dsig2[i] k^2) A(k) sin(phi(k)+2 dr[i]k) where i is the index to temperature, and the fit parameters are A(k), phi(k),

Re: [Ifeffit] errors in bond lengths

2020-04-11 Thread Matthew Marcus
The uncertainties reported by Artemis include as 'noise' the systematic deviation of FEFF calculation from the real thing. Even if FEFF were perfect, those FEFF calcs haven't been through the mutilations inflicted by data reduction, such as spline fitting. What I've done when looking at

Re: [Ifeffit] what happened to the website?

2020-01-29 Thread Matthew Marcus
OK, thanks. I figured that you removed it because it's obsolete. Are you sure the server isn't running Windows 7? :-) Sincerely, Matthew Marcus On 1/29/2020 3:48 PM, Matt Newville wrote: Hi Matthew, On Wed, Jan 29, 2020 at 4:39 PM Matthew Marcus mailto:mamar...@lbl.gov>>

Re: [Ifeffit] what happened to the website?

2020-01-29 Thread Matthew Marcus
bAtoms had a problem anyway - it wouldn't reliably handle more than 50 inequivalent sites. There are complicated mineral structures of low symmetry that easily blow past that. Sincerely, Matthew Marcus On 1/29/2020 3:09 PM, Jo Melville wrote: If you already have Demeter installed, it's reasonably e

[Ifeffit] what happened to the website?

2020-01-29 Thread Matthew Marcus
The http://millenia.cars.aps.anl.gov/ website seems to have gone off-line, which means that WebAtoms doesn't work anymore. Is there a replacement? Of course, I can use the stand-alone Atoms in Demeter. -- Sincerely, Matthew Marcus ___ Ifeffit

Re: [Ifeffit] selection of pixels by criteria

2019-11-21 Thread Matthew Marcus
A suggestion: Make a scatterplot available, plotting the pixel-by-pixel values of any two relevant quantities, and make it possible to define a polygon mask on that scatterplot. That often allows separation of chemically-distinct areas. Sincerely, Matthew Marcus On 11/21/2019 12:26 PM

[Ifeffit] Anyone use OCEAN?

2019-09-12 Thread Matthew Marcus
if this might be a good forum for getting advice on solving problems with this code. Unlike ABINIT, which is one of the ab-inito engines OCEAN can use, OCEAN doesn't have a forum of its own. -- Sincerely, Matthew Marcus ___ Ifeffit mailing list

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

2019-08-14 Thread Matthew Marcus
of three structures does this most resemble?'. I love the idea of blind analysis comparison. Sincerely, Matthew Marcus The answer you get will depend somewhat on the assumptions you make.  if you are truly provided with data and no other information about the sample, then the job is challenging

Re: [Ifeffit] EXAFS of solid-solution alloy

2019-02-08 Thread Matthew Marcus
each edge. Sincerely, Matthew Marcus Hi all, I have some problems in analyzing the EXAFS of solid-solution alloy, let us define as A0.5B0.5. I have searched the mailbox but cannot find similar discussion yet. So I post the question here and hope to get some suggestion from you.

Re: [Ifeffit] Bump/oscillating pattern at high energies of EXAFS

2018-11-01 Thread Matthew Marcus
Agreed. The low frequency and high amplitude at the end is implausible as EXAFS. Sincerely, Matthew Marcus It is an effect of inhomogeneity of the sample, that is, the variation in the metal density throughout the X-ray beam footprint. Anatoly On Thu, Nov 1, 2018 at 5:34 PM Raj kumar

Re: [Ifeffit] Interpreting old XANES data with missing standards

2018-06-08 Thread Matthew Marcus
would have sulfide in it? I'd think that it would have mostly sulfate and maybe sulfite. Check the peak position; it's a pretty reliable indicator of sulfite vs. sulfate vs. other. Here are some spectra taken in TEY mode with the calibration gypsum = 2482.75eV. Sincerely, Matthew Marcus

Re: [Ifeffit] EXAFS above 5 angstroms

2018-05-21 Thread Matthew Marcus
approaches give you the same criterion for the visibility of a distant shell. This effect is indeed significant for heavy elements, either at the L-edge (5d and actinides) or K-edge (4d and up). Sincerely, Matthew Marcus Daniel, Those distances are really far away and I think it would

[Ifeffit] current-amp recommendation

2017-11-14 Thread Matthew Marcus
I've gotten involved with a project in which stabilization of the position of a monochromatic, soft X-ray beam is needed. The offending frequencies seem to be vibration frequencies like 57 and 116Hz. We have in mind to use a thin Au film with a gap in the middle, measuring the drain current

Re: [Ifeffit] XAFS short course in BNL: Nov 1-3, 2017

2017-07-28 Thread Matthew Marcus
. It does sound interesting. My knowledge of XAS analysis has remained pretty static. Will there be anything that applies to soft X-rays? I'm moving to STXM, so will be dealing with soft X-rays. Sincerely, Matthew Marcus Dear subscribers: Please share with your group members or others

Re: [Ifeffit] E0 on linear combination fitting: fit or not?

2017-05-12 Thread Matthew Marcus
My experience on ALS 10.3.2 is that shifts of up to about 0.5eV are plausible and often improve the fit substantially. I assume you're talking XANES, not EXAFS. 6eV is right out and suggests either a misidentification of the species (false fit) or inconsistency of energy cal. One of my pet

Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 21

2017-04-21 Thread Matthew Marcus
[Ifeffit] Fwd: Ifeffit Digest, Vol 170, Issue 19 Message-ID: <ca+7esbopsw1p-9hzyyq+yobhcch++cohocyg2z-gexadn3l...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Matthew, On Thu, Apr 20, 2017 at 5:34 PM, Matthew Marcus <mamar...@lbl.gov> wrote: Does

Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 19

2017-04-20 Thread Matthew Marcus
Does Athena use a histogramming method for Fourier filtering? That's what I use. The idea is that to grid the data we don't interpolate but take averages over the data appearing within the bin, with interpolation only when there aren't any points within a bin. For those, you have to bridge

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:

Re: [Ifeffit] Peakfitting CeO2 data in Athena

2016-12-07 Thread Matthew Marcus
about 2-5 nm in diameter. Is there a good Ce(IV) ref for nanos that are in this size range? On Wed, Dec 7, 2016 at 2:37 PM, Matthew Marcus <mamar...@lbl.gov <mailto:mamar...@lbl.gov>> wrote: Instead of doing a bunch of peak fitting, try LSQ. Use CeO2 (bulk or nanos) for one ref

Re: [Ifeffit] Peakfitting CeO2 data in Athena

2016-12-07 Thread Matthew Marcus
Instead of doing a bunch of peak fitting, try LSQ. Use CeO2 (bulk or nanos) for one reference and some Ce(III) for the other. Consistency check: see that the Ce(III) fraction is consistent over some set of Ce(III) references. Ce(III) has an assymetric white line, so it doesn't really fit a

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] 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
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
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] 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] 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
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] 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] 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] 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

[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] 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.

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

[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] 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] 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 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] 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

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] 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] 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] 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] 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

[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] 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

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] 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] 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

[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] 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

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] 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] 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] 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] 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] 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] 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] 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,

[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] 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

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] 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

[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

2013-08-13 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

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] 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] 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] 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] 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] 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

2012-12-12 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

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