Re: [Ifeffit] Standardized Spectra

2022-08-08 Thread Robert Gordon
Is this what you had in mind? http://exafsmaterials.com/ReferenceSpectra.html Not all elements (nor all forms of a given element), but a good illustration. -R. On 2022-08-07 5:00 p.m., Kyle Draim wrote: Hello! I don't have any X-Ray data to analyze in your app, I'm just seeking a visual

Re: [Ifeffit] XAFS 2022: important deadlines

2022-04-01 Thread Robert Gordon
Matt's idea of an April Fool's joke no doubt... The XAFS2022 website indicates that the abstract deadline is April 17. Cheers, -R. On 2022-04-01 12:41 p.m., Matt Newville wrote: Hi Folks, ... and some reminders: Abstracts for XAFS 2022 are due April 19.  Please submit a presentation for

Re: [Ifeffit] Conduction band energy and deltae0

2022-03-12 Thread Robert Gordon
Hi Melike, If the 'before doping' system is a known material - i.e. a bulk standard - I would fix N's, let R's, sig^2's, dEo, and So^2 be variables to fit. While sig^2 may be similar between doped and undoped, I would not assume that no disorder has been introduced on doping. I would consider

Re: [Ifeffit] The possibility of the defect concentration estimation by feff

2022-01-16 Thread Robert Gordon
Hi Iraida, I am a little confused by your question. GaAs structure has 8 atoms in unit cell with a = 5.653 Ang. If I had a cluster 7 Ang in radius, that won't give 900 atoms...that is a volume less than 3 x 3 x 3 unit cells (216 atoms). You can calculate for substitutional and interstitial

Re: [Ifeffit] Any coorelation about 'white line" in K-edge XAS with oxidation states?

2021-12-11 Thread Robert Gordon
Hi Marco, Yes, a s - d transition is dipole forbidden, but the quadrupole transition can occur, as can a transition s - mixed p/d. The edge position in XAFS for metals like Ni and Cu is taken at the inflection point leading to the first main absorption feature, but is considered to have s - d

Re: [Ifeffit] XEOL

2021-11-25 Thread Robert Gordon
If you can move between Nd L3 and Br K, why not stop at Nd L1 if you want to see if a Nd s-type initial state has any influence on the XEOL? You should not need to go up to Nd K. Some references: https://aip.scitation.org/doi/abs/10.1063/1.477320?journalCode=jcp

Re: [Ifeffit] how to learn wavelet analysis

2021-11-10 Thread Robert Gordon
Try starting here: https://www.esrf.fr/UsersAndScience/Experiments/CRG/BM20/Software/Wavelets On 2021-11-10 6:48 p.m., 罗昕宇 wrote: Dear IFEFFIT members, I'm a fresh graduate student majoring in chemical engineering. I began to learn XAFS by myself one month ago. I bought and read the book

Re: [Ifeffit] Bi L3 standards

2021-06-29 Thread Robert Gordon
I have Bi metal foil and Bi2O3 you are welcome to use. Data were published in: dx.doi.org/10.1021/jp502996t|J. Phys. Chem. C2014, 118, 9696−9705 Some other standards are visible in here: *Journal of Nuclear Materials 420* (*2012*) *116*–122 ... *D.A. McKeown et al*. -R. On Tue, Jun 29, 2021 at

Re: [Ifeffit] How do I create a histogram based on R-space values

2020-12-09 Thread Robert Gordon
When i look at the files you included, I see R-value in the first column, then what I am assuming are the (magnitude of) Fourier transforms of different data sets selected for export, with vertical displacements of 10 or 25 between each data set. A histogram plot would involve extracting N and

Re: [Ifeffit] How to perform normalisation and background removal of data containing L3 and L2 edges

2020-12-07 Thread Robert Gordon
In checking the literature, has anyone indicated what data collection ranges they used, and what pre- and post-edge regions were selected for normalisation? Do you have more data below 2800eV that you are not showing? Starting data collection only 50 eV or so below the edge can be problematic

Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data

2020-12-07 Thread Robert Gordon
Data is just XANES at Ru L2...be better if it went to higher E for normalisation purposes Why are you trying to plot XANES data in k,q or R? On 2020-12-07 7:38 a.m., Ravel, Bruce wrote: Likeliest reason:

Re: [Ifeffit] Writing a Script for MD Simulations / Scripting Atoms

2020-07-28 Thread Robert Gordon
Are you specifying arguments for datoms.bat?  datoms [--output format] [--rmax #] [--cif --rec=#] [--wx] mydata.inp If no input or CIF file is specified at the command line, F in the current working directory will be used, if available. If the C<--wx> flag for running the GUI is given, all

Re: [Ifeffit] XAFS detection limit

2020-02-09 Thread Robert Gordon
You might also take a look at Steve Heald's article in JSR: https://dx.doi.org/10.1107%2FS1600577515001320 "Strategies and limitations for fluorescence detection of XAFS at high flux beamlines" -R. On 2020-02-09 8:00 a.m., Christian Wittee Lopes wrote: Hi Chris and Matt, Thank you for

Re: [Ifeffit] Unable to use 64-bit Demeter on Windows computer

2019-08-21 Thread Robert Gordon
Hi Brittaney, I downloaded the installer (in case Bruce put out a new version) and checked. It started up fine for me. Possible reasons why you may be having issues: 1. You might need to run the installer as administrator 2. Your antivirus program is blocking installation good luck! -R. On

Re: [Ifeffit] Dynamic XAFS Simulations?

2019-01-23 Thread Robert Gordon
Hi, Welcome to XAFS and all the excitement, thrills and adventure that implies! First, since you are new to the subject, I would strongly recommend you take a course on XAFS. Many synchrotron facilities offer such - e.g. The APS/IIT Summer school was held last July; the SSRL course was last

Re: [Ifeffit] Unwanted rescaling of energy axis when importing ascii file into Athena (Demeter 0.9.26)

2019-01-09 Thread Robert Gordon
Hi, I switched your data from keV to eV before importing, and that does not have the same issue. -R. On 2019-01-09 6:35 a.m., Lukas Grote wrote: Hello, I am reporting an apparent bug in Athena (Demeter 0.9.26, Windows 10). When I import high energy resolution XAS data from an ascii file,

Re: [Ifeffit] regarding installation

2018-12-23 Thread Robert Gordon
Dear Prof. Gupta, Could you provide more information, please? This is not a useful bug report. https://bruceravel.github.io/demeter/documents/SinglePage/bugs.html Many researchers use this software without issue. I have attached a test file for you to try. When you import it, please ensure the

Re: [Ifeffit] Looking of a K-edge spectrum of maghemite

2018-12-17 Thread Robert Gordon
Attached...foil measured simultaneously in transmission on 20BM at APS..only to about 12 invAng though. On 2018-12-17 9:08 a.m., Lorenzo Stievano wrote: Hi everybody, daes anybody have in his repository a Fe K-edge XAS spectrum of maghemite (gamma-Fe2O3)? I would need it as a reference

Re: [Ifeffit] data on CdS

2018-11-17 Thread Robert Gordon
CdS Mu(E) measured in FLY on 20BM in 2013...no simultaneous reference for energy calibration through...sorry... On Sat, Nov 17, 2018 at 8:58 AM Anatoly Frenkel < anatoly.fren...@stonybrook.edu> wrote: > Dear all - if someone could share raw Cd K-edge data of CdS, it would be > really helpful! >

Re: [Ifeffit] Problem with Athena - Weronica/difference

2018-10-30 Thread Robert Gordon
Hi Weronica, I tested this using the same scan loaded 3 times and was able to switch without issue. I tested this with a different additional scan on the same element, and was able to switch without issue. Please provide more information.

Re: [Ifeffit] Demeter on ubuntu 14.04

2018-08-08 Thread Robert Gordon
Hi Edmund, I installed on 16.04 LTS following this: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05851.html though this was 2 years ago. A more recent installation, I think, did not involve manually installing giflib-5.1.4. -R. On 2018-08-08 7:07 AM, Edmund Welter wrote:

Re: [Ifeffit] Making N (coordination number) a variable.

2018-08-01 Thread Robert Gordon
Or just swap...set N's to be the So^2 from a known coordination standard and define an amp for each shell... e.g. So^2 = 0.8 from standard so all N's set to 0.8, and shell 1 had amp1 in the So^2 position defined as guess, shell2 has amp2, etc On 2018-08-01 8:15 AM, Anatoly Frenkel wrote:

Re: [Ifeffit] Basic questions about the preliminary data processing in Athena

2018-07-27 Thread Robert Gordon
, Haifeng On Sun, Jul 22, 2018 at 5:45 PM, Robert Gordon <mailto:ragor...@alumni.sfu.ca>> wrote: Hi Haifeng, Here's my take on what you described: Two sample to be studied at the same edge using the same reference. Three scans on A and three on B are done with sim

Re: [Ifeffit] Basic questions about the preliminary data processing in Athena

2018-07-22 Thread Robert Gordon
Hi Haifeng, Here's my take on what you described: Two sample to be studied at the same edge using the same reference. Three scans on A and three on B are done with simultaneous reference. First: compare the three reference scans for A. If they agree, then compare the data scans. If they

Re: [Ifeffit] Athena programm for XAS data analysis

2018-05-08 Thread Robert Gordon
changing colour: Preferences --> gnuplot --> col7 and Set a desired colour then apply and savedisplayed "your value" might not update until you restart Athena, but the plot should. On Tue, May 8, 2018 at 3:07 AM, Stoll, Andreas (HIU) wrote: > Hi Jonas, > > > first

Re: [Ifeffit] Se reference XANES

2018-05-01 Thread Robert Gordon
Not personally, but there is a spectrum of it in these: https://academic.oup.com/jxb/article/66/15/4795/484381 http://aem.asm.org/content/71/5/2331 2nd one gives white line positions for ease of comparison On 5/1/2018 3:41 AM, desmau wrote: Hello everyone, would anybody have a reference XANES

Re: [Ifeffit] Sulfur EXAFS k oscillations

2018-04-09 Thread Robert Gordon
Large mono glitch around k ~ 13.8 A-1  (E~3200 eV) on 4-3   perhaps? On 4/9/2018 11:04 AM, Miller, Elizabeth Christine wrote: Hi all, I am analyzing some sulfur K-edge EXAFS data taken at 4-3 at SSRL. When I use a k-weight of k^3 to plot, my oscillations at high k reach over 100, which

Re: [Ifeffit] FeSe2 Se K-edge XANES request

2018-03-14 Thread Robert Gordon
Thank you, but we have measured an FeSe standard. We are seeing a small component in one sample that may be FeSe2-related and are looking for something to which to compare and possibly include in LCF. best regards, Robert On 3/14/2018 10:34 AM, Yasin Deep wrote: For Te doped FeSe we have this

[Ifeffit] FeSe2 Se K-edge XANES request

2018-03-14 Thread Robert Gordon
Hi Folks, Does anyone have a near-edge spectrum of FeSe2, Se K-edge, they could share? (Ideally with Se elemental reference measured simultaneous.) Thanks, -R. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov

Re: [Ifeffit] Artemis having trouble

2018-02-04 Thread Robert Gordon
t; Not sure what that mean. On Sat, Feb 3, 2018 at 4:14 PM, Robert Gordon <ragor...@alumni.sfu.ca <mailto:ragor...@alumni.sfu.ca>> wrote: When you reinstalled, did you delete the Demeter-related di

Re: [Ifeffit] Artemis having trouble

2018-02-03 Thread Robert Gordon
, Robert Gordon <ragor...@alumni.sfu.ca <mailto:ragor...@alumni.sfu.ca>> wrote: Opens fine for me... Have you tried the usual suspects? Accidentally minimised a window...Restarting the computer (or log off/on)... or sending the log file to see if there is an e

Re: [Ifeffit] Artemis having trouble

2018-02-03 Thread Robert Gordon
Opens fine for me... Have you tried the usual suspects? Accidentally minimised a window...Restarting the computer (or log off/on)... or sending the log file to see if there is an error message... not much to go on here... On 2/3/2018 3:29 PM, Sheraz Gul wrote: Can anyone please explain why

Re: [Ifeffit] Demeter 0.9.26 launch faillure

2017-12-06 Thread Robert Gordon
Hi, In case you don't know where you can make this change, if you can't start the program to edit it via the preferences, it is in the [gnuplot] section of demeter.ini which is in the same directory as the log. For me, the relevant line reads: program =

Re: [Ifeffit] Athena: Data cannot be imported by using plugin PFBL12C

2017-11-14 Thread Robert Gordon
Hi Yuri, You are probably running into the memory limit. This has been discussed  a number of times on this mailing list, e.g.: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03931.html https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05673.html Bruce's

Re: [Ifeffit] Hephaestus: Absorption Data Source

2017-11-13 Thread Robert Gordon
Spreadsheet attached...Adobe did most of the work... On 11/13/2017 11:13 AM, Matt Newville wrote: Anyone up for scanning the PDF of Krause and Oliver and cleaning up the data into machine readable values like a spreadsheet?  If so, I'd be happy to add them to the database. --Matt

Re: [Ifeffit] Hephaestus: Absorption Data Source

2017-11-13 Thread Robert Gordon
Another reference that might help: https://journals.aps.org/pra/abstract/10.1103/PhysRevA.22.1615 Core-level lifetimes as determined by x-ray photoelectron spectroscopy measurements John C. Fuggle and Santos F. Alvarado Phys. Rev. A 22, 1615 – Published 1 October 1980 X-ray photoelectron

Re: [Ifeffit] Hephaestus: Absorption Data Source

2017-11-12 Thread Robert Gordon
Hi, The documentation for Hephaestus lists the same paper as you indicated. (Access by going to Help-Document in Heph.) Another reference with values tabulated is: http://aip.scitation.org/doi/10.1063/1.95 Natural widths of atomic K and L levels, Kα X‐ray lines and several KLL Auger lines

[Ifeffit] flattened norm export issues

2017-10-22 Thread Robert Gordon
Hi, Encountered a difference on export of normalised data. Flattening does not seem to be preserved when saving current group as norm(E) but is when saving marked group. Example in norm.prj attached. original data set normalised and flattened...displaying "Normalized" as current group or as

[Ifeffit] space group 224 & Atoms

2017-10-22 Thread Robert Gordon
Hi, I was trying to simulate Cu2O...cubic...O tetrahedrally coordinated by Cu...Cu linearly coordinated by O. There are two origin choices for space group 224 (Pn-3m). If using origin choice 1, then atom positions would be O    0,0,0 Cu  0.25,0.25,0.25 If using origin choice 2, translate by

Re: [Ifeffit] Metal-Metal Peak Splitting in 5d Transition Metals

2017-09-19 Thread Robert Gordon
Ramsauer-Townsend effect Bruce gives some references at the end of this talk: https://speakerdeck.com/bruceravel/the-ramsauer-townsend-effect-in-x-ray-absorption-spectroscopy -R. On 9/19/2017 2:06 AM, Shoaib Muhammad wrote: Dear All, I have a question that is not directly related to Athena

Re: [Ifeffit] [IFEFIT]Chi(E) in version 0.9.25

2017-09-15 Thread Robert Gordon
This already happens in Athena. It was requested back in 2014: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04747.html and Bruce did include energy as a column in the exported chi file in a future release (present in 0.9.26)...e.g. # XDI/1.0 Athena/0.9.26 # Element.edge:

Re: [Ifeffit] Demeter on Windows with Inkscape (and possibly other programs)

2017-08-10 Thread Robert Gordon
Hi Bruce, I am not experiencing this issue. I have Athena and Inkscape both open right now. My environment variables list does not have FONTCONFIG_FILE in it. I have a vague recollection of deleting that env var some time ago when changing versions of Demeter. Regardless, Demeter is working

Re: [Ifeffit] FEFF8/FEFF9 in Demeter​

2017-06-15 Thread Robert Gordon
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06059.html -R. On Wed, Jun 14, 2017 at 11:55 PM, 이국승(에너지환경소재연구팀) wrote: > ​Dear Ifeffit users, > > > I remember that one of you have posted the method how we can use > FEFF8/FEFF9 in Demeter​ program. > >

Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 4

2017-06-09 Thread Robert Gordon
> > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > >1. Re: Error using Atoms (Robert Gordon) >2. Re: question about sigma2 and atomic distance (Robert Gordon) >

Re: [Ifeffit] question about sigma2 and atomic distance

2017-06-08 Thread Robert Gordon
I imagine they could, yes. Motivation to do so is another question entirely. Considering myself more of an experienced amateur, and a fan of the Socratic Method, let me ask you a few questions: What do you currently understand about the relationship between two atoms in a material and the mean

Re: [Ifeffit] Error using Atoms

2017-06-08 Thread Robert Gordon
Hi Adam, I opened the cif file you provided and Artemis/Atoms immediately gave the atoms.inp file attached. Running Atoms gave the feff.inpI don't see a problem. Could you provide more detail on how you achieved this erroneous result? i.e. step by step... e.g. I opened Artemis v0.9.25 I

Re: [Ifeffit] Silent Oxygen

2017-04-18 Thread Robert Gordon
Hi Fuxiang, Further to Bruce's note, I looked at your file. Your model splits the nearest oxygens by only 0.01A. Is that the magnitude of splitting you anticipate? Are you familiar with the resolution criteria for EXAFS? (k-range [deltak]) * (R-resolution [deltaR]) ~ pi/2 for identical near

Re: [Ifeffit] Conflicting FEFF calculation

2017-04-04 Thread Robert Gordon
/4/2017 11:23 AM, Bruce Ravel wrote: On 04/04/2017 11:58 AM, Robert Gordon wrote: Seems to be looking for gnuplot in the wrong location. Gnuplot was installed to: C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot not C:\Strawberry... Drat! I thought I had that working correctly. You

Re: [Ifeffit] Conflicting FEFF calculation

2017-04-04 Thread Robert Gordon
on https://github.com/bruceravel/WebAtoms, http://millenia.cars.aps.anl.gov/webatoms I don't really see the value of sifting through all that work to figure out what had an impact on Ashis' issue. If the newer code works -- that seems good enough to me. B On 04/03/2017 06:08 PM, Robert

Re: [Ifeffit] Conflicting FEFF calculation

2017-04-03 Thread Robert Gordon
Hi Ashis, I can reproduce what you are seeing. I exported the atoms.inp's for your two structures. If I import TAA first and run atoms, it looks ok. I then import TPA and run - ok. I re-run Atoms on TAA, it changes. In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I

Re: [Ifeffit] Space group type in Artemis

2017-03-11 Thread Robert Gordon
B11b in an alternate form of space group #9 (Cc or C1c1) Atoms does take Bb as the space group, but that could be Bb11 (which does not produce an error message) with unique x-axis instead of the unique z-axis in B11b. My suggestion: When I use a crystal structure in Atoms, I prefer to check the

Re: [Ifeffit] Bond length and Coordination number problems from EXAFS

2017-02-21 Thread Robert Gordon
21, 2017 at 3:30 AM, Robert Gordon <ragor...@alumni.sfu.ca <mailto:ragor...@alumni.sfu.ca>> wrote: Hi Fuxiang, I tried fitting just the first shell in your data: kmin 3.5 kmax 11.775 Rmin 1.25 Rmax 2.56 I used just Pd-Ni and Pd-Pd single scatter pa

Re: [Ifeffit] Bond length and Coordination number problems from EXAFS

2017-02-21 Thread Robert Gordon
Hi Fuxiang, I tried fitting just the first shell in your data: kmin 3.5 kmax 11.775 Rmin 1.25 Rmax 2.56 I used just Pd-Ni and Pd-Pd single scatter paths with one amplitude, one E, 2 delR's and 2 sigma-squareds for a 6 parameter fit. I didn't let Nni or Npd vary in a fit, but did change

Re: [Ifeffit] error when fitting in Artemis

2016-12-22 Thread Robert Gordon
Hi George, Your paths are not listed. I don't know why you cannot rerun FEFF directly, but you can export the feff.inp, Add it back in as a new feff calculation, and then run it. Discard the old path from the path list and drag the new path over to continue. -R. On 12/22/2016 9:11 AM,

Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

2016-12-21 Thread Robert Gordon
On 12/21/2016 12:58 PM, Bruce Ravel wrote: On 12/21/2016 02:50 PM, Robert Gordon wrote: So, for all but tetragonal, the orientation of the cluster can be identified with the orientation of the crystal axes. Does it not seem more logical to preserve the apparent orientation with respect to the cry

Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

2016-12-21 Thread Robert Gordon
in clusters that were rotated relative to one another. My answer, appropriate (I think) in that case, was to shrug. You seem to be commenting on something unrelated to the original question, but I'm not understanding the point. B On 12/21/2016 01:13 PM, Robert Gordon wrote: Hi Bruce

Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

2016-12-21 Thread Robert Gordon
, Robert Gordon wrote: What if one were to do this FEFF calculation using the POLARIZATION card? 1 0 0 means something different if the atom positions have been rotated by 45 degrees relative to the crystal axes along which the polarization is defined. Well ... you could rotate the polarization vector

Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

2016-12-19 Thread Robert Gordon
Hi Bruce, What if one were to do this FEFF calculation using the POLARIZATION card? 1 0 0 means something different if the atom positions have been rotated by 45 degrees relative to the crystal axes along which the polarization is defined. -R. On 12/16/2016 10:14 AM, Bruce Ravel wrote: On

Re: [Ifeffit] struggling to install demeter under ubuntu 16.04

2016-12-01 Thread Robert Gordon
Hi, I installed demeter recently under 16.04 lts. In response to Juan's issues, I described what I did here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-November/00.html One additional deviation was that I had already installed gfortran and gunplot (sudo apt install)

Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

2016-11-25 Thread Robert Gordon
Hi Juan, I can open your file. It displays without issue. My system is amd64 with ubuntu 16.04 LTS. The version of Demeter I cloned from git is 0.9.26 (using the git clone instruction), mostly following the 'David Hughes' guide" from here

Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

2016-11-23 Thread Robert Gordon
Hi Juan, I just installed demeter and larch on an Ubuntu 16.04lts system today. I can reproduce something like your error. I use the 10K Cu data in the examples folder. If I import it and don't select the numerator on import, the plot window has issues (~10^307 axis limit), but the file

Re: [Ifeffit] Bug Report importing file.

2016-07-24 Thread Robert Gordon
According to http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2013-August/006762.html limit is 8192 It is possible to rebin the data in Athena...in multiple steps...what it first imports, then export, then attach the missing higher E data, re-import, rebin...using a near edge step size of

Re: [Ifeffit] report bugs

2016-06-22 Thread Robert Gordon
HI, This was also reported earlier this month and Bruce has indicated it is on his .todo list. http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05587.html You can use the stand alone version to prepare and save the atoms.inp file. This file can then be imported (Add) in the

Re: [Ifeffit] Questions

2016-06-06 Thread Robert Gordon
Has it occurred to you to upgrade your version (and your colleague too)? Current version is 0.9.24. -R. On 6/6/2016 8:50 AM, dien...@srs.gov wrote: Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from

Re: [Ifeffit] Artemis/FEFF question

2016-05-03 Thread Robert Gordon
The Sc atom does not go at 0,0,0 in hcp. That is site 2a and has another atom at 0,0,0.5 which is what the calculation gave. If you use position 2c (0., 0.6667, 0.2500), you get 6 nn at 3.256A above and below the central atom. regards, Robert On 5/3/2016 6:02 PM, Dimitar Popmintchev

Re: [Ifeffit] Bug report

2016-04-11 Thread Robert Gordon
Hi Bruce, Sorry...should have suggested he back up the directory first. To that end, how about adding a statement or two to the faq along the lines of: Make a copy of the files in the AppData\Roaming\Demeter directory for help in diagnosing what caused a file corruption. -R. On 4/11/2016

Re: [Ifeffit] Bug report

2016-04-10 Thread Robert Gordon
Files\DemeterPerl\perl\site\bin\dathena.bat line 47 eval {...} called at C:\Program Files\DemeterPerl\perl\site\bin\dathena.bat line 47 -- Le 10/04/2016 07:53, Robert Gordon a écrit : The data file? On 4/9/2016 10:19 PM, Lorenzo Stievano wrote: Here it is. Le 09/04/2016 23:52, Robert

Re: [Ifeffit] Bug report

2016-04-09 Thread Robert Gordon
Another thought: Does this crash happen with other data files, or just this one? On 4/9/2016 10:19 PM, Lorenzo Stievano wrote: Here it is. Le 09/04/2016 23:52, Robert Gordon a écrit : Can you send the text file as well, please? On 4/9/2016 12:43 PM, Lorenzo Stievano wrote: Hi, I have

Re: [Ifeffit] Questions to Bruce

2016-03-23 Thread Robert Gordon
Hi Dien, To perhaps forestall a scolding from Bruce, let me point out the following advice on error reporting: https://bruceravel.github.io/demeter/pods/bugs.pod.html RE:1. I am able to import multiple scans with reference data. My test was to try 3 scans and associated reference data. I am

Re: [Ifeffit] Any XAFS schools in North America this year?

2016-03-07 Thread Robert Gordon
Thanks Anatoly! On 3/7/2016 10:14 AM, Anatoly I Frenkel wrote: Here is the info about the upcoming XAFS short course at Brookhaven (Nov 2-4, 2016): http://workshops.ps.bnl.gov/default.aspx?w=XAFS2016 Regards, Anatoly ___ Ifeffit mailing list

Re: [Ifeffit] Any XAFS schools in North America this year?

2016-02-28 Thread Robert Gordon
often. I'd like to be able to direct people to yours. Cheers, B Sent from my iPhone On Feb 28, 2016, at 08:05, Robert Gordon <ragor...@alumni.sfu.ca> wrote: Hi All, I have a couple of students who are novices. I was hoping that one could go to a school to learn and perhaps ge

[Ifeffit] Any XAFS schools in North America this year?

2016-02-28 Thread Robert Gordon
Hi All, I have a couple of students who are novices. I was hoping that one could go to a school to learn and perhaps get some hands-on experience before they get into the meat of their thesis work. I haven't seen any notices yet about schools taking place in the late spring or summer and was

Re: [Ifeffit] pi/2deltak

2016-02-01 Thread Robert Gordon
Hi Riti, A couple of caveats to Matt's answer: The EXAFS equation is not simply a sum of sine functions. I can think of two ways that the resolution criteria can be worked around: 1. Consider the case of two close near neighbours in a single-crystal environment whose close distances are

Re: [Ifeffit] Deglitching issues on Athena on latest Mac versions

2015-12-20 Thread Robert Gordon
” and the plotting window “X11”. So I could be wrong but my understanding is, even though X Quartz was the one installed, Athena is utilising it as x11. I thank you for your advice. Wuhib On 20 Dec 2015, at 21:01, Robert Gordon <ragor...@alumni.sfu.ca <mailto:ragor...@alumni.sfu.ca>> wrote: Hi

Re: [Ifeffit] Deglitching issues on Athena on latest Mac versions

2015-12-20 Thread Robert Gordon
s but on Windows [Sathish on Dec, 2013 / Shoaib May, 2015 / Martina or Robert Gordon Sep, 2015 / Eva October, 2015]. The problem that I am facing is the same as issues described before but on Mac. So I will describe it below. After moving to the "Deglitch and Truncate Data” window

Re: [Ifeffit] Opening "older" data files in the latest Athena version

2015-11-09 Thread Robert Gordon
Hi Marcelo, How did you save the data file? I can open Fe.060 without issue using 0.9.22 but in order to do so, I clicked on the fe.060 link, then selected RAW and then saved as text. If I just right-clicked and saved link as from the list page, I ended up with some html document. regards,

Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12

2015-11-09 Thread Robert Gordon
lder" data files in the latest Athena version (Marcelo Eduardo Alves) 2. Re: Opening "older" data files in the latest Athenaversion (Robert Gordon) 3. Re: Opening "older" data files in the latest Athena version (Guanghui Zhang

Re: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

2015-11-09 Thread Robert Gordon
Hi Carolyn, Do you see this behaviour even for standard samples, where the local co-odination of the zinc is known? If this is only happening for unknowns, then it could be telling you that you have heavier or more scatterers present than you have included in your fitting model. So^2, N and

Re: [Ifeffit] Athena open data project but not shown the curve

2015-11-05 Thread Robert Gordon
spectra already published in papers, should be the EXAFS the same or it depends on the range for the fourier transform. regards. 2015-11-05 18:50 GMT+01:00 Robert Gordon <ragor...@alumni.sfu.ca <mailto:ragor...@alumni.sfu.ca>>: Hi Carlos, Please clarify somethings for me re

Re: [Ifeffit] problems with deglitching in D-Athena 0.9.22

2015-10-03 Thread Robert Gordon
Hi Eva, I suspect, when searching the mailing list, the recent discussion on deglitching issues in 0.9.22 was overlooked. e.g. http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05193.html or http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05232.html or Bruce's

Re: [Ifeffit] Deglitching

2015-09-04 Thread Robert Gordon
resets to qt when restarting even though the ini file says wxt. -R. On 9/4/2015 11:06 AM, Bruce Ravel wrote: On 09/04/2015 01:37 PM, Robert Gordon wrote: I can confirm something funny is happening here. In 0.9.21, the deglitch menu would not display points. I upgraded to 0.9.22 today and degl

Re: [Ifeffit] Issues with Athena on high-performance systems

2015-06-25 Thread Robert Gordon
HI Nils, My laptop has i5 (2.4GHz)/Intel/16GB running win7prox64 and I have no issues, even with the first plot. How many files are you trying to plot? I test with just one and everything works fine. -R. On 6/25/2015 9:06 AM, Nils Skoglund wrote: Hi, I’m curious if anyone else is

Re: [Ifeffit] Reference for Setting k range in EXAFS analysis

2015-06-18 Thread Robert Gordon
Hi Navneet, You have asked a rather open-ended question. There are numerable resources available for learning about XAFS analysis that are straightforward to find. Setting the k-range is more specific and governed by several factors. The range chosen affects resolution and precision. In

Re: [Ifeffit] Ca EXAFS with Ge220 or InSb111 (Lisa Bovenkamp)

2015-05-11 Thread Robert Gordon
Another possibility is that the L-edges of In and Sb are giving considerable energy-dependence to the beam in the EXAFS region...any non-linearity between detectors will make extraction of the EXAFS problematic. Looking at CAMD's XAS beamline mono specs

Re: [Ifeffit] FEFF calculation for two inequivalent absorbing sites

2015-04-09 Thread Robert Gordon
Hi Eugenio, Quick question: Did you change the tags for the Co atoms so that they are different? If I do that, I get 4 and 6 coordinate results. you can import the cif file twice, run atoms on both sites (with tags different) and get the two feff inputs for running. -R. On Thu, Apr 9, 2015 at

Re: [Ifeffit] Exploring XANES data for getting EXAFS results

2015-01-16 Thread Robert Gordon
of a particular metal), R, N, and formal valence state are not independent quantities. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Dr. Robert Gordon Staff Scientist, CLS@APS

Re: [Ifeffit] D-Atoms program, common positions and occupancies

2014-04-07 Thread Robert Gordon
-- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 9700 S. Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 ph 630-252-0580 fax ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fit

2014-02-09 Thread Robert Gordon
: Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis (Robert Gordon) -- Message: 1 Date: Thu, 06 Feb 2014 16:05:30 -0600 From: Robert Gordon ragor...@alumni.sfu.ca

Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis

2014-02-06 Thread Robert Gordon
/mailman/listinfo/ifeffit -- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax todorokite.pdf Description: Adobe PDF document ___ Ifeffit mailing list Ifeffit

Re: [Ifeffit] Demeter not working on Windows 8.1 64bit

2014-01-14 Thread Robert Gordon
help to others if you did this --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E

Re: [Ifeffit] Demeter not working on Windows 8.1 64bit

2014-01-14 Thread Robert Gordon
for a clean install these plots, and gnuplot doesn't plot if no xrange. If I reset, then I can move around and use DAthena 9.19 without issue...DArtemis is still an unhappy DHuntress with fpj files... On 1/14/2014 3:28 PM, Bruce Ravel wrote: On 01/14/2014 04:11 PM, Robert Gordon wrote: Hi Matt

Re: [Ifeffit] error in ATOMS

2013-11-13 Thread Robert Gordon
@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax ___ Ifeffit mailing list Ifeffit

Re: [Ifeffit] modeling significant defects and molecules

2013-10-31 Thread Robert Gordon
___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax

Re: [Ifeffit] (D) Atoms crashing while running feff

2013-08-18 Thread Robert Gordon
HI Matt, That cif file is an old version of the structure. I can get DArtemis to crash if I use it too, but if I shift the origin by -1/8, -1/8, -1/8 it works. No crash when running Feff. Some more recent references for the structure: http://rruff.geo.arizona.edu/AMS/minerals/Hercynite Fd-3m

Re: [Ifeffit] data point limits in Athena?

2013-08-04 Thread Robert Gordon
Hi Jorg, Matt is on to the problem...Too many numbers... I deleted columns 2 - 58. Working with columns labelled Ioni1,2 and 3 was ok, with little problem reading it in to Athena 0.9.17 even with the 2460 lines. I say little because it does take several seconds on my system for Athena to read in