- Ifeffit - millenia.cars.aps.anl.gov

Re: Horae-058
by Bruce Ravel 23 Nov '05

23 Nov '05

On Wednesday 23 November 2005 07:35, you wrote: > Greetings from SPring-8 (getting chilly here, but no snow yet). We've got you beat here at the APS. There is snow on the ground right now! The Australian and Brazilian synchrotrons are looking awfully good right now.... > I tried downloading the latest tarball using your horae-update > script. It download a file with the right name, but that only > contains what appear to be sourceforge related web links. In other > words horae_update is broken (much like what happened before). SourceForge redesigned their web site. The screen scraper in horae_update no longer works. I am hesitant to just fix the current code -- it was a hand-built solution and, obviously, much too fragile. A better solution would require either using better html parsing tools from CPAN or figuring out how to gather information from SourceForge without needing to scrape their web pages. I am open to any suggestions or offers of coding help. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

4 4

that didn't take long...
by Bruce Ravel 23 Nov '05

23 Nov '05

Hi folks, I just discovered a fairly serious bug in the version of Athena I just released yesterday. The auto-alignment function is broken. Fortunately, alignment can still be done by hand using the +/- buttons in the alignment dialog. The fix is simple, but I won't be able to post updates until next week. (It's a holiday tomorrow here in the States and I am leaving for the airport soon.) My apologies to anyone who needs that feature in the next few days and especially to Paul who just did a bnch of work to make and post a new OSX installer. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

1 0

new tarball and windows updater
by Bruce Ravel 22 Nov '05

22 Nov '05

Hi folks, Today I made a release that is mostly for maintenence purposes on Athena. Most of the changes have to do with various bug fixes and small UI improvements. Artemis and Hephaestus are unchanged. The new tarball, version 58, is at my site and at SourceForge. I also built a new windows executable and an updater. See http://cars9.uchicago.edu/iffwiki/HoraeVersion058 for details about the release. Thanks to Shelly, Adam, and Norbert for their feedback on this release. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

1 0

graphics help
by crojasa＠unmsm.edu.pe 21 Nov '05

21 Nov '05

Hello help in: why in my graphics the fit curve is more differents that data curve?. If that fit is ok, but the fit curve(red) is very underneath that data curve(blue). Some idea Chachi P.D my graphis is in attachment -- Chachi Rojas GMC FCF UNMSM Tel.Mo.:97499347 email:crojasa@unmsm.edu.pe

2 1

RE: [Ifeffit] NiO data
by Kelly, Shelly D. 15 Nov '05

15 Nov '05

Hey Scott, Well, I botched the MRCAT part of the acknowledgement. Please use this one instead. Use of the APS was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-ENG-38. MRCAT operations are supported by the Department of Energy and the MRCAT member institutions. Thanks Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin > Sent: Monday, November 14, 2005 10:03 PM > To: XAFS Analysis using Ifeffit > Cc: SCalvin(a)slc.edu > Subject: RE: [Ifeffit] NiO data > > Thanks Shelly, Matt, and Jeremy! > > I'm using Shelly's data, since I need EXAFS. I've instructed the lead > author to include in the caption, > > "NiO data collected by S. Kelly at the MRCAT beamline of the APS." > > Good? > > --Scott Calvin > Sarah Lawrence College > > >Hi Scott, > > > >Here is some NiO data. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

RE: [Ifeffit] NiO data
by Kelly, Shelly D. 15 Nov '05

15 Nov '05

Hi Scott, I'm glad to help. Did any of the other data come from the APS? I would be great to add an acknowledgement to the APS/MRCAT funding, if you can swing it. Something like: Use of the APS was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-ENG-38. The Materials Research Collaborative Access Team is supported under grant number DE-FG02-04ER46106. Thanks Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin > Sent: Monday, November 14, 2005 10:03 PM > To: XAFS Analysis using Ifeffit > Cc: SCalvin(a)slc.edu > Subject: RE: [Ifeffit] NiO data > > Thanks Shelly, Matt, and Jeremy! > > I'm using Shelly's data, since I need EXAFS. I've instructed the lead > author to include in the caption, > > "NiO data collected by S. Kelly at the MRCAT beamline of the APS." > > Good? > > --Scott Calvin > Sarah Lawrence College > > >Hi Scott, > > > >Here is some NiO data. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

RE: [Ifeffit] NiO data
by Kelly, Shelly D. 15 Nov '05

15 Nov '05

Hi Scott, Here is some NiO data. There are several columns in the data files. They represent energy, I0, It, If, Iref. They were collected from MRCAT at the APS. Here are some beamline parameters. ID tapered 4 mm to decrease the change in x-ray energy over the scanned range. 1st harmonic of ID line used. double crystal Si(111) mono. Ph mirror to remove harmonics 0.7x0.7 mm slits to define x-ray cross-section 20/80 N2/H3 in Io, 100% N2 for It. quick scanning mode Ni filter of 6 absorption lengths was used in reference pin diode detector infront of I0. Reference signal is taken by log(Io/Iref). Cross and Frenkel have the reference for this. As far as I can tell, we haven't published this reference before. The log book mentions that the NiO particle size is less than 10 microns. I don't think that we ran XRD on it. The sample came from Aldrich (99% purity). Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Scott Calvin Sent: Sun 11/13/2005 5:50 PM To: XAFS Analysis using Ifeffit Cc: SCalvin(a)slc.edu Subject: [Ifeffit] NiO data Hi all, Anyone out there have spectra for a NiO standard? I bet one of you does, since there was a request for a NiO atoms.inp file a few months ago. I have a referee who wants to see that our data that matches Ni metal very well doesn't also match NiO well (I'm presuming this referee is not someone too familiar with EXAFS!). So anyway, also let me know how you'd like me to credit the data (e.g. a footnote listing you and the beamline it was collected on). Thanks! --Scott Calvin Sarah Lawrence College P.S. And no, Matt's database doesn't have NiO, and yes, the Lytle database does...but the Lytle data is not thoroughly documented and so I avoid it when possible. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

3 2

RE: [Ifeffit] N K-edge XANES, normalization parameters
by Barton, David (DG) 14 Nov '05

14 Nov '05

Peter, ATHENA is mainly written for EXAFS analysis, however...it is still quite useful for XANES analysis as well. I opened your project that you sent and there were a couple of obvious challenges with this dataset. First of all, you should read the section regarding Normalization in the ATHENA help POD if you haven't already. One useful feature in ATHENA is the ability to turn ON the Pre-edge and Post-edge plots. After looking at your two Plots in the file you sent it is obvious that the choice of the Post-edge region is quite poor for the dataset "merge21to27". The "Flattening" Normalization routine in Athena uses a Linear function for the pre-edge (Pre-edge Region) and a quadratic for the post-edge (Normalization Region). Flattening is the process of subtracting these two functions from your experimental dataset (subtracting pre-edge function at energies below Eo and subtracting the post-edge function above Eo) and then scaling the dataset to unity over the normalization range. Your dataset is a bit challenging because the pre-edge region has a limited range so that a when you fit a linear function to it, it crosses over your data set indicating that it is not a good representation of the sample background. I can't think of a quick workaround for this, but you may want to consider manually subtracting a linear function with a smaller slope from your raw dataset prior to opening in ATHENA and then adding a couple of points to the begin of the dataset that could be used for the pre-edge region in ATHENA to force a zero slope. Then you could look closer at your post-edge region (Normalization Range) to ensure the shape of the quadratic is reasonably fitting your dataset. At this point ATHENA only allows a linear pre-edge and a quadratic post-edge, however it does looks like Matt and Bruce are working on adding additional fitting functions to IFEFFIT and ATHENA. So if you cannot get a sufficient background normalization fitting with these functions! you will have to try some other tool. Finally, ATHENA likes to work in eV so you should adjust your energy scale, especially if you want to attempt to use CLNORM background subtraction. Hope this helps, Dave > -----Original Message----- > From: Peter Leinweber [mailto:peter.leinweber@uni-rostock.de] > Sent: Monday, November 14, 2005 3:25 PM > To: ATHENA Userlist > Cc: fan.walley(a)usask.ca > Subject: [Ifeffit] N K-edge XANES, normalization parameters > > > dear all, > i am a new XANES and ATHENA user. i didi N K-edge XANES of > soil samples. while feeling very good with data import, > deglitching, truncation, merging etc. i am insecure about > parameters for normalization. > in the attached project i did truncation of data before > 395900 (it is milli-eV), because these seem to be invalid, > and i set an E-shift of -900 sinc the beamline had -9.9 eV > off compared to the N K-edge of N2 gas. in this way i should > be right back on scale ? the i did set the pre-edge > parameters manually at start of the curve, and around 397000 > since non of the previously measured N standard substances > had edge steps below this value. > however, then i am insecure how to set the other parameters > for normalization properly. depending on how i play with the > parameters sometimes i get normalized spectra which look > pretty reasonable, sometimes the curves disappear completely > from the graphics window, and sometimes i get curves of a > shape never senn in the literature. is there easily > understandable advice for the setting of the normalization > parameters available; or can anybody more experienced check > my project and give me recommendations. thanks, peter > > Prof. Dr. Peter Leinweber > Institute for Land Use > Universitaet Rostock > D-18051 Rostock > > Present address: > Department of Soil Science > University of Saskatchewan > 51 Campus Drive > SK S7N 5A8 > Canada > > phone: 001-306-966-6866 > fax: 001-306-966-6881 >

1 0

N K-edge XANES, normalization parameters
by Peter Leinweber 14 Nov '05

14 Nov '05

dear all, i am a new XANES and ATHENA user. i didi N K-edge XANES of soil samples. while feeling very good with data import, deglitching, truncation, merging etc. i am insecure about parameters for normalization. in the attached project i did truncation of data before 395900 (it is milli-eV), because these seem to be invalid, and i set an E-shift of -900 sinc the beamline had -9.9 eV off compared to the N K-edge of N2 gas. in this way i should be right back on scale ? the i did set the pre-edge parameters manually at start of the curve, and around 397000 since non of the previously measured N standard substances had edge steps below this value. however, then i am insecure how to set the other parameters for normalization properly. depending on how i play with the parameters sometimes i get normalized spectra which look pretty reasonable, sometimes the curves disappear completely from the graphics window, and sometimes i get curves of a shape never senn in the literature. is there easily understandable advice for the setting of the normalization parameters available; or can anybody more experienced check my project and give me recommendations. thanks, peter Prof. Dr. Peter Leinweber Institute for Land Use Universitaet Rostock D-18051 Rostock Present address: Department of Soil Science University of Saskatchewan 51 Campus Drive SK S7N 5A8 Canada phone: 001-306-966-6866 fax: 001-306-966-6881

2 1

atoms and the alloys
by Mauro Rovezzi 13 Nov '05

13 Nov '05

Hi to all, I have noticed that Atoms fails to generate a correct "feff.inp" file in the case of alloys. For example, let's take the Ni_xCu_{1-x}, x=0.5, an fcc substitutional. If I put Ni as central atom and give 0.5 occupancy on the shared Cu-Ni site (0,0,0.5) the result is a normal Ni fcc without Cu. At the moment I modify my feff.inp by hand to simulate alloys, but maybe I'm just not using Atoms properly. If this is the case, it could be useful to insert your answer in the FAQ. Cheers, Mauro

6 7