Re: [Ifeffit] Question about Artemis
I am not sure there was an instance of Feff 9 directly on Artemis only Feff 8 as far as I can remember. Chris * Dr. Chris Patridge Associate Professor Department of Chemistry SASE 314 D’Youville University 320 Porter Ave Buffalo, NY 14201 716-829-8124 patri...@dyc.edu > On May 13, 2023, at 6:29 PM, María Elena Montero Cabrera > wrote: > > > Dear IFEFFIT-friends, > > I am working with Demeter version 0.9.26. > In older versions of Artemis, I remember being able to load FEFF9 to produce > the model for fitting, but I can't figure out how to do it in this version. I > have only found how to write the Atoms results to be read by FEFF8. > Is there a way to use the version of FEFF9 for this version of Artemis? Can > anyone tell me how it's done or instead recommend where to get documentation > on it? > Thank you very much in advance > Regards > > María Elena > > Dra. María Elena Montero Cabrera > Centro de Investigación en Materiales Avanzados (CIMAV) > Miguel de Cervantes 120, Complejo Industrial Chihuahua > Chihuahua CP 31136, Chih. México > Tel (614) 4391123 > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.cars.aps.anl.gov%2Fmailman%2Flistinfo%2Fifeffit=05%7C01%7Cpatridge%40g-mail.buffalo.edu%7C413be482c3aa4a8e98e708db5401905f%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638196137943514998%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=wO8aS3YaVBSTbICod%2Bttt2qzWYXVNefhCL5y51PEDUc%3D=0 > Unsubscribe: > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.cars.aps.anl.gov%2Fmailman%2Foptions%2Fifeffit=05%7C01%7Cpatridge%40g-mail.buffalo.edu%7C413be482c3aa4a8e98e708db5401905f%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638196137943514998%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ox6cfh8sIf%2FkbSAv57i5tndU8UlFhgrLONJXl7Ur898%3D=0 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Using larch for feff Fitting -> simple 4 parameter fit
Stefan, The simple 4 parameter fit typically involves just a single path such as the first coordination shell. Do you have multiple paths or multiple unique scatterers inside the first coordination? Chris > On Aug 18, 2022, at 7:50 AM, Mangold, Stefan (IPS) > wrote: > > Dear all, > > I try to use larch for Feff Fitting. For a first start, I liked the option of > Artemis with the „simple 4 parameter fit“. Larch produces for every path an > independent dear and sigma2. Is there a simple way to make this simple 4 > parameter fit also in larch? > > best regards > > Stefan Mangold > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.cars.aps.anl.gov%2Fmailman%2Flistinfo%2Fifeffitdata=05%7C01%7Cpatridge%40g-mail.buffalo.edu%7Ccccbc3cc26e4487ac00808da810fe8a1%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637964202583394046%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=UJUVs04UBZ%2BQxYkEUD0XDZLYdM%2BFj%2BYHnHZ86Gzw2zQ%3Dreserved=0 > Unsubscribe: > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.cars.aps.anl.gov%2Fmailman%2Foptions%2Fifeffitdata=05%7C01%7Cpatridge%40g-mail.buffalo.edu%7Ccccbc3cc26e4487ac00808da810fe8a1%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637964202583550284%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=fe6%2B9J1eoeiUe2SM80XtQcWQoSYcrCfQ18XzDr1sz5Y%3Dreserved=0 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] [ifeffit] Intensity difference in XANES
I think everyone might be able to help if you first give a more detailed explanation of how you extracted the data from the those papers as that might have much more influence Hope that helps, Chris * Dr. Chris Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave Buffalo, NY 14201 716-829-8096 patri...@dyc.edu > On Mar 7, 2022, at 6:51 AM, Chen, Danting wrote: > > > Dear All, > > I have been studied Zn XANES and EXAFS for my environmental samples. Due to > the unknow Zn speciation in my samples, called ‘A’, I do not have adequate Zn > reference materials. I found some Zn reference materials from others work, > called ‘B’, and extracted the data from their paper. > > I found quite similar features, e.g., the location of each peak and bottom. > However, the intensity of these peaks or bottoms does not correspond very > well. I am guessing that the features of XANES is mainly decided by the bond > lengths, ligands and oxidation states of the core atom. The intensity of > these features may be influenced by the multiple scattering from the > neighbouring atoms beyond the first coordination. Can I conclude that the Zn > speciation in my sample ‘A’ has a similar first coordination as other work > ‘B’, but the coordination environment beyond the first coordination may be > different. > > I compare their Fourier Transform ‘B’ with my samples ‘A’, and found each > peak location correspond well but the intensity is different. I am guessing > that their surrounding atoms are heavier than my samples. > > I am unsure if my explanation. Would you mind providing some suggestions > regarding the factors influencing the intensity and also the references for > this explanation? > > I will appreciate your help and many thanks. > > Best Wishes, > Danting > > Sent from Mail for Windows > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.cars.aps.anl.gov%2Fmailman%2Flistinfo%2Fifeffitdata=04%7C01%7Cpatridge%40g-mail.buffalo.edu%7Cf1974bdb5e38474fd3c508da0049e7a9%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637822614785929839%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=anonbOhqSF%2BupWRGGIw9eJSLQFOZJ3Ubj4HieoC6IaU%3Dreserved=0 > Unsubscribe: > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.cars.aps.anl.gov%2Fmailman%2Foptions%2Fifeffitdata=04%7C01%7Cpatridge%40g-mail.buffalo.edu%7Cf1974bdb5e38474fd3c508da0049e7a9%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637822614785929839%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=XkWLP0EoaP5Aa8yLGOjf9IFPF6BN2EXtKMf2rl9EuBg%3Dreserved=0 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Larch R plot
Thanks Stefan, The odd thing was because I saw slightly different things, I also imported the athena data to Larch directly to compared the plots but I think it might my own doing by changing the plot window parameters. Chris ** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patri...@dyc.edu www.dyc.edu <http://www.dyc.edu/> Social: Twitter <http://www.twitter.com/drpatridgc> > On Oct 25, 2021, at 9:17 AM, Mangold, Stefan (IPS) > wrote: > > Dear Chris, > > seen similar issues with Larch. The data (edge Jump 0.25), 200.k counts per > channel. Used Fluorescence signal for Athena and Larch. Used the same > parameter and got different result. Very similar to yours … > > best regards > > Stefan Mangold > >> Am 25.10.2021 um 14:41 schrieb Christopher Patridge > <mailto:patri...@buffalo.edu>>: >> >> Hello, >> >> I am using Larch and Athena together and I just have a question about the >> magnitude plots and its effect (if any) on EXAFS modeling. Below are plots >> of the same merged samples using the same setting values. I noted that the >> plot in Larch begins below 0 and just want to make sure this is not a >> setting I missed in Larch? >> >> >> Thank you, >> >> Chris >> >> ** >> Dr Christopher Patridge >> Associate Professor >> Dept of Chemistry >> SASE 315 >> 716-829-8096 | patri...@dyc.edu <mailto:patri...@dyc.edu> >> www.dyc.edu <http://www.dyc.edu/> >> >> Social: Twitter <http://www.twitter.com/drpatridgc> >> >> >> >> ___ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] TiFe EXELFS Two Phase Co-Refinement Question
Hi Catrina, I believe the weighting would/could be set using either the SO2 or N value. If the coordination is well known and reliable, you could create a variable x and (1-x) in So2 but of course, it could be more complicated. There are numerous examples of fitting two phases to a sample with a little googling. hope that helps, Chris ** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patri...@dyc.edu www.dyc.edu <http://www.dyc.edu/> Social: Twitter <http://www.twitter.com/drpatridgc> > On Jun 10, 2021, at 1:51 PM, Wilson, Catrina > wrote: > > Hello, > > I am using Artemis to fit EXELFS data on a TiFe alloy. There are multiple > interfaces between two phases (Im-3m, and P63/mmc) present in the data. I am > attempting to co-refine using both phases to create a path list and using > paths from both phases in the fit. My understanding of this process is that > the software uses a linear combination of each path. However, that would > imply that there is a weighting factor applied to each phase that would be > correlated to the phase weight for that region. > > I was wondering if there is a way to determine what the weighting factors > during a co-refinement to multiple phases are in Artemis, assuming my initial > understanding of the co-refinement process is correct? > > Thanks for your time, > Catrina Wilson > Ph.D. Candidate > The Ohio State University > Doan-Nguyen Group and McComb Group Materials Science and Engineering > Center for Electron Microscopy, 1305 Kinnear Rd., Columbus, OH 43212 > (614) 643-3110 Office > wilson.3...@osu.edu <mailto:wilson.3...@osu.edu> / osu.edu <http://osu.edu/> > Pronouns: she/her/hers > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Larch Energy calibration
Valerie, What type of energy range are you looking at? How far back do samples go? Chris ** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patri...@dyc.edu www.dyc.edu <http://www.dyc.edu/> Social: Twitter <http://www.twitter.com/drpatridgc> > On Mar 5, 2021, at 11:06 AM, Schoepfer, Valerie > wrote: > > Hi Matt, > > The backstory is that I'm trying to find which standards will define my > samples, so I am pulling standards from different beamlines and years to get > a basic linear combination fit, to run new standards myself when I have more > beamtime. > > I'm able to do it in Athena- where you more or less: > 1. Assign E0 to the first peak in the first derivative of your standard > reference foil. > 2. Calibrate one standard reference foil to the theoretical edge energy. > 3. Ensure E0 is right/adjust E0 for all samples and sample foils. > 4. Align reference foils to the standard reference foil, because the foil > will pull the sample with it. > > But in Larch, maybe I'm unsure about the groups function? I'm not convinced > the reference foils 'follow' the sample spectra. > If the reference and samples aren't tied together, how do you align samples > when your energies are off because of different beamlines or years or people > not as careful to calibrate the beamline energy? > My first thought was using the first derivative peak of your sample, but if > your edge energy shifts because of oxidation state changes, what do you use > then? > > > I'm still trying to form my question, so let me know if this still doesn't > make much sense. > Thanks! > Valerie > > > -Original Message- > From: Ifeffit On Behalf Of > ifeffit-requ...@millenia.cars.aps.anl.gov > Sent: Thursday, March 4, 2021 12:00 PM > To: ifeffit@millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 217, Issue 3 > > CAUTION: External to USask. Verify sender and use caution with links and > attachments. Forward suspicious emails to phish...@usask.ca > > > Send Ifeffit mailing list submissions to >ifeffit@millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to >ifeffit-requ...@millenia.cars.aps.anl.gov > > You can reach the person 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. Re: Larch energy calibration (Matt Newville) > > > -- > > Message: 1 > Date: Wed, 3 Mar 2021 18:38:24 -0600 > From: Matt Newville > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Larch energy calibration > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Valerie, > > On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < > valerie.schoep...@usask.ca> wrote: > >> Hi, >> >> >> >> I am using Larch XAS Viewer for the first time to analyze some Mo >> XANES data. It is fairly straightforward, however I am running into >> problems with energy calibration, which leads to problems with Linear >> Combination Fitting. >> >> >> >> Right now, which is likely wrong, I?m calibrating the energy of a >> standard to the theoretical edge, then auto-aligning the samples to the >> standard. >> But how do reference foils fit in here? Reference foils don?t seem to >> be tied to the sample like they are in Athena. Should I be manually aligning? >> >> >> >> Is there a general guidance or work flow? >> > > It's possible that I do not fully understand the question or that this answer > will veer a bit off the topic of your question. > > For sure, energies need to be aligned properly for any multi-spectra > comparison or linear method to work well. But it should be that you will have > groups of spectra that all share a consistent energy calibration, say from > the same beamline/beamtime. > > If you do have a reference channel for every measurement, you can compare > those reference channels. Ideally, these will not vary for every > measurement - that would indicate a serious problem. So, I think you > should be able to group spectra together as uniformly calibrated (hopefully > all data from a day or more of beamtime at a particular beamli
Re: [Ifeffit] How Artemis handle crystal structure data with partial occupancy in vorlanite (cubic CaUO4)
One way to import the data is to use separate calcs, one with Ca and one with U. To get the mixed, you might alter the Feff file and replace some U with Ca and vice versa. There are many others who probably have a better method but this will at least get over the partial occupancy problem in Artemis. Chris * Dr. Chris Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave Buffalo, NY 14201 716-829-8096 patri...@dyc.edu > On Apr 28, 2020, at 11:13 AM, "dien...@srnl.doe.gov" > wrote: > > > HI, Matthew and Bruce and Carlo > > As I want to fit a U L3-edge EXAFS spectrum using a crystal structure model > of vorlanite (cubic CaUO4), I was not able to load the crystal structure > data, with an error message of “could not input the data file because of > partial occupancy” or something like this. I believe that the reason is that > Ca and U are on the same site (coordination), and they are completely > disordered, it is like (Ca,U)O2, a CaF2 structure, and the occupancy for each > of Ca and U is 0.5. Is there any way to handling of such crystal structure > data in Artemis? Please see the attached crystal data file in cif. Thank you > so much for your instruction. > > Dien Li > Savannah River National Laboratory > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Fluorescence sample thickness
Hi Rachel, Do you have a good idea of the approximate mass percent of the elements you’re probing. A little more information, (edge, suspected surrounding environment) would probably get you a much better answer. When you say ‘control the concentration’ do you mean you can dictate how much sample you put in the capillary tube or how much of the absorption element? Otherwise, really the only answer is, “it depends.” hope that helps, Chris ** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patri...@dyc.edu www.dyc.edu <http://www.dyc.edu/> Social: Twitter <http://www.twitter.com/drpatridgc> > On Oct 1, 2019, at 1:10 PM, Wallick, Rachel wrote: > > I’m preparing for an XAS measurement in fluorescence of a solution-phase > sample that will be measured in a capillary tube. I anticipate being able to > control the concentration fairly easily, and I’m trying to figure out what > the best capillary diameter would be. Is there a good way to figure this out? > > Rachel Wallick > Chemistry Graduate Student > Van der Veen Group > University of Illinois at Urbana-Champaign > 3011 Materials Research Laboratory > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Demeter question and Larch
Thanks Matt, Is there a method in Larch GUI to create a difference spectrum between files? Thanks, Chris ** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patri...@dyc.edu > On Mar 27, 2019, at 9:08 AM, Matt Newville wrote: > > Hi Chris, > > On Tue, Mar 26, 2019 at 1:57 PM Patridge, Christopher <mailto:patri...@dyc.edu>> wrote: > Hi everyone, > > A Demeter question - Is the memory limit hard set in Athena? > > It is really set by the Ifeffit library, not by Athena itself. It should be > lifted if using Larch as a backend for Athena. That *ought* to work in that > simply by installing Larch, Demeter (latest version) *should* be able to find > and use it. I can believe that may not work perfectly, but if it is not > working, let's try to figure out why. > > I know that I can change the 50 dataset limit, but can I increase the memory > to handle more data as I have a relatively large set of spectra (~150)? I > have installed and tested Larch, but I do not see an option to run difference > spectra in Larch GUI unless I missed something? > > The Larch XAS Viewer app can definitely read in multiple spectra. It can also > read data from Athena project files (well "modern" Athena project files), and > write Athena project files. This app tries very hard to be compatible with > the functionality and concepts and terminology of Athena. There are some > areas that I think might be noticeable improvements over Athena, especially > a) the flexibility and robustness of pre-edge peak fitting, and b) the > interactivity and customizability of the plotting window, c) working on > MacOSX, and d) no limits on memory. There may be a few missing features > compared to Athena, especially in that the docs are not sufficient. But if > you (or anyone else) notices any missing features or has questions about > differences, or has any comments or suggestions, please let me know. > > I am running windows virtualization (win 7 - 64 bit) Demeter if that affects > the memory question. > > That should not be a problem unless you're pushing the amount of memory > allocated for the virtual machine. > > --Matt > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Advice on using Athena for XANES LCF on spectra with a small edge step?
Hi Mike, I would suggest that, as Carlo mentions, that because you cut off at 2200 eV, the post edge background function in purple might be skewed a bit. I might be use values ~2190 eV and 2164 eV? Though it appears to be a “flat” region where you place the points, it may actually not be all that flat if data was collected further out. Even if you were to collected new data, if this short range is used and the same approach to normalization is used, I don’t know if LCF would improve. Chris > On Jan 15, 2019, at 8:23 PM, Mike Massey wrote: > > Hi Scott, > > > I collect up to 2240 eV often, because that's about where the mirror stops, > but end up truncating it at 2200 eV before fitting because sometimes I end up > with all sorts of non-systematic background things at higher energies, > depending on the sample. > > I still collect the data because it helps me to troubleshoot, but I chop it > before fitting because 2200 eV is the limit of what I normally consider > consistently "good data." I end up with spectra that, to my eye anyway, are > comparable. For dilute samples, I don't usually trust it beyond that. For > concentrated samples, I don't have a problem. > > > Thanks, > > > > Mike > > > >> On Jan 15, 2019, at 5:12 PM, Scott Calvin wrote: >> >> Hi Mike, >> >> Is there a reason the data stops at 2200 eV—e.g., is there another edge just >> above that? >> >> —Scott >> >>> On Jan 15, 2019, at 8:02 PM, Mike Massey wrote: >>> >>> Thanks Riti and Carlo. >>> >>> Riti: will give it a go, thanks! I think the data are salvageable, it's >>> just a question of how... >>> >>> Carlo: Interesting point. In terms of how I'm fitting it, I just use the >>> LCF window to do a two-component fit. Nothing super fancy. >>> >>> But what you're suggesting is that maybe I have a misunderstanding in the >>> way I'm normalizing my data. That's entirely possible. I generally try to >>> get a nice flat background by following the "flat part" of the spectra but >>> in cases like this the pre- and post-edge lines end up not parallel. I can >>> force it to be parallel, and that helps the fit to behave better, but ends >>> up creating other normalization issues. >>> >>> >>> Much obliged for the responses so far. >>> >>> >>> >>> Mike >>> >>> >>> >>> On Jan 15, 2019, at 4:42 PM, Carlo Segre wrote: Hi Mike: How are you trying to fit it? It looks to me like the post edge line is not in the right place. You need to tune it by hand when you have such a short energy range after the edge since the normalization is critically dependent on how you set this line. carlo > On Tue, 15 Jan 2019, Mike Massey wrote: > > Hi All, > > > Does anyone have advice for LCF of spectra with a small edge step? > > I've recently found myself with more and more issues fitting spectra like > the one shown in the attached photo, where the spectrum is of good > quality, but the fits end up not working out due to normalization (as far > as I can tell). > > Sadly, I have so far ended up just throwing these fits out, but I'm > hoping there is a better solution out there that someone might be able to > recommend. > > One solution is "get more of the element of interest," as a beamline > scientist recently told me. I'm just reluctant to really load it up in > the data collection, because at 2 keV I get nervous about artifacts like > self-absorption. > > Is there a better way? What am I missing? > > Thanks for your thoughts, > > > > Mike -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498Fax: 312.567.3494 se...@iit.edu http://phys.iit.edu/~segre se...@debian.org ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >>> >>> ___ >>> Ifeffit mailing list >>> Ifeffit@millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> >> >> ___ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >
Re: [Ifeffit] EXAFS of wine
Should probably collect the data in triplicate…. Chris ** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patri...@dyc.edu > On Nov 1, 2018, at 7:34 PM, Simon James wrote: > > Thanks for sharing. Looks like pretty usable data. > > -Saj > > > > Simon James PhD > Senior Research Officer > NHMRC-ARC Dementia Research Development Fellow > > Molecular Gerontology Laboratory > > Melbourne Dementia Research Centre > University of Melbourne > The Florey Institute of Neuroscience and Mental Health > > Kenneth Myer Building > 30 Royal Parade > PARKVILLE VIC 3052, Australia > > Office: +61 (3) 9035 6420 > Mob: +61 (4) 3811 0982 > Web: www.florey.edu.au <http://www.florey.edu.au/> > simon.ja...@florey.edu.au <mailto:simon.ja...@florey.edu.au> > >> On 2 Nov 2018, at 10:11 am, Leandro Acu > <mailto:acu...@yahoo.com.ar>> wrote: >> >> I want one! Nothing better for a long synchrotron night! >> >> Enviado desde Yahoo Mail para Android >> <https://go.onelink.me/107872968?pid=InProduct=Global_Internal_YGrowth_AndroidEmailSig__AndroidUsers_wl=ym_sub1=Internal_sub2=Global_YGrowth_sub3=EmailSignature> >> El jue., 1 de nov. de 2018 a la(s) 19:37, Anatoly Frenkel >> mailto:anatoly.fren...@stonybrook.edu>> >> escribió: >> I thought this mailing list is an appropriate venue to post a picture of the >> bottle of wine I bought yesterday in a store on Long Island. >> >> >> Anatoly___ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> >> ___ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Athena problem
Hi Elien, I might not be correct but are the results you are showing in the 2nd screen shot coming from the combinatorics? That might be different than “fitting the data” since the combinatorics get those results by using each combination of standard and finding the best fits using those are particular standards. So across all the combinations, the D standard fits best by using a negative value which I think might be different. I am not sure but the tick box might not apply to the combinatorics. Maybe someone else can clarify or correct my interpretation, Chris ** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patri...@dyc.edu > On Oct 18, 2018, at 10:55 AM, Elien Lemmens > wrote: > > Dear, > > I was trying to do some linear combination fitting using Athena software. > Although the box “All weight between 0 and 1” is ticked I get negative weight > results. > I have read the online Athena’s User's Guide, but I did not find what the > issue can be. Do you have any ideas? > Below you can find some print screens of my actions. I also get an “error” > (print screen 2), which I don’t understand. > > Thanks in advance > Elien > > > > > > > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] EXAFS above 5 angstroms
Daniel, Those distances are really far away and I think it would really difficult to see in EXAFS even with pretty high quality data. Is there are other information from diffraction that suggests these distances? Chris ** Dr Christopher Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave. Buffalo, NY 14201 716-829-8096 / 315-529-0501 patri...@dyc.edu > On May 21, 2018, at 7:13 PM, Daniel Sneed <snee...@unlv.nevada.edu> wrote: > > Hello, > > This is my first time posting to the mailing list, so please forgive me if I > did not do it correctly. > > I am currently working on EXAFS of tin(IV) oxide, and I have what appears to > be high quality data out to 9 angstroms or so, but I am having some issues in > fitting the data above 4 angstroms. I am attempting to verify a crystal > structure with a= ~6 angstroms, and another structure with a=~9 angstroms. I > know that there is some inhibiting physics at such long distances, such as > inelastic scattering, and core-hole lifetime issues that can effect the data. > My question for the group is, is there any methodical way to deal with these > issues, other than incorporating Ei and the higher cumulants? Or is it even > possible to get results from such large R? > > Thank you for your time. > > regards, > > Daniel Sneed > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] install for mac error
Luke, Many thanks Luke. Error is gone and Athena didn't crash on open. Bruce, I am unsure how the two were related but I am good to go. Thanks for everyone's comments, Chris On Tue, Apr 3, 2018 at 12:47 PM, Luke Higgins <pml...@leeds.ac.uk> wrote: > Hi All, > > > > I see this error too. This is a bit of a bodge job, but if you replace: > > > > /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm > > > > With the attached template.pm from p5.24, it seems to work fine. I’d just > rename the old Template.pm in the same directory, rather than deleting it – > since another program may end up needing the most recent one. > > > > Cheers, > > > > Luke > > > > *From: *Ifeffit <ifeffit-boun...@millenia.cars.aps.anl.gov> on behalf of > Chris Patridge <patri...@buffalo.edu> > *Reply-To: *XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov > > > *Date: *Tuesday, 3 April 2018 at 19:22 > *To: *XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > *Subject: *Re: [Ifeffit] install for mac error > > > > Thank you for the input Matt. I am glad to hear that it is not “user > error”. I tried it again and I need to correct my earlier statement because > Artemis GUI will stay open after the warning however Athena > closes/crashes. > > I will try on a different system. > > > > Thanks again, > > > > Chris > > Sent from my iPhone > > > On Apr 3, 2018, at 11:52 AM, Matt Newville <newvi...@cars.uchicago.edu> > wrote: > > Hi Chris, > > > > On Mon, Apr 2, 2018 at 4:15 PM, Christopher Patridge <patri...@buffalo.edu> > wrote: > > Hello everyone, > > > > I tried to install demeter on my mac (running high Sierra) and it appeared > everything went well. However when I run either Athena or Artemis I get an > error shown below about Demeter::Templates: showing a error and I am not > sure how I can correct this error. Any help would be appreciated. > > > > Thanks in advanced, > > > > I can confirm this. I just did a fresh install of Macports on 10.13.3 > (high sierra). The MacPorts install was not super easy, but once it got to > the demeter install, that part went fine. > > I see the same problem with athena from demeter 0.9.25. I think the > warnings about "Demeter::Templates::F" and so forth are meant to be > warnings only -- I think they may not be related to the crash of athena. > For me, hephaestus gives the same sort of warnings, but runs fine. > > I can install and run Demeter 0.9.26 (including using Larch as a backend) > using Macports, though there are definitely some Mac-specific weirdness. > Anyway, I do not believe that "install from source" is a feasible approach > for demeter on OSX. I do not know enough about Macports to update the > existing package. I don't know that using some other system would be an > improvement. > > > > We keep seeing problems with demeter on OSX. I'm not sure what the right > answer is. Anyone have any suggestions? > > --Matt > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > -- Dr. Christopher Patridge Assistant Professor of Chemistry Math and Natural Science Dept BFAC 009 D'Youville College 320 Porter Ave., Buffalo, NY 14201 716-829-8096 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] install for mac error
Hello everyone, I tried to install demeter on my mac (running high Sierra) and it appeared everything went well. However when I run either Athena or Artemis I get an error shown below about Demeter::Templates: showing a error and I am not sure how I can correct this error. Any help would be appreciated. Thanks in advanced, Chris -- Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Chemistry SASE 315 D'Youville College 320 Porter Ave., Buffalo, NY 14201 716-829-8096 16:07:25: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236. 16:07:25: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236. 16:07:25: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236. 16:07:25: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236. 16:07:25: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236. 16:07:25: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Exploring XANES data for getting EXAFS results
Hi Marcelo, First and 2nd neighbor distances are usually modeled using EXAFS data in ARTEMIS. XANES might give you information about the coordination if you have some reference data to compare. More information or detail about your experiment might get you a better answer, thanks, Chris Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: patri...@dyc.edu On Jan 16, 2015, at 10:21 AM, Marcelo Alves meal...@gmail.com wrote: Hi all, I wonder if it is possible from XANES unusual data treatment to get information such as number and distances of neigbhors in the first and second shells. I think that could be very interesting for low Z elements such as P, S, Ca, K, Al, etc in diluted samples. Thanks in advance. Marcelo. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Possible bug in Athena during alignment
Leon, I am not sure I understand but from what you wrote, did you try to align the data sets to the NaBr standard or did you align the standard associated with each data set to the NaBr standard? Using the align tool in Athena, one should align the same type of data, i.e. the same sample such as NaBr. If the samples you try to align are different, then the align function will have some trouble, particularly if there are unique XANES features. On the other point, a 17 eV shift is not out of the ordinary and Athena does a fine job even as large as 25 eV in my experience with Ag K edge. calibrate and normalize can not be interchanged unless again I don't understand the problem completely. Calibrate has to do with the energy scale of the data and normalize has to do with the intensity of the signal at each energy point. please clarify, Chris Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: patri...@dyc.edu On Oct 15, 2014, at 10:21 AM, Leon Clarke l.cla...@mmu.ac.uk wrote: I’d like to report a possible bug within Athena. Last week I collected Br K-edge data at the APS and have experienced an issue with Athena during data alignment. The beamline energy required calibration and so I did the following data processing steps, in this order: 1. Completed pre- and post-edge corrections, using windows relative to the actual Br K-edge energy, on the raw data exported from the beamline. (In other words these windows were not energy offsets relative to the actual measured edge position). 2. Used the flatten post-edge feature within Athena. 3. ‘Calibrated’ (Normalised is a better term really) the first derivative of a NaBr measurement to the Br K-edge energy using the calibrate drop-down option. This resulted in the requirement for a -17.39 eV energy offset. 4. Tried to align all of the sample data to the NaBr ‘standard’ using the align drop-down option. The issue I have had is with step #4. When I aligned, for several samples the XAFS (XANES) plots went wrong. It seems that Athena was not transforming the pre- and post-edge windows correctly for such a large energy shift, i.e. didn’t shift these to lower energies by 17.39 eV, and I think this is a bug within Athena. I hope the above makes sense; I can provide an Athena project file, if required. Many thanks, Leon - Dr Leon J. Clarke Senior Lecturer in Environmental Analytical Chemistry Division of Chemistry and Environmental Sciences School of Science and the Environment Faculty of Science and Engineering Manchester Metropolitan University John Dalton East Oxford Road Manchester M1 5GD E-mail: l.cla...@mmu.ac.uk WWW: http://www.sste.mmu.ac.uk/ Tel: +44 (0)161 247 1412 Before acting on this email or opening any attachments you should read the Manchester Metropolitan University email disclaimer available on its websitehttp://www.mmu.ac.uk/emaildisclaimer ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] FEff
Carlos, you can only have one absorbing atom in a feff calculation. You must run each atom separately if you want an average structure for the the amorphous material. 24 feff calculations with each Ti as the absorber. Then average the spectra. Anyone else have a better method? hth, Chris Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: patri...@dyc.edu On Sep 29, 2014, at 11:44 AM, Carlos Triana Estupinan ctria...@unal.edu.co wrote: Dear Feff group I am Carlos Triana, and I want ask you the following. I am trying to calculate the feff.inp file for a theoretical amorphous structure composed by a supercell with 24 Ti atoms surrounding by 48 oxygen atoms with different coordination. In amorphous materials or materials with distortions from regular crystals, the absorbing atoms may have different surroundings. My question is how can I build the feff.inp file in this case, shall I define the 24 Ti atoms like absorbing atoms, because in this case the feff does not works. What can I do in this case, how can I build the feff.inp file with different environments I will be very grateful for your help -- Carlos Augusto Triana Estupiñan (C.A. Triana-E) Physicist M.Sc. In Physical Sciences-Research PhD Student-Research Ångströmlaboratoriet, Lägerhyddsv. 1 Solid State physics Uppsala University, Box 534 751 21 Uppsala, Sweden Tel: +46 018 471 3144 e-mail:carlos.tri...@angstrom.uu.se web:http://www.uu.se/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Itinerant vs localized XAFS
Hello, Could there be any information or insight in the XANES data? Localized electrons might significantly change the edge structure for the system. Just a thought, Chris Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: patri...@dyc.edu On Dec 9, 2013, at 10:02 AM, Maurits Boeije m.f.j.boe...@tudelft.nl wrote: Dear XAFS specialists, We’ve performed an experiment at the ESRF in Grenoble to find experimental evidence of an electronic change in our system. We suspect, from ab initio calculations, that there is a change in how electrons are allocated in our Mn/Fe system. Calculations show that some electrons change from being itinerant at high temperatures, to being localized at low temperatures. We performed an XAFS experiment and hope to see a difference between the low and high temperatures measurements. There is always difference because the cell parameters change as function of temperature, and I used your Artemis program to investigate the influence of the cell parameters on the EXAFS signal. I can get a decent fit using the crystallographic data we have, but I’m not sure if I’m not throwing away any evidence of our electronic change. I can interpret a fitted interatomic distance of 2.1 A (compared to 2.0 A we got from diffraction) as being the mean interatomic distance in our sample, but I could also interpret it as a 0.1 A difference because of our suspected electronic change. The challenge now lies in seeing an electronic difference despite the crystallographic change. What we would ideally do, is to keep the (known) atomic positions and cell parameters fixed, fit the EXAFS parameters and see if we can predict either the high or low temperature spectrum. Do you think this is possible? Are there any parameters which are calculated by IFEFFIT who are not precise enough for such a conclusion? It could be that the effect we are looking for is so small that they are nullified by the assumptions in the EXAFS equation. I would appreciate any insight you could have in this particular problem. With kind regards, Drs. MFJ Boeije Fundamental Aspects of Materials and Energy TU Delft T +31 (0)15 27 83793 No trees were killed to send this message, but a large number of electrons were terribly inconvenienced ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] error in ATOMS
Julius, I again did not find answer to the error but you could also try the following entity of ATOMS on the web which easily allows a huge number of sites http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi Chris Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: patri...@dyc.edu On Nov 13, 2013, at 12:19 PM, Julius Campecino jcampec...@gmail.com wrote: Hi everyone, Did anyone figure out how to fix Can't call method tag error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone. Thanks! Julius On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino jcampec...@gmail.com wrote: Hi Chris, Yeah, I did try add a site but it is not responding. Does anyone else experience this problem? Thank you, Chris. Julius On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge patri...@buffalo.edu wrote: Julius, While I am not certain what the error means, there is a button displayed right above the atom list which says ADD A SITE. I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS. Chris Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: patri...@dyc.edu On Nov 10, 2013, at 1:26 PM, Julius Campecino jcampec...@gmail.com wrote: Hi Bruce, Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms. When I click Run Atoms, it gives me this error Can't call method tag on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer. Thank you for your help! Julius Atoms.png___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Artemis in Demeter 0.9.17 Crashing Upon Loading Project File
Anthony, I would suggest instead of the artemis file that you sent, you instead send the Athena file showing the data structure for the samples. It does crash on my computer as well so any investigation might be rather difficult. Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 7/16/2013 2:17 PM, Anthony Ardizzi wrote: Dear Bruce and Ifeffit mailing list, I have just started experiencing a program crash in Artemis while trying to load a project I am working on. I am performing a fit on Sr2IrO4 data, and when I try to open the project file, it starts loading all of the usual stuff, and then when it gets to loading the path-lists/data sets screen for one of the two data sets I have, the entire program simply closes. I have attached both my project file, as well as the dartemis log file. I believe the relevant error in the log file is Illegal division by zero at C:/strawberry/perl/site/lib/Demeter/Data.pm line 922. I am running Windows 7 64-bit. Thanks for any help you can provide, Anthony ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] User interface question for Demeter
I am pretty sure you can delete old fits in the fit log. Check and remove them. Chris Patridge Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 7/3/2013 3:03 PM, Chachi Rojas wrote: Hi Bruce, I re-started use (D)Artemis last week, it is great work, But, I have the same problem with data list and path list, each time I open the project it change the order. And another point is about fit history, it is necessary save all old fits?, because if you have many data and feff calculations it is large file, Ok sometime is important for statistical report and I can discard some fits, but into compressed fpj file continue that fit directory with many files, So if you reopen project it is very slow each time you add more fits and sometimes paths included in the fit is lost. It may be my OS distribution or some configuration? Exist the way to dis-enable the automatic save fits, only save if I consider a good fit. Chachi On Wed, Jul 3, 2013 at 12:14 PM, Bruce Ravel bra...@bnl.gov mailto:bra...@bnl.gov wrote: On 07/03/2013 10:52 AM, Bare, Simon R wrote: In Athena it was Alt-k to move up and Alt-k to move down. In D(Athena) it is the reverse - Alt-k = down, Alt-j = up; these functions are not obvious. In new Athena it is done wrongly. See http://en.wikipedia.org/wiki/Arrow_keys#HJKL_keys This will be fixed in the next release (0.9.18). Sorry for that bit of confusion. And for those who have the backwards key binding in muscle memory when using Athena, I doubly apologize. But the meanings of j and k as down and up are well established. B -- Bruce Ravel bra...@bnl.gov mailto:bra...@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Disable duplicate data group check
Hi Jason, Would it fix the problem if you duplicate a dataset and rename the files in Athena instead of just trying to reimport the same dataset in Artemis? It appears to work for me. I loaded a dataset and then copied it in Athena and renamed it duplicate.026. I was able to import both and fit both with a crystal structure without any warning. It seems it would be easier to me to track the different treatments you use in Athena if you had different datasets from the start. Hope it helps, Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 6/21/2013 11:54 AM, Jason Gaudet wrote: Hi all, Not a bug this time, but a feature that occasionally frustrates me. Artemis does a sanity check prior to fitting, and if it detects a project has two instances of the same Athena data group, it will refuse to fit the new data. IME this is not a particularly helpful warning, and a major hassle if I'm trying a couple different treatments of the same data to see how the FEFF fit is affected. (The message is This data came from the the same source as another data group. You seem to be trying to increase your number of independent points by fitting the same data more than once in a multiple data set fit. But of course I'm not doing this; only one dupe is being fitted at a time.) I don't see any option in the Artemis preferences to disable this warning, which means I have to spend effort deleting and loading data sets, and keeping a dummy data set I don't really care about to collect all my paths in. Is the possibility of extremely novice users trying to fit multiple instances of the same data such a serious threat that this function needs to exist? Is there any possibility of disabling this check, or giving an option to disable it in the Preferences? It would save me from the occasional headache ... Thanks, Jason ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] bond angle
Hello Washington, Determining the bond angle is possible but there are vast resources and examples of bond angle models and calculations available to help to understand this. You should probably search EXAFS bond angles and it should keep you busy for quite a while. In general these kinds of questions don't get a great response because it sounds like you are asking us to help you do your research. Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 6/21/2013 1:33 PM, washington gomes wrote: Dear Colleagues, I am structure characterized of La0.8Ba0.2CoO3 by x-ray spectroscopy, used program IFFEFIT 1.2. 10. I wonderif it is possible to determine the bond angle Co-O-CO,used IFFEFIT code in the extended x -ray absorptionfine structure EXAFS. If possible, I would like you to indicate the material that shows examples of how to determine the bond angle Co-O-CO. Sincerely yours, Wahington ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] closing Artemis project
Hello, I have a question about (D)Artemis. After saving a project, I used the Close option under File. This does remove the datasets and feff calculations but it keeps the name of the project in main window header. Is there a way to begin a new project other than closing Artemis and/or beginning a project and use the save as option? One other thing, is there any possibility of extending the number of datasets for artemis? Thanks, Chris Patridge -- Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Opening XANES Files with Athena
Alex, Where was the XANES data collected? Unless the write format is really unique, I would suspect that you could just open the raw data in Athena without much trouble even if the data file extension is txt. The developer has made Athena pretty flexible for data import. Those extensions are for project files coming from Athena (prj) and Artemis (apj) not just the raw data you have. iXAFS has worked for a number of people on the list, myself included. Give it a try. buena salud, Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 5/24/2013 10:02 AM, Alex Kellum wrote: Hello All, I am working on an NSF-REU program this summer requiring me to analyze XANES spectra. My personal computer is a mac (w/ OS X 10.6.8). I am desperately trying to figure out how to even open an IFEFFIT program that will help me analyze the spectra. The spectra are saved in /.txt/ files--and I have no idea how to convert them to .apj or .prj files. Is it possible to analyze them with converting them? Right now I am using iXAFS Shell containing Athena, Artemis and Hephaestus. I realize there are newer versions available, but Demeter is only available on Windows and I spent a few hours trying to get Larch to work. Even after downloading python I had no idea how to get it to actually download and work. I do have X11 running on my computer. I realize you probably get a ton of emails from users, but any help would be greatly appreciated. Regards, Alex Kellum ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Problem with running Demeter
Quick note, I have been using this program for a few years and it has never removed needed DLL files from any of the computers I have used it on... I in fact used it the other day. Though I believe I have never checked a number of options that CCleaner gives you during it's cleaning. I have used the basic tools as Matt guessed and CC gives you options. I guess you selected several of these options and performed a much more judicious cleaning. Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 5/2/2013 8:02 AM, Matt Newville wrote: On Thu, May 2, 2013 at 2:00 AM, Alexander Riskin alexander.ris...@uhasselt.be wrote: Dear Amativa, Bruce is right, Ccleaner messed up your system and, unfortunately, beyond repair. Ccleaner promises indeed to remove unused DLL's from your system but is very bad at guessing which DLL's are really obsolete and has a tendency to assume DLL's are unused instead of playing it safe. Therefore, this piece of software needs to be handled by an expert hand, or you butcher your system as you seem to have done. I know this because I made the exact same mistake 16 years ago after which my windows 98 didn't even boot up anymore, so I'm even surprised your pc is still running. The solution to this problem? Complete reinstallation of your OS, trying to manually repair is very complicated and time consuming. You will probably run into similar problems with other applications as well because of missing DLL's. regards, Alexander -- dr. ir. Alexander Riskin Doctor-Navorser IMO - Inorganic and Physical Chemistry T +32(0)11 26 83 94 | F +32(0)11 26 83 23 http://www.uhasselt.be Universiteit Hasselt | Campus Diepenbeek Agoralaan Gebouw D | B-3590 Diepenbeek Kantoor G1.94 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Perhaps you're right, but this sounds a bit pessimistic to me. Surely, this program doesn't always mess up every computer to the point that the OS needs to be reinstalled. It's not clear to me that it removes DLLs it deems are not needed, or that this is what happened here. I've not used this particular tool, but it looks to me like it removes truly unneeded files (browser caches, temp folders) and the cleans the registry. If I had to, I'd guess the problem is in the registry, not in deleted files. The cleaner may have left a registry backup, or a system restore tool might help. But if the system is working fine and only Demeter is not, I doubt the OS needs to be reinstalled. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] L-edge soft X-ray data in Artemis and Athena
You can process the data but the L3-edge for 1st row transition elements (Mn and Ni) is only separated by 10-15 eV from the L2 edge so EXAFS analysis is not possible. good luck, Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 4/11/2013 7:46 AM, Shoaib Muhammad wrote: Hi, I am a research student and relatively new to XAFS. I have soft X-Ray L-edge data of Mn and Ni. Is it possible to process this data in Athena and then fit in Artemis like usual K-edge data? Thanks -- Shoaib ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] generating high res figures
Eva, I don't how flexible would consider exporting the fits you have completed and using a plotting software (Excel, Origin, Qplot, sigmaplot, Igor) to generate the number of adjustments you require. Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 3/26/2013 1:13 PM, Eva Vanamee wrote: Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? Can I change the figure legends? I used sample 1 and I want to give it a different name Can I use special characters (e.g. Greek letters)? Can I adjust the resolution for different formats (talk vs. publication)? I am running Demeter 0.9.9.9 under XP. Thanks in advance for the help! - Eva ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] MBACK and Athena
Cyril, Is the copper foil a separate file or is this file imported together with the other scans as a reference channel? If separate files, then there is not a clear relationship between sample and the foil since these were collected at different times and hence corrections for drift or other gremlins will not be the same. Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 3/8/2013 2:49 AM, Bajamundi Cyril wrote: Dear Bruce, The motivation for the question is that I'm concerned whether the shift in E values after calibration is conserved when the calibrated data has been saved in the .xmu file. But thanks to the link you have sent to me and your previous answer in the mailing list archive http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02755.html things are a bit clearer now. So here's a follow up. I have taken the following scans successively Cu foil Sample1_scan1 Sample1_scan2 Sample1_scan3 I then process the data in Athena, to begin I calibrated the Cu foil spectrum, such that the nice orange circle falls at the tabulated value of 8979 eV. This in turn gives some eshift value of -0.360. What is the relationship of this eshift to the spectra of sample 1, should I apply this eshift to the scans for sample 1 as? Definitely I can't apply the E0. This is still a bit vague in my mind, even after reading the basic data processing section in the documentation. Thank you in advance. Warm regards, Cyril -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Thursday, March 07, 2013 3:55 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] MBACK and Athena On Thursday, March 07, 2013 12:10:26 PM Bajamundi Cyril wrote: 1. Is this procedure valid? In the sense that no information or features of the spectrum are lost from merge.xmu to merged.xmu.mnor file. Do you have some reason to believe that might be happening? If so, perhaps you could ask a more explicit question. 2. How will the procedure Calibrate data affect this procedure? Calibration, as it is defined in Athena, is a procedure that changes *both* the E0 and the Eshift values so that a selected point in the spectrum has a selected energy value. http://bruceravel.github.com/demeter/aug/process/cal.html I'm not certain I've answered your question, but I am unclear what is motivating your question. B -- Bruce Ravel bravel at bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage:http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] MBACK and Athena
Hello Cyril, Is there a particular reason for moving the data to Matlab and using MBACK rather than the built-in procedure in Athena? From your email, it seems that you have the raw data which you then merge. I would feel confident in performing all the data processing in Athena. Your hope in merging data is remove noise and improve the confidence that features seen in the data are real. Someone may be able to comment on the impact of MBACK, but questions here mostly deal with ifeffit. Good luck, Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 3/7/2013 7:10 AM, Bajamundi Cyril wrote: Hello, I have 3 spectra taken from a single sample, I align, merge and save the merged data as merge.xmu file. I then normalize this merged data using the MBACK algorithm in Matlab, the results of which is stored as merged.xmu.mnor file. This file, I then import to ATHENA using the instructions in http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03523.html. I do this for all my samples and standards in order for me to perform LCF. My questions are 1. Is this procedure valid? In the sense that no information or features of the spectrum are lost from merge.xmu to merged.xmu.mnor file. 2. How will the procedure Calibrate data affect this procedure? Thank you for your time in answering my questions. Regards, Cyril PS: This query is in relation to my previous question [Ifeffit] Basic question in normalization and background removal ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Merging data in Athena
George, It seems rather unconventional to try and merge data which has different energy grid spacing? I thought the main point of merging data is to reduce the noise and uncertainty of a measurement. I am not sure how the exact method of merging data is implemented but I don't think it is fair to call this a bug as a result of a unique situation. Could you or have you reinterpolate one spectrum? Chris Patridge Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 2/26/2013 6:55 PM, George Sterbinsky wrote: I am writing to make you aware of what I believe to be a bug in (D)Athena. To demonstrate the problem, I have attached a project file containing two groups. Both groups have the same energy range but were measured with slightly different point spacings. Attempting to merge the two groups results in Athena excluding one of the groups from the merge for being too short. Thank you, George ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Error in second shell fit
Well that is interesting, As was asked earlier, what is the fitted reff from the model? It would be rather non-physical and probably suggest a poor model, but perhaps the bond length is shifted well beyond the rmax which you show sets as 7 A and that is why you are receiving the error. Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 2/20/2013 1:11 PM, Devender wrote: Bruce and Chris, Thanks for follow-up. I understand the frustration on your part. Reason for doubt is I am doing exactly the same thing Chris suggested even before posting the question here i.e. changing the rmax. I have changed rmax to even 9 A whereas shell I am trying to fit is only 5 A (please see attached screenshot) but still getting error log that reff is larger than rmax. I know by default it is set to 3 A but I have tried to change it values more then reff of path but still getting the same error. Please see attached screenshot where rmax I am using is 7 A where as Reff is only around 5 A but still getting the error log. Regards, Dev On Wed, Feb 20, 2013 at 12:49 PM, Bruce Ravel bra...@bnl.gov mailto:bra...@bnl.gov wrote: On Wednesday, February 20, 2013 10:54:02 AM Devender wrote: Dr. Patridge, Thanks for suggestion. I am not sure if I get completely, I do understand the difference of Rmax in artemis and feff. You mean make changes in rmax in feff input file? I did that and attached are screenshots for that but I am still getting the same error. Let me know if I interpreted your suggestion wrongly. Dr. Kicaj, I am studying doping problems and it's important I get fitting from second and subsequent shells as there are new peaks that shows up at higher radial distances. Regards, Dev Dev, I get the impression from your emails that you have not much availed yourself of the resources that are already available for learning how to use the software. At http://bruceravel.github.com/demeter/ you will find the Artemis manual. I'll admit, it's still pretty mediocre, but it's a start. You will also find some videos that go a long way towards explaining how the software works. You may find it useful to spend some time with those things. I certainly think some time spent with those resrouces would obviate a problem like I am not sure if I ... completely ... understand the difference of Rmax in artemis and feff. That, frankly, isn't a very good question. While it is certainly true that Artemis suffers from being a program written by a physicist who has no training in computer science, user experience engineering, or design, you would have found the answer to that question even in the fairly crappy Artemis manual. B -- Bruce Ravel bra...@bnl.gov mailto:bra...@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website https://sites.google.com/site/devendermaun/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Different R-factor values
Thank you for the discussion Matt and Jason, My main objective was to decide between the two different reported R-factors in some older Artemis fit file logs. I suspect that the analysis was prematurely completed because the user found small R-factor values printed out along with the other fit statistics near the beginning of the fit log. Scrolling down the log file to the area which gives; R-factor for this data set = ? k1,k2,k3 weightings R-factors = ? This R-factor is the average R-factor of the k-weights and much larger say, 0.01 above vs. 0.07-0.08 making a typical good fit to a single data set into a rather questionable one. Looking at more current fit logs from Demeter (attached, just a quick example), the R-factor which is printed near the beginning of the fit file is equal to the average R-factor for the k-weightings. Therefore the value found in the earlier Artemis file logs must have been faulty or buggy as was said so one should not rely on that value to evaluate the fits. Sorry for any confusion but this is all in the name of weeding out good/bad analysis Thanks again, Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 1/25/2013 12:04 PM, Matt Newville wrote: Hi Jason, Chris, On Fri, Jan 25, 2013 at 10:01 AM, Jason Gaudet jason.r.gau...@gmail.com wrote: Hi Chris, Might be helpful also to link to the archived thread you're talking about. http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2006-June/007048.html Bruce might have to correct me on this, but if I remember right there were individual-data-set R-factor and chi-square calculations at some point, which come not from IFEFFIT but from Bruce's own post-fit calculations, and these eventually were found to be pretty buggy and were dropped. I don't understand what the average over the k weights R factor is; analyzing the same data set with multiple k weights (which is pretty typical) still means a single fit result and a single statistical output in IFEFFIT, as far back as I can remember, anyhow. The discussion about multiple R-factors is for when you're simultaneously fitting multiple data sets (i.e. trying to fit a couple different data sets to some shared or partially shared set of guess variables). I think the overall residuals and chi-square are the more statistically meaningful values, as they are actually calculated by the same algorithm used to determine the guess variables - they're the quantities IFEFFIT is attempting to reduce. I don't believe I've reported the per-data-set residuals in my final results, as I only treated it as an internal check for myself. (It would be nice to have again, though...) -Jason I can understand the desire for per data set R-factors. I think there are a few reasons why this hasn't been done so far. First, The main purpose of chi-square and R-factor are to be simple, well-defined statistics that can be used to compare different fits. In the case of R-factor, the actual value can also be readily interpreted and so mapped to that's a good fit and that's a poor fit more easily (even if still imperfect). Second, it would be a slight technical challenge for Ifeffit to make these different statistics and decide what to call them. Third, this is really asking for information on different portions of the fit, and it's not necessarily obvious how to break the whole into parts. OK, for fitting multiple data sets, it might *seem* obvious how to break the whole. But, well, fitting with multiple k-weights *is* fitting different data. Also, multiple-data-set fits can mix fits in different fit spaces, with different k-weights, and so on. Should the chi-squared and R-factors be broken up for different k-weights too? Perhaps they should. You can different weights to different data sets in a fit, but how to best do this can quickly become a field of study on its own. I guess that's not a valid reason to not report these So, again, I think it's reasonable to ask for per-data-set and/or per-k-weight statistics, but not necessarily obvious what to report here. For example, you might also want to use other partial sums-of-squares (based on k- or R-range, for example) to see where a fit was better and worse.Of course, you can calculate any of the partial sums and R-factors yourself. This isn't so obvious with Artemis or DArtemis, but it is possible. It's much easier to do yourself and implement for others with larch than doing it in Ifeffit or Artemis. Patches welcome for this and/or any other advanced statistical analyses. Better visualizations of the fit and/or mis-fit might be useful to think about too. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Independent points : 6.8125000 Number of
[Ifeffit] Different R-factor values
Hello List, I know that Horae is no longer supported but I had quick question about the R-factor. I search the mailing list and found this post from 2006 concerning different R-factors in the fit log I have a question about Artemis log file. I noticed that two r-factors are reported in the log file. One is in the fifth line and it is called 'R-factor' and the other one is under the data set fitting conditions and it is called 'r-factor for this data set'. They have in general different values. What does it mean? Which is the difference between the two? It probably means that I am calculating something wrongly. Here's the concept. If you do a multiple data set fit and you have some value of R-factor, you would like to know how that misfit is partitioned among the data sets. That is, you'd like to know if one set is contributing to the misfit for significantly than the others. When Ifeffit computes the R-factor, it is for the entire fit. My idea in Artemis was to use the formula for R factor from page 18 of http://cars9.uchicago.edu/~newville/feffit/feffit.ps http://cars9.uchicago.edu/%7Enewville/feffit/feffit.ps on each data set in a multiple data set fit and report that in the log file. At some point, I must have convinced myself that I was doing the calulcation in Artemis identically to how it is done in Ifeffit. If you are seeing different values, it would seem I was mistaken. I'll make an entry in my to do list to look into that. I am reviewing some older analysis projects from artemis and just wanted to know which R-factor more accurately describes the misfit? I suspect the average over the k weights values since this was adopted in Demeter? Thanks, Chris Patridge -- Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 Project title : Fitting Cell_3_2_5V.003.chi Comment : Fit #1 Prepared by : Contact : Started : 11:07:39 on 23 February, 2011 This fit at : 17:46:41 on 8 November, 2011 Environment : Artemis 0.8.012 using Windows Vista, perl 5.008008, Tk 804.027, and Ifeffit 1.2.11 Data sets : Fe2_2_5V.021.chi Fit label : fit 5 Figure of merit : 5 Independent points = 4.502929688 Number of variables = 1.0 Chi-square =9463.223505940 Reduced Chi-square =2701.516830243 R-factor= 0.011247229 Measurement uncertainty (k) = 0.000419876 Measurement uncertainty (R) = 0.000780899 Number of data sets = 1.0 k-range = 3.000 - 11.000 dk = 1.000 k-window= hanning k-weight= 1,2,3 R-range = 1.335 - 2.243 dR = 0.000 R-window= hanning fitting space = R background function = none phase correction= none R-factor for this data set = 0.05390 R-factor with k-weight=1 for this data set = 0.01127 R-factor with k-weight=2 for this data set = 0.02877 R-factor with k-weight=3 for this data set = 0.12168 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Artemis crash and data set limit
Hi List, My project file crash about five minutes and I found the dartemis log file attached before opening the program again which I hope will explain the problem. is there a limit to the number of datasets in Artemis? Thanks, Chris -- Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 Win7Professional (64-bit) Service Pack 1Service Pack 16176012102561 PATH: C:\Program Files\ImageMagick-6.7.8-Q16;C:\Program Files (x86)\Gradkell Systems, Inc\DBsign Data Security Suite\Common\Lib\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\WIDCOMM\Bluetooth Software\;C:\Program Files\WIDCOMM\Bluetooth Software\syswow64;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;c:\Program Files\Intel\DMIX;c:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files (x86)\Intel\Services\IPT\;C:\Program Files (x86)\NTRU Cryptosystems\NTRU TCG Software Stack\bin\;C:\Program Files\NTRU Cryptosystems\NTRU TCG Software Stack\bin\;C:\Program Files\Dell\Dell Data Protection\Access\Advanced\Wave\Gemalto\Access Client\v5\;C:\Program Files (x86)\Common Files\Roxio Shared\DLLShared\;C:\Program Files (x86)\Common Files\Roxio Shared\OEM\DLLShared\;C:\Program Files (x86)\Common Files\Roxio Shared\OEM\DLLShared\;C:\Program Files (x86)\Common Files\Roxio Shared\OEM\12.0\DLLShared\;C:\Program Files (x86)\Roxio\OEM\AudioCore\;C:\Program Files\ActivIdentity\ActivClient\;C:\Program Files (x86)\ActivIdentity\ActivClient\;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\Program Files (x86)\MATLAB\MATLAB Component Runtime\v77\runtime\win32;C:\Program Files (x86)\QuickTime\QTSystem\;C:\Program Files (x86)\Mendeley Desktop\wordPlugin; perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib . Can't call method SetSizer on an undefined value at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Path.pm line 111. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Multiple Atom.inp in Feff
Hi all, Is there a way to remove data sets, feff.inp, or atoms.inp from the main window list? I know this question was raised at one of Bruce's XAFS seminars at Diamond. I looked at the current Demeter List of Things to Do and did not see specifically removing them, just reorganizing lists. I guess it is not really a bug, just annoying, but for some reason, probably user error and impatience, my artemis file saved several atoms.inp windows in the Feff list and now I cannot get rid of them. Thanks, Chris Patridge -- Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] k-range question R-factor
Thank you Scott, I guess that is a refinement of my question concerning R-factor.' Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 1/15/2013 9:39 AM, Scott Calvin wrote: Hi Chris, I don't see a reason to think that data is a glitch. For one thing, it's not consistent across datasets. The features also look smooth, and not so glitch-like. The spike around 8.2 inverse angstroms in some of the datasets looks a bit more like a glitch, but it's fairly modest and narrow enough not to mess you up too much. The spacing of those features look OK--there's a double feature in some of the datasets around 6-7 inverse angstroms; it's plausible there would be another reature like that above it. In fact, I can make an argument that there's some kind of beating going on that gives a shoulder at 3.5-5, a double peak at 5-7, and two peaks at 7-8 inverse angstroms. So I would recommend including that data and seeing what it does to your fits. If that range is garbage, your fits will probably reject it. As for your second question, R-factors are always a kind of average across the data, by definition. So total mismatch doesn't really make sense. Off-hand, though, I don't recall how ifeffit weights the data for the purposes of calculating R-factors for multiple datasets, and that may be your question. --Scott Calvin Sarah Lawrence College On Jan 15, 2013, at 9:21 AM, Christopher Patridge wrote: Hello Users, I was looking for an opinion about the chi(k) signal in a set of data I am analyzing. Brief background, this is a set of in-situ XAS data collected at the Fe K edge from a working electrochemical cell at a range of potentials during charge; I did not collect the data. I suspect the feature at ~ 8 angstroms-1, although present in all the spectra is noise or glitch and wondered if I am being overly cautious? My conservative range ( k = 2-7 and R = 1-2) really constrains the model Nidp = 3.31. Luckily, multiple datasets ( 8 ) to the rescue to give me some flexibility. In a multiple dataset fitting, is the R-factor of the whole set just the average or total mismatch across all the datasets or it calculated another way? Working towards happiness, Chris Patridge -- Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 Athena-plot.png___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] The degeneracy and the coordination number
Zhaomo Tan, I think you have to set the path degeneracy to 1 because the model you used for Cu in Artemis has already found that there are 12 degenerate paths which make up the first scattering distance. By setting it to one, you then create a fitting parameter for the coordination number CN. You also must constrain the amplitude factor SO2 to some value because these parameters, N and SO2, are correlated. SO2(somewhere between 0.8-1.0) * N (=1) * CN(guess parameter) - Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 12/26/2012 6:23 AM, Zhaomo Tian wrote: Dear all, I am confused about the degeneracy and the coordination number used in the Artemis program. I want to get the coordination number of 1st shell of my copper sample, so I set a guess number N1=12(initial guess) as the coordination number which will vary during the fitting iteration, but when I am looking at the 1st path's parameters, there is another N appear which may stand for the degeneracy.The 1st path of copper model is single scattering, so the degeneracy N equals coordination number . But when I set N=12, the guessed N1 will have a value which is closed to 1, only when I set N=1, the guessed N1 will have a value which is closed to 12. It seems that N and N1 are reciprocals. But I think N actually equals N1 in the single scattering case. So I am really confused, If I want to get coordination number of a shell in a fitting, how can I deal with floated coordination number and its path degeneracy N? Thanks so much. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Plot multiple fits in (D)Artemis and statistical errors
Hello Nilmar, You mention floating the so2 value between two values? Can you constrain that value and completely remove it from the fit? It can usually be reasonably determined by standards. You might also take a look at the correlations in your fit. As another general guideline, when posting issues you come across, a very helpful step is to find and attach the log file in the Demeter folder after the error occurs, such as the program closing, which gives detailed information of the problem. I don't remember the exact location for the file but if you search the mailing list for the DArtemislog or artemis log file, you should be able to find it. You also have many parameters that you are fitting. Could you establish any sorts of relationships or approximations between them in order to reduce the number? You have ss for In and Ir which are quite close in value as well as delrIn11 = 0.00235278 and delrIn12 = 0.00255704# +/- 0. [0] . You could set them equal to each other and this can reduce the uncertainty of the fit. buena salud, Chris On Fri, Oct 26, 2012 at 8:42 AM, Nilmar Camilo nil...@fis.ufu.br wrote: Dear Bruce, ** ** I am new in the list and really don’t know if the points raised below were already discussed. In the (D)Artemis (Demeter version 0.9.13) how may I: **- **Plot different fits with the experimental data (to visually compare the results) **- **I don’t know if this is a (new) bug of the program but when I try to restore a fit the program closes. In the log file the following line is written: “Can't use an undefined value as a HASH reference at C:/Strawberry/perl/site/lib/Demeter/Fit.pm line 1558.” Obs.: I am running Demeter in Windows 7 (Pro). ** ** Another problem is related to the statistical errors when constraining the S0^2 parameter to float between two limits. The program doesn’t return the error for all others parameters (but just zero as the error value) as you can see below: ** ** guess parameters: amp= 0.79284158# +/- 0. [0.95] enot = 5.29826510# +/- 0. [0] delrIn11 = 0.00235278# +/- 0. [0] ssIn11 = 0.00155959# +/- 0. [0.00300]*** * delrCe1= -0.00231455# +/- 0. [0] ssCe1 = 0.00192778# +/- 0. [0.00300]*** * delrIn11In11 = 0.02070081# +/- 0. [0] delrIr1= -0.00435502# +/- 0. [0] ssIr1 = 0.00386517# +/- 0. [0.00300]*** * delrIn31 = 0.00648507# +/- 0. [0] ssIn31 = 0.00669602# +/- 0. [0.00300]*** * delrIn12 = 0.00255704# +/- 0. [0] ssIn12 = 0.00305432# +/- 0. [0.00300]*** * ** ** def parameters: b = 0.8000# [min(max(0.8,amp),1.0)] ** ** ** ** Thanks so much in advance. Nilmar ** ** ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Christopher J. Patridge PhD. Contact: (315)-529-0501 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] difference spectra function in (D)Athena
If it helps to diagnose and fix the bug, I just applied the E shifts found after reference calibration to the difference spectra and it fixed the problem. thanks for the quick response, Chris On Wed, Apr 11, 2012 at 11:36 AM, Ravel, Bruce bra...@bnl.gov wrote: Hi Chris, Thanks for the bug report -- that is clearly a problem. I'll look into it and get back to you. B From: ifeffit-boun...@millenia.cars.aps.anl.gov [ ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Christopher Patridge [patri...@buffalo.edu] Sent: Wednesday, April 11, 2012 10:39 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] difference spectra function in (D)Athena Hello Mailing List, I have a question about the difference spectrum function. I chose difference spectrum in norm mu(E) in the Demeter pull down menu. I set the standard and chose another spectrum. Plotting both the difference and spectra gives me the image attached. Is the difference shifted significantly to lower energy? If so, why does it change its energy scale relative to the plotted spectra? Is there a setting I can change or could this be a small bug? Thank you all, buena salud, Chris Patridge -- Christopher J. Patridge PhD. Contact: (315)-529-0501 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Christopher J. Patridge PhD. Contact: (315)-529-0501 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Crystallographic data for V(CO)6
Ismael, You do really not need exact parameters which can is helpful in EXAFS. Can you find any references on the V-C bond length? Since CO is linear, the V-O and V-C-O scattering should be possible to roughly establish. I think a number of general inorganic textbooks might have information such as this on metal carbonyl bonding. If the lattice parameters are not too different, start with simple octahedral geometry and the quick first shell fit using V-C bond length. buena salud, Chris Patridge On Wed, Mar 7, 2012 at 1:39 PM, Ismael Graff gr...@fisica.ufpr.br wrote: Dear XAS fellows: I have to fit EXAFS data of a nanoparticle colloidal suspension. TEM and NMR data indicate that I have nanoparticles of V(CO)_6 (vanadium hexacarbonyl). The system is orthorhombic, space group Pnma (Nr. 62), and I know the nominal values for the lattice parameters. However, I need the different atomic positions/coordinates to enter in ATOMS. Usually I get such information from a CIF (Crystallographic Information File) card. But in this case, I didn´t find it in the open data banks. Is anyone out there that could help me? Cheers, Ismael. PS: A similar structure/material would also help (like Mo(CO)_6)! -- *Ismael Leandro Graff * * * * Universidade Federal do Paraná * * Departamento de Física, CP 19044 * * 81531-990, Curitiba, Brazil. * * Tel (office): +55 41 3361 3278 * * Tel (Lab): +55 41 3361 3427 * * Fax: +55 41 3361 3418* * http://fisica.ufpr.br/graff * ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Christopher J. Patridge PhD. Contact: (315)-529-0501 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] SCF convergence
Dear All, I recently starting using FEFF9 for XANES and I am trying to calculate LiCoO2 structure with deintercalation. The SCF iteration fails to converge at the 3rd iteration and I do not understand what setting I have used which is causing this hang up. I tried several different SCF radii in the attached feff input file and read in the manual that a cluster of about 30 atoms should be enough for a solid to reach convergence. Thank you in advance for any help, buena salud, Chris -- Christopher J. Patridge PhD. Contact: (315)-529-0501 feff.inp Description: Binary data ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] LCF E0
Pieter-Jan, Did you collect reference spectra along side the unknown samples? In that case just calibrate one of the reference channels and then use align spectra which shifts the the other selected reference spectrum to the calibrated one. Each reference channel will be shifted to the calibrated one along with corrsponding sample channel. buena salud, Chris Patridge On Thu, Aug 18, 2011 at 8:02 AM, Pieter-Jan Sabbe pieterjan.sa...@ugent.bewrote: Dear All I am trying to do a linear combination fit with Athena. To do that i want to first prepare my standard spectra. My unknown sample is (I presume) a combination of Cu and Cu(I)O (cuprite) and Cu(II)O (tenorite). I started with calibrating the Cu to 8979 eV as how the Athena manual say how to do it (I use the zero crossing point at the second derivative). This provided me an E0 and Eshift. I am doubting now for what I should do next: Cuprite and Tenorite have different oxidation states, meanin that the binding energies of the inner electrons will shift and in that way shifting the absorption edge of the compound. Should I look somewhere in a database (does that exist, or articles) for the absorption edge of cuprite and tenorite and set it like that or should I use the same E0 as i did for Cu? Another important thing for me, I have found some old data with some standard reference (powder spectra) measured in fluorescence mode, but my guess they are from different beamtimes, can I use data from different beamtimes/beamlines as standards in a linear combination fit? thank you in advance Pieter-Jan __**_ Ifeffit mailing list ifef...@millenia.cars.aps.anl.**gov Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.**gov/mailman/listinfo/ifeffithttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] dementer Artemis crashing on XP
Hello Bruce, I retested the crash to get the text file you mentioned. I think I found the right one which is attached. Hope this helps the debug. Chris On Thu, Aug 18, 2011 at 11:40 AM, Bruce Ravel bra...@bnl.gov wrote: Hi Chris, It turned out to be a small, easily fixed typo. I am planning on making yet another new release of Demeter this afternoon before going home. I'll add you to the list of people I email about it. For future reference, when the new codes crash, they try to write a file with names like dathena.log and so on. You can find this in %APPDATA%\demeter. On XP, %APPDATA% is something like C:\Documents and Settings\user name\Application Data That file gets overwritten the next time you fire up the program, so be sure to snag it before doing so. If you send along that file, it helps me figure out what's going wrong. B On Thursday, August 18, 2011 02:09:24 pm Christopher Patridge wrote: Hello all, I recently (yesterday) installed the new Dementer package with Strawberry perl on a freshly installed XP Pro SP3. I have tried to open a couple different old Artemis projects (.apj) and once chosen, (D) Artemis shuts down immediately with no warnings messages. The message line reads something like - converting data to Dementer fit serialization and then everything disappears. I have attached one of the projects I attempted to open. I can open data from previous Athena projects with no problem. Any help would be appreciated. buena salud, Chris Patridge -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage:http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit dartemis.log Description: Binary data ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Question about shift in E0
Brandon, I have a question about your method. You mention that you pick E0 based on the 1st peak of the derivative for each sample then extract chi(k). Have you tried constraining E0 across the set? I have thought that in order to make a good comparison between samples in a set, a common E0 should be chosen in order to replicate closely the background function across the whole set. Constraining may also provide a trend in the fitting. Buena salud, Chris On Jun 6, 2011, at 6:46 PM, Brandon Reese bjre...@gmail.com wrote: Kicaj and Matt, Thanks for the replies. It is certainly reasonable to ask about the experimental setup, that seems like a good first place to look for oddities. Sorry about using E0 in two different contexts (Athena and Artemis). I'll switch to using E0 for the chosen parameter in Athena's background subtraction and Enot for the guess parameter in Artemis. I aligned the scans in Athena using the reference foil absorption edge. I ended up shifting the scans in energy by ~1 eV or less based on the reference foil. I then set the E0 parameter in Athena to the peak of the first derivative. This value varied by about 0.5 eV (or less) between the different samples. This is what I considered when I made the statement about not seeing the oxidation change in the XANES. There is a shift of about 4 eV compared to the reference foil, which I would expect because I am looking at oxides. I then extracted the chi(k) into Artemis, and used the same Feff calculations/paths for each sample. In the Artemis fits I am seeing Enot shifts of 1-2 eV, which is a fair bit larger than the error bars. If I chose E0 at peak of the first derivative the Enot came out to be ~7 eV. Since this seemed a little on the big side, I also tried setting E0 to be the top of the white line, in that case Enot came out to be ~1 eV. The Enot shift between samples was about the same either way. Could an argument be made that there is a small shift in the overall oxidation state of the films, possibly contributing to the changes in the conductivity changes in the films? Does anyone have any references about using Enot shifts in this way? Scott - The amplitudes of the XANES features are very close. in the normalized spectrum the difference practically 0, and in the derivative the amplitudes are ~5% off. There is bit larger of a difference in amplitude between the samples (in fluorescence) and a pure In2O3 powder (in transmission) of ~10% in the first derivative. The samples are sputtered from oxide sources, so the presence of metallic In should be pretty small. I am interested about your comment on the relative sizes of the first derivative peaks. Comparing my samples to the foil the oxide peak amplitude is bigger than the metal peak by 10% or so. Could this be due to the differences between fluorescence and transmission or not optimizing the experiment to measure the foil? Or could it be due to something else more heinous? I noticed on individual fits that the dR for the first shell came out nearly the same (2.162 +/- .007 vs. 2.164) on the two samples, while the Enot's had the 1-2 eV shift between the samples. I tried to fit the two types of samples simultaneously while constraining the dR's (and a few 2nd shell parameters) to be equal to each other and letting the Enot's float. The relative Enot values came out close to what they were before. If I let dR values fit independantly, there was no real change present. In other words the multiple data set fit just made my EB's a bit smaller, but the relative shifts stayed about the same. Would there be some reasonable way in a multi-data set fit to constrain the Enot's? Brandon On Mon, Jun 6, 2011 at 9:04 AM, Matt Newville newvi...@cars.uchicago.edu wrote: HI Brandon, If I understand right (and to echo Darius's questions), it seems like you measure samples with a metal reference, and aligned the spectra in Athena so that the references matched. That's a fine way to go. I would ask: how big were the needed energy shifts? Are the experimental mu(E) spectra aligned well at this point? If you're studying metal oxides with different oxygen content, you might very well see oxidation in the XANES. If I understand correctly, you're saying you don't see this. Then, you extracted the chi(k) from the aligned spectra. How much did E0 vary for the shifted spectra in this background-subtraction step? Then, you pulled these chi(k) into Artemis, and see different E0 shifts in the fits. This E0 is a little different, in that it is the E0 shift applied to the Feff calculation to match the experimental spectra. If you use different paths or different calculations, such E0 shifts might happen, and wouldn't be highly meaningful. I know that's not a complete answer, but hopefully that and Darius's questions will help, --Matt PS on Q2: 1/ (kR)^2 vs 1
Re: [Ifeffit] What does FEFF stand for?
On 5/10/2011 2:49 PM, Francisco Garcia wrote: Dear all, I wish to ask a somewhat novice question: What does the acronym FEFF stand for? Thank you. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit I am pretty sure it stand for the calculated Effective Scattering factor F(*eff*)ective. buena salud, Chris Patridge ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
