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

Possibly non-reproduceable fits
by Godfrey, Ian 04 Aug '15

04 Aug '15

Dear All, Please bear with me here - it's possible I've done something stupid without spotting it - but I was fitting some data in Artemis and have two fits, that I am convinced should be identical (same data, same k and r windows, same paths, same GDS etc. etc.), but are not. What I did was as follows (fit numbers refer to the Artemis history file in the attached project): I set up a fit to some data, simultaneously refining at Au and Ag edges to Au-Au/Au-Ag/Ag-Au/Au-Ag paths (fits 1 & 2), and then tried a different fit, this time with Ag-Cl paths as well (fits 3&4). I then fitted the original model again (fit 5 - this was slightly different to 1 & 2, but not enough for me to notice at the time). I then closed Artemis and finished for the day. Today I came back, reloaded the project file, saved it in a new location, and tried to pick up where I left off. I performed one fit where I'd set the values to def, rather than guess, by mistake (fit 6) and then corrected this when I realised what I'd done. However when I tried to re-run the model with Ag-Cl paths I was getting wildly different results to the first time (Fits 7&8). As far as I can tell these models should be identical to fits 3&4. Both datasets were chi(k) data imported directly into Artemis. OS: Win 8.1 Ent x64 Demeter: 0.9.22 pre something x64 I've attached the following: Artemis project (artemis.fpj) Logs from fits 3 and 7 for comparison (fit3.txt, fit7.txt) Artemis log file (dartemis.log). (Also possibly worth noting is that Artemis seems to have lost the file locations (in the log files and the data window), first for the Au edge data, and then for both datasets; however when I plot the data it all seems present and correct!) Any insight gratefully received! Thanks, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Localisation issue with plots in Demeter 0.9.22
by Godfrey, Ian 04 Aug '15

04 Aug '15

Dear All, There seems to be an issue with the way plots are displayed on non-English computers: My office PC is Japanese (although set to English) and I'm seeing spurious katakana (Japanese) characters in the GNUPlot plots generated by Artemis (as well as an Angstrom that's missing its circle)! Screenshot attached. System: Demeter 0.9.22 x64, Win 8.1 Ent x64. Regards, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] Ifeffit Digest, Vol 150, Issue 3
by Abhijeet Gaur 04 Aug '15

04 Aug '15

Hi Max, Thanks for the explaning the probable reason of smaller particle sizes determined by EXAFS. I will also try to refine my fittings. Hi Anatoly, Can you please send me the link of that recent paper again as I am unable to find it in your earlier message. Abhijeet On Mon, Aug 3, 2015 at 6:04 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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: Ifeffit Digest, Vol 150, Issue 2 (Abhijeet Gaur) > 2. Re: Measuring particle size by coordination number (Maxim Boyanov) > 3. Re: Measuring particle size by coordination number > (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 3 Aug 2015 13:49:40 +0200 > From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 150, Issue 2 > Message-ID: > < > CAEq27Q1Fde2qTQyrgaAMaTJ1wUpoXydxOcS0v73MPXdAKJs_zA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > Thanks for your quick reply. So, I have to add more paths to > the fitting and then try to determine the size of the particle. > > Also, I want to add some analysis details to confirm that I am > on the right path. > > The value of amp is obtained from fitting of metal foil, i.e., > 0.84 (0.03) and is kept fixed during the fitting of the sample. > > S02 is defined by the formula S02 = > amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))). > > With thanks > > Abhijeet > > > > > > > > > > Message: 2 > > Date: Mon, 3 Aug 2015 07:11:53 -0400 > > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Measuring particle size by coordination number > > Message-ID: <C61F6046-713C-4EC2-8F7A-536ECC43DEA5(a)slc.edu> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Abhijeet, > > > > The formula looks poorly when it is only applied with one path. > > > > The strength of this approach, and of Anatoly Frenkel?s alternative > > strategy for finding particle sizes, is that it compares coordination > > numbers for different shells, helping to break the correlations between > N, > > S02, and sigma2. > > > > Even then, it tends to report sizes that are small compared to those > > provided by other techniques, but compares sizes between different > samples > > quite well. > > > > ?Scott Calvin > > Sarah Lawrence College > > > > > > > > > -- > *Dr. Abhijeet Gaur* > *Post doctoral fellow in the Institute for Chemical Technology and Polymer > Chemistry * > *Karlsruher Institut f?r Technologie (KIT), Karlsruhe Germany.* >

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Measuring particle size by coordination number
by Abhijeet Gaur 03 Aug '15

03 Aug '15

Hi all, Sorry, I may be asking a question already asked in the mailing list, but I am unable to get it from the earlier discussions. I am reading one of the research article ´´ Determination of crystallite size in a magnetic nanocomposite using extended x-ray absorption fine structure´´ .J. Appl. Phys,. vol 94, page 778, 2003 In this paper there is a formula N_nano = [1-3/4(r/R)+1/16(r/R)^3]N_bulk, which you said can be used in the Artemis for extracting the particle size. I am trying to use this formula for determination of size of Ni particles in an Ni / Al2O3 catalyst. From TEM the size determined is around 4 nm. So, I am trying to fit the theoretical model of Ni metal to the sample data in the Artemis I defined a guessed parameter R and then put the whole formula for S02 = amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))). The value of R I am getting is 0.81 (0.05) which is quite small. Is there something I am missing in the formula or I have to define the N seprately for sample cooridnation number. Currently, I am using only the first path in the fitting. With thanks Abhijeet Gaur -- *Dr. Abhijeet Gaur* *Post doctoral fellow in the Institute for Chemical Technology and Polymer Chemistry * *Karlsruher Institut für Technologie (KIT), Karlsruhe Germany.*

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Re: [Ifeffit] Ifeffit Digest, Vol 150, Issue 2
by Abhijeet Gaur 03 Aug '15

03 Aug '15

Hi Scott, Thanks for your quick reply. So, I have to add more paths to the fitting and then try to determine the size of the particle. Also, I want to add some analysis details to confirm that I am on the right path. The value of amp is obtained from fitting of metal foil, i.e., 0.84 (0.03) and is kept fixed during the fitting of the sample. S02 is defined by the formula S02 = amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))). With thanks Abhijeet > > > Message: 2 > Date: Mon, 3 Aug 2015 07:11:53 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Measuring particle size by coordination number > Message-ID: <C61F6046-713C-4EC2-8F7A-536ECC43DEA5(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Abhijeet, > > The formula looks poorly when it is only applied with one path. > > The strength of this approach, and of Anatoly Frenkel?s alternative > strategy for finding particle sizes, is that it compares coordination > numbers for different shells, helping to break the correlations between N, > S02, and sigma2. > > Even then, it tends to report sizes that are small compared to those > provided by other techniques, but compares sizes between different samples > quite well. > > ?Scott Calvin > Sarah Lawrence College > > > -- *Dr. Abhijeet Gaur* *Post doctoral fellow in the Institute for Chemical Technology and Polymer Chemistry * *Karlsruher Institut für Technologie (KIT), Karlsruhe Germany.*

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Vanadium-Chromium Prussian Blue Analog XANES fitting
by Adora Graham 31 Jul '15

31 Jul '15

Hello, First of all, I am still very new to XAS analysis, so please excuse any misunderstandings I may have. I have a series of compounds nominally consisting of KxVx[Cr(CN)6] Prussian blue analogs (where x is ~1) with Cr(III) and presumably V(II) present in the system. From other evidence, the V(II) may be oxidizing to V(III). I have XAS data collected at the V and Cr K-edges from APS and have been struggling through trying to analyze my data using Athena. I am trying to get two things out of this data: First, I would like to get the oxidation state of the Vanadium sites. If they are not V(II), to get the ratio of V(II) to V(III) present, if possible. I have been trying to follow a similar analysis to Wong (Phys. Rev. B, 1984, 30, 10, 5596-5610). However, I seem to be running into the issue of finding standards with a similar ligand set to my sample. I have XAS data for the following standards: VO, V2O3, V2O4, V2O5, V(acac)3, VO(acac), VOSO4, and VSO4. I start with VSO4 as my initial vanadium source, so that could be useful for a comparison. Our initial idea was to use the vanadium oxides to give a standard curve to then extrapolate the oxidation state of my compound, but using this gives me an oxidation state of ~4.2 which seems unreasonable for my system. I am kind of lost otherwise as to what else I could do with this. Second, I would like to get the ratio of V to Cr. I was told I could compare the un-normalized K-edge heights of the vanadium to that of the chromium to get this ratio. This doesn't seem right, as I would think that there should be some relative intensity factor involved. Also, this gives me a fairly unreasonable value of 4:1, since XPS measurements give me values of around 1:1. Can you point me in the right direction for these issues? I've also attached the project files for one of my samples. Thanks, Adora

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Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8)
by Fowler, Joseph W. 30 Jul '15

30 Jul '15

Dear Ie-Rang, I’m the demeter maintainer on MacPorts, but I admit I am anything but a MacPorts guru. I notice that the error you showed is a failure to install gcc49. I don’t know if that new GCC is compatible with your old version of OS X, but that’s an issue that’s beyond my expertise. You might edit your variants file (it’s /opt/local/etc/macports/variants.conf on my installation) to insist on an earlier version by adding a line containing, e.g., “+gcc47” or whatever is your installed and preferred version of GCC. In fact, the port demeter does not depend (directly) on gcc, which you can see by issuing the command > port echo depof:demeter > port echo depof:demeter-devel So it looks to me like you have several steps to get ready for installing demeter. I admit that I recently discovered—but have not fixed—a flaw in the demeter port description file. The code depends on ports p5.16-file-which and p5.16-math-round, but these are not made explicit. I need to figure out how to add these to the explicit dependency list. I’m just back from vacation and a conference, so I have no excuses now. If you get far enough that you can install *but not run* demeter’s executables, then a workaround for this is > sudo port install p5.16-file-which p5.16-math-round And for MacPorts users in general: I understand that the project as a whole is in the process of trying to move to Perl 5.22 instead of 5.16. I’ll be updating the port file to reflect that change, too. Joe Fowler NIST Boulder Laboratories On Jul 29, 2015, at 4:01 PM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto: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-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. HELP: failed to install gcc49 on mac (v10.6.8) (Ie-Rang Jeon) 2. Re: HELP: failed to install gcc49 on mac (v10.6.8) (Bruce Ravel) 3. Error in Running XANES on FEFF8.4 for Cobalt based cluster (Ganesh Subramanian) From: Ie-Rang Jeon <jeon(a)northwestern.edu> Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) Date: July 29, 2015 at 1:11:08 PM MDT To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) Date: July 29, 2015 at 1:21:06 PM MDT To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> On 07/29/2015 03:11 PM, Ie-Rang Jeon wrote: Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang Perhaps there's anything useful in that log file? B ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Error in Running XANES on FEFF8.4 for Cobalt based cluster
by Ganesh Subramanian 30 Jul '15

30 Jul '15

Dear all, I was trying to simulate XANES using FEFF8.4 at Cobalt K edge. This is for a cluster and not a crystal. I encountered two problems. 1. *Using the FOLP card*: The actual cluster size is about 180 atoms extending upto 18 A in radial distance from the central cobalt atom. But there are quite a few instances of Hydrogen atoms that are too close. I tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to get a syntax type error, that i cant figure out. I checked the crystal structure and the smallest hydrogen bond distance is 0.89 A. (I have attached the corresponding input and log file with suffix 'full cluster') 2. *SCF for small cluster*: Since the problem with the hydrogen distances persisted, I decided to run the calculation for a smaller cluster (about 50 atoms). I used the conditions as prescribed for small clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were too close (within this smaller cluster, there were about 3 of them, and none in the first or second shell of co-ordination) were removed manually. Now, I did not have the error on distances, did not require the FOLP card to be manually altered, but the log1 file seems to suggest that the SCF is not calculated. I cant figure why that is the case. (I have attached the corresponding input and log file with suffix 'small cluster') Sorry for the long email, and thank you for any suggestions. Ganesh

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HELP: failed to install gcc49 on mac (v10.6.8)
by Ie-Rang Jeon 29 Jul '15

29 Jul '15

Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed

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Setting ranges in peak fitting
by Kenneth Latham 28 Jul '15

28 Jul '15

Hi Bruce, To clarify this further, I am peak fitting a number of peaks under the carbon edge. For example, I know from the literature that the 1s-p transition for the C=C should be located between 284.5 to 285.5 eV, so I would fit a peak at about 285 eV to start with. I would then move on to fitting additional peaks based on their literature values with what I know about the material/where obvious peaks are in the NEXAFS. The problem now comes when I tell Athena to fit, it will start to move the peaks all over the place to obtain the best fit, typically placing them in locations where functionalities don't appear under the NEXAFS. In other words, it would move peaks away from where I would expect them to be based on the literature. This can be partially stopped by fixing all but one peak, fitting it and then and applying this procedure to every peak multiple times. What I was wondering is if Athena has the ability to set a range that each peak is allowed to move, i.e., the C=C center would be restricted to values between 284.5-285.5 eV. Hence I could set up the ranges and fit quickly based on those. Cheers, Ken Latham ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Saturday, 25 July 2015 3:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 149, Issue 23 Send Ifeffit mailing list submissions to ifeffit(a)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-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Setting ranges in peak fitting Athena (Kenneth Latham) 2. Re: Setting ranges in peak fitting Athena (Ravel, Bruce) 3. Re: Setting ranges in peak fitting Athena (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Jul 2015 00:14:18 +0000 From: Kenneth Latham <Kenneth.Latham(a)uon.edu.au> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Setting ranges in peak fitting Athena Message-ID: <CY1PR02MB1416E3DBC230406B078F9A07AA810(a)CY1PR02MB1416.namprd02.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken ------------------------------ Message: 2 Date: Fri, 24 Jul 2015 13:14:03 +0000 From: "Ravel, Bruce" <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Setting ranges in peak fitting Athena Message-ID: <xp7hq5h11j0ygmcc2btiht0f.1437743641853(a)email.android.com> Content-Type: text/plain; charset="us-ascii" Hi Ken, I'm sorry, but I don't quite understand your question. And I have no idea what casaXPS is, so that reference doesn't help me. Are you asking whether you can put gaps in the fit range? B On July 23, 2015, at 8:16 PM, Kenneth Latham <Kenneth.Latham(a)uon.edu.au> wrote: Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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