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

cannot run demeter 0.9.19
by Georges Siddiqi 10 Jan '14

10 Jan '14

Hi, I'd like to report a bug in which I can't run any of the demeter programs (athena, artemis, hephaestus) after updating to 0.9.19. My computer is running windows 7 - I either install Demeter 0.9.19 without removing 0.9.18 (the installer automatically uninstalls it anyways), or after removing 0.9.18 in add/remove programs - In either case I get an error message from perl.exe saying "This program can't start because libgcc_s_dw2-1.dll is missing from your computer. Try reinstalling the program to fix this problem" - i click ok and program closes I can re-install 0.9.18 and it works fine, but no matter what i've tried 0.9.19 wont run for me. I attached the logfile for artemis (identical to log file for athena) thanks for your help, georges

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Re: [Ifeffit] correlating number of nearest neighborst to the particle
by Rana, Jatinkumar Kantilal 10 Jan '14

10 Jan '14

Dear Scott and Anatoly, Thanks a lot for your valuable suggestions. I may get back to you for any questions, once I go through both the approaches in literature and implement them in the form of a fit. Best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 09 January, 2014 19:18 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 10 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: correlating number of nearest neighborst to the particle size (Scott Calvin) 2. Re: correlating number of nearest neighborst to the particle size (Anatoly I Frenkel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 9 Jan 2014 13:11:41 -0500 From: Scott Calvin <scalvin(a)sarahlawrence.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] correlating number of nearest neighborst to the particle size Message-ID: <E6FE5676-5821-46A2-ABAD-B383AE402183(a)slc.edu> Content-Type: text/plain; charset="utf-8" Hi Jatin, There are two strategies that have been used to do this that you can find in the literature, both of which are by members who frequent this list (myself and Anatoly Frenkel). I have published articles outlining a strategy where you assume the shape of the particles. Most often in my case that has been spheres, but it could be plates or hemispheres or whatever. Then you derive how the coordination number depends on dimensions for that shape (as I said, I an others have done that for spheres), and make those dimensions free parameters in an Ifeffit (e.g. Artemis) fit. Anatoly has published articles outlining a strategy where you treat the coordination numbers themselves as free parameters, and then check for consistency with various shapes. I think Anatoly's method is better when the nanoparticles are very consistent; i.e. they have a narrow size distribution and consistent shapes, and when data quality is good. I think my method may work better when the nanoparticles are "messier" or when the data is more limited, if only because it requires fewer free parameters. A typical reference for Anatoly's method is A View from the Inside:? Complexity in the Atomic Scale Ordering of Supported Metal Nanoparticles Anatoly I. Frenkel,*,?,?, Charles W. Hills,? and, and Ralph G. Nuzzo*,?,? The Journal of Physical Chemistry B 2001 105 (51), 12689-12703 A typical reference for my method is ?Estimating crystallite size in polydispersed samples using EXAFS,? S. Calvin, C. J. Riedel,* E. E. Carpenter, S. A. Morrison, R. M. Stroud, and V. G. Harris, Physica Scripta T115, 744 (2005). although that can be a little hard to find. Another reference which is more widely available is ?Comparison of extended X-ray absorption fine structure and Scherrer analysis of x-ray diffraction as methods for determining mean sizes of polydisperse nanoparticles,? S. Calvin, S. X. Luo, C. C. Broadbridge, J. K. McGuinness, E. Anderson, A. Lehman, K. H. Wee, S. A. Morrison, and L. K. Kurihara, Appl. Phys. Lett. 87, 233102 (2005). --Scott Calvin Sarah Lawrence College On Jan 9, 2014, at 12:55 PM, Rana, Jatinkumar Kantilal <jatinkumar.rana(a)helmholtz-berlin.de> wrote: > Hi All, > > I would like to estimate the size of Cu nanoparticles grown in my sample by EXAFS fitting. I can refine the number of nearest neighbors in these Cu nanoparticles up to 4 shells (say NN1, NN2, NN3 and NN4), by constraining S02 to the value obtained by fitting the data of Cu reference foil. But, how do I correlate the refined values of nearest neighbors to the actual size of Cu nanoparticles ? Any help in this regard would be much appreciated. > > Regards, > Jatin > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 09 January, 2014 17:51 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 131, Issue 8 > > 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. Query re: Athena and Artemis user guides (Leon Clarke) > 2. Re: Query re: Athena and Artemis user guides (Bruce Ravel) > 3. Re: Query re: Athena and Artemis user guides (Kathy Dardenne) > 4. Re: Demeter 0.9.19 (Schima, Frank) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 9 Jan 2014 15:56:29 +0000 > From: Leon Clarke <L.Clarke(a)mmu.ac.uk> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Query re: Athena and Artemis user guides > Message-ID: <83CF3E8AA2102C4598B316168B472EFE98BEEECD@drmb1> > Content-Type: text/plain; charset="us-ascii" > > Dear Dr Ravel and Demeter users, > > > > I recollect that the Athena and Artemis user guides used to be available as PDF files (which I found useful). Am I correct that the latest guides are now only accessible as internet pages, as I can't seem to find a download link? > > > > Best regards, Leon > > > ----- > Dr Leon J. Clarke > 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.clarke(a)mmu.ac.uk<mailto:l.clarke@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 website http://www.mmu.ac.uk/emaildisclaimer " > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201401 > 09/4361200f/attachment-0001.htm> > > ------------------------------ > > Message: 2 > Date: Thu, 09 Jan 2014 11:23:13 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Query re: Athena and Artemis user guides > Message-ID: <52CECCF1.3050502(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 01/09/2014 10:56 AM, Leon Clarke wrote: >> I recollect that the Athena and Artemis user guides used to be >> available as PDF files (which I found useful). Am I correct that the >> latest guides are now only accessible as internet pages, as I can?t >> seem to find a download link? >> > > I just put links to PDF copies of the two Users' Guides on the Demeter > home page: http://bruceravel.github.io/demeter/ > > A couple things to note: > > 1. When you install either from source or from the Windows installer, > full HTML copies of the users' guides get installed as well. > > 2. The PDF files are generated from the same source as the html. I > have spent a lot of time making the html look reasonable. (Not > great, but reasonable!) The PDF are pretty rough and have some > obvious layout problems. But I just skimmed through both of them. > They are usable, though certainly not beautiful. > > Thanks for asking. I had stopped updating the PDF versions because I didn't know that anyone was using them. How 'bout that! > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology Synchrotron Science > Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, > 11973 > > Homepage: http://xafs.org/BruceRavel > Software: https://github.com/bruceravel > > > ------------------------------ > > Message: 3 > Date: Thu, 9 Jan 2014 17:34:13 +0100 > From: Kathy Dardenne <kathy.dardenne(a)kit.edu> > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Query re: Athena and Artemis user guides > Message-ID: <001801cf0d58$a1499170$e3dcb450$(a)kit.edu> > Content-Type: text/plain; charset="us-ascii" > > Thanks a lot for the pdf version. > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce > Ravel > Sent: Thursday, January 09, 2014 5:23 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Query re: Athena and Artemis user guides > > On 01/09/2014 10:56 AM, Leon Clarke wrote: >> I recollect that the Athena and Artemis user guides used to be >> available as PDF files (which I found useful). Am I correct that the >> latest guides are now only accessible as internet pages, as I can't >> seem to find a download link? >> > > I just put links to PDF copies of the two Users' Guides on the Demeter > home > page: http://bruceravel.github.io/demeter/ > > A couple things to note: > > 1. When you install either from source or from the Windows installer, > full HTML copies of the users' guides get installed as well. > > 2. The PDF files are generated from the same source as the html. I > have spent a lot of time making the html look reasonable. (Not > great, but reasonable!) The PDF are pretty rough and have some > obvious layout problems. But I just skimmed through both of them. > They are usable, though certainly not beautiful. > > Thanks for asking. I had stopped updating the PDF versions because I didn't know that anyone was using them. How 'bout that! > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology Synchrotron Science > 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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ------------------------------ > > Message: 4 > Date: Thu, 9 Jan 2014 16:47:41 +0000 > From: "Schima, Frank" <frank.schima(a)nist.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter 0.9.19 > Message-ID: <DFAFEE64-6489-4E27-91B4-14CF762FADCD(a)nist.gov> > Content-Type: text/plain; charset="windows-1252" > > Hi all, > > On Jan 9, 2014, at 8:26 AM, Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> wrote: > > On Thu, Jan 9, 2014 at 8:04 AM, Bruce Ravel <bravel(a)bnl.gov<mailto:bravel@bnl.gov>> wrote: > On 01/09/2014 08:24 AM, Stefano Luciano Ciurli wrote: > > Hello Bruce and thank you for your hard work! > instructions to install on OS X 10.6.8? > > There is not a Mac package. I do not own a Mac and and so do not have the ability to develop a Mac package on my own. > > Over the years, no one has ever stepped up to help me develop a Mac > package for Demeter. (Or Debian packages, or RedHat packages, for > that matter.) > > Well, I have *tried* many times, and put a fair amount of time in > getting Demeter to work on a Mac. What I have not done is *succeed*. > I can tell you that getting wxPerl to work on Mac OSX is far from simple. Though Demeter is many years old now, and I've tried many times over the years (and I using wxPython on Mac all the time), it is only within the past few months that I have ever gotten wxPerl to actually build on any Mac, and this was a 10.8 machine. Currently (though I haven't looked at it in more than a month), getting the Ifeffit-Perl interface to build properly with Mac OS 10.8 has me stumped, as Apple is now using llvm/clang, making it challenging to work well with gfortran. > > Migrating Demeter to use Larch should simplify the situation, as it would remove the need for the Ifeffit-Perl interface. > > Frankly, the work I do on the Windows package takes a lot of time. The only way I can claim that time fits in my job description is because my group uses Windows machines at our beamlines. Help would be welcome to develop packages for Mac and other platforms, but despite repeated requests over many years, no one has ever volunteered and actually seen it through to completion. > > Yes, help building Demeter for Mac OSX would be great. > > I too have put a lot of work into making Demeter run on OS X. I have been attempting to make a port of it in Macports [1] so it is easy to install and/or have a package installer created. > > The good news is that along the way I have successfully created a port of ifeffit [2] that builds fine for me on 10.9 and should work all the way down to 10.6. I utilize gcc for gfortran. I believe the ifeffit-perl bindings [3] work too. After you install Macports [4], you can simply type: > > sudo port install p5.16-ifeffit > > The bad news is that my in progress Demeter port does not work yet. The problem I?m stuck on is getting the perl-wx port [5] built. I have not been able to get it built with the new wx-widgets version 3.0.0 that is in Macports. The perl-wx people apparently don?t have support for that version of wx yet and they never respond to my queries about it on the mailing list. > > I encourage people to test out ifeffit on OS X through Macports and give me feedback - positive or negative. Thanks to Bruce for his support during this endeavor. > > > Cheers! > Frank > > [1] <http://www.macports.org> > [2] > <https://trac.macports.org/browser/trunk/dports/science/ifeffit/Portfi > le> [3] > <https://trac.macports.org/browser/trunk/dports/perl/p5-ifeffit/Portfi > le> [4] <http://www.macports.org/install.php> > [5] > <https://trac.macports.org/browser/trunk/dports/perl/p5-wx/Portfile> > > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201401 > 09/59f05e5e/attachment.htm> > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 131, Issue 8 > *************************************** > > ________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, > stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas > Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ Message: 2 Date: Thu, 9 Jan 2014 18:16:37 +0000 From: Anatoly I Frenkel <afrenke2(a)yu.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] correlating number of nearest neighborst to the particle size Message-ID: <545F89325F51764C902D37B42C9F4D538EC6E017(a)YUWEXCPM11.yuad.uds.yu.edu> Content-Type: text/plain; charset="Windows-1252" Jatin, Estimating the size from EXAFS data alone may be very risky because you will have to assume a certain shape and morphology (say, 3D such as cuboctahedral, or oblate, such as truncated cuboctahedral) in order to find the size from EXAFS coordination numbers. They CNs are "indices" that describe not just size but the entire architecture, and there may be more than one such architecture that fits those four indices. The simplest architectures that you can consider for modeling purposes are closed shell clusters that can be constructed from a seed cluster of a given shape by adding more layers on it until your model CNs and experimental CNs match within the error bars. However, such analysis is predicated that you have excellent size and shape selectivity. Hence, you need an independent data such as TEM, to get statistical information about the size/shape distribution. Of course, you need to make synthesis also size-shape selective as well. If you do not have good control over size/shape, your analysis using 4 shells is an overkill. You can get average size by estimating it using Scott Calvin's equation in J. Appl. Phys. 94:778?83. If you do have a good control over size/shape you should first question your fitting process that gives you the CNs and their uncertainties. You have to check if you included the most important multiple scattering contributions, the stability of the fit results to the changes in your fitting scheme (e.g., the ways you constrain (or not) parameters of single and multiple scattering collinear paths). You may also decide to check your model on bulk Cu and see if you will obtain correct CNs if you vary them (by fixing the S02). If you find that the CNs in bulk Cu are not in agreement with the crystallography, you should not expect anything meaningful from the CNs in your nanoparticle if you obtain them using the same fitting scheme as for the bulk. After all the above is done, then you can do some modeling using CNs from 1st through 4th shell. Here are some references how to do that using EXAFS results: J. Phys. Chem. B, 105, 12689-12703 (2001). J. Synchrotron Rad., 6 , 293 (1999). Zeitschrift fur Kristallographie, 222, 605-611 (2007). Ann. Rev. Anal. Chem., 4, 23-39 (2011) J. Am. Chem. Soc. 132, 8747-8756 (2010) Anatoly ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Rana, Jatinkumar Kantilal [jatinkumar.rana(a)helmholtz-berlin.de] Sent: Thursday, January 09, 2014 12:55 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] correlating number of nearest neighborst to the particle size Hi All, I would like to estimate the size of Cu nanoparticles grown in my sample by EXAFS fitting. I can refine the number of nearest neighbors in these Cu nanoparticles up to 4 shells (say NN1, NN2, NN3 and NN4), by constraining S02 to the value obtained by fitting the data of Cu reference foil. But, how do I correlate the refined values of nearest neighbors to the actual size of Cu nanoparticles ? Any help in this regard would be much appreciated. Regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 09 January, 2014 17:51 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 8 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. Query re: Athena and Artemis user guides (Leon Clarke) 2. Re: Query re: Athena and Artemis user guides (Bruce Ravel) 3. Re: Query re: Athena and Artemis user guides (Kathy Dardenne) 4. Re: Demeter 0.9.19 (Schima, Frank) ---------------------------------------------------------------------- Message: 1 Date: Thu, 9 Jan 2014 15:56:29 +0000 From: Leon Clarke <L.Clarke(a)mmu.ac.uk> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Query re: Athena and Artemis user guides Message-ID: <83CF3E8AA2102C4598B316168B472EFE98BEEECD@drmb1> Content-Type: text/plain; charset="us-ascii" Dear Dr Ravel and Demeter users, I recollect that the Athena and Artemis user guides used to be available as PDF files (which I found useful). Am I correct that the latest guides are now only accessible as internet pages, as I can't seem to find a download link? Best regards, Leon ----- Dr Leon J. Clarke 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.clarke(a)mmu.ac.uk<mailto:l.clarke@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 website http://www.mmu.ac.uk/emaildisclaimer "

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correlating number of nearest neighborst to the particle size
by Rana, Jatinkumar Kantilal 09 Jan '14

09 Jan '14

Hi All, I would like to estimate the size of Cu nanoparticles grown in my sample by EXAFS fitting. I can refine the number of nearest neighbors in these Cu nanoparticles up to 4 shells (say NN1, NN2, NN3 and NN4), by constraining S02 to the value obtained by fitting the data of Cu reference foil. But, how do I correlate the refined values of nearest neighbors to the actual size of Cu nanoparticles ? Any help in this regard would be much appreciated. Regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 09 January, 2014 17:51 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 8 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. Query re: Athena and Artemis user guides (Leon Clarke) 2. Re: Query re: Athena and Artemis user guides (Bruce Ravel) 3. Re: Query re: Athena and Artemis user guides (Kathy Dardenne) 4. Re: Demeter 0.9.19 (Schima, Frank) ---------------------------------------------------------------------- Message: 1 Date: Thu, 9 Jan 2014 15:56:29 +0000 From: Leon Clarke <L.Clarke(a)mmu.ac.uk> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Query re: Athena and Artemis user guides Message-ID: <83CF3E8AA2102C4598B316168B472EFE98BEEECD@drmb1> Content-Type: text/plain; charset="us-ascii" Dear Dr Ravel and Demeter users, I recollect that the Athena and Artemis user guides used to be available as PDF files (which I found useful). Am I correct that the latest guides are now only accessible as internet pages, as I can't seem to find a download link? Best regards, Leon ----- Dr Leon J. Clarke 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.clarke(a)mmu.ac.uk<mailto:l.clarke@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 website http://www.mmu.ac.uk/emaildisclaimer "

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Query re: Athena and Artemis user guides
by Leon Clarke 09 Jan '14

09 Jan '14

Dear Dr Ravel and Demeter users, I recollect that the Athena and Artemis user guides used to be available as PDF files (which I found useful). Am I correct that the latest guides are now only accessible as internet pages, as I can't seem to find a download link? Best regards, Leon ----- Dr Leon J. Clarke 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.clarke(a)mmu.ac.uk<mailto:l.clarke@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 website http://www.mmu.ac.uk/emaildisclaimer "

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Demeter 0.9.19
by Bruce Ravel 08 Jan '14

08 Jan '14

Happy New Year, everyone! Today I released a new version of Demeter and it's programs, Athena, Artemis, and Hephaestus. See http://bruceravel.github.io/demeter/ A new Windows Installer can be found there. Please note that this is a full release, not an updater package. It's rather large because I have updated all of the software tools that Demeter depends upon. The installer will uninstall your earlier version, so it is not necessary to do so by hand. I have tagged a new release at github for those who use the source code. The list of changes can be found here: https://github.com/bruceravel/demeter/blob/master/Changes.org Along with a number of bug fixes and back end improvements, there are three interesting new user interface features in Athena: 1. keyboard shortcuts for merging mu(E), norm(E), and chi(k) -- Ctrl-Shift-m, Ctrl-Shift-n, and Ctrl-Shift-c 2. Right clicking on the plot buttons will display special plots from the Plot menu. For example, right clicking on the orange "kq" button will redisplay the quad plot for the current group. 3. Selecting "Shrink" from the plot options tab will hide the k-weight and plot options controls, allowing the group list to be taller, thus displaying more groups. As always, please report bugs to the mailing list with enough detail that I can reproduce the problem on my own computer. Enjoy! Happy 2014! Bruce -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Re: [Ifeffit] How to identify Mn Mn Corner edge paths in Artemis
by fred.mosselmans＠diamond.ac.uk 07 Jan '14

07 Jan '14

Hi Sathish, There are no corner sharing paths in your feff calculation as the "perfect" birnessite model you are using only has edge sharing octahedra. I am not a phyllomanganate expert so can't help with a structure suggestion to try but using google I would think you could find a structure with corner sharing MnO6. Then you could take the corner sharing path from there and the edge sharing from your original structure. In Sam Webb's paper he has refined his model to give shell occupancy numbers as he has a non totally crystalline structure. This is effectively the path degeneracy from the Feff calculation but you cannot refine this number in artemis, you have to refine Nmncor or some other variable the name is irrelevant and then define the path occupancy of the corner as 1 and the S02 for this path as amp * Nmncor . Bruce's videos are pretty good in getting started in fitting from scratch, which is really not the easiest thing to do, so keep going. I assume you have watched some of them. http://www.diamond.ac.uk/Home/Events/Past_events/XAS-workshop-2011.html?mgn… HTH Cheers Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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How to identify Mn Mn Corner edge paths in Artemis
by Sathish Mayanna 07 Jan '14

07 Jan '14

Dear all I am sorry for disturbing you all again, since I am self learning to fit multiple scattering for biogenic Mn oxides in Artemis, I am quite lost in understanding the basics of Mn Mn corner sharing path. All reports are included Mn-Mn Corner at ~ 3.4 A, which I cannot find in my Feff calcuation for Phyllomanganate layer (Na-Birnessite) model. Below are the crystallographic information of Na birnessite I used (*also available in the attachment*), Na is excluded. A = 5.174 B = 2.850 C = 7.336 and angles 90, 103.18 and 90 for alpha, beta, gamma respectively Parameters X Y Z Mn 0 0 0 O1 0.37600 0 0.1330 I have two questions 1) How to identify the Mn Mn corner paths from the Paths result. 2) Where can I find the Coordination Number for Mn Mn Corner, If i see in eg. Webb et al., 2005 ( http://www.intl-ammin.geoscienceworld.org/content/90/8-9/1342.short) the CN numbers for Mn-Mn Corner is 0.6(1.0) or 0.8(8), what does the number represent in the brackets? It will be looking forward for your help. Regards -- Sathish

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Re: [Ifeffit] Standard Mn(III) oxides for LCF fitting? problem in
by fred.mosselmans＠diamond.ac.uk 03 Jan '14

03 Jan '14

Dear Sathish, You are right to be dubious about your Mn2O3 spectra, it looks to have much too small a white line compared to literature data and thus probably suffers from Some sort of thickness effects. You can find some MnOxide spectra in Matt's data base http://cars9.uchicago.edu/cgi-bin/newville/Model-Search.cgi however the resolution may be different to wherever you collected your data, but the spectra should be better. Assuming all your data was collected at the same time the edge position of your sample suggests by inspection that it is mainly Mn(IV), In the recess of my mind i know people have published nicely correlated pictures of oxo-Mn compounds edge positions against oxidation states to get a nice linear plot. I am sure you can find this if you search for it in google scholar or the like. However there are several different isomorphs of MnO2 and they have different XANES/EXAFS , thus LCF will only work if you have spectra of all of them (or at least all the types in your sample) Thus unless you are sure that delta is the only type in your sample (by XRD?) , LCF is not likely to get you very far. Given the edge position ab initio fitting might work OK. Otherwise you need to track down absorption spectra of the other isomorphs and try again. For LCF to work well (or at all) you need to have a basis set of all the components in your sample not just one for each possible oxidation state. HTH Regards Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Standard Mn(III) oxides for LCF fitting? problem in fitting
by Sathish Mayanna 03 Jan '14

03 Jan '14

Dear all Wish you a very happy new year! I was trying to apply LCF for XANES or EXAFS for biogenic Mn oxides (layer type Mn oxides). Using the standards (Mn2O3, Aqueous Mn2+ and dMnO2) I cannot fit the LCF for my XANES or EXAFS data *(attachment)*. I am not really sure what are the problems with the standards (as I expect mainly Mn(III) or Mn(IV) in my samples). It would be really great, if anyone could provide me the Mn(III) oxide standard or have a look at the data and please let me know, if I have done any thing wrong. Best regards Sathish

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Athena deglitch problem
by Sathish Mayanna 03 Jan '14

03 Jan '14

Dear Matt After installing Demeter to other than C drive there is no problem with deglitching. For me its easier to rebin the data points and then deglitch the terrible glitch in my data. If I don't rebin I need hours to deglitch a single spectra since the data contains a big glitch. I believe the major problem is solved for now, thanks a lot for your help. Regards Sathish On Tue, Dec 17, 2013 at 7:00 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: Athena deglitch problem (Sathish Mayanna) > 2. Re: Athena deglitch problem (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 16 Dec 2013 19:42:25 +0100 > From: Sathish Mayanna <satty334(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Athena deglitch problem > Message-ID: > <CABVfawm9mL4XhhvBJoPX2= > ZZ-MNek5YCkRcTHUP6S1UL6+xcaQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > *Dear Matt* > > > > > > Now it seems working well except some minor things, I can remove the > > points > > > from the data, the random point selection by software works better for > > > rebinned data. I think the only problem I have now is I still cannot > move > > > the cursor after double click (I can only remove the points which the > > > software decides - at least now it choose the points where I double > > click). > > > When i move my mouse cursor on the plot, it shows the correct > > coordinates. > > > > I'm still a bit confused about whether this actually working for you. > > The data you sent has fairly large arrays (>2400 points), but all the > > data was well-ordered in energy... I think that should "just work", > > without needing re-binning. And it does for me, and I don't see how > > re-binning would affect this. > > > * If I don't rebin the data, Athena will not choose the point which I am > intend to remove (I think i have some minor issues here). If I rebin the > data from ~ 2400 to 350 points, Athena will work correctly.* > > > > > > > I think it's always been the case that you double-click near the point > > to be removed, and hope that Athena does select the one you intended. > > > > *This works perfect for rebinned data. * > > > > > > I have one clarifications, when u choose the option to deglitch the > data > > > (rebinned or non rebinned data), does the x(E) data plot looks like in > > the > > > attached file (line) or it looks like sets of blue round points same > > size as > > > cursor. > > > > For me, it looks very much like the image you attached. I do not see > > a series of dots. > > > > > I think, the issue is solved except that I cannot move the randomly > > chosen > > > point. > > > > Why can't you remove the point chosen? That seems like it's not > > working to me. Wasn't that the problem you were having? > > > > *I mentioned "MOVE" in my above sentence, (Just to be more specific, when I > double click on the plot to choose a point, sometimes Athena select its own > random points away from the point where I clicked, when I try to drag that > randomly chosen cursor to the point of my interest, it will not work), IS > THIS NORMAL? * > > *I will try to figure out all the possible ways for non-rebinned data, if > it does not work at least for now rebinned data works.* > > *Regards* > *Sathish* > > > > > > Again, it may be that I'm not understanding. Cheers, > > > > --Matt > > > > > > ------------------------------ > > > > Message: 2 > > Date: Mon, 16 Dec 2013 08:30:39 -0500 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Handling time resolved data > > Message-ID: <52AF007F.4050600(a)bnl.gov> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 12/13/2013 09:00 AM, Ditty Dixon wrote: > > > Dear Bruce, > > > > > > Recenetly we did some time resolved measurements, QEXAFS mode. While > > > the old Athena arranged the file as we want i.e file 1, 2, 3 etc, the > > > new did it bit different 1, 11 12 and again 2, 21 etc. Screenshot > > > attached. Why is it doing diffrently for the two version? Can it be > > > fixed some how. > > > > You haven't explained exactly where these data come from, so I am > > assuming that each scan was written to its own file and these files were > > imported into Athena. > > > > In Athena, data are imported in "ascii-betical" order, that is, sorted > > in order of characters in the ASCII chart: > > > > http://en.wikipedia.org/wiki/ASCII#ASCII_printable_characters > > > > In that sense, Athena sorted your data as expected. As Chris pointed > > out, if you want things like > > > > nr_1.spec > > nr_2.spec > > ... > > nr_10.spec > > > > to sort numerically by the number between the _ and the .spec, you need > > to format the them so that numerical and ascii-ordered sorting come out > > the same. This is done as > > > > nr_01.spec > > nr_02.spec > > ... > > nr_10.spec > > > > For a quick exafs experiment, two digits is probably not enough, so > > you'd want something like > > > > nr_00001.spec > > nr_00002.spec > > ... > > nr_00010.spec > > > > > > I don't recall quite how the sorting worked in the old version of Athena > > (it has been over 5 years since I stopped working on it), but my vague > > memory is that, on Windows, they were imported in the order that they > > were clicked upon the file selection dialog. The way it is currently > > done is much better in that it is reproducible. > > > > > > > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Science 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(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > End of Ifeffit Digest, Vol 130, Issue 22 > > **************************************** > > > > > > -- > Satty >

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Re: [Ifeffit] Athena deglitch problem
by Sathish Mayanna 16 Dec '13

16 Dec '13

*Dear Matt* > > > Now it seems working well except some minor things, I can remove the > points > > from the data, the random point selection by software works better for > > rebinned data. I think the only problem I have now is I still cannot move > > the cursor after double click (I can only remove the points which the > > software decides - at least now it choose the points where I double > click). > > When i move my mouse cursor on the plot, it shows the correct > coordinates. > > I'm still a bit confused about whether this actually working for you. > The data you sent has fairly large arrays (>2400 points), but all the > data was well-ordered in energy... I think that should "just work", > without needing re-binning. And it does for me, and I don't see how > re-binning would affect this. * If I don't rebin the data, Athena will not choose the point which I am intend to remove (I think i have some minor issues here). If I rebin the data from ~ 2400 to 350 points, Athena will work correctly.* > > I think it's always been the case that you double-click near the point > to be removed, and hope that Athena does select the one you intended. > *This works perfect for rebinned data. * > > > I have one clarifications, when u choose the option to deglitch the data > > (rebinned or non rebinned data), does the x(E) data plot looks like in > the > > attached file (line) or it looks like sets of blue round points same > size as > > cursor. > > For me, it looks very much like the image you attached. I do not see > a series of dots. > > > I think, the issue is solved except that I cannot move the randomly > chosen > > point. > > Why can't you remove the point chosen? That seems like it's not > working to me. Wasn't that the problem you were having? > *I mentioned "MOVE" in my above sentence, (Just to be more specific, when I double click on the plot to choose a point, sometimes Athena select its own random points away from the point where I clicked, when I try to drag that randomly chosen cursor to the point of my interest, it will not work), IS THIS NORMAL? * *I will try to figure out all the possible ways for non-rebinned data, if it does not work at least for now rebinned data works.* *Regards* *Sathish* > Again, it may be that I'm not understanding. Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Mon, 16 Dec 2013 08:30:39 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Handling time resolved data > Message-ID: <52AF007F.4050600(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 12/13/2013 09:00 AM, Ditty Dixon wrote: > > Dear Bruce, > > > > Recenetly we did some time resolved measurements, QEXAFS mode. While > > the old Athena arranged the file as we want i.e file 1, 2, 3 etc, the > > new did it bit different 1, 11 12 and again 2, 21 etc. Screenshot > > attached. Why is it doing diffrently for the two version? Can it be > > fixed some how. > > You haven't explained exactly where these data come from, so I am > assuming that each scan was written to its own file and these files were > imported into Athena. > > In Athena, data are imported in "ascii-betical" order, that is, sorted > in order of characters in the ASCII chart: > > http://en.wikipedia.org/wiki/ASCII#ASCII_printable_characters > > In that sense, Athena sorted your data as expected. As Chris pointed > out, if you want things like > > nr_1.spec > nr_2.spec > ... > nr_10.spec > > to sort numerically by the number between the _ and the .spec, you need > to format the them so that numerical and ascii-ordered sorting come out > the same. This is done as > > nr_01.spec > nr_02.spec > ... > nr_10.spec > > For a quick exafs experiment, two digits is probably not enough, so > you'd want something like > > nr_00001.spec > nr_00002.spec > ... > nr_00010.spec > > > I don't recall quite how the sorting worked in the old version of Athena > (it has been over 5 years since I stopped working on it), but my vague > memory is that, on Windows, they were imported in the order that they > were clicked upon the file selection dialog. The way it is currently > done is much better in that it is reproducible. > > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science 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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 130, Issue 22 > **************************************** > -- Satty

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Handling time resolved data
by Ditty Dixon 16 Dec '13

16 Dec '13

Dear Bruce, Recenetly we did some time resolved measurements, QEXAFS mode. While the old Athena arranged the file as we want i.e file 1, 2, 3 etc, the new did it bit different 1, 11 12 and again 2, 21 etc. Screenshot attached. Why is it doing diffrently for the two version? Can it be fixed some how. Thank you, Ditty -- Ditty Dixon, Anorganische Chemie Karlsruhe Institute of Technology Kaiserstr 12 Karlsruhe, Germany Ph no: 004972160848093

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Re: [Ifeffit] Demeter deglitch problem
by Sathish Mayanna 15 Dec '13

15 Dec '13

Dear Matt and Bruce Thanks a lot for your help, I noticed your suggestions, regarding the deglitch problem, I installed the Demeter in another drive than in drive C. Now it seems working well except some minor things, I can remove the points from the data, the random point selection by software works better for rebinned data. I think the only problem I have now is I still cannot move the cursor after double click (I can only remove the points which the software decides - at least now it choose the points where I double click). When i move my mouse cursor on the plot, it shows the correct coordinates. I have one clarifications, when u choose the option to deglitch the data (rebinned or non rebinned data), does the x(E) data plot looks like in the attached file (line) or it looks like sets of blue round points same size as cursor. I think, the issue is solved except that I cannot move the randomly chosen point. Thanks a lot Sathish On Fri, Dec 13, 2013 at 5:10 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: Fwd: Re: Demeter deglitch problem (Matt Newville) > 2. Handling time resolved data (Ditty Dixon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 12 Dec 2013 13:20:05 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>, > Sathish Mayanna <satty334(a)gmail.com> > Subject: Re: [Ifeffit] Fwd: Re: Demeter deglitch problem > Message-ID: > <CA+7ESbpvTztp7Q8zTvShm8DO9yEjuo_2J6VuxtgnDWUNqk= > 1qQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Sathish, Bruce, > > On Thu, Dec 12, 2013 at 12:51 PM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > > Sathish, > > > > I'm sorry, Sathish, but I simply don't see this behavior, on any of > > the computers I have tried. > > > > I have no trouble putting the cursor on the point in question. It can > > be a little tricky getting the cursor on, for example, one of the > > points from 6750 to 6770. That is because of the details of the > > algorithm that tries to find the actual data point that is closest to > > whatever point was clicked on. For a data point that is not a distant > > outlier, pretty good aim is required. > > > > That said, the two points near 6864 are distant outliers. Hitting one > > and not the other might be hard, but hitting one of them is easy. > > > > I am not disputing that you are having trouble. I am just saying that > > given the data you sent and the explanation you gave, I cannot > > reproduce the behavior, so I don't know what I can do to help. > > I made what I thought were two concrete suggestions / observations to > Satish, > a) I do not see k space data, and think you probably shouldn't either. > b) If you just move the mouse around on the plot window, > do you see the correct coordinates? > > I am sure Satish read Bruce's instructions on reporting bugs, but it > would have been polite if he had followed them. He did not answer the > questions designed to help diagnose the problem. He did not respond > not to the list, but directly to Bruce. In fact, he asked Bruce if > anyone else had seen the problem! > > Satish, it would be very much appreciated if this conversation > remained on the mailing list. If a problem happens for you, it is > possible that it will happen (or has happened) for someone else. > You'll get much better help and be helping others if you use the > mailing list. > > --Matt > > > ------------------------------ > > Message: 2 > Date: Fri, 13 Dec 2013 15:00:11 +0100 > From: Ditty Dixon <ditty.dixon(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Handling time resolved data > Message-ID: > <CABPBYUcg8DSWDnvdiK= > j9nfORORjG9n0RMYm4pVsaq6sYQYa3w(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Bruce, > > Recenetly we did some time resolved measurements, QEXAFS mode. While the > old Athena arranged the file as we want i.e file 1, 2, 3 etc, the new did > it bit different 1, 11 12 and again 2, 21 etc. Screenshot attached. Why is > it doing diffrently for the two version? Can it be fixed some how. > > Thank you, > > Ditty > > > > -- > Ditty Dixon, > Anorganische Chemie > Karlsruhe Institute of Technology > Kaiserstr 12 > Karlsruhe, Germany > Ph no: 004972160848093 >

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Fwd: Re: Demeter deglitch problem
by Bruce Ravel 12 Dec '13

12 Dec '13

Sathish, I'm sorry, Sathish, but I simply don't see this behavior, on any of the computers I have tried. I have no trouble putting the cursor on the point in question. It can be a little tricky getting the cursor on, for example, one of the points from 6750 to 6770. That is because of the details of the algorithm that tries to find the actual data point that is closest to whatever point was clicked on. For a data point that is not a distant outlier, pretty good aim is required. That said, the two points near 6864 are distant outliers. Hitting one and not the other might be hard, but hitting one of them is easy. I am not disputing that you are having trouble. I am just saying that given the data you sent and the explanation you gave, I cannot reproduce the behavior, so I don't know what I can do to help. B -------- Original Message -------- Subject: Re: Demeter deglitch problem Date: Wed, 11 Dec 2013 14:59:09 +0100 From: Sathish Mayanna <satty334(a)gmail.com> To: Bruce Ravel <bravel(a)bnl.gov> Dear Bruce Thanks a lot for your time. I am sorry, I am a beginner in the field of XAS, thus was confused. Please find the attachment of one of my glitch data and an image showing the randomly chosen point at 6705 eV by software even though i double clicked at 6864 eV and in addition, I cannot move the position of randomly chosen point. I have tried both in my windows laptop and PC, it does not work in both cases. I hope this time I have provided the details you expected? Thanks Sathish On Tue, Dec 10, 2013 at 8:13 PM, Bruce Ravel <bravel(a)bnl.gov <mailto:bravel@bnl.gov>> wrote: On 12/10/2013 12:58 PM, Sathish Mayanna wrote: Dear Bruce I am sorry to contact you here, I watched your whole XAS workshop 2011 at Diamond, it was very helpful. Regarding the problem, I could not understand your message, I read the link to reports bug, I understand you cannot reproduce my problem also, I just wanted to know, if anybody had same problem like me and have any solutions. I am just wondering, does your message also means that I should send the rawdata or print screen? -- Sathish Look, I'm happy to help, but you have to give me something to work with. Obviously, I think deglitching works, otherwise I would have said something different. If you cannot give me some way of reproducing what you see on one my own computers, there is no way that I can help you. I'm not asking for a differently detailed explanation, I am asking for data and a recipe that reproduces the problem. Without that, what could I possibly do to help? B -- Bruce Ravel ------------------------------__------ bravel(a)bnl.gov <mailto:bravel@bnl.gov> National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel -- Satty

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error in ATOMS
by Julius Campecino 12 Dec '13

12 Dec '13

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

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Re: [Ifeffit] athena error message.....
by Bruce Ravel 10 Dec '13

10 Dec '13

On 11/30/2013 05:17 PM, William Nash wrote: > Heya Bruce, > > I'm trying to use Athena to process some XANES data from the Diamond > Synchrotron (UK). I went to the demeter webpage and downloaded/ran the > installer and the updater. However, when I try to run athena, I get an > error message: > > (Window Title: "perl.exe - Entry Point Not Found") > > The procedure entry point __gxx_personality_v0 could not be located in > the dynamic link library libstdc++-6.dll. > > Is this an error you are familiar with? I don't seem to be able to get > around it. It time permits, would you mind giving me some guidance. > > Grateful thanks, > William > First off, please use the Ifeffit mailing list http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ which is the proper place to ask questions about and report problems with the software. As you can see, I have CCed my response to you and to the mailing list. Please continue correspondence on this topic via the mailing list. The most likely source of this problem is the one discussed here http://cars9.uchicago.edu/ifeffit/Demeter/MingwFix that is, that you have another version of MinGW installed on your computer, either that you yourself installed or that was installed by another application. This fellow, for example, had installed GnuPG and this triggered a similar conflict to what you see. http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04031.html Another possible problem is that you have another version of perl itself installed on you computer, again possibly as part of the installation of another package. HTH B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Re: [Ifeffit] Ifeffit Digest, Vol 130, Issue 13
by Sathish Mayanna 10 Dec '13

10 Dec '13

Dear Matt and Bruce Thanks, I thought its a common problem, i will be more specific in this message. I am using windows 7, 64 bits and/or 32 bits Operating System, installed with updating 0.9.18.2 Demeter, its in the folder C:\strawberry. To deglitch the single point of EXAFS data using Athena, after CHOOSE A POINT option, when I double click on the plot of k space, it does choose a point randomly and I can remove that particular point, but unfortunately, I cannot move or select the point which I want to remove. It always choose a random point by its own. Do I miss something here ? Regards Sathish On Mon, Dec 9, 2013 at 8:49 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. Athena 0.9.18.2 deglitch option (Sathish Mayanna) > 2. Re: Athena 0.9.18.2 deglitch option (Bruce Ravel) > 3. Re: Athena 0.9.18.2 deglitch option (Matt Newville) > 4. Re: Itinerant vs localized XAFS (Latta, Drew E.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Dec 2013 19:24:33 +0100 > From: Sathish Mayanna <satty334(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Athena 0.9.18.2 deglitch option > Message-ID: > <CABVfawmnabGT= > S+iEwy-1bv0f6jSLRQc9gga+hSg0KjmaE5Cdg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all > > I wondering, if anyone has problem with the option deglitch in Athena > especially for 32 or 64 bits Windows system? > > Would be really great, if anyone could help me to solve the problem, I have > a EXAFS data with huge glitch and the software do not choose/remove the > points and sometimes it crashes. > > Regards > Sathish >

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Artemis path like function crashing
by stephen.price＠diamond.ac.uk 10 Dec '13

10 Dec '13

Hi, I'm writing to report a crash of the path like function of Artemis, version 0.9.18 on Windows 7, 64 bit (the same thing also happened on my old windows XP machine). I have followed the procedure below several times on both machines and get the same result: · Load processed data from Athena of Pt nanoparticle, load and run Pt.inp in ATOMS (from atomsdb), run FEFF - click on path like tab · Make histograms from molecular dynamics time sequence - in this case from DL_POLY · Load HISTORY file from molecular dynamics - specify Rmin (e.g. 2.4 Å) Rmax (3.0) and bin size (0.005) · Plot RDF - in this case it loads in 503 time steps in increments of 10 and plots RDF after about 1 minute · I click on "Drag SS path from here" and drag to the path list - the message "making Fpaths n of 66" appears at the bottom of the window · As it is rebinning the last Fpath Artemis crashes with the log error "Can't locate object method "pathfinder_index" via package "Demeter::FPath" at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Path.pm line 254, <F> line 9" (dartemis.log attachment) · The final line mentioned in the dartemis.log sometimes varies e.g. <F> line 133 or <F> line 177 · This crash is independent of the Athena project, simulation HISTORY file (whether a 10 MB or a 100 MB file), choice of Rmin/max and bin size I can run a simple first/multi shell fit on the Pt nanoparticle, save and reopen the project (Pt test.fpj) but cannot save and reopen a project during any stage of the path like process as this crashes Artemis ("create RDF dartemis.log" and "Pt create RDF.fpj" attachments). I haven't attached a sample MD simulation file here as I don't want to fill everyone's inbox! Any help would be appreciated. Thank you, Steve Dr Stephen Price PDRA Beamline I18 Diamond Light Source -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Itinerant vs localized XAFS
by Maurits Boeije 09 Dec '13

09 Dec '13

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

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Athena 0.9.18.2 deglitch option
by Sathish Mayanna 09 Dec '13

09 Dec '13

Dear all I wondering, if anyone has problem with the option deglitch in Athena especially for 32 or 64 bits Windows system? Would be really great, if anyone could help me to solve the problem, I have a EXAFS data with huge glitch and the software do not choose/remove the points and sometimes it crashes. Regards Sathish

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problem running (D)Artemis on non-unicode machine
by Andrei Shiryaev 09 Dec '13

09 Dec '13

Dear colleagues, Again I have problems running (D)Artemis on two Win7 and on Win XP machines with non-unicode names. I've raised the issue in September and Matt Newville suggested some recipe (see IFEFFIT mailing list on Sept 6). The suggested solution was the following: ======= Edit the file C:/strawberry/perl/site/lib/Demeter/UI/Artemis.pm so that, near the top it reads: use Archive::Zip qw( :ERROR_CODES :CONSTANTS ); $Archive::Zip::UNICODE = 1; ======= The solution was great in the sense that DEMETER at least starts (it was not the case before). However, when I try to fit anything imported from old or new Athena (importing old style Artemis project does not work, this was apparently already reported to the list) I am getting the following error message (also see attached screenshot): ======= error writing zip-style project at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 104 Demeter::UI::Artemis::Project::save_project('HASH(0xaf38efc)', C:/Documents and setting/ NON-UNICODE NAME.......... ========== I would be grateful if an idea how to solve this obstacle. All the best, Andrei Shiryaev PS In the example above DArtemis is installed on D:, but standard installation on C: gives exactly the same result.

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Fe2(MoO4)3 and FeMoO4
by Anatoly I Frenkel 06 Dec '13

06 Dec '13

Dear IFEFFIT users, If anyone has Fe K-edge spectra of Fe2(MoO4)3 and/or FeMoO4, and could email me the raw data, it will be gratefully acknowledged! Thank you very much, Anatoly Frenkel

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Re: [Ifeffit] fitting a specific k range
by fred.mosselmans＠diamond.ac.uk 06 Dec '13

06 Dec '13

What I find reassuring about Bruce's warnings is they allow you to think properly about what you are doing. Fortunately, unlike Chris, I am not of a size where I have to worry about falling down rabbit holes, unless American rabbits are much bigger than English ones. I would commend Matt's original question as it opened a debate with 3 of the mainstays of the list. That may not have been the intention but it makes interesting reading for us mailing list voyeurs. Cheers Fred Sent from Samsung tablet

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fitting a specific k range
by Matt Frith 05 Dec '13

05 Dec '13

Dear All, I need some help in fitting an amorphous iron oxyhydoxide sample. I am having difficulty producing a good fit, particularly in the k=4-6 range. Fitting this region well is very important for me, because if I add another metal(+3 oxidation state) into my system, this is where I observe the most quantifiable changes (The shoulder @ 5 A^-1 and the min @ 5.6 A^-1). Thus far I have been unable to fit the shoulder well enough to make meaningful comparisons. I have been fitting in kq with kmin=2.566 And kmax=10.877, and Rmin=1 and Rmax=3.5, and using the goethite O1.1, Fe.1, and Fe.3 paths. Attached is an Artemis file (P41_006_merge_norm_TRANS.fpj) for an amorphous Fe oxyhydroxide sample (Fe only, no other metals). The data was collected at the Fe K-edge. *Is there a way to fit just this region (k~4-6 range) in k? If so what is the best method for doing this? If not, does anyone have suggestions as to how I can improve my fitting? Should I fit the data in k since the shoulder is less evident in kq?* Thank you for your time. Sincerely, Matt Frith

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Er2O3 standard spectra
by Carlo Segre 04 Dec '13

04 Dec '13

Hello All: Does anyone have a reference spectrum of Er2O3? I have one but I am a bit concerned about the resolution and wish to compare. Thanks, Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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