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

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 "

1 0

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 "

3 2

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 "

3 2

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

1 0

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

3 2

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

1 0

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

1 0

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

1 0

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 >

1 0

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

2 1