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@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 09 January, 2014 19:18 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 10 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@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 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] correlating number of nearest neighborst to the particle size Message-ID: 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 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@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 09 January, 2014 17:51 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 8

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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 To: "ifeffit@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@mmu.ac.ukmailto:l.clarke@mmu.ac.uk WWW: http://www.sste.mmu.ac.uk/ Tel: +44 (0)161 247 1412

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Message: 2 Date: Thu, 09 Jan 2014 11:23:13 -0500 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Query re: Athena and Artemis user guides Message-ID: <52CECCF1.3050502@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@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 To: "'XAFS Analysis using Ifeffit'" Subject: Re: [Ifeffit] Query re: Athena and Artemis user guides Message-ID: <001801cf0d58$a1499170$e3dcb450$@kit.edu> Content-Type: text/plain; charset="us-ascii"

Thanks a lot for the pdf version.

-----Original Message----- From: ifeffit-bounces@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@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Message: 4 Date: Thu, 9 Jan 2014 16:47:41 +0000 From: "Schima, Frank" To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Demeter 0.9.19 Message-ID: Content-Type: text/plain; charset="windows-1252"

Hi all,

On Jan 9, 2014, at 8:26 AM, Matt Newville mailto:newville@cars.uchicago.edu> wrote:

On Thu, Jan 9, 2014 at 8:04 AM, Bruce Ravel 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

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------------------------------ Message: 2 Date: Thu, 9 Jan 2014 18:16:37 +0000 From: Anatoly I Frenkel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] correlating number of nearest neighborst to the particle size Message-ID: <545F89325F51764C902D37B42C9F4D538EC6E017@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@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Rana, Jatinkumar Kantilal [jatinkumar.rana@helmholtz-berlin.de] Sent: Thursday, January 09, 2014 12:55 PM To: ifeffit@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@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 09 January, 2014 17:51 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 8 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@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 To: "ifeffit@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@mmu.ac.ukmailto: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 "