[Ifeffit] correlating number of nearest neighborst to the particle size

Thu Jan 9 12:11:41 CST 2014

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 at 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 at millenia.cars.aps.anl.gov [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request at millenia.cars.aps.anl.gov
> Sent: 09 January, 2014 17:51
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> 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 <L.Clarke at mmu.ac.uk>
> To: "ifeffit at millenia.cars.aps.anl.gov"
>        <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] Query re: Athena and Artemis user guides
> Message-ID: <83CF3E8AA2102C4598B316168B472EFE98BEEECD at 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 at mmu.ac.uk<mailto:l.clarke at 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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> ------------------------------
>
> Message: 2
> Date: Thu, 09 Jan 2014 11:23:13 -0500
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Query re: Athena and Artemis user guides
> Message-ID: <52CECCF1.3050502 at 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 at 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 at kit.edu>
> To: "'XAFS Analysis using Ifeffit'"
>        <ifeffit at millenia.cars.aps.anl.gov>
> 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 at millenia.cars.aps.anl.gov
> [mailto:ifeffit-bounces at 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 at 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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>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 9 Jan 2014 16:47:41 +0000
> From: "Schima, Frank" <frank.schima at nist.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Demeter 0.9.19
> Message-ID: <DFAFEE64-6489-4E27-91B4-14CF762FADCD at nist.gov>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi all,
>
> On Jan 9, 2014, at 8:26 AM, Matt Newville <newville at cars.uchicago.edu<mailto:newville at cars.uchicago.edu>> wrote:
>
> On Thu, Jan 9, 2014 at 8:04 AM, Bruce Ravel <bravel at bnl.gov<mailto:bravel at 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/Portfile>
> [3] <https://trac.macports.org/browser/trunk/dports/perl/p5-ifeffit/Portfile>
> [4] <http://www.macports.org/install.php>
> [5] <https://trac.macports.org/browser/trunk/dports/perl/p5-wx/Portfile>
>
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