[Ifeffit] determining reasonable fitting parameters

Wed Jul 27 14:53:32 CDT 2016

Thanks to everyone for all the previous responses to my emails, I've learned a lot in the few weeks I've been on this list! I was hoping to build off of the last point Bruce made in message 3 below by asking another question. I am fitting a CeO2 reference from paths generated by feff from a cif file. Since this is my starting point, I made SO2 the same for every path (and used the coordination numbers from the cif file). If I am generating what looks to be a reasonable fit, but my SO2 is in the 0.55-0.7 range, what is my fit trying to tell me? Am I doing something wrong in my initial background subtraction in Athena? 

I'm asking about the background subtraction because I recently discovered that there is a CeO2 reference provided in Hephaestus. I exported the data, and tried to fit it in Artemis using a similar methodology I used for my own sample, and I got an even lower SO2. So I don't think the small SO2 value is an artifact of the way the experiment was run (although I might be wrong, I wasn't present when the data was actually collected). The observed difference seems real because the magnitude of the signal in E-space, k-space, and R-space is lower for the Hephaestus sample compared to my experimental sample (see attached image... One note, I'm not sure why the signals are off set in the Energy plot. The Eo's are the same, and if I plot the spectra together in E-space alone, they are not offset. Maybe a bug?).

Neil

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Today's Topics:

   1. demeter installation in OSX El Capitan (Ping, Yuan)
   2. Re: determining reasonable fitting parameters (Bruce Ravel)
   3. Re: determining reasonable fitting parameters (Bruce Ravel)

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Message: 1
Date: Thu, 21 Jul 2016 05:37:10 +0000
From: "Ping, Yuan" <ping2 at llnl.gov>
To: "ifeffit at millenia.cars.aps.anl.gov"
	<ifeffit at millenia.cars.aps.anl.gov>
Subject: [Ifeffit] demeter installation in OSX El Capitan
Message-ID: <D3B5AD95.32BB2%ping2 at llnl.gov>
Content-Type: text/plain; charset="windows-1252"

Dear all,

I recently upgraded my mac to OSX El Capitan, and tried to install demeter following the steps at https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_demeter_&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=TCGdaYbJi7BT0F219p-mQqfSXpTu8VnSiBucuiAZxys&s=mJOf0GYWlZWRx9RR_r6Zd26d1gRzqee0VqmVe98TnjY&e= 

XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, ?sudo port -v self update?, ?port upgrade outdated? were all OK. When I tried ?sudo port install xorg-server demeter?, it showed:

--->  Computing dependencies for xorg-server

--->  Cleaning xorg-server

--->  Computing dependencies for demeter

--->  Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 
---> libcxx libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr 
---> pgplot gcc5 ... (a long list)

Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from various websites, it showed:

Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0

Error: Failed to install libcxx

Please see the log file for port libcxx for details:

   /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log

The log file is attached. What should I do to fix it? Any suggestion will be appreciated.

Thanks.
Yuan

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Message: 2
Date: Thu, 21 Jul 2016 08:38:40 -0400
From: Bruce Ravel <bravel at bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] determining reasonable fitting parameters
Message-ID: <59966720-fd90-d550-c717-9a91be236cd3 at bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 07/20/2016 06:59 PM, Neil M Schweitzer wrote:
> I found a bug in the log files in the history window. I am running 
> Demeter 0.9.21 on Windows 7. When I generate a new fit, if I change 
> the k-range of the fit, the k-range of previous fits in the history 
> window will also change to the current range (e.g. fit 19 was run from 
> 2.1-9.3, as shown in the data window. Fits 14-16 were run in smaller ranges).
> What?s even stranger, is if I go to a very old fit (i.e. fit 1 or 2 in 
> the project file) and then go back to the new fit, the log file will 
> report the k-range from the earlier fit, not the current fit. 
> Obviously, this is making it very difficult to keep track of fits 
> generated with different k-ranges. I have not tested to see if the 
> R-range behaves similarly.

Neil,

Thanks for reporting this.  The fit history mechanism is probably not one of the better tested parts of Artemis.  I'll look into it soon.

B

--
  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 743, Room 114
  Upton NY, 11973

  Homepage:    https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_home_&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=TCGdaYbJi7BT0F219p-mQqfSXpTu8VnSiBucuiAZxys&s=4932i4H5TyQaTp92YWNv9uj1eFsqVUgsgIOT0xU-K38&e= 
  Software:    https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bruceravel&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=TCGdaYbJi7BT0F219p-mQqfSXpTu8VnSiBucuiAZxys&s=_V-rZFwFbeDoCcnivvDWN7TB-NhKpoK-mpoe7whs0Rs&e= 
  Demeter:     https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_demeter_&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=TCGdaYbJi7BT0F219p-mQqfSXpTu8VnSiBucuiAZxys&s=mJOf0GYWlZWRx9RR_r6Zd26d1gRzqee0VqmVe98TnjY&e= 

------------------------------

Message: 3
Date: Thu, 21 Jul 2016 09:00:21 -0400
From: Bruce Ravel <bravel at bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] determining reasonable fitting parameters
Message-ID: <613fc1c2-eb51-1676-a0d5-f054ecfcccf7 at bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 07/20/2016 06:59 PM, Neil M Schweitzer wrote:
> In terms of the DWF?s in general, what value is considered too high? I 
> know the DWF?s have a component that relates to temperature induced 
> disorder in the scattering shell and a component that relates to 
> physical disorder in the scattering shell, but what value would be 
> considered too big for a sample measured at room temperature. I have 
> seen values as high as 0.03 and 0.04 in presentations (sorry, no
> references) but these seems too large to me. At some point, if the 
> sample is disordered enough, it seems like EXAFS is no longer an 
> appropriate characterization tool to use. What value of DWF would that 
> represent (for a sample measured at room temperature)?

This one is a bit easier than your first question, so I'll take a stab as I am drinking my morning coffee.

As you have certainly noticed, defensible sigma^2 values tend to be 0.00something.  Values for sigma^2 that are 0.0something tend to be very unrobust parameters in the sense that they cause so much attenuation that they more-or-less serve to remove the scattering path from the fit. 
  It is likely that the uncertainty will be similarly large in a fit like that.

One point I often try to get across when answering questions here is that often things that are presented as problems are actually useful information.  That is, a sigma^2 of 0.0something is trying to tell you that the Fourier components represented by the path are not represented (or represented very weakly) in the actual data.  A big sigma^2 is Artemis' way of suggesting one of your assumptions about the structural model might not be quite right.

In that case, it is likely that the fit will not change -- and might improve by virtue of reducing the count of guess parameters by one -- if you remove the path and remove the parameter.

To look at it another way: a result of "it's too disordered to measure" 
*is* a result.  It may not be quantitative.  It may not be what the boss is looking for.  But it's honest and it is a result.

HTH,
B

--
  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 743, Room 114
  Upton NY, 11973

  Homepage:    https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_home_&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=TCGdaYbJi7BT0F219p-mQqfSXpTu8VnSiBucuiAZxys&s=4932i4H5TyQaTp92YWNv9uj1eFsqVUgsgIOT0xU-K38&e= 
  Software:    https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bruceravel&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=TCGdaYbJi7BT0F219p-mQqfSXpTu8VnSiBucuiAZxys&s=_V-rZFwFbeDoCcnivvDWN7TB-NhKpoK-mpoe7whs0Rs&e= 
  Demeter:     https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_demeter_&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=TCGdaYbJi7BT0F219p-mQqfSXpTu8VnSiBucuiAZxys&s=mJOf0GYWlZWRx9RR_r6Zd26d1gRzqee0VqmVe98TnjY&e= 

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