Matt Newville | 23 May 22:44 2016
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Re: Question about H scattering

Hi Riti,


On Mon, May 23, 2016 at 1:50 PM, Ritimukta Sarangi <ritimukta-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hi Matt,
I have a question about FEFF and I hope you can shed some light on it. Several references point to the high muffin tin radius of H (0.77) in FEFF and say that it should be closer to 0.2. Is there a way of changing the MT radius of H in FEFF?
Thank you,
-Riti

I'm CCing this to the Ifeffit mailing list, because there are probably many people with more experience with this than me. 

I believe there is not a simple way to set the muffin tin radius for H or other atoms.  But, I think you can tweak this with the "FOLP" setting (usually a number between 1 and 1.25 or so, representing the amount of overlap between atoms).

My understanding is that Feff 9 handles hydrogen better than earlier versions, but I don't run very many calculations with H in the structures.  Hopefully someone who does will share some insight.

--Matt
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N independent variables

Dear list,

I made an EXAFS analysis in Artemis (in Demeter 0.9.22) using all the available variables. This is a fragment of the .log file I got:

Independent points          : 17.7666016
Number of variables         : 17
Chi-square                  : 265.0947132
Reduced chi-square          : 345.8050781                                       
R-factor                    : 0.0026486                                         
Number of data sets         : 1
: k-range               = 2.942 - 11.043
: dk                    = 1
: k-window              = hanning
: k-weight              = 1,2,3
: R-range               = 1.115 - 3.5
: dR                    = 0.0
: R-window              = hanning
: fitting space         = r
: background function   = yes
: phase correction      = no
: background removal    = E0: 20002.215, Rbkg: 1.0, range: [2.25:17.4039986832903], clamps: 0/24, kw: 2
: epsilon_k by k-weight = 3.189e-004
: epsilon_r by k-weight = 2.339e-001
: R-factor by k-weight  = 1 -> 0.00220,  2 -> 0.00224,  3 -> 0.00392

The problem is that when I use the Nyquist criterion 

Nind=2*deltak*deltar/pi + 1

for calculating the number of independent points the value I got is much lower and close to 13.

I was not aware of this discrepancy and it caused a reviewer to think I made up the fit!


Am I doing something wrong?
Is there another way to calculate the Nind that might have been used by Artemis?

I would really appreciate any help.

Yours

Jesús



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Consultation on Reduced Chi2

Dear list,

I am back with a new consultation on EXAFS fitting within Artemis.

I have made a fit and obtained a reduced Chi2 value of 391 and R-factor of 0.014 using 9 variables. Then I have added two more paths increasing the number of variables up to 12 and then I obtained a reduced Chi2 of 3039 and R-factor of 0.007.

I am a little surprised by the huge increase of reduced Chi2 while R-factor decreases down to half. 

What could be the cause of this large increase? 
Does it mean that it is not worth to add these new paths?

As always, thank you in advance

Yours,

Jesús





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Patel, Sunil | 16 May 11:54 2016
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Bug report ATHENA (Demeter 0.9.24)

Hello All,

I am using the latest version of Demeter (0.9.24) in Windows 7 Enterprise (64-bit).

In the process of doing LCF, the fit details (for ex. standards used for fitting, fitting range, phase fractions etc.) are not saved into the project file. This (very useful!) feature was available in the older version of ATHENA.

 

Please find attached a project file. To reproduce the problem:

  1. Open the project file in new ATHENA.

  2. Do LCF for marked datasets (Data_1 to Data_6) using standards (Standard_1 and Standard_2), with LCF range= -20 to 40 eV and hitting the “Fit marked groups” tab.

  3. Save the project file and close it.

  4. Re-open the file and go to the LCF page. The details are not saved. We need to re-do the fits to get the values.

  5. To check, open the ATHENA project file in older version of ATHENA and repeat the above steps. LCF details are shown on re-opening the file.

A similar bug report was made last year for an earlier version of Demeter (0.9.21).

(http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05057.html )

 

Thanks & regards,

Sunil Patel

 

Attachment (Bug Report_ATHENA_Demeter (0.9.24).prj): application/octet-stream, 188 KiB
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Christopher Thomas Chantler | 15 May 01:37 2016
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Re: Ifeffit Digest, Vol 159, Issue 5

Hi All

Most of them can be downloaded from either here

https://www.researchgate.net/profile/Christopher_Chantler/

or here

www.ph.unimelb.edu.au/~chantler/opticshome/papers.html

------------------------------------------------------------
Christopher Chantler, Professor, FAIP
Editor-in-Chief, Radiation Physics and Chemistry
Chair, International IUCr Commission on XAFS
President, International Radiation Physics Society
School of Physics, University of Melbourne
Parkville Victoria 3010 Australia
+61-3-83445437 FAX +61-3-93474783
chantler@... chantler@...
http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html
http://optics.ph.unimelb.edu.au/~chantler/home.html

________________________________________
From: Ifeffit [ifeffit-bounces@...]
on behalf of ifeffit-request@... [ifeffit-request@...]
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Today's Topics:

   1. Re: Ifeffit Digest, Vol 159, Issue 4 (Matteo Busi)

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

Message: 1
Date: Sun, 15 May 2016 01:20:03 +0200
From: Matteo Busi <basebush@...>
To: "ifeffit@..."
        <ifeffit@...>
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 159, Issue 4
Message-ID:
        <CAOyEiGgk5fqRzAoDAFTNibp_bctK=81Cp2+C4r-1T8v9+FyTbQ@...>
Content-Type: text/plain; charset="utf-8"

Dear Chris,
I would be glad to at least read the papers you mentioned. If it possible
you can send them here or at my email basebush@... when you have time.

Regards,
Matteo

Den l?rdag 14. mai 2016 skrev <ifeffit-request@...>
f?lgende:

> Send Ifeffit mailing list submissions to
>         ifeffit@... <javascript:;>
>
> 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
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>
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>         ifeffit-owner@... <javascript:;>
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ifeffit digest..."
>
>
> Today's Topics:
>
>    1. Re: Ifeffit Digest, Vol 159, Issue 3 (Christopher Thomas Chantler)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 13 May 2016 21:43:34 +0000
> From: Christopher Thomas Chantler <chantler@... <javascript:;>>
> To: "ifeffit@... <javascript:;>"
>         <ifeffit@... <javascript:;>>
> Cc: Christopher Thomas Chantler <chantler@... <javascript:;>>
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 159, Issue 3
> Message-ID:
>         <
> 1C86B7F795364B44940B1EAAB9D774FADEE724BE@...
> <javascript:;>>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear All, Matteo
>
> It is difficult to do post facto, but if you have a well-defined solid,
> foil or crystal then mapping the thickness, measuring the mass and hence
> determining the mass per unit area, for the exact region illuminated by the
> beam, provides accurate units. Usually you will need to make a measurement
> of the average m/A from (i) total mass and (ii) total area, and then (iii)
> map the whole sample with X-ray tomography and (iv) the region illuminated
> by the X-ray beam.
>
> We have a series of papers which explain more than one methodology for
> doing that within the XERT technique. If your sample is a solution it is a
> bit more tricky, and I would refer you to recent JSR and JPCC papers for
> our Hybrid technique. Both can work well but need a bit more care than a
> normal XAFS measurement.
>
> Best wishes
> Chris
> ------------------------------------------------------------
> Christopher Chantler, Professor, FAIP
> Editor-in-Chief, Radiation Physics and Chemistry
> Chair, International IUCr Commission on XAFS
> President, International Radiation Physics Society
> School of Physics, University of Melbourne
> Parkville Victoria 3010 Australia
> +61-3-83445437 FAX +61-3-93474783
> chantler@... <javascript:;>
chantler@... <javascript:;>
> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html
> http://optics.ph.unimelb.edu.au/~chantler/home.html
>
>
> ________________________________________
> From: Ifeffit [ifeffit-bounces@... <javascript:;>]
> on behalf of ifeffit-request@...
<javascript:;> [
> ifeffit-request@... <javascript:;>]
> Sent: Saturday, 14 May 2016 3:00 AM
> To: ifeffit@... <javascript:;>
> Subject: Ifeffit Digest, Vol 159, Issue 3
>
> Send Ifeffit mailing list submissions to
>         ifeffit@... <javascript:;>
>
> 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@... <javascript:;>
>
> You can reach the person managing the list at
>         ifeffit-owner@... <javascript:;>
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ifeffit digest..."
>
>
> Today's Topics:
>
>    1. How to assign measure unit to XAFS data (Matteo Busi)
>    2. Re: How to assign measure unit to XAFS data (Alexey Boubnov)
>    3. Re: How to assign measure unit to XAFS data (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 13 May 2016 02:11:39 +0200
> From: Matteo Busi <basebush@... <javascript:;>>
> To: ifeffit@... <javascript:;>
> Subject: [Ifeffit] How to assign measure unit to XAFS data
> Message-ID:
>         <CAOyEiGg1N7wL-tnzPXFBCrUYQD=6=
> bvsRFnDNEe3ZaCeguFU5Q@... <javascript:;>>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Bruce, Matt, and  mailing list readers,
>
> I have one question regarding the XAFS data. I have collected absorption
> coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however
> my question can be generalized to any compound).
> Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k) and
> \chi(R). I am wondering how can I assign a unit to the x\mu values. I would
> like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it with
> tabulated data for the Copper absorption coefficient and proceed with my
> studies.
>
> In case a treatment is needed for the normalized \mu , that would also suit
> my situation.
>
> My idea was to divide by the thickness of the sample but I don't find a
> reasonable justificiation for this.
>
> I really hope I made the question clear to any reader this time, and if
> that is not the case I apologyze in advance.
>
> Best Regards
> Matteo
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20160513/ce7b5ce8/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Fri, 13 May 2016 08:29:15 +0200
> From: Alexey Boubnov <alexeyboubnov@... <javascript:;>>
> To: XAFS Analysis using Ifeffit <ifeffit@...
> <javascript:;>>
> Subject: Re: [Ifeffit] How to assign measure unit to XAFS data
> Message-ID:
>         <
> CAJZPK0VrRQ2Ad-Mxr2q4kdZorjdT_ceaVroPO3m57LYuS_CiAg@...
> <javascript:;>>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Matteo,
>
> ?x that you measured is dimensionless: x in the thickness (in cm) and ? the
> Absorption coeffiecient (per cm). Indeed, if you want to know the
> Absorption coefficient ? of your sample, you should divide ?x by x.
>
> All the best,
> Alexey
>
> 2016-05-13 2:11 GMT+02:00 Matteo Busi <basebush@... <javascript:;>>:
>
> > Hi Bruce, Matt, and  mailing list readers,
> >
> > I have one question regarding the XAFS data. I have collected absorption
> > coefficient in fluorescence regime of a CuSO4 penta hydrate
> sample(however
> > my question can be generalized to any compound).
> > Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k)
> and
> > \chi(R). I am wondering how can I assign a unit to the x\mu values. I
> would
> > like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it
> with
> > tabulated data for the Copper absorption coefficient and proceed with my
> > studies.
> >
> > In case a treatment is needed for the normalized \mu , that would also
> > suit my situation.
> >
> > My idea was to divide by the thickness of the sample but I don't find a
> > reasonable justificiation for this.
> >
> > I really hope I made the question clear to any reader this time, and if
> > that is not the case I apologyze in advance.
> >
> > Best Regards
> > Matteo
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit@... <javascript:;>
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
> >
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20160513/e09233a7/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 3
> Date: Fri, 13 May 2016 07:13:08 -0500
> From: Matt Newville <newville@... <javascript:;>>
> To: XAFS Analysis using Ifeffit <ifeffit@...
> <javascript:;>>
> Subject: Re: [Ifeffit] How to assign measure unit to XAFS data
> Message-ID:
>         <
> CA+7ESbq84ZpYx9DvP8JvM7yNzO0U31jFCZZ-_X43b21sM43+og@...
> <javascript:;>>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Matteo,
>
>
> On Thu, May 12, 2016 at 7:11 PM, Matteo Busi <basebush@...
> <javascript:;>> wrote:
>
> > Hi Bruce, Matt, and  mailing list readers,
> >
> > I have one question regarding the XAFS data. I have collected absorption
> > coefficient in fluorescence regime of a CuSO4 penta hydrate
> sample(however
> > my question can be generalized to any compound).
> > Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k)
> and
> > \chi(R). I am wondering how can I assign a unit to the x\mu values. I
> would
> > like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it
> with
> > tabulated data for the Copper absorption coefficient and proceed with my
> > studies.
> >
>
>
> The analysis tools treat "xmu" as a dimensionless value.   To get values
> for the mu in cm^-1 or grm/cm^2, you'll have to convert the measured values
> used for XAFS analysis (say, readings from ion chambers) into actual X-ray
> intensities, and try to account for anything else in the beam path that
> will attenuate the X-rays.  For measurements made in transmission, this can
> be done.   In fact, for most transmission measurements, the *change* in
> -ln(I0 / I1) is usually a very good measure of the change in absorption of
> the sample, so that if the observed jump is a value of 2, the sample really
> did change its absorption by Delta_xmu = 2.    But the absolute values for
> xmu are definitely not in meaningful units.  Typically, the photo-current
> from the ion chamber or diode is converted to a voltage and then summed
> over some time period in a data acquisition system.   You'd have to know
> the details of that system to convert the "I0" and "I1" numbers into actual
> beam intensities.
>
> For fluorescence measurements, the situation is worse. You'd need a very
> good measure of the solid angle of your detector, fluorescence efficiency,
> and the attenuation of the fluorescence getting from the sample to the
> detector.  Depending on the detector type, you'd also need a good
> assessment of the backgrounds.   It's probably not impossible, but I think
> it would not be easy unless that was the actual point of the experiment and
> you made many careful measurements of the detection system.    If you're
> asking this question here, you'd didn't make those measurements.
>
>
>
> >
> > In case a treatment is needed for the normalized \mu , that would also
> > suit my situation.
> >
> > My idea was to divide by the thickness of the sample but I don't find a
> > reasonable justificiation for this.
> >
>
>
> If you're measuring in fluorescence, dividing by the thickness of the
> sample is not what you want.
>
>
> >
> > I really hope I made the question clear to any reader this time, and if
> > that is not the case I apologyze in advance.
> >
> >
>
> Cheers,
>
> --Matt
> -------------- next part --------------
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> Subject: Digest Footer
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> ------------------------------
>
> End of Ifeffit Digest, Vol 159, Issue 3
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>
>
> ------------------------------
>
> Subject: Digest Footer
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Matteo Busi | 15 May 01:20 2016
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Re: Ifeffit Digest, Vol 159, Issue 4

Dear Chris, 

I would be glad to at least read the papers you mentioned. If it possible you can send them here or at my email basebush-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org when you have time.

Regards,
Matteo

Den lørdag 14. mai 2016 skrev <ifeffit-request-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org> følgende:
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Today's Topics:

   1. Re: Ifeffit Digest, Vol 159, Issue 3 (Christopher Thomas Chantler)


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

Message: 1
Date: Fri, 13 May 2016 21:43:34 +0000
From: Christopher Thomas Chantler <chantler <at> unimelb.edu.au>
To: "ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa@public.gmane.orgv"
        <ifeffit <at> millenia.cars.aps.anl.gov>
Cc: Christopher Thomas Chantler <chantler <at> unimelb.edu.au>
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 159, Issue 3
Message-ID:
        <1C86B7F795364B44940B1EAAB9D774FADEE724BE <at> 000s-ex-mbx-qs1.unimelb.edu.au>

Content-Type: text/plain; charset="us-ascii"

Dear All, Matteo

It is difficult to do post facto, but if you have a well-defined solid, foil or crystal then mapping the thickness, measuring the mass and hence determining the mass per unit area, for the exact region illuminated by the beam, provides accurate units. Usually you will need to make a measurement of the average m/A from (i) total mass and (ii) total area, and then (iii) map the whole sample with X-ray tomography and (iv) the region illuminated by the X-ray beam.

We have a series of papers which explain more than one methodology for doing that within the XERT technique. If your sample is a solution it is a bit more tricky, and I would refer you to recent JSR and JPCC papers for our Hybrid technique. Both can work well but need a bit more care than a normal XAFS measurement.

Best wishes
Chris
------------------------------------------------------------
Christopher Chantler, Professor, FAIP
Editor-in-Chief, Radiation Physics and Chemistry
Chair, International IUCr Commission on XAFS
President, International Radiation Physics Society
School of Physics, University of Melbourne
Parkville Victoria 3010 Australia
+61-3-83445437 FAX +61-3-93474783
chantler-keaFvQtjc6i7NGdpmJTKYQ@public.gmane.org chantler-BUHhN+a2lJ4@public.gmane.org
http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html
http://optics.ph.unimelb.edu.au/~chantler/home.html


________________________________________
From: Ifeffit [ifeffit-bounces <at> millenia.cars.aps.anl.gov] on behalf of ifeffit-request-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org [ifeffit-request-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org]
Sent: Saturday, 14 May 2016 3:00 AM
To: ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org
Subject: Ifeffit Digest, Vol 159, Issue 3

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Today's Topics:

   1. How to assign measure unit to XAFS data (Matteo Busi)
   2. Re: How to assign measure unit to XAFS data (Alexey Boubnov)
   3. Re: How to assign measure unit to XAFS data (Matt Newville)


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

Message: 1
Date: Fri, 13 May 2016 02:11:39 +0200
From: Matteo Busi <basebush-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
To: ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org
Subject: [Ifeffit] How to assign measure unit to XAFS data
Message-ID:
        <CAOyEiGg1N7wL-tnzPXFBCrUYQD=6=bvsRFnDNEe3ZaCeguFU5Q-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
Content-Type: text/plain; charset="utf-8"

Hi Bruce, Matt, and  mailing list readers,

I have one question regarding the XAFS data. I have collected absorption
coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however
my question can be generalized to any compound).
Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k) and
\chi(R). I am wondering how can I assign a unit to the x\mu values. I would
like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it with
tabulated data for the Copper absorption coefficient and proceed with my
studies.

In case a treatment is needed for the normalized \mu , that would also suit
my situation.

My idea was to divide by the thickness of the sample but I don't find a
reasonable justificiation for this.

I really hope I made the question clear to any reader this time, and if
that is not the case I apologyze in advance.

Best Regards
Matteo
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Message: 2
Date: Fri, 13 May 2016 08:29:15 +0200
From: Alexey Boubnov <alexeyboubnov-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
To: XAFS Analysis using Ifeffit <ifeffit <at> millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] How to assign measure unit to XAFS data
Message-ID:
        <CAJZPK0VrRQ2Ad-Mxr2q4kdZorjdT_ceaVroPO3m57LYuS_CiAg <at> mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Matteo,

?x that you measured is dimensionless: x in the thickness (in cm) and ? the
Absorption coeffiecient (per cm). Indeed, if you want to know the
Absorption coefficient ? of your sample, you should divide ?x by x.

All the best,
Alexey

2016-05-13 2:11 GMT+02:00 Matteo Busi <basebush <at> gmail.com>:

> Hi Bruce, Matt, and  mailing list readers,
>
> I have one question regarding the XAFS data. I have collected absorption
> coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however
> my question can be generalized to any compound).
> Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k) and
> \chi(R). I am wondering how can I assign a unit to the x\mu values. I would
> like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it with
> tabulated data for the Copper absorption coefficient and proceed with my
> studies.
>
> In case a treatment is needed for the normalized \mu , that would also
> suit my situation.
>
> My idea was to divide by the thickness of the sample but I don't find a
> reasonable justificiation for this.
>
> I really hope I made the question clear to any reader this time, and if
> that is not the case I apologyze in advance.
>
> Best Regards
> Matteo
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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>
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Message: 3
Date: Fri, 13 May 2016 07:13:08 -0500
From: Matt Newville <newville-Gn9iRbd85Kk2LMHL4Co/2g@public.gmane.orgu>
To: XAFS Analysis using Ifeffit <ifeffit <at> millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] How to assign measure unit to XAFS data
Message-ID:
        <CA+7ESbq84ZpYx9DvP8JvM7yNzO0U31jFCZZ-_X43b21sM43+og <at> mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Matteo,


On Thu, May 12, 2016 at 7:11 PM, Matteo Busi <basebush <at> gmail.com> wrote:

> Hi Bruce, Matt, and  mailing list readers,
>
> I have one question regarding the XAFS data. I have collected absorption
> coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however
> my question can be generalized to any compound).
> Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k) and
> \chi(R). I am wondering how can I assign a unit to the x\mu values. I would
> like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it with
> tabulated data for the Copper absorption coefficient and proceed with my
> studies.
>


The analysis tools treat "xmu" as a dimensionless value.   To get values
for the mu in cm^-1 or grm/cm^2, you'll have to convert the measured values
used for XAFS analysis (say, readings from ion chambers) into actual X-ray
intensities, and try to account for anything else in the beam path that
will attenuate the X-rays.  For measurements made in transmission, this can
be done.   In fact, for most transmission measurements, the *change* in
-ln(I0 / I1) is usually a very good measure of the change in absorption of
the sample, so that if the observed jump is a value of 2, the sample really
did change its absorption by Delta_xmu = 2.    But the absolute values for
xmu are definitely not in meaningful units.  Typically, the photo-current
from the ion chamber or diode is converted to a voltage and then summed
over some time period in a data acquisition system.   You'd have to know
the details of that system to convert the "I0" and "I1" numbers into actual
beam intensities.

For fluorescence measurements, the situation is worse. You'd need a very
good measure of the solid angle of your detector, fluorescence efficiency,
and the attenuation of the fluorescence getting from the sample to the
detector.  Depending on the detector type, you'd also need a good
assessment of the backgrounds.   It's probably not impossible, but I think
it would not be easy unless that was the actual point of the experiment and
you made many careful measurements of the detection system.    If you're
asking this question here, you'd didn't make those measurements.



>
> In case a treatment is needed for the normalized \mu , that would also
> suit my situation.
>
> My idea was to divide by the thickness of the sample but I don't find a
> reasonable justificiation for this.
>


If you're measuring in fluorescence, dividing by the thickness of the
sample is not what you want.


>
> I really hope I made the question clear to any reader this time, and if
> that is not the case I apologyze in advance.
>
>

Cheers,

--Matt
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Christopher Thomas Chantler | 13 May 23:43 2016
Picon
Picon

Re: Ifeffit Digest, Vol 159, Issue 3

Dear All, Matteo

It is difficult to do post facto, but if you have a well-defined solid, foil or crystal then mapping the
thickness, measuring the mass and hence determining the mass per unit area, for the exact region
illuminated by the beam, provides accurate units. Usually you will need to make a measurement of the
average m/A from (i) total mass and (ii) total area, and then (iii) map the whole sample with X-ray
tomography and (iv) the region illuminated by the X-ray beam.

We have a series of papers which explain more than one methodology for doing that within the XERT technique.
If your sample is a solution it is a bit more tricky, and I would refer you to recent JSR and JPCC papers for our
Hybrid technique. Both can work well but need a bit more care than a normal XAFS measurement.

Best wishes
Chris
------------------------------------------------------------
Christopher Chantler, Professor, FAIP
Editor-in-Chief, Radiation Physics and Chemistry
Chair, International IUCr Commission on XAFS
President, International Radiation Physics Society
School of Physics, University of Melbourne
Parkville Victoria 3010 Australia
+61-3-83445437 FAX +61-3-93474783
chantler@... chantler@...
http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html
http://optics.ph.unimelb.edu.au/~chantler/home.html

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Today's Topics:

   1. How to assign measure unit to XAFS data (Matteo Busi)
   2. Re: How to assign measure unit to XAFS data (Alexey Boubnov)
   3. Re: How to assign measure unit to XAFS data (Matt Newville)

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

Message: 1
Date: Fri, 13 May 2016 02:11:39 +0200
From: Matteo Busi <basebush@...>
To: ifeffit@...
Subject: [Ifeffit] How to assign measure unit to XAFS data
Message-ID:
        <CAOyEiGg1N7wL-tnzPXFBCrUYQD=6=bvsRFnDNEe3ZaCeguFU5Q@...>
Content-Type: text/plain; charset="utf-8"

Hi Bruce, Matt, and  mailing list readers,

I have one question regarding the XAFS data. I have collected absorption
coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however
my question can be generalized to any compound).
Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k) and
\chi(R). I am wondering how can I assign a unit to the x\mu values. I would
like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it with
tabulated data for the Copper absorption coefficient and proceed with my
studies.

In case a treatment is needed for the normalized \mu , that would also suit
my situation.

My idea was to divide by the thickness of the sample but I don't find a
reasonable justificiation for this.

I really hope I made the question clear to any reader this time, and if
that is not the case I apologyze in advance.

Best Regards
Matteo
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------------------------------

Message: 2
Date: Fri, 13 May 2016 08:29:15 +0200
From: Alexey Boubnov <alexeyboubnov@...>
To: XAFS Analysis using Ifeffit <ifeffit@...>
Subject: Re: [Ifeffit] How to assign measure unit to XAFS data
Message-ID:
        <CAJZPK0VrRQ2Ad-Mxr2q4kdZorjdT_ceaVroPO3m57LYuS_CiAg@...>
Content-Type: text/plain; charset="utf-8"

Dear Matteo,

?x that you measured is dimensionless: x in the thickness (in cm) and ? the
Absorption coeffiecient (per cm). Indeed, if you want to know the
Absorption coefficient ? of your sample, you should divide ?x by x.

All the best,
Alexey

2016-05-13 2:11 GMT+02:00 Matteo Busi <basebush@...>:

> Hi Bruce, Matt, and  mailing list readers,
>
> I have one question regarding the XAFS data. I have collected absorption
> coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however
> my question can be generalized to any compound).
> Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k) and
> \chi(R). I am wondering how can I assign a unit to the x\mu values. I would
> like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it with
> tabulated data for the Copper absorption coefficient and proceed with my
> studies.
>
> In case a treatment is needed for the normalized \mu , that would also
> suit my situation.
>
> My idea was to divide by the thickness of the sample but I don't find a
> reasonable justificiation for this.
>
> I really hope I made the question clear to any reader this time, and if
> that is not the case I apologyze in advance.
>
> Best Regards
> Matteo
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@...
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
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Message: 3
Date: Fri, 13 May 2016 07:13:08 -0500
From: Matt Newville <newville@...>
To: XAFS Analysis using Ifeffit <ifeffit@...>
Subject: Re: [Ifeffit] How to assign measure unit to XAFS data
Message-ID:
        <CA+7ESbq84ZpYx9DvP8JvM7yNzO0U31jFCZZ-_X43b21sM43+og@...>
Content-Type: text/plain; charset="utf-8"

Hi Matteo,

On Thu, May 12, 2016 at 7:11 PM, Matteo Busi <basebush@...> wrote:

> Hi Bruce, Matt, and  mailing list readers,
>
> I have one question regarding the XAFS data. I have collected absorption
> coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however
> my question can be generalized to any compound).
> Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k) and
> \chi(R). I am wondering how can I assign a unit to the x\mu values. I would
> like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it with
> tabulated data for the Copper absorption coefficient and proceed with my
> studies.
>

The analysis tools treat "xmu" as a dimensionless value.   To get values
for the mu in cm^-1 or grm/cm^2, you'll have to convert the measured values
used for XAFS analysis (say, readings from ion chambers) into actual X-ray
intensities, and try to account for anything else in the beam path that
will attenuate the X-rays.  For measurements made in transmission, this can
be done.   In fact, for most transmission measurements, the *change* in
-ln(I0 / I1) is usually a very good measure of the change in absorption of
the sample, so that if the observed jump is a value of 2, the sample really
did change its absorption by Delta_xmu = 2.    But the absolute values for
xmu are definitely not in meaningful units.  Typically, the photo-current
from the ion chamber or diode is converted to a voltage and then summed
over some time period in a data acquisition system.   You'd have to know
the details of that system to convert the "I0" and "I1" numbers into actual
beam intensities.

For fluorescence measurements, the situation is worse. You'd need a very
good measure of the solid angle of your detector, fluorescence efficiency,
and the attenuation of the fluorescence getting from the sample to the
detector.  Depending on the detector type, you'd also need a good
assessment of the backgrounds.   It's probably not impossible, but I think
it would not be easy unless that was the actual point of the experiment and
you made many careful measurements of the detection system.    If you're
asking this question here, you'd didn't make those measurements.

>
> In case a treatment is needed for the normalized \mu , that would also
> suit my situation.
>
> My idea was to divide by the thickness of the sample but I don't find a
> reasonable justificiation for this.
>

If you're measuring in fluorescence, dividing by the thickness of the
sample is not what you want.

>
> I really hope I made the question clear to any reader this time, and if
> that is not the case I apologyze in advance.
>
>

Cheers,

--Matt
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Matteo Busi | 13 May 02:11 2016
Picon

How to assign measure unit to XAFS data

Hi Bruce, Matt, and  mailing list readers,

I have one question regarding the XAFS data. I have collected absorption coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however my question can be generalized to any compound). 
Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k) and \chi(R). I am wondering how can I assign a unit to the x\mu values. I would like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it with tabulated data for the Copper absorption coefficient and proceed with my studies. 

In case a treatment is needed for the normalized \mu , that would also suit my situation.

My idea was to divide by the thickness of the sample but I don't find a reasonable justificiation for this.

I really hope I made the question clear to any reader this time, and if that is not the case I apologyze in advance.

Best Regards
Matteo
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Dimitar Popmintchev | 4 May 03:02 2016
Picon

Artemis/FEFF question

Dear All,

The database at http://cars9.uchicago.edu/~newville/adb/search.html is down and I am trying to create an input file (for feff calculation) for pure scandium ( http://www.periodni.com/sc.html ).

The problem is when the 'atoms', and 'feff' in Artemis calculate the scattering paths, they shows distances smaller than the expected 3.256A nearest neighbor distance. What is the error in the input file attached below ?

Thank you.
Dimitar

 ATOMS                  * this list contains 117 atoms
 *   x          y          z     ipot tag           distance
    0.00000    0.00000    0.00000  0  Sc1           0.00000
    0.00000    0.00000    2.63650  1  Sc1.1         2.63650
    0.00000    0.00000   -2.63650  1  Sc1.1         2.63650
    2.86568    1.65450    0.00000  1  Sc1.2         3.30900
   -2.86568    1.65450    0.00000  1  Sc1.2         3.30900


Input file for scandium

## This Atoms file was generated by Demeter 0.9.22
## Demeter written by and copyright (c) Bruce Ravel, 2006-2015

title = name:     scandium
title = formula:  Sc
title = sites:    Sc1
title = refer1:   Kittel, ISSP
title = refer2:
title = schoen:
title = notes1:   metal, hcp
space = P63/mmc
a = 3.30900  c = 5.27300000
rmax  =   9.00000    core  = Sc1
atoms
# el.     x           y           z        tag
  Sc     0.00000     0.00000     0.00000   Sc1     
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Anatoly I Frenkel | 4 May 02:39 2016

Postdoctoral position

Dear IFEFFIT subscribers:

A postdoctoral position in my group will be available on July 1, 2016. The postdoc will be employed by
Yeshiva University in New York City. She or he will be stationed in Brookhaven National Laboratory on Long
Island and utilize XAFS and XRD/PDF techniques for studying mechanisms of electrostriction in novel
electromechanical materials. Prior experience with these methods, including high energy resolution
XAS, is required. This position is part of international collaboration, and will involve occasional
travel to research sites outside of the US. For all inquiries please contact me.

Anatoly Frenkel, Ph.D.
Professor and Chair, Department of Physics, Yeshiva University
245 Lexington Avenue, New York, NY 10016
https://yu.edu/faculty-bios/frenkel/
Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc
Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel@...
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Matt Newville | 27 Apr 17:52 2016
Gravatar

XASLIB (was Re: data availability)

Hi Nino,

Thanks for bringing this up and for the kind words.  I agree that not only is access to measured XAFS spectra a problem now, it's been a problem for a long time, as evidenced by the Farrel Lytle database.  In fact, it has long been a topic of discussion in the XAFS community of how to provide such databases, and developments over the past few years on data formats have been driven at least partly by the desire to have better spectral databases. 

For everyone: please try out XASLIB at  http://cars.uchicago.edu/xaslib  and let us know if you have any questions, comments, or suggestions for improving this database.   Right now, there is not a lot of data here, but it is enough to give you an idea of how it works.  

Comments can either come here or as github Issues at the source repository for this code:
   https://github.com/XraySpectroscopy/XASDataLibrary

There is a bit of documentation and wiki pages at
   https://github.com/XraySpectroscopy/XASDataLibrary/wiki


A longer explanation:

The standard XDI format for XAFS data (largely the work of Bruce)  was presented at an IXAS workshop (Q2XAFS) in Tsukuba, Japan in 2011.  At the most recent Q2XAFS meeting in Hamburg last August (as a satellite meeting of the XAFS conference), I presented an initial version of an on-line database based on this format, and intended for general use in the community.    With feedback from that meeting, the version linked above is now ready for beta testing and comments.

The plan is to move this to the IXAS Portal  http://www.ixasportal.net/ixas/,  but we'd like to get community suggestions and features and testing before we make that move.

The database uses proper relational database to store the actual data, and tries to use modern web technologies for the interface.

Some of the main features of this database are:
  -  spectra can be uploaded from XDI files through the web interface.  
  -  multiple spectra can be tagged as belonging to the same Suite.
  -  individual spectra or Suites can be rated and/or commented on by
     anyone, giving "Amazon-like" reviews.
  -  in order to upload or comment, one has to log in by email address.  

The ratings and reviews are meant to provide some mechanism for data quality assurance, but to avoid having one person "police" the data before it can be added.  This is trying to recognize that no one person can actually curate all the spectra, that truly bad data can be best identified by experts on that system, and also that there is actually some value to imperfect data.

The requirements for data to be uploaded are fairly minimal except that the data must be in XDI format (basically so that metadata can be parsed easily and the columns are well-labeled), and that the monochromator lattice constant must be provided (so that energy re-calibration can be done if needed).    We can help translate existing data into XDI so it can be uploaded into this database.

There are several features to add or improve including:
   - adding some information about energy resolution.
   - being able to export a Suite of spectra as a single zip file or Athena project.
   - better web page interface to setting citation information.
   - better web page interface to setting sample information.

But suggestions from anyone would be greatly appreciated.

Finally, although the database is meant to provide a public, on-line databases useful to anyone, and uses modern relational database engines as the backend, the software can actually run on an individual machine to provide a local, private database of XAS spectra, with the same web-based interface.  This is not very well documented at the moment, but if anyone is interested in trying to set such a database at their home institution, let me know.

--Matt Newville

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