Re: [Ifeffit] Interatomic distances from feff paths

[shelly Kelly]

Hi elsa,

You can open the cif file with a text editor and check the parameters in the 
atoms page against what you find in the cif file.

Sometimes a shift vector is needed. Check the messages in artemis for the 
possible values to try.

If none of these work. Try sending us the cif file.

Good luck
Shelly



On Sep 30, 2010 5:01 PM, Elsa E. Sileo  wrote:

I am trying to use the following CIF files to 

generate the feff path at the As edge:



1-  'Iron(III) arsenate(V) dihydrate', Scorodite, 

H4 As Fe O6'; space group P c a b; number 61; orthorhombic



and



2.  Iron(III) tris(dihydrogenarsenate) pentahydrate



Kaatialaite, Fe (H2 As O4)3 (H2 O)5, P 1 21/n 1, number 14; monoclinic





and in both cases, after running Feff, I obtain 

distances Fe-As that are not real.

For instance in scorodite I find a distance As-Fe = 1,71 A.

How can I overcome this problem?



Thanks,



Elsa





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>Today's Topics:

>

>1. Re: Ifeffit Digest, Vol 91, Issue 28 (Matt Newville)

>

>

>--

>

>Message: 1

>Date: Thu, 30 Sep 2010 11:28:28 -0500

>From: Matt Newville 

>To: XAFS Analysis using Ifeffit 

>Subject: Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28

>Message-ID:

> 


>Content-Type: text/plain; charset=ISO-8859-1

>

>Hi Elsa,

>

>On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo  wrote:

> >

> > Dear Matt,

> >

> > I have to perform EXAFS analysis, and when I tried to fit the first

> > shell, I found deltaE0 values of about 8 eV. Following the paper of

> > Kelly et al (Analysis of soils and minerals using X-ray absorption

> > spectroscopy. In Methods of soil analysis, Part 5: Mineralogical

> > methods; 2008; pp 446) I fitted the first shell obtaining values for

> > deltaE0, sigma^2; delta R and amplitude. Then, using the obtained

> > values, and making deltaE0=0, I got the theoretical signal.

>

>Why is important to have a theoretical spectra with deltaE0=0?

>

> > When I compare the experimental and theoretical spectrum I see a 
mismatch

> > between the position of the nodes at low wavenumbers.

>

>Yes, that is what E0 does.

>

> > Having done this, how I have to proceed to correct the experimental

> > data in order to obtain smalller delta E0 values?

>

>I think what you are trying to do (though I don't understand why) is

>to adjust E0 for the experimental data so that the fit to a particular

>theoretical standard gives deltaE0 close to zero.  If so, you want to

>adjust E0 in the background subtraction.  If you change E0 by 8eV

>there, you should end up with a deltaE0 in the fit that is close to

>zero.

>

>Hope that helps,

>

>--Matt

>

>

>--

>

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>

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>

>

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Dra. Elsa E. Sileo

Solidos Inorganicos

INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA

Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA

CABA - Argentina

Tel: (54 11) 4576 3380 ext. 113

Fax: (54 11) 4576 3341

e-mail: si...@qi.fcen.uba.ar









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[Ifeffit] Interatomic distances from feff paths

[Elsa E. Sileo]

I am trying to use the following CIF files to 
generate the feff path at the As edge:


1-  'Iron(III) arsenate(V) dihydrate', Scorodite, 
H4 As Fe O6'; space group P c a b; number 61; orthorhombic


and

2.  Iron(III) tris(dihydrogenarsenate) pentahydrate

Kaatialaite, Fe (H2 As O4)3 (H2 O)5, P 1 21/n 1, number 14; monoclinic


and in both cases, after running Feff, I obtain 
distances Fe-As that are not real.

For instance in scorodite I find a distance As-Fe = 1,71 A.
How can I overcome this problem?

Thanks,

Elsa


At 14:00 30/09/2010, you wrote:

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Today's Topics:

   1. Re: Ifeffit Digest, Vol 91, Issue 28 (Matt Newville)


--

Message: 1
Date: Thu, 30 Sep 2010 11:28:28 -0500
From: Matt Newville 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Hi Elsa,

On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo  wrote:
>
> Dear Matt,
>
> I have to perform EXAFS analysis, and when I tried to fit the first
> shell, I found deltaE0 values of about 8 eV. Following the paper of
> Kelly et al (Analysis of soils and minerals using X-ray absorption
> spectroscopy. In Methods of soil analysis, Part 5: Mineralogical
> methods; 2008; pp 446) I fitted the first shell obtaining values for
> deltaE0, sigma^2; delta R and amplitude. Then, using the obtained
> values, and making deltaE0=0, I got the theoretical signal.

Why is important to have a theoretical spectra with deltaE0=0?

> When I compare the experimental and theoretical spectrum I see a mismatch
> between the position of the nodes at low wavenumbers.

Yes, that is what E0 does.

> Having done this, how I have to proceed to correct the experimental
> data in order to obtain smalller delta E0 values?

I think what you are trying to do (though I don't understand why) is
to adjust E0 for the experimental data so that the fit to a particular
theoretical standard gives deltaE0 close to zero.  If so, you want to
adjust E0 in the background subtraction.  If you change E0 by 8eV
there, you should end up with a deltaE0 in the fit that is close to
zero.

Hope that helps,

--Matt


--

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End of Ifeffit Digest, Vol 91, Issue 30
***


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Checked by AVG - www.avg.com
Version: 8.5.445 / Virus Database: 271.1.1/3168 
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Dra. Elsa E. Sileo
Solidos Inorganicos
INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA
Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA
CABA - Argentina
Tel: (54 11) 4576 3380 ext. 113
Fax: (54 11) 4576 3341
e-mail: si...@qi.fcen.uba.ar




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Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 30

[Elsa E. Sileo]

Thanks Matt,

now I realize that I can directly change de Eo in the Athena window,
Elsa

At 14:00 30/09/2010, you wrote:

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Today's Topics:

   1. Re: Ifeffit Digest, Vol 91, Issue 28 (Matt Newville)


--

Message: 1
Date: Thu, 30 Sep 2010 11:28:28 -0500
From: Matt Newville 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Hi Elsa,

On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo  wrote:
>
> Dear Matt,
>
> I have to perform EXAFS analysis, and when I tried to fit the first
> shell, I found deltaE0 values of about 8 eV. Following the paper of
> Kelly et al (Analysis of soils and minerals using X-ray absorption
> spectroscopy. In Methods of soil analysis, Part 5: Mineralogical
> methods; 2008; pp 446) I fitted the first shell obtaining values for
> deltaE0, sigma^2; delta R and amplitude. Then, using the obtained
> values, and making deltaE0=0, I got the theoretical signal.

Why is important to have a theoretical spectra with deltaE0=0?

> When I compare the experimental and theoretical spectrum I see a mismatch
> between the position of the nodes at low wavenumbers.

Yes, that is what E0 does.

> Having done this, how I have to proceed to correct the experimental
> data in order to obtain smalller delta E0 values?

I think what you are trying to do (though I don't understand why) is
to adjust E0 for the experimental data so that the fit to a particular
theoretical standard gives deltaE0 close to zero.  If so, you want to
adjust E0 in the background subtraction.  If you change E0 by 8eV
there, you should end up with a deltaE0 in the fit that is close to
zero.

Hope that helps,

--Matt


--

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End of Ifeffit Digest, Vol 91, Issue 30
***


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Checked by AVG - www.avg.com
Version: 8.5.445 / Virus Database: 271.1.1/3168 
- Release Date: 09/30/10 06:34:00


Dra. Elsa E. Sileo
Solidos Inorganicos
INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA
Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA
CABA - Argentina
Tel: (54 11) 4576 3380 ext. 113
Fax: (54 11) 4576 3341
e-mail: si...@qi.fcen.uba.ar




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Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28

[Shelly Kelly]

Hi Elsa:

As Matt suggested, you want to change E0 in Athena to produce a new chi(k)
spectrum.  You can read the theoretical chi(k) spectrum that you made with
E0=0 into Athena, adjust E0 for the measurement, and then plot in k the data
and theory to see them match at low k.

I encourage you to poke around at the project files that I put at
www.xafs.org/ShellyKelly.  These project files show how to reproduce the
relevant figures in the book chapter.



Good luck,
Shelly

On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo  wrote:

> Dear Matt,
>
> I have to perform EXAFS analysis, and when I tried to fit the first shell,
> I found deltaE0 values of about 8 eV. Following the paper of Kelly et al
> (Analysis of soils and minerals using X-ray absorption spectroscopy. In
> Methods of soil analysis, Part 5: Mineralogical methods; 2008; pp 446)
> I fitted the first shell obtaining values for deltaE0, sigma^2; delta R
> and amplitude. Then, using the obtained values, and making deltaE0=0, I got
> the theoretical signal.
> When I compare the experimental and theoretical spectrum I see a mismatch
> between the position of the nodes at low wavenumbers.
> Having done this, how I have to proceed to correct the experimental data in
> order to obtain smalller delta E0 values?
>
> Thanks in advance,
>
> Elsa
>
> --- El *mié, 29/9/10, ifeffit-requ...@millenia.cars.aps.anl.gov <
> ifeffit-requ...@millenia.cars.aps.anl.gov>* escribió:
>
>
> De: ifeffit-requ...@millenia.cars.aps.anl.gov <
> ifeffit-requ...@millenia.cars.aps.anl.gov>
> Asunto: Ifeffit Digest, Vol 91, Issue 28
> Para: ifeffit@millenia.cars.aps.anl.gov
> Fecha: miércoles, 29 de septiembre, 2010 14:00
>
> 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-requ...@millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> 
> ifeffit-ow...@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: Aligning Energy scales (Matt Newville)
>
>
> --
>
> Message: 1
> Date: Tue, 28 Sep 2010 12:55:15 -0500
> From: Matt Newville 
> http://es.mc278.mail.yahoo.com/mc/compose?to=newvi...@cars.uchicago.edu>
> >
> To: XAFS Analysis using Ifeffit 
> http://es.mc278.mail.yahoo.com/mc/compose?to=ifef...@millenia.cars.aps.anl.gov>
> >
> Subject: Re: [Ifeffit] Aligning Energy scales
> Message-ID:
> 
> http://es.mc278.mail.yahoo.com/mc/compose?to=k-vb-0argwb9ac_w6bcblwgca...@mail.gmail.com>
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Elsa,
>
> It sounds like you want to adjust the data chi(k) so that deltaE0 is 0
> in a fit.  Is that correct, or are you trying to do something else
> (say, align the XANES)?If that assumption is correct, you want to
> change the E0 used to extract chi(k) from the experimental spectra --
> the E0 of the background subtraction.  That is what sets k for the
> data.
>
> If that's not clear or not the right question, let us know,
>
> --Matt
>
> On Mon, Sep 27, 2010 at 2:00 PM, Elsa E. Sileo 
> http://es.mc278.mail.yahoo.com/mc/compose?to=si...@qi.fcen.uba.ar>>
> wrote:
> > I need to align a measured spectra to a theoretically calculated spectra.
> > I fitted the first shell obtaining values for deltaE0, sigma^2; delta R
> and
> > amplitude.
> > Then, using the obtained values, and making deltaE0=0, I got the
> theoretical
> > signal.
> > But I do not know how to use this last theoretical fit to align the
> spectra.
> > Can somebody help me?
> >
> > Thanks,
> >
> > Elsa
> >
> >
> > Dra. Elsa E. Sileo
> > Solidos Inorganicos
> > INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA
> > Int. G?iraldes 2160, Pabell?n 2, Piso 3, Ciudad Universitaria - C1428EHA
> > CABA - Argentina
> > Tel: (54 11) 4576 3380 ext. 113
> > Fax: (54 11) 4576 3341
> > e-mail: 
> > si...@qi.fcen.uba.ar
> >
> >
> >
> >
> > ___
> > Ifeffit mailing list
> > Ifeffit@millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
>
>
>
> --
>
> ___
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Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28

[Matt Newville]

Hi Elsa,

On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo  wrote:
>
> Dear Matt,
>
> I have to perform EXAFS analysis, and when I tried to fit the first
> shell, I found deltaE0 values of about 8 eV. Following the paper of
> Kelly et al (Analysis of soils and minerals using X-ray absorption
> spectroscopy. In Methods of soil analysis, Part 5: Mineralogical
> methods; 2008; pp 446) I fitted the first shell obtaining values for
> deltaE0, sigma^2; delta R and amplitude. Then, using the obtained
> values, and making deltaE0=0, I got the theoretical signal.

Why is important to have a theoretical spectra with deltaE0=0?

> When I compare the experimental and theoretical spectrum I see a mismatch
> between the position of the nodes at low wavenumbers.

Yes, that is what E0 does.

> Having done this, how I have to proceed to correct the experimental
> data in order to obtain smalller delta E0 values?

I think what you are trying to do (though I don't understand why) is
to adjust E0 for the experimental data so that the fit to a particular
theoretical standard gives deltaE0 close to zero.  If so, you want to
adjust E0 in the background subtraction.  If you change E0 by 8eV
there, you should end up with a deltaE0 in the fit that is close to
zero.

Hope that helps,

--Matt
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Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28

[Frenkel, Anatoly]

It is because you made delta E0=0, but the fit gave you delta E0=8. Since the 
fit agrees with the data in k-space at low wavenumbers (I assume), then the 
signal with delta E0=0 should not, and vice versa. 
Anatoly
 


From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Elsa Sileo
Sent: Thu 9/30/2010 11:33 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28


Dear Matt,
 
I have to perform EXAFS analysis, and when I tried to fit the first shell, I 
found deltaE0 values of about 8 eV. Following the paper of Kelly et al 
(Analysis of soils and minerals using X-ray absorption spectroscopy. In Methods 
of soil analysis, Part 5: Mineralogical methods; 2008; pp 446) I fitted the 
first shell obtaining values for deltaE0, sigma^2; delta R and amplitude. Then, 
using the obtained values, and making deltaE0=0, I got the theoretical signal.
When I compare the experimental and theoretical spectrum I see a mismatch 
between the position of the nodes at low wavenumbers.
Having done this, how I have to proceed to correct the experimental data in 
order to obtain smalller delta E0 values?
 
Thanks in advance,
 
Elsa
 
--- El mié, 29/9/10, ifeffit-requ...@millenia.cars.aps.anl.gov 
 escribió:



De: ifeffit-requ...@millenia.cars.aps.anl.gov 

Asunto: Ifeffit Digest, Vol 91, Issue 28
Para: ifeffit@millenia.cars.aps.anl.gov
Fecha: miércoles, 29 de septiembre, 2010 14:00


Send Ifeffit mailing list submissions to
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Today's Topics:

   1. Re: Aligning Energy scales (Matt Newville)


--

Message: 1
Date: Tue, 28 Sep 2010 12:55:15 -0500
From: Matt Newville http://es.mc278.mail.yahoo.com/mc/compose?to=newvi...@cars.uchicago.edu> >
To: XAFS Analysis using Ifeffit http://es.mc278.mail.yahoo.com/mc/compose?to=ifef...@millenia.cars.aps.anl.gov>
 >
Subject: Re: [Ifeffit] Aligning Energy scales
Message-ID:
http://es.mc278.mail.yahoo.com/mc/compose?to=k-vb-0argwb9ac_w6bcblwgca...@mail.gmail.com>
 >
Content-Type: text/plain; charset=ISO-8859-1

Dear Elsa,

It sounds like you want to adjust the data chi(k) so that deltaE0 is 0
in a fit.  Is that correct, or are you trying to do something else
(say, align the XANES)?If that assumption is correct, you want to
change the E0 used to extract chi(k) from the experimental spectra --
the E0 of the background subtraction.  That is what sets k for the
data.

If that's not clear or not the right question, let us know,

--Matt

On Mon, Sep 27, 2010 at 2:00 PM, Elsa E. Sileo http://es.mc278.mail.yahoo.com/mc/compose?to=si...@qi.fcen.uba.ar> > wrote:
> I need to align a measured spectra to a theoretically calculated 
spectra.
> I fitted the first shell obtaining values for deltaE0, sigma^2; delta 
R and
> amplitude.
> Then, using the obtained values, and making deltaE0=0, I got the 
theoretical
> signal.
> But I do not know how to use this last theoretical fit to align the 
spectra.
> Can somebody help me?
>
> Thanks,
>
> Elsa
>
>
> Dra. Elsa E. Sileo
> Solidos Inorganicos
> INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA
> Int. G?iraldes 2160, Pabell?n 2, Piso 3, Ciudad Universitaria - 
C1428EHA
> CABA - Argentina
> Tel: (54 11) 4576 3380 ext. 113
> Fax: (54 11) 4576 3341
> e-mail: si...@qi.fcen.uba.ar 
 
>
>
>
>
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov 

 
> http

Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28

[Elsa Sileo]

Dear Matt,
 
I have to perform EXAFS analysis, and when I tried to fit the first shell, I 
found deltaE0 values of about 8 eV. Following the paper of Kelly et al 
(Analysis of soils and minerals using X-ray absorption spectroscopy. In Methods 
of soil analysis, Part 5: Mineralogical methods; 2008; pp 446) I fitted the 
first shell obtaining values for deltaE0, sigma^2; delta R and amplitude. Then, 
using the obtained values, and making deltaE0=0, I got the theoretical signal.
When I compare the experimental and theoretical spectrum I see a mismatch 
between the position of the nodes at low wavenumbers.
Having done this, how I have to proceed to correct the experimental data in 
order to obtain smalller delta E0 values?
 
Thanks in advance,
 
Elsa
 
--- El mié, 29/9/10, ifeffit-requ...@millenia.cars.aps.anl.gov 
 escribió:


De: ifeffit-requ...@millenia.cars.aps.anl.gov 

Asunto: Ifeffit Digest, Vol 91, Issue 28
Para: ifeffit@millenia.cars.aps.anl.gov
Fecha: miércoles, 29 de septiembre, 2010 14:00


Send Ifeffit mailing list submissions to
    ifeffit@millenia.cars.aps.anl.gov

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Today's Topics:

   1. Re: Aligning Energy scales (Matt Newville)


--

Message: 1
Date: Tue, 28 Sep 2010 12:55:15 -0500
From: Matt Newville 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Aligning Energy scales
Message-ID:
    
Content-Type: text/plain; charset=ISO-8859-1

Dear Elsa,

It sounds like you want to adjust the data chi(k) so that deltaE0 is 0
in a fit.  Is that correct, or are you trying to do something else
(say, align the XANES)?    If that assumption is correct, you want to
change the E0 used to extract chi(k) from the experimental spectra --
the E0 of the background subtraction.  That is what sets k for the
data.

If that's not clear or not the right question, let us know,

--Matt

On Mon, Sep 27, 2010 at 2:00 PM, Elsa E. Sileo  wrote:
> I need to align a measured spectra to a theoretically calculated spectra.
> I fitted the first shell obtaining values for deltaE0, sigma^2; delta R and
> amplitude.
> Then, using the obtained values, and making deltaE0=0, I got the theoretical
> signal.
> But I do not know how to use this last theoretical fit to align the spectra.
> Can somebody help me?
>
> Thanks,
>
> Elsa
>
>
> Dra. Elsa E. Sileo
> Solidos Inorganicos
> INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA
> Int. G?iraldes 2160, Pabell?n 2, Piso 3, Ciudad Universitaria - C1428EHA
> CABA - Argentina
> Tel: (54 11) 4576 3380 ext. 113
> Fax: (54 11) 4576 3341
> e-mail: si...@qi.fcen.uba.ar
>
>
>
>
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>



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End of Ifeffit Digest, Vol 91, Issue 28
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[Ifeffit] EXAFS spectrum of Fe foil (fcc)

[KONG Quingyu]

Dear All,

Does anyone has an EXAFS spectrum of gama Fe foil, or Fe foil spectrum measured 
at high temperature (more than 1000 degree). 
If you have this measurement, would you please send me a copy of the data. I 
would like to compare with our recent measured EXAFS spectrum.

Thanks a lot in advance,

Sincerely,
Qingyu Kong


Beamline ODE
Société civile Synchrotron SOLEIL
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 GIF-sur-YVETTE CEDEX
Tel: +33 (0)1 69 35 97 84 (office)
   +33 (0)1 69 35 97 16 (beamline)
email: k...@synchrotron-soleil.fr 


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