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Today's Topics:
1. Re: FOLP card (Joshua Kas)
2. Question on Glitch in FEFF for Ru EXAFS measurements
(Dooshaye Moonshiram)
3. Re: Question on Glitch in FEFF for Ru EXAFS measurements
(Bruce Ravel)
4. Re: Question on Glitch in FEFF for Ru EXAFS measurements
(Bobrik, Michael)
----------------------------------------------------------------------
Message: 1
Date: Mon, 26 Nov 2012 10:56:19 -0800
From: Joshua Kas <joshua.j.kas@gmail.com>
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] FOLP card
Message-ID:
<CAHuhYRkW5R6iSLjSc03aNnfVRmX+YWvUiNB4HDF7CDEJLNNSjw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi Enyuan,
I don't really know a rule of thumb for ionic bond v.s. covalent bond, but
by default, the FEFF code will automatically choose reasonable muffin tins
in most cases, and most of the time it overlaps them by ~15%, i.e. FOLP
1.15. In many cases, the overlap doesn't change the structure in the XANES
a lot until you get far from FOLP 1.0. However, there are some special
cases. For example, we have found that using FOLP 0.8 for hydrogen atoms
seem's to work reasonably well in the XANES. This is because of the short
bond lengths of H. In addition, there are cases where one atom is fairly
isolated from the others, i.e., cage like structures, where FEFF can't
overlap the potentials, and setting FOLP to something smaller than 1.0 is
essential to make the code run. I would start by letting the code choose
the muffin tins automatically, then change them and see how the results
change. If the changes in the XANES are small, you probably don't have to
worry about FOLP. Otherwise, this is probably a limitation of the spherical
muffin tin potential. The best thing to do in that case, is to compare the
DOS (LDOS) with a calculation from a full potential electronic structure
code, i.e., WIEN2K, ABINIT, QUANTUM ESPRESSO, etc.
This can give you confidence in the FEFF calculation, or lead you to the
best values for FOLP. You could also use the FOLP values to get the best
comparison to experiment, but in some cases you may be fitting many-body
effects, which can lead you to the wrong conclusions about your system.
Cheers,
Josh Kas
On Mon, Nov 26, 2012 at 7:53 AM,
<ifeffit-request@millenia.cars.aps.anl.gov>wrote:
> Re:
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Message: 2
Date: Mon, 26 Nov 2012 17:05:17 -0500
From: Dooshaye Moonshiram <dmoonshi@gmail.com>
To: Ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Question on Glitch in FEFF for Ru EXAFS
measurements
Message-ID:
<CAM3-ni4JtTk94CyDLnzT6gYzgH=Rst_bXNm=AYsVBd448=D0JQ@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear Bruce,
I recently collected EXAFS data on the *Tris(bipyridine)ruthenium(II)
dichloride Ru 2 compound-photosensitizer in solution form. In order to
compare EXAFS data to XRD data, I uploaded the XRD coordinates of this
crystal structure from cambridge database in a FEFF calculation page in
ARTEMIS. I ran FEFF on the x,y and z coordinates of this standard compound
in Artemis and summed all paths to compare with my experimental
data(collected in solution form in fluorescence mode)*
*I have 2 problems*
*1) I found a glitch when running FEFF in ARTEMIS. In order to compare XRD
coordinates to EXAFS data, I upload the XRD coordinates in a FEFF
calculation page, run FEFF and sum all paths. Now*
*a) **f I upload the XRD coordinates in a FEFF calculation page without
having the EXAFS artemis file present, I get different fits compared to*
*b) if I first upload the EXAFS experimental file and then run FEFF on
the XRD cartesian coordinates. It seems that **the sum of all paths from
the FEFF calculation page tend to mimic the experimental EXAFS file which
has first been uploaded and is not a true presentation of how the FT should
be.*
*
*
*-Please let me know if this is unclear and I can send you my EXAFS file as
well as the XRD coordinates which I obtained from Cambridge structural
databse*
*
*
*2) Another problem which I have with my EXAFS data is that I have a peak
at 2.5 Angstrom which does not match XRD coordinates and is not present if
I run FEFF on XRD coordinates only(true comparison as I don't add the the
experimental file in Artemis). Could this peak be due to the Ru standard
somehow? All measurements were done in fluorescence mode (F/Io) at 20 K in
cryostat using a germanium detector. I simultaneously collected EXAFS
measurements on Ru metal standard between Iref and IT ionization chambers.*
*
*
*Thank you for your help,*
*Sincerely*
*Best Regards*
*Dooshaye Moonshiram*
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Message: 3
Date: Mon, 26 Nov 2012 17:29:27 -0500
From: Bruce Ravel <bravel@bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Question on Glitch in FEFF for Ru EXAFS
measurements
Message-ID: <2060436.G3JCknhBQa@lachesis.bnl.gov>
Content-Type: text/plain; charset="us-ascii"
I'm sorry. No part of #1 was clear to me. I never really know how to
respond to these Joycean descriptions.
If you expect help from the people on this list you need to do a
better job asking questions. Some hints can be found at
http://bruceravel.github.com/demeter/pods/help.pod.html
As for #2, there are any number of reasons why your XAS and XRD data
may not say the same thing. If the XRD explained all aspects of the
coordination geometry, why bother measuring XAS? Or to say that
another way, since the XAS and XRD seem to be telling you different
stories, don't you now have a real research problem to work on?
Perhaps some of the Ru has precipitated out in another form. Perhaps
the XRD is faulty. Perhaps your sample suffered radiation damage and
changed form. Perhaps your sample wasn't what you thought it was. My
point is that you should at least consider challenging your experiment
and any assumptions about your sample before presuming Feff and Artemis
are to blame for your woes.
B
On Monday, November 26, 2012 05:05:17 PM Dooshaye Moonshiram wrote:
> Dear Bruce,
>
> I recently collected EXAFS data on the *Tris(bipyridine)ruthenium(II)
> dichloride Ru 2 compound-photosensitizer in solution form. In order to
> compare EXAFS data to XRD data, I uploaded the XRD coordinates of this
> crystal structure from cambridge database in a FEFF calculation page in
> ARTEMIS. I ran FEFF on the x,y and z coordinates of this standard compound
> in Artemis and summed all paths to compare with my experimental
> data(collected in solution form in fluorescence mode)*
> *I have 2 problems*
> *1) I found a glitch when running FEFF in ARTEMIS. In order to compare XRD
> coordinates to EXAFS data, I upload the XRD coordinates in a FEFF
> calculation page, run FEFF and sum all paths. Now*
> *a) **f I upload the XRD coordinates in a FEFF calculation page without
> having the EXAFS artemis file present, I get different fits compared to*
> *b) if I first upload the EXAFS experimental file and then run FEFF on
> the XRD cartesian coordinates. It seems that **the sum of all paths from
> the FEFF calculation page tend to mimic the experimental EXAFS file which
> has first been uploaded and is not a true presentation of how the FT should
> be.*
> *
> *
> *-Please let me know if this is unclear and I can send you my EXAFS file as
> well as the XRD coordinates which I obtained from Cambridge structural
> databse*
> *
> *
> *2) Another problem which I have with my EXAFS data is that I have a peak
> at 2.5 Angstrom which does not match XRD coordinates and is not present if
> I run FEFF on XRD coordinates only(true comparison as I don't add the the
> experimental file in Artemis). Could this peak be due to the Ru standard
> somehow? All measurements were done in fluorescence mode (F/Io) at 20 K in
> cryostat using a germanium detector. I simultaneously collected EXAFS
> measurements on Ru metal standard between Iref and IT ionization chambers.*
> *
> *
> *Thank you for your help,*
> *Sincerely*
> *Best Regards*
> *Dooshaye Moonshiram*
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Homepage: http://xafs.org/BruceRavel
Software: https://github.com/bruceravel
------------------------------
Message: 4
Date: Mon, 26 Nov 2012 22:33:32 +0000
From: "Bobrik, Michael" <mbobrik@sysplan.com>
To: "'ifeffit@millenia.cars.aps.anl.gov'"
<ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Question on Glitch in FEFF for Ru EXAFS
measurements
Message-ID:
<6CAB929B0FBCE744908066F17232F053927DA41C@AARDVARK.sysplan.com>
Content-Type: text/plain; charset="iso-8859-1"
There's no reason for anyone to assume solution XAFS and crystal XRD data will converge to the same results.
Indeed, the research problem now is how/why are they different?
--------------------------
Dr. Michael A. Bobrik
Sent from the BlackBerry
----- Original Message -----
From: Bruce Ravel [mailto:bravel@bnl.gov]
Sent: Monday, November 26, 2012 05:29 PM
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Question on Glitch in FEFF for Ru EXAFS measurements
I'm sorry. No part of #1 was clear to me. I never really know how to
respond to these Joycean descriptions.
If you expect help from the people on this list you need to do a
better job asking questions. Some hints can be found at
http://bruceravel.github.com/demeter/pods/help.pod.html
As for #2, there are any number of reasons why your XAS and XRD data
may not say the same thing. If the XRD explained all aspects of the
coordination geometry, why bother measuring XAS? Or to say that
another way, since the XAS and XRD seem to be telling you different
stories, don't you now have a real research problem to work on?
Perhaps some of the Ru has precipitated out in another form. Perhaps
the XRD is faulty. Perhaps your sample suffered radiation damage and
changed form. Perhaps your sample wasn't what you thought it was. My
point is that you should at least consider challenging your experiment
and any assumptions about your sample before presuming Feff and Artemis
are to blame for your woes.
B
On Monday, November 26, 2012 05:05:17 PM Dooshaye Moonshiram wrote:
> Dear Bruce,
>
> I recently collected EXAFS data on the *Tris(bipyridine)ruthenium(II)
> dichloride Ru 2 compound-photosensitizer in solution form. In order to
> compare EXAFS data to XRD data, I uploaded the XRD coordinates of this
> crystal structure from cambridge database in a FEFF calculation page in
> ARTEMIS. I ran FEFF on the x,y and z coordinates of this standard compound
> in Artemis and summed all paths to compare with my experimental
> data(collected in solution form in fluorescence mode)*
> *I have 2 problems*
> *1) I found a glitch when running FEFF in ARTEMIS. In order to compare XRD
> coordinates to EXAFS data, I upload the XRD coordinates in a FEFF
> calculation page, run FEFF and sum all paths. Now*
> *a) **f I upload the XRD coordinates in a FEFF calculation page without
> having the EXAFS artemis file present, I get different fits compared to*
> *b) if I first upload the EXAFS experimental file and then run FEFF on
> the XRD cartesian coordinates. It seems that **the sum of all paths from
> the FEFF calculation page tend to mimic the experimental EXAFS file which
> has first been uploaded and is not a true presentation of how the FT should
> be.*
> *
> *
> *-Please let me know if this is unclear and I can send you my EXAFS file as
> well as the XRD coordinates which I obtained from Cambridge structural
> databse*
> *
> *
> *2) Another problem which I have with my EXAFS data is that I have a peak
> at 2.5 Angstrom which does not match XRD coordinates and is not present if
> I run FEFF on XRD coordinates only(true comparison as I don't add the the
> experimental file in Artemis). Could this peak be due to the Ru standard
> somehow? All measurements were done in fluorescence mode (F/Io) at 20 K in
> cryostat using a germanium detector. I simultaneously collected EXAFS
> measurements on Ru metal standard between Iref and IT ionization chambers.*
> *
> *
> *Thank you for your help,*
> *Sincerely*
> *Best Regards*
> *Dooshaye Moonshiram*
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Methods 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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