[Ifeffit] Ifeffit Digest, Vol 117, Issue 24
Enyuan Hu
bearcharge at gmail.com
Tue Nov 27 10:46:00 CST 2012
Hi Joshua,
Thank you for your comment. Like you said, I tried FOLP with value from 1
to 1.3 and it didn't change the calculated spectrum much. It's very
time-consuming when FOLP reached 1.3, taking more than 3 hours to finish
the calculation on my laptop. On using 0.8 for hydrogen, actually I'm going
to calculated a sample with lots of Li in it. Do you suggest using a
similarly small number of FOLP for Li, in an analogy to H? The other thing
I want to ask is the CRITERIA card in Feff9. It seemed that once I asked
the program to calculate XANES, the CRITERIA card in the software cannot be
checked. It can only be checked if I selected EXAFS calculation mode. Is
there any way to solve this? thanks again for all your answers.
Enyuan
On Mon, Nov 26, 2012 at 5:33 PM,
<ifeffit-request at millenia.cars.aps.anl.gov>wrote:
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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 at gmail.com>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] FOLP card
> Message-ID:
> <
> CAHuhYRkW5R6iSLjSc03aNnfVRmX+YWvUiNB4HDF7CDEJLNNSjw at 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 at 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 at gmail.com>
> To: Ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] Question on Glitch in FEFF for Ru EXAFS
> measurements
> Message-ID:
> <CAM3-ni4JtTk94CyDLnzT6gYzgH=Rst_bXNm=AYsVBd448=
> D0JQ at 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 at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Question on Glitch in FEFF for Ru EXAFS
> measurements
> Message-ID: <2060436.G3JCknhBQa at 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 at 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 at sysplan.com>
> To: "'ifeffit at millenia.cars.aps.anl.gov'"
> <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Question on Glitch in FEFF for Ru EXAFS
> measurements
> Message-ID:
> <6CAB929B0FBCE744908066F17232F053927DA41C at 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 at bnl.gov]
> Sent: Monday, November 26, 2012 05:29 PM
> To: XAFS Analysis using Ifeffit <ifeffit at 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 at 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
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
>
> ------------------------------
>
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>
> End of Ifeffit Digest, Vol 117, Issue 24
> ****************************************
>
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