[Ifeffit] FOLP

Tue Nov 27 12:10:56 CST 2012

Hi Enyuan,
It is very strange that FOLP 1.3 is causing the code to take longer. There
really should be almost no difference in timing
between different values of FOLP. This has to be a bug. Would you mind
sending your input file?

As for the CRITERIA card, this effects the filtering of the path expansion.
The path expansion should only be used for EXAFS calculations, which is why
the CRITERIA card is greyed out for XANES calculations (which use full
multiple scattering). If you really want to run XANES with path expansion,
you can still do that using the text based input and running the code from
the command line. If you don't know how to do this, I can explain. Just let
me know what operating system you are using.
Cheers,
Josh

>
> 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:
> > -------------- next part --------------
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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*
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20121126/af55bf5f/attachment-0001.htm
> > >
> >
> > ------------------------------
> >
> > 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
> > _______________________________________________
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> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
> >
> > ------------------------------
> >
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> > Ifeffit at millenia.cars.aps.anl.gov
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> >
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