[Ifeffit] Re: Ifeffit Digest, Vol 11, Issue 5
Grant Bunker
bunker at biocat1.phys.iit.edu
Wed Jan 14 15:54:10 CST 2004
Hello, folks - In regard to Peter's question regarding multiple scattering
DWFs: Matt was correct that there have been two approaches (to my
knowledge) that attempt to directly address the problem: Poiarkova and
Rehr's approach, and our approach. There are pros and cons to each. We
(Nick Dimakis and I) have focussed on coordination complexes of metals with
amino acid and similar ligands to directly address metalloproteins. The
approach probably would work on other systems as well.
Our method works like this: we calculate using DFT the normal modes
(vibrational eigenvectors and eigenvaluesof model complexes as a function
of interatomic distance and bond angles (as needed). We started this
about ten years ago, and initially tried force constant models and various
approximate quantum mechanical methods but found them inadequate. DFT level
give sufficient accuracy and speed. Fortunately computers are fast and
cheap nowadays.
We have written a programs that take the eigenvalues and eigenvectors and
the feff output and generates MS DWFs for each path. We have found that
a "group fitting" approach works well, i.e. neglecting the inter-group
multiple scattering to a first approximation. It has worked well in the
cases we've tried.
Since it isn't really practical to expect people to do these DFT
calculations themselves (it's difficult to get convergence in many cases,
it's easy to get trapped in a local minimum, and the minimization
algorithms in the commercial codes are fairly antiquated), we have tried and
succeeded in parameterizing the DWF for each MS path as a function of distance
(and temperature). In almost all cases they are easily parameterized with
polynomials as a function of both distance and temperature.
So far we have done this with Zn coordinated to cysteine, histidine, and
carboxylate ligands (e.g. glu), and also Cu(I) and Cu(II). We are working
on Fe, Mn and other metal-ligand complexes as well, depending on funding.
Hope that helps.
Grant
On Wed, 14 Jan 2004 ifeffit-request at millenia.cars.aps.anl.gov wrote:
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> Today's Topics:
>
> 1. Spline clamps (SCalvin100 at aol.com)
> 2. Re: Spline clamps (Bruce Ravel)
> 3. Re: Spline clamps (Matt Newville)
> 4. Debye-Waller factors for MS paths (Peter Southon)
> 5. RE: Debye-Waller factors for MS paths (Kelly, Shelly D.)
> 6. Re: Debye-Waller factors for MS paths (Bruce Ravel)
> 7. Re: Debye-Waller factors for MS paths (Matt Newville)
> 8. linux: wouldn't it be cool... (Bruce Ravel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 13 Jan 2004 15:41:47 EST
> From: SCalvin100 at aol.com
> Subject: [Ifeffit] Spline clamps
> To: ifeffit at millenia.cars.aps.anl.gov
> Message-ID: <1cf.17c88a73.2d35b20b at aol.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi all,
>
> Happy New Year to all! I've been busy pushing the new versions of Artemis and
> Ifeffit pretty hard (3-edge fits, over 100 paths, also over 100 guess,def,set
> parameters) and they seem to be behaving pretty nicely. There are certainly
> some advantages and some disadvantages to this compared to the old FEFFIT
> package; one major advantage is this will certainly reduced the learning curve for
> new undergraduates in my group.
>
> I am posting now because I am not sure I understand the behavior of the
> spline clamps in Ifeffit. When I set a top end to the spline range that is below
> the top of the data range, the high spline clamp has very little, if any,
> effect. (As a simple example, if I take the "clamp.prj" project that comes with
> Athena and set all of the spline ranges to top out at 400 eV, all four backgrounds
> look the same.) Is this what should be happening, or is this a bug?
>
> In case this is a bug, here's the version information:
>
> Athena 0.8.024 and ifeffit 1.2.4 running on Windows XP.
>
> I'll also be glad to send a project file to Bruce or Matt if they wish,
> although it would just be the clamp.prj file with the top of the spline range
> changed...
>
> --Scott
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> ------------------------------
>
> Message: 2
> Date: Tue, 13 Jan 2004 15:57:01 -0500
> From: Bruce Ravel <ravel at phys.washington.edu>
> Subject: Re: [Ifeffit] Spline clamps
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <200401131557.01832.ravel at phys.washington.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Tuesday 13 January 2004 03:41 pm, SCalvin100 at aol.com wrote:
> > I am posting now because I am not sure I understand the behavior of the
> > spline clamps in Ifeffit. When I set a top end to the spline range that is
> > below the top of the data range, the high spline clamp has very little, if
> > any, effect. (As a simple example, if I take the "clamp.prj" project that
> > comes with Athena and set all of the spline ranges to top out at 400 eV,
> > all four backgrounds look the same.) Is this what should be happening, or
> > is this a bug?
>
> I don't know if it's a bug or not. (And if you think it is, I'd
> encourage you to make a minimal ifeffit script, perhaps with lines
> culled from Athena's ifeffit buffer, and send that to Matt. I suspect
> a minimal script would be most useful to him. And if you use a data
> file that comes with Athena's examples, like the one you mention, then
> you can send the script alone.) It would also be useful to check if
> the different clamp values lead to data that looks the same when
> plotted but has small numerical differences or if it is numerically
> identical.
>
> It is possible that it is not a bug and is, instead behaving as
> advertised. The clamp is a penalty applied to the chi-square that is
> calculated in determining the spline. The penalty is computed using
> (by default) the last five data points in the data range. The more
> those five points in the spline deviate from the data, the bigger the
> penalty. Thus, the sense in which it is a clamp is that it tries to
> coerce the spline to settle down to the level of the data at the end
> of the data range.
>
> If the spline is such that, with no clamp, the spline intersects the
> data points at the end of the spline range, then applying the clamp
> will have little effect. If the spline doesn't "want" to diverge from
> the data in any case, then adding a penalty for doing so won't be much
> of a penalty at all.
>
> The clamp.prj demo project works as a demo because the splines *do*
> diverge from the data near the end of the data set when the clamp is
> set to 0. That the splines don't do so 400 volts above the edge is
> not necessarily indicative of a problem with the clamps.
>
> B
>
> --
> Bruce Ravel ----------------------------------- ravel at phys.washington.edu
> Code 6134, Building 3, Room 222
> Naval Research Laboratory phone: (1) 202 767 5947
> Washington DC 20375, USA fax: (1) 202 767 1697
>
> NRL Synchrotron Radiation Consortium (NRL-SRC)
> Beamlines X11a, X11b, X23b
> National Synchrotron Light Source
> Brookhaven National Laboratory, Upton, NY 11973
>
> My homepage: http://feff.phys.washington.edu/~ravel
> EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 13 Jan 2004 15:36:16 -0600 (CST)
> From: Matt Newville <newville at cars.uchicago.edu>
> Subject: Re: [Ifeffit] Spline clamps
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID:
> <Pine.LNX.4.44.0401131520110.7613-100000 at millenia.cars.aps.anl.gov>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
> Hi Scott,
>
> The clamp uses the last data points, not the points near kmax (and
> similarly it uses the data points at above k=0, not k=kmin). I'm
> not sure if this is a bug (that is, it's not obvious what 'right' is
> here), but it's probably not the behavior you were hoping for ;).
>
> It's probably safe to assume that the clamps should persuade chi to
> be close to 0 at kmin and kmax (that is, this seems as safe as
> assuming chi should be near 0 at k=0 and k=last_data_point), so I
> don't see much reason to keep it like it is. I'll (try to) make the
> clamps use the points near kmax (and kmin) for 1.2.5
>
> --Matt
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 14 Jan 2004 10:32:15 +1100
> From: Peter Southon <p.southon at usyd.edu.au>
> Subject: [Ifeffit] Debye-Waller factors for MS paths
> To: ifeffit at millenia.cars.aps.anl.gov
> Message-ID: <6.0.0.22.2.20040114095950.01ada4f0 at pop.usyd.edu.au>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
>
> Dear everyone,
>
> One of the features of constructing models with Ifeffit is that we are
> forced to think long and hard about the parameters to use for each path. In
> particular I have had a great deal of difficulty in deciding how to
> approach the Debye-Waller factors for with multiple scattering (MS) paths.
>
> The ideal approach is to define the D-W factors for the MS paths in terms
> of the factors for the single scattering paths. That way you add no further
> variables to the model. But if you think about it you will realise that you
> cannot simply add all the relevant SS factors up to get a sum for your MS
> path - it all depends on the geometry, the direction of vibration,
> correlation of vibrations, etc. Its all a bit tricky for those of us
> dealing with intense MS paths.
>
> So what I am asking is, does anyone know of a general method or approach to
> define the Debye-Waller factors for MS paths (in terms of SS paths or
> otherwise)? How do all you Ifeffiters deal with the problem? I've found a
> few papers that discuss it (listed below) but they generally assume that
> all vibrations are uncorrelated, which is seldom a realistic situation in
> continuous solids.
>
> Munoz-Paez, A. (2000). Inorganic Chemistry 39(17): 3784-3790.
> Sakane, H. (1998). Journal of the American Chemical Society 120(40):
> 10397-10401.
> Haskel, D. (1998). PhD thesis, University of Washington. (appendix)
> http://www.aps.anl.gov/xfd/people/haskel/PS/thesis.ps
>
> Is there anything out there that I've missed? I'd be particularly
> interested in anything relating to continuous solids or correlated
> vibrations. Comments/questions/pearls of wisdom very welcome.
>
> Peter
>
>
> Peter Southon
> Research Fellow - School of Chemistry
> University of Sydney, NSW 2006, Australia
> +61 2 9351 4425
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 14 Jan 2004 10:04:56 -0600
> From: "Kelly, Shelly D." <SKelly at anl.gov>
> Subject: RE: [Ifeffit] Debye-Waller factors for MS paths
> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <1C1577844A0BDF448E14E8CCB2F7442409C756 at ANLMAIL.anl.gov>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Peter,
>
> Please see below:
> >
> > Dear everyone,
> >
> > One of the features of constructing models with Ifeffit is
> > that we are
> > forced to think long and hard about the parameters to use for
> > each path. In
> > particular I have had a great deal of difficulty in deciding how to
> > approach the Debye-Waller factors for with multiple
> > scattering (MS) paths.
> >
> > The ideal approach is to define the D-W factors for the MS
> > paths in terms
> > of the factors for the single scattering paths. That way you
> > add no further
> > variables to the model. But if you think about it you will
> > realise that you
> > cannot simply add all the relevant SS factors up to get a sum
> > for your MS
> > path - it all depends on the geometry, the direction of vibration,
> > correlation of vibrations, etc. Its all a bit tricky for those of us
> > dealing with intense MS paths.
> >
> > So what I am asking is, does anyone know of a general method
> > or approach to
> > define the Debye-Waller factors for MS paths (in terms of SS paths or
> > otherwise)? How do all you Ifeffiters deal with the problem?
> > I've found a
> > few papers that discuss it (listed below) but they generally
> > assume that
> > all vibrations are uncorrelated, which is seldom a realistic
> > situation in
> > continuous solids.
> >
> > Munoz-Paez, A. (2000). Inorganic Chemistry 39(17): 3784-3790.
> > Sakane, H. (1998). Journal of the American Chemical Society 120(40):
> > 10397-10401.
> > Haskel, D. (1998). PhD thesis, University of Washington. (appendix)
> > http://www.aps.anl.gov/xfd/people/haskel/PS/thesis.ps
> >
> > Is there anything out there that I've missed? I'd be particularly
> > interested in anything relating to continuous solids or correlated
> > vibrations. Comments/questions/pearls of wisdom very welcome.
> >
> > Peter
> >
> >
> > Peter Southon
> > Research Fellow - School of Chemistry
> > University of Sydney, NSW 2006, Australia
> > +61 2 9351 4425
> >
>
> There are a couple of ideas that I have found that work pretty well for
> determining sigma2 values for a lot of scattering paths.
>
> Idea 1: Try to use a correlated debye model or the eins model. You can
> have more than one debye/eins temperature depending on the atom types
> and path lengths.
>
> Idea 2: Group paths that are similar in distance and atom types and set
> their sigma2 values to the same value, including the M.S. paths.
> -use the abs function in defining a value for sigma2 to force it
> to be positive.
> sigma2 path1 abs(sig)
> guess sig 0.010
>
> Idea 3: Usually, the triangle paths that have a really large degeneracy
> end up with their own sigma2 value. Most models can be close to working
> without these paths, and then added them at the end to clean up the fit.
>
>
> Idea 4: Linear paths can be quantified in terms of the sigma2 values of
> the single scatting paths that contain the end atoms. Another paper that
> talks about this is:
> E A Hudson, J J Rehr and J J Bucher. "Multiple-scattering calculations
> of the uranium L3-edge X-ray-absorption near-edge structure." Phys. Rev.
> B 52(19): pp 13815-3826, 1995.
>
> -For a forward linear path A-B-C,
> sigma2(A-B-C-A)=sigma2(A-B-C-B-A)=sigma2(A-C-A)
> -For a backward scattering linear path B1-A-B2, and if A is a lot
> heavier than B then Sigma2(A-B1-A-B2-A)~sigma2(A-B1-B2-A)~2xsigma2(A-B),
> and sigma2(A-B1-A-B1-A)=4xsigma2(A-B) (John Rehr and I had a previous
> discussion about this with the subject "relation between DW factors in
> uranyls")
>
> Golden Rule: You have to try A LOT of different models, always try to
> start with the simplest model and make it more complex as the data
> requires. For example: Start with a eins model and use only one eins
> temp. See where the model works and were it fails. In the regions that
> it fails add another eins temp...and so on.
>
>
> Shelly Kelly
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 14 Jan 2004 11:22:57 -0500
> From: Bruce Ravel <ravel at phys.washington.edu>
> Subject: Re: [Ifeffit] Debye-Waller factors for MS paths
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <200401141122.57220.ravel at phys.washington.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Wednesday 14 January 2004 11:04 am, Kelly, Shelly D. wrote:
> > Golden Rule: You have to try A LOT of different models, always try to
> > start with the simplest model and make it more complex as the data
> > requires.
>
> Shelly's response to Peter's question about sigma^2 values was great.
> In particular I liked the snippet I quote above so much that I want to
> be sure that everyone on the mailing list reads it again. ;-)
>
> It would be difficult to overstate the wisdom of that sentence.
>
> And it is applicable to every aspect of fitting data in general and of
> using Ifeffit and Artemis in specific.
>
> B
>
>
>
> --
> Bruce Ravel ----------------------------------- ravel at phys.washington.edu
> Code 6134, Building 3, Room 222
> Naval Research Laboratory phone: (1) 202 767 5947
> Washington DC 20375, USA fax: (1) 202 767 1697
>
> NRL Synchrotron Radiation Consortium (NRL-SRC)
> Beamlines X11a, X11b, X23b
> National Synchrotron Light Source
> Brookhaven National Laboratory, Upton, NY 11973
>
> My homepage: http://feff.phys.washington.edu/~ravel
> EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 14 Jan 2004 11:25:05 -0600 (CST)
> From: Matt Newville <newville at cars.uchicago.edu>
> Subject: Re: [Ifeffit] Debye-Waller factors for MS paths
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID:
> <Pine.LNX.4.44.0401141058410.19052-100000 at millenia.cars.aps.anl.gov>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
> Hi Peter,
>
> On Wed, 14 Jan 2004, Peter Southon wrote:
>
> > So what I am asking is, does anyone know of a general method or approach to
> > define the Debye-Waller factors for MS paths (in terms of SS paths or
> > otherwise)? How do all you Ifeffiters deal with the problem? I've found a
> > few papers that discuss it (listed below) but they generally assume that
> > all vibrations are uncorrelated, which is seldom a realistic situation in
> > continuous solids.
>
> Shelly gave excellent advice for how to deal with this problem, but
> the overall answer to 'is there a general method for defining MS
> Debye-Waller Factors' is still no.
>
> > Is there anything out there that I've missed? I'd be particularly
> > interested in anything relating to continuous solids or correlated
> > vibrations. Comments/questions/pearls of wisdom very welcome.
>
> There has been some work to use a set of force constants to generate
> MS DWFS, and attempts made to generate these from (close to) first
> principles. There was work along these lines by A. Poiarkova and
> Rehr (including Poiarkova's thesis) which describes generating DWFs
> this way. Probably
> A Poiarkova and JJ Rehr, PRB 59 948-957 (1999)
>
> is the best reference. This approach aimed to calculate the DWFs,
> not to necessarily model/fit them. This work could, in principle,
> be turned around to allow a parameterized fit using a few force
> constants that generated the appropriate sigma2.
>
> Similar work has been done (or is being done) by N. Dimakis and G.
> Bunker (I'll probably get in trouble for calling them similar, as
> the approaches are pretty different, but both aim to calculate EXAFS
> DWFs from nearly first principles). I believe
> N Dimakis and G Bunker, PRB 65 201103(R) (2002)
>
> is the place to start. To me, this work seems to be a little more
> straightforward to parameterize for a fit, but it would be real work
> to try to put such capabilities into ifeffit.
>
> I don't have a good feel for how general either of these approaches
> is or what the prospects of using them "in general" is. Hopefully
> John or Grant can correct anything I've misrepresented!! It sure
> would be nice to have something like this available in ifeffit,
> wouldn't it?
>
> --Matt
>
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 14 Jan 2004 13:00:56 -0500
> From: Bruce Ravel <ravel at phys.washington.edu>
> Subject: [Ifeffit] linux: wouldn't it be cool...
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <200401141300.56900.ravel at phys.washington.edu>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Hi,
>
> I was just thinking that it would be nice to be able to install
> ifeffit and friends into either the KDE or GNOME menus. For example,
> one could imagine installing athena and artemis by doing
>
> perl Makefile.PL
> make
> make install
> make install-kde or make install-gnome
>
> where the last step makes the menu entries for the codes.
>
> Do any of the linux hacks out there know how this is done (at the
> level of a script -- I know how to do it by hand)?
>
> B
>
> --
> Bruce Ravel ----------------------------------- ravel at phys.washington.edu
> Code 6134, Building 3, Room 222
> Naval Research Laboratory phone: (1) 202 767 5947
> Washington DC 20375, USA fax: (1) 202 767 1697
>
> NRL Synchrotron Radiation Consortium (NRL-SRC)
> Beamlines X11a, X11b, X23b
> National Synchrotron Light Source
> Brookhaven National Laboratory, Upton, NY 11973
>
> My homepage: http://feff.phys.washington.edu/~ravel
> EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 11, Issue 5
> **************************************
>
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