[Ifeffit] RESTRAINTS IN IFEFFIT

Kelly, Shelly D. SKelly at anl.gov
Wed Jan 25 09:53:39 CST 2006


Hi Renato,

See below for some comments:

> 
> Hi Folks, this is my first message on the list. Perhaps someone could
help
> me. The subject is how to include restraints on exafs refinement.
There is
> just scanty information about this on the ifeffit reference manual.
> 
> I'm trying to refine the exafs data of a rhombohedral perovskite.
> 
> The main MS contributions to the signal at about 3.5 A (non phase
correct)
> arise from M - O - M  interactions  being  M the absorber .  We have a
> significant SS path, a two-legged and a three-legged path. The
structural
> parameters of these three terms are correlated since all refers to the
> same
> A-B-C triangle and the A-B and B-C distances must be that found for
> M-O1 nearest-neighbor configurations. For these reasons
> we constrained the photo electron path length for three-legged to the
> M-O nearest-neighbor distance:R(three-leg = 2*RM-O). 
[Kelly, Shelly D.] 

The three-leg path length is given by half the total path length.
Calculated as R = (distance_AB + distance_BC + distance_AC) * 0.5
You know the distance from A-B and the distance from B-C but the
distance from A-C is dependent on the angle of the triangle path.  You
can write an equation to determine the angle A.
a^2 = b^2 + c^2 -2bc cos(A)
where a=distance_AC, b=distance_AB, c=distance_BC and A is the angle
opposite of the AC side of the triangle.

Then the four leg path has a path length defined as
R = (2*distance_AB + 2*distance_BC)*0.5

The single path from A to B has the distance
R = (2*distance_AB)*0.5

The single path from A to C has the distance
R = (2*distance_AC)*0.5
Which also depends on the angle A and distance_AB as defined above.


So for your case you have one unknown length and one unknown bond angle
to describe these path lengths. i.e. distance_AB=distance_BC is unknown
and angle A is unknown.

HTH
Shelly

I'm trying to
> intoroduce the quantity  defined as delta =
R(three-legged)-R(two-legged)
> and thus define the SS half path length as a function of delta R(SS) =
R
> (three-legged) - 2*delta. I think it is a restraint not a constraint.
> So I defined (def) the delta function on the line above the command
FEFFIT
> also delr for the SS path. I introduced the restraint in the line
FEFFIT
> as
> restraint = delrSS). The fit produce the same results as obtainde
without
> the definition of delta and delrSS (function of delta).
> So I need to know how to introduce this restraint in the fit in order
to
> calculate de M - O - M bond angle (this angle should be calculated
using
> simple geometric relationships) - perhaps introduce the bond angle as
a
> restraint.
> Someone can say me where I introduce the definitions of restraint
> parameters?
> 
> Thank you very much for your kind attention
> 
> Renato Canha
> 
> Universidade Federal do Rio Grande doNorte
> Departamento de Quimica
> Natal - RN - BRAZIL
> Open WebMail Project (http://openwebmail.org)
> 
> 
> ---------- Original Message -----------
> From: ifeffit-request at millenia.cars.aps.anl.gov
> To: ifeffit at millenia.cars.aps.anl.gov
> Sent: Mon, 23 Jan 2006 12:00:13 -0600
> Subject: Ifeffit Digest, Vol 35, Issue 14
> 
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> > Today's Topics:
> >
> >    1. Re: Re: I should be able to find this somewhere... (Bruce
Ravel)
> >
> >
----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sun, 22 Jan 2006 16:58:07 -0600
> > From: Bruce Ravel <bravel at anl.gov>
> > Subject: Re: [Ifeffit] Re: I should be able to find this
somewhere...
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Message-ID: <200601221658.07513.bravel at anl.gov>
> > Content-Type: text/plain;  charset="iso-8859-1"
> >
> > Hi,
> >
> > In fact, Artemis and Athena both attempt to deal correctly with
input
> > chi(k) data that is not on the expected grid.  Both codes perform a
> > test to see if the data is on the standard grid and, if not,
> > front-loads the data with zeros and uses Ifeffit's boxcar rebinning
> > function to put the data on the expected grid.
> >
> > Alas, there was a bug in the rebinning macro used by A&A which
caused
> > it to fail in a particular situation met by the data in Matthew's
> > example.  This bug will be fixed in the next release.
> >
> > If you import mu(E) data into Athena and then import data from the
> > Athena project file into Artemis, you will never see the problem
that
> > Matthew reported.
> >
> > B
> >
> > On Tuesday 17 January 2006 16:09, Matt Newville wrote:
> > > Hi Matthew, Bruce,
> > >
> > > OK, I think it's a bug.  Well, maybe it's just a consequence of a
> > > "known but not well advertised" problem.
> > >
> > > The chi(k) data you have doesn't start at k=0.  By itself, this
should
> > > be OK, and the fit seems to be mostly fine.  There seems to be a
bug
> > > in Ifeffit that the output fit chi(k) has the same number of data
> > > points as the input chi(k) data. In this case is incorrect -- it
> > > should go to the last data point in k.  From looking at the code,
I'm
> > > pretty sure this has no effect on the fit and is only an error in
the
> > > output array.  But the shortened chi_fit(k) will have an impact on
the
> > > way Bruce is calculating the residual.   Even if that were fixed,
the
> > > residual would still be wrong, as the residual in Artemis is
> > > calculated as
> > >    set(data0_res.k = data0.k)
> > >    set(data0_res.chi = data0.chi - data0_fit.chi)
> > >
> > > and then Fourier transforming to R-space.   Since the data and fit
> > > aren't aligned in k-space, the residual is incorrect.  It should
be
> > >
> > >   set(data0_res.chi = data0.chi - interp(data0_fit.k,
data0_fit.chi,
> > > data0.k))
> > >
> > > or some variation on that.
> > >
> > > Sorry for the trouble.  It's definitely a result of
narrow-mindedly
> > > expecting that all chi(k) data comes from Ifeffit/Athena and will
> > > always start at k=0.  We should get this fixed (it's mostly
there!) so
> > > that data from other sources can be used.  Right now, the easiest
> > > work-around is to pre-pack the chi(k) data with zeros (starting
from
> > > k=0.00)
> > >
> > > --Matt
> > >
> > > _______________________________________________
> > > Ifeffit mailing list
> > > Ifeffit at millenia.cars.aps.anl.gov
> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> > --
> >  Bruce Ravel  ----------------------------------------------
> bravel at anl.gov
> >
> >  Molecular Environmental Science Group, Building 203, Room E-165
> >  MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007
> >
> >  Argonne National Laboratory         phone and voice mail: (1) 630
> > 252 5033 Argonne IL 60439, USA                                fax:
> > (1) 630 252 9793
> >
> >  My homepage:    http://cars9.uchicago.edu/~ravel
> >  EXAFS software: http://cars9.uchicago.edu/~ravel/software/
> >
> > ------------------------------
> >
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> >
> > End of Ifeffit Digest, Vol 35, Issue 14
> > ***************************************
> ------- End of Original Message -------
> 
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