My memory is that Yves Joly's FDMNES codes is available for the
asking, but the last time I looked at it (many years ago by now) I was
unable to get it compiled on my linux machine.

It is possible that Delphine Cabaret's pseudopotential approach may be
available for outside use as well, but I do not know for sure -- it's
been a while since I last spoke with her.

The folks associated with Rostov have codes for computing XANES
spectra.  I believe Victor Kraizman reads this list and may be able to
elaborate.

B


--
Bruce Ravel  ---------------------------------------------- bravel@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/




------------------------------

Message: 3
Date: Sat, 29 Jul 2006 22:42:44 -0500
From: Bruce Ravel <bravel@anl.gov >
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Message-ID: <200607292242.45091.bravel@anl.gov >
Content-Type: text/plain;  charset="iso-8859-1"

On Saturday 29 July 2006 17:24, you wrote:
> 4) The formalism underlying GNXAS is very elegant and reading the original
> papers is great. I suggest it is highly worth the effort.

This is true.  They are indeed very interesting papers.  The physics
or physical chemistry students reading this list would be well advised
to seek them out.

I would also put in a plug for the PRB from 1990 by Rehr and Albers
about the fast separable formalism for computing the photoelectron
propagator.  That paper was my constant companion for about a year in
grad school and is really quite lovely.

> 5) Regarding ease of use: is XAS amenable to a "black box" approach?
> Despite the fact that this clashes with what many of us teach to physics
> students, it might be very useful e.g. in the field of bioXAS. But can this
> be done? Or is the underlying physics too complex?

Ah!  The "black box" discussion.  That's a fun way to waste lots of
time. ;-)

The physics has its complicated parts, but I suspect that we have a
sufficient understanding of the problems.  There are many applications
where a black box is reasonable to consider and probably would even
work pretty well.  At the recent XAFS conference, the group from
Manchester, UK presented a high-throughput scheme that involves
automate processing of larfge quantities of data.  They seem to get
good results with minimal human intervention.  And Harald Funke gave a
really neat talk about Feff-based wavelets that could be a very useful
approach to a first-shell black-box.

There will always be a large part of exafs analysis that falls well
outside the scope the black box.  The sorts of crazy fits published by
some of the frequent contributors to this list (I am thinking
specifically of Scott Calvin and Shelly Kelly) will always defy
automation.

Well, that was my US$0.02 worth...
B


--
Bruce Ravel  ---------------------------------------------- bravel@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/




------------------------------

Message: 4
Date: Sun, 30 Jul 2006 08:20:58 -0400
From: Scott Calvin <SCalvin@slc.edu>
To: XAFS Analysis using Ifeffit < ifeffit@millenia.cars.aps.anl.gov>
Message-ID: <7.0.1.0.0.20060730075047.020630b8@slc.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed

Well, I have some time to waste, and since my name was just mentioned...

I think a black box is a wonderful idea for cases where the space of
possible solutions is very limited. At the same conference that the
UK group presented, Wolfram Meyer-Klaucke gave a very nice talk on a
black-box system for determining protein structure around an active
site. The talk was opposite the UK group's, so unfortunately no one saw both.

In any case, that's a perfect situation for automation: there are a
very limited number of ligands that could be present, and their
structures are very well understood. It's much more than
fingerprinting, since the combination of ligands might never have
seen before. Their system even allows for the ligands to be at
slightly unusual distances. But it only works because the
biochemistry is already pretty well understood and quite limited.
Although a very different system, I suspect the UK automation of
supported metal catalysts has similarly limited scope; neither system
would probably work very well when fed data meant for the other!

I think there's sometimes a wish for a system that acts like a Star
Trek tricorder: stick any spectrum in, and the computer can say "it
appears to be an oxide with coordination number 6." In my opinion,
that kind of system will never be developed, because there just isn't
that much information sitting in the EXAFS. (Some of you new to EXAFS
may be puzzled by that--it doesn't sound like very much information
at all. But if you're going to allow me the space of all possible
structures along with less-than-perfect data, it's hard to
distinguish disorder from coordination number changes, for example,
and it's in turn hard to distinguish true disorder from splitting
below the resolution of the data.)

In other words, current experts in EXAFS analysis don't act as black
boxes to the outside world. If <pick-your-favorite-expert> were
brought a spectrum and asked "OK, tell me the structure," the expert
would immediately start asking questions to gain additional
information (or would say "no," and walk off in a huff). If experts
don't act as black boxes, then neither can a computer.

OK, with my two cents added to Bruce, that now makes four...

--Scott Calvin
Sarah Lawrence College



>Ah!  The "black box" discussion.  That's a fun way to waste lots of
>time. ;-)
>
>The physics has its complicated parts, but I suspect that we have a
>sufficient understanding of the problems.  There are many applications
>where a black box is reasonable to consider and probably would even
>work pretty well.  At the recent XAFS conference, the group from
>Manchester, UK presented a high-throughput scheme that involves
>automate processing of larfge quantities of data.  They seem to get
>good results with minimal human intervention.  And Harald Funke gave a
>really neat talk about Feff-based wavelets that could be a very useful
>approach to a first-shell black-box.
>
>There will always be a large part of exafs analysis that falls well
>outside the scope the black box.  The sorts of crazy fits published by
>some of the frequent contributors to this list (I am thinking
>specifically of Scott Calvin and Shelly Kelly) will always defy
>automation.
>
>Well, that was my US$0.02 worth...
>B




------------------------------

Message: 5
Date: Sun, 30 Jul 2006 07:29:08 -0700
From: "Matthew Marcus" < mamarcus@lbl.gov>
To: "XAFS Analysis using Ifeffit" <ifeffit@millenia.cars.aps.anl.gov>
Message-ID: < 014401c6b3e4$86ef1a50$dd4cf383@lbl.gov>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
        reply-type=response

>> Including only bare-bones ASCII in/out is, IMHO, the only way to obtain
>> true portability,  and it has worked.  I vaguely recall that they use
>> some
>> sort of verifier on their code to screen out system dependencies.
>
> I don't understand this.

A verifier is a program that inspects programs, looking for probable bugs
such as un-initialized
variables, non-standard syntax, and system dependencies.  In fortran and C,
graphics is
not natively provided, so much be called from a library.  Such libraries
vary from system to system.

>
>> If it uses a g(r) approach, then I imagine that it doesn't handle
>> multiple
>> scattering.  On the
>> other hand, it could be argued that *in the EXAFS range* a system which
>> needs a g(r) approach
>> won't have detectable MS.  That still leaves XANES, though.
>
> Actually, GNXAS does handle MS.  It's not clear to me how well it handles
> small crystallographic distortions, mixed shells, and so on, but it does
> include MS.   I agree with you that requiring one of g(R) and MS seems
> to suggest that the other isn't necessary.

It may use MS for systems in which the atomic positions are defined, but
g(r) alone
does not define them.  To get both *at one time* would require some way of
specifying
baseline atoms positions plus some random distortions with specified
distributions, plus
models for how those distortions are correlated.  Essentially, calculating
MS requires assuming
things about 3-body correlations at least.
>
>> > That's not about "theory" as analysis. I don't know what theoretical
>> > advantages GNXAS might have.  I believe it includes curved wave
>> > effects,
>> > and that it uses the Hedin-Lunqvist exchange (perhaps the only
>> > option?).
>> > I think that it has a simple polarization model  (perhaps only
>> > dipole??).
>> > I
>> > believe it does multiple-scattering only out to four-leg paths  (good
>> > enough
>> > for almost  all cases), and don't know how it does this.  I recall from
>> > one of
>> > the GNXAS papers that they talked about correlating Debye-Waller
>> > factors
>> > for MS paths with those of SS paths, but I don't know that works in
>> > practice.
>>
>> All that sounds like what FEFF has.
>
> Err, no.  Feff has multiple options for exchange potentials, and decent
> models for loss terms.  Feff has polarization dependence beyond dipole,
> which is needed for L edges, and can do elliptical polarization fot XMCD.
> I think GNXAS has none of that.

I meant that FEFF's options are a superset, not that they are identical.

>
> For DW factors for MS paths, Feff can use the correlated Debye model.
> GNXAS claims to do something different and more complicated, but I've
> never understand this, or why that would be important for systems that
> needed to be treated with a g(R).

If GNXAS provides two different systems, one for disordered systems
described by g(r)
and one for systems described by atomic positions, then maybe the
'different&more complicated'
part is only for the atom-position case.
    mam



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