Re: [Ifeffit] Hexagonal WO3 (Carlo Segre)

22 Nov 2008

      Hi Carlo and Ying,

Does it means that if the sample is a random solid solution at experimental
temperature, in principle, you would be able to simulate the EXAFS spectra
whichever be the Mo/W ratio in the second shell coordination in the
Feff.inp, am I right?

Thanks, Yordy

2008/11/18 
...
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Today's Topics:
1. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b   on
     Ubuntu from source (Matt Newville)
  2. Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to
     ifeffit-1.2.11b on Ubuntu from source) (Matt Newville)
  3. Re: Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading
     to ifeffit-1.2.11b on Ubuntu from source) (Carlo Segre)
  4. Re: Ifeffit 1.2.11c (was Re: [PGPLOT build problem]       Upgrading
     to ifeffit-1.2.11b on Ubuntu from source) (Matt Newville)
  5. Hexagonal WO3 (Ying Zhou, Anorganisch-Chemisches Inst.)
  6. Re: Hexagonal WO3 (Carlo Segre)
----------------------------------------------------------------------
Message: 1
Date: Mon, 17 Nov 2008 12:30:20 -0600
From: "Matt Newville" 
Subject: Re: [Ifeffit] [PGPLOT build problem] Upgrading to
       ifeffit-1.2.11b on Ubuntu from source
To: "XAFS Analysis using Ifeffit" 
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1
Hi,
This is my fault... and I apologize for the sloppiness and for being
late in fixing this.   I've been mixing 'development/testing' and
'production'  versions, and haven't been very good at keeping them
cleanly separated.     I think I have this mostly under control now,
but I will have to work on a decent "test suite".
I think I found another reason to make a 1.2.11c version too, that the
mixing of "devel" and "production"
caused an experiment in how fitting was done to be the default, so
that the reported chi-square doesn't actually match the documentation
(instead of summing real and imaginary parts, it sums real and
magnitude components of the misfit, which is part of an experiment to
see how Feff8.5 worked for XAFS.  Using Magnitude as well Phase for
another way to report chi-square and misfits is potentially a useful
approach, but it's not what is documented.  Anyway, mixing devel and
production versions like this (for the past couple years, really) is
very sloppy on my part, and I apologize again.
I actually have an ubuntu box now, though I built pgplot from source,
and have never made a .deb file.
There is a new source kit at
http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz   I'll
post this to sourceforge this afternoon, and  I'll also make a new DLL
for Windows and post all of these on the download page. I'll also make
a new updater for Windows.
--Matt
On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi  wrote:
...
Carlo Segre wrote:
...
Hi Mauro:
I have now produced a package of ifeffit 1.2.11b.  It is in Debian
unstable and available for Ubuntu intrepid and jaunty in my repository
deb http://debian-xray.iit.edu intrepid main contrib non-free
Carlo,
Thank you very much for the package.
Actually, I was able to build/install ifeffit 1.2.11b from source but
not able to build than the Perl/Python wrappers and so no Horae&Friends
from Bruce SVN.
Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and
"python-ifeffit" from binaries and "libperlxray" "horae" and "demeter"
built from source (Bruce SVN).
Everything seems fine but I still do not understand why ifeffit 1.2.11
has all these "IFF str = *" output as stated also by Gareth in his
"Ifeffit 1.2.11b terminal output" post. Is it normal?
Cheers,
Mauro
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
Message: 2
Date: Mon, 17 Nov 2008 17:06:35 -0600
From: "Matt Newville" 
Subject: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem]
       Upgrading       to ifeffit-1.2.11b on Ubuntu from source)
To: "XAFS Analysis using Ifeffit" 
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1
Hi Folks,
I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu
and sourceforge.net download sites.
I have a Windows dll made for this bug fix version.  If anyone is
interested, this is currently at
 http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll
This should be a drop-in replacement for the
IFEFFIT_DIR\bin\ifeffit_12.dll   on your system.
Artemis.exe will not be updated from this dll, as it has this dlls
"compiled in".  Bruce will have to make a new Artemis.exe, and then
we'll make a automatic update.
Sorry for all the trouble,
--Matt
On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville
 wrote:
...
Hi,
This is my fault... and I apologize for the sloppiness and for being
late in fixing this.   I've been mixing 'development/testing' and
'production'  versions, and haven't been very good at keeping them
cleanly separated.     I think I have this mostly under control now,
but I will have to work on a decent "test suite".
I think I found another reason to make a 1.2.11c version too, that the
mixing of "devel" and "production"
caused an experiment in how fitting was done to be the default, so
that the reported chi-square doesn't actually match the documentation
(instead of summing real and imaginary parts, it sums real and
magnitude components of the misfit, which is part of an experiment to
see how Feff8.5 worked for XAFS.  Using Magnitude as well Phase for
another way to report chi-square and misfits is potentially a useful
approach, but it's not what is documented.  Anyway, mixing devel and
production versions like this (for the past couple years, really) is
very sloppy on my part, and I apologize again.
I actually have an ubuntu box now, though I built pgplot from source,
and have never made a .deb file.
There is a new source kit at
http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz   I'll
post this to sourceforge this afternoon, and  I'll also make a new DLL
for Windows and post all of these on the download page. I'll also make
a new updater for Windows.
--Matt
On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi  wrote:
...
Carlo Segre wrote:
...
Hi Mauro:
I have now produced a package of ifeffit 1.2.11b.  It is in Debian
unstable and available for Ubuntu intrepid and jaunty in my repository
deb http://debian-xray.iit.edu intrepid main contrib non-free
Carlo,
Thank you very much for the package.
Actually, I was able to build/install ifeffit 1.2.11b from source but
not able to build than the Perl/Python wrappers and so no Horae&Friends
from Bruce SVN.
Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and
"python-ifeffit" from binaries and "libperlxray" "horae" and "demeter"
built from source (Bruce SVN).
Everything seems fine but I still do not understand why ifeffit 1.2.11
has all these "IFF str = *" output as stated also by Gareth in his
"Ifeffit 1.2.11b terminal output" post. Is it normal?
Cheers,
Mauro
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
Message: 3
Date: Mon, 17 Nov 2008 20:03:06 -0600 (CST)
From: Carlo Segre 
Subject: Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem]
       Upgrading       to ifeffit-1.2.11b on Ubuntu from source)
To: Matt Newville 
Cc: XAFS Analysis using Ifeffit 
Message-ID: 
Content-Type: text/plain; charset=us-ascii; format=flowed
Debian packages have been uploaded to unstable and I am in the process of
building Ubuntu packages for my repository.  i expect that they will be up
tonight.
carlo
On Mon, 17 Nov 2008, Matt Newville wrote:
...
Hi Folks,
I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu
and sourceforge.net download sites.
I have a Windows dll made for this bug fix version.  If anyone is
interested, this is currently at
 http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll
This should be a drop-in replacement for the
IFEFFIT_DIR\bin\ifeffit_12.dll   on your system.
Artemis.exe will not be updated from this dll, as it has this dlls
"compiled in".  Bruce will have to make a new Artemis.exe, and then
we'll make a automatic update.
Sorry for all the trouble,
--Matt
On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville
 wrote:
...
Hi,
This is my fault... and I apologize for the sloppiness and for being
late in fixing this.   I've been mixing 'development/testing' and
'production'  versions, and haven't been very good at keeping them
cleanly separated.     I think I have this mostly under control now,
but I will have to work on a decent "test suite".
I think I found another reason to make a 1.2.11c version too, that the
mixing of "devel" and "production"
caused an experiment in how fitting was done to be the default, so
that the reported chi-square doesn't actually match the documentation
(instead of summing real and imaginary parts, it sums real and
magnitude components of the misfit, which is part of an experiment to
see how Feff8.5 worked for XAFS.  Using Magnitude as well Phase for
another way to report chi-square and misfits is potentially a useful
approach, but it's not what is documented.  Anyway, mixing devel and
production versions like this (for the past couple years, really) is
very sloppy on my part, and I apologize again.
I actually have an ubuntu box now, though I built pgplot from source,
and have never made a .deb file.
There is a new source kit at
http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz   I'll
post this to sourceforge this afternoon, and  I'll also make a new DLL
for Windows and post all of these on the download page. I'll also make
a new updater for Windows.
--Matt
On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi 
wrote:
...
Carlo Segre wrote:
...
Hi Mauro:
I have now produced a package of ifeffit 1.2.11b.  It is in Debian
unstable and available for Ubuntu intrepid and jaunty in my repository
deb http://debian-xray.iit.edu intrepid main contrib non-free
Carlo,
Thank you very much for the package.
Actually, I was able to build/install ifeffit 1.2.11b from source but
not able to build than the Perl/Python wrappers and so no Horae&Friends
from Bruce SVN.
Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and
"python-ifeffit" from binaries and "libperlxray" "horae" and "demeter"
built from source (Bruce SVN).
Everything seems fine but I still do not understand why ifeffit 1.2.11
has all these "IFF str = *" output as stated also by Gareth in his
"Ifeffit 1.2.11b terminal output" post. Is it normal?
Cheers,
Mauro
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--
Carlo U. Segre -- Professor of Physics
Associate Dean for Special Projects, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498            Fax: 312.567.3494
segre@iit.edu   http://www.iit.edu/~segre   segre@debian.org
------------------------------
Message: 4
Date: Mon, 17 Nov 2008 21:10:51 -0600
From: "Matt Newville" 
Subject: Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem]
       Upgrading to ifeffit-1.2.11b on Ubuntu from source)
To: segre@agni.phys.iit.edu
Cc: XAFS Analysis using Ifeffit 
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1
Thanks, Carlo!
--Matt
On Mon, Nov 17, 2008 at 8:03 PM, Carlo Segre  wrote:
...
Debian packages have been uploaded to unstable and I am in the process of
building Ubuntu packages for my repository.  i expect that they will be
up
...
tonight.
carlo
On Mon, 17 Nov 2008, Matt Newville wrote:
...
Hi Folks,
I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu
and sourceforge.net download sites.
I have a Windows dll made for this bug fix version.  If anyone is
interested, this is currently at
 http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll
This should be a drop-in replacement for the
IFEFFIT_DIR\bin\ifeffit_12.dll   on your system.
Artemis.exe will not be updated from this dll, as it has this dlls
"compiled in".  Bruce will have to make a new Artemis.exe, and then
we'll make a automatic update.
Sorry for all the trouble,
--Matt
On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville
 wrote:
...
Hi,
This is my fault... and I apologize for the sloppiness and for being
late in fixing this.   I've been mixing 'development/testing' and
'production'  versions, and haven't been very good at keeping them
cleanly separated.     I think I have this mostly under control now,
but I will have to work on a decent "test suite".
I think I found another reason to make a 1.2.11c version too, that the
mixing of "devel" and "production"
caused an experiment in how fitting was done to be the default, so
that the reported chi-square doesn't actually match the documentation
(instead of summing real and imaginary parts, it sums real and
magnitude components of the misfit, which is part of an experiment to
see how Feff8.5 worked for XAFS.  Using Magnitude as well Phase for
another way to report chi-square and misfits is potentially a useful
approach, but it's not what is documented.  Anyway, mixing devel and
production versions like this (for the past couple years, really) is
very sloppy on my part, and I apologize again.
I actually have an ubuntu box now, though I built pgplot from source,
and have never made a .deb file.
There is a new source kit at
http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz   I'll
post this to sourceforge this afternoon, and  I'll also make a new DLL
for Windows and post all of these on the download page. I'll also make
a new updater for Windows.
--Matt
On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi 
wrote:
...
...
Carlo Segre wrote:
...
Hi Mauro:
I have now produced a package of ifeffit 1.2.11b.  It is in Debian
unstable and available for Ubuntu intrepid and jaunty in my
repository
...
...
deb http://debian-xray.iit.edu intrepid main contrib non-free
Carlo,
Thank you very much for the package.
Actually, I was able to build/install ifeffit 1.2.11b from source but
not able to build than the Perl/Python wrappers and so no
Horae&Friends
from Bruce SVN.
Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and
"python-ifeffit" from binaries and "libperlxray" "horae" and "demeter"
built from source (Bruce SVN).
Everything seems fine but I still do not understand why ifeffit 1.2.11
has all these "IFF str = *" output as stated also by Gareth in his
"Ifeffit 1.2.11b terminal output" post. Is it normal?
Cheers,
Mauro
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--
Carlo U. Segre -- Professor of Physics
Associate Dean for Special Projects, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498            Fax: 312.567.3494
segre@iit.edu   http://www.iit.edu/~segre   segre@debian.org
------------------------------
Message: 5
Date: Tue, 18 Nov 2008 17:20:24 +0100
From: "Ying Zhou, Anorganisch-Chemisches Inst." 
Subject: [Ifeffit] Hexagonal WO3
To: ifeffit@millenia.cars.aps.anl.gov
Message-ID: 
Content-Type: text/plain;charset=iso-8859-1;format="flowed"
Dear All
Recently, I got one compound, W/Mo oxide, which has the similar structure
with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of this
compound. So, we use the hexagonal WO3 model to refine the structure of our
compounds. My question is that how can I get the FEFF file of this
compound.
Can I directly change some of W to Mo in FEFF file? or Do I need to add the
Mo in the atom file? I do appreciate your help.
Best wishes
Ying
------------------------------
Message: 6
Date: Tue, 18 Nov 2008 10:33:35 -0600 (CST)
From: Carlo Segre 
Subject: Re: [Ifeffit] Hexagonal WO3
To: XAFS Analysis using Ifeffit 
Message-ID: 
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Hi Ying:
On Tue, 18 Nov 2008, Ying Zhou, Anorganisch-Chemisches Inst. wrote:
...
Dear All
Recently, I got one compound, W/Mo oxide, which has the similar structure
with hexagonal WO3. We tested the EXAFS of W L3 edge and Mo K edge of
this
compound. So, we use the hexagonal WO3 model to refine the structure of
our
compounds. My question is that how can I get the FEFF file of this
compound.
Can I directly change some of W to Mo in FEFF file? or Do I need to add
the
Mo in the atom file? I do appreciate your help.
There are several ways to do this, depending on what you are trying to
find out.  If you change W to Mo in the atoms input file than you are
really making MoO3.  What it seems like you need to do is to generate the
FEFF input file from the WO3 structure, then replace the central atom with
Mo.  This will give you the first path which is likely oxygen.  The second
longest set of paths are likely to be W/Mo and you can do two things, one
is to generate a FEFF calculation with W in this position and then make a
second calculation with Mo and use both paths to fit the Mo environment.
You will have to be careful about multiplicities though since by starting
with the WO3 structure, you are assuming some degeneracies in the paths.
The advantage is that you potentially have some multiple scatteing paths
available to use.
Another approach is to generate the FEFF input file from WO3, look at the
near neighbors and then generate some "quick first shell" paths for the
nearest neighbor (oxygen) and then two fro the next near neighbor (one
with W and one with Mo).  The difference here is that you now have
uncorrelated paths with no implied degeneracies.  You cannot use this to
fit multiple scattering paths.
I guess that my approach would be to start with the latter, more simple
approach first to try to understand the problem.  If I see that the
environment looks like it is possible to fit with multiple scattering, I
would move to the first approach, being careful to realize that in a solid
sloution compound, the occupancy of the second shell of metal atoms is
probably random and not perfectly ordered like a FEFF input file with
substitutions would be.
Hope this helps.
Carlo
--
Carlo U. Segre -- Professor of Physics
Associate Dean for Special Projects, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498            Fax: 312.567.3494
segre@iit.edu   http://www.iit.edu/~segre   segre@debian.org
------------------------------
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
End of Ifeffit Digest, Vol 69, Issue 13
***************************************
-- 
Yordy E. Licea Fonseca
Departamento de Físico-Química
Instituto de Química-IQ/UFRJ
Laboratório de Catálise Heterogênea
Rio de Janeiro, RJ, CEP 21.949-909
Brasil
Email: yliceafonseca@gmail.com

Re: [Ifeffit] Hexagonal WO3 (Carlo Segre)

Yordy Licea Fonseca