[Ifeffit] Hexagonal WO3 (Carlo Segre)

Yordy Licea Fonseca yliceafonseca at gmail.com
Sat Nov 22 09:23:28 CST 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 <ifeffit-request at millenia.cars.aps.anl.gov>

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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" <newville at cars.uchicago.edu>
> Subject: Re: [Ifeffit] [PGPLOT build problem] Upgrading to
>        ifeffit-1.2.11b on Ubuntu from source
> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID:
>        <b8522e3d0811171030o2db1e183va43b9dcb4d99705e at mail.gmail.com>
> 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 <rovezzi at esrf.fr> 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 at 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" <newville at cars.uchicago.edu>
> 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" <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID:
>        <b8522e3d0811171506h438ba6abke90121bbb1744818 at mail.gmail.com>
> 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
> <newville at cars.uchicago.edu> 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 <rovezzi at esrf.fr> 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 at 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 <segre at iit.edu>
> 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 <newville at cars.uchicago.edu>
> Cc: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <alpine.DEB.2.00.0811172002240.3650 at hydride.iit.edu>
> 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
> > <newville at cars.uchicago.edu> 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 <rovezzi at esrf.fr>
> 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 at millenia.cars.aps.anl.gov
> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >>>
> >>>
> >>
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at 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 at iit.edu   http://www.iit.edu/~segre   segre at debian.org
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 17 Nov 2008 21:10:51 -0600
> From: "Matt Newville" <newville at cars.uchicago.edu>
> Subject: Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem]
>        Upgrading to ifeffit-1.2.11b on Ubuntu from source)
> To: segre at agni.phys.iit.edu
> Cc: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID:
>        <b8522e3d0811171910p4509bdacn3dc6ed65606d9580 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thanks, Carlo!
>
> --Matt
>
>
>
>
> On Mon, Nov 17, 2008 at 8:03 PM, Carlo Segre <segre at iit.edu> 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
> >> <newville at cars.uchicago.edu> 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 <rovezzi at esrf.fr>
> 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 at millenia.cars.aps.anl.gov
> >>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >>>>
> >>>>
> >>>
> >> _______________________________________________
> >> Ifeffit mailing list
> >> Ifeffit at 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 at iit.edu   http://www.iit.edu/~segre   segre at debian.org
> >
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 18 Nov 2008 17:20:24 +0100
> From: "Ying Zhou, Anorganisch-Chemisches Inst." <ying.zhou at aci.uzh.ch>
> Subject: [Ifeffit] Hexagonal WO3
> To: ifeffit at millenia.cars.aps.anl.gov
> Message-ID: <web-16292974 at idmailbe2b.unizh.ch>
> 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 <segre at iit.edu>
> Subject: Re: [Ifeffit] Hexagonal WO3
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <alpine.DEB.2.00.0811181023390.19806 at oxide.phys.iit.edu>
> 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 at iit.edu   http://www.iit.edu/~segre   segre at debian.org
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at 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 at gmail.com
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