2008/11/18 <ifeffit-request@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@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@millenia.cars.aps.anl.gov>
Message-ID:
<b8522e3d0811171030o2db1e183va43b9dcb4d99705e@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@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@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@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@millenia.cars.aps.anl.gov>
Message-ID:
<b8522e3d0811171506h438ba6abke90121bbb1744818@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@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@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@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@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@cars.uchicago.edu>
Cc: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Message-ID: <alpine.DEB.2.00.0811172002240.3650@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@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@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@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" <newville@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@agni.phys.iit.edu
Cc: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Message-ID:
<b8522e3d0811171910p4509bdacn3dc6ed65606d9580@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@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@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@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@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." <ying.zhou@aci.uzh.ch>
Subject: [Ifeffit] Hexagonal WO3
To: ifeffit@millenia.cars.aps.anl.gov
Message-ID: <web-16292974@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@iit.edu>
Subject: Re: [Ifeffit] Hexagonal WO3
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Message-ID: <alpine.DEB.2.00.0811181023390.19806@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@iit.edu http://www.iit.edu/~segre segre@debian.org

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

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Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
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End of Ifeffit Digest, Vol 69, Issue 13
***************************************