On 6 September 2011 22:30, <ifeffit-request@millenia.cars.aps.anl.gov> wrote:

Send Ifeffit mailing list submissions to
ifeffit@millenia.cars.aps.anl.gov

To subscribe or unsubscribe via the World Wide Web, visit
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
or, via email, send a message with subject or body 'help' to
ifeffit-request@millenia.cars.aps.anl.gov

You can reach the person managing the list at
ifeffit-owner@millenia.cars.aps.anl.gov

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Ifeffit digest..."

Today's Topics:

1. Re: Regarding the execution of Demos in PGPLOT (Matt Newville)
2. Re: Looking for reviewers for data reduction chapter (Wei Li)
3. Re: Question on GaN Artemis fit (esp. So2 factor) (Matt Newville)

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

Message: 1
Date: Tue, 6 Sep 2011 09:03:55 -0500
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Regarding the execution of Demos in PGPLOT
Message-ID:
<CA+7ESbqeQ87-wy8OvdDn_unfWXQtzg6DUVR-Os-TJf+v_rEmkg@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Rajesh,

On Tue, Sep 6, 2011 at 7:52 AM, Rajesh Kumar <rajesh.sdc@gmail.com> wrote:
> I recently installed
> 1. PGPLOT 5 (ver: 5.2.2-15) through Synaptic Package Manager from ubuntu -
> MOTU-Developers (Mathematics, Multiverse)
> 2. IFEFFIT from Carlo Segre < segre@debian.org>, (version
> 2:1.2.11d-6~lucid0 ) and
> 3. Horae-07-1 through Synaptic Package Manager from ubuntu - developers
> (Science, Multiverse)
> I am not able to run the demo programs. So I started running demo programs
> for PGPLOT first.
> My examples are in directory:
> /usr/share/doc/pgplot5/examples/pgdemo2.f.gz
> When I compile the program "depgplot10.f" and executed the file, the
> interaction on the console is attached in the file attached herewith.
> I need help in this regard and I am very very new to "xafs" as well as
> ubuntu.

As far as I can tell from the message you attached, you ran a PGPLOT
demo program that requires a cursor for user input, selected a device
that does not support user input, and got a message saying so. That
seems reasonable to me... you might try selecting the /XW device.

But, is running the PGPLOT demos your goal? What does that have to do
with Ifeffit? If running Ifeffit is the goal, what happens when you
try to run the programs ifeffit or athena? What does "I am not able
to run the demo programs" mean?

--Matt

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

Message: 2
Date: Tue, 6 Sep 2011 10:57:43 -0400
From: Wei Li <weili@udel.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Looking for reviewers for data reduction
chapter
Message-ID:
<CAG_WZxfBDkd4Vbr7GTSEV0n=-CT=FZ=9OrOMVoCt4OoM83AXxA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi, Scott,

I am also glad to read the chapter.

Wei

On Sat, Sep 3, 2011 at 7:13 PM, Lachlan MacLean <
Lachlan.MacLean@lightsource.ca> wrote:

> Hi Scott
>
> I'm in!
>
> Cheers
> Lachlan
> ________________________________________
> From: ifeffit-bounces@millenia.cars.aps.anl.gov [
> ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin [
> scalvin@sarahlawrence.edu]
> Sent: September 3, 2011 3:16 PM
> To: XAFS Analysis using Ifeffit
> Subject: [Ifeffit] Looking for reviewers for data reduction chapter
>
> Hi all,
>
> Once again, I have a draft of a chapter of my textbook ready for review.
> This chapter is on data reduction, including normalization, background
> subtraction, and Fourier transforms. This will be Chapter 4 in the book, so
> it should be suitable for near-beginners as well as those with more
> experience. This is also a chapter where I had to make a lot of decisions on
> nomenclature and presentation, so experts might be interested as well,
> particularly if you have strong opinions on that kind of thing! It is a bit
> more than 40 pages long, which makes it the longest so far.
>
> If you are interested in reviewing the chapter and can get feedback to me
> by 29 September, please contact me directly at SCalvin@slc.edu . As
> always, repeat reviewers are welcome!
>
> --Scott Calvin
> Sarah Lawrence College
> _______________________________________________
> 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
>

--
Wei Li

Postdoc researcher
Environmental Soil Chemistry Group
Delaware Environmental Institute
University of Delaware, Newark,19713
Tel:631-949-0663
http://ag.udel.edu/soilchem/li.html <http://ag.udel.edu/soilchem/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110906/e40fb50f/attachment.html>

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

Message: 3
Date: Tue, 6 Sep 2011 11:17:43 -0500
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Question on GaN Artemis fit (esp. So2 factor)
Message-ID:
<CA+7ESbqGAjbofXhoT9f0rfWnD4ooVeotH53j41UFHoSq-okJEw@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Alejandro,

On Fri, Sep 2, 2011 at 6:08 PM, Alejandro X Levander
<alevander@berkeley.edu> wrote:
> Dear ifeffit community;
> I am working on modeling the local structure of amorphous GaN(1-x)As(x)
> alloys. After helpful learning experiences at the SSRL XAS Summer School and
> reading Scott Calvin's doped material help page, I was able to model all of
> the data for the As K edge I had collected. However, I am now having issues
> modeling the Ga K edge spectra despite using similar methods. I expect the
> Ga to be tetrahedrally coordinated and bonded to a mixture of As and N based
> on the previously determined overall composition.
> To determine the SO2 parameters for the Ga K edge I am using data collected
> in fluorescence mode of a thin film (690 nm) of GaN on a sapphire (Al2O3 -
> 500um) substrate as a reference sample. I have fixed the first and second
> shell amplitudes in order to determine SO2. The SO2 parameter for the
> nitrogen shell appears too low to be physically correct (~0.5). When I use
> these values for SO2 to try and model my amorphous films, I get highly
> unexpected coordination values much larger than four when summed for As and
> N bonding since the model is compensating for the low SO2. I am concerned
> there may be an issue with the data processing in Athena (e.g.
> self-absorption or deglitching) or multiple-scattering, but cannot pin down
> the problem.
> I have attached the GaN (sample code sn281) Athena and Artemis files and an
> example of trying to fit the Ga K edge of amorphous GaN(0.55)As(0.45)
> material in Artemis (sample code sn404). The amorphous thin film was 220 nm
> thick on a 500um pyrex glass substrate measured in fluorescence mode.
> As a side note, I have also been having trouble with using ATOMS for the
> wurtzite crystal structure. Despite trying multiple appropriate .cif files
> from ICSD and making sure to use 1/3 instead of 0.33334 when I run ATOMS,
> there appear to be rounding errors that turn one coordination into three.
> Thus I have been manually changing the feff input.
> Any help is greatly appreciated,
> Alejandro

I didn't quite understand everything you were doing, but:

- It does look like the amplitude of k^2 chi(k) is much larger (4x)
for the SN281 sample than the SN404 sample.

- I don't quite understand why you are applying different S02
parameters *per path* / bond. That is, even
for the SN281 sample, the artemis project has different S02 for Ga-N
and Ga-Ga.

The usual approach would be to apply a single S02 for all paths, and
even for all Ga spectra measured under the same conditions.

Hope that helps,

--Matt

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

_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

End of Ifeffit Digest, Vol 103, Issue 7
***************************************

--
Wishing you best of life and time,

With regards
Rajesh Kumar