[Ifeffit] Ifeffit Digest, Vol 103, Issue 7

Rajesh Kumar rajesh.sdc at gmail.com
Tue Sep 6 13:07:07 CDT 2011


Dear Matt,
Thanks for your mail. I moved with your advice with PGPLOT a couple of weeks
back. After that I could install PGPLOT. Then I installed ATHENA, ARTEMIS
and there were some error messages when I was trying to run FIT in ARTEMIS.
I tried to resolve them, but then I thought of testing the installation of
PGPLOT and then I found that the demos were not working. Since at that time
I had tried to install different versions of IFEFFIT, ATHENA and DEMETER, my
system got cluttered.
So I cleaned the system. Removed all the programs.
I installed PGPLOT, HORAE though ubuntu afresh.
Then I started to run the demos of PGPLOT.
with advice from Pawel, I was able to run compile and execute the .f
programs.
with "I am not able to run the demo programs" meant that at that time I was
not able to run the  PGPLOT demos.
As I mentioned running PGPLOT demos was just a check, my goal is to use
IFEFFIT, ATHENA and now I would be moving to that.
With regards
Rajesh


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

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> 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 at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at 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 at 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 at 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 at 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 at udel.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Looking for reviewers for data reduction
>        chapter
> Message-ID:
>        <CAG_WZxfBDkd4Vbr7GTSEV0n=-CT=FZ=9OrOMVoCt4OoM83AXxA at 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 at lightsource.ca> wrote:
>
> > Hi Scott
> >
> > I'm in!
> >
> > Cheers
> > Lachlan
> > ________________________________________
> > From: ifeffit-bounces at millenia.cars.aps.anl.gov [
> > ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin [
> > scalvin at 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 at slc.edu . As
> > always, repeat reviewers are welcome!
> >
> > --Scott Calvin
> > Sarah Lawrence College
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
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> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
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> >
>
>
>
> --
> 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/>
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> ------------------------------
>
> Message: 3
> Date: Tue, 6 Sep 2011 11:17:43 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Question on GaN Artemis fit (esp. So2 factor)
> Message-ID:
>        <CA+7ESbqGAjbofXhoT9f0rfWnD4ooVeotH53j41UFHoSq-okJEw at 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 at 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
>
>
> ------------------------------
>
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> End of Ifeffit Digest, Vol 103, Issue 7
> ***************************************
>



-- 
Wishing you best of life and time,

With regards
Rajesh Kumar
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