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-requ...@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-requ...@millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-ow...@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 <newvi...@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_re...@mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Rajesh, > > > On Tue, Sep 6, 2011 at 7:52 AM, Rajesh Kumar <rajesh....@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 < se...@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 <we...@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=9oromvoct4oom83a...@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.macl...@lightsource.ca> wrote: > > > Hi Scott > > > > I'm in! > > > > Cheers > > Lachlan > > ________________________________________ > > From: ifeffit-boun...@millenia.cars.aps.anl.gov [ > > ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin [ > > scal...@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 scal...@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 <newvi...@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-ok...@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 > <alevan...@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
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