- Ifeffit - millenia.cars.aps.anl.gov

Creating Athena Projects from Ifeffit command line
by Matthew Ginder-Vogel 11 Sep '07

11 Sep '07

Hi Bruce and list, Has anyone written an Ifeffit wrapper and/or script that can take a series of data files and create an Athena project without actually having to use Athena? If you have, would you be willing to share it? I'm sure it's possible, but I don't want to recreate the wheel if I don't have to. Thanks, Matt -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

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Re: [Ifeffit] Atoms question
by Bruce Ravel 07 Sep '07

07 Sep '07

On Friday 07 September 2007, Saraiya, Neeraj M. wrote: > Hi Bruce, > I am somewhat of a first time user of the Ifeffit software package > and had a question regarding the Atoms package. I am trying to input > x,y,z coordinates for a crystal structure and I realized that the > coordinates are the same for two different elements - i.e. two elements > that can interchange with each other in the structure. How can I > account for the differing ratios of occupancy between the two elements? > Thanks in advance for addressing this question. > > Best, > Neeraj Neeraj, This is a common question, so I am taking the liberty of CCing my answer to the mailing list. Look at the last question ("How do I handle doped materials? Why doesn't Atoms handle doped materials?") on this FAQ page: http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling If you still have questions after reading that, go ahead and post your questions on the mailing list and we'll see what we can do about answering them. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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energy scale when averaging data
by Matthew Ginder-Vogel 07 Sep '07

07 Sep '07

Hello Everyone, I have a very large number of data files (>10,000) that I'm trying to average using Ifeffit. However, I'm having trouble coming up with the energy scale for the averaged file. The energy scale for each individual file is very similar, but not identical, so I'm not sure if it is the best idea to use the energy scale of a single file as the energy scale for the averaged file. I'm sure that I'm not the first person to deal with this problem, so I'm interested to hear how other people deal with this problem. I'm also sure that Bruce has already come up with a clever way of dealing with this problem in Athena, but unfortunately loading 50 files at a time into Athena to average is a too slow a process. So I'd rather do them 50 at a time from the command line. Thanks, Matt ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

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Linear Combination Fitting in Athena
by Skya Fawcett 06 Sep '07

06 Sep '07

A couple questions about linear combination fitting in Athena: 1. There is the option of floating an E0 for the standards, is there any way to restrict how much it floats, ie. constrain it to +/-0.4eV shifts during fitting? 2. If I am fitting normalized u(E), and only care about the XANES region at this point, is perfecting background removal needed? (I have, of course, carefully checked the pre-edge and normalization range). Thank you! Skya Fawcett PhD Candidate Department of Geological Sciences and Geological Engineering Queen's University, Kingston, Canada

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Can't change values in Athena and Artemis on Ubuntu(Feisty)
by Jun Lin 06 Sep '07

06 Sep '07

Hi Carlo Segre, I install Athena and Artemis from your compiled deb package for feisty. When I try to change values in Athena and Artemis, it doesn't work. The only way change the value is click on the plot canvas. I have tried to execute program as root user, but it also doesn't work. Looking forward for you help. Sincerely, Lin Jun -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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Re: [Ifeffit] Ifeffit Digest, Vol 54, Issue 21
by Jun Lin 31 Aug '07

31 Aug '07

Dear Caro, Thank you for your reply :) I followed your suggestion to double click or choose all text in the boxes, but still doesn't work. I installed the software in my two computers(both Ubuntu 7.04), but the symptoms are the same. Would you please tell me how to build deb package from source? Jun On 8/31/07, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > > > Message: 2 > Date: Wed, 29 Aug 2007 23:16:07 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > Subject: Re: [Ifeffit] Can't change values in Athena and Artemis on > Ubuntu(Feisty) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <Pine.LNX.4.64.0708292306530.2507(a)localhost.localdomain> > Content-Type: text/plain; charset=us-ascii; format=flowed > > > Hi Jun: > > Do you mean changing the values in the text boxes? Sometimes, I have > noticed that you have to double click on the box or select all of the text > in order to be able to change values using the keyboard. I haven't > figured out when this happens though, it seems sort of random to me. > > Carlo > > -- Shanghai Institute of Applied Physics, Chinese Academy of Sciences No. 2019, Baojia Road, Jiading District, Shanghai,China 201800

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Ifeffit and gfortran (was: iffefit compile on BlueWhite64)
by Matt Newville 27 Aug '07

27 Aug '07

Hi Chachi, all I believe I have a source kit that will build correctly for you using gfortran. I've tested on three different generations of Fedora/Redhat linux systems, one with only g77, one with only gfortran, and one with both, and the installation now works on all of them. Please try http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz With this tar ball, you will need to install pgplot: tar xvzf ifeffit-1.2.10_rc1.tar.gz cd ifeffit-1.2.10 sh PGPLOT_install ./configure make make install (doing the two 'install steps' with sufficient privilege). Again, you need to install PGPLOT with the provided script. Both the PGPLOT and Ifeffit installations will use gfortran if available, and g77 if gfortran is not available. I think it would not be too difficult to attempt to use Intel's ifort compiler or g95, though I do not know that it's needed-- all linux distribution come with gcc so have easy-to-use packages for gfortran (and, for "legacy", g77). I did get horae-065 and the python wrappers to build with no trouble (once the Tk modules were installed) on all systems, though I haven't done much more than trivial testing. Since I tested only on a few linux boxes, I'd be interested in hearing reports for other systems. I'll wait a few days (or more) to hear reports before uploading this as ifeffit-1.2.10. --Matt

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[Fwd: Ifeffit Ok on BlueWhite64, ...]
by Chachi Rojas 25 Aug '07

25 Aug '07

Hello list again Tk module run ok. Now, my problem is compling horae-065, error message: ... make[1]: Entering directory `/usr/local/src/ifeffit-1.2.10/horae-065/Absorption' /usr/bin/perl5.8.8 chantler2st.PL chantler.db Can't locate Chemistry/Elements.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl .) at chantler2st.PL line 40. BEGIN failed--compilation aborted at chantler2st.PL line 40. make[1]: *** [chantler.db] Error 2 make[1]: Leaving directory `/usr/local/src/ifeffit-1.2.10/horae-065/Absorption' make: *** [subdirs] Error 2 ch@pcbox:/usr/local/src/ifeffit-1.2.10/horae-065$ ...... it seems not to find Chemistry/Elements.pm file (module) Ch --------------------------------- Original Message --------------------------------- Subject: Ifeffit Ok on BlueWhite64, ... From: "Chachi Rojas" <crojasa(a)unmsm.edu.pe> Date: Fri, August 24, 2007 5:12 pm To: ifeffit(a)millenia.cars.aps.anl.gov ------------------------------------------------------------------------------------ Hi Matt Ifeffit run perfectely (thanks Matt) after installed by your scripts on RC1. Now, a question for Bruce try to install horae-065, but, error message is below: ---------- === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is linux. Checking dependencies ... Tk is not installed. Download the latest from http://search.cpan.org/search?module=Tk Failed dependencies. Not installing athena and artemis. ------ Tk modules (version 8.4.15) were installed on /usr, but perl Makefile.PL it does not recognize Some idea Ch. > Date: Wed, 22 Aug 2007 15:56:26 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on > BlueWhite64) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0708221356y37280877v86ac576fe9b6b96c(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chachi, all > > I believe I have a source kit that will build correctly for you using > gfortran. I've tested on three different generations of Fedora/Redhat > linux systems, one with only g77, one with only gfortran, and one with > both, and the installation now works on all of them. > > Please try > http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz > > With this tar ball, you will need to install pgplot: > tar xvzf ifeffit-1.2.10_rc1.tar.gz > cd ifeffit-1.2.10 > sh PGPLOT_install > ./configure > make > make install > > (doing the two 'install steps' with sufficient privilege). Again, you > need to install PGPLOT with the provided script. Both the PGPLOT and > Ifeffit installations will use gfortran if available, and g77 if > gfortran is not available. I think it would not be too difficult to > attempt to use Intel's ifort compiler or g95, though I do not know > that it's needed-- all linux distribution come with gcc so have > easy-to-use packages for gfortran (and, for "legacy", g77). > > I did get horae-065 and the python wrappers to build with no trouble > (once the Tk modules were installed) on all systems, though I haven't > done much more than trivial testing. > > Since I tested only on a few linux boxes, I'd be interested in hearing > reports for other systems. > > I'll wait a few days (or more) to hear reports before uploading this > as ifeffit-1.2.10. > > --Matt > -- Chachi Rojas Ayala GMC FCF UNMSM Claro:01-97489347 email:crojasa@unmsm.edu.pe chachi.rojas(a)gmail.com

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Re: [Ifeffit] Ifeffit Digest, Vol 54, Issue 15
by joshua jason kas 23 Aug '07

23 Aug '07

Hi Eckhard, Add the following card to your feff.inp file. FOLP 2 0.8 Our default overlap is not so good for hydrogen, and 0.8 is the recommended value given in the documentation. There is some instability in the calculation of the densities near the nucleus, which in hydrogen, turns out to be comparable to the total density, and gives negative densities. I don't know why folp 0.8 helps, but it does. Cheers, Josh > > Message: 1 > Date: Wed, 22 Aug 2007 14:21:14 +0200 (CEST) > From: s440697(a)stud.uni-goettingen.de > Subject: Re: [Ifeffit] log1.dat & program break > To: "Bruce Ravel" <bravel(a)anl.gov>, "XAFS Analysis using Ifeffit" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <54988.134.76.41.165.1187785274.squirrel(a)webmail.stud.uni-goettingen.de> > > Content-Type: text/plain;charset=iso-8859-1 > > Hi Bruce, > > maybe my mail was a little bit confusing. The log1.dat from the attachment > belongs to the first problem ("negative dens "). I found this message in > the log1.dat file. > > sincerely yours, > Eckhard > >> I don't know what the lines from the log file mean. As to the program >> crashing -- Josh addressed this in his email yesterday. >> > > > --------------------------------- > Eckhard Bosman > e.bosman(a)stud.uni-goettingen.de > +49 (0)551-39-14441 > Raum: E0.104 > Institut f?r R?ntgenphysik > Friedrich-Hund-Platz 1 > 37077 G?ttingen > Germany >

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iffefit compile on BlueWhite64
by Chachi Rojas 22 Aug '07

22 Aug '07

Hello list I try to install ifeffit 1.2.9 on Linux Bluewhite64 12.0 (slackware 12.0 based) PGPLOt run perfectely, ./configure ifeffit ok but when compile, error message: ... /usr/local/src/ifeffit-1.2.9/src/lib/iff_cursor.f:68: undefined reference to `_gfortran_concat_string' /usr/X11R6/lib/libgfortranbegin.a(fmain.o): In function `main': (.text+0x5): undefined reference to `_gfortran_set_args' /usr/local/pgplot//libpgplot.so: undefined reference to `_gfortran_pow_i4_i4' /usr/local/pgplot//libpgplot.so: undefined reference to `_gfortran_transfer_array' /usr/local/pgplot//libpgplot.so: undefined reference to `_gfortran_pow_r4_i4' collect2: ld returned 1 exit status make[3]: *** [ifftest1] Error 1 make[3]: Leaving directory `/usr/local/src/ifeffit-1.2.9/src/test' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/local/src/ifeffit-1.2.9/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/src/ifeffit-1.2.9' make: *** [all-recursive-am] Error 2 My computer: Linux chy 2.6.21.5 #1 SMP Fri Jun 15 08:49:16 EEST 2007 x86_64 Intel(R) Core(TM)2 CPU 6400 @ 2.13GHz GenuineIntel GNU/Linux Same idea about this error message, Thanks Ch -- Chachi Rojas Ayala GMC FCF UNMSM Claro:01-97489347 email:crojasa@unmsm.edu.pe chachi.rojas(a)gmail.com

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