March 2013 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 04 Dec '14

04 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

3 2

anisotropic Debye temperatures in reciprocal-space calculations
by Van Der Veen, Renske M. 29 Mar '13

29 Mar '13

Dear FEFF users! I am looking into the use of the DEBYE card in order to calculate the EELS spectrum of graphite at ~800 K. Obviously, graphite is highly anisotropic, such that it would be unphysical to use a single Debye temperature. However, the effective in-plane (a,b axes) and out-of-plane (c axis) Debye temperatures are known for graphite (2500 and 950 K, respectively). I was therefore wondering whether it is possible in FEFF9 to specify two Debye temperatures for the two different crystallographic directions. I am calculating the (oriented) EELS spectrum of graphite in reciprocal space using the RECIPROCAL, LATTICE and ATOMS cards; see feff.inp file below. I am using FEFF version 9.05. In case the use of Debye temperatures is not possible in this way, could anybody recommend another way to take into account the Debye-Waller factors for an anisotropic material such as graphite? Thanks! Best regards, Renske van der Veen -- Dr. Renske M. van der Veen California Institute of Technology Arthur Amos Noyes Laboratory of Chemical Physics 1200 E California Blvd MC 127-72, Pasadena, CA 91125, USA Office: (+1) (626) 395 6530 Mobile: (+1) (626) 808 2635 **** TITLE graphite * C K edge energy = 284.20 eV EDGE K 0.0 CONTROL 1 1 1 1 1 1 PRINT 1 1 1 1 1 1 COREHOLE RPA LDOS -20 10 0.05 * this calculates the density of states EGRID e_grid -3 17 0.3 e_grid last 30 0.4 e_grid last 58 1 ELNES 200 # beam energy in keV 0 0 1 # beam direction in the crystal frame 10 5 # collection semiangle, convergence semiangle (in mrad) 200 1 # q-integration mesh : radial size, angular size 0.0 0.0 # position of the detector (x,y angle in mrad) FMS 7.0 2 EXCHANGE 0 1 0.7 SCF 5 RPATH 0.2 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 6 C 3 2 0.01 1 6 C 3 2 2 2 6 C 3 2 2 RECIPROCAL KMESH 5000 MARKER 1 LATTICE P 2.4612 0.86603 -0.50000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 2.72546 ATOMS * this list contains 251 atoms * * x y z ipot tag distance 0.00000 0.00000 0.68160 1 C1 0.00000 0.00000 2.04479 1 C1 0.57735 0.00000 0.68160 2 C2 0.28868 0.50000 2.04479 2 C2 END

1 0

Demeter 0.9.16
by Bruce Ravel 29 Mar '13

29 Mar '13

Hi, I just tagged a new release of Demeter at https://github.com/bruceravel/demeter and made a link to the new Updater package for Windows at http://bruceravel.github.com/demeter/ This release fixes several issues that have bee raised in the last week or so. For details, see the change log at https://github.com/bruceravel/demeter/blob/master/Changes.org B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

1 0

Possible bug in atoms files generation by Artemis
by Devender 28 Mar '13

28 Mar '13

Hi, I ran updater for Demeter 0.9.15. I was using Artemis to calculate paths for Bi L3 in Bi2Te3. I saw now the option of using both (FEFF 6 and FEFF 8 style) for atoms. Previously, I was using only available option of FEFF6 style. When I tried to run atoms selecting FEFF 8, it generated atoms files but when I tried to run FEFF calculations it produced following errors. Error#1 " Unknown keyword: "EDGE" at line: EDGE L3" Error#2 "Unknown keyword: "exchange" at line: exchange" I worked around first error by replacing "EDGE L3 S02 1.0 "- which was generated by atoms when FEFF8 style is selected. with "HOLE 4 1.0" and deleting Exchange keyword from feff file. After making these edits in feff files, I was able to run FEFF without showing any errors. I have attached all the files with appropriate name. -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website <https://sites.google.com/site/devendermaun/>

5 10

Shifted data in Athena
by George Sterbinsky 27 Mar '13

27 Mar '13

Hello, I have attached an (D)Athena project with containing two groups, imported as a primary data set and a reference. The groups were therefore imported on the same energy grid. However, when plotted, the energy values of the data points for the two groups are clearly shifted with respect to each other. Can someone please explain the origin of this shift? Thank you, George

2 4

plotting
by Eva Vanamee 26 Mar '13

26 Mar '13

Thanks everyone for the helpful comments! I'll go with exporting to Origin. A final question. I am now a Mac user, is there a good alternative to Origin? Best, - Eva On Mar 26, 2013, at 2:45 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. generating high res figures (Eva Vanamee) > 2. Re: generating high res figures (Scott Calvin) > 3. Re: generating high res figures (Jason Gaudet) > 4. Re: generating high res figures (Christopher Patridge) > 5. Re: generating high res figures (Ravel, Bruce) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Mar 2013 13:13:17 -0400 > From: Eva Vanamee <eva.vanamee(a)mssm.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] generating high res figures > Message-ID: <C2797F03-A481-47C5-8631-B43292F375B2(a)mssm.edu> > Content-Type: text/plain; charset=us-ascii > > Hi, > > I'm in the happy stages of making figures. > I'd like to know how to change figure legends, make high resolution figures from a fit, etc. > > For instance: > I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? > Can I change the figure legends? I used sample 1 and I want to give it a different name > Can I use special characters (e.g. Greek letters)? > Can I adjust the resolution for different formats (talk vs. publication)? > > I am running Demeter 0.9.9.9 under XP. > > Thanks in advance for the help! > > - Eva > > > > > ------------------------------ > > Message: 2 > Date: Tue, 26 Mar 2013 13:25:01 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] generating high res figures > Message-ID: <CCDBA9E5-8A56-4438-A0EC-E1A9B3F6CB45(a)slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Eva, > > Demeter is not intended to be used to produce publication-quality figures. It's best to export the data, fits, etc., and then use a proper graphing program to generate figures. Even a spreadsheet will do in a pinch, although most of us use dedicated scientific graphing software. > > --Scott Calvin > Sarah Lawrence College > > On Mar 26, 2013, at 1:13 PM, Eva Vanamee <eva.vanamee(a)mssm.edu> wrote: > >> Hi, >> >> I'm in the happy stages of making figures. >> I'd like to know how to change figure legends, make high resolution figures from a fit, etc. >> >> For instance: >> I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? >> Can I change the figure legends? I used sample 1 and I want to give it a different name >> Can I use special characters (e.g. Greek letters)? >> Can I adjust the resolution for different formats (talk vs. publication)? >> >> I am running Demeter 0.9.9.9 under XP. >> >> Thanks in advance for the help! >> >> - Eva >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 3 > Date: Tue, 26 Mar 2013 13:51:36 -0400 > From: Jason Gaudet <jason.r.gaudet(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] generating high res figures > Message-ID: > <CANMcWtM=dO9GR-jSMC--dXEPWojAZ-78N44mPrAnV5ujHtMAmw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > And to do this, use the Artemis Plot dialog box to generate the chart you > want (e.g. the data and fit in magnitude R-space), click the "Save Next > Plot to File" button at the very bottom of the dialog box, and click the > correct plot button at the top (e.g. R). This lets you save the plot as an > ASCII file. > > -Jason > > On Tue, Mar 26, 2013 at 1:25 PM, Scott Calvin <scalvin(a)sarahlawrence.edu>wrote: > >> Hi Eva, >> >> Demeter is not intended to be used to produce publication-quality figures. >> It's best to export the data, fits, etc., and then use a proper graphing >> program to generate figures. Even a spreadsheet will do in a pinch, >> although most of us use dedicated scientific graphing software. >> >> --Scott Calvin >> Sarah Lawrence College >> >> On Mar 26, 2013, at 1:13 PM, Eva Vanamee <eva.vanamee(a)mssm.edu> wrote: >> >>> Hi, >>> >>> I'm in the happy stages of making figures. >>> I'd like to know how to change figure legends, make high resolution >> figures from a fit, etc. >>> >>> For instance: >>> I saved the session file. Can I go back to a particular fit to make a >> figure or do I need to rerun it? >>> Can I change the figure legends? I used sample 1 and I want to give it a >> different name >>> Can I use special characters (e.g. Greek letters)? >>> Can I adjust the resolution for different formats (talk vs. publication)? >>> >>> I am running Demeter 0.9.9.9 under XP. >>> >>> Thanks in advance for the help! >>> >>> - Eva >>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >

6 6

generating high res figures
by Eva Vanamee 26 Mar '13

26 Mar '13

Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? Can I change the figure legends? I used sample 1 and I want to give it a different name Can I use special characters (e.g. Greek letters)? Can I adjust the resolution for different formats (talk vs. publication)? I am running Demeter 0.9.9.9 under XP. Thanks in advance for the help! - Eva

5 4

Re: [Ifeffit] Building ifeffit Mac Mountain Lion
by Matt Newville 22 Mar '13

22 Mar '13

Hi Jeff, Hope it's OK, but I'm CCing this to the ifeffit mailing list. I've officially abandoned support for the Fortran version of Ifeffit, but I know many people are still using it, so I'll try to give some pointers. I haven't tried building on 10.8 (but Larch works fine for me on it). On Thu, Mar 21, 2013 at 3:34 PM, Jeff Terry <terryj(a)iit.edu> wrote: > Hi Matt, > > I am trying to build ifeffit for Mac OS 10.8 (Mountain Lion). I have built pgplot and the cpg library manually but cannot build it with your script. > > I get the following error when building with the script. > > Do you have any suggestions as to what might be causing this or another way that I can link pgplot to ifeffit? > > Thanks, > > Jeff > > > gfortran -c -O2 -fPIC /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/drivers/gidriv.f > /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:208.72: > > & RECL=255, FORM='BINARY', IOSTAT=IER) > 1 > Warning: FORM specifier in OPEN statement at (1) has invalid value 'BINARY' > /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:240.72: > > & RECL=255, FORM='BINARY', IOSTAT=IER) > 1 > Warning: FORM specifier in OPEN statement at (1) has invalid value 'BINARY' > /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:654.21: > > BLKOUT(0) = 254 > 1 > Error: Arithmetic overflow converting INTEGER(4) to INTEGER(1) at (1). This check can be disabled with the option -fno-range-check > make: *** [gidriv.o] Error 1 > gfortran -u -Wall -fPIC -O -o pgpack /Users/jterry/Downloads/ifeffit-1.2.11c/pgplot/fonts/pgpack.f > Undefined symbols for architecture x86_64: > "-Wall", referenced from: > -u command line option > ld: symbol(s) not found for architecture x86_64 > collect2: error: ld returned 1 exit status > make: *** [grfont.dat] Error 1 > = Cleaning up and preparing for test I think the last version of Ifeffi, from https://github.com/newville/ifeffit should work, at least to compile PGPLOT correctly. I've put most of the code I used to build Ifeffit on Mac OSX in the src/macosx directory on this repository: https://github.com/newville/ifeffit/tree/master/src/macosx Though, of course this makes many assumptions (such as, that gfortran and XCode are installed), and I really can't offer any support for these scripts and codes. Hope that helps, --Matt

4 4

Reduced chi square values versus F-tests for second shell fits
by Matt Siebecker 22 Mar '13

22 Mar '13

Dear All, Would it be recommended to compare reduced chi square (RCS) values from the fit of the second shell only? While fitting the second shell only, the differences between RCS values of different models can be greater than when including both the first and second shells in the fit. For example, the RCS values of model 1 and model 2 for fits of the first and second shells versus just the second shell are 45 and 18, and then 60 and 17, respectively. This to me indicates that fitting the second shell separately from the first gave me a slightly better description of the misfit in that R-range. Regardless of the fitting range the RCS values say model 2 improves the fit significantly. However, if I use an F-test to compare models while fitting the second shell only, I’ve found that the difference between the models is actually less important than when including both the first and second shells in the fit. For examples, the F-test values of model 1 versus model 2 for fits of the first and second shell versus just the second shell are P=0.047 and then P=0.113, respectively. This is perhaps caused by the small R-range and hence decreased Nind when fitting the second shell only. However, it also indicates to me that the F-test says perhaps one fitting model is not such an improvement on the fit as I thought it was based purely on the decrease in RCS value. I assume significant decreases in RCS values to be about >2x, and P <0.05 for the F-test. Should RCS values and F-tests for comparing fitting models only be used when fitting two shells together or can they be used when just fitting the second shell? Kind regards, Matt Siebecker

2 4

Core-Shell Spectroscopy session at Denver X-Ray Conference
by Carlo Segre 21 Mar '13

21 Mar '13

Hello All: This year we will once again have a core-shell spectroscopy session at the Denver X-ray Conference. The conference web site is http://www.dxcicdd.com/13/index.htm The conference organizers are accepting abstracts for talks and posters until April 5, 2013 (the web page says that submission is closed but it is really open for this specific session). Bruce Ravel and I are organizing the session and we would like to encourage you to submit your abstracts for talks and posters as soon as possible so that we can keep a yearly meeting where our community can present talks in North America. Denver is a nice centrally located venue where students can easily drive in from many places in North America (certainly from Chicago!) and save some travel costs. There are special student registration rates and there are also funds which students may apply for to defray expenses. I hope that you will participate and encourage your collegues in the field to do so as well. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

1 0