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

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 >> >

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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

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Re: [Ifeffit] Building ifeffit Mac Mountain Lion
by Matt Newville 23 Mar '13

23 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

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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

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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

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(no subject)
by davood dar 13 Mar '13

13 Mar '13

Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. * 1*. What is the ideal value of R- factor for any fit. 2. * 2. * Can we use (fit) the theoretical model generated from square pyramidal structure to EXAFS data of octahedral structure by assigning degeneracy of 2 for the apical atom. OR using octalhedral for square planar by not using apical path Yours faithfully Davood Ah. Dar EXAFS research scholar India

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questions related to ifeffit fitting
by davood dar 13 Mar '13

13 Mar '13

Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. What is the ideal value of R- factor for any fit. 2. * * Can we use (fit) the theoretical model generated from square pyramidal structure to EXAFS data of octahedral structure by assigning degeneracy of 2 for the apical atom. OR using octalhedral for square planar by not using apical path Yours faithfully Davood Ah. Dar EXAFS research scholar India

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questions regarding to ifeffit fitting
by davood dar 13 Mar '13

13 Mar '13

Respected Sir, I am new in the field of EXAFS. I have few questions regarding to IFEFFIT i.e., fitting of theoretical models to the experimental EXAFS data. 1. What is the ideal value of R- factor for any fit. 2. * * Can we use (fit) the theoretical model generated from square pyramidal structure to EXAFS data of octahedral structure by assigning degeneracy of 2 for the apical atom. OR using octalhedral for square planar by not using apical path Yours faithfully Davood Ah. Dar EXAFS research scholar India

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controls and data acquisition workshop ot SRI 2013
by Bruce Ravel 13 Mar '13

13 Mar '13

Hi! This year's Pan-American Synchrotron Radiation Instrumentation Conference will be held June 19-21 in Gaithersburg, MD, USA, with satellite workshops on June 17 and 18. Here's the URL: http://pml.nist.gov/Meetings/SRI2013/index.html I am organizing Workshop #8 on June 18th. It will be on the topic of software for beamline controls and data acquisition. If you work in this area, please consider submitting an abstract. Please pass word about this workshop to your favorite beamline scientist or to the controls and acquisition people at your synchrotron. Thanks! Bruce -- 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

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MBACK and Athena
by Bajamundi Cyril 12 Mar '13

12 Mar '13

Hello, I have 3 spectra taken from a single sample, I align, merge and save the merged data as merge.xmu file. I then normalize this merged data using the MBACK algorithm in Matlab, the results of which is stored as merged.xmu.mnor file. This file, I then import to ATHENA using the instructions in http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03523.html. I do this for all my samples and standards in order for me to perform LCF. My questions are 1. Is this procedure valid? In the sense that no information or features of the spectrum are lost from merge.xmu to merged.xmu.mnor file. 2. How will the procedure <Calibrate data> affect this procedure? Thank you for your time in answering my questions. Regards, Cyril PS: This query is in relation to my previous question [Ifeffit] Basic question in normalization and background removal

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