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

Question about FEFF6
by goodhei8＠gmail.com 13 Apr '11

13 Apr '11

Dear IFEFFIT Members, I have a strange problem with FEFF calculation. I am not sure if I made some mistakes in FEFF of input file, or FEFF did not handle it well. For Oxygen paths calculated with FEFF in Artemis by 3 input files, the results for O are supposed to be close, but I got a big difference, when I transform them into r space(k 2.5~10,kweight=2 in attachment). There are three input files for FEFF: #1, 6O only on xyz axis #2, + 1P besides 6O #3, + 6P besides 6O For O, #2 and #3 are close(almost same), but #1 is much bigger. (It would make sense to me if #1 #2 are close.) Thank a lot. Best, Jack Song

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Strategy to obtain cofigurationally averaged EXAFS from MD simulations
by Francisco Garcia 12 Apr '11

12 Apr '11

Dear users, I want to compute the “average EXAFS spectra” usin 500 snapshots of atomic coordinates from my MD simulations. The idea is to compute the EXAFS spectra for each snapshot and then average the spectra over all snapshots (the so-called "MD EXAFS" approach). I know how to use Artemis to generate the EXAFS spectrum of a single snapshot. However, generating the EXAFS data for each of the 500 snapshots individually will be too time consuming and messy (this is essentially a book-keeping approach). I was wondering if there is a time-saving strategy/script for computing the average EXAFS instead of the snapshot-by-snapshot approach. For example, is it possible to include the coordinates of all the snapshots in a single feff.inp file and feed it to Artemis? Or if I have the feff.inp file for each snapshot, is it possible to write a script for Artemis that will compute each EXAFS spectra individually and dump them in a specified directory? Thank you very much.

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XAS/XPS postdoc position at The University of Manchester
by Sven Schroeder 12 Apr '11

12 Apr '11

Dear all I would be grateful if you could bring this XAS/XPS post to the attention of suitable candidates. The post has been funded for 30 months and is available from 1 June 2011. Follow this link: http://www.manchester.ac.uk/aboutus/jobs/vacancies/research/vacancy/?ref=12… Research Associate (fixed term): Experimental and Computational Soft X-ray Spectroscopy (NEXAFS, XPS) of Corrosion Inhibition with Organic Molecules School of Chemical Engineering and Analytical Science, The University of Manchester Closing date: 06/05/2011 We are seeking to employ a Research Associate within the School of Chemical Engineering and Analytical Science (CEAS) on a full-time basis. The post is fixed-term for a period of 30 months commencing 1st June 2011. This post requires a PhD or equivalent in a relevant discipline (not limited to Physics or Chemistry) based on research in fundamental surface science or catalysis using ultra-high vacuum techniques. Experience with using ab initio soft X-ray spectroscopy data analysis packages such as StoBe, FEFF, CASTEP or similar methods is required. The project focuses on fundamental physicochemical studies of model surface systems in an industrially led project that involves organic chemists, computational chemists and chemical engineers at the Mexican Petroleum Institute (IMP). As such it requires a candidate with the ability to work both on their own initiative as well as a part of teams of varying size, and an ability to travel globally and regularly. Candidates should have an interest in working across the boundary between fundamental academic science and its practical application. Relevant peer-reviewed publications and experience in writing manuscripts for academic journal publications are essential. The candidate will take the lead in analysing the spectroscopic results through a combination of molecular modelling and calculations of core level shifts as well as associated X-ray absorption spectra. He/she will also be responsible for producing reports and presentations, and taking the lead in writing manuscripts for publications. On a day to day basis he/she will liaise directly with relevant contacts at IMP and within the University. Previous experience of operating NEXAFS and XPS equipment on a day to day basis, including minor repairs and vacuum management, would be an advantage. This work will include examination of these corrosion inhibitor/surface systems in simulated real-world environments, using equipment accessible at synchrotron radiation sources in the US and in Europe. The successful candidate will be integrated in the Manchester team, together with another project scientist and the Manchester investigators. He/she will contribute to applications for synchrotron radiation access and logistic coordinating of synchrotron radiation (SR) experiments and act as team leader during SR beamtimes. He/she will also carry out (or supervise) supporting measurements with home laboratory techniques (for example XRD, FTIR, electron microscopies, electrochemical techniques etc). The project requires quarterly reporting and presentations both in project meetings with the industrial partner and at academic conferences. Liaison with relevant contacts at the Mexican partner institute and participation in consortium project meetings twice a year will be required. The post is fixed-term for 30 months, available from 1st June 2011. -- Dr Sven L.M. Schroeder (mailto:s.schroeder@manchester.ac.uk) Reader School of Chemical Engineering and Analytical Science (CEAS) The University of Manchester, Manchester M13 9PL, United Kingdom http://www.slmslab.info Also at: School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom Tel +44 (161) 306 4502 Fax +44 (161) 306 8867 Office: Room C57 (Jackson's Mill) DISCLAIMER The views expressed within this message are those of the sender, not those of The University of Manchester or one of its units. While all emails and attachments are scanned for viruses before sending, we cannot accept any responsibility for viruses, so please scan all emails and attachments. This email is intended for the addressee only. If you are not the intended recipient, please notify the sender and delete this email immediately. END OF MESSAGE

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Re: [Ifeffit] Ifeffit Digest, Vol 98, Issue 8
by Guoqiang PAN 10 Apr '11

10 Apr '11

I did as the Bruce's advice, > 1. Check that Module::Build is indeed already on your system by > typing this at the command line: > perl -e "use Module::Build" > If it responds with noting (i.e. no error messages), then you are > fine. > > 2. Edit the files Bundle/LibPerlXrayBundle.pm and remove the line > with Module::Build beneath the "CONTENTS" header. > > 3. Try again. It's OK. Then to run ./build, it's easy to install artemis, athena and hephaestus. Thank you and Matt very much. Guoqiang On Fri, 2011-04-08 at 12:00 -0500, 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. Re: Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14) > (Guoqiang PAN) > 2. Installation Artemis, athena in Fedora 14 (Guoqiang PAN) > 3. Re: Installation Artemis, athena in Fedora 14 (Bruce Ravel) > 4. Re: Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14) > (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 08 Apr 2011 17:21:02 +0800 > From: Guoqiang PAN <gqpan(a)ustc.edu.cn> > To: Matt Newville <newville(a)cars.uchicago.edu> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>, > Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] Fwd: Re: Fwd: ifeffit installation in Linux > (Fedora 14) > Message-ID: <1302254462.5791.25.camel(a)localhost.localdomain> > Content-Type: text/plain; charset="UTF-8" > > Thanks lot to Matt and Bruce. > PGPLOT installation in Fedora 14 Linux case, can only be succeeded using > g77_gcc_aout. I tried every possible choice for fortran-compiler in my > case,only > /usr/local/src/pgplot/makemake /usr/local/src/pgplot linux g77_gcc_aout > could work! > Then PGPLOT_install script will use gfortran as default fortran > compiler, it stopped at > > gfortran -c -O2 -fPIC grexec.f > gfortran -c -O2 -fPIC /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f > /usr/local/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' > /usr/local/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' > /usr/local/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 /usr/local/ifeffit-1.2.11c/pgplot/fonts/pgpack.f > rm -f grfont.dat > ./pgpack </usr/local/ifeffit-1.2.11c/pgplot/fonts/grfont.txt > Characters defined: 996 > Array cells used: 26732 > rm -f pgpack > gfortran -fno-backslash -o > pgdemo1 /usr/local/ifeffit-1.2.11c/pgplot/examples/pgdemo1.f -L`pwd` > -lpgplot_iff -lpng -lz -L/usr/X11R6/lib -lX11 > /usr/bin/ld: cannot find -lpgplot_iff > collect2: ld returned 1 exit status > make: *** [pgdemo1] Error 1 > = Cleaning up and preparing for test > = = = = = = = = = = = = = = = = = = = = = = = = = = > = Uh-oh. PGPLOT is missing some important files! > = It looks like PGPLOT failed during building or > = is only partially installed. > = > = Please consult the PGPLOT installation instructions > = in the subdirectory pgplot/, and the log file: > = /usr/local/ifeffit-1.2.11c/PGPLOT_install.log > = which contains a full list of commands run. > = > = You may want to repeat these steps by hand or > = consult the PGPLOT installations instructions > = in install-unix.txt > > > So if I commented out these two lines (line 219 and 220) in > PGPLOT_install > gfortran -v > /dev/null 2>&1 > if [ $? = 0 ] ; then fcompl='gfortran'; fi > PGPLOT_install will be OK! > > As for installation ifeffit, I tried your suggestions > e.g. (./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot > -lpgplot_iff -lpng -lz -lX11') or ln -s libpgplot.a libpgplot_iff.a > ,but not successful. It stopped at > > gcc -g -O2 -o ifftest1 ifftest1.o ../lib/libifeffit.a > -L/usr/local/share/ifeffit/pgplot -lpgplot_iff -lpng -lz -lX11 > -L/usr/lib/gcc/i686-redhat-linux/4.5.1 > -L/usr/lib/gcc/i686-redhat-linux/4.5.1/../../.. -lgfortran -lm -lgcc_s > /usr/bin/ld: cannot find -lpgplot_iff > collect2: ld returned 1 exit status > make[3]: *** [ifftest1] Error 1 > make[3]: Leaving directory `/usr/local/ifeffit-1.2.11c/src/test' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/usr/local/ifeffit-1.2.11c/src' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/usr/local/ifeffit-1.2.11c' > make: *** [all-recursive-am] Error 2 > [root@localhost ifeffit-1.2.11c]# > > I think this also due to the gfortan, and I changed the fortran compiler > to g77: > ./configure --with-fortran=g77 > It is OK! > Best regards, > Guoqiang > > > On Thu, 2011-04-07 at 11:56 -0500, Matt Newville wrote: > > Guoqiang, > > > > Can we take a step back and try to figure out why PGPLOT_install > > didn't work for you? It does work for me on Fedora14. What part of > > PGPLOT_install did not work? > > > > It should be that ./configure --with-pgplot-link='LINKARGS' can be > > used to specify the PGPLOT_LIBS value, say > > > > ./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot > > -lpgplot_iff -lpng -lz -lX11' > > > > For PGPLOT installed with PGPLOT_install, or something like > > ./configure --with-pgplot-link='-L/usr/local/pgplot -lpgplot -lpng > > -lz -lX11' > > > > for a PGPLOT installed "by hand". > > > > An important difference between PGPLOT_install and most "by hand" > > installations is that PGPLOT_install will not build a shared library, > > but a static one only. This won't affect building, but can have an > > impact for runtime, as the shared library needs to be found at > > runtime, and so needs to be in the LD_LIBRARY_PATH, or configured with > > ldconfig. > > > > --Matt > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 08 Apr 2011 20:41:54 +0800 > From: Guoqiang PAN <gqpan(a)ustc.edu.cn> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: Bruce Ravel <bravel(a)bnl.gov> > Subject: [Ifeffit] Installation Artemis, athena in Fedora 14 > Message-ID: <1302266514.10181.10.camel(a)localhost.localdomain> > Content-Type: text/plain; charset="UTF-8" > > Hi,all > Main trouble for the installation Artemis, athena etc. in PC Linux > system (in my case is Fedora 14 ) is need to install all perl > pre-requisites from CPAN. Following the install instruction I did as > follows: perl -MCPAN -e 'install Bundle::XasPerlBundle' > But it stopped at 'DAGOLDEN': > > Warning: Prerequisite 'Module::Metadata => 1.000002' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing > 'DAGOLDEN/Module-Metadata-1.000004.tar.gz' with 'make_test => NO'. > Continuing, but chances to succeed are limited. > Warning: Prerequisite 'CPAN::Meta => 2.110420' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing > 'DAGOLDEN/CPAN-Meta-2.110930.tar.gz' with 'make_test => NO'. Continuing, > but chances to succeed are limited. > Warning: Prerequisite 'ExtUtils::CBuilder => 0.27' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > suspicious. Skipping another build attempt, to prevent looping > endlessly. > Warning: Prerequisite 'Parse::CPAN::Meta => 1.4401' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > suspicious. Skipping another build attempt, to prevent looping > endlessly. > Warning: Prerequisite 'version => 0.87' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > suspicious. Skipping another build attempt, to prevent looping > endlessly. > Warning: Prerequisite 'ExtUtils::ParseXS => 2.21' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > suspicious. Skipping another build attempt, to prevent looping > endlessly. > /usr/local/bin/perl Build --makefile_env_macros 1 > Can't locate Module/Metadata.pm in @INC (@INC contains: t/lib t/bundled > lib /usr/local/lib/perl5/5.10.1/i686-linux /usr/local/lib/perl5/5.10.1 /usr/local/lib/perl5/site_perl/5.10.1/i686-linux /usr/local/lib/perl5/site_perl/5.10.1 .) at lib/Module/Build/ModuleInfo.pm line 10. > Compilation failed in require at lib/Module/Build/Base.pm line 23. > BEGIN failed--compilation aborted at lib/Module/Build/Base.pm line 23. > Compilation failed in require at lib/Module/Build.pm line 15. > BEGIN failed--compilation aborted at lib/Module/Build.pm line 15. > Compilation failed in require at Build line 42. > BEGIN failed--compilation aborted at Build line 42. > make: *** [all] Error 2 > DAGOLDEN/Module-Build-0.3800.tar.gz > /usr/bin/make -- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > Running make test > Can't test without successful make > Running make install > Make had returned bad status, install seems impossible > > Guoqiang Pan > National Synchrotron Radiation Laboratory > University of Science & Technology of China > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 8 Apr 2011 09:37:01 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Installation Artemis, athena in Fedora 14 > Message-ID: <201104080937.01794.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="utf-8" > > > Guoqiang, > > Module::Build is the tool used to build and install my GUI software. > It is a standard perl module and should already be on your system. I > am surprised that your computer is finding it necessary to try to > download and reinstall it. > > I assume that you are at the step of installing the things I call > LibPerlXray and that you mis-typed. > > I suspect the fault is mine. I probably should not list Module::Build > in the file Bundle/LibPerlXrayBundle.pm. Try the following: > > 1. Check that Module::Build is indeed already on your system by > typing this at the command line: > perl -e "use Module::Build" > If it responds with noting (i.e. no error messages), then you are > fine. > > 2. Edit the files Bundle/LibPerlXrayBundle.pm and remove the line > with Module::Build beneath the "CONTENTS" header. > > 3. Try again. > > I apologize that this is so hard. I just don't have the resources to > test these things on all possible systems, so I rely on the users to > complain when they run into problems. Thanks for being patient. > > B > > > On Friday, April 08, 2011 08:41:54 am Guoqiang PAN wrote: > > Hi,all > > Main trouble for the installation Artemis, athena etc. in PC Linux > > system (in my case is Fedora 14 ) is need to install all perl > > pre-requisites from CPAN. Following the install instruction I did as > > follows: perl -MCPAN -e 'install Bundle::XasPerlBundle' > > But it stopped at 'DAGOLDEN': > > > > Warning: Prerequisite 'Module::Metadata => 1.000002' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing > > 'DAGOLDEN/Module-Metadata-1.000004.tar.gz' with 'make_test => NO'. > > Continuing, but chances to succeed are limited. > > Warning: Prerequisite 'CPAN::Meta => 2.110420' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing > > 'DAGOLDEN/CPAN-Meta-2.110930.tar.gz' with 'make_test => NO'. Continuing, > > but chances to succeed are limited. > > Warning: Prerequisite 'ExtUtils::CBuilder => 0.27' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > > suspicious. Skipping another build attempt, to prevent looping > > endlessly. > > Warning: Prerequisite 'Parse::CPAN::Meta => 1.4401' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > > suspicious. Skipping another build attempt, to prevent looping > > endlessly. > > Warning: Prerequisite 'version => 0.87' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > > suspicious. Skipping another build attempt, to prevent looping > > endlessly. > > Warning: Prerequisite 'ExtUtils::ParseXS => 2.21' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > > suspicious. Skipping another build attempt, to prevent looping > > endlessly. > > /usr/local/bin/perl Build --makefile_env_macros 1 > > Can't locate Module/Metadata.pm in @INC (@INC contains: t/lib t/bundled > > lib /usr/local/lib/perl5/5.10.1/i686-linux /usr/local/lib/perl5/5.10.1 > > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux > > /usr/local/lib/perl5/site_perl/5.10.1 .) at lib/Module/Build/ModuleInfo.pm > > line 10. Compilation failed in require at lib/Module/Build/Base.pm line > > 23. BEGIN failed--compilation aborted at lib/Module/Build/Base.pm line 23. > > Compilation failed in require at lib/Module/Build.pm line 15. > > BEGIN failed--compilation aborted at lib/Module/Build.pm line 15. > > Compilation failed in require at Build line 42. > > BEGIN failed--compilation aborted at Build line 42. > > make: *** [all] Error 2 > > DAGOLDEN/Module-Build-0.3800.tar.gz > > /usr/bin/make -- NOT OK > > Warning (usually harmless): 'YAML' not installed, will not store > > persistent state > > Running make test > > Can't test without successful make > > Running make install > > Make had returned bad status, install seems impossible > > > > Guoqiang Pan > > National Synchrotron Radiation Laboratory > > University of Science & Technology of China > > -- > > 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 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > ------------------------------ > > Message: 4 > Date: Fri, 8 Apr 2011 09:53:08 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: gqpan(a)ustc.edu.cn > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>, > Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] Fwd: Re: Fwd: ifeffit installation in Linux > (Fedora 14) > Message-ID: <BANLkTi=TERxR=UPKNfpdaybr6hsKtBFBrA(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Guoqiang, > > Ah, I see and sorry for the trouble, especially I have had a fix (so > that gfortran is used) for this for a while now. I believe you have > a reasonable solution, but the PGPLOT_install script in the svn > repository works better. I tried this on Fedora14 x86_64 yesterday > revealed another problem, that I think I have fixed. I'll try to get > that resolved and post a new PGPLOT_install script, and upload a > ifeffit 1.2.11d tarball. > > Thanks > > --Matt > > > > On Fri, Apr 8, 2011 at 4:21 AM, Guoqiang PAN <gqpan(a)ustc.edu.cn> wrote: > > Thanks lot to Matt and Bruce. > > PGPLOT installation in Fedora 14 Linux case, can only be succeeded using > > g77_gcc_aout. I tried every possible choice for fortran-compiler in my > > case,only > > /usr/local/src/pgplot/makemake /usr/local/src/pgplot linux g77_gcc_aout > > could work! > > Then PGPLOT_install script will use gfortran as default fortran > > compiler, it stopped at > > > > gfortran -c -O2 -fPIC grexec.f > > gfortran -c -O2 -fPIC /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f > > /usr/local/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' > > /usr/local/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' > > /usr/local/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 /usr/local/ifeffit-1.2.11c/pgplot/fonts/pgpack.f > > rm -f grfont.dat > > ./pgpack </usr/local/ifeffit-1.2.11c/pgplot/fonts/grfont.txt > > ?Characters defined: ? 996 > > ?Array cells used: ? 26732 > > rm -f pgpack > > gfortran -fno-backslash -o > > pgdemo1 /usr/local/ifeffit-1.2.11c/pgplot/examples/pgdemo1.f -L`pwd` > > -lpgplot_iff -lpng -lz -L/usr/X11R6/lib -lX11 > > /usr/bin/ld: cannot find -lpgplot_iff > > collect2: ld returned 1 exit status > > make: *** [pgdemo1] Error 1 > > ?= Cleaning up and preparing for test > > ?= = = = = = = = = = = = = = = = = = = = = = = = = = > > ?= Uh-oh. ?PGPLOT is missing some important files! > > ?= It looks like PGPLOT failed during building or > > ?= is only partially installed. > > ?= > > ?= Please consult the PGPLOT installation instructions > > ?= in the subdirectory ?pgplot/, and the log file: > > ?= ? ?/usr/local/ifeffit-1.2.11c/PGPLOT_install.log > > ?= which contains a full list of commands run. > > ?= > > ?= You may want to repeat these steps by hand or > > ?= consult the PGPLOT installations instructions > > ?= in install-unix.txt > > > > > > So if I commented out these two lines ?(line 219 and 220) in > > PGPLOT_install > > ? ?gfortran -v > /dev/null 2>&1 > > ? ?if [ $? = 0 ] ; then ?fcompl='gfortran'; fi > > PGPLOT_install will be OK! > > > > As for installation ifeffit, I tried your suggestions > > e.g. (./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot > > -lpgplot_iff -lpng -lz -lX11') or ln -s libpgplot.a libpgplot_iff.a > > ,but not successful. It stopped at > > > > gcc ?-g -O2 ?-o ifftest1 ?ifftest1.o ../lib/libifeffit.a > > -L/usr/local/share/ifeffit/pgplot -lpgplot_iff -lpng -lz -lX11 > > -L/usr/lib/gcc/i686-redhat-linux/4.5.1 > > -L/usr/lib/gcc/i686-redhat-linux/4.5.1/../../.. -lgfortran -lm -lgcc_s > > /usr/bin/ld: cannot find -lpgplot_iff > > collect2: ld returned 1 exit status > > make[3]: *** [ifftest1] Error 1 > > make[3]: Leaving directory `/usr/local/ifeffit-1.2.11c/src/test' > > make[2]: *** [all-recursive] Error 1 > > make[2]: Leaving directory `/usr/local/ifeffit-1.2.11c/src' > > make[1]: *** [all-recursive] Error 1 > > make[1]: Leaving directory `/usr/local/ifeffit-1.2.11c' > > make: *** [all-recursive-am] Error 2 > > [root@localhost ifeffit-1.2.11c]# > > > > I think this also due to the gfortan, and I changed the fortran compiler > > to g77: > > ./configure --with-fortran=g77 > > It is OK! > > Best regards, > > Guoqiang > > > > > > On Thu, 2011-04-07 at 11:56 -0500, Matt Newville wrote: > >> Guoqiang, > >> > >> Can we take a step back and try to figure out why PGPLOT_install > >> didn't work for you? ?It does work for me on Fedora14. ? What part of > >> PGPLOT_install did not work? > >> > >> It should be that ./configure --with-pgplot-link='LINKARGS' can be > >> used to specify the PGPLOT_LIBS value, say > >> > >> ? ? ./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot > >> -lpgplot_iff -lpng -lz -lX11' > >> > >> For PGPLOT installed with PGPLOT_install, or something like > >> ? ? ./configure --with-pgplot-link='-L/usr/local/pgplot -lpgplot -lpng > >> -lz -lX11' > >> > >> for a PGPLOT installed "by hand". > >> > >> An important difference between PGPLOT_install and most "by hand" > >> installations is that PGPLOT_install will not build a shared library, > >> but a static one only. ?This won't affect building, but can have an > >> impact for runtime, as the shared library needs to be found at > >> runtime, and so needs to be in the LD_LIBRARY_PATH, or configured with > >> ldconfig. > >> > >> --Matt > > > > > > > > > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 98, Issue 8 > **************************************

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Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14)
by Bruce Ravel 08 Apr '11

08 Apr '11

---------- Forwarded Message ---------- Subject: Re: Fwd: ifeffit installation in Linux (Fedora 14) Date: Thursday, April 07, 2011, 10:52:57 am From: Bruce Ravel <bravel(a)bnl.gov> To: gqpan(a)ustc.edu.cn On Thursday, April 07, 2011 10:23:20 am you wrote: > Thank you very much for your rapid reply. > Yes, I tried first with pgplot using > ./configure --with-pgplot=/usr/local/pgplot/, but failed with the 'make' > ../lib/libifeffit.a(iff_cursor.o): In function `iff_zoom_': > /usr/local/ifeffit-1.2.11c/src/lib/iff_cursor.f:134: undefined reference > to `pgband_' > /usr/local/ifeffit-1.2.11c/src/lib/iff_cursor.f:138: undefined reference > to `pgband_' > collect2: ld returned 1 exit status > make[3]: *** [ifftest1] Error 1 > make[3]: Leaving directory `/usr/local/ifeffit-1.2.11c/src/test' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/usr/local/ifeffit-1.2.11c/src' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/usr/local/ifeffit-1.2.11c' > make: *** [all-recursive-am] Error 2 > (more details in my previous make.log file) > Then I tried with ./configure --without-pgplot, which can > be done without any problem. That's the problem. > Regards, > Guoqiang Hmmm...... so it seems not to be linking with libpgplot.a. Odd. I notice on my computer that the pgplot library is called libpgplot_iff.a and that the Makefile in src/lib/ has this line: PGPLOT_LIBS = -L/usr/local/share/ifeffit/pgplot -lpgplot_iff -lpng -lz -lX11 I also see that Matt's PGPLOT_install script changes one of pgplot's files to use the installation location specified in PGPLOT_install as default location (i.e. the one that would be specified by setting the PGPLOT_DIR environment variable). The script then renames the library to have the "_iff". There are a number of ways to address. Here is one relatively simple suggestion: 1. cd to the location of libpgplot.a on your computer 2. make a symbolic link to libpgplot.a like so: ln -s libpgplot.a libpgplot_iff.a 3. set the PGPLOT_DIR environment variable to the directory containing libpgplot.a. This can be done either typing export PGPLOT_DIR=/location/of/pgplot at the commend line or putting it in a login script to make it permanent. (Of course, replace /location/of/pgplot with the correct thing on your computer.) 4. cd back to the location of the ifeffit source and try again to build it. All that is, of course, untested on my end. But I think it should work. If not, we'll keep trying until we figure it out! 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ----------------------------------------- -- 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Installation Artemis, athena in Fedora 14
by Guoqiang PAN 08 Apr '11

08 Apr '11

Hi,all Main trouble for the installation Artemis, athena etc. in PC Linux system (in my case is Fedora 14 ) is need to install all perl pre-requisites from CPAN. Following the install instruction I did as follows: perl -MCPAN -e 'install Bundle::XasPerlBundle' But it stopped at 'DAGOLDEN': Warning: Prerequisite 'Module::Metadata => 1.000002' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing 'DAGOLDEN/Module-Metadata-1.000004.tar.gz' with 'make_test => NO'. Continuing, but chances to succeed are limited. Warning: Prerequisite 'CPAN::Meta => 2.110420' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing 'DAGOLDEN/CPAN-Meta-2.110930.tar.gz' with 'make_test => NO'. Continuing, but chances to succeed are limited. Warning: Prerequisite 'ExtUtils::CBuilder => 0.27' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks suspicious. Skipping another build attempt, to prevent looping endlessly. Warning: Prerequisite 'Parse::CPAN::Meta => 1.4401' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks suspicious. Skipping another build attempt, to prevent looping endlessly. Warning: Prerequisite 'version => 0.87' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks suspicious. Skipping another build attempt, to prevent looping endlessly. Warning: Prerequisite 'ExtUtils::ParseXS => 2.21' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks suspicious. Skipping another build attempt, to prevent looping endlessly. /usr/local/bin/perl Build --makefile_env_macros 1 Can't locate Module/Metadata.pm in @INC (@INC contains: t/lib t/bundled lib /usr/local/lib/perl5/5.10.1/i686-linux /usr/local/lib/perl5/5.10.1 /usr/local/lib/perl5/site_perl/5.10.1/i686-linux /usr/local/lib/perl5/site_perl/5.10.1 .) at lib/Module/Build/ModuleInfo.pm line 10. Compilation failed in require at lib/Module/Build/Base.pm line 23. BEGIN failed--compilation aborted at lib/Module/Build/Base.pm line 23. Compilation failed in require at lib/Module/Build.pm line 15. BEGIN failed--compilation aborted at lib/Module/Build.pm line 15. Compilation failed in require at Build line 42. BEGIN failed--compilation aborted at Build line 42. make: *** [all] Error 2 DAGOLDEN/Module-Build-0.3800.tar.gz /usr/bin/make -- NOT OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make test Can't test without successful make Running make install Make had returned bad status, install seems impossible Guoqiang Pan National Synchrotron Radiation Laboratory University of Science & Technology of China

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Fwd: ifeffit installation in Linux (Fedora 14)
by Bruce Ravel 07 Apr '11

07 Apr '11

Guoqiang, First off, I am responding to you on the Ifeffit mailing list, which is the appropraite venue for questions about Ifeffit and related software. please use the mailing list for all future correspondance. I am not completely clear on what you are asking about, but I suspect that your problem is that Ifeffit isn't plotting anything. That is, I suspect that you have managed to compile pgplot and you have managed to compile Ifeffit, but you do not have pgplot and ifeffit talking to one another. The reason for this is that you said $ ./configure --without-pgplot This builds Ifeffit without pgplot support. What I think you want to do is to use the "--with-pgplot=dir" argument for "configure". That, you should do something like $ ./configure --with-pgplot=/usr/local/share/pgplot where you would, of course, specify, the actual installation location of pgplot on your computer. You will then need to remake and reinstall ifeffit. If that doesn't solve the problem, try asking again on the mailing list, where other knowledgeable people can offer their advice as well. Regards, 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] Third cumulant in DWF
by Joshua Kas 05 Apr '11

05 Apr '11

Hi all, I agree that adding debye waller factors in feff might be confusing, however, it can be useful if you are using a model for the DW factors that is not included in ifeffit, i.e., the spring constant, equation of motion, or dynamical matrix based methods. If these (or any of the other models in feff) are used, it will not change the path parameters used by ifeffit. The DWFs are only used in constructing chi(k), but the DWFs are printed out for each path so that they can be used in ifeffit/artemis if needed. Cheers, Josh > On Monday, April 04, 2011 06:51:23 pm Matthew Marcus wrote: > > Another question is whether, if you add a sigma2 to feff.inp, what > > does FEFF do? > > Ick! As good of a question as that might be, I have to recommend > against that practice in the strongest possible terms. Adding > sigma^2 <> 0 (or S0^2 <> 1, for that matter) to a Feff calculation > intended for use with Ifeffit/Artemis is highly likely to be highly > confusing. > > 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 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 98, Issue 4 > ************************************** >

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Third cumulant in DWF
by Ping, Yuan 05 Apr '11

05 Apr '11

Dear IFEFFIT experts: Is it possible to add a k^3 term in the phase for fitting to take into account anharmonic effect? The fitted coefficient will be proportional to the 3rd cumulant of Debye-Waller factor. I work with high-temperature high-pressure systems where anharmonic effect is not negligible. Thanks. Yuan Ping

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2011 XAFS Summer school
by sumitk＠barc.gov.in 05 Apr '11

05 Apr '11

Dear Members, I am interested to attend the 2011 APS/IIT XAFS Summer school. I have written to Dr. Bunker for details but however, i am not able to reach him. I have already written (e-mail) to him on bunker(a)iit.edu site but i did not get reply. If dr. Bunker is on the mail list, i expect to reach him through this or if some member has the correct e-mail id of him, it will be of help to me to reach him. Thanking Sumit Kumar Scientific Officer Radiochemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 0640 (O).

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Final Deadline for NASCCSC Oral Presentations
by Carlo Segre 03 Apr '11

03 Apr '11

Hello: The final abstract deadline for oral presentations to the 2011 North American Core Shell Spectroscopy Conference is today, Sunday, April 3, 2011. Poster abstracts will continue to be accepted after tonight. The Second Annual North American Core Shell Spectroscopy Conference will be held jointly with the Denver X-ray Conference in Colorado Springs August 1-5, 2011. The conference is centrally located, making it easily accessible from the entire continent and it is excellent opportunity to have young scientists present to the Core Shell Spectroscopy community. We hope that you can attend and make this event an ongoing success. More information can be found at http://www.dxcicdd.com/cssc/ Hope to see you there! Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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Final Deadline for NASCCSC Abstracts
by Carlo Segre 31 Mar '11

31 Mar '11

Hello: The final abstract deadline for the 2011 North American Core Shell Spectroscopy Conference has been extended to Sunday, April 3, 2011. The Second Annual North american Core Shell Spectroscopy Conference will be held jointly with the Denver X-ray Conference in Colorado Springs August 1-5, 2011. The conference is centrally located, making it easily accessible from the entire continent and it is excellent opportunity to have young scientists present to the Core Shell Spectroscopy community. We hope that you can attend and make this event an ongoing success. More information can be found at http://www.dxcicdd.com/cssc/ Hope to see you there! Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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Again some questions related to IFEFFIT_ ARTEMIS computer package program
by Nicolae Aldea 30 Mar '11

30 Mar '11

Dear Professor "Matt Newville The first I would like to thank for your mails sent me on Tue Mar 22, 2011 and On Sun, Mar 27, 2011. Now, I have had success for entering to ifeffit(a)millenia.cars.aps.anl.gov My new questions are: 1) Should I introduce in GDS degen parameter for fitting beside amp, enot, delr and ss? What happened when I want to obtain coordination number (CN) associated to some coordination shell. I thank that there is a difference some time between CN and degen. In some cases they are the same. Many journals as you know report CN. For a coordination shell I think that we have some times more paths, is it rue or false? Does dgen associate only for a path ? 2) I could to view the feffXXXX.dat in according with your indication in own folder of computer package program c:\Document andSettings\USERNAME\Application Data\horae\stash, but can I save directly them? I did not find a direct bottom for saving them, is it true or I did not see it? 3) The exafs signal is a real function from math. point of view. So, FT[chi(k)]= real_RDF_even(r)+i*RDF_odd(r). Then IFT[real_RDF_even(r)+i*RDF_odd(r)] = chi_real(k)+ i*zero, where i=sqrt(-1), is it true ? In affirmative case why you have in ARTEMIS plot region the both components ? Is not the imaginary part zero ? from math p. v. the module of chi(r) is a symmetrical signal. Even, we take into account only a region [rmin:rmax] for RDF(r) we obtain for IFT of RDF(r) only a real signal. Thanking you I advance I remain, Nick Aldea

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PhD position at KIT, INE in Germany
by tony vitova 25 Mar '11

25 Mar '11

Dear all, We are looking for a PhD candidate, who will work in a professional and friendly atmosphere in a young research group at the Karlsruhe Institute of Technology, Institute for Nuclear Waste Disposal with outstanding tradition in actinide research. The interested person should have background in physics, chemistry or related natural sciences, strong interest in instrumentation, method development and spectroscopy. Please see the attachment for additional information. many greetings from Karlsruhe Tonya

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NACSSC - Still 2 weeks for abstract submission
by Carlo Segre 22 Mar '11

22 Mar '11

Hello All: The Abstract Deadline has been extended for an additional 2 weeks until April 1, 2011, for oral presentations at the North American Core Shell Spectroscopy Conference to be held in conjunction with the 2011 Denver X-Ray Conference from August 1-5, 2011. http://www.dxcicdd.com/03/DXC_abstract.asp This conference is centrally located and an excellent opportunity for students and postdoctoral researchers to participate. This year, we are specifically interested in having presentations relating to 5f electron systems and catalysis. This conference is a great opportunity to meet with other practitioners of core-shell spectroscopy as well as a broader x-ray diffraction and fluorescence community. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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Please give us help
by 松浦真 21 Mar '11

21 Mar '11

Dear IFFEFIT members I'm a member of this mailing list and I engage in XAFS research in Tohoku University, in Japan. As you know incredible earthquake and subsequent Tsunami, the scale of which has never happened for hundreds years, has attacked Japan on March 11. More than 20 thousands of peoples are killed by this disaster and even now many victims are dieing being unable to extend a helping hand. Furthermore Tsunmai attacked Fukusima's nuclear reactors and residents within 30 km are evacuated due to radiational contamination. Through disparate effort thousands of fuel rods are successfully cooling down well, but straggling will still continue now. Japan faces triple crisis; earthquake, Tsunami and nuclear disaster, which have been never happened in our history after the second World War. Tohoku University in Sendai has suffered incredible damage by this earthquake. Though actual damage is not clear yet, I think it takes more than decade until complete reconstruction. Synchrotron radiation facility of KEK Tsukuba also seems to suffer serious damage. XAFS researchers in Japan now face to a unprecedented difficulty. I guess the damage of this disaster in Japan amounts total about 5 x 10^6 million US$. I believe Japanese can concur this disaster in future. But we need help to save numerous victims due to earthquake,Tsunami and nuclear disasters and need to help for reconstruction. I wish the colleges of XAFS in the world to notice this serious situation in Japan and I wish to appeal to other people to help Japanese. Thank you for your collaboration. Makoto Matsuura IMR, Tohoku University

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Looking for reviewers for XAFS textbook chapters
by Scott Calvin 09 Mar '11

09 Mar '11

Hi all, I am looking for people interested in reviewing portions of the XAFS textbook I am working on. I am particularly hoping that some people less experienced in XAFS will volunteer, so that I can get feedback on how well it teaches and how well it covers the topics you'd like to know more about. Experts are also welcome! The first chapter I've got ready is the chapter on sample preparation. If you are interested in reviewing this chapter and can get feedback back to me within two weeks, please email me at SCalvin(a)slc.edu . --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Looking for reviewers for XAFS textbook chapters
by Scott Calvin 08 Mar '11

08 Mar '11

Darn it! I did not mean to send the packet to the whole list. If anyone is interested in reviewing, please send a request to SCalvin(a)slc.edu . I apologize for spamming you all with a multi-MB file. --Scott On Mar 8, 2011, at 12:24 PM, Scott Calvin wrote: > Great! > > I'm attaching the review packet. The page numbering is a bit > chaotic, because it's actually several documents stitched together: > > The copyright notice. My publisher is allowing me to distribute > review copies, but only on the condition that reviewers not > redistribute them. > A detailed table of contents. This is more detailed than the final > version will be, but gives context to reviewers as to what will be > covered elsewhere. > An excerpt from the preface explaining the origin of the cartoon > characters. (Yes, there are cartoon characters...) > An introduction to the cartoon characters. > Chapter 3, on sample preparation. > References > > In the chapter, I've placed numbers along the margin to aid in > making comments. For example, you might want to comment on page 18, > lines 6-7. The numbers won't appear in the final version. > > If you have any questions about the context of the chapter, the > intended audience, or whatever, feel free to ask! > > --Scott Calvin > Sarah Lawrence College > <XAFSforEveryone_Chapter3_v2.pdf> > > On Mar 8, 2011, at 11:27 AM, Prof. Dr. Peter Leinweber wrote: > >> hello, i am interested in reviewing this. i am not experienced but i >> want to learn more. >> i look forward to hearing from you, peter leinweber >> >> Am 08.03.2011 04:13, schrieb Scott Calvin: >>> Hi all, >>> >>> I am looking for people interested in reviewing portions of the XAFS >>> textbook I am working on. I am particularly hoping that some people >>> less experienced in XAFS will volunteer, so that I can get >>> feedback on >>> how well it teaches and how well it covers the topics you'd like to >>> know more about. Experts are also welcome! >>> >>> The first chapter I've got ready is the chapter on sample >>> preparation. >>> If you are interested in reviewing this chapter and can get feedback >>> back to me within two weeks, please email me at SCalvin(a)slc.edu . >>> >>> --Scott Calvin >>> Sarah Lawrence College >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >> >> >> -- >> Prof. Dr. Peter Leinweber >> Soil Science >> Institute for Land Use >> University of Rostock >> D-18051 Rostock/Germany >> Tel.: +49 381 498 3120 >> Fax: +49 381 498 3122 >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

1 0

FEFF6L input keyword question
by YOON Zin Seok 03 Mar '11

03 Mar '11

Dear FEFF users, Hi, I am a beginner of FEFF6L. Usually depending on the manual provided by web site, I am managing to calculate spectrum, and there are too many difficulties...I would like to be advised from you, senior members. I have three questions. (1) I would like to control the temperature. In the manual, I see DEBYE 190 315 (Calculate Debye-Waller factors for Cu at 190 K??). Can I change the temperature simply by modifying the number "190"? Can I find a reference paper for this? (2) Where can I find Debye-Waller factors in the output files? (3) How can I change the ionic state? I would like to compare the output file, chi dat., between SF6 and SF6+ molecules. I hope I could have answers for my questions... Best wishes, Zin

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International Workshop on Improving Data Quality and Quantity , for XAFS Experiments (Q2XAFS2011), Tsukuba, Apr. 12-13, 2011
by Yohei Uemura 02 Mar '11

02 Mar '11

Dear ifeffit mailing list users, This is Yohei Uemura at Photon Factory, KEK, Japan. "Q2XAFS" workshop is going to be held on 12-13 April 2011 in Photon Factory, Tsukuba, Japan. This workshop aims to have worldwide discussions about measurements and data collection of XAFS to improve data quality and quantity. There will be also presentations about XAFS experiments on bio-systems and recent beamline developments. Please read the message from the organisers below. **************************************************************** Dear Colleagues It is our pleasure to inform you that "International Workshop on Improving Data Quality and Quantity for XAFS Experiments (Q2XAFS2011)" will be held during April 12-13, 2011 in Tsukuba, Japan. As you have been of great significance in the related topics of XAFS, we would be honored to ask your attendance and participation in our efforts aimed at quality and quantity improvements. We will welcome your early registration (reduced fee) at the Q2XAFS2011 web (http://pfwww.kek.jp/Q2XAFS2011/index.html) by February 28. The workshop is jointly organized by the IUCr XAFS Commission and the IXAS, inviting outstanding researchers representing synchrotron radiation facilities all over the world. Q2XAFS2011 focuses on Q2 (quality and quantity) control of EXAFS data collection, analyzing and exchange. Our goal is to assess the current status, to find fundamental problems and to propose a solution through standards and/or recommendation. The workshop will provide opportunities to fully discuss and exchange opinions on important categories of Q2 control. As the topics of the workshop are strongly dependent on beamlines and experimental stations, participation of experienced scientists based at facilities is essential. In particular, we will have a dedicated session for standard data format that would dramatically improve efficiency and security of data collection and exchange. Your participation in the workshop will be greatly appreciated. We look forward to seeing you in Tsukuba. Sincerely, yours Soich Wakatsuki, Chair of Q2XAFS2011, Director of Photon Factory Isabella Ascone, IUCr XAFS Commission, Chair Hiroyuki Oyanagi, IXAS, Chair **************************************************************** -- =========================================== 上村洋平所属: 高エネルギー加速器研究機構　物質構造科学研究所放射光科学研究施設（Photon Factory) 住所: 茨城県つくば市大穂1-1 Yohe'i Uemura (Ph.D) Affiliation : Photon Factory, Institute of Materials Science, KEK Adress : 1-1 Oho, Tsukuba-Shi, Ibaraki, Japan 305-0801 TEL&FAX: 029-879-6105 PHS: 029-864-5200 + 4956 Email : yuemura(a)post.kek.jp ===========================================

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Purple & Red E Derivatives
by Andrew Korinda 25 Feb '11

25 Feb '11

While working in Athena today I noticed something peculiar while looking at the derivative plots of mu(E) data. When I plot the current group (red button) the plot can be spiky. However, when I plot as marked group (purple button) everything is much smoother and more rounded. Smoothed data will do the same thing. It always happens whether I have mu(E) or norm(E) selected. I have never noticed a difference in how any of the other plots current when switching between marked and active plotting. I didn't see anything in the documentation about how the derivatives are calculated so I'm turning to all of you. Have any of you noticed this? Does anyone know if there is a difference in how the derivatives are calculated in each plotting function? Andy Korinda Notestein Lab Northwestern University

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parseval's theorem and athena
by kirshstein＠googlemail.com 17 Feb '11

17 Feb '11

Hello, I would like to use parseval's theorem (as described in a document called: Error Reporting Recommendations: A Report of the Standards and Criteria Committee, Adopted by the IXS Standards and Criteria Committee July 26, 2000 ) to quantify the statistical noise in my spectra. In section 3 (as shown in the attachment), it says that for the formula to work, the forward FT has to be normalized by sqrt(deltak/Pi). (delta k is the spacing of points in k space) What is the normalization used for FFT in athena? if it is not sqrt(deltak/Pi), what is it? how does the parseval theorem formula need to be modified as a function of FT normalization? Many thanks for answers! Regina

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FEFF question Te K edge
by Andrea L Foster 16 Feb '11

16 Feb '11

Hello All, sorry if this is not the correct venue...I tried to join a feffusers list I saw at http://leonardo.phys.washington.edu/feff/html/mailing_list.html but I got bounces when I subscribed and tried to post. my problem is below, and I'm sure one of the many knowledgeable folks on this group can help: I am starting to run FEFF6L calculations for Tellurium phases. I used published structure report of calaverite (AuTe2) and Na2TeO3_5H2O to generate ATOMS.INP files which I then used to generate FEFF.inp files. These two very different Te minerals gave me the following error when running FEFF6L (following is a copy of a little of the FEFF output): Running "C:\Program Files\Ifeffit\bin\feff6l.exe" feff.inp Feff 6L.02 Disodium Tellurite 5-hydrate Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 3 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... ...I have stopped copying the FEFF output there. I do not think that the problem is with the crystal structures as they are pretty simple (though human error is never to be minimized, especially mine ;). ATOMS returned no errors when it ran. The interatomic distances generated in feff match those reported in the crystal structure report...and the coordination numbers appear to be correct (for example the sodium tellurite structure should have 3 closest oxygen neighbors, and does, at the correct distances)... so I don' t know how to troubleshoot this error when nothing appears wrong geometrically. I have attached the 2 feff.inp files (which list the xtal structure info) in case that helps. They are slightly renamed. thanks for any help, andrea ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andrea L. Foster, Ph.D. U.S.G.S. WMESC 345 Middlfield Rd., MS 901 Menlo Park, CA 94025 T: 650-329-5437 F: 650-329-5491

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Re: [Ifeffit] Fe in glassy ceramics
by Scott Calvin 16 Feb '11

16 Feb '11

Hi Andrei, It's not unreasonable to model such a thing. Use a highly constrained model for the spinel, not allowing coordination numbers to float and using very few sigma2 parameters. I've published a model like that for fitting spinels here: http://prb.aps.org/abstract/PRB/v66/i22/e224405 My model is more complicated than yours needs to be, because you don't really have site disorder; all the sites are Fe. Then multiply the amplitudes by a guessed parameter representing the fraction of the iron that is in the spinel phase. The remaining amplitude gets used for the glassy phase, which can possibly be fit by a single iron-oxygen path, which can be cloned from one of the spinel near neighbor paths, but now with most parameters floated. You may very well need to fix S02 based on the value from a standard. Fit over a wide range in the Fourier transform, so that you take advantage of high R peaks to pin down the spinel part. Worth a shot, anyway. The key is being aggressive with assumptions and constraints, and then being honest about how that affects your uncertainties in the end. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Feb 16, 2011, at 4:53 AM, Andrei Shiryaev wrote: > Dear colleagues, > > Probably similar questions were already asked, but nevertheless I > would appreciate some advice how to solve the problem. > > We are looking at Fe environment in complex glasses, which underwent > partial crystallization. A fraction of Fe has precipitated as spinel- > like nanocrystals, another fraction remains in glass. Spinel itself > is already challenging for XAFS, but our task is to understand the > Fe fraction in glass (e.g., Fe-O bond length). > > We do not know the exact composition of the crystalline phases, thus > we can not record a suitable standard. Does anybody have an idea how > could we try to separate the Fe in glass from Fe(cryst) contributions? > > I fully realize that the problem is ill-posed, perhaps, some people > had somehow solved this problem. > > Thanks a lot, > Andrei Shiryaev > > Instituteof Physical Chemistry > Moscow > Russia

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Fe in glassy ceramics
by Andrei Shiryaev 16 Feb '11

16 Feb '11

Dear colleagues, Probably similar questions were already asked, but nevertheless I would appreciate some advice how to solve the problem. We are looking at Fe environment in complex glasses, which underwent partial crystallization. A fraction of Fe has precipitated as spinel-like nanocrystals, another fraction remains in glass. Spinel itself is already challenging for XAFS, but our task is to understand the Fe fraction in glass (e.g., Fe-O bond length). We do not know the exact composition of the crystalline phases, thus we can not record a suitable standard. Does anybody have an idea how could we try to separate the Fe in glass from Fe(cryst) contributions? I fully realize that the problem is ill-posed, perhaps, some people had somehow solved this problem. Thanks a lot, Andrei Shiryaev Instituteof Physical Chemistry Moscow Russia

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