April 2011 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Athena question
by Matt Newville 14 Apr '11

14 Apr '11

Hi Ganga, On Thu, Apr 14, 2011 at 5:17 AM, Ganga Hettiarachchi <ganga(a)k-state.edu> wrote: > Matt, > > Have you ever tried to save LC fitting results done using derivatives- we > did as we were doing for any fitting done using nor spectra- that is use > “write a report” option. However it does not save what we see in the LC > fitting graphic window. Why is that? How do we know what’s been saved when > we do that? How can we get it saved to generate stack plots on excel? > I'm not I've ever tried to get the report from a derivative LC fit, so I'll ask the Ifeffit mailing list. Anyone know how to extract this info easily? --Matt

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Re: [Ifeffit] Strategy to obtain cofigurationally averaged EXAFS from MD simulations
by Francisco Garcia 13 Apr '11

13 Apr '11

Dear Anatoly, Thank you very much for your reply. Unfortunately, your PRB references did not solve my problems. I am trying to reproduce the results of Cauet et al [J. Chem. Phys. 132, 194502 (2010)]. I basically have over 500 snapshots of a single Zn2+ ion (absorbing atom) in water (O atoms are the scattering atoms). I have the feff.inp file for each snapshot ready for Artemis. I basically want an efficient way to obtain the chi(k) of data for each snapshot and average the chi(k) as opposed to loading the feff.inp files one by one. Specifically a sample script/example will be of imense help. I could not find much information in the Artemis user manual. I must also state that I am an EXAFS novice so a step by step explanation will help me a lot. Thank you very much.

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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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