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

Fe2(MoO4)3 and FeMoO4
by Anatoly I Frenkel 06 Dec '13

06 Dec '13

Dear IFEFFIT users, If anyone has Fe K-edge spectra of Fe2(MoO4)3 and/or FeMoO4, and could email me the raw data, it will be gratefully acknowledged! Thank you very much, Anatoly Frenkel

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Re: [Ifeffit] fitting a specific k range
by fred.mosselmans＠diamond.ac.uk 06 Dec '13

06 Dec '13

What I find reassuring about Bruce's warnings is they allow you to think properly about what you are doing. Fortunately, unlike Chris, I am not of a size where I have to worry about falling down rabbit holes, unless American rabbits are much bigger than English ones. I would commend Matt's original question as it opened a debate with 3 of the mainstays of the list. That may not have been the intention but it makes interesting reading for us mailing list voyeurs. Cheers Fred Sent from Samsung tablet

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fitting a specific k range
by Matt Frith 05 Dec '13

05 Dec '13

Dear All, I need some help in fitting an amorphous iron oxyhydoxide sample. I am having difficulty producing a good fit, particularly in the k=4-6 range. Fitting this region well is very important for me, because if I add another metal(+3 oxidation state) into my system, this is where I observe the most quantifiable changes (The shoulder @ 5 A^-1 and the min @ 5.6 A^-1). Thus far I have been unable to fit the shoulder well enough to make meaningful comparisons. I have been fitting in kq with kmin=2.566 And kmax=10.877, and Rmin=1 and Rmax=3.5, and using the goethite O1.1, Fe.1, and Fe.3 paths. Attached is an Artemis file (P41_006_merge_norm_TRANS.fpj) for an amorphous Fe oxyhydroxide sample (Fe only, no other metals). The data was collected at the Fe K-edge. *Is there a way to fit just this region (k~4-6 range) in k? If so what is the best method for doing this? If not, does anyone have suggestions as to how I can improve my fitting? Should I fit the data in k since the shoulder is less evident in kq?* Thank you for your time. Sincerely, Matt Frith

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Er2O3 standard spectra
by Carlo Segre 04 Dec '13

04 Dec '13

Hello All: Does anyone have a reference spectrum of Er2O3? I have one but I am a bit concerned about the resolution and wish to compare. Thanks, Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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EXAFS spectra of uranyl standards
by Kate Tucker 02 Dec '13

02 Dec '13

Hi all, I was wondering if anyone has recorded an L3 edge for a single phase UO2Cl2 solid or solution, and a K edge for ZrCl4 and ZrO(NO3)2 solid or solution? I have already obtained my L3 and K edge data for the uranyl and zirconium containing systems, respectively. However, it has now become apparent that I may have something different going on to what was initially thought, so would really appreciate these spectra for use as standards. Many thanks, Kate

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dartemis crash
by René Genz 24 Nov '13

24 Nov '13

Hi Bruce, hi Matt, the other day a colleague encountered a problem. He measured a ZnO standard. I have the ZnO.fpj project file and can share the data. It is about 1.2 MB in size though. Shall I upload it to a public file hoster or sent it to your email account? At first I thought this is a problem with my installation steps on Fedora 18 x86_64, but I could reproduce the problem with Ubuntu 12.04 i686. The line numbers match, so I will post only the output from dartemis on Ubuntu. Note: this file was created with the Windows version of Demeter on Windows 7 Enterprise 32bit (running on Fedora 18 x86_64 as VirtualBox 4.2.18 virtual machine). Demeter crashes in the Windows version as well using the steps below. steps to reproduce: * start dartemis from a terminal * open project file in dartemis through 'Artemis [EXAFS data analysis]' window: File -- open project * in the 'Artemis [Plot]' window click on [R] button * in 'Artemis [Data] ZnO' window click on the bull's eye sign to the right of rmax window * wait about 10 seconds; dartemis will crash with the below error message ### Ubuntu 12.04 i686 test@test2:~$ dartemis Attribute (bft_rmax) does not pass the type constraint because: Num is not larger than 0 at accessor Demeter::Data::bft_rmax (defined at /home/test/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Data.pm line 406) line 7. Demeter::Data::bft_rmax(Demeter::Data=HASH(0x106540d8), -100000.000) called at /home/test/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis/Data.pm line 909 Demeter::UI::Artemis::Data::fetch_parameters(Demeter::UI::Artemis::Data=HASH(0x1085c3f4)) called at /home/test/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis/Data.pm line 662 Demeter::UI::Artemis::Data::Pluck(Demeter::UI::Artemis::Data=HASH(0x1085c3f4), Wx::CommandEvent=SCALAR(0x101c7ff8), "rmax") called at /home/test/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis/Data.pm line 362 Demeter::UI::Artemis::Data::__ANON__(Demeter::UI::Artemis::Data=HASH(0x1085c3f4), Wx::CommandEvent=SCALAR(0x101c7ff8)) called at /home/test/perl5/bin/dartemis line 39 eval {...} called at /home/test/perl5/bin/dartemis line 39 The installation steps on Ubuntu 12.04 i686 were: sudo apt-get install -y openssl-server # for my own pleasure sudo apt-get install -y gcc gfortran libx11-dev libncurses5 libncurses5-dev libpng3 libpng3-dev libgif4 libwxgtk2.8-dev git build-essential gnuplot perl cd git clone https://github.com/newville/ifeffit.git cd ifeffit sudo ./PGPLOT_install ./configure make sudo make install cd git clone git://github.com/bruceravel/demeter.git cd demeter sudo apt-get install -y liblocal-lib-perl sudo apt-get install -y libnet-ssleay-perl sudo apt-get install -y libssl-devl # due to 'SSLeay.xs:153:25: fatal error: openssl/err.h: No such file or directory' at Net::SSLeay sudo apt-get install -y libsoap-lite-perl # automatic installation fails due to missing/not installable dependencies, hence using package from repo sudo cpan o conf build_requires_install_policy yes o conf prerequisites_policy follow o conf commit perl ./Build.PL sudo ./Build installdeps perl ./Build.PL sudo ./Build installdeps perl Build.PL ./Build ./Build test sudo ./Build install If I should test something, let me know, please. Thanks a lot for your help :) -- Kind regards, René

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Fwd: problem compiling ifeffit
by Bruce Ravel 10 Nov '13

10 Nov '13

Rene, Support for the software is done via the Ifeffit Mailing List. This and all other questions should be asked in that forum. http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit please note that I am CCing my answer to the mailing list. All follow-up discussion should be on the mailing list rather than by responding to me directly. Regarding the problem with png files and PGPLOT, the solution of installing libpng12-devel is the much better solution. Regarding the problem compiling the file decod.f, I am going to blame Matt for that one. It seems he made a change to that file in August of 2012 (which is more recently than the last time I did a "git pull" on ifeffit!) Pulling and attempting to rebuild, I get the same result. Fixing the problem required editing the file encod.h to define the missing symbol "jtait". I just forked ifeffit, fixed the problem, and sent Matt a pull request. Here it is: https://github.com/newville/ifeffit/pull/4 If you follow the little link that says "97f6458", you'll see the diff. If you make the edit yourself, you should be able to finish compilation. Or wait for Matt to merge the pull request, do a git pull, then finish building. Regards, B -------- Original Message -------- Subject: problem compiling ifeffit Date: Thu, 31 Oct 2013 17:36:24 +0100 From: René Genz <liebundartig(a)freenet.de> To: <bravel(a)bnl.gov> Dear Mr. Ravel, today I tried to install the latest version of Demeter on Fedora 18 x86_64 following the instructions: http://bruceravel.github.io/demeter/pods/installation.pod.html In the past I could install ifeffit on Fedora 16 x86_64. But now I need your help. I encountered a problem in compiling ifeffit. This problem is reproducible on Ubuntu 12.04 i686. Furthermore, there are two minor things that I would like to mention as well: - PGPLOT_install does not set return code, if PGPLOT was not properly installed - ./configure of ifeffit echos the following line and continues without a problem "./configure: line 3355: #include: command not found" Details about the problem follow: I used the default installation selection for Fedora (Gnome Desktop). After installation I executed the following commands $ sudo yum install -y perl gnuplot gcc gcc-gfortran libX11-devel ncurses ncurses-devel libpng libpng-devel giflib wxGTK-devel git $ cd $ git clone https://github.com/newville/ifeffit.git $ cd ifeffit $ sudo ./PGPLOT_install The compilation started by the script fails. The attached file Demeter__F20__x86-64__PGPLOT_install.txt shows the last part of the output. I could work around this problem in two ways. Either a) sudo ./PGPLOT_install --no-png OR b) sudo yum install libpng12-devel ; sudo ./PGPLOT_install I used 'a)' and PGPLOT could be installed by the script. So I continued with the compilation of ifeffit. This is where I encountered a problem that I could not solve. $ ./configure was OK, just one line catched my attention "./configure: line 3355: #include: command not found" $ make The full output is in Demeter__F20_x86-64__ifeffit-configure-make.txt Here is the last part of the output: gfortran -g -O2 -fPIC -c iff_sync.f gfortran -g -O2 -fPIC -c decod.f decod.f:191.26: elseif (ic.eq.jtait) then 1 Error: Symbol 'jtait' at (1) has no IMPLICIT type make[3]: *** [decod.o] Error 1 make[3]: Leaving directory `/home/user/ifeffit/src/lib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/user/ifeffit/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/user/ifeffit' make: *** [all-recursive-am] Error 2 The error message refers to ./src/lib/decod.f I do not know how to solve this problem. Do you have a suggestions how to solve this? -- Kind regards, René

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Re: [Ifeffit] error in ATOMS
by Ravel, Bruce 10 Nov '13

10 Nov '13

Julius, I am CCing my response to the Ifeffit mailing list (http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) which is the appropriate venue for questions about the software. The problem you report is surprising to me and certainly not something I see normally. I will need to see an example on my own computer. If you could post an example of crystal data that triggers this, that would help. When you send this to the mailing list, also let us know what version of the software you are using. B Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ________________________________ From: Julius Campecino [jcampecino(a)gmail.com] Sent: Saturday, November 09, 2013 11:58 AM To: Ravel, Bruce Subject: error in ATOMS Hi Bruce, I am a new user of ATOMS (as well as Athena and Artemis). Whenever I try to run atoms it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 662." I do not know how to fix that or go around it. Hopefully you can help. Thank you, Bruce. Julius

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re Athena: Target transform function not working
by fred.mosselmans＠diamond.ac.uk 10 Nov '13

10 Nov '13

Dear Bruce, Following the instructions you gave John Hayes, I tried installing this fix on both a windows XP and Windows 7 machine today. Installing the PCA.pm file in the strawberry\perl\site\lib\Demeter folder seems to result in the crashing Athena when the pca tab is selected. I initially replaced both PCA.pm files and crashed the program then replaced one at a time and it is this file which causes the crash. Looking at github I see it was last changed yesterday I think, so suspect you may have altered it recently in a less than perfect manner. Log file attached. Thanks Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Re: [Ifeffit] Ifeffit Digest, Vol 129, Issue 9
by KONG Qingyu 08 Nov '13

08 Nov '13

Hello Jason, Thank you. Could one obtain x% directly from Artemis? We have tried to use a separate program to do linear combination fitting using feff calculated paths, but not the same quality of fitting from Artemis. Best regards, Qingyu Kong -----Message d'origine----- De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] De la part de ifeffit-request(a)millenia.cars.aps.anl.gov Envoyé : jeudi 7 novembre 2013 19:00 À : ifeffit(a)millenia.cars.aps.anl.gov Objet : Ifeffit Digest, Vol 129, Issue 9 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. linear combination fitting (KONG Qingyu) 2. Re: linear combination fitting (Jason Gaudet) ---------------------------------------------------------------------- Message: 1 Date: Wed, 6 Nov 2013 19:57:07 +0000 From: KONG Qingyu <qingyu.kong(a)synchrotron-soleil.fr> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] linear combination fitting Message-ID: <30F62EE734A9EA45A3F211513CB62003B134D787(a)SUN-DAG1.synchrotron-soleil.fr> Content-Type: text/plain; charset="iso-8859-1" Hello, We measured EXAFS of a mixed sample of Li2MoO3 and MO3, with Artemis we fitted the data with two FEFF calculations using the crystal structures of Li2MoO3 and MO3, the fitting results are quite good. We would like to know the weight of Li2MoO3 and MO3 in the sample, how can we get this value from Artemis? Thanks a lot in advance. Qingyu Kong Beamline ODE Soci?t? civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr ------------------------------ Message: 2 Date: Wed, 6 Nov 2013 18:03:53 -0500 From: Jason Gaudet <jason.r.gaudet(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] linear combination fitting Message-ID: <CANMcWtP0z6vALK5XMWtXp1TawruMo3NeMxNeZNoA1kvZpjT3wA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi Qingyu, Each Mo absorber contributes to the spectrum equally, so if you think you have a good analysis that indicates x% of Mo scatterers are most similar to Li2MoO3 and 100-x% are most similar to MoO3, those are simply atomic percentages. All you have to do is convert the atomic% to mass% using the formula weight of your components. -Jason On Wed, Nov 6, 2013 at 2:57 PM, KONG Qingyu < qingyu.kong(a)synchrotron-soleil.fr> wrote: > Hello, > > We measured EXAFS of a mixed sample of Li2MoO3 and MO3, with Artemis > we fitted the data with two FEFF calculations using the crystal > structures of > Li2MoO3 and MO3, the fitting results are quite good. We would like to > know the weight of Li2MoO3 and MO3 in the sample, how can we get this > value from Artemis? > > Thanks a lot in advance. > > > Qingyu Kong >

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