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

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

04 Dec '14

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

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error in ATOMS
by Julius Campecino 12 Dec '13

12 Dec '13

Hi Bruce, Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms. When I click "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 668.'' I am using the recent version 0.9.18.2 of the Demeter installer. Thank you for your help! Julius

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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 09 Nov '13

09 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 09 Nov '13

09 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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Re: [Ifeffit] LCF
by Jason Gaudet 07 Nov '13

07 Nov '13

It depends how you want to set up your guess-def-set parameters. For argument I'll describe a system of BCC Mo metal and MoO3, where you want to determine what fraction of Mo is in each. My usual method is just to set each path as N=1, SO2=amp_O for Mo-O, and N=1, SO2=amp_Mo for Mo-Mo. Then, in guess-def-set, I'd GUESS N_Mo = 8 N_O = 6 SET (SO2 as determined by my standards) so2=0.87 and DEFINE my amplitudes amp_Mo = N_Mo*so2 amp_O = N_O*so2 (And of course you want all the other parameters as well, I'm just showing the amplitude ones.) Then, once I get my N_Mo and N_O I can scale these to my expected coordination numbers and see if I get reasonable contributions for each. (Is N_Mo/8 + N_O/6 = 1?) If I had a really good reason to believe all Mo metal in my sample had an average Mo-Mo coordination of exactly 8 and all Mo oxide had an average Mo-O coordination of exactly 6, I could define things another way. SET N_Mo = 8 N_O = 6 so2=0.87 DEFINE amp_Mo = N_Mo*so2*Frac_metal amp_O = N_O*so2*(1-Frac_metal) GUESS Frac_metal=0.5 And that constrains all the amplitude parameters so the only result is what atomic fraction of Mo is present in the metal phase. Makes sense? -Jason On Thu, Nov 7, 2013 at 2:05 PM, KONG Qingyu < qingyu.kong(a)synchrotron-soleil.fr> wrote: > Hello Jason, > > Thanks a lot for your reply. > > What I can get from Artemis is the fitted parameters (amp, enot, ss^2, > delr) of each path, Mo-O, Mo-Mo, how can one get the percentage of Mo, x > from Li2MoO3 and 100-x from MoO3, from the fitted information. > > Best regards, > > > Qingyu > > Beamline ODE > Société 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 >

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linear combination fitting
by KONG Qingyu 06 Nov '13

06 Nov '13

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 Société 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

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Re: [Ifeffit] Is it possible to use ATOMS to solve this problem?
by Matt Newville 05 Nov '13

05 Nov '13

Hi Aderson, On Tue, Nov 5, 2013 at 8:16 AM, Áderson Miranda <aderson.mir(a)gmail.com>wrote: > Dear Prof. Newville, > I am a PhD. student from Brazil and I am trying to use ATOMS to a solve a > particular problem in my thesis. I would like to generate a big cubic > unitary cell with a S2O3 molecule surrounded by six water molecules in the > center of cell and to put heliums atoms in their six vertices. > > I have all the atoms positions optimized to my problem, except by the > helium atoms, that I want to place in a enough distance to have only one > molecule of S2O3 surrounded by water in the simulation of EXAFS. I tried to > insert the data in atoms and generate an input for the simulation of > EXAFS. I was not successful in my try, so is it possible to construct this > kind of cell and simulating the "EXAFS" for this specific problem? > > Sincerely, > > Áderson Miranda > > Yes, it should be possible to do this. It would be most helpful to see what you've tried and what worked and what did not. It's not obvious to me that helium will give a noticeable contribution to the EXAFS, but it's worth being able to calculate. I am using the Ifeffit mailing list to respond to this mail, as many people reading this have extensive experience constructing such molecular coordinates. --Matt

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