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

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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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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Header information data Lepidocrocite
by Florian Werner 05 Nov '13

05 Nov '13

Hi All, I'm trying to find my way into XAFS data processing with Athena, but I'm new to the topic. I hope someone can help me out with my questions. As background information: Currently I'm planning my beamtime experiment for XANES spectra about phosphorus speciation at SLRI in Thailand. I have made a tutorial with data from Bruce Ravel from scans of Lepidocrocite. I have a question regarding this data. For example in the header information of file Fe_lepidocrocite.000 (from Bruce Ravel's github site) there can be found the abbreviations SRB, SRSS and SPP. So my first question is: What do this abbreviations stand for? SRB is the sampling range (SR..?!), i guess, so what does 15k stand for (data ends at 7971.35723 keV, but how is this connected to "15k"?)? SRSS manages the step size (..SS?), but how does "0.05k" result in the given steps? I assume that this kind of "k"-settings may be limited to X-23A2 beamline (or BNL), but still I'm anxious to know how the data has been collected. Best regards, Florian

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Lead reference compounds
by Luxton, Todd 01 Nov '13

01 Nov '13

Hi All, I am looking for spectra of three lead compounds, and I am hoping someone has one or all of the spectra. I am looking for Coronadite (lead manganese oxide), Plumboferrite, (lead iron oxide), and Magnetoplumbite (Iead iron oxide). Any help would be greatly appreciated. Best Regards Todd Luxton "A nation that destroys its soils, destroys itself" Franklin D. Roosevelt

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modeling significant defects and molecules
by Carl Brozek 31 Oct '13

31 Oct '13

dear listhost, I would like to use Artemis/Atoms to simulate EXAFS of a crystalline material with significant defects that include additional atoms to the unit cell. Can I simulate this material without making a new cif file? Ideally, I would be able to input a DFT-optimized model cluster as xyz coordinates only -- no crystallographic information. This problem seems analogous to modeling discrete molecules. Can molecules be simulated by atoms/artemis? I know FEFF is capable of this, but I would like to use atoms for making my input file for feff. Carl -- PhD Candidate | Chemistry | MIT SB | 2010 | University of Chicago

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Athena crash report
by George Sterbinsky 31 Oct '13

31 Oct '13

Hello, I am writing to report a crash of Athena 0.9.18 running on Ubuntu 12.04 as a virtual machine. The terminal output is below. Let me know if I can provide any additional information. Thanks, George parallels@parallels-Parallels-Virtual-Platform:~$ dathena Attribute (bkg_nor1) does not pass the type constraint because: Validation failed for 'Num' with value 15. at accessor Demeter::Data::bkg_nor1 (defined at /home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 264) line 12, <F> line 1. Demeter::Data::bkg_nor1(Demeter::Data=HASH(0xd26a1b0), 15.) called at /home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Main.pm line 843 Demeter::UI::Athena::Main::OnParameter(Demeter::UI::Athena::Main=HASH(0xaf7f780), Wx::CommandEvent=SCALAR(0xc130520), Demeter::UI::Athena=HASH(0x186fad0), "bkg_nor1") called at /home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Main.pm line 341 Demeter::UI::Athena::Main::__ANON__(Demeter::UI::Athena::Main=HASH(0xaf7f780), Wx::CommandEvent=SCALAR(0xc130520)) called at /home/parallels/perl5/bin/dathena line 47 eval {...} called at /home/parallels/perl5/bin/dathena line 47 parallels@parallels-Parallels-Virtual-Platform:~$

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calculating particle size from coordination numbers
by Georges Siddiqi 31 Oct '13

31 Oct '13

Hi All, I'm trying to use EXAFS data I have of Cu nanoparticles dispersed on SiO2 and ZnO to calculate their particle size. Searching the archives, i've come by these topics and papers, which have helped immensely, but I'm still a little bit in the dark about the specifics of the fits: http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02994.html http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03430.html http://pubs.acs.org/doi/full/10.1021/jp012769j http://pubs.rsc.org/en/Content/ArticleLanding/1999/CP/a904654b#!divAbstract So these discussions and papers make it clear that CNs for the 2nd or 3rd coordination shells will give a more accurate picture of the particle size (and even shape). Also, just comparing SO2s between a foil and the sample isnt the most accurate. My initial thought was to get a good fitting model on Cu foil, obtain coordination numbers which are very close to 1, then apply that same fitting model to the Cu nanoparticles (for the Cu-SiO2 species we have TEM data I can again calibrate myself with) However, my specific problem is getting reasonable coordination numbers for the Cu foil. - I can set the SO2 to 1 and get a very good fit for the data, but this is not useful for the nanoparticles - I can give all paths the same SO2 variable, and get a fitted value close to 1, but this isnt useful for comparing first and second shell CNs, as the ratio will always be the same. - And finally, when I try to give each scattering shell its own independent CN, I again get a good fit, but while the first shell SO2 is close to 1, the 2nd shell value is closer to 1.5 I've been playing with which variables are the same between paths, etc, and I can get more reasonable numbers, but the problem then becomes that I cant easily justify my fitting model. Attached is my Artemis file for Cu foil. Any help or suggestions with how to proceed (specifically with how to group variables) would be much appreciated. I apologize in advance if i'm asking about a topic that's been covered extensively. thanks, Georges Siddiqui

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Bug when adding feff calculations
by Georges Siddiqi 31 Oct '13

31 Oct '13

Hi, I'd like to report 2 bugs that I have when dealing with Feff calculations. One is critical (program crashes), the other is more troublesome, but i've found ways around it. OS: Windows 7, SP1 Demeter version: 0.9.18 *1) Critical - Trying to add single scattering paths of arbitrary lengths. This used to work with an older version of the program, but now, no matter what I do, when I add a single scattering path with any length, the program crashes* I've attached the log file (dartemis.log)* * * * How to replicate: -import any file (i've attached Cu.inp for ease of comparison) -run atoms -run feff -load an athena file (i've attached Cu foil.apj) -go to "Path like" tab -input any bond distance, and drag path over to the path list *-*program should crash This problem occurs both with cif files and inp files (and several of both file types have been tried), and (so far) any type of data set I try to import into athena. I've just chosen the attached files for their simplicity. 2) Not critical - I deal with a lot of organometallic compounds whose cif files correspond of only 1 absorbing atom surrounded by a network of non-absorbing atoms. i.e. not a regular, repeating lattice.* *When I import the cif file for one of these compounds (*see attachment, schrock 1.cif*), the Atoms page is fine, but in the Feff page, the "potentials" lists the absorbing atom as ipot 0 and 1: POTENTIALS * ipot Z tag 0 74 W 1 74 W 2 8 O 3 7 N 4 6 C 5 1 H while in the atoms list, it only appears once as ipot 0. Naturally, if I just click "run Feff", the program returns an error. My workaround to this has been to copy the atoms list into notepad, save, import into excel, subtract 1 from the ipot column (besides ipot 0), and replace the old atoms list with the corrected atoms list. then I manually change the potentials to: POTENTIALS * ipot Z tag 0 74 W 1 8 O 2 7 N 3 6 C 4 1 H after this it works fine. So this isn't a big burden, after a bit of practice I've gotten pretty fast at editing the Feff file, but if there's some easier solution it would be great. This problem occurs with any monomeric compounds. If I run the feff on a dimeric organometallic compound, there's no problems. Please let me know if there's any additional information I can supply that would help with this. thanks, Georges Siddiqi

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Re: [Ifeffit] Ifeffit Digest, Vol 128, Issue 22
by Kyler Carroll 31 Oct '13

31 Oct '13

Hi Stefan, I had help from Tsu-Chein Weng (tsuchien(a)slac.stanford.edu) with this issue and his solution worked for me. Basically I had to unistall both iXAFS and XQuartz and reinstall and do a similar trick in terminal. Hope this helps! 1. Drag /Applications/iXAFS.app into the trash bin 2. Download iXAFS3.0.3.dmg and install the package 3. Drage /Applications/XQuartz.app and /opt/X11 into the trash bin 4. Download XQuartz-2.7.4.dmg and install the package 5. Launch Terminal.app 5.1 cd /Applications/Utilities 5.2 sudo rm -fr X11.app 5.3 sudo mkdir X11.app 5.4 cd X11.app 5.5 sudo ln -s ../XQuartz.app/Contents 5.6 open -a X11 5.7 open -a ixafs Thank you, Kyler J. Carroll, Ph.D. Research Scientist Chemical Engineering Massachusetts Institute of Technology, On Mon, Oct 28, 2013 at 10:47 AM, <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. Did anyone upgraded to SeaLion aka Mavericks (MacOS 10.9) > (Mangold, Stefan) > 2. Athena crash report (George Sterbinsky) > 3. Re: Athena crash report (Bruce Ravel) > 4. Re: Athena crash report (George Sterbinsky) > 5. Re: Athena crash report (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 27 Oct 2013 18:00:28 +0100 > From: "Mangold, Stefan" <stefan.mangold(a)kit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Did anyone upgraded to SeaLion aka Mavericks (MacOS > 10.9) > Message-ID: <6C20978B-32DC-4C87-A900-2499DFFF4EC9(a)kit.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > one question to the early adopter. Did anyone tried ifeffit already on > Mavericks? Is there any known issue beside the X11/Quartz issue? I have it > installed ifeffit on MoutainLion with the know trick to "emulate" the old > X11 (was on the mailing list). > > Best regards > > Stefan Mangold > > > Karlsruhe Institute of Technology (KIT) > ANKA Synchrotron Radiation Facility >

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Did anyone upgraded to SeaLion aka Mavericks (MacOS 10.9)
by Mangold, Stefan 27 Oct '13

27 Oct '13

Dear all, one question to the early adopter. Did anyone tried ifeffit already on Mavericks? Is there any known issue beside the X11/Quartz issue? I have it installed ifeffit on MoutainLion with the know trick to "emulate" the old X11 (was on the mailing list). Best regards Stefan Mangold Karlsruhe Institute of Technology (KIT) ANKA Synchrotron Radiation Facility

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Artemis Software Issue
by James Apollo 26 Oct '13

26 Oct '13

Hello, Bruce and co I am a user of extended xray edge EXAFS spectroscopy and I have what I hope is a well formulated question regarding your software that you have developed. I recently downloaded a fresh copy of Iffefit from the CARS website, but the same issue continues to persist. In version 0.8.012 of Atena, I have noticed that if I ever close the "graphics window #1" the program alerts me that "the window was closed" and the software shuts down. Afterwards, I cannot restart the software no matter how hard I try. I have lost a great deal of my extended xray XAFS and XANES work from this aggreviating software issue. Is there some kind of patch I can download? The updates don't seem to work when I startup the software. Is there a newer version of the software I could use? Please let me know how to fix the problem. Thanks!

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Problem with PCA tool in Athena
by Ismael Graff 25 Oct '13

25 Oct '13

Dear fellows, I have an issue with the PCA tool of Athena (using 0.9.18 version of Demeter, windows XP sp2). When I try to target-transform a standard/model compound the program simply ignores my choice of standard. The target transform is applied to the first sample file that I have used to get the different components, even having highlighted the standard compound of my choice. Also, there is no output for the TT coefficients in the text box. Is it a problem of my Demeter installation? Has anyone had the same issue? All the best, Ismael. -- ************************************ * Ismael Graff * * * * Universidade Federal do Paraná * * Departamento de Física, CP 19044 * * 81531-980, Curitiba, Brazil. * * Tel (office): +55 41 3361 3278 * * Tel (Lab): +55 41 3361 3427 * * Fax: +55 41 3361 3418 * * http://fisica.ufpr.br/graff * * * * "DOCENDO DISCIMUS" * ************************************

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Re: [Ifeffit] Report problem in Demeter install
by Bruce Ravel 25 Oct '13

25 Oct '13

Charles, It is a bad use of my time to answer questions about the software other than on the mailing list http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ You'll notice this email is CCed to the mailing list. Any further conversation on this topic must use the mailing list. On 10/25/2013 04:38 PM, Charles Le Losq wrote: > Hello, > > I tried to install the demeter software but when I seach for > dependencies with > > ./Build installdeps > > (as described here: > http://bruceravel.github.io/demeter/pods/installation.pod.html#Installing_f…) Am I to assume that you are trying to build from source? The link is to the part of that page that discusses NOT building from source.... > (step 3b) > > > > this command actually don't work and don't exist... I seach for > other commands with ./Build help but I did not found anything. What > should I do to fix that ? > All the standard questions apply. You really have to give me something to work with.... * Is this linux? * What version of linux? Or whatever operating system you are using. * What version of perl? (perl -v) * What version of gcc? (gcc -v) * Did you successfully install Ifeffit and Pgplot? (Step 1) * What happened when you did "perl Build.PL"? * Is cpan configured reasonably? (Step 3a) * Did you read this: https://gist.github.com/waveform80/3959252 ? It's really helpful -- Dave Hughes did a bang-up job. > In addition, I wanted to use this version in order to get the latest > version of Athena... I have a issue with the one I got, it did not > work when asking for normalization of more than 200 spectra in one > run... On linux and mac... Is it a memory limitation ? How can I > overpass that? I've answered this question over a billion times times on the mailing list. Ifeffit, the backend Athena uses for its XAS functionality, is written in Fortran. Fortran has static memory allocation. As normally delivered Ifeffit can handle about 60 groups, given the way Athena uses memory. You have two options. (1) Compile Ifeffit to use more memory. Instructions can be found by searching the mailing list. (2) Live with the fact that you cannot do 200 spectra at a time. As Matt has pointed out many times, Larch will fix this problem. The day when Athena can use Larch is fast approaching. I'm getting there, but I have a lot of things to do each day. So it takes time. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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FW: Problem opening Demeter in Windows - doesn't work at all
by Arjen van Veelen 25 Oct '13

25 Oct '13

Dear Bruce, Regarding my earlier mail this week, the log files of my problem. Also, when I go to command window in Windows 7, it says that it can't find the path specified. What should I do? Should I fix the paths and if yes, how do I do that? Arjen From: Arjen van Veelen Sent: 22 October, 2013 5:04 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: Problem opening Demeter in Windows - doesn't work at all Dear Bruce, > > I reinstalled Demeter today, since it didn't want to start up (it worked before as far as I know). I > re-installed it and still does not start up. > > I see a window appearing and disappearing, but not Athena or Artemis. > I am running this also at linux, but like to be able to use it in > windows as well, since I write and work mostly in Windows.... > > Is there a way around it, or is there a bug in the software? For the mean-time I am using linux > > Best wishes, > > Arjen ir. A. (Arjen) van Veelen | PhD student | University of Manchester | School of Earth, Atmospheric and Environmental Sciences | Oxford Road | Manchester | M13 9PL | United Kingdom | M +44 77 2037 3237 | arjen.vanveelen(a)postgrad.manchester.ac.uk<mailto:arjen.vanveelen@postgrad.manchester.ac.uk> | www.manchester.ac.uk<http://www.manchester.ac.uk>

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calculating particle size from coordination numbers
by Georges Siddiqi 24 Oct '13

24 Oct '13

Hi All, I'm trying to use EXAFS data I have of Cu nanoparticles dispersed on SiO2 and ZnO to calculate their particle size. Searching the archives, i've come by these topics and papers, which have helped immensely, but I'm still a little bit in the dark about the specifics of the fits: http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02994.html http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03430.html http://pubs.acs.org/doi/full/10.1021/jp012769j http://pubs.rsc.org/en/Content/ArticleLanding/1999/CP/a904654b#!divAbstract So these discussions and papers make it clear that CNs for the 2nd or 3rd coordination shells will give a more accurate picture of the particle size (and even shape). Also, just comparing SO2s between a foil and the sample isnt the most accurate. My initial thought was to get a good fitting model on Cu foil, obtain coordination numbers which are very close to 1, then apply that same fitting model to the Cu nanoparticles (for the Cu-SiO2 species we have TEM data I can again calibrate myself with) However, my specific problem is getting reasonable coordination numbers for the Cu foil. - I can set the SO2 to 1 and get a very good fit for the data, but this is not useful for the nanoparticles - I can give all paths the same SO2 variable, and get a fitted value close to 1, but this isnt useful for comparing first and second shell CNs, as the ratio will always be the same. - And finally, when I try to give each scattering shell its own independent CN, I again get a good fit, but while the first shell SO2 is close to 1, the 2nd shell value is closer to 1.5 I've been playing with which variables are the same between paths, etc, and I can get more reasonable numbers, but the problem then becomes that I cant easily justify my fitting model. Attached is my Artemis file for Cu foil. Any help or suggestions with how to proceed (specifically with how to group variables) would be much appreciated. I apologize in advance if i'm asking about a topic that's been covered extensively. thanks, Georges Siddiqui

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Problem opening Demeter in Windows - doesn't work at all
by Arjen van Veelen 22 Oct '13

22 Oct '13

Dear Bruce, > > I reinstalled Demeter today, since it didn't want to start up (it worked before as far as I know). I > re-installed it and still does not start up. > > I see a window appearing and disappearing, but not Athena or Artemis. > I am running this also at linux, but like to be able to use it in > windows as well, since I write and work mostly in Windows.... > > Is there a way around it, or is there a bug in the software? For the mean-time I am using linux > > Best wishes, > > Arjen ir. A. (Arjen) van Veelen | PhD student | University of Manchester | School of Earth, Atmospheric and Environmental Sciences | Oxford Road | Manchester | M13 9PL | United Kingdom | M +44 77 2037 3237 | arjen.vanveelen(a)postgrad.manchester.ac.uk<mailto:arjen.vanveelen@postgrad.manchester.ac.uk> | www.manchester.ac.uk<http://www.manchester.ac.uk>

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Problem opening Demeter in Windows - doesn't work at all (Arjen van Veelen)
by fred.mosselmans＠diamond.ac.uk 22 Oct '13

22 Oct '13

Hi Arjen the most common cause of this is the lack of a directory for the log file for either artemis or athena to write to. in windows 7. see the link bruce sent. if that directory doesn't exist ( or for some bizarre reason they cant write to it) ,neither program will create it and when you attempt to start them a "dos" window " opens then closes as it finds it cant create the log file. Obviously there could well be a different reason but the symptoms you describe are associated with this problem. Cheers 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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Athena: Target transform function not working
by John Hayes 17 Oct '13

17 Oct '13

Hi All, I am trying to use Athena to do some PCA work and am having trouble getting the target transform analysis to work. When I click the target transform button no TT coefficients are produced and only a residual that is shaped like the original spectrum to be transformed is plotted. This seems to happen for all of my standards. (For my data in norm3.prj I am doing the PCA on all the spectra that start with TMF and trying to target transform the other spectra.) I have also tried this with the cyanobacteria data in the XAS-Education folder (also attached) to ensure it wasn't just a problem with my data. I am still have the same problems with this file as well. The dathena.log file and screenshot come from trying to target transform using this file. I am running a 64-bit version of Windows 7 and am running the 0.9.18 version of Athena. Thank you for any help you can provide! Cheers! -- John Hayes The Grosvenor Group Dept. of Chemistry University of Saskatchewan “Somebody told me it was frightening how much topsoil we are losing each year, but I told that story around the campfire and nobody got scared.”

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