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

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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Renaming groups in Athena
by George Sterbinsky 17 Oct '13

17 Oct '13

Hello, I am writing to report what I believe to be a bug in Athena. In the attached project, there are two groups, a main group and a reference group. Changing the name of the first group does not change the name of the reference group. Changing the name of the reference group separately doesn't work well either. This results in an extra "Ref" being added to the beginning of the group name, which cannot be deleted. This happens every time one changes the name of the reference group, which can result in quite a long name for the reference. Let me know if any further information would be helpful. Thank you, George

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Demeter/Strawberry Perl in Windows 8
by Godfrey, Ian 15 Oct '13

15 Oct '13

Hi All, I was wondering if anyone has encountered the following error (screenshot attached) while trying to run Demeter applications (it seems to occur at least for both Artemis and Athena) under Windows 8. I know other members of my group have successfully managed to run Demeter under Windows 8 but have not encountered this message.: "perl.exe - Entry Point Not Found The procedure entry point __gxx_personality_v0 could not be located in the dynamic link library C:\strawberry\perl\site\lib\auto\Wx\Wx.dll" I have run the installer under Windows XP compatibility mode and used the Windows Compatibility Troubleshooter to no avail. I have tried installing the latest version of Strawberry Perl (I have tried both the x86 and x64 version, I have an x64 system) - this changes the symptoms so that the command prompts appear briefly on screen and then disappear. Re-running the Demeter installer than causes the original error message to begin appearing again. I have run all the installers as admin and have tried setting perl.exe both to admin and compatibility mode. I have authorised all UAC prompts that appear. Any help with this would be greatly appreciated. Regards, Ian Godfrey ---- Ian Godfrey MRes/PhD Student, Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London. i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> 02076 790053

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Export chi(R) with different kw
by Eugenio Otal 12 Oct '13

12 Oct '13

Hi, I am fitting results and I would like to export the chi(R) with different kw to show the change and remark the shell composed by light atoms from the one composed by heavy ones, Is this possible? Thanks in advance, euG

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Re: [Ifeffit] Ifeffit Digest, Vol 128, Issue 3
by Samson, Jan 04 Oct '13

04 Oct '13

Hello all, sorry for the late reply but Thursday is a holiday here. So I just come now to reply to the earlier question of Shoaib about my problem. I am using Win7 and Demeter in the version of 0.9.17. Think I missed the last update. Best regards, Jan -----Ursprüngliche Nachricht----- Von: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] Im Auftrag von ifeffit-request(a)millenia.cars.aps.anl.gov Gesendet: Mittwoch, 2. Oktober 2013 19:10 An: ifeffit(a)millenia.cars.aps.anl.gov Betreff: Ifeffit Digest, Vol 128, Issue 3 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: copied feff calculations in Artemis (Shoaib Muhammad) 2. Re: About ASCII Data Export in Athena 0.9.18 (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Oct 2013 16:41:37 +0900 From: Shoaib Muhammad <mshoaibce(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] copied feff calculations in Artemis Message-ID: <CAB+sMQeDh+jx9gcYCfhfBA=Ks2B9OS0tCSX-_LSUEjY6qYrw4g(a)mail.gmail.com> Content-Type: text/plain; charset="windows-1252" Hi Jan Samson, Are you using the latest version of Demeter that is 0.9.18.2? As far I know, the problem you have mentioned was a "known issue" in previous version and removed in the latest build. Regards, Shoaib On Wed, Oct 2, 2013 at 4:34 PM, Samson, Jan <jan.samson(a)tum.de> wrote: > Hello,**** > > ** ** > > I know it says on the webpage not to be vague about ones problems. The > problem is, I am not doing anything to the program. I do calculations > in a project of mine save and close it. When I load it sometimes the > program has copied the Feff calculation sheet. That is of course no > big problem but can be really annoying because the program sometimes > does not stop after copying it once but continues to do so. That can > make it really hard to stay on top of things. To make it more clear I > hereby sent a picture. The Feff calculation ?ARA_crystallstructureneu? > file was mysteriously copied.* > *** > > ** ** > > Thank you very much for any help,**** > > Jan Samson**** > > ** ** > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- Shoaib

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