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

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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About ASCII Data Export in Athena 0.9.18
by Shoaib Muhammad 03 Oct '13

03 Oct '13

Hi, I have Mn XAS data and I am trying to export this XAS data by using "File", "Save marked group as" and "norm E". My Mn XAS data shows some spikes around 7150eV other than main Mn K edge peak due to some Fe impurity. So it is hard to fit post edge and I have ticked "Flatten normalized data" to get a straight line post edge. After doing this I can see an almost straight line post edge in the Athena preview graph but when I export ASCII data to plot in OriginPro etc it seems like data is being exported with out "Flatten normalized data". I have attached relevant information. Am I missing some point or is it a software bug? Thanks -- Shoaib Muhammad Department of Energy Science Sungkyunkwan University South Korea

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copied feff calculations in Artemis
by Samson, Jan 02 Oct '13

02 Oct '13

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

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Problem with Demeter 0.9.18 pluck tool
by Denis Testemale 30 Sep '13

30 Sep '13

Dear members of the list, I finally got the opportunity to start using Dathena. I don't know if I've found a bug or if I'm doing something stupid (chances are not too low, actually...). - I am using Ubuntu 13.04 - Demeter 0.9.18 (I did the upgrade to 0.9.18 but ran into some error messages as reported on September 10th on this list, could they be related to the behaviour I am reporting here?). - I cannot say if it worked before the upgrade to 0.9.18 since I never took the time to use Demeter properly until now. I'm trying to pick/pluck a value from the graph. - When I first launch Dathena, and I press a pluck button for the first time I can see the expected message at the bottom of the GUI ("Double click on a point to pluck its value ..."): as hard as I tried (I tried many different combinations) I could never get the thing to work (parameter value in the 'box' never records the value where I double click). After 10s I see the 'Pluck timed out' message. - Then, when I click again on the pluck button, a value is recorded instantly in the 'box' without any double-clicking from me, and this value is crazy. An example: for a low k parameter of the FT I get -100000. The example in the attached screenshot shows a value for the normalization range low limit at -107112.52eV (note that the E0 value is 'integrated' in this number: the iron edge at 7112.52, see screenshot. I tried another set of data, silver K edge and the same thing occured: a weird number, with the E0 value inside, got recorded in the 'box). - Same problem with Dartemis. Tell me what I can do to help... or what I'm doing stupid. Thanks. denis

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Re: [Ifeffit] Problem with Demeter 0.9.18 pluck tool
by Denis Testemale 30 Sep '13

30 Sep '13

Bruce: many thanks, choosing wxt did the trick (I had x11 set). It now says (see screenshot): my value is 'wxt', Demeter value is 'x11' I definitely have to take the time to look into those preferences and options. I should have done my homework. Thanks again. Denis Le 28/09/2013 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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: Problem with Demeter 0.9.18 pluck tool (Bruce Ravel) > 2. Re: Problem with Demeter 0.9.18 pluck tool (Ravel, Bruce) > 3. Re: Problem with Demeter 0.9.18 pluck tool (Ravel, Bruce) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 27 Sep 2013 13:25:03 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Problem with Demeter 0.9.18 pluck tool > Message-ID: <5245BF6F.5010201(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Denis, > > I have 13.04 on several of my machines at work and at home. I do not > see the behavior you are describing. Let me try installing 13.04 > fresh on one of my computers and see if the same thing happens. If > not, I'll figure out how to troubleshoot. > > B > > > On 09/27/2013 08:24 AM, Denis Testemale wrote: >> Dear members of the list, >> I finally got the opportunity to start using Dathena. I don't know if >> I've found a bug or if I'm doing something stupid (chances are not too >> low, actually...). >> >> - I am using Ubuntu 13.04 >> - Demeter 0.9.18 (I did the upgrade to 0.9.18 but ran into some error >> messages as reported on September 10th on this list, could they be >> related to the behaviour I am reporting here?). >> - I cannot say if it worked before the upgrade to 0.9.18 since I never >> took the time to use Demeter properly until now. >> >> I'm trying to pick/pluck a value from the graph. >> - When I first launch Dathena, and I press a pluck button for the first >> time I can see the expected message at the bottom of the GUI ("Double >> click on a point to pluck its value ..."): as hard as I tried (I tried >> many different combinations) I could never get the thing to work >> (parameter value in the 'box' never records the value where I double >> click). After 10s I see the 'Pluck timed out' message. >> - Then, when I click again on the pluck button, a value is recorded >> instantly in the 'box' without any double-clicking from me, and this >> value is crazy. An example: for a low k parameter of the FT I get >> -100000. The example in the attached screenshot shows a value for the >> normalization range low limit at -107112.52eV (note that the E0 value is >> 'integrated' in this number: the iron edge at 7112.52, see screenshot. I >> tried another set of data, silver K edge and the same thing occured: a >> weird number, with the E0 value inside, got recorded in the 'box). >> - Same problem with Dartemis. >> >> Tell me what I can do to help... or what I'm doing stupid. >> Thanks. >> denis >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >

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