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

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

3 3

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

3 4

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

1 0

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

2 2

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

2 1

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

4 6

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 >> >

1 0

Athena fix edge step
by George Sterbinsky 24 Sep '13

24 Sep '13

Hello, I am writing to report what I believe to be a bug in Athena. I am using Demeter 0.9.18 and windows 8. To reproduce the behavior, open the attached project, and press the button to plot normalized marked groups in energy. One will observe that the fix edge step box is checked for the first group. Changing the edge step value for this group and pressing the button to replot the normalized data has no effect on the plot. If there is any further information I can provide to help determine why this is happening, let me know. Thank you, George

2 2

XANES relative peak energies
by Ross Devol 23 Sep '13

23 Sep '13

Hi everyone, I am using FEFF to calculate XANES spectra for calcium carbonates, and I am wondering how precisely I should expect the relative peak energies should be consistent with experiments. Is there anything I can do within FEFF to shift peaks relative to each other or to stretch/compress the entire spectrum? I've tried increasing l_fms (or lmax2), which helps some but not enough. Thank you! Ross DeVol University of Wisconsin-Madison

2 1

Re: [Ifeffit] XANES - relative peak energies
by Ross Devol 17 Sep '13

17 Sep '13

Thanks Josh and everyone else for the useful information! Here's another question: How precise should the relative peak energies be compared to experiment? If they don't match up, are there any parameters I can change that might stretch the spectrum or shift peaks relative to one another? Thanks Ross On 09/17/13, Joshua Kas wrote: > Hi Ross, > FEFF calculates the Edge energy, as well as the Fermi level. The edge > energy is accurate to about 1%, which means 1 to 10 eV for most edges > and systems. Feff also calculates the Fermi level, but does not give a > good estimate of the ionization potential. > > Also, in reference to your first question, as Bruce suggested, the > LDOS is a good quantity to look at. If a peak shows up strongly in the > Ca and the O LDOS, but only weakly in the C LDOS, that is an > indication that the peak is due to hybridization (bonding) between the > Ca and O states. > > Cheers, > Josh > > > > > > What about ionization potential? Does FEFF calculate it, or is there a way to extract it from the spectra? > > > > Thanks > > Ross > > > > On 09/13/13, Bruce Ravel > > wrote: > >> On 09/13/2013 03:25 PM, Ross Devol wrote: > >> > >> >Does anyone know whether FEFF can be used to assign peaks? In other > >> >words, is there a way to tell which peaks in a calcite O K-edge > >> >spectrum are due to CO bonds and which to CaO bonds? Also, does > >> >FEFF calculate the ionization potential and if so, where does it > >> >output this? > >> > >> Feff is a real-space multiple-scattering code. From the RSMS, your > >> question may not make a lot of sense. The XAS spectrum is a measure > >> of how the photoelectron interacts with its surroundings. In general, > >> peaks in the spectrum have something to do with all of the surroundings. > >> > >> One way to get a handle, in some sense, on your question is to run > >> Feff with successively larger values of the FMS parameter. That is, > >> see what features appear or change in the calculation as you increase > >> the radius of the cluster considered in the FMS calculation. > >> > >> Also of interest will be the partial densities of state as a function > >> of cluster size. That gives some hints of how Feff sees bonding in > >> your cluster. > >> > >> HTH, > >> 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 > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 17 Sep 2013 11:50:55 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] XANES - Peak assignment and ionization > > potential with FEFF > > Message-ID: <52387A5F.8(a)bnl.gov> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 09/17/2013 01:42 AM, Ross Devol wrote: > >> What about ionization potential? Does FEFF calculate it, or is there > >> a way to extract it from the spectra? > > > > Are you asking about edge energy on an absolute energy scale? Some > > measure of that can be found in xmu.dat, but I am not sure what the > > current state of Feff's ability to calculate that reliably is. > > Perhaps John, Kevin, or Josh might comment on that...? > > > > 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 > > > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > End of Ifeffit Digest, Vol 127, Issue 16 > > **************************************** > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0