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

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 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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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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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

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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

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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

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Re: [Ifeffit] XANES - Peak assignment and ionization potential with
by Joshua Kas 17 Sep '13

17 Sep '13

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 > ****************************************

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Re: [Ifeffit] XANES - Peak assignment and ionization potential with FEFF
by Ross Devol 17 Sep '13

17 Sep '13

Thanks Bruce! That answers my first question. 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

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Peak assignment and ionization potential with FEFF
by Ross Devol 13 Sep '13

13 Sep '13

Hi everyone, 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? Thanks! Ross DeVol University of Madison-Wisconsin

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atoms "bug" in 9.18.2
by fred.mosselmans＠diamond.ac.uk 12 Sep '13

12 Sep '13

Hi Bruce This is so minor that I am unsure whether to report it, but working on a windows xp computer the add a site button in atoms doesn't seem to work. I found it initially, when entering a partial occupancy containing cif where I was manually entering the atom positions as I am rubbish at editing the cif properly. The easy work round is to write out the partial .inp file and then edit the extra sites in a text file and read it back in. I then started a new artemis session and found the button still did nothing. I then read in an .inp file and the button still does nothing. I filled it up the six rows with meaningless sites so there were no blank sites left and .... I attach a log of that session. Though it doesn't seem to have much in it. And the project which is rather meaningless as it crashes artemis when I try to re-open it. (the log says there's a method group problem. But that's not the bug I am reporting. Copying and pasting rows keeps the no of empty rows as well so that's another way round it. By the way it's great atoms reads cif files without problems (except PO sites nowadays) Cheers Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK -- 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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