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

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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Re: [Ifeffit] Installation problems Ubuntu 12.04
by Denis Testemale 12 Sep '13

12 Sep '13

Dear list. I'm in a similar configuration (Ubuntu 13.04) and tried recently to upgrade Demeter (0.9.18). This is a short report. I ran in the exact same problems than David reported. I installed manually libsoap as suggested and it worked. I still have some fail messages during the building process though. See the attachments: - one is the output of the ./Build test command - one image is the corresponding screen snapshot which is a bit more verbose about the error. I was wondering if it could generate errors later when I use the softwares even if they seem to install fine. Another minor point is that the link about the Demeter homepage (in the "About" page) sent me to a page with an error (see 3rd attachment). Cheers denis Le 07/09/2013 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: Installation problems Ubuntu 12.04 (David Eveborn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Sep 2013 23:56:45 +0200 > From: David Eveborn <david.eveborn(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Installation problems Ubuntu 12.04 > Message-ID: > <CAGs9LMFwe12oyk3VDaxBVsR71tOdfCntJAaOymmo+sqffHMU_w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Bruce and Ivan > > By following your advice I was able to install the demeter package! > Installing libsoap-lite-perl by apt-get helped me out. Thank you! Look > forward to explore the demeter API now! > > Kind regards > > David >

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Using radius in FEFF to determine nanoparticles
by Lisa Bovenkamp 12 Sep '13

12 Sep '13

Hey all, I started working on modelling nanoparticles with FEFF. 1. Anybody have some useful links about this subject? 2. In 2 reports people were using the radius (i.e. number of atoms used in the calculations) as a measure for the size of the nanoparticles. Further they were discussing the absence of features due to the size. This strikes me odd. I thought that for a) a small SCF radius the feff code might not converge (which cannot give good results), b) when the FMS radius is small - and there are not many scatterers included - the resolution of the calculated XANES spectrum is "bad" and features are broad. I think that has nothing to do with the nanoparticles c) a correct real space feff table of xyz coordinates should include more than just one nanoparticle since the neighboring particles do have an effect on each other - or am I wrong? Thanks. Lisa

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Upon updating Demeter on 9/4, pluck results in both Artemis and Athena not responding
by Heidi Jensen 12 Sep '13

12 Sep '13

I wanted to see if anyone can help me with a problem that I am experiencing (log files below). I am running Demeter on Windows 7. I updated the Demeter package last week using the updater package (0.9.18.2) and have had issues when attempting to pluck points from plots since then. I am confident that at the time of update, I had the current version of the installer package. The window that usually pops up when you click on the pluck boxes does not come up and both Artemis and Athena stop responding for about 30 seconds and then return to normal function, but without allowing me to select any points in the plotting window. This does not crash either program completely. In Artemis, I tried to use the pluck command to select the fitting range. In Athena, I tried it with both selecting points for the k-range of the Forward Fourier transformation and in the Deglitching and truncation window. I think that I may try to uninstall the Demeter package and start over and see what that does. Thanks for your help. Heidi Jensen Artemis: Started at 2013-09-05T16:05:49 Win7Professional (64-bit) Service Pack 1 Service Pack 16176012102561 PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files\Intel\DMIX;C:\Program Files (x86)\PharosSystems\Core;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\Program Files (x86)\QuickTime\QTSystem\ perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib . Athena: Started at 2013-09-10T15:17:12 Win7Professional (64-bit) Service Pack 1 Service Pack 16176012102561 PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files\Intel\DMIX;C:\Program Files (x86)\PharosSystems\Core;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\Program Files (x86)\QuickTime\QTSystem\ perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib .

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