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

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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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 .

2 1

Re: [Ifeffit] X-ray natural circular dichroism by FEFF?
by Joshua Kas 11 Sep '13

11 Sep '13

Hi Matthew, XNCD is due to dipole-quadrupole interference terms. See for example, Ankudinov, Phys. Rev. B 62, 2437–2445 (2000) Cheers, Josh On Wed, Sep 11, 2013 at 12:18 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. X-ray natural circular dichroism by FEFF? (Joshua Kas) > 2. Re: X-ray natural circular dichroism by FEFF? (Matthew Marcus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 11 Sep 2013 10:59:37 -0700 > From: Joshua Kas <joshua.j.kas(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] X-ray natural circular dichroism by FEFF? > Message-ID: > <CAHuhYR=X20USCUMtorXtvTcY-yoguDcbEm+LTMrw1y2P2m_G=w(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Matthew, > Sorry it took a while to answer your questions. No one has used the > XNCD features of FEFF for quite some time, and the example files that > were lying around did not run correctly. However, I have now > reproduced the output from one for the LiIO3 example. Please see the > input below. The main things that are essential are: > 1. The setting > MULTIPOLE 2 > which turns on quadrupole effects. > 2. The XNCD card. > 3. The ELLIPTICITY card to tell the program the direction of x-ray > propagation, i.e., > ELLIPTICITY elipticity kx ky kz > for example, circular polarization in the z direction is specified by > ELLIPTICITY 1 0 0 1 > If you don't specify the ELLIPTICITY, and the XNCD card is > specified, the program will > assume circularly polarized light traveling in the z direction. > > I am also attaching the results that I get from FEFF9. The xncd signal > is in column 6. > > Cheers, > Josh Kas > > * Example feff input file for XNCD of LiIO3 > * This feff.inp file generated by ATOMS, version 2.46c > * ATOMS written by Bruce Ravel and copyright of The Univ. of Washington, 1994 > > * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * > * total mu = 112.7 cm^-1, delta mu = 92.0 cm^-1 > * specific gravity = 4.488, cluster contains 547 atoms. > * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * > * mcmaster corrections: 0.00014 ang^2 and 0.403E-07 ang^4 > * self-abs. corrections: amplitude factor = 4.652 > * 0.00011 ang^2 and 0.252E-07 ang^4 > * i0 corrections: 0.00006 ang^2 and 0.269E-07 ang^4 > * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * > * sum of corrections: 0.00031 ang^2 and 0.923E-07 ang^4 > * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * > > TITLE LiIO3 > > HOLE 4 1.0 I L3 edge, second number is S0^2 > SCF 4.0 > > * pot ph fms paths genfmt ff2chi > CONTROL 1 1 1 1 1 1 > > > XANES 5.5 0.05 0.5 > * absorption with averaging over left and right circular polarizations > *POLARIZATION 1 0 0 > MULTIPOLE 2 > ELLIPTICITY 1 0 0 1 > > * XNCD calculations; comment out for above average absorption > XNCD > > EXCHANGE 0 1 0.0 2 > RPATH 0.1 > > * 41-atom cluster > FMS 4.9 > > POTENTIALS > * ipot z label l_scmt l_fms > 0 53 I 3 3 0.01 > 1 8 O 2 2 3.00 > 2 3 Li 2 2 1.00 > 3 53 I 3 3 0.99 > > ATOMS > 0.00000 0.00000 0.00000 0 I 0.00000 > -0.40916 -1.44312 -0.88847 1 O 1.74338 > -1.13161 1.09916 -0.88847 1 O 1.81055 > 1.54125 0.34316 -0.88847 1 O 1.81179 > 0.04130 2.19081 1.85203 1 O 2.86903 > -2.03253 -0.99669 1.85203 1 O 2.92482 > 1.99171 -1.19491 1.85203 1 O 2.97064 > -1.58207 -2.53476 0.41875 2 Li 3.01717 > -1.58207 2.63724 0.41875 2 Li 3.10376 > 3.16461 -0.10326 0.41875 2 Li 3.19387 > 0.04130 -2.98119 1.85203 1 O 3.50988 > 2.71415 1.43481 1.85203 1 O 3.58543 > -2.75498 1.54559 1.85203 1 O 3.66180 > -1.58207 -2.53476 -2.32175 2 Li 3.78398 > -1.58207 2.63724 -2.32175 2 Li 3.85337 > -0.40916 3.72888 -0.88847 1 O 3.85504 > 3.16461 -0.10326 -2.32175 2 Li 3.92632 > -3.20544 -2.08834 -0.88847 1 O 3.92751 > 1.58207 2.53425 -2.74050 3 I 4.05410 > 1.58207 2.53425 2.74050 3 I 4.05410 > 3.61508 -1.64134 -0.88847 1 O 4.06843 > 1.58207 -2.63775 2.74050 3 I 4.11959 > 1.58207 -2.63775 -2.74050 3 I 4.11959 > -3.16461 0.10275 2.74050 3 I 4.18756 > -3.16461 0.10275 -2.74050 3 I 4.18756 > 0.04130 2.19081 -3.62897 1 O 4.23919 > -2.03253 -0.99669 -3.62897 1 O 4.27715 > 1.99171 -1.19491 -3.62897 1 O 4.30861 > -1.13161 -4.07284 -0.88847 1 O 4.31948 > -1.58207 -2.53476 3.15925 2 Li 4.34843 > -1.58207 2.63724 3.15925 2 Li 4.40895 > 3.16461 -0.10326 3.15925 2 Li 4.47284 > -3.20544 3.08366 -0.88847 1 O 4.53577 > 4.33752 0.98838 -0.88847 1 O 4.53656 > 0.04130 -2.98119 -3.62897 1 O 4.69666 > 2.71415 1.43481 -3.62897 1 O 4.75339 > -2.75498 1.54559 -3.62897 1 O 4.81125 > 1.99171 3.97709 1.85203 1 O 4.81811 > -0.40916 -1.44312 4.59253 1 O 4.83129 > -1.13161 1.09916 4.59253 1 O 4.85593 > 1.54125 0.34316 4.59253 1 O 4.85639 > -2.75498 -3.62641 1.85203 1 O 4.91638 > 2.71415 -3.73719 1.85203 1 O 4.97627 > -2.03253 4.17531 1.85203 1 O 4.99944 > -4.70539 -0.24069 1.85203 1 O 5.06247 > 3.61508 3.53066 -0.88847 1 O 5.13066 > 1.54125 -4.82884 -0.88847 1 O 5.14611 > 4.78798 -0.54969 1.85203 1 O 5.16304 > 0.00000 -5.17200 0.00000 3 I 5.17200 > 0.00000 5.17200 0.00000 3 I 5.17200 > -4.74669 -2.43150 0.00000 3 I 5.33322 > 4.74669 2.43150 0.00000 3 I 5.33322 > -5.15585 1.29738 -0.88847 1 O 5.39030 > 0.00000 0.00000 5.48100 3 I 5.48100 > 0.00000 0.00000 -5.48100 3 I 5.48100 > 4.74669 -2.74050 0.00000 3 I 5.48100 > -4.74669 2.74050 0.00000 3 I 5.48100 > 1.99171 3.97709 -3.62897 1 O 5.74052 > 1.54125 5.51516 -0.88847 1 O 5.79499 > -2.75498 -3.62641 -3.62897 1 O 5.82324 > 2.71415 -3.73719 -3.62897 1 O 5.87390 > -1.58207 -2.53476 -5.06225 2 Li 5.87830 > -2.03253 4.17531 -3.62897 1 O 5.89354 > -1.58207 2.63724 -5.06225 2 Li 5.92320 > -0.40916 3.72888 4.59253 1 O 5.92987 > -4.70539 -0.24069 -3.62897 1 O 5.94710 > 3.16461 -0.10326 -5.06225 2 Li 5.97092 > -3.20544 -2.08834 4.59253 1 O 5.97723 > 3.16461 5.06874 0.41875 2 Li 5.99018 > END > > On Tue, Sep 10, 2013 at 10:00 AM, > <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: >> 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. X-ray natural circular dichroism by FEFF? (Matthew Marcus) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 10 Sep 2013 09:28:44 -0700 >> From: Matthew Marcus <mamarcus(a)lbl.gov> >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: [Ifeffit] X-ray natural circular dichroism by FEFF? >> Message-ID: <522F48BC.8090402(a)lbl.gov> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Can FEFF calculate X-ray natural circular dichroism, which is the XCD that comes from structural chirality and not >> magnetism? I suppose I could simply try it, putting in coordinates for some simple molecule, but I'd like to know >> if any results would be meaningful. >> mam >> >> >> ------------------------------ >> >> _______________________________________________ >> 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 9 >> *************************************** >

1 0

X-ray natural circular dichroism by FEFF?
by Joshua Kas 11 Sep '13

11 Sep '13

Hi Matthew, Sorry it took a while to answer your questions. No one has used the XNCD features of FEFF for quite some time, and the example files that were lying around did not run correctly. However, I have now reproduced the output from one for the LiIO3 example. Please see the input below. The main things that are essential are: 1. The setting MULTIPOLE 2 which turns on quadrupole effects. 2. The XNCD card. 3. The ELLIPTICITY card to tell the program the direction of x-ray propagation, i.e., ELLIPTICITY elipticity kx ky kz for example, circular polarization in the z direction is specified by ELLIPTICITY 1 0 0 1 If you don't specify the ELLIPTICITY, and the XNCD card is specified, the program will assume circularly polarized light traveling in the z direction. I am also attaching the results that I get from FEFF9. The xncd signal is in column 6. Cheers, Josh Kas * Example feff input file for XNCD of LiIO3 * This feff.inp file generated by ATOMS, version 2.46c * ATOMS written by Bruce Ravel and copyright of The Univ. of Washington, 1994 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 112.7 cm^-1, delta mu = 92.0 cm^-1 * specific gravity = 4.488, cluster contains 547 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00014 ang^2 and 0.403E-07 ang^4 * self-abs. corrections: amplitude factor = 4.652 * 0.00011 ang^2 and 0.252E-07 ang^4 * i0 corrections: 0.00006 ang^2 and 0.269E-07 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * sum of corrections: 0.00031 ang^2 and 0.923E-07 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE LiIO3 HOLE 4 1.0 I L3 edge, second number is S0^2 SCF 4.0 * pot ph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 XANES 5.5 0.05 0.5 * absorption with averaging over left and right circular polarizations *POLARIZATION 1 0 0 MULTIPOLE 2 ELLIPTICITY 1 0 0 1 * XNCD calculations; comment out for above average absorption XNCD EXCHANGE 0 1 0.0 2 RPATH 0.1 * 41-atom cluster FMS 4.9 POTENTIALS * ipot z label l_scmt l_fms 0 53 I 3 3 0.01 1 8 O 2 2 3.00 2 3 Li 2 2 1.00 3 53 I 3 3 0.99 ATOMS 0.00000 0.00000 0.00000 0 I 0.00000 -0.40916 -1.44312 -0.88847 1 O 1.74338 -1.13161 1.09916 -0.88847 1 O 1.81055 1.54125 0.34316 -0.88847 1 O 1.81179 0.04130 2.19081 1.85203 1 O 2.86903 -2.03253 -0.99669 1.85203 1 O 2.92482 1.99171 -1.19491 1.85203 1 O 2.97064 -1.58207 -2.53476 0.41875 2 Li 3.01717 -1.58207 2.63724 0.41875 2 Li 3.10376 3.16461 -0.10326 0.41875 2 Li 3.19387 0.04130 -2.98119 1.85203 1 O 3.50988 2.71415 1.43481 1.85203 1 O 3.58543 -2.75498 1.54559 1.85203 1 O 3.66180 -1.58207 -2.53476 -2.32175 2 Li 3.78398 -1.58207 2.63724 -2.32175 2 Li 3.85337 -0.40916 3.72888 -0.88847 1 O 3.85504 3.16461 -0.10326 -2.32175 2 Li 3.92632 -3.20544 -2.08834 -0.88847 1 O 3.92751 1.58207 2.53425 -2.74050 3 I 4.05410 1.58207 2.53425 2.74050 3 I 4.05410 3.61508 -1.64134 -0.88847 1 O 4.06843 1.58207 -2.63775 2.74050 3 I 4.11959 1.58207 -2.63775 -2.74050 3 I 4.11959 -3.16461 0.10275 2.74050 3 I 4.18756 -3.16461 0.10275 -2.74050 3 I 4.18756 0.04130 2.19081 -3.62897 1 O 4.23919 -2.03253 -0.99669 -3.62897 1 O 4.27715 1.99171 -1.19491 -3.62897 1 O 4.30861 -1.13161 -4.07284 -0.88847 1 O 4.31948 -1.58207 -2.53476 3.15925 2 Li 4.34843 -1.58207 2.63724 3.15925 2 Li 4.40895 3.16461 -0.10326 3.15925 2 Li 4.47284 -3.20544 3.08366 -0.88847 1 O 4.53577 4.33752 0.98838 -0.88847 1 O 4.53656 0.04130 -2.98119 -3.62897 1 O 4.69666 2.71415 1.43481 -3.62897 1 O 4.75339 -2.75498 1.54559 -3.62897 1 O 4.81125 1.99171 3.97709 1.85203 1 O 4.81811 -0.40916 -1.44312 4.59253 1 O 4.83129 -1.13161 1.09916 4.59253 1 O 4.85593 1.54125 0.34316 4.59253 1 O 4.85639 -2.75498 -3.62641 1.85203 1 O 4.91638 2.71415 -3.73719 1.85203 1 O 4.97627 -2.03253 4.17531 1.85203 1 O 4.99944 -4.70539 -0.24069 1.85203 1 O 5.06247 3.61508 3.53066 -0.88847 1 O 5.13066 1.54125 -4.82884 -0.88847 1 O 5.14611 4.78798 -0.54969 1.85203 1 O 5.16304 0.00000 -5.17200 0.00000 3 I 5.17200 0.00000 5.17200 0.00000 3 I 5.17200 -4.74669 -2.43150 0.00000 3 I 5.33322 4.74669 2.43150 0.00000 3 I 5.33322 -5.15585 1.29738 -0.88847 1 O 5.39030 0.00000 0.00000 5.48100 3 I 5.48100 0.00000 0.00000 -5.48100 3 I 5.48100 4.74669 -2.74050 0.00000 3 I 5.48100 -4.74669 2.74050 0.00000 3 I 5.48100 1.99171 3.97709 -3.62897 1 O 5.74052 1.54125 5.51516 -0.88847 1 O 5.79499 -2.75498 -3.62641 -3.62897 1 O 5.82324 2.71415 -3.73719 -3.62897 1 O 5.87390 -1.58207 -2.53476 -5.06225 2 Li 5.87830 -2.03253 4.17531 -3.62897 1 O 5.89354 -1.58207 2.63724 -5.06225 2 Li 5.92320 -0.40916 3.72888 4.59253 1 O 5.92987 -4.70539 -0.24069 -3.62897 1 O 5.94710 3.16461 -0.10326 -5.06225 2 Li 5.97092 -3.20544 -2.08834 4.59253 1 O 5.97723 3.16461 5.06874 0.41875 2 Li 5.99018 END On Tue, Sep 10, 2013 at 10:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. X-ray natural circular dichroism by FEFF? (Matthew Marcus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Sep 2013 09:28:44 -0700 > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] X-ray natural circular dichroism by FEFF? > Message-ID: <522F48BC.8090402(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Can FEFF calculate X-ray natural circular dichroism, which is the XCD that comes from structural chirality and not > magnetism? I suppose I could simply try it, putting in coordinates for some simple molecule, but I'd like to know > if any results would be meaningful. > mam > > > ------------------------------ > > _______________________________________________ > 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 9 > ***************************************

2 1

problem with Demeter on non-unicode machine
by Andrei Shiryaev 08 Sep '13

08 Sep '13

Dear Bruce, I have a problem with running Demeter on non-unicode Win7/64 bit computer. The log file is attached. I am using the latest update and it is better than previous versions since at least something is happening, when I've tried previous Demeter versions, they just crashed immediately. I am not an expert in programming, but I suspect that similar problem existed in one of the old version of IFEFFIT as was discussed with you in July 2008 in the mail list: =============== A followup to the unicode issue: I use a tool called PerlApp to build stand-alone windows executables of my codes. While researching how it handles temporary directory creation, I came across the following: http://bugs.activestate.com/show_bug.cgi?id=43697 It would seem that the issue Kleper and Shiryaev are seeing is the result of that bug, which has been resolved in recent versions of PerlApp. I was certainly using a version of PerlApp that showed this problem when the previous installer was made. I am now using version 7.2, so things should work fine for non-ascii language speakers. I will communicate with Kleper and Shiryaev off the list to ask them to test the new installer. Regards, B ============== I would appreciate some advice how to handle the problem. Regards, Andrei ---------------------------------------------------------------------- -- Andrei Shiryaev

2 3

Installation problems Ubuntu 12.04
by David Eveborn 06 Sep '13

06 Sep '13

Hi! I am trying to install the demeter package from sources as described by Dave Huges https://gist.github.com/waveform80/3959252. I am doing this on a fresh install of ubuntu 12.04 (as a virtual machine if this could have any effect). Most things turns out as expected but I have encountered a problem. When I invoke the ./Build installdeps one single dependency refuses to install because of failing tests. The output from the terminal is attached in this e-mail. If anyone could lead me in how to handle this I would be very happy (I am not experienced in building from sources). Kind Regads David

3 5

chirality and XMCD with FEFF
by Ross Devol 04 Sep '13

04 Sep '13

Hi All, Does anyone know whether FEFF can be used to determine whether a crystal is chiral? I am trying to do this for monohydrocalcite (MHC) using the XMCD card. Would this be the correct approach? Also, while I have gotten FEFF to run with the XMCD card in the feff.inp file for other crystals, I keep getting the following error: "FOLP for POTENTIAL type 4 is too big. Reduce overlap using FOLP and rerun." I've tried FOLP 4 1, FOLP 4 0.8, FOLP 4 0.5, and even FOLP 4 0.2, but I keep getting the same error. Has anyone else had this problem and resolved it? Thank you! Ross DeVol University of Wisconsin-Madison

1 0

Artemis Bug -- Path Like Object
by mattie.peck＠huskers.unl.edu 30 Aug '13

30 Aug '13

Hey Everyone, I've found another bug in Artemis. When I try to add a path like object to the paths list the program crashes. I've attached the log file and copied the text of it below. I'm using the newest version of Artemis 0.9.18.2 and running Windows XP. Thanks, Mattie Peck LOG FILE TEXT BELOW: Started at 2013-08-30T11:27:21 WinXP/.NetMedia Center Edition Service Pack 3 Service Pack 35126002302561 PATH: C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Program Files\QuickTime\QTSystem\;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Zone Labs\ZoneAlarm\MailFrontier;C:\Program Files\Microsoft SQL Server\90\Tools\binn\;C:\Program Files\QuickTime\QTSystem\;C:\FullProf_Suite perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib . Can't locate object method "pathfinder_index" via package "Demeter::SSPath" at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Path.pm line 254.

2 1

Artemis Bug
by mattie.peck＠huskers.unl.edu 29 Aug '13

29 Aug '13

Hello, I've got another bug I think. Like I said I'm using the new version of Artemis to open old .apj files and I've noticed that the path information isn't importing correctly. I have opened several .apj files and this problem happens with all of them. I have attached the .apj file and a pdf with screen shots pointing out the discrepancies. I have the latest version of demeter 0.9.18 and I am running Windows XP. Thanks for the help. Sincerely, Mattie Peck

2 2