June 2009 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Primitive unit cell from .cif file
by joshua jason kas 19 Jun '09

19 Jun '09

Hi Bruce, > I don't really understand what you are driving at, but it seems as > though you want to express Diamond as a simple cubic cell with a two > atom basis? Yes, that would be the case for diamond, but for an arbitrary crystal structure specified as in a .cif I would like to find the primitive cell, i.e. the unit cell of smallest volume. > I don't really understand how that > will save you time in > abinit, but, of course, I am not a crystallographer.... Smaller volume means less bands to obtain the same energy range. > PS. Doesn't abinit understand crystal symmetry? Maybe. I couldn't get it to reproduce the diamond structure using only one atom in the cell, but I haven't been using it for very long, and will probably go to the abinit list for this. > Why can't you just tell it that it's diamond and has the symmetry of > diamond? For our application, we can't really use the symmetry at this point. Would be good if we can in the future, but for now we really need input that includes all atoms in the primitive unit cell. Again, thanks to everyone for your time. I hope this was not too far out in left field for this mailing list. Apologies if it was. Josh Kas > > -- > Bruce Ravel ----------------------------------- bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at Brookhaven National Laboratory > Building 535A > Upton NY, 11973 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of joshua jason kas > Sent: Thu 6/18/2009 2:41 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Primitive unit cell from .cif file > > Thanks everyone for your suggestions! I have tried the following things. > I used atoms (webATOMS) to generate a p1.inp file using diamond as an > example, but this gives me the conventional cell with 8 atoms in > it instead of the 2 atom primitive cell. Am I doing something wrong? > The input file came from the atoms database and the output is as follows: > > * > * "F d -3 m" appears in the International Tables with > * multiple choices of origin. If the atoms list seems wrong, you > * should use a shift vector of: > * -0.125, -0.125, -0.125 > * > * > ! This p1.inp file was generated by WebAtoms 1.8 (Atoms 3.0beta10) > ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 > title = name: diamond > title = formula: C > title = sites: C1 > title = refer1: Kittel, ISSP > title = refer2: > title = schoen: > title = notes1: diamond structure > space p 1 ! original space group: F d -3 m > a = 3.5670 b = 3.5670 c = 3.5670 > alpha = 90.0 beta = 90.0 gamma = 90.0 > core = C1_1 edge = K rmax = 6.0 > atoms > ! elem x y z tag occ > C 0.12500 0.12500 0.12500 C1_1 1 > C 0.12500 0.62500 0.62500 C1_2 1 > C 0.62500 0.12500 0.62500 C1_3 1 > C 0.62500 0.62500 0.12500 C1_4 1 > C 0.87500 0.37500 0.37500 C1_5 1 > C 0.87500 0.87500 0.87500 C1_6 1 > C 0.37500 0.37500 0.87500 C1_7 1 > C 0.37500 0.87500 0.37500 C1_8 1 > > I also tried the Mercury demo, but all editing features are disabled. > > I will try Diamond now. > > Just to give some motivation here, I am working with abinit (along with > feff) to produce optical spectra. If I use a conventional cell, the > calculations become much more time consuming, so ideally I want to use a > primitive cell. > Thanks again for all your help! > Josh > >> Hi Josh, >> You may try Diamond Demo version which is free. >> >> http://www.crystalimpact.com/diamond/download.htm > I will give this a try. > > >> >> Hi Josh, >> >> If I understand your question, I think that Atoms does what you want. Running the command line tool as "atoms -p" turns the attached cif file into the attached "p1.inp" file. You can do the same thing inside of Artemis using "write special output" in the Theory menu. > >> >> B >> >> -- >> Bruce Ravel ----------------------------------- bravel(a)bnl.gov >> >> National Institute of Standards and Technology >> Synchrotron Methods Group at Brookhaven National Laboratory >> Building 535A >> Upton NY, 11973 >> >> My homepage: http://cars9.uchicago.edu/~ravel >> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ >> >> >> >> >> -----Original Message----- >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of joshua jason kas >> Sent: Wed 6/17/2009 2:16 PM >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: [Ifeffit] Primitive unit cell from .cif file >> >> Hi everyone, >> I was wondering if there is a simple (free) utility for producing a >> primitive cell (not conventional) from an asymmetric cell and space group. >> Basically, I want to be able to easily go from a crystallographic >> information file to a primitive unit cell. I know that there are ways to >> do this within applications like material studio, but these are expensive. >> Any help would be appreciated. >> Thanks, >> Josh Kas >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >>

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Radial distribution
by Eugenio Otal 18 Jun '09

18 Jun '09

Hi Shelly, thanks, I will try this. Cheers, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

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Radial distribution
by Eugenio Otal 18 Jun '09

18 Jun '09

Hi, I performed EXAFS simulation and want to obtain the radial distribution of the signal. I tried with athena but I cannot process it like experimental signal. Is there any trick to transform the signal into radial distribution? Thanks, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

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Primitive unit cell from .cif file
by Eugenio Otal 18 Jun '09

18 Jun '09

Josh, you can also try with Mercury, has a free version at: http://www.ccdc.cam.ac.uk/products/mercury/ Hope it helps, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Hi Josh, You may try Diamond Demo version which is free. http://www.crystalimpact.com/diamond/download.htm Good luck, Mengqiang Zhu ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html ---- Original message ---- >*Date: Wed, 17 Jun 2009 11:16:49 -0700 (PDT) *>*From: ifeffit-bounces at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> (on behalf of joshua jason kas <hebhop at u.washington.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>>) *>*Subject: [Ifeffit] Primitive unit cell from .cif file *>*To: ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> *>* *>*Hi everyone, *>*I was wondering if there is a simple (free) utility for producing a *>*primitive cell (not conventional) from an asymmetric cell and space group. *>*Basically, I want to be able to easily go from a crystallographic *>*information file to a primitive unit cell. I know that there are ways to *>*do this within applications like material studio, but these are expensive. *>*Any help would be appreciated. *>*Thanks, *>*Josh Kas *>*_______________________________________________ *>*Ifeffit mailing list *>*Ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> *>*http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit *

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Primitive unit cell from .cif file
by joshua jason kas 17 Jun '09

17 Jun '09

Hi everyone, I was wondering if there is a simple (free) utility for producing a primitive cell (not conventional) from an asymmetric cell and space group. Basically, I want to be able to easily go from a crystallographic information file to a primitive unit cell. I know that there are ways to do this within applications like material studio, but these are expensive. Any help would be appreciated. Thanks, Josh Kas

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Re: [Ifeffit] how to reduce the core-hole lifetime broadening in feff8.2
by joshua jason kas 12 Jun '09

12 Jun '09

> And yet, the documentation for the CORRECTIONS keyword says: > > "The real energy shift vrcorr moves E0 in the final \chi(k) and > the imaginary energy shift vicorr adds broadening to the > result. The real energy shift is useful to correct the error in > FEFF's Fermi level estimate and the imaginary part can be used to > correct for experimental resolution or errors in the core-hole > lifetime." > > And a couple of sentences later: > > "The imaginary energy is typically used to correct for instrument > broadening or as a correction to the mean free path calculated by > feff." > > Perhaps the document should be updated to explain more clearly what > CORRECTIONS actually does. Thank you Bruce. I will try to clear up the documentation. Let me state more clearly how these two cards can be used to change the broadening of the spectrum. In the EXCHANGE card, the user can use negative values to offset the core hole broadening. The CORRECTIONS card can only be used to add to the total (previous) broadening, which is given by the half width at half max, Gamma_CH/2 + vi, where vi is the broadening from the EXCHANGE card and Gamma_CH is the core hole broadening. The benefit of using the CORRECTIONS card is that it is very fast since you can skip the matrix inversion for the FMS calculation. Thus a good way to use the two cards together is to reduce the broadening via EXCHANGE by a bit too much (use an overestimate as a first try), then use the CORRECTIONS card to fine tune the broadening. Cheers, Josh correctly. > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 76, Issue 8 > ************************************** >

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how to reduce the core-hole lifetime broadening in feff8.2
by joshua jason kas 11 Jun '09

11 Jun '09

Hi Tony, As mentioned already, you can use the EXCHANGE card with negative values to reduce the core-hole broadening. Note however that this will not work with the CORRECTIONS card. Josh Kas > Message: 1 > Date: Thu, 11 Jun 2009 05:58:53 -0700 (PDT) > From: tony vitova <tony_vitova(a)yahoo.com> > Subject: [Ifeffit] how to reduce the core-hole lifetime broadening in > feff8.2 > To: Ifeffit List <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <204685.79014.qm(a)web54505.mail.re2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear?all, > ? > Could somebody give me a hint how to reduce the core-hole lifetime broadening in feff8.2? Do I?need to change the source code? I have partial fluorescence yield XANES spectrum whose White Line is narrow than the one in the calculation. > ? > Thanks for any help > ? > Tonya > > > >

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how to reduce the core-hole lifetime broadening in feff8.2
by tony vitova 11 Jun '09

11 Jun '09

Dear all, Could somebody give me a hint how to reduce the core-hole lifetime broadening in feff8.2? Do I need to change the source code? I have partial fluorescence yield XANES spectrum whose White Line is narrow than the one in the calculation. Thanks for any help Tonya

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Re: [Ifeffit] how to reduce the core-hole lifetime broadening in feff8.2
by tony vitova 11 Jun '09

11 Jun '09

Hi Janine and Bruce, Thanks a lot! I didn't think that the EXCHANGE card might take and negative values... Tonya --- On Thu, 6/11/09, Janine GRATTAGE <janine.grattage(a)esrf.fr> wrote: From: Janine GRATTAGE <janine.grattage(a)esrf.fr> Subject: Re: [Ifeffit] how to reduce the core-hole lifetime broadening in feff8.2 To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Date: Thursday, June 11, 2009, 5:29 PM Hi Tonya, I use the EXCHANGE card to reduce the applied broadening in my spectra. If you set the third parameter in the card to a number less than zero (up to about -5 in my experience) then the broadening is reduced and you can calculate high resolution type XANES spectra. This applies only to some inherent limit in the calculations where further reducing the parameter has no effect. You can look up the EXCHANGE card on the feff wiki as it also can be used to change the exchange model and the position of the Fermi level. Hope that helps you! Janine tony vitova wrote: > Dear all, > > Could somebody give me a hint how to reduce the core-hole lifetime > broadening in feff8.2? Do I need to change the source code? I have > partial fluorescence yield XANES spectrum whose White Line is narrow > than the one in the calculation. > > Thanks for any help > > Tonya > > > ------------------------------------------------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > -- Dr Janine GRATTAGE Postdoctoral Fellow, ID26 European Synchrotron Radiation Facility (ESRF) Sector 26, BP 220 6, rue Jules Horowitz, 38043 Grenoble, Cedex 9, FRANCE Tel: +33(0)4 38 88 19 30 Email: janine.grattage(a)esrf.fr _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Xanes peaks fitting with Athena: no data on output
by Ismael Graff 10 Jun '09

10 Jun '09

Hi dears, I was using Athena (Ifeffit version 1.2.11) to fit XANES peaks and it worked very well. But, at the end when I try to "save fit as data group" the output is empty (or almost). The only thing that I get when I save the group data as "norm(E)" is the following: # Athena multicolumn data file -- Athena version 0.8.056 # This file contains normalized mu(E) from: # Peak hnvp (column 2) #------------------------ # energy Peak_hnvp I have no data in the output! Also, when I click the "save fit as data group" button, the plot window becomes blank/white, without plots! I have to have the fits to put them on a high-quality figure for publication. Interestingly, the fits appear in the plot window but I can not get the data corresponding to the fits. I can just save the window as GIF or PS files, and it works well. I use Athena on windows XP and Vista and the problem is the same for both. I´ve attached my data file in case someone would like to have a look on it. For sure I´m doing something stupid and I don´t see where is the fail! All the best, Ismael. -- Ismael Leandro Graff Departamento de Física - UFPR Centro Politécnico, CP 19044 81531-990, Curitiba, Brazil. Tel: +55 41 3361 3427 Fax: +55 41 3361 3418

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