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

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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pgplot on mac os x 10.5.7
by Matthew Ginder-Vogel 09 Jun '09

09 Jun '09

Hi Renske, Thanks for the info. It worked for me as well. However, now I'm running the older version of ifeffit. Has anyone had success with version 1.2.10? Thanks, Matt On Thu, Jun 4, 2009 at 1:00 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. Re: pgplot on mac os x 10.5.6 (Matthew Ginder-Vogel) > (Renske van der Veen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 04 Jun 2009 10:01:56 +0200 > From: Renske van der Veen <renske.vanderveen(a)psi.ch> > Subject: Re: [Ifeffit] pgplot on mac os x 10.5.6 (Matthew > Ginder-Vogel) > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <C64D4C14.B00%renske.vanderveen(a)psi.ch<C64D4C14.B00%25renske.vanderveen(a)psi.ch> > > > Content-Type: text/plain; charset="US-ASCII" > > Hello, > > I encountered the same problem with the 1.2.10 version of ifeffit > (ifeffit-1.2.10-Mac10.4_Intel_horae66.dmg downloaded via > http://cars9.uchicago.edu/ifeffit/Downloads) on my Mac (also Mac OS X > version 10.5.6). > > Instead I downloaded iXAFS (iXAFSinstall.tar.gz) from the same website for > which pgplot works fine. > > Best regards, > Renske > > > On 02.06.09 19:00, "ifeffit-request(a)millenia.cars.aps.anl.gov" > <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > > pgplot on mac os x 10.5.6 (Matthew Ginder-Vogel) > > Message: 1 > Date: Mon, 1 Jun 2009 15:53:33 -0400 > From: Matthew Ginder-Vogel <mattgv(a)udel.edu> > Subject: [Ifeffit] pgplot on mac os x 10.5.6 > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <f637a5340906011253m3b98d3deld2452f2511c3f355(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Everyone, > > Does anyone else have problems with pgplot on macs? > > There is no text on any plot that I make using Athena/Artemis. This > includes the axis labels, the legend, and the tick labels. > > I've tried on several macs and the problem is the same on all of them. > > Any advice? > > Thanks, > > Matt > > -- > ******************************************* > Matthew Ginder-Vogel > Post Doctoral Researcher > Center for Critical Zone Research > Environmental Soil Chemistry > University of Delaware > http://ag.udel.edu/SoilChem/gindervogel.html > (302) 831-0608 > mattgv(a)udel.edu > > > > ------------------------------ > > _______________________________________________ > 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 3 > ************************************** > -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

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Re: [Ifeffit] pgplot on mac os x 10.5.6 (Matthew Ginder-Vogel)
by Renske van der Veen 04 Jun '09

04 Jun '09

Hello, I encountered the same problem with the 1.2.10 version of ifeffit (ifeffit-1.2.10-Mac10.4_Intel_horae66.dmg downloaded via http://cars9.uchicago.edu/ifeffit/Downloads) on my Mac (also Mac OS X version 10.5.6). Instead I downloaded iXAFS (iXAFSinstall.tar.gz) from the same website for which pgplot works fine. Best regards, Renske On 02.06.09 19:00, "ifeffit-request(a)millenia.cars.aps.anl.gov" <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > pgplot on mac os x 10.5.6 (Matthew Ginder-Vogel) Message: 1 Date: Mon, 1 Jun 2009 15:53:33 -0400 From: Matthew Ginder-Vogel <mattgv(a)udel.edu> Subject: [Ifeffit] pgplot on mac os x 10.5.6 To: ifeffit(a)millenia.cars.aps.anl.gov Message-ID: <f637a5340906011253m3b98d3deld2452f2511c3f355(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello Everyone, Does anyone else have problems with pgplot on macs? There is no text on any plot that I make using Athena/Artemis. This includes the axis labels, the legend, and the tick labels. I've tried on several macs and the problem is the same on all of them. Any advice? Thanks, Matt -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu

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post-doc job postings
by Matt Newville 03 Jun '09

03 Jun '09

Hi, There are a couple of new listings for Post-Doc positions at http//xafs.org/Jobs. If you or someone you know may be interested, please pass these along. --Matt

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Re: [Ifeffit] Problems with potential overlap for small molecule
by joshua jason kas 02 Jun '09

02 Jun '09

Hi Renske, In order to solve the overlap problem, I tried some of the standard methods of fixing these problems, i.e. using the FOLP cards and such with no luck. This will take some time to debug, but we are looking into it. As for the negative density problem, this is something that we have worked on, and know how to fix, but will also take some time. Cheers, Josh Kas > Dear FEFF users, > > I have a FEFF8.4-related question concerning the abortion of the potential > module in a XANES calculation for a small molecule in solution. It might not > be totally appropriate for the ifeffit mailing list, but the FEFFusers > mailing list doesn?t seem to be used very often. I have looked through the > archive, but I haven?t found an entry with this specific problem. > > I am trying to simulate the L3-edge XANES spectrum for the linear I3- > molecule (I-I-I) embedded in a solvent with O-H groups. In order to simulate > the scattering from the solvent, I have put two O-H groups at either end of > the molecule with the H-atoms pointing towards the I-atoms (expected charge > transfer from I3- towards solvent). The I-H and I-O distances are taken from > ab initio calculations in the literature, the O-H distance is well-known and > amounts to 0.96 A. It is also known from the literature on similar ions in > solution that the H-atoms contribute to the XANES and should therefore be > included. > > I pasted my feff.inp file below. > > Running this file results in abortion at the beginning of the potential > module: > > ... > Number of processors = 12 > Calculating potentials ... > free atom potential and density for atom type 0 > MOVRLP-1 > Abnormal termination on processor 8 > [n7:09539] MPI_ABORT invoked on rank 8 in communicator MPI_COMM_WORLD with > errorcode 512 > ... > > It seems to occur when it is trying to overlap the potentials (MOVRLP-1). I > tried including the FOLP 2 0.8 card as suggested for H-atoms in the manual, > but this does not help. > > It seems like the O-H bond <1 A is too small: moving the O atoms further > away such that the O-H bond is 1.05 A ?solves? the problem, although this is > not what I want. But: moving the H atom closer to the I atom while keeping > the O positions fixed, which increases the O-H bond as well, does not help! > Also, to make things even more complicated, excluding the H-atoms fully, > i.e. putting only two O-atoms at 3.5 A from the iodines, results in the > WARNING during the SCF loop that the interstitial potential level lies > higher than the Fermi energy (moving the O atom closer to ca. 2 A removes > this message). In addition, certain combinations of H- and O- positions give > the output ?negative dens? during the SCF loop, for which I checked that > FOLP 2 0.8 did not help... > > It is obvious that FEFF has problems with generating the MT potentials for a > small and ?open? system such as the one here. Did somebody encounter similar > problems (abortion, Ei>Ef, negative dens) for systems like this? Is there > something wrong with my input cards? > > I?d appreciate any help. > > Best regards, > Renske van der Veen > > P.s. I am running the parallel version of FEFF8.4 on Linux > > *** > > TITLE I3- XANES spectrum > > * I L3 edge energy = 4557.0 eV > EDGE L3 > S02 1.0 > > CONTROL 1 1 1 1 1 1 > SIG2 0.01 > > PRINT 1 0 0 0 0 0 > EXCHANGE 0 0.0 0.0 0 > > SCF 10 1 30 0.2 1 > > LDOS -30 60 -1 > > XANES 6 > > FMS 10 1 > UNFR > > POTENTIALS > 0 53 I 3 4 > 1 53 I 3 4 > 2 1 H > 3 8 O 2 3 > > *FOLP 2 0.8 > > ATOMS > 0.0000 0.0000 0.0000 0 > -2.91 0.0000 0.0000 1 > 2.91 0.0000 0.0000 1 > -5.45 0.0000 0.0000 2 > 5.45 0.0000 0.0000 2 > -6.41 0.0000 0.0000 3 > 6.41 0.0000 0.0000 3 > END > >

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pgplot on mac os x 10.5.6
by Matthew Ginder-Vogel 01 Jun '09

01 Jun '09

Hello Everyone, Does anyone else have problems with pgplot on macs? There is no text on any plot that I make using Athena/Artemis. This includes the axis labels, the legend, and the tick labels. I've tried on several macs and the problem is the same on all of them. Any advice? Thanks, Matt -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

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Problems with potential overlap for small molecule
by Renske van der Veen 20 May '09

20 May '09

Dear FEFF users, I have a FEFF8.4-related question concerning the abortion of the potential module in a XANES calculation for a small molecule in solution. It might not be totally appropriate for the ifeffit mailing list, but the FEFFusers mailing list doesn¹t seem to be used very often. I have looked through the archive, but I haven¹t found an entry with this specific problem. I am trying to simulate the L3-edge XANES spectrum for the linear I3- molecule (I-I-I) embedded in a solvent with O-H groups. In order to simulate the scattering from the solvent, I have put two O-H groups at either end of the molecule with the H-atoms pointing towards the I-atoms (expected charge transfer from I3- towards solvent). The I-H and I-O distances are taken from ab initio calculations in the literature, the O-H distance is well-known and amounts to 0.96 A. It is also known from the literature on similar ions in solution that the H-atoms contribute to the XANES and should therefore be included. I pasted my feff.inp file below. Running this file results in abortion at the beginning of the potential module: ... Number of processors = 12 Calculating potentials ... free atom potential and density for atom type 0 MOVRLP-1 Abnormal termination on processor 8 [n7:09539] MPI_ABORT invoked on rank 8 in communicator MPI_COMM_WORLD with errorcode 512 ... It seems to occur when it is trying to overlap the potentials (MOVRLP-1). I tried including the FOLP 2 0.8 card as suggested for H-atoms in the manual, but this does not help. It seems like the O-H bond <1 A is too small: moving the O atoms further away such that the O-H bond is 1.05 A ³solves² the problem, although this is not what I want. But: moving the H atom closer to the I atom while keeping the O positions fixed, which increases the O-H bond as well, does not help! Also, to make things even more complicated, excluding the H-atoms fully, i.e. putting only two O-atoms at 3.5 A from the iodines, results in the WARNING during the SCF loop that the interstitial potential level lies higher than the Fermi energy (moving the O atom closer to ca. 2 A removes this message). In addition, certain combinations of H- and O- positions give the output ³negative dens² during the SCF loop, for which I checked that FOLP 2 0.8 did not help... It is obvious that FEFF has problems with generating the MT potentials for a small and ³open² system such as the one here. Did somebody encounter similar problems (abortion, Ei>Ef, negative dens) for systems like this? Is there something wrong with my input cards? I¹d appreciate any help. Best regards, Renske van der Veen P.s. I am running the parallel version of FEFF8.4 on Linux *** TITLE I3- XANES spectrum * I L3 edge energy = 4557.0 eV EDGE L3 S02 1.0 CONTROL 1 1 1 1 1 1 SIG2 0.01 PRINT 1 0 0 0 0 0 EXCHANGE 0 0.0 0.0 0 SCF 10 1 30 0.2 1 LDOS -30 60 -1 XANES 6 FMS 10 1 UNFR POTENTIALS 0 53 I 3 4 1 53 I 3 4 2 1 H 3 8 O 2 3 *FOLP 2 0.8 ATOMS 0.0000 0.0000 0.0000 0 -2.91 0.0000 0.0000 1 2.91 0.0000 0.0000 1 -5.45 0.0000 0.0000 2 5.45 0.0000 0.0000 2 -6.41 0.0000 0.0000 3 6.41 0.0000 0.0000 3 END

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Polarization vector in FEFF calculation
by Yun Luo 15 May '09

15 May '09

Dear All, I have a quick question regarding the polarization vector in FEFF calculation. There is a card of "POLARIZATION x y z" that we can use to count in polarization effect in FEFF calculation. I just want to make sure that the x, y, z coordinates of the polarization vector is in the crystal Cartesian base. For example, if the direction of the electric field of the incident beam is along the a axis of the crystal, then I can use the card "POLARIZATION 1 0 0" in the FEFF input file to do the calculation. Is this correct? Thank you very much! Best Yun

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Artemis and Athena
by Chris Patridge 08 May '09

08 May '09

Hello everyone, I am starting the tutorials that are provided with the ifeffit package. Do the examples in the package have additional text files to explain some of the steps involved with the various fits for the more complicated samples? Thank you all, Chris

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Fitting procedure
by abhijeet gaur 01 May '09

01 May '09

Hello Matt Sir, Thanks a lot. I will include the error bars in fitted value for sure. with regards Abhijeet Gaur

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