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

Re: [Ifeffit] Compiling Feff 8.4 on Linux
by prange 04 Mar '08

04 Mar '08

> Hi Adam, Feff 8.4 currently does not work with gfortran, but people have successfully used g95 (http://www.g95.org/) which is also free and open source, with feff 8.1 and 8.4. Good luck, Micah Prange University of Washington Physics > Hi all, > > I have having difficulty compiling feff 8.4. I am using gcc version > 4.1.1 20070105 (Red Hat 4.1.1-52) on Scientific Linux 5.0. It > compiles but gives many warnings like: > Warning: Obsolete: arithmetic IF statement at (1) > In file FEFF810.F:4208 > > if (i-1) 85,85,83 > > The compile finished however and I tried to run it. The input file > was a BN example file that came with Feff 8.1. It runs for a little > while and stops with: > Done with module 1: potentials. > Calculating LDOS ... > At line 47994 of file feff84.f > Fortran runtime error: Bad value during integer read > > I compiled using: gfortran -O2 -o feff84 feff84.f > > Has anyone seen this sort of thing? Or compiled Feff 8.4 with > gfortran? I did the same with feff 8.1 and it compiled and ran > correctly. > > Cheers, > Adam > > -- > ---------------------------------------------------------- > Dr. M. Adam Webb > HASYLAB at DESY > Notkestrasse 85 > D-22607 Hamburg > Germany > > Phone: +49 40 8998-1994, Fax: +49 40 8998-2787 > E-mail: adam.webb(a)desy.de > -----------------------------------------------------------

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Compiling Feff 8.4 on Linux
by Adam Webb 04 Mar '08

04 Mar '08

Hi all, I have having difficulty compiling feff 8.4. I am using gcc version 4.1.1 20070105 (Red Hat 4.1.1-52) on Scientific Linux 5.0. It compiles but gives many warnings like: Warning: Obsolete: arithmetic IF statement at (1) In file FEFF810.F:4208 if (i-1) 85,85,83 The compile finished however and I tried to run it. The input file was a BN example file that came with Feff 8.1. It runs for a little while and stops with: Done with module 1: potentials. Calculating LDOS ... At line 47994 of file feff84.f Fortran runtime error: Bad value during integer read I compiled using: gfortran -O2 -o feff84 feff84.f Has anyone seen this sort of thing? Or compiled Feff 8.4 with gfortran? I did the same with feff 8.1 and it compiled and ran correctly. Cheers, Adam -- ---------------------------------------------------------- Dr. M. Adam Webb HASYLAB at DESY Notkestrasse 85 D-22607 Hamburg Germany Phone: +49 40 8998-1994, Fax: +49 40 8998-2787 E-mail: adam.webb(a)desy.de -----------------------------------------------------------

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feff82 issue with perovskites
by Francesco Giannici 03 Mar '08

03 Mar '08

Hi all, when calculating paths around Ba (K-edge) in the cubic perovskite BaZrO3, the third path (Ba-Ba) is totally screwed up in the 2.6 - 3.8 ang^-1 range, with amplitude going up to 1000. You can find the input file at http://giannici.altervista.org/feff.inp Actually, this is also the case of Gd:BaCeO3, substituting one Gd for one Ce, and calculating paths for the Gd K-edge: the Gd-Ba path shows the same issue. This applies to Feff8.2 on Debian, Fedora, and MacOSX 10.4.11. I found that playing around with FOLPs seems to help, but I´m not very confident with that, and I´d like to hear your opinion on what the cause could be. (Yeah, just throwing away all those low-k data would also be a solution). On the other hand, Zr and In K-edge in Ba(In,Zr)O3 work just fine, as do Ce, Ba, Y and In K-edges in Ba(Y/In,Ce)O3. Also Gd K-edge in Gd2O3 works fine. Cheers from Stuttgart, -- Francesco Giannici Dip. di Chimica Inorganica e Analitica Università di Palermo / ISMN-CNR giannici(a)pa.ismn.cnr.it

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Query regarding inequivalent sites in the EXAFS fitting
by Bindu R. 29 Feb '08

29 Feb '08

Dear Bruce, Could you please tell me if there is an option to do the EXAFS fitting for a compound having the absorbing atoms at two inequivalent crystallographic sites. For example, In Ca3Co2O6 compound, the Co ion occupies two inequivalent crystallographic sites with the Co1-O bond distance at 1.960 and Co2-O at 2.09 Ang. How does one invoke the contribution of both the bond distances in the first shell fitting? Best regards Bindu Dr.Bindu R. Visiting Fellow DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830 --------------------------------- 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here.

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phase shift correction
by Bindu R. 24 Feb '08

24 Feb '08

Could you tell me... Why the peak in the Fourier transform of the experimental spectrum is less than the actual one. Why it is required to include the scattering phase shift correction in the experimental one? As it is expected that the experimental one should show the actual bond length. Bindu Dr.Bindu R. Visiting Scientist DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830 --------------------------------- Forgot the famous last words? Access your message archive online. Click here.

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Re: [Ifeffit] thanks for your posting
by Matt Newville 23 Feb '08

23 Feb '08

Hi Mustafa, On Fri, Feb 22, 2008 at 1:13 PM, Mustafa Hussein <mustafa.hussein86(a)yahoo.com> wrote: > Dear Prof Newville, > > Thanks for your reply. I have some questions, I am listing them below, OK. I'm going to forward with to the mailing list as well. > I am simulating the excited state dynamics of two platinum atoms, can I > specify two atoms as absorbing atoms? or I have to re-run the calculation > again to average over the two sites of absorption? You have to re-run the calculation again. > I used the Atoms.inp Archive, but I did not arrive at a molecule that might > be similar to mine. > So I need to build an input file? it is okay, I think I can deal with shell > scripting. That's fine. Using Pt metal might be a good place to start too. > What is meant by HOLE? and the values 1 and 1.0 are the default or they can > be changed? and at what basis? In HOLE 1 1.0 the first '1' means "Use the K edge (1s electron)" which is one of the most common edges used for EXAFS. For Pt you may want to simulate the more-commonly-measured L3 edge, which would use HOLE 4 The '1.0' means "multiply by a constant factor of 1.0", which is there to allow one to put in a factor (usually called S02) that multiplies the calculated EXAFS. For now, leave it as 1.0 -- it can be dealt with later or ignored for a pure simulation. There is some documentation for this on the Feff web page. > What do the 0.00000 coordinates for the absorbing atom mean? I suppose they > mean the atom is centered in a computational box or something, I do not know > exactly!! Feff needs only atomic coordinates of a "cluster of atoms" -- it could be a molecule, part of a crystalline solid, or coordinates from a simulation for a liqud, glass, etc. It does not need or implicitly impose periodic boundary conditions. So the coordinates are all in Angstroms, but relative to some arbitrary origin. It's common to put the absorbing atom at 0,0,0, but it is not necessary: "ipot = 0" specifies the absorbing atom. If you can generate x,y,z coordinates in Angstroms from your simulation, just use those. > You input six oxygen atoms, what are they? all bonded to two Mn atoms?? or > they are pertinent to solvent molecules? For the example I gave, those oxygens were bonded to the Mn. For EXAFS it generally does not matter a great deal whether the atoms are bonded or not, though for a gas or liquid 'residence time' is a factor, and the cluster should reflect a "snapshot" of the atomic arrangement on the timescale of the EXAFS measurement (which is femto-seconds). In many cases, the solvent is visible, especially for metals in water -- the hydration shell is seen. > I quote "generally feff needs no more than a few hundred atoms", of the > molecule in question, or including solvent molecules too? Actually, I am > doing my simulation in the gas phase, would this be okay with the input > requirements? Oh, sure. One potential (pun intended, sorry!) issue is that Feff does a real space calculation of the atomic potentials for the atoms in your cluster. For a gas phase (or non-condensed molecule) the 'emptiness' on the outside of the cluster can make the calculation a little less reliable. In my experience, I often put a few extra waters (well, O atoms) around a small molecule just to help the calculation. Also, note that for Feff6 that comes with Ifeffit/Artemis, it's recommended to take out all the H atoms -- they aren't see by the x-rays anyway and make the potentials calculation harder. I'm hope someone from the mailing list might be able to add more insight on simulations for small molecules.... Hope that helps, --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 60, Issue 4
by joshua jason kas 22 Feb '08

22 Feb '08

Another way to get feff to run is to define the stoichiometry. I found that the following cards work. Change the SCF definition to the following SCF 3.46808 0 30 0.05 and change the potential definition to POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 26 Fe -1 -1 1 1 26 Fe -1 -1 1000 2 29 Cu -1 -1 1 This makes feff assume that there are many Fe atoms for each Cu atom, which was what I was assuming from your feff.inp. Cheers, Josh > Message: 1 > Date: Thu, 21 Feb 2008 13:52:31 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] problem with feff.inp > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0802211152p6fa9c908v24ba67bc2dfc81b2(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > It looks like the SCF calculation is having a hard time with the new > potential. The input file you sent only has atoms out to 2.48 Ang > (though perhaps you truncated it when posting???), but the > > SCF 4 0 30 0.2 1 > > in your feff.inp means to make a self-consistent potential out to 4 > Ang. Without any atoms out that far, I can imagine it would have > problems. I think you'll probably need a larger cluster than a > single shell for a reasonable XANES simulation. > > Hope that helps, > > --Matt >

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sorting files in Athena
by Dominik Samuelis 22 Feb '08

22 Feb '08

Hi Dariusz, > I use Iffefit under Win XP, and every time when I open (import) more > files I have them in such order: 1, 11, 12, 13, ... , 19, 2, 20, 21, 22, > ... , 29, 3, 30, 31 ... etc. > So, my question is if there is some "hidden" way to sort automatically > files during importing or in the menue. Do you know something about? Is > the sorting lexigraphical (from Windows)? this is a typical problem with the Windows file selection dialog. Windows always puts the file, which is currently selected, at the first position of the files list. Now, when you're shift-clicking on your last file, you automatically select this one. That's why file 31 is in first position. The easiest workaround for this issue is to select your files backwards, i.e. first click on file 31, then shift-click on file 1. Now, with HASYLAB files, it gets a little more complicated, due to filenames like scan_00001rxx, where xx is the scan number during a QEXAFS scan. I usually just open them in two chunks, one with xx=1-9 and then xx=10-99. This way, you can use the lexical sorting of Windows. Cheers, dominik -- Dipl.-Ing. Dominik Samuelis samuelis(a)pc.rwth-aachen.de Physikalische Chemie I RWTH Aachen University Phone: +49-241-80-94840 Fax: +49-241-80-92128 Landoltweg 2 52074 Aachen Germany

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theoretical EXAFS spectra
by Mustafa Hussein 22 Feb '08

22 Feb '08

Dear all, I am doing a Car-Parinello MD simulation, and I want to generate an EXAFS spectrum using the MD trajectory data. I am not familiar with the realm of XAS data analysis software. I need to know what software to use (FEFF, IFEFFIT, etc, what is the difference?) and is there some interface that helps me to build input files easily (I am having very little time)? and some other plotting commands that can produce nice plots? any help is appreciated Sincerely, Mustafa Mustafa Hussein Muhammad Independent Research Student Quantum Chemistry Senior Undergraduate Faculty of Pharmacy Minia University Minia 61511, Egypt Cell: + (20) 10 187 6193 --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

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sorting files in Athena
by Zajac, Dariusz 22 Feb '08

22 Feb '08

Hi, I can not find one small thing - sorting files in Athena - it makes me crazy ;) I work with QEXAFS data - usualy few tens of files or even more. Files are named in such way: "file_name"rXX.fio where XX is next file number (1, 2, 3, ... ,10, 11, 12, ... , 20, 21, etc.). I use Iffefit under Win XP, and every time when I open (import) more files I have them in such order: 1, 11, 12, 13, ... , 19, 2, 20, 21, 22, ... , 29, 3, 30, 31 ... etc. So, my question is if there is some "hidden" way to sort automatically files during importing or in the menue. Do you know something about? Is the sorting lexigraphical (from Windows)? another problem which apears, is the limitation of the memmory... thanks for answer and greetings kicaj ------------------------------------------------------------------------ Zajac Dariusz A. Deutsches Elektronen-Synchrotron -Hasylab phone: +49-40-8998-2932 Notkestr. 85 fax: +49-40-8998-2787 22607 Hamburg e-mail: Germany ------------------------------------------------------------------------

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