[Ifeffit] problem with feeff.inp
Dear I have some problem with a very easy simulation. Everytime I try to introduce a potential with more elements, for instance POTENTIALS 0 26 Fe 1 26 Fe 2 29 Cu the program stops the simulation with a message that I do not understand and that is attached to this mail. This 'weird' behavior does not happen with a monoatomic potential like POTENTIALS 0 26 Fe 1 26 Fe and in this second case everything works perfectly. I would be very glad if you will have any suggestion. Thank you in advance Sebastiano Cammelli feff.inp1: this works well TITLE Fe CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 LDOS -30 20 0.2 EDGE K S02 1.0 SCF 4 0 30 0.2 1 XANES 4 0.07 0.0 FMS 6 0 POTENTIALS 0 26 Fe 1 26 Fe ATOMS 0.00.00.00 Fe 0.0 1.433251.433251.43325 1 Fe_12.48246 -1.433251.433251.43325 1 Fe_12.48246 1.43325 -1.433251.43325 1 Fe_12.48246 -1.43325 -1.433251.43325 1 Fe_12.48246 1.433251.43325 -1.43325 1 Fe_12.48246 -1.433251.43325 -1.43325 1 Fe_12.48246 1.43325 -1.43325 -1.43325 1 Fe_12.48246 -1.43325 -1.43325 -1.43325 1 Fe_12.48246 *... END feff.inp2: this does not work, the only difference is the atom of Cu in first shell. TITLE Fe CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 LDOS -30 20 0.2 EDGE K S02 1.0 SCF 4 0 30 0.2 1 XANES 4 0.07 0.0 FMS 6 0 POTENTIALS 0 26 Fe 1 26 Fe 2 29 Cu ATOMS 0.00.00.00 Fe 0.0 1.433251.433251.43325 1 Fe_12.48246 -1.433251.433251.43325 1 Fe_12.48246 1.43325 -1.433251.43325 1 Fe_12.48246 -1.43325 -1.433251.43325 2 Cu_12.48246 1.433251.43325 -1.43325 1 Fe_12.48246 -1.433251.43325 -1.43325 1 Fe_12.48246 1.43325 -1.43325 -1.43325 1 Fe_12.48246 -1.43325 -1.43325 -1.43325 1 Fe_12.48246 * END in this second case the message is: [EMAIL PROTECTED] 2]$ ./feff Feff 8.40 XANES: Fe in Fe 7 Calculating potentials ... free atom potential and density for atom type0 free atom potential and density for atom type1 free atom potential and density for atom type2 initial state energy overlapped potential and density for unique potential0 overlapped potential and density for unique potential1 overlapped potential and density for unique potential2 muffin tin radii and interstitial parameters iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph) 0 1.40339E+00 1.35427E+00 1.09245E+00 1 1.41347E+00 1.36196E+00 1.09680E+00 2 1.27400E+00 1.24500E+00 1.05748E+00 Core-valence separation mu_old= -11.483 SCF ITERATION NUMBER 1 OUT OF 30 Calculating energy and space dependent l-DOS. It takes time ... point # 1 energy = -40.000 Doing FMS for a cluster of 15 atoms around iph = 0 0 FMS matrix (LUD) at point 1, number of state kets = 135 Doing FMS for a cluster of 15 atoms around iph = 1 0 FMS matrix (LUD) at point 1, number of state kets = 135 Doing FMS for a cluster of 15 atoms around iph = 2 0 FMS matrix (LUD) at point 1, number of state kets = 135 point # 20 energy = -28.815 point # 40 energy = -16.459 point # 60 energy = -15.827 Electronic configuration iphil N_el 0 00.669 0 10.939 0 28.180 0 30.000 1 00.670 1 10.946 1 26.522 1 30.000 2 00.430 2 10.522 2 20.557 Found bad counts. Occupation number in getorb is10.000 Will repeat this iteration 2 30.000 ./feff: line 4: 12214 Segmentation fault $FeffPath/ffmod1 Calculating LDOS ... open: No such file or directory apparent state: unit 3 named pot.bin lately writing sequential formatted external IO ./feff: line 5: 12217 Aborted $FeffPath/ldos Calculating cross-section and phases... open: No such file or directory apparent state: unit 3 named pot.bin lately writing sequential formatted external IO ./feff: line 7: 12218 Aborted $FeffPath/ffmod2 Error opening file, phase.bin in module rdxsph Fatal error CHOPEN STOP statement executed Preparing plane wave scattering amplitudes... Error opening file, phase.bin in module rdxsph Fatal error CHOPEN STOP statement executed Calculating EXAFS parameters... Error opening file, phase.bin in module rdxsph Fatal error CHOPEN STOP statement executed Calculating chi... fmt: end of file apparent state: unit 8 named fort.8 last format: (A) lately reading sequential formatted external IO ./feff: line 11:
Re: [Ifeffit] Questions about Athena and XANES
Hi Jenny, I just wanted to add a bit to Matt's answer on TEY vs FY and suggest a couple of reference for you. There are three contributions to the TEY: photoelectrons, Auger Electrons, and secondary electrons. The secondary electrons will typically determine the maximum depth that you can observe in a TEY measurement. There is a good description of this in Jo Stohr's book, NEXAFS Spectroscopy which can be seen at google books. http://tiny.cc/44VGq There is also a quick synopsis of the book at: http://www-ssrl.slac.stanford.edu/stohr/nexafs.htm At this site, there is a photoelectron spectrum showing the relative intensity of Auger and Photopeaks. The secondaries are roughly a factor of 100 more intense than the other contributions. It is possible to measure both TEY and Auger electron yield (AEY) and you will see that the AEY is more surface sensitive that TEY. Measuring AEY requires an analyzer capable of discriminating the electron energy. AEY is typically performed at lower photon energies as there are not too many electron energy analyzers at hard x-ray facilities. It is actually pretty difficult to try to calculate the maximum analysis depth for TEY because of the three different contributions. Here is an attempt to understand the probe depth of TEY but neglects secondary electrons: http://www.icdd.com/resources/axa/vol44/v44_058.pdf For the K-edges in the hard x-ray regime, with TEY it would not be unrealistic to expect probe depths on the order of 1000 angstroms (100 nm). Jeff On Feb 20, 2008, at 6:33 PM, Jenny Cai wrote: Hi all, Could someone please answer my questions? I would really appreciate your help. 1. For linear combination fitting, there are three indicators for the goodness of fitting: R-factor, chi-square and reduced chi- square. Could anyone tell me how they work? 2. Since TEY is sensitive for the surface and FY for the bulk (and surface?), species detected by TEY should be also detected by FY, right? 3. How to calculate the maximum analysis depths for TEY and FY? Thank you in advance. Jenny Cai ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] sorting files in Athena
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_namerXX.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: +49-40-8998-2932Notkestr. 85 fax:+49-40-8998-2787 22607 Hamburg e-mail: Germany ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] sorting files in Athena
Check out the section on marking groups in the Athena manual to see if that meets your needs. This may not be the answer you're looking for, but it's a way to sort data by selecting data sets that have a common expression that matches your search parameters. The command is under Mark then mark regex I think. The Athena manual is found here http://cars9.uchicago.edu/iffwiki/Documentation Richard 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_namerXX.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: +49-40-8998-2932Notkestr. 85 fax:+49-40-8998-2787 22607 Hamburg e-mail: Germany ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Richard Mayes Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] problem with feff.inp
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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Questions about Athena and XANES
Hi Jeff, Thanks -- you're right. I was only considering Auger electrons which are more surface sensitive than the secondary electrons that actually dominate most TEY measurements. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] sorting files in Athena
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_namerXX.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)? The file selection dialog sorts alphabetically. There is no quick-n-easy way to resort the data groups once in Athena. The best solution would be to name the files in a way that alphabetical sorting will be the same as time sorting. The way to do that will be to name the first file f01.fio rather than r1.fio. another problem which apears, is the limitation of the memmory... That is a well known, well discussed problem. Ifeffit is written in fortran. Fortran does not have dynamic memory allocation. The only practical solution is tonot read so many data files in at a time. I wish it were different, but it's not. B -- Bruce Ravel --- [EMAIL PROTECTED] 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/ winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
