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

Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11
by Khalid, Syed 09 Sep '08

09 Sep '08

Anatoly: I will try your approach: Same problem I can address in a different way. Suppose the energy is not linear in case of a Pt-L3 scan. We can set Pt-L3 edge at known 11564 eV. Scanning all the way to L2 edge and say we find it 200 eV off (exaggerating), can we set in Athena the L2 edge at known 13273 eV, while the L3 edge is still at 11564 eV? -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, September 08, 2008 4:44 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 11 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. FW: enrgy-axis-expansion (Khalid, Syed) 2. Re: enrgy-axis-expansion (Bruce Ravel) 3. Re: enrgy-axis-expansion (Anatoly Frenkel) 4. Re: enrgy-axis-expansion (Bruce Ravel) 5. ODP: enrgy-axis-expansion (Zajac, Dariusz) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: [Ifeffit] FW: enrgy-axis-expansion To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" -----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081351.12614.bravel(a)bnl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 08 September 2008 12:20:47 Khalid, Syed wrote: > Is it possible in Athena to change the y-axis (energy > scale) at two different energy points of an EXAFS scan? > > I have a Ni foil spectrum as a function of time. > The edge can be set at 8333.0 eV, and I want to > to assign higher energy to a known feature in the Ni scan. I am not 100% certain I understand the question, but I think the question is about the calibration dialog. That is, you want to assign an energy shift, but not referenced to the edge energy position. Why can't you just set the energy shift by hand on Athena's main page? B -- 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/ ------------------------------ Message: 3 Date: Mon, 8 Sep 2008 13:59:42 -0400 From: "Anatoly Frenkel" <frenkel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <20080908175744.9B7E429C12(a)fe6.prod.mis.yu.edu> Content-Type: text/plain; charset="us-ascii" Khalid, what you can do is to note how much the higher energy (at energy E1) feature is shifted from what you think it should be (let's say by the amount of D eV), provided that you fixed the lower energy point to what you wanted (say, E0). Then, you should transfer the data into a spreadsheet and apply linear scaling: E --> E0 + (E-E0)*D It will ensure that in the range between E0 and E1 the data are linearly stretched or compressed, depending on the sign of D. Anatoly = _____ From: Khalid, Syed [mailto:khalid@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] enrgy-axis-expansion Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov _______________________________________________ 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] Ifeffit Digest, Vol 67, Issue 11
by Frenkel, Anatoly 09 Sep '08

09 Sep '08

No, if you enter any number in the energy shift window, the entire scale is shifted. This linear scaling can be done only for small shifts, in XANES region. For larger shifts you need parabolic correction, or even use a splice method where different corrections are applied to different sub-ranges of the data, and then the entire (supposedly, correct) energy range is spliced from Such corrected ranges. Suppose, you took data at the beamline where you discovered there is energy tracking problem, which is reproducible. Then you can fix it, assuming you collected also data in a reference foil and can compare such data against a "standard" data of the foil. It is very time consuming but doable. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue Sep 09 09:22:14 2008 Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11 Anatoly: I will try your approach: Same problem I can address in a different way. Suppose the energy is not linear in case of a Pt-L3 scan. We can set Pt-L3 edge at known 11564 eV. Scanning all the way to L2 edge and say we find it 200 eV off (exaggerating), can we set in Athena the L2 edge at known 13273 eV, while the L3 edge is still at 11564 eV? -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, September 08, 2008 4:44 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 11 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. FW: enrgy-axis-expansion (Khalid, Syed) 2. Re: enrgy-axis-expansion (Bruce Ravel) 3. Re: enrgy-axis-expansion (Anatoly Frenkel) 4. Re: enrgy-axis-expansion (Bruce Ravel) 5. ODP: enrgy-axis-expansion (Zajac, Dariusz) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: [Ifeffit] FW: enrgy-axis-expansion To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" -----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081351.12614.bravel(a)bnl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 08 September 2008 12:20:47 Khalid, Syed wrote: > Is it possible in Athena to change the y-axis (energy > scale) at two different energy points of an EXAFS scan? > > I have a Ni foil spectrum as a function of time. > The edge can be set at 8333.0 eV, and I want to > to assign higher energy to a known feature in the Ni scan. I am not 100% certain I understand the question, but I think the question is about the calibration dialog. That is, you want to assign an energy shift, but not referenced to the edge energy position. Why can't you just set the energy shift by hand on Athena's main page? B -- 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/ ------------------------------ Message: 3 Date: Mon, 8 Sep 2008 13:59:42 -0400 From: "Anatoly Frenkel" <frenkel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <20080908175744.9B7E429C12(a)fe6.prod.mis.yu.edu> Content-Type: text/plain; charset="us-ascii" Khalid, what you can do is to note how much the higher energy (at energy E1) feature is shifted from what you think it should be (let's say by the amount of D eV), provided that you fixed the lower energy point to what you wanted (say, E0). Then, you should transfer the data into a spreadsheet and apply linear scaling: E --> E0 + (E-E0)*D It will ensure that in the range between E0 and E1 the data are linearly stretched or compressed, depending on the sign of D. Anatoly = _____ From: Khalid, Syed [mailto:khalid@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] enrgy-axis-expansion Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Noise level in XANES spectrum
by Pushan Shah 09 Sep '08

09 Sep '08

Hello Everyone, I have a general question regarding noise level of XANES spectrum. I have collected XANES data for an element which is present in ppm level in my samples. Some samples are exhibiting varying degree of noise in XANES spectrum. Is the noise level of XANES spectrum would be proportional or consistent with the concentration of the sample? As XANES spectra for some of my samples with relatively higher concentration of this element are exhibiting greater level of noise than those with relatively lower concentrations. Will sample matrix play any role in the noise level? Thanks and I appreciate your help. regards, Pushan

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enrgy-axis-expansion
by Khalid, Syed 09 Sep '08

09 Sep '08

Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov

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Bugs in Athena under Windows
by Timna-Josua Kuehn 08 Sep '08

08 Sep '08

Hello, since the last two versions of Athena under Windows some serious bugs have appeared. Whenever I merge some datasets, Athena somehow breaks down afterwards. The window is still open, but I can not plot anything, nor do any other operation. The same happens when I try to align or convolute some spectrum. Thanks for checking this. Timna

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FW: enrgy-axis-expansion
by Khalid, Syed 08 Sep '08

08 Sep '08

-----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov

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A problem with Athena
by NIRAWAT THAMMAJAK 08 Sep '08

08 Sep '08

Hello, May I ask a short question here. I don't know why now Athena cannot open any data files. It is said "you have not used any memory yet" in the bottom.* *I have tried to go back and used the older version (1.2.10), which once it used to work very well, and it started to have the same problem. I've heard about bug stuff in a former mailing list, but i don't know how to solve it. It would be very grateful if you could let me know a short solution for this. Please accept my appreciation for your kindly help. Best Regards, Nirawat. -- Nirawat Thammajak Research and Academic Division, National Synchrotron Research Center, PO Box 93, Nakhon Ratchasima 30000 Thailand. Tel. (+66) 044-217040 ext. 504 Fax (+66) 044-217047

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Re: [Ifeffit] lanthanides convergence
by Eugenio Otal 06 Sep '08

06 Sep '08

Dear Micah, I attach six xmu.dat files and its feff.inp files. The atoms range is from 230 to 488 atoms. The convergence for SCF is achieved but not for FMS, I have some more files with problem to converge the FMS, but the server is in back up process in this moment, I will post them ASAP if necessary. I found the core-hole broadening in xmu.dat, but which is a correct criteria to choose the broadening for the LDOS? Thanks in advance, euG Eugenio, Can you post some of your xmu.dat files generated with various cluster sizes? That might give a clue as to what is going on. > If I increase the broadening for the LDOS, the default is 0.1eV for > the one exported by Arthemis and 0.2eV is shown in the manual, the > last one is still small compared with 4.16 eV. Which is a good > criteria to choose it and where I can find the core hole broadening > value? > The core-hole broadening in eV is reported in the header of xmu.dat as Gam_ch. Here is the relevant line from one of my files: # Gam_ch=8.302E+00 H-L exch Vi= 2.000E+00 Vr= 0.000E+00 > I will quit the LDOS card to obtain results faster, but pot.bin > will be generated anyway (I will leave the CONTROL card option on), > if not, is it needed for another calculation? The calculations > (without the LDOS) and the spectra will be obtained like before? > You can compute pot.bin once and do subsequent calculations with CONTROL 0 1 1 1 1 1. This will cause FEFF to skip the potentials calculation and use the result (saved in pot.bin) of the previous run. There is no need to recalculate the potentials for each run in a convergence test unless you are converging parameters relevant to the potentials calculation. Best Wishes, Micah Prange 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Lic. Eugenio H. Otal E-mail: eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

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Re: [Ifeffit] lanthanides convergence
by Eugenio Otal 05 Sep '08

05 Sep '08

Hi Joshua, I can not find convergence on the absorption spectra. It is very hard to believe that 500 atoms is not enough to find a converged spectra. If I increase the broadening for the LDOS, the default is 0.1eV for the one exported by Arthemis and 0.2eV is shown in the manual, the last one is still small compared with 4.16 eV. Which is a good criteria to choose it and where I can find the core hole broadening value? I will quit the LDOS card to obtain results faster, but pot.bin will be generated anyway (I will leave the CONTROL card option on), if not, is it needed for another calculation? The calculations (without the LDOS) and the spectra will be obtained like before? I will implement the lanczos algorithm too and parameter nex to obtain faster results with a bigger number of atoms. Cheers, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Lic. Eugenio H. Otal E-mail: eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Hi Eugenio, I have a question for you, When you say that convergence is not reached, do you mean convergence of the absoption spectrum or convergence of the LDOS? These are very different since the absorption has core-hole and self-energy broadening included. I noticed that you use 0.1 eV broadening for the LDOS, which is much smaller than the core hole broadening which is 4.16eV. Also, the calculation will be much quicker if you do not run LDOS since FEFF does the matrix inversion for each unique potential and energy when the LDOS card is present. Otherwise, the inversion is only done for the central atom potential at each energy. Cheers, Josh Kas > > Bruce, > > thanks for your answer, it is a great problem to increase the number of > atoms, huge CPU time is needed to finish a calculation. > > Here I pasted the header and the first lines of the atom list and attached > the whole file, if somebody could help me to reduce the calculation time I > will be grateful. > > Thanks in advance, euG > > * This feff8 input file was generated by Artemis 0.8.011 > * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 > > TITLE name: ZnO:Er 1 at no distortion d= 4.136 > TITLE formula: ZnO > TITLE sites: Zn1,O1 > TITLE refer1: wyckoff, vol 1, ch III, p 111 > TITLE refer2: > TITLE schoen: > TITLE notes1: > > * Er L3 edge energy = 8358.0 eV > EDGE L3 > S02 1.0 > > * pot xsph fms paths genfmt ff2chi > CONTROL 1 1 1 1 1 1 > PRINT 3 0 0 0 0 0 > > *** ixc=0 means to use Hedin-Lundqvist > * ixc [ Vr Vi ] > EXCHANGE 0 > > *** Radius of small cluster for > *** self-consistency calculation > *** A sphere including 2 shells is > *** a good choice > *** l_scf = 0 for a solid, 1 for a molecule > * r_scf [ l_scf n_scf ca ] > SCF 4.0 > > *** Upper limit of XANES calculation. > *** This *must* be uncommented to > *** make Feff calculate full multiple > *** scattering rather than a path expansion > * kmax [ delta_k delta_e ] > XANES 4.0 > > *** Radius of cluster for Full Multiple > *** Scattering calculation > *** l_fms = 0 for a solid, 1 for a molecule > * r_fms l_fms > FMS 5.00 0 > > *** Energy grid over which to calculate > *** DOS functions > * emin emax eimag > LDOS -30 20 0.1 > > *** for EXAFS: RMAX 12.0 and uncomment > *** the EXAFS card > RPATH 0.1 > *EXAFS 20 > > POTENTIALS > * ipot Z element l_scmt l_fms stoichiometry > 0 68 Er 3 3 0.001 > 1 30 Zn 2 2 2 > 2 8 O 1 1 2 > 3 68 Er 3 3 2 > > ATOMS * this list contains 902 atoms > * x y z ipot tag distance > 0.00000 0.00000 0.00000 0 Er 0.00000 0 > -0.93804 -1.62473 -0.49466 1 Zn1 1.94019 1 > 1.87611 0.00002 -0.49466 1 Zn1 1.94023 2 > -0.93804 1.62477 -0.49466 1 Zn1 1.94023 3 > -0.93804 -1.62473 1.30173 2 O1 2.28346 4 > 0.93804 1.62473 -1.30173 2 O1 2.28346 5 > 1.87611 0.00002 1.30173 2 O1 2.28348 6 > -0.93804 1.62477 1.30173 2 O1 2.28348 7 > -1.87611 -0.00002 -1.30173 2 O1 2.28348 8 > 0.93804 -1.62477 -1.30173 2 O1 2.28348 9 > 0.93804 1.62473 2.10879 1 Zn1 2.82253 12 > -1.87611 -0.00002 2.10879 1 Zn1 2.82255 13 > 0.93804 -1.62477 2.10879 1 Zn1 2.82255 14 > 0.93804 1.62473 -3.09811 1 Zn1 3.62187 21 > -1.87611 -0.00002 -3.09811 1 Zn1 3.62189 22 > 0.93804 -1.62477 -3.09811 1 Zn1 3.62189 23 > -3.75219 0.00002 -0.49466 1 Zn1 3.78466 24 > 1.87611 -3.24948 -0.49466 1 Zn1 3.78465 25 > 1.87611 3.24952 -0.49466 1 Zn1 3.78469 26 > -3.75219 0.00002 1.30173 2 O1 3.97158 27 > 1.87611 -3.24948 1.30173 2 O1 3.97158 28 > -1.87611 3.24948 -1.30173 2 O1 3.97158 29 > 3.75219 -0.00002 -1.30173 2 O1 3.97158 30 > 1.87611 3.24952 1.30173 2 O1 3.97161 31 > -1.87611 -3.24952 -1.30173 2 O1 3.97161 32 > 2.81415 1.62475 2.60345 3 Er 4.16380 33 > -1.87611 3.24948 2.10879 1 Zn1 4.30417 45 > 3.75219 -0.00002 2.10879 1 Zn1 4.30418 46 >

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chi(k) Athena bug?
by Olivier 04 Sep '08

04 Sep '08

Dear all, I recently performed FEFF calculations to model chi(k) spectra. The generated chi.dat files had chi(k) data starting at 1.4k. When importing the data (chi.dat) in Athena (version 0.8.056) using IFEFFIT 1.2.11 (XP OS), Athena was not able to interpolate the data from 0 to xk (x being the starting k value of the file, in my case 1.4). Thus Athena could only read the data in but no changes were visible in the plot window when changing parameters (e.g. k-weight, looking at the FT). The plot window just froze. Yet the echo and Ifeffit buffer indicated that the changes had been taken into account. I tried to uncheck the buffering and storing options in the plot window without success. In contrast, with the newest version of Artemis (i.e. 0.8.012, or previous versions of Athena, e.g. 0.8.054), I was able to read and play with any chi data. To look at the data in Athena 0.8.056 I simply added a 0-1.4k interval with a 0.05k grid and set chi(k) to 0 in this interval. Do you also experience this tiny Athena 0.8.056 (XP OS) bug? Or is there a workaround? Best regards, Oli ++++++++++++++++++++++++++++++++++++:-) Olivier Jacquat Soil Chemistry group Institut of Biogeochemistry and Pollutant Dynamics ETH Zürich Universitätstrasse 16, CHN F71 8092 Zürich-Switzerland Tel: +41 44 633 60 28 Fax: +41 44 633 11 18 Email: olivier.jacquat(a)env.ethz.ch

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Re: [Ifeffit] lanthanides convergence
by joshua jason kas 03 Sep '08

03 Sep '08

Hi Eugenio, I have a question for you, When you say that convergence is not reached, do you mean convergence of the absoption spectrum or convergence of the LDOS? These are very different since the absorption has core-hole and self-energy broadening included. I noticed that you use 0.1 eV broadening for the LDOS, which is much smaller than the core hole broadening which is 4.16eV. Also, the calculation will be much quicker if you do not run LDOS since FEFF does the matrix inversion for each unique potential and energy when the LDOS card is present. Otherwise, the inversion is only done for the central atom potential at each energy. Cheers, Josh Kas > > Bruce, > > thanks for your answer, it is a great problem to increase the number of > atoms, huge CPU time is needed to finish a calculation. > > Here I pasted the header and the first lines of the atom list and attached > the whole file, if somebody could help me to reduce the calculation time I > will be grateful. > > Thanks in advance, euG > > * This feff8 input file was generated by Artemis 0.8.011 > * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 > > TITLE name: ZnO:Er 1 at no distortion d= 4.136 > TITLE formula: ZnO > TITLE sites: Zn1,O1 > TITLE refer1: wyckoff, vol 1, ch III, p 111 > TITLE refer2: > TITLE schoen: > TITLE notes1: > > * Er L3 edge energy = 8358.0 eV > EDGE L3 > S02 1.0 > > * pot xsph fms paths genfmt ff2chi > CONTROL 1 1 1 1 1 1 > PRINT 3 0 0 0 0 0 > > *** ixc=0 means to use Hedin-Lundqvist > * ixc [ Vr Vi ] > EXCHANGE 0 > > *** Radius of small cluster for > *** self-consistency calculation > *** A sphere including 2 shells is > *** a good choice > *** l_scf = 0 for a solid, 1 for a molecule > * r_scf [ l_scf n_scf ca ] > SCF 4.0 > > *** Upper limit of XANES calculation. > *** This *must* be uncommented to > *** make Feff calculate full multiple > *** scattering rather than a path expansion > * kmax [ delta_k delta_e ] > XANES 4.0 > > *** Radius of cluster for Full Multiple > *** Scattering calculation > *** l_fms = 0 for a solid, 1 for a molecule > * r_fms l_fms > FMS 5.00 0 > > *** Energy grid over which to calculate > *** DOS functions > * emin emax eimag > LDOS -30 20 0.1 > > *** for EXAFS: RMAX 12.0 and uncomment > *** the EXAFS card > RPATH 0.1 > *EXAFS 20 > > POTENTIALS > * ipot Z element l_scmt l_fms stoichiometry > 0 68 Er 3 3 0.001 > 1 30 Zn 2 2 2 > 2 8 O 1 1 2 > 3 68 Er 3 3 2 > > ATOMS * this list contains 902 atoms > * x y z ipot tag distance > 0.00000 0.00000 0.00000 0 Er 0.00000 0 > -0.93804 -1.62473 -0.49466 1 Zn1 1.94019 1 > 1.87611 0.00002 -0.49466 1 Zn1 1.94023 2 > -0.93804 1.62477 -0.49466 1 Zn1 1.94023 3 > -0.93804 -1.62473 1.30173 2 O1 2.28346 4 > 0.93804 1.62473 -1.30173 2 O1 2.28346 5 > 1.87611 0.00002 1.30173 2 O1 2.28348 6 > -0.93804 1.62477 1.30173 2 O1 2.28348 7 > -1.87611 -0.00002 -1.30173 2 O1 2.28348 8 > 0.93804 -1.62477 -1.30173 2 O1 2.28348 9 > 0.93804 1.62473 2.10879 1 Zn1 2.82253 12 > -1.87611 -0.00002 2.10879 1 Zn1 2.82255 13 > 0.93804 -1.62477 2.10879 1 Zn1 2.82255 14 > 0.93804 1.62473 -3.09811 1 Zn1 3.62187 21 > -1.87611 -0.00002 -3.09811 1 Zn1 3.62189 22 > 0.93804 -1.62477 -3.09811 1 Zn1 3.62189 23 > -3.75219 0.00002 -0.49466 1 Zn1 3.78466 24 > 1.87611 -3.24948 -0.49466 1 Zn1 3.78465 25 > 1.87611 3.24952 -0.49466 1 Zn1 3.78469 26 > -3.75219 0.00002 1.30173 2 O1 3.97158 27 > 1.87611 -3.24948 1.30173 2 O1 3.97158 28 > -1.87611 3.24948 -1.30173 2 O1 3.97158 29 > 3.75219 -0.00002 -1.30173 2 O1 3.97158 30 > 1.87611 3.24952 1.30173 2 O1 3.97161 31 > -1.87611 -3.24952 -1.30173 2 O1 3.97161 32 > 2.81415 1.62475 2.60345 3 Er 4.16380 33 > -1.87611 3.24948 2.10879 1 Zn1 4.30417 45 > 3.75219 -0.00002 2.10879 1 Zn1 4.30418 46 >

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Re: [Ifeffit] Problem reproducing spectrum for Ti complex (Josh Kas)
by joshua jason kas 03 Sep '08

03 Sep '08

Hi Janine, I think that distortions could play a role here. When I shift the central Ti atom by 0.1 angstroms in plane (perpendicular to the Cl bonds) to break the planar symmetry, I get a clear double pre-edge peak. 0.1 angstroms may be a bit large but 0.05 is certainly not, since 0.003 angstroms**2 is a very reasonable value for sigma**2. You could also estimate the distortion if you have more information about the debye waller factors, or even better, you could perform a molecular dynamics simulation and do a configurational average of the XANES spectra from snapshots. Below is the feff.inp file that I used. You might want to play with shifting the Ti atom in different directions too. Cheers, Josh Kas TITLE TiPcCl2 molecule Geom1acc CONTROL 1 1 1 1 1 1 PRINT 5 0 0 0 0 0 FMS 9.0 1 *1 appropriate for molecules (wiki) MULTIPOLE 2 *Dipole and quadrupole EXCHANGE 0 0 0 0 *Dirac Hara, -1eV Fermi level shift, -3 broadening SCF 8.0 1 *includes second coordination shell XANES 6.0 0.03 0.001 AFOLP 1.2 CRITERION 0 0 RPATH 0.1 SIG2 0.005 * emin emax eimag * LDOS -20 20 0.2 POTENTIALS *absorbing atom is the Ti *ipot z tag 0 22 Ti 1 6 C 2 7 N 3 1 H 4 17 Cl ATOMS 0 0.1 0 0 0 -0.00040276 -2.1184 -0.28392 2 2.13734 -2.11835 0.00044201 -0.284329 2 2.13734 0.00049691 2.11839 -0.284036 2 2.13734 2.11844 -0.00045764 -0.283627 2 2.13734 -0.00040584 6.782e-05 2.45003 4 2.45003 0.00040523 -6.766e-05 -2.45005 4 2.45005 -1.14859 2.9207 -0.359915 1 3.159 -1.14983 -2.92023 -0.359755 1 3.159 -2.92016 1.14988 -0.36016 1 3.159 -2.92065 -1.14866 -0.360097 1 3.159 1.14871 -2.92072 -0.359374 1 3.159 1.14995 2.92021 -0.359534 1 3.159 2.92028 -1.1499 -0.359129 1 3.159 2.92077 1.14864 -0.359192 1 3.159 -2.49915 2.50027 -0.371632 2 3.5546 -2.50021 -2.49922 -0.371494 2 3.5546 2.49928 -2.50029 -0.370665 2 3.5546 2.50034 2.4992 -0.370803 2 3.5546 -0.692606 4.24003 -0.468777 1 4.32173 -0.694406 -4.23976 -0.468544 1 4.32173 -4.23967 0.694471 -0.469267 1 4.32173 -4.23997 -0.692696 -0.469229 1 4.32173 0.692761 -4.24006 -0.468314 1 4.32173 0.694562 4.23974 -0.468547 1 4.32173 4.23983 -0.694497 -0.467823 1 4.32173 4.24012 0.69267 -0.467862 1 4.32173 -1.42292 5.42169 -0.582346 1 5.63547 -1.42522 -5.42112 -0.582048 1 5.63547 -5.42101 1.4253 -0.582898 1 5.63547 -5.42161 -1.42303 -0.58282 1 5.63547 1.42311 -5.42172 -0.581576 1 5.63547 1.42541 5.42109 -0.581873 1 5.63547 5.4212 -1.42533 -0.581023 1 5.63547 5.42181 1.423 -0.581101 1 5.63547 -2.50314 5.41265 -0.586151 3 5.99217 -2.50544 -5.41162 -0.585854 3 5.99217 -5.41151 2.50552 -0.586554 3 5.99217 -5.41257 -2.50326 -0.586416 3 5.99217 2.50334 -5.41269 -0.585024 3 5.99217 2.50564 5.41159 -0.585321 3 5.99217 5.4117 -2.50555 -0.584622 3 5.99217 5.41277 2.50322 -0.584759 3 5.99217 -0.705001 6.62658 -0.692551 1 6.69987 -0.707815 -6.62632 -0.692187 1 6.69987 -6.62618 0.707911 -0.693369 1 6.69987 -6.62648 -0.705135 -0.69333 1 6.69987 0.70523 -6.62662 -0.691953 1 6.69987 0.708044 6.62628 -0.692316 1 6.69987 6.62641 -0.707949 -0.691134 1 6.69987 6.62671 0.705096 -0.691173 1 6.69987 -1.23945 7.56123 -0.780998 3 7.70184 -1.24266 -7.56074 -0.780583 3 7.70184 -7.56059 1.24277 -0.781872 3 7.70184 -7.56112 -1.2396 -0.781804 3 7.70184 1.23971 -7.56127 -0.780172 3 7.70184 1.24292 7.5607 -0.780587 3 7.70184 7.56085 -1.24281 -0.779298 3 7.70184 7.56138 1.23956 -0.779366 3 7.70184 END On Thu, 28 Aug 2008, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 1. Problem reproducing spectrum for Ti complex (Janine GRATTAGE) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 28 Aug 2008 10:42:31 +0200 > From: Janine GRATTAGE <janine.grattage(a)esrf.fr> > Subject: [Ifeffit] Problem reproducing spectrum for Ti complex > To: Ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <48B664F7.6010704(a)esrf.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Dear IFEFFIT mailing list, > > I have been trying to reproduce the XANES spectrum of a titanium > compound (titanium phthalocyanine dichloride) using FEFF 8.4. The > overall shape is reproduced reasonably well, but I wanted to ask the > mailing list users if they have any ideas as to how to improve the > details such as the pre-edge (to give two distinct peaks) and peak > positions over the absorption edge. > > I have attached a file showing the experimental spectrum, two FEFF input > files and the corresponding XMU output files. These two files have the > same atomic co-ordinates for the molecule, but one has 'standard' > broadening and the Fermi level has been shifted by -1eV (geom1) where > the other has reduced experimental broadening (-3) a shifted Fermi > level, and smaller step size (geom1acc). > > I have tried changing the geometry of the molecule by moving one or both > of the Cl atoms, and by trying a flat molecular geometry rather than the > 'umbrella' shape in the attached files, but the spectra attached are the > best match to experiment. Any help or suggestions on improvements would > be greatly appreciated. > > Best regards and thanks in advance, > > Janine Grattage > > -- > 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 > >

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Re: [Ifeffit] lanthanides convergence
by hebhop＠u.washington.edu 02 Sep '08

02 Sep '08

Hi Eugenio, You can use the lanczos algorithm for the matrix inverse. This is specified by setting the fourth option to the FMS card to 2. FMS 5.0 0 2 Also, make sure that the number of energy points is not set too large, that is check the parameter nex in the code. Set it to 150 or so. I have a feeling that it is set to 400. These two things should reduce the time by a factor of 4 at least. Cheers, Josh Kas > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: lanthanides convergence (Eugenio Otal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Sep 2008 23:58:55 -0300 > From: "Eugenio Otal" <eugenioh(a)gmail.com> > Subject: Re: [Ifeffit] lanthanides convergence > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <da22ad30809011958g484a5cfr750341645402fb74(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Bruce, > > thanks for your answer, it is a great problem to increase the number of > atoms, huge CPU time is needed to finish a calculation. > > Here I pasted the header and the first lines of the atom list and attached > the whole file, if somebody could help me to reduce the calculation time I > will be grateful. > > Thanks in advance, euG > > * This feff8 input file was generated by Artemis 0.8.011 > * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 > > TITLE name: ZnO:Er 1 at no distortion d= 4.136 > TITLE formula: ZnO > TITLE sites: Zn1,O1 > TITLE refer1: wyckoff, vol 1, ch III, p 111 > TITLE refer2: > TITLE schoen: > TITLE notes1: > > * Er L3 edge energy = 8358.0 eV > EDGE L3 > S02 1.0 > > * pot xsph fms paths genfmt ff2chi > CONTROL 1 1 1 1 1 1 > PRINT 3 0 0 0 0 0 > > *** ixc=0 means to use Hedin-Lundqvist > * ixc [ Vr Vi ] > EXCHANGE 0 > > *** Radius of small cluster for > *** self-consistency calculation > *** A sphere including 2 shells is > *** a good choice > *** l_scf = 0 for a solid, 1 for a molecule > * r_scf [ l_scf n_scf ca ] > SCF 4.0 > > *** Upper limit of XANES calculation. > *** This *must* be uncommented to > *** make Feff calculate full multiple > *** scattering rather than a path expansion > * kmax [ delta_k delta_e ] > XANES 4.0 > > *** Radius of cluster for Full Multiple > *** Scattering calculation > *** l_fms = 0 for a solid, 1 for a molecule > * r_fms l_fms > FMS 5.00 0 > > *** Energy grid over which to calculate > *** DOS functions > * emin emax eimag > LDOS -30 20 0.1 > > *** for EXAFS: RMAX 12.0 and uncomment > *** the EXAFS card > RPATH 0.1 > *EXAFS 20 > > POTENTIALS > * ipot Z element l_scmt l_fms stoichiometry > 0 68 Er 3 3 0.001 > 1 30 Zn 2 2 2 > 2 8 O 1 1 2 > 3 68 Er 3 3 2 > > ATOMS * this list contains 902 atoms > * x y z ipot tag distance > 0.00000 0.00000 0.00000 0 Er 0.00000 0 > -0.93804 -1.62473 -0.49466 1 Zn1 1.94019 1 > 1.87611 0.00002 -0.49466 1 Zn1 1.94023 2 > -0.93804 1.62477 -0.49466 1 Zn1 1.94023 3 > -0.93804 -1.62473 1.30173 2 O1 2.28346 4 > 0.93804 1.62473 -1.30173 2 O1 2.28346 5 > 1.87611 0.00002 1.30173 2 O1 2.28348 6 > -0.93804 1.62477 1.30173 2 O1 2.28348 7 > -1.87611 -0.00002 -1.30173 2 O1 2.28348 8 > 0.93804 -1.62477 -1.30173 2 O1 2.28348 9 > 0.93804 1.62473 2.10879 1 Zn1 2.82253 12 > -1.87611 -0.00002 2.10879 1 Zn1 2.82255 13 > 0.93804 -1.62477 2.10879 1 Zn1 2.82255 14 > 0.93804 1.62473 -3.09811 1 Zn1 3.62187 21 > -1.87611 -0.00002 -3.09811 1 Zn1 3.62189 22 > 0.93804 -1.62477 -3.09811 1 Zn1 3.62189 23 > -3.75219 0.00002 -0.49466 1 Zn1 3.78466 24 > 1.87611 -3.24948 -0.49466 1 Zn1 3.78465 25 > 1.87611 3.24952 -0.49466 1 Zn1 3.78469 26 > -3.75219 0.00002 1.30173 2 O1 3.97158 27 > 1.87611 -3.24948 1.30173 2 O1 3.97158 28 > -1.87611 3.24948 -1.30173 2 O1 3.97158 29 > 3.75219 -0.00002 -1.30173 2 O1 3.97158 30 > 1.87611 3.24952 1.30173 2 O1 3.97161 31 > -1.87611 -3.24952 -1.30173 2 O1 3.97161 32 > 2.81415 1.62475 2.60345 3 Er 4.16380 33 > -1.87611 3.24948 2.10879 1 Zn1 4.30417 45 > 3.75219 -0.00002 2.10879 1 Zn1 4.30418 46 >

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lanthanides convergence
by Eugenio Otal 02 Sep '08

02 Sep '08

Bruce, I am running feff to model XANES of Erbium doped ZnO. I have a big problem to find the convergence of FMS in this kind of systems. I increased the atoms number in feff code to nclusx=500 and still have not found convergence. Should I increase the nclusx to a bigger number?, is there a limit for this number independent from the computer RAM or I do have another chance?. Thanks for your time and patience. 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Eugenio H. Otal CINSO - CONICET - CITEFA eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

2 2

Problem reproducing spectrum for Ti complex
by Janine GRATTAGE 29 Aug '08

29 Aug '08

Dear IFEFFIT mailing list, I have been trying to reproduce the XANES spectrum of a titanium compound (titanium phthalocyanine dichloride) using FEFF 8.4. The overall shape is reproduced reasonably well, but I wanted to ask the mailing list users if they have any ideas as to how to improve the details such as the pre-edge (to give two distinct peaks) and peak positions over the absorption edge. I have attached a file showing the experimental spectrum, two FEFF input files and the corresponding XMU output files. These two files have the same atomic co-ordinates for the molecule, but one has 'standard' broadening and the Fermi level has been shifted by -1eV (geom1) where the other has reduced experimental broadening (-3) a shifted Fermi level, and smaller step size (geom1acc). I have tried changing the geometry of the molecule by moving one or both of the Cl atoms, and by trying a flat molecular geometry rather than the 'umbrella' shape in the attached files, but the spectra attached are the best match to experiment. Any help or suggestions on improvements would be greatly appreciated. Best regards and thanks in advance, Janine Grattage -- 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 TITLE TiPcCl2 molecule Geom1acc CONTROL 1 1 1 1 1 1 PRINT 5 0 0 0 0 0 FMS 8.0 1 *1 appropriate for molecules (wiki) MULTIPOLE 2 *Dipole and quadrupole EXCHANGE 0 1. -3. *Dirac Hara, -1eV Fermi level shift, -3 broadening SCF 4 *includes second coordination shell XANES 6.0 0.03 0.001 AFOLP 1.2 CRITERION 0 0 RPATH 0.1 * emin emax eimag LDOS -20 20 0.2 POTENTIALS *absorbing atom is the Ti *ipot z tag 0 22 Ti 1 6 C 2 7 N 3 1 H 4 17 Cl ATOMS *xmod ymod zmod ipot 0 0 0 0 2.11844236 -0.00045764 -0.28362660 2 0.00049691 2.11838749 -0.28403609 2 -2.11834820 0.00044201 -0.28432911 2 -0.00040276 -2.11840312 -0.28391961 2 2.50033703 2.49920371 -0.37080272 2 -2.49915235 2.50026531 -0.37163159 2 -2.50021397 -2.49922414 -0.37149421 2 2.49927541 -2.50028574 -0.37066535 2 2.92077159 1.14863904 -0.35919200 1 -1.14858929 2.92070211 -0.35991542 1 -2.92065235 -1.14865884 -0.36009724 1 1.14870854 -2.92072190 -0.35937383 1 2.92028351 -1.14989912 -0.35912883 1 1.14994884 2.92021403 -0.35953433 1 -2.92016426 1.14987932 -0.36016040 1 -1.14982959 -2.92023383 -0.35975490 1 4.24012097 0.69267038 -0.46786156 1 -0.69260556 4.24003046 -0.46877686 1 -4.23996562 -0.69269616 -0.46922925 1 0.69276092 -4.24005624 -0.46831395 1 4.23982641 -0.69449678 -0.46782344 1 0.69456158 4.23973590 -0.46854687 1 -4.23967106 0.69447100 -0.46926736 1 -0.69440621 -4.23976169 -0.46854393 1 5.42180506 1.42299661 -0.58110099 1 -1.42291609 5.42169266 -0.58234553 1 -5.42161213 -1.42302863 -0.58282014 1 1.42310907 -5.42172466 -0.58157559 1 5.42120023 -1.42533102 -0.58102274 1 1.42541150 5.42108783 -0.58187330 1 -5.42100730 1.42529900 -0.58289838 1 -1.42521852 -5.42111985 -0.58204782 1 6.62671213 0.70509648 -0.69117255 1 -0.70500071 6.62657845 -0.69255053 1 -6.62648265 -0.70513457 -0.69333050 1 0.70523027 -6.62661650 -0.69195251 1 6.62641208 -0.70794872 -0.69113373 1 0.70804448 6.62627840 -0.69231626 1 -6.62618259 0.70791063 -0.69336932 1 -0.70781492 -6.62631646 -0.69218678 1 5.41276801 2.50322415 -0.58475924 3 -2.50314311 5.41265491 -0.58615139 3 -5.41257388 -2.50325637 -0.58641595 3 2.50333729 -5.41268710 -0.58502379 3 5.41170441 -2.50555482 -0.58462164 3 2.50563579 5.41159131 -0.58532097 3 -5.41151028 2.50552260 -0.58655354 3 -2.50544161 -5.41162354 -0.58585421 3 7.56137780 1.23956000 -0.77936602 3 7.56085067 -1.24281398 -0.77929784 3 -7.56059192 1.24277103 -0.78187250 3 -7.56111904 -1.23960294 -0.78180432 3 -1.23945199 7.56122707 -0.78099842 3 1.24292195 7.56069994 -0.78058687 3 1.23971085 -7.56126996 -0.78017192 3 -1.24266309 -7.56074286 -0.78058347 3 0.00040523 -0.00006766 -2.45005490 4 -0.00040584 0.00006782 2.45002706 4 END # TiPcCl2 molecule Geom1acc Feff 8.40 # POT SCF 30 4.0000 0, core-hole, AFOLP (folp(0)= 1.200) # Abs Z=22 Rmt= 1.437 Rnm= 1.537 K shell # Pot 1 Z= 6 Rmt= 0.840 Rnm= 0.996 # Pot 2 Z= 7 Rmt= 0.885 Rnm= 1.008 # Pot 3 Z= 1 Rmt= 0.789 Rnm= 0.909 # Pot 4 Z=17 Rmt= 1.538 Rnm= 1.686 # Gam_ch=9.030E-01 H-L exch Vi=-3.000E+00 Vr= 1.000E+00 # Mu=-1.040E+01 kf=2.632E+00 Vint=-1.880E+01 Rs_int= 1.378 # FMS rfms= 8.0000 # PATH Rmax= 0.100, Keep_limit= 0.00, Heap_limit 0.00 Pwcrit= 0.00% # S02=1.000 Global_sig2= 0.00000 # file sig2 tot cw amp ratio deg nlegs reff inp sig2 # 0/ 0 paths used # xsedge+ 50, used to normalize mu 4.8609E-04 # ----------------------------------------------------------------------- # omega e k mu mu0 chi @# 4966.250 -12.512 -0.540 9.13165E-04 3.37112E-03 -2.45795E-03 4966.484 -12.279 -0.480 1.06274E-03 4.18380E-03 -3.12106E-03 4966.689 -12.074 -0.420 1.27282E-03 5.35021E-03 -4.07739E-03 4966.868 -11.895 -0.360 1.58625E-03 7.11910E-03 -5.53285E-03 4967.019 -11.744 -0.300 2.09217E-03 1.00069E-02 -7.91471E-03 4967.142 -11.621 -0.240 3.00252E-03 1.52351E-02 -1.22326E-02 4967.238 -11.525 -0.180 4.92381E-03 2.62777E-02 -2.13539E-02 4967.307 -11.456 -0.120 1.00982E-02 5.59015E-02 -4.58033E-02 4967.348 -11.415 -0.060 2.70590E-02 1.52513E-01 -1.25454E-01 4967.351 -11.412 -0.051 3.08226E-02 1.73905E-01 -1.43082E-01 4967.361 -11.402 0.000 4.35361E-02 2.46060E-01 -2.02524E-01 4967.365 -11.398 0.030 4.81925E-02 2.72502E-01 -2.24310E-01 4967.375 -11.388 0.060 5.99908E-02 3.39822E-01 -2.79831E-01 4967.392 -11.371 0.090 7.06798E-02 4.01939E-01 -3.31259E-01 4967.416 -11.347 0.120 7.66663E-02 4.38394E-01 -3.61727E-01 4967.447 -11.316 0.150 7.97483E-02 4.59111E-01 -3.79362E-01 4967.485 -11.278 0.180 8.14520E-02 4.72336E-01 -3.90884E-01 4967.529 -11.233 0.210 8.25377E-02 4.81982E-01 -3.99444E-01 4967.581 -11.182 0.240 8.33826E-02 4.89861E-01 -4.06478E-01 4967.639 -11.124 0.270 8.41397E-02 4.96841E-01 -4.12701E-01 4967.704 -11.059 0.300 8.48985E-02 5.03368E-01 -4.18469E-01 4967.776 -10.987 0.330 8.56237E-02 5.09640E-01 -4.24016E-01 4967.855 -10.908 0.360 8.62149E-02 5.15699E-01 -4.29484E-01 4967.941 -10.822 0.390 8.67731E-02 5.21557E-01 -4.34784E-01 4968.034 -10.729 0.420 8.78023E-02 5.27174E-01 -4.39371E-01 4968.133 -10.630 0.450 9.10340E-02 5.32553E-01 -4.41519E-01 4968.239 -10.524 0.480 1.04529E-01 5.37749E-01 -4.33220E-01 4968.352 -10.411 0.510 1.23575E-01 5.42866E-01 -4.19290E-01 4968.472 -10.291 0.540 1.10145E-01 5.48027E-01 -4.37883E-01 4968.599 -10.164 0.570 1.15424E-01 5.53380E-01 -4.37956E-01 4968.733 -10.030 0.600 1.29776E-01 5.59004E-01 -4.29228E-01 4968.874 -9.889 0.630 1.40253E-01 5.64967E-01 -4.24714E-01 4969.021 -9.742 0.660 1.30116E-01 5.71309E-01 -4.41194E-01 4969.175 -9.588 0.690 1.02880E-01 5.78006E-01 -4.75126E-01 4969.337 -9.426 0.720 7.82317E-02 5.85054E-01 -5.06823E-01 4969.505 -9.258 0.750 6.27424E-02 5.92438E-01 -5.29696E-01 4969.679 -9.084 0.780 5.40260E-02 6.00135E-01 -5.46109E-01 4969.861 -8.902 0.810 4.93417E-02 6.08094E-01 -5.58753E-01 4970.050 -8.713 0.840 4.72836E-02 6.16308E-01 -5.69025E-01 4970.245 -8.518 0.870 4.73852E-02 6.24726E-01 -5.77341E-01 4970.448 -8.315 0.900 5.02215E-02 6.33358E-01 -5.83136E-01 4970.657 -8.106 0.930 5.67812E-02 6.42152E-01 -5.85370E-01 4970.873 -7.890 0.960 6.13993E-02 6.51085E-01 -5.89686E-01 4971.096 -7.667 0.990 5.66943E-02 6.60139E-01 -6.03445E-01 4971.325 -7.438 1.020 6.16275E-02 6.69310E-01 -6.07683E-01 4971.562 -7.201 1.050 7.15826E-02 6.78561E-01 -6.06979E-01 4971.805 -6.958 1.080 6.00972E-02 6.87872E-01 -6.27775E-01 4972.056 -6.707 1.110 6.50374E-02 6.97223E-01 -6.32185E-01 4972.313 -6.450 1.140 7.38111E-02 7.06611E-01 -6.32800E-01 4972.577 -6.186 1.170 8.62661E-02 7.16016E-01 -6.29750E-01 4972.848 -5.915 1.200 1.03456E-01 7.25401E-01 -6.21944E-01 4973.126 -5.637 1.230 1.26524E-01 7.34746E-01 -6.08222E-01 4973.410 -5.353 1.260 1.54971E-01 7.44066E-01 -5.89095E-01 4973.702 -5.061 1.290 1.82740E-01 7.53341E-01 -5.70601E-01 4974.000 -4.763 1.320 2.00380E-01 7.62518E-01 -5.62138E-01 4974.305 -4.458 1.350 2.11141E-01 7.71629E-01 -5.60487E-01 4974.617 -4.146 1.380 2.30273E-01 7.80636E-01 -5.50363E-01 4974.936 -3.827 1.410 2.66899E-01 7.89521E-01 -5.22623E-01 4975.262 -3.501 1.440 3.21552E-01 7.98299E-01 -4.76747E-01 4975.594 -3.169 1.470 3.88177E-01 8.06915E-01 -4.18738E-01 4975.934 -2.829 1.500 4.53793E-01 8.15386E-01 -3.61592E-01 4976.280 -2.483 1.530 5.03101E-01 8.23710E-01 -3.20609E-01 4976.633 -2.130 1.560 5.32723E-01 8.31850E-01 -2.99127E-01 4976.993 -1.769 1.590 5.66560E-01 8.39805E-01 -2.73245E-01 4977.360 -1.403 1.620 6.34775E-01 8.47573E-01 -2.12798E-01 4977.734 -1.029 1.650 6.84473E-01 8.55136E-01 -1.70663E-01 4978.115 -0.648 1.680 6.71745E-01 8.62493E-01 -1.90748E-01 4978.502 -0.261 1.710 7.03172E-01 8.69644E-01 -1.66472E-01 4978.897 0.134 1.740 7.94749E-01 8.76587E-01 -8.18378E-02 4979.298 0.535 1.770 8.38553E-01 8.83285E-01 -4.47320E-02 4979.706 0.943 1.800 8.11564E-01 8.89757E-01 -7.81934E-02 4980.121 1.358 1.830 8.36275E-01 8.96019E-01 -5.97439E-02 4980.542 1.780 1.860 9.16563E-01 9.02018E-01 1.45451E-02 4980.971 2.208 1.890 1.00872E+00 9.07788E-01 1.00932E-01 4981.407 2.644 1.920 1.08114E+00 9.13312E-01 1.67828E-01 4981.849 3.086 1.950 1.11955E+00 9.18608E-01 2.00945E-01 4982.298 3.535 1.980 1.13308E+00 9.23657E-01 2.09423E-01 4982.754 3.991 2.010 1.14273E+00 9.28461E-01 2.14271E-01 4983.217 4.454 2.040 1.15283E+00 9.33035E-01 2.19790E-01 4983.687 4.924 2.070 1.15849E+00 9.37346E-01 2.21143E-01 4984.163 5.401 2.100 1.16452E+00 9.41447E-01 2.23068E-01 4984.647 5.884 2.130 1.18412E+00 9.45303E-01 2.38817E-01 4985.137 6.374 2.160 1.21498E+00 9.48932E-01 2.66044E-01 4985.634 6.872 2.190 1.24240E+00 9.52334E-01 2.90069E-01 4986.139 7.376 2.220 1.25155E+00 9.55511E-01 2.96036E-01 4986.649 7.887 2.250 1.23876E+00 9.58461E-01 2.80303E-01 4987.167 8.404 2.280 1.21617E+00 9.61204E-01 2.54969E-01 4987.692 8.929 2.310 1.20218E+00 9.63742E-01 2.38437E-01 4988.223 9.460 2.340 1.21246E+00 9.66074E-01 2.46388E-01 4988.762 9.999 2.370 1.25770E+00 9.68220E-01 2.89477E-01 4989.307 10.544 2.400 1.32791E+00 9.70161E-01 3.57749E-01 4989.859 11.096 2.430 1.38130E+00 9.71917E-01 4.09379E-01 4990.418 11.655 2.460 1.38220E+00 9.73507E-01 4.08696E-01 4990.984 12.221 2.490 1.34139E+00 9.74933E-01 3.66459E-01 4991.556 12.793 2.520 1.29626E+00 9.76174E-01 3.20089E-01 4992.136 13.373 2.550 1.27334E+00 9.77270E-01 2.96074E-01 4992.722 13.959 2.580 1.27044E+00 9.78222E-01 2.92220E-01 4993.315 14.552 2.610 1.26795E+00 9.79029E-01 2.88916E-01 4993.915 15.153 2.640 1.25051E+00 9.79692E-01 2.70818E-01 4994.522 15.759 2.670 1.21688E+00 9.80191E-01 2.36689E-01 TITLE TiPcCl2 molecule Geom1 CONTROL 1 1 1 1 1 1 PRINT 5 0 0 0 0 0 FMS 8.0 1 *1 appropriate for molecules (wiki) MULTIPOLE 2 *Dipole and quadrupole EXCHANGE 0 1 *Dirac Hara, -1eV Fermi level shift SCF 4 *includes second coordination shell XANES 6.0 0.05 0.01 AFOLP 1.2 CRITERION 0 0 *use all paths *RPATH 0.1 * emin emax eimag LDOS -20 20 0.2 POTENTIALS *absorbing atom is the Ti *ipot z tag 0 22 Ti 1 6 C 2 7 N 3 1 H 4 17 Cl ATOMS *xmod ymod zmod ipot 0 0 0 0 2.11844236 -0.00045764 -0.28362660 2 0.00049691 2.11838749 -0.28403609 2 -2.11834820 0.00044201 -0.28432911 2 -0.00040276 -2.11840312 -0.28391961 2 2.50033703 2.49920371 -0.37080272 2 -2.49915235 2.50026531 -0.37163159 2 -2.50021397 -2.49922414 -0.37149421 2 2.49927541 -2.50028574 -0.37066535 2 2.92077159 1.14863904 -0.35919200 1 -1.14858929 2.92070211 -0.35991542 1 -2.92065235 -1.14865884 -0.36009724 1 1.14870854 -2.92072190 -0.35937383 1 2.92028351 -1.14989912 -0.35912883 1 1.14994884 2.92021403 -0.35953433 1 -2.92016426 1.14987932 -0.36016040 1 -1.14982959 -2.92023383 -0.35975490 1 4.24012097 0.69267038 -0.46786156 1 -0.69260556 4.24003046 -0.46877686 1 -4.23996562 -0.69269616 -0.46922925 1 0.69276092 -4.24005624 -0.46831395 1 4.23982641 -0.69449678 -0.46782344 1 0.69456158 4.23973590 -0.46854687 1 -4.23967106 0.69447100 -0.46926736 1 -0.69440621 -4.23976169 -0.46854393 1 5.42180506 1.42299661 -0.58110099 1 -1.42291609 5.42169266 -0.58234553 1 -5.42161213 -1.42302863 -0.58282014 1 1.42310907 -5.42172466 -0.58157559 1 5.42120023 -1.42533102 -0.58102274 1 1.42541150 5.42108783 -0.58187330 1 -5.42100730 1.42529900 -0.58289838 1 -1.42521852 -5.42111985 -0.58204782 1 6.62671213 0.70509648 -0.69117255 1 -0.70500071 6.62657845 -0.69255053 1 -6.62648265 -0.70513457 -0.69333050 1 0.70523027 -6.62661650 -0.69195251 1 6.62641208 -0.70794872 -0.69113373 1 0.70804448 6.62627840 -0.69231626 1 -6.62618259 0.70791063 -0.69336932 1 -0.70781492 -6.62631646 -0.69218678 1 5.41276801 2.50322415 -0.58475924 3 -2.50314311 5.41265491 -0.58615139 3 -5.41257388 -2.50325637 -0.58641595 3 2.50333729 -5.41268710 -0.58502379 3 5.41170441 -2.50555482 -0.58462164 3 2.50563579 5.41159131 -0.58532097 3 -5.41151028 2.50552260 -0.58655354 3 -2.50544161 -5.41162354 -0.58585421 3 7.56137780 1.23956000 -0.77936602 3 7.56085067 -1.24281398 -0.77929784 3 -7.56059192 1.24277103 -0.78187250 3 -7.56111904 -1.23960294 -0.78180432 3 -1.23945199 7.56122707 -0.78099842 3 1.24292195 7.56069994 -0.78058687 3 1.23971085 -7.56126996 -0.78017192 3 -1.24266309 -7.56074286 -0.78058347 3 0.00040523 -0.00006766 -2.45005490 4 -0.00040584 0.00006782 2.45002706 4 END # TiPcCl2 molecule (positions calculated from ADF) Feff 8.40 # POT SCF 30 4.0000 0, core-hole, AFOLP (folp(0)= 1.200) # Abs Z=22 Rmt= 1.437 Rnm= 1.537 K shell # Pot 1 Z= 6 Rmt= 0.840 Rnm= 0.996 # Pot 2 Z= 7 Rmt= 0.885 Rnm= 1.008 # Pot 3 Z= 1 Rmt= 0.789 Rnm= 0.909 # Pot 4 Z=17 Rmt= 1.538 Rnm= 1.686 # Gam_ch=9.030E-01 H-L exch Vi= 0.000E+00 Vr= 1.000E+00 # Mu=-1.040E+01 kf=2.632E+00 Vint=-1.880E+01 Rs_int= 1.378 # FMS rfms= 8.0000 # PATH Rmax=-1.000, Keep_limit= 0.00, Heap_limit 0.00 Pwcrit= 0.00% # S02=1.000 Global_sig2= 0.00000 # file sig2 tot cw amp ratio deg nlegs reff inp sig2 # 0/ 0 paths used # xsedge+ 50, used to normalize mu 4.6992E-04 # ----------------------------------------------------------------------- # omega e k mu mu0 chi @# 4964.275 -14.488 -0.900 1.44077E-02 3.21565E-02 -1.77488E-02 4964.923 -13.840 -0.800 1.61993E-02 3.95010E-02 -2.33017E-02 4965.495 -13.268 -0.700 1.84771E-02 4.97434E-02 -3.12663E-02 4965.990 -12.773 -0.600 2.15278E-02 6.45932E-02 -4.30654E-02 4966.409 -12.354 -0.500 2.58451E-02 8.69527E-02 -6.11076E-02 4966.752 -12.011 -0.400 3.21686E-02 1.21157E-01 -8.89880E-02 4967.019 -11.744 -0.300 4.10037E-02 1.70217E-01 -1.29214E-01 4967.209 -11.554 -0.200 5.09103E-02 2.25913E-01 -1.75002E-01 4967.323 -11.440 -0.100 5.83015E-02 2.67539E-01 -2.09238E-01 4967.351 -11.412 -0.051 6.02274E-02 2.78296E-01 -2.18069E-01 4967.361 -11.402 0.000 6.09319E-02 2.82145E-01 -2.21213E-01 4967.371 -11.392 0.050 6.15821E-02 2.85805E-01 -2.24223E-01 4967.400 -11.363 0.100 6.35112E-02 2.96793E-01 -2.33281E-01 4967.447 -11.316 0.150 6.67307E-02 3.14931E-01 -2.48200E-01 4967.514 -11.249 0.200 7.10829E-02 3.39349E-01 -2.68267E-01 4967.600 -11.163 0.250 7.62645E-02 3.68148E-01 -2.91884E-01 4967.704 -11.059 0.300 8.19260E-02 3.98629E-01 -3.16703E-01 4967.828 -10.935 0.350 8.77714E-02 4.28185E-01 -3.40413E-01 4967.971 -10.792 0.400 9.37945E-02 4.55258E-01 -3.61463E-01 4968.133 -10.630 0.450 1.00145E-01 4.79354E-01 -3.79209E-01 4968.314 -10.449 0.500 1.06691E-01 5.00709E-01 -3.94018E-01 4968.514 -10.249 0.550 1.12394E-01 5.19879E-01 -4.07485E-01 4968.733 -10.030 0.600 1.15591E-01 5.37511E-01 -4.21920E-01 4968.971 -9.792 0.650 1.13910E-01 5.54177E-01 -4.40267E-01 4969.228 -9.535 0.700 1.06198E-01 5.70351E-01 -4.64152E-01 4969.505 -9.258 0.750 9.61631E-02 5.86343E-01 -4.90179E-01 4969.800 -8.963 0.800 8.86382E-02 6.02345E-01 -5.13707E-01 4970.114 -8.649 0.850 8.55330E-02 6.18458E-01 -5.32925E-01 4970.448 -8.315 0.900 8.67318E-02 6.34730E-01 -5.47998E-01 4970.800 -7.963 0.950 9.08250E-02 6.51152E-01 -5.60327E-01 4971.171 -7.592 1.000 9.64994E-02 6.67694E-01 -5.71195E-01 4971.562 -7.201 1.050 1.03277E-01 6.84334E-01 -5.81056E-01 4971.972 -6.791 1.100 1.11508E-01 7.01012E-01 -5.89504E-01 4972.400 -6.363 1.150 1.27017E-01 7.17678E-01 -5.90661E-01 4972.848 -5.915 1.200 1.51783E-01 7.34259E-01 -5.82476E-01 4973.315 -5.448 1.250 1.85121E-01 7.50729E-01 -5.65608E-01 4973.800 -4.963 1.300 2.22060E-01 7.66999E-01 -5.44939E-01 4974.305 -4.458 1.350 2.60104E-01 7.83015E-01 -5.22911E-01 4974.829 -3.934 1.400 3.10517E-01 7.98732E-01 -4.88216E-01 4975.372 -3.391 1.450 3.82202E-01 8.14085E-01 -4.31883E-01 4975.934 -2.829 1.500 4.63881E-01 8.29030E-01 -3.65149E-01 4976.515 -2.248 1.550 5.37065E-01 8.43501E-01 -3.06436E-01 4977.115 -1.648 1.600 6.07253E-01 8.57469E-01 -2.50216E-01 4977.734 -1.029 1.650 6.73937E-01 8.70893E-01 -1.96956E-01 4978.372 -0.391 1.700 7.30804E-01 8.83727E-01 -1.52923E-01 4979.030 0.267 1.750 8.02516E-01 8.95956E-01 -9.34395E-02 4979.706 0.943 1.800 8.54202E-01 9.07537E-01 -5.33342E-02 4980.401 1.638 1.850 9.26242E-01 9.18471E-01 7.77126E-03 4981.115 2.353 1.900 1.02684E+00 9.28720E-01 9.81182E-02 4981.849 3.086 1.950 1.10155E+00 9.38305E-01 1.63246E-01 4982.601 3.838 2.000 1.13866E+00 9.47198E-01 1.91459E-01 4983.373 4.610 2.050 1.16173E+00 9.55400E-01 2.06331E-01 4984.163 5.401 2.100 1.18362E+00 9.62930E-01 2.20694E-01 4984.973 6.210 2.150 1.21605E+00 9.69805E-01 2.46241E-01 4985.802 7.039 2.200 1.24599E+00 9.76015E-01 2.69973E-01 4986.649 7.887 2.250 1.25003E+00 9.81596E-01 2.68433E-01 4987.516 8.753 2.300 1.24364E+00 9.86570E-01 2.57068E-01 4988.402 9.639 2.350 1.26862E+00 9.90955E-01 2.77669E-01 4989.307 10.544 2.400 1.33164E+00 9.94768E-01 3.36871E-01 4990.231 11.468 2.450 1.36605E+00 9.98067E-01 3.67984E-01 4991.174 12.411 2.500 1.33716E+00 1.00084E+00 3.36318E-01 4992.136 13.373 2.550 1.30098E+00 1.00317E+00 2.97807E-01 4993.117 14.354 2.600 1.28188E+00 1.00505E+00 2.76824E-01 4994.117 15.354 2.650 1.24913E+00 1.00652E+00 2.42606E-01 4995.136 16.373 2.700 1.19116E+00 1.00762E+00 1.83538E-01 4996.174 17.412 2.750 1.12334E+00 1.00839E+00 1.14945E-01 4997.232 18.469 2.800 1.05879E+00 1.00886E+00 4.99339E-02 4998.308 19.545 2.850 1.00361E+00 1.00905E+00 -5.44234E-03 4999.403 20.640 2.900 9.66190E-01 1.00899E+00 -4.28024E-02 5000.518 21.755 2.950 9.53894E-01 1.00874E+00 -5.48451E-02 5001.651 22.888 3.000 9.61104E-01 1.00831E+00 -4.72049E-02 5002.804 24.041 3.050 9.70657E-01 1.00771E+00 -3.70537E-02 5003.975 25.212 3.100 9.65699E-01 1.00699E+00 -4.12896E-02 5005.166 26.403 3.150 9.43779E-01 1.00616E+00 -6.23849E-02 5006.376 27.613 3.200 9.12270E-01 1.00527E+00 -9.29971E-02 5007.604 28.841 3.250 8.79909E-01 1.00430E+00 -1.24395E-01 5008.852 30.089 3.300 8.53592E-01 1.00330E+00 -1.49707E-01 5010.119 31.356 3.350 8.37319E-01 1.00228E+00 -1.64962E-01 5011.405 32.642 3.400 8.32342E-01 1.00126E+00 -1.68915E-01 5012.710 33.947 3.450 8.37897E-01 1.00024E+00 -1.62341E-01 5014.034 35.271 3.500 8.52224E-01 9.99254E-01 -1.47030E-01 5015.377 36.614 3.550 8.73066E-01 9.98292E-01 -1.25226E-01 5016.739 37.976 3.600 8.98424E-01 9.97383E-01 -9.89589E-02 5018.120 39.357 3.650 9.25999E-01 9.96535E-01 -7.05367E-02 5019.520 40.757 3.700 9.53423E-01 9.95731E-01 -4.23079E-02 5020.939 42.176 3.750 9.78294E-01 9.94988E-01 -1.66939E-02 5022.378 43.615 3.800 9.98847E-01 9.94307E-01 4.53986E-03 5023.835 45.072 3.850 1.01451E+00 9.93705E-01 2.08018E-02 5025.311 46.548 3.900 1.02568E+00 9.93184E-01 3.25003E-02 5026.807 48.044 3.950 1.03332E+00 9.92711E-01 4.06132E-02 5028.321 49.558 4.000 1.03851E+00 9.92313E-01 4.61965E-02 5029.855 51.092 4.050 1.04223E+00 9.91980E-01 5.02542E-02 5031.407 52.644 4.100 1.04512E+00 9.91711E-01 5.34115E-02 5032.979 54.216 4.150 1.04746E+00 9.91501E-01 5.59600E-02 5034.570 55.807 4.200 1.04937E+00 9.91335E-01 5.80315E-02 5036.179 57.416 4.250 1.05095E+00 9.91211E-01 5.97411E-02 5037.808 59.045 4.300 1.05246E+00 9.91143E-01 6.13166E-02 5039.456 60.693 4.350 1.05412E+00 9.91101E-01 6.30208E-02 5041.123 62.360 4.400 1.05575E+00 9.91083E-01 6.46637E-02 5042.809 64.046 4.450 1.05588E+00 9.91095E-01 6.47840E-02

2 1

Comparison of "amp" between Feff8.40 and feff6 - Curved waves or Plane waves?
by Ying Zou 29 Aug '08

29 Aug '08

Dear all, Nice to get so prompt response from Bruce and Scott, thanks for their effort to make this list vital! Looks like "amp" is a factor which can be reduced. Then there is a question: how would all paths be sorted? by Reff or by "amp"? More techically related another question is then: can FEFFIT and FEFF work seamless together on this? Is there any presumption in FEFFIT (or more explicityly, ARTEMIS/ATHENA) which assumes all the paths have been sorted by descending "amp" down from 100% with ascending REFF? The background story behind this: using the same structural model (thanks Bruce!), I tried to fit either use paths from FEFF840 or from FEFF6. The fitting with FEFF6 paths does a quite good job, giving a R_factor~1%, reduced chi square~ 90. Yet the one with FEFF840 paths terminates abnormally because two parameters cannot be determined. Attached please find two ARTEMIS project files. And appreciate for comments! Ying Ying Zou Research Assoc., Dr. Phys. Physics Department, UWM

2 1

Re: [Ifeffit] Comparison of "amp" between Feff8.40 and feff6 - Curved waves or Plane waves?
by Ying Zou 29 Aug '08

29 Aug '08

Dear all, While I am calculating FEFF path through Feff8.40 using the "feff8.inp" as attached, I notice that the value of "amp" shown on "FEFF interpretation page" for some paths goes over 100%. For example, path 14 has a Reff=3.9317 far away from first shell, yet it has an "amp"=169.913. On the contrary, if I do the same in Artemis through embedded Feff6.0(using "feff6.inp"), none of paths has an "amp" over 100%. I am guessing this could be all right because Feff8 is using curved waves Feff6 instead plane waves. Any comments on this would be greatly appreciated! Ying Ying Zou Research Assoc., Dr.Phys. Physics Department, UWM =======================feff8.inp======================================= * This feff.inp file generated by ATOMS, version 2.50 * ATOMS written by and copyright (c) Bruce Ravel, 1992-1999 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 5194.4 cm^-1, delta mu = 761.6 cm^-1 * specific gravity = 7.942, cluster contains 25 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00093 ang^2 and 0.165E-05 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE Perovskite: PbTiO3 EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * r_scf [ l_scf n_scf ca ] SCF 3.88586 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 EXAFS RPATH 7.77172 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 3.88586 ******** * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 22 Ti -1 -1 0 1 8 O -1 -1 3 2 82 Pb -1 -1 1 3 22 Ti -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Ti 0.00000 0.00000 0.00000 -1.76630 1 Oapical 1.76630 1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 -1.95250 0.32417 1 Oplanar 1.97923 -1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 1.95250 0.32417 1 Oplanar 1.97923 0.00000 0.00000 2.38970 1 Oapical 2.38970 -1.95250 -1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 1.91592 2 Pb 3.36084 -1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 -2.24008 2 Pb 3.55563 -1.95250 1.95250 -2.24008 2 Pb 3.55563 -1.95250 -1.95250 -2.24008 2 Pb 3.55563 1.95250 1.95250 -2.24008 2 Pb 3.55563 -3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 3.90500 0.00000 3 Ti 3.90500 3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 -3.90500 0.00000 3 Ti 3.90500 0.00000 0.00000 4.15600 3 Ti 4.15600 0.00000 0.00000 -4.15600 3 Ti 4.15600 3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 -3.90500 -1.76630 1 Oapical 4.28589 -3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 3.90500 -1.76630 1 Oapical 4.28589 END ============================================================================ ========================feff6.inp========================================== * This feff6 input file was generated by Artemis 0.8.011 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu*x=1: 2.06 microns, unit edge step: 13.38 microns * specific gravity = 7.942 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00048 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * ----------------------------------------------------------------- * The following crystallographic data were used: * * title Pb Ti O3 * title Glazer A M * title # Powder profile refinement of lead zirconate titanate at several temperatures. * title # II. Pure PbTiO3 * title # Locality: synthetic * title # Sample: T = 25 C * space = P 4 m m * a = 3.9050 b = 3.9050 c = 4.1560 * alpha = 90.0 beta = 90.0 gamma = 90.0 * core = Ti edge = K * atoms * ! elem x y z tag occ * Pb 0.00000 0.00000 0.00000 Pb 1.00000 * Ti 0.50000 0.50000 0.53900 Ti 1.00000 * O 0.50000 0.50000 0.11400 Oapical 1.00000 * O 0.50000 0.00000 0.61700 Oplanar 1.00000 * ----------------------------------------------------------------- TITLE Pb Ti O3 TITLE Glazer A M TITLE # Powder profile refinement of lead zirconate titanate at several temperatures. TITLE # II. Pure PbTiO3 TITLE # Locality: synthetic TITLE # Sample: T = 25 C HOLE 1 1.0 * Ti K edge (4966.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 4.29550 *CRITERIA curved plane *DEBYE temp debye-temp NLEG 4 POTENTIALS * ipot Z element 0 22 Ti 1 82 Pb 2 22 Ti 3 8 O ATOMS * this list contains 25 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Ti 0.00000 0.00000 0.00000 -1.76630 3 Oapical_1 1.76630 1.95250 0.00000 0.32417 3 Oplanar_1 1.97923 -1.95250 0.00000 0.32417 3 Oplanar_1 1.97923 0.00000 1.95250 0.32417 3 Oplanar_1 1.97923 0.00000 -1.95250 0.32417 3 Oplanar_1 1.97923 0.00000 0.00000 2.38970 3 Oapical_2 2.38970 1.95250 1.95250 1.91592 1 Pb_1 3.36084 -1.95250 1.95250 1.91592 1 Pb_1 3.36084 1.95250 -1.95250 1.91592 1 Pb_1 3.36084 -1.95250 -1.95250 1.91592 1 Pb_1 3.36084 1.95250 1.95250 -2.24008 1 Pb_2 3.55563 -1.95250 1.95250 -2.24008 1 Pb_2 3.55563 1.95250 -1.95250 -2.24008 1 Pb_2 3.55563 -1.95250 -1.95250 -2.24008 1 Pb_2 3.55563 3.90500 0.00000 0.00000 2 Ti_1 3.90500 -3.90500 0.00000 0.00000 2 Ti_1 3.90500 0.00000 3.90500 0.00000 2 Ti_1 3.90500 0.00000 -3.90500 0.00000 2 Ti_1 3.90500 0.00000 0.00000 4.15600 2 Ti_2 4.15600 0.00000 0.00000 -4.15600 2 Ti_2 4.15600 3.90500 0.00000 -1.76630 3 Oapical_3 4.28589 -3.90500 0.00000 -1.76630 3 Oapical_3 4.28589 0.00000 3.90500 -1.76630 3 Oapical_3 4.28589 0.00000 -3.90500 -1.76630 3 Oapical_3 4.28589 END ========================================================================

4 3

Re: [Ifeffit] charge transfer by SCF in FEFF8 and simulation for charge disproportionation
by Ying Zou 28 Aug '08

28 Aug '08

Dear all, I am doing a SCF calculation by Feff8.40 for a model compound PbTiO3. However, the obtained charge transfer deviates far away from its well-known formal oxidation state. According to common electron negativity data, the oxidation state would be: Pb 2+ Ti 4+ O 2- The SCF run gave out charge transfer for those atoms as following: Pb 0.717 Ti 0.181 O -0.300 After I read through the existing threads on charge transfer in this list, I know that transfered charge FEFF gives out is just a portion of general formal oxidation state. Can we undderstand that this is just ionic portion for entire bonding? Such as for oxygen, "-0.300" is ionic bonding, while the rest of valency (-1.700) exists as covalent bonding, which doesn't have apparent charge transfer by definition. Another related question is then: is there any way in FEFF to take into account this "covalence" part? (maybe deriving from overlapping area of mufftin-potential?) I think this may be crucial for a self-consistent analysis of charge disproportionation. Any comments on this would be greatly appreciated. Attached please see"atom.inp" and "feff.inp". Thanks so much! Ying Ying Zou Research associate,Dr. Phys. Physics Department, UWM ***************atoms.inp*********************************** ! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = Perovskite: PbTiO3 space = p 4 m m a = 3.9050 b = 3.9050 c = 4.1560 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ti edge = K rmax = 4.2950 atoms ! elem x y z tag occ. Pb 0.00000 0.00000 0.00000 Pb 1.00000 Ti 0.50000 0.50000 0.53900 Ti 1.00000 O 0.50000 0.50000 0.11400 Oapical 1.00000 O 0.50000 0.00000 0.61700 Oplanar 1.00000 ****************************************************************** ************feff.inp*************************************** * This feff.inp file generated by ATOMS, version 2.50 * ATOMS written by and copyright (c) Bruce Ravel, 1992-1999 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 5194.4 cm^-1, delta mu = 761.6 cm^-1 * specific gravity = 7.942, cluster contains 25 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00093 ang^2 and 0.165E-05 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE Perovskite: PbTiO3 EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * r_scf [ l_scf n_scf ca ] SCF 3.88586 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 EXAFS RPATH 7.77172 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 3.88586 ******** * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 22 Ti -1 -1 0 1 8 O -1 -1 3 2 82 Pb -1 -1 1 3 22 Ti -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Ti 0.00000 0.00000 0.00000 -1.76630 1 Oapical 1.76630 1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 -1.95250 0.32417 1 Oplanar 1.97923 -1.95250 0.00000 0.32417 1 Oplanar 1.97923 0.00000 1.95250 0.32417 1 Oplanar 1.97923 0.00000 0.00000 2.38970 1 Oapical 2.38970 -1.95250 -1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 1.91592 2 Pb 3.36084 -1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 1.95250 1.91592 2 Pb 3.36084 1.95250 -1.95250 -2.24008 2 Pb 3.55563 -1.95250 1.95250 -2.24008 2 Pb 3.55563 -1.95250 -1.95250 -2.24008 2 Pb 3.55563 1.95250 1.95250 -2.24008 2 Pb 3.55563 -3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 3.90500 0.00000 3 Ti 3.90500 3.90500 0.00000 0.00000 3 Ti 3.90500 0.00000 -3.90500 0.00000 3 Ti 3.90500 0.00000 0.00000 4.15600 3 Ti 4.15600 0.00000 0.00000 -4.15600 3 Ti 4.15600 3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 -3.90500 -1.76630 1 Oapical 4.28589 -3.90500 0.00000 -1.76630 1 Oapical 4.28589 0.00000 3.90500 -1.76630 1 Oapical 4.28589 END *******************************************************************

2 1

Re: [Ifeffit] Quick question about atoms.exe and .cif files
by Bruce Ravel 26 Aug '08

26 Aug '08

On Tuesday 26 August 2008 01:44:03 you wrote: > Hi Bruce, > > I have atoms running well, but whenever I input a simple diamond > structure .cif file (like the attached silicon.cif file), I get the wrong > structure. I've tried everything that I could think of, but it doesn't > work. I'm not sure if it is something I'm doing wrong, or something > intrinsic in the .cif file. I'm currently running the command line program > with the command "atoms.exe -u -o "silicon.inf" "Silicon.cif"", with the > files being appropriately loaded. If you get the chance could you tell me > if it is an easy problem that I can quickly fix (and the solution), or if > it is something more in depth: I'd appreciate it. > > Zak I am forwarding this question to the Ifeffit mailing list. This is the sort of question for which that forum was created. Please make use of it. http://cars9.uchicago.edu/iffwiki/BruceRavel/FormLetters/HelpRequest As the warning message says, "F d -3 m" is one of those space groups in the International Tables that offers two choices for the position of the origin. There is no way to correct that from the command line, so your two options are: 1. Use Artemis to generate your unit cell file and apply the shift vector given in the warning message or 2. Edit the cif file to put the Si atom at (1/8,1/8,1/8) B -- 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/

1 0

(no subject)
by Hashem Stietiya 25 Aug '08

25 Aug '08

Dr. Calvin, I appreciate your prompt reply. I will work on your suggestions and get back to you soon. Meanwhile, can you please tell what is meant by 'A Bessel window with a smoothing parameter of 4?' I read that in a couple of publications where they indicate that is used to suppress artifacts. Is the smoothing parameter the dk? Thanks again. Regards, Hashem Stietiya Louisiana State University

2 1

asking questions effectively
by Bruce Ravel 25 Aug '08

25 Aug '08

Hi folks, When I returned from the dentist's office this afternoon, there were 2 questions on the mailing list. Both were interesting questions but neither really included enough information to definatively solve the problem. Please remember that the folks who answer questions on the maililng list can only do so effectively if you provide enough information that the problem can be reproduced on their own computers. Often, this involves attaching a small project file which demonstrates the problem to your email. B -- 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/

1 0

Background Subtraction
by Hashem Stietiya 25 Aug '08

25 Aug '08

Dear Dr. Ravel, I am trying to optimize background removal of my spectra by setting the Rbkg to half the distance of the first shell peak. However, when I import my spectra in ATHENA, I notice that the edge step is a very large number and when converting to R space there are no well defined peaks. If I click on 'fix step', the R space becomes comprehendible and peaks appear. Do I continue using the 'fix step' and then setting Rbkg to half the distance of the first shell peak? I appreciate your help. Regards, Hashem Stietiya

3 2

Re: [Ifeffit] Energy shift (???)
by Frommer Jakob 19 Aug '08

19 Aug '08

Hi eunsuk1986 (unfortunately you did not share your full name with us...) I had some trouble with reading your feff.inp. Nevertheless the problem of the absolute alignment of FEFF xmu and experimental data has been the subject of earlier questions. I' am citing form a list contribution of J. Rehr (Aug 3rd 2003): "The FEFF calculation of the absolute energy is not meant to be highly accurate, and errors of several eV for K-shells of large Z atoms are not unusal. Thus you did nothing wrong in the input file. To match FEFF and experiment you *always* have to shift the FEFF absolute threshold to match experiment.". There is no way (I am aware of) to tell FEFF do this absolute shift (you can and you often need to shift the position of the Fermi level though) but you can do this with every plot program. Thus you should not worry too much about the absolute energies in your xmu but a lot about relative energies (i.e. the positions of the single resonances). HTH Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Mon 8/18/2008 09:46 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 66, Issue 9 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. Energy shift (???) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Aug 2008 16:46:26 +0900 From: ??? <eunsuk1986(a)hotmail.com> Subject: [Ifeffit] Energy shift To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <COL101-W46347AB6CA04C793B53D5FDA6E0(a)phx.gbl> Content-Type: text/plain; charset="ks_c_5601-1987" Hi everyoneI am studying XANES at Zn K-edge in ZnO nanocrystal by using FEFF8. I wrote FEFF8 as following, and got xmu.dat. I found that there was a difference between experimental data and xmu.dat (check file) for the energy. I dont understand why the energy is shifted. I wish to adjust xmu.dat in FEFF8 to my experimental dat. If someone knows how to do, please contact me. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: zincite ZnO TITLE formula: ZnO TITLE sites: Zn1,O1 TITLE refer1: wyckoff, vol 1, ch III, p 111 TITLE refer2: TITLE schoen: TITLE notes1: EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 5.03864 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 2 0 0*EXAFS*RPATH 9.07729 * kmax [ delta_k delta_e ] XANES 4.0 ! 0.07 0.5 * r_fms [ l_fms ] FMS 5.53864 0 * *RPATH 0.10000 * emin emax resolution LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 30 Zn -1 -1 0 1 8 O -1 -1 1 2 30 Zn -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Zn1 0.00000 0.00000 0.00000 2.06302 1 O1 2.06302 -1.95951 0.00000 -0.65148 1 O1 2.06497 0.97978 -1.69700 -0.65148 1 O1 2.06500 0.97978 1.69700 -0.65148 1 O1 2.06500 0.97978 -1.69700 -2.71450 2 Zn1 3.34788 0.97978 1.69700 2.71450 2 Zn1 3.34788 0.97978 1.69700 -2.71450 2 Zn1 3.34788 0.97978 -1.69700 2.71450 2 Zn1 3.34788 _________________________________________________________________ ???? ???, ???? ?? ???? ???? ??? Windows Live Hotmail! ?? ???? ???! http://www.hotmail.com <http://www.hotmail.com/>

1 0

Energy shift
by 정은석 18 Aug '08

18 Aug '08

Hi everyoneI am studying XANES at Zn K-edge in ZnO nanocrystal by using FEFF8. I wrote FEFF8 as following, and got xmu.dat. I found that there was a difference between experimental data and xmu.dat (check file) for the energy. I dont understand why the energy is shifted. I wish to adjust xmu.dat in FEFF8 to my experimental dat. If someone knows how to do, please contact me. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: zincite ZnO TITLE formula: ZnO TITLE sites: Zn1,O1 TITLE refer1: wyckoff, vol 1, ch III, p 111 TITLE refer2: TITLE schoen: TITLE notes1: EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 5.03864 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 2 0 0*EXAFS*RPATH 9.07729 * kmax [ delta_k delta_e ] XANES 4.0 ! 0.07 0.5 * r_fms [ l_fms ] FMS 5.53864 0 * *RPATH 0.10000 * emin emax resolution LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 30 Zn -1 -1 0 1 8 O -1 -1 1 2 30 Zn -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Zn1 0.00000 0.00000 0.00000 2.06302 1 O1 2.06302 -1.95951 0.00000 -0.65148 1 O1 2.06497 0.97978 -1.69700 -0.65148 1 O1 2.06500 0.97978 1.69700 -0.65148 1 O1 2.06500 0.97978 -1.69700 -2.71450 2 Zn1 3.34788 0.97978 1.69700 2.71450 2 Zn1 3.34788 0.97978 1.69700 -2.71450 2 Zn1 3.34788 0.97978 -1.69700 2.71450 2 Zn1 3.34788 _________________________________________________________________ 강력해진 보안성, 아웃룩을 닮아 편리해진 기능들로 무장한 Windows Live Hotmail! 지금 로그인해 보세요! http://www.hotmail.com

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Artemis bug in new version
by van der Veen Renske 15 Aug '08

15 Aug '08

Hello! I just downloaded the new version of Ifeffit (1.2.11) and I am happy with it except for a small bug that wasn't present in the previous version. I am used to work with many different FEFF calculations for the same data set, all with the same fit model. I usually copy the path parameters from one calculation to all the others by using <right click> "Paths -> Export these path parameters... -> to SELECTED paths". Although a bit cumbersome for many paths and calculations, it worked fine in the previous version of Artemis. In the new version, it does exactly the opposite from what I want: it exports the path parameters to all the paths EXCEPT the ones I selected. Is there a chance to fix this, or does anybody know a more cunning way to copy the path parameters from one calculation to the others on a path-by-path basis? Thanks in advance! Renske Renske M. van der Veen PhD student EPFL / PSI Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3151 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

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