Question on GDS values: amp
Dear All, Just wondering what could I do to make the amp guess value as a positive number? If I run it and let it float (i.e. guess), the amp becomes negative in the resulting fits, but the fit has nice delr and ss values (i.e. make sense). If I restrict the amp value to 1, everything else doesn't fit. I am only fitting the first nearest neighbour in a measured standard; Gadolinium oxide. Regards, Nic Nicholas Tse Postgraduate Student, University of Melbourne CSIRO Materials Science and Engineering. Phone: +61 3 9545 2626 | Mobile: 0403 782 805 nicholas.tse@csiro.aumailto:nicholas.tse@csiro.au | www.csiro.auhttp://www.csiro.au | www.csiro.au/cmsehttp://www.csiro.au/cmht Address: Ian Wark Laboratories, Bayview Ave Clayton 3169 VIC [Postal: Private Bag 10, Clayton South VIC 3169] [Deliveries: Gate 3 Normanby Road, Clayton VIC 3168] Please consider the environment before printing this email.
Dear Nic, this sounds like your fit is shifted to the experimental chi(k) by half an oscillation period. Typically, you can recognize this by looking at the enot value. So what is your enot value like? Does it help changing the enot starting value by a couple of eV? Finally, (and this is a FAQ item) could you maybe post a sample Artemis project so that we can easily see what has happened? Regards, Dominik On 01.08.2011 06:36, Nicholas.Tse@csiro.au wrote:
Dear All,
Just wondering what could I do to make the amp guess value as a positive number? If I run it and let it float (i.e. guess), the amp becomes negative in the resulting fits, but the fit has nice delr and ss values (i.e. make sense). If I restrict the amp value to 1, everything else doesn’t fit. I am only fitting the first nearest neighbour in a measured standard; Gadolinium oxide.
Regards,
Nic
**
*Nicholas Tse* Postgraduate Student, University of Melbourne CSIRO Materials Science and Engineering.
Phone: +61 3 9545 2626 *| *Mobile: 0403 782 805 nicholas.tse@csiro.au mailto:nicholas.tse@csiro.au | www.csiro.au http://www.csiro.au | www.csiro.au/cmse http://www.csiro.au/cmht Address: Ian Wark Laboratories, Bayview Ave Clayton 3169 VIC [Postal: Private Bag 10, Clayton South VIC 3169] [Deliveries: Gate 3 Normanby Road, Clayton VIC 3168]
*Please consider the environment before printing this email.*
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-- Dr. Dominik Samuelis d.samuelis@fkf.mpg.de Max-Planck-Institut für Festkörperforschung Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/
On Monday, August 01, 2011 12:36:19 am Nicholas.Tse@csiro.au wrote:
Just wondering what could I do to make the amp guess value as a positive number? If I run it and let it float (i.e. guess), the amp becomes negative in the resulting fits, but the fit has nice delr and ss values (i.e. make sense). If I restrict the amp value to 1, everything else doesn't fit. I am only fitting the first nearest neighbour in a measured standard; Gadolinium oxide.
Are you sure that you ran the Feff calculation with the correct edge? You will find that the K edge and L3 edge calculations are roughly 180 degrees out of phase. That mistake (one I make annoyingly regularly) could account for a negative amplitude. B -- Bruce Ravel ------------------------------------ bravel@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/
Thank you all the suggestions. I believe the ATOM model used is representative of what it should be. I generated the FEFF file from the CIF file from the American Mineralogist X'stal DB. The generated FEFF has the edge L3 that should be fine. A simple summation of the scatter paths does roughly produce the pattern for the sample, except for the amplitudes. The enot was found to be 53.8995 +/- 2.7632. I have also included the .prj and .apj files for your inspection. Regards, Nic
Dear Nic, I've had a short look into your Artemis file. First of all, it seems that something's wrong with the Gd2O3 structure data in your feff.inp. Running feff on your feff.inp gives this error: Feff 8.40 ... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 8 14 8 2.24848E+00 2.70250E+00 0.00000E+00 14 2.47549E+00 2.70250E+00 0.00000E+00 Run continues in case you really meant it. WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 9 15 9 -2.24848E+00 -2.70250E+00 0.00000E+00 15 -2.47549E+00 -2.70250E+00 0.00000E+00 Run continues in case you really meant it. [...] It seems that all your "Gd2" atoms have a duplicate in your "Gd3" atoms, shifted only by ~0.2 angstroms in either x,y, or z direction. Looking further at your feff.inp, already your ATOMS input somehow looks broken: (your ATOMS list) * Gd 0.25000 0.25000 0.25000 Gd1 1.00000 * Gd 0.02100 0.00000 0.25000 Gd2 1.00000 * Gd 0.54200 0.00000 0.25000 Gd3 1.00000 * O 0.12500 0.12500 0.37500 O1 1.00000 * O 0.12500 0.37500 0.37500 O2 (my list, cif file from ICSD, Shuenn et al., J. Chin. Chem. Soc. 57 (2010), 938) Gd 0.25 0.25 0.25 Gd1 1.000 * (8b position) O 0.3904 0.1513 0.379 O1 1.000 * (48e position) Gd 0.9710 0 0.25 Gd2 1.000 * (24d position) Using this crystal data, I was able to fit your data reasonably well (didn't tweak to make the fit perfect though...) - see attached file! I've also attached the .cif file that I've used, in case you want to compare with yours. BTW, enot values of >20 eV shouldn't really happen in any fit. Best regards, Dominik On 02.08.2011 04:42, Nicholas.Tse@csiro.au wrote:
Thank you all the suggestions.
I believe the ATOM model used is representative of what it should be. I generated the FEFF file from the CIF file from the American Mineralogist X'stal DB. The generated FEFF has the edge L3 that should be fine. A simple summation of the scatter paths does roughly produce the pattern for the sample, except for the amplitudes.
The enot was found to be 53.8995 +/- 2.7632.
I have also included the .prj and .apj files for your inspection.
Regards,
Nic
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-- Dr. Dominik Samuelis d.samuelis@fkf.mpg.de Max-Planck-Institut für Festkörperforschung Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/
Thank you Dominik, I have had a play around with the data and this model is definitely the better model. Just a sidenote, is the general workflow for fitting XAFS data the following: Fit first shell and get reasonable Enot and Amp and then make set them, then incrementally add more of the scatter paths and adjust the delR for each path correspondingly. Adjusting degeneracy for atom assuming there are slight differences in the atoms spacing. I know the question is very trivial but I don't seem to be able to find a general guideline for knowing when the fitting process is over in these type of analysis. Many thanks, Nic -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Dominik Samuelis Sent: Tuesday, 2 August 2011 7:15 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Question on GDS values: amp Dear Nic, I've had a short look into your Artemis file. First of all, it seems that something's wrong with the Gd2O3 structure data in your feff.inp. Running feff on your feff.inp gives this error: Feff 8.40 ... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 8 14 8 2.24848E+00 2.70250E+00 0.00000E+00 14 2.47549E+00 2.70250E+00 0.00000E+00 Run continues in case you really meant it. WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 9 15 9 -2.24848E+00 -2.70250E+00 0.00000E+00 15 -2.47549E+00 -2.70250E+00 0.00000E+00 Run continues in case you really meant it. [...] It seems that all your "Gd2" atoms have a duplicate in your "Gd3" atoms, shifted only by ~0.2 angstroms in either x,y, or z direction. Looking further at your feff.inp, already your ATOMS input somehow looks broken: (your ATOMS list) * Gd 0.25000 0.25000 0.25000 Gd1 1.00000 * Gd 0.02100 0.00000 0.25000 Gd2 1.00000 * Gd 0.54200 0.00000 0.25000 Gd3 1.00000 * O 0.12500 0.12500 0.37500 O1 1.00000 * O 0.12500 0.37500 0.37500 O2 (my list, cif file from ICSD, Shuenn et al., J. Chin. Chem. Soc. 57 (2010), 938) Gd 0.25 0.25 0.25 Gd1 1.000 * (8b position) O 0.3904 0.1513 0.379 O1 1.000 * (48e position) Gd 0.9710 0 0.25 Gd2 1.000 * (24d position) Using this crystal data, I was able to fit your data reasonably well (didn't tweak to make the fit perfect though...) - see attached file! I've also attached the .cif file that I've used, in case you want to compare with yours. BTW, enot values of >20 eV shouldn't really happen in any fit. Best regards, Dominik On 02.08.2011 04:42, Nicholas.Tse@csiro.au wrote:
Thank you all the suggestions.
I believe the ATOM model used is representative of what it should be. I generated the FEFF file from the CIF file from the American Mineralogist X'stal DB. The generated FEFF has the edge L3 that should be fine. A simple summation of the scatter paths does roughly produce the pattern for the sample, except for the amplitudes.
The enot was found to be 53.8995 +/- 2.7632.
I have also included the .prj and .apj files for your inspection.
Regards,
Nic
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-- Dr. Dominik Samuelis d.samuelis@fkf.mpg.de Max-Planck-Institut für Festkörperforschung Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/
participants (3)
-
Bruce Ravel -
Dominik Samuelis -
Nicholas.Tse＠csiro.au