Re: [Ifeffit] how to built ATOM to obtian FEFF by using DFT model?
Hi everyone! can u please help me? I was so glad that Prof. J F W Mosselmans gave me advice about EXAFS analysis of complex solution system in last time. Here i have an another question about how to bulit ATOM to obtain FEFF by using DFT model. When getting a reasonable zinc complex model caculated by Density Functional Theory, i wish use it to clarify the experimental EXAFS data. But i don't know how to bulit ATOM file using this model. Except for the coordinates in the DFT output file, i don't know how to get the other structure information including space, cell parameter etc. ********************************* title=name space=? a=? b=? c=? alpha=? beta=? gamma=? ( How to get these data? ) rmax = 8.0 core = Zn1 atom Zn 0 -0.25 -0.125 Zn1 1 (I can get the atom coordinates from the DFT output file) ....... ******************************* Is there any other methods to create the corresponding ATOM file? Thank you very much. winejar 2012-03-09 发件人： Takahide Yamaguchi 发送时间： 2012-03-08 16:00:36 收件人： ifeffit 抄送： 主题： [Ifeffit] what is the reasonable arc-tan for edge jump Dear all, I was so glad that Bruce and Zajac gave me advice about MS path treatment in last time. Thank you very much. Now, I am working on analysis of Cu K edge by using EDG_FIT, following previous papers. I am wondering if someone gave me comment about current problem for me. And my question about XANES analysis is "what the reasonable arc-tan is as a back ground of XANES." In previous some papers, Cu K edge were deconvoluted by assuming arc-tan edge jump function. But I couldn't found the reasonable mention for the shape of arc-tan. For example of Cu(II), one paper (1), which has interest in the metalloproteins active site, the arc-tan were positioned around 8992 eV with 5 eV hwhm approximatly. But in another paper (2), which reported about high valence Cu(III), the arc-tan for Cu(II) complex looks having narrow hwhm at higher positons (around at 8984 eV). (1) J. Phys. Chem. B 2000, 104,10814-10819 (2) JACS 2000, 122, 5775-5787 Are there any reason which can explain these difference? I hope any comment and advice. Takahide
Hello, If you have done a DFT calculation, you can take the atom coordinates from the calculation and just put them directly into a Feff input file. No need to use atoms. If you are not sure how to build a feff input file, you can run a dummy atoms file with Zn to get a rough template and work with the Feff users manual to determine how to set the parameters. Jeff On Mar 8, 2012, at 11:13 PM, winejar8324 wrote:
Hi everyone! can u please help me?
I was so glad that Prof. J F W Mosselmans gave me advice about EXAFS analysis of complex solution system in last time.
Here i have an another question about how to bulit ATOM to obtain FEFF by using DFT model.
When getting a reasonable zinc complex model caculated by Density Functional Theory, i wish use it to clarify the experimental EXAFS data. But i don't know how to bulit ATOM file using this model. Except for the coordinates in the DFT output file, i don't know how to get the other structure information including space, cell parameter etc.
********************************* title=name space=? a=? b=? c=? alpha=? beta=? gamma=? ( How to get these data? ) rmax = 8.0 core = Zn1 atom Zn 0 -0.25 -0.125 Zn1 1 (I can get the atom coordinates from the DFT output file) .......
*******************************
Is there any other methods to create the corresponding ATOM file?
Thank you very much. winejar
2012-03-09 发件人： Takahide Yamaguchi 发送时间： 2012-03-08 16:00:36 收件人： ifeffit 抄送： 主题： [Ifeffit] what is the reasonable arc-tan for edge jump Dear all,
I was so glad that Bruce and Zajac gave me advice about MS path treatment in last time. Thank you very much.
Now, I am working on analysis of Cu K edge by using EDG_FIT, following previous papers. I am wondering if someone gave me comment about current problem for me. And my question about XANES analysis is "what the reasonable arc-tan is as a back ground of XANES."
In previous some papers, Cu K edge were deconvoluted by assuming arc-tan edge jump function. But I couldn't found the reasonable mention for the shape of arc-tan.
For example of Cu(II), one paper (1), which has interest in the metalloproteins active site, the arc-tan were positioned around 8992 eV with 5 eV hwhm approximatly. But in another paper (2), which reported about high valence Cu(III), the arc-tan for Cu(II) complex looks having narrow hwhm at higher positons (around at 8984 eV).
(1) J. Phys. Chem. B 2000, 104,10814-10819 (2) JACS 2000, 122, 5775-5787
Are there any reason which can explain these difference?
I hope any comment and advice.
Takahide _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hello, everyone Here I got the spectra of components in a mixture with linear combination fitting. Can i fit directly the component spectra (i.e. chi(k) of specific species) using Artemis to get the structure information of the specific component? I saw the manual (linear combination fitting) says that "The data group containing the fit result will be treated as normal data that can have a background removed or be Fourier transformed. When you save a fit using the derivative spectra, the fit group will be saved as a normal μ(E) spectrum". Does it mean that i can fit directly the data mentioned above? Thank you. winejar
Hi Winejar,
On Sat, Mar 10, 2012 at 9:05 AM, winejar8324
Hello, everyone
Here I got the spectra of components in a mixture with linear combination fitting.
Can i fit directly the component spectra (i.e. chi(k) of specific species) using Artemis to get the structure information of the specific component?
Yes. It may not be easy to do, as the chi(k) spectra is, well, a linear combination of two distinct chi(k) from two distinct phases. In general, that would require modeling the two components with different Feff calculations, combining the paths from those into two separate chi(k), and adding these together, weighted by the fraction of each phase. It *can* be done, and has been done many times, but it may not be easy in all cases.
I saw the manual (linear combination fitting) says that "The data group containing the fit result will be treated as normal data that can have a background removed or be Fourier transformed. When you save a fit using the derivative spectra, the fit group will be saved as a normal mu(E) spectrum".
Does it mean that i can fit directly the data mentioned above?
Yes. You can analyze the individual extracted components. --Matt
participants (3)
-
Jeff Terry -
Matt Newville -
winejar8324