How do I create a histogram based on R-space values
When i look at the files you included, I see R-value in the first column, then what I am assuming are the (magnitude of) Fourier transforms of different data sets selected for export, with vertical displacements of 10 or 25 between each data set. A histogram plot would involve extracting N and R values (and mean-square-relative-displacements and Eo-shift). So, some questions: Do these individual datasets comprise multiple scans for one sample? If so, do you plan on merging this data (typically, I do this before removing background and extracting chi(k))? else if they represent data that is to be kept separate (not to be merged)... Have you fit this data to get N and R (and...)? If you have a standard (e.g. only 1 target element), where you know N and R, and what a histogram plot of N vs R would be, have you tried examining that first to get a feel for what you need to do with your unknowns? On 2020-12-09 10:38 a.m., Deepak Varanasi wrote:
Good afternoon
I hope that everyone is safe and healthy.
I am trying to create a histogram of Number of atoms vs. the radial distance between the central atoms and their neighbours (in Angstroms). I have the R-space data for 3 of my “central atoms” but I do not know how to create a histogram using them as each of them has 8 columns of data and I do not know which one(s) to use.
Hence, may I ask for your guidance please?
Yours Sincerely
Deepak Varanasi
P.S.: I have appended an example file of an R-space reading to demonstrate what I mean .
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Good afternoon
Yes. The files I sent in my email belong to ones with multiple scans of the
same sample.
Moreover, this is my first time creating a histogram with such kind of data
and therefore, have no clue what to do or expect.
I honestly do not even know how to approach it and you all are my final
hope. Kindly guide me through the process, please.
Yours sincerely
Deepak Varanasi
On Wed, Dec 9, 2020, 13:21 Robert Gordon
When i look at the files you included, I see R-value in the first column, then what I am assuming are the (magnitude of) Fourier transforms of different data sets selected for export, with vertical displacements of 10 or 25 between each data set.
A histogram plot would involve extracting N and R values (and mean-square-relative-displacements and Eo-shift).
So, some questions: Do these individual datasets comprise multiple scans for one sample? If so, do you plan on merging this data (typically, I do this before removing background and extracting chi(k))?
else if they represent data that is to be kept separate (not to be merged)...
Have you fit this data to get N and R (and...)?
If you have a standard (e.g. only 1 target element), where you know N and R, and what a histogram plot of N vs R would be, have you tried examining that first to get a feel for what you need to do with your unknowns?
On 2020-12-09 10:38 a.m., Deepak Varanasi wrote:
Good afternoon
I hope that everyone is safe and healthy.
I am trying to create a histogram of Number of atoms vs. the radial distance between the central atoms and their neighbours (in Angstroms). I have the R-space data for 3 of my “central atoms” but I do not know how to create a histogram using them as each of them has 8 columns of data and I do not know which one(s) to use.
Hence, may I ask for your guidance please?
Yours Sincerely
Deepak Varanasi
P.S.: I have appended an example file of an R-space reading to demonstrate what I mean .
_______________________________________________ Ifeffit mailing listIfeffit@millenia.cars.aps.anl.govhttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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Deepak, The data files you sent appear to be plots of XAFS |chi(R)|, including offsets for the plotting. That is certainly a reasonable visualization to make for EXAFS data and Demeter can make those easily. But |chi(R)| is not a histogram of the number of atoms as a function of distance. That is sort of all of "EXAFS analysis" and unfortunately there is not a simple transform that converts |chi(R)| into g(R). I recommend looking at some of the on-line resources and books and review articles on EXAFS. Cheers, --Matt
Good evening
May I also know how to calculate the necessary ingredients in building a
histogram such as R and N?
I suppose R is just the R-space stuff so how do I calculate N? Is it simply
the number of peaks in my R-space graph or something else entirely?
I need to be able to construct the histogram to finish my thesis and
graduate but I am still stuck on it. Hence, may I request your guidance on
this please?
Yours sincerely
Deepak Varanasi
On Wed, Dec 9, 2020, 13:21 Robert Gordon
When i look at the files you included, I see R-value in the first column, then what I am assuming are the (magnitude of) Fourier transforms of different data sets selected for export, with vertical displacements of 10 or 25 between each data set.
A histogram plot would involve extracting N and R values (and mean-square-relative-displacements and Eo-shift).
So, some questions: Do these individual datasets comprise multiple scans for one sample? If so, do you plan on merging this data (typically, I do this before removing background and extracting chi(k))?
else if they represent data that is to be kept separate (not to be merged)...
Have you fit this data to get N and R (and...)?
If you have a standard (e.g. only 1 target element), where you know N and R, and what a histogram plot of N vs R would be, have you tried examining that first to get a feel for what you need to do with your unknowns?
On 2020-12-09 10:38 a.m., Deepak Varanasi wrote:
Good afternoon
I hope that everyone is safe and healthy.
I am trying to create a histogram of Number of atoms vs. the radial distance between the central atoms and their neighbours (in Angstroms). I have the R-space data for 3 of my “central atoms” but I do not know how to create a histogram using them as each of them has 8 columns of data and I do not know which one(s) to use.
Hence, may I ask for your guidance please?
Yours Sincerely
Deepak Varanasi
P.S.: I have appended an example file of an R-space reading to demonstrate what I mean .
_______________________________________________ Ifeffit mailing listIfeffit@millenia.cars.aps.anl.govhttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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Dear Deepak,
First add your affiliation in your email signature. It is the right thing to do. Next, ....
What do you mean by histogram?
What do you want to plot?
in other words....
What do you want on the x-axis and what's on the y-axis?
Mahendra
============================
Dr. Uma Mahendra Kumar
Asst Professor of Physics
School of Advanced Sciences
VIT University-Vellore 632 014
Bharat
VIT-Recognized as an Institution of Eminence (IoE),
________________________________
From: Ifeffit
Deepak,
On Wed, Dec 9, 2020 at 9:27 PM Deepak Varanasi
Good evening
May I also know how to calculate the necessary ingredients in building a histogram such as R and N?
The analysis of EXAFS to extract structural parameters is slightly complex. There is quite a bit of literature on how to do this. I may suggest looking at the books listed at https://xafs.xrayabsorption.org/tutorials.html, especially the two by Grant Bunker and Scott Calvin. I suppose R is just the R-space stuff so how do I calculate N?
Hm, well actually it kind of isn't.
Is it simply the number of peaks in my R-space graph or something else entirely?
No, it is not simply the number of peaks in the plot of |chi(R)|. The positions and intensities of those peaks do depend on the distribution of distances, g(R), but also depend in non-trivial ways on scattering factors of the photo-electron created in the absorption process.
I need to be able to construct the histogram to finish my thesis and graduate but I am still stuck on it. Hence, may I request your guidance on this please?
EXAFS data is not simply "converted" to a histogram of distances, g(R). EXAFS does depend on g(R) and an analysis of the EXAFS signals can provide information about the local structure. I hope that helps, but it appears you are confusing |chi(R)| (the magnitude of the Fourier transform of the EXAFS oscillations) with g(R). They are related, but that relationship is not simple enough to allow a simple conversion from |chi(R)| to g(R). --Matt
participants (4)
-
Deepak Varanasi -
Matt Newville -
Robert Gordon -
Uma Mahendra Kumar K