Re: [Ifeffit] How do I create a histogram based on R-space values
Deepak, On Wed, Dec 9, 2020 at 9:27 PM Deepak Varanasi wrote: > 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] How do I create a histogram based on R-space values
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 on behalf of Deepak Varanasi Sent: Thursday, December 10, 2020 8:56:55 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] How do I create a histogram based on R-space values 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 mailto:ragor...@alumni.sfu.ca>> wrote: 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 list Ifeffit@millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] How do I create a histogram based on R-space values
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 wrote: > 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 > listifef...@millenia.cars.aps.anl.govhttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] How do I create a histogram based on R-space values
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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] How do I create a histogram based on R-space values
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 wrote: > 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 > listifef...@millenia.cars.aps.anl.govhttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] 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 . ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] How do I create a histogram based on R-space values
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 SincerelyDeepak Varanasi P.S.: I have appended an example file of an R-space reading to demonstrate what I mean . Fe (R-space).dat Description: Binary data Mn - 2 (R-Space).dat Description: Binary data ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
