### Author Topic: Modeling Oxygen in Fanal  (Read 6054 times)

#### Probeman

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##### Modeling Oxygen in Fanal
« on: November 25, 2013, 01:45:41 PM »
Edit by John: due to a bug fix in my Fanal k-ratio extraction code (take off angle bug), you might want to jump down to this post:

http://probesoftware.com/smf/index.php?topic=119.msg1639#msg1639

where the newly output low energy data is posted. Feel free to read the older posts, but keep in mind that the current Fanal extracted k-ratios are more accurate!

Yes, one can model oxygen emission in the Calculate Penepma 2012 Fluorescence Couple Profiles, but you'll need to lower the Penepma minimum electron energy keyword in the Probewin.ini file as seen here:

In the [software] section change

PenepmaMinimumElectronEnergy="1.0"

to

PenepmaMinimumElectronEnergy="0.5"

This will change the minimum electron energy from 1 keV to 0.5 keV allowing oxygen x-rays to be modeled. For example, this is Fe metal adjacent to SiO2:

« Last Edit: September 12, 2014, 12:36:52 PM by John Donovan »
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#### Probeman

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##### Re: Modeling Oxygen in Fanal
« Reply #1 on: November 25, 2013, 02:18:20 PM »
Just for fun though, let's see what happens when we try a matrix model at these low energies. Let's model SiO2 for Si Ka and O Ka and compare them to a CalcZAF analytical model.

Using SiO2 for both our beam incident and boundary material (and Si as our primary standard to back out the matrix correction), we obtain this for Si Ka:

If we turn on the Send to Excel option we get this (among a whole lot of other numbers!):

So the two calculations are pretty close. What happens if we run the calculation with oxygen Ka? Basically the "wheels come off" at that point for the matrix correction.  Why?

Because the default PAR files that I've run, only calculate electron energies down to 1 keV, so we need to *re-calculate* our PAR files.

Stay tuned...
« Last Edit: September 12, 2014, 12:41:42 PM by John Donovan »
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#### Probeman

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##### Re: Modeling Oxygen in Fanal
« Reply #2 on: November 25, 2013, 02:49:26 PM »
So, I happen to have some PAR files that were calculated to 500 eV some time last year, but let's try them anyway.

We'll start with Mo La since that should be no problem, and again...

We see another small discrepancy between the MC model (Calc. Wt%) and one of the CalcZAF (JTA-Reed) analytical expressions (Meas. Wt%) for Mo La in MoO2.

Let's try oxygen Ka in MoO2:

Whoa, that is pretty good. In fact I'd say it's "spurious accuracy" meaning too good to be true considering that it's over 400% matrix correction!

« Last Edit: November 25, 2013, 07:32:01 PM by John Donovan »
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#### Probeman

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##### Re: Modeling Oxygen in Fanal
« Reply #3 on: November 25, 2013, 03:07:57 PM »
Just for fun, here's Mo Ka at 25 keV:

and Mo La at 25 keV:

Roughly the same difference as at 15 keV- it could be either that the Reed fluorescence correction in CalcZAF isn't quite good enough or that the fluorescence correction in Fanal is an analytical expression rather than Monte-Carlo and also not as accurate as in the full blown Penepma.

Hey, is someone willing to model Mo La and O Ka in MoO2 at 25 keV in Penepma for us?   Just run the MoO2, pure Mo and pure O (STP) material files at 25 keV in the Penepma12 "batch" window in Standard.exe and let us know what the intensities are for each material (see the pe-intens-01.dat file for each calculation). Explicit instructions for calculating k-ratios from Penepma 2012 runs are found here:

http://probesoftware.com/smf/index.php?topic=59.msg221#msg221

Or even better, does someone have some Mo and MoO2 measurements from their instrument?

What about oxygen at 25 keV?

Ok, so now we see that nasty absorption correction starting to kick in. Matrix correction here was 7.75 for Fanal and 9.0 for CalcZAF, but who is to say who is right?

For comparison I calculated O Ka in MoO2 using CalcZAF PAP and get 7.48 for the oxygen matrix correction at 25 keV, so maybe Penepma is doing great for absorption!

Edit by John: see below for an improved calculation of oxygen in MoO2 at 25 keV.
« Last Edit: September 12, 2014, 12:58:18 PM by John Donovan »
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#### Probeman

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##### Re: Modeling Oxygen in Fanal
« Reply #4 on: November 26, 2013, 12:19:50 PM »
As promised I ran some Penepma/Penfluor Monte-Carlo simulations overnight, using the PenepmaMinimumElectronEnergy keyword in the probewin.ini file set to 0.5 keV as described above in order to model oxygen emissions, and here are the results for Al2O3 matrix corrections for Al Ka and O Ka:

First Al Ka at 15 keV using the CalcZAF JTA-Reed analytical matrix correction (Meas. Wt%):

Now the same but using the CalcZAF XPP-Reed analytical matrix correction:

XPP definitely agrees better with the Penepma MC!

Now for O Ka, again first with JTA-Reed CalcZAF for the "Meas. Wt%":

Reasonable agreement for a 500 eV emission line (though remember we are *not* considering any chemical bonding effects with either model) and you will have difficulty seeing the difference for CalcZAF XPP seen here:

What we are probably seeing here are the limits to our knowledge of the photo-elastic absorption physics (scattering factors for Penepma and MACs for CalcZAF).

However, just for fun I loaded in an empirical Mass Absorption Coefficient (MAC) value from Bastin (1992) for O Ka in Al (6720) into CalcZAF (see Analytical | Empirical MACs menu) and the ZAF correction factor changed from 1.876 to 1.875, so maybe not!

Should we try O Ka in TiO2?
« Last Edit: April 19, 2015, 07:26:43 PM by John Donovan »
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#### Probeman

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##### Re: Modeling Oxygen in Fanal
« Reply #5 on: November 26, 2013, 03:16:06 PM »
Let's do this!

I'm going to try both the JTA and XPP analytical models in CalcZAF for O Ka in TiO2 and also apply Bastin's empirical MAC for O Ka in Ti which is 19900. Let's see how these compare to Penepma/Penfluor Monte-Carlo models.

Here is O Ka in TiO2 using CalcZAF's JTA analytical model (and Reed fluorescence):

Here is the same but using CalcZAF's XPP analytical model (and Reed fluorescence):

Now let's apply an empirically determined MAC from Bastin (1992):

Looks pretty good. Now let's try the same empirical MAC but with CalcZAF's JTA-Reed analytical model:

Not bad for an over 500% correction...
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#### John Donovan

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##### Re: Modeling Oxygen in Fanal
« Reply #6 on: November 27, 2013, 11:18:07 PM »

now contains a number of PAR files calculated down 500 eV in the "Penfluor\500 eV" folder.

The latest CalcZAF.msi installer/updater, also contains this Penepma12.Zip, but it will not automatically update the Penepma12 files for you... hmm, something I should add to the "to do list"!

In the meantime, just extract the Penepma12.zip file (it will be in the CalcZAF app folder) to your "User Data"\Penepma12 folder manually and click Yes To All to overwrite all files- it won't overwrite any of your own calculations!
john
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#### John Donovan

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##### Re: Modeling Oxygen in Fanal
« Reply #7 on: September 12, 2014, 11:11:10 AM »
To get a complete set of the available .PAR files that have been run below 1 keV, see this link here:

john
John J. Donovan, Pres.
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#### John Donovan

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##### Re: Modeling Oxygen in Fanal
« Reply #8 on: September 12, 2014, 11:38:19 AM »
Due to a bug fix (takeoff angle) in the Fanal extraction code, I will be re-calculating and re-posting the above low energy Penfluor/Fanal calculations. Fortunately this take off angle bug *does not* affect the already calculated PAR files!

So, here is the oxygen in TiO2 fanal extraction re-calculated down to 500 eV:

And here is oxygen Ka in SiO2 with the new Fanal extraction code:

And here is oxygen in Al2O3:

« Last Edit: September 12, 2014, 12:45:48 PM by John Donovan »
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#### John Donovan

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##### Re: Modeling Oxygen in Fanal
« Reply #9 on: September 12, 2014, 12:54:37 PM »
And here are the oxygen k-ratios in MoO2 at 25 keV, a rather large matrix correction around 800-900%!

and the Excel spreadsheet generated (note that the new Fanal couple extractions now incloude the takeoff angle in the folder name:

File attached below.
John J. Donovan, Pres.
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"Not Absolutely Certain, Yet Reliable"