Author Topic: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics  (Read 22966 times)

Probeman

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Chad Parish asks:

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I've recently found a very nice parameterization of K-shell electron-impact ionization cross-sections (Talukder et al., Int. J. Mass Spec., V269 (2008) P. 118 and V309 (2012) P. 212) which are very convenient to code into the computer.

I'm not finding similar good (or even fair) parameterizations for L or M-shells. Can anyone recommend good references from which to write code for X-ray cross-sections?

Xavier Llovet responds:

Quote
...might be interest in the attached paper. The complete cross section database will be available from NIST very soon (I'll let you know when). If he's interested in an analytical paramaterization, then Fortran subroutines are available from the on-line version of Ref.[31] (Bote et al. ATNDT 95, 871-909, 2009). As easy as it gets.

http://scitation.aip.org/content/aip/journal/jpcrd/43/1/10.1063/1.4832851
« Last Edit: March 11, 2014, 06:58:07 pm by John Donovan »
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Probeman

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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #1 on: March 10, 2014, 12:21:53 pm »
Chad,
For modeling thin films in for TEM at 80 to 300 keV you'll want to check this topic also:

http://probesoftware.com/smf/index.php?topic=57.0

To extract the k-ratios from the Penepma calculations I suggest using the "Batch Mode" dialog  as seen here:



and have all your calculations saved automatically as seen here (for a slightly different example):



Finally, to *manually* extract your intensities to create k-ratios, see this post here:

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

The above link is best for understanding the gritty details, but the next post describes a new feature which allows one to simply specify the element, x-ray, a folder containing the standard intensity and the folder containing the unknown samples (a separate sub folder for each Penepma batch run).

Easy!
« Last Edit: July 16, 2014, 11:44:07 am by Probeman »
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #2 on: July 16, 2014, 12:45:17 pm »
Here I describe a new feature which allows the user to simply specify a few parameters and the program will automatically extract k-ratios from multiple Penepma batch runs...

Starting from the Penepma Batch Mode window as seen here:



specify the element and x-ray to extract k-ratios for and click the Extract K-Ratios button.  The program will then ask for two folders, the first for the folder containing the (usually bulk geometry) standard intensity calculation from Penepma for that element as seen here:



Note that the current standard intensity folder containing the pe-intens-01.dat file is empty (indicated by the two closed parentheses), and the program first starts in the C:\UserData\Penepma12\Batch folder to begin with. Therefore the user must browse to the actual folder containing the standard intensity file as seen here:



Next the program will ask for the folder containing the unknown samples, and again it will start in the C:\UserData\Penepma12\Batch folder to begin with, so again, the user must browse to the actual folder containing the unknown intensities as seen here:



After specifying the unknown intensity folder (which contains sub folders created by the Penepma batch mode), the program will automatically output the calculated k-ratios for all samples to a tab delimited text file which can be edited further as necessary. An example of the output is shown here and attached below:



Note that if the user clicks the Extract K-ratios button a second time, the application will start at the last folder specified as seen here:

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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #3 on: July 23, 2014, 11:51:13 am »
A new method for Penepma compositional input has been added as seen here:



Using this method one can specify a "weight percent string" such as Fe1Ni99 to get 1 wt.% Fe and 99 wt.% Ni in a composition as seen here:



To differentiate this compositional name from a "formula string" such as Mg2SiO4, the program will automatically append the string "_atom" to formula composition names and the string "_weight" for weight percent string names as seen here:



I should also mention that I have a number of pure elements calculated by Penepma at 10, 15 and 20 keV for use as standards for k-ratio calculations if anyone needs them.
« Last Edit: July 23, 2014, 03:26:13 pm by Probeman »
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #4 on: July 25, 2014, 11:03:40 am »
As mentioned previously I have calculated a number of pure bulk element intensities at 10, 15 and 20 keV for use as standard intensities for typical Penepma k-ratio calculations. The current version of this ZIP file is here:

http://probesoftware.com/download/BulkPureElements.ZIP

It can be extracted to the Penepma folder (usually C:\UserData\Penepma12\Penepma), for example "C:\UserData\Penepma12\Penepma\BulkPureElements" and utilized in the above Extract K-Ratios button in the Penepma Batch Mode window.

Let me know if there are other pure elements we should pre-calculate and have available to save time...
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Probeman

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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #5 on: July 29, 2014, 02:02:17 pm »
A complete set of binary alpha factors is still being calculated, but the PAR files for the specific compositions in the POUCHOU2.DAT data set are complete and I thought I would show where we are so far...

Using the default JTA/Reed phi-rho-z as a starting point we get the following reasonable results:



Now using the Penfluor PAR files calculated for the specific compositions in the Pouchou data set, we obtain this result which includes a complete fluorescence correction with continuum:



Now, running the same calculation using the currently available binary PAR files and fitting them as a hyperbolic relationship we obtain this result:



Again, this is still using some phi-rho-z for the remaining uncalculated binaries, but it is showing promise!
« Last Edit: July 29, 2014, 08:46:41 pm by Probeman »
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #6 on: September 16, 2014, 11:53:48 am »
Sheri Singerling at UNM has created an excellent document on how to run Penepma to obtain k-ratios to compare with experimental measurements and this can be downloaded here:

http://probesoftware.com/smf/index.php?topic=322.msg1641#msg1641

Note that although Sheri is absolutely correct on how to locate the appropriate x-ray intensities for producing your k-ratios, there is now an automated method if you would prefer which is described here:

http://probesoftware.com/smf/index.php?topic=202.msg1506#msg1506
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #7 on: September 24, 2014, 12:45:12 pm »
As mentioned previously I have calculated a number of pure bulk element intensities at 10, 15 and 20 keV for use as standard intensities for typical Penepma k-ratio calculations. The current version of this ZIP file is here:

http://probesoftware.com/download/BulkPureElements.ZIP

It can be extracted to the Penepma folder (usually C:\UserData\Penepma12\Penepma), for example "C:\UserData\Penepma12\Penepma\BulkPureElements" and utilized in the above Extract K-Ratios button in the Penepma Batch Mode window.

Let me know if there are other pure elements we should pre-calculate and have available to save time...

I have updated the BulkPureElements ZIP file with many more pure element calculations (now 75 MB) for use in extracting k-ratios from Penepma calculations as described here:

http://probesoftware.com/smf/index.php?topic=202.msg1506#msg1506

Download the update ZIP file here:

http://probesoftware.com/download/BulkPureElements.ZIP
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #8 on: October 13, 2014, 05:54:26 pm »
I've updated the Bulk Pure Element ZIP file for Penepma. There are now 98 MB of pure elements calculated (at 40 degrees takeoff) and for 10, 15 and 20 keV.

These files can be utilized to automatically load intensities for "standards" for k-ratio extractions in Standard.exe. Download from here:

http://probesoftware.com/download/BulkPureElements.ZIP

Edit by John: Updated again Oct 28 2014 and now containing 102 MB of compressed Penepma pure element simulations for quant.
« Last Edit: October 28, 2014, 03:18:42 pm by John Donovan »
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #9 on: November 19, 2014, 01:55:50 pm »
I've been recalculating a large number of light element binaries (to include MC modeling down to the lowest energy edge emitter) and pure elements (at twice the precision as previously, i.e., 7200 sec per beam energy versus 3600 sec per beam energy) and the results look very encouraging.

As an example of "spurious accuracy" (that is, too good to be true, but happens to be the case) I tested the N-Cr binary (seriously, it was the first one I tested!), and the results calculated using the 1% N 99% Cr in Standard.exe are seen here:



Looks pretty good for such as large matrix correction (compare the k-ratio% to the wt%), but zooming in further reveals the "spurious accuracy" mentioned previously:



Edit by John: Note that Xavier Llovet and Cesc Salvat are fixing a bug in Penepma/Penfluor for calculation of B Ka intensities, so stay away from boron as an emitter until the new version is released.
« Last Edit: November 30, 2014, 12:06:25 pm by Probeman »
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #10 on: December 11, 2014, 11:51:45 am »
Again, remember that you should avoid modeling B Ka until the Penepma bug is fixed by Salvat and Llovet, but in the meantime you can easily model other low energy lines such as Cu La by following the instructions here:

http://probesoftware.com/smf/index.php?topic=47.msg2098#msg2098
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #11 on: December 19, 2014, 04:52:55 pm »
Xavier Llovet reports the following on the B ka issue in Penepma/Penfluor:

Quote
Just to let you know that actually you didn't find a bug in the program. The problem comes from the database that PENELOPE uses for X-rays (EADL from Lawrence Livermore lab) that starts at Z=6, i.e. for Carbon!!

This database contains the radiative and non-radiative probabilities for all possible electron transitions so we're now trying to find these data for B, Be and Li.

I'll keep you posted.
« Last Edit: December 20, 2014, 10:54:54 am by John Donovan »
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #12 on: June 24, 2015, 12:34:33 pm »
Here's something to think about.

Here are two plots of the k-ratio (%) for Cr ka in N for both 99% Cr and 1% Cr. Interesting in the 99% plot how much difference there is between the Penfluor/Fanal Monte-Carlo output and the CalcZAF analytical expressions. See the graph attachments (you need to log in to see attachments!).

I don't think the large difference at low overvoltages is due to precision issues as the curve is very smooth.  By the way, the standard (pure Cr) was calculated at 14400 sec per beam energy. Yes, 40 hours!
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #13 on: September 05, 2015, 03:07:38 pm »
I've calculated pure elements from V to Cu down to 500 eV (40 hours each simulation time) in the latest penepma12.zip file:

http://probesoftware.com/download/PENEPMA12.ZIP

These PAR files will be useful as standards for those that want to model L lines for these transition elements.
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« Last Edit: September 06, 2015, 12:51:32 pm by Probeman »
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Re: Penelope/Penepma/Penfluor/Fanal Monte-Carlo Software and Physics
« Reply #14 on: May 19, 2016, 05:38:44 am »
In case anyone is interested, I've attached a pdf of the Penepma/Penfluor tutorial presentation I gave at the EPMA 2016 topical conference this week in Madison (remember, you have to be logged in to see attachments).

The CalcZAF and Standard apps can be downloaded here:

http://www.probesoftware.com/download/CalcZAF.msi
« Last Edit: May 26, 2016, 06:50:49 pm by John Donovan »
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