Author Topic: Modeling Thin Films Intensities in Penepma (Standard.exe)  (Read 12263 times)

John Donovan

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Modeling Thin Films Intensities in Penepma (Standard.exe)
« on: September 18, 2013, 12:22:49 AM »
As many of you know, one can model thin film geometries using the Penepma 12 GUI in Standard.exe.

Provided are a number of Penepma thin film geometry files as follows:

bilayer_1nm.geo
bilayer_2nm.geo
bilayer_5nm.geo
bilayer_10nm.geo
bilayer_20nm.geo
bilayer_50nm.geo
bilayer_100nm.geo
bilayer_200nm.geo
bilayer_500nm.geo
bilayer_1000nm.geo
bilayer_2000nm.geo

The thin film calculations using these geometry files require two materials to be specified, the first is the thin film material and the second is the substrate:



This simple interface will get you started with thin film Monte-Carlo modeling. One thing to keep in mind: generally one will want to set the electron/photon minimum energies to be the same, usually just under the critical excitation energy of the lowest energy emission line to be observed.

Note: Some early versions of the Penepma12.zip distribution had a bug where if you tried to calculate a thin film model using the default bilayer_100nm.geo file, the Penepma app will run for about a 30 seconds and then close. The problem was that the bilayer_100nm.geo file was not in the Penepma folder where Penepma expected it to be, so it failed with an EOF error.

This has been fixed in the current CalcZAF distribution and Penepma12.ZIP download files, but to correct this problem on an existing installation simply click the geometry file Browse button and navigate up one folder level and select the bilayer_100nm.geo file, or any other bilayer_*.geo file.

A Monte-Carlo calculation using the above parameters will look like the attached screen shot.
« Last Edit: January 22, 2014, 05:07:27 PM by John Donovan »
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Re: Modeling Thin Films Intensities in Penepma (Standard.exe)
« Reply #1 on: September 21, 2013, 12:11:53 PM »
For details on how to extract the necessary photon intensities output by Penepma for the calculation of elemental k-ratios, please refer to this post in the particle/inclusion modeling thread:

http://probesoftware.com/smf/index.php?topic=59.msg221#msg221
« Last Edit: September 21, 2013, 12:14:32 PM by John Donovan »
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Probeman

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Re: Modeling Thin Films Intensities in Penepma (Standard.exe)
« Reply #2 on: November 25, 2013, 01:01:47 PM »
I just made a couple of "tri-layer" geo models for Penepma- thanks to Jon Wade!

They are 50 nm for the first layer (1st material), and 75 nm (and 30 nm) thick for the 2nd layer (2nd material) and then 1 cm of a 3rd material. 

In my case, that 3rd material would be air at say 1 Pascal so I can model a thin film on a TEM "Smart Grid", from Dune Sciences, which come in 15, 30 and 75 nm thick SiO2 and Si3N4 back thinned TEM grids (for the 2nd layer).

http://www.dunesciences.com/

This will allow us to deposit a thin film (here, Bi2Te3) directly on a back-thinned supporting structure to reduce continuum fluorescence and x-rays produced from substrate backscattered electrons.

We can't directly specify a three material input file in the Penepma12 GUI in Standard.exe, but all one needs to do is edit the input file using a text editor and add a third material (air at 1 Pascal, for example) to the material section and a step length for each layer (material).

So the input file created by the Penepma GUI outputs this using the default bilayer production files:

TITLE  Tri-layer Thin Film On 1 Pascal Air X-ray Production Model
       .
       >>>>>>>> Electron beam definition.
SENERG 1.50E+04                  [Energy of the electron beam, in eV]
SPOSIT 0.00E+00 0 1              [Coordinates of the electron source]
SDIREC 180 0              [Direction angles of the beam axis, in deg]
SAPERT 0                                      [Beam aperture, in deg]
       .
       >>>>>>>> Material data and simulation parameters.
                Up to 10 materials; 2 lines for each material.
MFNAME Bi2Te3.MAT                     [Material file, up to 20 chars]
MSIMPA 1.0E+3 1.0E+3 1E+3 0 0 0 -1E+2       [EABS(1:3),C1,C2,WCC,WCR]
MFNAME SiO2.mat                       [Material file, up to 20 chars]
MSIMPA 1.0E+3 1.0E+3 1E+3 0 0 0 -1E+2       [EABS(1:3),C1,C2,WCC,WCR]
       .
       >>>>>>>> Geometry of the sample.
GEOMFN trilayer_50_75nm.geo      [Geometry definition file, 20 chars]
DSMAX  1 1.0e-7             [IB, Maximum step length (cm) in body IB]
DSMAX  2 1.5e-7             [IB, Maximum step length (cm) in body IB]
       .
       >>>>>>>> Interaction forcing.
IFORCE 1 1 4 -10    0.1 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 1 1 5 -200  0.1 1.0            [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 1 2 2 -10   1e-4 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 1 2 3 -10   1e-4 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 1 4 -10    0.1 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 1 5 -200  0.1 1.0            [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 2 2 -10   1e-4 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 2 3 -10   1e-4 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
       .
       >>>>>>>> Emerging particles. Energy and angular distributions.
NBE    0   4e3 250                [E-interval and no. of energy bins]
NBTH   45                     [No. of bins for the polar angle THETA]
NBPH   30                   [No. of bins for the azimuthal angle PHI]
       .
       >>>>>>>> Photon detectors (up to 25 different detectors).
                IPSF=0, do not create a phase-space file.
                IPSF=1, creates a phase-space file.
       .
PDANGL 45.0 55.0 0.0 360.0 0           [Angular window, in deg, IPSF]
PDENER 0   20e3 1000                 [Energy window, no. of channels]
       .
       >>>>>>>> Job properties
RESUME dump1.dat               [Resume from this dump file, 20 chars]
DUMPTO dump1.dat                  [Generate this dump file, 20 chars]
DUMPP  120                                   [Dumping period, in sec]
       .
NSIMSH 2.0e+09                  [Desired number of simulated showers]
TIME   100000                      [Allotted simulation time, in sec]


And the input file after manual editing in a text editor looks like this:

TITLE  Tri-layer Thin Film On 1 Pascal Air X-ray Production Model
       .
       >>>>>>>> Electron beam definition.
SENERG 1.50E+04                  [Energy of the electron beam, in eV]
SPOSIT 0.00E+00 0 1              [Coordinates of the electron source]
SDIREC 180 0              [Direction angles of the beam axis, in deg]
SAPERT 0                                      [Beam aperture, in deg]
       .
       >>>>>>>> Material data and simulation parameters.
                Up to 10 materials; 2 lines for each material.
MFNAME Bi2Te3.MAT                     [Material file, up to 20 chars]
MSIMPA 1.0E+3 1.0E+3 1E+3 0 0 0 -1E+2       [EABS(1:3),C1,C2,WCC,WCR]
MFNAME SiO2.mat                       [Material file, up to 20 chars]
MSIMPA 1.0E+3 1.0E+3 1E+3 0 0 0 -1E+2       [EABS(1:3),C1,C2,WCC,WCR]
MFNAME Air (1 Pascal).mat             [Material file, up to 20 chars]
MSIMPA 1.0E+3 1.0E+3 1E+3 0 0 0 -1E+2       [EABS(1:3),C1,C2,WCC,WCR]
       .
       >>>>>>>> Geometry of the sample.
GEOMFN trilayer_50_75nm.geo      [Geometry definition file, 20 chars]
DSMAX  1 1.0e-7             [IB, Maximum step length (cm) in body IB]
DSMAX  2 1.5e-7             [IB, Maximum step length (cm) in body IB]
DSMAX  3 1.5e-2             [IB, Maximum step length (cm) in body IB]
       .
       >>>>>>>> Interaction forcing.
IFORCE 1 1 4 -10    0.1 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 1 1 5 -200  0.1 1.0            [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 1 2 2 -10   1e-4 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 1 2 3 -10   1e-4 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 1 4 -10    0.1 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 1 5 -200  0.1 1.0            [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 2 2 -10   1e-4 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 2 3 -10   1e-4 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
       .
       >>>>>>>> Emerging particles. Energy and angular distributions.
NBE    0   4e3 250                [E-interval and no. of energy bins]
NBTH   45                     [No. of bins for the polar angle THETA]
NBPH   30                   [No. of bins for the azimuthal angle PHI]
       .
       >>>>>>>> Photon detectors (up to 25 different detectors).
                IPSF=0, do not create a phase-space file.
                IPSF=1, creates a phase-space file.
       .
PDANGL 45.0 55.0 0.0 360.0 0           [Angular window, in deg, IPSF]
PDENER 0   20e3 1000                 [Energy window, no. of channels]
       .
       >>>>>>>> Job properties
RESUME dump1.dat               [Resume from this dump file, 20 chars]
DUMPTO dump1.dat                  [Generate this dump file, 20 chars]
DUMPP  120                                   [Dumping period, in sec]
       .
NSIMSH 2.0e+09                  [Desired number of simulated showers]
TIME   100000                      [Allotted simulation time, in sec]


See attached geo files. Note that any geo files you create must have file names (not counting the extension) less than 16 characters for Penepma12 to read it properly.
« Last Edit: July 06, 2015, 07:28:58 AM by John Donovan »
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Probeman

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Re: Modeling Thin Films Intensities in Penepma (Standard.exe)
« Reply #3 on: March 10, 2014, 12:18:23 PM »
Worth documenting is how to obtain k-ratios from the Penepma calculations...

One starts by running some calculations by creating one or more input file using the Penepma GUI as seen here:



Assuming one has utilized the Batch Mode dialog for running the Penepma Monte-Carlo calculations, one will have a folder for each calculation once it is complete as seen here:



The details on obtaining the necessary intensities to calculate k-ratios is found here:

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

As a slight aside, you might want to avail yourself of the tri-layer geometry for TEM as I did for these calculations:



More details on the tri-layer geometry are found in the post above and linked here:

http://probesoftware.com/smf/index.php?topic=57.msg478#msg478

« Last Edit: March 10, 2014, 01:39:21 PM by Probeman »
The only stupid question is the one not asked!

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Re: Modeling Thin Films Intensities in Penepma (Standard.exe)
« Reply #4 on: July 16, 2014, 12:49:11 PM »
Note a new method to automatically extract k-ratios from Penepma batch mode calculations:

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

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Re: Modeling Thin Films Intensities in Penepma (Standard.exe)
« Reply #5 on: November 30, 2014, 05:45:13 PM »
Hi Probeman,

I did similar with looking at the effect of the diameter of hemispherical calcium aluminates on the Ca:Al ratio (without a substrate=low pressure air).  I perceived an Ar peak in the output....

"Curiouser and curiouser", cried Alice.

Les

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Re: Modeling Thin Films Intensities in Penepma (Standard.exe)
« Reply #6 on: November 30, 2014, 06:20:53 PM »
I did similar with looking at the effect of the diameter of hemispherical calcium aluminates on the Ca:Al ratio (without a substrate=low pressure air).  I perceived an Ar peak in the output....

I don't quite understand how you could get an Ar peak without Ar in the physical model (unless your "low pressure air" composition contains the roughly 1% Ar as in the natural material)...

Have you tried it in Penepma? Can you post the data for us to examine?
« Last Edit: November 30, 2014, 06:26:23 PM by Probeman »
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Re: Modeling Thin Films Intensities in Penepma (Standard.exe)
« Reply #7 on: November 30, 2014, 10:40:19 PM »
Hi again,

From memory, I used the air.mat file and dropped the pressure by many orders of magnitude.
I will try and find the run output.

Have you tried running multiple layers of the same element and seeing if it matches the bulk*?
I have never turned on the phase space option, just what does it output?
What I would like is to know is just what initiated the X-Ray I am counting.  i.e. electron, background fluorescence or characteristic X-Ray fluoresence**.   

* GMRFILM was an interesting package in that if you specified multiple layers of the same material you could build up an idea of the prz yield for each element as a function of depth - quite a useful feature with widely differing element energies/lines.

** this question spurred my interest in GEANT4 but this is way beyond my pay grade.

Les

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Re: Modeling Thin Films Intensities in Penepma (Standard.exe)
« Reply #8 on: December 01, 2014, 08:08:04 AM »
Have you tried running multiple layers of the same element and seeing if it matches the bulk*?
I haven't but by definition it would have to. I have run many simulations in  Penepma and it does a good job compared to actual measurements. This is documented in the Pouchou posts.

I have never turned on the phase space option, just what does it output?
What do you mean by the "phase space option"?

What I would like is to know is just what initiated the X-Ray I am counting.  i.e. electron, background fluorescence or characteristic X-Ray fluoresence**.   
This information is in the pe-intens-01.dat file.  See this post:

http://probesoftware.com/smf/index.php?topic=151.msg632#msg632

* GMRFILM was an interesting package in that if you specified multiple layers of the same material you could build up an idea of the prz yield for each element as a function of depth - quite a useful feature with widely differing element energies/lines.
Yes, I used GMRFILM for a while, but Rick Waldo refused to add a file input/output capability so I switched to STRATAGem* where I can automate the quant process since about 60%of the work in our lab is thin films.

* © Copyright 1993-2016 SAMx
« Last Edit: February 06, 2016, 08:12:57 AM by John Donovan »
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