Penelope/Penepma material files

[Mike Matthews]

Has anyone generated a material file for epoxy resin (Epofix in particular)? The standard material list has polymethyl methacrilate (Perspex) but I don't know if this is similar enough - it doesn't have CL in which Epofix does.

[John Donovan]

Has anyone generated a material file for epoxy resin (Epofix in particular)? The standard material list has polymethyl methacrilate (Perspex) but I don't know if this is similar enough - it doesn't have CL in which Epofix does.

Hi Mike,
In the C:\UserData\Penepma12\Penfluor\Compound folder there is an "Epon 828 Epoxy.par" file.  Update your Penepma files using the CalcZAF Help menu if you need to.

If you need a different epoxy composition, it's just a 10 hour run...
john

[Probeman]

Instructions for creating PAR files for new compounds are described here:

http://probesoftware.com/smf/index.php?topic=58.msg214#msg214

By the way, the Epon 828 Epoxy in the Penepma12\Penfluor\Compound folder contains 0.3 wt% Cl:

St   29 Epon 828 Epoxy
TakeOff = 40.0  KiloVolt = 15.0  Density =  1.160

Elemental Composition

Average Total Oxygen:         .000     Average Total Weight%:  100.310
Average Calculated Oxygen:    .000     Average Atomic Number:    6.051
Average Excess Oxygen:        .000     Average Atomic Weight:    6.982
Oxygen Equiv. from Halogen:   .068

ELEM:        C       O      Cl       H
XRAY:      ka      ka      ka         
ELWT:   74.400  18.550    .300   7.060
KFAC:    .6261   .0443   .0025   .0000
ZCOR:   1.1883  4.1883  1.2150  1.0000
AT% :   43.118   8.070    .059  48.753

[Mike Matthews]

Thanks John,

Are these PAR files the same as the Penelope .mat files. If not can they be converted?

Mike

[Probeman]

Thanks John,

Are these PAR files the same as the Penelope .mat files. If not can they be converted?

Mike

Hi Mike,
I guess I should have asked if you are modeling using the Penepma GUI (the next to last menu under the Analytical menu in Standard.exe) or the using the Penfluor/Fanal secondary fluorescence GUI (the last menu under the Analytical menu in Standard.exe).

Both Penepma and Penfluor use .MAT files as input for performing the Monte Carlo simulation.   These .MAT files are the same for both applications.

However, in Penepma the .MAT file (and a .IN input file with the simulation conditions) is all you need to run the full Penepma simulation simulation. But the simulation is for a specific set of beam conditions and an X, Y and Z distance. In the Penfluor/Fanal secondary fluorescence simulations (and matrix correction simulations when the beam incident and adjacent materials are the same), the .MAT is used as the input to Penfluor, which then performs a Monter carlo simulation over a range of beam energies (currently 5 keV to 50 keV), and a range of take-off angles and for all emitted x-rays for all emitted elements (but only the primary and continuum intensity simulations, w/o the fluorescence simulations!).  These calculations are then saved to a .PAR file which is then used as input to Fanal to extract a specific emission line at a specified keV and takeoff angle, and also a specified range of distances from the boundary.

Before Penfluor/Fanal were developed, one would have to run a full Monte Carlo simulation for each element, each x-ray, each beam energy, each takeoff angle and for *each* distance from the boundary.  Very time consuming!

Please let me know if I haven't explained something clearly enough.  There's certainly a lot going on "under the hood" there!
john

[Mike Matthews]

Hi John,

I'm using the newly available PenNuc module to model the self-fluorescence component when analysing radioactive materials (a problem I'm sure we're all very familiar with🤔). Currently this has to be run from Penelope. Fortunately the .mat files are exactly the same as for Penelope.

Mike

[John Donovan]

Hi John,

I'm using the newly available PenNuc module to model the self-fluorescence component when analysing radioactive materials (a problem I'm sure we're all very familiar with🤔). Currently this has to be run from Penelope. Fortunately the .mat files are exactly the same as for Penelope.

Mike

Hi Mike,
Right.  I saw the poster on PenNuc at EMAS.   Pretty cool, or should I say, hot!?     

Is the executable file called Penepma.exe?  If so, maybe you can simply copy the PenNuc version of Penepma.exe to the Penepma12\Penepma folder and be able to utilize the Penepma GUI in Standard.exe?  I would guess that there's an additional sub folder with the radioactive data files.  Can you post the PenNuc zip file here?  I doesn't have such samples myself, but I would be interested in looking at the PenNuc files.
john

[Mike Matthews]

Hi John,

The executable is Penelope.exe. It uses the same structure as Penepma, i.e. a .in input file defining the conditions and a .geo file describing the sample geometry. However, both need additional terms compared to Penepma. For example, the detectors need to be explicitly described as bodies/modules in the .geo file and assigned materials in the .in file. Would your GUI be able to cope with these differences? It's be pretty cool if it could!

Mike

[John Donovan]

Hi John,

The executable is Penelope.exe. It uses the same structure as Penepma, i.e. a .in input file defining the conditions and a .geo file describing the sample geometry. However, both need additional terms compared to Penepma. For example, the detectors need to be explicitly described as bodies/modules in the .geo file and assigned materials in the .in file. Would your GUI be able to cope with these differences? It's be pretty cool if it could!

Mike

Hi Mike,
That should the same as for Penepma. See an example Penepma input file below. Please post the necessary PenNuc files and I'll take a look.
john

TITLE  Characteristic X-ray Production Model
       .
       >>>>>>>> Electron beam definition.
SENERG 2.00E+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.
MFNAME CuAu.mat                       [Material file, up to 20 chars]
MSIMPA 5.0E+1 1.8E+1 1E+3 0.1 0.1 1E+3 1E+3 [EABS(1:3),C1,C2,WCC,WCR]
       .
       >>>>>>>> Geometry of the sample.
GEOMFN bulk.geo                  [Geometry definition file, 20 chars]
DSMAX  1 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 -400   0.1 1.0           [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
       .
       >>>>>>>> Photon detectors (up to 10 different detectors).
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   300                         [Allotted simulation time, in sec]

[John Donovan]

Has anyone generated a material file for epoxy resin (Epofix in particular)? The standard material list has polymethyl methacrilate (Perspex) but I don't know if this is similar enough - it doesn't have CL in which Epofix does.

Hi Mike,
Below is attached the .mat file for the Epon epoxy.

Note that you can generate .mat files in Standard for any standard in the standard list from the the Penfluor/Fanal GUI secondary fluorescence window as seen here:



Or you can use the other button (just below) and type in the chemical formula, but if you do this formula entry method be sure to enter the correct density before you create the material file. Once the material file is created you can find it in the C:\UserData\Penepma12\Pendbase folder.

john

[Mike Matthews]

Thanks John,

It's useful to know I can generate the material files in PfE too.

The Penelope.in file is very similar to the Penepma one (Penepma is just a version of Penelope configured specifically for EPMA setups whereas Penelope is the full generic version that can be used for e.g. model the radiation dose received by different body tissues - I think this is what it was originally created for). In the Penelope.in file the main difference is how the detectors need to be defined using IMPDET, IDBODY and IDKPAR:

TITLE  AWE shuttle loaded with 8 4x10x10mm Pu98Ga samples
       >>>>>>>> Source definition.
SKPAR  1        [Primary particles: 1=electron, 2=photon, 3=positron]
SENERG 2.5e4            [Initial energy (monoenergetic sources only)]
SPOSIT 0.0 0.0 1.0                        [Coordinates of the source]
SCONE  180 0 0                          [Conical beam; angles in deg]
       .
       >>>>>>>> Material data and simulation parameters.
                Up to MAXMAT materials; 2 lines for each material.
MFNAME Pu98Ga.mat                     [Material file, up to 20 chars]
MSIMPA 1e3 1e3 1e3 0.2 0.2  1e3 1e3         [EABS(1:3),C1,C2,WCC,WCR]
MFNAME epoxy.mat                      [Material file, up to 20 chars]
MSIMPA 1e3 1e3 1e3 0.2 0.02 1e3 1e3         [EABS(1:3),C1,C2,WCC,WCR]
MFNAME Fe.mat                         [Material file, up to 20 chars]
MSIMPA 1e3 1e3 1e3 0.2 0.02 1e3 1e3         [EABS(1:3),C1,C2,WCC,WCR]
       .
       >>>>>>>> Geometry and local simulation parameters.
GEOMFN shuttle.geo                    [Geometry file, up to 20 chars]
DSMAX  1 1.0e-4             [IB, Maximum step length (cm) in body IB]
DSMAX  2 1.0e-4             [IB, Maximum step length (cm) in body IB]
       .
       >>>>>>>> Interaction forcing.
IFORCE 1 1 4 -5     0.9  1.0          [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 1 1 5 -5     0.9  1.0          [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 1 2 2  10    0.9  1.0          [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 1 2 2  10    0.9  1.0          [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 1 4 -5     0.9  1.0          [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 1 5 -5     0.9  1.0          [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 2 2  10    0.9  1.0          [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
IFORCE 2 2 2  10    0.9  1.0          [KB,KPAR,ICOL,FORCER,WLOW,WHIG]
       .
       >>>>>>>> Bremsstrahlung splitting.
IBRSPL 1 5                                      [KB,splitting factor]
IBRSPL 2 5                                      [KB,splitting factor]
       .
       >>>>>>>> X-ray splitting.
IXRSPL 1 5                                      [KB,splitting factor]
IXRSPL 2 5                                      [KB,splitting factor]
       .
       >>>>>>>> Emerging particles. Energy and angular distributions.
NBE    1e3 1e5 200                    [Energy window and no. of bins]
NBANGL 60 60               [No. of bins for the angles THETA and PHI]
       .
       >>>>>>>> Impact detectors (up to 25 different detectors).
       IPSF=0; no psf is created.
       IPSF=1; a psf is created (for only one detector).
       IDCUT=0; tracking is discontinued at the detector entrance.
       IDCUT=1; the detector does not affect the tracking.
       IDCUT=2; the detector does not affect tracking, the energy
                distribution of particle fluence (integrated over the
                volume of the detector) is calculated.
IMPDET 0 2e4 1000 0 0            [E-window, no. of bins, IPSF, IDCUT]
IDBODY 11                                               [Active body]
IDKPAR 2                                 [Kind of detected particles]
       .
       >>>>>>>> Job properties.
RESUME dump1.dmp               [Resume from this dump file, 20 chars]
DUMPTO dump1.dmp                  [Generate this dump file, 20 chars]
DUMPP  60                                    [Dumping period, in sec]
       .
NSIMSH 1e9                      [Desired number of simulated showers]
TIME   1e9                         [Allotted simulation time, in sec]
END                                  [Ends the reading of input data]

The IDBODY links the detector to a body/module in the .geo file that specifies the shape and position of the detector so, for example, the standard annular Penepma detector is modelled as the intersection between two concentric cone surfaces, two concentric spheres, and the z=0 plane:

SURFACE ( CD1)  Plane Z=0
INDICES=( 0, 0, 0, 1, 0)
0000000000000000000000000000000000000000000000000000000000000000
SURFACE ( CD2)  Cone, interior
INDICES=( 1, 1,-1, 0, 0)
X-SCALE=( 1.732050000000000E+00,   0)
Y-SCALE=( 1.732050000000000E+00,   0)
0000000000000000000000000000000000000000000000000000000000000000
SURFACE ( CD3)  Cone, exterior
INDICES=( 1, 1,-1, 0, 0)
X-SCALE=( 5.773502000000000E-01,   0)
Y-SCALE=( 5.773502000000000E-01,   0)
0000000000000000000000000000000000000000000000000000000000000000
SURFACE ( CD4)  Inner sphere
INDICES=( 1, 1, 1, 0,-1)
X-SCALE=( 1.000000000000000E+01,   0)
Y-SCALE=( 1.000000000000000E+01,   0)
Z-SCALE=( 1.000000000000000E+01,   0)
0000000000000000000000000000000000000000000000000000000000000000
SURFACE ( CD5)  Inner sphere
INDICES=( 1, 1, 1, 0,-1)
X-SCALE=( 1.010000000000000E+01,   0)
Y-SCALE=( 1.010000000000000E+01,   0)
Z-SCALE=( 1.010000000000000E+01,   0)
0000000000000000000000000000000000000000000000000000000000000000
BODY    ( CD1)  Cylindrical detector 1
MATERIAL(   3)
SURFACE ( CD1), SIDE POINTER=( 1)
SURFACE ( CD2), SIDE POINTER=(-1)
SURFACE ( CD3), SIDE POINTER=( 1)
SURFACE ( CD4), SIDE POINTER=( 1)
SURFACE ( CD5), SIDE POINTER=(-1)

(Thanks to Xavier for this - It would have taken me hours to work this out). All the other bodies that make up the sample are described exactly as for Penepma.

Mike