### Step 2: Filter events containing charged particles from the Geant4 output files
Run the executable produced from FilterExtrAp.f best with a steering text file. <br/>
Example with the executable produced above and the sample steering file **cox.dat**:
$ *~/bin/FilterExtrAp < cox.dat*
The first two lines are the numbers of files per case (PMMA thickness and primary energy) and of subdirectories (each corresponding to a combination of PMMA thickness and primary energy).
The third line is a flag that should be set to 0 if the results from the Geant4 simulations have been produced in different runs and are merged during the filtering. (In this case files named F_ExtractionScoringPlane_t*.dat resdiding in the output directories must be deleted before running FilterExtrAp.)
Example with the executable produced above and the sample steering file **cox.dat**:<br/>
$ *~/bin/FilterExtrAp < cox.dat*<br/>
The first two lines are the numbers of files per case (PMMA thickness and primary energy) and of subdirectories (each corresponding to a combination of PMMA thickness and primary energy). <br/>
The third line is a flag that should be set to 0 if the results from the Geant4 simulations have been produced in different runs and are merged during the filtering. (In this case files named F_ExtractionScoringPlane_t*.dat resdiding in the output directories must be deleted before running FilterExtrAp.)<br/>
The remaining even lines are the paths to the Geant4 simulation output files and the ensuing odd lines are the corresponding paths where the output files are written.
### Step 3: Run the simulations
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@@ -26,7 +26,7 @@ An example is provided here as the file **bco.dat**. (It will be necessary to ch
4. Open a terminal and navigate to the directory where the data files (produced by FilterExrAp) are situated. <br/>
5. Start the simulation.<br/>
Example with the steering file bco.dat: <br/>
$ ~/bin/PTra_HIT <bco.dat<br/>
$ *~/bin/PTra_HIT < bco.dat*<br/>
The output files of the simulation are written to the directory in which the filtered datafiles reside.