Update README.md

Simulation_Track_Structure/PTra_HIT/README.md

 ## How to get the code to run
 
+# Step 1: Download and compile the codes
 1. Download all *.f files into the same directory. <br />
 2. Open a terminal and navigate to this directory. <br />
-3. Compile the code using a Fortran 90/95 compatible compiler. <br />
-Example using gfortran and producing an executable named PTra_HIT: <br />
+3. Compile the codes FilterExtrAp.f and PTra_c3h8_20170608HIT.f using a Fortran 90/95 compatible compiler. <br />
+Example using gfortran and producing an executable PTra_HIT: <br />
    $ gfortran **PTra_c3h8_20170608HIT.f** > ~/bin/PTra_HIT 
-4. Create a text file containing the info on the simulation parameters. <br />
-An example is provided here as the file **HITEIN_240513.txt**. 
-5. Create a steering text file (to avoid manual input). <br />
+Example using gfortran and producing an executable PTra_HIT: <br />
+   $ gfortran **FilterExtrAp.f** > ~/bin/FilterExtrAp
+
+# Step 2: Filter events containing charged particles from the Geant4 output files (discarding neutrons and photons)
+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 normally be set to 1.
+
+# Step 3: Run the simulations
+1. Download the data file **nanodosimeter3_eff_HIT_1.2mbar-C3H8_drift_V4c_part-1-2_ds2v4508.dat** which contains the detection efficiency map. <br />
+2. Create a text file containing the info on the simulation parameters. <br />
+An example is provided here as the file **HITEIN_240513.txt**. It may be necessary to change the last line of the section "DETECTION EFFICIENCY" containing the path to the efficiency map. 
+3. Create a steering text file (to avoid manual input). <br />
 An example is provided here as the file **bco.dat**. (It will be necessary to change the first line to reflect the correct path to the text file containing the info on the simulation parameters.)
-6. Open a terminal and navigate to the directory where the data files (produced by FilterExrAp) are situated. <br />
-Start the simulation.<br />
+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
-
-   in 
+   $ ~/bin/PTra_HIT < bco.dat <br />
+The output files of the simulation are written to the directory in which the filtered datafiles reside.
 
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