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README.md

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+# IonTracks
+
+The code IonTracks consists of different parts, see below. The idea is to distribute charge carriers in ion tracks depending on the linear energy transfer (LET) and a Gaussian track radius (b).
+
+## Comparison with the Jaffé theory and initial (intra-track) recombination in a single track:
+- main.py compares IonTracks with the Jaffé theory for initial recombination.
+
+## Recombination in a pulsed beam:
+- main_pulsed.py distributes particle tracks in an array and computes the total initial and general recombination in a pulsed beam.
+- it is assumed, that the ionization of the medium between the electrodes is instantaneous.
+- the simulation can be improved by generating spectra (.spc) files where the scripts SH_spc_files.py and get_b_LET.py sample from the energy spectra and print corresponding LET and Gaussian track radii to a file
+
+## Dependencies
+- Generally, the simulation of charge carriers is computed with python3 and cython3 and is written on Ubuntu 16.04:
+    - sudo apt install python3 cython3
+    - python3 modules as scipy, numpy, matplotlib are required
+    - use the makefile to compile the cython files and run with "python3 main.py"
+- the sampling of particle parameters from .spc files requires installion of libamtrack:
+    - https://github.com/libamtrack/library
+- an example of .spc files can be downloaded here: 
+    - https://libamtrack.dkfz.org/libamtrack/index.php/Download
+- .spc files for a particular beam setup can be created with e.g. SHIELD-HIT:
+    - http://shieldhit.org/ 
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