Gabriele Cosmo\page Examplesdcounters Example sdcounters
Author: C. Velten \n Date: 7 April 2025 \n Email: cv2415@columbia.edu
The custom (spatially-aware) molecule counter used here is further described in:
- Radiat. Phys. Chem. 212 (2023) 111194 \n doi:10.1016/j.radphyschem.2023.111194
This example is provided by the Geant4-DNA collaboration (http://geant4-dna.org).
Any report or published results obtained using the Geant4-DNA software shall cite the following Geant4-DNA collaboration publications:\n Med. Phys. 45 (2018) e722-e739\n Phys. Med. 31 (2015) 861-874\n Med. Phys. 37 (2010) 4692-4708\n Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178\n
\Description:
Geometry
A box of liquid water with a 8 µm (radius) spherical cell placed at its center. The cell contains a 4 µm (radius) nucleus and 100 mitochondria.
Incident particles
Electrons with 1 keV energy, which can be changed in the simple_sbs.ini macro file. They are shot from the center of the box (inside the nucleus).
Physics
The default Geant4-DNA physics constructor 2 is used in the PhysicsList class with chemistry constructor 3.
Molecule Counters
Counters are defined and registered in the ActionInitialization class for master & workers using the BuildMoleculeCounters(), and BuildMultipleAndCustomMoleculeCounters() methods. To switch between either of these methods, change the boolean value of fBuildMultipleAndCustomMoleculeCounters in ActionInitialization.hh.
By default, the molecule counter manager will accumulate counts from
worker instances into the master instance. To facilitate this the user
must create a UserEventAction and UserRunAction and override
the (Begin|End)Of(Event|Run)Action methods and call the corresponding
method on the G4DNAChemistryManager::Instance(). See the example's
EventAction.hh and RunAction.(hh|cc) on how to do this.
__`BuildMoleculeCounters()`:__
* __[important]__ Reset counters before each event but not keep counter values between events. \
This is required since our scorers will read out the molecule counters using
their `EndOfEvent()` method and save the recorded molecules.
* Register a `G4MoleculeCounter` instance called "BasicCounter":
* set its time precision to 10 ps
* Register a `G4MoleculeCounter` instance called "BasicCounter_VariablePrecision":
* set its time precision to vary with global time:
```
<= 10 ps: 5 ps
<= 100 ps: 50 ps
<= 1 ns: 0.5 ns
<= 1 µs: 50 ns
```
* Register a `G4MoleculeReactionCounter` instance called "Reactions":
* set its time precision to 10 ps
Multifunctional Detector & Primitive Scorers:
Two scorers are defined for molecule (ScoreBasicMoleculeCounts) and
reaction (ScoreBasicReactionCounts) counts. The basic molecule scorers
are instantiated once for each molecule counter.
The results are saved as ROOT trees to a single file.
Execute the code by running:
./sdcounters [simple_sbs.in,simple_irt_syn_react.in]
The simple_sbs.in macro only includes molecule transport (diffusion)!
Output
Visualize the molecule and reaction counts using the Python notebook plotRoot.ipynb. It does not require a ROOT installation but the following packages:
matplotlib pandas seaborn uproot