Gabriele Cosmo
101 lines
3.9 KiB
Markdown
101 lines
3.9 KiB
Markdown
\page Examplebasic Example basic
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This molecule counter basic example is provided by the Geant4-DNA collaboration
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(http://geant4-dna.org).
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The custom (spatially-aware) molecule counter used here
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is further described in:
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- Radiat. Phys. Chem. 212 (2023) 111194 \
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doi:10.1016/j.radphyschem.2023.111194
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Any report or published results obtained using the Geant4-DNA software
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shall cite the following Geant4-DNA collaboration publications:\n
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Med. Phys. 51 (2024) 5873–5889\n
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Med. Phys. 45 (2018) e722-e739\n
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Phys. Med. 31 (2015) 861-874\n
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Med. Phys. 37 (2010) 4692-4708\n
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Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178\n
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\Description:
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## Geometry
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A box of liquid water with a 8 µm (radius) spherical cell placed at its center.
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The cell contains a 4 µm (radius) nucleus and 100 mitochondria.
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## Particles
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Electrons with 1 keV energy, which can be changed in
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the simple_sbs.ini macro file.
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They are shot from the center of the box (inside the nucleus).
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## Physics
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The default Geant4-DNA physics constructor 2 is used in
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the PhysicsList class with chemistry constructor 3.
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## Counters
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Counters are defined and registered in the ActionInitialization
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class for master & workers using the BuildMoleculeCounters(), and
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BuildMultipleAndCustomMoleculeCounters() methods.
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To switch between either of these methods, change the
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boolean value of fBuildMultipleAndCustomMoleculeCounters in
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ActionInitialization.hh.
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By default, the molecule counter manager will accumulate counts from
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worker instances into the master instance. To facilitate this the user
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__must__ create a `UserEventAction` and `UserRunAction` and override
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the `(Begin|End)Of(Event|Run)Action` methods and call the corresponding
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method on the `G4DNAChemistryManager::Instance()`. See the example's
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`EventAction.hh` and `RunAction.(hh|cc)` on how to do this.
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__Default Method: `BuildMoleculeCounters()`:__
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* Reset counters before each run but not keep counter values between events
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* Register a default `G4MoleculeCounter` instance called "Molecules"
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* Register a default `G4MoleculeReactionCounter` instance called "Reactions"
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__Alternative Method: `BuildMultipleAndCustomMoleculeCounters()`:__
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* Reset counters before each run but not keep counter values between events
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* Register a `G4MoleculeCounter` instance called "BasicCounter":
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* set its time precision to 25 ps
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* Register a `G4MoleculeCounter` instance called "BasicCounter_Restricted":
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* set its time precision to 25 ps
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* activate the counter for global times in [500 ps, 10 ns]
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* Register a `G4MoleculeCounter` instance called "BasicCounter_VariablePrecision":
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* set its time precision to vary with global time:
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```
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<= 10 ps: 5 ps
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<= 100 ps: 50 ps
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<= 1 ns: 0.5 ns
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<= 1 µs: 50 ns
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```
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* activate the counter for global times in [500 ps, 10 ns]
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* Register a custom `MoleculeCounter` instance called "MoleculeCounter"
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* set its time precision to vary with global time:
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```
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<= 10 ps: 5 ps
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<= 100 ps: 50 ps
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<= 1 ns: 0.5 ns
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<= 1 µs: 50 ns
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```
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* __(important)__ `SetSensitiveToStepping(true)` to change molecule count when traversing geometry boundaries
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* `SetIgnoreMoleculePosition(false)` if set to `true` the counter behaves like `G4MoleculeCounter`
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* `SetNegativeCountsAreFatal(true)` to throw a FatalException if any molecule count drops below 0 through misregistration
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* Register a `G4MoleculeReactionCounter` instance called "Reactions":
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* set its time precision to 50 ps
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* activate the counter for global times in [0 ps, 1 µs]
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## Execute the code by running:
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```
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./molcounters_basic [simple_sbs.in,simple_irt_syn_react.in]
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```
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The `simple_sbs.in` macro __only__ includes molecule transport (diffusion)!
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Contents of the molecule counters are dumped to `stdout`
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at the end of each run by the RunAction::EndOfRunAction()
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