\page Examplebasic Example basic

This molecule counter basic example is provided by the Geant4-DNA collaboration
  (http://geant4-dna.org).

The custom (spatially-aware) molecule counter used here
is further described in:
- Radiat. Phys. Chem. 212 (2023) 111194 \
doi:10.1016/j.radphyschem.2023.111194

  Any report or published results obtained using the Geant4-DNA software
  shall cite the following Geant4-DNA collaboration publications:\n
  Med. Phys. 51 (2024) 5873–5889\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.

## 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.

## 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.

    __Default Method: `BuildMoleculeCounters()`:__
    * Reset counters before each run but not keep counter values between events
    * Register a default `G4MoleculeCounter` instance called "Molecules"
    * Register a default `G4MoleculeReactionCounter` instance called "Reactions"


    __Alternative Method: `BuildMultipleAndCustomMoleculeCounters()`:__
    * Reset counters before each run but not keep counter values between events
    * Register a `G4MoleculeCounter` instance called "BasicCounter":
        * set its time precision to 25 ps
    * Register a `G4MoleculeCounter` instance called "BasicCounter_Restricted":
        * set its time precision to 25 ps
        * activate the counter for global times in [500 ps, 10 ns]
    * 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
        ```
        * activate the counter for global times in [500 ps, 10 ns]
    * Register a custom `MoleculeCounter` instance called "MoleculeCounter"
        * 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
        ```
        * __(important)__ `SetSensitiveToStepping(true)` to change molecule count when traversing geometry boundaries
        * `SetIgnoreMoleculePosition(false)` if set to `true` the counter behaves like `G4MoleculeCounter`
        * `SetNegativeCountsAreFatal(true)` to throw a FatalException if any molecule count drops below 0 through misregistration
    * Register a `G4MoleculeReactionCounter` instance called "Reactions":
        * set its time precision to 50 ps
        * activate the counter for global times in [0 ps, 1 µs]

## Execute the code by running:

```
./molcounters_basic [simple_sbs.in,simple_irt_syn_react.in]
```

The `simple_sbs.in` macro __only__ includes molecule transport (diffusion)!

Contents of the molecule counters are dumped to `stdout`
at the end of each run by the RunAction::EndOfRunAction()