Import Geant4 11.4.0 source tree

2025-12-05 08:54:02 +01:00
parent a499fb82e9
commit b4a16de652
6484 changed files with 232674 additions and 221097 deletions
@@ -1,8 +1,13 @@
+# Example molcounter-basic History

+See `CONTRIBUTING.rst` for details of **required** info/format for each entry,
+which **must** added in reverse chronological order (newest at the top).
+It must **not** be used as a substitute for writing good git commit messages!

-     =========================================================
-     Geant4 - an Object-Oriented Toolkit for Simulation in HEP
-     =========================================================
+-------------------------------------------------------------------------------
+
+## 2025-11-10 G Cosmo (molcounter-basic-V11-03-03)
+- Fixed coding conventions for tabs in MoleculeCounter source.

 ## 2025-05-28  H Tran (molcounter-basic-V11-03-02)
 - Fixed warning in windows
@@ -1,103 +0,0 @@
- -------------------------------------------------------------------
-
-      =========================================================
-      Geant4 - an Object-Oriented Toolkit for Simulation in HEP
-      =========================================================
-*** molcounters/basic example ***
-
-Author: C. Velten \
-Date: 7 April 2025 \
-Email: cv2415@columbia.edu
-
-(c) The Geant4-DNA collaboration.
-
-This example shows how to use the new molecule counter manager
-system and how to write custom molecule counters.
-
-This example is provided by the Geant4-DNA collaboration.
-
-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:
- Med. Phys. 51 (2024) 5873–5889 
- Med. Phys. 45 (2018) e722-e739 
- Phys. Med. 31 (2015) 861-874   
- Med. Phys. 37 (2010) 4692-4708 
- Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
-
-### Description:
-
-1. __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.
-
-2. __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).
-
-3. __Physics__:
-The default Geant4-DNA physics constructor 2 is used in
-the PhysicsList class with chemistry constructor 3.
-
-4. __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. \
-
-    __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]
-
-5. __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)!
-
-6. __Output__: Contents of the molecule counters are dumped to `stdout`
-at the end of each run by the RunAction::EndOfRunAction()
@@ -1,10 +1,6 @@
+\page Examplebasic Example basic

-///\file "medical/dna/molcounters/basic/.README.txt"
-///\brief Example molcounters basic README page
-
-/*! \page Examplebasic Example basic
-
-\ This example is provided by the Geant4-DNA collaboration
+This molecule counter basic example is provided by the Geant4-DNA collaboration
  (http://geant4-dna.org).

 The custom (spatially-aware) molecule counter used here
@@ -23,32 +19,37 @@ doi:10.1016/j.radphyschem.2023.111194
 \Description:


-\section 1. __Geometry__:
+## 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.

-\section2. __Incident particles__:
+## 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).

-\section3. __Physics__:
+## Physics
+
 The default Geant4-DNA physics constructor 2 is used in
 the PhysicsList class with chemistry constructor 3.

-\section4. __Molecule Counters__:
+## 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. \
+`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
@@ -87,9 +88,13 @@ method on the `G4DNAChemistryManager::Instance()`. See the example's
        * set its time precision to 50 ps
        * activate the counter for global times in [0 ps, 1 µs]

-\section5. __Execute__ the code by running:
-`./molcounters_basic [simple_sbs.in,simple_irt_syn_react.in]`
+## 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)!

-\section6. __Output__: Contents of the molecule counters are dumped to `stdout`
+Contents of the molecule counters are dumped to `stdout`
 at the end of each run by the RunAction::EndOfRunAction()
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file ActionInitialization.hh
+/// \brief Definition of the ActionInitialization class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file ChemistrySteppingAction.hh
+/// \brief Definition of the ChemistrySteppingAction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file ChemistryTrackingManager.hh
+/// \brief Definition of the ChemistryTrackingManager class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file DetectorConstruction.hh
+/// \brief Definition of the DetectorConstruction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file EventAction.hh
+/// \brief Definition of the EventAction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file MoleculeCounter.hh
+/// \brief Definition of the MoleculeCounter class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file PhysicsList.hh
+/// \brief Definition of the PhysicsList class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file PrimaryGeneratorAction.hh
+/// \brief Definition of the PrimaryGeneratorAction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file RunAction.hh
+/// \brief Definition of the RunAction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file StackingAction.hh
+/// \brief Definition of the StackingAction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file molcounters_basic.cc
+/// \brief Main program of the molcounters/basic example
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file ActionInitialization.cc
+/// \brief Implementation of the ActionInitialization class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -45,6 +48,7 @@
 #include "PrimaryGeneratorAction.hh"
 #include "RunAction.hh"
 #include "StackingAction.hh"
+#include "G4SystemOfUnits.hh"

 #include "G4DNAChemistryManager.hh"
 #include "G4H2O.hh"
@@ -186,4 +190,4 @@ void ActionInitialization::BuildMultipleAndCustomMoleculeCounters() const
    G4MoleculeCounterManager::Instance()->RegisterCounter(std::move(counter));
  }
 }
-//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file ChemistrySteppingAction.cc
+/// \brief Implementation of the ChemistrySteppingAction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file ChemistryTrackingManager.cc
+/// \brief Implementation of the ChemistryTrackingManager class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file DetectorConstruction.cc
+/// \brief Implementation of the DetectorConstruction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file MoleculeCounter.cc
+/// \brief Implementation of the MoleculeCounter class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -80,8 +83,8 @@ std::unique_ptr<G4VMoleculeCounterIndex> MoleculeCounter::BuildIndex(const G4Tra

    if (touchable == nullptr) touchable = aTrack->GetTouchable();
    if (touchable == nullptr) {
-	  auto touchableHandle = G4MoleculeLocator::Instance()->LocateMoleculeTrack(aTrack);
-	  touchable = touchableHandle();
+      auto touchableHandle = G4MoleculeLocator::Instance()->LocateMoleculeTrack(aTrack);
+      touchable = touchableHandle();
    }
    if (touchable == nullptr) {  // still not found -- should never fire
      G4ExceptionDescription errMsg;
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file PhysicsList.cc
+/// \brief Implementation of the PhysicsList class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file PrimaryGeneratorAction.cc
+/// \brief Implementation of the PrimaryGeneratorAction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file RunAction.cc
+/// \brief Implementation of the RunAction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.
@@ -23,6 +23,9 @@
 // * acceptance of all terms of the Geant4 Software license.          *
 // ********************************************************************
 //
+/// \file StackingAction.cc
+/// \brief Implementation of the StackingAction class
+
 // The `molcounters` example(s) are provided as part of Geant4-DNA
 // and any report or published result obtained using it shall cite
 // the respective Geant4-DNA collaboration publications.