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examples/extended/medical/dna/dnadamage2/src/TimeStepAction.cc

+//
+// ********************************************************************
+// * License and Disclaimer                                           *
+// *                                                                  *
+// * The  Geant4 software  is  copyright of the Copyright Holders  of *
+// * the Geant4 Collaboration.  It is provided  under  the terms  and *
+// * conditions of the Geant4 Software License,  included in the file *
+// * LICENSE and available at  http://cern.ch/geant4/license .  These *
+// * include a list of copyright holders.                             *
+// *                                                                  *
+// * Neither the authors of this software system, nor their employing *
+// * institutes,nor the agencies providing financial support for this *
+// * work  make  any representation or  warranty, express or implied, *
+// * regarding  this  software system or assume any liability for its *
+// * use.  Please see the license in the file  LICENSE  and URL above *
+// * for the full disclaimer and the limitation of liability.         *
+// *                                                                  *
+// * This  code  implementation is the result of  the  scientific and *
+// * technical work of the GEANT4 collaboration.                      *
+// * By using,  copying,  modifying or  distributing the software (or *
+// * any work based  on the software)  you  agree  to acknowledge its *
+// * use  in  resulting  scientific  publications,  and indicate your *
+// * acceptance of all terms of the Geant4 Software license.          *
+// ********************************************************************
+//
+// This example is provided by the Geant4-DNA collaboration
+// dnadamage3 example is derived from the chem6 example
+// chem6 example authors: W. G. Shin and S. Incerti (CENBG, France)
+//
+// Any report or published results obtained using the Geant4-DNA software
+// shall cite the following Geant4-DNA collaboration publication:
+// J. Appl. Phys. 125 (2019) 104301
+// Med. Phys. 45 (2018) e722-e739
+// J. Comput. Phys. 274 (2014) 841-882
+// Med. Phys. 37 (2010) 4692-4708
+// Int. J. Model. Simul. Sci. Comput. 1 (2010) 157-178
+// The Geant4-DNA web site is available at http://geant4-dna.org
+//
+// Authors: J. Naoki D. Kondo (UCSF, US)
+//          J. Ramos-Mendez and B. Faddegon (UCSF, US)
+//
+//
+/// \file TimeStepAction.hh
+/// \brief Implementation of the TimeStepAction class
+///  Filtering of molecules by material at the beggining of the chemical stage
+
+#include "TimeStepAction.hh"
+#include "G4Scheduler.hh"
+#include "G4UnitsTable.hh"
+#include "G4SystemOfUnits.hh"
+#include "G4Track.hh"
+#include "G4Molecule.hh"
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
+
+TimeStepAction::TimeStepAction() : G4UserTimeStepAction()
+{;}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
+
+TimeStepAction::~TimeStepAction()
+{;}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
+
+TimeStepAction::TimeStepAction(const TimeStepAction& other) :
+        G4UserTimeStepAction(other)
+{;}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
+
+TimeStepAction&
+TimeStepAction::operator=(const TimeStepAction& rhs)
+{
+  if (this == &rhs) return *this; // handle self assignment
+  //assignment operator
+  return *this;
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
+void TimeStepAction::UserPreTimeStepAction()
+{
+    G4int Steps = G4Scheduler::Instance()->GetNbSteps();
+
+    if (Steps == 1) {
+        G4int TotalMolecules = 0;
+        G4int KilledMolecules = 0;
+        G4int AcceptedMolecules = 0;
+        G4TrackManyList* trackList = G4ITTrackHolder::Instance()->GetMainList();
+        G4ManyFastLists<G4Track>::iterator it_begin = trackList->begin();
+        G4ManyFastLists<G4Track>::iterator it_end   = trackList->end();
+
+        for(;it_begin!=it_end;++it_begin) {
+            TotalMolecules++;
+            G4String Material = it_begin->GetStep()->
+                         GetPreStepPoint()->GetMaterial()->GetName();
+            G4String MoleculeName = GetMolecule(*it_begin)->GetName();
+            if (Material != "G4_WATER" && !G4StrUtil::contains(MoleculeName,"DNA")) {
+                KilledMolecules++;
+                it_begin->SetTrackStatus(fStopAndKill);
+            }
+            else {
+                AcceptedMolecules++;
+            }
+        }
+    }
+}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
+
+void TimeStepAction::UserPostTimeStepAction()
+{;}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
+
+void TimeStepAction::Clear()
+{;}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
+
+void TimeStepAction::UserReactionAction(const G4Track& /*trackA*/,
+    const G4Track& /*trackB*/,
+    const std::vector<G4Track*>* /*products*/)
+{;}
+
+//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....