moleculardna/src/TimeStepAction.cc

0001 //
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0025 //
0026 //
0027 #include "TimeStepAction.hh"
0028
0029 #include "ChromosomeMapper.hh"
0030 #include "DNAGeometry.hh"
0031 #include "DNAHit.hh"
0032 #include "DetectorConstruction.hh"
0033 #include "EventAction.hh"
0034 #include "OctreeNode.hh"
0035
0036 #include "G4DNAMolecularReactionTable.hh"
0037 #include "G4ITTrackHolder.hh"
0038 #include "G4ITTrackingManager.hh"
0039 #include "G4Molecule.hh"
0040 #include "G4RunManager.hh"
0041 #include "G4Scheduler.hh"
0042
0043 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0044 TimeStepAction::TimeStepAction(EventAction* event)
0045   : G4UserTimeStepAction(),
0046     fEventAction(event),
0047     fRadicalKillDistance(4.5 * nm),
0048     fpChemistryTrackHolder(G4ITTrackHolder::Instance())
0049 {
0050   //AddTimeStep(1 * picosecond, 0.5 * nanosecond);
0051   // ctor
0052 }
0053
0054 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0055
0056 TimeStepAction::~TimeStepAction() = default;
0057 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0058
0059 void TimeStepAction::StartProcessing()
0060 {
0061   auto det = dynamic_cast<const DetectorConstruction*>(
0062     G4RunManager::GetRunManager()->GetUserDetectorConstruction());
0063   fDNAGeometry = det->GetDNAGeometry();
0064   if (fDNAGeometry == nullptr) {
0065     G4ExceptionDescription exceptionDescription;
0066     exceptionDescription << "fDNAGeometry is null";
0067     G4Exception(
0068       "TimeStepAction"
0069       "StartProcessing",
0070       "no fDNAGeometry", FatalException, exceptionDescription);
0071   }
0072
0073   fRadicalKillDistance = fDNAGeometry->GetRadicalKillDistance();
0074 }
0075
0076 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0077
0078 void TimeStepAction::UserPostTimeStepAction()
0079 {
0080   RadicalKillDistance();
0081 }
0082
0083 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0084
0085 void TimeStepAction::UserPreTimeStepAction() {}
0086
0087 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0088
0089 void TimeStepAction::UserReactionAction(const G4Track&, const G4Track&,
0090                                         const std::vector<G4Track*>*)
0091 {}
0092
0093 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0094
0095 void TimeStepAction::RadicalKillDistance()
0096 {
0097   if (fpChemistryTrackHolder == nullptr) {
0098     G4ExceptionDescription exceptionDescription;
0099     exceptionDescription << "fpChemistryTrackHolder is null";
0100     G4Exception(
0101       "TimeStepAction"
0102       "RadicalKillDistance",
0103       "NO_fpChemistryTrackHolder", FatalException, exceptionDescription);
0104   }
0105   G4Track* trackToKill;
0106   G4TrackManyList::iterator it_begin = fpChemistryTrackHolder->GetMainList()->begin();
0107   G4TrackManyList::iterator it_end = fpChemistryTrackHolder->GetMainList()->end();
0108   while (it_begin != it_end) {
0109     trackToKill = nullptr;
0110
0111     const G4VTouchable* touchable = it_begin->GetTouchable();
0112     if (touchable == nullptr) {
0113       ++it_begin;
0114       continue;
0115     }
0116
0117     G4LogicalVolume* trackLV = touchable->GetVolume()->GetLogicalVolume();
0118     G4LogicalVolume* motherLV = touchable->GetVolume()->GetMotherLogical();
0119
0120     OctreeNode* octree_track = fDNAGeometry->GetTopOctreeNode(trackLV);
0121     OctreeNode* octree_mother = fDNAGeometry->GetTopOctreeNode(motherLV);
0122
0123     if ((octree_track == nullptr) && (octree_mother == nullptr)) {
0124       trackToKill = *it_begin;
0125     }
0126     else if (octree_track != nullptr) {
0127       const G4AffineTransform& trans = it_begin->GetTouchable()->GetHistory()->GetTopTransform();
0128       G4ThreeVector pos = trans.TransformPoint(it_begin->GetPosition());
0129       size_t n = octree_track->SearchOctree(pos, fRadicalKillDistance).size();
0130       if (n == 0) {
0131         trackToKill = *it_begin;
0132       }
0133       if (fDNAGeometry->IsInsideHistone(trackLV, pos)) {
0134         trackToKill = *it_begin;
0135       }
0136     }
0137     else {
0138       const G4AffineTransform& trans = it_begin->GetTouchable()->GetHistory()->GetTopTransform();
0139       G4ThreeVector pos = trans.TransformPoint(it_begin->GetPosition());
0140       if (fDNAGeometry->IsInsideHistone(trackLV, pos)) {
0141         trackToKill = *it_begin;
0142       }
0143     }
0144     ++it_begin;
0145     if (trackToKill != nullptr) {
0146       fpChemistryTrackHolder->PushToKill(trackToKill);
0147       G4Scheduler::Instance()->SetInteractionStep(true);
0148     }
0149   }
0150 }
0151
0152 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......