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1 // 1 //
2 // ******************************************* 2 // ********************************************************************
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18 // * This code implementation is the result 18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboratio 19 // * technical work of the GEANT4 collaboration. *
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24 // ******************************************* 24 // ********************************************************************
25 // 25 //
26 // This example is provided by the Geant4-DNA 26 // This example is provided by the Geant4-DNA collaboration
27 // Any report or published results obtained us 27 // Any report or published results obtained using the Geant4-DNA software
28 // shall cite the following Geant4-DNA collabo 28 // shall cite the following Geant4-DNA collaboration publication:
29 // Med. Phys. 37 (2010) 4692-4708 29 // Med. Phys. 37 (2010) 4692-4708
30 // Delage et al. PDB4DNA: implementation of DN 30 // Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
31 // Bank (PDB) description for 31 // Bank (PDB) description for Geant4-DNA Monte-Carlo
32 // simulations (submitted to 32 // simulations (submitted to Comput. Phys. Commun.)
33 // The Geant4-DNA web site is available at htt 33 // The Geant4-DNA web site is available at http://geant4-dna.org
34 // 34 //
35 // 35 //
36 /// \file SteppingAction.cc 36 /// \file SteppingAction.cc
37 /// \brief Implementation of the SteppingActio 37 /// \brief Implementation of the SteppingAction class
38 38
39 #include "SteppingAction.hh" 39 #include "SteppingAction.hh"
40 40
41 #include "DetectorConstruction.hh" 41 #include "DetectorConstruction.hh"
42 #include "EventAction.hh" <<
43 <<
44 #include "G4EventManager.hh" 42 #include "G4EventManager.hh"
>> 43 #include "EventAction.hh"
45 #include "G4LogicalVolumeStore.hh" 44 #include "G4LogicalVolumeStore.hh"
46 #include "G4RunManager.hh" 45 #include "G4RunManager.hh"
47 #include "G4SteppingManager.hh" 46 #include "G4SteppingManager.hh"
48 #include "G4SystemOfUnits.hh" 47 #include "G4SystemOfUnits.hh"
49 48
50 //....oooOO0OOooo........oooOO0OOooo........oo 49 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
51 50
52 SteppingAction::SteppingAction() 51 SteppingAction::SteppingAction()
53 : G4UserSteppingAction(), RunInitObserver(), << 52 :G4UserSteppingAction(),RunInitObserver(),fpEventAction(0),fpDetector(0)
54 {} << 53 {
>> 54 }
55 55
56 //....oooOO0OOooo........oooOO0OOooo........oo 56 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
57 57
58 SteppingAction::~SteppingAction() {} << 58 SteppingAction::~SteppingAction()
>> 59 {
>> 60 }
59 61
60 //....oooOO0OOooo........oooOO0OOooo........oo 62 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
61 63
62 void SteppingAction::Initialize() 64 void SteppingAction::Initialize()
63 { 65 {
64 fpEventAction = (EventAction*)G4EventManager << 66 fpEventAction = (EventAction*) G4EventManager::GetEventManager()->
65 fpDetector = (DetectorConstruction*)G4RunMan << 67 GetUserEventAction();
>> 68 fpDetector = (DetectorConstruction*)G4RunManager::GetRunManager()->
>> 69 GetUserDetectorConstruction();
66 } 70 }
67 71
68 //....oooOO0OOooo........oooOO0OOooo........oo 72 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
69 73
70 void SteppingAction::UserSteppingAction(const 74 void SteppingAction::UserSteppingAction(const G4Step* theStep)
71 { 75 {
72 if (theStep->GetPostStepPoint()->GetProcessD << 76 if(theStep->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()!=
>> 77 "Transportation")
>> 78 {
73 // Get position and edep of current step 79 // Get position and edep of current step
74 // 80 //
75 G4double x = theStep->GetPreStepPoint()->G << 81 G4double x = theStep->GetPreStepPoint()->GetPosition().x()/nanometer;
76 G4double y = theStep->GetPreStepPoint()->G << 82 G4double y = theStep->GetPreStepPoint()->GetPosition().y()/nanometer;
77 G4double z = theStep->GetPreStepPoint()->G << 83 G4double z = theStep->GetPreStepPoint()->GetPosition().z()/nanometer;
78 G4double edepStep = theStep->GetTotalEnerg << 84 G4double edepStep = theStep->GetTotalEnergyDeposit()/eV;
79 85
80 G4LogicalVolume* targetVolume = G4LogicalV << 86 G4LogicalVolume* targetVolume =
>> 87 G4LogicalVolumeStore::GetInstance()->GetVolume("BoundingLV");
81 G4LogicalVolume* theVolume = 88 G4LogicalVolume* theVolume =
82 theStep->GetPreStepPoint()->GetPhysicalV << 89 theStep->GetPreStepPoint()->GetPhysicalVolume()->GetLogicalVolume();
83 90
84 if ((edepStep > 0.) && (theVolume == targe << 91 if ((edepStep > 0.) && (theVolume==targetVolume))
>> 92 {
85 // Add edep to this event 93 // Add edep to this event
86 // 94 //
87 fpEventAction->AddEdepEvent(edepStep); 95 fpEventAction->AddEdepEvent(edepStep);
88 if (fpDetector->GetBarycenterList() == N << 96 if (fpDetector->GetBarycenterList()==NULL)
>> 97 {
89 G4cout << "Barycenter list is null!!!" 98 G4cout << "Barycenter list is null!!!" << G4endl;
90 } 99 }
91 else { << 100 else
92 CheckAndProcessDNAHit(x, y, z, edepSte << 101 {
>> 102 CheckAndProcessDNAHit(x,y,z,edepStep);
93 } 103 }
94 } 104 }
95 } 105 }
96 } 106 }
97 107
98 //....oooOO0OOooo........oooOO0OOooo........oo 108 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
99 109
100 G4bool SteppingAction::CheckAndProcessDNAHit(G << 110 G4bool SteppingAction::CheckAndProcessDNAHit(G4double x,G4double y, G4double z,
>> 111 G4double edepStep)
101 { 112 {
102 int numStrand = 0; << 113 int numStrand=0;
103 int numNucl = 0; << 114 int numNucl=0;
104 int intResidue = -1; // 0 for Phospat, 1 fo << 115 int intResidue=-1; // 0 for Phospat, 1 for Sugar, 2 for Base
105 unsigned short int hit = << 116 unsigned short int hit = (fpDetector->GetPDBlib()).ComputeMatchEdepDNA(
106 (fpDetector->GetPDBlib()) << 117 fpDetector->GetBarycenterList(),
107 .ComputeMatchEdepDNA(fpDetector->GetBary << 118 fpDetector->GetMoleculeList(),
108 y * 10., z * 10., << 119 x*10., y*10., z*10.,// x10 => angstrom<->nm
109 numStrand, numNucl, << 120 numStrand, numNucl, intResidue);
110 << 121
111 if (hit == 1) { << 122 if (hit==1)
112 if ((intResidue == 0) || (intResidue == 1) << 123 {
>> 124 if ((intResidue==0)||(intResidue==1)) //Edep in Phosphate or Sugar
113 { 125 {
114 fpEventAction->AddEdepToNucleotide(numSt << 126 fpEventAction->AddEdepToNucleotide(numStrand,numNucl,edepStep);
115 return true; 127 return true;
116 } 128 }
117 else { << 129 else
>> 130 {
118 return false; 131 return false;
119 } 132 }
120 } 133 }
121 else { << 134 else
>> 135 {
122 return false; 136 return false;
123 } 137 }
124 } 138 }
125 139