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1 // 1 //
2 // ******************************************* 2 // ********************************************************************
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4 // * 4 // * *
5 // * The Geant4 software is copyright of th 5 // * The Geant4 software is copyright of the Copyright Holders of *
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10 // * 10 // * *
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12 // * institutes,nor the agencies providing fin 12 // * institutes,nor the agencies providing financial support for this *
13 // * work make any representation or warran 13 // * work make any representation or warranty, express or implied, *
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16 // * for the full disclaimer and the limitatio 16 // * for the full disclaimer and the limitation of liability. *
17 // * 17 // * *
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. *
20 // * By using, copying, modifying or distri 20 // * By using, copying, modifying or distributing the software (or *
21 // * any work based on the software) you ag 21 // * any work based on the software) you agree to acknowledge its *
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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 // $Id$
35 // 36 //
36 /// \file SteppingAction.cc 37 /// \file SteppingAction.cc
37 /// \brief Implementation of the SteppingActio 38 /// \brief Implementation of the SteppingAction class
38 39
39 #include "SteppingAction.hh" 40 #include "SteppingAction.hh"
40 41
41 #include "DetectorConstruction.hh" 42 #include "DetectorConstruction.hh"
42 #include "EventAction.hh" <<
43 <<
44 #include "G4EventManager.hh" 43 #include "G4EventManager.hh"
>> 44 #include "EventAction.hh"
45 #include "G4LogicalVolumeStore.hh" 45 #include "G4LogicalVolumeStore.hh"
46 #include "G4RunManager.hh" 46 #include "G4RunManager.hh"
47 #include "G4SteppingManager.hh" 47 #include "G4SteppingManager.hh"
48 #include "G4SystemOfUnits.hh" 48 #include "G4SystemOfUnits.hh"
49 49
50 //....oooOO0OOooo........oooOO0OOooo........oo 50 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
51 51
52 SteppingAction::SteppingAction() 52 SteppingAction::SteppingAction()
53 : G4UserSteppingAction(), RunInitObserver(), << 53 :G4UserSteppingAction(),RunInitObserver(),fpEventAction(0),fpDetector(0)
54 {} << 54 {
>> 55 }
55 56
56 //....oooOO0OOooo........oooOO0OOooo........oo 57 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
57 58
58 SteppingAction::~SteppingAction() {} << 59 SteppingAction::~SteppingAction()
>> 60 {
>> 61 }
59 62
60 //....oooOO0OOooo........oooOO0OOooo........oo 63 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
61 64
62 void SteppingAction::Initialize() 65 void SteppingAction::Initialize()
63 { 66 {
64 fpEventAction = (EventAction*)G4EventManager << 67 fpEventAction = (EventAction*) G4EventManager::GetEventManager()->
65 fpDetector = (DetectorConstruction*)G4RunMan << 68 GetUserEventAction();
>> 69 fpDetector = (DetectorConstruction*)G4RunManager::GetRunManager()->
>> 70 GetUserDetectorConstruction();
66 } 71 }
67 72
68 //....oooOO0OOooo........oooOO0OOooo........oo 73 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
69 74
70 void SteppingAction::UserSteppingAction(const 75 void SteppingAction::UserSteppingAction(const G4Step* theStep)
71 { 76 {
72 if (theStep->GetPostStepPoint()->GetProcessD << 77 if(theStep->GetPostStepPoint()->GetProcessDefinedStep()->GetProcessName()!=
>> 78 "Transportation")
>> 79 {
73 // Get position and edep of current step 80 // Get position and edep of current step
74 // 81 //
75 G4double x = theStep->GetPreStepPoint()->G << 82 G4double x = theStep->GetPreStepPoint()->GetPosition().x()/nanometer;
76 G4double y = theStep->GetPreStepPoint()->G << 83 G4double y = theStep->GetPreStepPoint()->GetPosition().y()/nanometer;
77 G4double z = theStep->GetPreStepPoint()->G << 84 G4double z = theStep->GetPreStepPoint()->GetPosition().z()/nanometer;
78 G4double edepStep = theStep->GetTotalEnerg << 85 G4double edepStep = theStep->GetTotalEnergyDeposit()/eV;
79 86
80 G4LogicalVolume* targetVolume = G4LogicalV << 87 G4LogicalVolume* targetVolume =
>> 88 G4LogicalVolumeStore::GetInstance()->GetVolume("BoundingLV");
81 G4LogicalVolume* theVolume = 89 G4LogicalVolume* theVolume =
82 theStep->GetPreStepPoint()->GetPhysicalV << 90 theStep->GetPreStepPoint()->GetPhysicalVolume()->GetLogicalVolume();
83 91
84 if ((edepStep > 0.) && (theVolume == targe << 92 if ((edepStep > 0.) && (theVolume==targetVolume))
>> 93 {
85 // Add edep to this event 94 // Add edep to this event
86 // 95 //
87 fpEventAction->AddEdepEvent(edepStep); 96 fpEventAction->AddEdepEvent(edepStep);
88 if (fpDetector->GetBarycenterList() == N << 97 if (fpDetector->GetBarycenterList()==NULL)
>> 98 {
89 G4cout << "Barycenter list is null!!!" 99 G4cout << "Barycenter list is null!!!" << G4endl;
90 } 100 }
91 else { << 101 else
92 CheckAndProcessDNAHit(x, y, z, edepSte << 102 {
>> 103 CheckAndProcessDNAHit(x,y,z,edepStep);
93 } 104 }
94 } 105 }
95 } 106 }
96 } 107 }
97 108
98 //....oooOO0OOooo........oooOO0OOooo........oo 109 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
99 110
100 G4bool SteppingAction::CheckAndProcessDNAHit(G << 111 G4bool SteppingAction::CheckAndProcessDNAHit(G4double x,G4double y, G4double z,
>> 112 G4double edepStep)
101 { 113 {
102 int numStrand = 0; << 114 int numStrand=0;
103 int numNucl = 0; << 115 int numNucl=0;
104 int intResidue = -1; // 0 for Phospat, 1 fo << 116 int intResidue=-1; // 0 for Phospat, 1 for Sugar, 2 for Base
105 unsigned short int hit = << 117 unsigned short int hit = (fpDetector->GetPDBlib()).ComputeMatchEdepDNA(
106 (fpDetector->GetPDBlib()) << 118 fpDetector->GetBarycenterList(),
107 .ComputeMatchEdepDNA(fpDetector->GetBary << 119 fpDetector->GetMoleculeList(),
108 y * 10., z * 10., << 120 x*10., y*10., z*10.,// x10 => angstrom<->nm
109 numStrand, numNucl, << 121 numStrand, numNucl, intResidue);
110 << 122
111 if (hit == 1) { << 123 if (hit==1)
112 if ((intResidue == 0) || (intResidue == 1) << 124 {
>> 125 if ((intResidue==0)||(intResidue==1)) //Edep in Phosphate or Sugar
113 { 126 {
114 fpEventAction->AddEdepToNucleotide(numSt << 127 fpEventAction->AddEdepToNucleotide(numStrand,numNucl,edepStep);
115 return true; 128 return true;
116 } 129 }
117 else { << 130 else
>> 131 {
118 return false; 132 return false;
119 } 133 }
120 } 134 }
121 else { << 135 else
>> 136 {
122 return false; 137 return false;
123 } 138 }
124 } 139 }
125 140