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1 // 1 //
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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. *
20 // * By using, copying, modifying or distri 20 // * By using, copying, modifying or distributing the software (or *
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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 // J. Comput. Phys. 274 (2014) 841-882 30 // J. Comput. Phys. 274 (2014) 841-882
31 // The Geant4-DNA web site is available at htt 31 // The Geant4-DNA web site is available at http://geant4-dna.org
32 // 32 //
33 // $Id$ 33 // $Id$
34 // 34 //
35 /// \file TimeStepAction.hh 35 /// \file TimeStepAction.hh
36 /// \brief Implementation of the TimeStepActio 36 /// \brief Implementation of the TimeStepAction class
37 37
38 #include "TimeStepAction.hh" 38 #include "TimeStepAction.hh"
39 << 39 #include "G4UnitsTable.hh"
40 #include "DetectorConstruction.hh" << 40 #include "G4SystemOfUnits.hh"
41 <<
42 #include "G4AnalysisManager.hh" <<
43 #include "G4IT.hh" 41 #include "G4IT.hh"
>> 42
44 #include "G4ITTrackHolder.hh" 43 #include "G4ITTrackHolder.hh"
45 #include "G4Molecule.hh" 44 #include "G4Molecule.hh"
46 #include "G4RunManager.hh" <<
47 #include "G4Scheduler.hh" 45 #include "G4Scheduler.hh"
48 #include "G4SystemOfUnits.hh" << 46 #include "G4AnalysisManager.hh"
49 #include "G4UnitsTable.hh" <<
50 // using namespace G4DNAPARSER; <<
51 47
52 TimeStepAction::TimeStepAction() : G4UserTimeS << 48 #include "DetectorConstruction.hh"
53 { << 49 #include "G4RunManager.hh"
54 fpDetector = dynamic_cast<const DetectorCons << 50 //using namespace G4DNAPARSER;
55 G4RunManager::GetRunManager()->GetUserDete <<
56 51
57 AddTimeStep(1 * picosecond, 0.1 * picosecond << 52 TimeStepAction::TimeStepAction() :
58 AddTimeStep(10 * picosecond, 1 * picosecond) << 53 G4UserTimeStepAction(),
59 AddTimeStep(100 * picosecond, 3 * picosecond << 54 fpDetector(0)
60 AddTimeStep(1000 * picosecond, 10 * picoseco << 55 {
>> 56 fpDetector =
>> 57 dynamic_cast<const DetectorConstruction*>(G4RunManager::GetRunManager()
>> 58 ->GetUserDetectorConstruction());
>> 59
>> 60 AddTimeStep(1 * picosecond, 0.1 * picosecond);
>> 61 AddTimeStep(10 * picosecond, 1 * picosecond);
>> 62 AddTimeStep(100 * picosecond, 3 * picosecond);
>> 63 AddTimeStep(1000 * picosecond, 10 * picosecond);
61 AddTimeStep(10000 * picosecond, 100 * picose 64 AddTimeStep(10000 * picosecond, 100 * picosecond);
62 } 65 }
63 66
64 //....oooOO0OOooo........oooOO0OOooo........oo 67 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
65 68
66 TimeStepAction::~TimeStepAction() 69 TimeStepAction::~TimeStepAction()
67 { 70 {
68 // dtor << 71 //dtor
69 } 72 }
70 73
71 //....oooOO0OOooo........oooOO0OOooo........oo 74 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
72 75
73 TimeStepAction::TimeStepAction(const TimeStepA << 76 TimeStepAction::TimeStepAction(const TimeStepAction& other) :
>> 77 G4UserTimeStepAction(other)
74 { 78 {
75 // copy ctor << 79 //copy ctor
76 } 80 }
77 81
78 //....oooOO0OOooo........oooOO0OOooo........oo 82 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
79 83
80 TimeStepAction& TimeStepAction::operator=(cons << 84 TimeStepAction&
>> 85 TimeStepAction::operator=(const TimeStepAction& rhs)
81 { 86 {
82 if (this == &rhs) return *this; << 87 if (this == &rhs)
>> 88 return *this;
83 return *this; 89 return *this;
84 } 90 }
85 91
86 //....oooOO0OOooo........oooOO0OOooo........oo 92 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
87 93
88 void TimeStepAction::Save(G4MolecularConfigura 94 void TimeStepAction::Save(G4MolecularConfiguration* molconf)
89 { 95 {
90 G4int moleculeID = molconf->GetMoleculeID(); 96 G4int moleculeID = molconf->GetMoleculeID();
91 const G4String& moleculeName = molconf->GetF 97 const G4String& moleculeName = molconf->GetFormatedName();
92 G4TrackList* trackList = G4ITTrackHolder::In 98 G4TrackList* trackList = G4ITTrackHolder::Instance()->GetMainList(moleculeID);
93 99
94 if (trackList == 0) return; << 100 if(trackList == 0) return;
95 101
96 G4TrackList::iterator it = trackList->begin( << 102 G4TrackList::iterator it = trackList->begin();
97 G4TrackList::iterator end = trackList->end() 103 G4TrackList::iterator end = trackList->end();
98 104
99 for (; it != end; ++it) { << 105 for (; it != end; ++it)
>> 106 {
100 G4Track* track = *it; 107 G4Track* track = *it;
101 SaveMoleculeInfo(track, moleculeID, molecu 108 SaveMoleculeInfo(track, moleculeID, moleculeName);
102 } 109 }
103 } 110 }
104 111
105 //....oooOO0OOooo........oooOO0OOooo........oo 112 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
106 113
107 void TimeStepAction::SaveMoleculeInfo(G4Track* << 114 void TimeStepAction::SaveMoleculeInfo(
>> 115 G4Track* track, G4int molID, const G4String& /*moleculeName*/)
108 { 116 {
109 G4AnalysisManager* analysisManager = G4Analy 117 G4AnalysisManager* analysisManager = G4AnalysisManager::Instance();
110 if (!analysisManager->IsActive()) { << 118 if(!analysisManager->IsActive()) {return; }
111 return; <<
112 } <<
113 119
114 const G4ThreeVector& position = track->GetPo 120 const G4ThreeVector& position = track->GetPosition();
115 // H_{3}O^{1} ID = 0 << 121 //H_{3}O^{1} ID = 0
116 // OH^{-1} ID = 1 << 122 //OH^{-1} ID = 1
117 // OH^{0} ID = 2 << 123 //OH^{0} ID = 2
118 // e_{aq}^{1} ID = 3 << 124 //e_{aq}^{1} ID = 3
119 // H0 ID = 4 << 125 //H0 ID = 4
120 // H_{2}^{0} ID = 5 << 126 //H_{2}^{0} ID = 5
121 // H2O2 ID = 6 << 127 //H2O2 ID = 6
122 // H_{2}O^{0} or H_{2}O^{1} ID=7-17 << 128 //H_{2}O^{0} or H_{2}O^{1} ID=7-17
123 << 129
124 G4double xp = position.x(); << 130 G4double xp = position.x();
125 G4double yp = position.y(); << 131 G4double yp = position.y();
126 G4double zp = position.z(); << 132 G4double zp = position.z();
127 G4double R = std::sqrt(xp * xp + yp * yp + z << 133 G4double R = std::sqrt(xp*xp+yp*yp+zp*zp) /CLHEP::nm;
128 // G4double RNP = fpDetector->GetNPRadius( << 134 //G4double RNP = fpDetector->GetNPRadius()/CLHEP::nm;
129 << 135
130 G4int offset = 10; << 136 G4int offset = 10;
131 << 137
132 if (molID < 7) { << 138 if(molID<7){
133 analysisManager->FillH1(molID + offset, R) << 139 analysisManager->FillH1(molID+offset, R);
134 } << 140 }else{
135 else { << 141 analysisManager->FillH1(17, R);
136 analysisManager->FillH1(17, R); << 142 }
137 } <<
138 143
139 G4Scheduler::Instance()->Stop(); << 144 G4Scheduler::Instance()->Stop();
140 } 145 }
141 //....oooOO0OOooo........oooOO0OOooo........oo 146 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
142 147
143 void TimeStepAction::UserPreTimeStepAction() 148 void TimeStepAction::UserPreTimeStepAction()
144 { 149 {
145 // Loop over defined molecules 150 // Loop over defined molecules
146 G4ConfigurationIterator it = G4MoleculeTable << 151 G4ConfigurationIterator it
>> 152 = G4MoleculeTable::Instance()->GetConfigurationIterator();
147 153
148 G4double time = G4Scheduler::Instance()->Get 154 G4double time = G4Scheduler::Instance()->GetGlobalTime();
149 << 155
150 if (time == 1. * picosecond) { << 156 if(time == 1.*picosecond){
151 while (it()) { << 157 while(it())
>> 158 {
152 G4MolecularConfiguration* molconf = it.v 159 G4MolecularConfiguration* molconf = it.value();
153 Save(molconf); 160 Save(molconf);
154 } 161 }
155 } 162 }
156 } 163 }
157 164
158 //....oooOO0OOooo........oooOO0OOooo........oo 165 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
159 166
160 void TimeStepAction::UserReactionAction(const << 167 void TimeStepAction::UserReactionAction(
161 const << 168 const G4Track&,
162 {} << 169 const G4Track&,
>> 170 const std::vector<G4Track*>* /*products*/)
>> 171 {
>> 172 }
163 173