| Geant4 Cross Reference |
1 // 1 //
2 // ******************************************* 2 // ********************************************************************
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5 // * The Geant4 software is copyright of th 5 // * The Geant4 software is copyright of the Copyright Holders of *
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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 *
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23 // * acceptance of all terms of the Geant4 Sof 23 // * acceptance of all terms of the Geant4 Software license. *
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 // and the DNA geometry given in the Geom_DNA << 28 // and the DNA geometry given in the Geom_DNA example
29 // shall cite the following Geant4-DNA collabo 29 // shall cite the following Geant4-DNA collaboration publications:
30 // [1] NIM B 298 (2013) 47-54 30 // [1] NIM B 298 (2013) 47-54
31 // [2] Med. Phys. 37 (2010) 4692-4708 31 // [2] Med. Phys. 37 (2010) 4692-4708
32 // The Geant4-DNA web site is available at htt 32 // The Geant4-DNA web site is available at http://geant4-dna.org
33 // 33 //
>> 34 // $ID$
34 /// \file DetectorConstruction.cc 35 /// \file DetectorConstruction.cc
35 /// \brief Implementation of the DetectorConst 36 /// \brief Implementation of the DetectorConstruction class
36 37
37 #include "DetectorConstruction.hh" 38 #include "DetectorConstruction.hh"
38 39
39 // Geant4 40 // Geant4
>> 41 #include "globals.hh"
40 #include "CLHEP/Units/SystemOfUnits.h" 42 #include "CLHEP/Units/SystemOfUnits.h"
41 #include "ChromosomeParameterisation.hh" <<
42 <<
43 #include "G4Box.hh" <<
44 #include "G4Ellipsoid.hh" <<
45 #include "G4LogicalVolume.hh" 43 #include "G4LogicalVolume.hh"
46 #include "G4NistManager.hh" << 44 #include "G4UnionSolid.hh"
>> 45 #include "G4Box.hh"
47 #include "G4Orb.hh" 46 #include "G4Orb.hh"
>> 47 #include "G4Tubs.hh"
>> 48 #include "G4Ellipsoid.hh"
48 #include "G4PVParameterised.hh" 49 #include "G4PVParameterised.hh"
49 #include "G4PVPlacement.hh" 50 #include "G4PVPlacement.hh"
50 #include "G4RotationMatrix.hh" 51 #include "G4RotationMatrix.hh"
51 #include "G4Tubs.hh" <<
52 #include "G4UnionSolid.hh" <<
53 #include "G4VisAttributes.hh" 52 #include "G4VisAttributes.hh"
54 #include "globals.hh" << 53 #include "G4NistManager.hh"
>> 54 #include "ChromosomeParameterisation.hh"
55 55
56 #define countof(x) (sizeof(x) / sizeof(x[0])) 56 #define countof(x) (sizeof(x) / sizeof(x[0]))
57 57
58 using namespace std; 58 using namespace std;
59 using CLHEP::degree; <<
60 using CLHEP::micrometer; <<
61 using CLHEP::mm; 59 using CLHEP::mm;
>> 60 using CLHEP::degree;
62 using CLHEP::nanometer; 61 using CLHEP::nanometer;
>> 62 using CLHEP::micrometer;
63 63
64 static G4VisAttributes visInvBlue(false, G4Col 64 static G4VisAttributes visInvBlue(false, G4Colour(0.0, 0.0, 1.0));
65 static G4VisAttributes visInvWhite(false, G4Co 65 static G4VisAttributes visInvWhite(false, G4Colour(1.0, 1.0, 1.0));
66 static G4VisAttributes visInvPink(false, G4Col 66 static G4VisAttributes visInvPink(false, G4Colour(1.0, 0.0, 1.0));
67 static G4VisAttributes visInvCyan(false, G4Col 67 static G4VisAttributes visInvCyan(false, G4Colour(0.0, 1.0, 1.0));
68 static G4VisAttributes visInvRed(false, G4Colo 68 static G4VisAttributes visInvRed(false, G4Colour(1.0, 0.0, 0.0));
69 static G4VisAttributes visInvGreen(false, G4Co 69 static G4VisAttributes visInvGreen(false, G4Colour(0.0, 1.0, 0.0));
70 static G4VisAttributes visBlue(true, G4Colour( 70 static G4VisAttributes visBlue(true, G4Colour(0.0, 0.0, 1.0));
71 static G4VisAttributes visWhite(true, G4Colour 71 static G4VisAttributes visWhite(true, G4Colour(1.0, 1.0, 1.0));
72 static G4VisAttributes visPink(true, G4Colour( 72 static G4VisAttributes visPink(true, G4Colour(1.0, 0.0, 1.0));
73 static G4VisAttributes visCyan(true, G4Colour( 73 static G4VisAttributes visCyan(true, G4Colour(0.0, 1.0, 1.0));
74 static G4VisAttributes visRed(true, G4Colour(1 74 static G4VisAttributes visRed(true, G4Colour(1.0, 0.0, 0.0));
75 static G4VisAttributes visGreen(true, G4Colour 75 static G4VisAttributes visGreen(true, G4Colour(0.0, 1.0, 0.0));
76 76
>> 77
77 //....oooOO0OOooo........oooOO0OOooo........oo 78 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
78 79
79 DetectorConstruction::DetectorConstruction() << 80 DetectorConstruction::DetectorConstruction() :
80 : G4VUserDetectorConstruction(), fBuildChrom << 81 G4VUserDetectorConstruction(),
81 {} << 82 fBuildChromatineFiber(true),
>> 83 fBuildBases(false)
>> 84 {
>> 85 }
82 86
83 //....oooOO0OOooo........oooOO0OOooo........oo 87 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
84 88
85 DetectorConstruction::~DetectorConstruction() << 89 DetectorConstruction::~DetectorConstruction()
>> 90 {
>> 91 }
86 92
87 //....oooOO0OOooo........oooOO0OOooo........oo 93 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
88 94
89 G4VPhysicalVolume* DetectorConstruction::Const 95 G4VPhysicalVolume* DetectorConstruction::Construct()
90 { 96 {
91 DefineMaterials(); 97 DefineMaterials();
92 return ConstructDetector(); 98 return ConstructDetector();
93 } 99 }
94 100
95 //....oooOO0OOooo........oooOO0OOooo........oo 101 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
96 102
97 void DetectorConstruction::DefineMaterials() 103 void DetectorConstruction::DefineMaterials()
98 { 104 {
99 // Water is defined from NIST material datab 105 // Water is defined from NIST material database
100 G4NistManager* man = G4NistManager::Instance << 106 G4NistManager *man = G4NistManager::Instance();
101 man->FindOrBuildMaterial("G4_WATER"); 107 man->FindOrBuildMaterial("G4_WATER");
102 } 108 }
103 109
104 //....oooOO0OOooo........oooOO0OOooo........oo 110 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
105 111
106 void DetectorConstruction::LoadChromosome(cons << 112 void DetectorConstruction::LoadChromosome(const char* filename,
>> 113 G4VPhysicalVolume* chromBox,
107 G4Lo 114 G4LogicalVolume* logicBoxros)
108 { 115 {
109 ChromosomeParameterisation* cp = new Chromos 116 ChromosomeParameterisation* cp = new ChromosomeParameterisation(filename);
110 new G4PVParameterised("box ros", logicBoxros << 117 new G4PVParameterised("box ros",
>> 118 logicBoxros,
>> 119 chromBox,
>> 120 kUndefined,
>> 121 cp->GetNumRosettes(),
>> 122 cp);
111 123
112 G4cout << filename << " done" << G4endl; 124 G4cout << filename << " done" << G4endl;
113 } 125 }
114 126
115 //....oooOO0OOooo........oooOO0OOooo........oo 127 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
116 128
117 G4VPhysicalVolume* DetectorConstruction::Const 129 G4VPhysicalVolume* DetectorConstruction::ConstructDetector()
118 { 130 {
119 if (fBuildBases == false && fBuildChromatine << 131 if(fBuildBases == false && fBuildChromatineFiber == false)
120 G4cout << "=============================== << 132 {
121 G4cout << "WARNING from DetectorConstructi << 133 G4cout <<"======================================================" << G4endl;
122 G4cout << "As long as the flags fBuildBase << 134 G4cout <<"WARNING from DetectorConstruction::ConstructDetector:" << G4endl;
123 "false, the output root file wil << 135 G4cout << "As long as the flags fBuildBases and fBuildChromatineFiber are "
124 << G4endl; << 136 "false, the output root file will be empty" << G4endl;
125 G4cout << "This is intended for fast compu << 137 G4cout << "This is intended for fast computation, display, testing ..."
126 G4cout << "=============================== << 138 << G4endl;
>> 139 G4cout <<"======================================================" << G4endl;
127 } 140 }
128 141
129 G4String name; 142 G4String name;
130 143
131 /******************************************* 144 /***************************************************************************/
132 // World 145 // World
133 /******************************************* 146 /***************************************************************************/
134 147
135 DefineMaterials(); 148 DefineMaterials();
136 G4Material* waterMaterial = G4Material::GetM 149 G4Material* waterMaterial = G4Material::GetMaterial("G4_WATER");
137 150
138 G4Box* solidWorld = new G4Box("world", 10.0 151 G4Box* solidWorld = new G4Box("world", 10.0 * mm, 10.0 * mm, 10.0 * mm);
139 G4LogicalVolume* logicWorld = new G4LogicalV << 152 G4LogicalVolume* logicWorld = new G4LogicalVolume(solidWorld,
140 G4PVPlacement* physiWorld = << 153 waterMaterial,
141 new G4PVPlacement(0, G4ThreeVector(), "wor << 154 "world");
>> 155 G4PVPlacement* physiWorld = new G4PVPlacement(0,
>> 156 G4ThreeVector(),
>> 157 "world",
>> 158 logicWorld,
>> 159 0,
>> 160 false,
>> 161 0);
142 logicWorld->SetVisAttributes(&visInvWhite); 162 logicWorld->SetVisAttributes(&visInvWhite);
143 163
144 /******************************************* 164 /****************************************************************************/
145 // Box nucleus 165 // Box nucleus
146 /******************************************* 166 /****************************************************************************/
147 167
148 G4Box* solidTin = new G4Box("tin", 13 * micr << 168 G4Box* solidTin = new G4Box("tin",
149 G4LogicalVolume* logicTin = new G4LogicalVol << 169 13 * micrometer,
150 G4VPhysicalVolume* physiTin = << 170 10 * micrometer,
151 new G4PVPlacement(0, G4ThreeVector(), "tin << 171 5 * micrometer);
>> 172 G4LogicalVolume* logicTin = new G4LogicalVolume(solidTin,
>> 173 waterMaterial,
>> 174 "tin");
>> 175 G4VPhysicalVolume* physiTin = new G4PVPlacement(0,
>> 176 G4ThreeVector(),
>> 177 "tin",
>> 178 logicTin,
>> 179 physiWorld,
>> 180 false,
>> 181 0);
152 logicTin->SetVisAttributes(&visInvWhite); 182 logicTin->SetVisAttributes(&visInvWhite);
153 183
154 /******************************************* 184 /****************************************************************************/
155 // Cell nucleus 185 // Cell nucleus
156 /******************************************* 186 /****************************************************************************/
157 187
158 G4Ellipsoid* solidNucleus = << 188 G4Ellipsoid* solidNucleus = new G4Ellipsoid("nucleus",
159 new G4Ellipsoid("nucleus", 11.82 * microme << 189 11.82 * micrometer,
160 G4LogicalVolume* logicNucleus = new G4Logica << 190 8.52 * micrometer,
161 G4VPhysicalVolume* physiNucleus = << 191 3 * micrometer,
162 new G4PVPlacement(0, G4ThreeVector(), "phy << 192 0,
>> 193 0);
>> 194 G4LogicalVolume* logicNucleus = new G4LogicalVolume(solidNucleus,
>> 195 waterMaterial,
>> 196 "logic nucleus");
>> 197 G4VPhysicalVolume* physiNucleus = new G4PVPlacement(0,
>> 198 G4ThreeVector(),
>> 199 "physi nucleus",
>> 200 logicNucleus,
>> 201 physiTin,
>> 202 false,
>> 203 0);
163 logicNucleus->SetVisAttributes(&visPink); 204 logicNucleus->SetVisAttributes(&visPink);
164 205
165 /******************************************* 206 /****************************************************************************/
166 // Chromosomes territ 207 // Chromosomes territories
167 /******************************************* 208 /****************************************************************************/
168 // NOTE: The only supported values for the r 209 // NOTE: The only supported values for the rotation are
169 // 0 and 90 degrees on the Y axis. 210 // 0 and 90 degrees on the Y axis.
170 G4double chromosomePositionSizeRotation[][7] 211 G4double chromosomePositionSizeRotation[][7] = {
171 {4.467, 2.835, 0, 1.557, 1.557, 1.557, 90} << 212 {4.467, 2.835, 0, 1.557, 1.557, 1.557, 90},
172 {-4.467, 2.835, 0, 1.557, 1.557, 1.557, 0} << 213 {-4.467, 2.835, 0, 1.557, 1.557, 1.557, 0},
173 {4.423, -2.831, 0, 1.553, 1.553, 1.553, 90 << 214 {4.423, -2.831, 0, 1.553, 1.553, 1.553, 90},
174 {-4.423, -2.831, 0, 1.553, 1.553, 1.553, 0 << 215 {-4.423, -2.831, 0, 1.553, 1.553, 1.553, 0},
175 {1.455, 5.63, 0, 1.455, 1.455, 1.455, 0}, << 216 {1.455, 5.63, 0, 1.455, 1.455, 1.455, 0},
176 {-1.455, 5.63, 0, 1.455, 1.455, 1.455, 90} << 217 {-1.455, 5.63, 0, 1.455, 1.455, 1.455, 90},
177 {1.435, 0, 1.392, 1.435, 1.435, 1.435, 0}, << 218 {1.435, 0, 1.392, 1.435, 1.435, 1.435, 0},
178 {-1.435, 0, 1.392, 1.435, 1.435, 1.435, 90 << 219 {-1.435, 0, 1.392, 1.435, 1.435, 1.435, 90},
179 {1.407, 0, -1.450, 1.407, 1.407, 1.407, 90 << 220 {1.407, 0, -1.450, 1.407, 1.407, 1.407, 90}, // 5 right
180 {-1.407, 0, -1.450, 1.407, 1.407, 1.407, 0 << 221 {-1.407, 0, -1.450, 1.407, 1.407, 1.407, 0}, // 5 left
181 {1.380, -5.437, 0, 1.380, 1.380, 1.380, 0} << 222 {1.380, -5.437, 0, 1.380, 1.380, 1.380, 0},
182 {-1.380, -5.437, 0, 1.380, 1.380, 1.380, 9 << 223 {-1.380, -5.437, 0, 1.380, 1.380, 1.380, 90},
183 {1.347, 2.782, -1.150, 1.347, 1.347, 1.347 << 224 {1.347, 2.782, -1.150, 1.347, 1.347, 1.347, 90},
184 {-1.347, 2.782, -1.150, 1.347, 1.347, 1.34 << 225 {-1.347, 2.782, -1.150, 1.347, 1.347, 1.347, 0},
185 {1.311, -2.746, -1.220, 1.311, 1.311, 1.31 << 226 {1.311, -2.746, -1.220, 1.311, 1.311, 1.311, 90},
186 {-1.311, -2.746, -1.220, 1.311, 1.311, 1.3 << 227 {-1.311, -2.746, -1.220, 1.311, 1.311, 1.311, 0},
187 {7.251, -2.541, 0, 1.275, 1.275, 1.275, 0} << 228 {7.251, -2.541, 0, 1.275, 1.275, 1.275, 0},
188 {-6.701, 0, -0.85, 1.275, 1.275, 1.275, 90 << 229 {-6.701, 0, -0.85, 1.275, 1.275, 1.275, 90},
189 {4.148, 0, 1.278, 1.278, 1.278, 1.278, 90} << 230 {4.148, 0, 1.278, 1.278, 1.278, 1.278, 90}, // 10 right
190 {-4.148, 0, 1.278, 1.278, 1.278, 1.278, 0} << 231 {-4.148, 0, 1.278, 1.278, 1.278, 1.278, 0}, // 10 left
191 {4.147, 0, -1.277, 1.277, 1.277, 1.277, 0} << 232 {4.147, 0, -1.277, 1.277, 1.277, 1.277, 0},
192 {-4.147, 0, -1.277, 1.277, 1.277, 1.277, 9 << 233 {-4.147, 0, -1.277, 1.277, 1.277, 1.277, 90},
193 {8.930, 0.006, 0, 1.272, 1.272, 1.272, 90} << 234 {8.930, 0.006, 0, 1.272, 1.272, 1.272, 90},
194 {-7.296, 2.547, 0, 1.272, 1.272, 1.272, 90 << 235 {-7.296, 2.547, 0, 1.272, 1.272, 1.272, 90},
195 {1.207, -2.642, 1.298, 1.207, 1.207, 1.207 << 236 {1.207, -2.642, 1.298, 1.207, 1.207, 1.207, 0},
196 {-1.207, -2.642, 1.298, 1.207, 1.207, 1.20 << 237 {-1.207, -2.642, 1.298, 1.207, 1.207, 1.207, 90},
197 {1.176, 2.611, 1.368, 1.176, 1.176, 1.176, << 238 {1.176, 2.611, 1.368, 1.176, 1.176, 1.176, 0},
198 {-1.176, 2.611, 1.368, 1.176, 1.176, 1.176 << 239 {-1.176, 2.611, 1.368, 1.176, 1.176, 1.176, 90},
199 {4.065, 5.547, 0, 1.155, 1.155, 1.155, 90} << 240 {4.065, 5.547, 0, 1.155, 1.155, 1.155, 90}, // 15 right
200 {-4.065, 5.547, 0, 1.155, 1.155, 1.155, 0} << 241 {-4.065, 5.547, 0, 1.155, 1.155, 1.155, 0}, // 15 left
201 {6.542, 0.159, 1.116, 1.116, 1.116, 1.116, << 242 {6.542, 0.159, 1.116, 1.116, 1.116, 1.116, 0},
202 {-9.092, 0, 0, 1.116, 1.116, 1.116, 0}, << 243 {-9.092, 0, 0, 1.116, 1.116, 1.116, 0},
203 {6.507, 0.159, -1.081, 1.081, 1.081, 1.081 << 244 {6.507, 0.159, -1.081, 1.081, 1.081, 1.081, 90},
204 {-7.057, -2.356, 0, 1.081, 1.081, 1.081, 9 << 245 {-7.057, -2.356, 0, 1.081, 1.081, 1.081, 90},
205 {3.824, -5.448, 0, 1.064, 1.064, 1.064, 90 << 246 {3.824, -5.448, 0, 1.064, 1.064, 1.064, 90},
206 {-3.824, -5.448, 0, 1.064, 1.064, 1.064, 0 << 247 {-3.824, -5.448, 0, 1.064, 1.064, 1.064, 0},
207 {5.883, -5.379, 0, 0.995, 0.995, 0.995, 0} << 248 {5.883, -5.379, 0, 0.995, 0.995, 0.995, 0},
208 {-9.133, -2.111, 0, 0.995, 0.995, 0.995, 0 << 249 {-9.133, -2.111, 0, 0.995, 0.995, 0.995, 0},
209 {6.215, 5.387, 0, 0.995, 0.995, 0.995, 0}, << 250 {6.215, 5.387, 0, 0.995, 0.995, 0.995, 0}, // 20 right
210 {-6.971, -4.432, 0, 0.995, 0.995, 0.995, 9 << 251 {-6.971, -4.432, 0, 0.995, 0.995, 0.995, 90}, // 20 left
211 {9.583, 2.177, 0, 0.899, 0.899, 0.899, 90} << 252 {9.583, 2.177, 0, 0.899, 0.899, 0.899, 90},
212 {-9.467, 2.03, 0, 0.899, 0.899, 0.899, 0}, << 253 {-9.467, 2.03, 0, 0.899, 0.899, 0.899, 0},
213 {9.440, -2.180, 0, 0.914, 0.914, 0.914, 90 << 254 {9.440, -2.180, 0, 0.914, 0.914, 0.914, 90},
214 {-6.34, 0, 1.339, 0.914, 0.914, 0.914, 0}, << 255 {-6.34, 0, 1.339, 0.914, 0.914, 0.914, 0},
215 {-6.947, 4.742, 0, 0.923, 0.923, 0.923, 90 << 256 {-6.947, 4.742, 0, 0.923, 0.923, 0.923, 90}, // Y
216 {7.354, 2.605, 0, 1.330, 1.330, 1.330, 0} << 257 {7.354, 2.605, 0, 1.330, 1.330, 1.330, 0} // X
217 }; 258 };
218 259
219 G4RotationMatrix* rotch = new G4RotationMatr 260 G4RotationMatrix* rotch = new G4RotationMatrix;
220 rotch->rotateY(90 * degree); 261 rotch->rotateY(90 * degree);
221 262
222 vector<G4VPhysicalVolume*> physiBox(48); 263 vector<G4VPhysicalVolume*> physiBox(48);
223 264
224 for (unsigned int i = 0; i < countof(chromos << 265 for (unsigned int i = 0; i < countof(chromosomePositionSizeRotation); i++)
>> 266 {
225 G4double* p = &chromosomePositionSizeRotat 267 G4double* p = &chromosomePositionSizeRotation[i][0];
226 G4double* size = &chromosomePositionSizeRo 268 G4double* size = &chromosomePositionSizeRotation[i][3];
227 G4double rotation = chromosomePositionSize 269 G4double rotation = chromosomePositionSizeRotation[i][6];
228 G4ThreeVector pos(p[0] * micrometer, p[1] 270 G4ThreeVector pos(p[0] * micrometer, p[1] * micrometer, p[2] * micrometer);
229 G4RotationMatrix* rot = rotation == 0 ? 0 271 G4RotationMatrix* rot = rotation == 0 ? 0 : rotch;
230 272
231 ostringstream ss; 273 ostringstream ss;
232 ss << "box" << (i / 2) + 1 << (i % 2 ? 'l' 274 ss << "box" << (i / 2) + 1 << (i % 2 ? 'l' : 'r');
233 name = ss.str(); 275 name = ss.str();
234 ss.str(""); 276 ss.str("");
235 ss.clear(); 277 ss.clear();
236 278
237 /* 279 /*
238 snprintf(name, countof(name), "box%d%c", 280 snprintf(name, countof(name), "box%d%c",
239 (i / 2) + 1, i % 2 ? 'l' : 'r'); 281 (i / 2) + 1, i % 2 ? 'l' : 'r');
240 */ 282 */
241 G4Box* solidBox = << 283 G4Box* solidBox = new G4Box(name,
242 new G4Box(name, size[0] * micrometer, si << 284 size[0] * micrometer,
243 G4LogicalVolume* logicBox = new G4LogicalV << 285 size[1] * micrometer,
244 physiBox[i] = new G4PVPlacement(rot, pos, << 286 size[2] * micrometer);
>> 287 G4LogicalVolume* logicBox = new G4LogicalVolume(solidBox,
>> 288 waterMaterial,
>> 289 name);
>> 290 physiBox[i] = new G4PVPlacement(rot,
>> 291 pos,
>> 292 "chromo",
>> 293 logicBox,
>> 294 physiNucleus,
>> 295 false,
>> 296 0);
245 logicBox->SetVisAttributes(&visBlue); 297 logicBox->SetVisAttributes(&visBlue);
246 } 298 }
247 299
248 /******************************************* 300 /**************************************************************************/
249 // Box containing the chroma 301 // Box containing the chromatin flowers
250 /******************************************* 302 /**************************************************************************/
251 303
252 G4Tubs* solidBoxros = new G4Tubs("solid box << 304 G4Tubs* solidBoxros = new G4Tubs("solid box ros",
253 0 * degree, << 305 0 * nanometer,
254 G4LogicalVolume* logicBoxros = new G4Logical << 306 399 * nanometer,
>> 307 20 * nanometer,
>> 308 0 * degree,
>> 309 360 * degree);
>> 310 G4LogicalVolume* logicBoxros = new G4LogicalVolume(solidBoxros,
>> 311 waterMaterial,
>> 312 "box ros");
255 logicBoxros->SetVisAttributes(&visInvBlue); 313 logicBoxros->SetVisAttributes(&visInvBlue);
256 314
257 // Loading flower box position for each chro << 315 //Loading flower box position for each chromosome territory
258 316
259 for (int k = 0; k < 22; k++) { << 317 for (int k = 0; k < 22; k++)
>> 318 {
260 ostringstream oss; 319 ostringstream oss;
261 oss << "chromo" << k + 1 << ".dat"; 320 oss << "chromo" << k + 1 << ".dat";
262 name = oss.str(); 321 name = oss.str();
263 oss.str(""); 322 oss.str("");
264 oss.clear(); 323 oss.clear();
265 // snprintf(name, countof(name), "chromo%d << 324 //snprintf(name, countof(name), "chromo%d.dat", k + 1);
266 LoadChromosome(name.c_str(), physiBox[k * 325 LoadChromosome(name.c_str(), physiBox[k * 2], logicBoxros);
267 LoadChromosome(name.c_str(), physiBox[k * 326 LoadChromosome(name.c_str(), physiBox[k * 2 + 1], logicBoxros);
268 } 327 }
269 328
270 LoadChromosome("chromoY.dat", physiBox[44], 329 LoadChromosome("chromoY.dat", physiBox[44], logicBoxros);
271 LoadChromosome("chromoX.dat", physiBox[45], 330 LoadChromosome("chromoX.dat", physiBox[45], logicBoxros);
272 331
273 /******************************************* 332 /****************************************************************************/
274 if (fBuildChromatineFiber) { << 333 if (fBuildChromatineFiber)
>> 334 {
275 // chromatin fiber envelope 335 // chromatin fiber envelope
276 G4Tubs* solidEnv = new G4Tubs("chromatin f << 336 G4Tubs* solidEnv = new G4Tubs("chromatin fiber",
277 0 * degree, << 337 0,
278 G4LogicalVolume* logicEnv = new G4LogicalV << 338 15.4 * nanometer,
>> 339 80.5 * nanometer,
>> 340 0 * degree,
>> 341 360 * degree);
>> 342 G4LogicalVolume* logicEnv = new G4LogicalVolume(solidEnv,
>> 343 waterMaterial,
>> 344 "LV chromatin fiber");
279 logicEnv->SetVisAttributes(&visInvPink); 345 logicEnv->SetVisAttributes(&visInvPink);
280 346
281 // Chromatin fiber position 347 // Chromatin fiber position
282 for (G4int i = 0; i < 7; i++) { << 348 for (G4int i = 0; i < 7; i++)
>> 349 {
283 G4RotationMatrix* rotFiber = new G4Rotat 350 G4RotationMatrix* rotFiber = new G4RotationMatrix;
284 rotFiber->rotateX(90 * degree); 351 rotFiber->rotateX(90 * degree);
285 rotFiber->rotateY(i * 25.72 * degree); 352 rotFiber->rotateY(i * 25.72 * degree);
286 G4ThreeVector posFiber = G4ThreeVector(0 353 G4ThreeVector posFiber = G4ThreeVector(0, 152 * nanometer, 0);
287 posFiber.rotateZ(i * 25.72 * degree); 354 posFiber.rotateZ(i * 25.72 * degree);
288 new G4PVPlacement(rotFiber, posFiber, lo << 355 new G4PVPlacement(rotFiber,
>> 356 posFiber,
>> 357 logicEnv,
>> 358 "physi env",
>> 359 logicBoxros,
>> 360 false,
>> 361 0);
289 362
290 rotFiber = new G4RotationMatrix; 363 rotFiber = new G4RotationMatrix;
291 rotFiber->rotateX(90 * degree); 364 rotFiber->rotateX(90 * degree);
292 rotFiber->rotateY((7 + i) * 25.72 * degr 365 rotFiber->rotateY((7 + i) * 25.72 * degree);
293 posFiber = G4ThreeVector(0, 152 * nanome 366 posFiber = G4ThreeVector(0, 152 * nanometer, 0);
294 posFiber.rotateZ((7 + i) * 25.72 * degre 367 posFiber.rotateZ((7 + i) * 25.72 * degree);
295 new G4PVPlacement(rotFiber, posFiber, lo << 368 new G4PVPlacement(rotFiber,
>> 369 posFiber,
>> 370 logicEnv,
>> 371 "physi env",
>> 372 logicBoxros,
>> 373 false,
>> 374 0);
296 375
297 rotFiber = new G4RotationMatrix; 376 rotFiber = new G4RotationMatrix;
298 rotFiber->rotateX(90 * degree); 377 rotFiber->rotateX(90 * degree);
299 rotFiber->rotateY((25.72 + (i - 14) * 51 378 rotFiber->rotateY((25.72 + (i - 14) * 51.43) * degree);
300 posFiber = G4ThreeVector(-36.5 * nanomet 379 posFiber = G4ThreeVector(-36.5 * nanometer, 312 * nanometer, 0);
301 posFiber.rotateZ((i - 14) * 51.43 * degr 380 posFiber.rotateZ((i - 14) * 51.43 * degree);
302 new G4PVPlacement(rotFiber, posFiber, lo << 381 new G4PVPlacement(rotFiber,
>> 382 posFiber,
>> 383 logicEnv,
>> 384 "physi env",
>> 385 logicBoxros,
>> 386 false,
>> 387 0);
303 388
304 rotFiber = new G4RotationMatrix; 389 rotFiber = new G4RotationMatrix;
305 rotFiber->rotateX(90 * degree); 390 rotFiber->rotateX(90 * degree);
306 rotFiber->rotateY(180 * degree); 391 rotFiber->rotateY(180 * degree);
307 rotFiber->rotateY((i - 21) * 51.43 * deg 392 rotFiber->rotateY((i - 21) * 51.43 * degree);
308 posFiber = G4ThreeVector(-103 * nanomete 393 posFiber = G4ThreeVector(-103 * nanometer, 297 * nanometer, 0);
309 posFiber.rotateZ((i - 21) * 51.43 * degr 394 posFiber.rotateZ((i - 21) * 51.43 * degree);
310 new G4PVPlacement(rotFiber, posFiber, lo << 395 new G4PVPlacement(rotFiber,
>> 396 posFiber,
>> 397 logicEnv,
>> 398 "physi env",
>> 399 logicBoxros,
>> 400 false,
>> 401 0);
>> 402
311 } 403 }
312 404
313 if (fBuildBases) { << 405 if (fBuildBases)
>> 406 {
314 // Histones 407 // Histones
315 G4Tubs* solidHistone = new G4Tubs("solid << 408 G4Tubs* solidHistone = new G4Tubs("solid histone",
316 0 * de << 409 0,
317 G4LogicalVolume* logicHistone = << 410 3.25 * nanometer,
318 new G4LogicalVolume(solidHistone, wate << 411 2.85 * nanometer,
>> 412 0 * degree,
>> 413 360 * degree);
>> 414 G4LogicalVolume* logicHistone = new G4LogicalVolume(solidHistone,
>> 415 waterMaterial,
>> 416 "logic histone");
319 417
320 // Base pair << 418 //Base pair
321 G4Orb* solidBp1 = new G4Orb("blue sphere 419 G4Orb* solidBp1 = new G4Orb("blue sphere", 0.17 * nanometer);
322 G4LogicalVolume* logicBp1 = new G4Logica << 420 G4LogicalVolume* logicBp1 = new G4LogicalVolume(solidBp1,
>> 421 waterMaterial,
>> 422 "logic blue sphere");
323 G4Orb* solidBp2 = new G4Orb("pink sphere 423 G4Orb* solidBp2 = new G4Orb("pink sphere", 0.17 * nanometer);
324 G4LogicalVolume* logicBp2 = new G4Logica << 424 G4LogicalVolume* logicBp2 = new G4LogicalVolume(solidBp2,
>> 425 waterMaterial,
>> 426 "logic pink sphere");
325 427
326 // Phosphodiester group << 428 //Phosphodiester group
327 429
328 G4Orb* solidSugar_48em1_nm = new G4Orb(" 430 G4Orb* solidSugar_48em1_nm = new G4Orb("sugar", 0.48 * nanometer);
329 431
330 G4ThreeVector posi(0.180248 * nanometer, << 432 G4ThreeVector posi(0.180248 * nanometer,
331 G4UnionSolid* uniDNA = << 433 0.32422 * nanometer,
332 new G4UnionSolid("move", solidSugar_48 << 434 0.00784 * nanometer);
333 << 435 G4UnionSolid* uniDNA = new G4UnionSolid("move",
334 G4ThreeVector posi2(-0.128248 * nanomete << 436 solidSugar_48em1_nm,
335 G4UnionSolid* uniDNA2 = << 437 solidSugar_48em1_nm,
336 new G4UnionSolid("move2", solidSugar_4 << 438 0,
>> 439 posi);
>> 440
>> 441 G4ThreeVector posi2(-0.128248 * nanometer,
>> 442 0.41227 * nanometer,
>> 443 0.03584 * nanometer);
>> 444 G4UnionSolid* uniDNA2 = new G4UnionSolid("move2",
>> 445 solidSugar_48em1_nm,
>> 446 solidSugar_48em1_nm,
>> 447 0,
>> 448 posi2);
337 449
338 /*************************************** 450 /************************************************************************
339 Phosphodiester group Position 451 Phosphodiester group Position
340 *************************************** 452 ************************************************************************/
341 453
342 for (G4int n = 2; n < 200; n++) { << 454 for (G4int n = 2; n < 200; n++)
343 G4double SP1[2][3] = { << 455 {
344 {(-0.6 * nanometer) * cos(n * 0.26), << 456 G4double SP1[2][3] = {
345 {(0.6 * nanometer) * cos(n * 0.26), << 457 { (-0.6 * nanometer) * cos(n * 0.26),
346 G4double matriceSP1[3][3] = { << 458 0, (0.6* nanometer) * sin(n * 0.26) },
347 {cos(n * 0.076), -sin(n * 0.076), 0} << 459 { (0.6 * nanometer) * cos(n * 0.26),
348 G4double matriceSP2[2][3]; << 460 0, (-0.6 * nanometer) * sin(0.26 * n) }
349 << 461 };
350 for (G4int i = 0; i < 3; i++) { << 462 G4double matriceSP1[3][3] = {
351 G4double sumSP1 = 0; << 463 { cos(n * 0.076), -sin(n * 0.076), 0 },
352 G4double sumSP2 = 0; << 464 { sin(n * 0.076), cos(n * 0.076), 0 },
353 for (G4int j = 0; j < 3; j++) { << 465 { 0, 0, 1 }
354 sumSP1 += matriceSP1[i][j] * SP1[0 << 466 };
355 sumSP2 += matriceSP1[i][j] * SP1[1 << 467 G4double matriceSP2[2][3];
356 } << 468
357 matriceSP2[0][i] = sumSP1; << 469 for (G4int i = 0; i < 3; i++)
358 matriceSP2[1][i] = sumSP2; << 470 {
>> 471 G4double sumSP1 = 0;
>> 472 G4double sumSP2 = 0;
>> 473 for (G4int j = 0; j < 3; j++)
>> 474 {
>> 475 sumSP1 += matriceSP1[i][j] * SP1[0][j];
>> 476 sumSP2 += matriceSP1[i][j] * SP1[1][j];
359 } 477 }
360 << 478 matriceSP2[0][i] = sumSP1;
361 G4double heliceSP[3] = {(4.85 * nanome << 479 matriceSP2[1][i] = sumSP2;
362 (4.85 * nanome <<
363 <<
364 for (G4int i = 0; i < 3; i++) { <<
365 matriceSP2[0][i] += heliceSP[i]; <<
366 matriceSP2[1][i] += heliceSP[i]; <<
367 } <<
368 G4ThreeVector posSugar1(matriceSP2[0][ <<
369 (matriceSP2[0] <<
370 G4ThreeVector posSugar2(matriceSP2[1][ <<
371 (matriceSP2[1] <<
372 <<
373 ostringstream ss; <<
374 ss << "sugar_" << n; <<
375 name = ss.str().c_str(); <<
376 ss.str(""); <<
377 ss.clear(); <<
378 <<
379 // snprintf(name, countof(name), "sug <<
380 uniDNA = new G4UnionSolid(name, uniDNA <<
381 <<
382 ss << "sugar_" << n; <<
383 name = ss.str().c_str(); <<
384 ss.str(""); <<
385 ss.clear(); <<
386 <<
387 // snprintf(name, countof(name), "sug <<
388 uniDNA2 = new G4UnionSolid(name, uniDN <<
389 } 480 }
390 G4LogicalVolume* logicSphere3 = new G4Lo <<
391 G4LogicalVolume* logicSphere4 = new G4Lo <<
392 481
393 /*************************************** << 482 G4double heliceSP[3] = {
394 Base pair Position << 483 (4.85 * nanometer) * cos(n * 0.076),
395 *************************************** << 484 (4.85 * nanometer) * sin(n * 0.076),
396 for (G4int n = 0; n < 200; n++) { << 485 (n * 0.026 * nanometer)
>> 486 };
>> 487
>> 488 for (G4int i = 0; i < 3; i++)
>> 489 {
>> 490 matriceSP2[0][i] += heliceSP[i];
>> 491 matriceSP2[1][i] += heliceSP[i];
>> 492 }
>> 493 G4ThreeVector posSugar1(matriceSP2[0][2],
>> 494 matriceSP2[0][1],
>> 495 (matriceSP2[0][0]) - (4.25 * nanometer));
>> 496 G4ThreeVector posSugar2(matriceSP2[1][2],
>> 497 matriceSP2[1][1],
>> 498 (matriceSP2[1][0]) - (5.45 * nanometer));
>> 499
>> 500 ostringstream ss;
>> 501 ss << "sugar_" << n;
>> 502 name = ss.str().c_str();
>> 503 ss.str("");
>> 504 ss.clear();
>> 505
>> 506 // snprintf(name, countof(name), "sugar %d", n);
>> 507 uniDNA = new G4UnionSolid(name,
>> 508 uniDNA,
>> 509 solidSugar_48em1_nm,
>> 510 0,
>> 511 posSugar1);
>> 512
>> 513 ss << "sugar_" << n;
>> 514 name = ss.str().c_str();
>> 515 ss.str("");
>> 516 ss.clear();
>> 517
>> 518 // snprintf(name, countof(name), "sugar %d", n);
>> 519 uniDNA2 = new G4UnionSolid(name,
>> 520 uniDNA2,
>> 521 solidSugar_48em1_nm,
>> 522 0,
>> 523 posSugar2);
>> 524 }
>> 525 G4LogicalVolume* logicSphere3 = new G4LogicalVolume(uniDNA,
>> 526 waterMaterial,
>> 527 "logic sugar 2");
>> 528 G4LogicalVolume* logicSphere4 = new G4LogicalVolume(uniDNA2,
>> 529 waterMaterial,
>> 530 "logic sugar 4");
>> 531
>> 532 /**************************************************************************
>> 533 Base pair Position
>> 534 **************************************************************************/
>> 535 for (G4int n = 0; n < 200; n++)
>> 536 {
397 G4double bp1[2][3] = { 537 G4double bp1[2][3] = {
398 {(-0.34 * nanometer) * cos(n * 0.26) << 538 { (-0.34 * nanometer) * cos(n * 0.26),
399 {(0.34 * nanometer) * cos(n * 0.26), << 539 0, (0.34* nanometer) * sin(n * 0.26) },
>> 540 { (0.34 * nanometer) * cos(n * 0.26),
>> 541 0, (-0.34 * nanometer) * sin(0.26 * n) }
>> 542 };
400 G4double matriceBP1[3][3] = { 543 G4double matriceBP1[3][3] = {
401 {cos(n * 0.076), -sin(n * 0.076), 0} << 544 { cos(n * 0.076), -sin(n * 0.076), 0 },
>> 545 {sin(n * 0.076), cos(n * 0.076), 0 },
>> 546 { 0, 0, 1 }
>> 547 };
402 G4double matriceBP2[2][3]; 548 G4double matriceBP2[2][3];
403 549
404 for (G4int i = 0; i < 3; i++) { << 550 for (G4int i = 0; i < 3; i++)
>> 551 {
405 G4double sumBP1 = 0; 552 G4double sumBP1 = 0;
406 G4double sumBP2 = 0; 553 G4double sumBP2 = 0;
407 for (G4int j = 0; j < 3; j++) { << 554 for (G4int j = 0; j < 3; j++)
>> 555 {
408 sumBP1 += matriceBP1[i][j] * bp1[0 556 sumBP1 += matriceBP1[i][j] * bp1[0][j];
409 sumBP2 += matriceBP1[i][j] * bp1[1 557 sumBP2 += matriceBP1[i][j] * bp1[1][j];
410 } 558 }
411 matriceBP2[0][i] = sumBP1; 559 matriceBP2[0][i] = sumBP1;
412 matriceBP2[1][i] = sumBP2; 560 matriceBP2[1][i] = sumBP2;
413 } 561 }
414 G4double heliceBP[3] = {(4.8 * nanomet << 562 G4double heliceBP[3] = {
415 (4.8 * nanomet << 563 (4.8 * nanometer) * cos(n * 0.076),
>> 564 (4.8 * nanometer) * sin(n * 0.076),
>> 565 n * 0.026 * nanometer
>> 566 };
416 567
417 for (G4int i = 0; i < 3; i++) { << 568 for (G4int i = 0; i < 3; i++)
>> 569 {
418 matriceBP2[0][i] += heliceBP[i]; 570 matriceBP2[0][i] += heliceBP[i];
419 matriceBP2[1][i] += heliceBP[i]; 571 matriceBP2[1][i] += heliceBP[i];
420 } 572 }
421 G4ThreeVector position1(matriceBP2[0][ << 573 G4ThreeVector position1(matriceBP2[0][2],
>> 574 matriceBP2[0][1],
422 matriceBP2[0][ 575 matriceBP2[0][0] - (4.25 * nanometer));
423 G4ThreeVector position2(matriceBP2[1][ << 576 G4ThreeVector position2(matriceBP2[1][2],
>> 577 matriceBP2[1][1],
424 matriceBP2[1][ 578 matriceBP2[1][0] - (5.45 * nanometer));
425 579
426 new G4PVPlacement(0, position1, logicB << 580 new G4PVPlacement(0,
427 new G4PVPlacement(0, position2, logicB << 581 position1,
428 } << 582 logicBp1,
>> 583 "physi blue sphere",
>> 584 logicSphere3,
>> 585 false,
>> 586 0);
>> 587 new G4PVPlacement(0,
>> 588 position2,
>> 589 logicBp2,
>> 590 "physi pink sphere",
>> 591 logicSphere4,
>> 592 false,
>> 593 0);
>> 594 }
429 595
430 /*************************************** << 596 /****************************************************************************/
431 // Initial position of d << 597 // Initial position of different elements
432 /*************************************** << 598 /****************************************************************************/
433 // DNA and histone positions 599 // DNA and histone positions
434 for (int j = 0; j < 90; j++) { << 600 for (int j = 0; j < 90; j++)
>> 601 {
435 // DNA (bp-SP) 602 // DNA (bp-SP)
436 G4RotationMatrix* rotStrand1 = new G4R 603 G4RotationMatrix* rotStrand1 = new G4RotationMatrix;
437 rotStrand1->rotateZ(j * -51.43 * degre 604 rotStrand1->rotateZ(j * -51.43 * degree);
438 G4ThreeVector posStrand1(-2.7 * nanome << 605 G4ThreeVector posStrand1(-2.7 * nanometer,
>> 606 9.35 * nanometer,
439 (-69.9 * nano 607 (-69.9 * nanometer) + (j * 1.67 * nanometer));
440 posStrand1.rotateZ(j * 51.43 * degree) 608 posStrand1.rotateZ(j * 51.43 * degree);
441 new G4PVPlacement(rotStrand1, posStran << 609 new G4PVPlacement(rotStrand1,
>> 610 posStrand1,
>> 611 logicSphere3,
>> 612 "physi sugar 2",
>> 613 logicEnv,
>> 614 false,
442 0); 615 0);
443 616
444 G4RotationMatrix* rotStrand2 = new G4R 617 G4RotationMatrix* rotStrand2 = new G4RotationMatrix;
445 rotStrand2->rotateZ(j * -51.43 * degre 618 rotStrand2->rotateZ(j * -51.43 * degree);
446 G4ThreeVector posStrand2(-2.7 * nanome << 619 G4ThreeVector posStrand2(-2.7 * nanometer,
>> 620 9.35 * nanometer,
447 (-68.7 * nano 621 (-68.7 * nanometer) + (j * 1.67 * nanometer));
448 posStrand2.rotateZ(j * 51.43 * degree) 622 posStrand2.rotateZ(j * 51.43 * degree);
449 new G4PVPlacement(rotStrand2, posStran << 623 new G4PVPlacement(rotStrand2,
>> 624 posStrand2,
>> 625 logicSphere4,
>> 626 "physi sugar 4",
>> 627 logicEnv,
>> 628 false,
450 0); 629 0);
451 630
452 // histones 631 // histones
453 G4RotationMatrix* rotHistone = new G4R 632 G4RotationMatrix* rotHistone = new G4RotationMatrix;
454 rotHistone->rotateY(90 * degree); 633 rotHistone->rotateY(90 * degree);
455 rotHistone->rotateX(j * (-51.43 * degr 634 rotHistone->rotateX(j * (-51.43 * degree));
456 G4ThreeVector posHistone(0.0, 9.35 * n << 635 G4ThreeVector posHistone(0.0,
>> 636 9.35 * nanometer,
>> 637 (-74.15 + j * 1.67) * nanometer);
457 posHistone.rotateZ(j * 51.43 * degree) 638 posHistone.rotateZ(j * 51.43 * degree);
458 new G4PVPlacement(rotHistone, posHisto << 639 new G4PVPlacement(rotHistone,
>> 640 posHistone,
>> 641 logicHistone,
>> 642 "PV histone",
>> 643 logicEnv,
>> 644 false,
>> 645 0);
459 } 646 }
460 /*************************************** 647 /************************************************************************/
461 // Visualisation 648 // Visualisation colors
462 /*************************************** 649 /************************************************************************/
463 650
464 logicBp1->SetVisAttributes(&visInvCyan); 651 logicBp1->SetVisAttributes(&visInvCyan);
465 logicBp2->SetVisAttributes(&visInvPink); 652 logicBp2->SetVisAttributes(&visInvPink);
466 653
467 logicSphere3->SetVisAttributes(&visInvWh 654 logicSphere3->SetVisAttributes(&visInvWhite);
468 logicSphere4->SetVisAttributes(&visInvRe 655 logicSphere4->SetVisAttributes(&visInvRed);
469 656
470 logicHistone->SetVisAttributes(&visInvBl 657 logicHistone->SetVisAttributes(&visInvBlue);
471 } 658 }
472 } 659 }
473 660
474 G4cout << "Geometry has been loaded" << G4en 661 G4cout << "Geometry has been loaded" << G4endl;
475 return physiWorld; 662 return physiWorld;
476 } 663 }
477 664