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25 // 25 //
26 // Authors: J. Naoki D. Kondo (UCSF, US) : 10/ << 26 // Authors: J. Naoki D. Kondo (UCSF, US) : 10/10/2021
27 // J. Ramos-Mendez and B. Faddegon (U 27 // J. Ramos-Mendez and B. Faddegon (UCSF, US)
28 // 28 //
29 /// \file PhysGeoImport.cc 29 /// \file PhysGeoImport.cc
30 /// \brief Implementation of the plasmid load 30 /// \brief Implementation of the plasmid load methods for the geometry
31 31
32 #include "PhysGeoImport.hh" 32 #include "PhysGeoImport.hh"
33 <<
34 #include "G4DNAChemistryManager.hh" 33 #include "G4DNAChemistryManager.hh"
35 #include "G4Ellipsoid.hh" <<
36 #include "G4VPhysicalVolume.hh" 34 #include "G4VPhysicalVolume.hh"
>> 35 #include "G4Ellipsoid.hh"
37 #include "Randomize.hh" 36 #include "Randomize.hh"
38 37
39 //....oooOO0OOooo........oooOO0OOooo........oo 38 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
40 39
41 PhysGeoImport::PhysGeoImport() {} << 40 PhysGeoImport::PhysGeoImport()
>> 41 {}
42 42
43 //....oooOO0OOooo........oooOO0OOooo........oo 43 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
44 44
45 G4LogicalVolume* PhysGeoImport::CreateLogicVol << 45 G4LogicalVolume* PhysGeoImport::CreateLogicVolumeXYZ(G4String fileName) {
46 { << 46 G4NistManager * man = G4NistManager::Instance();
47 G4NistManager* man = G4NistManager::Instance <<
48 fEnvelopeWater = man->FindOrBuildMaterial("G 47 fEnvelopeWater = man->FindOrBuildMaterial("G4_WATER");
49 fpWater = << 48 fpWater = man->BuildMaterialWithNewDensity("G4_WATER_MODIFIED",
50 man->BuildMaterialWithNewDensity("G4_WATER << 49 "G4_WATER",1.0*g/cm/cm/cm);
51 50
52 ReadFile(fileName); 51 ReadFile(fileName);
53 52
54 G4double des1 = 1.1344640137963142; 53 G4double des1 = 1.1344640137963142;
55 G4double des2 = des1 + (CLHEP::pi * .5); << 54 G4double des2 = des1 + (CLHEP::pi*.5);
56 G4double ang = 0.6283185307179586; 55 G4double ang = 0.6283185307179586;
57 G4double bet1 = 0.6283185307179586 * 2; 56 G4double bet1 = 0.6283185307179586 * 2;
58 G4double posi = 1.0471975511965976; 57 G4double posi = 1.0471975511965976;
59 G4double sep = .1 * angstrom; << 58 G4double sep = .1*angstrom;
60 // Geometries Sizes << 59 //Geometries Sizes
61 G4double PxRs = 2.9389169420478556 * angstro << 60 G4double PxRs = 2.9389169420478556 * angstrom;
62 G4double PyRs = 2.9389169420478556 * angstro 61 G4double PyRs = 2.9389169420478556 * angstrom;
63 G4double PzRs = 2.9389169420478556 * angstro 62 G4double PzRs = 2.9389169420478556 * angstrom;
64 G4double PxYs = 2.7 * angstrom; 63 G4double PxYs = 2.7 * angstrom;
65 G4double PyYs = 2.7 * angstrom; 64 G4double PyYs = 2.7 * angstrom;
66 G4double PzYs = 2.7 * angstrom; 65 G4double PzYs = 2.7 * angstrom;
67 G4double PxBp = 2.45 * angstrom; 66 G4double PxBp = 2.45 * angstrom;
68 G4double PyBp = 2.45 * angstrom; 67 G4double PyBp = 2.45 * angstrom;
69 G4double PzBp = 2.45 * angstrom; 68 G4double PzBp = 2.45 * angstrom;
>> 69
70 70
71 G4double xin = -170 * angstrom; 71 G4double xin = -170 * angstrom;
72 G4double yin = -170 * angstrom; 72 G4double yin = -170 * angstrom;
73 G4double zin = -170 * angstrom; 73 G4double zin = -170 * angstrom;
74 G4double xfn = 170 * angstrom; << 74 G4double xfn = 170 * angstrom;
75 G4double yfn = 170 * angstrom; << 75 G4double yfn = 170 * angstrom;
76 G4double zfn = 170 * angstrom; << 76 G4double zfn = 170 * angstrom;
77 77
78 G4int nVertex = fVertexes.size(); 78 G4int nVertex = fVertexes.size();
79 79
80 // Envelope 80 // Envelope
81 81
82 std::string boxNameSolid = fGeoName + "_soli 82 std::string boxNameSolid = fGeoName + "_solid";
83 G4Box* box_solid = << 83 G4Box* box_solid = new G4Box(boxNameSolid, 0.5*(fXMax-fXMin)+0.5*3.4*nm,
84 new G4Box(boxNameSolid, 0.5 * (fXMax - fXM << 84 0.5*(fYMax-fYMin)+0.5*3.4*nm,
85 0.5 * (fYMax - fYMin) + 0.5 * 3. << 85 0.5*(fZMax-fZMin)+0.5*3.4*nm);
86 << 86
87 G4String boxNameLogic = fGeoName + "_logic"; << 87 G4String boxNameLogic = fGeoName + "_logic";
88 G4LogicalVolume* box_logic = << 88 G4LogicalVolume* box_logic = new G4LogicalVolume(box_solid,
89 new G4LogicalVolume(box_solid, fEnvelopeWa << 89 fEnvelopeWater,
90 << 90 boxNameLogic, 0,0,0);
91 // Desoxyribose << 91
92 << 92 //Desoxyribose
93 G4Ellipsoid* RSolidSugar = new G4Ellipsoid(" << 93
94 G4LogicalVolume* RSugar = new G4LogicalVolum << 94 G4Ellipsoid *RSolidSugar = new G4Ellipsoid("sdeoxyribose",
>> 95 PxRs,
>> 96 PyRs,
>> 97 PzRs, -PzRs, .445*PzRs);
>> 98 G4LogicalVolume* RSugar = new G4LogicalVolume(RSolidSugar,
>> 99 fpWater,
>> 100 "ldeoxyribose",
>> 101 0,0,0);
95 G4VisAttributes* MyVisAtt_Rs = new G4VisAttr 102 G4VisAttributes* MyVisAtt_Rs = new G4VisAttributes(G4Colour(G4Colour::Red()));
96 MyVisAtt_Rs->SetForceSolid(true); 103 MyVisAtt_Rs->SetForceSolid(true);
97 RSugar->SetVisAttributes(MyVisAtt_Rs); 104 RSugar->SetVisAttributes(MyVisAtt_Rs);
98 105
99 // Phosphoric Acid << 106 //Phosphoric Acid
100 <<
101 G4Ellipsoid* YSolidSugar = new G4Ellipsoid(" <<
102 107
103 G4LogicalVolume* YSugar = new G4LogicalVolum << 108 G4Ellipsoid *YSolidSugar = new G4Ellipsoid("sphosphate",
>> 109 PxYs,
>> 110 PyYs,
>> 111 PzYs,
>> 112 -PzYs,
>> 113 .9 * angstrom);
>> 114
>> 115 G4LogicalVolume* YSugar = new G4LogicalVolume(YSolidSugar,
>> 116 fpWater,
>> 117 "lphosphate",
>> 118 0,0,0);
104 G4VisAttributes* MyVisAtt_Ys = new G4VisAttr 119 G4VisAttributes* MyVisAtt_Ys = new G4VisAttributes(G4Colour(G4Colour::Yellow()));
105 MyVisAtt_Ys->SetForceSolid(true); 120 MyVisAtt_Ys->SetForceSolid(true);
106 YSugar->SetVisAttributes(MyVisAtt_Ys); 121 YSugar->SetVisAttributes(MyVisAtt_Ys);
107 122
108 // Base Pairs << 123 //Base Pairs
109 124
110 G4Ellipsoid* Base1a = new G4Ellipsoid("BaseP << 125 G4Ellipsoid* Base1a = new G4Ellipsoid("BasePair1a",
111 G4LogicalVolume* BaseP1a = new G4LogicalVolu << 126 PxBp,
>> 127 PyBp,
>> 128 PzBp,
>> 129 -PzBp,
>> 130 1.15 * angstrom);
>> 131 G4LogicalVolume* BaseP1a = new G4LogicalVolume(Base1a, fpWater, "BasePair1a", 0,0,0);
112 G4VisAttributes* MyVisAtt_Bp1a = new G4VisAt 132 G4VisAttributes* MyVisAtt_Bp1a = new G4VisAttributes(G4Colour(G4Colour::Green()));
113 MyVisAtt_Bp1a->SetForceSolid(true); 133 MyVisAtt_Bp1a->SetForceSolid(true);
114 BaseP1a->SetVisAttributes(MyVisAtt_Bp1a); 134 BaseP1a->SetVisAttributes(MyVisAtt_Bp1a);
115 135
116 G4Ellipsoid* Base1b = new G4Ellipsoid("BaseP << 136 G4Ellipsoid* Base1b= new G4Ellipsoid("BasePair1b",
117 G4LogicalVolume* BaseP1b = new G4LogicalVolu << 137 PxBp,
>> 138 PyBp,
>> 139 PzBp,
>> 140 1.15 * angstrom,
>> 141 PzBp);
>> 142 G4LogicalVolume* BaseP1b = new G4LogicalVolume(Base1b, fpWater, "BasePair1b", 0,0,0);
118 143
119 G4VisAttributes* MyVisAtt_Bp1b = new G4VisAt 144 G4VisAttributes* MyVisAtt_Bp1b = new G4VisAttributes(G4Colour(G4Colour::Green()));
120 MyVisAtt_Bp1b->SetForceSolid(true); 145 MyVisAtt_Bp1b->SetForceSolid(true);
121 BaseP1b->SetVisAttributes(MyVisAtt_Bp1b); 146 BaseP1b->SetVisAttributes(MyVisAtt_Bp1b);
122 147
123 G4int index = 0; << 148 G4int index = 0;
124 G4double cAngle = 0; 149 G4double cAngle = 0;
125 G4double pi = CLHEP::pi; << 150 G4double pi = CLHEP::pi;
126 for (int vertex = 0; vertex < nVertex - 1; v << 151 for (int vertex = 0; vertex < nVertex - 1; vertex++ ) {
127 xin = fVertexes[vertex][0] - fOffsetX; << 152 xin = fVertexes[vertex][0]-fOffsetX;
128 yin = fVertexes[vertex][1] - fOffsetY; << 153 yin = fVertexes[vertex][1]-fOffsetY;
129 zin = fVertexes[vertex][2] - fOffsetZ; << 154 zin = fVertexes[vertex][2]-fOffsetZ;
130 xfn = fVertexes[vertex + 1][0] - fOffsetX; << 155 xfn = fVertexes[vertex+1][0]-fOffsetX;
131 yfn = fVertexes[vertex + 1][1] - fOffsetY; << 156 yfn = fVertexes[vertex+1][1]-fOffsetY;
132 zfn = fVertexes[vertex + 1][2] - fOffsetZ; << 157 zfn = fVertexes[vertex+1][2]-fOffsetZ;
133 << 158
134 G4double phi0 = << 159 G4double phi0 = std::atan2(zfn-zin,std::sqrt(((xfn-xin)*(xfn-xin))+
135 std::atan2(zfn - zin, std::sqrt(((xfn - << 160 ((yfn-yin)*(yfn-yin))));
136 G4double theta0 = std::atan2(xfn - xin, yf << 161 G4double theta0 = std::atan2(xfn-xin,yfn-yin);
137 G4double lenght = std::sqrt(((xfn - xin) * << 162 G4double lenght = std::sqrt(((xfn-xin)*(xfn-xin))+
138 + ((zfn - zin) << 163 ((yfn-yin)*(yfn-yin))+
139 G4double dl = 1.0 / (lenght / (3.4 * angst << 164 ((zfn-zin)*(zfn-zin)));
140 G4int nChain = (fVertexes[vertex] - fVerte << 165 G4double dl = 1.0 / (lenght / (3.4*angstrom));
>> 166 G4int nChain = (fVertexes[vertex] - fVertexes[vertex+1]).mag() / (0.34 * nm);
141 167
142 for (G4int nseg = 0; nseg < nChain; nseg++ << 168 for (G4int nseg = 0; nseg < nChain ; nseg++) {
143 cAngle += ang; 169 cAngle += ang;
144 170
145 G4double theta = cAngle; 171 G4double theta = cAngle;
146 G4double x1 = 0; 172 G4double x1 = 0;
147 G4double y1 = 0; 173 G4double y1 = 0;
148 G4double z1 = ((2 * PzBp) + PzRs + sep); << 174 G4double z1 = ((2*PzBp) + PzRs + sep);
149 175
150 G4double x2 = 0; << 176 G4double x2 = 0;
151 G4double y2 = 0; << 177 G4double y2 = 0;
152 G4double z2 = ((2 * PzBp) + PzRs + sep); << 178 G4double z2 = ((2*PzBp) + PzRs + sep);
153 179
154 G4ThreeVector plus2 = G4ThreeVector(0, 0 << 180 G4ThreeVector plus2 = G4ThreeVector(0,0,(.5 * PzRs) + PzYs);
155 plus2.rotateX(-des1); 181 plus2.rotateX(-des1);
156 plus2.rotateZ(-posi); 182 plus2.rotateZ(-posi);
157 183
158 G4ThreeVector plus2alt = G4ThreeVector(0 << 184 G4ThreeVector plus2alt = G4ThreeVector(0,0,(.5 * PzRs) + PzYs);
159 plus2alt.rotateX(-des1); 185 plus2alt.rotateX(-des1);
160 plus2alt.rotateZ(posi); 186 plus2alt.rotateZ(posi);
161 187
162 G4double x3 = 0; 188 G4double x3 = 0;
163 G4double y3 = 0; 189 G4double y3 = 0;
164 G4double z3 = PzBp + sep; 190 G4double z3 = PzBp + sep;
165 191
166 G4ThreeVector position1i = G4ThreeVector << 192 G4ThreeVector position1i = G4ThreeVector(x1,y1,z1);
167 G4ThreeVector position2i = G4ThreeVector << 193 G4ThreeVector position2i = G4ThreeVector(x2,y2,z2)+plus2;
168 G4ThreeVector position2ialt = G4ThreeVec << 194 G4ThreeVector position2ialt = G4ThreeVector(x2,y2,-z2)-plus2alt;
169 G4ThreeVector position3i = G4ThreeVector << 195 G4ThreeVector position3i = G4ThreeVector(x3,y3,z3);
170 196
171 position1i.rotateY(theta); 197 position1i.rotateY(theta);
172 position2i.rotateY(theta); 198 position2i.rotateY(theta);
173 position2ialt.rotateY(theta); 199 position2ialt.rotateY(theta);
174 position3i.rotateY(theta); 200 position3i.rotateY(theta);
175 201
176 G4double x = dl * nseg * (xfn - xin) + x << 202 G4double x = dl*nseg*(xfn-xin)+xin;
177 G4double y = dl * nseg * (yfn - yin) + y << 203 G4double y = dl*nseg*(yfn-yin)+yin;
178 G4double z = dl * nseg * (zfn - zin) + z << 204 G4double z = dl*nseg*(zfn-zin)+zin;
179 205
180 position1i.rotateX(phi0); 206 position1i.rotateX(phi0);
181 position2i.rotateX(phi0); 207 position2i.rotateX(phi0);
182 position2ialt.rotateX(phi0); 208 position2ialt.rotateX(phi0);
183 position3i.rotateX(phi0); 209 position3i.rotateX(phi0);
184 210
185 position1i.rotateZ(-theta0); 211 position1i.rotateZ(-theta0);
186 position2i.rotateZ(-theta0); 212 position2i.rotateZ(-theta0);
187 position2ialt.rotateZ(-theta0); 213 position2ialt.rotateZ(-theta0);
188 position3i.rotateZ(-theta0); 214 position3i.rotateZ(-theta0);
189 215
190 G4double yrot1 = theta; 216 G4double yrot1 = theta;
191 G4double xrot1 = -des1; 217 G4double xrot1 = -des1;
192 G4RotationMatrix rotm1 = G4RotationMatri 218 G4RotationMatrix rotm1 = G4RotationMatrix();
193 rotm1.rotateX(xrot1); 219 rotm1.rotateX(xrot1);
194 rotm1.rotateZ(-posi); 220 rotm1.rotateZ(-posi);
195 rotm1.rotateY(yrot1); 221 rotm1.rotateY(yrot1);
196 rotm1.rotateX(phi0); 222 rotm1.rotateX(phi0);
197 rotm1.rotateZ(-theta0); 223 rotm1.rotateZ(-theta0);
198 G4ThreeVector position1 = position1i + G << 224 G4ThreeVector position1 = position1i + G4ThreeVector(x,y,z);
199 G4Transform3D transform1(rotm1, position 225 G4Transform3D transform1(rotm1, position1);
200 << 226
201 G4double yrot1alt = theta + pi; 227 G4double yrot1alt = theta + pi;
202 G4double xrot1alt = des1; 228 G4double xrot1alt = des1;
203 G4RotationMatrix rotm1alt = G4RotationMa 229 G4RotationMatrix rotm1alt = G4RotationMatrix();
204 rotm1alt.rotateX(xrot1alt); 230 rotm1alt.rotateX(xrot1alt);
205 rotm1alt.rotateZ(-posi); 231 rotm1alt.rotateZ(-posi);
206 rotm1alt.rotateY(yrot1alt); 232 rotm1alt.rotateY(yrot1alt);
207 rotm1alt.rotateX(phi0); 233 rotm1alt.rotateX(phi0);
208 rotm1alt.rotateZ(-theta0); 234 rotm1alt.rotateZ(-theta0);
209 G4ThreeVector position1alt = -position1i << 235 G4ThreeVector position1alt = -position1i + G4ThreeVector(x,y,z);
210 G4Transform3D transform1alt(rotm1alt, po << 236 G4Transform3D transform1alt(rotm1alt,position1alt);
211 237
212 G4double yrot2 = theta; 238 G4double yrot2 = theta;
213 G4double xrot2 = -des2; 239 G4double xrot2 = -des2;
214 G4RotationMatrix rotm2 = G4RotationMatri 240 G4RotationMatrix rotm2 = G4RotationMatrix();
215 rotm2.rotateX(xrot2); 241 rotm2.rotateX(xrot2);
216 rotm2.rotateY(yrot2 - bet1 + 0.872664625 242 rotm2.rotateY(yrot2 - bet1 + 0.8726646259971648);
217 rotm2.rotateX(phi0); 243 rotm2.rotateX(phi0);
218 rotm2.rotateZ(-theta0); 244 rotm2.rotateZ(-theta0);
219 G4ThreeVector position2 = position2i + G << 245 G4ThreeVector position2 = position2i + G4ThreeVector(x,y,z);
220 G4Transform3D transform2(rotm2, position << 246 G4Transform3D transform2(rotm2,position2);
221 247
222 G4double yrot2alt = theta + pi; 248 G4double yrot2alt = theta + pi;
223 G4double xrot2alt = des2; 249 G4double xrot2alt = des2;
224 G4RotationMatrix rotm2alt = G4RotationMa 250 G4RotationMatrix rotm2alt = G4RotationMatrix();
225 rotm2alt.rotateX(xrot2alt); 251 rotm2alt.rotateX(xrot2alt);
226 rotm2alt.rotateY(yrot2alt + bet1 - 0.872 252 rotm2alt.rotateY(yrot2alt + bet1 - 0.8726646259971648);
227 rotm2alt.rotateX(phi0); 253 rotm2alt.rotateX(phi0);
228 rotm2alt.rotateZ(-theta0); 254 rotm2alt.rotateZ(-theta0);
229 G4ThreeVector position2alt = position2ia << 255 G4ThreeVector position2alt = position2ialt + G4ThreeVector(x,y,z);
230 G4Transform3D transform2alt(rotm2alt, po << 256 G4Transform3D transform2alt(rotm2alt,position2alt);
231 257
232 G4double yrot3 = theta; 258 G4double yrot3 = theta;
233 G4RotationMatrix rotm3 = G4RotationMatri 259 G4RotationMatrix rotm3 = G4RotationMatrix();
234 rotm3.rotateX(-pi / 2); << 260 rotm3.rotateX(-pi/2);
235 rotm3.rotateZ(-ang); 261 rotm3.rotateZ(-ang);
236 rotm3.rotateY(yrot3); 262 rotm3.rotateY(yrot3);
237 rotm3.rotateX(phi0); 263 rotm3.rotateX(phi0);
238 rotm3.rotateZ(-theta0); 264 rotm3.rotateZ(-theta0);
239 G4ThreeVector position3 = position3i + G << 265 G4ThreeVector position3 = position3i + G4ThreeVector(x,y,z);
240 G4Transform3D transform3(rotm3, position << 266 G4Transform3D transform3(rotm3,position3);
241 267
242 G4double yrot3alt = theta + pi; 268 G4double yrot3alt = theta + pi;
243 G4RotationMatrix rotm3alt = G4RotationMa 269 G4RotationMatrix rotm3alt = G4RotationMatrix();
244 rotm3alt.rotateX(pi / 2); << 270 rotm3alt.rotateX(pi/2);
245 rotm3alt.rotateZ(-ang); 271 rotm3alt.rotateZ(-ang);
246 rotm3alt.rotateY(yrot3alt); 272 rotm3alt.rotateY(yrot3alt);
247 rotm3alt.rotateX(phi0); 273 rotm3alt.rotateX(phi0);
248 rotm3alt.rotateZ(-theta0); 274 rotm3alt.rotateZ(-theta0);
249 G4ThreeVector position3alt = -position3i << 275 G4ThreeVector position3alt = -position3i + G4ThreeVector(x,y,z);
250 G4Transform3D transform3alt(rotm3alt, po << 276 G4Transform3D transform3alt(rotm3alt,position3alt);
251 <<
252 new G4PVPlacement(transform1, RSugar, "d <<
253 <<
254 new G4PVPlacement(transform1alt, RSugar, <<
255 <<
256 new G4PVPlacement(transform3, BaseP1a, " <<
257 <<
258 new G4PVPlacement(transform3alt, BaseP1a <<
259 <<
260 new G4PVPlacement(transform2, YSugar, "p <<
261 277
262 new G4PVPlacement(transform2alt, YSugar, << 278
>> 279 new G4PVPlacement(transform1,
>> 280 RSugar,
>> 281 "deoxyribose1",
>> 282 box_logic,
>> 283 false,
>> 284 index,
>> 285 false);
>> 286
>> 287 new G4PVPlacement(transform1alt,
>> 288 RSugar,
>> 289 "deoxyribose2",
>> 290 box_logic,
>> 291 false,
>> 292 index,
>> 293 false);
>> 294
>> 295 new G4PVPlacement(transform3,
>> 296 BaseP1a,
>> 297 "BasePair1",
>> 298 box_logic,
>> 299 false,
>> 300 index,
>> 301 false);
>> 302
>> 303 new G4PVPlacement(transform3alt,
>> 304 BaseP1a,
>> 305 "BasePair2",
>> 306 box_logic,
>> 307 false,
>> 308 index,
>> 309 false);
>> 310
>> 311 new G4PVPlacement(transform2,
>> 312 YSugar,
>> 313 "phosphate1",
>> 314 box_logic,
>> 315 false,
>> 316 index,
>> 317 false);
>> 318
>> 319 new G4PVPlacement(transform2alt,
>> 320 YSugar,
>> 321 "phosphate2",
>> 322 box_logic,
>> 323 false,
>> 324 index,
>> 325 false);
263 326
264 G4ThreeVector Deoxy1 = position1; 327 G4ThreeVector Deoxy1 = position1;
265 G4ThreeVector Deoxy2 = position1alt; 328 G4ThreeVector Deoxy2 = position1alt;
266 329
267 fSampleDNAPositions.push_back(Deoxy1); 330 fSampleDNAPositions.push_back(Deoxy1);
268 fSampleDNAPositions.push_back(Deoxy2); 331 fSampleDNAPositions.push_back(Deoxy2);
269 fSampleDNANames.push_back("Deoxyribose") 332 fSampleDNANames.push_back("Deoxyribose");
270 fSampleDNANames.push_back("Deoxyribose") 333 fSampleDNANames.push_back("Deoxyribose");
271 fSampleDNADetails.push_back({-1, index, << 334 fSampleDNADetails.push_back({-1,index,1});
272 fSampleDNADetails.push_back({-1, index, << 335 fSampleDNADetails.push_back({-1,index,2});
273 336
274 index++; 337 index++;
>> 338
275 } 339 }
276 } 340 }
277 341
278 return box_logic; 342 return box_logic;
279 } 343 }
280 344
281 //....oooOO0OOooo........oooOO0OOooo........oo 345 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
282 346
283 void PhysGeoImport::ReadFile(G4String fileName << 347 void PhysGeoImport::ReadFile(G4String fileName) {
284 { <<
285 G4double x, y, z; 348 G4double x, y, z;
286 fXMin = 1 * mm, fYMin = 1 * mm, fZMin = 1 * << 349 fXMin = 1*mm, fYMin = 1*mm, fZMin = 1*mm;
287 fXMax = -1 * mm, fYMax = -1 * mm, fZMax = -1 << 350 fXMax =-1*mm, fYMax =-1*mm, fZMax =-1*mm;
288 std::ifstream plasmidFile(fileName); 351 std::ifstream plasmidFile(fileName);
289 while (true) { << 352 while(true) {
290 plasmidFile >> x >> y >> z; 353 plasmidFile >> x >> y >> z;
291 if (!plasmidFile.good()) break; << 354 if ( !plasmidFile.good() ) break;
292 x *= nm; 355 x *= nm;
293 y *= nm; 356 y *= nm;
294 z *= nm; 357 z *= nm;
295 fVertexes.push_back(G4ThreeVector(x, y, z) 358 fVertexes.push_back(G4ThreeVector(x, y, z));
296 if (fXMin > x) fXMin = x; << 359 if ( fXMin > x ) fXMin = x;
297 if (fXMax < x) fXMax = x; << 360 if ( fXMax < x ) fXMax = x;
298 if (fYMin > y) fYMin = y; << 361 if ( fYMin > y ) fYMin = y;
299 if (fYMax < y) fYMax = y; << 362 if ( fYMax < y ) fYMax = y;
300 if (fZMin > z) fZMin = z; << 363 if ( fZMin > z ) fZMin = z;
301 if (fZMax < z) fZMax = z; << 364 if ( fZMax < z ) fZMax = z;
302 } 365 }
303 plasmidFile.close(); 366 plasmidFile.close();
304 fOffsetX = (fXMin + fXMax) * 0.5; << 367 fOffsetX = (fXMin + fXMax)*0.5;
305 fOffsetY = (fYMin + fYMax) * 0.5; << 368 fOffsetY = (fYMin + fYMax)*0.5;
306 fOffsetZ = (fZMin + fZMax) * 0.5; << 369 fOffsetZ = (fZMin + fZMax)*0.5;
307 370
308 std::vector<G4ThreeVector> VertRed; 371 std::vector<G4ThreeVector> VertRed;
309 for (size_t i = 0; i < fVertexes.size(); i++ << 372 for(size_t i = 0; i < fVertexes.size(); i++) {
310 if (i % 15 == 0) VertRed.push_back(fVertex << 373 if (i % 15 == 0)
>> 374 VertRed.push_back(fVertexes[i]);
311 } 375 }
312 376
313 VertRed.push_back(fVertexes[0]); 377 VertRed.push_back(fVertexes[0]);
314 378
315 fVertexes = VertRed; 379 fVertexes = VertRed;
316 } 380 }
317 381
318 //....oooOO0OOooo........oooOO0OOooo........oo 382 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
319 383