| Geant4 Cross Reference |
1 // 1
2 // *******************************************
3 // * License and Disclaimer
4 // *
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6 // * the Geant4 Collaboration. It is provided
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14 // * regarding this software system or assum
15 // * use. Please see the license in the file
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17 // *
18 // * This code implementation is the result
19 // * technical work of the GEANT4 collaboratio
20 // * By using, copying, modifying or distri
21 // * any work based on the software) you ag
22 // * use in resulting scientific publicati
23 // * acceptance of all terms of the Geant4 Sof
24 // *******************************************
25 //
26 // This example is provided by the Geant4-DNA
27 // Any report or published results obtained us
28 // shall cite the following Geant4-DNA collabo
29 // Med. Phys. 37 (2010) 4692-4708
30 // and papers
31 // M. Batmunkh et al. J Radiat Res Appl Sci 8
32 // O. Belov et al. Physica Medica 32 (2016) 15
33 // The Geant4-DNA web site is available at htt
34 //
35 // -------------------------------------------
36 // November 2016
37 // -------------------------------------------
38 //
39 /// \file DetectorConstruction.cc
40 /// \brief Implementation of the DetectorConst
41
42 #include "DetectorConstruction.hh"
43
44 #include "G4Colour.hh"
45 #include "G4PhysicalConstants.hh"
46 #include "G4ProductionCuts.hh"
47 #include "G4Region.hh"
48 #include "G4RotationMatrix.hh"
49 #include "G4SystemOfUnits.hh"
50 #include "G4VisAttributes.hh"
51
52 #include <algorithm>
53 #include <iostream>
54
55 //....oooOO0OOooo........oooOO0OOooo........oo
56
57 DetectorConstruction::DetectorConstruction()
58 {
59 fNeuronLoadParamz = new NeuronLoadDataFile()
60 DefineMaterials();
61 }
62
63 //....oooOO0OOooo........oooOO0OOooo........oo
64
65 DetectorConstruction::~DetectorConstruction()
66 {
67 delete fNeuronLoadParamz;
68 }
69
70 //....oooOO0OOooo........oooOO0OOooo........oo
71
72 void DetectorConstruction::DefineMaterials()
73 {
74 // Water is defined from NIST material datab
75 G4NistManager* man = G4NistManager::Instance
76 fpWaterMaterial = man->FindOrBuildMaterial("
77 fpWorldMaterial = man->FindOrBuildMaterial("
78 }
79
80 //....oooOO0OOooo........oooOO0OOooo........oo
81
82 G4VPhysicalVolume* DetectorConstruction::Const
83 {
84 G4cout << " ---- Begin of Neuron Constructio
85 << "\n"
86 << " ================================
87
88 // =========================================
89 // WORLD VOLUME - filled by default material
90 // =========================================
91
92 // Dimensions of world volume are calculated
93
94 G4double worldSizeX;
95 worldSizeX = fNeuronLoadParamz->GetdiagnlLen
96
97 if (worldSizeX <= 0.0) {
98 worldSizeX = 10. * cm;
99 }
100
101 G4double worldSizeY = worldSizeX;
102 G4double worldSizeZ = worldSizeX;
103 G4cout << " Side length of word volume is ca
104 G4VSolid* worldS = new G4Box("World", worldS
105
106 G4LogicalVolume* worldLV = new G4LogicalVolu
107
108 // Visualization attributes
109 G4VisAttributes* worldVisAtt = new G4VisAttr
110 worldVisAtt->SetVisibility(true);
111 worldLV->SetVisAttributes(worldVisAtt);
112
113 G4VPhysicalVolume* worldPV = new G4PVPlaceme
114
115
116
117
118
119
120
121
122 // =========================================
123 // HOMOGENEOUS MEDIUM - LARGE SPHERE VOLUME
124 // =========================================
125
126 // Radius of water sphere calculated as over
127 fTotMassMedium = fNeuronLoadParamz->GetTotMa
128 fTotSurfMedium = fNeuronLoadParamz->GetTotSu
129 G4double RadiusMedium = fNeuronLoadParamz->G
130 G4cout << " Radius of homogeneous medium is
131 << G4endl;
132 G4VSolid* mediumS = new G4Orb("Medium", Radi
133
134 G4LogicalVolume* mediumLV = new G4LogicalVol
135
136 // Visualization attributes
137 G4VisAttributes* mediumVisAtt = new G4VisAtt
138 // mediumVisAtt->SetForceSolid(true);
139 // mediumVisAtt->SetForceWireframe (true);
140 mediumVisAtt->SetForceLineSegmentsPerCircle(
141 mediumVisAtt->SetVisibility(true);
142 mediumLV->SetVisAttributes(mediumVisAtt);
143
144 G4VPhysicalVolume* mediumPV =
145 new G4PVPlacement(0, G4ThreeVector(), "Med
146
147 // =========================================
148 // TARGET - BOUNDING SLICE including NEURON
149 // =========================================
150
151 // Dimensions of bounding slice volume defin
152
153 G4double TargetSizeX = fNeuronLoadParamz->Ge
154 G4double TargetSizeY = fNeuronLoadParamz->Ge
155 G4double TargetSizeZ = fNeuronLoadParamz->Ge
156 fTotMassSlice = fNeuronLoadParamz->GetTotMas
157 G4cout << " Overall dimensions (um) of neuro
158 << "\n"
159 << '\t' << " width = " << TargetSizeX
160 << " depth = " << TargetSizeZ / um <<
161
162 G4cout << " Volume (um3), surface (um2) and
163 << " calculated : "
164 << "\n"
165 << '\t' << fNeuronLoadParamz->GetTotV
166 << fNeuronLoadParamz->GetTotSurfSlice
167 << fNeuronLoadParamz->GetTotMassSlice
168
169 G4Box* boundingS =
170 new G4Box("BoundingSlice", TargetSizeX / 2
171
172 G4LogicalVolume* boundingLV = new G4LogicalV
173
174 // Visualization attributes with opacity!
175 G4VisAttributes* TargetVisAtt = new G4VisAtt
176 TargetVisAtt->SetForceSolid(true);
177 TargetVisAtt->SetVisibility(true);
178 boundingLV->SetVisAttributes(TargetVisAtt);
179 new G4PVPlacement(0, G4ThreeVector(), "Bound
180 fCheckOverlaps);
181
182 // =========================================
183 // NEURON MORPHOLOGY
184 // =========================================
185
186 G4cout << " Volume (um3), surface (um2) and
187 << "are calculated : "
188 << "\n"
189 << '\t' << fNeuronLoadParamz->GetTotV
190 << fNeuronLoadParamz->GetTotSurfNeuro
191 << fNeuronLoadParamz->GetTotMassNeuro
192 fTotMassNeuron = fNeuronLoadParamz->GetTotMa
193 G4cout << " Total number of compartments int
194 << G4endl;
195 G4cout << " Shift values (um) for Neuron tra
196 << "\n"
197 << '\t' << " shiftX = " << fNeuronLoa
198 << " shiftY = " << fNeuronLoadParamz-
199 << " shiftZ = " << fNeuronLoadParamz-
200
201 // Soma in Violet with opacity // 0.85,0.4
202 fSomaColour = new G4VisAttributes;
203 fSomaColour->SetColour(G4Colour(G4Colour(22
204 fSomaColour->SetForceSolid(true); // true
205 fSomaColour->SetVisibility(true);
206
207 // Dendrites in Dark-Blue
208 fDendColour = new G4VisAttributes;
209 fDendColour->SetColour(G4Colour(G4Colour(0.0
210 fDendColour->SetForceSolid(true);
211 // fDendColour->SetVisibility(true);
212
213 // Axon in Maroon
214 fAxonColour = new G4VisAttributes;
215 fAxonColour->SetColour(G4Colour(G4Colour(0.5
216 fAxonColour->SetForceSolid(true);
217 fAxonColour->SetVisibility(true);
218
219 // Spines in Dark-Green
220 fSpineColour = new G4VisAttributes;
221 fSpineColour->SetColour(G4Colour(G4Colour(0.
222 fSpineColour->SetForceSolid(true);
223 fSpineColour->SetVisibility(true);
224
225 // Whole neuron in semitransparent navy blue
226 fNeuronColour = new G4VisAttributes;
227 fNeuronColour->SetColour(G4Colour(G4Colour(0
228 fNeuronColour->SetForceSolid(true);
229 fNeuronColour->SetVisibility(true);
230
231 // Placement volumes: G4examples/extended/pa
232
233 // =========================================
234 // Structure-1: Soma
235
236 // Create Target G4Region and add logical vo
237 // Active Geant4-DNA processes in this regio
238 fpRegion = new G4Region("Soma");
239 G4ProductionCuts* cuts = new G4ProductionCut
240 G4double defCut = 1 * nanometer;
241 cuts->SetProductionCut(defCut, "gamma");
242 cuts->SetProductionCut(defCut, "e-");
243 cuts->SetProductionCut(defCut, "e+");
244 cuts->SetProductionCut(defCut, "proton");
245 fpRegion->SetProductionCuts(cuts);
246 G4ThreeVector shift(fNeuronLoadParamz->Getsh
247 fNeuronLoadParamz->Getsh
248
249 G4int n = fNeuronLoadParamz->GetnbSomacomp()
250 if (n <= 0) {
251 G4cout << " ---- Soma not found! ---- " <<
252 }
253 else {
254 G4cout << " ---- Soma for construction: --
255 G4cout << " Total number of compartments i
256 fnbSomacomp = n;
257 fMassSomaTot = fNeuronLoadParamz->GetMassS
258 fMassSomacomp.resize(n, 0.0);
259 fPosSomacomp.resize(n);
260 fsomaS.resize(n, nullptr);
261 fsomaLV.resize(n, nullptr);
262 fsomaPV.resize(n, nullptr);
263
264 for (G4int i = 0; i < n; ++i) {
265 fsomaS[i] = new G4Orb("Soma", fNeuronLoa
266 // you can change parameters of Soma wit
267 G4ThreeVector pos = (fNeuronLoadParamz->
268 fsomaLV[i] = new G4LogicalVolume(fsomaS[
269 fsomaLV[i]->SetVisAttributes(fSomaColour
270 fsomaPV[i] = new G4PVPlacement(0, // no
271 pos, fsom
272 fMassSomacomp[i] = fNeuronLoadParamz->Ge
273 fPosSomacomp[i] = fNeuronLoadParamz->Get
274 fpRegion->AddRootLogicalVolume(fsomaLV[i
275 }
276 }
277
278 // =========================================
279 // Structure-2: Dendrites
280
281 n = fNeuronLoadParamz->GetnbDendritecomp();
282 if (n <= 0) {
283 G4cout << " ---- Dendrites not found! ----
284 }
285 else {
286 fnbDendritecomp = n;
287 G4cout << " ---- Dendrites for constructio
288 G4cout << " Total number of compartments i
289
290 // Active Geant4-DNA processes in this reg
291 auto region = new G4Region("Dendrites");
292 region->SetProductionCuts(cuts);
293
294 fMassDendTot = fNeuronLoadParamz->GetMassD
295 fMassDendcomp.resize(n, 0.0);
296 fDistADendSoma.resize(n, 0.0);
297 fDistBDendSoma.resize(n, 0.0);
298 fPosDendcomp.resize(n);
299 fdendriteS.resize(n, nullptr);
300 fdendriteLV.resize(n, nullptr);
301 fdendritePV.resize(n, nullptr);
302 for (G4int i = 1; i < n; ++i) {
303 fdendriteS[i] = new G4Tubs("Dendrites",
304 fNeuronLoadPa
305 fdendriteLV[i] = new G4LogicalVolume(fde
306 fdendriteLV[i]->SetVisAttributes(fDendCo
307
308 G4ThreeVector pos = (fNeuronLoadParamz->
309 // rotation checking with function Compu
310 // RotationMatrix with Inverse
311 fdendritePV[i] = new G4PVPlacement(G4Tra
312 fdend
313 fMassDendcomp[i] = fNeuronLoadParamz->Ge
314 fPosDendcomp[i] = fNeuronLoadParamz->Get
315 fDistADendSoma[i] = fNeuronLoadParamz->G
316 fDistBDendSoma[i] = fNeuronLoadParamz->G
317 region->AddRootLogicalVolume(fdendriteLV
318 }
319 }
320
321 // =========================================
322 // Structure-3: Axon
323
324 n = fNeuronLoadParamz->GetnbAxoncomp();
325 if (n <= 0) {
326 G4cout << " ---- Axon not found! ---- " <<
327 }
328 else {
329 G4cout << " ---- Axon for construction: --
330 G4cout << " Total number of compartments i
331 // Active Geant4-DNA processes in this reg
332 auto region = new G4Region("Axon");
333 region->SetProductionCuts(cuts);
334
335 fnbAxoncomp = n;
336 fMassAxonTot = fNeuronLoadParamz->GetMassA
337 fMassAxoncomp.resize(n, 0.0);
338 fDistAxonsoma.resize(n, 0.0);
339 fPosAxoncomp.resize(n);
340 faxonS.resize(n, nullptr);
341 faxonLV.resize(n, nullptr);
342 faxonPV.resize(n, nullptr);
343
344 for (G4int i = 1; i < n; ++i) {
345 faxonS[i] = new G4Tubs("Axon", 0., fNeur
346 fNeuronLoadParamz
347 faxonLV[i] = new G4LogicalVolume(faxonS[
348 faxonLV[i]->SetVisAttributes(fAxonColour
349 // RotationMatrix with Inverse
350 G4ThreeVector pos = (fNeuronLoadParamz->
351 faxonPV[i] = new G4PVPlacement(G4Transfo
352 faxonLV[i
353 fMassAxoncomp[i] = fNeuronLoadParamz->Ge
354 fPosAxoncomp[i] = fNeuronLoadParamz->Get
355 fDistAxonsoma[i] = fNeuronLoadParamz->Ge
356 region->AddRootLogicalVolume(faxonLV[i])
357 }
358 }
359 // =========================================
360 // Structure-4: Spines
361 if (fNeuronLoadParamz->GetnbSpinecomp() == 0
362 G4cout << " ---- Spines not found! ---- "
363 }
364 else {
365 G4cout << " ---- Spines for construction:
366 G4cout << " Total number of compartments i
367 << G4endl;
368 }
369
370 G4cout << "\n ---- End of Neuron Constructio
371 << "\n ==============================
372 << G4endl;
373
374 // =========================================
375 // Active Geant4-DNA processes in BoundingSl
376 // fpRegion = new G4Region("BoundingSlice");
377 // fpRegion->SetProductionCuts(cuts);
378 // fpRegion->AddRootLogicalVolume(boundingLV
379
380 return worldPV;
381 }
382