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Jose Ramos MendezJose Ramos Mendez
Jose Ramos Mendez
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Jose Ramos Mendez
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First implementation of process for interactions with Gold
 And code cleaning new file: examples/processes/GoldNanoParticle.txt modified: geometry/dna/TsPlasmidSupercoiled/TsIRTPlasmidSupercoiled.cc modified: geometry/sampling/TsRandomCylindersInComponent.cc modified: primary/TsGeneratorUniformlyRandomAtVolume.cc modified: processes/TsEmDNAChemistryExtended.cc modified: processes/TsEmDNAPhysics.cc deleted: processes/TsEmDNAPhysics_opt1.cc deleted: processes/TsEmDNAPhysics_opt1.hh modified: processes/TsEmStandardPhysics_option4.cc modified: processes/TsIRTConfiguration.cc modified: scorers/TsScoreDNADamageWithIRT.cc modified: scorers/TsScoreWithIRTCummulative.cc
1 parent a1b1e84 commit 5d16656

12 files changed

+752
-1287
lines changed

‎examples/processes/GoldNanoParticle.txt

Lines changed: 41 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,41 @@
1+
# Test for using electron/photon interactions in Gold material
2+
# Note: Only electron and photon interactions are supported.
3+
4+
Ts/UseQt = "True"
5+
6+
s:Gr/view/Type = "OpenGL"
7+
Ge/World/HLX = 400 nm
8+
Ge/World/HLY = 400 nm
9+
Ge/World/HLZ = 400 nm
10+
Ge/World/Material = "G4_WATER"
11+
12+
s:Ge/MyBox/Type = "TsSphere"
13+
s:Ge/MyBox/Material = "G4_Au"
14+
s:Ge/MyBox/Parent = "World"
15+
d:Ge/MyBox/RMax = 150 nm
16+
s:Ge/MyBox/Color = "Yellow"
17+
18+
# It requires a region (use lower-case)
19+
s:Ge/MyBox/AssignToRegionNamed = "nanoparticle"
20+
21+
# Active the physics in region
22+
sv:Ph/Default/Modules = 1 "TsEmDNAPhysics"
23+
b:Ph/Default/PhysicsForGold/Active = "True"
24+
s:Ph/Default/PhysicsForGold/Region = Ge/MyBox/AssignToRegionNamed
25+
26+
# Set a beam, zero radius and zero divergence
27+
s:So/Demo/BeamParticle = "e-"
28+
s:So/Demo/BeamPositionDistribution = "None"
29+
s:So/Demo/BeamAngularDistribution = "None"
30+
d:So/Demo/BeamEnergy = 20 keV
31+
u:So/Demo/BeamEnergySpread = 0
32+
i:So/Demo/NumberOfHistoriesInRun = 10
33+
34+
s:Gr/ViewA/Type = "OpenGL"
35+
d:Gr/ViewA/Theta = 90 deg
36+
d:Gr/ViewA/Phi = 0 deg
37+
u:Gr/ViewA/Zoom = 2.
38+
39+
# Good practice, report the simulation time
40+
b:Ts/ShowCPUTime = "True"
41+

‎geometry/dna/TsPlasmidSupercoiled/TsIRTPlasmidSupercoiled.cc

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -163,22 +163,22 @@ G4LogicalVolume* TsIRTPlasmidSupercoiled::CreateLogicVolume(G4String, G4int copy
163163
G4int copyNum = fMolecules[i].fCopyNumber;
164164

165165
if ( solidPhosphate || solidPurinePyrimidine || solidDeoxyribose || solidHistone ) {
166-
if ( name.contains("phosphate") && solidPhosphate ) {
166+
if ( G4StrUtil::contains(name,"phosphate") && solidPhosphate ) {
167167
phosphate = new G4Orb("phosphate", radius);
168168
wphosphate = new G4Orb("wphosphate", waterRadius);
169169
solidPhosphate = false;
170170
G4cout << "#### Built phosphate" << G4endl;
171-
} else if ( name.contains("base") && solidPurinePyrimidine ) {
171+
} else if ( G4StrUtil::contains(name,"base") && solidPurinePyrimidine ) {
172172
purineAndPyrimidine = new G4Orb("purineandpyrimidine", radius);
173173
wpurineAndPyrimidine = new G4Orb("wpurineandpyrimidine", waterRadius);
174174
solidPurinePyrimidine = false;
175175
G4cout << "#### Built purines and pyrimidines" << G4endl;
176-
} else if ( name.contains("deoxyribose") && solidDeoxyribose ) {
176+
} else if ( G4StrUtil::contains(name, "deoxyribose") && solidDeoxyribose ) {
177177
deoxyribose = new G4Orb("deoxyribose", radius);
178178
wdeoxyribose = new G4Orb("wdeoxyribose", waterRadius);
179179
solidDeoxyribose = false;
180180
G4cout << "#### Built deoxyriboses" << G4endl;
181-
} else if ( name.contains("histone") && solidHistone ) {
181+
} else if ( G4StrUtil::contains(name, "histone") && solidHistone ) {
182182
histone = new G4Orb("histone", radius);
183183
solidHistone = false;
184184
}
@@ -192,11 +192,11 @@ G4LogicalVolume* TsIRTPlasmidSupercoiled::CreateLogicVolume(G4String, G4int copy
192192
if(waterRadius > (0 + tol)*nm)
193193
{
194194
G4String nameWaterSolid = name+"_waterShell";
195-
if ( name.contains("phosphate") ) {
195+
if ( G4StrUtil::contains(name, "phosphate") ) {
196196
moleculeWaterCut_solid = CreateCutSolid(wphosphate, fMolecules[i], fMolecules, false);
197-
} else if ( name.contains("base") ) {
197+
} else if ( G4StrUtil::contains(name, "base") ) {
198198
moleculeWaterCut_solid = CreateCutSolid(wpurineAndPyrimidine, fMolecules[i], fMolecules, false);
199-
} else if ( name.contains("deoxyribose") ) {
199+
} else if ( G4StrUtil::contains(name, "deoxyribose") ) {
200200
moleculeWaterCut_solid = CreateCutSolid(wdeoxyribose, fMolecules[i], fMolecules, false);
201201
}
202202

@@ -213,13 +213,13 @@ G4LogicalVolume* TsIRTPlasmidSupercoiled::CreateLogicVolume(G4String, G4int copy
213213
G4String nameLogic = name;
214214
G4LogicalVolume* molecule_logic = 0;
215215

216-
if ( name.contains("phosphate") ) {
216+
if ( G4StrUtil::contains(name,"phosphate") ) {
217217
moleculeCut_solid = CreateCutSolid(phosphate, fMolecules[i], fMolecules, true);
218-
} else if ( name.contains("base") ) {
218+
} else if ( G4StrUtil::contains(name,"base") ) {
219219
moleculeCut_solid = CreateCutSolid(purineAndPyrimidine, fMolecules[i], fMolecules, true);
220-
} else if ( name.contains("deoxyribose") ) {
220+
} else if ( G4StrUtil::contains(name,"deoxyribose") ) {
221221
moleculeCut_solid = CreateCutSolid(deoxyribose, fMolecules[i], fMolecules, true);
222-
} else if ( name.contains("histone") ) {
222+
} else if ( G4StrUtil::contains(name,"histone") ) {
223223
moleculeCut_solid = CreateCutSolid(histone, fMolecules[i], fMolecules, true);
224224
}
225225

‎geometry/sampling/TsRandomCylindersInComponent.cc

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -55,14 +55,14 @@ TsVGeometryComponent(pM, eM, mM, gM, parentComponent, parentVolume, name)
5555
fTHL = fPm->GetDoubleParameter(GetFullParmName("Cylinders/HL"), "Length");
5656

5757
fEnvelopeType = fPm->GetStringParameter(GetFullParmName("EnvelopeShape"));
58-
fEnvelopeType.toLower();
59-
if ( fEnvelopeType.contains("tssphere") ) {
58+
G4StrUtil::to_lower(fEnvelopeType);
59+
if ( G4StrUtil::contains(fEnvelopeType,"tssphere") ) {
6060
fRMax = fPm->GetDoubleParameter(GetFullParmName("RMax"), "Length");
61-
} else if (fEnvelopeType.contains("tsbox")) {
61+
} else if (G4StrUtil::contains(fEnvelopeType,"tsbox")) {
6262
fHLX = fPm->GetDoubleParameter(GetFullParmName("HLX"), "Length");
6363
fHLY = fPm->GetDoubleParameter(GetFullParmName("HLY"), "Length");
6464
fHLZ = fPm->GetDoubleParameter(GetFullParmName("HLZ"), "Length");
65-
} else if ( fEnvelopeType.contains("tscylinder")) {
65+
} else if ( G4StrUtil::contains(fEnvelopeType,"tscylinder")) {
6666
fRMax = fPm->GetDoubleParameter(GetFullParmName("RMax"), "Length");
6767
fHL = fPm->GetDoubleParameter(GetFullParmName("HL"), "Length");
6868
} else {
@@ -90,12 +90,12 @@ G4VPhysicalVolume* TsRandomCylindersInComponent::Construct()
9090
BeginConstruction();
9191

9292
G4double extensionX, extensionY, extensionZ;
93-
if ( fEnvelopeType.contains("tssphere" ) ) {
93+
if ( G4StrUtil::contains(fEnvelopeType,"tssphere" ) ) {
9494
fEnvelope = new G4Orb(fName, fRMax);
9595
extensionX = 2.0 * fRMax;
9696
extensionY = extensionX;
9797
extensionZ = extensionY;
98-
} else if ( fEnvelopeType.contains("tscylinder")) {
98+
} else if ( G4StrUtil::contains(fEnvelopeType,"tscylinder")) {
9999
fEnvelope = new G4Tubs(fName, 0.0, fRMax, fHL, 0.0, 360.0*deg);
100100
extensionX = 2.0 * fRMax;
101101
extensionY = extensionX;

‎primary/TsGeneratorUniformlyRandomAtVolume.cc

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@ void TsGeneratorUniformlyRandomAtVolume::ResolveParameters() {
4848
G4String generateOn = "volume";
4949
if ( fPm->ParameterExists(GetFullParmName("DistributePrimariesAtVolumeRegion")))
5050
generateOn = fPm->GetStringParameter(GetFullParmName("DistributePrimariesAtVolumeRegion"));
51-
generateOn.toLower();
51+
G4StrUtil::to_lower(generateOn);
5252

5353
if ( generateOn != "volume" && generateOn != "surface" ) {
5454
G4cerr << "Topas is exiting due to a serious error in source setup." << G4endl;
@@ -61,7 +61,7 @@ void TsGeneratorUniformlyRandomAtVolume::ResolveParameters() {
6161
fTheDirection = "isotropic";
6262
if ( fPm->ParameterExists(GetFullParmName("DirectPrimariesTo")))
6363
fTheDirection = fPm->GetStringParameter(GetFullParmName("DirectPrimariesTo"));
64-
fTheDirection.toLower();
64+
G4StrUtil::to_lower(fTheDirection);
6565

6666
if ( fTheDirection != "inside" && ( fTheDirection != "outside" && fTheDirection != "isotropic")) {
6767
G4cerr << "Topas is exiting due to a serious error in source setup." << G4endl;

‎processes/TsEmDNAChemistryExtended.cc

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -140,7 +140,7 @@ void TsEmDNAChemistryExtended::DefineParameters()
140140
"must match with " + GetFullParmName("DiffusionCoefficients/Values"));
141141

142142
for ( int i = 0; i < nbOfMolecules; i++ ) {
143-
molecules[i].toLower();
143+
G4StrUtil::to_lower(molecules[i]);
144144
if ( !MoleculeExists(molecules[i]) ) {
145145
Quit(GetFullParmName("DiffusionCoefficients/Molecules"), "\n--- Molecule: " + molecules[i] + " was not found in database");
146146
} else if ( molecules[i] == "water" ) {
@@ -164,7 +164,7 @@ void TsEmDNAChemistryExtended::DefineParameters()
164164
"must match with " + GetFullParmName("Radii/Values"));
165165

166166
for ( int i = 0; i < nbOfMolecules; i++ ) {
167-
molecules[i].toLower();
167+
G4StrUtil::to_lower(molecules[i]);
168168
if ( !MoleculeExists(molecules[i]) ) {
169169
Quit(GetFullParmName("Radii/Molecules"), "\n--- Molecule: " + molecules[i] + " was not found in database");
170170
} else if ( molecules[i] == "water" ) {
@@ -197,8 +197,8 @@ void TsEmDNAChemistryExtended::DefineParameters()
197197
std::vector<G4String> reactors;
198198
std::vector<G4String> products;
199199

200-
reactorA.toLower();
201-
reactorB.toLower();
200+
G4StrUtil::to_lower(reactorA);
201+
G4StrUtil::to_lower(reactorB);
202202
if ( !MoleculeExists(reactorA) )
203203
Quit(parName, "\n--- Molecule: " + reactorA + " was not found in database");
204204

@@ -209,7 +209,7 @@ void TsEmDNAChemistryExtended::DefineParameters()
209209
reactors.push_back(fExistingMolecules[reactorB]);
210210

211211
for ( int j = 0; j < nbOfProduct; j++ ) {
212-
product[j].toLower();
212+
G4StrUtil::to_lower(product[j]);
213213
if ( product[j] == "none" ) // Note on comparison of strings: See comment on ConstructReactionTable()
214214
products.push_back("none");
215215
else if ( product[j] == "water") {
@@ -242,7 +242,7 @@ void TsEmDNAChemistryExtended::DefineParameters()
242242
G4int nbOfScavenged = fPm->GetVectorLength(GetFullParmName("Scavenger/Molecules"));
243243
for ( int i = 0; i < nbOfScavenged; i++ ) {
244244
G4String aName = scavengedMolecules[i];
245-
aName.toLower();
245+
G4StrUtil::to_lower(aName);
246246
if ( !MoleculeExists(aName) ) {
247247
Quit(GetFullParmName("Scavenger/Molecules"), "\n--- Molecule name " + aName + " was not found");
248248
}

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