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This commit is contained in:
Gabriele Cosmo
2021-12-10 14:46:44 +01:00
committed by Ben Morgan
parent 6399a014b6
commit 80e2389dd8
3932 changed files with 202519 additions and 246221 deletions
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source/processes/electromagnetic/dna/models/src/G4DNAIRT.cc
+20 -12
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@@ -52,7 +52,7 @@ G4VITReactionProcess(),
fMolReactionTable(reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable)),
fpReactionModel(nullptr),
fTrackHolder(G4ITTrackHolder::Instance()),
fReactionSet(0)
fReactionSet(nullptr)
{
timeMin = G4Scheduler::Instance()->GetStartTime();
timeMax = G4Scheduler::Instance()->GetEndTime();
@@ -247,10 +247,11 @@ void G4DNAIRT::Sampling(G4Track* track){
for(size_t u=0; u<fReactionDatas->size();u++){
if((*fReactionDatas)[u]->GetReactant2()->GetDiffusionCoefficient() == 0){
G4double kObs = (*fReactionDatas)[u]->GetObservedReactionRateConstant();
if(kObs == 0) continue;
G4double time = -(std::log(1.0 - G4UniformRand())/kObs) + globalTime;
if( time < minTime && time >= globalTime && time < timeMax){
minTime = time;
index = (int) u;
index = (G4int)u;
}
}
}
@@ -277,18 +278,19 @@ G4double G4DNAIRT::GetIndependentReactionTime(const G4MolecularConfiguration* mo
G4double irt = -1 * ps;
G4double D = molA->GetDiffusionCoefficient() +
molB->GetDiffusionCoefficient();
if(D == 0) D += 1e-20*(m2/s);
G4double rc = fReactionData->GetOnsagerRadius();
if ( reactionType == 0){
G4double sigma = fReactionData->GetEffectiveReactionRadius();
if( rc != 0) r0 = -rc / (1-std::exp(rc/r0));
if(sigma > r0) return 0; // contact reaction
if( rc != 0) r0 = -rc / (1-std::exp(rc/r0));
G4double Winf = sigma/r0;
G4double W = G4UniformRand();
if ( W < Winf ) irt = (0.25/D) * std::pow( (r0-sigma)/erfc->erfcInv(r0*W/sigma), 2 );
if ( W > 0 && W < Winf ) irt = (0.25/D) * std::pow( (r0-sigma)/erfc->erfcInv(r0*W/sigma), 2 );
return irt;
}
@@ -319,8 +321,8 @@ G4double G4DNAIRT::GetIndependentReactionTime(const G4MolecularConfiguration* mo
Winf = sigma / r0 * kobs / kdif;
if(Winf > G4UniformRand()) irt = SamplePDC(a,b)/D;
return irt;
}
return irt;
}
return -1 * ps;
}
@@ -404,7 +406,7 @@ std::unique_ptr<G4ITReactionChange> G4DNAIRT::MakeReaction(const G4Track& trackA
G4double dt = globalTime - trackA.GetGlobalTime();
if(dt != 0){
if(dt != 0 && (D1 + D2) != 0 && r0 != 0){
G4double s12 = 2.0 * D1 * dt;
G4double s22 = 2.0 * D2 * dt;
if(s12 == 0) r2 = r1;
@@ -415,6 +417,9 @@ std::unique_ptr<G4ITReactionChange> G4DNAIRT::MakeReaction(const G4Track& trackA
G4RandGauss::shoot(0, s12 + s22 * s22 / s12),
G4RandGauss::shoot(0, s12 + s22 * s22 / s12));
if(alpha == 0){
return pChanges;
}
S1.setPhi(rad * G4UniformRand() * 2.0 * CLHEP::pi);
S1.setTheta(rad * std::acos(1.0 + 1./alpha * std::log(1.0 - G4UniformRand() * (1 - std::exp(-2.0 * alpha)))));
@@ -441,6 +446,9 @@ std::unique_ptr<G4ITReactionChange> G4DNAIRT::MakeReaction(const G4Track& trackA
const G4double sqrD1 = D1 == 0. ? 0. : std::sqrt(D1);
const G4double sqrD2 = D2 == 0. ? 0. : std::sqrt(D2);
if((sqrD1 + sqrD2) == 0){
return pChanges;
}
const G4double inv_numerator = 1./(sqrD1 + sqrD2);
const G4ThreeVector reactionSite = sqrD2 * inv_numerator * trackA.GetPosition()
+ sqrD1 * inv_numerator * trackB.GetPosition();
@@ -487,9 +495,9 @@ std::unique_ptr<G4ITReactionChange> G4DNAIRT::MakeReaction(const G4Track& trackA
std::vector<std::unique_ptr<G4ITReactionChange>> G4DNAIRT::FindReaction(
G4ITReactionSet* pReactionSet,
const double /*currentStepTime*/,
const double fGlobalTime,
const bool /*reachedUserStepTimeLimit*/)
const G4double /*currentStepTime*/,
const G4double fGlobalTime,
const G4bool /*reachedUserStepTimeLimit*/)
{
std::vector<std::unique_ptr<G4ITReactionChange>> fReactionInfo;
fReactionInfo.clear();
@@ -528,8 +536,8 @@ std::vector<std::unique_ptr<G4ITReactionChange>> G4DNAIRT::FindReaction(
G4bool G4DNAIRT::TestReactibility(const G4Track& /*trackA*/,
const G4Track& /*trackB*/,
double /*currentStepTime*/,
bool /*userStepTimeLimit*/) /*const*/
G4double /*currentStepTime*/,
G4bool /*userStepTimeLimit*/) /*const*/
{
return true;
}