G4DNAGillespieDirectMethod.cc

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#include "G4DNAMolecularReactionTable.hh"
#include "G4DNAGillespieDirectMethod.hh"
#include "Randomize.hh"
#include "G4PhysicalConstants.hh"
#include <memory>
#include <tuple>
#include "G4DNAEventSet.hh"
#include "G4UnitsTable.hh"
#include "G4DNAScavengerMaterial.hh"
#include "G4Scheduler.hh"
#include <cassert>
 
G4DNAGillespieDirectMethod::G4DNAGillespieDirectMethod()
  : fMolecularReactions(G4DNAMolecularReactionTable::Instance())
  , fpMesh(nullptr)
  , fTimeStep(0)
  , fpEventSet(nullptr)
  , fVerbose(0)
  , fpScavengerMaterial(nullptr)
{}
 
G4DNAGillespieDirectMethod::~G4DNAGillespieDirectMethod() = default;
 
void G4DNAGillespieDirectMethod::SetEventSet(G4DNAEventSet* pEventSet)
{
  fpEventSet = pEventSet;
}
 
//#define DEBUG 1
 
G4double G4DNAGillespieDirectMethod::VolumeOfNode(const Index& index)
{
  auto LengthY = fpMesh->GetBoundingBox(index).Getyhi() -
                 fpMesh->GetBoundingBox(index).Getylo();
  auto LengthX = fpMesh->GetBoundingBox(index).Getxhi() -
                 fpMesh->GetBoundingBox(index).Getxlo();
  auto LengthZ = fpMesh->GetBoundingBox(index).Getzhi() -
                 fpMesh->GetBoundingBox(index).Getzlo();
  G4double V = LengthY * LengthX * LengthZ;
  assert(V > 0);
  return V;
}
G4double G4DNAGillespieDirectMethod::PropensityFunction(const Index& index,
                                                        MolType moleType)
{
  if(moleType->GetDiffusionCoefficient() == 0)
  {
    return 0.;
  }
  const auto& node = fpMesh->GetVoxelMapList(index);
  G4double alpha   = 0;
  auto it          = node.find(moleType);
  if(it != node.end())
  {
    auto LengthY = fpMesh->GetBoundingBox(index).Getyhi() -
                   fpMesh->GetBoundingBox(index).Getylo();
    G4double d = it->first->GetDiffusionCoefficient() / std::pow(LengthY, 2);
    alpha      = d * it->second;
 
#ifdef DEBUG
    G4cout << it->first->GetName() << " " << it->second
           << " D : " << it->first->GetDiffusionCoefficient()
           << " LengthY : " << LengthY << " PropensityFunction : " << alpha
           << G4endl;
#endif
  }
  return alpha;
}
 
G4double G4DNAGillespieDirectMethod::PropensityFunction(const Index& index,
                                                        ReactionData* data)
{
  G4double value;
  auto ConfA               = data->GetReactant1();
  auto ConfB               = data->GetReactant2();
  G4double scavengerNumber = 0;
  auto typeANumber         = FindScavenging(index, ConfA, scavengerNumber)
                       ? scavengerNumber
                       : ComputeNumberInNode(index, ConfA);
 
  auto typeBNumber = FindScavenging(index, ConfB, scavengerNumber)
                       ? scavengerNumber
                       : ComputeNumberInNode(index, ConfB);
 
  if(typeANumber == 0 || typeBNumber == 0)
  {
    return 0;
  }
 
  auto k =
    data->GetObservedReactionRateConstant() / (Avogadro * VolumeOfNode(index));
  if(ConfA == ConfB)
  {
    value = typeANumber * (typeBNumber - 1) * k;
  }
  else
  {
    value = typeANumber * typeBNumber * k;
  }
 
  if(value < 0)
  {
    G4cout << "G4DNAGillespieDirectMethod::PropensityFunction for : "
           << ConfA->GetName() << "(" << typeANumber << ") + "
           << ConfB->GetName() << "(" << typeBNumber
           << ") : propensity : " << value
           << " GetObservedReactionRateConstant : "
           << data->GetObservedReactionRateConstant()
           << " GetEffectiveReactionRadius : "
           << G4BestUnit(data->GetEffectiveReactionRadius(), "Length")
           << " k : " << k << " volume : " << VolumeOfNode(index)
           << " Index : " << index << G4endl;
    assert(false);
  }
 
#ifdef DEBUG
  if(value > 0)
    G4cout << "G4DNAGillespieDirectMethod::PropensityFunction for : "
           << ConfA->GetName() << "(" << typeANumber << ") + "
           << ConfB->GetName() << "(" << typeBNumber
           << ") : propensity : " << value
           << "  Time to Reaction : " << G4BestUnit(timeToReaction, "Time")
           << " k : " << k << " Index : " << index << G4endl;
#endif
 
  return value;
}
 
void G4DNAGillespieDirectMethod::Initialize()
{
  // for Scavenger
  fpScavengerMaterial = dynamic_cast<G4DNAScavengerMaterial*>(
    G4Scheduler::Instance()->GetScavengerMaterial());
 
  auto begin = fpMesh->begin();
  auto end   = fpMesh->end();
  for(; begin != end; begin++)
  {
    auto key = begin->first;
#ifdef DEBUG
    fpMesh->PrintVoxel(fpMesh->GetIndex(key));
#endif
    CreateEvent(key);
  }
}
 
void G4DNAGillespieDirectMethod::SetTimeStep(const G4double& stepTime)
{
  fTimeStep = stepTime;
}
void G4DNAGillespieDirectMethod::CreateEvent(unsigned int key)
{
  G4double r1         = G4UniformRand();
  G4double r2         = G4UniformRand();
  auto index          = fpMesh->GetIndex(key);
  G4double dAlpha0    = DiffusiveJumping(index);
  G4double rAlpha0    = Reaction(index);
  G4double alphaTotal = dAlpha0 + rAlpha0;
 
  if(alphaTotal == 0)
  {
    return;
  }
  auto timeStep = ((1.0 / (alphaTotal)) * std::log(1.0 / r1)) + fTimeStep;
 
#ifdef DEBUG
  G4cout << "r2 : " << r2 << " rAlpha0 : " << rAlpha0
         << " dAlpha0 : " << dAlpha0 << "    rAlpha0 / (dAlpha0 + rAlpha0) : "
         << rAlpha0 / (dAlpha0 + rAlpha0) << G4endl;
#endif
  if(r2 < rAlpha0 / alphaTotal)
  {
    if(fVerbose > 1)
    {
      G4cout << "=>>>>reaction at : " << timeStep << " timeStep : "
             << G4BestUnit(((1.0 / alphaTotal) * std::log(1.0 / r1)), "Time")
             << G4endl;
    }
    auto rSelectedIter = fReactionDataMap.upper_bound(r2 * alphaTotal);
    fpEventSet->CreateEvent(timeStep, key, rSelectedIter->second);
  }
  else if(dAlpha0 > 0)
  {
    if(fVerbose > 1)
    {
      G4cout << "=>>>>jumping at : " << timeStep << " timeStep : "
             << G4BestUnit(((1.0 / alphaTotal) * std::log(1.0 / r1)), "Time")
             << G4endl;
    }
 
    auto dSelectedIter = fJumpingDataMap.upper_bound(r2 * alphaTotal - rAlpha0);
    auto pDSelected =
      std::make_unique<std::pair<MolType, Index>>(dSelectedIter->second);
    fpEventSet->CreateEvent(timeStep, key, std::move(pDSelected));
  }
#ifdef DEBUG
  G4cout << G4endl;
#endif
}
 
G4double G4DNAGillespieDirectMethod::Reaction(const Index& index)
{
  fReactionDataMap.clear();
  G4double alpha0 = 0;
  auto dataList   = fMolecularReactions->GetVectorOfReactionData();
  if(dataList.empty())
  {
    G4cout << "MolecularReactionTable empty" << G4endl;
    assert(false);
  }
  for(const auto& it : dataList)
  {
    auto propensity = PropensityFunction(index, it);
    if(propensity == 0)
    {
      continue;
    }
    alpha0 += propensity;
    fReactionDataMap[alpha0] = it;
  }
#ifdef DEBUG
  G4cout << "Reaction :alpha0 :  " << alpha0 << G4endl;
#endif
  return alpha0;
}
 
G4double G4DNAGillespieDirectMethod::DiffusiveJumping(const Index& index)
{
  fJumpingDataMap.clear();
  G4double alpha0        = 0;
  auto NeighboringVoxels = fpMesh->FindNeighboringVoxels(index);
  if(NeighboringVoxels.empty())
  {
    return 0;
  }
  auto iter = G4MoleculeTable::Instance()->GetConfigurationIterator();
  while(iter())
  {
    const auto conf = iter.value();
    auto propensity = PropensityFunction(index, conf);
    if(propensity == 0)
    {
      continue;
    }
    for(const auto& it_Neighbor : NeighboringVoxels)
    {
      alpha0 += propensity;
      fJumpingDataMap[alpha0] = std::make_pair(conf, it_Neighbor);
#ifdef DEBUG
      G4cout << "mole : " << conf->GetName()
             << " number : " << ComputeNumberInNode(index, conf)
             << " propensity : " << propensity << "  alpha0 : " << alpha0
             << G4endl;
#endif
    }
  }
#ifdef DEBUG
  G4cout << "DiffusiveJumping :alpha0 :  " << alpha0 << G4endl;
#endif
  return alpha0;
}
 
G4double G4DNAGillespieDirectMethod::ComputeNumberInNode(
  const Index& index, MolType type)  // depend node ?
{
  if(type->GetDiffusionCoefficient() != 0)
  {
    const auto& node = fpMesh->GetVoxelMapList(index);
    const auto& it   = node.find(type);
    return (it != node.end()) ? (it->second) : 0;
  }
  else
  {
    return 0;
  }
}
 
G4bool G4DNAGillespieDirectMethod::FindScavenging(const Index& index,
                                                  MolType moletype,
                                                  G4double& numberOfScavenger)
{
  numberOfScavenger = 0;
  if(fpScavengerMaterial == nullptr)
  {
    return false;
  }
  auto volumeOfNode = VolumeOfNode(index);
  if(G4MoleculeTable::Instance()->GetConfiguration("H2O") == moletype)
  {
    auto factor       = Avogadro * volumeOfNode;
    numberOfScavenger = factor;
    return true;
  }
 
  G4double totalNumber =
    fpScavengerMaterial->GetNumberMoleculePerVolumeUnitForMaterialConf(
      moletype);
  if(totalNumber == 0)
  {
    return false;
  }
  else
  {
    G4double numberInDouble =
      volumeOfNode * std::floor(totalNumber) / fpMesh->GetBoundingBox().Volume();
    auto numberInInterg = (int) (std::floor(numberInDouble));
    G4double ram          = G4UniformRand();
    G4double change       = numberInDouble - numberInInterg;
    if(ram > change)
    {
      numberOfScavenger = numberInInterg;
    }
    else
    {
      numberOfScavenger = numberInInterg + 1;
    }
    return true;
  }
}