G4EmDNAChemistry.cc

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//
#include "G4EmDNAChemistry.hh"

#include "G4PhysicalConstants.hh"
#include "G4SystemOfUnits.hh"

#include "G4DNAWaterDissociationDisplacer.hh"
#include "G4DNAChemistryManager.hh"
#include "G4DNAWaterExcitationStructure.hh"
#include "G4ProcessManager.hh"

#include "G4DNAGenericIonsManager.hh"

// *** Processes and models for Geant4-DNA

#include "G4DNAElectronSolvation.hh"

#include "G4DNAAttachment.hh"
#include "G4DNAVibExcitation.hh"

#include "G4DNAElastic.hh"
#include "G4DNAChampionElasticModel.hh"
#include "G4DNAScreenedRutherfordElasticModel.hh"
#include "G4DNAUeharaScreenedRutherfordElasticModel.hh"

#include "G4DNAMolecularDissociation.hh"
#include "G4DNABrownianTransportation.hh"
#include "G4DNAMolecularReactionTable.hh"
#include "G4DNAMolecularStepByStepModel.hh"
#include "G4VDNAReactionModel.hh"
#include "G4DNASmoluchowskiReactionModel.hh"

#include "G4DNAElectronHoleRecombination.hh"

// particles

#include "G4Electron.hh"
#include "G4Proton.hh"
#include "G4GenericIon.hh"

#include "G4MoleculeTable.hh"
#include "G4H2O.hh"
#include "G4H2.hh"
#include "G4Hydrogen.hh"
#include "G4OH.hh"
#include "G4H3O.hh"
#include "G4Electron_aq.hh"
#include "G4H2O2.hh"

#include "G4PhysicsListHelper.hh"
#include "G4BuilderType.hh"

/****/
#include "G4DNAMoleculeEncounterStepper.hh"
#include "G4ProcessVector.hh"
#include "G4ProcessTable.hh"
#include "G4DNASecondOrderReaction.hh"
#include "G4MolecularConfiguration.hh"
/****/

// factory
#include "G4PhysicsConstructorFactory.hh"

G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistry);

#include "G4Threading.hh"

G4EmDNAChemistry::G4EmDNAChemistry() :
    G4VUserChemistryList(true)
{
  G4DNAChemistryManager::Instance()->SetChemistryList(this);
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

G4EmDNAChemistry::~G4EmDNAChemistry()
{
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void G4EmDNAChemistry::ConstructMolecule()
{
  //-----------------------------------
  G4Electron::Definition(); // safety

  //-----------------------------------
  // Create the definition
  G4H2O::Definition();
  G4Hydrogen::Definition();
  G4H3O::Definition();
  G4OH::Definition();
  G4Electron_aq::Definition();
  G4H2O2::Definition();
  G4H2::Definition();

  //____________________________________________________________________________

  G4MoleculeTable::Instance()->CreateConfiguration("H3Op", G4H3O::Definition());
  G4MolecularConfiguration* OHm = G4MoleculeTable::Instance()->
      CreateConfiguration("OHm", // just a tag to store and retrieve from
                                 // G4MoleculeTable
                          G4OH::Definition(),
                          -1, // charge
                          5.0e-9 * (m2 / s));
  OHm->SetMass(17.0079 * g / Avogadro * c_squared);
  G4MoleculeTable::Instance()->CreateConfiguration("OH", G4OH::Definition());
  G4MoleculeTable::Instance()->CreateConfiguration("e_aq",
                                                   G4Electron_aq::Definition());
  G4MoleculeTable::Instance()->CreateConfiguration("H",
                                                   G4Hydrogen::Definition());
  G4MoleculeTable::Instance()->CreateConfiguration("H2", G4H2::Definition());
  G4MoleculeTable::Instance()->CreateConfiguration("H2O2", G4H2O2::Definition());
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void G4EmDNAChemistry::ConstructDissociationChannels()
{
  //-----------------------------------
  //Get the molecular configuration
  G4MolecularConfiguration* OH =
      G4MoleculeTable::Instance()->GetConfiguration("OH");
  G4MolecularConfiguration* OHm =
      G4MoleculeTable::Instance()->GetConfiguration("OHm");
  G4MolecularConfiguration* e_aq =
      G4MoleculeTable::Instance()->GetConfiguration("e_aq");
  G4MolecularConfiguration* H2 =
      G4MoleculeTable::Instance()->GetConfiguration("H2");
  G4MolecularConfiguration* H3O =
      G4MoleculeTable::Instance()->GetConfiguration("H3Op");
  G4MolecularConfiguration* H =
      G4MoleculeTable::Instance()->GetConfiguration("H");

  //-------------------------------------
  //Define the decay channels
  G4MoleculeDefinition* water = G4H2O::Definition();
  G4MolecularDissociationChannel* decCh1;
  G4MolecularDissociationChannel* decCh2;

  G4ElectronOccupancy* occ = new G4ElectronOccupancy(
      *(water->GetGroundStateElectronOccupancy()));

  //            EXCITATIONS                               //
  G4DNAWaterExcitationStructure waterExcitation;
  //--------------------------------------------------------
  //---------------Excitation on the fifth layer------------

  decCh1 = new G4MolecularDissociationChannel("A^1B_1_Relaxation");
  decCh2 = new G4MolecularDissociationChannel("A^1B_1_DissociativeDecay");
  //Decay 1 : OH + H
  decCh1->SetEnergy(waterExcitation.ExcitationEnergy(0));
  decCh1->SetProbability(0.35);
  decCh1->SetDisplacementType(G4DNAWaterDissociationDisplacer::NoDisplacement);

  decCh2->AddProduct(OH);
  decCh2->AddProduct(H);
  decCh2->SetProbability(0.65);
  decCh2->SetDisplacementType(
      G4DNAWaterDissociationDisplacer::A1B1_DissociationDecay);

//  water->AddExcitedState("A^1B_1");
  occ->RemoveElectron(4, 1); // this is the transition form ground state to
  occ->AddElectron(5, 1); // the first unoccupied orbital: A^1B_1

  water->NewConfigurationWithElectronOccupancy("A^1B_1", *occ);
  water->AddDecayChannel("A^1B_1", decCh1);
  water->AddDecayChannel("A^1B_1", decCh2);

  //--------------------------------------------------------
  //---------------Excitation on the fourth layer-----------
  decCh1 = new G4MolecularDissociationChannel("B^1A_1_Relaxation_Channel");
  decCh2 = new G4MolecularDissociationChannel("B^1A_1_DissociativeDecay");
  G4MolecularDissociationChannel* decCh3 = new G4MolecularDissociationChannel(
      "B^1A_1_AutoIonisation_Channel");

  //Decay 1 : energy
  decCh1->SetEnergy(waterExcitation.ExcitationEnergy(1));
  decCh1->SetProbability(0.3);

  //Decay 2 : 2OH + H_2
  decCh2->AddProduct(H2);
  decCh2->AddProduct(OH);
  decCh2->AddProduct(OH);
  decCh2->SetProbability(0.15);
  decCh2->SetDisplacementType(
      G4DNAWaterDissociationDisplacer::B1A1_DissociationDecay);

  //Decay 3 : OH + H_3Op + e_aq
  decCh3->AddProduct(OH);
  decCh3->AddProduct(H3O);
  decCh3->AddProduct(e_aq);
  decCh3->SetProbability(0.55);
  decCh3->SetDisplacementType(G4DNAWaterDissociationDisplacer::AutoIonisation);

  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->RemoveElectron(3); // this is the transition form ground state to
  occ->AddElectron(5, 1); // the first unoccupied orbital: B^1A_1

  water->NewConfigurationWithElectronOccupancy("B^1A_1", *occ);
  water->AddDecayChannel("B^1A_1", decCh1);
  water->AddDecayChannel("B^1A_1", decCh2);
  water->AddDecayChannel("B^1A_1", decCh3);

  //-------------------------------------------------------
  //-------------------Excitation of 3rd layer-----------------
  decCh1 = new G4MolecularDissociationChannel(
      "Excitation3rdLayer_AutoIonisation_Channel");
  decCh2 = new G4MolecularDissociationChannel(
      "Excitation3rdLayer_Relaxation_Channel");

  //Decay channel 1 : : OH + H_3Op + e_aq
  decCh1->AddProduct(OH);
  decCh1->AddProduct(H3O);
  decCh1->AddProduct(e_aq);

  decCh1->SetProbability(0.5);
  decCh1->SetDisplacementType(G4DNAWaterDissociationDisplacer::AutoIonisation);

  //Decay channel 2 : energy
  decCh2->SetEnergy(waterExcitation.ExcitationEnergy(2));
  decCh2->SetProbability(0.5);

  //Electronic configuration of this decay
  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->RemoveElectron(2, 1);
  occ->AddElectron(5, 1);

  //Configure the water molecule
  water->NewConfigurationWithElectronOccupancy("Excitation3rdLayer", *occ);
  water->AddDecayChannel("Excitation3rdLayer", decCh1);
  water->AddDecayChannel("Excitation3rdLayer", decCh2);

  //-------------------------------------------------------
  //-------------------Excitation of 2nd layer-----------------
  decCh1 = new G4MolecularDissociationChannel(
      "Excitation2ndLayer_AutoIonisation_Channel");
  decCh2 = new G4MolecularDissociationChannel(
      "Excitation2ndLayer_Relaxation_Channel");

  //Decay Channel 1 : : OH + H_3Op + e_aq
  decCh1->AddProduct(OH);
  decCh1->AddProduct(H3O);
  decCh1->AddProduct(e_aq);

  decCh1->SetProbability(0.5);
  decCh1->SetDisplacementType(G4DNAWaterDissociationDisplacer::AutoIonisation);

  //Decay channel 2 : energy
  decCh2->SetEnergy(waterExcitation.ExcitationEnergy(3));
  decCh2->SetProbability(0.5);

  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->RemoveElectron(1, 1);
  occ->AddElectron(5, 1);

  water->NewConfigurationWithElectronOccupancy("Excitation2ndLayer", *occ);
  water->AddDecayChannel("Excitation2ndLayer", decCh1);
  water->AddDecayChannel("Excitation2ndLayer", decCh2);

  //-------------------------------------------------------
  //-------------------Excitation of 1st layer-----------------
  decCh1 = new G4MolecularDissociationChannel(
      "Excitation1stLayer_AutoIonisation_Channel");
  decCh2 = new G4MolecularDissociationChannel(
      "Excitation1stLayer_Relaxation_Channel");

  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->RemoveElectron(0, 1);
  occ->AddElectron(5, 1);

  //Decay Channel 1 : : OH + H_3Op + e_aq
  decCh1->AddProduct(OH);
  decCh1->AddProduct(H3O);
  decCh1->AddProduct(e_aq);
  decCh1->SetProbability(0.5);
  decCh1->SetDisplacementType(G4DNAWaterDissociationDisplacer::AutoIonisation);

  //Decay channel 2 : energy
  decCh2->SetEnergy(waterExcitation.ExcitationEnergy(4));
  decCh2->SetProbability(0.5);

  water->NewConfigurationWithElectronOccupancy("Excitation1stLayer", *occ);
  water->AddDecayChannel("Excitation1stLayer", decCh1);
  water->AddDecayChannel("Excitation1stLayer", decCh2);

  //                  IONISATION                         //
  //--------------------------------------------------------
  //------------------- Ionisation -------------------------

  decCh1 = new G4MolecularDissociationChannel("Ionisation_Channel");

  //Decay Channel 1 : : OH + H_3Op
  decCh1->AddProduct(H3O);
  decCh1->AddProduct(OH);
  decCh1->SetProbability(1);
  decCh1->SetDisplacementType(
      G4DNAWaterDissociationDisplacer::Ionisation_DissociationDecay);

  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->RemoveElectron(4, 1);
  // this is a ionized h2O with a hole in its last orbital
  water->NewConfigurationWithElectronOccupancy("Ionisation5", *occ);
  water->AddDecayChannel("Ionisation5",
                         decCh1);

  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->RemoveElectron(3, 1);
  water->NewConfigurationWithElectronOccupancy("Ionisation4", *occ);
  water->AddDecayChannel("Ionisation4",
                         new G4MolecularDissociationChannel(*decCh1));

  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->RemoveElectron(2, 1);
  water->NewConfigurationWithElectronOccupancy("Ionisation3", *occ);
  water->AddDecayChannel("Ionisation3",
                         new G4MolecularDissociationChannel(*decCh1));

  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->RemoveElectron(1, 1);
  water->NewConfigurationWithElectronOccupancy("Ionisation2", *occ);
  water->AddDecayChannel("Ionisation2",
                         new G4MolecularDissociationChannel(*decCh1));

  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->RemoveElectron(0, 1);
  water->NewConfigurationWithElectronOccupancy("Ionisation1", *occ);
  water->AddDecayChannel("Ionisation1",
                         new G4MolecularDissociationChannel(*decCh1));

  //            Dissociative Attachment                   //
  decCh1 = new G4MolecularDissociationChannel("DissociativeAttachment");

  //Decay 1 : 2OH + H_2
  decCh1->AddProduct(H2);
  decCh1->AddProduct(OHm);
  decCh1->AddProduct(OH);
  decCh1->SetProbability(1);
  decCh1->SetDisplacementType(G4DNAWaterDissociationDisplacer::
                              DissociativeAttachment);

  *occ = *(water->GetGroundStateElectronOccupancy());
  occ->AddElectron(5, 1); // H_2O^-
  water->NewConfigurationWithElectronOccupancy("DissociativeAttachment", *occ);
  water->AddDecayChannel("DissociativeAttachment", decCh1);

  delete occ;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void G4EmDNAChemistry::ConstructReactionTable(G4DNAMolecularReactionTable*
                                              theReactionTable)
{
  //-----------------------------------
  //Get the molecular configuration
  G4MolecularConfiguration* OH =
   G4MoleculeTable::Instance()->GetConfiguration("OH");
  G4MolecularConfiguration* OHm =
   G4MoleculeTable::Instance()->GetConfiguration("OHm");
  G4MolecularConfiguration* e_aq =
   G4MoleculeTable::Instance()->GetConfiguration("e_aq");
  G4MolecularConfiguration* H2 =
   G4MoleculeTable::Instance()->GetConfiguration("H2");
  G4MolecularConfiguration* H3Op =
   G4MoleculeTable::Instance()->GetConfiguration("H3Op");
  G4MolecularConfiguration* H =
   G4MoleculeTable::Instance()->GetConfiguration("H");
  G4MolecularConfiguration* H2O2 =
   G4MoleculeTable::Instance()->GetConfiguration("H2O2");

  //------------------------------------------------------------------
  // e_aq + e_aq + 2H2O -> H2 + 2OH-
  G4DNAMolecularReactionData* reactionData =
   new G4DNAMolecularReactionData(0.5e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
  reactionData->AddProduct(OHm);
  reactionData->AddProduct(OHm);
  reactionData->AddProduct(H2);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // e_aq + *OH -> OH-
  reactionData = new G4DNAMolecularReactionData(
      2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
  reactionData->AddProduct(OHm);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // e_aq + H* + H2O -> H2 + OH-
  reactionData = new G4DNAMolecularReactionData(
      2.65e10 * (1e-3 * m3 / (mole * s)), e_aq, H);
  reactionData->AddProduct(OHm);
  reactionData->AddProduct(H2);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // e_aq + H3O+ -> H* + H2O
  reactionData = new G4DNAMolecularReactionData(
      2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
  reactionData->AddProduct(H);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // e_aq + H2O2 -> OH- + *OH
  reactionData = new G4DNAMolecularReactionData(
      1.41e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
  reactionData->AddProduct(OHm);
  reactionData->AddProduct(OH);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // *OH + *OH -> H2O2
  reactionData = new G4DNAMolecularReactionData(
      0.44e10 * (1e-3 * m3 / (mole * s)), OH, OH);
  reactionData->AddProduct(H2O2);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // *OH + *H -> H2O
  theReactionTable->SetReaction(1.44e10 * (1e-3 * m3 / (mole * s)), OH, H);
  //------------------------------------------------------------------
  // *H + *H -> H2
  reactionData = new G4DNAMolecularReactionData(
      1.20e10 * (1e-3 * m3 / (mole * s)), H, H);
  reactionData->AddProduct(H2);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // H3O+ + OH- -> 2H2O
  theReactionTable->SetReaction(1.43e11 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
  //------------------------------------------------------------------
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void G4EmDNAChemistry::ConstructProcess()
{
  G4PhysicsListHelper* ph = G4PhysicsListHelper::GetPhysicsListHelper();

  //===============================================================
  // Extend vibrational to low energy
  // Anyway, solvation of electrons is taken into account from 7.4 eV
  // So below this threshold, for now, no accurate modeling is done
  //
  G4VProcess* process =
      G4ProcessTable::GetProcessTable()->
        FindProcess("e-_G4DNAVibExcitation", "e-");

  if (process)
  {
    G4DNAVibExcitation* vibExcitation = (G4DNAVibExcitation*) process;
    G4VEmModel* model = vibExcitation->EmModel();
    G4DNASancheExcitationModel* sancheExcitationMod =
        dynamic_cast<G4DNASancheExcitationModel*>(model);
    if(sancheExcitationMod)
    {
      sancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
    }
  }

  //===============================================================
  // *** Electron Solvatation ***
  //
  process =
  G4ProcessTable::GetProcessTable()->
  FindProcess("e-_G4DNAElectronSolvation", "e-");
  
  if (process == 0)
  {
    ph->RegisterProcess(
        new G4DNAElectronSolvation("e-_G4DNAElectronSolvation"),
        G4Electron::Definition());
  }

  //===============================================================
  // Define processes for molecules
  //
  G4MoleculeTable* theMoleculeTable = G4MoleculeTable::Instance();
  G4MoleculeDefinitionIterator iterator =
      theMoleculeTable->GetDefintionIterator();
  iterator.reset();
  while (iterator())
  {
    G4MoleculeDefinition* moleculeDef = iterator.value();

    if (moleculeDef != G4H2O::Definition())
    {
      // G4cout << "Brownian motion added for : "
      //        << moleculeDef->GetName() << G4endl;
      G4DNABrownianTransportation* brown = new G4DNABrownianTransportation();
      //   brown->SetVerboseLevel(4);
      ph->RegisterProcess(brown, moleculeDef);
    }
    else
    {
      moleculeDef->GetProcessManager()
                      ->AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
      G4DNAMolecularDissociation* dissociationProcess =
          new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
      dissociationProcess->SetDecayDisplacer(
          moleculeDef, new G4DNAWaterDissociationDisplacer);
      dissociationProcess->SetVerboseLevel(1);
//      ph->RegisterProcess(dissociationProcess, moleculeDef);

      moleculeDef->GetProcessManager()
                ->AddRestProcess(dissociationProcess, 1);
    }
    /*
     * Warning : end of particles and processes are needed by
     * EM Physics builders
     */
  }

  G4DNAChemistryManager::Instance()->Initialize();
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void G4EmDNAChemistry::ConstructTimeStepModel(G4DNAMolecularReactionTable*
                                              reactionTable)
{

  //=========================================
  // Diffusion controlled reaction model
  //=========================================
  G4VDNAReactionModel* reactionRadiusComputer =
      new G4DNASmoluchowskiReactionModel();
  reactionTable->PrintTable(reactionRadiusComputer);

  G4DNAMolecularStepByStepModel* stepByStep =
      new G4DNAMolecularStepByStepModel();
  stepByStep->SetReactionModel(reactionRadiusComputer);
//  ((G4DNAMoleculeEncounterStepper*) stepByStep->GetTimeStepper())->
//  SetVerbose(5);

  RegisterTimeStepModel(stepByStep, 0);
}