G4EmDNAChemistry_option1 Class Reference

#include <G4EmDNAChemistry_option1.hh>

Inheritance diagram for G4EmDNAChemistry_option1:

Public Member Functions
	G4EmDNAChemistry_option1 ()
	~G4EmDNAChemistry_option1 () override=default
void	ConstructParticle () override
void	ConstructMolecule () override
void	ConstructProcess () override
void	ConstructDissociationChannels () override
void	ConstructReactionTable (G4DNAMolecularReactionTable *reactionTable) override
void	ConstructTimeStepModel (G4DNAMolecularReactionTable *reactionTable) override
Public Member Functions inherited from G4VUserChemistryList
	G4VUserChemistryList (G4bool flag=true)
virtual	~G4VUserChemistryList ()
bool	IsPhysicsConstructor ()
void	ThisIsAPhysicsConstructor (G4bool flag=true)
void	BuildPhysicsTable ()
Public Member Functions inherited from G4VPhysicsConstructor
	G4VPhysicsConstructor (const G4String &="")
	G4VPhysicsConstructor (const G4String &name, G4int physics_type)
virtual	~G4VPhysicsConstructor ()
void	SetPhysicsName (const G4String &="")
const G4String &	GetPhysicsName () const
void	SetPhysicsType (G4int)
G4int	GetPhysicsType () const
G4int	GetInstanceID () const
virtual void	TerminateWorker ()
void	SetVerboseLevel (G4int value)
G4int	GetVerboseLevel () const

Additional Inherited Members
Static Public Member Functions inherited from G4VPhysicsConstructor
static const G4VPCManager &	GetSubInstanceManager ()
Protected Types inherited from G4VPhysicsConstructor
using	PhysicsBuilder_V = G4VPCData::PhysicsBuilders_V
Protected Member Functions inherited from G4VUserChemistryList
void	BuildPhysicsTable (G4MoleculeDefinition *)
void	RegisterTimeStepModel (G4VITStepModel *timeStepModel, G4double startingTime=0)
Protected Member Functions inherited from G4VPhysicsConstructor
G4bool	RegisterProcess (G4VProcess *process, G4ParticleDefinition *particle)
G4ParticleTable::G4PTblDicIterator *	GetParticleIterator () const
PhysicsBuilder_V	GetBuilders () const
void	AddBuilder (G4PhysicsBuilderInterface *bld)
Protected Attributes inherited from G4VUserChemistryList
G4int	verboseLevel
G4bool	fIsPhysicsConstructor
Protected Attributes inherited from G4VPhysicsConstructor
G4int	verboseLevel = 0
G4String	namePhysics = ""
G4int	typePhysics = 0
G4ParticleTable *	theParticleTable = nullptr
G4int	g4vpcInstanceID = 0
Static Protected Attributes inherited from G4VPhysicsConstructor
static G4RUN_DLL G4VPCManager	subInstanceManager

Detailed Description

Definition at line 35 of file G4EmDNAChemistry_option1.hh.

Constructor & Destructor Documentation

G4EmDNAChemistry_option1()

G4EmDNAChemistry_option1::G4EmDNAChemistry_option1

(

)

Definition at line 65 of file G4EmDNAChemistry_option1.cc.

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

~G4EmDNAChemistry_option1()

G4EmDNAChemistry_option1::~G4EmDNAChemistry_option1 ( )

overridedefault

Member Function Documentation

ConstructDissociationChannels()

void G4EmDNAChemistry_option1::ConstructDissociationChannels ( )

overridevirtual

Reimplemented from G4VUserChemistryList.

Definition at line 93 of file G4EmDNAChemistry_option1.cc.

{
  G4ChemDissociationChannels::ConstructDissociationChannels();
}

ConstructMolecule()

void G4EmDNAChemistry_option1::ConstructMolecule ( )

overridevirtual

Reimplemented from G4VUserChemistryList.

Definition at line 73 of file G4EmDNAChemistry_option1.cc.

{
  G4ChemDissociationChannels::ConstructMolecule();
 
  //____________________________________________________________________________
 
  G4MoleculeTable::Instance()->GetConfiguration("H3Op")->SetDiffusionCoefficient(
                          9.46e-9 * (m2/s));
  G4MoleculeTable::Instance()->GetConfiguration("OHm")->SetDiffusionCoefficient(
    5.3e-9 * (m2 / s));
  G4MoleculeTable::Instance()->GetConfiguration("OH")->SetDiffusionCoefficient(
    2.2e-9 * (m2/s));
  G4MoleculeTable::Instance()->GetConfiguration("H2")->SetDiffusionCoefficient(
    4.8e-9 * (m2/s));
  G4MoleculeTable::Instance()->GetConfiguration("H2O2")->SetDiffusionCoefficient(
    2.3e-9 * (m2/s));
}

Referenced by ConstructParticle().

ConstructParticle()

void G4EmDNAChemistry_option1::ConstructParticle ( )

inlineoverridevirtual

Implements G4VPhysicsConstructor.

Definition at line 41 of file G4EmDNAChemistry_option1.hh.

  {
    ConstructMolecule();
  }

ConstructProcess()

void G4EmDNAChemistry_option1::ConstructProcess ( )

overridevirtual

Reimplemented from G4VUserChemistryList.

Definition at line 177 of file G4EmDNAChemistry_option1.cc.

{
  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->SetDisplacer(
          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();
}

ConstructReactionTable()

void G4EmDNAChemistry_option1::ConstructReactionTable ( G4DNAMolecularReactionTable * reactionTable )

overridevirtual

Implements G4VUserChemistryList.

Definition at line 100 of file G4EmDNAChemistry_option1.cc.

{
  //-----------------------------------
  //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(0.636e10 * (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(
      2.50e10 * (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(
      1.10e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
  reactionData->AddProduct(OHm);
  reactionData->AddProduct(OH);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // *OH + *OH -> H2O2
  reactionData = new G4DNAMolecularReactionData(
      0.55e10 * (1e-3 * m3 / (mole * s)), OH, OH);
  reactionData->AddProduct(H2O2);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // *OH + *H -> H2O
  theReactionTable->SetReaction(1.55e10 * (1e-3 * m3 / (mole * s)), OH, H);
  //------------------------------------------------------------------
  // *H + *H -> H2
  reactionData = new G4DNAMolecularReactionData(
      0.503e10 * (1e-3 * m3 / (mole * s)), H, H);
  reactionData->AddProduct(H2);
  theReactionTable->SetReaction(reactionData);
  //------------------------------------------------------------------
  // H3O+ + OH- -> 2H2O
  theReactionTable->SetReaction(1.13e11 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
  //------------------------------------------------------------------
}

ConstructTimeStepModel()

void G4EmDNAChemistry_option1::ConstructTimeStepModel ( G4DNAMolecularReactionTable * reactionTable )

overridevirtual

The reaction model defines how to compute the reaction range between molecules

The StepByStep model tells the step manager how to behave before and after each step, how to compute the time steps.

Implements G4VUserChemistryList.

Definition at line 260 of file G4EmDNAChemistry_option1.cc.

{
 
  //=========================================
  // Diffusion controlled reaction model
  //=========================================
  /**
   * The reaction model defines how to compute the reaction range between
   * molecules
   */
 
  G4VDNAReactionModel* reactionRadiusComputer =
      new G4DNASmoluchowskiReactionModel();
  reactionTable->PrintTable(reactionRadiusComputer);
 
  /**
   * The StepByStep model tells the step manager how to behave before and
   * after each step, how to compute the time steps.
   */
 
  G4DNAMolecularStepByStepModel* stepByStep =
      new G4DNAMolecularStepByStepModel();
  stepByStep->SetReactionModel(reactionRadiusComputer);
//  ((G4DNAMoleculeEncounterStepper*) stepByStep->GetTimeStepper())->
//  SetVerbose(5);
 
  RegisterTimeStepModel(stepByStep, 0);
}

---

The documentation for this class was generated from the following files:

• G4EmDNAChemistry_option1.hh
• G4EmDNAChemistry_option1.cc