G4DNAMolecularReactionData Class Reference

#include <G4DNAMolecularReactionTable.hh>

Collaboration diagram for G4DNAMolecularReactionData:

Public Types
typedef std::function< double(double)>	RateParam

Public Member Functions
	G4DNAMolecularReactionData (G4double reactionRate, G4MolecularConfiguration *reactive1, G4MolecularConfiguration *reactive2)
	G4DNAMolecularReactionData (G4double reactionRate, const G4String &reactive1, const G4String &reactive2)
	~G4DNAMolecularReactionData ()
int	GetReactionID () const
void	SetReactionID (int ID)
std::pair < G4MolecularConfiguration *, G4MolecularConfiguration * >	GetReactants ()
G4MolecularConfiguration *	GetReactant1 () const
G4MolecularConfiguration *	GetReactant2 () const
void	SetObservedReactionRateConstant (G4double rate)
G4double	GetObservedReactionRateConstant () const
G4double	GetEffectiveReactionRadius () const
void	SetEffectiveReactionRadius (G4double radius)
void	SetReactant1 (G4MolecularConfiguration *reactive)
void	SetReactant2 (G4MolecularConfiguration *reactive)
void	SetReactants (G4MolecularConfiguration *reactive1, G4MolecularConfiguration *reactive2)
void	AddProduct (G4MolecularConfiguration *molecule)
void	SetReactant1 (const G4String &reactive)
void	SetReactant2 (const G4String &reactive)
void	SetReactants (const G4String &reactive1, const G4String &reactive2)
void	AddProduct (const G4String &molecule)
G4int	GetNbProducts () const
G4MolecularConfiguration *	GetProduct (G4int i) const
const std::vector < G4MolecularConfiguration * > *	GetProducts () const
void	RemoveProducts ()
void	SetPolynomialParameterization (const std::vector< double > &P)
void	SetArrehniusParameterization (double A0, double E_R)
void	SetScaledParameterization (double temperature_K, double rateCste)
void	ScaleForNewTemperature (double temp_K)

Static Public Member Functions
static double	PolynomialParam (double temp_K, std::vector< double > P)
static double	ArrehniusParam (double temp_K, std::vector< double > P)
static double	ScaledParameterization (double temp_K, double temp_init, double rateCste_init)

Protected Member Functions
	G4DNAMolecularReactionData ()

Protected Attributes
G4MolecularConfiguration *	fReactant1
G4MolecularConfiguration *	fReactant2
G4double	fObservedReactionRate
G4double	fEffectiveReactionRadius
std::vector < G4MolecularConfiguration * > *	fProducts
RateParam	fRateParam
int	fReactionID

Detailed Description

G4DNAMolecularReactionData contains the information relative to a given reaction (eg : °OH + °OH -> H2O2)

Definition at line 67 of file G4DNAMolecularReactionTable.hh.

Member Typedef Documentation

typedef std::function<double(double)> G4DNAMolecularReactionData::RateParam

Definition at line 165 of file G4DNAMolecularReactionTable.hh.

Constructor & Destructor Documentation

G4DNAMolecularReactionData::G4DNAMolecularReactionData	(	G4double	reactionRate,
		G4MolecularConfiguration *	reactive1,
		G4MolecularConfiguration *	reactive2
	)

Definition at line 70 of file G4DNAMolecularReactionTable.cc.

                                                                :
    fProducts(0)
{
  fObservedReactionRate = reactionRate;
  SetReactant1(reactant1);
  SetReactant2(reactant2);

  G4double sumDiffCoeff(0.);

  if (reactant1 == reactant2)
  {
    sumDiffCoeff = reactant1->GetDiffusionCoefficient();
    fEffectiveReactionRadius = fObservedReactionRate
        / (4 * pi * sumDiffCoeff * Avogadro);
  }
  else
  {
    sumDiffCoeff = reactant1->GetDiffusionCoefficient()
        + reactant2->GetDiffusionCoefficient();
    fEffectiveReactionRadius = fObservedReactionRate /
        (4 * pi * sumDiffCoeff * Avogadro);
  }
  fReactionID = 0;
}

Here is the call graph for this function:

G4DNAMolecularReactionData::G4DNAMolecularReactionData	(	G4double	reactionRate,
		const G4String &	reactive1,
		const G4String &	reactive2
	)

Definition at line 100 of file G4DNAMolecularReactionTable.cc.

                                                      :
    fProducts(0)
{
  fObservedReactionRate = reactionRate;
  SetReactant1(reactant1);
  SetReactant2(reactant2);

  G4double sumDiffCoeff(0.);

  if (fReactant1 == fReactant2)
  {
    sumDiffCoeff = fReactant1->GetDiffusionCoefficient();
    fEffectiveReactionRadius = fObservedReactionRate
        / (4 * pi * sumDiffCoeff * Avogadro);
  }
  else
  {
    sumDiffCoeff = fReactant1->GetDiffusionCoefficient()
        + fReactant2->GetDiffusionCoefficient();
    fEffectiveReactionRadius = fObservedReactionRate /
        (4 * pi * sumDiffCoeff * Avogadro);
  }
  fReactionID = 0;
}

Here is the call graph for this function:

G4DNAMolecularReactionData::~G4DNAMolecularReactionData

(

)

Definition at line 127 of file G4DNAMolecularReactionTable.cc.

{
  if (fProducts)
  {
    fProducts->clear();
    delete fProducts;
    fProducts = 0;
  }
}

G4DNAMolecularReactionData::G4DNAMolecularReactionData ( )

protected

Definition at line 57 of file G4DNAMolecularReactionTable.cc.

                                                       :
    fReactant1(),
    fReactant2(),
    fObservedReactionRate(0.),
    fEffectiveReactionRadius(0.),
    fProducts(0)
{
  fReactionID = 0;
}

Member Function Documentation

void G4DNAMolecularReactionData::AddProduct

(

G4MolecularConfiguration *

molecule

)

Definition at line 155 of file G4DNAMolecularReactionTable.cc.

{
  if (!fProducts) fProducts = new std::vector<G4MolecularConfiguration*>();
  fProducts->push_back(molecule);
}

Here is the caller graph for this function:

void G4DNAMolecularReactionData::AddProduct

(

const G4String &

molecule

)

Definition at line 176 of file G4DNAMolecularReactionTable.cc.

{
  if (!fProducts) fProducts = new std::vector<G4MolecularConfiguration*>();
  fProducts->push_back(G4MoleculeTable::Instance()->GetConfiguration(molecule));
}

Here is the call graph for this function:

double G4DNAMolecularReactionData::ArrehniusParam ( double  temp_K, std::vector< double >  P  )

static

Definition at line 193 of file G4DNAMolecularReactionTable.cc.

 {
   return P[0]*G4Exp(P[1]/temp_K)*
          (1e-3 * CLHEP::m3 / (CLHEP::mole * CLHEP::s));
 }

Here is the call graph for this function:

Here is the caller graph for this function:

G4double G4DNAMolecularReactionData::GetEffectiveReactionRadius ( ) const

inline

Definition at line 112 of file G4DNAMolecularReactionTable.hh.

  {
    return fEffectiveReactionRadius;
  }

Here is the caller graph for this function:

G4int G4DNAMolecularReactionData::GetNbProducts ( ) const

inline

Definition at line 137 of file G4DNAMolecularReactionTable.hh.

  {
    if(fProducts) return fProducts->size();
    return 0;
  }

Here is the caller graph for this function:

G4double G4DNAMolecularReactionData::GetObservedReactionRateConstant ( ) const

inline

Definition at line 107 of file G4DNAMolecularReactionTable.hh.

  {
    return fObservedReactionRate;
  }

Here is the caller graph for this function:

G4MolecularConfiguration* G4DNAMolecularReactionData::GetProduct ( G4int  i ) const

inline

Definition at line 143 of file G4DNAMolecularReactionTable.hh.

  {
    if(fProducts) return (*fProducts)[i];
    return 0;
  }

Here is the caller graph for this function:

const std::vector<G4MolecularConfiguration*>* G4DNAMolecularReactionData::GetProducts ( ) const

inline

Definition at line 149 of file G4DNAMolecularReactionTable.hh.

  {
    return fProducts;
  }

G4MolecularConfiguration* G4DNAMolecularReactionData::GetReactant1 ( ) const

inline

Definition at line 93 of file G4DNAMolecularReactionTable.hh.

  {
    return fReactant1;
  }

Here is the caller graph for this function:

G4MolecularConfiguration* G4DNAMolecularReactionData::GetReactant2 ( ) const

inline

Definition at line 97 of file G4DNAMolecularReactionTable.hh.

  {
    return fReactant2;
  }

Here is the caller graph for this function:

std::pair<G4MolecularConfiguration*, G4MolecularConfiguration*> G4DNAMolecularReactionData::GetReactants ( )

inline

Definition at line 88 of file G4DNAMolecularReactionTable.hh.

  {
    return std::make_pair(fReactant1, fReactant2);
  }

int G4DNAMolecularReactionData::GetReactionID ( ) const

inline

Definition at line 83 of file G4DNAMolecularReactionTable.hh.

{ return fReactionID; }

double G4DNAMolecularReactionData::PolynomialParam ( double  temp_K, std::vector< double >  P  )

static

Definition at line 183 of file G4DNAMolecularReactionTable.cc.

 {
   double inv_temp = 1. / temp_K;

   return pow(10,
              P[0] + P[1] * inv_temp + P[2] * pow(inv_temp, 2)
              + P[3] * pow(inv_temp, 3) + P[4] * pow(inv_temp, 4))
          * (1e-3 * CLHEP::m3 / (CLHEP::mole * CLHEP::s));
 }

Here is the caller graph for this function:

void G4DNAMolecularReactionData::RemoveProducts ( )

inline

Definition at line 154 of file G4DNAMolecularReactionTable.hh.

  {
    if(fProducts)
    {
      fProducts->clear();
      delete fProducts;
    }
  }

double G4DNAMolecularReactionData::ScaledParameterization ( double  temp_K, double  temp_init, double  rateCste_init  )

static

Definition at line 199 of file G4DNAMolecularReactionTable.cc.

 {
   double D0 = G4MolecularConfiguration::DiffCoeffWater(temp_init);
   double Df = G4MolecularConfiguration::DiffCoeffWater(temp_K);
   return Df*rateCste_init/D0;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void G4DNAMolecularReactionData::ScaleForNewTemperature

(

double

temp_K

)

Definition at line 726 of file G4DNAMolecularReactionTable.cc.

{
  if(fRateParam)
  {
    SetObservedReactionRateConstant(fRateParam(temp_K));

//    G4cout <<"PROD RATE = " << fProductionRate << G4endl;
//
//    if(fProductionRate != DBL_MAX && fProductionRate !=0)
//    {
//      SetPartiallyDiffusionControlledReactionByActivation(fObservedReactionRate,
//                                                          fProductionRate);
//    }
  }
}

Here is the call graph for this function:

void G4DNAMolecularReactionData::SetArrehniusParameterization	(	double	A0,
		double	E_R
	)

Definition at line 689 of file G4DNAMolecularReactionTable.cc.

{
  std::vector<double> P = {A0, E_R};

  G4cout << "ici = " << P[0] << G4endl;
  G4cout << "A0 = " << A0 << G4endl;

  fRateParam = std::bind(ArrehniusParam, std::placeholders::_1, P);
}

Here is the call graph for this function:

Here is the caller graph for this function:

void G4DNAMolecularReactionData::SetEffectiveReactionRadius ( G4double  radius )

inline

Definition at line 117 of file G4DNAMolecularReactionTable.hh.

  {
    fEffectiveReactionRadius = radius;
  }

void G4DNAMolecularReactionData::SetObservedReactionRateConstant ( G4double  rate )

inline

Definition at line 102 of file G4DNAMolecularReactionTable.hh.

  {
    fObservedReactionRate = rate;
  }

Here is the caller graph for this function:

void G4DNAMolecularReactionData::SetPolynomialParameterization

(

const std::vector< double > &

P

)

Definition at line 682 of file G4DNAMolecularReactionTable.cc.

{
  fRateParam = std::bind(PolynomialParam, std::placeholders::_1, P);
}

Here is the call graph for this function:

Here is the caller graph for this function:

void G4DNAMolecularReactionData::SetReactant1

(

G4MolecularConfiguration *

reactive

)

Definition at line 137 of file G4DNAMolecularReactionTable.cc.

{
  fReactant1 = reactive;
}

Here is the caller graph for this function:

void G4DNAMolecularReactionData::SetReactant1

(

const G4String &

reactive

)

Definition at line 161 of file G4DNAMolecularReactionTable.cc.

{
  fReactant1 = G4MoleculeTable::Instance()->GetConfiguration(reactive);
}

Here is the call graph for this function:

void G4DNAMolecularReactionData::SetReactant2

(

G4MolecularConfiguration *

reactive

)

Definition at line 143 of file G4DNAMolecularReactionTable.cc.

{
  fReactant2 = reactive;
}

Here is the caller graph for this function:

void G4DNAMolecularReactionData::SetReactant2

(

const G4String &

reactive

)

Definition at line 165 of file G4DNAMolecularReactionTable.cc.

{
  fReactant2 = G4MoleculeTable::Instance()->GetConfiguration(reactive);
}

Here is the call graph for this function:

void G4DNAMolecularReactionData::SetReactants	(	G4MolecularConfiguration *	reactive1,
		G4MolecularConfiguration *	reactive2
	)

Definition at line 148 of file G4DNAMolecularReactionTable.cc.

{
  fReactant1 = reactant1;
  fReactant2 = reactant2;
}

void G4DNAMolecularReactionData::SetReactants	(	const G4String &	reactive1,
		const G4String &	reactive2
	)

Definition at line 169 of file G4DNAMolecularReactionTable.cc.

{
  fReactant1 = G4MoleculeTable::Instance()->GetConfiguration(reactant1);
  fReactant2 = G4MoleculeTable::Instance()->GetConfiguration(reactant2);
}

Here is the call graph for this function:

void G4DNAMolecularReactionData::SetReactionID ( int  ID )

inline

Definition at line 84 of file G4DNAMolecularReactionTable.hh.

{ fReactionID = ID; }

void G4DNAMolecularReactionData::SetScaledParameterization	(	double	temperature_K,
		double	rateCste
	)

Definition at line 702 of file G4DNAMolecularReactionTable.cc.

{
  fRateParam = std::bind(ScaledParameterization, 
                         std::placeholders::_1,
                         temperature_K,
                         rateCste);
}

Here is the call graph for this function:

Here is the caller graph for this function:

Member Data Documentation

G4double G4DNAMolecularReactionData::fEffectiveReactionRadius

protected

Definition at line 186 of file G4DNAMolecularReactionTable.hh.

G4double G4DNAMolecularReactionData::fObservedReactionRate

protected

Definition at line 185 of file G4DNAMolecularReactionTable.hh.

std::vector<G4MolecularConfiguration*>* G4DNAMolecularReactionData::fProducts

protected

Definition at line 188 of file G4DNAMolecularReactionTable.hh.

RateParam G4DNAMolecularReactionData::fRateParam

protected

Definition at line 190 of file G4DNAMolecularReactionTable.hh.

G4MolecularConfiguration* G4DNAMolecularReactionData::fReactant1

protected

Definition at line 183 of file G4DNAMolecularReactionTable.hh.

G4MolecularConfiguration* G4DNAMolecularReactionData::fReactant2

protected

Definition at line 184 of file G4DNAMolecularReactionTable.hh.

int G4DNAMolecularReactionData::fReactionID

protected

Definition at line 191 of file G4DNAMolecularReactionTable.hh.

---

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

• source/geant4.10.03.p03/source/processes/electromagnetic/dna/utils/include/G4DNAMolecularReactionTable.hh
• source/geant4.10.03.p03/source/processes/electromagnetic/dna/utils/src/G4DNAMolecularReactionTable.cc