G4MoleculeTable Class Reference

#include <G4MoleculeTable.hh>

Public Member Functions
G4MolecularConfiguration *	CreateConfiguration (const G4String &userIdentifier, const G4MoleculeDefinition *molDef, const G4String &configurationLabel, const G4ElectronOccupancy &eOcc)
G4MolecularConfiguration *	CreateConfiguration (const G4String &userIdentifier, G4MoleculeDefinition *)
G4MolecularConfiguration *	CreateConfiguration (const G4String &userIdentifier, G4MoleculeDefinition *, const G4String &configurationLabel, int charge=0)
G4MolecularConfiguration *	CreateConfiguration (const G4String &userIdentifier, G4MoleculeDefinition *, int charge, double diffusion_coefficient=-1)
G4MoleculeDefinition *	CreateMoleculeDefinition (const G4String &userIdentifier, double diffusion_coefficient)
void	Finalize ()
void	Finalize (G4MoleculeDefinition *)
G4MolecularConfiguration *	GetConfiguration (const G4String &, bool mustExist=true)
G4MolecularConfiguration *	GetConfiguration (G4int id)
G4ConfigurationIterator	GetConfigurationIterator ()
G4MoleculeDefinitionIterator	GetDefintionIterator ()
G4MoleculeDefinition *	GetMoleculeDefinition (const G4String &, bool mustExist=true)
int	GetNumberOfDefinedSpecies ()
void	Insert (G4MoleculeDefinition *)
void	PrepareMolecularConfiguration ()
virtual	~G4MoleculeTable ()

Static Public Member Functions
static G4MoleculeTable *	GetMoleculeTable ()
static G4MoleculeTable *	Instance ()

Protected Types
typedef std::map< G4String, G4MoleculeDefinition * >	MoleculeDefTable

Protected Member Functions
	G4MoleculeTable ()

Protected Attributes
MoleculeDefTable	fMoleculeDefTable

Static Protected Attributes
static G4MoleculeTable *	fpgMoleculeTable

Detailed Description

Definition at line 58 of file G4MoleculeTable.hh.

Member Typedef Documentation

MoleculeDefTable

typedef std::map<G4String, G4MoleculeDefinition*> G4MoleculeTable::MoleculeDefTable

protected

Definition at line 131 of file G4MoleculeTable.hh.

Constructor & Destructor Documentation

~G4MoleculeTable()

G4MoleculeTable::~G4MoleculeTable ( )

virtual

Definition at line 47 of file G4MoleculeTable.cc.

{
}

G4MoleculeTable()

G4MoleculeTable::G4MoleculeTable ( )

protected

Definition at line 41 of file G4MoleculeTable.cc.

{
}

Referenced by Instance().

Member Function Documentation

CreateConfiguration() [1/4]

G4MolecularConfiguration * G4MoleculeTable::CreateConfiguration	(	const G4String &	userIdentifier,
		const G4MoleculeDefinition *	molDef,
		const G4String &	configurationLabel,
		const G4ElectronOccupancy &	eOcc
	)

Definition at line 233 of file G4MoleculeTable.cc.

{
  bool alreadyCreated(false);
 
  G4MolecularConfiguration* molConf =
      G4MolecularConfiguration::CreateMolecularConfiguration(userIdentifier,
                                                             molDef,
                                                             configurationLabel,
                                                             eOcc,
                                                             alreadyCreated);
 
  return molConf;
}

References G4MolecularConfiguration::CreateMolecularConfiguration().

Referenced by G4EmDNAChemistry::ConstructMolecule(), G4EmDNAChemistry_option1::ConstructMolecule(), and G4EmDNAChemistry_option3::ConstructMolecule().

CreateConfiguration() [2/4]

G4MolecularConfiguration * G4MoleculeTable::CreateConfiguration	(	const G4String &	userIdentifier,
		G4MoleculeDefinition *	molDef
	)

Definition at line 173 of file G4MoleculeTable.cc.

{
  bool alreadyCreated(false);
 
  G4MolecularConfiguration* molConf =
      G4MolecularConfiguration::CreateMolecularConfiguration(userIdentifier,
                                                             molDef,
                                                             alreadyCreated);
 
  return molConf;
}

References G4MolecularConfiguration::CreateMolecularConfiguration().

CreateConfiguration() [3/4]

G4MolecularConfiguration * G4MoleculeTable::CreateConfiguration	(	const G4String &	userIdentifier,
		G4MoleculeDefinition *	molDef,
		const G4String &	configurationLabel,
		int	charge = 0
	)

Definition at line 189 of file G4MoleculeTable.cc.

{
  bool alreadyCreated(false);
 
  G4MolecularConfiguration* molConf =
      G4MolecularConfiguration::CreateMolecularConfiguration(userIdentifier,
                                                             molDef,
                                                             charge,
                                                             configurationLabel,
                                                             alreadyCreated);
 
  return molConf;
}

References G4MolecularConfiguration::CreateMolecularConfiguration().

CreateConfiguration() [4/4]

G4MolecularConfiguration * G4MoleculeTable::CreateConfiguration	(	const G4String &	userIdentifier,
		G4MoleculeDefinition *	molDef,
		int	charge,
		double	diffusion_coefficient = -1
	)

Definition at line 209 of file G4MoleculeTable.cc.

{
  bool alreadyCreated(false);
 
  G4MolecularConfiguration* molConf =
        G4MolecularConfiguration::CreateMolecularConfiguration(userIdentifier,
                                                               molDef,
                                                               charge,
                                                               userIdentifier,
                                                               alreadyCreated);
 
  if(diffusion_coefficient!=-1) // TODO
  {
    molConf->SetDiffusionCoefficient(diffusion_coefficient);
  }
  return molConf;
}

References G4MolecularConfiguration::CreateMolecularConfiguration(), and G4MolecularConfiguration::SetDiffusionCoefficient().

CreateMoleculeDefinition()

G4MoleculeDefinition * G4MoleculeTable::CreateMoleculeDefinition	(	const G4String &	userIdentifier,
		double	diffusion_coefficient
	)

Definition at line 69 of file G4MoleculeTable.cc.

{
  return new G4MoleculeDefinition(name, -1 /* mass*/,
                                  diffusion_coefficient);
}

References G4InuclParticleNames::name().

Finalize() [1/2]

void G4MoleculeTable::Finalize

(

)

Definition at line 252 of file G4MoleculeTable.cc.

{
  G4MolecularConfiguration::FinalizeAll();
}

References G4MolecularConfiguration::FinalizeAll().

Finalize() [2/2]

void G4MoleculeTable::Finalize ( G4MoleculeDefinition *  )

inline

Definition at line 112 of file G4MoleculeTable.hh.

{}

Referenced by G4MoleculeDefinition::Finalize(), G4DNAChemistryManager::InitializeThreadSharedData(), and G4DNAChemistryManager::Run().

GetConfiguration() [1/2]

G4MolecularConfiguration * G4MoleculeTable::GetConfiguration	(	const G4String &	name,
		bool	mustExist = true
	)

Definition at line 105 of file G4MoleculeTable.cc.

{
  G4MolecularConfiguration* species =
      G4MolecularConfiguration::GetMolecularConfiguration(name);
 
  if(species == 0 && mustExist)
  {
    // exception
    G4ExceptionDescription description;
    description << "The configuration " << name
                << " was not recorded in the table" << G4endl;
    G4Exception("G4MoleculeTable::GetConfiguration",
                "CONF_NOT_CREATED",
                FatalException,
                description);
  }
 
  return species;
}

References FatalException, G4endl, G4Exception(), G4MolecularConfiguration::GetMolecularConfiguration(), and G4InuclParticleNames::name().

Referenced by G4MoleculeGun::BuildAndPushTrack(), G4EmDNAChemistry::ConstructDissociationChannels(), G4EmDNAChemistry_option1::ConstructDissociationChannels(), G4EmDNAChemistry_option3::ConstructDissociationChannels(), G4EmDNAChemistry_option2::ConstructDissociationChannels(), G4EmDNAChemistry_option1::ConstructMolecule(), G4EmDNAChemistry_option3::ConstructMolecule(), G4EmDNAChemistry_option2::ConstructReactionTable(), G4EmDNAChemistry::ConstructReactionTable(), G4EmDNAChemistry_option1::ConstructReactionTable(), G4EmDNAChemistry_option3::ConstructReactionTable(), G4DNAMolecularReactionTable::GetReactionData(), G4DNAEventScheduler::RunInMesh(), G4DNAMolecularMaterial::SetMolecularConfiguration(), G4DNAMolecularReactionData::SetReactant1(), G4DNAMolecularReactionData::SetReactant2(), and G4DNAMolecularReactionData::SetReactants().

GetConfiguration() [2/2]

G4MolecularConfiguration * G4MoleculeTable::GetConfiguration

(

G4int

id

)

Definition at line 128 of file G4MoleculeTable.cc.

{
  G4MolecularConfiguration* species =
        G4MolecularConfiguration::GetMolecularConfiguration(id);
 
  return species;
}

References G4MolecularConfiguration::GetMolecularConfiguration().

GetConfigurationIterator()

G4ConfigurationIterator G4MoleculeTable::GetConfigurationIterator

(

)

Definition at line 259 of file G4MoleculeTable.cc.

{
  return G4ConfigurationIterator(G4MolecularConfiguration::GetUserIDTable());
}

References G4MolecularConfiguration::GetUserIDTable().

Referenced by G4DNAGillespieDirectMethod::DiffusiveJumping(), G4MoleculeCounter::Initialize(), G4DNAEventScheduler::RecordTime(), and G4MolecularConfiguration::ScaleAllDiffusionCoefficientsOnWater().

GetDefintionIterator()

G4MoleculeDefinitionIterator G4MoleculeTable::GetDefintionIterator ( )

inline

Definition at line 116 of file G4MoleculeTable.hh.

  {
    return G4MoleculeDefinitionIterator(this->fMoleculeDefTable);
  }

References fMoleculeDefTable.

Referenced by G4VUserChemistryList::BuildPhysicsTable(), G4EmDNAChemistry::ConstructProcess(), G4EmDNAChemistry_option1::ConstructProcess(), G4EmDNAChemistry_option3::ConstructProcess(), and G4EmDNAChemistry_option2::ConstructProcess().

GetMoleculeDefinition()

G4MoleculeDefinition * G4MoleculeTable::GetMoleculeDefinition	(	const G4String &	name,
		bool	mustExist = true
	)

Definition at line 79 of file G4MoleculeTable.cc.

{
  MoleculeDefTable::iterator it = fMoleculeDefTable.find(name);
  G4MoleculeDefinition* definition(0);
  if (it != fMoleculeDefTable.end())
  {
    definition = it->second;
  }
  else if(mustExist)
  {
    // exception
    G4ExceptionDescription description;
    description << "The molecule definition " << name
                << " was NOT recorded in the table" << G4endl;
    G4Exception("G4MoleculeTable::CreateMoleculeModel",
                "MOLECULE_DEFINITION_NOT_CREATED",
                FatalException,
                description);
  }
  return definition;
}

References FatalException, fMoleculeDefTable, G4endl, G4Exception(), and G4InuclParticleNames::name().

Referenced by G4MolecularConfiguration::Unserialize().

GetMoleculeTable()

G4MoleculeTable * G4MoleculeTable::GetMoleculeTable ( )

static

Definition at line 61 of file G4MoleculeTable.cc.

{
  return Instance();
}

References Instance().

Referenced by G4DNAMolecularReactionTable::GetReactionData().

GetNumberOfDefinedSpecies()

int G4MoleculeTable::GetNumberOfDefinedSpecies

(

)

Definition at line 266 of file G4MoleculeTable.cc.

{
  return G4MolecularConfiguration::GetNumberOfSpecies();
}

References G4MolecularConfiguration::GetNumberOfSpecies().

Insert()

void G4MoleculeTable::Insert

(

G4MoleculeDefinition *

moleculeDefinition

)

Definition at line 138 of file G4MoleculeTable.cc.

{
 
  const G4String& name = moleculeDefinition->GetName();
  MoleculeDefTable::iterator it = fMoleculeDefTable.find(name);
  if (it == fMoleculeDefTable.end())
  {
    fMoleculeDefTable[name] = moleculeDefinition;
  }
  else
  {
    // exception
    G4ExceptionDescription description;
    description << "The molecule definition " << name
                << " was already recorded in the table" << G4endl;
    G4Exception("G4MoleculeTable::CreateMoleculeDefinition",
                "DEFINITION_ALREADY_CREATED", FatalException, description);
  }
}

References FatalException, fMoleculeDefTable, G4endl, G4Exception(), G4MoleculeDefinition::GetName(), and G4InuclParticleNames::name().

Referenced by G4MoleculeDefinition::G4MoleculeDefinition().

Instance()

G4MoleculeTable * G4MoleculeTable::Instance ( )

static

Definition at line 53 of file G4MoleculeTable.cc.

{
  if (!fpgMoleculeTable) fpgMoleculeTable = new G4MoleculeTable;
  return fpgMoleculeTable;
}

References fpgMoleculeTable, and G4MoleculeTable().

Referenced by G4DNAScavengerMaterial::AddNumberMoleculePerVolumeUnitForMaterialConf(), G4DNAMolecularReactionData::AddProduct(), G4MoleculeGun::BuildAndPushTrack(), G4VUserChemistryList::BuildPhysicsTable(), G4EmDNAChemistry::ConstructDissociationChannels(), G4EmDNAChemistry_option1::ConstructDissociationChannels(), G4EmDNAChemistry_option3::ConstructDissociationChannels(), G4EmDNAChemistry_option2::ConstructDissociationChannels(), G4EmDNAChemistry::ConstructMolecule(), G4EmDNAChemistry_option1::ConstructMolecule(), G4EmDNAChemistry_option3::ConstructMolecule(), G4EmDNAChemistry_option2::ConstructMolecule(), G4EmDNAChemistry::ConstructProcess(), G4EmDNAChemistry_option1::ConstructProcess(), G4EmDNAChemistry_option3::ConstructProcess(), G4EmDNAChemistry_option2::ConstructProcess(), G4EmDNAChemistry_option2::ConstructReactionTable(), G4EmDNAChemistry::ConstructReactionTable(), G4EmDNAChemistry_option1::ConstructReactionTable(), G4EmDNAChemistry_option3::ConstructReactionTable(), G4DNAGillespieDirectMethod::DiffusiveJumping(), G4MoleculeDefinition::Finalize(), G4DNAGillespieDirectMethod::FindScavenging(), G4MoleculeDefinition::G4MoleculeDefinition(), GetMoleculeTable(), G4DNAScavengerMaterial::GetNumberMoleculePerVolumeUnitForMaterialConf(), G4MoleculeCounter::Initialize(), G4DNAChemistryManager::InitializeThreadSharedData(), G4DNAEventScheduler::RecordTime(), G4DNAScavengerMaterial::ReduceNumberMoleculePerVolumeUnitForMaterialConf(), G4DNAChemistryManager::Run(), G4DNAEventScheduler::RunInMesh(), G4DNAIRT_geometries::Sampling(), G4MolecularConfiguration::ScaleAllDiffusionCoefficientsOnWater(), G4DNAMolecularMaterial::SetMolecularConfiguration(), G4DNAMolecularReactionData::SetReactant1(), G4DNAMolecularReactionData::SetReactant2(), G4DNAMolecularReactionData::SetReactants(), and G4MolecularConfiguration::Unserialize().

PrepareMolecularConfiguration()

void G4MoleculeTable::PrepareMolecularConfiguration

(

)

Definition at line 160 of file G4MoleculeTable.cc.

{
  MoleculeDefTable::iterator it = fMoleculeDefTable.begin();
 
  for(; it != fMoleculeDefTable.end() ; ++it)
  {
    G4MolecularConfiguration::GetOrCreateMolecularConfiguration(it->second);
  }
}

References fMoleculeDefTable, and G4MolecularConfiguration::GetOrCreateMolecularConfiguration().

Referenced by G4DNAChemistryManager::InitializeThreadSharedData().

Field Documentation

fMoleculeDefTable

MoleculeDefTable G4MoleculeTable::fMoleculeDefTable

protected

Definition at line 133 of file G4MoleculeTable.hh.

Referenced by GetDefintionIterator(), GetMoleculeDefinition(), Insert(), and PrepareMolecularConfiguration().

fpgMoleculeTable

G4MoleculeTable * G4MoleculeTable::fpgMoleculeTable

staticprotected

Definition at line 130 of file G4MoleculeTable.hh.

Referenced by Instance().

---

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

• source/processes/electromagnetic/dna/molecules/management/include/G4MoleculeTable.hh
• source/processes/electromagnetic/dna/molecules/management/src/G4MoleculeTable.cc