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This commit is contained in:
Gabriele Cosmo
2019-06-28 11:59:04 +02:00
parent 28a70706e0
commit d0f911957d
1056 changed files with 95168 additions and 78160 deletions
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source/processes/electromagnetic/dna/utils/include/G4DNAChemistryManager.hh
+141 -186
View File
@@ -44,8 +44,7 @@
// J. Comput. Phys. 274 (2014) 841-882
// Prog. Nucl. Sci. Tec. 2 (2011) 503-508
#ifndef G4DNACHEMISTRYMANAGER_HH
#define G4DNACHEMISTRYMANAGER_HH
#pragma once
#include "globals.hh"
#include "G4ThreeVector.hh"
@@ -62,14 +61,15 @@ class G4VUserChemistryList;
class G4UIcmdWithABool;
class G4UIcmdWithADoubleAndUnit;
class G4UIcmdWithoutParameter;
class G4UIcmdWithAnInteger;
class G4ITGun;
class G4VPhysChemIO;
enum ElectronicModification
{
eIonizedMolecule,
eExcitedMolecule,
eDissociativeAttachment
eIonizedMolecule,
eExcitedMolecule,
eDissociativeAttachment
};
/**
@@ -84,217 +84,172 @@ enum ElectronicModification
* The user can also ask to create a file containing a information about the
* creation of water molecules and solvated electrons.
*/
class G4DNAChemistryManager: public G4UImessenger,
public G4VStateDependent
{
protected:
virtual ~G4DNAChemistryManager();
~G4DNAChemistryManager() override;
public:
//============================================================================
// STATIC METHODS
//============================================================================
static G4DNAChemistryManager* Instance();
static G4DNAChemistryManager* GetInstanceIfExists();
//============================================================================
// STATIC METHODS
//============================================================================
static G4DNAChemistryManager* Instance();
static G4DNAChemistryManager* GetInstanceIfExists();
/**
* You should rather use DeleteInstance than the destructor of this class
*/
static void DeleteInstance();
G4bool IsChemistryActivated();
void SetChemistryActivation(G4bool);
static G4bool IsActivated();
static void Activated(G4bool flag = true);
static void DeleteInstance();
static G4bool IsActivated();
//============================================================================
// VIRTUAL METHODS
//============================================================================
virtual G4bool Notify(G4ApplicationState requestedState);
virtual void SetNewValue(G4UIcommand*, G4String);
virtual G4String GetCurrentValue(G4UIcommand * command);
//============================================================================
// VIRTUAL METHODS
//============================================================================
// G4VStateDependent
G4bool Notify(G4ApplicationState requestedState) override;
// G4UImessenger
void SetNewValue(G4UIcommand*, G4String) override;
G4String GetCurrentValue(G4UIcommand* pCommand) override;
//============================================================================
// INITIALIZATION AND FINALIZATION METHODS
//============================================================================
void Initialize();
inline void SetChemistryList(G4VUserChemistryList*);
inline void Deregister(G4VUserChemistryList*);
void SetGlobalTemperature(G4double temp_K);
//============================================================================
// INITIALIZATION AND FINALIZATION METHODS
//============================================================================
G4bool IsChemistryActivated();
void SetChemistryActivation(G4bool);
inline void ForceMasterReinitialization();
inline void TagThreadForReinitialization();
/** Chemistry list is managed outside the chemistry manager (eg. constructor). */
void SetChemistryList(G4VUserChemistryList&);
void Run();
void Clear();
void Gun(G4ITGun*, bool physicsTableToBuild = true);
inline void ForceThreadReinitialization();
inline void ForceRebuildingPhysicsTable();
/** Not a constructor or when used in standalone? Prefer this method. */
void SetChemistryList(std::unique_ptr<G4VUserChemistryList>);
//============================================================================
// FILE OPERATIONS
//============================================================================
/**
* Tells the chemMan to write into a file
* the position and electronic state of the water molecule
* and the position thermalized or not of the solvated electron
*/
void WriteInto(const G4String&, std::ios_base::openmode mode =
std::ios_base::out);
void AddEmptyLineInOuputFile();
// [[deprecated]] : chemistry list should never be nullptr
void SetChemistryList(G4VUserChemistryList*);
/**
* Close the file specified with WriteInto
*/
void CloseFile();
void Deregister(G4VUserChemistryList&);
//============================================================================
// PUSH MOLECULES
//============================================================================
/**
* Method used by DNA physics model to create a water molecule.
* The ElectronicModification is a flag telling whether the molecule
* is ionized or excited, the electronic level is calculated by the
* model and the IncomingTrack is the track responsible for the creation
* of this molecule (electron, proton...).
*/
void CreateWaterMolecule(ElectronicModification,
G4int /*electronicLevel*/,
const G4Track* /*theIncomingTrack*/);
void Initialize();
void Run();
void Clear();
/**
* On the same idea as the previous method but for solvated electron.
* This method should be used by the physics model of the ElectronSolvatation
* process.
*/
void CreateSolvatedElectron(const G4Track* /*theIncomingTrack*/,
G4ThreeVector* finalPosition = 0);
/**
* @brief Inject custom species to the simulation
* @details This method should be called per thread, possibly from
* ActionInitialisation::Build.
* One can decide to set the same gun for all threads.
* It is the user responsibility to handle the pointer deletion.
*/
void SetGun(G4ITGun* pChemSpeciesGun);
/**
* WARNING : In case chemistry is not activated, PushMolecule will take care
* of deleting the transfered molecule.
* Before calling this method, it is also possible to check if the chemistry
* is activated through IsChemistryActived().
* This method will create the track corresponding to the transfered molecule
* and will be in charge of loading the new track to the system.
*/
void SetPhysChemIO(std::unique_ptr<G4VPhysChemIO> pPhysChemIO);
void PushMolecule(G4Molecule*& molecule,
G4double time,
const G4ThreeVector& position,
G4int parentID);
void SetVerbose(G4int verbose);
/**
* WARNING : In case chemistry is not activated, PushMoleculeAtParentTimeAndPlace
* will take care of deleting the transfered molecule.
* Before calling this method, it is also possible to check if the chemistry
* is activated through IsChemistryActived().
* This method will create the track corresponding to the transfered molecule
* and will be in charge of loading the new track to the system.
*/
void PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecule,
const G4Track* /*theIncomingTrack*/);
/**
* If the chemistry module is used in standalone (ie. without running the physics
* stage beforehand), the physics table still needs to be built.
* It is therefore necessary to flag the chemistry module as being run
* in standalone.
*/
void UseAsStandalone(G4bool flag);
G4bool IsCounterResetWhenRunEnds() const;
void ResetCounterWhenRunEnds(G4bool resetCounterWhenRunEnds);
inline void SetVerbose(G4int verbose)
{
fVerbose = verbose;
}
void ForceMasterReinitialization();
void TagThreadForReinitialization();
void ForceThreadReinitialization();
void ForceRebuildingPhysicsTable();
inline void SetBuildPhysicsTable(G4bool flag)
{fBuildPhysicsTable = flag;}
//============================================================================
// FILE OPERATIONS
//============================================================================
/**
* Tells the chemMan to write into a file
* the position and electronic state of the water molecule
* and the position thermalized or not of the solvated electron
*/
void WriteInto(const G4String&, std::ios_base::openmode mode =
std::ios_base::out);
void AddEmptyLineInOutputFile();
G4bool IsCounterResetWhenRunEnds() const
{
return fResetCounterWhenRunEnds;
}
/**
* Close the file specified with WriteInto
*/
void CloseFile();
void ResetCounterWhenRunEnds(G4bool resetCounterWhenRunEnds)
{
fResetCounterWhenRunEnds = resetCounterWhenRunEnds;
}
//============================================================================
// PUSH MOLECULES
//============================================================================
/**
* Method used by DNA physics model to create a water molecule.
* The ElectronicModification is a flag telling whether the molecule
* is ionized or excited, the electronic level is calculated by the
* model and the IncomingTrack is the track responsible for the creation
* of this molecule (electron, proton...).
*/
void CreateWaterMolecule(ElectronicModification,
G4int /*electronicLevel*/,
const G4Track* /*pIncomingTrack*/);
/**
* This method should be used by the physics model of the ElectronSolvatation
* process.
*/
void CreateSolvatedElectron(const G4Track* /*pIncomingTrack*/,
G4ThreeVector* pFinalPosition = nullptr);
void PushMolecule(std::unique_ptr<G4Molecule> pMolecule,
G4double time,
const G4ThreeVector& position,
G4int parentID);
void SetPhysChemIO(G4VPhysChemIO* physChemIO);
protected:
G4DNAWaterExcitationStructure* GetExcitationLevel();
G4DNAWaterIonisationStructure* GetIonisationLevel();
void InitializeFile();
void InitializeMaster();
void InitializeThread();
void HandleStandaloneInitialization();
void PushTrack(G4Track*);
void SetGlobalTemperature(G4double temperatureKelvin);
G4DNAChemistryManager();
G4DNAWaterExcitationStructure* GetExcitationLevel();
G4DNAWaterIonisationStructure* GetIonisationLevel();
void InitializeFile();
void InitializeMaster();
void InitializeThread();
void InitializeThreadSharedData();
G4DNAChemistryManager();
private:
G4UIdirectory* fpChemDNADirectory;
G4UIcmdWithABool* fpActivateChem;
G4UIcmdWithoutParameter* fpRunChem;
G4UIcmdWithoutParameter* fpSkipReactionsFromChemList;
//G4UIcmdWithADoubleAndUnit* fpGridSize; // not used in release
G4UIcmdWithADoubleAndUnit* fpScaleForNewTemperature;
G4UIcmdWithoutParameter* fpInitChem;
static G4DNAChemistryManager* fgInstance;
G4bool fActiveChemistry;
struct ThreadLocalData{
ThreadLocalData();
~ThreadLocalData();
G4VPhysChemIO* fpPhysChemIO;
G4bool fThreadInitialized_tl;
};
static G4ThreadLocal ThreadLocalData* fpThreadData;
G4bool fMasterInitialized;
G4bool fForceThreadReinitialization;
std::unique_ptr<G4UIdirectory> fpChemDNADirectory;
std::unique_ptr<G4UIcmdWithABool> fpActivateChem;
std::unique_ptr<G4UIcmdWithAnInteger> fpRunChem;
std::unique_ptr<G4UIcmdWithoutParameter> fpSkipReactionsFromChemList;
std::unique_ptr<G4UIcmdWithADoubleAndUnit> fpScaleForNewTemperature;
std::unique_ptr<G4UIcmdWithoutParameter> fpInitChem;
G4DNAWaterExcitationStructure* fpExcitationLevel;
G4DNAWaterIonisationStructure* fpIonisationLevel;
static G4DNAChemistryManager* fgInstance;
G4bool fActiveChemistry;
G4VUserChemistryList* fpUserChemistryList;
G4bool fBuildPhysicsTable;
G4bool fPhysicsTableBuilt;
G4bool fSkipReactions;
struct ThreadLocalData{
ThreadLocalData();
~ThreadLocalData();
std::unique_ptr<G4VPhysChemIO> fpPhysChemIO;
G4bool fThreadInitialized = false;
};
G4bool fGeometryClosed;
static G4ThreadLocal ThreadLocalData* fpThreadData;
G4int fVerbose;
G4bool fResetCounterWhenRunEnds;
G4bool fMasterInitialized;
G4bool fForceThreadReinitialization;
std::unique_ptr<G4DNAWaterExcitationStructure> fpExcitationLevel;
std::unique_ptr<G4DNAWaterIonisationStructure> fpIonisationLevel;
std::unique_ptr<G4VUserChemistryList> fpUserChemistryList;
G4bool fOwnChemistryList;
G4bool fUseInStandalone;
G4bool fPhysicsTableBuilt;
G4bool fSkipReactions;
G4bool fGeometryClosed;
G4int fVerbose;
G4bool fResetCounterWhenRunEnds;
};
//------------------------------------------------------------------------------
inline void G4DNAChemistryManager::ForceRebuildingPhysicsTable()
{
fPhysicsTableBuilt = false;
}
inline void G4DNAChemistryManager::SetChemistryList(G4VUserChemistryList* chemistryList)
{
fpUserChemistryList = chemistryList;
Activated();
}
inline void G4DNAChemistryManager::Deregister(G4VUserChemistryList* chemistryList)
{
if (fpUserChemistryList == chemistryList) fpUserChemistryList = 0;
}
inline void G4DNAChemistryManager::ForceMasterReinitialization()
{
fMasterInitialized = false;
InitializeMaster();
}
inline void G4DNAChemistryManager::ForceThreadReinitialization()
{
fForceThreadReinitialization = true;
}
inline void G4DNAChemistryManager::TagThreadForReinitialization()
{
fpThreadData->fThreadInitialized_tl = false;
}
#endif // G4DNACHEMISTRYMANAGER_HH