G4DNAChemistryManager.cc

Go to the documentation of this file.

//
// ********************************************************************
// * License and Disclaimer                                           *
// *                                                                  *
// * The  Geant4 software  is  copyright of the Copyright Holders  of *
// * the Geant4 Collaboration.  It is provided  under  the terms  and *
// * conditions of the Geant4 Software License,  included in the file *
// * LICENSE and available at  http://cern.ch/geant4/license .  These *
// * include a list of copyright holders.                             *
// *                                                                  *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work  make  any representation or  warranty, express or implied, *
// * regarding  this  software system or assume any liability for its *
// * use.  Please see the license in the file  LICENSE  and URL above *
// * for the full disclaimer and the limitation of liability.         *
// *                                                                  *
// * This  code  implementation is the result of  the  scientific and *
// * technical work of the GEANT4 collaboration.                      *
// * By using,  copying,  modifying or  distributing the software (or *
// * any work based  on the software)  you  agree  to acknowledge its *
// * use  in  resulting  scientific  publications,  and indicate your *
// * acceptance of all terms of the Geant4 Software license.          *
// ********************************************************************
//
// $Id: G4DNAChemistryManager.cc 75583 2013-11-04 12:16:46Z gcosmo $
//
// Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
//
// WARNING : This class is released as a prototype.
// It might strongly evolve or even disapear in the next releases.
//
// History:
// -----------
// 10 Oct 2011 M.Karamitros created
//
// -------------------------------------------------------------------

#include "G4DNAChemistryManager.hh"
#include "G4SystemOfUnits.hh"
#include "G4Molecule.hh"
#include "G4ITTrackHolder.hh"
#include "G4H2O.hh"
#include "G4DNAMolecularReactionTable.hh"
#include "G4DNAWaterExcitationStructure.hh"
#include "G4DNAWaterIonisationStructure.hh"
#include "G4Electron_aq.hh"
#include "G4ITManager.hh"
#include "G4MolecularConfiguration.hh"
#include "G4MoleculeCounter.hh"
#include "G4Tokenizer.hh"
#include "G4AutoLock.hh"

using namespace std;

auto_ptr<G4DNAChemistryManager> G4DNAChemistryManager::fInstance ;
G4ThreadLocal std::ofstream*  G4DNAChemistryManager::fOutput = 0;
G4Mutex chemManExistence;

G4DNAChemistryManager::G4DNAChemistryManager() :
        fActiveChemistry(false)
{
    fExcitationLevel = 0;
    fIonisationLevel = 0;
    fWriteFile       = false;
}

G4DNAChemistryManager* G4DNAChemistryManager::Instance()
{
    if (fInstance.get() == 0)
    {
        G4AutoLock lock(&chemManExistence);
        if(fInstance.get() == 0) // MT : double check at initialisation
        {
            fInstance = auto_ptr<G4DNAChemistryManager> (new G4DNAChemistryManager()) ;
        }
        lock.unlock();
    }
    return fInstance.get();
}

G4DNAChemistryManager::~G4DNAChemistryManager()
{
    if(fIonisationLevel) delete fIonisationLevel;
    if(fExcitationLevel) delete fExcitationLevel;
    G4DNAMolecularReactionTable::DeleteInstance();
    G4MoleculeHandleManager::DeleteInstance();
    G4MolecularConfiguration::DeleteManager();
    fInstance.release();
    G4MoleculeCounter::DeleteInstance();
}

void G4DNAChemistryManager::DeleteInstance()
{
    G4AutoLock lock(&chemManExistence);
    if(fInstance.get())
    {
        fInstance.reset();
    }
}

void G4DNAChemistryManager::InitializeFile()
{
    *fOutput << std::setprecision(6) << std::scientific;
    *fOutput << setw(11) << left << "#Parent ID"
            << setw(10) << "Molecule"
            << setw(14) << "Elec Modif"
            << setw(13) << "Energy (eV)"
            << setw(22) << "X pos of parent [nm]"
            << setw(22) << "Y pos of parent [nm]"
            << setw(22) << "Z pos of parent [nm]"
            << setw(14) << "X pos [nm]"
            << setw(14) << "Y pos [nm]"
            << setw(14) << "Z pos [nm]"
            << G4endl
            << setw(21) << "#"
            << setw(13) << "1)io/ex=0/1"
            << G4endl
            << setw(21) << "#"
            << setw(13) << "2)level=0...5"
            << G4endl;
}

void G4DNAChemistryManager::WriteInto(const G4String& output,
        ios_base::openmode mode)
{
    fOutput =  new std::ofstream();
    fOutput->open(output.data(), mode);
    fWriteFile = true;
}

void G4DNAChemistryManager::CloseFile()
{
    if (fOutput->is_open())
    {
        fOutput->close();
    }

    fWriteFile = false;
}

G4DNAWaterExcitationStructure* G4DNAChemistryManager::GetExcitationLevel()
{
    if(!fExcitationLevel)
    {
        fExcitationLevel = new G4DNAWaterExcitationStructure;
    }
    return fExcitationLevel;
}

G4DNAWaterIonisationStructure* G4DNAChemistryManager::GetIonisationLevel()
{
    if(!fIonisationLevel)
    {
        fIonisationLevel = new G4DNAWaterIonisationStructure;
    }
    return fIonisationLevel;
}

void G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modification,
        G4int electronicLevel,
        const G4Track* theIncomingTrack)
{
    if(fWriteFile)
    {
        G4double energy = -1.;

        switch (modification)
        {
        case eDissociativeAttachment:
            energy = -1;
            break;
        case eExcitedMolecule :
            energy = GetExcitationLevel()->ExcitationEnergy(electronicLevel);
            break;
        case eIonizedMolecule :
            energy = GetIonisationLevel()->IonisationEnergy(electronicLevel);
            break;
        }

        *fOutput << setw(11) << left << theIncomingTrack->GetTrackID()
                                                << setw(10) << "H2O"
                                                << left << modification
                                                << internal <<":"
                                                << right <<electronicLevel
                                                << left
                                                << setw(11) << ""
                                                << std::setprecision(2) << std::fixed
                                                << setw(13) << energy/eV
                                                << std::setprecision(6) << std::scientific
                                                << setw(22) << (theIncomingTrack->GetPosition().x())/nanometer
                                                << setw(22) << (theIncomingTrack->GetPosition().y())/nanometer
                                                << setw(22) << (theIncomingTrack->GetPosition().z())/nanometer
                                                << G4endl;
    }

    if(fActiveChemistry)
    {
        G4Molecule * H2O = new G4Molecule (G4H2O::Definition());

        switch (modification)
        {
        case eDissociativeAttachment:
            H2O -> AddElectron(5,1);
            break;
        case eExcitedMolecule :
            H2O -> ExciteMolecule(electronicLevel);
            break;
        case eIonizedMolecule :
            H2O -> IonizeMolecule(electronicLevel);
            break;
        }

        G4Track * H2OTrack = H2O->BuildTrack(1*picosecond,
                theIncomingTrack->GetPosition());

        H2OTrack -> SetParentID(theIncomingTrack->GetTrackID());
        H2OTrack -> SetTrackStatus(fStopButAlive);
        H2OTrack -> SetKineticEnergy(0.);

        G4ITTrackHolder::Instance()->PushTrack(H2OTrack);
    }
}

void G4DNAChemistryManager::CreateSolvatedElectron(const G4Track* theIncomingTrack,
        G4ThreeVector* finalPosition)
// finalPosition is a pointer because this argument is optional
{
    if(fWriteFile)
    {
        *fOutput << setw(11)<< theIncomingTrack->GetTrackID()
                                                << setw(10)<< "e_aq"
                                                << setw(14)<< -1
                                                << std::setprecision(2) << std::fixed
                                                << setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
                                                << std::setprecision(6) << std::scientific
                                                << setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
                                                << setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
                                                << setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer  ;

        if(finalPosition != 0)
        {
            *fOutput<< setw(14)<< (finalPosition->x())/nanometer
                    << setw(14)<< (finalPosition->y())/nanometer
                    << setw(14)<< (finalPosition->z())/nanometer ;
        }

        *fOutput << G4endl;
    }

    if(fActiveChemistry)
    {
        G4Molecule* e_aq = new G4Molecule(G4Electron_aq::Definition());
        G4Track * e_aqTrack(0);
        if(finalPosition)
        {
            e_aqTrack  = e_aq->BuildTrack(picosecond,*finalPosition);
        }
        else
        {
            e_aqTrack  = e_aq->BuildTrack(picosecond,theIncomingTrack->GetPosition());
        }
        e_aqTrack -> SetTrackStatus(fAlive);
        e_aqTrack -> SetParentID(theIncomingTrack->GetTrackID());
        G4ITTrackHolder::Instance()->PushTrack(e_aqTrack);
        G4ITManager<G4Molecule>::Instance()->Push(e_aqTrack);
    }
}


void G4DNAChemistryManager::PushMolecule(G4Molecule*& molecule, double time,
        const G4ThreeVector& position, int parentID)
{
    if(fWriteFile)
    {
        *fOutput << setw(11)<< parentID
                << setw(10)<< molecule->GetName()
                << setw(14)<< -1
                << std::setprecision(2) << std::fixed
                << setw(13)<< -1
                << std::setprecision(6) << std::scientific
                << setw(22)<< (position.x())/nanometer
                << setw(22)<< (position.y())/nanometer
                << setw(22)<< (position.z())/nanometer;
        *fOutput << G4endl;
    }

    if(fActiveChemistry)
    {
        G4Track* track = molecule->BuildTrack(time,position);
        track -> SetTrackStatus(fAlive);
        track -> SetParentID(parentID);
        G4ITTrackHolder::Instance()->PushTrack(track);
        G4ITManager<G4Molecule>::Instance()->Push(track);
    }
    else
    {
        delete molecule;
        molecule = 0;
    }
}

void G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecule,
        const G4Track* theIncomingTrack)
{
    if(fWriteFile)
    {
        *fOutput << setw(11)<< theIncomingTrack->GetTrackID()
                                                << setw(10)<< molecule->GetName()
                                                << setw(14)<< -1
                                                << std::setprecision(2) << std::fixed
                                                << setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
                                                << std::setprecision(6) << std::scientific
                                                << setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
                                                << setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
                                                << setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer  ;
        *fOutput << G4endl;
    }

    if(fActiveChemistry)
    {
        G4Track* track = molecule->BuildTrack(theIncomingTrack->GetGlobalTime(),theIncomingTrack->GetPosition());
        track -> SetTrackStatus(fAlive);
        track -> SetParentID(theIncomingTrack->GetTrackID());
        G4ITTrackHolder::Instance()->PushTrack(track);
        G4ITManager<G4Molecule>::Instance()->Push(track);
    }
    else
    {
        delete molecule;
        molecule = 0;
    }
}

void G4DNAChemistryManager::AddEmptyLineInOuputFile()
{
    if(fWriteFile)
    {
        *fOutput << G4endl;
    }
}