G4DNAChemistryManager.cc

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//
// $Id: G4DNAChemistryManager.cc 100802 2016-11-02 14:55:27Z 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 "G4Scheduler.hh"
#include "G4SystemOfUnits.hh"
#include "G4Molecule.hh"
#include "G4VITTrackHolder.hh"
#include "G4H2O.hh"
#include "G4DNAMolecularReactionTable.hh"
#include "G4DNAWaterExcitationStructure.hh"
#include "G4DNAWaterIonisationStructure.hh"
#include "G4Electron_aq.hh"
#include "G4MolecularConfiguration.hh"
#include "G4VMoleculeCounter.hh"
#include "G4VUserChemistryList.hh"
#include "G4AutoLock.hh"
#include "G4UIcmdWithABool.hh"
#include "G4UIcmdWithADoubleAndUnit.hh"
#include "G4UIcmdWithoutParameter.hh"
#include "G4GeometryManager.hh"
#include "G4StateManager.hh"
#include "G4MoleculeFinder.hh"
#include "G4MoleculeTable.hh"

using namespace std;

G4DNAChemistryManager* G4DNAChemistryManager::fgInstance;
G4ThreadLocal std::ofstream* G4DNAChemistryManager::fpgOutput_tl = 0;
G4ThreadLocal G4bool* G4DNAChemistryManager::fpgThreadInitialized_tl = 0;
G4Mutex chemManExistence;
//bool G4DNAChemistryManager::fActiveChemistry = false;

G4DNAChemistryManager::G4DNAChemistryManager() :
    G4UImessenger(), G4VStateDependent()
{
//==============================================================================
/* M.K: 24/11/2014
 * To work properly, the chemistry manager should be created and initialized on
 * the master thread only. If the static flag fActiveChemistry is on but the
 * chemistry manager singleton
 */
//==============================================================================

//  if (/*fActiveChemistry &&*/ G4Threading::IsWorkerThread()
//      && G4Threading::IsMultithreadedApplication())
//  {
//    G4Exception("G4DNAChemistryManager::G4DNAChemistryManager",
//                "G4DNAChemistryManager_MASTER_CREATION", FatalException,
//                "The chemistry manager should be created and initialized on the "
//                "master thread only");
//  }

  fpExcitationLevel = 0;
  fpIonisationLevel = 0;
  fWriteFile = false;
  fpUserChemistryList = 0;
  fMasterInitialized = false;
  fpChemDNADirectory = new G4UIdirectory("/chem/");
  fpActivateChem = new G4UIcmdWithABool("/chem/activate", this);
  fpRunChem = new G4UIcmdWithoutParameter("/chem/run", this);
  //fpGridSize = new G4UIcmdWithADoubleAndUnit("/chem/gridRes", this);
  fpScaleForNewTemperature = new G4UIcmdWithADoubleAndUnit("/chem/temperature",
                                                           this);
  fpSkipReactionsFromChemList =
      new G4UIcmdWithoutParameter("/chem/skipReactionsFromChemList", this);
  fpInitChem = new G4UIcmdWithoutParameter("/chem/init", this);
  //fDefaultGridResolution = -1;
  fBuildPhysicsTable = false;
  fGeometryClosed = false;
  fPhysicsTableBuilt = false;
  fForceThreadReinitialization = false;
  fFileInitialized = false;
  fVerbose = 0;
  fActiveChemistry = false;
  fSkipReactions = false;
  fResetCounterWhenRunEnds = true;
}

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

G4DNAChemistryManager*
G4DNAChemistryManager::GetInstanceIfExists()
{
  return fgInstance;
}

G4DNAChemistryManager::~G4DNAChemistryManager()
{
//  G4cout << "Deleting G4DNAChemistryManager" << G4endl;
  Clear();
  fgInstance = 0;
  /*
   * DEBUG : check that the chemistry manager has well been deregistered
   *  assert(G4StateManager::GetStateManager()->
   *  DeregisterDependent(this) == true);
   */
}

void G4DNAChemistryManager::Clear()
{
  if (fpIonisationLevel)
  {
    delete fpIonisationLevel;
    fpIonisationLevel = 0;

  }
  if (fpExcitationLevel)
  {
    delete fpExcitationLevel;
    fpExcitationLevel = 0;
  }
  if (fpUserChemistryList)
  {
    if(fpUserChemistryList->IsPhysicsConstructor() == false)
    {
      delete fpUserChemistryList;
    }
//    else
//    {
//   G4cout << "G4DNAChemistryManager will not delete the chemistry list "
//       "since it inherits from G4VPhysicsConstructor and it is then "
//       "expected to be the responsability to the G4VModularPhysics to handle"
//       " the chemistry list." << G4endl;
//    }
    fpUserChemistryList = 0;
  }
  if (fpChemDNADirectory)
  {
    delete fpChemDNADirectory;
    fpChemDNADirectory = 0;
  }
  if (fpActivateChem)
  {
    delete fpActivateChem;
    fpActivateChem = 0;
  }
  if(fpRunChem)
  {
    delete fpRunChem;
    fpRunChem = 0;
  }
  if(fpSkipReactionsFromChemList)
  {
    delete fpSkipReactionsFromChemList;
    fpSkipReactionsFromChemList = 0;
  }
  if(fpInitChem)
  {
    delete fpInitChem;
    fpInitChem = 0;
  }

  G4DNAMolecularReactionTable::DeleteInstance();
  //G4MoleculeHandleManager::DeleteInstance();
  G4MolecularConfiguration::DeleteManager();
  G4VMoleculeCounter::DeleteInstance();
}

void G4DNAChemistryManager::DeleteInstance()
{
  //G4cout << "G4DNAChemistryManager::DeleteInstance" << G4endl;

  G4AutoLock lock(&chemManExistence);

  if(fgInstance)
  {
    G4DNAChemistryManager* deleteMe = fgInstance;
    fgInstance = 0;
    lock.unlock();
    delete deleteMe;
  }
  else
  {
    G4cout << "G4DNAChemistryManager already deleted" << G4endl;
  }
  lock.unlock();
}

G4bool G4DNAChemistryManager::Notify(G4ApplicationState requestedState)
{
  if (requestedState == G4State_Quit)
  {
    if(fVerbose)
    G4cout << "G4DNAChemistryManager::Notify ---> received G4State_Quit"
           << G4endl;
    //DeleteInstance();
    Clear();
  }

  else if(requestedState == G4State_GeomClosed)
  {
    fGeometryClosed = true;
  }

  else if (requestedState == G4State_Idle)
  {
    G4MoleculeTable::Instance()->PrepareMolecularConfiguration();
  }

  return true;
}

void G4DNAChemistryManager::SetNewValue(G4UIcommand* command, G4String value)
{
  if (command == fpActivateChem)
  {
    Activated(G4UIcmdWithABool::GetNewBoolValue(value));
  }
  else if (command == fpRunChem)
  {
    Run();
  }
  /*
  else if(command == fpGridSize)
  {
    fDefaultGridResolution = fpGridSize->ConvertToDimensionedDouble(value);
  }*/
  else if (command == fpSkipReactionsFromChemList)
  {
    fSkipReactions = true;
  }
  else if(command == fpScaleForNewTemperature)
  {
    SetGlobalTemperature(fpScaleForNewTemperature->ConvertToDimensionedDouble(value));
  }
  else if(command == fpInitChem)
  {
    Initialize();
    InitializeThread();
  }
}

G4String G4DNAChemistryManager::GetCurrentValue(G4UIcommand* command)
{
  if (command == fpActivateChem)
  {
    return G4UIcmdWithABool::ConvertToString(fActiveChemistry);
  }

  return "";
}

void G4DNAChemistryManager::Run()
{
  if (fActiveChemistry)
  {
    InitializeThread();

    if (fMasterInitialized == false)
    {
      G4ExceptionDescription description;
      description << "Global components were not initialized.";
      G4Exception("G4DNAChemistryManager::Run", "MASTER_INIT", FatalException,
                  description);
    }

    if (fpgThreadInitialized_tl == 0)
    {
      G4ExceptionDescription description;
      description << "Thread local components were not initialized.";
      G4Exception("G4DNAChemistryManager::Run", "THREAD_INIT", FatalException,
                  description);
    }
    
    G4MoleculeTable::Instance()->Finalize();
    G4Scheduler::Instance()->Process();
    if(fResetCounterWhenRunEnds)
    {
      G4VMoleculeCounter::Instance()->ResetCounter();
    }
    CloseFile();
  }
}

void G4DNAChemistryManager::Gun(G4ITGun* gun, bool physicsTableToBuild)
{
  fBuildPhysicsTable = physicsTableToBuild;
  G4Scheduler::Instance()->SetGun(gun);
}

void G4DNAChemistryManager::Initialize()
{
  //===========================================================================
  // MT MODE
  //===========================================================================
  if(G4Threading::IsMultithreadedApplication())
  {
    //==========================================================================
    // ON WORKER THREAD
    //==========================================================================
    if(G4Threading::IsWorkerThread())
    {
      InitializeThread(); // Will create and initialize G4ITScheduler
      return;
    }
    //==========================================================================
    // ON MASTER THREAD
    //==========================================================================
    else
    {
      InitializeMaster();
      return;
    }
  }
  //===========================================================================
  // IS NOT IN MT MODE
  //===========================================================================
  else
  {
    InitializeMaster();
    // In this case: InitializeThread is called when Run() is called
    return;
  }

}

void G4DNAChemistryManager::InitializeMaster()
{
  if (fMasterInitialized == false)
  {
    if(fVerbose)
    {
     G4cout << "G4DNAChemistryManager::InitializeMaster() is called" << G4endl;
    }

    G4Scheduler::Instance(); 
    // creates a concrete object of the scheduler 
    // and track container

    if (fpUserChemistryList)
    {
      fpUserChemistryList->ConstructDissociationChannels();
      if(fSkipReactions == false)
      {
        fpUserChemistryList->ConstructReactionTable(
            G4DNAMolecularReactionTable::GetReactionTable());
      }
      else
      {
        G4DNAMolecularReactionTable::GetReactionTable(); // init pointer
      }
      fMasterInitialized = true;
    }
    else
    {
      if (fActiveChemistry)
      {
        G4ExceptionDescription description;
        description << "No user chemistry list has been provided.";
        G4Exception("G4DNAChemistryManager::InitializeMaster", "NO_CHEM_LIST",
                    FatalException, description);
      }
    }
  }
}

void G4DNAChemistryManager::InitializeThread()
{
  if (fpgThreadInitialized_tl == 0 || fForceThreadReinitialization == true)
  {
    if (fpUserChemistryList)
    {
      if(fVerbose)
      {
        G4cout << "G4DNAChemistryManager::InitializeThread() is called"
               << G4endl;
      }

      if (fBuildPhysicsTable && fPhysicsTableBuilt == false)
      {
        if(fVerbose)
        {
          G4cout << "G4DNAChemistryManager: Build the physics tables for "
              "molecules."
                 << G4endl;
        }

        fpUserChemistryList->BuildPhysicsTable();
        if (fGeometryClosed == false)
        {
          if(fVerbose)
          {
            G4cout << "G4DNAChemistryManager: Close geometry"
                   << G4endl;
          }

          G4GeometryManager* geomManager = G4GeometryManager::GetInstance();
          // G4cout << "Start closing geometry." << G4endl;
          geomManager->OpenGeometry();
          geomManager->CloseGeometry(true, true);
          fGeometryClosed = true;
        }

        fPhysicsTableBuilt = true;
      }
      fpUserChemistryList->ConstructTimeStepModel(
          G4DNAMolecularReactionTable::GetReactionTable());
      G4Scheduler::Instance()->Initialize();

      fpgThreadInitialized_tl = new G4bool(true);
    }
    else
    {
      G4ExceptionDescription description;
      description << "No user chemistry list has been provided.";
      G4Exception("G4DNAChemistryManager::InitializeThread", "NO_CHEM_LIST",
                  FatalException, description);
    }

    G4VMoleculeCounter::InitializeInstance();
  }

  InitializeFile();
}

void G4DNAChemistryManager::InitializeFile()
{
  if (fpgOutput_tl == 0 || fWriteFile == false || fFileInitialized)
  {
    return;
  }

  if(fVerbose)
  {
    G4cout << "G4DNAChemistryManager::InitializeFile() is called"
           << G4endl;
  }

  *fpgOutput_tl << std::setprecision(6) << std::scientific;
  *fpgOutput_tl << 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;

  fFileInitialized = true;
}

G4bool G4DNAChemistryManager::IsActivated()
{
  return Instance()->fActiveChemistry;
}

void G4DNAChemistryManager::Activated(G4bool flag)
{
  Instance()->fActiveChemistry = flag;
}

G4bool G4DNAChemistryManager::IsChemistryActivated()
{
  return fActiveChemistry;
}

void G4DNAChemistryManager::SetChemistryActivation(G4bool flag)
{
  fActiveChemistry = flag;
}

void G4DNAChemistryManager::WriteInto(const G4String& output,
                                      ios_base::openmode mode)
{
  if (fVerbose)
  {
    G4cout << "G4DNAChemistryManager: Write chemical stage into "
           << output.data() << G4endl;
  }

  fpgOutput_tl = new std::ofstream();
  fpgOutput_tl->open(output.data(), mode);
  fWriteFile = true;
  fFileInitialized = false;
}

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

void G4DNAChemistryManager::CloseFile()
{
  if (fpgOutput_tl == 0) return;

  if (fpgOutput_tl->is_open())
  {
    if (fVerbose)
    {
      G4cout << "G4DNAChemistryManager: Close File" << G4endl;
    }
    fpgOutput_tl->close();
  }
}

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

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

void G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modification,
                                                G4int electronicLevel,
                                                const G4Track* theIncomingTrack)
{
  if (fWriteFile)
  {
    if(!fFileInitialized) InitializeFile();

    G4double energy = -1.;

    switch (modification)
    {
      case eDissociativeAttachment:
        energy = 0;
        break;
      case eExcitedMolecule:
        energy = GetExcitationLevel()->ExcitationEnergy(electronicLevel);
        break;
      case eIonizedMolecule:
        energy = GetIonisationLevel()->IonisationEnergy(electronicLevel);
        break;
    }

    *fpgOutput_tl << 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(4-electronicLevel);
      break;
      case eIonizedMolecule :
      H2O -> IonizeMolecule(4-electronicLevel);
      break;
    }

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

    H2OTrack -> SetParentID(theIncomingTrack->GetTrackID());
    H2OTrack -> SetTrackStatus(fStopButAlive);
    H2OTrack -> SetKineticEnergy(0.);
    G4VITTrackHolder::Instance()->Push(H2OTrack);
  }
//  else
//  abort();
}

void G4DNAChemistryManager::CreateSolvatedElectron(const G4Track* theIncomingTrack,
                                                   G4ThreeVector* finalPosition)
// finalPosition is a pointer because this argument is optional
{
  if (fWriteFile)
  {
    if(!fFileInitialized) InitializeFile();

    *fpgOutput_tl << 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)
    {
      *fpgOutput_tl << setw(14) << (finalPosition->x()) / nanometer << setw(14)
                    << (finalPosition->y()) / nanometer << setw(14)
                    << (finalPosition->z()) / nanometer;
    }

    *fpgOutput_tl << 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());
    G4VITTrackHolder::Instance()->Push(e_aqTrack);
  }
}

void G4DNAChemistryManager::PushMolecule(G4Molecule*& molecule,
                                         double time,
                                         const G4ThreeVector& position,
                                         int parentID)
{
  if (fWriteFile)
  {
    if(!fFileInitialized) InitializeFile();

    *fpgOutput_tl << 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;
    *fpgOutput_tl << G4endl;
  }

  if(fActiveChemistry)
  {
    G4Track* track = molecule->BuildTrack(time,position);
    track -> SetTrackStatus(fAlive);
    track -> SetParentID(parentID);
    G4VITTrackHolder::Instance()->Push(track);
  }
  else
  {
    delete molecule;
    molecule = 0;
  }
}

void G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecule,
                                                             const G4Track* theIncomingTrack)
{
  if (fWriteFile)
  {
    if(!fFileInitialized) InitializeFile();

    *fpgOutput_tl << 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;
    *fpgOutput_tl << G4endl;
  }

  if(fActiveChemistry)
  {
    G4Track* track = molecule->BuildTrack(theIncomingTrack->GetGlobalTime(),
                                          theIncomingTrack->GetPosition());
    track -> SetTrackStatus(fAlive);
    track -> SetParentID(theIncomingTrack->GetTrackID());
    G4VITTrackHolder::Instance()->Push(track);
  }
  else
  {
    delete molecule;
    molecule = 0;
  }
}

void G4DNAChemistryManager::SetGlobalTemperature(double temp_K)
{
  G4MolecularConfiguration::SetGlobalTemperature(temp_K);
  G4DNAMolecularReactionTable::Instance()->ScaleReactionRateForNewTemperature(temp_K);
}