Gabriele Cosmo
770 lines
21 KiB
C++
770 lines
21 KiB
C++
//
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// ********************************************************************
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// * License and Disclaimer *
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// * *
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// * The Geant4 software is copyright of the Copyright Holders of *
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// * the Geant4 Collaboration. It is provided under the terms and *
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// * conditions of the Geant4 Software License, included in the file *
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// * LICENSE and available at http://cern.ch/geant4/license . These *
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// * include a list of copyright holders. *
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// * *
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// * Neither the authors of this software system, nor their employing *
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// * institutes,nor the agencies providing financial support for this *
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// * work make any representation or warranty, express or implied, *
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// * regarding this software system or assume any liability for its *
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// * use. Please see the license in the file LICENSE and URL above *
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// * for the full disclaimer and the limitation of liability. *
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// * *
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// * This code implementation is the result of the scientific and *
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// * technical work of the GEANT4 collaboration. *
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// * By using, copying, modifying or distributing the software (or *
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// * any work based on the software) you agree to acknowledge its *
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// * use in resulting scientific publications, and indicate your *
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// * acceptance of all terms of the Geant4 Software license. *
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// ********************************************************************
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//
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// $Id: G4DNAChemistryManager.cc 103042 2017-03-10 11:50:07Z gcosmo $
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//
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// Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
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//
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// WARNING : This class is released as a prototype.
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// It might strongly evolve or even disapear in the next releases.
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//
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// History:
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// -----------
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// 10 Oct 2011 M.Karamitros created
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//
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// -------------------------------------------------------------------
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#include "G4DNAChemistryManager.hh"
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#include "G4Scheduler.hh"
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#include "G4SystemOfUnits.hh"
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#include "G4Molecule.hh"
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#include "G4VITTrackHolder.hh"
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#include "G4H2O.hh"
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#include "G4DNAMolecularReactionTable.hh"
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#include "G4DNAWaterExcitationStructure.hh"
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#include "G4DNAWaterIonisationStructure.hh"
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#include "G4Electron_aq.hh"
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#include "G4MolecularConfiguration.hh"
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#include "G4VMoleculeCounter.hh"
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#include "G4VUserChemistryList.hh"
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#include "G4AutoLock.hh"
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#include "G4UIcmdWithABool.hh"
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#include "G4UIcmdWithADoubleAndUnit.hh"
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#include "G4UIcmdWithoutParameter.hh"
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#include "G4GeometryManager.hh"
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#include "G4StateManager.hh"
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#include "G4MoleculeFinder.hh"
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#include "G4MoleculeTable.hh"
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#include "G4PhysChemIO.hh"
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using namespace std;
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G4DNAChemistryManager* G4DNAChemistryManager::fgInstance;
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G4ThreadLocal G4DNAChemistryManager::ThreadLocalData*
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G4DNAChemistryManager::fpThreadData = 0;
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G4Mutex chemManExistence;
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//------------------------------------------------------------------------------
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G4DNAChemistryManager::ThreadLocalData::ThreadLocalData()
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{
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fpPhysChemIO = nullptr;
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fThreadInitialized_tl = false;
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}
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//------------------------------------------------------------------------------
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G4DNAChemistryManager::ThreadLocalData::~ThreadLocalData()
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{
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if(fpPhysChemIO) delete fpPhysChemIO;
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fThreadInitialized_tl = false;
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::SetPhysChemIO(G4VPhysChemIO* physChemIO)
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{
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if(fpThreadData->fpPhysChemIO)
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delete fpThreadData->fpPhysChemIO;
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fpThreadData->fpPhysChemIO = physChemIO;
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}
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//------------------------------------------------------------------------------
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G4DNAChemistryManager::G4DNAChemistryManager() :
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G4UImessenger(), G4VStateDependent()
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{
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//------------------------------------------------------------------------------
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/*
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* The chemistry manager is shared between threads
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* It is initialized both on the master thread and on the worker threads
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*/
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//------------------------------------------------------------------------------
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fpExcitationLevel = 0;
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fpIonisationLevel = 0;
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fpUserChemistryList = 0;
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fMasterInitialized = false;
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fpChemDNADirectory = new G4UIdirectory("/chem/");
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fpActivateChem = new G4UIcmdWithABool("/chem/activate", this);
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fpRunChem = new G4UIcmdWithoutParameter("/chem/run", this);
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//fpGridSize = new G4UIcmdWithADoubleAndUnit("/chem/gridRes", this);
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fpScaleForNewTemperature = new G4UIcmdWithADoubleAndUnit("/chem/temperature",
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this);
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fpSkipReactionsFromChemList =
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new G4UIcmdWithoutParameter("/chem/skipReactionsFromChemList", this);
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fpInitChem = new G4UIcmdWithoutParameter("/chem/init", this);
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//fDefaultGridResolution = -1;
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fBuildPhysicsTable = false;
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fGeometryClosed = false;
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fPhysicsTableBuilt = false;
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fForceThreadReinitialization = false;
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fVerbose = 0;
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fActiveChemistry = false;
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fSkipReactions = false;
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fResetCounterWhenRunEnds = true;
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}
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//------------------------------------------------------------------------------
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G4DNAChemistryManager*
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G4DNAChemistryManager::Instance()
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{
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if(fgInstance == 0)
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{
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G4AutoLock lock(&chemManExistence);
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if (fgInstance == 0) // MT : double check at initialisation
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{
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fgInstance = new G4DNAChemistryManager();
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}
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lock.unlock();
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}
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if(fpThreadData==0) fpThreadData = new ThreadLocalData();
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// make sure thread local data is initialized for all threads
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return fgInstance;
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}
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//------------------------------------------------------------------------------
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G4DNAChemistryManager*
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G4DNAChemistryManager::GetInstanceIfExists()
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{
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return fgInstance;
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}
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//------------------------------------------------------------------------------
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G4DNAChemistryManager::~G4DNAChemistryManager()
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{
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// G4cout << "Deleting G4DNAChemistryManager" << G4endl;
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Clear();
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fgInstance = 0;
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/*
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* DEBUG : check that the chemistry manager has well been deregistered
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* assert(G4StateManager::GetStateManager()->
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* DeregisterDependent(this) == true);
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*/
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::Clear()
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{
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if (fpIonisationLevel)
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{
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delete fpIonisationLevel;
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fpIonisationLevel = 0;
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}
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if (fpExcitationLevel)
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{
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delete fpExcitationLevel;
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fpExcitationLevel = 0;
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}
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if (fpUserChemistryList)
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{
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if(fpUserChemistryList->IsPhysicsConstructor() == false)
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{
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delete fpUserChemistryList;
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}
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// else
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// {
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// G4cout << "G4DNAChemistryManager will not delete the chemistry list "
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// "since it inherits from G4VPhysicsConstructor and it is then "
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// "expected to be the responsability to the G4VModularPhysics to handle"
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// " the chemistry list." << G4endl;
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// }
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fpUserChemistryList = 0;
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}
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if (fpChemDNADirectory)
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{
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delete fpChemDNADirectory;
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fpChemDNADirectory = 0;
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}
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if (fpActivateChem)
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{
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delete fpActivateChem;
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fpActivateChem = 0;
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}
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if(fpRunChem)
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{
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delete fpRunChem;
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fpRunChem = 0;
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}
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if(fpSkipReactionsFromChemList)
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{
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delete fpSkipReactionsFromChemList;
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fpSkipReactionsFromChemList = 0;
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}
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if(fpInitChem)
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{
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delete fpInitChem;
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fpInitChem = 0;
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}
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G4DNAMolecularReactionTable::DeleteInstance();
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//G4MoleculeHandleManager::DeleteInstance();
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G4MolecularConfiguration::DeleteManager();
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G4VMoleculeCounter::DeleteInstance();
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::DeleteInstance()
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{
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//G4cout << "G4DNAChemistryManager::DeleteInstance" << G4endl;
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G4AutoLock lock(&chemManExistence);
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if(fgInstance)
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{
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G4DNAChemistryManager* deleteMe = fgInstance;
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fgInstance = 0;
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lock.unlock();
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delete deleteMe;
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}
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else
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{
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G4cout << "G4DNAChemistryManager already deleted" << G4endl;
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}
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lock.unlock();
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}
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//------------------------------------------------------------------------------
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G4bool G4DNAChemistryManager::Notify(G4ApplicationState requestedState)
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{
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if (requestedState == G4State_Quit)
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{
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if(fVerbose)
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G4cout << "G4DNAChemistryManager::Notify ---> received G4State_Quit"
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<< G4endl;
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//DeleteInstance();
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Clear();
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}
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// else if(requestedState == G4State_EventProc)
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// Note: From here we can know that a new event is started
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// But the run and event IDs remain unknown
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// {
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// if(fpThreadData->fpPhysChemIO)
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// {
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//
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// }
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// }
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else if(requestedState == G4State_GeomClosed)
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{
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fGeometryClosed = true;
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}
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else if (requestedState == G4State_Idle)
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{
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G4MoleculeTable::Instance()->PrepareMolecularConfiguration();
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}
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return true;
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::SetNewValue(G4UIcommand* command, G4String value)
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{
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if (command == fpActivateChem)
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{
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Activated(G4UIcmdWithABool::GetNewBoolValue(value));
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}
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else if (command == fpRunChem)
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{
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Run();
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}
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/*
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else if(command == fpGridSize)
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{
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fDefaultGridResolution = fpGridSize->ConvertToDimensionedDouble(value);
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}*/
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else if (command == fpSkipReactionsFromChemList)
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{
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fSkipReactions = true;
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}
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else if(command == fpScaleForNewTemperature)
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{
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SetGlobalTemperature(fpScaleForNewTemperature->
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ConvertToDimensionedDouble(value));
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}
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else if(command == fpInitChem)
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{
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Initialize();
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InitializeThread();
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}
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}
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//------------------------------------------------------------------------------
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G4String G4DNAChemistryManager::GetCurrentValue(G4UIcommand* command)
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{
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if (command == fpActivateChem)
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{
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return G4UIcmdWithABool::ConvertToString(fActiveChemistry);
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}
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return "";
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::Run()
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{
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if (fActiveChemistry)
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{
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InitializeThread();
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if (fMasterInitialized == false)
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{
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G4ExceptionDescription description;
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description << "Global components were not initialized.";
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G4Exception("G4DNAChemistryManager::Run", "MASTER_INIT", FatalException,
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description);
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}
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if (fpThreadData->fThreadInitialized_tl == 0)
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{
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G4ExceptionDescription description;
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description << "Thread local components were not initialized.";
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G4Exception("G4DNAChemistryManager::Run", "THREAD_INIT", FatalException,
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description);
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}
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G4MoleculeTable::Instance()->Finalize();
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G4Scheduler::Instance()->Process();
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if(fResetCounterWhenRunEnds)
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{
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G4VMoleculeCounter::Instance()->ResetCounter();
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}
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CloseFile();
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}
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::Gun(G4ITGun* gun, bool physicsTableToBuild)
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{
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fBuildPhysicsTable = physicsTableToBuild;
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G4Scheduler::Instance()->SetGun(gun);
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::Initialize()
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{
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//===========================================================================
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// MT MODE
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//===========================================================================
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if(G4Threading::IsMultithreadedApplication())
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{
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//==========================================================================
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// ON WORKER THREAD
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//==========================================================================
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if(G4Threading::IsWorkerThread())
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{
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InitializeThread(); // Will create and initialize G4Scheduler
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return;
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}
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//==========================================================================
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// ON MASTER THREAD
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//==========================================================================
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else
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{
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InitializeMaster();
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return;
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}
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}
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//===========================================================================
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// IS NOT IN MT MODE
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//===========================================================================
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else
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{
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InitializeMaster();
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// In this case: InitializeThread is called when Run() is called
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return;
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}
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::InitializeMaster()
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{
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if (fMasterInitialized == false)
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{
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if(fVerbose)
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{
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G4cout << "G4DNAChemistryManager::InitializeMaster() is called" << G4endl;
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}
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G4Scheduler::Instance();
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// creates a concrete object of the scheduler
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if (fpUserChemistryList)
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{
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fpUserChemistryList->ConstructDissociationChannels();
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if(fSkipReactions == false)
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{
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fpUserChemistryList->ConstructReactionTable(
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G4DNAMolecularReactionTable::GetReactionTable());
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}
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else
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{
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G4DNAMolecularReactionTable::GetReactionTable(); // init pointer
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}
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fMasterInitialized = true;
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}
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else
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{
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if (fActiveChemistry)
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{
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G4ExceptionDescription description;
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description << "No user chemistry list has been provided.";
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G4Exception("G4DNAChemistryManager::InitializeMaster", "NO_CHEM_LIST",
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FatalException, description);
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}
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}
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}
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::InitializeThread()
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{
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if (fpThreadData->fThreadInitialized_tl == false
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|| fForceThreadReinitialization == true)
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{
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if (fpUserChemistryList)
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{
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if(fVerbose)
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{
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G4cout << "G4DNAChemistryManager::InitializeThread() is called"
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<< G4endl;
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}
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if (fBuildPhysicsTable && fPhysicsTableBuilt == false)
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{
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if(fVerbose)
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{
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G4cout << "G4DNAChemistryManager: Build the physics tables for "
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"molecules."
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<< G4endl;
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}
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fpUserChemistryList->BuildPhysicsTable();
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if (fGeometryClosed == false)
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{
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if(fVerbose)
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{
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G4cout << "G4DNAChemistryManager: Close geometry"
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<< G4endl;
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}
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G4GeometryManager* geomManager = G4GeometryManager::GetInstance();
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// G4cout << "Start closing geometry." << G4endl;
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geomManager->OpenGeometry();
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geomManager->CloseGeometry(true, true);
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fGeometryClosed = true;
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}
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fPhysicsTableBuilt = true;
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}
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fpUserChemistryList->ConstructTimeStepModel(
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G4DNAMolecularReactionTable::GetReactionTable());
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G4Scheduler::Instance()->Initialize();
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fpThreadData->fThreadInitialized_tl = true;
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}
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else
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{
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G4ExceptionDescription description;
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description << "No user chemistry list has been provided.";
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G4Exception("G4DNAChemistryManager::InitializeThread", "NO_CHEM_LIST",
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FatalException, description);
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}
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G4VMoleculeCounter::InitializeInstance();
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}
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InitializeFile();
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::InitializeFile()
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{
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if(fVerbose)
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{
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G4cout << "G4DNAChemistryManager::InitializeFile() is called"
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<< G4endl;
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}
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if(fpThreadData->fpPhysChemIO){
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fpThreadData->fpPhysChemIO->InitializeFile();
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}
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}
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//------------------------------------------------------------------------------
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G4bool G4DNAChemistryManager::IsActivated()
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{
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return Instance()->fActiveChemistry;
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::Activated(G4bool flag)
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{
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Instance()->fActiveChemistry = flag;
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}
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//------------------------------------------------------------------------------
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G4bool G4DNAChemistryManager::IsChemistryActivated()
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{
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return fActiveChemistry;
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::SetChemistryActivation(G4bool flag)
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{
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fActiveChemistry = flag;
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::WriteInto(const G4String& output,
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ios_base::openmode mode)
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{
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if (fVerbose)
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{
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G4cout << "G4DNAChemistryManager: Write chemical stage into "
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<< output.data() << G4endl;
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}
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if(fpThreadData->fpPhysChemIO){
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fpThreadData->fpPhysChemIO->WriteInto(output, mode);
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}
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else{
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fpThreadData->fpPhysChemIO = new G4PhysChemIO::FormattedText();
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fpThreadData->fpPhysChemIO->WriteInto(output, mode);
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}
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::AddEmptyLineInOuputFile()
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{
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if(fpThreadData->fpPhysChemIO){
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fpThreadData->fpPhysChemIO->AddEmptyLineInOuputFile();
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}
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}
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//------------------------------------------------------------------------------
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void G4DNAChemistryManager::CloseFile()
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|
{
|
|
if(fpThreadData->fpPhysChemIO){
|
|
fpThreadData->fpPhysChemIO->CloseFile();
|
|
}
|
|
}
|
|
|
|
//------------------------------------------------------------------------------
|
|
|
|
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(fpThreadData->fpPhysChemIO){
|
|
G4double energy = -1.;
|
|
|
|
switch (modification)
|
|
{
|
|
case eDissociativeAttachment:
|
|
energy = 0;
|
|
break;
|
|
case eExcitedMolecule:
|
|
energy = GetExcitationLevel()->ExcitationEnergy(electronicLevel);
|
|
break;
|
|
case eIonizedMolecule:
|
|
energy = GetIonisationLevel()->IonisationEnergy(electronicLevel);
|
|
break;
|
|
}
|
|
|
|
fpThreadData->fpPhysChemIO->CreateWaterMolecule(modification,
|
|
4-electronicLevel,
|
|
energy,
|
|
theIncomingTrack);
|
|
}
|
|
|
|
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);
|
|
}
|
|
}
|
|
|
|
//------------------------------------------------------------------------------
|
|
|
|
void
|
|
G4DNAChemistryManager::CreateSolvatedElectron(const G4Track* theIncomingTrack,
|
|
G4ThreeVector* finalPosition)
|
|
// finalPosition is a pointer because this argument is optional
|
|
{
|
|
if(fpThreadData->fpPhysChemIO){
|
|
fpThreadData->fpPhysChemIO->CreateSolvatedElectron(theIncomingTrack,
|
|
finalPosition);
|
|
}
|
|
|
|
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)
|
|
{
|
|
// TODO: PhysChemIO - method unused in the released code
|
|
|
|
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)
|
|
{
|
|
// TODO: PhysChemIO - method unused in the released code
|
|
|
|
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(G4double temp_K)
|
|
{
|
|
G4MolecularConfiguration::SetGlobalTemperature(temp_K);
|
|
G4DNAMolecularReactionTable::Instance()->
|
|
ScaleReactionRateForNewTemperature(temp_K);
|
|
}
|
|
|