Gabriele Cosmo
430 lines
14 KiB
C++
430 lines
14 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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//
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#include "G4DNAScavengerMaterial.hh"
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#include "G4DNABoundingBox.hh"
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#include "G4DNAMolecularMaterial.hh"
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#include "G4MolecularConfiguration.hh"
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#include "G4PhysicalConstants.hh"
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#include "G4Scheduler.hh"
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#include "G4StateManager.hh"
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#include "G4SystemOfUnits.hh"
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#include "G4UnitsTable.hh"
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#include "G4VChemistryWorld.hh"
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#include <memory>
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using namespace std;
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//------------------------------------------------------------------------------
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G4DNAScavengerMaterial::G4DNAScavengerMaterial(G4VChemistryWorld* pChemistryInfo)
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: fpChemistryInfo(pChemistryInfo), fIsInitialized(false), fCounterAgainstTime(false), fVerbose(0)
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{
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Initialize();
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}
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//------------------------------------------------------------------------------
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void G4DNAScavengerMaterial::Initialize()
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{
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if (fIsInitialized) {
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return;
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}
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if (fpChemistryInfo->size() == 0) {
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G4cout << "G4DNAScavengerMaterial existed but empty" << G4endl;
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}
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Reset();
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fIsInitialized = true;
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}
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G4double
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G4DNAScavengerMaterial::GetNumberMoleculePerVolumeUnitForMaterialConf(MolType matConf) const
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{
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// no change these molecules
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if (fH2O == matConf) {
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G4ExceptionDescription exceptionDescription;
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exceptionDescription << "matConf : " << matConf->GetName();
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G4Exception("G4DNAScavengerMaterial::GetNumberMoleculePerVolumeUnitForMaterialConf",
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"G4DNAScavengerMaterial001", FatalErrorInArgument, exceptionDescription);
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}
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auto iter = fScavengerTable.find(matConf);
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if (iter == fScavengerTable.end()) {
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return 0;
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}
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if (iter->second >= 1) {
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return (floor)(iter->second);
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}
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return 0;
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}
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void G4DNAScavengerMaterial::ReduceNumberMoleculePerVolumeUnitForMaterialConf(MolType matConf,
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G4double time)
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{
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// no change these molecules
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if (fH2O == matConf || fH3Op == matConf || // suppose that pH is not changed during simu
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fHOm == matConf)
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{
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// G4cout<<"moletype : "<<matConf->GetName()<<G4endl;
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// kobs is already counted these molecule concentrations
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return;
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}
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if (!find(matConf)) // matConf must greater than 0
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{
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return;
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}
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fScavengerTable[matConf]--;
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if (fScavengerTable[matConf] < 0) // projection
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{
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assert(false);
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}
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if (fCounterAgainstTime) {
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RemoveAMoleculeAtTime(matConf, time);
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}
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}
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void G4DNAScavengerMaterial::AddNumberMoleculePerVolumeUnitForMaterialConf(MolType matConf,
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G4double time)
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{
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// no change these molecules
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if (fH2O == matConf || fH3Op == matConf || // pH has no change
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G4MoleculeTable::Instance()->GetConfiguration("OHm(B)") == matConf)
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{
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// G4cout<<"moletype : "<<matConf->GetName()<<G4endl;
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// kobs is already counted these molecule concentrations
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return;
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}
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auto it = fScavengerTable.find(matConf);
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if (it == fScavengerTable.end()) // matConf must be in fScavengerTable
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{
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return;
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}
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fScavengerTable[matConf]++;
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if (fCounterAgainstTime) {
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AddAMoleculeAtTime(matConf, time);
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}
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}
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void G4DNAScavengerMaterial::PrintInfo()
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{
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auto pConfinedBox = fpChemistryInfo->GetChemistryBoundary();
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auto iter = fpChemistryInfo->begin();
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G4cout << "**************************************************************" << G4endl;
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for (; iter != fpChemistryInfo->end(); iter++) {
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auto containedConf = iter->first;
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// auto concentration = iter->second;
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auto concentration = fScavengerTable[containedConf] / (Avogadro * pConfinedBox->Volume());
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G4cout << "Scavenger:" << containedConf->GetName() << " : "
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<< concentration / 1.0e-6 /*mm3 to L*/ << " (M) with : "
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<< fScavengerTable[containedConf] << " (molecules)"
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<< "in: " << pConfinedBox->Volume() / (um * um * um) << " (um3)" << G4endl;
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if (fScavengerTable[containedConf] < 1) {
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G4cout << "!!!!!!!!!!!!! this molecule has less one molecule for "
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"considered volume"
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<< G4endl;
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// assert(false);
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}
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if (fVerbose != 0) {
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Dump();
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}
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}
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G4cout << "**************************************************************" << G4endl;
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}
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void G4DNAScavengerMaterial::Reset()
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{
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if (fpChemistryInfo == nullptr) {
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return;
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}
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if (fpChemistryInfo->size() == 0) {
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return;
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}
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fScavengerTable.clear();
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fCounterMap.clear();
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fpLastSearch.reset(nullptr);
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auto pConfinedBox = fpChemistryInfo->GetChemistryBoundary();
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auto iter = fpChemistryInfo->begin();
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for (; iter != fpChemistryInfo->end(); iter++) {
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auto containedConf = iter->first;
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auto concentration = iter->second;
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fScavengerTable[containedConf] = floor(Avogadro * concentration * pConfinedBox->Volume());
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fCounterMap[containedConf][1 * picosecond] =
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floor(Avogadro * concentration * pConfinedBox->Volume());
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}
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if (fVerbose != 0) {
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PrintInfo();
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}
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}
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//------------------------------------------------------------------------------
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void G4DNAScavengerMaterial::AddAMoleculeAtTime(MolType molecule, G4double time,
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const G4ThreeVector* /*position*/, int number)
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{
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if (fVerbose != 0) {
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G4cout << "G4DNAScavengerMaterial::AddAMoleculeAtTime : " << molecule->GetName()
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<< " at time : " << G4BestUnit(time, "Time") << G4endl;
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}
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auto counterMap_i = fCounterMap.find(molecule);
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if (counterMap_i == fCounterMap.end()) {
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fCounterMap[molecule][time] = number;
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}
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else if (counterMap_i->second.empty()) {
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counterMap_i->second[time] = number;
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}
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else {
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auto end = counterMap_i->second.rbegin();
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if (end->first <= time
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|| fabs(end->first - time) <= G4::MoleculeCounter::TimePrecision::fPrecision) {
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G4double newValue = end->second + number;
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counterMap_i->second[time] = newValue;
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if (newValue != (floor)(fScavengerTable[molecule])) // protection
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{
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G4String errMsg = "You are trying to add wrong molecule ";
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G4Exception("AddAMoleculeAtTime", "", FatalErrorInArgument, errMsg);
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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 G4DNAScavengerMaterial::RemoveAMoleculeAtTime(MolType pMolecule, G4double time,
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const G4ThreeVector* /*position*/, int number)
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{
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NbMoleculeInTime& nbMolPerTime = fCounterMap[pMolecule];
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if (fVerbose != 0) {
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auto it_ = nbMolPerTime.rbegin();
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G4cout << "G4DNAScavengerMaterial::RemoveAMoleculeAtTime : " << pMolecule->GetName()
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<< " at time : " << G4BestUnit(time, "Time")
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<< " form : " << it_->second << G4endl;
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}
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if (nbMolPerTime.empty()) {
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Dump();
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G4String errMsg = "You are trying to remove molecule " +
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pMolecule->GetName() +
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" from the counter while this kind of molecules has not "
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"been registered yet";
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G4Exception("G4DNAScavengerMaterial::RemoveAMoleculeAtTime", "", FatalErrorInArgument, errMsg);
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return;
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}
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auto it = nbMolPerTime.rbegin();
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if (it == nbMolPerTime.rend()) {
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it--;
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G4String errMsg = "There was no " + pMolecule->GetName()
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+ " recorded at the time or even before the time asked";
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G4Exception("G4DNAScavengerMaterial::RemoveAMoleculeAtTime", "", FatalErrorInArgument, errMsg);
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}
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G4double finalN = it->second - number;
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if (finalN < 0) {
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Dump();
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G4cout << "fScavengerTable : " << pMolecule->GetName() << " : " << (fScavengerTable[pMolecule])
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<< G4endl;
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G4ExceptionDescription errMsg;
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errMsg << "After removal of " << number << " species of "
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<< " " << it->second << " " << pMolecule->GetName() << " the final number at time "
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<< G4BestUnit(time, "Time") << " is less than zero and so not valid." << G4endl;
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G4cout << " Global time is " << G4BestUnit(G4Scheduler::Instance()->GetGlobalTime(), "Time")
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<< ". Previous selected time is " << G4BestUnit(it->first, "Time") << G4endl;
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G4Exception("G4DNAScavengerMaterial::RemoveAMoleculeAtTime", "N_INF_0", FatalException, errMsg);
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}
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nbMolPerTime[time] = finalN;
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if (finalN != (floor)(fScavengerTable[pMolecule])) // protection
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{
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assert(false);
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}
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}
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void G4DNAScavengerMaterial::Dump()
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{
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auto pConfinedBox = fpChemistryInfo->GetChemistryBoundary();
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auto V = pConfinedBox->Volume();
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for (const auto& it : fCounterMap) {
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auto pReactant = it.first;
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G4cout << " --- > For " << pReactant->GetName() << G4endl;
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for (const auto& it2 : it.second) {
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G4cout << " " << G4BestUnit(it2.first, "Time") << " "
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<< it2.second / (Avogadro * V * 1.0e-6 /*mm3 to L*/) << G4endl;
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}
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}
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}
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int64_t G4DNAScavengerMaterial::GetNMoleculesAtTime(MolType molecule, G4double time)
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{
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if (!fCounterAgainstTime) {
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G4cout << "fCounterAgainstTime == false" << G4endl;
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assert(false);
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}
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G4bool sameTypeOfMolecule = SearchTimeMap(molecule);
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auto output = SearchUpperBoundTime(time, sameTypeOfMolecule);
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if (output < 0) {
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G4ExceptionDescription errMsg;
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errMsg << "N molecules not valid < 0 : " << molecule->GetName() << " N : " << output << G4endl;
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G4Exception("G4DNAScavengerMaterial::GetNMoleculesAtTime", "", FatalErrorInArgument, errMsg);
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}
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return output;
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}
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G4bool G4DNAScavengerMaterial::SearchTimeMap(MolType molecule)
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{
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if (fpLastSearch == nullptr) {
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fpLastSearch = std::make_unique<Search>();
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}
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else {
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if (fpLastSearch->fLowerBoundSet && fpLastSearch->fLastMoleculeSearched->first == molecule) {
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return true;
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}
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}
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auto mol_it = fCounterMap.find(molecule);
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fpLastSearch->fLastMoleculeSearched = mol_it;
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if (mol_it != fCounterMap.end()) {
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fpLastSearch->fLowerBoundTime = fpLastSearch->fLastMoleculeSearched->second.end();
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fpLastSearch->fLowerBoundSet = true;
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}
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else {
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fpLastSearch->fLowerBoundSet = false;
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}
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return false;
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}
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//------------------------------------------------------------------------------
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int64_t G4DNAScavengerMaterial::SearchUpperBoundTime(G4double time, G4bool sameTypeOfMolecule)
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{
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auto mol_it = fpLastSearch->fLastMoleculeSearched;
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if (mol_it == fCounterMap.end()) {
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return 0;
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}
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NbMoleculeInTime& timeMap = mol_it->second;
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if (timeMap.empty()) {
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return 0;
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}
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if (sameTypeOfMolecule) {
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if (fpLastSearch->fLowerBoundSet && fpLastSearch->fLowerBoundTime != timeMap.end()) {
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if (fpLastSearch->fLowerBoundTime->first < time) {
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auto upperToLast = fpLastSearch->fLowerBoundTime;
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upperToLast++;
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if (upperToLast == timeMap.end()) {
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return fpLastSearch->fLowerBoundTime->second;
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}
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if (upperToLast->first > time) {
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return fpLastSearch->fLowerBoundTime->second;
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}
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}
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}
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}
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auto up_time_it = timeMap.upper_bound(time);
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if (up_time_it == timeMap.end()) {
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auto last_time = timeMap.rbegin();
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return last_time->second;
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}
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if (up_time_it == timeMap.begin()) {
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return 0;
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}
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up_time_it--;
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fpLastSearch->fLowerBoundTime = up_time_it;
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fpLastSearch->fLowerBoundSet = true;
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return fpLastSearch->fLowerBoundTime->second;
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}
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void G4DNAScavengerMaterial::WaterEquilibrium()
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{
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auto convertFactor = Avogadro * fpChemistryInfo->GetChemistryBoundary()->Volume() / liter;
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G4double kw = 1.01e-14;
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fScavengerTable[fHOm] = (kw / ((G4double)fScavengerTable[fH3Op] / convertFactor)) * convertFactor;
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G4cout << "pH : " << GetpH() << G4endl;
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return;
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}
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void G4DNAScavengerMaterial::SetpH(const G4int& ph)
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{
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auto volume = fpChemistryInfo->GetChemistryBoundary()->Volume();
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fScavengerTable[fH3Op] = floor(Avogadro * std::pow(10, -ph) * volume / liter);
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fScavengerTable[fHOm] = floor(Avogadro * std::pow(10, -(14 - ph)) * volume / liter);
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}
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G4double G4DNAScavengerMaterial::GetpH()
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{
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G4double volumeInLiter = fpChemistryInfo->GetChemistryBoundary()->Volume() / liter;
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G4double Cion = (G4double)fScavengerTable[fH3Op] / (Avogadro * volumeInLiter);
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G4double pH = std::log10(Cion);
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// G4cout<<"OH- : "<<fScavengerTable[fHOm]<<" H3O+ : "<<fScavengerTable[fH3Op]<<" pH :
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// "<<-pH<<G4endl;
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if (fScavengerTable[fH3Op] < 0) // protect me
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{
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G4Exception("G4DNAScavengerMaterial::GetpH()", "G4DNAScavengerMaterial001", JustWarning,
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"H3O+ < 0");
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fScavengerTable[fH3Op] = 0;
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}
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if (fScavengerTable[fHOm] < 0) // protect me
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{
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G4Exception("G4DNAScavengerMaterial::GetpH()", "G4DNAScavengerMaterial001", JustWarning,
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"HO- < 0");
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fScavengerTable[fHOm] = 0;
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}
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return -pH;
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} |