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This commit is contained in:
Gabriele Cosmo
2022-07-01 10:44:02 +02:00
parent b3bf75a2a1
commit c07cea1fe0
2172 changed files with 183300 additions and 123938 deletions
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source/processes/electromagnetic/dna/molecules/management/include/G4MolecularConfiguration.hh
+8 -1
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@@ -293,6 +293,9 @@ public:
inline void Finalize();
static void FinalizeAll();
static void PrintAll(); //hoang added
inline void UnFinalize();
void SetUserID(const G4String& userID);//hoang moved it to public
inline const G4String& GetUserID() const;
@@ -331,7 +334,6 @@ protected:
void CheckElectronOccupancy(const char* line) const;
void MakeExceptionIfFinalized();
void SetUserID(const G4String& userID);
void CreateDefaultDiffCoeffParam();
static void ScaleAllDiffusionCoefficientsOnWater(double temperature_K);
@@ -591,4 +593,9 @@ G4MolecularConfiguration::GetDiffusionCoefficient(const G4Material* material,
return fDiffParam(material, temperature, this);
}
inline void G4MolecularConfiguration::UnFinalize()
{
fIsFinalized = false;
}
#endif
source/processes/electromagnetic/dna/molecules/management/include/G4MoleculeTable.hh
+5
View File
@@ -49,8 +49,11 @@
#include "G4MoleculeIterator.hh"
#include "G4ElectronOccupancy.hh"
#include <memory>
class G4MoleculeDefinition;
class G4MolecularConfiguration;
class G4MoleculeTableMessenger;
typedef G4MoleculeIterator<G4MoleculeDefinition> G4MoleculeDefinitionIterator;
typedef G4MoleculeIterator<G4MolecularConfiguration> G4ConfigurationIterator;
@@ -131,6 +134,8 @@ protected:
typedef std::map<G4String, G4MoleculeDefinition*> MoleculeDefTable;
MoleculeDefTable fMoleculeDefTable;
std::unique_ptr<G4MoleculeTableMessenger> fMoleculeDefTableMessenger;
};
#endif /* G4MOLECULETABLE_HH_ */
source/processes/electromagnetic/dna/molecules/management/include/G4MoleculeTableMessenger.hh
+55
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@@ -0,0 +1,55 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
#ifndef _G4MOLECULETABLEMESSENGER_HH
#define _G4MOLECULETABLEMESSENGER_HH
#include <G4UImessenger.hh>
#include <memory>
class G4UIcmdWithAString;
class G4DNAMolecularReactionTable;
class G4UIcmdWithoutParameter;
class G4UIcmdWithADoubleAndUnit;
class G4UIcmdWithAnInteger;
class G4UIcmdWithABool;
class G4MoleculeTableMessenger : public G4UImessenger
{
public:
G4MoleculeTableMessenger();
~G4MoleculeTableMessenger() override;
void SetNewValue(G4UIcommand * command,G4String newValue) override;
protected:
std::unique_ptr<G4UIcmdWithoutParameter> fpPrintTable;
std::unique_ptr<G4UIcmdWithAString> fpSpecies;
};
#endif // GEANT4_G4MOLECULETABLEMESSENGER_HH
source/processes/electromagnetic/dna/molecules/management/include/G4VMoleculeCounter.hh
+3 -3
View File
@@ -44,7 +44,7 @@ class G4VMoleculeCounter
{
protected:
static G4ThreadLocal G4VMoleculeCounter* fpInstance;
static G4bool fUse;
G4bool fUse = false;
G4VMoleculeCounter() = default;
@@ -70,9 +70,9 @@ public:
* at every creation/deletion of a molecule to
* to increase/decrease the number at a given time.
*/
static void Use(G4bool flag = true);
void Use(G4bool flag = true);
static G4bool InUse();
G4bool InUse();
//----------------------------------------------------
source/processes/electromagnetic/dna/molecules/management/sources.cmake
+3 -1
View File
@@ -17,6 +17,7 @@ geant4_add_module(G4emdna-molman
G4Serialize.hh
G4VMolecularDissociationDisplacer.hh
G4VMoleculeCounter.hh
G4MoleculeTableMessenger.hh
SOURCES
G4MolecularConfiguration.cc
G4MolecularDissociationChannel.cc
@@ -28,7 +29,8 @@ geant4_add_module(G4emdna-molman
G4MoleculeTable.cc
G4Serialize.cc
G4VMolecularDissociationDisplacer.cc
G4VMoleculeCounter.cc)
G4VMoleculeCounter.cc
G4MoleculeTableMessenger.cc)
geant4_module_link_libraries(G4emdna-molman
PUBLIC
source/processes/electromagnetic/dna/molecules/management/src/G4MolecularConfiguration.cc
+20
View File
@@ -1553,3 +1553,23 @@ void G4MolecularConfiguration::FinalizeAll()
}
}
void G4MolecularConfiguration::PrintAll() //hoang added
{
const std::vector<G4MolecularConfiguration*>& species =
GetManager()->GetAllSpecies();
G4cout<<G4endl;
G4cout<<"Molecular Config"<<std::setw(25)<<" | Diffusion Coefficient (m2 / s) "<<std::setw(20)<<" | Radius (nm) "<<G4endl;
G4cout<<"__________________________________________"
"___________________________________"<<G4endl;
for(size_t i = 0; i < species.size() ; ++i)
{
G4cout<<species[i]->GetName()
<<std::setw(30 - species[i]->GetName().length())
<<right<<species[i]->GetDiffusionCoefficient() * 1.0e3<<std::setw(30)
<<species[i]->GetVanDerVaalsRadius()/CLHEP::nm<<G4endl;
G4cout<<"__________________________________________"
"___________________________________"<<G4endl;
}
}
source/processes/electromagnetic/dna/molecules/management/src/G4Molecule.cc
+1 -3
View File
@@ -56,8 +56,6 @@
using namespace std;
ITImp(G4Molecule)
G4Allocator<G4Molecule>*& aMoleculeAllocator()
{
G4ThreadLocalStatic G4Allocator<G4Molecule>* _instance = nullptr;
@@ -396,7 +394,7 @@ G4Track* G4Molecule::BuildTrack(G4double globalTime,
fpMolecularConfiguration->GetDefinition(), MomentumDirection,
KineticEnergy);
if (G4VMoleculeCounter::InUse())
if (G4VMoleculeCounter::Instance()->InUse())
{
G4VMoleculeCounter::Instance()->
AddAMoleculeAtTime(fpMolecularConfiguration,
source/processes/electromagnetic/dna/molecules/management/src/G4MoleculeTable.cc
+2
View File
@@ -33,12 +33,14 @@
#include "G4MoleculeTable.hh"
#include "G4MolecularConfiguration.hh"
#include "G4MoleculeDefinition.hh"
#include "G4MoleculeTableMessenger.hh"
G4MoleculeTable* G4MoleculeTable::fpgMoleculeTable(0);
//------------------------------------------------------------------------------
G4MoleculeTable::G4MoleculeTable()
: fMoleculeDefTableMessenger(new G4MoleculeTableMessenger())
{
}
source/processes/electromagnetic/dna/molecules/management/src/G4MoleculeTableMessenger.cc
+163
View File
@@ -0,0 +1,163 @@
//
// ********************************************************************
// * License and Disclaimer *
// * *
// * The Geant4 software is copyright of the Copyright Holders of *
// * the Geant4 Collaboration. It is provided under the terms and *
// * conditions of the Geant4 Software License, included in the file *
// * LICENSE and available at http://cern.ch/geant4/license . These *
// * include a list of copyright holders. *
// * *
// * Neither the authors of this software system, nor their employing *
// * institutes,nor the agencies providing financial support for this *
// * work make any representation or warranty, express or implied, *
// * regarding this software system or assume any liability for its *
// * use. Please see the license in the file LICENSE and URL above *
// * for the full disclaimer and the limitation of liability. *
// * *
// * This code implementation is the result of the scientific and *
// * technical work of the GEANT4 collaboration. *
// * By using, copying, modifying or distributing the software (or *
// * any work based on the software) you agree to acknowledge its *
// * use in resulting scientific publications, and indicate your *
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
#include "G4MoleculeTableMessenger.hh"
#include "G4UIcmdWithAString.hh"
#include <G4SystemOfUnits.hh>
#include <G4UIcmdWithoutParameter.hh>
#include "G4MoleculeTable.hh"
#include "G4MoleculeDefinition.hh"
#include "G4MolecularConfiguration.hh"
#include "G4ParticleTable.hh"
//------------------------------------------------------------------------------
G4MoleculeTableMessenger::G4MoleculeTableMessenger()
: G4UImessenger()
, fpPrintTable(new G4UIcmdWithoutParameter("/chem/PrintSpeciesTable", this))
, fpSpecies(new G4UIcmdWithAString("/chem/species", this))
{}
G4MoleculeTableMessenger::~G4MoleculeTableMessenger() = default;
//------------------------------------------------------------------------------
void G4MoleculeTableMessenger::SetNewValue(G4UIcommand* command,
G4String newValue)
{
if(command == fpPrintTable.get())
{
G4MolecularConfiguration::PrintAll();
}
if(command == fpSpecies.get())
{
std::istringstream iss(newValue);
G4String speciesName;
iss >> speciesName;
G4String marker;
iss >> marker; // must be [
if(marker != "[")
{
G4ExceptionDescription description;
description << " marker : " << marker << G4endl;
G4Exception("G4MoleculeTableMessenger::SetNewValue",
"FAIL_SPECIES_DEFINITION04", FatalException, description);
}
G4String speciesDefName;
iss >> speciesDefName;
iss >> marker; // peut etre |
G4int charge = 0;
if(marker == "|")
{
iss >> charge;
}
iss >> marker; // peut etre |
G4double diffusion_coefficient = 0;
if(marker == "|")
{
iss >> diffusion_coefficient;
}
iss >> marker; // peut etre |
G4double VanDerVaalsRadius = 0;
if(marker == "|")
{
iss >> VanDerVaalsRadius; // in nm
}
auto pConf =
G4MolecularConfiguration::GetMolecularConfiguration(speciesName);
if(pConf != nullptr)
{
pConf->UnFinalize();
if(VanDerVaalsRadius != 0)
{
pConf->SetVanDerVaalsRadius(VanDerVaalsRadius * nm);
}
if(diffusion_coefficient != 0)
{
pConf->SetDiffusionCoefficient(diffusion_coefficient * (m2 / s));
}
}
else
{
auto particleDef = dynamic_cast<G4MoleculeDefinition*>(
G4ParticleTable::GetParticleTable()->FindParticle(speciesDefName));
if(particleDef != nullptr)
{
auto molConf =
G4MolecularConfiguration::GetOrCreateMolecularConfiguration(
particleDef, charge);
if(molConf == nullptr)
{
G4ExceptionDescription description;
description << "This molecule has not been defined" << G4endl;
G4Exception("G4MoleculeTableMessenger::SetNewValue",
"FAIL_SPECIES_DEFINITION02", FatalException, description);
}
molConf->UnFinalize();
if(VanDerVaalsRadius != 0)
{
molConf->SetVanDerVaalsRadius(VanDerVaalsRadius * nm);
}
if(diffusion_coefficient != 0)
{
molConf->SetDiffusionCoefficient(diffusion_coefficient * (m2 / s));
}
auto usedName = molConf->GetUserID();
if(usedName != "")
{
molConf->PrintState();
G4ExceptionDescription description;
description << "This molecule has been defined by the name : "
<< usedName << " . Please, use this name." << G4endl;
G4Exception("G4MoleculeTableMessenger::SetNewValue",
"FAIL_SPECIES_DEFINITION", FatalException, description);
}
else
{
molConf->SetUserID(speciesName);
}
}
else
{
auto speciesDef =
new G4MoleculeDefinition(speciesDefName, /*mass no needed*/ 0,
/*D*/ diffusion_coefficient * (m * m / s),
/*charge*/ charge, 1,
/*electronL*/ 0,
/*radius*/ VanDerVaalsRadius * nm);
G4bool alreadyCreated(false);
G4MolecularConfiguration::CreateMolecularConfiguration(
speciesName, speciesDef, alreadyCreated);
}
}
}
}
source/processes/electromagnetic/dna/molecules/management/src/G4VMoleculeCounter.cc
-2
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@@ -32,8 +32,6 @@
#include "G4VMoleculeCounter.hh"
#include "G4MoleculeCounter.hh"
G4bool G4VMoleculeCounter::fUse = false;
G4ThreadLocal
G4VMoleculeCounter* G4VMoleculeCounter::fpInstance = nullptr;