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This commit is contained in:
Gabriele Cosmo
2017-06-30 10:49:55 +02:00
parent 3a5407696b
commit 1a1316fea4
2180 changed files with 237880 additions and 59109 deletions
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source/processes/electromagnetic/dna/utils/GNUmakefile
+3 -2
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@@ -1,4 +1,4 @@
# $Id: GNUmakefile 66892 2013-01-17 10:57:59Z gunter $
# $Id: GNUmakefile 103042 2017-03-10 11:50:07Z gcosmo $
# --------------------------------------------------------------------
# GNUmakefile for electromagnetic sub-library. John Allison, 25/6/98.
# --------------------------------------------------------------------
@@ -33,7 +33,8 @@ CPPFLAGS += -I$(G4BASE)/global/management/include \
-I$(G4BASE)/materials/include \
-I$(G4BASE)/processes/electromagnetic/dna/molecules/management/include \
-I$(G4BASE)/processes/electromagnetic/dna/molecules/types/include \
-I$(G4BASE)/processes/electromagnetic/dna/management/include
-I$(G4BASE)/processes/electromagnetic/dna/management/include \
-I$(G4BASE)/analysis/management/include
include $(G4INSTALL)/config/common.gmk
source/processes/electromagnetic/dna/utils/include/G4DNACPA100LogLogInterpolation.hh
+84
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@@ -0,0 +1,84 @@
//
// ********************************************************************
// * 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. *
// ********************************************************************
//
// Based on the work of M. Terrissol and M. C. Bordage
//
// Users are requested to cite the following papers:
// - M. Terrissol, A. Baudre, Radiat. Prot. Dosim. 31 (1990) 175-177
// - M.C. Bordage, J. Bordes, S. Edel, M. Terrissol, X. Franceries,
// M. Bardies, N. Lampe, S. Incerti, Phys. Med. 32 (2016) 1833-1840
//
// Authors of this class:
// M.C. Bordage, M. Terrissol, S. Edel, J. Bordes, S. Incerti
//
// 15.01.2014: creation
//
#ifndef G4LOGLOGINTERPOLATION_HH
#define G4LOGLOGINTERPOLATION_HH 1
#include "globals.hh"
#include "G4VDataSetAlgorithm.hh"
#include "G4DataVector.hh"
class G4DNACPA100LogLogInterpolation : public G4VDataSetAlgorithm {
public:
G4DNACPA100LogLogInterpolation();
~G4DNACPA100LogLogInterpolation();
G4double Calculate(G4double point, G4int bin,
const G4DataVector& energies,
const G4DataVector& data) const;
G4double Calculate(G4double point, G4int bin,
const G4DataVector& energies,
const G4DataVector& data,
const G4DataVector& log_energies,
const G4DataVector& log_data) const;
virtual G4VDataSetAlgorithm* Clone() const;
private:
// Hide copy constructor and assignment operator
};
#endif
source/processes/electromagnetic/dna/utils/include/G4DNACPA100WaterExcitationStructure.hh
+69
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@@ -0,0 +1,69 @@
//
// ********************************************************************
// * 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. *
// ********************************************************************
//
// Based on the work of M. Terrissol and M. C. Bordage
//
// Users are requested to cite the following papers:
// - M. Terrissol, A. Baudre, Radiat. Prot. Dosim. 31 (1990) 175-177
// - M.C. Bordage, J. Bordes, S. Edel, M. Terrissol, X. Franceries,
// M. Bardies, N. Lampe, S. Incerti, Phys. Med. 32 (2016) 1833-1840
//
// Authors of this class:
// M.C. Bordage, M. Terrissol, S. Edel, J. Bordes, S. Incerti
//
// 15.01.2014: creation
//
#ifndef G4DNACPA100WaterExcitationStructure_hh
#define G4DNACPA100WaterExcitationStructure_hh 1
#include "globals.hh"
#include <vector>
class G4DNACPA100WaterExcitationStructure
{
public:
G4DNACPA100WaterExcitationStructure();
virtual ~G4DNACPA100WaterExcitationStructure();
G4double ExcitationEnergy(G4int level);
G4int NumberOfLevels() { return nLevels; }
// Copy constructor and assignment operator to be added here
private:
// Number of excitation levels of the water molecule
G4int nLevels;
std::vector<G4double> energyConstant;
};
#endif
source/processes/electromagnetic/dna/utils/include/G4DNACPA100WaterIonisationStructure.hh
+72
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@@ -0,0 +1,72 @@
//
// ********************************************************************
// * 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. *
// ********************************************************************
//
// Based on the work of M. Terrissol and M. C. Bordage
//
// Users are requested to cite the following papers:
// - M. Terrissol, A. Baudre, Radiat. Prot. Dosim. 31 (1990) 175-177
// - M.C. Bordage, J. Bordes, S. Edel, M. Terrissol, X. Franceries,
// M. Bardies, N. Lampe, S. Incerti, Phys. Med. 32 (2016) 1833-1840
//
// Authors of this class:
// M.C. Bordage, M. Terrissol, S. Edel, J. Bordes, S. Incerti
//
// 15.01.2014: creation
//
#ifndef G4DNACPA100WaterIonisationStructure_hh
#define G4DNACPA100WaterIonisationStructure_hh 1
#include "globals.hh"
#include <vector>
class G4DNACPA100WaterIonisationStructure
{
public:
G4DNACPA100WaterIonisationStructure();
virtual ~G4DNACPA100WaterIonisationStructure();
G4double IonisationEnergy(G4int level);
G4double UEnergy(G4int level);
G4int NumberOfLevels() { return nLevels; }
// Copy constructor and assignment operator to be added here
private:
// Number of Ionisation levels of the water molecule
G4int nLevels;
std::vector<G4double> energyConstant;
std::vector<G4double> UConstant;
};
#endif
source/processes/electromagnetic/dna/utils/include/G4DNAChemistryManager.hh
+28 -18
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@@ -23,7 +23,7 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// $Id: G4DNAChemistryManager.hh 100802 2016-11-02 14:55:27Z gcosmo $
// $Id: G4DNAChemistryManager.hh 103042 2017-03-10 11:50:07Z gcosmo $
//
// Author: Mathieu Karamitros
@@ -64,6 +64,7 @@ class G4UIcmdWithABool;
class G4UIcmdWithADoubleAndUnit;
class G4UIcmdWithoutParameter;
class G4ITGun;
class G4VPhysChemIO;
enum ElectronicModification
{
@@ -85,7 +86,8 @@ enum ElectronicModification
* creation of water molecules and solvated electrons.
*/
class G4DNAChemistryManager : public G4UImessenger, public G4VStateDependent
class G4DNAChemistryManager: public G4UImessenger,
public G4VStateDependent
{
protected:
virtual ~G4DNAChemistryManager();
@@ -119,7 +121,7 @@ public:
void Initialize();
inline void SetChemistryList(G4VUserChemistryList*);
inline void Deregister(G4VUserChemistryList*);
void SetGlobalTemperature(double temp_K);
void SetGlobalTemperature(G4double temp_K);
inline void ForceMasterReinitialization();
inline void TagThreadForReinitialization();
@@ -152,10 +154,10 @@ public:
//============================================================================
/**
* Method used by DNA physics model to create a water molecule.
* The ElectronicModification is a flag telling wheter the molecule
* The ElectronicModification is a flag telling whether the molecule
* is ionized or excited, the electronic level is calculated by the
* model and the IncomingTrack is the track responsible for the creation
* of this molecule, for instance an electron.
* of this molecule (electron, proton...).
*/
void CreateWaterMolecule(ElectronicModification,
G4int /*electronicLevel*/,
@@ -179,9 +181,9 @@ public:
*/
void PushMolecule(G4Molecule*& molecule,
double time,
G4double time,
const G4ThreeVector& position,
int parentID);
G4int parentID);
/**
* WARNING : In case chemistry is not activated, PushMoleculeAtParentTimeAndPlace
@@ -200,7 +202,7 @@ public:
fVerbose = verbose;
}
inline void SetBuildPhysicsTable(bool flag)
inline void SetBuildPhysicsTable(G4bool flag)
{fBuildPhysicsTable = flag;}
G4bool IsCounterResetWhenRunEnds() const
@@ -213,6 +215,8 @@ public:
fResetCounterWhenRunEnds = resetCounterWhenRunEnds;
}
void SetPhysChemIO(G4VPhysChemIO* physChemIO);
protected:
G4DNAWaterExcitationStructure* GetExcitationLevel();
G4DNAWaterIonisationStructure* GetIonisationLevel();
@@ -227,17 +231,22 @@ private:
G4UIcmdWithABool* fpActivateChem;
G4UIcmdWithoutParameter* fpRunChem;
G4UIcmdWithoutParameter* fpSkipReactionsFromChemList;
//G4UIcmdWithADoubleAndUnit* fpGridSize;
//G4UIcmdWithADoubleAndUnit* fpGridSize; // not used in release
G4UIcmdWithADoubleAndUnit* fpScaleForNewTemperature;
G4UIcmdWithoutParameter* fpInitChem;
static G4DNAChemistryManager* fgInstance;
// static bool fActiveChemistry;
bool fActiveChemistry;
G4bool fFileInitialized;
G4bool fWriteFile;
static G4ThreadLocal std::ofstream* fpgOutput_tl;
static G4ThreadLocal G4bool* fpgThreadInitialized_tl;
G4bool fActiveChemistry;
struct ThreadLocalData{
ThreadLocalData();
~ThreadLocalData();
G4VPhysChemIO* fpPhysChemIO;
G4bool fThreadInitialized_tl;
};
static G4ThreadLocal ThreadLocalData* fpThreadData;
G4bool fMasterInitialized;
G4bool fForceThreadReinitialization;
@@ -255,6 +264,8 @@ private:
G4bool fResetCounterWhenRunEnds;
};
//------------------------------------------------------------------------------
inline void G4DNAChemistryManager::ForceRebuildingPhysicsTable()
{
fPhysicsTableBuilt = false;
@@ -279,13 +290,12 @@ inline void G4DNAChemistryManager::ForceMasterReinitialization()
inline void G4DNAChemistryManager::ForceThreadReinitialization()
{
// TODO
fForceThreadReinitialization = true;
}
inline void G4DNAChemistryManager::TagThreadForReinitialization()
{
if (fpgThreadInitialized_tl) delete fpgThreadInitialized_tl;
fpThreadData->fThreadInitialized_tl = false;
}
#endif // G4DNACHEMISTRYMANAGER_HH
source/processes/electromagnetic/dna/utils/include/G4DNAMolecularMaterial.hh
+129 -6
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@@ -23,7 +23,7 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// $Id: G4DNAMolecularMaterial.hh 101354 2016-11-15 08:27:51Z gcosmo $
// $Id: G4DNAMolecularMaterial.hh 103042 2017-03-10 11:50:07Z gcosmo $
//
// Author: Mathieu Karamitros
//
@@ -40,7 +40,7 @@
// reference papers on chemistry:
//
// J. Comput. Phys. 274 (2014) 841-882
// Prog. Nucl. Sci. Tec. 2 (2011) 503-508
// Prog. Nucl. Sci. Tec. 2 (2011) 503-508
#ifndef G4DNAMolecularMaterial_HH
#define G4DNAMolecularMaterial_HH
@@ -54,18 +54,46 @@
class G4Material;
class G4MolecularConfiguration;
/**
* \struct CompareMaterial
* \brief Materials can be described as a derivation of existing "parent"
* materials in order to alter few of their features, such as density.
* \p CompareMaterial compare materials taking into account
* their possible "affiliation".
*/
struct CompareMaterial
{
// If the materials derives from a base material,
// it should be able to find the derived material using the base material.
bool operator()(const G4Material* mat1, const G4Material* mat2) const;
};
typedef std::map<const G4Material*, double, CompareMaterial> ComponentMap;
// G4DNAMolecularMaterial is initialized when G4ApplicationState == G4State_Idle
/**
* \class G4DNAMolecularMaterial
* \brief G4DNAMolecularMaterial builds tables of molecular densities for chosen
* molecular materials. The class handles homogeneous, composite and
* derived materials. A material of interest is labeled as molecular if built
* using the number of atoms rather than the mass fractions.
*
* \details
* - Initialization:
* G4DNAMolecularMaterial is initialized when
* G4ApplicationState == G4State_Idle.
* It should be initialized on the master thread and used in read-only mode
* during stepping. The singleton is thread-shared.
*
* - For Developers:
* Use GetNumMolPerVolTableFor(molecule) in the concrete implementation of
* G4VEmModel::Initialise or G4VProcess::PreparePhysicsTable
* at run initialization to retrieve a read-only, thread-safe, table.
* The table is then built on the master thread at initialization time and
* shared between all threads and models.
*
* \note A G4material is labeled as molecular if built using the number of atoms
*
*/
class G4DNAMolecularMaterial : public G4VStateDependent
class G4DNAMolecularMaterial: public G4VStateDependent
{
public:
static G4DNAMolecularMaterial* Instance();
@@ -77,7 +105,39 @@ public:
//----------------------------------------------------------------------------
/**
* \fn const std::vector<double>* \
* GetDensityTableFor(const G4Material* searchedMaterial) const
* \brief Retrieve a table of volumetric mass densities (mass per unit volume)
* in the G4 unit system for chosen material.
*
* @param[in] searchedMaterial
* The material which you'd like to retrieve the volumic mass
* @pre The \p searchedMaterial used in parameter must be built as a
* molecular material, using the number of atoms rather than the density
* fractions.
* \return
* Pointer to a table of molecular densities for the \p searchedMaterial
* indexed on the (parent) material index.
*
*/
const std::vector<double>* GetDensityTableFor(const G4Material*) const;
/**
* \fn const std::vector<double>* \
* GetNumMolPerVolTableFor(const G4Material* searchedMaterial) const
* \brief Retrieve a table of molecular densities (number of molecules per
* unit volume) in the G4 unit system for chosen material.
*
* @param[in] searchedMaterial
* The material which you'd like to retrieve the molecular density
* @pre The \p searchedMaterial used in parameter must be built as a
* molecular material, using the number of atoms rather than the density
* fractions.
* \return
* Pointer to a table of molecular densities for the \p searchedMaterial
* indexed on the (parent) material index.
*/
const std::vector<double>* GetNumMolPerVolTableFor(const G4Material*) const;
inline const std::vector<ComponentMap>* GetMassFractionTable() const{
@@ -90,13 +150,75 @@ public:
//----------------------------------------------------------------------------
G4MolecularConfiguration* GetMolecularConfiguration(const G4Material*) const;
/**
* \fn void SetMolecularConfiguration(const G4Material* material, \
* G4MolecularConfiguration* molConf)
* \brief Associate a molecular configuration to a G4material.
*
* @param[in] material
* Pointer to a G4 material. The material
* does not need to be defined as a molecular material.
* @param[in] molConf
* The molecular configuration corresponding to
* the G4 \p material.
*/
void SetMolecularConfiguration(const G4Material*,
G4MolecularConfiguration*);
/**
* \fn void SetMolecularConfiguration(const G4Material* material, \
* const G4String& molConf)
* \brief Associate a molecular configuration to a G4material.
*
* @param[in] material
* Pointer to a G4 material. The material
* does not need to be defined as a molecular material.
* @param[in] molConf
* User ID of the molecular configuration corresponding to
* the G4 \p material.
*/
void SetMolecularConfiguration(const G4Material*,
const G4String&);
/**
* \fn void SetMolecularConfiguration(const G4Material* material, \
* const G4String& molConf)
* \brief Associate a molecular configuration to a G4material.
*
* @param[in] material
* Name of the G4 material. The material
* does not need to be defined as a molecular material.
* @param[in] molConf
* User ID of the molecular configuration corresponding to
* the G4 \p material.
*/
void SetMolecularConfiguration(const G4String& materialName,
const G4String& molUserIF);
//----------------------------------------------------------------------------
/**
* \brief Deprecated
* \deprecated Will return a G4 fatal exception.
* Use instead GetNumMolPerVolTableFor(molecule) at run
* initialization to retrieve a read-only, thread-safe, table.
* \note A G4material is labeled as molecular if built using
* the number of atoms.
*/
G4double GetNumMoleculePerVolumeUnitForMaterial(const G4Material *mat);
/**
* \brief Deprecated
* \deprecated Will return a G4 fatal exception.
* Use instead GetNumMolPerVolTableFor(molecule) at run
* initialization to retrieve a read-only, thread-safe, table.
* \note A G4material is labeled as molecular if built using
* the number of atoms.
*/
G4double GetNumMolPerVolForComponentInComposite(const G4Material *composite,
const G4Material *component,
G4double massFraction);
protected:
static G4DNAMolecularMaterial* fInstance;
@@ -119,6 +241,7 @@ protected:
void PrintNotAMolecularMaterial(const char* methodName,
const G4Material* lookForMaterial) const;
// Tables built for all molecular materials at initialization
std::vector<ComponentMap>* fpCompFractionTable;
std::vector<ComponentMap>* fpCompDensityTable;
std::vector<ComponentMap>* fpCompNumMolPerVolTable;
source/processes/electromagnetic/dna/utils/include/G4DNAPTBIonisationStructure.hh
+61
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@@ -0,0 +1,61 @@
///
// ********************************************************************
// * 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. *
// ********************************************************************
// Authors: S. Meylan and C. Villagrasa (IRSN, France)
// Models come from
// M. Bug et al, Rad. Phys and Chem. 130, 459-479 (2017)
#ifndef G4DNAPTBIonisationStructure_HH
#define G4DNAPTBIonisationStructure_HH 1
#include "globals.hh"
#include <vector>
#include <map>
class G4DNAPTBIonisationStructure
{
public:
G4DNAPTBIonisationStructure();
virtual ~G4DNAPTBIonisationStructure();
G4double IonisationEnergy(G4int level, const G4String &materialName);
G4int NumberOfLevels(const G4String& materialName);
// Copy constructor and assignment operator to be added here
private:
// Number of Ionisation levels of the water molecule
std::map<G4String, G4int> nLevels;
std::map<G4String, std::vector<G4double> > energyConstant;
G4String ReplaceMaterial(const G4String &materialName);
};
#endif
source/processes/electromagnetic/dna/utils/include/G4PhysChemIO.hh
+135
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@@ -0,0 +1,135 @@
/*
* G4PhysChemIO.hh
*
* Created on: 3 févr. 2017
* Author: matkara
*/
#ifndef G4PHYSCHEMIO_HH_
#define G4PHYSCHEMIO_HH_
#include "G4VPhysChemIO.hh"
//------------------------------------------------------------------------------
namespace G4PhysChemIO{
class FormattedText: public G4VPhysChemIO
{
public:
FormattedText();
virtual ~FormattedText();
virtual void InitializeMaster(){}
virtual void InitializeThread(){}
virtual void InitializeFile();
virtual void NewRun(){}
virtual void NewEvent(){}
/**
* When DNA physics model create a water molecule, you'll get a notification
* through this method.
* The ElectronicModification is a flag telling whether the molecule
* is ionized or excited, the electronic level is calculated by the
* model and the IncomingTrack is the track responsible for the creation
* of this molecule (electron, proton...)
*/
virtual void CreateWaterMolecule(G4int electronicModif,
G4int /*electronicLevel*/,
G4double energy,
const G4Track* /*theIncomingTrack*/);
/**
* Same idea as the previous method but for solvated electron.
* This method should be used by the physics model of the ElectronSolvatation
* process.
*/
virtual void CreateSolvatedElectron(const G4Track* /*theIncomingTrack*/,
G4ThreeVector* finalPosition = 0);
//============================================================================
// FILE OPERATIONS
//============================================================================
/**
* Tells the chemistry manager to write into a file
* the position and electronic state of the water molecule
* and the position thermalized or not of the solvated electron
*/
virtual void WriteInto(const G4String&,
std::ios_base::openmode mode = std::ios_base::out);
virtual void AddEmptyLineInOuputFile();
/**
* Close the file specified with WriteInto
*/
virtual void CloseFile();
protected:
G4int fRunID; // unused
G4int fEventID; // unused
G4bool fFileInitialized;
std::ofstream fOfstream;
};
//------------------------------------------------------------------------------
class G4Analysis: public G4VPhysChemIO
{
public:
G4Analysis(G4VAnalysisManager*);
virtual ~G4Analysis();
virtual void InitializeMaster(){}
virtual void InitializeThread(){}
virtual void InitializeFile();
virtual void NewRun(){}
virtual void NewEvent(){}
/**
* Method used by DNA physics model to create a water molecule.
* The ElectronicModification is a flag telling wheter the molecule
* is ionized or excited, the electronic level is calculated by the
* model and the IncomingTrack is the track responsible for the creation
* of this molecule, for instance an electron.
*/
virtual void CreateWaterMolecule(G4int electronicModif,
G4int /*electronicLevel*/,
G4double energy,
const G4Track* /*theIncomingTrack*/);
/**
* Same idea as the previous method but for solvated electron.
* This method should be used by the physics model of the ElectronSolvatation
* process.
*/
virtual void CreateSolvatedElectron(const G4Track* /*theIncomingTrack*/,
G4ThreeVector* finalPosition = 0);
//============================================================================
// FILE OPERATIONS
//============================================================================
/**
* Tells the chemMan to write into a file
* the position and electronic state of the water molecule
* and the position thermalized or not of the solvated electron
*/
virtual void WriteInto(const G4String&, std::ios_base::openmode mode =
std::ios_base::out);
virtual void AddEmptyLineInOuputFile(){}
/**
* Close the file specified with WriteInto
*/
virtual void CloseFile();
protected:
G4VAnalysisManager* fpAnalysisManager;
int fNtupleID;
G4bool fFileInitialized;
};
}
#endif // G4PHYSCHEMIO_HH_
source/processes/electromagnetic/dna/utils/include/G4VPhysChemIO.hh
+71
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@@ -0,0 +1,71 @@
/*
* G4VPhysChemIO.hh
*
* Created on: 3 févr. 2017
* Author: matkara
*/
#ifndef G4VPHYSCHEMIO_HH_
#define G4VPHYSCHEMIO_HH_
#include <fstream>
#include "globals.hh"
#include "G4ThreeVector.hh"
class G4Track;
class G4VAnalysisManager;
class G4VPhysChemIO
{
public:
G4VPhysChemIO();
virtual ~G4VPhysChemIO();
virtual void InitializeMaster(){}
virtual void InitializeThread(){}
virtual void InitializeFile() = 0;
virtual void NewRun() = 0;
virtual void NewEvent() = 0;
/**
* When DNA physics model create a water molecule, you'll get a notification
* through this method.
* The ElectronicModification is a flag telling whether the molecule
* is ionized or excited, the electronic level is calculated by the
* model and the IncomingTrack is the track responsible for the creation
* of this molecule (electron, proton...)
*/
virtual void CreateWaterMolecule(G4int electronicModif,
G4int /*electronicLevel*/,
G4double energy,
const G4Track* /*theIncomingTrack*/) = 0;
/**
* Same idea as the previous method but for solvated electron.
* This method should be used by the physics model of the ElectronSolvatation
* process.
*/
virtual void CreateSolvatedElectron(const G4Track* /*theIncomingTrack*/,
G4ThreeVector* finalPosition = 0) = 0;
//============================================================================
// FILE OPERATIONS
//============================================================================
/**
* Tells the chemistry manager to write into a file
* the position and electronic state of the water molecule
* and the position thermalized or not of the solvated electron
*/
virtual void WriteInto(const G4String&, std::ios_base::openmode mode =
std::ios_base::out) = 0;
virtual void AddEmptyLineInOuputFile(){};
/**
* Close the file specified with WriteInto
*/
virtual void CloseFile() = 0;
};
#endif // G4PHYSCHEMIO_HH_
source/processes/electromagnetic/dna/utils/sources.cmake
+18 -1
View File
@@ -11,7 +11,7 @@
#
# Generated on : 24/9/2010
#
# $Id: sources.cmake 101790 2016-11-28 15:33:44Z gcosmo $
# $Id: sources.cmake 103042 2017-03-10 11:50:07Z gcosmo $
#
#------------------------------------------------------------------------------
@@ -42,6 +42,8 @@ include_directories(${CMAKE_SOURCE_DIR}/source/processes/electromagnetic/dna/mol
include_directories(${CMAKE_SOURCE_DIR}/source/processes/electromagnetic/dna/molecules/types/include)
include_directories(${CMAKE_SOURCE_DIR}/source/track/include)
include_directories(${CMAKE_SOURCE_DIR}/source/analysis/management/include) # for physchemIO
#
# Define the Geant4 Module.
#
@@ -49,6 +51,9 @@ include(Geant4MacroDefineModule)
GEANT4_DEFINE_MODULE(NAME G4emdna-utils
HEADERS
G4DNAChemistryManager.hh
G4DNACPA100LogLogInterpolation.hh
G4DNACPA100WaterExcitationStructure.hh
G4DNACPA100WaterIonisationStructure.hh
G4DNACrossSectionDataSet.hh
G4DNADamage.hh
G4DNAGenericIonsManager.hh
@@ -57,6 +62,7 @@ GEANT4_DEFINE_MODULE(NAME G4emdna-utils
G4DNAMolecularReactionTable.hh
G4DNAEmfietzoglouWaterExcitationStructure.hh
G4DNAEmfietzoglouWaterIonisationStructure.hh
G4DNAPTBIonisationStructure.hh
G4DNARevertProbability.hh
G4DNAWaterExcitationStructure.hh
G4DNAWaterIonisationStructure.hh
@@ -65,8 +71,14 @@ GEANT4_DEFINE_MODULE(NAME G4emdna-utils
G4ReactionTableMessenger.hh
G4VDNAReactionModel.hh
G4VUserChemistryList.hh
# physchemIO
G4VPhysChemIO.hh
G4PhysChemIO.hh
SOURCES
G4DNAChemistryManager.cc
G4DNACPA100LogLogInterpolation.cc
G4DNACPA100WaterExcitationStructure.cc
G4DNACPA100WaterIonisationStructure.cc
G4DNACrossSectionDataSet.cc
G4DNADamage.cc
G4DNAGenericIonsManager.cc
@@ -75,6 +87,7 @@ GEANT4_DEFINE_MODULE(NAME G4emdna-utils
G4DNAMolecularReactionTable.cc
G4DNAEmfietzoglouWaterExcitationStructure.cc
G4DNAEmfietzoglouWaterIonisationStructure.cc
G4DNAPTBIonisationStructure.cc
G4DNAWaterExcitationStructure.cc
G4DNAWaterIonisationStructure.cc
G4MoleculeGun.cc
@@ -82,6 +95,9 @@ GEANT4_DEFINE_MODULE(NAME G4emdna-utils
G4ReactionTableMessenger.cc
G4VDNAReactionModel.cc
G4VUserChemistryList.cc
# physchemIO
G4VPhysChemIO.cc
G4PhysChemIO.cc
GRANULAR_DEPENDENCIES
G4baryons
G4bosons
@@ -104,6 +120,7 @@ GEANT4_DEFINE_MODULE(NAME G4emdna-utils
# G4emdna-molman
# G4emdna-moltypes
GLOBAL_DEPENDENCIES
G4analysis
G4geometry
G4global
G4intercoms
source/processes/electromagnetic/dna/utils/src/G4DNACPA100LogLogInterpolation.cc
+160
View File
@@ -0,0 +1,160 @@
//
// ********************************************************************
// * 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. *
// ********************************************************************
//
// Based on the work of M. Terrissol and M. C. Bordage
//
// Users are requested to cite the following papers:
// - M. Terrissol, A. Baudre, Radiat. Prot. Dosim. 31 (1990) 175-177
// - M.C. Bordage, J. Bordes, S. Edel, M. Terrissol, X. Franceries,
// M. Bardies, N. Lampe, S. Incerti, Phys. Med. 32 (2016) 1833-1840
//
// Authors of this class:
// M.C. Bordage, M. Terrissol, S. Edel, J. Bordes, S. Incerti
//
// 15.01.2014: creation
//
#include "G4DNACPA100LogLogInterpolation.hh"
// Constructor
G4DNACPA100LogLogInterpolation::G4DNACPA100LogLogInterpolation()
{ }
// Destructor
G4DNACPA100LogLogInterpolation::~G4DNACPA100LogLogInterpolation()
{ }
G4VDataSetAlgorithm* G4DNACPA100LogLogInterpolation::Clone() const
{ return new G4DNACPA100LogLogInterpolation; }
G4double G4DNACPA100LogLogInterpolation::Calculate(G4double x, G4int bin,
const G4DataVector& points,
const G4DataVector& data) const
{
//G4cout << "G4DNACPA100LogLogInterpolation is performed (2 arguments) " << G4endl;
G4int nBins = data.size() - 1;
//G4double oldresult = 0.;
G4double value = 0.;
if (x < points[0])
{
value = 0.;
}
else if (bin < nBins)
{
G4double e1 = points[bin];
G4double e2 = points[bin+1];
G4double d1 = data[bin];
G4double d2 = data[bin+1];
// Check of e1, e2, d1 and d2 values to avoid floating-point errors when estimating the interpolated value below -- S.I., Jun. 2008
if ((d1 > 0.) && (d2 > 0.) && (e1 > 0.) && (e2 > 0.))
{
// Streamline the Log-Log Interpolation formula in order to reduce the required number of log10() function calls
// Variable oldresult contains the result of old implementation of Log-Log interpolation -- M.G.P. Jun. 2001
// oldresult = (std::log10(d1)*std::log10(e2/x) + std::log10(d2)*std::log10(x/e1)) / std::log10(e2/e1);
// oldresult = std::pow(10.,oldresult);
// Variable value contains the result of new implementation, after streamlining the math operation -- N.A.K. Oct. 2008
value = std::log10(d1)+(std::log10(d2/d1)/std::log10(e2/e1)*std::log10(x/e1));
value = std::pow(10.,value);
// Test of the new implementation result (value variable) against the old one (oldresult) -- N.A.K. Dec. 2008
// G4double diffResult = value - oldresult;
// G4double relativeDiff = 1e-11;
// Comparison of the two values based on a max allowable relative difference
// if ( std::fabs(diffResult) > relativeDiff*std::fabs(oldresult) )
// {
// Abort comparison when at least one of two results is infinite
// if ((!std::isinf(oldresult)) && (!std::isinf(value)))
// {
// G4cout << "G4DNACPA100LogLogInterpolation> Old Interpolated Value is:" << oldresult << G4endl;
// G4cout << "G4DNACPA100LogLogInterpolation> New Interpolated Value is:" << value << G4endl << G4endl;
// G4cerr << "G4DNACPA100LogLogInterpolation> Error in Interpolation:" << G4endl;
// G4cerr << "The difference between new and old interpolated value is:" << diffResult << G4endl << G4endl;
// }
// }
}
else value = 0.;
}
else
{
value = data[nBins];
}
return value;
}
// Nicolas A. Karakatsanis: New implementation of log-log interpolation after directly loading
// logarithmic values from G4EMLOW dataset
G4double G4DNACPA100LogLogInterpolation::Calculate(G4double x, G4int bin,
const G4DataVector& points,
const G4DataVector& data,
const G4DataVector& log_points,
const G4DataVector& log_data) const
{
G4int nBins = data.size() - 1;
G4double value = 0.;
G4double log_x = std::log10(x);
if (x < points[0])
{
value = 0.;
}
else if (bin < nBins)
{
G4double log_e1 = log_points[bin];
//G4double log_e2 = log_points[bin+1];
G4double log_d1 = log_data[bin];
G4double log_d2 = log_data[bin+1];
//G4cout << "x = " << x << " , logx = " << log_x << " , bin = " << bin << G4endl;
//G4cout << "e1 = " << points[bin] << " d1 = " << data[bin] << G4endl;
//G4cout << "e2 = " << points[bin+1] << " d2 = " << data[bin+1] << G4endl;
//G4cout << "loge1 = " << log_e1 << " logd1 = " << log_d1 << G4endl;
//G4cout << "loge2 = " << log_e2 << " logd2 = " << log_d2 << G4endl;
//G4cout << "interpol " << log_d1 + (log_d2 - log_d1)*(log_x - log_e1)/(log_e2 - log_e1) << " " << G4endl;
// Values e1, e2, d1 and d2 are the log values of the corresponding
// original energy and data values. Simple linear interpolation performed
// on loagarithmic data should be equivalent to log-log interpolation
// CPA100 specific
//value = log_d1 + (log_d2 - log_d1)*(log_x - log_e1)/(log_e2 - log_e1);
// value = log_d1;
value = log_d2; // UPPER VALUE INTERPOLATION
if (log_x == log_e1) value = log_d1; // IN CASE OF EQUALITY
// Delogarithmize to obtain interpolated value
value = std::pow(10.,value);
}
else
{
value = data[nBins];
}
return value;
}
source/processes/electromagnetic/dna/utils/src/G4DNACPA100WaterExcitationStructure.cc
+74
View File
@@ -0,0 +1,74 @@
//
// ********************************************************************
// * 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. *
// ********************************************************************
//
// Based on the work of M. Terrissol and M. C. Bordage
//
// Users are requested to cite the following papers:
// - M. Terrissol, A. Baudre, Radiat. Prot. Dosim. 31 (1990) 175-177
// - M.C. Bordage, J. Bordes, S. Edel, M. Terrissol, X. Franceries,
// M. Bardies, N. Lampe, S. Incerti, Phys. Med. 32 (2016) 1833-1840
//
// Authors of this class:
// M.C. Bordage, M. Terrissol, S. Edel, J. Bordes, S. Incerti
//
// 15.01.2014: creation
//
#include "G4DNACPA100WaterExcitationStructure.hh"
#include "G4SystemOfUnits.hh"
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4DNACPA100WaterExcitationStructure::G4DNACPA100WaterExcitationStructure(): nLevels(5)
{
// The following values are extracted from the thesis of S. Edel,
// Paul Sabatier University, Toulouse, France, July 7, 2006
// Page 36
energyConstant.push_back(8.17*eV);
energyConstant.push_back(10.13*eV);
energyConstant.push_back(11.31*eV);
energyConstant.push_back(12.91*eV);
energyConstant.push_back(14.50*eV);
nLevels = energyConstant.size();
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4DNACPA100WaterExcitationStructure::~G4DNACPA100WaterExcitationStructure()
{ }
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4double G4DNACPA100WaterExcitationStructure::ExcitationEnergy(G4int level)
{
G4double excitation = 0.;
if (level >=0 && level < nLevels) excitation = energyConstant[level];
return excitation;
}
source/processes/electromagnetic/dna/utils/src/G4DNACPA100WaterIonisationStructure.cc
+85
View File
@@ -0,0 +1,85 @@
//
// ********************************************************************
// * 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. *
// ********************************************************************
//
// Based on the work of M. Terrissol and M. C. Bordage
//
// Users are requested to cite the following papers:
// - M. Terrissol, A. Baudre, Radiat. Prot. Dosim. 31 (1990) 175-177
// - M.C. Bordage, J. Bordes, S. Edel, M. Terrissol, X. Franceries,
// M. Bardies, N. Lampe, S. Incerti, Phys. Med. 32 (2016) 1833-1840
//
// Authors of this class:
// M.C. Bordage, M. Terrissol, S. Edel, J. Bordes, S. Incerti
//
// 15.01.2014: creation
//
#include "G4DNACPA100WaterIonisationStructure.hh"
#include "G4SystemOfUnits.hh"
G4DNACPA100WaterIonisationStructure::G4DNACPA100WaterIonisationStructure(): nLevels(5)
{
energyConstant.push_back(10.79*eV);
energyConstant.push_back(13.39*eV);
energyConstant.push_back(16.05*eV);
energyConstant.push_back(32.30*eV);
energyConstant.push_back(539.0*eV);
UConstant.push_back(61.91*eV);
UConstant.push_back(59.52*eV);
UConstant.push_back(48.36*eV);
UConstant.push_back(70.71*eV);
UConstant.push_back(796.2*eV);
nLevels = energyConstant.size();
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4DNACPA100WaterIonisationStructure::~G4DNACPA100WaterIonisationStructure()
{ }
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4double G4DNACPA100WaterIonisationStructure::IonisationEnergy(G4int level)
{
G4double ionisation = 0.;
if (level >=0 && level < nLevels) ionisation = energyConstant[level];
return ionisation;
}
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
G4double G4DNACPA100WaterIonisationStructure::UEnergy(G4int level)
{
G4double ionisation = 0.;
if (level >=0 && level < nLevels) ionisation = UConstant[level];
return ionisation;
}
source/processes/electromagnetic/dna/utils/src/G4DNAChemistryManager.cc
+158 -146
View File
@@ -23,7 +23,7 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// $Id: G4DNAChemistryManager.cc 100802 2016-11-02 14:55:27Z gcosmo $
// $Id: G4DNAChemistryManager.cc 103042 2017-03-10 11:50:07Z gcosmo $
//
// Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
//
@@ -58,38 +58,57 @@
#include "G4StateManager.hh"
#include "G4MoleculeFinder.hh"
#include "G4MoleculeTable.hh"
#include "G4PhysChemIO.hh"
using namespace std;
G4DNAChemistryManager* G4DNAChemistryManager::fgInstance;
G4ThreadLocal std::ofstream* G4DNAChemistryManager::fpgOutput_tl = 0;
G4ThreadLocal G4bool* G4DNAChemistryManager::fpgThreadInitialized_tl = 0;
G4ThreadLocal G4DNAChemistryManager::ThreadLocalData*
G4DNAChemistryManager::fpThreadData = 0;
G4Mutex chemManExistence;
//bool G4DNAChemistryManager::fActiveChemistry = false;
//------------------------------------------------------------------------------
G4DNAChemistryManager::ThreadLocalData::ThreadLocalData()
{
fpPhysChemIO = nullptr;
fThreadInitialized_tl = false;
}
//------------------------------------------------------------------------------
G4DNAChemistryManager::ThreadLocalData::~ThreadLocalData()
{
if(fpPhysChemIO) delete fpPhysChemIO;
fThreadInitialized_tl = false;
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::SetPhysChemIO(G4VPhysChemIO* physChemIO)
{
if(fpThreadData->fpPhysChemIO)
delete fpThreadData->fpPhysChemIO;
fpThreadData->fpPhysChemIO = physChemIO;
}
//------------------------------------------------------------------------------
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
//------------------------------------------------------------------------------
/*
* The chemistry manager is shared between threads
* It is initialized both on the master thread and on the worker threads
*/
//==============================================================================
// 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/");
@@ -106,17 +125,18 @@ G4DNAChemistryManager::G4DNAChemistryManager() :
fGeometryClosed = false;
fPhysicsTableBuilt = false;
fForceThreadReinitialization = false;
fFileInitialized = false;
fVerbose = 0;
fActiveChemistry = false;
fSkipReactions = false;
fResetCounterWhenRunEnds = true;
}
//------------------------------------------------------------------------------
G4DNAChemistryManager*
G4DNAChemistryManager::Instance()
{
if (fgInstance == 0)
if(fgInstance == 0)
{
G4AutoLock lock(&chemManExistence);
if (fgInstance == 0) // MT : double check at initialisation
@@ -125,15 +145,23 @@ G4DNAChemistryManager::Instance()
}
lock.unlock();
}
if(fpThreadData==0) fpThreadData = new ThreadLocalData();
// make sure thread local data is initialized for all threads
return fgInstance;
}
//------------------------------------------------------------------------------
G4DNAChemistryManager*
G4DNAChemistryManager::GetInstanceIfExists()
{
return fgInstance;
}
//------------------------------------------------------------------------------
G4DNAChemistryManager::~G4DNAChemistryManager()
{
// G4cout << "Deleting G4DNAChemistryManager" << G4endl;
@@ -146,6 +174,8 @@ G4DNAChemistryManager::~G4DNAChemistryManager()
*/
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::Clear()
{
if (fpIonisationLevel)
@@ -206,6 +236,8 @@ void G4DNAChemistryManager::Clear()
G4VMoleculeCounter::DeleteInstance();
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::DeleteInstance()
{
//G4cout << "G4DNAChemistryManager::DeleteInstance" << G4endl;
@@ -226,6 +258,8 @@ void G4DNAChemistryManager::DeleteInstance()
lock.unlock();
}
//------------------------------------------------------------------------------
G4bool G4DNAChemistryManager::Notify(G4ApplicationState requestedState)
{
if (requestedState == G4State_Quit)
@@ -236,7 +270,15 @@ G4bool G4DNAChemistryManager::Notify(G4ApplicationState requestedState)
//DeleteInstance();
Clear();
}
// else if(requestedState == G4State_EventProc)
// Note: From here we can know that a new event is started
// But the run and event IDs remain unknown
// {
// if(fpThreadData->fpPhysChemIO)
// {
//
// }
// }
else if(requestedState == G4State_GeomClosed)
{
fGeometryClosed = true;
@@ -250,6 +292,8 @@ G4bool G4DNAChemistryManager::Notify(G4ApplicationState requestedState)
return true;
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::SetNewValue(G4UIcommand* command, G4String value)
{
if (command == fpActivateChem)
@@ -271,7 +315,8 @@ void G4DNAChemistryManager::SetNewValue(G4UIcommand* command, G4String value)
}
else if(command == fpScaleForNewTemperature)
{
SetGlobalTemperature(fpScaleForNewTemperature->ConvertToDimensionedDouble(value));
SetGlobalTemperature(fpScaleForNewTemperature->
ConvertToDimensionedDouble(value));
}
else if(command == fpInitChem)
{
@@ -280,6 +325,8 @@ void G4DNAChemistryManager::SetNewValue(G4UIcommand* command, G4String value)
}
}
//------------------------------------------------------------------------------
G4String G4DNAChemistryManager::GetCurrentValue(G4UIcommand* command)
{
if (command == fpActivateChem)
@@ -290,6 +337,8 @@ G4String G4DNAChemistryManager::GetCurrentValue(G4UIcommand* command)
return "";
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::Run()
{
if (fActiveChemistry)
@@ -304,7 +353,7 @@ void G4DNAChemistryManager::Run()
description);
}
if (fpgThreadInitialized_tl == 0)
if (fpThreadData->fThreadInitialized_tl == 0)
{
G4ExceptionDescription description;
description << "Thread local components were not initialized.";
@@ -322,12 +371,16 @@ void G4DNAChemistryManager::Run()
}
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::Gun(G4ITGun* gun, bool physicsTableToBuild)
{
fBuildPhysicsTable = physicsTableToBuild;
G4Scheduler::Instance()->SetGun(gun);
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::Initialize()
{
//===========================================================================
@@ -340,7 +393,7 @@ void G4DNAChemistryManager::Initialize()
//==========================================================================
if(G4Threading::IsWorkerThread())
{
InitializeThread(); // Will create and initialize G4ITScheduler
InitializeThread(); // Will create and initialize G4Scheduler
return;
}
//==========================================================================
@@ -364,6 +417,8 @@ void G4DNAChemistryManager::Initialize()
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::InitializeMaster()
{
if (fMasterInitialized == false)
@@ -375,7 +430,6 @@ void G4DNAChemistryManager::InitializeMaster()
G4Scheduler::Instance();
// creates a concrete object of the scheduler
// and track container
if (fpUserChemistryList)
{
@@ -404,9 +458,12 @@ void G4DNAChemistryManager::InitializeMaster()
}
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::InitializeThread()
{
if (fpgThreadInitialized_tl == 0 || fForceThreadReinitialization == true)
if (fpThreadData->fThreadInitialized_tl == false
|| fForceThreadReinitialization == true)
{
if (fpUserChemistryList)
{
@@ -447,7 +504,7 @@ void G4DNAChemistryManager::InitializeThread()
G4DNAMolecularReactionTable::GetReactionTable());
G4Scheduler::Instance()->Initialize();
fpgThreadInitialized_tl = new G4bool(true);
fpThreadData->fThreadInitialized_tl = true;
}
else
{
@@ -463,55 +520,51 @@ void G4DNAChemistryManager::InitializeThread()
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;
if(fpThreadData->fpPhysChemIO){
fpThreadData->fpPhysChemIO->InitializeFile();
}
}
//------------------------------------------------------------------------------
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)
{
@@ -521,34 +574,35 @@ void G4DNAChemistryManager::WriteInto(const G4String& output,
<< output.data() << G4endl;
}
fpgOutput_tl = new std::ofstream();
fpgOutput_tl->open(output.data(), mode);
fWriteFile = true;
fFileInitialized = false;
if(fpThreadData->fpPhysChemIO){
fpThreadData->fpPhysChemIO->WriteInto(output, mode);
}
else{
fpThreadData->fpPhysChemIO = new G4PhysChemIO::FormattedText();
fpThreadData->fpPhysChemIO->WriteInto(output, mode);
}
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::AddEmptyLineInOuputFile()
{
if (fWriteFile)
{
*fpgOutput_tl << G4endl;
if(fpThreadData->fpPhysChemIO){
fpThreadData->fpPhysChemIO->AddEmptyLineInOuputFile();
}
}
//------------------------------------------------------------------------------
void G4DNAChemistryManager::CloseFile()
{
if (fpgOutput_tl == 0) return;
if (fpgOutput_tl->is_open())
{
if (fVerbose)
{
G4cout << "G4DNAChemistryManager: Close File" << G4endl;
}
fpgOutput_tl->close();
if(fpThreadData->fpPhysChemIO){
fpThreadData->fpPhysChemIO->CloseFile();
}
}
//------------------------------------------------------------------------------
G4DNAWaterExcitationStructure*
G4DNAChemistryManager::GetExcitationLevel()
{
@@ -559,6 +613,8 @@ G4DNAChemistryManager::GetExcitationLevel()
return fpExcitationLevel;
}
//------------------------------------------------------------------------------
G4DNAWaterIonisationStructure*
G4DNAChemistryManager::GetIonisationLevel()
{
@@ -569,14 +625,14 @@ G4DNAChemistryManager::GetIonisationLevel()
return fpIonisationLevel;
}
void G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modification,
G4int electronicLevel,
const G4Track* theIncomingTrack)
{
if (fWriteFile)
{
if(!fFileInitialized) InitializeFile();
//------------------------------------------------------------------------------
void
G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modification,
G4int electronicLevel,
const G4Track* theIncomingTrack)
{
if(fpThreadData->fpPhysChemIO){
G4double energy = -1.;
switch (modification)
@@ -591,19 +647,11 @@ void G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modificat
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;
fpThreadData->fpPhysChemIO->CreateWaterMolecule(modification,
4-electronicLevel,
energy,
theIncomingTrack);
}
if(fActiveChemistry)
@@ -631,37 +679,18 @@ void G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modificat
H2OTrack -> SetKineticEnergy(0.);
G4VITTrackHolder::Instance()->Push(H2OTrack);
}
// else
// abort();
}
void G4DNAChemistryManager::CreateSolvatedElectron(const G4Track* theIncomingTrack,
G4ThreeVector* finalPosition)
//------------------------------------------------------------------------------
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(fpThreadData->fpPhysChemIO){
fpThreadData->fpPhysChemIO->CreateSolvatedElectron(theIncomingTrack,
finalPosition);
}
if(fActiveChemistry)
@@ -682,24 +711,15 @@ void G4DNAChemistryManager::CreateSolvatedElectron(const G4Track* theIncomingTra
}
}
//------------------------------------------------------------------------------
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;
}
// TODO: PhysChemIO - method unused in the released code
if(fActiveChemistry)
{
G4Track* track = molecule->BuildTrack(time,position);
@@ -714,25 +734,14 @@ void G4DNAChemistryManager::PushMolecule(G4Molecule*& molecule,
}
}
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;
}
void G4DNAChemistryManager::
PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecule,
const G4Track* theIncomingTrack)
{
// TODO: PhysChemIO - method unused in the released code
if(fActiveChemistry)
{
@@ -749,9 +758,12 @@ void G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecu
}
}
void G4DNAChemistryManager::SetGlobalTemperature(double temp_K)
//------------------------------------------------------------------------------
void G4DNAChemistryManager::SetGlobalTemperature(G4double temp_K)
{
G4MolecularConfiguration::SetGlobalTemperature(temp_K);
G4DNAMolecularReactionTable::Instance()->ScaleReactionRateForNewTemperature(temp_K);
G4DNAMolecularReactionTable::Instance()->
ScaleReactionRateForNewTemperature(temp_K);
}
source/processes/electromagnetic/dna/utils/src/G4DNACrossSectionDataSet.cc
+21 -37
View File
@@ -25,7 +25,7 @@
//
//
// $Id: G4DNACrossSectionDataSet.cc 70171 2013-05-24 13:34:18Z gcosmo $
// $Id: G4DNACrossSectionDataSet.cc 104122 2017-05-11 13:50:22Z gcosmo $
//
// Author: Riccardo Capra <capra@ge.infn.it>
// Code review by MGP October 2007: removed inheritance from concrete class
@@ -160,31 +160,23 @@ G4bool G4DNACrossSectionDataSet::LoadData(const G4String & argFileName)
comment=false;
space=true;
break;
case '#':
comment=true;
break;
case '\t':
c=' ';
case ' ':
if (space)
break;
space = true;
break;
default:
if (comment)
break;
if (c==' ')
space=true;
else
{
if (space && (!first))
(*stream) << ' ';
first=false;
(*stream) << c;
space=false;
}
if (comment) { break; }
if (space && (!first)) { (*stream) << ' '; }
first=false;
(*stream) << c;
space=false;
}
}
}
@@ -318,31 +310,23 @@ G4bool G4DNACrossSectionDataSet::LoadNonLogData(const G4String & argFileName)
comment=false;
space=true;
break;
case '#':
comment=true;
break;
case '\t':
c=' ';
case ' ':
if (space)
break;
space = true;
break;
default:
if (comment)
break;
if (c==' ')
space=true;
else
{
if (space && (!first))
(*stream) << ' ';
first=false;
(*stream) << c;
space=false;
}
if (comment) { break; }
if (space && (!first)) { (*stream) << ' '; }
first=false;
(*stream) << c;
space=false;
}
}
}
source/processes/electromagnetic/dna/utils/src/G4DNAMolecularMaterial.cc
+40 -11
View File
@@ -23,10 +23,11 @@
// * acceptance of all terms of the Geant4 Software license. *
// ********************************************************************
//
// $Id: G4DNAMolecularMaterial.cc 101354 2016-11-15 08:27:51Z gcosmo $
// $Id: G4DNAMolecularMaterial.cc 103042 2017-03-10 11:50:07Z gcosmo $
//
// Author: Mathieu Karamitros
//
#include "G4DNAMolecularMaterial.hh"
#include "G4Material.hh"
#include <utility>
@@ -323,6 +324,7 @@ G4DNAMolecularMaterial::RecordMolecularMaterial(G4Material* parentMaterial,
}
else{
matComponent[molecularMaterial] = it->second + fraction;
// handle "base material"
}
}
@@ -332,30 +334,27 @@ void G4DNAMolecularMaterial::SearchMolecularMaterial(G4Material* parentMaterial,
G4Material* material,
double currentFraction)
{
if (material->GetMassOfMolecule() != 0.0){
if (material->GetMassOfMolecule() != 0.0){ // is a molecular material
RecordMolecularMaterial(parentMaterial, material, currentFraction);
return;
}
G4Material* compMat(0);
G4double fraction = -1;
G4Material* compMat(nullptr);
G4double fraction = -1.;
std::map<G4Material*, G4double> matComponent = material->GetMatComponents();
std::map<G4Material*, G4double>::iterator it = matComponent.begin();
for (; it != matComponent.end(); it++){
compMat = it->first;
fraction = it->second;
if (compMat->GetMassOfMolecule() == 0.0){
if (compMat->GetMassOfMolecule() == 0.0){ // is not a molecular material
SearchMolecularMaterial(parentMaterial, compMat,
currentFraction * fraction);
}
else{
else{ // is a molecular material
RecordMolecularMaterial(parentMaterial, compMat,
currentFraction * fraction);
}
//compMat = 0;
//fraction = -1;
}
}
@@ -438,7 +437,7 @@ const std::vector<double>* G4DNAMolecularMaterial::GetNumMolPerVolTableFor(
const G4Material* lookForMaterial) const
{
if(lookForMaterial==0) return nullptr;
if (!fpCompNumMolPerVolTable){
if (fIsInitialized){
G4ExceptionDescription exceptionDescription;
@@ -581,7 +580,7 @@ G4DNAMolecularMaterial::SetMolecularConfiguration(const G4String& materialName,
const G4String& molUserID)
{
G4Material* material = G4Material::GetMaterial(materialName);
if(material == 0){
G4cout<< "Material " << materialName
<< " was not found and therefore won't be linked to "
@@ -590,3 +589,33 @@ G4DNAMolecularMaterial::SetMolecularConfiguration(const G4String& materialName,
}
SetMolecularConfiguration(material, molUserID);
}
//------------------------------------------------------------------------------
G4double
G4DNAMolecularMaterial::
GetNumMoleculePerVolumeUnitForMaterial(const G4Material*)
{
G4Exception("G4DNAMolecularMaterial::GetNumMolPerVolForComponentInComposite",
"DEPRECATED",
FatalException,"Use standard method: GetNumMolPerVolTableFor"
" at the run initialization to retrieve a read-only table used"
" during stepping. The method is thread-safe.");
return 0;
}
//------------------------------------------------------------------------------
G4double
G4DNAMolecularMaterial::
GetNumMolPerVolForComponentInComposite(const G4Material*,
const G4Material*,
G4double)
{
G4Exception("G4DNAMolecularMaterial::GetNumMolPerVolForComponentInComposite",
"DEPRECATED",
FatalException,"Use standard method: GetNumMolPerVolTableFor"
" at the run initialization to retrieve a read-only table used"
" during stepping. The method is thread-safe.");
return 0;
}
source/processes/electromagnetic/dna/utils/src/G4DNAPTBIonisationStructure.cc
+213
View File
@@ -0,0 +1,213 @@
//
// ********************************************************************
// * 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. *
// ********************************************************************
// Authors: S. Meylan and C. Villagrasa (IRSN, France)
// Models come from
// M. Bug et al, Rad. Phys and Chem. 130, 459-479 (2017)
#include "G4DNAPTBIonisationStructure.hh"
#include "G4SystemOfUnits.hh"
G4DNAPTBIonisationStructure::G4DNAPTBIonisationStructure()
{
energyConstant["G4_WATER"].push_back(10.79*eV);
energyConstant["G4_WATER"].push_back(13.39*eV);
energyConstant["G4_WATER"].push_back(16.05*eV);
energyConstant["G4_WATER"].push_back(32.30*eV);
energyConstant["G4_WATER"].push_back(539.0*eV);
energyConstant["THF"].push_back(9.74*eV);
energyConstant["THF"].push_back(12.31*eV);
energyConstant["THF"].push_back(12.99*eV);
energyConstant["THF"].push_back(13.57*eV);
energyConstant["THF"].push_back(13.60*eV);
energyConstant["THF"].push_back(15.11*eV);
energyConstant["THF"].push_back(15.97*eV);
energyConstant["THF"].push_back(16.28*eV);
energyConstant["THF"].push_back(18.19*eV);
energyConstant["THF"].push_back(18.69*eV);
energyConstant["THF"].push_back(22.14*eV);
energyConstant["THF"].push_back(22.25*eV);
energyConstant["THF"].push_back(27.21*eV);
energyConstant["THF"].push_back(28.97*eV);
energyConstant["THF"].push_back(36.97*eV);
energyConstant["THF"].push_back(305.07*eV);
energyConstant["THF"].push_back(305.08*eV);
energyConstant["THF"].push_back(306.17*eV);
energyConstant["THF"].push_back(306.17*eV);
energyConstant["THF"].push_back(557.94*eV);
energyConstant["PY"].push_back(9.73*eV);
energyConstant["PY"].push_back(10.96*eV);
energyConstant["PY"].push_back(11.54*eV);
energyConstant["PY"].push_back(12.58*eV);
energyConstant["PY"].push_back(15.96*eV);
energyConstant["PY"].push_back(16.27*eV);
energyConstant["PY"].push_back(16.53*eV);
energyConstant["PY"].push_back(17.98*eV);
energyConstant["PY"].push_back(19.37*eV);
energyConstant["PY"].push_back(20.52*eV);
energyConstant["PY"].push_back(24.55*eV);
energyConstant["PY"].push_back(24.64*eV);
energyConstant["PY"].push_back(29.75*eV);
energyConstant["PY"].push_back(33.02*eV);
energyConstant["PY"].push_back(36.57*eV);
energyConstant["PY"].push_back(305.92*eV);
energyConstant["PY"].push_back(307.09*eV);
energyConstant["PY"].push_back(307.09*eV);
energyConstant["PY"].push_back(307.52*eV);
energyConstant["PY"].push_back(423.44*eV);
energyConstant["PY"].push_back(423.44*eV);
energyConstant["PU"].push_back(9.58*eV);
energyConstant["PU"].push_back(10.57*eV);
energyConstant["PU"].push_back(10.97*eV);
energyConstant["PU"].push_back(12.22*eV);
energyConstant["PU"].push_back(12.92*eV);
energyConstant["PU"].push_back(13.44*eV);
energyConstant["PU"].push_back(15.05*eV);
energyConstant["PU"].push_back(16.56*eV);
energyConstant["PU"].push_back(17.18*eV);
energyConstant["PU"].push_back(17.88*eV);
energyConstant["PU"].push_back(17.90*eV);
energyConstant["PU"].push_back(19.11*eV);
energyConstant["PU"].push_back(20.09*eV);
energyConstant["PU"].push_back(21.70*eV);
energyConstant["PU"].push_back(23.52*eV);
energyConstant["PU"].push_back(24.35*eV);
energyConstant["PU"].push_back(25.41*eV);
energyConstant["PU"].push_back(29.34*eV);
energyConstant["PU"].push_back(32.44*eV);
energyConstant["PU"].push_back(33.67*eV);
energyConstant["PU"].push_back(36.26*eV);
energyConstant["PU"].push_back(38.22*eV);
energyConstant["PU"].push_back(306.53*eV);
energyConstant["PU"].push_back(307.19*eV);
energyConstant["PU"].push_back(307.64*eV);
energyConstant["PU"].push_back(308.14*eV);
energyConstant["PU"].push_back(308.17*eV);
energyConstant["PU"].push_back(423.31*eV);
energyConstant["PU"].push_back(423.43*eV);
energyConstant["PU"].push_back(423.64*eV);
energyConstant["PU"].push_back(423.98*eV);
energyConstant["TMP"].push_back(10.81*eV);
energyConstant["TMP"].push_back(10.81*eV);
energyConstant["TMP"].push_back(12.90*eV);
energyConstant["TMP"].push_back(13.32*eV);
energyConstant["TMP"].push_back(13.32*eV);
energyConstant["TMP"].push_back(13.59*eV);
energyConstant["TMP"].push_back(14.33*eV);
energyConstant["TMP"].push_back(14.33*eV);
energyConstant["TMP"].push_back(15.90*eV);
energyConstant["TMP"].push_back(17.09*eV);
energyConstant["TMP"].push_back(17.09*eV);
energyConstant["TMP"].push_back(17.13*eV);
energyConstant["TMP"].push_back(17.85*eV);
energyConstant["TMP"].push_back(17.85*eV);
energyConstant["TMP"].push_back(18.44*eV);
energyConstant["TMP"].push_back(19.37*eV);
energyConstant["TMP"].push_back(19.37*eV);
energyConstant["TMP"].push_back(21.40*eV);
energyConstant["TMP"].push_back(26.20*eV);
energyConstant["TMP"].push_back(26.20*eV);
energyConstant["TMP"].push_back(27.43*eV);
energyConstant["TMP"].push_back(35.23*eV);
energyConstant["TMP"].push_back(37.67*eV);
energyConstant["TMP"].push_back(37.67*eV);
energyConstant["TMP"].push_back(39.64*eV);
energyConstant["TMP"].push_back(152.42*eV);
energyConstant["TMP"].push_back(152.42*eV);
energyConstant["TMP"].push_back(152.44*eV);
energyConstant["TMP"].push_back(209.59*eV);
energyConstant["TMP"].push_back(306.92*eV);
energyConstant["TMP"].push_back(306.92*eV);
energyConstant["TMP"].push_back(306.92*eV);
energyConstant["TMP"].push_back(557.34*eV);
energyConstant["TMP"].push_back(559.40*eV);
energyConstant["TMP"].push_back(559.40*eV);
energyConstant["TMP"].push_back(559.41*eV);
energyConstant["TMP"].push_back(2178.05*eV);
std::map<G4String, std::vector<G4double> >::iterator it;
for(it=energyConstant.begin();it!=energyConstant.end();it++)
{
nLevels[it->first] = (it->second).size();
}
}
G4DNAPTBIonisationStructure::~G4DNAPTBIonisationStructure()
{ }
G4double G4DNAPTBIonisationStructure::IonisationEnergy(G4int level, const G4String& materialName)
{
G4String matNameModif = ReplaceMaterial(materialName);
// check if the material exist in the map
if(energyConstant.find(matNameModif)==energyConstant.end())
{
std::ostringstream oss;
oss << "Material name was not found in energyConstantMap. Problematic material is: "<<matNameModif;
G4Exception("G4DNAPTBIonisationStructure::IonisationEnergy","em0002",
FatalException, oss.str().c_str());
}
G4double ionisation = 0.;
if (level >=0 && level < nLevels[matNameModif]) ionisation = energyConstant[matNameModif][level];
return ionisation;
}
G4int G4DNAPTBIonisationStructure::NumberOfLevels(const G4String& materialName)
{
G4String matNameModif = ReplaceMaterial(materialName);
// check if the material exist in the map
if(nLevels.find(matNameModif)==nLevels.end())
{
std::ostringstream oss;
oss << "Material name was not found in energyConstantMap. Problematic material is: "<<matNameModif;
G4Exception("G4DNAPTBIonisationStructure::NumberOfLevels","em0002",
FatalException, oss.str().c_str());
}
return nLevels[matNameModif];
}
G4String G4DNAPTBIonisationStructure::ReplaceMaterial(const G4String& materialName)
{
G4String materialNameModified (materialName);
if(materialName=="backbone_THF") materialNameModified = "THF";
else if(materialName=="backbone_TMP") materialNameModified = "TMP";
else if(materialName=="adenine_PU") materialNameModified = "PU";
else if(materialName=="guanine_PU") materialNameModified = "PU";
else if(materialName=="thymine_PY") materialNameModified = "PY";
else if(materialName=="cytosine_PY") materialNameModified = "PY";
return materialNameModified;
}
source/processes/electromagnetic/dna/utils/src/G4PhysChemIO.cc
+283
View File
@@ -0,0 +1,283 @@
/*
* G4PhysChemIO.cc
*
* Created on: 3 févr. 2017
* Author: matkara
*/
#include "G4PhysChemIO.hh"
#include "G4SystemOfUnits.hh"
#include "G4Track.hh"
#include "G4VAnalysisManager.hh"
using namespace std;
//------------------------------------------------------------------------------
namespace G4PhysChemIO{
FormattedText::FormattedText(){
fRunID = -1;
fEventID = -1;
fFileInitialized = false;
}
//------------------------------------------------------------------------------
FormattedText::~FormattedText(){
CloseFile();
}
//------------------------------------------------------------------------------
void FormattedText::InitializeFile()
{
if(fFileInitialized) return;
fOfstream << std::setprecision(6) << std::scientific;
fOfstream << 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;
}
//------------------------------------------------------------------------------
void FormattedText::WriteInto(const G4String& output,
ios_base::openmode mode)
{
fOfstream.open(output.data(), mode);
fFileInitialized = false;
}
//------------------------------------------------------------------------------
void FormattedText::AddEmptyLineInOuputFile()
{
if(fFileInitialized) fOfstream << G4endl;
}
//------------------------------------------------------------------------------
void FormattedText::CloseFile()
{
if (fFileInitialized == false) return;
if (fOfstream.is_open())
{
fOfstream.close();
}
}
//------------------------------------------------------------------------------
void FormattedText::CreateWaterMolecule(G4int modification,
G4int electronicLevel,
G4double energy,
const G4Track* theIncomingTrack)
{
if(!fFileInitialized) InitializeFile();
fOfstream << 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;
}
//------------------------------------------------------------------------------
void FormattedText::CreateSolvatedElectron(const G4Track* theIncomingTrack,
G4ThreeVector* finalPosition)
{
if(!fFileInitialized) InitializeFile();
fOfstream << 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)
{
fOfstream << setw(14) << (finalPosition->x()) / nanometer << setw(14)
<< (finalPosition->y()) / nanometer << setw(14)
<< (finalPosition->z()) / nanometer;
}
fOfstream << G4endl;
}
//------------------------------------------------------------------------------
//
// Using G4analysis
//
G4Analysis::G4Analysis(G4VAnalysisManager* analysisManager):
fpAnalysisManager(analysisManager)
{
fFileInitialized = false;
fNtupleID = -1;
}
//------------------------------------------------------------------------------
G4Analysis::~G4Analysis()
{
fpAnalysisManager = 0;
}
//------------------------------------------------------------------------------
void G4Analysis::InitializeFile()
{
if (fFileInitialized) return;
fNtupleID = fpAnalysisManager->CreateNtuple("PhysChem","PhysChem");
fpAnalysisManager->CreateNtupleIColumn(fNtupleID, "ParentID");
fpAnalysisManager->CreateNtupleSColumn(fNtupleID, "Molecule");
//----------------------------------------------------------------------------
// valid for H2O only
fpAnalysisManager->CreateNtupleIColumn(fNtupleID, "ElectronicModif");
// ionization = 0 / excitation = 1 / diss att = 2
fpAnalysisManager->CreateNtupleIColumn(fNtupleID, "level");
// valid for ion and exc only
fpAnalysisManager->CreateNtupleDColumn(fNtupleID, "Energy_eV");
// valid for ion and exc only
//----------------------------------------------------------------------------
fpAnalysisManager->CreateNtupleDColumn(fNtupleID, "x_parent_nm");
fpAnalysisManager->CreateNtupleDColumn(fNtupleID, "y_parent_nm");
fpAnalysisManager->CreateNtupleDColumn(fNtupleID, "z_parent_nm");
fpAnalysisManager->CreateNtupleDColumn(fNtupleID, "x_nm");
fpAnalysisManager->CreateNtupleDColumn(fNtupleID, "y_nm");
fpAnalysisManager->CreateNtupleDColumn(fNtupleID, "z_nm");
fpAnalysisManager->FinishNtuple(fNtupleID);
fFileInitialized = true;
}
//------------------------------------------------------------------------------
void G4Analysis::WriteInto(const G4String& output,
ios_base::openmode)
{
fpAnalysisManager->OpenFile(output);
fFileInitialized = false;
}
//------------------------------------------------------------------------------
void G4Analysis::CloseFile()
{
// fpAnalysisManager->Write();
// fpAnalysisManager->CloseFile();
}
//------------------------------------------------------------------------------
void G4Analysis::CreateWaterMolecule(G4int modification,
G4int electronicLevel,
G4double energy,
const G4Track* theIncomingTrack)
{
if(!fFileInitialized) InitializeFile();
// parent ID
fpAnalysisManager->FillNtupleIColumn(fNtupleID, 0,
theIncomingTrack->GetTrackID());
// molecule type
fpAnalysisManager->FillNtupleSColumn(fNtupleID, 1, "H2O");
//----------------------------------------------------------------------------
// valid for H2O only
// electronic modif
fpAnalysisManager->FillNtupleIColumn(fNtupleID, 2, modification);
// ionization = 0 / excitation = 1 / diss att = 2
fpAnalysisManager->FillNtupleIColumn(fNtupleID, 3, electronicLevel);
fpAnalysisManager->FillNtupleDColumn(fNtupleID, 4, energy / eV);
//----------------------------------------------------------------------------
const G4ThreeVector& parentPos = theIncomingTrack->GetPosition();
fpAnalysisManager->FillNtupleDColumn(fNtupleID,5,(parentPos.x())/nanometer);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,6,(parentPos.y())/nanometer);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,7,(parentPos.z())/nanometer);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,8,(parentPos.x())/nanometer);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,9,(parentPos.y())/nanometer);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,10,(parentPos.z())/nanometer);
fpAnalysisManager->AddNtupleRow(fNtupleID);
}
//------------------------------------------------------------------------------
void G4Analysis::CreateSolvatedElectron(const G4Track* electronTrack,
G4ThreeVector* finalPosition)
{
if(!fFileInitialized) InitializeFile();
// parent ID
fpAnalysisManager->FillNtupleIColumn(fNtupleID, 0,
electronTrack->GetTrackID());
// molecule type
fpAnalysisManager->FillNtupleSColumn(fNtupleID, 1, "e_aq");
//----------------------------------------------------------------------------
// valid for H2O only
// electronic modif
fpAnalysisManager->FillNtupleIColumn(fNtupleID, 2, -1); // electronic modif
fpAnalysisManager->FillNtupleIColumn(fNtupleID, 3, -1); // electronic level
fpAnalysisManager->FillNtupleDColumn(fNtupleID, 4,
electronTrack->GetKineticEnergy() / eV);
//----------------------------------------------------------------------------
const G4ThreeVector& parentPos = electronTrack->GetPosition();
const double i_nm = 1./nanometer;
fpAnalysisManager->FillNtupleDColumn(fNtupleID,5, parentPos.x() *i_nm);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,6, parentPos.y() *i_nm);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,7, parentPos.z() *i_nm);
if (finalPosition != 0)
{
fpAnalysisManager->FillNtupleDColumn(fNtupleID,8, finalPosition->x()*i_nm);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,9, finalPosition->y()*i_nm);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,10, finalPosition->z()*i_nm);
}
else
{
fpAnalysisManager->FillNtupleDColumn(fNtupleID,8, parentPos.x() *i_nm);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,9, parentPos.y() *i_nm);
fpAnalysisManager->FillNtupleDColumn(fNtupleID,10, parentPos.z() *i_nm);
}
fpAnalysisManager->AddNtupleRow(fNtupleID);
}
}
source/processes/electromagnetic/dna/utils/src/G4VPhysChemIO.cc
+20
View File
@@ -0,0 +1,20 @@
/*
* G4VPhysChemIO.cc
*
* Created on: 3 févr. 2017
* Author: matkara
*/
#include "G4VPhysChemIO.hh"
//------------------------------------------------------------------------------
G4VPhysChemIO::G4VPhysChemIO()
{
}
//------------------------------------------------------------------------------
G4VPhysChemIO::~G4VPhysChemIO()
{
}