Geant4 10.7.0
Toolkit for the simulation of the passage of particles through matter
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Public Member Functions | List of all members
G4EmDNAChemistry_option2 Class Reference

#include <G4EmDNAChemistry_option2.hh>

+ Inheritance diagram for G4EmDNAChemistry_option2:

Public Member Functions

 G4EmDNAChemistry_option2 ()
 
virtual ~G4EmDNAChemistry_option2 () override
 
void ConstructParticle () override
 
void ConstructMolecule () override
 
void ConstructProcess () override
 
void ConstructDissociationChannels () override
 
void ConstructReactionTable (G4DNAMolecularReactionTable *pTable) override
 
void ConstructTimeStepModel (G4DNAMolecularReactionTable *pTable) override
 
- Public Member Functions inherited from G4VUserChemistryList
 G4VUserChemistryList (bool flag=true)
 
virtual ~G4VUserChemistryList ()
 
bool IsPhysicsConstructor ()
 
void ThisIsAPhysicsConstructor (bool flag=true)
 
virtual void ConstructMolecule ()
 
virtual void ConstructProcess ()
 
virtual void ConstructDissociationChannels ()
 
virtual void ConstructReactionTable (G4DNAMolecularReactionTable *reactionTable)=0
 
virtual void ConstructTimeStepModel (G4DNAMolecularReactionTable *reactionTable)=0
 
void BuildPhysicsTable ()
 
- Public Member Functions inherited from G4VPhysicsConstructor
 G4VPhysicsConstructor (const G4String &="")
 
 G4VPhysicsConstructor (const G4String &name, G4int physics_type)
 
virtual ~G4VPhysicsConstructor ()
 
virtual void ConstructParticle ()=0
 
virtual void ConstructProcess ()=0
 
void SetPhysicsName (const G4String &="")
 
const G4String & GetPhysicsName () const
 
void SetPhysicsType (G4int)
 
G4int GetPhysicsType () const
 
void SetVerboseLevel (G4int value)
 
G4int GetVerboseLevel () const
 
G4int GetInstanceID () const
 
virtual void TerminateWorker ()
 

Additional Inherited Members

- Static Public Member Functions inherited from G4VPhysicsConstructor
static const G4VPCManager & GetSubInstanceManager ()
 
- Protected Types inherited from G4VPhysicsConstructor
using PhysicsBuilder_V = G4VPCData::PhysicsBuilders_V
 
- Protected Member Functions inherited from G4VUserChemistryList
void RegisterTimeStepModel (G4VITStepModel *timeStepModel, double startingTime=0)
 
void BuildPhysicsTable (G4MoleculeDefinition *)
 
- Protected Member Functions inherited from G4VPhysicsConstructor
G4bool RegisterProcess (G4VProcess *process, G4ParticleDefinition *particle)
 
G4ParticleTable::G4PTblDicIterator * GetParticleIterator () const
 
PhysicsBuilder_V GetBuilders () const
 
void AddBuilder (G4PhysicsBuilderInterface *bld)
 
- Protected Attributes inherited from G4VUserChemistryList
int verboseLevel
 
bool fIsPhysicsConstructor
 
- Protected Attributes inherited from G4VPhysicsConstructor
G4int verboseLevel
 
G4String namePhysics
 
G4int typePhysics
 
G4ParticleTable * theParticleTable
 
G4int g4vpcInstanceID
 
- Static Protected Attributes inherited from G4VPhysicsConstructor
static G4RUN_DLL G4VPCManager subInstanceManager
 

Detailed Description

Definition at line 37 of file G4EmDNAChemistry_option2.hh.

Constructor & Destructor Documentation

◆ G4EmDNAChemistry_option2()

G4EmDNAChemistry_option2::G4EmDNAChemistry_option2 ( )

Definition at line 63 of file G4EmDNAChemistry_option2.cc.

64 : G4VUserChemistryList(true)
65{
66 G4DNAChemistryManager::Instance()->SetChemistryList(this);
67}
G4DNAChemistryManager::Instance
static G4DNAChemistryManager * Instance()
Definition: G4DNAChemistryManager.cc:132
G4DNAChemistryManager::SetChemistryList
void SetChemistryList(G4VUserChemistryList &)
Definition: G4DNAChemistryManager.cc:714

◆ ~G4EmDNAChemistry_option2()

G4EmDNAChemistry_option2::~G4EmDNAChemistry_option2 ( )
overridevirtual

Definition at line 71 of file G4EmDNAChemistry_option2.cc.

72{}

Member Function Documentation

◆ ConstructDissociationChannels()

void G4EmDNAChemistry_option2::ConstructDissociationChannels ( )
overridevirtual

Reimplemented from G4VUserChemistryList.

Definition at line 162 of file G4EmDNAChemistry_option2.cc.

163{
164//-----------------------------------
165//Get the molecular configuration
166 G4MolecularConfiguration* OH =
167 G4MoleculeTable::Instance()->GetConfiguration("OH");
168 G4MolecularConfiguration* OHm =
169 G4MoleculeTable::Instance()->GetConfiguration("OHm");
170 G4MolecularConfiguration* e_aq =
171 G4MoleculeTable::Instance()->GetConfiguration("e_aq");
172 G4MolecularConfiguration* H2 =
173 G4MoleculeTable::Instance()->GetConfiguration("H2");
174 G4MolecularConfiguration* H3O =
175 G4MoleculeTable::Instance()->GetConfiguration("H3Op");
176 G4MolecularConfiguration* H =
177 G4MoleculeTable::Instance()->GetConfiguration("H");
178
179//-------------------------------------
180//Define the decay channels
181 G4MoleculeDefinition* water = G4H2O::Definition();
182 G4MolecularDissociationChannel* decCh1;
183 G4MolecularDissociationChannel* decCh2;
184
185 G4ElectronOccupancy* occ = new G4ElectronOccupancy(
186 *(water->GetGroundStateElectronOccupancy()));
187
188//////////////////////////////////////////////////////////
189// EXCITATIONS //
190//////////////////////////////////////////////////////////
191 G4DNAWaterExcitationStructure waterExcitation;
192//--------------------------------------------------------
193//---------------Excitation on the fifth layer------------
194
195 decCh1 = new G4MolecularDissociationChannel(
196 "A^1B_1_Relaxation");
197 decCh2 = new G4MolecularDissociationChannel(
198 "A^1B_1_DissociativeDecay");
199
200//Decay 1 : OH + H
201 decCh1->SetEnergy(waterExcitation.ExcitationEnergy(0));
202 decCh1->SetProbability(0.35);
203 decCh1->SetDisplacementType(
204 G4DNAWaterDissociationDisplacer::NoDisplacement);
205
206 decCh2->AddProduct(OH);
207 decCh2->AddProduct(H);
208 decCh2->SetProbability(0.65);
209 decCh2->SetDisplacementType(
210 G4DNAWaterDissociationDisplacer::A1B1_DissociationDecay);
211
212// water->AddExcitedState("A^1B_1");
213// this is the transition form ground state to
214 occ->RemoveElectron(4, 1);
215// the first unoccupied orbital: A^1B_1
216 occ->AddElectron(5, 1);
217
218 water->NewConfigurationWithElectronOccupancy("A^1B_1", *occ);
219 water->AddDecayChannel("A^1B_1", decCh1);
220 water->AddDecayChannel("A^1B_1", decCh2);
221
222//--------------------------------------------------------
223//---------------Excitation on the fourth layer-----------
224 decCh1 = new G4MolecularDissociationChannel(
225 "B^1A_1_Relaxation_Channel");
226 decCh2 = new G4MolecularDissociationChannel(
227 "B^1A_1_DissociativeDecay");
228 G4MolecularDissociationChannel* decCh3 =
229 new G4MolecularDissociationChannel("B^1A_1_AutoIonisation_Channel");
230
231//Decay 1 : energy
232 decCh1->SetEnergy(waterExcitation.ExcitationEnergy(1));
233 decCh1->SetProbability(0.3);
234
235//Decay 2 : 2OH + H_2
236 decCh2->AddProduct(H2);
237 decCh2->AddProduct(OH);
238 decCh2->AddProduct(OH);
239 decCh2->SetProbability(0.15);
240 decCh2->SetDisplacementType(
241 G4DNAWaterDissociationDisplacer::B1A1_DissociationDecay);
242
243//Decay 3 : OH + H_3Op + e_aq
244 decCh3->AddProduct(OH);
245 decCh3->AddProduct(H3O);
246 decCh3->AddProduct(e_aq);
247 decCh3->SetProbability(0.55);
248 decCh3->SetDisplacementType(
249 G4DNAWaterDissociationDisplacer::AutoIonisation);
250
251 *occ = *(water->GetGroundStateElectronOccupancy());
252 occ->RemoveElectron(3); // this is the transition form ground state to
253 occ->AddElectron(5, 1); // the first unoccupied orbital: B^1A_1
254
255 water->NewConfigurationWithElectronOccupancy("B^1A_1", *occ);
256 water->AddDecayChannel("B^1A_1", decCh1);
257 water->AddDecayChannel("B^1A_1", decCh2);
258 water->AddDecayChannel("B^1A_1", decCh3);
259
260//-------------------------------------------------------
261//-------------------Excitation of 3rd layer-----------------
262 decCh1 = new G4MolecularDissociationChannel(
263 "Excitation3rdLayer_AutoIonisation_Channel");
264 decCh2 = new G4MolecularDissociationChannel(
265 "Excitation3rdLayer_Relaxation_Channel");
266
267//Decay channel 1 : : OH + H_3Op + e_aq
268 decCh1->AddProduct(OH);
269 decCh1->AddProduct(H3O);
270 decCh1->AddProduct(e_aq);
271
272 decCh1->SetProbability(0.5);
273 decCh1->SetDisplacementType(
274 G4DNAWaterDissociationDisplacer::AutoIonisation);
275
276//Decay channel 2 : energy
277 decCh2->SetEnergy(waterExcitation.ExcitationEnergy(2));
278 decCh2->SetProbability(0.5);
279
280//Electronic configuration of this decay
281 *occ = *(water->GetGroundStateElectronOccupancy());
282 occ->RemoveElectron(2, 1);
283 occ->AddElectron(5, 1);
284
285//Configure the water molecule
286 water->NewConfigurationWithElectronOccupancy(
287 "Excitation3rdLayer", *occ);
288 water->AddDecayChannel("Excitation3rdLayer", decCh1);
289 water->AddDecayChannel("Excitation3rdLayer", decCh2);
290
291//-------------------------------------------------------
292//-------------------Excitation of 2nd layer-----------------
293 decCh1 = new G4MolecularDissociationChannel(
294 "Excitation2ndLayer_AutoIonisation_Channel");
295 decCh2 = new G4MolecularDissociationChannel(
296 "Excitation2ndLayer_Relaxation_Channel");
297
298//Decay Channel 1 : : OH + H_3Op + e_aq
299 decCh1->AddProduct(OH);
300 decCh1->AddProduct(H3O);
301 decCh1->AddProduct(e_aq);
302
303 decCh1->SetProbability(0.5);
304 decCh1->SetDisplacementType(
305 G4DNAWaterDissociationDisplacer::AutoIonisation);
306
307//Decay channel 2 : energy
308 decCh2->SetEnergy(waterExcitation.ExcitationEnergy(3));
309 decCh2->SetProbability(0.5);
310
311 *occ = *(water->GetGroundStateElectronOccupancy());
312 occ->RemoveElectron(1, 1);
313 occ->AddElectron(5, 1);
314
315 water->NewConfigurationWithElectronOccupancy(
316 "Excitation2ndLayer", *occ);
317 water->AddDecayChannel("Excitation2ndLayer", decCh1);
318 water->AddDecayChannel("Excitation2ndLayer", decCh2);
319
320//-------------------------------------------------------
321//-------------------Excitation of 1st layer-----------------
322 decCh1 = new G4MolecularDissociationChannel(
323 "Excitation1stLayer_AutoIonisation_Channel");
324 decCh2 = new G4MolecularDissociationChannel(
325 "Excitation1stLayer_Relaxation_Channel");
326
327 *occ = *(water->GetGroundStateElectronOccupancy());
328 occ->RemoveElectron(0, 1);
329 occ->AddElectron(5, 1);
330
331//Decay Channel 1 : : OH + H_3Op + e_aq
332 decCh1->AddProduct(OH);
333 decCh1->AddProduct(H3O);
334 decCh1->AddProduct(e_aq);
335 decCh1->SetProbability(0.5);
336 decCh1->SetDisplacementType(
337 G4DNAWaterDissociationDisplacer::AutoIonisation);
338
339//Decay channel 2 : energy
340 decCh2->SetEnergy(waterExcitation.ExcitationEnergy(4));
341 decCh2->SetProbability(0.5);
342
343 water->NewConfigurationWithElectronOccupancy(
344 "Excitation1stLayer", *occ);
345 water->AddDecayChannel("Excitation1stLayer", decCh1);
346 water->AddDecayChannel("Excitation1stLayer", decCh2);
347
348/////////////////////////////////////////////////////////
349// IONISATION //
350/////////////////////////////////////////////////////////
351//--------------------------------------------------------
352//------------------- Ionisation -------------------------
353
354 decCh1 = new G4MolecularDissociationChannel("Ionisation_Channel");
355
356//Decay Channel 1 : : OH + H_3Op
357 decCh1->AddProduct(H3O);
358 decCh1->AddProduct(OH);
359 decCh1->SetProbability(1);
360 decCh1->SetDisplacementType(
361 G4DNAWaterDissociationDisplacer::Ionisation_DissociationDecay);
362
363 *occ = *(water->GetGroundStateElectronOccupancy());
364 occ->RemoveElectron(4, 1);
365// this is a ionized h2O with a hole in its last orbital
366 water->NewConfigurationWithElectronOccupancy("Ionisation5", *occ);
367 water->AddDecayChannel("Ionisation5", decCh1);
368
369 *occ = *(water->GetGroundStateElectronOccupancy());
370 occ->RemoveElectron(3, 1);
371 water->NewConfigurationWithElectronOccupancy("Ionisation4", *occ);
372 water->AddDecayChannel("Ionisation4",
373 new G4MolecularDissociationChannel(*decCh1));
374
375 *occ = *(water->GetGroundStateElectronOccupancy());
376 occ->RemoveElectron(2, 1);
377 water->NewConfigurationWithElectronOccupancy("Ionisation3", *occ);
378 water->AddDecayChannel("Ionisation3",
379 new G4MolecularDissociationChannel(*decCh1));
380
381 *occ = *(water->GetGroundStateElectronOccupancy());
382 occ->RemoveElectron(1, 1);
383 water->NewConfigurationWithElectronOccupancy("Ionisation2", *occ);
384 water->AddDecayChannel("Ionisation2",
385 new G4MolecularDissociationChannel(*decCh1));
386
387 *occ = *(water->GetGroundStateElectronOccupancy());
388 occ->RemoveElectron(0, 1);
389 water->NewConfigurationWithElectronOccupancy("Ionisation1", *occ);
390 water->AddDecayChannel("Ionisation1",
391 new G4MolecularDissociationChannel(*decCh1));
392
393//////////////////////////////////////////////////////////
394// Dissociative Attachment //
395//////////////////////////////////////////////////////////
396 decCh1 = new G4MolecularDissociationChannel(
397 "DissociativeAttachment");
398
399//Decay 1 : 2OH + H_2
400 decCh1->AddProduct(H2);
401 decCh1->AddProduct(OHm);
402 decCh1->AddProduct(OH);
403 decCh1->SetProbability(1);
404 decCh1->SetDisplacementType(
405 G4DNAWaterDissociationDisplacer::DissociativeAttachment);
406
407 *occ = *(water->GetGroundStateElectronOccupancy());
408 occ->AddElectron(5, 1); // H_2O^-
409 water->NewConfigurationWithElectronOccupancy(
410 "DissociativeAttachment", *occ);
411 water->AddDecayChannel(
412 "DissociativeAttachment", decCh1);
413
414 delete occ;
415}
G4ElectronOccupancy::AddElectron
G4int AddElectron(G4int orbit, G4int number=1)
Definition: G4ElectronOccupancy.cc:139
G4ElectronOccupancy::RemoveElectron
G4int RemoveElectron(G4int orbit, G4int number=1)
Definition: G4ElectronOccupancy.cc:161
G4H2O::Definition
static G4H2O * Definition()
Definition: G4H2O.cc:42
G4MolecularDissociationChannel::AddProduct
void AddProduct(Product *, G4double displacement=0.)
Definition: G4MolecularDissociationChannel.cc:60
G4MoleculeDefinition::GetGroundStateElectronOccupancy
const G4ElectronOccupancy * GetGroundStateElectronOccupancy() const
Definition: G4MoleculeDefinition.hh:240
G4MoleculeDefinition::AddDecayChannel
void AddDecayChannel(const G4MolecularConfiguration *molConf, const G4MolecularDissociationChannel *channel)
Definition: G4MoleculeDefinition.cc:223
G4MoleculeDefinition::NewConfigurationWithElectronOccupancy
G4MolecularConfiguration * NewConfigurationWithElectronOccupancy(const G4String &excitedStateLabel, const G4ElectronOccupancy &, double decayTime=0.)
Definition: G4MoleculeDefinition.cc:170
G4MoleculeTable::GetConfiguration
G4MolecularConfiguration * GetConfiguration(const G4String &, bool mustExist=true)
Definition: G4MoleculeTable.cc:105
G4MoleculeTable::Instance
static G4MoleculeTable * Instance()
Definition: G4MoleculeTable.cc:53

◆ ConstructMolecule()

void G4EmDNAChemistry_option2::ConstructMolecule ( )
overridevirtual

Reimplemented from G4VUserChemistryList.

Definition at line 76 of file G4EmDNAChemistry_option2.cc.

77{
78 //-----------------------------------
79 G4Electron::Definition(); // safety
80 //-----------------------------------
81 G4H2O::Definition();
82 G4Hydrogen::Definition();
83 G4H3O::Definition();
84 G4OH::Definition();
85 G4Electron_aq::Definition();
86 G4H2O2::Definition();
87 G4H2::Definition();
88 G4Deoxyribose::Definition();
89 G4Phosphate::Definition();
90 G4Adenine::Definition();
91 G4Guanine::Definition();
92 G4Thymine::Definition();
93 G4Cytosine::Definition();
94 G4Histone::Definition();
95//damaged molecules
96 G4DamagedDeoxyribose::Definition();
97 G4DamagedAdenine::Definition();
98 G4DamagedGuanine::Definition();
99 G4DamagedThymine::Definition();
100 G4DamagedCytosine::Definition();
101 G4ModifiedHistone::Definition();
102
103//_________________species___________________________________________________________
104
105 G4MoleculeTable::Instance()->
106 CreateConfiguration("H3Op", G4H3O::Definition());
107 G4MolecularConfiguration* OHm = G4MoleculeTable::Instance()->
108 CreateConfiguration("OHm",
109 G4OH::Definition(),
110 -1, // charge
111 5.0e-9 * (m2 / s));
112 OHm->SetMass(17.0079 * g / Avogadro * c_squared);
113 G4MoleculeTable::Instance()->
114 CreateConfiguration("OH", G4OH::Definition());
115 G4MoleculeTable::Instance()->
116 CreateConfiguration("e_aq",G4Electron_aq::Definition());
117 G4MoleculeTable::Instance()->
118 CreateConfiguration("H",G4Hydrogen::Definition());
119 G4MoleculeTable::Instance()->
120 CreateConfiguration("H2", G4H2::Definition());
121 G4MoleculeTable::Instance()->
122 CreateConfiguration("H2O2", G4H2O2::Definition());
123
124//________________DNA_______________________________________________
125
126 G4MoleculeTable::Instance()->
127 CreateConfiguration("Deoxyribose",G4Deoxyribose::Definition());
128 G4MoleculeTable::Instance()->
129 CreateConfiguration("Phosphate",G4Phosphate::Definition());
130 G4MoleculeTable::Instance()->
131 CreateConfiguration("Adenine",G4Adenine::Definition());
132 G4MoleculeTable::Instance()->
133 CreateConfiguration("Thymine",G4Thymine::Definition());
134 G4MoleculeTable::Instance()->
135 CreateConfiguration("Guanine",G4Guanine::Definition());
136 G4MoleculeTable::Instance()->
137 CreateConfiguration("Cytosine",G4Cytosine::Definition());
138 G4MoleculeTable::Instance()->
139 CreateConfiguration("Histone",G4Histone::Definition());
140
141//damaged DNAElement Configuration
142
143 G4MoleculeTable::Instance()->
144 CreateConfiguration("Damaged_Deoxyribose",
145 G4DamagedDeoxyribose::Definition());
146 G4MoleculeTable::Instance()->
147 CreateConfiguration("Damaged_Adenine",
148 G4DamagedAdenine::Definition());
149 G4MoleculeTable::Instance()->
150 CreateConfiguration("Damaged_Thymine",
151 G4DamagedThymine::Definition());
152 G4MoleculeTable::Instance()->
153 CreateConfiguration("Damaged_Guanine",
154 G4DamagedGuanine::Definition());
155 G4MoleculeTable::Instance()->
156 CreateConfiguration("Damaged_Cytosine",
157 G4DamagedCytosine::Definition());
158}
G4Adenine::Definition
static G4Adenine * Definition()
Definition: G4DNAMolecule.cc:225
G4Cytosine::Definition
static G4Cytosine * Definition()
Definition: G4DNAMolecule.cc:305
G4DamagedAdenine::Definition
static G4DamagedAdenine * Definition()
Definition: G4DNAMolecule.cc:66
G4DamagedCytosine::Definition
static G4DamagedCytosine * Definition()
Definition: G4DNAMolecule.cc:146
G4DamagedDeoxyribose::Definition
static G4DamagedDeoxyribose * Definition()
Definition: G4DNAMolecule.cc:39
G4DamagedGuanine::Definition
static G4DamagedGuanine * Definition()
Definition: G4DNAMolecule.cc:93
G4DamagedThymine::Definition
static G4DamagedThymine * Definition()
Definition: G4DNAMolecule.cc:119
G4Deoxyribose::Definition
static G4Deoxyribose * Definition()
Definition: G4DNAMolecule.cc:173
G4Electron_aq::Definition
static G4Electron_aq * Definition()
Definition: G4Electron_aq.cc:45
G4Electron::Definition
static G4Electron * Definition()
Definition: G4Electron.cc:48
G4Guanine::Definition
static G4Guanine * Definition()
Definition: G4DNAMolecule.cc:251
G4H2O2::Definition
static G4H2O2 * Definition()
Definition: G4H2O2.cc:45
G4H2::Definition
static G4H2 * Definition()
Definition: G4H2.cc:45
G4H3O::Definition
static G4H3O * Definition()
Definition: G4H3O.cc:46
G4Histone::Definition
static G4Histone * Definition()
Definition: G4DNAMolecule.cc:358
G4Hydrogen::Definition
static G4Hydrogen * Definition()
Definition: G4Hydrogen.cc:45
G4ModifiedHistone::Definition
static G4ModifiedHistone * Definition()
Definition: G4DNAMolecule.cc:331
G4OH::Definition
static G4OH * Definition()
Definition: G4OH.cc:45
G4Phosphate::Definition
static G4Phosphate * Definition()
Definition: G4DNAMolecule.cc:199
G4Thymine::Definition
static G4Thymine * Definition()
Definition: G4DNAMolecule.cc:279

Referenced by ConstructParticle().

◆ ConstructParticle()

void G4EmDNAChemistry_option2::ConstructParticle ( )
inlineoverridevirtual

Implements G4VPhysicsConstructor.

Definition at line 45 of file G4EmDNAChemistry_option2.hh.

46 {
47 ConstructMolecule();
48 }
G4EmDNAChemistry_option2::ConstructMolecule
void ConstructMolecule() override
Definition: G4EmDNAChemistry_option2.cc:76

◆ ConstructProcess()

void G4EmDNAChemistry_option2::ConstructProcess ( )
overridevirtual

Reimplemented from G4VUserChemistryList.

Definition at line 669 of file G4EmDNAChemistry_option2.cc.

670{
671 auto pPhysicsListHelper =
672 G4PhysicsListHelper::GetPhysicsListHelper();
673 G4VProcess* pProcess =
674 G4ProcessTable::GetProcessTable()->
675 FindProcess("e-_G4DNAVibExcitation", "e-");
676
677 if (pProcess != nullptr)
678 {
679 G4DNAVibExcitation* pVibExcitation =
680 (G4DNAVibExcitation*) pProcess;
681 G4VEmModel* pModel = pVibExcitation->EmModel();
682 G4DNASancheExcitationModel* pSancheExcitationMod =
683 dynamic_cast<G4DNASancheExcitationModel*>(pModel);
684 if(pSancheExcitationMod != nullptr)
685 {
686 pSancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
687 }
688 }
689
690//===============================================================
691// Electron Solvatation
692//
693 pProcess = G4ProcessTable::GetProcessTable()->
694 FindProcess("e-_G4DNAElectronSolvation", "e-");
695
696 if (pProcess == nullptr)
697 {
698 pPhysicsListHelper->
699 RegisterProcess(new G4DNAElectronSolvation(
700 "e-_G4DNAElectronSolvation"), G4Electron::Definition());
701 }
702
703//===============================================================
704// Define processes for molecules
705//
706 G4MoleculeTable* pMoleculeTable =
707 G4MoleculeTable::Instance();
708 G4MoleculeDefinitionIterator iterator =
709 pMoleculeTable->GetDefintionIterator();
710 iterator.reset();
711 while (iterator())
712 {
713 G4MoleculeDefinition* pMoleculeDef = iterator.value();
714
715 if(pMoleculeDef != G4H2O::Definition())
716 {
717 G4DNABrownianTransportation* pBrownianTransport =
718 new G4DNABrownianTransportation();
719 pPhysicsListHelper->
720 RegisterProcess(pBrownianTransport, pMoleculeDef);
721 }
722 else
723 {
724 pMoleculeDef->GetProcessManager()->
725 AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
726 G4DNAMolecularDissociation* pDissociationProcess =
727 new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
728 pDissociationProcess->SetDisplacer(pMoleculeDef,
729 new G4DNAWaterDissociationDisplacer);
730 pDissociationProcess->SetVerboseLevel(1);
731
732 pMoleculeDef->GetProcessManager()->
733 AddRestProcess(pDissociationProcess, 1);
734 }
735 }
736 G4DNAChemistryManager::Instance()->Initialize();
737}
G4DNAMolecularDissociation::SetDisplacer
void SetDisplacer(Species *, Displacer *)
Definition: G4DNAMolecularDissociation.cc:284
G4MoleculeTable::GetDefintionIterator
G4MoleculeDefinitionIterator GetDefintionIterator()
Definition: G4MoleculeTable.hh:116
G4ParticleDefinition::GetProcessManager
G4ProcessManager * GetProcessManager() const
Definition: G4ParticleDefinition.cc:237
G4PhysicsListHelper::GetPhysicsListHelper
static G4PhysicsListHelper * GetPhysicsListHelper()
Definition: G4PhysicsListHelper.cc:92
G4ProcessTable::GetProcessTable
static G4ProcessTable * GetProcessTable()
Definition: G4ProcessTable.cc:108
G4VEmProcess::EmModel
G4VEmModel * EmModel(size_t index=0) const
Definition: G4VEmProcess.cc:211
G4VPhysicsConstructor::RegisterProcess
G4bool RegisterProcess(G4VProcess *process, G4ParticleDefinition *particle)
Definition: G4VPhysicsConstructor.hh:222
G4VProcess::SetVerboseLevel
void SetVerboseLevel(G4int value)
Definition: G4VProcess.hh:412

◆ ConstructReactionTable()

void G4EmDNAChemistry_option2::ConstructReactionTable ( G4DNAMolecularReactionTable *  pTable)
overridevirtual

Implements G4VUserChemistryList.

Definition at line 419 of file G4EmDNAChemistry_option2.cc.

421{
422//-----------------------------------
423//Get the molecular configuration
424 G4MolecularConfiguration* OH =
425 G4MoleculeTable::Instance()->GetConfiguration("OH");
426 G4MolecularConfiguration* OHm =
427 G4MoleculeTable::Instance()->GetConfiguration("OHm");
428 G4MolecularConfiguration* e_aq =
429 G4MoleculeTable::Instance()->GetConfiguration("e_aq");
430 G4MolecularConfiguration* H2 =
431 G4MoleculeTable::Instance()->GetConfiguration("H2");
432 G4MolecularConfiguration* H3Op =
433 G4MoleculeTable::Instance()->GetConfiguration("H3Op");
434 G4MolecularConfiguration* H =
435 G4MoleculeTable::Instance()->GetConfiguration("H");
436 G4MolecularConfiguration* H2O2 =
437 G4MoleculeTable::Instance()->GetConfiguration("H2O2");
438
439 G4MolecularConfiguration* deoxyribose =
440 G4MoleculeTable::Instance()->GetConfiguration("Deoxyribose");
441 G4MolecularConfiguration* adenine =
442 G4MoleculeTable::Instance()->GetConfiguration("Adenine");
443 G4MolecularConfiguration* guanine =
444 G4MoleculeTable::Instance()->GetConfiguration("Guanine");
445 G4MolecularConfiguration* thymine =
446 G4MoleculeTable::Instance()->GetConfiguration("Thymine");
447 G4MolecularConfiguration* cytosine =
448 G4MoleculeTable::Instance()->GetConfiguration("Cytosine");
449 G4MolecularConfiguration* histone =
450 G4MoleculeTable::Instance()->GetConfiguration("Histone");
451
452 G4MolecularConfiguration* damage_deoxyribose =
453 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Deoxyribose");
454 G4MolecularConfiguration* damage_adenine =
455 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Adenine");
456 G4MolecularConfiguration* damage_guanine =
457 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Guanine");
458 G4MolecularConfiguration* damage_thymine =
459 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Thymine");
460 G4MolecularConfiguration* damage_cytosine =
461 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Cytosine");
462
463//------------------------------------------------------------------
464// e_aq + e_aq + 2H2O -> H2 + 2OH-
465 G4DNAMolecularReactionData* reactionData =
466 new G4DNAMolecularReactionData(
467 0.5e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
468 reactionData->AddProduct(OHm);
469 reactionData->AddProduct(OHm);
470 reactionData->AddProduct(H2);
471 theReactionTable->SetReaction(reactionData);
472//------------------------------------------------------------------
473// e_aq + *OH -> OH-
474 reactionData = new G4DNAMolecularReactionData(
475 2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
476 reactionData->AddProduct(OHm);
477 theReactionTable->SetReaction(reactionData);
478//------------------------------------------------------------------
479// e_aq + H* + H2O -> H2 + OH-
480 reactionData = new G4DNAMolecularReactionData(
481 2.65e10 * (1e-3 * m3 / (mole * s)), e_aq, H);
482 reactionData->AddProduct(OHm);
483 reactionData->AddProduct(H2);
484 theReactionTable->SetReaction(reactionData);
485//------------------------------------------------------------------
486// e_aq + H3O+ -> H* + H2O
487 reactionData = new G4DNAMolecularReactionData(
488 2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
489 reactionData->AddProduct(H);
490 theReactionTable->SetReaction(reactionData);
491
492//------------------------------------------------------------------
493// e_aq + H2O2 -> OH- + *OH
494 reactionData = new G4DNAMolecularReactionData(
495 1.41e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
496 reactionData->AddProduct(OHm);
497 reactionData->AddProduct(OH);
498 theReactionTable->SetReaction(reactionData);
499//------------------------------------------------------------------
500// *OH + *OH -> H2O2
501 reactionData = new G4DNAMolecularReactionData(
502 0.44e10 * (1e-3 * m3 / (mole * s)), OH, OH);
503 reactionData->AddProduct(H2O2);
504 theReactionTable->SetReaction(reactionData);
505//------------------------------------------------------------------
506// *OH + *H -> H2O
507 theReactionTable->SetReaction(
508 1.44e10 * (1e-3 * m3 / (mole * s)), OH, H);
509//------------------------------------------------------------------
510// *H + *H -> H2
511 reactionData = new G4DNAMolecularReactionData(
512 1.20e10 * (1e-3 * m3 / (mole * s)), H, H);
513 reactionData->AddProduct(H2);
514 theReactionTable->SetReaction(reactionData);
515//------------------------------------------------------------------
516// H3O+ + OH- -> 2H2O
517 theReactionTable->SetReaction(
518 1.43e11 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
519//------------------------------------------------------------------
520
521// DNA additions
522
523// OH and DNA
524
525// 2-Deoxyribose + OH -> damagedDeoxyribose
526 reactionData = new G4DNAMolecularReactionData(
527 1.80e9*(1e-3*m3/(mole*s)), deoxyribose, OH);
528 reactionData->AddProduct(damage_deoxyribose);
529 theReactionTable->SetReaction(reactionData);
530
531 // adenine + OH -> ...
532 reactionData = new G4DNAMolecularReactionData(
533 6.10e9*(1e-3*m3/(mole*s)), adenine, OH);
534 reactionData->AddProduct(damage_adenine);
535 theReactionTable->SetReaction(reactionData);
536
537 // guanine + OH -> ...
538 reactionData = new G4DNAMolecularReactionData(
539 9.20e9*(1e-3*m3/(mole*s)), guanine, OH);
540 reactionData->AddProduct(damage_guanine);
541 theReactionTable->SetReaction(reactionData);
542
543 // thymine + OH -> ...
544 reactionData = new G4DNAMolecularReactionData(
545 6.40e9*(1e-3*m3/(mole*s)), thymine, OH);
546 reactionData->AddProduct(damage_thymine);
547 theReactionTable->SetReaction(reactionData);
548
549 // cytosine + OH -> ...
550 reactionData = new G4DNAMolecularReactionData(
551 6.10e9*(1e-3*m3/(mole*s)), cytosine, OH);
552 reactionData->AddProduct(damage_cytosine);
553 theReactionTable->SetReaction(reactionData);
554
555 // Hydrated e- and DNA
556
557 // Deoxyribose + Hydrated e- -> ...
558 reactionData = new G4DNAMolecularReactionData(
559 0.01e9*(1e-3*m3/(mole*s)), deoxyribose, e_aq);
560 reactionData->AddProduct(damage_deoxyribose);
561 theReactionTable->SetReaction(reactionData);
562
563 // adenine + Hydrated e- -> ...
564 reactionData = new G4DNAMolecularReactionData(
565 9e9*(1e-3*m3/(mole*s)), adenine, e_aq);
566 reactionData->AddProduct(damage_adenine);
567 theReactionTable->SetReaction(reactionData);
568
569 // guanine + Hydrated e- -> ...
570 reactionData = new G4DNAMolecularReactionData(
571 14e9*(1e-3*m3/(mole*s)), guanine, e_aq);
572 reactionData->AddProduct(damage_guanine);
573 theReactionTable->SetReaction(reactionData);
574
575 // thymine + Hydrated e- -> ...
576 reactionData = new G4DNAMolecularReactionData(
577 18e9*(1e-3*m3/(mole*s)), thymine, e_aq);
578 reactionData->AddProduct(damage_thymine);
579 theReactionTable->SetReaction(reactionData);
580
581 // cytosine + Hydrated e- -> ...
582 reactionData = new G4DNAMolecularReactionData(
583 13e9*(1e-3*m3/(mole*s)), cytosine, e_aq);
584 reactionData->AddProduct(damage_cytosine);
585 theReactionTable->SetReaction(reactionData);
586
587 // Radical H and DNA
588
589 // Deoxyribose + Radical H -> ...
590 reactionData = new G4DNAMolecularReactionData(
591 0.029e9*(1e-3*m3/(mole*s)), deoxyribose, H);
592 reactionData->AddProduct(damage_deoxyribose);
593 //eactionData->SetEffectiveReactionRadius(0);
594
595 theReactionTable->SetReaction(reactionData);
596
597 // adenine + Radical H -> ...
598 reactionData = new G4DNAMolecularReactionData(
599 0.10e9*(1e-3*m3/(mole*s)), adenine, H);
600 reactionData->AddProduct(damage_adenine);
601 theReactionTable->SetReaction(reactionData);
602
603 // thymine + Radical H -> ...
604 reactionData = new G4DNAMolecularReactionData(
605 0.57e9*(1e-3*m3/(mole*s)), thymine, H);
606 reactionData->AddProduct(damage_thymine);
607 theReactionTable->SetReaction(reactionData);
608
609 // cytosine + Radical H -> ...
610 reactionData = new G4DNAMolecularReactionData(
611 0.092e9*(1e-3*m3/(mole*s)), cytosine, H);
612 reactionData->AddProduct(damage_cytosine);
613 theReactionTable->SetReaction(reactionData);
614
615 //histone + all molecules -> modification(or "damage")
616
617 reactionData = new G4DNAMolecularReactionData(
618 0.0*(1e-3*m3/(mole*s)), histone, OH);
619 reactionData->AddProduct(histone);
620 reactionData->SetEffectiveReactionRadius(
621 2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
622 theReactionTable->SetReaction(reactionData);
623
624 reactionData = new G4DNAMolecularReactionData(
625 0.0*(1e-3*m3/(mole*s)), histone, OHm);
626 reactionData->AddProduct(histone);
627 reactionData->SetEffectiveReactionRadius(
628 2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
629 theReactionTable->SetReaction(reactionData);
630
631 reactionData = new G4DNAMolecularReactionData(
632 0.0*(1e-3*m3/(mole*s)), histone, e_aq);
633 reactionData->AddProduct(histone);
634 reactionData->SetEffectiveReactionRadius(
635 2.4*nm + G4Electron_aq::Definition()->GetVanDerVaalsRadius());
636 theReactionTable->SetReaction(reactionData);
637
638 reactionData = new G4DNAMolecularReactionData(
639 0.0*(1e-3*m3/(mole*s)), histone, H2);
640 reactionData->AddProduct(histone);
641 reactionData->SetEffectiveReactionRadius(
642 2.4*nm + G4H2::Definition()->GetVanDerVaalsRadius());
643 theReactionTable->SetReaction(reactionData);
644
645 reactionData = new G4DNAMolecularReactionData(
646 0.0*(1e-3*m3/(mole*s)), histone, H3Op);
647 reactionData->AddProduct(histone);
648 reactionData->SetEffectiveReactionRadius(
649 2.4*nm + G4H3O::Definition()->GetVanDerVaalsRadius());
650 theReactionTable->SetReaction(reactionData);
651
652 reactionData = new G4DNAMolecularReactionData(
653 0.0*(1e-3*m3/(mole*s)), histone, H);
654 reactionData->AddProduct(histone);
655 reactionData->SetEffectiveReactionRadius(
656 2.4*nm + G4Hydrogen::Definition()->GetVanDerVaalsRadius());
657 theReactionTable->SetReaction(reactionData);
658
659 reactionData = new G4DNAMolecularReactionData(
660 0.0*(1e-3*m3/(mole*s)), histone, H2O2);
661 reactionData->AddProduct(histone);
662 reactionData->SetEffectiveReactionRadius(
663 2.4*nm + G4H2O2::Definition()->GetVanDerVaalsRadius());
664 theReactionTable->SetReaction(reactionData);
665}
G4DNAMolecularReactionData::SetEffectiveReactionRadius
void SetEffectiveReactionRadius(G4double radius)
Definition: G4DNAMolecularReactionTable.cc:250

◆ ConstructTimeStepModel()

void G4EmDNAChemistry_option2::ConstructTimeStepModel ( G4DNAMolecularReactionTable *  pTable)
overridevirtual

Implements G4VUserChemistryList.

Definition at line 742 of file G4EmDNAChemistry_option2.cc.

744{
745 G4VDNAReactionModel* reactionRadiusComputer =
746 new G4DNASmoluchowskiReactionModel();
747 reactionTable->PrintTable(reactionRadiusComputer);
748
749 G4DNAMolecularStepByStepModel* stepByStep =
750 new G4DNAMolecularStepByStepModel();
751 stepByStep->SetReactionModel(reactionRadiusComputer);
752
753 RegisterTimeStepModel(stepByStep, 0);
754}
G4DNAMolecularStepByStepModel::SetReactionModel
void SetReactionModel(G4VDNAReactionModel *)
Definition: G4DNAMolecularStepByStepModel.cc:87
G4VUserChemistryList::RegisterTimeStepModel
void RegisterTimeStepModel(G4VITStepModel *timeStepModel, double startingTime=0)
Definition: G4VUserChemistryList.cc:56
The documentation for this class was generated from the following files: