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G4DNAChemistryManager.cc
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26 // $Id: G4DNAChemistryManager.cc 64057 2012-10-30 15:04:49Z gcosmo $
27 //
28 // Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
29 //
30 // WARNING : This class is released as a prototype.
31 // It might strongly evolve or even disapear in the next releases.
32 //
33 // History:
34 // -----------
35 // 10 Oct 2011 M.Karamitros created
36 //
37 // -------------------------------------------------------------------
38 
39 #include "G4DNAChemistryManager.hh"
40 #include "G4SystemOfUnits.hh"
41 #include "G4Molecule.hh"
42 #include "G4ITTrackHolder.hh"
43 #include "G4H2O.hh"
44 #include "G4DNAMolecularReactionTable.hh"
45 #include "G4DNAWaterExcitationStructure.hh"
46 #include "G4DNAWaterIonisationStructure.hh"
47 #include "G4Electron_aq.hh"
48 #include "G4ITManager.hh"
49 #include "G4MolecularConfiguration.hh"
50 #include "G4MoleculeCounter.hh"
51 
52 using namespace std;
53 
54 auto_ptr<G4DNAChemistryManager> G4DNAChemistryManager::fInstance(0);
55 
56 G4DNAChemistryManager::G4DNAChemistryManager() :
57  fActiveChemistry(false)
58 {
59  fExcitationLevel = 0;
60  fIonisationLevel = 0;
61  fWriteFile = false;
62 }
63 
64 G4DNAChemistryManager* G4DNAChemistryManager::Instance()
65 {
66  if(!fInstance.get()) fInstance = auto_ptr<G4DNAChemistryManager>(new G4DNAChemistryManager());
67  return fInstance.get();
68 }
69 
70 G4DNAChemistryManager::~G4DNAChemistryManager()
71 {
72  if (fOutput.is_open())
73  {
74  fOutput.close();
75  }
76  if(fIonisationLevel) delete fIonisationLevel;
77  if(fExcitationLevel) delete fExcitationLevel;
78  G4DNAMolecularReactionTable::DeleteInstance();
79  G4MoleculeHandleManager::DeleteInstance();
80  G4MolecularConfiguration::DeleteManager();
81  fInstance.release();
82  G4MoleculeCounter::DeleteInstance();
83 }
84 
85 void G4DNAChemistryManager::DeleteInstance()
86 {
87  if(fInstance.get())
88  fInstance.reset();
89 }
90 
91 void G4DNAChemistryManager::WriteInto(const G4String& output,
92  ios_base::openmode mode)
93 {
94  fOutput.open(output.data(), mode);
95  fOutput << std::setprecision(6) << std::scientific;
96 
97  fOutput << setw(11) << left << "#Parent ID"
98  << setw(10) << "Molecule"
99  << setw(14) << "Elec Modif"
100  << setw(13) << "Energy (eV)"
101  << setw(22) << "X pos of parent [nm]"
102  << setw(22) << "Y pos of parent [nm]"
103  << setw(22) << "Z pos of parent [nm]"
104  << setw(14) << "X pos [nm]"
105  << setw(14) << "Y pos [nm]"
106  << setw(14) << "Z pos [nm]"
107  << G4endl
108  << setw(21) << "#"
109  << setw(13) << "1)io/ex=0/1"
110  << G4endl
111  << setw(21) << "#"
112  << setw(13) << "2)level=0...5"
113  << G4endl;
114  fWriteFile = true;
115 }
116 
117 void G4DNAChemistryManager::CloseFile()
118 {
119  if (fOutput.is_open())
120  {
121  fOutput.close();
122  }
123  fWriteFile = false;
124 }
125 
126 G4DNAWaterExcitationStructure* G4DNAChemistryManager::GetExcitationLevel()
127 {
128  if(!fExcitationLevel)
129  {
130  fExcitationLevel = new G4DNAWaterExcitationStructure;
131  }
132  return fExcitationLevel;
133 }
134 
135 G4DNAWaterIonisationStructure* G4DNAChemistryManager::GetIonisationLevel()
136 {
137  if(!fIonisationLevel)
138  {
139  fIonisationLevel = new G4DNAWaterIonisationStructure;
140  }
141  return fIonisationLevel;
142 }
143 
144 void G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modification,
145  G4int electronicLevel,
146  const G4Track* theIncomingTrack)
147 {
148  if(fWriteFile)
149  {
150  G4double energy = -1.;
151 
152  switch (modification)
153  {
154  case eDissociativeAttachment:
155  energy = -1;
156  break;
157  case eExcitedMolecule :
158  energy = GetExcitationLevel()->ExcitationEnergy(electronicLevel);
159  break;
160  case eIonizedMolecule :
161  energy = GetIonisationLevel()->IonisationEnergy(electronicLevel);
162  break;
163  }
164 
165  fOutput << setw(11) << left << theIncomingTrack->GetTrackID()
166  << setw(10) << "H2O"
167  << left << modification
168  << internal <<":"
169  << right <<electronicLevel
170  << left
171  << setw(11) << ""
172  << std::setprecision(2) << std::fixed
173  << setw(13) << energy/eV
174  << std::setprecision(6) << std::scientific
175  << setw(22) << (theIncomingTrack->GetPosition().x())/nanometer
176  << setw(22) << (theIncomingTrack->GetPosition().y())/nanometer
177  << setw(22) << (theIncomingTrack->GetPosition().z())/nanometer
178  << G4endl;
179  }
180 
181  if(fActiveChemistry)
182  {
183  G4Molecule * H2O = new G4Molecule (G4H2O::Definition());
184 
185  switch (modification)
186  {
187  case eDissociativeAttachment:
188  H2O -> AddElectron(5,1);
189  break;
190  case eExcitedMolecule :
191  H2O -> ExciteMolecule(electronicLevel);
192  break;
193  case eIonizedMolecule :
194  H2O -> IonizeMolecule(electronicLevel);
195  break;
196  }
197 
198  G4Track * H2OTrack = H2O->BuildTrack(1*picosecond,
199  theIncomingTrack->GetPosition());
200 
201  H2OTrack -> SetParentID(theIncomingTrack->GetTrackID());
202  H2OTrack -> SetTrackStatus(fStopButAlive);
203  H2OTrack -> SetKineticEnergy(0.);
204 
205  G4ITTrackHolder::Instance()->PushTrack(H2OTrack);
206  }
207 }
208 
209 void G4DNAChemistryManager::CreateSolvatedElectron(const G4Track* theIncomingTrack,
210  G4ThreeVector* finalPosition)
211 // finalPosition is a pointer because this argument is optional
212 {
213  if(fWriteFile)
214  {
215  fOutput << setw(11)<< theIncomingTrack->GetTrackID()
216  << setw(10)<< "e_aq"
217  << setw(14)<< -1
218  << std::setprecision(2) << std::fixed
219  << setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
220  << std::setprecision(6) << std::scientific
221  << setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
222  << setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
223  << setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer ;
224 
225  if(finalPosition != 0)
226  {
227  fOutput<< setw(14)<< (finalPosition->x())/nanometer
228  << setw(14)<< (finalPosition->y())/nanometer
229  << setw(14)<< (finalPosition->z())/nanometer ;
230  }
231 
232  fOutput << G4endl;
233  }
234 
235  if(fActiveChemistry)
236  {
237  G4Molecule* e_aq = new G4Molecule(G4Electron_aq::Definition());
238  G4Track * e_aqTrack(0);
239  if(finalPosition)
240  {
241  e_aqTrack = e_aq->BuildTrack(picosecond,*finalPosition);
242  }
243  else
244  {
245  e_aqTrack = e_aq->BuildTrack(picosecond,theIncomingTrack->GetPosition());
246  }
247  e_aqTrack -> SetTrackStatus(fAlive);
248  e_aqTrack -> SetParentID(theIncomingTrack->GetTrackID());
249  G4ITTrackHolder::Instance()->PushTrack(e_aqTrack);
250  G4ITManager<G4Molecule>::Instance()->Push(e_aqTrack);
251  }
252 }
253 
254 
255 void G4DNAChemistryManager::PushMolecule(G4Molecule*& molecule, double time,
256  const G4ThreeVector& position, int parentID)
257 {
258  if(fWriteFile)
259  {
260  fOutput << setw(11)<< parentID
261  << setw(10)<< molecule->GetName()
262  << setw(14)<< -1
263  << std::setprecision(2) << std::fixed
264  << setw(13)<< -1
265  << std::setprecision(6) << std::scientific
266  << setw(22)<< (position.x())/nanometer
267  << setw(22)<< (position.y())/nanometer
268  << setw(22)<< (position.z())/nanometer;
269  fOutput << G4endl;
270  }
271 
272  if(fActiveChemistry)
273  {
274  G4Track* track = molecule->BuildTrack(time,position);
275  track -> SetTrackStatus(fAlive);
276  track -> SetParentID(parentID);
277  G4ITTrackHolder::Instance()->PushTrack(track);
278  G4ITManager<G4Molecule>::Instance()->Push(track);
279  }
280  else
281  {
282  delete molecule;
283  molecule = 0;
284  }
285 }
286 
287 void G4DNAChemistryManager::PushMoleculeAtParentTimeAndPlace(G4Molecule*& molecule,
288  const G4Track* theIncomingTrack)
289 {
290  if(fWriteFile)
291  {
292  fOutput << setw(11)<< theIncomingTrack->GetTrackID()
293  << setw(10)<< molecule->GetName()
294  << setw(14)<< -1
295  << std::setprecision(2) << std::fixed
296  << setw(13)<< theIncomingTrack->GetKineticEnergy()/eV
297  << std::setprecision(6) << std::scientific
298  << setw(22)<< (theIncomingTrack->GetPosition().x())/nanometer
299  << setw(22)<< (theIncomingTrack->GetPosition().y())/nanometer
300  << setw(22)<< (theIncomingTrack->GetPosition().z())/nanometer ;
301  fOutput << G4endl;
302  }
303 
304  if(fActiveChemistry)
305  {
306  G4Track* track = molecule->BuildTrack(theIncomingTrack->GetGlobalTime(),theIncomingTrack->GetPosition());
307  track -> SetTrackStatus(fAlive);
308  track -> SetParentID(theIncomingTrack->GetTrackID());
309  G4ITTrackHolder::Instance()->PushTrack(track);
310  G4ITManager<G4Molecule>::Instance()->Push(track);
311  }
312  else
313  {
314  delete molecule;
315  molecule = 0;
316  }
317 }
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