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Comparing branches/new_design/OOPSE-4/src/brains/SimInfo.cpp (file contents):
Revision 1710 by tim, Thu Nov 4 19:48:22 2004 UTC vs.
Revision 1725 by tim, Wed Nov 10 22:01:06 2004 UTC

# Line 64 | Line 64 | bool SimInfo::addMolecule(Molecule* mol) {
64          nCutoffGroups_ += mol->getNCutoffGroups();
65          nConstraints_ += mol->getNConstraints();
66  
67 +        globalIndexToMol_.insert(make_pair(mol->getGlobalIndex(), mol));
68          return true;
69      } else {
70          return false;
# Line 85 | Line 86 | bool SimInfo::removeMolecule(Molecule* mol) {
86          nCutoffGroups_ -= mol->getNCutoffGroups();
87          nConstraints_ -= mol->getNConstraints();
88  
89 +        globalIndexToMol_.erase(mol->getGlobalIndex());
90          return true;
91      } else {
92          return false;
# Line 105 | Line 107 | void SimInfo::calcNDF() {
107   }
108  
109  
110 < void SimInfo::calcNDF() {
110 > void SimInfo::calcNdf() {
111      int ndf_local;
112      std::vector<Molecule*>::iterator i;
113      std::vector<StuntDouble*>::iterator j;
# Line 146 | Line 148 | void SimInfo::calcNDFRaw() {
148  
149   }
150  
151 < void SimInfo::calcNDFRaw() {
151 > void SimInfo::calcNdfRaw() {
152      int ndfRaw_local;
153  
154      std::vector<Molecule*>::iterator i;
# Line 181 | Line 183 | void SimInfo::calcNDFTrans() {
183   #endif
184   }
185  
186 < void SimInfo::calcNDFTrans() {
186 > void SimInfo::calcNdfTrans() {
187      int ndfTrans_local;
188  
189      ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
# Line 197 | Line 199 | void SimInfo::calcNDFTrans() {
199  
200   }
201  
202 + void SimInfo::addExcludePairs(Molecule* mol) {
203 +    std::vector<Bond*>::iterator bondIter;
204 +    std::vector<Bend*>::iterator bendIter;
205 +    std::vector<Torsion*>::iterator torsionIter;
206 +    Bond* bond;
207 +    Bend* bend;
208 +    Torsion* torsion;
209 +    int a;
210 +    int b;
211 +    int c;
212 +    int d;
213 +    
214 +    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
215 +        a = bond->getAtomA()->getGlobalIndex();
216 +        b = bond->getAtomB()->getGlobalIndex();        
217 +        exclude_.addPair(a, b);
218 +    }
219  
220 +    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
221 +        a = bend->getAtomA()->getGlobalIndex();
222 +        b = bend->getAtomB()->getGlobalIndex();        
223 +        c = bend->getAtomC()->getGlobalIndex();
224 +
225 +        exclude_.addPair(a, b);
226 +        exclude_.addPair(a, c);
227 +        exclude_.addPair(b, c);        
228 +    }
229 +
230 +    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
231 +        a = torsion->getAtomA()->getGlobalIndex();
232 +        b = torsion->getAtomB()->getGlobalIndex();        
233 +        c = torsion->getAtomC()->getGlobalIndex();        
234 +        d = torsion->getAtomD()->getGlobalIndex();        
235 +
236 +        exclude_.addPair(a, b);
237 +        exclude_.addPair(a, c);
238 +        exclude_.addPair(a, d);
239 +        exclude_.addPair(b, c);
240 +        exclude_.addPair(b, d);
241 +        exclude_.addPair(c, d);        
242 +    }
243 +
244 +    
245 + }
246 +
247 + void SimInfo::removeExcludePairs(Molecule* mol) {
248 +    std::vector<Bond*>::iterator bondIter;
249 +    std::vector<Bend*>::iterator bendIter;
250 +    std::vector<Torsion*>::iterator torsionIter;
251 +    Bond* bond;
252 +    Bend* bend;
253 +    Torsion* torsion;
254 +    int a;
255 +    int b;
256 +    int c;
257 +    int d;
258 +    
259 +    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
260 +        a = bond->getAtomA()->getGlobalIndex();
261 +        b = bond->getAtomB()->getGlobalIndex();        
262 +        exclude_.removePair(a, b);
263 +    }
264 +
265 +    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
266 +        a = bend->getAtomA()->getGlobalIndex();
267 +        b = bend->getAtomB()->getGlobalIndex();        
268 +        c = bend->getAtomC()->getGlobalIndex();
269 +
270 +        exclude_.removePair(a, b);
271 +        exclude_.removePair(a, c);
272 +        exclude_.removePair(b, c);        
273 +    }
274 +
275 +    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
276 +        a = torsion->getAtomA()->getGlobalIndex();
277 +        b = torsion->getAtomB()->getGlobalIndex();        
278 +        c = torsion->getAtomC()->getGlobalIndex();        
279 +        d = torsion->getAtomD()->getGlobalIndex();        
280 +
281 +        exclude_.removePair(a, b);
282 +        exclude_.removePair(a, c);
283 +        exclude_.removePair(a, d);
284 +        exclude_.removePair(b, c);
285 +        exclude_.removePair(b, d);
286 +        exclude_.removePair(c, d);        
287 +    }
288 +
289 + }
290 +
291 +
292 + void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
293 +    int curStampId;
294 +
295 +    //index from 0
296 +    curStampId = molStampIds_.size();
297 +
298 +    moleculeStamps_.push_back(molStamp);
299 +    molStampIds_.insert(molStampIds_.end(), nmol, curStampId)
300 + }
301 +
302 + std::ostream& operator <<(ostream& o, SimInfo& info) {
303 +
304 +    return o;
305 + }
306 +
307   }//end namespace oopse

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