43 |
|
} |
44 |
|
|
45 |
|
SimInfo::~SimInfo() { |
46 |
< |
MemoryUtils::deleteVectorOfPointer(molecules_); |
46 |
> |
//MemoryUtils::deleteVectorOfPointer(molecules_); |
47 |
|
delete sman_; |
48 |
|
|
49 |
|
} |
50 |
|
|
51 |
|
|
52 |
|
bool SimInfo::addMolecule(Molecule* mol) { |
53 |
< |
std::vector<Molecule*>::iterator i; |
53 |
> |
MoleculeIterator i; |
54 |
|
i = std::find(molecules_.begin(), molecules_.end(), mol); |
55 |
|
if (i != molecules_.end() ) { |
56 |
– |
molecules_.push_back(mol); |
56 |
|
|
57 |
+ |
molecules_.insert(make_pair(mol->getGlobalIndex(), mol)); |
58 |
+ |
|
59 |
|
nAtoms_ += mol->getNAtoms(); |
60 |
|
nBonds_ += mol->getNBonds(); |
61 |
|
nBends_ += mol->getNBends(); |
72 |
|
} |
73 |
|
|
74 |
|
bool SimInfo::removeMolecule(Molecule* mol) { |
75 |
< |
std::vector<Molecule*>::iterator i; |
75 |
> |
MoleculeIterator i; |
76 |
|
i = std::find(molecules_.begin(), molecules_.end(), mol); |
77 |
|
|
78 |
|
if (i != molecules_.end() ) { |
79 |
< |
molecules_.push_back(mol); |
79 |
> |
|
80 |
|
nAtoms_ -= mol->getNAtoms(); |
81 |
|
nBonds_ -= mol->getNBonds(); |
82 |
|
nBends_ -= mol->getNBends(); |
86 |
|
nCutoffGroups_ -= mol->getNCutoffGroups(); |
87 |
|
nConstraints_ -= mol->getNConstraints(); |
88 |
|
|
89 |
+ |
molecules_.erase(mol->getGlobalIndex()); |
90 |
+ |
|
91 |
+ |
delete mol; |
92 |
+ |
|
93 |
|
return true; |
94 |
|
} else { |
95 |
|
return false; |
99 |
|
} |
100 |
|
|
101 |
|
|
102 |
< |
Molecule* SimInfo::beginMolecule(std::vector<Molecule*>::iterator& i) { |
102 |
> |
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
103 |
|
i = molecules_.begin(); |
104 |
|
return i == molecules_.end() ? NULL : *i; |
105 |
|
} |
106 |
|
|
107 |
< |
Molecule* SimInfo::nextMolecule(std::vector<Molecule*>::iterator& i) { |
107 |
> |
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
108 |
|
++i; |
109 |
|
return i == molecules_.end() ? NULL : *i; |
110 |
|
} |
111 |
|
|
112 |
|
|
113 |
< |
void SimInfo::calcNDF() { |
113 |
> |
void SimInfo::calcNdf() { |
114 |
|
int ndf_local; |
115 |
< |
std::vector<Molecule*>::iterator i; |
115 |
> |
MoleculeIterator i; |
116 |
|
std::vector<StuntDouble*>::iterator j; |
117 |
|
Molecule* mol; |
118 |
|
StuntDouble* integrableObject; |
151 |
|
|
152 |
|
} |
153 |
|
|
154 |
< |
void SimInfo::calcNDFRaw() { |
154 |
> |
void SimInfo::calcNdfRaw() { |
155 |
|
int ndfRaw_local; |
156 |
|
|
157 |
< |
std::vector<Molecule*>::iterator i; |
157 |
> |
MoleculeIterator i; |
158 |
|
std::vector<StuntDouble*>::iterator j; |
159 |
|
Molecule* mol; |
160 |
|
StuntDouble* integrableObject; |
186 |
|
#endif |
187 |
|
} |
188 |
|
|
189 |
< |
void SimInfo::calcNDFTrans() { |
189 |
> |
void SimInfo::calcNdfTrans() { |
190 |
|
int ndfTrans_local; |
191 |
|
|
192 |
|
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
200 |
|
|
201 |
|
ndfTrans_ = ndfTrans_ - 3 - nZconstraints; |
202 |
|
|
203 |
+ |
} |
204 |
+ |
|
205 |
+ |
void SimInfo::addExcludePairs(Molecule* mol) { |
206 |
+ |
std::vector<Bond*>::iterator bondIter; |
207 |
+ |
std::vector<Bend*>::iterator bendIter; |
208 |
+ |
std::vector<Torsion*>::iterator torsionIter; |
209 |
+ |
Bond* bond; |
210 |
+ |
Bend* bend; |
211 |
+ |
Torsion* torsion; |
212 |
+ |
int a; |
213 |
+ |
int b; |
214 |
+ |
int c; |
215 |
+ |
int d; |
216 |
+ |
|
217 |
+ |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
218 |
+ |
a = bond->getAtomA()->getGlobalIndex(); |
219 |
+ |
b = bond->getAtomB()->getGlobalIndex(); |
220 |
+ |
exclude_.addPair(a, b); |
221 |
+ |
} |
222 |
+ |
|
223 |
+ |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
224 |
+ |
a = bend->getAtomA()->getGlobalIndex(); |
225 |
+ |
b = bend->getAtomB()->getGlobalIndex(); |
226 |
+ |
c = bend->getAtomC()->getGlobalIndex(); |
227 |
+ |
|
228 |
+ |
exclude_.addPair(a, b); |
229 |
+ |
exclude_.addPair(a, c); |
230 |
+ |
exclude_.addPair(b, c); |
231 |
+ |
} |
232 |
+ |
|
233 |
+ |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
234 |
+ |
a = torsion->getAtomA()->getGlobalIndex(); |
235 |
+ |
b = torsion->getAtomB()->getGlobalIndex(); |
236 |
+ |
c = torsion->getAtomC()->getGlobalIndex(); |
237 |
+ |
d = torsion->getAtomD()->getGlobalIndex(); |
238 |
+ |
|
239 |
+ |
exclude_.addPair(a, b); |
240 |
+ |
exclude_.addPair(a, c); |
241 |
+ |
exclude_.addPair(a, d); |
242 |
+ |
exclude_.addPair(b, c); |
243 |
+ |
exclude_.addPair(b, d); |
244 |
+ |
exclude_.addPair(c, d); |
245 |
+ |
} |
246 |
+ |
|
247 |
+ |
|
248 |
+ |
} |
249 |
+ |
|
250 |
+ |
void SimInfo::removeExcludePairs(Molecule* mol) { |
251 |
+ |
std::vector<Bond*>::iterator bondIter; |
252 |
+ |
std::vector<Bend*>::iterator bendIter; |
253 |
+ |
std::vector<Torsion*>::iterator torsionIter; |
254 |
+ |
Bond* bond; |
255 |
+ |
Bend* bend; |
256 |
+ |
Torsion* torsion; |
257 |
+ |
int a; |
258 |
+ |
int b; |
259 |
+ |
int c; |
260 |
+ |
int d; |
261 |
+ |
|
262 |
+ |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
263 |
+ |
a = bond->getAtomA()->getGlobalIndex(); |
264 |
+ |
b = bond->getAtomB()->getGlobalIndex(); |
265 |
+ |
exclude_.removePair(a, b); |
266 |
+ |
} |
267 |
+ |
|
268 |
+ |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
269 |
+ |
a = bend->getAtomA()->getGlobalIndex(); |
270 |
+ |
b = bend->getAtomB()->getGlobalIndex(); |
271 |
+ |
c = bend->getAtomC()->getGlobalIndex(); |
272 |
+ |
|
273 |
+ |
exclude_.removePair(a, b); |
274 |
+ |
exclude_.removePair(a, c); |
275 |
+ |
exclude_.removePair(b, c); |
276 |
+ |
} |
277 |
+ |
|
278 |
+ |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
279 |
+ |
a = torsion->getAtomA()->getGlobalIndex(); |
280 |
+ |
b = torsion->getAtomB()->getGlobalIndex(); |
281 |
+ |
c = torsion->getAtomC()->getGlobalIndex(); |
282 |
+ |
d = torsion->getAtomD()->getGlobalIndex(); |
283 |
+ |
|
284 |
+ |
exclude_.removePair(a, b); |
285 |
+ |
exclude_.removePair(a, c); |
286 |
+ |
exclude_.removePair(a, d); |
287 |
+ |
exclude_.removePair(b, c); |
288 |
+ |
exclude_.removePair(b, d); |
289 |
+ |
exclude_.removePair(c, d); |
290 |
+ |
} |
291 |
+ |
|
292 |
|
} |
293 |
|
|
294 |
|
|
295 |
+ |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
296 |
+ |
int curStampId; |
297 |
+ |
|
298 |
+ |
//index from 0 |
299 |
+ |
curStampId = molStampIds_.size(); |
300 |
+ |
|
301 |
+ |
moleculeStamps_.push_back(molStamp); |
302 |
+ |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId) |
303 |
+ |
} |
304 |
+ |
|
305 |
+ |
void SimInfo::update() { |
306 |
+ |
|
307 |
+ |
|
308 |
+ |
|
309 |
+ |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
310 |
+ |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
311 |
+ |
std::vector<int> localToGlobalCutoffGroupIndex; |
312 |
+ |
typename SimInfo::MoleculeIterator mi; |
313 |
+ |
typename Molecule::AtomIterator ai; |
314 |
+ |
typename Molecule::CutoffGroupIterator ci; |
315 |
+ |
Molecule* mol; |
316 |
+ |
Atom* atom; |
317 |
+ |
CutoffGroup* cg; |
318 |
+ |
mpiSimData parallelData; |
319 |
+ |
int isError; |
320 |
+ |
|
321 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
322 |
+ |
|
323 |
+ |
//local index(index in DataStorge) of atom is important |
324 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
325 |
+ |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
326 |
+ |
} |
327 |
+ |
|
328 |
+ |
//local index of cutoff group is trivial, it only depends on the order of travesing |
329 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
330 |
+ |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
331 |
+ |
} |
332 |
+ |
|
333 |
+ |
} |
334 |
+ |
|
335 |
+ |
//Setup Parallel Data and pass the index arrays to fortran |
336 |
+ |
parallelData.nMolGlobal = getNMolGlobal(); |
337 |
+ |
parallelData.nMolLocal = ; |
338 |
+ |
parallelData.nAtomsGlobal = ; |
339 |
+ |
parallelData.nAtomsLocal = ; |
340 |
+ |
parallelData.nGroupsGlobal = ; |
341 |
+ |
parallelData.nGroupsLocal = ; |
342 |
+ |
parallelData.myNode = worldRank; |
343 |
+ |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors)); |
344 |
+ |
|
345 |
+ |
setFsimParallel(parallelData, &(parallelData->nAtomsLocal), |
346 |
+ |
&localToGlobalAtomIndex[0], &(parallelData->nGroupsLocal), |
347 |
+ |
&localToGlobalCutoffGroupIndex[0], &isError); |
348 |
+ |
|
349 |
+ |
if (isError) { |
350 |
+ |
sprintf(painCave.errMsg, |
351 |
+ |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
352 |
+ |
painCave.isFatal = 1; |
353 |
+ |
simError(); |
354 |
+ |
} |
355 |
+ |
|
356 |
+ |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
357 |
+ |
MPIcheckPoint(); |
358 |
+ |
|
359 |
+ |
|
360 |
+ |
} |
361 |
+ |
|
362 |
+ |
std::ostream& operator <<(ostream& o, SimInfo& info) { |
363 |
+ |
|
364 |
+ |
return o; |
365 |
+ |
} |
366 |
+ |
|
367 |
|
}//end namespace oopse |