255 |
|
|
256 |
|
/** Returns the center of the mass of the whole system.*/ |
257 |
|
Vector3d getCom(); |
258 |
– |
|
259 |
– |
/** Returns the seed (used for random number generator) */ |
260 |
– |
int getSeed() { |
261 |
– |
return seed_; |
262 |
– |
} |
263 |
– |
|
264 |
– |
/** Sets the seed*/ |
265 |
– |
void setSeed(int seed) { |
266 |
– |
seed_ = seed; |
267 |
– |
} |
258 |
|
|
259 |
|
/** main driver function to interact with fortran during the initialization and molecule migration */ |
260 |
|
void update(); |
400 |
|
void removeExcludePairs(Molecule* mol); |
401 |
|
|
402 |
|
|
403 |
< |
SelectionManager* getSelectionManager() { |
404 |
< |
return selectMan_; |
415 |
< |
} |
403 |
> |
/** Returns the unique atom types of local processor in an array */ |
404 |
> |
std::set<AtomType*> getUniqueAtomTypes(); |
405 |
|
|
406 |
|
friend std::ostream& operator <<(std::ostream& o, SimInfo& info); |
407 |
+ |
|
408 |
+ |
void getCutoff(double& rcut, double& rsw); |
409 |
|
|
410 |
|
private: |
411 |
|
|
421 |
– |
|
422 |
– |
/** Returns the unique atom types of local processor in an array */ |
423 |
– |
std::set<AtomType*> getUniqueAtomTypes(); |
424 |
– |
|
412 |
|
/** fill up the simtype struct*/ |
413 |
|
void setupSimType(); |
414 |
|
|
482 |
|
PropertyMap properties_; /**< Generic Property */ |
483 |
|
SnapshotManager* sman_; /**< SnapshotManager */ |
484 |
|
|
498 |
– |
int seed_; /**< seed for random number generator */ |
499 |
– |
|
485 |
|
/** |
486 |
|
* The reason to have a local index manager is that when molecule is migrating to other processors, |
487 |
|
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
500 |
|
|
501 |
|
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
502 |
|
|
518 |
– |
SelectionManager* selectMan_; |
503 |
|
#ifdef IS_MPI |
504 |
|
//in Parallel version, we need MolToProc |
505 |
|
public: |