| 270 |
|
SnapshotManager* getSnapshotManager() { |
| 271 |
|
return sman_; |
| 272 |
|
} |
| 273 |
< |
|
| 273 |
> |
/** Returns the storage layout (computed by SimCreator) */ |
| 274 |
> |
int getStorageLayout() { |
| 275 |
> |
return storageLayout_; |
| 276 |
> |
} |
| 277 |
> |
/** Sets the storage layout (computed by SimCreator) */ |
| 278 |
> |
void setStorageLayout(int sl) { |
| 279 |
> |
storageLayout_ = sl; |
| 280 |
> |
} |
| 281 |
> |
|
| 282 |
|
/** Sets the snapshot manager. */ |
| 283 |
|
void setSnapshotManager(SnapshotManager* sman); |
| 284 |
|
|
| 390 |
|
/** |
| 391 |
|
* Sets GlobalGroupMembership |
| 392 |
|
*/ |
| 393 |
< |
void setGlobalGroupMembership(const vector<int>& globalGroupMembership) { |
| 394 |
< |
assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
| 395 |
< |
globalGroupMembership_ = globalGroupMembership; |
| 393 |
> |
void setGlobalGroupMembership(const vector<int>& ggm) { |
| 394 |
> |
assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_)); |
| 395 |
> |
globalGroupMembership_ = ggm; |
| 396 |
|
} |
| 397 |
|
|
| 398 |
|
/** |
| 399 |
|
* Sets GlobalMolMembership |
| 400 |
|
*/ |
| 401 |
< |
void setGlobalMolMembership(const vector<int>& globalMolMembership) { |
| 402 |
< |
assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
| 403 |
< |
globalMolMembership_ = globalMolMembership; |
| 401 |
> |
void setGlobalMolMembership(const vector<int>& gmm) { |
| 402 |
> |
assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ + |
| 403 |
> |
nGlobalRigidBodies_))); |
| 404 |
> |
globalMolMembership_ = gmm; |
| 405 |
|
} |
| 406 |
|
|
| 407 |
|
|
| 468 |
|
|
| 469 |
|
/** Returns the set of atom types present in this simulation */ |
| 470 |
|
set<AtomType*> getSimulatedAtomTypes(); |
| 471 |
+ |
|
| 472 |
+ |
/** Returns the global count of atoms of a particular type */ |
| 473 |
+ |
int getGlobalCountOfType(AtomType* atype); |
| 474 |
|
|
| 475 |
|
friend ostream& operator <<(ostream& o, SimInfo& info); |
| 476 |
|
|
| 616 |
|
|
| 617 |
|
PropertyMap properties_; /**< Generic Properties can be added */ |
| 618 |
|
SnapshotManager* sman_; /**< SnapshotManager (handles particle positions, etc.) */ |
| 619 |
+ |
int storageLayout_; /**< Bits to tell how much data to store on each object */ |
| 620 |
|
|
| 621 |
|
/** |
| 622 |
|
* The reason to have a local index manager is that when molecule |
| 636 |
|
string dumpFileName_; |
| 637 |
|
string statFileName_; |
| 638 |
|
string restFileName_; |
| 626 |
– |
|
| 639 |
|
|
| 640 |
|
bool topologyDone_; /** flag to indicate whether the topology has |
| 641 |
|
been scanned and all the relevant |
