| 91 |
|
/** |
| 92 |
|
* Constructor of SimInfo |
| 93 |
|
* |
| 94 |
< |
* @param molStampPairs MoleculeStamp Array. The first element of |
| 95 |
< |
* the pair is molecule stamp, the second element is the total |
| 96 |
< |
* number of molecules with the same molecule stamp in the system |
| 97 |
< |
* |
| 98 |
< |
* @param ff pointer of a concrete ForceField instance |
| 94 |
> |
* @param ff pointer to a concrete ForceField instance |
| 95 |
|
* |
| 96 |
< |
* @param simParams |
| 96 |
> |
* @param simParams pointer to the simulation parameters in a Globals object |
| 97 |
|
*/ |
| 98 |
|
SimInfo(ForceField* ff, Globals* simParams); |
| 99 |
|
virtual ~SimInfo(); |
| 104 |
|
* @return return true if adding successfully, return false if the |
| 105 |
|
* molecule is already in SimInfo |
| 106 |
|
* |
| 107 |
< |
* @param mol molecule to be added |
| 107 |
> |
* @param mol Molecule to be added |
| 108 |
|
*/ |
| 109 |
|
bool addMolecule(Molecule* mol); |
| 110 |
|
|
| 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 |
|
|
| 389 |
|
|
| 390 |
|
/** |
| 391 |
|
* Sets GlobalGroupMembership |
| 392 |
< |
* @see #SimCreator::setGlobalIndex |
| 393 |
< |
*/ |
| 394 |
< |
void setGlobalGroupMembership(const vector<int>& globalGroupMembership) { |
| 395 |
< |
assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
| 392 |
< |
globalGroupMembership_ = globalGroupMembership; |
| 392 |
> |
*/ |
| 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 |
| 397 |
– |
* @see #SimCreator::setGlobalIndex |
| 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 |
|
|
| 613 |
|
|
| 614 |
|
PropertyMap properties_; /**< Generic Properties can be added */ |
| 615 |
|
SnapshotManager* sman_; /**< SnapshotManager (handles particle positions, etc.) */ |
| 616 |
+ |
int storageLayout_; /**< Bits to tell how much data to store on each object */ |
| 617 |
|
|
| 618 |
|
/** |
| 619 |
|
* The reason to have a local index manager is that when molecule |
| 633 |
|
string dumpFileName_; |
| 634 |
|
string statFileName_; |
| 635 |
|
string restFileName_; |
| 632 |
– |
|
| 636 |
|
|
| 637 |
|
bool topologyDone_; /** flag to indicate whether the topology has |
| 638 |
|
been scanned and all the relevant |
| 670 |
|
|
| 671 |
|
/** |
| 672 |
|
* Set MolToProcMap array |
| 670 |
– |
* @see #SimCreator::divideMolecules |
| 673 |
|
*/ |
| 674 |
|
void setMolToProcMap(const vector<int>& molToProcMap) { |
| 675 |
|
molToProcMap_ = molToProcMap; |
