| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 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 |
| 94 |
> |
* @param ff pointer to a concrete ForceField instance |
| 95 |
|
* |
| 96 |
< |
* @param ff pointer of a concrete ForceField instance |
| 99 |
< |
* |
| 100 |
< |
* @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 |
| 388 |
– |
* @see #SimCreator::setGlobalIndex |
| 392 |
|
*/ |
| 393 |
|
void setGlobalGroupMembership(const vector<int>& ggm) { |
| 394 |
|
assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_)); |
| 397 |
|
|
| 398 |
|
/** |
| 399 |
|
* Sets GlobalMolMembership |
| 397 |
– |
* @see #SimCreator::setGlobalIndex |
| 400 |
|
*/ |
| 401 |
|
void setGlobalMolMembership(const vector<int>& gmm) { |
| 402 |
|
assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ + |
| 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 |
|
|
| 588 |
|
vector<int> identArray_; |
| 589 |
|
public: |
| 590 |
|
vector<int> getIdentArray() { return identArray_; } |
| 591 |
+ |
|
| 592 |
+ |
/** |
| 593 |
+ |
* A vector that contains information about the local region of an |
| 594 |
+ |
* atom (used for fluctuating charges, etc.) |
| 595 |
+ |
*/ |
| 596 |
|
private: |
| 597 |
< |
|
| 597 |
> |
vector<int> regions_; |
| 598 |
> |
public: |
| 599 |
> |
vector<int> getRegions() { return regions_; } |
| 600 |
> |
private: |
| 601 |
|
/** |
| 602 |
|
* A vector which contains the fractional contribution of an |
| 603 |
|
* atom's mass to the total mass of the cutoffGroup that atom |
| 624 |
|
|
| 625 |
|
PropertyMap properties_; /**< Generic Properties can be added */ |
| 626 |
|
SnapshotManager* sman_; /**< SnapshotManager (handles particle positions, etc.) */ |
| 627 |
+ |
int storageLayout_; /**< Bits to tell how much data to store on each object */ |
| 628 |
|
|
| 629 |
|
/** |
| 630 |
|
* The reason to have a local index manager is that when molecule |
| 644 |
|
string dumpFileName_; |
| 645 |
|
string statFileName_; |
| 646 |
|
string restFileName_; |
| 633 |
– |
|
| 647 |
|
|
| 648 |
|
bool topologyDone_; /** flag to indicate whether the topology has |
| 649 |
|
been scanned and all the relevant |
| 681 |
|
|
| 682 |
|
/** |
| 683 |
|
* Set MolToProcMap array |
| 671 |
– |
* @see #SimCreator::divideMolecules |
| 684 |
|
*/ |
| 685 |
|
void setMolToProcMap(const vector<int>& molToProcMap) { |
| 686 |
|
molToProcMap_ = molToProcMap; |
