| 298 |
|
|
| 299 |
|
void update(); |
| 300 |
|
/** |
| 301 |
< |
* Setup Fortran Simulation |
| 301 |
> |
* Do final bookkeeping before Force managers need their data. |
| 302 |
|
*/ |
| 303 |
< |
void setupFortran(); |
| 303 |
> |
void prepareTopology(); |
| 304 |
|
|
| 305 |
|
|
| 306 |
|
/** Returns the local index manager */ |
| 351 |
|
* processor, these should be identical. |
| 352 |
|
*/ |
| 353 |
|
vector<int> getGlobalGroupIndices(); |
| 354 |
+ |
|
| 355 |
|
|
| 356 |
|
string getFinalConfigFileName() { |
| 357 |
|
return finalConfigFileName_; |
| 411 |
|
} |
| 412 |
|
|
| 413 |
|
|
| 414 |
< |
bool isFortranInitialized() { |
| 415 |
< |
return fortranInitialized_; |
| 414 |
> |
bool isTopologyDone() { |
| 415 |
> |
return topologyDone_; |
| 416 |
|
} |
| 417 |
|
|
| 418 |
|
bool getCalcBoxDipole() { |
| 586 |
|
vector<int> identArray_; |
| 587 |
|
public: |
| 588 |
|
vector<int> getIdentArray() { return identArray_; } |
| 589 |
+ |
private: |
| 590 |
+ |
|
| 591 |
+ |
/** |
| 592 |
+ |
* A vector which contains the fractional contribution of an |
| 593 |
+ |
* atom's mass to the total mass of the cutoffGroup that atom |
| 594 |
+ |
* belongs to. In the case of single atom cutoff groups, the mass |
| 595 |
+ |
* factor for that atom is 1. For massless atoms, the factor is |
| 596 |
+ |
* also 1. |
| 597 |
+ |
*/ |
| 598 |
+ |
vector<RealType> massFactors_; |
| 599 |
+ |
public: |
| 600 |
+ |
vector<RealType> getMassFactors() { return massFactors_; } |
| 601 |
+ |
|
| 602 |
+ |
PairList getExcludedInteractions() { return excludedInteractions_; } |
| 603 |
+ |
PairList getOneTwoInteractions() { return oneTwoInteractions_; } |
| 604 |
+ |
PairList getOneThreeInteractions() { return oneThreeInteractions_; } |
| 605 |
+ |
PairList getOneFourInteractions() { return oneFourInteractions_; } |
| 606 |
+ |
|
| 607 |
|
private: |
| 608 |
+ |
|
| 609 |
|
|
| 610 |
|
/// lists to handle atoms needing special treatment in the non-bonded interactions |
| 611 |
|
PairList excludedInteractions_; /**< atoms excluded from interacting with each other */ |
| 636 |
|
string restFileName_; |
| 637 |
|
|
| 638 |
|
|
| 639 |
< |
bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */ |
| 639 |
> |
bool topologyDone_; /** flag to indicate whether the topology has |
| 640 |
> |
been scanned and all the relevant |
| 641 |
> |
bookkeeping has been done*/ |
| 642 |
|
|
| 643 |
|
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate |
| 644 |
|
the simulation box dipole moment */ |
