| 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 |
|
|
| 229 |
|
return ndf_ - getFdf(); |
| 230 |
|
} |
| 231 |
|
|
| 232 |
+ |
/** Returns the number of degrees of freedom (LOCAL) */ |
| 233 |
+ |
int getNdfLocal() { |
| 234 |
+ |
return ndfLocal_; |
| 235 |
+ |
} |
| 236 |
+ |
|
| 237 |
|
/** Returns the number of raw degrees of freedom */ |
| 238 |
|
int getNdfRaw() { |
| 239 |
|
return ndfRaw_; |
| 282 |
|
Globals* getSimParams() { |
| 283 |
|
return simParams_; |
| 284 |
|
} |
| 284 |
– |
|
| 285 |
– |
/** Returns the velocity of center of mass of the whole system.*/ |
| 286 |
– |
Vector3d getComVel(); |
| 287 |
– |
|
| 288 |
– |
/** Returns the center of the mass of the whole system.*/ |
| 289 |
– |
Vector3d getCom(); |
| 290 |
– |
/** Returns the center of the mass and Center of Mass velocity of |
| 291 |
– |
the whole system.*/ |
| 292 |
– |
void getComAll(Vector3d& com,Vector3d& comVel); |
| 293 |
– |
|
| 294 |
– |
/** Returns intertia tensor for the entire system and system |
| 295 |
– |
Angular Momentum.*/ |
| 296 |
– |
void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum); |
| 297 |
– |
|
| 298 |
– |
/** Returns system angular momentum */ |
| 299 |
– |
Vector3d getAngularMomentum(); |
| 300 |
– |
|
| 301 |
– |
/** Returns volume of system as estimated by an ellipsoid defined |
| 302 |
– |
by the radii of gyration*/ |
| 303 |
– |
void getGyrationalVolume(RealType &vol); |
| 304 |
– |
/** Overloaded version of gyrational volume that also returns |
| 305 |
– |
det(I) so dV/dr can be calculated*/ |
| 306 |
– |
void getGyrationalVolume(RealType &vol, RealType &detI); |
| 285 |
|
|
| 286 |
|
void update(); |
| 287 |
|
/** |
| 381 |
|
|
| 382 |
|
/** |
| 383 |
|
* Sets GlobalGroupMembership |
| 406 |
– |
* @see #SimCreator::setGlobalIndex |
| 384 |
|
*/ |
| 385 |
|
void setGlobalGroupMembership(const vector<int>& globalGroupMembership) { |
| 386 |
|
assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
| 389 |
|
|
| 390 |
|
/** |
| 391 |
|
* Sets GlobalMolMembership |
| 415 |
– |
* @see #SimCreator::setGlobalIndex |
| 392 |
|
*/ |
| 393 |
|
void setGlobalMolMembership(const vector<int>& globalMolMembership) { |
| 394 |
|
assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
| 511 |
|
|
| 512 |
|
/// Degress of freedom |
| 513 |
|
int ndf_; /**< number of degress of freedom (excludes constraints) (LOCAL) */ |
| 514 |
+ |
int ndfLocal_; /**< number of degrees of freedom (LOCAL, excludes constraints) */ |
| 515 |
|
int fdf_local; /**< number of frozen degrees of freedom (LOCAL) */ |
| 516 |
|
int fdf_; /**< number of frozen degrees of freedom (GLOBAL) */ |
| 517 |
|
int ndfRaw_; /**< number of degress of freedom (includes constraints), (LOCAL) */ |
| 661 |
|
|
| 662 |
|
/** |
| 663 |
|
* Set MolToProcMap array |
| 687 |
– |
* @see #SimCreator::divideMolecules |
| 664 |
|
*/ |
| 665 |
|
void setMolToProcMap(const vector<int>& molToProcMap) { |
| 666 |
|
molToProcMap_ = molToProcMap; |
