| 77 |
|
/** |
| 78 |
|
* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
| 79 |
|
* @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules. |
| 80 |
< |
* The Molecule class maintains all of the concrete objects |
| 81 |
< |
* (atoms, bond, bend, torsions, rigid bodies, cutoff groups, constrains). |
| 82 |
< |
* In both the single and parallel versions, atoms and |
| 83 |
< |
* rigid bodies have both global and local indices. The local index is |
| 84 |
< |
* not relevant to molecules or cutoff groups. |
| 85 |
< |
*/ |
| 80 |
> |
* The Molecule class maintains all of the concrete objects |
| 81 |
> |
* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups, |
| 82 |
> |
* constraints). In both the single and parallel versions, atoms and |
| 83 |
> |
* rigid bodies have both global and local indices. The local index is |
| 84 |
> |
* not relevant to molecules or cutoff groups. |
| 85 |
> |
*/ |
| 86 |
|
class SimInfo { |
| 87 |
|
public: |
| 88 |
|
typedef std::map<int, Molecule*>::iterator MoleculeIterator; |
| 171 |
|
return nTorsions_; |
| 172 |
|
} |
| 173 |
|
|
| 174 |
+ |
/** Returns the number of local torsions */ |
| 175 |
+ |
unsigned int getNInversions() { |
| 176 |
+ |
return nInversions_; |
| 177 |
+ |
} |
| 178 |
|
/** Returns the number of local rigid bodies */ |
| 179 |
|
unsigned int getNRigidBodies() { |
| 180 |
|
return nRigidBodies_; |
| 276 |
|
/** Returns system angular momentum */ |
| 277 |
|
Vector3d getAngularMomentum(); |
| 278 |
|
|
| 279 |
+ |
/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/ |
| 280 |
+ |
void getGyrationalVolume(RealType &vol); |
| 281 |
+ |
/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/ |
| 282 |
+ |
void getGyrationalVolume(RealType &vol, RealType &detI); |
| 283 |
|
/** main driver function to interact with fortran during the initialization and molecule migration */ |
| 284 |
|
void update(); |
| 285 |
|
|
| 392 |
|
return calcBoxDipole_; |
| 393 |
|
} |
| 394 |
|
|
| 395 |
+ |
bool getUseAtomicVirial() { |
| 396 |
+ |
return useAtomicVirial_; |
| 397 |
+ |
} |
| 398 |
+ |
|
| 399 |
|
//below functions are just forward functions |
| 400 |
|
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
| 401 |
|
//the other hand, has-a relation need composing. |
| 527 |
|
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
| 528 |
|
|
| 529 |
|
//number of local objects |
| 530 |
< |
int nAtoms_; /**< number of atoms in local processor */ |
| 531 |
< |
int nBonds_; /**< number of bonds in local processor */ |
| 532 |
< |
int nBends_; /**< number of bends in local processor */ |
| 533 |
< |
int nTorsions_; /**< number of torsions in local processor */ |
| 534 |
< |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 535 |
< |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 536 |
< |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 537 |
< |
int nConstraints_; /**< number of constraints in local processors */ |
| 530 |
> |
int nAtoms_; /**< number of atoms in local processor */ |
| 531 |
> |
int nBonds_; /**< number of bonds in local processor */ |
| 532 |
> |
int nBends_; /**< number of bends in local processor */ |
| 533 |
> |
int nTorsions_; /**< number of torsions in local processor */ |
| 534 |
> |
int nInversions_; /**< number of inversions in local processor */ |
| 535 |
> |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 536 |
> |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 537 |
> |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 538 |
> |
int nConstraints_; /**< number of constraints in local processors */ |
| 539 |
|
|
| 540 |
|
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 541 |
|
Exclude exclude_; |
| 563 |
|
RealType rsw_; /**< radius of switching function*/ |
| 564 |
|
RealType rlist_; /**< neighbor list radius */ |
| 565 |
|
|
| 566 |
< |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
| 566 |
> |
bool ljsp_; /**< use shifted potential for LJ*/ |
| 567 |
> |
bool ljsf_; /**< use shifted force for LJ*/ |
| 568 |
|
|
| 569 |
< |
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate the simulation box dipole moment */ |
| 569 |
> |
bool fortranInitialized_; /**< flag indicate whether fortran side |
| 570 |
> |
is initialized */ |
| 571 |
> |
|
| 572 |
> |
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate |
| 573 |
> |
the simulation box dipole moment */ |
| 574 |
> |
|
| 575 |
> |
bool useAtomicVirial_; /**< flag to indicate whether or not we use |
| 576 |
> |
Atomic Virials to calculate the pressure */ |
| 577 |
|
|
| 578 |
|
public: |
| 579 |
|
/** |
| 594 |
|
//private: |
| 595 |
|
//std::vector<StuntDouble*> sdByGlobalIndex_; |
| 596 |
|
|
| 576 |
– |
#ifdef IS_MPI |
| 597 |
|
//in Parallel version, we need MolToProc |
| 598 |
|
public: |
| 599 |
|
|
| 614 |
|
void setMolToProcMap(const std::vector<int>& molToProcMap) { |
| 615 |
|
molToProcMap_ = molToProcMap; |
| 616 |
|
} |
| 597 |
– |
|
| 598 |
– |
|
| 617 |
|
|
| 618 |
|
private: |
| 619 |
|
|
| 620 |
|
void setupFortranParallel(); |
| 621 |
|
|
| 622 |
|
/** |
| 623 |
< |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
| 624 |
< |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
| 625 |
< |
* once. |
| 623 |
> |
* The size of molToProcMap_ is equal to total number of molecules |
| 624 |
> |
* in the system. It maps a molecule to the processor on which it |
| 625 |
> |
* resides. it is filled by SimCreator once and only once. |
| 626 |
|
*/ |
| 627 |
|
std::vector<int> molToProcMap_; |
| 628 |
|
|
| 611 |
– |
#endif |
| 629 |
|
|
| 630 |
|
}; |
| 631 |
|
|
