75 |
|
* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the |
76 |
|
* second element is the total number of molecules with the same molecule stamp in the system |
77 |
|
* @param ff pointer of a concrete ForceField instance |
78 |
< |
* @param globals |
78 |
> |
* @param simParams |
79 |
|
* @note |
80 |
|
*/ |
81 |
< |
SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals); |
81 |
> |
SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams); |
82 |
|
virtual ~SimInfo(); |
83 |
|
|
84 |
|
/** |
116 |
|
int getNGlobalIntegrableObjects() { |
117 |
|
return nGlobalIntegrableObjects_; |
118 |
|
} |
119 |
+ |
|
120 |
+ |
/** |
121 |
+ |
* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
122 |
+ |
* of atoms which do not belong to the rigid bodies) in the system |
123 |
+ |
*/ |
124 |
+ |
int getNGlobalRigidBodies() { |
125 |
+ |
return nGlobalRigidBodies_; |
126 |
+ |
} |
127 |
|
|
128 |
|
/** |
129 |
|
* Returns the number of local molecules. |
229 |
|
return forceField_; |
230 |
|
} |
231 |
|
|
232 |
< |
Globals* getGlobals() { |
233 |
< |
return globals_; |
232 |
> |
Globals* getSimParams() { |
233 |
> |
return simParams_; |
234 |
|
} |
235 |
|
|
236 |
|
/** Returns the velocity of center of mass of the whole system.*/ |
409 |
|
*/ |
410 |
|
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
411 |
|
|
412 |
+ |
ForceField* forceField_; |
413 |
+ |
Globals* simParams_; |
414 |
+ |
|
415 |
|
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
416 |
|
|
417 |
|
//degress of freedom |
425 |
|
int nGlobalAtoms_; /**< number of atoms in the system */ |
426 |
|
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
427 |
|
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
428 |
< |
|
428 |
> |
int nGlobalRigidBodies_; /**< number of rigid bodies in this system */ |
429 |
|
/** |
430 |
|
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
431 |
|
* corresponding content is the global index of cutoff group this atom belong to. |
455 |
|
int nConstraints_; /**< number of constraints in local processors */ |
456 |
|
|
457 |
|
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
458 |
< |
Exclude exclude_; |
448 |
< |
ForceField* forceField_; |
458 |
> |
Exclude exclude_; |
459 |
|
PropertyMap properties_; /**< Generic Property */ |
460 |
|
SnapshotManager* sman_; /**< SnapshotManager */ |
461 |
< |
Globals* globals_; |
461 |
> |
|
462 |
|
int seed_; /**< seed for random number generator */ |
463 |
|
|
464 |
|
/** |