51 |
|
*/ |
52 |
|
class SimInfo { |
53 |
|
public: |
54 |
+ |
typedef std::vector<Molecule*>::iterator MoleculeIterator; |
55 |
|
SimInfo(); |
56 |
|
virtual ~SimInfo(); |
57 |
|
|
68 |
|
*/ |
69 |
|
bool removeMolecule(Molecule* mol); |
70 |
|
|
71 |
+ |
/** Returns the total number of molecules in the system. */ |
72 |
+ |
int getNGlobalMolecules() { |
73 |
+ |
|
74 |
+ |
#ifdef IS_MPI |
75 |
+ |
int nmols; |
76 |
+ |
int totNMols; |
77 |
+ |
|
78 |
+ |
nmols = getNMolecules(); |
79 |
+ |
MPI_Allreduce(&nmols, &totNMols, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
80 |
+ |
|
81 |
+ |
return totNMols; |
82 |
+ |
#else |
83 |
+ |
return getNMolecules(); |
84 |
+ |
#endif |
85 |
+ |
} |
86 |
+ |
|
87 |
+ |
/** Returns the total number of atoms in the system. */ |
88 |
+ |
int getNGlobalAtoms() { |
89 |
+ |
|
90 |
+ |
#ifdef IS_MPI |
91 |
+ |
int totNAtoms; |
92 |
+ |
MPI_Allreduce(&nAtoms_, &totNAtoms, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
93 |
+ |
return totNAtoms; |
94 |
+ |
#else |
95 |
+ |
return nAtoms_; |
96 |
+ |
#endif |
97 |
+ |
} |
98 |
+ |
|
99 |
+ |
/** Returns the total number of cutoff groups in the system. */ |
100 |
+ |
int getNGlobalCutoffGroups() { |
101 |
+ |
#ifdef IS_MPI |
102 |
+ |
int totNGroups; |
103 |
+ |
MPI_Allreduce(&nCutoffGroups_, &totNGroups, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
104 |
+ |
return totNGroups; |
105 |
+ |
#else |
106 |
+ |
return nCutoffGroups_; |
107 |
+ |
#endif |
108 |
+ |
} |
109 |
+ |
|
110 |
|
/** |
111 |
< |
* Returns the number of molecules. |
112 |
< |
* @return the number of molecules in this SimInfo |
111 |
> |
* Returns the number of local molecules. |
112 |
> |
* @return the number of local molecules |
113 |
|
*/ |
114 |
|
int getNMolecules() { |
115 |
|
return molecules_.size(); |
116 |
|
} |
117 |
|
|
118 |
< |
/** Returns the total number of atoms in this SimInfo */ |
118 |
> |
/** Returns the number of local atoms */ |
119 |
|
unsigned int getNAtoms() { |
120 |
|
return nAtoms_; |
121 |
|
} |
122 |
|
|
123 |
< |
/** Returns the total number of bonds in this SimInfo */ |
123 |
> |
/** Returns the number of local bonds */ |
124 |
|
unsigned int getNBonds(){ |
125 |
|
return nBonds_; |
126 |
|
} |
127 |
|
|
128 |
< |
/** Returns the total number of bends in this SimInfo */ |
128 |
> |
/** Returns the number of local bends */ |
129 |
|
unsigned int getNBends() { |
130 |
|
return nBends_; |
131 |
|
} |
132 |
|
|
133 |
< |
/** Returns the total number of torsions in this SimInfo */ |
133 |
> |
/** Returns the number of local torsions */ |
134 |
|
unsigned int getNTorsions() { |
135 |
|
return nTorsions_; |
136 |
|
} |
137 |
|
|
138 |
< |
/** Returns the total number of rigid bodies in this SimInfo */ |
138 |
> |
/** Returns the number of local rigid bodies */ |
139 |
|
unsigned int getNRigidBodies() { |
140 |
|
return nRigidBodies_; |
141 |
|
} |
142 |
|
|
143 |
< |
/** Returns the total number of integrable objects in this SimInfo */ |
143 |
> |
/** Returns the number of local integrable objects */ |
144 |
|
unsigned int getNIntegrableObjects() { |
145 |
|
return nIntegrableObjects_; |
146 |
|
} |
147 |
|
|
148 |
< |
/** Returns the total number of cutoff groups in this SimInfo */ |
148 |
> |
/** Returns the number of local cutoff groups */ |
149 |
|
unsigned int getNCutoffGroups() { |
150 |
|
return nCutoffGroups_; |
151 |
|
} |
212 |
|
globals_ = globals; |
213 |
|
} |
214 |
|
|
215 |
< |
int* getExcludeList() { |
176 |
< |
return exclude_.getExcludeList(); |
177 |
< |
} |
178 |
< |
|
215 |
> |
/** Returns the velocity of center of mass of the whole system.*/ |
216 |
|
Vector3d getComVel(); |
217 |
< |
|
217 |
> |
|
218 |
> |
/** Returns the center of the mass of the whole system.*/ |
219 |
|
Vector3d getCom(); |
220 |
|
|
221 |
+ |
/** Returns the seed (used for random number generator) */ |
222 |
|
int getSeed() { |
223 |
|
return seed_; |
224 |
|
} |
225 |
|
|
226 |
+ |
/** Sets the seed*/ |
227 |
|
void setSeed(int seed) { |
228 |
|
seed_ = seed; |
229 |
+ |
} |
230 |
+ |
|
231 |
+ |
|
232 |
+ |
void update(); |
233 |
+ |
|
234 |
+ |
|
235 |
+ |
/** Returns the local index manager */ |
236 |
+ |
LocalIndexManager* getLocalIndexManager() { |
237 |
+ |
return localIndexMan_; |
238 |
|
} |
239 |
+ |
|
240 |
+ |
|
241 |
+ |
/** |
242 |
+ |
* |
243 |
+ |
*/ |
244 |
+ |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
245 |
+ |
|
246 |
+ |
int getMoleculeStampId(int globalIndex) { |
247 |
+ |
//assert(globalIndex < molStampIds_.size()) |
248 |
+ |
return molStampIds_[globalIndex]; |
249 |
+ |
} |
250 |
+ |
|
251 |
+ |
/** Returns the molecule stamp */ |
252 |
+ |
MoleculeStamp* getMoleculeStamp(int id) { |
253 |
+ |
return moleculeStamps_[id]; |
254 |
+ |
} |
255 |
|
|
256 |
+ |
/** |
257 |
+ |
* Finds the processor where a molecule resides |
258 |
+ |
* @return the id of the processor which contains the molecule |
259 |
+ |
* @param globalIndex global Index of the molecule |
260 |
+ |
*/ |
261 |
+ |
int getMolToProc(int globalIndex) { |
262 |
+ |
//assert(globalIndex < molToProcMap_.size()); |
263 |
+ |
return molToProcMap_[globalIndex]; |
264 |
+ |
} |
265 |
+ |
|
266 |
+ |
/** |
267 |
+ |
* Finds a molecule with a specified global index |
268 |
+ |
* @return a pointer point to found molecule |
269 |
+ |
* @param index |
270 |
+ |
*/ |
271 |
+ |
Molecule* getMoleculeByGlobalIndex(int index) { |
272 |
+ |
std::map<int, Molecule*> i; |
273 |
+ |
i = globalIndexToMol_.find(index); |
274 |
+ |
|
275 |
+ |
return i != globalIndexToMol_.end() ? i->second : NULL; |
276 |
+ |
} |
277 |
+ |
|
278 |
+ |
|
279 |
+ |
friend std::ostream& operator <<(ostream& o, SimInfo& info); |
280 |
+ |
|
281 |
|
private: |
282 |
|
|
283 |
|
void calcNdf(); |
284 |
|
void calcNdfRaw(); |
285 |
|
void calcNdfTrans(); |
286 |
|
|
287 |
+ |
int* getExcludeList() { |
288 |
+ |
return exclude_.getExcludeList(); |
289 |
+ |
} |
290 |
+ |
|
291 |
|
void addExcludePairs(Molecule* mol); |
292 |
|
void removeExcludePairs(Molecule* mol); |
293 |
|
|
294 |
< |
int ndf_; |
294 |
> |
//degress of freedom |
295 |
> |
int ndf_; /** number of degress of freedom */ |
296 |
|
int ndfRaw_; |
297 |
< |
int ndfTrans_; |
298 |
< |
|
297 |
> |
int ndfTrans_; /**< number of translation degress of freedom */ |
298 |
> |
|
299 |
> |
//number of local objects |
300 |
|
int nAtoms_; |
301 |
|
int nBonds_; |
302 |
|
int nBends_; |
311 |
|
ForceField* forceField_; |
312 |
|
|
313 |
|
std::vector<Molecule*> molecules_; /**< Molecule array */ |
314 |
< |
PropertyMap properties_; /** Generic Property */ |
315 |
< |
SnapshotManager* sman_; /** SnapshotManager */ |
314 |
> |
PropertyMap properties_; /**< Generic Property */ |
315 |
> |
SnapshotManager* sman_; /**< SnapshotManager */ |
316 |
|
|
221 |
– |
std::vector<std::pair<MoleculeStamp*, int> > moleculeStamps_; |
317 |
|
Globals* globals_; |
318 |
|
|
319 |
< |
int seed_; |
319 |
> |
int seed_; /**< seed for random number generator */ |
320 |
> |
|
321 |
> |
LocalIndexManager localIndexMan_; |
322 |
> |
|
323 |
> |
// |
324 |
> |
std::vector<int> molToProcMap_; |
325 |
> |
std::map<int, Molecule*> globalIndexToMol_; |
326 |
> |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
327 |
> |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
328 |
> |
|
329 |
|
}; |
330 |
|
|
331 |
|
} //namespace oopse |