51 |
|
*/ |
52 |
|
class SimInfo { |
53 |
|
public: |
54 |
< |
SimInfo(); |
54 |
> |
typedef MoleculeIterator MoleculeIterator; |
55 |
> |
|
56 |
> |
/** |
57 |
> |
* Constructor of SimInfo |
58 |
> |
* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the |
59 |
> |
* second element is the total number of molecules with the same molecule stamp in the system |
60 |
> |
* @param ff pointer of a concrete ForceField instance |
61 |
> |
* @param globals |
62 |
> |
* @note |
63 |
> |
* <p> |
64 |
> |
* The major change of SimInfo |
65 |
> |
* </p> |
66 |
> |
*/ |
67 |
> |
SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals); |
68 |
|
virtual ~SimInfo(); |
69 |
|
|
70 |
|
/** |
80 |
|
*/ |
81 |
|
bool removeMolecule(Molecule* mol); |
82 |
|
|
83 |
+ |
/** Returns the total number of molecules in the system. */ |
84 |
+ |
int getNGlobalMolecules() { |
85 |
+ |
return nGlobalMols_; |
86 |
+ |
} |
87 |
+ |
|
88 |
+ |
/** Returns the total number of atoms in the system. */ |
89 |
+ |
int getNGlobalAtoms() { |
90 |
+ |
return nGlobalAtoms_; |
91 |
+ |
} |
92 |
+ |
|
93 |
+ |
/** Returns the total number of cutoff groups in the system. */ |
94 |
+ |
int getNGlobalCutoffGroups() { |
95 |
+ |
return nGlobalCutoffGroups_; |
96 |
+ |
} |
97 |
+ |
|
98 |
|
/** |
99 |
< |
* Returns the number of molecules. |
100 |
< |
* @return the number of molecules in this SimInfo |
99 |
> |
* Returns the number of local molecules. |
100 |
> |
* @return the number of local molecules |
101 |
|
*/ |
102 |
|
int getNMolecules() { |
103 |
|
return molecules_.size(); |
104 |
|
} |
105 |
|
|
106 |
< |
/** Returns the total number of atoms in this SimInfo */ |
106 |
> |
/** Returns the number of local atoms */ |
107 |
|
unsigned int getNAtoms() { |
108 |
|
return nAtoms_; |
109 |
|
} |
110 |
|
|
111 |
< |
/** Returns the total number of bonds in this SimInfo */ |
111 |
> |
/** Returns the number of local bonds */ |
112 |
|
unsigned int getNBonds(){ |
113 |
|
return nBonds_; |
114 |
|
} |
115 |
|
|
116 |
< |
/** Returns the total number of bends in this SimInfo */ |
116 |
> |
/** Returns the number of local bends */ |
117 |
|
unsigned int getNBends() { |
118 |
|
return nBends_; |
119 |
|
} |
120 |
|
|
121 |
< |
/** Returns the total number of torsions in this SimInfo */ |
121 |
> |
/** Returns the number of local torsions */ |
122 |
|
unsigned int getNTorsions() { |
123 |
|
return nTorsions_; |
124 |
|
} |
125 |
|
|
126 |
< |
/** Returns the total number of rigid bodies in this SimInfo */ |
126 |
> |
/** Returns the number of local rigid bodies */ |
127 |
|
unsigned int getNRigidBodies() { |
128 |
|
return nRigidBodies_; |
129 |
|
} |
130 |
|
|
131 |
< |
/** Returns the total number of integrable objects in this SimInfo */ |
131 |
> |
/** Returns the number of local integrable objects */ |
132 |
|
unsigned int getNIntegrableObjects() { |
133 |
|
return nIntegrableObjects_; |
134 |
|
} |
135 |
|
|
136 |
< |
/** Returns the total number of cutoff groups in this SimInfo */ |
136 |
> |
/** Returns the number of local cutoff groups */ |
137 |
|
unsigned int getNCutoffGroups() { |
138 |
|
return nCutoffGroups_; |
139 |
|
} |
148 |
|
* @return the first molecule, return NULL if there is not molecule in this SimInfo |
149 |
|
* @param i the iterator of molecule array (user shouldn't change it) |
150 |
|
*/ |
151 |
< |
Molecule* beginMolecule(std::vector<Molecule*>::iterator& i); |
151 |
> |
Molecule* beginMolecule(MoleculeIterator& i); |
152 |
|
|
153 |
|
/** |
154 |
|
* Returns the next avaliable Molecule based on the iterator. |
155 |
|
* @return the next avaliable molecule, return NULL if reaching the end of the array |
156 |
|
* @param i the iterator of molecule array |
157 |
|
*/ |
158 |
< |
Molecule* nextMolecule(std::vector<Molecule*>::iterator& i); |
158 |
> |
Molecule* nextMolecule(MoleculeIterator& i); |
159 |
|
|
160 |
|
/** Returns the number of degrees of freedom */ |
161 |
|
int getNdf() { |
172 |
|
return ndfTrans_; |
173 |
|
} |
174 |
|
|
175 |
+ |
//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
176 |
+ |
|
177 |
+ |
/** Returns the total number of z-constraint molecules in the system */ |
178 |
+ |
int getNZconstraint() { |
179 |
+ |
return nZconstraint_; |
180 |
+ |
} |
181 |
+ |
|
182 |
+ |
/** |
183 |
+ |
* Sets the number of z-constraint molecules in the system. |
184 |
+ |
*/ |
185 |
+ |
int setNZconstraint(int nZconstraint) { |
186 |
+ |
nZconstraint_ = nZconstraint; |
187 |
+ |
} |
188 |
+ |
|
189 |
|
/** Returns the snapshot manager. */ |
190 |
|
SnapshotManager* getSnapshotManager() { |
191 |
|
return sman_; |
201 |
|
return forceField_; |
202 |
|
} |
203 |
|
|
162 |
– |
/** Sets the force field */ |
163 |
– |
void setForceField(ForceField* ff) { |
164 |
– |
forceField_ = ff; |
165 |
– |
} |
166 |
– |
|
204 |
|
Globals* getGlobals() { |
205 |
|
return globals_; |
206 |
|
} |
170 |
– |
|
171 |
– |
void setGlobals(Globals* globals) { |
172 |
– |
globals_ = globals; |
173 |
– |
} |
207 |
|
|
208 |
< |
int* getExcludeList() { |
176 |
< |
return exclude_.getExcludeList(); |
177 |
< |
} |
178 |
< |
|
208 |
> |
/** Returns the velocity of center of mass of the whole system.*/ |
209 |
|
Vector3d getComVel(); |
210 |
< |
|
210 |
> |
|
211 |
> |
/** Returns the center of the mass of the whole system.*/ |
212 |
|
Vector3d getCom(); |
213 |
|
|
214 |
+ |
/** Returns the seed (used for random number generator) */ |
215 |
|
int getSeed() { |
216 |
|
return seed_; |
217 |
|
} |
218 |
|
|
219 |
+ |
/** Sets the seed*/ |
220 |
|
void setSeed(int seed) { |
221 |
|
seed_ = seed; |
222 |
|
} |
223 |
+ |
|
224 |
+ |
/** main driver function to interact with fortran during the initialization and molecule migration */ |
225 |
+ |
void update(); |
226 |
+ |
|
227 |
+ |
/** Returns the local index manager */ |
228 |
+ |
LocalIndexManager* getLocalIndexManager() { |
229 |
+ |
return localIndexMan_; |
230 |
+ |
} |
231 |
+ |
|
232 |
+ |
int getMoleculeStampId(int globalIndex) { |
233 |
+ |
//assert(globalIndex < molStampIds_.size()) |
234 |
+ |
return molStampIds_[globalIndex]; |
235 |
+ |
} |
236 |
+ |
|
237 |
+ |
/** Returns the molecule stamp */ |
238 |
+ |
MoleculeStamp* getMoleculeStamp(int id) { |
239 |
+ |
return moleculeStamps_[id]; |
240 |
+ |
} |
241 |
|
|
242 |
+ |
/** |
243 |
+ |
* Finds a molecule with a specified global index |
244 |
+ |
* @return a pointer point to found molecule |
245 |
+ |
* @param index |
246 |
+ |
*/ |
247 |
+ |
Molecule* getMoleculeByGlobalIndex(int index) { |
248 |
+ |
std::map<int, Molecule*> i; |
249 |
+ |
i = molecules_.find(index); |
250 |
+ |
|
251 |
+ |
return i != molecules_.end() ? i->second : NULL; |
252 |
+ |
} |
253 |
+ |
|
254 |
+ |
/** Returns the unique atom types of local processor in an array */ |
255 |
+ |
std::set<AtomType*> SimInfo::getUniqueAtomTypes(); |
256 |
+ |
|
257 |
+ |
std::string getFinalConfigFileName() { |
258 |
+ |
return finalConfigFileName_; |
259 |
+ |
} |
260 |
+ |
|
261 |
+ |
void setFinalConfigFileName(const std::string& fileName) { |
262 |
+ |
finalConfigFileName_ = fileName; |
263 |
+ |
} |
264 |
+ |
|
265 |
+ |
|
266 |
+ |
std::string getDumpFileName() { |
267 |
+ |
return dumpFileName_; |
268 |
+ |
} |
269 |
+ |
|
270 |
+ |
void setDumpFileName(const std::string& fileName) { |
271 |
+ |
dumpFileName_ = fileName; |
272 |
+ |
} |
273 |
+ |
|
274 |
+ |
std::string getStatFileName() { |
275 |
+ |
return statFileName_; |
276 |
+ |
} |
277 |
+ |
|
278 |
+ |
void setStatFileName(const std::string& fileName) { |
279 |
+ |
statFileName_ = fileName; |
280 |
+ |
} |
281 |
+ |
|
282 |
+ |
int* getGlobalGroupMembershipPointer() { |
283 |
+ |
return globalGroupMembership_[0]; |
284 |
+ |
} |
285 |
+ |
|
286 |
+ |
//below functions are just forward functions |
287 |
+ |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
288 |
+ |
//the other hand, has-a relation need composing. |
289 |
+ |
/** |
290 |
+ |
* Adds property into property map |
291 |
+ |
* @param genData GenericData to be added into PropertyMap |
292 |
+ |
*/ |
293 |
+ |
void addProperty(GenericData* genData); |
294 |
+ |
|
295 |
+ |
/** |
296 |
+ |
* Removes property from PropertyMap by name |
297 |
+ |
* @param propName the name of property to be removed |
298 |
+ |
*/ |
299 |
+ |
void removeProperty(const std::string& propName); |
300 |
+ |
|
301 |
+ |
/** |
302 |
+ |
* clear all of the properties |
303 |
+ |
*/ |
304 |
+ |
void clearProperties(); |
305 |
+ |
|
306 |
+ |
/** |
307 |
+ |
* Returns all names of properties |
308 |
+ |
* @return all names of properties |
309 |
+ |
*/ |
310 |
+ |
std::vector<std::string> getPropertyNames(); |
311 |
+ |
|
312 |
+ |
/** |
313 |
+ |
* Returns all of the properties in PropertyMap |
314 |
+ |
* @return all of the properties in PropertyMap |
315 |
+ |
*/ |
316 |
+ |
std::vector<GenericData*> getProperties(); |
317 |
+ |
|
318 |
+ |
/** |
319 |
+ |
* Returns property |
320 |
+ |
* @param propName name of property |
321 |
+ |
* @return a pointer point to property with propName. If no property named propName |
322 |
+ |
* exists, return NULL |
323 |
+ |
*/ |
324 |
+ |
GenericData* getPropertyByName(const std::string& propName); |
325 |
+ |
|
326 |
+ |
friend std::ostream& operator <<(ostream& o, SimInfo& info); |
327 |
+ |
|
328 |
|
private: |
329 |
|
|
330 |
+ |
void setupSimType(); |
331 |
+ |
|
332 |
+ |
/** |
333 |
+ |
* Setup Fortran Simulation |
334 |
+ |
* @see #setupFortranParallel |
335 |
+ |
*/ |
336 |
+ |
void setupFortranSim(); |
337 |
+ |
|
338 |
+ |
/** Calculates the number of degress of freedom in the whole system */ |
339 |
|
void calcNdf(); |
340 |
|
void calcNdfRaw(); |
341 |
|
void calcNdfTrans(); |
343 |
|
void addExcludePairs(Molecule* mol); |
344 |
|
void removeExcludePairs(Molecule* mol); |
345 |
|
|
346 |
< |
int ndf_; |
347 |
< |
int ndfRaw_; |
348 |
< |
int ndfTrans_; |
346 |
> |
/** |
347 |
> |
* Adds molecule stamps into |
348 |
> |
*/ |
349 |
> |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
350 |
> |
|
351 |
> |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
352 |
|
|
353 |
< |
int nAtoms_; |
354 |
< |
int nBonds_; |
355 |
< |
int nBends_; |
356 |
< |
int nTorsions_; |
357 |
< |
int nRigidBodies_; |
358 |
< |
int nIntegrableObjects_; |
359 |
< |
int nCutoffGroups_; |
360 |
< |
int nConstraints_; |
353 |
> |
//degress of freedom |
354 |
> |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
355 |
> |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
356 |
> |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
357 |
> |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
358 |
> |
|
359 |
> |
//number of global objects |
360 |
> |
int nGlobalMols_; /**< number of molecules in the system */ |
361 |
> |
int nGlobalAtoms_; /**< number of atoms in the system */ |
362 |
> |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
363 |
|
|
364 |
< |
simtype fInfo_; |
365 |
< |
Exclude exclude_; |
366 |
< |
ForceField* forceField_; |
364 |
> |
/** |
365 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
366 |
> |
* corresponding content is the global index of cutoff group this atom belong to. |
367 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
368 |
> |
*/ |
369 |
> |
std::vector<int> globalGroupMembership_; |
370 |
|
|
371 |
< |
std::vector<Molecule*> molecules_; /**< Molecule array */ |
372 |
< |
PropertyMap properties_; /** Generic Property */ |
373 |
< |
SnapshotManager* sman_; /** SnapshotManager */ |
371 |
> |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
372 |
> |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
373 |
> |
|
374 |
> |
//number of local objects |
375 |
> |
int nAtoms_; /**< number of atoms in local processor */ |
376 |
> |
int nBonds_; /**< number of bonds in local processor */ |
377 |
> |
int nBends_; /**< number of bends in local processor */ |
378 |
> |
int nTorsions_; /**< number of torsions in local processor */ |
379 |
> |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
380 |
> |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
381 |
> |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
382 |
> |
int nConstraints_; /**< number of constraints in local processors */ |
383 |
|
|
384 |
< |
std::vector<std::pair<MoleculeStamp*, int> > moleculeStamps_; |
384 |
> |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
385 |
> |
Exclude exclude_; |
386 |
> |
ForceField* forceField_; |
387 |
> |
PropertyMap properties_; /**< Generic Property */ |
388 |
> |
SnapshotManager* sman_; /**< SnapshotManager */ |
389 |
|
Globals* globals_; |
390 |
+ |
int seed_; /**< seed for random number generator */ |
391 |
|
|
392 |
< |
int seed_; |
392 |
> |
LocalIndexManager localIndexMan_; |
393 |
> |
|
394 |
> |
std::string finalConfigFileName_; |
395 |
> |
std::string dumpFileName_; |
396 |
> |
std::string statFileName_; |
397 |
> |
|
398 |
> |
#ifdef IS_MPI |
399 |
> |
//in Parallel version, we need MolToProc |
400 |
> |
public: |
401 |
> |
|
402 |
> |
/** |
403 |
> |
* Finds the processor where a molecule resides |
404 |
> |
* @return the id of the processor which contains the molecule |
405 |
> |
* @param globalIndex global Index of the molecule |
406 |
> |
*/ |
407 |
> |
int getMolToProc(int globalIndex) { |
408 |
> |
//assert(globalIndex < molToProcMap_.size()); |
409 |
> |
return molToProcMap_[globalIndex]; |
410 |
> |
} |
411 |
> |
|
412 |
> |
int* getMolToProcMapPointer() { |
413 |
> |
return &molToProcMap_[0]; |
414 |
> |
} |
415 |
> |
|
416 |
> |
private: |
417 |
> |
|
418 |
> |
void setupFortranParallel(); |
419 |
> |
|
420 |
> |
/** |
421 |
> |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
422 |
> |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
423 |
> |
* once. |
424 |
> |
*/ |
425 |
> |
std::vector<int> molToProcMap_; |
426 |
> |
#endif |
427 |
> |
|
428 |
|
}; |
429 |
|
|
430 |
|
} //namespace oopse |