47 |
|
|
48 |
|
/** |
49 |
|
* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
50 |
< |
* @brief |
50 |
> |
* @brief As one of the heavy weight class of OOPSE, SimInfo |
51 |
> |
* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules. |
52 |
> |
* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies, |
53 |
> |
* cutoff groups, constrains). |
54 |
> |
* Another major change is the index. No matter single version or parallel version, atoms and |
55 |
> |
* rigid bodies have both global index and local index. Local index is not important to molecule as well as |
56 |
> |
* cutoff group. |
57 |
|
*/ |
58 |
|
class SimInfo { |
59 |
|
public: |
60 |
< |
typedef std::vector<Molecule*>::iterator MoleculeIterator; |
61 |
< |
SimInfo(); |
60 |
> |
typedef MoleculeIterator MoleculeIterator; |
61 |
> |
|
62 |
> |
/** |
63 |
> |
* Constructor of SimInfo |
64 |
> |
* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the |
65 |
> |
* second element is the total number of molecules with the same molecule stamp in the system |
66 |
> |
* @param ff pointer of a concrete ForceField instance |
67 |
> |
* @param globals |
68 |
> |
* @note |
69 |
> |
* <p> |
70 |
> |
* The major change of SimInfo |
71 |
> |
* </p> |
72 |
> |
*/ |
73 |
> |
SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals); |
74 |
|
virtual ~SimInfo(); |
75 |
|
|
76 |
|
/** |
88 |
|
|
89 |
|
/** Returns the total number of molecules in the system. */ |
90 |
|
int getNGlobalMolecules() { |
91 |
< |
|
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 |
91 |
> |
return nGlobalMols_; |
92 |
|
} |
93 |
|
|
94 |
|
/** Returns the total number of atoms in the system. */ |
95 |
|
int getNGlobalAtoms() { |
96 |
< |
|
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 |
96 |
> |
return nGlobalAtoms_; |
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 |
101 |
> |
return nGlobalCutoffGroups_; |
102 |
|
} |
103 |
|
|
104 |
|
/** |
154 |
|
* @return the first molecule, return NULL if there is not molecule in this SimInfo |
155 |
|
* @param i the iterator of molecule array (user shouldn't change it) |
156 |
|
*/ |
157 |
< |
Molecule* beginMolecule(std::vector<Molecule*>::iterator& i); |
157 |
> |
Molecule* beginMolecule(MoleculeIterator& i); |
158 |
|
|
159 |
|
/** |
160 |
|
* Returns the next avaliable Molecule based on the iterator. |
161 |
|
* @return the next avaliable molecule, return NULL if reaching the end of the array |
162 |
|
* @param i the iterator of molecule array |
163 |
|
*/ |
164 |
< |
Molecule* nextMolecule(std::vector<Molecule*>::iterator& i); |
164 |
> |
Molecule* nextMolecule(MoleculeIterator& i); |
165 |
|
|
166 |
|
/** Returns the number of degrees of freedom */ |
167 |
|
int getNdf() { |
178 |
|
return ndfTrans_; |
179 |
|
} |
180 |
|
|
181 |
+ |
//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
182 |
+ |
|
183 |
+ |
/** Returns the total number of z-constraint molecules in the system */ |
184 |
+ |
int getNZconstraint() { |
185 |
+ |
return nZconstraint_; |
186 |
+ |
} |
187 |
+ |
|
188 |
+ |
/** |
189 |
+ |
* Sets the number of z-constraint molecules in the system. |
190 |
+ |
*/ |
191 |
+ |
int setNZconstraint(int nZconstraint) { |
192 |
+ |
nZconstraint_ = nZconstraint; |
193 |
+ |
} |
194 |
+ |
|
195 |
|
/** Returns the snapshot manager. */ |
196 |
|
SnapshotManager* getSnapshotManager() { |
197 |
|
return sman_; |
207 |
|
return forceField_; |
208 |
|
} |
209 |
|
|
202 |
– |
/** Sets the force field */ |
203 |
– |
void setForceField(ForceField* ff) { |
204 |
– |
forceField_ = ff; |
205 |
– |
} |
206 |
– |
|
210 |
|
Globals* getGlobals() { |
211 |
|
return globals_; |
212 |
|
} |
210 |
– |
|
211 |
– |
void setGlobals(Globals* globals) { |
212 |
– |
globals_ = globals; |
213 |
– |
} |
213 |
|
|
214 |
|
/** Returns the velocity of center of mass of the whole system.*/ |
215 |
|
Vector3d getComVel(); |
227 |
|
seed_ = seed; |
228 |
|
} |
229 |
|
|
230 |
< |
|
230 |
> |
/** main driver function to interact with fortran during the initialization and molecule migration */ |
231 |
|
void update(); |
232 |
|
|
234 |
– |
|
233 |
|
/** Returns the local index manager */ |
234 |
|
LocalIndexManager* getLocalIndexManager() { |
235 |
< |
return localIndexMan_; |
235 |
> |
return &localIndexMan_; |
236 |
|
} |
239 |
– |
|
240 |
– |
|
241 |
– |
/** |
242 |
– |
* |
243 |
– |
*/ |
244 |
– |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
237 |
|
|
238 |
|
int getMoleculeStampId(int globalIndex) { |
239 |
|
//assert(globalIndex < molStampIds_.size()) |
246 |
|
} |
247 |
|
|
248 |
|
/** |
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 |
– |
/** |
249 |
|
* Finds a molecule with a specified global index |
250 |
|
* @return a pointer point to found molecule |
251 |
|
* @param index |
252 |
|
*/ |
253 |
|
Molecule* getMoleculeByGlobalIndex(int index) { |
254 |
|
std::map<int, Molecule*> i; |
255 |
< |
i = globalIndexToMol_.find(index); |
255 |
> |
i = molecules_.find(index); |
256 |
|
|
257 |
< |
return i != globalIndexToMol_.end() ? i->second : NULL; |
257 |
> |
return i != molecules_.end() ? i->second : NULL; |
258 |
|
} |
259 |
+ |
|
260 |
+ |
/** Calculate the maximum cutoff radius based on the atom types */ |
261 |
+ |
double calcMaxCutoffRadius(); |
262 |
+ |
|
263 |
+ |
double getRcut() { |
264 |
+ |
return rcut_; |
265 |
+ |
} |
266 |
+ |
|
267 |
+ |
void setRcut(double rcut) { |
268 |
+ |
rcut_ = rcut; |
269 |
+ |
} |
270 |
+ |
|
271 |
+ |
double getRsw() { |
272 |
+ |
return rsw_; |
273 |
+ |
} |
274 |
+ |
void setRsw(double rsw) { |
275 |
+ |
rsw_ = rsw; |
276 |
+ |
} |
277 |
+ |
|
278 |
+ |
std::string getFinalConfigFileName() { |
279 |
+ |
return finalConfigFileName_; |
280 |
+ |
} |
281 |
+ |
|
282 |
+ |
void setFinalConfigFileName(const std::string& fileName) { |
283 |
+ |
finalConfigFileName_ = fileName; |
284 |
+ |
} |
285 |
+ |
|
286 |
+ |
|
287 |
+ |
std::string getDumpFileName() { |
288 |
+ |
return dumpFileName_; |
289 |
+ |
} |
290 |
+ |
|
291 |
+ |
void setDumpFileName(const std::string& fileName) { |
292 |
+ |
dumpFileName_ = fileName; |
293 |
+ |
} |
294 |
+ |
|
295 |
+ |
std::string getStatFileName() { |
296 |
+ |
return statFileName_; |
297 |
+ |
} |
298 |
+ |
|
299 |
+ |
void setStatFileName(const std::string& fileName) { |
300 |
+ |
statFileName_ = fileName; |
301 |
+ |
} |
302 |
+ |
|
303 |
+ |
/** |
304 |
+ |
* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class |
305 |
+ |
* @see #SimCreator::setGlobalIndex |
306 |
+ |
*/ |
307 |
+ |
int* getGlobalGroupMembershipPointer() { |
308 |
+ |
return globalGroupMembership_[0]; |
309 |
+ |
} |
310 |
+ |
|
311 |
+ |
/** |
312 |
+ |
* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class |
313 |
+ |
* @see #SimCreator::setGlobalIndex |
314 |
+ |
*/ |
315 |
+ |
int* getGlobalMolMembershipPointer() { |
316 |
+ |
return globalMolMembership_[0]; |
317 |
+ |
} |
318 |
+ |
|
319 |
+ |
//below functions are just forward functions |
320 |
+ |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
321 |
+ |
//the other hand, has-a relation need composing. |
322 |
+ |
/** |
323 |
+ |
* Adds property into property map |
324 |
+ |
* @param genData GenericData to be added into PropertyMap |
325 |
+ |
*/ |
326 |
+ |
void addProperty(GenericData* genData); |
327 |
|
|
328 |
+ |
/** |
329 |
+ |
* Removes property from PropertyMap by name |
330 |
+ |
* @param propName the name of property to be removed |
331 |
+ |
*/ |
332 |
+ |
void removeProperty(const std::string& propName); |
333 |
|
|
334 |
+ |
/** |
335 |
+ |
* clear all of the properties |
336 |
+ |
*/ |
337 |
+ |
void clearProperties(); |
338 |
+ |
|
339 |
+ |
/** |
340 |
+ |
* Returns all names of properties |
341 |
+ |
* @return all names of properties |
342 |
+ |
*/ |
343 |
+ |
std::vector<std::string> getPropertyNames(); |
344 |
+ |
|
345 |
+ |
/** |
346 |
+ |
* Returns all of the properties in PropertyMap |
347 |
+ |
* @return all of the properties in PropertyMap |
348 |
+ |
*/ |
349 |
+ |
std::vector<GenericData*> getProperties(); |
350 |
+ |
|
351 |
+ |
/** |
352 |
+ |
* Returns property |
353 |
+ |
* @param propName name of property |
354 |
+ |
* @return a pointer point to property with propName. If no property named propName |
355 |
+ |
* exists, return NULL |
356 |
+ |
*/ |
357 |
+ |
GenericData* getPropertyByName(const std::string& propName); |
358 |
+ |
|
359 |
|
friend std::ostream& operator <<(ostream& o, SimInfo& info); |
360 |
|
|
361 |
|
private: |
362 |
|
|
363 |
+ |
|
364 |
+ |
/** Returns the unique atom types of local processor in an array */ |
365 |
+ |
std::set<AtomType*> SimInfo::getUniqueAtomTypes(); |
366 |
+ |
|
367 |
+ |
/** fill up the simtype struct*/ |
368 |
+ |
void setupSimType(); |
369 |
+ |
|
370 |
+ |
/** |
371 |
+ |
* Setup Fortran Simulation |
372 |
+ |
* @see #setupFortranParallel |
373 |
+ |
*/ |
374 |
+ |
void setupFortranSim(); |
375 |
+ |
|
376 |
+ |
/** Calculates the number of degress of freedom in the whole system */ |
377 |
|
void calcNdf(); |
378 |
|
void calcNdfRaw(); |
379 |
|
void calcNdfTrans(); |
380 |
|
|
287 |
– |
int* getExcludeList() { |
288 |
– |
return exclude_.getExcludeList(); |
289 |
– |
} |
290 |
– |
|
381 |
|
void addExcludePairs(Molecule* mol); |
382 |
|
void removeExcludePairs(Molecule* mol); |
383 |
|
|
384 |
+ |
/** |
385 |
+ |
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
386 |
+ |
* system. |
387 |
+ |
*/ |
388 |
+ |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
389 |
+ |
|
390 |
+ |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
391 |
+ |
|
392 |
|
//degress of freedom |
393 |
< |
int ndf_; /** number of degress of freedom */ |
394 |
< |
int ndfRaw_; |
395 |
< |
int ndfTrans_; /**< number of translation degress of freedom */ |
393 |
> |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
394 |
> |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
395 |
> |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
396 |
> |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
397 |
> |
|
398 |
> |
//number of global objects |
399 |
> |
int nGlobalMols_; /**< number of molecules in the system */ |
400 |
> |
int nGlobalAtoms_; /**< number of atoms in the system */ |
401 |
> |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
402 |
|
|
403 |
+ |
/** |
404 |
+ |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
405 |
+ |
* corresponding content is the global index of cutoff group this atom belong to. |
406 |
+ |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
407 |
+ |
*/ |
408 |
+ |
std::vector<int> globalGroupMembership_; |
409 |
+ |
|
410 |
+ |
/** |
411 |
+ |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
412 |
+ |
* corresponding content is the global index of molecule this atom belong to. |
413 |
+ |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
414 |
+ |
*/ |
415 |
+ |
std::vector<int> globalMolMembership_; |
416 |
+ |
|
417 |
+ |
|
418 |
+ |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
419 |
+ |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
420 |
+ |
|
421 |
|
//number of local objects |
422 |
< |
int nAtoms_; |
423 |
< |
int nBonds_; |
424 |
< |
int nBends_; |
425 |
< |
int nTorsions_; |
426 |
< |
int nRigidBodies_; |
427 |
< |
int nIntegrableObjects_; |
428 |
< |
int nCutoffGroups_; |
429 |
< |
int nConstraints_; |
422 |
> |
int nAtoms_; /**< number of atoms in local processor */ |
423 |
> |
int nBonds_; /**< number of bonds in local processor */ |
424 |
> |
int nBends_; /**< number of bends in local processor */ |
425 |
> |
int nTorsions_; /**< number of torsions in local processor */ |
426 |
> |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
427 |
> |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
428 |
> |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
429 |
> |
int nConstraints_; /**< number of constraints in local processors */ |
430 |
|
|
431 |
< |
simtype fInfo_; |
431 |
> |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
432 |
|
Exclude exclude_; |
433 |
< |
ForceField* forceField_; |
312 |
< |
|
313 |
< |
std::vector<Molecule*> molecules_; /**< Molecule array */ |
433 |
> |
ForceField* forceField_; |
434 |
|
PropertyMap properties_; /**< Generic Property */ |
435 |
|
SnapshotManager* sman_; /**< SnapshotManager */ |
316 |
– |
|
436 |
|
Globals* globals_; |
318 |
– |
|
437 |
|
int seed_; /**< seed for random number generator */ |
438 |
|
|
439 |
+ |
/** |
440 |
+ |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
441 |
+ |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
442 |
+ |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
443 |
+ |
* to make a efficient data moving plan. |
444 |
+ |
*/ |
445 |
|
LocalIndexManager localIndexMan_; |
446 |
|
|
447 |
< |
// |
448 |
< |
std::vector<int> molToProcMap_; |
449 |
< |
std::map<int, Molecule*> globalIndexToMol_; |
450 |
< |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
327 |
< |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
447 |
> |
//file names |
448 |
> |
std::string finalConfigFileName_; |
449 |
> |
std::string dumpFileName_; |
450 |
> |
std::string statFileName_; |
451 |
|
|
452 |
+ |
double rcut_; /**< cutoff radius*/ |
453 |
+ |
double rsw_; /**< radius of switching function*/ |
454 |
+ |
|
455 |
+ |
#ifdef IS_MPI |
456 |
+ |
//in Parallel version, we need MolToProc |
457 |
+ |
public: |
458 |
+ |
|
459 |
+ |
/** |
460 |
+ |
* Finds the processor where a molecule resides |
461 |
+ |
* @return the id of the processor which contains the molecule |
462 |
+ |
* @param globalIndex global Index of the molecule |
463 |
+ |
*/ |
464 |
+ |
int getMolToProc(int globalIndex) { |
465 |
+ |
//assert(globalIndex < molToProcMap_.size()); |
466 |
+ |
return molToProcMap_[globalIndex]; |
467 |
+ |
} |
468 |
+ |
|
469 |
+ |
/** |
470 |
+ |
* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class |
471 |
+ |
* @see #SimCreator::divideMolecules |
472 |
+ |
*/ |
473 |
+ |
int* getMolToProcMapPointer() { |
474 |
+ |
return &molToProcMap_[0]; |
475 |
+ |
} |
476 |
+ |
|
477 |
+ |
private: |
478 |
+ |
|
479 |
+ |
void setupFortranParallel(); |
480 |
+ |
|
481 |
+ |
/** |
482 |
+ |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
483 |
+ |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
484 |
+ |
* once. |
485 |
+ |
*/ |
486 |
+ |
std::vector<int> molToProcMap_; |
487 |
+ |
#endif |
488 |
+ |
|
489 |
|
}; |
490 |
|
|
491 |
|
} //namespace oopse |