| 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 |
< |
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 |
|
/** |
| 86 |
|
*/ |
| 87 |
|
bool removeMolecule(Molecule* mol); |
| 88 |
|
|
| 89 |
+ |
/** Returns the total number of molecules in the system. */ |
| 90 |
+ |
int getNGlobalMolecules() { |
| 91 |
+ |
return nGlobalMols_; |
| 92 |
+ |
} |
| 93 |
+ |
|
| 94 |
+ |
/** Returns the total number of atoms in the system. */ |
| 95 |
+ |
int getNGlobalAtoms() { |
| 96 |
+ |
return nGlobalAtoms_; |
| 97 |
+ |
} |
| 98 |
+ |
|
| 99 |
+ |
/** Returns the total number of cutoff groups in the system. */ |
| 100 |
+ |
int getNGlobalCutoffGroups() { |
| 101 |
+ |
return nGlobalCutoffGroups_; |
| 102 |
+ |
} |
| 103 |
+ |
|
| 104 |
|
/** |
| 105 |
< |
* Returns the number of molecules. |
| 106 |
< |
* @return the number of molecules in this SimInfo |
| 105 |
> |
* Returns the number of local molecules. |
| 106 |
> |
* @return the number of local molecules |
| 107 |
|
*/ |
| 108 |
|
int getNMolecules() { |
| 109 |
|
return molecules_.size(); |
| 110 |
|
} |
| 111 |
|
|
| 112 |
< |
/** Returns the total number of atoms in this SimInfo */ |
| 112 |
> |
/** Returns the number of local atoms */ |
| 113 |
|
unsigned int getNAtoms() { |
| 114 |
|
return nAtoms_; |
| 115 |
|
} |
| 116 |
|
|
| 117 |
< |
/** Returns the total number of bonds in this SimInfo */ |
| 117 |
> |
/** Returns the number of local bonds */ |
| 118 |
|
unsigned int getNBonds(){ |
| 119 |
|
return nBonds_; |
| 120 |
|
} |
| 121 |
|
|
| 122 |
< |
/** Returns the total number of bends in this SimInfo */ |
| 122 |
> |
/** Returns the number of local bends */ |
| 123 |
|
unsigned int getNBends() { |
| 124 |
|
return nBends_; |
| 125 |
|
} |
| 126 |
|
|
| 127 |
< |
/** Returns the total number of torsions in this SimInfo */ |
| 127 |
> |
/** Returns the number of local torsions */ |
| 128 |
|
unsigned int getNTorsions() { |
| 129 |
|
return nTorsions_; |
| 130 |
|
} |
| 131 |
|
|
| 132 |
< |
/** Returns the total number of rigid bodies in this SimInfo */ |
| 132 |
> |
/** Returns the number of local rigid bodies */ |
| 133 |
|
unsigned int getNRigidBodies() { |
| 134 |
|
return nRigidBodies_; |
| 135 |
|
} |
| 136 |
|
|
| 137 |
< |
/** Returns the total number of integrable objects in this SimInfo */ |
| 137 |
> |
/** Returns the number of local integrable objects */ |
| 138 |
|
unsigned int getNIntegrableObjects() { |
| 139 |
|
return nIntegrableObjects_; |
| 140 |
|
} |
| 141 |
|
|
| 142 |
< |
/** Returns the total number of cutoff groups in this SimInfo */ |
| 142 |
> |
/** Returns the number of local cutoff groups */ |
| 143 |
|
unsigned int getNCutoffGroups() { |
| 144 |
|
return nCutoffGroups_; |
| 145 |
|
} |
| 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() { |
| 167 |
> |
int getNdf() { |
| 168 |
|
return ndf_; |
| 169 |
|
} |
| 170 |
|
|
| 171 |
|
/** Returns the number of raw degrees of freedom */ |
| 172 |
< |
int getNDFRaw() { |
| 172 |
> |
int getNdfRaw() { |
| 173 |
|
return ndfRaw_; |
| 174 |
|
} |
| 175 |
|
|
| 176 |
|
/** Returns the number of translational degrees of freedom */ |
| 177 |
< |
int getNDFTrans() { |
| 177 |
> |
int getNdfTrans() { |
| 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 |
|
|
| 162 |
– |
/** Sets the force field */ |
| 163 |
– |
void setForceField(ForceField* ff) { |
| 164 |
– |
forceField_ = ff; |
| 165 |
– |
} |
| 166 |
– |
|
| 210 |
|
Globals* getGlobals() { |
| 211 |
|
return globals_; |
| 212 |
|
} |
| 213 |
< |
|
| 214 |
< |
void setGlobals(Globals* globals) { |
| 215 |
< |
globals_ = globals; |
| 213 |
> |
|
| 214 |
> |
/** Returns the velocity of center of mass of the whole system.*/ |
| 215 |
> |
Vector3d getComVel(); |
| 216 |
> |
|
| 217 |
> |
/** Returns the center of the mass of the whole system.*/ |
| 218 |
> |
Vector3d getCom(); |
| 219 |
> |
|
| 220 |
> |
/** Returns the seed (used for random number generator) */ |
| 221 |
> |
int getSeed() { |
| 222 |
> |
return seed_; |
| 223 |
|
} |
| 224 |
|
|
| 225 |
< |
int* getExcludeList() { |
| 226 |
< |
return exclude_.getExcludeList(); |
| 225 |
> |
/** Sets the seed*/ |
| 226 |
> |
void setSeed(int seed) { |
| 227 |
> |
seed_ = seed; |
| 228 |
|
} |
| 229 |
+ |
|
| 230 |
+ |
/** main driver function to interact with fortran during the initialization and molecule migration */ |
| 231 |
+ |
void update(); |
| 232 |
+ |
|
| 233 |
+ |
/** Returns the local index manager */ |
| 234 |
+ |
LocalIndexManager* getLocalIndexManager() { |
| 235 |
+ |
return &localIndexMan_; |
| 236 |
+ |
} |
| 237 |
+ |
|
| 238 |
+ |
int getMoleculeStampId(int globalIndex) { |
| 239 |
+ |
//assert(globalIndex < molStampIds_.size()) |
| 240 |
+ |
return molStampIds_[globalIndex]; |
| 241 |
+ |
} |
| 242 |
+ |
|
| 243 |
+ |
/** Returns the molecule stamp */ |
| 244 |
+ |
MoleculeStamp* getMoleculeStamp(int id) { |
| 245 |
+ |
return moleculeStamps_[id]; |
| 246 |
+ |
} |
| 247 |
|
|
| 248 |
< |
private: |
| 248 |
> |
/** |
| 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 = molecules_.find(index); |
| 256 |
|
|
| 257 |
< |
void calcNDF(); |
| 258 |
< |
void calcNDFRaw(); |
| 183 |
< |
void calcNDFTrans(); |
| 257 |
> |
return i != molecules_.end() ? i->second : NULL; |
| 258 |
> |
} |
| 259 |
|
|
| 260 |
< |
void addExcludePairs(Molecule* mol); |
| 261 |
< |
void removeExcludePairs(Molecule* mol); |
| 260 |
> |
/** Calculate the maximum cutoff radius based on the atom types */ |
| 261 |
> |
double calcMaxCutoffRadius(); |
| 262 |
|
|
| 263 |
< |
int ndf_; |
| 264 |
< |
int ndfRaw_; |
| 265 |
< |
int ndfTrans_; |
| 263 |
> |
double getRcut() { |
| 264 |
> |
return rcut_; |
| 265 |
> |
} |
| 266 |
|
|
| 267 |
< |
int nAtoms_; |
| 268 |
< |
int nBonds_; |
| 269 |
< |
int nBends_; |
| 195 |
< |
int nTorsions_; |
| 196 |
< |
int nRigidBodies_; |
| 197 |
< |
int nIntegrableObjects_; |
| 198 |
< |
int nCutoffGroups_; |
| 199 |
< |
int nConstraints_; |
| 267 |
> |
void setRcut(double rcut) { |
| 268 |
> |
rcut_ = rcut; |
| 269 |
> |
} |
| 270 |
|
|
| 271 |
< |
simtype fInfo_; |
| 272 |
< |
Exclude exclude_; |
| 273 |
< |
ForceField* forceField_; |
| 271 |
> |
double getRsw() { |
| 272 |
> |
return rsw_; |
| 273 |
> |
} |
| 274 |
> |
void setRsw(double rsw) { |
| 275 |
> |
rsw_ = rsw; |
| 276 |
> |
} |
| 277 |
|
|
| 278 |
< |
std::vector<Molecule*> molecules_; /**< Molecule array */ |
| 279 |
< |
PropertyMap properties_; /** Generic Property */ |
| 280 |
< |
SnapshotManager* sman_; /** SnapshotManager */ |
| 278 |
> |
std::string getFinalConfigFileName() { |
| 279 |
> |
return finalConfigFileName_; |
| 280 |
> |
} |
| 281 |
> |
|
| 282 |
> |
void setFinalConfigFileName(const std::string& fileName) { |
| 283 |
> |
finalConfigFileName_ = fileName; |
| 284 |
> |
} |
| 285 |
|
|
| 286 |
< |
std::vector<std::pair<MoleculeStamp*, int> > moleculeStamps_; |
| 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 |
> |
|
| 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 (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_; /**< 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_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 432 |
> |
Exclude exclude_; |
| 433 |
> |
ForceField* forceField_; |
| 434 |
> |
PropertyMap properties_; /**< Generic Property */ |
| 435 |
> |
SnapshotManager* sman_; /**< SnapshotManager */ |
| 436 |
|
Globals* globals_; |
| 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 |
+ |
//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 |
