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typedef std::vector<Torsion*>::iterator TorsionIterator; |
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typedef std::vector<RigidBody*>::iterator RigidBodyIterator; |
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typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
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typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
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typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
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typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator; |
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typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator; |
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Molecule(int stampId, int globalIndex, const std::string& molName); |
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virtual ~Molecule(); |
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/** |
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* Returns the global index of this molecule. |
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* @return the global index of this molecule |
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int getGlobalIndex() { |
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return globalIndex_; |
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} |
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/** |
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* Returns the stamp id of this molecule |
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* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its |
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* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor. |
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* @note Ideally, every molecule should keep a pointer of its |
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* molecule stamp instead of its stamp id. However, the pointer |
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* will become invalid, if the molecule migrate to other |
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* processor. |
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*/ |
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int getStampId() { |
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return stampId_; |
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} |
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/** Returns the name of the molecule */ |
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std::string getType() { |
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return moleculeName_; |
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} |
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/** |
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* Sets the global index of this molecule. |
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* @param new global index to be set |
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void setGlobalIndex(int index) { |
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globalIndex_ = index; |
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} |
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/** add an atom into this molecule */ |
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void addAtom(Atom* atom); |
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/** add a bond into this molecule */ |
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void addBond(Bond* bond); |
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/** add a bend into this molecule */ |
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void addBend(Bend* bend); |
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/** add a torsion into this molecule*/ |
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void addTorsion(Torsion* torsion); |
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/** add a rigidbody into this molecule */ |
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void addRigidBody(RigidBody *rb); |
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/** add a cutoff group into this molecule */ |
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void addCutoffGroup(CutoffGroup* cp); |
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void addConstraintPair(ConstraintPair* consPair); |
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void addConstraintElem(ConstraintElem* consElem); |
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/** */ |
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void complete(); |
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/** Returns the total number of atoms in this molecule */ |
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unsigned int getNAtoms() { |
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return atoms_.size(); |
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} |
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/** Returns the total number of bonds in this molecule */ |
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unsigned int getNBonds(){ |
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return bonds_.size(); |
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} |
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/** Returns the total number of bends in this molecule */ |
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unsigned int getNBends() { |
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return bends_.size(); |
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} |
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/** Returns the total number of torsions in this molecule */ |
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unsigned int getNTorsions() { |
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return torsions_.size(); |
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} |
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/** Returns the total number of rigid bodies in this molecule */ |
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unsigned int getNRigidBodies() { |
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return rigidBodies_.size(); |
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} |
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/** Returns the total number of integrable objects in this molecule */ |
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unsigned int getNIntegrableObjects() { |
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return integrableObjects_.size(); |
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} |
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> |
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/** Returns the total number of cutoff groups in this molecule */ |
| 177 |
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unsigned int getNCutoffGroups() { |
| 178 |
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return cutoffGroups_.size(); |
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} |
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/** Returns the total number of constraints in this molecule */ |
| 182 |
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unsigned int getNConstraintPairs() { |
| 183 |
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return constraintPairs_.size(); |
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} |
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< |
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Atom* getAtomAt(unsigned int i) { |
| 187 |
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assert(i < atoms_.size()); |
| 188 |
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return atoms_[i]; |
| 189 |
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} |
| 190 |
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| 190 |
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RigidBody* getRigidBodyAt(unsigned int i) { |
| 192 |
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assert(i < rigidBodies_.size()); |
| 193 |
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return rigidBodies_[i]; |
| 194 |
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} |
| 195 |
< |
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> |
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| 196 |
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Atom* beginAtom(std::vector<Atom*>::iterator& i) { |
| 197 |
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i = atoms_.begin(); |
| 198 |
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return (i == atoms_.end()) ? NULL : *i; |
| 199 |
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} |
| 200 |
< |
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| 200 |
> |
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| 201 |
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Atom* nextAtom(std::vector<Atom*>::iterator& i) { |
| 202 |
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++i; |
| 203 |
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return (i == atoms_.end()) ? NULL : *i; |
| 204 |
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} |
| 205 |
< |
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| 205 |
> |
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| 206 |
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Bond* beginBond(std::vector<Bond*>::iterator& i) { |
| 207 |
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i = bonds_.begin(); |
| 208 |
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return (i == bonds_.end()) ? NULL : *i; |
| 209 |
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} |
| 210 |
< |
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| 210 |
> |
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| 211 |
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Bond* nextBond(std::vector<Bond*>::iterator& i) { |
| 212 |
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++i; |
| 213 |
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return (i == bonds_.end()) ? NULL : *i; |
| 214 |
< |
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| 214 |
> |
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| 215 |
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} |
| 216 |
< |
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| 216 |
> |
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| 217 |
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Bend* beginBend(std::vector<Bend*>::iterator& i) { |
| 218 |
|
i = bends_.begin(); |
| 219 |
|
return (i == bends_.end()) ? NULL : *i; |
| 220 |
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} |
| 221 |
< |
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| 221 |
> |
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| 222 |
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Bend* nextBend(std::vector<Bend*>::iterator& i) { |
| 223 |
|
++i; |
| 224 |
|
return (i == bends_.end()) ? NULL : *i; |
| 225 |
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} |
| 226 |
< |
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| 226 |
> |
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| 227 |
|
Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) { |
| 228 |
|
i = torsions_.begin(); |
| 229 |
|
return (i == torsions_.end()) ? NULL : *i; |
| 230 |
|
} |
| 231 |
< |
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| 231 |
> |
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| 232 |
|
Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) { |
| 233 |
|
++i; |
| 234 |
|
return (i == torsions_.end()) ? NULL : *i; |
| 235 |
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} |
| 236 |
< |
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| 236 |
> |
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| 237 |
|
RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) { |
| 238 |
|
i = rigidBodies_.begin(); |
| 239 |
|
return (i == rigidBodies_.end()) ? NULL : *i; |
| 240 |
|
} |
| 241 |
< |
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| 241 |
> |
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| 242 |
|
RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) { |
| 243 |
|
++i; |
| 244 |
|
return (i == rigidBodies_.end()) ? NULL : *i; |
| 245 |
|
} |
| 246 |
< |
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| 246 |
> |
|
| 247 |
|
StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
| 248 |
|
i = integrableObjects_.begin(); |
| 249 |
|
return (i == integrableObjects_.end()) ? NULL : *i; |
| 250 |
|
} |
| 251 |
< |
|
| 251 |
> |
|
| 252 |
|
StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
| 253 |
|
++i; |
| 254 |
|
return (i == integrableObjects_.end()) ? NULL : *i; |
| 255 |
|
} |
| 256 |
< |
|
| 256 |
> |
|
| 257 |
|
CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 258 |
|
i = cutoffGroups_.begin(); |
| 259 |
|
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 260 |
|
} |
| 261 |
|
|
| 262 |
< |
CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 262 |
> |
CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 263 |
|
++i; |
| 264 |
|
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 265 |
|
} |
| 266 |
< |
|
| 266 |
> |
|
| 267 |
|
ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 268 |
|
i = constraintPairs_.begin(); |
| 269 |
|
return (i == constraintPairs_.end()) ? NULL : *i; |
| 270 |
|
} |
| 271 |
< |
|
| 271 |
> |
|
| 272 |
|
ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 273 |
|
++i; |
| 274 |
|
return (i == constraintPairs_.end()) ? NULL : *i; |
| 275 |
|
} |
| 276 |
< |
|
| 276 |
> |
|
| 277 |
|
ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 278 |
|
i = constraintElems_.begin(); |
| 279 |
|
return (i == constraintElems_.end()) ? NULL : *i; |
| 280 |
|
} |
| 281 |
< |
|
| 281 |
> |
|
| 282 |
|
ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 283 |
|
++i; |
| 284 |
|
return (i == constraintElems_.end()) ? NULL : *i; |
| 285 |
|
} |
| 286 |
< |
|
| 287 |
< |
/** return the total potential energy of short range interaction of this molecule */ |
| 286 |
> |
|
| 287 |
> |
/** |
| 288 |
> |
* Returns the total potential energy of short range interaction |
| 289 |
> |
* of this molecule |
| 290 |
> |
*/ |
| 291 |
|
RealType getPotential(); |
| 292 |
< |
|
| 292 |
> |
|
| 293 |
|
/** get total mass of this molecule */ |
| 294 |
|
RealType getMass(); |
| 295 |
< |
|
| 295 |
> |
|
| 296 |
|
/** return the center of mass of this molecule */ |
| 297 |
|
Vector3d getCom(); |
| 298 |
< |
|
| 298 |
> |
|
| 299 |
|
/** Moves the center of this molecule */ |
| 300 |
|
void moveCom(const Vector3d& delta); |
| 301 |
< |
|
| 301 |
> |
|
| 302 |
|
/** Returns the velocity of center of mass of this molecule */ |
| 303 |
|
Vector3d getComVel(); |
| 304 |
|
|
| 307 |
|
} |
| 308 |
|
|
| 309 |
|
friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
| 310 |
< |
|
| 310 |
> |
|
| 311 |
|
private: |
| 312 |
< |
|
| 312 |
> |
|
| 313 |
|
int globalIndex_; |
| 314 |
< |
|
| 314 |
> |
|
| 315 |
|
std::vector<Atom*> atoms_; |
| 316 |
|
std::vector<Bond*> bonds_; |
| 317 |
|
std::vector<Bend*> bends_; |
