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namespace oopse { |
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Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) |
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: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) { |
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} |
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} |
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Molecule::~Molecule() { |
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MemoryUtils::deletePointers(atoms_); |
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MemoryUtils::deletePointers(bonds_); |
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MemoryUtils::deletePointers(bends_); |
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MemoryUtils::deletePointers(cutoffGroups_); |
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MemoryUtils::deletePointers(constraintPairs_); |
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MemoryUtils::deletePointers(constraintElems_); |
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//integrableObjects_ don't own the objects |
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// integrableObjects_ don't own the objects |
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integrableObjects_.clear(); |
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} |
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void Molecule::addAtom(Atom* atom) { |
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if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) { |
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atoms_.push_back(atom); |
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} |
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} |
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void Molecule::addBond(Bond* bond) { |
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if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) { |
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bonds_.push_back(bond); |
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} |
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} |
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void Molecule::addBend(Bend* bend) { |
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if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) { |
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bends_.push_back(bend); |
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} |
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} |
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void Molecule::addTorsion(Torsion* torsion) { |
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if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) { |
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if (std::find(torsions_.begin(), torsions_.end(), torsion) == |
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torsions_.end()) { |
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torsions_.push_back(torsion); |
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} |
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} |
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void Molecule::addRigidBody(RigidBody *rb) { |
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if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) { |
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if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == |
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rigidBodies_.end()) { |
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rigidBodies_.push_back(rb); |
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} |
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} |
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void Molecule::addCutoffGroup(CutoffGroup* cp) { |
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if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) { |
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if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == |
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cutoffGroups_.end()) { |
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cutoffGroups_.push_back(cp); |
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} |
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} |
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} |
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void Molecule::addConstraintPair(ConstraintPair* cp) { |
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if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == constraintPairs_.end()) { |
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if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == |
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constraintPairs_.end()) { |
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constraintPairs_.push_back(cp); |
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} |
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} |
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} |
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void Molecule::addConstraintElem(ConstraintElem* cp) { |
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if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == constraintElems_.end()) { |
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if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == |
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constraintElems_.end()) { |
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constraintElems_.push_back(cp); |
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} |
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} |
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void Molecule::complete() { |
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std::set<Atom*> rigidAtoms; |
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for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
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rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); |
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} |
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Atom* atom; |
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AtomIterator ai; |
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for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
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if (rigidAtoms.find(*ai) == rigidAtoms.end()) { |
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//if an atom does not belong to a rigid body, it is an integrable object |
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|
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// If an atom does not belong to a rigid body, it is an |
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// integrable object |
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integrableObjects_.push_back(*ai); |
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} |
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} |
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//find all free atoms (which do not belong to rigid bodies) |
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//performs the "difference" operation from set theory, the output range contains a copy of every |
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//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in |
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< |
//[rigidAtoms.begin(), rigidAtoms.end()). |
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// performs the "difference" operation from set theory, the output |
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// range contains a copy of every element that is contained in |
| 156 |
> |
// [allAtoms.begin(), allAtoms.end()) and not contained in |
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// [rigidAtoms.begin(), rigidAtoms.end()). |
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//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), |
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// std::back_inserter(integrableObjects_)); |
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|
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//integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); |
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} |
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|
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< |
double Molecule::getMass() { |
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> |
RealType Molecule::getMass() { |
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StuntDouble* sd; |
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std::vector<StuntDouble*>::iterator i; |
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< |
double mass = 0.0; |
| 178 |
< |
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| 179 |
< |
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
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> |
RealType mass = 0.0; |
| 178 |
> |
|
| 179 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 180 |
> |
nextIntegrableObject(i)){ |
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mass += sd->getMass(); |
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} |
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< |
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< |
return mass; |
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> |
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> |
return mass; |
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} |
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|
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Vector3d Molecule::getCom() { |
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StuntDouble* sd; |
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std::vector<StuntDouble*>::iterator i; |
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Vector3d com; |
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< |
double totalMass = 0; |
| 192 |
< |
double mass; |
| 191 |
> |
RealType totalMass = 0; |
| 192 |
> |
RealType mass; |
| 193 |
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|
| 194 |
< |
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
| 194 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 195 |
> |
nextIntegrableObject(i)){ |
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mass = sd->getMass(); |
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totalMass += mass; |
| 198 |
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com += sd->getPos() * mass; |
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} |
| 200 |
< |
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> |
|
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com /= totalMass; |
| 202 |
|
|
| 203 |
|
return com; |
| 207 |
|
StuntDouble* sd; |
| 208 |
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std::vector<StuntDouble*>::iterator i; |
| 209 |
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|
| 210 |
< |
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
| 210 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 211 |
> |
nextIntegrableObject(i)){ |
| 212 |
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sd->setPos(sd->getPos() + delta); |
| 213 |
< |
} |
| 207 |
< |
|
| 213 |
> |
} |
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} |
| 215 |
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|
| 216 |
|
Vector3d Molecule::getComVel() { |
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StuntDouble* sd; |
| 218 |
|
std::vector<StuntDouble*>::iterator i; |
| 219 |
|
Vector3d velCom; |
| 220 |
< |
double totalMass = 0; |
| 221 |
< |
double mass; |
| 220 |
> |
RealType totalMass = 0; |
| 221 |
> |
RealType mass; |
| 222 |
|
|
| 223 |
< |
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
| 223 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 224 |
> |
nextIntegrableObject(i)){ |
| 225 |
|
mass = sd->getMass(); |
| 226 |
|
totalMass += mass; |
| 227 |
|
velCom += sd->getVel() * mass; |
| 228 |
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} |
| 229 |
< |
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| 229 |
> |
|
| 230 |
|
velCom /= totalMass; |
| 231 |
< |
|
| 231 |
> |
|
| 232 |
|
return velCom; |
| 233 |
|
} |
| 234 |
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|
| 235 |
< |
double Molecule::getPotential() { |
| 235 |
> |
RealType Molecule::getPotential() { |
| 236 |
|
|
| 237 |
|
Bond* bond; |
| 238 |
|
Bend* bend; |
| 241 |
|
Molecule::BendIterator bendIter; |
| 242 |
|
Molecule::TorsionIterator torsionIter; |
| 243 |
|
|
| 244 |
< |
double potential = 0.0; |
| 244 |
> |
RealType potential = 0.0; |
| 245 |
|
|
| 246 |
|
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
| 247 |
|
potential += bond->getPotential(); |
| 251 |
|
potential += bend->getPotential(); |
| 252 |
|
} |
| 253 |
|
|
| 254 |
< |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
| 254 |
> |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = |
| 255 |
> |
nextTorsion(torsionIter)) { |
| 256 |
|
potential += torsion->getPotential(); |
| 257 |
|
} |
| 258 |
< |
|
| 258 |
> |
|
| 259 |
|
return potential; |
| 260 |
< |
|
| 260 |
> |
|
| 261 |
|
} |
| 262 |
< |
|
| 262 |
> |
|
| 263 |
|
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
| 264 |
|
o << std::endl; |
| 265 |
|
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
| 273 |
|
o << mol.getNConstraintPairs() << "constraint pairs" << std::endl; |
| 274 |
|
return o; |
| 275 |
|
} |
| 276 |
< |
|
| 276 |
> |
|
| 277 |
|
}//end namespace oopse |
