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* @version 1.0 |
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*/ |
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#include "primitives/Molecule.hpp" |
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#include <algorithm> |
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#include <set> |
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#include "primitives/Molecule.hpp" |
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#include "utils/MemoryUtils.hpp" |
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namespace oopse { |
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Molecule::~Molecule() { |
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deleteVectorOfPointer(atoms_); |
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deleteVectorOfPointer(bonds_); |
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deleteVectorOfPointer(bends_); |
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deleteVectorOfPointer(torsions_); |
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deleteVectorOfPointer(rigidbodies_); |
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deleteVectorOfPointer(cutoffGroups_); |
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MemoryUtils::deleteVectorOfPointer(atoms_); |
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MemoryUtils::deleteVectorOfPointer(bonds_); |
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MemoryUtils::deleteVectorOfPointer(bends_); |
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MemoryUtils::deleteVectorOfPointer(torsions_); |
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MemoryUtils::deleteVectorOfPointer(rigidBodies_); |
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MemoryUtils::deleteVectorOfPointer(cutoffGroups_); |
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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 (atoms_.find(atom) == atoms_.end()) { |
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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 (bonds_.find(bond) == bonds_.end()) { |
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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 (bends_.find(bend) == bends_.end()) { |
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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 (torsions_.find(torsion) == torsions_.end()) { |
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if (std::find(torsions_.begin(), torsions_.end(), torsion) == 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 (rigidBodies_.find(bond) == bonds_.end()) { |
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if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == 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 (cutoffGroups_.find(bond) == bonds_.end()) { |
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if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) { |
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cutoffGroups_.push_back(cp); |
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} |
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std::set<Atom*> rigidAtoms; |
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RigidBody* rb; |
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std::vector<RigidBody*> rbIter; |
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std::vector<RigidBody*>::iterator rbIter; |
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for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
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rigidAtoms.insert(rb->beginAtomIter(), rb->endAtomIter()); |
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rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); |
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} |
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//find all free atoms (which do not belong to rigid bodies) |
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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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std::vector<RigidBody*> rbIter; |
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std::vector<Bond*> bondIter;; |
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std::vector<Bend*> bendIter; |
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std::vector<Torsion*> torsionIter; |
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std::vector<RigidBody*>::iterator rbIter; |
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std::vector<Bond*>::iterator bondIter;; |
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std::vector<Bend*>::iterator bendIter; |
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std::vector<Torsion*>::iterator torsionIter; |
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for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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Bend* bend; |
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Torsion* torsion; |
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//std::vector<RigidBody*> rbIter; |
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std::vector<Bond*> bondIter;; |
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std::vector<Bend*> bendIter; |
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std::vector<Torsion*> torsionIter; |
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std::vector<Bond*>::iterator bondIter;; |
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std::vector<Bend*>::iterator bendIter; |
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std::vector<Torsion*>::iterator torsionIter; |
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double potential = 0; |
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return com; |
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} |
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void Molecule::moveCom(const Vetor3d& delta) { |
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void Molecule::moveCom(const Vector3d& delta) { |
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StuntDouble* sd; |
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std::vector<StuntDouble*>::iterator i; |
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for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
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s->setPos(sd->getPos() + delta); |
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sd->setPos(sd->getPos() + delta); |
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} |
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} |
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return velCom; |
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} |
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std::ostream& operator <<(std::ostream& o, const Molecule& mol) { |
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std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
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o << std::endl; |
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o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
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o << mol.getNAtoms() << " atoms" << std::endl; |
