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#include "primitives/Molecule.hpp" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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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::deleteVectorOfPointer(atoms_); |
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if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) { |
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//Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
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sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); |
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return (i == cutoffGroups_.end()) ? NULL : *i; |
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} |
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void Molecule::calcForces() { |
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RigidBody* rb; |
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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*>::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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} |
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for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
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bond->calcForce(); |
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} |
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for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
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bend->calcForce(); |
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} |
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|
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for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
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torsion->calcForce(); |
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} |
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|
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} |
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|
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double Molecule::getPotential() { |
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//RigidBody* rb; |
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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*>::iterator bondIter;; |
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std::vector<Bend*>::iterator bendIter; |
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std::vector<Torsion*>::iterator torsionIter; |
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|
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double potential = 0; |
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|
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//for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
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// rb->updateAtoms(); |
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//} |
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|
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for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
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potential += bond->getPotential(); |
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} |
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|
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for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
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potential += bend->getPotential(); |
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} |
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|
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for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
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potential += torsion->getPotential(); |
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} |
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|
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return potential; |
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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; |
