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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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#include "utils/ElementsTable.hpp" |
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namespace OpenMD { |
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Molecule::Molecule(int stampId, int globalIndex, const std::string& molName, |
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std::set<Atom*> rigidAtoms; |
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Atom* atom; |
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AtomIterator ai; |
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Atom* atom1; |
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Atom* atom2; |
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AtomIterator ai, aj; |
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RigidBody* rb; |
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RigidBodyIterator rbIter; |
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Bond* bond; |
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BondIterator bi; |
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// Get list of all the atoms that are part of rigid bodies |
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fluctuatingCharges_.push_back( atom ); |
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} |
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} |
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// find the electronegative atoms and add them to the |
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// hBondAcceptors_ vector: |
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for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
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AtomType* at = atom->getAtomType(); |
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// get the chain of base types for this atom type: |
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std::vector<AtomType*> ayb = at->allYourBase(); |
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// use the last type in the chain of base types for the name: |
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std::string bn = ayb[ayb.size()-1]->getName(); |
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|
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if (bn.compare("O")==0 || bn.compare("N")==0 || bn.compare("F")==0) |
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hBondAcceptors_.push_back( atom ); |
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} |
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// find electronegative atoms that are either bonded to |
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// hydrogens or are present in the same rigid bodies: |
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for (bond = beginBond(bi); bond != NULL; bond = nextBond(bi)) { |
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Atom* atom1 = bond->getAtomA(); |
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Atom* atom2 = bond->getAtomB(); |
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AtomType* at1 = atom1->getAtomType(); |
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AtomType* at2 = atom1->getAtomType(); |
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// get the chain of base types for this atom type: |
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std::vector<AtomType*> ayb1 = at1->allYourBase(); |
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std::vector<AtomType*> ayb2 = at2->allYourBase(); |
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// use the last type in the chain of base types for the name: |
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std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
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std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
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|
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if (bn1.compare("H")==0) { |
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if (bn2.compare("O")==0 || bn2.compare("N")==0 |
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|| bn2.compare("F")==0) { |
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HBondDonor* donor = new HBondDonor(); |
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donor->donorAtom = atom2; |
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donor->donatedHydrogen = atom1; |
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hBondDonors_.push_back( donor ); |
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} |
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} |
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if (bn2.compare("H")==0) { |
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if (bn1.compare("O")==0 || bn1.compare("N")==0 |
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|| bn1.compare("F")==0) { |
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HBondDonor* donor = new HBondDonor(); |
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donor->donorAtom = atom1; |
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donor->donatedHydrogen = atom2; |
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hBondDonors_.push_back( donor ); |
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} |
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} |
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} |
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for (rb = beginRigidBody(rbIter); rb != NULL; |
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rb = nextRigidBody(rbIter)) { |
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for(atom1 = rb->beginAtom(ai); atom1 != NULL; |
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atom1 = rb->nextAtom(ai)) { |
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AtomType* at1 = atom1->getAtomType(); |
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// get the chain of base types for this atom type: |
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std::vector<AtomType*> ayb1 = at1->allYourBase(); |
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// use the last type in the chain of base types for the name: |
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std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
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|
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if (bn1.compare("O")==0 || bn1.compare("N")==0 |
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|| bn1.compare("F")==0) { |
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for(atom2 = rb->beginAtom(aj); atom2 != NULL; |
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atom2 = rb->nextAtom(aj)) { |
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AtomType* at2 = atom2->getAtomType(); |
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// get the chain of base types for this atom type: |
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std::vector<AtomType*> ayb2 = at2->allYourBase(); |
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// use the last type in the chain of base types for the name: |
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std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
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if (bn2.compare("H")==0) { |
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HBondDonor* donor = new HBondDonor(); |
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donor->donorAtom = atom1; |
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donor->donatedHydrogen = atom2; |
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hBondDonors_.push_back( donor ); |
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} |
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} |
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} |
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} |
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} |
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} |
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|
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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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return com; |
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} |
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|
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Vector3d Molecule::getCom(int snapshotNo) { |
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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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RealType totalMass = 0; |
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RealType mass; |
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|
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for (sd = beginIntegrableObject(i); sd != NULL; sd = |
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nextIntegrableObject(i)){ |
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mass = sd->getMass(); |
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totalMass += mass; |
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com += sd->getPos(snapshotNo) * mass; |
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} |
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com /= totalMass; |
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return com; |
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} |
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|
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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; |
