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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* Copyright (C) 2000-2009 The Open Molecular Dynamics Engine (OpenMD) project |
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* |
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* Contact: oopse@oopse.org |
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* Contact: gezelter@openscience.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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#ifndef PRIMITIVES_MOLECULE_HPP |
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#define PRIMITIVES_MOLECULE_HPP |
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#include <vector> |
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#include <iostream> |
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#include "math/Vector3.hpp" |
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namespace oopse{ |
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namespace OpenMD{ |
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/** |
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* @class Molecule Molecule.hpp "primitives/Molecule.hpp" |
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return localIndex_; |
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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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/** */ |
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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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/** Returns the total mass of this molecule */ |
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double getTotalMass(); |
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friend ostream& operator <<(ostream& o, const Molecule& mol); |
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friend std::ostream& operator <<(std::ostream& o, const Molecule& mol); |
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private: |
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int localIndex_; |
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std::vector<CutoffGroup*> cutoffGroups_; |
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}; |
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} //namespace oopse |
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} //namespace OpenMD |
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#endif // |
