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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.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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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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/** |
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* @file Molecule.hpp |
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* @author tlin |
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* @date 10/25/2004 |
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* @version 1.0 |
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*/ |
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|
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#include "primitives/Molecule.hpp" |
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|
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namespace oopse { |
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|
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Molecule::~Molecule() { |
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|
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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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|
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integrableObjects_.clear(); |
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|
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} |
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|
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|
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Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) { |
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i = atoms_.begin(); |
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return (i == atoms_.end()) ? NULL : *i; |
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} |
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|
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Atom* Molecule::nextAtom(std::vector<Atom*>::iterator& i) { |
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++i; |
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return (i == atoms_.end()) ? NULL : *i; |
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} |
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|
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Bond* Molecule::beginBond(std::vector<Bond*>::iterator& i) { |
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i = bonds_.begin(); |
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return (i == bonds_.end()) ? NULL : *i; |
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} |
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|
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Bond* Molecule::nextBond(std::vector<Bond*>::iterator& i) { |
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++i; |
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return (i == bonds_.end()) ? NULL : *i; |
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|
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} |
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|
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|
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Bend* Molecule::beginBend(std::vector<Bend*>::iterator& i) { |
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i = bends_.begin(); |
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return (i == bends_.end()) ? NULL : *i; |
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} |
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|
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Bend* Molecule::nextBend(std::vector<Bend*>::iterator& i) { |
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++i; |
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return (i == bends_.end()) ? NULL : *i; |
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} |
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|
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Torsion* Molecule::beginTorsion(std::vector<Torsion*>::iterator& i) { |
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i = torsions_.begin(); |
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return (i == torsions_.end()) ? NULL : *i; |
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} |
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|
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Torsion* Molecule::nextTorsion(std::vector<Torsion*>::iterator& i) { |
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++i; |
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return (i == torsions_.end()) ? NULL : *i; |
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} |
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|
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RigidBody* Molecule::beginRigidBody(std::vector<RigidBody*>::iterator& i) { |
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i = rigidBodies_.begin(); |
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return (i == rigidBodies_.end()) ? NULL : *i; |
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} |
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|
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RigidBody* Molecule::nextRigidBody(std::vector<RigidBody*>::iterator& i) { |
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++i; |
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return (i == rigidBodies_.end()) ? NULL : *i; |
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} |
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|
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StuntDouble* Molecule::beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
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i = integrableObjects_.begin(); |
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return (i == integrableObjects_.end()) ? NULL : *i; |
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} |
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|
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StuntDouble* Molecule::nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
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++i; |
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return (i == integrableObjects_.end()) ? NULL : *i; |
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} |
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|
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CutoffGroup* Molecule::beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
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i = cutoffGroups_.begin(); |
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return (i == cutoffGroups_.end()) ? NULL : *i; |
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} |
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|
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CutoffGroup* Molecule::nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
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++i; |
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return (i == cutoffGroups_.end()) ? NULL : *i; |
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} |
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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*> 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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|
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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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bond->calcForce(); |
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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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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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}//end namespace oopse |
