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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.cpp |
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* @author tlin |
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* @date 10/28/2004 |
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* @version 1.0 |
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*/ |
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|
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#include <algorithm> |
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#include <set> |
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|
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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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|
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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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|
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Molecule::~Molecule() { |
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|
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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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MemoryUtils::deleteVectorOfPointer(constraintPairs_); |
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MemoryUtils::deleteVectorOfPointer(constraintElems_); |
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//integrableObjects_ don't own the objects |
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integrableObjects_.clear(); |
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|
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} |
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|
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void Molecule::addAtom(Atom* atom) { |
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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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|
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void Molecule::addBond(Bond* bond) { |
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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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|
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void Molecule::addBend(Bend* bend) { |
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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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|
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void Molecule::addTorsion(Torsion* torsion) { |
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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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|
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void Molecule::addRigidBody(RigidBody *rb) { |
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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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|
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void Molecule::addCutoffGroup(CutoffGroup* cp) { |
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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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|
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} |
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|
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void Molecule::addConstraintPair(ConstraintPair* cp) { |
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if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == constraintPairs_.end()) { |
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constraintPairs_.push_back(cp); |
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} |
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|
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} |
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|
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void Molecule::addConstraintElem(ConstraintElem* cp) { |
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if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == constraintElems_.end()) { |
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constraintElems_.push_back(cp); |
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} |
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|
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} |
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|
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void Molecule::complete() { |
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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*>::iterator rbIter; |
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|
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|
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for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
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rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); |
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} |
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|
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Atom* atom; |
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AtomIterator ai; |
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for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
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|
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if (rigidAtoms.find(*ai) == rigidAtoms.end()) { |
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//if an atom does not belong to a rigid body, it is an integrable object |
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integrableObjects_.push_back(*ai); |
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} |
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} |
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|
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//find all free atoms (which do not belong to rigid bodies) |
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//performs the "difference" operation from set theory, the output range contains a copy of every |
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//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in |
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//[rigidAtoms.begin(), rigidAtoms.end()). |
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//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), |
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// std::back_inserter(integrableObjects_)); |
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|
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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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// |
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// painCave.isFatal = 1; |
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// simError(); |
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//} |
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|
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integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); |
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} |
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|
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double Molecule::getMass() { |
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StuntDouble* sd; |
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std::vector<StuntDouble*>::iterator i; |
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double mass = 0.0; |
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|
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for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
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mass += sd->getMass(); |
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} |
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|
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return mass; |
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|
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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; |
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Vector3d com; |
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double totalMass = 0; |
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double mass; |
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|
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for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
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mass = sd->getMass(); |
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totalMass += mass; |
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com += sd->getPos() * mass; |
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} |
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|
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com /= totalMass; |
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|
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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; |
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|
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for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
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sd->setPos(sd->getPos() + delta); |
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} |
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|
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} |
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|
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Vector3d Molecule::getComVel() { |
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StuntDouble* sd; |
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std::vector<StuntDouble*>::iterator i; |
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Vector3d velCom; |
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double totalMass = 0; |
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double mass; |
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|
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for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
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mass = sd->getMass(); |
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totalMass += mass; |
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velCom += sd->getVel() * mass; |
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} |
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|
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velCom /= totalMass; |
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|
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return velCom; |
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} |
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|
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double Molecule::getPotential() { |
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|
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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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Molecule::BondIterator bondIter;; |
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Molecule::BendIterator bendIter; |
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Molecule::TorsionIterator torsionIter; |
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|
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double potential = 0.0; |
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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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|
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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; |
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o << mol.getNBonds() << " bonds" << std::endl; |
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o << mol.getNBends() << " bends" << std::endl; |
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o << mol.getNTorsions() << " torsions" << std::endl; |
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o << mol.getNRigidBodies() << " rigid bodies" << std::endl; |
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o << mol.getNIntegrableObjects() << "integrable objects" << std::endl; |
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o << mol.getNCutoffGroups() << "cutoff groups" << std::endl; |
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o << mol.getNConstraintPairs() << "constraint pairs" << std::endl; |
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return o; |
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} |
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|
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}//end namespace oopse |
