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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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#include "utils/ElementsTable.hpp" |
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|
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namespace OpenMD { |
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Molecule::Molecule(int stampId, int globalIndex, const std::string& molName, |
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int region) : stampId_(stampId), |
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globalIndex_(globalIndex), |
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moleculeName_(molName), |
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region_(region), |
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constrainTotalCharge_(false) { |
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} |
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|
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Molecule::~Molecule() { |
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|
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MemoryUtils::deletePointers(atoms_); |
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MemoryUtils::deletePointers(bonds_); |
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MemoryUtils::deletePointers(bends_); |
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MemoryUtils::deletePointers(torsions_); |
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MemoryUtils::deletePointers(inversions_); |
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MemoryUtils::deletePointers(rigidBodies_); |
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MemoryUtils::deletePointers(cutoffGroups_); |
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MemoryUtils::deletePointers(constraintPairs_); |
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MemoryUtils::deletePointers(constraintElems_); |
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|
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// integrableObjects_ don't own the objects |
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integrableObjects_.clear(); |
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fluctuatingCharges_.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) == |
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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::addInversion(Inversion* inversion) { |
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if (std::find(inversions_.begin(), inversions_.end(), inversion) == |
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inversions_.end()) { |
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inversions_.push_back(inversion); |
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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) == |
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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) == |
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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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void Molecule::addConstraintPair(ConstraintPair* cp) { |
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if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == |
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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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void Molecule::addConstraintElem(ConstraintElem* cp) { |
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if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == |
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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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void Molecule::complete() { |
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|
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std::set<Atom*> rigidAtoms; |
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Atom* atom; |
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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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|
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// Get list of all the atoms that are part of rigid bodies |
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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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// add any atom that wasn't part of a rigid body to the list of integrableObjects |
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|
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for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
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|
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if (rigidAtoms.find(atom) == rigidAtoms.end()) { |
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|
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// If an atom does not belong to a rigid body, it is an |
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// integrable object |
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|
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integrableObjects_.push_back(atom); |
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} |
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} |
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|
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// then add the rigid bodies themselves to the integrableObjects |
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|
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for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
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integrableObjects_.push_back(rb); |
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} |
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|
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// find the atoms that are fluctuating charges and add them to the |
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// fluctuatingCharges_ vector |
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|
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for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
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if ( atom->isFluctuatingCharge() ) |
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fluctuatingCharges_.push_back( atom ); |
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} |
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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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|
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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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} |
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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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|
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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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|
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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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RealType mass = 0.0; |
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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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} |
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|
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return mass; |
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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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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() * 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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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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|
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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 = |
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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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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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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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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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RealType 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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Inversion* inversion; |
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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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Molecule::InversionIterator inversionIter; |
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|
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RealType 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 = |
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nextTorsion(torsionIter)) { |
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potential += torsion->getPotential(); |
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} |
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|
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for (inversion = beginInversion(inversionIter); torsion != NULL; |
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inversion = nextInversion(inversionIter)) { |
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potential += inversion->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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void Molecule::addProperty(GenericData* genData) { |
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properties_.addProperty(genData); |
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} |
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|
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void Molecule::removeProperty(const std::string& propName) { |
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properties_.removeProperty(propName); |
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} |
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|
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void Molecule::clearProperties() { |
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properties_.clearProperties(); |
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} |
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|
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std::vector<std::string> Molecule::getPropertyNames() { |
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return properties_.getPropertyNames(); |
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} |
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|
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std::vector<GenericData*> Molecule::getProperties() { |
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return properties_.getProperties(); |
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} |
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|
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GenericData* Molecule::getPropertyByName(const std::string& propName) { |
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return properties_.getPropertyByName(propName); |
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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.getNInversions() << " inversions" << 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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o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl; |
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return o; |
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} |
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|
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}//end namespace OpenMD |
