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#include <stdlib.h> |
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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, 24107 (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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|
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namespace OpenMD { |
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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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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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|
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Molecule::Molecule( void ){ |
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|
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myAtoms = NULL; |
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myBonds = NULL; |
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myBends = NULL; |
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myTorsions = NULL; |
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} |
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|
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Molecule::~Molecule( void ){ |
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int i; |
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CutoffGroup* cg; |
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vector<CutoffGroup*>::iterator iter; |
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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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if( myAtoms != NULL ){ |
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for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i]; |
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delete[] myAtoms; |
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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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if( myBonds != NULL ){ |
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for(i=0; i<nBonds; i++) if(myBonds[i] != NULL ) delete myBonds[i]; |
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delete[] myBonds; |
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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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if( myBends != NULL ){ |
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for(i=0; i<nBends; i++) if(myBends[i] != NULL ) delete myBends[i]; |
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delete[] myBends; |
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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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if( myTorsions != NULL ){ |
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for(i=0; i<nTorsions; i++) if(myTorsions[i] != NULL ) delete myTorsions[i]; |
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delete[] myTorsions; |
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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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for(cg = beginCutoffGroup(iter); cg != NULL; cg = nextCutoffGroup(iter)) |
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delete cg; |
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myCutoffGroups.clear(); |
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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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} |
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|
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|
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void Molecule::initialize( molInit &theInit ){ |
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|
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CutoffGroup* curCutoffGroup; |
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vector<CutoffGroup*>::iterator iterCutoff; |
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Atom* cutoffAtom; |
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vector<Atom*>::iterator iterAtom; |
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int atomIndex; |
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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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nAtoms = theInit.nAtoms; |
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nMembers = nAtoms; |
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nBonds = theInit.nBonds; |
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nBends = theInit.nBends; |
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nTorsions = theInit.nTorsions; |
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nRigidBodies = theInit.nRigidBodies; |
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nOriented = theInit.nOriented; |
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|
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myAtoms = theInit.myAtoms; |
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myBonds = theInit.myBonds; |
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myBends = theInit.myBends; |
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myTorsions = theInit.myTorsions; |
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myRigidBodies = theInit.myRigidBodies; |
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|
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myIntegrableObjects = theInit.myIntegrableObjects; |
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|
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for (int i = 0; i < myRigidBodies.size(); i++) |
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myRigidBodies[i]->calcRefCoords(); |
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|
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myCutoffGroups = theInit.myCutoffGroups; |
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nCutoffGroups = myCutoffGroups.size(); |
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|
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} |
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|
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void Molecule::calcForces( void ){ |
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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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int i; |
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double com[3]; |
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|
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for(i=0; i<myRigidBodies.size(); i++) { |
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myRigidBodies[i]->updateAtoms(); |
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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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for(i=0; i<nBonds; i++){ |
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myBonds[i]->calc_forces(); |
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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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AtomIterator ai; |
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RigidBody* rb; |
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RigidBodyIterator rbIter; |
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|
|
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< |
for(i=0; i<nBends; i++){ |
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myBends[i]->calc_forces(); |
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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(i=0; i<nTorsions; i++){ |
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myTorsions[i]->calc_forces(); |
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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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< |
// Rigid Body forces and torques are done after the fortran force loop |
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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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< |
} |
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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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< |
double Molecule::getPotential( void ){ |
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< |
|
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< |
int i; |
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double myPot = 0.0; |
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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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< |
for(i=0; i<myRigidBodies.size(); i++) { |
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myRigidBodies[i]->updateAtoms(); |
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< |
} |
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< |
|
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< |
for(i=0; i<nBonds; i++){ |
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< |
myPot += myBonds[i]->get_potential(); |
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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(i=0; i<nBends; i++){ |
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< |
myPot += myBends[i]->get_potential(); |
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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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|
|
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< |
for(i=0; i<nTorsions; i++){ |
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< |
myPot += myTorsions[i]->get_potential(); |
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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; |
| 188 |
> |
|
| 189 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 190 |
> |
nextIntegrableObject(i)){ |
| 191 |
> |
mass += sd->getMass(); |
| 192 |
> |
} |
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> |
|
| 194 |
> |
return mass; |
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|
} |
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|
|
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< |
return myPot; |
| 198 |
< |
} |
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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; |
| 202 |
> |
RealType mass; |
| 203 |
> |
|
| 204 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 205 |
> |
nextIntegrableObject(i)){ |
| 206 |
> |
mass = sd->getMass(); |
| 207 |
> |
totalMass += mass; |
| 208 |
> |
com += sd->getPos() * mass; |
| 209 |
> |
} |
| 210 |
> |
|
| 211 |
> |
com /= totalMass; |
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|
|
| 213 |
< |
void Molecule::printMe( void ){ |
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< |
|
| 133 |
< |
int i; |
| 134 |
< |
|
| 135 |
< |
for(i=0; i<nBonds; i++){ |
| 136 |
< |
myBonds[i]->printMe(); |
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> |
return com; |
| 214 |
|
} |
| 215 |
|
|
| 216 |
< |
for(i=0; i<nBends; i++){ |
| 217 |
< |
myBends[i]->printMe(); |
| 216 |
> |
void Molecule::moveCom(const Vector3d& delta) { |
| 217 |
> |
StuntDouble* sd; |
| 218 |
> |
std::vector<StuntDouble*>::iterator i; |
| 219 |
> |
|
| 220 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 221 |
> |
nextIntegrableObject(i)){ |
| 222 |
> |
sd->setPos(sd->getPos() + delta); |
| 223 |
> |
} |
| 224 |
|
} |
| 225 |
|
|
| 226 |
< |
for(i=0; i<nTorsions; i++){ |
| 227 |
< |
myTorsions[i]->printMe(); |
| 226 |
> |
Vector3d Molecule::getComVel() { |
| 227 |
> |
StuntDouble* sd; |
| 228 |
> |
std::vector<StuntDouble*>::iterator i; |
| 229 |
> |
Vector3d velCom; |
| 230 |
> |
RealType totalMass = 0; |
| 231 |
> |
RealType mass; |
| 232 |
> |
|
| 233 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 234 |
> |
nextIntegrableObject(i)){ |
| 235 |
> |
mass = sd->getMass(); |
| 236 |
> |
totalMass += mass; |
| 237 |
> |
velCom += sd->getVel() * mass; |
| 238 |
> |
} |
| 239 |
> |
|
| 240 |
> |
velCom /= totalMass; |
| 241 |
> |
|
| 242 |
> |
return velCom; |
| 243 |
|
} |
| 244 |
|
|
| 245 |
< |
} |
| 245 |
> |
RealType Molecule::getPotential() { |
| 246 |
|
|
| 247 |
< |
void Molecule::moveCOM(double delta[3]){ |
| 248 |
< |
double aPos[3]; |
| 249 |
< |
int i, j; |
| 247 |
> |
Bond* bond; |
| 248 |
> |
Bend* bend; |
| 249 |
> |
Torsion* torsion; |
| 250 |
> |
Inversion* inversion; |
| 251 |
> |
Molecule::BondIterator bondIter;; |
| 252 |
> |
Molecule::BendIterator bendIter; |
| 253 |
> |
Molecule::TorsionIterator torsionIter; |
| 254 |
> |
Molecule::InversionIterator inversionIter; |
| 255 |
|
|
| 256 |
< |
for(i=0; i<myIntegrableObjects.size(); i++) { |
| 154 |
< |
if(myIntegrableObjects[i] != NULL ) { |
| 155 |
< |
|
| 156 |
< |
myIntegrableObjects[i]->getPos( aPos ); |
| 157 |
< |
|
| 158 |
< |
for (j=0; j< 3; j++) |
| 159 |
< |
aPos[j] += delta[j]; |
| 256 |
> |
RealType potential = 0.0; |
| 257 |
|
|
| 258 |
< |
myIntegrableObjects[i]->setPos( aPos ); |
| 258 |
> |
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
| 259 |
> |
potential += bond->getPotential(); |
| 260 |
|
} |
| 163 |
– |
} |
| 261 |
|
|
| 262 |
< |
for(i=0; i<myRigidBodies.size(); i++) { |
| 262 |
> |
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
| 263 |
> |
potential += bend->getPotential(); |
| 264 |
> |
} |
| 265 |
|
|
| 266 |
< |
myRigidBodies[i]->getPos( aPos ); |
| 267 |
< |
|
| 268 |
< |
for (j=0; j< 3; j++) |
| 170 |
< |
aPos[j] += delta[j]; |
| 171 |
< |
|
| 172 |
< |
myRigidBodies[i]->setPos( aPos ); |
| 266 |
> |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = |
| 267 |
> |
nextTorsion(torsionIter)) { |
| 268 |
> |
potential += torsion->getPotential(); |
| 269 |
|
} |
| 270 |
< |
} |
| 270 |
> |
|
| 271 |
> |
for (inversion = beginInversion(inversionIter); torsion != NULL; |
| 272 |
> |
inversion = nextInversion(inversionIter)) { |
| 273 |
> |
potential += inversion->getPotential(); |
| 274 |
> |
} |
| 275 |
> |
|
| 276 |
> |
return potential; |
| 277 |
> |
|
| 278 |
> |
} |
| 279 |
> |
|
| 280 |
> |
void Molecule::addProperty(GenericData* genData) { |
| 281 |
> |
properties_.addProperty(genData); |
| 282 |
> |
} |
| 283 |
|
|
| 284 |
< |
void Molecule::atoms2rigidBodies( void ) { |
| 285 |
< |
int i; |
| 178 |
< |
for (i = 0; i < myRigidBodies.size(); i++) { |
| 179 |
< |
myRigidBodies[i]->calcForcesAndTorques(); |
| 284 |
> |
void Molecule::removeProperty(const std::string& propName) { |
| 285 |
> |
properties_.removeProperty(propName); |
| 286 |
|
} |
| 181 |
– |
} |
| 287 |
|
|
| 288 |
< |
void Molecule::getCOM( double COM[3] ) { |
| 288 |
> |
void Molecule::clearProperties() { |
| 289 |
> |
properties_.clearProperties(); |
| 290 |
> |
} |
| 291 |
|
|
| 292 |
< |
double mass, mtot; |
| 293 |
< |
double aPos[3]; |
| 294 |
< |
int i, j; |
| 188 |
< |
|
| 189 |
< |
for (j=0; j<3; j++) |
| 190 |
< |
COM[j] = 0.0; |
| 191 |
< |
|
| 192 |
< |
mtot = 0.0; |
| 193 |
< |
|
| 194 |
< |
for (i=0; i < myIntegrableObjects.size(); i++) { |
| 195 |
< |
if (myIntegrableObjects[i] != NULL) { |
| 196 |
< |
|
| 197 |
< |
mass = myIntegrableObjects[i]->getMass(); |
| 198 |
< |
mtot += mass; |
| 292 |
> |
std::vector<std::string> Molecule::getPropertyNames() { |
| 293 |
> |
return properties_.getPropertyNames(); |
| 294 |
> |
} |
| 295 |
|
|
| 296 |
< |
myIntegrableObjects[i]->getPos( aPos ); |
| 297 |
< |
|
| 202 |
< |
for( j = 0; j < 3; j++) |
| 203 |
< |
COM[j] += aPos[j] * mass; |
| 204 |
< |
|
| 205 |
< |
} |
| 296 |
> |
std::vector<GenericData*> Molecule::getProperties() { |
| 297 |
> |
return properties_.getProperties(); |
| 298 |
|
} |
| 299 |
|
|
| 300 |
< |
for (j = 0; j < 3; j++) |
| 301 |
< |
COM[j] /= mtot; |
| 210 |
< |
} |
| 211 |
< |
|
| 212 |
< |
double Molecule::getCOMvel( double COMvel[3] ) { |
| 213 |
< |
|
| 214 |
< |
double mass, mtot; |
| 215 |
< |
double aVel[3]; |
| 216 |
< |
int i, j; |
| 217 |
< |
|
| 218 |
< |
|
| 219 |
< |
for (j=0; j<3; j++) |
| 220 |
< |
COMvel[j] = 0.0; |
| 221 |
< |
|
| 222 |
< |
mtot = 0.0; |
| 223 |
< |
|
| 224 |
< |
for (i=0; i < myIntegrableObjects.size(); i++) { |
| 225 |
< |
if (myIntegrableObjects[i] != NULL) { |
| 226 |
< |
|
| 227 |
< |
mass = myIntegrableObjects[i]->getMass(); |
| 228 |
< |
mtot += mass; |
| 229 |
< |
|
| 230 |
< |
myIntegrableObjects[i]->getVel(aVel); |
| 231 |
< |
|
| 232 |
< |
for (j=0; j<3; j++) |
| 233 |
< |
COMvel[j] += aVel[j]*mass; |
| 234 |
< |
|
| 235 |
< |
} |
| 300 |
> |
GenericData* Molecule::getPropertyByName(const std::string& propName) { |
| 301 |
> |
return properties_.getPropertyByName(propName); |
| 302 |
|
} |
| 303 |
|
|
| 304 |
< |
for (j=0; j<3; j++) |
| 305 |
< |
COMvel[j] /= mtot; |
| 306 |
< |
|
| 307 |
< |
return mtot; |
| 308 |
< |
|
| 309 |
< |
} |
| 310 |
< |
|
| 311 |
< |
double Molecule::getTotalMass() |
| 312 |
< |
{ |
| 313 |
< |
|
| 314 |
< |
double totalMass; |
| 315 |
< |
|
| 316 |
< |
totalMass = 0; |
| 317 |
< |
for(int i =0; i < myIntegrableObjects.size(); i++){ |
| 252 |
< |
totalMass += myIntegrableObjects[i]->getMass(); |
| 304 |
> |
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
| 305 |
> |
o << std::endl; |
| 306 |
> |
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
| 307 |
> |
o << mol.getNAtoms() << " atoms" << std::endl; |
| 308 |
> |
o << mol.getNBonds() << " bonds" << std::endl; |
| 309 |
> |
o << mol.getNBends() << " bends" << std::endl; |
| 310 |
> |
o << mol.getNTorsions() << " torsions" << std::endl; |
| 311 |
> |
o << mol.getNInversions() << " inversions" << std::endl; |
| 312 |
> |
o << mol.getNRigidBodies() << " rigid bodies" << std::endl; |
| 313 |
> |
o << mol.getNIntegrableObjects() << " integrable objects" << std::endl; |
| 314 |
> |
o << mol.getNCutoffGroups() << " cutoff groups" << std::endl; |
| 315 |
> |
o << mol.getNConstraintPairs() << " constraint pairs" << std::endl; |
| 316 |
> |
o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl; |
| 317 |
> |
return o; |
| 318 |
|
} |
| 319 |
< |
|
| 320 |
< |
return totalMass; |
| 256 |
< |
} |
| 319 |
> |
|
| 320 |
> |
}//end namespace OpenMD |
