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#ifndef _MOLECULE_H_ |
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#define _MOLECULE_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] Vardeman & Gezelter, in progress (2009). |
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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 <set> |
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#ifndef PRIMITIVES_MOLECULE_HPP |
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#define PRIMITIVES_MOLECULE_HPP |
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#include <vector> |
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#include <iostream> |
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|
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#include "constraints/ConstraintPair.hpp" |
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#include "math/Vector3.hpp" |
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#include "primitives/Atom.hpp" |
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#include "primitives/SRI.hpp" |
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#include "types/MoleculeStamp.hpp" |
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#include "primitives/RigidBody.hpp" |
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#include "primitives/Bond.hpp" |
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#include "primitives/Bend.hpp" |
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#include "primitives/Torsion.hpp" |
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#include "primitives/Inversion.hpp" |
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#include "primitives/CutoffGroup.hpp" |
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#include "utils/PropertyMap.hpp" |
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|
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using namespace std; |
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namespace OpenMD{ |
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|
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typedef struct{ |
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|
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int stampID; // the ID in the BASS component stamp array |
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int nAtoms; // the number of atoms in the molecule |
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int nBonds; // ... .. .. . .bonds .. .. . . . . |
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int nBends; // . . . . .. . .bends . . . . .. . |
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int nTorsions; // .. . . .. . . torsions . . .. . . |
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int nRigidBodies; // .. .. .. . rigid bodies ... .. |
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int nOriented; // .. . . . .. . oriented atoms . . . |
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|
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Atom** myAtoms; // the array of atoms |
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Bond** myBonds; // arrays of all the short range interactions |
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Bend** myBends; |
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Torsion** myTorsions; |
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vector<RigidBody*> myRigidBodies; |
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vector<StuntDouble*> myIntegrableObjects; |
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vector<CutoffGroup*> myCutoffGroups; |
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} molInit; |
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class Constraint; |
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|
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class Molecule{ |
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/** |
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* @class Molecule Molecule.hpp "primitives/Molecule.hpp" |
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* @brief |
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*/ |
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class Molecule { |
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public: |
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|
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public: |
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|
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Molecule( void ); |
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~Molecule( void ); |
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typedef std::vector<Atom*>::iterator AtomIterator; |
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typedef std::vector<Bond*>::iterator BondIterator; |
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typedef std::vector<Bend*>::iterator BendIterator; |
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typedef std::vector<Torsion*>::iterator TorsionIterator; |
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typedef std::vector<Inversion*>::iterator InversionIterator; |
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typedef std::vector<RigidBody*>::iterator RigidBodyIterator; |
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typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
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typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
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typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator; |
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typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator; |
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|
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|
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Molecule(int stampId, int globalIndex, const std::string& molName); |
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virtual ~Molecule(); |
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|
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/** |
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* Returns the global index of this molecule. |
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* @return the global index of this molecule |
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*/ |
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int getGlobalIndex() { |
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return globalIndex_; |
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} |
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|
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/** |
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* Returns the stamp id of this molecule |
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* @note Ideally, every molecule should keep a pointer of its |
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* molecule stamp instead of its stamp id. However, the pointer |
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* will become invalid, if the molecule migrate to other |
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* processor. |
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*/ |
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int getStampId() { |
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return stampId_; |
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} |
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|
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/** Returns the name of the molecule */ |
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std::string getType() { |
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return moleculeName_; |
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} |
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|
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/** |
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* Sets the global index of this molecule. |
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* @param new global index to be set |
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*/ |
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void setGlobalIndex(int index) { |
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globalIndex_ = index; |
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} |
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|
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|
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/** add an atom into this molecule */ |
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void addAtom(Atom* atom); |
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|
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/** add a bond into this molecule */ |
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void addBond(Bond* bond); |
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|
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/** add a bend into this molecule */ |
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void addBend(Bend* bend); |
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|
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/** add a torsion into this molecule*/ |
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void addTorsion(Torsion* torsion); |
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|
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void initialize( molInit &theInit ); |
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/** add an improper torsion into this molecule*/ |
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void addInversion(Inversion* inversion); |
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|
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/** add a rigidbody into this molecule */ |
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void addRigidBody(RigidBody *rb); |
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|
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/** add a cutoff group into this molecule */ |
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void addCutoffGroup(CutoffGroup* cp); |
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|
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void addConstraintPair(ConstraintPair* consPair); |
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|
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void addConstraintElem(ConstraintElem* consElem); |
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|
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/** */ |
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void complete(); |
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|
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/** Returns the total number of atoms in this molecule */ |
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unsigned int getNAtoms() { |
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return atoms_.size(); |
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} |
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|
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/** Returns the total number of bonds in this molecule */ |
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unsigned int getNBonds(){ |
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return bonds_.size(); |
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} |
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|
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/** Returns the total number of bends in this molecule */ |
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unsigned int getNBends() { |
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return bends_.size(); |
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} |
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|
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/** Returns the total number of torsions in this molecule */ |
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unsigned int getNTorsions() { |
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return torsions_.size(); |
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} |
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|
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void setMyIndex( int theIndex ){ myIndex = theIndex;} |
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int getMyIndex( void ) { return myIndex; } |
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/** Returns the total number of improper torsions in this molecule */ |
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unsigned int getNInversions() { |
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return inversions_.size(); |
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} |
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|
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/** Returns the total number of rigid bodies in this molecule */ |
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unsigned int getNRigidBodies() { |
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return rigidBodies_.size(); |
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} |
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|
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/** Returns the total number of integrable objects in this molecule */ |
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unsigned int getNIntegrableObjects() { |
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return integrableObjects_.size(); |
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} |
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|
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/** Returns the total number of cutoff groups in this molecule */ |
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unsigned int getNCutoffGroups() { |
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return cutoffGroups_.size(); |
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} |
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|
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/** Returns the total number of constraints in this molecule */ |
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unsigned int getNConstraintPairs() { |
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return constraintPairs_.size(); |
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} |
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|
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Atom* getAtomAt(unsigned int i) { |
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assert(i < atoms_.size()); |
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return atoms_[i]; |
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} |
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|
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RigidBody* getRigidBodyAt(unsigned int i) { |
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assert(i < rigidBodies_.size()); |
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return rigidBodies_[i]; |
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} |
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|
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Atom* 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* 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* 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* 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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Bend* 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* 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* 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* 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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< |
int getGlobalIndex( void ) { return globalIndex; } |
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< |
void setGlobalIndex( int theIndex ) { globalIndex = theIndex; } |
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> |
Inversion* beginInversion(std::vector<Inversion*>::iterator& i) { |
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> |
i = inversions_.begin(); |
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> |
return (i == inversions_.end()) ? NULL : *i; |
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> |
} |
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> |
|
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Inversion* nextInversion(std::vector<Inversion*>::iterator& i) { |
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++i; |
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> |
return (i == inversions_.end()) ? NULL : *i; |
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} |
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> |
|
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> |
RigidBody* 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* 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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} |
| 267 |
> |
|
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> |
StuntDouble* 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* 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* 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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> |
} |
| 282 |
|
|
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< |
int getNAtoms ( void ) {return nAtoms;} |
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< |
int getNBonds ( void ) {return nBonds;} |
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< |
int getNBends ( void ) {return nBends;} |
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< |
int getNTorsions( void ) {return nTorsions;} |
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< |
int getNRigidBodies( void ) {return myRigidBodies.size();} |
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< |
int getNOriented( void ) {return nOriented;} |
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< |
int getNMembers ( void ) {return nMembers;} |
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< |
int getStampID ( void ) {return stampID;} |
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> |
CutoffGroup* 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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> |
} |
| 287 |
> |
|
| 288 |
> |
ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 289 |
> |
i = constraintPairs_.begin(); |
| 290 |
> |
return (i == constraintPairs_.end()) ? NULL : *i; |
| 291 |
> |
} |
| 292 |
> |
|
| 293 |
> |
ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 294 |
> |
++i; |
| 295 |
> |
return (i == constraintPairs_.end()) ? NULL : *i; |
| 296 |
> |
} |
| 297 |
> |
|
| 298 |
> |
ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 299 |
> |
i = constraintElems_.begin(); |
| 300 |
> |
return (i == constraintElems_.end()) ? NULL : *i; |
| 301 |
> |
} |
| 302 |
> |
|
| 303 |
> |
ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 304 |
> |
++i; |
| 305 |
> |
return (i == constraintElems_.end()) ? NULL : *i; |
| 306 |
> |
} |
| 307 |
> |
|
| 308 |
> |
/** |
| 309 |
> |
* Returns the total potential energy of short range interaction |
| 310 |
> |
* of this molecule |
| 311 |
> |
*/ |
| 312 |
> |
RealType getPotential(); |
| 313 |
> |
|
| 314 |
> |
/** get total mass of this molecule */ |
| 315 |
> |
RealType getMass(); |
| 316 |
> |
|
| 317 |
> |
/** return the center of mass of this molecule */ |
| 318 |
> |
Vector3d getCom(); |
| 319 |
> |
|
| 320 |
> |
/** Moves the center of this molecule */ |
| 321 |
> |
void moveCom(const Vector3d& delta); |
| 322 |
> |
|
| 323 |
> |
/** Returns the velocity of center of mass of this molecule */ |
| 324 |
> |
Vector3d getComVel(); |
| 325 |
|
|
| 326 |
< |
Atom** getMyAtoms ( void ) {return myAtoms;} |
| 327 |
< |
Bond** getMyBonds ( void ) {return myBonds;} |
| 328 |
< |
Bend** getMyBends ( void ) {return myBends;} |
| 329 |
< |
Torsion** getMyTorsions( void ) {return myTorsions;} |
| 330 |
< |
vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;} |
| 63 |
< |
vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;} |
| 326 |
> |
std::string getMoleculeName() { |
| 327 |
> |
return moleculeName_; |
| 328 |
> |
} |
| 329 |
> |
|
| 330 |
> |
friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
| 331 |
|
|
| 332 |
< |
//beginCutoffGroup return the first group and initialize the iterator |
| 333 |
< |
CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){ |
| 334 |
< |
i = myCutoffGroups.begin(); |
| 335 |
< |
return i != myCutoffGroups.end()? *i : NULL; |
| 336 |
< |
} |
| 332 |
> |
//below functions are just forward functions |
| 333 |
> |
/** |
| 334 |
> |
* Adds property into property map |
| 335 |
> |
* @param genData GenericData to be added into PropertyMap |
| 336 |
> |
*/ |
| 337 |
> |
void addProperty(GenericData* genData); |
| 338 |
|
|
| 339 |
< |
//nextCutoffGroup return next cutoff group based on the iterator |
| 340 |
< |
CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){ |
| 341 |
< |
i++; |
| 342 |
< |
return i != myCutoffGroups.end()? *i : NULL; |
| 343 |
< |
} |
| 339 |
> |
/** |
| 340 |
> |
* Removes property from PropertyMap by name |
| 341 |
> |
* @param propName the name of property to be removed |
| 342 |
> |
*/ |
| 343 |
> |
void removeProperty(const std::string& propName); |
| 344 |
|
|
| 345 |
< |
int getNCutoffGroups() {return nCutoffGroups;} |
| 345 |
> |
/** |
| 346 |
> |
* clear all of the properties |
| 347 |
> |
*/ |
| 348 |
> |
void clearProperties(); |
| 349 |
|
|
| 350 |
< |
void setStampID( int info ) {stampID = info;} |
| 350 |
> |
/** |
| 351 |
> |
* Returns all names of properties |
| 352 |
> |
* @return all names of properties |
| 353 |
> |
*/ |
| 354 |
> |
std::vector<std::string> getPropertyNames(); |
| 355 |
|
|
| 356 |
< |
void calcForces( void ); |
| 357 |
< |
void atoms2rigidBodies( void ); |
| 358 |
< |
double getPotential( void ); |
| 359 |
< |
|
| 360 |
< |
void printMe( void ); |
| 356 |
> |
/** |
| 357 |
> |
* Returns all of the properties in PropertyMap |
| 358 |
> |
* @return all of the properties in PropertyMap |
| 359 |
> |
*/ |
| 360 |
> |
std::vector<GenericData*> getProperties(); |
| 361 |
|
|
| 362 |
< |
void getCOM( double COM[3] ); |
| 363 |
< |
void moveCOM( double delta[3] ); |
| 364 |
< |
double getCOMvel( double COMvel[3] ); |
| 365 |
< |
|
| 366 |
< |
double getTotalMass(); |
| 362 |
> |
/** |
| 363 |
> |
* Returns property |
| 364 |
> |
* @param propName name of property |
| 365 |
> |
* @return a pointer point to property with propName. If no property named propName |
| 366 |
> |
* exists, return NULL |
| 367 |
> |
*/ |
| 368 |
> |
GenericData* getPropertyByName(const std::string& propName); |
| 369 |
> |
|
| 370 |
> |
private: |
| 371 |
> |
|
| 372 |
> |
int globalIndex_; |
| 373 |
> |
|
| 374 |
> |
std::vector<Atom*> atoms_; |
| 375 |
> |
std::vector<Bond*> bonds_; |
| 376 |
> |
std::vector<Bend*> bends_; |
| 377 |
> |
std::vector<Torsion*> torsions_; |
| 378 |
> |
std::vector<Inversion*> inversions_; |
| 379 |
> |
std::vector<RigidBody*> rigidBodies_; |
| 380 |
> |
std::vector<StuntDouble*> integrableObjects_; |
| 381 |
> |
std::vector<CutoffGroup*> cutoffGroups_; |
| 382 |
> |
std::vector<ConstraintPair*> constraintPairs_; |
| 383 |
> |
std::vector<ConstraintElem*> constraintElems_; |
| 384 |
> |
int stampId_; |
| 385 |
> |
std::string moleculeName_; |
| 386 |
> |
PropertyMap properties_; |
| 387 |
|
|
| 388 |
< |
private: |
| 388 |
> |
}; |
| 389 |
|
|
| 390 |
< |
int stampID; // the ID in the BASS component stamp array |
| 391 |
< |
int nAtoms; // the number of atoms in the molecule |
| 97 |
< |
int nBonds; // ... .. .. . .bonds .. .. . . . . |
| 98 |
< |
int nBends; // . . . . .. . .bends . . . . .. . |
| 99 |
< |
int nTorsions; // .. . . .. . . torsions . . .. . . |
| 100 |
< |
int nRigidBodies; // .. . . .. .rigid bodies . . .. . . |
| 101 |
< |
int nOriented; // .. . . . .. . oriented atoms . . . |
| 102 |
< |
int nMembers; // .. . . . . . .atoms (legacy code) . . . |
| 103 |
< |
int nCutoffGroups; |
| 104 |
< |
|
| 105 |
< |
int myIndex; // mostly just for debug (and for making pressure calcs work) |
| 106 |
< |
int globalIndex; |
| 107 |
< |
|
| 108 |
< |
Atom** myAtoms; // the array of atoms |
| 109 |
< |
Bond** myBonds; // arrays of all the short range interactions |
| 110 |
< |
Bend** myBends; |
| 111 |
< |
Torsion** myTorsions; |
| 112 |
< |
vector<RigidBody*> myRigidBodies; |
| 113 |
< |
vector<StuntDouble*> myIntegrableObjects; |
| 114 |
< |
vector<CutoffGroup*> myCutoffGroups; |
| 115 |
< |
}; |
| 116 |
< |
|
| 117 |
< |
#endif |
| 390 |
> |
} //namespace OpenMD |
| 391 |
> |
#endif // |
