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#ifndef _MOLECULE_H_ |
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#define _MOLECULE_H_ |
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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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#include <set> |
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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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#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 "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/CutoffGroup.hpp" |
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|
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using namespace std; |
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namespace oopse{ |
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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<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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void initialize( molInit &theInit ); |
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Molecule(int stampId, int globalIndex, const std::string& molName); |
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virtual ~Molecule(); |
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void setMyIndex( int theIndex ){ myIndex = theIndex;} |
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int getMyIndex( void ) { return myIndex; } |
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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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int getGlobalIndex( void ) { return globalIndex; } |
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void setGlobalIndex( int theIndex ) { globalIndex = theIndex; } |
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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 molecule stamp instead of its |
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* stamp id. However, the pointer will become invalid, if the molecule migrate to other 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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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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/** 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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int setGlobalIndex(int index) { |
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return globalIndex_; |
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} |
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|
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Atom** getMyAtoms ( void ) {return myAtoms;} |
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Bond** getMyBonds ( void ) {return myBonds;} |
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Bend** getMyBends ( void ) {return myBends;} |
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Torsion** getMyTorsions( void ) {return myTorsions;} |
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vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;} |
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vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;} |
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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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//beginCutoffGroup return the first group and initialize the iterator |
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CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){ |
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i = myCutoffGroups.begin(); |
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return i != myCutoffGroups.end()? *i : NULL; |
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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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//nextCutoffGroup return next cutoff group based on the iterator |
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CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){ |
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i++; |
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return i != myCutoffGroups.end()? *i : NULL; |
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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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int getNCutoffGroups() {return nCutoffGroups;} |
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/** add a torsion into this molecule*/ |
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void addTorsion(Torsion* torsion); |
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void setStampID( int info ) {stampID = info;} |
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/** add a rigidbody into this molecule */ |
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void addRigidBody(RigidBody *rb); |
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void calcForces( void ); |
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void atoms2rigidBodies( void ); |
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double getPotential( void ); |
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|
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void printMe( void ); |
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/** add a cutoff group into this molecule */ |
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void addCutoffGroup(CutoffGroup* cp); |
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void getCOM( double COM[3] ); |
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void moveCOM( double delta[3] ); |
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double getCOMvel( double COMvel[3] ); |
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|
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double getTotalMass(); |
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/** */ |
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void complete(); |
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private: |
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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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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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int nMembers; // .. . . . . . .atoms (legacy code) . . . |
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int nCutoffGroups; |
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|
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int myIndex; // mostly just for debug (and for making pressure calcs work) |
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int globalIndex; |
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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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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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/** 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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/** 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 getNConstraints() { |
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return constraints_.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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* Returns the first atom in this molecule and initialize the iterator. |
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* @return the first atom, return NULL if there is not cut off group in this molecule |
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* @param i iteraotr |
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*/ |
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Atom* beginAtom(std::vector<Atom*>::iterator& i); |
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|
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Atom* nextAtom(std::vector<Atom*>::iterator& i); |
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|
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/** |
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* Returns the first bond in this molecule and initialize the iterator. |
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* @return the first bond, return NULL if there is not cut off group in this molecule |
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* @param i iteraotr |
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*/ |
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Bond* beginBond(std::vector<Bond*>::iterator& i); |
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|
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Bond* nextBond(std::vector<Bond*>::iterator& i); |
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|
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/** |
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* Returns the first bend in this molecule and initialize the iterator. |
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* @return the first bend, return NULL if there is not cut off group in this molecule |
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* @param i iteraotr |
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*/ |
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Bend* beginBend(std::vector<Bend*>::iterator& i); |
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|
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Bend* nextBend(std::vector<Bend*>::iterator& i); |
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|
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/** |
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* Returns the first torsion in this molecule and initialize the iterator. |
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* @return the first torsion, return NULL if there is not cut off group in this molecule |
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* @param i iteraotr |
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*/ |
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Torsion* beginTorsion(std::vector<Torsion*>::iterator& i); |
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Torsion* nextTorsion(std::vector<Torsion*>::iterator& i); |
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|
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/** |
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* Returns the first rigid body in this molecule and initialize the iterator. |
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* @return the first rigid body, return NULL if there is not cut off group in this molecule |
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* @param i iteraotr |
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*/ |
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RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i); |
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|
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RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i); |
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|
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/** |
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* Returns the first integrable object in this molecule and initialize the iterator. |
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* @return the first integrable object, return NULL if there is not cut off group in this molecule |
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* @param i iteraotr |
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*/ |
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StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i); |
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|
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StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i); |
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|
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/** |
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* Returns the first cutoff group in this molecule and initialize the iterator. |
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* @return the first cutoff group, return NULL if there is not cut off group in this molecule |
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* @param i iteraotr |
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*/ |
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CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i); |
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|
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/** |
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* Returns next cutoff group based on the iterator |
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* @return next cutoff group |
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* @param i |
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*/ |
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CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i); |
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|
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Constraint* beginConstraint(std::vector<Constraint*>::iterator& i); |
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|
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Constraint* nextConstraint(std::vector<Constraint*>::iterator& i); |
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|
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|
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/** return the total potential energy of short range interaction of this molecule */ |
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double getPotential(); |
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|
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/** get total mass of this molecule */ |
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double getMass(); |
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|
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/** return the center of mass of this molecule */ |
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Vector3d getCom(); |
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|
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/** Moves the center of this molecule */ |
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void moveCom(const Vector3d& delta); |
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|
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/** Returns the velocity of center of mass of this molecule */ |
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Vector3d getComVel(); |
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|
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/** Returns the total mass of this molecule */ |
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double getTotalMass(); |
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|
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friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
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|
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private: |
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|
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int globalIndex_; |
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|
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std::vector<Atom*> atoms_; |
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std::vector<Bond*> bonds_; |
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std::vector<Bend*> bends_; |
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std::vector<Torsion*> torsions_; |
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std::vector<RigidBody*> rigidBodies_; |
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std::vector<StuntDouble*> integrableObjects_; |
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std::vector<CutoffGroup*> cutoffGroups_; |
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std::vector<Constraint*> constraints_; |
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|
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int stampId_; |
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std::string moleculeName_; |
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}; |
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|
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< |
#endif |
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} //namespace oopse |
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#endif // |
