src/primitives/Molecule.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file Molecule.hpp
 * @author    tlin
 * @date  10/25/2004
 * @version 1.0
 */ 

#ifndef PRIMITIVES_MOLECULE_HPP
#define PRIMITIVES_MOLECULE_HPP
#include <vector>
#include <iostream>

#include "constraints/ConstraintPair.hpp"
#include "math/Vector3.hpp"
#include "primitives/Atom.hpp"
#include "primitives/RigidBody.hpp"
#include "primitives/Bond.hpp"
#include "primitives/Bend.hpp"
#include "primitives/Torsion.hpp"
#include "primitives/Inversion.hpp"
#include "primitives/CutoffGroup.hpp"
#include "utils/PropertyMap.hpp"


namespace OpenMD{

  class Constraint;
  
  /**
   * @class Molecule Molecule.hpp "primitives/Molecule.hpp"
   * @brief
   */
  class Molecule {
  public:

    struct HBondDonor {
      Atom* donorAtom;
      Atom* donatedHydrogen;
    };

    typedef std::vector<Atom*>::iterator AtomIterator;
    typedef std::vector<Bond*>::iterator BondIterator;
    typedef std::vector<Bend*>::iterator BendIterator;
    typedef std::vector<Torsion*>::iterator TorsionIterator;
    typedef std::vector<Inversion*>::iterator InversionIterator;
    typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
    typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
    typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
    typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
    typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
    typedef std::vector<Atom*>::iterator FluctuatingChargeIterator;
    typedef std::vector<HBondDonor*>::iterator HBondDonorIterator;
    typedef std::vector<Atom*>::iterator HBondAcceptorIterator;

    Molecule(int stampId, int globalIndex, const std::string& molName, int region);
    virtual ~Molecule();

    /**
     * Returns the global index of this molecule.
     * @return  the global index of this molecule 
     */
    int getGlobalIndex() {
      return globalIndex_;
    }
    
    /**
     * Returns the stamp id of this molecule
     * @note Ideally, every molecule should keep a pointer of its
     * molecule stamp instead of its stamp id. However, the pointer
     * will become invalid, if the molecule migrate to other
     * processor.
     */
    int getStampId() {
      return stampId_;
    }
    int getRegion() {
      return region_;
    }
    
    /** Returns the name of the molecule */
    std::string getType() {
      return moleculeName_;
    }
    
    /**
     * Sets the global index of this molecule.
     * @param index new global index to be set
     */
    void setGlobalIndex(int index) {
      globalIndex_ = index;
    }

    void setConstrainTotalCharge(bool ctc) {
      constrainTotalCharge_ = ctc;
    }
    
    bool constrainTotalCharge() {
      return constrainTotalCharge_;
    }

    /** add an atom into this molecule */
    void addAtom(Atom* atom);
    
    /** add a bond into this molecule */
    void addBond(Bond* bond);
    
    /** add a bend into this molecule */
    void addBend(Bend* bend);
    
    /** add a torsion into this molecule*/
    void addTorsion(Torsion* torsion);

    /** add an improper torsion into this molecule*/
    void addInversion(Inversion* inversion);
    
    /** add a rigidbody into this molecule */
    void addRigidBody(RigidBody *rb);
    
    /** add a cutoff group into this molecule */
    void addCutoffGroup(CutoffGroup* cp);     
    
    void addConstraintPair(ConstraintPair* consPair);
    
    void addConstraintElem(ConstraintElem* consElem);
    
    /** */
    void complete();
    
    /** Returns the total number of atoms in this molecule */
    unsigned int getNAtoms() {
      return atoms_.size();
    }
    
    /** Returns the total number of bonds in this molecule */        
    unsigned int getNBonds(){
      return bonds_.size();
    }
    
    /** Returns the total number of bends in this molecule */        
    unsigned int getNBends() {
      return bends_.size();
    }
    
    /** Returns the total number of torsions in this molecule */        
    unsigned int getNTorsions() {
      return torsions_.size();
    }

    /** Returns the total number of improper torsions in this molecule */
    unsigned int getNInversions() {
      return inversions_.size();
    }
    
    /** Returns the total number of rigid bodies in this molecule */        
    unsigned int getNRigidBodies() {
      return rigidBodies_.size();
    }
    
    /** Returns the total number of integrable objects in this molecule */
    unsigned int getNIntegrableObjects() {
      return integrableObjects_.size();
    }
    
    /** Returns the total number of cutoff groups in this molecule */
    unsigned int getNCutoffGroups() {
      return cutoffGroups_.size();
    }
    
    /** Returns the total number of constraints in this molecule */
    unsigned int getNConstraintPairs() {
      return constraintPairs_.size();
    }

    /** Returns the total number of fluctuating charges in this molecule */
    unsigned int getNFluctuatingCharges() {
      return fluctuatingCharges_.size();
    }
    /** Returns the total number of Hydrogen Bond donors in this molecule */
    unsigned int getNHBondDonors() {
      return hBondDonors_.size();
    }
    
    /** Returns the total number of Hydrogen Bond acceptors in this molecule */
    unsigned int getNHBondAcceptors() {
      return hBondAcceptors_.size();
    }

    Atom* getAtomAt(unsigned int i) {
      assert(i < atoms_.size());
      return atoms_[i];
    }
    
    RigidBody* getRigidBodyAt(unsigned int i) {
      assert(i < rigidBodies_.size());
      return rigidBodies_[i];
    }
    
    Atom* beginAtom(std::vector<Atom*>::iterator& i) {
      i = atoms_.begin();
      return (i == atoms_.end()) ? NULL : *i;
    }
    
    Atom* nextAtom(std::vector<Atom*>::iterator& i) {
      ++i;
      return (i == atoms_.end()) ? NULL : *i;    
    }
    
    Bond* beginBond(std::vector<Bond*>::iterator& i) {
      i = bonds_.begin();
      return (i == bonds_.end()) ? NULL : *i;
    }
    
    Bond* nextBond(std::vector<Bond*>::iterator& i) {
      ++i;
      return (i == bonds_.end()) ? NULL : *i;    
      
    }
    
    Bend* beginBend(std::vector<Bend*>::iterator& i) {
      i = bends_.begin();
      return (i == bends_.end()) ? NULL : *i;
    }
    
    Bend* nextBend(std::vector<Bend*>::iterator& i) {
      ++i;
      return (i == bends_.end()) ? NULL : *i;    
    }
    
    Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
      i = torsions_.begin();
      return (i == torsions_.end()) ? NULL : *i;
    }
    
    Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
      ++i;
      return (i == torsions_.end()) ? NULL : *i;    
    }    

    Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
      i = inversions_.begin();
      return (i == inversions_.end()) ? NULL : *i;
    }
    
    Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
      ++i;
      return (i == inversions_.end()) ? NULL : *i;    
    }    
    
    RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
      i = rigidBodies_.begin();
      return (i == rigidBodies_.end()) ? NULL : *i;
    }
    
    RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
      ++i;
      return (i == rigidBodies_.end()) ? NULL : *i;    
    }
    
    StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
      i = integrableObjects_.begin();
      return (i == integrableObjects_.end()) ? NULL : *i;
    }
    
    StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
      ++i;
      return (i == integrableObjects_.end()) ? NULL : *i;    
    }    
    
    CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
      i = cutoffGroups_.begin();
      return (i == cutoffGroups_.end()) ? NULL : *i;
    }

    CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
      ++i;
      return (i == cutoffGroups_.end()) ? NULL : *i;    
    } 
    
    ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
      i = constraintPairs_.begin();
      return (i == constraintPairs_.end()) ? NULL : *i;
    }
    
    ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {            
      ++i;
      return (i == constraintPairs_.end()) ? NULL : *i;    
    }         
    
    ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
      i = constraintElems_.begin();
      return (i == constraintElems_.end()) ? NULL : *i;
    }
    
    ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {            
      ++i;
      return (i == constraintElems_.end()) ? NULL : *i;    
    }

    Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) {
      i = fluctuatingCharges_.begin();
      return (i == fluctuatingCharges_.end()) ? NULL : *i;
    }
    
    Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) {
      ++i;
      return (i == fluctuatingCharges_.end()) ? NULL : *i;    
    }

    HBondDonor* beginHBondDonor(std::vector<HBondDonor*>::iterator& i) {
      i = hBondDonors_.begin();
      return (i == hBondDonors_.end()) ? NULL : *i;
    }
    
    HBondDonor* nextHBondDonor(std::vector<HBondDonor*>::iterator& i) {
      ++i;
      return (i == hBondDonors_.end()) ? NULL : *i;    
    }
    
    Atom* beginHBondAcceptor(std::vector<Atom*>::iterator& i) {
      i = hBondAcceptors_.begin();
      return (i == hBondAcceptors_.end()) ? NULL : *i;
    }
    
    Atom* nextHBondAcceptor(std::vector<Atom*>::iterator& i) {
      ++i;
      return (i == hBondAcceptors_.end()) ? NULL : *i;    
    }

        
    /** 
     * Returns the total potential energy of short range interaction
     * of this molecule 
     */    
    RealType getPotential();
    
    /** get total mass of this molecule */        
    RealType getMass();
    
    /**
     * Returns the current center of mass position of this molecule.
     *
     * @return the center of mass position of this molecule.
     */    
    Vector3d getCom();
    
    /**
     * Returns the center of mass position of this molecule in
     * specified snapshot
     *
     * @return the center of mass position of this molecule
     * @param snapshotNo
     */    
    Vector3d getCom(int snapshotNo);

    
    /** Moves the center of this molecule */
    void moveCom(const Vector3d& delta);
    
    /** Returns the velocity of center of mass of this molecule */
    Vector3d getComVel();

    std::string getMoleculeName() { 
      return moleculeName_;
    }
        
    friend std::ostream& operator <<(std::ostream& o, Molecule& mol);

    //below functions are just forward functions
    /**
     * Adds property into property map
     * @param genData GenericData to be added into PropertyMap
     */
    void addProperty(GenericData* genData);

    /**
     * Removes property from PropertyMap by name
     * @param propName the name of property to be removed
     */
    void removeProperty(const std::string& propName);

    /**
     * clear all of the properties
     */
    void clearProperties();

    /**
     * Returns all names of properties
     * @return all names of properties
     */
    std::vector<std::string> getPropertyNames();

    /**
     * Returns all of the properties in PropertyMap
     * @return all of the properties in PropertyMap
     */      
    std::vector<GenericData*> getProperties();

    /**
     * Returns property 
     * @param propName name of property
     * @return a pointer point to property with propName. If no property named propName
     * exists, return NULL
     */      
    GenericData* getPropertyByName(const std::string& propName);
    
  private:
    
    int globalIndex_;
    
    std::vector<Atom*> atoms_;
    std::vector<Bond*> bonds_;
    std::vector<Bend*> bends_;
    std::vector<Torsion*> torsions_;
    std::vector<Inversion*> inversions_;
    std::vector<RigidBody*> rigidBodies_;
    std::vector<StuntDouble*> integrableObjects_;
    std::vector<CutoffGroup*> cutoffGroups_;
    std::vector<ConstraintPair*> constraintPairs_;
    std::vector<ConstraintElem*> constraintElems_;
    std::vector<Atom*> fluctuatingCharges_;
    std::vector<HBondDonor*> hBondDonors_;
    std::vector<Atom*> hBondAcceptors_;
    
    int stampId_;
    int region_;
    std::string moleculeName_;
    PropertyMap properties_;
    bool constrainTotalCharge_;

  };

} //namespace OpenMD
#endif //
Revision:	2052
Committed:	Fri Jan 9 19:06:35 2015 UTC (10 years, 6 months ago) by gezelter
File size:	14663 byte(s)
Log Message:	Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			/**
44			* @file Molecule.hpp
45			* @author tlin
46			* @date 10/25/2004
47			* @version 1.0
48			*/
49	gezelter	2
50	gezelter	246	#ifndef PRIMITIVES_MOLECULE_HPP
51			#define PRIMITIVES_MOLECULE_HPP
52	gezelter	2	#include <vector>
53	gezelter	246	#include <iostream>
54	gezelter	2
55	gezelter	246	#include "constraints/ConstraintPair.hpp"
56			#include "math/Vector3.hpp"
57	tim	3	#include "primitives/Atom.hpp"
58			#include "primitives/RigidBody.hpp"
59	gezelter	246	#include "primitives/Bond.hpp"
60			#include "primitives/Bend.hpp"
61			#include "primitives/Torsion.hpp"
62	cli2	1275	#include "primitives/Inversion.hpp"
63	tim	3	#include "primitives/CutoffGroup.hpp"
64	cli2	1360	#include "utils/PropertyMap.hpp"
65	gezelter	2
66	gezelter	2052
67	gezelter	1390	namespace OpenMD{
68	gezelter	2
69	gezelter	507	class Constraint;
70	gezelter	2052
71	gezelter	507	/**
72			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
73			* @brief
74			*/
75			class Molecule {
76			public:
77	gezelter	2
78	gezelter	2052	struct HBondDonor {
79			Atom* donorAtom;
80			Atom* donatedHydrogen;
81			};
82
83	gezelter	507	typedef std::vector<Atom*>::iterator AtomIterator;
84			typedef std::vector<Bond*>::iterator BondIterator;
85			typedef std::vector<Bend*>::iterator BendIterator;
86			typedef std::vector<Torsion*>::iterator TorsionIterator;
87	cli2	1275	typedef std::vector<Inversion*>::iterator InversionIterator;
88	gezelter	507	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
89			typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
90	gezelter	1211	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
91	gezelter	507	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
92			typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
93	gezelter	1782	typedef std::vector<Atom*>::iterator FluctuatingChargeIterator;
94	gezelter	2052	typedef std::vector<HBondDonor*>::iterator HBondDonorIterator;
95			typedef std::vector<Atom*>::iterator HBondAcceptorIterator;
96
97	gezelter	1908	Molecule(int stampId, int globalIndex, const std::string& molName, int region);
98	gezelter	507	virtual ~Molecule();
99	cli2	1407
100	gezelter	507	/**
101			* Returns the global index of this molecule.
102			* @return the global index of this molecule
103			*/
104			int getGlobalIndex() {
105			return globalIndex_;
106			}
107	gezelter	1211
108	gezelter	507	/**
109			* Returns the stamp id of this molecule
110	gezelter	1211	* @note Ideally, every molecule should keep a pointer of its
111			* molecule stamp instead of its stamp id. However, the pointer
112			* will become invalid, if the molecule migrate to other
113			* processor.
114	gezelter	507	*/
115			int getStampId() {
116			return stampId_;
117			}
118	gezelter	1908	int getRegion() {
119			return region_;
120			}
121	gezelter	1211
122	gezelter	507	/** Returns the name of the molecule */
123			std::string getType() {
124			return moleculeName_;
125			}
126	gezelter	1211
127	gezelter	507	/**
128			* Sets the global index of this molecule.
129	gezelter	1879	* @param index new global index to be set
130	gezelter	507	*/
131			void setGlobalIndex(int index) {
132			globalIndex_ = index;
133			}
134	gezelter	1782
135			void setConstrainTotalCharge(bool ctc) {
136			constrainTotalCharge_ = ctc;
137			}
138	gezelter	1211
139	gezelter	1782	bool constrainTotalCharge() {
140			return constrainTotalCharge_;
141			}
142
143	gezelter	507	/** add an atom into this molecule */
144			void addAtom(Atom* atom);
145	gezelter	1211
146	gezelter	507	/** add a bond into this molecule */
147			void addBond(Bond* bond);
148	gezelter	1211
149	gezelter	507	/** add a bend into this molecule */
150			void addBend(Bend* bend);
151	gezelter	1211
152	gezelter	507	/** add a torsion into this molecule*/
153			void addTorsion(Torsion* torsion);
154	cli2	1275
155			/** add an improper torsion into this molecule*/
156			void addInversion(Inversion* inversion);
157	gezelter	1211
158	gezelter	507	/** add a rigidbody into this molecule */
159			void addRigidBody(RigidBody *rb);
160	gezelter	1211
161	gezelter	507	/** add a cutoff group into this molecule */
162			void addCutoffGroup(CutoffGroup* cp);
163	gezelter	1211
164	gezelter	507	void addConstraintPair(ConstraintPair* consPair);
165	gezelter	1211
166	gezelter	507	void addConstraintElem(ConstraintElem* consElem);
167	gezelter	1211
168	gezelter	507	/** */
169			void complete();
170	gezelter	1211
171	gezelter	507	/** Returns the total number of atoms in this molecule */
172			unsigned int getNAtoms() {
173			return atoms_.size();
174			}
175	gezelter	1211
176	gezelter	507	/** Returns the total number of bonds in this molecule */
177			unsigned int getNBonds(){
178			return bonds_.size();
179			}
180	gezelter	1211
181	gezelter	507	/** Returns the total number of bends in this molecule */
182			unsigned int getNBends() {
183			return bends_.size();
184			}
185	gezelter	1211
186	gezelter	507	/** Returns the total number of torsions in this molecule */
187			unsigned int getNTorsions() {
188			return torsions_.size();
189			}
190	cli2	1275
191			/** Returns the total number of improper torsions in this molecule */
192			unsigned int getNInversions() {
193			return inversions_.size();
194			}
195	gezelter	1211
196	gezelter	507	/** Returns the total number of rigid bodies in this molecule */
197			unsigned int getNRigidBodies() {
198			return rigidBodies_.size();
199			}
200	gezelter	1211
201	gezelter	507	/** Returns the total number of integrable objects in this molecule */
202			unsigned int getNIntegrableObjects() {
203			return integrableObjects_.size();
204			}
205	gezelter	1211
206	gezelter	507	/** Returns the total number of cutoff groups in this molecule */
207			unsigned int getNCutoffGroups() {
208			return cutoffGroups_.size();
209			}
210	gezelter	1211
211	gezelter	507	/** Returns the total number of constraints in this molecule */
212			unsigned int getNConstraintPairs() {
213			return constraintPairs_.size();
214			}
215	gezelter	1782
216			/** Returns the total number of fluctuating charges in this molecule */
217			unsigned int getNFluctuatingCharges() {
218			return fluctuatingCharges_.size();
219			}
220	gezelter	2052	/** Returns the total number of Hydrogen Bond donors in this molecule */
221			unsigned int getNHBondDonors() {
222			return hBondDonors_.size();
223			}
224
225			/** Returns the total number of Hydrogen Bond acceptors in this molecule */
226			unsigned int getNHBondAcceptors() {
227			return hBondAcceptors_.size();
228			}
229	gezelter	1782
230	gezelter	507	Atom* getAtomAt(unsigned int i) {
231			assert(i < atoms_.size());
232			return atoms_[i];
233			}
234	gezelter	1211
235	gezelter	507	RigidBody* getRigidBodyAt(unsigned int i) {
236			assert(i < rigidBodies_.size());
237			return rigidBodies_[i];
238			}
239	gezelter	1211
240	gezelter	507	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
241			i = atoms_.begin();
242			return (i == atoms_.end()) ? NULL : *i;
243			}
244	gezelter	1211
245	gezelter	507	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
246			++i;
247			return (i == atoms_.end()) ? NULL : *i;
248			}
249	gezelter	1211
250	gezelter	507	Bond* beginBond(std::vector<Bond*>::iterator& i) {
251			i = bonds_.begin();
252			return (i == bonds_.end()) ? NULL : *i;
253			}
254	gezelter	1211
255	gezelter	507	Bond* nextBond(std::vector<Bond*>::iterator& i) {
256			++i;
257			return (i == bonds_.end()) ? NULL : *i;
258	gezelter	1211
259	gezelter	507	}
260	gezelter	1211
261	gezelter	507	Bend* beginBend(std::vector<Bend*>::iterator& i) {
262			i = bends_.begin();
263			return (i == bends_.end()) ? NULL : *i;
264			}
265	gezelter	1211
266	gezelter	507	Bend* nextBend(std::vector<Bend*>::iterator& i) {
267			++i;
268			return (i == bends_.end()) ? NULL : *i;
269			}
270	gezelter	1211
271	gezelter	507	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
272			i = torsions_.begin();
273			return (i == torsions_.end()) ? NULL : *i;
274			}
275	gezelter	1211
276	gezelter	507	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
277			++i;
278			return (i == torsions_.end()) ? NULL : *i;
279			}
280	cli2	1275
281			Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
282			i = inversions_.begin();
283			return (i == inversions_.end()) ? NULL : *i;
284			}
285	gezelter	1211
286	cli2	1275	Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
287			++i;
288			return (i == inversions_.end()) ? NULL : *i;
289			}
290
291	gezelter	507	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
292			i = rigidBodies_.begin();
293			return (i == rigidBodies_.end()) ? NULL : *i;
294			}
295	gezelter	1211
296	gezelter	507	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
297			++i;
298			return (i == rigidBodies_.end()) ? NULL : *i;
299			}
300	gezelter	1211
301	gezelter	507	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
302			i = integrableObjects_.begin();
303			return (i == integrableObjects_.end()) ? NULL : *i;
304			}
305	gezelter	1211
306	gezelter	507	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
307			++i;
308			return (i == integrableObjects_.end()) ? NULL : *i;
309			}
310	gezelter	1211
311	gezelter	507	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
312			i = cutoffGroups_.begin();
313			return (i == cutoffGroups_.end()) ? NULL : *i;
314			}
315	gezelter	246
316	gezelter	1211	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
317	gezelter	507	++i;
318			return (i == cutoffGroups_.end()) ? NULL : *i;
319			}
320	gezelter	1211
321	gezelter	507	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
322			i = constraintPairs_.begin();
323			return (i == constraintPairs_.end()) ? NULL : *i;
324			}
325	gezelter	1211
326	gezelter	507	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
327			++i;
328			return (i == constraintPairs_.end()) ? NULL : *i;
329			}
330	gezelter	1211
331	gezelter	507	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
332			i = constraintElems_.begin();
333			return (i == constraintElems_.end()) ? NULL : *i;
334			}
335	gezelter	1211
336	gezelter	507	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
337			++i;
338			return (i == constraintElems_.end()) ? NULL : *i;
339			}
340	gezelter	1782
341			Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) {
342			i = fluctuatingCharges_.begin();
343			return (i == fluctuatingCharges_.end()) ? NULL : *i;
344			}
345
346			Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) {
347			++i;
348			return (i == fluctuatingCharges_.end()) ? NULL : *i;
349			}
350
351	gezelter	2052	HBondDonor* beginHBondDonor(std::vector<HBondDonor*>::iterator& i) {
352			i = hBondDonors_.begin();
353			return (i == hBondDonors_.end()) ? NULL : *i;
354			}
355
356			HBondDonor* nextHBondDonor(std::vector<HBondDonor*>::iterator& i) {
357			++i;
358			return (i == hBondDonors_.end()) ? NULL : *i;
359			}
360
361			Atom* beginHBondAcceptor(std::vector<Atom*>::iterator& i) {
362			i = hBondAcceptors_.begin();
363			return (i == hBondAcceptors_.end()) ? NULL : *i;
364			}
365
366			Atom* nextHBondAcceptor(std::vector<Atom*>::iterator& i) {
367			++i;
368			return (i == hBondAcceptors_.end()) ? NULL : *i;
369			}
370
371	cli2	1360
372	gezelter	1211	/**
373			* Returns the total potential energy of short range interaction
374			* of this molecule
375			*/
376	tim	963	RealType getPotential();
377	gezelter	1211
378	gezelter	507	/** get total mass of this molecule */
379	tim	963	RealType getMass();
380	gezelter	1211
381	gezelter	2052	/**
382			* Returns the current center of mass position of this molecule.
383			*
384			* @return the center of mass position of this molecule.
385			*/
386	gezelter	507	Vector3d getCom();
387	gezelter	1211
388	gezelter	2052	/**
389			* Returns the center of mass position of this molecule in
390			* specified snapshot
391			*
392			* @return the center of mass position of this molecule
393			* @param snapshotNo
394			*/
395			Vector3d getCom(int snapshotNo);
396
397
398	gezelter	507	/** Moves the center of this molecule */
399			void moveCom(const Vector3d& delta);
400	gezelter	1211
401	gezelter	507	/** Returns the velocity of center of mass of this molecule */
402			Vector3d getComVel();
403	gezelter	246
404	gezelter	507	std::string getMoleculeName() {
405			return moleculeName_;
406			}
407	tim	289
408	gezelter	507	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
409	cli2	1360
410			//below functions are just forward functions
411			/**
412			* Adds property into property map
413			* @param genData GenericData to be added into PropertyMap
414			*/
415			void addProperty(GenericData* genData);
416
417			/**
418			* Removes property from PropertyMap by name
419			* @param propName the name of property to be removed
420			*/
421			void removeProperty(const std::string& propName);
422
423			/**
424			* clear all of the properties
425			*/
426			void clearProperties();
427
428			/**
429			* Returns all names of properties
430			* @return all names of properties
431			*/
432			std::vector<std::string> getPropertyNames();
433
434			/**
435			* Returns all of the properties in PropertyMap
436			* @return all of the properties in PropertyMap
437			*/
438			std::vector<GenericData*> getProperties();
439
440			/**
441			* Returns property
442			* @param propName name of property
443			* @return a pointer point to property with propName. If no property named propName
444			* exists, return NULL
445			*/
446			GenericData* getPropertyByName(const std::string& propName);
447	gezelter	1211
448	gezelter	507	private:
449	gezelter	1211
450	gezelter	507	int globalIndex_;
451	gezelter	1211
452	gezelter	507	std::vector<Atom*> atoms_;
453			std::vector<Bond*> bonds_;
454			std::vector<Bend*> bends_;
455			std::vector<Torsion*> torsions_;
456	cli2	1275	std::vector<Inversion*> inversions_;
457	gezelter	507	std::vector<RigidBody*> rigidBodies_;
458			std::vector<StuntDouble*> integrableObjects_;
459			std::vector<CutoffGroup*> cutoffGroups_;
460			std::vector<ConstraintPair*> constraintPairs_;
461			std::vector<ConstraintElem*> constraintElems_;
462	gezelter	1782	std::vector<Atom*> fluctuatingCharges_;
463	gezelter	2052	std::vector<HBondDonor*> hBondDonors_;
464			std::vector<Atom*> hBondAcceptors_;
465
466	gezelter	507	int stampId_;
467	gezelter	1908	int region_;
468	gezelter	507	std::string moleculeName_;
469	cli2	1360	PropertyMap properties_;
470	gezelter	1782	bool constrainTotalCharge_;
471	cli2	1360
472	gezelter	507	};
473	gezelter	2
474	gezelter	1390	} //namespace OpenMD
475	gezelter	246	#endif //