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:

    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;
    
    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();
    }

    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;    
    }

        
    /** 
     * Returns the total potential energy of short range interaction
     * of this molecule 
     */    
    RealType getPotential();
    
    /** get total mass of this molecule */        
    RealType getMass();
    
    /** return the center of mass of this molecule */
    Vector3d getCom();
    
    /** 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_;
    int stampId_;
    int region_;
    std::string moleculeName_;
    PropertyMap properties_;
    bool constrainTotalCharge_;

  };

} //namespace OpenMD
#endif //
Revision:	1908
Committed:	Fri Jul 19 21:25:45 2013 UTC (11 years, 9 months ago) by gezelter
File size:	13069 byte(s)
Log Message:	Added infrastructure for region-constrained fluctuating charges.
#	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	1390	namespace OpenMD{
67	gezelter	2
68	gezelter	507	class Constraint;
69	gezelter	2
70	gezelter	507	/**
71			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
72			* @brief
73			*/
74			class Molecule {
75			public:
76	gezelter	2
77	gezelter	507	typedef std::vector<Atom*>::iterator AtomIterator;
78			typedef std::vector<Bond*>::iterator BondIterator;
79			typedef std::vector<Bend*>::iterator BendIterator;
80			typedef std::vector<Torsion*>::iterator TorsionIterator;
81	cli2	1275	typedef std::vector<Inversion*>::iterator InversionIterator;
82	gezelter	507	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
83			typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
84	gezelter	1211	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
85	gezelter	507	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
86			typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
87	gezelter	1782	typedef std::vector<Atom*>::iterator FluctuatingChargeIterator;
88	gezelter	1211
89	gezelter	1908	Molecule(int stampId, int globalIndex, const std::string& molName, int region);
90	gezelter	507	virtual ~Molecule();
91	cli2	1407
92	gezelter	507	/**
93			* Returns the global index of this molecule.
94			* @return the global index of this molecule
95			*/
96			int getGlobalIndex() {
97			return globalIndex_;
98			}
99	gezelter	1211
100	gezelter	507	/**
101			* Returns the stamp id of this molecule
102	gezelter	1211	* @note Ideally, every molecule should keep a pointer of its
103			* molecule stamp instead of its stamp id. However, the pointer
104			* will become invalid, if the molecule migrate to other
105			* processor.
106	gezelter	507	*/
107			int getStampId() {
108			return stampId_;
109			}
110	gezelter	1908	int getRegion() {
111			return region_;
112			}
113	gezelter	1211
114	gezelter	507	/** Returns the name of the molecule */
115			std::string getType() {
116			return moleculeName_;
117			}
118	gezelter	1211
119	gezelter	507	/**
120			* Sets the global index of this molecule.
121	gezelter	1879	* @param index new global index to be set
122	gezelter	507	*/
123			void setGlobalIndex(int index) {
124			globalIndex_ = index;
125			}
126	gezelter	1782
127			void setConstrainTotalCharge(bool ctc) {
128			constrainTotalCharge_ = ctc;
129			}
130	gezelter	1211
131	gezelter	1782	bool constrainTotalCharge() {
132			return constrainTotalCharge_;
133			}
134
135	gezelter	507	/** add an atom into this molecule */
136			void addAtom(Atom* atom);
137	gezelter	1211
138	gezelter	507	/** add a bond into this molecule */
139			void addBond(Bond* bond);
140	gezelter	1211
141	gezelter	507	/** add a bend into this molecule */
142			void addBend(Bend* bend);
143	gezelter	1211
144	gezelter	507	/** add a torsion into this molecule*/
145			void addTorsion(Torsion* torsion);
146	cli2	1275
147			/** add an improper torsion into this molecule*/
148			void addInversion(Inversion* inversion);
149	gezelter	1211
150	gezelter	507	/** add a rigidbody into this molecule */
151			void addRigidBody(RigidBody *rb);
152	gezelter	1211
153	gezelter	507	/** add a cutoff group into this molecule */
154			void addCutoffGroup(CutoffGroup* cp);
155	gezelter	1211
156	gezelter	507	void addConstraintPair(ConstraintPair* consPair);
157	gezelter	1211
158	gezelter	507	void addConstraintElem(ConstraintElem* consElem);
159	gezelter	1211
160	gezelter	507	/** */
161			void complete();
162	gezelter	1211
163	gezelter	507	/** Returns the total number of atoms in this molecule */
164			unsigned int getNAtoms() {
165			return atoms_.size();
166			}
167	gezelter	1211
168	gezelter	507	/** Returns the total number of bonds in this molecule */
169			unsigned int getNBonds(){
170			return bonds_.size();
171			}
172	gezelter	1211
173	gezelter	507	/** Returns the total number of bends in this molecule */
174			unsigned int getNBends() {
175			return bends_.size();
176			}
177	gezelter	1211
178	gezelter	507	/** Returns the total number of torsions in this molecule */
179			unsigned int getNTorsions() {
180			return torsions_.size();
181			}
182	cli2	1275
183			/** Returns the total number of improper torsions in this molecule */
184			unsigned int getNInversions() {
185			return inversions_.size();
186			}
187	gezelter	1211
188	gezelter	507	/** Returns the total number of rigid bodies in this molecule */
189			unsigned int getNRigidBodies() {
190			return rigidBodies_.size();
191			}
192	gezelter	1211
193	gezelter	507	/** Returns the total number of integrable objects in this molecule */
194			unsigned int getNIntegrableObjects() {
195			return integrableObjects_.size();
196			}
197	gezelter	1211
198	gezelter	507	/** Returns the total number of cutoff groups in this molecule */
199			unsigned int getNCutoffGroups() {
200			return cutoffGroups_.size();
201			}
202	gezelter	1211
203	gezelter	507	/** Returns the total number of constraints in this molecule */
204			unsigned int getNConstraintPairs() {
205			return constraintPairs_.size();
206			}
207	gezelter	1782
208			/** Returns the total number of fluctuating charges in this molecule */
209			unsigned int getNFluctuatingCharges() {
210			return fluctuatingCharges_.size();
211			}
212
213	gezelter	507	Atom* getAtomAt(unsigned int i) {
214			assert(i < atoms_.size());
215			return atoms_[i];
216			}
217	gezelter	1211
218	gezelter	507	RigidBody* getRigidBodyAt(unsigned int i) {
219			assert(i < rigidBodies_.size());
220			return rigidBodies_[i];
221			}
222	gezelter	1211
223	gezelter	507	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
224			i = atoms_.begin();
225			return (i == atoms_.end()) ? NULL : *i;
226			}
227	gezelter	1211
228	gezelter	507	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
229			++i;
230			return (i == atoms_.end()) ? NULL : *i;
231			}
232	gezelter	1211
233	gezelter	507	Bond* beginBond(std::vector<Bond*>::iterator& i) {
234			i = bonds_.begin();
235			return (i == bonds_.end()) ? NULL : *i;
236			}
237	gezelter	1211
238	gezelter	507	Bond* nextBond(std::vector<Bond*>::iterator& i) {
239			++i;
240			return (i == bonds_.end()) ? NULL : *i;
241	gezelter	1211
242	gezelter	507	}
243	gezelter	1211
244	gezelter	507	Bend* beginBend(std::vector<Bend*>::iterator& i) {
245			i = bends_.begin();
246			return (i == bends_.end()) ? NULL : *i;
247			}
248	gezelter	1211
249	gezelter	507	Bend* nextBend(std::vector<Bend*>::iterator& i) {
250			++i;
251			return (i == bends_.end()) ? NULL : *i;
252			}
253	gezelter	1211
254	gezelter	507	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
255			i = torsions_.begin();
256			return (i == torsions_.end()) ? NULL : *i;
257			}
258	gezelter	1211
259	gezelter	507	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
260			++i;
261			return (i == torsions_.end()) ? NULL : *i;
262			}
263	cli2	1275
264			Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
265			i = inversions_.begin();
266			return (i == inversions_.end()) ? NULL : *i;
267			}
268	gezelter	1211
269	cli2	1275	Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
270			++i;
271			return (i == inversions_.end()) ? NULL : *i;
272			}
273
274	gezelter	507	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
275			i = rigidBodies_.begin();
276			return (i == rigidBodies_.end()) ? NULL : *i;
277			}
278	gezelter	1211
279	gezelter	507	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
280			++i;
281			return (i == rigidBodies_.end()) ? NULL : *i;
282			}
283	gezelter	1211
284	gezelter	507	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
285			i = integrableObjects_.begin();
286			return (i == integrableObjects_.end()) ? NULL : *i;
287			}
288	gezelter	1211
289	gezelter	507	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
290			++i;
291			return (i == integrableObjects_.end()) ? NULL : *i;
292			}
293	gezelter	1211
294	gezelter	507	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
295			i = cutoffGroups_.begin();
296			return (i == cutoffGroups_.end()) ? NULL : *i;
297			}
298	gezelter	246
299	gezelter	1211	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
300	gezelter	507	++i;
301			return (i == cutoffGroups_.end()) ? NULL : *i;
302			}
303	gezelter	1211
304	gezelter	507	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
305			i = constraintPairs_.begin();
306			return (i == constraintPairs_.end()) ? NULL : *i;
307			}
308	gezelter	1211
309	gezelter	507	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
310			++i;
311			return (i == constraintPairs_.end()) ? NULL : *i;
312			}
313	gezelter	1211
314	gezelter	507	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
315			i = constraintElems_.begin();
316			return (i == constraintElems_.end()) ? NULL : *i;
317			}
318	gezelter	1211
319	gezelter	507	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
320			++i;
321			return (i == constraintElems_.end()) ? NULL : *i;
322			}
323	gezelter	1782
324			Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) {
325			i = fluctuatingCharges_.begin();
326			return (i == fluctuatingCharges_.end()) ? NULL : *i;
327			}
328
329			Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) {
330			++i;
331			return (i == fluctuatingCharges_.end()) ? NULL : *i;
332			}
333
334	cli2	1360
335	gezelter	1211	/**
336			* Returns the total potential energy of short range interaction
337			* of this molecule
338			*/
339	tim	963	RealType getPotential();
340	gezelter	1211
341	gezelter	507	/** get total mass of this molecule */
342	tim	963	RealType getMass();
343	gezelter	1211
344	gezelter	507	/** return the center of mass of this molecule */
345			Vector3d getCom();
346	gezelter	1211
347	gezelter	507	/** Moves the center of this molecule */
348			void moveCom(const Vector3d& delta);
349	gezelter	1211
350	gezelter	507	/** Returns the velocity of center of mass of this molecule */
351			Vector3d getComVel();
352	gezelter	246
353	gezelter	507	std::string getMoleculeName() {
354			return moleculeName_;
355			}
356	tim	289
357	gezelter	507	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
358	cli2	1360
359			//below functions are just forward functions
360			/**
361			* Adds property into property map
362			* @param genData GenericData to be added into PropertyMap
363			*/
364			void addProperty(GenericData* genData);
365
366			/**
367			* Removes property from PropertyMap by name
368			* @param propName the name of property to be removed
369			*/
370			void removeProperty(const std::string& propName);
371
372			/**
373			* clear all of the properties
374			*/
375			void clearProperties();
376
377			/**
378			* Returns all names of properties
379			* @return all names of properties
380			*/
381			std::vector<std::string> getPropertyNames();
382
383			/**
384			* Returns all of the properties in PropertyMap
385			* @return all of the properties in PropertyMap
386			*/
387			std::vector<GenericData*> getProperties();
388
389			/**
390			* Returns property
391			* @param propName name of property
392			* @return a pointer point to property with propName. If no property named propName
393			* exists, return NULL
394			*/
395			GenericData* getPropertyByName(const std::string& propName);
396	gezelter	1211
397	gezelter	507	private:
398	gezelter	1211
399	gezelter	507	int globalIndex_;
400	gezelter	1211
401	gezelter	507	std::vector<Atom*> atoms_;
402			std::vector<Bond*> bonds_;
403			std::vector<Bend*> bends_;
404			std::vector<Torsion*> torsions_;
405	cli2	1275	std::vector<Inversion*> inversions_;
406	gezelter	507	std::vector<RigidBody*> rigidBodies_;
407			std::vector<StuntDouble*> integrableObjects_;
408			std::vector<CutoffGroup*> cutoffGroups_;
409			std::vector<ConstraintPair*> constraintPairs_;
410			std::vector<ConstraintElem*> constraintElems_;
411	gezelter	1782	std::vector<Atom*> fluctuatingCharges_;
412	gezelter	507	int stampId_;
413	gezelter	1908	int region_;
414	gezelter	507	std::string moleculeName_;
415	cli2	1360	PropertyMap properties_;
416	gezelter	1782	bool constrainTotalCharge_;
417	cli2	1360
418	gezelter	507	};
419	gezelter	2
420	gezelter	1390	} //namespace OpenMD
421	gezelter	246	#endif //