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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @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;
    
    
    Molecule(int stampId, int globalIndex, const std::string& molName);
    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_;
    }
    
    /** Returns the name of the molecule */
    std::string getType() {
      return moleculeName_;
    }
    
    /**
     * Sets the global index of this molecule.
     * @param new global index to be set
     */
    void setGlobalIndex(int index) {
      globalIndex_ = index;
    }
    
    
    /** 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();
    }
    
    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;    
    }
        
    /** 
     * 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_;
    int stampId_;
    std::string moleculeName_;
    PropertyMap properties_;

  };

} //namespace OpenMD
#endif //
Revision:	1407
Committed:	Wed Jan 20 16:04:40 2010 UTC (15 years, 9 months ago) by cli2
File size:	12129 byte(s)
Log Message:	Fixed bugs in Restraint, refactored RestReader and RestWriter
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42			/**
43			* @file Molecule.hpp
44			* @author tlin
45			* @date 10/25/2004
46			* @version 1.0
47			*/
48	gezelter	2
49	gezelter	246	#ifndef PRIMITIVES_MOLECULE_HPP
50			#define PRIMITIVES_MOLECULE_HPP
51	gezelter	2	#include <vector>
52	gezelter	246	#include <iostream>
53	gezelter	2
54	gezelter	246	#include "constraints/ConstraintPair.hpp"
55			#include "math/Vector3.hpp"
56	tim	3	#include "primitives/Atom.hpp"
57			#include "primitives/RigidBody.hpp"
58	gezelter	246	#include "primitives/Bond.hpp"
59			#include "primitives/Bend.hpp"
60			#include "primitives/Torsion.hpp"
61	cli2	1275	#include "primitives/Inversion.hpp"
62	tim	3	#include "primitives/CutoffGroup.hpp"
63	cli2	1360	#include "utils/PropertyMap.hpp"
64	gezelter	2
65	gezelter	1390	namespace OpenMD{
66	gezelter	2
67	gezelter	507	class Constraint;
68	gezelter	2
69	gezelter	507	/**
70			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
71			* @brief
72			*/
73			class Molecule {
74			public:
75	gezelter	2
76	gezelter	507	typedef std::vector<Atom*>::iterator AtomIterator;
77			typedef std::vector<Bond*>::iterator BondIterator;
78			typedef std::vector<Bend*>::iterator BendIterator;
79			typedef std::vector<Torsion*>::iterator TorsionIterator;
80	cli2	1275	typedef std::vector<Inversion*>::iterator InversionIterator;
81	gezelter	507	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
82			typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
83	gezelter	1211	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
84	gezelter	507	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
85			typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
86	gezelter	1211
87
88	gezelter	507	Molecule(int stampId, int globalIndex, const std::string& molName);
89			virtual ~Molecule();
90	cli2	1407
91	gezelter	507	/**
92			* Returns the global index of this molecule.
93			* @return the global index of this molecule
94			*/
95			int getGlobalIndex() {
96			return globalIndex_;
97			}
98	gezelter	1211
99	gezelter	507	/**
100			* Returns the stamp id of this molecule
101	gezelter	1211	* @note Ideally, every molecule should keep a pointer of its
102			* molecule stamp instead of its stamp id. However, the pointer
103			* will become invalid, if the molecule migrate to other
104			* processor.
105	gezelter	507	*/
106			int getStampId() {
107			return stampId_;
108			}
109	gezelter	1211
110	gezelter	507	/** Returns the name of the molecule */
111			std::string getType() {
112			return moleculeName_;
113			}
114	gezelter	1211
115	gezelter	507	/**
116			* Sets the global index of this molecule.
117			* @param new global index to be set
118			*/
119			void setGlobalIndex(int index) {
120			globalIndex_ = index;
121			}
122	gezelter	1211
123
124	gezelter	507	/** add an atom into this molecule */
125			void addAtom(Atom* atom);
126	gezelter	1211
127	gezelter	507	/** add a bond into this molecule */
128			void addBond(Bond* bond);
129	gezelter	1211
130	gezelter	507	/** add a bend into this molecule */
131			void addBend(Bend* bend);
132	gezelter	1211
133	gezelter	507	/** add a torsion into this molecule*/
134			void addTorsion(Torsion* torsion);
135	cli2	1275
136			/** add an improper torsion into this molecule*/
137			void addInversion(Inversion* inversion);
138	gezelter	1211
139	gezelter	507	/** add a rigidbody into this molecule */
140			void addRigidBody(RigidBody *rb);
141	gezelter	1211
142	gezelter	507	/** add a cutoff group into this molecule */
143			void addCutoffGroup(CutoffGroup* cp);
144	gezelter	1211
145	gezelter	507	void addConstraintPair(ConstraintPair* consPair);
146	gezelter	1211
147	gezelter	507	void addConstraintElem(ConstraintElem* consElem);
148	gezelter	1211
149	gezelter	507	/** */
150			void complete();
151	gezelter	1211
152	gezelter	507	/** Returns the total number of atoms in this molecule */
153			unsigned int getNAtoms() {
154			return atoms_.size();
155			}
156	gezelter	1211
157	gezelter	507	/** Returns the total number of bonds in this molecule */
158			unsigned int getNBonds(){
159			return bonds_.size();
160			}
161	gezelter	1211
162	gezelter	507	/** Returns the total number of bends in this molecule */
163			unsigned int getNBends() {
164			return bends_.size();
165			}
166	gezelter	1211
167	gezelter	507	/** Returns the total number of torsions in this molecule */
168			unsigned int getNTorsions() {
169			return torsions_.size();
170			}
171	cli2	1275
172			/** Returns the total number of improper torsions in this molecule */
173			unsigned int getNInversions() {
174			return inversions_.size();
175			}
176	gezelter	1211
177	gezelter	507	/** Returns the total number of rigid bodies in this molecule */
178			unsigned int getNRigidBodies() {
179			return rigidBodies_.size();
180			}
181	gezelter	1211
182	gezelter	507	/** Returns the total number of integrable objects in this molecule */
183			unsigned int getNIntegrableObjects() {
184			return integrableObjects_.size();
185			}
186	gezelter	1211
187	gezelter	507	/** Returns the total number of cutoff groups in this molecule */
188			unsigned int getNCutoffGroups() {
189			return cutoffGroups_.size();
190			}
191	gezelter	1211
192	gezelter	507	/** Returns the total number of constraints in this molecule */
193			unsigned int getNConstraintPairs() {
194			return constraintPairs_.size();
195			}
196	gezelter	1211
197	gezelter	507	Atom* getAtomAt(unsigned int i) {
198			assert(i < atoms_.size());
199			return atoms_[i];
200			}
201	gezelter	1211
202	gezelter	507	RigidBody* getRigidBodyAt(unsigned int i) {
203			assert(i < rigidBodies_.size());
204			return rigidBodies_[i];
205			}
206	gezelter	1211
207	gezelter	507	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
208			i = atoms_.begin();
209			return (i == atoms_.end()) ? NULL : *i;
210			}
211	gezelter	1211
212	gezelter	507	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
213			++i;
214			return (i == atoms_.end()) ? NULL : *i;
215			}
216	gezelter	1211
217	gezelter	507	Bond* beginBond(std::vector<Bond*>::iterator& i) {
218			i = bonds_.begin();
219			return (i == bonds_.end()) ? NULL : *i;
220			}
221	gezelter	1211
222	gezelter	507	Bond* nextBond(std::vector<Bond*>::iterator& i) {
223			++i;
224			return (i == bonds_.end()) ? NULL : *i;
225	gezelter	1211
226	gezelter	507	}
227	gezelter	1211
228	gezelter	507	Bend* beginBend(std::vector<Bend*>::iterator& i) {
229			i = bends_.begin();
230			return (i == bends_.end()) ? NULL : *i;
231			}
232	gezelter	1211
233	gezelter	507	Bend* nextBend(std::vector<Bend*>::iterator& i) {
234			++i;
235			return (i == bends_.end()) ? NULL : *i;
236			}
237	gezelter	1211
238	gezelter	507	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
239			i = torsions_.begin();
240			return (i == torsions_.end()) ? NULL : *i;
241			}
242	gezelter	1211
243	gezelter	507	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
244			++i;
245			return (i == torsions_.end()) ? NULL : *i;
246			}
247	cli2	1275
248			Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
249			i = inversions_.begin();
250			return (i == inversions_.end()) ? NULL : *i;
251			}
252	gezelter	1211
253	cli2	1275	Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
254			++i;
255			return (i == inversions_.end()) ? NULL : *i;
256			}
257
258	gezelter	507	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
259			i = rigidBodies_.begin();
260			return (i == rigidBodies_.end()) ? NULL : *i;
261			}
262	gezelter	1211
263	gezelter	507	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
264			++i;
265			return (i == rigidBodies_.end()) ? NULL : *i;
266			}
267	gezelter	1211
268	gezelter	507	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
269			i = integrableObjects_.begin();
270			return (i == integrableObjects_.end()) ? NULL : *i;
271			}
272	gezelter	1211
273	gezelter	507	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
274			++i;
275			return (i == integrableObjects_.end()) ? NULL : *i;
276			}
277	gezelter	1211
278	gezelter	507	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
279			i = cutoffGroups_.begin();
280			return (i == cutoffGroups_.end()) ? NULL : *i;
281			}
282	gezelter	246
283	gezelter	1211	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
284	gezelter	507	++i;
285			return (i == cutoffGroups_.end()) ? NULL : *i;
286			}
287	gezelter	1211
288	gezelter	507	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
289			i = constraintPairs_.begin();
290			return (i == constraintPairs_.end()) ? NULL : *i;
291			}
292	gezelter	1211
293	gezelter	507	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
294			++i;
295			return (i == constraintPairs_.end()) ? NULL : *i;
296			}
297	gezelter	1211
298	gezelter	507	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
299			i = constraintElems_.begin();
300			return (i == constraintElems_.end()) ? NULL : *i;
301			}
302	gezelter	1211
303	gezelter	507	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
304			++i;
305			return (i == constraintElems_.end()) ? NULL : *i;
306			}
307	cli2	1360
308	gezelter	1211	/**
309			* Returns the total potential energy of short range interaction
310			* of this molecule
311			*/
312	tim	963	RealType getPotential();
313	gezelter	1211
314	gezelter	507	/** get total mass of this molecule */
315	tim	963	RealType getMass();
316	gezelter	1211
317	gezelter	507	/** return the center of mass of this molecule */
318			Vector3d getCom();
319	gezelter	1211
320	gezelter	507	/** Moves the center of this molecule */
321			void moveCom(const Vector3d& delta);
322	gezelter	1211
323	gezelter	507	/** Returns the velocity of center of mass of this molecule */
324			Vector3d getComVel();
325	gezelter	246
326	gezelter	507	std::string getMoleculeName() {
327			return moleculeName_;
328			}
329	tim	289
330	gezelter	507	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
331	cli2	1360
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			/**
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			/**
346			* clear all of the properties
347			*/
348			void clearProperties();
349
350			/**
351			* Returns all names of properties
352			* @return all names of properties
353			*/
354			std::vector<std::string> getPropertyNames();
355
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			/**
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	gezelter	1211
370	gezelter	507	private:
371	gezelter	1211
372	gezelter	507	int globalIndex_;
373	gezelter	1211
374	gezelter	507	std::vector<Atom*> atoms_;
375			std::vector<Bond*> bonds_;
376			std::vector<Bend*> bends_;
377			std::vector<Torsion*> torsions_;
378	cli2	1275	std::vector<Inversion*> inversions_;
379	gezelter	507	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	cli2	1360	PropertyMap properties_;
387
388	gezelter	507	};
389	gezelter	2
390	gezelter	1390	} //namespace OpenMD
391	gezelter	246	#endif //