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, 3 months ago) by gezelter
File size:	14663 byte(s)
Log Message:	Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
#	Content
1	/*
2	* 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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/**
44	* @file Molecule.hpp
45	* @author tlin
46	* @date 10/25/2004
47	* @version 1.0
48	*/
49
50	#ifndef PRIMITIVES_MOLECULE_HPP
51	#define PRIMITIVES_MOLECULE_HPP
52	#include <vector>
53	#include <iostream>
54
55	#include "constraints/ConstraintPair.hpp"
56	#include "math/Vector3.hpp"
57	#include "primitives/Atom.hpp"
58	#include "primitives/RigidBody.hpp"
59	#include "primitives/Bond.hpp"
60	#include "primitives/Bend.hpp"
61	#include "primitives/Torsion.hpp"
62	#include "primitives/Inversion.hpp"
63	#include "primitives/CutoffGroup.hpp"
64	#include "utils/PropertyMap.hpp"
65
66
67	namespace OpenMD{
68
69	class Constraint;
70
71	/**
72	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
73	* @brief
74	*/
75	class Molecule {
76	public:
77
78	struct HBondDonor {
79	Atom* donorAtom;
80	Atom* donatedHydrogen;
81	};
82
83	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	typedef std::vector<Inversion*>::iterator InversionIterator;
88	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
89	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
90	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
91	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
92	typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
93	typedef std::vector<Atom*>::iterator FluctuatingChargeIterator;
94	typedef std::vector<HBondDonor*>::iterator HBondDonorIterator;
95	typedef std::vector<Atom*>::iterator HBondAcceptorIterator;
96
97	Molecule(int stampId, int globalIndex, const std::string& molName, int region);
98	virtual ~Molecule();
99
100	/**
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
108	/**
109	* Returns the stamp id of this molecule
110	* @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	*/
115	int getStampId() {
116	return stampId_;
117	}
118	int getRegion() {
119	return region_;
120	}
121
122	/** Returns the name of the molecule */
123	std::string getType() {
124	return moleculeName_;
125	}
126
127	/**
128	* Sets the global index of this molecule.
129	* @param index new global index to be set
130	*/
131	void setGlobalIndex(int index) {
132	globalIndex_ = index;
133	}
134
135	void setConstrainTotalCharge(bool ctc) {
136	constrainTotalCharge_ = ctc;
137	}
138
139	bool constrainTotalCharge() {
140	return constrainTotalCharge_;
141	}
142
143	/** add an atom into this molecule */
144	void addAtom(Atom* atom);
145
146	/** add a bond into this molecule */
147	void addBond(Bond* bond);
148
149	/** add a bend into this molecule */
150	void addBend(Bend* bend);
151
152	/** add a torsion into this molecule*/
153	void addTorsion(Torsion* torsion);
154
155	/** add an improper torsion into this molecule*/
156	void addInversion(Inversion* inversion);
157
158	/** add a rigidbody into this molecule */
159	void addRigidBody(RigidBody *rb);
160
161	/** add a cutoff group into this molecule */
162	void addCutoffGroup(CutoffGroup* cp);
163
164	void addConstraintPair(ConstraintPair* consPair);
165
166	void addConstraintElem(ConstraintElem* consElem);
167
168	/** */
169	void complete();
170
171	/** Returns the total number of atoms in this molecule */
172	unsigned int getNAtoms() {
173	return atoms_.size();
174	}
175
176	/** Returns the total number of bonds in this molecule */
177	unsigned int getNBonds(){
178	return bonds_.size();
179	}
180
181	/** Returns the total number of bends in this molecule */
182	unsigned int getNBends() {
183	return bends_.size();
184	}
185
186	/** Returns the total number of torsions in this molecule */
187	unsigned int getNTorsions() {
188	return torsions_.size();
189	}
190
191	/** Returns the total number of improper torsions in this molecule */
192	unsigned int getNInversions() {
193	return inversions_.size();
194	}
195
196	/** Returns the total number of rigid bodies in this molecule */
197	unsigned int getNRigidBodies() {
198	return rigidBodies_.size();
199	}
200
201	/** Returns the total number of integrable objects in this molecule */
202	unsigned int getNIntegrableObjects() {
203	return integrableObjects_.size();
204	}
205
206	/** Returns the total number of cutoff groups in this molecule */
207	unsigned int getNCutoffGroups() {
208	return cutoffGroups_.size();
209	}
210
211	/** Returns the total number of constraints in this molecule */
212	unsigned int getNConstraintPairs() {
213	return constraintPairs_.size();
214	}
215
216	/** Returns the total number of fluctuating charges in this molecule */
217	unsigned int getNFluctuatingCharges() {
218	return fluctuatingCharges_.size();
219	}
220	/** 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
230	Atom* getAtomAt(unsigned int i) {
231	assert(i < atoms_.size());
232	return atoms_[i];
233	}
234
235	RigidBody* getRigidBodyAt(unsigned int i) {
236	assert(i < rigidBodies_.size());
237	return rigidBodies_[i];
238	}
239
240	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
241	i = atoms_.begin();
242	return (i == atoms_.end()) ? NULL : *i;
243	}
244
245	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
246	++i;
247	return (i == atoms_.end()) ? NULL : *i;
248	}
249
250	Bond* beginBond(std::vector<Bond*>::iterator& i) {
251	i = bonds_.begin();
252	return (i == bonds_.end()) ? NULL : *i;
253	}
254
255	Bond* nextBond(std::vector<Bond*>::iterator& i) {
256	++i;
257	return (i == bonds_.end()) ? NULL : *i;
258
259	}
260
261	Bend* beginBend(std::vector<Bend*>::iterator& i) {
262	i = bends_.begin();
263	return (i == bends_.end()) ? NULL : *i;
264	}
265
266	Bend* nextBend(std::vector<Bend*>::iterator& i) {
267	++i;
268	return (i == bends_.end()) ? NULL : *i;
269	}
270
271	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
272	i = torsions_.begin();
273	return (i == torsions_.end()) ? NULL : *i;
274	}
275
276	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
277	++i;
278	return (i == torsions_.end()) ? NULL : *i;
279	}
280
281	Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
282	i = inversions_.begin();
283	return (i == inversions_.end()) ? NULL : *i;
284	}
285
286	Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
287	++i;
288	return (i == inversions_.end()) ? NULL : *i;
289	}
290
291	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
292	i = rigidBodies_.begin();
293	return (i == rigidBodies_.end()) ? NULL : *i;
294	}
295
296	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
297	++i;
298	return (i == rigidBodies_.end()) ? NULL : *i;
299	}
300
301	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
302	i = integrableObjects_.begin();
303	return (i == integrableObjects_.end()) ? NULL : *i;
304	}
305
306	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
307	++i;
308	return (i == integrableObjects_.end()) ? NULL : *i;
309	}
310
311	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
312	i = cutoffGroups_.begin();
313	return (i == cutoffGroups_.end()) ? NULL : *i;
314	}
315
316	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
317	++i;
318	return (i == cutoffGroups_.end()) ? NULL : *i;
319	}
320
321	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
322	i = constraintPairs_.begin();
323	return (i == constraintPairs_.end()) ? NULL : *i;
324	}
325
326	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
327	++i;
328	return (i == constraintPairs_.end()) ? NULL : *i;
329	}
330
331	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
332	i = constraintElems_.begin();
333	return (i == constraintElems_.end()) ? NULL : *i;
334	}
335
336	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
337	++i;
338	return (i == constraintElems_.end()) ? NULL : *i;
339	}
340
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	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
372	/**
373	* Returns the total potential energy of short range interaction
374	* of this molecule
375	*/
376	RealType getPotential();
377
378	/** get total mass of this molecule */
379	RealType getMass();
380
381	/**
382	* Returns the current center of mass position of this molecule.
383	*
384	* @return the center of mass position of this molecule.
385	*/
386	Vector3d getCom();
387
388	/**
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	/** Moves the center of this molecule */
399	void moveCom(const Vector3d& delta);
400
401	/** Returns the velocity of center of mass of this molecule */
402	Vector3d getComVel();
403
404	std::string getMoleculeName() {
405	return moleculeName_;
406	}
407
408	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
409
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
448	private:
449
450	int globalIndex_;
451
452	std::vector<Atom*> atoms_;
453	std::vector<Bond*> bonds_;
454	std::vector<Bend*> bends_;
455	std::vector<Torsion*> torsions_;
456	std::vector<Inversion*> inversions_;
457	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	std::vector<Atom*> fluctuatingCharges_;
463	std::vector<HBondDonor*> hBondDonors_;
464	std::vector<Atom*> hBondAcceptors_;
465
466	int stampId_;
467	int region_;
468	std::string moleculeName_;
469	PropertyMap properties_;
470	bool constrainTotalCharge_;
471
472	};
473
474	} //namespace OpenMD
475	#endif //