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root/OpenMD/branches/development/src/primitives/Molecule.hpp

Comparing:
trunk/src/primitives/Molecule.hpp (file contents), Revision 305 by tim, Mon Feb 7 22:39:19 2005 UTC vs.
branches/development/src/primitives/Molecule.hpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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, 24107 (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		/**
#	Line 58 | Line 59
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	<	namespace oopse{
66	>	namespace OpenMD{
67
68	<	class Constraint;
68	>	class Constraint;
69
70	<	/**
71	<	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
72	<	* @brief
73	<	*/
74	<	class Molecule {
75	<	public:
70	>	/**
71	>	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
72	>	* @brief
73	>	*/
74	>	class Molecule {
75	>	public:
76
77	<	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	<	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
82	<	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
83	<	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
84	<	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
85	<	typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
86	<
77	>	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	>	typedef std::vector<Inversion*>::iterator InversionIterator;
82	>	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
83	>	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
84	>	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
85	>	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
86	>	typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
87	>	typedef std::vector<Atom*>::iterator FluctuatingChargeIterator;
88	>
89	>	Molecule(int stampId, int globalIndex, const std::string& molName);
90	>	virtual ~Molecule();
91
92	<	Molecule(int stampId, int globalIndex, const std::string& molName);
93	<	virtual ~Molecule();
92	>	/**
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	>
100	>	/**
101	>	* Returns the stamp id of this molecule
102	>	* @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	>	*/
107	>	int getStampId() {
108	>	return stampId_;
109	>	}
110	>
111	>	/** Returns the name of the molecule */
112	>	std::string getType() {
113	>	return moleculeName_;
114	>	}
115	>
116	>	/**
117	>	* Sets the global index of this molecule.
118	>	* @param index new global index to be set
119	>	*/
120	>	void setGlobalIndex(int index) {
121	>	globalIndex_ = index;
122	>	}
123
124	<	/**
125	<	* Returns the global index of this molecule.
126	<	* @return  the global index of this molecule
127	<	*/
128	<	int getGlobalIndex() {
129	<	return globalIndex_;
130	<	}
124	>	void setConstrainTotalCharge(bool ctc) {
125	>	constrainTotalCharge_ = ctc;
126	>	}
127	>
128	>	bool constrainTotalCharge() {
129	>	return constrainTotalCharge_;
130	>	}
131
132	<	/**
133	<	* Returns the stamp id of this molecule
134	<	* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
135	<	* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
136	<	*/
137	<	int getStampId() {
138	<	return stampId_;
139	<	}
132	>	/** add an atom into this molecule */
133	>	void addAtom(Atom* atom);
134	>
135	>	/** add a bond into this molecule */
136	>	void addBond(Bond* bond);
137	>
138	>	/** add a bend into this molecule */
139	>	void addBend(Bend* bend);
140	>
141	>	/** add a torsion into this molecule*/
142	>	void addTorsion(Torsion* torsion);
143
144	<	/** Returns the name of the molecule */
145	<	std::string getType() {
146	<	return moleculeName_;
147	<	}
148	<
149	<	/**
150	<	* Sets the global index of this molecule.
151	<	* @param new global index to be set
152	<	*/
153	<	void setGlobalIndex(int index) {
154	<	globalIndex_ = index;
155	<	}
144	>	/** add an improper torsion into this molecule*/
145	>	void addInversion(Inversion* inversion);
146	>
147	>	/** add a rigidbody into this molecule */
148	>	void addRigidBody(RigidBody *rb);
149	>
150	>	/** add a cutoff group into this molecule */
151	>	void addCutoffGroup(CutoffGroup* cp);
152	>
153	>	void addConstraintPair(ConstraintPair* consPair);
154	>
155	>	void addConstraintElem(ConstraintElem* consElem);
156	>
157	>	/** */
158	>	void complete();
159	>
160	>	/** Returns the total number of atoms in this molecule */
161	>	unsigned int getNAtoms() {
162	>	return atoms_.size();
163	>	}
164	>
165	>	/** Returns the total number of bonds in this molecule */
166	>	unsigned int getNBonds(){
167	>	return bonds_.size();
168	>	}
169	>
170	>	/** Returns the total number of bends in this molecule */
171	>	unsigned int getNBends() {
172	>	return bends_.size();
173	>	}
174	>
175	>	/** Returns the total number of torsions in this molecule */
176	>	unsigned int getNTorsions() {
177	>	return torsions_.size();
178	>	}
179
180	<
181	<	/** add an atom into this molecule */
182	<	void addAtom(Atom* atom);
180	>	/** Returns the total number of improper torsions in this molecule */
181	>	unsigned int getNInversions() {
182	>	return inversions_.size();
183	>	}
184	>
185	>	/** Returns the total number of rigid bodies in this molecule */
186	>	unsigned int getNRigidBodies() {
187	>	return rigidBodies_.size();
188	>	}
189	>
190	>	/** Returns the total number of integrable objects in this molecule */
191	>	unsigned int getNIntegrableObjects() {
192	>	return integrableObjects_.size();
193	>	}
194	>
195	>	/** Returns the total number of cutoff groups in this molecule */
196	>	unsigned int getNCutoffGroups() {
197	>	return cutoffGroups_.size();
198	>	}
199	>
200	>	/** Returns the total number of constraints in this molecule */
201	>	unsigned int getNConstraintPairs() {
202	>	return constraintPairs_.size();
203	>	}
204
205	<	/** add a bond into this molecule */
206	<	void addBond(Bond* bond);
205	>	/** Returns the total number of fluctuating charges in this molecule */
206	>	unsigned int getNFluctuatingCharges() {
207	>	return fluctuatingCharges_.size();
208	>	}
209
210	<	/** add a bend into this molecule */
211	<	void addBend(Bend* bend);
210	>	Atom* getAtomAt(unsigned int i) {
211	>	assert(i < atoms_.size());
212	>	return atoms_[i];
213	>	}
214	>
215	>	RigidBody* getRigidBodyAt(unsigned int i) {
216	>	assert(i < rigidBodies_.size());
217	>	return rigidBodies_[i];
218	>	}
219	>
220	>	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
221	>	i = atoms_.begin();
222	>	return (i == atoms_.end()) ? NULL : *i;
223	>	}
224	>
225	>	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
226	>	++i;
227	>	return (i == atoms_.end()) ? NULL : *i;
228	>	}
229	>
230	>	Bond* beginBond(std::vector<Bond*>::iterator& i) {
231	>	i = bonds_.begin();
232	>	return (i == bonds_.end()) ? NULL : *i;
233	>	}
234	>
235	>	Bond* nextBond(std::vector<Bond*>::iterator& i) {
236	>	++i;
237	>	return (i == bonds_.end()) ? NULL : *i;
238	>
239	>	}
240	>
241	>	Bend* beginBend(std::vector<Bend*>::iterator& i) {
242	>	i = bends_.begin();
243	>	return (i == bends_.end()) ? NULL : *i;
244	>	}
245	>
246	>	Bend* nextBend(std::vector<Bend*>::iterator& i) {
247	>	++i;
248	>	return (i == bends_.end()) ? NULL : *i;
249	>	}
250	>
251	>	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
252	>	i = torsions_.begin();
253	>	return (i == torsions_.end()) ? NULL : *i;
254	>	}
255	>
256	>	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
257	>	++i;
258	>	return (i == torsions_.end()) ? NULL : *i;
259	>	}
260
261	<	/** add a torsion into this molecule*/
262	<	void addTorsion(Torsion* torsion);
261	>	Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
262	>	i = inversions_.begin();
263	>	return (i == inversions_.end()) ? NULL : *i;
264	>	}
265	>
266	>	Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
267	>	++i;
268	>	return (i == inversions_.end()) ? NULL : *i;
269	>	}
270	>
271	>	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
272	>	i = rigidBodies_.begin();
273	>	return (i == rigidBodies_.end()) ? NULL : *i;
274	>	}
275	>
276	>	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
277	>	++i;
278	>	return (i == rigidBodies_.end()) ? NULL : *i;
279	>	}
280	>
281	>	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
282	>	i = integrableObjects_.begin();
283	>	return (i == integrableObjects_.end()) ? NULL : *i;
284	>	}
285	>
286	>	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
287	>	++i;
288	>	return (i == integrableObjects_.end()) ? NULL : *i;
289	>	}
290	>
291	>	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
292	>	i = cutoffGroups_.begin();
293	>	return (i == cutoffGroups_.end()) ? NULL : *i;
294	>	}
295
296	<	/** add a rigidbody into this molecule */
297	<	void addRigidBody(RigidBody *rb);
298	<
299	<	/** add a cutoff group into this molecule */
300	<	void addCutoffGroup(CutoffGroup* cp);
296	>	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
297	>	++i;
298	>	return (i == cutoffGroups_.end()) ? NULL : *i;
299	>	}
300	>
301	>	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
302	>	i = constraintPairs_.begin();
303	>	return (i == constraintPairs_.end()) ? NULL : *i;
304	>	}
305	>
306	>	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
307	>	++i;
308	>	return (i == constraintPairs_.end()) ? NULL : *i;
309	>	}
310	>
311	>	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
312	>	i = constraintElems_.begin();
313	>	return (i == constraintElems_.end()) ? NULL : *i;
314	>	}
315	>
316	>	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
317	>	++i;
318	>	return (i == constraintElems_.end()) ? NULL : *i;
319	>	}
320
321	<	void addConstraintPair(ConstraintPair* consPair);
322	<
323	<	void addConstraintElem(ConstraintElem* consElem);
321	>	Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) {
322	>	i = fluctuatingCharges_.begin();
323	>	return (i == fluctuatingCharges_.end()) ? NULL : *i;
324	>	}
325	>
326	>	Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) {
327	>	++i;
328	>	return (i == fluctuatingCharges_.end()) ? NULL : *i;
329	>	}
330
141	–	/** */
142	–	void complete();
143	–
144	–	/** Returns the total number of atoms in this molecule */
145	–	unsigned int getNAtoms() {
146	–	return atoms_.size();
147	–	}
148	–
149	–	/** Returns the total number of bonds in this molecule */
150	–	unsigned int getNBonds(){
151	–	return bonds_.size();
152	–	}
153	–
154	–	/** Returns the total number of bends in this molecule */
155	–	unsigned int getNBends() {
156	–	return bends_.size();
157	–	}
158	–
159	–	/** Returns the total number of torsions in this molecule */
160	–	unsigned int getNTorsions() {
161	–	return torsions_.size();
162	–	}
163	–
164	–	/** Returns the total number of rigid bodies in this molecule */
165	–	unsigned int getNRigidBodies() {
166	–	return rigidBodies_.size();
167	–	}
168	–
169	–	/** Returns the total number of integrable objects in this molecule */
170	–	unsigned int getNIntegrableObjects() {
171	–	return integrableObjects_.size();
172	–	}
173	–
174	–	/** Returns the total number of cutoff groups in this molecule */
175	–	unsigned int getNCutoffGroups() {
176	–	return cutoffGroups_.size();
177	–	}
178	–
179	–	/** Returns the total number of constraints in this molecule */
180	–	unsigned int getNConstraintPairs() {
181	–	return constraintPairs_.size();
182	–	}
183	–
184	–	Atom* getAtomAt(unsigned int i) {
185	–	assert(i < atoms_.size());
186	–	return atoms_[i];
187	–	}
188	–
189	–	RigidBody* getRigidBodyAt(unsigned int i) {
190	–	assert(i < rigidBodies_.size());
191	–	return rigidBodies_[i];
192	–	}
331
332	<	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
333	<	i = atoms_.begin();
334	<	return (i == atoms_.end()) ? NULL : *i;
335	<	}
332	>	/**
333	>	* Returns the total potential energy of short range interaction
334	>	* of this molecule
335	>	*/
336	>	RealType getPotential();
337	>
338	>	/** get total mass of this molecule */
339	>	RealType getMass();
340	>
341	>	/** return the center of mass of this molecule */
342	>	Vector3d getCom();
343	>
344	>	/** Moves the center of this molecule */
345	>	void moveCom(const Vector3d& delta);
346	>
347	>	/** Returns the velocity of center of mass of this molecule */
348	>	Vector3d getComVel();
349
350	<	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
351	<	++i;
352	<	return (i == atoms_.end()) ? NULL : *i;
202	<	}
203	<
204	<	Bond* beginBond(std::vector<Bond*>::iterator& i) {
205	<	i = bonds_.begin();
206	<	return (i == bonds_.end()) ? NULL : *i;
207	<	}
208	<
209	<	Bond* nextBond(std::vector<Bond*>::iterator& i) {
210	<	++i;
211	<	return (i == bonds_.end()) ? NULL : *i;
212	<
213	<	}
214	<
215	<	Bend* beginBend(std::vector<Bend*>::iterator& i) {
216	<	i = bends_.begin();
217	<	return (i == bends_.end()) ? NULL : *i;
218	<	}
219	<
220	<	Bend* nextBend(std::vector<Bend*>::iterator& i) {
221	<	++i;
222	<	return (i == bends_.end()) ? NULL : *i;
223	<	}
224	<
225	<	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
226	<	i = torsions_.begin();
227	<	return (i == torsions_.end()) ? NULL : *i;
228	<	}
229	<
230	<	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
231	<	++i;
232	<	return (i == torsions_.end()) ? NULL : *i;
233	<	}
234	<
235	<	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
236	<	i = rigidBodies_.begin();
237	<	return (i == rigidBodies_.end()) ? NULL : *i;
238	<	}
239	<
240	<	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
241	<	++i;
242	<	return (i == rigidBodies_.end()) ? NULL : *i;
243	<	}
244	<
245	<	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
246	<	i = integrableObjects_.begin();
247	<	return (i == integrableObjects_.end()) ? NULL : *i;
248	<	}
249	<
250	<	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
251	<	++i;
252	<	return (i == integrableObjects_.end()) ? NULL : *i;
253	<	}
254	<
255	<	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
256	<	i = cutoffGroups_.begin();
257	<	return (i == cutoffGroups_.end()) ? NULL : *i;
258	<	}
259	<
260	<	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
261	<	++i;
262	<	return (i == cutoffGroups_.end()) ? NULL : *i;
263	<	}
264	<
265	<	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
266	<	i = constraintPairs_.begin();
267	<	return (i == constraintPairs_.end()) ? NULL : *i;
268	<	}
269	<
270	<	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
271	<	++i;
272	<	return (i == constraintPairs_.end()) ? NULL : *i;
273	<	}
274	<
275	<	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
276	<	i = constraintElems_.begin();
277	<	return (i == constraintElems_.end()) ? NULL : *i;
278	<	}
279	<
280	<	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
281	<	++i;
282	<	return (i == constraintElems_.end()) ? NULL : *i;
283	<	}
350	>	std::string getMoleculeName() {
351	>	return moleculeName_;
352	>	}
353
354	<	/** return the total potential energy of short range interaction of this molecule */
286	<	double getPotential();
354	>	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
355
356	<	/** get total mass of this molecule */
357	<	double getMass();
356	>	//below functions are just forward functions
357	>	/**
358	>	* Adds property into property map
359	>	* @param genData GenericData to be added into PropertyMap
360	>	*/
361	>	void addProperty(GenericData* genData);
362
363	<	/** return the center of mass of this molecule */
364	<	Vector3d getCom();
363	>	/**
364	>	* Removes property from PropertyMap by name
365	>	* @param propName the name of property to be removed
366	>	*/
367	>	void removeProperty(const std::string& propName);
368
369	<	/** Moves the center of this molecule */
370	<	void moveCom(const Vector3d& delta);
369	>	/**
370	>	* clear all of the properties
371	>	*/
372	>	void clearProperties();
373
374	<	/** Returns the velocity of center of mass of this molecule */
375	<	Vector3d getComVel();
374	>	/**
375	>	* Returns all names of properties
376	>	* @return all names of properties
377	>	*/
378	>	std::vector<std::string> getPropertyNames();
379
380	<	std::string getMoleculeName() {
381	<	return moleculeName_;
382	<	}
383	<
384	<	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
305	<
306	<	private:
307	<
308	<	int globalIndex_;
380	>	/**
381	>	* Returns all of the properties in PropertyMap
382	>	* @return all of the properties in PropertyMap
383	>	*/
384	>	std::vector<GenericData*> getProperties();
385
386	<	std::vector<Atom*> atoms_;
387	<	std::vector<Bond*> bonds_;
388	<	std::vector<Bend*> bends_;
389	<	std::vector<Torsion*> torsions_;
390	<	std::vector<RigidBody*> rigidBodies_;
391	<	std::vector<StuntDouble*> integrableObjects_;
392	<	std::vector<CutoffGroup*> cutoffGroups_;
393	<	std::vector<ConstraintPair*> constraintPairs_;
394	<	std::vector<ConstraintElem*> constraintElems_;
395	<	int stampId_;
396	<	std::string moleculeName_;
397	<	};
386	>	/**
387	>	* Returns property
388	>	* @param propName name of property
389	>	* @return a pointer point to property with propName. If no property named propName
390	>	* exists, return NULL
391	>	*/
392	>	GenericData* getPropertyByName(const std::string& propName);
393	>
394	>	private:
395	>
396	>	int globalIndex_;
397	>
398	>	std::vector<Atom*> atoms_;
399	>	std::vector<Bond*> bonds_;
400	>	std::vector<Bend*> bends_;
401	>	std::vector<Torsion*> torsions_;
402	>	std::vector<Inversion*> inversions_;
403	>	std::vector<RigidBody*> rigidBodies_;
404	>	std::vector<StuntDouble*> integrableObjects_;
405	>	std::vector<CutoffGroup*> cutoffGroups_;
406	>	std::vector<ConstraintPair*> constraintPairs_;
407	>	std::vector<ConstraintElem*> constraintElems_;
408	>	std::vector<Atom*> fluctuatingCharges_;
409	>	int stampId_;
410	>	std::string moleculeName_;
411	>	PropertyMap properties_;
412	>	bool constrainTotalCharge_;
413
414	<	} //namespace oopse
414	>	};
415	>
416	>	} //namespace OpenMD
417		#endif //

Comparing:
trunk/src/primitives/Molecule.hpp (property svn:keywords), Revision 305 by tim, Mon Feb 7 22:39:19 2005 UTC vs.
branches/development/src/primitives/Molecule.hpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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