ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/trunk/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.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 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, 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		/**
#	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, int region);
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	>	int getRegion() {
111	>	return region_;
112	>	}
113	>
114	>	/** Returns the name of the molecule */
115	>	std::string getType() {
116	>	return moleculeName_;
117	>	}
118	>
119	>	/**
120	>	* Sets the global index of this molecule.
121	>	* @param index new global index to be set
122	>	*/
123	>	void setGlobalIndex(int index) {
124	>	globalIndex_ = index;
125	>	}
126
127	<	/**
128	<	* Returns the global index of this molecule.
129	<	* @return  the global index of this molecule
130	<	*/
131	<	int getGlobalIndex() {
132	<	return globalIndex_;
133	<	}
127	>	void setConstrainTotalCharge(bool ctc) {
128	>	constrainTotalCharge_ = ctc;
129	>	}
130	>
131	>	bool constrainTotalCharge() {
132	>	return constrainTotalCharge_;
133	>	}
134
135	<	/**
136	<	* Returns the stamp id of this molecule
137	<	* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
138	<	* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
139	<	*/
140	<	int getStampId() {
141	<	return stampId_;
142	<	}
135	>	/** add an atom into this molecule */
136	>	void addAtom(Atom* atom);
137	>
138	>	/** add a bond into this molecule */
139	>	void addBond(Bond* bond);
140	>
141	>	/** add a bend into this molecule */
142	>	void addBend(Bend* bend);
143	>
144	>	/** add a torsion into this molecule*/
145	>	void addTorsion(Torsion* torsion);
146
147	<	/** Returns the name of the molecule */
148	<	std::string getType() {
149	<	return moleculeName_;
150	<	}
151	<
152	<	/**
153	<	* Sets the global index of this molecule.
154	<	* @param new global index to be set
155	<	*/
156	<	void setGlobalIndex(int index) {
157	<	globalIndex_ = index;
158	<	}
147	>	/** add an improper torsion into this molecule*/
148	>	void addInversion(Inversion* inversion);
149	>
150	>	/** add a rigidbody into this molecule */
151	>	void addRigidBody(RigidBody *rb);
152	>
153	>	/** add a cutoff group into this molecule */
154	>	void addCutoffGroup(CutoffGroup* cp);
155	>
156	>	void addConstraintPair(ConstraintPair* consPair);
157	>
158	>	void addConstraintElem(ConstraintElem* consElem);
159	>
160	>	/** */
161	>	void complete();
162	>
163	>	/** Returns the total number of atoms in this molecule */
164	>	unsigned int getNAtoms() {
165	>	return atoms_.size();
166	>	}
167	>
168	>	/** Returns the total number of bonds in this molecule */
169	>	unsigned int getNBonds(){
170	>	return bonds_.size();
171	>	}
172	>
173	>	/** Returns the total number of bends in this molecule */
174	>	unsigned int getNBends() {
175	>	return bends_.size();
176	>	}
177	>
178	>	/** Returns the total number of torsions in this molecule */
179	>	unsigned int getNTorsions() {
180	>	return torsions_.size();
181	>	}
182
183	<
184	<	/** add an atom into this molecule */
185	<	void addAtom(Atom* atom);
183	>	/** Returns the total number of improper torsions in this molecule */
184	>	unsigned int getNInversions() {
185	>	return inversions_.size();
186	>	}
187	>
188	>	/** Returns the total number of rigid bodies in this molecule */
189	>	unsigned int getNRigidBodies() {
190	>	return rigidBodies_.size();
191	>	}
192	>
193	>	/** Returns the total number of integrable objects in this molecule */
194	>	unsigned int getNIntegrableObjects() {
195	>	return integrableObjects_.size();
196	>	}
197	>
198	>	/** Returns the total number of cutoff groups in this molecule */
199	>	unsigned int getNCutoffGroups() {
200	>	return cutoffGroups_.size();
201	>	}
202	>
203	>	/** Returns the total number of constraints in this molecule */
204	>	unsigned int getNConstraintPairs() {
205	>	return constraintPairs_.size();
206	>	}
207
208	<	/** add a bond into this molecule */
209	<	void addBond(Bond* bond);
208	>	/** Returns the total number of fluctuating charges in this molecule */
209	>	unsigned int getNFluctuatingCharges() {
210	>	return fluctuatingCharges_.size();
211	>	}
212
213	<	/** add a bend into this molecule */
214	<	void addBend(Bend* bend);
213	>	Atom* getAtomAt(unsigned int i) {
214	>	assert(i < atoms_.size());
215	>	return atoms_[i];
216	>	}
217	>
218	>	RigidBody* getRigidBodyAt(unsigned int i) {
219	>	assert(i < rigidBodies_.size());
220	>	return rigidBodies_[i];
221	>	}
222	>
223	>	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
224	>	i = atoms_.begin();
225	>	return (i == atoms_.end()) ? NULL : *i;
226	>	}
227	>
228	>	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
229	>	++i;
230	>	return (i == atoms_.end()) ? NULL : *i;
231	>	}
232	>
233	>	Bond* beginBond(std::vector<Bond*>::iterator& i) {
234	>	i = bonds_.begin();
235	>	return (i == bonds_.end()) ? NULL : *i;
236	>	}
237	>
238	>	Bond* nextBond(std::vector<Bond*>::iterator& i) {
239	>	++i;
240	>	return (i == bonds_.end()) ? NULL : *i;
241	>
242	>	}
243	>
244	>	Bend* beginBend(std::vector<Bend*>::iterator& i) {
245	>	i = bends_.begin();
246	>	return (i == bends_.end()) ? NULL : *i;
247	>	}
248	>
249	>	Bend* nextBend(std::vector<Bend*>::iterator& i) {
250	>	++i;
251	>	return (i == bends_.end()) ? NULL : *i;
252	>	}
253	>
254	>	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
255	>	i = torsions_.begin();
256	>	return (i == torsions_.end()) ? NULL : *i;
257	>	}
258	>
259	>	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
260	>	++i;
261	>	return (i == torsions_.end()) ? NULL : *i;
262	>	}
263
264	<	/** add a torsion into this molecule*/
265	<	void addTorsion(Torsion* torsion);
264	>	Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
265	>	i = inversions_.begin();
266	>	return (i == inversions_.end()) ? NULL : *i;
267	>	}
268	>
269	>	Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
270	>	++i;
271	>	return (i == inversions_.end()) ? NULL : *i;
272	>	}
273	>
274	>	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
275	>	i = rigidBodies_.begin();
276	>	return (i == rigidBodies_.end()) ? NULL : *i;
277	>	}
278	>
279	>	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
280	>	++i;
281	>	return (i == rigidBodies_.end()) ? NULL : *i;
282	>	}
283	>
284	>	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
285	>	i = integrableObjects_.begin();
286	>	return (i == integrableObjects_.end()) ? NULL : *i;
287	>	}
288	>
289	>	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
290	>	++i;
291	>	return (i == integrableObjects_.end()) ? NULL : *i;
292	>	}
293	>
294	>	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
295	>	i = cutoffGroups_.begin();
296	>	return (i == cutoffGroups_.end()) ? NULL : *i;
297	>	}
298
299	<	/** add a rigidbody into this molecule */
300	<	void addRigidBody(RigidBody *rb);
301	<
302	<	/** add a cutoff group into this molecule */
303	<	void addCutoffGroup(CutoffGroup* cp);
299	>	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
300	>	++i;
301	>	return (i == cutoffGroups_.end()) ? NULL : *i;
302	>	}
303	>
304	>	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
305	>	i = constraintPairs_.begin();
306	>	return (i == constraintPairs_.end()) ? NULL : *i;
307	>	}
308	>
309	>	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
310	>	++i;
311	>	return (i == constraintPairs_.end()) ? NULL : *i;
312	>	}
313	>
314	>	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
315	>	i = constraintElems_.begin();
316	>	return (i == constraintElems_.end()) ? NULL : *i;
317	>	}
318	>
319	>	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
320	>	++i;
321	>	return (i == constraintElems_.end()) ? NULL : *i;
322	>	}
323
324	<	void addConstraintPair(ConstraintPair* consPair);
325	<
326	<	void addConstraintElem(ConstraintElem* consElem);
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
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	–	}
334
335	<	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
336	<	i = atoms_.begin();
337	<	return (i == atoms_.end()) ? NULL : *i;
338	<	}
335	>	/**
336	>	* Returns the total potential energy of short range interaction
337	>	* of this molecule
338	>	*/
339	>	RealType getPotential();
340	>
341	>	/** get total mass of this molecule */
342	>	RealType getMass();
343	>
344	>	/** return the center of mass of this molecule */
345	>	Vector3d getCom();
346	>
347	>	/** Moves the center of this molecule */
348	>	void moveCom(const Vector3d& delta);
349	>
350	>	/** Returns the velocity of center of mass of this molecule */
351	>	Vector3d getComVel();
352
353	<	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
354	<	++i;
355	<	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	<	}
353	>	std::string getMoleculeName() {
354	>	return moleculeName_;
355	>	}
356
357	<	/** return the total potential energy of short range interaction of this molecule */
286	<	double getPotential();
357	>	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
358
359	<	/** get total mass of this molecule */
360	<	double getMass();
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	<	/** return the center of mass of this molecule */
367	<	Vector3d getCom();
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	<	/** Moves the center of this molecule */
373	<	void moveCom(const Vector3d& delta);
372	>	/**
373	>	* clear all of the properties
374	>	*/
375	>	void clearProperties();
376
377	<	/** Returns the velocity of center of mass of this molecule */
378	<	Vector3d getComVel();
377	>	/**
378	>	* Returns all names of properties
379	>	* @return all names of properties
380	>	*/
381	>	std::vector<std::string> getPropertyNames();
382
383	<	std::string getMoleculeName() {
384	<	return moleculeName_;
385	<	}
386	<
387	<	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
305	<
306	<	private:
307	<
308	<	int globalIndex_;
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	<	std::vector<Atom*> atoms_;
390	<	std::vector<Bond*> bonds_;
391	<	std::vector<Bend*> bends_;
392	<	std::vector<Torsion*> torsions_;
393	<	std::vector<RigidBody*> rigidBodies_;
394	<	std::vector<StuntDouble*> integrableObjects_;
395	<	std::vector<CutoffGroup*> cutoffGroups_;
396	<	std::vector<ConstraintPair*> constraintPairs_;
397	<	std::vector<ConstraintElem*> constraintElems_;
398	<	int stampId_;
399	<	std::string moleculeName_;
400	<	};
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	>
397	>	private:
398	>
399	>	int globalIndex_;
400	>
401	>	std::vector<Atom*> atoms_;
402	>	std::vector<Bond*> bonds_;
403	>	std::vector<Bend*> bends_;
404	>	std::vector<Torsion*> torsions_;
405	>	std::vector<Inversion*> inversions_;
406	>	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	>	std::vector<Atom*> fluctuatingCharges_;
412	>	int stampId_;
413	>	int region_;
414	>	std::string moleculeName_;
415	>	PropertyMap properties_;
416	>	bool constrainTotalCharge_;
417
418	<	} //namespace oopse
418	>	};
419	>
420	>	} //namespace OpenMD
421		#endif //

Comparing trunk/src/primitives/Molecule.hpp (property svn:keywords):
Revision 305 by tim, Mon Feb 7 22:39:19 2005 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines