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 2052 by gezelter, Fri Jan 9 19:06:35 2015 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
63	–	namespace oopse{
66
67	<	class Constraint;
67	>	namespace OpenMD{
68
69	<	/**
70	<	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
71	<	* @brief
72	<	*/
73	<	class Molecule {
74	<	public:
69	>	class Constraint;
70	>
71	>	/**
72	>	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
73	>	* @brief
74	>	*/
75	>	class Molecule {
76	>	public:
77
78	<	typedef std::vector<Atom*>::iterator AtomIterator;
79	<	typedef std::vector<Bond*>::iterator BondIterator;
80	<	typedef std::vector<Bend*>::iterator BendIterator;
81	<	typedef std::vector<Torsion*>::iterator TorsionIterator;
78	<	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
79	<	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
80	<	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
81	<	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
82	<	typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
83	<
78	>	struct HBondDonor {
79	>	Atom* donorAtom;
80	>	Atom* donatedHydrogen;
81	>	};
82
83	<	Molecule(int stampId, int globalIndex, const std::string& molName);
84	<	virtual ~Molecule();
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	<	/**
98	<	* Returns the global index of this molecule.
90	<	* @return  the global index of this molecule
91	<	*/
92	<	int getGlobalIndex() {
93	<	return globalIndex_;
94	<	}
97	>	Molecule(int stampId, int globalIndex, const std::string& molName, int region);
98	>	virtual ~Molecule();
99
100	<	/**
101	<	* Returns the stamp id of this molecule
102	<	* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
103	<	* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
104	<	*/
105	<	int getStampId() {
106	<	return stampId_;
107	<	}
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	<	/** Returns the name of the molecule */
136	<	std::string getType() {
137	<	return moleculeName_;
138	<	}
139	<
140	<	/**
141	<	* Sets the global index of this molecule.
112	<	* @param new global index to be set
113	<	*/
114	<	void setGlobalIndex(int index) {
115	<	globalIndex_ = index;
116	<	}
135	>	void setConstrainTotalCharge(bool ctc) {
136	>	constrainTotalCharge_ = ctc;
137	>	}
138	>
139	>	bool constrainTotalCharge() {
140	>	return constrainTotalCharge_;
141	>	}
142
143	<
144	<	/** add an atom into this molecule */
145	<	void addAtom(Atom* atom);
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 a bond into this molecule */
156	<	void addBond(Bond* bond);
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	<	/** add a bend into this molecule */
192	<	void addBend(Bend* bend);
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	<	/** add a torsion into this molecule*/
217	<	void addTorsion(Torsion* torsion);
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	<	/** add a rigidbody into this molecule */
231	<	void addRigidBody(RigidBody *rb);
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	<	/** add a cutoff group into this molecule */
282	<	void addCutoffGroup(CutoffGroup* cp);
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	<	void addConstraintPair(ConstraintPair* consPair);
317	<
318	<	void addConstraintElem(ConstraintElem* consElem);
319	<
320	<	/** */
321	<	void complete();
322	<
323	<	/** Returns the total number of atoms in this molecule */
324	<	unsigned int getNAtoms() {
325	<	return atoms_.size();
326	<	}
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	<	/** Returns the total number of bonds in this molecule */
342	<	unsigned int getNBonds(){
343	<	return bonds_.size();
344	<	}
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	<	/** Returns the total number of bends in this molecule */
352	<	unsigned int getNBends() {
353	<	return bends_.size();
354	<	}
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
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	–	}
371
372	<	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
373	<	i = atoms_.begin();
374	<	return (i == atoms_.end()) ? NULL : *i;
375	<	}
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	<	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
398	<	++i;
399	<	return (i == atoms_.end()) ? NULL : *i;
400	<	}
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	<	Bond* beginBond(std::vector<Bond*>::iterator& i) {
405	<	i = bonds_.begin();
406	<	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	<	}
404	>	std::string getMoleculeName() {
405	>	return moleculeName_;
406	>	}
407
408	<	/** return the total potential energy of short range interaction of this molecule */
286	<	double getPotential();
408	>	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
409
410	<	/** get total mass of this molecule */
411	<	double getMass();
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	<	/** return the center of mass of this molecule */
418	<	Vector3d getCom();
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	<	/** Moves the center of this molecule */
424	<	void moveCom(const Vector3d& delta);
423	>	/**
424	>	* clear all of the properties
425	>	*/
426	>	void clearProperties();
427
428	<	/** Returns the velocity of center of mass of this molecule */
429	<	Vector3d getComVel();
428	>	/**
429	>	* Returns all names of properties
430	>	* @return all names of properties
431	>	*/
432	>	std::vector<std::string> getPropertyNames();
433
434	<	std::string getMoleculeName() {
435	<	return moleculeName_;
436	<	}
437	<
438	<	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
305	<
306	<	private:
307	<
308	<	int globalIndex_;
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	<	std::vector<Atom*> atoms_;
441	<	std::vector<Bond*> bonds_;
442	<	std::vector<Bend*> bends_;
443	<	std::vector<Torsion*> torsions_;
444	<	std::vector<RigidBody*> rigidBodies_;
445	<	std::vector<StuntDouble*> integrableObjects_;
446	<	std::vector<CutoffGroup*> cutoffGroups_;
447	<	std::vector<ConstraintPair*> constraintPairs_;
448	<	std::vector<ConstraintElem*> constraintElems_;
449	<	int stampId_;
450	<	std::string moleculeName_;
451	<	};
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	<	} //namespace oopse
472	>	};
473	>
474	>	} //namespace OpenMD
475		#endif //

Comparing trunk/src/primitives/Molecule.hpp (property svn:keywords):
Revision 305 by tim, Mon Feb 7 22:39:19 2005 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

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

Diff Legend

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