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

Comparing:
trunk/src/primitives/Molecule.hpp (file contents), Revision 259 by tim, Fri Jan 14 01:56:04 2005 UTC vs.
branches/development/src/primitives/Molecule.hpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 58 | Line 58
58		#include "primitives/Bond.hpp"
59		#include "primitives/Bend.hpp"
60		#include "primitives/Torsion.hpp"
61	+	#include "primitives/Inversion.hpp"
62		#include "primitives/CutoffGroup.hpp"
63	+	#include "utils/PropertyMap.hpp"
64
65	<	namespace oopse{
65	>	namespace OpenMD{
66
67	<	class Constraint;
67	>	class Constraint;
68
69	<	/**
70	<	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
71	<	* @brief
72	<	*/
73	<	class Molecule {
74	<	public:
69	>	/**
70	>	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
71	>	* @brief
72	>	*/
73	>	class Molecule {
74	>	public:
75
76	<	typedef std::vector<Atom*>::iterator AtomIterator;
77	<	typedef std::vector<Bond*>::iterator BondIterator;
78	<	typedef std::vector<Bend*>::iterator BendIterator;
79	<	typedef std::vector<Torsion*>::iterator TorsionIterator;
80	<	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
81	<	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
82	<	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
83	<	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
84	<	typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
85	<
76	>	typedef std::vector<Atom*>::iterator AtomIterator;
77	>	typedef std::vector<Bond*>::iterator BondIterator;
78	>	typedef std::vector<Bend*>::iterator BendIterator;
79	>	typedef std::vector<Torsion*>::iterator TorsionIterator;
80	>	typedef std::vector<Inversion*>::iterator InversionIterator;
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	>
87	>
88	>	Molecule(int stampId, int globalIndex, const std::string& molName);
89	>	virtual ~Molecule();
90
91	<	Molecule(int stampId, int globalIndex, const std::string& molName);
92	<	virtual ~Molecule();
91	>	/**
92	>	* Returns the global index of this molecule.
93	>	* @return  the global index of this molecule
94	>	*/
95	>	int getGlobalIndex() {
96	>	return globalIndex_;
97	>	}
98	>
99	>	/**
100	>	* Returns the stamp id of this molecule
101	>	* @note Ideally, every molecule should keep a pointer of its
102	>	* molecule stamp instead of its stamp id. However, the pointer
103	>	* will become invalid, if the molecule migrate to other
104	>	* processor.
105	>	*/
106	>	int getStampId() {
107	>	return stampId_;
108	>	}
109	>
110	>	/** Returns the name of the molecule */
111	>	std::string getType() {
112	>	return moleculeName_;
113	>	}
114	>
115	>	/**
116	>	* Sets the global index of this molecule.
117	>	* @param new global index to be set
118	>	*/
119	>	void setGlobalIndex(int index) {
120	>	globalIndex_ = index;
121	>	}
122	>
123	>
124	>	/** add an atom into this molecule */
125	>	void addAtom(Atom* atom);
126	>
127	>	/** add a bond into this molecule */
128	>	void addBond(Bond* bond);
129	>
130	>	/** add a bend into this molecule */
131	>	void addBend(Bend* bend);
132	>
133	>	/** add a torsion into this molecule*/
134	>	void addTorsion(Torsion* torsion);
135
136	<	/**
137	<	* Returns the global index of this molecule.
138	<	* @return  the global index of this molecule
139	<	*/
140	<	int getGlobalIndex() {
141	<	return globalIndex_;
142	<	}
136	>	/** add an improper torsion into this molecule*/
137	>	void addInversion(Inversion* inversion);
138	>
139	>	/** add a rigidbody into this molecule */
140	>	void addRigidBody(RigidBody *rb);
141	>
142	>	/** add a cutoff group into this molecule */
143	>	void addCutoffGroup(CutoffGroup* cp);
144	>
145	>	void addConstraintPair(ConstraintPair* consPair);
146	>
147	>	void addConstraintElem(ConstraintElem* consElem);
148	>
149	>	/** */
150	>	void complete();
151	>
152	>	/** Returns the total number of atoms in this molecule */
153	>	unsigned int getNAtoms() {
154	>	return atoms_.size();
155	>	}
156	>
157	>	/** Returns the total number of bonds in this molecule */
158	>	unsigned int getNBonds(){
159	>	return bonds_.size();
160	>	}
161	>
162	>	/** Returns the total number of bends in this molecule */
163	>	unsigned int getNBends() {
164	>	return bends_.size();
165	>	}
166	>
167	>	/** Returns the total number of torsions in this molecule */
168	>	unsigned int getNTorsions() {
169	>	return torsions_.size();
170	>	}
171
172	<	/**
173	<	* Returns the stamp id of this molecule
174	<	* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
175	<	* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
176	<	*/
177	<	int getStampId() {
178	<	return stampId_;
179	<	}
172	>	/** Returns the total number of improper torsions in this molecule */
173	>	unsigned int getNInversions() {
174	>	return inversions_.size();
175	>	}
176	>
177	>	/** Returns the total number of rigid bodies in this molecule */
178	>	unsigned int getNRigidBodies() {
179	>	return rigidBodies_.size();
180	>	}
181	>
182	>	/** Returns the total number of integrable objects in this molecule */
183	>	unsigned int getNIntegrableObjects() {
184	>	return integrableObjects_.size();
185	>	}
186	>
187	>	/** Returns the total number of cutoff groups in this molecule */
188	>	unsigned int getNCutoffGroups() {
189	>	return cutoffGroups_.size();
190	>	}
191	>
192	>	/** Returns the total number of constraints in this molecule */
193	>	unsigned int getNConstraintPairs() {
194	>	return constraintPairs_.size();
195	>	}
196	>
197	>	Atom* getAtomAt(unsigned int i) {
198	>	assert(i < atoms_.size());
199	>	return atoms_[i];
200	>	}
201	>
202	>	RigidBody* getRigidBodyAt(unsigned int i) {
203	>	assert(i < rigidBodies_.size());
204	>	return rigidBodies_[i];
205	>	}
206	>
207	>	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
208	>	i = atoms_.begin();
209	>	return (i == atoms_.end()) ? NULL : *i;
210	>	}
211	>
212	>	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
213	>	++i;
214	>	return (i == atoms_.end()) ? NULL : *i;
215	>	}
216	>
217	>	Bond* beginBond(std::vector<Bond*>::iterator& i) {
218	>	i = bonds_.begin();
219	>	return (i == bonds_.end()) ? NULL : *i;
220	>	}
221	>
222	>	Bond* nextBond(std::vector<Bond*>::iterator& i) {
223	>	++i;
224	>	return (i == bonds_.end()) ? NULL : *i;
225	>
226	>	}
227	>
228	>	Bend* beginBend(std::vector<Bend*>::iterator& i) {
229	>	i = bends_.begin();
230	>	return (i == bends_.end()) ? NULL : *i;
231	>	}
232	>
233	>	Bend* nextBend(std::vector<Bend*>::iterator& i) {
234	>	++i;
235	>	return (i == bends_.end()) ? NULL : *i;
236	>	}
237	>
238	>	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
239	>	i = torsions_.begin();
240	>	return (i == torsions_.end()) ? NULL : *i;
241	>	}
242	>
243	>	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
244	>	++i;
245	>	return (i == torsions_.end()) ? NULL : *i;
246	>	}
247
248	<	/** Returns the name of the molecule */
249	<	std::string getType() {
250	<	return moleculeName_;
251	<	}
252	<
253	<	/**
254	<	* Sets the global index of this molecule.
255	<	* @param new global index to be set
256	<	*/
257	<	void setGlobalIndex(int index) {
258	<	globalIndex_ = index;
259	<	}
248	>	Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
249	>	i = inversions_.begin();
250	>	return (i == inversions_.end()) ? NULL : *i;
251	>	}
252	>
253	>	Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
254	>	++i;
255	>	return (i == inversions_.end()) ? NULL : *i;
256	>	}
257	>
258	>	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
259	>	i = rigidBodies_.begin();
260	>	return (i == rigidBodies_.end()) ? NULL : *i;
261	>	}
262	>
263	>	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
264	>	++i;
265	>	return (i == rigidBodies_.end()) ? NULL : *i;
266	>	}
267	>
268	>	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
269	>	i = integrableObjects_.begin();
270	>	return (i == integrableObjects_.end()) ? NULL : *i;
271	>	}
272	>
273	>	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
274	>	++i;
275	>	return (i == integrableObjects_.end()) ? NULL : *i;
276	>	}
277	>
278	>	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
279	>	i = cutoffGroups_.begin();
280	>	return (i == cutoffGroups_.end()) ? NULL : *i;
281	>	}
282
283	<
284	<	/** add an atom into this molecule */
285	<	void addAtom(Atom* atom);
286	<
287	<	/** add a bond into this molecule */
288	<	void addBond(Bond* bond);
289	<
290	<	/** add a bend into this molecule */
291	<	void addBend(Bend* bend);
292	<
293	<	/** add a torsion into this molecule*/
294	<	void addTorsion(Torsion* torsion);
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);
301	<
302	<	void addConstraintPair(ConstraintPair* consPair);
283	>	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
284	>	++i;
285	>	return (i == cutoffGroups_.end()) ? NULL : *i;
286	>	}
287	>
288	>	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
289	>	i = constraintPairs_.begin();
290	>	return (i == constraintPairs_.end()) ? NULL : *i;
291	>	}
292	>
293	>	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
294	>	++i;
295	>	return (i == constraintPairs_.end()) ? NULL : *i;
296	>	}
297	>
298	>	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
299	>	i = constraintElems_.begin();
300	>	return (i == constraintElems_.end()) ? NULL : *i;
301	>	}
302	>
303	>	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
304	>	++i;
305	>	return (i == constraintElems_.end()) ? NULL : *i;
306	>	}
307
308	<	void addConstraintElem(ConstraintElem* consElem);
308	>	/**
309	>	* Returns the total potential energy of short range interaction
310	>	* of this molecule
311	>	*/
312	>	RealType getPotential();
313	>
314	>	/** get total mass of this molecule */
315	>	RealType getMass();
316	>
317	>	/** return the center of mass of this molecule */
318	>	Vector3d getCom();
319	>
320	>	/** Moves the center of this molecule */
321	>	void moveCom(const Vector3d& delta);
322	>
323	>	/** Returns the velocity of center of mass of this molecule */
324	>	Vector3d getComVel();
325
326	<	/** */
327	<	void complete();
328	<
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	<	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
190	<	i = atoms_.begin();
191	<	return (i == atoms_.end()) ? NULL : *i;
192	<	}
193	<
194	<	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
195	<	++i;
196	<	return (i == atoms_.end()) ? NULL : *i;
197	<	}
198	<
199	<	Bond* beginBond(std::vector<Bond*>::iterator& i) {
200	<	i = bonds_.begin();
201	<	return (i == bonds_.end()) ? NULL : *i;
202	<	}
203	<
204	<	Bond* nextBond(std::vector<Bond*>::iterator& i) {
205	<	++i;
206	<	return (i == bonds_.end()) ? NULL : *i;
207	<
208	<	}
209	<
210	<	Bend* beginBend(std::vector<Bend*>::iterator& i) {
211	<	i = bends_.begin();
212	<	return (i == bends_.end()) ? NULL : *i;
213	<	}
214	<
215	<	Bend* nextBend(std::vector<Bend*>::iterator& i) {
216	<	++i;
217	<	return (i == bends_.end()) ? NULL : *i;
218	<	}
219	<
220	<	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
221	<	i = torsions_.begin();
222	<	return (i == torsions_.end()) ? NULL : *i;
223	<	}
224	<
225	<	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
226	<	++i;
227	<	return (i == torsions_.end()) ? NULL : *i;
228	<	}
229	<
230	<	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
231	<	i = rigidBodies_.begin();
232	<	return (i == rigidBodies_.end()) ? NULL : *i;
233	<	}
234	<
235	<	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
236	<	++i;
237	<	return (i == rigidBodies_.end()) ? NULL : *i;
238	<	}
239	<
240	<	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
241	<	i = integrableObjects_.begin();
242	<	return (i == integrableObjects_.end()) ? NULL : *i;
243	<	}
244	<
245	<	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
246	<	++i;
247	<	return (i == integrableObjects_.end()) ? NULL : *i;
248	<	}
249	<
250	<	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
251	<	i = cutoffGroups_.begin();
252	<	return (i == cutoffGroups_.end()) ? NULL : *i;
253	<	}
254	<
255	<	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
256	<	++i;
257	<	return (i == cutoffGroups_.end()) ? NULL : *i;
258	<	}
259	<
260	<	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
261	<	i = constraintPairs_.begin();
262	<	return (i == constraintPairs_.end()) ? NULL : *i;
263	<	}
264	<
265	<	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
266	<	++i;
267	<	return (i == constraintPairs_.end()) ? NULL : *i;
268	<	}
269	<
270	<	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
271	<	i = constraintElems_.begin();
272	<	return (i == constraintElems_.end()) ? NULL : *i;
273	<	}
274	<
275	<	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
276	<	++i;
277	<	return (i == constraintElems_.end()) ? NULL : *i;
278	<	}
326	>	std::string getMoleculeName() {
327	>	return moleculeName_;
328	>	}
329
330	<	/** return the total potential energy of short range interaction of this molecule */
281	<	double getPotential();
330	>	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
331
332	<	/** get total mass of this molecule */
333	<	double getMass();
332	>	//below functions are just forward functions
333	>	/**
334	>	* Adds property into property map
335	>	* @param genData GenericData to be added into PropertyMap
336	>	*/
337	>	void addProperty(GenericData* genData);
338
339	<	/** return the center of mass of this molecule */
340	<	Vector3d getCom();
339	>	/**
340	>	* Removes property from PropertyMap by name
341	>	* @param propName the name of property to be removed
342	>	*/
343	>	void removeProperty(const std::string& propName);
344
345	<	/** Moves the center of this molecule */
346	<	void moveCom(const Vector3d& delta);
345	>	/**
346	>	* clear all of the properties
347	>	*/
348	>	void clearProperties();
349
350	<	/** Returns the velocity of center of mass of this molecule */
351	<	Vector3d getComVel();
350	>	/**
351	>	* Returns all names of properties
352	>	* @return all names of properties
353	>	*/
354	>	std::vector<std::string> getPropertyNames();
355
356	<	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
357	<
358	<	private:
359	<
360	<	int globalIndex_;
356	>	/**
357	>	* Returns all of the properties in PropertyMap
358	>	* @return all of the properties in PropertyMap
359	>	*/
360	>	std::vector<GenericData*> getProperties();
361
362	<	std::vector<Atom*> atoms_;
363	<	std::vector<Bond*> bonds_;
364	<	std::vector<Bend*> bends_;
365	<	std::vector<Torsion*> torsions_;
366	<	std::vector<RigidBody*> rigidBodies_;
367	<	std::vector<StuntDouble*> integrableObjects_;
368	<	std::vector<CutoffGroup*> cutoffGroups_;
369	<	std::vector<ConstraintPair*> constraintPairs_;
370	<	std::vector<ConstraintElem*> constraintElems_;
371	<	int stampId_;
372	<	std::string moleculeName_;
373	<	};
362	>	/**
363	>	* Returns property
364	>	* @param propName name of property
365	>	* @return a pointer point to property with propName. If no property named propName
366	>	* exists, return NULL
367	>	*/
368	>	GenericData* getPropertyByName(const std::string& propName);
369	>
370	>	private:
371	>
372	>	int globalIndex_;
373	>
374	>	std::vector<Atom*> atoms_;
375	>	std::vector<Bond*> bonds_;
376	>	std::vector<Bend*> bends_;
377	>	std::vector<Torsion*> torsions_;
378	>	std::vector<Inversion*> inversions_;
379	>	std::vector<RigidBody*> rigidBodies_;
380	>	std::vector<StuntDouble*> integrableObjects_;
381	>	std::vector<CutoffGroup*> cutoffGroups_;
382	>	std::vector<ConstraintPair*> constraintPairs_;
383	>	std::vector<ConstraintElem*> constraintElems_;
384	>	int stampId_;
385	>	std::string moleculeName_;
386	>	PropertyMap properties_;
387
388	<	} //namespace oopse
388	>	};
389	>
390	>	} //namespace OpenMD
391		#endif //

Comparing:
trunk/src/primitives/Molecule.hpp (property svn:keywords), Revision 259 by tim, Fri Jan 14 01:56:04 2005 UTC vs.
branches/development/src/primitives/Molecule.hpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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