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

Comparing:
trunk/src/primitives/Molecule.hpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/primitives/Molecule.hpp (file contents), Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

#	Line 1 | Line 1
1	<	#ifndef _MOLECULE_H_
2	<	#define _MOLECULE_H_
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	<	#include <set>
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"
8	–	#include "primitives/SRI.hpp"
9	–	#include "types/MoleculeStamp.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	<	using namespace std;
66	>	namespace OpenMD{
67
68	<	typedef struct{
16	<
17	<	int stampID;   // the ID in the BASS component stamp array
18	<	int nAtoms;    // the number of atoms in the molecule
19	<	int nBonds;    // ... .. ..  . .bonds .. .. . . . .
20	<	int nBends;    // . . . . .. . .bends . . . . .. .
21	<	int nTorsions; // .. . . .. . . torsions . . .. . .
22	<	int nRigidBodies; // .. .. .. . rigid bodies ... ..
23	<	int nOriented; // .. . . . .. . oriented atoms . . .
24	<
25	<	Atom** myAtoms;      // the array of atoms
26	<	Bond** myBonds;      // arrays of all the short range interactions
27	<	Bend** myBends;
28	<	Torsion** myTorsions;
29	<	vector<RigidBody*>   myRigidBodies;
30	<	vector<StuntDouble*> myIntegrableObjects;
31	<	vector<CutoffGroup*> myCutoffGroups;
32	<	} molInit;
68	>	class Constraint;
69
70	<	class Molecule{
70	>	/**
71	>	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
72	>	* @brief
73	>	*/
74	>	class Molecule {
75	>	public:
76
77	<	public:
78	<
79	<	Molecule( void );
80	<	~Molecule( void );
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	<	void initialize( molInit &theInit );
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	<	void setMyIndex( int theIndex ){ myIndex = theIndex;}
125	<	int getMyIndex( void ) { return myIndex; }
124	>	void setConstrainTotalCharge(bool ctc) {
125	>	constrainTotalCharge_ = ctc;
126	>	}
127	>
128	>	bool constrainTotalCharge() {
129	>	return constrainTotalCharge_;
130	>	}
131
132	<	int getGlobalIndex( void ) { return globalIndex; }
133	<	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
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	<	int getNAtoms   ( void )    {return nAtoms;}
145	<	int getNBonds   ( void )    {return nBonds;}
146	<	int getNBends   ( void )    {return nBends;}
147	<	int getNTorsions( void )    {return nTorsions;}
148	<	int getNRigidBodies( void ) {return myRigidBodies.size();}
149	<	int getNOriented( void )    {return nOriented;}
150	<	int getNMembers ( void )    {return nMembers;}
151	<	int getStampID  ( void )    {return stampID;}
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	<	Atom**      getMyAtoms   ( void )    {return myAtoms;}
181	<	Bond**      getMyBonds   ( void )    {return myBonds;}
182	<	Bend**      getMyBends   ( void )    {return myBends;}
183	<	Torsion**   getMyTorsions( void )    {return myTorsions;}
184	<	vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
185	<	vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
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	<	//beginCutoffGroup return the first group and initialize the iterator
206	<	CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
207	<	i = myCutoffGroups.begin();
208	<	return i != myCutoffGroups.end()? *i : NULL;
69	<	}
70	<
71	<	//nextCutoffGroup return next cutoff group based on the iterator
72	<	CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
73	<	i++;
74	<	return i != myCutoffGroups.end()? *i : NULL;
75	<	}
76	<
77	<	int getNCutoffGroups() {return nCutoffGroups;}
205	>	/** Returns the total number of fluctuating charges in this molecule */
206	>	unsigned int getNFluctuatingCharges() {
207	>	return fluctuatingCharges_.size();
208	>	}
209
210	<	void setStampID( int info ) {stampID = info;}
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	<	void calcForces( void );
262	<	void atoms2rigidBodies( void );
263	<	double getPotential( void );
264	<
265	<	void printMe( void );
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	<	void getCOM( double COM[3] );
297	<	void moveCOM( double delta[3] );
298	<	double getCOMvel( double COMvel[3] );
299	<
300	<	double getTotalMass();
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	<	private:
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
331	<	int stampID;   // the ID in the BASS component stamp array
332	<	int nAtoms;    // the number of atoms in the molecule
333	<	int nBonds;    // ... .. ..  . .bonds .. .. . . . .
334	<	int nBends;    // . . . . .. . .bends . . . . .. .
335	<	int nTorsions; // .. . . .. . . torsions . . .. . .
336	<	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
337	<	int nOriented; // .. . . . .. . oriented atoms . . .
338	<	int nMembers;  // .. . . . . . .atoms (legacy code) . . .
339	<	int nCutoffGroups;
340	<
341	<	int myIndex; // mostly just for debug (and for making pressure calcs work)
342	<	int globalIndex;
331	>
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** myAtoms;     // the array of atoms
351	<	Bond** myBonds;     // arrays of all the short range interactions
352	<	Bend** myBends;
353	<	Torsion** myTorsions;
354	<	vector<RigidBody*>   myRigidBodies;
113	<	vector<StuntDouble*> myIntegrableObjects;
114	<	vector<CutoffGroup*> myCutoffGroups;
115	<	};
350	>	std::string getMoleculeName() {
351	>	return moleculeName_;
352	>	}
353	>
354	>	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
355
356	<	#endif
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	>	/**
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	>	/**
370	>	* clear all of the properties
371	>	*/
372	>	void clearProperties();
373	>
374	>	/**
375	>	* Returns all names of properties
376	>	* @return all names of properties
377	>	*/
378	>	std::vector<std::string> getPropertyNames();
379	>
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	>	/**
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	>	};
415	>
416	>	} //namespace OpenMD
417	>	#endif //

Comparing:
trunk/src/primitives/Molecule.hpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/primitives/Molecule.hpp (property svn:keywords), Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

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