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Comparing trunk/src/primitives/Molecule.hpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 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, int region);
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	>	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	<	void setMyIndex( int theIndex ){ myIndex = theIndex;}
128	<	int getMyIndex( void ) { return myIndex; }
127	>	void setConstrainTotalCharge(bool ctc) {
128	>	constrainTotalCharge_ = ctc;
129	>	}
130	>
131	>	bool constrainTotalCharge() {
132	>	return constrainTotalCharge_;
133	>	}
134
135	<	int getGlobalIndex( void ) { return globalIndex; }
136	<	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
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	<	int getNAtoms   ( void )    {return nAtoms;}
148	<	int getNBonds   ( void )    {return nBonds;}
149	<	int getNBends   ( void )    {return nBends;}
150	<	int getNTorsions( void )    {return nTorsions;}
151	<	int getNRigidBodies( void ) {return myRigidBodies.size();}
152	<	int getNOriented( void )    {return nOriented;}
153	<	int getNMembers ( void )    {return nMembers;}
154	<	int getStampID  ( void )    {return stampID;}
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	<	Atom**      getMyAtoms   ( void )    {return myAtoms;}
184	<	Bond**      getMyBonds   ( void )    {return myBonds;}
185	<	Bend**      getMyBends   ( void )    {return myBends;}
186	<	Torsion**   getMyTorsions( void )    {return myTorsions;}
187	<	vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
188	<	vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
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	<	//beginCutoffGroup return the first group and initialize the iterator
209	<	CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
210	<	i = myCutoffGroups.begin();
211	<	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;}
208	>	/** Returns the total number of fluctuating charges in this molecule */
209	>	unsigned int getNFluctuatingCharges() {
210	>	return fluctuatingCharges_.size();
211	>	}
212
213	<	void setStampID( int info ) {stampID = info;}
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	<	void calcForces( void );
265	<	void atoms2rigidBodies( void );
266	<	double getPotential( void );
267	<
268	<	void printMe( void );
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	<	void getCOM( double COM[3] );
300	<	void moveCOM( double delta[3] );
301	<	double getCOMvel( double COMvel[3] );
302	<
303	<	double getTotalMass();
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	<	private:
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
334	<	int stampID;   // the ID in the BASS component stamp array
335	<	int nAtoms;    // the number of atoms in the molecule
336	<	int nBonds;    // ... .. ..  . .bonds .. .. . . . .
337	<	int nBends;    // . . . . .. . .bends . . . . .. .
338	<	int nTorsions; // .. . . .. . . torsions . . .. . .
339	<	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
340	<	int nOriented; // .. . . . .. . oriented atoms . . .
341	<	int nMembers;  // .. . . . . . .atoms (legacy code) . . .
342	<	int nCutoffGroups;
343	<
344	<	int myIndex; // mostly just for debug (and for making pressure calcs work)
345	<	int globalIndex;
334	>
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** myAtoms;     // the array of atoms
354	<	Bond** myBonds;     // arrays of all the short range interactions
355	<	Bend** myBends;
356	<	Torsion** myTorsions;
357	<	vector<RigidBody*>   myRigidBodies;
113	<	vector<StuntDouble*> myIntegrableObjects;
114	<	vector<CutoffGroup*> myCutoffGroups;
115	<	};
353	>	std::string getMoleculeName() {
354	>	return moleculeName_;
355	>	}
356	>
357	>	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
358
359	<	#endif
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	>	/**
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	>	/**
373	>	* clear all of the properties
374	>	*/
375	>	void clearProperties();
376	>
377	>	/**
378	>	* Returns all names of properties
379	>	* @return all names of properties
380	>	*/
381	>	std::vector<std::string> getPropertyNames();
382	>
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	>	/**
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	>	};
419	>
420	>	} //namespace OpenMD
421	>	#endif //

Comparing trunk/src/primitives/Molecule.hpp (property svn:keywords):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

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