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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 2052 by gezelter, Fri Jan 9 19:06:35 2015 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
13	–	using namespace std;
66
67	<	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;
67	>	namespace OpenMD{
68
69	<	class Molecule{
35	<
36	<	public:
69	>	class Constraint;
70
71	<	Molecule( void );
72	<	~Molecule( void );
71	>	/**
72	>	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
73	>	* @brief
74	>	*/
75	>	class Molecule {
76	>	public:
77
78	<	void initialize( molInit &theInit );
78	>	struct HBondDonor {
79	>	Atom* donorAtom;
80	>	Atom* donatedHydrogen;
81	>	};
82
83	<	void setMyIndex( int theIndex ){ myIndex = theIndex;}
84	<	int getMyIndex( void ) { return myIndex; }
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	<	int getGlobalIndex( void ) { return globalIndex; }
98	<	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
97	>	Molecule(int stampId, int globalIndex, const std::string& molName, int region);
98	>	virtual ~Molecule();
99
100	<	int getNAtoms   ( void )    {return nAtoms;}
101	<	int getNBonds   ( void )    {return nBonds;}
102	<	int getNBends   ( void )    {return nBends;}
103	<	int getNTorsions( void )    {return nTorsions;}
104	<	int getNRigidBodies( void ) {return myRigidBodies.size();}
105	<	int getNOriented( void )    {return nOriented;}
106	<	int getNMembers ( void )    {return nMembers;}
107	<	int getStampID  ( void )    {return stampID;}
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	<	Atom**      getMyAtoms   ( void )    {return myAtoms;}
136	<	Bond**      getMyBonds   ( void )    {return myBonds;}
137	<	Bend**      getMyBends   ( void )    {return myBends;}
138	<	Torsion**   getMyTorsions( void )    {return myTorsions;}
139	<	vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
140	<	vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
135	>	void setConstrainTotalCharge(bool ctc) {
136	>	constrainTotalCharge_ = ctc;
137	>	}
138	>
139	>	bool constrainTotalCharge() {
140	>	return constrainTotalCharge_;
141	>	}
142
143	<	//beginCutoffGroup return the first group and initialize the iterator
144	<	CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
145	<	i = myCutoffGroups.begin();
146	<	return i != myCutoffGroups.end()? *i : NULL;
147	<	}
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	<	//nextCutoffGroup return next cutoff group based on the iterator
156	<	CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
157	<	i++;
158	<	return i != myCutoffGroups.end()? *i : NULL;
159	<	}
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	<	int getNCutoffGroups() {return nCutoffGroups;}
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	<	void setStampID( int info ) {stampID = info;}
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	<	void calcForces( void );
231	<	void atoms2rigidBodies( void );
232	<	double getPotential( void );
233	<
234	<	void printMe( void );
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	<	void getCOM( double COM[3] );
282	<	void moveCOM( double delta[3] );
283	<	double getCOMvel( double COMvel[3] );
284	<
285	<	double getTotalMass();
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	<	private:
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	<	int stampID;   // the ID in the BASS component stamp array
342	<	int nAtoms;    // the number of atoms in the molecule
343	<	int nBonds;    // ... .. ..  . .bonds .. .. . . . .
344	<	int nBends;    // . . . . .. . .bends . . . . .. .
345	<	int nTorsions; // .. . . .. . . torsions . . .. . .
346	<	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
347	<	int nOriented; // .. . . . .. . oriented atoms . . .
348	<	int nMembers;  // .. . . . . . .atoms (legacy code) . . .
349	<	int nCutoffGroups;
104	<
105	<	int myIndex; // mostly just for debug (and for making pressure calcs work)
106	<	int globalIndex;
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	<	Atom** myAtoms;     // the array of atoms
352	<	Bond** myBonds;     // arrays of all the short range interactions
353	<	Bend** myBends;
354	<	Torsion** myTorsions;
355	<	vector<RigidBody*>   myRigidBodies;
356	<	vector<StuntDouble*> myIntegrableObjects;
357	<	vector<CutoffGroup*> myCutoffGroups;
358	<	};
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
371	<	#endif
371	>
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	>
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	>	std::string getMoleculeName() {
405	>	return moleculeName_;
406	>	}
407	>
408	>	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
409	>
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	>	/**
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	>	/**
424	>	* clear all of the properties
425	>	*/
426	>	void clearProperties();
427	>
428	>	/**
429	>	* Returns all names of properties
430	>	* @return all names of properties
431	>	*/
432	>	std::vector<std::string> getPropertyNames();
433	>
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	>	/**
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	>	};
473	>
474	>	} //namespace OpenMD
475	>	#endif //

Comparing trunk/src/primitives/Molecule.hpp (property svn:keywords):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

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