src/primitives/Molecule.hpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file Molecule.hpp
 * @author    tlin
 * @date  10/25/2004
 * @version 1.0
 */ 

#ifndef PRIMITIVES_MOLECULE_HPP
#define PRIMITIVES_MOLECULE_HPP
#include <vector>
#include <iostream>

#include "constraints/ConstraintPair.hpp"
#include "math/Vector3.hpp"
#include "primitives/Atom.hpp"
#include "primitives/RigidBody.hpp"
#include "primitives/Bond.hpp"
#include "primitives/Bend.hpp"
#include "primitives/Torsion.hpp"
#include "primitives/CutoffGroup.hpp"

namespace oopse{

class Constraint;

/**
 * @class Molecule Molecule.hpp "primitives/Molecule.hpp"
 * @brief
 */
class Molecule {
    public:

        typedef std::vector<Atom*>::iterator AtomIterator;
        typedef std::vector<Bond*>::iterator BondIterator;
        typedef std::vector<Bend*>::iterator BendIterator;
        typedef std::vector<Torsion*>::iterator TorsionIterator;
        typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
        typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
        typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;        
        typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
        typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
        

        Molecule(int stampId, int globalIndex, const std::string& molName);
        virtual ~Molecule();

        /**
         * Returns the global index of this molecule.
         * @return  the global index of this molecule 
         */
        int getGlobalIndex() {
            return globalIndex_;
        }

        /**
         * Returns the stamp id of this molecule
         * @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
         * stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
         */
        int getStampId() {
            return stampId_;
        }

        /** Returns the name of the molecule */
        std::string getType() {
            return moleculeName_;
        }
        
        /**
         * Sets the global index of this molecule.
         * @param new global index to be set
         */
        int setGlobalIndex(int index) {
            return globalIndex_;
        }

        
        /** add an atom into this molecule */
        void addAtom(Atom* atom);

        /** add a bond into this molecule */
        void addBond(Bond* bond);

        /** add a bend into this molecule */
        void addBend(Bend* bend);

        /** add a torsion into this molecule*/
        void addTorsion(Torsion* torsion);

        /** add a rigidbody into this molecule */
        void addRigidBody(RigidBody *rb);

        /** add a cutoff group into this molecule */
        void addCutoffGroup(CutoffGroup* cp);     

        void addConstraintPair(ConstraintPair* consPair);
        
        void addConstraintElem(ConstraintElem* consElem);

        /** */
        void complete();

        /** Returns the total number of atoms in this molecule */
        unsigned int getNAtoms() {
            return atoms_.size();
        }

        /** Returns the total number of bonds in this molecule */        
        unsigned int getNBonds(){
            return bonds_.size();
        }

        /** Returns the total number of bends in this molecule */        
        unsigned int getNBends() {
            return bends_.size();
        }

        /** Returns the total number of torsions in this molecule */        
        unsigned int getNTorsions() {
            return torsions_.size();
        }

        /** Returns the total number of rigid bodies in this molecule */        
        unsigned int getNRigidBodies() {
            return rigidBodies_.size();
        }

        /** Returns the total number of integrable objects in this molecule */
        unsigned int getNIntegrableObjects() {
            return integrableObjects_.size();
        }

        /** Returns the total number of cutoff groups in this molecule */
        unsigned int getNCutoffGroups() {
            return cutoffGroups_.size();
        }

        /** Returns the total number of constraints in this molecule */
        unsigned int getNConstraintPairs() {
            return constraintPairs_.size();
        }

        Atom* getAtomAt(unsigned int i) {
            assert(i < atoms_.size());
            return atoms_[i];
        }

        Atom* beginAtom(std::vector<Atom*>::iterator& i) {
            i = atoms_.begin();
            return (i == atoms_.end()) ? NULL : *i;
        }

        Atom* nextAtom(std::vector<Atom*>::iterator& i) {
            ++i;
            return (i == atoms_.end()) ? NULL : *i;    
        }

        Bond* beginBond(std::vector<Bond*>::iterator& i) {
            i = bonds_.begin();
            return (i == bonds_.end()) ? NULL : *i;
        }

        Bond* nextBond(std::vector<Bond*>::iterator& i) {
            ++i;
            return (i == bonds_.end()) ? NULL : *i;    

        }

        Bend* beginBend(std::vector<Bend*>::iterator& i) {
            i = bends_.begin();
            return (i == bends_.end()) ? NULL : *i;
        }

        Bend* nextBend(std::vector<Bend*>::iterator& i) {
            ++i;
            return (i == bends_.end()) ? NULL : *i;    
        }

        Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
            i = torsions_.begin();
            return (i == torsions_.end()) ? NULL : *i;
        }

        Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
            ++i;
            return (i == torsions_.end()) ? NULL : *i;    
        }    

        RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
            i = rigidBodies_.begin();
            return (i == rigidBodies_.end()) ? NULL : *i;
        }

        RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
            ++i;
            return (i == rigidBodies_.end()) ? NULL : *i;    
        }

        StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
            i = integrableObjects_.begin();
            return (i == integrableObjects_.end()) ? NULL : *i;
        }

        StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
            ++i;
            return (i == integrableObjects_.end()) ? NULL : *i;    
        }    

        CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
            i = cutoffGroups_.begin();
            return (i == cutoffGroups_.end()) ? NULL : *i;
        }

        CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {            
            ++i;
            return (i == cutoffGroups_.end()) ? NULL : *i;    
        } 

        ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
            i = constraintPairs_.begin();
            return (i == constraintPairs_.end()) ? NULL : *i;
        }

        ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {            
            ++i;
            return (i == constraintPairs_.end()) ? NULL : *i;    
        }         

        ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
            i = constraintElems_.begin();
            return (i == constraintElems_.end()) ? NULL : *i;
        }

        ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {            
            ++i;
            return (i == constraintElems_.end()) ? NULL : *i;    
        }
        
        /** return the total potential energy of short range interaction of this molecule */
        double getPotential();

        /** get total mass of this molecule */        
        double getMass();

        /** return the center of mass of this molecule */
        Vector3d getCom();

        /** Moves the center of this molecule */
        void moveCom(const Vector3d& delta);

        /** Returns the velocity of center of mass of this molecule */
        Vector3d getComVel();

        friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
        
    private:
        
        int globalIndex_;

        std::vector<Atom*> atoms_;
        std::vector<Bond*> bonds_;
        std::vector<Bend*> bends_;
        std::vector<Torsion*> torsions_;
        std::vector<RigidBody*> rigidBodies_;
        std::vector<StuntDouble*> integrableObjects_;
        std::vector<CutoffGroup*> cutoffGroups_;
        std::vector<ConstraintPair*> constraintPairs_;
        std::vector<ConstraintElem*> constraintElems_;
        int stampId_;
        std::string moleculeName_;
};

} //namespace oopse
#endif //
Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (20 years, 7 months ago) by tim
File size:	10710 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	1692	*
4	tim	1927	* 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. 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40	tim	1692	*/
41	tim	1927
42	tim	1692	/**
43			* @file Molecule.hpp
44			* @author tlin
45			* @date 10/25/2004
46			* @version 1.0
47			*/
48
49			#ifndef PRIMITIVES_MOLECULE_HPP
50			#define PRIMITIVES_MOLECULE_HPP
51	gezelter	1490	#include <vector>
52	tim	1692	#include <iostream>
53	gezelter	1490
54	tim	1901	#include "constraints/ConstraintPair.hpp"
55	tim	1692	#include "math/Vector3.hpp"
56	tim	1492	#include "primitives/Atom.hpp"
57			#include "primitives/RigidBody.hpp"
58	tim	1782	#include "primitives/Bond.hpp"
59			#include "primitives/Bend.hpp"
60			#include "primitives/Torsion.hpp"
61	tim	1695	#include "primitives/CutoffGroup.hpp"
62	gezelter	1490
63	tim	1692	namespace oopse{
64	gezelter	1490
65	tim	1701	class Constraint;
66
67	tim	1692	/**
68			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
69			* @brief
70			*/
71			class Molecule {
72			public:
73	gezelter	1490
74	tim	1725	typedef std::vector<Atom*>::iterator AtomIterator;
75			typedef std::vector<Bond*>::iterator BondIterator;
76			typedef std::vector<Bend*>::iterator BendIterator;
77			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	tim	1907	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
82			typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
83
84	tim	1725
85	tim	1733	Molecule(int stampId, int globalIndex, const std::string& molName);
86	tim	1692	virtual ~Molecule();
87	gezelter	1490
88	tim	1692	/**
89			* Returns the global index of this molecule.
90			* @return the global index of this molecule
91			*/
92			int getGlobalIndex() {
93			return globalIndex_;
94			}
95	gezelter	1490
96	tim	1692	/**
97	tim	1733	* Returns the stamp id of this molecule
98			* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
99			* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
100			*/
101			int getStampId() {
102			return stampId_;
103			}
104
105			/** Returns the name of the molecule */
106			std::string getType() {
107			return moleculeName_;
108			}
109
110			/**
111	tim	1692	* Sets the global index of this molecule.
112			* @param new global index to be set
113			*/
114	tim	1695	int setGlobalIndex(int index) {
115	tim	1692	return globalIndex_;
116			}
117	gezelter	1490
118	tim	1733
119	tim	1692	/** add an atom into this molecule */
120			void addAtom(Atom* atom);
121	gezelter	1490
122	tim	1692	/** add a bond into this molecule */
123			void addBond(Bond* bond);
124	gezelter	1490
125	tim	1692	/** add a bend into this molecule */
126			void addBend(Bend* bend);
127	gezelter	1490
128	tim	1692	/** add a torsion into this molecule*/
129			void addTorsion(Torsion* torsion);
130	gezelter	1490
131	tim	1692	/** add a rigidbody into this molecule */
132			void addRigidBody(RigidBody *rb);
133	gezelter	1490
134	tim	1692	/** add a cutoff group into this molecule */
135	tim	1901	void addCutoffGroup(CutoffGroup* cp);
136	gezelter	1490
137	tim	1901	void addConstraintPair(ConstraintPair* consPair);
138	tim	1907
139			void addConstraintElem(ConstraintElem* consElem);
140	tim	1901
141	tim	1692	/** */
142			void complete();
143	gezelter	1490
144	tim	1692	/** Returns the total number of atoms in this molecule */
145			unsigned int getNAtoms() {
146			return atoms_.size();
147			}
148	gezelter	1490
149	tim	1692	/** Returns the total number of bonds in this molecule */
150			unsigned int getNBonds(){
151			return bonds_.size();
152			}
153	gezelter	1490
154	tim	1692	/** Returns the total number of bends in this molecule */
155			unsigned int getNBends() {
156			return bends_.size();
157			}
158	gezelter	1490
159	tim	1692	/** Returns the total number of torsions in this molecule */
160			unsigned int getNTorsions() {
161			return torsions_.size();
162			}
163	gezelter	1490
164	tim	1692	/** Returns the total number of rigid bodies in this molecule */
165			unsigned int getNRigidBodies() {
166			return rigidBodies_.size();
167			}
168	gezelter	1490
169	tim	1692	/** 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	tim	1696	/** Returns the total number of constraints in this molecule */
180	tim	1901	unsigned int getNConstraintPairs() {
181			return constraintPairs_.size();
182	tim	1696	}
183	tim	1719
184			Atom* getAtomAt(unsigned int i) {
185			assert(i < atoms_.size());
186			return atoms_[i];
187			}
188	tim	1692
189	tim	1910	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
190	tim	1907	i = atoms_.begin();
191			return (i == atoms_.end()) ? NULL : *i;
192			}
193	tim	1692
194	tim	1910	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
195	tim	1907	++i;
196			return (i == atoms_.end()) ? NULL : *i;
197			}
198	tim	1692
199	tim	1910	Bond* beginBond(std::vector<Bond*>::iterator& i) {
200	tim	1907	i = bonds_.begin();
201			return (i == bonds_.end()) ? NULL : *i;
202			}
203	tim	1692
204	tim	1910	Bond* nextBond(std::vector<Bond*>::iterator& i) {
205	tim	1907	++i;
206			return (i == bonds_.end()) ? NULL : *i;
207	tim	1692
208	tim	1907	}
209	tim	1692
210	tim	1910	Bend* beginBend(std::vector<Bend*>::iterator& i) {
211	tim	1907	i = bends_.begin();
212			return (i == bends_.end()) ? NULL : *i;
213			}
214	tim	1692
215	tim	1910	Bend* nextBend(std::vector<Bend*>::iterator& i) {
216	tim	1907	++i;
217			return (i == bends_.end()) ? NULL : *i;
218			}
219	tim	1692
220	tim	1910	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
221	tim	1907	i = torsions_.begin();
222			return (i == torsions_.end()) ? NULL : *i;
223			}
224	tim	1692
225	tim	1910	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
226	tim	1907	++i;
227			return (i == torsions_.end()) ? NULL : *i;
228			}
229	tim	1692
230	tim	1910	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
231	tim	1907	i = rigidBodies_.begin();
232			return (i == rigidBodies_.end()) ? NULL : *i;
233			}
234	tim	1692
235	tim	1910	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
236	tim	1907	++i;
237			return (i == rigidBodies_.end()) ? NULL : *i;
238			}
239	tim	1692
240	tim	1910	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
241	tim	1907	i = integrableObjects_.begin();
242			return (i == integrableObjects_.end()) ? NULL : *i;
243			}
244	tim	1696
245	tim	1910	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
246	tim	1907	++i;
247			return (i == integrableObjects_.end()) ? NULL : *i;
248			}
249
250	tim	1910	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
251	tim	1907	i = cutoffGroups_.begin();
252			return (i == cutoffGroups_.end()) ? NULL : *i;
253			}
254
255	tim	1910	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
256	tim	1907	++i;
257			return (i == cutoffGroups_.end()) ? NULL : *i;
258			}
259
260	tim	1910	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
261	tim	1907	i = constraintPairs_.begin();
262			return (i == constraintPairs_.end()) ? NULL : *i;
263			}
264
265	tim	1910	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
266	tim	1907	++i;
267			return (i == constraintPairs_.end()) ? NULL : *i;
268			}
269
270	tim	1910	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
271	tim	1907	i = constraintElems_.begin();
272			return (i == constraintElems_.end()) ? NULL : *i;
273			}
274
275	tim	1910	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
276	tim	1907	++i;
277			return (i == constraintElems_.end()) ? NULL : *i;
278			}
279	tim	1696
280	tim	1692	/** return the total potential energy of short range interaction of this molecule */
281			double getPotential();
282
283	tim	1843	/** get total mass of this molecule */
284			double getMass();
285	tim	1692
286			/** return the center of mass of this molecule */
287			Vector3d getCom();
288
289			/** Moves the center of this molecule */
290	tim	1695	void moveCom(const Vector3d& delta);
291	tim	1692
292			/** Returns the velocity of center of mass of this molecule */
293			Vector3d getComVel();
294
295	tim	1695	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
296	tim	1692
297			private:
298	tim	1725
299	tim	1692	int globalIndex_;
300
301			std::vector<Atom*> atoms_;
302			std::vector<Bond*> bonds_;
303			std::vector<Bend*> bends_;
304			std::vector<Torsion*> torsions_;
305			std::vector<RigidBody*> rigidBodies_;
306			std::vector<StuntDouble*> integrableObjects_;
307			std::vector<CutoffGroup*> cutoffGroups_;
308	tim	1901	std::vector<ConstraintPair*> constraintPairs_;
309	tim	1907	std::vector<ConstraintElem*> constraintElems_;
310	tim	1733	int stampId_;
311			std::string moleculeName_;
312	gezelter	1490	};
313
314	tim	1692	} //namespace oopse
315			#endif //