src/primitives/Molecule.hpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

/**
 * @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:	1910
Committed:	Fri Jan 7 21:50:13 2005 UTC (19 years, 7 months ago) by tim
File size:	9780 byte(s)
Log Message:	ZConstraintForceManager in progress
#	Content
1	/*
2	* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3	*
4	* Contact: oopse@oopse.org
5	*
6	* This program is free software; you can redistribute it and/or
7	* modify it under the terms of the GNU Lesser General Public License
8	* as published by the Free Software Foundation; either version 2.1
9	* of the License, or (at your option) any later version.
10	* All we ask is that proper credit is given for our work, which includes
11	* - but is not limited to - adding the above copyright notice to the beginning
12	* of your source code files, and to any copyright notice that you may distribute
13	* with programs based on this work.
14	*
15	* This program is distributed in the hope that it will be useful,
16	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	* GNU Lesser General Public License for more details.
19	*
20	* You should have received a copy of the GNU Lesser General Public License
21	* along with this program; if not, write to the Free Software
22	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23	*
24	*/
25
26	/**
27	* @file Molecule.hpp
28	* @author tlin
29	* @date 10/25/2004
30	* @version 1.0
31	*/
32
33	#ifndef PRIMITIVES_MOLECULE_HPP
34	#define PRIMITIVES_MOLECULE_HPP
35	#include <vector>
36	#include <iostream>
37
38	#include "constraints/ConstraintPair.hpp"
39	#include "math/Vector3.hpp"
40	#include "primitives/Atom.hpp"
41	#include "primitives/RigidBody.hpp"
42	#include "primitives/Bond.hpp"
43	#include "primitives/Bend.hpp"
44	#include "primitives/Torsion.hpp"
45	#include "primitives/CutoffGroup.hpp"
46
47	namespace oopse{
48
49	class Constraint;
50
51	/**
52	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
53	* @brief
54	*/
55	class Molecule {
56	public:
57
58	typedef std::vector<Atom*>::iterator AtomIterator;
59	typedef std::vector<Bond*>::iterator BondIterator;
60	typedef std::vector<Bend*>::iterator BendIterator;
61	typedef std::vector<Torsion*>::iterator TorsionIterator;
62	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
63	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
64	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
65	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
66	typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
67
68
69	Molecule(int stampId, int globalIndex, const std::string& molName);
70	virtual ~Molecule();
71
72	/**
73	* Returns the global index of this molecule.
74	* @return the global index of this molecule
75	*/
76	int getGlobalIndex() {
77	return globalIndex_;
78	}
79
80	/**
81	* Returns the stamp id of this molecule
82	* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
83	* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
84	*/
85	int getStampId() {
86	return stampId_;
87	}
88
89	/** Returns the name of the molecule */
90	std::string getType() {
91	return moleculeName_;
92	}
93
94	/**
95	* Sets the global index of this molecule.
96	* @param new global index to be set
97	*/
98	int setGlobalIndex(int index) {
99	return globalIndex_;
100	}
101
102
103	/** add an atom into this molecule */
104	void addAtom(Atom* atom);
105
106	/** add a bond into this molecule */
107	void addBond(Bond* bond);
108
109	/** add a bend into this molecule */
110	void addBend(Bend* bend);
111
112	/** add a torsion into this molecule*/
113	void addTorsion(Torsion* torsion);
114
115	/** add a rigidbody into this molecule */
116	void addRigidBody(RigidBody *rb);
117
118	/** add a cutoff group into this molecule */
119	void addCutoffGroup(CutoffGroup* cp);
120
121	void addConstraintPair(ConstraintPair* consPair);
122
123	void addConstraintElem(ConstraintElem* consElem);
124
125	/** */
126	void complete();
127
128	/** Returns the total number of atoms in this molecule */
129	unsigned int getNAtoms() {
130	return atoms_.size();
131	}
132
133	/** Returns the total number of bonds in this molecule */
134	unsigned int getNBonds(){
135	return bonds_.size();
136	}
137
138	/** Returns the total number of bends in this molecule */
139	unsigned int getNBends() {
140	return bends_.size();
141	}
142
143	/** Returns the total number of torsions in this molecule */
144	unsigned int getNTorsions() {
145	return torsions_.size();
146	}
147
148	/** Returns the total number of rigid bodies in this molecule */
149	unsigned int getNRigidBodies() {
150	return rigidBodies_.size();
151	}
152
153	/** Returns the total number of integrable objects in this molecule */
154	unsigned int getNIntegrableObjects() {
155	return integrableObjects_.size();
156	}
157
158	/** Returns the total number of cutoff groups in this molecule */
159	unsigned int getNCutoffGroups() {
160	return cutoffGroups_.size();
161	}
162
163	/** Returns the total number of constraints in this molecule */
164	unsigned int getNConstraintPairs() {
165	return constraintPairs_.size();
166	}
167
168	Atom* getAtomAt(unsigned int i) {
169	assert(i < atoms_.size());
170	return atoms_[i];
171	}
172
173	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
174	i = atoms_.begin();
175	return (i == atoms_.end()) ? NULL : *i;
176	}
177
178	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
179	++i;
180	return (i == atoms_.end()) ? NULL : *i;
181	}
182
183	Bond* beginBond(std::vector<Bond*>::iterator& i) {
184	i = bonds_.begin();
185	return (i == bonds_.end()) ? NULL : *i;
186	}
187
188	Bond* nextBond(std::vector<Bond*>::iterator& i) {
189	++i;
190	return (i == bonds_.end()) ? NULL : *i;
191
192	}
193
194	Bend* beginBend(std::vector<Bend*>::iterator& i) {
195	i = bends_.begin();
196	return (i == bends_.end()) ? NULL : *i;
197	}
198
199	Bend* nextBend(std::vector<Bend*>::iterator& i) {
200	++i;
201	return (i == bends_.end()) ? NULL : *i;
202	}
203
204	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
205	i = torsions_.begin();
206	return (i == torsions_.end()) ? NULL : *i;
207	}
208
209	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
210	++i;
211	return (i == torsions_.end()) ? NULL : *i;
212	}
213
214	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
215	i = rigidBodies_.begin();
216	return (i == rigidBodies_.end()) ? NULL : *i;
217	}
218
219	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
220	++i;
221	return (i == rigidBodies_.end()) ? NULL : *i;
222	}
223
224	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
225	i = integrableObjects_.begin();
226	return (i == integrableObjects_.end()) ? NULL : *i;
227	}
228
229	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
230	++i;
231	return (i == integrableObjects_.end()) ? NULL : *i;
232	}
233
234	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
235	i = cutoffGroups_.begin();
236	return (i == cutoffGroups_.end()) ? NULL : *i;
237	}
238
239	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
240	++i;
241	return (i == cutoffGroups_.end()) ? NULL : *i;
242	}
243
244	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
245	i = constraintPairs_.begin();
246	return (i == constraintPairs_.end()) ? NULL : *i;
247	}
248
249	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
250	++i;
251	return (i == constraintPairs_.end()) ? NULL : *i;
252	}
253
254	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
255	i = constraintElems_.begin();
256	return (i == constraintElems_.end()) ? NULL : *i;
257	}
258
259	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
260	++i;
261	return (i == constraintElems_.end()) ? NULL : *i;
262	}
263
264	/** return the total potential energy of short range interaction of this molecule */
265	double getPotential();
266
267	/** get total mass of this molecule */
268	double getMass();
269
270	/** return the center of mass of this molecule */
271	Vector3d getCom();
272
273	/** Moves the center of this molecule */
274	void moveCom(const Vector3d& delta);
275
276	/** Returns the velocity of center of mass of this molecule */
277	Vector3d getComVel();
278
279	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
280
281	private:
282
283	int globalIndex_;
284
285	std::vector<Atom*> atoms_;
286	std::vector<Bond*> bonds_;
287	std::vector<Bend*> bends_;
288	std::vector<Torsion*> torsions_;
289	std::vector<RigidBody*> rigidBodies_;
290	std::vector<StuntDouble*> integrableObjects_;
291	std::vector<CutoffGroup*> cutoffGroups_;
292	std::vector<ConstraintPair*> constraintPairs_;
293	std::vector<ConstraintElem*> constraintElems_;
294	int stampId_;
295	std::string moleculeName_;
296	};
297
298	} //namespace oopse
299	#endif //