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 "math/Vector3.hpp"
#include "primitives/Atom.hpp"
#include "primitives/RigidBody.hpp"

namespace oopse{

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

        Molecule();
        virtual ~Molecule();

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

        /**
         * Sets the global index of this molecule.
         * @param new global index to be set
         */
        void setGlobalIndex(int index) {
            return globalIndex_;
        }
        
        /** 
         * Returns the local index of this molecule 
         * @return the local index of this molecule
         */
        int getLocalIndex() {
            return localIndex_;
        }

        /** 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 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 first atom in this molecule and initialize the iterator.
         * @return the first atom, return NULL if there is not cut off group in this molecule
         * @param i iteraotr
         */        
        Atom* beginAtom(std::vector<Atom*>::iterator& i);

        Atom* nextAtom(std::vector<Atom*>::iterator& i);

        /**
         * Returns the first bond in this molecule and initialize the iterator.
         * @return the first bond, return NULL if there is not cut off group in this molecule
         * @param i iteraotr
         */
        Bond* beginBond(std::vector<Bond*>::iterator& i);

        Bond* nextBond(std::vector<Bond*>::iterator& i);

        /**
         * Returns the first bend in this molecule and initialize the iterator.
         * @return the first bend, return NULL if there is not cut off group in this molecule
         * @param i iteraotr
         */
        Bend* beginBend(std::vector<Bend*>::iterator& i);

        Bend* nextBend(std::vector<Bend*>::iterator& i);

        /**
         * Returns the first torsion in this molecule and initialize the iterator.
         * @return the first torsion, return NULL if there is not cut off group in this molecule
         * @param i iteraotr
         */
        Torsion* beginTorsion(std::vector<Torsion*>::iterator& i);
        Torsion* nextTorsion(std::vector<Torsion*>::iterator& i);

        /**
         * Returns the first rigid body in this molecule and initialize the iterator.
         * @return the first rigid body, return NULL if there is not cut off group in this molecule
         * @param i iteraotr
         */
        RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i);

        RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i);

        /**
         * Returns the first integrable object in this molecule and initialize the iterator.
         * @return the first integrable object, return NULL if there is not cut off group in this molecule
         * @param i iteraotr
         */
        StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i);
        
        StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i);

        /**
         * Returns the first cutoff group in this molecule and initialize the iterator.
         * @return the first cutoff group, return NULL if there is not cut off group in this molecule
         * @param i iteraotr
         */
        CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i);

        /**
         * Returns next cutoff group based on the iterator 
         * @return next cutoff group
         * @param i 
         */        
        CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);

        //void setStampID( int info ) {stampID = info;} 

        void calcForces( void );

        void atoms2rigidBodies( void );

        /** return the total potential energy of short range interaction of this molecule */
        double getPotential();


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

        /** Moves the center of this molecule */
        void moveCom(const Vetor3d& delta);

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

        /** Returns the total mass of this molecule */
        double getTotalMass();

        friend std::ostream& operator <<(std::ostream& o, const Molecule& mol);
        
    private:
        int localIndex_;
        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_;
};

} //namespace oopse
#endif //
Revision:	1692
Committed:	Mon Nov 1 20:15:58 2004 UTC (19 years, 7 months ago) by tim
File size:	7833 byte(s)
Log Message:	break, break and break.....
#	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 "math/Vector3.hpp"
39	#include "primitives/Atom.hpp"
40	#include "primitives/RigidBody.hpp"
41
42	namespace oopse{
43
44	/**
45	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
46	* @brief
47	*/
48	class Molecule {
49	public:
50
51	Molecule();
52	virtual ~Molecule();
53
54	/**
55	* Returns the global index of this molecule.
56	* @return the global index of this molecule
57	*/
58	int getGlobalIndex() {
59	return globalIndex_;
60	}
61
62	/**
63	* Sets the global index of this molecule.
64	* @param new global index to be set
65	*/
66	void setGlobalIndex(int index) {
67	return globalIndex_;
68	}
69
70	/**
71	* Returns the local index of this molecule
72	* @return the local index of this molecule
73	*/
74	int getLocalIndex() {
75	return localIndex_;
76	}
77
78	/** add an atom into this molecule */
79	void addAtom(Atom* atom);
80
81	/** add a bond into this molecule */
82	void addBond(Bond* bond);
83
84	/** add a bend into this molecule */
85	void addBend(Bend* bend);
86
87	/** add a torsion into this molecule*/
88	void addTorsion(Torsion* torsion);
89
90	/** add a rigidbody into this molecule */
91	void addRigidBody(RigidBody *rb);
92
93	/** add a cutoff group into this molecule */
94	void addCutoffGroup(CutoffGroup* cp);
95
96	/** */
97	void complete();
98
99	/** Returns the total number of atoms in this molecule */
100	unsigned int getNAtoms() {
101	return atoms_.size();
102	}
103
104	/** Returns the total number of bonds in this molecule */
105	unsigned int getNBonds(){
106	return bonds_.size();
107	}
108
109	/** Returns the total number of bends in this molecule */
110	unsigned int getNBends() {
111	return bends_.size();
112	}
113
114	/** Returns the total number of torsions in this molecule */
115	unsigned int getNTorsions() {
116	return torsions_.size();
117	}
118
119	/** Returns the total number of rigid bodies in this molecule */
120	unsigned int getNRigidBodies() {
121	return rigidBodies_.size();
122	}
123
124	/** Returns the total number of integrable objects in this molecule */
125	unsigned int getNIntegrableObjects() {
126	return integrableObjects_.size();
127	}
128
129	/** Returns the total number of cutoff groups in this molecule */
130	unsigned int getNCutoffGroups() {
131	return cutoffGroups_.size();
132	}
133
134	/**
135	* Returns the first atom in this molecule and initialize the iterator.
136	* @return the first atom, return NULL if there is not cut off group in this molecule
137	* @param i iteraotr
138	*/
139	Atom* beginAtom(std::vector<Atom*>::iterator& i);
140
141	Atom* nextAtom(std::vector<Atom*>::iterator& i);
142
143	/**
144	* Returns the first bond in this molecule and initialize the iterator.
145	* @return the first bond, return NULL if there is not cut off group in this molecule
146	* @param i iteraotr
147	*/
148	Bond* beginBond(std::vector<Bond*>::iterator& i);
149
150	Bond* nextBond(std::vector<Bond*>::iterator& i);
151
152	/**
153	* Returns the first bend in this molecule and initialize the iterator.
154	* @return the first bend, return NULL if there is not cut off group in this molecule
155	* @param i iteraotr
156	*/
157	Bend* beginBend(std::vector<Bend*>::iterator& i);
158
159	Bend* nextBend(std::vector<Bend*>::iterator& i);
160
161	/**
162	* Returns the first torsion in this molecule and initialize the iterator.
163	* @return the first torsion, return NULL if there is not cut off group in this molecule
164	* @param i iteraotr
165	*/
166	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i);
167	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i);
168
169	/**
170	* Returns the first rigid body in this molecule and initialize the iterator.
171	* @return the first rigid body, return NULL if there is not cut off group in this molecule
172	* @param i iteraotr
173	*/
174	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i);
175
176	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i);
177
178	/**
179	* Returns the first integrable object in this molecule and initialize the iterator.
180	* @return the first integrable object, return NULL if there is not cut off group in this molecule
181	* @param i iteraotr
182	*/
183	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i);
184
185	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i);
186
187	/**
188	* Returns the first cutoff group in this molecule and initialize the iterator.
189	* @return the first cutoff group, return NULL if there is not cut off group in this molecule
190	* @param i iteraotr
191	*/
192	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
193
194	/**
195	* Returns next cutoff group based on the iterator
196	* @return next cutoff group
197	* @param i
198	*/
199	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
200
201	//void setStampID( int info ) {stampID = info;}
202
203	void calcForces( void );
204
205	void atoms2rigidBodies( void );
206
207	/** return the total potential energy of short range interaction of this molecule */
208	double getPotential();
209
210
211	/** return the center of mass of this molecule */
212	Vector3d getCom();
213
214	/** Moves the center of this molecule */
215	void moveCom(const Vetor3d& delta);
216
217	/** Returns the velocity of center of mass of this molecule */
218	Vector3d getComVel();
219
220	/** Returns the total mass of this molecule */
221	double getTotalMass();
222
223	friend std::ostream& operator <<(std::ostream& o, const Molecule& mol);
224
225	private:
226	int localIndex_;
227	int globalIndex_;
228
229	std::vector<Atom*> atoms_;
230	std::vector<Bond*> bonds_;
231	std::vector<Bend*> bends_;
232	std::vector<Torsion*> torsions_;
233	std::vector<RigidBody*> rigidBodies_;
234	std::vector<StuntDouble*> integrableObjects_;
235	std::vector<CutoffGroup*> cutoffGroups_;
236	};
237
238	} //namespace oopse
239	#endif //