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"
#include "primitives/Bond.hpp"
#include "primitives/Bend.hpp"
#include "primitives/Torsion.hpp"
#include "primitives/CutoffGroup.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
         */
        int 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 Vector3d& 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, 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:	1695
Committed:	Mon Nov 1 22:52:57 2004 UTC (19 years, 8 months ago) by tim
File size:	7961 byte(s)
Log Message:	Molecule, Atom, DirectionalAtom, RigidBody and StuntDouble classes get compiled
#	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	#include "primitives/Bond.hpp"
42	#include "primitives/Bend.hpp"
43	#include "primitives/Torsion.hpp"
44	#include "primitives/CutoffGroup.hpp"
45
46	namespace oopse{
47
48	/**
49	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
50	* @brief
51	*/
52	class Molecule {
53	public:
54
55	Molecule();
56	virtual ~Molecule();
57
58	/**
59	* Returns the global index of this molecule.
60	* @return the global index of this molecule
61	*/
62	int getGlobalIndex() {
63	return globalIndex_;
64	}
65
66	/**
67	* Sets the global index of this molecule.
68	* @param new global index to be set
69	*/
70	int setGlobalIndex(int index) {
71	return globalIndex_;
72	}
73
74	/**
75	* Returns the local index of this molecule
76	* @return the local index of this molecule
77	*/
78	int getLocalIndex() {
79	return localIndex_;
80	}
81
82	/** add an atom into this molecule */
83	void addAtom(Atom* atom);
84
85	/** add a bond into this molecule */
86	void addBond(Bond* bond);
87
88	/** add a bend into this molecule */
89	void addBend(Bend* bend);
90
91	/** add a torsion into this molecule*/
92	void addTorsion(Torsion* torsion);
93
94	/** add a rigidbody into this molecule */
95	void addRigidBody(RigidBody *rb);
96
97	/** add a cutoff group into this molecule */
98	void addCutoffGroup(CutoffGroup* cp);
99
100	/** */
101	void complete();
102
103	/** Returns the total number of atoms in this molecule */
104	unsigned int getNAtoms() {
105	return atoms_.size();
106	}
107
108	/** Returns the total number of bonds in this molecule */
109	unsigned int getNBonds(){
110	return bonds_.size();
111	}
112
113	/** Returns the total number of bends in this molecule */
114	unsigned int getNBends() {
115	return bends_.size();
116	}
117
118	/** Returns the total number of torsions in this molecule */
119	unsigned int getNTorsions() {
120	return torsions_.size();
121	}
122
123	/** Returns the total number of rigid bodies in this molecule */
124	unsigned int getNRigidBodies() {
125	return rigidBodies_.size();
126	}
127
128	/** Returns the total number of integrable objects in this molecule */
129	unsigned int getNIntegrableObjects() {
130	return integrableObjects_.size();
131	}
132
133	/** Returns the total number of cutoff groups in this molecule */
134	unsigned int getNCutoffGroups() {
135	return cutoffGroups_.size();
136	}
137
138	/**
139	* Returns the first atom in this molecule and initialize the iterator.
140	* @return the first atom, return NULL if there is not cut off group in this molecule
141	* @param i iteraotr
142	*/
143	Atom* beginAtom(std::vector<Atom*>::iterator& i);
144
145	Atom* nextAtom(std::vector<Atom*>::iterator& i);
146
147	/**
148	* Returns the first bond in this molecule and initialize the iterator.
149	* @return the first bond, return NULL if there is not cut off group in this molecule
150	* @param i iteraotr
151	*/
152	Bond* beginBond(std::vector<Bond*>::iterator& i);
153
154	Bond* nextBond(std::vector<Bond*>::iterator& i);
155
156	/**
157	* Returns the first bend in this molecule and initialize the iterator.
158	* @return the first bend, return NULL if there is not cut off group in this molecule
159	* @param i iteraotr
160	*/
161	Bend* beginBend(std::vector<Bend*>::iterator& i);
162
163	Bend* nextBend(std::vector<Bend*>::iterator& i);
164
165	/**
166	* Returns the first torsion in this molecule and initialize the iterator.
167	* @return the first torsion, return NULL if there is not cut off group in this molecule
168	* @param i iteraotr
169	*/
170	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i);
171	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i);
172
173	/**
174	* Returns the first rigid body in this molecule and initialize the iterator.
175	* @return the first rigid body, return NULL if there is not cut off group in this molecule
176	* @param i iteraotr
177	*/
178	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i);
179
180	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i);
181
182	/**
183	* Returns the first integrable object in this molecule and initialize the iterator.
184	* @return the first integrable object, return NULL if there is not cut off group in this molecule
185	* @param i iteraotr
186	*/
187	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i);
188
189	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i);
190
191	/**
192	* Returns the first cutoff group in this molecule and initialize the iterator.
193	* @return the first cutoff group, return NULL if there is not cut off group in this molecule
194	* @param i iteraotr
195	*/
196	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
197
198	/**
199	* Returns next cutoff group based on the iterator
200	* @return next cutoff group
201	* @param i
202	*/
203	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
204
205	//void setStampID( int info ) {stampID = info;}
206
207	void calcForces( void );
208
209	void atoms2rigidBodies( void );
210
211	/** return the total potential energy of short range interaction of this molecule */
212	double getPotential();
213
214
215	/** return the center of mass of this molecule */
216	Vector3d getCom();
217
218	/** Moves the center of this molecule */
219	void moveCom(const Vector3d& delta);
220
221	/** Returns the velocity of center of mass of this molecule */
222	Vector3d getComVel();
223
224	/** Returns the total mass of this molecule */
225	double getTotalMass();
226
227	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
228
229	private:
230	int localIndex_;
231	int globalIndex_;
232
233	std::vector<Atom*> atoms_;
234	std::vector<Bond*> bonds_;
235	std::vector<Bend*> bends_;
236	std::vector<Torsion*> torsions_;
237	std::vector<RigidBody*> rigidBodies_;
238	std::vector<StuntDouble*> integrableObjects_;
239	std::vector<CutoffGroup*> cutoffGroups_;
240	};
241
242	} //namespace oopse
243	#endif //