test/brains/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 "math/Vector3.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_;
        }

        /** 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 ostream& operator <<(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:	192
Committed:	Fri Oct 29 20:54:04 2004 UTC (20 years, 11 months ago) by tim
File size:	7161 byte(s)
Log Message:	rewrite Molecule class.
#	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
37	#include "math/Vector3.hpp"
38
39	namespace oopse{
40
41	/**
42	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
43	* @brief
44	*/
45	class Molecule {
46	public:
47
48	Molecule();
49	virtual ~Molecule();
50
51	/**
52	* Returns the global index of this molecule.
53	* @return the global index of this molecule
54	*/
55	int getGlobalIndex() {
56	return globalIndex_;
57	}
58
59	/**
60	* Sets the global index of this molecule.
61	* @param new global index to be set
62	*/
63	void setGlobalIndex(int index) {
64	return globalIndex_;
65	}
66
67	/**
68	* Returns the local index of this molecule
69	* @return the local index of this molecule
70	*/
71	int getLocalIndex() {
72	return localIndex_;
73	}
74
75	/** Returns the total number of atoms in this molecule */
76	unsigned int getNAtoms() {
77	return atoms_.size();
78	}
79
80	/** Returns the total number of bonds in this molecule */
81	unsigned int getNBonds(){
82	return bonds_.size();
83	}
84
85	/** Returns the total number of bends in this molecule */
86	unsigned int getNBends() {
87	return bends_.size();
88	}
89
90	/** Returns the total number of torsions in this molecule */
91	unsigned int getNTorsions() {
92	return torsions_.size();
93	}
94
95	/** Returns the total number of rigid bodies in this molecule */
96	unsigned int getNRigidBodies() {
97	return rigidBodies_.size();
98	}
99
100	/** Returns the total number of integrable objects in this molecule */
101	unsigned int getNIntegrableObjects() {
102	return integrableObjects_.size();
103	}
104
105	/** Returns the total number of cutoff groups in this molecule */
106	unsigned int getNCutoffGroups() {
107	return cutoffGroups_.size();
108	}
109
110	/**
111	* Returns the first atom in this molecule and initialize the iterator.
112	* @return the first atom, return NULL if there is not cut off group in this molecule
113	* @param i iteraotr
114	*/
115	Atom* beginAtom(std::vector<Atom*>::iterator& i);
116
117	Atom* nextAtom(std::vector<Atom*>::iterator& i);
118
119	/**
120	* Returns the first bond in this molecule and initialize the iterator.
121	* @return the first bond, return NULL if there is not cut off group in this molecule
122	* @param i iteraotr
123	*/
124	Bond* beginBond(std::vector<Bond*>::iterator& i);
125
126	Bond* nextBond(std::vector<Bond*>::iterator& i);
127
128	/**
129	* Returns the first bend in this molecule and initialize the iterator.
130	* @return the first bend, return NULL if there is not cut off group in this molecule
131	* @param i iteraotr
132	*/
133	Bend* beginBend(std::vector<Bend*>::iterator& i);
134
135	Bend* nextBend(std::vector<Bend*>::iterator& i);
136
137	/**
138	* Returns the first torsion in this molecule and initialize the iterator.
139	* @return the first torsion, return NULL if there is not cut off group in this molecule
140	* @param i iteraotr
141	*/
142	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i);
143	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i);
144
145	/**
146	* Returns the first rigid body in this molecule and initialize the iterator.
147	* @return the first rigid body, return NULL if there is not cut off group in this molecule
148	* @param i iteraotr
149	*/
150	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i);
151
152	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i);
153
154	/**
155	* Returns the first integrable object in this molecule and initialize the iterator.
156	* @return the first integrable object, return NULL if there is not cut off group in this molecule
157	* @param i iteraotr
158	*/
159	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i);
160
161	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i);
162
163	/**
164	* Returns the first cutoff group in this molecule and initialize the iterator.
165	* @return the first cutoff group, return NULL if there is not cut off group in this molecule
166	* @param i iteraotr
167	*/
168	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
169
170	/**
171	* Returns next cutoff group based on the iterator
172	* @return next cutoff group
173	* @param i
174	*/
175	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
176
177	//void setStampID( int info ) {stampID = info;}
178
179	void calcForces( void );
180
181	void atoms2rigidBodies( void );
182
183	/** return the total potential energy of short range interaction of this molecule */
184	double getPotential();
185
186
187	/** return the center of mass of this molecule */
188	Vector3d getCom();
189
190	/** Moves the center of this molecule */
191	void moveCom(const Vetor3d& delta);
192
193	/** Returns the velocity of center of mass of this molecule */
194	Vector3d getComVel();
195
196	/** Returns the total mass of this molecule */
197	double getTotalMass();
198
199	friend ostream& operator <<(ostream& o, const Molecule& mol);
200
201	private:
202	int localIndex_;
203	int globalIndex_;
204
205	std::vector<Atom*> atoms_;
206	std::vector<Bond*> bonds_;
207	std::vector<Bend*> bends_;
208	std::vector<Torsion*> torsions_;
209	std::vector<RigidBody*> rigidBodies_;
210	std::vector<StuntDouble*> integrableObjects_;
211	std::vector<CutoffGroup*> cutoffGroups_;
212	};
213
214	} //namespace oopse
215	#endif //