test/brains/Molecule.hpp

/*
 * Copyright (C) 2000-2009  The Open Molecular Dynamics Engine (OpenMD) project
 * 
 * Contact: gezelter@openscience.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"

namespace OpenMD{

/**
 * @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 OpenMD
#endif //
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/test/brains/Molecule.hpp*
File size:	7768 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	Content
1	/*
2	* Copyright (C) 2000-2009 The Open Molecular Dynamics Engine (OpenMD) project
3	*
4	* Contact: gezelter@openscience.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	#include "math/Vector3.hpp"
38
39	namespace OpenMD{
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	/** add an atom into this molecule */
76	void addAtom(Atom* atom);
77
78	/** add a bond into this molecule */
79	void addBond(Bond* bond);
80
81	/** add a bend into this molecule */
82	void addBend(Bend* bend);
83
84	/** add a torsion into this molecule*/
85	void addTorsion(Torsion* torsion);
86
87	/** add a rigidbody into this molecule */
88	void addRigidBody(RigidBody *rb);
89
90	/** add a cutoff group into this molecule */
91	void addCutoffGroup(CutoffGroup* cp)
92
93	/** */
94	void complete();
95
96	/** Returns the total number of atoms in this molecule */
97	unsigned int getNAtoms() {
98	return atoms_.size();
99	}
100
101	/** Returns the total number of bonds in this molecule */
102	unsigned int getNBonds(){
103	return bonds_.size();
104	}
105
106	/** Returns the total number of bends in this molecule */
107	unsigned int getNBends() {
108	return bends_.size();
109	}
110
111	/** Returns the total number of torsions in this molecule */
112	unsigned int getNTorsions() {
113	return torsions_.size();
114	}
115
116	/** Returns the total number of rigid bodies in this molecule */
117	unsigned int getNRigidBodies() {
118	return rigidBodies_.size();
119	}
120
121	/** Returns the total number of integrable objects in this molecule */
122	unsigned int getNIntegrableObjects() {
123	return integrableObjects_.size();
124	}
125
126	/** Returns the total number of cutoff groups in this molecule */
127	unsigned int getNCutoffGroups() {
128	return cutoffGroups_.size();
129	}
130
131	/**
132	* Returns the first atom in this molecule and initialize the iterator.
133	* @return the first atom, return NULL if there is not cut off group in this molecule
134	* @param i iteraotr
135	*/
136	Atom* beginAtom(std::vector<Atom*>::iterator& i);
137
138	Atom* nextAtom(std::vector<Atom*>::iterator& i);
139
140	/**
141	* Returns the first bond in this molecule and initialize the iterator.
142	* @return the first bond, return NULL if there is not cut off group in this molecule
143	* @param i iteraotr
144	*/
145	Bond* beginBond(std::vector<Bond*>::iterator& i);
146
147	Bond* nextBond(std::vector<Bond*>::iterator& i);
148
149	/**
150	* Returns the first bend in this molecule and initialize the iterator.
151	* @return the first bend, return NULL if there is not cut off group in this molecule
152	* @param i iteraotr
153	*/
154	Bend* beginBend(std::vector<Bend*>::iterator& i);
155
156	Bend* nextBend(std::vector<Bend*>::iterator& i);
157
158	/**
159	* Returns the first torsion in this molecule and initialize the iterator.
160	* @return the first torsion, return NULL if there is not cut off group in this molecule
161	* @param i iteraotr
162	*/
163	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i);
164	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i);
165
166	/**
167	* Returns the first rigid body in this molecule and initialize the iterator.
168	* @return the first rigid body, return NULL if there is not cut off group in this molecule
169	* @param i iteraotr
170	*/
171	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i);
172
173	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i);
174
175	/**
176	* Returns the first integrable object in this molecule and initialize the iterator.
177	* @return the first integrable object, return NULL if there is not cut off group in this molecule
178	* @param i iteraotr
179	*/
180	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i);
181
182	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i);
183
184	/**
185	* Returns the first cutoff group in this molecule and initialize the iterator.
186	* @return the first cutoff group, return NULL if there is not cut off group in this molecule
187	* @param i iteraotr
188	*/
189	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
190
191	/**
192	* Returns next cutoff group based on the iterator
193	* @return next cutoff group
194	* @param i
195	*/
196	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
197
198	//void setStampID( int info ) {stampID = info;}
199
200	void calcForces( void );
201
202	void atoms2rigidBodies( void );
203
204	/** return the total potential energy of short range interaction of this molecule */
205	double getPotential();
206
207
208	/** return the center of mass of this molecule */
209	Vector3d getCom();
210
211	/** Moves the center of this molecule */
212	void moveCom(const Vetor3d& delta);
213
214	/** Returns the velocity of center of mass of this molecule */
215	Vector3d getComVel();
216
217	/** Returns the total mass of this molecule */
218	double getTotalMass();
219
220	friend std::ostream& operator <<(std::ostream& o, const Molecule& mol);
221
222	private:
223	int localIndex_;
224	int globalIndex_;
225
226	std::vector<Atom*> atoms_;
227	std::vector<Bond*> bonds_;
228	std::vector<Bend*> bends_;
229	std::vector<Torsion*> torsions_;
230	std::vector<RigidBody*> rigidBodies_;
231	std::vector<StuntDouble*> integrableObjects_;
232	std::vector<CutoffGroup*> cutoffGroups_;
233	};
234
235	} //namespace OpenMD
236	#endif //