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 total number of constraints in this molecule */
        unsigned int getNConstraints() {
            return constraints_.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);

        Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);

        Constraint* nextConstraint(std::vector<Constraint*>::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_;
        std::vector<Constraint*> constraints_;
};

} //namespace oopse
#endif //
Revision:	1696
Committed:	Tue Nov 2 15:23:46 2004 UTC (19 years, 8 months ago) by tim
File size:	8341 byte(s)
Log Message:	adding SimModel(something similar as SimInfo)
#	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	/** Returns the total number of constraints in this molecule */
139	unsigned int getNConstraints() {
140	return constraints_.size();
141	}
142
143	/**
144	* Returns the first atom in this molecule and initialize the iterator.
145	* @return the first atom, return NULL if there is not cut off group in this molecule
146	* @param i iteraotr
147	*/
148	Atom* beginAtom(std::vector<Atom*>::iterator& i);
149
150	Atom* nextAtom(std::vector<Atom*>::iterator& i);
151
152	/**
153	* Returns the first bond in this molecule and initialize the iterator.
154	* @return the first bond, return NULL if there is not cut off group in this molecule
155	* @param i iteraotr
156	*/
157	Bond* beginBond(std::vector<Bond*>::iterator& i);
158
159	Bond* nextBond(std::vector<Bond*>::iterator& i);
160
161	/**
162	* Returns the first bend in this molecule and initialize the iterator.
163	* @return the first bend, return NULL if there is not cut off group in this molecule
164	* @param i iteraotr
165	*/
166	Bend* beginBend(std::vector<Bend*>::iterator& i);
167
168	Bend* nextBend(std::vector<Bend*>::iterator& i);
169
170	/**
171	* Returns the first torsion in this molecule and initialize the iterator.
172	* @return the first torsion, return NULL if there is not cut off group in this molecule
173	* @param i iteraotr
174	*/
175	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i);
176	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i);
177
178	/**
179	* Returns the first rigid body in this molecule and initialize the iterator.
180	* @return the first rigid body, return NULL if there is not cut off group in this molecule
181	* @param i iteraotr
182	*/
183	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i);
184
185	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i);
186
187	/**
188	* Returns the first integrable object in this molecule and initialize the iterator.
189	* @return the first integrable object, return NULL if there is not cut off group in this molecule
190	* @param i iteraotr
191	*/
192	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i);
193
194	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i);
195
196	/**
197	* Returns the first cutoff group in this molecule and initialize the iterator.
198	* @return the first cutoff group, return NULL if there is not cut off group in this molecule
199	* @param i iteraotr
200	*/
201	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
202
203	/**
204	* Returns next cutoff group based on the iterator
205	* @return next cutoff group
206	* @param i
207	*/
208	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
209
210	Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
211
212	Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
213
214	//void setStampID( int info ) {stampID = info;}
215
216	void calcForces( void );
217
218	void atoms2rigidBodies( void );
219
220	/** return the total potential energy of short range interaction of this molecule */
221	double getPotential();
222
223
224	/** return the center of mass of this molecule */
225	Vector3d getCom();
226
227	/** Moves the center of this molecule */
228	void moveCom(const Vector3d& delta);
229
230	/** Returns the velocity of center of mass of this molecule */
231	Vector3d getComVel();
232
233	/** Returns the total mass of this molecule */
234	double getTotalMass();
235
236	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
237
238	private:
239	int localIndex_;
240	int globalIndex_;
241
242	std::vector<Atom*> atoms_;
243	std::vector<Bond*> bonds_;
244	std::vector<Bend*> bends_;
245	std::vector<Torsion*> torsions_;
246	std::vector<RigidBody*> rigidBodies_;
247	std::vector<StuntDouble*> integrableObjects_;
248	std::vector<CutoffGroup*> cutoffGroups_;
249	std::vector<Constraint*> constraints_;
250	};
251
252	} //namespace oopse
253	#endif //