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, 8 months ago) by tim
File size:	7833 byte(s)
Log Message:	break, break and break.....
#	User	Rev	Content
1	tim	1692	/*
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	gezelter	1490
26	tim	1692	/**
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	gezelter	1490	#include <vector>
36	tim	1692	#include <iostream>
37	gezelter	1490
38	tim	1692	#include "math/Vector3.hpp"
39	tim	1492	#include "primitives/Atom.hpp"
40			#include "primitives/RigidBody.hpp"
41	gezelter	1490
42	tim	1692	namespace oopse{
43	gezelter	1490
44	tim	1692	/**
45			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
46			* @brief
47			*/
48			class Molecule {
49			public:
50	gezelter	1490
51	tim	1692	Molecule();
52			virtual ~Molecule();
53	gezelter	1490
54	tim	1692	/**
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	gezelter	1490
62	tim	1692	/**
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	gezelter	1490
78	tim	1692	/** add an atom into this molecule */
79			void addAtom(Atom* atom);
80	gezelter	1490
81	tim	1692	/** add a bond into this molecule */
82			void addBond(Bond* bond);
83	gezelter	1490
84	tim	1692	/** add a bend into this molecule */
85			void addBend(Bend* bend);
86	gezelter	1490
87	tim	1692	/** add a torsion into this molecule*/
88			void addTorsion(Torsion* torsion);
89	gezelter	1490
90	tim	1692	/** add a rigidbody into this molecule */
91			void addRigidBody(RigidBody *rb);
92	gezelter	1490
93	tim	1692	/** add a cutoff group into this molecule */
94			void addCutoffGroup(CutoffGroup* cp);
95	gezelter	1490
96	tim	1692	/** */
97			void complete();
98	gezelter	1490
99	tim	1692	/** Returns the total number of atoms in this molecule */
100			unsigned int getNAtoms() {
101			return atoms_.size();
102			}
103	gezelter	1490
104	tim	1692	/** Returns the total number of bonds in this molecule */
105			unsigned int getNBonds(){
106			return bonds_.size();
107			}
108	gezelter	1490
109	tim	1692	/** Returns the total number of bends in this molecule */
110			unsigned int getNBends() {
111			return bends_.size();
112			}
113	gezelter	1490
114	tim	1692	/** Returns the total number of torsions in this molecule */
115			unsigned int getNTorsions() {
116			return torsions_.size();
117			}
118	gezelter	1490
119	tim	1692	/** Returns the total number of rigid bodies in this molecule */
120			unsigned int getNRigidBodies() {
121			return rigidBodies_.size();
122			}
123	gezelter	1490
124	tim	1692	/** 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	gezelter	1490	};
237
238	tim	1692	} //namespace oopse
239			#endif //