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:	1686
Committed:	Fri Oct 29 20:54:04 2004 UTC (19 years, 8 months ago) by tim
File size:	7161 byte(s)
Log Message:	rewrite Molecule class.
#	User	Rev	Content
1	tim	1686	/*
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 //