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, 10 months ago) by tim
File size:	8341 byte(s)
Log Message:	adding SimModel(something similar as SimInfo)
#	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	tim	1695	#include "primitives/Bond.hpp"
42			#include "primitives/Bend.hpp"
43			#include "primitives/Torsion.hpp"
44			#include "primitives/CutoffGroup.hpp"
45	gezelter	1490
46	tim	1692	namespace oopse{
47	gezelter	1490
48	tim	1692	/**
49			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
50			* @brief
51			*/
52			class Molecule {
53			public:
54	gezelter	1490
55	tim	1692	Molecule();
56			virtual ~Molecule();
57	gezelter	1490
58	tim	1692	/**
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	gezelter	1490
66	tim	1692	/**
67			* Sets the global index of this molecule.
68			* @param new global index to be set
69			*/
70	tim	1695	int setGlobalIndex(int index) {
71	tim	1692	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	gezelter	1490
82	tim	1692	/** add an atom into this molecule */
83			void addAtom(Atom* atom);
84	gezelter	1490
85	tim	1692	/** add a bond into this molecule */
86			void addBond(Bond* bond);
87	gezelter	1490
88	tim	1692	/** add a bend into this molecule */
89			void addBend(Bend* bend);
90	gezelter	1490
91	tim	1692	/** add a torsion into this molecule*/
92			void addTorsion(Torsion* torsion);
93	gezelter	1490
94	tim	1692	/** add a rigidbody into this molecule */
95			void addRigidBody(RigidBody *rb);
96	gezelter	1490
97	tim	1692	/** add a cutoff group into this molecule */
98			void addCutoffGroup(CutoffGroup* cp);
99	gezelter	1490
100	tim	1692	/** */
101			void complete();
102	gezelter	1490
103	tim	1692	/** Returns the total number of atoms in this molecule */
104			unsigned int getNAtoms() {
105			return atoms_.size();
106			}
107	gezelter	1490
108	tim	1692	/** Returns the total number of bonds in this molecule */
109			unsigned int getNBonds(){
110			return bonds_.size();
111			}
112	gezelter	1490
113	tim	1692	/** Returns the total number of bends in this molecule */
114			unsigned int getNBends() {
115			return bends_.size();
116			}
117	gezelter	1490
118	tim	1692	/** Returns the total number of torsions in this molecule */
119			unsigned int getNTorsions() {
120			return torsions_.size();
121			}
122	gezelter	1490
123	tim	1692	/** Returns the total number of rigid bodies in this molecule */
124			unsigned int getNRigidBodies() {
125			return rigidBodies_.size();
126			}
127	gezelter	1490
128	tim	1692	/** 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	tim	1696	/** Returns the total number of constraints in this molecule */
139			unsigned int getNConstraints() {
140			return constraints_.size();
141			}
142
143	tim	1692	/**
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	tim	1696	Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
211
212			Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
213
214	tim	1692	//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	tim	1695	void moveCom(const Vector3d& delta);
229	tim	1692
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	tim	1695	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
237	tim	1692
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	tim	1696	std::vector<Constraint*> constraints_;
250	gezelter	1490	};
251
252	tim	1692	} //namespace oopse
253			#endif //