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/SRI.hpp"
#include "primitives/CutoffGroup.hpp"

namespace oopse{

class Constraint;

/**
 * @class Molecule Molecule.hpp "primitives/Molecule.hpp"
 * @brief
 */
class Molecule {
    public:

        Molecule(int stampId, int globalIndex);
        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();
        }

        Atom* getAtomAt(unsigned int i) {
            assert(i < atoms_.size());
            return atoms_[i];
        }
        /**
         * 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_;

        int stampID;
};

} //namespace oopse
#endif //
Revision:	1719
Committed:	Fri Nov 5 23:38:27 2004 UTC (19 years, 8 months ago) by tim
File size:	8559 byte(s)
Log Message:	Fix Exclude class etc.
#	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/SRI.hpp"
45	#include "primitives/CutoffGroup.hpp"
46
47	namespace oopse{
48
49	class Constraint;
50
51	/**
52	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
53	* @brief
54	*/
55	class Molecule {
56	public:
57
58	Molecule(int stampId, int globalIndex);
59	virtual ~Molecule();
60
61	/**
62	* Returns the global index of this molecule.
63	* @return the global index of this molecule
64	*/
65	int getGlobalIndex() {
66	return globalIndex_;
67	}
68
69	/**
70	* Sets the global index of this molecule.
71	* @param new global index to be set
72	*/
73	int setGlobalIndex(int index) {
74	return globalIndex_;
75	}
76
77	/**
78	* Returns the local index of this molecule
79	* @return the local index of this molecule
80	*/
81	int getLocalIndex() {
82	return localIndex_;
83	}
84
85	/** add an atom into this molecule */
86	void addAtom(Atom* atom);
87
88	/** add a bond into this molecule */
89	void addBond(Bond* bond);
90
91	/** add a bend into this molecule */
92	void addBend(Bend* bend);
93
94	/** add a torsion into this molecule*/
95	void addTorsion(Torsion* torsion);
96
97	/** add a rigidbody into this molecule */
98	void addRigidBody(RigidBody *rb);
99
100	/** add a cutoff group into this molecule */
101	void addCutoffGroup(CutoffGroup* cp);
102
103	/** */
104	void complete();
105
106	/** Returns the total number of atoms in this molecule */
107	unsigned int getNAtoms() {
108	return atoms_.size();
109	}
110
111	/** Returns the total number of bonds in this molecule */
112	unsigned int getNBonds(){
113	return bonds_.size();
114	}
115
116	/** Returns the total number of bends in this molecule */
117	unsigned int getNBends() {
118	return bends_.size();
119	}
120
121	/** Returns the total number of torsions in this molecule */
122	unsigned int getNTorsions() {
123	return torsions_.size();
124	}
125
126	/** Returns the total number of rigid bodies in this molecule */
127	unsigned int getNRigidBodies() {
128	return rigidBodies_.size();
129	}
130
131	/** Returns the total number of integrable objects in this molecule */
132	unsigned int getNIntegrableObjects() {
133	return integrableObjects_.size();
134	}
135
136	/** Returns the total number of cutoff groups in this molecule */
137	unsigned int getNCutoffGroups() {
138	return cutoffGroups_.size();
139	}
140
141	/** Returns the total number of constraints in this molecule */
142	unsigned int getNConstraints() {
143	return constraints_.size();
144	}
145
146	Atom* getAtomAt(unsigned int i) {
147	assert(i < atoms_.size());
148	return atoms_[i];
149	}
150	/**
151	* Returns the first atom in this molecule and initialize the iterator.
152	* @return the first atom, return NULL if there is not cut off group in this molecule
153	* @param i iteraotr
154	*/
155	Atom* beginAtom(std::vector<Atom*>::iterator& i);
156
157	Atom* nextAtom(std::vector<Atom*>::iterator& i);
158
159	/**
160	* Returns the first bond in this molecule and initialize the iterator.
161	* @return the first bond, return NULL if there is not cut off group in this molecule
162	* @param i iteraotr
163	*/
164	Bond* beginBond(std::vector<Bond*>::iterator& i);
165
166	Bond* nextBond(std::vector<Bond*>::iterator& i);
167
168	/**
169	* Returns the first bend in this molecule and initialize the iterator.
170	* @return the first bend, return NULL if there is not cut off group in this molecule
171	* @param i iteraotr
172	*/
173	Bend* beginBend(std::vector<Bend*>::iterator& i);
174
175	Bend* nextBend(std::vector<Bend*>::iterator& i);
176
177	/**
178	* Returns the first torsion in this molecule and initialize the iterator.
179	* @return the first torsion, return NULL if there is not cut off group in this molecule
180	* @param i iteraotr
181	*/
182	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i);
183	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i);
184
185	/**
186	* Returns the first rigid body in this molecule and initialize the iterator.
187	* @return the first rigid body, return NULL if there is not cut off group in this molecule
188	* @param i iteraotr
189	*/
190	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i);
191
192	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i);
193
194	/**
195	* Returns the first integrable object in this molecule and initialize the iterator.
196	* @return the first integrable object, return NULL if there is not cut off group in this molecule
197	* @param i iteraotr
198	*/
199	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i);
200
201	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i);
202
203	/**
204	* Returns the first cutoff group in this molecule and initialize the iterator.
205	* @return the first cutoff group, return NULL if there is not cut off group in this molecule
206	* @param i iteraotr
207	*/
208	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
209
210	/**
211	* Returns next cutoff group based on the iterator
212	* @return next cutoff group
213	* @param i
214	*/
215	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
216
217	Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
218
219	Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
220
221	//void setStampID( int info ) {stampID = info;}
222
223	void calcForces( void );
224
225	void atoms2rigidBodies( void );
226
227	/** return the total potential energy of short range interaction of this molecule */
228	double getPotential();
229
230
231	/** return the center of mass of this molecule */
232	Vector3d getCom();
233
234	/** Moves the center of this molecule */
235	void moveCom(const Vector3d& delta);
236
237	/** Returns the velocity of center of mass of this molecule */
238	Vector3d getComVel();
239
240	/** Returns the total mass of this molecule */
241	double getTotalMass();
242
243	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
244
245	private:
246	int localIndex_;
247	int globalIndex_;
248
249	std::vector<Atom*> atoms_;
250	std::vector<Bond*> bonds_;
251	std::vector<Bend*> bends_;
252	std::vector<Torsion*> torsions_;
253	std::vector<RigidBody*> rigidBodies_;
254	std::vector<StuntDouble*> integrableObjects_;
255	std::vector<CutoffGroup*> cutoffGroups_;
256	std::vector<Constraint*> constraints_;
257
258	int stampID;
259	};
260
261	} //namespace oopse
262	#endif //