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:

        typedef std::vector<Atom*>::iterator AtomIterator;
        typedef std::vector<Bond*>::iterator BondIterator;
        typedef std::vector<Bend*>::iterator BendIterator;
        typedef std::vector<Torsion*>::iterator TorsionIterator;
        typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
        typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
        typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;        

        Molecule(int stampId, int globalIndex, const std::string& molName);
        virtual ~Molecule();

        /**
         * Returns the global index of this molecule.
         * @return  the global index of this molecule 
         */
        int getGlobalIndex() {
            return globalIndex_;
        }

        /**
         * Returns the stamp id of this molecule
         * @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
         * stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
         */
        int getStampId() {
            return stampId_;
        }

        /** Returns the name of the molecule */
        std::string getType() {
            return moleculeName_;
        }
        
        /**
         * Sets the global index of this molecule.
         * @param new global index to be set
         */
        int setGlobalIndex(int index) {
            return globalIndex_;
        }

        
        /** 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 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_;
        std::string moleculeName_;
};

} //namespace oopse
#endif //
Revision:	1733
Committed:	Fri Nov 12 06:19:04 2004 UTC (19 years, 7 months ago) by tim
File size:	9356 byte(s)
Log Message:	OOPSE = Object-Obfuscated Parallel Simulation Engine
#	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	typedef std::vector<Atom*>::iterator AtomIterator;
59	typedef std::vector<Bond*>::iterator BondIterator;
60	typedef std::vector<Bend*>::iterator BendIterator;
61	typedef std::vector<Torsion*>::iterator TorsionIterator;
62	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
63	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
64	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
65
66	Molecule(int stampId, int globalIndex, const std::string& molName);
67	virtual ~Molecule();
68
69	/**
70	* Returns the global index of this molecule.
71	* @return the global index of this molecule
72	*/
73	int getGlobalIndex() {
74	return globalIndex_;
75	}
76
77	/**
78	* Returns the stamp id of this molecule
79	* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
80	* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
81	*/
82	int getStampId() {
83	return stampId_;
84	}
85
86	/** Returns the name of the molecule */
87	std::string getType() {
88	return moleculeName_;
89	}
90
91	/**
92	* Sets the global index of this molecule.
93	* @param new global index to be set
94	*/
95	int setGlobalIndex(int index) {
96	return globalIndex_;
97	}
98
99
100	/** add an atom into this molecule */
101	void addAtom(Atom* atom);
102
103	/** add a bond into this molecule */
104	void addBond(Bond* bond);
105
106	/** add a bend into this molecule */
107	void addBend(Bend* bend);
108
109	/** add a torsion into this molecule*/
110	void addTorsion(Torsion* torsion);
111
112	/** add a rigidbody into this molecule */
113	void addRigidBody(RigidBody *rb);
114
115	/** add a cutoff group into this molecule */
116	void addCutoffGroup(CutoffGroup* cp);
117
118	/** */
119	void complete();
120
121	/** Returns the total number of atoms in this molecule */
122	unsigned int getNAtoms() {
123	return atoms_.size();
124	}
125
126	/** Returns the total number of bonds in this molecule */
127	unsigned int getNBonds(){
128	return bonds_.size();
129	}
130
131	/** Returns the total number of bends in this molecule */
132	unsigned int getNBends() {
133	return bends_.size();
134	}
135
136	/** Returns the total number of torsions in this molecule */
137	unsigned int getNTorsions() {
138	return torsions_.size();
139	}
140
141	/** Returns the total number of rigid bodies in this molecule */
142	unsigned int getNRigidBodies() {
143	return rigidBodies_.size();
144	}
145
146	/** Returns the total number of integrable objects in this molecule */
147	unsigned int getNIntegrableObjects() {
148	return integrableObjects_.size();
149	}
150
151	/** Returns the total number of cutoff groups in this molecule */
152	unsigned int getNCutoffGroups() {
153	return cutoffGroups_.size();
154	}
155
156	/** Returns the total number of constraints in this molecule */
157	unsigned int getNConstraints() {
158	return constraints_.size();
159	}
160
161	Atom* getAtomAt(unsigned int i) {
162	assert(i < atoms_.size());
163	return atoms_[i];
164	}
165	/**
166	* Returns the first atom in this molecule and initialize the iterator.
167	* @return the first atom, return NULL if there is not cut off group in this molecule
168	* @param i iteraotr
169	*/
170	Atom* beginAtom(std::vector<Atom*>::iterator& i);
171
172	Atom* nextAtom(std::vector<Atom*>::iterator& i);
173
174	/**
175	* Returns the first bond in this molecule and initialize the iterator.
176	* @return the first bond, return NULL if there is not cut off group in this molecule
177	* @param i iteraotr
178	*/
179	Bond* beginBond(std::vector<Bond*>::iterator& i);
180
181	Bond* nextBond(std::vector<Bond*>::iterator& i);
182
183	/**
184	* Returns the first bend in this molecule and initialize the iterator.
185	* @return the first bend, return NULL if there is not cut off group in this molecule
186	* @param i iteraotr
187	*/
188	Bend* beginBend(std::vector<Bend*>::iterator& i);
189
190	Bend* nextBend(std::vector<Bend*>::iterator& i);
191
192	/**
193	* Returns the first torsion in this molecule and initialize the iterator.
194	* @return the first torsion, return NULL if there is not cut off group in this molecule
195	* @param i iteraotr
196	*/
197	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i);
198	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i);
199
200	/**
201	* Returns the first rigid body in this molecule and initialize the iterator.
202	* @return the first rigid body, return NULL if there is not cut off group in this molecule
203	* @param i iteraotr
204	*/
205	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i);
206
207	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i);
208
209	/**
210	* Returns the first integrable object in this molecule and initialize the iterator.
211	* @return the first integrable object, return NULL if there is not cut off group in this molecule
212	* @param i iteraotr
213	*/
214	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i);
215
216	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i);
217
218	/**
219	* Returns the first cutoff group in this molecule and initialize the iterator.
220	* @return the first cutoff group, return NULL if there is not cut off group in this molecule
221	* @param i iteraotr
222	*/
223	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
224
225	/**
226	* Returns next cutoff group based on the iterator
227	* @return next cutoff group
228	* @param i
229	*/
230	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
231
232	Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
233
234	Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
235
236	//void setStampID( int info ) {stampID = info;}
237
238	void calcForces( void );
239
240	void atoms2rigidBodies( void );
241
242	/** return the total potential energy of short range interaction of this molecule */
243	double getPotential();
244
245
246	/** return the center of mass of this molecule */
247	Vector3d getCom();
248
249	/** Moves the center of this molecule */
250	void moveCom(const Vector3d& delta);
251
252	/** Returns the velocity of center of mass of this molecule */
253	Vector3d getComVel();
254
255	/** Returns the total mass of this molecule */
256	double getTotalMass();
257
258	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
259
260	private:
261
262	int globalIndex_;
263
264	std::vector<Atom*> atoms_;
265	std::vector<Bond*> bonds_;
266	std::vector<Bend*> bends_;
267	std::vector<Torsion*> torsions_;
268	std::vector<RigidBody*> rigidBodies_;
269	std::vector<StuntDouble*> integrableObjects_;
270	std::vector<CutoffGroup*> cutoffGroups_;
271	std::vector<Constraint*> constraints_;
272
273	int stampId_;
274	std::string moleculeName_;
275	};
276
277	} //namespace oopse
278	#endif //