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 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);
        

        /** return the total potential energy of short range interaction of this molecule */
        double getPotential();

        /** get total mass of this molecule */        
        double getMass();

        /** 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:	1843
Committed:	Fri Dec 3 21:30:30 2004 UTC (19 years, 7 months ago) by tim
File size:	9269 byte(s)
Log Message:	more missing function get implemented
#	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/CutoffGroup.hpp"
45
46	namespace oopse{
47
48	class Constraint;
49
50	/**
51	* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
52	* @brief
53	*/
54	class Molecule {
55	public:
56
57	typedef std::vector<Atom*>::iterator AtomIterator;
58	typedef std::vector<Bond*>::iterator BondIterator;
59	typedef std::vector<Bend*>::iterator BendIterator;
60	typedef std::vector<Torsion*>::iterator TorsionIterator;
61	typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
62	typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
63	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
64
65	Molecule(int stampId, int globalIndex, const std::string& molName);
66	virtual ~Molecule();
67
68	/**
69	* Returns the global index of this molecule.
70	* @return the global index of this molecule
71	*/
72	int getGlobalIndex() {
73	return globalIndex_;
74	}
75
76	/**
77	* Returns the stamp id of this molecule
78	* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
79	* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
80	*/
81	int getStampId() {
82	return stampId_;
83	}
84
85	/** Returns the name of the molecule */
86	std::string getType() {
87	return moleculeName_;
88	}
89
90	/**
91	* Sets the global index of this molecule.
92	* @param new global index to be set
93	*/
94	int setGlobalIndex(int index) {
95	return globalIndex_;
96	}
97
98
99	/** add an atom into this molecule */
100	void addAtom(Atom* atom);
101
102	/** add a bond into this molecule */
103	void addBond(Bond* bond);
104
105	/** add a bend into this molecule */
106	void addBend(Bend* bend);
107
108	/** add a torsion into this molecule*/
109	void addTorsion(Torsion* torsion);
110
111	/** add a rigidbody into this molecule */
112	void addRigidBody(RigidBody *rb);
113
114	/** add a cutoff group into this molecule */
115	void addCutoffGroup(CutoffGroup* cp);
116
117	/** */
118	void complete();
119
120	/** Returns the total number of atoms in this molecule */
121	unsigned int getNAtoms() {
122	return atoms_.size();
123	}
124
125	/** Returns the total number of bonds in this molecule */
126	unsigned int getNBonds(){
127	return bonds_.size();
128	}
129
130	/** Returns the total number of bends in this molecule */
131	unsigned int getNBends() {
132	return bends_.size();
133	}
134
135	/** Returns the total number of torsions in this molecule */
136	unsigned int getNTorsions() {
137	return torsions_.size();
138	}
139
140	/** Returns the total number of rigid bodies in this molecule */
141	unsigned int getNRigidBodies() {
142	return rigidBodies_.size();
143	}
144
145	/** Returns the total number of integrable objects in this molecule */
146	unsigned int getNIntegrableObjects() {
147	return integrableObjects_.size();
148	}
149
150	/** Returns the total number of cutoff groups in this molecule */
151	unsigned int getNCutoffGroups() {
152	return cutoffGroups_.size();
153	}
154
155	/** Returns the total number of constraints in this molecule */
156	unsigned int getNConstraints() {
157	return constraints_.size();
158	}
159
160	Atom* getAtomAt(unsigned int i) {
161	assert(i < atoms_.size());
162	return atoms_[i];
163	}
164	/**
165	* Returns the first atom in this molecule and initialize the iterator.
166	* @return the first atom, return NULL if there is not cut off group in this molecule
167	* @param i iteraotr
168	*/
169	Atom* beginAtom(std::vector<Atom*>::iterator& i);
170
171	Atom* nextAtom(std::vector<Atom*>::iterator& i);
172
173	/**
174	* Returns the first bond in this molecule and initialize the iterator.
175	* @return the first bond, return NULL if there is not cut off group in this molecule
176	* @param i iteraotr
177	*/
178	Bond* beginBond(std::vector<Bond*>::iterator& i);
179
180	Bond* nextBond(std::vector<Bond*>::iterator& i);
181
182	/**
183	* Returns the first bend in this molecule and initialize the iterator.
184	* @return the first bend, return NULL if there is not cut off group in this molecule
185	* @param i iteraotr
186	*/
187	Bend* beginBend(std::vector<Bend*>::iterator& i);
188
189	Bend* nextBend(std::vector<Bend*>::iterator& i);
190
191	/**
192	* Returns the first torsion in this molecule and initialize the iterator.
193	* @return the first torsion, return NULL if there is not cut off group in this molecule
194	* @param i iteraotr
195	*/
196	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i);
197	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i);
198
199	/**
200	* Returns the first rigid body in this molecule and initialize the iterator.
201	* @return the first rigid body, return NULL if there is not cut off group in this molecule
202	* @param i iteraotr
203	*/
204	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i);
205
206	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i);
207
208	/**
209	* Returns the first integrable object in this molecule and initialize the iterator.
210	* @return the first integrable object, return NULL if there is not cut off group in this molecule
211	* @param i iteraotr
212	*/
213	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i);
214
215	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i);
216
217	/**
218	* Returns the first cutoff group in this molecule and initialize the iterator.
219	* @return the first cutoff group, return NULL if there is not cut off group in this molecule
220	* @param i iteraotr
221	*/
222	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
223
224	/**
225	* Returns next cutoff group based on the iterator
226	* @return next cutoff group
227	* @param i
228	*/
229	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
230
231	Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
232
233	Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
234
235
236	/** return the total potential energy of short range interaction of this molecule */
237	double getPotential();
238
239	/** get total mass of this molecule */
240	double getMass();
241
242	/** return the center of mass of this molecule */
243	Vector3d getCom();
244
245	/** Moves the center of this molecule */
246	void moveCom(const Vector3d& delta);
247
248	/** Returns the velocity of center of mass of this molecule */
249	Vector3d getComVel();
250
251	/** Returns the total mass of this molecule */
252	double getTotalMass();
253
254	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
255
256	private:
257
258	int globalIndex_;
259
260	std::vector<Atom*> atoms_;
261	std::vector<Bond*> bonds_;
262	std::vector<Bend*> bends_;
263	std::vector<Torsion*> torsions_;
264	std::vector<RigidBody*> rigidBodies_;
265	std::vector<StuntDouble*> integrableObjects_;
266	std::vector<CutoffGroup*> cutoffGroups_;
267	std::vector<Constraint*> constraints_;
268
269	int stampId_;
270	std::string moleculeName_;
271	};
272
273	} //namespace oopse
274	#endif //