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();


        /** 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:	1782
Committed:	Wed Nov 24 20:55:03 2004 UTC (19 years, 7 months ago) by tim
File size:	9188 byte(s)
Log Message:	types and primitives get built
#	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	1782	#include "primitives/Bond.hpp"
42			#include "primitives/Bend.hpp"
43			#include "primitives/Torsion.hpp"
44	tim	1695	#include "primitives/CutoffGroup.hpp"
45	gezelter	1490
46	tim	1692	namespace oopse{
47	gezelter	1490
48	tim	1701	class Constraint;
49
50	tim	1692	/**
51			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
52			* @brief
53			*/
54			class Molecule {
55			public:
56	gezelter	1490
57	tim	1725	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	tim	1733	Molecule(int stampId, int globalIndex, const std::string& molName);
66	tim	1692	virtual ~Molecule();
67	gezelter	1490
68	tim	1692	/**
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	gezelter	1490
76	tim	1692	/**
77	tim	1733	* 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	tim	1692	* Sets the global index of this molecule.
92			* @param new global index to be set
93			*/
94	tim	1695	int setGlobalIndex(int index) {
95	tim	1692	return globalIndex_;
96			}
97	gezelter	1490
98	tim	1733
99	tim	1692	/** add an atom into this molecule */
100			void addAtom(Atom* atom);
101	gezelter	1490
102	tim	1692	/** add a bond into this molecule */
103			void addBond(Bond* bond);
104	gezelter	1490
105	tim	1692	/** add a bend into this molecule */
106			void addBend(Bend* bend);
107	gezelter	1490
108	tim	1692	/** add a torsion into this molecule*/
109			void addTorsion(Torsion* torsion);
110	gezelter	1490
111	tim	1692	/** add a rigidbody into this molecule */
112			void addRigidBody(RigidBody *rb);
113	gezelter	1490
114	tim	1692	/** add a cutoff group into this molecule */
115			void addCutoffGroup(CutoffGroup* cp);
116	gezelter	1490
117	tim	1692	/** */
118			void complete();
119	gezelter	1490
120	tim	1692	/** Returns the total number of atoms in this molecule */
121			unsigned int getNAtoms() {
122			return atoms_.size();
123			}
124	gezelter	1490
125	tim	1692	/** Returns the total number of bonds in this molecule */
126			unsigned int getNBonds(){
127			return bonds_.size();
128			}
129	gezelter	1490
130	tim	1692	/** Returns the total number of bends in this molecule */
131			unsigned int getNBends() {
132			return bends_.size();
133			}
134	gezelter	1490
135	tim	1692	/** Returns the total number of torsions in this molecule */
136			unsigned int getNTorsions() {
137			return torsions_.size();
138			}
139	gezelter	1490
140	tim	1692	/** Returns the total number of rigid bodies in this molecule */
141			unsigned int getNRigidBodies() {
142			return rigidBodies_.size();
143			}
144	gezelter	1490
145	tim	1692	/** 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	tim	1696	/** Returns the total number of constraints in this molecule */
156			unsigned int getNConstraints() {
157			return constraints_.size();
158			}
159	tim	1719
160			Atom* getAtomAt(unsigned int i) {
161			assert(i < atoms_.size());
162			return atoms_[i];
163			}
164	tim	1692	/**
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	tim	1696	Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
232
233			Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
234
235	tim	1692
236			/** return the total potential energy of short range interaction of this molecule */
237			double getPotential();
238
239
240			/** return the center of mass of this molecule */
241			Vector3d getCom();
242
243			/** Moves the center of this molecule */
244	tim	1695	void moveCom(const Vector3d& delta);
245	tim	1692
246			/** Returns the velocity of center of mass of this molecule */
247			Vector3d getComVel();
248
249			/** Returns the total mass of this molecule */
250			double getTotalMass();
251
252	tim	1695	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
253	tim	1692
254			private:
255	tim	1725
256	tim	1692	int globalIndex_;
257
258			std::vector<Atom*> atoms_;
259			std::vector<Bond*> bonds_;
260			std::vector<Bend*> bends_;
261			std::vector<Torsion*> torsions_;
262			std::vector<RigidBody*> rigidBodies_;
263			std::vector<StuntDouble*> integrableObjects_;
264			std::vector<CutoffGroup*> cutoffGroups_;
265	tim	1696	std::vector<Constraint*> constraints_;
266	tim	1713
267	tim	1733	int stampId_;
268			std::string moleculeName_;
269	gezelter	1490	};
270
271	tim	1692	} //namespace oopse
272			#endif //