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);
        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_;
        }

        /** 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;
};

} //namespace oopse
#endif //
Revision:	1725
Committed:	Wed Nov 10 22:01:06 2004 UTC (19 years, 7 months ago) by tim
File size:	8803 byte(s)
Log Message:	another painful day (1) SimCreator, SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom File will be removed) (3) ForceField (at least LJ) and BondType, BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
#	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	1701	//#include "primitives/Bond.hpp"
42			//#include "primitives/Bend.hpp"
43			//#include "primitives/Torsion.hpp"
44			#include "primitives/SRI.hpp"
45	tim	1695	#include "primitives/CutoffGroup.hpp"
46	gezelter	1490
47	tim	1692	namespace oopse{
48	gezelter	1490
49	tim	1701	class Constraint;
50
51	tim	1692	/**
52			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
53			* @brief
54			*/
55			class Molecule {
56			public:
57	gezelter	1490
58	tim	1725	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	tim	1719	Molecule(int stampId, int globalIndex);
67	tim	1692	virtual ~Molecule();
68	gezelter	1490
69	tim	1692	/**
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	gezelter	1490
77	tim	1692	/**
78			* Sets the global index of this molecule.
79			* @param new global index to be set
80			*/
81	tim	1695	int setGlobalIndex(int index) {
82	tim	1692	return globalIndex_;
83			}
84	gezelter	1490
85	tim	1692	/** add an atom into this molecule */
86			void addAtom(Atom* atom);
87	gezelter	1490
88	tim	1692	/** add a bond into this molecule */
89			void addBond(Bond* bond);
90	gezelter	1490
91	tim	1692	/** add a bend into this molecule */
92			void addBend(Bend* bend);
93	gezelter	1490
94	tim	1692	/** add a torsion into this molecule*/
95			void addTorsion(Torsion* torsion);
96	gezelter	1490
97	tim	1692	/** add a rigidbody into this molecule */
98			void addRigidBody(RigidBody *rb);
99	gezelter	1490
100	tim	1692	/** add a cutoff group into this molecule */
101			void addCutoffGroup(CutoffGroup* cp);
102	gezelter	1490
103	tim	1692	/** */
104			void complete();
105	gezelter	1490
106	tim	1692	/** Returns the total number of atoms in this molecule */
107			unsigned int getNAtoms() {
108			return atoms_.size();
109			}
110	gezelter	1490
111	tim	1692	/** Returns the total number of bonds in this molecule */
112			unsigned int getNBonds(){
113			return bonds_.size();
114			}
115	gezelter	1490
116	tim	1692	/** Returns the total number of bends in this molecule */
117			unsigned int getNBends() {
118			return bends_.size();
119			}
120	gezelter	1490
121	tim	1692	/** Returns the total number of torsions in this molecule */
122			unsigned int getNTorsions() {
123			return torsions_.size();
124			}
125	gezelter	1490
126	tim	1692	/** Returns the total number of rigid bodies in this molecule */
127			unsigned int getNRigidBodies() {
128			return rigidBodies_.size();
129			}
130	gezelter	1490
131	tim	1692	/** 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	tim	1696	/** Returns the total number of constraints in this molecule */
142			unsigned int getNConstraints() {
143			return constraints_.size();
144			}
145	tim	1719
146			Atom* getAtomAt(unsigned int i) {
147			assert(i < atoms_.size());
148			return atoms_[i];
149			}
150	tim	1692	/**
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	tim	1696	Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
218
219			Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
220
221	tim	1692	//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	tim	1695	void moveCom(const Vector3d& delta);
236	tim	1692
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	tim	1695	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
244	tim	1692
245			private:
246	tim	1725
247	tim	1692	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	tim	1696	std::vector<Constraint*> constraints_;
257	tim	1713
258			int stampID;
259	gezelter	1490	};
260
261	tim	1692	} //namespace oopse
262			#endif //