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 "constraints/ConstraintPair.hpp"
#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;        
        typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
        typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
        

        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 addConstraintPair(ConstraintPair* consPair);
        
        void addConstraintElem(ConstraintElem* consElem);

        /** */
        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 getNConstraintPairs() {
            return constraintPairs_.size();
        }

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

        Atom* beginAtom(std::vector<Atom*>::iterator& i) {
            i = atoms_.begin();
            return (i == atoms_.end()) ? NULL : *i;
        }

        Atom* nextAtom(std::vector<Atom*>::iterator& i) {
            ++i;
            return (i == atoms_.end()) ? NULL : *i;    
        }

        Bond* beginBond(std::vector<Bond*>::iterator& i) {
            i = bonds_.begin();
            return (i == bonds_.end()) ? NULL : *i;
        }

        Bond* nextBond(std::vector<Bond*>::iterator& i) {
            ++i;
            return (i == bonds_.end()) ? NULL : *i;    

        }

        Bend* beginBend(std::vector<Bend*>::iterator& i) {
            i = bends_.begin();
            return (i == bends_.end()) ? NULL : *i;
        }

        Bend* nextBend(std::vector<Bend*>::iterator& i) {
            ++i;
            return (i == bends_.end()) ? NULL : *i;    
        }

        Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
            i = torsions_.begin();
            return (i == torsions_.end()) ? NULL : *i;
        }

        Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
            ++i;
            return (i == torsions_.end()) ? NULL : *i;    
        }    

        RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
            i = rigidBodies_.begin();
            return (i == rigidBodies_.end()) ? NULL : *i;
        }

        RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
            ++i;
            return (i == rigidBodies_.end()) ? NULL : *i;    
        }

        StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
            i = integrableObjects_.begin();
            return (i == integrableObjects_.end()) ? NULL : *i;
        }

        StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
            ++i;
            return (i == integrableObjects_.end()) ? NULL : *i;    
        }    

        CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
            i = cutoffGroups_.begin();
            return (i == cutoffGroups_.end()) ? NULL : *i;
        }

        CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {            
            ++i;
            return (i == cutoffGroups_.end()) ? NULL : *i;    
        } 

        ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
            i = constraintPairs_.begin();
            return (i == constraintPairs_.end()) ? NULL : *i;
        }

        ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {            
            ++i;
            return (i == constraintPairs_.end()) ? NULL : *i;    
        }         

        ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
            i = constraintElems_.begin();
            return (i == constraintElems_.end()) ? NULL : *i;
        }

        ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {            
            ++i;
            return (i == constraintElems_.end()) ? NULL : *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();

        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<ConstraintPair*> constraintPairs_;
        std::vector<ConstraintElem*> constraintElems_;
        int stampId_;
        std::string moleculeName_;
};

} //namespace oopse
#endif //
Revision:	1910
Committed:	Fri Jan 7 21:50:13 2005 UTC (20 years, 9 months ago) by tim
File size:	9780 byte(s)
Log Message:	ZConstraintForceManager in progress
#	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	1901	#include "constraints/ConstraintPair.hpp"
39	tim	1692	#include "math/Vector3.hpp"
40	tim	1492	#include "primitives/Atom.hpp"
41			#include "primitives/RigidBody.hpp"
42	tim	1782	#include "primitives/Bond.hpp"
43			#include "primitives/Bend.hpp"
44			#include "primitives/Torsion.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	tim	1907	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
66			typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
67
68	tim	1725
69	tim	1733	Molecule(int stampId, int globalIndex, const std::string& molName);
70	tim	1692	virtual ~Molecule();
71	gezelter	1490
72	tim	1692	/**
73			* Returns the global index of this molecule.
74			* @return the global index of this molecule
75			*/
76			int getGlobalIndex() {
77			return globalIndex_;
78			}
79	gezelter	1490
80	tim	1692	/**
81	tim	1733	* Returns the stamp id of this molecule
82			* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
83			* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
84			*/
85			int getStampId() {
86			return stampId_;
87			}
88
89			/** Returns the name of the molecule */
90			std::string getType() {
91			return moleculeName_;
92			}
93
94			/**
95	tim	1692	* Sets the global index of this molecule.
96			* @param new global index to be set
97			*/
98	tim	1695	int setGlobalIndex(int index) {
99	tim	1692	return globalIndex_;
100			}
101	gezelter	1490
102	tim	1733
103	tim	1692	/** add an atom into this molecule */
104			void addAtom(Atom* atom);
105	gezelter	1490
106	tim	1692	/** add a bond into this molecule */
107			void addBond(Bond* bond);
108	gezelter	1490
109	tim	1692	/** add a bend into this molecule */
110			void addBend(Bend* bend);
111	gezelter	1490
112	tim	1692	/** add a torsion into this molecule*/
113			void addTorsion(Torsion* torsion);
114	gezelter	1490
115	tim	1692	/** add a rigidbody into this molecule */
116			void addRigidBody(RigidBody *rb);
117	gezelter	1490
118	tim	1692	/** add a cutoff group into this molecule */
119	tim	1901	void addCutoffGroup(CutoffGroup* cp);
120	gezelter	1490
121	tim	1901	void addConstraintPair(ConstraintPair* consPair);
122	tim	1907
123			void addConstraintElem(ConstraintElem* consElem);
124	tim	1901
125	tim	1692	/** */
126			void complete();
127	gezelter	1490
128	tim	1692	/** Returns the total number of atoms in this molecule */
129			unsigned int getNAtoms() {
130			return atoms_.size();
131			}
132	gezelter	1490
133	tim	1692	/** Returns the total number of bonds in this molecule */
134			unsigned int getNBonds(){
135			return bonds_.size();
136			}
137	gezelter	1490
138	tim	1692	/** Returns the total number of bends in this molecule */
139			unsigned int getNBends() {
140			return bends_.size();
141			}
142	gezelter	1490
143	tim	1692	/** Returns the total number of torsions in this molecule */
144			unsigned int getNTorsions() {
145			return torsions_.size();
146			}
147	gezelter	1490
148	tim	1692	/** Returns the total number of rigid bodies in this molecule */
149			unsigned int getNRigidBodies() {
150			return rigidBodies_.size();
151			}
152	gezelter	1490
153	tim	1692	/** Returns the total number of integrable objects in this molecule */
154			unsigned int getNIntegrableObjects() {
155			return integrableObjects_.size();
156			}
157
158			/** Returns the total number of cutoff groups in this molecule */
159			unsigned int getNCutoffGroups() {
160			return cutoffGroups_.size();
161			}
162
163	tim	1696	/** Returns the total number of constraints in this molecule */
164	tim	1901	unsigned int getNConstraintPairs() {
165			return constraintPairs_.size();
166	tim	1696	}
167	tim	1719
168			Atom* getAtomAt(unsigned int i) {
169			assert(i < atoms_.size());
170			return atoms_[i];
171			}
172	tim	1692
173	tim	1910	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
174	tim	1907	i = atoms_.begin();
175			return (i == atoms_.end()) ? NULL : *i;
176			}
177	tim	1692
178	tim	1910	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
179	tim	1907	++i;
180			return (i == atoms_.end()) ? NULL : *i;
181			}
182	tim	1692
183	tim	1910	Bond* beginBond(std::vector<Bond*>::iterator& i) {
184	tim	1907	i = bonds_.begin();
185			return (i == bonds_.end()) ? NULL : *i;
186			}
187	tim	1692
188	tim	1910	Bond* nextBond(std::vector<Bond*>::iterator& i) {
189	tim	1907	++i;
190			return (i == bonds_.end()) ? NULL : *i;
191	tim	1692
192	tim	1907	}
193	tim	1692
194	tim	1910	Bend* beginBend(std::vector<Bend*>::iterator& i) {
195	tim	1907	i = bends_.begin();
196			return (i == bends_.end()) ? NULL : *i;
197			}
198	tim	1692
199	tim	1910	Bend* nextBend(std::vector<Bend*>::iterator& i) {
200	tim	1907	++i;
201			return (i == bends_.end()) ? NULL : *i;
202			}
203	tim	1692
204	tim	1910	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
205	tim	1907	i = torsions_.begin();
206			return (i == torsions_.end()) ? NULL : *i;
207			}
208	tim	1692
209	tim	1910	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
210	tim	1907	++i;
211			return (i == torsions_.end()) ? NULL : *i;
212			}
213	tim	1692
214	tim	1910	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
215	tim	1907	i = rigidBodies_.begin();
216			return (i == rigidBodies_.end()) ? NULL : *i;
217			}
218	tim	1692
219	tim	1910	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
220	tim	1907	++i;
221			return (i == rigidBodies_.end()) ? NULL : *i;
222			}
223	tim	1692
224	tim	1910	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
225	tim	1907	i = integrableObjects_.begin();
226			return (i == integrableObjects_.end()) ? NULL : *i;
227			}
228	tim	1696
229	tim	1910	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
230	tim	1907	++i;
231			return (i == integrableObjects_.end()) ? NULL : *i;
232			}
233
234	tim	1910	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
235	tim	1907	i = cutoffGroups_.begin();
236			return (i == cutoffGroups_.end()) ? NULL : *i;
237			}
238
239	tim	1910	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
240	tim	1907	++i;
241			return (i == cutoffGroups_.end()) ? NULL : *i;
242			}
243
244	tim	1910	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
245	tim	1907	i = constraintPairs_.begin();
246			return (i == constraintPairs_.end()) ? NULL : *i;
247			}
248
249	tim	1910	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
250	tim	1907	++i;
251			return (i == constraintPairs_.end()) ? NULL : *i;
252			}
253
254	tim	1910	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
255	tim	1907	i = constraintElems_.begin();
256			return (i == constraintElems_.end()) ? NULL : *i;
257			}
258
259	tim	1910	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
260	tim	1907	++i;
261			return (i == constraintElems_.end()) ? NULL : *i;
262			}
263	tim	1696
264	tim	1692	/** return the total potential energy of short range interaction of this molecule */
265			double getPotential();
266
267	tim	1843	/** get total mass of this molecule */
268			double getMass();
269	tim	1692
270			/** return the center of mass of this molecule */
271			Vector3d getCom();
272
273			/** Moves the center of this molecule */
274	tim	1695	void moveCom(const Vector3d& delta);
275	tim	1692
276			/** Returns the velocity of center of mass of this molecule */
277			Vector3d getComVel();
278
279	tim	1695	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
280	tim	1692
281			private:
282	tim	1725
283	tim	1692	int globalIndex_;
284
285			std::vector<Atom*> atoms_;
286			std::vector<Bond*> bonds_;
287			std::vector<Bend*> bends_;
288			std::vector<Torsion*> torsions_;
289			std::vector<RigidBody*> rigidBodies_;
290			std::vector<StuntDouble*> integrableObjects_;
291			std::vector<CutoffGroup*> cutoffGroups_;
292	tim	1901	std::vector<ConstraintPair*> constraintPairs_;
293	tim	1907	std::vector<ConstraintElem*> constraintElems_;
294	tim	1733	int stampId_;
295			std::string moleculeName_;
296	gezelter	1490	};
297
298	tim	1692	} //namespace oopse
299			#endif //