src/primitives/Molecule.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @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
     */
    void setGlobalIndex(int index) {
      globalIndex_ = index;
    }
    
    
    /** 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];
    }
    
    RigidBody* getRigidBodyAt(unsigned int i) {
      assert(i < rigidBodies_.size());
      return rigidBodies_[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;    
    }
    
    /** 
     * Returns the total potential energy of short range interaction
     * of this molecule 
     */    
    RealType getPotential();
    
    /** get total mass of this molecule */        
    RealType 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();

    std::string getMoleculeName() { 
      return moleculeName_;
    }
        
    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:	1211
Committed:	Wed Jan 23 16:38:22 2008 UTC (17 years, 3 months ago) by gezelter
File size:	10267 byte(s)
Log Message:	A few formatting changes to prettify the code
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file Molecule.hpp
44			* @author tlin
45			* @date 10/25/2004
46			* @version 1.0
47			*/
48	gezelter	2
49	gezelter	246	#ifndef PRIMITIVES_MOLECULE_HPP
50			#define PRIMITIVES_MOLECULE_HPP
51	gezelter	2	#include <vector>
52	gezelter	246	#include <iostream>
53	gezelter	2
54	gezelter	246	#include "constraints/ConstraintPair.hpp"
55			#include "math/Vector3.hpp"
56	tim	3	#include "primitives/Atom.hpp"
57			#include "primitives/RigidBody.hpp"
58	gezelter	246	#include "primitives/Bond.hpp"
59			#include "primitives/Bend.hpp"
60			#include "primitives/Torsion.hpp"
61	tim	3	#include "primitives/CutoffGroup.hpp"
62	gezelter	2
63	gezelter	246	namespace oopse{
64	gezelter	2
65	gezelter	507	class Constraint;
66	gezelter	2
67	gezelter	507	/**
68			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
69			* @brief
70			*/
71			class Molecule {
72			public:
73	gezelter	2
74	gezelter	507	typedef std::vector<Atom*>::iterator AtomIterator;
75			typedef std::vector<Bond*>::iterator BondIterator;
76			typedef std::vector<Bend*>::iterator BendIterator;
77			typedef std::vector<Torsion*>::iterator TorsionIterator;
78			typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
79			typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
80	gezelter	1211	typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
81	gezelter	507	typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
82			typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
83	gezelter	1211
84
85	gezelter	507	Molecule(int stampId, int globalIndex, const std::string& molName);
86			virtual ~Molecule();
87	gezelter	1211
88	gezelter	507	/**
89			* Returns the global index of this molecule.
90			* @return the global index of this molecule
91			*/
92			int getGlobalIndex() {
93			return globalIndex_;
94			}
95	gezelter	1211
96	gezelter	507	/**
97			* Returns the stamp id of this molecule
98	gezelter	1211	* @note Ideally, every molecule should keep a pointer of its
99			* molecule stamp instead of its stamp id. However, the pointer
100			* will become invalid, if the molecule migrate to other
101			* processor.
102	gezelter	507	*/
103			int getStampId() {
104			return stampId_;
105			}
106	gezelter	1211
107	gezelter	507	/** Returns the name of the molecule */
108			std::string getType() {
109			return moleculeName_;
110			}
111	gezelter	1211
112	gezelter	507	/**
113			* Sets the global index of this molecule.
114			* @param new global index to be set
115			*/
116			void setGlobalIndex(int index) {
117			globalIndex_ = index;
118			}
119	gezelter	1211
120
121	gezelter	507	/** add an atom into this molecule */
122			void addAtom(Atom* atom);
123	gezelter	1211
124	gezelter	507	/** add a bond into this molecule */
125			void addBond(Bond* bond);
126	gezelter	1211
127	gezelter	507	/** add a bend into this molecule */
128			void addBend(Bend* bend);
129	gezelter	1211
130	gezelter	507	/** add a torsion into this molecule*/
131			void addTorsion(Torsion* torsion);
132	gezelter	1211
133	gezelter	507	/** add a rigidbody into this molecule */
134			void addRigidBody(RigidBody *rb);
135	gezelter	1211
136	gezelter	507	/** add a cutoff group into this molecule */
137			void addCutoffGroup(CutoffGroup* cp);
138	gezelter	1211
139	gezelter	507	void addConstraintPair(ConstraintPair* consPair);
140	gezelter	1211
141	gezelter	507	void addConstraintElem(ConstraintElem* consElem);
142	gezelter	1211
143	gezelter	507	/** */
144			void complete();
145	gezelter	1211
146	gezelter	507	/** Returns the total number of atoms in this molecule */
147			unsigned int getNAtoms() {
148			return atoms_.size();
149			}
150	gezelter	1211
151	gezelter	507	/** Returns the total number of bonds in this molecule */
152			unsigned int getNBonds(){
153			return bonds_.size();
154			}
155	gezelter	1211
156	gezelter	507	/** Returns the total number of bends in this molecule */
157			unsigned int getNBends() {
158			return bends_.size();
159			}
160	gezelter	1211
161	gezelter	507	/** Returns the total number of torsions in this molecule */
162			unsigned int getNTorsions() {
163			return torsions_.size();
164			}
165	gezelter	1211
166	gezelter	507	/** Returns the total number of rigid bodies in this molecule */
167			unsigned int getNRigidBodies() {
168			return rigidBodies_.size();
169			}
170	gezelter	1211
171	gezelter	507	/** Returns the total number of integrable objects in this molecule */
172			unsigned int getNIntegrableObjects() {
173			return integrableObjects_.size();
174			}
175	gezelter	1211
176	gezelter	507	/** Returns the total number of cutoff groups in this molecule */
177			unsigned int getNCutoffGroups() {
178			return cutoffGroups_.size();
179			}
180	gezelter	1211
181	gezelter	507	/** Returns the total number of constraints in this molecule */
182			unsigned int getNConstraintPairs() {
183			return constraintPairs_.size();
184			}
185	gezelter	1211
186	gezelter	507	Atom* getAtomAt(unsigned int i) {
187			assert(i < atoms_.size());
188			return atoms_[i];
189			}
190	gezelter	1211
191	gezelter	507	RigidBody* getRigidBodyAt(unsigned int i) {
192			assert(i < rigidBodies_.size());
193			return rigidBodies_[i];
194			}
195	gezelter	1211
196	gezelter	507	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
197			i = atoms_.begin();
198			return (i == atoms_.end()) ? NULL : *i;
199			}
200	gezelter	1211
201	gezelter	507	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
202			++i;
203			return (i == atoms_.end()) ? NULL : *i;
204			}
205	gezelter	1211
206	gezelter	507	Bond* beginBond(std::vector<Bond*>::iterator& i) {
207			i = bonds_.begin();
208			return (i == bonds_.end()) ? NULL : *i;
209			}
210	gezelter	1211
211	gezelter	507	Bond* nextBond(std::vector<Bond*>::iterator& i) {
212			++i;
213			return (i == bonds_.end()) ? NULL : *i;
214	gezelter	1211
215	gezelter	507	}
216	gezelter	1211
217	gezelter	507	Bend* beginBend(std::vector<Bend*>::iterator& i) {
218			i = bends_.begin();
219			return (i == bends_.end()) ? NULL : *i;
220			}
221	gezelter	1211
222	gezelter	507	Bend* nextBend(std::vector<Bend*>::iterator& i) {
223			++i;
224			return (i == bends_.end()) ? NULL : *i;
225			}
226	gezelter	1211
227	gezelter	507	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
228			i = torsions_.begin();
229			return (i == torsions_.end()) ? NULL : *i;
230			}
231	gezelter	1211
232	gezelter	507	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
233			++i;
234			return (i == torsions_.end()) ? NULL : *i;
235			}
236	gezelter	1211
237	gezelter	507	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
238			i = rigidBodies_.begin();
239			return (i == rigidBodies_.end()) ? NULL : *i;
240			}
241	gezelter	1211
242	gezelter	507	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
243			++i;
244			return (i == rigidBodies_.end()) ? NULL : *i;
245			}
246	gezelter	1211
247	gezelter	507	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
248			i = integrableObjects_.begin();
249			return (i == integrableObjects_.end()) ? NULL : *i;
250			}
251	gezelter	1211
252	gezelter	507	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
253			++i;
254			return (i == integrableObjects_.end()) ? NULL : *i;
255			}
256	gezelter	1211
257	gezelter	507	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
258			i = cutoffGroups_.begin();
259			return (i == cutoffGroups_.end()) ? NULL : *i;
260			}
261	gezelter	246
262	gezelter	1211	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
263	gezelter	507	++i;
264			return (i == cutoffGroups_.end()) ? NULL : *i;
265			}
266	gezelter	1211
267	gezelter	507	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
268			i = constraintPairs_.begin();
269			return (i == constraintPairs_.end()) ? NULL : *i;
270			}
271	gezelter	1211
272	gezelter	507	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
273			++i;
274			return (i == constraintPairs_.end()) ? NULL : *i;
275			}
276	gezelter	1211
277	gezelter	507	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
278			i = constraintElems_.begin();
279			return (i == constraintElems_.end()) ? NULL : *i;
280			}
281	gezelter	1211
282	gezelter	507	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
283			++i;
284			return (i == constraintElems_.end()) ? NULL : *i;
285			}
286	gezelter	1211
287			/**
288			* Returns the total potential energy of short range interaction
289			* of this molecule
290			*/
291	tim	963	RealType getPotential();
292	gezelter	1211
293	gezelter	507	/** get total mass of this molecule */
294	tim	963	RealType getMass();
295	gezelter	1211
296	gezelter	507	/** return the center of mass of this molecule */
297			Vector3d getCom();
298	gezelter	1211
299	gezelter	507	/** Moves the center of this molecule */
300			void moveCom(const Vector3d& delta);
301	gezelter	1211
302	gezelter	507	/** Returns the velocity of center of mass of this molecule */
303			Vector3d getComVel();
304	gezelter	246
305	gezelter	507	std::string getMoleculeName() {
306			return moleculeName_;
307			}
308	tim	289
309	gezelter	507	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
310	gezelter	1211
311	gezelter	507	private:
312	gezelter	1211
313	gezelter	507	int globalIndex_;
314	gezelter	1211
315	gezelter	507	std::vector<Atom*> atoms_;
316			std::vector<Bond*> bonds_;
317			std::vector<Bend*> bends_;
318			std::vector<Torsion*> torsions_;
319			std::vector<RigidBody*> rigidBodies_;
320			std::vector<StuntDouble*> integrableObjects_;
321			std::vector<CutoffGroup*> cutoffGroups_;
322			std::vector<ConstraintPair*> constraintPairs_;
323			std::vector<ConstraintElem*> constraintElems_;
324			int stampId_;
325			std::string moleculeName_;
326			};
327	gezelter	2
328	gezelter	246	} //namespace oopse
329			#endif //