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;    
    }
        
    /** 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();

    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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	10097 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	1490
49	gezelter	1930	#ifndef PRIMITIVES_MOLECULE_HPP
50			#define PRIMITIVES_MOLECULE_HPP
51	gezelter	1490	#include <vector>
52	gezelter	1930	#include <iostream>
53	gezelter	1490
54	gezelter	1930	#include "constraints/ConstraintPair.hpp"
55			#include "math/Vector3.hpp"
56	tim	1492	#include "primitives/Atom.hpp"
57			#include "primitives/RigidBody.hpp"
58	gezelter	1930	#include "primitives/Bond.hpp"
59			#include "primitives/Bend.hpp"
60			#include "primitives/Torsion.hpp"
61	tim	1492	#include "primitives/CutoffGroup.hpp"
62	gezelter	1490
63	gezelter	1930	namespace oopse{
64	gezelter	1490
65	gezelter	2204	class Constraint;
66	gezelter	1490
67	gezelter	2204	/**
68			* @class Molecule Molecule.hpp "primitives/Molecule.hpp"
69			* @brief
70			*/
71			class Molecule {
72			public:
73	gezelter	1490
74	gezelter	2204	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			typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
81			typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
82			typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
83	gezelter	1930
84	gezelter	1490
85	gezelter	2204	Molecule(int stampId, int globalIndex, const std::string& molName);
86			virtual ~Molecule();
87	gezelter	1490
88	gezelter	2204	/**
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	1490
96	gezelter	2204	/**
97			* Returns the stamp id of this molecule
98			* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
99			* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
100			*/
101			int getStampId() {
102			return stampId_;
103			}
104	gezelter	1490
105	gezelter	2204	/** Returns the name of the molecule */
106			std::string getType() {
107			return moleculeName_;
108			}
109	gezelter	1930
110	gezelter	2204	/**
111			* Sets the global index of this molecule.
112			* @param new global index to be set
113			*/
114			void setGlobalIndex(int index) {
115			globalIndex_ = index;
116			}
117	gezelter	1490
118	gezelter	1930
119	gezelter	2204	/** add an atom into this molecule */
120			void addAtom(Atom* atom);
121	gezelter	1490
122	gezelter	2204	/** add a bond into this molecule */
123			void addBond(Bond* bond);
124	gezelter	1490
125	gezelter	2204	/** add a bend into this molecule */
126			void addBend(Bend* bend);
127	gezelter	1490
128	gezelter	2204	/** add a torsion into this molecule*/
129			void addTorsion(Torsion* torsion);
130	gezelter	1490
131	gezelter	2204	/** add a rigidbody into this molecule */
132			void addRigidBody(RigidBody *rb);
133	gezelter	1490
134	gezelter	2204	/** add a cutoff group into this molecule */
135			void addCutoffGroup(CutoffGroup* cp);
136	gezelter	1490
137	gezelter	2204	void addConstraintPair(ConstraintPair* consPair);
138	gezelter	1930
139	gezelter	2204	void addConstraintElem(ConstraintElem* consElem);
140	gezelter	1490
141	gezelter	2204	/** */
142			void complete();
143	gezelter	1490
144	gezelter	2204	/** Returns the total number of atoms in this molecule */
145			unsigned int getNAtoms() {
146			return atoms_.size();
147			}
148	gezelter	1490
149	gezelter	2204	/** Returns the total number of bonds in this molecule */
150			unsigned int getNBonds(){
151			return bonds_.size();
152			}
153	gezelter	1930
154	gezelter	2204	/** Returns the total number of bends in this molecule */
155			unsigned int getNBends() {
156			return bends_.size();
157			}
158	gezelter	1930
159	gezelter	2204	/** Returns the total number of torsions in this molecule */
160			unsigned int getNTorsions() {
161			return torsions_.size();
162			}
163	gezelter	1930
164	gezelter	2204	/** Returns the total number of rigid bodies in this molecule */
165			unsigned int getNRigidBodies() {
166			return rigidBodies_.size();
167			}
168	gezelter	1930
169	gezelter	2204	/** Returns the total number of integrable objects in this molecule */
170			unsigned int getNIntegrableObjects() {
171			return integrableObjects_.size();
172			}
173	gezelter	1930
174	gezelter	2204	/** Returns the total number of cutoff groups in this molecule */
175			unsigned int getNCutoffGroups() {
176			return cutoffGroups_.size();
177			}
178	gezelter	1930
179	gezelter	2204	/** Returns the total number of constraints in this molecule */
180			unsigned int getNConstraintPairs() {
181			return constraintPairs_.size();
182			}
183	gezelter	1930
184	gezelter	2204	Atom* getAtomAt(unsigned int i) {
185			assert(i < atoms_.size());
186			return atoms_[i];
187			}
188	gezelter	1930
189	gezelter	2204	RigidBody* getRigidBodyAt(unsigned int i) {
190			assert(i < rigidBodies_.size());
191			return rigidBodies_[i];
192			}
193	tim	1989
194	gezelter	2204	Atom* beginAtom(std::vector<Atom*>::iterator& i) {
195			i = atoms_.begin();
196			return (i == atoms_.end()) ? NULL : *i;
197			}
198	gezelter	1930
199	gezelter	2204	Atom* nextAtom(std::vector<Atom*>::iterator& i) {
200			++i;
201			return (i == atoms_.end()) ? NULL : *i;
202			}
203	gezelter	1930
204	gezelter	2204	Bond* beginBond(std::vector<Bond*>::iterator& i) {
205			i = bonds_.begin();
206			return (i == bonds_.end()) ? NULL : *i;
207			}
208	gezelter	1930
209	gezelter	2204	Bond* nextBond(std::vector<Bond*>::iterator& i) {
210			++i;
211			return (i == bonds_.end()) ? NULL : *i;
212	gezelter	1930
213	gezelter	2204	}
214	gezelter	1930
215	gezelter	2204	Bend* beginBend(std::vector<Bend*>::iterator& i) {
216			i = bends_.begin();
217			return (i == bends_.end()) ? NULL : *i;
218			}
219	gezelter	1930
220	gezelter	2204	Bend* nextBend(std::vector<Bend*>::iterator& i) {
221			++i;
222			return (i == bends_.end()) ? NULL : *i;
223			}
224	gezelter	1930
225	gezelter	2204	Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
226			i = torsions_.begin();
227			return (i == torsions_.end()) ? NULL : *i;
228			}
229	gezelter	1930
230	gezelter	2204	Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
231			++i;
232			return (i == torsions_.end()) ? NULL : *i;
233			}
234	gezelter	1930
235	gezelter	2204	RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
236			i = rigidBodies_.begin();
237			return (i == rigidBodies_.end()) ? NULL : *i;
238			}
239	gezelter	1930
240	gezelter	2204	RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
241			++i;
242			return (i == rigidBodies_.end()) ? NULL : *i;
243			}
244	gezelter	1930
245	gezelter	2204	StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
246			i = integrableObjects_.begin();
247			return (i == integrableObjects_.end()) ? NULL : *i;
248			}
249	gezelter	1930
250	gezelter	2204	StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
251			++i;
252			return (i == integrableObjects_.end()) ? NULL : *i;
253			}
254	gezelter	1930
255	gezelter	2204	CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
256			i = cutoffGroups_.begin();
257			return (i == cutoffGroups_.end()) ? NULL : *i;
258			}
259	gezelter	1930
260	gezelter	2204	CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
261			++i;
262			return (i == cutoffGroups_.end()) ? NULL : *i;
263			}
264	gezelter	1930
265	gezelter	2204	ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
266			i = constraintPairs_.begin();
267			return (i == constraintPairs_.end()) ? NULL : *i;
268			}
269	gezelter	1930
270	gezelter	2204	ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
271			++i;
272			return (i == constraintPairs_.end()) ? NULL : *i;
273			}
274	gezelter	1930
275	gezelter	2204	ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
276			i = constraintElems_.begin();
277			return (i == constraintElems_.end()) ? NULL : *i;
278			}
279	gezelter	1930
280	gezelter	2204	ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
281			++i;
282			return (i == constraintElems_.end()) ? NULL : *i;
283			}
284	gezelter	1930
285	gezelter	2204	/** return the total potential energy of short range interaction of this molecule */
286			double getPotential();
287	gezelter	1930
288	gezelter	2204	/** get total mass of this molecule */
289			double getMass();
290	gezelter	1930
291	gezelter	2204	/** return the center of mass of this molecule */
292			Vector3d getCom();
293	gezelter	1930
294	gezelter	2204	/** Moves the center of this molecule */
295			void moveCom(const Vector3d& delta);
296	gezelter	1930
297	gezelter	2204	/** Returns the velocity of center of mass of this molecule */
298			Vector3d getComVel();
299	gezelter	1930
300	gezelter	2204	std::string getMoleculeName() {
301			return moleculeName_;
302			}
303	tim	1973
304	gezelter	2204	friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
305	gezelter	1930
306	gezelter	2204	private:
307	gezelter	1930
308	gezelter	2204	int globalIndex_;
309	gezelter	1930
310	gezelter	2204	std::vector<Atom*> atoms_;
311			std::vector<Bond*> bonds_;
312			std::vector<Bend*> bends_;
313			std::vector<Torsion*> torsions_;
314			std::vector<RigidBody*> rigidBodies_;
315			std::vector<StuntDouble*> integrableObjects_;
316			std::vector<CutoffGroup*> cutoffGroups_;
317			std::vector<ConstraintPair*> constraintPairs_;
318			std::vector<ConstraintElem*> constraintElems_;
319			int stampId_;
320			std::string moleculeName_;
321			};
322	gezelter	1490
323	gezelter	1930	} //namespace oopse
324			#endif //