src/primitives/CutoffGroup.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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#ifndef PRIMITIVES_CUTOFFGROUP_HPP

#define PRIMITIVES_CUTOFFGROUP_HPP

#include "primitives/Atom.hpp"
#include "math/Vector3.hpp"

namespace OpenMD {
  class CutoffGroup {
  public:
    
    CutoffGroup() {
      haveTotalMass = false;
      totalMass = 0.0;
    }
    
    void addAtom(Atom *atom) {
      cutoffAtomList.push_back(atom);
    }
    
    Atom *beginAtom(std::vector<Atom *>::iterator & i) {
      i = cutoffAtomList.begin();
      return i != cutoffAtomList.end() ? *i : NULL;
    }
    
    Atom *nextAtom(std::vector<Atom *>::iterator & i) {
      i++;
      return i != cutoffAtomList.end() ? *i : NULL;
    }

    std::vector<Atom*> getAtoms() { return cutoffAtomList; }
    RealType getMass() {
      std::vector<Atom *>::iterator i;
      Atom * atom;
      RealType mass;
      
      if (!haveTotalMass) {
        totalMass = 0;
        
        for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
          mass = atom->getMass();
          totalMass += mass;
        }
        
        haveTotalMass = true;
      }
      
      return totalMass;
    }
    
    void getCOM(Vector3d & com) {
      std::vector<Atom *>::iterator i;
      Atom * atom;
      Vector3d pos;
      RealType mass;
      
      com[0] = 0;
      com[1] = 0;
      com[2] = 0;
      totalMass = getMass();
      
      if (cutoffAtomList.size() == 1) {
        com = beginAtom(i)->getPos();
      } else {
        for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
          mass = atom->getMass();
          pos = atom->getPos();
          com += pos * mass;
        }
        
        com /= totalMass;
      }
    }
    
    int getNumAtom() {
      return cutoffAtomList.size();
    }
    
    int getGlobalIndex() {
      return globalIndex;
    }
    
    void setGlobalIndex(int id) {
      this->globalIndex = id;
    }
    
  private:
    
    std::vector<Atom *>cutoffAtomList;
    bool haveTotalMass;
    RealType totalMass;
    int globalIndex;
  };  
} //end namespace OpenMD
#endif //PRIMITIVES_CUTOFFGROUP_HPP  
Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	4074 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42			#ifndef PRIMITIVES_CUTOFFGROUP_HPP
43
44			#define PRIMITIVES_CUTOFFGROUP_HPP
45
46	tim	3	#include "primitives/Atom.hpp"
47	gezelter	246	#include "math/Vector3.hpp"
48	gezelter	2
49	gezelter	1390	namespace OpenMD {
50	gezelter	507	class CutoffGroup {
51			public:
52	gezelter	1211
53	gezelter	507	CutoffGroup() {
54			haveTotalMass = false;
55			totalMass = 0.0;
56			}
57	gezelter	1211
58	gezelter	507	void addAtom(Atom *atom) {
59			cutoffAtomList.push_back(atom);
60			}
61	gezelter	1211
62	gezelter	507	Atom beginAtom(std::vector<Atom >::iterator & i) {
63			i = cutoffAtomList.begin();
64			return i != cutoffAtomList.end() ? *i : NULL;
65			}
66	gezelter	1211
67	gezelter	507	Atom nextAtom(std::vector<Atom >::iterator & i) {
68			i++;
69			return i != cutoffAtomList.end() ? *i : NULL;
70			}
71	gezelter	2
72	gezelter	507	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
73	tim	963	RealType getMass() {
74	gezelter	507	std::vector<Atom *>::iterator i;
75			Atom * atom;
76	tim	963	RealType mass;
77	gezelter	1211
78	gezelter	507	if (!haveTotalMass) {
79			totalMass = 0;
80	gezelter	1211
81	gezelter	507	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
82			mass = atom->getMass();
83			totalMass += mass;
84			}
85	gezelter	1211
86	gezelter	507	haveTotalMass = true;
87			}
88	gezelter	1211
89	gezelter	507	return totalMass;
90			}
91	gezelter	1211
92	gezelter	507	void getCOM(Vector3d & com) {
93			std::vector<Atom *>::iterator i;
94			Atom * atom;
95			Vector3d pos;
96	tim	963	RealType mass;
97	gezelter	1211
98	gezelter	507	com[0] = 0;
99			com[1] = 0;
100			com[2] = 0;
101			totalMass = getMass();
102	gezelter	1211
103	gezelter	507	if (cutoffAtomList.size() == 1) {
104			com = beginAtom(i)->getPos();
105			} else {
106			for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
107			mass = atom->getMass();
108			pos = atom->getPos();
109			com += pos * mass;
110			}
111	gezelter	1211
112	gezelter	507	com /= totalMass;
113			}
114			}
115	gezelter	1211
116	gezelter	507	int getNumAtom() {
117			return cutoffAtomList.size();
118			}
119	gezelter	1211
120	gezelter	507	int getGlobalIndex() {
121			return globalIndex;
122			}
123	gezelter	1211
124	gezelter	507	void setGlobalIndex(int id) {
125			this->globalIndex = id;
126			}
127	gezelter	1211
128	gezelter	507	private:
129	gezelter	1211
130	gezelter	507	std::vector<Atom *>cutoffAtomList;
131			bool haveTotalMass;
132	tim	963	RealType totalMass;
133	gezelter	507	int globalIndex;
134	gezelter	1211	};
135	gezelter	1390	} //end namespace OpenMD
136	gezelter	246	#endif //PRIMITIVES_CUTOFFGROUP_HPP