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root/group/trunk/OOPSE-4/src/primitives/CutoffGroup.hpp
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Comparing trunk/OOPSE-4/src/primitives/CutoffGroup.hpp (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2114 by tim, Thu Mar 10 23:56:42 2005 UTC

# Line 1 | Line 1
1 < #ifndef _CUTOFFGROUP_H_
2 < #define _CUTOFFGROUP_H_
3 < #include "Atom.hpp"
1 > /*
2 > * 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 > #ifndef PRIMITIVES_CUTOFFGROUP_HPP
43  
44 < class CutoffGroup{
6 < public:
7 <  
8 <  CutoffGroup() {
9 <    haveTotalMass = false;
10 <    totalMass = 0.0;
11 <  }
12 <  
13 <  void addAtom(Atom* atom) {cutoffAtomList.push_back(atom);}
14 <  
15 <  Atom* beginAtom(vector<Atom*>::iterator& i){
16 <    i = cutoffAtomList.begin();
17 <    return i != cutoffAtomList.end()? *i : NULL;
18 <  }
19 <  
20 <  Atom* nextAtom(vector<Atom*>::iterator& i){
21 <    i++;
22 <    return i != cutoffAtomList.end()? *i : NULL;
23 <  }
24 <  
25 <  double getMass(){
26 <    vector<Atom*>::iterator i;
27 <    Atom* atom;
28 <    double mass;
29 <    
30 <    if (!haveTotalMass) {
44 > #define PRIMITIVES_CUTOFFGROUP_HPP
45  
46 <      totalMass = 0;
47 <      
34 <      for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
35 <        mass = atom->getMass();
36 <        totalMass += mass;
37 <      }
46 > #include "primitives/Atom.hpp"
47 > #include "math/Vector3.hpp"
48  
49 <      haveTotalMass = true;
50 <    }
51 <    
42 <    return totalMass;
43 <  }
44 <  
45 <  void getCOM(double com[3]){
49 > namespace oopse {
50 > class CutoffGroup {
51 >    public:
52  
53 <    vector<Atom*>::iterator i;
54 <    Atom* atom;
55 <    double pos[3];
56 <    double mass;
51 <    
52 <    com[0] = 0;
53 <    com[1] = 0;
54 <    com[2] = 0;
55 <    totalMass = getMass();    
56 <    
57 <    if (cutoffAtomList.size() == 1) {
58 <      
59 <      beginAtom(i)->getPos(com);
60 <      
61 <    } else {
62 <      
63 <      for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
64 <        mass = atom->getMass();
65 <        atom->getPos(pos);
66 <        com[0] += pos[0] * mass;
67 <        com[1] += pos[1] * mass;
68 <        com[2] += pos[2] * mass;
69 <      }
70 <      
71 <      com[0] /= totalMass;
72 <      com[1] /= totalMass;
73 <      com[2] /= totalMass;
74 <    }
75 <    
76 <  }
77 <  
78 <  int getNumAtom() {return cutoffAtomList.size();}
53 >        CutoffGroup() {
54 >            haveTotalMass = false;
55 >            totalMass = 0.0;
56 >        }
57  
58 <  int getGlobalIndex() {return globalIndex;}
59 <  void setGlobalIndex(int id) {this->globalIndex = id;}
60 < private:
83 <  vector<Atom*> cutoffAtomList;
84 <  bool haveTotalMass;
85 <  double totalMass;
86 <  int globalIndex;
58 >        void addAtom(Atom *atom) {
59 >            cutoffAtomList.push_back(atom);
60 >        }
61  
62 +        Atom *beginAtom(std::vector<Atom *>::iterator & i) {
63 +            i = cutoffAtomList.begin();
64 +            return i != cutoffAtomList.end() ? *i : NULL;
65 +        }
66 +
67 +        Atom *nextAtom(std::vector<Atom *>::iterator & i) {
68 +            i++;
69 +            return i != cutoffAtomList.end() ? *i : NULL;
70 +        }
71 +
72 +        std::vector<Atom*> getAtoms() { return cutoffAtomList; }
73 +        double getMass() {
74 +            std::vector<Atom *>::iterator i;
75 +            Atom * atom;
76 +            double mass;
77 +
78 +            if (!haveTotalMass) {
79 +                totalMass = 0;
80 +
81 +                for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
82 +                    mass = atom->getMass();
83 +                    totalMass += mass;
84 +                }
85 +
86 +                haveTotalMass = true;
87 +            }
88 +
89 +            return totalMass;
90 +        }
91 +
92 +        void getCOM(Vector3d & com) {
93 +            std::vector<Atom *>::iterator i;
94 +            Atom * atom;
95 +            Vector3d pos;
96 +            double mass;
97 +
98 +            com[0] = 0;
99 +            com[1] = 0;
100 +            com[2] = 0;
101 +            totalMass = getMass();
102 +
103 +            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 +
112 +                com /= totalMass;
113 +            }
114 +        }
115 +
116 +        int getNumAtom() {
117 +            return cutoffAtomList.size();
118 +        }
119 +
120 +        int getGlobalIndex() {
121 +            return globalIndex;
122 +        }
123 +
124 +        void setGlobalIndex(int id) {
125 +            this->globalIndex = id;
126 +        }
127 +
128 +    private:
129 +
130 +        std::vector<Atom *>cutoffAtomList;
131 +        bool haveTotalMass;
132 +        double totalMass;
133 +        int globalIndex;
134   };
135  
136 < #endif
136 > }      //end namespace oopse
137 >
138 > #endif //PRIMITIVES_CUTOFFGROUP_HPP  

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