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Comparing trunk/src/primitives/CutoffGroup.hpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2065 by gezelter, Thu Mar 5 15:11:00 2015 UTC

# Line 6 | Line 6
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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
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 + *
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, 234107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #ifndef PRIMITIVES_CUTOFFGROUP_HPP
# Line 46 | Line 47
47   #include "primitives/Atom.hpp"
48   #include "math/Vector3.hpp"
49  
50 < namespace oopse {
50 > namespace OpenMD {
51    class CutoffGroup {
52    public:
53 +    
54 +    CutoffGroup() :  snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {
55  
56 <    CutoffGroup() {
56 >      storage_ = &Snapshot::cgData;
57        haveTotalMass = false;
58        totalMass = 0.0;
59      }
60 +    
61 +    /**
62 +     * Sets the Snapshot Manager of this cutoffGroup
63 +     */
64 +    void setSnapshotManager(SnapshotManager* sman) {
65 +      snapshotMan_ = sman;
66 +    }
67  
68 +
69      void addAtom(Atom *atom) {
70        cutoffAtomList.push_back(atom);
71      }
72 <
72 >    
73      Atom *beginAtom(std::vector<Atom *>::iterator & i) {
74        i = cutoffAtomList.begin();
75        return i != cutoffAtomList.end() ? *i : NULL;
76      }
77 <
77 >    
78      Atom *nextAtom(std::vector<Atom *>::iterator & i) {
79        i++;
80        return i != cutoffAtomList.end() ? *i : NULL;
# Line 71 | Line 82 | namespace oopse {
82  
83      std::vector<Atom*> getAtoms() { return cutoffAtomList; }
84      RealType getMass() {
85 <      std::vector<Atom *>::iterator i;
75 <      Atom * atom;
76 <      RealType mass;
77 <
85 >      
86        if (!haveTotalMass) {
87 <        totalMass = 0;
88 <
89 <        for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
90 <          mass = atom->getMass();
87 >        totalMass = 0.0;
88 >        
89 >        std::vector<Atom *>::iterator i;
90 >        for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
91 >          RealType mass = atom->getMass();
92            totalMass += mass;
93          }
94 <
94 >        
95          haveTotalMass = true;
96        }
97 <
97 >      
98        return totalMass;
99      }
100 +    
101 +    void updateCOM() {
102  
103 <    void getCOM(Vector3d & com) {
104 <      std::vector<Atom *>::iterator i;
105 <      Atom * atom;
95 <      Vector3d pos;
96 <      RealType mass;
103 >      DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
104 >      bool needsVel = false;
105 >      if (data.getStorageLayout() & DataStorage::dslVelocity) needsVel = true;
106  
98      com[0] = 0;
99      com[1] = 0;
100      com[2] = 0;
101      totalMass = getMass();
102
107        if (cutoffAtomList.size() == 1) {
108 <        com = beginAtom(i)->getPos();
108 >        data.position[localIndex_] = cutoffAtomList[0]->getPos();
109 >        if (needsVel)
110 >          data.velocity[localIndex_] = cutoffAtomList[0]->getVel();
111        } else {
112 +        std::vector<Atom *>::iterator i;
113 +        Atom * atom;
114 +        RealType totalMass = getMass();
115 +        data.position[localIndex_] = V3Zero;
116 +        if (needsVel) data.velocity[localIndex_] = V3Zero;
117 +        
118          for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
119 <          mass = atom->getMass();
120 <          pos = atom->getPos();
121 <          com += pos * mass;
122 <        }
123 <
124 <        com /= totalMass;
125 <      }
119 >          data.position[localIndex_] += atom->getMass() * atom->getPos();
120 >          if (needsVel)
121 >            data.velocity[localIndex_] += atom->getMass() * atom->getVel();
122 >        }    
123 >        data.position[localIndex_] /= totalMass;
124 >        if (needsVel) data.velocity[localIndex_] /= totalMass;          
125 >      }      
126      }
127  
128 +
129 +    Vector3d getPos() {
130 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];      
131 +    }
132 +    Vector3d getVel() {
133 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];      
134 +    }
135 +    
136      int getNumAtom() {
137        return cutoffAtomList.size();
138      }
139 <
139 >    
140      int getGlobalIndex() {
141        return globalIndex;
142      }
143 <
143 >    
144      void setGlobalIndex(int id) {
145        this->globalIndex = id;
146      }
147  
148 <  private:
148 >    /**
149 >     * Returns the local index of this cutoffGroup
150 >     * @return the local index of this cutoffGroup
151 >     */
152 >    int getLocalIndex() {
153 >      return localIndex_;
154 >    }
155  
156 +    /**
157 +     * Sets the local index of this cutoffGroup
158 +     * @param index new index to be set
159 +     */        
160 +    void setLocalIndex(int index) {
161 +      localIndex_ = index;
162 +    }
163 +    
164 +  private:
165 +    
166      std::vector<Atom *>cutoffAtomList;
167      bool haveTotalMass;
168      RealType totalMass;
169 <    int globalIndex;
134 <  };
169 >    int globalIndex;    
170  
171 < }      //end namespace oopse
171 >    int localIndex_;
172 >    DataStoragePointer storage_;
173 >    SnapshotManager* snapshotMan_;
174  
175 +  };  
176 + } //end namespace OpenMD
177   #endif //PRIMITIVES_CUTOFFGROUP_HPP  

Comparing trunk/src/primitives/CutoffGroup.hpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2065 by gezelter, Thu Mar 5 15:11:00 2015 UTC

# Line 0 | Line 1
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