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Comparing branches/development/src/primitives/CutoffGroup.hpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
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).                        
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 50 | Line 51 | namespace OpenMD {
51    class CutoffGroup {
52    public:
53      
54 <    CutoffGroup() {
54 >    CutoffGroup() :  snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {
55 >
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      }
# Line 89 | Line 100 | namespace OpenMD {
100        return totalMass;
101      }
102      
103 <    void getCOM(Vector3d & com) {
103 >    void updateCOM() {
104        std::vector<Atom *>::iterator i;
105        Atom * atom;
106 <      Vector3d pos;
107 <      RealType mass;
108 <      
109 <      com[0] = 0;
99 <      com[1] = 0;
100 <      com[2] = 0;
106 >
107 >      DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
108 >      int storageLayout = data.getStorageLayout();
109 >    
110        totalMass = getMass();
111        
112        if (cutoffAtomList.size() == 1) {
113 <        com = beginAtom(i)->getPos();
113 >        data.position[localIndex_] = beginAtom(i)->getPos();
114        } else {
115 +        data.position[localIndex_] = V3Zero;
116          for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
117 <          mass = atom->getMass();
118 <          pos = atom->getPos();
119 <          com += pos * mass;
110 <        }
111 <        
112 <        com /= totalMass;
117 >          data.position[localIndex_] += atom->getMass() * atom->getPos();
118 >        }        
119 >        data.position[localIndex_] /= totalMass;
120        }
121 +
122 +      if (storageLayout & DataStorage::dslVelocity) {
123 +        if (cutoffAtomList.size() == 1) {
124 +          data.velocity[localIndex_] = beginAtom(i)->getVel();
125 +        } else {
126 +          data.velocity[localIndex_] = V3Zero;
127 +          for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
128 +            data.velocity[localIndex_] += atom->getMass() * atom->getVel();
129 +          }        
130 +          data.velocity[localIndex_] /= totalMass;
131 +        }
132 +      }
133      }
134 +
135 +
136 +    Vector3d getPos() {
137 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];      
138 +    }
139 +    Vector3d getVel() {
140 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];      
141 +    }
142      
143      int getNumAtom() {
144        return cutoffAtomList.size();
# Line 124 | Line 151 | namespace OpenMD {
151      void setGlobalIndex(int id) {
152        this->globalIndex = id;
153      }
154 +
155 +    /**
156 +     * Returns the local index of this cutoffGroup
157 +     * @return the local index of this cutoffGroup
158 +     */
159 +    int getLocalIndex() {
160 +      return localIndex_;
161 +    }
162 +
163 +    /**
164 +     * Sets the local index of this cutoffGroup
165 +     * @param index new index to be set
166 +     */        
167 +    void setLocalIndex(int index) {
168 +      localIndex_ = index;
169 +    }
170      
171    private:
172      
173      std::vector<Atom *>cutoffAtomList;
174      bool haveTotalMass;
175      RealType totalMass;
176 <    int globalIndex;
176 >    int globalIndex;    
177 >
178 >    int localIndex_;
179 >    DataStoragePointer storage_;
180 >    SnapshotManager* snapshotMan_;
181 >
182    };  
183   } //end namespace OpenMD
184   #endif //PRIMITIVES_CUTOFFGROUP_HPP  

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