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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 1875 by gezelter, Fri May 17 14:41:42 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 72 | Line 83 | namespace OpenMD {
83      std::vector<Atom*> getAtoms() { return cutoffAtomList; }
84      RealType getMass() {
85        std::vector<Atom *>::iterator i;
75 –      Atom * atom;
76 –      RealType mass;
86        
87        if (!haveTotalMass) {
88          totalMass = 0;
89          
90 <        for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
91 <          mass = atom->getMass();
90 >        for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
91 >          RealType mass = atom->getMass();
92            totalMass += mass;
93          }
94          
# Line 89 | Line 98 | namespace OpenMD {
98        return totalMass;
99      }
100      
101 <    void getCOM(Vector3d & com) {
101 >    void updateCOM() {
102        std::vector<Atom *>::iterator i;
103        Atom * atom;
104 <      Vector3d pos;
105 <      RealType mass;
106 <      
107 <      com[0] = 0;
99 <      com[1] = 0;
100 <      com[2] = 0;
104 >
105 >      DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
106 >      int storageLayout = data.getStorageLayout();
107 >    
108        totalMass = getMass();
109        
110        if (cutoffAtomList.size() == 1) {
111 <        com = beginAtom(i)->getPos();
111 >        data.position[localIndex_] = beginAtom(i)->getPos();
112        } else {
113 +        data.position[localIndex_] = V3Zero;
114          for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
115 <          mass = atom->getMass();
116 <          pos = atom->getPos();
117 <          com += pos * mass;
110 <        }
111 <        
112 <        com /= totalMass;
115 >          data.position[localIndex_] += atom->getMass() * atom->getPos();
116 >        }        
117 >        data.position[localIndex_] /= totalMass;
118        }
119 +
120 +      if (storageLayout & DataStorage::dslVelocity) {
121 +        if (cutoffAtomList.size() == 1) {
122 +          data.velocity[localIndex_] = beginAtom(i)->getVel();
123 +        } else {
124 +          data.velocity[localIndex_] = V3Zero;
125 +          for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
126 +            data.velocity[localIndex_] += atom->getMass() * atom->getVel();
127 +          }        
128 +          data.velocity[localIndex_] /= totalMass;
129 +        }
130 +      }
131      }
132 +
133 +
134 +    Vector3d getPos() {
135 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];      
136 +    }
137 +    Vector3d getVel() {
138 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];      
139 +    }
140      
141      int getNumAtom() {
142        return cutoffAtomList.size();
# Line 124 | Line 149 | namespace OpenMD {
149      void setGlobalIndex(int id) {
150        this->globalIndex = id;
151      }
152 +
153 +    /**
154 +     * Returns the local index of this cutoffGroup
155 +     * @return the local index of this cutoffGroup
156 +     */
157 +    int getLocalIndex() {
158 +      return localIndex_;
159 +    }
160 +
161 +    /**
162 +     * Sets the local index of this cutoffGroup
163 +     * @param index new index to be set
164 +     */        
165 +    void setLocalIndex(int index) {
166 +      localIndex_ = index;
167 +    }
168      
169    private:
170      
171      std::vector<Atom *>cutoffAtomList;
172      bool haveTotalMass;
173      RealType totalMass;
174 <    int globalIndex;
174 >    int globalIndex;    
175 >
176 >    int localIndex_;
177 >    DataStoragePointer storage_;
178 >    SnapshotManager* snapshotMan_;
179 >
180    };  
181   } //end namespace OpenMD
182   #endif //PRIMITIVES_CUTOFFGROUP_HPP  

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