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root/OpenMD/branches/development/src/primitives/CutoffGroup.hpp
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Comparing branches/development/src/primitives/CutoffGroup.hpp (file contents):
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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).          
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   */
# Line 51 | Line 51 | namespace OpenMD {
51    class CutoffGroup {
52    public:
53      
54 <    CutoffGroup() :  snapshotMan_(NULL) {
54 >    CutoffGroup() :  snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {
55  
56        storage_ = &Snapshot::cgData;
57        haveTotalMass = false;
# Line 83 | Line 83 | namespace OpenMD {
83      std::vector<Atom*> getAtoms() { return cutoffAtomList; }
84      RealType getMass() {
85        std::vector<Atom *>::iterator i;
86 –      Atom * atom;
87 –      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 105 | Line 103 | namespace OpenMD {
103        Atom * atom;
104  
105        DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
106 +      int storageLayout = data.getStorageLayout();
107      
108        totalMass = getMass();
109        
# Line 117 | Line 116 | namespace OpenMD {
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();

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