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Comparing branches/development/src/primitives/CutoffGroup.hpp (file contents):
Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 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() :  snapshotMan_(NULL) {
54 >    CutoffGroup() :  snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {
55  
56        storage_ = &Snapshot::cgData;
56 – #ifdef IS_MPI
57 –      iStorage_ = &Snapshot::cgIData;
58 –      jStorage_ = &Snapshot::cgJData;
59 – #endif
57        haveTotalMass = false;
58        totalMass = 0.0;
59      }
# Line 108 | Line 105 | namespace OpenMD {
105        Atom * atom;
106  
107        DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
108 +      int storageLayout = data.getStorageLayout();
109      
110        totalMass = getMass();
111        
112        if (cutoffAtomList.size() == 1) {
115 –        std::cerr << "YO!\n";
116 –        std::cerr << "atipos = " << beginAtom(i)->getPos() << "\n";
117 –        std::cerr << "lI = " << localIndex_ << "\n";
118 –
113          data.position[localIndex_] = beginAtom(i)->getPos();
120 –        std::cerr << "YOYO!\n";
114        } else {
115          data.position[localIndex_] = V3Zero;
116          for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
# Line 125 | Line 118 | namespace OpenMD {
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 <    /**
132 <     * Returns the current position of this cutoffGroup for the outer
133 <     * iteration over the cutoff groups.  For Force decomposition,
134 <     * this is the position of the cutoff groups ordered by row index.
135 <     * For serial calculations, this is just the position of the
136 <     * cutoff group.
137 <     */    
138 <    Vector3d getPosI() {
139 < #ifdef IS_MPI
140 <      return ((snapshotMan_->getCurrentSnapshot())->*iStorage_).position[iIndex_];
141 < #else
136 >    Vector3d getPos() {
137        return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];      
143 – #endif
138      }
139 <
140 <    /**
147 <     * Returns the current position of this cutoffGroup for the inner
148 <     * iteration over the cutoff groups.  For Force decomposition,
149 <     * this is the position of the cutoff groups ordered by column
150 <     * index.  For serial calculations, this is just the position of
151 <     * the cutoff group.
152 <     */    
153 <    Vector3d getPosJ() {
154 < #ifdef IS_MPI
155 <      return ((snapshotMan_->getCurrentSnapshot())->*jStorage_).position[jIndex_];
156 < #else
157 <      return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];      
158 < #endif
139 >    Vector3d getVel() {
140 >      return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];      
141      }
142      
143      int getNumAtom() {
# Line 196 | Line 178 | namespace OpenMD {
178      int localIndex_;
179      DataStoragePointer storage_;
180      SnapshotManager* snapshotMan_;
199 – #ifdef IS_MPI
200 –    int iIndex_;
201 –    int jIndex_;
202 –    DataStoragePointer iStorage_;
203 –    DataStoragePointer jStorage_;
204 – #endif
181  
182    };  
183   } //end namespace OpenMD

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