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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

# Line 57 | Line 57 | namespace OpenMD {
57      nLocal_ = snap_->getNumberOfAtoms();
58      nGroups_ = snap_->getNumberOfCutoffGroups();
59  
60 +    // gather the information for atomtype IDs (atids):
61 +    vector<int> identsLocal = info_->getIdentArray();
62 +    AtomLocalToGlobal = info_->getGlobalAtomIndices();
63 +    cgLocalToGlobal = info_->getGlobalGroupIndices();
64 +    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
65 +    vector<RealType> massFactorsLocal = info_->getMassFactors();
66 +    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
67 +
68   #ifdef IS_MPI
69  
70      AtomCommIntRow = new Communicator<Row,int>(nLocal_);
# Line 93 | Line 101 | namespace OpenMD {
101                                        vector<RealType> (nAtomsInRow_, 0.0));
102      vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
103                                        vector<RealType> (nAtomsInCol_, 0.0));
96 –
97 –
98 –    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
104      
100 –    // gather the information for atomtype IDs (atids):
101 –    vector<int> identsLocal = info_->getIdentArray();
105      identsRow.reserve(nAtomsInRow_);
106      identsCol.reserve(nAtomsInCol_);
107      
108      AtomCommIntRow->gather(identsLocal, identsRow);
109      AtomCommIntColumn->gather(identsLocal, identsCol);
110      
108 –    AtomLocalToGlobal = info_->getGlobalAtomIndices();
111      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
112      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
113      
112 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
114      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
115      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
116  
117 +    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
118 +    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
119 +
120 +    groupListRow_.clear();
121 +    groupListRow_.reserve(nGroupsInRow_);
122 +    for (int i = 0; i < nGroupsInRow_; i++) {
123 +      int gid = cgRowToGlobal[i];
124 +      for (int j = 0; j < nAtomsInRow_; j++) {
125 +        int aid = AtomRowToGlobal[j];
126 +        if (globalGroupMembership[aid] == gid)
127 +          groupListRow_[i].push_back(j);
128 +      }      
129 +    }
130 +
131 +    groupListCol_.clear();
132 +    groupListCol_.reserve(nGroupsInCol_);
133 +    for (int i = 0; i < nGroupsInCol_; i++) {
134 +      int gid = cgColToGlobal[i];
135 +      for (int j = 0; j < nAtomsInCol_; j++) {
136 +        int aid = AtomColToGlobal[j];
137 +        if (globalGroupMembership[aid] == gid)
138 +          groupListCol_[i].push_back(j);
139 +      }      
140 +    }
141 +
142 + #endif
143 +
144 +    groupList_.clear();
145 +    groupList_.reserve(nGroups_);
146 +    for (int i = 0; i < nGroups_; i++) {
147 +      int gid = cgLocalToGlobal[i];
148 +      for (int j = 0; j < nLocal_; j++) {
149 +        int aid = AtomLocalToGlobal[j];
150 +        if (globalGroupMembership[aid] == gid)
151 +          groupList_[i].push_back(j);
152 +      }      
153 +    }
154 +
155 +  
156      // still need:
157      // topoDist
158      // exclude
159 < #endif
159 >
160    }
161      
162  
# Line 244 | Line 284 | namespace OpenMD {
284   #endif
285    }
286  
287 +  /**
288 +   * returns the list of atoms belonging to this group.  
289 +   */
290 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
291 + #ifdef IS_MPI
292 +    return groupListRow_[cg1];
293 + #else
294 +    return groupList_[cg1];
295 + #endif
296 +  }
297 +
298 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
299 + #ifdef IS_MPI
300 +    return groupListCol_[cg2];
301 + #else
302 +    return groupList_[cg2];
303 + #endif
304 +  }
305    
306    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
307      Vector3d d;
# Line 284 | Line 342 | namespace OpenMD {
342      
343      snap_->wrapVector(d);
344      return d;    
345 +  }
346 +
347 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
348 + #ifdef IS_MPI
349 +    return massFactorsRow[atom1];
350 + #else
351 +    return massFactorsLocal[atom1];
352 + #endif
353 +  }
354 +
355 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
356 + #ifdef IS_MPI
357 +    return massFactorsCol[atom2];
358 + #else
359 +    return massFactorsLocal[atom2];
360 + #endif
361 +
362    }
363      
364    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){

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