ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
(Generate patch)

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC vs.
Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

# Line 53 | Line 53 | namespace OpenMD {
53      // surrounding cells (not just the 14 upper triangular blocks that
54      // are used when the processor can see all pairs)
55   #ifdef IS_MPI
56 <    cellOffsets_.push_back( Vector3i(-1, 0, 0) );
57 <    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
58 <    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
59 <    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
60 <    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
61 <    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
56 >    cellOffsets_.clear();
57      cellOffsets_.push_back( Vector3i(-1,-1,-1) );
58      cellOffsets_.push_back( Vector3i( 0,-1,-1) );
59 <    cellOffsets_.push_back( Vector3i( 1,-1,-1) );
59 >    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
60 >    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
61 >    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
62      cellOffsets_.push_back( Vector3i( 1, 0,-1) );
66 –    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 –    cellOffsets_.push_back( Vector3i( 0, 1,-1) );
63      cellOffsets_.push_back( Vector3i(-1, 1,-1) );
64 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
65 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
66 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
67 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
68 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
69 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );      
70 +    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
71 +    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
72 +    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
73 +    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
74 +    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
75 +    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
76 +    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
77 +    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
78 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
79 +    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
80 +    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
81 +    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
82 +    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
83 +    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
84   #endif    
85    }
86  
# Line 153 | Line 168 | namespace OpenMD {
168      AtomColToGlobal.resize(nAtomsInCol_);
169      AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170      AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156 –
157 –    cerr << "Atoms in Local:\n";
158 –    for (int i = 0; i < AtomLocalToGlobal.size(); i++) {
159 –      cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
160 –    }
161 –    cerr << "Atoms in Row:\n";
162 –    for (int i = 0; i < AtomRowToGlobal.size(); i++) {
163 –      cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
164 –    }
165 –    cerr << "Atoms in Col:\n";
166 –    for (int i = 0; i < AtomColToGlobal.size(); i++) {
167 –      cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
168 –    }
171  
172      cgRowToGlobal.resize(nGroupsInRow_);
173      cgColToGlobal.resize(nGroupsInCol_);
174      cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175      cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176  
175 –    cerr << "Gruops in Local:\n";
176 –    for (int i = 0; i < cgLocalToGlobal.size(); i++) {
177 –      cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
178 –    }
179 –    cerr << "Groups in Row:\n";
180 –    for (int i = 0; i < cgRowToGlobal.size(); i++) {
181 –      cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
182 –    }
183 –    cerr << "Groups in Col:\n";
184 –    for (int i = 0; i < cgColToGlobal.size(); i++) {
185 –      cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
186 –    }
187 –
188 –
177      massFactorsRow.resize(nAtomsInRow_);
178      massFactorsCol.resize(nAtomsInCol_);
179      AtomPlanRealRow->gather(massFactors, massFactorsRow);
# Line 245 | Line 233 | namespace OpenMD {
233        }      
234      }
235  
236 < #endif
249 <
250 <    // allocate memory for the parallel objects
251 <    atypesLocal.resize(nLocal_);
252 <
253 <    for (int i = 0; i < nLocal_; i++)
254 <      atypesLocal[i] = ff_->getAtomType(idents[i]);
255 <
256 <    groupList_.clear();
257 <    groupList_.resize(nGroups_);
258 <    for (int i = 0; i < nGroups_; i++) {
259 <      int gid = cgLocalToGlobal[i];
260 <      for (int j = 0; j < nLocal_; j++) {
261 <        int aid = AtomLocalToGlobal[j];
262 <        if (globalGroupMembership[aid] == gid) {
263 <          groupList_[i].push_back(j);
264 <        }
265 <      }      
266 <    }
267 <
236 > #else
237      excludesForAtom.clear();
238      excludesForAtom.resize(nLocal_);
239      toposForAtom.clear();
# Line 278 | Line 247 | namespace OpenMD {
247        for (int j = 0; j < nLocal_; j++) {
248          int jglob = AtomLocalToGlobal[j];
249  
250 <        if (excludes->hasPair(iglob, jglob))
250 >        if (excludes->hasPair(iglob, jglob))          
251            excludesForAtom[i].push_back(j);              
252          
253 +        
254          if (oneTwo->hasPair(iglob, jglob)) {
255            toposForAtom[i].push_back(j);
256            topoDist[i].push_back(1);
# Line 297 | Line 267 | namespace OpenMD {
267          }
268        }      
269      }
270 <    
270 > #endif
271 >
272 >    // allocate memory for the parallel objects
273 >    atypesLocal.resize(nLocal_);
274 >
275 >    for (int i = 0; i < nLocal_; i++)
276 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
277 >
278 >    groupList_.clear();
279 >    groupList_.resize(nGroups_);
280 >    for (int i = 0; i < nGroups_; i++) {
281 >      int gid = cgLocalToGlobal[i];
282 >      for (int j = 0; j < nLocal_; j++) {
283 >        int aid = AtomLocalToGlobal[j];
284 >        if (globalGroupMembership[aid] == gid) {
285 >          groupList_[i].push_back(j);
286 >        }
287 >      }      
288 >    }
289 >
290 >
291      createGtypeCutoffMap();
292  
293    }
# Line 576 | Line 566 | namespace OpenMD {
566      
567      // gather up the cutoff group positions
568  
579 –    cerr  << "before gather\n";
580 –    for (int i = 0; i < snap_->cgData.position.size(); i++) {
581 –      cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
582 –    }
583 –
569      cgPlanVectorRow->gather(snap_->cgData.position,
570                              cgRowData.position);
571  
587 –    cerr  << "after gather\n";
588 –    for (int i = 0; i < cgRowData.position.size(); i++) {
589 –      cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590 –    }
591 –
572      cgPlanVectorColumn->gather(snap_->cgData.position,
573                                 cgColData.position);
594 –    for (int i = 0; i < cgColData.position.size(); i++) {
595 –      cerr << "cgCpos = " << cgColData.position[i] << "\n";
596 –    }
574  
575      
576      // if needed, gather the atomic rotation matrices
# Line 708 | Line 685 | namespace OpenMD {
685        }
686        
687        AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
688 <      for (int i = 0; i < ns; i++)
688 >      for (int i = 0; i < ns; i++)
689          snap_->atomData.skippedCharge[i] += skch_tmp[i];
690 +            
691      }
692      
693      nLocal_ = snap_->getNumberOfAtoms();
# Line 731 | Line 709 | namespace OpenMD {
709      
710      for (int ii = 0;  ii < pot_temp.size(); ii++ )
711        pairwisePot += pot_temp[ii];    
712 +    
713 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
714 +      RealType ploc1 = pairwisePot[ii];
715 +      RealType ploc2 = 0.0;
716 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
717 +      pairwisePot[ii] = ploc2;
718 +    }
719 +
720 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
721 +      RealType ploc1 = embeddingPot[ii];
722 +      RealType ploc2 = 0.0;
723 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
724 +      embeddingPot[ii] = ploc2;
725 +    }
726 +
727   #endif
728  
736 –    cerr << "pairwisePot = " <<  pairwisePot << "\n";
729    }
730  
731    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 768 | Line 760 | namespace OpenMD {
760      
761   #ifdef IS_MPI
762      d = cgColData.position[cg2] - cgRowData.position[cg1];
771 –    cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
772 –    cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
763   #else
764      d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
775 –    cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
776 –    cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
765   #endif
766      
767      snap_->wrapVector(d);
# Line 849 | Line 837 | namespace OpenMD {
837    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
838      int unique_id_1, unique_id_2;
839      
852 –
853 –    cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
840   #ifdef IS_MPI
841      // in MPI, we have to look up the unique IDs for each atom
842      unique_id_1 = AtomRowToGlobal[atom1];
843      unique_id_2 = AtomColToGlobal[atom2];
844  
859 –    cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
845      // this situation should only arise in MPI simulations
846      if (unique_id_1 == unique_id_2) return true;
847      
# Line 880 | Line 865 | namespace OpenMD {
865     * field) must still be handled for these pairs.
866     */
867    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
868 <    int unique_id_2;
869 < #ifdef IS_MPI
870 <    // in MPI, we have to look up the unique IDs for the row atom.
886 <    unique_id_2 = AtomColToGlobal[atom2];
887 < #else
888 <    // in the normal loop, the atom numbers are unique
889 <    unique_id_2 = atom2;
890 < #endif
868 >
869 >    // excludesForAtom was constructed to use row/column indices in the MPI
870 >    // version, and to use local IDs in the non-MPI version:
871      
872      for (vector<int>::iterator i = excludesForAtom[atom1].begin();
873           i != excludesForAtom[atom1].end(); ++i) {
874 <      if ( (*i) == unique_id_2 ) return true;
874 >      if ( (*i) == atom2 )  return true;
875      }
876  
877      return false;
# Line 1131 | Line 1111 | namespace OpenMD {
1111          // add this cutoff group to the list of groups in this cell;
1112          cellListCol_[cellIndex].push_back(i);
1113        }
1114 +    
1115   #else
1116        for (int i = 0; i < nGroups_; i++) {
1117          rs = snap_->cgData.position[i];
# Line 1156 | Line 1137 | namespace OpenMD {
1137          // add this cutoff group to the list of groups in this cell;
1138          cellList_[cellIndex].push_back(i);
1139        }
1140 +
1141   #endif
1142  
1143        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1168 | Line 1150 | namespace OpenMD {
1150                   os != cellOffsets_.end(); ++os) {
1151                
1152                Vector3i m2v = m1v + (*os);
1153 <              
1153 >            
1154 >
1155                if (m2v.x() >= nCells_.x()) {
1156                  m2v.x() = 0;          
1157                } else if (m2v.x() < 0) {
# Line 1186 | Line 1169 | namespace OpenMD {
1169                } else if (m2v.z() < 0) {
1170                  m2v.z() = nCells_.z() - 1;
1171                }
1172 <              
1172 >
1173                int m2 = Vlinear (m2v, nCells_);
1174                
1175   #ifdef IS_MPI
# Line 1195 | Line 1178 | namespace OpenMD {
1178                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1179                       j2 != cellListCol_[m2].end(); ++j2) {
1180                    
1181 <                  // In parallel, we need to visit *all* pairs of row &
1182 <                  // column indicies and will truncate later on.
1181 >                  // In parallel, we need to visit *all* pairs of row
1182 >                  // & column indicies and will divide labor in the
1183 >                  // force evaluation later.
1184                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1185                    snap_->wrapVector(dr);
1186                    cuts = getGroupCutoffs( (*j1), (*j2) );

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines