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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC vs.
Revision 1616 by gezelter, Tue Aug 30 15:45:35 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 154 | Line 169 | namespace OpenMD {
169      AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170      AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171  
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 –    }
169 –
172      cgRowToGlobal.resize(nGroupsInRow_);
173      cgColToGlobal.resize(nGroupsInCol_);
174      cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175      cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
174 –
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 –    }
176  
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 297 | Line 266 | namespace OpenMD {
266          }
267        }      
268      }
269 <    
269 > #endif
270 >
271 >    // allocate memory for the parallel objects
272 >    atypesLocal.resize(nLocal_);
273 >
274 >    for (int i = 0; i < nLocal_; i++)
275 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
276 >
277 >    groupList_.clear();
278 >    groupList_.resize(nGroups_);
279 >    for (int i = 0; i < nGroups_; i++) {
280 >      int gid = cgLocalToGlobal[i];
281 >      for (int j = 0; j < nLocal_; j++) {
282 >        int aid = AtomLocalToGlobal[j];
283 >        if (globalGroupMembership[aid] == gid) {
284 >          groupList_[i].push_back(j);
285 >        }
286 >      }      
287 >    }
288 >
289 >
290      createGtypeCutoffMap();
291  
292    }
# Line 575 | Line 564 | namespace OpenMD {
564                                   atomColData.position);
565      
566      // gather up the cutoff group positions
578 –
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 –    }
567  
568      cgPlanVectorRow->gather(snap_->cgData.position,
569                              cgRowData.position);
570  
587 –    cerr  << "after gather\n";
588 –    for (int i = 0; i < cgRowData.position.size(); i++) {
589 –      cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590 –    }
591 –
571      cgPlanVectorColumn->gather(snap_->cgData.position,
572                                 cgColData.position);
594 –    for (int i = 0; i < cgColData.position.size(); i++) {
595 –      cerr << "cgCpos = " << cgColData.position[i] << "\n";
596 –    }
573  
574      
575      // if needed, gather the atomic rotation matrices
# Line 708 | Line 684 | namespace OpenMD {
684        }
685        
686        AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
687 <      for (int i = 0; i < ns; i++)
687 >      for (int i = 0; i < ns; i++)
688          snap_->atomData.skippedCharge[i] += skch_tmp[i];
689 +            
690      }
691      
692      nLocal_ = snap_->getNumberOfAtoms();
# Line 731 | Line 708 | namespace OpenMD {
708      
709      for (int ii = 0;  ii < pot_temp.size(); ii++ )
710        pairwisePot += pot_temp[ii];    
711 +    
712 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
713 +      RealType ploc1 = pairwisePot[ii];
714 +      RealType ploc2 = 0.0;
715 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
716 +      pairwisePot[ii] = ploc2;
717 +    }
718 +
719 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
720 +      RealType ploc1 = embeddingPot[ii];
721 +      RealType ploc2 = 0.0;
722 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
723 +      embeddingPot[ii] = ploc2;
724 +    }
725 +
726   #endif
727  
736 –    cerr << "pairwisePot = " <<  pairwisePot << "\n";
728    }
729  
730    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 768 | Line 759 | namespace OpenMD {
759      
760   #ifdef IS_MPI
761      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";
762   #else
763      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";
764   #endif
765      
766      snap_->wrapVector(d);
# Line 848 | Line 835 | namespace OpenMD {
835     */
836    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
837      int unique_id_1, unique_id_2;
838 <    
852 <
853 <    cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
838 >        
839   #ifdef IS_MPI
840      // in MPI, we have to look up the unique IDs for each atom
841      unique_id_1 = AtomRowToGlobal[atom1];
842      unique_id_2 = AtomColToGlobal[atom2];
843 + #else
844 +    unique_id_1 = AtomLocalToGlobal[atom1];
845 +    unique_id_2 = AtomLocalToGlobal[atom2];
846 + #endif  
847  
859 –    cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
860 –    // this situation should only arise in MPI simulations
848      if (unique_id_1 == unique_id_2) return true;
849 <    
849 >
850 > #ifdef IS_MPI
851      // this prevents us from doing the pair on multiple processors
852      if (unique_id_1 < unique_id_2) {
853        if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
854      } else {
855 <      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
855 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
856      }
857   #endif
858 +    
859      return false;
860    }
861  
# Line 880 | Line 869 | namespace OpenMD {
869     * field) must still be handled for these pairs.
870     */
871    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
872 <    int unique_id_2;
873 < #ifdef IS_MPI
874 <    // 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
872 >
873 >    // excludesForAtom was constructed to use row/column indices in the MPI
874 >    // version, and to use local IDs in the non-MPI version:
875      
876      for (vector<int>::iterator i = excludesForAtom[atom1].begin();
877           i != excludesForAtom[atom1].end(); ++i) {
878 <      if ( (*i) == unique_id_2 ) return true;
878 >      if ( (*i) == atom2 ) return true;
879      }
880  
881      return false;
# Line 1131 | Line 1115 | namespace OpenMD {
1115          // add this cutoff group to the list of groups in this cell;
1116          cellListCol_[cellIndex].push_back(i);
1117        }
1118 +    
1119   #else
1120        for (int i = 0; i < nGroups_; i++) {
1121          rs = snap_->cgData.position[i];
# Line 1156 | Line 1141 | namespace OpenMD {
1141          // add this cutoff group to the list of groups in this cell;
1142          cellList_[cellIndex].push_back(i);
1143        }
1144 +
1145   #endif
1146  
1147        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1168 | Line 1154 | namespace OpenMD {
1154                   os != cellOffsets_.end(); ++os) {
1155                
1156                Vector3i m2v = m1v + (*os);
1157 <              
1157 >            
1158 >
1159                if (m2v.x() >= nCells_.x()) {
1160                  m2v.x() = 0;          
1161                } else if (m2v.x() < 0) {
# Line 1186 | Line 1173 | namespace OpenMD {
1173                } else if (m2v.z() < 0) {
1174                  m2v.z() = nCells_.z() - 1;
1175                }
1176 <              
1176 >
1177                int m2 = Vlinear (m2v, nCells_);
1178                
1179   #ifdef IS_MPI
# Line 1195 | Line 1182 | namespace OpenMD {
1182                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1183                       j2 != cellListCol_[m2].end(); ++j2) {
1184                    
1185 <                  // In parallel, we need to visit *all* pairs of row &
1186 <                  // column indicies and will truncate later on.
1185 >                  // In parallel, we need to visit *all* pairs of row
1186 >                  // & column indicies and will divide labor in the
1187 >                  // force evaluation later.
1188                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1189                    snap_->wrapVector(dr);
1190                    cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1206 | Line 1194 | namespace OpenMD {
1194                  }
1195                }
1196   #else
1209 –              
1197                for (vector<int>::iterator j1 = cellList_[m1].begin();
1198                     j1 != cellList_[m1].end(); ++j1) {
1199                  for (vector<int>::iterator j2 = cellList_[m2].begin();
1200                       j2 != cellList_[m2].end(); ++j2) {
1201 <                  
1201 >    
1202                    // Always do this if we're in different cells or if
1203 <                  // we're in the same cell and the global index of the
1204 <                  // j2 cutoff group is less than the j1 cutoff group
1205 <                  
1206 <                  if (m2 != m1 || (*j2) < (*j1)) {
1203 >                  // we're in the same cell and the global index of
1204 >                  // the j2 cutoff group is greater than or equal to
1205 >                  // the j1 cutoff group.  Note that Rappaport's code
1206 >                  // has a "less than" conditional here, but that
1207 >                  // deals with atom-by-atom computation.  OpenMD
1208 >                  // allows atoms within a single cutoff group to
1209 >                  // interact with each other.
1210 >
1211 >
1212 >
1213 >                  if (m2 != m1 || (*j2) >= (*j1) ) {
1214 >
1215                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1216                      snap_->wrapVector(dr);
1217                      cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1235 | Line 1230 | namespace OpenMD {
1230        // branch to do all cutoff group pairs
1231   #ifdef IS_MPI
1232        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1233 <        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1233 >        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1234            dr = cgColData.position[j2] - cgRowData.position[j1];
1235            snap_->wrapVector(dr);
1236            cuts = getGroupCutoffs( j1, j2 );
# Line 1243 | Line 1238 | namespace OpenMD {
1238              neighborList.push_back(make_pair(j1, j2));
1239            }
1240          }
1241 <      }
1241 >      }      
1242   #else
1243 <      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1244 <        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1243 >      // include all groups here.
1244 >      for (int j1 = 0; j1 < nGroups_; j1++) {
1245 >        // include self group interactions j2 == j1
1246 >        for (int j2 = j1; j2 < nGroups_; j2++) {
1247            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1248            snap_->wrapVector(dr);
1249            cuts = getGroupCutoffs( j1, j2 );
1250            if (dr.lengthSquare() < cuts.third) {
1251              neighborList.push_back(make_pair(j1, j2));
1252            }
1253 <        }
1254 <      }        
1253 >        }    
1254 >      }
1255   #endif
1256      }
1257        

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