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Revision 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC vs.
Revision 1706 by gezelter, Fri Apr 27 20:44:16 2012 UTC

# Line 36 | Line 36
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).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42   #include "parallel/ForceMatrixDecomposition.hpp"
43   #include "math/SquareMatrix3.hpp"
# Line 53 | Line 54 | namespace OpenMD {
54      // surrounding cells (not just the 14 upper triangular blocks that
55      // are used when the processor can see all pairs)
56   #ifdef IS_MPI
57 <    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) );
57 >    cellOffsets_.clear();
58      cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59      cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60 <    cellOffsets_.push_back( Vector3i( 1,-1,-1) );
60 >    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
61 >    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62 >    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63      cellOffsets_.push_back( Vector3i( 1, 0,-1) );
66 –    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 –    cellOffsets_.push_back( Vector3i( 0, 1,-1) );
64      cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
66 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );      
71 +    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72 +    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73 +    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74 +    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75 +    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76 +    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77 +    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78 +    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80 +    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81 +    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82 +    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83 +    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84 +    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85   #endif    
86    }
87  
# Line 154 | Line 170 | namespace OpenMD {
170      AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
171      AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
172  
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 –
173      cgRowToGlobal.resize(nGroupsInRow_);
174      cgColToGlobal.resize(nGroupsInCol_);
175      cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176      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 –    }
177  
188 –
178      massFactorsRow.resize(nAtomsInRow_);
179      massFactorsCol.resize(nAtomsInCol_);
180      AtomPlanRealRow->gather(massFactors, massFactorsRow);
# Line 245 | Line 234 | namespace OpenMD {
234        }      
235      }
236  
237 < #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 <
237 > #else
238      excludesForAtom.clear();
239      excludesForAtom.resize(nLocal_);
240      toposForAtom.clear();
# 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 547 | Line 537 | namespace OpenMD {
537        fill(snap_->atomData.density.begin(),
538             snap_->atomData.density.end(), 0.0);
539      }
540 +
541      if (storageLayout_ & DataStorage::dslFunctional) {
542        fill(snap_->atomData.functional.begin(),
543             snap_->atomData.functional.end(), 0.0);
544      }
545 +
546      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
547        fill(snap_->atomData.functionalDerivative.begin(),
548             snap_->atomData.functionalDerivative.end(), 0.0);
549      }
550 +
551      if (storageLayout_ & DataStorage::dslSkippedCharge) {      
552        fill(snap_->atomData.skippedCharge.begin(),
553             snap_->atomData.skippedCharge.end(), 0.0);
554      }
562 –    
555    }
556  
557  
# Line 576 | Line 568 | namespace OpenMD {
568      
569      // gather up the cutoff group positions
570  
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 –
571      cgPlanVectorRow->gather(snap_->cgData.position,
572                              cgRowData.position);
573  
587 –    cerr  << "after gather\n";
588 –    for (int i = 0; i < cgRowData.position.size(); i++) {
589 –      cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590 –    }
591 –
574      cgPlanVectorColumn->gather(snap_->cgData.position,
575                                 cgColData.position);
594 –    for (int i = 0; i < cgColData.position.size(); i++) {
595 –      cerr << "cgCpos = " << cgColData.position[i] << "\n";
596 –    }
576  
577      
578      // if needed, gather the atomic rotation matrices
# Line 708 | Line 687 | namespace OpenMD {
687        }
688        
689        AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
690 <      for (int i = 0; i < ns; i++)
690 >      for (int i = 0; i < ns; i++)
691          snap_->atomData.skippedCharge[i] += skch_tmp[i];
692 +            
693      }
694      
695      nLocal_ = snap_->getNumberOfAtoms();
# Line 731 | Line 711 | namespace OpenMD {
711      
712      for (int ii = 0;  ii < pot_temp.size(); ii++ )
713        pairwisePot += pot_temp[ii];    
714 +    
715 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
716 +      RealType ploc1 = pairwisePot[ii];
717 +      RealType ploc2 = 0.0;
718 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
719 +      pairwisePot[ii] = ploc2;
720 +    }
721 +
722 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
723 +      RealType ploc1 = embeddingPot[ii];
724 +      RealType ploc2 = 0.0;
725 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
726 +      embeddingPot[ii] = ploc2;
727 +    }
728 +
729   #endif
730  
736 –    cerr << "pairwisePot = " <<  pairwisePot << "\n";
731    }
732  
733    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 768 | Line 762 | namespace OpenMD {
762      
763   #ifdef IS_MPI
764      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";
765   #else
766      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";
767   #endif
768      
769      snap_->wrapVector(d);
# Line 848 | Line 838 | namespace OpenMD {
838     */
839    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
840      int unique_id_1, unique_id_2;
841 <    
852 <
853 <    cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
841 >        
842   #ifdef IS_MPI
843      // in MPI, we have to look up the unique IDs for each atom
844      unique_id_1 = AtomRowToGlobal[atom1];
845      unique_id_2 = AtomColToGlobal[atom2];
846 + #else
847 +    unique_id_1 = AtomLocalToGlobal[atom1];
848 +    unique_id_2 = AtomLocalToGlobal[atom2];
849 + #endif  
850  
859 –    cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
860 –    // this situation should only arise in MPI simulations
851      if (unique_id_1 == unique_id_2) return true;
852 <    
852 >
853 > #ifdef IS_MPI
854      // this prevents us from doing the pair on multiple processors
855      if (unique_id_1 < unique_id_2) {
856        if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
857      } else {
858 <      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
858 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
859      }
860   #endif
861 +    
862      return false;
863    }
864  
# Line 880 | Line 872 | namespace OpenMD {
872     * field) must still be handled for these pairs.
873     */
874    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
875 <    int unique_id_2;
876 < #ifdef IS_MPI
877 <    // 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
875 >
876 >    // excludesForAtom was constructed to use row/column indices in the MPI
877 >    // version, and to use local IDs in the non-MPI version:
878      
879      for (vector<int>::iterator i = excludesForAtom[atom1].begin();
880           i != excludesForAtom[atom1].end(); ++i) {
881 <      if ( (*i) == unique_id_2 ) return true;
881 >      if ( (*i) == atom2 ) return true;
882      }
883  
884      return false;
# Line 966 | Line 953 | namespace OpenMD {
953      }
954  
955   #else
956 +    
957 +
958 +    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
959 +    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
960 +    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
961  
962      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
963      //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
# Line 1016 | Line 1008 | namespace OpenMD {
1008    
1009    void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1010   #ifdef IS_MPI
1011 <    pot_row[atom1] += 0.5 *  *(idat.pot);
1012 <    pot_col[atom2] += 0.5 *  *(idat.pot);
1011 >    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1012 >    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1013  
1014      atomRowData.force[atom1] += *(idat.f1);
1015      atomColData.force[atom2] -= *(idat.f1);
# Line 1131 | Line 1123 | namespace OpenMD {
1123          // add this cutoff group to the list of groups in this cell;
1124          cellListCol_[cellIndex].push_back(i);
1125        }
1126 +    
1127   #else
1128        for (int i = 0; i < nGroups_; i++) {
1129          rs = snap_->cgData.position[i];
# Line 1156 | Line 1149 | namespace OpenMD {
1149          // add this cutoff group to the list of groups in this cell;
1150          cellList_[cellIndex].push_back(i);
1151        }
1152 +
1153   #endif
1154  
1155        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1168 | Line 1162 | namespace OpenMD {
1162                   os != cellOffsets_.end(); ++os) {
1163                
1164                Vector3i m2v = m1v + (*os);
1165 <              
1165 >            
1166 >
1167                if (m2v.x() >= nCells_.x()) {
1168                  m2v.x() = 0;          
1169                } else if (m2v.x() < 0) {
# Line 1186 | Line 1181 | namespace OpenMD {
1181                } else if (m2v.z() < 0) {
1182                  m2v.z() = nCells_.z() - 1;
1183                }
1184 <              
1184 >
1185                int m2 = Vlinear (m2v, nCells_);
1186                
1187   #ifdef IS_MPI
# Line 1195 | Line 1190 | namespace OpenMD {
1190                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1191                       j2 != cellListCol_[m2].end(); ++j2) {
1192                    
1193 <                  // In parallel, we need to visit *all* pairs of row &
1194 <                  // column indicies and will truncate later on.
1193 >                  // In parallel, we need to visit *all* pairs of row
1194 >                  // & column indicies and will divide labor in the
1195 >                  // force evaluation later.
1196                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1197                    snap_->wrapVector(dr);
1198                    cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1206 | Line 1202 | namespace OpenMD {
1202                  }
1203                }
1204   #else
1209 –              
1205                for (vector<int>::iterator j1 = cellList_[m1].begin();
1206                     j1 != cellList_[m1].end(); ++j1) {
1207                  for (vector<int>::iterator j2 = cellList_[m2].begin();
1208                       j2 != cellList_[m2].end(); ++j2) {
1209 <                  
1209 >    
1210                    // Always do this if we're in different cells or if
1211 <                  // we're in the same cell and the global index of the
1212 <                  // j2 cutoff group is less than the j1 cutoff group
1213 <                  
1214 <                  if (m2 != m1 || (*j2) < (*j1)) {
1211 >                  // we're in the same cell and the global index of
1212 >                  // the j2 cutoff group is greater than or equal to
1213 >                  // the j1 cutoff group.  Note that Rappaport's code
1214 >                  // has a "less than" conditional here, but that
1215 >                  // deals with atom-by-atom computation.  OpenMD
1216 >                  // allows atoms within a single cutoff group to
1217 >                  // interact with each other.
1218 >
1219 >
1220 >
1221 >                  if (m2 != m1 || (*j2) >= (*j1) ) {
1222 >
1223                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1224                      snap_->wrapVector(dr);
1225                      cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1235 | Line 1238 | namespace OpenMD {
1238        // branch to do all cutoff group pairs
1239   #ifdef IS_MPI
1240        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1241 <        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1241 >        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1242            dr = cgColData.position[j2] - cgRowData.position[j1];
1243            snap_->wrapVector(dr);
1244            cuts = getGroupCutoffs( j1, j2 );
# Line 1243 | Line 1246 | namespace OpenMD {
1246              neighborList.push_back(make_pair(j1, j2));
1247            }
1248          }
1249 <      }
1249 >      }      
1250   #else
1251 <      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1252 <        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1251 >      // include all groups here.
1252 >      for (int j1 = 0; j1 < nGroups_; j1++) {
1253 >        // include self group interactions j2 == j1
1254 >        for (int j2 = j1; j2 < nGroups_; j2++) {
1255            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1256            snap_->wrapVector(dr);
1257            cuts = getGroupCutoffs( j1, j2 );
1258            if (dr.lengthSquare() < cuts.third) {
1259              neighborList.push_back(make_pair(j1, j2));
1260            }
1261 <        }
1262 <      }        
1261 >        }    
1262 >      }
1263   #endif
1264      }
1265        

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