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Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC vs.
Revision 1668 by gezelter, Fri Jan 6 19:03:05 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 218 | Line 234 | namespace OpenMD {
234        }      
235      }
236  
237 < #endif
222 <
223 <    // allocate memory for the parallel objects
224 <    atypesLocal.resize(nLocal_);
225 <
226 <    for (int i = 0; i < nLocal_; i++)
227 <      atypesLocal[i] = ff_->getAtomType(idents[i]);
228 <
229 <    groupList_.clear();
230 <    groupList_.resize(nGroups_);
231 <    for (int i = 0; i < nGroups_; i++) {
232 <      int gid = cgLocalToGlobal[i];
233 <      for (int j = 0; j < nLocal_; j++) {
234 <        int aid = AtomLocalToGlobal[j];
235 <        if (globalGroupMembership[aid] == gid) {
236 <          groupList_[i].push_back(j);
237 <        }
238 <      }      
239 <    }
240 <
237 > #else
238      excludesForAtom.clear();
239      excludesForAtom.resize(nLocal_);
240      toposForAtom.clear();
# Line 270 | 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 668 | 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 697 | Line 715 | namespace OpenMD {
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
# Line 811 | Line 836 | namespace OpenMD {
836     */
837    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
838      int unique_id_1, unique_id_2;
839 <    
839 >        
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 + #else
845 +    unique_id_1 = AtomLocalToGlobal[atom1];
846 +    unique_id_2 = AtomLocalToGlobal[atom2];
847 + #endif  
848  
820 –    // this situation should only arise in MPI simulations
849      if (unique_id_1 == unique_id_2) return true;
850 <    
850 >
851 > #ifdef IS_MPI
852      // this prevents us from doing the pair on multiple processors
853      if (unique_id_1 < unique_id_2) {
854        if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
855      } else {
856 <      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
856 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
857      }
858   #endif
859 +    
860      return false;
861    }
862  
# Line 840 | Line 870 | namespace OpenMD {
870     * field) must still be handled for these pairs.
871     */
872    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
873 <    int unique_id_2;
874 < #ifdef IS_MPI
875 <    // in MPI, we have to look up the unique IDs for the row atom.
846 <    unique_id_2 = AtomColToGlobal[atom2];
847 < #else
848 <    // in the normal loop, the atom numbers are unique
849 <    unique_id_2 = atom2;
850 < #endif
873 >
874 >    // excludesForAtom was constructed to use row/column indices in the MPI
875 >    // version, and to use local IDs in the non-MPI version:
876      
877      for (vector<int>::iterator i = excludesForAtom[atom1].begin();
878           i != excludesForAtom[atom1].end(); ++i) {
879 <      if ( (*i) == unique_id_2 ) return true;
879 >      if ( (*i) == atom2 ) return true;
880      }
881  
882      return false;
# Line 976 | Line 1001 | namespace OpenMD {
1001    
1002    void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1003   #ifdef IS_MPI
1004 <    pot_row[atom1] += 0.5 *  *(idat.pot);
1005 <    pot_col[atom2] += 0.5 *  *(idat.pot);
1004 >    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1005 >    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1006  
1007      atomRowData.force[atom1] += *(idat.f1);
1008      atomColData.force[atom2] -= *(idat.f1);
# Line 1091 | Line 1116 | namespace OpenMD {
1116          // add this cutoff group to the list of groups in this cell;
1117          cellListCol_[cellIndex].push_back(i);
1118        }
1119 +    
1120   #else
1121        for (int i = 0; i < nGroups_; i++) {
1122          rs = snap_->cgData.position[i];
# Line 1116 | Line 1142 | namespace OpenMD {
1142          // add this cutoff group to the list of groups in this cell;
1143          cellList_[cellIndex].push_back(i);
1144        }
1145 +
1146   #endif
1147  
1148        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1128 | Line 1155 | namespace OpenMD {
1155                   os != cellOffsets_.end(); ++os) {
1156                
1157                Vector3i m2v = m1v + (*os);
1158 <              
1158 >            
1159 >
1160                if (m2v.x() >= nCells_.x()) {
1161                  m2v.x() = 0;          
1162                } else if (m2v.x() < 0) {
# Line 1146 | Line 1174 | namespace OpenMD {
1174                } else if (m2v.z() < 0) {
1175                  m2v.z() = nCells_.z() - 1;
1176                }
1177 <              
1177 >
1178                int m2 = Vlinear (m2v, nCells_);
1179                
1180   #ifdef IS_MPI
# Line 1155 | Line 1183 | namespace OpenMD {
1183                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1184                       j2 != cellListCol_[m2].end(); ++j2) {
1185                    
1186 <                  // In parallel, we need to visit *all* pairs of row &
1187 <                  // column indicies and will truncate later on.
1186 >                  // In parallel, we need to visit *all* pairs of row
1187 >                  // & column indicies and will divide labor in the
1188 >                  // force evaluation later.
1189                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1190                    snap_->wrapVector(dr);
1191                    cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1166 | Line 1195 | namespace OpenMD {
1195                  }
1196                }
1197   #else
1169 –              
1198                for (vector<int>::iterator j1 = cellList_[m1].begin();
1199                     j1 != cellList_[m1].end(); ++j1) {
1200                  for (vector<int>::iterator j2 = cellList_[m2].begin();
1201                       j2 != cellList_[m2].end(); ++j2) {
1202 <                  
1202 >    
1203                    // Always do this if we're in different cells or if
1204 <                  // we're in the same cell and the global index of the
1205 <                  // j2 cutoff group is less than the j1 cutoff group
1206 <                  
1207 <                  if (m2 != m1 || (*j2) < (*j1)) {
1204 >                  // we're in the same cell and the global index of
1205 >                  // the j2 cutoff group is greater than or equal to
1206 >                  // the j1 cutoff group.  Note that Rappaport's code
1207 >                  // has a "less than" conditional here, but that
1208 >                  // deals with atom-by-atom computation.  OpenMD
1209 >                  // allows atoms within a single cutoff group to
1210 >                  // interact with each other.
1211 >
1212 >
1213 >
1214 >                  if (m2 != m1 || (*j2) >= (*j1) ) {
1215 >
1216                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1217                      snap_->wrapVector(dr);
1218                      cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1195 | Line 1231 | namespace OpenMD {
1231        // branch to do all cutoff group pairs
1232   #ifdef IS_MPI
1233        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1234 <        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1234 >        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1235            dr = cgColData.position[j2] - cgRowData.position[j1];
1236            snap_->wrapVector(dr);
1237            cuts = getGroupCutoffs( j1, j2 );
# Line 1203 | Line 1239 | namespace OpenMD {
1239              neighborList.push_back(make_pair(j1, j2));
1240            }
1241          }
1242 <      }
1242 >      }      
1243   #else
1244 <      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1245 <        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1244 >      // include all groups here.
1245 >      for (int j1 = 0; j1 < nGroups_; j1++) {
1246 >        // include self group interactions j2 == j1
1247 >        for (int j2 = j1; j2 < nGroups_; j2++) {
1248            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1249            snap_->wrapVector(dr);
1250            cuts = getGroupCutoffs( j1, j2 );
1251            if (dr.lengthSquare() < cuts.third) {
1252              neighborList.push_back(make_pair(j1, j2));
1253            }
1254 <        }
1255 <      }        
1254 >        }    
1255 >      }
1256   #endif
1257      }
1258        

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