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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 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1582 by gezelter, Tue Jun 14 20:41:44 2011 UTC

# Line 57 | Line 57 | namespace OpenMD {
57      storageLayout_ = sman_->getStorageLayout();
58      ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60 –    nGroups_ = snap_->getNumberOfCutoffGroups();
60  
61 +    nGroups_ = info_->getNLocalCutoffGroups();
62 +    cerr << "in dId, nGroups = " << nGroups_ << "\n";
63      // gather the information for atomtype IDs (atids):
64      identsLocal = info_->getIdentArray();
65      AtomLocalToGlobal = info_->getGlobalAtomIndices();
66      cgLocalToGlobal = info_->getGlobalGroupIndices();
67      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68 <    vector<RealType> massFactorsLocal = info_->getMassFactors();
68 >    massFactors = info_->getMassFactors();
69      PairList excludes = info_->getExcludedInteractions();
70      PairList oneTwo = info_->getOneTwoInteractions();
71      PairList oneThree = info_->getOneThreeInteractions();
# Line 104 | Line 105 | namespace OpenMD {
105      cgColData.resize(nGroupsInCol_);
106      cgColData.setStorageLayout(DataStorage::dslPosition);
107          
108 <    identsRow.reserve(nAtomsInRow_);
109 <    identsCol.reserve(nAtomsInCol_);
108 >    identsRow.resize(nAtomsInRow_);
109 >    identsCol.resize(nAtomsInCol_);
110      
111      AtomCommIntRow->gather(identsLocal, identsRow);
112      AtomCommIntColumn->gather(identsLocal, identsCol);
# Line 116 | Line 117 | namespace OpenMD {
117      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
118      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
119  
120 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
121 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
120 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
121 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
122  
123      groupListRow_.clear();
124 <    groupListRow_.reserve(nGroupsInRow_);
124 >    groupListRow_.resize(nGroupsInRow_);
125      for (int i = 0; i < nGroupsInRow_; i++) {
126        int gid = cgRowToGlobal[i];
127        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 131 | Line 132 | namespace OpenMD {
132      }
133  
134      groupListCol_.clear();
135 <    groupListCol_.reserve(nGroupsInCol_);
135 >    groupListCol_.resize(nGroupsInCol_);
136      for (int i = 0; i < nGroupsInCol_; i++) {
137        int gid = cgColToGlobal[i];
138        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 141 | Line 142 | namespace OpenMD {
142        }      
143      }
144  
145 <    skipsForRowAtom.clear();
146 <    skipsForRowAtom.reserve(nAtomsInRow_);
145 >    skipsForAtom.clear();
146 >    skipsForAtom.resize(nAtomsInRow_);
147 >    toposForAtom.clear();
148 >    toposForAtom.resize(nAtomsInRow_);
149 >    topoDist.clear();
150 >    topoDist.resize(nAtomsInRow_);
151      for (int i = 0; i < nAtomsInRow_; i++) {
152        int iglob = AtomRowToGlobal[i];
148 –      for (int j = 0; j < nAtomsInCol_; j++) {
149 –        int jglob = AtomColToGlobal[j];        
150 –        if (excludes.hasPair(iglob, jglob))
151 –          skipsForRowAtom[i].push_back(j);      
152 –      }      
153 –    }
153  
155 –    toposForRowAtom.clear();
156 –    toposForRowAtom.reserve(nAtomsInRow_);
157 –    for (int i = 0; i < nAtomsInRow_; i++) {
158 –      int iglob = AtomRowToGlobal[i];
159 –      int nTopos = 0;
154        for (int j = 0; j < nAtomsInCol_; j++) {
155 <        int jglob = AtomColToGlobal[j];        
155 >        int jglob = AtomColToGlobal[j];
156 >
157 >        if (excludes.hasPair(iglob, jglob))
158 >          skipsForAtom[i].push_back(j);      
159 >        
160          if (oneTwo.hasPair(iglob, jglob)) {
161 <          toposForRowAtom[i].push_back(j);
162 <          topoDistRow[i][nTopos] = 1;
163 <          nTopos++;
161 >          toposForAtom[i].push_back(j);
162 >          topoDist[i].push_back(1);
163 >        } else {
164 >          if (oneThree.hasPair(iglob, jglob)) {
165 >            toposForAtom[i].push_back(j);
166 >            topoDist[i].push_back(2);
167 >          } else {
168 >            if (oneFour.hasPair(iglob, jglob)) {
169 >              toposForAtom[i].push_back(j);
170 >              topoDist[i].push_back(3);
171 >            }
172 >          }
173          }
167 –        if (oneThree.hasPair(iglob, jglob)) {
168 –          toposForRowAtom[i].push_back(j);
169 –          topoDistRow[i][nTopos] = 2;
170 –          nTopos++;
171 –        }
172 –        if (oneFour.hasPair(iglob, jglob)) {
173 –          toposForRowAtom[i].push_back(j);
174 –          topoDistRow[i][nTopos] = 3;
175 –          nTopos++;
176 –        }
174        }      
175      }
176  
177   #endif
178  
179      groupList_.clear();
180 <    groupList_.reserve(nGroups_);
180 >    groupList_.resize(nGroups_);
181      for (int i = 0; i < nGroups_; i++) {
182        int gid = cgLocalToGlobal[i];
183        for (int j = 0; j < nLocal_; j++) {
184          int aid = AtomLocalToGlobal[j];
185 <        if (globalGroupMembership[aid] == gid)
185 >        if (globalGroupMembership[aid] == gid) {
186            groupList_[i].push_back(j);
187 +        }
188        }      
189      }
190  
191 <    skipsForLocalAtom.clear();
192 <    skipsForLocalAtom.reserve(nLocal_);
191 >    skipsForAtom.clear();
192 >    skipsForAtom.resize(nLocal_);
193 >    toposForAtom.clear();
194 >    toposForAtom.resize(nLocal_);
195 >    topoDist.clear();
196 >    topoDist.resize(nLocal_);
197  
198      for (int i = 0; i < nLocal_; i++) {
199        int iglob = AtomLocalToGlobal[i];
198 –      for (int j = 0; j < nLocal_; j++) {
199 –        int jglob = AtomLocalToGlobal[j];        
200 –        if (excludes.hasPair(iglob, jglob))
201 –          skipsForLocalAtom[i].push_back(j);      
202 –      }      
203 –    }
200  
205 –    toposForLocalAtom.clear();
206 –    toposForLocalAtom.reserve(nLocal_);
207 –    for (int i = 0; i < nLocal_; i++) {
208 –      int iglob = AtomLocalToGlobal[i];
209 –      int nTopos = 0;
201        for (int j = 0; j < nLocal_; j++) {
202 <        int jglob = AtomLocalToGlobal[j];        
202 >        int jglob = AtomLocalToGlobal[j];
203 >
204 >        if (excludes.hasPair(iglob, jglob))
205 >          skipsForAtom[i].push_back(j);              
206 >        
207          if (oneTwo.hasPair(iglob, jglob)) {
208 <          toposForLocalAtom[i].push_back(j);
209 <          topoDistLocal[i][nTopos] = 1;
210 <          nTopos++;
208 >          toposForAtom[i].push_back(j);
209 >          topoDist[i].push_back(1);
210 >        } else {
211 >          if (oneThree.hasPair(iglob, jglob)) {
212 >            toposForAtom[i].push_back(j);
213 >            topoDist[i].push_back(2);
214 >          } else {
215 >            if (oneFour.hasPair(iglob, jglob)) {
216 >              toposForAtom[i].push_back(j);
217 >              topoDist[i].push_back(3);
218 >            }
219 >          }
220          }
217 –        if (oneThree.hasPair(iglob, jglob)) {
218 –          toposForLocalAtom[i].push_back(j);
219 –          topoDistLocal[i][nTopos] = 2;
220 –          nTopos++;
221 –        }
222 –        if (oneFour.hasPair(iglob, jglob)) {
223 –          toposForLocalAtom[i].push_back(j);
224 –          topoDistLocal[i][nTopos] = 3;
225 –          nTopos++;
226 –        }
221        }      
222 <    }    
223 <
222 >    }
223 >    
224 >    createGtypeCutoffMap();
225    }
226    
227    void ForceMatrixDecomposition::createGtypeCutoffMap() {
# Line 236 | Line 231 | namespace OpenMD {
231      int atid;
232      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
233      vector<RealType> atypeCutoff;
234 <    atypeCutoff.reserve( atypes.size() );
234 >    atypeCutoff.resize( atypes.size() );
235  
236 <    for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
236 >    for (set<AtomType*>::iterator at = atypes.begin();
237 >         at != atypes.end(); ++at){
238        rc = interactionMan_->getSuggestedCutoffRadius(*at);
239        atid = (*at)->getIdent();
240        atypeCutoff[atid] = rc;
# Line 250 | Line 246 | namespace OpenMD {
246      // largest cutoff for any atypes present in this group.
247   #ifdef IS_MPI
248      vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
249 +    groupRowToGtype.resize(nGroupsInRow_);
250      for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
251        vector<int> atomListRow = getAtomsInGroupRow(cg1);
252        for (vector<int>::iterator ia = atomListRow.begin();
# Line 275 | Line 272 | namespace OpenMD {
272        
273      }
274      vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
275 +    groupColToGtype.resize(nGroupsInCol_);
276      for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
277        vector<int> atomListCol = getAtomsInGroupColumn(cg2);
278        for (vector<int>::iterator jb = atomListCol.begin();
# Line 298 | Line 296 | namespace OpenMD {
296        }
297      }
298   #else
299 +
300      vector<RealType> groupCutoff(nGroups_, 0.0);
301 +    groupToGtype.resize(nGroups_);
302 +
303 +    cerr << "nGroups = " << nGroups_ << "\n";
304      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305 +
306        groupCutoff[cg1] = 0.0;
307        vector<int> atomList = getAtomsInGroupRow(cg1);
308 +
309        for (vector<int>::iterator ia = atomList.begin();
310             ia != atomList.end(); ++ia) {            
311          int atom1 = (*ia);
# Line 325 | Line 329 | namespace OpenMD {
329      }
330   #endif
331  
332 +    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
333      // Now we find the maximum group cutoff value present in the simulation
334  
335 <    vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
331 <    RealType groupMax = *groupMaxLoc;
335 >    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
336  
337   #ifdef IS_MPI
338      MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
# Line 337 | Line 341 | namespace OpenMD {
341      RealType tradRcut = groupMax;
342  
343      for (int i = 0; i < gTypeCutoffs.size();  i++) {
344 <      for (int j = 0; j < gTypeCutoffs.size();  j++) {
341 <        
344 >      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
345          RealType thisRcut;
346          switch(cutoffPolicy_) {
347          case TRADITIONAL:
348            thisRcut = tradRcut;
349 +          break;
350          case MIX:
351            thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
352 +          break;
353          case MAX:
354            thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
355 +          break;
356          default:
357            sprintf(painCave.errMsg,
358                    "ForceMatrixDecomposition::createGtypeCutoffMap "
359                    "hit an unknown cutoff policy!\n");
360            painCave.severity = OPENMD_ERROR;
361            painCave.isFatal = 1;
362 <          simError();              
362 >          simError();
363 >          break;
364          }
365  
366          pair<int,int> key = make_pair(i,j);
# Line 383 | Line 390 | namespace OpenMD {
390  
391  
392    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
393 <    int i, j;
387 <
393 >    int i, j;  
394   #ifdef IS_MPI
395      i = groupRowToGtype[cg1];
396      j = groupColToGtype[cg2];
397   #else
398      i = groupToGtype[cg1];
399      j = groupToGtype[cg2];
400 < #endif
395 <    
400 > #endif    
401      return gTypeCutoffMap[make_pair(i,j)];
402    }
403  
404 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
405 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
406 +      if (toposForAtom[atom1][j] == atom2)
407 +        return topoDist[atom1][j];
408 +    }
409 +    return 0;
410 +  }
411  
412    void ForceMatrixDecomposition::zeroWorkArrays() {
413  
# Line 679 | Line 691 | namespace OpenMD {
691   #ifdef IS_MPI
692      return massFactorsRow[atom1];
693   #else
694 <    return massFactorsLocal[atom1];
694 >    return massFactors[atom1];
695   #endif
696    }
697  
# Line 687 | Line 699 | namespace OpenMD {
699   #ifdef IS_MPI
700      return massFactorsCol[atom2];
701   #else
702 <    return massFactorsLocal[atom2];
702 >    return massFactors[atom2];
703   #endif
704  
705    }
# Line 705 | Line 717 | namespace OpenMD {
717      return d;    
718    }
719  
720 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
721 < #ifdef IS_MPI
710 <    return skipsForRowAtom[atom1];
711 < #else
712 <    return skipsForLocalAtom[atom1];
713 < #endif
720 >  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
721 >    return skipsForAtom[atom1];
722    }
723  
724    /**
# Line 743 | Line 751 | namespace OpenMD {
751      unique_id_2 = atom2;
752   #endif
753      
754 < #ifdef IS_MPI
755 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748 <         i != skipsForRowAtom[atom1].end(); ++i) {
754 >    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
755 >         i != skipsForAtom[atom1].end(); ++i) {
756        if ( (*i) == unique_id_2 ) return true;
757      }    
751 – #else
752 –    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
753 –         i != skipsForLocalAtom[atom1].end(); ++i) {
754 –      if ( (*i) == unique_id_2 ) return true;
755 –    }    
756 – #endif
757 –  }
758  
759 –  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
760 –    
761 – #ifdef IS_MPI
762 –    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
763 –      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
764 –    }
765 – #else
766 –    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
767 –      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
768 –    }
769 – #endif
770 –
771 –    // zero is default for unconnected (i.e. normal) pair interactions
772 –    return 0;
759    }
760  
761 +
762    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
763   #ifdef IS_MPI
764      atomRowData.force[atom1] += fg;
# Line 789 | Line 776 | namespace OpenMD {
776    }
777  
778      // filling interaction blocks with pointers
779 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
780 <    InteractionData idat;
794 <
779 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
780 >                                                     int atom1, int atom2) {    
781   #ifdef IS_MPI
782      
783      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
784                               ff_->getAtomType(identsCol[atom2]) );
799 –
785      
786      if (storageLayout_ & DataStorage::dslAmat) {
787        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 874 | Line 859 | namespace OpenMD {
859      }
860  
861   #endif
877 –    return idat;
862    }
863  
864    
865 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
865 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
866   #ifdef IS_MPI
867      pot_row[atom1] += 0.5 *  *(idat.pot);
868      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 895 | Line 879 | namespace OpenMD {
879    }
880  
881  
882 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
883 <
900 <    InteractionData idat;
882 >  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
883 >                                              int atom1, int atom2) {
884   #ifdef IS_MPI
885      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
886                               ff_->getAtomType(identsCol[atom2]) );
# Line 958 | Line 941 | namespace OpenMD {
941      Vector3d rs, scaled, dr;
942      Vector3i whichCell;
943      int cellIndex;
944 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
945  
946   #ifdef IS_MPI
947 +    cellListRow_.resize(nCtot);
948 +    cellListCol_.resize(nCtot);
949 + #else
950 +    cellList_.resize(nCtot);
951 + #endif
952 +
953 + #ifdef IS_MPI
954      for (int i = 0; i < nGroupsInRow_; i++) {
955        rs = cgRowData.position[i];
956 +
957        // scaled positions relative to the box vectors
958        scaled = invHmat * rs;
959 +
960        // wrap the vector back into the unit box by subtracting integer box
961        // numbers
962 <      for (int j = 0; j < 3; j++)
962 >      for (int j = 0; j < 3; j++) {
963          scaled[j] -= roundMe(scaled[j]);
964 +        scaled[j] += 0.5;
965 +      }
966      
967        // find xyz-indices of cell that cutoffGroup is in.
968        whichCell.x() = nCells_.x() * scaled.x();
# Line 976 | Line 971 | namespace OpenMD {
971  
972        // find single index of this cell:
973        cellIndex = Vlinear(whichCell, nCells_);
974 +
975        // add this cutoff group to the list of groups in this cell;
976        cellListRow_[cellIndex].push_back(i);
977      }
978  
979      for (int i = 0; i < nGroupsInCol_; i++) {
980        rs = cgColData.position[i];
981 +
982        // scaled positions relative to the box vectors
983        scaled = invHmat * rs;
984 +
985        // wrap the vector back into the unit box by subtracting integer box
986        // numbers
987 <      for (int j = 0; j < 3; j++)
987 >      for (int j = 0; j < 3; j++) {
988          scaled[j] -= roundMe(scaled[j]);
989 +        scaled[j] += 0.5;
990 +      }
991  
992        // find xyz-indices of cell that cutoffGroup is in.
993        whichCell.x() = nCells_.x() * scaled.x();
# Line 996 | Line 996 | namespace OpenMD {
996  
997        // find single index of this cell:
998        cellIndex = Vlinear(whichCell, nCells_);
999 +
1000        // add this cutoff group to the list of groups in this cell;
1001        cellListCol_[cellIndex].push_back(i);
1002      }
1003   #else
1004      for (int i = 0; i < nGroups_; i++) {
1005        rs = snap_->cgData.position[i];
1006 +
1007        // scaled positions relative to the box vectors
1008        scaled = invHmat * rs;
1009 +
1010        // wrap the vector back into the unit box by subtracting integer box
1011        // numbers
1012 <      for (int j = 0; j < 3; j++)
1012 >      for (int j = 0; j < 3; j++) {
1013          scaled[j] -= roundMe(scaled[j]);
1014 +        scaled[j] += 0.5;
1015 +      }
1016  
1017        // find xyz-indices of cell that cutoffGroup is in.
1018        whichCell.x() = nCells_.x() * scaled.x();
# Line 1015 | Line 1020 | namespace OpenMD {
1020        whichCell.z() = nCells_.z() * scaled.z();
1021  
1022        // find single index of this cell:
1023 <      cellIndex = Vlinear(whichCell, nCells_);
1023 >      cellIndex = Vlinear(whichCell, nCells_);      
1024 >
1025        // add this cutoff group to the list of groups in this cell;
1026        cellList_[cellIndex].push_back(i);
1027      }
# Line 1073 | Line 1079 | namespace OpenMD {
1079                }
1080              }
1081   #else
1082 +
1083              for (vector<int>::iterator j1 = cellList_[m1].begin();
1084                   j1 != cellList_[m1].end(); ++j1) {
1085                for (vector<int>::iterator j2 = cellList_[m2].begin();
1086                     j2 != cellList_[m2].end(); ++j2) {
1087 <                              
1087 >
1088                  // Always do this if we're in different cells or if
1089                  // we're in the same cell and the global index of the
1090                  // j2 cutoff group is less than the j1 cutoff group
# Line 1097 | Line 1104 | namespace OpenMD {
1104          }
1105        }
1106      }
1107 <
1107 >    
1108      // save the local cutoff group positions for the check that is
1109      // done on each loop:
1110      saved_CG_positions_.clear();
1111      for (int i = 0; i < nGroups_; i++)
1112        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1113 <
1113 >    
1114      return neighborList;
1115    }
1116   } //end namespace OpenMD

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