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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 1586 by gezelter, Tue Jun 21 06:34:35 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      // gather the information for atomtype IDs (atids):
63 <    identsLocal = info_->getIdentArray();
63 >    idents = info_->getIdentArray();
64      AtomLocalToGlobal = info_->getGlobalAtomIndices();
65      cgLocalToGlobal = info_->getGlobalGroupIndices();
66      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67 <    vector<RealType> massFactorsLocal = info_->getMassFactors();
67 >
68 >    massFactors = info_->getMassFactors();
69 >
70      PairList excludes = info_->getExcludedInteractions();
71      PairList oneTwo = info_->getOneTwoInteractions();
72      PairList oneThree = info_->getOneThreeInteractions();
# Line 104 | Line 106 | namespace OpenMD {
106      cgColData.resize(nGroupsInCol_);
107      cgColData.setStorageLayout(DataStorage::dslPosition);
108          
109 <    identsRow.reserve(nAtomsInRow_);
110 <    identsCol.reserve(nAtomsInCol_);
109 >    identsRow.resize(nAtomsInRow_);
110 >    identsCol.resize(nAtomsInCol_);
111      
112 <    AtomCommIntRow->gather(identsLocal, identsRow);
113 <    AtomCommIntColumn->gather(identsLocal, identsCol);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
115      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
# Line 116 | Line 118 | namespace OpenMD {
118      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120  
121 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
122 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
121 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
122 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
123  
124      groupListRow_.clear();
125 <    groupListRow_.reserve(nGroupsInRow_);
125 >    groupListRow_.resize(nGroupsInRow_);
126      for (int i = 0; i < nGroupsInRow_; i++) {
127        int gid = cgRowToGlobal[i];
128        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 131 | Line 133 | namespace OpenMD {
133      }
134  
135      groupListCol_.clear();
136 <    groupListCol_.reserve(nGroupsInCol_);
136 >    groupListCol_.resize(nGroupsInCol_);
137      for (int i = 0; i < nGroupsInCol_; i++) {
138        int gid = cgColToGlobal[i];
139        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 141 | Line 143 | namespace OpenMD {
143        }      
144      }
145  
146 <    skipsForRowAtom.clear();
147 <    skipsForRowAtom.reserve(nAtomsInRow_);
146 >    skipsForAtom.clear();
147 >    skipsForAtom.resize(nAtomsInRow_);
148 >    toposForAtom.clear();
149 >    toposForAtom.resize(nAtomsInRow_);
150 >    topoDist.clear();
151 >    topoDist.resize(nAtomsInRow_);
152      for (int i = 0; i < nAtomsInRow_; i++) {
153        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 –    }
154  
155 –    toposForRowAtom.clear();
156 –    toposForRowAtom.reserve(nAtomsInRow_);
157 –    for (int i = 0; i < nAtomsInRow_; i++) {
158 –      int iglob = AtomRowToGlobal[i];
159 –      int nTopos = 0;
155        for (int j = 0; j < nAtomsInCol_; j++) {
156 <        int jglob = AtomColToGlobal[j];        
156 >        int jglob = AtomColToGlobal[j];
157 >
158 >        if (excludes.hasPair(iglob, jglob))
159 >          skipsForAtom[i].push_back(j);      
160 >        
161          if (oneTwo.hasPair(iglob, jglob)) {
162 <          toposForRowAtom[i].push_back(j);
163 <          topoDistRow[i][nTopos] = 1;
164 <          nTopos++;
162 >          toposForAtom[i].push_back(j);
163 >          topoDist[i].push_back(1);
164 >        } else {
165 >          if (oneThree.hasPair(iglob, jglob)) {
166 >            toposForAtom[i].push_back(j);
167 >            topoDist[i].push_back(2);
168 >          } else {
169 >            if (oneFour.hasPair(iglob, jglob)) {
170 >              toposForAtom[i].push_back(j);
171 >              topoDist[i].push_back(3);
172 >            }
173 >          }
174          }
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 –        }
175        }      
176      }
177  
178   #endif
179  
180      groupList_.clear();
181 <    groupList_.reserve(nGroups_);
181 >    groupList_.resize(nGroups_);
182      for (int i = 0; i < nGroups_; i++) {
183        int gid = cgLocalToGlobal[i];
184        for (int j = 0; j < nLocal_; j++) {
185          int aid = AtomLocalToGlobal[j];
186 <        if (globalGroupMembership[aid] == gid)
186 >        if (globalGroupMembership[aid] == gid) {
187            groupList_[i].push_back(j);
188 +        }
189        }      
190      }
191  
192 <    skipsForLocalAtom.clear();
193 <    skipsForLocalAtom.reserve(nLocal_);
192 >    skipsForAtom.clear();
193 >    skipsForAtom.resize(nLocal_);
194 >    toposForAtom.clear();
195 >    toposForAtom.resize(nLocal_);
196 >    topoDist.clear();
197 >    topoDist.resize(nLocal_);
198  
199      for (int i = 0; i < nLocal_; i++) {
200        int iglob = AtomLocalToGlobal[i];
201 +
202        for (int j = 0; j < nLocal_; j++) {
203 <        int jglob = AtomLocalToGlobal[j];        
203 >        int jglob = AtomLocalToGlobal[j];
204 >
205          if (excludes.hasPair(iglob, jglob))
206 <          skipsForLocalAtom[i].push_back(j);      
207 <      }      
203 <    }
204 <
205 <    toposForLocalAtom.clear();
206 <    toposForLocalAtom.reserve(nLocal_);
207 <    for (int i = 0; i < nLocal_; i++) {
208 <      int iglob = AtomLocalToGlobal[i];
209 <      int nTopos = 0;
210 <      for (int j = 0; j < nLocal_; j++) {
211 <        int jglob = AtomLocalToGlobal[j];        
206 >          skipsForAtom[i].push_back(j);              
207 >        
208          if (oneTwo.hasPair(iglob, jglob)) {
209 <          toposForLocalAtom[i].push_back(j);
210 <          topoDistLocal[i][nTopos] = 1;
211 <          nTopos++;
209 >          toposForAtom[i].push_back(j);
210 >          topoDist[i].push_back(1);
211 >        } else {
212 >          if (oneThree.hasPair(iglob, jglob)) {
213 >            toposForAtom[i].push_back(j);
214 >            topoDist[i].push_back(2);
215 >          } else {
216 >            if (oneFour.hasPair(iglob, jglob)) {
217 >              toposForAtom[i].push_back(j);
218 >              topoDist[i].push_back(3);
219 >            }
220 >          }
221          }
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 –        }
222        }      
223 <    }    
224 <
223 >    }
224 >    
225 >    createGtypeCutoffMap();
226    }
227    
228    void ForceMatrixDecomposition::createGtypeCutoffMap() {
229 <
229 >    
230      RealType tol = 1e-6;
231      RealType rc;
232      int atid;
233      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
234      vector<RealType> atypeCutoff;
235 <    atypeCutoff.reserve( atypes.size() );
236 <
237 <    for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
238 <      rc = interactionMan_->getSuggestedCutoffRadius(*at);
235 >    atypeCutoff.resize( atypes.size() );
236 >      
237 >    for (set<AtomType*>::iterator at = atypes.begin();
238 >         at != atypes.end(); ++at){
239        atid = (*at)->getIdent();
240 <      atypeCutoff[atid] = rc;
240 >
241 >      if (userChoseCutoff_)
242 >        atypeCutoff[atid] = userCutoff_;
243 >      else
244 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
245      }
246  
247      vector<RealType> gTypeCutoffs;
# Line 250 | Line 250 | namespace OpenMD {
250      // largest cutoff for any atypes present in this group.
251   #ifdef IS_MPI
252      vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
253 +    groupRowToGtype.resize(nGroupsInRow_);
254      for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
255        vector<int> atomListRow = getAtomsInGroupRow(cg1);
256        for (vector<int>::iterator ia = atomListRow.begin();
# Line 275 | Line 276 | namespace OpenMD {
276        
277      }
278      vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
279 +    groupColToGtype.resize(nGroupsInCol_);
280      for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
281        vector<int> atomListCol = getAtomsInGroupColumn(cg2);
282        for (vector<int>::iterator jb = atomListCol.begin();
# Line 298 | Line 300 | namespace OpenMD {
300        }
301      }
302   #else
303 +
304      vector<RealType> groupCutoff(nGroups_, 0.0);
305 +    groupToGtype.resize(nGroups_);
306 +
307      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
308 +
309        groupCutoff[cg1] = 0.0;
310        vector<int> atomList = getAtomsInGroupRow(cg1);
311 +
312        for (vector<int>::iterator ia = atomList.begin();
313             ia != atomList.end(); ++ia) {            
314          int atom1 = (*ia);
315 <        atid = identsLocal[atom1];
315 >        atid = idents[atom1];
316          if (atypeCutoff[atid] > groupCutoff[cg1]) {
317            groupCutoff[cg1] = atypeCutoff[atid];
318          }
# Line 327 | Line 334 | namespace OpenMD {
334  
335      // Now we find the maximum group cutoff value present in the simulation
336  
337 <    vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
331 <    RealType groupMax = *groupMaxLoc;
337 >    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
338  
339   #ifdef IS_MPI
340      MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
# Line 337 | Line 343 | namespace OpenMD {
343      RealType tradRcut = groupMax;
344  
345      for (int i = 0; i < gTypeCutoffs.size();  i++) {
346 <      for (int j = 0; j < gTypeCutoffs.size();  j++) {
341 <        
346 >      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
347          RealType thisRcut;
348          switch(cutoffPolicy_) {
349          case TRADITIONAL:
350            thisRcut = tradRcut;
351 +          break;
352          case MIX:
353            thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
354 +          break;
355          case MAX:
356            thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
357 +          break;
358          default:
359            sprintf(painCave.errMsg,
360                    "ForceMatrixDecomposition::createGtypeCutoffMap "
361                    "hit an unknown cutoff policy!\n");
362            painCave.severity = OPENMD_ERROR;
363            painCave.isFatal = 1;
364 <          simError();              
364 >          simError();
365 >          break;
366          }
367  
368          pair<int,int> key = make_pair(i,j);
# Line 371 | Line 380 | namespace OpenMD {
380            if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
381              sprintf(painCave.errMsg,
382                      "ForceMatrixDecomposition::createGtypeCutoffMap "
383 <                    "user-specified rCut does not match computed group Cutoff\n");
383 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
384              painCave.severity = OPENMD_ERROR;
385              painCave.isFatal = 1;
386              simError();            
# Line 383 | Line 392 | namespace OpenMD {
392  
393  
394    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
395 <    int i, j;
387 <
395 >    int i, j;  
396   #ifdef IS_MPI
397      i = groupRowToGtype[cg1];
398      j = groupColToGtype[cg2];
399   #else
400      i = groupToGtype[cg1];
401      j = groupToGtype[cg2];
402 < #endif
395 <    
402 > #endif    
403      return gTypeCutoffMap[make_pair(i,j)];
404    }
405  
406 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
407 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
408 +      if (toposForAtom[atom1][j] == atom2)
409 +        return topoDist[atom1][j];
410 +    }
411 +    return 0;
412 +  }
413  
414    void ForceMatrixDecomposition::zeroWorkArrays() {
415 +    pairwisePot = 0.0;
416 +    embeddingPot = 0.0;
417  
402 –    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403 –      longRangePot_[j] = 0.0;
404 –    }
405 –
418   #ifdef IS_MPI
419      if (storageLayout_ & DataStorage::dslForce) {
420        fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
# Line 418 | Line 430 | namespace OpenMD {
430           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
431  
432      fill(pot_col.begin(), pot_col.end(),
433 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422 <    
423 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
433 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
434  
435      if (storageLayout_ & DataStorage::dslParticlePot) {    
436        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
# Line 444 | Line 454 | namespace OpenMD {
454             atomColData.functionalDerivative.end(), 0.0);
455      }
456  
457 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
458 +      fill(atomRowData.skippedCharge.begin(), atomRowData.skippedCharge.end(), 0.0);
459 +      fill(atomColData.skippedCharge.begin(), atomColData.skippedCharge.end(), 0.0);
460 +    }
461 +
462   #else
463      
464      if (storageLayout_ & DataStorage::dslParticlePot) {      
# Line 463 | Line 478 | namespace OpenMD {
478        fill(snap_->atomData.functionalDerivative.begin(),
479             snap_->atomData.functionalDerivative.end(), 0.0);
480      }
481 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
482 +      fill(snap_->atomData.skippedCharge.begin(),
483 +           snap_->atomData.skippedCharge.end(), 0.0);
484 +    }
485   #endif
486      
487    }
# Line 594 | Line 613 | namespace OpenMD {
613      AtomCommPotRow->scatter(pot_row, pot_temp);
614  
615      for (int ii = 0;  ii < pot_temp.size(); ii++ )
616 <      pot_local += pot_temp[ii];
616 >      pairwisePot += pot_temp[ii];
617      
618      fill(pot_temp.begin(), pot_temp.end(),
619           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
# Line 602 | Line 621 | namespace OpenMD {
621      AtomCommPotColumn->scatter(pot_col, pot_temp);    
622      
623      for (int ii = 0;  ii < pot_temp.size(); ii++ )
624 <      pot_local += pot_temp[ii];
606 <    
624 >      pairwisePot += pot_temp[ii];    
625   #endif
626 +
627    }
628  
629    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 679 | Line 698 | namespace OpenMD {
698   #ifdef IS_MPI
699      return massFactorsRow[atom1];
700   #else
701 <    return massFactorsLocal[atom1];
701 >    return massFactors[atom1];
702   #endif
703    }
704  
# Line 687 | Line 706 | namespace OpenMD {
706   #ifdef IS_MPI
707      return massFactorsCol[atom2];
708   #else
709 <    return massFactorsLocal[atom2];
709 >    return massFactors[atom2];
710   #endif
711  
712    }
# Line 705 | Line 724 | namespace OpenMD {
724      return d;    
725    }
726  
727 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
728 < #ifdef IS_MPI
710 <    return skipsForRowAtom[atom1];
711 < #else
712 <    return skipsForLocalAtom[atom1];
713 < #endif
727 >  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
728 >    return skipsForAtom[atom1];
729    }
730  
731    /**
# Line 743 | Line 758 | namespace OpenMD {
758      unique_id_2 = atom2;
759   #endif
760      
761 < #ifdef IS_MPI
762 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748 <         i != skipsForRowAtom[atom1].end(); ++i) {
761 >    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
762 >         i != skipsForAtom[atom1].end(); ++i) {
763        if ( (*i) == unique_id_2 ) return true;
750 –    }    
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
765  
766 <    // zero is default for unconnected (i.e. normal) pair interactions
772 <    return 0;
766 >    return false;
767    }
768  
769 +
770    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
771   #ifdef IS_MPI
772      atomRowData.force[atom1] += fg;
# Line 789 | Line 784 | namespace OpenMD {
784    }
785  
786      // filling interaction blocks with pointers
787 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
788 <    InteractionData idat;
794 <
787 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
788 >                                                     int atom1, int atom2) {    
789   #ifdef IS_MPI
790      
791      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
792                               ff_->getAtomType(identsCol[atom2]) );
799 –
793      
794      if (storageLayout_ & DataStorage::dslAmat) {
795        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 835 | Line 828 | namespace OpenMD {
828  
829   #else
830  
831 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
832 <                             ff_->getAtomType(identsLocal[atom2]) );
831 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
832 >                             ff_->getAtomType(idents[atom2]) );
833  
834      if (storageLayout_ & DataStorage::dslAmat) {
835        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 853 | Line 846 | namespace OpenMD {
846        idat.t2 = &(snap_->atomData.torque[atom2]);
847      }
848  
849 <    if (storageLayout_ & DataStorage::dslDensity) {
849 >    if (storageLayout_ & DataStorage::dslDensity) {    
850        idat.rho1 = &(snap_->atomData.density[atom1]);
851        idat.rho2 = &(snap_->atomData.density[atom2]);
852      }
# Line 874 | Line 867 | namespace OpenMD {
867      }
868  
869   #endif
877 –    return idat;
870    }
871  
872    
873 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
873 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
874   #ifdef IS_MPI
875      pot_row[atom1] += 0.5 *  *(idat.pot);
876      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 886 | Line 878 | namespace OpenMD {
878      atomRowData.force[atom1] += *(idat.f1);
879      atomColData.force[atom2] -= *(idat.f1);
880   #else
881 <    longRangePot_ += *(idat.pot);
882 <    
881 >    pairwisePot += *(idat.pot);
882 >
883      snap_->atomData.force[atom1] += *(idat.f1);
884      snap_->atomData.force[atom2] -= *(idat.f1);
885   #endif
886 <
886 >    
887    }
888  
889  
890 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
891 <
900 <    InteractionData idat;
890 >  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
891 >                                              int atom1, int atom2) {
892   #ifdef IS_MPI
893      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
894                               ff_->getAtomType(identsCol[atom2]) );
# Line 906 | Line 897 | namespace OpenMD {
897        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
898        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
899      }
900 +
901      if (storageLayout_ & DataStorage::dslTorque) {
902        idat.t1 = &(atomRowData.torque[atom1]);
903        idat.t2 = &(atomColData.torque[atom2]);
904      }
905 +
906 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
907 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
908 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
909 +    }
910   #else
911 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
912 <                             ff_->getAtomType(identsLocal[atom2]) );
911 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
912 >                             ff_->getAtomType(idents[atom2]) );
913  
914      if (storageLayout_ & DataStorage::dslElectroFrame) {
915        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
916        idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
917      }
918 +
919      if (storageLayout_ & DataStorage::dslTorque) {
920        idat.t1 = &(snap_->atomData.torque[atom1]);
921        idat.t2 = &(snap_->atomData.torque[atom2]);
922      }
923 +
924 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
925 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
926 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
927 +    }
928   #endif    
929    }
930  
931 +
932 +  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
933 + #ifdef IS_MPI
934 +    pot_row[atom1] += 0.5 *  *(idat.pot);
935 +    pot_col[atom2] += 0.5 *  *(idat.pot);
936 + #else
937 +    pairwisePot += *(idat.pot);  
938 + #endif
939 +
940 +  }
941 +
942 +
943    /*
944     * buildNeighborList
945     *
# Line 958 | Line 973 | namespace OpenMD {
973      Vector3d rs, scaled, dr;
974      Vector3i whichCell;
975      int cellIndex;
976 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
977  
978   #ifdef IS_MPI
979 +    cellListRow_.resize(nCtot);
980 +    cellListCol_.resize(nCtot);
981 + #else
982 +    cellList_.resize(nCtot);
983 + #endif
984 +
985 + #ifdef IS_MPI
986      for (int i = 0; i < nGroupsInRow_; i++) {
987        rs = cgRowData.position[i];
988 +
989        // scaled positions relative to the box vectors
990        scaled = invHmat * rs;
991 +
992        // wrap the vector back into the unit box by subtracting integer box
993        // numbers
994 <      for (int j = 0; j < 3; j++)
994 >      for (int j = 0; j < 3; j++) {
995          scaled[j] -= roundMe(scaled[j]);
996 +        scaled[j] += 0.5;
997 +      }
998      
999        // find xyz-indices of cell that cutoffGroup is in.
1000        whichCell.x() = nCells_.x() * scaled.x();
# Line 976 | Line 1003 | namespace OpenMD {
1003  
1004        // find single index of this cell:
1005        cellIndex = Vlinear(whichCell, nCells_);
1006 +
1007        // add this cutoff group to the list of groups in this cell;
1008        cellListRow_[cellIndex].push_back(i);
1009      }
1010  
1011      for (int i = 0; i < nGroupsInCol_; i++) {
1012        rs = cgColData.position[i];
1013 +
1014        // scaled positions relative to the box vectors
1015        scaled = invHmat * rs;
1016 +
1017        // wrap the vector back into the unit box by subtracting integer box
1018        // numbers
1019 <      for (int j = 0; j < 3; j++)
1019 >      for (int j = 0; j < 3; j++) {
1020          scaled[j] -= roundMe(scaled[j]);
1021 +        scaled[j] += 0.5;
1022 +      }
1023  
1024        // find xyz-indices of cell that cutoffGroup is in.
1025        whichCell.x() = nCells_.x() * scaled.x();
# Line 996 | Line 1028 | namespace OpenMD {
1028  
1029        // find single index of this cell:
1030        cellIndex = Vlinear(whichCell, nCells_);
1031 +
1032        // add this cutoff group to the list of groups in this cell;
1033        cellListCol_[cellIndex].push_back(i);
1034      }
1035   #else
1036      for (int i = 0; i < nGroups_; i++) {
1037        rs = snap_->cgData.position[i];
1038 +
1039        // scaled positions relative to the box vectors
1040        scaled = invHmat * rs;
1041 +
1042        // wrap the vector back into the unit box by subtracting integer box
1043        // numbers
1044 <      for (int j = 0; j < 3; j++)
1044 >      for (int j = 0; j < 3; j++) {
1045          scaled[j] -= roundMe(scaled[j]);
1046 +        scaled[j] += 0.5;
1047 +      }
1048  
1049        // find xyz-indices of cell that cutoffGroup is in.
1050        whichCell.x() = nCells_.x() * scaled.x();
# Line 1015 | Line 1052 | namespace OpenMD {
1052        whichCell.z() = nCells_.z() * scaled.z();
1053  
1054        // find single index of this cell:
1055 <      cellIndex = Vlinear(whichCell, nCells_);
1055 >      cellIndex = Vlinear(whichCell, nCells_);      
1056 >
1057        // add this cutoff group to the list of groups in this cell;
1058        cellList_[cellIndex].push_back(i);
1059      }
# Line 1073 | Line 1111 | namespace OpenMD {
1111                }
1112              }
1113   #else
1114 +
1115              for (vector<int>::iterator j1 = cellList_[m1].begin();
1116                   j1 != cellList_[m1].end(); ++j1) {
1117                for (vector<int>::iterator j2 = cellList_[m2].begin();
1118                     j2 != cellList_[m2].end(); ++j2) {
1119 <                              
1119 >
1120                  // Always do this if we're in different cells or if
1121                  // we're in the same cell and the global index of the
1122                  // j2 cutoff group is less than the j1 cutoff group
# Line 1097 | Line 1136 | namespace OpenMD {
1136          }
1137        }
1138      }
1139 <
1139 >    
1140      // save the local cutoff group positions for the check that is
1141      // done on each loop:
1142      saved_CG_positions_.clear();
1143      for (int i = 0; i < nGroups_; i++)
1144        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1145 <
1145 >  
1146      return neighborList;
1147    }
1148   } //end namespace OpenMD

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