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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 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC vs.
Revision 1592 by gezelter, Tue Jul 12 20:33:14 2011 UTC

# Line 57 | Line 57 | namespace OpenMD {
57      storageLayout_ = sman_->getStorageLayout();
58      ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60 <
60 >    
61      nGroups_ = info_->getNLocalCutoffGroups();
62 –    cerr << "in dId, nGroups = " << nGroups_ << "\n";
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 +
68      massFactors = info_->getMassFactors();
69 –    PairList excludes = info_->getExcludedInteractions();
70 –    PairList oneTwo = info_->getOneTwoInteractions();
71 –    PairList oneThree = info_->getOneThreeInteractions();
72 –    PairList oneFour = info_->getOneFourInteractions();
69  
70 +    PairList* excludes = info_->getExcludedInteractions();
71 +    PairList* oneTwo = info_->getOneTwoInteractions();
72 +    PairList* oneThree = info_->getOneThreeInteractions();
73 +    PairList* oneFour = info_->getOneFourInteractions();
74 +
75   #ifdef IS_MPI
76  
77      AtomCommIntRow = new Communicator<Row,int>(nLocal_);
# Line 108 | Line 109 | namespace OpenMD {
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 +    // allocate memory for the parallel objects
116 +    atypesRow.resize(nAtomsInRow_);
117 +    atypesCol.resize(nAtomsInCol_);
118 +
119 +    for (int i = 0; i < nAtomsInRow_; i++)
120 +      atypesRow[i] = ff_->getAtomType(identsRow[i]);
121 +    for (int i = 0; i < nAtomsInCol_; i++)
122 +      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
123 +
124 +    pot_row.resize(nAtomsInRow_);
125 +    pot_col.resize(nAtomsInCol_);
126 +
127 +    AtomRowToGlobal.resize(nAtomsInRow_);
128 +    AtomColToGlobal.resize(nAtomsInCol_);
129      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
130      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
131      
132 +    cgRowToGlobal.resize(nGroupsInRow_);
133 +    cgColToGlobal.resize(nGroupsInCol_);
134      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
135      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
136  
137 +    massFactorsRow.resize(nAtomsInRow_);
138 +    massFactorsCol.resize(nAtomsInCol_);
139      AtomCommRealRow->gather(massFactors, massFactorsRow);
140      AtomCommRealColumn->gather(massFactors, massFactorsCol);
141  
# Line 142 | Line 161 | namespace OpenMD {
161        }      
162      }
163  
164 <    skipsForAtom.clear();
165 <    skipsForAtom.resize(nAtomsInRow_);
164 >    excludesForAtom.clear();
165 >    excludesForAtom.resize(nAtomsInRow_);
166      toposForAtom.clear();
167      toposForAtom.resize(nAtomsInRow_);
168      topoDist.clear();
# Line 154 | Line 173 | namespace OpenMD {
173        for (int j = 0; j < nAtomsInCol_; j++) {
174          int jglob = AtomColToGlobal[j];
175  
176 <        if (excludes.hasPair(iglob, jglob))
177 <          skipsForAtom[i].push_back(j);      
176 >        if (excludes->hasPair(iglob, jglob))
177 >          excludesForAtom[i].push_back(j);      
178          
179 <        if (oneTwo.hasPair(iglob, jglob)) {
179 >        if (oneTwo->hasPair(iglob, jglob)) {
180            toposForAtom[i].push_back(j);
181            topoDist[i].push_back(1);
182          } else {
183 <          if (oneThree.hasPair(iglob, jglob)) {
183 >          if (oneThree->hasPair(iglob, jglob)) {
184              toposForAtom[i].push_back(j);
185              topoDist[i].push_back(2);
186            } else {
187 <            if (oneFour.hasPair(iglob, jglob)) {
187 >            if (oneFour->hasPair(iglob, jglob)) {
188                toposForAtom[i].push_back(j);
189                topoDist[i].push_back(3);
190              }
# Line 176 | Line 195 | namespace OpenMD {
195  
196   #endif
197  
198 +    // allocate memory for the parallel objects
199 +    atypesLocal.resize(nLocal_);
200 +
201 +    for (int i = 0; i < nLocal_; i++)
202 +      atypesLocal[i] = ff_->getAtomType(idents[i]);
203 +
204      groupList_.clear();
205      groupList_.resize(nGroups_);
206      for (int i = 0; i < nGroups_; i++) {
# Line 188 | Line 213 | namespace OpenMD {
213        }      
214      }
215  
216 <    skipsForAtom.clear();
217 <    skipsForAtom.resize(nLocal_);
216 >    excludesForAtom.clear();
217 >    excludesForAtom.resize(nLocal_);
218      toposForAtom.clear();
219      toposForAtom.resize(nLocal_);
220      topoDist.clear();
# Line 201 | Line 226 | namespace OpenMD {
226        for (int j = 0; j < nLocal_; j++) {
227          int jglob = AtomLocalToGlobal[j];
228  
229 <        if (excludes.hasPair(iglob, jglob))
230 <          skipsForAtom[i].push_back(j);              
229 >        if (excludes->hasPair(iglob, jglob))
230 >          excludesForAtom[i].push_back(j);              
231          
232 <        if (oneTwo.hasPair(iglob, jglob)) {
232 >        if (oneTwo->hasPair(iglob, jglob)) {
233            toposForAtom[i].push_back(j);
234            topoDist[i].push_back(1);
235          } else {
236 <          if (oneThree.hasPair(iglob, jglob)) {
236 >          if (oneThree->hasPair(iglob, jglob)) {
237              toposForAtom[i].push_back(j);
238              topoDist[i].push_back(2);
239            } else {
240 <            if (oneFour.hasPair(iglob, jglob)) {
240 >            if (oneFour->hasPair(iglob, jglob)) {
241                toposForAtom[i].push_back(j);
242                topoDist[i].push_back(3);
243              }
# Line 222 | Line 247 | namespace OpenMD {
247      }
248      
249      createGtypeCutoffMap();
250 +
251    }
252    
253    void ForceMatrixDecomposition::createGtypeCutoffMap() {
254 <
254 >    
255      RealType tol = 1e-6;
256 +    largestRcut_ = 0.0;
257      RealType rc;
258      int atid;
259      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
260 <    vector<RealType> atypeCutoff;
261 <    atypeCutoff.resize( atypes.size() );
262 <
260 >    
261 >    map<int, RealType> atypeCutoff;
262 >      
263      for (set<AtomType*>::iterator at = atypes.begin();
264           at != atypes.end(); ++at){
238 –      rc = interactionMan_->getSuggestedCutoffRadius(*at);
265        atid = (*at)->getIdent();
266 <      atypeCutoff[atid] = rc;
266 >      if (userChoseCutoff_)
267 >        atypeCutoff[atid] = userCutoff_;
268 >      else
269 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
270      }
271 <
271 >    
272      vector<RealType> gTypeCutoffs;
244 –
273      // first we do a single loop over the cutoff groups to find the
274      // largest cutoff for any atypes present in this group.
275   #ifdef IS_MPI
# Line 299 | Line 327 | namespace OpenMD {
327  
328      vector<RealType> groupCutoff(nGroups_, 0.0);
329      groupToGtype.resize(nGroups_);
302 –
303 –    cerr << "nGroups = " << nGroups_ << "\n";
330      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305 –
331        groupCutoff[cg1] = 0.0;
332        vector<int> atomList = getAtomsInGroupRow(cg1);
308 –
333        for (vector<int>::iterator ia = atomList.begin();
334             ia != atomList.end(); ++ia) {            
335          int atom1 = (*ia);
336 <        atid = identsLocal[atom1];
337 <        if (atypeCutoff[atid] > groupCutoff[cg1]) {
336 >        atid = idents[atom1];
337 >        if (atypeCutoff[atid] > groupCutoff[cg1])
338            groupCutoff[cg1] = atypeCutoff[atid];
315 –        }
339        }
340 <
340 >      
341        bool gTypeFound = false;
342        for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
343          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
# Line 322 | Line 345 | namespace OpenMD {
345            gTypeFound = true;
346          }
347        }
348 <      if (!gTypeFound) {
348 >      if (!gTypeFound) {      
349          gTypeCutoffs.push_back( groupCutoff[cg1] );
350          groupToGtype[cg1] = gTypeCutoffs.size() - 1;
351        }      
352      }
353   #endif
354  
332 –    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
355      // Now we find the maximum group cutoff value present in the simulation
356  
357 <    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
357 >    RealType groupMax = *max_element(gTypeCutoffs.begin(),
358 >                                     gTypeCutoffs.end());
359  
360   #ifdef IS_MPI
361 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
361 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
362 >                              MPI::MAX);
363   #endif
364      
365      RealType tradRcut = groupMax;
# Line 365 | Line 389 | namespace OpenMD {
389  
390          pair<int,int> key = make_pair(i,j);
391          gTypeCutoffMap[key].first = thisRcut;
368 –
392          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
370 –
393          gTypeCutoffMap[key].second = thisRcut*thisRcut;
372 –        
394          gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
374 –
395          // sanity check
396          
397          if (userChoseCutoff_) {
398            if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
399              sprintf(painCave.errMsg,
400                      "ForceMatrixDecomposition::createGtypeCutoffMap "
401 <                    "user-specified rCut does not match computed group Cutoff\n");
401 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
402              painCave.severity = OPENMD_ERROR;
403              painCave.isFatal = 1;
404              simError();            
# Line 410 | Line 430 | namespace OpenMD {
430    }
431  
432    void ForceMatrixDecomposition::zeroWorkArrays() {
433 <
434 <    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415 <      longRangePot_[j] = 0.0;
416 <    }
433 >    pairwisePot = 0.0;
434 >    embeddingPot = 0.0;
435  
436   #ifdef IS_MPI
437      if (storageLayout_ & DataStorage::dslForce) {
# Line 430 | Line 448 | namespace OpenMD {
448           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
449  
450      fill(pot_col.begin(), pot_col.end(),
451 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434 <    
435 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
451 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
452  
453      if (storageLayout_ & DataStorage::dslParticlePot) {    
454 <      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
455 <      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
454 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
455 >           0.0);
456 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
457 >           0.0);
458      }
459  
460      if (storageLayout_ & DataStorage::dslDensity) {      
# Line 445 | Line 463 | namespace OpenMD {
463      }
464  
465      if (storageLayout_ & DataStorage::dslFunctional) {  
466 <      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
467 <      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
466 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
467 >           0.0);
468 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
469 >           0.0);
470      }
471  
472      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
# Line 456 | Line 476 | namespace OpenMD {
476             atomColData.functionalDerivative.end(), 0.0);
477      }
478  
479 < #else
480 <    
479 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
480 >      fill(atomRowData.skippedCharge.begin(),
481 >           atomRowData.skippedCharge.end(), 0.0);
482 >      fill(atomColData.skippedCharge.begin(),
483 >           atomColData.skippedCharge.end(), 0.0);
484 >    }
485 >
486 > #endif
487 >    // even in parallel, we need to zero out the local arrays:
488 >
489      if (storageLayout_ & DataStorage::dslParticlePot) {      
490        fill(snap_->atomData.particlePot.begin(),
491             snap_->atomData.particlePot.end(), 0.0);
# Line 475 | Line 503 | namespace OpenMD {
503        fill(snap_->atomData.functionalDerivative.begin(),
504             snap_->atomData.functionalDerivative.end(), 0.0);
505      }
506 < #endif
506 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
507 >      fill(snap_->atomData.skippedCharge.begin(),
508 >           snap_->atomData.skippedCharge.end(), 0.0);
509 >    }
510      
511    }
512  
# Line 512 | Line 543 | namespace OpenMD {
543        AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
544                                     atomColData.electroFrame);
545      }
546 +
547   #endif      
548    }
549    
# Line 578 | Line 610 | namespace OpenMD {
610      AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
611      for (int i = 0; i < n; i++)
612        snap_->atomData.force[i] += frc_tmp[i];
613 <    
582 <    
613 >        
614      if (storageLayout_ & DataStorage::dslTorque) {
615  
616 <      int nt = snap_->atomData.force.size();
616 >      int nt = snap_->atomData.torque.size();
617        vector<Vector3d> trq_tmp(nt, V3Zero);
618  
619        AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
620 <      for (int i = 0; i < n; i++) {
620 >      for (int i = 0; i < nt; i++) {
621          snap_->atomData.torque[i] += trq_tmp[i];
622          trq_tmp[i] = 0.0;
623        }
624        
625        AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
626 <      for (int i = 0; i < n; i++)
626 >      for (int i = 0; i < nt; i++)
627          snap_->atomData.torque[i] += trq_tmp[i];
628      }
629 +
630 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
631 +
632 +      int ns = snap_->atomData.skippedCharge.size();
633 +      vector<RealType> skch_tmp(ns, 0.0);
634 +
635 +      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
636 +      for (int i = 0; i < ns; i++) {
637 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
638 +        skch_tmp[i] = 0.0;
639 +      }
640 +      
641 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
642 +      for (int i = 0; i < ns; i++)
643 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
644 +    }
645      
646      nLocal_ = snap_->getNumberOfAtoms();
647  
# Line 606 | Line 653 | namespace OpenMD {
653      AtomCommPotRow->scatter(pot_row, pot_temp);
654  
655      for (int ii = 0;  ii < pot_temp.size(); ii++ )
656 <      pot_local += pot_temp[ii];
656 >      pairwisePot += pot_temp[ii];
657      
658      fill(pot_temp.begin(), pot_temp.end(),
659           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
# Line 614 | Line 661 | namespace OpenMD {
661      AtomCommPotColumn->scatter(pot_col, pot_temp);    
662      
663      for (int ii = 0;  ii < pot_temp.size(); ii++ )
664 <      pot_local += pot_temp[ii];
618 <    
664 >      pairwisePot += pot_temp[ii];    
665   #endif
666 +
667    }
668  
669    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 717 | Line 764 | namespace OpenMD {
764      return d;    
765    }
766  
767 <  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
768 <    return skipsForAtom[atom1];
767 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
768 >    return excludesForAtom[atom1];
769    }
770  
771    /**
772 <   * There are a number of reasons to skip a pair or a
726 <   * particle. Mostly we do this to exclude atoms who are involved in
727 <   * short range interactions (bonds, bends, torsions), but we also
728 <   * need to exclude some overcounted interactions that result from
772 >   * We need to exclude some overcounted interactions that result from
773     * the parallel decomposition.
774     */
775    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
# Line 745 | Line 789 | namespace OpenMD {
789      } else {
790        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
791      }
792 + #endif
793 +    return false;
794 +  }
795 +
796 +  /**
797 +   * We need to handle the interactions for atoms who are involved in
798 +   * the same rigid body as well as some short range interactions
799 +   * (bonds, bends, torsions) differently from other interactions.
800 +   * We'll still visit the pairwise routines, but with a flag that
801 +   * tells those routines to exclude the pair from direct long range
802 +   * interactions.  Some indirect interactions (notably reaction
803 +   * field) must still be handled for these pairs.
804 +   */
805 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
806 +    int unique_id_2;
807 +    
808 + #ifdef IS_MPI
809 +    // in MPI, we have to look up the unique IDs for the row atom.
810 +    unique_id_2 = AtomColToGlobal[atom2];
811   #else
812      // in the normal loop, the atom numbers are unique
750 –    unique_id_1 = atom1;
813      unique_id_2 = atom2;
814   #endif
815      
816 <    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
817 <         i != skipsForAtom[atom1].end(); ++i) {
816 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
817 >         i != excludesForAtom[atom1].end(); ++i) {
818        if ( (*i) == unique_id_2 ) return true;
819 <    }    
819 >    }
820  
821 +    return false;
822    }
823  
824  
# Line 776 | Line 839 | namespace OpenMD {
839    }
840  
841      // filling interaction blocks with pointers
842 <  void ForceMatrixDecomposition::fillInteractionData(InteractionData idat,
843 <                                                     int atom1, int atom2) {    
842 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
843 >                                                     int atom1, int atom2) {
844 >
845 >    idat.excluded = excludeAtomPair(atom1, atom2);
846 >  
847   #ifdef IS_MPI
848 <    
849 <    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
850 <                             ff_->getAtomType(identsCol[atom2]) );
848 >    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
849 >    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
850 >    //                         ff_->getAtomType(identsCol[atom2]) );
851      
852      if (storageLayout_ & DataStorage::dslAmat) {
853        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 818 | Line 884 | namespace OpenMD {
884        idat.particlePot2 = &(atomColData.particlePot[atom2]);
885      }
886  
887 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
888 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
889 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
890 +    }
891 +
892   #else
893  
894 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
895 <                             ff_->getAtomType(identsLocal[atom2]) );
894 >    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
895 >    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
896 >    //                         ff_->getAtomType(idents[atom2]) );
897  
898      if (storageLayout_ & DataStorage::dslAmat) {
899        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 838 | Line 910 | namespace OpenMD {
910        idat.t2 = &(snap_->atomData.torque[atom2]);
911      }
912  
913 <    if (storageLayout_ & DataStorage::dslDensity) {
913 >    if (storageLayout_ & DataStorage::dslDensity) {    
914        idat.rho1 = &(snap_->atomData.density[atom1]);
915        idat.rho2 = &(snap_->atomData.density[atom2]);
916      }
# Line 858 | Line 930 | namespace OpenMD {
930        idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
931      }
932  
933 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
934 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
935 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
936 +    }
937   #endif
938    }
939  
940    
941 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
941 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
942   #ifdef IS_MPI
943      pot_row[atom1] += 0.5 *  *(idat.pot);
944      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 870 | Line 946 | namespace OpenMD {
946      atomRowData.force[atom1] += *(idat.f1);
947      atomColData.force[atom2] -= *(idat.f1);
948   #else
949 <    longRangePot_ += *(idat.pot);
950 <    
949 >    pairwisePot += *(idat.pot);
950 >
951      snap_->atomData.force[atom1] += *(idat.f1);
952      snap_->atomData.force[atom2] -= *(idat.f1);
953   #endif
954 <
954 >    
955    }
956  
881 –
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]) );
887 –
888 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
889 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
890 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
891 –    }
892 –    if (storageLayout_ & DataStorage::dslTorque) {
893 –      idat.t1 = &(atomRowData.torque[atom1]);
894 –      idat.t2 = &(atomColData.torque[atom2]);
895 –    }
896 – #else
897 –    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
898 –                             ff_->getAtomType(identsLocal[atom2]) );
899 –
900 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
901 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
902 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
903 –    }
904 –    if (storageLayout_ & DataStorage::dslTorque) {
905 –      idat.t1 = &(snap_->atomData.torque[atom1]);
906 –      idat.t2 = &(snap_->atomData.torque[atom2]);
907 –    }
908 – #endif    
909 –  }
910 –
957    /*
958     * buildNeighborList
959     *
# Line 918 | Line 964 | namespace OpenMD {
964        
965      vector<pair<int, int> > neighborList;
966      groupCutoffs cuts;
967 +    bool doAllPairs = false;
968 +
969   #ifdef IS_MPI
970      cellListRow_.clear();
971      cellListCol_.clear();
# Line 937 | Line 985 | namespace OpenMD {
985      nCells_.y() = (int) ( Hy.length() )/ rList_;
986      nCells_.z() = (int) ( Hz.length() )/ rList_;
987  
988 +    // handle small boxes where the cell offsets can end up repeating cells
989 +    
990 +    if (nCells_.x() < 3) doAllPairs = true;
991 +    if (nCells_.y() < 3) doAllPairs = true;
992 +    if (nCells_.z() < 3) doAllPairs = true;
993 +
994      Mat3x3d invHmat = snap_->getInvHmat();
995      Vector3d rs, scaled, dr;
996      Vector3i whichCell;
997      int cellIndex;
998      int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
999  
946 –    cerr << "flag1\n";
1000   #ifdef IS_MPI
1001      cellListRow_.resize(nCtot);
1002      cellListCol_.resize(nCtot);
1003   #else
1004      cellList_.resize(nCtot);
1005   #endif
1006 <    cerr << "flag2\n";
1006 >
1007 >    if (!doAllPairs) {
1008   #ifdef IS_MPI
955 –    for (int i = 0; i < nGroupsInRow_; i++) {
956 –      rs = cgRowData.position[i];
1009  
1010 <      // scaled positions relative to the box vectors
1011 <      scaled = invHmat * rs;
1012 <
1013 <      // wrap the vector back into the unit box by subtracting integer box
1014 <      // numbers
1015 <      for (int j = 0; j < 3; j++) {
1016 <        scaled[j] -= roundMe(scaled[j]);
1017 <        scaled[j] += 0.5;
1010 >      for (int i = 0; i < nGroupsInRow_; i++) {
1011 >        rs = cgRowData.position[i];
1012 >        
1013 >        // scaled positions relative to the box vectors
1014 >        scaled = invHmat * rs;
1015 >        
1016 >        // wrap the vector back into the unit box by subtracting integer box
1017 >        // numbers
1018 >        for (int j = 0; j < 3; j++) {
1019 >          scaled[j] -= roundMe(scaled[j]);
1020 >          scaled[j] += 0.5;
1021 >        }
1022 >        
1023 >        // find xyz-indices of cell that cutoffGroup is in.
1024 >        whichCell.x() = nCells_.x() * scaled.x();
1025 >        whichCell.y() = nCells_.y() * scaled.y();
1026 >        whichCell.z() = nCells_.z() * scaled.z();
1027 >        
1028 >        // find single index of this cell:
1029 >        cellIndex = Vlinear(whichCell, nCells_);
1030 >        
1031 >        // add this cutoff group to the list of groups in this cell;
1032 >        cellListRow_[cellIndex].push_back(i);
1033        }
1034 <    
1035 <      // find xyz-indices of cell that cutoffGroup is in.
1036 <      whichCell.x() = nCells_.x() * scaled.x();
1037 <      whichCell.y() = nCells_.y() * scaled.y();
1038 <      whichCell.z() = nCells_.z() * scaled.z();
1039 <
1040 <      // find single index of this cell:
1041 <      cellIndex = Vlinear(whichCell, nCells_);
1042 <
1043 <      // add this cutoff group to the list of groups in this cell;
1044 <      cellListRow_[cellIndex].push_back(i);
1045 <    }
1046 <
1047 <    for (int i = 0; i < nGroupsInCol_; i++) {
1048 <      rs = cgColData.position[i];
1049 <
1050 <      // scaled positions relative to the box vectors
1051 <      scaled = invHmat * rs;
1052 <
1053 <      // wrap the vector back into the unit box by subtracting integer box
1054 <      // numbers
1055 <      for (int j = 0; j < 3; j++) {
1056 <        scaled[j] -= roundMe(scaled[j]);
1057 <        scaled[j] += 0.5;
1034 >      
1035 >      for (int i = 0; i < nGroupsInCol_; i++) {
1036 >        rs = cgColData.position[i];
1037 >        
1038 >        // scaled positions relative to the box vectors
1039 >        scaled = invHmat * rs;
1040 >        
1041 >        // wrap the vector back into the unit box by subtracting integer box
1042 >        // numbers
1043 >        for (int j = 0; j < 3; j++) {
1044 >          scaled[j] -= roundMe(scaled[j]);
1045 >          scaled[j] += 0.5;
1046 >        }
1047 >        
1048 >        // find xyz-indices of cell that cutoffGroup is in.
1049 >        whichCell.x() = nCells_.x() * scaled.x();
1050 >        whichCell.y() = nCells_.y() * scaled.y();
1051 >        whichCell.z() = nCells_.z() * scaled.z();
1052 >        
1053 >        // find single index of this cell:
1054 >        cellIndex = Vlinear(whichCell, nCells_);
1055 >        
1056 >        // add this cutoff group to the list of groups in this cell;
1057 >        cellListCol_[cellIndex].push_back(i);
1058        }
992 –
993 –      // find xyz-indices of cell that cutoffGroup is in.
994 –      whichCell.x() = nCells_.x() * scaled.x();
995 –      whichCell.y() = nCells_.y() * scaled.y();
996 –      whichCell.z() = nCells_.z() * scaled.z();
997 –
998 –      // find single index of this cell:
999 –      cellIndex = Vlinear(whichCell, nCells_);
1000 –
1001 –      // add this cutoff group to the list of groups in this cell;
1002 –      cellListCol_[cellIndex].push_back(i);
1003 –    }
1059   #else
1060 <    for (int i = 0; i < nGroups_; i++) {
1061 <      rs = snap_->cgData.position[i];
1062 <
1063 <      // scaled positions relative to the box vectors
1064 <      scaled = invHmat * rs;
1065 <
1066 <      // wrap the vector back into the unit box by subtracting integer box
1067 <      // numbers
1068 <      for (int j = 0; j < 3; j++) {
1069 <        scaled[j] -= roundMe(scaled[j]);
1070 <        scaled[j] += 0.5;
1060 >      for (int i = 0; i < nGroups_; i++) {
1061 >        rs = snap_->cgData.position[i];
1062 >        
1063 >        // scaled positions relative to the box vectors
1064 >        scaled = invHmat * rs;
1065 >        
1066 >        // wrap the vector back into the unit box by subtracting integer box
1067 >        // numbers
1068 >        for (int j = 0; j < 3; j++) {
1069 >          scaled[j] -= roundMe(scaled[j]);
1070 >          scaled[j] += 0.5;
1071 >        }
1072 >        
1073 >        // find xyz-indices of cell that cutoffGroup is in.
1074 >        whichCell.x() = nCells_.x() * scaled.x();
1075 >        whichCell.y() = nCells_.y() * scaled.y();
1076 >        whichCell.z() = nCells_.z() * scaled.z();
1077 >        
1078 >        // find single index of this cell:
1079 >        cellIndex = Vlinear(whichCell, nCells_);      
1080 >        
1081 >        // add this cutoff group to the list of groups in this cell;
1082 >        cellList_[cellIndex].push_back(i);
1083        }
1017 –
1018 –      // find xyz-indices of cell that cutoffGroup is in.
1019 –      whichCell.x() = nCells_.x() * scaled.x();
1020 –      whichCell.y() = nCells_.y() * scaled.y();
1021 –      whichCell.z() = nCells_.z() * scaled.z();
1022 –
1023 –      // find single index of this cell:
1024 –      cellIndex = Vlinear(whichCell, nCells_);      
1025 –
1026 –      // add this cutoff group to the list of groups in this cell;
1027 –      cellList_[cellIndex].push_back(i);
1028 –    }
1084   #endif
1085  
1086 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1087 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1088 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1089 <          Vector3i m1v(m1x, m1y, m1z);
1090 <          int m1 = Vlinear(m1v, nCells_);
1036 <
1037 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1038 <               os != cellOffsets_.end(); ++os) {
1086 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1087 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1088 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1089 >            Vector3i m1v(m1x, m1y, m1z);
1090 >            int m1 = Vlinear(m1v, nCells_);
1091              
1092 <            Vector3i m2v = m1v + (*os);
1093 <            
1094 <            if (m2v.x() >= nCells_.x()) {
1095 <              m2v.x() = 0;          
1096 <            } else if (m2v.x() < 0) {
1097 <              m2v.x() = nCells_.x() - 1;
1098 <            }
1099 <            
1100 <            if (m2v.y() >= nCells_.y()) {
1101 <              m2v.y() = 0;          
1102 <            } else if (m2v.y() < 0) {
1103 <              m2v.y() = nCells_.y() - 1;
1104 <            }
1105 <            
1106 <            if (m2v.z() >= nCells_.z()) {
1107 <              m2v.z() = 0;          
1108 <            } else if (m2v.z() < 0) {
1109 <              m2v.z() = nCells_.z() - 1;
1110 <            }
1111 <            
1112 <            int m2 = Vlinear (m2v, nCells_);
1113 <
1092 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1093 >                 os != cellOffsets_.end(); ++os) {
1094 >              
1095 >              Vector3i m2v = m1v + (*os);
1096 >              
1097 >              if (m2v.x() >= nCells_.x()) {
1098 >                m2v.x() = 0;          
1099 >              } else if (m2v.x() < 0) {
1100 >                m2v.x() = nCells_.x() - 1;
1101 >              }
1102 >              
1103 >              if (m2v.y() >= nCells_.y()) {
1104 >                m2v.y() = 0;          
1105 >              } else if (m2v.y() < 0) {
1106 >                m2v.y() = nCells_.y() - 1;
1107 >              }
1108 >              
1109 >              if (m2v.z() >= nCells_.z()) {
1110 >                m2v.z() = 0;          
1111 >              } else if (m2v.z() < 0) {
1112 >                m2v.z() = nCells_.z() - 1;
1113 >              }
1114 >              
1115 >              int m2 = Vlinear (m2v, nCells_);
1116 >              
1117   #ifdef IS_MPI
1118 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1119 <                 j1 != cellListRow_[m1].end(); ++j1) {
1120 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1121 <                   j2 != cellListCol_[m2].end(); ++j2) {
1122 <                              
1123 <                // Always do this if we're in different cells or if
1124 <                // we're in the same cell and the global index of the
1125 <                // j2 cutoff group is less than the j1 cutoff group
1126 <
1127 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1128 <                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1129 <                  snap_->wrapVector(dr);
1130 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1131 <                  if (dr.lengthSquare() < cuts.third) {
1132 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1118 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1119 >                   j1 != cellListRow_[m1].end(); ++j1) {
1120 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1121 >                     j2 != cellListCol_[m2].end(); ++j2) {
1122 >                  
1123 >                  // Always do this if we're in different cells or if
1124 >                  // we're in the same cell and the global index of the
1125 >                  // j2 cutoff group is less than the j1 cutoff group
1126 >                  
1127 >                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1128 >                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1129 >                    snap_->wrapVector(dr);
1130 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1131 >                    if (dr.lengthSquare() < cuts.third) {
1132 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1133 >                    }
1134                    }
1135                  }
1136                }
1081 –            }
1137   #else
1138 <
1139 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1140 <                 j1 != cellList_[m1].end(); ++j1) {
1141 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1142 <                   j2 != cellList_[m2].end(); ++j2) {
1143 <
1144 <                // Always do this if we're in different cells or if
1145 <                // we're in the same cell and the global index of the
1146 <                // j2 cutoff group is less than the j1 cutoff group
1147 <
1148 <                if (m2 != m1 || (*j2) < (*j1)) {
1149 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1150 <                  snap_->wrapVector(dr);
1151 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1152 <                  if (dr.lengthSquare() < cuts.third) {
1153 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1138 >              
1139 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1140 >                   j1 != cellList_[m1].end(); ++j1) {
1141 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1142 >                     j2 != cellList_[m2].end(); ++j2) {
1143 >                  
1144 >                  // Always do this if we're in different cells or if
1145 >                  // we're in the same cell and the global index of the
1146 >                  // j2 cutoff group is less than the j1 cutoff group
1147 >                  
1148 >                  if (m2 != m1 || (*j2) < (*j1)) {
1149 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1150 >                    snap_->wrapVector(dr);
1151 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1152 >                    if (dr.lengthSquare() < cuts.third) {
1153 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1154 >                    }
1155                    }
1156                  }
1157                }
1102 –            }
1158   #endif
1159 +            }
1160            }
1161          }
1162        }
1163 +    } else {
1164 +      // branch to do all cutoff group pairs
1165 + #ifdef IS_MPI
1166 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1167 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1168 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1169 +          snap_->wrapVector(dr);
1170 +          cuts = getGroupCutoffs( j1, j2 );
1171 +          if (dr.lengthSquare() < cuts.third) {
1172 +            neighborList.push_back(make_pair(j1, j2));
1173 +          }
1174 +        }
1175 +      }
1176 + #else
1177 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1178 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1179 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1180 +          snap_->wrapVector(dr);
1181 +          cuts = getGroupCutoffs( j1, j2 );
1182 +          if (dr.lengthSquare() < cuts.third) {
1183 +            neighborList.push_back(make_pair(j1, j2));
1184 +          }
1185 +        }
1186 +      }        
1187 + #endif
1188      }
1189 <    
1189 >      
1190      // save the local cutoff group positions for the check that is
1191      // done on each loop:
1192      saved_CG_positions_.clear();

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