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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 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
Revision 1590 by gezelter, Mon Jul 11 01:39:49 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();
68 –    vector<RealType> massFactorsLocal = info_->getMassFactors();
69 –    PairList excludes = info_->getExcludedInteractions();
70 –    PairList oneTwo = info_->getOneTwoInteractions();
71 –    PairList oneThree = info_->getOneThreeInteractions();
72 –    PairList oneFour = info_->getOneFourInteractions();
67  
68 +    massFactors = info_->getMassFactors();
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 +    AtomRowToGlobal.resize(nAtomsInRow_);
117 +    AtomColToGlobal.resize(nAtomsInCol_);
118 +    cgRowToGlobal.resize(nGroupsInRow_);
119 +    cgColToGlobal.resize(nGroupsInCol_);
120 +    massFactorsRow.resize(nAtomsInRow_);
121 +    massFactorsCol.resize(nAtomsInCol_);
122 +    pot_row.resize(nAtomsInRow_);
123 +    pot_col.resize(nAtomsInCol_);
124 +
125      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
126      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
127      
128      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
129      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
130  
131 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
132 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
131 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
132 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
133  
134      groupListRow_.clear();
135      groupListRow_.resize(nGroupsInRow_);
# Line 142 | Line 153 | namespace OpenMD {
153        }      
154      }
155  
156 <    skipsForAtom.clear();
157 <    skipsForAtom.resize(nAtomsInRow_);
156 >    excludesForAtom.clear();
157 >    excludesForAtom.resize(nAtomsInRow_);
158      toposForAtom.clear();
159      toposForAtom.resize(nAtomsInRow_);
160      topoDist.clear();
# Line 154 | Line 165 | namespace OpenMD {
165        for (int j = 0; j < nAtomsInCol_; j++) {
166          int jglob = AtomColToGlobal[j];
167  
168 <        if (excludes.hasPair(iglob, jglob))
169 <          skipsForAtom[i].push_back(j);      
168 >        if (excludes->hasPair(iglob, jglob))
169 >          excludesForAtom[i].push_back(j);      
170          
171 <        if (oneTwo.hasPair(iglob, jglob)) {
171 >        if (oneTwo->hasPair(iglob, jglob)) {
172            toposForAtom[i].push_back(j);
173            topoDist[i].push_back(1);
174          } else {
175 <          if (oneThree.hasPair(iglob, jglob)) {
175 >          if (oneThree->hasPair(iglob, jglob)) {
176              toposForAtom[i].push_back(j);
177              topoDist[i].push_back(2);
178            } else {
179 <            if (oneFour.hasPair(iglob, jglob)) {
179 >            if (oneFour->hasPair(iglob, jglob)) {
180                toposForAtom[i].push_back(j);
181                topoDist[i].push_back(3);
182              }
# Line 188 | Line 199 | namespace OpenMD {
199        }      
200      }
201  
202 <    skipsForAtom.clear();
203 <    skipsForAtom.resize(nLocal_);
202 >    excludesForAtom.clear();
203 >    excludesForAtom.resize(nLocal_);
204      toposForAtom.clear();
205      toposForAtom.resize(nLocal_);
206      topoDist.clear();
# Line 201 | Line 212 | namespace OpenMD {
212        for (int j = 0; j < nLocal_; j++) {
213          int jglob = AtomLocalToGlobal[j];
214  
215 <        if (excludes.hasPair(iglob, jglob))
216 <          skipsForAtom[i].push_back(j);              
215 >        if (excludes->hasPair(iglob, jglob))
216 >          excludesForAtom[i].push_back(j);              
217          
218 <        if (oneTwo.hasPair(iglob, jglob)) {
218 >        if (oneTwo->hasPair(iglob, jglob)) {
219            toposForAtom[i].push_back(j);
220            topoDist[i].push_back(1);
221          } else {
222 <          if (oneThree.hasPair(iglob, jglob)) {
222 >          if (oneThree->hasPair(iglob, jglob)) {
223              toposForAtom[i].push_back(j);
224              topoDist[i].push_back(2);
225            } else {
226 <            if (oneFour.hasPair(iglob, jglob)) {
226 >            if (oneFour->hasPair(iglob, jglob)) {
227                toposForAtom[i].push_back(j);
228                topoDist[i].push_back(3);
229              }
# Line 222 | Line 233 | namespace OpenMD {
233      }
234      
235      createGtypeCutoffMap();
236 +
237    }
238    
239    void ForceMatrixDecomposition::createGtypeCutoffMap() {
240 <
240 >    
241      RealType tol = 1e-6;
242      RealType rc;
243      int atid;
244      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
245 <    vector<RealType> atypeCutoff;
246 <    atypeCutoff.resize( atypes.size() );
235 <
245 >    map<int, RealType> atypeCutoff;
246 >      
247      for (set<AtomType*>::iterator at = atypes.begin();
248           at != atypes.end(); ++at){
238 –      rc = interactionMan_->getSuggestedCutoffRadius(*at);
249        atid = (*at)->getIdent();
250 <      atypeCutoff[atid] = rc;
250 >      if (userChoseCutoff_)
251 >        atypeCutoff[atid] = userCutoff_;
252 >      else
253 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
254      }
255  
256      vector<RealType> gTypeCutoffs;
244 –
257      // first we do a single loop over the cutoff groups to find the
258      // largest cutoff for any atypes present in this group.
259   #ifdef IS_MPI
# Line 299 | Line 311 | namespace OpenMD {
311  
312      vector<RealType> groupCutoff(nGroups_, 0.0);
313      groupToGtype.resize(nGroups_);
302 –
303 –    cerr << "nGroups = " << nGroups_ << "\n";
314      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
315  
316        groupCutoff[cg1] = 0.0;
# Line 309 | Line 319 | namespace OpenMD {
319        for (vector<int>::iterator ia = atomList.begin();
320             ia != atomList.end(); ++ia) {            
321          int atom1 = (*ia);
322 <        atid = identsLocal[atom1];
322 >        atid = idents[atom1];
323          if (atypeCutoff[atid] > groupCutoff[cg1]) {
324            groupCutoff[cg1] = atypeCutoff[atid];
325          }
# Line 329 | Line 339 | namespace OpenMD {
339      }
340   #endif
341  
332 –    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
342      // Now we find the maximum group cutoff value present in the simulation
343  
344 <    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
344 >    RealType groupMax = *max_element(gTypeCutoffs.begin(),
345 >                                     gTypeCutoffs.end());
346  
347   #ifdef IS_MPI
348 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
348 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
349 >                              MPI::MAX);
350   #endif
351      
352      RealType tradRcut = groupMax;
# Line 378 | Line 389 | namespace OpenMD {
389            if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
390              sprintf(painCave.errMsg,
391                      "ForceMatrixDecomposition::createGtypeCutoffMap "
392 <                    "user-specified rCut does not match computed group Cutoff\n");
392 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
393              painCave.severity = OPENMD_ERROR;
394              painCave.isFatal = 1;
395              simError();            
# Line 410 | Line 421 | namespace OpenMD {
421    }
422  
423    void ForceMatrixDecomposition::zeroWorkArrays() {
424 +    pairwisePot = 0.0;
425 +    embeddingPot = 0.0;
426  
414 –    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415 –      longRangePot_[j] = 0.0;
416 –    }
417 –
427   #ifdef IS_MPI
428      if (storageLayout_ & DataStorage::dslForce) {
429        fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
# Line 430 | Line 439 | namespace OpenMD {
439           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
440  
441      fill(pot_col.begin(), pot_col.end(),
442 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434 <    
435 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
442 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
443  
444      if (storageLayout_ & DataStorage::dslParticlePot) {    
445 <      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
446 <      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
445 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
446 >           0.0);
447 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
448 >           0.0);
449      }
450  
451      if (storageLayout_ & DataStorage::dslDensity) {      
# Line 445 | Line 454 | namespace OpenMD {
454      }
455  
456      if (storageLayout_ & DataStorage::dslFunctional) {  
457 <      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
458 <      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
457 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
458 >           0.0);
459 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
460 >           0.0);
461      }
462  
463      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
# Line 456 | Line 467 | namespace OpenMD {
467             atomColData.functionalDerivative.end(), 0.0);
468      }
469  
470 < #else
471 <    
470 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
471 >      fill(atomRowData.skippedCharge.begin(),
472 >           atomRowData.skippedCharge.end(), 0.0);
473 >      fill(atomColData.skippedCharge.begin(),
474 >           atomColData.skippedCharge.end(), 0.0);
475 >    }
476 >
477 > #endif
478 >    // even in parallel, we need to zero out the local arrays:
479 >
480      if (storageLayout_ & DataStorage::dslParticlePot) {      
481        fill(snap_->atomData.particlePot.begin(),
482             snap_->atomData.particlePot.end(), 0.0);
# Line 475 | Line 494 | namespace OpenMD {
494        fill(snap_->atomData.functionalDerivative.begin(),
495             snap_->atomData.functionalDerivative.end(), 0.0);
496      }
497 < #endif
497 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
498 >      fill(snap_->atomData.skippedCharge.begin(),
499 >           snap_->atomData.skippedCharge.end(), 0.0);
500 >    }
501      
502    }
503  
# Line 512 | Line 534 | namespace OpenMD {
534        AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
535                                     atomColData.electroFrame);
536      }
537 +
538   #endif      
539    }
540    
# Line 578 | Line 601 | namespace OpenMD {
601      AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
602      for (int i = 0; i < n; i++)
603        snap_->atomData.force[i] += frc_tmp[i];
604 <    
582 <    
604 >        
605      if (storageLayout_ & DataStorage::dslTorque) {
606  
607 <      int nt = snap_->atomData.force.size();
607 >      int nt = snap_->atomData.torque.size();
608        vector<Vector3d> trq_tmp(nt, V3Zero);
609  
610        AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
611 <      for (int i = 0; i < n; i++) {
611 >      for (int i = 0; i < nt; i++) {
612          snap_->atomData.torque[i] += trq_tmp[i];
613          trq_tmp[i] = 0.0;
614        }
615        
616        AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
617 <      for (int i = 0; i < n; i++)
617 >      for (int i = 0; i < nt; i++)
618          snap_->atomData.torque[i] += trq_tmp[i];
619 +    }
620 +
621 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
622 +
623 +      int ns = snap_->atomData.skippedCharge.size();
624 +      vector<RealType> skch_tmp(ns, 0.0);
625 +
626 +      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
627 +      for (int i = 0; i < ns; i++) {
628 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
629 +        skch_tmp[i] = 0.0;
630 +      }
631 +      
632 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
633 +      for (int i = 0; i < ns; i++)
634 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
635      }
636      
637      nLocal_ = snap_->getNumberOfAtoms();
# Line 606 | Line 644 | namespace OpenMD {
644      AtomCommPotRow->scatter(pot_row, pot_temp);
645  
646      for (int ii = 0;  ii < pot_temp.size(); ii++ )
647 <      pot_local += pot_temp[ii];
647 >      pairwisePot += pot_temp[ii];
648      
649      fill(pot_temp.begin(), pot_temp.end(),
650           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
# Line 614 | Line 652 | namespace OpenMD {
652      AtomCommPotColumn->scatter(pot_col, pot_temp);    
653      
654      for (int ii = 0;  ii < pot_temp.size(); ii++ )
655 <      pot_local += pot_temp[ii];
618 <    
655 >      pairwisePot += pot_temp[ii];    
656   #endif
657 +
658    }
659  
660    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 691 | Line 729 | namespace OpenMD {
729   #ifdef IS_MPI
730      return massFactorsRow[atom1];
731   #else
732 <    return massFactorsLocal[atom1];
732 >    return massFactors[atom1];
733   #endif
734    }
735  
# Line 699 | Line 737 | namespace OpenMD {
737   #ifdef IS_MPI
738      return massFactorsCol[atom2];
739   #else
740 <    return massFactorsLocal[atom2];
740 >    return massFactors[atom2];
741   #endif
742  
743    }
# Line 717 | Line 755 | namespace OpenMD {
755      return d;    
756    }
757  
758 <  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
759 <    return skipsForAtom[atom1];
758 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
759 >    return excludesForAtom[atom1];
760    }
761  
762    /**
763 <   * 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
763 >   * We need to exclude some overcounted interactions that result from
764     * the parallel decomposition.
765     */
766    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
# Line 745 | Line 780 | namespace OpenMD {
780      } else {
781        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
782      }
783 + #endif
784 +    return false;
785 +  }
786 +
787 +  /**
788 +   * We need to handle the interactions for atoms who are involved in
789 +   * the same rigid body as well as some short range interactions
790 +   * (bonds, bends, torsions) differently from other interactions.
791 +   * We'll still visit the pairwise routines, but with a flag that
792 +   * tells those routines to exclude the pair from direct long range
793 +   * interactions.  Some indirect interactions (notably reaction
794 +   * field) must still be handled for these pairs.
795 +   */
796 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
797 +    int unique_id_2;
798 +    
799 + #ifdef IS_MPI
800 +    // in MPI, we have to look up the unique IDs for the row atom.
801 +    unique_id_2 = AtomColToGlobal[atom2];
802   #else
803      // in the normal loop, the atom numbers are unique
750 –    unique_id_1 = atom1;
804      unique_id_2 = atom2;
805   #endif
806      
807 <    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
808 <         i != skipsForAtom[atom1].end(); ++i) {
807 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
808 >         i != excludesForAtom[atom1].end(); ++i) {
809        if ( (*i) == unique_id_2 ) return true;
810 <    }    
810 >    }
811  
812 +    return false;
813    }
814  
815  
# Line 776 | Line 830 | namespace OpenMD {
830    }
831  
832      // filling interaction blocks with pointers
833 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
834 <    InteractionData idat;
833 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
834 >                                                     int atom1, int atom2) {
835  
836 +    idat.excluded = excludeAtomPair(atom1, atom2);
837 +  
838   #ifdef IS_MPI
839      
840      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
841                               ff_->getAtomType(identsCol[atom2]) );
786 –
842      
843      if (storageLayout_ & DataStorage::dslAmat) {
844        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 820 | Line 875 | namespace OpenMD {
875        idat.particlePot2 = &(atomColData.particlePot[atom2]);
876      }
877  
878 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
879 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
880 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
881 +    }
882 +
883   #else
884  
885 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
886 <                             ff_->getAtomType(identsLocal[atom2]) );
885 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
886 >                             ff_->getAtomType(idents[atom2]) );
887  
888      if (storageLayout_ & DataStorage::dslAmat) {
889        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 840 | Line 900 | namespace OpenMD {
900        idat.t2 = &(snap_->atomData.torque[atom2]);
901      }
902  
903 <    if (storageLayout_ & DataStorage::dslDensity) {
903 >    if (storageLayout_ & DataStorage::dslDensity) {    
904        idat.rho1 = &(snap_->atomData.density[atom1]);
905        idat.rho2 = &(snap_->atomData.density[atom2]);
906      }
# Line 860 | Line 920 | namespace OpenMD {
920        idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
921      }
922  
923 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
924 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
925 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
926 +    }
927   #endif
864 –    return idat;
928    }
929  
930    
931 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
931 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
932   #ifdef IS_MPI
933      pot_row[atom1] += 0.5 *  *(idat.pot);
934      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 873 | Line 936 | namespace OpenMD {
936      atomRowData.force[atom1] += *(idat.f1);
937      atomColData.force[atom2] -= *(idat.f1);
938   #else
939 <    longRangePot_ += *(idat.pot);
940 <    
939 >    pairwisePot += *(idat.pot);
940 >
941      snap_->atomData.force[atom1] += *(idat.f1);
942      snap_->atomData.force[atom2] -= *(idat.f1);
943   #endif
944 <
944 >    
945    }
946  
884 –
885 –  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
886 –
887 –    InteractionData idat;
888 – #ifdef IS_MPI
889 –    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
890 –                             ff_->getAtomType(identsCol[atom2]) );
891 –
892 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
893 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
894 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
895 –    }
896 –    if (storageLayout_ & DataStorage::dslTorque) {
897 –      idat.t1 = &(atomRowData.torque[atom1]);
898 –      idat.t2 = &(atomColData.torque[atom2]);
899 –    }
900 – #else
901 –    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
902 –                             ff_->getAtomType(identsLocal[atom2]) );
903 –
904 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
905 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
906 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
907 –    }
908 –    if (storageLayout_ & DataStorage::dslTorque) {
909 –      idat.t1 = &(snap_->atomData.torque[atom1]);
910 –      idat.t2 = &(snap_->atomData.torque[atom2]);
911 –    }
912 – #endif    
913 –  }
914 –
947    /*
948     * buildNeighborList
949     *
# Line 922 | Line 954 | namespace OpenMD {
954        
955      vector<pair<int, int> > neighborList;
956      groupCutoffs cuts;
957 +    bool doAllPairs = false;
958 +
959   #ifdef IS_MPI
960      cellListRow_.clear();
961      cellListCol_.clear();
# Line 941 | Line 975 | namespace OpenMD {
975      nCells_.y() = (int) ( Hy.length() )/ rList_;
976      nCells_.z() = (int) ( Hz.length() )/ rList_;
977  
978 +    // handle small boxes where the cell offsets can end up repeating cells
979 +    
980 +    if (nCells_.x() < 3) doAllPairs = true;
981 +    if (nCells_.y() < 3) doAllPairs = true;
982 +    if (nCells_.z() < 3) doAllPairs = true;
983 +
984      Mat3x3d invHmat = snap_->getInvHmat();
985      Vector3d rs, scaled, dr;
986      Vector3i whichCell;
# Line 954 | Line 994 | namespace OpenMD {
994      cellList_.resize(nCtot);
995   #endif
996  
997 +    if (!doAllPairs) {
998   #ifdef IS_MPI
999 <    for (int i = 0; i < nGroupsInRow_; i++) {
1000 <      rs = cgRowData.position[i];
1001 <      // scaled positions relative to the box vectors
1002 <      scaled = invHmat * rs;
1003 <      // wrap the vector back into the unit box by subtracting integer box
1004 <      // numbers
1005 <      for (int j = 0; j < 3; j++)
1006 <        scaled[j] -= roundMe(scaled[j]);
1007 <    
1008 <      // find xyz-indices of cell that cutoffGroup is in.
1009 <      whichCell.x() = nCells_.x() * scaled.x();
1010 <      whichCell.y() = nCells_.y() * scaled.y();
1011 <      whichCell.z() = nCells_.z() * scaled.z();
1012 <
1013 <      // find single index of this cell:
1014 <      cellIndex = Vlinear(whichCell, nCells_);
1015 <      // add this cutoff group to the list of groups in this cell;
1016 <      cellListRow_[cellIndex].push_back(i);
1017 <    }
1018 <
1019 <    for (int i = 0; i < nGroupsInCol_; i++) {
1020 <      rs = cgColData.position[i];
1021 <      // scaled positions relative to the box vectors
1022 <      scaled = invHmat * rs;
1023 <      // wrap the vector back into the unit box by subtracting integer box
1024 <      // numbers
1025 <      for (int j = 0; j < 3; j++)
1026 <        scaled[j] -= roundMe(scaled[j]);
1027 <
1028 <      // find xyz-indices of cell that cutoffGroup is in.
1029 <      whichCell.x() = nCells_.x() * scaled.x();
1030 <      whichCell.y() = nCells_.y() * scaled.y();
1031 <      whichCell.z() = nCells_.z() * scaled.z();
1032 <
1033 <      // find single index of this cell:
1034 <      cellIndex = Vlinear(whichCell, nCells_);
1035 <      // add this cutoff group to the list of groups in this cell;
1036 <      cellListCol_[cellIndex].push_back(i);
1037 <    }
999 >
1000 >      for (int i = 0; i < nGroupsInRow_; i++) {
1001 >        rs = cgRowData.position[i];
1002 >        
1003 >        // scaled positions relative to the box vectors
1004 >        scaled = invHmat * rs;
1005 >        
1006 >        // wrap the vector back into the unit box by subtracting integer box
1007 >        // numbers
1008 >        for (int j = 0; j < 3; j++) {
1009 >          scaled[j] -= roundMe(scaled[j]);
1010 >          scaled[j] += 0.5;
1011 >        }
1012 >        
1013 >        // find xyz-indices of cell that cutoffGroup is in.
1014 >        whichCell.x() = nCells_.x() * scaled.x();
1015 >        whichCell.y() = nCells_.y() * scaled.y();
1016 >        whichCell.z() = nCells_.z() * scaled.z();
1017 >        
1018 >        // find single index of this cell:
1019 >        cellIndex = Vlinear(whichCell, nCells_);
1020 >        
1021 >        // add this cutoff group to the list of groups in this cell;
1022 >        cellListRow_[cellIndex].push_back(i);
1023 >      }
1024 >      
1025 >      for (int i = 0; i < nGroupsInCol_; i++) {
1026 >        rs = cgColData.position[i];
1027 >        
1028 >        // scaled positions relative to the box vectors
1029 >        scaled = invHmat * rs;
1030 >        
1031 >        // wrap the vector back into the unit box by subtracting integer box
1032 >        // numbers
1033 >        for (int j = 0; j < 3; j++) {
1034 >          scaled[j] -= roundMe(scaled[j]);
1035 >          scaled[j] += 0.5;
1036 >        }
1037 >        
1038 >        // find xyz-indices of cell that cutoffGroup is in.
1039 >        whichCell.x() = nCells_.x() * scaled.x();
1040 >        whichCell.y() = nCells_.y() * scaled.y();
1041 >        whichCell.z() = nCells_.z() * scaled.z();
1042 >        
1043 >        // find single index of this cell:
1044 >        cellIndex = Vlinear(whichCell, nCells_);
1045 >        
1046 >        // add this cutoff group to the list of groups in this cell;
1047 >        cellListCol_[cellIndex].push_back(i);
1048 >      }
1049   #else
1050 <    for (int i = 0; i < nGroups_; i++) {
1051 <      rs = snap_->cgData.position[i];
1052 <      // scaled positions relative to the box vectors
1053 <      scaled = invHmat * rs;
1054 <      // wrap the vector back into the unit box by subtracting integer box
1055 <      // numbers
1056 <      for (int j = 0; j < 3; j++)
1057 <        scaled[j] -= roundMe(scaled[j]);
1058 <
1059 <      // find xyz-indices of cell that cutoffGroup is in.
1060 <      whichCell.x() = nCells_.x() * scaled.x();
1061 <      whichCell.y() = nCells_.y() * scaled.y();
1062 <      whichCell.z() = nCells_.z() * scaled.z();
1063 <
1064 <      // find single index of this cell:
1065 <      cellIndex = Vlinear(whichCell, nCells_);
1066 <      // add this cutoff group to the list of groups in this cell;
1067 <      cellList_[cellIndex].push_back(i);
1068 <    }
1050 >      for (int i = 0; i < nGroups_; i++) {
1051 >        rs = snap_->cgData.position[i];
1052 >        
1053 >        // scaled positions relative to the box vectors
1054 >        scaled = invHmat * rs;
1055 >        
1056 >        // wrap the vector back into the unit box by subtracting integer box
1057 >        // numbers
1058 >        for (int j = 0; j < 3; j++) {
1059 >          scaled[j] -= roundMe(scaled[j]);
1060 >          scaled[j] += 0.5;
1061 >        }
1062 >        
1063 >        // find xyz-indices of cell that cutoffGroup is in.
1064 >        whichCell.x() = nCells_.x() * scaled.x();
1065 >        whichCell.y() = nCells_.y() * scaled.y();
1066 >        whichCell.z() = nCells_.z() * scaled.z();
1067 >        
1068 >        // find single index of this cell:
1069 >        cellIndex = Vlinear(whichCell, nCells_);      
1070 >        
1071 >        // add this cutoff group to the list of groups in this cell;
1072 >        cellList_[cellIndex].push_back(i);
1073 >      }
1074   #endif
1075  
1076 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1077 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1078 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1079 <          Vector3i m1v(m1x, m1y, m1z);
1080 <          int m1 = Vlinear(m1v, nCells_);
1024 <
1025 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1026 <               os != cellOffsets_.end(); ++os) {
1076 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1077 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1078 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1079 >            Vector3i m1v(m1x, m1y, m1z);
1080 >            int m1 = Vlinear(m1v, nCells_);
1081              
1082 <            Vector3i m2v = m1v + (*os);
1083 <            
1084 <            if (m2v.x() >= nCells_.x()) {
1085 <              m2v.x() = 0;          
1086 <            } else if (m2v.x() < 0) {
1087 <              m2v.x() = nCells_.x() - 1;
1088 <            }
1089 <            
1090 <            if (m2v.y() >= nCells_.y()) {
1091 <              m2v.y() = 0;          
1092 <            } else if (m2v.y() < 0) {
1093 <              m2v.y() = nCells_.y() - 1;
1094 <            }
1095 <            
1096 <            if (m2v.z() >= nCells_.z()) {
1097 <              m2v.z() = 0;          
1098 <            } else if (m2v.z() < 0) {
1099 <              m2v.z() = nCells_.z() - 1;
1100 <            }
1101 <            
1102 <            int m2 = Vlinear (m2v, nCells_);
1103 <
1082 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1083 >                 os != cellOffsets_.end(); ++os) {
1084 >              
1085 >              Vector3i m2v = m1v + (*os);
1086 >              
1087 >              if (m2v.x() >= nCells_.x()) {
1088 >                m2v.x() = 0;          
1089 >              } else if (m2v.x() < 0) {
1090 >                m2v.x() = nCells_.x() - 1;
1091 >              }
1092 >              
1093 >              if (m2v.y() >= nCells_.y()) {
1094 >                m2v.y() = 0;          
1095 >              } else if (m2v.y() < 0) {
1096 >                m2v.y() = nCells_.y() - 1;
1097 >              }
1098 >              
1099 >              if (m2v.z() >= nCells_.z()) {
1100 >                m2v.z() = 0;          
1101 >              } else if (m2v.z() < 0) {
1102 >                m2v.z() = nCells_.z() - 1;
1103 >              }
1104 >              
1105 >              int m2 = Vlinear (m2v, nCells_);
1106 >              
1107   #ifdef IS_MPI
1108 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1109 <                 j1 != cellListRow_[m1].end(); ++j1) {
1110 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1111 <                   j2 != cellListCol_[m2].end(); ++j2) {
1112 <                              
1113 <                // Always do this if we're in different cells or if
1114 <                // we're in the same cell and the global index of the
1115 <                // j2 cutoff group is less than the j1 cutoff group
1116 <
1117 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1118 <                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1119 <                  snap_->wrapVector(dr);
1120 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1121 <                  if (dr.lengthSquare() < cuts.third) {
1122 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1108 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1109 >                   j1 != cellListRow_[m1].end(); ++j1) {
1110 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1111 >                     j2 != cellListCol_[m2].end(); ++j2) {
1112 >                  
1113 >                  // Always do this if we're in different cells or if
1114 >                  // we're in the same cell and the global index of the
1115 >                  // j2 cutoff group is less than the j1 cutoff group
1116 >                  
1117 >                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1118 >                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1119 >                    snap_->wrapVector(dr);
1120 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1121 >                    if (dr.lengthSquare() < cuts.third) {
1122 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1123 >                    }
1124                    }
1125                  }
1126                }
1069 –            }
1127   #else
1128 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1129 <                 j1 != cellList_[m1].end(); ++j1) {
1130 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1131 <                   j2 != cellList_[m2].end(); ++j2) {
1132 <                              
1133 <                // Always do this if we're in different cells or if
1134 <                // we're in the same cell and the global index of the
1135 <                // j2 cutoff group is less than the j1 cutoff group
1136 <
1137 <                if (m2 != m1 || (*j2) < (*j1)) {
1138 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1139 <                  snap_->wrapVector(dr);
1140 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1141 <                  if (dr.lengthSquare() < cuts.third) {
1142 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1128 >              
1129 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1130 >                   j1 != cellList_[m1].end(); ++j1) {
1131 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1132 >                     j2 != cellList_[m2].end(); ++j2) {
1133 >                  
1134 >                  // Always do this if we're in different cells or if
1135 >                  // we're in the same cell and the global index of the
1136 >                  // j2 cutoff group is less than the j1 cutoff group
1137 >                  
1138 >                  if (m2 != m1 || (*j2) < (*j1)) {
1139 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1140 >                    snap_->wrapVector(dr);
1141 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1142 >                    if (dr.lengthSquare() < cuts.third) {
1143 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1144 >                    }
1145                    }
1146                  }
1147                }
1089 –            }
1148   #endif
1149 +            }
1150            }
1151          }
1152        }
1153 +    } else {
1154 +      // branch to do all cutoff group pairs
1155 + #ifdef IS_MPI
1156 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1157 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1158 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1159 +          snap_->wrapVector(dr);
1160 +          cuts = getGroupCutoffs( j1, j2 );
1161 +          if (dr.lengthSquare() < cuts.third) {
1162 +            neighborList.push_back(make_pair(j1, j2));
1163 +          }
1164 +        }
1165 +      }
1166 + #else
1167 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1168 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1169 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1170 +          snap_->wrapVector(dr);
1171 +          cuts = getGroupCutoffs( j1, j2 );
1172 +          if (dr.lengthSquare() < cuts.third) {
1173 +            neighborList.push_back(make_pair(j1, j2));
1174 +          }
1175 +        }
1176 +      }        
1177 + #endif
1178      }
1179 <
1179 >      
1180      // save the local cutoff group positions for the check that is
1181      // done on each loop:
1182      saved_CG_positions_.clear();
1183      for (int i = 0; i < nGroups_; i++)
1184        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1185 <
1185 >    
1186      return neighborList;
1187    }
1188   } //end namespace OpenMD

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