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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 1562 by gezelter, Thu May 12 17:00:14 2011 UTC vs.
Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC

# Line 42 | Line 42
42   #include "math/SquareMatrix3.hpp"
43   #include "nonbonded/NonBondedInteraction.hpp"
44   #include "brains/SnapshotManager.hpp"
45 + #include "brains/PairList.hpp"
46  
47   using namespace std;
48   namespace OpenMD {
# Line 54 | Line 55 | namespace OpenMD {
55    void ForceMatrixDecomposition::distributeInitialData() {
56      snap_ = sman_->getCurrentSnapshot();
57      storageLayout_ = sman_->getStorageLayout();
58 < #ifdef IS_MPI    
59 <    int nLocal = snap_->getNumberOfAtoms();
60 <    int nGroups = snap_->getNumberOfCutoffGroups();
60 <    
61 <    AtomCommIntRow = new Communicator<Row,int>(nLocal);
62 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
63 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
64 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
58 >    ff_ = info_->getForceField();
59 >    nLocal_ = snap_->getNumberOfAtoms();
60 >    nGroups_ = snap_->getNumberOfCutoffGroups();
61  
62 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
63 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
64 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
65 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
62 >    // gather the information for atomtype IDs (atids):
63 >    identsLocal = info_->getIdentArray();
64 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
65 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
66 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67 >    vector<RealType> massFactorsLocal = info_->getMassFactors();
68 >    PairList excludes = info_->getExcludedInteractions();
69 >    PairList oneTwo = info_->getOneTwoInteractions();
70 >    PairList oneThree = info_->getOneThreeInteractions();
71 >    PairList oneFour = info_->getOneFourInteractions();
72 >    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
73  
74 <    cgCommIntRow = new Communicator<Row,int>(nGroups);
75 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
76 <    cgCommIntColumn = new Communicator<Column,int>(nGroups);
77 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
74 > #ifdef IS_MPI
75 >
76 >    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
77 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
78 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
79 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
80  
81 <    int nAtomsInRow = AtomCommIntRow->getSize();
82 <    int nAtomsInCol = AtomCommIntColumn->getSize();
83 <    int nGroupsInRow = cgCommIntRow->getSize();
84 <    int nGroupsInCol = cgCommIntColumn->getSize();
81 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
82 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
83 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
84 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
85  
86 +    cgCommIntRow = new Communicator<Row,int>(nGroups_);
87 +    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
88 +    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
89 +    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
90 +
91 +    nAtomsInRow_ = AtomCommIntRow->getSize();
92 +    nAtomsInCol_ = AtomCommIntColumn->getSize();
93 +    nGroupsInRow_ = cgCommIntRow->getSize();
94 +    nGroupsInCol_ = cgCommIntColumn->getSize();
95 +
96      // Modify the data storage objects with the correct layouts and sizes:
97 <    atomRowData.resize(nAtomsInRow);
97 >    atomRowData.resize(nAtomsInRow_);
98      atomRowData.setStorageLayout(storageLayout_);
99 <    atomColData.resize(nAtomsInCol);
99 >    atomColData.resize(nAtomsInCol_);
100      atomColData.setStorageLayout(storageLayout_);
101 <    cgRowData.resize(nGroupsInRow);
101 >    cgRowData.resize(nGroupsInRow_);
102      cgRowData.setStorageLayout(DataStorage::dslPosition);
103 <    cgColData.resize(nGroupsInCol);
103 >    cgColData.resize(nGroupsInCol_);
104      cgColData.setStorageLayout(DataStorage::dslPosition);
105      
106      vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
107 <                                      vector<RealType> (nAtomsInRow, 0.0));
107 >                                      vector<RealType> (nAtomsInRow_, 0.0));
108      vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
109 <                                      vector<RealType> (nAtomsInCol, 0.0));
95 <
96 <
97 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
109 >                                      vector<RealType> (nAtomsInCol_, 0.0));
110      
111 <    // gather the information for atomtype IDs (atids):
112 <    vector<int> identsLocal = info_->getIdentArray();
101 <    identsRow.reserve(nAtomsInRow);
102 <    identsCol.reserve(nAtomsInCol);
111 >    identsRow.reserve(nAtomsInRow_);
112 >    identsCol.reserve(nAtomsInCol_);
113      
114      AtomCommIntRow->gather(identsLocal, identsRow);
115      AtomCommIntColumn->gather(identsLocal, identsCol);
116      
107 –    AtomLocalToGlobal = info_->getGlobalAtomIndices();
117      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
118      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
119      
111 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
120      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
121      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
122  
123 <    // still need:
124 <    // topoDist
125 <    // exclude
123 >    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
124 >    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
125 >
126 >    groupListRow_.clear();
127 >    groupListRow_.reserve(nGroupsInRow_);
128 >    for (int i = 0; i < nGroupsInRow_; i++) {
129 >      int gid = cgRowToGlobal[i];
130 >      for (int j = 0; j < nAtomsInRow_; j++) {
131 >        int aid = AtomRowToGlobal[j];
132 >        if (globalGroupMembership[aid] == gid)
133 >          groupListRow_[i].push_back(j);
134 >      }      
135 >    }
136 >
137 >    groupListCol_.clear();
138 >    groupListCol_.reserve(nGroupsInCol_);
139 >    for (int i = 0; i < nGroupsInCol_; i++) {
140 >      int gid = cgColToGlobal[i];
141 >      for (int j = 0; j < nAtomsInCol_; j++) {
142 >        int aid = AtomColToGlobal[j];
143 >        if (globalGroupMembership[aid] == gid)
144 >          groupListCol_[i].push_back(j);
145 >      }      
146 >    }
147 >
148 >    skipsForRowAtom.clear();
149 >    skipsForRowAtom.reserve(nAtomsInRow_);
150 >    for (int i = 0; i < nAtomsInRow_; i++) {
151 >      int iglob = AtomRowToGlobal[i];
152 >      for (int j = 0; j < nAtomsInCol_; j++) {
153 >        int jglob = AtomColToGlobal[j];        
154 >        if (excludes.hasPair(iglob, jglob))
155 >          skipsForRowAtom[i].push_back(j);      
156 >      }      
157 >    }
158 >
159 >    toposForRowAtom.clear();
160 >    toposForRowAtom.reserve(nAtomsInRow_);
161 >    for (int i = 0; i < nAtomsInRow_; i++) {
162 >      int iglob = AtomRowToGlobal[i];
163 >      int nTopos = 0;
164 >      for (int j = 0; j < nAtomsInCol_; j++) {
165 >        int jglob = AtomColToGlobal[j];        
166 >        if (oneTwo.hasPair(iglob, jglob)) {
167 >          toposForRowAtom[i].push_back(j);
168 >          topoDistRow[i][nTopos] = 1;
169 >          nTopos++;
170 >        }
171 >        if (oneThree.hasPair(iglob, jglob)) {
172 >          toposForRowAtom[i].push_back(j);
173 >          topoDistRow[i][nTopos] = 2;
174 >          nTopos++;
175 >        }
176 >        if (oneFour.hasPair(iglob, jglob)) {
177 >          toposForRowAtom[i].push_back(j);
178 >          topoDistRow[i][nTopos] = 3;
179 >          nTopos++;
180 >        }
181 >      }      
182 >    }
183 >
184   #endif
119 –  }
120 –    
185  
186 +    groupList_.clear();
187 +    groupList_.reserve(nGroups_);
188 +    for (int i = 0; i < nGroups_; i++) {
189 +      int gid = cgLocalToGlobal[i];
190 +      for (int j = 0; j < nLocal_; j++) {
191 +        int aid = AtomLocalToGlobal[j];
192 +        if (globalGroupMembership[aid] == gid)
193 +          groupList_[i].push_back(j);
194 +      }      
195 +    }
196  
197 +    skipsForLocalAtom.clear();
198 +    skipsForLocalAtom.reserve(nLocal_);
199 +
200 +    for (int i = 0; i < nLocal_; i++) {
201 +      int iglob = AtomLocalToGlobal[i];
202 +      for (int j = 0; j < nLocal_; j++) {
203 +        int jglob = AtomLocalToGlobal[j];        
204 +        if (excludes.hasPair(iglob, jglob))
205 +          skipsForLocalAtom[i].push_back(j);      
206 +      }      
207 +    }
208 +
209 +    toposForLocalAtom.clear();
210 +    toposForLocalAtom.reserve(nLocal_);
211 +    for (int i = 0; i < nLocal_; i++) {
212 +      int iglob = AtomLocalToGlobal[i];
213 +      int nTopos = 0;
214 +      for (int j = 0; j < nLocal_; j++) {
215 +        int jglob = AtomLocalToGlobal[j];        
216 +        if (oneTwo.hasPair(iglob, jglob)) {
217 +          toposForLocalAtom[i].push_back(j);
218 +          topoDistLocal[i][nTopos] = 1;
219 +          nTopos++;
220 +        }
221 +        if (oneThree.hasPair(iglob, jglob)) {
222 +          toposForLocalAtom[i].push_back(j);
223 +          topoDistLocal[i][nTopos] = 2;
224 +          nTopos++;
225 +        }
226 +        if (oneFour.hasPair(iglob, jglob)) {
227 +          toposForLocalAtom[i].push_back(j);
228 +          topoDistLocal[i][nTopos] = 3;
229 +          nTopos++;
230 +        }
231 +      }      
232 +    }
233 +  }
234 +  
235    void ForceMatrixDecomposition::distributeData()  {
236      snap_ = sman_->getCurrentSnapshot();
237      storageLayout_ = sman_->getStorageLayout();
# Line 229 | Line 341 | namespace OpenMD {
341          snap_->atomData.torque[i] += trq_tmp[i];
342      }
343      
344 <    int nLocal = snap_->getNumberOfAtoms();
344 >    nLocal_ = snap_->getNumberOfAtoms();
345  
346      vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
347 <                                       vector<RealType> (nLocal, 0.0));
347 >                                       vector<RealType> (nLocal_, 0.0));
348      
349      for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
350        AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
# Line 243 | Line 355 | namespace OpenMD {
355   #endif
356    }
357  
358 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
359 + #ifdef IS_MPI
360 +    return nAtomsInRow_;
361 + #else
362 +    return nLocal_;
363 + #endif
364 +  }
365 +
366 +  /**
367 +   * returns the list of atoms belonging to this group.  
368 +   */
369 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
370 + #ifdef IS_MPI
371 +    return groupListRow_[cg1];
372 + #else
373 +    return groupList_[cg1];
374 + #endif
375 +  }
376 +
377 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
378 + #ifdef IS_MPI
379 +    return groupListCol_[cg2];
380 + #else
381 +    return groupList_[cg2];
382 + #endif
383 +  }
384    
385    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
386      Vector3d d;
# Line 284 | Line 422 | namespace OpenMD {
422      snap_->wrapVector(d);
423      return d;    
424    }
425 +
426 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
427 + #ifdef IS_MPI
428 +    return massFactorsRow[atom1];
429 + #else
430 +    return massFactorsLocal[atom1];
431 + #endif
432 +  }
433 +
434 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
435 + #ifdef IS_MPI
436 +    return massFactorsCol[atom2];
437 + #else
438 +    return massFactorsLocal[atom2];
439 + #endif
440 +
441 +  }
442      
443    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
444      Vector3d d;
# Line 298 | Line 453 | namespace OpenMD {
453      return d;    
454    }
455  
456 +  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
457 + #ifdef IS_MPI
458 +    return skipsForRowAtom[atom1];
459 + #else
460 +    return skipsForLocalAtom[atom1];
461 + #endif
462 +  }
463 +
464 +  /**
465 +   * there are a number of reasons to skip a pair or a particle mostly
466 +   * we do this to exclude atoms who are involved in short range
467 +   * interactions (bonds, bends, torsions), but we also need to
468 +   * exclude some overcounted interactions that result from the
469 +   * parallel decomposition.
470 +   */
471 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
472 +    int unique_id_1, unique_id_2;
473 +
474 + #ifdef IS_MPI
475 +    // in MPI, we have to look up the unique IDs for each atom
476 +    unique_id_1 = AtomRowToGlobal[atom1];
477 +    unique_id_2 = AtomColToGlobal[atom2];
478 +
479 +    // this situation should only arise in MPI simulations
480 +    if (unique_id_1 == unique_id_2) return true;
481 +    
482 +    // this prevents us from doing the pair on multiple processors
483 +    if (unique_id_1 < unique_id_2) {
484 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
485 +    } else {
486 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
487 +    }
488 + #else
489 +    // in the normal loop, the atom numbers are unique
490 +    unique_id_1 = atom1;
491 +    unique_id_2 = atom2;
492 + #endif
493 +    
494 + #ifdef IS_MPI
495 +    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
496 +         i != skipsForRowAtom[atom1].end(); ++i) {
497 +      if ( (*i) == unique_id_2 ) return true;
498 +    }    
499 + #else
500 +    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
501 +         i != skipsForLocalAtom[atom1].end(); ++i) {
502 +      if ( (*i) == unique_id_2 ) return true;
503 +    }    
504 + #endif
505 +  }
506 +
507 +  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
508 +    
509 + #ifdef IS_MPI
510 +    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
511 +      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
512 +    }
513 + #else
514 +    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
515 +      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
516 +    }
517 + #endif
518 +
519 +    // zero is default for unconnected (i.e. normal) pair interactions
520 +    return 0;
521 +  }
522 +
523    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
524   #ifdef IS_MPI
525      atomRowData.force[atom1] += fg;
# Line 312 | Line 534 | namespace OpenMD {
534   #else
535      snap_->atomData.force[atom2] += fg;
536   #endif
315 –
537    }
538  
539      // filling interaction blocks with pointers
540    InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
320 –
541      InteractionData idat;
542 +
543   #ifdef IS_MPI
544 +    
545 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
546 +                             ff_->getAtomType(identsCol[atom2]) );
547 +
548      if (storageLayout_ & DataStorage::dslAmat) {
549        idat.A1 = &(atomRowData.aMat[atom1]);
550        idat.A2 = &(atomColData.aMat[atom2]);
551      }
552 <
552 >    
553      if (storageLayout_ & DataStorage::dslElectroFrame) {
554        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
555        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 344 | Line 569 | namespace OpenMD {
569        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
570        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
571      }
572 +
573   #else
574 +
575 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
576 +                             ff_->getAtomType(identsLocal[atom2]) );
577 +
578      if (storageLayout_ & DataStorage::dslAmat) {
579        idat.A1 = &(snap_->atomData.aMat[atom1]);
580        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 370 | Line 600 | namespace OpenMD {
600        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
601      }
602   #endif
603 <    
603 >    return idat;
604    }
605 +
606    InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
607 +
608      InteractionData idat;
377 –    skippedCharge1
378 –      skippedCharge2
379 –      rij
380 –      d
381 –    electroMult
382 –    sw
383 –    f
609   #ifdef IS_MPI
610 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
611 +                             ff_->getAtomType(identsCol[atom2]) );
612  
613      if (storageLayout_ & DataStorage::dslElectroFrame) {
614        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
# Line 391 | Line 618 | namespace OpenMD {
618        idat.t1 = &(atomRowData.torque[atom1]);
619        idat.t2 = &(atomColData.torque[atom2]);
620      }
621 +    if (storageLayout_ & DataStorage::dslForce) {
622 +      idat.t1 = &(atomRowData.force[atom1]);
623 +      idat.t2 = &(atomColData.force[atom2]);
624 +    }
625 + #else
626 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
627 +                             ff_->getAtomType(identsLocal[atom2]) );
628  
629 <    
629 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
630 >      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
631 >      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
632 >    }
633 >    if (storageLayout_ & DataStorage::dslTorque) {
634 >      idat.t1 = &(snap_->atomData.torque[atom1]);
635 >      idat.t2 = &(snap_->atomData.torque[atom2]);
636 >    }
637 >    if (storageLayout_ & DataStorage::dslForce) {
638 >      idat.t1 = &(snap_->atomData.force[atom1]);
639 >      idat.t2 = &(snap_->atomData.force[atom2]);
640 >    }
641 > #endif    
642    }
397 –  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
398 –  }
643  
400 –
644    /*
645     * buildNeighborList
646     *
647     * first element of pair is row-indexed CutoffGroup
648     * second element of pair is column-indexed CutoffGroup
649     */
650 <  vector<pair<int, int> >  buildNeighborList() {
651 <    Vector3d dr, invWid, rs, shift;
652 <    Vector3i cc, m1v, m2s;
653 <    RealType rrNebr;
654 <    int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
650 >  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
651 >      
652 >    vector<pair<int, int> > neighborList;
653 > #ifdef IS_MPI
654 >    cellListRow_.clear();
655 >    cellListCol_.clear();
656 > #else
657 >    cellList_.clear();
658 > #endif
659  
660 <
661 <    vector<pair<int, int> > neighborList;  
662 <    Vector3i nCells;
663 <    Vector3d invWid, r;
664 <
665 <    rList_ = (rCut_ + skinThickness_);
419 <    rl2 = rList_ * rList_;
420 <
421 <    snap_ = sman_->getCurrentSnapshot();
660 >    // dangerous to not do error checking.
661 >    RealType rCut_;
662 >
663 >    RealType rList_ = (rCut_ + skinThickness_);
664 >    RealType rl2 = rList_ * rList_;
665 >    Snapshot* snap_ = sman_->getCurrentSnapshot();
666      Mat3x3d Hmat = snap_->getHmat();
667      Vector3d Hx = Hmat.getColumn(0);
668      Vector3d Hy = Hmat.getColumn(1);
669      Vector3d Hz = Hmat.getColumn(2);
670  
671 <    nCells.x() = (int) ( Hx.length() )/ rList_;
672 <    nCells.y() = (int) ( Hy.length() )/ rList_;
673 <    nCells.z() = (int) ( Hz.length() )/ rList_;
671 >    nCells_.x() = (int) ( Hx.length() )/ rList_;
672 >    nCells_.y() = (int) ( Hy.length() )/ rList_;
673 >    nCells_.z() = (int) ( Hz.length() )/ rList_;
674  
675 <    for (i = 0; i < nGroupsInRow; i++) {
675 >    Mat3x3d invHmat = snap_->getInvHmat();
676 >    Vector3d rs, scaled, dr;
677 >    Vector3i whichCell;
678 >    int cellIndex;
679 >
680 > #ifdef IS_MPI
681 >    for (int i = 0; i < nGroupsInRow_; i++) {
682        rs = cgRowData.position[i];
683 <      snap_->scaleVector(rs);    
683 >      // scaled positions relative to the box vectors
684 >      scaled = invHmat * rs;
685 >      // wrap the vector back into the unit box by subtracting integer box
686 >      // numbers
687 >      for (int j = 0; j < 3; j++)
688 >        scaled[j] -= roundMe(scaled[j]);
689 >    
690 >      // find xyz-indices of cell that cutoffGroup is in.
691 >      whichCell.x() = nCells_.x() * scaled.x();
692 >      whichCell.y() = nCells_.y() * scaled.y();
693 >      whichCell.z() = nCells_.z() * scaled.z();
694 >
695 >      // find single index of this cell:
696 >      cellIndex = Vlinear(whichCell, nCells_);
697 >      // add this cutoff group to the list of groups in this cell;
698 >      cellListRow_[cellIndex].push_back(i);
699      }
435 –    
700  
701 <    VDiv (invWid, cells, region);
702 <    for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
703 <    for (n = 0; n < nMol; n ++) {
704 <      VSAdd (rs, mol[n].r, 0.5, region);
705 <      VMul (cc, rs, invWid);
706 <      c = VLinear (cc, cells) + nMol;
707 <      cellList[n] = cellList[c];
708 <      cellList[c] = n;
701 >    for (int i = 0; i < nGroupsInCol_; i++) {
702 >      rs = cgColData.position[i];
703 >      // scaled positions relative to the box vectors
704 >      scaled = invHmat * rs;
705 >      // wrap the vector back into the unit box by subtracting integer box
706 >      // numbers
707 >      for (int j = 0; j < 3; j++)
708 >        scaled[j] -= roundMe(scaled[j]);
709 >
710 >      // find xyz-indices of cell that cutoffGroup is in.
711 >      whichCell.x() = nCells_.x() * scaled.x();
712 >      whichCell.y() = nCells_.y() * scaled.y();
713 >      whichCell.z() = nCells_.z() * scaled.z();
714 >
715 >      // find single index of this cell:
716 >      cellIndex = Vlinear(whichCell, nCells_);
717 >      // add this cutoff group to the list of groups in this cell;
718 >      cellListCol_[cellIndex].push_back(i);
719      }
720 <    nebrTabLen = 0;
721 <    for (m1z = 0; m1z < cells.z(); m1z++) {
722 <      for (m1y = 0; m1y < cells.y(); m1y++) {
723 <        for (m1x = 0; m1x < cells.x(); m1x++) {
720 > #else
721 >    for (int i = 0; i < nGroups_; i++) {
722 >      rs = snap_->cgData.position[i];
723 >      // scaled positions relative to the box vectors
724 >      scaled = invHmat * rs;
725 >      // wrap the vector back into the unit box by subtracting integer box
726 >      // numbers
727 >      for (int j = 0; j < 3; j++)
728 >        scaled[j] -= roundMe(scaled[j]);
729 >
730 >      // find xyz-indices of cell that cutoffGroup is in.
731 >      whichCell.x() = nCells_.x() * scaled.x();
732 >      whichCell.y() = nCells_.y() * scaled.y();
733 >      whichCell.z() = nCells_.z() * scaled.z();
734 >
735 >      // find single index of this cell:
736 >      cellIndex = Vlinear(whichCell, nCells_);
737 >      // add this cutoff group to the list of groups in this cell;
738 >      cellList_[cellIndex].push_back(i);
739 >    }
740 > #endif
741 >
742 >
743 >
744 >    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
745 >      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
746 >        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
747            Vector3i m1v(m1x, m1y, m1z);
748 <          m1 = VLinear(m1v, cells) + nMol;
452 <          for (offset = 0; offset < nOffset_; offset++) {
453 <            m2v = m1v + cellOffsets_[offset];
454 <            shift = V3Zero();
748 >          int m1 = Vlinear(m1v, nCells_);
749  
750 <            if (m2v.x() >= cells.x) {
750 >          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
751 >               os != cellOffsets_.end(); ++os) {
752 >            
753 >            Vector3i m2v = m1v + (*os);
754 >            
755 >            if (m2v.x() >= nCells_.x()) {
756                m2v.x() = 0;          
458 –              shift.x() = region.x();  
757              } else if (m2v.x() < 0) {
758 <              m2v.x() = cells.x() - 1;
461 <              shift.x() = - region.x();
758 >              m2v.x() = nCells_.x() - 1;
759              }
760 <
761 <            if (m2v.y() >= cells.y()) {
760 >            
761 >            if (m2v.y() >= nCells_.y()) {
762                m2v.y() = 0;          
466 –              shift.y() = region.y();  
763              } else if (m2v.y() < 0) {
764 <              m2v.y() = cells.y() - 1;
469 <              shift.y() = - region.y();
764 >              m2v.y() = nCells_.y() - 1;
765              }
766 +            
767 +            if (m2v.z() >= nCells_.z()) {
768 +              m2v.z() = 0;          
769 +            } else if (m2v.z() < 0) {
770 +              m2v.z() = nCells_.z() - 1;
771 +            }
772 +            
773 +            int m2 = Vlinear (m2v, nCells_);
774  
775 <            m2 = VLinear (m2v, cells) + nMol;
776 <            for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
777 <              for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
778 <                if (m1 != m2 || j2 < j1) {
779 <                  dr = mol[j1].r - mol[j2].r;
780 <                  VSub (dr, mol[j1].r, mol[j2].r);
781 <                  VVSub (dr, shift);
782 <                  if (VLenSq (dr) < rrNebr) {
783 <                    neighborList.push_back(make_pair(j1, j2));
775 > #ifdef IS_MPI
776 >            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
777 >                 j1 != cellListRow_[m1].end(); ++j1) {
778 >              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
779 >                   j2 != cellListCol_[m2].end(); ++j2) {
780 >                              
781 >                // Always do this if we're in different cells or if
782 >                // we're in the same cell and the global index of the
783 >                // j2 cutoff group is less than the j1 cutoff group
784 >
785 >                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
786 >                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
787 >                  snap_->wrapVector(dr);
788 >                  if (dr.lengthSquare() < rl2) {
789 >                    neighborList.push_back(make_pair((*j1), (*j2)));
790                    }
791                  }
792                }
793              }
794 + #else
795 +            for (vector<int>::iterator j1 = cellList_[m1].begin();
796 +                 j1 != cellList_[m1].end(); ++j1) {
797 +              for (vector<int>::iterator j2 = cellList_[m2].begin();
798 +                   j2 != cellList_[m2].end(); ++j2) {
799 +                              
800 +                // Always do this if we're in different cells or if
801 +                // we're in the same cell and the global index of the
802 +                // j2 cutoff group is less than the j1 cutoff group
803 +
804 +                if (m2 != m1 || (*j2) < (*j1)) {
805 +                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
806 +                  snap_->wrapVector(dr);
807 +                  if (dr.lengthSquare() < rl2) {
808 +                    neighborList.push_back(make_pair((*j1), (*j2)));
809 +                  }
810 +                }
811 +              }
812 +            }
813 + #endif
814            }
815          }
816        }
817      }
489 –  }
818  
819 <  
819 >    // save the local cutoff group positions for the check that is
820 >    // done on each loop:
821 >    saved_CG_positions_.clear();
822 >    for (int i = 0; i < nGroups_; i++)
823 >      saved_CG_positions_.push_back(snap_->cgData.position[i]);
824 >
825 >    return neighborList;
826 >  }
827   } //end namespace OpenMD

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