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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 1554 by gezelter, Sat Apr 30 02:54:02 2011 UTC vs.
Revision 1575 by gezelter, Fri Jun 3 21:39:49 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  
73 <    cgCommIntRow = new Communicator<Row,int>(nGroups);
74 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
75 <    cgCommIntColumn = new Communicator<Column,int>(nGroups);
76 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
73 > #ifdef IS_MPI
74 >
75 >    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
76 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
77 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
78 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
79 >    AtomCommPotRow = new Communicator<Row,potVec>(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 >    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
86  
87 +    cgCommIntRow = new Communicator<Row,int>(nGroups_);
88 +    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
89 +    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
90 +    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
91 +
92 +    nAtomsInRow_ = AtomCommIntRow->getSize();
93 +    nAtomsInCol_ = AtomCommIntColumn->getSize();
94 +    nGroupsInRow_ = cgCommIntRow->getSize();
95 +    nGroupsInCol_ = cgCommIntColumn->getSize();
96 +
97      // Modify the data storage objects with the correct layouts and sizes:
98 <    atomRowData.resize(nAtomsInRow);
98 >    atomRowData.resize(nAtomsInRow_);
99      atomRowData.setStorageLayout(storageLayout_);
100 <    atomColData.resize(nAtomsInCol);
100 >    atomColData.resize(nAtomsInCol_);
101      atomColData.setStorageLayout(storageLayout_);
102 <    cgRowData.resize(nGroupsInRow);
102 >    cgRowData.resize(nGroupsInRow_);
103      cgRowData.setStorageLayout(DataStorage::dslPosition);
104 <    cgColData.resize(nGroupsInCol);
104 >    cgColData.resize(nGroupsInCol_);
105      cgColData.setStorageLayout(DataStorage::dslPosition);
106 +        
107 +    identsRow.reserve(nAtomsInRow_);
108 +    identsCol.reserve(nAtomsInCol_);
109      
91 –    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
92 –                                      vector<RealType> (nAtomsInRow, 0.0));
93 –    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
94 –                                      vector<RealType> (nAtomsInCol, 0.0));
95 –
96 –
97 –    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
98 –    
99 –    // gather the information for atomtype IDs (atids):
100 –    vector<int> identsLocal = info_->getIdentArray();
101 –    identsRow.reserve(nAtomsInRow);
102 –    identsCol.reserve(nAtomsInCol);
103 –    
110      AtomCommIntRow->gather(identsLocal, identsRow);
111      AtomCommIntColumn->gather(identsLocal, identsCol);
112      
107 –    AtomLocalToGlobal = info_->getGlobalAtomIndices();
113      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
114      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
115      
111 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
116      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
117      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
118  
119 <    // still need:
120 <    // topoDist
121 <    // exclude
119 >    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
120 >    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
121 >
122 >    groupListRow_.clear();
123 >    groupListRow_.reserve(nGroupsInRow_);
124 >    for (int i = 0; i < nGroupsInRow_; i++) {
125 >      int gid = cgRowToGlobal[i];
126 >      for (int j = 0; j < nAtomsInRow_; j++) {
127 >        int aid = AtomRowToGlobal[j];
128 >        if (globalGroupMembership[aid] == gid)
129 >          groupListRow_[i].push_back(j);
130 >      }      
131 >    }
132 >
133 >    groupListCol_.clear();
134 >    groupListCol_.reserve(nGroupsInCol_);
135 >    for (int i = 0; i < nGroupsInCol_; i++) {
136 >      int gid = cgColToGlobal[i];
137 >      for (int j = 0; j < nAtomsInCol_; j++) {
138 >        int aid = AtomColToGlobal[j];
139 >        if (globalGroupMembership[aid] == gid)
140 >          groupListCol_[i].push_back(j);
141 >      }      
142 >    }
143 >
144 >    skipsForRowAtom.clear();
145 >    skipsForRowAtom.reserve(nAtomsInRow_);
146 >    for (int i = 0; i < nAtomsInRow_; i++) {
147 >      int iglob = AtomRowToGlobal[i];
148 >      for (int j = 0; j < nAtomsInCol_; j++) {
149 >        int jglob = AtomColToGlobal[j];        
150 >        if (excludes.hasPair(iglob, jglob))
151 >          skipsForRowAtom[i].push_back(j);      
152 >      }      
153 >    }
154 >
155 >    toposForRowAtom.clear();
156 >    toposForRowAtom.reserve(nAtomsInRow_);
157 >    for (int i = 0; i < nAtomsInRow_; i++) {
158 >      int iglob = AtomRowToGlobal[i];
159 >      int nTopos = 0;
160 >      for (int j = 0; j < nAtomsInCol_; j++) {
161 >        int jglob = AtomColToGlobal[j];        
162 >        if (oneTwo.hasPair(iglob, jglob)) {
163 >          toposForRowAtom[i].push_back(j);
164 >          topoDistRow[i][nTopos] = 1;
165 >          nTopos++;
166 >        }
167 >        if (oneThree.hasPair(iglob, jglob)) {
168 >          toposForRowAtom[i].push_back(j);
169 >          topoDistRow[i][nTopos] = 2;
170 >          nTopos++;
171 >        }
172 >        if (oneFour.hasPair(iglob, jglob)) {
173 >          toposForRowAtom[i].push_back(j);
174 >          topoDistRow[i][nTopos] = 3;
175 >          nTopos++;
176 >        }
177 >      }      
178 >    }
179 >
180   #endif
181 +
182 +    groupList_.clear();
183 +    groupList_.reserve(nGroups_);
184 +    for (int i = 0; i < nGroups_; i++) {
185 +      int gid = cgLocalToGlobal[i];
186 +      for (int j = 0; j < nLocal_; j++) {
187 +        int aid = AtomLocalToGlobal[j];
188 +        if (globalGroupMembership[aid] == gid)
189 +          groupList_[i].push_back(j);
190 +      }      
191 +    }
192 +
193 +    skipsForLocalAtom.clear();
194 +    skipsForLocalAtom.reserve(nLocal_);
195 +
196 +    for (int i = 0; i < nLocal_; i++) {
197 +      int iglob = AtomLocalToGlobal[i];
198 +      for (int j = 0; j < nLocal_; j++) {
199 +        int jglob = AtomLocalToGlobal[j];        
200 +        if (excludes.hasPair(iglob, jglob))
201 +          skipsForLocalAtom[i].push_back(j);      
202 +      }      
203 +    }
204 +
205 +    toposForLocalAtom.clear();
206 +    toposForLocalAtom.reserve(nLocal_);
207 +    for (int i = 0; i < nLocal_; i++) {
208 +      int iglob = AtomLocalToGlobal[i];
209 +      int nTopos = 0;
210 +      for (int j = 0; j < nLocal_; j++) {
211 +        int jglob = AtomLocalToGlobal[j];        
212 +        if (oneTwo.hasPair(iglob, jglob)) {
213 +          toposForLocalAtom[i].push_back(j);
214 +          topoDistLocal[i][nTopos] = 1;
215 +          nTopos++;
216 +        }
217 +        if (oneThree.hasPair(iglob, jglob)) {
218 +          toposForLocalAtom[i].push_back(j);
219 +          topoDistLocal[i][nTopos] = 2;
220 +          nTopos++;
221 +        }
222 +        if (oneFour.hasPair(iglob, jglob)) {
223 +          toposForLocalAtom[i].push_back(j);
224 +          topoDistLocal[i][nTopos] = 3;
225 +          nTopos++;
226 +        }
227 +      }      
228 +    }
229    }
230 +  
231 +  void ForceMatrixDecomposition::zeroWorkArrays() {
232 +
233 +    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
234 +      longRangePot_[j] = 0.0;
235 +    }
236 +
237 + #ifdef IS_MPI
238 +    if (storageLayout_ & DataStorage::dslForce) {
239 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
240 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
241 +    }
242 +
243 +    if (storageLayout_ & DataStorage::dslTorque) {
244 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
245 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
246 +    }
247      
248 +    fill(pot_row.begin(), pot_row.end(),
249 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
250  
251 +    fill(pot_col.begin(), pot_col.end(),
252 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
253 +    
254 +    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
255  
256 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
257 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
258 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
259 +    }
260 +
261 +    if (storageLayout_ & DataStorage::dslDensity) {      
262 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
263 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
264 +    }
265 +
266 +    if (storageLayout_ & DataStorage::dslFunctional) {  
267 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
268 +      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
269 +    }
270 +
271 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
272 +      fill(atomRowData.functionalDerivative.begin(),
273 +           atomRowData.functionalDerivative.end(), 0.0);
274 +      fill(atomColData.functionalDerivative.begin(),
275 +           atomColData.functionalDerivative.end(), 0.0);
276 +    }
277 +
278 + #else
279 +    
280 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
281 +      fill(snap_->atomData.particlePot.begin(),
282 +           snap_->atomData.particlePot.end(), 0.0);
283 +    }
284 +    
285 +    if (storageLayout_ & DataStorage::dslDensity) {      
286 +      fill(snap_->atomData.density.begin(),
287 +           snap_->atomData.density.end(), 0.0);
288 +    }
289 +    if (storageLayout_ & DataStorage::dslFunctional) {
290 +      fill(snap_->atomData.functional.begin(),
291 +           snap_->atomData.functional.end(), 0.0);
292 +    }
293 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
294 +      fill(snap_->atomData.functionalDerivative.begin(),
295 +           snap_->atomData.functionalDerivative.end(), 0.0);
296 +    }
297 + #endif
298 +    
299 +  }
300 +
301 +
302    void ForceMatrixDecomposition::distributeData()  {
303      snap_ = sman_->getCurrentSnapshot();
304      storageLayout_ = sman_->getStorageLayout();
# Line 155 | Line 334 | namespace OpenMD {
334   #endif      
335    }
336    
337 +  /* collects information obtained during the pre-pair loop onto local
338 +   * data structures.
339 +   */
340    void ForceMatrixDecomposition::collectIntermediateData() {
341      snap_ = sman_->getCurrentSnapshot();
342      storageLayout_ = sman_->getStorageLayout();
# Line 166 | Line 348 | namespace OpenMD {
348                                 snap_->atomData.density);
349        
350        int n = snap_->atomData.density.size();
351 <      std::vector<RealType> rho_tmp(n, 0.0);
351 >      vector<RealType> rho_tmp(n, 0.0);
352        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
353        for (int i = 0; i < n; i++)
354          snap_->atomData.density[i] += rho_tmp[i];
355      }
356   #endif
357    }
358 <  
358 >
359 >  /*
360 >   * redistributes information obtained during the pre-pair loop out to
361 >   * row and column-indexed data structures
362 >   */
363    void ForceMatrixDecomposition::distributeIntermediateData() {
364      snap_ = sman_->getCurrentSnapshot();
365      storageLayout_ = sman_->getStorageLayout();
# Line 229 | Line 415 | namespace OpenMD {
415          snap_->atomData.torque[i] += trq_tmp[i];
416      }
417      
418 <    int nLocal = snap_->getNumberOfAtoms();
418 >    nLocal_ = snap_->getNumberOfAtoms();
419  
420 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
421 <                                       vector<RealType> (nLocal, 0.0));
420 >    vector<potVec> pot_temp(nLocal_,
421 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422 >
423 >    // scatter/gather pot_row into the members of my column
424 >          
425 >    AtomCommPotRow->scatter(pot_row, pot_temp);
426 >
427 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
428 >      pot_local += pot_temp[ii];
429      
430 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
431 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
432 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
433 <        pot_local[i] += pot_temp[i][ii];
434 <      }
435 <    }
430 >    fill(pot_temp.begin(), pot_temp.end(),
431 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
432 >      
433 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
434 >    
435 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
436 >      pot_local += pot_temp[ii];
437 >    
438   #endif
439    }
440  
441 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
442 + #ifdef IS_MPI
443 +    return nAtomsInRow_;
444 + #else
445 +    return nLocal_;
446 + #endif
447 +  }
448 +
449 +  /**
450 +   * returns the list of atoms belonging to this group.  
451 +   */
452 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
453 + #ifdef IS_MPI
454 +    return groupListRow_[cg1];
455 + #else
456 +    return groupList_[cg1];
457 + #endif
458 +  }
459 +
460 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
461 + #ifdef IS_MPI
462 +    return groupListCol_[cg2];
463 + #else
464 +    return groupList_[cg2];
465 + #endif
466 +  }
467    
468    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
469      Vector3d d;
# Line 284 | Line 505 | namespace OpenMD {
505      snap_->wrapVector(d);
506      return d;    
507    }
508 +
509 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
510 + #ifdef IS_MPI
511 +    return massFactorsRow[atom1];
512 + #else
513 +    return massFactorsLocal[atom1];
514 + #endif
515 +  }
516 +
517 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
518 + #ifdef IS_MPI
519 +    return massFactorsCol[atom2];
520 + #else
521 +    return massFactorsLocal[atom2];
522 + #endif
523 +
524 +  }
525      
526    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
527      Vector3d d;
# Line 296 | Line 534 | namespace OpenMD {
534  
535      snap_->wrapVector(d);
536      return d;    
537 +  }
538 +
539 +  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
540 + #ifdef IS_MPI
541 +    return skipsForRowAtom[atom1];
542 + #else
543 +    return skipsForLocalAtom[atom1];
544 + #endif
545    }
546  
547 +  /**
548 +   * There are a number of reasons to skip a pair or a
549 +   * particle. Mostly we do this to exclude atoms who are involved in
550 +   * short range interactions (bonds, bends, torsions), but we also
551 +   * need to exclude some overcounted interactions that result from
552 +   * the parallel decomposition.
553 +   */
554 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
555 +    int unique_id_1, unique_id_2;
556 +
557 + #ifdef IS_MPI
558 +    // in MPI, we have to look up the unique IDs for each atom
559 +    unique_id_1 = AtomRowToGlobal[atom1];
560 +    unique_id_2 = AtomColToGlobal[atom2];
561 +
562 +    // this situation should only arise in MPI simulations
563 +    if (unique_id_1 == unique_id_2) return true;
564 +    
565 +    // this prevents us from doing the pair on multiple processors
566 +    if (unique_id_1 < unique_id_2) {
567 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
568 +    } else {
569 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
570 +    }
571 + #else
572 +    // in the normal loop, the atom numbers are unique
573 +    unique_id_1 = atom1;
574 +    unique_id_2 = atom2;
575 + #endif
576 +    
577 + #ifdef IS_MPI
578 +    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579 +         i != skipsForRowAtom[atom1].end(); ++i) {
580 +      if ( (*i) == unique_id_2 ) return true;
581 +    }    
582 + #else
583 +    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
584 +         i != skipsForLocalAtom[atom1].end(); ++i) {
585 +      if ( (*i) == unique_id_2 ) return true;
586 +    }    
587 + #endif
588 +  }
589 +
590 +  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
591 +    
592 + #ifdef IS_MPI
593 +    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
594 +      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
595 +    }
596 + #else
597 +    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
598 +      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
599 +    }
600 + #endif
601 +
602 +    // zero is default for unconnected (i.e. normal) pair interactions
603 +    return 0;
604 +  }
605 +
606    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
607   #ifdef IS_MPI
608      atomRowData.force[atom1] += fg;
# Line 312 | Line 617 | namespace OpenMD {
617   #else
618      snap_->atomData.force[atom2] += fg;
619   #endif
315 –
620    }
621  
622      // filling interaction blocks with pointers
623    InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
320 –
624      InteractionData idat;
625 +
626   #ifdef IS_MPI
627 +    
628 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
629 +                             ff_->getAtomType(identsCol[atom2]) );
630 +
631 +    
632      if (storageLayout_ & DataStorage::dslAmat) {
633        idat.A1 = &(atomRowData.aMat[atom1]);
634        idat.A2 = &(atomColData.aMat[atom2]);
635      }
636 <
636 >    
637      if (storageLayout_ & DataStorage::dslElectroFrame) {
638        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
639        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 340 | Line 649 | namespace OpenMD {
649        idat.rho2 = &(atomColData.density[atom2]);
650      }
651  
652 +    if (storageLayout_ & DataStorage::dslFunctional) {
653 +      idat.frho1 = &(atomRowData.functional[atom1]);
654 +      idat.frho2 = &(atomColData.functional[atom2]);
655 +    }
656 +
657      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
658        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
659        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
660      }
661 +
662 +    if (storageLayout_ & DataStorage::dslParticlePot) {
663 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
664 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
665 +    }
666 +
667 + #else
668 +
669 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
670 +                             ff_->getAtomType(identsLocal[atom2]) );
671 +
672 +    if (storageLayout_ & DataStorage::dslAmat) {
673 +      idat.A1 = &(snap_->atomData.aMat[atom1]);
674 +      idat.A2 = &(snap_->atomData.aMat[atom2]);
675 +    }
676 +
677 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
678 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
679 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
680 +    }
681 +
682 +    if (storageLayout_ & DataStorage::dslTorque) {
683 +      idat.t1 = &(snap_->atomData.torque[atom1]);
684 +      idat.t2 = &(snap_->atomData.torque[atom2]);
685 +    }
686 +
687 +    if (storageLayout_ & DataStorage::dslDensity) {
688 +      idat.rho1 = &(snap_->atomData.density[atom1]);
689 +      idat.rho2 = &(snap_->atomData.density[atom2]);
690 +    }
691 +
692 +    if (storageLayout_ & DataStorage::dslFunctional) {
693 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
694 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
695 +    }
696 +
697 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
698 +      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
699 +      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
700 +    }
701 +
702 +    if (storageLayout_ & DataStorage::dslParticlePot) {
703 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
704 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
705 +    }
706 +
707   #endif
708 +    return idat;
709 +  }
710 +
711 +  
712 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
713 + #ifdef IS_MPI
714 +    pot_row[atom1] += 0.5 *  *(idat.pot);
715 +    pot_col[atom2] += 0.5 *  *(idat.pot);
716 +
717 +    atomRowData.force[atom1] += *(idat.f1);
718 +    atomColData.force[atom2] -= *(idat.f1);
719 + #else
720 +    longRangePot_ += *(idat.pot);
721      
722 +    snap_->atomData.force[atom1] += *(idat.f1);
723 +    snap_->atomData.force[atom2] -= *(idat.f1);
724 + #endif
725 +
726    }
727 +
728 +
729    InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
730 +
731 +    InteractionData idat;
732 + #ifdef IS_MPI
733 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
734 +                             ff_->getAtomType(identsCol[atom2]) );
735 +
736 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
737 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
738 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
739 +    }
740 +    if (storageLayout_ & DataStorage::dslTorque) {
741 +      idat.t1 = &(atomRowData.torque[atom1]);
742 +      idat.t2 = &(atomColData.torque[atom2]);
743 +    }
744 + #else
745 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
746 +                             ff_->getAtomType(identsLocal[atom2]) );
747 +
748 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
749 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
750 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
751 +    }
752 +    if (storageLayout_ & DataStorage::dslTorque) {
753 +      idat.t1 = &(snap_->atomData.torque[atom1]);
754 +      idat.t2 = &(snap_->atomData.torque[atom2]);
755 +    }
756 + #endif    
757    }
352 –  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
353 –  }
758  
759 <  
759 >  /*
760 >   * buildNeighborList
761 >   *
762 >   * first element of pair is row-indexed CutoffGroup
763 >   * second element of pair is column-indexed CutoffGroup
764 >   */
765 >  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
766 >      
767 >    vector<pair<int, int> > neighborList;
768 > #ifdef IS_MPI
769 >    cellListRow_.clear();
770 >    cellListCol_.clear();
771 > #else
772 >    cellList_.clear();
773 > #endif
774 >
775 >    // dangerous to not do error checking.
776 >    RealType rCut_;
777 >
778 >    RealType rList_ = (rCut_ + skinThickness_);
779 >    RealType rl2 = rList_ * rList_;
780 >    Snapshot* snap_ = sman_->getCurrentSnapshot();
781 >    Mat3x3d Hmat = snap_->getHmat();
782 >    Vector3d Hx = Hmat.getColumn(0);
783 >    Vector3d Hy = Hmat.getColumn(1);
784 >    Vector3d Hz = Hmat.getColumn(2);
785 >
786 >    nCells_.x() = (int) ( Hx.length() )/ rList_;
787 >    nCells_.y() = (int) ( Hy.length() )/ rList_;
788 >    nCells_.z() = (int) ( Hz.length() )/ rList_;
789 >
790 >    Mat3x3d invHmat = snap_->getInvHmat();
791 >    Vector3d rs, scaled, dr;
792 >    Vector3i whichCell;
793 >    int cellIndex;
794 >
795 > #ifdef IS_MPI
796 >    for (int i = 0; i < nGroupsInRow_; i++) {
797 >      rs = cgRowData.position[i];
798 >      // scaled positions relative to the box vectors
799 >      scaled = invHmat * rs;
800 >      // wrap the vector back into the unit box by subtracting integer box
801 >      // numbers
802 >      for (int j = 0; j < 3; j++)
803 >        scaled[j] -= roundMe(scaled[j]);
804 >    
805 >      // find xyz-indices of cell that cutoffGroup is in.
806 >      whichCell.x() = nCells_.x() * scaled.x();
807 >      whichCell.y() = nCells_.y() * scaled.y();
808 >      whichCell.z() = nCells_.z() * scaled.z();
809 >
810 >      // find single index of this cell:
811 >      cellIndex = Vlinear(whichCell, nCells_);
812 >      // add this cutoff group to the list of groups in this cell;
813 >      cellListRow_[cellIndex].push_back(i);
814 >    }
815 >
816 >    for (int i = 0; i < nGroupsInCol_; i++) {
817 >      rs = cgColData.position[i];
818 >      // scaled positions relative to the box vectors
819 >      scaled = invHmat * rs;
820 >      // wrap the vector back into the unit box by subtracting integer box
821 >      // numbers
822 >      for (int j = 0; j < 3; j++)
823 >        scaled[j] -= roundMe(scaled[j]);
824 >
825 >      // find xyz-indices of cell that cutoffGroup is in.
826 >      whichCell.x() = nCells_.x() * scaled.x();
827 >      whichCell.y() = nCells_.y() * scaled.y();
828 >      whichCell.z() = nCells_.z() * scaled.z();
829 >
830 >      // find single index of this cell:
831 >      cellIndex = Vlinear(whichCell, nCells_);
832 >      // add this cutoff group to the list of groups in this cell;
833 >      cellListCol_[cellIndex].push_back(i);
834 >    }
835 > #else
836 >    for (int i = 0; i < nGroups_; i++) {
837 >      rs = snap_->cgData.position[i];
838 >      // scaled positions relative to the box vectors
839 >      scaled = invHmat * rs;
840 >      // wrap the vector back into the unit box by subtracting integer box
841 >      // numbers
842 >      for (int j = 0; j < 3; j++)
843 >        scaled[j] -= roundMe(scaled[j]);
844 >
845 >      // find xyz-indices of cell that cutoffGroup is in.
846 >      whichCell.x() = nCells_.x() * scaled.x();
847 >      whichCell.y() = nCells_.y() * scaled.y();
848 >      whichCell.z() = nCells_.z() * scaled.z();
849 >
850 >      // find single index of this cell:
851 >      cellIndex = Vlinear(whichCell, nCells_);
852 >      // add this cutoff group to the list of groups in this cell;
853 >      cellList_[cellIndex].push_back(i);
854 >    }
855 > #endif
856 >
857 >    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
858 >      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
859 >        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
860 >          Vector3i m1v(m1x, m1y, m1z);
861 >          int m1 = Vlinear(m1v, nCells_);
862 >
863 >          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
864 >               os != cellOffsets_.end(); ++os) {
865 >            
866 >            Vector3i m2v = m1v + (*os);
867 >            
868 >            if (m2v.x() >= nCells_.x()) {
869 >              m2v.x() = 0;          
870 >            } else if (m2v.x() < 0) {
871 >              m2v.x() = nCells_.x() - 1;
872 >            }
873 >            
874 >            if (m2v.y() >= nCells_.y()) {
875 >              m2v.y() = 0;          
876 >            } else if (m2v.y() < 0) {
877 >              m2v.y() = nCells_.y() - 1;
878 >            }
879 >            
880 >            if (m2v.z() >= nCells_.z()) {
881 >              m2v.z() = 0;          
882 >            } else if (m2v.z() < 0) {
883 >              m2v.z() = nCells_.z() - 1;
884 >            }
885 >            
886 >            int m2 = Vlinear (m2v, nCells_);
887 >
888 > #ifdef IS_MPI
889 >            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
890 >                 j1 != cellListRow_[m1].end(); ++j1) {
891 >              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
892 >                   j2 != cellListCol_[m2].end(); ++j2) {
893 >                              
894 >                // Always do this if we're in different cells or if
895 >                // we're in the same cell and the global index of the
896 >                // j2 cutoff group is less than the j1 cutoff group
897 >
898 >                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
899 >                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
900 >                  snap_->wrapVector(dr);
901 >                  if (dr.lengthSquare() < rl2) {
902 >                    neighborList.push_back(make_pair((*j1), (*j2)));
903 >                  }
904 >                }
905 >              }
906 >            }
907 > #else
908 >            for (vector<int>::iterator j1 = cellList_[m1].begin();
909 >                 j1 != cellList_[m1].end(); ++j1) {
910 >              for (vector<int>::iterator j2 = cellList_[m2].begin();
911 >                   j2 != cellList_[m2].end(); ++j2) {
912 >                              
913 >                // Always do this if we're in different cells or if
914 >                // we're in the same cell and the global index of the
915 >                // j2 cutoff group is less than the j1 cutoff group
916 >
917 >                if (m2 != m1 || (*j2) < (*j1)) {
918 >                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
919 >                  snap_->wrapVector(dr);
920 >                  if (dr.lengthSquare() < rl2) {
921 >                    neighborList.push_back(make_pair((*j1), (*j2)));
922 >                  }
923 >                }
924 >              }
925 >            }
926 > #endif
927 >          }
928 >        }
929 >      }
930 >    }
931 >
932 >    // save the local cutoff group positions for the check that is
933 >    // done on each loop:
934 >    saved_CG_positions_.clear();
935 >    for (int i = 0; i < nGroups_; i++)
936 >      saved_CG_positions_.push_back(snap_->cgData.position[i]);
937 >
938 >    return neighborList;
939 >  }
940   } //end namespace OpenMD

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