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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 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC vs.
Revision 1756 by gezelter, Mon Jun 18 18:23:20 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42   #include "parallel/ForceMatrixDecomposition.hpp"
43   #include "math/SquareMatrix3.hpp"
# Line 47 | Line 48 | namespace OpenMD {
48   using namespace std;
49   namespace OpenMD {
50  
51 +  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52 +
53 +    // In a parallel computation, row and colum scans must visit all
54 +    // surrounding cells (not just the 14 upper triangular blocks that
55 +    // are used when the processor can see all pairs)
56 + #ifdef IS_MPI
57 +    cellOffsets_.clear();
58 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
61 +    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
66 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );      
71 +    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72 +    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73 +    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74 +    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75 +    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76 +    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77 +    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78 +    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80 +    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81 +    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82 +    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83 +    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84 +    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85 + #endif    
86 +  }
87 +
88 +
89    /**
90     * distributeInitialData is essentially a copy of the older fortran
91     * SimulationSetup
92     */
54 –  
93    void ForceMatrixDecomposition::distributeInitialData() {
94      snap_ = sman_->getCurrentSnapshot();
95      storageLayout_ = sman_->getStorageLayout();
96      ff_ = info_->getForceField();
97      nLocal_ = snap_->getNumberOfAtoms();
98 <
98 >  
99      nGroups_ = info_->getNLocalCutoffGroups();
62 –    cerr << "in dId, nGroups = " << nGroups_ << "\n";
100      // gather the information for atomtype IDs (atids):
101      idents = info_->getIdentArray();
102      AtomLocalToGlobal = info_->getGlobalAtomIndices();
103      cgLocalToGlobal = info_->getGlobalGroupIndices();
104      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
105 +
106      massFactors = info_->getMassFactors();
69 –    PairList excludes = info_->getExcludedInteractions();
70 –    PairList oneTwo = info_->getOneTwoInteractions();
71 –    PairList oneThree = info_->getOneThreeInteractions();
72 –    PairList oneFour = info_->getOneFourInteractions();
107  
108 +    PairList* excludes = info_->getExcludedInteractions();
109 +    PairList* oneTwo = info_->getOneTwoInteractions();
110 +    PairList* oneThree = info_->getOneThreeInteractions();
111 +    PairList* oneFour = info_->getOneFourInteractions();
112 +    
113 +    if (needVelocities_)
114 +      snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115 +                                     DataStorage::dslVelocity);
116 +    else
117 +      snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118 +    
119   #ifdef IS_MPI
120  
121 <    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
122 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
78 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
79 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
80 <    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
121 >    MPI::Intracomm row = rowComm.getComm();
122 >    MPI::Intracomm col = colComm.getComm();
123  
124 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
125 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
126 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
127 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
128 <    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
124 >    AtomPlanIntRow = new Plan<int>(row, nLocal_);
125 >    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
126 >    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
127 >    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
128 >    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
129  
130 <    cgCommIntRow = new Communicator<Row,int>(nGroups_);
131 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
132 <    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
133 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
130 >    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
131 >    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
132 >    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
133 >    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
134 >    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
135  
136 <    nAtomsInRow_ = AtomCommIntRow->getSize();
137 <    nAtomsInCol_ = AtomCommIntColumn->getSize();
138 <    nGroupsInRow_ = cgCommIntRow->getSize();
139 <    nGroupsInCol_ = cgCommIntColumn->getSize();
136 >    cgPlanIntRow = new Plan<int>(row, nGroups_);
137 >    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
138 >    cgPlanIntColumn = new Plan<int>(col, nGroups_);
139 >    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
140  
141 +    nAtomsInRow_ = AtomPlanIntRow->getSize();
142 +    nAtomsInCol_ = AtomPlanIntColumn->getSize();
143 +    nGroupsInRow_ = cgPlanIntRow->getSize();
144 +    nGroupsInCol_ = cgPlanIntColumn->getSize();
145 +
146      // Modify the data storage objects with the correct layouts and sizes:
147      atomRowData.resize(nAtomsInRow_);
148      atomRowData.setStorageLayout(storageLayout_);
# Line 103 | Line 151 | namespace OpenMD {
151      cgRowData.resize(nGroupsInRow_);
152      cgRowData.setStorageLayout(DataStorage::dslPosition);
153      cgColData.resize(nGroupsInCol_);
154 <    cgColData.setStorageLayout(DataStorage::dslPosition);
155 <        
154 >    if (needVelocities_)
155 >      // we only need column velocities if we need them.
156 >      cgColData.setStorageLayout(DataStorage::dslPosition |
157 >                                 DataStorage::dslVelocity);
158 >    else    
159 >      cgColData.setStorageLayout(DataStorage::dslPosition);
160 >      
161      identsRow.resize(nAtomsInRow_);
162      identsCol.resize(nAtomsInCol_);
163      
164 <    AtomCommIntRow->gather(idents, identsRow);
165 <    AtomCommIntColumn->gather(idents, identsCol);
164 >    AtomPlanIntRow->gather(idents, identsRow);
165 >    AtomPlanIntColumn->gather(idents, identsCol);
166      
167 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
168 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
169 <    
117 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
118 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
167 >    // allocate memory for the parallel objects
168 >    atypesRow.resize(nAtomsInRow_);
169 >    atypesCol.resize(nAtomsInCol_);
170  
171 <    AtomCommRealRow->gather(massFactors, massFactorsRow);
172 <    AtomCommRealColumn->gather(massFactors, massFactorsCol);
171 >    for (int i = 0; i < nAtomsInRow_; i++)
172 >      atypesRow[i] = ff_->getAtomType(identsRow[i]);
173 >    for (int i = 0; i < nAtomsInCol_; i++)
174 >      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
175 >
176 >    pot_row.resize(nAtomsInRow_);
177 >    pot_col.resize(nAtomsInCol_);
178 >
179 >    AtomRowToGlobal.resize(nAtomsInRow_);
180 >    AtomColToGlobal.resize(nAtomsInCol_);
181 >    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
182 >    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
183 >
184 >    cgRowToGlobal.resize(nGroupsInRow_);
185 >    cgColToGlobal.resize(nGroupsInCol_);
186 >    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
187 >    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
188  
189 +    massFactorsRow.resize(nAtomsInRow_);
190 +    massFactorsCol.resize(nAtomsInCol_);
191 +    AtomPlanRealRow->gather(massFactors, massFactorsRow);
192 +    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
193 +
194      groupListRow_.clear();
195      groupListRow_.resize(nGroupsInRow_);
196      for (int i = 0; i < nGroupsInRow_; i++) {
# Line 142 | Line 213 | namespace OpenMD {
213        }      
214      }
215  
216 <    skipsForAtom.clear();
217 <    skipsForAtom.resize(nAtomsInRow_);
216 >    excludesForAtom.clear();
217 >    excludesForAtom.resize(nAtomsInRow_);
218      toposForAtom.clear();
219      toposForAtom.resize(nAtomsInRow_);
220      topoDist.clear();
# Line 154 | Line 225 | namespace OpenMD {
225        for (int j = 0; j < nAtomsInCol_; j++) {
226          int jglob = AtomColToGlobal[j];
227  
228 <        if (excludes.hasPair(iglob, jglob))
229 <          skipsForAtom[i].push_back(j);      
228 >        if (excludes->hasPair(iglob, jglob))
229 >          excludesForAtom[i].push_back(j);      
230          
231 <        if (oneTwo.hasPair(iglob, jglob)) {
231 >        if (oneTwo->hasPair(iglob, jglob)) {
232            toposForAtom[i].push_back(j);
233            topoDist[i].push_back(1);
234          } else {
235 <          if (oneThree.hasPair(iglob, jglob)) {
235 >          if (oneThree->hasPair(iglob, jglob)) {
236              toposForAtom[i].push_back(j);
237              topoDist[i].push_back(2);
238            } else {
239 <            if (oneFour.hasPair(iglob, jglob)) {
239 >            if (oneFour->hasPair(iglob, jglob)) {
240                toposForAtom[i].push_back(j);
241                topoDist[i].push_back(3);
242              }
# Line 174 | Line 245 | namespace OpenMD {
245        }      
246      }
247  
248 < #endif
249 <
250 <    groupList_.clear();
180 <    groupList_.resize(nGroups_);
181 <    for (int i = 0; i < nGroups_; i++) {
182 <      int gid = cgLocalToGlobal[i];
183 <      for (int j = 0; j < nLocal_; j++) {
184 <        int aid = AtomLocalToGlobal[j];
185 <        if (globalGroupMembership[aid] == gid) {
186 <          groupList_[i].push_back(j);
187 <        }
188 <      }      
189 <    }
190 <
191 <    skipsForAtom.clear();
192 <    skipsForAtom.resize(nLocal_);
248 > #else
249 >    excludesForAtom.clear();
250 >    excludesForAtom.resize(nLocal_);
251      toposForAtom.clear();
252      toposForAtom.resize(nLocal_);
253      topoDist.clear();
# Line 201 | Line 259 | namespace OpenMD {
259        for (int j = 0; j < nLocal_; j++) {
260          int jglob = AtomLocalToGlobal[j];
261  
262 <        if (excludes.hasPair(iglob, jglob))
263 <          skipsForAtom[i].push_back(j);              
262 >        if (excludes->hasPair(iglob, jglob))
263 >          excludesForAtom[i].push_back(j);              
264          
265 <        if (oneTwo.hasPair(iglob, jglob)) {
265 >        if (oneTwo->hasPair(iglob, jglob)) {
266            toposForAtom[i].push_back(j);
267            topoDist[i].push_back(1);
268          } else {
269 <          if (oneThree.hasPair(iglob, jglob)) {
269 >          if (oneThree->hasPair(iglob, jglob)) {
270              toposForAtom[i].push_back(j);
271              topoDist[i].push_back(2);
272            } else {
273 <            if (oneFour.hasPair(iglob, jglob)) {
273 >            if (oneFour->hasPair(iglob, jglob)) {
274                toposForAtom[i].push_back(j);
275                topoDist[i].push_back(3);
276              }
# Line 220 | Line 278 | namespace OpenMD {
278          }
279        }      
280      }
281 <    
281 > #endif
282 >
283 >    // allocate memory for the parallel objects
284 >    atypesLocal.resize(nLocal_);
285 >
286 >    for (int i = 0; i < nLocal_; i++)
287 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
288 >
289 >    groupList_.clear();
290 >    groupList_.resize(nGroups_);
291 >    for (int i = 0; i < nGroups_; i++) {
292 >      int gid = cgLocalToGlobal[i];
293 >      for (int j = 0; j < nLocal_; j++) {
294 >        int aid = AtomLocalToGlobal[j];
295 >        if (globalGroupMembership[aid] == gid) {
296 >          groupList_[i].push_back(j);
297 >        }
298 >      }      
299 >    }
300 >
301 >
302      createGtypeCutoffMap();
303 +
304    }
305    
306    void ForceMatrixDecomposition::createGtypeCutoffMap() {
307 <
307 >    
308      RealType tol = 1e-6;
309 +    largestRcut_ = 0.0;
310      RealType rc;
311      int atid;
312      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
313 <    vector<RealType> atypeCutoff;
314 <    atypeCutoff.resize( atypes.size() );
313 >    
314 >    map<int, RealType> atypeCutoff;
315        
316      for (set<AtomType*>::iterator at = atypes.begin();
317           at != atypes.end(); ++at){
318        atid = (*at)->getIdent();
319 <
240 <      if (userChoseCutoff_)
319 >      if (userChoseCutoff_)
320          atypeCutoff[atid] = userCutoff_;
321        else
322          atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
323      }
324 <
324 >    
325      vector<RealType> gTypeCutoffs;
247 –
326      // first we do a single loop over the cutoff groups to find the
327      // largest cutoff for any atypes present in this group.
328   #ifdef IS_MPI
# Line 302 | Line 380 | namespace OpenMD {
380  
381      vector<RealType> groupCutoff(nGroups_, 0.0);
382      groupToGtype.resize(nGroups_);
305 –
306 –    cerr << "nGroups = " << nGroups_ << "\n";
383      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
308 –
384        groupCutoff[cg1] = 0.0;
385        vector<int> atomList = getAtomsInGroupRow(cg1);
311 –
386        for (vector<int>::iterator ia = atomList.begin();
387             ia != atomList.end(); ++ia) {            
388          int atom1 = (*ia);
389          atid = idents[atom1];
390 <        if (atypeCutoff[atid] > groupCutoff[cg1]) {
390 >        if (atypeCutoff[atid] > groupCutoff[cg1])
391            groupCutoff[cg1] = atypeCutoff[atid];
318 –        }
392        }
393 <
393 >      
394        bool gTypeFound = false;
395        for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
396          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
# Line 325 | Line 398 | namespace OpenMD {
398            gTypeFound = true;
399          }
400        }
401 <      if (!gTypeFound) {
401 >      if (!gTypeFound) {      
402          gTypeCutoffs.push_back( groupCutoff[cg1] );
403          groupToGtype[cg1] = gTypeCutoffs.size() - 1;
404        }      
405      }
406   #endif
407  
335 –    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
408      // Now we find the maximum group cutoff value present in the simulation
409  
410 <    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
410 >    RealType groupMax = *max_element(gTypeCutoffs.begin(),
411 >                                     gTypeCutoffs.end());
412  
413   #ifdef IS_MPI
414 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
414 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
415 >                              MPI::MAX);
416   #endif
417      
418      RealType tradRcut = groupMax;
# Line 368 | Line 442 | namespace OpenMD {
442  
443          pair<int,int> key = make_pair(i,j);
444          gTypeCutoffMap[key].first = thisRcut;
371 –
445          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
373 –
446          gTypeCutoffMap[key].second = thisRcut*thisRcut;
375 –        
447          gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
377 –
448          // sanity check
449          
450          if (userChoseCutoff_) {
# Line 391 | Line 461 | namespace OpenMD {
461      }
462    }
463  
394 –
464    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
465      int i, j;  
466   #ifdef IS_MPI
# Line 434 | Line 503 | namespace OpenMD {
503           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
504  
505      if (storageLayout_ & DataStorage::dslParticlePot) {    
506 <      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
507 <      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
506 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
507 >           0.0);
508 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
509 >           0.0);
510      }
511  
512      if (storageLayout_ & DataStorage::dslDensity) {      
# Line 444 | Line 515 | namespace OpenMD {
515      }
516  
517      if (storageLayout_ & DataStorage::dslFunctional) {  
518 <      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
519 <      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
518 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
519 >           0.0);
520 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
521 >           0.0);
522      }
523  
524      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
# Line 455 | Line 528 | namespace OpenMD {
528             atomColData.functionalDerivative.end(), 0.0);
529      }
530  
531 < #else
532 <    
531 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
532 >      fill(atomRowData.skippedCharge.begin(),
533 >           atomRowData.skippedCharge.end(), 0.0);
534 >      fill(atomColData.skippedCharge.begin(),
535 >           atomColData.skippedCharge.end(), 0.0);
536 >    }
537 >
538 >    if (storageLayout_ & DataStorage::dslFlucQForce) {      
539 >      fill(atomRowData.flucQFrc.begin(),
540 >           atomRowData.flucQFrc.end(), 0.0);
541 >      fill(atomColData.flucQFrc.begin(),
542 >           atomColData.flucQFrc.end(), 0.0);
543 >    }
544 >
545 >    if (storageLayout_ & DataStorage::dslElectricField) {    
546 >      fill(atomRowData.electricField.begin(),
547 >           atomRowData.electricField.end(), V3Zero);
548 >      fill(atomColData.electricField.begin(),
549 >           atomColData.electricField.end(), V3Zero);
550 >    }
551 >
552 >    if (storageLayout_ & DataStorage::dslFlucQForce) {    
553 >      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
554 >           0.0);
555 >      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
556 >           0.0);
557 >    }
558 >
559 > #endif
560 >    // even in parallel, we need to zero out the local arrays:
561 >
562      if (storageLayout_ & DataStorage::dslParticlePot) {      
563        fill(snap_->atomData.particlePot.begin(),
564             snap_->atomData.particlePot.end(), 0.0);
# Line 466 | Line 568 | namespace OpenMD {
568        fill(snap_->atomData.density.begin(),
569             snap_->atomData.density.end(), 0.0);
570      }
571 +
572      if (storageLayout_ & DataStorage::dslFunctional) {
573        fill(snap_->atomData.functional.begin(),
574             snap_->atomData.functional.end(), 0.0);
575      }
576 +
577      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
578        fill(snap_->atomData.functionalDerivative.begin(),
579             snap_->atomData.functionalDerivative.end(), 0.0);
580      }
581 < #endif
582 <    
581 >
582 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
583 >      fill(snap_->atomData.skippedCharge.begin(),
584 >           snap_->atomData.skippedCharge.end(), 0.0);
585 >    }
586 >
587 >    if (storageLayout_ & DataStorage::dslElectricField) {      
588 >      fill(snap_->atomData.electricField.begin(),
589 >           snap_->atomData.electricField.end(), V3Zero);
590 >    }
591    }
592  
593  
# Line 485 | Line 597 | namespace OpenMD {
597   #ifdef IS_MPI
598      
599      // gather up the atomic positions
600 <    AtomCommVectorRow->gather(snap_->atomData.position,
600 >    AtomPlanVectorRow->gather(snap_->atomData.position,
601                                atomRowData.position);
602 <    AtomCommVectorColumn->gather(snap_->atomData.position,
602 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
603                                   atomColData.position);
604      
605      // gather up the cutoff group positions
606 <    cgCommVectorRow->gather(snap_->cgData.position,
606 >
607 >    cgPlanVectorRow->gather(snap_->cgData.position,
608                              cgRowData.position);
609 <    cgCommVectorColumn->gather(snap_->cgData.position,
609 >
610 >    cgPlanVectorColumn->gather(snap_->cgData.position,
611                                 cgColData.position);
612 +
613 +
614 +
615 +    if (needVelocities_) {
616 +      // gather up the atomic velocities
617 +      AtomPlanVectorColumn->gather(snap_->atomData.velocity,
618 +                                   atomColData.velocity);
619 +      
620 +      cgPlanVectorColumn->gather(snap_->cgData.velocity,
621 +                                 cgColData.velocity);
622 +    }
623 +
624      
625      // if needed, gather the atomic rotation matrices
626      if (storageLayout_ & DataStorage::dslAmat) {
627 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
627 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
628                                  atomRowData.aMat);
629 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
629 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
630                                     atomColData.aMat);
631      }
632      
633      // if needed, gather the atomic eletrostatic frames
634      if (storageLayout_ & DataStorage::dslElectroFrame) {
635 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
635 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
636                                  atomRowData.electroFrame);
637 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
637 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
638                                     atomColData.electroFrame);
639      }
640 +
641 +    // if needed, gather the atomic fluctuating charge values
642 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {
643 +      AtomPlanRealRow->gather(snap_->atomData.flucQPos,
644 +                              atomRowData.flucQPos);
645 +      AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
646 +                                 atomColData.flucQPos);
647 +    }
648 +
649   #endif      
650    }
651    
# Line 524 | Line 659 | namespace OpenMD {
659      
660      if (storageLayout_ & DataStorage::dslDensity) {
661        
662 <      AtomCommRealRow->scatter(atomRowData.density,
662 >      AtomPlanRealRow->scatter(atomRowData.density,
663                                 snap_->atomData.density);
664        
665        int n = snap_->atomData.density.size();
666        vector<RealType> rho_tmp(n, 0.0);
667 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
667 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
668        for (int i = 0; i < n; i++)
669          snap_->atomData.density[i] += rho_tmp[i];
670      }
671 +
672 +    if (storageLayout_ & DataStorage::dslElectricField) {
673 +      
674 +      AtomPlanVectorRow->scatter(atomRowData.electricField,
675 +                                 snap_->atomData.electricField);
676 +      
677 +      int n = snap_->atomData.electricField.size();
678 +      vector<Vector3d> field_tmp(n, V3Zero);
679 +      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
680 +      for (int i = 0; i < n; i++)
681 +        snap_->atomData.electricField[i] += field_tmp[i];
682 +    }
683   #endif
684    }
685  
# Line 545 | Line 692 | namespace OpenMD {
692      storageLayout_ = sman_->getStorageLayout();
693   #ifdef IS_MPI
694      if (storageLayout_ & DataStorage::dslFunctional) {
695 <      AtomCommRealRow->gather(snap_->atomData.functional,
695 >      AtomPlanRealRow->gather(snap_->atomData.functional,
696                                atomRowData.functional);
697 <      AtomCommRealColumn->gather(snap_->atomData.functional,
697 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
698                                   atomColData.functional);
699      }
700      
701      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
702 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
702 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
703                                atomRowData.functionalDerivative);
704 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
704 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
705                                   atomColData.functionalDerivative);
706      }
707   #endif
# Line 568 | Line 715 | namespace OpenMD {
715      int n = snap_->atomData.force.size();
716      vector<Vector3d> frc_tmp(n, V3Zero);
717      
718 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
718 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
719      for (int i = 0; i < n; i++) {
720        snap_->atomData.force[i] += frc_tmp[i];
721        frc_tmp[i] = 0.0;
722      }
723      
724 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
725 <    for (int i = 0; i < n; i++)
724 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
725 >    for (int i = 0; i < n; i++) {
726        snap_->atomData.force[i] += frc_tmp[i];
727 <    
728 <    
727 >    }
728 >        
729      if (storageLayout_ & DataStorage::dslTorque) {
730  
731 <      int nt = snap_->atomData.force.size();
731 >      int nt = snap_->atomData.torque.size();
732        vector<Vector3d> trq_tmp(nt, V3Zero);
733  
734 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
735 <      for (int i = 0; i < n; i++) {
734 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
735 >      for (int i = 0; i < nt; i++) {
736          snap_->atomData.torque[i] += trq_tmp[i];
737          trq_tmp[i] = 0.0;
738        }
739        
740 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
741 <      for (int i = 0; i < n; i++)
740 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
741 >      for (int i = 0; i < nt; i++)
742          snap_->atomData.torque[i] += trq_tmp[i];
743      }
744 +
745 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
746 +
747 +      int ns = snap_->atomData.skippedCharge.size();
748 +      vector<RealType> skch_tmp(ns, 0.0);
749 +
750 +      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
751 +      for (int i = 0; i < ns; i++) {
752 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
753 +        skch_tmp[i] = 0.0;
754 +      }
755 +      
756 +      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
757 +      for (int i = 0; i < ns; i++)
758 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
759 +            
760 +    }
761      
762 +    if (storageLayout_ & DataStorage::dslFlucQForce) {
763 +
764 +      int nq = snap_->atomData.flucQFrc.size();
765 +      vector<RealType> fqfrc_tmp(nq, 0.0);
766 +
767 +      AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
768 +      for (int i = 0; i < nq; i++) {
769 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
770 +        fqfrc_tmp[i] = 0.0;
771 +      }
772 +      
773 +      AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
774 +      for (int i = 0; i < nq; i++)
775 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
776 +            
777 +    }
778 +
779      nLocal_ = snap_->getNumberOfAtoms();
780  
781      vector<potVec> pot_temp(nLocal_,
# Line 602 | Line 783 | namespace OpenMD {
783  
784      // scatter/gather pot_row into the members of my column
785            
786 <    AtomCommPotRow->scatter(pot_row, pot_temp);
786 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
787  
788      for (int ii = 0;  ii < pot_temp.size(); ii++ )
789        pairwisePot += pot_temp[ii];
790 <    
790 >        
791 >    if (storageLayout_ & DataStorage::dslParticlePot) {
792 >      // This is the pairwise contribution to the particle pot.  The
793 >      // embedding contribution is added in each of the low level
794 >      // non-bonded routines.  In single processor, this is done in
795 >      // unpackInteractionData, not in collectData.
796 >      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
797 >        for (int i = 0; i < nLocal_; i++) {
798 >          // factor of two is because the total potential terms are divided
799 >          // by 2 in parallel due to row/ column scatter      
800 >          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
801 >        }
802 >      }
803 >    }
804 >
805      fill(pot_temp.begin(), pot_temp.end(),
806           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
807        
808 <    AtomCommPotColumn->scatter(pot_col, pot_temp);    
808 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
809      
810      for (int ii = 0;  ii < pot_temp.size(); ii++ )
811        pairwisePot += pot_temp[ii];    
812 +
813 +    if (storageLayout_ & DataStorage::dslParticlePot) {
814 +      // This is the pairwise contribution to the particle pot.  The
815 +      // embedding contribution is added in each of the low level
816 +      // non-bonded routines.  In single processor, this is done in
817 +      // unpackInteractionData, not in collectData.
818 +      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
819 +        for (int i = 0; i < nLocal_; i++) {
820 +          // factor of two is because the total potential terms are divided
821 +          // by 2 in parallel due to row/ column scatter      
822 +          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
823 +        }
824 +      }
825 +    }
826 +    
827 +    if (storageLayout_ & DataStorage::dslParticlePot) {
828 +      int npp = snap_->atomData.particlePot.size();
829 +      vector<RealType> ppot_temp(npp, 0.0);
830 +
831 +      // This is the direct or embedding contribution to the particle
832 +      // pot.
833 +      
834 +      AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
835 +      for (int i = 0; i < npp; i++) {
836 +        snap_->atomData.particlePot[i] += ppot_temp[i];
837 +      }
838 +
839 +      fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
840 +      
841 +      AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
842 +      for (int i = 0; i < npp; i++) {
843 +        snap_->atomData.particlePot[i] += ppot_temp[i];
844 +      }
845 +    }
846 +
847 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
848 +      RealType ploc1 = pairwisePot[ii];
849 +      RealType ploc2 = 0.0;
850 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
851 +      pairwisePot[ii] = ploc2;
852 +    }
853 +
854 +    // Here be dragons.
855 +    MPI::Intracomm col = colComm.getComm();
856 +
857 +    col.Allreduce(MPI::IN_PLACE,
858 +                  &snap_->frameData.conductiveHeatFlux[0], 3,
859 +                  MPI::REALTYPE, MPI::SUM);
860 +
861 +
862   #endif
863  
864 +  }
865 +
866 +  /**
867 +   * Collects information obtained during the post-pair (and embedding
868 +   * functional) loops onto local data structures.
869 +   */
870 +  void ForceMatrixDecomposition::collectSelfData() {
871 +    snap_ = sman_->getCurrentSnapshot();
872 +    storageLayout_ = sman_->getStorageLayout();
873 +
874 + #ifdef IS_MPI
875 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
876 +      RealType ploc1 = embeddingPot[ii];
877 +      RealType ploc2 = 0.0;
878 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
879 +      embeddingPot[ii] = ploc2;
880 +    }    
881 + #endif
882 +    
883    }
884  
885 +
886 +
887    int ForceMatrixDecomposition::getNAtomsInRow() {  
888   #ifdef IS_MPI
889      return nAtomsInRow_;
# Line 658 | Line 924 | namespace OpenMD {
924      return d;    
925    }
926  
927 +  Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
928 + #ifdef IS_MPI
929 +    return cgColData.velocity[cg2];
930 + #else
931 +    return snap_->cgData.velocity[cg2];
932 + #endif
933 +  }
934  
935 +  Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
936 + #ifdef IS_MPI
937 +    return atomColData.velocity[atom2];
938 + #else
939 +    return snap_->atomData.velocity[atom2];
940 + #endif
941 +  }
942 +
943 +
944    Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
945  
946      Vector3d d;
# Line 716 | Line 998 | namespace OpenMD {
998      return d;    
999    }
1000  
1001 <  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
1002 <    return skipsForAtom[atom1];
1001 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1002 >    return excludesForAtom[atom1];
1003    }
1004  
1005    /**
1006 <   * There are a number of reasons to skip a pair or a
725 <   * particle. Mostly we do this to exclude atoms who are involved in
726 <   * short range interactions (bonds, bends, torsions), but we also
727 <   * need to exclude some overcounted interactions that result from
1006 >   * We need to exclude some overcounted interactions that result from
1007     * the parallel decomposition.
1008     */
1009 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1010 <    int unique_id_1, unique_id_2;
1011 <
1009 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1010 >    int unique_id_1, unique_id_2, group1, group2;
1011 >        
1012   #ifdef IS_MPI
1013      // in MPI, we have to look up the unique IDs for each atom
1014      unique_id_1 = AtomRowToGlobal[atom1];
1015      unique_id_2 = AtomColToGlobal[atom2];
1016 +    group1 = cgRowToGlobal[cg1];
1017 +    group2 = cgColToGlobal[cg2];
1018 + #else
1019 +    unique_id_1 = AtomLocalToGlobal[atom1];
1020 +    unique_id_2 = AtomLocalToGlobal[atom2];
1021 +    group1 = cgLocalToGlobal[cg1];
1022 +    group2 = cgLocalToGlobal[cg2];
1023 + #endif  
1024  
738 –    // this situation should only arise in MPI simulations
1025      if (unique_id_1 == unique_id_2) return true;
1026 <    
1026 >
1027 > #ifdef IS_MPI
1028      // this prevents us from doing the pair on multiple processors
1029      if (unique_id_1 < unique_id_2) {
1030        if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1031      } else {
1032 <      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1032 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1033      }
1034 < #else
1035 <    // in the normal loop, the atom numbers are unique
1036 <    unique_id_1 = atom1;
1037 <    unique_id_2 = atom2;
1034 > #endif    
1035 >
1036 > #ifndef IS_MPI
1037 >    if (group1 == group2) {
1038 >      if (unique_id_1 < unique_id_2) return true;
1039 >    }
1040   #endif
1041      
1042 <    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
1043 <         i != skipsForAtom[atom1].end(); ++i) {
1044 <      if ( (*i) == unique_id_2 ) return true;
1042 >    return false;
1043 >  }
1044 >
1045 >  /**
1046 >   * We need to handle the interactions for atoms who are involved in
1047 >   * the same rigid body as well as some short range interactions
1048 >   * (bonds, bends, torsions) differently from other interactions.
1049 >   * We'll still visit the pairwise routines, but with a flag that
1050 >   * tells those routines to exclude the pair from direct long range
1051 >   * interactions.  Some indirect interactions (notably reaction
1052 >   * field) must still be handled for these pairs.
1053 >   */
1054 >  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1055 >
1056 >    // excludesForAtom was constructed to use row/column indices in the MPI
1057 >    // version, and to use local IDs in the non-MPI version:
1058 >    
1059 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1060 >         i != excludesForAtom[atom1].end(); ++i) {
1061 >      if ( (*i) == atom2 ) return true;
1062      }
1063  
1064      return false;
# Line 777 | Line 1083 | namespace OpenMD {
1083  
1084      // filling interaction blocks with pointers
1085    void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1086 <                                                     int atom1, int atom2) {    
1086 >                                                     int atom1, int atom2) {
1087 >
1088 >    idat.excluded = excludeAtomPair(atom1, atom2);
1089 >  
1090   #ifdef IS_MPI
1091 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1092 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1093 +    //                         ff_->getAtomType(identsCol[atom2]) );
1094      
783 –    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
784 –                             ff_->getAtomType(identsCol[atom2]) );
785 –    
1095      if (storageLayout_ & DataStorage::dslAmat) {
1096        idat.A1 = &(atomRowData.aMat[atom1]);
1097        idat.A2 = &(atomColData.aMat[atom2]);
# Line 818 | Line 1127 | namespace OpenMD {
1127        idat.particlePot2 = &(atomColData.particlePot[atom2]);
1128      }
1129  
1130 < #else
1130 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
1131 >      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1132 >      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1133 >    }
1134  
1135 <    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1136 <                             ff_->getAtomType(idents[atom2]) );
1135 >    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
1136 >      idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1137 >      idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1138 >    }
1139  
1140 + #else
1141 +    
1142 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1143 +
1144      if (storageLayout_ & DataStorage::dslAmat) {
1145        idat.A1 = &(snap_->atomData.aMat[atom1]);
1146        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 858 | Line 1176 | namespace OpenMD {
1176        idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1177      }
1178  
1179 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
1180 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1181 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1182 +    }
1183 +
1184 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
1185 +      idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1186 +      idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1187 +    }
1188 +
1189   #endif
1190    }
1191  
1192    
1193    void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1194   #ifdef IS_MPI
1195 <    pot_row[atom1] += 0.5 *  *(idat.pot);
1196 <    pot_col[atom2] += 0.5 *  *(idat.pot);
1195 >    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1196 >    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1197  
1198      atomRowData.force[atom1] += *(idat.f1);
1199      atomColData.force[atom2] -= *(idat.f1);
1200 +
1201 +    if (storageLayout_ & DataStorage::dslFlucQForce) {              
1202 +      atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1203 +      atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1204 +    }
1205 +
1206 +    if (storageLayout_ & DataStorage::dslElectricField) {              
1207 +      atomRowData.electricField[atom1] += *(idat.eField1);
1208 +      atomColData.electricField[atom2] += *(idat.eField2);
1209 +    }
1210 +
1211   #else
1212      pairwisePot += *(idat.pot);
1213  
1214      snap_->atomData.force[atom1] += *(idat.f1);
1215      snap_->atomData.force[atom2] -= *(idat.f1);
877 – #endif
1216  
1217 <  }
1218 <
1219 <
1220 <  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
1221 <                                              int atom1, int atom2) {
1222 <    // Still Missing:: skippedCharge fill must be added to DataStorage
1223 < #ifdef IS_MPI
886 <    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
887 <                             ff_->getAtomType(identsCol[atom2]) );
888 <
889 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
890 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
891 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1217 >    if (idat.doParticlePot) {
1218 >      // This is the pairwise contribution to the particle pot.  The
1219 >      // embedding contribution is added in each of the low level
1220 >      // non-bonded routines.  In parallel, this calculation is done
1221 >      // in collectData, not in unpackInteractionData.
1222 >      snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1223 >      snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1224      }
1225 <    if (storageLayout_ & DataStorage::dslTorque) {
1226 <      idat.t1 = &(atomRowData.torque[atom1]);
1227 <      idat.t2 = &(atomColData.torque[atom2]);
1225 >    
1226 >    if (storageLayout_ & DataStorage::dslFlucQForce) {              
1227 >      snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1228 >      snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1229      }
897 – #else
898 –    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
899 –                             ff_->getAtomType(idents[atom2]) );
1230  
1231 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1232 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1233 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1231 >    if (storageLayout_ & DataStorage::dslElectricField) {              
1232 >      snap_->atomData.electricField[atom1] += *(idat.eField1);
1233 >      snap_->atomData.electricField[atom2] += *(idat.eField2);
1234      }
905 –    if (storageLayout_ & DataStorage::dslTorque) {
906 –      idat.t1 = &(snap_->atomData.torque[atom1]);
907 –      idat.t2 = &(snap_->atomData.torque[atom2]);
908 –    }
909 – #endif    
910 –  }
1235  
912 –
913 –  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
914 – #ifdef IS_MPI
915 –    pot_row[atom1] += 0.5 *  *(idat.pot);
916 –    pot_col[atom2] += 0.5 *  *(idat.pot);
917 – #else
918 –    pairwisePot += *(idat.pot);  
1236   #endif
1237 <
1237 >    
1238    }
1239  
923 –
1240    /*
1241     * buildNeighborList
1242     *
# Line 931 | Line 1247 | namespace OpenMD {
1247        
1248      vector<pair<int, int> > neighborList;
1249      groupCutoffs cuts;
1250 +    bool doAllPairs = false;
1251 +
1252   #ifdef IS_MPI
1253      cellListRow_.clear();
1254      cellListCol_.clear();
# Line 950 | Line 1268 | namespace OpenMD {
1268      nCells_.y() = (int) ( Hy.length() )/ rList_;
1269      nCells_.z() = (int) ( Hz.length() )/ rList_;
1270  
1271 +    // handle small boxes where the cell offsets can end up repeating cells
1272 +    
1273 +    if (nCells_.x() < 3) doAllPairs = true;
1274 +    if (nCells_.y() < 3) doAllPairs = true;
1275 +    if (nCells_.z() < 3) doAllPairs = true;
1276 +
1277      Mat3x3d invHmat = snap_->getInvHmat();
1278      Vector3d rs, scaled, dr;
1279      Vector3i whichCell;
# Line 963 | Line 1287 | namespace OpenMD {
1287      cellList_.resize(nCtot);
1288   #endif
1289  
1290 +    if (!doAllPairs) {
1291   #ifdef IS_MPI
967 –    for (int i = 0; i < nGroupsInRow_; i++) {
968 –      rs = cgRowData.position[i];
1292  
1293 <      // scaled positions relative to the box vectors
1294 <      scaled = invHmat * rs;
1295 <
1296 <      // wrap the vector back into the unit box by subtracting integer box
1297 <      // numbers
1298 <      for (int j = 0; j < 3; j++) {
1299 <        scaled[j] -= roundMe(scaled[j]);
1300 <        scaled[j] += 0.5;
1293 >      for (int i = 0; i < nGroupsInRow_; i++) {
1294 >        rs = cgRowData.position[i];
1295 >        
1296 >        // scaled positions relative to the box vectors
1297 >        scaled = invHmat * rs;
1298 >        
1299 >        // wrap the vector back into the unit box by subtracting integer box
1300 >        // numbers
1301 >        for (int j = 0; j < 3; j++) {
1302 >          scaled[j] -= roundMe(scaled[j]);
1303 >          scaled[j] += 0.5;
1304 >        }
1305 >        
1306 >        // find xyz-indices of cell that cutoffGroup is in.
1307 >        whichCell.x() = nCells_.x() * scaled.x();
1308 >        whichCell.y() = nCells_.y() * scaled.y();
1309 >        whichCell.z() = nCells_.z() * scaled.z();
1310 >        
1311 >        // find single index of this cell:
1312 >        cellIndex = Vlinear(whichCell, nCells_);
1313 >        
1314 >        // add this cutoff group to the list of groups in this cell;
1315 >        cellListRow_[cellIndex].push_back(i);
1316        }
1317 <    
1318 <      // find xyz-indices of cell that cutoffGroup is in.
1319 <      whichCell.x() = nCells_.x() * scaled.x();
1320 <      whichCell.y() = nCells_.y() * scaled.y();
1321 <      whichCell.z() = nCells_.z() * scaled.z();
1322 <
1323 <      // find single index of this cell:
1324 <      cellIndex = Vlinear(whichCell, nCells_);
1325 <
1326 <      // add this cutoff group to the list of groups in this cell;
1327 <      cellListRow_[cellIndex].push_back(i);
1328 <    }
1329 <
1330 <    for (int i = 0; i < nGroupsInCol_; i++) {
1331 <      rs = cgColData.position[i];
1332 <
1333 <      // scaled positions relative to the box vectors
1334 <      scaled = invHmat * rs;
1335 <
1336 <      // wrap the vector back into the unit box by subtracting integer box
1337 <      // numbers
1338 <      for (int j = 0; j < 3; j++) {
1339 <        scaled[j] -= roundMe(scaled[j]);
1002 <        scaled[j] += 0.5;
1317 >      for (int i = 0; i < nGroupsInCol_; i++) {
1318 >        rs = cgColData.position[i];
1319 >        
1320 >        // scaled positions relative to the box vectors
1321 >        scaled = invHmat * rs;
1322 >        
1323 >        // wrap the vector back into the unit box by subtracting integer box
1324 >        // numbers
1325 >        for (int j = 0; j < 3; j++) {
1326 >          scaled[j] -= roundMe(scaled[j]);
1327 >          scaled[j] += 0.5;
1328 >        }
1329 >        
1330 >        // find xyz-indices of cell that cutoffGroup is in.
1331 >        whichCell.x() = nCells_.x() * scaled.x();
1332 >        whichCell.y() = nCells_.y() * scaled.y();
1333 >        whichCell.z() = nCells_.z() * scaled.z();
1334 >        
1335 >        // find single index of this cell:
1336 >        cellIndex = Vlinear(whichCell, nCells_);
1337 >        
1338 >        // add this cutoff group to the list of groups in this cell;
1339 >        cellListCol_[cellIndex].push_back(i);
1340        }
1341 <
1005 <      // find xyz-indices of cell that cutoffGroup is in.
1006 <      whichCell.x() = nCells_.x() * scaled.x();
1007 <      whichCell.y() = nCells_.y() * scaled.y();
1008 <      whichCell.z() = nCells_.z() * scaled.z();
1009 <
1010 <      // find single index of this cell:
1011 <      cellIndex = Vlinear(whichCell, nCells_);
1012 <
1013 <      // add this cutoff group to the list of groups in this cell;
1014 <      cellListCol_[cellIndex].push_back(i);
1015 <    }
1341 >    
1342   #else
1343 <    for (int i = 0; i < nGroups_; i++) {
1344 <      rs = snap_->cgData.position[i];
1345 <
1346 <      // scaled positions relative to the box vectors
1347 <      scaled = invHmat * rs;
1348 <
1349 <      // wrap the vector back into the unit box by subtracting integer box
1350 <      // numbers
1351 <      for (int j = 0; j < 3; j++) {
1352 <        scaled[j] -= roundMe(scaled[j]);
1353 <        scaled[j] += 0.5;
1343 >      for (int i = 0; i < nGroups_; i++) {
1344 >        rs = snap_->cgData.position[i];
1345 >        
1346 >        // scaled positions relative to the box vectors
1347 >        scaled = invHmat * rs;
1348 >        
1349 >        // wrap the vector back into the unit box by subtracting integer box
1350 >        // numbers
1351 >        for (int j = 0; j < 3; j++) {
1352 >          scaled[j] -= roundMe(scaled[j]);
1353 >          scaled[j] += 0.5;
1354 >        }
1355 >        
1356 >        // find xyz-indices of cell that cutoffGroup is in.
1357 >        whichCell.x() = nCells_.x() * scaled.x();
1358 >        whichCell.y() = nCells_.y() * scaled.y();
1359 >        whichCell.z() = nCells_.z() * scaled.z();
1360 >        
1361 >        // find single index of this cell:
1362 >        cellIndex = Vlinear(whichCell, nCells_);
1363 >        
1364 >        // add this cutoff group to the list of groups in this cell;
1365 >        cellList_[cellIndex].push_back(i);
1366        }
1367  
1030 –      // find xyz-indices of cell that cutoffGroup is in.
1031 –      whichCell.x() = nCells_.x() * scaled.x();
1032 –      whichCell.y() = nCells_.y() * scaled.y();
1033 –      whichCell.z() = nCells_.z() * scaled.z();
1034 –
1035 –      // find single index of this cell:
1036 –      cellIndex = Vlinear(whichCell, nCells_);      
1037 –
1038 –      // add this cutoff group to the list of groups in this cell;
1039 –      cellList_[cellIndex].push_back(i);
1040 –    }
1368   #endif
1369  
1370 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1371 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1372 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1373 <          Vector3i m1v(m1x, m1y, m1z);
1374 <          int m1 = Vlinear(m1v, nCells_);
1048 <
1049 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1050 <               os != cellOffsets_.end(); ++os) {
1370 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1371 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1372 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1373 >            Vector3i m1v(m1x, m1y, m1z);
1374 >            int m1 = Vlinear(m1v, nCells_);
1375              
1376 <            Vector3i m2v = m1v + (*os);
1377 <            
1378 <            if (m2v.x() >= nCells_.x()) {
1379 <              m2v.x() = 0;          
1380 <            } else if (m2v.x() < 0) {
1057 <              m2v.x() = nCells_.x() - 1;
1058 <            }
1059 <            
1060 <            if (m2v.y() >= nCells_.y()) {
1061 <              m2v.y() = 0;          
1062 <            } else if (m2v.y() < 0) {
1063 <              m2v.y() = nCells_.y() - 1;
1064 <            }
1065 <            
1066 <            if (m2v.z() >= nCells_.z()) {
1067 <              m2v.z() = 0;          
1068 <            } else if (m2v.z() < 0) {
1069 <              m2v.z() = nCells_.z() - 1;
1070 <            }
1071 <            
1072 <            int m2 = Vlinear (m2v, nCells_);
1376 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1377 >                 os != cellOffsets_.end(); ++os) {
1378 >              
1379 >              Vector3i m2v = m1v + (*os);
1380 >            
1381  
1382 < #ifdef IS_MPI
1383 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1384 <                 j1 != cellListRow_[m1].end(); ++j1) {
1385 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1386 <                   j2 != cellListCol_[m2].end(); ++j2) {
1387 <                              
1388 <                // Always do this if we're in different cells or if
1389 <                // we're in the same cell and the global index of the
1390 <                // j2 cutoff group is less than the j1 cutoff group
1382 >              if (m2v.x() >= nCells_.x()) {
1383 >                m2v.x() = 0;          
1384 >              } else if (m2v.x() < 0) {
1385 >                m2v.x() = nCells_.x() - 1;
1386 >              }
1387 >              
1388 >              if (m2v.y() >= nCells_.y()) {
1389 >                m2v.y() = 0;          
1390 >              } else if (m2v.y() < 0) {
1391 >                m2v.y() = nCells_.y() - 1;
1392 >              }
1393 >              
1394 >              if (m2v.z() >= nCells_.z()) {
1395 >                m2v.z() = 0;          
1396 >              } else if (m2v.z() < 0) {
1397 >                m2v.z() = nCells_.z() - 1;
1398 >              }
1399  
1400 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1400 >              int m2 = Vlinear (m2v, nCells_);
1401 >              
1402 > #ifdef IS_MPI
1403 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1404 >                   j1 != cellListRow_[m1].end(); ++j1) {
1405 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1406 >                     j2 != cellListCol_[m2].end(); ++j2) {
1407 >                  
1408 >                  // In parallel, we need to visit *all* pairs of row
1409 >                  // & column indicies and will divide labor in the
1410 >                  // force evaluation later.
1411                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1412                    snap_->wrapVector(dr);
1413                    cuts = getGroupCutoffs( (*j1), (*j2) );
1414                    if (dr.lengthSquare() < cuts.third) {
1415                      neighborList.push_back(make_pair((*j1), (*j2)));
1416 <                  }
1416 >                  }                  
1417                  }
1418                }
1093 –            }
1419   #else
1420 +              for (vector<int>::iterator j1 = cellList_[m1].begin();
1421 +                   j1 != cellList_[m1].end(); ++j1) {
1422 +                for (vector<int>::iterator j2 = cellList_[m2].begin();
1423 +                     j2 != cellList_[m2].end(); ++j2) {
1424 +    
1425 +                  // Always do this if we're in different cells or if
1426 +                  // we're in the same cell and the global index of
1427 +                  // the j2 cutoff group is greater than or equal to
1428 +                  // the j1 cutoff group.  Note that Rappaport's code
1429 +                  // has a "less than" conditional here, but that
1430 +                  // deals with atom-by-atom computation.  OpenMD
1431 +                  // allows atoms within a single cutoff group to
1432 +                  // interact with each other.
1433  
1096 –            for (vector<int>::iterator j1 = cellList_[m1].begin();
1097 –                 j1 != cellList_[m1].end(); ++j1) {
1098 –              for (vector<int>::iterator j2 = cellList_[m2].begin();
1099 –                   j2 != cellList_[m2].end(); ++j2) {
1434  
1101 –                // Always do this if we're in different cells or if
1102 –                // we're in the same cell and the global index of the
1103 –                // j2 cutoff group is less than the j1 cutoff group
1435  
1436 <                if (m2 != m1 || (*j2) < (*j1)) {
1437 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1438 <                  snap_->wrapVector(dr);
1439 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1440 <                  if (dr.lengthSquare() < cuts.third) {
1441 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1436 >                  if (m2 != m1 || (*j2) >= (*j1) ) {
1437 >
1438 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1439 >                    snap_->wrapVector(dr);
1440 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1441 >                    if (dr.lengthSquare() < cuts.third) {
1442 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1443 >                    }
1444                    }
1445                  }
1446                }
1114 –            }
1447   #endif
1448 +            }
1449            }
1450          }
1451        }
1452 +    } else {
1453 +      // branch to do all cutoff group pairs
1454 + #ifdef IS_MPI
1455 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1456 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1457 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1458 +          snap_->wrapVector(dr);
1459 +          cuts = getGroupCutoffs( j1, j2 );
1460 +          if (dr.lengthSquare() < cuts.third) {
1461 +            neighborList.push_back(make_pair(j1, j2));
1462 +          }
1463 +        }
1464 +      }      
1465 + #else
1466 +      // include all groups here.
1467 +      for (int j1 = 0; j1 < nGroups_; j1++) {
1468 +        // include self group interactions j2 == j1
1469 +        for (int j2 = j1; j2 < nGroups_; j2++) {
1470 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1471 +          snap_->wrapVector(dr);
1472 +          cuts = getGroupCutoffs( j1, j2 );
1473 +          if (dr.lengthSquare() < cuts.third) {
1474 +            neighborList.push_back(make_pair(j1, j2));
1475 +          }
1476 +        }    
1477 +      }
1478 + #endif
1479      }
1480 <    
1480 >      
1481      // save the local cutoff group positions for the check that is
1482      // done on each loop:
1483      saved_CG_positions_.clear();
1484      for (int i = 0; i < nGroups_; i++)
1485        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1486 <  
1486 >    
1487      return neighborList;
1488    }
1489   } //end namespace OpenMD

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