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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 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs.
Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

# Line 47 | Line 47 | namespace OpenMD {
47   using namespace std;
48   namespace OpenMD {
49  
50 +  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51 +
52 +    // In a parallel computation, row and colum scans must visit all
53 +    // surrounding cells (not just the 14 upper triangular blocks that
54 +    // are used when the processor can see all pairs)
55 + #ifdef IS_MPI
56 +    cellOffsets_.clear();
57 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
58 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
59 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
60 +    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
61 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
62 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
63 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
64 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
65 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
66 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
67 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
68 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
69 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );      
70 +    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
71 +    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
72 +    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
73 +    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
74 +    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
75 +    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
76 +    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
77 +    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
78 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
79 +    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
80 +    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
81 +    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
82 +    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
83 +    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
84 + #endif    
85 +  }
86 +
87 +
88    /**
89     * distributeInitialData is essentially a copy of the older fortran
90     * SimulationSetup
91     */
54 –  
92    void ForceMatrixDecomposition::distributeInitialData() {
93      snap_ = sman_->getCurrentSnapshot();
94      storageLayout_ = sman_->getStorageLayout();
95      ff_ = info_->getForceField();
96      nLocal_ = snap_->getNumberOfAtoms();
97 <
97 >    
98      nGroups_ = info_->getNLocalCutoffGroups();
99      // gather the information for atomtype IDs (atids):
100 <    identsLocal = info_->getIdentArray();
100 >    idents = info_->getIdentArray();
101      AtomLocalToGlobal = info_->getGlobalAtomIndices();
102      cgLocalToGlobal = info_->getGlobalGroupIndices();
103      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();
104  
105 +    massFactors = info_->getMassFactors();
106 +
107 +    PairList* excludes = info_->getExcludedInteractions();
108 +    PairList* oneTwo = info_->getOneTwoInteractions();
109 +    PairList* oneThree = info_->getOneThreeInteractions();
110 +    PairList* oneFour = info_->getOneFourInteractions();
111 +
112   #ifdef IS_MPI
113  
114 <    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
115 <    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_);
114 >    MPI::Intracomm row = rowComm.getComm();
115 >    MPI::Intracomm col = colComm.getComm();
116  
117 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
118 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
119 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
120 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
121 <    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
117 >    AtomPlanIntRow = new Plan<int>(row, nLocal_);
118 >    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
119 >    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
120 >    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
121 >    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
122  
123 <    cgCommIntRow = new Communicator<Row,int>(nGroups_);
124 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
125 <    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
126 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
123 >    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
124 >    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
125 >    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
126 >    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
127 >    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
128  
129 <    nAtomsInRow_ = AtomCommIntRow->getSize();
130 <    nAtomsInCol_ = AtomCommIntColumn->getSize();
131 <    nGroupsInRow_ = cgCommIntRow->getSize();
132 <    nGroupsInCol_ = cgCommIntColumn->getSize();
129 >    cgPlanIntRow = new Plan<int>(row, nGroups_);
130 >    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
131 >    cgPlanIntColumn = new Plan<int>(col, nGroups_);
132 >    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
133  
134 +    nAtomsInRow_ = AtomPlanIntRow->getSize();
135 +    nAtomsInCol_ = AtomPlanIntColumn->getSize();
136 +    nGroupsInRow_ = cgPlanIntRow->getSize();
137 +    nGroupsInCol_ = cgPlanIntColumn->getSize();
138 +
139      // Modify the data storage objects with the correct layouts and sizes:
140      atomRowData.resize(nAtomsInRow_);
141      atomRowData.setStorageLayout(storageLayout_);
# Line 107 | Line 149 | namespace OpenMD {
149      identsRow.resize(nAtomsInRow_);
150      identsCol.resize(nAtomsInCol_);
151      
152 <    AtomCommIntRow->gather(identsLocal, identsRow);
153 <    AtomCommIntColumn->gather(identsLocal, identsCol);
152 >    AtomPlanIntRow->gather(idents, identsRow);
153 >    AtomPlanIntColumn->gather(idents, identsCol);
154      
155 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
156 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
157 <    
116 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
117 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
155 >    // allocate memory for the parallel objects
156 >    atypesRow.resize(nAtomsInRow_);
157 >    atypesCol.resize(nAtomsInCol_);
158  
159 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
160 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
159 >    for (int i = 0; i < nAtomsInRow_; i++)
160 >      atypesRow[i] = ff_->getAtomType(identsRow[i]);
161 >    for (int i = 0; i < nAtomsInCol_; i++)
162 >      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
163  
164 +    pot_row.resize(nAtomsInRow_);
165 +    pot_col.resize(nAtomsInCol_);
166 +
167 +    AtomRowToGlobal.resize(nAtomsInRow_);
168 +    AtomColToGlobal.resize(nAtomsInCol_);
169 +    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170 +    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171 +
172 +    cgRowToGlobal.resize(nGroupsInRow_);
173 +    cgColToGlobal.resize(nGroupsInCol_);
174 +    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175 +    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176 +
177 +    massFactorsRow.resize(nAtomsInRow_);
178 +    massFactorsCol.resize(nAtomsInCol_);
179 +    AtomPlanRealRow->gather(massFactors, massFactorsRow);
180 +    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
181 +
182      groupListRow_.clear();
183      groupListRow_.resize(nGroupsInRow_);
184      for (int i = 0; i < nGroupsInRow_; i++) {
# Line 141 | Line 201 | namespace OpenMD {
201        }      
202      }
203  
204 <    skipsForRowAtom.clear();
205 <    skipsForRowAtom.resize(nAtomsInRow_);
204 >    excludesForAtom.clear();
205 >    excludesForAtom.resize(nAtomsInRow_);
206 >    toposForAtom.clear();
207 >    toposForAtom.resize(nAtomsInRow_);
208 >    topoDist.clear();
209 >    topoDist.resize(nAtomsInRow_);
210      for (int i = 0; i < nAtomsInRow_; i++) {
211        int iglob = AtomRowToGlobal[i];
212 +
213        for (int j = 0; j < nAtomsInCol_; j++) {
214 <        int jglob = AtomColToGlobal[j];        
215 <        if (excludes.hasPair(iglob, jglob))
216 <          skipsForRowAtom[i].push_back(j);      
214 >        int jglob = AtomColToGlobal[j];
215 >
216 >        if (excludes->hasPair(iglob, jglob))
217 >          excludesForAtom[i].push_back(j);      
218 >        
219 >        if (oneTwo->hasPair(iglob, jglob)) {
220 >          toposForAtom[i].push_back(j);
221 >          topoDist[i].push_back(1);
222 >        } else {
223 >          if (oneThree->hasPair(iglob, jglob)) {
224 >            toposForAtom[i].push_back(j);
225 >            topoDist[i].push_back(2);
226 >          } else {
227 >            if (oneFour->hasPair(iglob, jglob)) {
228 >              toposForAtom[i].push_back(j);
229 >              topoDist[i].push_back(3);
230 >            }
231 >          }
232 >        }
233        }      
234      }
235  
236 <    toposForRowAtom.clear();
237 <    toposForRowAtom.resize(nAtomsInRow_);
238 <    for (int i = 0; i < nAtomsInRow_; i++) {
239 <      int iglob = AtomRowToGlobal[i];
240 <      int nTopos = 0;
241 <      for (int j = 0; j < nAtomsInCol_; j++) {
242 <        int jglob = AtomColToGlobal[j];        
243 <        if (oneTwo.hasPair(iglob, jglob)) {
244 <          toposForRowAtom[i].push_back(j);
245 <          topoDistRow[i][nTopos] = 1;
246 <          nTopos++;
236 > #else
237 >    excludesForAtom.clear();
238 >    excludesForAtom.resize(nLocal_);
239 >    toposForAtom.clear();
240 >    toposForAtom.resize(nLocal_);
241 >    topoDist.clear();
242 >    topoDist.resize(nLocal_);
243 >
244 >    for (int i = 0; i < nLocal_; i++) {
245 >      int iglob = AtomLocalToGlobal[i];
246 >
247 >      for (int j = 0; j < nLocal_; j++) {
248 >        int jglob = AtomLocalToGlobal[j];
249 >
250 >        if (excludes->hasPair(iglob, jglob))          
251 >          excludesForAtom[i].push_back(j);              
252 >        
253 >        
254 >        if (oneTwo->hasPair(iglob, jglob)) {
255 >          toposForAtom[i].push_back(j);
256 >          topoDist[i].push_back(1);
257 >        } else {
258 >          if (oneThree->hasPair(iglob, jglob)) {
259 >            toposForAtom[i].push_back(j);
260 >            topoDist[i].push_back(2);
261 >          } else {
262 >            if (oneFour->hasPair(iglob, jglob)) {
263 >              toposForAtom[i].push_back(j);
264 >              topoDist[i].push_back(3);
265 >            }
266 >          }
267          }
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 –        }
268        }      
269      }
179 –
270   #endif
271 +
272 +    // allocate memory for the parallel objects
273 +    atypesLocal.resize(nLocal_);
274 +
275 +    for (int i = 0; i < nLocal_; i++)
276 +      atypesLocal[i] = ff_->getAtomType(idents[i]);
277 +
278      groupList_.clear();
279      groupList_.resize(nGroups_);
280      for (int i = 0; i < nGroups_; i++) {
# Line 186 | Line 283 | namespace OpenMD {
283          int aid = AtomLocalToGlobal[j];
284          if (globalGroupMembership[aid] == gid) {
285            groupList_[i].push_back(j);
189 –
286          }
287        }      
288      }
289  
194 –    skipsForLocalAtom.clear();
195 –    skipsForLocalAtom.resize(nLocal_);
290  
291 <    for (int i = 0; i < nLocal_; i++) {
198 <      int iglob = AtomLocalToGlobal[i];
199 <      for (int j = 0; j < nLocal_; j++) {
200 <        int jglob = AtomLocalToGlobal[j];        
201 <        if (excludes.hasPair(iglob, jglob))
202 <          skipsForLocalAtom[i].push_back(j);      
203 <      }      
204 <    }
205 <    toposForLocalAtom.clear();
206 <    toposForLocalAtom.resize(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 <    }    
291 >    createGtypeCutoffMap();
292  
293    }
294    
295    void ForceMatrixDecomposition::createGtypeCutoffMap() {
296 <
296 >    
297      RealType tol = 1e-6;
298 +    largestRcut_ = 0.0;
299      RealType rc;
300      int atid;
301      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302 <    vector<RealType> atypeCutoff;
303 <    atypeCutoff.resize( atypes.size() );
304 <
305 <    for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
306 <      rc = interactionMan_->getSuggestedCutoffRadius(*at);
302 >    
303 >    map<int, RealType> atypeCutoff;
304 >      
305 >    for (set<AtomType*>::iterator at = atypes.begin();
306 >         at != atypes.end(); ++at){
307        atid = (*at)->getIdent();
308 <      atypeCutoff[atid] = rc;
308 >      if (userChoseCutoff_)
309 >        atypeCutoff[atid] = userCutoff_;
310 >      else
311 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312      }
313 <
313 >    
314      vector<RealType> gTypeCutoffs;
248 –
315      // first we do a single loop over the cutoff groups to find the
316      // largest cutoff for any atypes present in this group.
317   #ifdef IS_MPI
318      vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
319 +    groupRowToGtype.resize(nGroupsInRow_);
320      for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
321        vector<int> atomListRow = getAtomsInGroupRow(cg1);
322        for (vector<int>::iterator ia = atomListRow.begin();
# Line 275 | Line 342 | namespace OpenMD {
342        
343      }
344      vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
345 +    groupColToGtype.resize(nGroupsInCol_);
346      for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
347        vector<int> atomListCol = getAtomsInGroupColumn(cg2);
348        for (vector<int>::iterator jb = atomListCol.begin();
# Line 298 | Line 366 | namespace OpenMD {
366        }
367      }
368   #else
369 +
370      vector<RealType> groupCutoff(nGroups_, 0.0);
371 +    groupToGtype.resize(nGroups_);
372      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
373        groupCutoff[cg1] = 0.0;
374        vector<int> atomList = getAtomsInGroupRow(cg1);
375        for (vector<int>::iterator ia = atomList.begin();
376             ia != atomList.end(); ++ia) {            
377          int atom1 = (*ia);
378 <        atid = identsLocal[atom1];
379 <        if (atypeCutoff[atid] > groupCutoff[cg1]) {
378 >        atid = idents[atom1];
379 >        if (atypeCutoff[atid] > groupCutoff[cg1])
380            groupCutoff[cg1] = atypeCutoff[atid];
311 –        }
381        }
382 <
382 >      
383        bool gTypeFound = false;
384        for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
# Line 318 | Line 387 | namespace OpenMD {
387            gTypeFound = true;
388          }
389        }
390 <      if (!gTypeFound) {
390 >      if (!gTypeFound) {      
391          gTypeCutoffs.push_back( groupCutoff[cg1] );
392          groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393        }      
# Line 327 | Line 396 | namespace OpenMD {
396  
397      // Now we find the maximum group cutoff value present in the simulation
398  
399 <    vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
400 <    RealType groupMax = *groupMaxLoc;
399 >    RealType groupMax = *max_element(gTypeCutoffs.begin(),
400 >                                     gTypeCutoffs.end());
401  
402   #ifdef IS_MPI
403 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
403 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404 >                              MPI::MAX);
405   #endif
406      
407      RealType tradRcut = groupMax;
408  
409      for (int i = 0; i < gTypeCutoffs.size();  i++) {
410 <      for (int j = 0; j < gTypeCutoffs.size();  j++) {
341 <        
410 >      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
411          RealType thisRcut;
412          switch(cutoffPolicy_) {
413          case TRADITIONAL:
414            thisRcut = tradRcut;
415 +          break;
416          case MIX:
417            thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
418 +          break;
419          case MAX:
420            thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
421 +          break;
422          default:
423            sprintf(painCave.errMsg,
424                    "ForceMatrixDecomposition::createGtypeCutoffMap "
425                    "hit an unknown cutoff policy!\n");
426            painCave.severity = OPENMD_ERROR;
427            painCave.isFatal = 1;
428 <          simError();              
428 >          simError();
429 >          break;
430          }
431  
432          pair<int,int> key = make_pair(i,j);
433          gTypeCutoffMap[key].first = thisRcut;
361 –
434          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
363 –
435          gTypeCutoffMap[key].second = thisRcut*thisRcut;
365 –        
436          gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367 –
437          // sanity check
438          
439          if (userChoseCutoff_) {
440            if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
441              sprintf(painCave.errMsg,
442                      "ForceMatrixDecomposition::createGtypeCutoffMap "
443 <                    "user-specified rCut does not match computed group Cutoff\n");
443 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
444              painCave.severity = OPENMD_ERROR;
445              painCave.isFatal = 1;
446              simError();            
# Line 383 | Line 452 | namespace OpenMD {
452  
453  
454    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
455 <    int i, j;
387 <
455 >    int i, j;  
456   #ifdef IS_MPI
457      i = groupRowToGtype[cg1];
458      j = groupColToGtype[cg2];
459   #else
460      i = groupToGtype[cg1];
461      j = groupToGtype[cg2];
462 < #endif
395 <    
462 > #endif    
463      return gTypeCutoffMap[make_pair(i,j)];
464    }
465  
466 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
467 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
468 +      if (toposForAtom[atom1][j] == atom2)
469 +        return topoDist[atom1][j];
470 +    }
471 +    return 0;
472 +  }
473  
474    void ForceMatrixDecomposition::zeroWorkArrays() {
475 +    pairwisePot = 0.0;
476 +    embeddingPot = 0.0;
477  
402 –    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403 –      longRangePot_[j] = 0.0;
404 –    }
405 –
478   #ifdef IS_MPI
479      if (storageLayout_ & DataStorage::dslForce) {
480        fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
# Line 418 | Line 490 | namespace OpenMD {
490           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
491  
492      fill(pot_col.begin(), pot_col.end(),
493 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422 <    
423 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
493 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
494  
495      if (storageLayout_ & DataStorage::dslParticlePot) {    
496 <      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
497 <      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
496 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
497 >           0.0);
498 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
499 >           0.0);
500      }
501  
502      if (storageLayout_ & DataStorage::dslDensity) {      
# Line 433 | Line 505 | namespace OpenMD {
505      }
506  
507      if (storageLayout_ & DataStorage::dslFunctional) {  
508 <      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
509 <      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
508 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
509 >           0.0);
510 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
511 >           0.0);
512      }
513  
514      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
# Line 444 | Line 518 | namespace OpenMD {
518             atomColData.functionalDerivative.end(), 0.0);
519      }
520  
521 < #else
522 <    
521 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
522 >      fill(atomRowData.skippedCharge.begin(),
523 >           atomRowData.skippedCharge.end(), 0.0);
524 >      fill(atomColData.skippedCharge.begin(),
525 >           atomColData.skippedCharge.end(), 0.0);
526 >    }
527 >
528 > #endif
529 >    // even in parallel, we need to zero out the local arrays:
530 >
531      if (storageLayout_ & DataStorage::dslParticlePot) {      
532        fill(snap_->atomData.particlePot.begin(),
533             snap_->atomData.particlePot.end(), 0.0);
# Line 463 | Line 545 | namespace OpenMD {
545        fill(snap_->atomData.functionalDerivative.begin(),
546             snap_->atomData.functionalDerivative.end(), 0.0);
547      }
548 < #endif
548 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
549 >      fill(snap_->atomData.skippedCharge.begin(),
550 >           snap_->atomData.skippedCharge.end(), 0.0);
551 >    }
552      
553    }
554  
# Line 474 | Line 559 | namespace OpenMD {
559   #ifdef IS_MPI
560      
561      // gather up the atomic positions
562 <    AtomCommVectorRow->gather(snap_->atomData.position,
562 >    AtomPlanVectorRow->gather(snap_->atomData.position,
563                                atomRowData.position);
564 <    AtomCommVectorColumn->gather(snap_->atomData.position,
564 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
565                                   atomColData.position);
566      
567      // gather up the cutoff group positions
568 <    cgCommVectorRow->gather(snap_->cgData.position,
568 >
569 >    cgPlanVectorRow->gather(snap_->cgData.position,
570                              cgRowData.position);
571 <    cgCommVectorColumn->gather(snap_->cgData.position,
571 >
572 >    cgPlanVectorColumn->gather(snap_->cgData.position,
573                                 cgColData.position);
574 +
575      
576      // if needed, gather the atomic rotation matrices
577      if (storageLayout_ & DataStorage::dslAmat) {
578 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
578 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
579                                  atomRowData.aMat);
580 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
580 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
581                                     atomColData.aMat);
582      }
583      
584      // if needed, gather the atomic eletrostatic frames
585      if (storageLayout_ & DataStorage::dslElectroFrame) {
586 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
586 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
587                                  atomRowData.electroFrame);
588 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
588 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
589                                     atomColData.electroFrame);
590      }
591 +
592   #endif      
593    }
594    
# Line 513 | Line 602 | namespace OpenMD {
602      
603      if (storageLayout_ & DataStorage::dslDensity) {
604        
605 <      AtomCommRealRow->scatter(atomRowData.density,
605 >      AtomPlanRealRow->scatter(atomRowData.density,
606                                 snap_->atomData.density);
607        
608        int n = snap_->atomData.density.size();
609        vector<RealType> rho_tmp(n, 0.0);
610 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
610 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
611        for (int i = 0; i < n; i++)
612          snap_->atomData.density[i] += rho_tmp[i];
613      }
# Line 534 | Line 623 | namespace OpenMD {
623      storageLayout_ = sman_->getStorageLayout();
624   #ifdef IS_MPI
625      if (storageLayout_ & DataStorage::dslFunctional) {
626 <      AtomCommRealRow->gather(snap_->atomData.functional,
626 >      AtomPlanRealRow->gather(snap_->atomData.functional,
627                                atomRowData.functional);
628 <      AtomCommRealColumn->gather(snap_->atomData.functional,
628 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
629                                   atomColData.functional);
630      }
631      
632      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
633 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
633 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
634                                atomRowData.functionalDerivative);
635 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
635 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
636                                   atomColData.functionalDerivative);
637      }
638   #endif
# Line 557 | Line 646 | namespace OpenMD {
646      int n = snap_->atomData.force.size();
647      vector<Vector3d> frc_tmp(n, V3Zero);
648      
649 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
649 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
650      for (int i = 0; i < n; i++) {
651        snap_->atomData.force[i] += frc_tmp[i];
652        frc_tmp[i] = 0.0;
653      }
654      
655 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
656 <    for (int i = 0; i < n; i++)
655 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
656 >    for (int i = 0; i < n; i++) {
657        snap_->atomData.force[i] += frc_tmp[i];
658 <    
659 <    
658 >    }
659 >        
660      if (storageLayout_ & DataStorage::dslTorque) {
661  
662 <      int nt = snap_->atomData.force.size();
662 >      int nt = snap_->atomData.torque.size();
663        vector<Vector3d> trq_tmp(nt, V3Zero);
664  
665 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
666 <      for (int i = 0; i < n; i++) {
665 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
666 >      for (int i = 0; i < nt; i++) {
667          snap_->atomData.torque[i] += trq_tmp[i];
668          trq_tmp[i] = 0.0;
669        }
670        
671 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
672 <      for (int i = 0; i < n; i++)
671 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
672 >      for (int i = 0; i < nt; i++)
673          snap_->atomData.torque[i] += trq_tmp[i];
674      }
675 +
676 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
677 +
678 +      int ns = snap_->atomData.skippedCharge.size();
679 +      vector<RealType> skch_tmp(ns, 0.0);
680 +
681 +      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
682 +      for (int i = 0; i < ns; i++) {
683 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
684 +        skch_tmp[i] = 0.0;
685 +      }
686 +      
687 +      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
688 +      for (int i = 0; i < ns; i++)
689 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
690 +            
691 +    }
692      
693      nLocal_ = snap_->getNumberOfAtoms();
694  
# Line 591 | Line 697 | namespace OpenMD {
697  
698      // scatter/gather pot_row into the members of my column
699            
700 <    AtomCommPotRow->scatter(pot_row, pot_temp);
700 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
701  
702      for (int ii = 0;  ii < pot_temp.size(); ii++ )
703 <      pot_local += pot_temp[ii];
703 >      pairwisePot += pot_temp[ii];
704      
705      fill(pot_temp.begin(), pot_temp.end(),
706           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
707        
708 <    AtomCommPotColumn->scatter(pot_col, pot_temp);    
708 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
709      
710      for (int ii = 0;  ii < pot_temp.size(); ii++ )
711 <      pot_local += pot_temp[ii];
711 >      pairwisePot += pot_temp[ii];    
712      
713 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
714 +      RealType ploc1 = pairwisePot[ii];
715 +      RealType ploc2 = 0.0;
716 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
717 +      pairwisePot[ii] = ploc2;
718 +    }
719 +
720 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
721 +      RealType ploc1 = embeddingPot[ii];
722 +      RealType ploc2 = 0.0;
723 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
724 +      embeddingPot[ii] = ploc2;
725 +    }
726 +
727   #endif
728 +
729    }
730  
731    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 679 | Line 800 | namespace OpenMD {
800   #ifdef IS_MPI
801      return massFactorsRow[atom1];
802   #else
803 <    return massFactorsLocal[atom1];
803 >    return massFactors[atom1];
804   #endif
805    }
806  
# Line 687 | Line 808 | namespace OpenMD {
808   #ifdef IS_MPI
809      return massFactorsCol[atom2];
810   #else
811 <    return massFactorsLocal[atom2];
811 >    return massFactors[atom2];
812   #endif
813  
814    }
# Line 705 | Line 826 | namespace OpenMD {
826      return d;    
827    }
828  
829 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
830 < #ifdef IS_MPI
710 <    return skipsForRowAtom[atom1];
711 < #else
712 <    return skipsForLocalAtom[atom1];
713 < #endif
829 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
830 >    return excludesForAtom[atom1];
831    }
832  
833    /**
834 <   * There are a number of reasons to skip a pair or a
718 <   * particle. Mostly we do this to exclude atoms who are involved in
719 <   * short range interactions (bonds, bends, torsions), but we also
720 <   * need to exclude some overcounted interactions that result from
834 >   * We need to exclude some overcounted interactions that result from
835     * the parallel decomposition.
836     */
837    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
838      int unique_id_1, unique_id_2;
839 <
839 >    
840   #ifdef IS_MPI
841      // in MPI, we have to look up the unique IDs for each atom
842      unique_id_1 = AtomRowToGlobal[atom1];
# Line 737 | Line 851 | namespace OpenMD {
851      } else {
852        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
853      }
740 – #else
741 –    // in the normal loop, the atom numbers are unique
742 –    unique_id_1 = atom1;
743 –    unique_id_2 = atom2;
854   #endif
855 <    
746 < #ifdef IS_MPI
747 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748 <         i != skipsForRowAtom[atom1].end(); ++i) {
749 <      if ( (*i) == unique_id_2 ) return true;
750 <    }    
751 < #else
752 <    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
753 <         i != skipsForLocalAtom[atom1].end(); ++i) {
754 <      if ( (*i) == unique_id_2 ) return true;
755 <    }    
756 < #endif
855 >    return false;
856    }
857  
858 <  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
859 <    
860 < #ifdef IS_MPI
861 <    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
862 <      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
863 <    }
864 < #else
865 <    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
866 <      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
858 >  /**
859 >   * We need to handle the interactions for atoms who are involved in
860 >   * the same rigid body as well as some short range interactions
861 >   * (bonds, bends, torsions) differently from other interactions.
862 >   * We'll still visit the pairwise routines, but with a flag that
863 >   * tells those routines to exclude the pair from direct long range
864 >   * interactions.  Some indirect interactions (notably reaction
865 >   * field) must still be handled for these pairs.
866 >   */
867 >  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
868 >
869 >    // excludesForAtom was constructed to use row/column indices in the MPI
870 >    // version, and to use local IDs in the non-MPI version:
871 >    
872 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
873 >         i != excludesForAtom[atom1].end(); ++i) {
874 >      if ( (*i) == atom2 )  return true;
875      }
769 – #endif
876  
877 <    // zero is default for unconnected (i.e. normal) pair interactions
772 <    return 0;
877 >    return false;
878    }
879  
880 +
881    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
882   #ifdef IS_MPI
883      atomRowData.force[atom1] += fg;
# Line 789 | Line 895 | namespace OpenMD {
895    }
896  
897      // filling interaction blocks with pointers
898 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
899 <    InteractionData idat;
898 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
899 >                                                     int atom1, int atom2) {
900  
901 +    idat.excluded = excludeAtomPair(atom1, atom2);
902 +  
903   #ifdef IS_MPI
904 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
905 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
906 +    //                         ff_->getAtomType(identsCol[atom2]) );
907      
797 –    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
798 –                             ff_->getAtomType(identsCol[atom2]) );
799 –
800 –    
908      if (storageLayout_ & DataStorage::dslAmat) {
909        idat.A1 = &(atomRowData.aMat[atom1]);
910        idat.A2 = &(atomColData.aMat[atom2]);
# Line 833 | Line 940 | namespace OpenMD {
940        idat.particlePot2 = &(atomColData.particlePot[atom2]);
941      }
942  
943 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
944 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
945 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
946 +    }
947 +
948   #else
949  
950 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
951 <                             ff_->getAtomType(identsLocal[atom2]) );
950 >    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
951 >    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
952 >    //                         ff_->getAtomType(idents[atom2]) );
953  
954      if (storageLayout_ & DataStorage::dslAmat) {
955        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 853 | Line 966 | namespace OpenMD {
966        idat.t2 = &(snap_->atomData.torque[atom2]);
967      }
968  
969 <    if (storageLayout_ & DataStorage::dslDensity) {
969 >    if (storageLayout_ & DataStorage::dslDensity) {    
970        idat.rho1 = &(snap_->atomData.density[atom1]);
971        idat.rho2 = &(snap_->atomData.density[atom2]);
972      }
# Line 873 | Line 986 | namespace OpenMD {
986        idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
987      }
988  
989 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
990 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
991 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
992 +    }
993   #endif
877 –    return idat;
994    }
995  
996    
997 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
997 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
998   #ifdef IS_MPI
999      pot_row[atom1] += 0.5 *  *(idat.pot);
1000      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 886 | Line 1002 | namespace OpenMD {
1002      atomRowData.force[atom1] += *(idat.f1);
1003      atomColData.force[atom2] -= *(idat.f1);
1004   #else
1005 <    longRangePot_ += *(idat.pot);
1006 <    
1005 >    pairwisePot += *(idat.pot);
1006 >
1007      snap_->atomData.force[atom1] += *(idat.f1);
1008      snap_->atomData.force[atom2] -= *(idat.f1);
1009   #endif
1010 <
1010 >    
1011    }
1012  
897 –
898 –  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
899 –
900 –    InteractionData idat;
901 – #ifdef IS_MPI
902 –    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903 –                             ff_->getAtomType(identsCol[atom2]) );
904 –
905 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
906 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
907 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
908 –    }
909 –    if (storageLayout_ & DataStorage::dslTorque) {
910 –      idat.t1 = &(atomRowData.torque[atom1]);
911 –      idat.t2 = &(atomColData.torque[atom2]);
912 –    }
913 – #else
914 –    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915 –                             ff_->getAtomType(identsLocal[atom2]) );
916 –
917 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
918 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
919 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
920 –    }
921 –    if (storageLayout_ & DataStorage::dslTorque) {
922 –      idat.t1 = &(snap_->atomData.torque[atom1]);
923 –      idat.t2 = &(snap_->atomData.torque[atom2]);
924 –    }
925 – #endif    
926 –  }
927 –
1013    /*
1014     * buildNeighborList
1015     *
# Line 935 | Line 1020 | namespace OpenMD {
1020        
1021      vector<pair<int, int> > neighborList;
1022      groupCutoffs cuts;
1023 +    bool doAllPairs = false;
1024 +
1025   #ifdef IS_MPI
1026      cellListRow_.clear();
1027      cellListCol_.clear();
# Line 954 | Line 1041 | namespace OpenMD {
1041      nCells_.y() = (int) ( Hy.length() )/ rList_;
1042      nCells_.z() = (int) ( Hz.length() )/ rList_;
1043  
1044 +    // handle small boxes where the cell offsets can end up repeating cells
1045 +    
1046 +    if (nCells_.x() < 3) doAllPairs = true;
1047 +    if (nCells_.y() < 3) doAllPairs = true;
1048 +    if (nCells_.z() < 3) doAllPairs = true;
1049 +
1050      Mat3x3d invHmat = snap_->getInvHmat();
1051      Vector3d rs, scaled, dr;
1052      Vector3i whichCell;
1053      int cellIndex;
1054 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1055  
1056   #ifdef IS_MPI
1057 <    for (int i = 0; i < nGroupsInRow_; i++) {
1058 <      rs = cgRowData.position[i];
1059 <      // scaled positions relative to the box vectors
1060 <      scaled = invHmat * rs;
1061 <      // wrap the vector back into the unit box by subtracting integer box
968 <      // numbers
969 <      for (int j = 0; j < 3; j++)
970 <        scaled[j] -= roundMe(scaled[j]);
971 <    
972 <      // find xyz-indices of cell that cutoffGroup is in.
973 <      whichCell.x() = nCells_.x() * scaled.x();
974 <      whichCell.y() = nCells_.y() * scaled.y();
975 <      whichCell.z() = nCells_.z() * scaled.z();
1057 >    cellListRow_.resize(nCtot);
1058 >    cellListCol_.resize(nCtot);
1059 > #else
1060 >    cellList_.resize(nCtot);
1061 > #endif
1062  
1063 <      // find single index of this cell:
1064 <      cellIndex = Vlinear(whichCell, nCells_);
979 <      // add this cutoff group to the list of groups in this cell;
980 <      cellListRow_[cellIndex].push_back(i);
981 <    }
1063 >    if (!doAllPairs) {
1064 > #ifdef IS_MPI
1065  
1066 <    for (int i = 0; i < nGroupsInCol_; i++) {
1067 <      rs = cgColData.position[i];
1068 <      // scaled positions relative to the box vectors
1069 <      scaled = invHmat * rs;
1070 <      // wrap the vector back into the unit box by subtracting integer box
1071 <      // numbers
1072 <      for (int j = 0; j < 3; j++)
1073 <        scaled[j] -= roundMe(scaled[j]);
1074 <
1075 <      // find xyz-indices of cell that cutoffGroup is in.
1076 <      whichCell.x() = nCells_.x() * scaled.x();
1077 <      whichCell.y() = nCells_.y() * scaled.y();
1078 <      whichCell.z() = nCells_.z() * scaled.z();
1079 <
1080 <      // find single index of this cell:
1081 <      cellIndex = Vlinear(whichCell, nCells_);
1082 <      // add this cutoff group to the list of groups in this cell;
1083 <      cellListCol_[cellIndex].push_back(i);
1084 <    }
1066 >      for (int i = 0; i < nGroupsInRow_; i++) {
1067 >        rs = cgRowData.position[i];
1068 >        
1069 >        // scaled positions relative to the box vectors
1070 >        scaled = invHmat * rs;
1071 >        
1072 >        // wrap the vector back into the unit box by subtracting integer box
1073 >        // numbers
1074 >        for (int j = 0; j < 3; j++) {
1075 >          scaled[j] -= roundMe(scaled[j]);
1076 >          scaled[j] += 0.5;
1077 >        }
1078 >        
1079 >        // find xyz-indices of cell that cutoffGroup is in.
1080 >        whichCell.x() = nCells_.x() * scaled.x();
1081 >        whichCell.y() = nCells_.y() * scaled.y();
1082 >        whichCell.z() = nCells_.z() * scaled.z();
1083 >        
1084 >        // find single index of this cell:
1085 >        cellIndex = Vlinear(whichCell, nCells_);
1086 >        
1087 >        // add this cutoff group to the list of groups in this cell;
1088 >        cellListRow_[cellIndex].push_back(i);
1089 >      }
1090 >      for (int i = 0; i < nGroupsInCol_; i++) {
1091 >        rs = cgColData.position[i];
1092 >        
1093 >        // scaled positions relative to the box vectors
1094 >        scaled = invHmat * rs;
1095 >        
1096 >        // wrap the vector back into the unit box by subtracting integer box
1097 >        // numbers
1098 >        for (int j = 0; j < 3; j++) {
1099 >          scaled[j] -= roundMe(scaled[j]);
1100 >          scaled[j] += 0.5;
1101 >        }
1102 >        
1103 >        // find xyz-indices of cell that cutoffGroup is in.
1104 >        whichCell.x() = nCells_.x() * scaled.x();
1105 >        whichCell.y() = nCells_.y() * scaled.y();
1106 >        whichCell.z() = nCells_.z() * scaled.z();
1107 >        
1108 >        // find single index of this cell:
1109 >        cellIndex = Vlinear(whichCell, nCells_);
1110 >        
1111 >        // add this cutoff group to the list of groups in this cell;
1112 >        cellListCol_[cellIndex].push_back(i);
1113 >      }
1114 >    
1115   #else
1116 <    for (int i = 0; i < nGroups_; i++) {
1117 <      rs = snap_->cgData.position[i];
1118 <      // scaled positions relative to the box vectors
1119 <      scaled = invHmat * rs;
1120 <      // wrap the vector back into the unit box by subtracting integer box
1121 <      // numbers
1122 <      for (int j = 0; j < 3; j++)
1123 <        scaled[j] -= roundMe(scaled[j]);
1116 >      for (int i = 0; i < nGroups_; i++) {
1117 >        rs = snap_->cgData.position[i];
1118 >        
1119 >        // scaled positions relative to the box vectors
1120 >        scaled = invHmat * rs;
1121 >        
1122 >        // wrap the vector back into the unit box by subtracting integer box
1123 >        // numbers
1124 >        for (int j = 0; j < 3; j++) {
1125 >          scaled[j] -= roundMe(scaled[j]);
1126 >          scaled[j] += 0.5;
1127 >        }
1128 >        
1129 >        // find xyz-indices of cell that cutoffGroup is in.
1130 >        whichCell.x() = nCells_.x() * scaled.x();
1131 >        whichCell.y() = nCells_.y() * scaled.y();
1132 >        whichCell.z() = nCells_.z() * scaled.z();
1133 >        
1134 >        // find single index of this cell:
1135 >        cellIndex = Vlinear(whichCell, nCells_);
1136 >        
1137 >        // add this cutoff group to the list of groups in this cell;
1138 >        cellList_[cellIndex].push_back(i);
1139 >      }
1140  
1012 –      // find xyz-indices of cell that cutoffGroup is in.
1013 –      whichCell.x() = nCells_.x() * scaled.x();
1014 –      whichCell.y() = nCells_.y() * scaled.y();
1015 –      whichCell.z() = nCells_.z() * scaled.z();
1016 –
1017 –      // find single index of this cell:
1018 –      cellIndex = Vlinear(whichCell, nCells_);
1019 –      // add this cutoff group to the list of groups in this cell;
1020 –      cellList_[cellIndex].push_back(i);
1021 –    }
1141   #endif
1142  
1143 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1144 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1145 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1146 <          Vector3i m1v(m1x, m1y, m1z);
1147 <          int m1 = Vlinear(m1v, nCells_);
1029 <
1030 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1031 <               os != cellOffsets_.end(); ++os) {
1143 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1144 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1145 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1146 >            Vector3i m1v(m1x, m1y, m1z);
1147 >            int m1 = Vlinear(m1v, nCells_);
1148              
1149 <            Vector3i m2v = m1v + (*os);
1150 <            
1151 <            if (m2v.x() >= nCells_.x()) {
1152 <              m2v.x() = 0;          
1153 <            } else if (m2v.x() < 0) {
1038 <              m2v.x() = nCells_.x() - 1;
1039 <            }
1040 <            
1041 <            if (m2v.y() >= nCells_.y()) {
1042 <              m2v.y() = 0;          
1043 <            } else if (m2v.y() < 0) {
1044 <              m2v.y() = nCells_.y() - 1;
1045 <            }
1046 <            
1047 <            if (m2v.z() >= nCells_.z()) {
1048 <              m2v.z() = 0;          
1049 <            } else if (m2v.z() < 0) {
1050 <              m2v.z() = nCells_.z() - 1;
1051 <            }
1052 <            
1053 <            int m2 = Vlinear (m2v, nCells_);
1149 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1150 >                 os != cellOffsets_.end(); ++os) {
1151 >              
1152 >              Vector3i m2v = m1v + (*os);
1153 >            
1154  
1155 < #ifdef IS_MPI
1156 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1157 <                 j1 != cellListRow_[m1].end(); ++j1) {
1158 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1159 <                   j2 != cellListCol_[m2].end(); ++j2) {
1160 <                              
1161 <                // Always do this if we're in different cells or if
1162 <                // we're in the same cell and the global index of the
1163 <                // j2 cutoff group is less than the j1 cutoff group
1155 >              if (m2v.x() >= nCells_.x()) {
1156 >                m2v.x() = 0;          
1157 >              } else if (m2v.x() < 0) {
1158 >                m2v.x() = nCells_.x() - 1;
1159 >              }
1160 >              
1161 >              if (m2v.y() >= nCells_.y()) {
1162 >                m2v.y() = 0;          
1163 >              } else if (m2v.y() < 0) {
1164 >                m2v.y() = nCells_.y() - 1;
1165 >              }
1166 >              
1167 >              if (m2v.z() >= nCells_.z()) {
1168 >                m2v.z() = 0;          
1169 >              } else if (m2v.z() < 0) {
1170 >                m2v.z() = nCells_.z() - 1;
1171 >              }
1172  
1173 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1173 >              int m2 = Vlinear (m2v, nCells_);
1174 >              
1175 > #ifdef IS_MPI
1176 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1177 >                   j1 != cellListRow_[m1].end(); ++j1) {
1178 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1179 >                     j2 != cellListCol_[m2].end(); ++j2) {
1180 >                  
1181 >                  // In parallel, we need to visit *all* pairs of row
1182 >                  // & column indicies and will divide labor in the
1183 >                  // force evaluation later.
1184                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1185                    snap_->wrapVector(dr);
1186                    cuts = getGroupCutoffs( (*j1), (*j2) );
1187                    if (dr.lengthSquare() < cuts.third) {
1188                      neighborList.push_back(make_pair((*j1), (*j2)));
1189 <                  }
1189 >                  }                  
1190                  }
1191                }
1074 –            }
1192   #else
1193 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1194 <                 j1 != cellList_[m1].end(); ++j1) {
1195 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1196 <                   j2 != cellList_[m2].end(); ++j2) {
1197 <                              
1198 <                // Always do this if we're in different cells or if
1199 <                // we're in the same cell and the global index of the
1200 <                // j2 cutoff group is less than the j1 cutoff group
1201 <
1202 <                if (m2 != m1 || (*j2) < (*j1)) {
1203 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1204 <                  snap_->wrapVector(dr);
1205 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1206 <                  if (dr.lengthSquare() < cuts.third) {
1207 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1193 >              
1194 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1195 >                   j1 != cellList_[m1].end(); ++j1) {
1196 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1197 >                     j2 != cellList_[m2].end(); ++j2) {
1198 >                  
1199 >                  // Always do this if we're in different cells or if
1200 >                  // we're in the same cell and the global index of the
1201 >                  // j2 cutoff group is less than the j1 cutoff group
1202 >                  
1203 >                  if (m2 != m1 || (*j2) < (*j1)) {
1204 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1205 >                    snap_->wrapVector(dr);
1206 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1207 >                    if (dr.lengthSquare() < cuts.third) {
1208 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1209 >                    }
1210                    }
1211                  }
1212                }
1094 –            }
1213   #endif
1214 +            }
1215            }
1216          }
1217        }
1218 +    } else {
1219 +      // branch to do all cutoff group pairs
1220 + #ifdef IS_MPI
1221 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1222 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1223 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1224 +          snap_->wrapVector(dr);
1225 +          cuts = getGroupCutoffs( j1, j2 );
1226 +          if (dr.lengthSquare() < cuts.third) {
1227 +            neighborList.push_back(make_pair(j1, j2));
1228 +          }
1229 +        }
1230 +      }
1231 + #else
1232 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1233 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1234 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1235 +          snap_->wrapVector(dr);
1236 +          cuts = getGroupCutoffs( j1, j2 );
1237 +          if (dr.lengthSquare() < cuts.third) {
1238 +            neighborList.push_back(make_pair(j1, j2));
1239 +          }
1240 +        }
1241 +      }        
1242 + #endif
1243      }
1244 <
1244 >      
1245      // save the local cutoff group positions for the check that is
1246      // done on each loop:
1247      saved_CG_positions_.clear();
1248      for (int i = 0; i < nGroups_; i++)
1249        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1250 <
1250 >    
1251      return neighborList;
1252    }
1253   } //end namespace OpenMD

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