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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 1570 by gezelter, Thu May 26 21:56:04 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 <    nGroups_ = snap_->getNumberOfCutoffGroups();
98 <
97 >    
98 >    nGroups_ = info_->getNLocalCutoffGroups();
99      // gather the information for atomtype IDs (atids):
100 <    vector<int> identsLocal = info_->getIdentArray();
100 >    idents = info_->getIdentArray();
101      AtomLocalToGlobal = info_->getGlobalAtomIndices();
102      cgLocalToGlobal = info_->getGlobalGroupIndices();
103      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
66 –    vector<RealType> massFactorsLocal = info_->getMassFactors();
67 –    PairList excludes = info_->getExcludedInteractions();
68 –    PairList oneTwo = info_->getOneTwoInteractions();
69 –    PairList oneThree = info_->getOneThreeInteractions();
70 –    PairList oneFour = info_->getOneFourInteractions();
71 –    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
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_);
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_);
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 101 | Line 145 | namespace OpenMD {
145      cgRowData.setStorageLayout(DataStorage::dslPosition);
146      cgColData.resize(nGroupsInCol_);
147      cgColData.setStorageLayout(DataStorage::dslPosition);
148 +        
149 +    identsRow.resize(nAtomsInRow_);
150 +    identsCol.resize(nAtomsInCol_);
151      
152 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
153 <                                      vector<RealType> (nAtomsInRow_, 0.0));
107 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
108 <                                      vector<RealType> (nAtomsInCol_, 0.0));
152 >    AtomPlanIntRow->gather(idents, identsRow);
153 >    AtomPlanIntColumn->gather(idents, identsCol);
154      
155 <    identsRow.reserve(nAtomsInRow_);
156 <    identsCol.reserve(nAtomsInCol_);
157 <    
113 <    AtomCommIntRow->gather(identsLocal, identsRow);
114 <    AtomCommIntColumn->gather(identsLocal, identsCol);
115 <    
116 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
117 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
118 <    
119 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
120 <    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_.reserve(nGroupsInRow_);
183 >    groupListRow_.resize(nGroupsInRow_);
184      for (int i = 0; i < nGroupsInRow_; i++) {
185        int gid = cgRowToGlobal[i];
186        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 134 | Line 191 | namespace OpenMD {
191      }
192  
193      groupListCol_.clear();
194 <    groupListCol_.reserve(nGroupsInCol_);
194 >    groupListCol_.resize(nGroupsInCol_);
195      for (int i = 0; i < nGroupsInCol_; i++) {
196        int gid = cgColToGlobal[i];
197        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 144 | Line 201 | namespace OpenMD {
201        }      
202      }
203  
204 <    skipsForRowAtom.clear();
205 <    skipsForRowAtom.reserve(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 = AtomColToGlobal[i];
211 >      int iglob = AtomRowToGlobal[i];
212 >
213        for (int j = 0; j < nAtomsInCol_; j++) {
214 <        int jglob = AtomRowToGlobal[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.reserve(nAtomsInRow_);
238 <    for (int i = 0; i < nAtomsInRow_; i++) {
239 <      int iglob = AtomColToGlobal[i];
240 <      int nTopos = 0;
241 <      for (int j = 0; j < nAtomsInCol_; j++) {
242 <        int jglob = AtomRowToGlobal[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          }
170 –        if (oneThree.hasPair(iglob, jglob)) {
171 –          toposForRowAtom[i].push_back(j);
172 –          topoDistRow[i][nTopos] = 2;
173 –          nTopos++;
174 –        }
175 –        if (oneFour.hasPair(iglob, jglob)) {
176 –          toposForRowAtom[i].push_back(j);
177 –          topoDistRow[i][nTopos] = 3;
178 –          nTopos++;
179 –        }
268        }      
269      }
182 –
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_.reserve(nGroups_);
279 >    groupList_.resize(nGroups_);
280      for (int i = 0; i < nGroups_; i++) {
281        int gid = cgLocalToGlobal[i];
282        for (int j = 0; j < nLocal_; j++) {
283          int aid = AtomLocalToGlobal[j];
284 <        if (globalGroupMembership[aid] == gid)
284 >        if (globalGroupMembership[aid] == gid) {
285            groupList_[i].push_back(j);
286 +        }
287        }      
288      }
289  
196 –    skipsForLocalAtom.clear();
197 –    skipsForLocalAtom.reserve(nLocal_);
290  
291 <    for (int i = 0; i < nLocal_; i++) {
200 <      int iglob = AtomLocalToGlobal[i];
201 <      for (int j = 0; j < nLocal_; j++) {
202 <        int jglob = AtomLocalToGlobal[j];        
203 <        if (excludes.hasPair(iglob, jglob))
204 <          skipsForLocalAtom[i].push_back(j);      
205 <      }      
206 <    }
291 >    createGtypeCutoffMap();
292  
293 <    toposForLocalAtom.clear();
294 <    toposForLocalAtom.reserve(nLocal_);
295 <    for (int i = 0; i < nLocal_; i++) {
296 <      int iglob = AtomLocalToGlobal[i];
297 <      int nTopos = 0;
298 <      for (int j = 0; j < nLocal_; j++) {
299 <        int jglob = AtomLocalToGlobal[j];        
300 <        if (oneTwo.hasPair(iglob, jglob)) {
301 <          toposForLocalAtom[i].push_back(j);
302 <          topoDistLocal[i][nTopos] = 1;
303 <          nTopos++;
304 <        }
305 <        if (oneThree.hasPair(iglob, jglob)) {
306 <          toposForLocalAtom[i].push_back(j);
307 <          topoDistLocal[i][nTopos] = 2;
308 <          nTopos++;
309 <        }
310 <        if (oneFour.hasPair(iglob, jglob)) {
311 <          toposForLocalAtom[i].push_back(j);
312 <          topoDistLocal[i][nTopos] = 3;
313 <          nTopos++;
293 >  }
294 >  
295 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
296 >    
297 >    RealType tol = 1e-6;
298 >    largestRcut_ = 0.0;
299 >    RealType rc;
300 >    int atid;
301 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
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 >      if (userChoseCutoff_)
309 >        atypeCutoff[atid] = userCutoff_;
310 >      else
311 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312 >    }
313 >    
314 >    vector<RealType> gTypeCutoffs;
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();
323 >           ia != atomListRow.end(); ++ia) {            
324 >        int atom1 = (*ia);
325 >        atid = identsRow[atom1];
326 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
327 >          groupCutoffRow[cg1] = atypeCutoff[atid];
328          }
329 +      }
330 +
331 +      bool gTypeFound = false;
332 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
333 +        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
334 +          groupRowToGtype[cg1] = gt;
335 +          gTypeFound = true;
336 +        }
337 +      }
338 +      if (!gTypeFound) {
339 +        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
340 +        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
341 +      }
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();
349 +           jb != atomListCol.end(); ++jb) {            
350 +        int atom2 = (*jb);
351 +        atid = identsCol[atom2];
352 +        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
353 +          groupCutoffCol[cg2] = atypeCutoff[atid];
354 +        }
355 +      }
356 +      bool gTypeFound = false;
357 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
358 +        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
359 +          groupColToGtype[cg2] = gt;
360 +          gTypeFound = true;
361 +        }
362 +      }
363 +      if (!gTypeFound) {
364 +        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
365 +        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
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 = idents[atom1];
379 +        if (atypeCutoff[atid] > groupCutoff[cg1])
380 +          groupCutoff[cg1] = atypeCutoff[atid];
381 +      }
382 +      
383 +      bool gTypeFound = false;
384 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
386 +          groupToGtype[cg1] = gt;
387 +          gTypeFound = true;
388 +        }
389 +      }
390 +      if (!gTypeFound) {      
391 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
392 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393        }      
394      }
395 + #endif
396 +
397 +    // Now we find the maximum group cutoff value present in the simulation
398 +
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,
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++) {      
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();
429 +          break;
430 +        }
431 +
432 +        pair<int,int> key = make_pair(i,j);
433 +        gTypeCutoffMap[key].first = thisRcut;
434 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
435 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
436 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
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 (%lf) does not match computed group Cutoff\n", userCutoff_);
444 +            painCave.severity = OPENMD_ERROR;
445 +            painCave.isFatal = 1;
446 +            simError();            
447 +          }
448 +        }
449 +      }
450 +    }
451    }
452 <  
452 >
453 >
454 >  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
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    
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 >
478 > #ifdef IS_MPI
479 >    if (storageLayout_ & DataStorage::dslForce) {
480 >      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
481 >      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
482 >    }
483 >
484 >    if (storageLayout_ & DataStorage::dslTorque) {
485 >      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
486 >      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
487 >    }
488 >    
489 >    fill(pot_row.begin(), pot_row.end(),
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));  
494 >
495 >    if (storageLayout_ & DataStorage::dslParticlePot) {    
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) {      
503 >      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
504 >      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
505 >    }
506 >
507 >    if (storageLayout_ & DataStorage::dslFunctional) {  
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) {      
515 >      fill(atomRowData.functionalDerivative.begin(),
516 >           atomRowData.functionalDerivative.end(), 0.0);
517 >      fill(atomColData.functionalDerivative.begin(),
518 >           atomColData.functionalDerivative.end(), 0.0);
519 >    }
520 >
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);
534 >    }
535 >    
536 >    if (storageLayout_ & DataStorage::dslDensity) {      
537 >      fill(snap_->atomData.density.begin(),
538 >           snap_->atomData.density.end(), 0.0);
539 >    }
540 >    if (storageLayout_ & DataStorage::dslFunctional) {
541 >      fill(snap_->atomData.functional.begin(),
542 >           snap_->atomData.functional.end(), 0.0);
543 >    }
544 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
545 >      fill(snap_->atomData.functionalDerivative.begin(),
546 >           snap_->atomData.functionalDerivative.end(), 0.0);
547 >    }
548 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
549 >      fill(snap_->atomData.skippedCharge.begin(),
550 >           snap_->atomData.skippedCharge.end(), 0.0);
551 >    }
552 >    
553 >  }
554 >
555 >
556    void ForceMatrixDecomposition::distributeData()  {
557      snap_ = sman_->getCurrentSnapshot();
558      storageLayout_ = sman_->getStorageLayout();
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    
595 +  /* collects information obtained during the pre-pair loop onto local
596 +   * data structures.
597 +   */
598    void ForceMatrixDecomposition::collectIntermediateData() {
599      snap_ = sman_->getCurrentSnapshot();
600      storageLayout_ = sman_->getStorageLayout();
# Line 273 | 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 <      std::vector<RealType> rho_tmp(n, 0.0);
610 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
609 >      vector<RealType> rho_tmp(n, 0.0);
610 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
611        for (int i = 0; i < n; i++)
612          snap_->atomData.density[i] += rho_tmp[i];
613      }
614   #endif
615    }
616 <  
616 >
617 >  /*
618 >   * redistributes information obtained during the pre-pair loop out to
619 >   * row and column-indexed data structures
620 >   */
621    void ForceMatrixDecomposition::distributeIntermediateData() {
622      snap_ = sman_->getCurrentSnapshot();
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 313 | 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  
695 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
696 <                                       vector<RealType> (nLocal_, 0.0));
695 >    vector<potVec> pot_temp(nLocal_,
696 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
697 >
698 >    // scatter/gather pot_row into the members of my column
699 >          
700 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
701 >
702 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
703 >      pairwisePot += pot_temp[ii];
704      
705 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
706 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
707 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
708 <        pot_local[i] += pot_temp[i][ii];
709 <      }
705 >    fill(pot_temp.begin(), pot_temp.end(),
706 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
707 >      
708 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
709 >    
710 >    for (int ii = 0;  ii < pot_temp.size(); 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 426 | 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 434 | 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 452 | Line 826 | namespace OpenMD {
826      return d;    
827    }
828  
829 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
830 < #ifdef IS_MPI
457 <    return skipsForRowAtom[atom1];
458 < #else
459 <    return skipsForLocalAtom[atom1];
460 < #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 particle mostly
835 <   * we do this to exclude atoms who are involved in short range
466 <   * interactions (bonds, bends, torsions), but we also need to
467 <   * exclude some overcounted interactions that result from the
468 <   * parallel decomposition.
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 484 | Line 851 | namespace OpenMD {
851      } else {
852        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
853      }
487 – #else
488 –    // in the normal loop, the atom numbers are unique
489 –    unique_id_1 = atom1;
490 –    unique_id_2 = atom2;
854   #endif
855 <    
493 < #ifdef IS_MPI
494 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
495 <         i != skipsForRowAtom[atom1].end(); ++i) {
496 <      if ( (*i) == unique_id_2 ) return true;
497 <    }    
498 < #else
499 <    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
500 <         i != skipsForLocalAtom[atom1].end(); ++i) {
501 <      if ( (*i) == unique_id_2 ) return true;
502 <    }    
503 < #endif
855 >    return false;
856    }
857  
858 <  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
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 < #ifdef IS_MPI
873 <    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
874 <      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
872 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
873 >         i != excludesForAtom[atom1].end(); ++i) {
874 >      if ( (*i) == atom2 )  return true;
875      }
512 – #else
513 –    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
514 –      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
515 –    }
516 – #endif
876  
877 <    // zero is default for unconnected (i.e. normal) pair interactions
519 <    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 536 | 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 +    
908      if (storageLayout_ & DataStorage::dslAmat) {
909        idat.A1 = &(atomRowData.aMat[atom1]);
910        idat.A2 = &(atomColData.aMat[atom2]);
# Line 560 | Line 925 | namespace OpenMD {
925        idat.rho2 = &(atomColData.density[atom2]);
926      }
927  
928 +    if (storageLayout_ & DataStorage::dslFunctional) {
929 +      idat.frho1 = &(atomRowData.functional[atom1]);
930 +      idat.frho2 = &(atomColData.functional[atom2]);
931 +    }
932 +
933      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
934        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
935        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
936      }
937  
938 +    if (storageLayout_ & DataStorage::dslParticlePot) {
939 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
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( 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]);
956        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 581 | 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      }
973  
974 +    if (storageLayout_ & DataStorage::dslFunctional) {
975 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
976 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
977 +    }
978 +
979      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
980        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
981        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
982      }
983 +
984 +    if (storageLayout_ & DataStorage::dslParticlePot) {
985 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
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
594 –    return idat;
994    }
995  
996 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
997 <
599 <    InteractionData idat;
996 >  
997 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
998   #ifdef IS_MPI
999 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1000 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1001 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1002 <    }
1003 <    if (storageLayout_ & DataStorage::dslTorque) {
606 <      idat.t1 = &(atomRowData.torque[atom1]);
607 <      idat.t2 = &(atomColData.torque[atom2]);
608 <    }
609 <    if (storageLayout_ & DataStorage::dslForce) {
610 <      idat.t1 = &(atomRowData.force[atom1]);
611 <      idat.t2 = &(atomColData.force[atom2]);
612 <    }
999 >    pot_row[atom1] += 0.5 *  *(idat.pot);
1000 >    pot_col[atom2] += 0.5 *  *(idat.pot);
1001 >
1002 >    atomRowData.force[atom1] += *(idat.f1);
1003 >    atomColData.force[atom2] -= *(idat.f1);
1004   #else
1005 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1006 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1007 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1008 <    }
618 <    if (storageLayout_ & DataStorage::dslTorque) {
619 <      idat.t1 = &(snap_->atomData.torque[atom1]);
620 <      idat.t2 = &(snap_->atomData.torque[atom2]);
621 <    }
622 <    if (storageLayout_ & DataStorage::dslForce) {
623 <      idat.t1 = &(snap_->atomData.force[atom1]);
624 <      idat.t2 = &(snap_->atomData.force[atom2]);
625 <    }
1005 >    pairwisePot += *(idat.pot);
1006 >
1007 >    snap_->atomData.force[atom1] += *(idat.f1);
1008 >    snap_->atomData.force[atom2] -= *(idat.f1);
1009   #endif
1010      
1011    }
1012  
630 –
631 –
632 –
1013    /*
1014     * buildNeighborList
1015     *
# Line 639 | Line 1019 | namespace OpenMD {
1019    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
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 646 | Line 1029 | namespace OpenMD {
1029      cellList_.clear();
1030   #endif
1031  
1032 <    // dangerous to not do error checking.
650 <    RealType rCut_;
651 <
652 <    RealType rList_ = (rCut_ + skinThickness_);
1032 >    RealType rList_ = (largestRcut_ + skinThickness_);
1033      RealType rl2 = rList_ * rList_;
1034      Snapshot* snap_ = sman_->getCurrentSnapshot();
1035      Mat3x3d Hmat = snap_->getHmat();
# Line 661 | 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
675 <      // numbers
676 <      for (int j = 0; j < 3; j++)
677 <        scaled[j] -= roundMe(scaled[j]);
678 <    
679 <      // find xyz-indices of cell that cutoffGroup is in.
680 <      whichCell.x() = nCells_.x() * scaled.x();
681 <      whichCell.y() = nCells_.y() * scaled.y();
682 <      whichCell.z() = nCells_.z() * scaled.z();
683 <
684 <      // find single index of this cell:
685 <      cellIndex = Vlinear(whichCell, nCells_);
686 <      // add this cutoff group to the list of groups in this cell;
687 <      cellListRow_[cellIndex].push_back(i);
688 <    }
1057 >    cellListRow_.resize(nCtot);
1058 >    cellListCol_.resize(nCtot);
1059 > #else
1060 >    cellList_.resize(nCtot);
1061 > #endif
1062  
1063 <    for (int i = 0; i < nGroupsInCol_; i++) {
1064 <      rs = cgColData.position[i];
692 <      // scaled positions relative to the box vectors
693 <      scaled = invHmat * rs;
694 <      // wrap the vector back into the unit box by subtracting integer box
695 <      // numbers
696 <      for (int j = 0; j < 3; j++)
697 <        scaled[j] -= roundMe(scaled[j]);
1063 >    if (!doAllPairs) {
1064 > #ifdef IS_MPI
1065  
1066 <      // find xyz-indices of cell that cutoffGroup is in.
1067 <      whichCell.x() = nCells_.x() * scaled.x();
1068 <      whichCell.y() = nCells_.y() * scaled.y();
1069 <      whichCell.z() = nCells_.z() * scaled.z();
1070 <
1071 <      // find single index of this cell:
1072 <      cellIndex = Vlinear(whichCell, nCells_);
1073 <      // add this cutoff group to the list of groups in this cell;
1074 <      cellListCol_[cellIndex].push_back(i);
1075 <    }
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  
719 –      // find xyz-indices of cell that cutoffGroup is in.
720 –      whichCell.x() = nCells_.x() * scaled.x();
721 –      whichCell.y() = nCells_.y() * scaled.y();
722 –      whichCell.z() = nCells_.z() * scaled.z();
723 –
724 –      // find single index of this cell:
725 –      cellIndex = Vlinear(whichCell, nCells_);
726 –      // add this cutoff group to the list of groups in this cell;
727 –      cellList_[cellIndex].push_back(i);
728 –    }
1141   #endif
1142  
1143 <
1144 <
1145 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1146 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1147 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
736 <          Vector3i m1v(m1x, m1y, m1z);
737 <          int m1 = Vlinear(m1v, nCells_);
738 <
739 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
740 <               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) {
747 <              m2v.x() = nCells_.x() - 1;
748 <            }
749 <            
750 <            if (m2v.y() >= nCells_.y()) {
751 <              m2v.y() = 0;          
752 <            } else if (m2v.y() < 0) {
753 <              m2v.y() = nCells_.y() - 1;
754 <            }
755 <            
756 <            if (m2v.z() >= nCells_.z()) {
757 <              m2v.z() = 0;          
758 <            } else if (m2v.z() < 0) {
759 <              m2v.z() = nCells_.z() - 1;
760 <            }
761 <            
762 <            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 <                  if (dr.lengthSquare() < rl2) {
1186 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1187 >                  if (dr.lengthSquare() < cuts.third) {
1188                      neighborList.push_back(make_pair((*j1), (*j2)));
1189 <                  }
1189 >                  }                  
1190                  }
1191                }
782 –            }
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 <                  if (dr.lengthSquare() < rl2) {
1206 <                    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                }
801 –            }
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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