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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 1612 by gezelter, Fri Aug 12 19:59:56 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];
151 <      for (int j = 0; j < nAtomsInCol_; j++) {
152 <        int jglob = AtomRowToGlobal[j];        
153 <        if (excludes.hasPair(iglob, jglob))
154 <          skipsForRowAtom[i].push_back(j);      
155 <      }      
156 <    }
211 >      int iglob = AtomRowToGlobal[i];
212  
158 –    toposForRowAtom.clear();
159 –    toposForRowAtom.reserve(nAtomsInRow_);
160 –    for (int i = 0; i < nAtomsInRow_; i++) {
161 –      int iglob = AtomColToGlobal[i];
162 –      int nTopos = 0;
213        for (int j = 0; j < nAtomsInCol_; j++) {
214 <        int jglob = AtomRowToGlobal[j];        
215 <        if (oneTwo.hasPair(iglob, jglob)) {
216 <          toposForRowAtom[i].push_back(j);
217 <          topoDistRow[i][nTopos] = 1;
218 <          nTopos++;
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          }
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 –        }
233        }      
234      }
235  
236   #endif
237  
238 +    // allocate memory for the parallel objects
239 +    atypesLocal.resize(nLocal_);
240 +
241 +    for (int i = 0; i < nLocal_; i++)
242 +      atypesLocal[i] = ff_->getAtomType(idents[i]);
243 +
244      groupList_.clear();
245 <    groupList_.reserve(nGroups_);
245 >    groupList_.resize(nGroups_);
246      for (int i = 0; i < nGroups_; i++) {
247        int gid = cgLocalToGlobal[i];
248        for (int j = 0; j < nLocal_; j++) {
249          int aid = AtomLocalToGlobal[j];
250 <        if (globalGroupMembership[aid] == gid)
250 >        if (globalGroupMembership[aid] == gid) {
251            groupList_[i].push_back(j);
252 +        }
253        }      
254      }
255  
256 <    skipsForLocalAtom.clear();
257 <    skipsForLocalAtom.reserve(nLocal_);
256 >    excludesForAtom.clear();
257 >    excludesForAtom.resize(nLocal_);
258 >    toposForAtom.clear();
259 >    toposForAtom.resize(nLocal_);
260 >    topoDist.clear();
261 >    topoDist.resize(nLocal_);
262  
263      for (int i = 0; i < nLocal_; i++) {
264        int iglob = AtomLocalToGlobal[i];
265 +
266        for (int j = 0; j < nLocal_; j++) {
267 <        int jglob = AtomLocalToGlobal[j];        
268 <        if (excludes.hasPair(iglob, jglob))
269 <          skipsForLocalAtom[i].push_back(j);      
267 >        int jglob = AtomLocalToGlobal[j];
268 >
269 >        if (excludes->hasPair(iglob, jglob))
270 >          excludesForAtom[i].push_back(j);              
271 >        
272 >        if (oneTwo->hasPair(iglob, jglob)) {
273 >          toposForAtom[i].push_back(j);
274 >          topoDist[i].push_back(1);
275 >        } else {
276 >          if (oneThree->hasPair(iglob, jglob)) {
277 >            toposForAtom[i].push_back(j);
278 >            topoDist[i].push_back(2);
279 >          } else {
280 >            if (oneFour->hasPair(iglob, jglob)) {
281 >              toposForAtom[i].push_back(j);
282 >              topoDist[i].push_back(3);
283 >            }
284 >          }
285 >        }
286        }      
287      }
288 +    
289 +    createGtypeCutoffMap();
290  
291 <    toposForLocalAtom.clear();
292 <    toposForLocalAtom.reserve(nLocal_);
293 <    for (int i = 0; i < nLocal_; i++) {
294 <      int iglob = AtomLocalToGlobal[i];
295 <      int nTopos = 0;
296 <      for (int j = 0; j < nLocal_; j++) {
297 <        int jglob = AtomLocalToGlobal[j];        
298 <        if (oneTwo.hasPair(iglob, jglob)) {
299 <          toposForLocalAtom[i].push_back(j);
300 <          topoDistLocal[i][nTopos] = 1;
301 <          nTopos++;
302 <        }
303 <        if (oneThree.hasPair(iglob, jglob)) {
304 <          toposForLocalAtom[i].push_back(j);
305 <          topoDistLocal[i][nTopos] = 2;
306 <          nTopos++;
307 <        }
308 <        if (oneFour.hasPair(iglob, jglob)) {
309 <          toposForLocalAtom[i].push_back(j);
310 <          topoDistLocal[i][nTopos] = 3;
311 <          nTopos++;
291 >  }
292 >  
293 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
294 >    
295 >    RealType tol = 1e-6;
296 >    largestRcut_ = 0.0;
297 >    RealType rc;
298 >    int atid;
299 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
300 >    
301 >    map<int, RealType> atypeCutoff;
302 >      
303 >    for (set<AtomType*>::iterator at = atypes.begin();
304 >         at != atypes.end(); ++at){
305 >      atid = (*at)->getIdent();
306 >      if (userChoseCutoff_)
307 >        atypeCutoff[atid] = userCutoff_;
308 >      else
309 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
310 >    }
311 >    
312 >    vector<RealType> gTypeCutoffs;
313 >    // first we do a single loop over the cutoff groups to find the
314 >    // largest cutoff for any atypes present in this group.
315 > #ifdef IS_MPI
316 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
317 >    groupRowToGtype.resize(nGroupsInRow_);
318 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
319 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
320 >      for (vector<int>::iterator ia = atomListRow.begin();
321 >           ia != atomListRow.end(); ++ia) {            
322 >        int atom1 = (*ia);
323 >        atid = identsRow[atom1];
324 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
325 >          groupCutoffRow[cg1] = atypeCutoff[atid];
326          }
327 +      }
328 +
329 +      bool gTypeFound = false;
330 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
331 +        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
332 +          groupRowToGtype[cg1] = gt;
333 +          gTypeFound = true;
334 +        }
335 +      }
336 +      if (!gTypeFound) {
337 +        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
338 +        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
339 +      }
340 +      
341 +    }
342 +    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
343 +    groupColToGtype.resize(nGroupsInCol_);
344 +    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
345 +      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
346 +      for (vector<int>::iterator jb = atomListCol.begin();
347 +           jb != atomListCol.end(); ++jb) {            
348 +        int atom2 = (*jb);
349 +        atid = identsCol[atom2];
350 +        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
351 +          groupCutoffCol[cg2] = atypeCutoff[atid];
352 +        }
353 +      }
354 +      bool gTypeFound = false;
355 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
356 +        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
357 +          groupColToGtype[cg2] = gt;
358 +          gTypeFound = true;
359 +        }
360 +      }
361 +      if (!gTypeFound) {
362 +        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
363 +        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
364 +      }
365 +    }
366 + #else
367 +
368 +    vector<RealType> groupCutoff(nGroups_, 0.0);
369 +    groupToGtype.resize(nGroups_);
370 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
371 +      groupCutoff[cg1] = 0.0;
372 +      vector<int> atomList = getAtomsInGroupRow(cg1);
373 +      for (vector<int>::iterator ia = atomList.begin();
374 +           ia != atomList.end(); ++ia) {            
375 +        int atom1 = (*ia);
376 +        atid = idents[atom1];
377 +        if (atypeCutoff[atid] > groupCutoff[cg1])
378 +          groupCutoff[cg1] = atypeCutoff[atid];
379 +      }
380 +      
381 +      bool gTypeFound = false;
382 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
383 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
384 +          groupToGtype[cg1] = gt;
385 +          gTypeFound = true;
386 +        }
387 +      }
388 +      if (!gTypeFound) {      
389 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
390 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
391        }      
392      }
393 + #endif
394 +
395 +    // Now we find the maximum group cutoff value present in the simulation
396 +
397 +    RealType groupMax = *max_element(gTypeCutoffs.begin(),
398 +                                     gTypeCutoffs.end());
399 +
400 + #ifdef IS_MPI
401 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
402 +                              MPI::MAX);
403 + #endif
404 +    
405 +    RealType tradRcut = groupMax;
406 +
407 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
408 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
409 +        RealType thisRcut;
410 +        switch(cutoffPolicy_) {
411 +        case TRADITIONAL:
412 +          thisRcut = tradRcut;
413 +          break;
414 +        case MIX:
415 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
416 +          break;
417 +        case MAX:
418 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
419 +          break;
420 +        default:
421 +          sprintf(painCave.errMsg,
422 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
423 +                  "hit an unknown cutoff policy!\n");
424 +          painCave.severity = OPENMD_ERROR;
425 +          painCave.isFatal = 1;
426 +          simError();
427 +          break;
428 +        }
429 +
430 +        pair<int,int> key = make_pair(i,j);
431 +        gTypeCutoffMap[key].first = thisRcut;
432 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
433 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
434 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
435 +        // sanity check
436 +        
437 +        if (userChoseCutoff_) {
438 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
439 +            sprintf(painCave.errMsg,
440 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
441 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
442 +            painCave.severity = OPENMD_ERROR;
443 +            painCave.isFatal = 1;
444 +            simError();            
445 +          }
446 +        }
447 +      }
448 +    }
449    }
450 <  
450 >
451 >
452 >  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
453 >    int i, j;  
454 > #ifdef IS_MPI
455 >    i = groupRowToGtype[cg1];
456 >    j = groupColToGtype[cg2];
457 > #else
458 >    i = groupToGtype[cg1];
459 >    j = groupToGtype[cg2];
460 > #endif    
461 >    return gTypeCutoffMap[make_pair(i,j)];
462 >  }
463 >
464 >  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
465 >    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
466 >      if (toposForAtom[atom1][j] == atom2)
467 >        return topoDist[atom1][j];
468 >    }
469 >    return 0;
470 >  }
471 >
472 >  void ForceMatrixDecomposition::zeroWorkArrays() {
473 >    pairwisePot = 0.0;
474 >    embeddingPot = 0.0;
475 >
476 > #ifdef IS_MPI
477 >    if (storageLayout_ & DataStorage::dslForce) {
478 >      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
479 >      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
480 >    }
481 >
482 >    if (storageLayout_ & DataStorage::dslTorque) {
483 >      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
484 >      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
485 >    }
486 >    
487 >    fill(pot_row.begin(), pot_row.end(),
488 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
489 >
490 >    fill(pot_col.begin(), pot_col.end(),
491 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
492 >
493 >    if (storageLayout_ & DataStorage::dslParticlePot) {    
494 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
495 >           0.0);
496 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
497 >           0.0);
498 >    }
499 >
500 >    if (storageLayout_ & DataStorage::dslDensity) {      
501 >      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
502 >      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
503 >    }
504 >
505 >    if (storageLayout_ & DataStorage::dslFunctional) {  
506 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
507 >           0.0);
508 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
509 >           0.0);
510 >    }
511 >
512 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
513 >      fill(atomRowData.functionalDerivative.begin(),
514 >           atomRowData.functionalDerivative.end(), 0.0);
515 >      fill(atomColData.functionalDerivative.begin(),
516 >           atomColData.functionalDerivative.end(), 0.0);
517 >    }
518 >
519 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
520 >      fill(atomRowData.skippedCharge.begin(),
521 >           atomRowData.skippedCharge.end(), 0.0);
522 >      fill(atomColData.skippedCharge.begin(),
523 >           atomColData.skippedCharge.end(), 0.0);
524 >    }
525 >
526 > #endif
527 >    // even in parallel, we need to zero out the local arrays:
528 >
529 >    if (storageLayout_ & DataStorage::dslParticlePot) {      
530 >      fill(snap_->atomData.particlePot.begin(),
531 >           snap_->atomData.particlePot.end(), 0.0);
532 >    }
533 >    
534 >    if (storageLayout_ & DataStorage::dslDensity) {      
535 >      fill(snap_->atomData.density.begin(),
536 >           snap_->atomData.density.end(), 0.0);
537 >    }
538 >    if (storageLayout_ & DataStorage::dslFunctional) {
539 >      fill(snap_->atomData.functional.begin(),
540 >           snap_->atomData.functional.end(), 0.0);
541 >    }
542 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
543 >      fill(snap_->atomData.functionalDerivative.begin(),
544 >           snap_->atomData.functionalDerivative.end(), 0.0);
545 >    }
546 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
547 >      fill(snap_->atomData.skippedCharge.begin(),
548 >           snap_->atomData.skippedCharge.end(), 0.0);
549 >    }
550 >    
551 >  }
552 >
553 >
554    void ForceMatrixDecomposition::distributeData()  {
555      snap_ = sman_->getCurrentSnapshot();
556      storageLayout_ = sman_->getStorageLayout();
557   #ifdef IS_MPI
558      
559      // gather up the atomic positions
560 <    AtomCommVectorRow->gather(snap_->atomData.position,
560 >    AtomPlanVectorRow->gather(snap_->atomData.position,
561                                atomRowData.position);
562 <    AtomCommVectorColumn->gather(snap_->atomData.position,
562 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
563                                   atomColData.position);
564      
565      // gather up the cutoff group positions
566 <    cgCommVectorRow->gather(snap_->cgData.position,
566 >
567 >    cgPlanVectorRow->gather(snap_->cgData.position,
568                              cgRowData.position);
569 <    cgCommVectorColumn->gather(snap_->cgData.position,
569 >
570 >    cgPlanVectorColumn->gather(snap_->cgData.position,
571                                 cgColData.position);
572 +
573      
574      // if needed, gather the atomic rotation matrices
575      if (storageLayout_ & DataStorage::dslAmat) {
576 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
576 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
577                                  atomRowData.aMat);
578 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
578 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
579                                     atomColData.aMat);
580      }
581      
582      // if needed, gather the atomic eletrostatic frames
583      if (storageLayout_ & DataStorage::dslElectroFrame) {
584 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
584 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
585                                  atomRowData.electroFrame);
586 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
586 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
587                                     atomColData.electroFrame);
588      }
589 +
590   #endif      
591    }
592    
593 +  /* collects information obtained during the pre-pair loop onto local
594 +   * data structures.
595 +   */
596    void ForceMatrixDecomposition::collectIntermediateData() {
597      snap_ = sman_->getCurrentSnapshot();
598      storageLayout_ = sman_->getStorageLayout();
# Line 273 | Line 600 | namespace OpenMD {
600      
601      if (storageLayout_ & DataStorage::dslDensity) {
602        
603 <      AtomCommRealRow->scatter(atomRowData.density,
603 >      AtomPlanRealRow->scatter(atomRowData.density,
604                                 snap_->atomData.density);
605        
606        int n = snap_->atomData.density.size();
607 <      std::vector<RealType> rho_tmp(n, 0.0);
608 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
607 >      vector<RealType> rho_tmp(n, 0.0);
608 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
609        for (int i = 0; i < n; i++)
610          snap_->atomData.density[i] += rho_tmp[i];
611      }
612   #endif
613    }
614 <  
614 >
615 >  /*
616 >   * redistributes information obtained during the pre-pair loop out to
617 >   * row and column-indexed data structures
618 >   */
619    void ForceMatrixDecomposition::distributeIntermediateData() {
620      snap_ = sman_->getCurrentSnapshot();
621      storageLayout_ = sman_->getStorageLayout();
622   #ifdef IS_MPI
623      if (storageLayout_ & DataStorage::dslFunctional) {
624 <      AtomCommRealRow->gather(snap_->atomData.functional,
624 >      AtomPlanRealRow->gather(snap_->atomData.functional,
625                                atomRowData.functional);
626 <      AtomCommRealColumn->gather(snap_->atomData.functional,
626 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
627                                   atomColData.functional);
628      }
629      
630      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
631 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
631 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
632                                atomRowData.functionalDerivative);
633 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
633 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
634                                   atomColData.functionalDerivative);
635      }
636   #endif
# Line 313 | Line 644 | namespace OpenMD {
644      int n = snap_->atomData.force.size();
645      vector<Vector3d> frc_tmp(n, V3Zero);
646      
647 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
647 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
648      for (int i = 0; i < n; i++) {
649        snap_->atomData.force[i] += frc_tmp[i];
650        frc_tmp[i] = 0.0;
651      }
652      
653 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
654 <    for (int i = 0; i < n; i++)
653 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
654 >    for (int i = 0; i < n; i++) {
655        snap_->atomData.force[i] += frc_tmp[i];
656 <    
657 <    
656 >    }
657 >        
658      if (storageLayout_ & DataStorage::dslTorque) {
659  
660 <      int nt = snap_->atomData.force.size();
660 >      int nt = snap_->atomData.torque.size();
661        vector<Vector3d> trq_tmp(nt, V3Zero);
662  
663 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
664 <      for (int i = 0; i < n; i++) {
663 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
664 >      for (int i = 0; i < nt; i++) {
665          snap_->atomData.torque[i] += trq_tmp[i];
666          trq_tmp[i] = 0.0;
667        }
668        
669 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
670 <      for (int i = 0; i < n; i++)
669 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
670 >      for (int i = 0; i < nt; i++)
671          snap_->atomData.torque[i] += trq_tmp[i];
672      }
673 +
674 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
675 +
676 +      int ns = snap_->atomData.skippedCharge.size();
677 +      vector<RealType> skch_tmp(ns, 0.0);
678 +
679 +      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
680 +      for (int i = 0; i < ns; i++) {
681 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
682 +        skch_tmp[i] = 0.0;
683 +      }
684 +      
685 +      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
686 +      for (int i = 0; i < ns; i++)
687 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
688 +    }
689      
690      nLocal_ = snap_->getNumberOfAtoms();
691  
692 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
693 <                                       vector<RealType> (nLocal_, 0.0));
692 >    vector<potVec> pot_temp(nLocal_,
693 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
694 >
695 >    // scatter/gather pot_row into the members of my column
696 >          
697 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
698 >
699 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
700 >      pairwisePot += pot_temp[ii];
701      
702 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
703 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
704 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
705 <        pot_local[i] += pot_temp[i][ii];
706 <      }
702 >    fill(pot_temp.begin(), pot_temp.end(),
703 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
704 >      
705 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
706 >    
707 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
708 >      pairwisePot += pot_temp[ii];    
709 >    
710 >    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
711 >      RealType ploc1 = pairwisePot[ii];
712 >      RealType ploc2 = 0.0;
713 >      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
714 >      pairwisePot[ii] = ploc2;
715      }
716 +
717   #endif
718 +
719    }
720  
721    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 426 | Line 790 | namespace OpenMD {
790   #ifdef IS_MPI
791      return massFactorsRow[atom1];
792   #else
793 <    return massFactorsLocal[atom1];
793 >    return massFactors[atom1];
794   #endif
795    }
796  
# Line 434 | Line 798 | namespace OpenMD {
798   #ifdef IS_MPI
799      return massFactorsCol[atom2];
800   #else
801 <    return massFactorsLocal[atom2];
801 >    return massFactors[atom2];
802   #endif
803  
804    }
# Line 452 | Line 816 | namespace OpenMD {
816      return d;    
817    }
818  
819 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
820 < #ifdef IS_MPI
457 <    return skipsForRowAtom[atom1];
458 < #else
459 <    return skipsForLocalAtom[atom1];
460 < #endif
819 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
820 >    return excludesForAtom[atom1];
821    }
822  
823    /**
824 <   * there are a number of reasons to skip a pair or a particle mostly
825 <   * 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.
824 >   * We need to exclude some overcounted interactions that result from
825 >   * the parallel decomposition.
826     */
827    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
828      int unique_id_1, unique_id_2;
829 <
829 >    
830   #ifdef IS_MPI
831      // in MPI, we have to look up the unique IDs for each atom
832      unique_id_1 = AtomRowToGlobal[atom1];
# Line 484 | Line 841 | namespace OpenMD {
841      } else {
842        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
843      }
844 + #endif
845 +    return false;
846 +  }
847 +
848 +  /**
849 +   * We need to handle the interactions for atoms who are involved in
850 +   * the same rigid body as well as some short range interactions
851 +   * (bonds, bends, torsions) differently from other interactions.
852 +   * We'll still visit the pairwise routines, but with a flag that
853 +   * tells those routines to exclude the pair from direct long range
854 +   * interactions.  Some indirect interactions (notably reaction
855 +   * field) must still be handled for these pairs.
856 +   */
857 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
858 +    int unique_id_2;
859 + #ifdef IS_MPI
860 +    // in MPI, we have to look up the unique IDs for the row atom.
861 +    unique_id_2 = AtomColToGlobal[atom2];
862   #else
863      // in the normal loop, the atom numbers are unique
489 –    unique_id_1 = atom1;
864      unique_id_2 = atom2;
865   #endif
866      
867 < #ifdef IS_MPI
868 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
495 <         i != skipsForRowAtom[atom1].end(); ++i) {
867 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
868 >         i != excludesForAtom[atom1].end(); ++i) {
869        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
504 –  }
505 –
506 –  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
507 –    
508 – #ifdef IS_MPI
509 –    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
510 –      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
870      }
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
871  
872 <    // zero is default for unconnected (i.e. normal) pair interactions
519 <    return 0;
872 >    return false;
873    }
874  
875 +
876    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
877   #ifdef IS_MPI
878      atomRowData.force[atom1] += fg;
# Line 536 | Line 890 | namespace OpenMD {
890    }
891  
892      // filling interaction blocks with pointers
893 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
894 <    InteractionData idat;
893 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
894 >                                                     int atom1, int atom2) {
895  
896 +    idat.excluded = excludeAtomPair(atom1, atom2);
897 +  
898   #ifdef IS_MPI
899 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
900 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
901 +    //                         ff_->getAtomType(identsCol[atom2]) );
902 +    
903      if (storageLayout_ & DataStorage::dslAmat) {
904        idat.A1 = &(atomRowData.aMat[atom1]);
905        idat.A2 = &(atomColData.aMat[atom2]);
# Line 560 | Line 920 | namespace OpenMD {
920        idat.rho2 = &(atomColData.density[atom2]);
921      }
922  
923 +    if (storageLayout_ & DataStorage::dslFunctional) {
924 +      idat.frho1 = &(atomRowData.functional[atom1]);
925 +      idat.frho2 = &(atomColData.functional[atom2]);
926 +    }
927 +
928      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
929        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
930        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
931      }
932  
933 +    if (storageLayout_ & DataStorage::dslParticlePot) {
934 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
935 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
936 +    }
937 +
938 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
939 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
940 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
941 +    }
942 +
943   #else
944 +
945 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
946 +    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
947 +    //                         ff_->getAtomType(idents[atom2]) );
948 +
949      if (storageLayout_ & DataStorage::dslAmat) {
950        idat.A1 = &(snap_->atomData.aMat[atom1]);
951        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 581 | Line 961 | namespace OpenMD {
961        idat.t2 = &(snap_->atomData.torque[atom2]);
962      }
963  
964 <    if (storageLayout_ & DataStorage::dslDensity) {
964 >    if (storageLayout_ & DataStorage::dslDensity) {    
965        idat.rho1 = &(snap_->atomData.density[atom1]);
966        idat.rho2 = &(snap_->atomData.density[atom2]);
967      }
968  
969 +    if (storageLayout_ & DataStorage::dslFunctional) {
970 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
971 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
972 +    }
973 +
974      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
975        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
976        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
977      }
978 +
979 +    if (storageLayout_ & DataStorage::dslParticlePot) {
980 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
981 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
982 +    }
983 +
984 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
985 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
986 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
987 +    }
988   #endif
594 –    return idat;
989    }
990  
991 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
992 <
599 <    InteractionData idat;
991 >  
992 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
993   #ifdef IS_MPI
994 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
995 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
996 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
997 <    }
998 <    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 <    }
994 >    pot_row[atom1] += 0.5 *  *(idat.pot);
995 >    pot_col[atom2] += 0.5 *  *(idat.pot);
996 >
997 >    atomRowData.force[atom1] += *(idat.f1);
998 >    atomColData.force[atom2] -= *(idat.f1);
999   #else
1000 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1001 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1002 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1003 <    }
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 <    }
1000 >    pairwisePot += *(idat.pot);
1001 >
1002 >    snap_->atomData.force[atom1] += *(idat.f1);
1003 >    snap_->atomData.force[atom2] -= *(idat.f1);
1004   #endif
1005      
1006    }
1007  
630 –
631 –
632 –
1008    /*
1009     * buildNeighborList
1010     *
# Line 639 | Line 1014 | namespace OpenMD {
1014    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1015        
1016      vector<pair<int, int> > neighborList;
1017 +    groupCutoffs cuts;
1018 +    bool doAllPairs = false;
1019 +
1020   #ifdef IS_MPI
1021      cellListRow_.clear();
1022      cellListCol_.clear();
# Line 646 | Line 1024 | namespace OpenMD {
1024      cellList_.clear();
1025   #endif
1026  
1027 <    // dangerous to not do error checking.
650 <    RealType rCut_;
651 <
652 <    RealType rList_ = (rCut_ + skinThickness_);
1027 >    RealType rList_ = (largestRcut_ + skinThickness_);
1028      RealType rl2 = rList_ * rList_;
1029      Snapshot* snap_ = sman_->getCurrentSnapshot();
1030      Mat3x3d Hmat = snap_->getHmat();
# Line 661 | Line 1036 | namespace OpenMD {
1036      nCells_.y() = (int) ( Hy.length() )/ rList_;
1037      nCells_.z() = (int) ( Hz.length() )/ rList_;
1038  
1039 +    // handle small boxes where the cell offsets can end up repeating cells
1040 +    
1041 +    if (nCells_.x() < 3) doAllPairs = true;
1042 +    if (nCells_.y() < 3) doAllPairs = true;
1043 +    if (nCells_.z() < 3) doAllPairs = true;
1044 +
1045      Mat3x3d invHmat = snap_->getInvHmat();
1046      Vector3d rs, scaled, dr;
1047      Vector3i whichCell;
1048      int cellIndex;
1049 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1050  
1051   #ifdef IS_MPI
1052 <    for (int i = 0; i < nGroupsInRow_; i++) {
1053 <      rs = cgRowData.position[i];
1054 <      // scaled positions relative to the box vectors
1055 <      scaled = invHmat * rs;
1056 <      // 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 <    }
1052 >    cellListRow_.resize(nCtot);
1053 >    cellListCol_.resize(nCtot);
1054 > #else
1055 >    cellList_.resize(nCtot);
1056 > #endif
1057  
1058 <    for (int i = 0; i < nGroupsInCol_; i++) {
1059 <      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]);
1058 >    if (!doAllPairs) {
1059 > #ifdef IS_MPI
1060  
1061 <      // find xyz-indices of cell that cutoffGroup is in.
1062 <      whichCell.x() = nCells_.x() * scaled.x();
1063 <      whichCell.y() = nCells_.y() * scaled.y();
1064 <      whichCell.z() = nCells_.z() * scaled.z();
1065 <
1066 <      // find single index of this cell:
1067 <      cellIndex = Vlinear(whichCell, nCells_);
1068 <      // add this cutoff group to the list of groups in this cell;
1069 <      cellListCol_[cellIndex].push_back(i);
1070 <    }
1061 >      for (int i = 0; i < nGroupsInRow_; i++) {
1062 >        rs = cgRowData.position[i];
1063 >        
1064 >        // scaled positions relative to the box vectors
1065 >        scaled = invHmat * rs;
1066 >        
1067 >        // wrap the vector back into the unit box by subtracting integer box
1068 >        // numbers
1069 >        for (int j = 0; j < 3; j++) {
1070 >          scaled[j] -= roundMe(scaled[j]);
1071 >          scaled[j] += 0.5;
1072 >        }
1073 >        
1074 >        // find xyz-indices of cell that cutoffGroup is in.
1075 >        whichCell.x() = nCells_.x() * scaled.x();
1076 >        whichCell.y() = nCells_.y() * scaled.y();
1077 >        whichCell.z() = nCells_.z() * scaled.z();
1078 >        
1079 >        // find single index of this cell:
1080 >        cellIndex = Vlinear(whichCell, nCells_);
1081 >        
1082 >        // add this cutoff group to the list of groups in this cell;
1083 >        cellListRow_[cellIndex].push_back(i);
1084 >      }
1085 >      for (int i = 0; i < nGroupsInCol_; i++) {
1086 >        rs = cgColData.position[i];
1087 >        
1088 >        // scaled positions relative to the box vectors
1089 >        scaled = invHmat * rs;
1090 >        
1091 >        // wrap the vector back into the unit box by subtracting integer box
1092 >        // numbers
1093 >        for (int j = 0; j < 3; j++) {
1094 >          scaled[j] -= roundMe(scaled[j]);
1095 >          scaled[j] += 0.5;
1096 >        }
1097 >        
1098 >        // find xyz-indices of cell that cutoffGroup is in.
1099 >        whichCell.x() = nCells_.x() * scaled.x();
1100 >        whichCell.y() = nCells_.y() * scaled.y();
1101 >        whichCell.z() = nCells_.z() * scaled.z();
1102 >        
1103 >        // find single index of this cell:
1104 >        cellIndex = Vlinear(whichCell, nCells_);
1105 >        
1106 >        // add this cutoff group to the list of groups in this cell;
1107 >        cellListCol_[cellIndex].push_back(i);
1108 >      }
1109 >    
1110   #else
1111 <    for (int i = 0; i < nGroups_; i++) {
1112 <      rs = snap_->cgData.position[i];
1113 <      // scaled positions relative to the box vectors
1114 <      scaled = invHmat * rs;
1115 <      // wrap the vector back into the unit box by subtracting integer box
1116 <      // numbers
1117 <      for (int j = 0; j < 3; j++)
1118 <        scaled[j] -= roundMe(scaled[j]);
1111 >      for (int i = 0; i < nGroups_; i++) {
1112 >        rs = snap_->cgData.position[i];
1113 >        
1114 >        // scaled positions relative to the box vectors
1115 >        scaled = invHmat * rs;
1116 >        
1117 >        // wrap the vector back into the unit box by subtracting integer box
1118 >        // numbers
1119 >        for (int j = 0; j < 3; j++) {
1120 >          scaled[j] -= roundMe(scaled[j]);
1121 >          scaled[j] += 0.5;
1122 >        }
1123 >        
1124 >        // find xyz-indices of cell that cutoffGroup is in.
1125 >        whichCell.x() = nCells_.x() * scaled.x();
1126 >        whichCell.y() = nCells_.y() * scaled.y();
1127 >        whichCell.z() = nCells_.z() * scaled.z();
1128 >        
1129 >        // find single index of this cell:
1130 >        cellIndex = Vlinear(whichCell, nCells_);
1131 >        
1132 >        // add this cutoff group to the list of groups in this cell;
1133 >        cellList_[cellIndex].push_back(i);
1134 >      }
1135  
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 –    }
1136   #endif
1137  
1138 <
1139 <
1140 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1141 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1142 <        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) {
1138 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1139 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1140 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1141 >            Vector3i m1v(m1x, m1y, m1z);
1142 >            int m1 = Vlinear(m1v, nCells_);
1143              
1144 <            Vector3i m2v = m1v + (*os);
1145 <            
1146 <            if (m2v.x() >= nCells_.x()) {
1147 <              m2v.x() = 0;          
1148 <            } 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_);
1144 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1145 >                 os != cellOffsets_.end(); ++os) {
1146 >              
1147 >              Vector3i m2v = m1v + (*os);
1148 >            
1149  
1150 < #ifdef IS_MPI
1151 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1152 <                 j1 != cellListRow_[m1].end(); ++j1) {
1153 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1154 <                   j2 != cellListCol_[m2].end(); ++j2) {
1155 <                              
1156 <                // Always do this if we're in different cells or if
1157 <                // we're in the same cell and the global index of the
1158 <                // j2 cutoff group is less than the j1 cutoff group
1150 >              if (m2v.x() >= nCells_.x()) {
1151 >                m2v.x() = 0;          
1152 >              } else if (m2v.x() < 0) {
1153 >                m2v.x() = nCells_.x() - 1;
1154 >              }
1155 >              
1156 >              if (m2v.y() >= nCells_.y()) {
1157 >                m2v.y() = 0;          
1158 >              } else if (m2v.y() < 0) {
1159 >                m2v.y() = nCells_.y() - 1;
1160 >              }
1161 >              
1162 >              if (m2v.z() >= nCells_.z()) {
1163 >                m2v.z() = 0;          
1164 >              } else if (m2v.z() < 0) {
1165 >                m2v.z() = nCells_.z() - 1;
1166 >              }
1167  
1168 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1168 >              int m2 = Vlinear (m2v, nCells_);
1169 >              
1170 > #ifdef IS_MPI
1171 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1172 >                   j1 != cellListRow_[m1].end(); ++j1) {
1173 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1174 >                     j2 != cellListCol_[m2].end(); ++j2) {
1175 >                  
1176 >                  // In parallel, we need to visit *all* pairs of row
1177 >                  // & column indicies and will divide labor in the
1178 >                  // force evaluation later.
1179                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1180                    snap_->wrapVector(dr);
1181 <                  if (dr.lengthSquare() < rl2) {
1181 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1182 >                  if (dr.lengthSquare() < cuts.third) {
1183                      neighborList.push_back(make_pair((*j1), (*j2)));
1184 <                  }
1184 >                  }                  
1185                  }
1186                }
782 –            }
1187   #else
1188 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1189 <                 j1 != cellList_[m1].end(); ++j1) {
1190 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1191 <                   j2 != cellList_[m2].end(); ++j2) {
1192 <                              
1193 <                // Always do this if we're in different cells or if
1194 <                // we're in the same cell and the global index of the
1195 <                // j2 cutoff group is less than the j1 cutoff group
1196 <
1197 <                if (m2 != m1 || (*j2) < (*j1)) {
1198 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1199 <                  snap_->wrapVector(dr);
1200 <                  if (dr.lengthSquare() < rl2) {
1201 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1188 >              
1189 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1190 >                   j1 != cellList_[m1].end(); ++j1) {
1191 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1192 >                     j2 != cellList_[m2].end(); ++j2) {
1193 >                  
1194 >                  // Always do this if we're in different cells or if
1195 >                  // we're in the same cell and the global index of the
1196 >                  // j2 cutoff group is less than the j1 cutoff group
1197 >                  
1198 >                  if (m2 != m1 || (*j2) < (*j1)) {
1199 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1200 >                    snap_->wrapVector(dr);
1201 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1202 >                    if (dr.lengthSquare() < cuts.third) {
1203 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1204 >                    }
1205                    }
1206                  }
1207                }
801 –            }
1208   #endif
1209 +            }
1210            }
1211          }
1212        }
1213 +    } else {
1214 +      // branch to do all cutoff group pairs
1215 + #ifdef IS_MPI
1216 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1217 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1218 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1219 +          snap_->wrapVector(dr);
1220 +          cuts = getGroupCutoffs( j1, j2 );
1221 +          if (dr.lengthSquare() < cuts.third) {
1222 +            neighborList.push_back(make_pair(j1, j2));
1223 +          }
1224 +        }
1225 +      }
1226 + #else
1227 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1228 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1229 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1230 +          snap_->wrapVector(dr);
1231 +          cuts = getGroupCutoffs( j1, j2 );
1232 +          if (dr.lengthSquare() < cuts.third) {
1233 +            neighborList.push_back(make_pair(j1, j2));
1234 +          }
1235 +        }
1236 +      }        
1237 + #endif
1238      }
1239 <
1239 >      
1240      // save the local cutoff group positions for the check that is
1241      // done on each loop:
1242      saved_CG_positions_.clear();
1243      for (int i = 0; i < nGroups_; i++)
1244        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1245 <
1245 >    
1246      return neighborList;
1247    }
1248   } //end namespace OpenMD

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