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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 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC

# Line 57 | Line 57 | namespace OpenMD {
57      storageLayout_ = sman_->getStorageLayout();
58      ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60 –    nGroups_ = snap_->getNumberOfCutoffGroups();
60  
61 +    nGroups_ = info_->getNLocalCutoffGroups();
62 +    cerr << "in dId, nGroups = " << nGroups_ << "\n";
63      // gather the information for atomtype IDs (atids):
64 <    identsLocal = info_->getIdentArray();
64 >    idents = info_->getIdentArray();
65      AtomLocalToGlobal = info_->getGlobalAtomIndices();
66      cgLocalToGlobal = info_->getGlobalGroupIndices();
67      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68 <    vector<RealType> massFactorsLocal = info_->getMassFactors();
68 >    massFactors = info_->getMassFactors();
69 >
70      PairList excludes = info_->getExcludedInteractions();
71      PairList oneTwo = info_->getOneTwoInteractions();
72      PairList oneThree = info_->getOneThreeInteractions();
# Line 104 | Line 106 | namespace OpenMD {
106      cgColData.resize(nGroupsInCol_);
107      cgColData.setStorageLayout(DataStorage::dslPosition);
108          
109 <    identsRow.reserve(nAtomsInRow_);
110 <    identsCol.reserve(nAtomsInCol_);
109 >    identsRow.resize(nAtomsInRow_);
110 >    identsCol.resize(nAtomsInCol_);
111      
112 <    AtomCommIntRow->gather(identsLocal, identsRow);
113 <    AtomCommIntColumn->gather(identsLocal, identsCol);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
115      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
# Line 116 | Line 118 | namespace OpenMD {
118      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120  
121 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
122 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
121 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
122 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
123  
124      groupListRow_.clear();
125 <    groupListRow_.reserve(nGroupsInRow_);
125 >    groupListRow_.resize(nGroupsInRow_);
126      for (int i = 0; i < nGroupsInRow_; i++) {
127        int gid = cgRowToGlobal[i];
128        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 131 | Line 133 | namespace OpenMD {
133      }
134  
135      groupListCol_.clear();
136 <    groupListCol_.reserve(nGroupsInCol_);
136 >    groupListCol_.resize(nGroupsInCol_);
137      for (int i = 0; i < nGroupsInCol_; i++) {
138        int gid = cgColToGlobal[i];
139        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 141 | Line 143 | namespace OpenMD {
143        }      
144      }
145  
146 <    skipsForRowAtom.clear();
147 <    skipsForRowAtom.reserve(nAtomsInRow_);
146 >    skipsForAtom.clear();
147 >    skipsForAtom.resize(nAtomsInRow_);
148 >    toposForAtom.clear();
149 >    toposForAtom.resize(nAtomsInRow_);
150 >    topoDist.clear();
151 >    topoDist.resize(nAtomsInRow_);
152      for (int i = 0; i < nAtomsInRow_; i++) {
153        int iglob = AtomRowToGlobal[i];
148 –      for (int j = 0; j < nAtomsInCol_; j++) {
149 –        int jglob = AtomColToGlobal[j];        
150 –        if (excludes.hasPair(iglob, jglob))
151 –          skipsForRowAtom[i].push_back(j);      
152 –      }      
153 –    }
154  
155 –    toposForRowAtom.clear();
156 –    toposForRowAtom.reserve(nAtomsInRow_);
157 –    for (int i = 0; i < nAtomsInRow_; i++) {
158 –      int iglob = AtomRowToGlobal[i];
159 –      int nTopos = 0;
155        for (int j = 0; j < nAtomsInCol_; j++) {
156 <        int jglob = AtomColToGlobal[j];        
156 >        int jglob = AtomColToGlobal[j];
157 >
158 >        if (excludes.hasPair(iglob, jglob))
159 >          skipsForAtom[i].push_back(j);      
160 >        
161          if (oneTwo.hasPair(iglob, jglob)) {
162 <          toposForRowAtom[i].push_back(j);
163 <          topoDistRow[i][nTopos] = 1;
164 <          nTopos++;
162 >          toposForAtom[i].push_back(j);
163 >          topoDist[i].push_back(1);
164 >        } else {
165 >          if (oneThree.hasPair(iglob, jglob)) {
166 >            toposForAtom[i].push_back(j);
167 >            topoDist[i].push_back(2);
168 >          } else {
169 >            if (oneFour.hasPair(iglob, jglob)) {
170 >              toposForAtom[i].push_back(j);
171 >              topoDist[i].push_back(3);
172 >            }
173 >          }
174          }
167 –        if (oneThree.hasPair(iglob, jglob)) {
168 –          toposForRowAtom[i].push_back(j);
169 –          topoDistRow[i][nTopos] = 2;
170 –          nTopos++;
171 –        }
172 –        if (oneFour.hasPair(iglob, jglob)) {
173 –          toposForRowAtom[i].push_back(j);
174 –          topoDistRow[i][nTopos] = 3;
175 –          nTopos++;
176 –        }
175        }      
176      }
177  
178   #endif
179  
180      groupList_.clear();
181 <    groupList_.reserve(nGroups_);
181 >    groupList_.resize(nGroups_);
182      for (int i = 0; i < nGroups_; i++) {
183        int gid = cgLocalToGlobal[i];
184        for (int j = 0; j < nLocal_; j++) {
185          int aid = AtomLocalToGlobal[j];
186 <        if (globalGroupMembership[aid] == gid)
186 >        if (globalGroupMembership[aid] == gid) {
187            groupList_[i].push_back(j);
188 +        }
189        }      
190      }
191  
192 <    skipsForLocalAtom.clear();
193 <    skipsForLocalAtom.reserve(nLocal_);
192 >    skipsForAtom.clear();
193 >    skipsForAtom.resize(nLocal_);
194 >    toposForAtom.clear();
195 >    toposForAtom.resize(nLocal_);
196 >    topoDist.clear();
197 >    topoDist.resize(nLocal_);
198  
199      for (int i = 0; i < nLocal_; i++) {
200        int iglob = AtomLocalToGlobal[i];
198 –      for (int j = 0; j < nLocal_; j++) {
199 –        int jglob = AtomLocalToGlobal[j];        
200 –        if (excludes.hasPair(iglob, jglob))
201 –          skipsForLocalAtom[i].push_back(j);      
202 –      }      
203 –    }
201  
205 –    toposForLocalAtom.clear();
206 –    toposForLocalAtom.reserve(nLocal_);
207 –    for (int i = 0; i < nLocal_; i++) {
208 –      int iglob = AtomLocalToGlobal[i];
209 –      int nTopos = 0;
202        for (int j = 0; j < nLocal_; j++) {
203 <        int jglob = AtomLocalToGlobal[j];        
203 >        int jglob = AtomLocalToGlobal[j];
204 >
205 >        if (excludes.hasPair(iglob, jglob))
206 >          skipsForAtom[i].push_back(j);              
207 >        
208          if (oneTwo.hasPair(iglob, jglob)) {
209 <          toposForLocalAtom[i].push_back(j);
210 <          topoDistLocal[i][nTopos] = 1;
211 <          nTopos++;
212 <        }
213 <        if (oneThree.hasPair(iglob, jglob)) {
214 <          toposForLocalAtom[i].push_back(j);
215 <          topoDistLocal[i][nTopos] = 2;
216 <          nTopos++;
217 <        }
218 <        if (oneFour.hasPair(iglob, jglob)) {
219 <          toposForLocalAtom[i].push_back(j);
220 <          topoDistLocal[i][nTopos] = 3;
225 <          nTopos++;
209 >          toposForAtom[i].push_back(j);
210 >          topoDist[i].push_back(1);
211 >        } else {
212 >          if (oneThree.hasPair(iglob, jglob)) {
213 >            toposForAtom[i].push_back(j);
214 >            topoDist[i].push_back(2);
215 >          } else {
216 >            if (oneFour.hasPair(iglob, jglob)) {
217 >              toposForAtom[i].push_back(j);
218 >              topoDist[i].push_back(3);
219 >            }
220 >          }
221          }
222        }      
223      }
224 +    
225 +    createGtypeCutoffMap();
226    }
227    
228 <  void ForceMatrixDecomposition::zeroWorkArrays() {
228 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
229  
230 <    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
231 <      longRangePot_[j] = 0.0;
230 >    RealType tol = 1e-6;
231 >    RealType rc;
232 >    int atid;
233 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
234 >    vector<RealType> atypeCutoff;
235 >    atypeCutoff.resize( atypes.size() );
236 >      
237 >    for (set<AtomType*>::iterator at = atypes.begin();
238 >         at != atypes.end(); ++at){
239 >      atid = (*at)->getIdent();
240 >
241 >      if (userChoseCutoff_)
242 >        atypeCutoff[atid] = userCutoff_;
243 >      else
244 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
245 >    }
246 >
247 >    vector<RealType> gTypeCutoffs;
248 >
249 >    // first we do a single loop over the cutoff groups to find the
250 >    // largest cutoff for any atypes present in this group.
251 > #ifdef IS_MPI
252 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
253 >    groupRowToGtype.resize(nGroupsInRow_);
254 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
255 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
256 >      for (vector<int>::iterator ia = atomListRow.begin();
257 >           ia != atomListRow.end(); ++ia) {            
258 >        int atom1 = (*ia);
259 >        atid = identsRow[atom1];
260 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
261 >          groupCutoffRow[cg1] = atypeCutoff[atid];
262 >        }
263 >      }
264 >
265 >      bool gTypeFound = false;
266 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
267 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
268 >          groupRowToGtype[cg1] = gt;
269 >          gTypeFound = true;
270 >        }
271 >      }
272 >      if (!gTypeFound) {
273 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
274 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
275 >      }
276 >      
277 >    }
278 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
279 >    groupColToGtype.resize(nGroupsInCol_);
280 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
281 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
282 >      for (vector<int>::iterator jb = atomListCol.begin();
283 >           jb != atomListCol.end(); ++jb) {            
284 >        int atom2 = (*jb);
285 >        atid = identsCol[atom2];
286 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
287 >          groupCutoffCol[cg2] = atypeCutoff[atid];
288 >        }
289 >      }
290 >      bool gTypeFound = false;
291 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
292 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
293 >          groupColToGtype[cg2] = gt;
294 >          gTypeFound = true;
295 >        }
296 >      }
297 >      if (!gTypeFound) {
298 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
299 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
300 >      }
301 >    }
302 > #else
303 >
304 >    vector<RealType> groupCutoff(nGroups_, 0.0);
305 >    groupToGtype.resize(nGroups_);
306 >
307 >    cerr << "nGroups = " << nGroups_ << "\n";
308 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
309 >
310 >      groupCutoff[cg1] = 0.0;
311 >      vector<int> atomList = getAtomsInGroupRow(cg1);
312 >
313 >      for (vector<int>::iterator ia = atomList.begin();
314 >           ia != atomList.end(); ++ia) {            
315 >        int atom1 = (*ia);
316 >        atid = idents[atom1];
317 >        if (atypeCutoff[atid] > groupCutoff[cg1]) {
318 >          groupCutoff[cg1] = atypeCutoff[atid];
319 >        }
320 >      }
321 >
322 >      bool gTypeFound = false;
323 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
324 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
325 >          groupToGtype[cg1] = gt;
326 >          gTypeFound = true;
327 >        }
328 >      }
329 >      if (!gTypeFound) {
330 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
331 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
332 >      }      
333 >    }
334 > #endif
335 >
336 >    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
337 >    // Now we find the maximum group cutoff value present in the simulation
338 >
339 >    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
340 >
341 > #ifdef IS_MPI
342 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
343 > #endif
344 >    
345 >    RealType tradRcut = groupMax;
346 >
347 >    for (int i = 0; i < gTypeCutoffs.size();  i++) {
348 >      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
349 >        RealType thisRcut;
350 >        switch(cutoffPolicy_) {
351 >        case TRADITIONAL:
352 >          thisRcut = tradRcut;
353 >          break;
354 >        case MIX:
355 >          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
356 >          break;
357 >        case MAX:
358 >          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
359 >          break;
360 >        default:
361 >          sprintf(painCave.errMsg,
362 >                  "ForceMatrixDecomposition::createGtypeCutoffMap "
363 >                  "hit an unknown cutoff policy!\n");
364 >          painCave.severity = OPENMD_ERROR;
365 >          painCave.isFatal = 1;
366 >          simError();
367 >          break;
368 >        }
369 >
370 >        pair<int,int> key = make_pair(i,j);
371 >        gTypeCutoffMap[key].first = thisRcut;
372 >
373 >        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
374 >
375 >        gTypeCutoffMap[key].second = thisRcut*thisRcut;
376 >        
377 >        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
378 >
379 >        // sanity check
380 >        
381 >        if (userChoseCutoff_) {
382 >          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
383 >            sprintf(painCave.errMsg,
384 >                    "ForceMatrixDecomposition::createGtypeCutoffMap "
385 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
386 >            painCave.severity = OPENMD_ERROR;
387 >            painCave.isFatal = 1;
388 >            simError();            
389 >          }
390 >        }
391 >      }
392 >    }
393 >  }
394 >
395 >
396 >  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
397 >    int i, j;  
398 > #ifdef IS_MPI
399 >    i = groupRowToGtype[cg1];
400 >    j = groupColToGtype[cg2];
401 > #else
402 >    i = groupToGtype[cg1];
403 >    j = groupToGtype[cg2];
404 > #endif    
405 >    return gTypeCutoffMap[make_pair(i,j)];
406 >  }
407 >
408 >  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
409 >    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
410 >      if (toposForAtom[atom1][j] == atom2)
411 >        return topoDist[atom1][j];
412      }
413 +    return 0;
414 +  }
415 +
416 +  void ForceMatrixDecomposition::zeroWorkArrays() {
417 +    pairwisePot = 0.0;
418 +    embeddingPot = 0.0;
419  
420   #ifdef IS_MPI
421      if (storageLayout_ & DataStorage::dslForce) {
# Line 249 | Line 432 | namespace OpenMD {
432           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
433  
434      fill(pot_col.begin(), pot_col.end(),
435 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
253 <    
254 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
435 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
436  
437      if (storageLayout_ & DataStorage::dslParticlePot) {    
438        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
# Line 425 | Line 606 | namespace OpenMD {
606      AtomCommPotRow->scatter(pot_row, pot_temp);
607  
608      for (int ii = 0;  ii < pot_temp.size(); ii++ )
609 <      pot_local += pot_temp[ii];
609 >      pairwisePot += pot_temp[ii];
610      
611      fill(pot_temp.begin(), pot_temp.end(),
612           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
# Line 433 | Line 614 | namespace OpenMD {
614      AtomCommPotColumn->scatter(pot_col, pot_temp);    
615      
616      for (int ii = 0;  ii < pot_temp.size(); ii++ )
617 <      pot_local += pot_temp[ii];
437 <    
617 >      pairwisePot += pot_temp[ii];    
618   #endif
619 +
620    }
621  
622    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 510 | Line 691 | namespace OpenMD {
691   #ifdef IS_MPI
692      return massFactorsRow[atom1];
693   #else
694 <    return massFactorsLocal[atom1];
694 >    cerr << "mfs = " << massFactors.size() << " atom1 = " << atom1 << "\n";
695 >    return massFactors[atom1];
696   #endif
697    }
698  
# Line 518 | Line 700 | namespace OpenMD {
700   #ifdef IS_MPI
701      return massFactorsCol[atom2];
702   #else
703 <    return massFactorsLocal[atom2];
703 >    return massFactors[atom2];
704   #endif
705  
706    }
# Line 536 | Line 718 | namespace OpenMD {
718      return d;    
719    }
720  
721 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
722 < #ifdef IS_MPI
541 <    return skipsForRowAtom[atom1];
542 < #else
543 <    return skipsForLocalAtom[atom1];
544 < #endif
721 >  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
722 >    return skipsForAtom[atom1];
723    }
724  
725    /**
# Line 574 | Line 752 | namespace OpenMD {
752      unique_id_2 = atom2;
753   #endif
754      
755 < #ifdef IS_MPI
756 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579 <         i != skipsForRowAtom[atom1].end(); ++i) {
755 >    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
756 >         i != skipsForAtom[atom1].end(); ++i) {
757        if ( (*i) == unique_id_2 ) return true;
581 –    }    
582 – #else
583 –    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
584 –         i != skipsForLocalAtom[atom1].end(); ++i) {
585 –      if ( (*i) == unique_id_2 ) return true;
586 –    }    
587 – #endif
588 –  }
589 –
590 –  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
591 –    
592 – #ifdef IS_MPI
593 –    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
594 –      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
758      }
596 – #else
597 –    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
598 –      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
599 –    }
600 – #endif
759  
760 <    // zero is default for unconnected (i.e. normal) pair interactions
603 <    return 0;
760 >    return false;
761    }
762  
763 +
764    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
765   #ifdef IS_MPI
766      atomRowData.force[atom1] += fg;
# Line 620 | Line 778 | namespace OpenMD {
778    }
779  
780      // filling interaction blocks with pointers
781 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
782 <    InteractionData idat;
625 <
781 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
782 >                                                     int atom1, int atom2) {    
783   #ifdef IS_MPI
784      
785      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
786                               ff_->getAtomType(identsCol[atom2]) );
630 –
787      
788      if (storageLayout_ & DataStorage::dslAmat) {
789        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 666 | Line 822 | namespace OpenMD {
822  
823   #else
824  
825 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
826 <                             ff_->getAtomType(identsLocal[atom2]) );
825 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
826 >                             ff_->getAtomType(idents[atom2]) );
827  
828      if (storageLayout_ & DataStorage::dslAmat) {
829        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 684 | Line 840 | namespace OpenMD {
840        idat.t2 = &(snap_->atomData.torque[atom2]);
841      }
842  
843 <    if (storageLayout_ & DataStorage::dslDensity) {
843 >    if (storageLayout_ & DataStorage::dslDensity) {    
844        idat.rho1 = &(snap_->atomData.density[atom1]);
845        idat.rho2 = &(snap_->atomData.density[atom2]);
846      }
# Line 705 | Line 861 | namespace OpenMD {
861      }
862  
863   #endif
708 –    return idat;
864    }
865  
866    
867 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
867 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
868   #ifdef IS_MPI
869      pot_row[atom1] += 0.5 *  *(idat.pot);
870      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 717 | Line 872 | namespace OpenMD {
872      atomRowData.force[atom1] += *(idat.f1);
873      atomColData.force[atom2] -= *(idat.f1);
874   #else
875 <    longRangePot_ += *(idat.pot);
876 <    
875 >    pairwisePot += *(idat.pot);
876 >
877      snap_->atomData.force[atom1] += *(idat.f1);
878      snap_->atomData.force[atom2] -= *(idat.f1);
879   #endif
# Line 726 | Line 881 | namespace OpenMD {
881    }
882  
883  
884 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
885 <
731 <    InteractionData idat;
884 >  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
885 >                                              int atom1, int atom2) {
886   #ifdef IS_MPI
887      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
888                               ff_->getAtomType(identsCol[atom2]) );
# Line 737 | Line 891 | namespace OpenMD {
891        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
892        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
893      }
894 +
895      if (storageLayout_ & DataStorage::dslTorque) {
896        idat.t1 = &(atomRowData.torque[atom1]);
897        idat.t2 = &(atomColData.torque[atom2]);
898      }
899 +
900 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
901 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
902 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
903 +    }
904   #else
905 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
906 <                             ff_->getAtomType(identsLocal[atom2]) );
905 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
906 >                             ff_->getAtomType(idents[atom2]) );
907  
908      if (storageLayout_ & DataStorage::dslElectroFrame) {
909        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
910        idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
911      }
912 +
913      if (storageLayout_ & DataStorage::dslTorque) {
914        idat.t1 = &(snap_->atomData.torque[atom1]);
915        idat.t2 = &(snap_->atomData.torque[atom2]);
916      }
917 +
918 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
919 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
920 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
921 +    }
922   #endif    
923 +  }
924 +
925 +
926 +  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
927 + #ifdef IS_MPI
928 +    pot_row[atom1] += 0.5 *  *(idat.pot);
929 +    pot_col[atom2] += 0.5 *  *(idat.pot);
930 + #else
931 +    pairwisePot += *(idat.pot);  
932 + #endif
933 +
934    }
935  
936 +
937    /*
938     * buildNeighborList
939     *
# Line 765 | Line 943 | namespace OpenMD {
943    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
944        
945      vector<pair<int, int> > neighborList;
946 +    groupCutoffs cuts;
947   #ifdef IS_MPI
948      cellListRow_.clear();
949      cellListCol_.clear();
# Line 772 | Line 951 | namespace OpenMD {
951      cellList_.clear();
952   #endif
953  
954 <    // dangerous to not do error checking.
776 <    RealType rCut_;
777 <
778 <    RealType rList_ = (rCut_ + skinThickness_);
954 >    RealType rList_ = (largestRcut_ + skinThickness_);
955      RealType rl2 = rList_ * rList_;
956      Snapshot* snap_ = sman_->getCurrentSnapshot();
957      Mat3x3d Hmat = snap_->getHmat();
# Line 791 | Line 967 | namespace OpenMD {
967      Vector3d rs, scaled, dr;
968      Vector3i whichCell;
969      int cellIndex;
970 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
971  
972   #ifdef IS_MPI
973 +    cellListRow_.resize(nCtot);
974 +    cellListCol_.resize(nCtot);
975 + #else
976 +    cellList_.resize(nCtot);
977 + #endif
978 +
979 + #ifdef IS_MPI
980      for (int i = 0; i < nGroupsInRow_; i++) {
981        rs = cgRowData.position[i];
982 +
983        // scaled positions relative to the box vectors
984        scaled = invHmat * rs;
985 +
986        // wrap the vector back into the unit box by subtracting integer box
987        // numbers
988 <      for (int j = 0; j < 3; j++)
988 >      for (int j = 0; j < 3; j++) {
989          scaled[j] -= roundMe(scaled[j]);
990 +        scaled[j] += 0.5;
991 +      }
992      
993        // find xyz-indices of cell that cutoffGroup is in.
994        whichCell.x() = nCells_.x() * scaled.x();
# Line 809 | Line 997 | namespace OpenMD {
997  
998        // find single index of this cell:
999        cellIndex = Vlinear(whichCell, nCells_);
1000 +
1001        // add this cutoff group to the list of groups in this cell;
1002        cellListRow_[cellIndex].push_back(i);
1003      }
1004  
1005      for (int i = 0; i < nGroupsInCol_; i++) {
1006        rs = cgColData.position[i];
1007 +
1008        // scaled positions relative to the box vectors
1009        scaled = invHmat * rs;
1010 +
1011        // wrap the vector back into the unit box by subtracting integer box
1012        // numbers
1013 <      for (int j = 0; j < 3; j++)
1013 >      for (int j = 0; j < 3; j++) {
1014          scaled[j] -= roundMe(scaled[j]);
1015 +        scaled[j] += 0.5;
1016 +      }
1017  
1018        // find xyz-indices of cell that cutoffGroup is in.
1019        whichCell.x() = nCells_.x() * scaled.x();
# Line 829 | Line 1022 | namespace OpenMD {
1022  
1023        // find single index of this cell:
1024        cellIndex = Vlinear(whichCell, nCells_);
1025 +
1026        // add this cutoff group to the list of groups in this cell;
1027        cellListCol_[cellIndex].push_back(i);
1028      }
1029   #else
1030      for (int i = 0; i < nGroups_; i++) {
1031        rs = snap_->cgData.position[i];
1032 +
1033        // scaled positions relative to the box vectors
1034        scaled = invHmat * rs;
1035 +
1036        // wrap the vector back into the unit box by subtracting integer box
1037        // numbers
1038 <      for (int j = 0; j < 3; j++)
1038 >      for (int j = 0; j < 3; j++) {
1039          scaled[j] -= roundMe(scaled[j]);
1040 +        scaled[j] += 0.5;
1041 +      }
1042  
1043        // find xyz-indices of cell that cutoffGroup is in.
1044        whichCell.x() = nCells_.x() * scaled.x();
# Line 848 | Line 1046 | namespace OpenMD {
1046        whichCell.z() = nCells_.z() * scaled.z();
1047  
1048        // find single index of this cell:
1049 <      cellIndex = Vlinear(whichCell, nCells_);
1049 >      cellIndex = Vlinear(whichCell, nCells_);      
1050 >
1051        // add this cutoff group to the list of groups in this cell;
1052        cellList_[cellIndex].push_back(i);
1053      }
# Line 898 | Line 1097 | namespace OpenMD {
1097                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1098                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1099                    snap_->wrapVector(dr);
1100 <                  if (dr.lengthSquare() < rl2) {
1100 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1101 >                  if (dr.lengthSquare() < cuts.third) {
1102                      neighborList.push_back(make_pair((*j1), (*j2)));
1103                    }
1104                  }
1105                }
1106              }
1107   #else
1108 +
1109              for (vector<int>::iterator j1 = cellList_[m1].begin();
1110                   j1 != cellList_[m1].end(); ++j1) {
1111                for (vector<int>::iterator j2 = cellList_[m2].begin();
1112                     j2 != cellList_[m2].end(); ++j2) {
1113 <                              
1113 >
1114                  // Always do this if we're in different cells or if
1115                  // we're in the same cell and the global index of the
1116                  // j2 cutoff group is less than the j1 cutoff group
# Line 917 | Line 1118 | namespace OpenMD {
1118                  if (m2 != m1 || (*j2) < (*j1)) {
1119                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1120                    snap_->wrapVector(dr);
1121 <                  if (dr.lengthSquare() < rl2) {
1121 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1122 >                  if (dr.lengthSquare() < cuts.third) {
1123                      neighborList.push_back(make_pair((*j1), (*j2)));
1124                    }
1125                  }
# Line 928 | Line 1130 | namespace OpenMD {
1130          }
1131        }
1132      }
1133 <
1133 >    
1134      // save the local cutoff group positions for the check that is
1135      // done on each loop:
1136      saved_CG_positions_.clear();
1137      for (int i = 0; i < nGroups_; i++)
1138        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1139 <
1139 >  
1140      return neighborList;
1141    }
1142   } //end namespace OpenMD

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