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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 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC

# Line 55 | Line 55 | namespace OpenMD {
55    void ForceMatrixDecomposition::distributeInitialData() {
56      snap_ = sman_->getCurrentSnapshot();
57      storageLayout_ = sman_->getStorageLayout();
58 +    ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
59 –    nGroups_ = snap_->getNumberOfCutoffGroups();
60  
61 +    nGroups_ = info_->getNLocalCutoffGroups();
62 +    cerr << "in dId, nGroups = " << nGroups_ << "\n";
63      // gather the information for atomtype IDs (atids):
64 <    vector<int> 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      PairList excludes = info_->getExcludedInteractions();
70      PairList oneTwo = info_->getOneTwoInteractions();
71      PairList oneThree = info_->getOneThreeInteractions();
72      PairList oneFour = info_->getOneFourInteractions();
71 –    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
73  
74   #ifdef IS_MPI
75  
# Line 76 | Line 77 | namespace OpenMD {
77      AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
78      AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
79      AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
80 +    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
81  
82      AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
83      AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
84      AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
85      AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
86 +    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
87  
88      cgCommIntRow = new Communicator<Row,int>(nGroups_);
89      cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
# Line 101 | Line 104 | namespace OpenMD {
104      cgRowData.setStorageLayout(DataStorage::dslPosition);
105      cgColData.resize(nGroupsInCol_);
106      cgColData.setStorageLayout(DataStorage::dslPosition);
107 +        
108 +    identsRow.resize(nAtomsInRow_);
109 +    identsCol.resize(nAtomsInCol_);
110      
111 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
112 <                                      vector<RealType> (nAtomsInRow_, 0.0));
107 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
108 <                                      vector<RealType> (nAtomsInCol_, 0.0));
111 >    AtomCommIntRow->gather(idents, identsRow);
112 >    AtomCommIntColumn->gather(idents, identsCol);
113      
110 –    identsRow.reserve(nAtomsInRow_);
111 –    identsCol.reserve(nAtomsInCol_);
112 –    
113 –    AtomCommIntRow->gather(identsLocal, identsRow);
114 –    AtomCommIntColumn->gather(identsLocal, identsCol);
115 –    
114      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
115      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
116      
117      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
118      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
119  
120 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
121 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
120 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
121 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
122  
123      groupListRow_.clear();
124 <    groupListRow_.reserve(nGroupsInRow_);
124 >    groupListRow_.resize(nGroupsInRow_);
125      for (int i = 0; i < nGroupsInRow_; i++) {
126        int gid = cgRowToGlobal[i];
127        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 134 | Line 132 | namespace OpenMD {
132      }
133  
134      groupListCol_.clear();
135 <    groupListCol_.reserve(nGroupsInCol_);
135 >    groupListCol_.resize(nGroupsInCol_);
136      for (int i = 0; i < nGroupsInCol_; i++) {
137        int gid = cgColToGlobal[i];
138        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 144 | Line 142 | namespace OpenMD {
142        }      
143      }
144  
145 <    skipsForRowAtom.clear();
146 <    skipsForRowAtom.reserve(nAtomsInRow_);
145 >    skipsForAtom.clear();
146 >    skipsForAtom.resize(nAtomsInRow_);
147 >    toposForAtom.clear();
148 >    toposForAtom.resize(nAtomsInRow_);
149 >    topoDist.clear();
150 >    topoDist.resize(nAtomsInRow_);
151      for (int i = 0; i < nAtomsInRow_; i++) {
152 <      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 <    }
152 >      int iglob = AtomRowToGlobal[i];
153  
158 –    toposForRowAtom.clear();
159 –    toposForRowAtom.reserve(nAtomsInRow_);
160 –    for (int i = 0; i < nAtomsInRow_; i++) {
161 –      int iglob = AtomColToGlobal[i];
162 –      int nTopos = 0;
154        for (int j = 0; j < nAtomsInCol_; j++) {
155 <        int jglob = AtomRowToGlobal[j];        
155 >        int jglob = AtomColToGlobal[j];
156 >
157 >        if (excludes.hasPair(iglob, jglob))
158 >          skipsForAtom[i].push_back(j);      
159 >        
160          if (oneTwo.hasPair(iglob, jglob)) {
161 <          toposForRowAtom[i].push_back(j);
162 <          topoDistRow[i][nTopos] = 1;
163 <          nTopos++;
161 >          toposForAtom[i].push_back(j);
162 >          topoDist[i].push_back(1);
163 >        } else {
164 >          if (oneThree.hasPair(iglob, jglob)) {
165 >            toposForAtom[i].push_back(j);
166 >            topoDist[i].push_back(2);
167 >          } else {
168 >            if (oneFour.hasPair(iglob, jglob)) {
169 >              toposForAtom[i].push_back(j);
170 >              topoDist[i].push_back(3);
171 >            }
172 >          }
173          }
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 –        }
174        }      
175      }
176  
177   #endif
178  
179      groupList_.clear();
180 <    groupList_.reserve(nGroups_);
180 >    groupList_.resize(nGroups_);
181      for (int i = 0; i < nGroups_; i++) {
182        int gid = cgLocalToGlobal[i];
183        for (int j = 0; j < nLocal_; j++) {
184          int aid = AtomLocalToGlobal[j];
185 <        if (globalGroupMembership[aid] == gid)
185 >        if (globalGroupMembership[aid] == gid) {
186            groupList_[i].push_back(j);
187 +        }
188        }      
189      }
190  
191 <    skipsForLocalAtom.clear();
192 <    skipsForLocalAtom.reserve(nLocal_);
191 >    skipsForAtom.clear();
192 >    skipsForAtom.resize(nLocal_);
193 >    toposForAtom.clear();
194 >    toposForAtom.resize(nLocal_);
195 >    topoDist.clear();
196 >    topoDist.resize(nLocal_);
197  
198      for (int i = 0; i < nLocal_; i++) {
199        int iglob = AtomLocalToGlobal[i];
200 +
201        for (int j = 0; j < nLocal_; j++) {
202 <        int jglob = AtomLocalToGlobal[j];        
202 >        int jglob = AtomLocalToGlobal[j];
203 >
204          if (excludes.hasPair(iglob, jglob))
205 <          skipsForLocalAtom[i].push_back(j);      
205 >          skipsForAtom[i].push_back(j);              
206 >        
207 >        if (oneTwo.hasPair(iglob, jglob)) {
208 >          toposForAtom[i].push_back(j);
209 >          topoDist[i].push_back(1);
210 >        } else {
211 >          if (oneThree.hasPair(iglob, jglob)) {
212 >            toposForAtom[i].push_back(j);
213 >            topoDist[i].push_back(2);
214 >          } else {
215 >            if (oneFour.hasPair(iglob, jglob)) {
216 >              toposForAtom[i].push_back(j);
217 >              topoDist[i].push_back(3);
218 >            }
219 >          }
220 >        }
221        }      
222      }
223 +    
224 +    createGtypeCutoffMap();
225 +  }
226 +  
227 +  void ForceMatrixDecomposition::createGtypeCutoffMap() {
228  
229 <    toposForLocalAtom.clear();
230 <    toposForLocalAtom.reserve(nLocal_);
231 <    for (int i = 0; i < nLocal_; i++) {
232 <      int iglob = AtomLocalToGlobal[i];
233 <      int nTopos = 0;
234 <      for (int j = 0; j < nLocal_; j++) {
235 <        int jglob = AtomLocalToGlobal[j];        
236 <        if (oneTwo.hasPair(iglob, jglob)) {
237 <          toposForLocalAtom[i].push_back(j);
238 <          topoDistLocal[i][nTopos] = 1;
239 <          nTopos++;
240 <        }
241 <        if (oneThree.hasPair(iglob, jglob)) {
242 <          toposForLocalAtom[i].push_back(j);
243 <          topoDistLocal[i][nTopos] = 2;
244 <          nTopos++;
245 <        }
246 <        if (oneFour.hasPair(iglob, jglob)) {
247 <          toposForLocalAtom[i].push_back(j);
248 <          topoDistLocal[i][nTopos] = 3;
249 <          nTopos++;
229 >    RealType tol = 1e-6;
230 >    RealType rc;
231 >    int atid;
232 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
233 >    vector<RealType> atypeCutoff;
234 >    atypeCutoff.resize( atypes.size() );
235 >      
236 >    for (set<AtomType*>::iterator at = atypes.begin();
237 >         at != atypes.end(); ++at){
238 >      atid = (*at)->getIdent();
239 >
240 >      if (userChoseCutoff_)
241 >        atypeCutoff[atid] = userCutoff_;
242 >      else
243 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
244 >    }
245 >
246 >    vector<RealType> gTypeCutoffs;
247 >
248 >    // first we do a single loop over the cutoff groups to find the
249 >    // largest cutoff for any atypes present in this group.
250 > #ifdef IS_MPI
251 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
252 >    groupRowToGtype.resize(nGroupsInRow_);
253 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
254 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
255 >      for (vector<int>::iterator ia = atomListRow.begin();
256 >           ia != atomListRow.end(); ++ia) {            
257 >        int atom1 = (*ia);
258 >        atid = identsRow[atom1];
259 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
260 >          groupCutoffRow[cg1] = atypeCutoff[atid];
261          }
262 +      }
263 +
264 +      bool gTypeFound = false;
265 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
266 +        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
267 +          groupRowToGtype[cg1] = gt;
268 +          gTypeFound = true;
269 +        }
270 +      }
271 +      if (!gTypeFound) {
272 +        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
273 +        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
274 +      }
275 +      
276 +    }
277 +    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
278 +    groupColToGtype.resize(nGroupsInCol_);
279 +    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
280 +      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
281 +      for (vector<int>::iterator jb = atomListCol.begin();
282 +           jb != atomListCol.end(); ++jb) {            
283 +        int atom2 = (*jb);
284 +        atid = identsCol[atom2];
285 +        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
286 +          groupCutoffCol[cg2] = atypeCutoff[atid];
287 +        }
288 +      }
289 +      bool gTypeFound = false;
290 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
291 +        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
292 +          groupColToGtype[cg2] = gt;
293 +          gTypeFound = true;
294 +        }
295 +      }
296 +      if (!gTypeFound) {
297 +        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
298 +        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
299 +      }
300 +    }
301 + #else
302 +
303 +    vector<RealType> groupCutoff(nGroups_, 0.0);
304 +    groupToGtype.resize(nGroups_);
305 +
306 +    cerr << "nGroups = " << nGroups_ << "\n";
307 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
308 +
309 +      groupCutoff[cg1] = 0.0;
310 +      vector<int> atomList = getAtomsInGroupRow(cg1);
311 +
312 +      for (vector<int>::iterator ia = atomList.begin();
313 +           ia != atomList.end(); ++ia) {            
314 +        int atom1 = (*ia);
315 +        atid = idents[atom1];
316 +        if (atypeCutoff[atid] > groupCutoff[cg1]) {
317 +          groupCutoff[cg1] = atypeCutoff[atid];
318 +        }
319 +      }
320 +
321 +      bool gTypeFound = false;
322 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
323 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
324 +          groupToGtype[cg1] = gt;
325 +          gTypeFound = true;
326 +        }
327 +      }
328 +      if (!gTypeFound) {
329 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
330 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
331        }      
332      }
333 + #endif
334 +
335 +    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
336 +    // Now we find the maximum group cutoff value present in the simulation
337 +
338 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
339 +
340 + #ifdef IS_MPI
341 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
342 + #endif
343 +    
344 +    RealType tradRcut = groupMax;
345 +
346 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
347 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
348 +        RealType thisRcut;
349 +        switch(cutoffPolicy_) {
350 +        case TRADITIONAL:
351 +          thisRcut = tradRcut;
352 +          break;
353 +        case MIX:
354 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
355 +          break;
356 +        case MAX:
357 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
358 +          break;
359 +        default:
360 +          sprintf(painCave.errMsg,
361 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
362 +                  "hit an unknown cutoff policy!\n");
363 +          painCave.severity = OPENMD_ERROR;
364 +          painCave.isFatal = 1;
365 +          simError();
366 +          break;
367 +        }
368 +
369 +        pair<int,int> key = make_pair(i,j);
370 +        gTypeCutoffMap[key].first = thisRcut;
371 +
372 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
373 +
374 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
375 +        
376 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
377 +
378 +        // sanity check
379 +        
380 +        if (userChoseCutoff_) {
381 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
382 +            sprintf(painCave.errMsg,
383 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
384 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
385 +            painCave.severity = OPENMD_ERROR;
386 +            painCave.isFatal = 1;
387 +            simError();            
388 +          }
389 +        }
390 +      }
391 +    }
392    }
393 <  
393 >
394 >
395 >  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
396 >    int i, j;  
397 > #ifdef IS_MPI
398 >    i = groupRowToGtype[cg1];
399 >    j = groupColToGtype[cg2];
400 > #else
401 >    i = groupToGtype[cg1];
402 >    j = groupToGtype[cg2];
403 > #endif    
404 >    return gTypeCutoffMap[make_pair(i,j)];
405 >  }
406 >
407 >  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
408 >    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
409 >      if (toposForAtom[atom1][j] == atom2)
410 >        return topoDist[atom1][j];
411 >    }
412 >    return 0;
413 >  }
414 >
415 >  void ForceMatrixDecomposition::zeroWorkArrays() {
416 >    pairwisePot = 0.0;
417 >    embeddingPot = 0.0;
418 >
419 > #ifdef IS_MPI
420 >    if (storageLayout_ & DataStorage::dslForce) {
421 >      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
422 >      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
423 >    }
424 >
425 >    if (storageLayout_ & DataStorage::dslTorque) {
426 >      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
427 >      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
428 >    }
429 >    
430 >    fill(pot_row.begin(), pot_row.end(),
431 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
432 >
433 >    fill(pot_col.begin(), pot_col.end(),
434 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
435 >
436 >    if (storageLayout_ & DataStorage::dslParticlePot) {    
437 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
438 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
439 >    }
440 >
441 >    if (storageLayout_ & DataStorage::dslDensity) {      
442 >      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
443 >      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
444 >    }
445 >
446 >    if (storageLayout_ & DataStorage::dslFunctional) {  
447 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
448 >      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
449 >    }
450 >
451 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
452 >      fill(atomRowData.functionalDerivative.begin(),
453 >           atomRowData.functionalDerivative.end(), 0.0);
454 >      fill(atomColData.functionalDerivative.begin(),
455 >           atomColData.functionalDerivative.end(), 0.0);
456 >    }
457 >
458 > #else
459 >    
460 >    if (storageLayout_ & DataStorage::dslParticlePot) {      
461 >      fill(snap_->atomData.particlePot.begin(),
462 >           snap_->atomData.particlePot.end(), 0.0);
463 >    }
464 >    
465 >    if (storageLayout_ & DataStorage::dslDensity) {      
466 >      fill(snap_->atomData.density.begin(),
467 >           snap_->atomData.density.end(), 0.0);
468 >    }
469 >    if (storageLayout_ & DataStorage::dslFunctional) {
470 >      fill(snap_->atomData.functional.begin(),
471 >           snap_->atomData.functional.end(), 0.0);
472 >    }
473 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
474 >      fill(snap_->atomData.functionalDerivative.begin(),
475 >           snap_->atomData.functionalDerivative.end(), 0.0);
476 >    }
477 > #endif
478 >    
479 >  }
480 >
481 >
482    void ForceMatrixDecomposition::distributeData()  {
483      snap_ = sman_->getCurrentSnapshot();
484      storageLayout_ = sman_->getStorageLayout();
# Line 266 | Line 514 | namespace OpenMD {
514   #endif      
515    }
516    
517 +  /* collects information obtained during the pre-pair loop onto local
518 +   * data structures.
519 +   */
520    void ForceMatrixDecomposition::collectIntermediateData() {
521      snap_ = sman_->getCurrentSnapshot();
522      storageLayout_ = sman_->getStorageLayout();
# Line 277 | Line 528 | namespace OpenMD {
528                                 snap_->atomData.density);
529        
530        int n = snap_->atomData.density.size();
531 <      std::vector<RealType> rho_tmp(n, 0.0);
531 >      vector<RealType> rho_tmp(n, 0.0);
532        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
533        for (int i = 0; i < n; i++)
534          snap_->atomData.density[i] += rho_tmp[i];
535      }
536   #endif
537    }
538 <  
538 >
539 >  /*
540 >   * redistributes information obtained during the pre-pair loop out to
541 >   * row and column-indexed data structures
542 >   */
543    void ForceMatrixDecomposition::distributeIntermediateData() {
544      snap_ = sman_->getCurrentSnapshot();
545      storageLayout_ = sman_->getStorageLayout();
# Line 342 | Line 597 | namespace OpenMD {
597      
598      nLocal_ = snap_->getNumberOfAtoms();
599  
600 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
601 <                                       vector<RealType> (nLocal_, 0.0));
600 >    vector<potVec> pot_temp(nLocal_,
601 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
602 >
603 >    // scatter/gather pot_row into the members of my column
604 >          
605 >    AtomCommPotRow->scatter(pot_row, pot_temp);
606 >
607 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
608 >      pairwisePot += pot_temp[ii];
609      
610 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
611 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
612 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
613 <        pot_local[i] += pot_temp[i][ii];
614 <      }
615 <    }
610 >    fill(pot_temp.begin(), pot_temp.end(),
611 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
612 >      
613 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
614 >    
615 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
616 >      pairwisePot += pot_temp[ii];    
617   #endif
618 +
619    }
620  
621    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 426 | Line 690 | namespace OpenMD {
690   #ifdef IS_MPI
691      return massFactorsRow[atom1];
692   #else
693 <    return massFactorsLocal[atom1];
693 >    return massFactors[atom1];
694   #endif
695    }
696  
# Line 434 | Line 698 | namespace OpenMD {
698   #ifdef IS_MPI
699      return massFactorsCol[atom2];
700   #else
701 <    return massFactorsLocal[atom2];
701 >    return massFactors[atom2];
702   #endif
703  
704    }
# Line 452 | Line 716 | namespace OpenMD {
716      return d;    
717    }
718  
719 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
720 < #ifdef IS_MPI
457 <    return skipsForRowAtom[atom1];
458 < #else
459 <    return skipsForLocalAtom[atom1];
460 < #endif
719 >  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
720 >    return skipsForAtom[atom1];
721    }
722  
723    /**
724 <   * there are a number of reasons to skip a pair or a particle mostly
725 <   * we do this to exclude atoms who are involved in short range
726 <   * interactions (bonds, bends, torsions), but we also need to
727 <   * exclude some overcounted interactions that result from the
728 <   * parallel decomposition.
724 >   * There are a number of reasons to skip a pair or a
725 >   * particle. Mostly we do this to exclude atoms who are involved in
726 >   * short range interactions (bonds, bends, torsions), but we also
727 >   * need to exclude some overcounted interactions that result from
728 >   * the parallel decomposition.
729     */
730    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
731      int unique_id_1, unique_id_2;
# Line 490 | Line 750 | namespace OpenMD {
750      unique_id_2 = atom2;
751   #endif
752      
753 < #ifdef IS_MPI
754 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
495 <         i != skipsForRowAtom[atom1].end(); ++i) {
753 >    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
754 >         i != skipsForAtom[atom1].end(); ++i) {
755        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];
756      }
757 < #else
758 <    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
514 <      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
515 <    }
516 < #endif
517 <
518 <    // zero is default for unconnected (i.e. normal) pair interactions
519 <    return 0;
757 >
758 >    return false;
759    }
760  
761 +
762    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
763   #ifdef IS_MPI
764      atomRowData.force[atom1] += fg;
# Line 536 | Line 776 | namespace OpenMD {
776    }
777  
778      // filling interaction blocks with pointers
779 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
780 <    InteractionData idat;
541 <
779 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
780 >                                                     int atom1, int atom2) {    
781   #ifdef IS_MPI
782 +    
783 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
784 +                             ff_->getAtomType(identsCol[atom2]) );
785 +    
786      if (storageLayout_ & DataStorage::dslAmat) {
787        idat.A1 = &(atomRowData.aMat[atom1]);
788        idat.A2 = &(atomColData.aMat[atom2]);
# Line 560 | Line 803 | namespace OpenMD {
803        idat.rho2 = &(atomColData.density[atom2]);
804      }
805  
806 +    if (storageLayout_ & DataStorage::dslFunctional) {
807 +      idat.frho1 = &(atomRowData.functional[atom1]);
808 +      idat.frho2 = &(atomColData.functional[atom2]);
809 +    }
810 +
811      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
812        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
813        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
814      }
815  
816 +    if (storageLayout_ & DataStorage::dslParticlePot) {
817 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
818 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
819 +    }
820 +
821   #else
822 +
823 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
824 +                             ff_->getAtomType(idents[atom2]) );
825 +
826      if (storageLayout_ & DataStorage::dslAmat) {
827        idat.A1 = &(snap_->atomData.aMat[atom1]);
828        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 581 | Line 838 | namespace OpenMD {
838        idat.t2 = &(snap_->atomData.torque[atom2]);
839      }
840  
841 <    if (storageLayout_ & DataStorage::dslDensity) {
841 >    if (storageLayout_ & DataStorage::dslDensity) {    
842        idat.rho1 = &(snap_->atomData.density[atom1]);
843        idat.rho2 = &(snap_->atomData.density[atom2]);
844      }
845  
846 +    if (storageLayout_ & DataStorage::dslFunctional) {
847 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
848 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
849 +    }
850 +
851      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
852        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
853        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
854      }
855 +
856 +    if (storageLayout_ & DataStorage::dslParticlePot) {
857 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
858 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
859 +    }
860 +
861   #endif
594 –    return idat;
862    }
863  
864 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
864 >  
865 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
866 > #ifdef IS_MPI
867 >    pot_row[atom1] += 0.5 *  *(idat.pot);
868 >    pot_col[atom2] += 0.5 *  *(idat.pot);
869  
870 <    InteractionData idat;
870 >    atomRowData.force[atom1] += *(idat.f1);
871 >    atomColData.force[atom2] -= *(idat.f1);
872 > #else
873 >    pairwisePot += *(idat.pot);
874 >
875 >    snap_->atomData.force[atom1] += *(idat.f1);
876 >    snap_->atomData.force[atom2] -= *(idat.f1);
877 > #endif
878 >
879 >  }
880 >
881 >
882 >  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
883 >                                              int atom1, int atom2) {
884 >    // Still Missing:: skippedCharge fill must be added to DataStorage
885   #ifdef IS_MPI
886 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
887 +                             ff_->getAtomType(identsCol[atom2]) );
888 +
889      if (storageLayout_ & DataStorage::dslElectroFrame) {
890        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
891        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 606 | Line 894 | namespace OpenMD {
894        idat.t1 = &(atomRowData.torque[atom1]);
895        idat.t2 = &(atomColData.torque[atom2]);
896      }
609 –    if (storageLayout_ & DataStorage::dslForce) {
610 –      idat.t1 = &(atomRowData.force[atom1]);
611 –      idat.t2 = &(atomColData.force[atom2]);
612 –    }
897   #else
898 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
899 +                             ff_->getAtomType(idents[atom2]) );
900 +
901      if (storageLayout_ & DataStorage::dslElectroFrame) {
902        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
903        idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
# Line 619 | Line 906 | namespace OpenMD {
906        idat.t1 = &(snap_->atomData.torque[atom1]);
907        idat.t2 = &(snap_->atomData.torque[atom2]);
908      }
909 <    if (storageLayout_ & DataStorage::dslForce) {
623 <      idat.t1 = &(snap_->atomData.force[atom1]);
624 <      idat.t2 = &(snap_->atomData.force[atom2]);
625 <    }
626 < #endif
627 <    
909 > #endif    
910    }
911  
912  
913 +  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
914 + #ifdef IS_MPI
915 +    pot_row[atom1] += 0.5 *  *(idat.pot);
916 +    pot_col[atom2] += 0.5 *  *(idat.pot);
917 + #else
918 +    pairwisePot += *(idat.pot);  
919 + #endif
920  
921 +  }
922  
923 +
924    /*
925     * buildNeighborList
926     *
# Line 639 | Line 930 | namespace OpenMD {
930    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
931        
932      vector<pair<int, int> > neighborList;
933 +    groupCutoffs cuts;
934   #ifdef IS_MPI
935      cellListRow_.clear();
936      cellListCol_.clear();
# Line 646 | Line 938 | namespace OpenMD {
938      cellList_.clear();
939   #endif
940  
941 <    // dangerous to not do error checking.
650 <    RealType rCut_;
651 <
652 <    RealType rList_ = (rCut_ + skinThickness_);
941 >    RealType rList_ = (largestRcut_ + skinThickness_);
942      RealType rl2 = rList_ * rList_;
943      Snapshot* snap_ = sman_->getCurrentSnapshot();
944      Mat3x3d Hmat = snap_->getHmat();
# Line 665 | Line 954 | namespace OpenMD {
954      Vector3d rs, scaled, dr;
955      Vector3i whichCell;
956      int cellIndex;
957 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
958  
959   #ifdef IS_MPI
960 +    cellListRow_.resize(nCtot);
961 +    cellListCol_.resize(nCtot);
962 + #else
963 +    cellList_.resize(nCtot);
964 + #endif
965 +
966 + #ifdef IS_MPI
967      for (int i = 0; i < nGroupsInRow_; i++) {
968        rs = cgRowData.position[i];
969 +
970        // scaled positions relative to the box vectors
971        scaled = invHmat * rs;
972 +
973        // wrap the vector back into the unit box by subtracting integer box
974        // numbers
975 <      for (int j = 0; j < 3; j++)
975 >      for (int j = 0; j < 3; j++) {
976          scaled[j] -= roundMe(scaled[j]);
977 +        scaled[j] += 0.5;
978 +      }
979      
980        // find xyz-indices of cell that cutoffGroup is in.
981        whichCell.x() = nCells_.x() * scaled.x();
# Line 683 | Line 984 | namespace OpenMD {
984  
985        // find single index of this cell:
986        cellIndex = Vlinear(whichCell, nCells_);
987 +
988        // add this cutoff group to the list of groups in this cell;
989        cellListRow_[cellIndex].push_back(i);
990      }
991  
992      for (int i = 0; i < nGroupsInCol_; i++) {
993        rs = cgColData.position[i];
994 +
995        // scaled positions relative to the box vectors
996        scaled = invHmat * rs;
997 +
998        // wrap the vector back into the unit box by subtracting integer box
999        // numbers
1000 <      for (int j = 0; j < 3; j++)
1000 >      for (int j = 0; j < 3; j++) {
1001          scaled[j] -= roundMe(scaled[j]);
1002 +        scaled[j] += 0.5;
1003 +      }
1004  
1005        // find xyz-indices of cell that cutoffGroup is in.
1006        whichCell.x() = nCells_.x() * scaled.x();
# Line 703 | Line 1009 | namespace OpenMD {
1009  
1010        // find single index of this cell:
1011        cellIndex = Vlinear(whichCell, nCells_);
1012 +
1013        // add this cutoff group to the list of groups in this cell;
1014        cellListCol_[cellIndex].push_back(i);
1015      }
1016   #else
1017      for (int i = 0; i < nGroups_; i++) {
1018        rs = snap_->cgData.position[i];
1019 +
1020        // scaled positions relative to the box vectors
1021        scaled = invHmat * rs;
1022 +
1023        // wrap the vector back into the unit box by subtracting integer box
1024        // numbers
1025 <      for (int j = 0; j < 3; j++)
1025 >      for (int j = 0; j < 3; j++) {
1026          scaled[j] -= roundMe(scaled[j]);
1027 +        scaled[j] += 0.5;
1028 +      }
1029  
1030        // find xyz-indices of cell that cutoffGroup is in.
1031        whichCell.x() = nCells_.x() * scaled.x();
# Line 722 | Line 1033 | namespace OpenMD {
1033        whichCell.z() = nCells_.z() * scaled.z();
1034  
1035        // find single index of this cell:
1036 <      cellIndex = Vlinear(whichCell, nCells_);
1036 >      cellIndex = Vlinear(whichCell, nCells_);      
1037 >
1038        // add this cutoff group to the list of groups in this cell;
1039        cellList_[cellIndex].push_back(i);
1040      }
1041   #endif
1042  
731 –
732 –
1043      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1044        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1045          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
# Line 774 | Line 1084 | namespace OpenMD {
1084                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1085                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1086                    snap_->wrapVector(dr);
1087 <                  if (dr.lengthSquare() < rl2) {
1087 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1088 >                  if (dr.lengthSquare() < cuts.third) {
1089                      neighborList.push_back(make_pair((*j1), (*j2)));
1090                    }
1091                  }
1092                }
1093              }
1094   #else
1095 +
1096              for (vector<int>::iterator j1 = cellList_[m1].begin();
1097                   j1 != cellList_[m1].end(); ++j1) {
1098                for (vector<int>::iterator j2 = cellList_[m2].begin();
1099                     j2 != cellList_[m2].end(); ++j2) {
1100 <                              
1100 >
1101                  // Always do this if we're in different cells or if
1102                  // we're in the same cell and the global index of the
1103                  // j2 cutoff group is less than the j1 cutoff group
# Line 793 | Line 1105 | namespace OpenMD {
1105                  if (m2 != m1 || (*j2) < (*j1)) {
1106                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1107                    snap_->wrapVector(dr);
1108 <                  if (dr.lengthSquare() < rl2) {
1108 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1109 >                  if (dr.lengthSquare() < cuts.third) {
1110                      neighborList.push_back(make_pair((*j1), (*j2)));
1111                    }
1112                  }
# Line 804 | Line 1117 | namespace OpenMD {
1117          }
1118        }
1119      }
1120 <
1120 >    
1121      // save the local cutoff group positions for the check that is
1122      // done on each loop:
1123      saved_CG_positions_.clear();
1124      for (int i = 0; i < nGroups_; i++)
1125        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1126 <
1126 >  
1127      return neighborList;
1128    }
1129   } //end namespace OpenMD

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