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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 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC

# Line 42 | Line 42
42   #include "math/SquareMatrix3.hpp"
43   #include "nonbonded/NonBondedInteraction.hpp"
44   #include "brains/SnapshotManager.hpp"
45 + #include "brains/PairList.hpp"
46  
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_.push_back( Vector3i(-1, 0, 0) );
57 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
58 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
59 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
60 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
61 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
62 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
63 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
64 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );
65 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
66 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );
68 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
69 + #endif    
70 +  }
71 +
72 +
73    /**
74     * distributeInitialData is essentially a copy of the older fortran
75     * SimulationSetup
76     */
53 –  
77    void ForceMatrixDecomposition::distributeInitialData() {
78      snap_ = sman_->getCurrentSnapshot();
79      storageLayout_ = sman_->getStorageLayout();
80 +    ff_ = info_->getForceField();
81      nLocal_ = snap_->getNumberOfAtoms();
82 <    nGroups_ = snap_->getNumberOfCutoffGroups();
82 >    
83 >    nGroups_ = info_->getNLocalCutoffGroups();
84 >    // gather the information for atomtype IDs (atids):
85 >    idents = info_->getIdentArray();
86 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
87 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
88 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
89  
90 +    massFactors = info_->getMassFactors();
91 +
92 +    PairList* excludes = info_->getExcludedInteractions();
93 +    PairList* oneTwo = info_->getOneTwoInteractions();
94 +    PairList* oneThree = info_->getOneThreeInteractions();
95 +    PairList* oneFour = info_->getOneFourInteractions();
96 +
97   #ifdef IS_MPI
98  
99 <    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
100 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
64 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
65 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
99 >    MPI::Intracomm row = rowComm.getComm();
100 >    MPI::Intracomm col = colComm.getComm();
101  
102 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
103 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
104 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
105 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
102 >    AtomPlanIntRow = new Plan<int>(row, nLocal_);
103 >    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
104 >    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
105 >    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
106 >    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
107  
108 <    cgCommIntRow = new Communicator<Row,int>(nGroups_);
109 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
110 <    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
111 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
108 >    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
109 >    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
110 >    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
111 >    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
112 >    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
113  
114 <    nAtomsInRow_ = AtomCommIntRow->getSize();
115 <    nAtomsInCol_ = AtomCommIntColumn->getSize();
116 <    nGroupsInRow_ = cgCommIntRow->getSize();
117 <    nGroupsInCol_ = cgCommIntColumn->getSize();
114 >    cgPlanIntRow = new Plan<int>(row, nGroups_);
115 >    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
116 >    cgPlanIntColumn = new Plan<int>(col, nGroups_);
117 >    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
118  
119 +    nAtomsInRow_ = AtomPlanIntRow->getSize();
120 +    nAtomsInCol_ = AtomPlanIntColumn->getSize();
121 +    nGroupsInRow_ = cgPlanIntRow->getSize();
122 +    nGroupsInCol_ = cgPlanIntColumn->getSize();
123 +
124      // Modify the data storage objects with the correct layouts and sizes:
125      atomRowData.resize(nAtomsInRow_);
126      atomRowData.setStorageLayout(storageLayout_);
# Line 88 | Line 130 | namespace OpenMD {
130      cgRowData.setStorageLayout(DataStorage::dslPosition);
131      cgColData.resize(nGroupsInCol_);
132      cgColData.setStorageLayout(DataStorage::dslPosition);
133 +        
134 +    identsRow.resize(nAtomsInRow_);
135 +    identsCol.resize(nAtomsInCol_);
136      
137 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
138 <                                      vector<RealType> (nAtomsInRow_, 0.0));
139 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
140 <                                      vector<RealType> (nAtomsInCol_, 0.0));
137 >    AtomPlanIntRow->gather(idents, identsRow);
138 >    AtomPlanIntColumn->gather(idents, identsCol);
139 >    
140 >    // allocate memory for the parallel objects
141 >    atypesRow.resize(nAtomsInRow_);
142 >    atypesCol.resize(nAtomsInCol_);
143  
144 +    for (int i = 0; i < nAtomsInRow_; i++)
145 +      atypesRow[i] = ff_->getAtomType(identsRow[i]);
146 +    for (int i = 0; i < nAtomsInCol_; i++)
147 +      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
148  
149 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
149 >    pot_row.resize(nAtomsInRow_);
150 >    pot_col.resize(nAtomsInCol_);
151 >
152 >    AtomRowToGlobal.resize(nAtomsInRow_);
153 >    AtomColToGlobal.resize(nAtomsInCol_);
154 >    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155 >    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156 >
157 >    cerr << "Atoms in Local:\n";
158 >    for (int i = 0; i < AtomLocalToGlobal.size(); i++) {
159 >      cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
160 >    }
161 >    cerr << "Atoms in Row:\n";
162 >    for (int i = 0; i < AtomRowToGlobal.size(); i++) {
163 >      cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
164 >    }
165 >    cerr << "Atoms in Col:\n";
166 >    for (int i = 0; i < AtomColToGlobal.size(); i++) {
167 >      cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
168 >    }
169 >
170 >    cgRowToGlobal.resize(nGroupsInRow_);
171 >    cgColToGlobal.resize(nGroupsInCol_);
172 >    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
173 >    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
174 >
175 >    cerr << "Gruops in Local:\n";
176 >    for (int i = 0; i < cgLocalToGlobal.size(); i++) {
177 >      cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
178 >    }
179 >    cerr << "Groups in Row:\n";
180 >    for (int i = 0; i < cgRowToGlobal.size(); i++) {
181 >      cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
182 >    }
183 >    cerr << "Groups in Col:\n";
184 >    for (int i = 0; i < cgColToGlobal.size(); i++) {
185 >      cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
186 >    }
187 >
188 >
189 >    massFactorsRow.resize(nAtomsInRow_);
190 >    massFactorsCol.resize(nAtomsInCol_);
191 >    AtomPlanRealRow->gather(massFactors, massFactorsRow);
192 >    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
193 >
194 >    groupListRow_.clear();
195 >    groupListRow_.resize(nGroupsInRow_);
196 >    for (int i = 0; i < nGroupsInRow_; i++) {
197 >      int gid = cgRowToGlobal[i];
198 >      for (int j = 0; j < nAtomsInRow_; j++) {
199 >        int aid = AtomRowToGlobal[j];
200 >        if (globalGroupMembership[aid] == gid)
201 >          groupListRow_[i].push_back(j);
202 >      }      
203 >    }
204 >
205 >    groupListCol_.clear();
206 >    groupListCol_.resize(nGroupsInCol_);
207 >    for (int i = 0; i < nGroupsInCol_; i++) {
208 >      int gid = cgColToGlobal[i];
209 >      for (int j = 0; j < nAtomsInCol_; j++) {
210 >        int aid = AtomColToGlobal[j];
211 >        if (globalGroupMembership[aid] == gid)
212 >          groupListCol_[i].push_back(j);
213 >      }      
214 >    }
215 >
216 >    excludesForAtom.clear();
217 >    excludesForAtom.resize(nAtomsInRow_);
218 >    toposForAtom.clear();
219 >    toposForAtom.resize(nAtomsInRow_);
220 >    topoDist.clear();
221 >    topoDist.resize(nAtomsInRow_);
222 >    for (int i = 0; i < nAtomsInRow_; i++) {
223 >      int iglob = AtomRowToGlobal[i];
224 >
225 >      for (int j = 0; j < nAtomsInCol_; j++) {
226 >        int jglob = AtomColToGlobal[j];
227 >
228 >        if (excludes->hasPair(iglob, jglob))
229 >          excludesForAtom[i].push_back(j);      
230 >        
231 >        if (oneTwo->hasPair(iglob, jglob)) {
232 >          toposForAtom[i].push_back(j);
233 >          topoDist[i].push_back(1);
234 >        } else {
235 >          if (oneThree->hasPair(iglob, jglob)) {
236 >            toposForAtom[i].push_back(j);
237 >            topoDist[i].push_back(2);
238 >          } else {
239 >            if (oneFour->hasPair(iglob, jglob)) {
240 >              toposForAtom[i].push_back(j);
241 >              topoDist[i].push_back(3);
242 >            }
243 >          }
244 >        }
245 >      }      
246 >    }
247 >
248 > #endif
249 >
250 >    // allocate memory for the parallel objects
251 >    atypesLocal.resize(nLocal_);
252 >
253 >    for (int i = 0; i < nLocal_; i++)
254 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
255 >
256 >    groupList_.clear();
257 >    groupList_.resize(nGroups_);
258 >    for (int i = 0; i < nGroups_; i++) {
259 >      int gid = cgLocalToGlobal[i];
260 >      for (int j = 0; j < nLocal_; j++) {
261 >        int aid = AtomLocalToGlobal[j];
262 >        if (globalGroupMembership[aid] == gid) {
263 >          groupList_[i].push_back(j);
264 >        }
265 >      }      
266 >    }
267 >
268 >    excludesForAtom.clear();
269 >    excludesForAtom.resize(nLocal_);
270 >    toposForAtom.clear();
271 >    toposForAtom.resize(nLocal_);
272 >    topoDist.clear();
273 >    topoDist.resize(nLocal_);
274 >
275 >    for (int i = 0; i < nLocal_; i++) {
276 >      int iglob = AtomLocalToGlobal[i];
277 >
278 >      for (int j = 0; j < nLocal_; j++) {
279 >        int jglob = AtomLocalToGlobal[j];
280 >
281 >        if (excludes->hasPair(iglob, jglob))
282 >          excludesForAtom[i].push_back(j);              
283 >        
284 >        if (oneTwo->hasPair(iglob, jglob)) {
285 >          toposForAtom[i].push_back(j);
286 >          topoDist[i].push_back(1);
287 >        } else {
288 >          if (oneThree->hasPair(iglob, jglob)) {
289 >            toposForAtom[i].push_back(j);
290 >            topoDist[i].push_back(2);
291 >          } else {
292 >            if (oneFour->hasPair(iglob, jglob)) {
293 >              toposForAtom[i].push_back(j);
294 >              topoDist[i].push_back(3);
295 >            }
296 >          }
297 >        }
298 >      }      
299 >    }
300      
301 <    // gather the information for atomtype IDs (atids):
302 <    vector<int> identsLocal = info_->getIdentArray();
303 <    identsRow.reserve(nAtomsInRow_);
304 <    identsCol.reserve(nAtomsInCol_);
301 >    createGtypeCutoffMap();
302 >
303 >  }
304 >  
305 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
306      
307 <    AtomCommIntRow->gather(identsLocal, identsRow);
308 <    AtomCommIntColumn->gather(identsLocal, identsCol);
307 >    RealType tol = 1e-6;
308 >    largestRcut_ = 0.0;
309 >    RealType rc;
310 >    int atid;
311 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
312      
313 <    AtomLocalToGlobal = info_->getGlobalAtomIndices();
314 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
315 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
313 >    map<int, RealType> atypeCutoff;
314 >      
315 >    for (set<AtomType*>::iterator at = atypes.begin();
316 >         at != atypes.end(); ++at){
317 >      atid = (*at)->getIdent();
318 >      if (userChoseCutoff_)
319 >        atypeCutoff[atid] = userCutoff_;
320 >      else
321 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
322 >    }
323      
324 <    cgLocalToGlobal = info_->getGlobalGroupIndices();
325 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
326 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
327 <
328 <    // still need:
329 <    // topoDist
330 <    // exclude
324 >    vector<RealType> gTypeCutoffs;
325 >    // first we do a single loop over the cutoff groups to find the
326 >    // largest cutoff for any atypes present in this group.
327 > #ifdef IS_MPI
328 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
329 >    groupRowToGtype.resize(nGroupsInRow_);
330 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
331 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
332 >      for (vector<int>::iterator ia = atomListRow.begin();
333 >           ia != atomListRow.end(); ++ia) {            
334 >        int atom1 = (*ia);
335 >        atid = identsRow[atom1];
336 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
337 >          groupCutoffRow[cg1] = atypeCutoff[atid];
338 >        }
339 >      }
340 >
341 >      bool gTypeFound = false;
342 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
343 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
344 >          groupRowToGtype[cg1] = gt;
345 >          gTypeFound = true;
346 >        }
347 >      }
348 >      if (!gTypeFound) {
349 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
350 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
351 >      }
352 >      
353 >    }
354 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
355 >    groupColToGtype.resize(nGroupsInCol_);
356 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
357 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
358 >      for (vector<int>::iterator jb = atomListCol.begin();
359 >           jb != atomListCol.end(); ++jb) {            
360 >        int atom2 = (*jb);
361 >        atid = identsCol[atom2];
362 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
363 >          groupCutoffCol[cg2] = atypeCutoff[atid];
364 >        }
365 >      }
366 >      bool gTypeFound = false;
367 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
368 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
369 >          groupColToGtype[cg2] = gt;
370 >          gTypeFound = true;
371 >        }
372 >      }
373 >      if (!gTypeFound) {
374 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
375 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
376 >      }
377 >    }
378 > #else
379 >
380 >    vector<RealType> groupCutoff(nGroups_, 0.0);
381 >    groupToGtype.resize(nGroups_);
382 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
383 >      groupCutoff[cg1] = 0.0;
384 >      vector<int> atomList = getAtomsInGroupRow(cg1);
385 >      for (vector<int>::iterator ia = atomList.begin();
386 >           ia != atomList.end(); ++ia) {            
387 >        int atom1 = (*ia);
388 >        atid = idents[atom1];
389 >        if (atypeCutoff[atid] > groupCutoff[cg1])
390 >          groupCutoff[cg1] = atypeCutoff[atid];
391 >      }
392 >      
393 >      bool gTypeFound = false;
394 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
395 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
396 >          groupToGtype[cg1] = gt;
397 >          gTypeFound = true;
398 >        }
399 >      }
400 >      if (!gTypeFound) {      
401 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
402 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
403 >      }      
404 >    }
405   #endif
406 +
407 +    // Now we find the maximum group cutoff value present in the simulation
408 +
409 +    RealType groupMax = *max_element(gTypeCutoffs.begin(),
410 +                                     gTypeCutoffs.end());
411 +
412 + #ifdef IS_MPI
413 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
414 +                              MPI::MAX);
415 + #endif
416 +    
417 +    RealType tradRcut = groupMax;
418 +
419 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
420 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
421 +        RealType thisRcut;
422 +        switch(cutoffPolicy_) {
423 +        case TRADITIONAL:
424 +          thisRcut = tradRcut;
425 +          break;
426 +        case MIX:
427 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
428 +          break;
429 +        case MAX:
430 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
431 +          break;
432 +        default:
433 +          sprintf(painCave.errMsg,
434 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
435 +                  "hit an unknown cutoff policy!\n");
436 +          painCave.severity = OPENMD_ERROR;
437 +          painCave.isFatal = 1;
438 +          simError();
439 +          break;
440 +        }
441 +
442 +        pair<int,int> key = make_pair(i,j);
443 +        gTypeCutoffMap[key].first = thisRcut;
444 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
445 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
446 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
447 +        // sanity check
448 +        
449 +        if (userChoseCutoff_) {
450 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
451 +            sprintf(painCave.errMsg,
452 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
453 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
454 +            painCave.severity = OPENMD_ERROR;
455 +            painCave.isFatal = 1;
456 +            simError();            
457 +          }
458 +        }
459 +      }
460 +    }
461    }
462 +
463 +
464 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
465 +    int i, j;  
466 + #ifdef IS_MPI
467 +    i = groupRowToGtype[cg1];
468 +    j = groupColToGtype[cg2];
469 + #else
470 +    i = groupToGtype[cg1];
471 +    j = groupToGtype[cg2];
472 + #endif    
473 +    return gTypeCutoffMap[make_pair(i,j)];
474 +  }
475 +
476 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
477 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
478 +      if (toposForAtom[atom1][j] == atom2)
479 +        return topoDist[atom1][j];
480 +    }
481 +    return 0;
482 +  }
483 +
484 +  void ForceMatrixDecomposition::zeroWorkArrays() {
485 +    pairwisePot = 0.0;
486 +    embeddingPot = 0.0;
487 +
488 + #ifdef IS_MPI
489 +    if (storageLayout_ & DataStorage::dslForce) {
490 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
491 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
492 +    }
493 +
494 +    if (storageLayout_ & DataStorage::dslTorque) {
495 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
496 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
497 +    }
498      
499 +    fill(pot_row.begin(), pot_row.end(),
500 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
501  
502 +    fill(pot_col.begin(), pot_col.end(),
503 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
504  
505 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
506 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
507 +           0.0);
508 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
509 +           0.0);
510 +    }
511 +
512 +    if (storageLayout_ & DataStorage::dslDensity) {      
513 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
514 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
515 +    }
516 +
517 +    if (storageLayout_ & DataStorage::dslFunctional) {  
518 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
519 +           0.0);
520 +      fill(atomColData.functional.begin(), atomColData.functional.end(),
521 +           0.0);
522 +    }
523 +
524 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
525 +      fill(atomRowData.functionalDerivative.begin(),
526 +           atomRowData.functionalDerivative.end(), 0.0);
527 +      fill(atomColData.functionalDerivative.begin(),
528 +           atomColData.functionalDerivative.end(), 0.0);
529 +    }
530 +
531 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
532 +      fill(atomRowData.skippedCharge.begin(),
533 +           atomRowData.skippedCharge.end(), 0.0);
534 +      fill(atomColData.skippedCharge.begin(),
535 +           atomColData.skippedCharge.end(), 0.0);
536 +    }
537 +
538 + #endif
539 +    // even in parallel, we need to zero out the local arrays:
540 +
541 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
542 +      fill(snap_->atomData.particlePot.begin(),
543 +           snap_->atomData.particlePot.end(), 0.0);
544 +    }
545 +    
546 +    if (storageLayout_ & DataStorage::dslDensity) {      
547 +      fill(snap_->atomData.density.begin(),
548 +           snap_->atomData.density.end(), 0.0);
549 +    }
550 +    if (storageLayout_ & DataStorage::dslFunctional) {
551 +      fill(snap_->atomData.functional.begin(),
552 +           snap_->atomData.functional.end(), 0.0);
553 +    }
554 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
555 +      fill(snap_->atomData.functionalDerivative.begin(),
556 +           snap_->atomData.functionalDerivative.end(), 0.0);
557 +    }
558 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
559 +      fill(snap_->atomData.skippedCharge.begin(),
560 +           snap_->atomData.skippedCharge.end(), 0.0);
561 +    }
562 +    
563 +  }
564 +
565 +
566    void ForceMatrixDecomposition::distributeData()  {
567      snap_ = sman_->getCurrentSnapshot();
568      storageLayout_ = sman_->getStorageLayout();
569   #ifdef IS_MPI
570      
571      // gather up the atomic positions
572 <    AtomCommVectorRow->gather(snap_->atomData.position,
572 >    AtomPlanVectorRow->gather(snap_->atomData.position,
573                                atomRowData.position);
574 <    AtomCommVectorColumn->gather(snap_->atomData.position,
574 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
575                                   atomColData.position);
576      
577      // gather up the cutoff group positions
578 <    cgCommVectorRow->gather(snap_->cgData.position,
578 >
579 >    cerr  << "before gather\n";
580 >    for (int i = 0; i < snap_->cgData.position.size(); i++) {
581 >      cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
582 >    }
583 >
584 >    cgPlanVectorRow->gather(snap_->cgData.position,
585                              cgRowData.position);
586 <    cgCommVectorColumn->gather(snap_->cgData.position,
586 >
587 >    cerr  << "after gather\n";
588 >    for (int i = 0; i < cgRowData.position.size(); i++) {
589 >      cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590 >    }
591 >
592 >    cgPlanVectorColumn->gather(snap_->cgData.position,
593                                 cgColData.position);
594 +    for (int i = 0; i < cgColData.position.size(); i++) {
595 +      cerr << "cgCpos = " << cgColData.position[i] << "\n";
596 +    }
597 +
598      
599      // if needed, gather the atomic rotation matrices
600      if (storageLayout_ & DataStorage::dslAmat) {
601 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
601 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
602                                  atomRowData.aMat);
603 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
603 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
604                                     atomColData.aMat);
605      }
606      
607      // if needed, gather the atomic eletrostatic frames
608      if (storageLayout_ & DataStorage::dslElectroFrame) {
609 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
609 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
610                                  atomRowData.electroFrame);
611 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
611 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
612                                     atomColData.electroFrame);
613      }
614 +
615   #endif      
616    }
617    
618 +  /* collects information obtained during the pre-pair loop onto local
619 +   * data structures.
620 +   */
621    void ForceMatrixDecomposition::collectIntermediateData() {
622      snap_ = sman_->getCurrentSnapshot();
623      storageLayout_ = sman_->getStorageLayout();
# Line 163 | Line 625 | namespace OpenMD {
625      
626      if (storageLayout_ & DataStorage::dslDensity) {
627        
628 <      AtomCommRealRow->scatter(atomRowData.density,
628 >      AtomPlanRealRow->scatter(atomRowData.density,
629                                 snap_->atomData.density);
630        
631        int n = snap_->atomData.density.size();
632 <      std::vector<RealType> rho_tmp(n, 0.0);
633 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
632 >      vector<RealType> rho_tmp(n, 0.0);
633 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
634        for (int i = 0; i < n; i++)
635          snap_->atomData.density[i] += rho_tmp[i];
636      }
637   #endif
638    }
639 <  
639 >
640 >  /*
641 >   * redistributes information obtained during the pre-pair loop out to
642 >   * row and column-indexed data structures
643 >   */
644    void ForceMatrixDecomposition::distributeIntermediateData() {
645      snap_ = sman_->getCurrentSnapshot();
646      storageLayout_ = sman_->getStorageLayout();
647   #ifdef IS_MPI
648      if (storageLayout_ & DataStorage::dslFunctional) {
649 <      AtomCommRealRow->gather(snap_->atomData.functional,
649 >      AtomPlanRealRow->gather(snap_->atomData.functional,
650                                atomRowData.functional);
651 <      AtomCommRealColumn->gather(snap_->atomData.functional,
651 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
652                                   atomColData.functional);
653      }
654      
655      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
656 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
656 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
657                                atomRowData.functionalDerivative);
658 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
658 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
659                                   atomColData.functionalDerivative);
660      }
661   #endif
# Line 203 | Line 669 | namespace OpenMD {
669      int n = snap_->atomData.force.size();
670      vector<Vector3d> frc_tmp(n, V3Zero);
671      
672 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
672 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
673      for (int i = 0; i < n; i++) {
674        snap_->atomData.force[i] += frc_tmp[i];
675        frc_tmp[i] = 0.0;
676      }
677      
678 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
679 <    for (int i = 0; i < n; i++)
678 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
679 >    for (int i = 0; i < n; i++) {
680        snap_->atomData.force[i] += frc_tmp[i];
681 <    
682 <    
681 >    }
682 >        
683      if (storageLayout_ & DataStorage::dslTorque) {
684  
685 <      int nt = snap_->atomData.force.size();
685 >      int nt = snap_->atomData.torque.size();
686        vector<Vector3d> trq_tmp(nt, V3Zero);
687  
688 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
689 <      for (int i = 0; i < n; i++) {
688 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
689 >      for (int i = 0; i < nt; i++) {
690          snap_->atomData.torque[i] += trq_tmp[i];
691          trq_tmp[i] = 0.0;
692        }
693        
694 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
695 <      for (int i = 0; i < n; i++)
694 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
695 >      for (int i = 0; i < nt; i++)
696          snap_->atomData.torque[i] += trq_tmp[i];
697      }
698 +
699 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
700 +
701 +      int ns = snap_->atomData.skippedCharge.size();
702 +      vector<RealType> skch_tmp(ns, 0.0);
703 +
704 +      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
705 +      for (int i = 0; i < ns; i++) {
706 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
707 +        skch_tmp[i] = 0.0;
708 +      }
709 +      
710 +      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
711 +      for (int i = 0; i < ns; i++)
712 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
713 +    }
714      
715      nLocal_ = snap_->getNumberOfAtoms();
716  
717 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
718 <                                       vector<RealType> (nLocal_, 0.0));
717 >    vector<potVec> pot_temp(nLocal_,
718 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
719 >
720 >    // scatter/gather pot_row into the members of my column
721 >          
722 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
723 >
724 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
725 >      pairwisePot += pot_temp[ii];
726      
727 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
728 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
729 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
730 <        pot_local[i] += pot_temp[i][ii];
731 <      }
732 <    }
727 >    fill(pot_temp.begin(), pot_temp.end(),
728 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
729 >      
730 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
731 >    
732 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
733 >      pairwisePot += pot_temp[ii];    
734   #endif
735 +
736 +    cerr << "pairwisePot = " <<  pairwisePot << "\n";
737    }
738  
739 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
740 + #ifdef IS_MPI
741 +    return nAtomsInRow_;
742 + #else
743 +    return nLocal_;
744 + #endif
745 +  }
746 +
747 +  /**
748 +   * returns the list of atoms belonging to this group.  
749 +   */
750 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
751 + #ifdef IS_MPI
752 +    return groupListRow_[cg1];
753 + #else
754 +    return groupList_[cg1];
755 + #endif
756 +  }
757 +
758 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
759 + #ifdef IS_MPI
760 +    return groupListCol_[cg2];
761 + #else
762 +    return groupList_[cg2];
763 + #endif
764 +  }
765    
766    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
767      Vector3d d;
768      
769   #ifdef IS_MPI
770      d = cgColData.position[cg2] - cgRowData.position[cg1];
771 +    cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
772 +    cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
773   #else
774      d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
775 +    cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
776 +    cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
777   #endif
778      
779      snap_->wrapVector(d);
# Line 285 | Line 807 | namespace OpenMD {
807      snap_->wrapVector(d);
808      return d;    
809    }
810 +
811 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
812 + #ifdef IS_MPI
813 +    return massFactorsRow[atom1];
814 + #else
815 +    return massFactors[atom1];
816 + #endif
817 +  }
818 +
819 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
820 + #ifdef IS_MPI
821 +    return massFactorsCol[atom2];
822 + #else
823 +    return massFactors[atom2];
824 + #endif
825 +
826 +  }
827      
828    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
829      Vector3d d;
# Line 299 | Line 838 | namespace OpenMD {
838      return d;    
839    }
840  
841 +  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
842 +    return excludesForAtom[atom1];
843 +  }
844 +
845 +  /**
846 +   * We need to exclude some overcounted interactions that result from
847 +   * the parallel decomposition.
848 +   */
849 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
850 +    int unique_id_1, unique_id_2;
851 +    
852 +
853 +    cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
854 + #ifdef IS_MPI
855 +    // in MPI, we have to look up the unique IDs for each atom
856 +    unique_id_1 = AtomRowToGlobal[atom1];
857 +    unique_id_2 = AtomColToGlobal[atom2];
858 +
859 +    cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
860 +    // this situation should only arise in MPI simulations
861 +    if (unique_id_1 == unique_id_2) return true;
862 +    
863 +    // this prevents us from doing the pair on multiple processors
864 +    if (unique_id_1 < unique_id_2) {
865 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
866 +    } else {
867 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
868 +    }
869 + #endif
870 +    return false;
871 +  }
872 +
873 +  /**
874 +   * We need to handle the interactions for atoms who are involved in
875 +   * the same rigid body as well as some short range interactions
876 +   * (bonds, bends, torsions) differently from other interactions.
877 +   * We'll still visit the pairwise routines, but with a flag that
878 +   * tells those routines to exclude the pair from direct long range
879 +   * interactions.  Some indirect interactions (notably reaction
880 +   * field) must still be handled for these pairs.
881 +   */
882 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
883 +    int unique_id_2;
884 + #ifdef IS_MPI
885 +    // in MPI, we have to look up the unique IDs for the row atom.
886 +    unique_id_2 = AtomColToGlobal[atom2];
887 + #else
888 +    // in the normal loop, the atom numbers are unique
889 +    unique_id_2 = atom2;
890 + #endif
891 +    
892 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
893 +         i != excludesForAtom[atom1].end(); ++i) {
894 +      if ( (*i) == unique_id_2 ) return true;
895 +    }
896 +
897 +    return false;
898 +  }
899 +
900 +
901    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
902   #ifdef IS_MPI
903      atomRowData.force[atom1] += fg;
# Line 316 | Line 915 | namespace OpenMD {
915    }
916  
917      // filling interaction blocks with pointers
918 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
919 <    InteractionData idat;
918 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
919 >                                                     int atom1, int atom2) {
920  
921 +    idat.excluded = excludeAtomPair(atom1, atom2);
922 +  
923   #ifdef IS_MPI
924 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
925 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
926 +    //                         ff_->getAtomType(identsCol[atom2]) );
927 +    
928      if (storageLayout_ & DataStorage::dslAmat) {
929        idat.A1 = &(atomRowData.aMat[atom1]);
930        idat.A2 = &(atomColData.aMat[atom2]);
# Line 340 | Line 945 | namespace OpenMD {
945        idat.rho2 = &(atomColData.density[atom2]);
946      }
947  
948 +    if (storageLayout_ & DataStorage::dslFunctional) {
949 +      idat.frho1 = &(atomRowData.functional[atom1]);
950 +      idat.frho2 = &(atomColData.functional[atom2]);
951 +    }
952 +
953      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
954        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
955        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
956      }
957 +
958 +    if (storageLayout_ & DataStorage::dslParticlePot) {
959 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
960 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
961 +    }
962 +
963 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
964 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
965 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
966 +    }
967 +
968   #else
969 +
970 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
971 +    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
972 +    //                         ff_->getAtomType(idents[atom2]) );
973 +
974      if (storageLayout_ & DataStorage::dslAmat) {
975        idat.A1 = &(snap_->atomData.aMat[atom1]);
976        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 360 | Line 986 | namespace OpenMD {
986        idat.t2 = &(snap_->atomData.torque[atom2]);
987      }
988  
989 <    if (storageLayout_ & DataStorage::dslDensity) {
989 >    if (storageLayout_ & DataStorage::dslDensity) {    
990        idat.rho1 = &(snap_->atomData.density[atom1]);
991        idat.rho2 = &(snap_->atomData.density[atom2]);
992      }
993  
994 +    if (storageLayout_ & DataStorage::dslFunctional) {
995 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
996 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
997 +    }
998 +
999      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1000        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1001        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1002      }
1003 +
1004 +    if (storageLayout_ & DataStorage::dslParticlePot) {
1005 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1006 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1007 +    }
1008 +
1009 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
1010 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1011 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1012 +    }
1013   #endif
373 –    return idat;
1014    }
1015  
1016 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1017 <
378 <    InteractionData idat;
1016 >  
1017 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1018   #ifdef IS_MPI
1019 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1020 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1021 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1022 <    }
1023 <    if (storageLayout_ & DataStorage::dslTorque) {
385 <      idat.t1 = &(atomRowData.torque[atom1]);
386 <      idat.t2 = &(atomColData.torque[atom2]);
387 <    }
388 <    if (storageLayout_ & DataStorage::dslForce) {
389 <      idat.t1 = &(atomRowData.force[atom1]);
390 <      idat.t2 = &(atomColData.force[atom2]);
391 <    }
1019 >    pot_row[atom1] += 0.5 *  *(idat.pot);
1020 >    pot_col[atom2] += 0.5 *  *(idat.pot);
1021 >
1022 >    atomRowData.force[atom1] += *(idat.f1);
1023 >    atomColData.force[atom2] -= *(idat.f1);
1024   #else
1025 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1026 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1027 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1028 <    }
397 <    if (storageLayout_ & DataStorage::dslTorque) {
398 <      idat.t1 = &(snap_->atomData.torque[atom1]);
399 <      idat.t2 = &(snap_->atomData.torque[atom2]);
400 <    }
401 <    if (storageLayout_ & DataStorage::dslForce) {
402 <      idat.t1 = &(snap_->atomData.force[atom1]);
403 <      idat.t2 = &(snap_->atomData.force[atom2]);
404 <    }
1025 >    pairwisePot += *(idat.pot);
1026 >
1027 >    snap_->atomData.force[atom1] += *(idat.f1);
1028 >    snap_->atomData.force[atom2] -= *(idat.f1);
1029   #endif
1030      
1031    }
1032  
409 –
410 –
411 –
1033    /*
1034     * buildNeighborList
1035     *
# Line 418 | Line 1039 | namespace OpenMD {
1039    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1040        
1041      vector<pair<int, int> > neighborList;
1042 +    groupCutoffs cuts;
1043 +    bool doAllPairs = false;
1044 +
1045   #ifdef IS_MPI
1046      cellListRow_.clear();
1047      cellListCol_.clear();
# Line 425 | Line 1049 | namespace OpenMD {
1049      cellList_.clear();
1050   #endif
1051  
1052 <    // dangerous to not do error checking.
429 <    RealType rCut_;
430 <
431 <    RealType rList_ = (rCut_ + skinThickness_);
1052 >    RealType rList_ = (largestRcut_ + skinThickness_);
1053      RealType rl2 = rList_ * rList_;
1054      Snapshot* snap_ = sman_->getCurrentSnapshot();
1055      Mat3x3d Hmat = snap_->getHmat();
# Line 440 | Line 1061 | namespace OpenMD {
1061      nCells_.y() = (int) ( Hy.length() )/ rList_;
1062      nCells_.z() = (int) ( Hz.length() )/ rList_;
1063  
1064 +    // handle small boxes where the cell offsets can end up repeating cells
1065 +    
1066 +    if (nCells_.x() < 3) doAllPairs = true;
1067 +    if (nCells_.y() < 3) doAllPairs = true;
1068 +    if (nCells_.z() < 3) doAllPairs = true;
1069 +
1070      Mat3x3d invHmat = snap_->getInvHmat();
1071      Vector3d rs, scaled, dr;
1072      Vector3i whichCell;
1073      int cellIndex;
1074 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1075  
1076   #ifdef IS_MPI
1077 <    for (int i = 0; i < nGroupsInRow_; i++) {
1078 <      rs = cgRowData.position[i];
451 <      // scaled positions relative to the box vectors
452 <      scaled = invHmat * rs;
453 <      // wrap the vector back into the unit box by subtracting integer box
454 <      // numbers
455 <      for (int j = 0; j < 3; j++)
456 <        scaled[j] -= roundMe(scaled[j]);
457 <    
458 <      // find xyz-indices of cell that cutoffGroup is in.
459 <      whichCell.x() = nCells_.x() * scaled.x();
460 <      whichCell.y() = nCells_.y() * scaled.y();
461 <      whichCell.z() = nCells_.z() * scaled.z();
462 <
463 <      // find single index of this cell:
464 <      cellIndex = Vlinear(whichCell, nCells_);
465 <      // add this cutoff group to the list of groups in this cell;
466 <      cellListRow_[cellIndex].push_back(i);
467 <    }
468 <
469 <    for (int i = 0; i < nGroupsInCol_; i++) {
470 <      rs = cgColData.position[i];
471 <      // scaled positions relative to the box vectors
472 <      scaled = invHmat * rs;
473 <      // wrap the vector back into the unit box by subtracting integer box
474 <      // numbers
475 <      for (int j = 0; j < 3; j++)
476 <        scaled[j] -= roundMe(scaled[j]);
477 <
478 <      // find xyz-indices of cell that cutoffGroup is in.
479 <      whichCell.x() = nCells_.x() * scaled.x();
480 <      whichCell.y() = nCells_.y() * scaled.y();
481 <      whichCell.z() = nCells_.z() * scaled.z();
482 <
483 <      // find single index of this cell:
484 <      cellIndex = Vlinear(whichCell, nCells_);
485 <      // add this cutoff group to the list of groups in this cell;
486 <      cellListCol_[cellIndex].push_back(i);
487 <    }
1077 >    cellListRow_.resize(nCtot);
1078 >    cellListCol_.resize(nCtot);
1079   #else
1080 <    for (int i = 0; i < nGroups_; i++) {
1081 <      rs = snap_->cgData.position[i];
491 <      // scaled positions relative to the box vectors
492 <      scaled = invHmat * rs;
493 <      // wrap the vector back into the unit box by subtracting integer box
494 <      // numbers
495 <      for (int j = 0; j < 3; j++)
496 <        scaled[j] -= roundMe(scaled[j]);
1080 >    cellList_.resize(nCtot);
1081 > #endif
1082  
1083 <      // find xyz-indices of cell that cutoffGroup is in.
1084 <      whichCell.x() = nCells_.x() * scaled.x();
500 <      whichCell.y() = nCells_.y() * scaled.y();
501 <      whichCell.z() = nCells_.z() * scaled.z();
1083 >    if (!doAllPairs) {
1084 > #ifdef IS_MPI
1085  
1086 <      // find single index of this cell:
1087 <      cellIndex = Vlinear(whichCell, nCells_);
1088 <      // add this cutoff group to the list of groups in this cell;
1089 <      cellList_[cellIndex].push_back(i);
1090 <    }
1086 >      for (int i = 0; i < nGroupsInRow_; i++) {
1087 >        rs = cgRowData.position[i];
1088 >        
1089 >        // scaled positions relative to the box vectors
1090 >        scaled = invHmat * rs;
1091 >        
1092 >        // wrap the vector back into the unit box by subtracting integer box
1093 >        // numbers
1094 >        for (int j = 0; j < 3; j++) {
1095 >          scaled[j] -= roundMe(scaled[j]);
1096 >          scaled[j] += 0.5;
1097 >        }
1098 >        
1099 >        // find xyz-indices of cell that cutoffGroup is in.
1100 >        whichCell.x() = nCells_.x() * scaled.x();
1101 >        whichCell.y() = nCells_.y() * scaled.y();
1102 >        whichCell.z() = nCells_.z() * scaled.z();
1103 >        
1104 >        // find single index of this cell:
1105 >        cellIndex = Vlinear(whichCell, nCells_);
1106 >        
1107 >        // add this cutoff group to the list of groups in this cell;
1108 >        cellListRow_[cellIndex].push_back(i);
1109 >      }
1110 >      for (int i = 0; i < nGroupsInCol_; i++) {
1111 >        rs = cgColData.position[i];
1112 >        
1113 >        // scaled positions relative to the box vectors
1114 >        scaled = invHmat * rs;
1115 >        
1116 >        // wrap the vector back into the unit box by subtracting integer box
1117 >        // numbers
1118 >        for (int j = 0; j < 3; j++) {
1119 >          scaled[j] -= roundMe(scaled[j]);
1120 >          scaled[j] += 0.5;
1121 >        }
1122 >        
1123 >        // find xyz-indices of cell that cutoffGroup is in.
1124 >        whichCell.x() = nCells_.x() * scaled.x();
1125 >        whichCell.y() = nCells_.y() * scaled.y();
1126 >        whichCell.z() = nCells_.z() * scaled.z();
1127 >        
1128 >        // find single index of this cell:
1129 >        cellIndex = Vlinear(whichCell, nCells_);
1130 >        
1131 >        // add this cutoff group to the list of groups in this cell;
1132 >        cellListCol_[cellIndex].push_back(i);
1133 >      }
1134 > #else
1135 >      for (int i = 0; i < nGroups_; i++) {
1136 >        rs = snap_->cgData.position[i];
1137 >        
1138 >        // scaled positions relative to the box vectors
1139 >        scaled = invHmat * rs;
1140 >        
1141 >        // wrap the vector back into the unit box by subtracting integer box
1142 >        // numbers
1143 >        for (int j = 0; j < 3; j++) {
1144 >          scaled[j] -= roundMe(scaled[j]);
1145 >          scaled[j] += 0.5;
1146 >        }
1147 >        
1148 >        // find xyz-indices of cell that cutoffGroup is in.
1149 >        whichCell.x() = nCells_.x() * scaled.x();
1150 >        whichCell.y() = nCells_.y() * scaled.y();
1151 >        whichCell.z() = nCells_.z() * scaled.z();
1152 >        
1153 >        // find single index of this cell:
1154 >        cellIndex = Vlinear(whichCell, nCells_);
1155 >        
1156 >        // add this cutoff group to the list of groups in this cell;
1157 >        cellList_[cellIndex].push_back(i);
1158 >      }
1159   #endif
1160  
1161 <
1162 <
1163 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1164 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1165 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
515 <          Vector3i m1v(m1x, m1y, m1z);
516 <          int m1 = Vlinear(m1v, nCells_);
517 <
518 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
519 <               os != cellOffsets_.end(); ++os) {
1161 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1162 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1163 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1164 >            Vector3i m1v(m1x, m1y, m1z);
1165 >            int m1 = Vlinear(m1v, nCells_);
1166              
1167 <            Vector3i m2v = m1v + (*os);
1168 <            
1169 <            if (m2v.x() >= nCells_.x()) {
1170 <              m2v.x() = 0;          
1171 <            } else if (m2v.x() < 0) {
1172 <              m2v.x() = nCells_.x() - 1;
1173 <            }
1174 <            
1175 <            if (m2v.y() >= nCells_.y()) {
1176 <              m2v.y() = 0;          
1177 <            } else if (m2v.y() < 0) {
1178 <              m2v.y() = nCells_.y() - 1;
1179 <            }
1180 <            
1181 <            if (m2v.z() >= nCells_.z()) {
1182 <              m2v.z() = 0;          
1183 <            } else if (m2v.z() < 0) {
1184 <              m2v.z() = nCells_.z() - 1;
1185 <            }
1186 <            
1187 <            int m2 = Vlinear (m2v, nCells_);
1188 <
1167 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1168 >                 os != cellOffsets_.end(); ++os) {
1169 >              
1170 >              Vector3i m2v = m1v + (*os);
1171 >              
1172 >              if (m2v.x() >= nCells_.x()) {
1173 >                m2v.x() = 0;          
1174 >              } else if (m2v.x() < 0) {
1175 >                m2v.x() = nCells_.x() - 1;
1176 >              }
1177 >              
1178 >              if (m2v.y() >= nCells_.y()) {
1179 >                m2v.y() = 0;          
1180 >              } else if (m2v.y() < 0) {
1181 >                m2v.y() = nCells_.y() - 1;
1182 >              }
1183 >              
1184 >              if (m2v.z() >= nCells_.z()) {
1185 >                m2v.z() = 0;          
1186 >              } else if (m2v.z() < 0) {
1187 >                m2v.z() = nCells_.z() - 1;
1188 >              }
1189 >              
1190 >              int m2 = Vlinear (m2v, nCells_);
1191 >              
1192   #ifdef IS_MPI
1193 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1194 <                 j1 != cellListRow_[m1].end(); ++j1) {
1195 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1196 <                   j2 != cellListCol_[m2].end(); ++j2) {
1197 <                              
1198 <                // Always do this if we're in different cells or if
1199 <                // we're in the same cell and the global index of the
551 <                // j2 cutoff group is less than the j1 cutoff group
552 <
553 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1193 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1194 >                   j1 != cellListRow_[m1].end(); ++j1) {
1195 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1196 >                     j2 != cellListCol_[m2].end(); ++j2) {
1197 >                  
1198 >                  // In parallel, we need to visit *all* pairs of row &
1199 >                  // column indicies and will truncate later on.
1200                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1201                    snap_->wrapVector(dr);
1202 <                  if (dr.lengthSquare() < rl2) {
1202 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1203 >                  if (dr.lengthSquare() < cuts.third) {
1204                      neighborList.push_back(make_pair((*j1), (*j2)));
1205 <                  }
1205 >                  }                  
1206                  }
1207                }
561 –            }
1208   #else
1209 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1210 <                 j1 != cellList_[m1].end(); ++j1) {
1211 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1212 <                   j2 != cellList_[m2].end(); ++j2) {
1213 <                              
1214 <                // Always do this if we're in different cells or if
1215 <                // we're in the same cell and the global index of the
1216 <                // j2 cutoff group is less than the j1 cutoff group
1217 <
1218 <                if (m2 != m1 || (*j2) < (*j1)) {
1219 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1220 <                  snap_->wrapVector(dr);
1221 <                  if (dr.lengthSquare() < rl2) {
1222 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1209 >              
1210 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1211 >                   j1 != cellList_[m1].end(); ++j1) {
1212 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1213 >                     j2 != cellList_[m2].end(); ++j2) {
1214 >                  
1215 >                  // Always do this if we're in different cells or if
1216 >                  // we're in the same cell and the global index of the
1217 >                  // j2 cutoff group is less than the j1 cutoff group
1218 >                  
1219 >                  if (m2 != m1 || (*j2) < (*j1)) {
1220 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1221 >                    snap_->wrapVector(dr);
1222 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1223 >                    if (dr.lengthSquare() < cuts.third) {
1224 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1225 >                    }
1226                    }
1227                  }
1228                }
580 –            }
1229   #endif
1230 +            }
1231            }
1232          }
1233        }
1234 +    } else {
1235 +      // branch to do all cutoff group pairs
1236 + #ifdef IS_MPI
1237 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1238 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1239 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1240 +          snap_->wrapVector(dr);
1241 +          cuts = getGroupCutoffs( j1, j2 );
1242 +          if (dr.lengthSquare() < cuts.third) {
1243 +            neighborList.push_back(make_pair(j1, j2));
1244 +          }
1245 +        }
1246 +      }
1247 + #else
1248 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1249 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1250 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1251 +          snap_->wrapVector(dr);
1252 +          cuts = getGroupCutoffs( j1, j2 );
1253 +          if (dr.lengthSquare() < cuts.third) {
1254 +            neighborList.push_back(make_pair(j1, j2));
1255 +          }
1256 +        }
1257 +      }        
1258 + #endif
1259      }
1260 <
1260 >      
1261      // save the local cutoff group positions for the check that is
1262      // done on each loop:
1263      saved_CG_positions_.clear();
1264      for (int i = 0; i < nGroups_; i++)
1265        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1266 <
1266 >    
1267      return neighborList;
1268    }
1269   } //end namespace OpenMD

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