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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 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC vs.
Revision 1588 by gezelter, Sat Jul 9 15:05:59 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 {
# Line 52 | Line 53 | namespace OpenMD {
53     */
54    
55    void ForceMatrixDecomposition::distributeInitialData() {
56 < #ifdef IS_MPI    
57 <    Snapshot* snap = sman_->getCurrentSnapshot();
58 <    int nLocal = snap->getNumberOfAtoms();
59 <    int nGroups = snap->getNumberOfCutoffGroups();
56 >    snap_ = sman_->getCurrentSnapshot();
57 >    storageLayout_ = sman_->getStorageLayout();
58 >    ff_ = info_->getForceField();
59 >    nLocal_ = snap_->getNumberOfAtoms();
60 >    
61 >    nGroups_ = info_->getNLocalCutoffGroups();
62 >    // gather the information for atomtype IDs (atids):
63 >    idents = info_->getIdentArray();
64 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
65 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
66 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67  
68 <    AtomCommIntRow = new Communicator<Row,int>(nLocal);
61 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
62 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
63 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
68 >    massFactors = info_->getMassFactors();
69  
70 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
71 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
72 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
73 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
70 >    PairList* excludes = info_->getExcludedInteractions();
71 >    PairList* oneTwo = info_->getOneTwoInteractions();
72 >    PairList* oneThree = info_->getOneThreeInteractions();
73 >    PairList* oneFour = info_->getOneFourInteractions();
74  
75 <    cgCommIntRow = new Communicator<Row,int>(nGroups);
76 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
77 <    cgCommIntColumn = new Communicator<Column,int>(nGroups);
78 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
75 > #ifdef IS_MPI
76 >
77 >    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
78 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81 >    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
82  
83 <    int nAtomsInRow = AtomCommIntRow->getSize();
84 <    int nAtomsInCol = AtomCommIntColumn->getSize();
85 <    int nGroupsInRow = cgCommIntRow->getSize();
86 <    int nGroupsInCol = cgCommIntColumn->getSize();
83 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
84 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
85 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
86 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
87 >    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
88 >
89 >    cgCommIntRow = new Communicator<Row,int>(nGroups_);
90 >    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
91 >    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
92 >    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
93 >
94 >    nAtomsInRow_ = AtomCommIntRow->getSize();
95 >    nAtomsInCol_ = AtomCommIntColumn->getSize();
96 >    nGroupsInRow_ = cgCommIntRow->getSize();
97 >    nGroupsInCol_ = cgCommIntColumn->getSize();
98 >
99 >    // Modify the data storage objects with the correct layouts and sizes:
100 >    atomRowData.resize(nAtomsInRow_);
101 >    atomRowData.setStorageLayout(storageLayout_);
102 >    atomColData.resize(nAtomsInCol_);
103 >    atomColData.setStorageLayout(storageLayout_);
104 >    cgRowData.resize(nGroupsInRow_);
105 >    cgRowData.setStorageLayout(DataStorage::dslPosition);
106 >    cgColData.resize(nGroupsInCol_);
107 >    cgColData.setStorageLayout(DataStorage::dslPosition);
108 >        
109 >    identsRow.resize(nAtomsInRow_);
110 >    identsCol.resize(nAtomsInCol_);
111      
112 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
113 <                                      vector<RealType> (nAtomsInRow, 0.0));
82 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
83 <                                      vector<RealType> (nAtomsInCol, 0.0));
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
115 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
116 <    
117 <    // gather the information for atomtype IDs (atids):
118 <    vector<int> identsLocal = info_->getIdentArray();
89 <    identsRow.reserve(nAtomsInRow);
90 <    identsCol.reserve(nAtomsInCol);
91 <    
92 <    AtomCommIntRow->gather(identsLocal, identsRow);
93 <    AtomCommIntColumn->gather(identsLocal, identsCol);
94 <    
95 <    AtomLocalToGlobal = info_->getGlobalAtomIndices();
115 >    vector<int>::iterator it;
116 >    for (it = AtomLocalToGlobal.begin(); it != AtomLocalToGlobal.end(); ++it) {
117 >      cerr << "my AtomLocalToGlobal = " << (*it) << "\n";
118 >    }
119      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
120      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
121      
99 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
122      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
123      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
124  
125 <    // still need:
126 <    // topoDist
127 <    // exclude
125 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
126 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
127 >
128 >    groupListRow_.clear();
129 >    groupListRow_.resize(nGroupsInRow_);
130 >    for (int i = 0; i < nGroupsInRow_; i++) {
131 >      int gid = cgRowToGlobal[i];
132 >      for (int j = 0; j < nAtomsInRow_; j++) {
133 >        int aid = AtomRowToGlobal[j];
134 >        if (globalGroupMembership[aid] == gid)
135 >          groupListRow_[i].push_back(j);
136 >      }      
137 >    }
138 >
139 >    groupListCol_.clear();
140 >    groupListCol_.resize(nGroupsInCol_);
141 >    for (int i = 0; i < nGroupsInCol_; i++) {
142 >      int gid = cgColToGlobal[i];
143 >      for (int j = 0; j < nAtomsInCol_; j++) {
144 >        int aid = AtomColToGlobal[j];
145 >        if (globalGroupMembership[aid] == gid)
146 >          groupListCol_[i].push_back(j);
147 >      }      
148 >    }
149 >
150 >    excludesForAtom.clear();
151 >    excludesForAtom.resize(nAtomsInRow_);
152 >    toposForAtom.clear();
153 >    toposForAtom.resize(nAtomsInRow_);
154 >    topoDist.clear();
155 >    topoDist.resize(nAtomsInRow_);
156 >    for (int i = 0; i < nAtomsInRow_; i++) {
157 >      int iglob = AtomRowToGlobal[i];
158 >
159 >      for (int j = 0; j < nAtomsInCol_; j++) {
160 >        int jglob = AtomColToGlobal[j];
161 >
162 >        if (excludes->hasPair(iglob, jglob))
163 >          excludesForAtom[i].push_back(j);      
164 >        
165 >        if (oneTwo->hasPair(iglob, jglob)) {
166 >          toposForAtom[i].push_back(j);
167 >          topoDist[i].push_back(1);
168 >        } else {
169 >          if (oneThree->hasPair(iglob, jglob)) {
170 >            toposForAtom[i].push_back(j);
171 >            topoDist[i].push_back(2);
172 >          } else {
173 >            if (oneFour->hasPair(iglob, jglob)) {
174 >              toposForAtom[i].push_back(j);
175 >              topoDist[i].push_back(3);
176 >            }
177 >          }
178 >        }
179 >      }      
180 >    }
181 >
182   #endif
183 +
184 +    groupList_.clear();
185 +    groupList_.resize(nGroups_);
186 +    for (int i = 0; i < nGroups_; i++) {
187 +      int gid = cgLocalToGlobal[i];
188 +      for (int j = 0; j < nLocal_; j++) {
189 +        int aid = AtomLocalToGlobal[j];
190 +        if (globalGroupMembership[aid] == gid) {
191 +          groupList_[i].push_back(j);
192 +        }
193 +      }      
194 +    }
195 +
196 +    excludesForAtom.clear();
197 +    excludesForAtom.resize(nLocal_);
198 +    toposForAtom.clear();
199 +    toposForAtom.resize(nLocal_);
200 +    topoDist.clear();
201 +    topoDist.resize(nLocal_);
202 +
203 +    for (int i = 0; i < nLocal_; i++) {
204 +      int iglob = AtomLocalToGlobal[i];
205 +
206 +      for (int j = 0; j < nLocal_; j++) {
207 +        int jglob = AtomLocalToGlobal[j];
208 +
209 +        if (excludes->hasPair(iglob, jglob))
210 +          excludesForAtom[i].push_back(j);              
211 +        
212 +        if (oneTwo->hasPair(iglob, jglob)) {
213 +          toposForAtom[i].push_back(j);
214 +          topoDist[i].push_back(1);
215 +        } else {
216 +          if (oneThree->hasPair(iglob, jglob)) {
217 +            toposForAtom[i].push_back(j);
218 +            topoDist[i].push_back(2);
219 +          } else {
220 +            if (oneFour->hasPair(iglob, jglob)) {
221 +              toposForAtom[i].push_back(j);
222 +              topoDist[i].push_back(3);
223 +            }
224 +          }
225 +        }
226 +      }      
227 +    }
228 +    
229 +    createGtypeCutoffMap();
230 +
231    }
232 +  
233 +  void ForceMatrixDecomposition::createGtypeCutoffMap() {
234      
235 +    RealType tol = 1e-6;
236 +    RealType rc;
237 +    int atid;
238 +    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
239 +    map<int, RealType> atypeCutoff;
240 +      
241 +    for (set<AtomType*>::iterator at = atypes.begin();
242 +         at != atypes.end(); ++at){
243 +      atid = (*at)->getIdent();
244 +      if (userChoseCutoff_)
245 +        atypeCutoff[atid] = userCutoff_;
246 +      else
247 +        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
248 +    }
249  
250 +    vector<RealType> gTypeCutoffs;
251 +    // first we do a single loop over the cutoff groups to find the
252 +    // largest cutoff for any atypes present in this group.
253 + #ifdef IS_MPI
254 +    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
255 +    groupRowToGtype.resize(nGroupsInRow_);
256 +    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
257 +      vector<int> atomListRow = getAtomsInGroupRow(cg1);
258 +      for (vector<int>::iterator ia = atomListRow.begin();
259 +           ia != atomListRow.end(); ++ia) {            
260 +        int atom1 = (*ia);
261 +        atid = identsRow[atom1];
262 +        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
263 +          groupCutoffRow[cg1] = atypeCutoff[atid];
264 +        }
265 +      }
266  
267 +      bool gTypeFound = false;
268 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
269 +        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
270 +          groupRowToGtype[cg1] = gt;
271 +          gTypeFound = true;
272 +        }
273 +      }
274 +      if (!gTypeFound) {
275 +        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
276 +        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
277 +      }
278 +      
279 +    }
280 +    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
281 +    groupColToGtype.resize(nGroupsInCol_);
282 +    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
283 +      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
284 +      for (vector<int>::iterator jb = atomListCol.begin();
285 +           jb != atomListCol.end(); ++jb) {            
286 +        int atom2 = (*jb);
287 +        atid = identsCol[atom2];
288 +        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
289 +          groupCutoffCol[cg2] = atypeCutoff[atid];
290 +        }
291 +      }
292 +      bool gTypeFound = false;
293 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
294 +        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
295 +          groupColToGtype[cg2] = gt;
296 +          gTypeFound = true;
297 +        }
298 +      }
299 +      if (!gTypeFound) {
300 +        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
301 +        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
302 +      }
303 +    }
304 + #else
305 +
306 +    vector<RealType> groupCutoff(nGroups_, 0.0);
307 +    groupToGtype.resize(nGroups_);
308 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
309 +
310 +      groupCutoff[cg1] = 0.0;
311 +      vector<int> atomList = getAtomsInGroupRow(cg1);
312 +
313 +      for (vector<int>::iterator ia = atomList.begin();
314 +           ia != atomList.end(); ++ia) {            
315 +        int atom1 = (*ia);
316 +        atid = idents[atom1];
317 +        if (atypeCutoff[atid] > groupCutoff[cg1]) {
318 +          groupCutoff[cg1] = atypeCutoff[atid];
319 +        }
320 +      }
321 +
322 +      bool gTypeFound = false;
323 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
324 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
325 +          groupToGtype[cg1] = gt;
326 +          gTypeFound = true;
327 +        }
328 +      }
329 +      if (!gTypeFound) {
330 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
331 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
332 +      }      
333 +    }
334 + #endif
335 +
336 +    // 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 +
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 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
459 +      fill(atomRowData.skippedCharge.begin(),
460 +           atomRowData.skippedCharge.end(), 0.0);
461 +      fill(atomColData.skippedCharge.begin(),
462 +           atomColData.skippedCharge.end(), 0.0);
463 +    }
464 +
465 + #else
466 +    
467 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
468 +      fill(snap_->atomData.particlePot.begin(),
469 +           snap_->atomData.particlePot.end(), 0.0);
470 +    }
471 +    
472 +    if (storageLayout_ & DataStorage::dslDensity) {      
473 +      fill(snap_->atomData.density.begin(),
474 +           snap_->atomData.density.end(), 0.0);
475 +    }
476 +    if (storageLayout_ & DataStorage::dslFunctional) {
477 +      fill(snap_->atomData.functional.begin(),
478 +           snap_->atomData.functional.end(), 0.0);
479 +    }
480 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
481 +      fill(snap_->atomData.functionalDerivative.begin(),
482 +           snap_->atomData.functionalDerivative.end(), 0.0);
483 +    }
484 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
485 +      fill(snap_->atomData.skippedCharge.begin(),
486 +           snap_->atomData.skippedCharge.end(), 0.0);
487 +    }
488 + #endif
489 +    
490 +  }
491 +
492 +
493    void ForceMatrixDecomposition::distributeData()  {
494 +    snap_ = sman_->getCurrentSnapshot();
495 +    storageLayout_ = sman_->getStorageLayout();
496   #ifdef IS_MPI
113 –    Snapshot* snap = sman_->getCurrentSnapshot();
497      
498      // gather up the atomic positions
499 <    AtomCommVectorRow->gather(snap->atomData.position,
500 <                            snap->atomIData.position);
501 <    AtomCommVectorColumn->gather(snap->atomData.position,
502 <                            snap->atomJData.position);
499 >    AtomCommVectorRow->gather(snap_->atomData.position,
500 >                              atomRowData.position);
501 >    AtomCommVectorColumn->gather(snap_->atomData.position,
502 >                                 atomColData.position);
503      
504      // gather up the cutoff group positions
505 <    cgCommVectorRow->gather(snap->cgData.position,
506 <                          snap->cgIData.position);
507 <    cgCommVectorColumn->gather(snap->cgData.position,
508 <                          snap->cgJData.position);
505 >    cgCommVectorRow->gather(snap_->cgData.position,
506 >                            cgRowData.position);
507 >    cgCommVectorColumn->gather(snap_->cgData.position,
508 >                               cgColData.position);
509      
510      // if needed, gather the atomic rotation matrices
511 <    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
512 <      AtomCommMatrixRow->gather(snap->atomData.aMat,
513 <                              snap->atomIData.aMat);
514 <      AtomCommMatrixColumn->gather(snap->atomData.aMat,
515 <                              snap->atomJData.aMat);
511 >    if (storageLayout_ & DataStorage::dslAmat) {
512 >      AtomCommMatrixRow->gather(snap_->atomData.aMat,
513 >                                atomRowData.aMat);
514 >      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
515 >                                   atomColData.aMat);
516      }
517      
518      // if needed, gather the atomic eletrostatic frames
519 <    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
520 <      AtomCommMatrixRow->gather(snap->atomData.electroFrame,
521 <                              snap->atomIData.electroFrame);
522 <      AtomCommMatrixColumn->gather(snap->atomData.electroFrame,
523 <                              snap->atomJData.electroFrame);
519 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
520 >      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
521 >                                atomRowData.electroFrame);
522 >      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
523 >                                   atomColData.electroFrame);
524      }
525   #endif      
526    }
527    
528 +  /* collects information obtained during the pre-pair loop onto local
529 +   * data structures.
530 +   */
531    void ForceMatrixDecomposition::collectIntermediateData() {
532 +    snap_ = sman_->getCurrentSnapshot();
533 +    storageLayout_ = sman_->getStorageLayout();
534   #ifdef IS_MPI
147 –    Snapshot* snap = sman_->getCurrentSnapshot();
535      
536 <    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
537 <
538 <      AtomCommRealRow->scatter(snap->atomIData.density,
539 <                             snap->atomData.density);
540 <
541 <      int n = snap->atomData.density.size();
542 <      std::vector<RealType> rho_tmp(n, 0.0);
543 <      AtomCommRealColumn->scatter(snap->atomJData.density, rho_tmp);
536 >    if (storageLayout_ & DataStorage::dslDensity) {
537 >      
538 >      AtomCommRealRow->scatter(atomRowData.density,
539 >                               snap_->atomData.density);
540 >      
541 >      int n = snap_->atomData.density.size();
542 >      vector<RealType> rho_tmp(n, 0.0);
543 >      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
544        for (int i = 0; i < n; i++)
545 <        snap->atomData.density[i] += rho_tmp[i];
545 >        snap_->atomData.density[i] += rho_tmp[i];
546      }
547   #endif
548    }
549 <  
549 >
550 >  /*
551 >   * redistributes information obtained during the pre-pair loop out to
552 >   * row and column-indexed data structures
553 >   */
554    void ForceMatrixDecomposition::distributeIntermediateData() {
555 +    snap_ = sman_->getCurrentSnapshot();
556 +    storageLayout_ = sman_->getStorageLayout();
557   #ifdef IS_MPI
558 <    Snapshot* snap = sman_->getCurrentSnapshot();
559 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
560 <      AtomCommRealRow->gather(snap->atomData.functional,
561 <                            snap->atomIData.functional);
562 <      AtomCommRealColumn->gather(snap->atomData.functional,
170 <                            snap->atomJData.functional);
558 >    if (storageLayout_ & DataStorage::dslFunctional) {
559 >      AtomCommRealRow->gather(snap_->atomData.functional,
560 >                              atomRowData.functional);
561 >      AtomCommRealColumn->gather(snap_->atomData.functional,
562 >                                 atomColData.functional);
563      }
564      
565 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
566 <      AtomCommRealRow->gather(snap->atomData.functionalDerivative,
567 <                            snap->atomIData.functionalDerivative);
568 <      AtomCommRealColumn->gather(snap->atomData.functionalDerivative,
569 <                            snap->atomJData.functionalDerivative);
565 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
566 >      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
567 >                              atomRowData.functionalDerivative);
568 >      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
569 >                                 atomColData.functionalDerivative);
570      }
571   #endif
572    }
573    
574    
575    void ForceMatrixDecomposition::collectData() {
576 < #ifdef IS_MPI
577 <    Snapshot* snap = sman_->getCurrentSnapshot();
578 <    
579 <    int n = snap->atomData.force.size();
576 >    snap_ = sman_->getCurrentSnapshot();
577 >    storageLayout_ = sman_->getStorageLayout();
578 > #ifdef IS_MPI    
579 >    int n = snap_->atomData.force.size();
580      vector<Vector3d> frc_tmp(n, V3Zero);
581      
582 <    AtomCommVectorRow->scatter(snap->atomIData.force, frc_tmp);
582 >    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
583      for (int i = 0; i < n; i++) {
584 <      snap->atomData.force[i] += frc_tmp[i];
584 >      snap_->atomData.force[i] += frc_tmp[i];
585        frc_tmp[i] = 0.0;
586      }
587      
588 <    AtomCommVectorColumn->scatter(snap->atomJData.force, frc_tmp);
588 >    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
589      for (int i = 0; i < n; i++)
590 <      snap->atomData.force[i] += frc_tmp[i];
590 >      snap_->atomData.force[i] += frc_tmp[i];
591      
592      
593 <    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
593 >    if (storageLayout_ & DataStorage::dslTorque) {
594  
595 <      int nt = snap->atomData.force.size();
595 >      int nt = snap_->atomData.torque.size();
596        vector<Vector3d> trq_tmp(nt, V3Zero);
597  
598 <      AtomCommVectorRow->scatter(snap->atomIData.torque, trq_tmp);
599 <      for (int i = 0; i < n; i++) {
600 <        snap->atomData.torque[i] += trq_tmp[i];
598 >      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
599 >      for (int i = 0; i < nt; i++) {
600 >        snap_->atomData.torque[i] += trq_tmp[i];
601          trq_tmp[i] = 0.0;
602        }
603        
604 <      AtomCommVectorColumn->scatter(snap->atomJData.torque, trq_tmp);
605 <      for (int i = 0; i < n; i++)
606 <        snap->atomData.torque[i] += trq_tmp[i];
604 >      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
605 >      for (int i = 0; i < nt; i++)
606 >        snap_->atomData.torque[i] += trq_tmp[i];
607      }
608 +
609 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
610 +
611 +      int ns = snap_->atomData.skippedCharge.size();
612 +      vector<RealType> skch_tmp(ns, 0.0);
613 +
614 +      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
615 +      for (int i = 0; i < ns; i++) {
616 +        snap_->atomData.skippedCharge[i] = skch_tmp[i];
617 +        skch_tmp[i] = 0.0;
618 +      }
619 +      
620 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
621 +      for (int i = 0; i < ns; i++)
622 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
623 +    }
624      
625 <    int nLocal = snap->getNumberOfAtoms();
625 >    nLocal_ = snap_->getNumberOfAtoms();
626  
627 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
628 <                                       vector<RealType> (nLocal, 0.0));
627 >    vector<potVec> pot_temp(nLocal_,
628 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
629 >
630 >    // scatter/gather pot_row into the members of my column
631 >          
632 >    AtomCommPotRow->scatter(pot_row, pot_temp);
633 >
634 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
635 >      pairwisePot += pot_temp[ii];
636      
637 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
638 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
639 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
640 <        pot_local[i] += pot_temp[i][ii];
641 <      }
637 >    fill(pot_temp.begin(), pot_temp.end(),
638 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
639 >      
640 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
641 >    
642 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
643 >      pairwisePot += pot_temp[ii];    
644 > #endif
645 >
646 >  }
647 >
648 >  int ForceMatrixDecomposition::getNAtomsInRow() {  
649 > #ifdef IS_MPI
650 >    return nAtomsInRow_;
651 > #else
652 >    return nLocal_;
653 > #endif
654 >  }
655 >
656 >  /**
657 >   * returns the list of atoms belonging to this group.  
658 >   */
659 >  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
660 > #ifdef IS_MPI
661 >    return groupListRow_[cg1];
662 > #else
663 >    return groupList_[cg1];
664 > #endif
665 >  }
666 >
667 >  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
668 > #ifdef IS_MPI
669 >    return groupListCol_[cg2];
670 > #else
671 >    return groupList_[cg2];
672 > #endif
673 >  }
674 >  
675 >  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
676 >    Vector3d d;
677 >    
678 > #ifdef IS_MPI
679 >    d = cgColData.position[cg2] - cgRowData.position[cg1];
680 > #else
681 >    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
682 > #endif
683 >    
684 >    snap_->wrapVector(d);
685 >    return d;    
686 >  }
687 >
688 >
689 >  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
690 >
691 >    Vector3d d;
692 >    
693 > #ifdef IS_MPI
694 >    d = cgRowData.position[cg1] - atomRowData.position[atom1];
695 > #else
696 >    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
697 > #endif
698 >
699 >    snap_->wrapVector(d);
700 >    return d;    
701 >  }
702 >  
703 >  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
704 >    Vector3d d;
705 >    
706 > #ifdef IS_MPI
707 >    d = cgColData.position[cg2] - atomColData.position[atom2];
708 > #else
709 >    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
710 > #endif
711 >    
712 >    snap_->wrapVector(d);
713 >    return d;    
714 >  }
715 >
716 >  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
717 > #ifdef IS_MPI
718 >    return massFactorsRow[atom1];
719 > #else
720 >    return massFactors[atom1];
721 > #endif
722 >  }
723 >
724 >  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
725 > #ifdef IS_MPI
726 >    return massFactorsCol[atom2];
727 > #else
728 >    return massFactors[atom2];
729 > #endif
730 >
731 >  }
732 >    
733 >  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
734 >    Vector3d d;
735 >    
736 > #ifdef IS_MPI
737 >    d = atomColData.position[atom2] - atomRowData.position[atom1];
738 > #else
739 >    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
740 > #endif
741 >
742 >    snap_->wrapVector(d);
743 >    return d;    
744 >  }
745 >
746 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
747 >    return excludesForAtom[atom1];
748 >  }
749 >
750 >  /**
751 >   * We need to exclude some overcounted interactions that result from
752 >   * the parallel decomposition.
753 >   */
754 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
755 >    int unique_id_1, unique_id_2;
756 >
757 > #ifdef IS_MPI
758 >    // in MPI, we have to look up the unique IDs for each atom
759 >    unique_id_1 = AtomRowToGlobal[atom1];
760 >    unique_id_2 = AtomColToGlobal[atom2];
761 >
762 >    // this situation should only arise in MPI simulations
763 >    if (unique_id_1 == unique_id_2) return true;
764 >    
765 >    // this prevents us from doing the pair on multiple processors
766 >    if (unique_id_1 < unique_id_2) {
767 >      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
768 >    } else {
769 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
770      }
771   #endif
772 +    return false;
773    }
774 +
775 +  /**
776 +   * We need to handle the interactions for atoms who are involved in
777 +   * the same rigid body as well as some short range interactions
778 +   * (bonds, bends, torsions) differently from other interactions.
779 +   * We'll still visit the pairwise routines, but with a flag that
780 +   * tells those routines to exclude the pair from direct long range
781 +   * interactions.  Some indirect interactions (notably reaction
782 +   * field) must still be handled for these pairs.
783 +   */
784 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
785 +    int unique_id_2;
786 +    
787 + #ifdef IS_MPI
788 +    // in MPI, we have to look up the unique IDs for the row atom.
789 +    unique_id_2 = AtomColToGlobal[atom2];
790 + #else
791 +    // in the normal loop, the atom numbers are unique
792 +    unique_id_2 = atom2;
793 + #endif
794 +    
795 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
796 +         i != excludesForAtom[atom1].end(); ++i) {
797 +      if ( (*i) == unique_id_2 ) return true;
798 +    }
799 +
800 +    return false;
801 +  }
802 +
803 +
804 +  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
805 + #ifdef IS_MPI
806 +    atomRowData.force[atom1] += fg;
807 + #else
808 +    snap_->atomData.force[atom1] += fg;
809 + #endif
810 +  }
811 +
812 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
813 + #ifdef IS_MPI
814 +    atomColData.force[atom2] += fg;
815 + #else
816 +    snap_->atomData.force[atom2] += fg;
817 + #endif
818 +  }
819 +
820 +    // filling interaction blocks with pointers
821 +  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
822 +                                                     int atom1, int atom2) {
823 +
824 +    idat.excluded = excludeAtomPair(atom1, atom2);
825 +  
826 + #ifdef IS_MPI
827 +    
828 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
829 +                             ff_->getAtomType(identsCol[atom2]) );
830 +    
831 +    if (storageLayout_ & DataStorage::dslAmat) {
832 +      idat.A1 = &(atomRowData.aMat[atom1]);
833 +      idat.A2 = &(atomColData.aMat[atom2]);
834 +    }
835 +    
836 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
837 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
838 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
839 +    }
840 +
841 +    if (storageLayout_ & DataStorage::dslTorque) {
842 +      idat.t1 = &(atomRowData.torque[atom1]);
843 +      idat.t2 = &(atomColData.torque[atom2]);
844 +    }
845 +
846 +    if (storageLayout_ & DataStorage::dslDensity) {
847 +      idat.rho1 = &(atomRowData.density[atom1]);
848 +      idat.rho2 = &(atomColData.density[atom2]);
849 +    }
850 +
851 +    if (storageLayout_ & DataStorage::dslFunctional) {
852 +      idat.frho1 = &(atomRowData.functional[atom1]);
853 +      idat.frho2 = &(atomColData.functional[atom2]);
854 +    }
855 +
856 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
857 +      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
858 +      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
859 +    }
860 +
861 +    if (storageLayout_ & DataStorage::dslParticlePot) {
862 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
863 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
864 +    }
865 +
866 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
867 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
868 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
869 +    }
870 +
871 + #else
872 +
873 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
874 +                             ff_->getAtomType(idents[atom2]) );
875 +
876 +    if (storageLayout_ & DataStorage::dslAmat) {
877 +      idat.A1 = &(snap_->atomData.aMat[atom1]);
878 +      idat.A2 = &(snap_->atomData.aMat[atom2]);
879 +    }
880 +
881 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
882 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
883 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
884 +    }
885 +
886 +    if (storageLayout_ & DataStorage::dslTorque) {
887 +      idat.t1 = &(snap_->atomData.torque[atom1]);
888 +      idat.t2 = &(snap_->atomData.torque[atom2]);
889 +    }
890 +
891 +    if (storageLayout_ & DataStorage::dslDensity) {    
892 +      idat.rho1 = &(snap_->atomData.density[atom1]);
893 +      idat.rho2 = &(snap_->atomData.density[atom2]);
894 +    }
895 +
896 +    if (storageLayout_ & DataStorage::dslFunctional) {
897 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
898 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
899 +    }
900 +
901 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
902 +      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
903 +      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
904 +    }
905 +
906 +    if (storageLayout_ & DataStorage::dslParticlePot) {
907 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
908 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
909 +    }
910 +
911 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
912 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
913 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
914 +    }
915 + #endif
916 +  }
917 +
918    
919 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
920 + #ifdef IS_MPI
921 +    pot_row[atom1] += 0.5 *  *(idat.pot);
922 +    pot_col[atom2] += 0.5 *  *(idat.pot);
923 +
924 +    atomRowData.force[atom1] += *(idat.f1);
925 +    atomColData.force[atom2] -= *(idat.f1);
926 + #else
927 +    pairwisePot += *(idat.pot);
928 +
929 +    snap_->atomData.force[atom1] += *(idat.f1);
930 +    snap_->atomData.force[atom2] -= *(idat.f1);
931 + #endif
932 +    
933 +  }
934 +
935 +  /*
936 +   * buildNeighborList
937 +   *
938 +   * first element of pair is row-indexed CutoffGroup
939 +   * second element of pair is column-indexed CutoffGroup
940 +   */
941 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
942 +      
943 +    vector<pair<int, int> > neighborList;
944 +    groupCutoffs cuts;
945 +    bool doAllPairs = false;
946 +
947 + #ifdef IS_MPI
948 +    cellListRow_.clear();
949 +    cellListCol_.clear();
950 + #else
951 +    cellList_.clear();
952 + #endif
953 +
954 +    RealType rList_ = (largestRcut_ + skinThickness_);
955 +    RealType rl2 = rList_ * rList_;
956 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
957 +    Mat3x3d Hmat = snap_->getHmat();
958 +    Vector3d Hx = Hmat.getColumn(0);
959 +    Vector3d Hy = Hmat.getColumn(1);
960 +    Vector3d Hz = Hmat.getColumn(2);
961 +
962 +    nCells_.x() = (int) ( Hx.length() )/ rList_;
963 +    nCells_.y() = (int) ( Hy.length() )/ rList_;
964 +    nCells_.z() = (int) ( Hz.length() )/ rList_;
965 +
966 +    // handle small boxes where the cell offsets can end up repeating cells
967 +    
968 +    if (nCells_.x() < 3) doAllPairs = true;
969 +    if (nCells_.y() < 3) doAllPairs = true;
970 +    if (nCells_.z() < 3) doAllPairs = true;
971 +
972 +    Mat3x3d invHmat = snap_->getInvHmat();
973 +    Vector3d rs, scaled, dr;
974 +    Vector3i whichCell;
975 +    int cellIndex;
976 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
977 +
978 + #ifdef IS_MPI
979 +    cellListRow_.resize(nCtot);
980 +    cellListCol_.resize(nCtot);
981 + #else
982 +    cellList_.resize(nCtot);
983 + #endif
984 +
985 +    if (!doAllPairs) {
986 + #ifdef IS_MPI
987 +
988 +      for (int i = 0; i < nGroupsInRow_; i++) {
989 +        rs = cgRowData.position[i];
990 +        
991 +        // scaled positions relative to the box vectors
992 +        scaled = invHmat * rs;
993 +        
994 +        // wrap the vector back into the unit box by subtracting integer box
995 +        // numbers
996 +        for (int j = 0; j < 3; j++) {
997 +          scaled[j] -= roundMe(scaled[j]);
998 +          scaled[j] += 0.5;
999 +        }
1000 +        
1001 +        // find xyz-indices of cell that cutoffGroup is in.
1002 +        whichCell.x() = nCells_.x() * scaled.x();
1003 +        whichCell.y() = nCells_.y() * scaled.y();
1004 +        whichCell.z() = nCells_.z() * scaled.z();
1005 +        
1006 +        // find single index of this cell:
1007 +        cellIndex = Vlinear(whichCell, nCells_);
1008 +        
1009 +        // add this cutoff group to the list of groups in this cell;
1010 +        cellListRow_[cellIndex].push_back(i);
1011 +      }
1012 +      
1013 +      for (int i = 0; i < nGroupsInCol_; i++) {
1014 +        rs = cgColData.position[i];
1015 +        
1016 +        // scaled positions relative to the box vectors
1017 +        scaled = invHmat * rs;
1018 +        
1019 +        // wrap the vector back into the unit box by subtracting integer box
1020 +        // numbers
1021 +        for (int j = 0; j < 3; j++) {
1022 +          scaled[j] -= roundMe(scaled[j]);
1023 +          scaled[j] += 0.5;
1024 +        }
1025 +        
1026 +        // find xyz-indices of cell that cutoffGroup is in.
1027 +        whichCell.x() = nCells_.x() * scaled.x();
1028 +        whichCell.y() = nCells_.y() * scaled.y();
1029 +        whichCell.z() = nCells_.z() * scaled.z();
1030 +        
1031 +        // find single index of this cell:
1032 +        cellIndex = Vlinear(whichCell, nCells_);
1033 +        
1034 +        // add this cutoff group to the list of groups in this cell;
1035 +        cellListCol_[cellIndex].push_back(i);
1036 +      }
1037 + #else
1038 +      for (int i = 0; i < nGroups_; i++) {
1039 +        rs = snap_->cgData.position[i];
1040 +        
1041 +        // scaled positions relative to the box vectors
1042 +        scaled = invHmat * rs;
1043 +        
1044 +        // wrap the vector back into the unit box by subtracting integer box
1045 +        // numbers
1046 +        for (int j = 0; j < 3; j++) {
1047 +          scaled[j] -= roundMe(scaled[j]);
1048 +          scaled[j] += 0.5;
1049 +        }
1050 +        
1051 +        // find xyz-indices of cell that cutoffGroup is in.
1052 +        whichCell.x() = nCells_.x() * scaled.x();
1053 +        whichCell.y() = nCells_.y() * scaled.y();
1054 +        whichCell.z() = nCells_.z() * scaled.z();
1055 +        
1056 +        // find single index of this cell:
1057 +        cellIndex = Vlinear(whichCell, nCells_);      
1058 +        
1059 +        // add this cutoff group to the list of groups in this cell;
1060 +        cellList_[cellIndex].push_back(i);
1061 +      }
1062 + #endif
1063 +
1064 +      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1065 +        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1066 +          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1067 +            Vector3i m1v(m1x, m1y, m1z);
1068 +            int m1 = Vlinear(m1v, nCells_);
1069 +            
1070 +            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1071 +                 os != cellOffsets_.end(); ++os) {
1072 +              
1073 +              Vector3i m2v = m1v + (*os);
1074 +              
1075 +              if (m2v.x() >= nCells_.x()) {
1076 +                m2v.x() = 0;          
1077 +              } else if (m2v.x() < 0) {
1078 +                m2v.x() = nCells_.x() - 1;
1079 +              }
1080 +              
1081 +              if (m2v.y() >= nCells_.y()) {
1082 +                m2v.y() = 0;          
1083 +              } else if (m2v.y() < 0) {
1084 +                m2v.y() = nCells_.y() - 1;
1085 +              }
1086 +              
1087 +              if (m2v.z() >= nCells_.z()) {
1088 +                m2v.z() = 0;          
1089 +              } else if (m2v.z() < 0) {
1090 +                m2v.z() = nCells_.z() - 1;
1091 +              }
1092 +              
1093 +              int m2 = Vlinear (m2v, nCells_);
1094 +              
1095 + #ifdef IS_MPI
1096 +              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1097 +                   j1 != cellListRow_[m1].end(); ++j1) {
1098 +                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1099 +                     j2 != cellListCol_[m2].end(); ++j2) {
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
1104 +                  
1105 +                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1106 +                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1107 +                    snap_->wrapVector(dr);
1108 +                    cuts = getGroupCutoffs( (*j1), (*j2) );
1109 +                    if (dr.lengthSquare() < cuts.third) {
1110 +                      neighborList.push_back(make_pair((*j1), (*j2)));
1111 +                    }
1112 +                  }
1113 +                }
1114 +              }
1115 + #else
1116 +              
1117 +              for (vector<int>::iterator j1 = cellList_[m1].begin();
1118 +                   j1 != cellList_[m1].end(); ++j1) {
1119 +                for (vector<int>::iterator j2 = cellList_[m2].begin();
1120 +                     j2 != cellList_[m2].end(); ++j2) {
1121 +                  
1122 +                  // Always do this if we're in different cells or if
1123 +                  // we're in the same cell and the global index of the
1124 +                  // j2 cutoff group is less than the j1 cutoff group
1125 +                  
1126 +                  if (m2 != m1 || (*j2) < (*j1)) {
1127 +                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1128 +                    snap_->wrapVector(dr);
1129 +                    cuts = getGroupCutoffs( (*j1), (*j2) );
1130 +                    if (dr.lengthSquare() < cuts.third) {
1131 +                      neighborList.push_back(make_pair((*j1), (*j2)));
1132 +                    }
1133 +                  }
1134 +                }
1135 +              }
1136 + #endif
1137 +            }
1138 +          }
1139 +        }
1140 +      }
1141 +    } else {
1142 +      // branch to do all cutoff group pairs
1143 + #ifdef IS_MPI
1144 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1145 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1146 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1147 +          snap_->wrapVector(dr);
1148 +          cuts = getGroupCutoffs( j1, j2 );
1149 +          if (dr.lengthSquare() < cuts.third) {
1150 +            neighborList.push_back(make_pair(j1, j2));
1151 +          }
1152 +        }
1153 +      }
1154 + #else
1155 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1156 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1157 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1158 +          snap_->wrapVector(dr);
1159 +          cuts = getGroupCutoffs( j1, j2 );
1160 +          if (dr.lengthSquare() < cuts.third) {
1161 +            neighborList.push_back(make_pair(j1, j2));
1162 +          }
1163 +        }
1164 +      }        
1165 + #endif
1166 +    }
1167 +      
1168 +    // save the local cutoff group positions for the check that is
1169 +    // done on each loop:
1170 +    saved_CG_positions_.clear();
1171 +    for (int i = 0; i < nGroups_; i++)
1172 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1173 +    
1174 +    return neighborList;
1175 +  }
1176   } //end namespace OpenMD

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