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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1582 by gezelter, Tue Jun 14 20:41:44 2011 UTC

# Line 38 | Line 38
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39   * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41 < #include "parallel/ForceDecomposition.hpp"
41 > #include "parallel/ForceMatrixDecomposition.hpp"
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 51 | Line 52 | namespace OpenMD {
52     * SimulationSetup
53     */
54    
55 <  void ForceDecomposition::distributeInitialData() {
56 < #ifdef IS_MPI    
57 <    Snapshot* snap = sman_->getCurrentSnapshot();
58 <    int nLocal = snap->getNumberOfAtoms();
59 <    int nGroups = snap->getNumberOfCutoffGroups();
55 >  void ForceMatrixDecomposition::distributeInitialData() {
56 >    snap_ = sman_->getCurrentSnapshot();
57 >    storageLayout_ = sman_->getStorageLayout();
58 >    ff_ = info_->getForceField();
59 >    nLocal_ = snap_->getNumberOfAtoms();
60  
61 <    AtomCommIntI = new Communicator<Row,int>(nLocal);
62 <    AtomCommRealI = new Communicator<Row,RealType>(nLocal);
63 <    AtomCommVectorI = new Communicator<Row,Vector3d>(nLocal);
64 <    AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nLocal);
61 >    nGroups_ = info_->getNLocalCutoffGroups();
62 >    cerr << "in dId, nGroups = " << nGroups_ << "\n";
63 >    // gather the information for atomtype IDs (atids):
64 >    identsLocal = info_->getIdentArray();
65 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
66 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
67 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68 >    massFactors = info_->getMassFactors();
69 >    PairList excludes = info_->getExcludedInteractions();
70 >    PairList oneTwo = info_->getOneTwoInteractions();
71 >    PairList oneThree = info_->getOneThreeInteractions();
72 >    PairList oneFour = info_->getOneFourInteractions();
73  
74 <    AtomCommIntJ = new Communicator<Column,int>(nLocal);
75 <    AtomCommRealJ = new Communicator<Column,RealType>(nLocal);
76 <    AtomCommVectorJ = new Communicator<Column,Vector3d>(nLocal);
77 <    AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nLocal);
74 > #ifdef IS_MPI
75 >
76 >    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
77 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
78 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
79 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
80 >    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
81  
82 <    cgCommIntI = new Communicator<Row,int>(nGroups);
83 <    cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
84 <    cgCommIntJ = new Communicator<Column,int>(nGroups);
85 <    cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
82 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
83 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
84 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
85 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
86 >    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
87  
88 <    int nAtomsInRow = AtomCommIntI->getSize();
89 <    int nAtomsInCol = AtomCommIntJ->getSize();
90 <    int nGroupsInRow = cgCommIntI->getSize();
91 <    int nGroupsInCol = cgCommIntJ->getSize();
88 >    cgCommIntRow = new Communicator<Row,int>(nGroups_);
89 >    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
90 >    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
91 >    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
92  
93 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
94 <                                      vector<RealType> (nAtomsInRow, 0.0));
95 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
96 <                                      vector<RealType> (nAtomsInCol, 0.0));
93 >    nAtomsInRow_ = AtomCommIntRow->getSize();
94 >    nAtomsInCol_ = AtomCommIntColumn->getSize();
95 >    nGroupsInRow_ = cgCommIntRow->getSize();
96 >    nGroupsInCol_ = cgCommIntColumn->getSize();
97 >
98 >    // Modify the data storage objects with the correct layouts and sizes:
99 >    atomRowData.resize(nAtomsInRow_);
100 >    atomRowData.setStorageLayout(storageLayout_);
101 >    atomColData.resize(nAtomsInCol_);
102 >    atomColData.setStorageLayout(storageLayout_);
103 >    cgRowData.resize(nGroupsInRow_);
104 >    cgRowData.setStorageLayout(DataStorage::dslPosition);
105 >    cgColData.resize(nGroupsInCol_);
106 >    cgColData.setStorageLayout(DataStorage::dslPosition);
107 >        
108 >    identsRow.resize(nAtomsInRow_);
109 >    identsCol.resize(nAtomsInCol_);
110      
111 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
111 >    AtomCommIntRow->gather(identsLocal, identsRow);
112 >    AtomCommIntColumn->gather(identsLocal, identsCol);
113 >    
114 >    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
115 >    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
116 >    
117 >    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
118 >    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
119  
120 <    // gather the information for atomtype IDs (atids):
121 <    AtomCommIntI->gather(info_->getIdentArray(), identsRow);
89 <    AtomCommIntJ->gather(info_->getIdentArray(), identsCol);
120 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
121 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
122  
123 <    AtomLocalToGlobal = info_->getLocalToGlobalAtomIndex();
124 <    AtomCommIntI->gather(AtomLocalToGlobal, AtomRowToGlobal);
125 <    AtomCommIntJ->gather(AtomLocalToGlobal, AtomColToGlobal);
123 >    groupListRow_.clear();
124 >    groupListRow_.resize(nGroupsInRow_);
125 >    for (int i = 0; i < nGroupsInRow_; i++) {
126 >      int gid = cgRowToGlobal[i];
127 >      for (int j = 0; j < nAtomsInRow_; j++) {
128 >        int aid = AtomRowToGlobal[j];
129 >        if (globalGroupMembership[aid] == gid)
130 >          groupListRow_[i].push_back(j);
131 >      }      
132 >    }
133  
134 <    cgLocalToGlobal = info_->getLocalToGlobalCutoffGroupIndex();
135 <    cgCommIntI->gather(cgLocalToGlobal, cgRowToGlobal);
136 <    cgCommIntJ->gather(cgLocalToGlobal, cgColToGlobal);
134 >    groupListCol_.clear();
135 >    groupListCol_.resize(nGroupsInCol_);
136 >    for (int i = 0; i < nGroupsInCol_; i++) {
137 >      int gid = cgColToGlobal[i];
138 >      for (int j = 0; j < nAtomsInCol_; j++) {
139 >        int aid = AtomColToGlobal[j];
140 >        if (globalGroupMembership[aid] == gid)
141 >          groupListCol_[i].push_back(j);
142 >      }      
143 >    }
144  
145 +    skipsForAtom.clear();
146 +    skipsForAtom.resize(nAtomsInRow_);
147 +    toposForAtom.clear();
148 +    toposForAtom.resize(nAtomsInRow_);
149 +    topoDist.clear();
150 +    topoDist.resize(nAtomsInRow_);
151 +    for (int i = 0; i < nAtomsInRow_; i++) {
152 +      int iglob = AtomRowToGlobal[i];
153 +
154 +      for (int j = 0; j < nAtomsInCol_; j++) {
155 +        int jglob = AtomColToGlobal[j];
156 +
157 +        if (excludes.hasPair(iglob, jglob))
158 +          skipsForAtom[i].push_back(j);      
159 +        
160 +        if (oneTwo.hasPair(iglob, jglob)) {
161 +          toposForAtom[i].push_back(j);
162 +          topoDist[i].push_back(1);
163 +        } else {
164 +          if (oneThree.hasPair(iglob, jglob)) {
165 +            toposForAtom[i].push_back(j);
166 +            topoDist[i].push_back(2);
167 +          } else {
168 +            if (oneFour.hasPair(iglob, jglob)) {
169 +              toposForAtom[i].push_back(j);
170 +              topoDist[i].push_back(3);
171 +            }
172 +          }
173 +        }
174 +      }      
175 +    }
176 +
177 + #endif
178 +
179 +    groupList_.clear();
180 +    groupList_.resize(nGroups_);
181 +    for (int i = 0; i < nGroups_; i++) {
182 +      int gid = cgLocalToGlobal[i];
183 +      for (int j = 0; j < nLocal_; j++) {
184 +        int aid = AtomLocalToGlobal[j];
185 +        if (globalGroupMembership[aid] == gid) {
186 +          groupList_[i].push_back(j);
187 +        }
188 +      }      
189 +    }
190 +
191 +    skipsForAtom.clear();
192 +    skipsForAtom.resize(nLocal_);
193 +    toposForAtom.clear();
194 +    toposForAtom.resize(nLocal_);
195 +    topoDist.clear();
196 +    topoDist.resize(nLocal_);
197 +
198 +    for (int i = 0; i < nLocal_; i++) {
199 +      int iglob = AtomLocalToGlobal[i];
200 +
201 +      for (int j = 0; j < nLocal_; j++) {
202 +        int jglob = AtomLocalToGlobal[j];
203 +
204 +        if (excludes.hasPair(iglob, jglob))
205 +          skipsForAtom[i].push_back(j);              
206 +        
207 +        if (oneTwo.hasPair(iglob, jglob)) {
208 +          toposForAtom[i].push_back(j);
209 +          topoDist[i].push_back(1);
210 +        } else {
211 +          if (oneThree.hasPair(iglob, jglob)) {
212 +            toposForAtom[i].push_back(j);
213 +            topoDist[i].push_back(2);
214 +          } else {
215 +            if (oneFour.hasPair(iglob, jglob)) {
216 +              toposForAtom[i].push_back(j);
217 +              topoDist[i].push_back(3);
218 +            }
219 +          }
220 +        }
221 +      }      
222 +    }
223 +    
224 +    createGtypeCutoffMap();
225 +  }
226 +  
227 +  void ForceMatrixDecomposition::createGtypeCutoffMap() {
228 +
229 +    RealType tol = 1e-6;
230 +    RealType rc;
231 +    int atid;
232 +    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
233 +    vector<RealType> atypeCutoff;
234 +    atypeCutoff.resize( atypes.size() );
235 +
236 +    for (set<AtomType*>::iterator at = atypes.begin();
237 +         at != atypes.end(); ++at){
238 +      rc = interactionMan_->getSuggestedCutoffRadius(*at);
239 +      atid = (*at)->getIdent();
240 +      atypeCutoff[atid] = rc;
241 +    }
242 +
243 +    vector<RealType> gTypeCutoffs;
244 +
245 +    // first we do a single loop over the cutoff groups to find the
246 +    // largest cutoff for any atypes present in this group.
247 + #ifdef IS_MPI
248 +    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
249 +    groupRowToGtype.resize(nGroupsInRow_);
250 +    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
251 +      vector<int> atomListRow = getAtomsInGroupRow(cg1);
252 +      for (vector<int>::iterator ia = atomListRow.begin();
253 +           ia != atomListRow.end(); ++ia) {            
254 +        int atom1 = (*ia);
255 +        atid = identsRow[atom1];
256 +        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
257 +          groupCutoffRow[cg1] = atypeCutoff[atid];
258 +        }
259 +      }
260 +
261 +      bool gTypeFound = false;
262 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
263 +        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
264 +          groupRowToGtype[cg1] = gt;
265 +          gTypeFound = true;
266 +        }
267 +      }
268 +      if (!gTypeFound) {
269 +        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
270 +        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
271 +      }
272        
273 <      
273 >    }
274 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
275 >    groupColToGtype.resize(nGroupsInCol_);
276 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
277 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
278 >      for (vector<int>::iterator jb = atomListCol.begin();
279 >           jb != atomListCol.end(); ++jb) {            
280 >        int atom2 = (*jb);
281 >        atid = identsCol[atom2];
282 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
283 >          groupCutoffCol[cg2] = atypeCutoff[atid];
284 >        }
285 >      }
286 >      bool gTypeFound = false;
287 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
288 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
289 >          groupColToGtype[cg2] = gt;
290 >          gTypeFound = true;
291 >        }
292 >      }
293 >      if (!gTypeFound) {
294 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
295 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
296 >      }
297 >    }
298 > #else
299  
300 +    vector<RealType> groupCutoff(nGroups_, 0.0);
301 +    groupToGtype.resize(nGroups_);
302  
303 +    cerr << "nGroups = " << nGroups_ << "\n";
304 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305  
306 <    // still need:
307 <    // topoDist
308 <    // exclude
306 >      groupCutoff[cg1] = 0.0;
307 >      vector<int> atomList = getAtomsInGroupRow(cg1);
308 >
309 >      for (vector<int>::iterator ia = atomList.begin();
310 >           ia != atomList.end(); ++ia) {            
311 >        int atom1 = (*ia);
312 >        atid = identsLocal[atom1];
313 >        if (atypeCutoff[atid] > groupCutoff[cg1]) {
314 >          groupCutoff[cg1] = atypeCutoff[atid];
315 >        }
316 >      }
317 >
318 >      bool gTypeFound = false;
319 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
320 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
321 >          groupToGtype[cg1] = gt;
322 >          gTypeFound = true;
323 >        }
324 >      }
325 >      if (!gTypeFound) {
326 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
327 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
328 >      }      
329 >    }
330   #endif
331 +
332 +    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
333 +    // Now we find the maximum group cutoff value present in the simulation
334 +
335 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
336 +
337 + #ifdef IS_MPI
338 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
339 + #endif
340 +    
341 +    RealType tradRcut = groupMax;
342 +
343 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
344 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
345 +        RealType thisRcut;
346 +        switch(cutoffPolicy_) {
347 +        case TRADITIONAL:
348 +          thisRcut = tradRcut;
349 +          break;
350 +        case MIX:
351 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
352 +          break;
353 +        case MAX:
354 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
355 +          break;
356 +        default:
357 +          sprintf(painCave.errMsg,
358 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
359 +                  "hit an unknown cutoff policy!\n");
360 +          painCave.severity = OPENMD_ERROR;
361 +          painCave.isFatal = 1;
362 +          simError();
363 +          break;
364 +        }
365 +
366 +        pair<int,int> key = make_pair(i,j);
367 +        gTypeCutoffMap[key].first = thisRcut;
368 +
369 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
370 +
371 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
372 +        
373 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
374 +
375 +        // sanity check
376 +        
377 +        if (userChoseCutoff_) {
378 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
379 +            sprintf(painCave.errMsg,
380 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
381 +                    "user-specified rCut does not match computed group Cutoff\n");
382 +            painCave.severity = OPENMD_ERROR;
383 +            painCave.isFatal = 1;
384 +            simError();            
385 +          }
386 +        }
387 +      }
388 +    }
389    }
390 +
391 +
392 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
393 +    int i, j;  
394 + #ifdef IS_MPI
395 +    i = groupRowToGtype[cg1];
396 +    j = groupColToGtype[cg2];
397 + #else
398 +    i = groupToGtype[cg1];
399 +    j = groupToGtype[cg2];
400 + #endif    
401 +    return gTypeCutoffMap[make_pair(i,j)];
402 +  }
403 +
404 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
405 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
406 +      if (toposForAtom[atom1][j] == atom2)
407 +        return topoDist[atom1][j];
408 +    }
409 +    return 0;
410 +  }
411 +
412 +  void ForceMatrixDecomposition::zeroWorkArrays() {
413 +
414 +    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415 +      longRangePot_[j] = 0.0;
416 +    }
417 +
418 + #ifdef IS_MPI
419 +    if (storageLayout_ & DataStorage::dslForce) {
420 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
421 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
422 +    }
423 +
424 +    if (storageLayout_ & DataStorage::dslTorque) {
425 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
426 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
427 +    }
428      
429 +    fill(pot_row.begin(), pot_row.end(),
430 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
431  
432 +    fill(pot_col.begin(), pot_col.end(),
433 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434 +    
435 +    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
436  
437 <  void ForceDecomposition::distributeData()  {
437 >    if (storageLayout_ & DataStorage::dslParticlePot) {    
438 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
439 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
440 >    }
441 >
442 >    if (storageLayout_ & DataStorage::dslDensity) {      
443 >      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
444 >      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
445 >    }
446 >
447 >    if (storageLayout_ & DataStorage::dslFunctional) {  
448 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
449 >      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
450 >    }
451 >
452 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
453 >      fill(atomRowData.functionalDerivative.begin(),
454 >           atomRowData.functionalDerivative.end(), 0.0);
455 >      fill(atomColData.functionalDerivative.begin(),
456 >           atomColData.functionalDerivative.end(), 0.0);
457 >    }
458 >
459 > #else
460 >    
461 >    if (storageLayout_ & DataStorage::dslParticlePot) {      
462 >      fill(snap_->atomData.particlePot.begin(),
463 >           snap_->atomData.particlePot.end(), 0.0);
464 >    }
465 >    
466 >    if (storageLayout_ & DataStorage::dslDensity) {      
467 >      fill(snap_->atomData.density.begin(),
468 >           snap_->atomData.density.end(), 0.0);
469 >    }
470 >    if (storageLayout_ & DataStorage::dslFunctional) {
471 >      fill(snap_->atomData.functional.begin(),
472 >           snap_->atomData.functional.end(), 0.0);
473 >    }
474 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
475 >      fill(snap_->atomData.functionalDerivative.begin(),
476 >           snap_->atomData.functionalDerivative.end(), 0.0);
477 >    }
478 > #endif
479 >    
480 >  }
481 >
482 >
483 >  void ForceMatrixDecomposition::distributeData()  {
484 >    snap_ = sman_->getCurrentSnapshot();
485 >    storageLayout_ = sman_->getStorageLayout();
486   #ifdef IS_MPI
114 –    Snapshot* snap = sman_->getCurrentSnapshot();
487      
488      // gather up the atomic positions
489 <    AtomCommVectorI->gather(snap->atomData.position,
490 <                            snap->atomIData.position);
491 <    AtomCommVectorJ->gather(snap->atomData.position,
492 <                            snap->atomJData.position);
489 >    AtomCommVectorRow->gather(snap_->atomData.position,
490 >                              atomRowData.position);
491 >    AtomCommVectorColumn->gather(snap_->atomData.position,
492 >                                 atomColData.position);
493      
494      // gather up the cutoff group positions
495 <    cgCommVectorI->gather(snap->cgData.position,
496 <                          snap->cgIData.position);
497 <    cgCommVectorJ->gather(snap->cgData.position,
498 <                          snap->cgJData.position);
495 >    cgCommVectorRow->gather(snap_->cgData.position,
496 >                            cgRowData.position);
497 >    cgCommVectorColumn->gather(snap_->cgData.position,
498 >                               cgColData.position);
499      
500      // if needed, gather the atomic rotation matrices
501 <    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
502 <      AtomCommMatrixI->gather(snap->atomData.aMat,
503 <                              snap->atomIData.aMat);
504 <      AtomCommMatrixJ->gather(snap->atomData.aMat,
505 <                              snap->atomJData.aMat);
501 >    if (storageLayout_ & DataStorage::dslAmat) {
502 >      AtomCommMatrixRow->gather(snap_->atomData.aMat,
503 >                                atomRowData.aMat);
504 >      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
505 >                                   atomColData.aMat);
506      }
507      
508      // if needed, gather the atomic eletrostatic frames
509 <    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
510 <      AtomCommMatrixI->gather(snap->atomData.electroFrame,
511 <                              snap->atomIData.electroFrame);
512 <      AtomCommMatrixJ->gather(snap->atomData.electroFrame,
513 <                              snap->atomJData.electroFrame);
509 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
510 >      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
511 >                                atomRowData.electroFrame);
512 >      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
513 >                                   atomColData.electroFrame);
514      }
515   #endif      
516    }
517    
518 <  void ForceDecomposition::collectIntermediateData() {
518 >  /* collects information obtained during the pre-pair loop onto local
519 >   * data structures.
520 >   */
521 >  void ForceMatrixDecomposition::collectIntermediateData() {
522 >    snap_ = sman_->getCurrentSnapshot();
523 >    storageLayout_ = sman_->getStorageLayout();
524   #ifdef IS_MPI
148 –    Snapshot* snap = sman_->getCurrentSnapshot();
525      
526 <    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
527 <
528 <      AtomCommRealI->scatter(snap->atomIData.density,
529 <                             snap->atomData.density);
530 <
531 <      int n = snap->atomData.density.size();
532 <      std::vector<RealType> rho_tmp(n, 0.0);
533 <      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
526 >    if (storageLayout_ & DataStorage::dslDensity) {
527 >      
528 >      AtomCommRealRow->scatter(atomRowData.density,
529 >                               snap_->atomData.density);
530 >      
531 >      int n = snap_->atomData.density.size();
532 >      vector<RealType> rho_tmp(n, 0.0);
533 >      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
534        for (int i = 0; i < n; i++)
535 <        snap->atomData.density[i] += rho_tmp[i];
535 >        snap_->atomData.density[i] += rho_tmp[i];
536      }
537   #endif
538    }
539 <  
540 <  void ForceDecomposition::distributeIntermediateData() {
539 >
540 >  /*
541 >   * redistributes information obtained during the pre-pair loop out to
542 >   * row and column-indexed data structures
543 >   */
544 >  void ForceMatrixDecomposition::distributeIntermediateData() {
545 >    snap_ = sman_->getCurrentSnapshot();
546 >    storageLayout_ = sman_->getStorageLayout();
547   #ifdef IS_MPI
548 <    Snapshot* snap = sman_->getCurrentSnapshot();
549 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
550 <      AtomCommRealI->gather(snap->atomData.functional,
551 <                            snap->atomIData.functional);
552 <      AtomCommRealJ->gather(snap->atomData.functional,
171 <                            snap->atomJData.functional);
548 >    if (storageLayout_ & DataStorage::dslFunctional) {
549 >      AtomCommRealRow->gather(snap_->atomData.functional,
550 >                              atomRowData.functional);
551 >      AtomCommRealColumn->gather(snap_->atomData.functional,
552 >                                 atomColData.functional);
553      }
554      
555 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
556 <      AtomCommRealI->gather(snap->atomData.functionalDerivative,
557 <                            snap->atomIData.functionalDerivative);
558 <      AtomCommRealJ->gather(snap->atomData.functionalDerivative,
559 <                            snap->atomJData.functionalDerivative);
555 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
556 >      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
557 >                              atomRowData.functionalDerivative);
558 >      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
559 >                                 atomColData.functionalDerivative);
560      }
561   #endif
562    }
563    
564    
565 <  void ForceDecomposition::collectData() {
566 < #ifdef IS_MPI
567 <    Snapshot* snap = sman_->getCurrentSnapshot();
568 <    
569 <    int n = snap->atomData.force.size();
565 >  void ForceMatrixDecomposition::collectData() {
566 >    snap_ = sman_->getCurrentSnapshot();
567 >    storageLayout_ = sman_->getStorageLayout();
568 > #ifdef IS_MPI    
569 >    int n = snap_->atomData.force.size();
570      vector<Vector3d> frc_tmp(n, V3Zero);
571      
572 <    AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
572 >    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
573      for (int i = 0; i < n; i++) {
574 <      snap->atomData.force[i] += frc_tmp[i];
574 >      snap_->atomData.force[i] += frc_tmp[i];
575        frc_tmp[i] = 0.0;
576      }
577      
578 <    AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
578 >    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
579      for (int i = 0; i < n; i++)
580 <      snap->atomData.force[i] += frc_tmp[i];
580 >      snap_->atomData.force[i] += frc_tmp[i];
581      
582      
583 <    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
583 >    if (storageLayout_ & DataStorage::dslTorque) {
584  
585 <      int nt = snap->atomData.force.size();
585 >      int nt = snap_->atomData.force.size();
586        vector<Vector3d> trq_tmp(nt, V3Zero);
587  
588 <      AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
588 >      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
589        for (int i = 0; i < n; i++) {
590 <        snap->atomData.torque[i] += trq_tmp[i];
590 >        snap_->atomData.torque[i] += trq_tmp[i];
591          trq_tmp[i] = 0.0;
592        }
593        
594 <      AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
594 >      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
595        for (int i = 0; i < n; i++)
596 <        snap->atomData.torque[i] += trq_tmp[i];
596 >        snap_->atomData.torque[i] += trq_tmp[i];
597      }
598      
599 <    int nLocal = snap->getNumberOfAtoms();
599 >    nLocal_ = snap_->getNumberOfAtoms();
600  
601 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
602 <                                       vector<RealType> (nLocal, 0.0));
601 >    vector<potVec> pot_temp(nLocal_,
602 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
603 >
604 >    // scatter/gather pot_row into the members of my column
605 >          
606 >    AtomCommPotRow->scatter(pot_row, pot_temp);
607 >
608 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
609 >      pot_local += pot_temp[ii];
610      
611 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
612 <      AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
613 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
614 <        pot_local[i] += pot_temp[i][ii];
615 <      }
611 >    fill(pot_temp.begin(), pot_temp.end(),
612 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
613 >      
614 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
615 >    
616 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
617 >      pot_local += pot_temp[ii];
618 >    
619 > #endif
620 >  }
621 >
622 >  int ForceMatrixDecomposition::getNAtomsInRow() {  
623 > #ifdef IS_MPI
624 >    return nAtomsInRow_;
625 > #else
626 >    return nLocal_;
627 > #endif
628 >  }
629 >
630 >  /**
631 >   * returns the list of atoms belonging to this group.  
632 >   */
633 >  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
634 > #ifdef IS_MPI
635 >    return groupListRow_[cg1];
636 > #else
637 >    return groupList_[cg1];
638 > #endif
639 >  }
640 >
641 >  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
642 > #ifdef IS_MPI
643 >    return groupListCol_[cg2];
644 > #else
645 >    return groupList_[cg2];
646 > #endif
647 >  }
648 >  
649 >  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
650 >    Vector3d d;
651 >    
652 > #ifdef IS_MPI
653 >    d = cgColData.position[cg2] - cgRowData.position[cg1];
654 > #else
655 >    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
656 > #endif
657 >    
658 >    snap_->wrapVector(d);
659 >    return d;    
660 >  }
661 >
662 >
663 >  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
664 >
665 >    Vector3d d;
666 >    
667 > #ifdef IS_MPI
668 >    d = cgRowData.position[cg1] - atomRowData.position[atom1];
669 > #else
670 >    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
671 > #endif
672 >
673 >    snap_->wrapVector(d);
674 >    return d;    
675 >  }
676 >  
677 >  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
678 >    Vector3d d;
679 >    
680 > #ifdef IS_MPI
681 >    d = cgColData.position[cg2] - atomColData.position[atom2];
682 > #else
683 >    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
684 > #endif
685 >    
686 >    snap_->wrapVector(d);
687 >    return d;    
688 >  }
689 >
690 >  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
691 > #ifdef IS_MPI
692 >    return massFactorsRow[atom1];
693 > #else
694 >    return massFactors[atom1];
695 > #endif
696 >  }
697 >
698 >  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
699 > #ifdef IS_MPI
700 >    return massFactorsCol[atom2];
701 > #else
702 >    return massFactors[atom2];
703 > #endif
704 >
705 >  }
706 >    
707 >  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
708 >    Vector3d d;
709 >    
710 > #ifdef IS_MPI
711 >    d = atomColData.position[atom2] - atomRowData.position[atom1];
712 > #else
713 >    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
714 > #endif
715 >
716 >    snap_->wrapVector(d);
717 >    return d;    
718 >  }
719 >
720 >  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
721 >    return skipsForAtom[atom1];
722 >  }
723 >
724 >  /**
725 >   * There are a number of reasons to skip a pair or a
726 >   * particle. Mostly we do this to exclude atoms who are involved in
727 >   * short range interactions (bonds, bends, torsions), but we also
728 >   * need to exclude some overcounted interactions that result from
729 >   * the parallel decomposition.
730 >   */
731 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
732 >    int unique_id_1, unique_id_2;
733 >
734 > #ifdef IS_MPI
735 >    // in MPI, we have to look up the unique IDs for each atom
736 >    unique_id_1 = AtomRowToGlobal[atom1];
737 >    unique_id_2 = AtomColToGlobal[atom2];
738 >
739 >    // this situation should only arise in MPI simulations
740 >    if (unique_id_1 == unique_id_2) return true;
741 >    
742 >    // this prevents us from doing the pair on multiple processors
743 >    if (unique_id_1 < unique_id_2) {
744 >      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
745 >    } else {
746 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
747      }
748 + #else
749 +    // in the normal loop, the atom numbers are unique
750 +    unique_id_1 = atom1;
751 +    unique_id_2 = atom2;
752   #endif
753 +    
754 +    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
755 +         i != skipsForAtom[atom1].end(); ++i) {
756 +      if ( (*i) == unique_id_2 ) return true;
757 +    }    
758 +
759    }
760 +
761 +
762 +  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
763 + #ifdef IS_MPI
764 +    atomRowData.force[atom1] += fg;
765 + #else
766 +    snap_->atomData.force[atom1] += fg;
767 + #endif
768 +  }
769 +
770 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
771 + #ifdef IS_MPI
772 +    atomColData.force[atom2] += fg;
773 + #else
774 +    snap_->atomData.force[atom2] += fg;
775 + #endif
776 +  }
777 +
778 +    // filling interaction blocks with pointers
779 +  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
780 +                                                     int atom1, int atom2) {    
781 + #ifdef IS_MPI
782 +    
783 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
784 +                             ff_->getAtomType(identsCol[atom2]) );
785 +    
786 +    if (storageLayout_ & DataStorage::dslAmat) {
787 +      idat.A1 = &(atomRowData.aMat[atom1]);
788 +      idat.A2 = &(atomColData.aMat[atom2]);
789 +    }
790 +    
791 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
792 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
793 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
794 +    }
795 +
796 +    if (storageLayout_ & DataStorage::dslTorque) {
797 +      idat.t1 = &(atomRowData.torque[atom1]);
798 +      idat.t2 = &(atomColData.torque[atom2]);
799 +    }
800 +
801 +    if (storageLayout_ & DataStorage::dslDensity) {
802 +      idat.rho1 = &(atomRowData.density[atom1]);
803 +      idat.rho2 = &(atomColData.density[atom2]);
804 +    }
805 +
806 +    if (storageLayout_ & DataStorage::dslFunctional) {
807 +      idat.frho1 = &(atomRowData.functional[atom1]);
808 +      idat.frho2 = &(atomColData.functional[atom2]);
809 +    }
810 +
811 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
812 +      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
813 +      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
814 +    }
815 +
816 +    if (storageLayout_ & DataStorage::dslParticlePot) {
817 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
818 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
819 +    }
820 +
821 + #else
822 +
823 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
824 +                             ff_->getAtomType(identsLocal[atom2]) );
825 +
826 +    if (storageLayout_ & DataStorage::dslAmat) {
827 +      idat.A1 = &(snap_->atomData.aMat[atom1]);
828 +      idat.A2 = &(snap_->atomData.aMat[atom2]);
829 +    }
830 +
831 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
832 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
833 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
834 +    }
835 +
836 +    if (storageLayout_ & DataStorage::dslTorque) {
837 +      idat.t1 = &(snap_->atomData.torque[atom1]);
838 +      idat.t2 = &(snap_->atomData.torque[atom2]);
839 +    }
840 +
841 +    if (storageLayout_ & DataStorage::dslDensity) {
842 +      idat.rho1 = &(snap_->atomData.density[atom1]);
843 +      idat.rho2 = &(snap_->atomData.density[atom2]);
844 +    }
845 +
846 +    if (storageLayout_ & DataStorage::dslFunctional) {
847 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
848 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
849 +    }
850 +
851 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
852 +      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
853 +      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
854 +    }
855 +
856 +    if (storageLayout_ & DataStorage::dslParticlePot) {
857 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
858 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
859 +    }
860 +
861 + #endif
862 +  }
863 +
864    
865 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
866 + #ifdef IS_MPI
867 +    pot_row[atom1] += 0.5 *  *(idat.pot);
868 +    pot_col[atom2] += 0.5 *  *(idat.pot);
869 +
870 +    atomRowData.force[atom1] += *(idat.f1);
871 +    atomColData.force[atom2] -= *(idat.f1);
872 + #else
873 +    longRangePot_ += *(idat.pot);
874 +    
875 +    snap_->atomData.force[atom1] += *(idat.f1);
876 +    snap_->atomData.force[atom2] -= *(idat.f1);
877 + #endif
878 +
879 +  }
880 +
881 +
882 +  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
883 +                                              int atom1, int atom2) {
884 + #ifdef IS_MPI
885 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
886 +                             ff_->getAtomType(identsCol[atom2]) );
887 +
888 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
889 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
890 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
891 +    }
892 +    if (storageLayout_ & DataStorage::dslTorque) {
893 +      idat.t1 = &(atomRowData.torque[atom1]);
894 +      idat.t2 = &(atomColData.torque[atom2]);
895 +    }
896 + #else
897 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
898 +                             ff_->getAtomType(identsLocal[atom2]) );
899 +
900 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
901 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
902 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
903 +    }
904 +    if (storageLayout_ & DataStorage::dslTorque) {
905 +      idat.t1 = &(snap_->atomData.torque[atom1]);
906 +      idat.t2 = &(snap_->atomData.torque[atom2]);
907 +    }
908 + #endif    
909 +  }
910 +
911 +  /*
912 +   * buildNeighborList
913 +   *
914 +   * first element of pair is row-indexed CutoffGroup
915 +   * second element of pair is column-indexed CutoffGroup
916 +   */
917 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
918 +      
919 +    vector<pair<int, int> > neighborList;
920 +    groupCutoffs cuts;
921 + #ifdef IS_MPI
922 +    cellListRow_.clear();
923 +    cellListCol_.clear();
924 + #else
925 +    cellList_.clear();
926 + #endif
927 +
928 +    RealType rList_ = (largestRcut_ + skinThickness_);
929 +    RealType rl2 = rList_ * rList_;
930 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
931 +    Mat3x3d Hmat = snap_->getHmat();
932 +    Vector3d Hx = Hmat.getColumn(0);
933 +    Vector3d Hy = Hmat.getColumn(1);
934 +    Vector3d Hz = Hmat.getColumn(2);
935 +
936 +    nCells_.x() = (int) ( Hx.length() )/ rList_;
937 +    nCells_.y() = (int) ( Hy.length() )/ rList_;
938 +    nCells_.z() = (int) ( Hz.length() )/ rList_;
939 +
940 +    Mat3x3d invHmat = snap_->getInvHmat();
941 +    Vector3d rs, scaled, dr;
942 +    Vector3i whichCell;
943 +    int cellIndex;
944 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
945 +
946 + #ifdef IS_MPI
947 +    cellListRow_.resize(nCtot);
948 +    cellListCol_.resize(nCtot);
949 + #else
950 +    cellList_.resize(nCtot);
951 + #endif
952 +
953 + #ifdef IS_MPI
954 +    for (int i = 0; i < nGroupsInRow_; i++) {
955 +      rs = cgRowData.position[i];
956 +
957 +      // scaled positions relative to the box vectors
958 +      scaled = invHmat * rs;
959 +
960 +      // wrap the vector back into the unit box by subtracting integer box
961 +      // numbers
962 +      for (int j = 0; j < 3; j++) {
963 +        scaled[j] -= roundMe(scaled[j]);
964 +        scaled[j] += 0.5;
965 +      }
966 +    
967 +      // find xyz-indices of cell that cutoffGroup is in.
968 +      whichCell.x() = nCells_.x() * scaled.x();
969 +      whichCell.y() = nCells_.y() * scaled.y();
970 +      whichCell.z() = nCells_.z() * scaled.z();
971 +
972 +      // find single index of this cell:
973 +      cellIndex = Vlinear(whichCell, nCells_);
974 +
975 +      // add this cutoff group to the list of groups in this cell;
976 +      cellListRow_[cellIndex].push_back(i);
977 +    }
978 +
979 +    for (int i = 0; i < nGroupsInCol_; i++) {
980 +      rs = cgColData.position[i];
981 +
982 +      // scaled positions relative to the box vectors
983 +      scaled = invHmat * rs;
984 +
985 +      // wrap the vector back into the unit box by subtracting integer box
986 +      // numbers
987 +      for (int j = 0; j < 3; j++) {
988 +        scaled[j] -= roundMe(scaled[j]);
989 +        scaled[j] += 0.5;
990 +      }
991 +
992 +      // find xyz-indices of cell that cutoffGroup is in.
993 +      whichCell.x() = nCells_.x() * scaled.x();
994 +      whichCell.y() = nCells_.y() * scaled.y();
995 +      whichCell.z() = nCells_.z() * scaled.z();
996 +
997 +      // find single index of this cell:
998 +      cellIndex = Vlinear(whichCell, nCells_);
999 +
1000 +      // add this cutoff group to the list of groups in this cell;
1001 +      cellListCol_[cellIndex].push_back(i);
1002 +    }
1003 + #else
1004 +    for (int i = 0; i < nGroups_; i++) {
1005 +      rs = snap_->cgData.position[i];
1006 +
1007 +      // scaled positions relative to the box vectors
1008 +      scaled = invHmat * rs;
1009 +
1010 +      // wrap the vector back into the unit box by subtracting integer box
1011 +      // numbers
1012 +      for (int j = 0; j < 3; j++) {
1013 +        scaled[j] -= roundMe(scaled[j]);
1014 +        scaled[j] += 0.5;
1015 +      }
1016 +
1017 +      // find xyz-indices of cell that cutoffGroup is in.
1018 +      whichCell.x() = nCells_.x() * scaled.x();
1019 +      whichCell.y() = nCells_.y() * scaled.y();
1020 +      whichCell.z() = nCells_.z() * scaled.z();
1021 +
1022 +      // find single index of this cell:
1023 +      cellIndex = Vlinear(whichCell, nCells_);      
1024 +
1025 +      // add this cutoff group to the list of groups in this cell;
1026 +      cellList_[cellIndex].push_back(i);
1027 +    }
1028 + #endif
1029 +
1030 +    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1031 +      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1032 +        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1033 +          Vector3i m1v(m1x, m1y, m1z);
1034 +          int m1 = Vlinear(m1v, nCells_);
1035 +
1036 +          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1037 +               os != cellOffsets_.end(); ++os) {
1038 +            
1039 +            Vector3i m2v = m1v + (*os);
1040 +            
1041 +            if (m2v.x() >= nCells_.x()) {
1042 +              m2v.x() = 0;          
1043 +            } else if (m2v.x() < 0) {
1044 +              m2v.x() = nCells_.x() - 1;
1045 +            }
1046 +            
1047 +            if (m2v.y() >= nCells_.y()) {
1048 +              m2v.y() = 0;          
1049 +            } else if (m2v.y() < 0) {
1050 +              m2v.y() = nCells_.y() - 1;
1051 +            }
1052 +            
1053 +            if (m2v.z() >= nCells_.z()) {
1054 +              m2v.z() = 0;          
1055 +            } else if (m2v.z() < 0) {
1056 +              m2v.z() = nCells_.z() - 1;
1057 +            }
1058 +            
1059 +            int m2 = Vlinear (m2v, nCells_);
1060 +
1061 + #ifdef IS_MPI
1062 +            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1063 +                 j1 != cellListRow_[m1].end(); ++j1) {
1064 +              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1065 +                   j2 != cellListCol_[m2].end(); ++j2) {
1066 +                              
1067 +                // Always do this if we're in different cells or if
1068 +                // we're in the same cell and the global index of the
1069 +                // j2 cutoff group is less than the j1 cutoff group
1070 +
1071 +                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1072 +                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1073 +                  snap_->wrapVector(dr);
1074 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1075 +                  if (dr.lengthSquare() < cuts.third) {
1076 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1077 +                  }
1078 +                }
1079 +              }
1080 +            }
1081 + #else
1082 +
1083 +            for (vector<int>::iterator j1 = cellList_[m1].begin();
1084 +                 j1 != cellList_[m1].end(); ++j1) {
1085 +              for (vector<int>::iterator j2 = cellList_[m2].begin();
1086 +                   j2 != cellList_[m2].end(); ++j2) {
1087 +
1088 +                // Always do this if we're in different cells or if
1089 +                // we're in the same cell and the global index of the
1090 +                // j2 cutoff group is less than the j1 cutoff group
1091 +
1092 +                if (m2 != m1 || (*j2) < (*j1)) {
1093 +                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1094 +                  snap_->wrapVector(dr);
1095 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1096 +                  if (dr.lengthSquare() < cuts.third) {
1097 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1098 +                  }
1099 +                }
1100 +              }
1101 +            }
1102 + #endif
1103 +          }
1104 +        }
1105 +      }
1106 +    }
1107 +    
1108 +    // save the local cutoff group positions for the check that is
1109 +    // done on each loop:
1110 +    saved_CG_positions_.clear();
1111 +    for (int i = 0; i < nGroups_; i++)
1112 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1113 +    
1114 +    return neighborList;
1115 +  }
1116   } //end namespace OpenMD

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