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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1539 by gezelter, Fri Jan 14 22:31:31 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1668 by gezelter, Fri Jan 6 19:03:05 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42 < #include "parallel/ForceDecomposition.hpp"
42 < #include "parallel/Communicator.hpp"
42 > #include "parallel/ForceMatrixDecomposition.hpp"
43   #include "math/SquareMatrix3.hpp"
44 + #include "nonbonded/NonBondedInteraction.hpp"
45 + #include "brains/SnapshotManager.hpp"
46 + #include "brains/PairList.hpp"
47  
48 + using namespace std;
49   namespace OpenMD {
50  
51 <  void ForceDecomposition::distributeInitialData() {
51 >  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52 >
53 >    // In a parallel computation, row and colum scans must visit all
54 >    // surrounding cells (not just the 14 upper triangular blocks that
55 >    // are used when the processor can see all pairs)
56   #ifdef IS_MPI
57 +    cellOffsets_.clear();
58 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
61 +    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
66 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );      
71 +    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72 +    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73 +    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74 +    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75 +    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76 +    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77 +    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78 +    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80 +    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81 +    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82 +    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83 +    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84 +    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85 + #endif    
86 +  }
87  
50 –    int nAtoms;
51 –    int nGroups;
88  
89 <    AtomCommRealI = new Comm<I,RealType>(nAtoms);
90 <    AtomCommVectorI = new Comm<I,Vector3d>(nAtoms);
91 <    AtomCommMatrixI = new Comm<I,Mat3x3d>(nAtoms);
89 >  /**
90 >   * distributeInitialData is essentially a copy of the older fortran
91 >   * SimulationSetup
92 >   */
93 >  void ForceMatrixDecomposition::distributeInitialData() {
94 >    snap_ = sman_->getCurrentSnapshot();
95 >    storageLayout_ = sman_->getStorageLayout();
96 >    ff_ = info_->getForceField();
97 >    nLocal_ = snap_->getNumberOfAtoms();
98 >    
99 >    nGroups_ = info_->getNLocalCutoffGroups();
100 >    // gather the information for atomtype IDs (atids):
101 >    idents = info_->getIdentArray();
102 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
103 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
104 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
105  
106 <    AtomCommRealJ = new Comm<J,RealType>(nAtoms);
58 <    AtomCommVectorJ = new Comm<J,Vector3d>(nAtoms);
59 <    AtomCommMatrixJ = new Comm<J,Mat3x3d>(nAtoms);
106 >    massFactors = info_->getMassFactors();
107  
108 <    cgCommVectorI = new Comm<I,Vector3d>(nGroups);
109 <    cgCommVectorJ = new Comm<J,Vector3d>(nGroups);
110 <    // more to come
108 >    PairList* excludes = info_->getExcludedInteractions();
109 >    PairList* oneTwo = info_->getOneTwoInteractions();
110 >    PairList* oneThree = info_->getOneThreeInteractions();
111 >    PairList* oneFour = info_->getOneFourInteractions();
112 >
113 > #ifdef IS_MPI
114 >
115 >    MPI::Intracomm row = rowComm.getComm();
116 >    MPI::Intracomm col = colComm.getComm();
117 >
118 >    AtomPlanIntRow = new Plan<int>(row, nLocal_);
119 >    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
120 >    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
121 >    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
122 >    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
123 >
124 >    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
125 >    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
126 >    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
127 >    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
128 >    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
129 >
130 >    cgPlanIntRow = new Plan<int>(row, nGroups_);
131 >    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
132 >    cgPlanIntColumn = new Plan<int>(col, nGroups_);
133 >    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
134 >
135 >    nAtomsInRow_ = AtomPlanIntRow->getSize();
136 >    nAtomsInCol_ = AtomPlanIntColumn->getSize();
137 >    nGroupsInRow_ = cgPlanIntRow->getSize();
138 >    nGroupsInCol_ = cgPlanIntColumn->getSize();
139 >
140 >    // Modify the data storage objects with the correct layouts and sizes:
141 >    atomRowData.resize(nAtomsInRow_);
142 >    atomRowData.setStorageLayout(storageLayout_);
143 >    atomColData.resize(nAtomsInCol_);
144 >    atomColData.setStorageLayout(storageLayout_);
145 >    cgRowData.resize(nGroupsInRow_);
146 >    cgRowData.setStorageLayout(DataStorage::dslPosition);
147 >    cgColData.resize(nGroupsInCol_);
148 >    cgColData.setStorageLayout(DataStorage::dslPosition);
149 >        
150 >    identsRow.resize(nAtomsInRow_);
151 >    identsCol.resize(nAtomsInCol_);
152 >    
153 >    AtomPlanIntRow->gather(idents, identsRow);
154 >    AtomPlanIntColumn->gather(idents, identsCol);
155 >    
156 >    // allocate memory for the parallel objects
157 >    atypesRow.resize(nAtomsInRow_);
158 >    atypesCol.resize(nAtomsInCol_);
159 >
160 >    for (int i = 0; i < nAtomsInRow_; i++)
161 >      atypesRow[i] = ff_->getAtomType(identsRow[i]);
162 >    for (int i = 0; i < nAtomsInCol_; i++)
163 >      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
164 >
165 >    pot_row.resize(nAtomsInRow_);
166 >    pot_col.resize(nAtomsInCol_);
167 >
168 >    AtomRowToGlobal.resize(nAtomsInRow_);
169 >    AtomColToGlobal.resize(nAtomsInCol_);
170 >    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
171 >    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
172 >
173 >    cgRowToGlobal.resize(nGroupsInRow_);
174 >    cgColToGlobal.resize(nGroupsInCol_);
175 >    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176 >    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177 >
178 >    massFactorsRow.resize(nAtomsInRow_);
179 >    massFactorsCol.resize(nAtomsInCol_);
180 >    AtomPlanRealRow->gather(massFactors, massFactorsRow);
181 >    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
182 >
183 >    groupListRow_.clear();
184 >    groupListRow_.resize(nGroupsInRow_);
185 >    for (int i = 0; i < nGroupsInRow_; i++) {
186 >      int gid = cgRowToGlobal[i];
187 >      for (int j = 0; j < nAtomsInRow_; j++) {
188 >        int aid = AtomRowToGlobal[j];
189 >        if (globalGroupMembership[aid] == gid)
190 >          groupListRow_[i].push_back(j);
191 >      }      
192 >    }
193 >
194 >    groupListCol_.clear();
195 >    groupListCol_.resize(nGroupsInCol_);
196 >    for (int i = 0; i < nGroupsInCol_; i++) {
197 >      int gid = cgColToGlobal[i];
198 >      for (int j = 0; j < nAtomsInCol_; j++) {
199 >        int aid = AtomColToGlobal[j];
200 >        if (globalGroupMembership[aid] == gid)
201 >          groupListCol_[i].push_back(j);
202 >      }      
203 >    }
204 >
205 >    excludesForAtom.clear();
206 >    excludesForAtom.resize(nAtomsInRow_);
207 >    toposForAtom.clear();
208 >    toposForAtom.resize(nAtomsInRow_);
209 >    topoDist.clear();
210 >    topoDist.resize(nAtomsInRow_);
211 >    for (int i = 0; i < nAtomsInRow_; i++) {
212 >      int iglob = AtomRowToGlobal[i];
213 >
214 >      for (int j = 0; j < nAtomsInCol_; j++) {
215 >        int jglob = AtomColToGlobal[j];
216 >
217 >        if (excludes->hasPair(iglob, jglob))
218 >          excludesForAtom[i].push_back(j);      
219 >        
220 >        if (oneTwo->hasPair(iglob, jglob)) {
221 >          toposForAtom[i].push_back(j);
222 >          topoDist[i].push_back(1);
223 >        } else {
224 >          if (oneThree->hasPair(iglob, jglob)) {
225 >            toposForAtom[i].push_back(j);
226 >            topoDist[i].push_back(2);
227 >          } else {
228 >            if (oneFour->hasPair(iglob, jglob)) {
229 >              toposForAtom[i].push_back(j);
230 >              topoDist[i].push_back(3);
231 >            }
232 >          }
233 >        }
234 >      }      
235 >    }
236 >
237 > #else
238 >    excludesForAtom.clear();
239 >    excludesForAtom.resize(nLocal_);
240 >    toposForAtom.clear();
241 >    toposForAtom.resize(nLocal_);
242 >    topoDist.clear();
243 >    topoDist.resize(nLocal_);
244 >
245 >    for (int i = 0; i < nLocal_; i++) {
246 >      int iglob = AtomLocalToGlobal[i];
247 >
248 >      for (int j = 0; j < nLocal_; j++) {
249 >        int jglob = AtomLocalToGlobal[j];
250 >
251 >        if (excludes->hasPair(iglob, jglob))
252 >          excludesForAtom[i].push_back(j);              
253 >        
254 >        if (oneTwo->hasPair(iglob, jglob)) {
255 >          toposForAtom[i].push_back(j);
256 >          topoDist[i].push_back(1);
257 >        } else {
258 >          if (oneThree->hasPair(iglob, jglob)) {
259 >            toposForAtom[i].push_back(j);
260 >            topoDist[i].push_back(2);
261 >          } else {
262 >            if (oneFour->hasPair(iglob, jglob)) {
263 >              toposForAtom[i].push_back(j);
264 >              topoDist[i].push_back(3);
265 >            }
266 >          }
267 >        }
268 >      }      
269 >    }
270   #endif
271 +
272 +    // allocate memory for the parallel objects
273 +    atypesLocal.resize(nLocal_);
274 +
275 +    for (int i = 0; i < nLocal_; i++)
276 +      atypesLocal[i] = ff_->getAtomType(idents[i]);
277 +
278 +    groupList_.clear();
279 +    groupList_.resize(nGroups_);
280 +    for (int i = 0; i < nGroups_; i++) {
281 +      int gid = cgLocalToGlobal[i];
282 +      for (int j = 0; j < nLocal_; j++) {
283 +        int aid = AtomLocalToGlobal[j];
284 +        if (globalGroupMembership[aid] == gid) {
285 +          groupList_[i].push_back(j);
286 +        }
287 +      }      
288 +    }
289 +
290 +
291 +    createGtypeCutoffMap();
292 +
293    }
294 +  
295 +  void ForceMatrixDecomposition::createGtypeCutoffMap() {
296      
297 +    RealType tol = 1e-6;
298 +    largestRcut_ = 0.0;
299 +    RealType rc;
300 +    int atid;
301 +    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302 +    
303 +    map<int, RealType> atypeCutoff;
304 +      
305 +    for (set<AtomType*>::iterator at = atypes.begin();
306 +         at != atypes.end(); ++at){
307 +      atid = (*at)->getIdent();
308 +      if (userChoseCutoff_)
309 +        atypeCutoff[atid] = userCutoff_;
310 +      else
311 +        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312 +    }
313 +    
314 +    vector<RealType> gTypeCutoffs;
315 +    // first we do a single loop over the cutoff groups to find the
316 +    // largest cutoff for any atypes present in this group.
317 + #ifdef IS_MPI
318 +    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
319 +    groupRowToGtype.resize(nGroupsInRow_);
320 +    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
321 +      vector<int> atomListRow = getAtomsInGroupRow(cg1);
322 +      for (vector<int>::iterator ia = atomListRow.begin();
323 +           ia != atomListRow.end(); ++ia) {            
324 +        int atom1 = (*ia);
325 +        atid = identsRow[atom1];
326 +        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
327 +          groupCutoffRow[cg1] = atypeCutoff[atid];
328 +        }
329 +      }
330  
331 <
332 <  void ForceDecomposition::distributeData()  {
331 >      bool gTypeFound = false;
332 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
333 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
334 >          groupRowToGtype[cg1] = gt;
335 >          gTypeFound = true;
336 >        }
337 >      }
338 >      if (!gTypeFound) {
339 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
340 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
341 >      }
342 >      
343 >    }
344 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
345 >    groupColToGtype.resize(nGroupsInCol_);
346 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
347 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
348 >      for (vector<int>::iterator jb = atomListCol.begin();
349 >           jb != atomListCol.end(); ++jb) {            
350 >        int atom2 = (*jb);
351 >        atid = identsCol[atom2];
352 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
353 >          groupCutoffCol[cg2] = atypeCutoff[atid];
354 >        }
355 >      }
356 >      bool gTypeFound = false;
357 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
358 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
359 >          groupColToGtype[cg2] = gt;
360 >          gTypeFound = true;
361 >        }
362 >      }
363 >      if (!gTypeFound) {
364 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
365 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
366 >      }
367 >    }
368 > #else
369 >
370 >    vector<RealType> groupCutoff(nGroups_, 0.0);
371 >    groupToGtype.resize(nGroups_);
372 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
373 >      groupCutoff[cg1] = 0.0;
374 >      vector<int> atomList = getAtomsInGroupRow(cg1);
375 >      for (vector<int>::iterator ia = atomList.begin();
376 >           ia != atomList.end(); ++ia) {            
377 >        int atom1 = (*ia);
378 >        atid = idents[atom1];
379 >        if (atypeCutoff[atid] > groupCutoff[cg1])
380 >          groupCutoff[cg1] = atypeCutoff[atid];
381 >      }
382 >      
383 >      bool gTypeFound = false;
384 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
386 >          groupToGtype[cg1] = gt;
387 >          gTypeFound = true;
388 >        }
389 >      }
390 >      if (!gTypeFound) {      
391 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
392 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393 >      }      
394 >    }
395 > #endif
396 >
397 >    // Now we find the maximum group cutoff value present in the simulation
398 >
399 >    RealType groupMax = *max_element(gTypeCutoffs.begin(),
400 >                                     gTypeCutoffs.end());
401 >
402   #ifdef IS_MPI
403 <    Snapshot* snap = sman_->getCurrentSnapshot();
403 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404 >                              MPI::MAX);
405 > #endif
406 >    
407 >    RealType tradRcut = groupMax;
408  
409 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
410 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
411 +        RealType thisRcut;
412 +        switch(cutoffPolicy_) {
413 +        case TRADITIONAL:
414 +          thisRcut = tradRcut;
415 +          break;
416 +        case MIX:
417 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
418 +          break;
419 +        case MAX:
420 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
421 +          break;
422 +        default:
423 +          sprintf(painCave.errMsg,
424 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
425 +                  "hit an unknown cutoff policy!\n");
426 +          painCave.severity = OPENMD_ERROR;
427 +          painCave.isFatal = 1;
428 +          simError();
429 +          break;
430 +        }
431 +
432 +        pair<int,int> key = make_pair(i,j);
433 +        gTypeCutoffMap[key].first = thisRcut;
434 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
435 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
436 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
437 +        // sanity check
438 +        
439 +        if (userChoseCutoff_) {
440 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
441 +            sprintf(painCave.errMsg,
442 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
443 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
444 +            painCave.severity = OPENMD_ERROR;
445 +            painCave.isFatal = 1;
446 +            simError();            
447 +          }
448 +        }
449 +      }
450 +    }
451 +  }
452 +
453 +
454 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
455 +    int i, j;  
456 + #ifdef IS_MPI
457 +    i = groupRowToGtype[cg1];
458 +    j = groupColToGtype[cg2];
459 + #else
460 +    i = groupToGtype[cg1];
461 +    j = groupToGtype[cg2];
462 + #endif    
463 +    return gTypeCutoffMap[make_pair(i,j)];
464 +  }
465 +
466 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
467 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
468 +      if (toposForAtom[atom1][j] == atom2)
469 +        return topoDist[atom1][j];
470 +    }
471 +    return 0;
472 +  }
473 +
474 +  void ForceMatrixDecomposition::zeroWorkArrays() {
475 +    pairwisePot = 0.0;
476 +    embeddingPot = 0.0;
477 +
478 + #ifdef IS_MPI
479 +    if (storageLayout_ & DataStorage::dslForce) {
480 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
481 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
482 +    }
483 +
484 +    if (storageLayout_ & DataStorage::dslTorque) {
485 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
486 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
487 +    }
488 +    
489 +    fill(pot_row.begin(), pot_row.end(),
490 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
491 +
492 +    fill(pot_col.begin(), pot_col.end(),
493 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
494 +
495 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
496 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
497 +           0.0);
498 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
499 +           0.0);
500 +    }
501 +
502 +    if (storageLayout_ & DataStorage::dslDensity) {      
503 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
504 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
505 +    }
506 +
507 +    if (storageLayout_ & DataStorage::dslFunctional) {  
508 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
509 +           0.0);
510 +      fill(atomColData.functional.begin(), atomColData.functional.end(),
511 +           0.0);
512 +    }
513 +
514 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
515 +      fill(atomRowData.functionalDerivative.begin(),
516 +           atomRowData.functionalDerivative.end(), 0.0);
517 +      fill(atomColData.functionalDerivative.begin(),
518 +           atomColData.functionalDerivative.end(), 0.0);
519 +    }
520 +
521 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
522 +      fill(atomRowData.skippedCharge.begin(),
523 +           atomRowData.skippedCharge.end(), 0.0);
524 +      fill(atomColData.skippedCharge.begin(),
525 +           atomColData.skippedCharge.end(), 0.0);
526 +    }
527 +
528 + #endif
529 +    // even in parallel, we need to zero out the local arrays:
530 +
531 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
532 +      fill(snap_->atomData.particlePot.begin(),
533 +           snap_->atomData.particlePot.end(), 0.0);
534 +    }
535 +    
536 +    if (storageLayout_ & DataStorage::dslDensity) {      
537 +      fill(snap_->atomData.density.begin(),
538 +           snap_->atomData.density.end(), 0.0);
539 +    }
540 +    if (storageLayout_ & DataStorage::dslFunctional) {
541 +      fill(snap_->atomData.functional.begin(),
542 +           snap_->atomData.functional.end(), 0.0);
543 +    }
544 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
545 +      fill(snap_->atomData.functionalDerivative.begin(),
546 +           snap_->atomData.functionalDerivative.end(), 0.0);
547 +    }
548 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
549 +      fill(snap_->atomData.skippedCharge.begin(),
550 +           snap_->atomData.skippedCharge.end(), 0.0);
551 +    }
552 +    
553 +  }
554 +
555 +
556 +  void ForceMatrixDecomposition::distributeData()  {
557 +    snap_ = sman_->getCurrentSnapshot();
558 +    storageLayout_ = sman_->getStorageLayout();
559 + #ifdef IS_MPI
560 +    
561      // gather up the atomic positions
562 <    AtomCommVectorI->gather(snap->atomData.position,
563 <                            snap->atomIData.position);
564 <    AtomCommVectorJ->gather(snap->atomData.position,
565 <                           snap->atomJData.position);
562 >    AtomPlanVectorRow->gather(snap_->atomData.position,
563 >                              atomRowData.position);
564 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
565 >                                 atomColData.position);
566      
567      // gather up the cutoff group positions
568 <    cgCommVectorI->gather(snap->cgData.position,
569 <                         snap->cgIData.position);
570 <    cgCommVectorJ->gather(snap->cgData.position,
571 <                         snap->cgJData.position);
568 >
569 >    cgPlanVectorRow->gather(snap_->cgData.position,
570 >                            cgRowData.position);
571 >
572 >    cgPlanVectorColumn->gather(snap_->cgData.position,
573 >                               cgColData.position);
574 >
575      
576      // if needed, gather the atomic rotation matrices
577 <    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
578 <      AtomCommMatrixI->gather(snap->atomData.aMat,
579 <                             snap->atomIData.aMat);
580 <      AtomCommMatrixJ->gather(snap->atomData.aMat,
581 <                             snap->atomJData.aMat);
577 >    if (storageLayout_ & DataStorage::dslAmat) {
578 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
579 >                                atomRowData.aMat);
580 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
581 >                                   atomColData.aMat);
582      }
583      
584      // if needed, gather the atomic eletrostatic frames
585 <    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
586 <      AtomCommMatrixI->gather(snap->atomData.electroFrame,
587 <                             snap->atomIData.electroFrame);
588 <      AtomCommMatrixJ->gather(snap->atomData.electroFrame,
589 <                             snap->atomJData.electroFrame);
585 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
586 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
587 >                                atomRowData.electroFrame);
588 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
589 >                                   atomColData.electroFrame);
590      }
591 +
592   #endif      
593    }
594    
595 <  void ForceDecomposition::collectIntermediateData() {
595 >  /* collects information obtained during the pre-pair loop onto local
596 >   * data structures.
597 >   */
598 >  void ForceMatrixDecomposition::collectIntermediateData() {
599 >    snap_ = sman_->getCurrentSnapshot();
600 >    storageLayout_ = sman_->getStorageLayout();
601   #ifdef IS_MPI
105 –    Snapshot* snap = sman_->getCurrentSnapshot();
106 –    // gather up the atomic positions
602      
603 <    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
604 <      AtomCommRealI->scatter(snap->atomIData.density,
605 <                            snap->atomData.density);
606 <      std::vector<RealType> rho_tmp;
607 <      int n = snap->getNumberOfAtoms();
608 <      rho_tmp.reserve( n );
609 <      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
603 >    if (storageLayout_ & DataStorage::dslDensity) {
604 >      
605 >      AtomPlanRealRow->scatter(atomRowData.density,
606 >                               snap_->atomData.density);
607 >      
608 >      int n = snap_->atomData.density.size();
609 >      vector<RealType> rho_tmp(n, 0.0);
610 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
611        for (int i = 0; i < n; i++)
612 <        snap->atomData.density[i] += rho_tmp[i];
612 >        snap_->atomData.density[i] += rho_tmp[i];
613      }
614   #endif
615    }
616 <  
617 <  void ForceDecomposition::distributeIntermediateData() {
616 >
617 >  /*
618 >   * redistributes information obtained during the pre-pair loop out to
619 >   * row and column-indexed data structures
620 >   */
621 >  void ForceMatrixDecomposition::distributeIntermediateData() {
622 >    snap_ = sman_->getCurrentSnapshot();
623 >    storageLayout_ = sman_->getStorageLayout();
624   #ifdef IS_MPI
625 <    Snapshot* snap = sman_->getCurrentSnapshot();
626 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
627 <      AtomCommRealI->gather(snap->atomData.functional,
628 <                           snap->atomIData.functional);
629 <      AtomCommRealJ->gather(snap->atomData.functional,
128 <                           snap->atomJData.functional);
625 >    if (storageLayout_ & DataStorage::dslFunctional) {
626 >      AtomPlanRealRow->gather(snap_->atomData.functional,
627 >                              atomRowData.functional);
628 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
629 >                                 atomColData.functional);
630      }
631      
632 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
633 <      AtomCommRealI->gather(snap->atomData.functionalDerivative,
634 <                           snap->atomIData.functionalDerivative);
635 <      AtomCommRealJ->gather(snap->atomData.functionalDerivative,
636 <                           snap->atomJData.functionalDerivative);
632 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
633 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
634 >                              atomRowData.functionalDerivative);
635 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
636 >                                 atomColData.functionalDerivative);
637      }
638   #endif
639    }
640    
641    
642 <  void ForceDecomposition::collectData() {
642 >  void ForceMatrixDecomposition::collectData() {
643 >    snap_ = sman_->getCurrentSnapshot();
644 >    storageLayout_ = sman_->getStorageLayout();
645 > #ifdef IS_MPI    
646 >    int n = snap_->atomData.force.size();
647 >    vector<Vector3d> frc_tmp(n, V3Zero);
648 >    
649 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
650 >    for (int i = 0; i < n; i++) {
651 >      snap_->atomData.force[i] += frc_tmp[i];
652 >      frc_tmp[i] = 0.0;
653 >    }
654 >    
655 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
656 >    for (int i = 0; i < n; i++) {
657 >      snap_->atomData.force[i] += frc_tmp[i];
658 >    }
659 >        
660 >    if (storageLayout_ & DataStorage::dslTorque) {
661 >
662 >      int nt = snap_->atomData.torque.size();
663 >      vector<Vector3d> trq_tmp(nt, V3Zero);
664 >
665 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
666 >      for (int i = 0; i < nt; i++) {
667 >        snap_->atomData.torque[i] += trq_tmp[i];
668 >        trq_tmp[i] = 0.0;
669 >      }
670 >      
671 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
672 >      for (int i = 0; i < nt; i++)
673 >        snap_->atomData.torque[i] += trq_tmp[i];
674 >    }
675 >
676 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {
677 >
678 >      int ns = snap_->atomData.skippedCharge.size();
679 >      vector<RealType> skch_tmp(ns, 0.0);
680 >
681 >      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
682 >      for (int i = 0; i < ns; i++) {
683 >        snap_->atomData.skippedCharge[i] += skch_tmp[i];
684 >        skch_tmp[i] = 0.0;
685 >      }
686 >      
687 >      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
688 >      for (int i = 0; i < ns; i++)
689 >        snap_->atomData.skippedCharge[i] += skch_tmp[i];
690 >            
691 >    }
692 >    
693 >    nLocal_ = snap_->getNumberOfAtoms();
694 >
695 >    vector<potVec> pot_temp(nLocal_,
696 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
697 >
698 >    // scatter/gather pot_row into the members of my column
699 >          
700 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
701 >
702 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
703 >      pairwisePot += pot_temp[ii];
704 >    
705 >    fill(pot_temp.begin(), pot_temp.end(),
706 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
707 >      
708 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
709 >    
710 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
711 >      pairwisePot += pot_temp[ii];    
712 >    
713 >    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
714 >      RealType ploc1 = pairwisePot[ii];
715 >      RealType ploc2 = 0.0;
716 >      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
717 >      pairwisePot[ii] = ploc2;
718 >    }
719 >
720 >    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
721 >      RealType ploc1 = embeddingPot[ii];
722 >      RealType ploc2 = 0.0;
723 >      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
724 >      embeddingPot[ii] = ploc2;
725 >    }
726 >
727 > #endif
728 >
729 >  }
730 >
731 >  int ForceMatrixDecomposition::getNAtomsInRow() {  
732   #ifdef IS_MPI
733 +    return nAtomsInRow_;
734 + #else
735 +    return nLocal_;
736 + #endif
737 +  }
738 +
739 +  /**
740 +   * returns the list of atoms belonging to this group.  
741 +   */
742 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
743 + #ifdef IS_MPI
744 +    return groupListRow_[cg1];
745 + #else
746 +    return groupList_[cg1];
747 + #endif
748 +  }
749 +
750 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
751 + #ifdef IS_MPI
752 +    return groupListCol_[cg2];
753 + #else
754 +    return groupList_[cg2];
755 + #endif
756 +  }
757 +  
758 +  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
759 +    Vector3d d;
760 +    
761 + #ifdef IS_MPI
762 +    d = cgColData.position[cg2] - cgRowData.position[cg1];
763 + #else
764 +    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
765 + #endif
766 +    
767 +    snap_->wrapVector(d);
768 +    return d;    
769 +  }
770 +
771 +
772 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
773 +
774 +    Vector3d d;
775 +    
776 + #ifdef IS_MPI
777 +    d = cgRowData.position[cg1] - atomRowData.position[atom1];
778 + #else
779 +    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
780 + #endif
781 +
782 +    snap_->wrapVector(d);
783 +    return d;    
784 +  }
785 +  
786 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
787 +    Vector3d d;
788 +    
789 + #ifdef IS_MPI
790 +    d = cgColData.position[cg2] - atomColData.position[atom2];
791 + #else
792 +    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
793 + #endif
794 +    
795 +    snap_->wrapVector(d);
796 +    return d;    
797 +  }
798 +
799 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
800 + #ifdef IS_MPI
801 +    return massFactorsRow[atom1];
802 + #else
803 +    return massFactors[atom1];
804 + #endif
805 +  }
806 +
807 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
808 + #ifdef IS_MPI
809 +    return massFactorsCol[atom2];
810 + #else
811 +    return massFactors[atom2];
812 + #endif
813 +
814 +  }
815 +    
816 +  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
817 +    Vector3d d;
818 +    
819 + #ifdef IS_MPI
820 +    d = atomColData.position[atom2] - atomRowData.position[atom1];
821 + #else
822 +    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
823 + #endif
824 +
825 +    snap_->wrapVector(d);
826 +    return d;    
827 +  }
828 +
829 +  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
830 +    return excludesForAtom[atom1];
831 +  }
832 +
833 +  /**
834 +   * We need to exclude some overcounted interactions that result from
835 +   * the parallel decomposition.
836 +   */
837 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
838 +    int unique_id_1, unique_id_2;
839 +        
840 + #ifdef IS_MPI
841 +    // in MPI, we have to look up the unique IDs for each atom
842 +    unique_id_1 = AtomRowToGlobal[atom1];
843 +    unique_id_2 = AtomColToGlobal[atom2];
844 + #else
845 +    unique_id_1 = AtomLocalToGlobal[atom1];
846 +    unique_id_2 = AtomLocalToGlobal[atom2];
847 + #endif  
848 +
849 +    if (unique_id_1 == unique_id_2) return true;
850 +
851 + #ifdef IS_MPI
852 +    // this prevents us from doing the pair on multiple processors
853 +    if (unique_id_1 < unique_id_2) {
854 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
855 +    } else {
856 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
857 +    }
858 + #endif
859 +    
860 +    return false;
861 +  }
862 +
863 +  /**
864 +   * We need to handle the interactions for atoms who are involved in
865 +   * the same rigid body as well as some short range interactions
866 +   * (bonds, bends, torsions) differently from other interactions.
867 +   * We'll still visit the pairwise routines, but with a flag that
868 +   * tells those routines to exclude the pair from direct long range
869 +   * interactions.  Some indirect interactions (notably reaction
870 +   * field) must still be handled for these pairs.
871 +   */
872 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
873 +
874 +    // excludesForAtom was constructed to use row/column indices in the MPI
875 +    // version, and to use local IDs in the non-MPI version:
876 +    
877 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
878 +         i != excludesForAtom[atom1].end(); ++i) {
879 +      if ( (*i) == atom2 ) return true;
880 +    }
881 +
882 +    return false;
883 +  }
884 +
885 +
886 +  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
887 + #ifdef IS_MPI
888 +    atomRowData.force[atom1] += fg;
889 + #else
890 +    snap_->atomData.force[atom1] += fg;
891 + #endif
892 +  }
893 +
894 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
895 + #ifdef IS_MPI
896 +    atomColData.force[atom2] += fg;
897 + #else
898 +    snap_->atomData.force[atom2] += fg;
899 + #endif
900 +  }
901 +
902 +    // filling interaction blocks with pointers
903 +  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
904 +                                                     int atom1, int atom2) {
905 +
906 +    idat.excluded = excludeAtomPair(atom1, atom2);
907 +  
908 + #ifdef IS_MPI
909 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
910 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
911 +    //                         ff_->getAtomType(identsCol[atom2]) );
912 +    
913 +    if (storageLayout_ & DataStorage::dslAmat) {
914 +      idat.A1 = &(atomRowData.aMat[atom1]);
915 +      idat.A2 = &(atomColData.aMat[atom2]);
916 +    }
917 +    
918 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
919 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
920 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
921 +    }
922 +
923 +    if (storageLayout_ & DataStorage::dslTorque) {
924 +      idat.t1 = &(atomRowData.torque[atom1]);
925 +      idat.t2 = &(atomColData.torque[atom2]);
926 +    }
927 +
928 +    if (storageLayout_ & DataStorage::dslDensity) {
929 +      idat.rho1 = &(atomRowData.density[atom1]);
930 +      idat.rho2 = &(atomColData.density[atom2]);
931 +    }
932 +
933 +    if (storageLayout_ & DataStorage::dslFunctional) {
934 +      idat.frho1 = &(atomRowData.functional[atom1]);
935 +      idat.frho2 = &(atomColData.functional[atom2]);
936 +    }
937 +
938 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
939 +      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
940 +      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
941 +    }
942 +
943 +    if (storageLayout_ & DataStorage::dslParticlePot) {
944 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
945 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
946 +    }
947 +
948 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
949 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
950 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
951 +    }
952 +
953 + #else
954 +
955 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
956 +    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
957 +    //                         ff_->getAtomType(idents[atom2]) );
958 +
959 +    if (storageLayout_ & DataStorage::dslAmat) {
960 +      idat.A1 = &(snap_->atomData.aMat[atom1]);
961 +      idat.A2 = &(snap_->atomData.aMat[atom2]);
962 +    }
963 +
964 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
965 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
966 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
967 +    }
968 +
969 +    if (storageLayout_ & DataStorage::dslTorque) {
970 +      idat.t1 = &(snap_->atomData.torque[atom1]);
971 +      idat.t2 = &(snap_->atomData.torque[atom2]);
972 +    }
973 +
974 +    if (storageLayout_ & DataStorage::dslDensity) {    
975 +      idat.rho1 = &(snap_->atomData.density[atom1]);
976 +      idat.rho2 = &(snap_->atomData.density[atom2]);
977 +    }
978 +
979 +    if (storageLayout_ & DataStorage::dslFunctional) {
980 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
981 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
982 +    }
983 +
984 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
985 +      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
986 +      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
987 +    }
988 +
989 +    if (storageLayout_ & DataStorage::dslParticlePot) {
990 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
991 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
992 +    }
993 +
994 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
995 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
996 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
997 +    }
998   #endif
999    }
1000 +
1001    
1002 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1003 + #ifdef IS_MPI
1004 +    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1005 +    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1006 +
1007 +    atomRowData.force[atom1] += *(idat.f1);
1008 +    atomColData.force[atom2] -= *(idat.f1);
1009 + #else
1010 +    pairwisePot += *(idat.pot);
1011 +
1012 +    snap_->atomData.force[atom1] += *(idat.f1);
1013 +    snap_->atomData.force[atom2] -= *(idat.f1);
1014 + #endif
1015 +    
1016 +  }
1017 +
1018 +  /*
1019 +   * buildNeighborList
1020 +   *
1021 +   * first element of pair is row-indexed CutoffGroup
1022 +   * second element of pair is column-indexed CutoffGroup
1023 +   */
1024 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1025 +      
1026 +    vector<pair<int, int> > neighborList;
1027 +    groupCutoffs cuts;
1028 +    bool doAllPairs = false;
1029 +
1030 + #ifdef IS_MPI
1031 +    cellListRow_.clear();
1032 +    cellListCol_.clear();
1033 + #else
1034 +    cellList_.clear();
1035 + #endif
1036 +
1037 +    RealType rList_ = (largestRcut_ + skinThickness_);
1038 +    RealType rl2 = rList_ * rList_;
1039 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1040 +    Mat3x3d Hmat = snap_->getHmat();
1041 +    Vector3d Hx = Hmat.getColumn(0);
1042 +    Vector3d Hy = Hmat.getColumn(1);
1043 +    Vector3d Hz = Hmat.getColumn(2);
1044 +
1045 +    nCells_.x() = (int) ( Hx.length() )/ rList_;
1046 +    nCells_.y() = (int) ( Hy.length() )/ rList_;
1047 +    nCells_.z() = (int) ( Hz.length() )/ rList_;
1048 +
1049 +    // handle small boxes where the cell offsets can end up repeating cells
1050 +    
1051 +    if (nCells_.x() < 3) doAllPairs = true;
1052 +    if (nCells_.y() < 3) doAllPairs = true;
1053 +    if (nCells_.z() < 3) doAllPairs = true;
1054 +
1055 +    Mat3x3d invHmat = snap_->getInvHmat();
1056 +    Vector3d rs, scaled, dr;
1057 +    Vector3i whichCell;
1058 +    int cellIndex;
1059 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1060 +
1061 + #ifdef IS_MPI
1062 +    cellListRow_.resize(nCtot);
1063 +    cellListCol_.resize(nCtot);
1064 + #else
1065 +    cellList_.resize(nCtot);
1066 + #endif
1067 +
1068 +    if (!doAllPairs) {
1069 + #ifdef IS_MPI
1070 +
1071 +      for (int i = 0; i < nGroupsInRow_; i++) {
1072 +        rs = cgRowData.position[i];
1073 +        
1074 +        // scaled positions relative to the box vectors
1075 +        scaled = invHmat * rs;
1076 +        
1077 +        // wrap the vector back into the unit box by subtracting integer box
1078 +        // numbers
1079 +        for (int j = 0; j < 3; j++) {
1080 +          scaled[j] -= roundMe(scaled[j]);
1081 +          scaled[j] += 0.5;
1082 +        }
1083 +        
1084 +        // find xyz-indices of cell that cutoffGroup is in.
1085 +        whichCell.x() = nCells_.x() * scaled.x();
1086 +        whichCell.y() = nCells_.y() * scaled.y();
1087 +        whichCell.z() = nCells_.z() * scaled.z();
1088 +        
1089 +        // find single index of this cell:
1090 +        cellIndex = Vlinear(whichCell, nCells_);
1091 +        
1092 +        // add this cutoff group to the list of groups in this cell;
1093 +        cellListRow_[cellIndex].push_back(i);
1094 +      }
1095 +      for (int i = 0; i < nGroupsInCol_; i++) {
1096 +        rs = cgColData.position[i];
1097 +        
1098 +        // scaled positions relative to the box vectors
1099 +        scaled = invHmat * rs;
1100 +        
1101 +        // wrap the vector back into the unit box by subtracting integer box
1102 +        // numbers
1103 +        for (int j = 0; j < 3; j++) {
1104 +          scaled[j] -= roundMe(scaled[j]);
1105 +          scaled[j] += 0.5;
1106 +        }
1107 +        
1108 +        // find xyz-indices of cell that cutoffGroup is in.
1109 +        whichCell.x() = nCells_.x() * scaled.x();
1110 +        whichCell.y() = nCells_.y() * scaled.y();
1111 +        whichCell.z() = nCells_.z() * scaled.z();
1112 +        
1113 +        // find single index of this cell:
1114 +        cellIndex = Vlinear(whichCell, nCells_);
1115 +        
1116 +        // add this cutoff group to the list of groups in this cell;
1117 +        cellListCol_[cellIndex].push_back(i);
1118 +      }
1119 +    
1120 + #else
1121 +      for (int i = 0; i < nGroups_; i++) {
1122 +        rs = snap_->cgData.position[i];
1123 +        
1124 +        // scaled positions relative to the box vectors
1125 +        scaled = invHmat * rs;
1126 +        
1127 +        // wrap the vector back into the unit box by subtracting integer box
1128 +        // numbers
1129 +        for (int j = 0; j < 3; j++) {
1130 +          scaled[j] -= roundMe(scaled[j]);
1131 +          scaled[j] += 0.5;
1132 +        }
1133 +        
1134 +        // find xyz-indices of cell that cutoffGroup is in.
1135 +        whichCell.x() = nCells_.x() * scaled.x();
1136 +        whichCell.y() = nCells_.y() * scaled.y();
1137 +        whichCell.z() = nCells_.z() * scaled.z();
1138 +        
1139 +        // find single index of this cell:
1140 +        cellIndex = Vlinear(whichCell, nCells_);
1141 +        
1142 +        // add this cutoff group to the list of groups in this cell;
1143 +        cellList_[cellIndex].push_back(i);
1144 +      }
1145 +
1146 + #endif
1147 +
1148 +      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1149 +        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1150 +          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1151 +            Vector3i m1v(m1x, m1y, m1z);
1152 +            int m1 = Vlinear(m1v, nCells_);
1153 +            
1154 +            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1155 +                 os != cellOffsets_.end(); ++os) {
1156 +              
1157 +              Vector3i m2v = m1v + (*os);
1158 +            
1159 +
1160 +              if (m2v.x() >= nCells_.x()) {
1161 +                m2v.x() = 0;          
1162 +              } else if (m2v.x() < 0) {
1163 +                m2v.x() = nCells_.x() - 1;
1164 +              }
1165 +              
1166 +              if (m2v.y() >= nCells_.y()) {
1167 +                m2v.y() = 0;          
1168 +              } else if (m2v.y() < 0) {
1169 +                m2v.y() = nCells_.y() - 1;
1170 +              }
1171 +              
1172 +              if (m2v.z() >= nCells_.z()) {
1173 +                m2v.z() = 0;          
1174 +              } else if (m2v.z() < 0) {
1175 +                m2v.z() = nCells_.z() - 1;
1176 +              }
1177 +
1178 +              int m2 = Vlinear (m2v, nCells_);
1179 +              
1180 + #ifdef IS_MPI
1181 +              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1182 +                   j1 != cellListRow_[m1].end(); ++j1) {
1183 +                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1184 +                     j2 != cellListCol_[m2].end(); ++j2) {
1185 +                  
1186 +                  // In parallel, we need to visit *all* pairs of row
1187 +                  // & column indicies and will divide labor in the
1188 +                  // force evaluation later.
1189 +                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1190 +                  snap_->wrapVector(dr);
1191 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1192 +                  if (dr.lengthSquare() < cuts.third) {
1193 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1194 +                  }                  
1195 +                }
1196 +              }
1197 + #else
1198 +              for (vector<int>::iterator j1 = cellList_[m1].begin();
1199 +                   j1 != cellList_[m1].end(); ++j1) {
1200 +                for (vector<int>::iterator j2 = cellList_[m2].begin();
1201 +                     j2 != cellList_[m2].end(); ++j2) {
1202 +    
1203 +                  // Always do this if we're in different cells or if
1204 +                  // we're in the same cell and the global index of
1205 +                  // the j2 cutoff group is greater than or equal to
1206 +                  // the j1 cutoff group.  Note that Rappaport's code
1207 +                  // has a "less than" conditional here, but that
1208 +                  // deals with atom-by-atom computation.  OpenMD
1209 +                  // allows atoms within a single cutoff group to
1210 +                  // interact with each other.
1211 +
1212 +
1213 +
1214 +                  if (m2 != m1 || (*j2) >= (*j1) ) {
1215 +
1216 +                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1217 +                    snap_->wrapVector(dr);
1218 +                    cuts = getGroupCutoffs( (*j1), (*j2) );
1219 +                    if (dr.lengthSquare() < cuts.third) {
1220 +                      neighborList.push_back(make_pair((*j1), (*j2)));
1221 +                    }
1222 +                  }
1223 +                }
1224 +              }
1225 + #endif
1226 +            }
1227 +          }
1228 +        }
1229 +      }
1230 +    } else {
1231 +      // branch to do all cutoff group pairs
1232 + #ifdef IS_MPI
1233 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1234 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1235 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1236 +          snap_->wrapVector(dr);
1237 +          cuts = getGroupCutoffs( j1, j2 );
1238 +          if (dr.lengthSquare() < cuts.third) {
1239 +            neighborList.push_back(make_pair(j1, j2));
1240 +          }
1241 +        }
1242 +      }      
1243 + #else
1244 +      // include all groups here.
1245 +      for (int j1 = 0; j1 < nGroups_; j1++) {
1246 +        // include self group interactions j2 == j1
1247 +        for (int j2 = j1; j2 < nGroups_; j2++) {
1248 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1249 +          snap_->wrapVector(dr);
1250 +          cuts = getGroupCutoffs( j1, j2 );
1251 +          if (dr.lengthSquare() < cuts.third) {
1252 +            neighborList.push_back(make_pair(j1, j2));
1253 +          }
1254 +        }    
1255 +      }
1256 + #endif
1257 +    }
1258 +      
1259 +    // save the local cutoff group positions for the check that is
1260 +    // done on each loop:
1261 +    saved_CG_positions_.clear();
1262 +    for (int i = 0; i < nGroups_; i++)
1263 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1264 +    
1265 +    return neighborList;
1266 +  }
1267   } //end namespace OpenMD

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