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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1541 by gezelter, Fri Feb 4 20:04:56 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1706 by gezelter, Fri Apr 27 20:44:16 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 <    Snapshot* snap = sman_->getCurrentSnapshot();
58 <    int nAtoms = snap->getNumberOfAtoms();
59 <    int nGroups = snap->getNumberOfCutoffGroups();
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  
54 –    AtomCommRealI = new Communicator<Row,RealType>(nAtoms);
55 –    AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms);
56 –    AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nAtoms);
88  
89 <    AtomCommRealJ = new Communicator<Column,RealType>(nAtoms);
90 <    AtomCommVectorJ = new Communicator<Column,Vector3d>(nAtoms);
91 <    AtomCommMatrixJ = new Communicator<Column,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 <    cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
63 <    cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
106 >    massFactors = info_->getMassFactors();
107  
108 <    int nInRow = AtomCommRealI.getSize();
109 <    int nInCol = AtomCommRealJ.getSize();
108 >    PairList* excludes = info_->getExcludedInteractions();
109 >    PairList* oneTwo = info_->getOneTwoInteractions();
110 >    PairList* oneThree = info_->getOneThreeInteractions();
111 >    PairList* oneFour = info_->getOneFourInteractions();
112  
113 <    vector<vector<RealType> > pot_row(LR_POT_TYPES,
114 <                                      vector<RealType> (nInRow, 0.0));
115 <    vector<vector<RealType> > pot_col(LR_POT_TYPES,
116 <                                      vector<RealType> (nInCol, 0.0));
113 > #ifdef IS_MPI
114 >
115 >    MPI::Intracomm row = rowComm.getComm();
116 >    MPI::Intracomm col = colComm.getComm();
117  
118 <    vector<vector<RealType> > pot_local(LR_POT_TYPES,
119 <                                        vector<RealType> (nAtoms, 0.0));
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 +      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 <  void ForceDecomposition::distributeData()  {
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 +
541 +    if (storageLayout_ & DataStorage::dslFunctional) {
542 +      fill(snap_->atomData.functional.begin(),
543 +           snap_->atomData.functional.end(), 0.0);
544 +    }
545 +
546 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
547 +      fill(snap_->atomData.functionalDerivative.begin(),
548 +           snap_->atomData.functionalDerivative.end(), 0.0);
549 +    }
550 +
551 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
552 +      fill(snap_->atomData.skippedCharge.begin(),
553 +           snap_->atomData.skippedCharge.end(), 0.0);
554 +    }
555 +  }
556 +
557 +
558 +  void ForceMatrixDecomposition::distributeData()  {
559 +    snap_ = sman_->getCurrentSnapshot();
560 +    storageLayout_ = sman_->getStorageLayout();
561 + #ifdef IS_MPI
562 +    
563      // gather up the atomic positions
564 <    AtomCommVectorI->gather(snap->atomData.position,
565 <                            snap->atomIData.position);
566 <    AtomCommVectorJ->gather(snap->atomData.position,
567 <                            snap->atomJData.position);
564 >    AtomPlanVectorRow->gather(snap_->atomData.position,
565 >                              atomRowData.position);
566 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
567 >                                 atomColData.position);
568      
569      // gather up the cutoff group positions
570 <    cgCommVectorI->gather(snap->cgData.position,
571 <                          snap->cgIData.position);
572 <    cgCommVectorJ->gather(snap->cgData.position,
573 <                          snap->cgJData.position);
570 >
571 >    cgPlanVectorRow->gather(snap_->cgData.position,
572 >                            cgRowData.position);
573 >
574 >    cgPlanVectorColumn->gather(snap_->cgData.position,
575 >                               cgColData.position);
576 >
577      
578      // if needed, gather the atomic rotation matrices
579 <    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
580 <      AtomCommMatrixI->gather(snap->atomData.aMat,
581 <                              snap->atomIData.aMat);
582 <      AtomCommMatrixJ->gather(snap->atomData.aMat,
583 <                              snap->atomJData.aMat);
579 >    if (storageLayout_ & DataStorage::dslAmat) {
580 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
581 >                                atomRowData.aMat);
582 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
583 >                                   atomColData.aMat);
584      }
585      
586      // if needed, gather the atomic eletrostatic frames
587 <    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
588 <      AtomCommMatrixI->gather(snap->atomData.electroFrame,
589 <                              snap->atomIData.electroFrame);
590 <      AtomCommMatrixJ->gather(snap->atomData.electroFrame,
591 <                              snap->atomJData.electroFrame);
587 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
588 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
589 >                                atomRowData.electroFrame);
590 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
591 >                                   atomColData.electroFrame);
592      }
593 +
594   #endif      
595    }
596    
597 <  void ForceDecomposition::collectIntermediateData() {
597 >  /* collects information obtained during the pre-pair loop onto local
598 >   * data structures.
599 >   */
600 >  void ForceMatrixDecomposition::collectIntermediateData() {
601 >    snap_ = sman_->getCurrentSnapshot();
602 >    storageLayout_ = sman_->getStorageLayout();
603   #ifdef IS_MPI
117 –    Snapshot* snap = sman_->getCurrentSnapshot();
604      
605 <    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
606 <
607 <      AtomCommRealI->scatter(snap->atomIData.density,
608 <                             snap->atomData.density);
609 <
610 <      int n = snap->atomData.density.size();
611 <      std::vector<RealType> rho_tmp(n, 0.0);
612 <      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
605 >    if (storageLayout_ & DataStorage::dslDensity) {
606 >      
607 >      AtomPlanRealRow->scatter(atomRowData.density,
608 >                               snap_->atomData.density);
609 >      
610 >      int n = snap_->atomData.density.size();
611 >      vector<RealType> rho_tmp(n, 0.0);
612 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
613        for (int i = 0; i < n; i++)
614 <        snap->atomData.density[i] += rho_tmp[i];
614 >        snap_->atomData.density[i] += rho_tmp[i];
615      }
616   #endif
617    }
618 <  
619 <  void ForceDecomposition::distributeIntermediateData() {
618 >
619 >  /*
620 >   * redistributes information obtained during the pre-pair loop out to
621 >   * row and column-indexed data structures
622 >   */
623 >  void ForceMatrixDecomposition::distributeIntermediateData() {
624 >    snap_ = sman_->getCurrentSnapshot();
625 >    storageLayout_ = sman_->getStorageLayout();
626   #ifdef IS_MPI
627 <    Snapshot* snap = sman_->getCurrentSnapshot();
628 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
629 <      AtomCommRealI->gather(snap->atomData.functional,
630 <                            snap->atomIData.functional);
631 <      AtomCommRealJ->gather(snap->atomData.functional,
140 <                            snap->atomJData.functional);
627 >    if (storageLayout_ & DataStorage::dslFunctional) {
628 >      AtomPlanRealRow->gather(snap_->atomData.functional,
629 >                              atomRowData.functional);
630 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
631 >                                 atomColData.functional);
632      }
633      
634 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
635 <      AtomCommRealI->gather(snap->atomData.functionalDerivative,
636 <                            snap->atomIData.functionalDerivative);
637 <      AtomCommRealJ->gather(snap->atomData.functionalDerivative,
638 <                            snap->atomJData.functionalDerivative);
634 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
635 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
636 >                              atomRowData.functionalDerivative);
637 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
638 >                                 atomColData.functionalDerivative);
639      }
640   #endif
641    }
642    
643    
644 <  void ForceDecomposition::collectData() {
645 < #ifdef IS_MPI
646 <    Snapshot* snap = sman_->getCurrentSnapshot();
647 <    
648 <    int n = snap->atomData.force.size();
649 <    std::vector<Vector3d> frc_tmp(n, 0.0);
650 <    
651 <    AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
644 >  void ForceMatrixDecomposition::collectData() {
645 >    snap_ = sman_->getCurrentSnapshot();
646 >    storageLayout_ = sman_->getStorageLayout();
647 > #ifdef IS_MPI    
648 >    int n = snap_->atomData.force.size();
649 >    vector<Vector3d> frc_tmp(n, V3Zero);
650 >    
651 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
652      for (int i = 0; i < n; i++) {
653 <      snap->atomData.force[i] += frc_tmp[i];
653 >      snap_->atomData.force[i] += frc_tmp[i];
654        frc_tmp[i] = 0.0;
655      }
656      
657 <    AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
658 <    for (int i = 0; i < n; i++)
659 <      snap->atomData.force[i] += frc_tmp[i];
660 <    
661 <    
662 <    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
657 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
658 >    for (int i = 0; i < n; i++) {
659 >      snap_->atomData.force[i] += frc_tmp[i];
660 >    }
661 >        
662 >    if (storageLayout_ & DataStorage::dslTorque) {
663  
664 <      int nt = snap->atomData.force.size();
665 <      std::vector<Vector3d> trq_tmp(nt, 0.0);
664 >      int nt = snap_->atomData.torque.size();
665 >      vector<Vector3d> trq_tmp(nt, V3Zero);
666  
667 <      AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
668 <      for (int i = 0; i < n; i++) {
669 <        snap->atomData.torque[i] += trq_tmp[i];
667 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
668 >      for (int i = 0; i < nt; i++) {
669 >        snap_->atomData.torque[i] += trq_tmp[i];
670          trq_tmp[i] = 0.0;
671        }
672        
673 <      AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
674 <      for (int i = 0; i < n; i++)
675 <        snap->atomData.torque[i] += trq_tmp[i];
673 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
674 >      for (int i = 0; i < nt; i++)
675 >        snap_->atomData.torque[i] += trq_tmp[i];
676      }
677 +
678 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
679 +
680 +      int ns = snap_->atomData.skippedCharge.size();
681 +      vector<RealType> skch_tmp(ns, 0.0);
682 +
683 +      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
684 +      for (int i = 0; i < ns; i++) {
685 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
686 +        skch_tmp[i] = 0.0;
687 +      }
688 +      
689 +      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
690 +      for (int i = 0; i < ns; i++)
691 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
692 +            
693 +    }
694      
695 +    nLocal_ = snap_->getNumberOfAtoms();
696 +
697 +    vector<potVec> pot_temp(nLocal_,
698 +                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
699 +
700 +    // scatter/gather pot_row into the members of my column
701 +          
702 +    AtomPlanPotRow->scatter(pot_row, pot_temp);
703 +
704 +    for (int ii = 0;  ii < pot_temp.size(); ii++ )
705 +      pairwisePot += pot_temp[ii];
706      
707 <    vector<vector<RealType> > pot_temp(LR_POT_TYPES,
708 <                                       vector<RealType> (nAtoms, 0.0));
707 >    fill(pot_temp.begin(), pot_temp.end(),
708 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
709 >      
710 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
711      
712 <    for (int i = 0; i < LR_POT_TYPES; i++) {
713 <      AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
714 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
715 <        pot_local[i] += pot_temp[i][ii];
716 <      }
712 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
713 >      pairwisePot += pot_temp[ii];    
714 >    
715 >    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
716 >      RealType ploc1 = pairwisePot[ii];
717 >      RealType ploc2 = 0.0;
718 >      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
719 >      pairwisePot[ii] = ploc2;
720      }
721 +
722 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
723 +      RealType ploc1 = embeddingPot[ii];
724 +      RealType ploc2 = 0.0;
725 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
726 +      embeddingPot[ii] = ploc2;
727 +    }
728 +
729 + #endif
730 +
731 +  }
732 +
733 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
734 + #ifdef IS_MPI
735 +    return nAtomsInRow_;
736 + #else
737 +    return nLocal_;
738 + #endif
739 +  }
740 +
741 +  /**
742 +   * returns the list of atoms belonging to this group.  
743 +   */
744 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
745 + #ifdef IS_MPI
746 +    return groupListRow_[cg1];
747 + #else
748 +    return groupList_[cg1];
749 + #endif
750 +  }
751 +
752 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
753 + #ifdef IS_MPI
754 +    return groupListCol_[cg2];
755 + #else
756 +    return groupList_[cg2];
757 + #endif
758 +  }
759 +  
760 +  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
761 +    Vector3d d;
762      
763 + #ifdef IS_MPI
764 +    d = cgColData.position[cg2] - cgRowData.position[cg1];
765 + #else
766 +    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
767 + #endif
768 +    
769 +    snap_->wrapVector(d);
770 +    return d;    
771 +  }
772  
773  
774 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
775 +
776 +    Vector3d d;
777 +    
778 + #ifdef IS_MPI
779 +    d = cgRowData.position[cg1] - atomRowData.position[atom1];
780 + #else
781 +    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
782   #endif
783 +
784 +    snap_->wrapVector(d);
785 +    return d;    
786    }
787    
788 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
789 +    Vector3d d;
790 +    
791 + #ifdef IS_MPI
792 +    d = cgColData.position[cg2] - atomColData.position[atom2];
793 + #else
794 +    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
795 + #endif
796 +    
797 +    snap_->wrapVector(d);
798 +    return d;    
799 +  }
800 +
801 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
802 + #ifdef IS_MPI
803 +    return massFactorsRow[atom1];
804 + #else
805 +    return massFactors[atom1];
806 + #endif
807 +  }
808 +
809 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
810 + #ifdef IS_MPI
811 +    return massFactorsCol[atom2];
812 + #else
813 +    return massFactors[atom2];
814 + #endif
815 +
816 +  }
817 +    
818 +  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
819 +    Vector3d d;
820 +    
821 + #ifdef IS_MPI
822 +    d = atomColData.position[atom2] - atomRowData.position[atom1];
823 + #else
824 +    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
825 + #endif
826 +
827 +    snap_->wrapVector(d);
828 +    return d;    
829 +  }
830 +
831 +  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
832 +    return excludesForAtom[atom1];
833 +  }
834 +
835 +  /**
836 +   * We need to exclude some overcounted interactions that result from
837 +   * the parallel decomposition.
838 +   */
839 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
840 +    int unique_id_1, unique_id_2;
841 +        
842 + #ifdef IS_MPI
843 +    // in MPI, we have to look up the unique IDs for each atom
844 +    unique_id_1 = AtomRowToGlobal[atom1];
845 +    unique_id_2 = AtomColToGlobal[atom2];
846 + #else
847 +    unique_id_1 = AtomLocalToGlobal[atom1];
848 +    unique_id_2 = AtomLocalToGlobal[atom2];
849 + #endif  
850 +
851 +    if (unique_id_1 == unique_id_2) return true;
852 +
853 + #ifdef IS_MPI
854 +    // this prevents us from doing the pair on multiple processors
855 +    if (unique_id_1 < unique_id_2) {
856 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
857 +    } else {
858 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
859 +    }
860 + #endif
861 +    
862 +    return false;
863 +  }
864 +
865 +  /**
866 +   * We need to handle the interactions for atoms who are involved in
867 +   * the same rigid body as well as some short range interactions
868 +   * (bonds, bends, torsions) differently from other interactions.
869 +   * We'll still visit the pairwise routines, but with a flag that
870 +   * tells those routines to exclude the pair from direct long range
871 +   * interactions.  Some indirect interactions (notably reaction
872 +   * field) must still be handled for these pairs.
873 +   */
874 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
875 +
876 +    // excludesForAtom was constructed to use row/column indices in the MPI
877 +    // version, and to use local IDs in the non-MPI version:
878 +    
879 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
880 +         i != excludesForAtom[atom1].end(); ++i) {
881 +      if ( (*i) == atom2 ) return true;
882 +    }
883 +
884 +    return false;
885 +  }
886 +
887 +
888 +  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
889 + #ifdef IS_MPI
890 +    atomRowData.force[atom1] += fg;
891 + #else
892 +    snap_->atomData.force[atom1] += fg;
893 + #endif
894 +  }
895 +
896 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
897 + #ifdef IS_MPI
898 +    atomColData.force[atom2] += fg;
899 + #else
900 +    snap_->atomData.force[atom2] += fg;
901 + #endif
902 +  }
903 +
904 +    // filling interaction blocks with pointers
905 +  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
906 +                                                     int atom1, int atom2) {
907 +
908 +    idat.excluded = excludeAtomPair(atom1, atom2);
909 +  
910 + #ifdef IS_MPI
911 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
912 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
913 +    //                         ff_->getAtomType(identsCol[atom2]) );
914 +    
915 +    if (storageLayout_ & DataStorage::dslAmat) {
916 +      idat.A1 = &(atomRowData.aMat[atom1]);
917 +      idat.A2 = &(atomColData.aMat[atom2]);
918 +    }
919 +    
920 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
921 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
922 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
923 +    }
924 +
925 +    if (storageLayout_ & DataStorage::dslTorque) {
926 +      idat.t1 = &(atomRowData.torque[atom1]);
927 +      idat.t2 = &(atomColData.torque[atom2]);
928 +    }
929 +
930 +    if (storageLayout_ & DataStorage::dslDensity) {
931 +      idat.rho1 = &(atomRowData.density[atom1]);
932 +      idat.rho2 = &(atomColData.density[atom2]);
933 +    }
934 +
935 +    if (storageLayout_ & DataStorage::dslFunctional) {
936 +      idat.frho1 = &(atomRowData.functional[atom1]);
937 +      idat.frho2 = &(atomColData.functional[atom2]);
938 +    }
939 +
940 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
941 +      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
942 +      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
943 +    }
944 +
945 +    if (storageLayout_ & DataStorage::dslParticlePot) {
946 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
947 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
948 +    }
949 +
950 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
951 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
952 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
953 +    }
954 +
955 + #else
956 +    
957 +
958 +    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
959 +    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
960 +    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
961 +
962 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
963 +    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
964 +    //                         ff_->getAtomType(idents[atom2]) );
965 +
966 +    if (storageLayout_ & DataStorage::dslAmat) {
967 +      idat.A1 = &(snap_->atomData.aMat[atom1]);
968 +      idat.A2 = &(snap_->atomData.aMat[atom2]);
969 +    }
970 +
971 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
972 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
973 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
974 +    }
975 +
976 +    if (storageLayout_ & DataStorage::dslTorque) {
977 +      idat.t1 = &(snap_->atomData.torque[atom1]);
978 +      idat.t2 = &(snap_->atomData.torque[atom2]);
979 +    }
980 +
981 +    if (storageLayout_ & DataStorage::dslDensity) {    
982 +      idat.rho1 = &(snap_->atomData.density[atom1]);
983 +      idat.rho2 = &(snap_->atomData.density[atom2]);
984 +    }
985 +
986 +    if (storageLayout_ & DataStorage::dslFunctional) {
987 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
988 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
989 +    }
990 +
991 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
992 +      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
993 +      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
994 +    }
995 +
996 +    if (storageLayout_ & DataStorage::dslParticlePot) {
997 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
998 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
999 +    }
1000 +
1001 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
1002 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1003 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1004 +    }
1005 + #endif
1006 +  }
1007 +
1008 +  
1009 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1010 + #ifdef IS_MPI
1011 +    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1012 +    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1013 +
1014 +    atomRowData.force[atom1] += *(idat.f1);
1015 +    atomColData.force[atom2] -= *(idat.f1);
1016 + #else
1017 +    pairwisePot += *(idat.pot);
1018 +
1019 +    snap_->atomData.force[atom1] += *(idat.f1);
1020 +    snap_->atomData.force[atom2] -= *(idat.f1);
1021 + #endif
1022 +    
1023 +  }
1024 +
1025 +  /*
1026 +   * buildNeighborList
1027 +   *
1028 +   * first element of pair is row-indexed CutoffGroup
1029 +   * second element of pair is column-indexed CutoffGroup
1030 +   */
1031 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1032 +      
1033 +    vector<pair<int, int> > neighborList;
1034 +    groupCutoffs cuts;
1035 +    bool doAllPairs = false;
1036 +
1037 + #ifdef IS_MPI
1038 +    cellListRow_.clear();
1039 +    cellListCol_.clear();
1040 + #else
1041 +    cellList_.clear();
1042 + #endif
1043 +
1044 +    RealType rList_ = (largestRcut_ + skinThickness_);
1045 +    RealType rl2 = rList_ * rList_;
1046 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1047 +    Mat3x3d Hmat = snap_->getHmat();
1048 +    Vector3d Hx = Hmat.getColumn(0);
1049 +    Vector3d Hy = Hmat.getColumn(1);
1050 +    Vector3d Hz = Hmat.getColumn(2);
1051 +
1052 +    nCells_.x() = (int) ( Hx.length() )/ rList_;
1053 +    nCells_.y() = (int) ( Hy.length() )/ rList_;
1054 +    nCells_.z() = (int) ( Hz.length() )/ rList_;
1055 +
1056 +    // handle small boxes where the cell offsets can end up repeating cells
1057 +    
1058 +    if (nCells_.x() < 3) doAllPairs = true;
1059 +    if (nCells_.y() < 3) doAllPairs = true;
1060 +    if (nCells_.z() < 3) doAllPairs = true;
1061 +
1062 +    Mat3x3d invHmat = snap_->getInvHmat();
1063 +    Vector3d rs, scaled, dr;
1064 +    Vector3i whichCell;
1065 +    int cellIndex;
1066 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1067 +
1068 + #ifdef IS_MPI
1069 +    cellListRow_.resize(nCtot);
1070 +    cellListCol_.resize(nCtot);
1071 + #else
1072 +    cellList_.resize(nCtot);
1073 + #endif
1074 +
1075 +    if (!doAllPairs) {
1076 + #ifdef IS_MPI
1077 +
1078 +      for (int i = 0; i < nGroupsInRow_; i++) {
1079 +        rs = cgRowData.position[i];
1080 +        
1081 +        // scaled positions relative to the box vectors
1082 +        scaled = invHmat * rs;
1083 +        
1084 +        // wrap the vector back into the unit box by subtracting integer box
1085 +        // numbers
1086 +        for (int j = 0; j < 3; j++) {
1087 +          scaled[j] -= roundMe(scaled[j]);
1088 +          scaled[j] += 0.5;
1089 +        }
1090 +        
1091 +        // find xyz-indices of cell that cutoffGroup is in.
1092 +        whichCell.x() = nCells_.x() * scaled.x();
1093 +        whichCell.y() = nCells_.y() * scaled.y();
1094 +        whichCell.z() = nCells_.z() * scaled.z();
1095 +        
1096 +        // find single index of this cell:
1097 +        cellIndex = Vlinear(whichCell, nCells_);
1098 +        
1099 +        // add this cutoff group to the list of groups in this cell;
1100 +        cellListRow_[cellIndex].push_back(i);
1101 +      }
1102 +      for (int i = 0; i < nGroupsInCol_; i++) {
1103 +        rs = cgColData.position[i];
1104 +        
1105 +        // scaled positions relative to the box vectors
1106 +        scaled = invHmat * rs;
1107 +        
1108 +        // wrap the vector back into the unit box by subtracting integer box
1109 +        // numbers
1110 +        for (int j = 0; j < 3; j++) {
1111 +          scaled[j] -= roundMe(scaled[j]);
1112 +          scaled[j] += 0.5;
1113 +        }
1114 +        
1115 +        // find xyz-indices of cell that cutoffGroup is in.
1116 +        whichCell.x() = nCells_.x() * scaled.x();
1117 +        whichCell.y() = nCells_.y() * scaled.y();
1118 +        whichCell.z() = nCells_.z() * scaled.z();
1119 +        
1120 +        // find single index of this cell:
1121 +        cellIndex = Vlinear(whichCell, nCells_);
1122 +        
1123 +        // add this cutoff group to the list of groups in this cell;
1124 +        cellListCol_[cellIndex].push_back(i);
1125 +      }
1126 +    
1127 + #else
1128 +      for (int i = 0; i < nGroups_; i++) {
1129 +        rs = snap_->cgData.position[i];
1130 +        
1131 +        // scaled positions relative to the box vectors
1132 +        scaled = invHmat * rs;
1133 +        
1134 +        // wrap the vector back into the unit box by subtracting integer box
1135 +        // numbers
1136 +        for (int j = 0; j < 3; j++) {
1137 +          scaled[j] -= roundMe(scaled[j]);
1138 +          scaled[j] += 0.5;
1139 +        }
1140 +        
1141 +        // find xyz-indices of cell that cutoffGroup is in.
1142 +        whichCell.x() = nCells_.x() * scaled.x();
1143 +        whichCell.y() = nCells_.y() * scaled.y();
1144 +        whichCell.z() = nCells_.z() * scaled.z();
1145 +        
1146 +        // find single index of this cell:
1147 +        cellIndex = Vlinear(whichCell, nCells_);
1148 +        
1149 +        // add this cutoff group to the list of groups in this cell;
1150 +        cellList_[cellIndex].push_back(i);
1151 +      }
1152 +
1153 + #endif
1154 +
1155 +      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1156 +        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1157 +          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1158 +            Vector3i m1v(m1x, m1y, m1z);
1159 +            int m1 = Vlinear(m1v, nCells_);
1160 +            
1161 +            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1162 +                 os != cellOffsets_.end(); ++os) {
1163 +              
1164 +              Vector3i m2v = m1v + (*os);
1165 +            
1166 +
1167 +              if (m2v.x() >= nCells_.x()) {
1168 +                m2v.x() = 0;          
1169 +              } else if (m2v.x() < 0) {
1170 +                m2v.x() = nCells_.x() - 1;
1171 +              }
1172 +              
1173 +              if (m2v.y() >= nCells_.y()) {
1174 +                m2v.y() = 0;          
1175 +              } else if (m2v.y() < 0) {
1176 +                m2v.y() = nCells_.y() - 1;
1177 +              }
1178 +              
1179 +              if (m2v.z() >= nCells_.z()) {
1180 +                m2v.z() = 0;          
1181 +              } else if (m2v.z() < 0) {
1182 +                m2v.z() = nCells_.z() - 1;
1183 +              }
1184 +
1185 +              int m2 = Vlinear (m2v, nCells_);
1186 +              
1187 + #ifdef IS_MPI
1188 +              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1189 +                   j1 != cellListRow_[m1].end(); ++j1) {
1190 +                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1191 +                     j2 != cellListCol_[m2].end(); ++j2) {
1192 +                  
1193 +                  // In parallel, we need to visit *all* pairs of row
1194 +                  // & column indicies and will divide labor in the
1195 +                  // force evaluation later.
1196 +                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1197 +                  snap_->wrapVector(dr);
1198 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1199 +                  if (dr.lengthSquare() < cuts.third) {
1200 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1201 +                  }                  
1202 +                }
1203 +              }
1204 + #else
1205 +              for (vector<int>::iterator j1 = cellList_[m1].begin();
1206 +                   j1 != cellList_[m1].end(); ++j1) {
1207 +                for (vector<int>::iterator j2 = cellList_[m2].begin();
1208 +                     j2 != cellList_[m2].end(); ++j2) {
1209 +    
1210 +                  // Always do this if we're in different cells or if
1211 +                  // we're in the same cell and the global index of
1212 +                  // the j2 cutoff group is greater than or equal to
1213 +                  // the j1 cutoff group.  Note that Rappaport's code
1214 +                  // has a "less than" conditional here, but that
1215 +                  // deals with atom-by-atom computation.  OpenMD
1216 +                  // allows atoms within a single cutoff group to
1217 +                  // interact with each other.
1218 +
1219 +
1220 +
1221 +                  if (m2 != m1 || (*j2) >= (*j1) ) {
1222 +
1223 +                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1224 +                    snap_->wrapVector(dr);
1225 +                    cuts = getGroupCutoffs( (*j1), (*j2) );
1226 +                    if (dr.lengthSquare() < cuts.third) {
1227 +                      neighborList.push_back(make_pair((*j1), (*j2)));
1228 +                    }
1229 +                  }
1230 +                }
1231 +              }
1232 + #endif
1233 +            }
1234 +          }
1235 +        }
1236 +      }
1237 +    } else {
1238 +      // branch to do all cutoff group pairs
1239 + #ifdef IS_MPI
1240 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1241 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1242 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1243 +          snap_->wrapVector(dr);
1244 +          cuts = getGroupCutoffs( j1, j2 );
1245 +          if (dr.lengthSquare() < cuts.third) {
1246 +            neighborList.push_back(make_pair(j1, j2));
1247 +          }
1248 +        }
1249 +      }      
1250 + #else
1251 +      // include all groups here.
1252 +      for (int j1 = 0; j1 < nGroups_; j1++) {
1253 +        // include self group interactions j2 == j1
1254 +        for (int j2 = j1; j2 < nGroups_; j2++) {
1255 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1256 +          snap_->wrapVector(dr);
1257 +          cuts = getGroupCutoffs( j1, j2 );
1258 +          if (dr.lengthSquare() < cuts.third) {
1259 +            neighborList.push_back(make_pair(j1, j2));
1260 +          }
1261 +        }    
1262 +      }
1263 + #endif
1264 +    }
1265 +      
1266 +    // save the local cutoff group positions for the check that is
1267 +    // done on each loop:
1268 +    saved_CG_positions_.clear();
1269 +    for (int i = 0; i < nGroups_; i++)
1270 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1271 +    
1272 +    return neighborList;
1273 +  }
1274   } //end namespace OpenMD

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