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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC vs.
Revision 1713 by gezelter, Sat May 19 14:21:02 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/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 +  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 +
88 +
89    /**
90     * distributeInitialData is essentially a copy of the older fortran
91     * SimulationSetup
92     */
53 –  
93    void ForceMatrixDecomposition::distributeInitialData() {
94      snap_ = sman_->getCurrentSnapshot();
95      storageLayout_ = sman_->getStorageLayout();
96 < #ifdef IS_MPI    
97 <    int nLocal = snap_->getNumberOfAtoms();
59 <    int nGroups = snap_->getNumberOfCutoffGroups();
96 >    ff_ = info_->getForceField();
97 >    nLocal_ = snap_->getNumberOfAtoms();
98      
99 <    AtomCommIntRow = new Communicator<Row,int>(nLocal);
100 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
101 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
102 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
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 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
67 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
68 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
69 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
106 >    massFactors = info_->getMassFactors();
107  
108 <    cgCommIntRow = new Communicator<Row,int>(nGroups);
109 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
110 <    cgCommIntColumn = new Communicator<Column,int>(nGroups);
111 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
108 >    PairList* excludes = info_->getExcludedInteractions();
109 >    PairList* oneTwo = info_->getOneTwoInteractions();
110 >    PairList* oneThree = info_->getOneThreeInteractions();
111 >    PairList* oneFour = info_->getOneFourInteractions();
112  
113 <    int nAtomsInRow = AtomCommIntRow->getSize();
114 <    int nAtomsInCol = AtomCommIntColumn->getSize();
115 <    int nGroupsInRow = cgCommIntRow->getSize();
116 <    int nGroupsInCol = cgCommIntColumn->getSize();
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);
141 >    atomRowData.resize(nAtomsInRow_);
142      atomRowData.setStorageLayout(storageLayout_);
143 <    atomColData.resize(nAtomsInCol);
143 >    atomColData.resize(nAtomsInCol_);
144      atomColData.setStorageLayout(storageLayout_);
145 <    cgRowData.resize(nGroupsInRow);
145 >    cgRowData.resize(nGroupsInRow_);
146      cgRowData.setStorageLayout(DataStorage::dslPosition);
147 <    cgColData.resize(nGroupsInCol);
147 >    cgColData.resize(nGroupsInCol_);
148      cgColData.setStorageLayout(DataStorage::dslPosition);
149 +        
150 +    identsRow.resize(nAtomsInRow_);
151 +    identsCol.resize(nAtomsInCol_);
152      
153 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
154 <                                      vector<RealType> (nAtomsInRow, 0.0));
155 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
156 <                                      vector<RealType> (nAtomsInCol, 0.0));
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 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
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 <    // gather the information for atomtype IDs (atids):
298 <    vector<int> identsLocal = info_->getIdentArray();
299 <    identsRow.reserve(nAtomsInRow);
300 <    identsCol.reserve(nAtomsInCol);
297 >    RealType tol = 1e-6;
298 >    largestRcut_ = 0.0;
299 >    RealType rc;
300 >    int atid;
301 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302      
303 <    AtomCommIntRow->gather(identsLocal, identsRow);
304 <    AtomCommIntColumn->gather(identsLocal, identsCol);
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 <    AtomLocalToGlobal = info_->getGlobalAtomIndices();
315 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
316 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
317 <    
318 <    cgLocalToGlobal = info_->getGlobalGroupIndices();
319 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
320 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
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 <    // still need:
332 <    // topoDist
333 <    // exclude
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 +    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 +    if (storageLayout_ & DataStorage::dslElectricField) {    
529 +      fill(atomRowData.electricField.begin(),
530 +           atomRowData.electricField.end(), V3Zero);
531 +      fill(atomColData.electricField.begin(),
532 +           atomColData.electricField.end(), V3Zero);
533 +    }
534 +    if (storageLayout_ & DataStorage::dslFlucQForce) {    
535 +      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
536 +           0.0);
537 +      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
538 +           0.0);
539 +    }
540 +
541 + #endif
542 +    // even in parallel, we need to zero out the local arrays:
543 +
544 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
545 +      fill(snap_->atomData.particlePot.begin(),
546 +           snap_->atomData.particlePot.end(), 0.0);
547 +    }
548 +    
549 +    if (storageLayout_ & DataStorage::dslDensity) {      
550 +      fill(snap_->atomData.density.begin(),
551 +           snap_->atomData.density.end(), 0.0);
552 +    }
553 +
554 +    if (storageLayout_ & DataStorage::dslFunctional) {
555 +      fill(snap_->atomData.functional.begin(),
556 +           snap_->atomData.functional.end(), 0.0);
557 +    }
558 +
559 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
560 +      fill(snap_->atomData.functionalDerivative.begin(),
561 +           snap_->atomData.functionalDerivative.end(), 0.0);
562 +    }
563 +
564 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
565 +      fill(snap_->atomData.skippedCharge.begin(),
566 +           snap_->atomData.skippedCharge.end(), 0.0);
567 +    }
568 +
569 +    if (storageLayout_ & DataStorage::dslElectricField) {      
570 +      fill(snap_->atomData.electricField.begin(),
571 +           snap_->atomData.electricField.end(), V3Zero);
572 +    }
573 +  }
574 +
575 +
576    void ForceMatrixDecomposition::distributeData()  {
577      snap_ = sman_->getCurrentSnapshot();
578      storageLayout_ = sman_->getStorageLayout();
579   #ifdef IS_MPI
580      
581      // gather up the atomic positions
582 <    AtomCommVectorRow->gather(snap_->atomData.position,
582 >    AtomPlanVectorRow->gather(snap_->atomData.position,
583                                atomRowData.position);
584 <    AtomCommVectorColumn->gather(snap_->atomData.position,
584 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
585                                   atomColData.position);
586      
587      // gather up the cutoff group positions
588 <    cgCommVectorRow->gather(snap_->cgData.position,
588 >
589 >    cgPlanVectorRow->gather(snap_->cgData.position,
590                              cgRowData.position);
591 <    cgCommVectorColumn->gather(snap_->cgData.position,
591 >
592 >    cgPlanVectorColumn->gather(snap_->cgData.position,
593                                 cgColData.position);
594 +
595      
596      // if needed, gather the atomic rotation matrices
597      if (storageLayout_ & DataStorage::dslAmat) {
598 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
598 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
599                                  atomRowData.aMat);
600 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
600 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
601                                     atomColData.aMat);
602      }
603      
604      // if needed, gather the atomic eletrostatic frames
605      if (storageLayout_ & DataStorage::dslElectroFrame) {
606 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
606 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
607                                  atomRowData.electroFrame);
608 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
608 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
609                                     atomColData.electroFrame);
610      }
611 +
612 +    // if needed, gather the atomic fluctuating charge values
613 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {
614 +      AtomPlanRealRow->gather(snap_->atomData.flucQPos,
615 +                              atomRowData.flucQPos);
616 +      AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
617 +                                 atomColData.flucQPos);
618 +    }
619 +
620   #endif      
621    }
622    
623 +  /* collects information obtained during the pre-pair loop onto local
624 +   * data structures.
625 +   */
626    void ForceMatrixDecomposition::collectIntermediateData() {
627      snap_ = sman_->getCurrentSnapshot();
628      storageLayout_ = sman_->getStorageLayout();
# Line 162 | Line 630 | namespace OpenMD {
630      
631      if (storageLayout_ & DataStorage::dslDensity) {
632        
633 <      AtomCommRealRow->scatter(atomRowData.density,
633 >      AtomPlanRealRow->scatter(atomRowData.density,
634                                 snap_->atomData.density);
635        
636        int n = snap_->atomData.density.size();
637 <      std::vector<RealType> rho_tmp(n, 0.0);
638 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
637 >      vector<RealType> rho_tmp(n, 0.0);
638 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
639        for (int i = 0; i < n; i++)
640          snap_->atomData.density[i] += rho_tmp[i];
641      }
642 +
643 +    if (storageLayout_ & DataStorage::dslElectricField) {
644 +      
645 +      AtomPlanVectorRow->scatter(atomRowData.electricField,
646 +                                 snap_->atomData.electricField);
647 +      
648 +      int n = snap_->atomData.electricField.size();
649 +      vector<Vector3d> field_tmp(n, V3Zero);
650 +      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
651 +      for (int i = 0; i < n; i++)
652 +        snap_->atomData.electricField[i] += field_tmp[i];
653 +    }
654   #endif
655    }
656 <  
656 >
657 >  /*
658 >   * redistributes information obtained during the pre-pair loop out to
659 >   * row and column-indexed data structures
660 >   */
661    void ForceMatrixDecomposition::distributeIntermediateData() {
662      snap_ = sman_->getCurrentSnapshot();
663      storageLayout_ = sman_->getStorageLayout();
664   #ifdef IS_MPI
665      if (storageLayout_ & DataStorage::dslFunctional) {
666 <      AtomCommRealRow->gather(snap_->atomData.functional,
666 >      AtomPlanRealRow->gather(snap_->atomData.functional,
667                                atomRowData.functional);
668 <      AtomCommRealColumn->gather(snap_->atomData.functional,
668 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
669                                   atomColData.functional);
670      }
671      
672      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
673 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
673 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
674                                atomRowData.functionalDerivative);
675 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
675 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
676                                   atomColData.functionalDerivative);
677      }
678   #endif
# Line 202 | Line 686 | namespace OpenMD {
686      int n = snap_->atomData.force.size();
687      vector<Vector3d> frc_tmp(n, V3Zero);
688      
689 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
689 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
690      for (int i = 0; i < n; i++) {
691        snap_->atomData.force[i] += frc_tmp[i];
692        frc_tmp[i] = 0.0;
693      }
694      
695 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
696 <    for (int i = 0; i < n; i++)
695 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
696 >    for (int i = 0; i < n; i++) {
697        snap_->atomData.force[i] += frc_tmp[i];
698 <    
699 <    
698 >    }
699 >        
700      if (storageLayout_ & DataStorage::dslTorque) {
701  
702 <      int nt = snap_->atomData.force.size();
702 >      int nt = snap_->atomData.torque.size();
703        vector<Vector3d> trq_tmp(nt, V3Zero);
704  
705 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
706 <      for (int i = 0; i < n; i++) {
705 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
706 >      for (int i = 0; i < nt; i++) {
707          snap_->atomData.torque[i] += trq_tmp[i];
708          trq_tmp[i] = 0.0;
709        }
710        
711 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
712 <      for (int i = 0; i < n; i++)
711 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
712 >      for (int i = 0; i < nt; i++)
713          snap_->atomData.torque[i] += trq_tmp[i];
714      }
231 –    
232 –    int nLocal = snap_->getNumberOfAtoms();
715  
716 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
717 <                                       vector<RealType> (nLocal, 0.0));
716 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {
717 >
718 >      int ns = snap_->atomData.skippedCharge.size();
719 >      vector<RealType> skch_tmp(ns, 0.0);
720 >
721 >      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
722 >      for (int i = 0; i < ns; i++) {
723 >        snap_->atomData.skippedCharge[i] += skch_tmp[i];
724 >        skch_tmp[i] = 0.0;
725 >      }
726 >      
727 >      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
728 >      for (int i = 0; i < ns; i++)
729 >        snap_->atomData.skippedCharge[i] += skch_tmp[i];
730 >            
731 >    }
732      
733 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
734 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
735 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
736 <        pot_local[i] += pot_temp[i][ii];
733 >    if (storageLayout_ & DataStorage::dslFlucQForce) {
734 >
735 >      int nq = snap_->atomData.flucQFrc.size();
736 >      vector<RealType> fqfrc_tmp(nq, 0.0);
737 >
738 >      AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
739 >      for (int i = 0; i < nq; i++) {
740 >        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
741 >        fqfrc_tmp[i] = 0.0;
742        }
743 +      
744 +      AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
745 +      for (int i = 0; i < nq; i++)
746 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
747 +            
748      }
749 +
750 +    nLocal_ = snap_->getNumberOfAtoms();
751 +
752 +    vector<potVec> pot_temp(nLocal_,
753 +                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
754 +
755 +    // scatter/gather pot_row into the members of my column
756 +          
757 +    AtomPlanPotRow->scatter(pot_row, pot_temp);
758 +
759 +    for (int ii = 0;  ii < pot_temp.size(); ii++ )
760 +      pairwisePot += pot_temp[ii];
761 +    
762 +    fill(pot_temp.begin(), pot_temp.end(),
763 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
764 +      
765 +    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
766 +    
767 +    for (int ii = 0;  ii < pot_temp.size(); ii++ )
768 +      pairwisePot += pot_temp[ii];    
769 +    
770 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
771 +      RealType ploc1 = pairwisePot[ii];
772 +      RealType ploc2 = 0.0;
773 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
774 +      pairwisePot[ii] = ploc2;
775 +    }
776 +
777 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
778 +      RealType ploc1 = embeddingPot[ii];
779 +      RealType ploc2 = 0.0;
780 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
781 +      embeddingPot[ii] = ploc2;
782 +    }
783 +
784   #endif
785 +
786    }
787  
788 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
789 + #ifdef IS_MPI
790 +    return nAtomsInRow_;
791 + #else
792 +    return nLocal_;
793 + #endif
794 +  }
795 +
796 +  /**
797 +   * returns the list of atoms belonging to this group.  
798 +   */
799 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
800 + #ifdef IS_MPI
801 +    return groupListRow_[cg1];
802 + #else
803 +    return groupList_[cg1];
804 + #endif
805 +  }
806 +
807 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
808 + #ifdef IS_MPI
809 +    return groupListCol_[cg2];
810 + #else
811 +    return groupList_[cg2];
812 + #endif
813 +  }
814    
815    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
816      Vector3d d;
# Line 284 | Line 852 | namespace OpenMD {
852      snap_->wrapVector(d);
853      return d;    
854    }
855 +
856 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
857 + #ifdef IS_MPI
858 +    return massFactorsRow[atom1];
859 + #else
860 +    return massFactors[atom1];
861 + #endif
862 +  }
863 +
864 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
865 + #ifdef IS_MPI
866 +    return massFactorsCol[atom2];
867 + #else
868 +    return massFactors[atom2];
869 + #endif
870 +
871 +  }
872      
873    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
874      Vector3d d;
# Line 296 | Line 881 | namespace OpenMD {
881  
882      snap_->wrapVector(d);
883      return d;    
884 +  }
885 +
886 +  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
887 +    return excludesForAtom[atom1];
888 +  }
889 +
890 +  /**
891 +   * We need to exclude some overcounted interactions that result from
892 +   * the parallel decomposition.
893 +   */
894 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
895 +    int unique_id_1, unique_id_2;
896 +        
897 + #ifdef IS_MPI
898 +    // in MPI, we have to look up the unique IDs for each atom
899 +    unique_id_1 = AtomRowToGlobal[atom1];
900 +    unique_id_2 = AtomColToGlobal[atom2];
901 + #else
902 +    unique_id_1 = AtomLocalToGlobal[atom1];
903 +    unique_id_2 = AtomLocalToGlobal[atom2];
904 + #endif  
905 +
906 +    if (unique_id_1 == unique_id_2) return true;
907 +
908 + #ifdef IS_MPI
909 +    // this prevents us from doing the pair on multiple processors
910 +    if (unique_id_1 < unique_id_2) {
911 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
912 +    } else {
913 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
914 +    }
915 + #endif
916 +    
917 +    return false;
918    }
919  
920 +  /**
921 +   * We need to handle the interactions for atoms who are involved in
922 +   * the same rigid body as well as some short range interactions
923 +   * (bonds, bends, torsions) differently from other interactions.
924 +   * We'll still visit the pairwise routines, but with a flag that
925 +   * tells those routines to exclude the pair from direct long range
926 +   * interactions.  Some indirect interactions (notably reaction
927 +   * field) must still be handled for these pairs.
928 +   */
929 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
930 +
931 +    // excludesForAtom was constructed to use row/column indices in the MPI
932 +    // version, and to use local IDs in the non-MPI version:
933 +    
934 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
935 +         i != excludesForAtom[atom1].end(); ++i) {
936 +      if ( (*i) == atom2 ) return true;
937 +    }
938 +
939 +    return false;
940 +  }
941 +
942 +
943    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
944   #ifdef IS_MPI
945      atomRowData.force[atom1] += fg;
# Line 312 | Line 954 | namespace OpenMD {
954   #else
955      snap_->atomData.force[atom2] += fg;
956   #endif
315 –
957    }
958  
959      // filling interaction blocks with pointers
960 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
960 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
961 >                                                     int atom1, int atom2) {
962  
963 <    InteractionData idat;
963 >    idat.excluded = excludeAtomPair(atom1, atom2);
964 >  
965   #ifdef IS_MPI
966 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
967 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
968 +    //                         ff_->getAtomType(identsCol[atom2]) );
969 +    
970      if (storageLayout_ & DataStorage::dslAmat) {
971 <      idat.A1 = atomRowData.aMat[atom1];
972 <      idat.A2 = atomColData.aMat[atom2];
971 >      idat.A1 = &(atomRowData.aMat[atom1]);
972 >      idat.A2 = &(atomColData.aMat[atom2]);
973      }
974 <
974 >    
975      if (storageLayout_ & DataStorage::dslElectroFrame) {
976 <      idat.eFrame1 = atomRowData.electroFrame[atom1];
977 <      idat.eFrame2 = atomColData.electroFrame[atom2];
976 >      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
977 >      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
978      }
979  
980      if (storageLayout_ & DataStorage::dslTorque) {
981 <      idat.t1 = atomRowData.torque[atom1];
982 <      idat.t2 = atomColData.torque[atom2];
981 >      idat.t1 = &(atomRowData.torque[atom1]);
982 >      idat.t2 = &(atomColData.torque[atom2]);
983      }
984  
985      if (storageLayout_ & DataStorage::dslDensity) {
986 <      idat.rho1 = atomRowData.density[atom1];
987 <      idat.rho2 = atomColData.density[atom2];
986 >      idat.rho1 = &(atomRowData.density[atom1]);
987 >      idat.rho2 = &(atomColData.density[atom2]);
988      }
989  
990 +    if (storageLayout_ & DataStorage::dslFunctional) {
991 +      idat.frho1 = &(atomRowData.functional[atom1]);
992 +      idat.frho2 = &(atomColData.functional[atom2]);
993 +    }
994 +
995      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
996 <      idat.dfrho1 = atomRowData.functionalDerivative[atom1];
997 <      idat.dfrho2 = atomColData.functionalDerivative[atom2];
996 >      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
997 >      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
998      }
999 < #endif
999 >
1000 >    if (storageLayout_ & DataStorage::dslParticlePot) {
1001 >      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1002 >      idat.particlePot2 = &(atomColData.particlePot[atom2]);
1003 >    }
1004 >
1005 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
1006 >      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1007 >      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1008 >    }
1009 >
1010 > #else
1011      
1012 <  }
1013 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1014 <  }
1015 <  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
1012 >
1013 >    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1014 >    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1015 >    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1016 >
1017 >    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1018 >    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1019 >    //                         ff_->getAtomType(idents[atom2]) );
1020 >
1021 >    if (storageLayout_ & DataStorage::dslAmat) {
1022 >      idat.A1 = &(snap_->atomData.aMat[atom1]);
1023 >      idat.A2 = &(snap_->atomData.aMat[atom2]);
1024 >    }
1025 >
1026 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
1027 >      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1028 >      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1029 >    }
1030 >
1031 >    if (storageLayout_ & DataStorage::dslTorque) {
1032 >      idat.t1 = &(snap_->atomData.torque[atom1]);
1033 >      idat.t2 = &(snap_->atomData.torque[atom2]);
1034 >    }
1035 >
1036 >    if (storageLayout_ & DataStorage::dslDensity) {    
1037 >      idat.rho1 = &(snap_->atomData.density[atom1]);
1038 >      idat.rho2 = &(snap_->atomData.density[atom2]);
1039 >    }
1040 >
1041 >    if (storageLayout_ & DataStorage::dslFunctional) {
1042 >      idat.frho1 = &(snap_->atomData.functional[atom1]);
1043 >      idat.frho2 = &(snap_->atomData.functional[atom2]);
1044 >    }
1045 >
1046 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1047 >      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1048 >      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1049 >    }
1050 >
1051 >    if (storageLayout_ & DataStorage::dslParticlePot) {
1052 >      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1053 >      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1054 >    }
1055 >
1056 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {
1057 >      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1058 >      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1059 >    }
1060 > #endif
1061    }
1062  
1063    
1064 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1065 + #ifdef IS_MPI
1066 +    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1067 +    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1068 +
1069 +    atomRowData.force[atom1] += *(idat.f1);
1070 +    atomColData.force[atom2] -= *(idat.f1);
1071 +
1072 +    // should particle pot be done here also?
1073 + #else
1074 +    pairwisePot += *(idat.pot);
1075 +
1076 +    snap_->atomData.force[atom1] += *(idat.f1);
1077 +    snap_->atomData.force[atom2] -= *(idat.f1);
1078 +
1079 +    if (idat.doParticlePot) {
1080 +      snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1081 +      snap_->atomData.particlePot[atom2] -= *(idat.vpair) * *(idat.sw);
1082 +    }
1083 +      
1084 + #endif
1085 +    
1086 +  }
1087 +
1088 +  /*
1089 +   * buildNeighborList
1090 +   *
1091 +   * first element of pair is row-indexed CutoffGroup
1092 +   * second element of pair is column-indexed CutoffGroup
1093 +   */
1094 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1095 +      
1096 +    vector<pair<int, int> > neighborList;
1097 +    groupCutoffs cuts;
1098 +    bool doAllPairs = false;
1099 +
1100 + #ifdef IS_MPI
1101 +    cellListRow_.clear();
1102 +    cellListCol_.clear();
1103 + #else
1104 +    cellList_.clear();
1105 + #endif
1106 +
1107 +    RealType rList_ = (largestRcut_ + skinThickness_);
1108 +    RealType rl2 = rList_ * rList_;
1109 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1110 +    Mat3x3d Hmat = snap_->getHmat();
1111 +    Vector3d Hx = Hmat.getColumn(0);
1112 +    Vector3d Hy = Hmat.getColumn(1);
1113 +    Vector3d Hz = Hmat.getColumn(2);
1114 +
1115 +    nCells_.x() = (int) ( Hx.length() )/ rList_;
1116 +    nCells_.y() = (int) ( Hy.length() )/ rList_;
1117 +    nCells_.z() = (int) ( Hz.length() )/ rList_;
1118 +
1119 +    // handle small boxes where the cell offsets can end up repeating cells
1120 +    
1121 +    if (nCells_.x() < 3) doAllPairs = true;
1122 +    if (nCells_.y() < 3) doAllPairs = true;
1123 +    if (nCells_.z() < 3) doAllPairs = true;
1124 +
1125 +    Mat3x3d invHmat = snap_->getInvHmat();
1126 +    Vector3d rs, scaled, dr;
1127 +    Vector3i whichCell;
1128 +    int cellIndex;
1129 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1130 +
1131 + #ifdef IS_MPI
1132 +    cellListRow_.resize(nCtot);
1133 +    cellListCol_.resize(nCtot);
1134 + #else
1135 +    cellList_.resize(nCtot);
1136 + #endif
1137 +
1138 +    if (!doAllPairs) {
1139 + #ifdef IS_MPI
1140 +
1141 +      for (int i = 0; i < nGroupsInRow_; i++) {
1142 +        rs = cgRowData.position[i];
1143 +        
1144 +        // scaled positions relative to the box vectors
1145 +        scaled = invHmat * rs;
1146 +        
1147 +        // wrap the vector back into the unit box by subtracting integer box
1148 +        // numbers
1149 +        for (int j = 0; j < 3; j++) {
1150 +          scaled[j] -= roundMe(scaled[j]);
1151 +          scaled[j] += 0.5;
1152 +        }
1153 +        
1154 +        // find xyz-indices of cell that cutoffGroup is in.
1155 +        whichCell.x() = nCells_.x() * scaled.x();
1156 +        whichCell.y() = nCells_.y() * scaled.y();
1157 +        whichCell.z() = nCells_.z() * scaled.z();
1158 +        
1159 +        // find single index of this cell:
1160 +        cellIndex = Vlinear(whichCell, nCells_);
1161 +        
1162 +        // add this cutoff group to the list of groups in this cell;
1163 +        cellListRow_[cellIndex].push_back(i);
1164 +      }
1165 +      for (int i = 0; i < nGroupsInCol_; i++) {
1166 +        rs = cgColData.position[i];
1167 +        
1168 +        // scaled positions relative to the box vectors
1169 +        scaled = invHmat * rs;
1170 +        
1171 +        // wrap the vector back into the unit box by subtracting integer box
1172 +        // numbers
1173 +        for (int j = 0; j < 3; j++) {
1174 +          scaled[j] -= roundMe(scaled[j]);
1175 +          scaled[j] += 0.5;
1176 +        }
1177 +        
1178 +        // find xyz-indices of cell that cutoffGroup is in.
1179 +        whichCell.x() = nCells_.x() * scaled.x();
1180 +        whichCell.y() = nCells_.y() * scaled.y();
1181 +        whichCell.z() = nCells_.z() * scaled.z();
1182 +        
1183 +        // find single index of this cell:
1184 +        cellIndex = Vlinear(whichCell, nCells_);
1185 +        
1186 +        // add this cutoff group to the list of groups in this cell;
1187 +        cellListCol_[cellIndex].push_back(i);
1188 +      }
1189 +    
1190 + #else
1191 +      for (int i = 0; i < nGroups_; i++) {
1192 +        rs = snap_->cgData.position[i];
1193 +        
1194 +        // scaled positions relative to the box vectors
1195 +        scaled = invHmat * rs;
1196 +        
1197 +        // wrap the vector back into the unit box by subtracting integer box
1198 +        // numbers
1199 +        for (int j = 0; j < 3; j++) {
1200 +          scaled[j] -= roundMe(scaled[j]);
1201 +          scaled[j] += 0.5;
1202 +        }
1203 +        
1204 +        // find xyz-indices of cell that cutoffGroup is in.
1205 +        whichCell.x() = nCells_.x() * scaled.x();
1206 +        whichCell.y() = nCells_.y() * scaled.y();
1207 +        whichCell.z() = nCells_.z() * scaled.z();
1208 +        
1209 +        // find single index of this cell:
1210 +        cellIndex = Vlinear(whichCell, nCells_);
1211 +        
1212 +        // add this cutoff group to the list of groups in this cell;
1213 +        cellList_[cellIndex].push_back(i);
1214 +      }
1215 +
1216 + #endif
1217 +
1218 +      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1219 +        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1220 +          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1221 +            Vector3i m1v(m1x, m1y, m1z);
1222 +            int m1 = Vlinear(m1v, nCells_);
1223 +            
1224 +            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1225 +                 os != cellOffsets_.end(); ++os) {
1226 +              
1227 +              Vector3i m2v = m1v + (*os);
1228 +            
1229 +
1230 +              if (m2v.x() >= nCells_.x()) {
1231 +                m2v.x() = 0;          
1232 +              } else if (m2v.x() < 0) {
1233 +                m2v.x() = nCells_.x() - 1;
1234 +              }
1235 +              
1236 +              if (m2v.y() >= nCells_.y()) {
1237 +                m2v.y() = 0;          
1238 +              } else if (m2v.y() < 0) {
1239 +                m2v.y() = nCells_.y() - 1;
1240 +              }
1241 +              
1242 +              if (m2v.z() >= nCells_.z()) {
1243 +                m2v.z() = 0;          
1244 +              } else if (m2v.z() < 0) {
1245 +                m2v.z() = nCells_.z() - 1;
1246 +              }
1247 +
1248 +              int m2 = Vlinear (m2v, nCells_);
1249 +              
1250 + #ifdef IS_MPI
1251 +              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1252 +                   j1 != cellListRow_[m1].end(); ++j1) {
1253 +                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1254 +                     j2 != cellListCol_[m2].end(); ++j2) {
1255 +                  
1256 +                  // In parallel, we need to visit *all* pairs of row
1257 +                  // & column indicies and will divide labor in the
1258 +                  // force evaluation later.
1259 +                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1260 +                  snap_->wrapVector(dr);
1261 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1262 +                  if (dr.lengthSquare() < cuts.third) {
1263 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1264 +                  }                  
1265 +                }
1266 +              }
1267 + #else
1268 +              for (vector<int>::iterator j1 = cellList_[m1].begin();
1269 +                   j1 != cellList_[m1].end(); ++j1) {
1270 +                for (vector<int>::iterator j2 = cellList_[m2].begin();
1271 +                     j2 != cellList_[m2].end(); ++j2) {
1272 +    
1273 +                  // Always do this if we're in different cells or if
1274 +                  // we're in the same cell and the global index of
1275 +                  // the j2 cutoff group is greater than or equal to
1276 +                  // the j1 cutoff group.  Note that Rappaport's code
1277 +                  // has a "less than" conditional here, but that
1278 +                  // deals with atom-by-atom computation.  OpenMD
1279 +                  // allows atoms within a single cutoff group to
1280 +                  // interact with each other.
1281 +
1282 +
1283 +
1284 +                  if (m2 != m1 || (*j2) >= (*j1) ) {
1285 +
1286 +                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1287 +                    snap_->wrapVector(dr);
1288 +                    cuts = getGroupCutoffs( (*j1), (*j2) );
1289 +                    if (dr.lengthSquare() < cuts.third) {
1290 +                      neighborList.push_back(make_pair((*j1), (*j2)));
1291 +                    }
1292 +                  }
1293 +                }
1294 +              }
1295 + #endif
1296 +            }
1297 +          }
1298 +        }
1299 +      }
1300 +    } else {
1301 +      // branch to do all cutoff group pairs
1302 + #ifdef IS_MPI
1303 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1304 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1305 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1306 +          snap_->wrapVector(dr);
1307 +          cuts = getGroupCutoffs( j1, j2 );
1308 +          if (dr.lengthSquare() < cuts.third) {
1309 +            neighborList.push_back(make_pair(j1, j2));
1310 +          }
1311 +        }
1312 +      }      
1313 + #else
1314 +      // include all groups here.
1315 +      for (int j1 = 0; j1 < nGroups_; j1++) {
1316 +        // include self group interactions j2 == j1
1317 +        for (int j2 = j1; j2 < nGroups_; j2++) {
1318 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1319 +          snap_->wrapVector(dr);
1320 +          cuts = getGroupCutoffs( j1, j2 );
1321 +          if (dr.lengthSquare() < cuts.third) {
1322 +            neighborList.push_back(make_pair(j1, j2));
1323 +          }
1324 +        }    
1325 +      }
1326 + #endif
1327 +    }
1328 +      
1329 +    // save the local cutoff group positions for the check that is
1330 +    // done on each loop:
1331 +    saved_CG_positions_.clear();
1332 +    for (int i = 0; i < nGroups_; i++)
1333 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1334 +    
1335 +    return neighborList;
1336 +  }
1337   } //end namespace OpenMD

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