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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 1562 by gezelter, Thu May 12 17:00:14 2011 UTC vs.
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/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);
321 <
322 <    // still need:
323 <    // topoDist
324 <    // exclude
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 >    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 + #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 <    AtomCommVectorRow->gather(snap_->atomData.position,
564 >    AtomPlanVectorRow->gather(snap_->atomData.position,
565                                atomRowData.position);
566 <    AtomCommVectorColumn->gather(snap_->atomData.position,
566 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
567                                   atomColData.position);
568      
569      // gather up the cutoff group positions
570 <    cgCommVectorRow->gather(snap_->cgData.position,
570 >
571 >    cgPlanVectorRow->gather(snap_->cgData.position,
572                              cgRowData.position);
573 <    cgCommVectorColumn->gather(snap_->cgData.position,
573 >
574 >    cgPlanVectorColumn->gather(snap_->cgData.position,
575                                 cgColData.position);
576 +
577      
578      // if needed, gather the atomic rotation matrices
579      if (storageLayout_ & DataStorage::dslAmat) {
580 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
580 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
581                                  atomRowData.aMat);
582 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
582 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
583                                     atomColData.aMat);
584      }
585      
586      // if needed, gather the atomic eletrostatic frames
587      if (storageLayout_ & DataStorage::dslElectroFrame) {
588 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
588 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
589                                  atomRowData.electroFrame);
590 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
590 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
591                                     atomColData.electroFrame);
592      }
593 +
594   #endif      
595    }
596    
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();
# Line 162 | Line 604 | namespace OpenMD {
604      
605      if (storageLayout_ & DataStorage::dslDensity) {
606        
607 <      AtomCommRealRow->scatter(atomRowData.density,
607 >      AtomPlanRealRow->scatter(atomRowData.density,
608                                 snap_->atomData.density);
609        
610        int n = snap_->atomData.density.size();
611 <      std::vector<RealType> rho_tmp(n, 0.0);
612 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
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];
615      }
616   #endif
617    }
618 <  
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      if (storageLayout_ & DataStorage::dslFunctional) {
628 <      AtomCommRealRow->gather(snap_->atomData.functional,
628 >      AtomPlanRealRow->gather(snap_->atomData.functional,
629                                atomRowData.functional);
630 <      AtomCommRealColumn->gather(snap_->atomData.functional,
630 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
631                                   atomColData.functional);
632      }
633      
634      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
635 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
635 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
636                                atomRowData.functionalDerivative);
637 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
637 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
638                                   atomColData.functionalDerivative);
639      }
640   #endif
# Line 202 | Line 648 | namespace OpenMD {
648      int n = snap_->atomData.force.size();
649      vector<Vector3d> frc_tmp(n, V3Zero);
650      
651 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
651 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
652      for (int i = 0; i < n; i++) {
653        snap_->atomData.force[i] += frc_tmp[i];
654        frc_tmp[i] = 0.0;
655      }
656      
657 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
658 <    for (int i = 0; i < n; i++)
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 <    
660 >    }
661 >        
662      if (storageLayout_ & DataStorage::dslTorque) {
663  
664 <      int nt = snap_->atomData.force.size();
664 >      int nt = snap_->atomData.torque.size();
665        vector<Vector3d> trq_tmp(nt, V3Zero);
666  
667 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
668 <      for (int i = 0; i < n; 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 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
674 <      for (int i = 0; i < n; 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 <    int nLocal = snap_->getNumberOfAtoms();
695 >    nLocal_ = snap_->getNumberOfAtoms();
696  
697 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
698 <                                       vector<RealType> (nLocal, 0.0));
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 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
708 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
709 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
710 <        pot_local[i] += pot_temp[i][ii];
711 <      }
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 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;
# Line 284 | Line 797 | namespace OpenMD {
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;
# Line 296 | Line 826 | namespace OpenMD {
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;
# Line 312 | Line 899 | namespace OpenMD {
899   #else
900      snap_->atomData.force[atom2] += fg;
901   #endif
315 –
902    }
903  
904      // filling interaction blocks with pointers
905 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
905 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
906 >                                                     int atom1, int atom2) {
907  
908 <    InteractionData idat;
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 <
919 >    
920      if (storageLayout_ & DataStorage::dslElectroFrame) {
921        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
922        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 340 | Line 932 | namespace OpenMD {
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]);
# Line 360 | Line 978 | namespace OpenMD {
978        idat.t2 = &(snap_->atomData.torque[atom2]);
979      }
980  
981 <    if (storageLayout_ & DataStorage::dslDensity) {
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
373 –    
1006    }
1007 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1008 <    InteractionData idat;
1009 <    skippedCharge1
378 <      skippedCharge2
379 <      rij
380 <      d
381 <    electroMult
382 <    sw
383 <    f
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 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1015 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1016 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1017 <    }
390 <    if (storageLayout_ & DataStorage::dslTorque) {
391 <      idat.t1 = &(atomRowData.torque[atom1]);
392 <      idat.t2 = &(atomColData.torque[atom2]);
393 <    }
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    }
397 –  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
398 –  }
1024  
400 –
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> >  buildNeighborList() {
1032 <    Vector3d dr, invWid, rs, shift;
1033 <    Vector3i cc, m1v, m2s;
1034 <    RealType rrNebr;
1035 <    int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
1031 >  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1032 >      
1033 >    vector<pair<int, int> > neighborList;
1034 >    groupCutoffs cuts;
1035 >    bool doAllPairs = false;
1036  
1037 <
1038 <    vector<pair<int, int> > neighborList;  
1039 <    Vector3i nCells;
1040 <    Vector3d invWid, r;
1041 <
1042 <    rList_ = (rCut_ + skinThickness_);
419 <    rl2 = rList_ * rList_;
1037 > #ifdef IS_MPI
1038 >    cellListRow_.clear();
1039 >    cellListCol_.clear();
1040 > #else
1041 >    cellList_.clear();
1042 > #endif
1043  
1044 <    snap_ = sman_->getCurrentSnapshot();
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_;
1052 >    nCells_.x() = (int) ( Hx.length() )/ rList_;
1053 >    nCells_.y() = (int) ( Hy.length() )/ rList_;
1054 >    nCells_.z() = (int) ( Hz.length() )/ rList_;
1055  
1056 <    for (i = 0; i < nGroupsInRow; i++) {
432 <      rs = cgRowData.position[i];
433 <      snap_->scaleVector(rs);    
434 <    }
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 <    VDiv (invWid, cells, region);
1063 <    for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
1064 <    for (n = 0; n < nMol; n ++) {
1065 <      VSAdd (rs, mol[n].r, 0.5, region);
1066 <      VMul (cc, rs, invWid);
442 <      c = VLinear (cc, cells) + nMol;
443 <      cellList[n] = cellList[c];
444 <      cellList[c] = n;
445 <    }
446 <    nebrTabLen = 0;
447 <    for (m1z = 0; m1z < cells.z(); m1z++) {
448 <      for (m1y = 0; m1y < cells.y(); m1y++) {
449 <        for (m1x = 0; m1x < cells.x(); m1x++) {
450 <          Vector3i m1v(m1x, m1y, m1z);
451 <          m1 = VLinear(m1v, cells) + nMol;
452 <          for (offset = 0; offset < nOffset_; offset++) {
453 <            m2v = m1v + cellOffsets_[offset];
454 <            shift = V3Zero();
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 <            if (m2v.x() >= cells.x) {
1069 <              m2v.x() = 0;          
1070 <              shift.x() = region.x();  
1071 <            } else if (m2v.x() < 0) {
1072 <              m2v.x() = cells.x() - 1;
1073 <              shift.x() = - region.x();
462 <            }
1068 > #ifdef IS_MPI
1069 >    cellListRow_.resize(nCtot);
1070 >    cellListCol_.resize(nCtot);
1071 > #else
1072 >    cellList_.resize(nCtot);
1073 > #endif
1074  
1075 <            if (m2v.y() >= cells.y()) {
1076 <              m2v.y() = 0;          
466 <              shift.y() = region.y();  
467 <            } else if (m2v.y() < 0) {
468 <              m2v.y() = cells.y() - 1;
469 <              shift.y() = - region.y();
470 <            }
1075 >    if (!doAllPairs) {
1076 > #ifdef IS_MPI
1077  
1078 <            m2 = VLinear (m2v, cells) + nMol;
1079 <            for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
1080 <              for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
1081 <                if (m1 != m2 || j2 < j1) {
1082 <                  dr = mol[j1].r - mol[j2].r;
1083 <                  VSub (dr, mol[j1].r, mol[j2].r);
1084 <                  VVSub (dr, shift);
1085 <                  if (VLenSq (dr) < rrNebr) {
1086 <                    neighborList.push_back(make_pair(j1, j2));
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    }
490 –
491 –  
1274   } //end namespace OpenMD

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