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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 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC

# Line 42 | Line 42
42   #include "math/SquareMatrix3.hpp"
43   #include "nonbonded/NonBondedInteraction.hpp"
44   #include "brains/SnapshotManager.hpp"
45 + #include "brains/PairList.hpp"
46  
47   using namespace std;
48   namespace OpenMD {
# Line 54 | Line 55 | namespace OpenMD {
55    void ForceMatrixDecomposition::distributeInitialData() {
56      snap_ = sman_->getCurrentSnapshot();
57      storageLayout_ = sman_->getStorageLayout();
58 +    ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
58 –    nGroups_ = snap_->getNumberOfCutoffGroups();
60  
61 +    nGroups_ = info_->getNLocalCutoffGroups();
62 +    cerr << "in dId, nGroups = " << nGroups_ << "\n";
63 +    // gather the information for atomtype IDs (atids):
64 +    idents = info_->getIdentArray();
65 +    AtomLocalToGlobal = info_->getGlobalAtomIndices();
66 +    cgLocalToGlobal = info_->getGlobalGroupIndices();
67 +    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68 +    massFactors = info_->getMassFactors();
69 +
70 +    PairList excludes = info_->getExcludedInteractions();
71 +    PairList oneTwo = info_->getOneTwoInteractions();
72 +    PairList oneThree = info_->getOneThreeInteractions();
73 +    PairList oneFour = info_->getOneFourInteractions();
74 +
75   #ifdef IS_MPI
76  
77      AtomCommIntRow = new Communicator<Row,int>(nLocal_);
78      AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79      AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80      AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81 +    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
82  
83      AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
84      AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
85      AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
86      AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
87 +    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
88  
89      cgCommIntRow = new Communicator<Row,int>(nGroups_);
90      cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
# Line 88 | Line 105 | namespace OpenMD {
105      cgRowData.setStorageLayout(DataStorage::dslPosition);
106      cgColData.resize(nGroupsInCol_);
107      cgColData.setStorageLayout(DataStorage::dslPosition);
108 +        
109 +    identsRow.resize(nAtomsInRow_);
110 +    identsCol.resize(nAtomsInCol_);
111      
112 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
113 <                                      vector<RealType> (nAtomsInRow_, 0.0));
94 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
95 <                                      vector<RealType> (nAtomsInCol_, 0.0));
96 <
97 <
98 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
100 –    // gather the information for atomtype IDs (atids):
101 –    vector<int> identsLocal = info_->getIdentArray();
102 –    identsRow.reserve(nAtomsInRow_);
103 –    identsCol.reserve(nAtomsInCol_);
104 –    
105 –    AtomCommIntRow->gather(identsLocal, identsRow);
106 –    AtomCommIntColumn->gather(identsLocal, identsCol);
107 –    
108 –    AtomLocalToGlobal = info_->getGlobalAtomIndices();
115      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
117      
112 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
118      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120  
121 <    // still need:
122 <    // topoDist
123 <    // exclude
121 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
122 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
123 >
124 >    groupListRow_.clear();
125 >    groupListRow_.resize(nGroupsInRow_);
126 >    for (int i = 0; i < nGroupsInRow_; i++) {
127 >      int gid = cgRowToGlobal[i];
128 >      for (int j = 0; j < nAtomsInRow_; j++) {
129 >        int aid = AtomRowToGlobal[j];
130 >        if (globalGroupMembership[aid] == gid)
131 >          groupListRow_[i].push_back(j);
132 >      }      
133 >    }
134 >
135 >    groupListCol_.clear();
136 >    groupListCol_.resize(nGroupsInCol_);
137 >    for (int i = 0; i < nGroupsInCol_; i++) {
138 >      int gid = cgColToGlobal[i];
139 >      for (int j = 0; j < nAtomsInCol_; j++) {
140 >        int aid = AtomColToGlobal[j];
141 >        if (globalGroupMembership[aid] == gid)
142 >          groupListCol_[i].push_back(j);
143 >      }      
144 >    }
145 >
146 >    skipsForAtom.clear();
147 >    skipsForAtom.resize(nAtomsInRow_);
148 >    toposForAtom.clear();
149 >    toposForAtom.resize(nAtomsInRow_);
150 >    topoDist.clear();
151 >    topoDist.resize(nAtomsInRow_);
152 >    for (int i = 0; i < nAtomsInRow_; i++) {
153 >      int iglob = AtomRowToGlobal[i];
154 >
155 >      for (int j = 0; j < nAtomsInCol_; j++) {
156 >        int jglob = AtomColToGlobal[j];
157 >
158 >        if (excludes.hasPair(iglob, jglob))
159 >          skipsForAtom[i].push_back(j);      
160 >        
161 >        if (oneTwo.hasPair(iglob, jglob)) {
162 >          toposForAtom[i].push_back(j);
163 >          topoDist[i].push_back(1);
164 >        } else {
165 >          if (oneThree.hasPair(iglob, jglob)) {
166 >            toposForAtom[i].push_back(j);
167 >            topoDist[i].push_back(2);
168 >          } else {
169 >            if (oneFour.hasPair(iglob, jglob)) {
170 >              toposForAtom[i].push_back(j);
171 >              topoDist[i].push_back(3);
172 >            }
173 >          }
174 >        }
175 >      }      
176 >    }
177 >
178   #endif
179 +
180 +    groupList_.clear();
181 +    groupList_.resize(nGroups_);
182 +    for (int i = 0; i < nGroups_; i++) {
183 +      int gid = cgLocalToGlobal[i];
184 +      for (int j = 0; j < nLocal_; j++) {
185 +        int aid = AtomLocalToGlobal[j];
186 +        if (globalGroupMembership[aid] == gid) {
187 +          groupList_[i].push_back(j);
188 +        }
189 +      }      
190 +    }
191 +
192 +    skipsForAtom.clear();
193 +    skipsForAtom.resize(nLocal_);
194 +    toposForAtom.clear();
195 +    toposForAtom.resize(nLocal_);
196 +    topoDist.clear();
197 +    topoDist.resize(nLocal_);
198 +
199 +    for (int i = 0; i < nLocal_; i++) {
200 +      int iglob = AtomLocalToGlobal[i];
201 +
202 +      for (int j = 0; j < nLocal_; j++) {
203 +        int jglob = AtomLocalToGlobal[j];
204 +
205 +        if (excludes.hasPair(iglob, jglob))
206 +          skipsForAtom[i].push_back(j);              
207 +        
208 +        if (oneTwo.hasPair(iglob, jglob)) {
209 +          toposForAtom[i].push_back(j);
210 +          topoDist[i].push_back(1);
211 +        } else {
212 +          if (oneThree.hasPair(iglob, jglob)) {
213 +            toposForAtom[i].push_back(j);
214 +            topoDist[i].push_back(2);
215 +          } else {
216 +            if (oneFour.hasPair(iglob, jglob)) {
217 +              toposForAtom[i].push_back(j);
218 +              topoDist[i].push_back(3);
219 +            }
220 +          }
221 +        }
222 +      }      
223 +    }
224 +    
225 +    createGtypeCutoffMap();
226    }
227 +  
228 +  void ForceMatrixDecomposition::createGtypeCutoffMap() {
229 +
230 +    RealType tol = 1e-6;
231 +    RealType rc;
232 +    int atid;
233 +    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
234 +    vector<RealType> atypeCutoff;
235 +    atypeCutoff.resize( atypes.size() );
236 +      
237 +    for (set<AtomType*>::iterator at = atypes.begin();
238 +         at != atypes.end(); ++at){
239 +      atid = (*at)->getIdent();
240 +
241 +      if (userChoseCutoff_)
242 +        atypeCutoff[atid] = userCutoff_;
243 +      else
244 +        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
245 +    }
246 +
247 +    vector<RealType> gTypeCutoffs;
248 +
249 +    // first we do a single loop over the cutoff groups to find the
250 +    // largest cutoff for any atypes present in this group.
251 + #ifdef IS_MPI
252 +    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
253 +    groupRowToGtype.resize(nGroupsInRow_);
254 +    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
255 +      vector<int> atomListRow = getAtomsInGroupRow(cg1);
256 +      for (vector<int>::iterator ia = atomListRow.begin();
257 +           ia != atomListRow.end(); ++ia) {            
258 +        int atom1 = (*ia);
259 +        atid = identsRow[atom1];
260 +        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
261 +          groupCutoffRow[cg1] = atypeCutoff[atid];
262 +        }
263 +      }
264 +
265 +      bool gTypeFound = false;
266 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
267 +        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
268 +          groupRowToGtype[cg1] = gt;
269 +          gTypeFound = true;
270 +        }
271 +      }
272 +      if (!gTypeFound) {
273 +        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
274 +        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
275 +      }
276 +      
277 +    }
278 +    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
279 +    groupColToGtype.resize(nGroupsInCol_);
280 +    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
281 +      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
282 +      for (vector<int>::iterator jb = atomListCol.begin();
283 +           jb != atomListCol.end(); ++jb) {            
284 +        int atom2 = (*jb);
285 +        atid = identsCol[atom2];
286 +        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
287 +          groupCutoffCol[cg2] = atypeCutoff[atid];
288 +        }
289 +      }
290 +      bool gTypeFound = false;
291 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
292 +        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
293 +          groupColToGtype[cg2] = gt;
294 +          gTypeFound = true;
295 +        }
296 +      }
297 +      if (!gTypeFound) {
298 +        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
299 +        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
300 +      }
301 +    }
302 + #else
303 +
304 +    vector<RealType> groupCutoff(nGroups_, 0.0);
305 +    groupToGtype.resize(nGroups_);
306 +
307 +    cerr << "nGroups = " << nGroups_ << "\n";
308 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
309 +
310 +      groupCutoff[cg1] = 0.0;
311 +      vector<int> atomList = getAtomsInGroupRow(cg1);
312 +
313 +      for (vector<int>::iterator ia = atomList.begin();
314 +           ia != atomList.end(); ++ia) {            
315 +        int atom1 = (*ia);
316 +        atid = idents[atom1];
317 +        if (atypeCutoff[atid] > groupCutoff[cg1]) {
318 +          groupCutoff[cg1] = atypeCutoff[atid];
319 +        }
320 +      }
321 +
322 +      bool gTypeFound = false;
323 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
324 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
325 +          groupToGtype[cg1] = gt;
326 +          gTypeFound = true;
327 +        }
328 +      }
329 +      if (!gTypeFound) {
330 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
331 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
332 +      }      
333 +    }
334 + #endif
335 +
336 +    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
337 +    // Now we find the maximum group cutoff value present in the simulation
338 +
339 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
340 +
341 + #ifdef IS_MPI
342 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
343 + #endif
344      
345 +    RealType tradRcut = groupMax;
346  
347 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
348 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
349 +        RealType thisRcut;
350 +        switch(cutoffPolicy_) {
351 +        case TRADITIONAL:
352 +          thisRcut = tradRcut;
353 +          break;
354 +        case MIX:
355 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
356 +          break;
357 +        case MAX:
358 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
359 +          break;
360 +        default:
361 +          sprintf(painCave.errMsg,
362 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
363 +                  "hit an unknown cutoff policy!\n");
364 +          painCave.severity = OPENMD_ERROR;
365 +          painCave.isFatal = 1;
366 +          simError();
367 +          break;
368 +        }
369  
370 +        pair<int,int> key = make_pair(i,j);
371 +        gTypeCutoffMap[key].first = thisRcut;
372 +
373 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
374 +
375 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
376 +        
377 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
378 +
379 +        // sanity check
380 +        
381 +        if (userChoseCutoff_) {
382 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
383 +            sprintf(painCave.errMsg,
384 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
385 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
386 +            painCave.severity = OPENMD_ERROR;
387 +            painCave.isFatal = 1;
388 +            simError();            
389 +          }
390 +        }
391 +      }
392 +    }
393 +  }
394 +
395 +
396 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
397 +    int i, j;  
398 + #ifdef IS_MPI
399 +    i = groupRowToGtype[cg1];
400 +    j = groupColToGtype[cg2];
401 + #else
402 +    i = groupToGtype[cg1];
403 +    j = groupToGtype[cg2];
404 + #endif    
405 +    return gTypeCutoffMap[make_pair(i,j)];
406 +  }
407 +
408 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
409 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
410 +      if (toposForAtom[atom1][j] == atom2)
411 +        return topoDist[atom1][j];
412 +    }
413 +    return 0;
414 +  }
415 +
416 +  void ForceMatrixDecomposition::zeroWorkArrays() {
417 +    pairwisePot = 0.0;
418 +    embeddingPot = 0.0;
419 +
420 + #ifdef IS_MPI
421 +    if (storageLayout_ & DataStorage::dslForce) {
422 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
423 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
424 +    }
425 +
426 +    if (storageLayout_ & DataStorage::dslTorque) {
427 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
428 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
429 +    }
430 +    
431 +    fill(pot_row.begin(), pot_row.end(),
432 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
433 +
434 +    fill(pot_col.begin(), pot_col.end(),
435 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
436 +
437 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
438 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
439 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
440 +    }
441 +
442 +    if (storageLayout_ & DataStorage::dslDensity) {      
443 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
444 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
445 +    }
446 +
447 +    if (storageLayout_ & DataStorage::dslFunctional) {  
448 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
449 +      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
450 +    }
451 +
452 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
453 +      fill(atomRowData.functionalDerivative.begin(),
454 +           atomRowData.functionalDerivative.end(), 0.0);
455 +      fill(atomColData.functionalDerivative.begin(),
456 +           atomColData.functionalDerivative.end(), 0.0);
457 +    }
458 +
459 + #else
460 +    
461 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
462 +      fill(snap_->atomData.particlePot.begin(),
463 +           snap_->atomData.particlePot.end(), 0.0);
464 +    }
465 +    
466 +    if (storageLayout_ & DataStorage::dslDensity) {      
467 +      fill(snap_->atomData.density.begin(),
468 +           snap_->atomData.density.end(), 0.0);
469 +    }
470 +    if (storageLayout_ & DataStorage::dslFunctional) {
471 +      fill(snap_->atomData.functional.begin(),
472 +           snap_->atomData.functional.end(), 0.0);
473 +    }
474 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
475 +      fill(snap_->atomData.functionalDerivative.begin(),
476 +           snap_->atomData.functionalDerivative.end(), 0.0);
477 +    }
478 + #endif
479 +    
480 +  }
481 +
482 +
483    void ForceMatrixDecomposition::distributeData()  {
484      snap_ = sman_->getCurrentSnapshot();
485      storageLayout_ = sman_->getStorageLayout();
# Line 156 | Line 515 | namespace OpenMD {
515   #endif      
516    }
517    
518 +  /* collects information obtained during the pre-pair loop onto local
519 +   * data structures.
520 +   */
521    void ForceMatrixDecomposition::collectIntermediateData() {
522      snap_ = sman_->getCurrentSnapshot();
523      storageLayout_ = sman_->getStorageLayout();
# Line 167 | Line 529 | namespace OpenMD {
529                                 snap_->atomData.density);
530        
531        int n = snap_->atomData.density.size();
532 <      std::vector<RealType> rho_tmp(n, 0.0);
532 >      vector<RealType> rho_tmp(n, 0.0);
533        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
534        for (int i = 0; i < n; i++)
535          snap_->atomData.density[i] += rho_tmp[i];
536      }
537   #endif
538    }
539 <  
539 >
540 >  /*
541 >   * redistributes information obtained during the pre-pair loop out to
542 >   * row and column-indexed data structures
543 >   */
544    void ForceMatrixDecomposition::distributeIntermediateData() {
545      snap_ = sman_->getCurrentSnapshot();
546      storageLayout_ = sman_->getStorageLayout();
# Line 232 | Line 598 | namespace OpenMD {
598      
599      nLocal_ = snap_->getNumberOfAtoms();
600  
601 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
602 <                                       vector<RealType> (nLocal_, 0.0));
601 >    vector<potVec> pot_temp(nLocal_,
602 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
603 >
604 >    // scatter/gather pot_row into the members of my column
605 >          
606 >    AtomCommPotRow->scatter(pot_row, pot_temp);
607 >
608 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
609 >      pairwisePot += pot_temp[ii];
610      
611 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
612 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
613 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
614 <        pot_local[i] += pot_temp[i][ii];
615 <      }
616 <    }
611 >    fill(pot_temp.begin(), pot_temp.end(),
612 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
613 >      
614 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
615 >    
616 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
617 >      pairwisePot += pot_temp[ii];    
618   #endif
619 +
620    }
621  
622 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
623 + #ifdef IS_MPI
624 +    return nAtomsInRow_;
625 + #else
626 +    return nLocal_;
627 + #endif
628 +  }
629 +
630 +  /**
631 +   * returns the list of atoms belonging to this group.  
632 +   */
633 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
634 + #ifdef IS_MPI
635 +    return groupListRow_[cg1];
636 + #else
637 +    return groupList_[cg1];
638 + #endif
639 +  }
640 +
641 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
642 + #ifdef IS_MPI
643 +    return groupListCol_[cg2];
644 + #else
645 +    return groupList_[cg2];
646 + #endif
647 +  }
648    
649    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
650      Vector3d d;
# Line 285 | Line 686 | namespace OpenMD {
686      snap_->wrapVector(d);
687      return d;    
688    }
689 +
690 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
691 + #ifdef IS_MPI
692 +    return massFactorsRow[atom1];
693 + #else
694 +    cerr << "mfs = " << massFactors.size() << " atom1 = " << atom1 << "\n";
695 +    return massFactors[atom1];
696 + #endif
697 +  }
698 +
699 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
700 + #ifdef IS_MPI
701 +    return massFactorsCol[atom2];
702 + #else
703 +    return massFactors[atom2];
704 + #endif
705 +
706 +  }
707      
708    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
709      Vector3d d;
# Line 299 | Line 718 | namespace OpenMD {
718      return d;    
719    }
720  
721 +  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
722 +    return skipsForAtom[atom1];
723 +  }
724 +
725 +  /**
726 +   * There are a number of reasons to skip a pair or a
727 +   * particle. Mostly we do this to exclude atoms who are involved in
728 +   * short range interactions (bonds, bends, torsions), but we also
729 +   * need to exclude some overcounted interactions that result from
730 +   * the parallel decomposition.
731 +   */
732 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
733 +    int unique_id_1, unique_id_2;
734 +
735 + #ifdef IS_MPI
736 +    // in MPI, we have to look up the unique IDs for each atom
737 +    unique_id_1 = AtomRowToGlobal[atom1];
738 +    unique_id_2 = AtomColToGlobal[atom2];
739 +
740 +    // this situation should only arise in MPI simulations
741 +    if (unique_id_1 == unique_id_2) return true;
742 +    
743 +    // this prevents us from doing the pair on multiple processors
744 +    if (unique_id_1 < unique_id_2) {
745 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
746 +    } else {
747 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
748 +    }
749 + #else
750 +    // in the normal loop, the atom numbers are unique
751 +    unique_id_1 = atom1;
752 +    unique_id_2 = atom2;
753 + #endif
754 +    
755 +    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
756 +         i != skipsForAtom[atom1].end(); ++i) {
757 +      if ( (*i) == unique_id_2 ) return true;
758 +    }
759 +
760 +    return false;
761 +  }
762 +
763 +
764    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
765   #ifdef IS_MPI
766      atomRowData.force[atom1] += fg;
# Line 316 | Line 778 | namespace OpenMD {
778    }
779  
780      // filling interaction blocks with pointers
781 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
782 <    InteractionData idat;
321 <
781 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
782 >                                                     int atom1, int atom2) {    
783   #ifdef IS_MPI
784 +    
785 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
786 +                             ff_->getAtomType(identsCol[atom2]) );
787 +    
788      if (storageLayout_ & DataStorage::dslAmat) {
789        idat.A1 = &(atomRowData.aMat[atom1]);
790        idat.A2 = &(atomColData.aMat[atom2]);
# Line 340 | Line 805 | namespace OpenMD {
805        idat.rho2 = &(atomColData.density[atom2]);
806      }
807  
808 +    if (storageLayout_ & DataStorage::dslFunctional) {
809 +      idat.frho1 = &(atomRowData.functional[atom1]);
810 +      idat.frho2 = &(atomColData.functional[atom2]);
811 +    }
812 +
813      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
814        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
815        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
816      }
817 +
818 +    if (storageLayout_ & DataStorage::dslParticlePot) {
819 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
820 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
821 +    }
822 +
823   #else
824 +
825 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
826 +                             ff_->getAtomType(idents[atom2]) );
827 +
828      if (storageLayout_ & DataStorage::dslAmat) {
829        idat.A1 = &(snap_->atomData.aMat[atom1]);
830        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 360 | Line 840 | namespace OpenMD {
840        idat.t2 = &(snap_->atomData.torque[atom2]);
841      }
842  
843 <    if (storageLayout_ & DataStorage::dslDensity) {
843 >    if (storageLayout_ & DataStorage::dslDensity) {    
844        idat.rho1 = &(snap_->atomData.density[atom1]);
845        idat.rho2 = &(snap_->atomData.density[atom2]);
846      }
847  
848 +    if (storageLayout_ & DataStorage::dslFunctional) {
849 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
850 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
851 +    }
852 +
853      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
854        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
855        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
856      }
857 +
858 +    if (storageLayout_ & DataStorage::dslParticlePot) {
859 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
860 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
861 +    }
862 +
863   #endif
373 –    return idat;
864    }
865  
866 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
866 >  
867 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
868 > #ifdef IS_MPI
869 >    pot_row[atom1] += 0.5 *  *(idat.pot);
870 >    pot_col[atom2] += 0.5 *  *(idat.pot);
871  
872 <    InteractionData idat;
872 >    atomRowData.force[atom1] += *(idat.f1);
873 >    atomColData.force[atom2] -= *(idat.f1);
874 > #else
875 >    pairwisePot += *(idat.pot);
876 >
877 >    snap_->atomData.force[atom1] += *(idat.f1);
878 >    snap_->atomData.force[atom2] -= *(idat.f1);
879 > #endif
880 >
881 >  }
882 >
883 >
884 >  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
885 >                                              int atom1, int atom2) {
886   #ifdef IS_MPI
887 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
888 +                             ff_->getAtomType(identsCol[atom2]) );
889 +
890      if (storageLayout_ & DataStorage::dslElectroFrame) {
891        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
892        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
893      }
894 +
895      if (storageLayout_ & DataStorage::dslTorque) {
896        idat.t1 = &(atomRowData.torque[atom1]);
897        idat.t2 = &(atomColData.torque[atom2]);
898      }
899 <    if (storageLayout_ & DataStorage::dslForce) {
900 <      idat.t1 = &(atomRowData.force[atom1]);
901 <      idat.t2 = &(atomColData.force[atom2]);
899 >
900 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {
901 >      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
902 >      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
903      }
904   #else
905 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
906 +                             ff_->getAtomType(idents[atom2]) );
907 +
908      if (storageLayout_ & DataStorage::dslElectroFrame) {
909        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
910        idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
911      }
912 +
913      if (storageLayout_ & DataStorage::dslTorque) {
914        idat.t1 = &(snap_->atomData.torque[atom1]);
915        idat.t2 = &(snap_->atomData.torque[atom2]);
916      }
917 <    if (storageLayout_ & DataStorage::dslForce) {
918 <      idat.t1 = &(snap_->atomData.force[atom1]);
919 <      idat.t2 = &(snap_->atomData.force[atom2]);
917 >
918 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {
919 >      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
920 >      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
921      }
922 < #endif
406 <    
922 > #endif    
923    }
924  
925  
926 +  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
927 + #ifdef IS_MPI
928 +    pot_row[atom1] += 0.5 *  *(idat.pot);
929 +    pot_col[atom2] += 0.5 *  *(idat.pot);
930 + #else
931 +    pairwisePot += *(idat.pot);  
932 + #endif
933  
934 +  }
935  
936 +
937    /*
938     * buildNeighborList
939     *
# Line 418 | Line 943 | namespace OpenMD {
943    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
944        
945      vector<pair<int, int> > neighborList;
946 +    groupCutoffs cuts;
947   #ifdef IS_MPI
948      cellListRow_.clear();
949      cellListCol_.clear();
# Line 425 | Line 951 | namespace OpenMD {
951      cellList_.clear();
952   #endif
953  
954 <    // dangerous to not do error checking.
429 <    RealType rCut_;
430 <
431 <    RealType rList_ = (rCut_ + skinThickness_);
954 >    RealType rList_ = (largestRcut_ + skinThickness_);
955      RealType rl2 = rList_ * rList_;
956      Snapshot* snap_ = sman_->getCurrentSnapshot();
957      Mat3x3d Hmat = snap_->getHmat();
# Line 444 | Line 967 | namespace OpenMD {
967      Vector3d rs, scaled, dr;
968      Vector3i whichCell;
969      int cellIndex;
970 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
971  
972   #ifdef IS_MPI
973 +    cellListRow_.resize(nCtot);
974 +    cellListCol_.resize(nCtot);
975 + #else
976 +    cellList_.resize(nCtot);
977 + #endif
978 +
979 + #ifdef IS_MPI
980      for (int i = 0; i < nGroupsInRow_; i++) {
981        rs = cgRowData.position[i];
982 +
983        // scaled positions relative to the box vectors
984        scaled = invHmat * rs;
985 +
986        // wrap the vector back into the unit box by subtracting integer box
987        // numbers
988 <      for (int j = 0; j < 3; j++)
988 >      for (int j = 0; j < 3; j++) {
989          scaled[j] -= roundMe(scaled[j]);
990 +        scaled[j] += 0.5;
991 +      }
992      
993        // find xyz-indices of cell that cutoffGroup is in.
994        whichCell.x() = nCells_.x() * scaled.x();
# Line 462 | Line 997 | namespace OpenMD {
997  
998        // find single index of this cell:
999        cellIndex = Vlinear(whichCell, nCells_);
1000 +
1001        // add this cutoff group to the list of groups in this cell;
1002        cellListRow_[cellIndex].push_back(i);
1003      }
1004  
1005      for (int i = 0; i < nGroupsInCol_; i++) {
1006        rs = cgColData.position[i];
1007 +
1008        // scaled positions relative to the box vectors
1009        scaled = invHmat * rs;
1010 +
1011        // wrap the vector back into the unit box by subtracting integer box
1012        // numbers
1013 <      for (int j = 0; j < 3; j++)
1013 >      for (int j = 0; j < 3; j++) {
1014          scaled[j] -= roundMe(scaled[j]);
1015 +        scaled[j] += 0.5;
1016 +      }
1017  
1018        // find xyz-indices of cell that cutoffGroup is in.
1019        whichCell.x() = nCells_.x() * scaled.x();
# Line 482 | Line 1022 | namespace OpenMD {
1022  
1023        // find single index of this cell:
1024        cellIndex = Vlinear(whichCell, nCells_);
1025 +
1026        // add this cutoff group to the list of groups in this cell;
1027        cellListCol_[cellIndex].push_back(i);
1028      }
1029   #else
1030      for (int i = 0; i < nGroups_; i++) {
1031        rs = snap_->cgData.position[i];
1032 +
1033        // scaled positions relative to the box vectors
1034        scaled = invHmat * rs;
1035 +
1036        // wrap the vector back into the unit box by subtracting integer box
1037        // numbers
1038 <      for (int j = 0; j < 3; j++)
1038 >      for (int j = 0; j < 3; j++) {
1039          scaled[j] -= roundMe(scaled[j]);
1040 +        scaled[j] += 0.5;
1041 +      }
1042  
1043        // find xyz-indices of cell that cutoffGroup is in.
1044        whichCell.x() = nCells_.x() * scaled.x();
# Line 501 | Line 1046 | namespace OpenMD {
1046        whichCell.z() = nCells_.z() * scaled.z();
1047  
1048        // find single index of this cell:
1049 <      cellIndex = Vlinear(whichCell, nCells_);
1049 >      cellIndex = Vlinear(whichCell, nCells_);      
1050 >
1051        // add this cutoff group to the list of groups in this cell;
1052        cellList_[cellIndex].push_back(i);
1053      }
1054   #endif
1055  
510 –
511 –
1056      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1057        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1058          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
# Line 553 | Line 1097 | namespace OpenMD {
1097                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1098                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1099                    snap_->wrapVector(dr);
1100 <                  if (dr.lengthSquare() < rl2) {
1100 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1101 >                  if (dr.lengthSquare() < cuts.third) {
1102                      neighborList.push_back(make_pair((*j1), (*j2)));
1103                    }
1104                  }
1105                }
1106              }
1107   #else
1108 +
1109              for (vector<int>::iterator j1 = cellList_[m1].begin();
1110                   j1 != cellList_[m1].end(); ++j1) {
1111                for (vector<int>::iterator j2 = cellList_[m2].begin();
1112                     j2 != cellList_[m2].end(); ++j2) {
1113 <                              
1113 >
1114                  // Always do this if we're in different cells or if
1115                  // we're in the same cell and the global index of the
1116                  // j2 cutoff group is less than the j1 cutoff group
# Line 572 | Line 1118 | namespace OpenMD {
1118                  if (m2 != m1 || (*j2) < (*j1)) {
1119                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1120                    snap_->wrapVector(dr);
1121 <                  if (dr.lengthSquare() < rl2) {
1121 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1122 >                  if (dr.lengthSquare() < cuts.third) {
1123                      neighborList.push_back(make_pair((*j1), (*j2)));
1124                    }
1125                  }
# Line 583 | Line 1130 | namespace OpenMD {
1130          }
1131        }
1132      }
1133 <
1133 >    
1134      // save the local cutoff group positions for the check that is
1135      // done on each loop:
1136      saved_CG_positions_.clear();
1137      for (int i = 0; i < nGroups_; i++)
1138        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1139 <
1139 >  
1140      return neighborList;
1141    }
1142   } //end namespace OpenMD

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