ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
(Generate patch)

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1581 by gezelter, Mon Jun 13 22:13:12 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 <    vector<int> identsLocal = info_->getIdentArray();
64 >    identsLocal = info_->getIdentArray();
65      AtomLocalToGlobal = info_->getGlobalAtomIndices();
66      cgLocalToGlobal = info_->getGlobalGroupIndices();
67      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68 <    vector<RealType> massFactorsLocal = info_->getMassFactors();
69 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
68 >    massFactors = info_->getMassFactors();
69 >    PairList excludes = info_->getExcludedInteractions();
70 >    PairList oneTwo = info_->getOneTwoInteractions();
71 >    PairList oneThree = info_->getOneThreeInteractions();
72 >    PairList oneFour = info_->getOneFourInteractions();
73  
74   #ifdef IS_MPI
75  
# Line 71 | Line 77 | namespace OpenMD {
77      AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
78      AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
79      AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
80 +    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
81  
82      AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
83      AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
84      AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
85      AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
86 +    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
87  
88      cgCommIntRow = new Communicator<Row,int>(nGroups_);
89      cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
# Line 96 | Line 104 | namespace OpenMD {
104      cgRowData.setStorageLayout(DataStorage::dslPosition);
105      cgColData.resize(nGroupsInCol_);
106      cgColData.setStorageLayout(DataStorage::dslPosition);
107 +        
108 +    identsRow.resize(nAtomsInRow_);
109 +    identsCol.resize(nAtomsInCol_);
110      
100 –    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
101 –                                      vector<RealType> (nAtomsInRow_, 0.0));
102 –    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
103 –                                      vector<RealType> (nAtomsInCol_, 0.0));
104 –    
105 –    identsRow.reserve(nAtomsInRow_);
106 –    identsCol.reserve(nAtomsInCol_);
107 –    
111      AtomCommIntRow->gather(identsLocal, identsRow);
112      AtomCommIntColumn->gather(identsLocal, identsCol);
113      
# Line 114 | Line 117 | namespace OpenMD {
117      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
118      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
119  
120 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
121 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
120 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
121 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
122  
123      groupListRow_.clear();
124 <    groupListRow_.reserve(nGroupsInRow_);
124 >    groupListRow_.resize(nGroupsInRow_);
125      for (int i = 0; i < nGroupsInRow_; i++) {
126        int gid = cgRowToGlobal[i];
127        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 129 | Line 132 | namespace OpenMD {
132      }
133  
134      groupListCol_.clear();
135 <    groupListCol_.reserve(nGroupsInCol_);
135 >    groupListCol_.resize(nGroupsInCol_);
136      for (int i = 0; i < nGroupsInCol_; i++) {
137        int gid = cgColToGlobal[i];
138        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 139 | Line 142 | namespace OpenMD {
142        }      
143      }
144  
145 +    skipsForAtom.clear();
146 +    skipsForAtom.resize(nAtomsInRow_);
147 +    toposForAtom.clear();
148 +    toposForAtom.resize(nAtomsInRow_);
149 +    topoDist.clear();
150 +    topoDist.resize(nAtomsInRow_);
151 +    for (int i = 0; i < nAtomsInRow_; i++) {
152 +      int iglob = AtomRowToGlobal[i];
153 +
154 +      for (int j = 0; j < nAtomsInCol_; j++) {
155 +        int jglob = AtomColToGlobal[j];
156 +
157 +        if (excludes.hasPair(iglob, jglob))
158 +          skipsForAtom[i].push_back(j);      
159 +        
160 +        if (oneTwo.hasPair(iglob, jglob)) {
161 +          toposForAtom[i].push_back(j);
162 +          topoDist[i].push_back(1);
163 +        } else {
164 +          if (oneThree.hasPair(iglob, jglob)) {
165 +            toposForAtom[i].push_back(j);
166 +            topoDist[i].push_back(2);
167 +          } else {
168 +            if (oneFour.hasPair(iglob, jglob)) {
169 +              toposForAtom[i].push_back(j);
170 +              topoDist[i].push_back(3);
171 +            }
172 +          }
173 +        }
174 +      }      
175 +    }
176 +
177   #endif
178  
179      groupList_.clear();
180 <    groupList_.reserve(nGroups_);
180 >    groupList_.resize(nGroups_);
181      for (int i = 0; i < nGroups_; i++) {
182        int gid = cgLocalToGlobal[i];
183        for (int j = 0; j < nLocal_; j++) {
184          int aid = AtomLocalToGlobal[j];
185 <        if (globalGroupMembership[aid] == gid)
185 >        if (globalGroupMembership[aid] == gid) {
186            groupList_[i].push_back(j);
187 +        }
188        }      
189      }
190  
191 +    skipsForAtom.clear();
192 +    skipsForAtom.resize(nLocal_);
193 +    toposForAtom.clear();
194 +    toposForAtom.resize(nLocal_);
195 +    topoDist.clear();
196 +    topoDist.resize(nLocal_);
197 +
198 +    for (int i = 0; i < nLocal_; i++) {
199 +      int iglob = AtomLocalToGlobal[i];
200 +
201 +      for (int j = 0; j < nLocal_; j++) {
202 +        int jglob = AtomLocalToGlobal[j];
203 +
204 +        if (excludes.hasPair(iglob, jglob))
205 +          skipsForAtom[i].push_back(j);              
206 +        
207 +        if (oneTwo.hasPair(iglob, jglob)) {
208 +          toposForAtom[i].push_back(j);
209 +          topoDist[i].push_back(1);
210 +        } else {
211 +          if (oneThree.hasPair(iglob, jglob)) {
212 +            toposForAtom[i].push_back(j);
213 +            topoDist[i].push_back(2);
214 +          } else {
215 +            if (oneFour.hasPair(iglob, jglob)) {
216 +              toposForAtom[i].push_back(j);
217 +              topoDist[i].push_back(3);
218 +            }
219 +          }
220 +        }
221 +      }      
222 +    }
223 +    
224 +    createGtypeCutoffMap();
225 +  }
226    
227 <    // still need:
228 <    // topoDist
229 <    // exclude
227 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
228 >
229 >    RealType tol = 1e-6;
230 >    RealType rc;
231 >    int atid;
232 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
233 >    vector<RealType> atypeCutoff;
234 >    atypeCutoff.resize( atypes.size() );
235 >
236 >    for (set<AtomType*>::iterator at = atypes.begin();
237 >         at != atypes.end(); ++at){
238 >      rc = interactionMan_->getSuggestedCutoffRadius(*at);
239 >      atid = (*at)->getIdent();
240 >      atypeCutoff[atid] = rc;
241 >    }
242 >
243 >    vector<RealType> gTypeCutoffs;
244 >
245 >    // first we do a single loop over the cutoff groups to find the
246 >    // largest cutoff for any atypes present in this group.
247 > #ifdef IS_MPI
248 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
249 >    groupRowToGtype.resize(nGroupsInRow_);
250 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
251 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
252 >      for (vector<int>::iterator ia = atomListRow.begin();
253 >           ia != atomListRow.end(); ++ia) {            
254 >        int atom1 = (*ia);
255 >        atid = identsRow[atom1];
256 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
257 >          groupCutoffRow[cg1] = atypeCutoff[atid];
258 >        }
259 >      }
260 >
261 >      bool gTypeFound = false;
262 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
263 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
264 >          groupRowToGtype[cg1] = gt;
265 >          gTypeFound = true;
266 >        }
267 >      }
268 >      if (!gTypeFound) {
269 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
270 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
271 >      }
272 >      
273 >    }
274 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
275 >    groupColToGtype.resize(nGroupsInCol_);
276 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
277 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
278 >      for (vector<int>::iterator jb = atomListCol.begin();
279 >           jb != atomListCol.end(); ++jb) {            
280 >        int atom2 = (*jb);
281 >        atid = identsCol[atom2];
282 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
283 >          groupCutoffCol[cg2] = atypeCutoff[atid];
284 >        }
285 >      }
286 >      bool gTypeFound = false;
287 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
288 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
289 >          groupColToGtype[cg2] = gt;
290 >          gTypeFound = true;
291 >        }
292 >      }
293 >      if (!gTypeFound) {
294 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
295 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
296 >      }
297 >    }
298 > #else
299  
300 +    vector<RealType> groupCutoff(nGroups_, 0.0);
301 +    groupToGtype.resize(nGroups_);
302 +
303 +    cerr << "nGroups = " << nGroups_ << "\n";
304 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305 +
306 +      groupCutoff[cg1] = 0.0;
307 +      vector<int> atomList = getAtomsInGroupRow(cg1);
308 +
309 +      for (vector<int>::iterator ia = atomList.begin();
310 +           ia != atomList.end(); ++ia) {            
311 +        int atom1 = (*ia);
312 +        atid = identsLocal[atom1];
313 +        if (atypeCutoff[atid] > groupCutoff[cg1]) {
314 +          groupCutoff[cg1] = atypeCutoff[atid];
315 +        }
316 +      }
317 +
318 +      bool gTypeFound = false;
319 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
320 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
321 +          groupToGtype[cg1] = gt;
322 +          gTypeFound = true;
323 +        }
324 +      }
325 +      if (!gTypeFound) {
326 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
327 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
328 +      }      
329 +    }
330 + #endif
331 +
332 +    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
333 +    // Now we find the maximum group cutoff value present in the simulation
334 +
335 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
336 +
337 + #ifdef IS_MPI
338 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
339 + #endif
340 +    
341 +    RealType tradRcut = groupMax;
342 +
343 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
344 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
345 +        RealType thisRcut;
346 +        switch(cutoffPolicy_) {
347 +        case TRADITIONAL:
348 +          thisRcut = tradRcut;
349 +          break;
350 +        case MIX:
351 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
352 +          break;
353 +        case MAX:
354 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
355 +          break;
356 +        default:
357 +          sprintf(painCave.errMsg,
358 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
359 +                  "hit an unknown cutoff policy!\n");
360 +          painCave.severity = OPENMD_ERROR;
361 +          painCave.isFatal = 1;
362 +          simError();
363 +          break;
364 +        }
365 +
366 +        pair<int,int> key = make_pair(i,j);
367 +        gTypeCutoffMap[key].first = thisRcut;
368 +
369 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
370 +
371 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
372 +        
373 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
374 +
375 +        // sanity check
376 +        
377 +        if (userChoseCutoff_) {
378 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
379 +            sprintf(painCave.errMsg,
380 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
381 +                    "user-specified rCut does not match computed group Cutoff\n");
382 +            painCave.severity = OPENMD_ERROR;
383 +            painCave.isFatal = 1;
384 +            simError();            
385 +          }
386 +        }
387 +      }
388 +    }
389    }
390 +
391 +
392 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
393 +    int i, j;  
394 + #ifdef IS_MPI
395 +    i = groupRowToGtype[cg1];
396 +    j = groupColToGtype[cg2];
397 + #else
398 +    i = groupToGtype[cg1];
399 +    j = groupToGtype[cg2];
400 + #endif    
401 +    return gTypeCutoffMap[make_pair(i,j)];
402 +  }
403 +
404 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
405 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
406 +      if (toposForAtom[atom1][j] == atom2)
407 +        return topoDist[atom1][j];
408 +    }
409 +    return 0;
410 +  }
411 +
412 +  void ForceMatrixDecomposition::zeroWorkArrays() {
413 +
414 +    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415 +      longRangePot_[j] = 0.0;
416 +    }
417 +
418 + #ifdef IS_MPI
419 +    if (storageLayout_ & DataStorage::dslForce) {
420 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
421 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
422 +    }
423 +
424 +    if (storageLayout_ & DataStorage::dslTorque) {
425 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
426 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
427 +    }
428      
429 +    fill(pot_row.begin(), pot_row.end(),
430 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
431  
432 +    fill(pot_col.begin(), pot_col.end(),
433 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434 +    
435 +    pot_local = 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 196 | 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 207 | 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 272 | 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 >      pot_local += 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 >      pot_local += pot_temp[ii];
618 >    
619   #endif
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     */
# Line 348 | Line 691 | namespace OpenMD {
691   #ifdef IS_MPI
692      return massFactorsRow[atom1];
693   #else
694 <    return massFactorsLocal[atom1];
694 >    return massFactors[atom1];
695   #endif
696    }
697  
# Line 356 | Line 699 | namespace OpenMD {
699   #ifdef IS_MPI
700      return massFactorsCol[atom2];
701   #else
702 <    return massFactorsLocal[atom2];
702 >    return massFactors[atom2];
703   #endif
704  
705    }
# Line 372 | Line 715 | namespace OpenMD {
715  
716      snap_->wrapVector(d);
717      return d;    
718 +  }
719 +
720 +  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
721 +    return skipsForAtom[atom1];
722 +  }
723 +
724 +  /**
725 +   * There are a number of reasons to skip a pair or a
726 +   * particle. Mostly we do this to exclude atoms who are involved in
727 +   * short range interactions (bonds, bends, torsions), but we also
728 +   * need to exclude some overcounted interactions that result from
729 +   * the parallel decomposition.
730 +   */
731 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
732 +    int unique_id_1, unique_id_2;
733 +
734 + #ifdef IS_MPI
735 +    // in MPI, we have to look up the unique IDs for each atom
736 +    unique_id_1 = AtomRowToGlobal[atom1];
737 +    unique_id_2 = AtomColToGlobal[atom2];
738 +
739 +    // this situation should only arise in MPI simulations
740 +    if (unique_id_1 == unique_id_2) return true;
741 +    
742 +    // this prevents us from doing the pair on multiple processors
743 +    if (unique_id_1 < unique_id_2) {
744 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
745 +    } else {
746 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
747 +    }
748 + #else
749 +    // in the normal loop, the atom numbers are unique
750 +    unique_id_1 = atom1;
751 +    unique_id_2 = atom2;
752 + #endif
753 +    
754 +    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
755 +         i != skipsForAtom[atom1].end(); ++i) {
756 +      if ( (*i) == unique_id_2 ) return true;
757 +    }    
758 +
759    }
760  
761 +
762    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
763   #ifdef IS_MPI
764      atomRowData.force[atom1] += fg;
# Line 391 | Line 776 | namespace OpenMD {
776    }
777  
778      // filling interaction blocks with pointers
779 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
780 <    InteractionData idat;
396 <
779 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData idat,
780 >                                                     int atom1, int atom2) {    
781   #ifdef IS_MPI
782 +    
783 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
784 +                             ff_->getAtomType(identsCol[atom2]) );
785 +    
786      if (storageLayout_ & DataStorage::dslAmat) {
787        idat.A1 = &(atomRowData.aMat[atom1]);
788        idat.A2 = &(atomColData.aMat[atom2]);
# Line 415 | Line 803 | namespace OpenMD {
803        idat.rho2 = &(atomColData.density[atom2]);
804      }
805  
806 +    if (storageLayout_ & DataStorage::dslFunctional) {
807 +      idat.frho1 = &(atomRowData.functional[atom1]);
808 +      idat.frho2 = &(atomColData.functional[atom2]);
809 +    }
810 +
811      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
812        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
813        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
814      }
815 +
816 +    if (storageLayout_ & DataStorage::dslParticlePot) {
817 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
818 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
819 +    }
820 +
821   #else
822 +
823 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
824 +                             ff_->getAtomType(identsLocal[atom2]) );
825 +
826      if (storageLayout_ & DataStorage::dslAmat) {
827        idat.A1 = &(snap_->atomData.aMat[atom1]);
828        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 440 | Line 843 | namespace OpenMD {
843        idat.rho2 = &(snap_->atomData.density[atom2]);
844      }
845  
846 +    if (storageLayout_ & DataStorage::dslFunctional) {
847 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
848 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
849 +    }
850 +
851      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
852        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
853        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
854      }
855 +
856 +    if (storageLayout_ & DataStorage::dslParticlePot) {
857 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
858 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
859 +    }
860 +
861   #endif
448 –    return idat;
862    }
863  
864 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
864 >  
865 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
866 > #ifdef IS_MPI
867 >    pot_row[atom1] += 0.5 *  *(idat.pot);
868 >    pot_col[atom2] += 0.5 *  *(idat.pot);
869  
870 <    InteractionData idat;
870 >    atomRowData.force[atom1] += *(idat.f1);
871 >    atomColData.force[atom2] -= *(idat.f1);
872 > #else
873 >    longRangePot_ += *(idat.pot);
874 >    
875 >    snap_->atomData.force[atom1] += *(idat.f1);
876 >    snap_->atomData.force[atom2] -= *(idat.f1);
877 > #endif
878 >
879 >  }
880 >
881 >
882 >  void ForceMatrixDecomposition::fillSkipData(InteractionData idat,
883 >                                              int atom1, int atom2) {
884   #ifdef IS_MPI
885 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
886 +                             ff_->getAtomType(identsCol[atom2]) );
887 +
888      if (storageLayout_ & DataStorage::dslElectroFrame) {
889        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
890        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 460 | Line 893 | namespace OpenMD {
893        idat.t1 = &(atomRowData.torque[atom1]);
894        idat.t2 = &(atomColData.torque[atom2]);
895      }
463 –    if (storageLayout_ & DataStorage::dslForce) {
464 –      idat.t1 = &(atomRowData.force[atom1]);
465 –      idat.t2 = &(atomColData.force[atom2]);
466 –    }
896   #else
897 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
898 +                             ff_->getAtomType(identsLocal[atom2]) );
899 +
900      if (storageLayout_ & DataStorage::dslElectroFrame) {
901        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
902        idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
# Line 473 | Line 905 | namespace OpenMD {
905        idat.t1 = &(snap_->atomData.torque[atom1]);
906        idat.t2 = &(snap_->atomData.torque[atom2]);
907      }
908 <    if (storageLayout_ & DataStorage::dslForce) {
477 <      idat.t1 = &(snap_->atomData.force[atom1]);
478 <      idat.t2 = &(snap_->atomData.force[atom2]);
479 <    }
480 < #endif
481 <    
908 > #endif    
909    }
910  
484 –
485 –
486 –
911    /*
912     * buildNeighborList
913     *
# Line 493 | Line 917 | namespace OpenMD {
917    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
918        
919      vector<pair<int, int> > neighborList;
920 +    groupCutoffs cuts;
921   #ifdef IS_MPI
922      cellListRow_.clear();
923      cellListCol_.clear();
# Line 500 | Line 925 | namespace OpenMD {
925      cellList_.clear();
926   #endif
927  
928 <    // dangerous to not do error checking.
504 <    RealType rCut_;
505 <
506 <    RealType rList_ = (rCut_ + skinThickness_);
928 >    RealType rList_ = (largestRcut_ + skinThickness_);
929      RealType rl2 = rList_ * rList_;
930      Snapshot* snap_ = sman_->getCurrentSnapshot();
931      Mat3x3d Hmat = snap_->getHmat();
# Line 519 | Line 941 | namespace OpenMD {
941      Vector3d rs, scaled, dr;
942      Vector3i whichCell;
943      int cellIndex;
944 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
945  
946 +    cerr << "flag1\n";
947   #ifdef IS_MPI
948 +    cellListRow_.resize(nCtot);
949 +    cellListCol_.resize(nCtot);
950 + #else
951 +    cellList_.resize(nCtot);
952 + #endif
953 +    cerr << "flag2\n";
954 + #ifdef IS_MPI
955      for (int i = 0; i < nGroupsInRow_; i++) {
956        rs = cgRowData.position[i];
957 +
958        // scaled positions relative to the box vectors
959        scaled = invHmat * rs;
960 +
961        // wrap the vector back into the unit box by subtracting integer box
962        // numbers
963 <      for (int j = 0; j < 3; j++)
963 >      for (int j = 0; j < 3; j++) {
964          scaled[j] -= roundMe(scaled[j]);
965 +        scaled[j] += 0.5;
966 +      }
967      
968        // find xyz-indices of cell that cutoffGroup is in.
969        whichCell.x() = nCells_.x() * scaled.x();
# Line 537 | Line 972 | namespace OpenMD {
972  
973        // find single index of this cell:
974        cellIndex = Vlinear(whichCell, nCells_);
975 +
976        // add this cutoff group to the list of groups in this cell;
977        cellListRow_[cellIndex].push_back(i);
978      }
979  
980      for (int i = 0; i < nGroupsInCol_; i++) {
981        rs = cgColData.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 557 | 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        cellListCol_[cellIndex].push_back(i);
1003      }
1004   #else
1005      for (int i = 0; i < nGroups_; i++) {
1006        rs = snap_->cgData.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 576 | Line 1021 | namespace OpenMD {
1021        whichCell.z() = nCells_.z() * scaled.z();
1022  
1023        // find single index of this cell:
1024 <      cellIndex = Vlinear(whichCell, nCells_);
1024 >      cellIndex = Vlinear(whichCell, nCells_);      
1025 >
1026        // add this cutoff group to the list of groups in this cell;
1027        cellList_[cellIndex].push_back(i);
1028      }
1029   #endif
1030  
585 –
586 –
1031      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1032        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1033          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
# Line 628 | Line 1072 | namespace OpenMD {
1072                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1073                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1074                    snap_->wrapVector(dr);
1075 <                  if (dr.lengthSquare() < rl2) {
1075 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1076 >                  if (dr.lengthSquare() < cuts.third) {
1077                      neighborList.push_back(make_pair((*j1), (*j2)));
1078                    }
1079                  }
1080                }
1081              }
1082   #else
1083 +
1084              for (vector<int>::iterator j1 = cellList_[m1].begin();
1085                   j1 != cellList_[m1].end(); ++j1) {
1086                for (vector<int>::iterator j2 = cellList_[m2].begin();
1087                     j2 != cellList_[m2].end(); ++j2) {
1088 <                              
1088 >
1089                  // Always do this if we're in different cells or if
1090                  // we're in the same cell and the global index of the
1091                  // j2 cutoff group is less than the j1 cutoff group
# Line 647 | Line 1093 | namespace OpenMD {
1093                  if (m2 != m1 || (*j2) < (*j1)) {
1094                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1095                    snap_->wrapVector(dr);
1096 <                  if (dr.lengthSquare() < rl2) {
1096 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1097 >                  if (dr.lengthSquare() < cuts.third) {
1098                      neighborList.push_back(make_pair((*j1), (*j2)));
1099                    }
1100                  }
# Line 658 | Line 1105 | namespace OpenMD {
1105          }
1106        }
1107      }
1108 <
1108 >    
1109      // save the local cutoff group positions for the check that is
1110      // done on each loop:
1111      saved_CG_positions_.clear();
1112      for (int i = 0; i < nGroups_; i++)
1113        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1114 <
1114 >    
1115      return neighborList;
1116    }
1117   } //end namespace OpenMD

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines