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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 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1575 by gezelter, Fri Jun 3 21:39:49 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();
60      nGroups_ = snap_->getNumberOfCutoffGroups();
61  
62      // gather the information for atomtype IDs (atids):
63 <    vector<int> identsLocal = info_->getIdentArray();
63 >    identsLocal = info_->getIdentArray();
64      AtomLocalToGlobal = info_->getGlobalAtomIndices();
65      cgLocalToGlobal = info_->getGlobalGroupIndices();
66      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67      vector<RealType> massFactorsLocal = info_->getMassFactors();
68 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
68 >    PairList excludes = info_->getExcludedInteractions();
69 >    PairList oneTwo = info_->getOneTwoInteractions();
70 >    PairList oneThree = info_->getOneThreeInteractions();
71 >    PairList oneFour = info_->getOneFourInteractions();
72  
73   #ifdef IS_MPI
74  
# Line 71 | Line 76 | namespace OpenMD {
76      AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
77      AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
78      AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
79 +    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
80  
81      AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
82      AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
83      AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
84      AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
85 +    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
86  
87      cgCommIntRow = new Communicator<Row,int>(nGroups_);
88      cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
# Line 96 | Line 103 | namespace OpenMD {
103      cgRowData.setStorageLayout(DataStorage::dslPosition);
104      cgColData.resize(nGroupsInCol_);
105      cgColData.setStorageLayout(DataStorage::dslPosition);
106 <    
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 <    
106 >        
107      identsRow.reserve(nAtomsInRow_);
108      identsCol.reserve(nAtomsInCol_);
109      
# Line 139 | Line 141 | namespace OpenMD {
141        }      
142      }
143  
144 +    skipsForRowAtom.clear();
145 +    skipsForRowAtom.reserve(nAtomsInRow_);
146 +    for (int i = 0; i < nAtomsInRow_; i++) {
147 +      int iglob = AtomRowToGlobal[i];
148 +      for (int j = 0; j < nAtomsInCol_; j++) {
149 +        int jglob = AtomColToGlobal[j];        
150 +        if (excludes.hasPair(iglob, jglob))
151 +          skipsForRowAtom[i].push_back(j);      
152 +      }      
153 +    }
154 +
155 +    toposForRowAtom.clear();
156 +    toposForRowAtom.reserve(nAtomsInRow_);
157 +    for (int i = 0; i < nAtomsInRow_; i++) {
158 +      int iglob = AtomRowToGlobal[i];
159 +      int nTopos = 0;
160 +      for (int j = 0; j < nAtomsInCol_; j++) {
161 +        int jglob = AtomColToGlobal[j];        
162 +        if (oneTwo.hasPair(iglob, jglob)) {
163 +          toposForRowAtom[i].push_back(j);
164 +          topoDistRow[i][nTopos] = 1;
165 +          nTopos++;
166 +        }
167 +        if (oneThree.hasPair(iglob, jglob)) {
168 +          toposForRowAtom[i].push_back(j);
169 +          topoDistRow[i][nTopos] = 2;
170 +          nTopos++;
171 +        }
172 +        if (oneFour.hasPair(iglob, jglob)) {
173 +          toposForRowAtom[i].push_back(j);
174 +          topoDistRow[i][nTopos] = 3;
175 +          nTopos++;
176 +        }
177 +      }      
178 +    }
179 +
180   #endif
181  
182      groupList_.clear();
# Line 152 | Line 190 | namespace OpenMD {
190        }      
191      }
192  
193 <  
194 <    // still need:
157 <    // topoDist
158 <    // exclude
193 >    skipsForLocalAtom.clear();
194 >    skipsForLocalAtom.reserve(nLocal_);
195  
196 +    for (int i = 0; i < nLocal_; i++) {
197 +      int iglob = AtomLocalToGlobal[i];
198 +      for (int j = 0; j < nLocal_; j++) {
199 +        int jglob = AtomLocalToGlobal[j];        
200 +        if (excludes.hasPair(iglob, jglob))
201 +          skipsForLocalAtom[i].push_back(j);      
202 +      }      
203 +    }
204 +
205 +    toposForLocalAtom.clear();
206 +    toposForLocalAtom.reserve(nLocal_);
207 +    for (int i = 0; i < nLocal_; i++) {
208 +      int iglob = AtomLocalToGlobal[i];
209 +      int nTopos = 0;
210 +      for (int j = 0; j < nLocal_; j++) {
211 +        int jglob = AtomLocalToGlobal[j];        
212 +        if (oneTwo.hasPair(iglob, jglob)) {
213 +          toposForLocalAtom[i].push_back(j);
214 +          topoDistLocal[i][nTopos] = 1;
215 +          nTopos++;
216 +        }
217 +        if (oneThree.hasPair(iglob, jglob)) {
218 +          toposForLocalAtom[i].push_back(j);
219 +          topoDistLocal[i][nTopos] = 2;
220 +          nTopos++;
221 +        }
222 +        if (oneFour.hasPair(iglob, jglob)) {
223 +          toposForLocalAtom[i].push_back(j);
224 +          topoDistLocal[i][nTopos] = 3;
225 +          nTopos++;
226 +        }
227 +      }      
228 +    }
229    }
230 +  
231 +  void ForceMatrixDecomposition::zeroWorkArrays() {
232 +
233 +    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
234 +      longRangePot_[j] = 0.0;
235 +    }
236 +
237 + #ifdef IS_MPI
238 +    if (storageLayout_ & DataStorage::dslForce) {
239 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
240 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
241 +    }
242 +
243 +    if (storageLayout_ & DataStorage::dslTorque) {
244 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
245 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
246 +    }
247      
248 +    fill(pot_row.begin(), pot_row.end(),
249 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
250  
251 +    fill(pot_col.begin(), pot_col.end(),
252 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
253 +    
254 +    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
255  
256 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
257 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
258 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
259 +    }
260 +
261 +    if (storageLayout_ & DataStorage::dslDensity) {      
262 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
263 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
264 +    }
265 +
266 +    if (storageLayout_ & DataStorage::dslFunctional) {  
267 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
268 +      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
269 +    }
270 +
271 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
272 +      fill(atomRowData.functionalDerivative.begin(),
273 +           atomRowData.functionalDerivative.end(), 0.0);
274 +      fill(atomColData.functionalDerivative.begin(),
275 +           atomColData.functionalDerivative.end(), 0.0);
276 +    }
277 +
278 + #else
279 +    
280 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
281 +      fill(snap_->atomData.particlePot.begin(),
282 +           snap_->atomData.particlePot.end(), 0.0);
283 +    }
284 +    
285 +    if (storageLayout_ & DataStorage::dslDensity) {      
286 +      fill(snap_->atomData.density.begin(),
287 +           snap_->atomData.density.end(), 0.0);
288 +    }
289 +    if (storageLayout_ & DataStorage::dslFunctional) {
290 +      fill(snap_->atomData.functional.begin(),
291 +           snap_->atomData.functional.end(), 0.0);
292 +    }
293 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
294 +      fill(snap_->atomData.functionalDerivative.begin(),
295 +           snap_->atomData.functionalDerivative.end(), 0.0);
296 +    }
297 + #endif
298 +    
299 +  }
300 +
301 +
302    void ForceMatrixDecomposition::distributeData()  {
303      snap_ = sman_->getCurrentSnapshot();
304      storageLayout_ = sman_->getStorageLayout();
# Line 196 | Line 334 | namespace OpenMD {
334   #endif      
335    }
336    
337 +  /* collects information obtained during the pre-pair loop onto local
338 +   * data structures.
339 +   */
340    void ForceMatrixDecomposition::collectIntermediateData() {
341      snap_ = sman_->getCurrentSnapshot();
342      storageLayout_ = sman_->getStorageLayout();
# Line 207 | Line 348 | namespace OpenMD {
348                                 snap_->atomData.density);
349        
350        int n = snap_->atomData.density.size();
351 <      std::vector<RealType> rho_tmp(n, 0.0);
351 >      vector<RealType> rho_tmp(n, 0.0);
352        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
353        for (int i = 0; i < n; i++)
354          snap_->atomData.density[i] += rho_tmp[i];
355      }
356   #endif
357    }
358 <  
358 >
359 >  /*
360 >   * redistributes information obtained during the pre-pair loop out to
361 >   * row and column-indexed data structures
362 >   */
363    void ForceMatrixDecomposition::distributeIntermediateData() {
364      snap_ = sman_->getCurrentSnapshot();
365      storageLayout_ = sman_->getStorageLayout();
# Line 272 | Line 417 | namespace OpenMD {
417      
418      nLocal_ = snap_->getNumberOfAtoms();
419  
420 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
421 <                                       vector<RealType> (nLocal_, 0.0));
420 >    vector<potVec> pot_temp(nLocal_,
421 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422 >
423 >    // scatter/gather pot_row into the members of my column
424 >          
425 >    AtomCommPotRow->scatter(pot_row, pot_temp);
426 >
427 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
428 >      pot_local += pot_temp[ii];
429      
430 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
431 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
432 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
433 <        pot_local[i] += pot_temp[i][ii];
434 <      }
435 <    }
430 >    fill(pot_temp.begin(), pot_temp.end(),
431 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
432 >      
433 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
434 >    
435 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
436 >      pot_local += pot_temp[ii];
437 >    
438   #endif
439    }
440  
441 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
442 + #ifdef IS_MPI
443 +    return nAtomsInRow_;
444 + #else
445 +    return nLocal_;
446 + #endif
447 +  }
448 +
449    /**
450     * returns the list of atoms belonging to this group.  
451     */
# Line 374 | Line 536 | namespace OpenMD {
536      return d;    
537    }
538  
539 +  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
540 + #ifdef IS_MPI
541 +    return skipsForRowAtom[atom1];
542 + #else
543 +    return skipsForLocalAtom[atom1];
544 + #endif
545 +  }
546 +
547 +  /**
548 +   * There are a number of reasons to skip a pair or a
549 +   * particle. Mostly we do this to exclude atoms who are involved in
550 +   * short range interactions (bonds, bends, torsions), but we also
551 +   * need to exclude some overcounted interactions that result from
552 +   * the parallel decomposition.
553 +   */
554 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
555 +    int unique_id_1, unique_id_2;
556 +
557 + #ifdef IS_MPI
558 +    // in MPI, we have to look up the unique IDs for each atom
559 +    unique_id_1 = AtomRowToGlobal[atom1];
560 +    unique_id_2 = AtomColToGlobal[atom2];
561 +
562 +    // this situation should only arise in MPI simulations
563 +    if (unique_id_1 == unique_id_2) return true;
564 +    
565 +    // this prevents us from doing the pair on multiple processors
566 +    if (unique_id_1 < unique_id_2) {
567 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
568 +    } else {
569 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
570 +    }
571 + #else
572 +    // in the normal loop, the atom numbers are unique
573 +    unique_id_1 = atom1;
574 +    unique_id_2 = atom2;
575 + #endif
576 +    
577 + #ifdef IS_MPI
578 +    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579 +         i != skipsForRowAtom[atom1].end(); ++i) {
580 +      if ( (*i) == unique_id_2 ) return true;
581 +    }    
582 + #else
583 +    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
584 +         i != skipsForLocalAtom[atom1].end(); ++i) {
585 +      if ( (*i) == unique_id_2 ) return true;
586 +    }    
587 + #endif
588 +  }
589 +
590 +  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
591 +    
592 + #ifdef IS_MPI
593 +    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
594 +      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
595 +    }
596 + #else
597 +    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
598 +      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
599 +    }
600 + #endif
601 +
602 +    // zero is default for unconnected (i.e. normal) pair interactions
603 +    return 0;
604 +  }
605 +
606    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
607   #ifdef IS_MPI
608      atomRowData.force[atom1] += fg;
# Line 395 | Line 624 | namespace OpenMD {
624      InteractionData idat;
625  
626   #ifdef IS_MPI
627 +    
628 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
629 +                             ff_->getAtomType(identsCol[atom2]) );
630 +
631 +    
632      if (storageLayout_ & DataStorage::dslAmat) {
633        idat.A1 = &(atomRowData.aMat[atom1]);
634        idat.A2 = &(atomColData.aMat[atom2]);
# Line 415 | Line 649 | namespace OpenMD {
649        idat.rho2 = &(atomColData.density[atom2]);
650      }
651  
652 +    if (storageLayout_ & DataStorage::dslFunctional) {
653 +      idat.frho1 = &(atomRowData.functional[atom1]);
654 +      idat.frho2 = &(atomColData.functional[atom2]);
655 +    }
656 +
657      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
658        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
659        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
660      }
661 +
662 +    if (storageLayout_ & DataStorage::dslParticlePot) {
663 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
664 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
665 +    }
666 +
667   #else
668 +
669 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
670 +                             ff_->getAtomType(identsLocal[atom2]) );
671 +
672      if (storageLayout_ & DataStorage::dslAmat) {
673        idat.A1 = &(snap_->atomData.aMat[atom1]);
674        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 440 | Line 689 | namespace OpenMD {
689        idat.rho2 = &(snap_->atomData.density[atom2]);
690      }
691  
692 +    if (storageLayout_ & DataStorage::dslFunctional) {
693 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
694 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
695 +    }
696 +
697      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
698        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
699        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
700      }
701 +
702 +    if (storageLayout_ & DataStorage::dslParticlePot) {
703 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
704 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
705 +    }
706 +
707   #endif
708      return idat;
709    }
710  
711 +  
712 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
713 + #ifdef IS_MPI
714 +    pot_row[atom1] += 0.5 *  *(idat.pot);
715 +    pot_col[atom2] += 0.5 *  *(idat.pot);
716 +
717 +    atomRowData.force[atom1] += *(idat.f1);
718 +    atomColData.force[atom2] -= *(idat.f1);
719 + #else
720 +    longRangePot_ += *(idat.pot);
721 +    
722 +    snap_->atomData.force[atom1] += *(idat.f1);
723 +    snap_->atomData.force[atom2] -= *(idat.f1);
724 + #endif
725 +
726 +  }
727 +
728 +
729    InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
730  
731      InteractionData idat;
732   #ifdef IS_MPI
733 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
734 +                             ff_->getAtomType(identsCol[atom2]) );
735 +
736      if (storageLayout_ & DataStorage::dslElectroFrame) {
737        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
738        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 460 | Line 741 | namespace OpenMD {
741        idat.t1 = &(atomRowData.torque[atom1]);
742        idat.t2 = &(atomColData.torque[atom2]);
743      }
463 –    if (storageLayout_ & DataStorage::dslForce) {
464 –      idat.t1 = &(atomRowData.force[atom1]);
465 –      idat.t2 = &(atomColData.force[atom2]);
466 –    }
744   #else
745 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
746 +                             ff_->getAtomType(identsLocal[atom2]) );
747 +
748      if (storageLayout_ & DataStorage::dslElectroFrame) {
749        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
750        idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
# Line 473 | Line 753 | namespace OpenMD {
753        idat.t1 = &(snap_->atomData.torque[atom1]);
754        idat.t2 = &(snap_->atomData.torque[atom2]);
755      }
756 <    if (storageLayout_ & DataStorage::dslForce) {
477 <      idat.t1 = &(snap_->atomData.force[atom1]);
478 <      idat.t2 = &(snap_->atomData.force[atom2]);
479 <    }
480 < #endif
481 <    
756 > #endif    
757    }
758  
484 –
485 –
486 –
759    /*
760     * buildNeighborList
761     *
# Line 582 | Line 854 | namespace OpenMD {
854      }
855   #endif
856  
585 –
586 –
857      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
858        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
859          for (int m1x = 0; m1x < nCells_.x(); m1x++) {

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