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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 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC

# Line 55 | 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();
# Line 68 | Line 69 | namespace OpenMD {
69      PairList oneTwo = info_->getOneTwoInteractions();
70      PairList oneThree = info_->getOneThreeInteractions();
71      PairList oneFour = info_->getOneFourInteractions();
71 –    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
72  
73   #ifdef IS_MPI
74  
# Line 76 | 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 101 | Line 103 | namespace OpenMD {
103      cgRowData.setStorageLayout(DataStorage::dslPosition);
104      cgColData.resize(nGroupsInCol_);
105      cgColData.setStorageLayout(DataStorage::dslPosition);
106 <    
105 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
106 <                                      vector<RealType> (nAtomsInRow_, 0.0));
107 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
108 <                                      vector<RealType> (nAtomsInCol_, 0.0));
109 <    
106 >        
107      identsRow.reserve(nAtomsInRow_);
108      identsCol.reserve(nAtomsInCol_);
109      
# Line 147 | Line 144 | namespace OpenMD {
144      skipsForRowAtom.clear();
145      skipsForRowAtom.reserve(nAtomsInRow_);
146      for (int i = 0; i < nAtomsInRow_; i++) {
147 <      int iglob = AtomColToGlobal[i];
147 >      int iglob = AtomRowToGlobal[i];
148        for (int j = 0; j < nAtomsInCol_; j++) {
149 <        int jglob = AtomRowToGlobal[j];        
149 >        int jglob = AtomColToGlobal[j];        
150          if (excludes.hasPair(iglob, jglob))
151            skipsForRowAtom[i].push_back(j);      
152        }      
# Line 158 | Line 155 | namespace OpenMD {
155      toposForRowAtom.clear();
156      toposForRowAtom.reserve(nAtomsInRow_);
157      for (int i = 0; i < nAtomsInRow_; i++) {
158 <      int iglob = AtomColToGlobal[i];
158 >      int iglob = AtomRowToGlobal[i];
159        int nTopos = 0;
160        for (int j = 0; j < nAtomsInCol_; j++) {
161 <        int jglob = AtomRowToGlobal[j];        
161 >        int jglob = AtomColToGlobal[j];        
162          if (oneTwo.hasPair(iglob, jglob)) {
163            toposForRowAtom[i].push_back(j);
164            topoDistRow[i][nTopos] = 1;
# Line 231 | Line 228 | namespace OpenMD {
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 266 | 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 277 | 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 342 | 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  
# Line 461 | Line 545 | namespace OpenMD {
545    }
546  
547    /**
548 <   * there are a number of reasons to skip a pair or a particle mostly
549 <   * we do this to exclude atoms who are involved in short range
550 <   * interactions (bonds, bends, torsions), but we also need to
551 <   * exclude some overcounted interactions that result from the
552 <   * parallel decomposition.
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;
# Line 540 | 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 560 | 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 586 | 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 606 | Line 741 | namespace OpenMD {
741        idat.t1 = &(atomRowData.torque[atom1]);
742        idat.t2 = &(atomColData.torque[atom2]);
743      }
609 –    if (storageLayout_ & DataStorage::dslForce) {
610 –      idat.t1 = &(atomRowData.force[atom1]);
611 –      idat.t2 = &(atomColData.force[atom2]);
612 –    }
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 619 | Line 753 | namespace OpenMD {
753        idat.t1 = &(snap_->atomData.torque[atom1]);
754        idat.t2 = &(snap_->atomData.torque[atom2]);
755      }
756 <    if (storageLayout_ & DataStorage::dslForce) {
623 <      idat.t1 = &(snap_->atomData.force[atom1]);
624 <      idat.t2 = &(snap_->atomData.force[atom2]);
625 <    }
626 < #endif
627 <    
756 > #endif    
757    }
758  
630 –
631 –
632 –
759    /*
760     * buildNeighborList
761     *
# Line 728 | Line 854 | namespace OpenMD {
854      }
855   #endif
856  
731 –
732 –
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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