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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 1567 by gezelter, Tue May 24 21:24:45 2011 UTC vs.
Revision 1570 by gezelter, Thu May 26 21:56:04 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 57 | Line 58 | namespace OpenMD {
58      nLocal_ = snap_->getNumberOfAtoms();
59      nGroups_ = snap_->getNumberOfCutoffGroups();
60  
61 +    // gather the information for atomtype IDs (atids):
62 +    vector<int> identsLocal = info_->getIdentArray();
63 +    AtomLocalToGlobal = info_->getGlobalAtomIndices();
64 +    cgLocalToGlobal = info_->getGlobalGroupIndices();
65 +    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
66 +    vector<RealType> massFactorsLocal = info_->getMassFactors();
67 +    PairList excludes = info_->getExcludedInteractions();
68 +    PairList oneTwo = info_->getOneTwoInteractions();
69 +    PairList oneThree = info_->getOneThreeInteractions();
70 +    PairList oneFour = info_->getOneFourInteractions();
71 +    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
72 +
73   #ifdef IS_MPI
74  
75      AtomCommIntRow = new Communicator<Row,int>(nLocal_);
# Line 93 | Line 106 | namespace OpenMD {
106                                        vector<RealType> (nAtomsInRow_, 0.0));
107      vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
108                                        vector<RealType> (nAtomsInCol_, 0.0));
96 –
97 –
98 –    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
109      
100 –    // gather the information for atomtype IDs (atids):
101 –    vector<int> identsLocal = info_->getIdentArray();
110      identsRow.reserve(nAtomsInRow_);
111      identsCol.reserve(nAtomsInCol_);
112      
113      AtomCommIntRow->gather(identsLocal, identsRow);
114      AtomCommIntColumn->gather(identsLocal, identsCol);
115      
108 –    AtomLocalToGlobal = info_->getGlobalAtomIndices();
116      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
117      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
118      
112 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
119      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
120      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
121  
122 <    // still need:
123 <    // topoDist
124 <    // exclude
122 >    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
123 >    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
124 >
125 >    groupListRow_.clear();
126 >    groupListRow_.reserve(nGroupsInRow_);
127 >    for (int i = 0; i < nGroupsInRow_; i++) {
128 >      int gid = cgRowToGlobal[i];
129 >      for (int j = 0; j < nAtomsInRow_; j++) {
130 >        int aid = AtomRowToGlobal[j];
131 >        if (globalGroupMembership[aid] == gid)
132 >          groupListRow_[i].push_back(j);
133 >      }      
134 >    }
135 >
136 >    groupListCol_.clear();
137 >    groupListCol_.reserve(nGroupsInCol_);
138 >    for (int i = 0; i < nGroupsInCol_; i++) {
139 >      int gid = cgColToGlobal[i];
140 >      for (int j = 0; j < nAtomsInCol_; j++) {
141 >        int aid = AtomColToGlobal[j];
142 >        if (globalGroupMembership[aid] == gid)
143 >          groupListCol_[i].push_back(j);
144 >      }      
145 >    }
146 >
147 >    skipsForRowAtom.clear();
148 >    skipsForRowAtom.reserve(nAtomsInRow_);
149 >    for (int i = 0; i < nAtomsInRow_; i++) {
150 >      int iglob = AtomColToGlobal[i];
151 >      for (int j = 0; j < nAtomsInCol_; j++) {
152 >        int jglob = AtomRowToGlobal[j];        
153 >        if (excludes.hasPair(iglob, jglob))
154 >          skipsForRowAtom[i].push_back(j);      
155 >      }      
156 >    }
157 >
158 >    toposForRowAtom.clear();
159 >    toposForRowAtom.reserve(nAtomsInRow_);
160 >    for (int i = 0; i < nAtomsInRow_; i++) {
161 >      int iglob = AtomColToGlobal[i];
162 >      int nTopos = 0;
163 >      for (int j = 0; j < nAtomsInCol_; j++) {
164 >        int jglob = AtomRowToGlobal[j];        
165 >        if (oneTwo.hasPair(iglob, jglob)) {
166 >          toposForRowAtom[i].push_back(j);
167 >          topoDistRow[i][nTopos] = 1;
168 >          nTopos++;
169 >        }
170 >        if (oneThree.hasPair(iglob, jglob)) {
171 >          toposForRowAtom[i].push_back(j);
172 >          topoDistRow[i][nTopos] = 2;
173 >          nTopos++;
174 >        }
175 >        if (oneFour.hasPair(iglob, jglob)) {
176 >          toposForRowAtom[i].push_back(j);
177 >          topoDistRow[i][nTopos] = 3;
178 >          nTopos++;
179 >        }
180 >      }      
181 >    }
182 >
183   #endif
184 <  }
185 <    
184 >
185 >    groupList_.clear();
186 >    groupList_.reserve(nGroups_);
187 >    for (int i = 0; i < nGroups_; i++) {
188 >      int gid = cgLocalToGlobal[i];
189 >      for (int j = 0; j < nLocal_; j++) {
190 >        int aid = AtomLocalToGlobal[j];
191 >        if (globalGroupMembership[aid] == gid)
192 >          groupList_[i].push_back(j);
193 >      }      
194 >    }
195 >
196 >    skipsForLocalAtom.clear();
197 >    skipsForLocalAtom.reserve(nLocal_);
198  
199 +    for (int i = 0; i < nLocal_; i++) {
200 +      int iglob = AtomLocalToGlobal[i];
201 +      for (int j = 0; j < nLocal_; j++) {
202 +        int jglob = AtomLocalToGlobal[j];        
203 +        if (excludes.hasPair(iglob, jglob))
204 +          skipsForLocalAtom[i].push_back(j);      
205 +      }      
206 +    }
207  
208 +    toposForLocalAtom.clear();
209 +    toposForLocalAtom.reserve(nLocal_);
210 +    for (int i = 0; i < nLocal_; i++) {
211 +      int iglob = AtomLocalToGlobal[i];
212 +      int nTopos = 0;
213 +      for (int j = 0; j < nLocal_; j++) {
214 +        int jglob = AtomLocalToGlobal[j];        
215 +        if (oneTwo.hasPair(iglob, jglob)) {
216 +          toposForLocalAtom[i].push_back(j);
217 +          topoDistLocal[i][nTopos] = 1;
218 +          nTopos++;
219 +        }
220 +        if (oneThree.hasPair(iglob, jglob)) {
221 +          toposForLocalAtom[i].push_back(j);
222 +          topoDistLocal[i][nTopos] = 2;
223 +          nTopos++;
224 +        }
225 +        if (oneFour.hasPair(iglob, jglob)) {
226 +          toposForLocalAtom[i].push_back(j);
227 +          topoDistLocal[i][nTopos] = 3;
228 +          nTopos++;
229 +        }
230 +      }      
231 +    }
232 +  }
233 +  
234    void ForceMatrixDecomposition::distributeData()  {
235      snap_ = sman_->getCurrentSnapshot();
236      storageLayout_ = sman_->getStorageLayout();
# Line 244 | Line 354 | namespace OpenMD {
354   #endif
355    }
356  
357 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
358 + #ifdef IS_MPI
359 +    return nAtomsInRow_;
360 + #else
361 +    return nLocal_;
362 + #endif
363 +  }
364 +
365 +  /**
366 +   * returns the list of atoms belonging to this group.  
367 +   */
368 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
369 + #ifdef IS_MPI
370 +    return groupListRow_[cg1];
371 + #else
372 +    return groupList_[cg1];
373 + #endif
374 +  }
375 +
376 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
377 + #ifdef IS_MPI
378 +    return groupListCol_[cg2];
379 + #else
380 +    return groupList_[cg2];
381 + #endif
382 +  }
383    
384    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
385      Vector3d d;
# Line 285 | Line 421 | namespace OpenMD {
421      snap_->wrapVector(d);
422      return d;    
423    }
424 +
425 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
426 + #ifdef IS_MPI
427 +    return massFactorsRow[atom1];
428 + #else
429 +    return massFactorsLocal[atom1];
430 + #endif
431 +  }
432 +
433 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
434 + #ifdef IS_MPI
435 +    return massFactorsCol[atom2];
436 + #else
437 +    return massFactorsLocal[atom2];
438 + #endif
439 +
440 +  }
441      
442    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
443      Vector3d d;
# Line 297 | Line 450 | namespace OpenMD {
450  
451      snap_->wrapVector(d);
452      return d;    
453 +  }
454 +
455 +  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
456 + #ifdef IS_MPI
457 +    return skipsForRowAtom[atom1];
458 + #else
459 +    return skipsForLocalAtom[atom1];
460 + #endif
461 +  }
462 +
463 +  /**
464 +   * there are a number of reasons to skip a pair or a particle mostly
465 +   * we do this to exclude atoms who are involved in short range
466 +   * interactions (bonds, bends, torsions), but we also need to
467 +   * exclude some overcounted interactions that result from the
468 +   * parallel decomposition.
469 +   */
470 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
471 +    int unique_id_1, unique_id_2;
472 +
473 + #ifdef IS_MPI
474 +    // in MPI, we have to look up the unique IDs for each atom
475 +    unique_id_1 = AtomRowToGlobal[atom1];
476 +    unique_id_2 = AtomColToGlobal[atom2];
477 +
478 +    // this situation should only arise in MPI simulations
479 +    if (unique_id_1 == unique_id_2) return true;
480 +    
481 +    // this prevents us from doing the pair on multiple processors
482 +    if (unique_id_1 < unique_id_2) {
483 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
484 +    } else {
485 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
486 +    }
487 + #else
488 +    // in the normal loop, the atom numbers are unique
489 +    unique_id_1 = atom1;
490 +    unique_id_2 = atom2;
491 + #endif
492 +    
493 + #ifdef IS_MPI
494 +    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
495 +         i != skipsForRowAtom[atom1].end(); ++i) {
496 +      if ( (*i) == unique_id_2 ) return true;
497 +    }    
498 + #else
499 +    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
500 +         i != skipsForLocalAtom[atom1].end(); ++i) {
501 +      if ( (*i) == unique_id_2 ) return true;
502 +    }    
503 + #endif
504    }
505  
506 +  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
507 +    
508 + #ifdef IS_MPI
509 +    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
510 +      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
511 +    }
512 + #else
513 +    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
514 +      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
515 +    }
516 + #endif
517 +
518 +    // zero is default for unconnected (i.e. normal) pair interactions
519 +    return 0;
520 +  }
521 +
522    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
523   #ifdef IS_MPI
524      atomRowData.force[atom1] += fg;
# Line 344 | Line 564 | namespace OpenMD {
564        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
565        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
566      }
567 +
568   #else
569      if (storageLayout_ & DataStorage::dslAmat) {
570        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 406 | Line 627 | namespace OpenMD {
627      
628    }
629  
409 –  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
410 –    SelfData sdat;
411 –    // Still Missing atype, skippedCharge, potVec pot,
412 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
413 –      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
414 –    }
415 –    
416 –    if (storageLayout_ & DataStorage::dslTorque) {
417 –      sdat.t = &(snap_->atomData.torque[atom1]);
418 –    }
419 –    
420 –    if (storageLayout_ & DataStorage::dslDensity) {
421 –      sdat.rho = &(snap_->atomData.density[atom1]);
422 –    }
423 –    
424 –    if (storageLayout_ & DataStorage::dslFunctional) {
425 –      sdat.frho = &(snap_->atomData.functional[atom1]);
426 –    }
427 –    
428 –    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
429 –      sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
430 –    }
630  
432 –    return sdat;    
433 –  }
631  
632  
436 –
633    /*
634     * buildNeighborList
635     *
# Line 444 | Line 640 | namespace OpenMD {
640        
641      vector<pair<int, int> > neighborList;
642   #ifdef IS_MPI
643 <    CellListRow.clear();
644 <    CellListCol.clear();
643 >    cellListRow_.clear();
644 >    cellListCol_.clear();
645   #else
646 <    CellList.clear();
646 >    cellList_.clear();
647   #endif
648  
649      // dangerous to not do error checking.
454 –    RealType skinThickness_ = info_->getSimParams()->getSkinThickness();
650      RealType rCut_;
651  
652      RealType rList_ = (rCut_ + skinThickness_);
# Line 461 | Line 656 | namespace OpenMD {
656      Vector3d Hx = Hmat.getColumn(0);
657      Vector3d Hy = Hmat.getColumn(1);
658      Vector3d Hz = Hmat.getColumn(2);
464 –    Vector3i nCells;
659  
660 <    nCells.x() = (int) ( Hx.length() )/ rList_;
661 <    nCells.y() = (int) ( Hy.length() )/ rList_;
662 <    nCells.z() = (int) ( Hz.length() )/ rList_;
660 >    nCells_.x() = (int) ( Hx.length() )/ rList_;
661 >    nCells_.y() = (int) ( Hy.length() )/ rList_;
662 >    nCells_.z() = (int) ( Hz.length() )/ rList_;
663  
664      Mat3x3d invHmat = snap_->getInvHmat();
665      Vector3d rs, scaled, dr;
# Line 483 | Line 677 | namespace OpenMD {
677          scaled[j] -= roundMe(scaled[j]);
678      
679        // find xyz-indices of cell that cutoffGroup is in.
680 <      whichCell.x() = nCells.x() * scaled.x();
681 <      whichCell.y() = nCells.y() * scaled.y();
682 <      whichCell.z() = nCells.z() * scaled.z();
680 >      whichCell.x() = nCells_.x() * scaled.x();
681 >      whichCell.y() = nCells_.y() * scaled.y();
682 >      whichCell.z() = nCells_.z() * scaled.z();
683  
684        // find single index of this cell:
685 <      cellIndex = Vlinear(whichCell, nCells);
685 >      cellIndex = Vlinear(whichCell, nCells_);
686        // add this cutoff group to the list of groups in this cell;
687 <      CellListRow[cellIndex].push_back(i);
687 >      cellListRow_[cellIndex].push_back(i);
688      }
689  
690      for (int i = 0; i < nGroupsInCol_; i++) {
# Line 503 | Line 697 | namespace OpenMD {
697          scaled[j] -= roundMe(scaled[j]);
698  
699        // find xyz-indices of cell that cutoffGroup is in.
700 <      whichCell.x() = nCells.x() * scaled.x();
701 <      whichCell.y() = nCells.y() * scaled.y();
702 <      whichCell.z() = nCells.z() * scaled.z();
700 >      whichCell.x() = nCells_.x() * scaled.x();
701 >      whichCell.y() = nCells_.y() * scaled.y();
702 >      whichCell.z() = nCells_.z() * scaled.z();
703  
704        // find single index of this cell:
705 <      cellIndex = Vlinear(whichCell, nCells);
705 >      cellIndex = Vlinear(whichCell, nCells_);
706        // add this cutoff group to the list of groups in this cell;
707 <      CellListCol[cellIndex].push_back(i);
707 >      cellListCol_[cellIndex].push_back(i);
708      }
709   #else
710      for (int i = 0; i < nGroups_; i++) {
# Line 523 | Line 717 | namespace OpenMD {
717          scaled[j] -= roundMe(scaled[j]);
718  
719        // find xyz-indices of cell that cutoffGroup is in.
720 <      whichCell.x() = nCells.x() * scaled.x();
721 <      whichCell.y() = nCells.y() * scaled.y();
722 <      whichCell.z() = nCells.z() * scaled.z();
720 >      whichCell.x() = nCells_.x() * scaled.x();
721 >      whichCell.y() = nCells_.y() * scaled.y();
722 >      whichCell.z() = nCells_.z() * scaled.z();
723  
724        // find single index of this cell:
725 <      cellIndex = Vlinear(whichCell, nCells);
725 >      cellIndex = Vlinear(whichCell, nCells_);
726        // add this cutoff group to the list of groups in this cell;
727 <      CellList[cellIndex].push_back(i);
727 >      cellList_[cellIndex].push_back(i);
728      }
729   #endif
730  
731  
732  
733 <    for (int m1z = 0; m1z < nCells.z(); m1z++) {
734 <      for (int m1y = 0; m1y < nCells.y(); m1y++) {
735 <        for (int m1x = 0; m1x < nCells.x(); m1x++) {
733 >    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
734 >      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
735 >        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
736            Vector3i m1v(m1x, m1y, m1z);
737 <          int m1 = Vlinear(m1v, nCells);
544 <          for (int offset = 0; offset < nOffset_; offset++) {
545 <            Vector3i m2v = m1v + cellOffsets_[offset];
737 >          int m1 = Vlinear(m1v, nCells_);
738  
739 <            if (m2v.x() >= nCells.x()) {
739 >          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
740 >               os != cellOffsets_.end(); ++os) {
741 >            
742 >            Vector3i m2v = m1v + (*os);
743 >            
744 >            if (m2v.x() >= nCells_.x()) {
745                m2v.x() = 0;          
746              } else if (m2v.x() < 0) {
747 <              m2v.x() = nCells.x() - 1;
747 >              m2v.x() = nCells_.x() - 1;
748              }
749 <
750 <            if (m2v.y() >= nCells.y()) {
749 >            
750 >            if (m2v.y() >= nCells_.y()) {
751                m2v.y() = 0;          
752              } else if (m2v.y() < 0) {
753 <              m2v.y() = nCells.y() - 1;
753 >              m2v.y() = nCells_.y() - 1;
754              }
755 <
756 <            if (m2v.z() >= nCells.z()) {
755 >            
756 >            if (m2v.z() >= nCells_.z()) {
757                m2v.z() = 0;          
758              } else if (m2v.z() < 0) {
759 <              m2v.z() = nCells.z() - 1;
759 >              m2v.z() = nCells_.z() - 1;
760              }
761 +            
762 +            int m2 = Vlinear (m2v, nCells_);
763  
565 –            int m2 = Vlinear (m2v, nCells);
566 –
764   #ifdef IS_MPI
765 <            for (vector<int>::iterator j1 = CellListRow[m1].begin();
766 <                 j1 != CellListRow[m1].end(); ++j1) {
767 <              for (vector<int>::iterator j2 = CellListCol[m2].begin();
768 <                   j2 != CellListCol[m2].end(); ++j2) {
765 >            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
766 >                 j1 != cellListRow_[m1].end(); ++j1) {
767 >              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
768 >                   j2 != cellListCol_[m2].end(); ++j2) {
769                                
770                  // Always do this if we're in different cells or if
771                  // we're in the same cell and the global index of the
# Line 584 | Line 781 | namespace OpenMD {
781                }
782              }
783   #else
784 <            for (vector<int>::iterator j1 = CellList[m1].begin();
785 <                 j1 != CellList[m1].end(); ++j1) {
786 <              for (vector<int>::iterator j2 = CellList[m2].begin();
787 <                   j2 != CellList[m2].end(); ++j2) {
784 >            for (vector<int>::iterator j1 = cellList_[m1].begin();
785 >                 j1 != cellList_[m1].end(); ++j1) {
786 >              for (vector<int>::iterator j2 = cellList_[m2].begin();
787 >                   j2 != cellList_[m2].end(); ++j2) {
788                                
789                  // Always do this if we're in different cells or if
790                  // we're in the same cell and the global index of the
# Line 607 | Line 804 | namespace OpenMD {
804          }
805        }
806      }
807 +
808 +    // save the local cutoff group positions for the check that is
809 +    // done on each loop:
810 +    saved_CG_positions_.clear();
811 +    for (int i = 0; i < nGroups_; i++)
812 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
813 +
814      return neighborList;
815    }
816   } //end namespace OpenMD

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