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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 1566 by gezelter, Thu May 12 17:00:14 2011 UTC vs.
Revision 1567 by gezelter, Tue May 24 21:24:45 2011 UTC

# Line 54 | Line 54 | namespace OpenMD {
54    void ForceMatrixDecomposition::distributeInitialData() {
55      snap_ = sman_->getCurrentSnapshot();
56      storageLayout_ = sman_->getStorageLayout();
57 < #ifdef IS_MPI    
58 <    int nLocal = snap_->getNumberOfAtoms();
59 <    int nGroups = snap_->getNumberOfCutoffGroups();
60 <    
61 <    AtomCommIntRow = new Communicator<Row,int>(nLocal);
62 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
63 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
64 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
57 >    nLocal_ = snap_->getNumberOfAtoms();
58 >    nGroups_ = snap_->getNumberOfCutoffGroups();
59  
60 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
61 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
62 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
63 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
60 > #ifdef IS_MPI
61 >
62 >    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
63 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
64 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
65 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
66  
67 <    cgCommIntRow = new Communicator<Row,int>(nGroups);
68 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
69 <    cgCommIntColumn = new Communicator<Column,int>(nGroups);
70 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
67 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
68 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
69 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
70 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
71  
72 <    int nAtomsInRow = AtomCommIntRow->getSize();
73 <    int nAtomsInCol = AtomCommIntColumn->getSize();
74 <    int nGroupsInRow = cgCommIntRow->getSize();
75 <    int nGroupsInCol = cgCommIntColumn->getSize();
72 >    cgCommIntRow = new Communicator<Row,int>(nGroups_);
73 >    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
74 >    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
75 >    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
76  
77 +    nAtomsInRow_ = AtomCommIntRow->getSize();
78 +    nAtomsInCol_ = AtomCommIntColumn->getSize();
79 +    nGroupsInRow_ = cgCommIntRow->getSize();
80 +    nGroupsInCol_ = cgCommIntColumn->getSize();
81 +
82      // Modify the data storage objects with the correct layouts and sizes:
83 <    atomRowData.resize(nAtomsInRow);
83 >    atomRowData.resize(nAtomsInRow_);
84      atomRowData.setStorageLayout(storageLayout_);
85 <    atomColData.resize(nAtomsInCol);
85 >    atomColData.resize(nAtomsInCol_);
86      atomColData.setStorageLayout(storageLayout_);
87 <    cgRowData.resize(nGroupsInRow);
87 >    cgRowData.resize(nGroupsInRow_);
88      cgRowData.setStorageLayout(DataStorage::dslPosition);
89 <    cgColData.resize(nGroupsInCol);
89 >    cgColData.resize(nGroupsInCol_);
90      cgColData.setStorageLayout(DataStorage::dslPosition);
91      
92      vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
93 <                                      vector<RealType> (nAtomsInRow, 0.0));
93 >                                      vector<RealType> (nAtomsInRow_, 0.0));
94      vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
95 <                                      vector<RealType> (nAtomsInCol, 0.0));
95 >                                      vector<RealType> (nAtomsInCol_, 0.0));
96  
97  
98      vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
99      
100      // gather the information for atomtype IDs (atids):
101      vector<int> identsLocal = info_->getIdentArray();
102 <    identsRow.reserve(nAtomsInRow);
103 <    identsCol.reserve(nAtomsInCol);
102 >    identsRow.reserve(nAtomsInRow_);
103 >    identsCol.reserve(nAtomsInCol_);
104      
105      AtomCommIntRow->gather(identsLocal, identsRow);
106      AtomCommIntColumn->gather(identsLocal, identsCol);
# Line 229 | Line 230 | namespace OpenMD {
230          snap_->atomData.torque[i] += trq_tmp[i];
231      }
232      
233 <    int nLocal = snap_->getNumberOfAtoms();
233 >    nLocal_ = snap_->getNumberOfAtoms();
234  
235      vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
236 <                                       vector<RealType> (nLocal, 0.0));
236 >                                       vector<RealType> (nLocal_, 0.0));
237      
238      for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
239        AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
# Line 312 | Line 313 | namespace OpenMD {
313   #else
314      snap_->atomData.force[atom2] += fg;
315   #endif
315 –
316    }
317  
318      // filling interaction blocks with pointers
319    InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
320 –
320      InteractionData idat;
321 +
322   #ifdef IS_MPI
323      if (storageLayout_ & DataStorage::dslAmat) {
324        idat.A1 = &(atomRowData.aMat[atom1]);
325        idat.A2 = &(atomColData.aMat[atom2]);
326      }
327 <
327 >    
328      if (storageLayout_ & DataStorage::dslElectroFrame) {
329        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
330        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 370 | Line 370 | namespace OpenMD {
370        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
371      }
372   #endif
373 <    
373 >    return idat;
374    }
375 +
376    InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
377 +
378      InteractionData idat;
377 –    skippedCharge1
378 –      skippedCharge2
379 –      rij
380 –      d
381 –    electroMult
382 –    sw
383 –    f
379   #ifdef IS_MPI
385 –
380      if (storageLayout_ & DataStorage::dslElectroFrame) {
381        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
382        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 391 | Line 385 | namespace OpenMD {
385        idat.t1 = &(atomRowData.torque[atom1]);
386        idat.t2 = &(atomColData.torque[atom2]);
387      }
388 <
388 >    if (storageLayout_ & DataStorage::dslForce) {
389 >      idat.t1 = &(atomRowData.force[atom1]);
390 >      idat.t2 = &(atomColData.force[atom2]);
391 >    }
392 > #else
393 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
394 >      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
395 >      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
396 >    }
397 >    if (storageLayout_ & DataStorage::dslTorque) {
398 >      idat.t1 = &(snap_->atomData.torque[atom1]);
399 >      idat.t2 = &(snap_->atomData.torque[atom2]);
400 >    }
401 >    if (storageLayout_ & DataStorage::dslForce) {
402 >      idat.t1 = &(snap_->atomData.force[atom1]);
403 >      idat.t2 = &(snap_->atomData.force[atom2]);
404 >    }
405 > #endif
406      
407    }
408 +
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 +    }
431 +
432 +    return sdat;    
433    }
434  
435  
436 +
437    /*
438     * buildNeighborList
439     *
440     * first element of pair is row-indexed CutoffGroup
441     * second element of pair is column-indexed CutoffGroup
442     */
443 <  vector<pair<int, int> >  buildNeighborList() {
444 <    Vector3d dr, invWid, rs, shift;
445 <    Vector3i cc, m1v, m2s;
446 <    RealType rrNebr;
447 <    int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
443 >  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
444 >      
445 >    vector<pair<int, int> > neighborList;
446 > #ifdef IS_MPI
447 >    CellListRow.clear();
448 >    CellListCol.clear();
449 > #else
450 >    CellList.clear();
451 > #endif
452  
453 <
454 <    vector<pair<int, int> > neighborList;  
455 <    Vector3i nCells;
456 <    Vector3d invWid, r;
457 <
458 <    rList_ = (rCut_ + skinThickness_);
459 <    rl2 = rList_ * rList_;
420 <
421 <    snap_ = sman_->getCurrentSnapshot();
453 >    // dangerous to not do error checking.
454 >    RealType skinThickness_ = info_->getSimParams()->getSkinThickness();
455 >    RealType rCut_;
456 >
457 >    RealType rList_ = (rCut_ + skinThickness_);
458 >    RealType rl2 = rList_ * rList_;
459 >    Snapshot* snap_ = sman_->getCurrentSnapshot();
460      Mat3x3d Hmat = snap_->getHmat();
461      Vector3d Hx = Hmat.getColumn(0);
462      Vector3d Hy = Hmat.getColumn(1);
463      Vector3d Hz = Hmat.getColumn(2);
464 +    Vector3i nCells;
465  
466      nCells.x() = (int) ( Hx.length() )/ rList_;
467      nCells.y() = (int) ( Hy.length() )/ rList_;
468      nCells.z() = (int) ( Hz.length() )/ rList_;
469  
470 <    for (i = 0; i < nGroupsInRow; i++) {
470 >    Mat3x3d invHmat = snap_->getInvHmat();
471 >    Vector3d rs, scaled, dr;
472 >    Vector3i whichCell;
473 >    int cellIndex;
474 >
475 > #ifdef IS_MPI
476 >    for (int i = 0; i < nGroupsInRow_; i++) {
477        rs = cgRowData.position[i];
478 <      snap_->scaleVector(rs);    
479 <    }
480 <    
478 >      // scaled positions relative to the box vectors
479 >      scaled = invHmat * rs;
480 >      // wrap the vector back into the unit box by subtracting integer box
481 >      // numbers
482 >      for (int j = 0; j < 3; j++)
483 >        scaled[j] -= roundMe(scaled[j]);
484 >    
485 >      // find xyz-indices of cell that cutoffGroup is in.
486 >      whichCell.x() = nCells.x() * scaled.x();
487 >      whichCell.y() = nCells.y() * scaled.y();
488 >      whichCell.z() = nCells.z() * scaled.z();
489  
490 <    VDiv (invWid, cells, region);
491 <    for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
492 <    for (n = 0; n < nMol; n ++) {
493 <      VSAdd (rs, mol[n].r, 0.5, region);
441 <      VMul (cc, rs, invWid);
442 <      c = VLinear (cc, cells) + nMol;
443 <      cellList[n] = cellList[c];
444 <      cellList[c] = n;
490 >      // find single index of this cell:
491 >      cellIndex = Vlinear(whichCell, nCells);
492 >      // add this cutoff group to the list of groups in this cell;
493 >      CellListRow[cellIndex].push_back(i);
494      }
495 <    nebrTabLen = 0;
496 <    for (m1z = 0; m1z < cells.z(); m1z++) {
497 <      for (m1y = 0; m1y < cells.y(); m1y++) {
498 <        for (m1x = 0; m1x < cells.x(); m1x++) {
495 >
496 >    for (int i = 0; i < nGroupsInCol_; i++) {
497 >      rs = cgColData.position[i];
498 >      // scaled positions relative to the box vectors
499 >      scaled = invHmat * rs;
500 >      // wrap the vector back into the unit box by subtracting integer box
501 >      // numbers
502 >      for (int j = 0; j < 3; j++)
503 >        scaled[j] -= roundMe(scaled[j]);
504 >
505 >      // find xyz-indices of cell that cutoffGroup is in.
506 >      whichCell.x() = nCells.x() * scaled.x();
507 >      whichCell.y() = nCells.y() * scaled.y();
508 >      whichCell.z() = nCells.z() * scaled.z();
509 >
510 >      // find single index of this cell:
511 >      cellIndex = Vlinear(whichCell, nCells);
512 >      // add this cutoff group to the list of groups in this cell;
513 >      CellListCol[cellIndex].push_back(i);
514 >    }
515 > #else
516 >    for (int i = 0; i < nGroups_; i++) {
517 >      rs = snap_->cgData.position[i];
518 >      // scaled positions relative to the box vectors
519 >      scaled = invHmat * rs;
520 >      // wrap the vector back into the unit box by subtracting integer box
521 >      // numbers
522 >      for (int j = 0; j < 3; j++)
523 >        scaled[j] -= roundMe(scaled[j]);
524 >
525 >      // find xyz-indices of cell that cutoffGroup is in.
526 >      whichCell.x() = nCells.x() * scaled.x();
527 >      whichCell.y() = nCells.y() * scaled.y();
528 >      whichCell.z() = nCells.z() * scaled.z();
529 >
530 >      // find single index of this cell:
531 >      cellIndex = Vlinear(whichCell, nCells);
532 >      // add this cutoff group to the list of groups in this cell;
533 >      CellList[cellIndex].push_back(i);
534 >    }
535 > #endif
536 >
537 >
538 >
539 >    for (int m1z = 0; m1z < nCells.z(); m1z++) {
540 >      for (int m1y = 0; m1y < nCells.y(); m1y++) {
541 >        for (int m1x = 0; m1x < nCells.x(); m1x++) {
542            Vector3i m1v(m1x, m1y, m1z);
543 <          m1 = VLinear(m1v, cells) + nMol;
544 <          for (offset = 0; offset < nOffset_; offset++) {
545 <            m2v = m1v + cellOffsets_[offset];
454 <            shift = V3Zero();
543 >          int m1 = Vlinear(m1v, nCells);
544 >          for (int offset = 0; offset < nOffset_; offset++) {
545 >            Vector3i m2v = m1v + cellOffsets_[offset];
546  
547 <            if (m2v.x() >= cells.x) {
547 >            if (m2v.x() >= nCells.x()) {
548                m2v.x() = 0;          
458 –              shift.x() = region.x();  
549              } else if (m2v.x() < 0) {
550 <              m2v.x() = cells.x() - 1;
461 <              shift.x() = - region.x();
550 >              m2v.x() = nCells.x() - 1;
551              }
552  
553 <            if (m2v.y() >= cells.y()) {
553 >            if (m2v.y() >= nCells.y()) {
554                m2v.y() = 0;          
466 –              shift.y() = region.y();  
555              } else if (m2v.y() < 0) {
556 <              m2v.y() = cells.y() - 1;
469 <              shift.y() = - region.y();
556 >              m2v.y() = nCells.y() - 1;
557              }
558  
559 <            m2 = VLinear (m2v, cells) + nMol;
560 <            for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
561 <              for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
562 <                if (m1 != m2 || j2 < j1) {
563 <                  dr = mol[j1].r - mol[j2].r;
564 <                  VSub (dr, mol[j1].r, mol[j2].r);
565 <                  VVSub (dr, shift);
566 <                  if (VLenSq (dr) < rrNebr) {
567 <                    neighborList.push_back(make_pair(j1, j2));
559 >            if (m2v.z() >= nCells.z()) {
560 >              m2v.z() = 0;          
561 >            } else if (m2v.z() < 0) {
562 >              m2v.z() = nCells.z() - 1;
563 >            }
564 >
565 >            int m2 = Vlinear (m2v, nCells);
566 >
567 > #ifdef IS_MPI
568 >            for (vector<int>::iterator j1 = CellListRow[m1].begin();
569 >                 j1 != CellListRow[m1].end(); ++j1) {
570 >              for (vector<int>::iterator j2 = CellListCol[m2].begin();
571 >                   j2 != CellListCol[m2].end(); ++j2) {
572 >                              
573 >                // Always do this if we're in different cells or if
574 >                // we're in the same cell and the global index of the
575 >                // j2 cutoff group is less than the j1 cutoff group
576 >
577 >                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
578 >                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
579 >                  snap_->wrapVector(dr);
580 >                  if (dr.lengthSquare() < rl2) {
581 >                    neighborList.push_back(make_pair((*j1), (*j2)));
582                    }
583                  }
584                }
585              }
586 + #else
587 +            for (vector<int>::iterator j1 = CellList[m1].begin();
588 +                 j1 != CellList[m1].end(); ++j1) {
589 +              for (vector<int>::iterator j2 = CellList[m2].begin();
590 +                   j2 != CellList[m2].end(); ++j2) {
591 +                              
592 +                // Always do this if we're in different cells or if
593 +                // we're in the same cell and the global index of the
594 +                // j2 cutoff group is less than the j1 cutoff group
595 +
596 +                if (m2 != m1 || (*j2) < (*j1)) {
597 +                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
598 +                  snap_->wrapVector(dr);
599 +                  if (dr.lengthSquare() < rl2) {
600 +                    neighborList.push_back(make_pair((*j1), (*j2)));
601 +                  }
602 +                }
603 +              }
604 +            }
605 + #endif
606            }
607          }
608        }
609      }
610 +    return neighborList;
611    }
490 –
491 –  
612   } //end namespace OpenMD

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