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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1893 by gezelter, Wed Jun 19 17:19:07 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 310 | Line 310 | namespace OpenMD {
310      
311      RealType tol = 1e-6;
312      largestRcut_ = 0.0;
313 –    RealType rc;
313      int atid;
314      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315      
# Line 395 | Line 394 | namespace OpenMD {
394        }
395        
396        bool gTypeFound = false;
397 <      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
397 >      for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
398          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
399            groupToGtype[cg1] = gt;
400            gTypeFound = true;
# Line 420 | Line 419 | namespace OpenMD {
419      
420      RealType tradRcut = groupMax;
421  
422 <    for (int i = 0; i < gTypeCutoffs.size();  i++) {
423 <      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
422 >    for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
423 >      for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {      
424          RealType thisRcut;
425          switch(cutoffPolicy_) {
426          case TRADITIONAL:
# Line 477 | Line 476 | namespace OpenMD {
476    }
477  
478    int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
479 <    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
479 >    for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
480        if (toposForAtom[atom1][j] == atom2)
481          return topoDist[atom1][j];
482 <    }
482 >    }                                          
483      return 0;
484    }
485  
# Line 488 | Line 487 | namespace OpenMD {
487      pairwisePot = 0.0;
488      embeddingPot = 0.0;
489      excludedPot = 0.0;
490 +    excludedSelfPot = 0.0;
491  
492   #ifdef IS_MPI
493      if (storageLayout_ & DataStorage::dslForce) {
# Line 559 | Line 559 | namespace OpenMD {
559             atomColData.electricField.end(), V3Zero);
560      }
561  
562 –    if (storageLayout_ & DataStorage::dslFlucQForce) {    
563 –      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
564 –           0.0);
565 –      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
566 –           0.0);
567 –    }
568 –
562   #endif
563      // even in parallel, we need to zero out the local arrays:
564  
# Line 639 | Line 632 | namespace OpenMD {
632        AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633                                     atomColData.aMat);
634      }
635 <    
636 <    // if needed, gather the atomic eletrostatic frames
637 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
638 <      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
639 <                                atomRowData.electroFrame);
640 <      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
641 <                                   atomColData.electroFrame);
635 >
636 >    // if needed, gather the atomic eletrostatic information
637 >    if (storageLayout_ & DataStorage::dslDipole) {
638 >      AtomPlanVectorRow->gather(snap_->atomData.dipole,
639 >                                atomRowData.dipole);
640 >      AtomPlanVectorColumn->gather(snap_->atomData.dipole,
641 >                                   atomColData.dipole);
642      }
643  
644 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
645 +      AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
646 +                                atomRowData.quadrupole);
647 +      AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
648 +                                   atomColData.quadrupole);
649 +    }
650 +        
651      // if needed, gather the atomic fluctuating charge values
652      if (storageLayout_ & DataStorage::dslFlucQPosition) {
653        AtomPlanRealRow->gather(snap_->atomData.flucQPos,
# Line 679 | Line 679 | namespace OpenMD {
679          snap_->atomData.density[i] += rho_tmp[i];
680      }
681  
682 +    // this isn't necessary if we don't have polarizable atoms, but
683 +    // we'll leave it here for now.
684      if (storageLayout_ & DataStorage::dslElectricField) {
685        
686        AtomPlanVectorRow->scatter(atomRowData.electricField,
# Line 686 | Line 688 | namespace OpenMD {
688        
689        int n = snap_->atomData.electricField.size();
690        vector<Vector3d> field_tmp(n, V3Zero);
691 <      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
691 >      AtomPlanVectorColumn->scatter(atomColData.electricField,
692 >                                    field_tmp);
693        for (int i = 0; i < n; i++)
694          snap_->atomData.electricField[i] += field_tmp[i];
695      }
# Line 784 | Line 787 | namespace OpenMD {
787        for (int i = 0; i < nq; i++)
788          snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
789              
790 +    }
791 +
792 +    if (storageLayout_ & DataStorage::dslElectricField) {
793 +
794 +      int nef = snap_->atomData.electricField.size();
795 +      vector<Vector3d> efield_tmp(nef, V3Zero);
796 +
797 +      AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
798 +      for (int i = 0; i < nef; i++) {
799 +        snap_->atomData.electricField[i] += efield_tmp[i];
800 +        efield_tmp[i] = 0.0;
801 +      }
802 +      
803 +      AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
804 +      for (int i = 0; i < nef; i++)
805 +        snap_->atomData.electricField[i] += efield_tmp[i];
806      }
807  
808 +
809      nLocal_ = snap_->getNumberOfAtoms();
810  
811      vector<potVec> pot_temp(nLocal_,
# Line 907 | Line 927 | namespace OpenMD {
927        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
928        embeddingPot[ii] = ploc2;
929      }    
930 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
931 +      RealType ploc1 = excludedSelfPot[ii];
932 +      RealType ploc2 = 0.0;
933 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
934 +      excludedSelfPot[ii] = ploc2;
935 +    }    
936   #endif
937      
938    }
939  
940  
941  
942 <  int ForceMatrixDecomposition::getNAtomsInRow() {  
942 >  int& ForceMatrixDecomposition::getNAtomsInRow() {  
943   #ifdef IS_MPI
944      return nAtomsInRow_;
945   #else
# Line 924 | Line 950 | namespace OpenMD {
950    /**
951     * returns the list of atoms belonging to this group.  
952     */
953 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
953 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
954   #ifdef IS_MPI
955      return groupListRow_[cg1];
956   #else
# Line 932 | Line 958 | namespace OpenMD {
958   #endif
959    }
960  
961 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
961 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
962   #ifdef IS_MPI
963      return groupListCol_[cg2];
964   #else
# Line 949 | Line 975 | namespace OpenMD {
975      d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
976   #endif
977      
978 <    snap_->wrapVector(d);
978 >    if (usePeriodicBoundaryConditions_) {
979 >      snap_->wrapVector(d);
980 >    }
981      return d;    
982    }
983  
984 <  Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
984 >  Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
985   #ifdef IS_MPI
986      return cgColData.velocity[cg2];
987   #else
# Line 961 | Line 989 | namespace OpenMD {
989   #endif
990    }
991  
992 <  Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
992 >  Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
993   #ifdef IS_MPI
994      return atomColData.velocity[atom2];
995   #else
# Line 979 | Line 1007 | namespace OpenMD {
1007   #else
1008      d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1009   #endif
1010 <
1011 <    snap_->wrapVector(d);
1010 >    if (usePeriodicBoundaryConditions_) {
1011 >      snap_->wrapVector(d);
1012 >    }
1013      return d;    
1014    }
1015    
# Line 992 | Line 1021 | namespace OpenMD {
1021   #else
1022      d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1023   #endif
1024 <    
1025 <    snap_->wrapVector(d);
1024 >    if (usePeriodicBoundaryConditions_) {
1025 >      snap_->wrapVector(d);
1026 >    }
1027      return d;    
1028    }
1029  
1030 <  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1030 >  RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1031   #ifdef IS_MPI
1032      return massFactorsRow[atom1];
1033   #else
# Line 1005 | Line 1035 | namespace OpenMD {
1035   #endif
1036    }
1037  
1038 <  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1038 >  RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1039   #ifdef IS_MPI
1040      return massFactorsCol[atom2];
1041   #else
# Line 1022 | Line 1052 | namespace OpenMD {
1052   #else
1053      d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1054   #endif
1055 <
1056 <    snap_->wrapVector(d);
1055 >    if (usePeriodicBoundaryConditions_) {
1056 >      snap_->wrapVector(d);
1057 >    }
1058      return d;    
1059    }
1060  
1061 <  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1061 >  vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1062      return excludesForAtom[atom1];
1063    }
1064  
# Line 1036 | Line 1067 | namespace OpenMD {
1067     * the parallel decomposition.
1068     */
1069    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1070 <    int unique_id_1, unique_id_2, group1, group2;
1070 >    int unique_id_1, unique_id_2;
1071          
1072   #ifdef IS_MPI
1073      // in MPI, we have to look up the unique IDs for each atom
1074      unique_id_1 = AtomRowToGlobal[atom1];
1075      unique_id_2 = AtomColToGlobal[atom2];
1076 <    group1 = cgRowToGlobal[cg1];
1077 <    group2 = cgColToGlobal[cg2];
1076 >    // group1 = cgRowToGlobal[cg1];
1077 >    // group2 = cgColToGlobal[cg2];
1078   #else
1079      unique_id_1 = AtomLocalToGlobal[atom1];
1080      unique_id_2 = AtomLocalToGlobal[atom2];
1081 <    group1 = cgLocalToGlobal[cg1];
1082 <    group2 = cgLocalToGlobal[cg2];
1081 >    int group1 = cgLocalToGlobal[cg1];
1082 >    int group2 = cgLocalToGlobal[cg2];
1083   #endif  
1084  
1085      if (unique_id_1 == unique_id_2) return true;
# Line 1126 | Line 1157 | namespace OpenMD {
1157        idat.A2 = &(atomColData.aMat[atom2]);
1158      }
1159      
1129 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1130 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1131 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1132 –    }
1133 –
1160      if (storageLayout_ & DataStorage::dslTorque) {
1161        idat.t1 = &(atomRowData.torque[atom1]);
1162        idat.t2 = &(atomColData.torque[atom2]);
1163      }
1164  
1165 +    if (storageLayout_ & DataStorage::dslDipole) {
1166 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1167 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1168 +    }
1169 +
1170 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1171 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1172 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1173 +    }
1174 +
1175      if (storageLayout_ & DataStorage::dslDensity) {
1176        idat.rho1 = &(atomRowData.density[atom1]);
1177        idat.rho2 = &(atomColData.density[atom2]);
# Line 1175 | Line 1211 | namespace OpenMD {
1211        idat.A2 = &(snap_->atomData.aMat[atom2]);
1212      }
1213  
1178 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1179 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1180 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1181 –    }
1182 –
1214      if (storageLayout_ & DataStorage::dslTorque) {
1215        idat.t1 = &(snap_->atomData.torque[atom1]);
1216        idat.t2 = &(snap_->atomData.torque[atom2]);
1217      }
1218  
1219 +    if (storageLayout_ & DataStorage::dslDipole) {
1220 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1221 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1222 +    }
1223 +
1224 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1225 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1226 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1227 +    }
1228 +
1229      if (storageLayout_ & DataStorage::dslDensity) {    
1230        idat.rho1 = &(snap_->atomData.density[atom1]);
1231        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1281 | Line 1322 | namespace OpenMD {
1322      groupCutoffs cuts;
1323      bool doAllPairs = false;
1324  
1325 +    RealType rList_ = (largestRcut_ + skinThickness_);
1326 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1327 +    Mat3x3d box;
1328 +    Mat3x3d invBox;
1329 +
1330 +    Vector3d rs, scaled, dr;
1331 +    Vector3i whichCell;
1332 +    int cellIndex;
1333 +
1334   #ifdef IS_MPI
1335      cellListRow_.clear();
1336      cellListCol_.clear();
1337   #else
1338      cellList_.clear();
1339   #endif
1340 <
1341 <    RealType rList_ = (largestRcut_ + skinThickness_);
1342 <    RealType rl2 = rList_ * rList_;
1343 <    Snapshot* snap_ = sman_->getCurrentSnapshot();
1344 <    Mat3x3d Hmat = snap_->getHmat();
1345 <    Vector3d Hx = Hmat.getColumn(0);
1346 <    Vector3d Hy = Hmat.getColumn(1);
1347 <    Vector3d Hz = Hmat.getColumn(2);
1348 <
1349 <    nCells_.x() = (int) ( Hx.length() )/ rList_;
1350 <    nCells_.y() = (int) ( Hy.length() )/ rList_;
1351 <    nCells_.z() = (int) ( Hz.length() )/ rList_;
1352 <
1340 >    
1341 >    if (!usePeriodicBoundaryConditions_) {
1342 >      box = snap_->getBoundingBox();
1343 >      invBox = snap_->getInvBoundingBox();
1344 >    } else {
1345 >      box = snap_->getHmat();
1346 >      invBox = snap_->getInvHmat();
1347 >    }
1348 >    
1349 >    Vector3d boxX = box.getColumn(0);
1350 >    Vector3d boxY = box.getColumn(1);
1351 >    Vector3d boxZ = box.getColumn(2);
1352 >    
1353 >    nCells_.x() = (int) ( boxX.length() )/ rList_;
1354 >    nCells_.y() = (int) ( boxY.length() )/ rList_;
1355 >    nCells_.z() = (int) ( boxZ.length() )/ rList_;
1356 >    
1357      // handle small boxes where the cell offsets can end up repeating cells
1358      
1359      if (nCells_.x() < 3) doAllPairs = true;
1360      if (nCells_.y() < 3) doAllPairs = true;
1361      if (nCells_.z() < 3) doAllPairs = true;
1362 <
1309 <    Mat3x3d invHmat = snap_->getInvHmat();
1310 <    Vector3d rs, scaled, dr;
1311 <    Vector3i whichCell;
1312 <    int cellIndex;
1362 >    
1363      int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1364 <
1364 >    
1365   #ifdef IS_MPI
1366      cellListRow_.resize(nCtot);
1367      cellListCol_.resize(nCtot);
1368   #else
1369      cellList_.resize(nCtot);
1370   #endif
1371 <
1371 >    
1372      if (!doAllPairs) {
1373   #ifdef IS_MPI
1374 <
1374 >      
1375        for (int i = 0; i < nGroupsInRow_; i++) {
1376          rs = cgRowData.position[i];
1377          
1378          // scaled positions relative to the box vectors
1379 <        scaled = invHmat * rs;
1379 >        scaled = invBox * rs;
1380          
1381          // wrap the vector back into the unit box by subtracting integer box
1382          // numbers
1383          for (int j = 0; j < 3; j++) {
1384            scaled[j] -= roundMe(scaled[j]);
1385            scaled[j] += 0.5;
1386 +          // Handle the special case when an object is exactly on the
1387 +          // boundary (a scaled coordinate of 1.0 is the same as
1388 +          // scaled coordinate of 0.0)
1389 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1390          }
1391          
1392          // find xyz-indices of cell that cutoffGroup is in.
# Line 1350 | Line 1404 | namespace OpenMD {
1404          rs = cgColData.position[i];
1405          
1406          // scaled positions relative to the box vectors
1407 <        scaled = invHmat * rs;
1407 >        scaled = invBox * rs;
1408          
1409          // wrap the vector back into the unit box by subtracting integer box
1410          // numbers
1411          for (int j = 0; j < 3; j++) {
1412            scaled[j] -= roundMe(scaled[j]);
1413            scaled[j] += 0.5;
1414 +          // Handle the special case when an object is exactly on the
1415 +          // boundary (a scaled coordinate of 1.0 is the same as
1416 +          // scaled coordinate of 0.0)
1417 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1418          }
1419          
1420          // find xyz-indices of cell that cutoffGroup is in.
# Line 1370 | Line 1428 | namespace OpenMD {
1428          // add this cutoff group to the list of groups in this cell;
1429          cellListCol_[cellIndex].push_back(i);
1430        }
1431 <    
1431 >      
1432   #else
1433        for (int i = 0; i < nGroups_; i++) {
1434          rs = snap_->cgData.position[i];
1435          
1436          // scaled positions relative to the box vectors
1437 <        scaled = invHmat * rs;
1437 >        scaled = invBox * rs;
1438          
1439          // wrap the vector back into the unit box by subtracting integer box
1440          // numbers
1441          for (int j = 0; j < 3; j++) {
1442            scaled[j] -= roundMe(scaled[j]);
1443            scaled[j] += 0.5;
1444 +          // Handle the special case when an object is exactly on the
1445 +          // boundary (a scaled coordinate of 1.0 is the same as
1446 +          // scaled coordinate of 0.0)
1447 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1448          }
1449          
1450          // find xyz-indices of cell that cutoffGroup is in.
# Line 1441 | Line 1503 | namespace OpenMD {
1503                    // & column indicies and will divide labor in the
1504                    // force evaluation later.
1505                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1506 <                  snap_->wrapVector(dr);
1506 >                  if (usePeriodicBoundaryConditions_) {
1507 >                    snap_->wrapVector(dr);
1508 >                  }
1509                    cuts = getGroupCutoffs( (*j1), (*j2) );
1510                    if (dr.lengthSquare() < cuts.third) {
1511                      neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1463 | Line 1527 | namespace OpenMD {
1527                    // allows atoms within a single cutoff group to
1528                    // interact with each other.
1529  
1466 –
1467 –
1530                    if (m2 != m1 || (*j2) >= (*j1) ) {
1531  
1532                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1533 <                    snap_->wrapVector(dr);
1533 >                    if (usePeriodicBoundaryConditions_) {
1534 >                      snap_->wrapVector(dr);
1535 >                    }
1536                      cuts = getGroupCutoffs( (*j1), (*j2) );
1537                      if (dr.lengthSquare() < cuts.third) {
1538                        neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1487 | Line 1551 | namespace OpenMD {
1551        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1552          for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1553            dr = cgColData.position[j2] - cgRowData.position[j1];
1554 <          snap_->wrapVector(dr);
1554 >          if (usePeriodicBoundaryConditions_) {
1555 >            snap_->wrapVector(dr);
1556 >          }
1557            cuts = getGroupCutoffs( j1, j2 );
1558            if (dr.lengthSquare() < cuts.third) {
1559              neighborList.push_back(make_pair(j1, j2));
# Line 1500 | Line 1566 | namespace OpenMD {
1566          // include self group interactions j2 == j1
1567          for (int j2 = j1; j2 < nGroups_; j2++) {
1568            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1569 <          snap_->wrapVector(dr);
1569 >          if (usePeriodicBoundaryConditions_) {
1570 >            snap_->wrapVector(dr);
1571 >          }
1572            cuts = getGroupCutoffs( j1, j2 );
1573            if (dr.lengthSquare() < cuts.third) {
1574              neighborList.push_back(make_pair(j1, j2));

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