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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1771 by gezelter, Fri Jul 27 17:34:10 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 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 479 | Line 479 | namespace OpenMD {
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 557 | Line 557 | namespace OpenMD {
557             atomRowData.electricField.end(), V3Zero);
558        fill(atomColData.electricField.begin(),
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);
560      }
561  
562   #endif
# 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 919 | Line 939 | namespace OpenMD {
939  
940  
941  
942 <  int ForceMatrixDecomposition::getNAtomsInRow() {  
942 >  int& ForceMatrixDecomposition::getNAtomsInRow() {  
943   #ifdef IS_MPI
944      return nAtomsInRow_;
945   #else
# Line 930 | 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 938 | 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 955 | 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 967 | 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 985 | 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 998 | 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 1011 | 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 1028 | 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 1042 | 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 1124 | Line 1149 | namespace OpenMD {
1149    
1150   #ifdef IS_MPI
1151      idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1152 +    idat.atid1 = identsRow[atom1];
1153 +    idat.atid2 = identsCol[atom2];
1154      //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1155      //                         ff_->getAtomType(identsCol[atom2]) );
1156      
# Line 1132 | Line 1159 | namespace OpenMD {
1159        idat.A2 = &(atomColData.aMat[atom2]);
1160      }
1161      
1135 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1136 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1137 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1138 –    }
1139 –
1162      if (storageLayout_ & DataStorage::dslTorque) {
1163        idat.t1 = &(atomRowData.torque[atom1]);
1164        idat.t2 = &(atomColData.torque[atom2]);
1165 +    }
1166 +
1167 +    if (storageLayout_ & DataStorage::dslDipole) {
1168 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1169 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1170 +    }
1171 +
1172 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1173 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1174 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1175      }
1176  
1177      if (storageLayout_ & DataStorage::dslDensity) {
# Line 1175 | Line 1207 | namespace OpenMD {
1207   #else
1208      
1209      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1210 +    idat.atid1 = idents[atom1];
1211 +    idat.atid2 = idents[atom2];
1212  
1213      if (storageLayout_ & DataStorage::dslAmat) {
1214        idat.A1 = &(snap_->atomData.aMat[atom1]);
1215        idat.A2 = &(snap_->atomData.aMat[atom2]);
1216      }
1217  
1184 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1185 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1186 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1187 –    }
1188 –
1218      if (storageLayout_ & DataStorage::dslTorque) {
1219        idat.t1 = &(snap_->atomData.torque[atom1]);
1220        idat.t2 = &(snap_->atomData.torque[atom2]);
1221      }
1222  
1223 +    if (storageLayout_ & DataStorage::dslDipole) {
1224 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1225 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1226 +    }
1227 +
1228 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1229 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1230 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1231 +    }
1232 +
1233      if (storageLayout_ & DataStorage::dslDensity) {    
1234        idat.rho1 = &(snap_->atomData.density[atom1]);
1235        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1281 | Line 1320 | namespace OpenMD {
1320     * first element of pair is row-indexed CutoffGroup
1321     * second element of pair is column-indexed CutoffGroup
1322     */
1323 <  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1324 <      
1325 <    vector<pair<int, int> > neighborList;
1323 >  void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1324 >    
1325 >    neighborList.clear();
1326      groupCutoffs cuts;
1327      bool doAllPairs = false;
1328  
1329 +    RealType rList_ = (largestRcut_ + skinThickness_);
1330 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1331 +    Mat3x3d box;
1332 +    Mat3x3d invBox;
1333 +
1334 +    Vector3d rs, scaled, dr;
1335 +    Vector3i whichCell;
1336 +    int cellIndex;
1337 +
1338   #ifdef IS_MPI
1339      cellListRow_.clear();
1340      cellListCol_.clear();
1341   #else
1342      cellList_.clear();
1343   #endif
1344 <
1345 <    RealType rList_ = (largestRcut_ + skinThickness_);
1346 <    RealType rl2 = rList_ * rList_;
1347 <    Snapshot* snap_ = sman_->getCurrentSnapshot();
1348 <    Mat3x3d Hmat = snap_->getHmat();
1349 <    Vector3d Hx = Hmat.getColumn(0);
1350 <    Vector3d Hy = Hmat.getColumn(1);
1351 <    Vector3d Hz = Hmat.getColumn(2);
1352 <
1353 <    nCells_.x() = (int) ( Hx.length() )/ rList_;
1354 <    nCells_.y() = (int) ( Hy.length() )/ rList_;
1355 <    nCells_.z() = (int) ( Hz.length() )/ rList_;
1356 <
1344 >    
1345 >    if (!usePeriodicBoundaryConditions_) {
1346 >      box = snap_->getBoundingBox();
1347 >      invBox = snap_->getInvBoundingBox();
1348 >    } else {
1349 >      box = snap_->getHmat();
1350 >      invBox = snap_->getInvHmat();
1351 >    }
1352 >    
1353 >    Vector3d boxX = box.getColumn(0);
1354 >    Vector3d boxY = box.getColumn(1);
1355 >    Vector3d boxZ = box.getColumn(2);
1356 >    
1357 >    nCells_.x() = (int) ( boxX.length() )/ rList_;
1358 >    nCells_.y() = (int) ( boxY.length() )/ rList_;
1359 >    nCells_.z() = (int) ( boxZ.length() )/ rList_;
1360 >    
1361      // handle small boxes where the cell offsets can end up repeating cells
1362      
1363      if (nCells_.x() < 3) doAllPairs = true;
1364      if (nCells_.y() < 3) doAllPairs = true;
1365      if (nCells_.z() < 3) doAllPairs = true;
1366 <
1315 <    Mat3x3d invHmat = snap_->getInvHmat();
1316 <    Vector3d rs, scaled, dr;
1317 <    Vector3i whichCell;
1318 <    int cellIndex;
1366 >    
1367      int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1368 <
1368 >    
1369   #ifdef IS_MPI
1370      cellListRow_.resize(nCtot);
1371      cellListCol_.resize(nCtot);
1372   #else
1373      cellList_.resize(nCtot);
1374   #endif
1375 <
1375 >    
1376      if (!doAllPairs) {
1377   #ifdef IS_MPI
1378 <
1378 >      
1379        for (int i = 0; i < nGroupsInRow_; i++) {
1380          rs = cgRowData.position[i];
1381          
1382          // scaled positions relative to the box vectors
1383 <        scaled = invHmat * rs;
1383 >        scaled = invBox * rs;
1384          
1385          // wrap the vector back into the unit box by subtracting integer box
1386          // numbers
1387          for (int j = 0; j < 3; j++) {
1388            scaled[j] -= roundMe(scaled[j]);
1389            scaled[j] += 0.5;
1390 +          // Handle the special case when an object is exactly on the
1391 +          // boundary (a scaled coordinate of 1.0 is the same as
1392 +          // scaled coordinate of 0.0)
1393 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1394          }
1395          
1396          // find xyz-indices of cell that cutoffGroup is in.
# Line 1356 | Line 1408 | namespace OpenMD {
1408          rs = cgColData.position[i];
1409          
1410          // scaled positions relative to the box vectors
1411 <        scaled = invHmat * rs;
1411 >        scaled = invBox * rs;
1412          
1413          // wrap the vector back into the unit box by subtracting integer box
1414          // numbers
1415          for (int j = 0; j < 3; j++) {
1416            scaled[j] -= roundMe(scaled[j]);
1417            scaled[j] += 0.5;
1418 +          // Handle the special case when an object is exactly on the
1419 +          // boundary (a scaled coordinate of 1.0 is the same as
1420 +          // scaled coordinate of 0.0)
1421 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1422          }
1423          
1424          // find xyz-indices of cell that cutoffGroup is in.
# Line 1376 | Line 1432 | namespace OpenMD {
1432          // add this cutoff group to the list of groups in this cell;
1433          cellListCol_[cellIndex].push_back(i);
1434        }
1435 <    
1435 >      
1436   #else
1437        for (int i = 0; i < nGroups_; i++) {
1438          rs = snap_->cgData.position[i];
1439          
1440          // scaled positions relative to the box vectors
1441 <        scaled = invHmat * rs;
1441 >        scaled = invBox * rs;
1442          
1443          // wrap the vector back into the unit box by subtracting integer box
1444          // numbers
# Line 1451 | Line 1507 | namespace OpenMD {
1507                    // & column indicies and will divide labor in the
1508                    // force evaluation later.
1509                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1510 <                  snap_->wrapVector(dr);
1510 >                  if (usePeriodicBoundaryConditions_) {
1511 >                    snap_->wrapVector(dr);
1512 >                  }
1513                    cuts = getGroupCutoffs( (*j1), (*j2) );
1514                    if (dr.lengthSquare() < cuts.third) {
1515                      neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1473 | Line 1531 | namespace OpenMD {
1531                    // allows atoms within a single cutoff group to
1532                    // interact with each other.
1533  
1476 –
1477 –
1534                    if (m2 != m1 || (*j2) >= (*j1) ) {
1535  
1536                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1537 <                    snap_->wrapVector(dr);
1537 >                    if (usePeriodicBoundaryConditions_) {
1538 >                      snap_->wrapVector(dr);
1539 >                    }
1540                      cuts = getGroupCutoffs( (*j1), (*j2) );
1541                      if (dr.lengthSquare() < cuts.third) {
1542                        neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1497 | Line 1555 | namespace OpenMD {
1555        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1556          for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1557            dr = cgColData.position[j2] - cgRowData.position[j1];
1558 <          snap_->wrapVector(dr);
1558 >          if (usePeriodicBoundaryConditions_) {
1559 >            snap_->wrapVector(dr);
1560 >          }
1561            cuts = getGroupCutoffs( j1, j2 );
1562            if (dr.lengthSquare() < cuts.third) {
1563              neighborList.push_back(make_pair(j1, j2));
# Line 1510 | Line 1570 | namespace OpenMD {
1570          // include self group interactions j2 == j1
1571          for (int j2 = j1; j2 < nGroups_; j2++) {
1572            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1573 <          snap_->wrapVector(dr);
1573 >          if (usePeriodicBoundaryConditions_) {
1574 >            snap_->wrapVector(dr);
1575 >          }
1576            cuts = getGroupCutoffs( j1, j2 );
1577            if (dr.lengthSquare() < cuts.third) {
1578              neighborList.push_back(make_pair(j1, j2));
# Line 1525 | Line 1587 | namespace OpenMD {
1587      saved_CG_positions_.clear();
1588      for (int i = 0; i < nGroups_; i++)
1589        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1528 –    
1529 –    return neighborList;
1590    }
1591   } //end namespace OpenMD

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