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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1771 by gezelter, Fri Jul 27 17:34:10 2012 UTC vs.
Revision 1856 by gezelter, Tue Apr 2 21:30:34 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 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 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  
# 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  
# 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  
# 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 1132 | Line 1157 | namespace OpenMD {
1157        idat.A2 = &(atomColData.aMat[atom2]);
1158      }
1159      
1135 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1136 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1137 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1138 –    }
1139 –
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 1179 | Line 1209 | namespace OpenMD {
1209      if (storageLayout_ & DataStorage::dslAmat) {
1210        idat.A1 = &(snap_->atomData.aMat[atom1]);
1211        idat.A2 = &(snap_->atomData.aMat[atom2]);
1182 –    }
1183 –
1184 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1185 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1186 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1212      }
1213  
1214      if (storageLayout_ & DataStorage::dslTorque) {
# Line 1191 | Line 1216 | namespace OpenMD {
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 1287 | Line 1322 | namespace OpenMD {
1322      groupCutoffs cuts;
1323      bool doAllPairs = false;
1324  
1290 – #ifdef IS_MPI
1291 –    cellListRow_.clear();
1292 –    cellListCol_.clear();
1293 – #else
1294 –    cellList_.clear();
1295 – #endif
1296 –
1325      RealType rList_ = (largestRcut_ + skinThickness_);
1298 –    RealType rl2 = rList_ * rList_;
1326      Snapshot* snap_ = sman_->getCurrentSnapshot();
1300 –    Mat3x3d Hmat = snap_->getHmat();
1301 –    Vector3d Hx = Hmat.getColumn(0);
1302 –    Vector3d Hy = Hmat.getColumn(1);
1303 –    Vector3d Hz = Hmat.getColumn(2);
1304 –
1305 –    nCells_.x() = (int) ( Hx.length() )/ rList_;
1306 –    nCells_.y() = (int) ( Hy.length() )/ rList_;
1307 –    nCells_.z() = (int) ( Hz.length() )/ rList_;
1308 –
1309 –    // handle small boxes where the cell offsets can end up repeating cells
1310 –    
1311 –    if (nCells_.x() < 3) doAllPairs = true;
1312 –    if (nCells_.y() < 3) doAllPairs = true;
1313 –    if (nCells_.z() < 3) doAllPairs = true;
1314 –
1327      Mat3x3d invHmat = snap_->getInvHmat();
1328      Vector3d rs, scaled, dr;
1329      Vector3i whichCell;
1330      int cellIndex;
1319 –    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1331  
1332   #ifdef IS_MPI
1333 <    cellListRow_.resize(nCtot);
1334 <    cellListCol_.resize(nCtot);
1333 >    cellListRow_.clear();
1334 >    cellListCol_.clear();
1335   #else
1336 <    cellList_.resize(nCtot);
1336 >    cellList_.clear();
1337   #endif
1338  
1339 +    if (!usePeriodicBoundaryConditions_) {
1340 +      doAllPairs = true;
1341 +    } else {
1342 +
1343 +      Mat3x3d Hmat = snap_->getHmat();
1344 +      Vector3d Hx = Hmat.getColumn(0);
1345 +      Vector3d Hy = Hmat.getColumn(1);
1346 +      Vector3d Hz = Hmat.getColumn(2);
1347 +
1348 +      nCells_.x() = (int) ( Hx.length() )/ rList_;
1349 +      nCells_.y() = (int) ( Hy.length() )/ rList_;
1350 +      nCells_.z() = (int) ( Hz.length() )/ rList_;
1351 +      
1352 +      // handle small boxes where the cell offsets can end up repeating cells
1353 +      
1354 +      if (nCells_.x() < 3) doAllPairs = true;
1355 +      if (nCells_.y() < 3) doAllPairs = true;
1356 +      if (nCells_.z() < 3) doAllPairs = true;
1357 +      
1358 +      int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1359 +      
1360 + #ifdef IS_MPI
1361 +      cellListRow_.resize(nCtot);
1362 +      cellListCol_.resize(nCtot);
1363 + #else
1364 +      cellList_.resize(nCtot);
1365 + #endif
1366 +    }
1367 +
1368      if (!doAllPairs) {
1369   #ifdef IS_MPI
1370  
# Line 1339 | Line 1379 | namespace OpenMD {
1379          for (int j = 0; j < 3; j++) {
1380            scaled[j] -= roundMe(scaled[j]);
1381            scaled[j] += 0.5;
1382 +          // Handle the special case when an object is exactly on the
1383 +          // boundary (a scaled coordinate of 1.0 is the same as
1384 +          // scaled coordinate of 0.0)
1385 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1386          }
1387          
1388          // find xyz-indices of cell that cutoffGroup is in.
# Line 1363 | Line 1407 | namespace OpenMD {
1407          for (int j = 0; j < 3; j++) {
1408            scaled[j] -= roundMe(scaled[j]);
1409            scaled[j] += 0.5;
1410 +          // Handle the special case when an object is exactly on the
1411 +          // boundary (a scaled coordinate of 1.0 is the same as
1412 +          // scaled coordinate of 0.0)
1413 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1414          }
1415          
1416          // find xyz-indices of cell that cutoffGroup is in.
# Line 1451 | Line 1499 | namespace OpenMD {
1499                    // & column indicies and will divide labor in the
1500                    // force evaluation later.
1501                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1502 <                  snap_->wrapVector(dr);
1502 >                  if (usePeriodicBoundaryConditions_) {
1503 >                    snap_->wrapVector(dr);
1504 >                  }
1505                    cuts = getGroupCutoffs( (*j1), (*j2) );
1506                    if (dr.lengthSquare() < cuts.third) {
1507                      neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1478 | Line 1528 | namespace OpenMD {
1528                    if (m2 != m1 || (*j2) >= (*j1) ) {
1529  
1530                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1531 <                    snap_->wrapVector(dr);
1531 >                    if (usePeriodicBoundaryConditions_) {
1532 >                      snap_->wrapVector(dr);
1533 >                    }
1534                      cuts = getGroupCutoffs( (*j1), (*j2) );
1535                      if (dr.lengthSquare() < cuts.third) {
1536                        neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1497 | Line 1549 | namespace OpenMD {
1549        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1550          for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1551            dr = cgColData.position[j2] - cgRowData.position[j1];
1552 <          snap_->wrapVector(dr);
1552 >          if (usePeriodicBoundaryConditions_) {
1553 >            snap_->wrapVector(dr);
1554 >          }
1555            cuts = getGroupCutoffs( j1, j2 );
1556            if (dr.lengthSquare() < cuts.third) {
1557              neighborList.push_back(make_pair(j1, j2));
# Line 1510 | Line 1564 | namespace OpenMD {
1564          // include self group interactions j2 == j1
1565          for (int j2 = j1; j2 < nGroups_; j2++) {
1566            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1567 <          snap_->wrapVector(dr);
1567 >          if (usePeriodicBoundaryConditions_) {
1568 >            snap_->wrapVector(dr);
1569 >          }
1570            cuts = getGroupCutoffs( j1, j2 );
1571            if (dr.lengthSquare() < cuts.third) {
1572              neighborList.push_back(make_pair(j1, j2));

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