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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 1756 by gezelter, Mon Jun 18 18:23:20 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC

# Line 175 | Line 175 | namespace OpenMD {
175  
176      pot_row.resize(nAtomsInRow_);
177      pot_col.resize(nAtomsInCol_);
178 +
179 +    expot_row.resize(nAtomsInRow_);
180 +    expot_col.resize(nAtomsInCol_);
181  
182      AtomRowToGlobal.resize(nAtomsInRow_);
183      AtomColToGlobal.resize(nAtomsInCol_);
# Line 307 | Line 310 | namespace OpenMD {
310      
311      RealType tol = 1e-6;
312      largestRcut_ = 0.0;
310 –    RealType rc;
313      int atid;
314      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315      
# Line 392 | 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 417 | 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 474 | 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      }
# Line 484 | Line 486 | namespace OpenMD {
486    void ForceMatrixDecomposition::zeroWorkArrays() {
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 502 | Line 506 | namespace OpenMD {
506      fill(pot_col.begin(), pot_col.end(),
507           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
508  
509 +    fill(expot_row.begin(), expot_row.end(),
510 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
511 +
512 +    fill(expot_col.begin(), expot_col.end(),
513 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
514 +
515      if (storageLayout_ & DataStorage::dslParticlePot) {    
516        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
517             0.0);
# Line 780 | Line 790 | namespace OpenMD {
790  
791      vector<potVec> pot_temp(nLocal_,
792                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
793 +    vector<potVec> expot_temp(nLocal_,
794 +                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
795  
796      // scatter/gather pot_row into the members of my column
797            
798      AtomPlanPotRow->scatter(pot_row, pot_temp);
799 +    AtomPlanPotRow->scatter(expot_row, expot_temp);
800  
801 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
801 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
802        pairwisePot += pot_temp[ii];
803 +
804 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
805 +      excludedPot += expot_temp[ii];
806          
807      if (storageLayout_ & DataStorage::dslParticlePot) {
808        // This is the pairwise contribution to the particle pot.  The
# Line 804 | Line 820 | namespace OpenMD {
820  
821      fill(pot_temp.begin(), pot_temp.end(),
822           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
823 +    fill(expot_temp.begin(), expot_temp.end(),
824 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
825        
826      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
827 +    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
828      
829      for (int ii = 0;  ii < pot_temp.size(); ii++ )
830        pairwisePot += pot_temp[ii];    
831  
832 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
833 +      excludedPot += expot_temp[ii];    
834 +
835      if (storageLayout_ & DataStorage::dslParticlePot) {
836        // This is the pairwise contribution to the particle pot.  The
837        // embedding contribution is added in each of the low level
# Line 851 | Line 873 | namespace OpenMD {
873        pairwisePot[ii] = ploc2;
874      }
875  
876 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
877 +      RealType ploc1 = excludedPot[ii];
878 +      RealType ploc2 = 0.0;
879 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
880 +      excludedPot[ii] = ploc2;
881 +    }
882 +
883      // Here be dragons.
884      MPI::Intracomm col = colComm.getComm();
885  
# Line 878 | Line 907 | namespace OpenMD {
907        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
908        embeddingPot[ii] = ploc2;
909      }    
910 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
911 +      RealType ploc1 = excludedSelfPot[ii];
912 +      RealType ploc2 = 0.0;
913 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
914 +      excludedSelfPot[ii] = ploc2;
915 +    }    
916   #endif
917      
918    }
# Line 1194 | Line 1229 | namespace OpenMD {
1229   #ifdef IS_MPI
1230      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1231      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1232 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1233 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1234  
1235      atomRowData.force[atom1] += *(idat.f1);
1236      atomColData.force[atom2] -= *(idat.f1);
# Line 1210 | Line 1247 | namespace OpenMD {
1247  
1248   #else
1249      pairwisePot += *(idat.pot);
1250 +    excludedPot += *(idat.excludedPot);
1251  
1252      snap_->atomData.force[atom1] += *(idat.f1);
1253      snap_->atomData.force[atom2] -= *(idat.f1);
# Line 1257 | Line 1295 | namespace OpenMD {
1295   #endif
1296  
1297      RealType rList_ = (largestRcut_ + skinThickness_);
1260 –    RealType rl2 = rList_ * rList_;
1298      Snapshot* snap_ = sman_->getCurrentSnapshot();
1299      Mat3x3d Hmat = snap_->getHmat();
1300      Vector3d Hx = Hmat.getColumn(0);
# Line 1301 | Line 1338 | namespace OpenMD {
1338          for (int j = 0; j < 3; j++) {
1339            scaled[j] -= roundMe(scaled[j]);
1340            scaled[j] += 0.5;
1341 +          // Handle the special case when an object is exactly on the
1342 +          // boundary (a scaled coordinate of 1.0 is the same as
1343 +          // scaled coordinate of 0.0)
1344 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1345          }
1346          
1347          // find xyz-indices of cell that cutoffGroup is in.
# Line 1325 | Line 1366 | namespace OpenMD {
1366          for (int j = 0; j < 3; j++) {
1367            scaled[j] -= roundMe(scaled[j]);
1368            scaled[j] += 0.5;
1369 +          // Handle the special case when an object is exactly on the
1370 +          // boundary (a scaled coordinate of 1.0 is the same as
1371 +          // scaled coordinate of 0.0)
1372 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1373          }
1374          
1375          // find xyz-indices of cell that cutoffGroup is in.
# Line 1351 | Line 1396 | namespace OpenMD {
1396          for (int j = 0; j < 3; j++) {
1397            scaled[j] -= roundMe(scaled[j]);
1398            scaled[j] += 0.5;
1399 +          // Handle the special case when an object is exactly on the
1400 +          // boundary (a scaled coordinate of 1.0 is the same as
1401 +          // scaled coordinate of 0.0)
1402 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1403          }
1404          
1405          // find xyz-indices of cell that cutoffGroup is in.

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