ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
(Generate patch)

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC vs.
Revision 1713 by gezelter, Sat May 19 14:21:02 2012 UTC

# Line 36 | Line 36
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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42   #include "parallel/ForceMatrixDecomposition.hpp"
43   #include "math/SquareMatrix3.hpp"
# Line 524 | Line 525 | namespace OpenMD {
525             atomColData.skippedCharge.end(), 0.0);
526      }
527  
528 +    if (storageLayout_ & DataStorage::dslElectricField) {    
529 +      fill(atomRowData.electricField.begin(),
530 +           atomRowData.electricField.end(), V3Zero);
531 +      fill(atomColData.electricField.begin(),
532 +           atomColData.electricField.end(), V3Zero);
533 +    }
534 +    if (storageLayout_ & DataStorage::dslFlucQForce) {    
535 +      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
536 +           0.0);
537 +      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
538 +           0.0);
539 +    }
540 +
541   #endif
542      // even in parallel, we need to zero out the local arrays:
543  
# Line 536 | Line 550 | namespace OpenMD {
550        fill(snap_->atomData.density.begin(),
551             snap_->atomData.density.end(), 0.0);
552      }
553 +
554      if (storageLayout_ & DataStorage::dslFunctional) {
555        fill(snap_->atomData.functional.begin(),
556             snap_->atomData.functional.end(), 0.0);
557      }
558 +
559      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
560        fill(snap_->atomData.functionalDerivative.begin(),
561             snap_->atomData.functionalDerivative.end(), 0.0);
562      }
563 +
564      if (storageLayout_ & DataStorage::dslSkippedCharge) {      
565        fill(snap_->atomData.skippedCharge.begin(),
566             snap_->atomData.skippedCharge.end(), 0.0);
567      }
568 <    
568 >
569 >    if (storageLayout_ & DataStorage::dslElectricField) {      
570 >      fill(snap_->atomData.electricField.begin(),
571 >           snap_->atomData.electricField.end(), V3Zero);
572 >    }
573    }
574  
575  
# Line 588 | Line 609 | namespace OpenMD {
609                                     atomColData.electroFrame);
610      }
611  
612 +    // if needed, gather the atomic fluctuating charge values
613 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {
614 +      AtomPlanRealRow->gather(snap_->atomData.flucQPos,
615 +                              atomRowData.flucQPos);
616 +      AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
617 +                                 atomColData.flucQPos);
618 +    }
619 +
620   #endif      
621    }
622    
# Line 610 | Line 639 | namespace OpenMD {
639        for (int i = 0; i < n; i++)
640          snap_->atomData.density[i] += rho_tmp[i];
641      }
642 +
643 +    if (storageLayout_ & DataStorage::dslElectricField) {
644 +      
645 +      AtomPlanVectorRow->scatter(atomRowData.electricField,
646 +                                 snap_->atomData.electricField);
647 +      
648 +      int n = snap_->atomData.electricField.size();
649 +      vector<Vector3d> field_tmp(n, V3Zero);
650 +      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
651 +      for (int i = 0; i < n; i++)
652 +        snap_->atomData.electricField[i] += field_tmp[i];
653 +    }
654   #endif
655    }
656  
# Line 689 | Line 730 | namespace OpenMD {
730              
731      }
732      
733 +    if (storageLayout_ & DataStorage::dslFlucQForce) {
734 +
735 +      int nq = snap_->atomData.flucQFrc.size();
736 +      vector<RealType> fqfrc_tmp(nq, 0.0);
737 +
738 +      AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
739 +      for (int i = 0; i < nq; i++) {
740 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
741 +        fqfrc_tmp[i] = 0.0;
742 +      }
743 +      
744 +      AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
745 +      for (int i = 0; i < nq; i++)
746 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
747 +            
748 +    }
749 +
750      nLocal_ = snap_->getNumberOfAtoms();
751  
752      vector<potVec> pot_temp(nLocal_,
# Line 950 | Line 1008 | namespace OpenMD {
1008      }
1009  
1010   #else
1011 +    
1012  
1013 +    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1014 +    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1015 +    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1016 +
1017      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1018      //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1019      //                         ff_->getAtomType(idents[atom2]) );
# Line 1000 | Line 1063 | namespace OpenMD {
1063    
1064    void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1065   #ifdef IS_MPI
1066 <    pot_row[atom1] += 0.5 *  *(idat.pot);
1067 <    pot_col[atom2] += 0.5 *  *(idat.pot);
1066 >    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1067 >    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1068  
1069      atomRowData.force[atom1] += *(idat.f1);
1070      atomColData.force[atom2] -= *(idat.f1);
1071 +
1072 +    // should particle pot be done here also?
1073   #else
1074      pairwisePot += *(idat.pot);
1075  
1076      snap_->atomData.force[atom1] += *(idat.f1);
1077      snap_->atomData.force[atom2] -= *(idat.f1);
1078 +
1079 +    if (idat.doParticlePot) {
1080 +      snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1081 +      snap_->atomData.particlePot[atom2] -= *(idat.vpair) * *(idat.sw);
1082 +    }
1083 +      
1084   #endif
1085      
1086    }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines