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root/OpenMD/branches/development/src/brains/ForceManager.cpp
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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1756 by gezelter, Mon Jun 18 18:23:20 2012 UTC vs.
Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

# Line 449 | Line 449 | namespace OpenMD {
449      Molecule::CutoffGroupIterator ci;
450      CutoffGroup* cg;
451      
452 <    // forces are zeroed here, before any are accumulated.
452 >    // forces and potentials are zeroed here, before any are
453 >    // accumulated.
454      
455 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
456 +
457 +    snap->setBondPotential(0.0);
458 +    snap->setBendPotential(0.0);
459 +    snap->setTorsionPotential(0.0);
460 +    snap->setInversionPotential(0.0);
461 +
462 +    potVec zeroPot(0.0);
463 +    snap->setLongRangePotential(zeroPot);
464 +    snap->setExcludedPotentials(zeroPot);
465 +
466 +    snap->setRestraintPotential(0.0);
467 +    snap->setRawPotential(0.0);
468 +
469      for (mol = info_->beginMolecule(mi); mol != NULL;
470           mol = info_->nextMolecule(mi)) {
471        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 586 | Line 601 | namespace OpenMD {
601          }      
602        }      
603      }
604 <    
605 <    RealType  shortRangePotential = bondPotential + bendPotential +
606 <      torsionPotential +  inversionPotential;    
604 >
605 > #ifdef IS_MPI
606 >    // Collect from all nodes.  This should eventually be moved into a
607 >    // SystemDecomposition, but this is a better place than in
608 >    // Thermo to do the collection.
609 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
610 >                              MPI::SUM);
611 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
612 >                              MPI::SUM);
613 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
614 >                              MPI::REALTYPE, MPI::SUM);
615 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
616 >                              MPI::REALTYPE, MPI::SUM);
617 > #endif
618 >
619      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
620 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
621 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
622 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
623 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
624 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
620 >
621 >    curSnapshot->setBondPotential(bondPotential);
622 >    curSnapshot->setBendPotential(bendPotential);
623 >    curSnapshot->setTorsionPotential(torsionPotential);
624 >    curSnapshot->setInversionPotential(inversionPotential);
625 >    
626 >    // RealType shortRangePotential = bondPotential + bendPotential +
627 >    //   torsionPotential +  inversionPotential;    
628 >
629 >    // curSnapshot->setShortRangePotential(shortRangePotential);
630    }
631    
632    void ForceManager::longRangeInteractions() {
# Line 649 | Line 681 | namespace OpenMD {
681      RealType dVdFQ2(0.0);
682      potVec longRangePotential(0.0);
683      potVec workPot(0.0);
684 +    potVec exPot(0.0);
685      vector<int>::iterator ia, jb;
686  
687      int loopStart, loopEnd;
# Line 656 | Line 689 | namespace OpenMD {
689      idat.vdwMult = &vdwMult;
690      idat.electroMult = &electroMult;
691      idat.pot = &workPot;
692 +    idat.excludedPot = &exPot;
693      sdat.pot = fDecomp_->getEmbeddingPotential();
694 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
695      idat.vpair = &vpair;
696      idat.dVdFQ1 = &dVdFQ1;
697      idat.dVdFQ2 = &dVdFQ2;
# Line 723 | Line 758 | namespace OpenMD {
758  
759                  vpair = 0.0;
760                  workPot = 0.0;
761 +                exPot = 0.0;
762                  f1 = V3Zero;
763                  dVdFQ1 = 0.0;
764                  dVdFQ2 = 0.0;
# Line 860 | Line 896 | namespace OpenMD {
896      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
897        *(fDecomp_->getPairwisePotential());
898  
899 <    lrPot = longRangePotential.sum();
899 >    curSnapshot->setLongRangePotential(longRangePotential);
900  
901 <    //store the stressTensor and long range potential    
902 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
903 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
904 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
901 >    // lrPot = longRangePotential.sum();
902 >
903 >    // //store the long range potential  
904 >    // curSnapshot->setLongRangePotential(lrPot);
905 >    
906 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
907 >                                         *(fDecomp_->getExcludedPotential()));
908 >
909    }
910  
911    
# Line 875 | Line 915 | namespace OpenMD {
915      Molecule::RigidBodyIterator rbIter;
916      RigidBody* rb;
917      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
918 <    
918 >  
919      // collect the atomic forces onto rigid bodies
920      
921      for (mol = info_->beginMolecule(mi); mol != NULL;

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