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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC vs.
Revision 1761 by gezelter, Fri Jun 22 20:01:37 2012 UTC

# Line 110 | Line 110 | namespace OpenMD {
110      Globals* simParams_ = info_->getSimParams();
111      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112      int mdFileVersion;
113 +    rCut_ = 0.0; //Needs a value for a later max() call;  
114      
115      if (simParams_->haveMDfileVersion())
116        mdFileVersion = simParams_->getMDfileVersion();
# Line 390 | Line 391 | namespace OpenMD {
391        info_->prepareTopology();      
392  
393        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
394 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
395 +      if (doHeatFlux_) doParticlePot_ = true;
396    
397      }
398  
# Line 471 | Line 474 | namespace OpenMD {
474      }
475      
476      // Zero out the stress tensor
477 <    tau *= 0.0;
478 <    
477 >    stressTensor *= 0.0;
478 >    // Zero out the heatFlux
479 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
480    }
481    
482    void ForceManager::shortRangeInteractions() {
# Line 582 | Line 586 | namespace OpenMD {
586          }      
587        }      
588      }
589 +
590 + #ifdef IS_MPI
591 +    // Collect from all nodes.  This should eventually be moved into a
592 +    // SystemDecomposition, but this is a better place than in
593 +    // Thermo to do the collection.
594 +    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
595 +                              MPI::SUM);
596 +    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
597 +                              MPI::SUM);
598 +    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
599 +                              MPI::REALTYPE, MPI::SUM);
600 +    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
601 +                              MPI::REALTYPE, MPI::SUM);
602 + #endif
603 +
604 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
605 +
606 +    curSnapshot->setBondPotential(bondPotential);
607 +    curSnapshot->setBendPotential(bendPotential);
608 +    curSnapshot->setTorsionPotential(torsionPotential);
609 +    curSnapshot->setInversionPotential(inversionPotential);
610      
611 <    RealType  shortRangePotential = bondPotential + bendPotential +
611 >    RealType shortRangePotential = bondPotential + bendPotential +
612        torsionPotential +  inversionPotential;    
613 <    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
614 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
590 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
591 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
592 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
593 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
613 >
614 >    curSnapshot->setShortRangePotential(shortRangePotential);
615    }
616    
617    void ForceManager::longRangeInteractions() {
618  
619 +
620      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
621      DataStorage* config = &(curSnapshot->atomData);
622      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 618 | Line 640 | namespace OpenMD {
640        // center of mass of the group is the same as position of the atom  
641        // if cutoff group does not exist
642        cgConfig->position = config->position;
643 +      cgConfig->velocity = config->velocity;
644      }
645  
646      fDecomp_->zeroWorkArrays();
647      fDecomp_->distributeData();
648      
649      int cg1, cg2, atom1, atom2, topoDist;
650 <    Vector3d d_grp, dag, d;
650 >    Vector3d d_grp, dag, d, gvel2, vel2;
651      RealType rgrpsq, rgrp, r2, r;
652      RealType electroMult, vdwMult;
653      RealType vij;
# Line 639 | Line 662 | namespace OpenMD {
662      RealType mf;
663      RealType lrPot;
664      RealType vpair;
665 +    RealType dVdFQ1(0.0);
666 +    RealType dVdFQ2(0.0);
667      potVec longRangePotential(0.0);
668      potVec workPot(0.0);
669 +    potVec exPot(0.0);
670      vector<int>::iterator ia, jb;
671  
672      int loopStart, loopEnd;
# Line 648 | Line 674 | namespace OpenMD {
674      idat.vdwMult = &vdwMult;
675      idat.electroMult = &electroMult;
676      idat.pot = &workPot;
677 +    idat.excludedPot = &exPot;
678      sdat.pot = fDecomp_->getEmbeddingPotential();
679 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
680      idat.vpair = &vpair;
681 +    idat.dVdFQ1 = &dVdFQ1;
682 +    idat.dVdFQ2 = &dVdFQ2;
683      idat.f1 = &f1;
684      idat.sw = &sw;
685      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
# Line 663 | Line 693 | namespace OpenMD {
693      } else {
694        loopStart = PAIR_LOOP;
695      }
666 –  
696      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
697      
698        if (iLoop == loopStart) {
# Line 695 | Line 724 | namespace OpenMD {
724            
725            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
726                                                       rgrp);
727 <          
727 >
728            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
729            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
730  
731 +          if (doHeatFlux_)
732 +            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
733 +
734            for (ia = atomListRow.begin();
735                 ia != atomListRow.end(); ++ia) {            
736              atom1 = (*ia);
737 <            
737 >
738              for (jb = atomListColumn.begin();
739                   jb != atomListColumn.end(); ++jb) {              
740                atom2 = (*jb);
741  
742 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
742 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
743 >
744                  vpair = 0.0;
745                  workPot = 0.0;
746 +                exPot = 0.0;
747                  f1 = V3Zero;
748 +                dVdFQ1 = 0.0;
749 +                dVdFQ2 = 0.0;
750  
751                  fDecomp_->fillInteractionData(idat, atom1, atom2);
752 <                
752 >
753                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
754                  vdwMult = vdwScale_[topoDist];
755                  electroMult = electrostaticScale_[topoDist];
# Line 721 | Line 757 | namespace OpenMD {
757                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
758                    idat.d = &d_grp;
759                    idat.r2 = &rgrpsq;
760 +                  if (doHeatFlux_)
761 +                    vel2 = gvel2;
762                  } else {
763                    d = fDecomp_->getInteratomicVector(atom1, atom2);
764                    curSnapshot->wrapVector( d );
765                    r2 = d.lengthSquare();
766                    idat.d = &d;
767                    idat.r2 = &r2;
768 +                  if (doHeatFlux_)
769 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
770                  }
771                
772                  r = sqrt( *(idat.r2) );
# Line 739 | Line 779 | namespace OpenMD {
779                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
780                    vij += vpair;
781                    fij += f1;
782 <                  tau -= outProduct( *(idat.d), f1);
782 >                  stressTensor -= outProduct( *(idat.d), f1);
783 >                  if (doHeatFlux_)
784 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
785                  }
786                }
787              }
# Line 752 | Line 794 | namespace OpenMD {
794                fij += fg;
795  
796                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
797 <                tau -= outProduct( *(idat.d), fg);
797 >                stressTensor -= outProduct( *(idat.d), fg);
798 >                if (doHeatFlux_)
799 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
800 >                
801                }
802            
803                for (ia = atomListRow.begin();
# Line 768 | Line 813 | namespace OpenMD {
813                      // find the distance between the atom
814                      // and the center of the cutoff group:
815                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
816 <                    tau -= outProduct(dag, fg);
816 >                    stressTensor -= outProduct(dag, fg);
817 >                    if (doHeatFlux_)
818 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
819                    }
820                  }
821                }
# Line 786 | Line 833 | namespace OpenMD {
833                      // find the distance between the atom
834                      // and the center of the cutoff group:
835                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
836 <                    tau -= outProduct(dag, fg);
836 >                    stressTensor -= outProduct(dag, fg);
837 >                    if (doHeatFlux_)
838 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
839                    }
840                  }
841                }
842              }
843              //if (!info_->usesAtomicVirial()) {
844 <            //  tau -= outProduct(d_grp, fij);
844 >            //  stressTensor -= outProduct(d_grp, fij);
845 >            //  if (doHeatFlux_)
846 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
847              //}
848            }
849          }
# Line 814 | Line 865 | namespace OpenMD {
865        }
866      }
867      
868 +    // collects pairwise information
869      fDecomp_->collectData();
870          
871      if (info_->requiresSelfCorrection()) {
872 <
821 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
872 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
873          fDecomp_->fillSelfData(sdat, atom1);
874          interactionMan_->doSelfCorrection(sdat);
875        }
825 –
876      }
877  
878 +    // collects single-atom information
879 +    fDecomp_->collectSelfData();
880 +
881      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
882        *(fDecomp_->getPairwisePotential());
883  
884 +    curSnapshot->setLongRangePotentialFamilies(longRangePotential);
885 +
886      lrPot = longRangePotential.sum();
887  
888 <    //store the tau and long range potential    
889 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
890 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
891 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
888 >    //store the long range potential  
889 >    curSnapshot->setLongRangePotential(lrPot);
890 >    
891 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
892 >                                         *(fDecomp_->getExcludedPotential()));
893 >
894    }
895  
896    
# Line 851 | Line 908 | namespace OpenMD {
908        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
909             rb = mol->nextRigidBody(rbIter)) {
910          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
911 <        tau += rbTau;
911 >        stressTensor += rbTau;
912        }
913      }
914      
915   #ifdef IS_MPI
916 <    Mat3x3d tmpTau(tau);
917 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
861 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
916 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
917 >                              MPI::REALTYPE, MPI::SUM);
918   #endif
919 <    curSnapshot->setTau(tau);
919 >    curSnapshot->setStressTensor(stressTensor);
920 >    
921    }
922  
923   } //end namespace OpenMD

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