ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/ForceManager.cpp
(Generate patch)

Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC vs.
Revision 1760 by gezelter, Thu Jun 21 19:26:46 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      idat.vpair = &vpair;
680 +    idat.dVdFQ1 = &dVdFQ1;
681 +    idat.dVdFQ2 = &dVdFQ2;
682      idat.f1 = &f1;
683      idat.sw = &sw;
684      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
# Line 663 | Line 692 | namespace OpenMD {
692      } else {
693        loopStart = PAIR_LOOP;
694      }
666 –  
695      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
696      
697        if (iLoop == loopStart) {
# Line 695 | Line 723 | namespace OpenMD {
723            
724            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
725                                                       rgrp);
726 <          
726 >
727            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
728            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
729  
730 +          if (doHeatFlux_)
731 +            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
732 +
733            for (ia = atomListRow.begin();
734                 ia != atomListRow.end(); ++ia) {            
735              atom1 = (*ia);
736 <            
736 >
737              for (jb = atomListColumn.begin();
738                   jb != atomListColumn.end(); ++jb) {              
739                atom2 = (*jb);
740  
741 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
741 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
742 >
743                  vpair = 0.0;
744                  workPot = 0.0;
745 +                exPot = 0.0;
746                  f1 = V3Zero;
747 +                dVdFQ1 = 0.0;
748 +                dVdFQ2 = 0.0;
749  
750                  fDecomp_->fillInteractionData(idat, atom1, atom2);
751 <                
751 >
752                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
753                  vdwMult = vdwScale_[topoDist];
754                  electroMult = electrostaticScale_[topoDist];
# Line 721 | Line 756 | namespace OpenMD {
756                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
757                    idat.d = &d_grp;
758                    idat.r2 = &rgrpsq;
759 +                  if (doHeatFlux_)
760 +                    vel2 = gvel2;
761                  } else {
762                    d = fDecomp_->getInteratomicVector(atom1, atom2);
763                    curSnapshot->wrapVector( d );
764                    r2 = d.lengthSquare();
765                    idat.d = &d;
766                    idat.r2 = &r2;
767 +                  if (doHeatFlux_)
768 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
769                  }
770                
771                  r = sqrt( *(idat.r2) );
# Line 739 | Line 778 | namespace OpenMD {
778                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
779                    vij += vpair;
780                    fij += f1;
781 <                  tau -= outProduct( *(idat.d), f1);
781 >                  stressTensor -= outProduct( *(idat.d), f1);
782 >                  if (doHeatFlux_)
783 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
784                  }
785                }
786              }
# Line 752 | Line 793 | namespace OpenMD {
793                fij += fg;
794  
795                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
796 <                tau -= outProduct( *(idat.d), fg);
796 >                stressTensor -= outProduct( *(idat.d), fg);
797 >                if (doHeatFlux_)
798 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
799 >                
800                }
801            
802                for (ia = atomListRow.begin();
# Line 768 | Line 812 | namespace OpenMD {
812                      // find the distance between the atom
813                      // and the center of the cutoff group:
814                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
815 <                    tau -= outProduct(dag, fg);
815 >                    stressTensor -= outProduct(dag, fg);
816 >                    if (doHeatFlux_)
817 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
818                    }
819                  }
820                }
# Line 786 | Line 832 | namespace OpenMD {
832                      // find the distance between the atom
833                      // and the center of the cutoff group:
834                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
835 <                    tau -= outProduct(dag, fg);
835 >                    stressTensor -= outProduct(dag, fg);
836 >                    if (doHeatFlux_)
837 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
838                    }
839                  }
840                }
841              }
842              //if (!info_->usesAtomicVirial()) {
843 <            //  tau -= outProduct(d_grp, fij);
843 >            //  stressTensor -= outProduct(d_grp, fij);
844 >            //  if (doHeatFlux_)
845 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
846              //}
847            }
848          }
# Line 814 | Line 864 | namespace OpenMD {
864        }
865      }
866      
867 +    // collects pairwise information
868      fDecomp_->collectData();
869          
870      if (info_->requiresSelfCorrection()) {
871 <
821 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
871 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
872          fDecomp_->fillSelfData(sdat, atom1);
873          interactionMan_->doSelfCorrection(sdat);
874        }
825 –
875      }
876  
877 +    // collects single-atom information
878 +    fDecomp_->collectSelfData();
879 +
880      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
881        *(fDecomp_->getPairwisePotential());
882  
883 +    curSnapshot->setLongRangePotentialFamilies(longRangePotential);
884 +
885      lrPot = longRangePotential.sum();
886  
887 <    //store the tau and long range potential    
888 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
889 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
890 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
887 >    //store the long range potential  
888 >    curSnapshot->setLongRangePotential(lrPot);
889 >
890 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedPotential()));
891 >
892    }
893  
894    
# Line 851 | Line 906 | namespace OpenMD {
906        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
907             rb = mol->nextRigidBody(rbIter)) {
908          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
909 <        tau += rbTau;
909 >        stressTensor += rbTau;
910        }
911      }
912      
913   #ifdef IS_MPI
914 <    Mat3x3d tmpTau(tau);
915 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
861 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
914 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
915 >                              MPI::REALTYPE, MPI::SUM);
916   #endif
917 <    curSnapshot->setTau(tau);
917 >    curSnapshot->setStressTensor(stressTensor);
918 >    
919    }
920  
921   } //end namespace OpenMD

Diff Legend

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