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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC vs.
Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

# Line 58 | Line 58
58   #include "primitives/Torsion.hpp"
59   #include "primitives/Inversion.hpp"
60   #include "nonbonded/NonBondedInteraction.hpp"
61 + #include "perturbations/ElectricField.hpp"
62   #include "parallel/ForceMatrixDecomposition.hpp"
63  
64   #include <cstdio>
# Line 110 | Line 111 | namespace OpenMD {
111      Globals* simParams_ = info_->getSimParams();
112      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113      int mdFileVersion;
114 +    rCut_ = 0.0; //Needs a value for a later max() call;  
115      
116      if (simParams_->haveMDfileVersion())
117        mdFileVersion = simParams_->getMDfileVersion();
# Line 368 | Line 370 | namespace OpenMD {
370      }
371      switcher_->setSwitchType(sft_);
372      switcher_->setSwitch(rSwitch_, rCut_);
371 –    interactionMan_->setSwitchingRadius(rSwitch_);
373    }
374  
375  
# Line 388 | Line 389 | namespace OpenMD {
389        setupCutoffs();
390  
391        info_->prepareTopology();      
392 +
393 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
394 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
395 +      if (doHeatFlux_) doParticlePot_ = true;
396 +
397 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
398 +  
399      }
400  
401      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
# Line 417 | Line 425 | namespace OpenMD {
425      electrostaticScale_[2] = fopts.getelectrostatic13scale();
426      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
427      
428 +    if (info_->getSimParams()->haveElectricField()) {
429 +      ElectricField* eField = new ElectricField(info_);
430 +      perturbations_.push_back(eField);
431 +    }
432 +
433      fDecomp_->distributeInitialData();
434  
435      initialized_ = true;
# Line 443 | Line 456 | namespace OpenMD {
456      Molecule::CutoffGroupIterator ci;
457      CutoffGroup* cg;
458      
459 <    // forces are zeroed here, before any are accumulated.
459 >    // forces and potentials are zeroed here, before any are
460 >    // accumulated.
461      
462 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
463 +
464 +    snap->setBondPotential(0.0);
465 +    snap->setBendPotential(0.0);
466 +    snap->setTorsionPotential(0.0);
467 +    snap->setInversionPotential(0.0);
468 +
469 +    potVec zeroPot(0.0);
470 +    snap->setLongRangePotential(zeroPot);
471 +    snap->setExcludedPotentials(zeroPot);
472 +
473 +    snap->setRestraintPotential(0.0);
474 +    snap->setRawPotential(0.0);
475 +
476      for (mol = info_->beginMolecule(mi); mol != NULL;
477           mol = info_->nextMolecule(mi)) {
478        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 468 | Line 496 | namespace OpenMD {
496      }
497      
498      // Zero out the stress tensor
499 <    tau *= 0.0;
500 <    
499 >    stressTensor *= 0.0;
500 >    // Zero out the heatFlux
501 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
502    }
503    
504    void ForceManager::shortRangeInteractions() {
# Line 502 | Line 531 | namespace OpenMD {
531  
532        for (bond = mol->beginBond(bondIter); bond != NULL;
533             bond = mol->nextBond(bondIter)) {
534 <        bond->calcForce();
534 >        bond->calcForce(doParticlePot_);
535          bondPotential += bond->getPotential();
536        }
537  
# Line 510 | Line 539 | namespace OpenMD {
539             bend = mol->nextBend(bendIter)) {
540          
541          RealType angle;
542 <        bend->calcForce(angle);
542 >        bend->calcForce(angle, doParticlePot_);
543          RealType currBendPot = bend->getPotential();          
544          
545          bendPotential += bend->getPotential();
# Line 535 | Line 564 | namespace OpenMD {
564        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
565             torsion = mol->nextTorsion(torsionIter)) {
566          RealType angle;
567 <        torsion->calcForce(angle);
567 >        torsion->calcForce(angle, doParticlePot_);
568          RealType currTorsionPot = torsion->getPotential();
569          torsionPotential += torsion->getPotential();
570          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 559 | Line 588 | namespace OpenMD {
588             inversion != NULL;
589             inversion = mol->nextInversion(inversionIter)) {
590          RealType angle;
591 <        inversion->calcForce(angle);
591 >        inversion->calcForce(angle, doParticlePot_);
592          RealType currInversionPot = inversion->getPotential();
593          inversionPotential += inversion->getPotential();
594          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 579 | Line 608 | namespace OpenMD {
608          }      
609        }      
610      }
611 <    
612 <    RealType  shortRangePotential = bondPotential + bendPotential +
613 <      torsionPotential +  inversionPotential;    
611 >
612 > #ifdef IS_MPI
613 >    // Collect from all nodes.  This should eventually be moved into a
614 >    // SystemDecomposition, but this is a better place than in
615 >    // Thermo to do the collection.
616 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
617 >                              MPI::SUM);
618 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
619 >                              MPI::SUM);
620 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
621 >                              MPI::REALTYPE, MPI::SUM);
622 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
623 >                              MPI::REALTYPE, MPI::SUM);
624 > #endif
625 >
626      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
627 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
628 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
629 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
630 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
631 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
627 >
628 >    curSnapshot->setBondPotential(bondPotential);
629 >    curSnapshot->setBendPotential(bendPotential);
630 >    curSnapshot->setTorsionPotential(torsionPotential);
631 >    curSnapshot->setInversionPotential(inversionPotential);
632 >    
633 >    // RealType shortRangePotential = bondPotential + bendPotential +
634 >    //   torsionPotential +  inversionPotential;    
635 >
636 >    // curSnapshot->setShortRangePotential(shortRangePotential);
637    }
638    
639    void ForceManager::longRangeInteractions() {
640  
641 +
642      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
643      DataStorage* config = &(curSnapshot->atomData);
644      DataStorage* cgConfig = &(curSnapshot->cgData);
# Line 615 | Line 662 | namespace OpenMD {
662        // center of mass of the group is the same as position of the atom  
663        // if cutoff group does not exist
664        cgConfig->position = config->position;
665 +      cgConfig->velocity = config->velocity;
666      }
667  
668      fDecomp_->zeroWorkArrays();
669      fDecomp_->distributeData();
670      
671      int cg1, cg2, atom1, atom2, topoDist;
672 <    Vector3d d_grp, dag, d;
672 >    Vector3d d_grp, dag, d, gvel2, vel2;
673      RealType rgrpsq, rgrp, r2, r;
674      RealType electroMult, vdwMult;
675      RealType vij;
# Line 634 | Line 682 | namespace OpenMD {
682      InteractionData idat;
683      SelfData sdat;
684      RealType mf;
637 –    RealType lrPot;
685      RealType vpair;
686 +    RealType dVdFQ1(0.0);
687 +    RealType dVdFQ2(0.0);
688      potVec longRangePotential(0.0);
689      potVec workPot(0.0);
690 +    potVec exPot(0.0);
691 +    Vector3d eField1(0.0);
692 +    Vector3d eField2(0.0);
693 +    vector<int>::iterator ia, jb;
694  
695      int loopStart, loopEnd;
696  
697      idat.vdwMult = &vdwMult;
698      idat.electroMult = &electroMult;
699      idat.pot = &workPot;
700 +    idat.excludedPot = &exPot;
701      sdat.pot = fDecomp_->getEmbeddingPotential();
702 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
703      idat.vpair = &vpair;
704 +    idat.dVdFQ1 = &dVdFQ1;
705 +    idat.dVdFQ2 = &dVdFQ2;
706 +    idat.eField1 = &eField1;
707 +    idat.eField2 = &eField2;  
708      idat.f1 = &f1;
709      idat.sw = &sw;
710      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
711      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
712 +    idat.doParticlePot = doParticlePot_;
713 +    idat.doElectricField = doElectricField_;
714 +    sdat.doParticlePot = doParticlePot_;
715      
716      loopEnd = PAIR_LOOP;
717      if (info_->requiresPrepair() ) {
# Line 657 | Line 719 | namespace OpenMD {
719      } else {
720        loopStart = PAIR_LOOP;
721      }
660 –  
722      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
723      
724        if (iLoop == loopStart) {
# Line 689 | Line 750 | namespace OpenMD {
750            
751            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
752                                                       rgrp);
753 <          
753 >
754            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
755            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
756  
757 <          for (vector<int>::iterator ia = atomListRow.begin();
757 >          if (doHeatFlux_)
758 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
759 >
760 >          for (ia = atomListRow.begin();
761                 ia != atomListRow.end(); ++ia) {            
762              atom1 = (*ia);
763 <            
764 <            for (vector<int>::iterator jb = atomListColumn.begin();
763 >
764 >            for (jb = atomListColumn.begin();
765                   jb != atomListColumn.end(); ++jb) {              
766                atom2 = (*jb);
767  
768 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
768 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
769 >
770                  vpair = 0.0;
771                  workPot = 0.0;
772 +                exPot = 0.0;
773                  f1 = V3Zero;
774 +                dVdFQ1 = 0.0;
775 +                dVdFQ2 = 0.0;
776  
777                  fDecomp_->fillInteractionData(idat, atom1, atom2);
778 <                
778 >
779                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
780                  vdwMult = vdwScale_[topoDist];
781                  electroMult = electrostaticScale_[topoDist];
# Line 715 | Line 783 | namespace OpenMD {
783                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
784                    idat.d = &d_grp;
785                    idat.r2 = &rgrpsq;
786 +                  if (doHeatFlux_)
787 +                    vel2 = gvel2;
788                  } else {
789                    d = fDecomp_->getInteratomicVector(atom1, atom2);
790                    curSnapshot->wrapVector( d );
791                    r2 = d.lengthSquare();
792                    idat.d = &d;
793                    idat.r2 = &r2;
794 +                  if (doHeatFlux_)
795 +                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
796                  }
797                
798                  r = sqrt( *(idat.r2) );
# Line 733 | Line 805 | namespace OpenMD {
805                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
806                    vij += vpair;
807                    fij += f1;
808 <                  tau -= outProduct( *(idat.d), f1);
808 >                  stressTensor -= outProduct( *(idat.d), f1);
809 >                  if (doHeatFlux_)
810 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
811                  }
812                }
813              }
# Line 746 | Line 820 | namespace OpenMD {
820                fij += fg;
821  
822                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
823 <                tau -= outProduct( *(idat.d), fg);
823 >                stressTensor -= outProduct( *(idat.d), fg);
824 >                if (doHeatFlux_)
825 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
826 >                
827                }
828            
829 <              for (vector<int>::iterator ia = atomListRow.begin();
829 >              for (ia = atomListRow.begin();
830                     ia != atomListRow.end(); ++ia) {            
831                  atom1 = (*ia);                
832                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 762 | Line 839 | namespace OpenMD {
839                      // find the distance between the atom
840                      // and the center of the cutoff group:
841                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
842 <                    tau -= outProduct(dag, fg);
842 >                    stressTensor -= outProduct(dag, fg);
843 >                    if (doHeatFlux_)
844 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
845                    }
846                  }
847                }
848 <              for (vector<int>::iterator jb = atomListColumn.begin();
848 >              for (jb = atomListColumn.begin();
849                     jb != atomListColumn.end(); ++jb) {              
850                  atom2 = (*jb);
851                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 780 | Line 859 | namespace OpenMD {
859                      // find the distance between the atom
860                      // and the center of the cutoff group:
861                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
862 <                    tau -= outProduct(dag, fg);
862 >                    stressTensor -= outProduct(dag, fg);
863 >                    if (doHeatFlux_)
864 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
865                    }
866                  }
867                }
868              }
869              //if (!info_->usesAtomicVirial()) {
870 <            //  tau -= outProduct(d_grp, fij);
870 >            //  stressTensor -= outProduct(d_grp, fij);
871 >            //  if (doHeatFlux_)
872 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
873              //}
874            }
875          }
# Line 797 | Line 880 | namespace OpenMD {
880  
881            fDecomp_->collectIntermediateData();
882  
883 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
883 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
884              fDecomp_->fillSelfData(sdat, atom1);
885              interactionMan_->doPreForce(sdat);
886            }
# Line 808 | Line 891 | namespace OpenMD {
891        }
892      }
893      
894 +    // collects pairwise information
895      fDecomp_->collectData();
896          
897      if (info_->requiresSelfCorrection()) {
898 <
815 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
898 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
899          fDecomp_->fillSelfData(sdat, atom1);
900          interactionMan_->doSelfCorrection(sdat);
901        }
819 –
902      }
903  
904 +    // collects single-atom information
905 +    fDecomp_->collectSelfData();
906 +
907      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
908        *(fDecomp_->getPairwisePotential());
909  
910 <    lrPot = longRangePotential.sum();
910 >    curSnapshot->setLongRangePotential(longRangePotential);
911 >    
912 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
913 >                                         *(fDecomp_->getExcludedPotential()));
914  
827 –    //store the tau and long range potential    
828 –    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
829 –    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
830 –    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
915    }
916  
917    
918    void ForceManager::postCalculation() {
919 +
920 +    vector<Perturbation*>::iterator pi;
921 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
922 +      (*pi)->applyPerturbation();
923 +    }
924 +
925      SimInfo::MoleculeIterator mi;
926      Molecule* mol;
927      Molecule::RigidBodyIterator rbIter;
928      RigidBody* rb;
929      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
930 <    
930 >  
931      // collect the atomic forces onto rigid bodies
932      
933      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 845 | Line 935 | namespace OpenMD {
935        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
936             rb = mol->nextRigidBody(rbIter)) {
937          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
938 <        tau += rbTau;
938 >        stressTensor += rbTau;
939        }
940      }
941      
942   #ifdef IS_MPI
943 <    Mat3x3d tmpTau(tau);
944 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
855 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
943 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
944 >                              MPI::REALTYPE, MPI::SUM);
945   #endif
946 <    curSnapshot->setTau(tau);
946 >    curSnapshot->setStressTensor(stressTensor);
947 >    
948    }
859 –
949   } //end namespace OpenMD

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