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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 1723 by gezelter, Thu May 24 20:59:54 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 392 | Line 393 | namespace OpenMD {
393        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
394        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
395        if (doHeatFlux_) doParticlePot_ = true;
396 +
397 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
398    
399      }
400  
# Line 422 | 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 448 | 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 475 | Line 498 | namespace OpenMD {
498      // Zero out the stress tensor
499      stressTensor *= 0.0;
500      // Zero out the heatFlux
501 <    fDecomp_->setHeatFlux( V3Zero );    
501 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
502    }
503    
504    void ForceManager::shortRangeInteractions() {
# Line 585 | 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() {
# Line 642 | Line 682 | namespace OpenMD {
682      InteractionData idat;
683      SelfData sdat;
684      RealType mf;
645 –    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;
# Line 653 | Line 697 | namespace OpenMD {
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;
# Line 668 | Line 719 | namespace OpenMD {
719      } else {
720        loopStart = PAIR_LOOP;
721      }
671 –  
722      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
723      
724        if (iLoop == loopStart) {
# Line 700 | 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            if (doHeatFlux_)
758              gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
759 <        
759 >
760            for (ia = atomListRow.begin();
761                 ia != atomListRow.end(); ++ia) {            
762              atom1 = (*ia);
763 <            
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 826 | 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 837 | Line 891 | namespace OpenMD {
891        }
892      }
893      
894 +    // collects pairwise information
895      fDecomp_->collectData();
896          
897      if (info_->requiresSelfCorrection()) {
898 <
844 <      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        }
848 –
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  
856 –    //store the stressTensor and long range potential    
857 –    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
858 –    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
859 –    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 879 | Line 940 | namespace OpenMD {
940      }
941      
942   #ifdef IS_MPI
882 –
943      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
944                                MPI::REALTYPE, MPI::SUM);
945   #endif
946      curSnapshot->setStressTensor(stressTensor);
947      
948    }
889 –
949   } //end namespace OpenMD

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