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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1733 by jmichalk, Tue Jun 5 17:48:40 2012 UTC vs.
Revision 1812 by gezelter, Fri Nov 16 21:18:42 2012 UTC

# Line 44 | Line 44
44   * @file ForceManager.cpp
45   * @author tlin
46   * @date 11/09/2004
47 – * @time 10:39am
47   * @version 1.0
48   */
49  
# Line 58 | Line 57
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59   #include "nonbonded/NonBondedInteraction.hpp"
60 + #include "perturbations/ElectricField.hpp"
61   #include "parallel/ForceMatrixDecomposition.hpp"
62  
63   #include <cstdio>
# 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 368 | Line 369 | namespace OpenMD {
369      }
370      switcher_->setSwitchType(sft_);
371      switcher_->setSwitch(rSwitch_, rCut_);
371 –    interactionMan_->setSwitchingRadius(rSwitch_);
372    }
373  
374  
# Line 392 | Line 392 | namespace OpenMD {
392        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
394        if (doHeatFlux_) doParticlePot_ = true;
395 +
396 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
397    
398      }
399  
# Line 422 | Line 424 | namespace OpenMD {
424      electrostaticScale_[2] = fopts.getelectrostatic13scale();
425      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
426      
427 +    if (info_->getSimParams()->haveElectricField()) {
428 +      ElectricField* eField = new ElectricField(info_);
429 +      perturbations_.push_back(eField);
430 +    }
431 +
432      fDecomp_->distributeInitialData();
433  
434      initialized_ = true;
# Line 448 | Line 455 | namespace OpenMD {
455      Molecule::CutoffGroupIterator ci;
456      CutoffGroup* cg;
457      
458 <    // forces are zeroed here, before any are accumulated.
458 >    // forces and potentials are zeroed here, before any are
459 >    // accumulated.
460      
461 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
462 +
463 +    snap->setBondPotential(0.0);
464 +    snap->setBendPotential(0.0);
465 +    snap->setTorsionPotential(0.0);
466 +    snap->setInversionPotential(0.0);
467 +
468 +    potVec zeroPot(0.0);
469 +    snap->setLongRangePotential(zeroPot);
470 +    snap->setExcludedPotentials(zeroPot);
471 +
472 +    snap->setRestraintPotential(0.0);
473 +    snap->setRawPotential(0.0);
474 +
475      for (mol = info_->beginMolecule(mi); mol != NULL;
476           mol = info_->nextMolecule(mi)) {
477        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 475 | Line 497 | namespace OpenMD {
497      // Zero out the stress tensor
498      stressTensor *= 0.0;
499      // Zero out the heatFlux
500 <    fDecomp_->setHeatFlux( V3Zero );    
500 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
501    }
502    
503    void ForceManager::shortRangeInteractions() {
# Line 585 | Line 607 | namespace OpenMD {
607          }      
608        }      
609      }
610 <    
611 <    RealType  shortRangePotential = bondPotential + bendPotential +
612 <      torsionPotential +  inversionPotential;    
610 >
611 > #ifdef IS_MPI
612 >    // Collect from all nodes.  This should eventually be moved into a
613 >    // SystemDecomposition, but this is a better place than in
614 >    // Thermo to do the collection.
615 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
616 >                              MPI::SUM);
617 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
618 >                              MPI::SUM);
619 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
620 >                              MPI::REALTYPE, MPI::SUM);
621 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
622 >                              MPI::REALTYPE, MPI::SUM);
623 > #endif
624 >
625      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
626 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
627 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
628 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
629 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
630 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
626 >
627 >    curSnapshot->setBondPotential(bondPotential);
628 >    curSnapshot->setBendPotential(bendPotential);
629 >    curSnapshot->setTorsionPotential(torsionPotential);
630 >    curSnapshot->setInversionPotential(inversionPotential);
631 >    
632 >    // RealType shortRangePotential = bondPotential + bendPotential +
633 >    //   torsionPotential +  inversionPotential;    
634 >
635 >    // curSnapshot->setShortRangePotential(shortRangePotential);
636    }
637    
638    void ForceManager::longRangeInteractions() {
# Line 642 | Line 681 | namespace OpenMD {
681      InteractionData idat;
682      SelfData sdat;
683      RealType mf;
645 –    RealType lrPot;
684      RealType vpair;
685      RealType dVdFQ1(0.0);
686      RealType dVdFQ2(0.0);
687      potVec longRangePotential(0.0);
688      potVec workPot(0.0);
689 +    potVec exPot(0.0);
690 +    Vector3d eField1(0.0);
691 +    Vector3d eField2(0.0);
692      vector<int>::iterator ia, jb;
693  
694      int loopStart, loopEnd;
# Line 655 | Line 696 | namespace OpenMD {
696      idat.vdwMult = &vdwMult;
697      idat.electroMult = &electroMult;
698      idat.pot = &workPot;
699 +    idat.excludedPot = &exPot;
700      sdat.pot = fDecomp_->getEmbeddingPotential();
701 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
702      idat.vpair = &vpair;
703      idat.dVdFQ1 = &dVdFQ1;
704      idat.dVdFQ2 = &dVdFQ2;
705 +    idat.eField1 = &eField1;
706 +    idat.eField2 = &eField2;  
707      idat.f1 = &f1;
708      idat.sw = &sw;
709      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
710      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
711      idat.doParticlePot = doParticlePot_;
712 +    idat.doElectricField = doElectricField_;
713      sdat.doParticlePot = doParticlePot_;
714      
715      loopEnd = PAIR_LOOP;
# Line 672 | Line 718 | namespace OpenMD {
718      } else {
719        loopStart = PAIR_LOOP;
720      }
675 –  
721      for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
722      
723        if (iLoop == loopStart) {
# Line 704 | Line 749 | namespace OpenMD {
749            
750            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
751                                                       rgrp);
752 <          
752 >
753            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
754            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
755  
756            if (doHeatFlux_)
757              gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
758 <        
758 >
759            for (ia = atomListRow.begin();
760                 ia != atomListRow.end(); ++ia) {            
761              atom1 = (*ia);
762 <            
762 >
763              for (jb = atomListColumn.begin();
764                   jb != atomListColumn.end(); ++jb) {              
765                atom2 = (*jb);
766  
767 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
767 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
768 >
769                  vpair = 0.0;
770                  workPot = 0.0;
771 +                exPot = 0.0;
772                  f1 = V3Zero;
773                  dVdFQ1 = 0.0;
774                  dVdFQ2 = 0.0;
775  
776                  fDecomp_->fillInteractionData(idat, atom1, atom2);
777 <                
777 >
778                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
779                  vdwMult = vdwScale_[topoDist];
780                  electroMult = electrostaticScale_[topoDist];
# Line 772 | Line 819 | namespace OpenMD {
819                fij += fg;
820  
821                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
822 <                stressTensor -= outProduct( *(idat.d), fg);
823 <                if (doHeatFlux_)
824 <                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
825 <                
822 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
823 >                                            atomListColumn[0],
824 >                                            cg1, cg2)) {
825 >                  stressTensor -= outProduct( *(idat.d), fg);
826 >                  if (doHeatFlux_)
827 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
828 >                }                
829                }
830            
831                for (ia = atomListRow.begin();
# Line 832 | Line 882 | namespace OpenMD {
882  
883            fDecomp_->collectIntermediateData();
884  
885 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
885 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
886              fDecomp_->fillSelfData(sdat, atom1);
887              interactionMan_->doPreForce(sdat);
888            }
# Line 843 | Line 893 | namespace OpenMD {
893        }
894      }
895      
896 +    // collects pairwise information
897      fDecomp_->collectData();
898          
899      if (info_->requiresSelfCorrection()) {
900 <
850 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
900 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
901          fDecomp_->fillSelfData(sdat, atom1);
902          interactionMan_->doSelfCorrection(sdat);
903        }
854 –
904      }
905  
906 +    // collects single-atom information
907 +    fDecomp_->collectSelfData();
908 +
909      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
910        *(fDecomp_->getPairwisePotential());
911  
912 <    lrPot = longRangePotential.sum();
912 >    curSnapshot->setLongRangePotential(longRangePotential);
913  
914 <    //store the stressTensor and long range potential    
915 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
916 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
917 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
914 >    // collects single-atom information
915 >    fDecomp_->collectSelfData();
916 >
917 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
918 >      *(fDecomp_->getPairwisePotential());
919 >
920 >    curSnapshot->setLongRangePotential(longRangePotential);
921 >    
922 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
923 >                                         *(fDecomp_->getExcludedPotential()));
924 >
925    }
926  
927    
928    void ForceManager::postCalculation() {
929 +
930 +    vector<Perturbation*>::iterator pi;
931 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
932 +      (*pi)->applyPerturbation();
933 +    }
934 +
935      SimInfo::MoleculeIterator mi;
936      Molecule* mol;
937      Molecule::RigidBodyIterator rbIter;
938      RigidBody* rb;
939      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
940 <    
940 >  
941      // collect the atomic forces onto rigid bodies
942      
943      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 885 | Line 950 | namespace OpenMD {
950      }
951      
952   #ifdef IS_MPI
888 –
953      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
954                                MPI::REALTYPE, MPI::SUM);
955   #endif
956      curSnapshot->setStressTensor(stressTensor);
957      
958    }
895 –
959   } //end namespace OpenMD

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