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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1749 by gezelter, Thu Jun 7 02:47:21 2012 UTC vs.
Revision 1849 by gezelter, Wed Feb 20 13:52:51 2013 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();
117      else
118        mdFileVersion = 0;
119    
120 +    // We need the list of simulated atom types to figure out cutoffs
121 +    // as well as long range corrections.
122 +
123 +    set<AtomType*>::iterator i;
124 +    set<AtomType*> atomTypes_;
125 +    atomTypes_ = info_->getSimulatedAtomTypes();
126 +
127      if (simParams_->haveCutoffRadius()) {
128        rCut_ = simParams_->getCutoffRadius();
129      } else {      
# Line 130 | Line 138 | namespace OpenMD {
138          rCut_ = 12.0;
139        } else {
140          RealType thisCut;
141 <        set<AtomType*>::iterator i;
134 <        set<AtomType*> atomTypes;
135 <        atomTypes = info_->getSimulatedAtomTypes();        
136 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
141 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
142            thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
143            rCut_ = max(thisCut, rCut_);
144          }
# Line 368 | Line 373 | namespace OpenMD {
373      }
374      switcher_->setSwitchType(sft_);
375      switcher_->setSwitch(rSwitch_, rCut_);
371 –    interactionMan_->setSwitchingRadius(rSwitch_);
376    }
377  
378  
# Line 392 | Line 396 | namespace OpenMD {
396        doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
397        doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
398        if (doHeatFlux_) doParticlePot_ = true;
399 +
400 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
401    
402      }
403  
# Line 422 | Line 428 | namespace OpenMD {
428      electrostaticScale_[2] = fopts.getelectrostatic13scale();
429      electrostaticScale_[3] = fopts.getelectrostatic14scale();    
430      
431 +    if (info_->getSimParams()->haveElectricField()) {
432 +      ElectricField* eField = new ElectricField(info_);
433 +      perturbations_.push_back(eField);
434 +    }
435 +
436      fDecomp_->distributeInitialData();
437  
438      initialized_ = true;
# Line 448 | Line 459 | namespace OpenMD {
459      Molecule::CutoffGroupIterator ci;
460      CutoffGroup* cg;
461      
462 <    // forces are zeroed here, before any are accumulated.
462 >    // forces and potentials are zeroed here, before any are
463 >    // accumulated.
464      
465 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
466 +
467 +    snap->setBondPotential(0.0);
468 +    snap->setBendPotential(0.0);
469 +    snap->setTorsionPotential(0.0);
470 +    snap->setInversionPotential(0.0);
471 +
472 +    potVec zeroPot(0.0);
473 +    snap->setLongRangePotential(zeroPot);
474 +    snap->setExcludedPotentials(zeroPot);
475 +
476 +    snap->setRestraintPotential(0.0);
477 +    snap->setRawPotential(0.0);
478 +
479      for (mol = info_->beginMolecule(mi); mol != NULL;
480           mol = info_->nextMolecule(mi)) {
481        for(atom = mol->beginAtom(ai); atom != NULL;
# Line 585 | Line 611 | namespace OpenMD {
611          }      
612        }      
613      }
614 <    
615 <    RealType  shortRangePotential = bondPotential + bendPotential +
616 <      torsionPotential +  inversionPotential;    
614 >
615 > #ifdef IS_MPI
616 >    // Collect from all nodes.  This should eventually be moved into a
617 >    // SystemDecomposition, but this is a better place than in
618 >    // Thermo to do the collection.
619 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
620 >                              MPI::SUM);
621 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
622 >                              MPI::SUM);
623 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
624 >                              MPI::REALTYPE, MPI::SUM);
625 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
626 >                              MPI::REALTYPE, MPI::SUM);
627 > #endif
628 >
629      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
630 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
631 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
632 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
633 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
634 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
630 >
631 >    curSnapshot->setBondPotential(bondPotential);
632 >    curSnapshot->setBendPotential(bendPotential);
633 >    curSnapshot->setTorsionPotential(torsionPotential);
634 >    curSnapshot->setInversionPotential(inversionPotential);
635 >    
636 >    // RealType shortRangePotential = bondPotential + bendPotential +
637 >    //   torsionPotential +  inversionPotential;    
638 >
639 >    // curSnapshot->setShortRangePotential(shortRangePotential);
640    }
641    
642    void ForceManager::longRangeInteractions() {
# Line 642 | Line 685 | namespace OpenMD {
685      InteractionData idat;
686      SelfData sdat;
687      RealType mf;
645 –    RealType lrPot;
688      RealType vpair;
689      RealType dVdFQ1(0.0);
690      RealType dVdFQ2(0.0);
691      potVec longRangePotential(0.0);
692      potVec workPot(0.0);
693 +    potVec exPot(0.0);
694 +    Vector3d eField1(0.0);
695 +    Vector3d eField2(0.0);
696      vector<int>::iterator ia, jb;
697  
698      int loopStart, loopEnd;
# Line 655 | Line 700 | namespace OpenMD {
700      idat.vdwMult = &vdwMult;
701      idat.electroMult = &electroMult;
702      idat.pot = &workPot;
703 +    idat.excludedPot = &exPot;
704      sdat.pot = fDecomp_->getEmbeddingPotential();
705 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
706      idat.vpair = &vpair;
707      idat.dVdFQ1 = &dVdFQ1;
708      idat.dVdFQ2 = &dVdFQ2;
709 +    idat.eField1 = &eField1;
710 +    idat.eField2 = &eField2;  
711      idat.f1 = &f1;
712      idat.sw = &sw;
713      idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
714      idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
715      idat.doParticlePot = doParticlePot_;
716 +    idat.doElectricField = doElectricField_;
717      sdat.doParticlePot = doParticlePot_;
718      
719      loopEnd = PAIR_LOOP;
# Line 699 | Line 749 | namespace OpenMD {
749            if (iLoop == PAIR_LOOP) {
750              vij = 0.0;
751              fij = V3Zero;
752 +            eField1 = V3Zero;
753 +            eField2 = V3Zero;
754            }
755            
756            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
757                                                       rgrp);
758 +
759            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
760            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
761  
# Line 717 | Line 770 | namespace OpenMD {
770                   jb != atomListColumn.end(); ++jb) {              
771                atom2 = (*jb);
772  
773 <              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
773 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
774 >
775                  vpair = 0.0;
776                  workPot = 0.0;
777 +                exPot = 0.0;
778                  f1 = V3Zero;
779                  dVdFQ1 = 0.0;
780                  dVdFQ2 = 0.0;
# Line 770 | Line 825 | namespace OpenMD {
825                fij += fg;
826  
827                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
828 <                stressTensor -= outProduct( *(idat.d), fg);
829 <                if (doHeatFlux_)
830 <                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
831 <                
828 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
829 >                                            atomListColumn[0],
830 >                                            cg1, cg2)) {
831 >                  stressTensor -= outProduct( *(idat.d), fg);
832 >                  if (doHeatFlux_)
833 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
834 >                }                
835                }
836            
837                for (ia = atomListRow.begin();
# Line 830 | Line 888 | namespace OpenMD {
888  
889            fDecomp_->collectIntermediateData();
890  
891 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
891 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
892              fDecomp_->fillSelfData(sdat, atom1);
893              interactionMan_->doPreForce(sdat);
894            }
# Line 841 | Line 899 | namespace OpenMD {
899        }
900      }
901      
902 +    // collects pairwise information
903      fDecomp_->collectData();
904          
905      if (info_->requiresSelfCorrection()) {
906 <
848 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
906 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907          fDecomp_->fillSelfData(sdat, atom1);
908          interactionMan_->doSelfCorrection(sdat);
909        }
852 –
910      }
911  
912 +    // collects single-atom information
913 +    fDecomp_->collectSelfData();
914 +
915      longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
916        *(fDecomp_->getPairwisePotential());
917  
918 <    lrPot = longRangePotential.sum();
918 >    curSnapshot->setLongRangePotential(longRangePotential);
919 >    
920 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
921 >                                         *(fDecomp_->getExcludedPotential()));
922  
860 –    //store the stressTensor and long range potential    
861 –    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
862 –    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
863 –    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
923    }
924  
925    
926    void ForceManager::postCalculation() {
927 +
928 +    vector<Perturbation*>::iterator pi;
929 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
930 +      (*pi)->applyPerturbation();
931 +    }
932 +
933      SimInfo::MoleculeIterator mi;
934      Molecule* mol;
935      Molecule::RigidBodyIterator rbIter;
936      RigidBody* rb;
937      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
938 <    
938 >  
939      // collect the atomic forces onto rigid bodies
940      
941      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 883 | Line 948 | namespace OpenMD {
948      }
949      
950   #ifdef IS_MPI
886 –
951      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
952                                MPI::REALTYPE, MPI::SUM);
953   #endif
954      curSnapshot->setStressTensor(stressTensor);
955      
956 <  }
956 >    if (info_->getSimParams()->getUseLongRangeCorrections()) {
957 >      /*
958 >      RealType vol = curSnapshot->getVolume();
959 >      RealType Elrc(0.0);
960 >      RealType Wlrc(0.0);
961  
962 < } //end namespace OpenMD
962 >      set<AtomType*>::iterator i;
963 >      set<AtomType*>::iterator j;
964 >    
965 >      RealType n_i, n_j;
966 >      RealType rho_i, rho_j;
967 >      pair<RealType, RealType> LRI;
968 >      
969 >      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
970 >        n_i = RealType(info_->getGlobalCountOfType(*i));
971 >        rho_i = n_i /  vol;
972 >        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
973 >          n_j = RealType(info_->getGlobalCountOfType(*j));
974 >          rho_j = n_j / vol;
975 >          
976 >          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
977 >
978 >          Elrc += n_i   * rho_j * LRI.first;
979 >          Wlrc -= rho_i * rho_j * LRI.second;
980 >        }
981 >      }
982 >      Elrc *= 2.0 * NumericConstant::PI;
983 >      Wlrc *= 2.0 * NumericConstant::PI;
984 >
985 >      RealType lrp = curSnapshot->getLongRangePotential();
986 >      curSnapshot->setLongRangePotential(lrp + Elrc);
987 >      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
988 >      curSnapshot->setStressTensor(stressTensor);
989 >      */
990 >    
991 >    }
992 >  }
993 > }

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